gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC1 UCLA
section Grant Year
Start Grant Year 2 :milestone, m1, 2024-03-31, 0d
Start Grant Year 3 :milestone, m1, 2025-03-31, 0d
Start Grant Year 4 :milestone, m1, 2026-03-31, 0d
Start Grant Year 5 :milestone, m1, 2027-04-01, 0d
section AIM 1
Generate stable clonal iPSC lines for 10 gene mutations in KOLF2.2J (Capstone; Batch A) : t1, 2024-01-01, 2024-07-01
Generate stable clonal iPSC lines for 10 gene mutations in CIRM line (Capstone; Batch A) : t2, 2024-01-01, 2024-07-01
Generate stable clonal iPSC lines for additional 25 gene mutations in KOLF2.2J and CIRM (Batch B) : t3, 2024-04-01, 2024-09-30
QC of Capstone lines to date pending : t4, 2024-04-01, 39w
Generate and QC stable clonal iPSC lines for additional 65 gene mutations in KOLF2.2J and CIRM : t6, after t3, 52w
QC of all generated lines to date pending : t7, after t3, 78w
Share 20 BatchA gene edited iPSC lines (10 NPD genes x 2 iPSC backgrounds) : t8, after t4, 26w
Share 180 Batch B+C gene edited iPSC lines (90 NPD genes x 2 iPSC backgrounds) : t10, after t8, 39w
Troubleshoot and perform 2nd attempt of difficult KO genes : t11, after t10, 13w
section AIM 2
Quantify proliferation rates of NPCs from 10 Capstone iPSC clonal lines : t5, after t1, 26w
Quantify proliferation rates of NPCs from all iPSC clonal lines from all batches : t9, after t4, 52w
Bulk RNA-seq profiles (4 replicates per gene x (10 NPD iPSC lines + 2 controls) x 1 background (KOLF2.2J) iPSC background lines; fastq)) : t20, after t2, 52w
Submit data from first capstone experiment (KOLF2.2J background) :crit, t22, after t20, 13w
Bulk RNA-seq profiles ((4 replicates per gene x (10 NPD iPSC lines + 2 controls) x 1 background (CIRM line) iPSC background lines; fastq)) : t21, after t3, 39w
Submit data from first capstone experiment (CIRM background) :crit, t23, after t21, 13w
Begin villages : t24, 2024-07-01,13w
Complete villages : t25, after t24,13w
Perform StimScope Ephys Experiments for all lines : t32, 2025-10-01,30w
Submit data on RNA-seq profiles from Batch B and C :crit, t33, 2025-10-01,13w
ADGC1_I_8 Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from Capstone Lines (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_I_8, 2025-03-31, 0d
ADGC1_JK_8 Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from batch B (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_JK_8, 2025-10-01, 0d
ADGC1_LM_8 Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from batch C (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_LM_8, 2026-04-01, 0d
ADGC1_NO_8 Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from batch D (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_NO_8, 2026-10-01, 0d
ADGC1_P_8 Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from batch E (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_P_8, 2026-12-31, 0d
ADGC1_Q_8 Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from batch F (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_Q_8, 2027-04-01, 0d
ADGC1_LM_111213 Submit L0-L1 from Batch B, producing bulk RNA-seq profiles (3 technical replicates, 4 biological replicates per gene x (20 NPD iPSC lines + 2 controls) x 2 backgrounds (KOLF2.2J/CIRM) iPSC background lines; fastq)) : crit, milestone, ADGC1_LM_111213, 2026-04-01, 0d
ADGC1_NO_111213 Submit L0-L1 from Batch C, producing bulk RNA-seq profiles (3 technical replicates, 4 biological replicates per gene x (20 NPD iPSC lines + 2 controls) x 2 backgrounds (KOLF2.2J/CIRM) iPSC background lines; fastq)) : crit, milestone, ADGC1_NO_111213, 2026-10-01, 0d
ADGC1_P_111213 Submit L0-L1 from Batch D, producing bulk RNA-seq profiles (3 technical replicates, 4 biological replicates per gene x (20 NPD iPSC lines + 2 controls) x 2 backgrounds (KOLF2.2J/CIRM) iPSC background lines; fastq)) : crit, milestone, ADGC1_P_111213, 2026-12-31, 0d
ADGC1_Q_111213 Submit L0-L1 from Batch E-G, producing bulk RNA-seq profiles (3 technical replicates, 4 biological replicates per gene x (20 NPD iPSC lines + 2 controls) x 2 backgrounds (KOLF2.2J/CIRM) iPSC background lines; fastq)) : crit, milestone, ADGC1_Q_111213, 2027-04-01, 0d
ADGC1_JK_14 Complete villages (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_JK_14, 2025-10-01, 0d
ADGC1_LM_14 Village Analysis (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_LM_14, 2026-04-01, 0d
ADGC1_K_15 Calcium Imaging Capstone Analysis (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_K_15, 2025-09-30, 0d
ADGC1_M_15 Calcium Imaging analysis excitatory/inhibitory neurons - Capstone Analysis (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_M_15, 2026-04-01, 0d
ADGC1_NOPQ_15 Calcium Imaging Experiments and analysis of future batches (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) (Submit L0-L4 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_NOPQ_15, 2027-04-01, 0d
section AIM 3
Begin organoids first 20 : t26, 2024-07-01,13w
Prepare samples for RNAseq : t27, after t26,13w
Perform RNAseq : t28, after t27,13w
Begin RNAseq Analysis : t29, after t28,13w
Prepare samples for CODEX: t30, after t27,13w
Perform CODEX: t31, after t30,13w
Submit first Spatial Imaging data: crit, t32, after t31,13w
ADGC1_J_161718 Perform codex Capstone Lines (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; qptiff format) (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_J_161718, 2025-07-01, 0d
ADGC1_K_161718 Spatial Proteomics Analysis Capstone Lines (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_K_161718, 2025-09-30, 0d
ADGC1_L_161718 Perform codex Batch B (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; qptiff format) (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_L_161718, 2025-12-31, 0d
ADGC1_M_161718 Spatial Proteomics Analysis Batch B (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_M_161718, 2026-04-01, 0d
ADGC1_N_161718 Perform codex Batch C (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; qptiff format) (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_N_161718, 2027-04-01, 0d
ADGC1_O_161718 Spatial Proteomics Analysis Batch C (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_O_161718, 2027-04-01, 0d
ADGC1_Q_161718 Perform codex and analysis for future batches (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_Q_161718, 2027-04-01, 0d
ADGC1_J_1920 Organoid snRNAseq analysis for Capstone Genes (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_J_1920, 2025-07-01, 0d
ADGC1_K_1920 Perform snRNAseq for batch B (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 2-4 organoid replicates/line; tif format) (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_K_1920, 2025-09-30, 0d
ADGC1_L_1920 Organoid snRNAseq analysis for batch B (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_L_1920, 2025-12-31, 0d
ADGC1_M_1920 Perform snRNAseq for batch C (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 2-4 organoid replicates/line; tif format) (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_M_1920, 2026-04-01, 0d
ADGC1_N_1920 Organoid snRNAseq analysis C (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_N_1920, 2027-04-01, 0d
ADGC1_O_1920 Perform Integrative analysis across first 30 genes and across experimental modalities (Spatial and snRNAseq). Submit L3-L4 level data by this time at the latest : crit, milestone, ADGC1_O_1920, 2027-04-01, 0d
ADGC1_P_1920 Perform snRNAseq for future batches (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_P_1920, 2026-12-31, 0d
ADGC1_Q_1920 Organoid snRNAseq Analysis for future batches (Submit L0-L1 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_Q_1920, 2027-04-01, 0d
gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC2 MiNND
section Grant Year
Start Grant Year 2 :milestone, m1, 2024-03-31, 0d
Start Grant Year 3 :milestone, m1, 2025-03-31, 0d
Start Grant Year 4 :milestone, m1, 2026-03-31, 0d
Start Grant Year 5 :milestone, m1, 2027-04-01, 0d
section Aim 1
Generated 217 new lines including 10 NTC (total 332 lines). We generated iNs from 180 lines. :done, IIt1, 2024-01-01, 2025-04-01
Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt2, after IIt1,13w
Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt3, after IIt2,13w
Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt4, after IIt3,13w
Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt5, after IIt4,13w
section Aim 2
Submitted scRNA-seq data for 157 lines to the DRACC. : done, IIt6, 2024-04-01,52w
Submit scRNA-seq data for 72 edited lines (3×23 gene mutations + 1 NTC) from last quarter. :crit, IIt7, after IIt6,13w
Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last year. :crit, IIt8, after IIt7,13w
Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last quarter. :crit, IIt9, after IIt8,13w
Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last quarter. :crit, IIt10, after IIt9,13w
Submitted 113 lines morphometrics imaging data. :done, IIt11, 2024-04-01,52w
Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt12, after IIt11,13w
Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt13, after IIt12,13w
Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt14, after IIt13,13w
Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt15, after IIt14,13w
Pilot CODEX LoF risk variants : II_codex1, 2024-10-01,39w
CODEX 30-50 patient-specific LoF variants KOLF2.2J : II_codex2, after II_codex1,13w
CODEX 12mm coverslips iNs, 30-50 SNPs (SNP/neuron), 3x reps : II_codex3, after II_codex2,13w
CODEX 3x data to BIL, generate LoF variants in 1-2 new lines : crit, II_codex4, after II_codex3,13w
section Aim 3
Submitted 46 lines of Synaptic Optical sensors imaging data : done, IIt16, 2024-04-01,52w
Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt17, after IIt16,13w
Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt18, after IIt17,13w
Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt19, after IIt18,13w
Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt20, after IIt19,13w
section Aim4
Submit PatchSeq data for 192 NTC lines L0 data :crit, IIv20, 2025-04-01,52w
Submit PatchSeq data for 192 cells L1-L3 : crit, IIv21, 2025-07-01,39w
gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC3 Yale
section Grant Year
Start Grant Year 2 :milestone, m1, 2024-03-31, 0d
Start Grant Year 3 :milestone, m1, 2025-03-31, 0d
Start Grant Year 4 :milestone, m1, 2026-03-31, 0d
Start Grant Year 5 :milestone, m1, 2027-04-01, 0d
section Aim 1
Validate gRNA library, lentivirus, pool for 10 capstone ASD genes : done, IIIt1, 2024-01-01,13w
Generate NPC lines from KOLF2.2J and CW20107 for 10 ASD genes : done, IIIt2, 2024-04-01,26w
SUSPENDED - ECCITEseq in hiPSC-NPCs of 10 ASD genes scRNA-seq profiles : active, IIIt3, after IIIt2,13w
SUSPENDED - Sequence and analysis poooled CRISPR screen of 10 NPD genes in hiPSC-NPCs : active, IIIt5, after IIIt3,13w
SUSPENDED - Submit data from multi-omic CRISPR screen of NPD genes in NPCs :active, IIIt8, after IIIt5, 13w
ECCITEseq in day 21 iGLUTs of 10 ASD genes scRNA-seq profiles : done, IIIt4, after IIIt3,13w
DELAYED - Sequence and analysis of pooled CRISPR screen of 10 NPD genes in NPC-iGLUTs : IIIt7, after IIIt5,13w
Submit data from multi-omic CRISPR screen of 29 NDD genes in iGLUTs 3182-3-clone5 & 553-3-clone34 :crit, IIIt9, after IIIt7,13w
DELAYED - dCas9-KRAB hiPSCs with dox-inducible ASCL1/DLX2 from KOLF2.2J and CW20107 hiPSCs : IIIt6, after IIIt4,13w
ECCITEseq in day 35 iGABA 10 genes scRNA-seq : IIIt10, after IIIt6,13w
ADGC3_N_5 Submit initial data (L0, L1) CRISPRi MEA and calcium imaging of 15 ASD genes in iGLUTs and/or iGABAs (ARID1B, ASH1L, CHD8, CUL3, DYRK1A, KMT5B, POGZ, PTEN, ANK2, CACNA1G, GRIA3, GRIN2A, NRXN1, SCN2A, SHANK3) : crit, milestone, ADGC3_N_5, 2027-04-01, 0d
ADGC3_K_6 Submit initial data (L0, L1) CRISPRi ECCITEseq, KOLF2.2J and CW20107 in iGLUTs (fastq), 10 capstone genes (ARID1B, ASXL3, CACNA1G, CHD8, DLL1, GABRA1, KMT2C, SCN2A, SHANK3, SMARCC2) : crit, milestone, ADGC3_K_6, 2025-10-01, 0d
ADGC3_N_6 Submit initial data (L0, L1) CRISPRi organoid models ECCITEseq of 10 capstone genes (ARID1B, ASXL3, CACNA1G, CHD8, DLL1, GABRA1, KMT2C, SCN2A, SHANK3, SMARCC2) genes in KOLF2.2J : crit, milestone, ADGC3_N_6, 2027-04-01, 0d
ADGC3_I_7 Submit ECCITEseq data (L0, L1) to DRACC for 29 NDD genes (ANK3, ARID1B, ASH1L, ASXL3, BCL11A, CHD2, CHD8, CREBBP, DPYSL2, FOXP2, KMT5B (SUV420H1), KDM5B, KDM6B, KMT2C, MBD5, MED13L, NRXN1, PHF12, PHF21A, POGZ, PPP2R5D, SCN2A, SETD5, SHANK3, SIN3A, SKI, SLC6A1, SMARCC2, WAC) in induced NPCs, glutamatergic neurons, and GABAergic neurons; iGLUT 3182-3-clone5 (iNPC, d7 iGLUT and d21 iGLUT) and iGABA 553-3-clone34 (d36 iGABA) : crit, milestone, ADGC3_I_7, 2025-04-01, 0d
ADGC3_K_7 Submit L3/L4 data from iGLUT manuscript : crit, milestone, ADGC3_K_7, 2025-10-01, 0d
section Aim 2
Generate zebrafish F0 mutants for 10 NPD genes in parallel with hiPSCs : IIIv16, 2024-01-01,13w
Submit data from high-throughput behavioral profiling of F0 mutants for 10 NPD genes : crit, IIIv17, 2024-01-01,13w
Design CRISPRs targeting another 20 genes in parallel with hiPSCs : IIIv18, 2024-01-01,13w
Design CRISPRs targeting another 10 NPD genes in parallel with hiPSCs : done, IIIv19, after IIIv18,13w
Submit data [acquired - not submitted] from high-throughput behavioral profiling for mutants of 10 NPD genes : crit, IIIv20, after IIIv17,13w
Generate zebrafish F0 mutants for 10 more NPD genes in parallel with hiPSCs: done, IIIv21, after IIIv19,13w
Behavioral profiling of zebrafish F0 mutants for another 10 NPD genes : done, IIIv22, after IIIv20,13w
Whole-brain mapping of zebrafish F0 mutants and stable lines for 5 NPD genes : done, IIIv23, 2024-07-01,13w
Design CRISPRs targeting of 10 more NPD genes in parallel with hiPSCs : done, IIIv24, after IIIv21,13w
Generate zebrafish F0 mutants for 10 more NPD genes in parallel with hiPSCs : done, IIIv25, after IIIv22,13w
Generate stable zebrafish mutant lines for 5 NPD genes with the most robust phenotypes : done, IIIv26, 2024-10-01,13w
Behavioral profiling of zebrafish F0 mutants for another 10 NPD genes : done, IIIv27, after IIIv24,13w
Submit data from high-throughput behavioral profiling for F0 mutants of 10 NPD genes : crit, IIIv28, after IIIv25,13w
ONGOING - Whole-brain mapping of zebrafish F0 mutants and stable lines for 5 NPD genes : IIIv29, 2025-01-01,13w
Generate stable zebrafish mutant lines for 5 NPD genes with the most robust phenotypes : done, IIIv30, after IIIv26,13w
Generate zebrafish F0 mutants for 20 more NPD genes in parallel with hiPSCs : IIIv31, after IIIv27,13w
Submit data from high-throughput behavioral profiling for F0 mutants of 20 more NPD genes : crit, IIIv32, after IIIv28,13w
Whole-brain mapping of zebrafish F0 mutants and stable lines for 10 NPD genes : IIIv33, after IIIv29,13w
Generate stable zebrafish mutant lines for 10 NPD genes with the most robust phenotypes : IIIv34, after IIIv30,13w
Submit data from whole-brain structure and activity mapping of zebrafish mutants of 10 NPD genes : crit, IIIv35, after IIIv33,13w
ADGC3_I_12 Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 10 stable mutant lines (ADNP, ARID1B, ASH1L, GRIN2A, KMT2C, KMT5B, NRXN1, PTEN, SHANK3, SYNGAP1) : crit, milestone, ADGC3_I_12, 2025-04-01, 0d
ADGC3_J_14 Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes (ANK2, AUTS2, BCL11A, CHD2, CREBBP, CTNNB1, DDX3X, DNMT3, FOXP2, GABRA1, GRIA3, KDM6B, MBD5, NLGN4, PHF12, PHF21, PIK3C, PPP2R5D, SIN3A, SMARCC2) : crit, milestone, ADGC3_J_14, 2025-07-01, 0d
ADGC3_K_14 Submit data (L0, L1) Whole-brain structure and activity mapping (.LIF, .XLS), zebrafish, 5 NPD genes (ADNP, ASH1L, FOXP2, KMT5B, NRXN1) : crit, milestone, ADGC3_K_14, 2025-10-01, 0d
ADGC3_L_14 Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes (AKAP11, ANKRD11, BCKDK, CACNA1G, CASK, CUL1, DLG4, DLL1, DSCAM, FOXP1, KCNB1, KCNQ3, KMT2A, RFX3, SETD5, SKI, SLC6A1, STXBP1, TRIO, WAC) : crit, milestone, ADGC3_L_14, 2025-12-31, 0d
ADGC3_M_14 Submit data (L0, L1) Whole-brain structure and activity mapping (.LIF, .XLS), zebrafish, 5 NPD genes (PPP2R5D, PTEN, ARID1B, GABRA1, MBD5) : crit, milestone, ADGC3_M_14, 2026-03-31, 0d
ADGC3_K_15 Submit L3/L4 data from 40 NPD gene manuscript : crit, milestone, ADGC3_K_15, 2025-10-01, 0d
ADGC3_N_15 Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes (CASKIN1, CTCF, DEAF1, DYNC1H1, FMR1, GIGYF1, HERC1, IRF2BPL, KCNMA1, MECP2, MED13L, NF1, RB1CC1, SETD1A, SP4, TAOK1, TCF20, TCF7L2, TLK2, XPO7) : crit, milestone, ADGC3_N_15, 2027-04-01, 0d
ADGC3_N_17 Submit data (L0, L1) Whole-brain RNA-seq, zebrafish, 10 NPD genes (CHD8, ARID1B, ASH1L, FOXP2, GABRA1, MBD5, PPP2R5D, PTEN, SHANK3, SMARCC2) : crit, milestone, ADGC3_N_17, 2027-04-01, 0d
section Aim 3
ONGOING - Optimize spatial transcriptomic and epigenomic analysis of larval zebrafish using DBiT-Seq : IIIv11, 2024-01-01,52w
ONGOING - Submit 5 DBiT RNA-seq and 5 DBiT ATAC-seq profiles : crit, IIIv12, after IIIv11,13w
Optimize spatial transcriptomic and epigenomic analysis of larval zebrafish using DBiT-Seq : III_v11_new1, 2025-04-01,26w
Produce 5-10 DBiT RNA-seq profiles (fastq) and 5-10 DBiT ATAC-seq profiles (fastq). : III_v11_new2, after III_v11_new1,13w
Submit another 5 DBiT RNA-seq and 5 DBiT ATAC-seq profiles : crit, IIIv13, after III_v11_new2,13w
Submit data [10-20 DBiT RNA-seq profiles (fastq) and 10-20 DBiT ATAC-seq profiles (fastq)] : crit, IIIv13_new1, after IIIv13,52w
Optimize multi-omic CRISPR screen of NPD genes in hiPSC-NPCs : IIIv14, 2024-04-01,78w
Produce 5-10 DBiT RNA-seq profiles (fastq) and 5-10 DBiT ATAC-seq profiles (fastq) : IIIv14_new1, after IIIv14,13w
Submit data from multi-omic CRISPR screen of NPD genes in hiPSCs :crit, IIIv15, after IIIv14_new1,13w
Submit data [10-20 DBiT RNA-seq profiles (fastq) and 10-20 DBiT ATAC-seq profiles (fastq)] : crit, IIIv16, after IIIv15,52w
ADGC3_M_22 Submit data (L0, L1) Transcriptomic and epigenomic analysis (5 DBiT RNA-seq profiles (fastq) and 5 DBiT ATAC-seq profiles (fastq)), zebrafish, one NPD gene (CHD8) : crit, milestone, ADGC3_M_22, 2026-03-31, 0d
ADGC3_N_22 Submit data (L0, L1) Transcriptomic and epigenomic analysis (10-20 DBiT RNA-seq profiles (fastq) and 10-20 DBiT ATAC-seq profiles (fastq)), zebrafish, two NPD genes (TBD, possibly SMARCC2, SHANK3) : crit, milestone, ADGC3_N_22, 2027-04-01, 0d
ADGC3_M_23 Submit data (L0, L1) CRISPRi organoid transcriptomic and epigenomic analysis (5-10 DBiT RNA-seq profiles (fastq) and 5-10 DBiT ATAC-seq profiles (fastq)), one NPD gene (CHD8) : crit, milestone, ADGC3_M_23, 2026-03-31, 0d
ADGC3_N_23 Submit data (L0, L1) CRISPRi organoid transcriptomic and epigenomic analysis (10-20 DBiT RNA-seq profiles (fastq) and 10-20 DBiT ATAC-seq profiles (fastq)), two NPD genes (TBD, possibly SMARCC2, SHANK3) : crit, milestone, ADGC3_N_23, 2027-04-01, 0d
gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC4 Broad
section Grant Year
Start Grant Year 2 :milestone, m1, 2024-03-31, 0d
Start Grant Year 3 :milestone, m1, 2025-03-31, 0d
Start Grant Year 4 :milestone, m1, 2026-03-31, 0d
Start Grant Year 5 :milestone, m1, 2027-04-01, 0d
section Aim 1
Performed pilot morpholgy screen in 20 genes : done, IVt1, 2024-01-01,13w
Perform perturb-seq screen of ~150 genes in 4 cell types : IVt2, 2024-04-01,52w
Submit 100,000 scRNA-seq profiles per cell type (fastq) - PARTIALLY COMPLETE (191 GENES, 3 CELL TYPES)/ TRANSFER STARTED : crit, IVt2b, after IVt2,3w
Submit 100,000 scRNA-seq profiles per cell type (fastq) of 191 genes in 3 cell types : crit, IVt2_year4, 2026-03-15,3w
Develop protocol for scaling up screen size : done, IVt5, 2024-04-01,52w
Validation of initial 20 gene morphological screen : done, IVt3, 2024-04-01,52w
Submit image dataset of 40 TB - DONE, DATA TRANSFER STARTED : crit, IVt4, after IVt3,3w
Submit image dataset of 120 TB (443 genes in 3 cells 5 million profiles) : crit, IVt6, 2026-03-15,3w
Submit remaining image datasets : crit, IVt7, 2027-03-15,3w
section Aim 2
Developed Perturb-FISH screens : done, IVt8, 2024-01-01,13w
Perform perturb-seq screen of ~150 genes in 4 cell types - PARTIALLY COMPLETE : IVt9, 2024-04-01,52w
Submit 100,000 scRNA-seq profiles per cell type of 191 genes in 3 cell types (fastq) : crit, IVt9b_year4, 2026-03-15,3w
Perform Perturb-FISH screen of ASD genes in iPS derived astrocytes : done, IVt10, 2024-04-01, 52w
Submit 50 TB of calcium imaging and MERFISH data : done, IVt11, after IVt10, 3w
Perform pilot 10 gene electrophysiology screen - PARTIALLY COMPLETE : IVt12, 2024-04-01,52w
Submit 5 TB of optical electrophysiology data - DATA QUALITY BEING ASSESSED : crit, IVt13, after IVt12, 3w
Submit 5 TB of optical electrophysiology data : crit, IVt14, 2026-03-15,3w
Submit remaining optical electrophysiology data : crit, IVt15, 2027-03-15,3w
section Aim 3
Perform scRNAseq (dropulation) screen of ~40 line village of CIRM lines - PARTIALLY COMPLETE : IVt16, 2024-04-01,52w
Submit RNA-seq profiles - ANALYSIS / SUBMISSION UNDERWAY : crit, IVt16b, after IVt16, 3w
Submit RNA-seq profiles from >10,000 cells : crit, IVt17, 2026-03-15,3w
Submit remaining RNA-seq profiles : crit, IVt17_yearEnd, 2027-03-15,3w
Morphological profiles of ~40 line village of CIRM lines : IVt18a, 2025-04-01,52w
Submit ~10 TB of associated images to DRACC : crit, IVt18b, after IVt18a,3w
Submit remaining morphology imaging : crit, IVt19, 2027-03-15,3w
gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC5 Scripps/Broad
section Grant Year
Start Grant Year 2 :milestone, m1, 2024-03-31, 0d
Start Grant Year 3 :milestone, m1, 2025-03-31, 0d
Start Grant Year 4 :milestone, m1, 2026-03-31, 0d
Start Grant Year 5 :milestone, m1, 2027-04-01, 0d
section Scripps/Broad Reporting Year
End Scripps/Broad Reporting Year 1 :milestone, m1, 2025-03-31, 0d
End Scripps/Broad Reporting Year 2 :milestone, m1, 2026-03-31, 0d
End Scripps/Broad Reporting Year 3 :milestone, m1, 2027-04-01, 0d
section Aim 1
Refine AAV-based Perturb-seq, test v1 and v2, assess data quality, finalize method : Vt1, 2024-09-01,2025-04-01
Design gRNAs and generate vectors for Perturb-seq : Vt2, 2024-09-01,2025-04-01
Choose single cell technology; test, validate with finalized Perturb-seq method : Vt3, 2024-09-01,2025-04-01
Test gRNA efficacy in vitro; nominate final perturbation vectors to be used : Vt4, 2024-09-01,2025-04-01
Discuss within and across ADGC groups to choose genes to target among list of 259 genes; finalize gene selection for this project : Vt5, 2024-09-01,2025-04-01
Generate multiomics data for 50 genes in 1 brain region at 1 time point : V_Y2t1, 2025-04-01,52w
Submit L0/L1 data to DRACC (Restricted) ~175 FASTQ for ~75TB overall : crit, V_Y2t2, 2025-04-01,52w
section Aim 2
Refine brain clearing experiments (1) test CUBIC method and assess data quality : Vt6, 2024-09-01,2025-04-01
Refine brain clearing experiments (2) test LifeCanvas (CLARITY) method and assess data quality : Vt7, 2024-09-01,2025-04-01
Establish data analysis pipeline through semi-automatic image tracing and segmentation : Vt8, 2024-09-01,2025-04-01
Establish approaches to integrate single-cell omic data with spatial morphometric data : Vt9, 2024-09-01,2025-04-01
Select first 5 ASD risk genes to be included in the study : Vt10, 2024-09-01,2025-04-01
Test gRNA efficacy in vitro, nominate final vectors, collect brain samples : V_Y2t3, 2025-04-01,52w
Implement functional pipeline for analyzing Perturb-seq multiomics data : V_Y2t4,2025-04-01,52w
Develop methods for GRN analysis of multiomics data : V_Y2t5, 2025-04-01,52w
Identify datasets to be used to build GRNs from developing human brains : V_Y2t6, 2025-04-01,52w
Generate raw TIFF format and 3D swc files for 100 neurons on 3 genes : V_Y2t7, 2025-04-01,52w
gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC6 Cross-Scale Interrogation of NPD Genes (SING) - PSU/JAX/UTSW/NYU
section Grant Year
Start Grant Year 2 :milestone, m1, 2024-03-31, 0d
Start Grant Year 3 :milestone, m1, 2025-03-31, 0d
Start Grant Year 4 :milestone, m1, 2026-03-31, 0d
Start Grant Year 5 :milestone, m1, 2027-04-01, 0d
section SING Reporting Year
End SING Reporting Year 1 :milestone, m1, 2025-12-31, 0d
End SING Reporting Year 2 :milestone, m1, 2026-12-31, 0d
section Aim 1
ADGC6_C_7 Initial discussion with DRACC for data transfer complete : crit, milestone, ADGC6_C_7, 2025-06-31, 0d
ADGC6_D_8 DRACC data transfer of C57 control MERFISH : crit, milestone, ADGC6_D_8, 2025-10-01, 0d
ADGC6_E_7 DRACC data transfer of first 5 KO mice MERFISH data : crit, milestone, ADGC6_E_7, 2026-01-01, 0d
ADGC6_F_7 DRACC data transfer of 2025 Q4 and 20026 Q1-Q3 KO mice MERFISH data : crit, milestone, ADGC6_F_7, 2027-01-01, 0d
ADGC6_D_10 DRACC data transfer of C57 control 10x Flex : crit, milestone, ADGC6_D_10, 2025-10-01, 0d
ADGC6_F_10 DRACC data transfer of 10x Flex from 2025 and 2026Q1-Q2 : crit, milestone, ADGC6_F_10, 2027-01-01, 0d
section Aim 2
ADGC6_C_16 Initial discussion with DRACC for data transfer complete : crit, milestone, ADGC6_C_16, 2025-06-31, 0d
ADGC6_D_16 DRACC data transfer of C57 control MRI and LSFM data : crit, milestone, ADGC6_D_16, 2025-10-01, 0d
ADGC6_E_16 DRACC data transfer of first 5 KO mice MRI and LSFM data : crit, milestone, ADGC6_E_16, 2026-01-01, 0d
ADGC6_F_16 DRACC data transfer of 2025 Q4 and 20026 Q1-Q3 KO mice MRI and LSFM data : crit, milestone, ADGC6_F_16, 2027-01-01, 0d
section Aim 3
ADGC6_C_23 Initial discussion with DRACC for data transfer complete : crit, milestone, ADGC6_C_23, 2025-06-31, 0d
ADGC6_D_23 DRACC data transfer of C57 control behavioral data : crit, milestone, ADGC6_D_23, 2025-10-01, 0d
ADGC6_E_23 DRACC data transfer of first 5 KO lines behavioral data : crit, milestone, ADGC6_E_23, 2026-01-01, 0d
ADGC6_F_23 DRACC data transfer of 2025 Q4 and 20026 Q1-Q3 KO line behavioral data : crit, milestone, ADGC6_F_23, 2027-01-01, 0d
gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC7 Washington Univ. St Louis - WUSTL
section Grant Year
Start Grant Year 2 :milestone, m1, 2024-03-31, 0d
Start Grant Year 3 :milestone, m1, 2025-03-31, 0d
Start Grant Year 4 :milestone, m1, 2026-03-31, 0d
Start Grant Year 5 :milestone, m1, 2027-04-01, 0d
section WUSTL Reporting Year
End WUSTL Reporting Year 1 :milestone, m1, 2025-12-31, 0d
End WUSTL Reporting Year 2 :milestone, m1, 2026-12-31, 0d
- section FULL-TEXT WUSTL
- ADGC7_E_12 L0, L1 Data from last quarter submitted, and 3 more lines collected : crit, milestone, ADGC7_E_12, 2027-04-01, 0d
- ADGC7_F_12 L0, L1 Data from last quarter submitted, and 4 more lines collected : crit, milestone, ADGC7_F_12, 2027-04-01, 0d
- ADGC7_F_13 L2, L3 from prior L0,L1 data submitted : crit, milestone, ADGC7_F_13, 2027-04-01, 0d
- ADGC7_C_17 Home Cage Behavior L0-L1 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_C_17, 2027-04-01, 0d
- ADGC7_D_17 Home Cage Behavior L0-L1 Data to DRACC for line 3-4 : crit, milestone, ADGC7_D_17, 2027-04-01, 0d
- ADGC7_E_17 Home Cage Behavior L0-L1 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_E_17, 2027-04-01, 0d
- ADGC7_D_18 Home Cage Behavior L3 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_D_18, 2027-04-01, 0d
- ADGC7_E_18 Home Cage Behavior L3 Data to DRACC for line3-4 : crit, milestone, ADGC7_E_18, 2027-04-01, 0d
- ADGC7_F_18 Home Cage Behavior L3 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_F_18, 2027-04-01, 0d
- ADGC7_E_19 Home Cage Behavior L4 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_E_19, 2027-04-01, 0d
- ADGC7_F_19 Home Cage Behavior L4 Data to DRACC for lines 3-4 : crit, milestone, ADGC7_F_19, 2027-04-01, 0d
- ADGC7_C_20 IB & SI L0 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_C_20, 2027-04-01, 0d
- ADGC7_D_20 IB & SI L1 & L3 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_D_20, 2027-04-01, 0d
- ADGC7_E_20 IB & SI L4 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_E_20, 2027-04-01, 0d
- ADGC7_D_21 IB & SI L0 Data to DRACC for line 3-4 : crit, milestone, ADGC7_D_21, 2027-04-01, 0d
- ADGC7_E_21 IB & SI L1 & L3 Data to DRACC for line 3-4 : crit, milestone, ADGC7_E_21, 2027-04-01, 0d
- ADGC7_F_21 IB & SI L4 Data to DRACC for line 3-4 : crit, milestone, ADGC7_F_21, 2027-04-01, 0d
- ADGC7_E_22 IB & SI L0 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_E_22, 2027-04-01, 0d
- ADGC7_F_22 IB & SI L1 & L3 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_F_22, 2027-04-01, 0d
- ADGC7_D_27 Imaging L0, L1 data collected for 3 lines : crit, milestone, ADGC7_D_27, 2027-04-01, 0d
- ADGC7_E_27 L0, L1 Data from last quarter submitted, and 4 more lines collected : crit, milestone, ADGC7_E_27, 2027-04-01, 0d
- ADGC7_F_27 L0, L1 Data from last quarter submitted, and 4 more lines collected : crit, milestone, ADGC7_F_27, 2027-04-01, 0d
- ADGC7_F_28 L2, L3 from prior L0,L1 data submitted : crit, milestone, ADGC7_F_28, 2027-04-01, 0d
+ section Aim 1
+ ADGC7_E_12 L0, L1 Data from last quarter submitted, and 3 more lines collected : crit, milestone, ADGC7_E_12, 2025-12-31, 0d
+ ADGC7_F_12 L0, L1 Data from last quarter submitted, and 4 more lines collected : crit, milestone, ADGC7_F_12, 2026-03-31, 0d
+ ADGC7_F_13 L2, L3 from prior L0,L1 data submitted : crit, milestone, ADGC7_F_13, 2026-03-31, 0d
+
+ section Aim 2
+ ADGC7_C_17 Home Cage Behavior L0-L1 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_C_17, 2025-07-01, 0d
+ ADGC7_D_17 Home Cage Behavior L0-L1 Data to DRACC for line 3-4 : crit, milestone, ADGC7_D_17, 2025-09-31, 0d
+ ADGC7_E_17 Home Cage Behavior L0-L1 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_E_17, 2025-12-31, 0d
+ ADGC7_D_18 Home Cage Behavior L3 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_D_18, 2025-09-31, 0d
+ ADGC7_E_18 Home Cage Behavior L3 Data to DRACC for line3-4 : crit, milestone, ADGC7_E_18, 2025-12-31, 0d
+ ADGC7_F_18 Home Cage Behavior L3 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_F_18, 2026-03-31, 0d
+ ADGC7_E_19 Home Cage Behavior L4 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_E_19, 2025-12-31, 0d
+ ADGC7_F_19 Home Cage Behavior L4 Data to DRACC for lines 3-4 : crit, milestone, ADGC7_F_19, 2026-03-31, 0d
+ ADGC7_C_20 IB & SI L0 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_C_20, 2025-07-01, 0d
+ ADGC7_D_20 IB & SI L1 & L3 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_D_20, 2025-09-31, 0d
+ ADGC7_E_20 IB & SI L4 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_E_20, 2025-12-31, 0d
+ ADGC7_D_21 IB & SI L0 Data to DRACC for line 3-4 : crit, milestone, ADGC7_D_21, 2025-09-31, 0d
+ ADGC7_E_21 IB & SI L1 & L3 Data to DRACC for line 3-4 : crit, milestone, ADGC7_E_21, 2025-12-31, 0d
+ ADGC7_F_21 IB & SI L4 Data to DRACC for line 3-4 : crit, milestone, ADGC7_F_21, 2026-03-31, 0d
+ ADGC7_E_22 IB & SI L0 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_E_22, 2025-12-31, 0d
+ ADGC7_F_22 IB & SI L1 & L3 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_F_22, 2026-03-31, 0d
+
+ section Aim 3
+ ADGC7_D_27 Imaging L0, L1 data collected for 3 lines : crit, milestone, ADGC7_D_27, 2025-09-31, 0d
+ ADGC7_E_27 L0, L1 Data from last quarter submitted, and 4 more lines collected : crit, milestone, ADGC7_E_27, 2025-12-31, 0d
+ ADGC7_F_27 L0, L1 Data from last quarter submitted, and 4 more lines collected : crit, milestone, ADGC7_F_27, 2026-03-31, 0d
+ ADGC7_F_28 L2, L3 from prior L0,L1 data submitted : crit, milestone, ADGC7_F_28, 2026-03-31, 0d