16ae9a2464995949ec09f739683d0b09282a379d brianlee Mon Jan 26 13:27:34 2026 -0800 Stripping timeline chart down to just submission milestones for clarity diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index 6771aea6f68..5b603df9d01 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -27,73 +27,49 @@ gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC1 UCLA [RM1MH132651] section Grant Year Start Grant Year 2 :milestone, m1, 2024-03-31, 0d Start Grant Year 3 :milestone, year3_ucla, 2025-03-31, 0d Start Grant Year 4 :milestone, m1, 2026-03-31, 0d Start Grant Year 5 :milestone, m1, 2027-03-31, 0d click year3_ucla href "https://docs.google.com/spreadsheets/d/1Ml_UXDHE4UZo2kjLp1aZLa0KxLtLSnVi/edit?gid=1138387919#gid=1138387919&range=J1:M20" section AIM 1 - Generate stable clonal iPSC lines for additional 25 gene mutations in KOLF2.2J and CIRM (BATCH B) : t3, 2024-03-31, 2024-09-30 - QC of Capstone lines to date pending : t4, 2024-03-31, 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, 2025-09-30,30w - Submit data on RNA-seq profiles from BATCH B and C :crit, t33, 2025-09-30,13w Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from Capstone Lines 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_I_8, 2025-03-31, 0d Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from BATCH B 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_JK_8, 2025-09-30, 0d Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from BATCH C 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_LM_8, 2026-03-31, 0d Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from BATCH D 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_NO_8, 2026-10-01, 0d Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from BATCH E 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_P_8, 2026-12-31, 0d Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from BATCH F 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_Q_8, 2027-03-31, 0d Submit L0-L1 from BATCH B, producing bulk RNA-seq profiles 3 tech reps, 4 bio reps/gene × (20 NPD + 2 ctrl) × 2 (KOLF2.2J/CIRM) iPSC lines; .fastq : crit, milestone, ADGC1_LM_111213, 2026-03-31, 0d Submit L0-L1 from BATCH C, producing bulk RNA-seq profiles 3 tech reps, 4 bio reps/gene × (20 NPD + 2 ctrl) × 2 (KOLF2.2J/CIRM) iPSC lines; .fastq : crit, milestone, ADGC1_NO_111213, 2026-10-01, 0d Submit L0-L1 from BATCH D, producing bulk RNA-seq profiles 3 tech reps, 4 bio reps/gene × (20 NPD + 2 ctrl) × 2 (KOLF2.2J/CIRM) iPSC lines; .fastq : crit, milestone, ADGC1_P_111213, 2026-12-31, 0d Submit L0-L1 from BATCH E-G, producing bulk RNA-seq profiles 3 tech reps, 4 bio reps/gene × (20 NPD + 2 ctrl) × 2 (KOLF2.2J/CIRM) iPSC lines; .fastq : crit, milestone, ADGC1_Q_111213, 2027-03-31, 0d Complete villages - submit L0-L1 to DRACC : crit, milestone, ADGC1_JK_14, 2025-09-30, 0d Village Analysis - submit L0-L1 to DRACC : crit, milestone, ADGC1_LM_14, 2026-03-31, 0d Calcium Imaging Capstone Analysis 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_K_15, 2025-09-30, 0d Calcium Imaging analysis excitatory/inhibitory neurons - Capstone Analysis 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_M_15, 2026-03-31, 0d Calcium Imaging Experiments and analysis of future batches 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds (Submit L0-L4 to DRACC) : crit, milestone, ADGC1_NOPQ_15, 2027-03-31, 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 Perform codex Capstone Lines (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; qptiff format) : crit, milestone, ADGC1_J_161718, 2025-07-01, 0d Spatial Proteomics Analysis Capstone Lines : crit, milestone, ADGC1_K_161718, 2025-09-30, 0d Perform codex BATCH B (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; qptiff format) : crit, milestone, ADGC1_L_161718, 2025-12-31, 0d Spatial Proteomics Analysis BATCH B : crit, milestone, ADGC1_M_161718, 2026-03-31, 0d Perform codex BATCH C (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; qptiff format) : crit, milestone, ADGC1_N_161718, 2027-03-31, 0d Spatial Proteomics Analysis BATCH C : crit, milestone, ADGC1_O_161718, 2027-03-31, 0d Perform codex and analysis for future batches : crit, milestone, ADGC1_Q_161718, 2027-03-31, 0d Organoid snRNAseq analysis for Capstone Genes : crit, milestone, ADGC1_J_1920, 2025-07-01, 0d 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) : crit, milestone, ADGC1_K_1920, 2025-09-30, 0d Organoid snRNAseq analysis for BATCH B : crit, milestone, ADGC1_L_1920, 2025-12-31, 0d 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) : crit, milestone, ADGC1_M_1920, 2026-03-31, 0d Organoid snRNAseq analysis C : crit, milestone, ADGC1_N_1920, 2027-03-31, 0d 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, 2027-03-31, 0d Perform snRNAseq for future batches : crit, milestone, ADGC1_P_1920, 2026-12-31, 0d Organoid snRNAseq Analysis for future batches : crit, milestone, ADGC1_Q_1920, 2027-03-31, 0d @@ -109,35 +85,30 @@ <pre class="mermaid"> gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC2 MiNND [RM1MH133065] section Grant Year Start Grant Year 2 :milestone, m1, 2024-03-31, 0d Start Grant Year 3 :milestone, year3_minnd, 2025-03-31, 0d Start Grant Year 4 :milestone, m1, 2026-03-31, 0d Start Grant Year 5 :milestone, m1, 2027-03-31, 0d click year3_minnd href "https://docs.google.com/spreadsheets/d/1GNrJaIjs6nPlFY4j2AlZSlTDf2-mi17d/edit?gid=1137576441#gid=1137576441&range=J1:M34" section Aim 1 - Generated 217 new lines including 10 NTC (total 332 lines). We generated iNs from 180 lines. :done, IIt1, 2024-03-31, 2025-03-31 - 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, 2024-03-31,52w 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, 2024-03-31,52w 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 @@ -164,137 +135,91 @@ <pre class="mermaid"> gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC3 Yale [RM1MH132648] section Grant Year Start Grant Year 2 :milestone, m1, 2024-03-31, 0d Start Grant Year 3 :milestone, year3_yale, 2025-03-31, 0d Start Grant Year 4 :milestone, m1, 2026-03-31, 0d Start Grant Year 5 :milestone, m1, 2027-03-31, 0d click year3_yale href "https://docs.google.com/spreadsheets/d/10xWymZXsDlDQ9uwU5YPAKwyflUMzpDS4/edit?gid=1305684354#gid=1305684354&range=J1:M25" section Aim 1 - Generate NPC lines from KOLF2.2J and CW20107 for 10 ASD genes : done, IIIt2, 2024-03-31,26w - 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 Submit initial data (L0, L1) CRISPRi MEA and calcium imaging of 15 ASD genes in iGLUTs and/or iGABAs (ARID1B - SHANK3) : crit, milestone, ADGC3_N_5, 2027-03-31, 0d Submit initial data (L0, L1) CRISPRi ECCITEseq, KOLF2.2J and CW20107 in iGLUTs (fastq), 10 capstone genes (ARID1B - SMARCC2) : crit, milestone, ADGC3_K_6, 2025-09-30, 0d Submit initial data (L0, L1) CRISPRi organoid models ECCITEseq of 10 capstone genes (ARID1B - SMARCC2) genes in KOLF2.2J : crit, milestone, ADGC3_N_6, 2027-03-31, 0d Submit ECCITEseq data (L0, L1) to DRACC for 29 NDD genes (ANK3 - 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) : done, milestone, ADGC3_I_7, 2025-03-31, 0d Submit L3/L4 data from iGLUT manuscript : crit, milestone, ADGC3_K_7, 2025-09-30, 0d section Aim 2 - 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 Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 10 stable mutant lines (ADNP - SYNGAP1) : crit, milestone, ADGC3_I_12, 2025-03-31, 0d Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes (ANK2 - SMARCC2) : crit, milestone, ADGC3_J_14, 2025-07-01, 0d Submit data (L0, L1) Whole-brain structure and activity mapping (.LIF, .XLS), zebrafish, 5 NPD genes (ADNP - NRXN1) : crit, milestone, ADGC3_K_14, 2025-09-30, 0d Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes (AKAP11 - WAC) : crit, milestone, ADGC3_L_14, 2025-12-31, 0d Submit data (L0, L1) Whole-brain structure and activity mapping (.LIF, .XLS), zebrafish, 5 NPD genes (PPP2R5D - MBD5) : crit, milestone, ADGC3_M_14, 2026-03-31, 0d Submit L3/L4 data from 40 NPD gene manuscript : crit, milestone, ADGC3_K_15, 2025-09-30, 0d Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes (CASKIN1 - XPO7) : crit, milestone, ADGC3_N_15, 2027-03-31, 0d Submit data (L0, L1) Whole-brain RNA-seq, zebrafish, 10 NPD genes (CHD8 - SMARCC2) : crit, milestone, ADGC3_N_17, 2027-03-31, 0d section Aim 3 - ONGOING - Optimize spatial transcriptomic and epigenomic analysis of larval zebrafish using DBiT-Seq : IIIv11, 2024-03-31,52w - 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, 2025-03-31,26w - 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, 2024-03-31,78w - Produce 5-10 DBiT RNA-seq profiles (fastq) and 5-10 DBiT ATAC-seq profiles : 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 Submit data (L0, L1) Transcriptomic and epigenomic analysis 5 DBiT RNA-seq, 5 DBiT ATAC-seq, zebrafish CHD8 : crit, milestone, ADGC3_M_22, 2026-03-31, 0d Submit data (L0, L1) Transcriptomic and epigenomic analysis 10-20 DBiT RNA-seq and DBiT ATAC-seq profiles, zebrafish 2 TBD genes : crit, milestone, ADGC3_N_22, 2027-03-31, 0d Submit data (L0, L1) CRISPRi organoid transcriptomic and epigenomic analysis 5-10 DBiT RNA-seq profiles and DBiT ATAC-seq profiles, CHD8 : crit, milestone, ADGC3_M_23, 2026-03-31, 0d Submit data (L0, L1) CRISPRi organoid transcriptomic and epigenomic analysis 10-20 DBiT RNA-seq and DBiT ATAC-seq, two TBD genes : crit, milestone, ADGC3_N_23, 2027-03-31, 0d </pre> </div> </div> <a name="ADGC4"></a> <!-- Start of ADGC4 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC4 Broad timeline</h5></div> <div class="row"> <div class="col-md-12"> <pre class="mermaid"> gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC4 Broad [R01MH128366] section Grant Year Start Grant Year 2 :milestone, m1, 2024-03-31, 0d Start Grant Year 3 :milestone, year3_broad, 2025-03-31, 0d Start Grant Year 4 :milestone, m1, 2026-03-31, 0d Start Grant Year 5 :milestone, m1, 2027-03-31, 0d click year3_broad href "https://docs.google.com/spreadsheets/d/1BwaO6rgn0o5nTulC2M6dQe5UMGUWEy-o/edit?gid=2037309850#gid=2037309850&range=D1:D16" section Aim 1 - Perform perturb-seq screen of 150 genes in 4 cell types : IVt2, 2024-03-31,52w - 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, milestone, ADGC4_Aim1_year4_item1, 2026-03-31, 0d - Develop protocol for scaling up screen size : done, IVt5, 2024-03-31,52w - Validation of initial 20 gene morphological screen : done, IVt3, 2024-03-31,52w - 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, milestone, ADGC4_Aim1_year4_item2, 2026-03-31, 0d Submit remaining image datasets : crit, milestone, ADGC4_Aim1_year5_item1, 2027-03-31, 0d section Aim 2 - Perform perturb-seq screen of 150 genes in 4 cell types - PARTIALLY COMPLETE : IVt9, 2024-03-31,52w Submit 100,000 scRNA-seq profiles per cell type of 191 genes in 3 cell types (fastq) : crit, milestone, ADGC4_Aim2_year4_item1, 2026-03-31, 0d - Perform Perturb-FISH screen of ASD genes in iPS derived astrocytes : done, IVt10, 2024-03-31, 52w - Submit 50 TB of calcium imaging and MERFISH data : done, IVt11, after IVt10, 3w - Perform pilot 10 gene electrophysiology screen - PARTIALLY COMPLETE : IVt12, 2024-03-31,52w - Submit 5 TB of optical electrophysiology data - DATA QUALITY BEING ASSESSED : crit, IVt13, after IVt12, 3w + Submit 50 TB of calcium imaging and MERFISH data : done, milestone, ADGC4_Aim2_year3_item1, 2025-03-31, 0d + Submit 5 TB of optical electrophysiology data - DATA QUALITY BEING ASSESSED : crit, milestone, ADGC4_Aim2_year3_item2, 2026-03-31, 0d Submit 5 TB of optical electrophysiology data : crit, milestone, ADGC4_Aim2_year4_item2, 2026-03-31, 0d Submit remaining optical electrophysiology data : crit, milestone, ADGC4_Aim2_year5_item1, 2027-03-31, 0d section Aim 3 - Perform scRNAseq (dropulation) screen of 40 line village of CIRM lines - PARTIALLY COMPLETE : IVt16, 2024-03-31,52w - Submit RNA-seq profiles - ANALYSIS / SUBMISSION UNDERWAY : crit, IVt16b, after IVt16, 3w + Submit RNA-seq profiles - ANALYSIS / SUBMISSION UNDERWAY : crit, milestone, ADGC4_Aim3_year3_item1, 2025-03-31, 0d Submit RNA-seq profiles from >10,000 cells : crit, milestone, ADGC4_Aim3_year4_item1, 2026-03-31, 0d Submit remaining RNA-seq profiles : crit, milestone, ADGC4_Aim3_year5_item1, 2027-03-31, 0d - Morphological profiles of 40 line village of CIRM lines : IVt18a, 2025-03-31,52w Submit 10 TB of associated images to DRACC : crit, milestone, ADGC4_Aim3_year4_item2, 2026-03-31, 0d Submit remaining morphology imaging : crit, milestone, ADGC4_Aim3_year5_item2, 2027-03-31, 0d </pre> </div> </div> <a name="ADGC5"></a> <!-- Start of ADGC5 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC5 Scripps/Broad timeline</h5></div> <div class="row"> <div class="col-md-12"> <pre class="mermaid"> gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q @@ -302,105 +227,87 @@ 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, 2027-03-31, 0d section Scripps/Broad Reporting Year End Scripps/Broad Reporting Year 1 :milestone, year1_scripps, 2025-03-31, 0d End Scripps/Broad Reporting Year 2 :milestone, m1, 2026-03-31, 0d End Scripps/Broad Reporting Year 3 :milestone, m1, 2027-03-31, 0d click year1_scripps href "https://docs.google.com/spreadsheets/d/19RWN6-DjIyMpFV2JP4yY5Ta5Xfthieds/edit?gid=744607405#gid=744607405&range=C2:C15" section Aim 1 - Refine AAV-based Perturb-seq, test v1 and v2, assess data quality, finalize method : Vt1, 2024-09-01,2025-03-31 - Design gRNAs and generate vectors for Perturb-seq : Vt2, 2024-09-01,2025-03-31 - Choose single cell technology; test, validate with finalized Perturb-seq method : Vt3, 2024-09-01,2025-03-31 - Test gRNA efficacy in vitro; nominate final perturbation vectors to be used : Vt4, 2024-09-01,2025-03-31 - Discuss within and across ADGC groups to choose genes to target among list of 259 genes; finalize gene selection for this project : Vt5, 2024-09-01,2025-03-31 Generate multiomics data for 50 genes in 1 brain region at 1 time point : V_Y2t1, 2025-03-31,52w Submit L0/L1 data to DRACC (Restricted) 175 FASTQ for 75TB overall : crit, milestone, ADGC5_Aim1_year4_item1, 2026-03-31, 0d section Aim 2 - Refine brain clearing experiments (1) test CUBIC method and assess data quality : Vt6, 2024-09-01,2025-03-31 - Refine brain clearing experiments (2) test LifeCanvas (CLARITY) method and assess data quality : Vt7, 2024-09-01,2025-03-31 - Establish data analysis pipeline through semi-automatic image tracing and segmentation : Vt8, 2024-09-01,2025-03-31 - Establish approaches to integrate single-cell omic data with spatial morphometric data : Vt9, 2024-09-01,2025-03-31 - Select first 5 ASD risk genes to be included in the study : Vt10, 2024-09-01,2025-03-31 - - Test gRNA efficacy in vitro, nominate final vectors, collect brain samples : V_Y2t3, 2025-03-31,52w - Implement functional pipeline for analyzing Perturb-seq multiomics data : V_Y2t4,2025-03-31,52w - Develop methods for GRN analysis of multiomics data : V_Y2t5, 2025-03-31,52w - Identify datasets to be used to build GRNs from developing human brains : V_Y2t6, 2025-03-31,52w Generate raw TIFF format and 3D swc files for 100 neurons on 3 genes : V_Y2t7, 2025-03-31,52w </pre> </div> </div> <a name="ADGC6"></a> <!-- Start of ADGC6 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC6 SING Timeline</h5></div> <div class="row"> <div class="col-md-12"> <pre class="mermaid"> gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC6 Cross-Scale Interrogation of NPD Genes (SING) - PSU/JAX/UTSW/NYU [RM1MH138309] 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, 2027-03-31, 0d section SING Reporting Year End SING Reporting Year 1 :milestone, year1_SING, 2025-12-31, 0d End SING Reporting Year 2 :milestone, m1, 2026-12-31, 0d click year1_SING href "https://docs.google.com/spreadsheets/d/1pw1muwglklo-gXrC5hadYjSqBjhZOKeh/edit?gid=1827916005#gid=1827916005&range=C2:E23" section Aim 1 - Initial discussion with DRACC for data transfer complete : crit, milestone, ADGC6_C_7, 2025-06-30, 0d DRACC data transfer of C57 control MERFISH : crit, milestone, ADGC6_D_8, 2025-09-30, 0d DRACC data transfer of first 5 KO mice MERFISH data : crit, milestone, ADGC6_E_7, 2025-12-31, 0d DRACC data transfer of 2025 Q4 and 20026 Q1-Q3 KO mice MERFISH data : crit, milestone, ADGC6_F_7, 2026-12-31, 0d DRACC data transfer of C57 control 10x Flex : crit, milestone, ADGC6_D_10, 2025-09-30, 0d DRACC data transfer of 10x Flex from 2025 and 2026Q1-Q2 : crit, milestone, ADGC6_F_10, 2026-12-31, 0d DRACC data transfer of C57 control L0 1TB, L1 0.5TB spatial txn : crit, milestone, ADGC6_Y2_B_4, 2026-03-31, 0d DRACC data transfer of 1st-4th KO L0 4TB, L1 2TB spatial txn : crit, milestone, ADGC6_Y2_C_5, 2026-07-01, 0d DRACC data transfer of 1st-4th scRNA-seq L0 0.8TB data, L1 0.4TB : crit, milestone, ADGC6_Y2_D_6, 2026-09-30, 0d DRACC data transfer of 5th-8th KO L0 4TB, L1 2TB spatial txn : crit, milestone, ADGC6_Y2_D_7, 2026-09-30, 0d DRACC data transfer of 5th-8th line scRNA-seq L0 0.8TB data, L1 0.4TB : crit, milestone, ADGC6_Y2_E_6, 2026-12-31, 0d DRACC data transfer of 9th - 12th KO L0 4TB, L1 2TB spatial txn : crit, milestone, ADGC6_Y2_E_7, 2026-12-31, 0d section Aim 2 - Initial discussion with DRACC for data transfer complete : crit, milestone, ADGC6_C_16, 2025-06-30, 0d DRACC data transfer of C57 control MRI and LSFM data : crit, milestone, ADGC6_D_16, 2025-09-30, 0d DRACC data transfer of first 5 KO mice MRI and LSFM data : crit, milestone, ADGC6_E_16, 2025-12-31, 0d DRACC data transfer of 2025 Q4 and 20026 Q1-Q3 KO mice MRI and LSFM data : crit, milestone, ADGC6_F_16, 2026-12-31, 0d DRACC data transfer of 1st-5th MRI L0 0.24TB data, L1 0.2TB, initial analysis 20 mouse brains : crit, milestone, ADGC6_Y2_B_11, 2026-03-31, 0d DRACC data transfer of 6th-10th MRI L0 0.5TB data, L1 0.5TB : crit, milestone, ADGC6_Y2_C_11, 2026-07-01, 0d DRACC data transfer of 6th-10th LSFM L1 5TB data, L2 0.5TB CCF mapped 1st-5th lines : crit, milestone, ADGC6_Y2_C_15, 2026-07-01, 0d DRACC data transfer of 11th-15th MRI L0 0.5TB data, L1 0.5TB : crit, milestone, ADGC6_Y2_D_11, 2026-09-30, 0d DRACC data transfer of 16th-20th MRI L0 0.5TB data, L1 0.5TB : crit, milestone, ADGC6_Y2_E_11, 2026-12-31, 0d DRACC data transfer of 16th-20th LSFM L1 5TB data, L2 0.5TB CCF mapped 11th-15th lines : crit, milestone, ADGC6_Y2_E_15, 2026-12-31, 0d section Aim 3 - Initial discussion with DRACC for data transfer complete : crit, milestone, ADGC6_C_23, 2025-06-30, 0d DRACC data transfer of C57 control behavioral data : crit, milestone, ADGC6_D_23, 2025-09-30, 0d DRACC data transfer of first 5 KO lines behavioral data : crit, milestone, ADGC6_E_23, 2025-12-31, 0d DRACC data transfer of 2025 Q4 and 20026 Q1-Q3 KO line behavioral data : crit, milestone, ADGC6_F_23, 2026-12-31, 0d DRACC data transfer of L0 Video, L1 tracking behavior from lines : crit, milestone, ADGC6_Y2_B_22, 2026-03-31, 0d DRACC data transfer of L0 Video, L1 tracking behavior from lines : crit, milestone, ADGC6_Y2_C_22, 2026-07-01, 0d DRACC data transfer of L0 Video, L1 tracking behavior from lines : crit, milestone, ADGC6_Y2_D_22, 2026-09-30, 0d DRACC data transfer of L0 Video, L1 tracking behavior from lines : crit, milestone, ADGC6_Y2_E_22, 2026-12-31, 0d </pre> </div> </div> <!-- Start of ADGC7 Henry Gantt Chart--> <a name="ADGC7"></a> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC7 WUSTL Timeline</h5></div>