4878284d04625dce770834a5819934b485650936 brianlee Mon Jun 9 15:12:56 2025 -0700 Moving Full Text Yale/UCLA milestones to respective AIMs sections diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index acd4fff9d5f..4d7fc22123a 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -46,57 +46,54 @@ 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 - - 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 - - section FULL TEXT to add UCLA updates 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_JK_8 SHORTENED BUT MEANINGLESS - Submit L0-L1 to DRACC 2025 Q3 (Jul-Sep) : 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 @@ -173,80 +170,78 @@ 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 - - section FULL TEXT YALE new submits - 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 - 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 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 </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