9ab37a5c7846963ba7f24a36d5b4c7f49e306fda brianlee Thu Mar 26 07:46:38 2026 -0700 Code Review changes per browser-code-reviews-group diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index bd03c667a93..b80ab12cc5a 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -162,66 +162,66 @@ title ADGC3 Yale [RM1MH132648] section Grant Year 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 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 : active, milestone, ADGC3_K_7, 2025-09-30, 0d - Submit initial data (L0, L1) GLUT 10 capstone genes (ARID1B, ASXL3, CACNA1G, CHD8, DLL1, GABRA1, KMT2C, SCN2A, SHANK3, SMARCC2). Across four donors, KOLF2.2J, CW20107, 2607, 553, ECCITEseq resolved 7,985, 3,834, 232, and 8,902 iGLUTs, expected to further increase with final alignments.QC metrics resolved good gRNA representation and high quality/glutamatergic neurons : crit, milestone, ADGC3_Y4_N_4, 2026-06-30, 0d - Submit initial data (L0, L1) CRISPRko calcium imaging of 15 ASD genes in iGLUTs (ARID1B, ASH1L, CHD8, CUL3, DYRK1A, KMT5B,, POGZ, PTEN, ANK2, CACNA1G, GRIA3, GRIN2A, NRXN1, SCN2A, SHANK3) and MEA iGLUT (SCN2A) - matrix CSV file : crit, milestone, ADGC3_Y4_N_5, 2026-06-30, 0d + Submit initial data (L0, L1) iGLUT 10 capstone genes (ARID1B, ASXL3, CACNA1G, CHD8, DLL1, GABRA1, KMT2C, SCN2A, SHANK3, SMARCC2). Across four donors, KOLF2.2J, CW20107, 2607, 553, ECCITEseq resolved 7,985, 3,834, 232, and 8,902 iGLUTs, expected to further increase with final alignments. QC metrics resolved good gRNA representation and high quality/glutamatergic neurons : crit, milestone, ADGC3_Y4_N_4, 2026-06-30, 0d + Submit initial data (L0, L1) CRISPRko calcium imaging of 15 ASD genes in iGLUTs (ARID1B, ASH1L, CHD8, CUL3, DYRK1A, KMT5B, POGZ, PTEN, ANK2, CACNA1G, GRIA3, GRIN2A, NRXN1, SCN2A, SHANK3) and MEA iGLUT (SCN2A) - matrix CSV file : crit, milestone, ADGC3_Y4_N_5, 2026-06-30, 0d Submit L3/L4 data from manuscript describing capstone ECCITEseq of 10 capstone genes in KOLF2.2J : crit, milestone, ADGC3_Y4_Q_4, 2027-03-31, 0d - Submit L3/L4 data from estradiol pre-print describing calcium imaging of 15 ASD genes and MEA of 1 gene in iGLUTs : crit, milestone, ADGC3_Y4_Q_4, 2027-03-31, 0d -%% For successful screens, submit initial data (L0. L1) CRISPR amplicon-seq of 36/250/whole genome NDD genes for neurongenesis, mitochondrial function, and/or neuronal activity : crit, milestone, ADGC3_Y4_R_6, 2028-03-31, 0d + Submit L3/L4 data from estradiol pre-print describing calcium imaging of 15 ASD genes and MEA of 1 gene in iGLUTs : crit, milestone, ADGC3_Y4_Q_5, 2027-03-31, 0d +%% For successful screens, submit initial data (L0, L1) CRISPR amplicon-seq of 36/250/whole genome NDD genes for neurogenesis, mitochondrial function, and/or neuronal activity : crit, milestone, ADGC3_Y4_R_6, 2028-03-31, 0d %% Submit L3/L4 data from manuscript describing phenotyping of all genes across zebrafish + hiPSCs  : crit, milestone, ADGC3_Y4_R_7, 2028-03-31, 0d section Aim 2 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) : active, milestone, ADGC3_J_14, 2025-06-30, 0d Submit data (L0, L1) Whole-brain structure and activity mapping (.LIF, .XLS), zebrafish, 5 NPD genes (ADNP - NRXN1) : active, 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) : active, 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 - Submit data (L0, L1) Whole-brain RNA-seq, zebrafish, 10 genes, including 9 pilot "capstone" genes - ARID1B, CACNA1G, CHD8, DLL1, GABRA1, KMT2C, SCN2A, SHANK3, SMARCC2, PTEN : crit, milestone, ADGC3_Y4_N_14, 2026-06-30, 0 + Submit data (L0, L1) Whole-brain RNA-seq, zebrafish, 10 genes, including 9 pilot "capstone" genes - ARID1B, CACNA1G, CHD8, DLL1, GABRA1, KMT2C, SCN2A, SHANK3, SMARCC2, PTEN : crit, milestone, ADGC3_Y4_N_14, 2026-06-30, 0d Submit data (L0, L1) Whole-brain structure and activity mapping, zebrafish, 5 NPD genes (FMR1, DLL1, KCNQ3, SHANK3, SMARCC2) : crit, milestone, ADGC3_Y4_O_14, 2026-09-30, 0d Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS) for 20 NPD genes (CASKIN1, CTCF, DEAF1, DYNC1H1, EBF3, FMR1, GIGYF1, HERC1, KCNMA1, IRF2BPL, MECP2, MED13L, NF1, RB1CC1, SETD1A, SP4, TANC2, TAOK1, TCF20, TCF7L2) : crit, milestone, ADGC3_Y4_P_14, 2026-12-31, 0d Submit data (L0, L1) Whole-brain structure and activity mapping, zebrafish, 5 NPD genes (CHD2, GIGYF1, KMT2C, MECP2, CACNA1G) : crit, milestone, ADGC3_Y4_Q_14, 2027-03-31, 0d Submit data (L0, L1) Whole-brain RNA-seq, zebrafish, 10 NPD genes (ADNP, ASH1L, CHD2, DLG4, DYRK1A, MECP2, NRXN1, POGZ, PPP2R5D, SYNGAP1) : crit, milestone, ADGC3_Y4_Q_15, 2027-03-31, 0d Submit L3/L4 data from manuscript describing phenotyping of first 40 NPD genes : crit, milestone, ADGC3_Y4_Q_17, 2027-03-31, 0d %% Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes. : crit, milestone, ADGC3_Y4_R_15, 2028-03-31, 0d %% Submit data (L0, L1) Whole-brain structure and activity mapping, zebrafish, 10 NPD genes. : crit, milestone, ADGC3_Y4_R_16, 2028-03-31, 0d %% Submit data (L0, L1) Whole-brain RNA-seq, zebrafish, 20 NPD genes : crit, milestone, ADGC3_Y4_R_17, 2028-03-31, 0d %% Submit L3/L4 data from manuscript describing phenotyping of all genes across zebrafish + hiPSCs : crit, milestone, ADGC3_Y4_R_19, 2028-03-31, 0d section Aim 3 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 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 CHD8, SCN2A, SHANK3). : crit, milestone, ADGC3_Y4_Q_20, 2027-03-31, 0d Submit data (L0, L1) CRISPRko organoid Perturb-DBIT (4-8 DBiT RNA-seq profiles (fastq)), calcium imaging, and matched single cell ECCITEseq, across developmental timepoints and 36 pooled NPD genes : crit, milestone, ADGC3_Y4_Q_21, 2027-03-31, 0d %% Submit L3/L4 data from manuscript describing spatial transcriptomic analysis of NPD genes in zebrafish : crit, milestone, ADGC3_Y4_R_20, 2028-03-31, 0d -%% Submit L3/L4 data from manuscript describing integration of spatial and single cells pooled CRISPRko organoid NDD gene analysis : crit, milestone, ADGC3_Y4_R_21, 2028-03-31, 0d +%% Submit L3/L4 data from manuscript describing integration of spatial and single-cells pooled CRISPRko organoid NDD gene analysis : crit, milestone, ADGC3_Y4_R_21, 2028-03-31, 0d
ADGC4 Broad timeline
    
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         title       ADGC4  Broad [R01MH128366]