cb132eebcd2484023c6e828e92d63bbc90a42e73 brianlee Wed Jul 23 16:29:31 2025 -0700 Shortening AIM2 Yale gene lists to make more readable (Gene1 - Gene20; vs listing all 20) diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index 7a297d1b712..2cf7060083d 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -198,38 +198,38 @@ 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 + Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 10 stable mutant lines (ADNP - SYNGAP1) : crit, milestone, ADGC3_I_12, 2025-04-01, 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, 2025-10-01, 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, 2025-10-01, 0d + Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes (CASKIN1 - XPO7) : crit, milestone, ADGC3_N_15, 2027-04-01, 0d + Submit data (L0, L1) Whole-brain RNA-seq, zebrafish, 10 NPD genes (CHD8 - 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