0994a55f413ccb2180614edc5b7d3fed8928c3c8 brianlee Fri Jun 6 11:25:48 2025 -0700 UCLA new milestones, ADGC1_NO_111213 = column N/O, where O = end-date: 2026Q3(Jul-Sep) thus 2026-10-01 (equiv 2026-09-31) and 111213 refers to rows 11,12,13 per UCLA sspsygene_milestones_yr2_RM1MH132651_JMM_DHG_JMM_V5 excel from NIMH diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index 398be8d44fd..acd4fff9d5f 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -56,30 +56,63 @@ 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 +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 + </pre> </div> </div> <a name="ADGC2"></a> <!-- Start of ADGC2 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC2 MiNND timeline</h5></div> <div class="row"> <div class="col-md-12"> <pre class="mermaid"> gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC2 MiNND section Grant Year @@ -175,30 +208,50 @@ 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 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 dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC4 Broad section Grant Year @@ -294,33 +347,32 @@ <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 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, 2024-12-31, 0d - End SING Reporting Year 2 :milestone, m1, 2025-12-31, 0d - End SING Reporting Year 3 :milestone, m1, 2026-12-31, 0d + 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