96002a53528b7a6f42b53fa1379f76b6bfd12664 brianlee Thu Sep 4 12:35:04 2025 -0700 Aligning Q3 end to 2025-09-30 vs 2025-10-01 (which is start Q4) for SSPsyGene milestones diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index ff96a46b9b3..004d94f4efc 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -44,43 +44,43 @@ 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, 2025-10-01,30w - Submit data on RNA-seq profiles from BATCH B and C :crit, t33, 2025-10-01,13w + 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, 2025-10-01, 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, 2026-04-01, 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, 2027-04-01, 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, 2026-04-01, 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, 2027-04-01, 0d - Complete villages - submit L0-L1 to DRACC : crit, milestone, ADGC1_JK_14, 2025-10-01, 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, 2026-04-01, 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, 2026-04-01, 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, 2027-04-01, 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 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 @@ -171,63 +171,63 @@ 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 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, 2027-04-01, 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, 2025-10-01, 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, 2027-04-01, 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, 2025-04-01, 0d - Submit L3/L4 data from iGLUT manuscript : crit, milestone, ADGC3_K_7, 2025-10-01, 0d + Submit L3/L4 data from iGLUT manuscript : crit, milestone, ADGC3_K_7, 2025-09-30, 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 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) 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, 2025-10-01, 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, 2027-04-01, 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 : 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 @@ -347,44 +347,44 @@ 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, 2025-12-31, 0d End SING Reporting Year 2 :milestone, m1, 2026-12-31, 0d 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, 2025-10-01, 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, 2026-01-01, 0d DRACC data transfer of 2025 Q4 and 20026 Q1-Q3 KO mice MERFISH data : crit, milestone, ADGC6_F_7, 2027-01-01, 0d - DRACC data transfer of C57 control 10x Flex : crit, milestone, ADGC6_D_10, 2025-10-01, 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, 2027-01-01, 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, 2025-10-01, 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, 2026-01-01, 0d 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 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, 2025-10-01, 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, 2026-01-01, 0d DRACC data transfer of 2025 Q4 and 20026 Q1-Q3 KO line behavioral data : crit, milestone, ADGC6_F_23, 2027-01-01, 0d </pre> </div> </div> <!-- Start of ADGC7 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC7 WUSTL Timeline</h5></div> <div class="row"> <div class="col-md-12"> <pre class="mermaid"> gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC7 Washington Univ. St Louis - WUSTL