373e06aadc70142ac8221261992b2815a343cf1d brianlee Wed Dec 10 14:23:46 2025 -0800 Adding RM references to ADGCs on timeline diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index 16266ba5c42..5082cfcde18 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -15,31 +15,31 @@ </head> <div class="cirm-page-body"> <div class="cirm-page-title back-dark-pink"> <h5 class="cirm-page-title-text">SSPsyGene Milestone Charts</h5> </div> <a name="ADGC1"></a> <!-- Start of ADGC1 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC1 UCLA Chart</h5></div> <div class="row"> <div class="col-md-12"> <pre class="mermaid"> gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q - title ADGC1 UCLA + title ADGC1 UCLA [RM1MH132651] section Grant Year Start Grant Year 2 :milestone, m1, 2024-03-31, 0d Start Grant Year 3 :milestone, year3_ucla, 2025-03-31, 0d Start Grant Year 4 :milestone, m1, 2026-03-31, 0d Start Grant Year 5 :milestone, m1, 2027-04-01, 0d click year3_ucla href "https://docs.google.com/spreadsheets/d/1Ml_UXDHE4UZo2kjLp1aZLa0KxLtLSnVi/edit?gid=1138387919#gid=1138387919&range=J1:M20" section AIM 1 Generate stable clonal iPSC lines for additional 25 gene mutations in KOLF2.2J and CIRM (BATCH B) : t3, 2024-04-01, 2024-09-30 QC of Capstone lines to date pending : t4, 2024-04-01, 39w 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 @@ -98,31 +98,31 @@ Perform snRNAseq for future batches : crit, milestone, ADGC1_P_1920, 2026-12-31, 0d Organoid snRNAseq Analysis for future batches : 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 + title ADGC2 MiNND [RM1MH133065] section Grant Year Start Grant Year 2 :milestone, m1, 2024-03-31, 0d Start Grant Year 3 :milestone, year3_minnd, 2025-03-31, 0d Start Grant Year 4 :milestone, m1, 2026-03-31, 0d Start Grant Year 5 :milestone, m1, 2027-04-01, 0d click year3_minnd href "https://docs.google.com/spreadsheets/d/1GNrJaIjs6nPlFY4j2AlZSlTDf2-mi17d/edit?gid=1137576441#gid=1137576441&range=J1:M34" section Aim 1 Generated 217 new lines including 10 NTC (total 332 lines). We generated iNs from 180 lines. :done, IIt1, 2024-04-01, 2025-04-01 Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt2, after IIt1,13w Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt3, after IIt2,13w Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt4, after IIt3,13w Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt5, after IIt4,13w @@ -153,31 +153,31 @@ section Aim4 Submit PatchSeq data for 192 NTC lines L0 data :crit, IIv20, 2025-04-01,52w Submit PatchSeq data for 192 cells L1-L3 : crit, IIv21, 2025-07-01,39w </pre> </div> </div> <a name="ADGC3"></a> <!-- Start of ADGC3 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC3 Yale timeline</h5></div> <div class="row"> <div class="col-md-12"> <pre class="mermaid"> gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q - title ADGC3 Yale + title ADGC3 Yale [RM1MH132648] section Grant Year Start Grant Year 2 :milestone, m1, 2024-03-31, 0d 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, 2027-04-01, 0d click year3_yale href "https://docs.google.com/spreadsheets/d/10xWymZXsDlDQ9uwU5YPAKwyflUMzpDS4/edit?gid=1305684354#gid=1305684354&range=J1:M25" section Aim 1 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 @@ -235,31 +235,31 @@ 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, 2027-04-01, 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 + title ADGC4 Broad [R01MH128366] section Grant Year Start Grant Year 2 :milestone, m1, 2024-03-31, 0d Start Grant Year 3 :milestone, year3_broad, 2025-03-31, 0d Start Grant Year 4 :milestone, m1, 2026-03-31, 0d Start Grant Year 5 :milestone, m1, 2027-04-01, 0d click year3_broad href "https://docs.google.com/spreadsheets/d/1BwaO6rgn0o5nTulC2M6dQe5UMGUWEy-o/edit?gid=2037309850#gid=2037309850&range=D1:D16" section Aim 1 Perform perturb-seq screen of 150 genes in 4 cell types : IVt2, 2024-04-01,52w Submit 100,000 scRNA-seq profiles per cell type (fastq) - PARTIALLY COMPLETE (191 GENES, 3 CELL TYPES)/ TRANSFER STARTED : crit, IVt2b, after IVt2,3w Submit 100,000 scRNA-seq profiles per cell type (fastq) of 191 genes in 3 cell types : crit, milestone, ADGC4_Aim1_year4_item1, 2026-03-31, 0d Develop protocol for scaling up screen size : done, IVt5, 2024-04-01,52w Validation of initial 20 gene morphological screen : done, IVt3, 2024-04-01,52w @@ -286,31 +286,31 @@ Submit 10 TB of associated images to DRACC : crit, milestone, ADGC4_Aim3_year4_item2, 2026-03-31, 0d Submit remaining morphology imaging : crit, milestone, ADGC4_Aim3_year5_item2, 2027-03-31, 0d </pre> </div> </div> <a name="ADGC5"></a> <!-- Start of ADGC5 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC5 Scripps/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 ADGC5 Scripps/Broad + title ADGC5 Scripps/Broad [R01MH137042-01/-02] 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 Scripps/Broad Reporting Year End Scripps/Broad Reporting Year 1 :milestone, year1_scripps, 2025-03-31, 0d End Scripps/Broad Reporting Year 2 :milestone, m1, 2026-03-31, 0d End Scripps/Broad Reporting Year 3 :milestone, m1, 2027-04-01, 0d click year1_scripps href "https://docs.google.com/spreadsheets/d/19RWN6-DjIyMpFV2JP4yY5Ta5Xfthieds/edit?gid=744607405#gid=744607405&range=C2:C15" section Aim 1 @@ -334,31 +334,31 @@ Develop methods for GRN analysis of multiomics data : V_Y2t5, 2025-04-01,52w Identify datasets to be used to build GRNs from developing human brains : V_Y2t6, 2025-04-01,52w Generate raw TIFF format and 3D swc files for 100 neurons on 3 genes : V_Y2t7, 2025-04-01,52w </pre> </div> </div> <a name="ADGC6"></a> <!-- Start of ADGC6 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC6 SING Timeline</h5></div> <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 + title ADGC6 Cross-Scale Interrogation of NPD Genes (SING) - PSU/JAX/UTSW/NYU [RM1MH138309] 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, year1_SING, 2025-12-31, 0d End SING Reporting Year 2 :milestone, m1, 2026-12-31, 0d click year1_SING href "https://docs.google.com/spreadsheets/d/1pw1muwglklo-gXrC5hadYjSqBjhZOKeh/edit?gid=1827916005#gid=1827916005&range=C2:E23" section Aim 1 Initial discussion with DRACC for data transfer complete : crit, milestone, ADGC6_C_7, 2025-06-30, 0d @@ -378,31 +378,31 @@ 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 + title ADGC7 Washington Univ. St Louis - WUSTL [RM1MH138313] 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 WUSTL Reporting Year End WUSTL Reporting Year 1 :milestone, year1_wustl, 2025-12-31, 0d End WUSTL Reporting Year 2 :milestone, m1, 2026-12-31, 0d click year1_wustl href "https://docs.google.com/spreadsheets/d/1ae4bX4Ful2AWlqzeH_JOo4jFssmEsojd/edit?gid=1888128068#gid=1888128068&range=C2:E27" section Aim 1 L0, L1 Data from last quarter submitted, and 3 more lines collected : crit, milestone, ADGC7_E_12, 2025-12-31, 0d