a4ff8fa3139e52d36188b26841fb2a362b1d700b brianlee Fri Oct 31 13:00:45 2025 -0700 Adding links to jump to dates in milestones in Google Docs of each ADGCs on SSPsyGene milestones for quicker reference diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index adf7691e575..16266ba5c42 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -24,31 +24,31 @@ <div class="row"> <div class="col-md-12"> <pre class="mermaid"> gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC1 UCLA 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" + 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 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 @@ -106,31 +106,31 @@ <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 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" + 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 section Aim 2 Submitted scRNA-seq data for 157 lines to the DRACC. : done, IIt6, 2024-04-01,52w Submit scRNA-seq data for 72 edited lines (3×23 gene mutations + 1 NTC) from last quarter. :crit, IIt7, after IIt6,13w Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last year. :crit, IIt8, after IIt7,13w Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last quarter. :crit, IIt9, after IIt8,13w Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last quarter. :crit, IIt10, after IIt9,13w Submitted 113 lines morphometrics imaging data. :done, IIt11, 2024-04-01,52w @@ -161,31 +161,31 @@ <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 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" + 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 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, 2025-09-30, 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 @@ -243,31 +243,31 @@ <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 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" + 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 Submit image dataset of 40 TB - DONE, DATA TRANSFER STARTED : crit, IVt4, after IVt3,3w Submit image dataset of 120 TB (443 genes in 3 cells 5 million profiles) : crit, milestone, ADGC4_Aim1_year4_item2, 2026-03-31, 0d Submit remaining image datasets : crit, milestone, ADGC4_Aim1_year5_item1, 2027-03-31, 0d section Aim 2 Perform perturb-seq screen of 150 genes in 4 cell types - PARTIALLY COMPLETE : IVt9, 2024-04-01,52w Submit 100,000 scRNA-seq profiles per cell type of 191 genes in 3 cell types (fastq) : crit, milestone, ADGC4_Aim2_year4_item1, 2026-03-31, 0d Perform Perturb-FISH screen of ASD genes in iPS derived astrocytes : done, IVt10, 2024-04-01, 52w @@ -299,31 +299,31 @@ dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC5 Scripps/Broad 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" + click year1_scripps href "https://docs.google.com/spreadsheets/d/19RWN6-DjIyMpFV2JP4yY5Ta5Xfthieds/edit?gid=744607405#gid=744607405&range=C2:C15" section Aim 1 Refine AAV-based Perturb-seq, test v1 and v2, assess data quality, finalize method : Vt1, 2024-09-01,2025-04-01 Design gRNAs and generate vectors for Perturb-seq : Vt2, 2024-09-01,2025-04-01 Choose single cell technology; test, validate with finalized Perturb-seq method : Vt3, 2024-09-01,2025-04-01 Test gRNA efficacy in vitro; nominate final perturbation vectors to be used : Vt4, 2024-09-01,2025-04-01 Discuss within and across ADGC groups to choose genes to target among list of 259 genes; finalize gene selection for this project : Vt5, 2024-09-01,2025-04-01 Generate multiomics data for 50 genes in 1 brain region at 1 time point : V_Y2t1, 2025-04-01,52w Submit L0/L1 data to DRACC (Restricted) 175 FASTQ for 75TB overall : crit, milestone, ADGC5_Aim1_year4_item1, 2026-03-31, 0d section Aim 2 Refine brain clearing experiments (1) test CUBIC method and assess data quality : Vt6, 2024-09-01,2025-04-01 Refine brain clearing experiments (2) test LifeCanvas (CLARITY) method and assess data quality : Vt7, 2024-09-01,2025-04-01 Establish data analysis pipeline through semi-automatic image tracing and segmentation : Vt8, 2024-09-01,2025-04-01 Establish approaches to integrate single-cell omic data with spatial morphometric data : Vt9, 2024-09-01,2025-04-01 @@ -346,31 +346,31 @@ 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, 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" + 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 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, 2025-09-30, 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, 2025-09-30, 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 @@ -390,31 +390,31 @@ gantt dateFormat YYYY-MM-DD axisFormat %Y-Q%q title ADGC7 Washington Univ. St Louis - WUSTL 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" + 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 L0, L1 Data from last quarter submitted, and 4 more lines collected : crit, milestone, ADGC7_F_12, 2026-03-31, 0d L2, L3 from prior L0,L1 data submitted : crit, milestone, ADGC7_F_13, 2026-03-31, 0d section Aim 2 Home Cage Behavior L0-L1 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_C_17, 2025-07-01, 0d Home Cage Behavior L0-L1 Data to DRACC for line 3-4 : crit, milestone, ADGC7_D_17, 2025-09-30, 0d Home Cage Behavior L0-L1 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_E_17, 2025-12-31, 0d Home Cage Behavior L3 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_D_18, 2025-09-30, 0d Home Cage Behavior L3 Data to DRACC for line3-4 : crit, milestone, ADGC7_E_18, 2025-12-31, 0d Home Cage Behavior L3 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_F_18, 2026-03-31, 0d Home Cage Behavior L4 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_E_19, 2025-12-31, 0d Home Cage Behavior L4 Data to DRACC for lines 3-4 : crit, milestone, ADGC7_F_19, 2026-03-31, 0d