fba6fb06141cf261a967e1b7e9742f98cd492e06 brianlee Wed May 21 16:17:16 2025 -0700 Fix to mermaid code specific to Safari, Firefox/Chrome add the 01, Safari needs 2025-07-01 date 01 format diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index 6f87b66a60a..827667742ac 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -1,292 +1,291 @@ <!DOCTYPE html> <!--#set var="TITLE" value="CIRM CESCG People and Labs" --> <!--#include virtual="setRoot.html" --> <!--#include virtual="${ROOT}inc/header.html" --> <head> <meta charset="UTF-8"> <title>Mermaid Gantt Chart</title> <script src="https://cdn.jsdelivr.net/npm/mermaid/dist/mermaid.min.js"></script> <script> mermaid.initialize({ startOnLoad: true }); </script> </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">ADGC 1 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 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 AIM 1 Generate stable clonal iPSC lines for 10 gene mutations in KOLF2.2J (Capstone; Batch A) : t1, 2024-01-01, 2024-07-01 Generate stable clonal iPSC lines for 10 gene mutations in CIRM line (Capstone; Batch A) : t2, 2024-01-01, 2024-07-01 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 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 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 </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 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 Aim 1 Generated 217 new lines including 10 NTC (total 332 lines). We generated iNs from 180 lines. :done, IIt1, 2024-01-01, 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 Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt12, after IIt11,13w Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt13, after IIt12,13w Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt14, after IIt13,13w Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt15, after IIt14,13w Pilot CODEX LoF risk variants : II_codex1, 2024-10-01,39w CODEX 30-50 patient-specific LoF variants KOLF2.2J : II_codex2, after II_codex1,13w CODEX 12mm coverslips iNs, 30-50 SNPs (SNP/neuron), 3x reps : II_codex3, after II_codex2,13w CODEX 3x data to BIL, generate LoF variants in 1-2 new lines : crit, II_codex4, after II_codex3,13w section Aim 3 Submitted 46 lines of Synaptic Optical sensors imaging data : done, IIt16, 2024-04-01,52w Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt17, after IIt16,13w Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt18, after IIt17,13w Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt19, after IIt18,13w Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt20, after IIt19,13w 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, 2025-07-1,39w - + 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 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 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 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 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 </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 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 Aim 1 Performed pilot morpholgy screen in 20 genes : done, IVt1, 2024-01-01,13w 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, IVt2_year4, 2026-03-15,3w 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, IVt6, 2026-03-15,3w Submit remaining image datasets : crit, IVt7, 2027-03-15,3w section Aim 2 Developed Perturb-FISH screens : done, IVt8, 2024-01-01,13w 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, IVt9b_year4, 2026-03-15,3w Perform Perturb-FISH screen of ASD genes in iPS derived astrocytes : done, IVt10, 2024-04-01, 52w Submit 50 TB of calcium imaging and MERFISH data : done, IVt11, after IVt10, 3w Perform pilot 10 gene electrophysiology screen - PARTIALLY COMPLETE : IVt12, 2024-04-01,52w Submit 5 TB of optical electrophysiology data - DATA QUALITY BEING ASSESSED : crit, IVt13, after IVt12, 3w Submit 5 TB of optical electrophysiology data : crit, IVt14, 2026-03-15,3w Submit remaining optical electrophysiology data : crit, IVt15, 2027-03-15,3w section Aim 3 Perform scRNAseq (dropulation) screen of ~40 line village of CIRM lines - PARTIALLY COMPLETE : IVt16, 2024-04-01,52w Submit RNA-seq profiles - ANALYSIS / SUBMISSION UNDERWAY : crit, IVt16b, after IVt16, 3w Submit RNA-seq profiles from >10,000 cells : crit, IVt17, 2026-03-15,3w Submit remaining RNA-seq profiles : crit, IVt17_yearEnd, 2027-03-15,3w Morphological profiles of ~40 line village of CIRM lines : IVt18a, 2025-04-01,52w Submit ~10 TB of associated images to DRACC : crit, IVt18b, after IVt18a,3w Submit remaining morphology imaging : crit, IVt19, 2027-03-15,3w </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 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, m1, 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 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, V_Y2t2, 2025-04-01,52w 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 Select first 5 ASD risk genes to be included in the study : Vt10, 2024-09-01,2025-04-01 Test gRNA efficacy in vitro, nominate final vectors, collect brain samples : V_Y2t3, 2025-04-01,52w Implement functional pipeline for analyzing Perturb-seq multiomics data : V_Y2t4,2025-04-01,52w 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> <!--#include virtual="${ROOT}inc/footer.html" -->