697565bdd3b78419adda01dd9b709c6bf1a6503d brianlee Mon Sep 29 13:54:15 2025 -0700 Removing tilde which caused mermaid code display issue diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index 077637a9fa1..03ff42ccc66 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -238,56 +238,56 @@ <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 - Perform perturb-seq screen of ~150 genes in 4 cell types : IVt2, 2024-04-01,52w + 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 + 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 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, milestone, ADGC4_Aim2_year4_item2, 2026-03-31, 0d Submit remaining optical electrophysiology data : crit, milestone, ADGC4_Aim2_year5_item1, 2027-03-31, 0d section Aim 3 - Perform scRNAseq (dropulation) screen of ~40 line village of CIRM lines - PARTIALLY COMPLETE : IVt16, 2024-04-01,52w + 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, milestone, ADGC4_Aim3_year4_item1, 2026-03-31, 0d Submit remaining RNA-seq profiles : crit, milestone, ADGC4_Aim3_year5_item1, 2027-03-31, 0d - Morphological profiles of ~40 line village of CIRM lines : IVt18a, 2025-04-01,52w - Submit ~10 TB of associated images to DRACC : crit, milestone, ADGC4_Aim3_year4_item2, 2026-03-31, 0d + Morphological profiles of 40 line village of CIRM lines : IVt18a, 2025-04-01,52w + 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 @@ -298,31 +298,31 @@ 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, milestone, ADGC5_Aim1_year4_item1, 2026-03-31, 0d + 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 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>