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 @@ 
    
         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
ADGC5 Scripps/Broad timeline
         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