31b411ea6756d18925d33cce11834319376700ee brianlee Tue Oct 14 14:59:51 2025 -0700 Adding scripps, broad, sing links to 2025 milestone spreadsheet in mermaid code timeline page diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index 1af11b9003e..1032a536bdb 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -235,34 +235,36 @@ </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 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" + 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 Submit 50 TB of calcium imaging and MERFISH data : done, IVt11, after IVt10, 3w @@ -289,34 +291,36 @@ <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 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" + 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 Select first 5 ASD risk genes to be included in the study : Vt10, 2024-09-01,2025-04-01 @@ -335,33 +339,35 @@ <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 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, m1, 2025-12-31, 0d + 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" + 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 Initial discussion with DRACC for data transfer complete : crit, milestone, ADGC6_C_23, 2025-06-30, 0d