94100fbd46c1b07ed9ca5021ca7800b4c6f57084 brianlee Tue Jun 9 09:31:11 2026 -0700 Aligning Broad/Sing timeline/milestones to Year3 -newer ADGC5 diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index 94cea23bc30..d9e2d84d04c 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -58,41 +58,41 @@ section AIM 2 Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from Capstone Lines 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_I_8, 2025-03-31, 0d Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from BATCH B 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : active, milestone, ADGC1_JK_8, 2025-09-30, 0d Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from BATCH C 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_LM_8, 2026-03-31, 0d Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from BATCH D 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_NO_8, 2026-09-30, 0d Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from BATCH E 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_P_8, 2026-12-31, 0d Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from BATCH F 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_Q_8, 2027-03-31, 0d Quantify proliferation rates for batch H and share data with DRACC: crit, milestone, ADGC1_Y4_Q_9, 2027-03-31, 0d Submit L0-L1 from BATCH B, producing bulk RNA-seq profiles 3 tech reps, 4 bio reps/gene × (20 NPD + 2 ctrl) × 2 (KOLF2.2J/CIRM) iPSC lines; .fastq : crit, milestone, ADGC1_LM_111213, 2026-03-31, 0d Submit L0-L1 from BATCH C, producing bulk RNA-seq profiles 3 tech reps, 4 bio reps/gene × (20 NPD + 2 ctrl) × 2 (KOLF2.2J/CIRM) iPSC lines; .fastq : crit, milestone, ADGC1_NO_111213, 2026-09-30, 0d Submit L0-L1 from BATCH D, producing bulk RNA-seq profiles 3 tech reps, 4 bio reps/gene × (20 NPD + 2 ctrl) × 2 (KOLF2.2J/CIRM) iPSC lines; .fastq : crit, milestone, ADGC1_P_111213, 2026-12-31, 0d %% Submit L0-L1 from BATCH E-G, producing bulk RNA-seq profiles 3 tech reps, 4 bio reps/gene × (20 NPD + 2 ctrl) × 2 (KOLF2.2J/CIRM) iPSC lines; .fastq : crit, milestone, ADGC1_Q_111213, 2027-03-31, 0d Submit Batch F, producing bulk RNA-seq profiles 4 reps/gene x (10 NPD + 2 ctrl) x 1 (KOLF2.2J/CIRM) iPSC background lines; fastq : crit, milestone, ADGC1_Y4_O_13, 2026-09-30, 0d Submit data from Batch G, producing bulk RNA-seq profiles (4 replicates per gene x (10 NPD iPSC lines + 2 controls) x 1 background (KOLF2.2J/CIRM) iPSC background lines; fastq) : crit, milestone, ADGC1_Y4_P_13, 2026-12-31, 0d - Submit data from Batch H, producing bulk RNA-seq profiles (4 replicates per gene x (10 NPD iPSC lines + 2 controls) x 1 background (KOLF2.2J/CIRM) iPSC background lines; fastq)) : crit, milestone, ADGC1_Y4_Q_13, 2027-03-31, 0d + Submit data from Batch H, producing bulk RNA-seq profiles (4 replicates per gene x (10 NPD iPSC lines + 2 controls) x 1 background (KOLF2.2J/CIRM) iPSC background lines; fastq) : crit, milestone, ADGC1_Y4_Q_13, 2027-03-31, 0d Complete villages - submit L0-L1 to DRACC : crit, milestone, ADGC1_JK_14, 2025-09-30, 0d Village Analysis - submit L0-L1 to DRACC : crit, milestone, ADGC1_LM_14, 2026-03-31, 0d Calcium Imaging Capstone Analysis 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_K_15, 2025-09-30, 0d Calcium Imaging analysis excitatory/inhibitory neurons - Capstone Analysis 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : crit, milestone, ADGC1_M_15, 2026-03-31, 0d Calcium Imaging Experiments and analysis of future batches 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds (Submit L0-L4 to DRACC) : crit, milestone, ADGC1_NOPQ_15, 2027-03-31, 0d Calcium Imaging excitatory neurons Batch F 2 time points, 4 replicates/gene, 4 NPD + 2 control iPSC lines, 2 backgrounds; TIFF : crit, milestone, ADGC1_Y4_O_15, 2026-09-30, 0d Calcium Imaging excitatory neurons Batch G 2 time points, 4 replicates/gene, 4 NPD + 2 control iPSC lines, 2 backgrounds; TIFF : crit, milestone, ADGC1_Y4_P_15, 2026-12-31, 0d Calcium Imaging excitatory neurons Batch H 2 time points, 4 replicates/gene, 4 NPD + 2 control iPSC lines, 2 backgrounds; TIFF : crit, milestone, ADGC1_Y4_Q_15, 2027-03-31, 0d Perform StimScope ephys on lines with excitatory calcium imaging (Batches B–E); submit all data levels to DRACC : crit, milestone, ADGC1_Y4_O_16, 2026-09-30, 0d - Perform StimScope Ephys Analysis for lines with signifiant differences in Excitatory Calcium Imaging Data in batch B-E. Submit All Levels of Data to DRACC : crit, milestone, ADGC1_Y4_Q_16, 2027-03-31, 0d + Perform StimScope Ephys Analysis for lines with significant differences in Excitatory Calcium Imaging Data in batch B-E. Submit All Levels of Data to DRACC : crit, milestone, ADGC1_Y4_Q_16, 2027-03-31, 0d section AIM 3 Perform codex Capstone Lines (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; qptiff format) : crit, milestone, ADGC1_J_161718, 2025-06-30, 0d Spatial Proteomics Analysis Capstone Lines : crit, milestone, ADGC1_K_161718, 2025-09-30, 0d Perform codex BATCH B (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; qptiff format) : crit, milestone, ADGC1_L_161718, 2025-12-31, 0d Spatial Proteomics Analysis BATCH B : crit, milestone, ADGC1_M_161718, 2026-03-31, 0d Perform codex BATCH C (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; qptiff format) : crit, milestone, ADGC1_N_161718, 2027-03-31, 0d Spatial Proteomics Analysis BATCH C : crit, milestone, ADGC1_O_161718, 2027-03-31, 0d Perform codex and analysis for future batches : crit, milestone, ADGC1_Q_161718, 2027-03-31, 0d Spatial Proteomics Analysis for Batch A-C - Submit L2-L4 Data to DRACC Upon Completion : crit, milestone, ADGC1_Y4_O_19, 2026-09-30, 0d Perform Spatial Proteomics for Batch D-E and transfer all data files to DRACC : crit, milestone, ADGC1_Y4_P_19, 2026-12-31, 0d Spatial Proteomics Analysis for Batch D-E (Submit L2-L4 Data to DRACC Upon Completion) : crit, milestone, ADGC1_Y4_Q_19, 2027-03-31, 0d Organoid snRNAseq analysis for Capstone Genes : crit, milestone, ADGC1_J_1920, 2025-06-30, 0d Perform snRNAseq for BATCH B (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 2-4 organoid replicates/line; tif format) : crit, milestone, ADGC1_K_1920, 2025-09-30, 0d Organoid snRNAseq analysis for BATCH B : crit, milestone, ADGC1_L_1920, 2025-12-31, 0d @@ -268,39 +268,39 @@ </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 [R01MH137042-01/-02] - section Grant Year - 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, 2027-03-31, 0d + section SSPsyGene Year + Start SSPsyGene Year 3 :milestone, m1, 2025-03-31, 0d + Start SSPsyGene Year 4 :milestone, m1, 2026-03-31, 0d + Start SSPsyGene Year 5 :milestone, m1, 2027-03-31, 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, 2027-03-31, 0d + section ADGC5 + Scripps/Broad Milestones Year 1 :milestone, year1_scripps, 2025-03-31, 0d + Scripps/Broad Milestones Year 2 :milestone, m1, 2026-03-31, 0d click year1_scripps href "https://docs.google.com/spreadsheets/d/19RWN6-DjIyMpFV2JP4yY5Ta5Xfthieds/edit?gid=744607405#gid=744607405&range=C2:C15" section Aim 1 Generate multiomics data for 50 genes in 1 brain region at 1 time point : V_Y2t1, 2025-03-31,52w 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 Generate raw TIFF format and 3D swc files for 100 neurons on 3 genes : V_Y2t7, 2025-03-31,52w </pre> </div> </div> <a name="ADGC6"></a> <!-- Start of ADGC6 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC6 SING Timeline</h5></div>