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>