2e8750b60612a2c59ef7bceb93d3b865ab9f45b8 brianlee Wed Aug 12 10:17:14 2026 -0700 Active items,reflecting data flow: ADGC1_M_15 --> UCLA Calcium Imaging Capstone Analysis, ADGC2_L_11 --> MiNND scRNA-seq 72 lines, ADGC2_L_27 --> MiNND PatchSeq 192 NTC L0, ADGC6_Y2_B_22 -->SING L0 Video diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index 59a7b825100..f829b38b0c9 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -65,31 +65,31 @@ 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 Complete villages - submit L0-L1 to DRACC : crit, milestone, ADGC1_JK_14, 2025-09-30, 0d Village Analysis - submit L0-L1 to DRACC : active, 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 analysis excitatory/inhibitory neurons - Capstone Analysis 10 genes, 22 iPSC lines (20 NPD + 2 ctrl) × 2 backgrounds : active, 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 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 @@ -123,54 +123,54 @@ section Grant Year Start Grant Year 3 :milestone, year3_minnd, 2025-03-31, 0d Start Grant Year 4 :milestone, year4_minnd, 2026-03-31, 0d Start Grant Year 5 :milestone, m1, 2027-03-31, 0d click year3_minnd href "https://docs.google.com/spreadsheets/d/1GNrJaIjs6nPlFY4j2AlZSlTDf2-mi17d/edit?gid=1137576441#gid=1137576441&range=J1:M34" click year4_minnd href "https://docs.google.com/spreadsheets/d/1XjUJYSy8xPxKOBBOgHEdzbzNFG_cqqLn/edit?gid=1137576441#gid=1137576441&range=N1" section Aim 1 section Aim 2 Submit scRNA-seq data for 72 edited lines (3×23 gene mutations + 1 NTC) from last quarter. : active, milestone, ADGC2_J_11, 2025-06-30, 0d Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last year. : crit, milestone, ADGC2_K_11, 2025-09-30, 0d - Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last quarter : crit, milestone, ADGC2_L_11, 2025-12-31, 0d + Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last quarter : active, milestone, ADGC2_L_11, 2025-12-31, 0d Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last quarter : crit, milestone, ADGC2_M_11, 2026-03-31, 0d Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 : active, milestone, ADGC2_J_12, 2025-06-30, 0d Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 : crit, milestone, ADGC2_K_12, 2025-09-30, 0d Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 : crit, milestone, ADGC2_L_12, 2025-12-31, 0d Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 : crit, milestone, ADGC2_M_12, 2026-03-31, 0d CODEX 3x data to BIL, generate LoF variants in 1-2 new lines : crit, milestone, ADGC2_M_13, 2026-03-31, 0d section Aim 3 Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) : active, milestone, ADGC2_J_19, 2025-06-30, 0d Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) : crit, milestone, ADGC2_K_19, 2025-09-30, 0d Begin to upload L1-L3 analysis for data from previous year : crit, milestone, ADGC2_K_20, 2025-09-30, 0d Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) : crit, milestone, ADGC2_L_19, 2025-12-31, 0d Continue upload L1-L3 analysis for data from previous year : crit, milestone, ADGC2_L_20, 2025-12-31, 0d Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) : crit, milestone, ADGC2_M_19, 2026-03-31, 0d Continue upload L1-L3 analysis for data from previous year : crit, milestone, ADGC2_M_20, 2026-03-31, 0d section Aim4 Submit PatchSeq data for 192 NTC lines L0 data : crit, milestone, ADGC2_J_27, 2025-06-30, 0d Submit PatchSeq data for 192 NTC lines L0 data : crit, milestone, ADGC2_K_27, 2025-09-30, 0d - Submit PatchSeq data for 192 NTC lines L0 data : crit, milestone, ADGC2_L_27, 2025-12-31, 0d + Submit PatchSeq data for 192 NTC lines L0 data : active, milestone, ADGC2_L_27, 2025-12-31, 0d Submit PatchSeq data for 192 NTC lines L0 data : active, milestone, ADGC2_M_27, 2026-03-31, 0d Submit PatchSeq data for 192 cells L1-L3 : crit, milestone, ADGC2_K_28, 2025-09-30, 0d Submit PatchSeq data for 192 cells L1-L3 : crit, milestone, ADGC2_L_28, 2025-12-31, 0d Submit PatchSeq data for 192 cells L1-L3 : crit, milestone, ADGC2_M_28, 2026-03-31, 0d
ADGC3 Yale timeline
    
@@ -349,31 +349,31 @@
         section Aim 2
         DRACC data transfer of C57 control MRI and LSFM data : active, milestone, ADGC6_D_16, 2025-09-30, 0d
         DRACC data transfer of first 5 KO mice MRI and LSFM data : active, milestone, ADGC6_E_16, 2025-12-31, 0d
         DRACC data transfer of 2025 Q4 and 2026 Q1-Q3 KO mice MRI and LSFM data : crit, milestone, ADGC6_F_16, 2026-12-31, 0d
         DRACC data transfer of 1st-5th MRI L0 0.24TB data, L1 0.2TB, initial analysis 20 mouse brains : active, milestone, ADGC6_Y2_B_11, 2026-03-31, 0d
         DRACC data transfer of 6th-10th MRI L0 0.5TB data, L1 0.5TB : crit, milestone, ADGC6_Y2_C_11, 2026-06-30, 0d
         DRACC data transfer of 6th-10th LSFM L1 5TB data, L2 0.5TB CCF mapped 1st-5th lines : crit, milestone, ADGC6_Y2_C_15, 2026-06-30, 0d
         DRACC data transfer of 11th-15th MRI L0 0.5TB data, L1 0.5TB : crit, milestone, ADGC6_Y2_D_11, 2026-09-30, 0d
         DRACC data transfer of 16th-20th MRI L0 0.5TB data, L1 0.5TB : crit, milestone, ADGC6_Y2_E_11, 2026-12-31, 0d
         DRACC data transfer of 16th-20th LSFM L1 5TB data, L2 0.5TB CCF mapped 11th-15th lines : crit, milestone, ADGC6_Y2_E_15, 2026-12-31, 0d
         
         section Aim 3
         DRACC data transfer of C57 control behavioral data : active, milestone, ADGC6_D_23, 2025-09-30, 0d
         DRACC data transfer of first 5 KO lines behavioral data : crit, milestone, ADGC6_E_23, 2025-12-31, 0d
         DRACC data transfer of 2025 Q4 and 2026 Q1-Q3 KO line behavioral data : crit, milestone, ADGC6_F_23, 2026-12-31, 0d
-        DRACC data transfer of L0 Video, L1 tracking behavior from lines : crit, milestone, ADGC6_Y2_B_22, 2026-03-31, 0d
+        DRACC data transfer of L0 Video, L1 tracking behavior from lines : active, milestone, ADGC6_Y2_B_22, 2026-03-31, 0d
         DRACC data transfer of L0 Video, L1 tracking behavior from lines : crit, milestone, ADGC6_Y2_C_22, 2026-06-30, 0d
         DRACC data transfer of L0 Video, L1 tracking behavior from lines : crit, milestone, ADGC6_Y2_D_22, 2026-09-30, 0d
         DRACC data transfer of L0 Video, L1 tracking behavior from lines : crit, milestone, ADGC6_Y2_E_22, 2026-12-31, 0d
ADGC7 WUSTL Timeline
         gantt
@@ -404,31 +404,31 @@
 %%        L2, L3 from lines 6-10 submitted : crit, milestone, ADGC7_Y2_F_14, 2027-12-31, 0d
 
         section Aim 2
         Home Cage Behavior L0-L1 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_C_17, 2025-06-30, 0d
         Home Cage Behavior L3 Data to DRACC for lines 1-2 : active, milestone, ADGC7_D_18, 2025-09-30, 0d
         Home Cage Behavior L4 Data to DRACC for lines 1-2 : active, milestone, ADGC7_E_19, 2025-12-31, 0d
         Home Cage Behavior L0-L1 Data to DRACC for line 3-4 : active, milestone, ADGC7_D_17, 2025-09-30, 0d
 
         Home Cage Behavior L3 Data to DRACC for lines 3-4 : active, milestone, ADGC7_E_18, 2025-12-31, 0d
         Home Cage Behavior L4 Data to DRACC for lines 3-4: active, milestone, ADGC7_Y2_B_19, 2026-03-31, 0d
         
         Home Cage Behavior L0-L1 Data to DRACC for lines 5-7 : crit, milestone, ADGC7_E_17, 2025-12-31, 0d
         Home Cage Behavior L3 Data to DRACC for lines 5-7: crit, milestone, ADGC7_Y2_B_18, 2026-03-31, 0d 
         Home Cage Behavior L4 Data to DRACC for lines 5-7 : active, milestone, ADGC7_Y2_C_19, 2026-06-30, 0d
         
-        Home Cage Behavior L0-L1 Data to DRACC for lines 8-12: crit, milestone, ADGC7_Y2_B_17, 2026-03-31,
+        Home Cage Behavior L0-L1 Data to DRACC for lines 8-12: crit, milestone, ADGC7_Y2_B_17, 2026-03-31, 0d
         Home Cage Behavior L3 Data to DRACC for line 8-12 : crit, milestone, ADGC7_Y2_C_18, 2026-06-30, 0d
         Home Cage Behavior L4 Data to DRACC for lines 8-12  : crit, milestone, ADGC7_Y2_D_19, 2026-09-30, 0d
 
         Home Cage Behavior L0-L1 Data to DRACC for lines 13-16 : crit, milestone, ADGC7_Y2_C_17, 2026-06-30, 0d
         Home Cage Behavior L3 Data to DRACC for line 13-16 : crit, milestone, ADGC7_Y2_D_18, 2026-09-30, 0d
         Home Cage Behavior L4 Data to DRACC for lines 13-16 : crit, milestone, ADGC7_Y2_E_19, 2026-12-31, 0d
 
         Home Cage Behavior L0-L1 Data to DRACC for lines 17-22 : crit, milestone, ADGC7_Y2_D_17, 2026-09-30, 0d
         Home Cage Behavior L3 Data to DRACC for line 17-22 : crit, milestone, ADGC7_Y2_E_18, 2026-12-31, 0d
 %%      Home Cage Behavior L4 Data to DRACC for lines 17-22 : crit, milestone, ADGC7_Y2_F_19, 2027-12-31, 0d
         
         Home Cage Behavior L0-L1 Data to DRACC for lines 23-27 : crit, milestone, ADGC7_Y2_E_17, 2026-12-31, 0d
 %%        Home Cage Behavior L3 Data to DRACC for line 23-27 : crit, milestone, ADGC7_Y2_F_18, 2027-12-31, 0d
 %%        Home Cage Behavior L0-L1 data to DRACC for lines 28-32 : crit, milestone, ADGC7_Y2_F_17, 2027-12-31, 0d