f6a269c29b553a8d1f5357e908e15ee1c76f602e brianlee Mon Aug 10 11:00:18 2026 -0700 ADGC1_LM_14,ADGC2_M_27,ADGC3_Y4_N_4,ADGC6_Y2_B_11,ADGC7_Y2_C_19 updates in timeline to reflect active work diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index c77620eada3..6bc2b4318ee 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -63,31 +63,31 @@ 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 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 + 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 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 @@ -147,31 +147,31 @@ 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 : crit, milestone, ADGC2_M_27, 2026-03-31, 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 </pre> </div> </div> <a name="ADGC3"></a> <!-- Start of ADGC3 Henry Gantt Chart--> <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC3 Yale timeline</h5></div> <div class="row"> <div class="col-md-12"> <pre class="mermaid"> gantt @@ -181,31 +181,31 @@ section Grant Year Start Grant Year 3 :milestone, year3_yale, 2025-03-31, 0d Start Grant Year 4 :milestone, year4_yale, 2026-03-31, 0d Start Grant Year 5 :milestone, m1, 2027-03-31, 0d click year3_yale href "https://docs.google.com/spreadsheets/d/10xWymZXsDlDQ9uwU5YPAKwyflUMzpDS4/edit?gid=1305684354#gid=1305684354&range=J1:M25" click year4_yale href "https://docs.google.com/spreadsheets/d/1eXIL5rCpqCD2rp331q_iruQJ29UPOy70/edit?gid=1400272468#gid=1400272468&range=N1" section Aim 1 Submit initial data (L0, L1) CRISPRi MEA and calcium imaging of 15 ASD genes in iGLUTs and/or iGABAs (ARID1B - SHANK3) : crit, milestone, ADGC3_N_5, 2027-03-31, 0d Submit initial data (L0, L1) CRISPRi ECCITEseq, KOLF2.2J and CW20107 in iGLUTs (fastq), 10 capstone genes (ARID1B - SMARCC2) : crit, milestone, ADGC3_K_6, 2025-09-30, 0d Submit initial data (L0, L1) CRISPRi organoid models ECCITEseq of 10 capstone genes (ARID1B - SMARCC2) genes in KOLF2.2J : crit, milestone, ADGC3_N_6, 2027-03-31, 0d Submit ECCITEseq data (L0, L1) to DRACC for 29 NDD genes (ANK3 - WAC) in induced NPCs, glutamatergic neurons, and GABAergic neurons; iGLUT 3182-3-clone5 (iNPC, d7 iGLUT and d21 iGLUT) and iGABA 553-3-clone34 (d36 iGABA) : done, milestone, ADGC3_I_7, 2025-03-31, 0d Submit L3/L4 data from iGLUT manuscript : active, milestone, ADGC3_K_7, 2025-09-30, 0d - Submit initial data (L0, L1) iGLUT 10 capstone genes (ARID1B, ASXL3, CACNA1G, CHD8, DLL1, GABRA1, KMT2C, SCN2A, SHANK3, SMARCC2). Across four donors, KOLF2.2J, CW20107, 2607, 553, ECCITEseq resolved 7,985, 3,834, 232, and 8,902 iGLUTs, expected to further increase with final alignments. QC metrics resolved good gRNA representation and high quality/glutamatergic neurons : crit, milestone, ADGC3_Y4_N_4, 2026-06-30, 0d + Submit initial data (L0, L1) iGLUT 10 capstone genes (ARID1B, ASXL3, CACNA1G, CHD8, DLL1, GABRA1, KMT2C, SCN2A, SHANK3, SMARCC2). Across four donors, KOLF2.2J, CW20107, 2607, 553, ECCITEseq resolved 7,985, 3,834, 232, and 8,902 iGLUTs, expected to further increase with final alignments. QC metrics resolved good gRNA representation and high quality/glutamatergic neurons : active, milestone, ADGC3_Y4_N_4, 2026-06-30, 0d Submit initial data (L0, L1) CRISPRko calcium imaging of 15 ASD genes in iGLUTs (ARID1B, ASH1L, CHD8, CUL3, DYRK1A, KMT5B, POGZ, PTEN, ANK2, CACNA1G, GRIA3, GRIN2A, NRXN1, SCN2A, SHANK3) and MEA iGLUT (SCN2A) - matrix CSV file : crit, milestone, ADGC3_Y4_N_5, 2026-06-30, 0d Submit L3/L4 data from manuscript describing capstone ECCITEseq of 10 capstone genes in KOLF2.2J : crit, milestone, ADGC3_Y4_Q_4, 2027-03-31, 0d Submit L3/L4 data from estradiol pre-print describing calcium imaging of 15 ASD genes and MEA of 1 gene in iGLUTs : crit, milestone, ADGC3_Y4_Q_5, 2027-03-31, 0d %% For successful screens, submit initial data (L0, L1) CRISPR amplicon-seq of 36/250/whole genome NDD genes for neurogenesis, mitochondrial function, and/or neuronal activity : crit, milestone, ADGC3_Y4_R_6, 2028-03-31, 0d %% Submit L3/L4 data from manuscript describing phenotyping of all genes across zebrafish + hiPSCs : crit, milestone, ADGC3_Y4_R_7, 2028-03-31, 0d section Aim 2 Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 10 stable mutant lines (ADNP - SYNGAP1) : crit, milestone, ADGC3_I_12, 2025-03-31, 0d Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes (ANK2 - SMARCC2) : active, milestone, ADGC3_J_14, 2025-06-30, 0d Submit data (L0, L1) Whole-brain structure and activity mapping (.LIF, .XLS), zebrafish, 5 NPD genes (ADNP - NRXN1) : active, milestone, ADGC3_K_14, 2025-09-30, 0d Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes (AKAP11 - WAC) : active, milestone, ADGC3_L_14, 2025-12-31, 0d Submit data (L0, L1) Whole-brain structure and activity mapping (.LIF, .XLS), zebrafish, 5 NPD genes (PPP2R5D - MBD5) : crit, milestone, ADGC3_M_14, 2026-03-31, 0d Submit L3/L4 data from 40 NPD gene manuscript : crit, milestone, ADGC3_K_15, 2025-09-30, 0d Submit data (L0, L1) High-throughput quantitative behavioral profiling (.raw, .XLS), zebrafish, 20 NPD genes (CASKIN1 - XPO7) : crit, milestone, ADGC3_N_15, 2027-03-31, 0d Submit data (L0, L1) Whole-brain RNA-seq, zebrafish, 10 NPD genes (CHD8 - SMARCC2) : crit, milestone, ADGC3_N_17, 2027-03-31, 0d @@ -338,31 +338,31 @@ DRACC data transfer of 2025 Q4 and 2026 Q1-Q3 KO mice MERFISH data : crit, milestone, ADGC6_F_7, 2026-12-31, 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, 2026-12-31, 0d DRACC data transfer of C57 control L0 1TB, L1 0.5TB spatial txn : crit, milestone, ADGC6_Y2_B_4, 2026-03-31, 0d DRACC data transfer of 1st-4th KO L0 4TB, L1 2TB spatial txn : crit, milestone, ADGC6_Y2_C_5, 2026-06-30, 0d DRACC data transfer of 1st-4th scRNA-seq L0 0.8TB data, L1 0.4TB : crit, milestone, ADGC6_Y2_D_6, 2026-09-30, 0d DRACC data transfer of 5th-8th KO L0 4TB, L1 2TB spatial txn : crit, milestone, ADGC6_Y2_D_7, 2026-09-30, 0d DRACC data transfer of 5th-8th line scRNA-seq L0 0.8TB data, L1 0.4TB : crit, milestone, ADGC6_Y2_E_6, 2026-12-31, 0d DRACC data transfer of 9th - 12th KO L0 4TB, L1 2TB spatial txn : crit, milestone, ADGC6_Y2_E_7, 2026-12-31, 0d 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 : crit, milestone, ADGC6_Y2_B_11, 2026-03-31, 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 : 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 @@ -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 : crit, milestone, ADGC7_D_18, 2025-09-30, 0d Home Cage Behavior L4 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_E_19, 2025-12-31, 0d Home Cage Behavior L0-L1 Data to DRACC for line 3-4 : crit, milestone, ADGC7_D_17, 2025-09-30, 0d Home Cage Behavior L3 Data to DRACC for lines 3-4 : crit, milestone, ADGC7_E_18, 2025-12-31, 0d %% Home Cage Behavior L4 Data to DRACC for lines 3-4 : crit, milestone, ADGC7_F_19, 2026-03-31, 0d Home Cage Behavior L4 Data to DRACC for lines 3-4: crit, 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_F_18, 2026-03-31, 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 : crit, milestone, ADGC7_Y2_C_19, 2026-06-30, 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 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