gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC1 UCLA
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 AIM 1
- Generate stable clonal iPSC lines for 10 gene mutations in KOLF2.2J (Capstone; Batch A) : t1, 2024-01-01, 2024-07-01
- Generate stable clonal iPSC lines for 10 gene mutations in CIRM line (Capstone; Batch A) : t2, 2024-01-01, 2024-07-01
- Generate stable clonal iPSC lines for additional 25 gene mutations in KOLF2.2J and CIRM (Batch B) : t3, 2024-04-01, 2024-09-30
+ Generate stable clonal iPSC lines for 10 gene mutations in KOLF2.2J (Capstone; BATCH A) : t1, 2024-01-01, 2024-07-01
+ Generate stable clonal iPSC lines for 10 gene mutations in CIRM line (Capstone; BATCH A) : t2, 2024-01-01, 2024-07-01
+ Generate stable clonal iPSC lines for additional 25 gene mutations in KOLF2.2J and CIRM (BATCH B) : t3, 2024-04-01, 2024-09-30
QC of Capstone lines to date pending : t4, 2024-04-01, 39w
Generate and QC stable clonal iPSC lines for additional 65 gene mutations in KOLF2.2J and CIRM : t6, after t3, 52w
QC of all generated lines to date pending : t7, after t3, 78w
- Share 20 BatchA gene edited iPSC lines (10 NPD genes x 2 iPSC backgrounds) : t8, after t4, 26w
- Share 180 Batch B+C gene edited iPSC lines (90 NPD genes x 2 iPSC backgrounds) : t10, after t8, 39w
+ Share 20 BATCHA gene edited iPSC lines (10 NPD genes x 2 iPSC backgrounds) : t8, after t4, 26w
+ Share 180 BATCH B+C gene edited iPSC lines (90 NPD genes x 2 iPSC backgrounds) : t10, after t8, 39w
Troubleshoot and perform 2nd attempt of difficult KO genes : t11, after t10, 13w
section AIM 2
Quantify proliferation rates of NPCs from 10 Capstone iPSC clonal lines : t5, after t1, 26w
Quantify proliferation rates of NPCs from all iPSC clonal lines from all batches : t9, after t4, 52w
Bulk RNA-seq profiles (4 replicates per gene x (10 NPD iPSC lines + 2 controls) x 1 background (KOLF2.2J) iPSC background lines; fastq)) : t20, after t2, 52w
Submit data from first capstone experiment (KOLF2.2J background) :crit, t22, after t20, 13w
Bulk RNA-seq profiles ((4 replicates per gene x (10 NPD iPSC lines + 2 controls) x 1 background (CIRM line) iPSC background lines; fastq)) : t21, after t3, 39w
Submit data from first capstone experiment (CIRM background) :crit, t23, after t21, 13w
Begin villages : t24, 2024-07-01,13w
Complete villages : t25, after t24,13w
Perform StimScope Ephys Experiments for all lines : t32, 2025-10-01,30w
- Submit data on RNA-seq profiles from Batch B and C :crit, t33, 2025-10-01,13w
- Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from Capstone Lines (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_I_8, 2025-03-31, 0d
- Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from batch B (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_JK_8, 2025-10-01, 0d
- Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from batch C (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_LM_8, 2026-04-01, 0d
- Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from batch D (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_NO_8, 2026-10-01, 0d
- Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from batch E (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_P_8, 2026-12-31, 0d
- Quantify proliferation rates/IF/morphology of IPSC/NPC/Neurons from batch F (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_Q_8, 2027-04-01, 0d
-ADGC1_LM_111213 Submit L0-L1 from Batch B, producing bulk RNA-seq profiles (3 technical replicates, 4 biological replicates per gene x (20 NPD iPSC lines + 2 controls) x 2 backgrounds (KOLF2.2J/CIRM) iPSC background lines; fastq)) : crit, milestone, ADGC1_LM_111213, 2026-04-01, 0d
- Submit L0-L1 from Batch C, producing bulk RNA-seq profiles (3 technical replicates, 4 biological replicates per gene x (20 NPD iPSC lines + 2 controls) x 2 backgrounds (KOLF2.2J/CIRM) iPSC background lines; fastq)) : crit, milestone, ADGC1_NO_111213, 2026-10-01, 0d
- Submit L0-L1 from Batch D, producing bulk RNA-seq profiles (3 technical replicates, 4 biological replicates per gene x (20 NPD iPSC lines + 2 controls) x 2 backgrounds (KOLF2.2J/CIRM) iPSC background lines; fastq)) : crit, milestone, ADGC1_P_111213, 2026-12-31, 0d
- Submit L0-L1 from Batch E-G, producing bulk RNA-seq profiles (3 technical replicates, 4 biological replicates per gene x (20 NPD iPSC lines + 2 controls) x 2 backgrounds (KOLF2.2J/CIRM) iPSC background lines; fastq)) : crit, milestone, ADGC1_Q_111213, 2027-04-01, 0d
+ Submit data on RNA-seq profiles from BATCH B and C :crit, t33, 2025-10-01,13w
+ 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 : crit, milestone, ADGC1_JK_8, 2025-10-01, 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, 2026-04-01, 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, 2026-10-01, 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, 2027-04-01, 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, 2026-04-01, 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, 2026-10-01, 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, 2027-04-01, 0d
Complete villages - submit L0-L1 to DRACC : crit, milestone, ADGC1_JK_14, 2025-10-01, 0d
Village Analysis - submit L0-L1 to DRACC : crit, milestone, ADGC1_LM_14, 2026-04-01, 0d
- Calcium Imaging Capstone Analysis (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_K_15, 2025-09-30, 0d
- Calcium Imaging analysis excitatory/inhibitory neurons - Capstone Analysis (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) : crit, milestone, ADGC1_M_15, 2026-04-01, 0d
- Calcium Imaging Experiments and analysis of future batches (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 4 well replicates/line; tif format) (Submit L0-L4 to DRACC on a rolling basis once completed during this timeframe) : crit, milestone, ADGC1_NOPQ_15, 2027-04-01, 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, 2026-04-01, 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, 2027-04-01, 0d
section AIM 3
Begin organoids first 20 : t26, 2024-07-01,13w
Prepare samples for RNAseq : t27, after t26,13w
Perform RNAseq : t28, after t27,13w
Begin RNAseq Analysis : t29, after t28,13w
Prepare samples for CODEX: t30, after t27,13w
Perform CODEX: t31, after t30,13w
Submit first Spatial Imaging data: crit, t32, after t31,13w
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, 2025-07-01, 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, 2026-04-01, 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, 2027-04-01, 0d
- Spatial Proteomics Analysis Batch C : crit, milestone, ADGC1_O_161718, 2027-04-01, 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, 2026-04-01, 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, 2027-04-01, 0d
+ Spatial Proteomics Analysis BATCH C : crit, milestone, ADGC1_O_161718, 2027-04-01, 0d
Perform codex and analysis for future batches : crit, milestone, ADGC1_Q_161718, 2027-04-01, 0d
Organoid snRNAseq analysis for Capstone Genes : crit, milestone, ADGC1_J_1920, 2025-07-01, 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
- Perform snRNAseq for batch C (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 2-4 organoid replicates/line; tif format) : crit, milestone, ADGC1_M_1920, 2026-04-01, 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
+ Perform snRNAseq for BATCH C (10 Genes, 20 NPD iPSC lines + 2 control lines) x 2 iPSC background lines; 2-4 organoid replicates/line; tif format) : crit, milestone, ADGC1_M_1920, 2026-04-01, 0d
Organoid snRNAseq analysis C : crit, milestone, ADGC1_N_1920, 2027-04-01, 0d
Perform Integrative analysis across first 30 genes and across experimental modalities (Spatial and snRNAseq). Submit L3-L4 level data by this time at the latest : crit, milestone, ADGC1_O_1920, 2027-04-01, 0d
Perform snRNAseq for future batches : crit, milestone, ADGC1_P_1920, 2026-12-31, 0d
Organoid snRNAseq Analysis for future batches : crit, milestone, ADGC1_Q_1920, 2027-04-01, 0d