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
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
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
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
gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC2 MiNND
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
Generated 217 new lines including 10 NTC (total 332 lines). We generated iNs from 180 lines. :done, IIt1, 2024-01-01, 2025-04-01
Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt2, after IIt1,13w
Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt3, after IIt2,13w
Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt4, after IIt3,13w
Production of 72 iPSC lines on average per quarter (3 batches of 23 gene mutations + 1 NTC) : IIt5, after IIt4,13w
section Aim 2
Submitted scRNA-seq data for 157 lines to the DRACC. : done, IIt6, 2024-04-01,52w
Submit scRNA-seq data for 72 edited lines (3×23 gene mutations + 1 NTC) from last quarter. :crit, IIt7, after IIt6,13w
Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last year. :crit, IIt8, after IIt7,13w
Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last quarter. :crit, IIt9, after IIt8,13w
Submit scRNA-seq data for 72 edited lines (3×23 mutations + 1 NTC) & L1-L3 datasets (fastq, RDS, Excel) from last quarter. :crit, IIt10, after IIt9,13w
Submitted 113 lines morphometrics imaging data. :done, IIt11, 2024-04-01,52w
Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt12, after IIt11,13w
Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt13, after IIt12,13w
Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt14, after IIt13,13w
Submit Imaging of 72 iPSC lines (3×23 mutations + 1 NTC) & prior quarter L1-L3 :crit, IIt15, after IIt14,13w
Pilot CODEX LoF risk variants : II_codex1, 2024-10-01,39w
CODEX 30-50 patient-specific LoF variants KOLF2.2J : II_codex2, after II_codex1,13w
CODEX 12mm coverslips iNs, 30-50 SNPs (SNP/neuron), 3x reps : II_codex3, after II_codex2,13w
CODEX 3x data to BIL, generate LoF variants in 1-2 new lines : crit, II_codex4, after II_codex3,13w
section Aim 3
Submitted 46 lines of Synaptic Optical sensors imaging data : done, IIt16, 2024-04-01,52w
Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt17, after IIt16,13w
Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt18, after IIt17,13w
Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt19, after IIt18,13w
Submit Synaptic Optical Imaging of 72 iPSC (3×23 mutations + 1 NTC) :crit, IIt20, after IIt19,13w
section Aim4
Submit PatchSeq data for 192 NTC lines L0 data :crit, IIv20, 2025-04-01,52w
Submit Patchseq data for 192 cells L1-L3 : crit, IIv21, 2025-07-1,39w
gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC3 Yale
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
Validate gRNA library, lentivirus, pool for 10 capstone ASD genes : done, IIIt1, 2024-01-01,13w
Generate NPC lines from KOLF2.2J and CW20107 for 10 ASD genes : done, IIIt2, 2024-04-01,26w
SUSPENDED - ECCITEseq in hiPSC-NPCs of 10 ASD genes scRNA-seq profiles : active, IIIt3, after IIIt2,13w
SUSPENDED - Sequence and analysis poooled CRISPR screen of 10 NPD genes in hiPSC-NPCs : active, IIIt5, after IIIt3,13w
SUSPENDED - Submit data from multi-omic CRISPR screen of NPD genes in NPCs :active, IIIt8, after IIIt5, 13w
ECCITEseq in day 21 iGLUTs of 10 ASD genes scRNA-seq profiles : done, IIIt4, after IIIt3,13w
DELAYED - Sequence and analysis of pooled CRISPR screen of 10 NPD genes in NPC-iGLUTs : IIIt7, after IIIt5,13w
Submit data from multi-omic CRISPR screen of 29 NDD genes in iGLUTs 3182-3-clone5 & 553-3-clone34 :crit, IIIt9, after IIIt7,13w
DELAYED - dCas9-KRAB hiPSCs with dox-inducible ASCL1/DLX2 from KOLF2.2J and CW20107 hiPSCs : IIIt6, after IIIt4,13w
ECCITEseq in day 35 iGABA 10 genes scRNA-seq : IIIt10, after IIIt6,13w
section Aim 2
Generate zebrafish F0 mutants for 10 NPD genes in parallel with hiPSCs : IIIv16, 2024-01-01,13w
Submit data from high-throughput behavioral profiling of F0 mutants for 10 NPD genes : crit, IIIv17, 2024-01-01,13w
Design CRISPRs targeting another 20 genes in parallel with hiPSCs : IIIv18, 2024-01-01,13w
Design CRISPRs targeting another 10 NPD genes in parallel with hiPSCs : done, IIIv19, after IIIv18,13w
Submit data [acquired - not submitted] from high-throughput behavioral profiling for mutants of 10 NPD genes : crit, IIIv20, after IIIv17,13w
Generate zebrafish F0 mutants for 10 more NPD genes in parallel with hiPSCs: done, IIIv21, after IIIv19,13w
Behavioral profiling of zebrafish F0 mutants for another 10 NPD genes : done, IIIv22, after IIIv20,13w
Whole-brain mapping of zebrafish F0 mutants and stable lines for 5 NPD genes : done, IIIv23, 2024-07-01,13w
Design CRISPRs targeting of 10 more NPD genes in parallel with hiPSCs : done, IIIv24, after IIIv21,13w
Generate zebrafish F0 mutants for 10 more NPD genes in parallel with hiPSCs : done, IIIv25, after IIIv22,13w
Generate stable zebrafish mutant lines for 5 NPD genes with the most robust phenotypes : done, IIIv26, 2024-10-01,13w
Behavioral profiling of zebrafish F0 mutants for another 10 NPD genes : done, IIIv27, after IIIv24,13w
Submit data from high-throughput behavioral profiling for F0 mutants of 10 NPD genes : crit, IIIv28, after IIIv25,13w
ONGOING - Whole-brain mapping of zebrafish F0 mutants and stable lines for 5 NPD genes : IIIv29, 2025-01-01,13w
Generate stable zebrafish mutant lines for 5 NPD genes with the most robust phenotypes : done, IIIv30, after IIIv26,13w
Generate zebrafish F0 mutants for 20 more NPD genes in parallel with hiPSCs : IIIv31, after IIIv27,13w
Submit data from high-throughput behavioral profiling for F0 mutants of 20 more NPD genes : crit, IIIv32, after IIIv28,13w
Whole-brain mapping of zebrafish F0 mutants and stable lines for 10 NPD genes : IIIv33, after IIIv29,13w
Generate stable zebrafish mutant lines for 10 NPD genes with the most robust phenotypes : IIIv34, after IIIv30,13w
Submit data from whole-brain structure and activity mapping of zebrafish mutants of 10 NPD genes : crit, IIIv35, after IIIv33,13w
section Aim 3
ONGOING - Optimize spatial transcriptomic and epigenomic analysis of larval zebrafish using DBiT-Seq : IIIv11, 2024-01-01,52w
ONGOING - Submit 5 DBiT RNA-seq and 5 DBiT ATAC-seq profiles : crit, IIIv12, after IIIv11,13w
Optimize spatial transcriptomic and epigenomic analysis of larval zebrafish using DBiT-Seq : III_v11_new1, 2025-04-01,26w
Produce 5-10 DBiT RNA-seq profiles (fastq) and 5-10 DBiT ATAC-seq profiles (fastq). : III_v11_new2, after III_v11_new1,13w
Submit another 5 DBiT RNA-seq and 5 DBiT ATAC-seq profiles : crit, IIIv13, after III_v11_new2,13w
Submit data [10-20 DBiT RNA-seq profiles (fastq) and 10-20 DBiT ATAC-seq profiles (fastq)] : crit, IIIv13_new1, after IIIv13,52w
Optimize multi-omic CRISPR screen of NPD genes in hiPSC-NPCs : IIIv14, 2024-04-01,78w
Produce 5-10 DBiT RNA-seq profiles (fastq) and 5-10 DBiT ATAC-seq profiles (fastq) : IIIv14_new1, after IIIv14,13w
Submit data from multi-omic CRISPR screen of NPD genes in hiPSCs :crit, IIIv15, after IIIv14_new1,13w
Submit data [10-20 DBiT RNA-seq profiles (fastq) and 10-20 DBiT ATAC-seq profiles (fastq)] : crit, IIIv16, after IIIv15,52w
gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC4 Broad
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
Performed pilot morpholgy screen in 20 genes : done, IVt1, 2024-01-01,13w
Perform perturb-seq screen of ~150 genes in 4 cell types : IVt2, 2024-04-01,52w
- Develop protocol for scaling up screen size : IVt5, 2024-04-01,52w
- Validation of initial 20 gene morphological screen : IVt3, 2024-04-01,52w
- Submit image dataset of 40 TB : crit, IVt4, after IVt3,3w
- Submit image dataset of 40 TB : crit, IVt6, 2026-03-15,3w
- Submit image dataset of 80 TB : crit, IVt7, 2027-03-15,3w
+ Submit 100,000 scRNA-seq profiles per cell type (fastq) - PARTIALLY COMPLETE (191 GENES, 3 CELL TYPES)/ TRANSFER STARTED : crit, IVt2b, after IVt2,3w
+ Submit 100,000 scRNA-seq profiles per cell type (fastq) of 191 genes in 3 cell types : crit, IVt2_year4, 2026-03-15,3w
+ Develop protocol for scaling up screen size : done, IVt5, 2024-04-01,52w
+ Validation of initial 20 gene morphological screen : done, IVt3, 2024-04-01,52w
+ Submit image dataset of 40 TB - DONE, DATA TRANSFER STARTED : crit, IVt4, after IVt3,3w
+ Submit image dataset of 120 TB (443 genes in 3 cells 5 million profiles) : crit, IVt6, 2026-03-15,3w
+ Submit remaining image datasets : crit, IVt7, 2027-03-15,3w
section Aim 2
Developed Perturb-FISH screens : done, IVt8, 2024-01-01,13w
- Perform perturb-seq screen of ~150 genes in 4 cell types : IVt9, 2024-04-01,52w
- Perform Perturb-FISH screen of ASD genes in iPS derived astrocytes : IVt10, 2024-04-01, 52w
- Submit 50 TB of calcium imaging and MERFISH data :crit, IVt11, after IVt10, 3w
- Perform pilot 10 gene electrophysiology screen : IVt12, 2024-04-01,52w
- Submit 5 TB of optical electrophysiology data : crit, IVt13, after IVt12, 3w
+ Perform perturb-seq screen of ~150 genes in 4 cell types - PARTIALLY COMPLETE : IVt9, 2024-04-01,52w
+ Submit 100,000 scRNA-seq profiles per cell type of 191 genes in 3 cell types (fastq) : crit, IVt9b_year4, 2026-03-15,3w
+ Perform Perturb-FISH screen of ASD genes in iPS derived astrocytes : done, IVt10, 2024-04-01, 52w
+ Submit 50 TB of calcium imaging and MERFISH data : done, IVt11, after IVt10, 3w
+ Perform pilot 10 gene electrophysiology screen - PARTIALLY COMPLETE : IVt12, 2024-04-01,52w
+ Submit 5 TB of optical electrophysiology data - DATA QUALITY BEING ASSESSED : crit, IVt13, after IVt12, 3w
Submit 5 TB of optical electrophysiology data : crit, IVt14, 2026-03-15,3w
- Submit 5 TB of optical electrophysiology data : crit, IVt15, 2027-03-15,3w
+ Submit remaining optical electrophysiology data : crit, IVt15, 2027-03-15,3w
section Aim 3
- Perform census-seq screen of 40 line village RNA-seq : IVt16, 2024-04-01,52w
- Submit census-seq RNA-seq profiles : crit, IVt16b, after IVt16, 3w
- Submit 2 TB of morphology imaging : crit, IVt17, 2026-03-15,3w
- Submit 2 TB of optical ephys : crit, IVt18, 2026-03-15,3w
- Submit 2 TB of morphology imaging : crit, IVt19, 2027-03-15,3w
- Submit 2 TB of optical ephys : crit, IVt20, 2027-03-15,3w
+ Perform scRNAseq (dropulation) screen of ~40 line village of CIRM lines - PARTIALLY COMPLETE : IVt16, 2024-04-01,52w
+ Submit RNA-seq profiles - ANALYSIS / SUBMISSION UNDERWAY : crit, IVt16b, after IVt16, 3w
+ Submit RNA-seq profiles from >10,000 cells : crit, IVt17, 2026-03-15,3w
+ Submit remaining RNA-seq profiles : crit, IVt17_yearEnd, 2027-03-15,3w
+ Morphological profiles of ~40 line village of CIRM lines : IVt18a, 2025-04-01,52w
+ Submit ~10 TB of associated images to DRACC : crit, IVt18b, after IVt18a,3w
+ Submit remaining morphology imaging : crit, IVt19, 2027-03-15,3w
gantt
dateFormat YYYY-MM-DD
axisFormat %Y-Q%q
title ADGC5 Scripps/Broad
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 Scripps/Broad Reporting Year
End Scripps/Broad Reporting Year 1 :milestone, m1, 2025-03-31, 0d
End Scripps/Broad Reporting Year 2 :milestone, m1, 2026-03-31, 0d
End Scripps/Broad Reporting Year 3 :milestone, m1, 2027-04-01, 0d
section Aim 1
Refine AAV-based Perturb-seq, test v1 and v2, assess data quality, finalize method : Vt1, 2024-09-01,2025-04-01
Design gRNAs and generate vectors for Perturb-seq : Vt2, 2024-09-01,2025-04-01
Choose single cell technology; test, validate with finalized Perturb-seq method : Vt3, 2024-09-01,2025-04-01
Test gRNA efficacy in vitro; nominate final perturbation vectors to be used : Vt4, 2024-09-01,2025-04-01
Discuss within and across ADGC groups to choose genes to target among list of 259 genes; finalize gene selection for this project : Vt5, 2024-09-01,2025-04-01
Generate multiomics data for 50 genes in 1 brain region at 1 time point : V_Y2t1, 2025-04-01,52w
Submit L0/L1 data to DRACC (Restricted) ~175 FASTQ for ~75TB overall : crit, V_Y2t2, 2025-04-01,52w
section Aim 2
Refine brain clearing experiments (1) test CUBIC method and assess data quality : Vt6, 2024-09-01,2025-04-01
Refine brain clearing experiments (2) test LifeCanvas (CLARITY) method and assess data quality : Vt7, 2024-09-01,2025-04-01
Establish data analysis pipeline through semi-automatic image tracing and segmentation : Vt8, 2024-09-01,2025-04-01
Establish approaches to integrate single-cell omic data with spatial morphometric data : Vt9, 2024-09-01,2025-04-01
Select first 5 ASD risk genes to be included in the study : Vt10, 2024-09-01,2025-04-01
Test gRNA efficacy in vitro, nominate final vectors, collect brain samples : V_Y2t3, 2025-04-01,52w
Implement functional pipeline for analyzing Perturb-seq multiomics data : V_Y2t4,2025-04-01,52w
Develop methods for GRN analysis of multiomics data : V_Y2t5, 2025-04-01,52w
Identify datasets to be used to build GRNs from developing human brains : V_Y2t6, 2025-04-01,52w
Generate raw TIFF format and 3D swc files for 100 neurons on 3 genes : V_Y2t7, 2025-04-01,52w