c545c9e19e779833f77cac8832136f95e4f3390b brianlee Wed May 7 14:11:28 2025 -0700 Updates to MiNND SSPsyGene AIM1 & AIM2 milestones per 2025 NIMH docs diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index 13a86b5f6ed..52572d23660 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -77,47 +77,51 @@ 
    
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         dateFormat  YYYY-MM-DD
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         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 115 lines (22 targeted genes +1 NTC)     :done, IIt1, 2024-01-01, 2024-04-01
-        Production of 72 iPSC lines on average per quarter :   IIt2, after IIt1,13w 
-        Production of 72 iPSC lines on average per quarter :   IIt3, after IIt2,13w 
-        Production of 72 iPSC lines on average per quarter :   IIt4, after IIt3,13w
-        Production of 72 iPSC lines on average per quarter :   IIt5, after IIt4,13w 
+        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
-        Submit 22 lines of scRNA-seq  :crit, IIt6, 2024-04-01,13w
-        Submit scRNA-seq of 72 iPSC lines on average per quarter :crit,   IIt7, after IIt6,13w 
-        Submit scRNA-seq of 72 iPSC lines on average per quarter :crit,   IIt8, after IIt7,13w 
-        Submit scRNA-seq of 72 iPSC lines on average per quarter :crit,   IIt9, after IIt8,13w
-        Submit scRNA-seq of 72 iPSC lines on average per quarter :crit,   IIt10, after IIt9,13w 
-        Submit 22 lines morphometrics imaging data   :done, IIt11, 2024-04-01,13w
-        Submit Imaging of 72 iPSC lines on average per quarter :crit,   IIt12, after IIt11,13w 
-        Submit Imaging of 72 iPSC lines on average per quarter :crit,   IIt13, after IIt12,13w 
-        Submit Imaging of 72 iPSC lines on average per quarter :crit,   IIt14, after IIt13,13w 
-        Submit Imaging of 72 iPSC lines on average per quarter :crit,   IIt15, after IIt14,13w 
+        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
         Submit Synaptic Optical sensors imaging data :done, IIt16, 2024-04-01,13w 
         Submit Synaptic Optical Imaging of 72 iPSC lines on average per quarter :crit,   IIt17, after IIt16,13w
         Submit Synaptic Optical Imaging of 72 iPSC lines on average per quarter :crit,   IIt18, after IIt17,13w
         Submit Synaptic Optical Imaging of 72 iPSC lines on average per quarter :crit,   IIt19, after IIt18,13w
         Submit Synaptic Optical Imaging of 72 iPSC lines on average per quarter :crit,   IIt20, after IIt19,13w
 
         section Aim4
         Submit PatchSeq data for first set of 96 edited lines :crit, IIv20, 2024-04-01,13w
         Submit Patchseq data for 192 cells : crit, IIv21, after IIv20,39w
@@ -142,54 +146,54 @@ 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 : IIIv19, after IIIv18,13w - Submit data 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: IIIv21, after IIIv19,13w - Behavioral profiling of zebrafish F0 mutants for another 10 NPD genes : IIIv22, after IIIv20,13w - Whole-brain mapping of zebrafish F0 mutants and stable lines for 5 NPD genes : IIIv23, 2024-07-01,13w - Design CRISPRs targeting of 10 more NPD genes in parallel with hiPSCs : IIIv24, after IIIv21,13w - Generate zebrafish F0 mutants for 10 more NPD genes in parallel with hiPSCs : IIIv25, after IIIv22,13w - Generate stable zebrafish mutant lines for 5 NPD genes with the most robust phenotypes : IIIv26, 2024-10-01,13w - Behavioral profiling of zebrafish F0 mutants for another 10 NPD genes : IIIv27, after IIIv24,13w - Submit data from high-throughput behavioral profiling for F0 mutants of 20 more NPD genes : crit, IIIv28, after IIIv25,13w - 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 : IIIv30, after IIIv26,13w + 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 - Optimize spatial transcriptomic and epigenomic analysis of larval zebrafish using DBiT-Seq : IIIv11, 2024-01-01,52w - Submit 5 DBiT RNA-seq and 5 DBiT ATAC-seq profiles : crit, IIIv12, after IIIv11,13w + 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 Submit another 5 DBiT RNA-seq and 5 DBiT ATAC-seq profiles : crit, IIIv13, after IIIv12,13w - Optimize multi-omic CRISPR screen of NPD genes in hiPSC-NPCs : IIIv14, 2024-04-01,52w + ONGOING - Optimize multi-omic CRISPR screen of NPD genes in hiPSC-NPCs : IIIv14, 2024-04-01,52w Submit data from multi-omic CRISPR screen of NPD genes in hiPSCs :crit, IIIv15, after IIIv14,13w
ADGC4 Broad timeline
    
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         title       ADGC4  Broad