ce8f3ea0b9a92fdeae5257a2035b11dedc78b5b0 brianlee Thu Sep 19 08:47:11 2024 -0700 Adding a SSPsyGene Timeline graphic fo SSPsyGene portal, and links in footer, and CGI page footer; Commit Approved by Max in email 9/19/24 diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html new file mode 100755 index 0000000..3b92d48 --- /dev/null +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -0,0 +1,233 @@ +<!DOCTYPE html> +<!--#set var="TITLE" value="CIRM CESCG People and Labs" --> + +<!--#include virtual="setRoot.html" --> + +<!--#include virtual="${ROOT}inc/header.html" --> + +<head> + <meta charset="UTF-8"> + <title>Mermaid Gantt Chart</title> + <script src="https://cdn.jsdelivr.net/npm/mermaid/dist/mermaid.min.js"></script> + <script> + mermaid.initialize({ startOnLoad: true }); + </script> +</head> + +<div class="cirm-page-body"> + <div class="cirm-page-title back-dark-pink"> + <h5 class="cirm-page-title-text">SSPsyGene Milestone Charts</h5> + </div> + <a name="ADGC1"></a> + <!-- Start of ADGC1 Gnatt Chart--> + <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC 1 UCLA Chart</h5></div> + <div class="row"> + <div class="col-md-12"> + <pre class="mermaid"> + 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 + + </pre> + </div> + </div> + <a name="ADGC2"></a> + <!-- Start of ADGC2 Gnatt Chart--> + <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC2 MiNND timeline</h5></div> + <div class="row"> + <div class="col-md-12"> + <pre class="mermaid"> + 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 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 + + 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 :crit, 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 + + section Aim 3 + Submit Synaptic Optical sensors imaging data :crit, 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 + + </pre> + </div> + </div> + <a name="ADGC3"></a> + <!-- Start of ADGC3 Gnatt 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 + 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 : IIIt1, 2024-01-01,13w + Generate NPC lines from KOLF2.2J and CW20107 for 10 ASD genes : IIIt2, 2024-04-01,26w + ECCITEseq in hiPSC-NPCs of 10 ASD genes scRNA-seq profiles : IIIt3, after IIIt2,13w + Sequence and analysis poooled CRISPR screen of 10 NPD genes in hiPSC-NPCs : IIIt5, after IIIt3,13w + Submit data from multi-omic CRISPR screen of NPD genes in NPCs :crit, IIIt8, after IIIt5, 13w + ECCITEseq in day 21 iGLUTs of 10 ASD genes scRNA-seq profiles : IIIt4, after IIIt3,13w + 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 NPD genes in iGLUTs :crit, IIIt9, after IIIt7,13w + 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 + 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 + 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 + Submit data from multi-omic CRISPR screen of NPD genes in hiPSCs :crit, IIIv15, after IIIv14,13w + + </pre> + </div> + </div> + <a name="ADGC4"></a> + <!-- Start of ADGC4 Gnatt Chart--> + <div class="cirm-page-title back-light-blue"><h5 class="cirm-page-title-text">ADGC4 Broad timeline</h5></div> + <div class="row"> + <div class="col-md-12"> + <pre class="mermaid"> + 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 + + 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 + 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 + + 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 + + </pre> + </div> + </div> +<!--#include virtual="${ROOT}inc/footer.html" -->