a4ff8fa3139e52d36188b26841fb2a362b1d700b brianlee Fri Oct 31 13:00:45 2025 -0700 Adding links to jump to dates in milestones in Google Docs of each ADGCs on SSPsyGene milestones for quicker reference diff --git src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html index adf7691e575..16266ba5c42 100755 --- src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html +++ src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html @@ -24,31 +24,31 @@ 
     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, year3_ucla, 2025-03-31, 0d                                       
     Start Grant Year 4     :milestone, m1, 2026-03-31, 0d                                        
     Start Grant Year 5     :milestone, m1, 2027-04-01, 0d
 
-    click year3_ucla href "https://docs.google.com/spreadsheets/d/1Ml_UXDHE4UZo2kjLp1aZLa0KxLtLSnVi/edit?gid=1138387919#gid=1138387919"
+    click year3_ucla href "https://docs.google.com/spreadsheets/d/1Ml_UXDHE4UZo2kjLp1aZLa0KxLtLSnVi/edit?gid=1138387919#gid=1138387919&range=J1:M20"
         
     section AIM 1 
     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
@@ -106,31 +106,31 @@
   
ADGC2 MiNND timeline

   

     

       
    
         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, year3_minnd, 2025-03-31, 0d
         Start Grant Year 4     :milestone, m1, 2026-03-31, 0d
         Start Grant Year 5     :milestone, m1, 2027-04-01, 0d
 
-        click year3_minnd href "https://docs.google.com/spreadsheets/d/1GNrJaIjs6nPlFY4j2AlZSlTDf2-mi17d/edit?gid=1137576441#gid=1137576441"
+        click year3_minnd href "https://docs.google.com/spreadsheets/d/1GNrJaIjs6nPlFY4j2AlZSlTDf2-mi17d/edit?gid=1137576441#gid=1137576441&range=J1:M34"
         
         section Aim 1
         Generated 217 new lines including 10 NTC (total 332 lines). We generated iNs from 180 lines.  :done, IIt1, 2024-04-01, 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
@@ -161,31 +161,31 @@
   
ADGC3 Yale timeline

   

     

       
    
         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, year3_yale, 2025-03-31, 0d
         Start Grant Year 4     :milestone, m1, 2026-03-31, 0d
         Start Grant Year 5     :milestone, m1, 2027-04-01, 0d
 
-        click year3_yale href "https://docs.google.com/spreadsheets/d/10xWymZXsDlDQ9uwU5YPAKwyflUMzpDS4/edit?gid=1305684354#gid=1305684354"
+        click year3_yale href "https://docs.google.com/spreadsheets/d/10xWymZXsDlDQ9uwU5YPAKwyflUMzpDS4/edit?gid=1305684354#gid=1305684354&range=J1:M25"
 
         section Aim 1
         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
         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, 2027-04-01, 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, 2027-04-01, 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, 2025-04-01, 0d
@@ -243,31 +243,31 @@
   
ADGC4 Broad timeline

   

     

       
    
         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, year3_broad, 2025-03-31, 0d
         Start Grant Year 4     :milestone, m1, 2026-03-31, 0d
         Start Grant Year 5     :milestone, m1, 2027-04-01, 0d
 
-        click year3_broad href "https://docs.google.com/spreadsheets/d/1BwaO6rgn0o5nTulC2M6dQe5UMGUWEy-o/edit?gid=2037309850#gid=2037309850"
+        click year3_broad href "https://docs.google.com/spreadsheets/d/1BwaO6rgn0o5nTulC2M6dQe5UMGUWEy-o/edit?gid=2037309850#gid=2037309850&range=D1:D16"
 
         section Aim 1
         Perform perturb-seq screen of 150 genes in 4 cell types : IVt2, 2024-04-01,52w
         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, milestone, ADGC4_Aim1_year4_item1, 2026-03-31, 0d
         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, milestone, ADGC4_Aim1_year4_item2, 2026-03-31, 0d 
         Submit remaining image datasets : crit, milestone, ADGC4_Aim1_year5_item1, 2027-03-31, 0d 
 
         section Aim 2
         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, milestone, ADGC4_Aim2_year4_item1, 2026-03-31, 0d
         Perform Perturb-FISH screen of ASD genes in iPS derived astrocytes : done, IVt10, 2024-04-01, 52w
@@ -299,31 +299,31 @@
         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, year1_scripps, 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
 
-        click year1_scripps href "https://docs.google.com/spreadsheets/d/19RWN6-DjIyMpFV2JP4yY5Ta5Xfthieds/edit?gid=744607405#gid=744607405"
+        click year1_scripps href "https://docs.google.com/spreadsheets/d/19RWN6-DjIyMpFV2JP4yY5Ta5Xfthieds/edit?gid=744607405#gid=744607405&range=C2:C15"
         
         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, milestone, ADGC5_Aim1_year4_item1, 2026-03-31, 0d
 
         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
@@ -346,31 +346,31 @@
         gantt
         dateFormat  YYYY-MM-DD
         axisFormat  %Y-Q%q
         title       ADGC6  Cross-Scale Interrogation of NPD Genes (SING) - PSU/JAX/UTSW/NYU 
 
         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 SING Reporting Year
         End SING Reporting Year 1      :milestone, year1_SING, 2025-12-31, 0d
         End SING Reporting Year 2      :milestone, m1, 2026-12-31, 0d
 
-        click year1_SING href "https://docs.google.com/spreadsheets/d/1pw1muwglklo-gXrC5hadYjSqBjhZOKeh/edit?gid=1827916005#gid=1827916005"
+        click year1_SING href "https://docs.google.com/spreadsheets/d/1pw1muwglklo-gXrC5hadYjSqBjhZOKeh/edit?gid=1827916005#gid=1827916005&range=C2:E23"
 
         section Aim 1
         Initial discussion with DRACC for data transfer complete : crit, milestone, ADGC6_C_7, 2025-06-30, 0d
         DRACC data transfer of C57 control MERFISH : crit, milestone, ADGC6_D_8, 2025-09-30, 0d
         DRACC data transfer of first 5 KO mice MERFISH data : crit, milestone, ADGC6_E_7, 2026-01-01, 0d
         DRACC data transfer of 2025 Q4 and 20026 Q1-Q3 KO mice MERFISH data : crit, milestone, ADGC6_F_7, 2027-01-01, 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, 2027-01-01, 0d
 
         section Aim 2
         Initial discussion with DRACC for data transfer complete : crit, milestone, ADGC6_C_16, 2025-06-30, 0d
         DRACC data transfer of C57 control MRI and LSFM data : crit, milestone, ADGC6_D_16, 2025-09-30, 0d
         DRACC data transfer of first 5 KO mice MRI and LSFM data : crit, milestone, ADGC6_E_16, 2026-01-01, 0d
         DRACC data transfer of 2025 Q4 and 20026 Q1-Q3 KO mice MRI and LSFM data : crit, milestone, ADGC6_F_16, 2027-01-01, 0d
         section Aim 3
@@ -390,31 +390,31 @@
         gantt
         dateFormat  YYYY-MM-DD
         axisFormat  %Y-Q%q
         title       ADGC7  Washington Univ. St Louis - WUSTL
 
         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 WUSTL Reporting Year
         End WUSTL Reporting Year 1      :milestone, year1_wustl, 2025-12-31, 0d
         End WUSTL Reporting Year 2      :milestone, m1, 2026-12-31, 0d
 
-        click year1_wustl href "https://docs.google.com/spreadsheets/d/1ae4bX4Ful2AWlqzeH_JOo4jFssmEsojd/edit?gid=1888128068#gid=1888128068"
+        click year1_wustl href "https://docs.google.com/spreadsheets/d/1ae4bX4Ful2AWlqzeH_JOo4jFssmEsojd/edit?gid=1888128068#gid=1888128068&range=C2:E27"
 
         section Aim 1
         L0, L1 Data from last quarter submitted, and 3 more lines collected : crit, milestone, ADGC7_E_12, 2025-12-31, 0d
         L0, L1 Data from last quarter submitted, and 4 more lines collected : crit, milestone, ADGC7_F_12, 2026-03-31, 0d
         L2, L3 from prior L0,L1 data submitted : crit, milestone, ADGC7_F_13,  2026-03-31, 0d
 
         section Aim 2
         Home Cage Behavior L0-L1 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_C_17, 2025-07-01, 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 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 1-2 : crit, milestone, ADGC7_D_18, 2025-09-30, 0d
         Home Cage Behavior L3 Data to DRACC for line3-4 : crit, milestone, ADGC7_E_18, 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 L4 Data to DRACC for lines 1-2 : crit, milestone, ADGC7_E_19, 2025-12-31, 0d
         Home Cage Behavior L4 Data to DRACC for lines 3-4 : crit, milestone, ADGC7_F_19,  2026-03-31, 0d