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Sample GSM8770312 Query DataSets for GSM8770312
Status Public on Feb 03, 2025
Title Sample_L_transcriptome, KO
Sample type SRA
 
Source name ESC
Organism Homo sapiens
Characteristics cell line: H1_L_3DEC, HUES8_L_3DEC
cell type: ESC
editing strategy: enhancer, gene body
altered gene_symbol: PDX1, HES1, NEUROD1, PAX6, NKX2-2, ARX, GATA6, GATA4, FOXA2, FOXA1, RFX6, GLIS3, HHEX, UBA6, OTUD5, TADA2B, KDM2B, GSC, ONECUT1, MNX1, TET1, TET2, TET3, NANOG, BCOR, NEUROG3, BMPR1A, TLE3, NKX6-1, PBX1, QSER1, PROSER1, HNF4A
time (day): 18, 18
model system: immature SC-islet (stage 5), immature SC-islet (stage 5)
parental cell_line: H1, HUES8
pooled samples: 2
Extracted molecule total RNA
Extraction protocol Chromium Next GEM Single Cell 3สน GEM, Library & Gel Bead Kit v3.1
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Library name: Sample_L_transcriptome
L_1_star_unfiltered_counts.h5ad
L_1_star_unfiltered_features.h5ad
L_2_star_unfiltered_counts.h5ad
L_2_star_unfiltered_features.h5ad
Data processing Unfiltered counts and feature counts (LARRY barcodes) generated for each library using STAR. Feature counts have been very slightly corrected for an edge case that affects about 1 in 10,000 counts. QC has been added and uploaded for the feature assignments. Feature assignment has also been done directly from the scRNA-seq expression as a control for the targeted sequence method (which is the main value in the features counts file). These are available in the 'expression' layer. Assignments have been provided for the features. These follow the original MSK criterion (minimum 10 counts - second best count no more than half of maximum). A second less restrictive assignment has also been provided using a minimum 4 counts - second best count no more than half of maximum). These are provided as obs 'feature-10' and 'feature-4'. These are provided as a convenience - filtering can still be done using whatever criteria the user wishes from the feature_counts file data.
https://github.com/morphic-bio/process_features
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: Unfiltered counts and feature counts per library as h5ad files. Zip folder includes QC files (.txt and .png) for expression feature assignments and targeted feature assignments.
 
Submission date Feb 03, 2025
Last update date Feb 03, 2025
Contact name MorPhiC Consortium
Organization name EMBL-EBI
Street address Wellcome Genome Campus
City Hinxton
ZIP/Postal code CB10 1SD
Country United Kingdom
 
Platform ID GPL24676
Series (1)
GSE288587 Mapping the Temporal Impact of Perturbations on Lineage Plasticity and Gene Regulation
Relations
BioSample SAMEA117610456
SRA ERX13563863

Supplementary file Size Download File type/resource
GSM8770312_L_1_star_unfiltered_counts.h5ad 3.8 Gb (ftp)(http) H5AD
GSM8770312_L_1_star_unfiltered_features.h5ad 289.7 Mb (ftp)(http) H5AD
GSM8770312_L_2_star_unfiltered_counts.h5ad 3.6 Gb (ftp)(http) H5AD
GSM8770312_L_2_star_unfiltered_features.h5ad 271.6 Mb (ftp)(http) H5AD
SRA Run SelectorHelp
Raw data are available in SRA

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