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Sample GSM6681047 Query DataSets for GSM6681047
Status Public on Jan 05, 2023
Title 180124_TFmap
Sample type SRA
 
Source name HUES66 human embryonic stem cells
Organism Homo sapiens
Characteristics cell type: HUES66 human embryonic stem cells
perturbation: overexpression of a library with 90 transcription factors
perturbation time point: 7 days
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics 120237)
single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics 120237). Cells were mapped to their respective transcription factor perturbations by PCR amplifying the transcription factor and cell barcodes from the cDNA prior to tagmentation
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model NextSeq 550
 
Data processing Cell Ranger Single cell Software Suite v3.1.0
Scanpy v1.7.2
Custom Python script for mapping cells to transcription factor ORFs
Assembly: hg38
Supplementary files format and content: Raw count matrix generated by Cell Ranger (mtx and tsv) and annotated processed data generated by Scanpy (h5ad). Map of cells to transcription factor ORFs produced by a custom Python script (csv)
Library strategy: AMPLICON
 
Submission date Oct 26, 2022
Last update date Jan 05, 2023
Contact name Julia Joung
E-mail(s) julia@joung.science
Organization name Broad Institute
Street address 75 Ames St
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL21697
Series (2)
GSE216481 A Transcription Factor Atlas of Directed Differentiation
GSE216595 A Transcription Factor Atlas of Directed Differentiation [10XscRNA_180124_perturb]
Relations
BioSample SAMN31460141
SRA SRX18032372

Supplementary file Size Download File type/resource
GSM6681047_180124_TFmap.csv.gz 532.8 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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