|
| Status |
Public on Jan 05, 2023 |
| Title |
180124_perturb_S3 |
| 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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
180124_perturb.h5ad
|
| 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)
|
| |
|
| 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 |
SAMN31460147 |
| SRA |
SRX18032366 |
