|
| Status |
Public on Jan 12, 2023 |
| Title |
CROP-seq RNA + sgRNA |
| Sample type |
SRA |
| |
|
| Source name |
lymphoblasts
|
| Organism |
Homo sapiens |
| Characteristics |
strain: K-562 cells
Sex: Female
age: 53
|
| Treatment protocol |
K562 CRISPRi cells were transduced with a lentivirus library containing 138 sgRNA32 at a multiplicity of infection of 0.1.
|
| Growth protocol |
RPMI-1640 (Gibco #11875093) with 10% FBS (Thermo Fisher Scientific, #10438026) and 1% penicillin/streptomycin (Thermo Fisher Scientific, #15140148) in an incubator at 37C with 5% CO2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
PIP-seq
PIP-seq + sgRNA recovery
PIP-seq + separate sgRNA library preparation
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
immortalized myelogenous leukemia cel line
|
| Data processing |
The sample is aligned to human GRCh38.p13 with Salmon and quantified with alevin v1.2.0 using an index modified to include the guide RNAs. sgRNA calling was performed according to Datinger et al. Nature Biotechnology
Assembly: GRCh38.p13
Supplementary files format and content: The filtered matrix consists of a zipped folder with 3 files: (1) sparse matrix, (2) barcodes file, (3) genes file. sgRNA counts have been pre-merged with the gene expression (GEX) counts. sgRNA counts can be isolated from using the GEX counts by subsetting feature names containing the following distinct patterns: "_-_", "_+_", or "neg_ctrl". Raw data are gzipped fastqs, with 1 file per read for both the original gene expression sample and the derived sgRNA library for a total of 4 files.
|
| |
|
| Submission date |
May 12, 2022 |
| Last update date |
Mar 15, 2023 |
| Contact name |
Iain Christopher Clark |
| Organization name |
University of California, Berkeley
|
| Street address |
374 Stanley Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE202915 |
CROP-seq + PIP-seq |
| GSE202919 |
Microfluidics-free single-cell genomics with templated emulsification |
|
| Relations |
| BioSample |
SAMN28215402 |
| SRA |
SRX15245761 |
