|
| Status |
Public on Jan 13, 2024 |
| Title |
HEK_RAF_ER_12h_R1_GE |
| Sample type |
SRA |
| |
|
| Source name |
HEK-RAF-ER
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK-RAF-ER
library type: mRNA
treatment: 4OHT (tamoxifen)
replicate: R1
time: 12h
|
| Treatment protocol |
Cells were treated with tamoxifen to induce RAF/MAPK signalling for various times (6-18hrs)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Approximately 20.000 cells were encapsulated in Gel Beads-in-emulsion (GEMs) and GEX and CRISPR libraries were generated using the 10x Chromium Single Cell 3' V3 with Feature Barcoding technology
Gene expression libraries were constructed as per manufacturers instruction. Targeted libraries were amplified with custom primers from the amplified cDNA library. Guide libraries were constructed using the direct capture method.
Direct Capture Perturb-seq: scRNA-seq, CRISPR-guides, targeted scRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Gene expression library
|
| Data processing |
Raw sequences reads were analysed using cellranger-6.1.1 with feature calling using the guide sequences as in feature_ref.csv.gz; standard 10x gene expression libraries were processed alone and together with the targeted sequencing results
Effects of individual KO (represented by the CRISPR guides) on gene expression were assessed using pseudo-bulk analysis in R using the package glmGamPoi.
Assembly: GRCh38
Supplementary files format and content: *.h5 files contain the single cell gene expression matrices. Untargeted contain only data from the standard runs.
Supplementary files format and content: *.protospacer_calls_per_cell.csv.gz contain the guide / feature assignement of cells
|
| |
|
| Submission date |
Dec 19, 2023 |
| Last update date |
Jan 13, 2024 |
| Contact name |
Nils Blüthgen |
| E-mail(s) |
nils.bluethgen@charite.de
|
| Organization name |
Charite Universitätsmedizin Berlin
|
| Department |
Institute of Pathology
|
| Street address |
Chariteplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE250558 |
Targeted Perturb-seq of regulators of the transcriptional network downstream of RAF-MAPK signaling [perturb_seq] |
| GSE250559 |
MAPK |
|
| Relations |
| BioSample |
SAMN38927507 |
| SRA |
SRX22964138 |
