|
| Status |
Public on Apr 26, 2022 |
| Title |
416B_Chd7_sg3_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
416B
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 416B
condition: Chd7sg3
|
| Treatment protocol |
416B cells stably expressing Cas9 protein were infected with lentiviruses (made in Perturb-Seq GBC plasmid background) containing expression cassettes for sgRNAs targeting Chd7, Runx1 or GFP genes (control). After 4 days in culture the cells were harvested for RNA-Seq
|
| Growth protocol |
416B cells were cultured in media consisting of: RPMI1640, 10% FBS and 1% Penicillin/Streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
75 cells sorted directly into lysis buffer (Smart-Seq2 protocol Picelli et al. 2014)
As in Smart-Seq2 protocol (Picelli et al. 2014), with 13 PCR amplification cycles
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Bulk 416B cells transduced with sgRNAs in Perturb-Seq GBC constructs
RBG16272
|
| Data processing |
QC perfomed with custom R script (available upon request). Samples were thresholded based on minimal fraction of mapped reads (15%), minimal number of reads (200,000), maximal number of mitochondrial reads (20%) and number of expressed genes (3000 genes > 10 cpm)
Reads were aligned to mouse genome (mm10) using GSNAP and reads overlapping exons (ENSEMBL m38.81) were counted using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with counts for each gene (how many aligned reads overlap its exons) generated using HTSeq
|
| |
|
| Submission date |
May 05, 2019 |
| Last update date |
Apr 26, 2022 |
| Contact name |
Bertie Gottgens |
| E-mail(s) |
bg200@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Street address |
Jeffrey Cheah Biomedical Centre
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE130719 |
CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation |
|
| Relations |
| BioSample |
SAMN11578350 |
| SRA |
SRX5793798 |
