|
| Status |
Public on Dec 18, 2023 |
| Title |
RNAseq_K562_115_IGHMBP2_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
K-562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K-562
cell type: lymphoblast cells
genotype: IGHMBP2 KO; expression is fully deleted in K-562 expressing CRISPRi machinery (doi: 10.1016/j.cell.2014.09.029)
treatment: None
|
| Treatment protocol |
Cells were seeded in fresh media 16 hr prior to harvest. Cell count was measured near 0.3E6 cells/mL per cell line at time of harvest, reflecting active growth conditions.
|
| Growth protocol |
RPMI 1640 (Gibco) containing L-glutamine and 25 mM HEPES, supplemented with 10% FBS and 1% penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Refer to manuscript for RNA-seq and Ribo-seq RNA extraction protocols
Refer to manuscript for RNA-seq and Ribo-seq library construction protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FASTQ files were converted to FASTA format. Adapter sequences from Ribo-seq FASTQ files were removed with cutadapt. Using cutadapt, adapter sequences were removed from RNA-seq and Ribo-seq sample reads, and reads were filtered to a minimum length of 22 nt. Reads were collapsed by UMI, which were then removed. Ribosomal RNAs, repeat RNAs and other non-coding RNAs were aligned against and removed with repeatmasker using bowtie2 2.4.1. Index files were generated using STAR 2.7.5a, GRCh38 primary assembly genome.fa file, and a GENCODE v25 .gtf annotation file with --sjdbOverhang set to 64 or 29 for RNA-seq and Ribo-seq indices, respectively. Filtered reads were then mapped to corresponding indices, generating annotated .bam files for analysis.
To determine localized read mapping coverage for specific genes, bamCoverage from deeptools was used to convert RNA-seq and Ribo-seq pre-processed .bam files to .bigwig files, where reads were normalized to counts per million (CPM).
Assembly: hg38
Supplementary files format and content: Processed data are bw
|
| |
|
| Submission date |
Nov 29, 2023 |
| Last update date |
Dec 18, 2023 |
| Contact name |
Jesslyn Park |
| E-mail(s) |
jesslyn.park@ucsf.edu, stephen.floor@ucsf.edu
|
| Organization name |
University of California, San Francisco
|
| Department |
Cell and Tissue Biology
|
| Lab |
Stephen Floor
|
| Street address |
513 Parnassus Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE248889 |
IGHMBP2 deletion suppresses translation and activates the integrated stress response [RNA-Seq] |
| GSE248890 |
IGHMBP2 deletion suppresses translation and activates the integrated stress response |
|
| Relations |
| BioSample |
SAMN38483276 |
| SRA |
SRX22672470 |
