|
| Status |
Public on Mar 08, 2023 |
| Title |
K562 CEBPA reporter cell line, PELO sgRNA ribo RNAseI, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
cell type: myeloid leukemia cells
genotype: PELO knockdown
treatment: RNAseI
|
| Growth protocol |
Human K562 cells were grown in RPMI-1640 with L-glutamine (ThermoFisher Scientific) supplemented with 10% FBS, 1% sodium pyruvate, 100 units/mL penicillin and 100 mg/mL streptomycin and grown at 37C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
30ug of RNA for ribosome profiling was harvested by TRIzol extraction; 1ug of RNA for RNA-seq was harvested by phenol-chloroform extraction.
Ribosome footprint libraries were prepared by PCR amplifcation from circularized cDNA using NEBNext Multiplex oligos; matched RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit following the manufacturer's protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
rpf_pelo_1
pelokd_rnase1_ribo_cds_grch38_cnt_all.csv
|
| Data processing |
Ribosome profiling reads were first trimmed using Cutadapt to remove adapter sequences.
Trimmed ribosome footprint reads and RNA-Seq reads were then aligned to ribosomal, transfer and noncoding RNA references. The remaining reads were subsequently aligned to the GRCh38 transcriptome using STAR.
Footprint and RNA-Seq transcript abundance were quantified from these alignments by RSEM.
Assembly: hg18
Supplementary files format and content: Comma-delimited text file containing raw, unnormalized read counts for each sample.
Library strategy: Ribo-Seq
|
| |
|
| Submission date |
Mar 01, 2023 |
| Last update date |
Mar 08, 2023 |
| Contact name |
Nicholas T Ingolia |
| E-mail(s) |
ingolia@berkeley.edu
|
| Organization name |
University of California, Berkeley
|
| Department |
Molecular and Cell Biology
|
| Street address |
1 Barker Hall #3202
|
| City |
Berkeley |
| ZIP/Postal code |
94709 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE226436 |
Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPα [riboprofiling] |
| GSE226437 |
Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPα |
|
| Relations |
| BioSample |
SAMN33556623 |
| SRA |
SRX19541055 |
