|
| Status |
Public on Oct 17, 2024 |
| Title |
Disomes_CHX1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK294T flip in
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: wild type
treatment: CHX 1 uM
cell type: HEK294T flip in
|
| Treatment protocol |
Cells were treated with DMSO solvent or indicated concentration of girolline for 2 hrs
|
| Growth protocol |
HEK294T flip in cells grown in DMSO with 10% FBS and antibiotics at 37 deg C under 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected in lysis buffer, cleared of debris and lysates were snap frozen with liquid nitrogen and stored at -80 deg C
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification. For RNA-Seq, Poly(A) selection and cDNA synthesis were performed using Illumina Stranded mRNA Prep, Ligation (Illumina) and subsequent steps were performed by TruSeq Stranded Total RNA Library Prep Gold (Illumina).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Data processing |
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: Human Genome hg38
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribosome profiling
|
| |
|
| Submission date |
Apr 17, 2024 |
| Last update date |
Oct 17, 2024 |
| Contact name |
Tilman Schneider-Poetsch |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
RIKEN
|
| Department |
Center for Sustainable Resource Science
|
| Lab |
Chemical Genomics Research Group
|
| Street address |
2-1 Hirosawa
|
| City |
Wako-shi |
| State/province |
Saitam |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
| |
|
| Platform ID |
GPL34284 |
| Series (1) |
| GSE264204 |
Girolline is a sequence-context specific modulator of eIF5A activity |
|
| Relations |
| BioSample |
SAMN40994840 |
| SRA |
SRX24287236 |
