|
| Status |
Public on Nov 14, 2024 |
| Title |
U2OS Cells_G3BP-mutated + Arsenite |
| Sample type |
SRA |
| |
|
| Source name |
U2OS Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS Cells
genotype: G3BP1 mutant
treatment: Arsenite
|
| Treatment protocol |
For arsenite treatment, 80-85% confluent HeLa cells were treated with 500 µM of arsenite (Sigma) whereas for combined arsenite and cycloheximide treatment, cells were treated with 500 µM of HeLa cells and 25 µg/ml of cycloheximide for 1 hour. Similarly for combined arsenite and ISRIB treatment, cells were treated with 500 µM of arsenite and 200 nM of ISRIB for 1 hour.
|
| Growth protocol |
HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from HeLa cells was isolated using Trizol reaget (Invitrogen, Cat# 15596-018) following the manufacturer’s protocl. 75 µg of total RNA was used to isolate poly(A) mRNAs. 500-1000 ng of poly(A) mRNA was used for library preparation
RNA libraries for dRNA-Seq were prepared using direct RNA sequencing kit (Oxford Nanopore Technologies, SQK-RNA002) following manufacturer's protocols.
Long read direct RNA-seq using Oxford Nanopore Technology
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
Basecalled using Guppy (v3.4.5)
5’ adaptors were identified and removed using Cutadapt (v2.8)
Reads were first aligned against ribosomal sequences obtained from SILVA. Non-ribosomal reads were subsequently mapped against the human genome hg38 using minimap2 (version 2.17)
Reads were also aligned against the human transcriptome.
The poly(A) tail lengths were extracted from sequenced reads using the nanopolish polya package, with quality control scores as “PASS” selectively used in our analysis.
Assembly: hg38 for homo sapiens and mm10 for mouse.
Supplementary files format and content: Tab-delimited text files include transcript id based raw counts and respective average trasncript length values for each Sample
Supplementary files format and content: Counts and lengths for each trasncript were calculated.
|
| |
|
| Submission date |
Sep 17, 2024 |
| Last update date |
Nov 14, 2024 |
| Contact name |
Emmanouil Maragkakis |
| E-mail(s) |
[email protected]
|
| Phone |
+1 410-454-8429
|
| Organization name |
National Institute on aging
|
| Department |
Laboratory of Genetics and Genomics (LGG)
|
| Lab |
Computational Genomics Unit
|
| Street address |
251 Bayview Blvd, 10B133 Baltimore
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE204785 |
Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress |
|
| Relations |
| BioSample |
SAMN43803666 |
| SRA |
SRX26110109 |
