|
| Status |
Public on May 27, 2024 |
| Title |
Post-UV 12mins RNA-Seq Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cervix
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cervix
cell line: HeLa-S3
cell type: cancer
treatment: UV
|
| Treatment protocol |
With the cover off, cells were placed under a germicidal lamp emitting 254-nm UV (1 J/m2/s) for 20 s.
|
| Growth protocol |
HeLa-S3 cells were maintained in Dulbeco’s modified Eagle’s medium (PAN-P04-03500) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (PAN-P30-3304), 100 U/ml penicillin/streptomycin (PAN-P06-07100), 2 mM L-glutamine (PAN-P04-80100) and 1x MEM non-essential amino acid (Gibco 11140-35) solution. Cells were maintained at 37 °C with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA isolation was carried out using Genezol RNA isolation reagent (Geneaid GZR100) following the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
fastq files were first preprocessed to QC with fastp with flag --detect_adapter_for_pe.
Reads have been aligned to human genome and its corresponding annotation file, with STAR aligner version 2.7.6a with arguments --genomeLoad NoSharedMemory --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM SortedByCoordinate
Transcripts (transcripts per million) were quantified using Salmon version 1.6.0
Assembly: GRCh38, Gencode v35
Supplementary files format and content: Salmon output files, contain TPM values for each transcript
|
| |
|
| Submission date |
May 25, 2024 |
| Last update date |
May 27, 2024 |
| Contact name |
Ogun Adebali |
| E-mail(s) |
oadebali@sabanciuniv.edu
|
| Organization name |
Sabanci University
|
| Department |
Mol. Bio. Genetics & Bioeng.
|
| Lab |
Adebali Lab
|
| Street address |
Orta Mahalle, Üniversite Caddesi No:27 Tuzla, Sabancı Üniversitesi
|
| City |
Istanbul |
| ZIP/Postal code |
34956 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE268349 |
UV-induced reorganization of 3D genome mediates DNA damage response [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN38862435 |
| SRA |
SRX22913304 |
