|
| Status |
Public on Feb 01, 2021 |
| Title |
HeLa_polyA_siWdr82_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: human cervix, epitheloid carcinoma
treatment: siWdr82
|
| Treatment protocol |
Cells were left untreated.
|
| Growth protocol |
HeLa cells were cultured in DMEM containing 10% South American origin Foetal Bovine Serum, 1% L-Glutamax solution and 1% PenicillinStreptomycin solution.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Zymo Quick-RNA Mini Prep kit (Cat no. R1055) with on-column DNAse digestion.
After oligodT-based selection of polyadenylated transcripts from 3-5 ug total RNA, library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
polyA-RNAseq HeLa siWdr82 rep 3
|
| Data processing |
Strand specific paired end reads (76nt) were trimmed for removing the adapter sequence and discarding low quality bases using Trimmomatic v0.27 with PE option (PMID:24695404)
Read quality was then checked for each sample using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High-quality reads were then aligned with TopHat2 v2.1.0 (–very-sensitive --library-type fr-firststrand -r 200 --segment-length 35 --microexon-search --no-mixed --no-discordant -g 1 --coverage-search) (PMID:23618408). Indels due to sequencing errors were identifies using Bowtie2 v.2.6 (PMID: 19261174).
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Genome_build: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary_files_format_and_content: Strand specific tracks (bigWig)
|
| |
|
| Submission date |
Oct 28, 2020 |
| Last update date |
Feb 02, 2021 |
| Contact name |
Viviana Piccolo |
| E-mail(s) |
viviana.piccolo@ieo.it
|
| Organization name |
European Institute of Oncology (IEO)
|
| Department |
Department of Experimental Oncology
|
| Lab |
Gioacchino Natoli Lab
|
| Street address |
Via Adamello 16
|
| City |
Milano |
| State/province |
Milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE133109 |
A first exon termination checkpoint that preferentially suppresses extragenic transcription |
| GSE133139 |
A first exon termination checkpoint that preferentially suppresses extragenic transcription [RNASEQ_HELA_polyA] |
|
| Relations |
| BioSample |
SAMN16584292 |
| SRA |
SRX9391084 |
