|
| Status |
Public on Nov 28, 2017 |
| Title |
Strand-specific RNA-seq in senescent cells- Replicate #2 |
| Sample type |
SRA |
| |
|
| Source name |
senescent WI38 hTERT RAF1-ER cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WI38 hTERT RAF1-ER
state: senescent
|
| Growth protocol |
WI38 hTERT RAF1-ER cells were grown for three days in prescence (to induce senescence) or abscence (proliferative cells) of 4-hydroxytamoxifen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were prepared using the MasterPure RNA Purification Kit (Epicentre Biotechnologies) supplemented with Baseline-ZERO DNAse (Epicentre). BGI or EMBL-GeneCore treated the RNA by Ribozero kit to remove ribosomal RNA.
Strand-specific RNA-seq, including the library construction, which is based on UTP incorporation in the second strand cDNA, was performed at BGI (HONG KONG) for the first replicates (lncRNA-seq) and at EMBL-GeneCore (Heidelberg, Germany) for the second replicates (stranded rRNA-minus RNA-seq).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
total RNA (ribosomal RNA depleted)
Strand-specific RNA-sequencing in senescent cells was performed paired-end (HMKMGBGXY_Sen_16s005986-1-1_Nicolas_lane116s005986_1_sequence.txt and HMKMGBGXY_Sen_16s005986-1-1_Nicolas_lane116s005986_2_sequence.txt) by Illumina’s NextSeq 500 technology at EMBL-GeneCore (stranded rRNA-minus RNA-seq) with ~100 millions paired reads per library. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2a_modified, depending on the strand of the genome, 2 files were generated (minus (HMKMGBGXY_Sen_16s005986-1-1_Nicolas_lane116s005986_minus_normalized_hg38.bw) and plus (HMKMGBGXY_Sen_16s005986-1-1_Nicolas_lane116s005986_plus_normalized_hg38.bw)).
|
| Data processing |
Paired-end reads of the strand-specific RNA-Seq (senescence or proliferation) data were aligned using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2a_modified. For these alignments all parameters were kept as default.
After the alignment, we applied on all aligned datasets several steps using samtools software: we converted aligned file from Sequence Alignments/Map (sam) format into the Binary Alignment/Map (bam) format which stores the same data in a compressed, indexed, binary form and a cutoff was applied to keep only reads with MAPQ > 25. We sorted data by position on the genome, and created an index of each bam file (bai format). We then converted these cleaned files in wiggle files using R via the rtracklayer bioconductor package. On each dataset, we applied for each base position of the genome a normalization factor (100,000,000 / total numbers of aligned reads).
Genome_build: hg38
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
Sep 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Estelle Nicolas |
| E-mail(s) |
estelle.nicolas@univ-tlse3.fr
|
| Phone |
+33 5 61 55 81 11
|
| Organization name |
INSERM
|
| Lab |
UMR5077, MCD, CBI
|
| Street address |
118 route de Narbonne
|
| City |
Toulouse |
| ZIP/Postal code |
31062 |
| Country |
France |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE85082 |
Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes [RNA-Seq PROLIF-SEN] |
| GSE85085 |
Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes |
|
| Relations |
| BioSample |
SAMN07638088 |
| SRA |
SRX3182082 |
