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Sample GSM2781951 Query DataSets for GSM2781951
Status Public on Nov 28, 2017
Title Strand-specific RNA-seq in proliferative cells- Replicate #1
Sample type SRA
Source name proliferative WI38 hTERT RAF1-ER cells
Organism Homo sapiens
Characteristics cell line: WI38 hTERT RAF1-ER
state: proliferative
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 HiSeq 2000
Description total RNA (ribosomal RNA depleted)
Strand-specific RNA-sequencing in proliferative cells was performed paired-end (READS1( CONT_L1_1.fq) and READS 2 (CONT_L1_2.fq) by Illumina’s HiSeq technology at BGI (lncRNA-seq) with at least 50 millions clean reads (after removing adaptor pollution and low quality sequence). 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 ( and plus (
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
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 GPL11154
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
BioSample SAMN07638091
SRA SRX3182079

Supplementary file Size Download File type/resource 154.3 Mb (ftp)(http) BW 161.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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