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| Status |
Public on Apr 15, 2020 |
| Title |
RNA-seq_Experiment 3 - control condition (24h) |
| Sample type |
SRA |
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| Source name |
EndoC-BH1 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: EndoC-BH1
treatment: control
timepoint: 24h
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| Treatment protocol |
EndoC-BH1 cells were exposed or not to interferon-alpha (2.000U/ml) for 2, 8 or 24h.
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| Growth protocol |
The EndoC-βH1 cells were cultured in DMEM containing 5.6 mmol/l glucose (Gibco, Thermo-Fisher Scientific, Paisley, UK), 2% BSA fraction V, fatty acid free (Roche, Manheim, Germany), 50 μmol/l 2-mercaptoethanol (Sigma-Aldrich, Poole, UK), 10 mmol/l nicotinamide (Calbiochem, Darmstadt, Germany), 5.5 μg/ml transferrin (Sigma-Aldrich), 6.7 ng/ml selenite (Sigma-Aldrich), 100 units/ml penicillin and 100 μg/ml streptomycin (Lonza, Leusden, Netherlands) in Matrigel-fibronectin-coated plates
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from EndoC-Bh1 cells using the RNeasy Mini kit (Qiagen, Venlo, The Netherlands) which favours purification of RNA molecules longer than 200 nucleotides. mRNA was purified from 1 μg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments.
mRNA was purified from 1 µg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 39- monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bio- analyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 µl cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on an Illumina HiSeq 2500 system
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequencing reads were mapped to the Homo sapiens genome (version GRCh37/hg19) using the program Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) using default options the GENCODE 18 annotation of genes transcripts. The Tophat mapper reports all mappings and split-mappings.
GTF files: Mapped reads were used to quantify human transcripts from the GENCODE 18 annotation dataset, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.
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| Submission date |
Jun 24, 2019 |
| Last update date |
Apr 16, 2020 |
| Contact name |
Maikel Luis Colli |
| E-mail(s) |
mcolli@ulb.ac.be
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| Organization name |
Universite Libre de Bruxelles
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| Department |
Faculty of Medicine
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| Lab |
Center for Diabetes Research
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| Street address |
Route de Lennik, 808
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| City |
Brussels |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE133218 |
An integrated multi-omics approach identifies the landscape of interferon-a-mediated responses of human pancreatic beta cells [RNA-seq] |
| GSE133221 |
An integrated multi-omics approach identifies the landscape of interferon-a-mediated responses of human pancreatic beta cells |
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| Relations |
| BioSample |
SAMN12127417 |
| SRA |
SRX6355753 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3902481_Ctl_24h_3.gtf.gz |
4.3 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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