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Sample GSM4301363 Query DataSets for GSM4301363
Status Public on Dec 07, 2020
Title neonatal pancreatic islets, S35171_b
Sample type SRA
 
Source name Pancreas
Organism Sus scrofa
Characteristics tissue: neonatal pancreatic islets
treatment: Fet-A
timepoint of culture: day 10
tissue status: maturated
Extracted molecule total RNA
Extraction protocol Total cellular RNA was extracted from porcine islets using a commercial kit for RNA isolation (Macherey Nagel RNA isolation kit).
The mRNA was isolated from 0.2 ug total RNA with an integrity number of ≥ 9 by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module in accordance with the manufacturer’s instructions. Final elution was done in 15 µl 2x first strand cDNA synthesis buffer (NEBnext, NEB). Samples were then directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep II, NEB). Following ligation, adapters were depleted by a 1X XP bead purification (Beckman Coulter). Indexing was carried out during the following PCR enrichment (15 cycles, 65 °C).Following two further bead based purifications (1X XP beads) libraries were quantified using Qubit dsDNA HS Assay Kit (Invitrogen), equimolarly pooled and used for 75bp single read sequencing on Illumina NextSeq 500 resulting in an average 28 Mio sequenced fragments per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description QJFAM033A2
Data processing The data was processed with the RNA-Seq nf-core (v18.10.1) workflow, which can be found at https://github.com/nf-core/rnaseq.
Quality control was done with FASTQC (v0.11.8) and adapter trimming was performed by Trim Galore! (v0.5)
STAR (v2.6.1) was used for aligning the reads to the pig reference genome Ensembl release 94.
dupRadar (v1.10.0) was used for scanning RNA-Seq data for PCR clonal artifacts and the discovered duplicates were highlighted with Picard MarkDuplicates (v2.18.15).
Read counting on features (e.g. genes) was performed with featureCounts (v1.6.2).
For the differential expression analysis the raw read count table resulting from featureCounts was used and fed into the R package DESeq2 (v1.22.1).
Genome_build: Pig genome Ensembl release 94.
Supplementary_files_format_and_content: The tab-delimited text file that includes the raw read counts.
 
Submission date Feb 07, 2020
Last update date Dec 07, 2020
Contact name Stefan Czemmel
Organization name Quantitative Biology Center (QBiC)
Department University of Tuebingen
Street address Auf der Morgenstelle 10
City Tuebingen
ZIP/Postal code 72076
Country Germany
 
Platform ID GPL20983
Series (1)
GSE144950 Hepatokine Fetuin-A disrupts functional maturation of pancreatic β-cells
Relations
BioSample SAMN14057324
SRA SRX7692539

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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