|
| Status |
Public on Dec 07, 2020 |
| Title |
neonatal pancreatic islets, S35168 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: neonatal pancreatic islets
treatment: HSA + SB + LDN
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 |
QJFAM030AC
|
| 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 |
SAMN14057300 |
| SRA |
SRX7692533 |
