|
| Status |
Public on Sep 15, 2021 |
| Title |
WT-1_1995_liver |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype: HuR WT
tissue: Liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed and stored in -80° C until RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel).
mRNA enrichment and reverse-transcription into cDNA was done with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
WT-1_1995
processed data file: bfx1090.mm10.e81.txt
|
| Data processing |
Basecalls were performed using Illumina bcl2fastq version 2.19.1.
Reads were aligned to the mouse genome assembly (mm10) using GSNAP (2017-03-17; parameters: --gunzip -A sam --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 1 -n 1 -s EnsemblGene-81.ss.mm10.iit) with known splice sites from Ensembl (v81) as support.
Uniquely aligned fragments and gene annotations from Ensembl (v81) were used for featureCounts (v1.5.1; parameters: -a EnsemblGene-81.mm10.TR.gtf -s 2 -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bfx1090.mm10.e81.txt: Tab-delimited counts table from featureCounts with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Gene Length, then all sample counts; comments start with '#'.
|
| |
|
| Submission date |
Jan 09, 2020 |
| Last update date |
Sep 15, 2021 |
| Contact name |
Triantafyllos Chavakis |
| E-mail(s) |
[email protected]
|
| Organization name |
Medizinische Fakultät der TU Dresden
|
| Department |
Klinische Pathobiochemie
|
| Lab |
Chavakis Lab
|
| Street address |
Fiedlerstraße 42
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE143358 |
Sequencing of liver RNA from HuR WT and HuR KO mice |
|
| Relations |
| BioSample |
SAMN13808698 |
| SRA |
SRX7527649 |
