|
| Status |
Public on Jul 09, 2021 |
| Title |
REU4502A13 (RN091) |
| Sample type |
SRA |
| |
|
| Source name |
FS120
|
| Organism |
Rattus norvegicus |
| Characteristics |
group: FS120
Sex: Male
strain: Wistar
tissue: Whole hippocampus
conditions: 120 min following onset of FS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from hippocampus tissue using TRI reagent as per manufacturer's instructions. The resulting RNA pellets were dissolved in 50 μl of nuclease-free water (Ambion). Purified RNA was treated with DNase I (Qiagen, Germany) and incubated for 10 min at room temperature. DNase was inactivated by the addition of EDTA (Final conc. 5mM) for 10 min at 70°C and RNA was purified over MinElute spin column as per manufacturer’s instructions (Qiagen, Germany).
Total RNA was depleted of ribosomal RNA using Ribo-Zero rRNA Removal Kit (Epicentre/Illumina, Human/Mouse/Rat). Library preparation was completed using TruSeq Stranded Total RNA kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Real time Analysis (RTA): HiSeq 4000 - RTA v2.7.7, Application Version: HD 3.4.0.38
Base-calling: bcl2fastq v2.17.1.14
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.4 with default parameters to the Rat genome Rnor_6.0, Ensembl release 81.
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 81 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: Read counts were normalized to counts per million (CPM) and Transcripts per Million (TPM) by dividing each gene-count by total reads mapped (uniquely mapped to exonic regions) per million and using ENSEMBL annotated read-lengths
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: exon_counts.txt: Gene expression counts using reads aligning to annotated exon features of 32546 genes
Supplementary_files_format_and_content: intron_counts.txt: Gene expression counts using reads aligning to intron features of 22971 genes
Supplementary_files_format_and_content: QC_Table.xlsx: Contains two excel sheets with Sheet 1 = sample information with information regarding sequencing depth and mapping QC metrics
Supplementary_files_format_and_content: QC_Table.xlsx: Sheet2= Contains description of column headers of cell metadata in Sheet 1
|
| |
|
| Submission date |
Feb 18, 2019 |
| Last update date |
Jul 09, 2021 |
| Contact name |
Johannes Reul |
| Organization name |
University of Bristol
|
| Department |
Bristol Medical School
|
| Lab |
Neuro-Epigenetics Research Group
|
| Street address |
Dorothy Hodgkin Building, Whitson Street
|
| City |
Bristol |
| ZIP/Postal code |
BS1 3NY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22396 |
| Series (2) |
| GSE126705 |
Glucocorticoid action in the hippocampus revealed by integrated genome-wide ChIP and RNA analysis (RNA-seq) |
| GSE126706 |
Glucocorticoid action in the hippocampus revealed by integrated genome-wide ChIP and RNA analysis |
|
| Relations |
| BioSample |
SAMN10962758 |
| SRA |
SRX5388893 |
