 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 08, 2021 |
| Title |
Corticosterone RNA - 792_pulsatile_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
Sex: Male
tissue: Liver
treatment: Corticosterone infusion - pulsatile - 180min
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA_Seq RNA extraction Frozen liver sections were homogenised (Polytron, PT-2100, Kinematica, CH) in TRIzol (ThermoFisher Scientific, USA). The aqueous phase was separated via chloroform extraction (Sigma-Aldritch, UK) and centrifugation (10,000 rpm, 40C), total RNA extracted, and DNA digested (miRNAeasy mini, Qiagen, US).
RNA_Seq Libraries were constructed from 1 µg total RNA (TrueSeq Stranded Total RNA kit, Illumina, USA) and filtered for a RIN score > 8 and < 10 (Agilent Tape Station, Bioanalyzer, UK) for sequencing (HiSeq 2500, Illumina UK).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA-Seq
|
| Data processing |
Basecalling RTA 1.13.48 with default filter and quality settings
Adapters removed by bbduk (BBMap v38.22) tpe tbo
Aligned to rn6 using STAR v020201, default parameters
strand specific read counts calculated by featureCounts v1.6.2, exonic boundaries identified in Ensemble Rnor 6.0.92 release
Genes filtered for counts > 10 across conditions and DESeq2 normalisation, differenrial analysis assesed by DESeq2 using defualt parameters (n=3)
AllFinalCounts.gene represents matrix of exonic read counts (featureCounts), genes filtered for counts >10 across conditions and differential results from DESeq2 analysis are formatted as Gene ID, base mean, log2 fold change, standard error of log2 fold change values, Wald statistic, Wald test p-value and Benjamin-Hochberg adjusted p-value for pulsatile VEH difference to constant VEH (ExonRNAData_PULSVEH_CONSVEH.txt), pulsatile CORT change to pulsatile VEH (ExonRNAData_PULSCORT_PLSVEH.txt) and constant CORT change to constant VEH (ExonRNAData_CNSCORT_CNSVEH.txt)
Genome_build: rn6
|
| |
|
| Submission date |
Apr 07, 2021 |
| Last update date |
Apr 08, 2021 |
| Contact name |
Benjamin P Flynn |
| E-mail(s) |
ben.flynn@bristol.ac.uk
|
| Organization name |
University of Bristol
|
| Street address |
Dorothy Hodgkin Building, Whitson street
|
| City |
Bristol |
| State/province |
County (optional) |
| ZIP/Postal code |
BS13NY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE171647 |
Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regualtion |
|
| Relations |
| BioSample |
SAMN18649189 |
| SRA |
SRX10533697 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
