 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 29, 2020 |
| Title |
416L |
| Sample type |
SRA |
| |
|
| Source name |
RNA derived from Rattus norvegicus tibialis anterior muscle
|
| Organism |
Rattus norvegicus |
| Characteristics |
animal identifier: 416
vdr status: Sham VDR knock-in
|
| Treatment protocol |
In vivo electroporation was used to knock out (ko) or knock in (ki) the vitmain D receptor in the tibialis anterior muscle of one hindlimb in rats. VDR-KD groups received VDR shRNA (Table S1) in right leg TAM and scramble shRNA in left leg TAM. VDR-OE groups received pCAGGS-mVDR in right leg TAM, and empty pCAGGS controls in left leg TAM. Immediately following, one HV (900 V/cm, 100 ยต-sec pulse), and four LV (90 V/cm, 100 m-sec) pulses were administered across the distal limb via tweezer-electrodes attached to an ECM-830 electroporator (BTX, Holliston, MA). Animals subsequently received a subcutaneous injection of carprofen (50mg/kg), before recovery from anesthesia. RNA-seq was carried out with the contrast of interest being either ko v control limb or ki v control limb.
|
| Growth protocol |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from muscle using Qiagen RNEasy kit. RNA was quantified using the nanodrop instrument and RNA quality was assesed using the Agilent bioanalyser.
The RNA library was prepared for RNA-sequencin using the Illumina Tru-Seq kit following the manufacturers directions.
RNA-Sequencing was carried out using the Illumina HiSeq 4000 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Text file of raw RNA-seq derived counts for genes in the rat genome (ver 6.0) (Ensembl release 89)
|
| Data processing |
The core facility carried out the following conversion and quality control steps on the raw data. Per-cycle base call files were converted to fastq using the bcl2fastq software (v2.17.1.14), library content was checked with the fastq_screen utility (v0.4.2) and fastq file quality was examined using FastQC (0.11.5). After data delivery FastQC (0.11.5) was used to assess quality and trimmotmatic was used to remove contaminating adapter sequences.
Reads were aligned to the rat genome (version 6, Ensembl release 89) and gene counts generated using the R package Rsubread (1.26.1) with the following settings: phredOffset=33, input_format = "gzFASTQ", output_format = 'BAM', output_file = output.files, nthreads=4, nTrim5=12 (for alignment) and isGTFAnnotationFile=TRUE, isPairedEnd=TRUE, strandSpecific=2, nthreads=4 (for counts).
Genes with fewer than 10 reads per million bases we removed before further analysis.
Genome_build: Rattus norvegicus genome version 6, Ensembl 89
Supplementary_files_format_and_content: CSV files generated using edgeR (3.18.1). Gene counts were filtered to remove genes with low counts by identifying the CPM at a count of 10 in line with guidelines published by the edgeR authors (Lun, Chen, Smyth, 2016). The dataset was then normalised using TMM normalisation (Robinson and Oshlack 2010).
|
| |
|
| Submission date |
Feb 12, 2018 |
| Last update date |
Sep 29, 2020 |
| Contact name |
Iain Gallagher |
| E-mail(s) |
iaingallagher@gmail.com
|
| Phone |
00 44 1786 46 6024
|
| Organization name |
University of Stirling
|
| Department |
Faculty of Health Sciences and Sport
|
| Street address |
Room 4B133 Cottrell Building, University of Stirling, Airthrey Road
|
| City |
Stirling |
| ZIP/Postal code |
FK9 4LA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE110507 |
The vitamin D receptor (VDR) autonomously regulates skeletal muscle mass |
|
| Relations |
| BioSample |
SAMN08522248 |
| SRA |
SRX3686715 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2994929_416L_gene_counts.txt.gz |
152.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
