|
Status |
Public on May 03, 2021 |
Title |
Hira_KO_rep1 |
Sample type |
SRA |
|
|
Source name |
Hira_KO
|
Organism |
Mus musculus |
Characteristics |
strain source: C3H cell line: C2C12 cell type: skeletal muscle cell line genotype: Hira -/-
|
Treatment protocol |
none
|
Growth protocol |
C2C12 control and C2C12 Hira KO cell lines were collected when grown in high serum medium at low density (proliferating conditions)
|
Extracted molecule |
total RNA |
Extraction protocol |
C2C12 cells were collected for RNA extraction using Machery Nagel NucleoSpin RNA purification kit Libraries were prepared with TruSeq Stranded Total RNA Sample preparation kit according to supplier recommendations. Briefly, the key stages of this protocol are successively, the removal of ribosomal RNA fraction from 1µg of total RNA using the Ribo-Zero Gold Kit; fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces; double strand cDNA synthesis using reverse transcriptase and random primers, and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
FASTQ groomer tool (https://usegalaxy.org) BOWTIE2 v2.3.4.2 (https://usegalaxy.org) featureCounts v1.6.3+galaxy2 (https://usegalaxy.org) Genome_build: mm10 Supplementary_files_format_and_content: DESeq2 v2.11.40.6+galaxy1 (https://usegalaxy.org)
|
|
|
Submission date |
Nov 08, 2020 |
Last update date |
May 03, 2021 |
Contact name |
Joana Esteves de Lima |
E-mail(s) |
joanaesteveslima@gmail.com
|
Organization name |
INSERM
|
Department |
IMRB INSERM U955
|
Lab |
Team RELAIX
|
Street address |
8 rue du general sarrail
|
City |
Creteil |
ZIP/Postal code |
94000 |
Country |
France |
|
|
Platform ID |
GPL21103 |
Series (2) |
GSE161055 |
Analysis of the transcriptomic changes of myoblasts lacking Hira [RNA-seq] |
GSE161056 |
ATAC-seq, ChIP-seq and RNA-seq studies in myoblasts lacking Hira |
|
Relations |
BioSample |
SAMN16706616 |
SRA |
SRX9460306 |