|
| Status |
Public on Jul 21, 2020 |
| Title |
GM-IP-2 |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
m6a antibody: anti-m6A (Cat: 202 003, Synaptic Systems, Goettingen, Germany)
|
| Treatment protocol |
Proliferation samples were taken when C2C12 myoblasts were 50% confluent and maintained in a medium of high glucose DMEM supplemented with 10% fetal bovine serum. 3d Differentiation samples were taken after C2C12 myoblasts had reached >90% confluence and were switched to a high glucose DMEM supplemented with 2% horse serum for 3 days.
|
| Growth protocol |
C2C12 myoblasts were seeded on collagen (Type 1 rat tail) coated dishes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using an Omega E.Z.N.A.® Total RNA Kit I. mRNA was isolated using Arraystar Seq-StarTM poly(A) mRNA Isolation Kit .
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The KAPA Stranded mRNA-seq Kit (Illumina, San Diego, CA, USA) was used to prepare the RNA-seq libraries for m6A immunoprecipitated mRNA and input control mRNA libraries. Quality of the libraries was determined using an Agilent 2100 Bioanalyzer. The HiSeq 3000/4000 PE Cluster Kit (Illumina, San Diego, CA, USA) was used to generate clusters from the prepared libraries following the manufacturer’s instructions. The clustered libraries were sequenced on an Illumina HiSeq 4000 system.
MeRIP-seq or RNA-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Proliferation Replicate 2
GM-IP_2-peaks.txt
|
| Data processing |
The 5’, 3’-adaptor trimmed reads were aligned to the mm10 reference genome using HISAT2 (v2.1.0).
ExomePeak was used for MeRIP peak calling and statistically significant MeRIP enriched regions (MeRIP peaks) were identified at the sample level with a significance threshold of P≤0.05
ExomePeak was also used to compare transcripts which were differentially m6A-modified between the GM and 3d DM samples with significance set at P≤0.05
For RNA-seq - The input control RNA-sequencing results were subjected to differential gene expression analysis using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TMM values for RNA-seq output and peak values for MeRIP-seq
|
| |
|
| Submission date |
Jul 20, 2020 |
| Last update date |
Jul 21, 2020 |
| Contact name |
Anna E Thalacker-Merc er |
| Organization name |
University of Alabama at Birmingham
|
| Street address |
1720 University Blvd
|
| City |
Birmingham |
| State/province |
Alabama |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE154720 |
meRIP-seq and RNA-seq on proliferating and differentiating cultured C2C12 cells |
|
| Relations |
| BioSample |
SAMN15581719 |
| SRA |
SRX8772335 |
