|
| Status |
Public on Oct 16, 2015 |
| Title |
GM_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
developmental stage: Myoblast (MB)
antibody: NA
|
| Treatment protocol |
C2C12 myoblasts were induced to differentiate by culturing in differentiation medium (DMEM, 2% horse serum and 1% pen/strep)
|
| Growth protocol |
C2C12 myoblasts were growed in gowth medium containing DMEM, 10% FBS and 1% pen/srep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chromatins from myoblasts and myotubes were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies
Purified RNA was fragmented and the cDNA was synthesized by reverse transcription. The resulting double-stranded DNA fragments were end-repaired and A-nucleotide overhangs were added.
ChIP-seq libraries were constructed closely according to the standard illumina pair-end ChIP-seq procedure
After the attachment of anchor sequences, fragments were PCR-amplified using Illumina primers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
cDNA
PolyA+ selected
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads by ChIP-seq were mapped to mm9 genome using SOAP2 with parameters: -v 2 -r 0 -m 0 -p 20
Peaks were called using MACS2 (v1.4.2), a p-value of 10^-5 is used as the cutoff
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation. Overlaping analysis was performed using in-house programs and the maximum distance limitation is set to 1000bp.
RNA-seq reads were first aligned to the mm9 genome using TopHat (v2.0.4) then merged with Others C2C12 RNA-seq data (GEO accession: GSE20846). Then ab initio assembly (for GM/DM RNA-seq) was conducted using Cufflinks (v2.1.1).
The assembled transcripts were then processed by Sebnif (v1.2.1) and annotated by Histone markers, EST Tags and MyoD bindings for novel lincRNA discovery.
Differentially expression between siNC and siLinc-Yy1 was conducted using Cuffdiff (v2.0.4) against RefSeq genes.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS, scores represent -10*log(p)
|
| |
|
| Submission date |
Oct 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Sun |
| E-mail(s) |
sunkun@szbl.ac.cn
|
| Organization name |
Shenzhen Bay Laboratory
|
| Department |
Cancer Research
|
| Lab |
Kun Sun
|
| Street address |
Rm B505, No. 9 Duxue Road, Nanshan District
|
| City |
Shenzhen |
| ZIP/Postal code |
518107 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE74049 |
Transcriptome Analysis Identifies Linc-Yy1, A Novel Functional LincRNA During Myogenesis |
|
| Relations |
| BioSample |
SAMN04167186 |
| SRA |
SRX1337879 |
