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| Status |
Public on Jan 30, 2015 |
| Title |
WT Cul_RNASeq3 |
| Sample type |
SRA |
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| Source name |
Satellite cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: proliferating satellite cells
strain: C57Bl/6 background
genotype/variation: WT
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| Treatment protocol |
For differentiation, cells were placed in Hams F-10 media (Gibco) with 2% horse serum (Gibco) for 24 hrs.
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| Growth protocol |
FACS isolated satellite cells were grown in Hams F-10 media (Gibco), 20% fetal bovine serum (FBS, Gibco), bFGF (12.5ng/mL), Penicillin/streptomycin (1x, Gibco).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For ChIPSeq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNASeq, RNA was extracted according to TRIzol protocol (invitrogen).
For ChIPSeq, cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments. Histone-DNA complexes were isolated with H4K16ac antibody (Millipore, CS204361) or Sirt1 antibody (Upstate, 07-131) Purified DNA was processed according to manufacturer's protocol. For polyA RNA-Seq, Illumina protocol was followed.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
PolyA RNA sequencing
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using Bowtie (Langmead B, et.al 2009) , and TopHat(Trapnell C, et.al 2009) for RNA-Seq
H4K16ac data peaks were called using SICER Algorithm ( Zang et al, 2009) with the following setting: window size (200bp), window pvalue (0.2), gap size(600bp) and the FDR of 0.05, Sirt1 ChIP were analyzed using MACS ( Zhang et al, 2008), with pvalue of 10^-5, --gsize mm, and the rest were defualt setting, input data reads were shuffled and down sampled to adujst for difference in read coverage.
FPKM (RPKM) and differential expression analysis was done using Cufflink/Cuffdiff (Trapnell C, et.al 2009) with multi-reads correction and geometric normalization
Genome_build: mm9
Supplementary_files_format_and_content: RNA-Seq processed data files are bigWig format and in text format generated from Cuffdiff, and for ChIP-Seq data wig files were generated using filtered reads residing in enriched regions
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| Submission date |
Dec 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Hossein Zare |
| E-mail(s) |
hzare@mail.nih.gov
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| Organization name |
NIH
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| Street address |
5o South Dr #1347
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| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE64379 |
The NAD+-Dependent SIRT1 Deacetylase Translates a Metabolic Switch into Regulatory Epigenetics in Skeletal Muscle Stem Cells |
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| Relations |
| Reanalyzed by |
GSE80797 |
| BioSample |
SAMN03269539 |
| SRA |
SRX818817 |
| Named Annotation |
GSM1569858_WTA-RNA_rep3.bw |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1569858_WTA-RNA_rep3.bw |
355.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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