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| Status |
Public on Dec 05, 2013 |
| Title |
transcriptome_DMSO |
| Sample type |
SRA |
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| Source name |
MRC-5_transcriptome_DMSO
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MRC-5
cell type: human fetal lung fibroblast Cell
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| Treatment protocol |
TCBQ powder was dissolved in DMSO with the concentration of 20mM for stock. MRC-5 cells with about 50% confluence were treated with TCBQ or DMSO diluted in culture media to the final concentration of 20uM for 24 hours.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from TCBQ/DMSO treated MRC-5 cells using RNAzol (Molecular Research Center, Inc.)
Poly(A) RNA from 1 ug of total RNA was used to generate the cDNA library according to TruSeq RNA Sample Prep Kit protocol which was then sequenced using the Illumina system.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
processed data file: gene_exp.diff.txt
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| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using BWA version 0.5.9-r16
Peaks were called using MACS version 1.4.2 with default parameter
We aligned those high quality reads to the masked Homo sapiens reference genome (hg19) genome and junction sequences using BWA 0.5.8 software allowing up to four mismatches. All the uniquely mapped reads were used to define gene expression level based on our developed method. We modified the RPKM (measured in reads per kilobase of exon per million mapped sequence reads, which is a normalized measure of exonic read density) calculation described by Mortazavi and colleagues to include junction fragments. By including reads that map to junction fragments, we ensure that genes with many introns are not under represented in the RPKM estimate. To examine differential expression, we used a MARS (MA-plot-based method with Random Sampling model) method to identify differentially expressed genes which described in DEGseq. For each gene, the P-value and Q-value were computed, and the fold changes were also calculated. Those genes with p < 0.001 and q-value < 0.05 were defined as DEGs.
Genome_build: hg19
Supplementary_files_format_and_content: The files are generated by MACS version 1.4.2, including chr, start, end, length, summit, tags, -10*log10(pvalue),fold_enrichment. The file of differitially expressed genes includes Gene, GeneNames, value1, value2, log2(Fold_change), log2(Fold_change) normalized, z-score, p-value, q-value(Benjamini et al. 1995), q-value(Storey et al. 2003), Signature(p-value < 0.001).
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| Submission date |
Feb 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Zechen Chong |
| Organization name |
Beijing Institute of Genomics
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| Street address |
NO. 7 Beitucheng West Road
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| City |
Beijing |
| ZIP/Postal code |
100029 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE44457 |
Cellular generation of 5-Hydroxymethylcytosine by redox-active chemicals via an unprecedent non-enzymatic mechanism |
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| Relations |
| SRA |
SRX243746 |
| BioSample |
SAMN01923908 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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