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| Status |
Public on Jun 21, 2013 |
| Title |
Veh_2 |
| Sample type |
SRA |
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| Source name |
Immortalized human breast cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: Vehicle
replicate: 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
After 1 hour of E2 or Vehicle treatment, nuclei from C4-12/Flag-ERβ cells were extracted and processed with nuclear run-on assay.
Run-on RNA was ligated with adapters and reverse transcribed to generate cDNA library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
GROseq - Global run-on followed by sequencing
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| Data processing |
Alignment: Short-reads were aligned to the human reference genome (hg18, NCBI36), including autosomes, X-chromosome, and one complete copy of an rDNA repeat (GenBank ID: U13369.1). The SOAP2 software package was used to align reads with the following options: (1) all non-unique mappings were removed (-r 0), (2) three mismatches were allowed in each mapped read (-v 3), (3) low-quality reads with more than 10 ambiguous bases were removed (-N 10), and (4) for reads failing to align over the entire length of the read, the first 32 bp was used (-l 32). SOAP2 output was processed using custom Perl scripts, and imported into R for most the analysis. In order to identify E2-regulated genes, we focused on RefSeq-annotated genes, counting reads in a fixed window between +1 kb and +13 kb relative to the transcription start site of each gene, so as to avoid possible complications introduced by paused polymerases, and to allow easy side-by-side comparison among samples. The normalized expression value of 1e-5 (normalized against the sample total read counts) was used as the threshold to select genes for further analyses. Comparing E2 treated samples versus vehicle treated samples, genes with FC>1.2 were considered upregulated; those with FC<0.8 were considered downregulated.
Genome_build: hg18
Supplementary_files_format_and_content: txt: read locations, count reads
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| Submission date |
Jun 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Thien Le |
| E-mail(s) |
lethien@uchicago.edu
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| Organization name |
University of Chicago
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| Lab |
Geoffrey Greene
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| Street address |
929 E 57th St W325D
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE48159 |
Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor [Gro-Seq] |
| GSE48161 |
Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor |
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| Relations |
| BioSample |
SAMN02209909 |
| SRA |
SRX312097 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1171525_GEOarchive_TL_GROseq_Veh_2.txt.gz |
512.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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