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| Status |
Public on Jun 05, 2014 |
| Title |
PR-ChIP-seq |
| Sample type |
SRA |
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| Source name |
T47D cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D
cell type: breast cancer cell line
passages: 5-8
chip antibody: PR
chip antibody catalog #: sc-7208
chip antibody manufacturer: Santa Cruz
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| Treatment protocol |
R5020 (progestin) or EtOH
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| Growth protocol |
RPMI+10% fetal calf serum
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Trizol extraction for RNA and ChIPs with an antibody against the progesterone receptor for immunoprecipitated DNA
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
For ChIP-seq data, reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.1.2 with default parameters
For RNA-seq data, reads reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Refseq database using TopHat with own junction and gene annotation model
For ChIP-seq data, SAM tools were used for filtering uniquely mapped, paired end reads. MACS was used for peak calling with default parameters.
For RNA-seq data the Cufflinks suite was used for transcript annotation
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq data BED files were generated with the genomic coordinates for PR binding sites.
Supplementary_files_format_and_content: For RNA-seq data, txt files were generated with FPKM values for all transcripts
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| Submission date |
Oct 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Angeliki Magklara |
| E-mail(s) |
amagklara@gmail.com
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| Organization name |
University of Ioannina
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| Department |
Medicine
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| Lab |
Clinical Chemistry
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| Street address |
University Campus
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| City |
Ioannina |
| ZIP/Postal code |
45221 |
| Country |
Greece |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE51428 |
Transcriptomic profiling reveals new aspects of progestin signaling in breast cancer |
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| Relations |
| BioSample |
SAMN02378270 |
| SRA |
SRX365497 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1245253_PR_binding_sites.txt.gz |
153.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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