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Sample GSM2915382 Query DataSets for GSM2915382
Status Public on Jan 09, 2018
Title DSP460_E2_30_ERa_N2
Sample type SRA
 
Source name breast cancer cells
Organism Homo sapiens
Characteristics cell type: MCF-7 cells
chip antibody: ERα HC-20 (Santa Cruz Biotechnology sc-543)
Treatment protocol MCF-7 cells were treated with 5 nM E2 for 30 min
Growth protocol MCF-7 cells were maintained at 37°C, 5% CO2 in AMEM supplemented with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin. Three days before experiments, cells were switched to phenol red-free DMEM containing charcoal-stripped FBS, 2% L-glutamine and 1% penicillin-streptomycin.
Extracted molecule genomic DNA
Extraction protocol Nuclei were lysed. ERα-DNA complexes complexes were isolated with the appropriate antibody.
Libraries were prepared according to Roche's instructions. KAPA DNA HyperPrep Library Kit.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description genomic DNA
Data processing ChIP-seq reads were trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters were removed from the reads, and all reads were required to have a length of at least 50 bp using Timmomatic. The trimmed reads were mapped onto the hg19 reference genome using the aligner BWA. Properly paired reads were identified as inward-facing reads that are on the same chromosome and separated by a distance less than 600 bp. The number of fragments overlapping each 50 bp window was counted for each library along each standard chromosome and excluding blacklisted regions 2. The starts of adjacent windows were separated by 50 bp. To remove composition biases between libraries, reads were counted into 2 kbp bins over the genome for each library. Windows were filtered to retain only those with a 4-fold or greater increase in the average abundance above the scaled background estimate.
Gene expression was computed with Kallisto with default parameters (100 bootstraps) on the reference genome GRCh38 with the annotation of Ensembl v85 (with cdna and rna). 
Genome_build: hg19 for chipseq and GRCh38 for rnaseq
Supplementary_files_format_and_content: Tab-delimited text file for the chiseq experiment include counts per 50bp window for each sample and calculated using the csaw bioconductor package as described above
Supplementary_files_format_and_content: Tab-delimited text file for the rnaseq experiment include abundance estimate for each sample using kallisto as described above
 
Submission date Jan 08, 2018
Last update date Jan 23, 2018
Contact name Sylvie Mader
E-mail(s) sylvie.mader@umontreal.ca
Phone 514 3437166
Organization name Université de Montréal
Department Biochemistry and Molecular Medicine
Lab Molecular targeting in breast cancer
Street address CP 6128 Succursale centre ville
City MONTREAL
State/province QC
ZIP/Postal code H3C 3J7
Country Canada
 
Platform ID GPL18573
Series (1)
GSE108883 Role of SUMOylation in differential ERα transcriptional repression by SERMs and pure antiestrogens in breast cancer cells
Relations
BioSample SAMN08327232
SRA SRX3541101

Supplementary file Size Download File type/resource
GSM2915382_DSP460_E2_30_ERa_N2_count_data.txt.gz 1.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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