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Sample GSM4551115 Query DataSets for GSM4551115
Status Public on May 14, 2020
Title 229_11_R5020+proclactin
Sample type SRA
Source name T47D breast cancer cells
Organism Homo sapiens
Characteristics cell line: T47D
cell type: breast cancer cells
Treatment protocol T47D breast cancer cells were treated with vehicle (water for prolactin and EtOH for R5020), 100 ng/ml prolactin, 10nM R5020, or both, for 6 hrs. RNA was isolated immediately following treatment.
Growth protocol Cell were maintained and passed in appropriate culture media, as described in the manuscript.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description 229_11
Data processing 51 bp single end sequencing run with Illumina HiSeq 3000 platform and CASAVA was employed to generate the fastq file for each sample
RNA-seq FASTQ files were aligned to hg19 using TopHat (version 2.0.14) and only uniquely mapped reads were used for the further downstream analysis
summarizeOverlaps function (of GenomicAlignments package) in R/Bioconductor was utilized to count the reads that mapped to exonic regions only to generate a raw count matrix
DESeq2, whose default and recommended normalization method is relative log expression (RLE), was then utilized to identify differentially expressed genes (DEGs). The genes with log2FoldChange>=1, after rounding all log2FoldChange values to one decimal point, and adjusted p-value<0.05 were considered DEGs
Functional annotation of DEGs was performed using ClueGO (v2.5.4) plug-in of Cytoscape
Genome_build: hg19
Supplementary_files_format_and_content: read counts
Submission date May 13, 2020
Last update date May 14, 2020
Contact name Bakhtiyor Nosirov
Organization name BDR RIKEN, Japan
Street address Minatojima-minamimachi, 2-2-3
City Chuo-ku, Kobe
State/province Hyogo
ZIP/Postal code 650-0046
Country Japan
Platform ID GPL21290
Series (1)
GSE150477 Reciprocal fine-tuning of progesterone and prolactin-regulated gene expression in breast cancer cells
BioSample SAMN14911343
SRA SRX8336329

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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