 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 14, 2020 |
| Title |
229_06_R5020 |
| 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_06
|
| 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 |
|
| Relations |
| BioSample |
SAMN14911348 |
| SRA |
SRX8336324 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
