|
| Status |
Public on Dec 01, 2016 |
| Title |
MDA-MB-231_CONT_3 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231_CONT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: breast cancer cell line MDA-MB-231
breast cancer subtype: Basal type
er status: ER-ve
treatment: control-siRNA
|
| Treatment protocol |
To obtain RORC knockdown, Control-siRNA or RORC-siRNA was transfected for 48h as described. For over-expression, CMV-empty or CMV-RORC was transfected for 48h. For antagonization of RORC protein, selective inhibitor (SR2211) was treated for 24h in MCF-7 and data was compared to DMSO treated cells.
|
| Growth protocol |
Cell lines were maintained in complete media as described.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat. no. RS-122-2101 and RS-122-2102) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Part oo. 15031047 Rev. E October 2013).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped against the reference genome (GRCh38.p2) using STAR.
SAM was tranformed to BAM with samtools.
BAM data was sorted with Picard.
read counts for each gene in the Ensembl annotation were generated using htseq-count in the HTSeq python package.
Differential expression was detected using the DESeq2.
Genome_build: GENCODE GRCh38.p2
Supplementary_files_format_and_content: text files with raw count numbers by Htseq version 0.6.1.
|
| |
|
| Submission date |
Nov 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tae Gyu Oh |
| E-mail(s) |
t.oh@uq.edu.au
|
| Organization name |
Institute for Molecular Bioscience
|
| Street address |
306 Carmody Rd
|
| City |
St Lucia |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE74981 |
Next generation sequencing to elucidate the novel function of RORC (RORgamma) in breast cancer |
|
| Relations |
| BioSample |
SAMN04266618 |
| SRA |
SRX1432829 |
