|
| Status |
Public on Oct 28, 2022 |
| Title |
control cells 1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: basal breast cancer cell line
transduction: lentiviral-GFP-luciferase control vector
treatment: doxycycline
time: 3 days
|
| Treatment protocol |
Cells were treated with doxycycline for 3 days.
Cells were treated with CLI for 24 hours.
|
| Growth protocol |
MDA-MB-231 cells lentivirally transduced with dox-inducible expression of GFP-luciferase-estrogen receptor β isoform 1 or control GFP-luciferase were cultured in DMEM+5%FBS + 100 ng/ml doxycycline + pen/strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol protocol, followed by DNase treatment. RNA was then re-purified with an aqueous column-based protocol followed by gel analysis to analyze purity and quality of the RNA.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand. The libraries were pooled; quantitated by qPCR and sequenced on one S2 lane for 101 cycles from one end of the fragments on a NovaSeq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calling and de-multiplexing of samples within each lane were done with bcl2fastq v2.20 Conversion Software (Illumina).
Fastqc files containing raw RNA sequencing data were trimmed using Trimmomatic (version 0.38).
Reads were pseudo-mapped to the Homo sapiens reference transcriptome (GRCh38; Gencode v34) using Salmon (v1.2.1) with the entire GRCh38 genome as the decoy sequence. Transcript-level counts were summed to the gene level while adjusting for effective lengths using tximport's (v1.16.1) "lengthScaledTPM" method.
Gene-level counts underwent quality control and normalization in R (v4.0.2) using edgeR (Version 3.30.3). Genes were filtered out if they did not have expression levels above 0.25 CPM in at least 2 samples.
Assembly: GRCh38
Supplementary files format and content: Raw_gene_counts.xlsx
Supplementary files format and content: TMM_normalized_logCPM_data.xlsx
|
| |
|
| Submission date |
Jul 29, 2022 |
| Last update date |
Oct 28, 2022 |
| Contact name |
Yvonne Ziegler |
| E-mail(s) |
yziegler@illinois.edu
|
| Organization name |
University of Illinois
|
| Department |
MIP
|
| Lab |
Katzenellenbogen
|
| Street address |
407 S Goodwin Ave.
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE210092 |
Estrogen Receptor Beta 1: A Potential Therapeutic Target for Triple Negative Breast Cancer |
|
| Relations |
| BioSample |
SAMN30056045 |
| SRA |
SRX16736054 |
