|
Status |
Public on Oct 28, 2022 |
Title |
β1 transduced+CLI 3 |
Sample type |
SRA |
|
|
Source name |
MDA-MB-239
|
Organism |
Homo sapiens |
Characteristics |
cell line: MDA-MB-239 cell type: basal breast cancer cell line transduction: lentiviral-GFP-luciferase-estrogen receptor beta1 vector treatment: doxycycline+CLI ligand time: 3 days, 24 hr ligand treatment
|
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.
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|
|
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
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|
|
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 |
SAMN30056037 |
SRA |
SRX16736053 |