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Sample GSM4006661 Query DataSets for GSM4006661
Status Public on Jun 23, 2020
Title MCF7, dDBD_Veh_rep2 (RNA-Seq)
Sample type SRA
 
Source name MCF7
Organism Homo sapiens
Characteristics cell line: MCF7
transfection: Cells were infected with dDBD ER
treatment: Veh
Treatment protocol MCF7 cells were first infected with lentivirus-based ER truncations, and then transiently infected shControl(for vector group) or shER(for WT and dDBD group) targeting 3'UTR to knock down endogenous ER. Cells were kept in hormone stripped condition for at least three days before treating with 100 nM estradiol or corresponding condition of ethanol for six hours.
Growth protocol MCF7 obtained from ATCC were cultured in DMEM media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.
Extracted molecule total RNA
Extraction protocol total RNA was extracted by Trizol Reagent from Invitrogen (Cat no 15596026).
RNA library was prepared by the KAPA Stranded mRNA-Seq kit (KK8421), according to the manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes reads counts for each Sample
 
Submission date Aug 03, 2019
Last update date Jun 23, 2020
Contact name Kexin Xu
Organization name UT Health Science Center at San Antonio
Department Molecular Medicine
Street address 7703 Floyd Curl, MC 8257
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
 
Platform ID GPL21290
Series (2)
GSE135339 Enhancer RNA mediate estrogen-induced transcriptional repression by recruiting ERa and its cofactor to selective enhancers [RNA-Seq]
GSE135341 Enhancer RNAs mediate estrogen-induced decommissioning of selective enhancers by recruiting ER and its cofactor
Relations
BioSample SAMN12491199

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

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