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Sample GSM2425620 Query DataSets for GSM2425620
Status Public on Dec 01, 2017
Title shCtrl rep1
Sample type SRA
Source name tamoxifen-resistant breast cancer cells
Organism Homo sapiens
Characteristics cell line: TamR MCF-7
transfection: Cells were infected with scrambled control shRNAs
Treatment protocol TamR MCF-7 cells were stably transfected with shCtrl and shEZH2 and maintained in phenol-red-free RPMI 1640 supplemented with 100 nM of 4-OHT.
Growth protocol Cells were cultured in phenol-red-free RPMI 1640 supplemented with 10% charcoal stripped FBS and 1% PSG (Penicillin-Streptomycin-L-Glutamine). 100 nM of 4-hydroxytamoxifen was added to maintain the tamoxifen resistant feature. Cells were 1:3 split twice per week.
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 (Cat.# RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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
Data processing Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using Tophat 2.0.10 with parameters -G. 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 edgeR with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample
Submission date Dec 13, 2016
Last update date May 15, 2019
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)
GSE92316 The transcriptome effect of knocking down EZH2 in TamR MCF7L
GSE103243 Tamoxifen Resistance in Breast Cancer is Regulated by the EZH2-ERa-GREB1 Transcriptional Axis
BioSample SAMN06134779
SRA SRX2417206

Supplementary file Size Download File type/resource
GSM2425620_shCtrl_rep1_readCounts.txt.gz 194.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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