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Sample GSM5738224 Query DataSets for GSM5738224
Status Public on Mar 03, 2022
Title 231-Con-1
Sample type SRA
Source name Breast cancer cell-line MDA-MB-231
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
treatment: control non-targeted shRNA
shRNA: Stable tranfection were generated using puromycin selection
Growth protocol MDA-MB-231 control-shRNA and PELP1-shRNA cells were cultured in RPMI medium supplemented with 10% FBS
Extracted molecule total RNA
Extraction protocol Total RNA from MDA-MB-231 control-shRNA and PELP1-shRNA cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Data processing Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
Submission date Dec 16, 2021
Last update date Mar 03, 2022
Contact name YI ZOU
Organization name UTHSA-GCCRI
Street address 8403 Floyd Curl Drive
State/province TX
ZIP/Postal code 78229
Country USA
Platform ID GPL21290
Series (1)
GSE191066 Global genomic and proteomic analysis of TNBC cells identifies the critical role of PELP1 in ribosome biogenesis
BioSample SAMN24139220
SRA SRX13427219

Supplementary file Size Download File type/resource
GSM5738224_231_Con_1_Genes_ReadCount.txt.gz 91.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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