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Sample GSM4476221 Query DataSets for GSM4476221
Status Public on Mar 29, 2021
Title CD44 KO MDA-MB-231 rep 1
Sample type SRA
 
Source name MDA-MB-231
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
cell type: Breast cancer cell line
cd44 status: knockout
Treatment protocol CD44 was deleted from the Hs578T and MDA-MB-231 cells using CRISPR/Cas9 -based techniques and sorted to generate populations of CD44 knockout cells. Knockout was confirmed by flow cytometry and Western blot.
Growth protocol Hs578T and MDA-MB-231 cells were grown per ATCC recommendations in Dulbecco's Modified Eagle's Medium, 10% fetal bovine serum, and 1% Pen/Strep.
Extracted molecule total RNA
Extraction protocol RNA was harvested using the RNeasy Mini Kit (Qiagen #74104) and 2000ng RNA was submitted per sample. Twelve dual-indexed Illumina TruSeq stranded mRNA libraries were pooled for sequencing on 1 lane of a HiSeq 2500 using v4 chemistry to generate 2x50 bp paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 231_CD44negative_1
231_CD44negative_12
Tissue: mammary gland/breast
Cancer subtype: triple negative breast cancer
processed data file: CD44_KO_subread.txt
Data processing Fastq files were mapped to the hg38 human reference genome using HiSat2 (v. 2.1.0).
Counts were estimated using the Subread featureCounts (v1.6.2) tool using the gencode.v28.GRCh38.annotation.gtf annotation.
Count data were filtered to only keep genes that were less than 300 nt in length and had a cpm (counts per million) value greater than 1 cpm in at least 2 sample replicates across all experimental conditions.
Genome_build: GRCh38
Supplementary_files_format_and_content: CD44_KO_subread.txt: Tab-delimited text file includes abundance measurements.
 
Submission date Apr 14, 2020
Last update date Mar 29, 2021
Contact name Sarah Munro
Organization name University of Minnesota
Street address 117 Pleasant Street SE
City Minneapolis
State/province MN
ZIP/Postal code 55455
Country USA
 
Platform ID GPL16791
Series (1)
GSE148657 Hyaluronan-CD44 signaling promotes pro-tumor inflammation in breast cancer
Relations
BioSample SAMN14596675
SRA SRX8114671

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

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