|
| Status |
Public on Mar 29, 2021 |
| Title |
CD44 KO MDA-MB-231 rep 3 |
| 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_3
231_CD44negative_8
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 |
SAMN14596673 |
| SRA |
SRX8114673 |
