NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7528038 Query DataSets for GSM7528038
Status Public on Jul 06, 2023
Title sgILRAP rep 2
Sample type SRA
 
Source name breast
Organism Homo sapiens
Characteristics tissue: breast
cell line: MCF10A
cell type: epithelial cell
genotype: IL1RAP KO
treatment: no
Treatment protocol Cells were seeded in 6-well plates 1 day before RT, which was performed by a Precision X-RAD 320 Biological Irradiator. For a single high dose of RT, cells were irradiated at a single dose of 20 Gy at one time.
Growth protocol MCF10A normal breast epithelial cells were grown in DMEM/F12 medium supplemented with 20 ng/ml epithelial growth factor (EGF; Fisher Scientific), 100 ng/ml cholera toxin (Sigma-Aldrich), 10 μg/ml insulin (Sigma-Aldrich), 0.5 mg/ml hydrocortisone (Sigma-Aldrich), and 5% horse serum (Fisher Scientific).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted (Qiagen)
An Illumina TruSeq Stranded Total RNA Library Prep Kit was used to prepare the library after rRNA depletion.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Description MCF10A-85-2_S18
Data processing Sequence reads were trimmed for adapter content and low quality bases using Cutadapt version 1.15
Trimmed sequence reads were mapped to GRCh38 using STAR version 2.5.3a
Reads count extraction was done using HTseq-count
The raw reads were normalized using DESeq2 for which there are > 5 reads in at least one sample
Assembly: GRCh38
Supplementary files format and content: tab delimited text file include TPM values for each sample
 
Submission date Jul 03, 2023
Last update date Jul 06, 2023
Contact name Citu .
E-mail(s) guliasitu40@gmail.com
Organization name University of Texas Health Science Centre
Department McWilliams School of Biomedical Informatics
Street address 7000 Fannin Street
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL21697
Series (1)
GSE236331 Genome-wide CRISPR screen reveals tumor-intrinsic responses to radiotherapy
Relations
BioSample SAMN36271105
SRA SRX20866491

Supplementary file Size Download File type/resource
GSM7528038_MCF10A-85-2_S18.txt.gz 213.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap