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Sample GSM2181590 Query DataSets for GSM2181590
Status Public on May 30, 2017
Title HCC1143_BEZ235
Sample type SRA
 
Source name HCC1143 cell line
Organism Homo sapiens
Characteristics cell_type: basal-like breast cancer
cell_line: HCC1143
treatment: BEZ235
Treatment protocol Two plates of each line were then treated with 1μM Trametinib, two plates with 1μM BEZ235, two plates with 1μM of both agents, and two plates with 0.05% DMSO as a control. Plates were incubated for 6 days, with media changed and drug replenished after 72hr. Following the incubation total RNA was isolated with TriZol reagent and lysates from the two biological replicate plates were combined. cDNA libraries were then created and samples were run through high throughput sequencing.
Growth protocol HCC1143 cells were cultured in RPMI 1640 + 10% fetal bovine serum and 10g/ml penn/strep, SUM149PT were cultured in HAMS F12 + 5% fetal bovine serum, 4g/ml insulin, 0.5g/ml hydrocortisone, 10mM HEPES and 10g/ml penn/strep. Cells were maintained at 37°C in a 5% CO2 atmosphere. Each line was typsinized and plated in 8 10cm plates and allowed to adhere for 18hr.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with TriZol reagent.
Libraries were made with Agilent SureSelect Strand Specific RNA kits under manufacturer's protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description BEZ235 treatment for cell line HCC1143.
Data processing Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
Reads were trimmed to 44 bases (first 4 bases were discared, next 44 were kept, and remaining bases were also discarded).
Trimmed reads were aligned to hg19 with Bowtie version 1.0.0 (Up to 3 mismatches were allowed, but unique best matches were required.)
R scripts were used to count tags that aligned to the exons of UCSC RefSeq gene models and calculate RPKM values. Processed files contain the in exon tag counts and the RPKM nomalized values for each RefSeq gene model.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary files are tab delimited text files with tag counts and RPKM values for each RefSeq gene model.
 
Submission date May 30, 2016
Last update date May 15, 2019
Contact name Tyler Risom
E-mail(s) tyler.risom@gmail.com
Organization name Oregon Health & Science University
Department Molecular Medical Genetics
Lab Dr. Rosalie Sears
Street address 2730 SW Moody Ave
City Portland
State/province Oregon
ZIP/Postal code 97201
Country USA
 
Platform ID GPL11154
Series (1)
GSE82032 Human basal-like breast cancer cell line HCC1143 treated with BET inhibitor JQ1 in combination with MEK inhibitor Trametinib or PI3K/mTOR inhibitor BEZ235
Relations
BioSample SAMN05187273
SRA SRX1808183

Supplementary file Size Download File type/resource
GSM2181590_HCC1143_BEZ235.txt.gz 805.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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