NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2630673 Query DataSets for GSM2630673
Status Public on May 30, 2017
Title D3
Sample type SRA
 
Source name HCC1143 cell line
Organism Homo sapiens
Characteristics treatment: DMSO
cell line: HCC1143
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 72hr, then total RNA was isolated using the QIAGEN RNeasy mini kit according to manufacturers instructions.
Growth protocol HCC1143 cells were cultured in RPMI 1640 + 10% fetal bovine serum and 10g/ml penn/strep, cells were maintained at 37°C in a 5% CO2 atmosphere.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the QIAGEN Rneasy mini kit according to manufacturers protocol
Libraries were made with the Illumina Truseq Samples Prep v2 kit with 150ng RNA using manufacturer's protocol.
Poly A capture: total RNA was run on the Bioanalyzer (Agilent) to verify intactness. Following this test, RNA-seq libraries were constructed using the TruSeq RNA sample prep protocol (Illumina). Poly(A)+ RNA was isolated using oligo-dT bound to magnetic beads. Poly(A)+ RNA was then chemically fragmented. RNA fragments were converted to double stranded cDNA using random hexamer priming. Fragment ends were treated to remove overhanging nucleotides and then a single “A” was added to the 3’ end of each strand to facilitate ligation. Illumina adaptors with barcode sequences was ligated to the fragments. The resulting libraries were then amplified using polymerase chain reaction with a limited number of rounds. Unincorporated nucleotides and adaptor dimers were removed using AMPure XP beads (Agencourt). Libraries were combined for multiplexing and sequenced on the NextSeq 500
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description DMSO control
Data processing Base calling - using Illumina RTA version 2.4.11
Demultiplexing was done with Bcl2fastq 2.17.1.14
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.
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 17, 2017
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 GPL18573
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 SAMN07138549
SRA SRX2832113

Supplementary file Size Download File type/resource
GSM2630673_D3.txt.gz 1.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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