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Sample GSM1519357 Query DataSets for GSM1519357
Status Public on Jan 15, 2015
Title HCC1419_DTEP_L1P7
Sample type SRA
 
Source name HCC1419
Organism Homo sapiens
Characteristics cell line: HCC1419
treatment: 1μM Lapatinib indefinitely
sample id: dep_mgA6
Growth protocol HCC1419 cells (ATCC, CRL-2326, purchased 1/31/11) were grown in RPMI containing 1% penicillin streptomycin (PenStrep) and 10% Gibco certified fetal bovine serum (FBS) (Invitrogen) (RPMI-complete) conditioned with mouse embryonic fibroblasts (MEF). Media was changed every 3 days.
Extracted molecule total RNA
Extraction protocol Trizol + RNEasy cleanup, followed by ribozero rRNA depletion
Strand-specific dUTP followed by TruSeq DNA library prep kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing The input Illumina fastq files consisted of paired end reads with each end containing 100 bp, which were reduced to 80x80bp by trimming 20bp from the 3' end of each read to improve mapping of fragments shorter than 100nt.
Fragments that mapped to elements in the repeatMasker human library, using Bowtie2, were removed.
Bowtie2 was used to map the remaining fragments against a version of the human transcriptome derived from the UCSC Known Genes track of the GRCh37hg19 human assembly by using the target generation script supplied with RSEM.
Only mappings with both read ends aligned were kept.
Potential PCR duplicates (mappings of more than one fragment with identical positions for both read ends) were removed with the samtools “rmdup” function, keeping only one of any potential duplicates.
The final set of mapped paired end reads for a sample were converted to transcript and gene expression estimates using RSEM.
For input to DESeq all genes with non-zero counts in any sample were considered.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RSEM expression estimates and DESeq results
 
Submission date Oct 06, 2014
Last update date May 15, 2019
Contact name Mia Grifford
E-mail(s) mgrifford@gmail.com
Organization name UCSC
Street address 1156 High Street
City San
State/province CA
ZIP/Postal code 95064
Country USA
 
Platform ID GPL11154
Series (1)
GSE62074 Mutation independent activation of the Notch pathway is associated with Lapatinib resistance in Her2+ breast cancer cell lines
Relations
BioSample SAMN03097375
SRA SRX722674

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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