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Sample GSM2179004 Query DataSets for GSM2179004
Status Public on Feb 07, 2017
Title BT5sh4minus
Sample type SRA
 
Source name breast cancer cell line
Organism Homo sapiens
Characteristics cell line name: BT549
doxycycline added: minus dox
gene target of shrna: SF3B1
Treatment protocol for doxycycline samples, treated with 100 ng/mL for 4 days to induce SF3B1 suppression
Growth protocol RPMI 10% FBS
Extracted molecule total RNA
Extraction protocol Qiangen RNA easy extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sequenced reads were trimmed for adaptor sequence, FASTQ files were aligned using TOPHAT v1.4 with parameters "--mate-inner- dist 300 --mate-std-dev 500 --no-sort-bam --no-convert-bam -p 4" and aligned to hg19
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using RNASeqMetrics 44
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample in .gct file format
 
Submission date May 27, 2016
Last update date May 15, 2019
Contact name Brenton Paolella
Organization name Dana-Farber Cancer Institute
Lab Rameen Beroukhim
Street address 450 Brookline Ave. Smith 1010
City Boston
State/province Massachusetts
ZIP/Postal code 02215
Country USA
 
Platform ID GPL18573
Series (1)
GSE81978 Effect of SF3B1 suppression in cancer cells with different SF3B1 copy-number levels
Relations
BioSample SAMN05187202
SRA SRX1808066

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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