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Sample GSM2179009 Query DataSets for GSM2179009
Status Public on Feb 07, 2017
Title C51sh3plus
Sample type SRA
Source name breast cancer cell line
Organism Homo sapiens
Characteristics cell line name: Cal51
doxycycline added: plus 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
BioSample SAMN05187207
SRA SRX1808071

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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