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Sample GSM1817339 Query DataSets for GSM1817339
Status Public on Jul 11, 2015
Title SET2 cells persistent to INC424_replicate 2
Sample type SRA
 
Source name SET2 cell line
Organism Homo sapiens
Characteristics inhibitor exposure: chronic
cell line: SET-2
Growth protocol SET2 cells were cultured in RPMI1640 media + 20% FCS. For persistent cell lines, the respective type I JAK inhibitor was added to the culture media for continuous growth in presence of inhibitor. For acute exposures with inhibitor, DMSO was used as a control
Extracted molecule total RNA
Extraction protocol SET2 cells were lysed in Trizol and processed according to instructions with reagent.
poly(A) RNA was isolated using Dynabeads® mRNA DIRECTTM Micro Kit (Life Technologies) from 1 μg of total RNA. mRNA was then fragmentated using RNaseIII and purified. The fragmented samples’ quality and yield were evaluated using Agilent BioAnalyzer. Subsequently, the fragmented material underwent whole transcriptome library preparation according to the Ion Total RNA-Seq Kit v2 protocol (Life Technologies), with 16 cycles of PCR. Samples were barcoded, template-positive Ion PITM Ion SphereTM Particles (ISPs) were prepared using the ion one touch system II and Ion PITMTemplate OT2 200kit v2 Kit (Life Technologies). Enriched particles were sequenced on a Proton sequencing system using 200 bp version 2 chemistry.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description s_SET2_INC_per2
Data processing All sequenced library were mapped to the human genome (hg19) using rnaStar. Unmapped reads were mapped again to the same genome using BWA MEM (version 0.7.5.1)
HTSeq v0.5.3p3 (options -s y -m intersection-strict) is used for feature counting using the Homo_sapiens.GRCh37.69_ENSEMBL gene model also used at the mapping stage
DESeq (v1.10.1) is used for the normalization of count table.
Genome_build: hg19
Supplementary_files_format_and_content: text file with normalized count tables from each experiment
 
Submission date Jul 10, 2015
Last update date May 15, 2019
Contact name Jeffrey Zhao
Organization name Memorial Sloan Kettering Cancer Center
Department Genomics Core
Street address 1275 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL17303
Series (1)
GSE69827 Differential expression profiles of type I JAK inhibitor persistent vs. naïve MPN cells
Relations
BioSample SAMN03854218
SRA SRX1091683

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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