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Sample GSM1968786 Query DataSets for GSM1968786
Status Public on Mar 31, 2016
Title treated sample #28 TT
Sample type SRA
Source name lymphoblastoid cell line HG3
Organism Homo sapiens
Characteristics strain: HG3
cell line: lymphoblastoid cell line HG3
sample type: fludarabine-resistant
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using an RNeasy Plus Mini kit (Qiagen). The RNA integrity and concentration was determined on a Bioanalyzer instrument (Agilent) using an RNA 6000 Nano kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description treated sample #28 TT
Data processing The reads were aligned to the human genome hg19 assembly ( using Tophat2 software (version 2.0.4)
The FPKM summary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
The RNAseq read count quantification was performed using the HTSeq tool (version 0.6.1)
To identify the gene expression differences between the three pairs of HG3 pools, DESeq2 software was used. (Love, Huber et al. 2014)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each Sample.
Submission date Dec 09, 2015
Last update date May 15, 2019
Contact name L. H.
Organization name Uppsala University
Street address Dag Hammarskjölds Väg 20
City Uppsala
ZIP/Postal code 751 85
Country Sweden
Platform ID GPL17303
Series (1)
GSE75844 Transposon mutagenesis reveals fludarabine-resistance mechanisms in chronic lymphocytic leukemia
BioSample SAMN04327459
SRA SRX1472499

Supplementary file Size Download File type/resource
GSM1968786_28TT_FPKM.txt.gz 138.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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