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Sample GSM2991450 Query DataSets for GSM2991450
Status Public on Feb 12, 2019
Sample type SRA
Source name cell line
Organism Mus musculus
Characteristics strain: Balb/c
cell line: SCLL cell line derived from BM of disease mice
agent: DMSO
Treatment protocol The BBC2, ZNF112 and BCRF8C cells were treated with 30nM, 3nM and 1.5nM BGJ398 or DMSO for 24h, then the cells were harvested for analysis.
Growth protocol The BBC2, ZNF112 and BCRF8C cells were cultured in RPMI 1640 medium containing 10% FBS, 100 U/ml penicillin and 100 U/ml streptomycin.
Extracted molecule total RNA
Extraction protocol RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Illumina Casava1.8.2 software used for basecalling, bcl2fastq2_v2 software used for demultiplexing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NCBIM37 whole genome using tophat-2.0.12 with parameters --library-type fr-firststrand
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Combined FPKMs of all samples into one combinedfpkm table
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values combined for all Samples ...
Submission date Feb 12, 2018
Last update date Feb 12, 2019
Contact name John Cowell
Phone 7067214381
Organization name Augusta University
Street address 1410 Laney-Walker Blvd
City Augusta
State/province GA
ZIP/Postal code 30912
Country USA
Platform ID GPL17021
Series (1)
GSE110457 Identification of transcriptional network regulated by FGFR1 fusion kinase in stem cell leukemia and lymphoma (SCLL)
BioSample SAMN08517578
SRA SRX3680449

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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