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Status |
Public on Feb 12, 2019 |
Title |
ZNFBGJ |
Sample type |
SRA |
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Source name |
cell line
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Organism |
Mus musculus |
Characteristics |
strain: Balb/c cell line: SCLL cell line derived from BM of disease mice agent: BGJ398
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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.
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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.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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 ...
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Submission date |
Feb 12, 2018 |
Last update date |
Feb 12, 2019 |
Contact name |
John Cowell |
E-mail(s) |
jcowell@augusta.edu
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Phone |
7067214381
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Organization name |
Augusta University
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Street address |
1410 Laney-Walker Blvd
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City |
Augusta |
State/province |
GA |
ZIP/Postal code |
30912 |
Country |
USA |
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Platform ID |
GPL17021 |
Series (1) |
GSE110457 |
Identification of transcriptional network regulated by FGFR1 fusion kinase in stem cell leukemia and lymphoma (SCLL) |
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Relations |
BioSample |
SAMN08517583 |
SRA |
SRX3680450 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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