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Sample GSM1387804 Query DataSets for GSM1387804
Status Public on Mar 18, 2015
Title BZLF1 B cell RNASeq biological replicate 2
Sample type SRA
Source name modified Burkitt's lymphoma cell line
Organism Homo sapiens
Characteristics cell line: modified Burkitt's lymphoma cell line (Akata)
genotype/variation: harboring BZLF1 tet inducible gene
construct: pRTS-CD2-BZLF1
Treatment protocol 500ng/ml doxycycline for 24h and enrichment on anti-NGFR MACS beads.
Growth protocol Maintained in RPMI medium supplemented with 10% (v/v) fetal bovine serum, 100units/ml penicillin, 100_g/ml streptomycin and 2mM L-glutamine (Life Technologies) at 370C with 5% CO2.
Extracted molecule polyA RNA
Extraction protocol Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
The RNA-Seq libraries were prepared with the Illumina stranded mRNA kit. The mRNA was purified using oligo-dT beads and fragmented using elevated temperatures. The first strand of cDNA is generated from the mRNA using random hexamer primers. The second strand was synthesized without the use of dUTP so strand specificity is not encoded. Double stranded cDNA was ligated to standard Illumina adapters and amplified by PCR using 15 cycles of amplification. The libraries were subjected to cluster formation and then 100bp paired-end sequencing on the HiSeq 2500 using the v3 chemistry.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description processed data files: CONTROLvsBZLF1.RNASeq.genes.counts.tsv, CONTROLvsBZLF1.RNASeq.edgeR.DE_results.tsv
Data processing Alignments were performed to human RefSeq genes archived in the Illumina iGenomes resource using RSEM (version 1.2.4; Li and Dewey 2011).
An existing pipeline developed within the Trinity software package (Grabherr et al., 2011) was used to perform differential expression analysis with edgeR (Robinson et al., 2010) which is available as part of the Bioconductor project (Gentleman et al., 2004) developed within the R programming language (version 3.01).
Genes with a read count less than ten across all samples were removed before differential expression analysis with edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: CONTROLvsBZLF1.RNASeq.genes.counts.tsv: Tab-delimited text file containing gene names as rows and columns that represent read counts generated by RSEM for all samples with respect to the RefSeq annotation.
Supplementary_files_format_and_content: CONTROLvsBZLF1.RNASeq.edgeR.DE_results.tsv: Tab-delimited text file containing gene names as rows and columns that represent the output from edgeR.
Submission date May 16, 2014
Last update date May 15, 2019
Contact name Alison Jane Sinclair
Organization name University of Sussex
Department School of Life Sciences
Lab Biochemistry and Bioscience
Street address University of Sussex
City Brighton
State/province E. Sussex
ZIP/Postal code BN1 9QG
Country United Kingdom
Platform ID GPL16791
Series (2)
GSE57732 Genomic-scale identification of host genes regulated by EBV during lytic cycle [RNA-Seq]
GSE58246 Genomic-scale identification of host genes regulated by EBV during the lytic cycle
BioSample SAMN02782210
SRA SRX545690

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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