|
| 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 |
| E-mail(s) |
a.j.sinclair@sussex.ac.uk
|
| 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 |
|
| Relations |
| BioSample |
SAMN02782210 |
| SRA |
SRX545690 |
