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Status |
Public on Aug 12, 2023 |
Title |
Lytic_AKATA_input1 |
Sample type |
SRA |
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Source name |
EBV-positive Burkitt's lymphoma cell line
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Organism |
human gammaherpesvirus 4 |
Characteristics |
cell type: EBV-positive Burkitt's lymphoma cell line passage: 12--15 rip antibody: non
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Treatment protocol |
To reactivate EBV, TPA (20 ng/ml) and Butyric acid (BA, 2.5 mM) were used to treat the cells for 48 hours.
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Growth protocol |
LCL cells were generated in our laboratory. These B-cell lines and PBMC were cultured in RPMI 1640 media (Hyclone, Logan, UT) with 10% BGS (HyClone Bovine Growth Serum).
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Extracted molecule |
total RNA |
Extraction protocol |
The total RNA extraction was performed using Trizol reagent (Invitrogen, Inc., Carlsbad, CA) and treated with DNase I (Invitrogen, Inc., Carlsbad, CA). cDNA was prepared with Superscript II reverse transcriptase kit (Invitrogen, Inc., Carlsbad, CA) according to the manufacturer’s protocol. The library was prepared using the TruSeq stranded mRNA kit (Illumina, San Diego, CA) according to the manufacturer’s protocol. First, the elute-frag-prime stage was done at 80°C for 2 min to allow annealing without causing fragmentation [12]. RNA was reverse transcribed into first strand cDNA using reverse transcriptase and random primers. This was followed by the second strand cDNA synthesis using DNA Polymerase I and RNase H. The cDNA fragments were used for end repair process with the addition of a single ‘A’ base followed by ligation of adapters. The products were then purified and enriched by PCR amplification for 12 cycles to generate the final RNA-seq library. cDNA libraries were quantified and pooled and subsequent sequencing on an Illumina HiSeq3000 platform 50 bp single read sequencing module.
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Library strategy |
RIP-Seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 3000 |
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Description |
AKATA_lytic_vs_latent
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Data processing |
After sequencing, the first step is quality and adapter trimming. Trimming was conducted by Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low-quality bases (bases with < 20 quality score will be removed). After trimming, the MeRIP-seq reads were aligned to EBV reference genome by the aligner HISAT2 [39] with the annotation of the splice sites (the EBV reference genome and annotation were downloaded from https://www.ncbi.nlm.nih.gov/nuccore/NC_007605.1). The m6A peaks were called by a graphical model-based peak calling method – MeTPeak [40], with the parameters of window width = 50, sliding step = 50 and read length = 50. The peaks were visualized in IGV (http://www.broadinstitute.org/igv). Genome_build: EBV genome NC_007605.1 Supplementary_files_format_and_content: peka, rpkm
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Submission date |
Apr 02, 2019 |
Last update date |
Aug 12, 2023 |
Contact name |
Fengchao Lang |
E-mail(s) |
flang@upenn.edu
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Organization name |
University of Pennsylvania
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Street address |
3610 Hamilton Walk
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City |
PHILADELPHIA |
State/province |
PA |
ZIP/Postal code |
19104 |
Country |
USA |
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Platform ID |
GPL26377 |
Series (1) |
GSE129217 |
m6A modification of EBV transcripts |
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Relations |
BioSample |
SAMN11317984 |
SRA |
SRX5624908 |
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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