|
Status |
Public on Jul 01, 2019 |
Title |
HIV CEM cells PA-m6A-seq |
Sample type |
SRA |
|
|
Source name |
PA-m6A-seq of cellular RNA from HIV infected CEM cells
|
Organism |
Human immunodeficiency virus |
Characteristics |
human cell line: CEM virus: HIV technique: PA-m6A-seq par-clip antibody: anti-m6A, Synaptic Systems, Cat No 202111, Lot No, 202111/4 transfection: polyA RNA
|
Extracted molecule |
total RNA |
Extraction protocol |
PAR-CLIP protocol All samples were processed with the Illumina Tru-seq small RNA-seq kit
|
|
|
Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Aligned to the HIV genome
|
Data processing |
Library strategy: PA-m6A-seq CASAVA 1.8.2 fastx toolkit Bowtie (1) Aligned to hg19 genome to remove human reads Aligned remainder of the reads to the HIV genome Genome_build: HIV genome from Genbank AF324493.2 Supplementary_files_format_and_content: bed files, aligned to the HIV genome. Column 4 includes the read abundance normalised to the total number of reads.
|
|
|
Submission date |
May 09, 2019 |
Last update date |
Jul 02, 2019 |
Contact name |
Bryan R Cullen |
Organization name |
Duke University
|
Department |
Molecular Genetics & Microbiology
|
Lab |
Cullen Lab
|
Street address |
213 Research Drive
|
City |
Durham |
State/province |
NC |
ZIP/Postal code |
27710 |
Country |
USA |
|
|
Platform ID |
GPL26648 |
Series (1) |
GSE130972 |
Mapping of m6A and m5C on HIV with PA-antibody-seq |
|
Relations |
BioSample |
SAMN11613147 |
SRA |
SRX5813540 |