|
| Status |
Public on Jul 01, 2019 |
| Title |
HIV CEM virions PA-m6A-seq |
| Sample type |
SRA |
| |
|
| Source name |
PA-m6A-seq of virion 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: virion 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 |
SAMN11613146 |
| SRA |
SRX5813541 |
