|
| Status |
Public on Jun 21, 2021 |
| Title |
HIV YTHDC1 PAR-CLIP repeat |
| Sample type |
SRA |
| |
|
| Source name |
293T
|
| Organisms |
Homo sapiens; Human immunodeficiency virus 1 |
| Characteristics |
virus strain: HIV-1 NL4-3
cell line: 293T
technique: PAR-CLIP
pulldown antibody: anti-Flag, clone M2, Sigma, Cat No F1804
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PAR-CLIP
All samples were processed with the Illumina Truseq small RNA-seq library prep kit
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Aligned to the HIV-1 NL4-3 genome, with one copy of LTR, U3 sequence on the 5' end, R-U5 on the 3' end
|
| Data processing |
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 0.12.7: bowtie -m 8 -a --best --strata --chunkmbs 10000
hg19 non-aligning reads aligned to the HIV-1 NL4-3 genome using Bowtie 0.12.7: bowtie -m 3 -v 1 -a --best --strata --chunkmbs 10000
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
Genome_build: NL4-3 genome: 551-9626nt of GenBank AF324493.2
Supplementary_files_format_and_content: bed files, aligned to HIV-1 NL4-3 genome
|
| |
|
| Submission date |
Jan 25, 2021 |
| Last update date |
Jun 21, 2021 |
| Contact name |
Kevin Tsai |
| E-mail(s) |
kevtsai@ibms.sinica.edu.tw
|
| Organization name |
Academia Sinica
|
| Department |
Institute of Biomedical Sciences
|
| Lab |
R414
|
| Street address |
128 Sec. 2, Academia Rd. Nankang
|
| City |
Taipei |
| ZIP/Postal code |
115 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL18160 |
| Series (1) |
| GSE165473 |
Epitranscriptomic addition of m6A regulates HIV-1 RNA stability and alternative splicing |
|
| Relations |
| BioSample |
SAMN17530812 |
| SRA |
SRX9933708 |
