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| Status |
Public on Jun 10, 2014 |
| Title |
HIV_12hr_rep2 |
| Sample type |
SRA |
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| Source name |
Total RNA from HIV-infected SUPT1 at 12 hours post-infection
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| Organisms |
Homo sapiens; Human immunodeficiency virus 1 |
| Characteristics |
human cell line: SUPT1
human cell type: CD4+ T cell line
infection: HIV-1
time: 12 hours post-infection
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| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 20 μg of total RNA from each sample was submitted to the Beijing Genomics Institute (BGI) for sequencing. In brief, ribosomal RNAs (rRNAs) were depleted using the RiboMinus™ Human/Mouse Transcriptome Isolation Kit (Invitrogen, CA).
rRNA-depleted RNAs were fragmented, and cDNA synthesis was primed using random hexamers. Short fragments were purified for an average insert size of 200 nt, and then ligated with proprietary adapters. The 2x90 nt paired-end sequencing was done using an Illumina HiSeq™ 2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
12_8
HIV-1 infection
Total RNA-seq
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| Data processing |
mRNA-seq data was processed previously and is part of a different study. It was referenced in this study. The mRNA-seq data can be found in GEO GSE38006. This data set refers to the Whole Transcriptome data from similar samples.
Reads were aligned to the human reference genome (hg19, build GRCh37) using the gapped aligner software TopHat and Ht-seq, HIV-1 genome (GenBank accession no. K02013), and Human Non-coding ENCODE project (Gencode v17).
We trimmed from 90nt to 75nt. We then mapped the 75-nt reads to human ribosomal sequences using the short-read aligner software Bowtie to remove potential rRNA sequences. We also removed sequences that mapped to the HIV-1 genome. To quantify transcript expressions, we mapped all reads that remained unmapped to the human reference genome (hg19, build GRCh37, downloaded from UCSC genome browser, http://genome.ucsc.edu) using the gapped aligner software TopHat. RefSeq transcript annotations were supplied to facilitate the mapping of reads spanning known splicing junctions. Based on these human genome mapping results, we then estimated the expression abundances at both transcript and locus levels for RefSeq-annotated genes using the transcript assembly software Cufflinks. Read sequences that mapped to more than one genomic location were excluded from expression quantification. For visualization, BAM files were generated using TopHat and samtools and displayed using the UCSC genome browser.
Genome_build: GRCh37 (human), GenBank K02013 (HIV-1), Gencode v17 (human non-coding ENCODE project).
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each Sample using Htseq.
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| Submission date |
Jan 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Katze |
| E-mail(s) |
data@viromics.washington.edu
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| Organization name |
University of Washington
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| Department |
Microbiology
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| Lab |
Michael G. Katze, Ph.D
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| Street address |
Rosen Building 960 Republican St.
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-4325 |
| Country |
USA |
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| Platform ID |
GPL18160 |
| Series (1) |
| GSE53993 |
Comparative total RNA and mRNA sequencing and systems analysis reveals nascent transcriptional response to early HIV-1 infection in a CD4+ T cell line |
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| Relations |
| BioSample |
SAMN02581471 |
| SRA |
SRX424927 |
| 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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