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| Status |
Public on Jun 13, 2014 |
| Title |
U937, D137N 1h |
| Sample type |
SRA |
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| Source name |
U937 monocytic cells infected with HIV-1-GFP
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| Organism |
Homo sapiens |
| Characteristics |
cell type: U937
time points post-infection: 1h
transduced gene: SAMHD1 D137N
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| Growth protocol |
U937 cells were grown in RPMI1640 supplemented with 10% fetal bovine serum, 100U/ml of penicillin, 100㎍/ml of streptomycin, and 2 mM GlutaMAX-I(Gibco). U937 cells (0.5 x 106 cells/ml) were seeded in 12-well plates and differentiated for 20 h in PMA (30 ng/ml). The cells were infected with 100 ng of viruses for 2 h and harvested at indicated time.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence, then mapped to hg19 with HIV genome using Tophat v.2.0.9 with parameters -p 4 --b2-very-sensitive
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using bam2rpkm v.0.06 from the University of Liverpool. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 with HIV-1 NL4-3
Supplementary_files_format_and_content: tab-delimited text files include genes, transcripts, and RPKM values for each sample.
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| Submission date |
Jun 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Daekwan Seo |
| E-mail(s) |
daekwan.seo@psomagen.com
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| Phone |
+1-301-251-1007
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| Organization name |
Psomagen Inc
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| Department |
Bioinformatics
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| Lab |
BI
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| Street address |
1330 Piccard Dr., Ste 103
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| City |
Rockville |
| State/province |
MARYLAND |
| ZIP/Postal code |
20850 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE58418 |
The ribonuclease activity of SAMHD1 is required for HIV-1 restriction |
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| Relations |
| BioSample |
SAMN02851326 |
| SRA |
SRX591648 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1410591_D137N_1h_rpkm.txt.gz |
358.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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