|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jun 13, 2014 |
Title |
U937, WT 1h |
Sample type |
SRA |
|
|
Source name |
U937 monocytic cells infected with HIV-1-GFP
|
Organism |
Homo sapiens |
Characteristics |
cell type: U937 time points post-infection: 1h transduced gene: SAMHD1 Wild Type
|
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.
|
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
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
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.
|
|
|
Submission date |
Jun 12, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Daekwan Seo |
E-mail(s) |
daekwan.seo@psomagen.com
|
Phone |
+1-301-251-1007
|
Organization name |
Psomagen Inc
|
Department |
Bioinformatics
|
Lab |
BI
|
Street address |
1330 Piccard Dr., Ste 103
|
City |
Rockville |
State/province |
MARYLAND |
ZIP/Postal code |
20850 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE58418 |
The ribonuclease activity of SAMHD1 is required for HIV-1 restriction |
|
Relations |
BioSample |
SAMN02851321 |
SRA |
SRX591642 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1410585_WT_1h_rpkm.txt.gz |
365.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|