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Status |
Public on May 10, 2024 |
Title |
57_GE34_ARV_CD4N ATAC |
Sample type |
SRA |
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Source name |
peripheral blood
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Organism |
Macaca mulatta |
Characteristics |
tissue: peripheral blood cell type: CD4 naiveT cell disease state: ARV
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Extracted molecule |
genomic DNA |
Extraction protocol |
Up to 10,000 sorted cells from each population were pelleted and resuspended in 2x Tagmentation Buffer (Illumina), 0.02% Digitonin, and 0.1% Tween-20, with Tagment DNA TDE1 Enzyme (Illumina) and incubating at 37°C for one hour. The mix was then incubated with proteinase K for 30 minutes at 40°C. High molecular weight DNA was removed with a 0.7x selection ratio of Agencourt AMPureXP beads (Beckman Coulter) and low molecular weight DNA was isolated from the remainder with a 1.2x selection ratio. Library amplification was performed with KAPA HiFi HotStart ReadyMix (KAPA) and i5 and i7 indexing primers (Nextera DNA CD Indexes) for 11-15 total cycles depending on the sample concentration reached after 5 cycles (KAPA Library Quantification kit). Library DNA was purified with a 1x selection ratio of AMPureXP beads. The final library was verified by High Sensitivity DNA Bioanalyzer (Agilent).
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
57_GE34_ARV_CD4N
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Data processing |
ATAC-seq samples were sequenced as 151bp paired-end libraries on a Novaseq S4. All samples had over ?? million reads. Samples were trimmed for adapters using Cutadapt v 1.18 before alignment. The trimmed reads were aligned to the RheMac10 reference using Bowtie2 v2.3.4.1 with flag -k 10. Assembly: RheMac10 Supplementary files format and content: The peaks were called using Genrich v0.6 with the following flags -j -y -r -v -d 150 -m 5 -e chrM,chrY. Supplementary files format and content: Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.
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Submission date |
Apr 23, 2024 |
Last update date |
Jul 01, 2024 |
Contact name |
Jason Brenchley |
E-mail(s) |
jbrenchl@niaid.nih.gov
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Organization name |
NIAID
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Street address |
4 Center Drive
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City |
Bethesda |
State/province |
MD |
ZIP/Postal code |
20892 |
Country |
USA |
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Platform ID |
GPL27943 |
Series (1) |
GSE264656 |
SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells in vivo (ATAC-Seq) |
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Relations |
BioSample |
SAMN41062630 |
SRA |
SRX24348391 |
Supplementary file |
Size |
Download |
File type/resource |
GSM8224652_57_GE34_ARV_CD4N.genrich.RPM.bw |
486.3 Mb |
(ftp)(http) |
BW |
GSM8224652_57_GE34_ARV_CD4N.narrowPeak.gz |
1.0 Mb |
(ftp)(http) |
NARROWPEAK |
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