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| Status |
Public on May 10, 2024 |
| Title |
3_A11263_SIV_CD8N ATAC |
| Sample type |
SRA |
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| Source name |
peripheral blood
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| Organism |
Macaca nemestrina |
| Characteristics |
tissue: peripheral blood
cell type: CD8 naiveT cell
disease state: SIV
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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 |
3_A11263_SIV_CD8N
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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 |
GPL33261 |
| 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 |
SAMN41062684 |
| SRA |
SRX24348369 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8224598_3_A11263_SIV_CD8N.genrich.RPM.bw |
518.7 Mb |
(ftp)(http) |
BW |
| GSM8224598_3_A11263_SIV_CD8N.narrowPeak.gz |
958.5 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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