|
Status |
Public on Jun 12, 2023 |
Title |
RhM22_Post Kleptose_CD8M |
Sample type |
SRA |
|
|
Source name |
peripheral blood
|
Organism |
Macaca mulatta |
Characteristics |
tissue: peripheral blood cell type: CD8+ memory T cell treatment: 2-hydroxypropyl-beta-cyclodextrin
|
Treatment protocol |
2-hydroxypropyl-beta-cyclodextrin-treated animals received 15% (w/w) KleptoseTM HBP parenteral grade (Roquette #346111109D) subcutaneously at 1 ml/kg/day for up to 120 days.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
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).
|
|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
ATAC-seq samples were sequenced as 151bp paired-end libraries on a Novaseq S4. All samples had over 60 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. The peaks were called using Genrich v0.6 with the following flags -j -y -r -v -d 150 -m 5 -e chrM,chrY. Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization. Assembly: RheMac10 Supplementary files format and content: bigWig, narrowPeak
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|
|
Submission date |
May 25, 2023 |
Last update date |
Jul 10, 2023 |
Contact name |
Jason Brenchley |
E-mail(s) |
jbrenchl@niaid.nih.gov
|
Organization name |
NIAID
|
Street address |
4 Center Drive
|
City |
Bethesda |
State/province |
MD |
ZIP/Postal code |
20892 |
Country |
USA |
|
|
Platform ID |
GPL27943 |
Series (2) |
GSE233449 |
2-hydroxypropyl-beta-cyclodextrin treatment induces modest immune activation in healthy rhesus macaques [ATAC-seq] |
GSE233467 |
2-hydroxypropyl-beta-cyclodextrin treatment induces modest immune activation in healthy rhesus macaques |
|
Relations |
BioSample |
SAMN35365604 |
SRA |
SRX20516498 |