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| Status |
Public on Dec 05, 2023 |
| Title |
NK Pt03 Pop4 [CHIP_S104] |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
cell type: CD56dim CD16+ NK cells
participant id: Pt03
participant phenotype: HIVN
antibody: IgG
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, isolated NK cells from ECs, HAARTs and HIVNs were bound to concanavalin A-coated magnetic beads (Bangs Laboratories), followed by cell permeabilization using 0.01% digitonin (Millipore) in wash buffer. Primary antibodies against intracellular H3K27ac, H3K27me3 and H3K4me3 histone marks (Cell Signaling Technology) were added and cells were incubated at 4oC for overnight. Guinea pig anti-rabbit IgG antibody (Antibodies-online) was used as a negative control. The next day, fusion protein CUTANA pA/G-MNase (20x) (Epicypher) was added and cells were incubated at 4oC for 1 hour, followed by chromatin digestion using 100mM CaCl2 (Fisher Scientific). Stop buffer was then added to stop the chromatin digestion. DNA fragments were extracted using phenol chloroform (Invitrogen) and the extracted DNA was eluted in 1mM Tris-HCl pH 8.0 (Fisher Scientific) + 0.1 mM EDTA (Sigma Aldrich).
The DNA library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina Sequencing (New England Biolabs).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
library strategy: CUT&RUN
Raw reads in the FASTQ files were trimmed using trimmomatic (v0.36) and aligned to human reference genome (hg38) using bowtie2 (v2.2.9).
Duplicated reads were marked using Picard (v2.8.0).
Peaks were called using macs2 (v2.1.1.20160309).
Assembly: GRCh38
Supplementary files format and content: peaks
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| Submission date |
May 19, 2023 |
| Last update date |
Dec 05, 2023 |
| Contact name |
Ce Gao |
| E-mail(s) |
CGAO4@MGH.HARVARD.EDU
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| Organization name |
Ragon Institute of MGH, MIT and Harvard
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| Lab |
Yu/Lichterfeld Labs
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| Street address |
400 Technology Square
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE232915 |
IL-15-DEPENDENT IMMUNE CROSS-TALK BETWEEN NK CELLS AND DENDRITIC CELLS IN HIV-1 ELITE CONTROLLERS [CUT&RUN] |
| GSE232916 |
IL-15-DEPENDENT IMMUNE CROSS-TALK BETWEEN NK CELLS AND DENDRITIC CELLS IN HIV-1 ELITE CONTROLLERS |
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| Relations |
| BioSample |
SAMN35216026 |
| SRA |
SRX20439675 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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