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| Status |
Public on Jul 18, 2024 |
| Title |
VAV05_12d |
| Sample type |
SRA |
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| Source name |
Peripheral Blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral Blood
cell type: Cd14+ Monocyte
treatment: ChAdox1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
To prepare nuclei, we spun 50,000 cells at 500 × g for 5 min, washed the cells with 50 mL of cold 1× PBS, and then centrifuged them at 500 × g for 5 min. Cells were lysed with cold lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 × g for 10 min in a refrigerated centrifuge. Immediately following nuclei preparation, the pellet was resuspended in transposase reaction mix (Illumina). The transposition reaction was carried out for 30 min at 37°C.
ATAC-seq library was constructed by using illumina Tag DNA Enzyme & Buffer kit.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Raw fastq file is trimmed by skewer to get eliminate adaptor sequence of TN5
trimmed fastq file is aligned on Hg19 reference genome by bowtie 2 software
Homer software constructed Tag directories based on aligned bam files
Homer software transformed Tag directories to bedgraph
Assembly: hg19
Supplementary files format and content: bedgraph.gz
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| Submission date |
Oct 25, 2023 |
| Last update date |
Jul 18, 2024 |
| Contact name |
Wonhyo Lee |
| E-mail(s) |
wonhyo6446@unist.ac.kr
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| Organization name |
UNIST
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| Department |
Biological Sciences
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| Street address |
Unist-gil 50
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| City |
Ulju-gun |
| State/province |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE244965 |
Longitudinal Immune Profiling and Corticosteroid Modulation of the Immediate Innate Immune Response to ChAdOx1 nCoV-19 |
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| Relations |
| BioSample |
SAMN37982114 |
| SRA |
SRX22219558 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7864875_VAV05_AZ_12d.bedGraph.gz |
44.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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