|
| Status |
Public on Jun 03, 2022 |
| Title |
control [N04] |
| Sample type |
SRA |
| |
|
| Source name |
cord blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cord blood
disease state: healthy
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cord blood (approximately 50-75ml) were collected from each donor during delivery. Lymphoprep (Serumwerk Bernburg cat.1858) was used to isolate mononuclear cells (MNCs) from the cord blood. Red blood cells were lysed using RBC lysing buffer (Biolegend cat. 420310). Cells were recovered from liquid nitrogen.
Approximately 10K cells were processed following the established ATAC-Seq protocol [Buenrostro et al. Nat. Methods 2013]
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
MGISEQ-2000RS |
| |
|
| Data processing |
Raw ATAC-seq reads were mapped to hg38 reference genome using Bowtie
Duplicates were removed with MarkDuplicates function from Picard Tools (version:2.26.11) with default parameters
Low quality reads with mapping quality (mapQ) lower than 30 were removed using samtools. Reads mapped to ChrX, Y and Random were filtered.
MACS2 (version: 2.2.7.1) was used for peak calling with parameters -nomodel -shift -100 -extsize 200.
HTseq-count(version: 1.99.2) was used for counting reads within each peak.
Assembly: hg38
|
| |
|
| Submission date |
Mar 26, 2022 |
| Last update date |
Jun 03, 2022 |
| Contact name |
Xiaonan Wang |
| E-mail(s) |
xiaonanwang@shsmu.edu.cn
|
| Organization name |
Shanghai Jiaotong University
|
| Department |
School of Public Health, School of Medicine
|
| Street address |
227 Chongqing South Road
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL30209 |
| Series (1) |
| GSE199479 |
Preliminary Interpretations of Epigenetic Profiling of Cord Blood in Preeclampsia |
|
| Relations |
| BioSample |
SAMN26982645 |
| SRA |
SRX14624397 |
