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| Status |
Public on May 16, 2023 |
| Title |
905 |
| Sample type |
SRA |
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| Source name |
plasma
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| Organism |
Homo sapiens |
| Characteristics |
subject id: 5
tissue: plasma
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Circulating cfDNA was isolated using the QIAamp Circulating Nucleic Acid Kit (Qiagen) from 0.5 mL of frozen serum per study subject. Genomic DNA (gDNA) was isolated from ~5 mg of frozen DLPFC using the Monarch Genomic DNA Purification Kit (New England Biolabs).
To obtain sequencing-amenable ~200 bp fragments of gDNA from brain samples, we performed enzymatic fragmentation using the KAPA HyperPlus Kit (Roche). After ligation of unique dual index barcoded sequencing adapters, DNA fragments proceeded through the 5hmC-Seal protocol to construct sequencing libraries.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
library strategy: 5hmC-Seal-seq
Bcl2fastq v2.17 software used to change the bcl files to fastq files.
Sequenced reads were trimmed for adaptor sequence using software trimmomatic v0.36, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using bowtie v2.26
Duplicate reads were marked using picard v1.141. The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts v1.5.0-p3.
Assembly: hg19
Supplementary files format and content: A CSV file include edgR normalized 5hmC levels for all sample.
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| Submission date |
May 18, 2022 |
| Last update date |
May 23, 2023 |
| Contact name |
Zhou Zhang |
| E-mail(s) |
[email protected]
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| Organization name |
Northwestern University
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| Department |
Preventive Medicine
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| Street address |
680 North Lake Shore Drive, Suite 1400
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE203337 |
Genome-wide Mapping Implicates 5-Hydroxymethylcytosines in Diabetes and Alzheimer’s Disease |
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| Relations |
| BioSample |
SAMN28535083 |
| Supplementary data files not provided |
| Processed data are available on Series record |
| Raw data not provided for this record |
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