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| Status |
Public on Oct 03, 2023 |
| Title |
input |
| Sample type |
SRA |
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| Source name |
cortex
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| Organism |
Mus musculus |
| Characteristics |
tissue: cortex
genotype: WT
Sex: male
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed with 600ul of lysis buffer contaning 100mM Tris-HCl, Ph8.5, 5mM EDTA, 0.2% SDS, 200mM NaCl, and 25ul of protease K.Following lysis, RNase A was added and phenol:chloroform:isoamyl alcohol (25:24:1) was used to extract DNA. The Covaris ME220 was used to sonicate gDNA into ~200-300bp fragments. 5hmC was labeled with UDP-6-N3-Glu βGT and biotin. Invitrogen Dynabeads® MyOne™ Streptavidin C1 were used to pull down the biotin labeled 5hmC.
5hmC capture libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® manufacturers protocol
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
WT3
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| Data processing |
Paired end reads were trimmed using Trimmomatic/0.36. Illumina adapters were removed from reads, bases with a pred score below 20 were trimmed off the end of the read, and a sliding window set at 4:15 was used to remove remaining low-quality bases.
owtie2 was used to align the paired-end reads to NCBI37v1/mm9 genome.
Samtools/1.9 was used to remove duplicate reads, sort, and index the reads mapped
5hmC peaks were called on grouped samples using the MACS2 peak calling software with 5hmC capture and non-pulldown input libraries (q <=0.05)
Differential peak analysis was performed using bdgdiff within the MACS2 peak calling software
Assembly: mm9
Supplementary files format and content: narrowPeak (except for Input sample)
Library strategy: 5hmC-Capture
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| Submission date |
Feb 24, 2023 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Matthew J Armstrong |
| E-mail(s) |
[email protected]
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| Organization name |
Emory University
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| Street address |
615 Michael St
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| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE226043 |
Role of TET1-mediated epigenetic modulation in Alzheimer’s disease [5hmC-Capture] |
| GSE226056 |
Role of TET1-mediated epigenetic modulation in Alzheimer's disease |
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| Relations |
| BioSample |
SAMN33435070 |
| SRA |
SRX19495352 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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