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| Status |
Public on Apr 17, 2019 |
| Title |
Filtered_air_sample_6-6 |
| Sample type |
SRA |
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| Source name |
Neonatal cardiomyocytes
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| Organism |
Mus musculus |
| Characteristics |
tissue: Neonatal cardiomyocytes
treatment: Filtered air
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| Biomaterial provider |
University of Washington (Seattle, WA, USA)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from frozen p0 isolated cardiomyocytes using Qiagen (Germantown; MD, USA) DNeasy Blood and Tissue kit, according to the manufacturer’s protocol.
500ng of DNA was digested overnight with MspI (New England BioLabs Inc., Ipswich, MA, USA) and then directly prepared with the KAPA Hyper Library prep protocol (KAPA Biosystems, Wilmington, MA, USA). Samples were then adapter-ligated using SeqCap Adapters (Roche-Nimblegen, Pleasanton, CA, USA), and cleaned using a 2.5X post-ligation Agencourt AMPure XP bead cleanup (Beckman Coulter, Indianapolis, IN). Size selection was performed to a size range of 160bp-340bp on a 2% Pippin Prep gel (Sage Science, Beverly, MA, USA), followed by bisulfite conversion using the Zymo EZ DNA Methylation Lightning kit (Zymo Research, Irvine, CA, USA). The converted DNA was then put back into the KAPA Hyper Library prep protocol at the library amplification step, and amplification was performed with 19 PCR cycles using 2X KAPA Hifi HotStart Uracil+ ReadyMix (KAPA Biosystems, Wilmington, MA, USA). Post-amplification cleanup was performed with 0.8X Agencourt AMPure XP beads (Beckman Coulter). Library size distributions were validated using the Agilent High Sensitivity D1000 ScreenTape run on an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA, USA). Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies- Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sample libraries were sequenced on the Illumina HiSeq 2500. Sequences were processed by discarding the low quality reads using Illumina’s base call quality filter, and raw reads were trimmed of adapter sequences and flanking low quality base reads using the trimmomatic read trimmer, discarding any reads less than 25nt. Reads were aligned to the mm10 genome using the Bismark aligner. Output from Bismark is bedGraph format consisting of five lines; CHR, START, END, %METHYLATION, COUNT METHYLATED, COUNT UNMETHYLATED.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files consist of Bismark bedGraph coverage files.
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| Submission date |
Feb 19, 2018 |
| Last update date |
Apr 17, 2019 |
| Contact name |
James William MacDonald |
| E-mail(s) |
[email protected]
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| Organization name |
University of Washington
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| Department |
Environmental and Occupational Health Sciences
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| Street address |
4225 Roosevelt Way NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105-6099 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE110792 |
In utero exposure to diesel exhaust particulates is associated with alterations of the neonatal cardiomyocyte transcriptome, metabolic parturbation and a global decrease in DNA methylation. [RRBS] |
| GSE110793 |
In utero exposure to diesel exhaust particulates is associated with alterations of the neonatal cardiomyocyte transcriptome, metabolic parturbation and a global decrease in DNA methylation. |
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| Relations |
| BioSample |
SAMN08564257 |
| SRA |
SRX3721323 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3016965_Sample_FA06-6_bismark_merged.bismark.cov.gz |
25.6 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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