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| Status |
Public on Jan 21, 2021 |
| Title |
1: Vehicle-Naive1_WGBS |
| Sample type |
SRA |
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| Source name |
Vehicle-Naive
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| Organism |
Mus musculus |
| Characteristics |
tissue: CD4+ T cells
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| Treatment protocol |
Impregnated and lactating dams were gavaged with vehicle (peanut oil) or 1ug 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)/kg body weight on gestational day 0, 7, 14, and post natal day 2. Offspring were aged to maturity (6-10 weeks old), and CD4+ T cells were purified from naive mice or mice infected with 120 HAU Influenza A virus (HKx31).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Peripheral lymph nodes (cervical, axillary, brachial, inguinal, and sacral) were harvested from naïve adult developmentally exposed mice. Mediastinal lymph nodes were harvested from adult developmentally exposed mice on day 9 post IAV infection. Lymph nodes were processed to single cell suspensions, and CD4+ T cells were purified to >90% purity using the MojoSort Mouse CD4+ T cell negative selection isolation kit protocol (BioLegend, San Diego, CA). DNA was isolated using the DNeasy blood and tissue kit (Qiagen, Valencia, CA), and then processed for whole genome bisulfite sequencing. Genomic DNA was quantified using the Qubit fluorometer (Life Technologies, Grand Island, NY). DNA integrity was determined using the TapeStation with genomics DNA tape reagents (Agilent, Santa Clara, CA).
Methylation libraries were generated with Illumina’s TruSeq DNA Methylation Kit.Briefly, bisulfite conversion was carried out on 100 ng of genomics DNA using Zymo EZ DNA Methylation Gold per manufacturer’s recommendations (Zymo Research, Irvine, CA) and conversion efficiency was determined with the Bioanalyzer 2100 (Agilent, Santa Clara, CA). Single-stranded cDNA was generated and tagged from Bisulfite converted DNA using random hexamers containing a 5` tag followed by terminal tagging to mark the 3` end of the DNA. Illumina specific adaptors were added during PCR amplification. DNA libraries were purified with AmpureXP beads and quantified with Bioanalyzer 2100 and Qubit fluorometer. The amplified libraries were hybridized to the Illumina pair end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Pair end reads of 126nt were generated on the Illumina HiSeq2500 for each sample.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
bcltofastq-2.19.0
trim_galore-0.4.3, "--paired --clip_r1 8 --clip_r2 8 --three_prime_clip_r1 8 --three_prime_clip_r2 8"
bismark-0.18.1, bismark "--bowtie2 --maxins 1000 --multicore 3"
bismark-0.18.1, filter_non_conversion
bismark-0.18.1, deduplicate_bismark
smtools-1.4.1, sort
MethylKit-1.4.0, processBismarkAln "save.context="CpG",read.context="CpG",nolap=TRUE,mincov=2,minqual=10,phred64=FALSE"
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited, MethylKit CpG extracted data
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| Submission date |
Jan 17, 2020 |
| Last update date |
Jan 21, 2021 |
| Contact name |
B. Paige Lawrence |
| E-mail(s) |
Paige_Lawrence@URMC.Rochester.edu
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| Organization name |
University of Rochester
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| Street address |
601 Elmwood Ave.
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| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14624 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE143893 |
Whole Genome Bisulfite Sequencing of CD4+ T cells from mice developmentally exposed to vehicle or TCDD prior to and during influenza infection |
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| Relations |
| BioSample |
SAMN13878776 |
| SRA |
SRX7578538 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4276332_Vehicle-Naive1_CpG.txt.gz |
201.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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