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| Status |
Public on Mar 01, 2022 |
| Title |
DtRum |
| Sample type |
SRA |
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| Source name |
Rumen
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| Organism |
Bos taurus |
| Characteristics |
breed: Hereford
tissue: Rumen
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The qualified genomic DNA from somatic tissues and sperm were used to construct libraries. Briefly, 3 μg of genomic DNA spiked with unmethylated lambda DNA were fragmented into 200-300 bp using a Covaris S220 (Covaris, Inc., Woburn, MA, USA), followed by teriminal repairing and A-ligation. Different cytosine methylated barcodes were ligated to sonicated DNA for different samples. The DNA bisufite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). Then single-stranded DNA fragments were amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2 X) (Kapa Biosystems, Wilmington, MA, USA). The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and qPCR (iCycler, BioRad Laboratories, Hercules, CA, USA), and the insert size was checked using the Agilent 2100.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Programs FastQC (0.11.5) and Trim Galore (0.4.5) were used to generate sequence quality reports and to trim/filter the sequences, respectively.
The cleaned data for each sample were merged and aligned to the reference genome (Bos taurus ARS-UCD1.2) using bowtie2 under the Bismark software (0.19.0)
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position,strand, coverage for methylated cytosine, coverage for unmethylated cytosine, CG type, three bases near the cytosine.
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| Submission date |
Jul 21, 2021 |
| Last update date |
Mar 01, 2022 |
| Contact name |
George E. Liu |
| E-mail(s) |
george.liu@usda.gov
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| Phone |
301-504-9843
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| Organization name |
USDA-ARS
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| Lab |
Animal Genomics and improvement Lab.
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| Street address |
10300 Baltimore Ave Bldg 306
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| City |
Beltsville |
| State/province |
Maryland (MD) |
| ZIP/Postal code |
20705 |
| Country |
USA |
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| Platform ID |
GPL24230 |
| Series (1) |
| GSE180577 |
Whole genome bisulfite sequencing of rumen, muscle, placenta, sperm tissues in cattle |
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| Relations |
| BioSample |
SAMN20342760 |
| SRA |
SRX11515761 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5465079_Rumen_DtRum_1_val_1_bismark_bt2_pe.deduplicated.CpG_report.txt.CpG_report.txt.gz |
249.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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