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| Status |
Public on Apr 30, 2020 |
| Title |
Analyses of methylomes of multiple tissues in cattle |
| Organism |
Bos taurus |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
In this study, we generated whole genome bisulfite sequencing data of 19 samples for 13 tissues in Holstein cattle. We analyzed the variations of DNA methylation among tissues.
In this study, we generated whole genome bisulfite sequencing data of 6 samples for 5 tissues in Hereford cattle. We analyzed the variations of DNA methylation among tissues.
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| Overall design |
Genomic DNA for each tissue was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA). The quality of DNA samples was evaluated using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) including degradation, and potential RNA contamination, and purity (OD260/OD280), and concentration using a spectrophotometer (NanoDrop Technologies, Rockland, DE) to meet the requirements for library construction. The qualified genomic DNA from somatic tissues and sperm were used to construct a library. The library different lanes of a HiSeq X Ten (Illumina, San Diego, CA, USA) to generate 150-bp paired-end reads by Novogene (Novogene, Beijing, China).
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| Citation(s) |
32631327, 32620158 |
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| Submission date |
Mar 17, 2020 |
| Last update date |
Aug 02, 2020 |
| 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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| Platforms (1) |
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| Samples (25)
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| GSM4238272 |
Holstein, Blood_2_WGBS |
| GSM4238273 |
Holstein, Heart_1_WGBS |
| GSM4238274 |
Holstein, Ileum_1_WGBS |
| GSM4238275 |
Holstein, Kidney_1_WGBS |
| GSM4238276 |
Holstein, Ldorsi_1_WGBS |
| GSM4238277 |
Holstein, Ldorsi_2_WGBS |
| GSM4238278 |
Holstein, Liver_1_WGBS |
| GSM4238279 |
Holstein, Lung_1_WGBS |
| GSM4238280 |
Holstein, Lung_2_WGBS |
| GSM4238281 |
Holstein, Ovary_1_WGBS |
| GSM4238282 |
Holstein, Rumen_1_WGBS |
| GSM4238283 |
Holstein, Rumen_2_WGBS |
| GSM4238284 |
Holstein, Spleen_1_WGBS |
| GSM4238285 |
Holstein, Uterus_1_WGBS |
| GSM4238286 |
Holstein, Placenta_1_WGBS |
| GSM4238287 |
Holstein, Placenta_2_WGBS |
| GSM4416578 |
Hereford, Adipose_Dt, WGBS |
| GSM4416579 |
Hereford, Heart_Dt, WGBS |
| GSM4416580 |
Hereford, Jejun_Do, WGBS |
| GSM4416581 |
Hereford, Jejun_Dt, WGBS |
| GSM4416582 |
Hereford, Kidney_Dt, WGBS |
| GSM4416583 |
Hereford, Liver_Do, WGBS |
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| Relations |
| BioProject |
PRJNA612978 |
| SRA |
SRP254023 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE147087_RAW.tar |
6.4 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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