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| Status |
Public on Jan 17, 2023 |
| Title |
PITUITARY_3218_MOET |
| Sample type |
SRA |
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| Source name |
Pituitary
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| Organism |
Bos taurus |
| Characteristics |
tissue: Pituitary
embryo origin: MOET
age (days): 102
weight at_birth_(kg): 33
weight at_sample_collection_(kg): 108
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissues samples were shipped in dry ice to the BGI TECH SOLUTIONS Company (Hong Kong), which performed the gDNA extraction, quality control, library preparation, and sequencing. All samples met the requirements for library preparation (GC content between 35%-65% for extracted gDNA).
The gDNA samples were subjected to Whole Genome Bisulfite Sequencing (WGBS), through bisulfite library preparation and PE100 sequencing with 45Gb clean data per sample on DNBSEQ. After library preparation and sequencing, raw data with adapter sequences or low-quality sequences were filtered to remove contamination and obtain valid data. This step was completed by the SOAPnuke software developed by the BGI Company.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
DNBSEQ-G400 |
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| Data processing |
The WGBS clean reads were aligned to the bovine reference genome (bosTau 9) using the Bismark Bisulfite Read Marker (v 0.22.3)
The percent of methylated cytosines was calculated as the number of methylated cytosines/total number of cytosines x 100.
Cytosines were annotated with the nearest (no specific cut-off) transcription start site (TSS) and with gene structures (promoter, exon, intron, CpG islands or shores) through Genomation (Bioconductor/R). Promoters and CpG shore were defined as ± 1000 bp and ± 2000 bp of the TSS and CpG islands, respectively.
Assembly: bosTau 9
Supplementary files format and content: tab delimited text file listing the genomic positions, and the corresponding annotation, the number of methylated cytosines, the total number of cytosines, and the percentage of methylated cytosines at each position.
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| Submission date |
Jan 17, 2023 |
| Last update date |
Jan 18, 2023 |
| Contact name |
Maria Belen Rabaglino |
| E-mail(s) |
m.b.rabaglino@uu.nl
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| Organization name |
Utrecht University
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| Department |
Population Health Science
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| Street address |
Yalelaan 7
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| City |
Utrecht |
| ZIP/Postal code |
3584 CL |
| Country |
Netherlands |
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| Platform ID |
GPL28857 |
| Series (1) |
| GSE223098 |
Epigenomics of metabolic organs from in vitro or in vivo-produced dairy male calves |
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| Relations |
| BioSample |
SAMN32771679 |
| SRA |
SRX19053714 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6939624_PITUITARY_3218_MOET.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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