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| Status |
Public on Apr 07, 2021 |
| Title |
Sample1 |
| Sample type |
SRA |
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| Source name |
Endometrium
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| Organism |
Bos taurus |
| Characteristics |
tissue: Endometrium
breed: Angus x Brahman
p4: 0.72
block: 1
pregnancy: 1
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using RNeasy Mini Kit (Qiagen, Valencia, CA). RNA concentration and quality were determined using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, Waltham, MA). Bioanalyzer and Qubit RNA integrity numbers ranged between 5.6 and 8.7, and between 6.9 and 9.4, respectively.
All the RNA-sequencing procedures were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China). Sequencing libraries were prepared using a Poly-A tail capture method and sequenced with NovaSeq 6000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using Hisat2 sofware (version 2.1.0).
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Bovine genome assembly: (ARS-UCD1.2)
Supplementary_files_format_and_content: Tab-delimited text files including ensembl gene id and number of mapped reads
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| Submission date |
Apr 06, 2021 |
| Last update date |
Apr 07, 2021 |
| Contact name |
Francisco Peñagaricano |
| E-mail(s) |
fpenagarican@wisc.edu
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| Organization name |
University of Wisconsin-Madison
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| Department |
Animal and Dairy Sciences
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| Street address |
1675 Observatory Drive
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| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE171577 |
Endometrial luminal epithelium transcriptome during early diestrus defines pregnancy outcome in cattle |
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| Relations |
| BioSample |
SAMN18636357 |
| SRA |
SRX10522925 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5227638_Sample1.txt.gz |
111.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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