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| Status |
Public on Apr 13, 2022 |
| Title |
Endometrium, r-18 |
| Sample type |
SRA |
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| Source name |
Endometrium
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| Organism |
Bos taurus |
| Characteristics |
tissue: Endometrium
cell type: luminal epithelial cell
cow id: 4-126
time: day 14
treatment: L
p4: 5.58
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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 spectrophotometry (NanoDrop 2000 Spectrophotometer, Thermo Fisher Scientific, Waltham, MA, USA) by absorbance at 260 nm and the 260/280 nm ratios, respectively. Absorbance ratios ranged from 1.8 to 2.1.
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).
Assembly: 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 07, 2022 |
| Last update date |
Apr 13, 2022 |
| 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) |
| GSE200361 |
Concentrations of progesterone prior to luteolysis modulates the uterine luminal transcriptome in the subsequent cycle in cattle |
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| Relations |
| BioSample |
SAMN27401873 |
| SRA |
SRX14774723 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6032056_r_18.txt.gz |
110.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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