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| Status |
Public on Jul 13, 2022 |
| Title |
BEND77 |
| Sample type |
SRA |
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| Source name |
Uterus
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| Organism |
Bos taurus |
| Characteristics |
tissue: Non-Pregnant
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen tissues (60-100 mg) using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The total RNA concentration was determined using NanoDrop One (Thermo Fisher Scientific, Madison, WI). RNA quality was determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France).
RNA libraries were prepared for sequencing using standard lllumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
hisat2-build was used too index genome (Bos_taurus.ARS-UCD1.2.dna.toplevel.fa)
hisat2 was used to align against the genome
samtools was used to sort SAM files
htseq_counts was used to produce raw counts
DESeq2 was used for differential gene expression analysis
Genome_build: Bos_taurus.ARS-UCD1.2
Supplementary_files_format_and_content: xlsx; contains raw read counts and DESeq2 results
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| Submission date |
Feb 15, 2022 |
| Last update date |
Jul 13, 2022 |
| Contact name |
Vedbar S Khadka |
| E-mail(s) |
[email protected]
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| Phone |
8086921462
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| Organization name |
JABSOM Bioinformatics Core, University of Hawaii
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| Lab |
Vedbar S Khadka
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| Street address |
651 IIalo Street
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| City |
Honolulu |
| State/province |
HI |
| ZIP/Postal code |
96813 |
| Country |
USA |
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| Platform ID |
GPL23055 |
| Series (1) |
| GSE196789 |
RNA-Sequencing based analysis of bovine endometrium during the maternal recognition of pregnancy |
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| Relations |
| BioSample |
SAMN25977552 |
| SRA |
SRX14191156 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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