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| Status |
Public on Aug 01, 2022 |
| Title |
Healthy cow - rep3 |
| Sample type |
SRA |
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| Source name |
Healthy cow
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| Organism |
Bos taurus |
| Characteristics |
tissue: placenta
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| Extracted molecule |
total RNA |
| Extraction protocol |
Placentome were collected after parturtion. Small cuboid samples were taken from the fetomaternal conjunction sites of placentome. The samples from each cow pooled and snap frozen in liquid nitrogen. RNAs harvested from the samples were used for RNA-sequencing using Illumina HiSeq 2500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
SO_Healthy3_1881_R1
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| Data processing |
Illumina Casava1.7 software used for basecalling.
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left for further analyzes. Then, the sequences were mapped to ARS-UCD1.2 whole bovine genome using HISAT2.
Read counts obtained using featureCounts and finally raw read counts were used for DEG analysis using edgeR.
Genome_build: HISAT2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jan 19, 2022 |
| Last update date |
Aug 01, 2022 |
| Contact name |
Mehdi Moradi |
| Organization name |
University of Tehran
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| Department |
Animal Science
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| Street address |
Daneshkadeh st.
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| City |
Karaj |
| State/province |
Alborz |
| ZIP/Postal code |
31587-77871 |
| Country |
Iran |
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| Platform ID |
GPL24230 |
| Series (1) |
| GSE194033 |
RNA-seq study on the placentomes collected from the cows with or without retained placenta |
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| Relations |
| BioSample |
SAMN25124857 |
| SRA |
SRX13833712 |
| 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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