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| Status |
Public on Dec 12, 2017 |
| Title |
NP-IF (#11807) |
| Sample type |
SRA |
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| Source name |
Infertile_Non-pregnant_Endometrium
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| Organism |
Bos taurus |
| Characteristics |
breed: Heifer cow
fertility: Infertile
pregnancy: Non-pregnant
tissue: Endometrium
hf conceptus size: N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the endometrium samples was extracted using the Isol-RNA Lysis Reagent (5Prime, Hamburg, Germany). Total RNA from the conceptuses was extracted using the AllPrep DNA/RNA/Protein Mini kit (Qiagen, Valencia, CA).
RNA library preparation and sequencing was conducted by the University of Missouri DNA Core facility. Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded sample preparation kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
807_S2
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| Data processing |
The raw sequences (fastq) were subjected to adapter removal and quality trimming using fqtrim (https://ccb.jhu.edu/software/fqtrim/).
The quality reads were then mapped to the bovine reference genome UMD3.1 using Hisat2 mapper (https://ccb.jhu.edu/software/hisat2/) .
To produce a global gene annotation file (GTF) for comprehensive quantification of gene expressions across the samples, the sorted binary alignment maps of sequence reads from each sample were assembled to generate transcriptomes those were then merged, along with the gene annotations from reference genome assembly.
The transcript assembly step was accomplished using the software ‘Stringtie’ (https://ccb.jhu.edu/software/stringtie/) .
The merged global transcriptome was then used in Stringtie to quantify transcript abundance of each sample. Differential expression analysis between sample groups were performed by robustly fitting the expression data to a weighted generalized linear model using edgeR robust.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-limited text file of read count data.
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| Submission date |
Dec 11, 2017 |
| Last update date |
Dec 14, 2017 |
| Contact name |
Thomas Spencer |
| E-mail(s) |
spencerte@missouri.edu
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| Organization name |
University of Missouri
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| Department |
Animal Sciences
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| Lab |
ASRC 158
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| Street address |
920 East Campus Drive
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| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
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| Platform ID |
GPL23055 |
| Series (1) |
| GSE107891 |
Uterine Influences on Conceptus Development in Fertility-Classified Animals |
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| Relations |
| BioSample |
SAMN08159679 |
| SRA |
SRX3461000 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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