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| Status |
Public on Nov 13, 2014 |
| Title |
1153 |
| Sample type |
SRA |
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| Source name |
endometrium
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| Organism |
Bos taurus |
| Characteristics |
tissue: ipsilateral uterine horn
timepoint: day 7 oestrus
fertility group: Fert- ('low fertility')
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| Treatment protocol |
Washed in PBS, connective tissue removed, snap-frozen in liquid nitrogen, stored -80 freezer
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| Growth protocol |
See Cummins et al doi:10.3168/jds.2011-4742
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Standard trizol extraction see Chomczynski doi:10.1016/0003-2697(87)90021-2
Illumina TruSeq v1 kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
E_4
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| Data processing |
Basecalls using CASAVA 1.4
Alignment; STAR, Dobin et al doi:10.1093/bioinformatics/bts635, version 2.2.0; default run except --outFilterMismatchNmax 2; only first fastq files usd in case of paired-end data
Count generation; HTSeq-count, version 0.3p7; -m union -t exon -i gene_id -s no
Filtering by RPKM; removal of bottom 25% of lowest abundance genes ranked by RPKM calculated as ((10^9*count)/(total counts in sample*length of gene)) following TMM normalisation of the library using edgeR; bottom 25% per condition removed, excluding E_5 of Fert-; 15,524 bovine genes retained
Genome_build: UMD3.1.69
Supplementary_files_format_and_content: Format: tab separated; content: column1=bovine gene ID, column2=number of sequence reads overlapping bovine gene ID as defined by GTF, using the HTSeq-count 'union' method
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| Submission date |
Nov 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Bruce Moran |
| E-mail(s) |
bruce.moran@gmail.com
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| Organization name |
St. Vincent's University Hospital
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| Department |
Dept. of Pathology
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| Lab |
Molecular Lab
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| Street address |
Nutley Lane, Dublin 4
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| City |
Dublin |
| ZIP/Postal code |
D4 |
| Country |
Ireland |
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| Platform ID |
GPL15750 |
| Series (1) |
| GSE52438 |
Endometrial gene expression and cow fertility |
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| Relations |
| BioSample |
SAMN02404550 |
| SRA |
SRX378131 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1266822_E_4.de.counts.txt.gz |
73.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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