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Status |
Public on Oct 08, 2015 |
Title |
164_M_4 |
Sample type |
SRA |
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Source name |
Muscle_Late Pregnancy_Fert-
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Organism |
Bos taurus |
Characteristics |
breed: Holstein tissue: Muscle timepoint: Late Pregnancy fertility group: Fert-
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Treatment protocol |
Percutaneuos punch [PMID: 22365213]
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Growth protocol |
PMID: 22365213
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Extracted molecule |
polyA RNA |
Extraction protocol |
Standard trizol extraction [PMID:2440339] Illumina TruSeq v2 kit
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
semitendinosus muscle (PMID: 22720928)
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Data processing |
Basecalls using CASAVA 1.8 Trimming; Trimmomtatic sliding window from end 30 or below removed; Alignment; STAR, Dobin et al doi:10.1093/bioinformatics/bts635, version 2.2.0; default run except ‘--outFilterMismatchNoverLmax’ set to 0.02 (i.e. 2 mismatches per 100bp) Count generation; featureCounts, flags -p, -P, -C, and with a maximum insert size of 590 kb flag –D Filtering by FPKM following TMM normalisation of the library using edgeR, retained 18,000 genes Genome_build: UMD3.1.70 (close to Bos_taurus_UMD_3.1 with the ENsembl build version 70) 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 Supplementary_files_format_and_content: The *1-48.count.txt files contain all 48 counts files from each tissue group.
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Submission date |
Oct 08, 2014 |
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 |
GPL15749 |
Series (1) |
GSE62159 |
Liver and muscle gene expression and cow fertility at late pregnancy, early lactation and mid lactation |
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Relations |
BioSample |
SAMN03099638 |
SRA |
SRX728652 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1520650_M_4.counts.txt.gz |
95.5 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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