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| Status |
Public on Oct 08, 2015 |
| Title |
1000_L_32 |
| Sample type |
SRA |
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| Source name |
Liver_Early Lactation_Fert-
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| Organism |
Bos taurus |
| Characteristics |
breed: Holstein
tissue: Liver
timepoint: Early Lactation
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 |
liver by percutaneuos punch (PMID: 12545545)
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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 |
SAMN03099618 |
| SRA |
SRX728632 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1520630_L_32.counts.txt.gz |
95.3 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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