|
| Status |
Public on Apr 25, 2012 |
| Title |
SNEB3 |
| Sample type |
SRA |
| |
|
| Source name |
experimental:14d post-calving with restricted diet
|
| Organism |
Bos taurus |
| Characteristics |
energy balance: severe negative
tissue: liver
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from frozen liver tissue by homogenisation in Trizol. RNA was then DNAse treated and purified using Qiagen RNeasy spin columns. Standard Illumina single read mRNA-seq libraries were constructed from cDNA which was made from mRNA which had been purified from total RNA by two rounds of polyA tail selection using oligo dT beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
experimental:14d post-caliving with restricted diet
|
| Data processing |
Basecalls performed using CASAVA version 1.4
RNAseq reads were aligned to Btau4.0 genome using Bowtie (settings: -S -m 1 -n 2 --solexa1.3-quals), sorted and possible PCR duplicates were removed using Samtools.
Raw counts were enumerated using HTSEQ-count (settings: mode = union)
Genome_build: Btau_4.0
Supplementary_files_format_and_content: Tab delimited txt files: First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene.
|
| |
|
| Submission date |
Apr 24, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris Creevey |
| E-mail(s) |
chris.creevey@teagasc.ie
|
| Organization name |
Teagasc
|
| Department |
Animal & Bioscience Research Department
|
| Street address |
Grange
|
| City |
Dunsany |
| State/province |
Co. Meath |
| ZIP/Postal code |
Ireland |
| Country |
Ireland |
| |
|
| Platform ID |
GPL9323 |
| Series (1) |
| GSE37544 |
RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance |
|
| Relations |
| SRA |
SRX144214 |
| BioSample |
SAMN00862585 |
