|
| Status |
Public on Jul 22, 2015 |
| Title |
Low gain, low intake [20113092] |
| Sample type |
SRA |
| |
|
| Source name |
Low gain_low intake
|
| Organism |
Bos taurus |
| Characteristics |
breed: Crossbred
gender type: male; steer
age: 344 ± 48-days
feed gain and intake group: Low gain_low intake
tissue: rumen papillae
|
| Treatment protocol |
No specific treatment. Animals were chosen for this study based on the cartesian quadrant that they were allocated to based on their gain and dry matter intake.
|
| Growth protocol |
Steers had ad libitum access to a ration consisting of: 57.35% dry-rolled corn, 30% wet distillers grains soluble, 8% alfalfa hay, 4.25% steakmaker (Land O'Lakes Feed LLC, Gray Summit, MO, USA), and 0.4% urea.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Papillae were clipped from the rumen wall and immediately frozen in liquid nitrogen. 50-100mg of tissue were homogenized in TriZol reagent. Manufacturers protocol was followed.
oligo-dt beads were used to select poly-adenylated RNA to be sheared to appropriate size for the synthesis of cDNA. The resulting double stranded cDNA was end-repaired and A-tailed in preparation for adaptor ligation. Adaptors were indexed and ligated to the cDNA, which was then size selected on a 2% SizeSelect™ E-Gel (Invitrogen, Carlsbad, CA, USA). The size selected cDNA was amplified via polymerase chain reaction. Library quality was assessed by measuring nanomolar concentration and the fragment size in base pairs. All 16 samples were sequenced at 1×50 basepairs per sequence read.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Sequences were mapped to the reference Bos taurus genome UMD 3.1 using tophat (version 2.08b)
align reads across splice junctions between exons annotated by Ensembl (version 3.1.70)
The resulting alignments were combined to create clusters of reads (or patches), which represented non-redundant genomic regions in the reference genome sequence. Cluster boundaries were created by taking all samples into account during the cluster generation to define the left-most and right-most end coordinates of each cluster. Only uniquely mapped reads were taken into consideration.
Clusters created in this manner underwent linear normalization by multiplying each sample’s locus coverage by the total reads of the lowest read-count sample divided by the respective sample's total reads. This normalized expression data was the basis for the expression comparison.
The comparative expression approach stepped through each cluster and compared every possible pairing of samples and generated a log2 (A/B), where A and B were the two normalized average coverage of each sample, A and B. Pairwise P-values were determined among the samples using Welch's t-test for unequal variance. The resulting comparative expressions were visualized in ActiveSite (Cofactor Genomics).
Genome_build: UMD3.1 Genome Assembly
|
| |
|
| Submission date |
Jul 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Amanda K Lindholm-Perrry |
| E-mail(s) |
amanda.lindholm@ars.usda.gov
|
| Phone |
402-762-4189
|
| Organization name |
USMARC
|
| Department |
NEMRU
|
| Street address |
State Spur 18D
|
| City |
Clay Center |
| State/province |
NE |
| ZIP/Postal code |
68933 |
| Country |
USA |
| |
|
| Platform ID |
GPL11153 |
| Series (1) |
| GSE71153 |
Transcriptome differences in the rumen of beef steers with variation in feed intake and gain |
|
| Relations |
| BioSample |
SAMN03892188 |
| SRA |
SRX1113895 |
