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| Status |
Public on Jan 01, 2017 |
| Title |
299 |
| Sample type |
SRA |
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| Source name |
Rumen
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| Organism |
Bos taurus |
| Characteristics |
residual feed intake: Low RFI
tissue: rumen epithelial tissue
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| Extracted molecule |
total RNA |
| Extraction protocol |
rumen tissue samples were frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
All the reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
Paired end fastq files were mapped to refenrence genome by using Tophat 2.0.10 with default parameters.
The output mapping files from the TopHat2 alignment, along with the GTF file from ENSEMBL (http://uswest.ensembl.org/) rat gene annotation v75.30, were used in the htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) to count the total number of reads mapped to each gene.
The expression level of mRNAs in each library was obtained by normalizing reads number to counts per million reads (CPM): CPM = (gene reads number / total mapped reads number per library) × 1,000,000.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample
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| Submission date |
Jan 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Guanxiang Liang |
| E-mail(s) |
liangguanxiang@gmail.com
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| Organization name |
University of Alberta
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| Street address |
410 Agriculture/Forestry Centre
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| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G 2P5 |
| Country |
Canada |
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| Platform ID |
GPL15749 |
| Series (1) |
| GSE76501 |
Transcriptome Profiling of the Rumen Epithelial Tissues of Beef Cattle Differing in Residual Feed Intake |
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| Relations |
| BioSample |
SAMN04383553 |
| SRA |
SRX1515300 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2027124_299.txt.gz |
136.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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