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| Status |
Public on May 05, 2021 |
| Title |
CHR2 |
| Sample type |
SRA |
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| Source name |
rumen epithelium
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| Organism |
Bos taurus |
| Characteristics |
tissue: rumen epithelium
feed efficiency: Low
breed: Charolais
backfat_thickness_mm: 6.67
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| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 100 mg of frozen tissue samples were ground to fine powder in a sterilized mortar and then rumen epithelium, liver, and muscle tissue samples were applied to isolate the total RNA using a mirVana total RNA Isolation Kit (Ambion, Carlsbad, CA, USA) while backfat tissue was applied to isolate total RNA using RNeasy Lipid Tissue Mini Kit (Qiagen, Germany) following the manufacturer’s instructions. The RNA was quantified using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and checked for purity and integrity using the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). RNA with the ration of 28S/18S ranging from 1.7 to 2.4 and the RNA integrity number greater than 7.0 was used for RNA-Seq library construction.
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 4000 |
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| Description |
R34_accepted_hits.bed
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| Data processing |
Low-quality bases and adapter sequence was trimmed and quality of reads was filtered using fastq-mcf with parameters quality score ³ 20 and length ³ 75
The cleaned reads were then aligned to the reference bovine genome UMD3.1 (http://bovinegenome.org/?q=umd_downloads) and assembled with TopHat2 (v2.0.9) software package
Samtools (v1.1) was then applied to generate BAM alignment files and convert them into SAM format
HTSeq-count (v0.6.1) was used to quantify the number of mapped reads per each bovine gene
the number of mapped reads was normalized into counts per million (CPM) according to the formula: CPM = (number of reads mapped to a gene) ÷ (total number of reads mapped to all annotated genes) × 106.
Genome_build: bovine genome UMD3.1 (http://bovinegenome.org/?q=umd_downloads)
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample
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| Submission date |
Jul 09, 2018 |
| Last update date |
May 05, 2021 |
| Contact name |
Huizeng Sun |
| E-mail(s) |
huizeng@zju.edu.cn
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| Organization name |
Zhejiang University
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| Department |
College of Animal Sciences
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| Lab |
Functional Genomics and Microbiology
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| Street address |
866 Yuhangtang Road
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL23295 |
| Series (1) |
| GSE116775 |
Beef cattle multi-tissue transcriptome |
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| Relations |
| BioSample |
SAMN09630944 |
| SRA |
SRX4367549 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3261641_E34_ht_test.txt.gz |
97.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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