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| Status |
Public on Nov 01, 2021 |
| Title |
F24 |
| Sample type |
SRA |
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| Source name |
subcutaneous backfat tissue
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| Organism |
Bos taurus |
| Characteristics |
tissue: subcutaneous backfat tissue
cell type: Adipocytes
breed: Angus
phenotype: Low RFIfat (-1.09 kg)
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| Growth protocol |
Backfat tissue were from Angus, Charolais, and Kinsella composite, including high-RFIfat and low-RFIfat in each breed.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Backfat tissue were applied to isolate total RNA using RNeasy Lipid Tissue Mini Kit.
The isolated RNA from each sample was used to construct a cDNA library for RNA-seq according to the protocol of TruSeq Standed Total RNA Sample Prep Kit. Briefly, the steps included removement of rRNA using Ribo-Zero Gold rRNA Removal Kit (Epicentre Technologies), RNA fragmentation, and cDNA synthesis. The resulting double-stranded cDNA was subjected to end repair and addition of a single A base at 3’-end, followed by ligation of bar-coded adapters. To guarantee the high quality of libraries, cDNA was amplified by 15 cycles of PCR to check its size using Agilent 2200 TapeStation. And cDNA libraries were quantified with a Qubit fluorometer using a Qubit dsDNA HS Assay Kit.
The cDNA libraries with effective concentration (³ 2 nM) were sequenced in 4 lanes on Illumina HiSeqTM 4000 platform to obtain 100-bp paired-end reads (average phred quality score ≥ 33) at the McGill University and Genome Quebec Innovation Centre (Montreal, Quebec, Canada).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Adapter sequence was removed and quality of reads was filtered using fastq-mcf with parameters quality score ³ 20 and length ³ 75.
The remaining reads were aligned to reference bovine genome UMD3.1 and assembled by software package TopHat2 (v2.0.9).
Samtools (v1.1) was used to sort BAM alignment files and then convert them to SAM format.
HTSeq-count (v0.6.1) was used to quantify the number of mapped reads per each bovine gene.
Genome_build: Bovine genome UMD3.1
Supplementary_files_format_and_content: Bam files were generated using TopHat2 (v2.0.9). Sam files were generated using Samtools (v1.1). Txt files were generated using HTSeq-count (v0.6.1).
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| Submission date |
Nov 22, 2017 |
| Last update date |
Nov 01, 2021 |
| Contact name |
Zhi Zhu |
| E-mail(s) |
zhuzhi612@163.com
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| Organization name |
University of Alberta
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| Department |
AFNS
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| Street address |
116 St and 85 Ave
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| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G 2P5 |
| Country |
Canada |
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| Platform ID |
GPL23295 |
| Series (1) |
| GSE107268 |
RNA-seq of backfat tissue in beef cattle |
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| Relations |
| BioSample |
SAMN08057414 |
| SRA |
SRX3415780 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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