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| Status |
Public on Dec 31, 2014 |
| Title |
Rex rabbit, back skin, 42 days, black color(B) |
| Sample type |
SRA |
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| Source name |
Back skin
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| Organism |
Oryctolagus cuniculus |
| Characteristics |
age (days): 42 days
phenotype: black color(B)
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| Treatment protocol |
For anesthesia, 5 ml 0.5% sodium pentobarbital solution was injected into the ear vein of the rabbits. After anesthesia, a 1-cm2 skin tissue sample was obtained from the backs of the animals, placed immediately in liquid nitrogen, and preserved at –80°C until use. An iodine solution was smeared on the resultant lesion to prevent bacterial infection.
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| Growth protocol |
The three Rex rabbits used for this study were purchased from Yuyao Xinnong Rabbit Co., Ltd. (Zhejiang, China). These animals were healthy, were born in the same nest by one mother, and were raised under the same conditions for 42 days (at the first molt) to minimize the impact of genetic background and environment on fur color.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the back skin of the Rex rabbits using TRIzol reagent (Invitrogen, USA). A Qubit fluorometer (Invitrogen, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., USA) were used to determine the quality and quantity of the RNA. The mRNA was enriched using oligo (dT) magnetic beads, then fragmented into short fragments (approximately 200-700 nt) using fragmentation buffer (Invitrogen, USA). Double-stranded cDNA product was synthetized and purified .
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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| Description |
Gene expression about back skin of black Rex rabbit in 42 days
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| Data processing |
The library was sequenced using IlluminaHiSeqTM 2000 (Illumina, USA)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then mapped to the rabbit genome in the Ensembl database.
If the alignment results passed the QC assessment, the samples were then subjected to downstream analysis, including gene expression, gene structure refinement, alternative splicing, novel transcript prediction and annotation, and SNP detection.
The level of gene expression was calculated as RPKM (reads per kilobase transcriptome per million mapped reads), differentially expressed Genes (DEGs) were identified using an FDR≤0.001 (false discovery rate no greater than 0.05)
Cluster v3.0 and javaTreeview v1.1.1 were used forExpression pattern analysis of DEGs. Gene Ontology functional analysis was based on GO::TermFinder. KEGG (major public pathway-related database) is used in our pipeline to perform pathway enrichment analysis of DEGs for further understand genes biological functions.
Genome_build: The rabbit genome in the Ensembl database
Supplementary_files_format_and_content: Tables include RPKM values, coverage for each Sample.
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| Submission date |
Mar 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lizhi Qin |
| E-mail(s) |
qlz814709954@163.com
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| Phone |
15052510276
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| Organization name |
Yangzhou University
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| Department |
College of Animal Science and Technology
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| Street address |
No.48 Wenhui East Road
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| City |
Yangzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
225009 |
| Country |
China |
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| Platform ID |
GPL18453 |
| Series (1) |
| GSE55927 |
Analysis of genes that control fur color formation in domestic rabbits using Solexa sequencing |
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| Relations |
| BioSample |
SAMN02693835 |
| SRA |
SRX498112 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1356023_Sample_B.Gene.rpkm.txt.gz |
266.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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