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| Status |
Public on Dec 31, 2018 |
| Title |
hibernation adipose DGE |
| Sample type |
SRA |
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| Source name |
adipose tissue
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| Organism |
Myotis ricketti |
| Characteristics |
state: hibernation
developmental stage: adult
tissue: adipose
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| Treatment protocol |
Tissues of Myotis ricketti in hibernating and aroused states, which were collected and stored at -80 ºC, were used for RNA extraction and library preparation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
According to the manufacturerâs instruction, total RNA was isolated from bat brain and adipose tissues of hibernating and active states by the RNAiso kit (TakaRa). Five microgram total RNA of each was incubated with oligo-dT beads to capture the polyadenlyated RNA fraction, and double strand cDNA were synthesized while the RNA was bound to the beads. Then cDNA fragments were digested with NlaIII to bring a CATG site at the most 3â end, and ligated with the GEX adapter 1 which contains MmeI restriction site. After digested with MmeI, 21 nt fragments (contains a 17 nt tag) were extracted by dephosphorylation and phenol, and ligated with the GEX adapter 2 which contains the sequencing primers. Subsequently, the PCR was performed with two primers that anneal to the ends of the GEX adapter 2 to selectively enrich the cDNA tags. Finally, the Illumina Cluster Station and Solexa Genome Analyzer II were programmed for subsequent cDNA tags sequencing and the quantitative expression level of the unique transcripts was demonstrated by the number of times the sequence was detected.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Solexa Digital Gene Expression (DGE) sequencing
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| Data processing |
Total 17,792 genes were annotated based on the current 1.7 Ã coverage genome of microbat (Myotis lucifugus) and used as reference genes (Hubbard et al. 2002). According to the Solexa tags preparation, the 3â most CATG sites within 3 Kb of 3â UTR for each reference gene were identified by in-house Perl script and used to construct the reference tag dataset. After removing the adapter contaminants and the low quality tags (containing Ns), the clean Solexa tags of each library were mapped onto the gene reference tag dataset separately by SOAP (Li et al. 2008). Only perfect matches were considered, and no mismatches were allowed. For genes that have multi-tags were found in Solexa tags, only the 3â most expressed tags were taken into account as the gene expression value. Whereas, for tags that mapped onto different genes, the mean value of tag number was used as the expression level for each gene.
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| Submission date |
May 04, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Lihong Yuan |
| E-mail(s) |
yuanlh@gdei.gd.cn
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| Phone |
13005180367
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| Organization name |
Guangdong Entomological Institute
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| Street address |
105 Xin-gang Xi road
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510260 |
| Country |
China |
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| Platform ID |
GPL18718 |
| Series (1) |
| GSE29052 |
Screen of differential expression genes on bat hibernating regulation |
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| Relations |
| SRA |
SRX060865 |
| BioSample |
SAMN00263094 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM720037_dge_MY1-ZF_Clean_Tag.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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