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| Status |
Public on Dec 26, 2020 |
| Title |
S43-3 |
| Sample type |
SRA |
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| Source name |
S43, dorsal muscle
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| Organism |
Microhyla fissipes |
| Characteristics |
developmental stage: Stage 43
collection site: Shuangliu, Chengdu, China (30.5825o N, 103.8438o E)
tissue: dorsal muscle
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| Growth protocol |
Tadpoles were fed with spirulina powder once daily
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each sample was extracted and purified using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. After purified with poly-T oligo-attached magnetic beads, the mRNAs were fragmented.
First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H−). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3′ ends of the DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To preferentially select cDNA fragments of 150–200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then, PCR was performed with a Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) primer. Finally, PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq 4000 platform by NovoGene (Beijing), and paired-end reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
dorsal muscle of S43
Microhyla_fissipes_unigene.fasta
Microhyla_fissipes_merged_fpkm.txt
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The total clean reads from all libraries were assembled using Trinity as a reference transcriptome.
The expression level of each unigene was expressed as fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: de novo assembly (.fasta file includes the sequences of all unigenes)
Supplementary_files_format_and_content: .txt file includes FPKM values for all Samples
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| Submission date |
Dec 26, 2017 |
| Last update date |
Dec 26, 2020 |
| Contact name |
xungang wang |
| E-mail(s) |
wangxgucas@163.com
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| Organization name |
Chengdu Institute of Biology, Chinese Academy of Sciences
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| Street address |
No.9 Section 4, Renmin Nan Road
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| City |
Chengdu |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL24441 |
| Series (1) |
| GSE108552 |
Transcriptomic insight into molecular processes of dorsal muscle remodeling during Microhyla fissipes metamorphosis |
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| Relations |
| BioSample |
SAMN08243467 |
| SRA |
SRX3516176 |
| 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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