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| Status |
Public on Nov 04, 2016 |
| Title |
M_N3 |
| Sample type |
SRA |
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| Source name |
Upper jaw skin
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| Organism |
Leptobrachium boringii |
| Characteristics |
strain: wild type
tissue: Upper jaw skin
developmental stage: Breeding period
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues of brain, testis and upper jaw skin were removed, and RNA was harvested using Trizol reagent. Illumina NEBNext® Ultra™ RNA Library Prep Kit (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
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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| Data processing |
Illumina CASVA 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence through in-house perl scripts, then mapped to the assembled Unigene sequences using RSEM 1.2.0 with Bowtie allowing mismatchs of no more than two bases (Bowtie default parameter).
The left files (read1 file) from all samples were pooled into one big left.fq file, and right files (read2 file) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (r2012-10-05) with min_kmer_cov set to 2 by default and all other parameters set defalut.Unigenes was selected from the longest transcript copy of each gene clusters using in-house Perl scripts to avoid redundant transcripts.
Gene expression level for each sample were estimated using the software package RSEM (v 1.2.0) based on the expectation-maximization (EM) algorithm. Firstly, clean reads of each sample were mapped back onto the assembled transcripts. Then, the read count for each gene was obtained from the mapping results. The gene expression level was estimated by calculating the fragments per kb per million reads (FPKM).
Genome_build: Assembly Unigene.fasta
Supplementary_files_format_and_content: xls files include Readcount and FPKM values for each Sample,and fasta file is the assembled Unigene sequence.
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| Submission date |
Oct 21, 2016 |
| Last update date |
Nov 04, 2016 |
| Contact name |
Wei Zhang |
| E-mail(s) |
454130770@qq.com
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| Organization name |
Central China Normal University
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| Street address |
Luoyu
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| City |
Wuhan |
| State/province |
Hubei Province |
| ZIP/Postal code |
430079 |
| Country |
China |
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| Platform ID |
GPL22593 |
| Series (1) |
| GSE89016 |
Transcriptome analysis reveals the genetic basis underlying the seasonal development of keratinized nuptial spines in Leptobrachium boringii |
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| Relations |
| BioSample |
SAMN05933047 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2357429_M_CN.Readcount_FPKM.txt.gz |
466.7 Kb |
(ftp)(http) |
TXT |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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