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Sample GSM1103228

Query DataSets for GSM1103228

Status

Public on Apr 01, 2013

Title

Surface_fish_eye

Sample type

SRA

Source name

eye

Organism

Sinocyclocheilus angustiporus

Characteristics

tissue: eye
age: adult
sample type: surface fish

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated using a TRIzol reagent (Invitrogen) from whole eye and brain of adult surface and cave species respectively. Two individuals were used in each species. Oligo(dT) selection was performed by using MicroPoly(A) PuristTM (Ambion) according to the manufacturer's protocol. Superscript III First-Strand Synthesis System (Invitrogen) was used to create first-strand cDNA. The second-strand cDNA was synthesized using random primers and Klenow exo- polymerase (Epicentre). cDNA was sheared to short fragments with Biorupter® Sonicator, and then the fragments were connected with sequencing adapters. After size selection, suitable fragments were used as templates for PCR amplification. Finally, four libraries (200 – 400 bp insert) were sequenced using Illumina sequencer GA-II paired-end 80-nt or HiSeq 2000 paired-ed 100-nt (Illumina Inc., San Diego, CA, USA).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

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, then de novo assembled or mapped to de novo assembled transcriptome using bowtie v0.12.2 with parameters -v 3 -k 1 -e 100 -a --best
Reads Per Kilobase of exon per Megabase of library size (RPKM (Reads Per Kilobase of exon per Million mapped sequence reads) were calculated using a protocol from Mortazavi et al., Nat Methods , 2008. In short, we merged the number of reads of surface fish and cavefish that mapped to the same unigene of either our Sinocyclocheilus transcriptome or the zebrafish unigene database, and converted mapped read numbers to RPKM values.
Genome_build: de novo assembled Sinocyclocheilus transcriptome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

Submission date

Mar 20, 2013

Last update date

May 15, 2019

Contact name

Fanwei Meng

E-mail(s)

mengfw@ioz.ac.cn

Organization name

Institue of Zoology, Chinese Academy of Sciences

Department

State Key Laboratory of Biomembrane and Membrane Biotechnology