DRA SearchDRASearch

  • Search Home
  • DRA Home

ERX1749513

FASTQ

SRA

Experiment Detail

TitleIllumina HiSeq 1000 paired end sequencing; Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
Design DescriptionEvidence of Late Pleistocene origin of Astyanax mexicanus cavefish
OrganismAstyanax mexicanus

Library Description

NameESF_p
StrategyRNA-Seq
SourceTRANSCRIPTOMIC
SelectionRANDOM
LayoutPAIRED
Orientation
Nominal Length300
Nominal Sdev250
Construction ProtocolHyphessobrycon anisitsi and Astyanax mexicanus Pachon cave and Texas surface morphs were used. Sample collection included embryos and larvae encompassing stages from 10hpf (hours post-fertilisation) to 17dpf (days post-fertilisation), as well as dissected brains and olfactory epithelia from adults. Samples were immersed in Trizol (Invitrogen) and freezed at -80°C. Total RNA was extracted from the samples according to the manufacturer's instructions for Trizol Reagent (Invitrogen) mRNA were purified from total RNA (FastTrack mRNA isolation kit (Thermo Fischer)), fragmented (NEBNext Magnesium RNA fragmentation module, NEB) and treated with the TruSeq small RNA library preparation Kit (Illumina) according to the manufacturer recommendations. Final libraries were purified with AMPureXP kit (Beckman Coulter) instead of gel purification to recover all fragments. Library quality has been assessed on a bioanalyzer instrument (Agilent).

Platform

PlatformILLUMINA
Instrument ModelIllumina HiSeq 1000

Processing

Base Calls
Sequence Space
Base Caller

Spot Information

Number of Reads per Spots0
Spot Length202

Read Spec

Read Index 0
Read Label
Read ClassApplication Read
Read TypeForward
Base Coord1
Read Index 1
Read Label
Read ClassApplication Read
Read TypeReverse
Base Coord102

Navigation

Submission ERA732768 FTP
Study ERP017705
Sample ERS1403021
Run ERR1679845 FASTQ SRA
Website policy | © DNA Data Bank of Japan