Experiment Detail
| Title | Illumina HiSeq 1000 paired end sequencing; Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish |
| Design Description | Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish |
| Organism | Astyanax mexicanus |
Library Description
| Name | Pa1_B_p |
| Strategy | RNA-Seq |
| Source | TRANSCRIPTOMIC |
| Selection | RANDOM |
| Layout | PAIRED |
| Orientation | |
| Nominal Length | 300 |
| Nominal Sdev | 250 |
| Construction Protocol | Hyphessobrycon 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
| Platform | ILLUMINA |
| Instrument Model | Illumina HiSeq 1000 |
Processing
| Base Calls | |
|---|---|
| Sequence Space | |
| Base Caller | |
Spot Information
| Number of Reads per Spots | 0 |
| Spot Length | 202 |
Read Spec
| Read Index 0 | |
|---|---|
| Read Label | |
| Read Class | Application Read |
| Read Type | Forward |
| Base Coord | 1 |
| Read Index 1 | |
| Read Label | |
| Read Class | Application Read |
| Read Type | Reverse |
| Base Coord | 102 |
Navigation
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Submission | ERA732768 |
 FTP
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Study | ERP017705 | ||
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Sample | ERS1403022 | ||
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Run | ERR1679846 |
FASTQ
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SRA
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