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| Status |
Public on Nov 07, 2019 |
| Title |
RNA seq species 9 |
| Sample type |
SRA |
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| Source name |
Cerebellum
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| Organism |
Python regius |
| Characteristics |
tissue: Cerebellum
age: Adult
genotype: Wild-type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cerebella were dissected, flash frozen in liquid nitrogen, and RNA was harvested using the RNeasy Plus Micro Kit (Qiagen, Germany). RNA Integrity Number (RIN) values were determined using Agilent 2100 Bioanalyzer (Agilent Technologies, U.S.A.).
Libraries were produced using the TruSeq Stranded Total RNA Kit with Ribo-Zero (Human/Mouse/Rat; Illumina, U.S.A.).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Quality trimming and adapter sequence removal of reads were done using the Trimmomatic tool, and the SortMeRNA pipeline was used for ribosomal RNA (rRNA) filtering.
Quality trimmed and rRNA-filtered reads were de novo assembled in contigs with the Trinity software v2.8.5, using its default parameters.
The coding (CDS) and protein sequence of unigenes were then predicted using the TransDecoder program implemented in Trinity software.
The OrthoFinder algorithm was used for inferring orthologous and species-specific unigenes from protein sequences.
The relative abundance of transcripts were evaluated for each species as FPKM using the RNA-Seq by Expectation Maximization (RSEM) software.
Supplementary_files_format_and_content: Excel file including FPKM values for each squamate species.
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| Submission date |
Oct 29, 2019 |
| Last update date |
Nov 07, 2019 |
| Contact name |
Nicolas Di-Poi |
| E-mail(s) |
nicolas.di-poi@helsinki.fi
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| Organization name |
University of Helsinki
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| Department |
Institute of Biotechnology, Helsinki Institute of Life Sciences
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| Street address |
Viikinkaari 1
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| City |
University of Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
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| Platform ID |
GPL27701 |
| Series (1) |
| GSE139570 |
Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization |
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| Relations |
| BioSample |
SAMN13153854 |
| SRA |
SRX7070006 |
| 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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