|
| Status |
Public on Aug 14, 2014 |
| Title |
aLBe1_mRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
embryonic tissue
|
| Organism |
Anolis carolinensis |
| Characteristics |
tissue type: hindlimb bud
Stage: stage 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Life Technologies) and enriched for mRNA fraction using MPG mRNA Purification Kit (PureBiotech)
Multiplexed RNA-seq libraries were produced using the SPIA cDNA synthesis kit and the Ovation Ultralow DR Multiplex system (NuGen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
base calling using standard Illumina software
Adaptor sequences were trimmed using FASTX_trimmer (Hannon lab)
Reads were mapped to genome builds mm9 (Mus musculus; using UCSC mm9 refseq annotation) and Anocar2.0 (Anolis carolinensis; using ASU_Acar version 2.1 annotation) using RNA-Seq unified mapper (RUM) verison 1.11 (Grant et al., 2011)
To account for species-specific differences in non-uniquely mapping (NU) reads, we redistributed NU reads based on the number of uniquely mapping (U) reads mapping to the respective loci, following the logic outlined in Brawand et al, 2011
Only orthologous genes found in both species were used for further analyses
Genome_build: mm9, Anocar2.0
Supplementary_files_format_and_content: tab-delimited text files including total read counts for all samples of the same species
|
| |
|
| Submission date |
Aug 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick Tschopp |
| E-mail(s) |
patrick.tschopp@unibas.ch
|
| Organization name |
University of Basel
|
| Department |
Department of Environmental Sciences
|
| Lab |
Laboratory of Regulatory Evolution
|
| Street address |
Vesalgasse 1
|
| City |
Basel |
| ZIP/Postal code |
4051 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL15001 |
| Series (1) |
| GSE60373 |
A relative shift in cloacal location repositions external genitalia in amniote evolution |
|
| Relations |
| BioSample |
SAMN02988828 |
| SRA |
SRX679291 |
