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Sample GSM1477380 Query DataSets for GSM1477380
Status Public on Aug 14, 2014
Title aLBl2_mRNAseq
Sample type SRA
 
Source name embryonic tissue
Organism Anolis carolinensis
Characteristics tissue type: hindlimb bud
Stage: stage 5
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) tschopp@genetics.med.harvard.edu
Organization name Harvard Medical School
Department Department of Genetics
Lab Tabin lab
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL15001
Series (1)
GSE60373 A relative shift in cloacal location repositions external genitalia in amniote evolution
Relations
BioSample SAMN02988831
SRA SRX679294

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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