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Sample GSM946003 Query DataSets for GSM946003
Status Public on Sep 23, 2013
Title stage 10 mRNA-seq
Sample type SRA
 
Source name Whole embryos
Organism Xenopus tropicalis
Characteristics genotype/variation: wild-type
developmental stage: Embryonic stage 10
tissue: Whole embryos
molecule subtype: Polyadenylated total RNA
Treatment protocol Embryos were not treated.
Growth protocol X. tropicalis embryos were obtained by in vitro fertilization, de-jellied in 2.2% cysteine and cultured in 1/20 x MMR + gentamycin until the indicated stage as described (Khokha et al. 2002).
Extracted molecule total RNA
Extraction protocol Total RNA was obtained by Trizol extraction from X. tropicalis embryos and the mRNA-seq sample prep kit (Illumina) was used to prepare the mRNA libraries. Briefly, polyadenylated RNA was selected, fragmented and cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen). Double-stranded cDNA was then synthesized using T4 DNA polymerase and used for Illumina sample preparation.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description mRNA-seq
Sample 7
Data processing small RNA-seq reads were trimmed to remove sequencing adapters and aligned to the X. tropicalis genome allowing for zero mismatches using the bwa alignment program (Li and Durbin 2009).
Normalised abundance measurements were generated to allow comparison across the libraries using a linear scaling whereby the raw reads were multiplied by the greatest number of genomic alignments in any library divided by the number of genomic alignments in the library of interest.
mRNA-seq reads were aligned to the X. tropicalis genome using bowtie (Langmead et al. 2009) allowing up to 2 mismatches. mRNA-seq reads over splice junctions were aligned using TopHat (Trapnell et al. 2009).
mRNA-seq reads over splice junctions were aligned to the X. tropicalis genome using TopHat (Trapnell et al. 2009). Up to two sequence mismatches were permitted.
Normalised abundance measurements of mRNA reads were generated using the reads per kilobase per million of exon (RPKM) method for each gene annotated in RefSeq to normalize for transcript length and total read number (Mortazavi et al. 2008).
Genome_build: X. tropicalis genome, Joint Genome Institute assembly version 4.1 (Hellsten et al. 2010)
Supplementary_files_format_and_content: BED files were generated using bedtools software and contain alignments of trimmed small RNA reads to the X. tropicalis genome or alignments of trimmed mRNA-seq reads including reads spanning exon-exon junctions.
 
Submission date Jun 08, 2012
Last update date May 15, 2019
Contact name Caroline Hill
E-mail(s) caroline.hill@cancer.org.uk
Phone +44 20 7269 2941
Organization name Cancer Research UK London Research Institute
Lab Developmental Signalling
Street address 44 Lincoln's Inn Fields
City London
ZIP/Postal code WC2A 3LY
Country United Kingdom
 
Platform ID GPL13741
Series (1)
GSE38605 Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos
Relations
SRA SRX152569
BioSample SAMN01041913

Supplementary file Size Download File type/resource
GSM946003_mRNA_Stage10.bed.gz 62.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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