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Sample GSM1357548 Query DataSets for GSM1357548
Status Public on Mar 27, 2014
Title s_2_00_2.5_polyA
Sample type SRA
 
Source name Whole embryo
Organism Xenopus tropicalis
Characteristics series: 2
time/hpf: 2.5
Extracted molecule polyA RNA
Extraction protocol Series 1&2: total RNA was isolated using TriPure (Invitrogen) followed by LiCl precipitation. RNA was dissolved in 100 µl H2O, and 10 µg total RNA from each sample was used for PolyA+ RNA library preparation using Illumina kit RS-930-1001
Series 3: total RNA was extracted, samples were suspended in 40 µl DEPC H2O, and 1 µg was taken for library preparation. PolyA+ RNA was isolated using beads from TruSeq RNA Sample Prep Kit v2 (Illumina kit RS-122-2001), and PolyA+ RNA-seq libraries were prepared using Epicentre ScriptSeq v2. Ribosomal RNA depleted RNA-seq libraries were prepared using Epicentre ScriptSeq Complete Kit (BHMR1224) combining Ribo-Zero and ScriptSeq v2.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description Series_2_Sample_00_2.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 2497.754984
Data processing Series 1&2 basecalling performed with Illumina RTA 1.9.35
Series 3 basecalling performed with Illumina RTA 1.17.21.3
Read pairs were aligned to a transcriptome containing Xenopus Tropicalis v7 gene models and additional off-genome EST sequences with Bowtie 0.12.7 with parameters -a -y --best -v 3 -X 0 -I 10000. The assembly of these off-genome ESTs is described here: "Gilchrist, M. J., Zorn, A. M., Voigt, J., Smith, J. C., Papalopulu, N. and Amaya, E. (2004). Defining a large set of full-length clones from a Xenopus tropicalis EST project. Dev Biol 271, 498-516." The assembled contigs themselves do not have accession numbers, but the contig sequences will be included in a supplemental file with our paper.
Pairs aligning to transcripts from more than one gene were discarded, pairs aligning to one or more transcripts from the same gene were counted once.
Reads were normalized by total mapped reads to a standard library size of 25 million reads.
Genome_build: Xtropicalis_v7
Supplementary_files_format_and_content: Tab delimited .txt files containing raw and normalized read counts for each sample
 
Submission date Mar 26, 2014
Last update date May 15, 2019
Contact name Nick Owens
Organization name University of Exeter Medical School
Street address Barrack Road
City Exeter
State/province Exeter
ZIP/Postal code EX2 5DW
Country United Kingdom
 
Platform ID GPL13741
Series (1)
GSE56242 High-resolution analysis of gene activity during the Xenopus mid-blastula transition
Relations
BioSample SAMN02708784
SRA SRX501604

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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