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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