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Status |
Public on Mar 27, 2014 |
Title |
s_2_00_2.5_polyA |
Sample type |
SRA |
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Source name |
Whole embryo
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Organism |
Xenopus tropicalis |
Characteristics |
series: 2 time/hpf: 2.5
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer IIx |
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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
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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
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Submission date |
Mar 26, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Nick Owens |
Organization name |
University of Exeter Medical School
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Street address |
Barrack Road
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City |
Exeter |
State/province |
Exeter |
ZIP/Postal code |
EX2 5DW |
Country |
United Kingdom |
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Platform ID |
GPL13741 |
Series (1) |
GSE56242 |
High-resolution analysis of gene activity during the Xenopus mid-blastula transition |
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Relations |
BioSample |
SAMN02708784 |
SRA |
SRX501604 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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