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Sample GSM389472

Query DataSets for GSM389472

Status

Public on Sep 01, 2009

Title

X. tropicalis Egg Extract Small RNAs

Sample type

SRA

Source name

Small RNAs from X.tropicalis Egg Extract

Organism

Xenopus tropicalis

Characteristics

tissue: egg extract
sequencing technology: 454

Extracted molecule

total RNA

Extraction protocol

Small RNA library from X.tropicalis egg extract. Xenopus egg extract was prepared by crushing mature eggs laid in frog water in a centrifuge and pulling cytoplasmic layer with a needle and syringe. The egg extract was mixed with Trizol to obtain total RNA. Small RNAs were ligated with linkers and converted to cDNA by reverse transcription. cDNA library was amplified by PCR.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

454 GS FLX

Description

cDNA library was sequenced on a 454 Genome Sequencer FLX platform, according to Margulies et. al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005 Sep 15;437(7057):376-80. Epub 2005 Jul 31. Analysis of this file is described in the manuscript "Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi".

Data processing

Base quality filtering, linker sequence removal, and structural RNA culling was performed with in-house scripts developed by Toshihiro Ohsumi and Mark Borowsky.

Submission date

Apr 05, 2009

Last update date

Jun 11, 2013

Contact name

Nelson C Lau

Organization name

Brandeis University

Department

Biology

Lab

Nelson Lau Lab

Street address

415 South St MS029

City

Waltham

State/province

ZIP/Postal code

02454

Country

USA

Platform ID

GPL9406

Series (1)

GSE15556

Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi

Relations

BioSample

SAMN02197819

Data table header descriptions
SEQUENCE
COUNT	Frequency of read sequenced

Data table
SEQUENCE	COUNT
GGGAAAGGAAATGAGCCTTTGCGAGTGCGG	334
TGCAGAGAGACTGGATGGGAGCTTCTCCGC	333
TGAAGTGGAAGACTGCCCTTGTGATGGCCC	261
GGGAAAGGAAATGAGCCTTTGCGAGTGCA	191
TGAAGTGGAAGACTGCCCTTGTGATGGCC	146
TCACTGAACCTTCCACAGATCGACGTTGCA	110
TGCTAGGTCTACCTGGGTTTTGGTTCCCTG	97
TGAGTAAAGTCCCTTTTGCTGGTGATCCC	97
TGTGAATATTCAATATGCAGCTGGTACCA	94
CCCCGCGCAGGTTCGTATCCTGCCGACTACGCCA	93
TGGAGGTTTTACACAAGCAGTCTTGTTGGT	90
TGCGTAGACGTCTTATGGTTCTTTATGCC	88
TGGAAAAGACCAGATCCTAGGAAATGCCCA	85
TGCAAATGAGTCAATGGTGGAGGCTAGTA	83
TGAGTAAAGTCCCTTTTGCTGGTGATCCCC	80
TGTAAGGAAGTCATGTGTGTCTTTCGTA	78
TAAGAAGGTATGATCCAATCAGAATGGTA	77
TGCATGAAAGAGTGTGACATTCCTTAGCA	77
GGGAAAGGAAATGAGCCTTTGTGAGTGCGG	74
GGGAAAGGAAATGAGCCTTTGCGAGTGCG	72

Total number of rows: 33317

Table truncated, full table size 1046 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM389472_fasta.FA.gz	1.5 Mb	(ftp)(http)	FA
Processed data included within Sample table
Raw data provided as supplementary file