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Sample GSM744253

Query DataSets for GSM744253

Status

Public on Jun 18, 2011

Title

Gastrula_dorsal_explant

Sample type

SRA

Source name

Embryo, dorsal

Organism

Xenopus tropicalis

Characteristics

tissue: gastrula
developmental stage: stage 10
explant: dorsal

Extracted molecule

total RNA

Extraction protocol

All samples were prepared and sequenced at GeneWorks (Adelaide, Australia), a commercial sequencing provider. Libraries were generated using the v1.5 Illumina small RNA sequencing kit (Part # 15002615) and adaptor (5' ATCTCGTATGCCGTCTTCTGCTTG 3') according to the manufacturer's instructions. Small RNA size selection was performed using a modified ladder, which has additional markers at 14, 18 and 21 bp to facilitate sequencing of very small RNA species.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina Genome Analyzer IIx

Description

DMZ

Data processing

After removing the adapters (using a set of in-house scripts) and merging identical reads, the sequences were filtered by length (20 - 32nt), sequence complexity and then mapped to the Xenopus tropicalis genome (Assembly 4.1v) allowing only exact matches. This will consolidate the summary table for each library. Each summary table contains two columns: (1) Nucleotide sequence, and (2) Counts of the sequence in the library.

Submission date

Jun 17, 2011

Last update date

May 15, 2019

Contact name

Juan Larrain

E-mail(s)

[email protected]

Phone

56-2-6862126

Fax

56-2-6862824

Organization name

P. Universidad Catolica de Chile

Department

Cell and Molecular Biology

Lab

Developmental Biology and Regeneration

Street address

Alameda 340

City

Santiago

ZIP/Postal code

8331150

Country

Chile

Platform ID

GPL13741

Series (1)

GSE30067

Deep sequencing of small RNAs in the Xenopus tropicalis gastrula

Relations

SRA

SRX077929

BioSample

SAMN00627863

Data table header descriptions
SEQUENCE	Sequence read
COUNT	Sequence count

Data table
SEQUENCE	COUNT
AAAAAAAAAAACTCTTTACGCAGATGCA	1
AAAAAAAAAAATTTTTTAGACAGTTGAGACA	2
AAAAAAAAAAGACTGCCAGAGAAAGCAAAG	1
AAAAAAAAAAGACTGCCAGAGAAAGCAAAGA	1
AAAAAAAAAAGACTTAGAAGAAGCAGGGA	1
AAAAAAAAAAGCTTACTTTCTGATGGCA	1
AAAAAAAAAAGTGATCTCTGGTTGGTGC	1
AAAAAAAAAAGTGATCTCTGGTTGGTGCTG	1
AAAAAAAAAATAAAACCCAACAGTTACAAA	1
AAAAAAAAAATACTGTGCTGGGGGA	1
AAAAAAAAAATCAGACAGCAGAAGTACT	1
AAAAAAAAAATGAATGAAGAAATGTCCAAC	1
AAAAAAAAAATGACTAGATAGGATTAAAA	1
AAAAAAAAAATTCCAGAAAC	1
AAAAAAAAACCTGAATGCATAGTCACCC	1
AAAAAAAAACCTTCTGCACTACATTTAT	1
AAAAAAAAAGACTGCCAGAGAAAGCAA	1
AAAAAAAAAGACTGCCAGAGAAAGCAAA	1
AAAAAAAAAGACTGCCAGAGAAAGCAAAG	2
AAAAAAAAAGACTGCCAGAGAAAGCAAAGA	2

Total number of rows: 1739435

Table truncated, full table size 51292 Kbytes.

Supplementary data files not provided

SRA Run Selector

Raw data are available in SRA

Processed data included within Sample table