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Sample GSM753518

Query DataSets for GSM753518

Status

Public on Jul 16, 2012

Title

20mm length flower of hermaphrodite

Sample type

SRA

Source name

flower bud

Organism

Carica papaya

Characteristics

cultivar: Sunrise solo
gender: hermaphrodite

Growth protocol

Plants were grown in greenhouse.

Extracted molecule

total RNA

Extraction protocol

Double-stranded cDNA was synthesized from total RNA using the biotinylated adapter-oligo dT primer. Purified cDNA was digested with NlaIII, resulting fragments were bound to streptavidin-coated beads, and non-biotinylated cDNA fragments were removed by washing. Adapter-2SLD was ligated to cDNA fragments on the beads and after washing digested with EcoP15I. EcoP15I-digested and released fragments (adapter-2SLD-tags) were ligated to adapters-1SLD with defined index sequences for sample identification. Tags sandwiched between two adapters were amplified by PCR. The PCR regime consisted of 98oC for 1min, 12 cycles at 98oC for 30sec, and 60oC for 30sec. Eight tubes from this PCR amplification (each 15ml) were pooled and concentrated PCR products were run on an 8% non-denaturing polyacrylamide gel. The band at 160bp was cut out from the gel, and DNA purified after its elution from the gel pieces. Equal concentrations of PCR products from all the samples were mixed and applied to SOLiD3 sequencing.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

AB SOLiD System 3.0

Description

digital trasncript profiling using 26-bp tags

Data processing

Once csfasta-formatted sequence files from SOLiD3 were converted to fasta-formatted files for further analysis. Sorting of sequence reads based on indexed sequences and the subsequent extraction of sequence tags from reads was conducted using a script written in Perl (Matsumura et al. 2010).

Submission date

Jul 01, 2011

Last update date

Jun 11, 2013

Contact name

Hideo Matsumura

E-mail(s)

hideoma@shinshu-u.ac.jp

Phone

81-268-21-5800

Organization name

Shinshu University

Department

Gene Research Center

Street address

Tokita 3-15-1

City

Ueda

State/province

Nagano

ZIP/Postal code

3868567

Country

Japan

Platform ID

GPL13809

Series (1)

GSE30366

Digital transcriptome analysis of genes on sex chromosomes in papaya (Carica papaya)

Relations

BioSample

SAMN02198197

Data table header descriptions
SEQUENCE	sequence
COUNT	count

Data table
SEQUENCE	COUNT
CATGGGGTCCAGGATGGGGTGAGAAT	35355
CATGGGAACGCGCCGAGGTTCGCAGA	32237
CATGCGGGCGTCGTCGTAAGACAATA	30538
CATGTGATCTGTACGTTGTGTGCTAC	17823
CATGCGCCAGACTGTTGCTGTTGGTG	17646
CATGTGTAAGTATGAACTAATTCAGA	16570
CATGTTGGGCAGAAGGGCAAGAAGTG	14970
CATGAGACTGAAAAGACAATCTGGCA	13856
CATGCGGGCGTGTATTGCCTGCGTCT	12416
CATGGACGAGGGTGGCATACTGGCCT	11668
CATGACCACCGTCCTGCTGTCTTAAT	8731
CATGTCCGGCCGGCGGAGCCCTAGAT	8698
CATGAGTTTTGCGGAGAAGACAACGA	8176
CATGGCTTCCACACTGTCACTTAGAT	7566
CATGGGCTTTACAAGATCACAGAACA	5860
CATGTGGGAGCAGGAGCAACTGTGCC	4813
CATGTCCTTCCGTGTCCCCACCGTTG	4581
CATGGCGGTAAGTTCACGTGGTCCGG	4464
CATGGCGATGGTGGCGGCTGCTTTGG	4166
CATGTACGCAGGGTGCGTCAGCGACC	4110

Total number of rows: 139087

Table truncated, full table size 3951 Kbytes.

Supplementary data files not provided

Raw data not provided for this record

Processed data included within Sample table