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Sample GSM753513

Query DataSets for GSM753513

Status

Public on Jul 16, 2012

Title

7mm length flower of male

Sample type

SRA

Source name

flower bud

Organism

Carica papaya

Characteristics

cultivar: TM1
gender: male

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

SAMN02198226

Data table header descriptions
SEQUENCE	sequence
COUNT	count

Data table
SEQUENCE	COUNT
CATGGACGAGGGTGGCATACTGGCCT	40248
CATGGGAACGCGCCGAGGTTCGCAGA	35537
CATGGCTGCAGGTGGCACCAGCACCA	35006
CATGGCTTCCACACTGTCACTTAGAT	21601
CATGCGCCAGACTGTTGCTGTTGGTG	19807
CATGTGTAAGTATGAACTAATTCAGA	19422
CATGCGGGCGTCGTCGTAAGACAATA	16483
CATGCGGGCGTGTATTGCCTGCATCT	12583
CATGTGGGAGCAGGAGCAACTGTGCC	12319
CATGGGGTCCAGGATGGGGTGAGAAT	11305
CATGAGACTGAAAAGACAATCTGGCA	10020
CATGAGTTTTGCGGAGAAGACAACGA	9767
CATGTGATCTGTACGTTGTGTGCTAC	9222
CATGAGAGGATGTCGAGCCTCAATCT	9068
CATGTCCGGCCGGCGGAGCCCTAGAT	7917
CATGTTGGGCAGAAGGGCAAGAAGTG	7756
CATGGAACGCCAGCGTTTCGCTGAAA	7469
CATGGCGGTAAGTTCACGTGGTCCGG	7398
CATGTAGCTCTTTTGTGTTCATCCAA	7102
CATGGGGTGAGCTTCCTTGGTGATCC	6921

Total number of rows: 190431

Table truncated, full table size 5409 Kbytes.

Supplementary data files not provided

Raw data not provided for this record

Processed data included within Sample table