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| Status |
Public on Sep 27, 2013 |
| Title |
JFY-10 |
| Sample type |
SRA |
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| Source name |
somatic torpedo-shaped embryos
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| Organism |
Gossypium hirsutum |
| Characteristics |
cultivar: YZ1
tissue: somatic embryo
developmental stage: torpedo-shaped stage
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| Growth protocol |
The cotton plants (Gossypium hirsutum cv. YZ1), used for zygotic embryos collection, were cultivated in the field under normal farming condition during growing seasons in Wuhan, China. Tissue culture was carried out for somatic embryos collection using hypocotyls excised from germfree seedlings. The explants were cultured on MSB (MS medium plus B5 vitamins) medium supplemented with the combination of 1.0 mg/L IBA plus 0.1 mg/L kinetin. After 40 d of culture, all explants were transferred to fresh MSB medium for induction of embryogenic calli (ECs). The ECs were subcultured monthly on MSB medium, with KNO3 doubled but NH4NO3 removed, and supplemented with 3% (w/v) glucose, 0.25% (w/v) Phytagel, 0.5 mg/L IBA, 0.15 mg/L kinetin, 1.0g/L glutamine and 0.5 g/L asparagines, for embryo maturation. All media were autoclaved at 121°C for 15 min. Cultures were maintained in a room at 28 ± 2 °C under a 14-h photoperiod (irradiance of 135 μmol/m∙s). Different stages of somatic embryos were sampled.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Guanidine thiocyanate method was used to extract total RNA
Approximate 20ug of total RNA was sent to Beijing Genomics Institute (Shenzhen, China) where the tag libraries were prepared and sequenced. Before construction of library, RNA quality and quantity were determined by Agilent 2100 with rRNA ratio [28s/18s] > 1.0 and RNA Integrity Number (RIN) > 7. Then mRNA were enriched by using the oligo(dT) magnetic beads, and interrupted by adding the fragmentation buffer to short segments (about 200bp) which were used as templates to synthesize double strand cDNA tags by random hexamer-primer. After purified, washed for end repair and single nucleotide A (adenine) addition, and attached the sequencing adaptors, the library required fragments were enriched by PCR amplification. Millions of raw reads with a length approximate 50bp were generated via Illumina HiSeq™ 2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Gossypium hirsutum cv. YZ1
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| Data processing |
Millions of raw reads with a length approximate 50bp were generated via Illumina HiSeq™ 2000
Clean reads occupied > 98% of raw reads were produced after filtering dirty raw reads
By using SOAPaligner/soap2, all clean reads were mapped to the reference sequences which were cotton unigenes collected from NCBI, supporting up to 2 bases mismatches in the alignment.
Transcription levels were calculated in RPKM (reads per kilobase of exon model per million mapped reads) which was able to get rid of the disturbance of different gene length and sequencing discrepancy on the calculation of gene expression
Genome_build: Gossypium hirsutum: UniGene Build #11
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample
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| Submission date |
Apr 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Fangyan Jin |
| E-mail(s) |
lantian5963@163.com
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| Organization name |
Huazhong Agriculture University
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| Lab |
National Key Laboratory of Crop Genetic Improvement
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| Street address |
No.1, Shizishan Street
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL16485 |
| Series (1) |
| GSE45671 |
Expression profiling of genes involved in somatic and zygotic embryo development in cotton |
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| Relations |
| SRA |
SRX257606 |
| BioSample |
SAMN01995744 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1111704_JFY-10_Gene_rpkm.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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