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| Status |
Public on May 31, 2012 |
| Title |
yxy-6 |
| Sample type |
SRA |
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| Source name |
embryogenic calli
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| Organism |
Gossypium hirsutum |
| Characteristics |
varieties/line: YZ1
tissue: embryogenic calli
developmental stages: embryogenic calli
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| Growth protocol |
Sterilized seeds of YZ1 (Gossypium hirsutum L.) were germinated on 1/2 MS (1/2 macro salts plus 15 g of glucose, pH 6.0) and cultured at 28°C in the dark for 6 d. Hypocotyls were excised from germfree seedlings and cut into 5-7 mm segments. The explants were then 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 explants during initial cellular dedifferentiation (0 h, 6 h, 24 h, 48 h), NECs (40 d), ECs and somatic embryos [globular embryos (GEs), torpedo embryos (TEs) and cotyledon embryos (CEs)] were sampled
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from each sample by using a modified guanidine thiocyanate method, Twenty micrograms of total RNA was sent to Beijing Genomics Institute (Shenzhen) where the libraries were constructed and sequenced using Illumina’s Genome Analyzer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequencing output raw data were first filtered to remove adaptor tags, low quality sequences (tags with unknown sequences 'N') and tags with a copy number of 1 (probably sequencing error).
all tags were mapped to the reference sequences (cotton unigenes from NCBI) and allowed no more than one nucleotide mismatch. All the tags mapped to reference sequences from multiple genes were filtered and the remaining tags were designed as unambiguous tags.
For gene expression analysis, the number of expressed tags was calculated and then normalized to TPM (number of transcripts per million clean tags). To minimize false positives and negatives, we estimated that statistical analysis was reliable when applied to genes showing a TPM ≥ 20 in at least one of these stages
To obtain statistical confirmation of the differences in gene expression among the developmental stages, we then compared the TPM-derived read count all the timepoints/stages to ck (0h) using a threshold value of P ≤ 0.001 and the absolute value of log2Ratio ≥1 based on the FDR < 0.05.
Genome_build: geneme unavailable, use cotton unigenes from NCBI for reads alignment
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample, and a matrix nomalized tablelist for differentially expressed gene from all timepoints/stages
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| Submission date |
May 24, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiyan Yang |
| E-mail(s) |
[email protected]
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| Organization name |
Huazhong Agricultural University
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| Street address |
Shizishan 1, Hongshan
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL9362 |
| Series (1) |
| GSE38209 |
Expression profiling of genes involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton |
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| Relations |
| SRA |
SRX149427 |
| BioSample |
SAMN00998318 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM936807_yxy-6.GeneExpression.txt.gz |
609.1 Kb |
(ftp)(http) |
TXT |
| GSM936807_yxy-6_TagCopyNumber.txt.gz |
848.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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