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| Status |
Public on Jun 27, 2019 |
| Title |
Sporangium_s_1 |
| Sample type |
SRA |
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| Source name |
Sporophyll
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| Organism |
Selaginella moellendorffii |
| Characteristics |
developmental stge: Sporangium small
genotype/variation: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs of a series of sporangia at different developmental stages and young leaves were extracted using the TRIzol solution.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina HiSeqTM2000 software used for basecalling. Raw reads were processed to remove adaptors, low-quality reads and reads with unknown bases.
The clean reads of S. moellendorfii were aligned to the genome sequence of S. moellendorfii at JGI database (ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Smoellendorffii/annotation/) using the assembling program SOAPaligner/SOAP2 from Li et al, Bioinformatics, 2009.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nucleic Acids Research, 2008.
Fold changes in gene expression were determined from RPKM ratios. Genes were considered to be differentially expressed if they had an FDR < 0.05, P-value < 0.05, and the absolute value of log2Ratio ≥ 1.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample
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| Submission date |
Jun 27, 2016 |
| Last update date |
Jun 27, 2019 |
| Contact name |
luoyan zhang |
| E-mail(s) |
10110700021@fudan.edu.cn
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| Phone |
086-021-51630695
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| Organization name |
fudan university
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| Street address |
songhu Road 2005
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| City |
shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
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| Platform ID |
GPL19601 |
| Series (1) |
| GSE83783 |
RNA-Sequencing analysis of reproduction/meiosis in Selaginella moellendorffii |
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| Relations |
| BioSample |
SAMN05296686 |
| SRA |
SRX1880796 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2218795_Sporangium_s_1_RPKM.txt.gz |
149.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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