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| Status |
Public on Mar 31, 2014 |
| Title |
Actively Growing Vascular Cambium |
| Sample type |
SRA |
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| Source name |
actively growing vascular cambium
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| Organism |
Cunninghamia lanceolata |
| Characteristics |
tissue: vascular cambium
Stage: active
age: 16 years old
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| Growth protocol |
~16 years old, 15 m tall, 12 cm in diameter) growing under natural conditions
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| Extracted molecule |
total RNA |
| Extraction protocol |
After extracting the total RNA from dormant, reactivating and actively growing vascular cambium of C. lanceolata using tangential cryosections, mRNA of eukaryotes is enriched by using the oligo(dT) magnetic beads and mRNA of prokaryotes is enriched just by removing rRNAs from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythesize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis 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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| Data processing |
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to transcriptome using SOAPaligner/soap2 with and mismatches of only 1 bp were considered
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nucleic Acids Research, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: C. lanceolata transcriptome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Apr 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinxing Lin |
| E-mail(s) |
linjx@ibcas.ac.cn
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| Phone |
+86-10-62836211
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| Fax |
+86-10-62836211
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| URL |
http://dmdb.ibcas.ac.cn/linj.htm
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| Organization name |
Institute of botany
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| Street address |
No.20 Nanxincun, Xiangshan
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| City |
Beijing |
| ZIP/Postal code |
100093 |
| Country |
China |
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| Platform ID |
GPL15423 |
| Series (1) |
| GSE37152 |
The regulation of cambial activity in Cunninghamia lanceolata involves extensive transcriptome remodeling |
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| Relations |
| SRA |
SRX139886 |
| BioSample |
SAMN00854715 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM912555_active.Gene.rpkm.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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