|
| Status |
Public on Sep 22, 2010 |
| Title |
Orange_MT_170DAF |
| Sample type |
SRA |
| |
|
| Source name |
fruits
|
| Organism |
Citrus sinensis |
| Characteristics |
genotype: red-flesh mutant
tissue: fruits, 170 DAF (days after flowering)
|
| Growth protocol |
The orange fruits were pick up from 3 different trees which cultivated at the Institute of Citrus Research located in Guilin, Guangxi Province, China
|
| Extracted molecule |
total RNA |
| Extraction protocol |
small RNAs with 16-30 nt in length were isolated from the total RNA of WT and MT samples by size fractionation with 15% Tris-borate-EDTA urea polyacrylamide gel (TBU). After extraction from the gel, sRNA was dephosphorylatd by alkaline phosphatase (New England Biolabs Inc.). Then the small RNAs were ligated sequentially to 5’ and 3’ RNA/DNA chimeric oligonucleotide adaptors (Illumina). The ligation products were purified from 10% TBE urea polyacrylamide gel. Reverse transcription was performed with the ligated sRNAs as templates. The obtained cDNAs were sequenced using the Illumina 1 G Genome Analyzer by Beijing Genomics Institute (BGI) (Shenzhen, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
small RNAs with 16-30 nt in length were isolated from the total RNA of WT and MT samples by size fractionation with 15% Tris-borate-EDTA urea polyacrylamide gel (TBU). After extraction from the gel, sRNA was dephosphorylatd by alkaline phosphatase (New England Biolabs Inc.). Then the small RNAs were ligated sequentially to 5? and 3? RNA/DNA chimeric oligonucleotide adaptors (Illumina). The ligation products were purified from 10% TBE urea polyacrylamide gel. Reverse transcription was performed with the ligated sRNAs as templates. The obtained cDNAs were sequenced using the Illumina 1 G Genome Analyzer by Beijing Genomics Institute (BGI) (Shenzhen, China).
|
| Data processing |
Sequences without adapters were discarded. The adapter-containing tags were used for further analysis after removement of 5' and 3' adapters.
|
| |
|
| Submission date |
Sep 22, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Qiang Xu |
| E-mail(s) |
qx32@cornell.edu
|
| Phone |
607-254-5057
|
| Organization name |
Cornell University
|
| Street address |
Tower Road, Cornell University
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL9256 |
| Series (1) |
| GSE18207 |
Discovery and comparative profiling of microRNAs in sweet oranges |
|
| Relations |
| SRA |
SRX019196 |
| BioSample |
SAMN00011288 |
