|
| Status |
Public on May 27, 2014 |
| Title |
Bol-Stem |
| Sample type |
SRA |
| |
|
| Source name |
Stem tissues of Brassica oleracea
|
| Organism |
Brassica oleracea |
| Characteristics |
tissue: stem
age: 7-week old
|
| Treatment protocol |
total RNA is extracted by TRIzol Reagent
|
| Growth protocol |
The flower, leaf, root, silique, stem, bud from the Brassica oleracea plants, which were grown in the greenhouse under condition of temperature,15-25℃ and sunlight. The tissue of callus were generated in the illumination box under the 25℃ using tissue culture. All the tissues were generated by Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences,China in 2010.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sequenced reads were generated from stem tissue of 7-week old Brassica oleracea plant
|
| Data processing |
Used Brassica oleracea genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat-1.0.13 with default parameters except -N 1, -r 20, -p 4, --coverage-search, --microexon-search
Supplementary_files_format_and_content: bedgraph and counts
|
| |
|
| Submission date |
Dec 12, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhangyan Wu |
| E-mail(s) |
Joanna.wu@genomics.cn
|
| Phone |
+8613265797662
|
| Organization name |
Beijing Genomics Institute
|
| Street address |
Yantian district, Shenzhen
|
| City |
Shenzhen |
| ZIP/Postal code |
518083 |
| Country |
China |
| |
|
| Platform ID |
GPL16360 |
| Series (1) |
| GSE42891 |
Transcriptome sequencing of Brassica oleracea tissues |
|
| Relations |
| SRA |
SRX209696 |
| BioSample |
SAMN01831068 |
