|
| Status |
Public on Sep 16, 2016 |
| Title |
CM-NEI-br1 |
| Sample type |
SRA |
| |
|
| Source name |
Ovules_Nour clementina (Citrus Clementine)
|
| Organism |
Citrus x clementina |
| Characteristics |
cultivar: Nour
tissue: ovules
age: 7 DAF (days after flowering)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Trizol method
Small RNA libraries were constructed for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
replicate 1 for ovules at nucellar embryo initiation stage
Low Molecular Weight RNA
|
| Data processing |
To obtain clean reads, low quality reads, filtering the contaminants and the adaptor sequences were filtered first.
The clean sRNAs mapped to Rfam10.1 (ftp://ftp.ebi.ac.uk/pub/databases/Rfam) with no more than two mismatches,which were identified as non-coding RNAs (ncRNA), were excluded.
The leftover high-quality clean reads of GF and PU were mapped to the genome of Citrus Sinensis, while PK and CM were mapped to Clementine genome.
Genome_build: Reference genome sequences of Citrus Sinensis were downloaded from http://citrus.hzau.edu.cn/orange/download/data.php, while Clementine genome sequences were downloaded from http://phytozome.jgi.doe.gov/pz/portal.html.
Supplementary_files_format_and_content: tab-delimited text files include raw count and length for each read
|
| |
|
| Submission date |
Oct 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jianmei Long |
| E-mail(s) |
[email protected]
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
shizishan street NO.1
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL21044 |
| Series (1) |
| GSE74132 |
Exploring miRNAs involved in citrus nucellar embryo initiation by high-throughput small RNA sequencing |
|
| Relations |
| BioSample |
SAMN04194087 |
| SRA |
SRX1353675 |
