|
| Status |
Public on Feb 22, 2018 |
| Title |
FRE-2 |
| Sample type |
SRA |
| |
|
| Source name |
Gametophores
|
| Organism |
Physcomitrium patens |
| Characteristics |
treatment: fully rehydrated tissues
|
| Treatment protocol |
Plants growing in BCD mediums were subjected to hydrated (HD), mild dehydrated (MDH), severe dehydrated (SDH), partially rehydrated (PRE) and fully rehydrated (FRE) treatments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total extracted from hydrated (HD), mild dehydrated (MDH), severe dehydrated (SDH), partially rehydrated (PRE) and fully rehydrated (FRE) gametophores of moss P. patens.
Illumina standard protocol for HiSeq 2000 platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using the Illumina GA Pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity (unknown bases are less than 10%) or low-quality sequence (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read), then mapped to Bhy_V1.0 (unpublished) whole genome using SOAPaligner/soap2.
The transcript abundance of each gene were normalized by RPKM.
Genome_build: phytozome V1.6
Supplementary_files_format_and_content: tab-delimited text files include read number and annotations for each Sample.
|
| |
|
| Submission date |
Mar 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lihong Xiao |
| E-mail(s) |
xiaolihong6290@gmail.com
|
| Organization name |
Capital Normal University
|
| Street address |
No.105 North Road of West 3rd-ring Road.Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100048 |
| Country |
China |
| |
|
| Platform ID |
GPL14798 |
| Series (1) |
| GSE66467 |
Genome-wide transcriptome analysis during dehydration and recovery in gametophores of Physcomitrella patens |
|
| Relations |
| BioSample |
SAMN03383430 |
| SRA |
SRX895711 |
