 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 12, 2024 |
| Title |
Col-0_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
age: 12-day-old seedlings
genotype: WT
|
| Growth protocol |
All the plant seeds were sown and grown on 1/2 MS medium containing 1% sucrose. The seedlings were grown under a long- (16 h light/8 h dark) photoperiod at 23 °C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were extracted from 12-day-old seedlings grown during long days using a RNeasy Plant Mini kit (Qiagen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Col_1
|
| Data processing |
RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer’s instructions
Then clean reads were separately aligned to reference genome with orientation mode using TopHat
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method
RSEM was used to quantify gene abundances. R statistical package software EdgeR was utilized for differential expression analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: excel table with FPKM value
|
| |
|
| Submission date |
Mar 15, 2021 |
| Last update date |
Mar 12, 2024 |
| Contact name |
li peng |
| E-mail(s) |
lipeng@psc.ac.cn
|
| Phone |
18721062615
|
| Organization name |
PSC
|
| Street address |
NO.38888,chenhualu
|
| City |
shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (2) |
| GSE168891 |
RNA-seq analysis of WT, jmj28-3 in Arabidopsis |
| GSE168893 |
RNA-seq analysis of jmj28-3 and genome-wide occupancy of JMJ28 in Arabidopsis |
|
| Relations |
| BioSample |
SAMN18310690 |
| SRA |
SRX10340426 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
