|
| Status |
Public on Jan 25, 2023 |
| Title |
leaf tissue, pGLCT2 knock out, permanent light, biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
leaf tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaf tissue
ecotype: Col-0
genotype: pGLCT2 knock out
treatment: permament light
|
| Treatment protocol |
To apply an artificial continuous light condition, 24 -day-old plants grown under short day were transferred to a specific growth chamber (percival) with a continous light intensity of 100-120 µmol quanta m-2 s-1 for 10-12 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from leaves or leaf discs using the NucleoSpin® RNA Plant Kit (Macherey-Nagel) according to the manufacturer's instructions. 50 mg of fresh plant material was used for this purpose. The RNA was eluted from the column with 40 μl of RNase-free ddH2O
Directional library construction was perfomed by Novogene Sequencing Service. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
PR3_KO78
|
| Data processing |
The data processing steps are according to Novogene methods: Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Alignment: Algorithm for mapping sequences: HISAT2 is selected to map the filtered sequenced reads to the reference genome. In general, HISAT2 supports genomes of any size, including those larger than 4 billion bases and most of the parameters are set to default. Spliced reads of RNA Seq data can be effictively aligned using HISAT2. HISAT2 v2.0.5 was run using the --dta --phred33 parameters.
Novel gene prediction was performed with StringTie v.1.3.3 and GffCompare v0.10.6 using default parameters
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: tab-delimited xls files include RPKM values for each Sample
|
| |
|
| Submission date |
Jan 20, 2023 |
| Last update date |
Jan 25, 2023 |
| Contact name |
Benjamin Pommerrenig |
| E-mail(s) |
pommerre@bio.uni-kl.de
|
| Organization name |
University of Kaiserslautern
|
| Department |
Biology
|
| Lab |
Ekkehard Neuhaus
|
| Street address |
Paul-Ehrlich-Str. 22
|
| City |
Kaiserslautern |
| ZIP/Postal code |
67663 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE223330 |
The novel chloroplast glucose transporter pGlcT2 affects adaptation to extended light periods |
|
| Relations |
| BioSample |
SAMN32810976 |
| SRA |
SRX19099531 |
