|
| Status |
Public on Feb 07, 2024 |
| Title |
G8.N.day3.1_S22 |
| Sample type |
SRA |
| |
|
| Source name |
PHB pathway harbouring cell line G8
|
| Organism |
Phaeodactylum tricornutum CCAP 1055/1 |
| Characteristics |
time: Day 3 post induction
cell type: diatom
genotype: PHB pathway expression
treatment: N-limitation + P-limitation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A volume relative to 10^8 cells was added to 0.9% NaCl solution (-4°C) and centrifuged for 3 min. Total RNA extraction was done using Trizol aget following the protocol of the RNAeasy mini purification kit (Quiagen).
Samples were converted into libraries using the Illumina stranded mRNA library kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
1x75 bp format
|
| Data processing |
Trimgalore! was used to to trim Fastq files using default parameters.
FastQC was used to for quality control of fastq files pre- and post trimming. Reports were compiled by MultiQC v1.11.
Subsequently the reads were pseudo-aligned to the Phaeodactylum-tricornutum.ASM15095v2 transcriptome using kallisto v0.44.0 to give gene-level counts. Counts were combined for multiple transcripts.
Genes were filtered as follows: at least 10 counts in at least 3 out of 4 replicates.
Assembly: ASM15095v2
Supplementary files format and content: All presented counts are voom-transformed.
|
| |
|
| Submission date |
Feb 08, 2023 |
| Last update date |
Feb 07, 2024 |
| Contact name |
Matthias Windhagauer |
| Organization name |
University of Technology Sydney
|
| Department |
C3
|
| Lab |
COAST
|
| Street address |
745 Harris St
|
| City |
Sydney, Chippendale |
| State/province |
NSW |
| ZIP/Postal code |
2007 |
| Country |
Australia |
| |
|
| Platform ID |
GPL33107 |
| Series (1) |
| GSE224880 |
Metabolic and transcriptional response to the induction of a heterologous poly-3-hydroxybutyrate pathway in Phaeodactylum tricornutum |
|
| Relations |
| BioSample |
SAMN33214266 |
| SRA |
SRX19315538 |
