|
| Status |
Public on Mar 27, 2024 |
| Title |
HDC1 KO mutant, control media, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 3 days old
tissue: seedlings
genotype: HDC1 knockout
treatment: control
|
| Treatment protocol |
Sterilized seeds were then sown on 1/2 MS 1% sucrose plates with or without 100 mM NaCl.
At day 3 after sowing the seeds were harvested and and snap-frozen with liquid N2.
|
| Growth protocol |
Seeds were sterilised with 50% bleach solution, wash with dH2O water three times and stored at 4C for two days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using hot phenol method and treated with DNAse I. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
hdc1-1, C, 3
|
| Data processing |
Fastq files were generated with bcl2fastq v.1.8.4 Illumina software
The raw fastq files were pre-processed to trim the 3’ end adapter and to trim the low quality reads using Cutadapt (version 1.5) and Sickle (version 0.940; flags -q 10 -l 54), respectively.
Transcript expression quantification was performed using Kallisto (version 0.43.0) against the TAIR10 transcriptome.
Read counts related to TAIR10 transcripts were collected, rounded, and summarized into gene-specific read counts.
Differential gene expression was analysewd using DESeq2 (version 1.24.0).
Assembly: TAIR10
Supplementary files format and content: Comma-delimited text fille containing raw gene-count for each sample separately
|
| |
|
| Submission date |
Jun 11, 2022 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Pawel Herzyk |
| E-mail(s) |
[email protected]
|
| Phone |
00441413303180
|
| Organization name |
University of Glasgow
|
| Department |
College of Medical, Veterinary and Life Sciences
|
| Lab |
Glasgow Polyomics
|
| Street address |
Wolfson Wohl Cancer Research Centre, Garscube Estate
|
| City |
Bearsden |
| ZIP/Postal code |
G61 1QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE205893 |
Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [RNA-Seq] |
| GSE206055 |
Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process |
|
| Relations |
| BioSample |
SAMN28986039 |
| SRA |
SRX15679903 |
