|
| Status |
Public on Apr 29, 2021 |
| Title |
RNA_seq_Col0_clf_shoot_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
RNA_seq_Col0_clf_shoot_rep2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Col0
|
| Growth protocol |
RNAseq assays were performed on shoot or root of 14‐day‐old seedlings
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction using Nucleospin RNA kit from Macherey Nagel
Libraries were produced using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Trimmomatic-0.38 : Minimum length of 30 bp; Mean Phred quality score > 30; Leading and trailing bases removal with base quality <5. STAR aligner was used to mapped the reads to TAIR10 genome assembly. Raw read counts were then extracted using featureCounts based on the gene annotations in Araport11_GFF3_genes_transposons.201606.gtf. DESeq2 to identify differentially expressed genes. Genes having read counts ≥ 50 in atleast 2 samples were considered for differential expression analysis.
Genome_build: TAIR10
|
| |
|
| Submission date |
Jul 31, 2020 |
| Last update date |
Apr 29, 2021 |
| Contact name |
Sanchari Sircar |
| E-mail(s) |
sancharisircar24@gmail.com
|
| Organization name |
IPS2
|
| Lab |
Chromosome Dynamics
|
| Street address |
Batiment 630 Rue Noetzlin
|
| City |
Orsay |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE155502 |
Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis |
|
| Relations |
| BioSample |
SAMN15689615 |
| SRA |
SRX8860847 |
