|
| Status |
Public on Mar 04, 2024 |
| Title |
Bdnrpd1-2, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Brachypodium distachyon |
| Characteristics |
tissue: leaves
age: 4-week-old
genotype: Bdnrpd1-2
|
| Growth protocol |
Brachypodium distachyon seeds (Bd21-3 background) were germinated 4 days on wet Whatman filter paper at room temperature, then the plants were grown on soil for 4 weeks in a walk-in growth chamber with a day/night cycle of 20 h/4 h at temperatures of 26°C/20°C under 6x OSRAM FQ 49W/965HO Lumilux de Lux Cool Daylight lighting (40 cm distance to light tubes).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from young emerging leaves (4-week-old) was extracted with TRIzol reagent, treated with DNaseI, and then purified again via phenol-chloroform extraction and ethanol precipitation.
DNAase-treated total RNA were subjected to poly(A)-tail selection, followed by library construction using Illumina TruSeq Stranded mRNA Library Prep kit.
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Bd07_AFVA-89
featureCounts_genes.tsv
featureCounts_TEs.tsv
|
| Data processing |
trim_galore --length 100 --fastqc --paired
hisat2 --max-intronlen 5000 --rna-strandness RF
samtools sort -O BAM
featureCounts -p -M
Assembly: Bdistachyon_314_v3.1
Supplementary files format and content: tab-delimited text file including count values for each Sample on each TE/gene annotation
|
| |
|
| Submission date |
Sep 21, 2023 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Todd L Blevins |
| E-mail(s) |
[email protected]
|
| Organization name |
CNRS
|
| Lab |
Institut de biologie moléculaire des plantes
|
| Street address |
12 Rue du Général-Zimmer
|
| City |
Strasbourg |
| ZIP/Postal code |
67000 |
| Country |
France |
| |
|
| Platform ID |
GPL33763 |
| Series (1) |
| GSE243693 |
Epigenomic profiles of Brachypodium distachyon mutants deficient in RNA polymerase IV (Pol IV) |
|
| Relations |
| BioSample |
SAMN37503342 |
| SRA |
SRX21855165 |
