|
| Status |
Public on May 22, 2020 |
| Title |
Col0_B |
| Sample type |
SRA |
| |
|
| Source name |
Col0 replicate 2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: wild type
developmental stage: Boyes: 1.0
tissue: roots
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
Media = MS/10 +P (KH2PO4 500µM), hygrometry = 33% humidity, Temperature = 24°C day/ 21°c night, Light = 16 hours day / 8 hours night.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Roots 50µg (QuickRNA Zymo).
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases. Ribosomal RNA were removed using SortMeRNA (v2.1).
Trimmed reads were aligned to the TAIR10 genome using STAR (2.5.2b).
Reads were counted using featureCounts from subreads package (v1.6.5) using strand specific mode.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files include raw count values by gene for each Sample.
|
| |
|
| Submission date |
May 21, 2020 |
| Last update date |
May 22, 2020 |
| Contact name |
Thomas Blein |
| E-mail(s) |
thomas.blein@cnrs.fr
|
| Organization name |
CNRS
|
| Lab |
IPS2
|
| Street address |
Avenue des Sciences
|
| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE151005 |
Analysis of NPC48 overexpressing in Arabidopsis roots |
|
| Relations |
| BioSample |
SAMN14992923 |
| SRA |
SRX8377625 |
