|
| Status |
Public on Jun 05, 2019 |
| Title |
Ncviv_ENV_F1 |
| Sample type |
SRA |
| |
|
| Source name |
Ncviv_ENV_leaf
|
| Organism |
Noccaea caerulescens |
| Characteristics |
subspecies/plant: Viviez
phenotype: non-nickel-accumulator
geographical location: Viviez, Aveyron, France
gps location: N 44 32.724, E 2 12.870
collection date: 5-Jun-2014
sample type: Environmental sample
tissue: Leaf
|
| Treatment protocol |
Environmental samples were stabilized in in RNAlater (Sigma). The stabilization solution was removed at the laboratory and samples were stored at -80°C before RNA extraction. Hydroponic culture samples were directly frozen in liquid nitrogen and stored at -80°C before RNA extraction.
|
| Growth protocol |
Plant samples were collected in their natural environment (serpentine soil or zinc mining site). Leaves and roots were also collected from Noccaea caerulescens subsp. firmensis and Noccaea montana hydroponically grown (Araponics, Liège, Belgium) with modified Hoagland’s solution, supplemented with 20 μM Fe-HBED and 37.5 μM NiCl2 during 7 weeks.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA were extracted using RNeasy Plant Mini kit (Qiagen, Hilden, Germany) and treated with DNAseI.
Libraries were constructed using 1 µg total RNA with Illumina TruSeq Stranded mRNA kit by the POPS transcriptomic plateform (IPS2, Orsay, France) following Illumina kit recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
BLB_NOSW_5_*_C52YGACXX.IND7_noribo
|
| Data processing |
Illumina HiSeq 2000 100bp paired-end mode
Adaptors and low quality pair-end sequences were removed from the raw reads and the ribosomal RNA was filtered using the SortMeRNA algorithm (Kopylova, E., Noé, L. & Touzet, H. (2012) SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217).
To generate transcriptome sequences, paired-end reads originating from roots and leaves from one individual plant of Noccaea caerulescens subsp. fimiensis (Ncfi) and Noccaea montana (Nmon) were assembled de novo using CLC Genomic Workbench 9 with Lenght fraction:0.75; Similarity fraction: 0.95; word size: 30 (Ncfi), 24 (Nmon). Contig sequences were annotated using Blast2GO using BlastX with E-value≤10-6.
Paired-end reads of all independent samples were mapped to the Ncfi_transcriptome_v1. using CLC Genomic Workbench 9 with Lenght fraction 0.5 and Similarity fraction 0.875. Read counts are used for abundance measurements.
Genome_build: de novo transcriptome assembly:
Ncfi_transcriptome_v1.fasta
Nmon_transcriptome_v1.fasta
|
| |
|
| Submission date |
Jun 06, 2018 |
| Last update date |
Jun 06, 2019 |
| Contact name |
Sylvain MERLOT |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
CNRS
|
| Department |
Biological Sciences
|
| Lab |
LRSV
|
| Street address |
24, chemin de Borde Rouge
|
| City |
Auzeville Tolosane |
| ZIP/Postal code |
31320 |
| Country |
France |
| |
|
| Platform ID |
GPL25153 |
| Series (2) |
| GSE115411 |
Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from the Noccaea genus (Brassicaceae) from France |
| GSE116054 |
Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from diverse genera and geographic locations |
|
| Relations |
| BioSample |
SAMN09375119 |
| SRA |
SRX4174675 |
