|
| Status |
Public on Apr 17, 2020 |
| Title |
Control_6hr_Replicate1 [24_6_rep1] |
| Sample type |
SRA |
| |
|
| Source name |
Control_6hr_protonema
|
| Organism |
Physcomitrium patens |
| Characteristics |
strain: Gransden
cell type: protonema
treatment: Control_6hour
|
| Growth protocol |
protonemata were cultivated axenically in petri dishes containing PpNH4 medium supplemented with 7g.L-1 agar in a growth chamber maintained at 24 °C under a photoperiod of 16/8 h and an irradiance of 100 µmol.m-2.s-1. Harvest at 6H.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total moss RNA was extracted from 100 mg of P. patens 7-day protonemal tissues from control or heat-treated samples using Nucleospin® RNA plant (Macherey-Nagel-Germany).
Sequencing was carried out by Eurofin (Germany) using one channel and Illumina Illumina HiSeq 2500 2x 100 bp paired-end. RNA libraries were prepared for sequencing using standard Illumina protocols
strand-specific cDNA libraries; RNA selection using polyA selection. RNAseq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
24_6_rep1_CTGAAGCT-CCTATCCT_L008
|
| Data processing |
basecalling Illumina RTA 1.18.64
demultiplexing software bcl2fastq-1.8.4. Sequences are demultiplexed according to the 2x8 bp index code with 1 mismatch allowed.
Mapping of reads to the reference genome using BWA-MEM (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1)
Raw read counts created using featureCounts on a Galaxy web server (Galaxy Tool Version: 1.4.6.p5) with default parameters and feature type filter = gene. The annotation version 3.3 of P. patens genome (file Ppatens_318_v3.3.gene.gff3 was downloaded from http://plants.ensembl.org).
Genome_build: Ppatens_318_v3 (https://genome.jgi.doe.gov/)
Supplementary_files_format_and_content: featureCounts. gene level expression estimates; tab-delimited text
|
| |
|
| Submission date |
Oct 05, 2019 |
| Last update date |
Apr 17, 2020 |
| Contact name |
Said Mouzeyar |
| E-mail(s) |
[email protected]
|
| Organization name |
Université Clermont Auvergne
|
| Department |
Biology
|
| Lab |
UMR GDEC 1095 INRA-UCA
|
| Street address |
1 Impasse Amélie Murat
|
| City |
Aubière |
| ZIP/Postal code |
63178 |
| Country |
France |
| |
|
| Platform ID |
GPL17793 |
| Series (1) |
| GSE138467 |
Dynamics of the transcriptome response to heat in the moss, Physcomitrella Patens |
|
| Relations |
| BioSample |
SAMN12920292 |
| SRA |
SRX6954701 |
