 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 14, 2019 |
| Title |
col_T2h_2 |
| Sample type |
SRA |
| |
|
| Source name |
col_T2h_2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
time: 2h
ecotype: Columbia
genotype: wild type
developmental stage: boyes: 1.0
tissue: roots
|
| Treatment protocol |
Name:MS/10-P media 2h - time course study - compound addition,phosphate:time 2hour . Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen. Plants were sowed in line on nylon mesh (100µ) (about 150-200 seeds/line). The nylon mesh were put on a MS/10+P media. Seeds were synchronized 24h at 4°C obscurity then plates were transfered into phytotron (16hd/8hn, 24°C/21°C, 33%humidity). Plants were grown for 7 days. Then the nylon mesh with plants were transfered to a new MS/10+P media (for T0 time) or MS/10-P media (for T1h or T2h). Root apices (about 0.5cm) were harvested and frozen into liquide nitrogen.
|
| 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 |
col_T2h_2(10ug)
rna_selection:selection polyA, paired-end, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Genome_build: genome of Arabidopsis thaliana TAIR10
Mapping and counts of reads by locus gene (tophat2/bowtie2). If PE reads, count only consistent PE reads
Supplementary_files_format_and_content: type:count file (txt); content:gene ID,length of Gene,nb single reads,nb PE reads
|
| |
|
| Submission date |
Mar 13, 2019 |
| Last update date |
Mar 14, 2019 |
| Contact name |
Thomas Blein |
| E-mail(s) |
thomas.blein@cnrs.fr
|
| Organization name |
CNRS
|
| Lab |
IPS2
|
| Street address |
rue de Noetzlin
|
| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE128250 |
rnadapt-Non-coding RNAs in the adaptation of root growth to phosphate starvation |
|
| Relations |
| BioSample |
SAMN11119331 |
| SRA |
SRX5516582 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3669297_rawcount_col_T2h_2.txt.gz |
126.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
