|
| Status |
Public on Nov 15, 2017 |
| Title |
dex3 |
| Sample type |
SRA |
| |
|
| Source name |
inflorescence
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia-0
tissue: inflorescence
age: 30 days after germination
developmental stage: until flower stage 3-4
|
| Treatment protocol |
0.01% ethanol,0.015% Silwet, with or without 10µM dexamethasone,
|
| Growth protocol |
23°C; 65% humidity; 16h light/8h dark; LED lights 200µE
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy plant mini kit according to manufacturer instructions (Qiagen, Hilden, Germany)
The RNA were poly A selected using the NEB Poly (A) Magnetic isolation module (7490), then the NEBnext Ultra Direction RNA Prep Kit (E7420) for Illumina with the NEBnext Multiplex Oligo's for Illumina (E7335). For RNA 1 µg inout was used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality control: FastQC
Read alignment: TOPHAT2
BAM SAM conversion: samtools
Read table reconstruction: HT-seq
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with normalized read count table
|
| |
|
| Submission date |
Jan 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jan Lohmann |
| E-mail(s) |
jan.lohmann@cos.uni-heidelberg.de
|
| Phone |
+49186784234
|
| Organization name |
Centre for Organismal Studies
|
| Department |
Stem Cell Biology
|
| Lab |
Jan Lohmann
|
| Street address |
Im Neuenheimer Feld, 230
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE94309 |
Control of plant cell fate transitions by transcriptional and hormonal signals [RNA-seq: mock_vs_dex_3h] |
| GSE94311 |
Control of plant cell fate transitions by transcriptional and hormonal signals |
|
| Relations |
| BioSample |
SAMN06284161 |
| SRA |
SRX2529379 |
