 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 12, 2018 |
| Title |
WTCol0-0-1 |
| Sample type |
SRA |
| |
|
| Source name |
6 day-old aerial parts
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: Wild type
|
| Growth protocol |
Seeds are stratified for 3 days at 4°C in darkness before transfer to growth chamber for 6 days (16hL/8hD: 8 am-12 pm, ~80 µE, ~65% humidity, ~21°C). Media: Murashige and Skoog (MS) 1/2, 1% sucrose, 0,4% phytagel or 0.8% Agar
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy kit (Qiagen®, Hilden, Germany) according to the supplier’s instruction
TruSeq Stranded mRNA SamplePrep Guide 15031047 D protocol (Illumina®, California, U.S.A.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNAseq_caa39_Vs_WT.xlsx
|
| Data processing |
Trimming of library adapters with fastQC (0.10.1) and reads with a Phred Quality score>20 and lenght > 30 bases were kept
Alignement with Bowtie 2 against TAIR10 transcriptome with one isoform per gene
Quatification with edgeR (1.12.0)
Quantification of transposable element transcripts unsing Tetranscripts (Jin et al, 2015) with prior alignement against TAIR10_TE.gtf. Multi-read alignement allowed.
Genome_build: TAIR10-31
Supplementary_files_format_and_content: bigwig files, Excel file containing gene and TE transcript quantification in the mutant versus the wt
|
| |
|
| Submission date |
Sep 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Christophe Laloi |
| E-mail(s) |
christophe.laloi@univ-amu.fr
|
| Phone |
+334 91 82 95 64
|
| Organization name |
Aix-Marseille Université
|
| Department |
Biology
|
| Lab |
LGBP
|
| Street address |
163 avenue de Luminy
|
| City |
Marseille |
| State/province |
France |
| ZIP/Postal code |
13009 |
| Country |
France |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE103924 |
Topoisomerase VI participates to a chromatin barrier-like function that prevents heterochromatin spreading in euchromatic islands (HTS) |
| GSE129249 |
Topoisomerase VI participates to a chromatin barrier-like function that prevents heterochromatin spreading in euchromatic islands |
|
| Relations |
| BioSample |
SAMN07656249 |
| SRA |
SRX3190294 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
|
|
|
|
 |
