|
| Status |
Public on May 24, 2017 |
| Title |
WT_seedlings_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
7 days old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype/genotype: WT Col-0
developmental stage: 7 days old seedlings
|
| Treatment protocol |
-
|
| Growth protocol |
7 days old seedlings growing on 1/2 MS medium with 0,8% phytoagar on continuous light conditions at 22°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with Direct-zol™ RNA MiniPrep Kit (Zymo Research) and 4 µg was used to isolate polyadenylated RNAs with NEBNext Oligo d(T)25 Magnetic Beads (E7490, Biolabs).
The libraries were done with ScriptSeq™ Plant Leaf kit (Epicentre) following the manufacturer's instruction. Single end sequencing was performed on an Illumina HiSeq2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
tophat (v2.0.10) was used for spliced alignments against A. thaliana reference genome (TAIR10)
cufflinks (version 2.2.1) was used to extract FPKM counts
Genome_build: TAIR10
Supplementary_files_format_and_content: text files, cufflinks output files
|
| |
|
| Submission date |
May 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Eva-Maria Willing |
| E-mail(s) |
willing@mpipz.mpg.de
|
| Organization name |
MPIPZ
|
| Street address |
Carl-von-Linne Weg 10
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE98779 |
LUC7 is an U1snRNP component that plays a role in alternative splicing and terminal introns removal in plants |
|
| Relations |
| BioSample |
SAMN06927734 |
| SRA |
SRX2796077 |
