|
| Status |
Public on Nov 23, 2021 |
| Title |
atxr5/6 (W)_R1_SxaQSEQsYA038L4_index_12 |
| Sample type |
SRA |
| |
|
| Source name |
cotyledons
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: two-week-old
tissue: cotyledons
genotype: atxr5/6 (W)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. A single replicate was collected for each genotype.Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the NeoPrep Library Prep System (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
SxaQSEQsYA038L4_index_12
|
| Data processing |
Reads were aligned using Tophat by allowing up to two mismatches and mapping only to one location. Chromosome mitochondria and chloroplast were exluded from alignments.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each genes generated by Cufflinks
|
| |
|
| Submission date |
Feb 16, 2021 |
| Last update date |
Nov 23, 2021 |
| Contact name |
magdalena ewelina potok |
| Organization name |
UCLA
|
| Department |
MCDB
|
| Lab |
Jacobsen lab
|
| Street address |
4045 Terasaki Life Sciences Building
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7239 |
| Country |
USA |
| |
|
| Platform ID |
GPL21785 |
| Series (2) |
| GSE166884 |
The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_5_6] |
| GSE166897 |
The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis |
|
| Relations |
| BioSample |
SAMN17927470 |
| SRA |
SRX10112833 |
