|
Status |
Public on Nov 23, 2021 |
Title |
ddm1-2_R3_SxaQSEQsYAP054L7_index_25 |
Sample type |
SRA |
|
|
Source name |
cotyledons
|
Organism |
Arabidopsis thaliana |
Characteristics |
developmental stage: two-week-old tissue: cotyledons genotype: ddm1-2
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was extracted from two-week-old cotyledons grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype. Each replicate conisted of ~ 20 cotyledons. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo). RNA for stubl2-3 atxr5/6 (W) genotype was successfully extracted for only two out of four replicates. 1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina) .
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
SxaQSEQsYAP054L7_index_25
|
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
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|
|
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) |
GSE166891 |
The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq_17-18] |
GSE166897 |
The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis |
|
Relations |
BioSample |
SAMN17927594 |
SRA |
SRX10112900 |