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Sample GSM5087602 Query DataSets for GSM5087602
Status Public on Nov 23, 2021
Title WT_R2_SxaQSEQsYB052L8_index_23
Sample type SRA
 
Source name roots
Organism Arabidopsis thaliana
Characteristics developmental stage: two-week-old
tissue: roots
genotype: WT
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from two-week-old roots grown on 1%MS under long day conditions. Four replicates, grown on separate plates were collected for each genotype.Each replicate conisted of ~ 10 roots from individual plants. RNA was extracted using Direct-zol RNA Miniprep kit (Zymo)
1ug of total RNA was used to prepare libraries using the TrueSeq Stranded mRNA-Seq kit (Illumina) .
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description SxaQSEQsYB052L8_index_23
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)
GSE166887 The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis [RNA-seq-12_13]
GSE166897 The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis
Relations
BioSample SAMN17927487
SRA SRX10112767

Supplementary file Size Download File type/resource
GSM5087602_SxaQSEQsYB052L8_index_23_genes.fpkm_tracking.gz 622.1 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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