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Sample GSM5087552 Query DataSets for GSM5087552
Status Public on Nov 23, 2021
Title T2: SAC3b:SAC3B-Flag in sac3b-3 atxr5/6 (W)_SxaQSEQsYA038L4_index_25
Sample type SRA
 
Source name cotyledons
Organism Arabidopsis thaliana
Characteristics developmental stage: two-week-old
tissue: cotyledons
genotype: T2: SAC3b:SAC3B-Flag in sac3b-3 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 SxaQSEQsYA038L5_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
 
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 SAMN17927469
SRA SRX10112834

Supplementary file Size Download File type/resource
GSM5087552_SxaQSEQsYA038L5_index_25_genes.fpkm_tracking.gz 911.4 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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