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Sample GSM4671830 Query DataSets for GSM4671830
Status Public on May 26, 2021
Title rh27-2_shoot apices_sRNA-seq_rep3
Sample type SRA
Source name Shoot apices of 5-day old seedlings
Organism Arabidopsis thaliana
Characteristics tissue: shoot apices
developmental stage: 5 days after germination
genotype: rh27-2
Treatment protocol The seedlings grown at 21-22°C under a 16 h light and 8 h dark cycle.
Growth protocol The wild-type and rh27-2 line were grown on 1/2 Murashige and Skoog plates with 1% sucrose for 5 days after germination.
Extracted molecule total RNA
Extraction protocol The shoot apices or root tips were ground into fine powder in liquid nitrogen and processed using miRNeasy Mini Kit (217004, Qiagen).
Both small RNA-sequencing and mRNA-sequencing libraries generated from Col-0 wild-type and rh27-2 samples constructed following standard protocols (Berry Genomics).
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
Description high-throughput profiling of small RNA in rh27-2 (mutant) shoot apices
Data processing RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count. Differentially expressed genes were detected using R package edgeR.
Small RNA sequencing reads were aligned to the Arabidopsis genome (TAIR10) using Bowtie2. miRNA were aligned to mature miRNA sequence from miRBase using NCBI blast. miRNAs with RPM fold change over 1.5 were defined as differentially expressed miRNAs.
Genome_build: TAIR10
Supplementary_files_format_and_content: read count files were generated using htseq-count program. miRNA abundance files were generated using miRNA counts normalized against total mapped reads.
Submission date Jul 15, 2020
Last update date May 26, 2021
Contact name Jing Sun
Organization name Chinese Academy of Sciences
Department IGDB
Street address No. 1 West Beichen Road
City Beijing
ZIP/Postal code 100101
Country China
Platform ID GPL19580
Series (1)
GSE154473 DEAD-box RNA helicase 27-Mediated MicroRNA Biogenesis Is Essential for Zygote Division and Stem Cell Homeostasis in Arabidopsis
BioSample SAMN15543035
SRA SRX8736713

Supplementary file Size Download File type/resource
GSM4671830_FS3.txt.gz 1.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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