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Sample GSM4705391 Query DataSets for GSM4705391
Status Public on Apr 29, 2021
Title RNA_seq_ref6_shoot_rep1
Sample type SRA
Source name RNA_seq_ref6_shoot_rep1
Organism Arabidopsis thaliana
Characteristics genotype: ref6 mutant
Growth protocol RNAseq assays were performed on shoot or root of 14‐day‐old seedlings
Extracted molecule total RNA
Extraction protocol RNA extraction using Nucleospin RNA kit from Macherey Nagel
Libraries were produced using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Trimmomatic-0.38 : Minimum length of 30 bp; Mean Phred quality score > 30; Leading and trailing bases removal with base quality <5. STAR aligner was used to mapped the reads to TAIR10 genome assembly. Raw read counts were then extracted using featureCounts based on the gene annotations in Araport11_GFF3_genes_transposons.201606.gtf. DESeq2 to identify differentially expressed genes. Genes having read counts ≥ 50 in atleast 2 samples were considered for differential expression analysis.
Genome_build: TAIR10
Submission date Jul 31, 2020
Last update date Apr 29, 2021
Contact name Sanchari Sircar
Organization name IPS2
Lab Chromosome Dynamics
Street address Batiment 630 Rue Noetzlin
City Orsay
ZIP/Postal code 75015
Country France
Platform ID GPL19580
Series (1)
GSE155502 Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis
BioSample SAMN15689637
SRA SRX8860851

Supplementary file Size Download File type/resource
GSM4705391_ref6_Shoot_rep1.txt.gz 195.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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