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Sample GSM3070163 Query DataSets for GSM3070163
Status Public on Aug 08, 2019
Title bdr1_rep1
Sample type SRA
Source name bdr1 single mutant (SALK_142108C)_seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype/variation: bdr1 single mutant (SALK_142108C)
age: Eight-day old
tissue: seedlings
Growth protocol Seeds were sown on MS plates and stratified for 4 days at 4°C in the dark. Plates were transfered to a growth chamber at 21°C and grown for 8 days under long day conditions (16h light/8h dark).
Extracted molecule total RNA
Extraction protocol The seedlings were ground into fine powder in liquid nitrogen. Total RNA was extracted using Trizol reagent following the manufacturer's instructions
Libraries were prepared from 1.5µg of total RNA using Illumina TruSeq Stranded mRNA Library Prep kit. Libraries were sequenced on a NextSeq500 instrument at Indiana University Center for Genomics and Bioinformatics.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description GSF1238-2_S2
Data processing Alignment : STAR v2.5.2b (Dobin et al., Bioinformatics, 2013) with default parameters
Filtering : samtools v1.3.1 was used to keep only primary alignments of reads with mapping quality above 10 (MapQ>10)
Counting: featureCounts from the Rsubread package (v 1.24.2) of R (v. 3.3.2) / Bioconductor (v. 3.4) was used to count uniquely mapping read pairs on TAIR10 annotated genes.
DE analysis : Differential expression analysis was performed using the DESeq2 package (v1.14.1) on protein-coding genes (excluding genes with zero counts in all samples or overlapping with blacklisted regions)
Genome_build: TAIR10
Supplementary_files_format_and_content: GSF1238_RawCounts_bdrs.txt contains the raw counts from featureCounts
Supplementary_files_format_and_content: GSF1238_NormalizedCounts_bdrs.txt contains the DESeq2-normalized counts
Submission date Mar 28, 2018
Last update date Aug 08, 2019
Contact name Pascal GP Martin
Organization name INRAE
Department UMR1332 BFP
Street address 71 avenue Edouard Bourlaux
City Villenave d'Ornon
ZIP/Postal code 33140
Country France
Platform ID GPL19580
Series (2)
GSE112441 Gene expression profiling by RNA-seq of wild-type, fpa mutant, bdr1 mutant, bdr2 mutant, bdr3 mutant and bdrs triple mutant Arabidopsis seedlings
GSE112443 RNA-seq, ChIP-seq and MNase-seq in WT, fpa mutant and bdr1,2,3 mutant Arabidopsis seedlings
BioSample SAMN08805278
SRA SRX3856938

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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