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Sample GSM3070159 Query DataSets for GSM3070159
Status Public on Aug 08, 2019
Title fpa_8
Sample type SRA
Source name fpa single mutant (fpa-7)_seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype/variation: fpa single mutant (fpa-7)
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 with Plant/Fungi Total RNA purification kit (Norgen) following the manufacturer's instructions
Libraries were prepared from 3µg of total RNA using Illumina RNA TruSeq Sample Prep kit. Libraries were sequenced on a HiSeq2000 instrument at the Beijing Genomics Institute.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description fpa_8
Data processing Alignment : Tophat v2.0.8 (Trapnell et al., Bioinformatics, 2009)
Filtering : samtools v1.2 and grep unix command on tag "NH :i :1" were used to keep only uniquely mapped reads
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 mapped reads on TAIR10 annotated genes using option strandSpecific=0 (non stranded).
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). Sample WT_12 was removed from the DE analysis because of its low sequencing depth.
Genome_build: TAIR10
Supplementary_files_format_and_content: GSF509_RawCounts.txt contains the raw counts from featureCounts
Supplementary_files_format_and_content: GSF509_NormalizedCounts.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 GPL13222
Series (2)
GSE112440 Gene expression profiling in wild-type, fpa 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 SAMN08805277
SRA SRX3856933

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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