Study : Transcriptional Regulation of Nitrogen and Nitrogen-Related Metabolism in Arabidopsis

Identification

• Name: Transcriptional Regulation of Nitrogen and Nitrogen-Related Metabolism in Arabidopsis
• Identifier: dXJuOkVWQS9zdHVkeS9QUkpOQTQyMjExOA==
• Data link: Link to this study on EBI European Nucleotide Archive
• Description: Purpose: Investigate transcriptional changes by genetic perturbation of specific transcription factors under sufficient and limiting nitrate conditions. Methods: 9 day old roots were harvested between 1-2pm (get hours after “sunrise”) and frozen in liquid N2. RNA-seq libraries were prepared following the BRAD-Seq DGE protocol (four biological replicates per genotype and treatment). Libraries were sequenced using the Ilummina HiSeq 3000 in SR50 mode. Two technical replicates libraries were created from each RNA sample; after assessing sufficient reproducibility, counts across technical replicates were pooled together. Reads were processed with fastx_trimmer for barcode removal (-f 9 -v -Q 33) and trimmed by quality with reaper (paremeters: -geom no-bc -dust-suffix-late 10/ACTG -dust-suffix 10/ACTG --noqc -nnn-check 1/1 -qqq-check 33/10 -clean-length 30 -tri 20 -polya 5 --bcq-late), then mapped to the reference genome of Arabidopsis thaliana (TAIR v10) using bowtie (-a --best --strata -n 1 -m 1 -p 4 --sam --tryhard) with subsequent conversion to BAM format using samtools and counts were obtained with HTSeq-count. Overall design: Wild-type and 12 T-DNA insertion lines were grown in media with 1 or 10 mM KNO3. mRNA from 9 days old roots was collected for RNA-seq libraries using BRAD-seq.
• Data files: SRR6369541; SRR6369540; SRR6369539; SRR6369538; SRR6369537; SRR6369536; SRR6369535; SRR6369534; SRR6369530; SRR6369529; SRR6369528; SRR6369470; SRR6369469; SRR6369468; SRR6369467; SRR6369466; SRR6369465; SRR6369464; SRR6369463; SRR6369462; ERZ1080650; ERZ1178852; ERZ1080601; ERZ1179078; ERZ1080619; ERZ1178729; ERZ1080613; ERZ1179060; ERZ1080612; ERZ1179065; ERZ1080510; ERZ1179087; ERZ1080608; ERZ1179063; ERZ1080564; ERZ1178726; ERZ1080523; ERZ1178713; ERZ1080668; ERZ1178909

Genotype

Accession number	Name	Taxon
	GABI_513E07	Arabidopsis thaliana
	GABI_699B09	Arabidopsis thaliana
	GABI_868	Arabidopsis thaliana
	SAIL_1207	Arabidopsis thaliana
	SALK_012253	Arabidopsis thaliana
	SALK_015182	Arabidopsis thaliana
	SALK_035980	Arabidopsis thaliana
	SALK_070847C	Arabidopsis thaliana
	SALK_085964C	Arabidopsis thaliana
	SALK_094437C	Arabidopsis thaliana
	SALK_100002	Arabidopsis thaliana
	SALK_146141	Arabidopsis thaliana