7 protocols
AccessionNameType
P-GSE42410-6
feature_extraction
mRNA-seq reads were uniquely mapped to the genome using Bowtie (Langmead et al., 2009) allowing two mismatches. For smRNA-seq reads, adapter sequences were trimmed first, and then were uniquely mapped to the genome using Bowtie allowing no mismatches, and reads were categorized by their lengths for analyses Genome_build: MSU 6.1 Supplementary_files_format_and_content: Column 1 is the read sequence. Column 2 is the number of reads with the given sequence.
P-GSE42410-3
feature_extraction
BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to MSU6.1 chr1..12, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Identical reads were collapsed into single reads. Genome_build: MSU 6.1 Supplementary_files_format_and_content: Column 1 is chromosome (1..12). Column 2 is the coordinate of the genomic cytosine. Column 3 is genomic strand (+/-) of the cytosine. Column 4 is context (CG, CHG, or CHH) of the genomic cytosine. Column 5 is #Cs. Column 6 is #Ts.
P-GSE42410-4
specified_biomaterial_action
RNA-seq libraries were constructed from total RNA isolated using TRIzol reagent (Invitrogen, Life Technologies, USA) from leaf tissues
P-GSE42410-7
nucleic acid library construction protocol
Total RNA (10 ug) for each sample was used to purify poly-A mRNA; this mRNA was used for synthesis and amplification of cDNA. The RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit from Illumina (San Diego, CA).
P-GSE42410-5
nucleic acid library construction protocol
smRNA-seq libraries were constructed from total RNA isolated from the same tissues as described for the mRNA libraries, using the TruSeq Small RNA Sample Prep Kit from Illumina (San Diego, CA).
P-GSE42410-2
nucleic acid library construction protocol
Fragmented genomic DNA library as described in Cokus et al., Nature 2008, except directly with pre-methylated final adapters (see Feng et al., Methods Mol. Biol. 2011;733:223-38 for further information)
P-GSE42410-1
specified_biomaterial_action
Genomic DNA was extracted using Qiagen Plant DNeasy Maxi Kit.