title: GSM1232785: WT_mRNA; Arabidopsis thaliana; RNA-Seq
library_construction_protocol: ChIP-seq: 2 grams of expanded leaves were ground in liquid nitrogen and fixed in 1% formaldehyde for 10 minutes. The reaction was stopped by adding 0.125 M glycine. Nuclei were extracted by filtration through Miracloth and iteratively washed and centrifuged at 2,000g.  Nuclei were lysed in SDS buffer. DNA was sonicated for 10 cycles of 0.5 minute on and 1 minute off with an UCD-200TM-EX Bioruptor (Diagenode) on medium power, at 0 to 4°C. Sonicated chromatin was incubated overnight with either anti-H2As or anti-H3 (ab1791, Abcam) antibodies. After pre-clearing, magnetic protein A-beads (Dynabeads protein A, Invitrogen) were incubated with the antibodies-chromatin mix for 3 hours. After precipitation of the beads on a magnetic rack (MagnaRack, Invitrogen) and washes with increasing stringency, DNA was eluted at 65°C and reverse cross-linked with proteinase K (Fermentas). Immunoprecipitated DNA was treated with RNase A (Fermentas) and purified with the QIAquick purification kit (Qiagen). ChIP-seq libraries were generated as per manufacturer’s instructions (Illumina). Bisulfite-seq: 0.1g of mature rosette leaves were collected, and genomic DNA was extracted using Plant DNeasey mini purification kit (Qiagen). Libraries were generated and sequenced as previously described (Feng et al., Methods Mol Biol. 2011;733:223-38.). RNA-seq: RNA-seq experiments were performed in two biological replicates for each genotype. Tissue was ground in Trizol (Invitrogen).  Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina Truseq).
attributes.tag: GEO Accession
attributes.value: GSM1232785