title: GSM2981908: methylome_35S_TET1_3_rep1; Arabidopsis thaliana; OTHER
library_construction_protocol: Genomic DNA libraries were prepared following the MethylC-seq protocol without use of the bisulfite conversion step. MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). TAB-seq libraries were prepared as previously described in (Yu et al. 2012). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer's instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. ChIP library preparation. Leaves were treated with formaldehyde to covalently link protein to DNA, washed several times with distilled water, patted dry and ground into fine powder in liquid nitrogen. Chromatin was extracted with a series of extraction buffers and sonicated. The final chromatin solution was incubated overnight with anti-H3K9me2 antibody (Cell Signaling Technology, 9753S) coated Dynabeads protein A (Life Technologies, 10002D) to precipitate the immune complex. After a few washes, the immune complex was eluted and incubated at 65 degrees in the presence of a high concentration of NaCl in a water-bath overnight. After degrading the proteins with proteinase K, DNA was recovered by phenol/chloroform/isoamyl alcohol extraction followed by ethanol precipitation. The DNA pellet was then dissolved in 30µl of nuclease-free water.
attributes.tag: GEO Accession
attributes.value: GSM2981908