WebA second antibody used in ChIP-seq experiments on PAX5 in our lab is PAX5 (C-20) sc-1974, a goat polyclonal antibody with epitope mapping at the C-terminus of PAX-5 of human origin. Irreproducible Discovery Rate (IDR) analysis results for two ChIP-seq experiments using these two antibodies, each in GM12878, are as follows: WebGM12878 cell culture NOTES: A. Upon receipt, cells should be expanded for a few days (see #3 below) and then frozen in aliquots (see #6 below). B. Cell density is critical for …
ENCODE and modENCODE Guidelines For Experiments …
Webtype Cell type Dataset identifier Protocol Correlation between Chip-seq and qPCR Positive predictive value (PPV) BATF ChIP GM12878 SL839 PCR1x 0.84 0.978 GABP ChIP … WebChIP-on-chip (also known as ChIP-chip) is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray ("chip").Like regular ChIP, ChIP-on … pond balance water treatment
ENCSR000BGY – ENCODE
WebFeb 13, 2024 · The EBNA2 and EBNA3 in MutuIII, PolII and H3K27ac in GM12878, and gene density are not correlated with the enrichment of MutuI 4C peaks (Fig. 3a, c). 4C peaks containing EBNA1 binding sites were ... WebGrowth protocol. GM12878 cells were grown in RPMI media containing 15% FBS. Extracted molecule. genomic DNA. Extraction protocol. Nuclei were isolated from cross-linked (1% formaldehyde for 10 minutes at room temperature) GM12878 cells. Nuclei were lysed in RIPA buffer and extracted chromatin was sonicated using Branson Sonifier 250. WebHere, we detail (i) the experimental protocol for preparing quality control spike-in chromatin from Drosophila melanogaster cells and (ii) the computational protocol to compare … pond balls