title: GSM2151671: NELF-EKD_VEH_GFP_NELFE_2; Homo sapiens; ChIP-Seq
library_construction_protocol: PARP-1 ChIP-seq:  Following mock ADP-ribosylation in intact nuclei from MEFs as described above, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and chromatin was used for chromatin immunoprecipitation.  Click-ChIP-seq:  Following 8-Bu(3-yne)T-ADP-ribosylation in intact nuclei from MEFs as described above, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and bound to streptavidin-conjugated magnetic beads.  Following extensive washing, the beads were collected in a magnetic field and de-crosslinked overnight at 65°C.  DNA was to be sequenced was recovered by magnetic separation from the beads and purified by PCIAA extraction and ethanol precipitation. All Other ChIP-seq:  Cells were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and chromatin was used for chromatin immunoprecipitation. After purification, 50 ng of ChIP’d DNA for each condition was used to generate libraries for sequencing, as previously described  {Robertson, 2007 #41}, with some modifications.  Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated with Ilumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250 ± 25 bp) was size-selected by agarose gel electrophoresis and extraction, amplified by PCR, and purified using AmPure beads (Beckman Coulter).  The final libraries were subjected to QC (size, purity, adapter contamination) and sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.
attributes.tag: GEO Accession
attributes.value: GSM2151671