GSM3263218: Rec-1 ChIPseq input WO rep1; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Input control
Antigen
Input control
Cell type
Cell type Class
Blood
Cell type
REC-1
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma B-cell
Attributes by original data submitter
Sample
source_name
Rec-1 cell line
cell line
Rec-1
cell type
Mantle cell lymphoma cell line
chip antibody
input
drug treatment
GSI-washout
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq was performed as previously described (Ryan et al., 2017). Briefly, chromatin samples prepared from appropriate number of fixed cells (107 for histone modifications and 4 x 107 for transcription factors) were sonicated and cleared with recombinant protein G–conjugated Agarose beads (Invitrogen, cat# 15920-010) and subsequently immunoprecipitated with antibodies recognizing Notch1 (Wang et al., 2014), RBPJ (D10A4) (CST, cat# 5313), H3K27ac (Active Motif, cat# 39133), H3K27me3 (EMD Millipore cat# 07-449), H3K4me1 (Abcam, cat# ab8895), Smc1a (Bethyl, cat# A300-055A) and CTCF (EMD Millipore cat# 07-729). Antibody-chromatin complexes were captured with recombinant protein G–conjugated Agarose beads, washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and TE buffer with 50mM NaCl and eluted. Input sample was prepared by the same approach without immunoprecipitation. After reversal of cross-linking, RNase and Proteinase K (Invitrogen, cat# 25530-049) treatment were performed and DNA was purified with QIAquick PCR Purification Kit (Qiagen, cat# 28106). Libraries were then prepared using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB, cat# E7645S). Two replicates were performed for each condition. Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Single end sequencing (75 bp) or Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.