Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Sp1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
mESCs, differentiated
NA
NA

Attributes by original data submitter

Sample

source_name
Sp1 from E14 Flk1Plus
cell type
E14 FLK1+
strain
C57BL/6
chip antibody
anti-Sp1 antibody (Santa Cruz sc-17824X)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Flk1+ve sorted cells and c-kit+ve sorted floating progenitors from Day 3 blast culture were used for ChIP-seq analysis. Cells were crosslinked for 10 min at room temperature with 1% formaldehyde (Pierce, Rockford, IL, USA) and quenched with 1/10th volume 2 M glycine. Nuclei were prepared essentially as described in Lefevre et al 2003, sonicated using a Bioruptor water bath in immunoprecipitation buffer I (25 mM Tris 1 M, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1 % TritonX-100 and 0.25 % SDS). After centrifugation the sheared 0.5-2 kb chromatin fragments (1-2 x 106 cells) were diluted with 2 volumes immunoprecipitation buffer II (25 mM Tris, pH 8.0, 150mM NaCl, 2 mM EDTA, pH 8.0, 1% TritonX-100, 7.5% glycerol) and precipitation was carried out for 2-3 hours at 4 °C using 2 µg anti-Sp1 antibody (Santa Cruz sc-17824X) coupled to 15 µl Protein-G dynabeads. Beads were washed with low salt buffer (20 mM Tris 1 M, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1% TritonX-100, 0.1% SDS), high salt buffer (20 mM Tris, pH 8.0, 500 mM NaCl, 2 mM EDTA, pH 8.0, 1% TritonX-100, 0.1% SDS), LiCl buffer (10 mM Tris, pH 8.0, 250 mM lithium chloride, 1 mM EDTA, pH 8.0, 0.5% NP40, 0.5 % sodium-deoxycholate) and TE pH 8.0 containing 50 mM sodium chloride. The immune complexes were eluted in 100 µl elution buffer (100 mM NaHCO3, 1 % SDS) and after adding 5 µl 5M sodium chloride and proteinase K, the crosslinks were reversed at 65°C overnight. DNA was extracted using the Ampure PCR purification kit (Beckman Coulter) according to manufacturer’s instructions and analysed by qRT-PCR. Libraries of DNA fragments from chromatin immunoprecipitation were prepared from approximately 10 ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Ampure PCR purification kit (Beckman Coulter). ‘A’ bases were added to 3’ ends of fragments using Klenow Fragment (3´- 5´ exo-), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further Ampure clean up to remove excess adaptors, fragments were amplified in an 18-cycle PCR reaction using adapter-specific primers (5’-CAAGCAGAAGACGGCATACGAGCTCTTCCGATC*T and 5’-AATGATACGGCGACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T). The libraries were purified and adapter dimers removed by running the PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Libraries were validated using quantitative PCR for known targets, and quality assessed by running 1 µl of each sample on an Agilent Technologies 2100 Bioanalyser. Once prepared, DNA libraries were subjected to massively parallel DNA sequencing on an Illumina Genome Analyzer IIx. DNA from in vivo treated cells was run on an agarose gel and fragments were excised and isolated. This DNA was used to prepare the libraries, according to Illumina's sample preparation protocol

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
25495768
Reads aligned (%)
95.7
Duplicates removed (%)
16.4
Number of peaks
14825 (qval < 1E-05)

mm9

Number of total reads
25495768
Reads aligned (%)
95.5
Duplicates removed (%)
16.5
Number of peaks
14844 (qval < 1E-05)

Base call quality data from DBCLS SRA