GSM1174714: FBio-CHD5 ChIPSeq; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
Biotin
Cell type
Cell type Class
Neural
Cell type
SH-SY5Y
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma
Attributes by original data submitter
Sample
source_name
FBio-CHD5 expressing SH-SY5Y cells
cell type
neuroblastoma cell line
cell line
SH-SY5Y
expression
FBio-CHD5
treatment
Retinoic Acid treatmeant (8 Days)
chip antibody
Streptavidin (Dynabeads, M-280)
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Differentiated SH-SY5Y cells cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin from FBio-CHD5 and Fbio-Ctrl expressing SH-SY5Y cells was precipitated with magnetic streptavidin beads (Invitrogen) or the H3K27me3 antibody and recovered DNA and an Input DNA control were used for high throughput sequencing. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 14 cycles and library fragments of 150-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was sent to BGI genomics for sequencing on an Illumina Hi-Seq 2000 platform.