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Sample GSM1174715 Query DataSets for GSM1174715
Status Public on Aug 26, 2013
Title Fbio-Ctrl_ChIPSeq
Sample type SRA
 
Source name Fbio-Ctrl expressing SH-SY5Y cells
Organism Homo sapiens
Characteristics cell type: neuroblastoma cell line
cell line: SH-SY5Y
expression: FBio-Ctrl
treatment: Retinoic Acid treatmeant (8 Days)
chip antibody: Streptavidin (Dynabeads, M-280)
Treatment protocol SH-SY5Y cells were treated for 8 days in the presence of 10uM Retinoic Acid (Media was changed on Days 2, 4, 6)
Growth protocol SH-SY5Y cells were grown in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin
Extracted molecule genomic DNA
Extraction 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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Alignment; 50bp short reads were mapped onto the Human genome (hg19, Feb 2009) using the burrows-wheeler alignment tool, allowing for up to two mismatches in each read.
Peak detection was performed using MACS (Zhang et al. 2008) where the FBio-Ctrl or Input_DNA datasets served as a normalization controls for the FBio-CHD5 and H3K27me3 datasets, respectively.
Tag density files for each dataset were generated using the IGV toolkit.
Genome_build: hg19, Feb 2009
Supplementary_files_format_and_content: tag density files
 
Submission date Jun 26, 2013
Last update date May 15, 2019
Contact name Adrian P. Bracken
Organization name Trinity College Dublin
Department Department of Genetics
Lab Bracken Lab
Street address 1 Lincoln Place
City Dublin
ZIP/Postal code Dublin 2
Country Ireland
 
Platform ID GPL11154
Series (1)
GSE48314 CHD5 is required for neurogenesis and has a dual role in facilitating gene expression and Polycomb gene repression
Relations
BioSample SAMN02213965
SRA SRX315188

Supplementary file Size Download File type/resource
GSM1174715_Fbio-Empty.tdf 376.2 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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