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Sample GSM1542270 Query DataSets for GSM1542270
Status Public on Jun 05, 2015
Title Sample_LSD1_SH-SY5Y_B0_S63
Sample type SRA
 
Source name Cultured SH-SY5Y cells
Organism Homo sapiens
Characteristics cell line: SH-SY5Y
antibody: LSD1 (ab-17721; Abcam)
infection: control shRNA
neuronal maturation: B0
Treatment protocol SH-SY5Y cells were seeded onto collagen-coated plates at an initial density of 104 cells/cm2. Retinoic acid (RA) (Sigma) was added at a final concentration of 10 μM the next day after plating. After 4 days, the cells were washed three times with PBS and incubated with 50 ng/mL of Brain Derived Neural Factor (BDNF) (Millipore) in serum-free medium for 3 days.
Growth protocol SH-SY5Y were maintained in Dulbecco's Modified Eagle Medium (DMEM) containing 4,500 mg/L glucose, 10% heat-inactivated fetal bovine serum, 110 mg/L sodium pyruvate, 2 mM L-glutamine and 1% penicillin-streptomycin.
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde for 10 minutes at room temperature before termination with 0.125 M glycine. Cells were then lysed in ChIP buffer (0.6% SDS, 10 mM EDTA, and 50 mM Tris-HCl, pH 8.1) and cross-linked chromatin was sonicated to obtain DNA fragments of 300–800 bp. Immunoprecipitations were performed following the Upstate protocol (http://www.upstate.com). DNA was recovered by phenol-chloroform extraction and ethanol precipitation.
ChIP-seq libraries were prepared using NEBNext DNA library preparation reagents (E6000) and the protocol and reagents concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. After PCR amplification, 300-600 bp DNA fragments were selected on an agarose gel. Libraries were quantified by Qubit (Invitrogen), and library size was assessed by Bioanalyzer (Agilent). Libraries were sequenced using a HiSeq 2000 (Illumina) to generate 50 bp single end reads.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description LSD1 ChIP-seq is done in SH-SY5Y infected control shRNA at B0
Data processing base_calling: CASAVA package (Illumina v1.6)
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-1.0.0
peaks were called using macs14 with the following setting:--pvalue=1e-5
Genome_build: hg19
Supplementary_files_format_and_content: txt and peak list; bedgraph files.
 
Submission date Nov 10, 2014
Last update date May 15, 2019
Contact name Ruitu Lyu
E-mail(s) lvruitu@gmail.com
Organization name Institutes of Biomedical Sciences Fudan University
Lab Epigenetics lab
Street address 138 Yixueyuan Road Xuhui District
City Shanghai
ZIP/Postal code 200030
Country China
 
Platform ID GPL16791
Series (2)
GSE58258 The LSD1/KDM1A neuro-specific isoform regulates neuronal differentiation through H3K9 demethylation [ChIP-Seq]
GSE63153 The LSD1/KDM1A neuro-specific isoform regulates neuronal differentiation through H3K9 demethylation
Relations
BioSample SAMN03174684
SRA SRX757045

Supplementary file Size Download File type/resource
GSM1542270_Sample_LSD1_SH-SY5Y_B0_S63.bedgraph.gz 99.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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