|
| Status |
Public on Jun 05, 2015 |
| Title |
Sample_H3K9me2_Input_shLSD18a_B0_I18 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured SH-SY5Y cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y
infection: LSD1+8a 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 |
input
|
| 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 |
SAMN03174674 |
| SRA |
SRX757026 |
