|
| Status |
Public on Aug 02, 2021 |
| Title |
SHSY5Y - PARIS-Flag2 magnetic beads rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SHSY5Y neuroblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow-derived metastatic cancer tissue
chip antibody: Flag antibody
genotype: PARIS-flag
treatment: transfected with flag-PARIS
|
| Treatment protocol |
For transient transfection, cells were transfected with indicated amounts of either flag-PARIS or flag using Fugene HD (Promega, Madison, WI) according to manufacturer’s instructions. After 48 hours incubation, SHSY-5Y cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and 125 mM glycine were then added to inactivate the formaldehyde.
|
| Growth protocol |
Human SHSY-5Y neuroblastoma cells were purchased from American Type Culture Collection (ATCC, Manassas, VA) and cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % heat-inactivated fetal bovine serum (FBS) and 1 % penicillin/streptomycin (Gibco-Invitrogen, Carlsbad, CA).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After cross-linking and fractionation steps, PARIS DNA binding sites were enriched by immunoprecipitation of the DNA-PARIS complexes using magnetic beads and flag antibodies. The same protocol was used for the control sample. Protein-bound DNA was extracted for the preparation of sequencing libraries.
CHIP-seq high sensitivity kit (ab185908, Abcam) was further used for ChIP-Seq library preparation according to manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq 2000 sequencer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4.
For each sample, after quality control as mentioned above, reads were separately aligned to the latest human genome (NCBI; GRCh38) using Bowtie with the parameter “-m 1” to retain uniquely mapped reads only. The R packages ChIPQC v1.20.0 and PhantomPeakQualTools v1.2.2 were used to confirm the quality of the aligned bam files based on the ChIP-seq guidelines by ENCODE consortium (NSC >= 1.05; RSC >= 0.8, Qtag={-2,-1,0,1,2}). QC-confirmed bam files were subject to differential peak calling using MACS v1.4.220 with the following parameters: -t Sample.sam -c Control.sam --format SAM -g hs -B -S --call-subpeaks. Peak annotation and visualization were done using the R packages ChIPseeker v1.20.0 and clusterProfiler v3.12.0, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: Bedgraph files generated from peak files built from reads mapping uniquely to the genome contain coordinates of the genomic location of each peak called
|
| |
|
| Submission date |
May 25, 2021 |
| Last update date |
Aug 02, 2021 |
| Contact name |
Karin M Danzer |
| Organization name |
University of Ulm / DZNE, Ulm
|
| Department |
Department of Neurology
|
| Lab |
Danzer Lab
|
| Street address |
University of Ulm Campus, Building N24, R3306 Albert-Einstein-Allee 11
|
| City |
Ulm |
| State/province |
Baden-Wurttemberg |
| ZIP/Postal code |
89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE175555 |
Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression dissects recognition of multiple PPAR-γ associated gene regulation (ChIP-Seq). |
| GSE175556 |
Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of multiple PPAR-γ associated gene regulation |
|
| Relations |
| BioSample |
SAMN19337890 |
