|
| Status |
Public on Sep 28, 2022 |
| Title |
Wild-type SHSY5Y H3K4me3 Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SHSY5Y cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SHSY5Y cells
conditions: Wild-type
antibody: anti-H3K4me3 (Cell signaling, C42D8)
|
| Growth protocol |
SH-SY5Y cells were cultured in DMEM medium with 10% FBS and 1% Glutmax at 37℃ in a humidified atmosphere containing 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked by 1% formaldehyde (ThermoFisher scientific) and sonicated in RIPA buffer (10 mM Tris-HCl, 1 mM EDTA, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40, 1× Protease inhibitor cocktail (Roche), pH 8.0) to 200-500 bp. The sonicated lysate was subjected to immunoprecipitation with specific antibody. The immunoprecipitated DNA (at least 1ng) was purified and subjected to libraries generation.
ChIP-seq libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Reads qualities of ChIP-seq data in fastq files were assessed using QoRTs (v1.2.37). Raw reads were aligned to the hg19 genome assembly using BWA (v0.7.17). Alignment quality was analyzed and unmapped reads were filtered using samtools (v1.12).
ChIP-seq peaks calling were analyzed using MACS2 (v2.1.1.20160309)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files
|
| |
|
| Submission date |
Sep 28, 2021 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Fubo Cheng |
| E-mail(s) |
fubo.cheng@med.uni-tuebingen.de
|
| Organization name |
University of Tuebingen
|
| Department |
Institute of Medical Genetics and Applied Genomics
|
| Street address |
Calwerstrasse 7
|
| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE184957 |
THAP1 is cell type dependent regulator of SP1 family crucial for dystonic syndromes in human and rat [SHSY5Y_ChIP-seq] |
| GSE184961 |
THAP1 is cell type dependent regulator of SP1 family crucial for dystonic syndromes in human and rat |
|
| Relations |
| SRA |
SRX12391704 |
