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Sample GSM4200330 Query DataSets for GSM4200330
Status Public on Sep 28, 2022
Title 4C-seq wild-type repeat 1
Sample type SRA
Source name SH-SY5Y cells
Organism Homo sapiens
Characteristics cell type: SH-SY5Y cells
restriction enzyme: NlaIII
condition: wild-type
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 The 4C-seq was performed as previously reported with some modifications (van de Werken et al, Methods Enzymol. 2012; 513:89-112.). NlaIII and BfaI were selected as the first and second restriction enzymes, respectively.
Before generating 4C-seq libraries for sequencing, 4C template of viewer point (VP: SNCA promoter) were PCR amplified by 6 cycles using specific primers. Final 4C-seq libraries were generated by PCR amplified by 24 cycles using indexed primers (P5 and P7).
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing Library strategy: 4C-Seq
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Raw reads were separated into individual sample FastQ Files by barcode sequences.
Raw reads were filtered by retaining VP-specific PR amplicons (GGAGGGGGTGGTGCTGC), trimmed to remove nucleotide sequences belongs to the VP restriction fragment,
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files showed the distribtuion of raw reads in whole genome
Submission date Dec 02, 2019
Last update date Sep 28, 2022
Contact name Fubo Cheng
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 GPL18573
Series (2)
GSE141277 Transcription regulation of SNCA by dystonia type 6 gene product THAP1 [4C-Seq]
GSE141278 Transcription regulation of SNCA by dystonia type 6 gene product THAP1
BioSample SAMN13381797
SRA SRX7208524

Supplementary file Size Download File type/resource
GSM4200330_wild-type_rep1_nearbait_norm_counts.bedGraph.gz 12.7 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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