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Status |
Public on Sep 28, 2022 |
Title |
4C-seq wild-type repeat 2 |
Sample type |
SRA |
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|
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).
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|
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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
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|
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Submission date |
Dec 02, 2019 |
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 |
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 |
|
Relations |
BioSample |
SAMN13381797 |
SRA |
SRX7208525 |