|
| Status |
Public on Sep 28, 2022 |
| Title |
4C-seq wild-type repeat 2 |
| 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 |
| 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 |
