|
| Status |
Public on May 29, 2019 |
| Title |
416B_2_Sfpi1-Prom |
| Sample type |
SRA |
| |
|
| Source name |
myeloid progenitor cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 416B
cell type: myeloid progenitor cell line
4c-seq viewpoint: PU.1 Promoter
|
| Growth protocol |
416B cells were cultured under standard conditions using DMEM medium supplemented with 20% FCS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
4C-seq was performed as previously described (PMID: 22609568). For chromatin digestion NlaIII (NEB) and Csp6I (Thermo Scientific) were used as first and second restriction endonucleases. Inverse PCR was performed to amplify the specific viewpoint at the PU.1 promoter. Single-end sequencing was performed using the Illumina HiSeq2500 platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: 4C-seq
Base calling was performed with Illumina's CASAVA 1.7.
4C-seq reads were aligned against the mouse reference genome (mm10 /GRCm38.69) using BWA-mem (bwa v. 0.7.12; default settings)
Aligned reads were mapped to a virtual restriction fragment library based on the chosen restriction enzyme sequences with the R/Bioconductor package Basic4Cseq.
Fragment data was RPM-normalized and filtered: Only uniquely aligned reads were kept for analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bed files were created with the R/Bioconductor package Basic4Cseq and include running median RPM values per valid fragment in the chosen near-cis region for the experiment's viewpoint.
|
| |
|
| Submission date |
Nov 29, 2018 |
| Last update date |
Oct 28, 2021 |
| Contact name |
Frank Rosenbauer |
| E-mail(s) |
frank.rosenbauer@ukmuenster.de
|
| Organization name |
University Hospital Münster
|
| Department |
Institute of Molecular Tumor Biology
|
| Street address |
Robert-Koch-Str. 43
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE123131 |
Benchmarking of 4C-seq pipelines based on real and simulated data |
|
| Relations |
| BioSample |
SAMN10499730 |
| SRA |
SRX5079887 |
