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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 01, 2023 |
| Title |
CaptureC_cDC2_2 |
| Sample type |
SRA |
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| Source name |
Classical dendritic cell
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| Organism |
Mus musculus |
| Characteristics |
cell type: Classical dendritic cell
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
NuTi Capture-C combines 3C library preparation with oligonucleotide capture for IRF8 promoter viewpoint restriction fragments, as described in Downes et al., Nat. Commun. 12, 1-15, 2021 and Downes et al., Nat. Protoc. 17, 445-475, 2022.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Data processing |
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2 -v 3) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Assembly: mm9
Supplementary files format and content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
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| Submission date |
Apr 01, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Zhijian Li |
| E-mail(s) |
zhijian.li@rwth-aachen.de
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| Organization name |
RWTH Aachen University
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| Lab |
Institute for Computational Genomics
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| Street address |
Pauwelsstr. 19
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| City |
Aachen |
| State/province |
North Rhine-Westphal |
| ZIP/Postal code |
52062 |
| Country |
Germany |
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| Platform ID |
GPL21626 |
| Series (1) |
| GSE198651 |
A lncRNA identifies Irf8 enhancer element in negative feedback control of dendritic cell differentiation |
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| Relations |
| BioSample |
SAMN27176236 |
| SRA |
SRX14708261 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5993819_cDC2-promoter_BR2_IRF8p_normalised.bigWig |
418.2 Kb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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