Data Summary
- Genome build
- Data source/consortium
- Tissue/cell type category
- Biosample types
- Assay type
- Data description
- Acknowledgements
Experimental assays
Listed below are experimental assay categories and specific assay types contained in FILER. The assay descriptions are provided based on OBI and EFO ontologies.
| 3D chromatin structure | ||
| 5C | 5C stands for Chromosome conformation capture carbon copy. It is an extension of the original 3C technique that studies 3-dimensional organisation and interaction of chromatin in a cell. It detects interactions among all loci by ligating universal primers to all fragments. As a result, the whole genome is covered, albeit at a relatively low coverage. The 5C technique overcomes the junctional problems at the intramolecular ligation step and is useful for constructing complex interactions of specific loci of interest. | http://www.ebi.ac.uk/efo/EFO_0007692 |
| ChIA-PET | ChIA-PET (chromatin interaction analysis by paired-end tag sequencing) is a type of chromosome conformation capture assay that uses chromatin immunoprecipitation to enrich for protein-specific chromatin complexes after digestion, followed by nuclear proximity ligation and high-throughput paired-end-tag sequencing. | http://www.ebi.ac.uk/efo/EFO_0008684 |
| DNA accesibility | ||
| ATAC-seq | Assay for transposase-accessible chromatin using sequencing (ATAC-seq), is a method based on direct in vitro transposition of sequencing adaptors into native chromatin, and is a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol. | http://www.ebi.ac.uk/efo/EFO_0007045 |
| DNase-seq | An assay in which DNA is the input molecule derived from a DNase-hypersensitivity digest of chromatin with the aim of identifying regulatory elements. | http://www.ebi.ac.uk/efo/EFO_0003752 |
| FAIRE-seq | FAIRE-Seq (Formaldehyde-Assisted Isolation of Regulatory Elements) is an assay used for determining the sequences of DNA regions associated with regulatory activity. This is enabled by the isolation of nucleosome-depleted DNA from total genomic dna to access actively transcribed dna. | http://www.ebi.ac.uk/efo/EFO_0004428 |
| GM DNase-seq [genetic modification followed by DNase-seq] | An assay in which DNA is the input molecule derived from a DNase-hypersensitivity digest of chromatin with the aim of identifying regulatory elements. | http://www.ebi.ac.uk/efo/EFO_0003752 |
| DNA binding | ||
| ChIP-seq | ChIP-seq is an assay in which chromatin immunoprecipitation with high throughput sequencing is used to identify the cistrome of DNA-associated proteins. | http://www.ebi.ac.uk/efo/EFO_0002692 |
| DNA methylation | ||
| RRBS | Reduced representation bisulfite sequencing (RRBS-Seq) | http://www.ebi.ac.uk/efo/EFO_0008900 |
| Genome annotation | ||
| Annotation | Genome annotation | NA |
| repeats | repeat regions annotation | NA |
| Genotyping | ||
| CGH [comparative genomic hybridization by array] | copy number variation | http://www.ebi.ac.uk/efo/EFO_0010937 |
| Genotyping | An assay in which variation in a part of or the whole genome is analysed | http://www.ebi.ac.uk/efo/EFO_0000750 |
| Quantitative trait loci | ||
| eQTL | expression quantitative trait loci | NA |
| sQTL | splicing quantitative trait loci | NA |
| Reference genome sequence | ||
| Reference genome sequence | Reference genome sequence | NA |
| RNA binding | ||
| eCLIP | eCLIP maps the binding sites of RBPs on their target RNAs using a modified individual nucleotide resolution CLIP (iCLIP) protocol, improving efficiency and decreasing execution complexity | http://www.ebi.ac.uk/efo/EFO_0009998 |
| iCLIP | Individual nucleotide resolution CLIP (iCLIP) | http://www.ebi.ac.uk/efo/EFO_0008774 |
| RIP-chip | RNA-binding protein immunoprecipitation array profiling assay | http://purl.obolibrary.org/obo/OBI_0001918 |
| RIP-seq | A method used for finding which RNA species interact with a particular RNA-binding protein. It involves immunoprecipitation with antibodies for the protein and then isolation of the RNAs associated with the protein. Unlike CLIP-seq, no cross-linking of RNAs and proteins is carried out prior to immunoprecipitation. | http://www.ebi.ac.uk/efo/EFO_0005310 |
| Switchgear | RNA binding | NA |
| TargetScan | biological targets of miRNAs | NA |
| Transcription | ||
| CAGEScan | CAGEscan: a mate-pair adaptation of nanoCAGE that captures the transcript 5_ ends linked to a downstream region | http://www.ebi.ac.uk/efo/EFO_0008669 |
| CAGE-Seq | High throughput Cap-analysis gene expression (CAGE) | http://www.ebi.ac.uk/efo/EFO_0008708 |
| CAGE | High throughput Cap-analysis gene expression (CAGE) | http://www.ebi.ac.uk/efo/EFO_0008708 |
| hCAGE | High throughput Cap-analysis gene expression (CAGE) | http://www.ebi.ac.uk/efo/EFO_0008708 |
| LQhCAGE | High throughput Cap-analysis gene expression (CAGE) | http://www.ebi.ac.uk/efo/EFO_0008708 |
| microRNA counts | miRNA expression | NA |
| RAMPAGE | RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay | http://purl.obolibrary.org/obo/OBI_0001864 |
| RNA-microarray [transcription profiling by array assay] | transcription profiling by an array assay | NA |
| RNA-PET | transcript analysis by paired-end tag sequencing assay | http://purl.obolibrary.org/obo/OBI_0001850 |
| short total RNA-Seq | short total RNA-seq | NA |
| Small RNA-Seq | small RNA-seq | NA |
| Transcription factor binding | ||
| Homer known motif | HOMER transcription binding sites | NA |
Data glossary
For descriptions of the main output data types, experimental targets and genomic feature types, please refer to data glossary and data terms.
Acknowledgements
We acknowledge the original publications of data sources available in FILER and the funding they received. If you use FILER in your research, please cite the FILER paper as well as the orginal publications producing the raw data and aknowledge the funding that they received.