HOME> Products> Molecular Biology> Special probes for a novel epigenomic analysis (ChIL : Chromatin Integration labeling)
High sensitive epigenomic analysis more than than ChIP Special probes for a novel epigenomic analysis (ChIL : Chromatin Integration labeling)
Date：June 10 2026Web Page No：562533
ChIL probe is a newly developed probe for Chromatin Integration labeling (ChIL) method. This method enables to perform more sensitive epigenomic analysis than ChIP without special equipment. This product has two options, anti-mouse IgG antibody or anti-rabbit IgG antibody, depending on the type of your primary antibody.
- Problems with conventional Chromatin immunoprecipitation (ChIP)
- Principe of ChIL
- Features
- Comparison with ChIL-seq and ChIP-seq
- Application note
- Reference
- Product information
Problems with conventional Chromatin immunoprecipitation (ChIP)
ChIP (Chromatin Immunoprecipitation) is widely used to analyze interaction between specific regions of genomic DNA and DNA binding proteins such as histone proteins and transcriptional factors. ChIP is the way to isolate DNA by immunoprecipitation using a specific antibody to DNA-protein complex, and it is possible to obtain neighbor DNA of the target protein binding site from genomic DNA contained in chromatin. Although ChIP specifically isolates target DNA using an antigen-antibody reaction, it cannot yield more DNA than was originally present in the sample, as it lacks an amplification step. Therefore, this method is not sensitive enough for extremely small samples, and a more sensitive technique is required.
ChIL (Chromatin Integration Labeling) is a method for analyzing target sequences after amplification by using special ChIP probes. It is now possible to detect target sequences from small amounts of samples via the amplification step.
Principe of ChIL
In ChIL, amplification of target sequences is accomplished by in vitro transcription initiated from the T7 promoter sequence inserted into the adjacent target DNA sequence on the genomic DNA of the sample. The structure of the ChIL probe is an antibody labeled with an oligo DNA and a fluorescent dye (TAMRA). The oligo DNA contains the T7 promoter sequence and Tn5 transposase binding region sequence.
Structure of ChIL probe
Outline of the procedures for amplification and analysis of target DNA sequences by ChIL
- Please refer to the reference2) for detailed procedures and required materials.
- After fix cell or tissue samples, perform permeabilization and blocking to the samples.
- Add a primary antibody to the blocked samples to bind a target DNA binding protein.
- Add a ChIL probe compatible with the primary antibody to the samples and observe the staining image.
- Add Tn5 transposase* to the samples. (An oligo DNA sequence present on the ChIL probe is inserted by transposase activity into the genomic DNA adjacent to the probe bound to the primary antibody.)
- T7 RNA polymerase* is added to the samples and reacted. The target sequences of the DNA- binding protein bound to the primary antibody are amplified by in vitro transcription initiated from the T7 promoter region contained in the oligo DNA.
- Purify the transcribed RNA, prepare NGS library*, and analyze the obtained sequencing data.
* Tn5 transposase, T7 RNA polymerase, and a NGS library preparation kit etc. are also required.
Flow of ChIL analysis
Features
- It is more sensitive than ChIP and compatible for very low input samples.
- No need for fragmentation of chromatin, so no special equipment is required.
- As the probe is labeled by a fluorescent dye (TAMRA), the samples can be analyzed after observation by a fluorescence microscope.
- The products are available in anti-mouse IgG and anti-rabbit IgG formats, and are compatible with a wide range of antibodies.
Comparison with ChIL-seq and ChIP-seq
| Method | Required cell numbers | Chromatin fragmentation |
|---|---|---|
| ChIP-seq | 1,000 cells or more （Usually required more than 100,000 cell） |
Required |
| ChIL-seq | At least single cell （Recommended to prepare around 1,000 cells usually） | Unrequired |
Application note
C2C12 cells were stained with anti-histone antibody (as primary antibody) and ChIL probe (as secondary antibody). Nuclei were stained in the sample with the primary antibody (left figure). In contrast, nuclei were not stained in the sample without the primary antibody (right figure).
Immunostaining of C2C12 cells by ChIL probe
Primary antibody : Anti-histone antibody (only for the left figure)
Secondary antibody : ChIL probe
Counterstain : DAPI
Reference
- Harada, A., et al., Nat. Cell Biol., 21(2), 287(2019). PMID:30532068
“A chromatin integration labelling method enables epigenomic profiling with lower input” - Handa, T., et al., Nat. Protoc., 15(10), 3334(2020). PMID:32807906
“Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input” - Maehara, K., et al., Mol. Syst. Biol., 17(11), e10323(2021). PMID:34730297
“Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections”
Product information
Anti-mouse IgG antibody format
[Date : June 15 2026 00:07]
| Detail | Product Name | Product Code | Supplier | Size | Price | ||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ChIL Probe #AH001M-12 DatasheetThis may not be the latest data sheet. |
AH001M-12 | TXO | 12 µl | $649 | |||||||||||||||||||||||||||||||
|
|
|
||||||||||||||||||||||||||||||||||
|
ChIL Probe #AH001M-60 |
AH001M-60 | TXO | 60 µl | $2,416 | |||||||||||||||||||||||||||||||
|
|
|
||||||||||||||||||||||||||||||||||
[Date : June 15 2026 00:07]
ChIL Probe #AH001M-12
DatasheetThis may not be the latest data sheet.
- Product Code: AH001M-12
- Supplier: TXO
- Size: 12µl
- Price: $649
| Description |
Anti-mouse IgG antibody-based probe for use in the Chromatin Insertion and Labeling (Chromatin Integration Labeling, ChIL) method, a new epigenomic analysis technique. Corresponds to mouse IgG antibody (primary antibody). |
||
|---|---|---|---|
| Storage | -20°C,Dark Storage | CAS | |
| Link |
|
||
ChIL Probe #AH001M-60
- Product Code: AH001M-60
- Supplier: TXO
- Size: 60µl
- Price: $2,416
| Description |
Anti-mouse IgG antibody-based probe for use in the Chromatin Insertion and Labeling (Chromatin Integration Labeling, ChIL) method, a new epigenomic analysis technique. Corresponds to mouse IgG antibody (primary antibody). |
||
|---|---|---|---|
| Storage | -20°C,Dark Storage | CAS | |
| Link |
|
||
Anti-rabbit IgG antibody format
[Date : June 15 2026 00:07]
| Detail | Product Name | Product Code | Supplier | Size | Price | ||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ChIL Probe #AH001R-12 DatasheetThis may not be the latest data sheet. |
AH001R-12 | TXO | 12 µl | $649 | |||||||||||||||||||||||||||||||
|
|
|
||||||||||||||||||||||||||||||||||
|
ChIL Probe #AH001R-60 |
AH001R-60 | TXO | 60 µl | $2,416 | |||||||||||||||||||||||||||||||
|
|
|
||||||||||||||||||||||||||||||||||
[Date : June 15 2026 00:07]
ChIL Probe #AH001R-12
DatasheetThis may not be the latest data sheet.
- Product Code: AH001R-12
- Supplier: TXO
- Size: 12µl
- Price: $649
| Description |
Anti-rabbit IgG antibody-based probe for use in the Chromatin Insertion and Labeling (Chromatin Integration Labeling, ChIL) method, a new epigenomic analysis technique. Corresponds to rabbit IgG antibody (primary antibody). |
||
|---|---|---|---|
| Storage | -20°C,Dark Storage | CAS | |
| Link |
|
||
ChIL Probe #AH001R-60
- Product Code: AH001R-60
- Supplier: TXO
- Size: 60µl
- Price: $2,416
| Description |
Anti-rabbit IgG antibody-based probe for use in the Chromatin Insertion and Labeling (Chromatin Integration Labeling, ChIL) method, a new epigenomic analysis technique. Corresponds to rabbit IgG antibody (primary antibody). |
||
|---|---|---|---|
| Storage | -20°C,Dark Storage | CAS | |
| Link |
|
||
CONTACT
export@funakoshi.co.jp
- ※Prices on our website are for your reference only. Please inquire your distributor for your prices.
- ※Please note that Product Information or Price may change without notice.