Truseq chip kit

Manufactured by Illumina

The TruSeq ChIP kit is a next-generation sequencing (NGS) library preparation kit designed for chromatin immunoprecipitation (ChIP) experiments. The kit enables the preparation of high-quality ChIP-seq libraries from small amounts of input material.

Automatically generated - may contain errors

Lab products found in correlation

Qubit 2.0 fluorometer, by Thermo Fisher Scientific (4 mentions) Qubit fluorimeter, by Thermo Fisher Scientific (1 mentions) Hiseq 4000, by Illumina (1 mentions) Hiseq 4000 sequencer, by Illumina (1 mentions) Tapestation 2200, by Agilent Technologies (1 mentions) Bioruptor pico sonicator, by Diagenode (1 mentions) Anti stat3, by Cell Signaling Technology (1 mentions) Anti ezh2, by Cell Signaling Technology (1 mentions) Casava v1, by Illumina (1 mentions) Qubit fluorometric quantitation system, by Thermo Fisher Scientific (1 mentions) Hiseq 2000, by Illumina (1 mentions) Anti rnapiis2p, by Abcam (1 mentions) Anti gfp, by Abcam (1 mentions)

8 protocols using truseq chip kit

ChIP-seq Library Preparation and Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

The single-end read libraries were prepared using the TruSeq ChIP kit from Illumina (catalog ID: IP-202-1024), with DNA size selection made with lab-made Serapure magnetic beads. Library concentration were assayed using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and normalized to 1.7 Nano gram per microliter. Six multiplexed libraries were sequenced per lane on a HiSeq 2000.

Xie M., Chen H., Huang L., O’Neil R.C., Shokhirev M.N, & Ecker J.R. (2018). A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. Nature Communications, 9, 1604.

+ Open protocol

+ Expand

H3K27Ac ChIP-seq protocol with sonication

Check if the same lab product or an alternative is used in the 5 most similar protocols

5 × 10⁵ fixed nuclei were sonicated to a 200–500 bp length with the Bioruptor Pico sonicator (Diagenode). H3K27Ac ChIP (Diagenode C15410174) was performed as previously described^{48 (link),49 (link)}, using 1/500 dilution of the antibody, with the addition of 5 mM of Na-Butyrate to all buffers. Libraries were then prepared following the Illumina ChIP TruSeq protocol and sequenced as 50 bp single-end reads on a illumina HiSeq 4000. Libraries were prepared starting with below <10 ng quantities of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications. Libraries were validated on a Tapestation 2200 (Agilent) and a Qubit fluorimeter (Invitrogen – Thermofisher Scientific). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

Rouco R., Bompadre O., Rauseo A., Fazio O., Peraldi R., Thorel F, & Andrey G. (2021). Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer. Nature Communications, 12, 7235.

+ Open protocol

+ Expand

ChIP-seq Library Preparation and Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

+ Open protocol

+ Expand

ChIP-seq Library Preparation Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

TruSeq ChIP kit from Illumina was used to perform library preparation according to the manufacturer’s recommendations. Briefly, IP and input DNA were first size selected using SPRIselect beads (Agencourt) in order to have fragments between 100 and 500 bp after BioAnalyzer profiling. one to ten nanogram of DNA were used in the first step of end-repair followed by the adenylation of 3′ end, allowing further ligation of specific Illumina adapters required for sequencing. These adapters contain specific indexes (barcodes) different for each sample, so that library from different samples can be mixed together before sequencing. After PCR amplification (12–15 cycles), quality assessment of DNA libraries was achieved using BioAnalyzer profiling and Qubit quantification. After equimolar pooling of libraries, the final dilution was accurately quantified using Kapa library quantification kit. Sequencing was performed on HiSeq 2500 instrument on rapid flow cells using single-read 50 or paired-read 100 nucleotides for reading mode SR50 or PE100 (see Table S1). Raw sequencing data were then used as Fastq files for further bioinformatic analysis. High-throughput sequencing was performed by the NGS platform of the Institute Curie supported by the grants ANR-10-EQPX-03, and ANR10-INBS-09-08 from the Agence Nationale de le Recherche and by the Canceropole Ile-de-France.

El-Daher M.T., Cagnard N., Gil M., Da Cruz M.C., Leveau C., Sepulveda F., Zarhrate M., Tores F., Legoix P., Baulande S., de Villartay J.P., Almouzni G., Quivy J.P., Fischer A, & de Saint Basile G. (2018). Tetratricopeptide repeat domain 7A is a nuclear factor that modulates transcription and chromatin structure. Cell Discovery, 4, 61.

+ Open protocol

+ Expand

ChIP-seq Profiling of Stat3 and Ezh2 Binding

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Ten million cells were used for each ChIP and were prepared using the protocol from Lee et. al. ^{26 (link)}. Briefly, cells were lysed and sheared using a probe sonicator to achieve a size of 200–300 bp, and chromatin was isolated using phenol: chloroform for library preparation. Immunoprecipitations were performed overnight at 4°C using anti-Stat3 (Cell Signaling #9139) and anti-Ezh2 (Cell Signaling #5246) antibodies at 1:100 dilution. Libraries were prepared using TruSeq ChIP kit (Illumina) and multiplexed for sequencing using 50-bp single reads. Libraries were sequenced on a Hi-Seq 2000 at the Genome Access Center of Washington University in St. Louis. Processing of ChIP-seq data was carried out using Encode standards. Binding sites were identified using MACS2. The functional significance of Ezh2 and Stat3 binding sites/peaks was evaluated using the Genomic Regions Enrichment of Annotations Tool (GREAT) ²⁷. Data was visualized using the Integrated Genomics viewer ²⁸. De novo motif analysis was carried out using HOMER ^{29 (link)}. The Ezh2 and Stat3 differentially bound peaks were annotated with the R package ChipSeeker. For ChIP-qPCR and sequential ChIP (ChIP-reChIP), forty million cells per sample were used and prepared according to Furlan-Magaril et al. ^{30 (link)}

Zimmerman S.M., Nixon S.J., Chen P.Y., Raj L., Smith S.R., Paolini R.L., Nay Lin P, & Souroullas G.P. (2022). Ezh2Y641F mutations co-operate with Stat3 to regulate MHC Class I antigen processing and alter the tumor immune response in melanoma. Oncogene, 41(46), 4983-4993.

+ Open protocol

+ Expand

ChIP-Seq Library Preparation and Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

For ChIP-Seq, the ChIP part of the protocol was conducted as described previously (Wang et al., 2012a (link), Wang et al., 2012b (link)) with minor modifications. Briefly, nine cell lysate samples of 100 μl were combined, immunoprecipitated and the final purified IP DNA was resuspended in 30 μl of distilled water. The DNA concentration of the anti-FLAG (7.2 ng/μl) and input (23.0 ng/μl) samples were determined using the Qubit® Fluorometric Quantitation System (Life Technologies). The anti-FLAG IP DNA and input DNA were used for library preparation for Illumina sequencing using the TruSeq ChIP kit (Illumina, San Diego, CA) following manufacturer’s protocol. Briefly, 20 ng of ChIP DNA samples were end repaired-ligated to Illumina adaptors and selected for a fragment size of approximately 300 bp by gel extraction. Multiplex Illumina primers were used to amplify gel-extracted products. The amplified ChIP-Seq libraries were quantitated by qPCR and loaded to a concentration of 2.5 pM per lane in the Illumina HiSeq2000 platform. A standard paired-end sequencing reaction was performed to generate 50 bp of sequence in each direction. The raw data was converted from .bcl file format to .fastq format for downstream analysis. This was done using CASAVA v1.8.2 software from Illumina.

Ayala J.C., Wang H., Silva A.J, & Benitez J.A. (2015). Repression by H-NS of genes required for the biosynthesis of the Vibrio cholerae biofilm matrix is modulated by the second messenger cyclic diguanylic acid. Molecular microbiology, 97(4), 630-645.

+ Open protocol

+ Expand

ChIP-seq Protocol for Epigenetic Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols

ChIP assay was carried out as described previously (71 ). Briefly, the cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and formaldehyde was then inactivated by the addition of 125 mM glycine. Chromatin extracts containing DNA fragments with an average size of 200 to 500 base pairs were immunoprecipitated using anti-RARα, anti-RXRα, anti-H3K27ace, or anti-p300 antibody. The ChIP-enriched DNA was then decross-linked and used for library preparation using an Illumina TruSeq ChIP kit followed by analysis using Illumina sequencing or used for real-time PCR.

Loo S.Y., Toh L.P., Xie W.H., Pathak E., Tan W., Ma S., Lee M.Y., Shatishwaran S., Yeo J.Z., Yuan J., Ho Y.Y., Peh E.K., Muniandy M., Torta F., Chan J., Tan T.J., Sim Y., Tan V., Tan B., Madhukumar P., Yong W.S., Ong K.W., Wong C.Y., Tan P.H., Yap Y.S., Deng L.W., Dent R., Foo R., Wenk M.R., Lee S.C., Ho Y.S., Lim E.H, & Tam W.L. (2021). Fatty acid oxidation is a druggable gateway regulating cellular plasticity for driving metastasis in breast cancer. Science Advances, 7(41), eabh2443.

+ Open protocol

+ Expand

CENP-A Chromatin Immunoprecipitation Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

ChIPs were performed using the MAGnify kit (Life Technologies). 10⁶ cells (~10μg DNA) was used for each IP and chromatin was sheared to fragments 100–300bp long. 1μl of anti-CENP-A (rabbit, Active Motif), anti-SSRP1 (Nakayama et al., 2007 (link)), anti-GFP (Abcam), or anti-RNAPIIS2p (Abcam) were coupled to 10μl beads for 2h and mixed with chromatin overnight at 4°C. Immunoprecipitated DNA was eluted in 50μl of elution buffer, and analyzed by qPCR. Normalization was performed using the formula:

100 \times AE^(averageCT INPUT - averageCT IP)

, where AE is the amplification efficiency calculated by the formula

AE = 10^(- 1 / slope)

. The values obtained for induced were normalized by those for uninduced cells to calculate enrichment. For ChIP-seq, DNA from three independent ChIPs were pooled and made into libraries with the TruSeq ChIP kit (Illumina). Samples were ran on a MiSeq using Reagent Kit v3. See supplementary experimental procedures for mapping information.

Chen C.C., Bowers S., Lipinszki Z., Palladino J., Trusiak S., Bettini E., Rosin L., Przewloka M.R., Glover D.M., O’Neill R.J, & Mellone B.G. (2015). Establishment of centromeric chromatin by the CENP-A assembly factor CAL1 requires FACT-mediated transcription. Developmental cell, 34(1), 73-84.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!