Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative multiplexed ChIP-Seq (MINUTE-ChIP) from formaldehyde-fixed material

ABSTRACT: Quantitative multiplexed ChIP-Seq (MINUTE-ChIP) from formaldehyde-fixed material

PROVIDER: PRJNA1026104 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR26324368.fastq.gz	Fastqsanger.gz
	SRR26324368_1.fastq.gz	Fastqsanger.gz
	SRR26324368_2.fastq.gz	Fastqsanger.gz
	SRR26324369.fastq.gz	Fastqsanger.gz
	SRR26324369_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Quantitative multiplexed ChIP-Seq (MINUTE-ChIP) from formaldehyde-fixed material

Project description:In crosslinked MINUTE-ChIP, formaldehyde-fixed chromatin is fragmented using sonication, blunted and ligated to double-stranded DNA adaptors that include a T7 RNA polymerase promoter and a sample barcode sequence. Finally, samples are combined and subsequent ChIP reactions are performed with the pooled samples. ChIP material is prepared into an Illumina-compatible library using linear amplification by virtue of T7 RNA polymerase, reverse transcription and a low-cycle library PCR amplification. Here, we demonstrate a MINUTE-ChIP for Nanog from formaldehyde-fixed cells using fragmentation by sonication.

2024-02-11 | GSE244908 | GEO

Quantitative multiplexed ChIP-Seq (MINUTE-ChIP) Calibration Experiment

Project description:In MINUTE-ChIP, native chromatin is fragmented using Micrococcal nuclease, and subsequently blunted and ligated to double-stranded DNA adaptors that include a T7 RNA polymerase promoter and a sample barcode sequence. Finally, samples are combined and subsequent ChIP reactions are performed with the pooled samples. ChIP material is prepared into an Illumina-compatible library using linear amplification by virtue of T7 RNA polymerase, reverse transcription and a low-cycle library PCR amplification. Native MINUTE-ChIP is based on Mint-ChIP, developed by the Bernstein lab (van Galen et al., 2016; PMID: 26687680). We have introduce unique molecule (UMI) counting and paired-end mapping of the chromatin fragments to this method, which we then termed MINUTE-ChIP for multiplexed indexed unique molecule T7 amplification end-to-end sequencing. Here, we generate a standard curve for H3K27me3 and demonstrate that MINUTE-ChIP has a large linear dynamic range, thus MINUTE-ChIP quantitation is proportional to real quantities.

2019-06-21 | GSE133056 | GEO

Quantitative multiplexed ChIP-Seq (MINUTE-ChIP) Calibration Experiment

Project description:Quantitative multiplexed ChIP-Seq (MINUTE-ChIP) Calibration Experiment

| PRJNA549856 | ENA

PAT-ChIP-Seq: a novel tool for the epigenetic profiling of formaldehyde-fixed and paraffin-embedded (FFPE) pathology samples

Project description:Epigenetic alterations in the pattern of DNA and histone modifications play a crucial role in cancer development. Analysis of patient samples, however, is hampered by technical limitations in the study of chromatin structure from pathology archives that typically consist of heavily fixed, paraffin-embedded material. ChIP assays (with anti-H3K4me3 and anti-H3K27me3 antibodies) were performed by using formaldehyde-fixed paraffin-embedded (FFPE) mouse spleen sections (half portion of the spleen) and comparing it to the canonical ChIP procedure applied by using isolated cells from the other portion of the same spleen.

2010-12-02 | E-GEOD-21449 | biostudies-arrayexpress

Analysis of RNA quantitation in formaldehyde-fixed cells

Project description:Fluorescence-activated cell sorting (FACS) is a sensitive and valuable technique to characterize cellular subpopulations and great advances have been made using this approach. Cells are often fixed with formaldehyde prior to the sorting process to preserve cell morphology and maintain the expression of surface molecules, as well as to ensure safety in the sorting of infected cells. It is widely recognized that formaldehyde fixation alters RNA and DNA structure and integrity, thus analyzing gene expression in these cells has been difficult. We therefore examined the effects of formaldehyde fixation on the stability and quantitation of nucleic acids in cell lines, primary leukocytes and also cells isolated from SIV-infected pigtailed macaques. We developed a method to extract RNA from fixed cells that yielded the same amount of RNA as our common method of RNA isolation from fresh cells. Quantitation of RNA by RT-qPCR in fixed cells was not always comparable with that in unfixed cells. In comparison, when RNA was measured by the probe-based NanoString system, there was no significant difference in RNA quantitation. In addition, we demonstrated that quantitation of proviral DNA in fixed cells by qPCR is comparable to that in unfixed cells when normalized by a single-copy cellular gene. These results provide a systematic procedure to quantitate gene expression in cells that have been fixed with formaldehyde and sorted by FACS.

2013-09-09 | GSE50690 | GEO

Analysis of RNA quantitation in formaldehyde-fixed cells

2013-09-09 | E-GEOD-50690 | biostudies-arrayexpress

Gene expression profiles of gliomas in formalin-fixed paraffin-embedded material

Project description:In this study we have performed expression analysis using paired FF-FFPE glioma samples. We show that expression data from FFPE glioma material is concordant with expression data from matched FF tissue, and can be used for molecular profiling in gliomas.

2012-07-01 | GSE30472 | GEO

Dynamic antagonism between key repressive pathways maintains the placental epigenome (MINUTE-ChIP)

Project description:Dynamic antagonism between key repressive pathways maintains the placental epigenome (MINUTE-ChIP)

| PRJNA838412 | ENA

Aquifer material

Project description:Aquifer material Metagenome

| PRJNA720508 | ENA

Parallel-factor ER ChIP-seq of Breast Cancer PDX Material

Project description:Parallel-factor ER ChIP-seq of Breast Cancer PDX Material

| PRJNA434662 | ENA