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Series GSE112633 Query DataSets for GSE112633
Status Public on Apr 11, 2018
Title TAF-ChIP: An ultra low input approach for genome wide chromatin immunoprecipitation assay
Organisms Drosophila melanogaster; Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The transcriptional regulation is often controlled by the epigenetic modifications or by chromatin associated proteins. To understand this regulation, chromatin immunoprecipitation (ChIP) followed by next generation sequencing is an invaluable and powerful technique. However, the major limitation of this approach is often the requirement of large amount of starting material for generating high-quality datasets, and often the workflow is laborious. This limitation also results in application of this approach to study of rare cell populations even more challenging, if not impossible. Here, we present a tagmentation-assisted fragmentation ChIP (TAF-ChIP) and sequencing method to generate high quality dataset from as few as 100 human and 1000 Drosophila cells. The method itself is straightforward and is by far less labor-intensive than conventional library preparation, and other contemporary low amount ChIP-Seq methods. Furthermore, this approach can be applied directly on 100 cells rather than relying on de-multiplexing strategies to generate the profile from limited number of cells. This can be extremely useful when the access to the starting material is very restricted, for example clinically isolated cells from patients. Using this approach we generated the H3K4Me3 and H3K9Me3 profiles from 100 K562 cells and 1000 sorted neural stem cells (NSC) from Drosophila. We benchmarked our TAF-ChIP datasets from K562 cells against the Encode datasets. For validating the TAF-ChIP datasets obtained from Drosophila NSCs we took advantage of Notch induced over proliferation specifically in type II NSCs. The epigenetic profile obtained from conventional ChIP-Seq approach and TAF-ChIP approach shows high degree of agreement, thereby underlining the utility of this approach for generating ChIP-Seq profiles from very low cell numbers.
Overall design ChIP Seq datasets from sorted Neural stem cells (NSCs) from Drosophila larval brain and sorted K562 cells. To benchmark the TAF-ChIP dataset, previously published datasets from ENCODE consortium and CUT&RUN (Nature Protocols volume 13, pages 1006?1019 (2018)) was donwloaded and processed identically as the TAF-ChIP datasets.
Contributor(s) Akhtar J
Citation(s) 31331983
Junaid Akhtar, Piyush More, Apurva Kulkarni, Federico Marini, Waldemaar Kaiser, and Christian Berger. TAF-ChIP: An ultra-low input approach for genome wide chromatin immunoprecipitation assay. bioRxiv 299727. doi:10.1101/299727
Submission date Apr 03, 2018
Last update date Aug 07, 2019
Contact name Junaid Akhtar
Organization name University of Mainz
Department Institute of Neurobiology and Developmental Biology
Street address Johannes-Joachim-Becherweg, 32
City Mainz
State/province Rheinland-Pflaz
ZIP/Postal code 55128
Country Germany
Platforms (3)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (23)
GSM3576635 Tum_1K_H3K4Me3_R1
GSM3576636 Tum_1K_H3K4Me3_R2
GSM3576637 Tum_1K_H3K9Me3_R1
BioProject PRJNA448587
SRA SRP137008

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 93.8 Mb (ftp)(http) BW 158.0 Mb (ftp)(http) BW 120.6 Mb (ftp)(http) BW 248.3 Mb (ftp)(http) BW 236.3 Mb (ftp)(http) BW 260.9 Mb (ftp)(http) BW 236.3 Mb (ftp)(http) BW
GSE112633_RAW.tar 1.5 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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