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Series GSE144244 Query DataSets for GSE144244
Status Public on Jul 28, 2021
Title m6A RNA methylation regulates promoter proximal pausing of RNA Pol II (ChIP-Seq)
Organism Drosophila melanogaster
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 HA ChIP-seq with S2R+ cell extracts transfected with HA tagged Mettl3, Mettl14, fl2d, Ythdc1 and Control. Pol II ChIP-seq in cells depleted for either Mettl3, Mettl14, fl2d, Ythdc1 and Control. Ser2P ChIP-seq with S2R+ cell extract where Mettl3, Mettl14, fl2d were depleted along with control knockdwon condition.
Contributor(s) Akhtar J
Citation(s) 34297910
Submission date Jan 24, 2020
Last update date Jul 28, 2021
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 (1)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (44)
GSM4284351 Mettl14HAChIP_Rep1
GSM4284352 Mettl14HAChIP_Rep2
GSM4284353 Mettl14HAInput
This SubSeries is part of SuperSeries:
GSE144246 m6A RNA methylation regulates promoter proximal pausing of RNA Pol II
BioProject PRJNA603118
SRA SRP244718

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Supplementary file Size Download File type/resource 21.4 Mb (ftp)(http) BW 22.0 Mb (ftp)(http) BW 22.3 Mb (ftp)(http) BW
GSE144244_H3K36Me3_1.sorted.bam 1.6 Gb (ftp)(http) BAM
GSE144244_H3K36Me3_2.sorted.bam 2.0 Gb (ftp)(http) BAM
GSE144244_H3K36Me3_Input.bam 1.9 Gb (ftp)(http) BAM 22.0 Mb (ftp)(http) BW 22.1 Mb (ftp)(http) BW 22.2 Mb (ftp)(http) BW 21.9 Mb (ftp)(http) BW 21.6 Mb (ftp)(http) BW 21.8 Mb (ftp)(http) BW 22.2 Mb (ftp)(http) BW 22.3 Mb (ftp)(http) BW 21.5 Mb (ftp)(http) BW 22.0 Mb (ftp)(http) BW 21.5 Mb (ftp)(http) BW 22.0 Mb (ftp)(http) BW 22.3 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data provided as supplementary file

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