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MINUTE-ChIP example data

dataset
posted on 2024-05-07, 12:40 authored by Carmen Navarro LuzonCarmen Navarro Luzon, Simon ElsässerSimon Elsässer

This collection contains an example MINUTE-ChIP dataset to run minute pipeline on, provided as supporting material to help users understand the results of a MINUTE-ChIP experiment from raw data to a primary analysis that yields the relevant files for downstream analysis along with summarized QC indicators.

Example primary non-demultiplexed FASTQ files provided here were used to generate GSM5493452-GSM5493463 (H3K27m3) and GSM5823907-GSM5823918 (Input), deposited on GEO with the minute pipeline all together under series GSE181241.

For more information about MINUTE-ChIP, you can check the publication relevant to this dataset:

Kumar, Banushree, et al. "Polycomb repressive complex 2 shields naïve human pluripotent cells from trophectoderm differentiation." Nature Cell Biology 24.6 (2022): 845-857.

If you want more information about the minute pipeline, there is a public biorXiv and a GitHub repository and official documentation.

Funding

Stiftelsen för Strategisk Forskning (FFL7)

Knut och Alice Wallenbergs Stiftelse, Sweden

KI Research Foundation Grants (2022-01826)

The Ragnar Söderbergs Stiftelse, Sweden

Dynamic interplay of Polycomb complexes in establishing and maintaining cellular memory

Swedish Research Council

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NAISS

Swedish Research Council

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NAISS Storage projects: SNIC 2022/6-14, NAISS 2023/6-19, NAISS 2024/6-20

NAISS Compute projects: SNIC 2020/15-9, NAISS 2023/22-84, NAISS 2024/22-108

History

Publisher

Karolinska Institutet

SciLifeLab acknowledgement

  • Bioinformatics platform (NBIS)

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