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Series GSE235876 Query DataSets for GSE235876
Status Public on Sep 08, 2023
Title Epigenomic analysis of Formalin-Fixed Paraffin-Embedded samples by CUT&Tag
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary For more than a century, Formalin Fixed Paraffin Embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our single-tube CUTAC protocol are sufficient to produce high-resolution maps of paused RNA Polymerase II (RNAPII) at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumor specimens and identify regulatory element markers with high confidence and precision. Our simple workflow is suitable for automation, making possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
Overall design We used FFPE-CUTAC, a modification of the CUT&Tag chromatin profiling strategy, whereby antibody-targeted controlled integration of DNA sequencing adapters at sites of paused RNA Polymerase II or between nucleosomes flanking open chromatin sites produces libraries for paired-end sequencing from Formalin-Fixed Paraffin-Embedded (FFPE) sections.

Grant information: T32CA009515 - Ronald M. Paranal - National Cancer Institute

Web link
Contributor(s) Henikoff S, Ahmad K, Henikoff JG, Paranal RM, Janssens DH, Russell ZR, Szulzewsky F, Kugel S, Holland EC
Citation(s) 37739938
Submission date Jun 26, 2023
Last update date Sep 24, 2023
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platforms (2)
GPL30172 NextSeq 2000 (Mus musculus)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (192)
GSM7511134 3T3_H3K27me3_3T3_nuclei_(230417_SH_Mm_K27m3_3T3_0405)
GSM7511135 3T3_H3K36me3_3T3_nuclei_(230417_SH_Mm_K36m3_3T3_0405)
GSM7511136 3T3_H3K4me2_3T3_nuclei_(230417_SH_Mm_K4m2_3T3_0405)
BioProject PRJNA987816

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
GSE235876_FFPE_80deg.pdf 1.8 Mb (ftp)(http) PDF
GSE235876_FFPE_85deg.pdf 2.0 Mb (ftp)(http) PDF
GSE235876_FFPE_90deg.pdf 4.1 Mb (ftp)(http) PDF
GSE235876_FFPE_beadtest.pdf 74.1 Kb (ftp)(http) PDF
GSE235876_FFPE_heating_series_20221204.pdf 2.4 Mb (ftp)(http) PDF
GSE235876_FFPE_on-slide.pdf 105.1 Kb (ftp)(http) PDF
GSE235876_FFPE_temp_mineraloil.pdf 7.8 Mb (ftp)(http) PDF
GSE235876_RAW.tar 9.2 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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