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Series GSE140806 Query DataSets for GSE140806
Status Public on Jun 26, 2020
Title FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [human]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Fixed-Tissue ChIP-seq for H3K27Ac profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in FFPE tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27Ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65°C in more stringent detergent conditions and a minimized sonication step, to produce robust genome-wide H3K27Ac maps from clinical samples. We demonstrate FiTAc-seq suitability to generate high quality enhancer landscapes and SE annotation in a number of archived FFPE samples from distinct tumor types. This approach will be of great interest both for basic and clinical researchers. The entire protocol from FFPE blocks to sequence ready library can be accomplished within 4 days.
Overall design 3 samples per tissue type for bladder, melanoma, and seminoma. 1 brain cancer breast metastasis sample. RT4 cell line open chromatin assessed to compare bladder.
Contributor(s) Font-Tello A, Kesten NG, Cejas P, Long HW
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Submission date Nov 21, 2019
Last update date Jun 28, 2020
Contact name Henry Long
E-mail(s) Henry_Long@DFCI.HARVARD.EDU
Organization name Dana Farber Cancer Institute
Street address 450 Brookline ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (13)
GSM4186519 BlCa_1
GSM4186521 BlCa_2
GSM4186523 BlCa_3
This SubSeries is part of SuperSeries:
GSE140808 FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues
BioProject PRJNA590996
SRA SRP231165

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

Supplementary file Size Download File type/resource
GSE140806_RAW.tar 1.7 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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