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Series GSE136251 Query DataSets for GSE136251
Status Public on Aug 24, 2019
Title Demonstration of CUT&RUN motif footprint analysis using key blood progenitor transcription factors
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We introduce CUT&RUNTools (https://bitbucket.org/qzhudfci/cutruntools/) as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. We illustrate the functionality of CUT&RUNTools through analysis of CUT&RUN data acquired for GATA1, a master regulator in erythroid lineage cells. Results were compared initially to published GATA1 ChIP-seq data for cells under the same conditions. We performed de novo analysis of CUT&RUN peaks to retrieve not only GATA1’s primary motif, but also the GATA1-TAL1 composite motif, and co-factor motifs GCCCCGCCTC, CMCDCCC, and RTGASTCA that correspond to SP1, KLF1, and NFE2 co-factors. Cofactor binding was verified by independent TAL1 and KLF1 CUT&RUN, and other ChIP-seq experiments. CUT&RUNTools also generated base-pair resolution motif footprint for sequence-specific binding factors, and located likely direct binding sites by quantifying log-odds of binding scores. Overall, CUT&RUNTools should enable biologists to realize advantages of cleavage data provided by CUT&RUN, and make high-quality footprinting analysis accessible to a broad audience.
 
Overall design We performed CUT&RUN using GATA1, TAL1, and KLF1 antibodies in primary human stem/progenitor CD34+ cells after 7 days of erythroid differentiation, and in erythroid progenitor HUDEP2 cells followed by 4 days of erythroid differentiation.
 
Contributor(s) Zhu Q, Liu N, Yuan G, Orkin S
Citation(s) 31500663
Submission date Aug 23, 2019
Last update date Sep 18, 2019
Contact name Stuart Orkin
Organization name Boston Childrens Hospital
Department Hematology and Oncology
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (5)
GSM4043375 GATA1_CD34_rep1: CD34+ differentiated
GSM4043376 GATA1_CD34_rep2: CD34+ differentiated
GSM4043377 TAL1_HUDEP2: HUDEP2 differentiated
Relations
BioProject PRJNA561759
SRA SRP219873

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
GSE136251_RAW.tar 6.5 Mb (http)(custom) TAR (of NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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