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Series GSE151287 Query DataSets for GSE151287
Status Public on Jun 09, 2020
Title Screening of PCRP transcription factor antibodies in biochemical assays
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Antibodies offer a powerful means to interrogate specific proteins in a complex milieu, and where epitope tagging is impractical. However, antibody reliability is problematic. The Protein Capture Reagents Program (PCRP) has generated over a thousand renewable monoclonal antibodies against presumptive chromatin proteins in an effort to improve reliability. However, these reagents have not been widely field tested. We therefore screened them in a variety of chromatin-based assays. 887 unique antibodies against 681 unique chromatin targets were assayed by ChIP-exo. A subset was further tested in ChIP-seq, CUT&RUN, STORM super-resolution microscopy, immunoblots, and PBM protein-DNA interaction assays. At least 5% of the tested antibodies were clearly validated by the most stringent of criteria. However, many others produced data that was distinctly different from background, but whose validity was ambiguous. We demonstrate and discuss the metrics and limitation to antibody validation in chromatin-based assays.
Overall design Large scale screen of PCRP antibodies with ChIP-exo
Contributor(s) Lai WK, Kuntala PK, Blanda TR, Bocklund K, Mairose J, Dweikat S, Mistretta K, Pugh BF
Citation(s) 34426512
Submission date May 27, 2020
Last update date Aug 31, 2021
Contact name B. Franklin Pugh
Organization name Cornell University
Department Molecular Biology and Genetics
Lab B. Franklin Pugh
Street address 465 Biotechnology Bldg.
City Ithaca
State/province New York
ZIP/Postal code 14853
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (1666)
GSM4570399 19159_EIF4E_K562
GSM4570400 19158_ZBTB17_K562
GSM4570401 19155_VDR_K562
BioProject PRJNA635402
SRA SRP264978

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Supplementary file Size Download File type/resource
GSE151287_bed.tar.gz 14.4 Mb (ftp)(http) TAR
GSE151287_processed_data1_bw.tar.gz 1.4 Gb (ftp)(http) TAR
GSE151287_processed_data2_bw.tar.gz 1.1 Gb (ftp)(http) TAR
GSE151287_processed_data3_bw.tar.gz 1.1 Gb (ftp)(http) TAR
GSE151287_processed_data4_bw.tar.gz 950.2 Mb (ftp)(http) TAR
GSE151287_processed_data5_bw.tar.gz 1.4 Gb (ftp)(http) TAR
GSE151287_processed_data6_bw.tar.gz 1.6 Gb (ftp)(http) TAR
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Raw data are available in SRA
Processed data are available on Series record

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