|
|
GEO help: Mouse over screen elements for information. |
|
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 |
|
https://doi.org/10.1101/2020.06.08.140046
|
|
Submission date |
May 27, 2020 |
Last update date |
Aug 31, 2021 |
Contact name |
B. Franklin Pugh |
E-mail(s) |
fp265@cornell.edu
|
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)
|
|
Relations |
BioProject |
PRJNA635402 |
SRA |
SRP264978 |
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 |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|