ENCAB000BLL

Homo sapiens

any cell type or tissue

partially characterized

Homo sapiens

K562, HepG2

not characterized to standards

Method: motif enrichment

compliant

Caption: The motif for target NRF1 is represented by the attached position weight matrix (PWM) derived from ENCFF803TIA. Motif enrichment analysis was done by Dr. Zhizhuo Zhang (Broad Institute, Kellis Lab) using known motifs (http://compbio.mit.edu/encode-motifs/) and previously published ChIP-seq data (http://www.broadinstitute.org/~zzhang/motifpipeline/data/TrainSetInfo.txt). The accept probability score of the given transcription factor was calculated using a Bayesian approach. This analysis also includes three motif enrichment scores, computed by overlapping the motif instances with the given ChIP-seq peak locations. For more information on the underlying statistical methods, please see the attached document. Accept probability score: 0.91960821639, Global enrichment Z-score: 6.36881734605, Positional bias Z-score: 14.4329962635, Peak rank bias Z-score: 14.8942315546, Enrichment rank: 1.0.
Submitted by: Aditi Narayanan
Lab: Richard Myers, HAIB
Grant: U54HG006998
Download: ENCAB000BLL.pdf
Documents: encode:Antibody_Characterization_ENCODE3_August2015.pdf
encode:motif_enrichment_method

K562HepG2

Method: immunoprecipitation

not compliant

Caption: An immunoprecipitation followed by Western blot was performed with CDI R157.1.3H1 (lot 011513-RAP) antibody against NRF1 in HepG2 and K562 whole cell lysate. The expected size of NRF1 is 84 kDa. A band of ~75 kDa was detected. The experiment was repeated and this band was analyzed by mass spec in the secondary validation.
Submitter comment: non specific bands and no IgG control
Submitted by: Flo Pauli-Behn
Lab: Richard Myers, HAIB
Grant: U54HG006998
Download: NRF1_R157.1.3H1_011513-RAP_IP-Western.png
Documents: encode:Antibody_Characterization_ENCODE3_February2014.pdf

Method: immunoblot

not submitted for review by lab

Caption: a) Western blot analysis of nuclear lysates prepared from multiple cells lines loaded in the order: GM12878, K562, HepG2, HelaS3, MCF7, Liver using the antibody R157.1.3H1.
Submitted by: Trupti Kawli
Lab: Michael Snyder, Stanford
Grant: U54HG006996
Download: NRF1_R157.1.3H1_WB_a.jpg

Method: immunoprecipitation

not submitted for review by lab

Caption: b) Immunoprecipitation was performed on nuclear extracts from the cell line: K562, using the antibody R157.1.3H1 .The blot shows western blot analysis of input, flowthrough, immunoprecipitate and mock immunoprecipitate using IgG.
Submitted by: Trupti Kawli
Lab: Michael Snyder, Stanford
Grant: U54HG006996
Download: NRF1_R157.1.3H1_WB_b.jpg