Anandi Bhattacharya

Treventis Corporation.

We developed and optimized a high-throughput project workflow to generate renewable recombinant antibodies to human proteins involved in epigenetic signalling. Three different strategies to produce phage display compatible protein antigens in bacterial systems were compared, and we found that in vivo biotinylation through the use of an Avi tag was...

Antibodies are used in multiple cell biology applications, but there are no standardized methods to assess antibody quality-an absence that risks data integrity and reproducibility. We describe a mass spectrometry-based standard operating procedure for scoring immunoprecipitation antibody quality. We quantified the abundance of all the proteins in...

The Lim domain only 2 (Lmo2) gene encodes a transcriptional cofactor critical for the development of hematopoietic stem cells. Several distal regulatory elements have been identified upstream of the Lmo2 gene in the human and mouse genomes that are capable of enhancing reporter gene expression in erythroid cells and may be responsible for the high...

The Caprin1 TSS does not interact with distal regulatory elements upstream of Lmo2. Quantitative chromosome conformation capture (3C) was performed to detect chromatin-chromatin interactions between the Caprin1 TSS and distal regulatory elements (DRE). The profile of interactions identified in anaemic spleen (red) and kidney (blue) is displayed. Bl...

The Lmo2/Caprin1 region on mouse chromosome 2. Primers used in chromosome conformation capture (3C) and HindIII restriction sites are shown across the Lmo2/Caprin1 region of mouse chromosome 2. Promoters and distal regulatory elements (DRE) are depicted in red and black respectively. Anchor fragments used in the Caprin1, 75 DRE and Lmo2 3C experime...

CTCF bound upstream of Lmo2 in different cell types. The mouse Lmo2 upstream region on chromosome 2 is depicted with chromosome coordinates shown at the top. HindIII restriction sites are indicated by blue lines. The two Lmo2 promoters are indicated by red boxes. Distal regulatory element (DRE) homology regions are indicated by black boxes joined b...

Distal regulatory elements upstream of Lmo2 overlap transcription factor bound regions in HPC7 hematopoietic progenitor cells. The mouse Lmo2-Caprin1 region. Distal regulatory element (DRE) homology regions are indicated by black boxes joined by a line to delineate the human enhancer construct used in the generation of transgenic mice. Coloured box...

Restriction digestion efficiency in chromosome conformation capture. Restriction digestion efficiency was between 85 and 95% at several HindIII restriction sites. Lmo2 proximal promoter (pP), Distal regulatory element (DRE), Caprin1 promoter (Caprin1P). “U” denotes a restriction fragment upstream of the indicated element. (PDF)

Coordinates of the Lmo2 proximal and distal promoters in the mouse genome. The coordintes of proximal promoters and distal promoters for the Lmo2 gene in the mouse genome are listed in the table. Coordinates are given for homology regions identified by BLAT. All fragments were mapped in NCBI m37 mouse assembly (mm9). (PDF)

Coordinates of distal regulatory elements located upstream of the Lmo2 promoter in the mouse genome. Distal regulatory elements are named acording to their distance upstream of the annotated Lmo2 transcription start site overlapping the proximal promoter. Coordinates are given for homology regions identified by BLAT. All fragments were mapped in NC...

Chromatin immunoprecipitation sequencing data. Transcription factor binding sites have been obtained from three different cell types; differentiated murine erythroleukemia cells (MEL), hematopoietic progenitor cells (HPC7), and GIE-ER4 a GATA1-null erythroblast cell line in which GATA1 activity was restored. CTCF, DNaseI hypersensitivity, p300 and...

Relative transcript abundance in intergenic regions upstream of Lmo2 . (PDF)

Primers. Specific primers are listed for the chromosome conformation capture (3C) and RT-qPCR analyses. Left primer (L), right primer (R), primers used to test HindIII restriction digestion efficiency are marked as REX. (PDF)