ABSTRACT: Nano LC-MS/MS was carried out, which A549 cell lysates were immunoprecipitated with mouse anti-kindlin-2 antibody (clone 3A3.538) or control mouse IgG (Santa Cruz, Cat# sc-2025).
INSTRUMENT(S): Southern University of Science and Technology
Project description:The NuRD complex is required for efficient and timely myelination in the peripheral nervous system. ChIP-chip assays were performed on rat sciatic nerve at P15, a peak timepoint of myelination, for binding of Chd4 to genes involved in regulating myelin formation. This experiment includes two custom ChIP-chip design incorporating many genes that are dynamically regulated during myelination. The antibodies used in this platform were Chd3/4 (Santa Cruz sc-11378) Chd4 (gift from Paul Wade), Mta2 (Santa Cruz sc-9447), and Nab2 (Santa Cruz sc-22815).
Project description:We immunoprecipitated exogenously expressed Myc-FGL1 using Anti-Myc-Tag monoclonal antibody (DIA-AN, Wuhan, China, Cat#2097) from 293T cells cocultured with tumor associated macrophages (TAMs) for 16 hr. No FGL1 protein was identified in protein lysates in which normal mouse IgG (Santa Cruz, California, USA, Cat#sc-2025) was added. Thus, protein lysates of 293T cells cocultured with TAMs added to mouse IgG were utilized as the negative control. A high-throughput technology, LC/MS (MS), was applied to identify the candidate interacting proteins of FGL1.
Project description:Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration Mouse G1E or G1ER cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total Smad1 (Santa Cruz SC-7965), Gata1 (Santa Cruz SC-265), or Gata2 (Santa Cruz SC-9008). This represents the Mouse ChIP-seq portion of this dataset.
Project description:The oncogenic transcription factor TAL1/SCL is aberrantly overexpressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing the importance of the TAL1-regulated transcriptional program in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, GATA3, ETS1 and RUNX1 in T-ALL cells. We find that TAL1 forms an interconnected auto-regulatory loop with its partners, which contributes to the sustained upregulation of its direct target genes. Importantly, we also find the MYB oncogenic transcription factor is directly activated by the TAL1 complex and positively regulates many of the same target genes, thus forming a feed-forward positive regulatory loop that further promotes the TAL1-regulated oncogenic program. Human T-ALL cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total TAL1 (Santa Cruz SC-12984), TCF12/HEB (Santa Cruz SC-357),TCF3/E2A (Santa Cruz SC-349X), LMO1 (Santa Cruz SC-10494), LMO2 (R&D Systems AF2726), GATA3 (Santa Cruz SC-22206) and RUNX1 (Santa Cruz SC-8563). This represents the ChIP-seq portion of this dataset. Human Jurkat cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total TAL1 (Santa Cruz SC-12984), TCF12/HEB (Santa Cruz SC-357),TCF3/E2A (Santa Cruz SC-349X), LMO1 (Santa Cruz SC-10494), GATA3 (Santa Cruz SC-22206) and RUNX1 (Santa Cruz SC-8563). This represents the ChIP-seq portion of this dataset.
Project description:The project was aimed at identifying the N-terminus of a truncated form of SLX4 (termed SLX4Nter) in HeLa KO30 cells. The HeLa KO30 cell line comes from a clone of HeLa Flp-In T-Rex cells (termed FITo) obtained through a CRISPR-Cas9 approach using commercially available plasmids from Santa Cruz Biotechnology (sc-404395 and sc-404395-HDR). This allows the integration of an exogenous plasmid conferring Puromycin resistance at the endogenous SLX4 locus. Unexpectedly, this strategy allowed us to retrieve several Puromycin-resistant clones (including KO30) displaying a shorter form of endogenous SLX4 that is N-terminally truncated (SLX4Nter). To identify the proximal peptide of SLX4Nter, FITo and KO30 nuclear extracts were immunoprecipitated with anti-SLX4 antibodies and N-terminus of SLX4Nter was further identified by LC-MSMS analysis.
Project description:Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. This represents the human CD34 ChIP-seq portion of this dataset. Human hematopoietic cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total Smad1 (Santa Cruz SC-7965), Tcf7l2 (Santa Cruz SC-8631),Gata1 (Santa Cruz SC-265), Gata2 (Santa Cruz SC-9008) or CEBPA (SC-9314).
Project description:Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. This represents the human ChIP-seq portion of this dataset on leukemia cell lines. Human hematopoietic cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total Smad1 (Santa Cruz SC-7965), Tcf7l2 (Santa Cruz SC-8631),Gata1 (Santa Cruz SC-265), Gata2 (Santa Cruz SC-9008), CEBPA (SC-9314) or H3K4me1 (Abcam ab8895).
Project description:ChIP-Seq study in human MCF7 and HEPG2 cells using antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314)
Project description:ChIP-Seq study in human MCF7 and HEPG2 cells using antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314) ArrayExpress Release Date: 2010-05-12 Publication Title: A CTCF-independent role for cohesin in tissue-specific transcription Publication Author List: Dominic Schmidt, Petra C. Schwalie, Caryn S. Ross-Innes, Antoni Hurtado, Gordon D. Brown, Jason S. Carroll, Paul Flicek and Duncan T. Odom Person Roles: submitter Person Last Name: Schwalie Person First Name: Petra Catalina Person Email: schwalie@ebi.ac.uk Person Address: Person Affiliation: EBI
Project description:The oncogenic transcription factor TAL1/SCL is aberrantly expressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing its importance in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, LMO1, LMO2, GATA3 and RUNX1 in T-ALL cells. We show that TAL1 forms an interconnected auto-regulatory loop with its partners, and that the TAL1 complex directly activates the MYB oncogene, forming a feed-forward positive regulatory loop that further promotes the TAL1-regulated oncogenic program. one of the cirtical downstream targets in this circuitry is the TRIB2 gene, which is oppositely regulated by TAL1 and HEB/E2A, and is essential for the survival of T-ALL cells. Human T-ALL cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total TAL1 (Santa Cruz SC-12984), TCF12/HEB (Santa Cruz SC-357),TCF3/E2A (Santa Cruz SC-349X), LMO1 (Santa Cruz SC-10494), LMO2 (R&D AF2726),GATA3 (Santa Cruz SC-22206) and RUNX1 (Santa Cruz SC-8563). This represents the ChIP-seq portion of this dataset.