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HOXA9 protein, human

The HOXA9 protein is a transcription factor that plays a key role in regulating gene expression during embryonic development and hematopoiesis.
It is a member of the homeobox gene family and is involved in the patterning of the anterior-posterior axis.
The HOXA9 protein has been implicated in the pathogenesis of certain leukemias and solid tumors, making it an important target for cancer research.
This protein is also believed to be involved in the regulation of stem cell self-renewal and differentiation.
Researchers can optimize their HOXA9 protein research using PubCompare.ai's AI-driven protocol comparison platform, which helps locate relevant protocols from literature, preprints, and patents, and provides intelligent comparisons to identify the best protocols and products for their experiments, simplifying the research process and unlocking new insights.

Most cited protocols related to «HOXA9 protein, human»

Informed consent from MM patients was obtained in line with the Declaration of Helsinki. DNA was extracted from bone marrow aspirate (tumor) and blood (normal). WGS libraries (370-410 bp inserts) and WES libraries (200-350 bp inserts) were constructed and sequenced on an Illumina GA-II sequencer using 101 and 76 bp paired-end reads, respectively. Sequencing reads were procesed with the Firehose pipeline, identifying somatic point mutations, indels, and other structural chromosomal rearrangements. Structural rearrangements affecting protein-coding regions were then subjected to manual review to exclude alignment artifacts. True positive mutation rates were estimated by Sequenom mass spectrometry genotyping of randomly selected mutations. HOXA9 shRNAs were introduced into MM cell lines using lentiviral infection using standard methods.
A complete description of the materials and methods are provided in the Supplementary Information.
Publication 2011
BLOOD Bone Marrow Cell Lines Chromosomes Diploid Cell Gene Rearrangement HOXA9 protein, human INDEL Mutation Infection Mass Spectrometry Multiple Acyl Coenzyme A Dehydrogenase Deficiency Mutation Neoplasms Open Reading Frames Patients Point Mutation Short Hairpin RNA
Informed consent from MM patients was obtained in line with the Declaration of Helsinki. DNA was extracted from bone marrow aspirate (tumor) and blood (normal). WGS libraries (370-410 bp inserts) and WES libraries (200-350 bp inserts) were constructed and sequenced on an Illumina GA-II sequencer using 101 and 76 bp paired-end reads, respectively. Sequencing reads were procesed with the Firehose pipeline, identifying somatic point mutations, indels, and other structural chromosomal rearrangements. Structural rearrangements affecting protein-coding regions were then subjected to manual review to exclude alignment artifacts. True positive mutation rates were estimated by Sequenom mass spectrometry genotyping of randomly selected mutations. HOXA9 shRNAs were introduced into MM cell lines using lentiviral infection using standard methods.
A complete description of the materials and methods are provided in the Supplementary Information.
Publication 2011
BLOOD Bone Marrow Cell Lines Chromosomes Diploid Cell Gene Rearrangement HOXA9 protein, human INDEL Mutation Infection Mass Spectrometry Multiple Acyl Coenzyme A Dehydrogenase Deficiency Mutation Neoplasms Open Reading Frames Patients Point Mutation Short Hairpin RNA
ORCA builds on recent innovations in RNA and DNA FISH, taking advantage of array-derived oligonucleotide (oligo) probes (Oligopaints)9 ,13 (link),18 (link),20 ,21 . ORCA reconstructs the trajectory of a genomic region of interest (100–700 kb), by tiling the region in short sections (2–10 kb) with primary probes that have unique barcodes20 (Fig. 1a, Extended Data Fig. 1a-c, Supplementary Data Tables 1-5). These barcodes are labelled with a fluorophore and imaged. The signal is then removed via strand displacement (Supplementary Data Table 6). The process repeats for each barcode. This is conceptually similar to recent18 (link) and concurrent work17 (link),19 (link), though with improved genomic resolution (Fig. 1b). With high-precision fiducial registration (Extended Data Fig. 1a-c), sequential imaging allows barcoded sections within a diffraction-limited volume to be resolved, as in STORM, while adding sequence resolution across the domain (Fig. 1b). We represent the measured 3D positions of the barcodes as spheres, pseudo-coloured per barcode and linked with a smooth polymer (Fig. 1c), and as distance maps (Fig. 1d).
We applied ORCA to visualize the nanoscale DNA path of the BX-C at 10-kb and 2-kb resolution in 6-µm cryosections of Drosophila embryos 10–12 hours post-fertilization (hpf). The 10-kb step size allowed a 700-kb region, including flanking domains of the BX-C, to be traced with 70 barcodes (Fig 1d, e). The 2-kb step size enhanced the resolution over a 130-kb regulatory region spanning abd-A to Abd-B (Fig.1a, g, h). Missed detection events (Fig. 1d, g, grey lines) were largely stochastic – showing no significant variation between embryos, cell types, or probesets, and limited variation between barcodes (Extended Data Fig. 2). Replicate experiments yielded reproducible measurements (Pearson’s r > 0.95) (Extended Data Fig. 1d). Comparisons to published Hi-C22 (link) across a range of contact thresholds revealed qualitatively similar features and quantitatively similar contact distributions (Fig. 1e, f, h, i, Extended Data Fig.1 e, f). In Drosophila chromosomes, which are predominantly paired in interphase, our ORCA images reveal that paired homologs follow a common trajectory to within ~50 nm. (Extended Data Fig. 3). Additional ORCA experiments in mouse embryonic stem cells tracing the region containing Sox2 at 5-kb resolution (Extended Data Fig. 4) exhibited strong correspondence with published Hi-C data23 (link) (Pearson’s r = 0.96), illustrating versatility across cell types.
Publication 2019
Cells Chromosomes Cryoultramicrotomy DNA Replication Drosophila Embryo Fertilization Fishes Genome HOXA9 protein, human Innovativeness Interphase Microtubule-Associated Proteins Mouse Embryonic Stem Cells Oligonucleotide Probes Orcinus orca Polymers Regulatory Sequences, Nucleic Acid SOX2 protein, human
Mouse models of CML were generated by transducing bone marrow stem and progenitor cells with retroviruses carrying BCR-ABL (chronic phase), or BCR-ABL and NUP98-HOXA9 (blast crisis phase) and transplanted into irradiated recipient mice. The development of CML was confirmed by flow cytometry and histopathology. For Msi2 knockdown experiments, lineage negative blast crisis CML cells were infected with Msi2 or control Luciferase shRNA retroviral constructs and leukemia incidence monitored. ChIP assays were performed using the myeloid leukemia cell line M1. DNA was crosslinked and immunoprecipitated with control or anti-HOXA9 antibodies and analyzed by PCR for regions of interest. CML patient samples were obtained from the Korean Leukemia Bank (Korea), the Hammersmith MRD Lab Sample Archive (United Kingdom), the Fred Hutchinson Cancer Research Center (United States) and the Singapore General Hospital (Singapore). Gene expression in human chronic and blast crisis CML was analyzed by PCR or by DNA microarrays.
Publication 2010
Anti-Antibodies Blast Phase Bone Marrow Cell Lines DNA Chips Flow Cytometry Gene Expression Homo sapiens HOXA9 protein, human Immunoprecipitation, Chromatin Koreans Leukemia Luciferases Malignant Neoplasms Mus Myeloid Leukemia Nup98 protein, human Patients Retroviridae Short Hairpin RNA Stem, Plant Stem Cells Transplant Recipients

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Publication 2012
ARID1A protein, human BLOOD Bone Marrow Cells Common Cold DNA Replication Genome HOXA9 protein, human Infection Mus NRG1 protein, human Nup98 protein, human Polybrene Puromycin RNA Interference Sequence Analysis Serum Short Hairpin RNA Virus

Most recents protocols related to «HOXA9 protein, human»

Dorsal abdomen specimens were dissected from pupae between the P14 and P15(i) developmental stages [12 (link),16 (link),50 ]. Male and female specimens were combined, and females were distinguished by the removal of their wings. The ensuing steps were done with male and female specimens together in the same tubes or plate in order to expose to identical conditions. Specimens were fixed for 35 min in PBST solution (phosphate buffered saline with 0.3% Triton X-100) with 4% paraformaldehyde (Electron Microscopy Services). After fixation, specimens were washed twice with PBST and then blocked for 1 hour at room temperature in a blocking solution (PBST with 1% Bovine Serum Albumin). Specimens were then incubated overnight at 4°C with a primary antibody in PBST. These were either mouse monoclonal anti-Abd-B (Developmental Studies Hybridoma Bank, 1A2E9) at a dilution of 1:200 of a concentrated stock, rabbit anti-Bab1 primary antibody [11 (link)] at a 1:200 dilution, and rabbit anti-Trx [39 (link)] at a 1:200 dilution.
After four washes with PBST and then 1 hour in blocking solution, specimens were incubated with either goat anti-mouse Alexa Fluor 647 (Invitrogen, #A21236) secondary antibody, or goat anti-rabbit Alexa Fluor 646 (Invitrogen, #A21244) secondary antibody. These secondary antibodies were used at a 1:500 dilution in PBST, and incubated for 2 hours at room temperature. Following four washes with PBST, the specimens were equilibrated for ten minutes at room temperature in Glycerol Mount:PBST (50% glycerol, 50% PBST) solution. Specimens were then transferred to the glycerol mount (80% glycerol) before being situated between a glass cover slip and slide for imaging with a confocal microscope. Cover slip and slides were separated by one piece of double-sided sticky tape, for which a hole was cut out in the center by a razor blade. Specimens are situated in the hole with their cuticle towards the cover slip side.
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Publication 2023
Abdomen Alexa Fluor 647 Antibodies Antibodies, Anti-Idiotypic Cardiac Arrest Electron Microscopy Females Glycerin Goat HOXA9 protein, human Hybridomas Immunoglobulins Males Mice, House Microscopy, Confocal paraform Phosphates Pupa Rabbits Saline Solution Serum Albumin, Bovine Technique, Dilution Triton X-100
The following antibodies were used for immunohistochemistry in this study: mouse anti-Scr (1:50; 6H-4.1, DSHB), mouse anti-Ubx (1:40; FP3-38, DSHB), mouse anti-Abd-A (1:100; 6A8.12, DSHB), mouse anti-Abd-B (1:40; 1A2E9, DSHB), mouse anti-EcR-B1 (1:50; AD4.4, DSHB), mouse anti-FasII (1:50; 1D4, DSHB), mouse anti-Cut (1:50; 2B10, DSHB), mouse anti-Knot/Collier (1:100, a gift from A. Vincent), Guinea pig anti-Sox14 (1:200), Guinea pig anti-Mical (1:500), Rabbit anti-GFP (1:1000, A-11122, Invitrogen), Rabbit anti-Scm (1:20; a gift from J. Muller). Fluorescein isothiocyanate (FITC)-, Cy3- and Cy5-conjugated secondary antibodies (111–545-003, 115–165-003, 111–165-003, 106–165-003 and 123–605-021, Jackson ImmunoResearch) were used at 1:500 dilution.
For immunohistochemistry, pupae or larvae were dissected in cold PBS and fixed in 4% formaldehyde for 20 min, followed by washing with 0.5% Triton-X-containing PBS (PBST) for 3 times. Control and sample fillets/brains for each set of experiment were washed and stained in the same tube. Primary antibodies were added into blocking buffer (5% BSA in PBST) after 30 min blocking and were incubated at 4 °C overnight. Secondary antibodies were incubated on the second day at room temperature for 2–6 h. Samples were mounted using VectaShield mounting medium and imaged using either Leica SPE II or Olympus FV3000 confocal microscope. Images were taken from projected z-stacks (1.5-µm intervals) to cover the whole da neuron. Images of the same experiment set were taken with the same settings and processed in parallel.
Measurement of fluorescence intensity was done using ImageJ. Contours of cell nuclei (Ubx/ Abd-A/ Abd-B/ Scr/ EcR-B1/ Sox14/ Cut/ Knot immunostaining) or whole soma (Mical immunostaining) were drawn on the GFP channel. To quantify the fluorescence intensity of Scr, Cut and Knot background (rolling ball radius = 50) was subtracted on the whole image of that channel before measuring the mean grey value in the marked region of ddaC nuclei was measured. To quantify the fluorescence intensity of Ubx, Abd-A, EcR-B1, Sox14 and Mical, background (rolling ball radius = 50) was subtracted on the whole image of that channel before measuring the mean grey value in the marked region of ddaC and ddaE, their ratio was subsequently calculated. The values were then normalized to their corresponding mean control values and subjected to statistical analysis.
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Publication 2023
Antibodies Brain Buffers Carisoprodol Cavia porcellus Cell Nucleus Cold Temperature Fluorescein Fluorescence Formaldehyde HOXA9 protein, human Immunohistochemistry iodine-131-tositumomab isothiocyanate Larva Mice, House Microscopy, Confocal N,N-dimethyl-N-hexadecyl-1-octadecylammonium chloride Neurons Pupa Rabbits Radius Technique, Dilution
All Drosophila stocks and crosses were maintained in standard cornmeal media at 25 °C. The third instar larvae or early pupae at 0, 6, 16, 20 or 24 h APF (both male and female) were used in this study. The following stocks were requested from other labs: UAS-MicalN−ter (non-functional N-terminal Mical fragment as a UAS-control transgene), UAS-MicalFL [78 (link)], ppk-Gal4 [79 (link)], SOP-flp [80 (link)], 71G10-Gal4 [23 (link)], mhc-Gal80 [81 (link)], ScmD1, ScmM56 [43 (link)], ph505 [37 (link), 48 (link)], E(z)73 [82 (link)].
The following stocks were obtained from Bloomington Drosophila Stock Center (BDSC): UAS-mCD8-GFP, UAS-Dicer2, tubP-Gal80, FRT19A, FRT42D, FRT2A, FRT82B, GSG2295-Gal4 (BL#40,266), ppk-CD4-tdGFP (BL#35,843), 201Y-Gal4 (BL#4440), ctrl RNAi (mCherry, BL#35,785), Df(3R)by10 (BL#1931), Df(3R)BSC468 (BL#24,972), Pc15 (BL#24,468), E(z)731 (BL#24,470), Su(z)122 (BL#24,159), Su(z)124 (BL#24,469), Scm RNAi #1 (BL#55,278), Scm RNAi #2 (BL#35,389), Scm RNAi #3 (BL#31,614), Psc-Su(z)21.b8 (BL#24,467), Psc RNAi (BL#35,297), Psc RNAi (BL#31,611), Psc RNAi (BL#38,261), Sce RNAi (BL#35,446), Sce RNAi (BL#31,612), ph-d RNAi (BL#63,018), ph-d RNAi (BL#31,190), ph-p RNAi (BL#35,207), ph-p RNAi (BL#33,669), ph-p RNAi (BL#31,608), PcRNAi (BL#31,110), Psc-Su(z)21.b8 (BL#24,467), esc21 (BL#3623), Df(2L)Exel6030 (BL#7513), UAS-Abd-B (BL#913), UAS-abd-A (BL#912), UAS-Ubx (BL#911), UAS-Scr (BL#7302), Abd-B RNAi (BL#26,746), Scr RNAi (BL#50,662).
The following stocks were obtained from Vienna Drosophila Resource Centre (VDRC): ph RNAi (v50028), Su(z)2 RNAi (v50368), Sce RNAi (v106328), Su(z)2 RNAi (v100096), control RNAi (v25271, γ-tub37C).
Genotypes of the fly strains shown in each figure are listed in Supplementary Methods.
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Publication 2023
Drosophila Females Genotype HOXA9 protein, human Larva Males Pupa RNA Interference Strains Transgenes
Immunoprecipitates, chromatin extracts, total protein lysates and RIPA cell lysates samples were separated by SDS-PAGE (7.5 to 10% acrylamide) and subsequently transferred to polyvinylidene difluoride (PVDF) membranes (Amersham Hybond, GE Healthcare Europe, Solingen, Germany) with a PerfectBlue™ tank electro blotter (Peqlab Biotechnologie, Erlangen, Germany). Membranes were probed with the following primary antibodies: anti-c-fos (ab134122, Abcam, Cambridge, UK), anti-c-myc (Invitrogen 13-2500, Thermo Fisher Scientific, Dreieich, Germany), anti-Cyclin E (32-1600, Thermo Fisher Scientific, Dreieich, Germany), anti-ERα (NBP1-84827, Novus Biologicals, Wiesbaden, Germany), anti-GFP (sc-9996, Santa Cruz Biotechnology, Heidelberg, Germany), anti-HA (ab9110, Abcam, Cambridge, UK), anti-Histone H3 K4 trimethylation (9751, Cell signaling Technology, Leiden, The Netherlands), anti-HOXA9 (ab140631, Abcam, Cambridge, UK), anti-MLL/KMT2A (NB600-248, Novus Biologicals, Wiesbaden, Germany), anti-Nucleolin (ab22758, Abcam, Cambridge, UK), anti-Nucleophosmin1/B23 (sc-47725, Santa Cruz Biotechnology, Heidelberg, Germany), anti-Topoisomerase IIα/β (ab109524, Abcam, Cambridge, UK), anti-Topoisomerase IIα (sc-365071, Santa Cruz Biotechnology, Heidelberg, Germany), anti-Topoisomerase IIβ (sc-365916, Santa Cruz Biotechnology, Heidelberg, Germany), anti-Taspase1 (AP11325PU-N, OriGene Technologies, Herford, Germany), anti-α-Tubulin (T6074, Sigma-Aldrich, Taufkirchen, Germany) or anti-γH2AX (613402, BioLegend, Amsterdam, The Netherlands).
For visualization of immune complexes, HRP-conjugated secondary antibodies were applied (NXA931 and NA934, GE Healthcare Europe, Solingen, Germany), and detected with the PierceTM ECL Plus Western Blotting Substrate or SuperSignalTM West Femto Maximum Sensitivity Substrate from Thermo Fisher Scientific, Dreieich, Germany and the ChemiDoc MP Imaging System (Bio-Rad Laboratories, Feldkirchen, Germany).
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Publication 2023
Acrylamide alpha-Tubulin Antibodies Biological Factors CCNE1 protein, human Cells Chromatin Complex, Immune DNA Topoisomerase II alpha DNA Topoisomerase II beta Histone H3 HOXA9 protein, human Hypersensitivity MLL protein, human Novus nucleolin polyvinylidene fluoride Proteins Radioimmunoprecipitation Assay SDS-PAGE Tissue, Membrane
The myeloid progenitor transformation assay was carried out as previously described52 (link). Bone marrow cells were harvested from the femurs and tibiae of 5-week-old female C57BL/6 mice (purchased from CLEA Japan, Inc). c-Kit-positive cells were enriched using magnetic beads conjugated with an anti-c-Kit antibody (Miltenyi Biotec, 1:50 dilution), transduced with a recombinant retrovirus by spinoculation, and then plated in a methylcellulose medium (Iscove’s Modified Dulbecco’s Medium, 20% FBS, 1.6% methylcellulose, and 100 µM β-mercaptoethanol) containing murine stem cell factors, interleukin-3, and granulocyte-macrophage colony-stimulating factor (10 ng ml−1 of each). G418 (1 mg ml−1) was added to the first round of culture to select for transduced cells. Hoxa9 expression was quantified by RT-qPCR after the first round of culture. Colony-forming units (CFUs) were quantified per 104 plated cells after 4–6 days in culture. This protocol was approved by the National Cancer Center Institutional Animal Care and Use Committee of the National Cancer Center, Tsuruoka, Japan.
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Publication 2023
2-Mercaptoethanol anti-c antibody antibiotic G 418 Biological Assay Bone Marrow Cells Cells Femur Granulocyte-Macrophage Colony-Stimulating Factor HOXA9 protein, human Institutional Animal Care and Use Committees Interleukin-3 Malignant Neoplasms Methylcellulose Mice, Inbred C57BL Mus Proto-Oncogene Protein c-kit Retroviridae Stem Cell Factor Technique, Dilution Tibia Woman

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HOXA9 is a protein-coding gene that plays a role in regulating gene expression, cell differentiation, and embryonic development. It is often used in research applications to study these biological processes.
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More about "HOXA9 protein, human"

The HOXA9 gene encodes a critical transcription factor that plays a pivotal role in regulating gene expression during embryonic development and hematopoiesis (blood cell formation).
As a member of the homeobox gene family, HOXA9 is essential for patterning the anterior-posterior axis.
This protein has been implicated in the pathogenesis of certain leukemias and solid tumors, making it an important target for cancer research.
HOXA9 is also believed to be involved in the regulation of stem cell self-renewal and differentiation.
Researchers can optimize their HOXA9 protein research using PubCompare.ai's AI-driven protocol comparison platform, which helps locate relevant protocols from literature, preprints, and patents, and provides intelligent comparisons to identify the best protocols and products for their experiments.
This simplifies the research process and unlocks new insights.
To study HOXA9, researchers often use techniques like RNA extraction with the RNeasy Mini Kit or TRIzol reagent, cDNA synthesis with the High-Capacity cDNA Reverse Transcription Kit, and transfection with Lipofectamine 2000 or SuperFect.
Antibodies like Ab140631 can be used for HOXA9 detection and quantification.
The Luciferase Assay System is also a valuable tool for evaluating HOXA9-related transcriptional activity.
By leveraging these resources and the power of PubCompare.ai, scientists can efficiently advance their understanding of this critical transcription factor and its role in development, hematopoiesis, and cancer.