We developed a text-mining-based data parsing workflow and collected tumor scRNA-seq datasets of human from GEO (16 (link)) and ArrayExpress (17 (link)). We searched the single-cell-related keywords such as ‘single cell RNA sequencing’ or ‘scRNAseq’ or ‘single cell’ or ‘single-cell’, as well as the technology-related keywords like ‘microfluidics’, ‘10X Genomics’ and ‘SMARTseq’, and the tumor-related keywords such as ‘tumor’ or ‘cancer’ or ‘carcinoma’ in the description page of GEO or ArrayExpress. Each dataset was then manually confirmed and curated. A total of 118 cancer-related scRNA-seq datasets were obtained initially and were further filtered to keep the datasets with >1000 high-quality cells. To expand the utility of TISCH, we also included the scRNA-seq datasets of mice treated with immunotherapy and three scRNA-seq datasets of human peripheral blood mononuclear cells (PBMC) from 10X Genomics. Overall, the TISCH database contains 76 high-quality tumor datasets across 27 cancer types and three PBMC datasets (Supplementary Table S1 ). We downloaded the expression matrix of the raw count, TPM or FPKM (if available) for each dataset. We collected sample information from databases or the original studies, such as the patient ID, tissue origin, treatment condition, response groups and the original cell-type annotation. Notably, we processed each cancer type separately if a dataset contained multiple cancer types. The source code for processing all the collected scRNA-seq datasets are deposited at the Github repository (https://github.com/DongqingSun96/TISCH/tree/master/code )
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Chemicals & Drugs
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Organic Chemical
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7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine is a synthetic compound with potential therapeutic applications.
This heterocyclic molecule contains a benzazepine core and features chloro, hydroxy, iodophenyl, and methyl substituents.
Reserachers can use PubCompre.ai's AI-driven tools to optimize their work with this compound, including locating protocols from literature, preprints, and patents, and identifying the best methods and products to ensure reproducibility and streamline their research process.
This heterocyclic molecule contains a benzazepine core and features chloro, hydroxy, iodophenyl, and methyl substituents.
Reserachers can use PubCompre.ai's AI-driven tools to optimize their work with this compound, including locating protocols from literature, preprints, and patents, and identifying the best methods and products to ensure reproducibility and streamline their research process.
Most cited protocols related to «7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine»
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
Carcinoma
Cells
Homo sapiens
Immunotherapy
Malignant Neoplasms
Mus
Neoplasms
Patients
PBMC Peripheral Blood Mononuclear Cells
Single-Cell RNA-Seq
Tissues
Trees
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
Anaplastic Oligodendroglioma
Astrocytoma
Astrocytoma, Anaplastic
Biological Assay
BLOOD
Brain Neoplasms
Brain Tumor, Primary
CDKN2A Gene
Chronic Lymphocytic Leukemia
Colorectal Carcinoma
Deletion Mutation
Diploid Cell
EGFR protein, human
Ethics Committees, Research
Exons
Gastric Cancer
Genes
Glioblastoma
Glioma
Grade II Astrocytomas
Heterografts
IDH2, human
Leukemia, Myelocytic, Acute
Leukemias, Chronic Granulocytic
Loss of Heterozygosity
Lung Cancer
Lymphocyte
Malignant Neoplasm of Breast
Medulloblastoma
Mutation
Neoplasms
Neuropathologist
Oligodendroglioma
Ovarian Cancer
Pancreatic Cancer
Patients
Polymerase Chain Reaction
Precursor Cell Lymphoblastic Leukemia Lymphoma
Prostate Cancer
PTEN protein, human
Real-Time Polymerase Chain Reaction
Tissues
TP53 protein, human
3-(2-phenylethyl)-4-methylsydnone
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
Biopharmaceuticals
Cyclonic Storms
Decompression Sickness
Fingers
Impacted Tooth
Medical Devices
Nebulizers
Needles
Polonium-210
Polytetrafluoroethylene
Pressure
Technique, Dilution
Tissue, Membrane
XR 5000
To characterize the functions of distinct cell-type populations, we performed gene set enrichment analysis (31 (link),32 (link)) according to the rank of genes based on the fold-change from the differential analysis. We totally collected 16 626 gene-sets for GSEA, including 186 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (33 (link)), 50 hallmark pathways, 10 192 Gene Ontology terms (BP: 7530; CC: 999; MF: 1663), 4872 immunologic signatures, 189 oncogenic signatures and 1137 transcriptional factor targets from the Molecular Signatures Database (MSigDB v7.1; 34 (link)). Significant up-regulated, and down-regulated pathways (FDR ≤ 0.05) in each cluster were identified and visualized to enable the functional enrichment analysis between different clusters. In addition, we also performed functional enrichment analysis of each cell-type between pre- and post-treatment, or responder and non-responder for the datasets with treatment information. Notably, we performed hierarchical clustering on the enriched GO terms due to the high similarity across ontology terms. The term with the longest paths to the root within a GO subtree will be considered as a representative term and labeled in the heatmap (35 (link)). This analysis was fulfilled by GSEA v4.0.3 for Linux, and figures were generated by the ComplexHeatmap R package v1.99.5 (36 (link)). In addition to performing GSEA at the cluster level, we also employed Single-Cell Signature Explorer (37 (link)) to calculate gene-set enrichment scores at the single-cell level. Only the visualizations on hallmark pathways are available in TISCH due to the limited computational resource.
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
Cells
Genes
Genome
Lanugo
Oncogenes
Physiology, Cell
Plant Roots
Population Group
Transcription Factor
This study examines a subset of 180 PUF–PAS samples collected
in the metropolitan Chicago area to evaluate the model with active
sampling comparison and characterize the model’s function under
varying meteorological scenarios. The “flying saucer”
PAS sampler design (with a 24 cm top bowl and 19.5 cm bottom bowl)
is based on the “Harner” PUF–PAS Design.3 (link),9 (link),12 (link),14 (link),23 (link)−25 (link) The PUF disk were purchased
from Tisch Environmental (Cleves, OH). Dimensions, 14 cm diameter
× 1.3 cm thick; surface area of 365 cm2; and density
of 0.0236 g cm–3. Samples were collected in approximately
6-week intervals (average of 45 days) from January 2012 to January
2014. All samples were collected in pairs with one sample remaining
at the University of Iowa for analysis, and the other sample being
sent to Indiana University for analysis for a different suite of environmental
contaminants.8 (link) A subset of 10 samples were
analyzed for PCBs at both laboratories.
Prior to deployment of the samplers, the sampling media (PUF disk)
was cleaned with multiple 24 h Soxhlet extractions, dried by low-flow
nitrogen blow-down, wrapped in aluminum foil, and stored in a freezer
until shipment and deployment.30 (link),31 (link) After collection, samples
were wrapped in combusted aluminum foil and shipped back to the University
of Iowa, where they were kept refrigerated at −20 °C until
extraction. The PUF samples were spiked with 50 ng of surrogate standards
(PCB14 (3,5-dichlorobiphenyl), PCB65-d5 (2,3,5,6-tetrachlorabiphenyl-d5,
deuterated), and PCB166 (2,3,4,4′,5,6-hexachlorobiphenyl)),
extracted with a 1:1 hexane:acetone mixture in an accelerated solvent
extractor, cleaned with an acidified silica column, and concentrated
with a Caliper TurboVap II.7 (link),30 (link),32 (link) The samples were then spiked with 50 ng of internal standard (PCB30-d5
(2,4,6-trichlorobiphenyl-2′,3′,4′,5′,6′-d5,
deuterated) and PCB204 (2,2′,3,4,4′,5,6,6′-octachlorobiphenyl))
just prior to analysis by gas chromatography with tandem mass spectrometry
(GC-MS/MS, Agilent 6890N Quattro Micro GC, Waters Micromass MS Technologies)
using a modified EPA method 1668a.33 All
209 PCB congeners were quantified as a collection of 156 individual
or coeluting chromatographic peaks.
in the metropolitan Chicago area to evaluate the model with active
sampling comparison and characterize the model’s function under
varying meteorological scenarios. The “flying saucer”
PAS sampler design (with a 24 cm top bowl and 19.5 cm bottom bowl)
is based on the “Harner” PUF–PAS Design.3 (link),9 (link),12 (link),14 (link),23 (link)−25 (link) The PUF disk were purchased
from Tisch Environmental (Cleves, OH). Dimensions, 14 cm diameter
× 1.3 cm thick; surface area of 365 cm2; and density
of 0.0236 g cm–3. Samples were collected in approximately
6-week intervals (average of 45 days) from January 2012 to January
2014. All samples were collected in pairs with one sample remaining
at the University of Iowa for analysis, and the other sample being
sent to Indiana University for analysis for a different suite of environmental
contaminants.8 (link) A subset of 10 samples were
analyzed for PCBs at both laboratories.
Prior to deployment of the samplers, the sampling media (PUF disk)
was cleaned with multiple 24 h Soxhlet extractions, dried by low-flow
nitrogen blow-down, wrapped in aluminum foil, and stored in a freezer
until shipment and deployment.30 (link),31 (link) After collection, samples
were wrapped in combusted aluminum foil and shipped back to the University
of Iowa, where they were kept refrigerated at −20 °C until
extraction. The PUF samples were spiked with 50 ng of surrogate standards
(PCB14 (3,5-dichlorobiphenyl), PCB65-d5 (2,3,5,6-tetrachlorabiphenyl-d5,
deuterated), and PCB166 (2,3,4,4′,5,6-hexachlorobiphenyl)),
extracted with a 1:1 hexane:acetone mixture in an accelerated solvent
extractor, cleaned with an acidified silica column, and concentrated
with a Caliper TurboVap II.7 (link),30 (link),32 (link) The samples were then spiked with 50 ng of internal standard (PCB30-d5
(2,4,6-trichlorobiphenyl-2′,3′,4′,5′,6′-d5,
deuterated) and PCB204 (2,2′,3,4,4′,5,6,6′-octachlorobiphenyl))
just prior to analysis by gas chromatography with tandem mass spectrometry
(GC-MS/MS, Agilent 6890N Quattro Micro GC, Waters Micromass MS Technologies)
using a modified EPA method 1668a.33 All
209 PCB congeners were quantified as a collection of 156 individual
or coeluting chromatographic peaks.
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
Acetone
Aluminum
Chromatography
Cocaine
Gas Chromatography-Mass Spectrometry
Hexanes
Silicon Dioxide
Tandem Mass Spectrometry
Most recents protocols related to «7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine»
To evaluate the relationship between the CRG_score and TME, the “CIBERSORT” R package (29 (link)) was used to evaluate the abundance of immune cells infiltrating tumors in high- and low-risk samples. The correlation between the score and infiltrating cell abundance was analyzed using linear analysis and a heatmap. Simultaneously, the immune cells, matrix, and ESTIMATE scores of patients with BC were calculated using the ESTIMATE algorithm. In addition, we analyzed the differences in the expression of immune test genes in the different CRG_score groups.The single-cell tumor microenvironment expression of cuproptosis-related genes in the tumor microenvironment was analyzed using the TISCH database(http://tisch.comp-genomics.org/ ).
Full text: Click here
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
COMP protocol
Gene Expression
Neoplasms
Patients
Tumor Microenvironment
The effect of prognostic CRGs on the expression of single cell subsets in the TME was investigated using TISCH (http://tisch.comp-genomics.org/ ) (Sun et al., 2021 (link)). TISCH is a scRNA-seq database focused on the TME, providing detailed cell-type annotation at the single-cell level, which is beneficial for exploring the TME in different cancer types. In this dataset, three main cell types are present, such as immune cells, stromal cells, and malignant cells. In this study, the t-distributed stochastic neighborhood embedding (t-SNE) map of LIHC_GSE125449_aPDL1aCTLA4 and the heatmap of LIHC_GSE125449_aPDL1aCTLA4 were displayed through the TISCH database to demonstrate the effect of CRGs on the TME of HCC.
Full text: Click here
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
Cells
COMP protocol
Malignant Neoplasms
Single-Cell RNA-Seq
Stromal Cells
Samples for various chemical analyses
were collected once a week from the influent and the bioreactor content
during the ASBR mixing phase and two to three times a week from the
effluent during the ASBR settling phase. sCOD analyses were conducted
using Lovibond medium-range (0–1500 mg L–1) COD digestion vials (Tintometer, Germany). Carboxylic acids (C2–C8,
including iso-forms of C4 and C5) and ethanol concentrations were
determined by an Agilent Technologies 7890B gas chromatograph (Santa
Clara, CA) equipped with a stabilwax-DA column (Restex) and a flame
ionization detector (GC-FID). The samples for GC-FID and sCOD were
acidified with phosphoric acid and sulfuric acid, respectively, centrifuged,
and filtered through 0.45 μm nylon membrane filters (TISCH Scientific,
North Bend, OH) before analyses. The concentrations of SCCAs and MCCAs
are reported as the sum of undissociated carboxylic acids and dissociated
carboxylates, even though we refer to them by their dissociated carboxylate
names for simplicity. The concentrations of SCCAs (including acetate,
propionate, n-butyrate, and n-valerate) and MCCAs (including caproate,
enanthate, and caprylate) are expressed on a molar basis. To determine
net acetate concentrations, the influent concentrations were subtracted
from the corresponding effluent concentrations. Gas collected in the
Tedlar gas bag was measured daily with a 0.1 L gas-tight glass syringe.
Gas composition (H2, CO2, and CH4) was determined two to three times a week using a Gow-Mac Series
gas chromatography (Bethlehem, PA) equipped with a thermal conductivity
detector. PH2 was calculated by considering the H2 percentages in the gas and assuming that the headspace in the bioreactor
was at atmospheric pressure. Detailed information on both of the gas
chromatographs is given in theSI .
were collected once a week from the influent and the bioreactor content
during the ASBR mixing phase and two to three times a week from the
effluent during the ASBR settling phase. sCOD analyses were conducted
using Lovibond medium-range (0–1500 mg L–1) COD digestion vials (Tintometer, Germany). Carboxylic acids (C2–C8,
including iso-forms of C4 and C5) and ethanol concentrations were
determined by an Agilent Technologies 7890B gas chromatograph (Santa
Clara, CA) equipped with a stabilwax-DA column (Restex) and a flame
ionization detector (GC-FID). The samples for GC-FID and sCOD were
acidified with phosphoric acid and sulfuric acid, respectively, centrifuged,
and filtered through 0.45 μm nylon membrane filters (TISCH Scientific,
North Bend, OH) before analyses. The concentrations of SCCAs and MCCAs
are reported as the sum of undissociated carboxylic acids and dissociated
carboxylates, even though we refer to them by their dissociated carboxylate
names for simplicity. The concentrations of SCCAs (including acetate,
propionate, n-butyrate, and n-valerate) and MCCAs (including caproate,
enanthate, and caprylate) are expressed on a molar basis. To determine
net acetate concentrations, the influent concentrations were subtracted
from the corresponding effluent concentrations. Gas collected in the
Tedlar gas bag was measured daily with a 0.1 L gas-tight glass syringe.
Gas composition (H2, CO2, and CH4) was determined two to three times a week using a Gow-Mac Series
gas chromatography (Bethlehem, PA) equipped with a thermal conductivity
detector. PH2 was calculated by considering the H2 percentages in the gas and assuming that the headspace in the bioreactor
was at atmospheric pressure. Detailed information on both of the gas
chromatographs is given in the
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
Acetate
Atmospheric Pressure
Bioreactors
Carboxylic Acids
Chromatography
Decompression Sickness
Digestion
Ethanol
Gas Chromatography
Heptanoates
hexanoate
Molar
n-Butyrate
Nylons
octanoate
Phosphoric Acids
Propionate
Sulfuric Acids
Syringes
Tissue, Membrane
Valerates
Obtain the FPKM expression matrix for lung adenocarcinoma from the Genomic Data Commons (GDC) repository (https://portal.gdc.cancer.gov/ ). Gene expression profiles of lung adenocarcinoma were queried from the GEO Gene Expression Dataset (https://www.ncbi.nlm.nih.gov/geo/ ) and microarray and high-throughput sequencing transcriptome data GSE42127, GSE72094, GSE26939, GSE31547, GSE19188, GSE14814, GSE37745, GSE5828 (BULK transcriptome data for validation), GSE135222, PRJEB23709, phs000452 (BULK transcriptome data for validation of impact on immunotherapy); we applied a text-mining-based data parsing workflow to collect the TISCH2 database (http://tisch.compgenomics.org/ ) of GSE117570 lung adenocarcinoma single-cell dataset, with all genes expressed in at least 3 cells, at least 200 genes per cell, UMIs retaining reads in the range 500-6500 depending on distribution, and percentage of mitochondrial reads < 80%; single-cell data as UMI transcript matrices as well as cellular information matrices, merged into Seraut objects required for analysis, using LogNormalize to normalise the data and check for batch effects between samples by UMAP and found no significant batch effects between samples.
Full text: Click here
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
Adenocarcinoma of Lung
Cells
Cytoskeleton
Cytosol
Dietary Fiber
Gene Expression
Genes
Genome
Immunotherapy
Malignant Neoplasms
Microarray Analysis
Mitochondrial Inheritance
Transcriptome
The evaluation of specific genes at the single-cell level was conducted based on the Tumor Immune Single-cell Hub website (http://tisch.comp-genomics.org/home/ ) (18 (link)).
Full text: Click here
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine
Cells
COMP protocol
Genes
Neoplasms
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More about "7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine"
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine is a synthetic compound with potential therapeutic applications.
This heterocyclic molecule contains a benzazepine core and features chloro, hydroxy, iodophenyl, and methyl substituents.
Researchers can utilize PubCompare.ai's AI-driven tools to optimize their work with this compound, including locating protocols from literature, preprints, and patents, and identifying the best methods and products to ensure reproducibility and streamline their research process.
For example, the C57BL/6J mouse strain is a commonly used model in research related to this compound, and the GoTaq qPCR Master Mix or RNeasy Plant Mini Kit could be employed for gene expression analysis.
Qbase+ software and DNase I treatment may also be relevant for data analysis and RNA purification, respectively.
Additionally, tert-butyl peroxide is a potential oxidative agent that could be used in studies involving this compound.
Researchers can further utilize the HiSeq X Ten sequencing platform and NOD.Cd11c-YFP mouse model to investigate the compound's mechanisms of action and potential therapeutic applications.
The R language 4.0.5 could be employed for bioinformatic analysis and data visualization.
By leveraging PubCompare.ai's AI-driven tools and related technologies, researchers can optimize their workflows, ensure reproducibility, and accelerate their progress in exploring the therapeutic potential of 7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine.
This heterocyclic molecule contains a benzazepine core and features chloro, hydroxy, iodophenyl, and methyl substituents.
Researchers can utilize PubCompare.ai's AI-driven tools to optimize their work with this compound, including locating protocols from literature, preprints, and patents, and identifying the best methods and products to ensure reproducibility and streamline their research process.
For example, the C57BL/6J mouse strain is a commonly used model in research related to this compound, and the GoTaq qPCR Master Mix or RNeasy Plant Mini Kit could be employed for gene expression analysis.
Qbase+ software and DNase I treatment may also be relevant for data analysis and RNA purification, respectively.
Additionally, tert-butyl peroxide is a potential oxidative agent that could be used in studies involving this compound.
Researchers can further utilize the HiSeq X Ten sequencing platform and NOD.Cd11c-YFP mouse model to investigate the compound's mechanisms of action and potential therapeutic applications.
The R language 4.0.5 could be employed for bioinformatic analysis and data visualization.
By leveraging PubCompare.ai's AI-driven tools and related technologies, researchers can optimize their workflows, ensure reproducibility, and accelerate their progress in exploring the therapeutic potential of 7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine.