BioTuring's Blog

Data analysis made easy. For biologists, especially.

Category Archives: Single Cell Analysis

November 22, 2021 By Minh-Hien Tran

Zooming in the intratumoral heterogeneity of liver cancer with BBrowser single cell database

intratumoral heterogeneity - liver cancer cell composition

Introduction Why are tumors so resilient against available cancer therapies? One answer lies in intratumoral heterogeneity. Intratumoral heterogeneity describes the diversity in tumor cell populations. Cancer cells exhibit startling distinctions in their types, shape, metabolic activities, transcriptomic profiles, and more. The causes of intratumoral heterogeneity are both heritable (clonal expansion […]

February 2, 2021 By biomembers

B cell subsets in the lungs: What are they?

Single Cell Analysis, Single-cell RNA-seq tutorials

B cells are like key ‘defenders’ in a soccer match. They play a critical role in supporting T cells, the ‘strikers’, in their battle against diseases, by producing antibodies to block specific antigens. Yet there are different types of defenders. Some form the memory that remembers the same pathogen for […]

November 9, 2020 By biomembers

Explore 10X Visium Spatial Transcriptomics data at ease with BioTuring Browser

Single Cell Analysis, Single-cell RNA-seq tutorials, Visium Spatial Transcriptomics Analysis

Cells don’t function independently. They belong to a complex and interconnected network. This makes gene expression profiling of individual cells not enough for understanding their activities and crosstalk in the tissue context. Like a marriage between imaging and RNA sequencing, Spatial Transcriptomics is a revolutionized method to map gene activity […]

October 20, 2020 By biomembers

A tiny world inside non-small cell lung cancer revealed by single-cell omics: 35 cell types, and their marker genes

Single Cell Analysis, Single-cell RNA-seq tutorials

Take a non-small cell lung tumor. What do we see? To answer this challenging question, a lot of single-cell omics experiments have been conducted, yielding significant insights into the heterogeneity of non-small cell lung cancer (NSCLC) microenvironment. While each successfully characterizes a facet of this ecosystem, until now no work […]

September 8, 2020 By biomembers

Immunoglobulin genes up-regulated in lung adenocarcinoma infiltrating T cells: A report from BioTuring lung cancer single cell database

Single Cell Analysis, Single-cell RNA-seq tutorials

Highlights: In every biology textbook, expression of the B cell receptor (BCR) defines B cells, and the T cell receptor (TCR) defines T cells. However, in 2019, Ahmed et al. discovered a strange cell population in Type I Diabetes that coexpresses the BCR and TCR, and key lineage markers of […]

July 27, 2020 By biomembers

Is Survivin (BIRC5) linked to tumor resistance at single-cell resolution?

Single Cell Analysis

BIRC5, known as Survivin, is one member of the Inhibitor of apoptosis protein family and plays an important role in preventing cell death (Jaiswal et al., 2015) and poor survival in cancers (Supplementary). For this reason, BIRC5 can be hypothesized to be associated with tumor resistance to cancer treatments. With […]

July 7, 2020 By biomembers

Revisiting AML single-cell datasets in BBrowser to learn how monocytic AML survives Venetoclax

Single Cell Analysis

Acute myeloid leukemia (AML) happens when the myeloid precursor cells in the bone marrow grow abnormally (making up myeloblasts). A common treatment for AML is Venetoclax. This drug inhibits BCL2, an oncoprotein that prevents cell death and is often overexpressed in the majority of blasts from AML patients (Bensi et […]

May 4, 2020 By biomembers

BioTuring Big Data Portal: Exploring huge public single-cell data sets without limits

Single Cell Analysis

Single-cell data sets are exploding in size. From a few thousand cells, we now see more than 1 million data points being generated (Cao et. al., 2019). Large single-cell atlases are valuable resources for exploration and insights, but also pose a great challenge to anyone who wants to view and […]

March 30, 2020 By biomembers

Single-cell analysis of CD8+ T cells in immune checkpoint blockade: some reproducible insights from BioTuring Database

Single Cell Analysis

Cancer treatment, as challenging as it sounds, has been revolutionized by recent advances in immune checkpoint blockade (ICB) therapies, which use monoclonal antibodies (mAb) to block the suppressive immune checkpoints, helping the patient’s immune system to kill cancer cells. However, despite several clinical case studies of success, some patients still […]

March 2, 2020 By biomembers

Interactive CITE-Seq data analysis with BioTuring Browser

Single Cell Analysis

Nominated as Method of the year by Nature in 2019, single-cell multimodal omics has enabled scientists to uncover many facets of the cells by simultaneously measuring multiple modalities in one single-cell experiment. One candidate for multimodal analysis is CITE-Seq, a technique that layers cell surface protein information on top of […]

January 15, 2020 By biomembers

BioTuring Cell Search: a new tool to search for similar populations in public single-cell data sets

Single Cell Analysis

A machine learning model for cell type classification? When analyzing single-cell transcriptomic data, scientists often perform cell type annotations by checking individual marker genes. However, marker genes are not even consistent among different literature sources. Six months ago, armed with the largest curated single-cell transcriptomic data, BioTuring single-cell team naively […]

December 25, 2019 By biomembers

How to explore “Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution” (Duclos et. al 2019) | BioTuring Cellpedia

BioTuring Cellpedia, Single Cell Analysis, Single-cell RNA-seq tutorials

Multiple studies have shown smoking’s effects on the human bronchi. However, few have characterized its precise impact at cellular resolution. Published recently on Science Advances, a study by Duclos and colleagues has employed single-cell RNA sequencing into exploring the cellular changes in the human bronchial epithelium between current and never […]