Healthy and B-cell precursor Acute Lymphoblastic Leukemia (ALL) cells analyzed via CyTOF

This is a dataset of 1,108,853 blood and bone marrow cells collected from 3 pediatric B-cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) patients and 3 healthy controls. Each ALL sample is made up of a mixture of cancer cells and healthy cells, whereas the healthy samples do not contain and cancer cells. This dataset can be used to evaluate models trained to classify cells as either cancerous or non-cancerous.  Each BCP-ALL patient has samples collected from 3 timepoints and 2 tissues: diagnosis (bone marrow and blood), day 8 post-treatment initiation with chemotherapy (blood), and day 15 post-treatment initiation (blood). Healthy patients only have samples collected from a single timepoint (the time of donation) and one tissue (bone marrow). These different tissues and timepoints can be used to assess a classifier's ability to generalize to new contexts (i.e. from bone marrow to blood, or from the diagnostic timepoint to a timepoint later in treatment). , All cells have been analyzed for the presence of 28 proteins as previously described using mass cytometry (CyTOF), a high-dimensional cytometry platform similar to multicolor flow cytometers commonly used to analyze leukemic tissue specimens in clinical laboratories. CyTOF analysis allows a high-dimensional sample characterization, extending the capabilities beyond those of conventional multicolor flow cytometers, typically employed for the analysis of leukemic tissue specimens in clinical laboratories. The files are in the flow cytometry standard (.FCS) file format and include information about 28 proteins as read off the mass cytometer (unit: ion counts) and an additional column called ('cell_type') that encodes healthy cells with a value of 0 and cancerous cells as a value of 1. These labels were manually annotated by an expert BCP-ALL cytometrist and verified by a physician-scientist board-certified in pediatric hematology and oncology. The samples were extracted, debarcoded, and fi..., , # Healthy and B-cell precursor Acute Lymphoblastic Leukemia cells analyzed via CyTOF [https://doi.org/10.5061/dryad.8gtht76vw](https://doi.org/10.5061/dryad.8gtht76vw) This repository contains 15 .FCS (Flow Cytometry Standard) data files. Each of these files represents a sample collected from a BCP-ALL patient or a healthy control patient. Each BCP-ALL patient has samples collected from 3 timepoints and 2 tissues: diagnosis (bone marrow and blood), day 8 post-treatment initiation with chemotherapy (blood), and day 15 post-treatment initiation (blood). Healthy patients only have samples collected from a single timepoint (the time of donation) and one tissue (bone marrow). ## Description of the data and file structure The information about the patient, timepoint, and tissue information about each sample is encoded in the .FCS filename. The .FCS filename is a string formatted as follows: **{patient_name}_{tissue}_{timepoint}.fcs.** In this string, **{patient_name}** is one of the fo..., All human samples and associated data in this study were collected under protocols approved by the Stanford University Institutional Review Board (IRB). Informed consent was obtained from all participants or their legal guardians, including explicit consent to publish de-identified data in public repositories. The data shared in this submission have been fully de-identified in accordance with applicable legal and ethical standards. No personally identifiable information, including names, dates of birth, medical record numbers, or geographic identifiers, is included. Sample identifiers (e.g., ID numbers) are randomly assigned codes that cannot be traced back to individual participants. Only single-cell protein expression data derived from mass cytometry are included. These data do not contain genetic information or any direct or indirect identifiers.本数据集包含1,108,853份血液与骨髓细胞样本，采集自3名儿科B细胞前体急性淋巴细胞白血病（B-cell Precursor Acute Lymphoblastic Leukemia, BCP-ALL）患者与3名健康对照者。所有BCP-ALL样本均由癌细胞与正常细胞混合而成，而健康样本不含任何癌细胞。本数据集可用于评估针对癌细胞与正常细胞分类任务训练的模型性能。 每位BCP-ALL患者的样本采集自3个时间节点与2种组织：诊断阶段（骨髓与血液）、化疗启动后第8天（血液）、化疗启动后第15天（血液）。健康对照者仅在单个时间节点（捐献时）采集单一种组织（骨髓）的样本。上述不同组织与时间节点可用于评估分类器对新场景的泛化能力，例如从骨髓到血液，或从诊断时间节点到治疗后期时间节点。 所有细胞均通过质谱流式细胞术（mass cytometry, CyTOF）完成28种蛋白质的表达分析，具体方法如前文所述。CyTOF是一种高维流式细胞术平台，类似于临床实验室中常用于分析白血病组织标本的多色流式细胞仪；其可实现高维度样本表征，性能优于传统多色流式细胞仪——后者通常用于临床实验室的白血病组织标本分析。 样本文件采用流式细胞术标准格式（Flow Cytometry Standard, .FCS），包含质谱流式细胞仪读取的28种蛋白质的表达信息（单位：离子计数），以及一个名为`cell_type`的附加列：健康细胞编码为0，癌细胞编码为1。上述标签由资深BCP-ALL细胞计量学家手动标注，并经儿科血液学与肿瘤学委员会认证的医师科学家验证。样本经提取、去条码处理及[原文此处未完成]。 # 经CyTOF分析的健康细胞与B细胞前体急性淋巴细胞白血病细胞 [https://doi.org/10.5061/dryad.8gtht76vw](https://doi.org/10.5061/dryad.8gtht76vw) 本数据集仓库包含15个.FCS（流式细胞术标准格式）数据文件，每个文件对应1份取自BCP-ALL患者或健康对照者的样本。 每位BCP-ALL患者的样本采集自3个时间节点与2种组织：诊断阶段（骨髓与血液）、化疗启动后第8天（血液）、化疗启动后第15天（血液）。健康对照者仅在单个时间节点（捐献时）采集单一种组织（骨髓）的样本。 ## 数据与文件结构说明 每份样本的患者信息、时间节点与组织信息均编码于.FCS文件名中，文件名格式如下： **{患者姓名}_{组织}_{时间节点}.fcs** 在此格式中，**{患者姓名}**为以下所列之一[原文此处未完成]。 本研究中所有人类样本及相关数据均经斯坦福大学机构审查委员会（Institutional Review Board, IRB）批准的方案采集。所有参与者或其法定监护人均已签署知情同意书，其中明确同意将去标识化数据发布至公共数据集仓库。 本次提交共享的数据已按照适用的法律与伦理标准完成去标识化处理，不包含任何个人可识别信息，包括姓名、出生日期、病历号或地理标识。样本标识符（如ID编号）均为随机分配的代码，无法追溯至具体参与者。 本数据集仅包含源自质谱流式细胞术的单细胞蛋白表达数据，不包含遗传信息或任何直接/间接标识符。