DOI: 10.5061/dryad.h9w0vt4t2
title: RNA-seq of bone marrow samples from acute myeloid leukemia patients and healthy individuals

description: Acute myeloid leukemia (AML) is the most common type of acute leukemia in
 adults, characterized by the malignant transformation and uncontrolled
 proliferation of abnormal myeloid hematopoietic progenitor cells in the
 bone marrow. This study aims to analyze the pathogenesis and prognosis of
 AML by performing RNA-seq on bone marrow samples from both AML patients
 and healthy individuals. We collected a total of 20 bone marrow samples,
 consisting of 10 samples from AML patients and 10 from healthy controls,
 all of which were stored in liquid nitrogen. The study received ethical
 approval (Ethical Approval Number: KY2024070), and all participants signed
 informed consent forms. This dataset includes the RNA-seq data
 from these samples. By analyzing the gene expression characteristics of
 myeloid progenitor cells, we attempt to construct a prognostic model to
 guide clinical treatment. These data not only aid in further exploring the
 molecular mechanisms of AML but also serve to identify new biomarkers and
 develop prognostic models, which are valuable for understanding the gene
 expression differences between AML and healthy bone marrow samples. The
 sharing of data from this study strictly adheres to ethical guidelines,
 with all sample collection and usage approved by the ethics committee and
 consented to by the participants.
description: A total of 20 bone marrow samples were collected for this study,
 consisting of 10 bone marrow samples from patients with acute myeloid
 leukemia (AML) (AML group), and 10 bone marrow samples from healthy
 individuals (control group). All AML patients were diagnosed by bone
 marrow smear morphology and cytogenetic testing, and individuals in the
 healthy control group underwent a thorough physical examination to exclude
 any history of blood disorders and tumors. The samples were stored in
 liquid nitrogen for further processing. All subjects signed an informed
 consent form, and the study was approved by the Ethics Committee of the
 Affiliated Hospital of Southwest Medical University (Ethics Approval No.
 KY2024070).<br><br>Total RNA was extracted from frozen bone
 marrow samples using TRIzol reagent (Thermo Fisher Scientific, USA) for
 RNA extraction according to the manufacturer's instructions. The
 quality of extracted RNA was assessed by Agilent 2100 Bioanalyzer to
 ensure that the RNA Integrity Index (RIN) was greater than 7.0.RNA
 concentration was quantified using Qubit 2.0 (Thermo Fisher Scientific) to
 ensure that sequencing requirements were met.RNA library construction was
 performed using the Illumina TruSeq RNA Library Prep Kit (Illumina, USA),
 and library quality control was performed by Qubit and Bioanalyzer. All
 samples were bipartite sequenced on the Illumina NovaSeq 6000 platform
 with a read length of 150 bp and a target sequencing depth of 50M reads
 per sample.
description: # RNA-seq of bone marrow samples from acute myeloid leukemia patients and
 healthy individuals
 [https://doi.org/10.5061/dryad.h9w0vt4t2](https://doi.org/10.5061/dryad.h9w0vt4t2) ## Description of the data and file structure ### Files and variables #### File: AML.txt **Description:** RNA-seq expression matrix, rows are sample names, columns are gene names. ##### Variables * Gene_Name: gene name * Patient1: Bone marrow sample from patient 1 with acute myeloid leukemia * Patient2: Bone marrow sample from patient 2 with acute myeloid leukemia * Patient3: Bone marrow sample from patient 3 with acute myeloid leukemia * Patient4: Bone marrow sample from patient 4 with acute myeloid leukemia * Patient5: Bone marrow sample from patient 5 with acute myeloid leukemia * Patient6: Bone marrow sample from patient 6 with acute myeloid leukemia * Patient7: Bone marrow sample from patient 7 with acute myeloid leukemia * Patient8: Bone marrow sample from patient 8 with acute myeloid leukemia * Patient9: Bone marrow sample from patient 9 with acute myeloid leukemia * Patient10: Bone marrow sample from patient 10 with acute myeloid leukemia * Control1: Bone marrow sample from healthy person 1 * Control2: Bone marrow sample from healthy person 2 * Control3: Bone marrow sample from healthy person 3 * Control4: Bone marrow sample from healthy person 4 * Control5: Bone marrow sample from healthy person 5 * Control6: Bone marrow sample from healthy person 6 * Control7: Bone marrow sample from healthy person 7 * Control8: Bone marrow sample from healthy person 8 * Control9: Bone marrow sample from healthy person 9 * Control10: Bone marrow sample from healthy person 10 #### File: sample.txt **Description:** Sample Description Form ##### Variables * P: Bone marrow sample from a patient with acute myeloid leukemia * C: Bone marrow sample from a healthy person #### File: Raw\_data.zip **Description:** In the Raw data section, we provide two TPM-formatted gene expression matrix files: "gene.TPM.matrix.annot.xls" includes the annotation of probes to gene names, while "gene.tpm.matrix.xls" contains the unannotated raw data. ##### Variables * gene_id: Unique identifiers for genes * gene_name: Name of the gene * description: Description or functional annotation of the gene * length: Length of the gene * Patient1 to Patient10: These columns represent the samples from 10 patients, with each column name followed by the corresponding patient number. These columns contain the expression levels of the gene in each patient sample, measured in TPM (Transcripts Per Million) units. * Control1 to Control10: These columns represent the samples from 10 normal individuals, with each column name followed by the corresponding normal individual number. They also contain the expression levels of the gene in each sample, in TPM units. * Control: The average expression level across all normal samples. * Patient: The average expression level across all patient samples. * nr: Likely refers to the identifier from the Non-Redundant Protein Sequence Database. * go: Gene Ontology terms describing the function, process, and location of the gene. * KO_id: KEGG Orthology ID used for classification in the KEGG database for enzymes and biological pathways. * KO_name: The name corresponding to the KEGG Orthology. * paths: The biological pathways in which the gene is involved. * cog: Likely an abbreviation for Cluster of Orthologous Groups, used for classification and functional annotation. * cog_description: The description of the cog. * pfam: Identifier from the Pfam database, a database of protein families. * uniprot: Protein identifier from the UniProt database, which provides protein sequence and functional information. * entrez: Entrez Gene ID, a gene identifier in the NCBI (National Center for Biotechnology Information) gene database.