README ====== Dataset title: Single-cell sequencing reveals transcriptional and immunogenetic diversity in stereotyped chronic lymphocytic leukemia Recommended Citation: Rosenquist, R. (2026). Data for: Single-cell sequencing reveals transcriptional and immunogenetic diversity in stereotyped chronic lymphocytic leukemia (Version 1) [Dataset]. Karolinska Institutet. https://doi.org/10.48723/ep36-6r74 See the Researchdata.se catalogue entry for this dataset - accessible via the DOI link above - for complete metadata, including the dataset description, contact information and information about how to obtain the dataset. Responsible organization: Karolinska Institutet, Stockholm, Sweden Description: The dataset comprises raw single-cell sequencing data generated from patient-derived chronic lymphocytic leukemia (CLL) samples representing stereotyped subsets #1, #2, and #4. Access restrictions: This dataset contains pseudonymized human sequencing data and is subject to legal protections. This dataset can be requested from the Researchdata.se research data catalogue using the link above. Essential information for dataset reuse ---------------------------------------- Single-cell libraries were generated using the 10x Genomics Chromium Single Cell 5′ workflow and include gene expression (GEX), B-cell receptor immunoglobulin (BcR IG), and T-cell receptor (TCR) libraries. Sequencing data are provided as compressed FASTQ files (.fastq.gz). Paired-end sequencing files are identified by R1 and R2 in the filenames. Where a library was sequenced across multiple sequencing lanes, the lane is indicated by identifiers such as L001, L002, etc. A separate Metadata.csv file links each sequencing file to its pseudonymized study case identifier, stereotyped subset, sequencing information, batch, and library/data type. The data type field indicates whether the corresponding FASTQ file belongs to a gene expression (GEX), B-cell receptor immunoglobulin (BcR IG), or T-cell receptor (TCR) library. The FASTQ files can be processed using 10x Genomics Cell Ranger or other software compatible with 10x Genomics Chromium Single Cell 5′ gene expression and immune-receptor sequencing data. All patient identifiers have been replaced by study-specific case identifiers. These identifiers are pseudonyms used within the study and should not be interpreted as clinical or direct personal identifiers. For details of the experimental design, sample selection, library preparation, sequencing, quality control, and downstream analyses, please refer to the associated publication. Datafile descriptions ---------------------- The .fastq.gz files contain raw sequencing reads generated from 10x Genomics Chromium Single Cell 5′ gene expression (GEX), B-cell receptor immunoglobulin (BcR IG), and T-cell receptor (TCR) libraries. Each FASTQ file is linked to its corresponding sample and library information through Metadata.csv. The dataset consists of 138 FASTQ files with a total size of approximately 511 GB. Metadata.csv contains one row for each FASTQ file and provides the following variables: - File: Filename. - Sequencing ID: Sequencing ID of the corresponding FASTQ sequencing file. - Batch: Sequencing batch associated with the file. - Data type: Type of 10x Genomics library. GEX denotes gene expression, BcR IG denotes B-cell receptor immunoglobulin V(D)J sequencing, and TCR denotes T-cell receptor V(D)J sequencing. - Case ID: Study-specific pseudonymized identifier for the patient sample. - Stereotyped subset: CLL stereotyped subset assigned to the case (#1, #2, or #4). Reference information --------------------- Abbreviations: CLL: Chronic lymphocytic leukemia GEX: Gene expression BcR IG: B-cell receptor immunoglobulin TCR: T-cell receptor V(D)J: Variable, diversity, and joining gene segments of antigen receptor genes R1/R2: Read 1 and Read 2 L001, L002, etc.: Sequencing lane identifiers Data quality: The sequencing data were subjected to quality control and processing as described in the associated publication. The deposited FASTQ files represent the raw sequencing data used in the study. For detailed information on sample processing, sequencing, quality control, and downstream analyses, please refer to the associated publication.