Data for: ALK R1275Q mutation drives expansion of SCP-like cells during sympathoadrenal commitment and primes neuroblastoma initiation
https://doi.org/10.48723/9bm1-gr40
Overview This dataset contains raw and processed transcriptomic profiling data generated from a human induced pluripotent stem cell (iPSC)-based model of sympathoadrenal (SA) lineage differentiation. The study investigates the role of the ALK R1275Q mutation in Neuroblastoma initiation. The dataset includes single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing data derived from healthy control iPSCs and patient-derived iPSCs carrying the germline ALK R1275Q mutation.
The dataset consists of approximately 500 files totalling approximately 486 GB
Data Generation and Methods Human iPSCs (Control lines: Ctrl7, Ctrl10, Ctrl14; Patient lines: NB1, NB2, NB4) were differentiated into trunk neural crest cells (tNCCs), sympathoadrenal progenitors (SAPs), and mature sympathoadrenal cells (SAMs).
Single-Cell RNA Sequencing (scRNA-seq):
Platform: 10x Genomics Single Cell 3' v3.1.
Sequencing: Performed on MGI DNBSEQ PE100.
Samples: Collected at four developmental stages: tNCC, SAP, Day 8 (D8), and Day 12 (D12) from Ctrl10, NB1, NB2, and NB4.
Bulk RNA Sequencing:
Platform: Illumina PE150 sequencing.
Samples: Collected at six developmental stages: tNCC, SAP, Day 6, Day 8, Day 10 and Day 12 from Ctrl7, Ctrl10, Ctrl14, NB1, NB2, and NB4
File Content and Organization The dataset consists of the following file types:
Raw Sequencing Data (FASTQ):
Unprocessed sequencing reads in .fastq.gz format.
For scRNA-seq: Paired-end reads (e.g., R1 containing cell barcodes/UMIs, R2 containing the transcript insert).
For Bulk RNA-seq: Paired-end reads (R1/R2).
Filenames typically indicate sample ID, library (GE or HTO), lane number, and read direction (e.g., SampleID_GE/HTO_L001_R1_001.fastq.gz).
Processed Data:
Gene Expression Matrices: Count matrices (e.g., .mtx, .tsv) generated by Cell Ranger (for scRNA-seq) or Salmon (for bulk RNA-seq).
Metadata: Tables containing sample information and differentiation time points.
Documentation files
Documentation files
Citation and access
Citation and access
Data access level:
Creator/Principal investigator(s):
Research principal:
Data contains personal data:
Yes
Type of personal data:
Sensitive Personal Data (Health Data): The data consists of transcriptomic sequences (bulk and single-cell RNA-seq) derived from patient-specific induced pluripotent stem cells (iPSCs). This includes genetic information relating to a specific diagnosis (Neuroblastoma) and mutation status (e.g., germline ALK R1275Q mutation). Indirect Identifiers: While direct identifiers (names, ID numbers) have been removed and replaced with codes (e.g., NB1, NB2), the combination of rare disease diagnosis, specific genetic mutation, and biological characteristics could potentially be used to re-identify individuals if combined with other registries.
Sensitive personal data:
Yes
Citation:
Language:
Method and outcome
Method and outcome
Unit of analysis:
Population:
Human induced pluripotent stem cell (iPSC) lines derived from patients with Neuroblastoma carrying the germline ALK R1275Q mutation, as well as iPSC lines from healthy control individuals. (Refers to specific cell lines: NB1, NB2, NB4 and Ctrl7, Ctrl10, Ctrl14)
Study design:
- Case-control study
- Experimental study
- Preclinical study
- Observational study
Description of study design:
This is a preclinical experimental study utilizing a human induced pluripotent stem cell (iPSC) model. The study employs a case-control design, comparing iPSC lines derived from neuroblastoma patients carrying the ALK R1275Q mutation with iPSC lines from healthy donors. An in vitro time-course design was applied to monitor the differentiation process along the sympathoadrenal lineage. Samples were collected and analyzed using single-cell and bulk RNA sequencing at four specific developmental stages: trunk neural crest cells (tNCC), sympathoadrenal progenitors (SAP), and differentiated sympathoadrenal cells (Day 8 and Day 12).
Sampling procedure:
Description of sampling:
A non-probability, purposive sampling strategy was employed. The study utilized specific human induced pluripotent stem cell (iPSC) lines selected based on their genetic profile to model Neuroblastoma initiation. The sample consists of: Patient-derived lines (n=3): Established from skin biopsies of patients diagnosed with Neuroblastoma carrying the germline ALK R1275Q mutation (Cell lines: NB1, NB2, NB4). Control lines (n=3): Established from healthy individuals to serve as experimental controls (Cell lines: Ctrl7, Ctrl10, Ctrl14). The patient samples were collected at Karolinska University Hospital after informed consent and according to ethical approval (EPN 2009/1369-31/1, EPN 2022-07254-01). Ctrl iPS cell lines were obtained from Karolinska Institutet iPS Core facility (EPN 2012/208-31/3).
Variables:
33538
Number of individuals/objects:
6
Weighting:
No
Description of the response rate/participation rate:
Not applicable. This is an experimental study using established cell lines, not a population survey.
Samples/material - Existing from scientific collection/biobank
Samples/material - Existing from scientific collection/biobank
Name:
Research collection
Type(s) of sample:
Human induced Pluripotent Stem Cells (iPSC) and differentiated derivatives (Trunk neural crest cells, Sympathoadrenal progenitors, Sympathoadrenal cells). (Originally established from patient skin biopsies/fibroblasts).
Administrative information
Administrative information
Responsible department/unit:
Department of Microbiology, Tumor and Cell Biology [C1]
Other research principals:
Ethical Review
Ethical Review
Reviewer:
- Stockholm Ethical Review Board
Registration number:
2009/1369-31/1
Reviewer:
- Stockholm Ethical Review Board
Registration number:
2012/208-31/3
Reviewer:
- Swedish Ethical Review Authority
components.catalogue.resource.content.administrativeInformation.ethicalReview.rorId.srText
ROR
Registration number:
2022-07254-01
