|
| Status |
Public on Aug 08, 2023 |
| Title |
Tumor type and cell type-specific gene expression alterations in diverse pediatric central nervous system tumors identified using single nuclei RNA-seq |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Central nervous system (CNS) tumors are the leading cause of pediatric cancer death, and these patients have an increased risk for developing secondary neoplasms. Due to the low prevalence of pediatric CNS tumors, major advances in targeted therapies have been lagging compared to other adult tumors. We collected single nuclei RNA-seq data from 35 pediatric CNS tumors and three non-tumoral pediatric brain tissues (84,700 nuclei) and characterized tumor heterogeneity and transcriptomic alterations. We distinguished cell subpopulations associated with specific tumor types including radial glial cells in ependymomas and oligodendrocyte precursor cells in astrocytomas. In tumors, we observed pathways important in neural stem cell-like populations, a cell type previously associated with therapy resistance. Lastly, we identified transcriptomic alterations among pediatric CNS tumor types compared to non-tumor tissues, while accounting for cell type effects on gene expression. Our results suggest potential tumor type and cell type-specific targets for pediatric CNS tumor treatment.
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| |
|
| Overall design |
Nuclei were isolated from pediatric central nervous system tumors and non-tumor pediatric brain tissue and analyzed using single nuclei RNA-seq (following 10X Genomics 3' VDJ protocol). Majority of the samples were multiplexed into a single 10x run. Please refer to the published paper for the details on the samples that were pooled into the same run.
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| |
|
| Contributor(s) |
Min Kyung L, Brock C |
| Citation(s) |
36865335, 38688903 |
| |
| Submission date |
Aug 16, 2022 |
| Last update date |
May 24, 2024 |
| Contact name |
Min Kyung Lee |
| E-mail(s) |
min.kyung.lee.gr@dartmouth.edu, sarahminkyunglee@gmail.com
|
| Organization name |
Dartmouth College
|
| Street address |
1 Medical Center Dr
|
| City |
Lebanon |
| State/province |
NH |
| ZIP/Postal code |
03756 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (38)
|
| GSM6467392 |
Pool 2, HTO derived cDNA |
| GSM6467393 |
Pool 3, mRNA derived cDNA |
| GSM6467394 |
Pool 3, HTO derived cDNA |
| GSM6467395 |
Pool 4, mRNA derived cDNA |
| GSM6467396 |
Pool 4, HTO derived cDNA |
| GSM6467397 |
Pool 5, mRNA derived cDNA |
| GSM6467398 |
Pool 5, HTO derived cDNA |
| GSM6467399 |
Pool 6, mRNA derived cDNA |
| GSM6467400 |
Pool 6, HTO derived cDNA |
| GSM6467401 |
Pool 9, mRNA derived cDNA |
| GSM6467402 |
Pool 9, HTO derived cDNA |
| GSM6467403 |
Pool 10, mRNA derived cDNA |
| GSM6467404 |
Pool 10, HTO derived cDNA |
| GSM6467405 |
Pool 11, mRNA derived cDNA |
| GSM6467406 |
Pool 11, HTO derived cDNA |
| GSM6467407 |
Pool 12, mRNA derived cDNA |
| GSM6467408 |
Pool 12, HTO derived cDNA |
| GSM6467409 |
Pool 13, mRNA derived cDNA |
| GSM6467410 |
Pool 13, HTO derived cDNA |
| GSM6467411 |
Pool 15, mRNA derived cDNA |
| GSM6467412 |
Pool 15, HTO derived cDNA |
| GSM6467413 |
Pool 18, mRNA derived cDNA |
| GSM6467414 |
Pool 18, HTO derived cDNA |
| GSM6467415 |
Pool 19, mRNA derived cDNA |
| GSM6467416 |
Pool 19, HTO derived cDNA |
| GSM6467417 |
Pool 20, mRNA derived cDNA |
| GSM6467418 |
Pool 20, HTO derived cDNA |
| GSM6467419 |
Pool 21, mRNA derived cDNA |
| GSM6467420 |
Pool 21, HTO derived cDNA |
| GSM6467421 |
Pool 22, mRNA derived cDNA |
| GSM6467422 |
Pool 22, HTO derived cDNA |
| GSM6467423 |
Sample 1, mRNA derived cDNA |
| GSM6467424 |
Sample 3, mRNA derived cDNA |
| GSM6467425 |
Sample 5, mRNA derived cDNA |
| GSM6467426 |
Sample 18, mRNA derived cDNA |
|
| Relations |
| BioProject |
PRJNA869964 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE211362_Pool10_barcodes.tsv.gz |
62.1 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool10_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool10_matrix.mtx.gz |
70.5 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool11_barcodes.tsv.gz |
56.7 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool11_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool11_matrix.mtx.gz |
74.2 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool12_barcodes.tsv.gz |
89.6 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool12_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool12_matrix.mtx.gz |
135.3 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool13_barcodes.tsv.gz |
79.0 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool13_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool13_matrix.mtx.gz |
151.6 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool15_barcodes.tsv.gz |
19.0 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool15_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool15_matrix.mtx.gz |
23.9 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool18_barcodes.tsv.gz |
26.0 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool18_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool18_matrix.mtx.gz |
38.4 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool19_barcodes.tsv.gz |
25.1 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool19_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool19_matrix.mtx.gz |
37.4 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool1_barcodes.tsv.gz |
69.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool1_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool1_matrix.mtx.gz |
160.0 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool20_barcodes.tsv.gz |
21.3 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool20_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool20_matrix.mtx.gz |
19.5 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool21_barcodes.tsv.gz |
26.4 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool21_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool21_matrix.mtx.gz |
25.6 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool22_barcodes.tsv.gz |
26.3 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool22_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool22_matrix.mtx.gz |
22.9 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool2_barcodes.tsv.gz |
50.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool2_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool2_matrix.mtx.gz |
105.4 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool3_barcodes.tsv.gz |
18.1 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool3_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool3_matrix.mtx.gz |
18.8 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool4_barcodes.tsv.gz |
15.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool4_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool4_matrix.mtx.gz |
16.4 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool5_barcodes.tsv.gz |
55.2 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool5_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool5_matrix.mtx.gz |
78.5 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool6_barcodes.tsv.gz |
58.0 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool6_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool6_matrix.mtx.gz |
97.8 Mb |
(ftp)(http) |
MTX |
| GSE211362_Pool9_barcodes.tsv.gz |
63.5 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool9_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Pool9_matrix.mtx.gz |
86.8 Mb |
(ftp)(http) |
MTX |
| GSE211362_Sample18_barcodes.tsv.gz |
20.3 Kb |
(ftp)(http) |
TSV |
| GSE211362_Sample18_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Sample18_matrix.mtx.gz |
35.4 Mb |
(ftp)(http) |
MTX |
| GSE211362_Sample1_barcodes.tsv.gz |
142.7 Kb |
(ftp)(http) |
TSV |
| GSE211362_Sample1_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Sample1_matrix.mtx.gz |
84.6 Mb |
(ftp)(http) |
MTX |
| GSE211362_Sample3_barcodes.tsv.gz |
12.1 Kb |
(ftp)(http) |
TSV |
| GSE211362_Sample3_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Sample3_matrix.mtx.gz |
12.7 Mb |
(ftp)(http) |
MTX |
| GSE211362_Sample5_barcodes.tsv.gz |
10.0 Kb |
(ftp)(http) |
TSV |
| GSE211362_Sample5_features.tsv.gz |
325.8 Kb |
(ftp)(http) |
TSV |
| GSE211362_Sample5_matrix.mtx.gz |
9.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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