|
| Status |
Public on May 03, 2023 |
| Title |
Molecular fingerprints for bone marrow cells, pediatric acute lymphoblastic leukemia |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
The overall goal of this study was to characterize bone marrow cells based on their transcriptome, surface protein expression and BCR- and TCR VDJ-profile for accurate identification of clinically relevant cell states. This submission includes pediatric B-cell acute lymphoblastic leukemia samples. This project has received funding from the European Union Horizon 2020 research and innovation programme under grant agreement No 824110 (EASI-Genomics)
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| |
|
| Overall design |
CITE-seq (scRNA-seq, scADT-seq) and scVDJ-seq samples were generated from bone marrow and blood mononuclear cells using the 10X Genomics Chromium platform and protocols. Bone marrow and blood samples were collected from donors treated with NOPHO2008 protocol at diagnosis and at day 2 (blood) and day 15 (bone marrow) during induction chemotherapy. Cells were stained with specific surface antibodies and hashtag antibodies to label donors. Single cell suspensions representing donor pools (2 per pool) were loaded and processed for sequencing. Sample annotation follows tissue term ontology from EFO https://www.ebi.ac.uk/efo/
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Authors state the following:
Submission of sensitive patient data, only processed cell ranger output files provided. Raw data with sample metadata is deposited to EGA (see Data Access Committee)
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| |
|
| Contributor(s) |
Heinäniemi M, Lohi O, Lahnalampi M, Suhonen J, Ivanov K, Sipola M |
| Citation(s) |
38822412 |
| |
| Submission date |
Apr 21, 2023 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Merja Heinäniemi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Eastern Finland
|
| Department |
School of Medicine, Institute of Biomedicine
|
| Lab |
Systems Genomics - Heinäniemi lab
|
| Street address |
Yliopistonranta 1E
|
| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA958206 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE230295_L10Ball_contig_annotations.csv.gz |
850.9 Kb |
(ftp)(http) |
CSV |
| GSE230295_L10Tall_contig_annotations.csv.gz |
165.3 Kb |
(ftp)(http) |
CSV |
| GSE230295_L10barcodes.tsv.gz |
2.2 Mb |
(ftp)(http) |
TSV |
| GSE230295_L10features.tsv.gz |
267.3 Kb |
(ftp)(http) |
TSV |
| GSE230295_L10matrix.mtx.gz |
147.8 Mb |
(ftp)(http) |
MTX |
| GSE230295_L5Ball_contig_annotations.csv.gz |
1.6 Mb |
(ftp)(http) |
CSV |
| GSE230295_L5Tall_contig_annotations.csv.gz |
813.4 Kb |
(ftp)(http) |
CSV |
| GSE230295_L5barcodes.tsv.gz |
2.2 Mb |
(ftp)(http) |
TSV |
| GSE230295_L5features.tsv.gz |
267.3 Kb |
(ftp)(http) |
TSV |
| GSE230295_L5matrix.mtx.gz |
115.9 Mb |
(ftp)(http) |
MTX |
| GSE230295_L6Ball_contig_annotations.csv.gz |
342.7 Kb |
(ftp)(http) |
CSV |
| GSE230295_L6Tall_contig_annotations.csv.gz |
540.9 Kb |
(ftp)(http) |
CSV |
| GSE230295_L6barcodes.tsv.gz |
2.2 Mb |
(ftp)(http) |
TSV |
| GSE230295_L6features.tsv.gz |
267.3 Kb |
(ftp)(http) |
TSV |
| GSE230295_L6matrix.mtx.gz |
98.5 Mb |
(ftp)(http) |
MTX |
| GSE230295_L7Ball_contig_annotations.csv.gz |
846.1 Kb |
(ftp)(http) |
CSV |
| GSE230295_L7Tall_contig_annotations.csv.gz |
836.3 Kb |
(ftp)(http) |
CSV |
| GSE230295_L7barcodes.tsv.gz |
2.1 Mb |
(ftp)(http) |
TSV |
| GSE230295_L7features.tsv.gz |
267.3 Kb |
(ftp)(http) |
TSV |
| GSE230295_L7matrix.mtx.gz |
88.7 Mb |
(ftp)(http) |
MTX |
| GSE230295_L8Ball_contig_annotations.csv.gz |
419.9 Kb |
(ftp)(http) |
CSV |
| GSE230295_L8Tall_contig_annotations.csv.gz |
329.0 Kb |
(ftp)(http) |
CSV |
| GSE230295_L8barcodes.tsv.gz |
2.1 Mb |
(ftp)(http) |
TSV |
| GSE230295_L8features.tsv.gz |
267.3 Kb |
(ftp)(http) |
TSV |
| GSE230295_L8matrix.mtx.gz |
89.0 Mb |
(ftp)(http) |
MTX |
| GSE230295_L9Ball_contig_annotations.csv.gz |
345.8 Kb |
(ftp)(http) |
CSV |
| GSE230295_L9Tall_contig_annotations.csv.gz |
484.6 Kb |
(ftp)(http) |
CSV |
| GSE230295_L9barcodes.tsv.gz |
2.2 Mb |
(ftp)(http) |
TSV |
| GSE230295_L9features.tsv.gz |
267.3 Kb |
(ftp)(http) |
TSV |
| GSE230295_L9matrix.mtx.gz |
100.0 Mb |
(ftp)(http) |
MTX |
| GSE230295_ab_barcodes.csv.gz |
630 b |
(ftp)(http) |
CSV |
| Raw data not provided for this record |
| Processed data are available on Series record |
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