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| Status |
Public on Jun 14, 2024 |
| Title |
Cranioencephalic functional lymphoid units in glioblastoma |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We used single cell RNA sequencing to profile the immune cell repertoire of tumor tissue, peripheral blood mononuclear cells (PBMC), bone marrow mononuclear cells (BMMC) from distal bone and cranial (skull) bone from human treatment-naive glioblastoma patients. For comparison, we obtained and analyzed control samples (cranial bone and PBMC) from human non-malignant intracranial disease.
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| Overall design |
CD45+ cells were derived by magnetic cell separation from fresh clinical samples (tumor tissue, cranial bone, PBMC, BMMC) and analyzed using the 10x Genomics Chromium Next GEM Single Cell 3´ Reagent Kits v3.1 or the 10x Genomics Chromium Next GEM Single Cell 5´ Reagent Kits v2. A second set of data was derived from CD45+ single cell suspensions that underwent additional magnetic depletion of myeloid cells (CD14 negative flowthrough) and were further analyzed using the 10x Genomics Chromium Next GEM Single Cell 5´ Reagent Kits v2.
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| Contributor(s) |
Dobersalske C, Rauschenbach L, Hua Y, Rambow F, Sure U, Scheffler B |
| Citation(s) |
39085419 |
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| Submission date |
May 24, 2023 |
| Last update date |
Sep 13, 2024 |
| Contact name |
Björn Scheffler |
| Organization name |
DKFZ (German Cancer Research Center)
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| Department |
DKTK Division Translational Neurooncology at the WTZ
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| Street address |
Hufelandstrasse 55
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| City |
Essen |
| ZIP/Postal code |
45147 |
| Country |
Germany |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (55)
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| GSM7421860 |
Patient 1, Cranial Bone CD45+, 3' GEX scRNAseq |
| GSM7421861 |
Patient 1, Tumor CD45+, 3' GEX scRNAseq |
| GSM7421862 |
Patient 1, PBMCs CD45+, 3' GEX scRNAseq |
| GSM7421863 |
Patient 2, Cranial Bone CD45+, 3' GEX scRNAseq |
| GSM7421864 |
Patient 2, Tumor CD45+, 3' GEX scRNAseq |
| GSM7421865 |
Patient 2, PBMCs CD45+, 3' GEX scRNAseq |
| GSM7421866 |
Patient 7, Cranial Bone CD45+, 3' GEX scRNAseq |
| GSM7421867 |
Patient 8, Cranial Bone CD45+, 3' GEX scRNAseq |
| GSM7421868 |
Patient 9, Cranial Bone CD45+, 3' GEX scRNAseq |
| GSM7421869 |
Patient 9, Tumor CD45+, 3' GEX scRNAseq |
| GSM7421870 |
Patient 9, PBMCs CD45+, 3' GEX scRNAseq |
| GSM7421871 |
Patient c4, Control Cranial Bone CD45+, 3' GEX scRNAseq |
| GSM7421872 |
Patient c4, Control PBMCs CD45+, 3' GEX scRNAseq |
| GSM7421873 |
Patient c5, Control Cranial Bone CD45+, 3' GEX scRNAseq |
| GSM7421874 |
Patient c5, Control PBMCs CD45+, 3' GEX scRNAseq |
| GSM8244370 |
Patient c8, Control Cranial Bone CD45+, 3' GEX scRNAseq |
| GSM8244371 |
Patient c8, Control PBMC CD45+, 3' GEX scRNAseq |
| GSM8244372 |
Patient c9, Control Cranial Bone CD45+, 3' GEX scRNAseq |
| GSM8244373 |
Patient c9, Control PBMC CD45+, 3' GEX scRNAseq |
| GSM8244374 |
Patient c10, Control Cranial Bone CD45+, 3' GEX scRNAseq |
| GSM8244375 |
Patient c10, Control PBMC CD45+, 3' GEX scRNAseq |
| GSM8244376 |
Patient 4, Cranial Bone CD45+, 5' GEX scRNAseq |
| GSM8244377 |
Patient 4, Cranial Bone CD45+, 5' TCR scV(D)Jseq |
| GSM8244378 |
Patient 4, Tumor CD45+, 5' GEX scRNAseq |
| GSM8244379 |
Patient 4, Tumor CD45+, 5' TCR scV(D)Jseq |
| GSM8244380 |
Patient 15, Cranial Bone CD45+, 5' GEX scRNAseq |
| GSM8244381 |
Patient 15, Cranial Bone CD45+, 5' TCR scV(D)Jseq |
| GSM8244382 |
Patient 15, Tumor CD45+, 5' GEX scRNAseq |
| GSM8244383 |
Patient 15, Tumor CD45+, 5' TCR scV(D)Jseq |
| GSM8244384 |
Patient 15, PBMC CD45+, 5' GEX scRNAseq |
| GSM8244385 |
Patient 15, PBMC CD45+, 5' TCR scV(D)Jseq |
| GSM8244386 |
Patient 16, Cranial Bone CD45+, 5' GEX scRNAseq |
| GSM8244387 |
Patient 16, Cranial Bone CD45+, 5' TCR scV(D)Jseq |
| GSM8244388 |
Patient 16, Tumor CD45+, 5' GEX scRNAseq |
| GSM8244389 |
Patient 16, Tumor CD45+, 5' TCR scV(D)Jseq |
| GSM8244390 |
Patient 16, PBMC CD45+, 5' GEX scRNAseq |
| GSM8244391 |
Patient 16, PBMC CD45+, 5' TCR scV(D)Jseq |
| GSM8244392 |
Patient 21, Cranial Bone CD45+ CD14-, 5' GEX scRNAseq |
| GSM8244393 |
Patient 21, Cranial Bone CD45+ CD14-, 5' TCR scV(D)Jseq |
| GSM8244394 |
Patient 21, Tumor CD45+ CD14-, 5' GEX scRNAseq |
| GSM8244395 |
Patient 21, Tumor CD45+ CD14-, 5' TCR scV(D)Jseq |
| GSM8244396 |
Patient 21, BMMC CD45+ CD14-, 5' GEX scRNAseq |
| GSM8244397 |
Patient 21, BMMC CD45+ CD14-, 5' TCR scV(D)Jseq |
| GSM8244398 |
Patient 22, Cranial Bone CD45+ CD14-, 5' GEX scRNAseq |
| GSM8244399 |
Patient 22, Cranial Bone CD45+ CD14-, 5' TCR scV(D)Jseq |
| GSM8244400 |
Patient 22, Tumor CD45+ CD14-, 5' GEX scRNAseq |
| GSM8244401 |
Patient 22, Tumor CD45+ CD14-, 5' TCR scV(D)Jseq |
| GSM8244402 |
Patient 22, BMMC CD45+ CD14-, 5' GEX scRNAseq |
| GSM8244403 |
Patient 22, BMMC CD45+ CD14-, 5' TCR scV(D)Jseq |
| GSM8244404 |
Patient 24, Cranial Bone CD45+ CD14-, 5' GEX scRNAseq |
| GSM8244405 |
Patient 24, Cranial Bone CD45+ CD14-, 5' TCR scV(D)Jseq |
| GSM8244406 |
Patient 24, Tumor CD45+ CD14-, 5' GEX scRNAseq |
| GSM8244407 |
Patient 24, Tumor CD45+ CD14-, 5' TCR scV(D)Jseq |
| GSM8244408 |
Patient 24, BMMC CD45+ CD14-, 5' GEX scRNAseq |
| GSM8244409 |
Patient 24, BMMC CD45+ CD14-, 5' TCR scV(D)Jseq |
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| Relations |
| BioProject |
PRJNA975835 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE233304_RAW.tar |
2.2 Gb |
(http)(custom) |
TAR (of CSV, H5, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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