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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 29, 2020 |
| Title |
Analysis of RNA-seq of human neuroblastomas from mouse-human neural crest chimeric mice model and in other neuroblastoma models |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To confirm the neuroblastomas (NB) identity of human neuroblastomas from mouse-human neural crest chimeric mice model (CHNBs) we characterized their gene expression profiles by RNA-Seq (CHNBs MYCN+ALKF1174L; n=8). For a global comparison of gene expression profiles of CHNBs with other NB models, we further collected RNA-seq data from patient derived xenografts of neuroblastoma (PDX NBs ; MYCNamp+ALKwt PDX; n=2, and MYCNamp+ALKF1174L PDX; n=3), neuroblastomas from genetically engineered mouse model (GEMM NBs; Th-MYCN+ALKF1174L; n=3), neuroblastoma established cell lines (n=2; Kelly, MYCNamp+ALKF1174L; SH-SY5Y, MYCNwt+ ALKF1174L), human pluripotent derived human neural crest cells (hNCCs; wt hNCCs; n=2, and MYCN+ALKF1174L hNCCs, with Dox; n=2) and from hNCC xenografts (MYCN+ALKF1174L; n=5).
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| Overall design |
RNA samples were collectd from 28 biological samples, including: 8 samples for CHNB (4 with technical replicates), 5 samples of PDX NBs (with technical replicates), 3 samples of mouse GEMM NBs (with technical replicates), 2 samples of NB cell lines, 5 samples of hNCCS xenografts (one with biological replicate and 2 with technical replicates) and 4 samples of hNCCs (2 with oncogenes and Dox, and 2 wt with technical replicates), and one mouse wt adernal gland (control) .
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| Contributor(s) |
Jaenisch R, Cohen MA |
| Citation(s) |
32142683 |
| Submission date |
Jan 28, 2020 |
| Last update date |
May 11, 2020 |
| Contact name |
Malkiel Cohen |
| E-mail(s) |
wibr-bioinformatics@wi.mit.edu
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| Organization name |
Whitehead Institute
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| Lab |
Jaenisch
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| Street address |
455 Main St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (3) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL22245 |
Illumina HiSeq 2500 (Homo sapiens; Mus musculus) |
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| Samples (29)
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| Relations |
| BioProject |
PRJNA603497 |
| SRA |
SRP245586 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144366_Cohen_human_gene_counts.txt.gz |
1007.0 Kb |
(ftp)(http) |
TXT |
| GSE144366_Cohen_mouse_gene_counts.txt.gz |
909.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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