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| Status |
Public on Nov 07, 2022 |
| Title |
3 mo NPE mut SN1 |
| Sample type |
SRA |
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| Source name |
Peripheral nerve tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: Peripheral nerve tumor:sciatic nerves
strain: Nf1fl/fl;P53fl/fl;Eed fl/fl;Dhh-Cre;ccGFP
age: 14 weeks
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| Extracted molecule |
total RNA |
| Extraction protocol |
For mouse samples, tumor tissues were dissected and transported in DMEM to the laboratory. For scRNA-seq, the tissues were dissociated into single cells suspensions using a cocktail of collagenase type I (156 U/ml, Worthington) and dispase II protease (1.25 U/ml, Sigma) at 37oC with agitation. Cell concentration was adjusted to a final concentration of 140,000 cells/ml for Dropseq. The libraries were purified, quantified, and then sequenced on an Illumina NextSeq500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
For Dropseq data, FASTQ sequencing reads were processed, aligned to the mouse genome (mm10), and converted to digital gene expression matrices using the Drop-seq tools (version 1.12, http://mccarrolllab.com/dropseq/) with settings as described in the Drop-seq Alignment Cookbook (version 1.2, January 2016 http://mccarrolllab.com/dropseq/).
Genome_build: mm10
Supplementary_files_format_and_content: expression matrix
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| Submission date |
Jun 28, 2021 |
| Last update date |
Nov 07, 2022 |
| Contact name |
Lai Man (Natalie) Wu |
| E-mail(s) |
laiman.wu@cchmc.org
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| Organization name |
CCHMC
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| Street address |
3333 Burnet Avenue, MLC7013,Lu lab, T6.525
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| City |
CINCINNATI |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE179041 |
Transcriptional programs dictating Schwann cell transformation in MPNST [Dropseq scRNAseq] |
| GSE179043 |
Transcriptional programs dictating Schwann cell transformation in MPNST |
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| Relations |
| BioSample |
SAMN19918682 |
| SRA |
SRX11243563 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5404425_P98-NPE_SN_out_gene_exon_tagged.dge.txt.gz |
8.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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