 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 15, 2024 |
| Title |
RPM GBC Allograft rep1 |
| Sample type |
SRA |
| |
|
| Source name |
allograft tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: allograft tumor
genotype: Rb1 fl/fl; Trp53 fl/fl; Myc T58A (RPM)
treatment: Ad5-CMV-Cre
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Allograft tumor was subject to enzymatic/mechanical digestion into a single cell suspension. 10x Genomics gel beads and reverse transcription reagents were added to cell suspensions and loaded to a chromium single cell controller to form gel-bead-in emulsions (GEMs). From GEMs, cDNA was generated from barcoded mRNA and subsequent A tailing, end repair, adaptor ligation, and sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D5000 ScreenTape on an Agilent Tech 2200 tapestation system and quantified by Kapa Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000 w 2x150 paired end seq.
10X Genomics Single-Cell 3' RNA Dual Index v3
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X Genomic 3' GEX
|
| Data processing |
Demulitplexed with 10x cellranger mkfastq to create fastq files with sample index (I1, I2) and read files (R1, R2).
Reads were aligned to the custom mouse genome (refdata-cellranger-mm10) from 10X Genomics plus GFP.CDS and CellTag.UTR sequences (as described in Kong et al., Nature Protocols, 2020) and firefly Luciferase (fLuc) and Venus from our Myc and Ascl1 alleles, respectively, using cellranger mkref. Count barcodes and UMIs were then generated using cellranger count v7.0.0.
Downstream visualization and further analysis of scRNA seq data was performed in R with Seurat and/or Python with Scanpy.
Assembly: Custom mm10-2020-A plus GFP.CDS, CellTag.UTR, firefly Luciferase (fLuc), and Venus sequences as indicators of Cre-mediated recombination for the Myc allele (fLuc) or Ascl1 allele (Venus).
Supplementary files format and content: Filtered feature-barcode matrices from cellranger count.
|
| |
|
| Submission date |
Mar 15, 2024 |
| Last update date |
May 15, 2024 |
| Contact name |
Trudy Oliver |
| E-mail(s) |
tgo@duke.edu, trudy.oliver@duke.edu
|
| Phone |
6174607487
|
| Organization name |
Duke University
|
| Department |
Pharmacology & Cancer Biology
|
| Lab |
theoliverlab
|
| Street address |
Duke University, Box 3813, LSRC Room C138B, 308 Research Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE244119 |
Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer [Single cell RNA seq on RPM and RPMA GBC-derived allograft tumors, CellTagged] |
| GSE244123 |
Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer |
|
| Relations |
| BioSample |
SAMN40473176 |
| SRA |
SRX23962837 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8149580_RPM_GBC_Allograft_rep1.tar.gz |
98.6 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
