|
| Status |
Public on May 28, 2020 |
| Title |
15844X1 Day17 (time-series cells) |
| Sample type |
SRA |
| |
|
| Source name |
RPM-CAS9 GEMM
|
| Organism |
Mus musculus |
| Characteristics |
ID: 15844X1
mouse genotype: Rb1 fl/fl;Trp53 fl/fl;MycT58A LSL/LSL-Cas9-Ires-GFP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Enzymatic/mechanical digestion into single cell suspension then immediate sequencing for bulk tumors, or growth in culture for transition timepoints
10X Chromium Single Cell Gene Expression Solution with 3’ chemistry, version 3
Targeted cell recovery of 8k cells, 10x gel beads and reverse transcription reagents were added to cell suspensions and loaded to 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, sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D1000 ScreenTape on Agilent tech 2200 tapestation system and quantified KAPA Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000 w 2x150 paired end seq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Single-cell RNA seq
Filtered_TimeCourse_barcodes.tsv.gz
Filtered_TimeCourse_features.tsv.gz
Filtered_TimeCourse_matrix.mtx.gz
|
| Data processing |
Demulitplexed with 10x cellranger mkfastq version 3.1.0 to create fastq files with the I1 sample index, R1 cell barcode+UMI and R2 sequence
Reads were aligned to the mouse genome (refdata-cellranger-mm10-3.0.0 from 10X Genomics with EGFP+Cas9 added) and count barcodes and UMIs were generated using cellranger count 3.1.0 with expected-cells set to 8000 per library
tumor cells were identified in the Loupe browser and with Seurat and combined into a single experiment containing all timepoints
Genome_build: mm10 with EGFP+Cas9
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MEX format from cellranger count. The time course samples from day 4 to 21 are aggregated into one feature barcode matrix
|
| |
|
| Submission date |
Apr 23, 2020 |
| Last update date |
Sep 12, 2023 |
| Contact name |
Trudy Oliver |
| E-mail(s) |
[email protected], [email protected]
|
| 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) |
| GSE149179 |
MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate [Single Cell RNA seq on RPM time-series cells and 4 RPM bulk tumors] |
| GSE149180 |
MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate [SuperSeries] |
|
| Relations |
| BioSample |
SAMN14677162 |
| SRA |
SRX8161344 |
