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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 09, 2020 |
| Title |
Exp2_SQ_Li_1_GEXL |
| Sample type |
SRA |
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| Source name |
SQ tumor
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
sort selection: CD45+ CD3+
tumor group: SQ only
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
FACS-sorted live CD45+ tumor infiltrating cells from the subcutaneous tumor were washed and resuspended in PBS with 0.04% BSA to a concentration of 1000 cell/μL
Libraries were prepared using 10x Genomics Chromium Single Cell 5’ Reagent (GEX + VDJ) Kit according to manufacturer’s protocol
10x Genomics Chromium Single Cell 5’
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Experiment 2
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| Data processing |
Fastq files from 10x gene expression library were processed with Cell Ranger, using default parameters.
Genome_build: FASTQ were aligned using the Cell Ranger pipeline (10x Genomics, Inc., version 3.0.2) using mouse genome reference dataset (GRCm38/Ensembl/10x, 3.0.2)
Supplementary_files_format_and_content: For each sample, gene expression (GEX) tar file contains a named count matrix of genes by cells for all cells passing filter
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| Submission date |
Sep 08, 2020 |
| Last update date |
Sep 09, 2020 |
| Contact name |
Jennifer Anne Smith |
| E-mail(s) |
jennifer.bridge@ucsf.edu
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| Organization name |
University of California, San Francisco
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| Department |
Diabetes Center
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| Street address |
513 Parnassus Ave HS1102
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE157653 |
Single Cell RNA sequencing of mouse SQ tumor from C57BL/6 with or with liver tumor. |
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| Relations |
| BioSample |
SAMN16081324 |
| SRA |
SRX9091903 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4772112_Exp2_SQ_Li_1_GEXL.tar.gz |
8.4 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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