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Series GSE184398 Query DataSets for GSE184398
Status Public on Dec 29, 2021
Title RNA-sequencing of tumor infiltrating cells across 12 different solid tumors type
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary To identify patterns of gene expression within six broadly defined cell populations, we also performed cell sorting for bulk RNA-sequencing including compartments denoted: 1. “Live”: All viable cells at the time of sorting, 2. “Tconv”: sorted conventional CD4+ and CD8+ T cells, 3. “Treg”: CD25+ CD4+ (enriched for regulatory) T cells, 4. “Myeloid”: Lymphocyte-negative HLA-DR+ (enriched for myeloid) cells, 5. “Stromal”: CD45- CD44+Thy1+ cells, and 6. “Tumor”: all other CD45- cells
 
Overall design Tumor samples for the Immunoprofiler was transported from various cancer operating rooms (ORs) as well as from outpatient clinics. All patients consented by the UCSF IPI clinical coordinator group for tissue collection under a UCSF IRB approved protocol (UCSF IRB# 20-31740). Tumor or metastatic tissue was thoroughly chopped with surgical scissors and transferred to GentleMACs C Tubes (Miltenyi Biotec) containing 20 uL/mL Liberase TL (5 mg/ml, Roche) and 50 U/ml DNAse I (Roche) in RPMI 1640 per 0.3 g tissue. GentleMACs C Tubes were then installed onto the GentleMACs Octo Dissociator (Miltenyi Biotec) and incubated for 45min according to the manufacturer’s instructions. Samples were then quenched with 15 mL of sort buffer (PBS/2% FCS/2mM EDTA), filtered through 100 um filters and spun down. Red blood cell lysis was performed with 175 mM ammonium chloride if needed. Cells were then incubated with Human FcX (Biolegend) to prevent non-specific antibody binding. Cells were then washed in DPBS and incubated with Zombie Aqua Fixable Viability Dye (Thermo). Following viability dye, cells were washed with sort buffer and incubated with cell surface antibodies mix diluted in the BV stain buffer (BD Biosciences) following manufacturer instruction for 30 minutes on ice in the dark and subsequently fixed in either Fixation Buffer (BD Biosciences) or in Foxp3/Transcription Factor Staining Buffer Set (eBioscience) if intracellular staining was required.
 
Contributor(s) Combes AJ, Krummel MF, Samad B
Citation(s) 34963056
Submission date Sep 19, 2021
Last update date Jul 20, 2023
Contact name Bushra Samad
E-mail(s) Bushra.Samad@ucsf.edu
Organization name USCF Immunoprofiler
Street address 505 Parnassus Ave
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (1072)
GSM5585901 ADR002T1_St_S12
GSM5585902 BLAD006T1Li2_S8
GSM5585903 BLAD006T1Tc_S10
Relations
BioProject PRJNA764510
SRA SRP337782

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE184398_RAW.tar 316.4 Mb (http)(custom) TAR (of MTX, TSV)
GSE184398_pancan_all_pc_genes_Live_TPM_Aug_3_20.tsv.gz 14.7 Mb (ftp)(http) TSV
GSE184398_pancan_all_pc_genes_Myeloid_TPM_Aug_5_20.tsv.gz 10.0 Mb (ftp)(http) TSV
GSE184398_pancan_all_pc_genes_Tcell_TPM_July_27_20.tsv.gz 6.3 Mb (ftp)(http) TSV
GSE184398_pancan_all_pc_genes_Treg_TPM_July_27_20.tsv.gz 4.7 Mb (ftp)(http) TSV
GSE184398_pancan_all_pc_genes_tumor_epcam_TPM_Aug_27_20.tsv.gz 5.2 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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