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Sample GSM6859012 Query DataSets for GSM6859012
Status Public on Sep 27, 2023
Title Control sample of Tumor liver (Mouse 2)
Sample type SRA
 
Source name Liver containing metastases of CRC origin
Organism Mus musculus
Characteristics tissue: Liver containing metastases of CRC origin
condition: Control
Extracted molecule total RNA
Extraction protocol Liver metastases were isolated and dissociated into single cells by physical (chopping the tissue into small pieces) and enzymatic (collagenase, Dispase II and DNAse) digestion followed by a filtering step using a 0.4mm cell strainer. No antibody staining was performed, single cells were resuspended in autoMACS running buffer containing 7AAD (BioLegend/ 420404) in a 1/50 dilution. Viable cells were sorted based by gating on single 7AAD negative cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1, 10x Genomics, ref. CG000204). Briefly, sorted cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Dec 19, 2022
Last update date Sep 27, 2023
Contact name Stefano Beretta
E-mail(s) beretta.stefano1@hsr.it
Organization name San Raffaele Telethon Institute for Gene Therapy
Street address Via Olgettina, 60
City Milan
ZIP/Postal code 20132
Country Italy
 
Platform ID GPL24247
Series (2)
GSE221357 In vivo macrophage engineering reshapes the tumor microenvironment leading to eradication of liver metastases [scRNA-seq]
GSE221360 In vivo macrophage engineering reshapes the tumor microenvironment leading to eradication of liver metastases
Relations
BioSample SAMN32316014
SRA SRX18777273

Supplementary file Size Download File type/resource
GSM6859012_Sample7_barcodes.tsv.gz 35.8 Kb (ftp)(http) TSV
GSM6859012_Sample7_features.tsv.gz 191.5 Kb (ftp)(http) TSV
GSM6859012_Sample7_matrix.mtx.gz 36.8 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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