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Sample GSM7727713 Query DataSets for GSM7727713
Status Public on May 28, 2024
Title Empty vector Bone Marrow 3
Sample type SRA
Source name bone marrow
Organism Mus musculus
Characteristics tissue: bone marrow
cell line: EV-BM
cell type: total BMC
genotype: mixed WT and EV
treatment: TBI + BMT
strain: Balb/cAnN
Treatment protocol Mice received sub-lethal total body irradiation and subsequent bone marrow transplantation (100.000 transduced cells + 1*10^6 wt BM cells). On day 10 past transplantation blood was taken to check for engraftment and on day 21 past TP bone marrow was isolated
Growth protocol Donor mice are treated with 5-FU. Donor bone marrow are isolated on day four after treatment and cultured in RPMI, 10%FCS, 1%P/S supplemented with IL-3 (10ng/ml), IL-6 (10ng/ml) and mSCF (14ng/ml). EV or MPL+Calr(del52) expression constructs are transduced using a retroviral vector system with polybrene to increase transduction efficiency.
Extracted molecule total RNA
Extraction protocol Bone marrow cells were isolated from femur, tibia and hip bone on day 21 past BMT. Erythrocytes were removed using erythrocyte lysis buffer. Cells were strained through a 75 µm cell strainer to receive single cell suspension. For all steps cells were treated according to 10xGenomics Cell preparation guidelines.
Samples were processed using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index – 10x Genomics) following manufactures protocol. In short: GEM´s were generated using a Chromium Controller (10x Genomics) at a target cell recovery rate of 10.000. GEM-RT and subsequent clean-up was performed. cDNA was amplified and 3’ Gene Expression Dual Index Library Construction was performed. Illumina paired-end, dual indexing was performed. For all amplification steps a Veriti 96 Well Thermal Cycler (appledbiosystems) and for all quality control steps a 2200 TapeStation (Agilent Technologies) was used.
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Paired fastq files were processed with cellRanger (6.1.2) with the transcriptome index from Mouse mm10 (2020-A) downloaded from 10xgenomics website.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Submission date Aug 21, 2023
Last update date May 28, 2024
Contact name Geoffroy Andrieux
Organization name University clinics Freiburg
Street address Breisacherstr 153
City Freiburg
ZIP/Postal code 79110
Country Germany
Platform ID GPL24247
Series (2)
GSE241364 Oncogenic Calreticulin Induces Immune Escape by Stimulating TGF-β Expression and Regulatory T Cell Expansion in the Bone Marrow Microenvironment - scRNAseq
GSE241365 Oncogenic Calreticulin Induces Immune Escape by Stimulating TGF-β Expression and Regulatory T Cell Expansion in the Bone Marrow Microenvironment
BioSample SAMN37097556
SRA SRX21438973

Supplementary file Size Download File type/resource
GSM7727713_EV3_barcodes.tsv.gz 33.6 Kb (ftp)(http) TSV
GSM7727713_EV3_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM7727713_EV3_matrix.mtx.gz 50.6 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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