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Sample GSM5091227 Query DataSets for GSM5091227
Status Public on Apr 30, 2022
Title PT_2 tumor VDJ
Sample type SRA
 
Source name human breast cancer
Organism Homo sapiens
Characteristics sequencing_type: VDJ-seq
donor: patient_2
site: Primary tumor
pathological type: Invasive ductal carcinoma
Extracted molecule total RNA
Extraction protocol Cells suspension from primary tumor and paired lymph node metastasis samples were loaded into the 10X Chromium Controller using the Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics), Samples with gene expression and T cell receptor sequencing, the Chromium Single Cell V(D)J protocol was used. 10X Chromium Single Cell V(D)J kits (5' gene expression with paired T cell receptor sequencing)
RNA libraries were prepared for sequencing using 10x chromium single cell 5' Library or V(D)J protocals and standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Raw sequencing data for each sample were converted to matrices of expression using cellranger (version 3.1.0, 10x Genomics), for GEX-seq data using cellranger count parameter and for VDJ-seq data using cellragner vdj parameter
doublet removal with Scrublet (version 0.2.3)
removal of ambient mRNA with SoupX (version 1.3.6)
normalization, logtransform, variable genes calling with Scanpy (version 1.4.1)
Integrate samples with bbknn
cells cluster with leiden
different gene analysis with Seurat (version 3.1.1)
Genome_build: GRCh38 human reference genome (official Cell Ranger reference, version 3.0.0)
Supplementary_files_format_and_content: Raw counts of filtered cell barcodes and features were provided in cell_counts_matrix.mtx. Cells annotation meta infomation were provided in meta_all.csv as comma separated text files. Cell of vdj annotaion were provided in meta_tcr.csv as comma separated text file
 
Submission date Feb 18, 2021
Last update date Apr 30, 2022
Contact name Hongquan Zhang
E-mail(s) hongquan.zhang@bjmu.edu.cn
Organization name Peking University
Department Department of Anatomy and embryology
Street address School of Basic Medical Sciences. Peking University Health Science Center NO. 38, XUEYUAN Road
City Beijing
State/province Beijing
ZIP/Postal code 100191
Country China
 
Platform ID GPL24676
Series (2)
GSE167036 Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients(10x RNA and TCR)
GSE190870 Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients
Relations
BioSample SAMN17978295
SRA SRX10124724

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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