|
| Status |
Public on Apr 30, 2022 |
| Title |
PT_3 LNM VDJ |
| Sample type |
SRA |
| |
|
| Source name |
human breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
sequencing_type: VDJ-seq
donor: patient_3
site: Lymph node metastasis
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 |
SAMN17978318 |
| SRA |
SRX10124733 |
