|
| Status |
Public on May 13, 2022 |
| Title |
s0248_mouse29_HBRX3078_Lung CTRL_1cells |
| Sample type |
SRA |
| |
|
| Source name |
Metastases
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Metastases
cell line: PDX1
cell type: cancer cells
|
| Growth protocol |
MDA-MB-231 and PDX models were implanted in the 4th mammary fat pad (cleared) of 4-8 week-old NSG mice. Primary tumors were resected. Lung metastasis cells were isolated out of the dissected lung at a later time (when mice reached ethical endpoints)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Primary tumors and lung metastases were mechanically and enzymatically digested with a collagenase/hyaluronidase solution (Stem Cell Technologies, 07912). Human cancer cells were recovered by FACS sorting, based CD298 or GFP expression.
Single cell isolation was performed on the Fluidigm C1 platform according to manufacturer protocol. mRNA was isolated with the Takara SMART-Seq Ultra Low RNA kit (Takara Bio; 634833) . Libraries for Illumina sequencing were prepared with the Nextera XT DNA Library Preparation Kit (Illumina; FC-131-1096).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Fluidigm C1 platform
well2965
|
| Data processing |
Reads were aligned to human genom with STAR. Following observation under the microscope, wells containing more than 1 cell or debris were marked and removed from further analyses.
Following observation under the microscope, wells containing more than 1 cell or debris were marked and removed from further analyses.
Cell cycle of individual cells were inferred using sets of known cell cycle-regulated genes known to peak in transcription at given cell cycle stages obtained from (PMID: 12058064, PMID:11416145)
The cell cycle and library complexity (percentage of detected genes) were modeled as covariates and regressed out of the log-normalized counts using glm.fit (R package glm).
Differential gene expression between single cell clusters was performed using pairwise t-test implemented in FindMarkers function from R package scran.
Gene set enrichment was performed with bioconductor packages fgsea and msigdb
Assembly: hg38
Supplementary files format and content: counts_raw.csv is a matrix containing raw counts after alignment. counts_afterQC are counts for the cells passing QC. Cccorected_logcounts.csv contains logcounts of the cells that passed QC after the cell-cycle correction. metadata.csv contains addition information on the column names of counts_raw.csv and CCcorected_logcounts.csv.
|
| |
|
| Submission date |
May 10, 2022 |
| Last update date |
May 13, 2022 |
| Contact name |
Mohamed Bentires-Alj |
| E-mail(s) |
bentireslab.data@gmail.com
|
| Organization name |
University Hospital Basel
|
| Department |
DBM
|
| Lab |
THMR
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| ZIP/Postal code |
4031 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE202695 |
Single-cell analysis reveals inter- and intra-tumor heterogeneity in metastatic breast cancer |
|
| Relations |
| BioSample |
SAMN28183999 |
| SRA |
SRX15230710 |
