|
| Status |
Public on Aug 11, 2018 |
| Title |
PT089_P3_G05_S365 |
| Sample type |
SRA |
| |
|
| Source name |
breast
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast
breast cancer subtype: TNBC
patient: PT089
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresly collected human tumor samples were mechanically and enzymatically digested using tumor dissociation kit (Miltenyi Biotec). Single cells were sorted by flow cytometry, lysed and snap frozen on dry ice immediately.
RNA libraries were prepared using Smart-seq2 protocol (Picelli et al., 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Fastq files were quantified to transcript per million (TPM) expression values with RSEM with default parameters
Low quality cells were filtered as follows: 4 median absolute deviations (MADs) below the median for any of the three metrics concering: i) library size; ii) number of expressed genes; iii) total amount of mRNA
Unexpressed genes were removed as follows: a gene was considered unexpressed if log2(TPM+1) < 0.1 in at least 95% of cells separately for each patient
Data was normalized following a three-step combination approach: i) Transform the TPM values into relative counts with the Census algorithm (Qiu et al, 2017); ii) Normalize the Census counts with the deconvolution strategy implemented in scran (Lun et al 2016); iii) Remove additional sources of variation with RUVSeq (Risso et al, 2014)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files representing: TPM values (tpm_rsem.txt); counts (counts_rsem.txt); normalized data as described above (norm_data.txt)
|
| |
|
| Submission date |
Aug 10, 2018 |
| Last update date |
Aug 12, 2018 |
| Contact name |
Simona Cristea |
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Biostatistics and Computational Biology
|
| Street address |
450 Brookline Ave.
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE118389 |
Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq [RNA-Seq] |
| GSE118390 |
Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq |
|
| Relations |
| BioSample |
SAMN09790191 |
| SRA |
SRX4527004 |
