|
| Status |
Public on Aug 27, 2024 |
| Title |
SH889_TR_GU02CTC |
| Sample type |
SRA |
| |
|
| Source name |
CTC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: CTC
donor: GU-2
cell type: EpCAM+ and/or PSMA+
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were picked or sorted into lysate buffer and RNA was released.
single cell cDNA was amplified using SMART-seq2 protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina CASAVA version 1.8 were used to do the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases. For single cell RNA-seq, the cleaned reads were aligned to the human hg19 reference using Tophat (v2.0.12) with default settings and the --no-novel-juncs argument (Trapnell et al., 2009).
PCR duplicates were removed using samtools (v1.3.1)(Li et al., 2009), gene counts were computed using HTseq (v0.6.1) (Anders et al., 2015)
Assembly: hg19
Supplementary files format and content: counts.csv is a comma-separated-values file with rows corresponding to a gene, columns corresponding to a sample, and values giving the number of reads aligned to the gene.
|
| |
|
| Submission date |
Aug 06, 2024 |
| Last update date |
Aug 27, 2024 |
| Contact name |
Ben S. Wittner |
| E-mail(s) |
wittner.ben@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Center for Cancer Research
|
| Lab |
Lawrence
|
| Street address |
149 13th Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE255889 |
Tumor cell-based liquid biopsy using high-throughput microfluidic enrichment of entire leukapheresis product |
|
| Relations |
| BioSample |
SAMN43074453 |
| SRA |
SRX25635674 |
