|
| Status |
Public on Jul 12, 2017 |
| Title |
met_RHH1595 |
| Sample type |
SRA |
| |
|
| Source name |
squamous cell carcinoma, metastatic tumor
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: squamous cell carcinoma
tissue: metastatic lymph node tumor
sample type: single cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolated from cells using the SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech).
Library construction: In accordance to protocol from Fluidigm describing the use of the C1 system to generate cDNA library for single cell RNA-seq. Briefly, cDNA was synthesized using SMARTer Ultra Low RNA Kit for the Fluidigm C1 System from Clontech; library was constructed using Nextera XT DNA Sample Preparation Kit and Nextera XT DNA Library Preparation Index Kits from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Metastatic cancer
PolyA+ RNA
Processed data file: expression.txt
|
| Data processing |
BAM files produced using Tophat-2.1.0.
FPKM obtained using Cuffdiff-2.2.1.
The RefSeq genes are tracked for analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: expression.txt: The tab-delimited text file contains the log2(1+pQ normalized FPKM) expression matrix for all individual cells. For details about pQ normalization, see Sengupta, Debarka, et al. "Fast, scalable and accurate differential expression analysis for single cells." bioRxiv (2016): 049734.
|
| |
|
| Submission date |
Jul 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Debarka Sengupta |
| E-mail(s) |
debarka@gmail.com
|
| Organization name |
Indraprastha Institute of Information Technology
|
| Department |
Computational Biology and Computer Science
|
| Street address |
IIIT Delhi, Okhla Phase 3
|
| City |
Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110020 |
| Country |
India |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE84323 |
Phenotype-driven precision oncology in patient-derived tumor models predict therapeutic response in squamous cell carcinoma |
|
| Relations |
| BioSample |
SAMN05391939 |
| SRA |
SRX1949071 |
