|
| Status |
Public on Jun 11, 2018 |
| Title |
H1TNSC3 |
| Sample type |
SRA |
| |
|
| Source name |
HuH-1 triple negative single cell 3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: hepatcellular carcinoma
cell line: HuH-1
cell surface marker: TripleNeg
cell number: 1
cell status: single-cell
|
| Growth protocol |
HuH-1 and HuH-7 were grown in DMEM medium plus 10% fetal bovine serum and 1% antibiotics. At 80% confluence, the cell were harvested for flow cytometry sorting
|
| Extracted molecule |
total RNA |
| Extraction protocol |
no RNA extraction step droplet-based single-cell RNA-seq (SMART-seq)
Cells were lysed in ice-cold lysis buffer. SMART-seq protolcol was performed on single or pooled sorted cells following the manufacturere's instructions with some modification. Briefly, whole transcriptome was amplified with the SMART-seq v4 Ultra Low Input RNA kit (Clonetech), purified (Beckman Coulter, A63881) and barcoded (Illumina, FC-131-1096). Finally, libraries were pooled and sequenced on Illumina Hiseq2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
H1TNSC3
|
| Data processing |
Basecalling performed by RTA version 1.18.66.3
Demultiplexing performed by Bcl2fastq version 1.8.4
Adaptor trimming and quality control by Trimmomatic version 0.30
Read alignment performed by STAR version 2.5.1
Transcript quantification performed by RSEM version 1.2.22
Data normalized by median normalization
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file of RSEM values for each single cell
|
| |
|
| Submission date |
Sep 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xin Wei Wang |
| E-mail(s) |
xw3u@nih.gov
|
| Phone |
240-760-6858
|
| Organization name |
National Cancer Institute
|
| Department |
Laboratory of Human Carcinogenesis
|
| Lab |
Liver Carcinogenesis Unit
|
| Street address |
37 Convent Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-4255 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE103591 |
Single cell analysis reveals cancer cell heterogeneities in hepatcellular carcinoma |
| GSE103866 |
Single cell analysis reveals cancer cell heterogeneities in hepatocellular carcinoma [SMART-seq] |
|
| Relations |
| BioSample |
SAMN07647883 |
| SRA |
SRX3187396 |
