|
| Status |
Public on May 28, 2021 |
| Title |
PDX1-CD276-low/EpCAM+ |
| Sample type |
SRA |
| |
|
| Source name |
Head and neck squamous cell carcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
strain: HNSCC PDX1
tissue: Head and neck squamous cell carcinoma
|
| Treatment protocol |
To isolate single cells from HNSCC PDXs, mice were euthanized and tumors were dissected and isolated. Tumors were chopped into small pieces with scalpels in petri dishes on ice, and then dissociated in to single cell suspension using Tumor Dissociation Kit (Miltenyi, cat# 130-095-929). The cell suspension was filtered through a 100 micro meter mesh filter and then followed by a 40 micro meter mesh filter. Red blood cells were removed using a RBC Lysis Buffer (Santa Cruz Biotechnology, cat#sc-296258). Subsequently, tumor cells were stained with the anti-CD276-PE and anti-EpCAM-APC antibodies. The CD276+/EpCAM+ and the CD276+/EpCAM- cells were isolated throug FACS sorting.
|
| Growth protocol |
Two cases of Human HNSCC PDXs were maintined in NOD/SCID mice. The discarded human HNSCC primary tissues were obtained from the UCLA Translational Pathological Core and subcutaneously inoculated into flank of 6-week-old NOD/SCID mice to generate the PDXs of HNSCC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Mini Kit (Qiagen, cat#74104).
Sequencing libraries were generated using a KAPA RNA-Seq Library Preparation Kits (KAPA Biosystems, cat#07960140001)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
RNAs were single-end sequenced on Illumina HiSeq 3000 machines
Reads was aligned using Tophat with the hg18 build of the human genome.
Transcript assembly and differential expression were determined using Cufflinks with Refseq mRNAs.
RNA-seq data was analyzed using the cummeRbund package in R.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jun 12, 2019 |
| Last update date |
May 28, 2021 |
| Contact name |
Jiong Li |
| E-mail(s) |
jli29@vcu.edu
|
| Phone |
3105617186
|
| Organization name |
VCU
|
| Street address |
800 E Leigh Street, suite 212
|
| City |
Richmond |
| State/province |
Virginia |
| ZIP/Postal code |
23298 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE132627 |
RNA-seq analysis of CD276-high/EpCAM+ cells from HNSCC patient-derived-xenograft |
|
| Relations |
| BioSample |
SAMN12042572 |
| SRA |
SRX6055585 |
