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| Status |
Public on Jul 10, 2017 |
| Title |
EpCAM+Tomato+ _2 |
| Sample type |
SRA |
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| Source name |
Oral cancer
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
sample type: Oral cancer
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| Extracted molecule |
total RNA |
| Extraction protocol |
Oral cancer samples were minced in cold PBS and digested into single cells using collagenase and dispase. Cells were stained with anti-EpCAM sorted based on EpCAM and Tomato expression. mRNA were isolated using Qiagen RNeasy Micro Kit.
RNA libraries were prepared for sequencing using KAPA kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using Tophat
Differential expression were calculated using cuffdiff.
Genome_build: mm9
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| Submission date |
Nov 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cunyu Wang |
| E-mail(s) |
cwang@dentistry.ucla.edu
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| Phone |
3108256317
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| Organization name |
UCLA
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| Department |
School of Dentistry
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| Lab |
CHS 56-200
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| Street address |
10833 Le Conte Ave
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE89549 |
RNA-Seq Analysis of the Transcriptomes of Tomato+ and Tomato- HNSCC cells |
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| Relations |
| BioSample |
SAMN05981933 |
| SRA |
SRX2328242 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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