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Sample GSM2375752 Query DataSets for GSM2375752
Status Public on Jul 10, 2017
Title EpCAM+Tomato- _1
Sample type SRA
 
Source name Oral cancer
Organism Mus musculus
Characteristics strain: C57BL/6
sample type: Oral cancer
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
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
 
Submission date Nov 04, 2016
Last update date May 15, 2019
Contact name Cunyu Wang
E-mail(s) cwang@dentistry.ucla.edu
Phone 3108256317
Organization name UCLA
Department School of Dentistry
Lab CHS 56-200
Street address 10833 Le Conte Ave
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL21493
Series (1)
GSE89549 RNA-Seq Analysis of the Transcriptomes of Tomato+ and Tomato- HNSCC cells
Relations
BioSample SAMN05981936
SRA SRX2328239

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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