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Sample GSM1966875 Query DataSets for GSM1966875
Status Public on Dec 07, 2016
Title control+1:100 Conditioned Medium 8h rep1
Sample type SRA
 
Source name TRAMP-C2_control+1:100 Conditioned Medium 8h
Organism Mus musculus
Characteristics cell line: TRAMP-C2
cell type: mouse prostate cancer cells
passages: five to six
treated with: control+1:100 Conditioned Medium for 8hrs
Treatment protocol For sutherlandia and Hh-CM treatment, cells are plated in 60mm petri dishes until confluent; TRAMPC2 cells are treated with ethnol control, 8ug/ml suterlandia extrat, 80ug/ml sutherlandia extract, Hh-CM, 8ug/ml suterlandia extrat+Hh-CM, 80ug/ml sutherlandia extract+Hh-CM for 8hr or 24 hr.
Growth protocol TRAMPC2 cells were obtained from the American Type Culture Collection (ATCC). TRAMPC2 cells are cultured in RPMI1640 media with DHT and insulin(Invitrogen, Grand Island, NY) with 10% Fetal Bovine Serum (FBS) (GE Healthcare Life Sciences, Logan, Utah). 70% confluent TRAMPC2 cells were treated with indicated treatment.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using Rneasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description TC2_1_CM_8h
TC2_7_GTGGCC_L001_R1_001.tar.gz
Data processing Illumina Casava1.7 software used for basecalling.
Sequencing adaptor seuqence were trimmed off, then low qualtiy basecall was trimmed off, at last, low qualtiy sequence reads were filtered out.
Short sequencing reads were aligned to mus musculus genome mm9, gene expression value is quantified as raw read.
Differentially gene expression was analyzed using EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: csv, raw gene expression read
 
Submission date Dec 07, 2015
Last update date May 15, 2019
Contact name Yuan Lu
Organization name Xiphophorus Genetic Stock Center
Street address university drive
City San Marcos
State/province TX
ZIP/Postal code 78666
Country USA
 
Platform ID GPL13112
Series (1)
GSE75760 Sutherlanida extract inhibits Hedgehog signaling target genes
Relations
BioSample SAMN04323303
SRA SRX1467128

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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