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Sample GSM2831503 Query DataSets for GSM2831503
Status Public on Dec 20, 2017
Title tumor from scrambled siRNA-treated mouse #4959 [miRNA]
Sample type RNA
Source name patient-derived xenograft tumor from scrambled siRNA-treated mouse #4959
Organism Homo sapiens
Characteristics tissue: breast cancer tumor tissue
genotype: Triple-negative breast cancer
xenograft type: BCM2665
Treatment protocol Groups (0) and (1) (n=10) were treated with 5 µg/mouse DOPC nanoliposomal siRNA IP injection twice a week for 3 weeks. Mice were sacrificed on day 21. Tumors were harvested and snap frozen.
Growth protocol In docetaxel-resistant BCM2665 PDX xenografts, tumors were transplanted into the mammary fat pad of SCID-Beige mice. Mice were randomized into 5 groups when tumor volume reached 150-200mm3: (0)scrambled siRNA, (1)HN1L siRNA.
Extracted molecule total RNA
Extraction protocol Extraction of miRNA from each frozen tumor sample was performed using miRNeasy Mini kit from Qiagen following manufacturer instruction.
Label biotin
Label protocol Biotinylated miRNA were prepared according to the standard Affymetrix protocol.
Hybridization protocol hybridization,washing and staining were done following Affymetrix protocol for Genechip miRNA 4.0 arrays.
Scan protocol Scanning was done on Affymetrix Genechip Scanner model 7G, Affymetrix Genechip command console(AGCC) software was used for instrument control, data acquisition and quality control.
Description miRNA expression data from TNBC tumor sample of scramble-siRNA treated mouse model BCM2665
Data processing Expression values were processed and normalized using the affy library in R statistical software. Only human probes were isolated, from the multispecies miRNA profiling by the miRNA array 4.0, for the purpose of the analysis. Differential expression analysis was then performed using limma package in R. The most significantly differentially expressed miRNAs were selected based on a cut off log fold change > 1 and FDR < 0.2.
Submission date Oct 26, 2017
Last update date Jan 23, 2018
Contact name Jenny Chang
Organization name Houston Methodist Hospital
Department Houston Methodist Cancer Center
Street address 6670 Bertner Ave.
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platform ID GPL19117
Series (2)
GSE106199 MicroRNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples
GSE106200 RNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

Data table header descriptions
VALUE Values were processed and normalized using the affy library in R statistical software, presented as normalized log2 expression value

Data table
MIMAT0021116_st 1.030100328
MIMAT0021117_st 3.081774518
MIMAT0021118_st 0.573067221
MIMAT0021119_st 0.597932217
MIMAT0021120_st 8.062063846
MIMAT0027088_st 0.665226147
MIMAT0021121_st 1.824115767
MIMAT0021122_st 0.724545722
MIMAT0019853_st 3.995948683
MIMAT0019854_st 0.682467166
MIMAT0019855_st 7.217639536
MIMAT0019856_st 1.362506727
MIMAT0019857_st 0.991521352
MIMAT0019858_st 0.670641756
MIMAT0019859_st 12.29145846
MIMAT0019860_st 0.589038731
MIMAT0019861_st 1.084951077
MIMAT0019862_st 1.011520785
MIMAT0019863_st 0.862787414
MIMAT0019864_st 6.649168684

Total number of rows: 6631

Table truncated, full table size 178 Kbytes.

Supplementary file Size Download File type/resource
GSM2831503_0_4959_miRNA-4_0_.CEL.gz 815.0 Kb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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