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Sample GSM2831509 Query DataSets for GSM2831509
Status Public on Dec 20, 2017
Title tumor from HN1L siRNA-treated mouse #4950 [miRNA]
Sample type RNA
Source name patient-derived xenograft tumor from HN1L siRNA-treated mouse #4950
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 HN1L-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 0.579376735
MIMAT0021117_st 3.764510959
MIMAT0021118_st 1.169859889
MIMAT0021119_st 1.142942253
MIMAT0021120_st 7.877689942
MIMAT0027088_st 0.742315217
MIMAT0021121_st 1.176781503
MIMAT0021122_st 1.182729722
MIMAT0019853_st 3.415128666
MIMAT0019854_st 0.989728789
MIMAT0019855_st 6.465931348
MIMAT0019856_st 2.442409826
MIMAT0019857_st 0.809492896
MIMAT0019858_st 1.472019932
MIMAT0019859_st 12.20705003
MIMAT0019860_st 0.450173769
MIMAT0019861_st 0.824133682
MIMAT0019862_st 0.921360662
MIMAT0019863_st 0.682467166
MIMAT0019864_st 6.725375492

Total number of rows: 6631

Table truncated, full table size 178 Kbytes.

Supplementary file Size Download File type/resource
GSM2831509_1_4950_miRNA-4_0_.CEL.gz 811.1 Kb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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