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Sample GSM2829797 Query DataSets for GSM2829797
Status Public on Dec 20, 2017
Title tumor from HN1L siRNA-treated mouse #4814 [mRNA]
Sample type RNA
 
Source name patient-derived xenograft tumor from HN1L siRNA-treated mouse #4814
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 total RNA from each frozen tumor sample was performed using RNeasy Mini kit from Qiagen following manufacturer instruction.
Label biotin
Label protocol Biotinylated cDNA were prepared according to Ovation Pico WTA system V2 and FL-Ovation cDNABtiotin Module V2 from NUGEN Technologies
 
Hybridization protocol Affymetrix Hybridization,cocktail assembly and Fluidics protocol for Standard Array( 49 format) with minor modifications provided by NUGEN's FL-Ovation cDNA biotin module V2 protocol
Scan protocol Genechips were scanned using Affymetrix Genechip Scanner model 7G, Genechip command console (AGCC)software provided instrument control, data acquisition and first order data anaylsis
Description mRNA expression data from TNBC tumor sample of HN1L-siRNA treated mouse model BCM2665
Data processing The array data were evaluated using the commercial software suite, Partek Genomics Suite. Specifically, data were normalized by using the RMA (robust multichip averaging) method. Gene-expression levels were analyzed on a logarithmic scale. ANOVA was used to identify differentially expressed genes. Genes with P value less than 0.05 in each comparison were selected for further functional and pathway analyses by Ingenuity Pathway Analysis (IPA) tools.
 
Submission date Oct 24, 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 GPL570
Series (2)
GSE106106 mRNA 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
ID_REF
VALUE Data were normalized by using the RMA (robust multichip averaging) method. Gene-expression levels were analyzed on a logarithmic scale.

Data table
ID_REF VALUE
1007_s_at 10.93483582
1053_at 8.246142446
117_at 7.580732809
121_at 7.429539892
1255_g_at 2.499010521
1294_at 6.55277604
1316_at 8.939155163
1320_at 6.541310311
1405_i_at 4.068589534
1431_at 4.064810617
1438_at 7.822698055
1487_at 7.386333375
1494_f_at 3.955744431
1552256_a_at 8.330889084
1552257_a_at 9.198825994
1552258_at 4.910844661
1552261_at 5.383732811
1552263_at 5.647423686
1552264_a_at 10.10412821
1552266_at 6.19648244

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM2829797_1_4814.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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