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Sample GSM6670345 Query DataSets for GSM6670345
Status Public on Jan 12, 2023
Title pdx_breast_tumor_TNBC032
Sample type RNA
 
Source name pdx established from pre-treatment breast tumor biopsy
Organism Homo sapiens
Characteristics xenograft: TNBC032
disease state: breast cancer
Growth protocol Tumor cells were engrafted into NOD/SCID mice and passaged through three generations.
Extracted molecule total RNA
Extraction protocol Fresh tumor core biopsies were placed into a 1.5 ml vial of RNAlater (Qiagen) at room temperature, then held in a 4°C refrigerator (6-72 hours) and after that stored frozen at -20°C until use. RNA was extracted using PicoPure RNA isolation kit (ThermoFisher Scientific, Waltham, MA) following the manufacturer's instructions.
Label biotin
Label protocol We performed an in vitro transcription reaction to produce biotin-labeled cRNA from the cDNA.
 
Hybridization protocol The cRNA is hybridized to the oligonucleotide probes on the array.
Scan protocol Immediately following the hybridization, the hybridized probe arrays undergo an automated washing and staining protocol on the fluidic station and are then scanned on the GeneChip Scanner.
Description PDX tumor
Data processing RMA signal calculated using R/Bioconductor.
 
Submission date Oct 21, 2022
Last update date Jan 12, 2023
Contact name Jeffrey Chang
E-mail(s) jeffrey.t.chang@uth.tmc.edu
Organization name University of Texas
Street address 6431 Fannin St
City Houston
ZIP/Postal code 77019
Country USA
 
Platform ID GPL96
Series (1)
GSE216333 Predictors of success in establishing orthotopic patient-derived xenograft models of triple negative breast cancer

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
1007_s_at 9.11495471
1053_at 8.114969414
117_at 7.359008096
121_at 8.574630304
1255_g_at 4.074021945
1294_at 8.069837207
1316_at 6.184935437
1320_at 5.208288431
1405_i_at 9.850193438
1431_at 4.240357126
1438_at 7.779871157
1487_at 8.510538148
1494_f_at 6.741658512
1598_g_at 10.05212667
160020_at 8.880850167
1729_at 8.4348612
177_at 5.799099086
1773_at 7.028859658
179_at 9.034736556
1861_at 7.395381909

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM6670345_TNBC032.cel.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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