NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6670325 Query DataSets for GSM6670325
Status Public on Jan 12, 2023
Title pdx_breast_tumor_TNBC005
Sample type RNA
 
Source name pdx established from pre-treatment breast tumor biopsy
Organism Homo sapiens
Characteristics xenograft: TNBC005
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 9.898831448
1053_at 7.954802299
117_at 7.613101526
121_at 8.753695864
1255_g_at 4.422401449
1294_at 9.0815214
1316_at 5.955828832
1320_at 5.08361304
1405_i_at 9.131203149
1431_at 4.15667284
1438_at 7.940667386
1487_at 8.259363524
1494_f_at 7.154806237
1598_g_at 9.868459622
160020_at 9.888441868
1729_at 8.52690583
177_at 5.780701923
1773_at 7.074956913
179_at 9.247229708
1861_at 7.108738824

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM6670325_TNBC005.cel.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap