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Sample GSM3502406 Query DataSets for GSM3502406
Status Public on Jul 14, 2020
Title miRNA PDAC fibroblast IMDM Biological remiRNA P 3
Sample type RNA
 
Source name Cultured human fibroblasts from PDAC
Organism Homo sapiens
Characteristics cell line: PDAC
media: IMDM
Growth protocol Disease-associated fibroblasts from PDAC, CP and PAT were isolated using the outgrowth method, these cells were grown in IMDM supplemented with 10% FBS, 2% L-glutamine, 1% penicillin-streptomycin. In addition, normal PSCs were isolated using the density gradient method and cultured in the same media.These normal PSC were expanded in culture for more than 15 days to achieve adequate yield and purity and referred to as normal-activated (NA) fibroblast. Samples used for array experiments were used from early passages (P1 or P2). Commercial normal fibroblasts (NF) were grown using low serum medium (LSM) (MSC-GRO, Vitro Biopharma) and IMDM supplemented with 10% FBS, 2% L-glutamine, 1% penicillin-streptomycin.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the high pure miRNA isolation kit (one-column protocol) (Qiagen) for the isolation of total RNA (containing small RNAs) following the manufacturer’s instructions. Purified total RNA was cleaned from genomic DNA using the DNA-freeTM DNA removal kit (ThermoFisher Scientific) following the manufacturer’s instruction.
Label Bioitin
Label protocol 130ng of total RNA (free from DNA) was labelled using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix). This process begins with a brief tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.
 
Hybridization protocol Biotin-labelled samples and controls were added to a hybridisation mix and hybridized to Affymetrix GeneChip miRNA 4.0 arrays for 18 hours at 48˚C and 60rpm in an Affymetrix GeneChip hybridisation oven 645.
Scan protocol Following hybridisation the arrays were washed and stained on an Affymetrix GeneChip Fluidics Station 450 using a FS450_0002 script and scanned in an Affymetrix Genechip Scanner 3000G.
Description Gene expression from disese-associated cultured fibroblasts
Data processing Data were RMA normalised in Partek Genomics Suite
 
Submission date Dec 05, 2018
Last update date Jul 14, 2020
Contact name Eithne Costello
E-mail(s) ecostell@liverpool.ac.uk
Organization name University of Liverpool
Department Department of Molecular and Clinical Cancer Medicine
Street address Ashton Street
City Liverpool
ZIP/Postal code L69 3GE
Country United Kingdom
 
Platform ID GPL19117
Series (2)
GSE123377 Disease associated fibroblasts from various pancreatic disorders exhibit subtype specific genetic profile [miRNA]
GSE123378 Disease associated fibroblasts from various pancreatic disorders exhibit subtype specific genetic profile

Data table header descriptions
ID_REF
VALUE Log2 RM signal

Data table
ID_REF VALUE
14q0_st 1.31062
14qI-1_st 1.3136
14qI-1_x_st 1.28492
14qI-2_st 1.40227
14qI-3_x_st 1.12953
14qI-4_st 1.78156
14qI-4_x_st 1.73681
14qI-5_st 1.55302
14qI-6_st 1.75416
14qI-7_st 3.12214
14qI-8_st 1.39016
14qI-8_x_st 1.35311
14qI-9_x_st 1.64173
14qII-10_st 1.17936
14qII-11_st 0.937666
14qII-12_st 2.34635
14qII-12_x_st 2.79579
14qII-13_st 1.35957
14qII-14_st 4.8485
14qII-14_x_st 3.31405

Total number of rows: 36353

Table truncated, full table size 854 Kbytes.




Supplementary file Size Download File type/resource
GSM3502406_4877_8_miRNA-4_0_.CEL.gz 740.3 Kb (ftp)(http) CEL
Processed data included within Sample table

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