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Sample GSM4467271 Query DataSets for GSM4467271
Status Public on Apr 01, 2022
Title 222-TE: Tumour epithelium_sample_222
Sample type RNA
 
Channel 1
Source name Invasive Lobular Carcinoma fresh frozen tumor
Organism Homo sapiens
Characteristics tissue: Tumour epithelium
patient age: 72
tumor size: 8
nuclear grade: II
er status: pos
pr status: neg
her2 status: neg
Treatment protocol Tissue specimens were microdissected into epithelium and stroma using a PixCell IIe LCM system (Arcturus). All microdissections were performed within two hours following tissue staining.
Growth protocol Breast tumor tissue samples were obtained at primary surgery from patients providing written informed consent.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from each population of microdissected cells in RNase-free eppendorf containing 50 µl of extraction buffer and placed for 30 min at 42 ºC (Arcturus). After RNA extraction, RNA was isolated and subjected to DNaseI treatment (PicoPure RNA isolation kit, Arcturus). Samples were concentrated to a final volume of 6 µl using a refrigerated CentriVap concentrator (LabConco) at 4 ºC for 10 min. Agilent RNA 6000 Pico kit was used for Bioanalyzer quality control (Agilent).
Label Cy3
Label protocol RNA was amplified using the T-7 based RiboAmp HS Plus RNA amplification kit (Arcturus) and quality control Agilent RNA 6000 Nano kit was used (Agilent). RNA was labelled with Cy3 dye (Turbo labeling kit Cy3, Life Technologies) according to the manufacturer’s procedure. The amount of Cy3-labeled aRNA was quantified using a NanoDrop.
 
Channel 2
Source name Universal Human Reference RNA Sample
Organism Homo sapiens
Characteristics supplier: Stratagene, #740000, La Jolla, California, USA
Treatment protocol Tissue specimens were microdissected into epithelium and stroma using a PixCell IIe LCM system (Arcturus). All microdissections were performed within two hours following tissue staining.
Growth protocol Breast tumor tissue samples were obtained at primary surgery from patients providing written informed consent.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from each population of microdissected cells in RNase-free eppendorf containing 50 µl of extraction buffer and placed for 30 min at 42 ºC (Arcturus). After RNA extraction, RNA was isolated and subjected to DNaseI treatment (PicoPure RNA isolation kit, Arcturus). Samples were concentrated to a final volume of 6 µl using a refrigerated CentriVap concentrator (LabConco) at 4 ºC for 10 min. Agilent RNA 6000 Pico kit was used for Bioanalyzer quality control (Agilent).
Label Cy5
Label protocol RNA was amplified using the T-7 based RiboAmp HS Plus RNA amplification kit (Arcturus) and quality control Agilent RNA 6000 Nano kit was used (Agilent). RNA was labelled with Cy3 dye (Turbo labeling kit Cy3, Life Technologies) according to the manufacturer’s procedure. The amount of Cy3-labeled aRNA was quantified using a NanoDrop.
 
 
Hybridization protocol SurePrint G3 Human GE 8x60K microarray kit with SurePrint technology (Agilent Technologies, #G4851-60510) were used for all the experiments. Two-color microarray-based gene expression hybridization kit was used to perform the hybridizations (Agilent, #5188-5242). The 2 dyes used were Cy3 and Cy5. The aRNA of interest (300 ng) was labelled with Cy3. The reference sample used (300 ng) was a universal human reference RNA sample (Stratagene, #740000, La Jolla, California, USA) that was previously amplified using the RiboAmp HS plus kit and labelled with Cy5 dye using the Arcturus Cy5 Turbo Labeling Kit (Life Technologies, #KIT0610).
Scan protocol Microarray data were feature extracted using Feature Extraction Software (v. 9.5.3) from Agilent with the default parameters.
Data processing The microarray experiments were carried out in 3 batches and pre-processed using Agilent GeneSpring Software. Raw data was normalised, log2 transformed and filtered, and quality control analyses were carried out. HGNC gene annotations were applied and the mean was taken when multiple probes were present for the same gene. Finally, the batch effect was corrected using ComBat.
 
Submission date Apr 09, 2020
Last update date Apr 01, 2022
Contact name Andrew H Sims
E-mail(s) andrew.sims@ed.ac.uk
Organization name University of Edinburgh
Department Institute of Genetics and Molecular Medicine
Lab Applied Bioinformatics of Cancer
Street address Carrington Crescent
City Edinburgh
ZIP/Postal code EH4 2XR
Country United Kingdom
 
Platform ID GPL14550
Series (1)
GSE148398 Gene expression of invasive lobular carcinoma tumor epithelium and tumor stroma isolated by laser-capture microdissection

Data table header descriptions
ID_REF
VALUE normalized log2 Cy3/Cy5

Data table
ID_REF VALUE
A_33_P3685216 1.464137944
A_24_P721699 -0.900291271
A_23_P104224 -2.54680214
A_23_P116898 -0.332609246
A_33_P3280950 0.632709311
A_33_P3525263 0.301317134
A_24_P16184 -0.012306456
A_33_P3294002 1.295157745
A_23_P58046 0.019392023
A_23_P64799 -1.199120383
A_33_P3403392 0.524849899
A_33_P3302290 -1.602373705
A_23_P80570 0.492465281
A_23_P91970 -0.037426964
A_33_P3307960 1.703416157
A_33_P3312601 0.094784509
A_33_P3300916 -0.045923759
A_23_P253484 -0.547325876
A_24_P169343 -0.466877181
A_23_P37545 1.104727369

Total number of rows: 22263

Table truncated, full table size 555 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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