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Sample GSM1584949 Query DataSets for GSM1584949
Status Public on Sep 15, 2015
Title ZF of ADR026
Sample type RNA
 
Source name Pheochromocytoma_ZF
Organism Homo sapiens
Characteristics disease: Pheochromocytoma
patient/tissue id: ADR026
tissue: Human adrenal tissue
tissue subtype: Zona Fasciculata
Extracted molecule total RNA
Extraction protocol Adrenal collection protocol: The aldosterone-producing adenoma (APA) and their paired adjacent adrenal gland (for ZG and ZF) or adrenal gland cortex adjacent to pheochromocytomas were sanp-frozen by liquid nitrogen and collected from the Human Research Tissue Bank in Addenbrooke's hospital. Local ethical approval and informed consent were obtained for each patient.
Laser capture microdissection was used to acquire samples. For differentiation of ZG from ZF, sections were stained with cresyl violet using the LCM Staining Kit (AM1935, Ambion, USA). The acquired cell samples were stored in RNAlater (Ambion, USA) and TRIzol® reagent (Life Technologies, USA) at -70°C till extracted for RNA. Total DNA-free RNA was isolated using the PureLink® RNA Mini Kit and DNase Set (Life Technologies, USA) according to manufacturer’s instruction. Reverse transcription was performed using the Reverse Transcription System (Promega, USA) with a 1:1 mixture of random hexamer and oligo-dT primers according to manufacturer’s instruction. One RNA sample from the ZG of ADR121 was not analyzed as it did not pass quality control.
Label biotin
Label protocol Total RNA obtained through LCM were sent to Genomics Corelab, Cambridge Biomedical Research Centre for microarray measurement. Each RNA sample (total RNA, 1 µg) was converted to cDNA by reverse transcription. NuGEN Technologies’ Ovation Pico WTA System V2 kit was used to generate the first strand cDNA from total RNA. A DNA/RNA hetero-duplex-tagged double strand cDNA was then generated and amplified using a DNA/RNA chimeric primer (SPIA® primer), DNA polymerase and RNase H. This cDNA was fragmented by a chemical and enzymatic process using the NuGEN Technologies Encore Biotin Module to fragments between 50 and 100 base pairs in length. These fragmented products were then labeled via enzymatic attachment of a biotin-labeled nucleotide to the 3-hydroxyl ends of the fragments.
 
Hybridization protocol Hybridization cocktails containing the fragmented and labeled cDNA and additional Affymetrix hybridization controls, were incubated on the Affymetrix arrays for 17hrs +/- 1hr at 45°C.
Scan protocol GeneChips were scanned using the GeneChip® (GCS3000) Scanner.
Description Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-15
Data processing Data processing and analysis was performed using AffymetrixGeneChip Command Console Software and PartekGenomicSuite 6.5 (Partek Inc., St. Louis, MO).
Gene expressions were portrayed as the summarized log-signal of the Robust Multichip Average (RMA) with quantile normalisation and median polish for probe set summarisation.
 
Submission date Jan 14, 2015
Last update date Sep 15, 2015
Contact name Junhua Zhou
Organization name University of Cambridge
Street address CPU, Level 6, ACCI, Addenbrooke’s Hospital
City Cambridge
State/province Cambridgeshire
ZIP/Postal code CB2 0QQ
Country United Kingdom
 
Platform ID GPL10739
Series (1)
GSE64957 Microarray study of human adrenal zona glomerulosa (ZG), zona fasciculata (ZF) and aldosterone-producing adenomas (APA)

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
7917119 4.19872
7917118 5.87316
7917104 4.79727
7917105 5.6548
7917106 3.78743
7917107 7.68054
7917108 8.28828
7917109 7.20856
7917110 7.02454
7917111 7.83648
7917112 5.02145
7917113 5.70937
7917114 7.83953
7917115 3.80225
7917116 2.7523
7917117 4.933
8011598 7.76504
8003847 5.29728
8011543 5.86625
8011544 6.6362

Total number of rows: 257430

Table truncated, full table size 3992 Kbytes.




Supplementary file Size Download File type/resource
GSM1584949_Affy0257-15.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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