Experiment Section
domain ebi.ac.uk
accession E-TABM-134
quality_control
experiment_design_type "genotyping_design, disease_state_design, optimization_design"
name WGA-LCM and Genomewide Survey of Lung Cancer
description A series of experiments were performed to validate whole genome amplification of genomic DNA from laser captured microdissectates and the technique was then applied to serial samples of developing lung cancers to identify early events. 10K Affymetrix SNP arrays were used.
release_date 2006-10-01
submission_date 2006-08-11
submitter Helen Bird
submitter_email H.E.Bird@warwick.ac.uk
organization Warwick University
publication_title Validation of a method for processing laser captures microdissected samples for analysis using high density single nucleotide polymorphism arrays & Genomewide loss of heterozygosity in small cell and non-small cell lung cancer and precursor bronchial epithelium
authors Bird H; Snead DRJ; Hey Y; Brown PE; Davis SA; James S; Knowles MA; Hurst CD; Blanks A; Pepper SD & Snead DRJ; Brown PE; James S; Davis SA; Suortamo S; Pandey S; Blanks A; Grammatopoulos D; Vohra H; Bird H
journal in submission to Journal of Pathology
volume
issue
pages
year
Protocol Section
accession text name parameters
P-EXML-2 "Resected tumour, tissue of bronchial origin and lymph node were snap frozen in liquid nitrogen. Frozen sections were cut and stained with haematoxylin and eosin." Patient Sample Processing
P-EXML-3 "LCM was performed using the Nikon Slµ cut instrument (Nikon UK Ltd.) on frozen sections which had been stored at -80ºC. Target lesions were visualised directly, excised and captured on to the adhesive cap of the LCM tubes (Nikon UK Ltd.). Captured cells were stored at -80ºC prior to WGA and microarray analysis." Laser Capture Microdissection
P-EXML-4 "For cell lines: DNA was extracted from the bladder tumour-derived cell line, J82, and from the patient-matched normal cell line (J82EBV, immortalised normal lymphoblasts). Aliquots of J82 tumour cell line DNA and of J82EBV normal cell line DNA were adjusted to either 250ng/5µL (for non-WGA controls), 3ng/3µL or 1ng/3µL (for WGA) to start the next step of the protocol.
For patient tissue: For non-WGA controls, complete sections were taken and DNA extracted using the DNeasy Tissue Kit (Qiagen, Crawley, UK).
For WGA samples: Captured cells were resuspended in 15µL proteinase K buffer.
For all WGA samples: Triplicate 5µL aliquots of material were subject to WGA, pooled and quantified. 1ng or 3ng cell line DNA was diluted and triplicate WGA reactions were set up as before. The recommended reaction volumes were increased by by 2.5-fold (GE Healthcare, Amersham, UK) according to Rook et al, Am J Path (2004)." DNA Extraction & WGA amount_of_starting_material;amplification_method;processing_centre
P-EXML-6 "Protocol was followed exactly according to manufacturer's instructions (Affymetrix, High Wycombe, UK), starting with 250ng DNA in all cases." "Digestion, Ligation, PCR, Purification, Labeling, Fragmentation"
P-EXML-8 "80µL hybridisation cocktail was hybridisaed overnight at 48ºC according to manufacturer's instructions (Affymetrix, High Wycombe, UK). Mapping10K_Xba131 arrays were processed with DNAARRAY_WS2 on Fluidics 400" Washing & Staining_131
P-EXML-9 "80µL hybridisation cocktail was hybridisaed overnight at 48ºC according to manufacturer's instructions (Affymetrix, High Wycombe, UK). Mapping10K_Xba142 arrays were processed with Mini_Mapping10Kv1_450 on Fluidics 450" Washing & Staining_142
P-EXML-10 "CEL files were analysed in GDAS using the same default settings for Xba131 and Xba142 arrays: HCRBound = 0.070000, CallZoneBound=0.800000, DSBound = 0.080000, GenderAttributeName = Gender, MaleAttributeValue = M, FemaleAttributeValue = F" Data Processing
Hybridization Section
File[raw] File[normalized] File[cdf] Array[accession] Array[serial] BioSource BioMaterialCharacteristics[DiseaseStaging] FactorValue[DiseaseStaging] BioMaterialCharacteristics[Individual] FactorValue[Individual] BioMaterialCharacteristics[Organism] BioSourceMaterial BioMaterialCharacteristics[OrganismPart] BioMaterialCharacteristics[DiseaseState] FactorValue[DiseaseState] BioMaterialCharacteristics[TumourGrading] BioMaterialCharacteristics[Sex] BioMaterialCharacteristics[Age] BioMaterialCharacteristics[TimeUnit] BioMaterialCharacteristics[ClinicalHistory] Protocol[grow] Protocol[treatment] Protocol[extraction] Parameter[amount_of_starting_material] Parameter[amplification_method] FactorValue[linear_amplification] Parameter[processing_centre] Protocol[labeling] Protocol[hybridization] Protocol[scanning]
nJ82_P.CEL nJ82_P.CHP Mapping10K_Xba131.CDF A-AFFY-64 3003935 nJ82_P not applicable patient J82 patient J82 Homo sapiens cell_line tumour cell line tumour cell line P-EXML-4 250ng DNA none none PICR P-EXML-6 P-EXML-8 P-EXML-10
nJ82ebv_P.CEL nJ82ebv_P.CHP Mapping10K_Xba131.CDF A-AFFY-64 3003935 nJ82ebv_P not applicable patient J82 patient J82 Homo sapiens cell_line immortalised cell line immortalised cell line P-EXML-4 250ng DNA none none PICR P-EXML-6 P-EXML-8 P-EXML-10
aJ82_1_W.CEL aJ82_1_W.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 aJ82_1_W not applicable patient J82 patient J82 Homo sapiens cell_line tumour cell line tumour cell line P-EXML-4 1ng DNA WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
aJ82ebv_1_W.CEL aJ82ebv_1_W.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 aJ82ebv_1_W not applicable patient J82 patient J82 Homo sapiens cell_line immortalised cell line immortalised cell line P-EXML-4 1ng DNA WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
aJ82_3_W.CEL aJ82_3_W.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 aJ82_3_W not applicable patient J82 patient J82 Homo sapiens cell_line tumour cell line tumour cell line P-EXML-4 3ng DNA WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
nJ82_W.CEL nJ82_W.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 nJ82_W not applicable patient J82 patient J82 Homo sapiens cell_line tumour cell line tumour cell line P-EXML-4 250ng DNA none none Warwick P-EXML-6 P-EXML-8 P-EXML-10
0904_MK18_10K_90J82.CEL 0904_MK18_10K_90J82.CHP Mapping10K_Xba131.CDF A-AFFY-64 3003935 0904_MK18_10K_90J82 not applicable patient J82 patient J82 Homo sapiens cell_line mixed source cell line mixed source cell line P-EXML-4 250ng DNA none none PICR P-EXML-6 P-EXML-8 P-EXML-10
0904_MK19_10K_80J82.CEL 0904_MK19_10K_80J82.CHP Mapping10K_Xba131.CDF A-AFFY-64 3003935 0904_MK19_10K_80J82 not applicable patient J82 patient J82 Homo sapiens cell_line mixed source cell line mixed source cell line P-EXML-4 250ng DNA none none PICR P-EXML-6 P-EXML-8 P-EXML-10
0904_MK20_10K_70J82.CEL 0904_MK20_10K_70J82.CHP Mapping10K_Xba131.CDF A-AFFY-64 3003935 0904_MK20_10K_70J82 not applicable patient J82 patient J82 Homo sapiens cell_line mixed source cell line mixed source cell line P-EXML-4 250ng DNA none none PICR P-EXML-6 P-EXML-8 P-EXML-10
Case1_aLN.CEL Case1_aLN.CHP Mapping10K_Xba131.CDF A-AFFY-64 3003935 Case1_aLN aLN aLN case 1 case 1 Homo sapiens organism_part lymph node squamous cell carcinoma squamous cell carcinoma "T2, N0, stage 1b" male 65 years smoking history: 50 pack years P-EXML-2 P-EXML-3 P-EXML-4 1035 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case1_aHYP.CEL Case1_aHYP.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case1_aHYP aHYP aHYP case 1 case 1 Homo sapiens organism_part lung squamous cell carcinoma squamous cell carcinoma "T2, N0, stage 1b" male 65 years smoking history: 50 pack years P-EXML-2 P-EXML-3 P-EXML-4 816 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case1_aTUM.CEL Case1_aTUM.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case1_aTUM aTUM aTUM case 1 case 1 Homo sapiens organism_part lung squamous cell carcinoma squamous cell carcinoma "T2, N0, stage 1b" male 65 years smoking history: 50 pack years P-EXML-2 P-EXML-3 P-EXML-4 1136 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case2_aAVM.CEL Case2_aAVM.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case2_aAVM aAVM aAVM case 2 case 2 Homo sapiens organism_part macrophage large cell neuroendocrine carcinoma large cell neuroendocrine carcinoma "T2, N0, M0, stage 1b" female 70 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 558 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case2_aBE.CEL Case2_aBE.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case2_aBE aBE aBE case 2 case 2 Homo sapiens organism_part lung large cell neuroendocrine carcinoma large cell neuroendocrine carcinoma "T2, N0, M0, stage 1b" female 70 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 nk WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case2_aOE.CEL Case2_aOE.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case2_aOE aOE aOE case 2 case 2 Homo sapiens organism_part lung large cell neuroendocrine carcinoma large cell neuroendocrine carcinoma "T2, N0, M0, stage 1b" female 70 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 419 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case2_aTUM1.CEL Case2_aTUM1.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case2_aTUM1 aTUM1 aTUM1 case 2 case 2 Homo sapiens organism_part lung large cell neuroendocrine carcinoma large cell neuroendocrine carcinoma "T2, N0, M0, stage 1b" female 70 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 446 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case2_aTUM2.CEL Case2_aTUM2.CHP Mapping10K_Xba142.CDF A-AFFY-65 4008473 Case2_aTUM2 aTUM2 aTUM2 case 2 case 2 Homo sapiens organism_part lung large cell neuroendocrine carcinoma large cell neuroendocrine carcinoma "T2, N0, M0, stage 1b" female 70 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 498 cells WGA WGA Warwick P-EXML-6 P-EXML-9 P-EXML-10
Case3_nLN.CEL Case3_nLN.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case3_nLN nLN nLN case 3 case 3 Homo sapiens organism_part lymph node small cell lung cancer small cell lung cancer "T1, N2, M0, stage 3" female 47 years smoking history: 30 pack years P-EXML-2 P-EXML-4 250ng DNA none none Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case3_aLN.CEL Case3_aLN.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case3_aLN aLN aLN case 3 case 3 Homo sapiens organism_part lymph node small cell lung cancer small cell lung cancer "T1, N2, M0, stage 3" female 47 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 545 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case3_aBE.CEL Case3_aBE.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case3_aBE aBE aBE case 3 case 3 Homo sapiens organism_part lung small cell lung cancer small cell lung cancer "T1, N2, M0, stage 3" female 47 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 843 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case3_aOE.CEL Case3_aOE.CHP Mapping10K_Xba142.CDF A-AFFY-65 4008473 Case3_aOE aOE aOE case 3 case 3 Homo sapiens organism_part lung small cell lung cancer small cell lung cancer "T1, N2, M0, stage 3" female 47 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 200 cells WGA WGA Warwick P-EXML-6 P-EXML-9 P-EXML-10
Case3_nTB.CEL Case3_nTB.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case3_nTB nTB nTB case 3 case 3 Homo sapiens organism_part lung small cell lung cancer small cell lung cancer "T1, N2, M0, stage 3" female 47 years smoking history: 30 pack years P-EXML-2 P-EXML-4 250ng DNA none none Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case3_aTUM1.CEL Case3_aTUM1.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case3_aTUM1 aTUM1 aTUM1 case 3 case 3 Homo sapiens organism_part lung small cell lung cancer small cell lung cancer "T1, N2, M0, stage 3" female 47 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 1300 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case3_aTUM2.CEL Case3_aTUM2.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case3_aTUM2 aTUM2 aTUM2 case 3 case 3 Homo sapiens organism_part lung small cell lung cancer small cell lung cancer "T1, N2, M0, stage 3" female 47 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 997 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10
Case3_aTUM3.CEL Case3_aTUM3.CHP Mapping10K_Xba131.CDF A-AFFY-64 3002019 Case3_aTUM3 aTUM3 aTUM3 case 3 case 3 Homo sapiens organism_part lung small cell lung cancer small cell lung cancer "T1, N2, M0, stage 3" female 47 years smoking history: 30 pack years P-EXML-2 P-EXML-3 P-EXML-4 350 cells WGA WGA Warwick P-EXML-6 P-EXML-8 P-EXML-10