title: TB11.0135_germline

description:
whole blood sample from patient TB11.0135
processed data file: A1942_4_processed_matrix.txt, column TB11.0135_G


title: TB08.0949_germline 2

status: Public on Sep 14 2015

type: genomic

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description:
whole blood sample from patient TB08.0949, second sample
processed data file: A1942_4_processed_matrix.txt, second column of TB08.0949_G

hyb_protocol: Standard Illumina hyb protocol; samples run by AROS (Denmark)

scan_protocol: Standard Illumina scan protocol; samples run by AROS (Denmark)

data_processing:
Data were pre-processed and quality checked using ‘Call Rate QC’ (AROS), gender calls from PennCNV (Wang et al., 2007); sample pairings were confirmed using BADGER (Lynch et al., 2012).
Processed data files include Genotype: AA,AB,BB,or NC (no call), GC_Score,  Theta, R, B_Allele_Freq and Log_R_Ratio.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: Standard Illumina label protocol; samples run by AROS (Denmark)

extract_protocol: Qiagen AllPrep, according to manufacturer's instructions.

treatment_protocol: When available (i.e not CRPC samples), matched tumour and benign tissues were identified and prepared from RP surgical tissue as described in Warren et al. (2013).  The Prostate.  73:  194-202.  Matched whole blood samples were obtained from selected samples at treatment clinics.

tag: tissue

value: blood

tag: sample type

tag: tumour gleason

tag: tumour %

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

value: see matched tumour sample

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)

tag: time to bcr (months)

value: ERG gene fusion status:see matched tumour sample


title: TB11.1083_germline

description:
whole blood sample from patient TB11.1083
processed data file: A1942_4_processed_matrix.txt, column TB11.1083_G


title: TB10.0230_germline

description:
whole blood sample from patient TB10.0230
processed data file: A1942_4_processed_matrix.txt, column TB10.0230_G


title: TB09.0720_germline

description:
whole blood sample from patient TB09.0720
processed data file: A1942_4_processed_matrix.txt, column TB09.0720_G


title: TB11.0308_germline

description:
whole blood sample from patient TB11.0308
processed data file: A1942_4_processed_matrix.txt, column TB11.0308_G


title: TB09.1408_germline

description:
whole blood sample from patient TB09.1408
processed data file: A1942_4_processed_matrix.txt, column TB09.1408_G


title: TB12.0170_germline

description:
whole blood sample from patient TB12.0170
processed data file: A1942_4_processed_matrix.txt, column TB12.0170_G


title: TB11.1437_germline

description:
whole blood sample from patient TB11.1437
processed data file: A1942_4_processed_matrix.txt, column TB11.1437_G


title: TB11.1693_germline

description:
whole blood sample from patient TB11.1693
processed data file: A1942_4_processed_matrix.txt, column TB11.1693_G


title: TB11.1861_germline

description:
whole blood sample from patient TB11.1861
processed data file: A1942_4_processed_matrix.txt, column TB11.1861_G


title: TB08.0598_germline

description:
whole blood sample from patient TB08.0598
processed data file: A1942_4_processed_matrix.txt, column TB08.0598_G


title: TB08.0872_germline

description:
whole blood sample from patient TB08.0872
processed data file: A1942_4_processed_matrix.txt, column TB08.0872_G


title: TB12.1408_germline

description:
whole blood sample from patient TB12.1408
processed data file: A1942_3_processed_matrix.txt, column TB12.1408_G


title: TB10.0529_germline

description:
whole blood sample from patient TB10.0529
processed data file: A1942_4_processed_matrix.txt, column TB10.0529_G


title: TB11.2279_germline

description:
whole blood sample from patient TB11.2279
processed data file: A1942_3_processed_matrix.txt, column TB11.2279_G


title: ALCaP04_germline

description:
whole blood sample from patient ALCaP04
processed data file: A1942_3_processed_matrix.txt, column ALCaP04_G


title: TB08.1054_germline

description:
whole blood sample from patient ARM099
processed data file: A1942_3_processed_matrix.txt, column ARM099_TB08.1054_G


title: NS021_germline

description:
whole blood sample from patient NS021
processed data file: A1942_3_processed_matrix.txt, column NS021_G


title: NS028_germline

description:
whole blood sample from patient NS028
processed data file: A1942_3_processed_matrix.txt, column NS028_G


title: NS019_germline

description:
whole blood sample from patient NS019
processed data file: A1942_3_processed_matrix.txt, column NS019_G


title: NS022_germline

description:
whole blood sample from patient NS022
processed data file: A1942_3_processed_matrix.txt, column NS022_G


title: NS017_germline

description:
whole blood sample from patient NS017
processed data file: A1942_3_processed_matrix.txt, column NS017_G


title: NS026_germline

description:
whole blood sample from patient NS026
processed data file: A1942_3_processed_matrix.txt, column NS026_G


title: NS020_germline

description:
whole blood sample from patient NS020
processed data file: A1942_3_processed_matrix.txt, column NS020_G


title: NS015_germline

description:
whole blood sample from patient NS015
processed data file: A1942_3_processed_matrix.txt, column NS015_G


title: ARM002_germline

description:
whole blood sample from patient ARM002
processed data file: A1942_3_processed_matrix.txt, column ARM002_G


title: TB11.0461_germline

description:
whole blood sample from patient TB11.0461
processed data file: A1942_4_processed_matrix.txt, column TB11.0461_G


title: NS015_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient NS015
processed data file: A1942_3_processed_matrix.txt, column NS015_T

source_name: tissue core

value: prostate

value: tumour

value: unknown

value: N

value: ERG gene fusion status:unknown


title: ALB9_37_benign

description:
HoLep (holmium enucleation of the prostate) tissue from patient ALB9_37
processed data file: A1942_3_processed_matrix.txt, column ALB9_37_B

value: benign

value: ERG gene fusion status:N/A


title: NS014_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient NS014
processed data file: A1942_3_processed_matrix.txt, column NS014_T


title: NS014_germline

description:
whole blood sample from patient NS014
processed data file: A1942_3_processed_matrix.txt, column NS014_G


title: ALCaP09_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient ALCaP09
processed data file: A1942_3_processed_matrix.txt, column ALCaP09_T

value: neuroendocrine


title: TB08.1054_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient TB08.1054
processed data file: A1942_3_processed_matrix.txt, column ARM099_TB08.1054_T


title: NS031_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient NS031
processed data file: A1942_3_processed_matrix.txt, column NS031_T


title: ARM003_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient ARM003
processed data file: A1942_3_processed_matrix.txt, column ARM003_T


title: NS017_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient NS017
processed data file: A1942_3_processed_matrix.txt, column NS017_T


title: TB09.0217_germline

description:
whole blood sample from patient TB09.0217
processed data file: A1942_3_processed_matrix.txt, column TB09.0217_G


title: NS028_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient NS028
processed data file: A1942_3_processed_matrix.txt, column NS028_T


title: NS026_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient NS026
processed data file: A1942_3_processed_matrix.txt, column NS026_T


title: NS019_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient NS019
processed data file: A1942_3_processed_matrix.txt, column NS019_T

value: Y


title: ARM001_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient ARM001
processed data file: A1942_3_processed_matrix.txt, column ARM001_T

value: small cell


title: NS020_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient NS020
processed data file: A1942_3_processed_matrix.txt, column NS020_T


title: ALCaP10_tumour

description:
chTURP (channel transurethral resection of the prostate) tissue from patient ALCaP10
processed data file: A1942_3_processed_matrix.txt, column ALCaP10_T


title: ALB9_39_benign

description:
HoLep (holmium enucleation of the prostate) tissue from patient ALB9_39
processed data file: A1942_3_processed_matrix.txt, column ALB9_39_B


title: ALB9_27_benign

description:
HoLep (holmium enucleation of the prostate) tissue from patient ALB9_27
processed data file: A1942_3_processed_matrix.txt, column ALB9_27_B


title: ALB9_15_benign

description:
HoLep (holmium enucleation of the prostate) tissue from patient ALB9_15
processed data file: A1942_3_processed_matrix.txt, column ALB9_15_B


title: TB09.0962_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0962
processed data file: A1942_3_processed_matrix.txt, column TB09.0962_B


title: TB09.0774_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0774
processed data file: A1942_3_processed_matrix.txt, column TB09.0774_B


title: TB09.0462_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0462
processed data file: A1942_2_processed_matrix.txt, column TB09.0462_B


title: TB09.0405_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0405
processed data file: A1942_2_processed_matrix.txt, column TB09.0405_B


title: TB09.0219_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0219
processed data file: A1942_2_processed_matrix.txt, column TB09.0219_B


title: TB09.0448_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0448
processed data file: A1942_2_processed_matrix.txt, column TB09.0448_B


title: TB08.1083_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1083
processed data file: A1942_2_processed_matrix.txt, column TB08.1083_B


title: TB09.0295_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0295
processed data file: A1942_2_processed_matrix.txt, column TB09.0295_B


title: TB09.0413_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0413
processed data file: A1942_2_processed_matrix.txt, column TB09.0413_B


title: TB08.1116_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1116
processed data file: A1942_2_processed_matrix.txt, column TB08.1116_B


title: TB08.0993_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0993
processed data file: A1942_2_processed_matrix.txt, column TB08.0993_B


title: TB08.0601_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0601
processed data file: A1942_2_processed_matrix.txt, column TB08.0601_B


title: TB08.0986_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0986
processed data file: A1942_2_processed_matrix.txt, column TB08.0986_B


title: TB08.0501_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0501
processed data file: A1942_2_processed_matrix.txt, column TB08.0501_B


title: TB08.0332_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0332
processed data file: A1942_2_processed_matrix.txt, column TB08.0332_B


title: TB08.0327_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0327
processed data file: A1942_2_processed_matrix.txt, column TB08.0327_B


title: TB08.0311_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0311
processed data file: A1942_2_processed_matrix.txt, column TB08.0311_B


title: TB08.0359_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0359
processed data file: A1942_2_processed_matrix.txt, column TB08.0359_B


title: TB08.0588_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0588
processed data file: A1942_2_processed_matrix.txt, column TB08.0588_B


title: TB09.0421_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0421
processed data file: A1942_2_processed_matrix.txt, column TB09.0421_5_B


title: TB08.1063_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1063
processed data file: A1942_2_processed_matrix.txt, column TB08.1063_13_B


title: TB08.0817_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0817
processed data file: A1942_2_processed_matrix.txt, column TB08.0817_10_B


title: TB09.0706_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0706
processed data file: A1942_2_processed_matrix.txt, column TB09.0706_15_B


title: TB08.0271_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0271
processed data file: A1942_2_processed_matrix.txt, column TB08.0271_B


title: TB08.0393_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0393
processed data file: A1942_2_processed_matrix.txt, column TB08.0393_B


title: TB09.0550_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0550
processed data file: A1942_2_processed_matrix.txt, column TB09.0550_5_B


title: TB10.1217_benign

description:
benign robotic radical prostatectomy tissue from patient TB10.1217
processed data file: A1942_7_processed_matrix.txt, column TB10.1217_11_B


title: TB08.0870_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0870
processed data file: A1942_2_processed_matrix.txt, column TB08.0870_9_B


title: TB08.0958_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0958
processed data file: A1942_2_processed_matrix.txt, column TB08.0958_6_B


title: TB08.0609_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0609
processed data file: A1942_2_processed_matrix.txt, column TB08.0609_3_B


title: TB08.0691_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0691
processed data file: A1942_2_processed_matrix.txt, column TB08.0691_4_B


title: TB08.0997_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0997
processed data file: A1942_2_processed_matrix.txt, column TB08.0997_8_B


title: TB08.0763_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0763
processed data file: A1942_2_processed_matrix.txt, column TB08.0763_7_B


title: TB08.0987_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0987
processed data file: A1942_2_processed_matrix.txt, column TB08.0987_4_B


title: TB08.1026_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1026
processed data file: A1942_2_processed_matrix.txt, column TB08.1026_6_B


title: TB08.0879_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0879
processed data file: A1942_2_processed_matrix.txt, column TB08.0879_1_B


title: TB08.0716_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0716
processed data file: A1942_1_processed_matrix.txt, column TB08.0716_13_B


title: TB09.0721_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0721
processed data file: A1942_2_processed_matrix.txt, column TB09.0721_9_B


title: TB09.0471_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0471
processed data file: A1942_1_processed_matrix.txt, column TB09.0471_6_B


title: TB08.0598_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0598
processed data file: A1942_1_processed_matrix.txt, column TB08.0598_2_B


title: TB08.0999_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0999
processed data file: A1942_1_processed_matrix.txt, column TB08.0999_8_B


title: TB08.0533_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0533
processed data file: A1942_2_processed_matrix.txt, column TB08.0533_B


title: TB08.0589_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0589
processed data file: A1942_2_processed_matrix.txt, column TB08.0589_8_B


title: TB08.0816_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0816
processed data file: A1942_1_processed_matrix.txt, column TB08.0816_4_B


title: TB08.0872_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0872
processed data file: A1942_2_processed_matrix.txt, column TB08.0872_12_B


title: TB08.1019_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1019
processed data file: A1942_1_processed_matrix.txt, column TB08.1019_6_B


title: TB08.0848_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0848
processed data file: A1942_1_processed_matrix.txt, column TB08.0848_7_B


title: TB09.0272_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0272
processed data file: A1942_1_processed_matrix.txt, column TB09.0272_17_B


title: TB08.1015_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1015
processed data file: A1942_1_processed_matrix.txt, column TB08.1015_2_B


title: TB09.0559_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0559
processed data file: A1942_1_processed_matrix.txt, column TB09.0559_7_B


title: TB08.0667_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0667
processed data file: A1942_1_processed_matrix.txt, column TB08.0667_2_B


title: TB09.0443_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0443
processed data file: A1942_1_processed_matrix.txt, column TB09.0443_15_B


title: TB09.0606_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0606
processed data file: A1942_1_processed_matrix.txt, column TB09.0606_17_B


title: TB09.0238_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0238
processed data file: A1942_1_processed_matrix.txt, column TB09.0238_4_B


title: TB08.0268_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0268
processed data file: A1942_2_processed_matrix.txt, column TB08.0268_B


title: TB08.0978_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0978
processed data file: A1942_2_processed_matrix.txt, column TB08.0978_14_B


title: TB09.0217_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0217
processed data file: A1942_1_processed_matrix.txt, column TB09.0217_3_B


title: TB08.1044_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1044
processed data file: A1942_1_processed_matrix.txt, column TB08.1044_12_B


title: TB08.1053_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1053
processed data file: A1942_1_processed_matrix.txt, column TB08.1053_2_B


title: TB08.1128_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1128
processed data file: A1942_1_processed_matrix.txt, column TB08.1128_8_B


title: TB08.0719_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0719
processed data file: A1942_1_processed_matrix.txt, column TB08.0719_3_B


title: TB08.0944_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0944
processed data file: A1942_1_processed_matrix.txt, column TB08.0944_1_B


title: TB08.0689_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0689
processed data file: A1942_1_processed_matrix.txt, column TB08.0689_10_B


title: TB08.0731_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0731
processed data file: A1942_1_processed_matrix.txt, column TB08.0731_4_B


title: TB09.0725_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0725
processed data file: A1942_1_processed_matrix.txt, column TB09.0725_2_B


title: TB08.0973_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0973
processed data file: A1942_1_processed_matrix.txt, column TB08.0973_5_B


title: TB08.0869_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0869
processed data file: A1942_1_processed_matrix.txt, column TB08.0869_5_B


title: TB09.0504_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0504
processed data file: A1942_1_processed_matrix.txt, column TB09.0504_8_B


title: TB09.0720_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0720
processed data file: A1942_1_processed_matrix.txt, column TB09.0720_9_B


title: TB08.0927_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0927
processed data file: A1942_1_processed_matrix.txt, column TB08.0927_10_B


title: TB08.0429_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0429
processed data file: A1942_1_processed_matrix.txt, column TB08.0429_5_B


title: TB08.0386_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0386
processed data file: A1942_1_processed_matrix.txt, column TB08.0386_3_B


title: TB08.0341_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0341
processed data file: A1942_1_processed_matrix.txt, column TB08.0341_4_B


title: TB08.0508_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0508
processed data file: A1942_1_processed_matrix.txt, column TB08.0508_3_B


title: TB08.0489_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0489
processed data file: A1942_1_processed_matrix.txt, column TB08.0489_7_B


title: TB08.0338_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0338
processed data file: A1942_1_processed_matrix.txt, column TB08.0338_2_B


title: TB08.0262_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0262
processed data file: A1942_1_processed_matrix.txt, column TB08.0262_1_B


title: TB08.0234_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0234
processed data file: A1942_1_processed_matrix.txt, column TB08.0234_1_B


title: TB08.0884_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0884
processed data file: A1942_1_processed_matrix.txt, column TB08.0884_8_B


title: TB08.1159_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1159
processed data file: A1942_1_processed_matrix.txt, column TB08.1159_18_B


title: TB08.0943_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0943
processed data file: A1942_1_processed_matrix.txt, column TB08.0943_13_B


title: TB08.0877_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0877
processed data file: A1942_1_processed_matrix.txt, column TB08.0877_11_B


title: RctB binding DNA (Cy5) vs total DNA (input, Cy3) in wildtype_replicate 3

city: Bethesda

first: Jonghwan

last: Baek

state: MD

address: 37 Convent Dr

department: NCI

country: USA

institute: NIH

description:
RctB WT Rep3
biological replicate 3 of 3
Vibrio cholerae N16961 (CVC209)

hyb_protocol: After adding hybridization buffer (Agilent), samples were applied to microarrays and incubated at 60°C for 17 hr following manufacturer's instructions.

scan_protocol: After washing, scanning was done using  Agilent scanner and Agilent Feature Extraction Software following manufacturer's instructions as described by Venkova-Canoca et al. [Venkova-Canoca et al., PLoS Genet 9: e1003579 (2013)] .

data_processing: Agilent Feature Extraction Software was used for background subtraction and normalization.

organism: Vibrio cholerae O1 biovar El Tor str. N16961

source_name: Genomic DNA precipitated by using RctB antibody

label_protocol: Amplified DNA was labelled with either Cy3 or Cy5 as described by Venkova-Canoca et al. [Venkova-Canoca et al., PLoS Genet 9: e1003579 (2013)]

growth_protocol: Cells of V. cholerae WT (CVC209) and MCH1 (CVC2099) were cultivated in L broth at 37°C to exponential phase.

extract_protocol: After cell lysis (2.5 mg/ml lysozyme, 37°C, 30 min) and sonication (5x20 sec), ParB2-DNA or RctB-DNA complexes were precipitated with antibody against ParB2 or RctB using Dynabeads-Protein G magnetic beads (Invitrogen) following manufacturer's instructions.

treatment_protocol: Exponential cells were cross-linked with 1% formaldehyde (roome temperature, 30 min).

tag: strain

tag: genotype/variation

value: wildtype

tag: chip antibody

value: RctB

source_name: total, input


title: RctB binding DNA (Cy5) vs total DNA (input, Cy3) in MCH1_replicate 1

description:
RctB MCH1 Rep1
biological replicate 1 of 2
Vibrio cholerae N16961 MCH1 (CVC2099)

value: rctB-deletion


title: RctB binding DNA (Cy5) vs total DNA (input, Cy3) in wildtype_replicate 1

description:
RctB WT Rep1
biological replicate 1 of 3
Vibrio cholerae N16961 (CVC209)


title: RctB binding DNA (Cy5) vs total DNA (input, Cy3) in wildtype_replicate 2

description:
RctB WT Rep2
biological replicate 2 of 3
Vibrio cholerae N16961 (CVC209)


title: Tumor biopsy [P-538]

type: RNA

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

label: biotin

molecule: total RNA

source_name: Cervical tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: 1-4 tumor samples wer collected from each patient at the time of diagnosis

extract_protocol: In cohort 1, RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. In cohort 2, RNA was extracted by use of the miRNeasy mini kit. RNA from different biopsies of the same tumor was pooled. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis.

tag: figo stage

tag: histology

value: Squamous cell carcinoma

tag: cohort

value: cohort 2


title: Tumor biopsy [P-532]


title: Tumor biopsy [P-533]


title: Tumor biopsy [P-535]


title: Tumor biopsy [P-531]


title: ParB2 binding DNA (Cy5) vs total DNA (input, Cy3) in wildtype_replicate 3

description:
ParB2 WT Rep3
biological replicate 3 of 3
Vibrio cholerae N16961 (CVC209)

source_name: Genomic DNA precipitated by using ParB2 antibody


title: ParB2 binding DNA (Cy5) vs total DNA (input, Cy3) in wildtype_replicate 2

description:
ParB2 WT Rep2
biological replicate 2 of 3
Vibrio cholerae N16961 (CVC209)


title: ParB2 binding DNA (Cy5) vs total DNA (input, Cy3) in wildtype_replicate 1

description:
ParB2 WT Rep1
biological replicate 1 of 3
Vibrio cholerae N16961 (CVC209)


title: Tumor biopsy [P-536]


title: Tumor biopsy [P-519]


title: Tumor biopsy [P-529]


title: Tumor biopsy [P-524]


title: Tumor biopsy [P-518]


title: RctB binding DNA (Cy5) vs total DNA (input, Cy3) in MCH1_replicate 2

description:
RctB MCH1 Rep2
biological replicate 2 of 2
Vibrio cholerae N16961 MCH1 (CVC2099)


title: Tumor biopsy [P-527]


title: Tumor biopsy [P-526]


title: Tumor biopsy [P-520]


title: Tumor biopsy [P-512]


title: Tumor biopsy [P-537]


title: Tumor biopsy [P-525]


title: Tumor biopsy [P-510]


title: Tumor biopsy [P-516]


title: Tumor biopsy [P-513]


title: Tumor biopsy [P-509]


title: Tumor biopsy [P-505]


title: Tumor biopsy [P-507]


title: Tumor biopsy [P-506]


title: Tumor biopsy [P-504]


title: Tumor biopsy [P-493]


title: Tumor biopsy [P-496]


title: Tumor biopsy (P-535)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data processing was performed using the pipeline developed by Touleimat and Tost 2012.

label: biotin and DNP

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted according to a standard protocol with proteinase K, phenol, chloroform and isoamylalcohol (cohort 1) or by the use of Purelink Genomic DNA Mini Kit (cohort 2)


title: Tumor biopsy [P-491]


title: Tumor biopsy [P-500]


title: Tumor biopsy [P-503]


title: Tumor biopsy (P-538)


title: Tumor biopsy [P-488]


title: Tumor biopsy [P-487]


title: Tumor biopsy (P-537)


title: Tumor biopsy [P-485]


title: Tumor biopsy (P-536)


title: Tumor biopsy [P-483]


title: Tumor biopsy (P-527)


title: Tumor biopsy (P-533)


title: Tumor biopsy [P-482]


title: Tumor biopsy [P-484]


title: Tumor biopsy (P-531)


title: Tumor biopsy [P-481]


title: Tumor biopsy (P-526)


title: Tumor biopsy (P-525)


title: Tumor biopsy (P-529)


title: Tumor biopsy (P-519)


title: Tumor biopsy (P-516)


title: Tumor biopsy (P-532)


title: Tumor biopsy [P-474]


title: Tumor biopsy (P-509)


title: Tumor biopsy (P-524)


title: Tumor biopsy (P-506)


title: Tumor biopsy (P-520)


title: Tumor biopsy [P-475]


title: Tumor biopsy (P-510)


title: Tumor biopsy [P-479]


title: Tumor biopsy (P-513)


title: Tumor biopsy [P-471]


title: Tumor biopsy [P-478]


title: Tumor biopsy (P-512)


title: Tumor biopsy [P-468]


title: Tumor biopsy [P-467]


title: Tumor biopsy [P-464]


title: Tumor biopsy (P-518)


title: Tumor biopsy [P-469]


title: Tumor biopsy [P-462]


title: Tumor biopsy [P-460]


title: Tumor biopsy [P-466]


title: Tumor biopsy (P-500)


title: Tumor biopsy [P-457]


title: Tumor biopsy (P-505)


title: Tumor biopsy (P-496)


title: Tumor biopsy [P-456]


title: Tumor biopsy (P-504)


title: Tumor biopsy [P-454]


title: Tumor biopsy (P-487)


title: Tumor biopsy [P-445]


title: Tumor biopsy (P-485)


title: Tumor biopsy (P-507)


title: Tumor biopsy [P-443]


title: Tumor biopsy (P-503)


title: Tumor biopsy (P-493)


title: Tumor biopsy [P-438]


title: Tumor biopsy [P-442]


title: Tumor biopsy (P-475)


title: Tumor biopsy (P-491)


title: Tumor biopsy (P-478)


title: Tumor biopsy [P-429]


title: Tumor biopsy (P-482)


title: Tumor biopsy (P-483)


title: Tumor biopsy (P-488)


title: Tumor biopsy (P-474)


title: Tumor biopsy [P-433]


title: Tumor biopsy [P-427]


title: Tumor biopsy [P-426]


title: Tumor biopsy (P-479)


title: Tumor biopsy (P-471)


title: Tumor biopsy [P-422]


title: Tumor biopsy [P-455]


title: Tumor biopsy [P-420]


title: Tumor biopsy (P-481)


title: Tumor biopsy (P-469)


title: Tumor biopsy [P-434]


title: Tumor biopsy [P-421]


title: Tumor biopsy (P-484)


title: Tumor biopsy [P-417]


title: Tumor biopsy (P-462)


title: Tumor biopsy (P-468)


title: Tumor biopsy (P-467)


title: Tumor biopsy (P-456)


title: Tumor biopsy (P-454)


title: Tumor biopsy [P-413]


title: Tumor biopsy (P-443)


title: Tumor biopsy (P-464)


title: Tumor biopsy (P-466)


title: Tumor biopsy (P-455)


title: Tumor biopsy [P-410]


title: Tumor biopsy [P-411]


title: Tumor biopsy [P-423]


title: Tumor biopsy [P-412]


title: Tumor biopsy [P-409]


title: Tumor biopsy [P-418]


title: Tumor biopsy [P-408]


title: Tumor biopsy (P-460)


title: Tumor biopsy (P-445)


title: Tumor biopsy (P-438)


title: Tumor biopsy [P-401]


title: Tumor biopsy [P-416]


title: Tumor biopsy (P-442)


title: Tumor biopsy (P-457)


title: Tumor biopsy (P-434)


title: Tumor biopsy [P-386]


title: Tumor biopsy [P-395]


title: Tumor biopsy [P-367]


title: Tumor biopsy [P-370]


title: Tumor biopsy [P-397]


title: Tumor biopsy [P-366]


title: Tumor biopsy (P-418)


title: Tumor biopsy [P-399]


title: Tumor biopsy (P-427)


title: Tumor biopsy (P-433)


title: Tumor biopsy (P-426)


title: Tumor biopsy [P-354]


title: Tumor biopsy (P-422)


title: Tumor biopsy (P-423)


title: Tumor biopsy [P-358]


title: Tumor biopsy [P-337]


title: Tumor biopsy [P-353]


title: Tumor biopsy [P-336]


title: Tumor biopsy (P-412)


title: Tumor biopsy [P-406]


title: Tumor biopsy (P-417)


title: Tumor biopsy (P-411)


title: Tumor biopsy [P-335]


title: Tumor biopsy [P-310]


title: Tumor biopsy (P-416)


title: Tumor biopsy [P-298]


title: Tumor biopsy (P-421)


title: Tumor biopsy [P-297]


title: Tumor biopsy [P-282]


title: Tumor biopsy (P-406)


title: Tumor biopsy (P-413)


title: Tumor biopsy (P-408)


title: Tumor biopsy [P-280]


title: Tumor biopsy (P-399)


title: Tumor biopsy [P-300]


title: Tumor biopsy (P-409)


title: Tumor biopsy (P-420)


title: Tumor biopsy (P-429)


title: Tumor biopsy (P-401)


title: Tumor biopsy [P-269]


title: Tumor biopsy [P-263]


title: Tumor biopsy [P-266]


title: Tumor biopsy [P-254]


title: Tumor biopsy (P-397)


title: Tumor biopsy [P-262]


title: Tumor biopsy (P-370)


title: Tumor biopsy [P-277]


title: Tumor biopsy [P-255]


title: Tumor biopsy (P-410)


title: Tumor biopsy (P-337)


title: Tumor biopsy [P-264]


title: Tumor biopsy (P-367)


title: Tumor biopsy (P-395)


title: Tumor biopsy [P-267]


title: Tumor biopsy (P-386)


title: Tumor biopsy [P-218 ]


title: Tumor biopsy [P-229]


title: Tumor biopsy (P-335)


title: Tumor biopsy (P-354)


title: Tumor biopsy (P-358)


title: Tumor biopsy [P-207]


title: Tumor biopsy (P-336)


title: Tumor biopsy (P-353)


title: Tumor biopsy (P-298)


title: Tumor biopsy (P-310)


title: Tumor biopsy [P-211]


title: Tumor biopsy (P-300)


title: Tumor biopsy [P-206 ]


title: Tumor biopsy [P-201]


title: Tumor biopsy (P-280)


title: Tumor biopsy [P-179]


title: Tumor biopsy [P-163]


title: Tumor biopsy [P-243]


title: Tumor biopsy (P-264)


title: Tumor biopsy (P-297)


title: Tumor biopsy (P-282)


title: Tumor biopsy (P-269)


title: Tumor biopsy [P-060]


title: Tumor biopsy [P-081]


title: Tumor biopsy [P-097]


title: Tumor biopsy [P-226]


title: Tumor biopsy (P-263)


title: Tumor biopsy [P-009]


title: Tumor biopsy [P-041]


title: Tumor biopsy [P-008]


title: Tumor biopsy (P-366)


title: Tumor biopsy (P-266)


title: Tumor biopsy [P-003]


title: Tumor biopsy (P-262)


title: Tumor biopsy (P-254)


title: Tumor biopsy (P-226)


title: Tumor biopsy (P-229)


title: Tumor biopsy (P-255)


title: Tumor biopsy (P-206 )


title: Tumor biopsy (P-243)


title: Tumor biopsy (P-218 )


title: Tumor biopsy (P-211)


title: Tumor biopsy (P-060)


title: Tumor biopsy (P-201)


title: Tumor biopsy (P-008)


title: Tumor biopsy (P-081)


title: Tumor biopsy (P-163)


title: Tumor biopsy (P-041)


title: Tumor biopsy (P-204)


title: Tumor biopsy (P-003)


title: Tumor biopsy (P-179)


title: Tumor biopsy (P-392)

value: cohort 1


title: Tumor biopsy (P-389)


title: Tumor biopsy (P-134)


title: Tumor biopsy (P-391)


title: Tumor biopsy (P-277)


title: Tumor biopsy (P-009)


title: Tumor biopsy (P-267)


title: Tumor biopsy (P-387)


title: Tumor biopsy (P-376)


title: Tumor biopsy (P-384)


title: Tumor biopsy (P-207)


title: Tumor biopsy (P-372)


title: Tumor biopsy (P-371)


title: Tumor biopsy (P-363)


title: Tumor biopsy (P-368)


title: Tumor biopsy (P-390)


title: Tumor biopsy (P-097)


title: Tumor biopsy (P-349)


title: Tumor biopsy (P-355)


title: Tumor biopsy (P-352)


title: Tumor biopsy (P-361)


title: Sox7-/-Gata6GR_+DEXday4_rep3

city: Kobe

first: Hitoshi

last: Niwa

state: Hyogo

address: 2-2-3 Minatojima-minamimachi,Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description: Gene expression after 4days with Gata6 induction in Sox7-/- mouse embryonic stem cells

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air dried.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505C) at the resolution of 3um.

data_processing: The scanned images were quantified with Feature Extraction Software 10.7.3.1 (Agilent).

organism: Mus musculus

source_name: Embryonic stem cells, Sox7-/-, +Gata6, day4, replicate3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini column purification (QIAGEN, Valencia, CA).

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genotype

value: Sox7-/-; Gata6-GR


title: Tumor biopsy (P-360)


title: Tumor biopsy (P-332)


title: Tumor biopsy (P-350)


title: Sox7-/-Gata6GR_+DEXday4_rep2

source_name: Embryonic stem cells, Sox7-/-, +Gata6, day4, replicate2


title: Tumor biopsy (P-351)


title: Tumor biopsy (P-343)


title: Tumor biopsy (P-303)


title: Tumor biopsy (P-340)


title: Tumor biopsy (P-331)


title: Tumor biopsy (P-322)


title: Tumor biopsy (P-318)


title: Tumor biopsy (P-308)


title: Sox7-/-Gata6GR_-DEXday4_rep2

description: Gene expression without Gata6 induction in Sox7-/- mouse embryonic stem cells

source_name: Embryonic stem cells, Sox7-/-, -Gata6, day4, replicate2


title: Tumor biopsy (P-346)


title: Sox7+/-Gata6GR_+DEXday4_rep2

description: Gene expression after 4days with Gata6 induction in Sox7+/- mouse embryonic stem cells

source_name: Embryonic stem cells, Sox7+/-, +Gata6, day4, replicate2

value: Sox7+/-; Gata6-GR


title: Sox7+/-Gata6GR_+DEXday4_rep3

source_name: Embryonic stem cells, Sox7+/-, +Gata6, day4, replicate3


title: Tumor biopsy (P-333)


title: Sox7+/-Gata6GR_+DEXday4_rep1

source_name: Embryonic stem cells, Sox7+/-, +Gata6, day4, replicate1


title: Sox7+/-Gata6GR_-DEXday4_rep3

description: Gene expression without Gata6 induction in Sox7+/- mouse embryonic stem cells

source_name: Embryonic stem cells, Sox7+/-, -Gata6, day4, replicate1


title: Tumor biopsy (P-325)


title: Sox7-/-Gata6GR_+DEXday4_rep1

source_name: Embryonic stem cells, Sox7-/-, +Gata6, day4, replicate1


title: Sox7-/-Gata6GR_-DEXday4_rep3

source_name: Embryonic stem cells, Sox7-/-, -Gata6, day4, replicate3


title: Tumor biopsy (P-326)


title: Tumor biopsy (P-347)


title: Tumor biopsy (P-293)


title: Tumor biopsy (P-292)


title: Sox7-/-Gata6GR_-DEXday4_rep1

source_name: Embryonic stem cells, Sox7-/-, -Gata6, day4, replicate1


title: Sox7+/-Gata6GR_-DEXday4_rep1


title: Sox7+/-Gata6GR_-DEXday4_rep2


title: Tumor biopsy (P-294)


title: Tumor biopsy (P-285)


title: Tumor biopsy (P-291)


title: Tumor biopsy (P-302)


title: Tumor biopsy (P-288)


title: Tumor biopsy (P-290)


title: Tumor biopsy (P-281)


title: Tumor biopsy (P-319)


title: Tumor biopsy (P-261)


title: Tumor biopsy (P-289)


title: Tumor biopsy (P-274)


title: Tumor biopsy (P-283)


title: Tumor biopsy (P-270)


title: Tumor biopsy (P-278)


title: Tumor biopsy (P-247)


title: Tumor biopsy (P-244)


title: Tumor biopsy (P-279)


title: Tumor biopsy (P-276)


title: Tumor biopsy (P-265)


title: Tumor biopsy (P-272)


title: Tumor biopsy (P-284)


title: Tumor biopsy (P-275)


title: Tumor biopsy (P-240)


title: Tumor biopsy (P-246)


title: Tumor biopsy (P-374)


title: Tumor biopsy (P-258)


title: Tumor biopsy (P-252)


title: Tumor biopsy (P-239)


title: Tumor biopsy (P-257)


title: Tumor biopsy (P-251)


title: Tumor biopsy (P-236)


title: Tumor biopsy (P-227)


title: Tumor biopsy (P-235)


title: Tumor biopsy (P-232)


title: Tumor biopsy (P-231)


title: Tumor biopsy (P-220)


title: Tumor biopsy (P-213)


title: Tumor biopsy (P-221)


title: Tumor biopsy (P-228)


title: Tumor biopsy (P-215)


title: Tumor biopsy (P-210)


title: Tumor biopsy (P-202)


title: Tumor biopsy (P-222)


title: Tumor biopsy (P-199)


title: Tumor biopsy (P-197)


title: Tumor biopsy (P-198)


title: Tumor biopsy (P-203)


title: Tumor biopsy (P-193)


title: Tumor biopsy (P-182)


title: Tumor biopsy (P-208)


title: Tumor biopsy (P-195)


title: Tumor biopsy (P-192)


title: Tumor biopsy (P-190)


title: Tumor biopsy (P-214)


title: Tumor biopsy (P-194)


title: Tumor biopsy (P-184)


title: Tumor biopsy (P-191)


title: Tumor biopsy (P-200)


title: Tumor biopsy (P-174)


title: Tumor biopsy (P-188)


title: Tumor biopsy (P-180)


title: Tumor biopsy (P-189)


title: Tumor biopsy (P-196)


title: Tumor biopsy (P-177)


title: 28T

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5

department: Department of Biochemistry and Molecular Biology Institute of Basic Medical Sciences

country: China

institute: Peking Union Medical College & Chinese Academy of Medical Sciences

hyb_protocol: Set the Hybridization System to 42°C. With the cover closed, allow at least 3 hours for the temperature to stabilize. Resuspend 6ug dried MeDIP sample and 6ug Input sample pellet in 5ul water. Vortex well and spin to collect contents in bottom of the tube. Using components from a NimbleGen Hybridization Kit, prepare the hybridization solution master mix. Add the appropriate amount of hybridization solution to each sample. Vortex well (~15 seconds) and spin to collect contents in bottom of the tube. Incubate at 95°C for 5 minutes, protected from light. Vortex, spin, and place the tube in the Hybridization System sample block (pre-heated to 42°C) until ready for sample loading.

scan_protocol: Arrays were scanned on an GenePix 4000B scanner per manufacturer's protocol

data_processing:
After scaled log2 ratio data is generated a modified ACME algorithm (Method Enzymol. 2006; 411:270-282) is employed where a fixed-length window is slided along the length of each chromosome, testing at each probe using a one-sided Kolmogorov-Smirnov (KS) test whether the surrounding window is enriched for high-intensity probes relative to the rest of the array. Each probe has a corresponding p-value score (-log10) and a threshold is set to select regions that are enriched (i.e. methylated) in the test sample. In this case, if the number in ACME_output.txt > 0, this means the region is highly methylated modified, vice versa. ACME_output.txt is linked as a supplementary file on the Series record.
There is no normalization of DNA methylation data. However, we do scale the GFF files by subtracting the bi-weight mean for the log-ratio values from each log-ratio value. This effectively centers the log-ratio values around zero.

source_name: MeDIP DNA from tumor tissue

label_protocol: Dilute Cy3 and Cy5 dye-labeled 9mers to 1 O.D./42μl Random 9mer Buffer. Aliquot to 40μl individual reaction volumes in 0.2ml thin-walled PCR tubes and store at -20°C, protected from light. Assemble “MeDIP” and “Input” samples in separate 0.2ml thin-walled PCR tubes. Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quick-chill in an ice-water bath for 10 minutes. Add 20μl of the dNTP/Klenow master mix to each of the denatured samples. Keep on ice. Mix well by pipetting up and down 10 times. Quick-spin to force contents to bottom of the tube. Incubate for 2 hours at 37°C in a thermocycler protected from light. Stop the reaction by addition of 0.5M EDTA.

extract_protocol: Cut tissue into small pieces, and place in a 1.5 ml microcentrifuge tube, Add 20 μl proteinase K. Mix thoroughly by vortexing, and incubate at 56°C until the tissue is completely lysed. Vortex occasionally during incubation to disperse the sample, or place in a shaking water bath. Lysis time varies depending on the type of tissue processed. Add 4 μl RNase A (100 mg/ml), mix by vortexing, and incubate for 2 min at room temperature. Vortex for 15 s. Add 200 μl Buffer AL to the sample, and mix thoroughly by vortexing. Then add 200μl ethanol (96–100%), and mix again thoroughly by vortexing. Pipet the mixture (including any precipitate) into the DNeasy Mini spin column placed in a 2 ml collection tube. Centrifuge at 6000 x g for 1 min. Discard flow-through and collection tube. Place the DNeasy Mini spin column in a new 2 ml collection tube, add 500 μl Buffer AW1, and centrifuge for 1 min at 6000 x g. Discard flow-through and collection tube. Place the DNeasy Mini spin column in a new 2 ml collection tube, add 500 μl Buffer AW2, and centrifuge for 3 min at 20,000 x g to dry the DNeasy membrane, Remove the DNeasy Mini spin column carefully so that the column does not come into contact with the flow-through, Discard flow-through and collection tube. Place the DNeasy Mini spin column in a clean 1.5 ml microcentrifuge tube, and pipet 200 μl Buffer AE directly onto the DNeasy membrane. Incubate at room temperature for 1 min, and then centrifuge for 1 min at 6000 x g to elute.

tag: disease state

value: gastric cancer

tag: pair id

value: tumor

tag: fraction

value: MeDIP

tag: tumor grade

value: Adenocarcinoma III

tag: age

tag: gender

value: male

tag: lymphatic invasion

value: Negative

tag: perineural invasion

value: Positive

tag: classification

value: Ulcer

tag: location

value: Body

tag: Stage

value: III

source_name: Input DNA from tumor tissue

value: input


title: Tumor biopsy (P-151)


title: 28N

source_name: MeDIP DNA from adjacent normal tissue

tag: tissue

value: adjacent normal

value: Normal

source_name: Input DNA from adjacent normal tissue


title: 3T

value: Adenocarcinoma II

value: Proximal


title: 3N


title: Tumor biopsy (P-144)

value: Squamous cell carcinoma

value: cohort 1


title: Tumor biopsy (P-169)


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 2) rep4

city: MAIDSTONE

first: KERRY

middle: STEVEN

last: BURTON

address: NEW ROAD, EAST MALLING

institute: EAST MALLING RESEARCH

hyb_protocol: Agilent standard protocols

scan_protocol: Agilent Technologies Scanner G2505B US45102900

data_processing: Feature Extraction software v.9.5.3 (Agilent).

organism: Agaricus bisporus

source_name: fruitbody (non-symptomatic)

label_protocol: One-Colour Microarray-based Gene Expression Analysis protocol v.5.5 (Agilent Technologies).

extract_protocol: Total RNA isolated by the TRIZOL extraction method (Chomczynski, 1993) and purified and concentrated using the Qiagen RNEasy MinElute method

tag: strain

tag: sample type

value: showing no diseased symptoms growing in a disease-free environment


title: 4N

value: gastric cancer


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 3) rep3


title: 4T

value: tumor

value: MeDIP

value: Poorly differentiated adenocarcinoma


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 3) rep2


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 2) rep3


title: Tumor biopsy (P-136)

source_name: Cervical tumor

tag: figo stage

tag: histology


title: Tumor biopsy (P-130)

tag: cohort


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 2) rep1


title: Tumor biopsy (P-162)


title: Tumor biopsy (P-141)


title: Tumor biopsy (P-138)


title: Tumor biopsy (P-133)


title: Tumor biopsy (P-166)


title: Tumor biopsy (P-129)


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 2) rep2


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 1) rep3


title: Tumor biopsy (P-142)


title: Tumor biopsy (P-125)


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 3) rep4


title: Tumor biopsy (P-149)


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 1) rep1


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 1) rep2


title: Agaricus bisporus fruitbody (diseased) Farm 5 rep4 (flush 1)

source_name: fruitbody (diseased)

value: carrying a viral infection related to farm 5


title: Agaricus bisporus fruitbody (diseased) Farm 5 rep3 (flush 1)


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 1) rep4


title: Agaricus bisporus fruitbody (diseased) Farm 5 rep2 (flush 1)


title: Tumor biopsy (P-120)


title: Tumor biopsy (P-146)


title: Tumor biopsy (P-101)


title: Agaricus bisporus fruitbody (diseased) Farm 5 rep1 (flush 1)


title: Tumor biopsy (P-121)


title: Tumor biopsy (P-148)


title: Agaricus bisporus fruitbody (non-symptomatic) Farm HRI (flush 3) rep1


title: Tumor biopsy (P-115)


title: Tumor biopsy (P-124)


title: Agaricus bisporus fruitbody (diseased) Farm 4 rep2 (flush 1)

value: carrying a viral infection related to farm 4


title: Agaricus bisporus fruitbody (diseased) Farm 4 rep4 (flush 1)


title: Agaricus bisporus fruitbody (diseased) Farm 4 rep3 (flush 1)


title: Agaricus bisporus fruitbody (diseased) Farm 4 rep1 (flush 1)


title: Agaricus bisporus fruitbody (diseased) Farm 3 rep4 (flush 3)

value: carrying a viral infection related to farm 3


title: Tumor biopsy (P-126)


title: Agaricus bisporus fruitbody (diseased) Farm 3 rep3 (flush 3)


title: Agaricus bisporus fruitbody (diseased) Farm 3 rep2 (flush 3)


title: Tumor biopsy (P-091)


title: Agaricus bisporus fruitbody (diseased) Farm 2 rep4 (flush 1)

value: carrying a viral infection related to farm 2


title: Agaricus bisporus fruitbody (diseased) Farm 3 rep1 (flush 3)


title: Agaricus bisporus fruitbody (diseased) Farm 2 rep3 (flush 1)


title: Tumor biopsy (P-087)


title: iPS cell line3, biological rep2

first: Xiuying

last: Liu

address: Yard 28, Science Park Road, Changping District

institute: Changping Laboratory

description:
EiP11-10-2
Gene expression data from integration-free iPS cells in early passage

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: One integration-free iPS cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: ES cells and iPS cells were maintained using N2B27 medium plus mouse lif in 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were collected using 0.25% trypsin/EDTA and then washed with PBS for two times. Then the collected cells were placed on ice in the Trizol solution (GibcoBRL).

value: male

tag: cell line

value: iPS cell line3


title: Tumor biopsy (P-084)


title: Tumor biopsy (P-093)


title: Tumor biopsy (P-080)


title: Tumor biopsy (P-074)


title: Tumor biopsy (P-083)


title: Tumor biopsy (P-072)


title: Agaricus bisporus fruitbody (diseased) Farm 2 rep2 (flush 1)


title: Tumor biopsy (P-098)


title: Tumor biopsy (P-068)


title: Agaricus bisporus fruitbody (diseased) Farm 1 rep4 (flush 2)

value: carrying a viral infection related to farm 1


title: Tumor biopsy (P-078)


title: iPS cell line1, biological rep2

description:
EiP11-1-2
Gene expression data from integration-free iPS cells in early passage

value: iPS cell line1


title: Tumor biopsy (P-067)


title: iPS cell line2, biological rep2

description:
EiP11-9-2
Gene expression data from integration-free iPS cells in early passage

value: iPS cell line2


title: Agaricus bisporus fruitbody (diseased) Farm 1 rep3 (flush 2)


title: Agaricus bisporus fruitbody (diseased) Farm 2 rep1 (flush 1)


title: Agaricus bisporus fruitbody (diseased) Farm 1 rep2 (flush 2)


title: Agaricus bisporus fruitbody (diseased) Farm 1 rep1 (flush 2)


title: Tumor biopsy (P-058)


title: Tumor biopsy (P-063)


title: iPS cell line1, biological rep1

description:
EiP11-1-1
Gene expression data from integration-free iPS cells in early passage


title: ES control, biological rep1

description:
ES1-1-1
Gene expression data from normal ES cells in early passage

source_name: Normal ES cell line

value: ES control


title: iPS cell line2, biological rep1

description:
EiP11-9-1
Gene expression data from integration-free iPS cells in early passage


title: ES control, biological rep2

description:
ES1-1-2
Gene expression data from normal ES cells in early passage


title: male X75

status: Public on Sep 13 2015

city: Amsterdam

first: Philip

middle: C

last: Schouten

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: According to manufacterer's protocol (Nimblegen Roche)

scan_protocol: 2 um double pass

data_processing: Nimblescan, grid tiff files, generate pair reports followed by using the NimbleScan DNAcopy procedure at default settings

source_name: Breast Cancer aCGH

label_protocol: With the ENZO 42760 labeling kit for array CGH: 20 uL primers (vial 1) with 500 ng of genomic tumor DNA or Promega Female reference DNA (GG1521) in 19 ul of nuclease free water for 10 minutes at 99 C in pcr machine, followed by 10 minutes of cooling to 4 degrees. Snap freeze and spin. While on ice add 11 ul Cy3 mix (10ul Cy3+1ul Klenow DNA pol (vial 4)) to tumor DNA, and 11 ul Cy5 mix (10ul Cy3+1ul Klenow DNA pol (vial 4)) to reference DNA and incubate in PCR machine for 4 hours at 37 C. Then add 5ul stop buffer (vial 5).  To remove excess nucleotides with Qiagen MinElute PCR purification kit add 275 uL binding buffer (PB) to sample and reference. Put on minElute column and spin 60 sec on 16000 rcf. Add 700 ul Wash Buffer (PE) and centrifuge 60 secs at 16000 rcf. Dry columns by spinning another 60 secs at 16000 rcf. Elute the DNA in 2 steps by adding 2x 10.5 ul of elution buffer (EB). Pool equal amounts of tumor and reference DNA and speedvac into a pellet.

extract_protocol: 10 x 10 u slices containing at least 60% tumour cells were cleared of paraffin (2 x 5 min xylene, 2 x 30 s 100% ethanol, 30s 90% ethanol, 30 s 70% ethanol, and rinsed with H2O), treated with 1 M NaSCN at 37 C overnight, and sections of interest (>70% tumour cells) were scraped in 200 ul buffer ATL (Qiagen, cat. no. 51304).  27 ul of proteinase K (15 ug/ull, Roche, cat. no.3115879001) was immediately added, as well as at the end of the day, and at the beginning and end of the next day; samples were constantly shaken at 37 C during the time of digestion. The following day, 40 ul RNase A (20 ug/ul, Sigma, cat. no. R5500) was added to the sample, vortexed, and incubated for 2 min at room temperature. 400 ul of buffer AL (Qiagen, cat.no.51304) was added and incubated for 10 min at 70 C. 420 ul of 100% ethanol was added and vortexed. The sample mixture was spun on a spincolumn (Qiagen, cat. no. 51304) for 1 min at 8,000 rpm. The column was sequentially washed with 500 ul of the following reagents and spun for 1 min at 8,000 rpm: AW1, AW2, and  twice with 80% ethanol. The column was spun dry for 3 min at 14,000 rpm. The sample was eluted with 50 ul of AE buffer by spinning for 1 min at 8,000 rpm.  (Joosse, SA et al, Breast Cancer Res Treat, 2009)

tag: bloom richardson grade

tag: er

tag: pr

value: breast cancer tumor

source_name: Promega Male Reference genomic DNA G1471

value: pooled Male Reference DNA


title: Tumor biopsy (P-053)

value: Squamous cell carcinoma

value: cohort 1


title: Tumor biopsy (P-042)


title: Tumor biopsy (P-055)


title: male X74


title: male X70


title: male X71


title: Tumor biopsy (P-028)


title: male X66


title: male X68


title: male X69


title: Tumor biopsy (P-024)


title: Tumor biopsy (P-172)


title: Tumor biopsy (P-018)


title: male X64


title: male X67


title: Tumor biopsy (P-062)


title: male X65


title: male X63


title: male X62


title: Tumor biopsy (P-014)


title: male X61


title: Tumor biopsy (P-004)


title: Tumor biopsy (P-002)


title: Tumor biopsy (P-032)


title: male X56


title: male X60


title: male X55


title: male X57


title: male X49


title: male X59


title: male X48


title: iPS cell line3, biological rep1

description:
EiP11-10-1
Gene expression data from integration-free iPS cells in early passage


title: male X46


title: male X47


title: male X45


title: male X58


title: male X43


title: male X52


title: male X42


title: male X73


title: male X50


title: Tumor biopsy (P-073)


title: male X51


title: male X53


title: male X44


title: male X54


title: Tumor biopsy (P-005)


title: male X34


title: male X35


title: male X40


title: male X38


title: male X39


title: male X32


title: male X37


title: male X33


title: male X36


title: male X31


title: male X29


title: male X30


title: male X72


title: male X23


title: male X28


title: male X15


title: male X25


title: male X24


title: male X20


title: male X26


title: male X19


title: male X22


title: male X27


title: male X18


title: male X13


title: male X14


title: male X17


title: male X16


title: male X11


title: male X10


title: CD8+YFPneg Replicate 4

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

description: CD8+YFPneg 4

hyb_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

source_name: CD8+YFPneg T cells, from Liver, Spleen & LNs, Day 7 post-allogeneic transplant

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

tag: cell type

value: CD8+YFPneg T cells


title: male X12


title: male X41


title: CD8+YFPneg Replicate 2

description: CD8+YFPneg 2

scan_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.


title: male X8


title: CD8+YFPneg Replicate 3

description: CD8+YFPneg 3


title: male X9


title: male X21


title: male X7


title: CD8+YFP+ Replicate 4

description: CD8+YFP+ 4

source_name: CD8+YFP+ T cells, from Liver, Spleen & LNs, Day 7 post-allogeneic transplant

value: CD8+YFP+ T cells


title: male X6


title: male X4


title: CD8+YFP+ Replicate 2

description: CD8+YFP+ 2


title: CD8+YFP+ Replicate 1

description: CD8+YFP+ 1


title: CD8+YFPneg Replicate 1

description: CD8+YFPneg 1


title: male X2


title: male X3


title: KO_TIFAB_LSK_rep2

status: Public on Sep 12 2015

city: Cincinnati

first: Daniel

middle: T

last: Starczynowski

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: 3.5 ug of fragmented cDNA were hybridized to a Mouse Gene 2.0 ST arrays (Affymetrix). Probe arrays were incubated at 45°C for 18 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0002. The Stain and Antibody solutions are produced by Affymetrix and contained in the Genechip Hybridization Wash and Stain Kit.

scan_protocol: Genechips were scanned using the Affymetrix GeneChip Scanner 3000 7G, and data were collected with Genechip Operating Software (Affymetrix)

data_processing:
The .cel were created by Command Console (Affymetrix). The .cel files were analyzed by Expression Console (Affymetrix) to create the .chp files. Data analysis was performed using GeneSpring GX 11.5 software (Agilent Technologies). Gene set enrichment analysis was performed on a JAVA-based dataset supported by the Broad Institute(Subramanian et al., 2005).
MoGene-2_0-st.pgf
MoGene-2_0-st.csv

source_name: TIFAB-/- (KO) LSK BM cells

label_protocol: Total RNA was reversed transcribed and labeled with the Ovation Pico WTA System v2 (Nugen).  The Encore Biotin Module (NuGEN) chemically fragmented and labeled the target cDNA.

growth_protocol: Animals were bred and housed in the Association for Assessment and Accreditation of Laboratory Animal Care-accredited animal facility of Cincinnati Children’s Hospital Medical Center.

extract_protocol: Total RNA was extracted and purified with Quick-RNA MiniPrep Kit from Zymo Research (Cat#R1054) according to the manufacturer's instructions.

treatment_protocol: Sorted LSK isolated from 3-month-old mice transplanted with Tifab+/+ or Tifab-/- BM cells (n = 3 mice/group) were injected i.v. into lethally-radiated (7.0 Gy and 4.75 Gy after 3 hours) syngeneic recipient Boy/J mice.

tag: genotype

value: TIFAB-/- (KO)

value: sorted lineage-Sca1+cKit+ (LSK) isolated from bone marrow (BM)


title: male X5


title: WT_TIFAB_LSK_rep3

source_name: TIFAB+/+ (WT) LSK BM cells

value: TIFAB+/+ (WT)


title: male X1


title: KO_TIFAB_LSK_rep1


title: WT_TIFAB_LSK_rep1


title: CD8+YFP+ Replicate 3

description: CD8+YFP+ 3


title: KO_TIFAB_LSK_rep3


title: WT_TIFAB_LSK_rep2


title: Murine ES Cells: Control vs. ETV4/5 double KO

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: normalized log2 ratio (PE15-2/PE9)

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal (3D-Gene Extraction software, Toray Industries).

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: ES cells were cultured on gelatin-coated dishes with LIF-supplemented Dulbecco’s modified Eagle’s medium (DMEM) as described previously.

extract_protocol: Total RNA was extracted using Sepasol-RNA I Super G following manufacturer's instructions

tag: strain background

value: embryonic stem cells

tag: genotype/variation

value: control

value: ETV4/5 double KO


title: ES-CM coculture-2

status: Public on Sep 11 2015

city: Tainan

first: Desy

middle: S

last: Lee

address: University Road

country: Taiwan

institute: NCKU

description: ES-CM cultured alone was used as control to identify miRNA that expressed differently following coculture with endothelial cells for 25 hours

hyb_protocol: The labeled samples were hybridized on the miRCURY LNA™ microRNA Array V11.0.

scan_protocol: Hybridization signals were detected by fluorescence using an GenePix 4000B scanner (Molecular Devices). Scanner images were quantified by GenePix Pro 6 (Molecular Devices)

data_processing: GPR files were loaded into GeneSpring 11.5 (Agilent Technologies, Santa Clara, CA) and normalized using the global Lowess algorithm.

source_name: embryonic stem cells-derived cardiomyocytes cultured alone

label_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Cat #208032-A, Exiqon) according to manufacturer's instructions.

growth_protocol: Mouse embryonic stem cells-derived cardiomyocytes were cultured alone (control) or along with endothelial cells

extract_protocol: RNA were extracted using Trizol reagent and further cleaned up using Qiagen RNAse Clean Up kit with the protocol that did not exclude the small RNAs

treatment_protocol: Both cells were cultured for 24 hours. ES-CMs with aMHC-GFP reporter were sorted out from coculture cells using FACS

tag: cultured

value: alone

source_name: embryonic stem cells-derived cardiomyocytes cultured along with endothelial cells

value: cultured along with endothelial cells


title: ES-CM coculture-3

description: ES-CM cultured alone was used as control to identify miRNA that expressed differently following coculture with endothelial cells for 26 hours


title: ES-CM coculture-1

description: ES-CM cultured alone was used as control to identify miRNA that expressed differently following coculture with endothelial cells for 24 hours


title: embryo 5_5 blastomere C

city: New York

first: Dieter

last: Egli

state: NY

address: 116th St & Broadway

institute: Columbia University

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was digested with the NspI restriction enzyme, ligated to an adapter molecule, PCR amplified, fragmented with DNase I, labeled and hybridized to each array according to the manufacturer's instructions (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

scan_protocol: Each array was washed using Affymetrix fluidics station 640, and scanned using the Gene Chip Scanner 7G as recommended (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

data_processing: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls. Copy number was calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual) analysis against a reference set at a 5Mb Gaussian smoothing for aneuploid screening and 1Mb Gaussian smoothing for microdeletion detection. Both sets of CN and LOH files have been included. The reference set consisted of three normal females from in house gDNA bank, 11 normal females from Coriel cell lines and 16 normal females from the HapMap database (www.hapmap.org). The 16 normal females are NA10855, NA10863, NA11832, NA12057, NA12234, NA12717, NA12813, NA18505, NA18508, NA18517, NA19137, NA19152, NE00088, NE00091, NE00403, and NE01119.

source_name: cleavage stage embryo blastomere

label_protocol: Fragmented DNA was biotinylated using the manufacturers recommendations (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930)

extract_protocol: Biopsied blastomere samples underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).  Whole genome amplification was performed as previously described (Treff et al., 2010, Fertil. Steril., In Press).

tag: predicted karyotype


title: embryo 5_5 blastomere D

description: Hybridized to 250K_Nsp


title: embryo 5_5 blastomere F

description: Hybridized to 250K_Nsp


title: embryo 5_3 blastomere C

description: Hybridized to 250K_Nsp

value: complex aneuploid


title: embryo 5_5 blastomere G

description: Hybridized to 250K_Nsp


title: embryo 5_4 blastomere F

description: Hybridized to 250K_Nsp


title: embryo 5_5 blastomere A

description: Hybridized to 250K_Nsp


title: embryo 5_5 blastomere B

description: Hybridized to 250K_Nsp


title: embryo 5_4 blastomere E

description: Hybridized to 250K_Nsp


title: embryo 5_4 blastomere C

description: Hybridized to 250K_Nsp


title: embryo 5_2 blastomere F

description: Hybridized to 250K_Nsp


title: embryo 5_4 blastomere D

description: Hybridized to 250K_Nsp


title: embryo 5_5 blastomere E

description: Hybridized to 250K_Nsp


title: embryo 5_4 blastomere G

description: Hybridized to 250K_Nsp


title: embryo 5_3 blastomere E

description: Hybridized to 250K_Nsp


title: embryo 5_3 blastomere G

description: Hybridized to 250K_Nsp


title: embryo 5_2 blastomere G

description: Hybridized to 250K_Nsp


title: embryo 5_2 blastomere B

description: Hybridized to 250K_Nsp


title: embryo 5_4 blastomere A

description: Hybridized to 250K_Nsp


title: embryo 5_3 blastomere B

description: Hybridized to 250K_Nsp

value: nonconcurrent


title: embryo 5_2 blastomere E

description: Hybridized to 250K_Nsp


title: embryo 5_4 blastomere B

description: Hybridized to 250K_Nsp


title: embryo 5_2 blastomere H

description: Hybridized to 250K_Nsp


title: RNA C MITO3 (control) vs RNA MITO3

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

country: Spain

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

organism: Acinetobacter baumannii

source_name: RNA C MITO3 (control) Second Dnase-treated RNA obtained from cultures treated with water (solvent of the mitomycin C).

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

growth_protocol: 50 ng of the Dnase-treated RNA was obtained from mid exponential growth phase cultures (optical density of 0.5 at 600 nm).

extract_protocol: Dnase-treated RNA from late log-phase culture (OD=0.4-0.6) by using the High Pure RNA Isolation Kit (Roche, Germany)

treatment_protocol: The cultures were treated with mitomycin C (MMC), at a final concentration of 10 μg ml-1, and incubated for an additional 1 h before samples were removed for RNA extraction.  A mixture of acyl homoseine lactones (AHLs) was prepared in ethyl acetate acidified with 0.1% (vol/vol) acetic acid containing N-(butyl, heptanoyl, hexanoyl, β-ketocaproyl, octanoyl and tetradecanoyl)-DL-homoserine lactones (Sigma-Aldrich, Inc), and each was added to a final concentration of 1μM in the medium.

tag: treatment

source_name: RNA MITO3 Second Dnase-treated RNA obtained from cultures treated with mitomycin C.


title: embryo 5_3 blastomere I

description: Hybridized to 250K_Nsp


title: embryo 5_2 blastomere A

description: Hybridized to 250K_Nsp


title: embryo 5_3 blastomere A

description: Hybridized to 250K_Nsp


title: embryo 5_2 blastomere D

description: Hybridized to 250K_Nsp


title: RNA C MITO4 (control) vs RNA MITO4

source_name: RNA C MITO4 (control) First Dnase-treated RNA obtained from cultures treated with water (solvent of the mitomycin C).

source_name: RNA MITO4 First Dnase-treated RNA obtained from cultures treated with mitomycin C.


title: embryo 5_3 blastomere D

description: Hybridized to 250K_Nsp


title: embryo 5_2 blastomere C

description: Hybridized to 250K_Nsp


title: RNA MITO5 vs RNA C MITO5 (control)

source_name: RNA MITO5 First Dnase-treated RNA obtained from cultures treated with mitomycin C.

source_name: RNA C MITO5 (control) First Dnase-treated RNA obtained from cultures treated with water (solvent of the mitomycin C).


title: embryo 5_3 blastomere H

description: Hybridized to 250K_Nsp


title: RNA MITO6 vs RNA C MITO6 (control)

source_name: RNA MITO6 Second Dnase-treated RNA obtained from cultures treated with mitomycin C.

source_name: RNA C MITO6 (control) Second Dnase-treated RNA obtained from cultures treated with water (solvent of the mitomycin C).


title: embryo 2_2 blastomere D

description: Hybridized to 250K_Nsp


title: embryo 2_2 blastomere A

description: Hybridized to 250K_Nsp


title: LV5_b

city: Evry

last: Stockholm

address: 1bis rue de l'Internationale

department: R&D

country: France

institute: Genethon - EPHE

description:
CD34+ Transduced sample b with vector LV5
Vector Type: LV
Production System: Quadri Chro
Initial Name: fLV5_b
Chip Name: f

hyb_protocol: Hybridisation to Illumina Infinium Human Methylation450k Beadchip used standard Illumina protocol.

scan_protocol: Beachips were scanned using an iScan

data_processing: Normalized Raw beta values exported from GenomeStudio software were imported into R and analyzed with our homemade scripts. Probes on chromosomes X and Y were removed. Probes with a detection P-value > 0.01 exceeding 5% of the samples were also filtered out.

source_name: CD34+ purified cells from mobilized peripheral blood cells #8 treated with LV

label_protocol: From each sample 500ng genomic DNA was bisulfite treated using EZ DNA methylation kit.

growth_protocol: 1x106 cells of CD34+ purified cells were pre-activated overnight at 37C° in X-VIVO culture medium, supplemented with antibiotics and cytokines  (Flt3-ligand (300 ng/ml), stem cell factor (300 ng/ml), trombopoietin (100 ng/ml) and IL3 (20ng/ml)).

extract_protocol: Genomic DNA was prepared using Nucleospin TissuXS kit (Nacherey Nagel).

treatment_protocol: Transduction was performed in the presence of 4ug/ml genomic DNA (Sigma) with 5x107 IG/ml (infectious genome) LV. A 2nd round of transduction was performed in the same conditions 6h later. Transduction reaction was stopped 24h after the beginning of the first round of transfection and cells were collected.

tag: tissue type

value: cord blood


title: embryo 2_2 blastomere E

description: Hybridized to 250K_Nsp


title: LV4b_a

description:
CD34+ Transduced sample a with vector LV4b
Vector Type: LV
Production System: Quadri Chro
Initial Name: fLV4b_a
Chip Name: f

source_name: CD34+ purified cells from mobilized peripheral blood cells #7 treated with LV


title: LV4b_c

description:
CD34+ Transduced sample c with vector LV4b
Vector Type: LV
Production System: Quadri Chro
Initial Name: fLV4b_c
Chip Name: f

source_name: CD34+ purified cells from mobilized peripheral blood cells #9 treated with LV


title: embryo 2_1 blastomere B

description: Hybridized to 250K_Nsp


title: embryo 2_1 blastomere F

description: Hybridized to 250K_Nsp

value: 47,XY,+9 (indeterminate)


title: LV5_a

description:
CD34+ Transduced sample a with vector LV5
Vector Type: LV
Production System: Quadri Chro
Initial Name: fLV5_a
Chip Name: f


title: embryo 1_6 blastomere E

description: Hybridized to 250K_Nsp


title: embryo 1_6 blastomere H

description: Hybridized to 250K_Nsp


title: embryo 2_1 blastomere C

description: Hybridized to 250K_Nsp


title: embryo 1_6 blastomere C

description: Hybridized to 250K_Nsp


title: embryo 1_6 blastomere B

description: Hybridized to 250K_Nsp


title: embryo 1_6 blastomere D

description: Hybridized to 250K_Nsp


title: embryo 1_6 blastomere F

description: Hybridized to 250K_Nsp


title: embryo 2_2 blastomere B

description: Hybridized to 250K_Nsp


title: embryo 6_5 blastomere A

description: Hybridized to 250K_Nsp


title: embryo 6_5 blastomere C

description: Hybridized to 250K_Nsp


title: LV4a_b

description:
CD34+ Transduced sample b with vector LV4a
Vector Type: LV
Production System: Quadri Chro
Initial Name: b2GMP.20
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #2 treated with LV


title: LV4b_b

description:
CD34+ Transduced sample b with vector LV4b
Vector Type: LV
Production System: Quadri Chro
Initial Name: fLV4b_b
Chip Name: f


title: embryo 6_5 blastomere B

description: Hybridized to 250K_Nsp


title: LV5_c

description:
CD34+ Transduced sample c with vector LV5
Vector Type: LV
Production System: Quadri Chro
Initial Name: fLV5_c
Chip Name: f


title: embryo 4 blastomere C

description: Hybridized to 250K_Nsp


title: LV3b_a

description:
CD34+ Transduced sample a with vector LV3b
Vector Type: LV
Production System: Tri UC
Initial Name: fLV3_a
Chip Name: f


title: embryo 2_1 blastomere A

description: Hybridized to 250K_Nsp


title: LV3b_b

description:
CD34+ Transduced sample b with vector LV3b
Vector Type: LV
Production System: Tri UC
Initial Name: fLV3_b
Chip Name: f


title: LV4a_c

description:
CD34+ Transduced sample c with vector LV4a
Vector Type: LV
Production System: Quadri Chro
Initial Name: b2GMP.21
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #3 treated with LV


title: embryo 4 blastomere E

description: Hybridized to 250K_Nsp


title: LV4a_a

description:
CD34+ Transduced sample a with vector LV4a
Vector Type: LV
Production System: Quadri Chro
Initial Name: b2GMP.19
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #1 treated with LV


title: embryo 2_2 blastomere C

description: Hybridized to 250K_Nsp


title: LV3a_c

description:
CD34+ Transduced sample c with vector LV3a
Vector Type: LV
Production System: Tri UC
Initial Name: cUC2c
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #12 treated with LV


title: LV3a_a

description:
CD34+ Transduced sample a with vector LV3a
Vector Type: LV
Production System: Tri UC
Initial Name: cUC2a
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #10 treated with LV


title: embryo 1_3 blastomere C

description: Hybridized to 250K_Nsp

source_name: cleavage stage embryo blastomere


title: embryo 2_1 blastomere E

description: Hybridized to 250K_Nsp


title: embryo 6_5 blastomere D

description: Hybridized to 250K_Nsp


title: embryo 1_3 blastomere G

description: Hybridized to 250K_Nsp


title: embryo 4 blastomere F

description: Hybridized to 250K_Nsp


title: embryo 1_3 blastomere E

description: Hybridized to 250K_Nsp


title: embryo 1_3 blastomere B

description: Hybridized to 250K_Nsp


title: embryo 1_3 blastomere F

description: Hybridized to 250K_Nsp


title: LV1b_c

description:
CD34+ Transduced sample c with vector LV1b
Vector Type: LV
Production System: Tri UC
Initial Name: cUC1c
Chip Name: c


title: LV1b_b

description:
CD34+ Transduced sample b with vector LV1b
Vector Type: LV
Production System: Tri UC
Initial Name: cUC1b
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #11 treated with LV


title: LV2_a

description:
CD34+ Transduced sample a with vector LV2
Vector Type: LV
Production System: Quadri UC
Initial Name: b2UC.16
Chip Name: ab


title: LV3a_b

description:
CD34+ Transduced sample b with vector LV3a
Vector Type: LV
Production System: Tri UC
Initial Name: cUC2b
Chip Name: c


title: LV1b_a

description:
CD34+ Transduced sample a with vector LV1b
Vector Type: LV
Production System: Tri UC
Initial Name: cUC1a
Chip Name: c


title: AR42J cells, +dexamethasone rep3

city: Kansas City

first: Robert

last: De Lisle

state: KS

address: 3901 Rainbow Blvd

department: Anatomy & Cell Biology

institute: Univ Kansas Med Ctr

description:
Gene expression from dexamethasone-induced AR42J cells
Dex3-230

hyb_protocol: GeneChip was prehybridized with Hybridization buffer at 45C 10min. Denatured Hybridization cocktail was applied to GeneChip. GeneChip was hybridized 16 hr at 45C in GeneChip Hybridization Oven 640. Washing and Staining: Automated process using the GeneChip Fluidics Station 400 with the Standard Array Format.

scan_protocol: Automated process conducted using the Agilent GeneArray Scanner. Pixel value = 3um Wavelength = 570nm

data_processing: Primary analysis was by GCOS with 'Scaling - All Probe Sets: Target Signal = 500'; 'Normalization – User Defined: Scale Factor = 1' using MAS 5.0.

organism: Rattus norvegicus

source_name: AR42J_100 nM dexamethasone_48hrs

label_protocol: The standard labeling protocol was used.

growth_protocol: AR42J cells were obtained from the ATCC. The experiment was repeated 3 times over a period of 5 months, using cells revived from frozen stocks at passage 29 for each experiment. Cells were seeded at 1.25 x 10^5 cells/cm^2 in 25 cm^2 flasks, with 20% FBS in F-12K medium (Kaighn's Modification of Ham's F-12 medium) plus penicillin/streptomycin.

extract_protocol: The flask was rinsed 2x with PBS and 3 mL Trizol reagent added. The flask was agitated until the cells were lysed and total RNA isolated as per the supplier's protocol.

treatment_protocol: After 24h, the medium was replaced with 5% FBS in DMEM, 4.5g glucose/L plus penicillin/streptomycin, and without (control) or with (induced) dexamethasone at 100 nM for a further 48h.

value: rat pancreatic cell line

tag: induced with

value: 100nM dexamethasone for 48h


title: cell line_RuT7_24h_3

city: Belgrade

first: Miljana

last: Tanic

address: Pasterova 14

department: Experimental Oncology

country: Serbia

institute: Institute for Oncology and Radiology of Serbia (IORS)

description: Gene expression after 24h in RuT7  treated Hela cell line

hyb_protocol: For each sample 600 ng of Cy3-labelled cRNA was mixed, fragmented for 1 h at 60 ⁰C for 30 min and hybridized at 65 ⁰C for 17 h.

scan_protocol: microarray slides were washed according to protocol provided by the manufacturer and scanned using Agilent SureScan Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA). Images were processed using Agilent Feature Extraction v.11 software.

data_processing: Raw data files were imported in Agilent GeneSpring, flagged probes and control probes were filtered out and background corrected data was normalized by scaling to 75th percentile and log 2 transformed. Probes where at least 70.0 percent of samples have flags and low expressed probes (bottom 20 %) were filtered out, retaining 41929 probes.

source_name: cell line

label_protocol: 100 ng of total RNA was amplified and labeled with Cyanine-3 (Cy3) fluorescent dye using Low Input Quick Amp Labeling Kit (Agilent Technologies). Fluorescently labeled samples were purified using QIAGEN’s RNeasy Mini spin columns and eluted in 30 µl of nuclease-free water, and cRNA quantity and Cy3 incorporation level was determined using BioSpec Nano (Shimadzu Scientific Instruments).

growth_protocol: 1 x 106 and 0.7 x 106 HeLa cells/25 cm2 falcon dish were seeded (Thermo Scientific Nunc™) for 12 and 24 h treatment, respectively.

extract_protocol: Total RNA was extracted from frozen cell pellets using Trizol reagent (Invitrogen) and RNA cleanup was performed using RNeasy Mini Kit (QIAGEN). RNA quantity and quality was estimated using BioSpec Nano (Shimadzu Scientific Instruments) and 1% agarose gel electrophoresis.

treatment_protocol: After 24 h stabilization period, cells were treated with the RuT7 complex and CDDP at concentrations equal to 0.5 x IC50. Control samples were left untreated. Following 12 and 24 h, cells were harvested by trypsinization, washed by ice cold PBS and cell pellet was collected by centrifugation at 2000 rpm, 10 min at 4 ˚C and frozen at -80 ˚C.

value: Hela cell line


title: LV1a_c

description:
CD34+ Transduced sample c with vector LV1a
Vector Type: LV
Production System: Tri UC
Initial Name: aWTr.12
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #6 treated with LV


title: LV2_b

description:
CD34+ Transduced sample b with vector LV2
Vector Type: LV
Production System: Quadri UC
Initial Name: b2UC.17
Chip Name: ab


title: embryo 1_4 blastomere G

description: Hybridized to 250K_Nsp


title: embryo 1_4 blastomere F

description: Hybridized to 250K_Nsp


title: embryo 1_3 blastomere D

description: Hybridized to 250K_Nsp


title: AR42J cells, control rep3

description:
Gene expression from uninduced AR42J cells
Con3-230

source_name: AR42J_control conditions (without dexamethasone)

value: none (not induced)


title: AR42J cells, control rep2

description:
Gene expression from uninduced AR42J cells
Con2-230


title: dINT2_b

description:
CD34+ Transduced sample b with vector dINT2
Vector Type: dINT
Production System: Tri UC
Initial Name: cINT2b
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #11 treated with dINT


title: embryo 1_4 blastomere A

description: Hybridized to 250K_Nsp


title: AR42J cells, +dexamethasone rep2

description:
Gene expression from dexamethasone-induced AR42J cells
Dex2-230


title: embryo 1_4 blastomere D

description: Hybridized to 250K_Nsp


title: embryo 1_4 blastomere B

description: Hybridized to 250K_Nsp


title: cell line_RuT7_12h_3

description: Gene expression after 12h in RuT7  treated Hela cell line


title: dINT2_a

description:
CD34+ Transduced sample a with vector dINT2
Vector Type: dINT
Production System: Tri UC
Initial Name: cINT2a
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #10 treated with dINT


title: embryo 1_4 blastomere H

description: Hybridized to 250K_Nsp


title: AR42J cells, control rep1

description:
Gene expression from uninduced AR42J cells
Con1-230


title: cell line_RuT7_24h_1


title: cell line_RuT7_24h_2


title: dINT2_c

description:
CD34+ Transduced sample c with vector dINT2
Vector Type: dINT
Production System: Tri UC
Initial Name: cINT2c
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #12 treated with dINT


title: dINT1b_c

description:
CD34+ Transduced sample c with vector dINT1b
Vector Type: dINT
Production System: Tri UC
Initial Name: cINT1c
Chip Name: c


title: embryo 1_1 blastomere E

description: Hybridized to 250K_Nsp


title: dINT1b_b

description:
CD34+ Transduced sample b with vector dINT1b
Vector Type: dINT
Production System: Tri UC
Initial Name: cINT1b
Chip Name: c


title: embryo 1_4 blastomere E

description: Hybridized to 250K_Nsp


title: cell line_RuT7_12h_1


title: embryo 1_4 blastomere C

description: Hybridized to 250K_Nsp


title: cell line_Control_12h_2

description: Gene expression after 12h in Control  treated Hela cell line


title: LV3b_c

description:
CD34+ Transduced sample c with vector LV3b
Vector Type: LV
Production System: Tri UC
Initial Name: fLV3_c
Chip Name: f


title: LV1a_a

description:
CD34+ Transduced sample a with vector LV1a
Vector Type: LV
Production System: Tri UC
Initial Name: aWTr.10
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #4 treated with LV


title: cell line_Control_24h_1

description: Gene expression after 24h in Control  treated Hela cell line


title: embryo 1_1 blastomere C

description: Hybridized to 250K_Nsp


title: LV2_c

description:
CD34+ Transduced sample c with vector LV2
Vector Type: LV
Production System: Quadri UC
Initial Name: b2UC.18
Chip Name: ab


title: LV1a_b

description:
CD34+ Transduced sample b with vector LV1a
Vector Type: LV
Production System: Tri UC
Initial Name: aWTr.11
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #5 treated with LV


title: cell line_Control_24h_3


title: cell line_Control_24h_2


title: cell line_Control_12h_1


title: cell line_CDDP_12h_3

description: Gene expression after 12h in CDDP treated Hela cell line


title: dINT1b_a

description:
CD34+ Transduced sample a with vector dINT1b
Vector Type: dINT
Production System: Tri UC
Initial Name: cINT1a
Chip Name: c


title: cell line_CDDP_24h_3

description: Gene expression after 24h in CDDP treated Hela cell line


title: cell line_CDDP_24h_2


title: cell line_RuT7_12h_2


title: comp6_ANT-comp6_AL

city: Bochum

first: Henrik

last: Rudolf

address: Universitätsstr. 150

department: Medical computer science, Biometry and Epidemiology

country: Germany

institute: Ruhr-Universität Bochum

hyb_protocol: We hybridized 3 µg of each labeled RNA on a single microarray slide.

scan_protocol: Slides were scanned (Axon 4000B Scanner), and raw hybridization signals were extracted (GenePix Pro 6.0 software, Agilent Technologies).

data_processing: Quantile normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. R-software package Limma was used.

organism: Apis mellifera

label_protocol: A total of 1 µg of RNA was amplified and labeled with mono-reactive cy3 and cy5 fluorophore dyes (Amersham, GE Healthcare), following the protocol of the supplier (MessageAmp II aRNA Amplification kit, Ambion).

extract_protocol: Total RNA was isolated from individual brains (including the suboesophal ganglion and the optical lobes, excluding the retina) using a standard Trizol protocol with subsequent purification by filter columns (Qiagen, Germany) and column removal of DNA by DNAse digestion.

tag: tissue

value: Antennae (ANT)

value: antennal lobe (AL)


title: AR42J cells, +dexamethasone rep1

description:
Gene expression from dexamethasone-induced AR42J cells
Dex1-230


title: embryo 1_1 blastomere A

description: Hybridized to 250K_Nsp


title: comp6_AL-comp6_MB

value: mushroom body (MB)


title: dGEN2_b

description:
CD34+ Transduced sample b with vector dGEN2
Vector Type: dGEN
Production System: Tri UC
Initial Name: cADN2b
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #11 treated with dGEN


title: cell line_CDDP_24h_1


title: dGEN2_c

description:
CD34+ Transduced sample c with vector dGEN2
Vector Type: dGEN
Production System: Tri UC
Initial Name: cADN2c
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #12 treated with dGEN


title: comp6_MB-comp6_ANT


title: dGEN2_a

description:
CD34+ Transduced sample a with vector dGEN2
Vector Type: dGEN
Production System: Tri UC
Initial Name: cADN2a
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #10 treated with dGEN


title: embryo 1_1 blastomere B

description: Hybridized to 250K_Nsp


title: comp5_MB-comp5_AL


title: comp5_ANT-comp5_MB


title: comp5_MB-comp4_MB


title: cell line_CDDP_12h_1


title: comp6_MB-comp5_MB


title: dINT1a_b

description:
CD34+ Transduced sample b with vector dINT1a
Vector Type: dINT
Production System: Tri UC
Initial Name: aWTin.14
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #5 treated with dINT


title: comp3_AL-comp6_AL


title: comp6_AL-comp5_AL


title: dGEN1b_c

description:
CD34+ Transduced sample c with vector dGEN1b
Vector Type: dGEN
Production System: Tri UC
Initial Name: cADN1c
Chip Name: c


title: dGEN1b_a

description:
CD34+ Transduced sample a with vector dGEN1b
Vector Type: dGEN
Production System: Tri UC
Initial Name: cADN1a
Chip Name: c


title: dINT1a_a

description:
CD34+ Transduced sample a with vector dINT1a
Vector Type: dINT
Production System: Tri UC
Initial Name: aWTin.13
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #4 treated with dINT


title: embryo 1_1 blastomere D

description: Hybridized to 250K_Nsp


title: dGEN1b_b

description:
CD34+ Transduced sample b with vector dGEN1b
Vector Type: dGEN
Production System: Tri UC
Initial Name: cADN1b
Chip Name: c


title: comp5_AL-comp4_AL


title: dGEN1a_b

description:
CD34+ Transduced sample b with vector dGEN1a
Vector Type: dGEN
Production System: Tri UC
Initial Name: aADN.8
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #5 treated with dGEN


title: comp3_MB-comp6_MB


title: comp5_AL-comp5_ANT


title: comp5_ANT-comp4_ANT


title: dENV3_c

description:
CD34+ Transduced sample c with vector dENV3
Vector Type: dENV
Production System: Quadri UC
Initial Name: fENV3_c
Chip Name: f

source_name: CD34+ purified cells from mobilized peripheral blood cells #9 treated with dENV


title: comp4_ANT-comp3_ANT


title: comp6_ANT-comp5_ANT


title: dGEN1a_a

description:
CD34+ Transduced sample a with vector dGEN1a
Vector Type: dGEN
Production System: Tri UC
Initial Name: aADN.7
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #4 treated with dGEN


title: comp3_ANT-comp2_ANT


title: dENV2_c

description:
CD34+ Transduced sample c with vector dENV2
Vector Type: dENV
Production System: Quadri UC
Initial Name: fENV2_c
Chip Name: f


title: comp1_ANT-comp6_ANT


title: dENV3_a

description:
CD34+ Transduced sample a with vector dENV3
Vector Type: dENV
Production System: Quadri UC
Initial Name: fENV3_a
Chip Name: f

source_name: CD34+ purified cells from mobilized peripheral blood cells #7 treated with dENV


title: dENV1b_c

description:
CD34+ Transduced sample c with vector dENV1
Vector Type: dENV
Production System: Tri UC
Initial Name: cENVc
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #12 treated with dENV


title: comp2_ANT-comp1_ANT


title: comp4_AL-comp3_AL


title: comp4_MB-comp3_MB


title: comp2_MB-comp1_MB


title: dENV2_b

description:
CD34+ Transduced sample b with vector dENV2
Vector Type: dENV
Production System: Quadri UC
Initial Name: fENV2_b
Chip Name: f

source_name: CD34+ purified cells from mobilized peripheral blood cells #8 treated with dENV


title: comp3_MB-comp2_MB


title: dENV1b_b

description:
CD34+ Transduced sample b with vector dENV1
Vector Type: dENV
Production System: Tri UC
Initial Name: cENVb
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #11 treated with dENV


title: dENV1b_a

description:
CD34+ Transduced sample a with vector dENV1
Vector Type: dENV
Production System: Tri UC
Initial Name: cENVa
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #10 treated with dENV


title: dINT1a_c

description:
CD34+ Transduced sample c with vector dINT1a
Vector Type: dINT
Production System: Tri UC
Initial Name: aWTin.15
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #6 treated with dINT


title: Transgenic fish 7, brain

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

institute: Nofima AS

hyb_protocol: Following One-Color Microarray-Based Gene Expression Analysis protocol Version 6.6 (Agilent p/n G4140-90040), 1650 ng of labeled cRNA was hybridized with the Zeno Custom Gene Expression Microarray

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565C) according to the manufacturer’s protocol Metric Set GE1_QCMT_ Oct12.

data_processing: Data were extracted using Agilent Feature Extraction Software 11.5.1.1 following the Agilent protocol GE1_1050_Oct12, grid template 044138_D_F_20121017 and the QC

organism: Danio rerio

source_name: Brain of transgenic fish

label_protocol: 150 ng of total RNA were used to produce Cyanine 3-CTP-labeled cRNA using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305) according to the manufacturer’s instructions.

growth_protocol: Twenty ASIP1 (5 males + 5 females) and wildtype (5 males + 5 females) zebrafish were placed in 6-liter tanks and acclimated during 30 days prior to sampling to minimize physiological differences.

extract_protocol: RNA was extracted with Tri-Reargent (Sigma) following manufacturer protocol and treated with DNAse (Promega). Subsequently, RNA total were quantified by spectrometry (NanoDrop ND1000) and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies) assay

treatment_protocol: The sampling day, animals were sacrificed and the brain + pituitary dissected under the stereo microscope, placed in trizol and stored at -80C until RNA extraction.

value: brain

value: transgenic


title: Transgenic fish 7, skin

source_name: Skin of transgenic fish

value: skin


title: dENV1a_c

description:
CD34+ Transduced sample c with vector dENV1
Vector Type: dENV
Production System: Tri UC
Initial Name: aEnv.18
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #6 treated with dENV