title: Blood_BKV_1

description:
173V0Pax
Gene expression data from BKV viremia blood sample


title: non tumoral sample 160

status: Public on May 23 2013

type: RNA

city: Nantes

first: Boris

last: HALGAND

address: 1, rue Gaston Veil

country: France

institute: INSERM

description:
NT_160_10296_1_4
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_1_4.txt

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanner Agilent G2565CA Feature extraction 10.7

data_processing: Feature extraction 10.7 with protocol GE_107_sep09 and grid 039494_G2_D_F_20120628. Both positive and negative control probes were excluded from data normalization and data was filtered by the average of the median of the samples (79.1490322580645).  The features which at least 50% of the samples have values above the cut were included (resulting in 28,782 data rows in the sample data table).

molecule: total RNA

organism: Homo sapiens

source_name: sample of human liver from resection and transplantation

label_protocol: labelling protocol  was agilent protocol 'G4140-90050_GeneExpression_Two_Color_v6.5-mai 2010' and the labelling was pseudo mono color (1/2 of the sample with Cy3 and 1/2 of the sample with Cy5)

extract_protocol:
liver from human biospies and transplantation
Total RNA was extracted using Mirvana extraction kit following manufacturer protocol

tag: patient id

tag: tissue

value: liver

tag: tissue subtype

value: non tumoral


title: non tumoral sample 216

description:
NT_216_10295_2_4
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_2_4.txt


title: Surviving HIV- case replicate 2

city: Liverpool

first: Benard

last: Kulohoma

address: Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital

country: United Kingdom

institute: University of Liverpool

description: Gene expression data from a surviving HIV- case with invasive pneumococcal disease.

hyb_protocol: Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM  Hybridization Oven 640 (Affymetrix, High Wycombe, UK).  Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).

scan_protocol: GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).

data_processing: The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.

label: biotin

source_name: Surviving HIV- case replicate 2

label_protocol: RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines.  The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).

growth_protocol: Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.

extract_protocol: Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK),  according to the manufacturer's instructions.

treatment_protocol: Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.

value: Host peripheral blood

tag: hiv status

value: HIV-

tag: disease outcome

value: Alive

tag: disease state


title: non tumoral sample 200

description:
NT_200_10295_2_3
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_2_3.txt


title: Surviving HIV- case replicate 1

source_name: Surviving HIV- case replicate 1

value: HIV- case with invasive pneumococcal disease


title: non tumoral sample 164

description:
NT_164_10295_2_1
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_2_1.txt


title: non tumoral sample 170

description:
NT_170_10295_2_2
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_2_2.txt


title: Deceased HIV- case replicate 2

description: Gene expression data from a deceased HIV- case with invasive pneumococcal disease.

source_name: Deceased HIV- case replicate 2

value: Dead


title: non tumoral sample 186

description:
NT_186_10296_1_1
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_1_1.txt


title: Deceased HIV- case replicate 1

source_name: Deceased HIV- case replicate 1


title: Healthy control replicate 2

description: Gene expression data from a healthy control without invasive pneumococcal disease.

source_name: Healthy control replicate 2


title: Surviving HIV+ case replicate 3

description: Gene expression data from a surviving HIV+ case with invasive pneumococcal disease.

source_name: Surviving HIV+ case replicate 3

value: HIV+


title: non tumoral sample 178

description:
NT_178_10296_2_2
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_2_2.txt


title: Healthy control replicate 1

source_name: Healthy control replicate 1

value: healthy control without invasive pneumococcal disease


title: Surviving HIV+ case replicate 2

source_name: Surviving HIV+ case replicate 2

value: HIV+ case with invasive pneumococcal disease


title: Deceased HIV+ case replicate 3

description: Gene expression data from a deceased HIV+ case with invasive pneumococcal disease.

source_name: Deceased HIV+ case replicate 3


title: Deceased HIV+ case replicate 2

source_name: Deceased HIV+ case replicate 2


title: Surviving HIV+ case replicate 1

source_name: Surviving HIV+ case replicate 1


title: non tumoral sample 140

description:
NT_140_10296_1_2
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_1_2.txt


title: Surviving HIV- case replicate 3

source_name: Surviving HIV- case replicate 3


title: Deceased HIV- case replicate 3

source_name: Deceased HIV- case replicate 3


title: Healthy control replicate 3

source_name: Healthy control replicate 3


title: non tumoral sample 68

description:
NT_68_10295_1_1
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_1_1.txt


title: tumoral sample 91

description:
T_91_10295_1_4
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_1_4.txt

value: tumoral


title: non tumoral sample 100

description:
NT_100_10294_2_1
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_2_1.txt


title: non tumoral sample 134

description:
NT_134_10294_2_2
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_2_2.txt


title: non tumoral sample 76

description:
NT_76_10295_1_3
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_1_3.txt


title: non tumoral sample 36 rep

description:
NT_36_10294_1_1
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_1_1.txt


title: non tumoral sample 80

description:
NT_80_10294_1_4
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_1_4.txt


title: non tumoral sample 190

description:
NT_190_10293_2_1
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_2_1.txt


title: non tumoral sample 222

description:
NT_222_10293_2_3
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_2_3.txt


title: Deceased HIV+ case replicate 1

source_name: Deceased HIV+ case replicate 1


title: non tumoral sample 42

description:
NT_42_10293_1_1
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_1_1.txt


title: non tumoral sample 130

description:
NT_130_10268_1_4
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_1_4.txt


title: non tumoral sample 196

description:
NT_196_10291_2_4
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_2_4.txt


title: non tumoral sample 208

description:
NT_208_10268_2_4
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_2_4.txt


title: Freeze-4

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

country: USA

institute: Uniformed Services University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25510.gif

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Vibrio cholerae

source_name: 2.0 ug starting cDNA

label_protocol: not provided

extract_protocol: not provided

tag: strain

source_name: 2.0 ug slowly frozen cDNA

tag: treatment

value: slowly frozen


title: non tumoral sample 48

description:
NT_48_10268_1_1
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_1_1.txt

source_name: sample of human liver from resection and transplantation


title: non tumoral sample 204

description:
NT_204_10268_2_3
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_2_3.txt


title: non tumoral sample 58

description:
NT_58_10291_1_3
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_1_3.txt


title: non tumoral sample 212

description:
NT_212_10292_2_3
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_2_3.txt


title: Freeze-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25507.gif


title: non tumoral sample 36

description:
NT_36_10267_2_2
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_2_2.txt


title: non tumoral sample 162

description:
NT_162_10296_2_4
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_2_4.txt


title: Exponential-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24209.gif

source_name: 2.0 ug Nadia exponential cDNA(exponentially growing 92A1552 V. cholerae strain)

source_name: 2.0 ug O1 Inaba exponential cDNA

tag: media

value: lab culture (exponential)


title: Stationary-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24212.gif

source_name: 2.0 ug O1 Inaba stationary cDNA

value: lab culture (stationary)


title: non tumoral sample 144

description:
NT_144_10268_2_2
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_2_2.txt


title: non tumoral sample 114

description:
NT_114_10268_1_3
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_1_3.txt


title: Freeze-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25508.gif


title: Stationary-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24059.gif


title: Exponential-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24058.gif


title: non tumoral sample 84

description:
NT_84_10267_1_1
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_1_1.txt


title: non tumoral sample 150

description:
NT_150_10293_1_3
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_1_3.txt


title: Stationary-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24060.gif


title: non tumoral sample 94

description:
NT_94_10267_2_1
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_2_1.txt


title: Vaccine Trial N16961-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24052.gif

value: stool


title: Freeze-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25509.gif


title: non tumoral sample 52

description:
NT_52_10267_1_4
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_1_4.txt


title: Stationary-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24211.gif

value: lab culture  (stationary)


title: ICDDR,B O139 A-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24208.gif

source_name: 2.0 ug O139 cDNA


title: ICDDR,B O139 A-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24207.gif

value: stool (stationary)


title: Vaccine Trial N16961-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24051.gif


title: untreated

city: Liverpoo

first: Kehinde

last: Ross

address: Byrom Street

department: Pharmacy and Biomolecular Sciences

institute: Liverpool John Moores University

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their SDS software, version 2.3.
The software performs threshold setting, delta Ct, delta delta Ct and RQ calculations automatically
Target microRNA signals normalized to the average small nucleolar RNA RNU44 (SNORD44) signals on each array
Matrix delta Ct reports the signal from target microRNA normalized to small nucleolar RNA RNU44; Ct_Target-Ct_RNU44
Matrix delta delta Ct reports the normalized signal from target microRNA in treated samples against the normalized signal in untreated samples = deltadeltaCt = deltaCt_treated delta deltaCt_untreated
Matrix RQ and Fold change reports the relative quantification (2^-deltadeltaCt) and the log thereof, respectively

label: TaqMan

source_name: Primary keratinocytes

label_protocol: TaqMan Low Density Array Human MicroRNA Panel v1.0

growth_protocol: Reconstituted  human epidermis purchased from Mattek; primary keratinocytes cultured in EpiLife (Invitrogen) and used at passage 4

extract_protocol: miRVana total RNA extraction (Ambion) including enrichment for small RNA

tag: agent

value: untreated

tag: dose

tag: time


title: IL-22

description: Test

source_name: Reconstituted human epidermis

value: 50 ng/ml


title: starved

description: Test

value: starved

value: culture medium (EpiLife) with no growth factors


title: LPS

description: Test

value: LPS

value: 1 microgram/ml

value: 8 h


title: Exponential-4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24210.gif


title: UV

description: Test

value: UV

value: 8 suberthymal doses

value: 24 h post-irradiation


title: non tumoral sample 82

description:
NT_82_10296_2_2
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_2_2.txt

value: liver

value: non tumoral


title: chalcone

description: Test

value: chalcone

value: 1 micromolar


title: non tumoral sample 198

description:
NT_198_10295_2_4
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_2_4.txt


title: non tumoral sample 142

description:
NT_142_10295_2_3
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_2_3.txt


title: non tumoral sample 50

description:
NT_50_10295_1_4
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_1_4.txt


title: non tumoral sample 166

description:
NT_166_10294_2_3
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_2_3.txt


title: non tumoral sample 44

description:
NT_44_10294_2_4
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_2_4.txt


title: Exponential-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24057.gif

value: lab culture (exponential)


title: non tumoral sample 40

description:
NT_40_10296_2_1
raw data file: US82400123_253949410296_S01_GE2_107_Sep09_2_1.txt


title: tumoral sample 163

description:
T_163_10294_2_2
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_2_2.txt

value: tumoral


title: respiration deficient pool-yeast extract and peptone with ethanol and copper sulfate-biological rep 3

type: genomic

city: Palo Alto

first: Ulrich

last: Schlecht

address: 3165 Porter Drive

department: Biochemistry

institute: Stanford University

description:
RD.Cu.9G.3
Respiration deficient deletion pool-9 generations yeast extract and peptone with ethanol and 500 uM copper sulfate-replicate 3

hyb_protocol: PCR reactions of up- and down-tags were mixed in equal volumes (30 ul each) and hybridized overnight to custom-built TAG4 microarrays (Affymetrix).

scan_protocol: After hybridization, arrays were stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix).

data_processing: The majority of strains carry two tags that hybridize to the array, an “uptag” and a “downtag”. From each array, we extracted the fluorescence intensity values for every uptag and downtag associated with the 5050 strains in the complete homozygous deletion pool, or in the case of the respiration-deficient deletion pool, the up- and downtags associated with the 331 strains in that pool. In total, this amounted to 9937, and 675 tags, respectively. The number of tags is not exactly twice the number of strains because some strains contain only one tag. These raw fluorescence values were then log2-transformed, and quantile-normalized using the normalize.quantiles function of the preprocessCore package in R. Quantile normalization was performed on four separate groups of tags; uptags from the complete deletion pool samples, downtags from the complete deletion pool samples, uptags from the respiration deficient deletion pool samples, and downtags from the respiration deficient deletion pool samples.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: The strain-specific barcodes contained in the DNA were amplified by PCR using a set of biotinylated primers.

growth_protocol: Growth in yeast extract and peptone (YP) media supplemented with 2% of either glucose, ethanol, glycerol, or lactate at 30°C with vigorouse shaking. Measurements of optical density at 595 nm (OD595) to monitor growth every 15 min. Samples were harvested after precisely 9 pool generations.

extract_protocol: Genomic DNA was extracted from cell pellets using the YeaStar Genomic DNA kit from Zymo Research (D2002).

treatment_protocol: 500 uM copper sulfate were incorporated into growth media in the treatment samples, 3 biological replicates each, for 9 generations of growth.

tag: pool

value: homozygous gene deletion collection

tag: growth stage

value: 9 generations


title: non tumoral sample 70

description:
NT_70_10295_2_2
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_2_2.txt


title: Intestinal non-EGFP cells rep2

city: Durham

first: Rashmi

last: Chandra

state: NC

address: Research Drive

department: Medicine/GI

institute: Duke University Medical Center

description: enteroendocrine

hyb_protocol: Affymetrix hybridization protocol (year 2008)

scan_protocol: Affymetrix scanning protocol (year 2008)

data_processing: GeneSpring GX (2008) was used to RMA normalized the data and perform analysis

organism: Mus musculus

source_name: adult SW_intestinal non-EGFP cells

label_protocol: Nugen WT-oviation Pico RNA amplification kit (2008) was used to label the picogram levels of total RNA from the samples.

extract_protocol: Qiagen Micro RNA kit

treatment_protocol: Intestinal cells were dissociated with enzymes and FACS purified

tag: strain background

value: Swiss Webster (SW)

tag: genotype/variation

value: CCK-EGFP transgenic

tag: age

value: adult

value: intestine

tag: cell type

value: non-EGFP intestinal cells (GFP negative)


title: non tumoral sample 188

description:
NT_188_10295_1_2
raw data file: US82400123_253949410295_S01_GE2_107_Sep09_1_2.txt

tag: patient id

tag: tissue


title: Izmir-3 tumor sample

city: Ankara

first: Mehmet

last: Ozturk

address: Faculty of Science Building

department: BilGen Genetics and Biotechnology Research Center

country: Turkey

institute: Bilkent University

description: Gene expression data from 65 years old age male HCC tissue

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.

source_name: Izmir HCC tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.

extract_protocol: Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.

treatment_protocol: Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.

value: Liver

tag: genotype

value: HBV positive

value: Male 66


title: Intestinal CCK-EGFP cells rep3

description: enteroendocrine

source_name: adult SW_intestinal CCK-EGFP cells

value: FACS-sorted CCK-EGFP intestinal cells


title: Ankara-1 tumor sample

description: Gene expression data from 45 years old age male HCC tissue

source_name: Ankara HCC tissue

value: Male 45


title: Izmir-4 cirrhosis sample

description: Gene expression data from 52 years old age female cirrhosis tissue

source_name: Izmir cirrhosis tissue

value: HCV positive

value: Female 52


title: non tumoral sample 32 rep

description:
NT_32_10294_1_1
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_1_1.txt

value: liver

tag: tissue subtype

value: non tumoral


title: non tumoral sample 116

description:
NT_116_10294_1_4
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_1_4.txt


title: Intestinal non-EGFP cells rep3

description: enteroendocrine


title: Izmir-4 tumor sample

description: Gene expression data from 52 years old age female HCC tissue


title: Izmir-8 cirrhosis sample

description: Gene expression data from 48 years old age female cirrhosis tissue

value: Female 48


title: Ankara-1 cirrhosis sample

description: Gene expression data from 45 years old age male cirrhosis tissue

source_name: Ankara cirrhosis tissue


title: non tumoral sample 156

description:
NT_156_10294_1_2
raw data file: US82400123_253949410294_S01_GE2_107_Sep09_1_2.txt


title: Intestinal non-EGFP cells rep1

description: enteroendocrine


title: Intestinal CCK-EGFP cells rep2

description: enteroendocrine


title: Ankara-7 tumor sample

description: Gene expression data from 69 years old age male HCC tissue

value: Male 69


title: respiration deficient pool-yeast extract and peptone with ethanol and copper sulfate-biological rep 2

description:
RD.Cu.9G.2
Respiration deficient deletion pool-9 generations yeast extract and peptone with ethanol and 500 uM copper sulfate-replicate 2

value: homozygous gene deletion collection

value: 9 generations


title: Izmir-5 cirrhosis sample

description: Gene expression data from male patient cirrhosis tissue

value: Male


title: respiration deficient pool-yeast extract and peptone with ethanol-biological rep 2

description:
RD.9G.2
Respiration deficient deletion pool-9 generations yeast extract and peptone with ethanol-replicate 2

value: yeast extract and peptone with ethanol


title: Intestinal CCK-EGFP cells rep1

description: enteroendocrine

value: Swiss Webster (SW)

value: CCK-EGFP transgenic

value: adult

value: intestine


title: respiration deficient pool-yeast extract and peptone with ethanol-biological rep 1

description:
RD.9G.1
Respiration deficient deletion pool-9 generations yeast extract and peptone with ethanol-replicate 1


title: Ankara-5 tumor sample

description: Gene expression data from male patient HCC tissue

value: Liver


title: Izmir-9 cirrhosis sample

description: Gene expression data from 52 years old age male cirrhosis tissue

value: HBV positive

value: Male 52


title: respiration deficient pool-yeast extract and peptone with ethanol-biological rep 3

description:
RD.9G.3
Respiration deficient deletion pool-9 generations yeast extract and peptone with ethanol-replicate 3


title: respiration deficient pool-yeast extract and peptone with ethanol and copper sulfate-biological rep 1

description:
RD.Cu.9G.1
Respiration deficient deletion pool-9 generations yeast extract and peptone with ethanol and 500 uM copper sulfate-replicate 1


title: non tumoral sample 146

description:
NT_146_10293_2_2
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_2_2.txt


title: non tumoral sample 92

description:
NT_92_10293_2_3
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_2_3.txt


title: non tumoral sample 206

description:
NT_206_10293_1_2
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_1_2.txt


title: non tumoral sample 192

description:
NT_192_10293_1_4
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_1_4.txt


title: Izmir-10 cirrhosis sample

description: Gene expression data from 48 years old age male cirrhosis tissue

value: Male 48


title: Ankara-10 tumor sample

description: Gene expression data from 64 years old age male HCC tissue

value: Male 64


title: Izmir-11 cirrhosis sample

description: Gene expression data from 50 years old age male cirrhosis tissue

value: Male 50


title: blank_7

city: Groton

first: Thomas

middle: A

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

description: 2 week shRNA treatment

hyb_protocol: Five (5) ug of fragmented, biotin-labeled cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 Gene Chips for 18 hours, then washed/stained according to manufacturer's recommendations using the Affymetrix 450 fluidics station.

scan_protocol: Gene chips were scanned using an Affymetrix 3000 array scanner.

data_processing: R/Bioconductor was used to apply the Robust Multi-Array Average (RMA) methodology to generate expression values for the combined samples.

source_name: primary cortical neurons, naïve

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed.

tag: days in vitro

value: E16 embryonic cortex

value: naïve


title: non tumoral sample 210

description:
NT_210_10293_1_1
raw data file: US82400123_253949410293_S01_GE2_107_Sep09_1_1.txt

value: liver

value: non tumoral


title: blank_5

description: 2 week shRNA treatment

tag: strain


title: blank_6

description: 2 week shRNA treatment

tag: treatment


title: mef2a_4

description: 2 week shRNA treatment

source_name: primary cortical neurons, MEF2A shRNA

value: MEF2A shRNA


title: Izmir-7 cirrhosis sample

description: Gene expression data from 41 years old age male cirrhosis tissue

value: HBV+HDV positive

value: Male 41


title: complete pool-yeast extract and peptone with lactate and copper sulfate-biological rep 3

description:
YPL.Cu.9G.3
Homozygous deletion pool-9 generations yeast extract and peptone with lactate and 500 uM copper sulfate-replicate 3

value: homozygous gene deletion collection

value: 9 generations


title: Ankara-4 tumor sample

description: Gene expression data from 60 years old age male HCC tissue

value: Male 60


title: non tumoral sample 56

description:
NT_56_10292_2_4
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_2_4.txt


title: Ankara-9 tumor sample

description: Gene expression data from 62 years old age male HCC tissue

value: HCV positive

value: Male 62


title: complete pool-yeast extract and peptone with lactate and copper sulfate-biological rep 1

description:
YPL.Cu.9G.1
Homozygous deletion pool-9 generations yeast extract and peptone with lactate and 500 uM copper sulfate-replicate 1


title: mef2a_2

description: 2 week shRNA treatment


title: complete pool-yeast extract and peptone with lactate-biological rep 3

description:
YPL.9G.3
Homozygous deletion pool-9 generations yeast extract and peptone with lactate-replicate 3

value: yeast extract and peptone with lactate


title: complete pool-yeast extract and peptone with lactate and copper sulfate-biological rep 2

description:
YPL.Cu.9G.2
Homozygous deletion pool-9 generations yeast extract and peptone with lactate and 500 uM copper sulfate-replicate 2


title: med2d_3

description: 2 week shRNA treatment

source_name: primary cortical neurons, MEF2D shRNA

value: MEF2D shRNA


title: complete pool-yeast extract and peptone with lactate-biological rep 2

description:
YPL.9G.2
Homozygous deletion pool-9 generations yeast extract and peptone with lactate-replicate 2


title: mef2a_1

description: 2 week shRNA treatment


title: Ankara-4 cirrhosis sample

description: Gene expression data from 60 years old age male cirrhosis tissue

value: Liver

value: HBV positive


title: non tumoral sample 104

description:
NT_104_10292_2_2
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_2_2.txt


title: mef2a_3

description: 2 week shRNA treatment


title: complete pool-yeast extract and peptone with lactate-biological rep 1

description:
YPL.9G.1
Homozygous deletion pool-9 generations yeast extract and peptone with lactate-replicate 1


title: complete pool-yeast extract and peptone with glycerol and copper sulfate-biological rep 3

description:
YPG.Cu.9G.3
Homozygous deletion pool-9 generations yeast extract and peptone with glycerol and 500 uM copper sulfate-replicate 3


title: med2d_2

description: 2 week shRNA treatment


title: Izmir-6 cirrhosis sample

description: Gene expression data from 64 years old age male cirrhosis tissue

value: Male 64


title: complete pool-yeast extract and peptone with glycerol and copper sulfate-biological rep 2

description:
YPG.Cu.9G.2
Homozygous deletion pool-9 generations yeast extract and peptone with glycerol and 500 uM copper sulfate-replicate 2


title: non tumoral sample 136

description:
NT_136_10292_1_4
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_1_4.txt


title: Izmir-12 cirrhosis sample

description: Gene expression data from female patient cirrhosis tissue

value: Female


title: complete pool-yeast extract and peptone with glycerol and copper sulfate-biological rep 1

description:
YPG.Cu.9G.1
Homozygous deletion pool-9 generations yeast extract and peptone with glycerol and 500 uM copper sulfate-replicate 1


title: complete pool-yeast extract and peptone with glycerol-biological rep 3

description:
YPG.9G.3
Homozygous deletion pool-9 generations yeast extract and peptone with glycerol-replicate 3

value: yeast extract and peptone with glycerol


title: SHANK3_3

description: 2 week shRNA treatment

source_name: primary cortical neurons, SHANK3 shRNA

value: E16 embryonic cortex

value: SHANK3 shRNA


title: non tumoral sample 172

description:
NT_172_10292_1_2
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_1_2.txt

source_name: sample of human liver from resection and transplantation

value: liver

value: non tumoral


title: Izmir-2 cirrhosis sample

description: Gene expression data from 44 years old age female cirrhosis tissue

value: Female 44


title: non tumoral sample 132

description:
NT_132_10292_2_1
raw data file: US82400123_253949410292_S01_GE2_107_Sep09_2_1.txt


title: Izmir-11 tumor sample

description: Gene expression data from 59 years old age male HCC tissue

value: Male 59


title: complete pool-yeast extract and peptone with ethanol and copper sulfate-biological rep 3

description:
YPE.Cu.9G.3
Homozygous deletion pool-9 generations yeast extract and peptone with ethanol and 500 uM copper sulfate-replicate 3

value: homozygous gene deletion collection

value: 9 generations


title: complete pool-yeast extract and peptone with glycerol-biological rep 2

description:
YPG.9G.2
Homozygous deletion pool-9 generations yeast extract and peptone with glycerol-replicate 2


title: SHANK3_1

description: 2 week shRNA treatment


title: med2d_1

description: 2 week shRNA treatment


title: non tumoral sample 78

description:
NT_78_10291_2_3
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_2_3.txt


title: PTEN_3

description: 2 week shRNA treatment

source_name: primary cortical neurons, PTEN shRNA

value: PTEN shRNA


title: Ankara-2 tumor sample

description: Gene expression data from 52 years old age male HCC tissue

value: Male 52


title: Ankara-11 tumor samle

description: Gene expression data from male patient HCC tissue

value: Male


title: PTEN_1

description: 2 week shRNA treatment


title: PTEN_4

description: 2 week shRNA treatment


title: Ankara-2 cirrhosis sample

description: Gene expression data from 52 years old age male cirrhosis tissue


title: PTEN_2

description: 2 week shRNA treatment


title: SHANK3_2

description: 2 week shRNA treatment


title: NLGN3_4

description: 2 week shRNA treatment

source_name: primary cortical neurons, NLGN3 shRNA

value: NLGN3 shRNA


title: complete pool-yeast extract and peptone with glycerol-biological rep 1

description:
YPG.9G.1
Homozygous deletion pool-9 generations yeast extract and peptone with glycerol-replicate 1


title: Izmir-1 tumor sample

description: Gene expression data from 56 years old age male HCC tissue

value: Liver

value: Male 56


title: complete pool-yeast extract and peptone with ethanol and copper sulfate-biological rep 2

description:
YPE.Cu.9G.2
Homozygous deletion pool-9 generations yeast extract and peptone with ethanol and 500 uM copper sulfate-replicate 2


title: complete pool-yeast extract and peptone with ethanol and copper sulfate-biological rep 1

description:
YPE.Cu.9G.1
Homozygous deletion pool-9 generations yeast extract and peptone with ethanol and 500 uM copper sulfate-replicate 1


title: Izmir-1 cirrhosis sample

description: Gene expression data from 56 years old age male cirrhosis tissue

value: HBV positive


title: Ankara-3 tumor sample

description: Gene expression data from 62 years old age male HCC tissue

value: HCV positive

value: Male 62


title: non tumoral sample 184

description:
NT_184_10291_1_4
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_1_4.txt


title: NLGN3_2

description: 2 week shRNA treatment

value: E16 embryonic cortex


title: complete pool-yeast extract and peptone with ethanol-biological rep 3

description:
YPE.9G.3
Homozygous deletion pool-9 generations yeast extract and peptone with ethanol-replicate 3

value: yeast extract and peptone with ethanol


title: complete pool-yeast extract and peptone with ethanol-biological rep 2

description:
YPE.9G.2
Homozygous deletion pool-9 generations yeast extract and peptone with ethanol-replicate 2


title: NLGN3_3

description: 2 week shRNA treatment


title: non tumoral sample 218

description:
NT_218_10291_1_2
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_1_2.txt

value: liver


title: Izmir-10 tumor sample

description: Gene expression data from 49 years old age male HCC tissue

value: Male 49


title: NLGN3_1

description: 2 week shRNA treatment


title: complete pool-yeast extract and peptone with glucose and copper sulfate-biological rep 2

description:
YPD.Cu.9G.2
Homozygous deletion pool-9 generations yeast extract and peptone with glucose and 500 uM copper sulfate-replicate 2


title: complete pool-yeast extract and peptone with glucose and copper sulfate-biological rep 3

description:
YPD.Cu.9G.3
Homozygous deletion pool-9 generations yeast extract and peptone with glucose and 500 uM copper sulfate-replicate 3


title: NLGN1_4

description: 2 week shRNA treatment

source_name: primary cortical neurons, NLGN1 shRNA

value: NLGN1 shRNA


title: non tumoral sample 224

description:
NT_224_10291_1_1
raw data file: US82400123_253949410291_S01_GE2_107_Sep09_1_1.txt

value: non tumoral


title: complete pool-yeast extract and peptone with glucose and copper sulfate-biological rep 1

description:
YPD.Cu.9G.1
Homozygous deletion pool-9 generations yeast extract and peptone with glucose and 500 uM copper sulfate-replicate 1

value: homozygous gene deletion collection


title: complete pool-yeast extract and peptone with ethanol-biological rep 1

description:
YPE.9G.1
Homozygous deletion pool-9 generations yeast extract and peptone with ethanol-replicate 1

value: 9 generations


title: complete pool-yeast extract and peptone with glucose-biological rep 3

description:
YPD.9G.3
Homozygous deletion pool-9 generations yeast extract and peptone with glucose-replicate 3

value: yeast extract and peptone with glucose


title: non tumoral sample 202

description:
NT_202_10268_2_2
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_2_2.txt


title: Ankara-6 cirrhosis sample

description: Gene expression data from 50 years old age male cirrhosis tissue

value: Male 50


title: NLGN1_1

description: 2 week shRNA treatment


title: complete pool-yeast extract and peptone with glucose-biological rep 2

description:
YPD.9G.2
Homozygous deletion pool-9 generations yeast extract and peptone with glucose-replicate 2


title: C3 senescent clone, biological rep3

description: Gene expression data from senescent isogenic clones

source_name: senescent Huh7 clone with >50% SABG pos.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The isogenic clones were plated in 10 cm plates in DMEM medium containing 10% FCS, 1% Penicillin/Streptomycin and 1% non-essential aminoacid, and stored in incubator at 37 C, 5% CO2.

extract_protocol: The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.

treatment_protocol: The cells were washed with 1XPBS three times and, detacched from plate using tyripsine. They were pelletted by centrifuging at 4 degree at 5000 rpm for 5 minutes.

value: Liver cancer cell line isogenic clone

tag: gender

value: M

value: isogenic clone after PD>60


title: C3 senescent clone, biological rep2


title: MeCP2_3

description: 2 week shRNA treatment

source_name: primary cortical neurons, MeCP2 shRNA

value: MeCP2 shRNA


title: complete pool-yeast extract and peptone with glucose-biological rep 1

description:
YPD.9G.1
Homozygous deletion pool-9 generations yeast extract and peptone with glucose-replicate 1

tag: agent


title: C1 immortal clone, biological rep2

description: Gene expression data from immortal isogenic clones

source_name: immortal Huh7 clone after PD >150

value: isogenic clone after PD>150


title: C3 senescent clone, biological rep1


title: MeCP2_2

description: 2 week shRNA treatment


title: MeCP2_1

description: 2 week shRNA treatment


title: Ankara-6 tumor sample

description: Gene expression data from 50 years old age male HCC tissue

value: Liver

value: HBV positive


title: MeCP2_4

description: 2 week shRNA treatment

value: E16 embryonic cortex


title: non tumoral sample 96

description:
NT_96_10268_1_3
raw data file: US82400123_253949410268_S01_GE2_107_Sep09_1_3.txt


title: NLGN1_2

description: 2 week shRNA treatment


title: C1 immortal clone, biological rep3


title: G12 senescence clone, biological rep2


title: non tumoral sample 60

description:
NT_60_10267_2_1
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_2_1.txt


title: G11 immortal clone, biological rep1


title: lucif_4

description: 2 week shRNA treatment

source_name: primary cortical neurons, luciferase shRNA

value: luciferase shRNA


title: G12 senescence clone, biological rep1


title: C1 immortal clone, biological rep1


title: lucif_3

description: 2 week shRNA treatment


title: FMR1_4

description: 2 week shRNA treatment

source_name: primary cortical neurons, FMR1 shRNA

value: FMR1 shRNA


title: R. sphaeroides 2.4.1 -Fe vs. R. sphaeroides 2.4.1 replicate 2

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

description: biological sample 4-6

hyb_protocol: The RNA of three independent experiments of Rhodobacter sphaeroides 2.4.1 under iron limitation and normal (control) conditions were pooled and hybridized to one array. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: R with Limma package was used for data evaluation. LOWESS normalized and background subtracted.

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides 2.4.1 -Fe total cells

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation

growth_protocol: R. sphaeroides strains grown anaerobically in presence and absence of iron

extract_protocol: Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. For microarray analysis the RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.

treatment_protocol: R. sphaeroides was grown anaerobically without external iron but with the iron chelator 2,2’-dipyridyl (30 µM). Anaerobic growth was provided using dimethyl sulfoxide (DMSO) as electron acceptor at a final concentration of 60 mM.

tag: culture

value: anaerobic without iron

source_name: R. sphaeroides 2.4.1 total cells

value: anaerobic with iron


title: lucif_2

description: 2 week shRNA treatment


title: non tumoral sample 32

description:
NT_32_10267_2_2
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_2_2.txt

value: liver

value: non tumoral


title: G11 immortal clone, biological rep3


title: R. sphaeroides 2.4.1 -Fe vs. R. sphaeroides 2.4.1 replicate 1

description: biological sample 1-3


title: non tumoral sample 214

description:
NT_214_10267_1_4
raw data file: US82400123_253949410267_S01_GE2_107_Sep09_1_4.txt


title: G11 immortal clone, biological rep2


title: FMR1_3

description: 2 week shRNA treatment


title: G12 senescence clone, biological rep3


title: lucif_1

description: 2 week shRNA treatment


title: FMR1_2

description: 2 week shRNA treatment


title: T_D7006

status: Public on May 22 2013

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

hyb_protocol: All the steps of hybridization and washing were performed following the Agilent protocol for chip-on-chip analysis.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B.

data_processing: The value is background subtracted and log2-quantile normalized using the limma Bioconductor package.

source_name: T cell_meDIP_high_aggressivity

label_protocol: 2ug of each of the input and bound fractions were labeled for the microarray hybridization. Cy3-dUTP and Cy5-dUTP (Perkin Elmer) were used to label the input and the bound fractions respectively. Cot-1 DNA was added to the hybridization mix to minimize cross-hybridization between repetitive elements.

extract_protocol: 20 ml of blood were drawn in EDTA coated-tubes for each subjects. PBMC (whole mononuclear cells from peripheral blood) and T cell isolation procedures were adapted from Current Protocols in Immunology (1997, sections 7.1 and 7.5.1-7.5.11). Briefly, PBMC isolation was done by centrifugation with Ficoll-Paque (GE healthcare) and washed twice with HBSS (Hanks balanced salt solution, GIBCO). T cells were isolated from the PBMCs by immunomagnetic isolation using CD3 dynabeads (Dynal). The beads were washed 3 times and incubated with the PBMCs for 45 min on a rotator at 4C. Coated CD3+ cells with the dynabeads were isolated using a strong magnet (Steam Cell Technology) and washed 5 times with PBS/FBS. CD3+ cells coated with the dynabeads were then frozen at -80C until DNA extraction. To isolate monocyte cells, B cells were extracted away from the remaining PBMCs with CD9 dynabeads (Dynal) following the same procedure as for T cells isolation and then frozen at -80C until DNA extraction. Monocytes and T cells DNA was extracted with Wizard Genomic DNA Purification kit (Promega) following the manufacturer's protocol. For MeDIP analysis, 2 ug of each of the T cells and monocytes DNA were sonicated and methylated DNA was immunoprecipitated with 10 Âµg of anti-5methylCytosine (Calbiochem, Cat. # NA81, Lot: D00048001). Prior to sonication, two control plasmids were added to the DNA (6ug each), an unmethylated GFP plasmid and an in vitro methylated Luciferase plasmid. The DNA-antibody complex was immunoprecipitated with 5 mg protein A and the methylated DNA was eluted with 150 ul of TE at 1.5% SDS. The input and bound fractions were then purified and validated by PCR analysis for two control genes, H19 (methylated control) and Beta-actin (unmethylated control) and the two added plasmid, GFP (unmethylated control) and Luciferase (in vitro methylated control) using the following primers: H19: forward (5'-TTGGTGGAACACGCTGTGATCA-3'), reverse (5'-GAGCCGCACCAGGTCTTCAG-3'); Beta-actin: forward (5'-AGCCATAAAAGGCAACTTTCG-3'), reverse (5'-CCAACGCCAAAACTCTCCC-3'); GFP: forward (CCAACGCCAAAACTCTCCC), reverse (AGCCATAAAAGGCAACTTTCG); Luciferase: forward (5'-AGAGATACGCCCTGGTTCC-3'), reverse (5'-CCAACACCGGCATAAAGAA-3'). The input and bound fractions were then amplified in triplicate using the Whole Genome Amplification kit (Sigma). The amplified input and bound fractions were labeled for microarray hybridization with either Cy3-dUTP or Cy5-dUTP (Perkin Elmer) respectively using the CGH labeling kit (Invitrogen) following the manufacturer's instructions.

tag: race

value: Caucasian

tag: history of behaviour

value: high aggressivity

value: T cell

source_name: T cell_input_DNA_high_aggressivity


title: FMR1_1

description: 2 week shRNA treatment


title: T_D5705

source_name: T cell_meDIP_chronic_aggressivity

value: chronic aggressivity

source_name: T cell_input_DNA_chronic_aggressivity


title: T_D5011

source_name: T cell_meDIP_low_aggressivity

value: low aggressivity

source_name: T cell_input_DNA_low_aggressivity


title: T_D8214

source_name: T cell_meDIP_moderate_aggressivity

value: moderate aggressivity

source_name: T cell_input_DNA_moderate_aggressivity


title: T_D5020


title: T_501


title: CellStrain_siControl_24hEGF_rep1

city: Bunkyo-ku

first: Jun

last: Iwaki

state: Tokyo

address: 1-1-5 Sendagi

country: Japan

institute: Nippon Medical School

description: Gene expression of siControl transfectant after 24h exposed by EGF

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 55 μl containing 2.2 μl of 25x Agilent fragmentation buffer, 11 μl of 10x Agilent blocking agent and 41.8 μl Nuclease-free water following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Human GE 4×44 K, v2 Microarray (G4845) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: The slide was scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44 K array slides (Scan Area 61x21.6 mm, Scan resolution 5 μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20110325).

source_name: CellStrain, siControl, 24h, 24hEGF, replicate1

label_protocol: Two hundred ng of total RNA was used for labeling reaction using One-Color Microarray-Based Gene Expression Analysis: Low Input Quick Amp Labeling Kit, (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: HuCCT1 cells were cultured at 37 ºC with 5% CO2 in RPMI 1640 medium containing 10% heat-inactivated fetal bovine serum.

extract_protocol: Total RNA was extracted from each sample using RNAiso plus (Takara Bio, Ohtsu, Japan) according to the manufacturer’s instructions.

treatment_protocol: HuCCT1 cells were transfected with the pre-miR-376c or GRB2-siRNA (Qiagen, Valencia, CA, USA) at final concentrations of 30 nM using Lipofectamine 2000 (Invitrogen). Pre-miR-negative control and a nonspecific non-silencing siRNA (AllStars Negative Control siRNA, Qiagen) were used as negative controls. After 24 hours of transfection, the cells were treated in the medium containing RPMI 1640 supplemented with 0.1% fetal bovine serum and EGF (5 ng/ml, R&D Systems, Minneapolis, USA). The cells were harvested after 24 hours of EGF-treatment, and gene expression profiling of the cells were conducted using an Agilent microarray (Human GE 4×44 K, v2).

tag: cell line

tag: disease type

value: cholangiocarcinoma

tag: transfection

value: siControl

value: 24hr of EGF


title: T_D8417


title: T_6494


title: T_D4425


title: T_8703


title: T_7050


title: T_6993


title: CellStrain_mir-376c_24hEGF_rep1

description: Gene expression of mir-376c transfectant after 24h exposed by EGF

source_name: CellStrain, mir-376c, 24h, 24hEGF, replicate1


title: CellStrain_miControl_24hEGF_rep1

description: Gene expression of miControl transfectant after 24h exposed by EGF

source_name: CellStrain, miControl, 24h, 24hEGF, replicate1

value: miControl


title: T_733


title: PB_D8417

value: monocyte


title: ΔSTM2239p2239_ΔSTM2239pFLAG_3

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: third replicate

hyb_protocol: Labelled cDNAs were hybridized to S. Typhimurium 14028 high-density oligo arrays in formamide-containing hybridization buffer overnight at 42°C, following standard protocols (Roche Nimblegen).

scan_protocol: Arrays were scanned using the Axon GenePix 4000B scanner (Molecular Devices LLC; Sunnyvale, CA).

data_processing: Image analysis and feature extraction was performed with the Axon GenePix Pro software (Molecular Devices).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

label_protocol: Approximately 20 μg of total RNA was pre-incubated with 2.4 μg random hexamers (Life Technologies) at 70°C for 10 minutes, then placed on ice for 2 min. The RNA mix was then combined with the Superscript II mastermix which was composed of the following: 4 μL dye labeled 1 mM dCTP (Cy3/Cy5), 6 μL 0.1M DTT, 12 μL 1st Strand Buffer (Life Technologies),1.2 μL nucleotide mix (25 mM dATP, dTTP, dGTP / 10mM dCTP), 4 μL Superscript II reverse transcriptase (Life Technologies), 2 μL Rnasin (Roche), and 0.8 μL nuclease-free water. The reaction was incubated at 42oC for 1 h, followed by addition of 2 μL Superscript II and a second incubation at 42oC for 1 h. Exactly 3 μL of fresh 1 M NaOH was added. The suspension was then incubated at 70°C for 10 min, followed by reaction neutralization with 3 μL of 1 M HCl. The cDNA was purified using the Qiagen PCR Purification Kit according to manufacturer’s directions (Qiagen).

growth_protocol: Salmonella strains carrying either pFLAG-CTC (empty vector control) or pFLAG-STM2239 were grown in 10 mL LB ampicillin for 1.5 h at 37°C, 225 rpm to an OD600~0.1, then IPTG (1 mM) was added and the culture was incubated for 1.5 h to an OD600~0.5 to induce expression of STM2239.

extract_protocol: Exactly 1 mL of 95% ethanol/5% acidic phenol (pH 4.3) (v/v) solution (Sigma) was added per 5 mL of culture, and this mixture was incubated at 4°C for 20 min. Bacteria were isolated by centrifugation, then resuspended in 200 μL 10 mM Tris, pH 8.0 with lysozyme (1 mg/mL) and incubated for 10 min at 37C. RNA was isolated using the Roche High Pure RNA Isolation Kit (Roche) as per manufacturer’s instructions for bacterial RNA, including on-column DNase I treatment. Purified RNA was subjected to two additional rounds of DNase I treatment using the TURBO DNA-Free kit (Ambion).

value: ΔSTM2239, pFLAG (control)

value: ΔSTM2239, pFLAG-STM2239 (exp)


title: T_3321


title: T_3292


title: CellStrain_siGRB2_24hEGF_rep1

description: Gene expression of siGRB2 transfectant after 24h exposed by EGF

source_name: CellStrain, siGRB2, 24h, 24hEGF, replicate1


title: ΔSTM2239p2239_ΔSTM2239pFLAG_2

description: second replicate


title: T_5720

description: Replicate arrays combined during processing.


title: PB_D5705


title: PB_D3215


title: PB_D5011


title: PB_D7006


title: T_6251


title: PB_D8214


title: PB_D5020


title: PB_D4425


title: PB_8703


title: PB_8630


title: NLGN1_3

description: 2 week shRNA treatment

source_name: primary cortical neurons, NLGN1 shRNA

value: E16 embryonic cortex

value: NLGN1 shRNA


title: PB_5720


title: PB_6494


title: PB_6251


title: PB_7050


title: PB_501


title: TGFbeta rep1

city: Bangalore

first: Neeraj

last: KUMAR

address: Indian Institute of Science Bangalore

department: MRDG

country: India

institute: Indian Institute of Science Bangalore

hyb_protocol: 750 ng of labelled cRNA each from treated and untreated were mixed with blocking agent and fragmentation buffer followd by incubation at 65 °C for 30 min. This is followed by addition of 55 ul of 2x GEx Hybridization Buffer HI-RPM to stop the fragmentation reaction. Later 100 ul of the above mix were added to each array.

scan_protocol: standard Agilent protocol

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: HaCaT cells

label_protocol: 200 ng of RNA each from untreated and treated samples were used. Labeling of the probes was done using the Low RNA Input Linear Amplification Kit (Agilent Technologies, USA). Briefly 200 ng of RNA were reverse transcribed using T7promoter attached Oligo-dT primers at 40 °C for 2 hrs followed by 65 °C for 15 min. This cDNA were transcribed using T7 polymerase with respective labelled nucleotides at 40 °C for 2hrs. This synthesized labelled cRNA were purified using RNeasy mini column.

growth_protocol: human keratinocytes (HaCaT) were maintained in DMEM (Sigma-Aldrich, USA) supplemented with 10% fetal bovine serum (Certified grade, Invitrogen corporation, USA.  Heat inactivated for HaCaT cells), 100 units/mL penicillin and 100ug/mL streptomycin (Invitrogen Life Sciences, USA) at 37°C in a humidified chamber with 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: For treatments, HaCaT cells were serum starved for 24 hr and treated with 5 ug/ ml areca nut water extracts, 5ng/ml TGF-beta (R&D systems, USA) for 48. For treatment with ALK5 inhibitor (TbetaRI inhibitor, Sigma-Aldrich, SB 431542), cells were pre-treated with 10uM of SB 431542 for 2 hr prior to the addition of the respective factors

value: immortalized human keratinocytes

value: HaCaT

value: untreated

value: TGF-beta (5 ng/ml)


title: PB_3292

value: Caucasian

value: high aggressivity


title: PB_3321


title: 5H rep2

value: 5H (5 ug/ml areca nut water extract)


title: PB_733

value: chronic aggressivity


title: 5H+ALK5 inhibitor rep1

value: 5H (5 ug/ml areca nut water extract)+ALK5 inhibitor


title: ALK5 inhibitor rep2

value: ALK5 inhibitor


title: 5H+ALK5 inhibitor rep2


title: ALK5 inhibitor rep1


title: Total bone marrow ttt119

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430 v2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were RMA summarized and batch corrected with Partek Genomics Suite 6.6

label: Biotin

source_name: Total bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

extract_protocol: Total RNA was extracted from mouse tumors using Trizol reagent (Invitrogen) with two washes with 75% ethanol. RNA quality was confirmed by analysis on the Agilient 2100 Bioanalyzer.

value: total bone marrow

tag: th-mycn mouse genotype

value: deficient caspase-8


title: TGFbeta rep2

tag: cell type


title: Total bone marrow ttt120a


title: 5H rep1


title: C5

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: SAMPLE 12

data_processing:
Cycle threshold values were calculated using SDS 2.4 software with manual baseline (3-15) and threshold (0.2) settings. Undetected miRNAs (average Ct > 35 in either the recurrence or no recurrence groups) were removed from the analysis. Normalisation of the data was as follows: 1) the A plates and B plates were normalised to each other using the Ct values for U6 snRNA, which is amplified on both plates; 2) all data was then scaled to the spiked-in cel-miR-39 to correct for differences in extraction efficiency, 3) finally, the mean Ct value of all miRNAs with a Ct value < 30 for each array was determined and used to normalise the arrays.
Matrix normalized worksheet reports normalized signal (described above).
Fold Change worksheet reports recurrence/no recurrence ratios.

label: SYBR Green

source_name: Serum

label_protocol: PCR assays were performed using theTaqMan Array Human MicroRNA A+B Cards Set v2.0 (Applied Biosystems), as per the manufacturer’s instructions. We used 3ul of serum miRNA as input for the Megaplex reverse transcription (RT) reactions. After RT and pre-amplification, quantitative PCR was carried out on an Applied Biosystems 7900HT.

extract_protocol: Total RNA was extracted from serum essentially as described previously (Selth et al, Int J Cancer, 131, 652–661, 2012), with some minor modifications. Serum was centrifuged at 3,000g for 5 min at 4°C prior to extraction. A serum:Qiazol ratio of 1:5 was used to denature the samples. miRNAs were extracted from 500 ml serum spiked with 25 fmol synthetic cel-miR-39 (Integrated DNA Technologies) and eluted in 35 ml RNase-free water.

tag: group

value: No biochemical recurrence


title: C4

description: SAMPLE 11


title: C7

description: SAMPLE 14


title: primary abdominal NB tumor ttt116

source_name: primary abdominal NB tumor

tag: tissue

value: primary abdominal NB tumor


title: primary abdominal NB tumor ttt110

value: wild type caspase-8


title: C2

description: SAMPLE 9


title: primary abdominal NB tumor ttt117


title: primary abdominal NB tumor ttt111


title: Total bone marrow ttt118


title: Total bone marrow ttt114a


title: Total bone marrow ttt112


title: primary abdominal NB tumor ttt115


title: primary abdominal NB tumor ttt109a


title: R5

description: SAMPLE 5

value: Rapid biochemical recurrence


title: primary abdominal NB tumor ttt107


title: primary abdominal NB tumor ttt106


title: primary abdominal NB tumor ttt108


title: C8

description: SAMPLE 15


title: C1

description: SAMPLE 8


title: R3

description: SAMPLE 3


title: R4

description: SAMPLE 4


title: R2

description: SAMPLE 2


title: R6

description: SAMPLE 6


title: R7

description: SAMPLE 7


title: C3

description: SAMPLE 10


title: R1

description: SAMPLE 1


title: primary abdominal NB tumor ttt104


title: primary abdominal NB tumor ttt102


title: C6

description: SAMPLE 13


title: primary abdominal NB tumor ttt018


title: primary abdominal NB tumor ttt021


title: primary abdominal NB tumor ttt101


title: primary abdominal NB tumor ttt020


title: E.albidus_Ag-NPs 200_3

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

description: E.albidus gene expression exposed to 200 mg/Kg of silver nanoparticles (Ag-NPs).

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit . 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-030589 Custom Gene Expression Array for Enchytraeus albidus 8x15k, for 17 hours at 65°C in a rotating Agilent 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 dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies) using default parameters (protocol GE1_105_Dec08 and Grid: 030589_D_F_20101007) to obtain background subtracted and spatially detrended Processed Signal intensities. Processing of the data and statistical analysis were performed using BRB Array Tools version 4.2.1 Stable Release (http://linus.nci.nih.gov/BRB-ArrayTools.html). After background subtraction, the replicated spots within each array were averaged and the intensities were log2 transformed (spots with a value of intensity bellow 1 were excluded from the analysis).

organism: Enchytraeus albidus

source_name: E. albidus_Ag-NPs 200 mg/Kg_rep3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Isolation of total RNA from each replicate was performed through the Trizol extraction method (Invitrogen, Belgium). This RNA followed a DNAse treatment (Fermentas, Germany) and further purification steps consisting of phenol/chloroform extractions. The quantity and purity of the isolated RNA were measured spectrophotometrically with nanodrop (NanoDrop ND-1000 Spectrophotometer) and its integrity was checked on a denaturing formaldehyde agarose gel electrophoresis.

treatment_protocol: Ten adult worms with well developed clitellum were introduced in each test vessel, containing 25 g moist soil (control or spiked soil with silver nanoparticles_Ag-NPs or silver nitrate_AgNO3). The worms were exposed during 2 days at 20ºC and a 16:8h photoperiod. Three biological replicates per exposure condition (including controls) were performed. At test end, organisms of each replicate were carefully removed, rinsed in deionised water, stored in RNA later (Ambion, USA) containing criotubes and frozen in liquid Nitrogen. All the samples were stored at -80C till further analysis.

value: Whole body extracts

tag: developmental stage

value: Adult organisms with well developed clitellum


title: primary abdominal NB tumor ttt017


title: primary abdominal NB tumor ttt100


title: primary abdominal NB tumor ttt015


title: primary abdominal NB tumor ttt105


title: primary abdominal NB tumor ttt019


title: E.albidus_Ag-NPs 200_2

source_name: E. albidus_Ag-NPs 200 mg/Kg_rep2


title: E.albidus_Ag-NPs 100_3

description: E.albidus gene expression exposed to 100 mg/Kg of silver nanoparticles (Ag-NPs).

source_name: E. albidus_Ag-NPs 100 mg/Kg_rep3


title: primary abdominal NB tumor ttt016


title: E.albidus_Ag-NPs 100_1

source_name: E. albidus_Ag-NPs 100 mg/Kg_rep1


title: E.albidus_Ag-NPs 200_1

source_name: E. albidus_Ag-NPs 200 mg/Kg_rep1


title: primary abdominal NB tumor ttt013


title: E.albidus_AgNO3 100_3

description: E.albidus gene expression exposed to 100 mg/Kg of silver nitrate (AgNO3).

source_name: E. albidus_AgNO3 100 mg/Kg_rep3


title: E.albidus_Ag-NPs 100_2

source_name: E. albidus_Ag-NPs 100 mg/Kg_rep2


title: E.albidus_AgNO3 200_2

description: E.albidus gene expression exposed to 200 mg/Kg of silver nitrate (AgNO3).

source_name: E. albidus_AgNO3 200 mg/Kg_rep2


title: ΔSTM2239p2239_ΔSTM2239pFLAG_1

description: first replicate

tag: genotype

value: ΔSTM2239, pFLAG-STM2239 (exp)

value: ΔSTM2239, pFLAG (control)


title: primary abdominal NB tumor ttt010


title: primary abdominal NB tumor ttt012


title: E.albidus_AgNO3 200_1

source_name: E. albidus_AgNO3 200 mg/Kg_rep1


title: Hepatocellular carcinoma 488T

city: San Diego

first: Kai

last: Wang

address: 10646 Science Center Dr

department: Oncology Research

description: Genomic DNA was genotyped using Illumina HumanOmni1-Quad BeadChip.

hyb_protocol: Samples were processed according to the manufacturers’ instructions (Illumina).

data_processing: Genomic DNA was genotyped using Infinium HD HumanOmni1-Quad Genotyping BeadChips (Illumina). Genotype: AA, AB, BB, or NC (no call)

label: C-Bio and A-DNP

extract_protocol: Extraction of genomic DNA was performed the QIAamp DNA mini kit.

value: Male

value: Liver

tag: disease state

value: Hepatocellular carcinoma


title: Non-tumor adjacent tissue 489N

scan_protocol: Samples were processed according to the manufacturers’ instructions (Illumina).

value: Non-tumor adjacent tissue


title: E.albidus_AgNO3 100_2

source_name: E. albidus_AgNO3 100 mg/Kg_rep2


title: E.albidus_AgNO3 100_1

source_name: E. albidus_AgNO3 100 mg/Kg_rep1


title: Non-tumor adjacent tissue 488N

label_protocol: Samples were processed according to the manufacturers’ instructions (Illumina).


title: E.albidus_AgNO3 200_3

source_name: E. albidus_AgNO3 200 mg/Kg_rep3


title: E.albidus_CT_3

description: E.albidus gene expression under control conditions

source_name: E. albidus_control_rep3


title: Hepatocellular carcinoma 487T


title: E.albidus_CT_2

source_name: E. albidus_control_rep2


title: Hepatocellular carcinoma 489T


title: Non-tumor adjacent tissue 485N


title: Hepatocellular carcinoma 485T


title: E.albidus_CT_1

source_name: E. albidus_control_rep1


title: Hepatocellular carcinoma 482T


title: Non-tumor adjacent tissue 487N


title: Non-tumor adjacent tissue 482N


title: Hepatocellular carcinoma 481T


title: donor4 stimulated + inhibited

city: Wuerzburg

first: Susanne

last: Kneitz

address: Am Hubland, Biocenter

department: Physiological Chemistry I

institute: University of Wuerzburg

description: Human peripheral blood mononuclear cells, stimulated and inhibited

hyb_protocol: hybridization according to the standard Affymetrix protocol on GeneChip Human Exon 1.0 ST  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were summarized using the Expression console software (Affymetrix) (method=plier) and quantile-quantile as normalization method

label_protocol: labeling according to the standard Affymetrix protocol

extract_protocol: RNA was extracted with the miRNeasy kit (Qiagen) according to the manufacturer`s instructions

treatment_protocol:
Human peripheral blood mononuclear cells obtained after leukapheresis from healthy donors served as the source for T cells. These were enriched on nylon wool columns (purity of CD3+ cells: on average 85%)
Individual samples maintained in RPMI1640/10% FCS were halved: one half was stimulated for 24h with 40 ng/ml PMA (Calbiochem) and 0.5 mM ionomycin (Sigma), the other half was stimulated after a 2 h exposure to 50 mM LY200492 (New England Biolabs, Frankfurt, Germany)

value: stimulated for 24h with 40 ng/ml PMA (Calbiochem) and 0.5 mM ionomycin (Sigma) after a 2 h exposure to 50 uM LY200492 (New England Biolabs, Frankfurt, Germany)

value: peripheral blood mononuclear cell

tag: donor


title: Non-tumor adjacent tissue 481N


title: Hepatocellular carcinoma 480T

value: Female


title: donor2 stimulated + inhibited

source_name: Human peripheral blood mononuclear cells obtained after leukapheresis from healthy donors

tag: treatment


title: Non-tumor adjacent tissue 480N

tag: gender


title: donor4 stimulated

description: Human peripheral blood mononuclear cells, stimulated

value: stimulated for 24h with 40 ng/ml PMA (Calbiochem) and 0.5 mM ionomycin (Sigma)


title: donor3 stimulated + inhibited


title: Hepatocellular carcinoma 479T


title: donor1 stimulated + inhibited


title: Non-tumor adjacent tissue 479N


title: hmNPCs_AAV2/9_2h_rep3

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Gene expression data from hmNPCs cells transduced with AAV2/9 and collection at 2 hour

hyb_protocol: labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix) according to the manufacturer's protocol.

data_processing: Expression data (CEL files) were analysed by the Robust Multiarray Average (RMA) method of Irrizarry using the R/Bioconductor suite of packages.

source_name: hmNPCs cells, transduction, AAV2/9, 2h

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

extract_protocol: Total RNA was isolated by using the RNeasy Mini Kit (Qiagen)

value: human midbrain neuroprogenitor cells

value: embryonic midbrain tissue


title: hmNPCs_LV_5d_rep2

description: Gene expression data from hmNPCs cells transduced with LV and collection at 5 days

source_name: hmNPCs cells, transduction, LV, 5d


title: Hepatocellular carcinoma 474T


title: donor1 stimulated


title: hmNPCs_LV_5d_rep3


title: hmNPCs_AAV2/9_2h_rep2


title: hmNPCs_LV_2h_rep3

description: Gene expression data from hmNPCs cells transduced with LV and collection at 2 hour

source_name: hmNPCs cells, transduction, LV, 2h


title: hmNPCs_AAV2/9_5d_rep1

description: Gene expression data from hmNPCs cells transduced with AAV2/9 and collection at 5 days

source_name: hmNPCs cells, transduction, AAV2/9, 5d


title: hmNPCs_LV_2h_rep1


title: hmNPCs_AAV2/9_2h_rep1


title: Non-tumor adjacent tissue 474N


title: donor2 stimulated


title: hmNPCs_HD-HAd_5d_rep2

description: Gene expression data from hmNPCs cells transduced with HD-HAd and collection at 5 days

source_name: hmNPCs cells, transduction, HD-HAd, 5d


title: Hepatocellular carcinoma 454T


title: hmNPCs_HD-HAd_5d_rep3


title: Non-tumor adjacent tissue 454N


title: hmNPCs_AAV2/9_5d_rep3


title: Hepatocellular carcinoma 450T


title: hmNPCs_AAV2/9_5d_rep2


title: Non-tumor adjacent tissue 450N


title: Hepatocellular carcinoma 391T


title: Non-tumor adjacent tissue 391N


title: donor3 stimulated


title: Hepatocellular carcinoma 385T


title: Non-tumor adjacent tissue 385N


title: Non-tumor adjacent tissue 349N


title: hmNPCs_HD-HAd_5d_rep1


title: hmNPCs_HD-CAV-2_5d_rep3

description: Gene expression data from hmNPCs cells transduced with HD-CAV-2 and collection at 5 days

source_name: hmNPCs cells, transduction, HD-CAV-2, 5d


title: hmNPCs_HD-HAd_2h_rep2

description: Gene expression data from hmNPCs cells transduced with HD-HAd and collection at 2 hour

source_name: hmNPCs cells, transduction, HD-HAd, 2h


title: Hepatocellular carcinoma 346T


title: hmNPCs_HD-HAd_2h_rep1


title: hmNPCs_HD-HAd_2h_rep3


title: hmNPCs_LV_2h_rep2


title: hmNPCs_HD-CAV-2_2h_rep2

description: Gene expression data from hmNPCs cells transduced with HD-CAV-2 and collection at 2 hour

source_name: hmNPCs cells, transduction, HD-CAV-2, 2h


title: Non-tumor adjacent tissue 346N


title: hmNPCs_HD-CAV-2_5d_rep2


title: hmNPCs_untreated_5d_rep3

description: Gene expression data from hmNPCs cells without transduction and collection at 5 days

source_name: hmNPCs cells, no transduction, 5d


title: hmNPCs_HD-CAV-2_5d_rep1


title: Hepatocellular carcinoma 319T


title: hmNPCs_HD-CAV-2_2h_rep3


title: Non-tumor adjacent tissue 319N


title: hmNPCs_HD-CAV-2_2h_rep1


title: Hepatocellular carcinoma 255T


title: Non-tumor adjacent tissue 255N


title: Hepatocellular carcinoma 199T


title: Non-tumor adjacent tissue 199N


title: hmNPCs_untreated_5d_rep2


title: Hepatocellular carcinoma 197T


title: Non-tumor adjacent tissue 197N


title: Non-tumor adjacent tissue 196N


title: Hepatocellular carcinoma 196T


title: hmNPCs_untreated_5d_rep1


title: Hepatocellular carcinoma 507T


title: hmNPCs_untreated_2h_rep3

description: Gene expression data from hmNPCs cells without transduction and collection at 2 hour

source_name: hmNPCs cells, no transduction, 2h


title: hmNPCs_untreated_2h_rep1


title: hmNPCs_untreated_2h_rep2


title: Non-tumor adjacent tissue 507N


title: Hepatocellular carcinoma 505T


title: Non-tumor adjacent tissue 505N


title: Non-tumor adjacent tissue 504N


title: Hepatocellular carcinoma 506T


title: MKN28-NC

city: Xi'an

first: Wang

last: Simeng

address: Changle Road

department: Xijing Hospital of Digestive Diseases

country: China

institute: Fourth Military Medical University

description: F 7.29

hyb_protocol: Hybridization with Affymetrix Hybridization Oven 640 according to the standard Affymetrix protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Robust Multichip Analysis（RMA）

growth_protocol: Human gastric cancer cell lines MKN28 were cultured at 37°C in an atmosphere of 5% CO2 in RPMI1640 (HyClone) supplemented with 10% fetal bovine serum, 100 unit penicillin, and 100 μg/mL streptomycin (Gibco BRL, Life Technologies, New York, USA).

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

treatment_protocol: MKN28 cell cultures expressing Sox2 were generated by infecting MKN28 cells with lenti-Sox2 (GOSL24628, Shanghai GeneChem Co., Ltd) using puromycin (2μg/mL) selection for 3-5 days. The lentivirus Sox2 provides the puromycin resistance.

value: gastric cancer cell line MKN28

tag: genotype/variation

value: control


title: Hepatocellular carcinoma 504T


title: MKN28-Sox2

description: S 7.29

value: Sox2 overexpression


title: Hepatocellular carcinoma 502T


title: Non-tumor adjacent tissue 503N


title: Non-tumor adjacent tissue 502N


title: Hepatocellular carcinoma 501T


title: Non-tumor adjacent tissue 501N


title: Non-tumor adjacent tissue 500N


title: Hepatocellular carcinoma 500T


title: Non-tumor adjacent tissue 499N


title: Hepatocellular carcinoma 497T


title: Hepatocellular carcinoma 499T


title: Non-tumor adjacent tissue 498N


title: Non-tumor adjacent tissue 497N


title: Non-tumor adjacent tissue 506N


title: Non-tumor adjacent tissue 496N


title: Hepatocellular carcinoma 496T


title: Hepatocellular carcinoma 503T


title: Hepatocellular carcinoma 495T


title: Non-tumor adjacent tissue 495N


title: Hepatocellular carcinoma 494T


title: Non-tumor adjacent tissue 494N


title: Hepatocellular carcinoma 498T


title: Hepatocellular carcinoma 493T


title: Non-tumor adjacent tissue 493N


title: Hepatocellular carcinoma 492T


title: Hepatocellular carcinoma 484T


title: Non-tumor adjacent tissue 490N


title: Hepatocellular carcinoma 483T


title: Non-tumor adjacent tissue 484N


title: Hepatocellular carcinoma 490T


title: Hepatocellular carcinoma 491T


title: Hepatocellular carcinoma 477T


title: Non-tumor adjacent tissue 477N


title: Non-tumor adjacent tissue 492N


title: Non-tumor adjacent tissue 476N


title: Non-tumor adjacent tissue 475N


title: Hepatocellular carcinoma 475T


title: Non-tumor adjacent tissue 491N


title: Hepatocellular carcinoma 473T


title: Hepatocellular carcinoma 476T


title: Hepatocellular carcinoma 472T


title: Non-tumor adjacent tissue 472N


title: Non-tumor adjacent tissue 473N


title: Hepatocellular carcinoma 471T


title: Non-tumor adjacent tissue 483N


title: hmNPCs_LV_5d_rep1


title: Hepatocellular carcinoma 468T


title: Non-tumor adjacent tissue 468N


title: Hepatocellular carcinoma 466T


title: Non-tumor adjacent tissue 466N


title: Hepatocellular carcinoma 464T


title: Non-tumor adjacent tissue 461N


title: Hepatocellular carcinoma 460T


title: Hepatocellular carcinoma 455T


title: Hepatocellular carcinoma 449T


title: Hepatocellular carcinoma 451T


title: Non-tumor adjacent tissue 451N


title: Hepatocellular carcinoma 461T


title: Non-tumor adjacent tissue 455N


title: Non-tumor adjacent tissue 460N


title: Non-tumor adjacent tissue 449N


title: Non-tumor adjacent tissue 444N


title: Non-tumor adjacent tissue 459N


title: Hepatocellular carcinoma 444T


title: Hepatocellular carcinoma 445T


title: Non-tumor adjacent tissue 445N


title: Non-tumor adjacent tissue 471N


title: Hepatocellular carcinoma 442T


title: Non-tumor adjacent tissue 441N


title: Non-tumor adjacent tissue 442N


title: Hepatocellular carcinoma 439T


title: Hepatocellular carcinoma 443T


title: Non-tumor adjacent tissue 464N


title: Non-tumor adjacent tissue 439N


title: Hepatocellular carcinoma 459T


title: Hepatocellular carcinoma 437T


title: Non-tumor adjacent tissue 437N


title: Hepatocellular carcinoma 434T


title: Non-tumor adjacent tissue 434N


title: Non-tumor adjacent tissue 435N


title: Non-tumor adjacent tissue 443N


title: Hepatocellular carcinoma 431T


title: Non-tumor adjacent tissue 430N


title: Hepatocellular carcinoma 430T


title: Non-tumor adjacent tissue 429N


title: Hepatocellular carcinoma 441T


title: Hepatocellular carcinoma 435T


title: Hepatocellular carcinoma 426T


title: Non-tumor adjacent tissue 428N


title: Hepatocellular carcinoma 427T


title: Non-tumor adjacent tissue 427N


title: Non-tumor adjacent tissue 426N


title: Hepatocellular carcinoma 425T


title: Non-tumor adjacent tissue 421N


title: Hepatocellular carcinoma 428T


title: Hepatocellular carcinoma 421T


title: Non-tumor adjacent tissue 425N


title: Non-tumor adjacent tissue 418N


title: Non-tumor adjacent tissue 419N


title: Non-tumor adjacent tissue 416N


title: Hepatocellular carcinoma 416T


title: Hepatocellular carcinoma 418T


title: Hepatocellular carcinoma 419T


title: Hepatocellular carcinoma 415T


title: Non-tumor adjacent tissue 431N


title: Non-tumor adjacent tissue 415N


title: Hepatocellular carcinoma 429T


title: Hepatocellular carcinoma 414T


title: Non-tumor adjacent tissue 414N


title: Hepatocellular carcinoma 412T


title: Hepatocellular carcinoma 413T


title: Non-tumor adjacent tissue 412N


title: Non-tumor adjacent tissue 410N


title: Non-tumor adjacent tissue 411N


title: Hepatocellular carcinoma 410T


title: Non-tumor adjacent tissue 408N


title: Hepatocellular carcinoma 411T


title: Non-tumor adjacent tissue 407N


title: Non-tumor adjacent tissue 409N


title: Hepatocellular carcinoma 405T


title: Hepatocellular carcinoma 407T


title: Hepatocellular carcinoma 403T


title: Non-tumor adjacent tissue 403N


title: Non-tumor adjacent tissue 402N


title: Non-tumor adjacent tissue 413N


title: Hepatocellular carcinoma 401T


title: Non-tumor adjacent tissue 401N


title: Hepatocellular carcinoma 396T


title: Hepatocellular carcinoma 402T


title: Non-tumor adjacent tissue 396N


title: Non-tumor adjacent tissue 405N


title: Hepatocellular carcinoma 399T


title: Hepatocellular carcinoma 409T


title: Non-tumor adjacent tissue 395N


title: Hepatocellular carcinoma 395T


title: Hepatocellular carcinoma 349T


title: Hepatocellular carcinoma 393T


title: Non-tumor adjacent tissue 394N


title: Hepatocellular carcinoma 408T


title: Non-tumor adjacent tissue 399N


title: Hepatocellular carcinoma 394T


title: Hepatocellular carcinoma 406T


title: Non-tumor adjacent tissue 406N


title: Non-tumor adjacent tissue 393N


title: Non-tumor adjacent tissue 386N


title: Non-tumor adjacent tissue 392N


title: Hepatocellular carcinoma 384T


title: Hepatocellular carcinoma 383T


title: Non-tumor adjacent tissue 383N


title: Non-tumor adjacent tissue 384N


title: Hepatocellular carcinoma 382T


title: Non-tumor adjacent tissue 382N


title: Hepatocellular carcinoma 381T


title: Non-tumor adjacent tissue 381N


title: Non-tumor adjacent tissue 373N


title: Hepatocellular carcinoma 374T


title: Hepatocellular carcinoma 373T


title: Hepatocellular carcinoma 378T


title: Non-tumor adjacent tissue 378N


title: Hepatocellular carcinoma 392T


title: Non-tumor adjacent tissue 374N


title: Hepatocellular carcinoma 386T


title: Non-tumor adjacent tissue 372N


title: Hepatocellular carcinoma 370T


title: Non-tumor adjacent tissue 365N


title: Non-tumor adjacent tissue 370N


title: Non-tumor adjacent tissue 371N


title: Hepatocellular carcinoma 363T


title: Hepatocellular carcinoma 362T


title: Hepatocellular carcinoma 364T


title: Non-tumor adjacent tissue 363N


title: Non-tumor adjacent tissue 364N


title: Hepatocellular carcinoma 365T


title: Non-tumor adjacent tissue 361N


title: Hepatocellular carcinoma 361T


title: Non-tumor adjacent tissue 362N


title: Hepatocellular carcinoma 360T


title: Non-tumor adjacent tissue 360N


title: Non-tumor adjacent tissue 359N


title: Hepatocellular carcinoma 356T


title: Hepatocellular carcinoma 371T


title: Non-tumor adjacent tissue 356N


title: Hepatocellular carcinoma 372T


title: Hepatocellular carcinoma 355T


title: Non-tumor adjacent tissue 355N


title: Non-tumor adjacent tissue 353N


title: Hepatocellular carcinoma 353T


title: Hepatocellular carcinoma 350T


title: Hepatocellular carcinoma 345T


title: Non-tumor adjacent tissue 354N


title: Hepatocellular carcinoma 344T


title: Non-tumor adjacent tissue 342N


title: Non-tumor adjacent tissue 345N


title: Hepatocellular carcinoma 342T


title: Hepatocellular carcinoma 340T


title: Non-tumor adjacent tissue 340N


title: Non-tumor adjacent tissue 344N


title: Non-tumor adjacent tissue 351N


title: Hepatocellular carcinoma 343T


title: Non-tumor adjacent tissue 343N


title: Non-tumor adjacent tissue 337N


title: Non-tumor adjacent tissue 339N


title: Hepatocellular carcinoma 336T


title: Non-tumor adjacent tissue 336N


title: Hepatocellular carcinoma 359T


title: Hepatocellular carcinoma 335T


title: Non-tumor adjacent tissue 335N


title: Hepatocellular carcinoma 333T


title: Hepatocellular carcinoma 354T


title: Hepatocellular carcinoma 351T


title: Hepatocellular carcinoma 332T


title: Non-tumor adjacent tissue 333N


title: Non-tumor adjacent tissue 350N


title: Hepatocellular carcinoma 337T


title: Hepatocellular carcinoma 329T


title: Non-tumor adjacent tissue 326N


title: Hepatocellular carcinoma 326T


title: Hepatocellular carcinoma 325T


title: Hepatocellular carcinoma 322T


title: Hepatocellular carcinoma 323T


title: Hepatocellular carcinoma 324T


title: Non-tumor adjacent tissue 328N


title: Non-tumor adjacent tissue 322N


title: Hepatocellular carcinoma 321T


title: Non-tumor adjacent tissue 323N


title: Non-tumor adjacent tissue 332N


title: Non-tumor adjacent tissue 321N


title: Non-tumor adjacent tissue 325N


title: Non-tumor adjacent tissue 320N


title: Hepatocellular carcinoma 318T


title: Hepatocellular carcinoma 339T


title: Hepatocellular carcinoma 320T


title: Non-tumor adjacent tissue 324N


title: Non-tumor adjacent tissue 314N


title: Hepatocellular carcinoma 312T


title: Hepatocellular carcinoma 311T


title: Non-tumor adjacent tissue 312N


title: Hepatocellular carcinoma 314T


title: Hepatocellular carcinoma 328T


title: Non-tumor adjacent tissue 311N


title: Non-tumor adjacent tissue 329N


title: Hepatocellular carcinoma 307T


title: Hepatocellular carcinoma 302T


title: Non-tumor adjacent tissue 306N


title: Non-tumor adjacent tissue 305N


title: Hepatocellular carcinoma 306T


title: Non-tumor adjacent tissue 318N


title: Hepatocellular carcinoma 305T


title: Hepatocellular carcinoma 300T


title: Non-tumor adjacent tissue 302N


title: Non-tumor adjacent tissue 300N


title: Hepatocellular carcinoma 297T


title: Non-tumor adjacent tissue 298N


title: Hepatocellular carcinoma 295T


title: Non-tumor adjacent tissue 295N


title: Non-tumor adjacent tissue 294N


title: Hepatocellular carcinoma 294T


title: Non-tumor adjacent tissue 297N


title: Hepatocellular carcinoma 298T


title: Non-tumor adjacent tissue 292N


title: Hepatocellular carcinoma 290T


title: Hepatocellular carcinoma 292T


title: Hepatocellular carcinoma 289T


title: Non-tumor adjacent tissue 290N


title: Non-tumor adjacent tissue 289N


title: Hepatocellular carcinoma 288T


title: Hepatocellular carcinoma 287T


title: Hepatocellular carcinoma 285T


title: Non-tumor adjacent tissue 287N


title: Non-tumor adjacent tissue 285N


title: Non-tumor adjacent tissue 307N


title: Non-tumor adjacent tissue 283N


title: Hepatocellular carcinoma 283T


title: Hepatocellular carcinoma 281T


title: Hepatocellular carcinoma 279T


title: Non-tumor adjacent tissue 279N


title: Hepatocellular carcinoma 276T


title: Non-tumor adjacent tissue 282N


title: Non-tumor adjacent tissue 276N


title: Non-tumor adjacent tissue 266N


title: Hepatocellular carcinoma 269T


title: Non-tumor adjacent tissue 281N


title: Hepatocellular carcinoma 270T


title: Hepatocellular carcinoma 266T


title: Non-tumor adjacent tissue 270N


title: Non-tumor adjacent tissue 267N


title: Hepatocellular carcinoma 271T


title: Non-tumor adjacent tissue 269N


title: Hepatocellular carcinoma 272T


title: Hepatocellular carcinoma 267T


title: Non-tumor adjacent tissue 271N


title: Non-tumor adjacent tissue 265N


title: Non-tumor adjacent tissue 264N


title: Non-tumor adjacent tissue 260N


title: Hepatocellular carcinoma 260T


title: Non-tumor adjacent tissue 288N


title: Hepatocellular carcinoma 264T


title: Hepatocellular carcinoma 265T


title: Hepatocellular carcinoma 259T


title: Hepatocellular carcinoma 282T


title: Non-tumor adjacent tissue 259N


title: Non-tumor adjacent tissue 258N


title: Non-tumor adjacent tissue 256N


title: Hepatocellular carcinoma 256T


title: Hepatocellular carcinoma 252T


title: Non-tumor adjacent tissue 272N


title: Non-tumor adjacent tissue 252N


title: Hepatocellular carcinoma 251T


title: Non-tumor adjacent tissue 251N


title: Non-tumor adjacent tissue 246N


title: Hepatocellular carcinoma 247T


title: Non-tumor adjacent tissue 245N


title: Non-tumor adjacent tissue 244N


title: Hepatocellular carcinoma 250T


title: Hepatocellular carcinoma 243T


title: Hepatocellular carcinoma 246T


title: Hepatocellular carcinoma 245T


title: Non-tumor adjacent tissue 247N


title: Non-tumor adjacent tissue 242N


title: Hepatocellular carcinoma 241T


title: Non-tumor adjacent tissue 243N


title: Non-tumor adjacent tissue 240N


title: Hepatocellular carcinoma 239T


title: Hepatocellular carcinoma 242T


title: Hepatocellular carcinoma 240T


title: Non-tumor adjacent tissue 241N


title: Non-tumor adjacent tissue 239N


title: Hepatocellular carcinoma 258T


title: Hepatocellular carcinoma 238T


title: Non-tumor adjacent tissue 238N


title: Non-tumor adjacent tissue 235N


title: Non-tumor adjacent tissue 237N


title: Hepatocellular carcinoma 234T


title: Non-tumor adjacent tissue 234N


title: Non-tumor adjacent tissue 250N


title: Hepatocellular carcinoma 244T


title: Hepatocellular carcinoma 233T


title: Non-tumor adjacent tissue 233N


title: Non-tumor adjacent tissue 232N


title: Hepatocellular carcinoma 228T


title: Hepatocellular carcinoma 227T


title: Non-tumor adjacent tissue 230N


title: Hepatocellular carcinoma 232T


title: Non-tumor adjacent tissue 229N


title: Hepatocellular carcinoma 230T


title: Non-tumor adjacent tissue 228N


title: Hepatocellular carcinoma 229T


title: Non-tumor adjacent tissue 225N


title: Hepatocellular carcinoma 226T


title: Non-tumor adjacent tissue 224N


title: Non-tumor adjacent tissue 227N


title: Non-tumor adjacent tissue 226N


title: Hepatocellular carcinoma 222T


title: Hepatocellular carcinoma 225T


title: Hepatocellular carcinoma 224T


title: Non-tumor adjacent tissue 222N


title: Hepatocellular carcinoma 235T


title: Non-tumor adjacent tissue 221N


title: Hepatocellular carcinoma 221T


title: Hepatocellular carcinoma 220T


title: Hepatocellular carcinoma 219T


title: Non-tumor adjacent tissue 220N


title: Non-tumor adjacent tissue 219N


title: Hepatocellular carcinoma 217T


title: Non-tumor adjacent tissue 217N


title: Hepatocellular carcinoma 237T


title: Hepatocellular carcinoma 216T


title: Non-tumor adjacent tissue 216N


title: Non-tumor adjacent tissue 214N


title: Hepatocellular carcinoma 214T


title: Non-tumor adjacent tissue 215N


title: Hepatocellular carcinoma 212T


title: Hepatocellular carcinoma 200T


title: Non-tumor adjacent tissue 212N


title: Hepatocellular carcinoma 205T


title: Non-tumor adjacent tissue 210N


title: Non-tumor adjacent tissue 207N


title: Non-tumor adjacent tissue 189N


title: Hepatocellular carcinoma 207T


title: Non-tumor adjacent tissue 192N


title: Hepatocellular carcinoma 210T


title: Non-tumor adjacent tissue 193N


title: Hepatocellular carcinoma 188T


title: Hepatocellular carcinoma 189T


title: Non-tumor adjacent tissue 211N


title: Hepatocellular carcinoma 193T


title: Non-tumor adjacent tissue 200N


title: Hepatocellular carcinoma 186T


title: Hepatocellular carcinoma 192T


title: Non-tumor adjacent tissue 188N


title: Non-tumor adjacent tissue 187N


title: Hepatocellular carcinoma 187T


title: Non-tumor adjacent tissue 186N


title: Hepatocellular carcinoma 215T


title: Hepatocellular carcinoma 211T


title: Non-tumor adjacent tissue 185N


title: Non-tumor adjacent tissue 205N


title: Hepatocellular carcinoma 185T


title: Non-tumor adjacent tissue 184N


title: Non-tumor adjacent tissue 183N


title: Non-tumor adjacent tissue 182N


title: Hepatocellular carcinoma 182T


title: Non-tumor adjacent tissue 181N


title: Non-tumor adjacent tissue 180N


title: Hepatocellular carcinoma 180T


title: Hepatocellular carcinoma 178T


title: Non-tumor adjacent tissue 178N


title: Hepatocellular carcinoma 177T


title: Hepatocellular carcinoma 184T


title: Non-tumor adjacent tissue 177N


title: Hepatocellular carcinoma 183T


title: Hepatocellular carcinoma 176T


title: Hepatocellular carcinoma 181T


title: CIT554

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

description: Array Version: CIT-CGH Homo sapiens 5.9K V7

hyb_protocol: After ethanol-coprecipitation with 140 µg of Human Cot-1 DNA (Roche, Basel, Switzerland), resuspension in 72.5 µl of hybridization buffer, denaturation at 100°C for 10 minutes and prehybridization at 37°C for 90 minutes, probes were hybridized on treated microarray slides in a humidity chamber at 37°C for 24 hours.

scan_protocol: After washing, slides were scanned with a GenePix 4000B scanner (Axon Instruments Inc., Union City, CA, USA) and analyzed with GenePix Pro 5.1 image analysis software, which defined the spots and determined the median intensities for the Cy3 and Cy5 signals of each BAC clone.

data_processing: Raw log2-ratio feature values were filtered from further analyses using a signal-to-noise threshold of 2.0 for the reference channel. The remaining values were normalized using the lowess within-print tip group method {Yang, 2002 #39}. For BACs in which more than 1 feature value remained after filtering and that yielded an inter-feature standard deviation of less than 0.25, an average normalized log2-ratio value was calculated. The iterative, data-adaptive smoothing technique Adaptive Weights Smoothing (AWS,Polzehl and Spokoiny) was applied to the normalized log2-ratio values [as adapted in the R GLAD package v1.8 {Hupe, 2004 #40}]. This yields smoothed log2-ratios values in homogeneous segments along the chromosome. We then determined the level of normal genomic ratios (copy number of 2) for each sample. This value corresponds to the first mode of the distribution of the normalized log2-ratio values across all chromosomes. The standard deviations of the smoothed log2-ratio segments are used as a threshold of determining breakpoints. All segments that are above or below this threshold are then classed as gains or losses, respectively. Outliers are classed manually and correspond to individual BACs that yielded log2-ratios three times the standard deviation threshold. This method allows for the partitioning of the smoothed CGH data into 3 different groups: gain (value=1), no change (value=0) or loss (value=-1).

source_name: Frozen tissue of primary colorectal Adenocarcinoma

label_protocol: Tumor DNAs were labeled by the random priming method (Bioprime DNA labelling system; Invitrogen, Cergy-Pontoise, France) with cyanine-5 (CyDye dCTP Multipack, Amersham GE Healthcare, Buckinghamshire, UK). Using the same procedure, we labeled control DNA with cyanine-3.

growth_protocol: Samples stored at -80 C

extract_protocol: E2: Manual-Phenol/Chloroform

tag: dataset

value: validation

tag: Sex

value: M

value: distal

value: N

value: pMMR

tag: cit-coloncancermolecularsubtype

source_name: common reference

tag: reference

value: sex-matched gDNA pool human variation panel caucasian


title: CIT561

value: F


title: CIT564

description: Array Version: CIT-CGH Homo sapiens 4.7K V6

extract_protocol: E1: Manual-QIAamp DNA Mini (Qiagen)

value: Y

value: pool of 20 sex-matched patients


title: CIT563


title: CIT560


title: CIT566

value: proximal


title: CIT565


title: CIT555


title: Hepatocellular carcinoma 175T

value: Male

value: Liver

value: Hepatocellular carcinoma


title: CIT557


title: CIT558


title: CIT553


title: CIT549


title: Non-tumor adjacent tissue 175N

value: Non-tumor adjacent tissue


title: CIT562


title: CIT552


title: Hepatocellular carcinoma 173T


title: CIT546


title: CIT551

value: dMMR


title: Non-tumor adjacent tissue 176N


title: CIT548


title: Non-tumor adjacent tissue 173N


title: Non-tumor adjacent tissue 167N


title: CIT545


title: CIT542


title: CIT543


title: CIT541


title: CIT544


title: Non-tumor adjacent tissue 166N


title: Hepatocellular carcinoma 163T


title: CIT540


title: CIT539


title: Non-tumor adjacent tissue 163N


title: CIT534


title: CIT538


title: CIT536


title: CIT537


title: CIT535


title: Hepatocellular carcinoma 161T

value: Female


title: CIT533


title: CIT532


title: Hepatocellular carcinoma 166T


title: Hepatocellular carcinoma 167T


title: CIT530


title: CIT531


title: CIT528


title: CIT527


title: Non-tumor adjacent tissue 161N


title: CIT526


title: CIT525


title: Hepatocellular carcinoma 158T


title: Non-tumor adjacent tissue 158N


title: CIT524


title: CIT523


title: CIT522


title: CIT529


title: Hepatocellular carcinoma 156T


title: Non-tumor adjacent tissue 156N


title: Hepatocellular carcinoma 155T


title: CIT521


title: CIT518


title: CIT520


title: CIT519


title: CIT517


title: CIT516


title: Non-tumor adjacent tissue 155N


title: CIT511


title: CIT514


title: CIT512


title: CIT515


title: CIT510


title: Non-tumor adjacent tissue 154N


title: Hepatocellular carcinoma 153T


title: CIT509


title: CIT508


title: Hepatocellular carcinoma 152T


title: Non-tumor adjacent tissue 153N


title: Non-tumor adjacent tissue 152N


title: CIT507


title: Hepatocellular carcinoma 151T


title: CIT504


title: CIT502


title: CIT503


title: CIT513


title: Hepatocellular carcinoma 154T


title: CIT506


title: Non-tumor adjacent tissue 151N


title: CIT498


title: CIT500


title: CIT501


title: CIT499


title: CIT505


title: Non-tumor adjacent tissue 149N


title: Hepatocellular carcinoma 149T


title: Hepatocellular carcinoma 146T


title: CIT494


title: CIT496


title: CIT495


title: CIT490

value: DELA (bone marrow XY)


title: Hepatocellular carcinoma 145T


title: Non-tumor adjacent tissue 145N


title: Hepatocellular carcinoma 144T


title: CIT497

value: validation


title: CIT493


title: CIT491

value: M


title: CIT492


title: CIT482


title: CIT489


title: Non-tumor adjacent tissue 144N


title: Hepatocellular carcinoma 142T


title: CIT487

value: distal


title: Non-tumor adjacent tissue 146N


title: CIT488


title: Non-tumor adjacent tissue 142N


title: Hepatocellular carcinoma 140T


title: CIT480

value: N


title: CIT479

value: pMMR


title: CIT475


title: CIT476


title: Non-tumor adjacent tissue 140N


title: CIT473


title: CIT471


title: CIT472


title: CIT466


title: CIT485


title: CIT474


title: CIT470


title: CIT481


title: CIT465


title: Non-tumor adjacent tissue 139N


title: CIT462


title: Hepatocellular carcinoma 138T


title: Non-tumor adjacent tissue 138N


title: Hepatocellular carcinoma 139T


title: CIT461


title: CIT464


title: CIT468


title: Hepatocellular carcinoma 137T


title: Non-tumor adjacent tissue 137N


title: Hepatocellular carcinoma 136T


title: CIT454

value: pool XX (20 healthy women)


title: Hepatocellular carcinoma 135T


title: Non-tumor adjacent tissue 136N


title: CIT460


title: CIT453

value: F


title: Non-tumor adjacent tissue 135N


title: Hepatocellular carcinoma 133T


title: Non-tumor adjacent tissue 133N


title: Hepatocellular carcinoma 132T


title: Non-tumor adjacent tissue 132N


title: Hepatocellular carcinoma 131T


title: CIT439

value: discovery

value: Y

value: sex-matched gDNA pool human variation panel caucasian


title: CIT440

value: proximal

value: pool of 20 sex-matched patients


title: CIT463


title: CIT451


title: CIT450


title: CIT441


title: CIT434


title: CIT433


title: CIT446

value: pool XY (20 healthy men)


title: CIT432


title: CIT445


title: CIT449


title: CIT444

value: Pool XX (20 patients)


title: CIT448


title: CIT442


title: CIT452


title: CIT443


title: CIT447


title: CIT431


title: CIT458


title: CIT435

value: dMMR


title: CIT437


title: CIT438


title: CIT436


title: CIT430


title: Non-tumor adjacent tissue 131N

value: Male

value: Liver

value: Non-tumor adjacent tissue


title: CIT429

value: M


title: CIT427

value: distal


title: Hepatocellular carcinoma 130T

value: Hepatocellular carcinoma


title: Hepatocellular carcinoma 128T


title: Non-tumor adjacent tissue 130N