title: HuCCT1_control-2

description: Sample name: HuCCT1_Z0-2


title: HuCCT1_control-1

status: Public on Mar 24 2015

type: genomic

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

description: Sample name: HuCCT1_Z0-1

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting.

data_processing:
Genome Studio V2011.2
The methylation level of each of the > 480,000 CpG sites was calculated using the GenomeStudio Methylation Module 1.9.0 (Illumina). Normalization was performed using "Normalization to Internal Controls" and "Background Subtraction" options implemented in the Methylation Module 1.9.0.
GSE60446_methylated_unmethylated_signals: Unmethylated and methylated signal intensities.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: An intrahepatic cholangiocarcinoma-derived cell line, HuCCT1, without zebularine treatment

label_protocol: Standard Illumina labelling protocol.

growth_protocol: TFK-1 cells (extrahepatic bile duct, RCB2537) and HuCCT1 cells (intrahepatic bile duct, RCB1960) were provided by the RIKEN BRC though the National Bio-Resource Project of the MEXT, Japan, and were maintained at 37oC under an atmosphere of 95% air and 5% CO2 in RPMI1069 containing 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin. Cells were immersed in a culture medium containing zebularine (1000 μM) for 72 h or in a culture medium without zebularine as a control.

extract_protocol: Genomic DNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen).

tag: cell line

tag: cell type

value: intrahepatic cholangiocarcinoma cell line

tag: treatment


title: TFK1_zebularine1000μM_72h-2

description: Sample name: TFK1_Z1000-2

source_name: An extrahepatic cholangiocarcinoma-derived cell line, TFK1, with zebularine treatment (1000μM for 72h)

value: extrahepatic cholangiocarcinoma cell line

value: zebularine


title: FRESH_Donor8_4_PB1

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor8_4_PB1_exp 6-258045B_bottom_Cy3_female_fused.txt
sample vs male reference: FRESH_Donor8_4_PB1_exp 6-258045B_bottom_Cy3_male_fused.txt
combined: FRESH_Donor8_4_PB1_exp 6-258045B_bottom_Cy3_combined_fused.txt

hyb_protocol: After ethanol precipitation, samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Agilent dual laser DNA microarray scanner G2566AA was used for scanning the arrays, data was stored as .TIFF files

data_processing: .TIFF files were imported in BlueFuse Multi 3.0

source_name: Fertilized Embryo

label_protocol: Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

extract_protocol: Extraction was done following standard 24sure v3 protocol. In brief, 2.5µl extraction buffer and 5µl extraction cocktail were added per sample, followed by 10min incubation at 75°C and 4min at 95°C.

tag: tissue

value: Fertilized Embryo

tag: sample

tag: assayed molecule

value: Amplified DNA

source_name: female/male reference

value: reference


title: TFK1_control-3

description: Sample name: TFK1_Z0-3

source_name: An extrahepatic cholangiocarcinoma-derived cell line, TFK1, without zebularine treatment


title: HuCCT1_zebularine1000μM_72h-1

description: Sample name: HuCCT1_Z1000-1

source_name: An intrahepatic cholangiocarcinoma-derived cell line, HuCCT1, with zebularine treatment (1000μM for 72h)


title: FRESH_Donor7_1_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor7_1_PB2_exp 6-258044B_top_Cy5_female_fused.txt
sample vs male reference: FRESH_Donor7_1_PB2_exp 6-258044B_top_Cy5_male_fused.txt
combined: FRESH_Donor7_1_PB2_exp 6-258044B_top_Cy5_combined_fused.txt


title: FRESH_Donor8_4_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor8_4_PB2_exp 6-258045B_bottom_Cy5_female_fused.txt
sample vs male reference: FRESH_Donor8_4_PB2_exp 6-258045B_bottom_Cy5_male_fused.txt
combined: FRESH_Donor8_4_PB2_exp 6-258045B_bottom_Cy5_combined_fused.txt


title: FRESH_Donor6_17_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor6_17_PB2_exp 6-258043B_bottom_Cy5_female_fused.txt
sample vs male reference: FRESH_Donor6_17_PB2_exp 6-258043B_bottom_Cy5_male_fused.txt
combined: FRESH_Donor6_17_PB2_exp 6-258043B_bottom_Cy5_combined_fused.txt


title: ERCC1-proficient_2

type: RNA

city: Rotterdam

first: Jurgen

middle: R

last: Haanstra

address: Dr. Molewaterplein 50

department: Hematology

country: Netherlands

institute: ErasmusMC

description: gene expression data from LSK cells sorted from lineage-depleted bone marrow

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

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

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: LSKs isolated from Ercc1-proficient mice; littermate of Ercc1-/d_2

label_protocol: Standard Affymetrix protocol

growth_protocol: mice were bred and housed according to institutional guidelines

extract_protocol: RNA was extracted with the RNeasy Micro Kit (Qiagen). After two steps of linear amplification with the RNA MessageAmp II aRNA Kit (Ambion, Applied Biosystems), aRNA was labelled and hybridized on the Mouse Genome 430 Affymetrix 2.0 Array according to Affymetrix standard protocols.

treatment_protocol: Bone marrow was harvested from 20- to 22-week-old mice. After lineage depletion, cells were stained with fluorochrome-labelled anti-c-Kit and anti-Sca-1 monoclonal antibodies to mark LSK cells and sorted by FACS. Cells were immediately sorted into RLT buffer (Qiagen).

tag: strain

value: F1 from a crossing of  C57BL/6 x FVB/n

tag: genotype

value: ERCC1-proficient (+/+)

tag: age

value: 20 weeks

value: bone marrow

value: LSK hematopoietic stem cells


title: ERCC1-deficient_2

source_name: LSKs isolated from Ercc1-deficient mice; littermate of Ercc1wt_2

value: ERCC1-deficient (-/d)


title: genomic DNA from stimulated Tcell P7/R2

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

description:
P7/R2 PD
Stimulated T cells

hyb_protocol: bisulphite converted DNA (EZ DNA methylation gold) was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol.

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

data_processing: GenomeStudio software v2010.3 with the Methylation module. Intergenic CpG-sites, CpG-sites at chromosome X and Y, Detection P-value > 0.05 and nbeads<=3 were filtered (set to NA). Probe type normalization was performed using the BMIQ Method.

label: Cy5 and Cy3

source_name: Stimulated T cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted according to standard protocols and DNA purity and concentration determined by spechtrophotometry.

tag: tissue/cell type

value: Stimulated T cells

tag: sample type

value: Control

tag: cimp subgroup

value: CIMP-


title: TFK1_control-2

description: Sample name: TFK1_Z0-2


title: TFK1_zebularine1000μM_72h-3

description: Sample name: TFK1_Z1000-3


title: genomic DNA from T-ALL sample 41

description:
41
BM T-ALL sample

source_name: clinical T-ALL sample

value: clinical T-cell acute lymphoblastic leukemia (T-ALL)

value: Tumor

value: CIMP+


title: genomic DNA from T-ALL sample 36

description:
36
BM T-ALL sample


title: FRESH_Donor6_16_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor6_16_PB1_exp 5-258042B_bottom_Cy3_female_fused.txt
sample vs male reference: FRESH_Donor6_16_PB1_exp 5-258042B_bottom_Cy3_male_fused.txt
combined: FRESH_Donor6_16_PB1_exp 5-258042B_bottom_Cy3_combined_fused.txt


title: EAAE_estradiol_2h_rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: gene expression in EAAE ovariectomized E2 2 hour treated uterus

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: EAAE uterus, E2 treated 2 hours

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: WT and EAAE mice were ovariectomized and rested for 10-14 days to clear endogenous ovarian hormones

extract_protocol: frozen uterine tissue was pulverized and each uterus was homogenized in 800 ul of Trizol (Invitrogen) with 250 ug/ml glycogen. Extraction proceeded as descibed in manufacturer's protocol. Following resuspension of RNA pellet, a second preciptation was done  RNA was DNAse treated and cleaned up using Rneasy kits

treatment_protocol: mice were injected with 100 ul saline of 100 ul E2 and uteri were collected 2 hours later and snap frozen in liquid nitrogen

tag: esr1 genotype

value: EAAE

value: adult (10+ weeks)

tag: gender

value: female (ovariectomized)

tag: agent

value: uterus


title: genomic DNA from T-ALL sample 31

description:
31
BM T-ALL sample


title: FRESH_Donor5_11_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor5_11_PB2_exp 4-258039B_bottom_Cy5_female_fused.txt
sample vs male reference: FRESH_Donor5_11_PB2_exp 4-258039B_bottom_Cy5_male_fused.txt
combined: FRESH_Donor5_11_PB2_exp 4-258039B_bottom_Cy5_combined_fused.txt

value: Fertilized Embryo

value: Amplified DNA

value: reference


title: FRESH_Donor7_1_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor7_1_PB1_exp 6-258044B_top_Cy3_female_fused.txt
sample vs male reference: FRESH_Donor7_1_PB1_exp 6-258044B_top_Cy3_male_fused.txt
combined: FRESH_Donor7_1_PB1_exp 6-258044B_top_Cy3_combined_fused.txt


title: ERCC1-deficient_1

source_name: LSKs isolated from Ercc1-deficient mice; littermate of Ercc1wt_1

value: F1 from a crossing of  C57BL/6 x FVB/n

value: 22 weeks


title: TFK1_control-1

description: Sample name: TFK1_Z0-1

value: extrahepatic cholangiocarcinoma cell line


title: EAAE_estradiol_2h_rep1


title: FRESH_Donor5_11_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor5_11_PB1_exp 4-258039B_bottom_Cy3_female_fused.txt
sample vs male reference: FRESH_Donor5_11_PB1_exp 4-258039B_bottom_Cy3_male_fused.txt
combined: FRESH_Donor5_11_PB1_exp 4-258039B_bottom_Cy3_combined_fused.txt


title: EAAE_estradiol_2h_rep2


title: Fresh_donor4_7_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: fresh_donor4_7_PB2_2nd exp-102023B_top_Cy5_female_fused.txt
sample vs male reference: fresh_donor4_7_PB2_2nd exp-102023B_top_Cy5_male_fused.txt
combined: fresh_donor4_7_PB2_2nd exp-102023B_top_Cy5_combined_fused.txt


title: EAAE_Saline_2h_rep3

description: gene expression in EAAE ovariectomized saline vehicle treated uterus

source_name: EAAE uterus, saline control

value: control


title: ERCC1-proficient_1

source_name: LSKs isolated from Ercc1-proficient mice; littermate of Ercc1-/d_1

value: ERCC1-proficient (+/+)

value: bone marrow

value: LSK hematopoietic stem cells


title: genomic DNA from T-ALL sample 29

description:
29
BM T-ALL sample

value: clinical T-cell acute lymphoblastic leukemia (T-ALL)


title: FRESH_Donor8-1_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH-Donor8-1_PB1_exp 6-258045B_top_Cy3_female_fused.txt
sample vs male reference: FRESH-Donor8-1_PB1_exp 6-258045B_top_Cy3_male_fused.txt
combined: FRESH-Donor8-1_PB1_258045exp 6-258045B_top_Cy3_combined_fused.txt

value: top


title: genomic DNA from T-ALL sample 20

description:
20
BM T-ALL sample

value: Tumor

value: CIMP-


title: genomic DNA from T-ALL sample 9

description:
9
BM T-ALL sample

value: CIMP+


title: EAAE_Saline_2h_rep2

value: EAAE

value: adult (10+ weeks)

value: female (ovariectomized)


title: Fresh_donor4_7_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: fresh_donor4_7_PB1_2nd exp-102023B_top_Cy3_female_fused.txt
sample vs male reference: fresh_donor4_7_PB1_2nd exp-102023B_top_Cy3_male_fused.txt
combined: fresh_donor4_7_PB1_2nd exp-102023B_top_Cy3_combined_fused.txt

value: Fertilized Embryo

value: Amplified DNA


title: genomic DNA from T-ALL sample 19

description:
19
BM T-ALL sample


title: FRESH_Donor10_4_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor10_4_PB2_PbH manual 4.2-258051B_bottom_Cy5_female_fused.txt
sample vs male reference: FRESH_Donor10_4_PB2_PbH manual 4.2-258051B_bottom_Cy5_male_fused.txt
combined: FRESH_Donor10_4_PB2_PbHe manual 4.2-258051B_bottom_Cy5_combined_fused.txt

value: reference


title: FRESH_Donor3_1_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor3_1_PB2_exp 4-258037B_bottom_Cy5_female_fused.txt
sample vs male reference: FRESH_Donor3_1_PB2_exp 4-258037B_bottom_Cy5_male_fused.txt
combined: FRESH_Donor3_1_PB2_exp 4-258037B_bottom_Cy5_combined_fused.txt


title: WT_estradiol_2h_rep3

description: gene expression in WT ovariectomized E2 2 hour treated uterus

source_name: WT uterus, E2 treated 2 hours

value: WT

value: uterus


title: genomic DNA from T-ALL sample 23

description:
23
BM T-ALL sample


title: FRESH_Donor10_4_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor10_4_PB1_PB H manual 4.1-258051B_bottom_Cy3_female_fused.txt
sample vs male reference: FRESH_Donor10_4_PB1_PB H manual 4.1-258051B_bottom_Cy3_male_fused.txt
combined: FRESH_Donor10_4_PB1_PB H manual 4.1-258051B_bottom_Cy3_combined_fused.txt


title: Fresh_donor1_4_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: fresh_donor1_4_PB2_121417-102020B_bottom_Cy5_female_fused.txt
sample vs male reference: fresh_donor1_4_PB2_121417-102020B_bottom_Cy5_male_fused.txt
combined: fresh_donor1_4_PB2_121417-102020B_bottom_Cy5_combined_fused.txt


title: EAAE_Saline_2h_rep1

value: control


title: WT_estradiol_2h_rep1


title: WT_estradiol_2h_rep2


title: genomic DNA from T-ALL sample 4

description:
4
BM T-ALL sample


title: Fresh_donor1_4_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: fresh_donor1_4_PB1_121417-102020B_bottom_Cy3_female_fused.txt
sample vs male reference: fresh_donor1_4_PB1_121417-102020B_bottom_Cy3_male_fused.txt
combined: fresh_donor1_4_PB1_121417-102020B_bottom_Cy3_combined_fused.txt


title: WT_Saline_2h_rep3

description: gene expression in WT ovariectomized saline vehicle treated uterus

source_name: WT uterus, saline control


title: genomic DNA from T-ALL sample 3

description:
3
BM T-ALL sample


title: genomic DNA from S4 68 PD

description:
S4 68 PD
Post-crisis cell culture sample

source_name: Post-crisis T-cell culture

value: Post-crisis T-cell culture

value: cell culture


title: WT_Saline_2h_rep1


title: WT_Saline_2h_rep2


title: FRESH_Donor6_16_PB2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor6_16_PB2_exp 5-258042B_bottom_Cy5_female_fused.txt
sample vs male reference: FRESH_Donor6_16_PB2_exp 5-258042B_bottom_Cy5_male_fused.txt
combined: FRESH_Donor6_16_PB2_exp 5-258042B_bottom_Cy5_combined_fused.txt


title: genomic DNA from S4 223 PD

description:
S4 223 PD
Post-crisis cell culture sample


title: genomic DNA from S4 48 PD

description:
S4 48 PD
Pre-crisis cell culture sample

source_name: Pre-crisis T-cell culture

value: Pre-crisis T-cell culture


title: genomic DNA from S3R 192 PD

description:
S3R 192 PD
Post-crisis cell culture sample


title: genomic DNA from S3R 76 PD

description:
S3R 76 PD
Post-crisis cell culture sample


title: genomic DNA from S3R 27 PD

description:
S3R 27 PD
Post-crisis cell culture sample


title: genomic DNA from S4 18 PD

description:
S4 18 PD
Pre-crisis cell culture sample


title: FRESH_Donor6_17_PB1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample vs female reference: FRESH_Donor6_17_PB1_exp 6-258043B_bottom_Cy3_female_fused.txt
sample vs male reference: FRESH_Donor6_17_PB1_exp 6-258043B_bottom_Cy3_male_fused.txt
combined: FRESH_Donor6_17_PB1_exp 6-258043B_bottom_Cy3_combined_fused.txt


title: 1841_p_2

status: Public on Mar 23 2015

city: Chiba

first: Shuhei

last: Noda

state: Chiba

address: Anagawa 4-9-1

department: Frontier research center

institute: National institute of radiological sciences

description: prior to treatment, radiotherapy alone

data_processing: global median normalization

source_name: biopsy, prior to treatment, radiotherapy alone

tag: female, cervical cancer


title: 1841_d_1

description: during treatment, radiotherapy alone

source_name: biopsy, during treatment, radiotherapy alone


title: 1992_p_1

description: prior to treatment, radiotherapy alone


title: 1841_p_1

description: prior to treatment, radiotherapy alone


title: 1841_d_2

description: during treatment, radiotherapy alone


title: 1992_p_2

description: prior to treatment, radiotherapy alone


title: 2776_p_2

description: prior to treatment, chemoradiotherapy

source_name: biopsy, prior to treatment, chemoradiotherapy


title: 2776_p_1

description: prior to treatment, chemoradiotherapy


title: genomic DNA from S3R 17 PD

description:
S3R 17 PD
Pre-crisis cell culture sample


title: 1348_p_2

description: prior to treatment, radiotherapy alone


title: 1348_d_2

description: during treatment, radiotherapy alone


title: 1348_p_1

description: prior to treatment, radiotherapy alone


title: 2775_d_2

description: during treatment, chemoradiotherapy

source_name: biopsy, during treatment, chemoradiotherapy


title: 2776_d_1

description: during treatment, chemoradiotherapy


title: 2789_p_2

description: prior to treatment, chemoradiotherapy


title: 1992_d_1

description: during treatment, radiotherapy alone


title: 1348_d_1

description: during treatment, radiotherapy alone


title: 2776_d_2

description: during treatment, chemoradiotherapy


title: 2789_d_1

description: during treatment, chemoradiotherapy


title: 2773_d_1

description: during treatment, chemoradiotherapy


title: 2789_d_2

description: during treatment, chemoradiotherapy


title: 1986_p_1

description: prior to treatment, chemoradiotherapy


title: 1986_d_1

description: during treatment, chemoradiotherapy


title: 1850_p_2

description: prior to treatment, chemoradiotherapy


title: 1986_d_2

description: during treatment, chemoradiotherapy


title: 1850_p_1

description: prior to treatment, chemoradiotherapy


title: 2773_d_2

description: during treatment, chemoradiotherapy


title: 1850_d_2

description: during treatment, chemoradiotherapy


title: 1850_d_1

description: during treatment, chemoradiotherapy


title: 2034_p_2

description: prior to treatment, chemoradiotherapy

extract_protocol: ISOGEN(NIPPON GENE)+RNeasy(QIAGEN)


title: 2034_p_1

description: prior to treatment, chemoradiotherapy


title: 1986_p_2

description: prior to treatment, chemoradiotherapy


title: 1994_p_2

description: prior to treatment, chemoradiotherapy


title: 1351_d_1

description: during treatment, chemoradiotherapy


title: 1994_p_1

description: prior to treatment, chemoradiotherapy


title: genomic DNA from S4 12 PD

description:
S4 12 PD
Pre-crisis cell culture sample


title: 2790_p_1

description: prior to treatment, chemoradiotherapy


title: 1591_d_2

description: during treatment, chemoradiotherapy


title: 1351_p_2

description: prior to treatment, chemoradiotherapy


title: 1995_d_1

description: during treatment, radiotherapy alone


title: 2789_p_1

description: prior to treatment, chemoradiotherapy


title: 2654_p_2

description: prior to treatment, chemoradiotherapy


title: 2790_p_2

description: prior to treatment, chemoradiotherapy


title: 2516_p_2

description: prior to treatment, chemoradiotherapy


title: 2516_p_1

description: prior to treatment, chemoradiotherapy


title: 2654_p_1

description: prior to treatment, chemoradiotherapy


title: 1591_d_1

description: during treatment, chemoradiotherapy


title: 2775_d_1

description: during treatment, chemoradiotherapy


title: 1351_d_2

description: during treatment, chemoradiotherapy


title: 1351_p_1

description: prior to treatment, chemoradiotherapy


title: 2318_p_2

description: prior to treatment, radiotherapy alone


title: 2318_p_1

description: prior to treatment, radiotherapy alone


title: 2313_p_2

source_name: biopsy, prior to treatment, chemotherapy + carbon-ion radiotherapy


title: 1995_d_2

description: during treatment, radiotherapy alone


title: 487_p_1

description: prior to treatment, radiotherapy alone


title: 1845_p_2

description: prior to treatment, radiotherapy alone


title: 487_p_2

description: prior to treatment, radiotherapy alone


title: 1350_p_2

description: prior to treatment, radiotherapy alone


title: 1603_p_1

description: prior to treatment, radiotherapy alone


title: 2313_p_1

description: prior to treatment, chemotherapy + carbon-ion radiotherapy


title: 1846_d_2

description: during treatment, chemoradiotherapy


title: 1845_p_1

description: prior to treatment, radiotherapy alone


title: 2897_p_1

description: prior to treatment, radiotherapy alone


title: 2772_d_2

source_name: biopsy, during treatment, carbon-ion radiotherapy


title: 2772_p_1

source_name: biopsy, prior to treatment, carbon-ion radiotherapy


title: 2897_p_2

description: prior to treatment, radiotherapy alone


title: 2515_d_2

description: during treatment, carbon-ion radiotherapy


title: 2312_d_2


title: 2515_d_1


title: 1350_p_1

description: prior to treatment, radiotherapy alone


title: 2036_d_2


title: 2038_d_1


title: 2036_d_1


title: 2029_d_1


title: 2312_d_1


title: 1244_d_2


title: 1586_d_1


title: 2772_p_2

description: prior to treatment, carbon-ion radiotherapy


title: HEK293_siRNA (siWRN387) against WRN (biol_repl 1) / HEK293_scrambled control siRNA (biol_repl 1)

city: Quebec

first: Michel

last: Lebel

state: Qc

address: 2705 Laurier Blvd, Local T-2-04

department: Centre Hospitalier de l’Université Laval (CHUL)

country: Canada

institute: Centre de Recherche du CHU de Québec

description:
Sample name: 387-1-C
Biological siRNA (siWRN387 molecule) replicate 1 of 2. Biological control siRNA replicate 1 of 2.
HEK293 cells transfected with a siRNA (siWRN387) against WRN (biological replicate one) / HEK293 cells transfected with a scrambled control siRNA (biological replicate one)

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Axon GenePix® 4000B. Data were extracted from images using GenePix® version 6.0 with local background estimation.

data_processing: Data were processed using limma in BioConductor (www.bioconductor.org). The data were background subtracted using normexp and also normalized using the loess method.

source_name: Human 293 embryonic kidney cells (HEK293)

label_protocol: Protocol from Agilent

growth_protocol: Human 293 embryonic kidney cells were maintained in DMEM high glucose supplemented with 10% fetal bovine serum, penicillin (50 IU/mL), and streptomycin (50 µg/mL) at 37°C in atmosphere of 5% CO2.

extract_protocol: Extraction of total RNA protocol described in Sambrook et al., 1989. Molecular cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press.

treatment_protocol: Cells were transfected using 25-mer small interference RNAs specific to WRN mRNA or scrambled siRNAs and left 72 hours in fresh media before mRNA extraction

tag: sirna

value: siRNA (siWRN387 molecule) against WRN mRNA

value: scrambled siRNA


title: 2513_d_1

description: during treatment, radiotherapy alone


title: 2772_d_1


title: HEK293_siRNA (siWRN385) against WRN (biol_repl 2) / HEK293_scrambled control siRNA (biol_repl 2)

description:
Sample name: 385-2-C
Biological siRNA (siWRN385 molecule) replicate 2 of 2. Biological control siRNA replicate 2 of 2.
HEK293 cells transfected with a siRNA (siWRN385) against WRN (biological replicate two) / HEK293 cells transfected with a scrambled control siRNA (biological replicate two)

tag: cell line

value: siRNA (siWRN385 molecule) against WRN mRNA


title: 176_d_2


title: 2513_d_2

description: during treatment, radiotherapy alone


title: 2029_d_2


title: 1846_d_1

description: during treatment, chemoradiotherapy


title: 1586_d_2


title: HEK293_scrambled control siRNA (biol_repl 2) / HEK293_siRNA (siWRN387) against WRN (biol_repl 2)

description:
Sample name: C-387-2
Biological control siRNA replicate 2 of 2. Biological siRNA (siWRN387 molecule) replicate 2 of 2.
HEK293 cells transfected with a scrambled control siRNA (biological replicate two) / HEK293 cells transfected with a siRNA (siWRN387) against WRN (biological replicate two)


title: 2038_d_2


title: Rt_b_treated_2

city: Agripolis - Legnaro (PD)

first: Mery

last: Giantin

state: Padova

address: Viale Università, 16

department: Dip. Biomedicina Comparata e Alimentazione

country: Italy

institute: University of Padova

description:
Rn_6528_004
Whole blood collected in PaxGene tube from male rat and stored at -20°C until extraction.

hyb_protocol: Hybridized according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned using the Agilent scanner G2565BA according to the standard Agilent protocol at a resolution of 5 microns, modifying the default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%).

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.9.2 statistical software.

organism: Rattus norvegicus

source_name: Male rat blood, treated with amiodarone

label_protocol: Amplified and labeled according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

extract_protocol: Heart RNA was extracted according to the Qiagen RNA easy MiniKit protocol for tissues samples, while blood RNA was extracted according to the Qiagen PAXgene Blood RNA kit.

treatment_protocol: Male Sprague-Dawley (CD) rats, which were 10 weeks old and weighed 290-320 grams at the beginning of the study, were treated for ten days with amiodarone by oral route at a dose of 300mg/Kg/die. The control group received the vehicle (methylcellulose 1%, w/v).

value: Sprague-Dawley

value: male

value: 11 weeks

tag: weight

value: whole blood

value: amiodarone


title: HEK293_scrambled control siRNA (biol_repl 1) / HEK293_siRNA (siWRN387) against WRN (biol_repl 1)

description:
Sample name: C-387-1
Biological control siRNA replicate 1 of 2. Biological siRNA (siWRN387 molecule) replicate 1 of 2.
HEK293 cells transfected with a scrambled control siRNA (biological replicate one)/HEK293 cells transfected with a siRNA (siWRN387) against WRN (biological replicate one)


title: 176_d_1


title: Rt_b_treated_3

description:
Rn_6529_002
Whole blood collected in PaxGene tube from male rat and stored at -20°C until extraction.

tag: treatment


title: HEK293_siRNA (siWRN385) against WRN (biol_repl 1) / HEK293_scrambled control siRNA (biol_repl 1)

description:
Sample name: 385-1-C
Biological siRNA (siWRN385 molecule) replicate 1 of 2. Biological control siRNA replicate 1 of 2.
HEK293 cells transfected with a siRNA (siWRN385) against WRN (biological replicate one) / HEK293 cells transfected with a scrambled control siRNA (biological replicate one)


title: 1992_d_2

description: during treatment, radiotherapy alone


title: 2032_d_2


title: 2032_d_1


title: 1244_d_1


title: SNU398

city: Rochester

first: Kuang-Hsiang

last: Chuang

state: NY

address: 601 Elmwood Ave

department: Wilmot Cancer Institute

institute: University of Rochester

hyb_protocol: miRNAs were hybridized to Affymetrix GeneChip miRNA 1.0 microarrays (Affymetrix, Santa Clara, CA, USA). These arrays are comprised of 46,228 probe sets representing over 6703 miRNA sequences (71 organisms) from the Sanger miRNA database (V.11) and an additional 922 sequences of human snoRNA and scaRNA from the Ensemble database and snoRNABase.

scan_protocol: Arrays were scanned with a GeneChip Scanner 7G Plus. Data files (.cel files) were generated using the miRNA-1_0_2X gain library file.

data_processing: Array signal intensities and present calls were produced by using AffyMetrix miRNA QCTool program (version 1.0.33.0, Affymetrix, Santa Clara, CA, USA). The normalization algorithm used was the default setting in AffyMetrix miRNA QCTool program, which is background adjustment, BC-CG Adjust; normalization, Quantile; summarization, median polish. The data processing was carried out on all 46,228 probe sets, after which non-human probe sets were removed leaving 847 human miRNA probe sets.

source_name: HCC cell line

label_protocol: miRNAs were labeled using the FlashTag Biotin RNA labeling kit (Affymetrix, Santa Clara, CA, USA) by following the manufacture’s protocol

extract_protocol: miRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each. One to four extractions were carried out for each tumor to generate sufficient miRNA for microarray analysis

tag: tumor vascular invasion/invasiveness

value: No


title: SNU449

value: Yes


title: Hep3B


title: Rt_b_ctrl_3

description:
Rn_6529_001
Whole blood collected in PaxGene tube from male rat and stored at -20°C until extraction.

source_name: Male rat blood, control, vehicle administration

tag: tissue

value: vehicle control


title: 1603_p_2

description: prior to treatment, radiotherapy alone


title: HEK293_siRNA (siWRN387) against WRN (biol_repl 2) / HEK293_scrambled control siRNA (biol_repl 2)

description:
Sample name: 387-2-C
Biological siRNA (siWRN387 molecule) replicate 2 of 2. Biological control siRNA replicate 2 of 2.
HEK293 cells transfected with a siRNA (siWRN387) against WRN (biological replicate two) / HEK293 cells transfected with a scrambled control siRNA (biological replicate two)


title: HepG2


title: HEK293_scrambled control siRNA (biol_repl 2) / HEK293_siRNA (siWRN385) against WRN (biol_repl 2)

description:
Sample name: C-385-2
Biological control siRNA replicate 2 of 2. Biological siRNA (siWRN385 molecule) replicate 2 of 2.
HEK293 cells transfected with a scrambled control siRNA (biological replicate two) / HEK293 cells transfected with a siRNA (siWRN385) against WRN (biological replicate two)


title: HCC0172_VI+

source_name: HCC tumor


title: SNU423


title: HCC0171_VI+


title: Rt_h_treated_1

description:
Rn_6490_003
Heart sample collected from male rat, submerged in RNAlater and stored at -20°C until extraction.

source_name: Male rat heart, treated with amiodarone

value: heart, left ventricle


title: Rt_h_treated_2

description:
Rn_6490_004
Heart sample collected from male rat, submerged in RNAlater and stored at -20°C until extraction.


title: HCC0169_VI+


title: HCC0170_VI+


title: HEK293_scrambled control siRNA (biol_repl 1) / HEK293_siRNA (siWRN385) against WRN (biol_repl 1)

description:
Sample name: C-385-1
Biological control siRNA replicate 1 of 2. Biological siRNA (siWRN385 molecule) replicate 1 of 2.
HEK293 cells transfected with a scrambled control siRNA (biological replicate one)/HEK293 cells transfected with a siRNA (siWRN385) against WRN (biological replicate one)


title: Rt_b_ctrl_1

description:
Rn_6528_001
Whole blood collected in PaxGene tube from male rat and stored at -20°C until extraction.


title: Rt_h_ctrl_1

description:
Rn_6490_001
Heart sample collected from male rat, submerged in RNAlater and stored at -20°C until extraction.

source_name: Male rat heart, control, vehicle administration


title: Rt_h_ctrl_2

description:
Rn_6490_002
Heart sample collected from male rat, submerged in RNAlater and stored at -20°C until extraction.


title: Rt_h_ctrl_3

description:
Rn_6526_001
Heart sample collected from male rat, submerged in RNAlater and stored at -20°C until extraction.


title: Rice seedlings roots_V Replicate 1

city: Tainan City

first: Chung-Yi

last: Lin

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

description: Biological replicate 1 of 3. Rice seedling roots treated with 1 mM V

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rice Oligo 4×44K Microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA).

data_processing: An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

organism: Oryza sativa

source_name: Roots of rice seedlings were exposed to 1 mM V

label_protocol: 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process. Sample RNA was labeled by Cy5 and RNA from control RNA was labeled by Cy3. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60℃ for 30 minutes.

growth_protocol: 6-day-old seedlings

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Rice roots exposed to  1 mM V

value: 6 day

tag: cultivar

value: exposed to 1 mM Vanadium

source_name: Rice seedlings roots were exposed to water

value: exposed to water


title: Rt_h_treated_3

description:
Rn_6526_002
Heart sample collected from male rat, submerged in RNAlater and stored at -20°C until extraction.

tag: strain


title: Rice seedlings roots_V Replicate 2

description: Biological replicate 2 of 3. Rice seedling roots treated with 1 mM V


title: Rt_b_treated_1

description:
Rn_6528_003
Whole blood collected in PaxGene tube from male rat and stored at -20°C until extraction.


title: HCC0166_VI+


title: HCC0168_VI+


title: HCC0165_VI+


title: HCC0164_VI+


title: HCC0167_VI+


title: HCC0158_VI+


title: HCC0159_VI+


title: HCC0160_VI+


title: HCC0157_VI+


title: HCC0162_VI+


title: HCC0161_VI+


title: HCC0163_VI+


title: Rt_b_ctrl_2

description:
Rn_6528_002
Whole blood collected in PaxGene tube from male rat and stored at -20°C until extraction.


title: HCC0156_VI+


title: HCC0151_VI+


title: HCC0154_VI+


title: HCC0152_VI+


title: HCC0153_VI+


title: HCC0155_VI+


title: SCC induced spontaneously in C3H/He mouse, 23 days after gamma irradiation at 50Gy (g_scc7_50_23d_1)

first: Kazunori

last: Nojiri

address: 4-9-1, Anagawa, Inage-ku

institute: National Institute of Radiological Sciences

description: 23days after gamma irradiation at 50Gy

hyb_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection

scan_protocol: Scanning CodeLink Bioarrays on Agilent G2565 microarray scanner

source_name: Murine tumor

label_protocol: CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation

tag: Squamous cell carcinoma developed spontaneously in C3H/He mouse etablished by Dr. L. Milas from the University of Texas, M. D. Anderson Cancer Center, Huston, USA"


title: Rice seedlings roots_V Replicate 3

description: Biological replicate 3 of 3. Rice seedling roots treated with 1 mM V

tag: age


title: SCC induced spontaneously in C3H/He mouse, 23 days after gamma irradiation at 50Gy (g_scc7_50_23d_2)

description: 23days after gamma irradiation at 50Gy


title: HCC0150_VI+


title: SCC induced spontaneously in C3H/He mouse, 35 days after gamma irradiation at 50Gy (g_scc7_50_35d_2)

description: 35days after gamma irradiation at 50Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 25 days after gamma irradiation at 50Gy (g_mca4_50_25d_3)

description: 25days after gamma irradiation at 50Gy

tag: Mammary Carcinoma developed spontaneously in C3H/He mouse etablished by National Institute of Radiological Science, Chiba, Japan "


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 41 days after gamma irradiation at 50Gy (g_mca4_50_41d_1)

description: 41days after gamma irradiation at 50Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50Gy (g_mca4_50_1d_2)

description: 1day after gamma irradiation at 50Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 25 days after gamma irradiation at 50Gy (g_mca4_50_25d_2)

description: 25days after gamma irradiation at 50Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30Gy (g_mca4_30_1d_2)

description: 1day after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 25 days after gamma irradiation at 50Gy (g_mca4_50_25d_1)

description: 25days after gamma irradiation at 50Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 70Gy (g_mca4_70_1d_2)

description: 1day after gamma irradiation at 70Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 11 days after gamma irradiation at 30Gy (g_mca4_30_11d_2)

description: 11days after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 11 days after gamma irradiation at 30Gy (g_mca4_30_11d_3)

description: 11days after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 70Gy (g_mca4_70_1d_1)

description: 1day after gamma irradiation at 70Gy


title: SCC induced spontaneously in C3H/He mouse, 35 days after gamma irradiation at 50Gy (g_scc7_50_35d_1)

description: 35days after gamma irradiation at 50Gy


title: HCC0147_VI+


title: HCC0148_VI+


title: HCC0146_VI+


title: SCC induced spontaneously in C3H/He mouse, 8 days after gamma irradiation at 30Gy (g_scc7_30_8d_2)

description: 8days after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 41 days after gamma irradiation at 50Gy (g_mca4_50_41d_2)

description: 41days after gamma irradiation at 50Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, no irradiation (g_mca4_0_1d_2)

description: no irradiation


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 11 days after gamma irradiation at 30Gy (g_mca4_30_11d_1)

description: 11days after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50Gy (g_mca4_50_1d_1)

description: 1day after gamma irradiation at 50Gy


title: HCC0149_VI+


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 70Gy (g_nfsa_70_1d_2)

description: 1day after gamma irradiation at 70Gy

tag: Fibrosarcoma developed spontaneously in C3H/He mouse etablished by Dr. L. Milas from the University of Texas, M. D. Anderson Cancer Center, Huston, USA


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 70Gy (g_nfsa_70_1d_1)

description: 1day after gamma irradiation at 70Gy


title: HCC0143_VI+


title: HCC0142_VI+


title: HCC0144_VI+


title: HCC0140_VI+


title: HCC0141_VI+


title: HCC0145_VI+


title: SCC induced spontaneously in C3H/He mouse, 8 days after gamma irradiation at 30Gy (g_scc7_30_8d_1)

description: 8days after gamma irradiation at 30Gy


title: HCC0139_VI+


title: HCC0138_VI+


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 9 days after gamma irradiation at 50Gy (g_nfsa_50_9d_1)

description: 9days after gamma irradiation at 50Gy


title: HCC0137_VI+


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 9 days after gamma irradiation at 50Gy (g_nfsa_50_9d_3)

description: 9days after gamma irradiation at 50Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 4 days after gamma irradiation at 50Gy (g_nfsa_50_4d_3)

description: 4days after gamma irradiation at 50Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 4 days after gamma irradiation at 50Gy (g_nfsa_50_4d_2)

description: 4days after gamma irradiation at 50Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 9 days after gamma irradiation at 50Gy (g_nfsa_50_9d_2)

description: 9days after gamma irradiation at 50Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 4 days after gamma irradiation at 50Gy (g_nfsa_50_4d_1)

description: 4days after gamma irradiation at 50Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50Gy (g_nfsa_50_1d_1)

description: 1day after gamma irradiation at 50Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 9 days after gamma irradiation at 30Gy (g_nfsa_30_9d_2)

description: 9days after gamma irradiation at 30Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 9 days after gamma irradiation at 30Gy (g_nfsa_30_9d_3)

description: 9days after gamma irradiation at 30Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 9 days after gamma irradiation at 30Gy (g_nfsa_30_9d_1)

description: 9days after gamma irradiation at 30Gy


title: R. sphaeroides pRCcsR1-4 vs. R. sphaeroides 2.4.1 pRK415- aerobic conditions - replicate 1

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

description: Biologial sample 1-3

hyb_protocol: A total of two arrays were hybridized to RNA from a total of six 2.4.1 pRK415 cultures. In the same way two arrays were hybridized to RNA from a total of six 2.4.1 pRCcsR1-4 cultures. 2 µg of the pooled RNA were incubated with Cy3 dye (2.4.1 pCcsRa-d) or Cy5 dye (2.4.1) for 15 min at 85°C in the dark. Labeled RNAs were purified using KREApure columns, and the dye incorporation was measured using the nanodrop. Equal quantities of Cy3/Cy5 incorporated RNAs were mixed and incubated with fragmentation buffer for 30 min at 60°C. The samples were mixed with hybridization buffer (Agilent), hybridized onto microarray glass slides, and incubated overnight (17 hrs) at 65°C in a hybridization oven.

scan_protocol: Scanned on an Genepix 3100 scanner. Images were quantified using GenePix Pro 7 Acquisition and Analysis Microarray Software.

data_processing: R with the LIMMA package was used for data evaluation. LOESS normalized, background subtracted.

organism: Cereibacter sphaeroides

source_name: R. sphaeroides pRCcsR1-4 (total cells)

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech, Amsterdam, Netherlands) was used for RNA labeling and fragmentation. 2 µg of the pooled RNA were incubated with Cy3 dye (2.4.1 pRCcsR1-4) or Cy5 dye (2.4.1 pRK415) for 15 min at 85°C in the dark. Labeled RNAs were purified using KREApure columns, and the dye incorporation was measured using the nanodrop.

growth_protocol: Cells were grown under aerobic conditions (100% oxygen) to an OD660 of 0.4

extract_protocol: Total RNA was isolated by the hot phenol method (Janzon et al., 1986). After DNaseI treatment, RNA was purified by phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen).

source_name: R. sphaeroides 2.4.1 pRK415


title: R. sphaeroides pRCcsR1-4 vs. R. sphaeroides 2.4.1 pRK415- aerobic conditions - replicate 2

description: Biologial sample 4-6


title: HCC0132_VI+


title: HCC0134_VI+


title: HCC0136_VI+


title: HCC0135_VI+


title: HCC0133_VI+


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50Gy (g_nfsa_50_1d_2)

description: 1day after gamma irradiation at 50Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, no irradiation (g_nfsa_0_1d_2)

description: no irradiation


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30Gy (g_mca4_30_1d_1)

description: 1day after gamma irradiation at 30Gy


title: HCC0131_VI+


title: HCC0130_VI+


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30Gy (g_nfsa_30_1d_1)

description: 1day after gamma irradiation at 30Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 4 days after gamma irradiation at 30Gy (g_nfsa_30_4d_3)

description: 4days after gamma irradiation at 30Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 4 days after gamma irradiation at 30Gy (g_nfsa_30_4d_2)

description: 4days after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 70Gy (g_mmca_70_1d_1)

description: 1day after gamma irradiation at 70Gy

tag: Mammary Carcinoma developed spontaneously in C3H/He mouse etablished by Dr. L. Milas from the University of Texas, M. D. Anderson Cancer Center, Huston, USA


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 19 days after gamma irradiation at 50Gy (g_mmca_50_19d_3)

description: 19days after gamma irradiation at 50Gy


title: HCC0129_VI+


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 4 days after gamma irradiation at 30Gy (g_nfsa_30_4d_1)

description: 4days after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 70Gy (g_mmca_70_1d_2)

description: 1day after gamma irradiation at 70Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 19 days after gamma irradiation at 50Gy (g_mmca_50_19d_2)

description: 19days after gamma irradiation at 50Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 19 days after gamma irradiation at 50Gy (g_mmca_50_19d_1)

description: 19days after gamma irradiation at 50Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, no irradiation (g_nfsa_0_1d_1)

description: no irradiation


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50Gy (g_mmca_50_1d_2)

description: 1day after gamma irradiation at 50Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30Gy (g_nfsa_30_1d_2)

description: 1day after gamma irradiation at 30Gy


title: HCC0128_VI+


title: genomic DNA from normal scalp skin

city: Baltimore

first: Andrew

last: Feinberg

state: Maryland

address: 855 N. Wolfe St

institute: Johns Hopkins University School of Medicine

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

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Minfi Package

source_name: normal scalp skin

extract_protocol: Genomic DNA was purified using EpiCentre MasterPure kit according to manufactuerer's instructions.

treatment_protocol: preserved in OCT immediately after biopsy

value: normal scalp skin

tag: body site

value: Scalp


title: genomic DNA from normal lip skin

source_name: normal lip skin

value: normal lip skin

tag: gender

value: female

value: Lip


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30Gy (g_mmca_30_1d_1)

description: 1day after gamma irradiation at 30Gy


title: HCC0127_VI+


title: HCC0126_VI+


title: HCC0125_VI+


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50Gy (g_mmca_50_1d_1)

description: 1day after gamma irradiation at 50Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30Gy (g_mmca_30_1d_2)

description: 1day after gamma irradiation at 30Gy


title: genomic DNA from normal leg skin 2

source_name: normal leg skin

value: normal leg skin

value: Leg


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 9 days after gamma irradiation at 30Gy (g_mmca_30_9d_2)

description: 9days after gamma irradiation at 30Gy


title: HCC0124_VI+


title: genomic DNA from scalp squamous cell carcinoma

source_name: scalp squamous cell carcinoma

value: scalp squamous cell carcinoma

value: male


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 9 days after gamma irradiation at 30Gy (g_mmca_30_9d_1)

description: 9days after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, no irradiation (g_mmca_0_1d_1)

description: no irradiation


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 9 days after no irradiation (g_mmca_0_9d_2)

description: 9days after no irradiation


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 9 days after gamma irradiation at 30Gy (g_mmca_30_9d_3)

description: 9days after gamma irradiation at 30Gy


title: genomic DNA from leg squamous cell carcinoma 2

source_name: leg squamous cell carcinoma

value: leg squamous cell carcinoma


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, no irradiation (g_mmca_0_1d_2)

description: no irradiation


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after gamma irradiation at 70Gy (g_8520_70_1d_2)

description: 1day after gamma irradiation at 70Gy

tag: Radiation induced C3H mouse Fibrosarcoma eatablished by National Institute of Radiological Science, Chiba, Japan


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after gamma irradiation at 70Gy (g_8520_70_1d_1)

description: 1day after gamma irradiation at 70Gy


title: Radiation induced C3H mouse Fibrosarcoma, 22 days after gamma irradiation at 50Gy (g_8520_50_22d_3)

description: 22days after gamma irradiation at 50Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, no irradiation (g_mca4_0_1d_1)

description: no irradiation


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 9 days after no irradiation (g_mmca_0_9d_1)

description: 9days after no irradiation


title: HCC0122_VI+


title: genomic DNA from normal leg skin 1


title: genomic DNA from neck squamous cell carcinoma

source_name: neck squamous cell carcinoma

value: neck squamous cell carcinoma

value: Neck


title: HCC0121_VI+

value: Yes


title: HCC0120_VI+


title: HCC0123_VI+


title: genomic DNA from normal arm skin

source_name: normal arm skin

value: normal arm skin

value: Arm


title: Radiation induced C3H mouse Fibrosarcoma, 22 days after gamma irradiation at 50Gy (g_8520_50_22d_2)

description: 22days after gamma irradiation at 50Gy


title: genomic DNA from arm squamous cell carcinoma

source_name: arm squamous cell carcinoma

value: arm squamous cell carcinoma


title: HCC0119_VI+


title: HCC0118_VI+


title: Radiation induced C3H mouse Fibrosarcoma, 16 days after gamma irradiation at 30Gy (g_8520_30_16d_2)

description: 16days after gamma irradiation at 30Gy


title: Radiation induced C3H mouse Fibrosarcoma, 16 days after gamma irradiation at 30Gy (g_8520_30_16d_3)

description: 16days after gamma irradiation at 30Gy


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after gamma irradiation at 50Gy (g_8520_50_1d_1)

description: 1day after gamma irradiation at 50Gy


title: Radiation induced C3H mouse Fibrosarcoma, 22 days after gamma irradiation at 50Gy (g_8520_50_22d_1)

description: 22days after gamma irradiation at 50Gy


title: genomic DNA from calf squamous cell carcinoma

source_name: calf squamous cell carcinoma

value: calf squamous cell carcinoma

value: Calf


title: Radiation induced C3H mouse Fibrosarcoma, 8 days after gamma irradiation at 30Gy (g_8520_30_8d_2)

description: 8days after gamma irradiation at 30Gy


title: genomic DNA from normal neck skin

source_name: normal neck skin

value: normal neck skin


title: HCC0116_VI+

source_name: HCC tumor


title: genomic DNA from leg squamous cell carcinoma 1


title: Radiation induced C3H mouse Fibrosarcoma, 8 days after gamma irradiation at 30Gy (g_8520_30_8d_1)

description: 8days after gamma irradiation at 30Gy


title: Radiation induced C3H mouse Fibrosarcoma, 8 days after gamma irradiation at 30Gy (g_8520_30_8d_3)

description: 8days after gamma irradiation at 30Gy


title: HCC0115_VI+


title: HCC0114_VI-

value: No


title: Radiation induced C3H mouse Fibrosarcoma, no irradiation (g_8520_0_1d_1)

description: no irradiation


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after gamma irradiation at 30Gy (g_8520_30_1d_1)

description: 1day after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 20 days after carbon-ion irradiation at 30Gy (c_mca4_30_d20_1)

description: 20days after carbon-ion irradiation at 30Gy

tag: Mammary Carcinoma developed spontaneously in C3H/He mouse etablished by National Institute of Radiological Science, Chiba, Japan


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after gamma irradiation at 50Gy (g_8520_50_1d_2)

description: 1day after gamma irradiation at 50Gy


title: HCC0113_VI-


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 5 days after carbon-ion irradiation at 30Gy (c_mca4_30_d5_2)

description: 5days after carbon-ion irradiation at 30Gy


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after gamma irradiation at 30Gy (g_8520_30_1d_2)

description: 1day after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 3 days after carbon-ion irradiation at 30Gy (c_mca4_30_d3_1)

description: 3days after carbon-ion irradiation at 30Gy


title: Radiation induced C3H mouse Fibrosarcoma, no irradiation (g_8520_0_1d_2)

description: no irradiation


title: genomic DNA from old sun exposed epidermis 9

source_name: old sun exposed epidermis

treatment_protocol: Overnight incubation in dispase at 4 degrees C followed by seperation of epidermal and dermal layers.

value: female

tag: exposure

value: sun exposed

value: epidermis


title: Radiation induced C3H mouse Fibrosarcoma, 16 days after gamma irradiation at 30Gy (g_8520_30_16d_1)

description: 16days after gamma irradiation at 30Gy


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after carbon-ion irradiation at 30Gy (c_mca4_30_d1_1)

description: 1day after carbon-ion irradiation at 30Gy


title: genomic DNA from old sun exposed epidermis 10


title: HCC0111_VI-


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 3 days after carbon-ion irradiation at 30Gy (c_mca4_30_d3_2)


title: genomic DNA from old sun exposed epidermis 7


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 6hours after carbon-ion irradiation at 30Gy (c_mca4_30_6h_1)


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 20 days after carbon-ion irradiation at 30Gy (c_mca4_30_d20_2)


title: HCC0117_VI+


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after carbon-ion irradiation at 30Gy (c_mca4_30_d1_2)


title: HCC0110_VI-


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 6hours after carbon-ion irradiation at 30Gy (c_mca4_30_6h_2)


title: genomic DNA from lip squamous cell carcinoma

source_name: lip squamous cell carcinoma

value: lip squamous cell carcinoma

value: Lip


title: genomic DNA from old sun exposed epidermis 8

value: male


title: genomic DNA from old sun exposed epidermis 6


title: HCC0108_VI-


title: genomic DNA from old sun exposed epidermis 3


title: HCC0107_VI-


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 20 days after carbon-ion irradiation at 30Gy (c_mmca_30_d20_1)


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 5 days after carbon-ion irradiation at 30Gy (c_mca4_30_d5_1)


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, no irradiation (c_mca4_30_0h_2)

description: no irradiation


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 5 days after carbon-ion irradiation at 30Gy (c_mmca_30_d5_1)


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 20 days after carbon-ion irradiation at 30Gy (c_mmca_30_d20_2)


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 5 days after carbon-ion irradiation at 30Gy (c_mmca_30_d5_2)


title: genomic DNA from old sun exposed epidermis 4


title: HCC0109_VI-


title: genomic DNA from old sun exposed epidermis 5


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, no irradiation (c_mca4_30_0h_1)

description: no irradiation


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after carbon-ion irradiation at 30Gy (c_mmca_30_d1_2)


title: HCC0106_VI-


title: HCC0112_VI-


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 3 days after carbon-ion irradiation at 30Gy (c_mmca_30_d3_2)


title: genomic DNA from old sun exposed epidermis 2


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 3 days after carbon-ion irradiation at 30Gy (c_mmca_30_d3_1)


title: HCC0105_VI-


title: HCC0104_VI-


title: genomic DNA from old sun protected epidermis 10

source_name: old sun protected epidermis

value: sun protected


title: genomic DNA from old sun exposed epidermis 1


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 6hours after carbon-ion irradiation at 30Gy (c_mmca_30_6h_1)

source_name: Murine tumor


title: HCC0103_VI-


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 6hours after carbon-ion irradiation at 30Gy (c_mmca_30_6h_2)


title: genomic DNA from old sun protected epidermis 8


title: HCC0102_VI-


title: genomic DNA from old sun protected epidermis 9


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, no irradiation (c_mmca_30_0h_1)

description: no irradiation


title: HCC0101_VI-


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, 1 day after carbon-ion irradiation at 30Gy (c_mmca_30_d1_1)


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 5 days after carbon-ion irradiation at 30Gy (c_nfsa_30_d5_1)


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 20 days after carbon-ion irradiation at 30Gy (c_nfsa_30_d20_2)


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 20 days after carbon-ion irradiation at 30Gy (c_nfsa_30_d20_1)


title: HCC0100_VI-


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 5 days after carbon-ion irradiation at 30Gy (c_nfsa_30_d5_2)


title: genomic DNA from old sun protected epidermis 7


title: leukocytes dog 10-stimulated-biological replicate 10

city: The University of Sydney

first: Peter

last: Williamson

state: NSW

address: Rm 552 RMC Gunn Building B19

department: Faculty of Veterinary Science

country: Australia

institute: University of Sydney

hyb_protocol: Labelled and hybridized to an Affymetrix® Canine Gene 1.0 ST Array according to the manufacturer’s instructions.

scan_protocol: Genechips were scanned using GeneChip Scanner 3000 (Affymetrix). Probe intensities were obtained using GCOS operating software (Affymetrix)

data_processing: RMA

organism: Canis lupus familiaris

source_name: Canine leukocytes, stimulated

extract_protocol: RNA was isolated from samples using a modified extraction procedure and micro-spin columns (QIAmp; Qiagen, Melbourne, Vic). The lysate was pipetted directly into a QIAshredder spin column following incubation in a 37˚C water bath until completely thawed and salts dissolved. 70% ethanol was added to the homogenized lysate before it was transferred into a QIAamp spin column and washed using a high-salt buffering system allowing RNA to bind to the QIAmp membrane as contaminants are removed. Purified RNA was eluted in 30 μl of RNase-free water followed by a second elution in 50 μl and stored at    -80˚C.

treatment_protocol: Blood was collected into EDTA coated vacutainers, and the leukocyte fraction was isolated by gradient centrifugation. Cells were divided into two aliquots and each were resuspended in 1 ml Dulbecco’s Modified Eagle Medium media. Both were incubated for 4 hours, one in the presence of 5μg/ml of PHA, a mitogen for T-cell activation, the other served as non-stimulated control cells. After incubation the cells were collected by centrifugation, and then lysed in RLT buffer (QIAmp; Qiagen Aust). Once lysed samples were immediately frozen until further use (within 48hr).

tag: cell type

value: T-cells

tag: age (years)

tag: breed

value: Bullmastiff

tag: treament

value: T-cells stimulated with PHA


title: Mammary Carcinoma induced spontaneously in C3H/He mouse, no irradiation (c_mmca_30_0h_2)

description: no irradiation


title: genomic DNA from old sun protected epidermis 6

tag: tissue


title: leukocytes dog 10-control-biological replicate 10

source_name: Canine leukocytes

label_protocol: Labelled and hybridized to an Affymetrix® Canine Gene 1.0 ST Array according to the manufacturer’s instructions.

value: non-stimulated


title: Radiation induced C3H mouse Fibrosarcoma, 20 days after carbon-ion irradiation at 30Gy (c_8520_30_d20_2)


title: Radiation induced C3H mouse Fibrosarcoma, 20 days after carbon-ion irradiation at 30Gy (c_8520_30_d20_1)


title: HCC0098_VI-

tag: tumor vascular invasion/invasiveness


title: metR_vs_metR+metZ

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

hyb_protocol: Labeled probes were hybridized to microarrays in 8x15k format, custom made by Agilent (Design ID: 049514) using Gene Expression Hybridization Kit, Hybridization Chamber and Hybridization oven (all from Agilent) for 17 hours at 65°C.

scan_protocol: After washing using Gene Expression Wash Buffer Set (Agilent) the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5μm and 100% laser power. PMT gain was set to around 600 and 750 for 532 nm and 635 nm excitation respectively with minor adjustments to normalize images. Feature extraction was done using GenePix Pro 6.1 (Molecular Devices, USA).

data_processing: GPR files were analyzed further with Acuity 4.0 software starting with lowess normalization. Normalized log2 ratio data from biological replicates and technical replicates (dye swap) were averaged and the statistical significance (p-value) was calculated.

organism: Aspergillus nidulans

source_name: mycelium

label_protocol: Samples of total RNA (5μg) were labeled with QuickAmp Labeling Kit, Two-Color (Agilent) with Cy3- and Cy5-UTP according to the manufacturer’s protocol.

growth_protocol: 100 ml of minimal medium (MM-S) supplemented with 0.3 mM methionine and 0.0005 mg/ml pyridoxine in 300-ml Erlenmeyer flasks was inoculated with 2-5x108 conidia collected with 2-3 ml of 0,01% Tween-80 from fresh (48-72h, 37oC) solid complete medium cultures. Mycelia were grown for 18-19 h at 30oC in orbital shaker set to 200 rpm up to approximately 0.8 g of wet weight. Mycelia were then harvested by filtration, washed with distilled water, dried on filter paper, weighed, frozen in liquid nitrogen and kept at –80oC.

extract_protocol: 300 mg of mycelia were powdered in liquid nitrogen and total RNA was isolated using TRI Reagent (Molecular Research Center) according to the manufacturer’s protocol. RNA was further purified by precipitation with lithium chloride added to a final concentration of 3.42 M. Purified RNA was stored at -80°C.

tag: strain

value: K1 (delmetR,pyr-4+)


title: Radiation induced C3H mouse Fibrosarcoma, 5 days after carbon-ion irradiation at 30Gy (c_8520_30_d5_2)


title: HCC0097_VI-


title: genomic DNA from old sun protected epidermis 5


title: HCC0096_VI-


title: genomic DNA from old sun protected epidermis 1


title: leukocytes dog 8-stimulated-biological replicate 8


title: leukocytes dog 8-control-biological replicate 8


title: leukocytes dog 9-stimulated-biological replicate 9


title: SCC induced spontaneously in C3H/He mouse, 5 days after carbon-ion irradiation at 30Gy (c_scc7_30_d5_2)

tag: Squamous cell carcinoma developed spontaneously in C3H/He mouse etablished by Dr. L. Milas from the University of Texas, M. D. Anderson Cancer Center, Huston, USA


title: genomic DNA from old sun protected epidermis 4

tag: age


title: HCC0094_VI-


title: HCC0095_VI-


title: SCC induced spontaneously in C3H/He mouse, 42 days after carbon-ion irradiation at 30Gy (c_scc7_30_d42_1)

description: 42days after carbon-ion irradiation at 30Gy


title: genomic DNA from old sun protected epidermis 2


title: leukocytes dog 11-stimulated-biological replicate 11


title: leukocytes dog 7-stimulated-biological replicate 7


title: leukocytes dog 9-control-biological replicate 9


title: SCC induced spontaneously in C3H/He mouse, 42 days after carbon-ion irradiation at 30Gy (c_scc7_30_d42_2)


title: Radiation induced C3H mouse Fibrosarcoma, 5 days after carbon-ion irradiation at 30Gy (c_8520_30_d5_1)


title: HCC0093_VI-


title: SCC induced spontaneously in C3H/He mouse, 5 days after carbon-ion irradiation at 30Gy (c_scc7_30_d5_1)


title: genomic DNA from old sun protected epidermis 3


title: HCC0099_VI-


title: HCC0092_VI-


title: leukocytes dog 6-stimulated-biological replicate 6


title: SCC induced spontaneously in C3H/He mouse, 20 days after carbon-ion irradiation at 30Gy (c_nrs1_30_d20_2)

tag: Squamous cell carcinoma developed spontaneously in C3H/He mouse etablished by National Institute of Radiological Science, Chiba, Japan


title: genomic DNA from young sun exposed epidermis 8

source_name: young sun exposed epidermis


title: HCC0089_VI-


title: genomic DNA from young sun exposed epidermis 6


title: genomic DNA from young sun exposed epidermis 5


title: leukocytes dog 5-control-biological replicate 5


title: genomic DNA from young sun exposed epidermis 3


title: HCC0088_VI-


title: genomic DNA from young sun exposed epidermis 4


title: SCC induced spontaneously in C3H/He mouse, 15 days after gamma irradiation at 50Gy (g_nrs1_50_15d_3)

description: 15days after gamma irradiation at 50Gy


title: SCC induced spontaneously in C3H/He mouse, 5 days after carbon-ion irradiation at 30Gy (c_nrs1_30_d5_1)


title: genomic DNA from young sun exposed epidermis 9


title: leukocytes dog 7-control-biological replicate 7


title: genomic DNA from young sun exposed epidermis 1


title: SCC induced spontaneously in C3H/He mouse, 20 days after carbon-ion irradiation at 30Gy (c_nrs1_30_d20_1)


title: genomic DNA from young sun protected epidermis 8

source_name: young sun protected epidermis


title: genomic DNA from young sun exposed epidermis 7


title: leukocytes dog 4-control-biological replicate 4


title: HCC0086_VI-


title: genomic DNA from young sun protected epidermis 9


title: genomic DNA from young sun protected epidermis 5


title: HCC0090_VI-


title: SCC induced spontaneously in C3H/He mouse, 5 days after carbon-ion irradiation at 30Gy (c_nrs1_30_d5_2)


title: db/db4

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

description: Gene expression data from male db/db liver, 4

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 h at 45°C to mouse 430_2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner(7G).

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and all prone sets scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: mouse liver biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2010, Affymetrix).

growth_protocol: C57BL/KSlepr+/+ (BKS) and BKS.Cg-Leprdb (db/db) mice were bred and maintained in a regular 12h light/dark cycle under constant temperature and humidity (22°C ± 1°C, 50% ± 5% humidity) with unrestricted access to water and standart chow.

extract_protocol: Total RNA extraction was performed with Qiazol tissue lysis and RNeasy affinity column purification (Qiagen). For Array experiments 8µg total RNA were used.

treatment_protocol: At 14 weeks of age male  mice were sacrifced by CO2 asphyxation, liver was isolated and 100 mg aliquots were snap frozen in liquid nitrogen. Samples were stored at -80°C until processing.

value: BKS.Cg-Leprdb (db/db)

value: 14 weeks

value: liver


title: leukocytes dog 5-stimulated-biological replicate 5


title: HCC0084_VI-


title: HCC0087_VI-


title: HCC0091_VI-


title: leukocytes dog 2-stimulated-biological replicate 2


title: db/db3

description: Gene expression data from male db/db liver, 3


title: leukocytes dog 6-control-biological replicate 6


title: genomic DNA from young sun protected epidermis 6


title: SCC induced spontaneously in C3H/He mouse, 15 days after gamma irradiation at 50Gy (g_nrs1_50_15d_2)

description: 15days after gamma irradiation at 50Gy


title: leukocytes dog 3-stimulated-biological replicate 3


title: db/db2

description: Gene expression data from male db/db liver, 2


title: HCC0082_VI-


title: leukocytes dog 4-stimulated-biological replicate 4


title: HCC0085_VI-


title: leukocytes dog 3-control-biological replicate 3


title: HCC0081_VI-


title: SCC induced spontaneously in C3H/He mouse, 8 days after gamma irradiation at 30Gy (g_nrs1_30_8d_2)

description: 8days after gamma irradiation at 30Gy


title: leukocytes dog 1-stimulated-biological replicate 1


title: db/db1

description: Gene expression data from male db/db liver, 1


title: leukocytes dog 2-control-biological replicate 2


title: SCC induced spontaneously in C3H/He mouse, 8 days after gamma irradiation at 30Gy (g_nrs1_30_8d_1)

description: 8days after gamma irradiation at 30Gy


title: SCC induced spontaneously in C3H/He mouse, 8 days after gamma irradiation at 30Gy (g_nrs1_30_8d_3)

description: 8days after gamma irradiation at 30Gy


title: HCC0083_VI-


title: genomic DNA from young sun protected epidermis 1


title: genomic DNA from young sun exposed epidermis 2


title: SCC induced spontaneously in C3H/He mouse, 15 days after gamma irradiation at 50Gy (g_nrs1_50_15d_1)

description: 15days after gamma irradiation at 50Gy


title: BKS4

description: Gene expression data from male BKS liver, 4

value: C57BL/KSlepr+/+ (BKS)


title: HCC0077_VI-

value: No


title: HCC0078_VI-


title: HCC0080_VI-


title: BKS5

description: Gene expression data from male BKS liver, 5


title: leukocytes dog 1-control-biological replicate 1


title: BKS1

description: Gene expression data from male BKS liver, 1


title: BKS2

description: Gene expression data from male BKS liver, 2


title: BKS3

description: Gene expression data from male BKS liver, 3


title: RNA from older, sun-protected epidermis 4

description: sun-protected

hyb_protocol: affymetrix hyb protocol

scan_protocol: affymetrix 7G gene chip scanner

data_processing: data were processed using the frma package from Bioconductor, using the frma method described in McCall MN, Bolstad BM, and Irizarry RA (2010). Frozen Robust Multi-Array Analysis (fRMA), Biostatistics, 11(2):242-253, and the barcode method (used for presence/absence calls) described in McCall MN, Uppal K, Jaffee HA, Zilliox MJ, and Irizarry RA (2011). The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes, Nucleic Acids Research, 39:D1011-5.

source_name: Older, sun-protected epidermis 4

label_protocol: 3 prime IVT express

extract_protocol: Trizol extraction of total RNA followed by cleanup and Dnase treatment using Qiagen Rneasy columns according to manufacturer's instructions.

value: dispase separated epidermis

tag: Sex

value: female

value: sun-protected


title: RNA from older, sun-protected epidermis 5

description: sun-protected

source_name: Older, sun-protected epidermis 5


title: RNA from older, sun-protected epidermis 3

description: sun-protected

source_name: Older, sun-protected epidermis 3


title: HCC0076_VI-


title: genomic DNA from young sun protected epidermis 3

value: epidermis


title: HCC0079_VI-


title: HCC0075_VI-


title: RNA from older, sun-protected epidermis 2

description: sun-protected

source_name: Older, sun-protected epidermis 2


title: genomic DNA from old sun exposed dermis 10

source_name: old sun exposed dermis

value: sun exposed

value: dermis


title: genomic DNA from young sun protected epidermis 2

value: sun protected


title: mPAC-notinfected-rep3

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

description: mouse pancreatic duct (mPAC) cells not-infected, biological replicate 3

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: Raw data was background adjusted, normalized and summarized by Robust Multi-array Analysis (RMA) using the Affy package from Bioconductor on R language.

source_name: mouse pancreatic duct (mPAC) cells

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

growth_protocol: Mouse pancreatic duct mPAC L20 cells were cultured in DMEM supplemented with 10% fetal bovine serum and antibiotics as previously described (Proc Natl Acad Sci U S A, 2004. 101(36): p. 13245-50)

extract_protocol: Rneasy kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: For viral treatment, 250000 mPAC cells were seeded onto 6-well plates the day before infection. Adenovirus were added at a multiplicity of infection (moi) of 40 and incubated for 2 h at 37ºC in culture medium. Then, cells were cultured for an additional 44-46 h period.  Double infections were conducted using moi=40 for each individual adenovirus. In overexpression experiments, the two adenoviruses were added to cells simultaneously.  Adenovirus expressing intact mouse Atoh8 and human Neurog3 were previously described (Proc Natl Acad Sci U S A, 2004. 101(36): p. 13245-50, PLoS One, 2008. 3(6): p. e2430). Control adenoviruses AdCMV-Bgal were kindly provided by Dr. CB.Newgard (Duke University, NC, USA).

tag: treatment

value: control

tag: cell line

value: mPAC L20


title: genomic DNA from old sun exposed dermis 8

tag: gender

value: male


title: genomic DNA from young sun protected epidermis 4


title: genomic DNA from young sun protected epidermis 7


title: mPAC-notinfected-rep2

description: mouse pancreatic duct (mPAC) cells not-infected, biological replicate 2


title: mPAC-notinfected-rep1

description: mouse pancreatic duct (mPAC) cells not-infected, biological replicate 1


title: RNA from younger, sun-protected epidermis 2

description: sun-protected

source_name: Younger, sun-protected epidermis 2


title: RNA from older, sun-protected epidermis 1

description: sun-protected

source_name: Older, sun-protected epidermis 1


title: RNA from younger, sun-protected epidermis 3

description: sun-protected

source_name: Younger, sun-protected epidermis 3


title: HCC0073_VI-

source_name: HCC tumor


title: HCC0074_VI-


title: mPAC-Ngn3+Atoh8-rep3

description: mouse pancreatic duct (mPAC) cells infected with adenoviruses coding forNeurogenin 3 and Atonal Homolog 8, biological replicate 3

value: Neurogenin3 and Atonal Homolog 8 overexpression


title: HCC0072_VI-


title: RNA from younger, sun-protected epidermis 1

description: sun-protected

source_name: Younger, sun-protected epidermis 1


title: RNA from younger, sun-exposed epidermis 4

description: sun-exposed

source_name: Younger, sun-exposed epidermis 4

value: sun-exposed


title: mPAC-Ngn3+Atoh8-rep1

description: mouse pancreatic duct (mPAC) cells infected with adenoviruses coding forNeurogenin 3 and Atonal Homolog 8, biological replicate 1


title: mPAC-Ngn3+Atoh8-rep2

description: mouse pancreatic duct (mPAC) cells infected with adenoviruses coding forNeurogenin 3 and Atonal Homolog 8, biological replicate 2


title: HCC0070_VI-


title: RNA from older, sun-exposed epidermis 4

description: sun-exposed

source_name: Older, sun-exposed epidermis 4


title: HCC0069_VI-


title: HCC0071_VI-


title: genomic DNA from old sun exposed dermis 9


title: RNA from older, sun-exposed epidermis 3

description: sun-exposed

source_name: Older, sun-exposed epidermis 3


title: RNA from older, sun-exposed epidermis 2

description: sun-exposed

source_name: Older, sun-exposed epidermis 2


title: mPAC-Bgal+Ngn3-rep3

description: mouse pancreatic duct (mPAC) cells infected with adenoviruses coding for β-galactosidase and Neurogenin 3, biological replicate 3

value: β-galactosidase and Neurogenin3 overexpression


title: genomic DNA from old sun exposed dermis 4


title: HCC0068_VI-


title: genomic DNA from old sun exposed dermis 2


title: genomic DNA from old sun exposed dermis 6


title: HCC0067_VI-


title: mPAC-Bgal+Ngn3-rep1

description: mouse pancreatic duct (mPAC) cells infected with adenoviruses coding for β-galactosidase and Neurogenin 3, biological replicate 1


title: genomic DNA from old sun exposed dermis 7


title: mPAC-Bgal+Ngn3-rep2

description: mouse pancreatic duct (mPAC) cells infected with adenoviruses coding for β-galactosidase and Neurogenin 3, biological replicate 2


title: RNA from older, sun-exposed epidermis 1

description: sun-exposed

source_name: Older, sun-exposed epidermis 1


title: mPAC-Ngn3-rep3

description: mouse pancreatic duct (mPAC) cells infected with an adenovirus coding for Neurogenin 3, biological replicate 3

value: Neurogenin3 overexpression


title: HCC0066_VI-


title: mPAC-Ngn3-rep2

description: mouse pancreatic duct (mPAC) cells infected with an adenovirus coding for Neurogenin 3, biological replicate 2


title: genomic DNA from old sun exposed dermis 5


title: RNA from younger, sun-exposed epidermis 2

description: sun-exposed

source_name: Younger, sun-exposed epidermis 2


title: genomic DNA from old sun exposed dermis 3


title: HCC0065_VI-


title: RNA from younger, sun-exposed epidermis 3

description: sun-exposed

source_name: Younger, sun-exposed epidermis 3


title: HCC0064_VI-


title: mPAC-Ngn3-rep1

description: mouse pancreatic duct (mPAC) cells infected with an adenovirus coding for Neurogenin 3, biological replicate 1


title: RNA from younger, sun-exposed epidermis 1

description: sun-exposed

source_name: Younger, sun-exposed epidermis 1


title: mPAC-Atoh8-rep3

description: mouse pancreatic duct (mPAC) cells infected with an adenovirus coding for Atonal homolog 8, biological replicate 3

value: Atonal Homolog 8  overexpression


title: MDA-MB-231 cells siYAP/TAZ#2, biological replica C

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

description: Gene expression data from MDA-MB-231 cells depleted of endogenous YAP and TAZ by siRNA mix #2

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GeneChip Command Console Software (AGCC)

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: MDA-MB-231 breast cancer cells

label_protocol: Biotinylated cRNA were prepared using the 3'IVT Kit ( Affymetrix, Santa Clara, USA, CA) according to manufacturer's intructions.

growth_protocol: Cells were seeded at low confluence on day 1 in standard growth medium (DMEM/F12 with 2mM Glutamine, 17.5mM D-glucose, without antibiotics, 10% Fetal Bovine Serum).

extract_protocol: Trizol extraction of total RNA, followed by DNAseI digestion to reduce genomic DNA contaminations, was performed according to the manufacturer's instructions.

treatment_protocol: Cells were transfected on day 2 with siRNA oligonucleotides (final concentration 33nM) by using RNAi MAX (Life Technologies), following a direct transfection protocol as indicated by manifacturer's instructions. On day 3, medium was renewed. On day 4, cells were washed with 1XHBSS and harvested for RNA extraction.

tag: transfection

value: YAP/TAZ siRNA #2


title: mPAC-Atoh8-rep1

description: mouse pancreatic duct (mPAC) cells infected with an adenovirus coding for Atonal homolog 8, biological replicate 1


title: genomic DNA from old sun protected dermis 8

source_name: old sun protected dermis


title: HCC0062_VI-

value: No


title: mPAC-Atoh8-rep2

description: mouse pancreatic duct (mPAC) cells infected with an adenovirus coding for Atonal homolog 8, biological replicate 2


title: HCC0061_VI-


title: genomic DNA from old sun protected dermis 9


title: genomic DNA from old sun protected dermis 10


title: HCC0060_VI-


title: genomic DNA from old sun exposed dermis 1

source_name: old sun exposed dermis


title: MDA-MB-231 cells siYAP/TAZ#2, biological replica A


title: MDA-MB-231 cells siYAP/TAZ#2, biological replica B


title: mPAC-Bgal-rep3

description: mouse pancreatic duct (mPAC) cells infected with an adenovirus coding for β-galactosidase, biological replicate 3

source_name: mouse pancreatic duct (mPAC) cells

value: β-galactosidase overexpression


title: genomic DNA from old sun protected dermis 6

value: female


title: MDA-MB-231 cells siYAP/TAZ#1, biological replica D

description: Gene expression data from MDA-MB-231 cells depleted of endogenous YAP and TAZ by siRNA mix #1

value: YAP/TAZ siRNA #1


title: HCC0059_VI-


title: MDA-MB-231 cells siYAP/TAZ#2, biological replica D


title: mPAC-Bgal-rep1

description: mouse pancreatic duct (mPAC) cells infected with an adenovirus coding for β-galactosidase, biological replicate 1


title: mPAC-Bgal-rep2

description: mouse pancreatic duct (mPAC) cells infected with an adenovirus coding for β-galactosidase, biological replicate 2


title: genomic DNA from old sun protected dermis 4


title: HCC0058_VI-


title: genomic DNA from old sun protected dermis 7


title: HCC0057_VI+

value: Yes


title: LPS_Stimulated_Overfed_Zebrafish_Liver_rep4

city: Leiden

first: Gabriel

last: Forn-Cuní

state: Zuid-Holland

address: Einsteinweg 55

department: IBL-ASH-CO

institute: Universiteit Leiden

hyb_protocol: Each amplified and labelled sample was briefly hybridized at 65 °C for 17 hours following manufacturer instructions.

scan_protocol: Microarray slides were scanned with Agilent Technologies Scanner model G2505B.

data_processing: Spot intensities and other quality control features were extracted with the Feature Extraction software version 10.4.0.0 (Agilent). The results for the fluorescence intensity data and quality annotations were imported into GeneSpring GX version 12.6 (Agilent Technologies). All of the control features (including the positive and negative controls and the landing lights) were excluded from subsequent analyses. Normalization was then carried out by a percentile shift at the 75th percentile. Entities with an expression between the 20 and 95th percentile in the raw data were retained and further analyzed at gene level (i.e. merging the signal values of the different probes for the same gene). The gene-level analysis results are provided in the 'gene_level_analysis.txt' along with the data processing details in the 'readme.txt'.

organism: Danio rerio

source_name: Liver Diet Induced Obesity LPS Stimulated Adult Zebrafish 3hpi

label_protocol: Total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit according to manufacturer's instructions.

extract_protocol: RNA was extracted with TRIzol reagent (Life Technologies, Madrid, Spain) following the TRIzol manufacturer’s specifications in combination with the RNeasy Mini Kit (Qiagen, Madrid), and preserved at -80 ºC until use. After DNase I treatment, RNA quality was assessed with the Agilent 2100 Bioanalyzer and kept frozen at -80 °C until all of the experiments could be hybridized and processed simultaneously.

treatment_protocol: Control fish were fed two times a day, one with Artemia and the other with standard fish chow while obese fish were fed fish chow two more times a day. After 8 months of differential diet, PBS or 10 μg of pure LPS (Sigma) was intraperitoneally injected in both control and obese fish. For every treatment, 4 biological replicates of livers from 3 fish were pooled 3 hours post injection and conserved at -80ºC until use.

tag: diet

value: Overfed

tag: stimulated with

value: 10 μg of pure LPS

tag: time point

value: 3 hours post injection (hpi)

value: liver


title: MDA-MB-231 cells siYAP/TAZ#1, biological replica C


title: MDA-MB-231 cells siYAP/TAZ#1, biological replica A


title: LPS_Stimulated_Overfed_Zebrafish_Liver_rep3


title: genomic DNA from old sun protected dermis 2

tag: exposure

value: sun protected

value: dermis


title: genomic DNA from old sun protected dermis 3

value: male


title: genomic DNA from old sun protected dermis 5


title: HCC0055_VI+


title: HCC0056_VI+


title: LPS_Stimulated_Overfed_Zebrafish_Liver_rep2


title: LPS_Stimulated_Overfed_Zebrafish_Liver_rep1


title: genomic DNA from young sun exposed dermis 9

source_name: young sun exposed dermis

value: sun exposed


title: HCC0054_VI+


title: MDA-MB-231 cells siControl, biological replica D

description: Gene expression data from control MDA-MB-231 cells

value: Control siRNA


title: MDA-MB-231 cells siControl, biological replica B


title: genomic DNA from young sun exposed dermis 10


title: HCC0053_VI+


title: HCC0063_VI-


title: genomic DNA from young sun exposed dermis 8


title: genomic DNA from young sun exposed dermis 7


title: MDA-MB-231 cells siControl, biological replica C


title: LPS_Stimulated_Zebrafish_Liver_rep4

source_name: Liver Healthy LPS Stimulated Adult Zebrafish 3hpi

value: Normal


title: LPS_Stimulated_Zebrafish_Liver_rep3


title: HCC0051_VI+

source_name: HCC tumor


title: genomic DNA from old sun protected dermis 1


title: genomic DNA from young sun exposed dermis 4


title: MDA-MB-231 cells siYAP/TAZ#1, biological replica B


title: LPS_Stimulated_Zebrafish_Liver_rep2


title: MDA-MB-231 cells siControl, biological replica A


title: LPS_Stimulated_Zebrafish_Liver_rep1


title: MCF10A cells siYAP/TAZ#2, biological replica D

description: Gene expression data from MCF10A cells depleted of endogenous YAP and TAZ by siRNA mix #2

source_name: MCF10A immortalized human mammary epithelial cells

growth_protocol: Cells were seeded at low confluence on day 1 in standard growth medium (DMEM/F12 with 1mM Glutamine, 17.5mM D-glucose, without antibiotics, 5% Horse Serum, Insulin, hEGF, Cholera Toxin and Hydrocortisone as in Debnath et al., Methods 2003 DOI:10.1016/S1046-2023(03)00032-X).


title: MCF10A cells siYAP/TAZ#2, biological replica C


title: HCC0050_VI+


title: Overfed_Zebrafish_Liver_rep4

source_name: Liver Diet Induced Obesity Adult Zebrafish

value: PBS (control)


title: HCC0048_VI+


title: HCC0049_VI+


title: HCC0052_VI+


title: genomic DNA from young sun exposed dermis 3


title: Overfed_Zebrafish_Liver_rep3


title: HCC0047_VI+


title: genomic DNA from young sun exposed dermis 1


title: MCF10A cells siYAP/TAZ#2, biological replica A

value: YAP/TAZ siRNA #2


title: MCF10A cells siYAP/TAZ#1, biological replica D

description: Gene expression data from MCF10A cells depleted of endogenous YAP and TAZ by siRNA mix #1


title: Overfed_Zebrafish_Liver_rep2


title: HCC0046_VI+


title: MCF10A cells siYAP/TAZ#2, biological replica B


title: genomic DNA from young sun exposed dermis 5


title: Overfed_Zebrafish_Liver_rep1


title: HCC0045_VI+


title: Healthy_Zebrafish_Liver_rep4

source_name: Liver Healthy Adult Zebrafish


title: genomic DNA from young sun exposed dermis 2


title: MCF10A cells siYAP/TAZ#1, biological replica B


title: Healthy_Zebrafish_Liver_rep3


title: HCC0044_VI+


title: HCC0043_VI+


title: HCMa-hypoxia 120 hr

city: Singapore

first: Lee Lee

last: Wong

address: 14 Medical Drive, 08-01

department: Medicine

country: Singapore

institute: National University of Singapore

description:
KJLab_2011-12-21_14h37m47_14312446_5#U00b5m_CMC-120hrpoint2hypoxia.txt
Total RNA (1 µg) was 3′-end–labeled with Hy3 dye and hybridized on miRCURY LNA™ Arrays

hyb_protocol: Samples were then hybridized on miRCURY LNATM Arrays using MAUI® hybridization system

scan_protocol: The microarray chips were then washed and scanned using InnoScan700, microarray scanner (Innopsys, Carbonne, France) and analysed on Mapix® Ver4.5 software (Innopsys, Carbonne, France).

data_processing: Background-subtracted median signal intensities were normalized using endogenous normalization. The differentially expressed miRNAs were selected based an absolute fold change ≥ 1.2 and ≤ -1.2.

label: Hy 3

source_name: Cardiomyocytes

label_protocol: Total RNA (1 µg) was 3′-end–labeled with Hy3 dye using the miRCURY LNATM Power Labeling Kit (Exiqon, Denmark)

growth_protocol: Primary human adult cardiac myocytes (HCMa) were originated from ScienCellTM Research Laboratories (Carlsbad, CA, USA). HCMa cells were cultured in cardiac myocyte medium (CMM, ScienCell Research Laboratories, Carlsbad, CA, US) supplemented with cell-specific growth factors according to the manufacturer’s protocol.  Cells were cultured at 37˚C in an incubator maintained at 5% CO2.

extract_protocol: Cells were harvested lysed by TRIZOL reagent (Invitrogen, Life Technologies Inc., Frederick, MA, USA). Total RNA + miRNAs was extracted according to manufacturer’s protocol, followed by treatment with Dnase I (Rnase-free 2U/µL, Life Technologies Inc., Carlsbad, CA, US).

treatment_protocol: Cells were incubated at 37˚C in a controlled chamber maintained with 0.2% O2 and 5% CO2 using OXc system (BioSpheric, Lacona, NY, USA) for the indicated time points in experiments.

value: Hypoxia


title: HCMa-normoxia

description:
KJLab_2011-12-21_15h22m26_14312447_5#U00b5m_CMC-Ctrlforpoint2hypoxia.txt
Total RNA (1 µg) was 3′-end–labeled with Hy3 dye and hybridized on miRCURY LNA™ Arrays

value: Normoxia


title: Healthy_Zebrafish_Liver_rep1


title: MCF10A cells siControl, biological replica D

description: Gene expression data from control MCF10A cells


title: MCF10A cells siControl, biological replica B


title: MCF10A cells siControl, biological replica C


title: Healthy_Zebrafish_Liver_rep2


title: genomic DNA from young sun protected dermis 6

source_name: young sun protected dermis


title: HCC0042_VI+


title: HCC0040_VI+


title: 2DG treated MDA-MB-231, biological replica D

description: Gene expression data from control MDA-MB-231 cells, cultured for 24 hours in medium containing 2DG to inhibit glucose metabolism

growth_protocol: Cells were seeded at low confluence on day 1 in standard growth medium (for MDA-MB-231: DMEM/F12 with 2mM Glutamine, 17.5mM D-glucose, antibiotics, 10% FBS; for MCF10A: DMEM/F12 with 1mM Glutamine, 17.5mM D-glucose, antibiotics, 5% Horse Serum, Insulin, hEGF, Cholera Toxin and Hydrocortisone as in Debnath et al., Methods 2003 DOI:10.1016/S1046-2023(03)00032-X).

treatment_protocol: On day 2, cells were supplemented with 50mM 2-deoxy-glucose (2DG) or the same amount of vehicle (water). On day 3, after 24 hours, cells were washed with 1X HBSS and harvested for RNA extraction.


title: HCC0041_VI+


title: genomic DNA from young sun protected dermis 7

value: female


title: genomic DNA from young sun protected dermis 4


title: HCC0039_VI+


title: MEF+fKOSM(Sh0to100_25d)_79d_2

city: Tsukuba, Ibaraki

first: Ken

last: Nishimura

address: 1-1-1 Tennodai

institute: University of Tsukuba

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalized using GenomeStudio Gene Expression Module v1.0 and the report was created using GEO Data Submission Report Plug-in v2.0.0

label: Biotin

source_name: paused iPSC

label_protocol: cRNA was prepared by reverse-transcription and labeling using Illumina TotalPrep RNA Amplification Kit (Life Technologies).

extract_protocol: Total RNA was purified by ReliaPrep RNA Cell Miniprep System (Promega).

tag: vector infection

value: Day 79

tag: shield1 addition

value: 0 to 100 nM at Day 25


title: MCF10A cells siControl, biological replica A


title: genomic DNA from young sun protected dermis 5

label_protocol: Standard Illumina Protocol

tag: tissue


title: HCC0038_VI+

tag: tumor vascular invasion/invasiveness

value: Yes


title: 2DG treated MDA-MB-231, biological replica B


title: MEF+fKOSM(Sh0)_79d_2

description: replicate 2

value: 0 nM


title: MCF10A cells siYAP/TAZ#1, biological replica A

value: YAP/TAZ siRNA #1


title: MEF+fKOSM(Sh0)_79d_1

description: replicate 1


title: HCC0036_VI+


title: HCC0037_VI+


title: genomic DNA from young sun protected dermis 3


title: genomic DNA from young sun protected dermis 8


title: MEF+fKOSM(Sh0)_22d_1

description: replicate 1

value: Day 22


title: HCC0034_VI-

value: No


title: MEF+fKOSM(Sh0)_22d_2

description: replicate 2


title: MEF+fKOSM(Sh0to100_25d)_79d_1

description: replicate 1


title: HCC0035_VI+


title: MEF+fKOSM(Sh10)_22d_2

description: replicate 2

value: 10 nM


title: 2DG treated MDA-MB-231, biological replica A


title: MDA-MB-231, biological replica D

value: water (vehicle)


title: MDA-MB-231, biological replica C


title: MDA-MB-231, biological replica B


title: HCC0033_VI-


title: HCC0032_VI-


title: MDA-MB-231, biological replica A


title: MEF+fKOSM(Sh30)_22d_2

description: replicate 2

value: 30 nM


title: 2DG treated MDA-MB-231, biological replica C


title: genomic DNA from young sun protected dermis 2

value: sun protected

value: dermis


title: HCC0030_VI-


title: genomic DNA from young sun protected dermis 9


title: MEF+fKOSM(Sh10)_22d_1

description: replicate 1


title: HCC0031_VI-


title: 2DG treated MCF10A, biological replica C

description: Gene expression data from control MCF10A cells, cultured for 24 hours in medium containing 2DG to inhibit glucose metabolism


title: MEF+fKOSM(Sh100)_22d_1

description: replicate 1


title: HCC0029_VI-


title: HCC0028_VI-


title: MEF+fKOSM(Sh100)_22d_2

description: replicate 2


title: 2DG treated MCF10A, biological replica D


title: genomic DNA from young sun exposed dermis 6

value: male

value: sun exposed


title: MCF10A cells siYAP/TAZ#1, biological replica C


title: HCC0027_VI-


title: MEF+fKOSM(Sh30)_22d_1

description: replicate 1


title: 2DG treated MCF10A, biological replica B


title: MCF10A, biological replica D


title: MEF+KOSM_33d_1

description: replicate 1

source_name: iPSC intermediate

value: Day 33


title: MEF+KOSM_33d_2

description: replicate 2


title: Mn/KOSM#24_1

description: replicate 1

source_name: iPSC


title: Mn/KOSM#24_2

description: replicate 2


title: MCF10A, biological replica C


title: MCF10A, biological replica B


title: 2DG treated MCF10A, biological replica A


title: MCF10A, biological replica A


title: HCC0025_VI-


title: HCC0024_VI-


title: genomic DNA from young sun protected dermis 10


title: HCC0021_VI-


title: HCC0022_VI-


title: MEF+KOSM_8d_2

description: replicate 2

value: Day 8


title: MEF+KOSM_19d_2

description: replicate 2

value: Day 19


title: HCC0020_VI-


title: HCC0026_VI-