title: Patient 23 NCCRI_2012-054_52

value: Patient 23

tag: age (yrs)

tag: tissue

value: IIB


title: Patient 25 NCCRI_2012-054_54

status: Public on Apr 15 2015

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

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

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

molecule: total RNA

organism: Homo sapiens

source_name: responder_primary lung cancer

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Total RNA was extracted from human lungs using QIAzol and the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. The purity and concentration of all RNA samples were quantified using NanoDrop ND-1000 (Thermo Scientific). Detection of RNA from human lungs was performed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). Prior to the analysis, total RNA was prepared with the Agilent RNA 6000 Pico kit (Agilent Technologies) according to the manufacturer’s protocol. All clinical samples exhibited RNA Integrity Numbers > 6.0.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: Twenty-nine patients who received four or more courses of first-line platinum-based chemotherapy after postoperative recurrence were divided into two groups (responder (n=17) and non-responder group (n=12)).

tag: subject id

value: Patient 25

tag: therapeutic response

value: responder

tag: gender

value: Male

value: primary lung cancer

tag: pathological type

value: squamous cell carcinoma (SQ)

tag: pathological stage


title: Patient 26 NCCRI_2012-054_55

value: Patient 26

value: adenocarcinoma (AD)

value: IB


title: Patient 27 NCCRI_2012-054_56

value: Patient 27


title: 24h - Dexamethasone - 7.5 mM (+S9) - Pooled Replicate

city: Ottawa

first: Julie

last: Buick

state: Ontario

address: 50 Colombine Driveway

department: Mechanistic Studies Division

country: Canada

institute: Health Canada

description:
Co-hybridized with vehicle control pool (DMSO +S9)
array 1_3: Cy3 Dex7.5 (+S9) and Cy5 VCP1 (+S9) array 2_3: Cy5 Dex7.5 (+S9) and Cy3 VCP1 (+S9)

hyb_protocol: Labelled cRNA samples (325 ng of cyanine-3 labelled cRNA and 325 ng of cyanine-5 labelled cRNA) were hybridized to Agilent SurePrint G3 Human GE 8x60K oligonucleotide microarrays (Agilent Catalogue No: G4851A, Agilent Microarray Design ID: 028004; Agilent Technologies, Mississauga, ON, Canada) at 65oC for 17 hours.

scan_protocol: Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner at 3 μm resolution. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.

data_processing: The log2 of the ratio using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.  After normalization the log2 ratios for the dye swap were averaged yielding a ratio representing the treatment relative to the vehicle control.

source_name: TK6 lymphoblastoid cell line

label_protocol: Gene expression profiles were generated using a two-colour dye swap design [Kerr and Churchill, 2001]. Microarray analysis was conducted on one pooled replicate from each condition at 24h (n=3 per concentration and time point), along with the corresponding pooled vehicle and positive controls. Agilent Low-Input Quick Amp Labelling kits were used to ultimately generate cyanine-3 and cyanine-5 labelled cRNA from 100 ng of total RNA, according to the manufacturer’s instructions (Agilent Technologies, Mississauga, ON, Canada).

growth_protocol: TK6 cells, a human lymphoblastoid cell line, were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA, USA). TK6 cells were maintained as described elsewhere [Ellinger-Ziegelbauer et al., 2009]. Briefly, cells were cultured and maintained in RPMI 1640 medium containing 10% heat inactivated horse serum, in addition to 0.1% pluronics, sodium pyruvate and antibiotics (penicillin at 20 units/ml and streptomycin at 20 µg/ml) at 37 ± 1oC and 6 ± 1% CO2 in air. Immediately prior to chemical exposure, cells were seeded at a density of 4 (± 0.5) x 105 cells/ml in twelve-well plates with a final volume of 3 ml per well. Given that TK6 cells are not metabolically competent cells and that BaP requires metabolic activation to form reactive metabolites, all cellular exposures were conducted in the presence of 1% 5,6 benzoflavone-/phenobarbital-induced rat liver S9 (Moltox, Boone, NC, USA) with NADPH generating system cofactors. The in vitro cellular exposures were performed by Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, NC, USA), in addition to the associated cytotoxicity and genotoxicity testing.

extract_protocol: Following cellular exposures, total RNA was isolated from treated and control TK6 cells at the 24h time point. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.6 to 10 and A260/280 absorbance ratios >2.0 were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to vehicle control (DMSO (±S9)), 10 μg/ml benzo[a]pyrene (-S9) and 7.5 mM dexamethasone (+S9) (n = 3 for each condition at 24h). Separate plates were used for exposures to negative and vehicle controls (NC (±S9), VC (±S9)). The time points was named as follows: 24h = four hours of exposure, media replaced and sampled 20 hours later. Benzo[a]pyrene was done in the absence of 1% BF/PB-induced rat liver S9 with NADPH generating system cofactors to verify that benzo[a]pyrene was not metabolically activated in the absence of S9, as TK6 cells do not have inherent metabolic capacity, in addition to its associated vehicle control). Dexamethasone was done in the presence of 1% BF/PB-induced rat liver S9 with NADPH generating system cofactors to test a higher concentraion of this non-genotoxic chemical, in addition to its associated vehicle control. Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of the 4h exposure, the exposed and control TK6 cells for the 24h time point were removed by centrifugation and the cells were rinsed in PBS. The 24h samples were re-suspended in 3 ml of media and re-incubated for an additional 20 ± 0.5 before being harvested for RNA and cytotoxicity/MN assays. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 106 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.

tag: cell line

value: TK6 lymphoblastoid

tag: time

value: 24h with dexamethasone with S9 (+S9)

tag: concentration

value: 24h vehicle control with VCP1 (+S9)

value: DMSO (+S9)


title: Patient 28 NCCRI_2012-054_57

value: Patient 28

value: IIIA


title: 24h - Benzo[a]pyrene - 10 μg/ml (-S9) - Pooled Replicate

description:
Co-hybridized with negative vehicle control pool (DMSO -S9)
array 1_2: Cy3 BaP10 (-S9) and Cy5 VCP2 (-S9) array 2_2: Cy5 BaP10 (-S9) and Cy3 VCP2 (-S9)

value: 24h with BaP 10 without S9 (-S9)

value: 24h vehicle control without VCP2 (-S9)

value: DMSO (-S9)


title: HSMCs, nicotine-treated vs. control cells

description: The differentiated HSMC is treated or untreated by nicotine.

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

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

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

growth_protocol: SmBM with supplements and growth factors (hEGF, insulin,hFGF-B, FBS andgentamicin/amphotericin-B).

extract_protocol: Total RNA extracted using RNeasy Plus (Qiagen) according to manufacturer's instructions.

treatment_protocol: After HSMCs were deprived of all supplements and growth factors for 24 h, differentiation into the contractile type by adding 1 ng/ml of TGF-β for 48 hours. Nicotine was added to the differentiated HSMCs and harvest the cells after 48 hours.

tag: cell type

value: normal human aortic smooth muscle cells (Lonza)

tag: treatment

value: control

value: nicotine


title: MDAMB231_1

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: MDA-MB-231 culture cells

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

growth_protocol: Both cells were maintained in DMEM supplemented with 10% FCS

extract_protocol: RNA were extracted from cells using pure link RNA mini kit (Ambion)

treatment_protocol: human SUV420H2 was transfected in MDA-MB-231 cells and stably expressing cells were cloned  and termed H2#9

value: breast cancer MDA-MB-231 cells

tag: genotype/variation

value: parental control


title: 24h - Cisplatin - 24 μg/ml - Control Pool

description: Sample 22

data_processing: The log2 of the ratio using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.  After normalization the log2 ratios for the dye swap were averaged yielding a ratio representing the treatment relative to the vehicle control [the sample-dye assignment information for each of the raw data files is included in the 'readme.txt' (available as Series supplementary file)].

source_name: TK6_24h_Cisplatin_24 μg/ml_Control Pool

label_protocol: Gene expression profiles were generated using a two-colour dye swap design [Kerr and Churchill, 2001]. Microarray analysis was conducted on all time points from the definitive studies (n=3 per concentration and time point), along with the corresponding pooled vehicle and positive controls. Agilent Low-Input Quick Amp Labelling kits were used to ultimately generate cyanine-3 and cyanine-5 labelled cRNA from 100 ng of total RNA, according to the manufacturer’s instructions (Agilent Technologies, Mississauga, ON, Canada).

extract_protocol: Following DEX cellular exposures, total RNA was isolated from treated and control TK6 cells at the 4, 8 and 24h time points. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.6 to 10 and A260/280 absorbance ratios >2.0 were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to 2 concentrations of DEX (n = 3 for DEX at 4, 8 & 24h) as follows:  0.63 mM and 1 mM. Separate plates were used for exposures to negative and positive controls (NC (±S9), VC (±S9), PC-1 (-S9) and PC-24(-S9)). Time points were named as follows: 4h = four hours of exposure and immediate sample collection; 8h = four hours of exposure, media replaced and sampled 4 hours later; 24h = four hours of exposure, media replaced, and sampling 20 hours later. All exposures were done in the presence of 1% BF/PB-induced rat liver S9 with NADPH generating system cofactors to act as a metabolic activation system (MAS), as TK6 cells do not have inherent metabolic capacity (except for the direct-acting positive control and its associated negative and vehicle controls). Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of each 4h exposure, the exposed and control TK6 cells for each time point were removed by centrifugation and the cells were rinsed in PBS. The 4h samples were immediately harvested and flash frozen for RNA collection and a portion was used for measurement of cytotoxicity. The 8 and 24h samples were re-suspended in 3 ml of media and re-incubated for an additional 4 ± 0.5 and 20 ± 0.5 hours, respectively, before being harvested for RNA and cytotoxicity/MN assays. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 106 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.

value: human lymphoblastoid cells

tag: exposed to

value: 24 μg/ml Cisplatin for 4 hrs

tag: harvest time

value: after 20h recovery in fresh media

source_name: TK6_negative vehicle control pool (DMSO -S9)

tag: sample type


title: 8h - DEX - 0.63 mM - Replicate 1

description: Sample 18

value: 0.63 mM Dexamethasone for 4 hrs

value: after 4h recovery in fresh media

source_name: TK6_negative vehicle control pool (DMSO +S9)


title: 8h - Cisplatin - 24 μg/ml - Control Pool

description: Sample 20

source_name: TK6_8h_Cisplatin_24 μg/ml_Control Pool

value: negative vehicle control pool (DMSO -S9)


title: Sample 9

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given mRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: SUV420H2 stably over-expressing MDA-MB-231 culture cells

tag: expression

value: SUV420H2 stably over-expressing


title: Sample 231


title: Patient 24 NCCRI_2012-054_53

value: Patient 24

value: responder

value: Female

tag: age (yrs)

value: primary lung cancer

value: adenocarcinoma (AD)

value: IIIB


title: MDAMB231_2


title: 24h - DEX - 1 mM - Replicate 2

description: Sample 10

source_name: TK6_24h_DEX_1 mM

value: 1 mM Dexamethasone for 4 hrs

value: negative vehicle control pool (DMSO +S9)


title: 8h - DEX - 0.63 mM - Replicate 3

description: Sample 13


title: 4h - Cisplatin 24 μg/ml - Control Pool

description: Sample 19

source_name: TK6_4h_Cisplatin 24 μg/ml_Control Pool

value: immediate sample collection (after chemical exposure)


title: 8h - DEX - 1 mM - Replicate 3

description: Sample 14

source_name: TK6_8h_DEX_1 mM


title: 4h - DEX - 0.63 mM - Replicate 1

description: Sample 17


title: 4h - DEX - 1 mM - Replicate 3

description: Sample 12

source_name: TK6_4h_DEX_1 mM


title: 24h - Cisplatin - 1 μg/ml - Control Pool

description: Sample 21

source_name: TK6_24h_Cisplatin_1 μg/ml_Control Pool

value: 1 μg/ml Cisplatin for 4 hrs


title: 24h - DEX - 0.63 mM - Replicate 3

description: Sample 15

value: human lymphoblastoid cells


title: 4h - DEX - 0.63 mM - Replicate 3

description: Sample 11


title: 24h - DEX - 1 mM - Replicate 3

description: Sample 16


title: Patient 21 NCCRI_2012-054_50

value: Patient 21

value: Male

tag: tissue


title: Patient 20 NCCRI_2012-054_49

tag: subject id

value: Patient 20


title: Patient 17 NCCRI_2012-054_46

value: Patient 17

tag: therapeutic response

value: squamous cell carcinoma (SQ)

value: IIB


title: Patient 19 NCCRI_2012-054_48

value: Patient 19

tag: gender


title: 24h - DEX - 0.63 mM - Replicate 2

description: Sample 9

value: 0.63 mM Dexamethasone for 4 hrs

value: after 20h recovery in fresh media


title: Patient 22 NCCRI_2012-054_51

value: Patient 22

value: responder

value: primary lung cancer

tag: pathological type


title: Patient 13 NCCRI_2012-054_42

value: Patient 13

value: Female

value: adenocarcinoma (AD)

tag: pathological stage

value: IIIA


title: Patient 15 NCCRI_2012-054_44

value: Patient 15

value: IA


title: Patient 14 NCCRI_2012-054_43

value: Patient 14

value: Male


title: Patient 18 NCCRI_2012-054_47

value: Patient 18


title: Patient 16 NCCRI_2012-054_45

value: Patient 16


title: Patient 28 NCCRI_2012-054_40

source_name: responder_adjacent normal tissue

value: Patient 28

value: adjacent normal tissue


title: Patient 29 NCCRI_2012-054_41

value: Patient 29


title: 4h - DEX - 0.63 mM - Replicate 2

description: Sample 3

tag: cell line

value: human lymphoblastoid cells

value: 0.63 mM Dexamethasone for 4 hrs

value: immediate sample collection (after chemical exposure)

value: negative vehicle control pool (DMSO +S9)


title: 4h - DEX - 1 mM - Replicate 1

description: Sample 1

value: 1 mM Dexamethasone for 4 hrs


title: 4h - DEX - 1 mM - Replicate 2

description: Sample 4

value: after 4h recovery in fresh media


title: 8h - DEX - 1 mM - Replicate 2

description: Sample 8


title: Patient 27 NCCRI_2012-054_39

value: Patient 27

value: responder


title: 24h - DEX - 0.63 mM - Replicate 1

description: Sample 5

value: after 20h recovery in fresh media


title: 24h - DEX - 1 mM - Replicate 1

description: Sample 6


title: 8h - DEX - 1 mM - Replicate 1

description: Sample 2


title: 8h - DEX - 0.63 mM - Replicate 2

description: Sample 7


title: 8h - Cisplatin - 24 μg/ml - Positive Control Pool

description: Sample 8

source_name: TK6_8h_Cisplatin_24 μg/ml_Positive Control Pool

extract_protocol: Following BaP cellular exposures, total RNA was isolated from treated and control TK6 cells at the 8h time point. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.6 to 10 and A260/280 absorbance ratios >2.0 were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to 3 concentrations of BaP (n = 3 for BaP at 8h) as follows: 0.45 μg/ml (low), 1.4 μg/ml (medium) and 10 μg/ml (high). Separate plates were used for exposures to negative and positive controls (NC (±S9), VC (±S9), PC-1 (-S9) and PC-24(-S9)). The time points was named as follows: 8h = four hours of exposure, media replaced and sampled 4 hours later. All exposures were done in the presence of 1% BF/PB-induced rat liver S9 with NADPH generating system cofactors to act as a metabolic activation system (MAS), as TK6 cells do not have inherent metabolic capacity (except for the direct-acting positive control and its associated negative and vehicle controls). Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of the 4h exposure, the exposed and control TK6 cells for the 8h time point were removed by centrifugation and the cells were rinsed in PBS. The 8h samples were re-suspended in 3 ml of media and re-incubated for an additional 4 ± 0.5 before being harvested for RNA and cytotoxicity/MN assays. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 106 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.

value: 24 μg/ml Benzo[a]pyrene for 4 hrs

value: negative vehicle control pool (DMSO -S9)


title: 8h - Benzo[a]pyrene - 10 μg/ml - Replicate 3

description: Sample 9

source_name: TK6_8h_Benzo[a]pyrene_10 μg/ml

value: 10 μg/ml Benzo[a]pyrene for 4 hrs


title: 24h - Cisplatin - 24 μg/ml - Positive Control Pool

description: Sample 10

source_name: TK6_24h_Cisplatin_24 μg/ml_Positive Control Pool

value: 24 μg/ml Cisplatin for 4 hrs


title: Patient 19 NCCRI_2012-054_31

value: Patient 19

value: Female


title: Patient 21 NCCRI_2012-054_33

value: Patient 21

value: Male

value: adjacent normal tissue


title: Patient 20 NCCRI_2012-054_32

value: Patient 20


title: Patient 18 NCCRI_2012-054_30

value: Patient 18


title: Patient 22 NCCRI_2012-054_34

value: Patient 22


title: 8h - Benzo[a]pyrene - 1.4 μg/ml - Replicate 3

description: Sample 12

source_name: TK6_8h_Benzo[a]pyrene_1.4 μg/ml

value: human lymphoblastoid cells

value: 1.4 μg/ml Benzo[a]pyrene for 4 hrs

value: negative vehicle control pool (DMSO +S9)


title: 8h - Benzo[a]pyrene - 0.45 μg/ml - Replicate 3

description: Sample 11

source_name: TK6_8h_Benzo[a]pyrene_0.45 μg/ml

value: 0.45 μg/ml Benzo[a]pyrene for 4 hrs

value: after 4h recovery in fresh media


title: 8h - Benzo[a]pyrene - 0.45 μg/ml - Replicate 1

description: Sample 1


title: 8h - Benzo[a]pyrene - 1.4 μg/ml - Replicate 2

description: Sample 6


title: 4h - Benzo[a]pyrene - 1.4 μg/ml - Replicate 2

description:
Sample 23
Co-hybridized with negative vehicle control pool (DMSO +S9)

source_name: TK6_4h_Benzo[a]pyrene_1.4 μg/ml

extract_protocol: Following BaP cellular exposures, total RNA was isolated from treated and control TK6 cells at the 4 and 24h time points. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.6 to 10 and A260/280 absorbance ratios >2.0 were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to 3 concentrations of BaP (n = 3 for BaP at 4h and 24h) as follows: 0.45 μg/ml (low), 1.4 μg/ml (medium) and 10 μg/ml (high). Separate plates were used for exposures to negative and positive controls (NC (±S9), VC (±S9), PC-1 (-S9) and PC-24(-S9)). Time points were named as follows: 4h = four hours of exposure and immediate sample collection; 24h = four hours of exposure, media replaced, and sampling 20 hours later. All exposures were done in the presence of 1% BF/PB-induced rat liver S9 with NADPH generating system cofactors to act as a metabolic activation system (MAS), as TK6 cells do not have inherent metabolic capacity (except for the direct-acting positive control and its associated negative and vehicle controls). Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of each 4h exposure, the exposed and control TK6 cells for each time point were removed by centrifugation and the cells were rinsed in PBS. The 4h samples were immediately harvested and flash frozen for RNA collection and a portion was used for measurement of cytotoxicity. The 24h samples were re-suspended in 3 ml of media and re-incubated for an additional 20 ± 0.5 hours before being harvested for RNA and cytotoxicity/MN assays. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 106 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.

value: immediate sample collection (after chemical exposure)


title: Patient 23 NCCRI_2012-054_35

value: Patient 23

value: responder


title: Patient 24 NCCRI_2012-054_36

value: Patient 24


title: Patient 26 NCCRI_2012-054_38

value: Patient 26


title: Patient 25 NCCRI_2012-054_37

value: Patient 25


title: 8h - Benzo[a]pyrene - 10 μg/ml - Replicate 2

description: Sample 7

value: 10 μg/ml Benzo[a]pyrene for 4 hrs


title: Patient 8 NCCRI_2012-054_20

source_name: non-responder_primary lung cancer

value: Patient 8

value: non-responder

value: Male

value: primary lung cancer

value: adenocarcinoma (AD)

value: IIIB


title: 8h - Benzo[a]pyrene - 0.45 μg/ml - Replicate 2

description: Sample 5

value: human lymphoblastoid cells


title: Patient 9 NCCRI_2012-054_21

value: Patient 9

value: IB


title: Patient 10 NCCRI_2012-054_22

value: Patient 10

value: IA


title: Patient 13 NCCRI_2012-054_25

value: Patient 13

value: Female

value: adjacent normal tissue


title: Patient 14 NCCRI_2012-054_26

value: Patient 14

value: responder


title: Patient 16 NCCRI_2012-054_28

value: Patient 16


title: Patient 17 NCCRI_2012-054_29

value: Patient 17


title: Patient 7 NCCRI_2012-054_19

value: Patient 7

value: non-responder

value: IIIA


title: Patient 11 NCCRI_2012-054_23

value: Patient 11

value: Male

value: primary lung cancer

value: squamous cell carcinoma (SQ)

value: IIB


title: Patient 15 NCCRI_2012-054_27

value: Patient 15


title: Patient 12 NCCRI_2012-054_24

value: Patient 12

value: adenocarcinoma (AD)


title: 4h - Benzo[a]pyrene - 0.45 μg/ml - Replicate 1

description:
Sample 20
Co-hybridized with negative vehicle control pool (DMSO +S9)

source_name: TK6_4h_Benzo[a]pyrene_0.45 μg/ml

value: human lymphoblastoid cells

value: 0.45 μg/ml Benzo[a]pyrene for 4 hrs

value: immediate sample collection (after chemical exposure)


title: Patient 6 NCCRI_2012-054_18

value: Patient 6

value: IIIB


title: 24h - Cisplatin - 1 μg/ml - Replicate 3

description:
Sample 17
Co-hybridized with negative vehicle control pool (DMSO -S9)

source_name: TK6_24h_Cisplatin_1 μg/ml

value: 1 μg/ml Cisplatin for 4 hrs

value: after 20h recovery in fresh media

source_name: TK6_negative vehicle control pool (DMSO -S9)


title: 4h - Cisplatin - 1 μg/ml - Replicate 1

description:
Sample 21
Co-hybridized with negative vehicle control pool (DMSO -S9)

source_name: TK6_4h_Cisplatin_1 μg/ml


title: 24h - Benzo[a]pyrene - 0.45 μg/ml - Replicate 3

description:
Sample 18
Co-hybridized with negative vehicle control pool (DMSO +S9)

source_name: TK6_24h_Benzo[a]pyrene_0.45 μg/ml

source_name: TK6_negative vehicle control pool (DMSO +S9)


title: 24h - Benzo[a]pyrene - 1.4 μg/ml - Replicate 3

description:
Sample 19
Co-hybridized with negative vehicle control pool (DMSO +S9)

source_name: TK6_24h_Benzo[a]pyrene_1.4 μg/ml

value: 1.4 μg/ml Benzo[a]pyrene for 4 hrs


title: 4h - Benzo[a]pyrene - 0.45 μg/ml - Replicate 2

description:
Sample 22
Co-hybridized with negative vehicle control pool (DMSO +S9)


title: Patient 4 NCCRI_2012-054_16

value: Patient 4

value: non-responder

value: IB


title: Patient 5 NCCRI_2012-054_17

value: Patient 5

value: Male

value: primary lung cancer


title: 8h - Benzo[a]pyrene - 1.4 μg/ml - Replicate 1

description: Sample 2

value: after 4h recovery in fresh media

value: negative vehicle control pool (DMSO +S9)


title: Patient 12 NCCRI_2012-054_12

source_name: non-responder_adjacent normal tissue

value: Patient 12

value: Female

value: adjacent normal tissue


title: Patient 2 NCCRI_2012-054_14

value: Patient 2

value: adenocarcinoma (AD)


title: Patient 10 NCCRI_2012-054_10

value: Patient 10


title: Patient 3 NCCRI_2012-054_15

value: Patient 3

value: IA


title: 24h - Benzo[a]pyrene - 10 μg/ml - Replicate 2

description:
Sample 15
Co-hybridized with negative vehicle control pool (DMSO +S9)

source_name: TK6_24h_Benzo[a]pyrene_10 μg/ml

value: human lymphoblastoid cells

value: 10 μg/ml Benzo[a]pyrene for 4 hrs

value: after 20h recovery in fresh media


title: 8h - Benzo[a]pyrene - 10 μg/ml - Replicate 1

description: Sample 3


title: 24h - Benzo[a]pyrene - 1.4 μg/ml - Replicate 2

description:
Sample 14
Co-hybridized with negative vehicle control pool (DMSO +S9)

value: 1.4 μg/ml Benzo[a]pyrene for 4 hrs


title: Patient 11 NCCRI_2012-054_11

value: Patient 11

value: non-responder


title: 24h - Benzo[a]pyrene - 0.45 μg/ml - Replicate 2

description:
Sample 13
Co-hybridized with negative vehicle control pool (DMSO +S9)

value: 0.45 μg/ml Benzo[a]pyrene for 4 hrs


title: 24h - Benzo[a]pyrene - 10 μg/ml - Replicate 1

description:
Sample 11
Co-hybridized with negative vehicle control pool (DMSO +S9)


title: 8h - Cisplatin - 1 μg/ml - Positive Control Pool

description: Sample 4

source_name: TK6_8h_Cisplatin_1 μg/ml_Positive Control Pool

value: 1 μg/ml Cisplatin for 4 hrs

value: after 4h recovery in fresh media

value: negative vehicle control pool (DMSO -S9)


title: 24h - Benzo[a]pyrene - 10 μg/ml - Replicate 3

description:
Sample 16
Co-hybridized with negative vehicle control pool (DMSO +S9)


title: 4h - Cisplatin - 1 μg/ml - Replicate 3

description:
Sample 6
Co-hybridized with negative vehicle control pool (DMSO -S9)

value: immediate sample collection (after chemical exposure)


title: Patient 9 NCCRI_2012-054_09

value: Patient 9

value: Male

value: adjacent normal tissue


title: 4h - Cisplatin - 1 μg/ml - Replicate 2

description:
Sample 3
Co-hybridized with negative vehicle control pool (DMSO -S9)


title: 4h - Benzo[a]pyrene - 1.4 μg/ml - Replicate 3

description:
Sample 8
Co-hybridized with negative vehicle control pool (DMSO +S9)


title: 4h - Benzo[a]pyrene - 10 μg/ml - Replicate 3

description:
Sample 5
Co-hybridized with negative vehicle control pool (DMSO +S9)

source_name: TK6_4h_Benzo[a]pyrene_10 μg/ml


title: 4h - Benzo[a]pyrene - 0.45 μg/ml - Replicate 3

description:
Sample 7
Co-hybridized with negative vehicle control pool (DMSO +S9)


title: 24h - Cisplatin - 1 μg/ml - Replicate 2

description:
Sample 12
Co-hybridized with negative vehicle control pool (DMSO -S9)


title: 24h - Benzo[a]pyrene - 0.45 μg/ml - Replicate 1

description:
Sample 9
Co-hybridized with negative vehicle control pool (DMSO +S9)


title: 24h - Aflatoxin B1 - 0.075 μM - Replicate 3

description: Sample 30

source_name: TK6_24h_Aflatoxin B1_0.075 μM

growth_protocol: TK6 cells, a human lymphoblastoid cell line, were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA, USA). TK6 cells were maintained as described elsewhere [Ellinger-Ziegelbauer et al., 2009]. Briefly, cells were cultured and maintained in RPMI 1640 medium containing 10% heat inactivated horse serum, in addition to 0.1% pluronics, sodium pyruvate and antibiotics (penicillin at 20 units/ml and streptomycin at 20 µg/ml) at 37 ± 1C and 6 ± 1% CO2 in air. Immediately prior to chemical exposure, cells were seeded at a density of 4 (± 0.5) x 10^5 cells/ml in twelve-well plates with a final volume of 3 ml per well. Given that TK6 cells are not metabolically competent cells and that BaP requires metabolic activation to form reactive metabolites, all cellular exposures were conducted in the presence of 1% 5,6 benzoflavone-/phenobarbital-induced rat liver S9 (Moltox, Boone, NC, USA) with NADPH generating system cofactors. The in vitro cellular exposures were performed by Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, NC, USA), in addition to the associated cytotoxicity and genotoxicity testing.

extract_protocol: Following AFB1 cellular exposures, total RNA was isolated from treated and control TK6 cells at the 4, 8 and 24h time points. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.6 to 10 and A260/280 absorbance ratios >2.0 were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to 3 concentrations of AFB1 (n = 3 for AFB1 at 4, 8 & 24h) as follows:  0.025 μM (low), 0.075 μM (medium) and 0.1 μM (high). Separate plates were used for exposures to negative and positive controls (NC (±S9), VC (±S9), PC-1 (-S9) and PC-24(-S9)). Time points were named as follows: 4h = four hours of exposure and immediate sample collection; 8h = four hours of exposure, media replaced and sampled 4 hours later; 24h = four hours of exposure, media replaced, and sampling 20 hours later. All exposures were done in the presence of 1% BF/PB-induced rat liver S9 with NADPH generating system cofactors to act as a metabolic activation system (MAS), as TK6 cells do not have inherent metabolic capacity (except for the direct-acting positive control and its associated negative and vehicle controls). Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of each 4h exposure, the exposed and control TK6 cells for each time point were removed by centrifugation and the cells were rinsed in PBS. The 4h samples were immediately harvested and flash frozen for RNA collection and a portion was used for measurement of cytotoxicity. The 8 and 24h samples were re-suspended in 3 ml of media and re-incubated for an additional 4 ± 0.5 and 20 ± 0.5 hours, respectively, before being harvested for RNA and cytotoxicity/MN assays. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 10^6 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.

value: 0.075 µM Aflatoxin B1 for 4 hrs

value: negative vehicle control pool (DMSO +S9)


title: Patient 4 NCCRI_2012-054_04

value: Patient 4


title: Patient 5 NCCRI_2012-054_05

value: Patient 5


title: Patient 6 NCCRI_2012-054_06

value: Patient 6


title: Patient 3 NCCRI_2012-054_03

value: Patient 3


title: Patient 8 NCCRI_2012-054_08

value: Patient 8


title: Patient 2 NCCRI_2012-054_02

value: Patient 2

value: Female


title: Patient 7 NCCRI_2012-054_07

value: Patient 7

value: non-responder


title: 24h - Benzo[a]pyrene - 1.4 μg/ml - Replicate 1

description:
Sample 10
Co-hybridized with negative vehicle control pool (DMSO +S9)

value: human lymphoblastoid cells

value: 1.4 μg/ml Benzo[a]pyrene for 4 hrs

value: after 20h recovery in fresh media


title: 4h - Benzo[a]pyrene - 1.4 μg/ml - Replicate 1

description:
Sample 1
Co-hybridized with negative vehicle control pool (DMSO +S9)

value: immediate sample collection (after chemical exposure)


title: 24h - Aflatoxin B1 - 0.075 μM - Replicate 2

description: Sample 28


title: 4h - Benzo[a]pyrene - 10 μg/ml - Replicate 2

description:
Sample 4
Co-hybridized with negative vehicle control pool (DMSO +S9)

value: 10 μg/ml Benzo[a]pyrene for 4 hrs


title: 24h - Aflatoxin B1 - 0.1 μM - Replicate 3

description: Sample 27

source_name: TK6_24h_Aflatoxin B1_0.1 μM

value: 0.1 µM Aflatoxin B1 for 4 hrs


title: Patient 1 NCCRI_2012-054_01

value: Patient 1

value: Male

value: adjacent normal tissue


title: 24h - Cisplatin Ctrl Pool - 1 μg/ml - Pool 1

description: Sample 24

source_name: TK6_24h_Cisplatin Ctrl Pool_1 μg/ml_Pool 1

value: 1 µg/ml Cisplatin

value: negative vehicle control pool (DMSO -S9)


title: 24h - Aflatoxin B1 - 0.025 μM - Replicate 2

description: Sample 25

source_name: TK6_24h_Aflatoxin B1_0.025 μM

value: 0.025 µM Aflatoxin B1 for 4 hrs

value: negative vehicle control pool (DMSO +S9)


title: 24h - Aflatoxin B1 - 0.1 μM - Replicate 2

description: Sample 26


title: 24h - Aflatoxin B1 - 0.025 μM - Replicate 3

description: Sample 29


title: iPSC PiZZ T24 2

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

country: USA

institute: Boston University School of Medicine

description:
Sample name: 102 T24
microRNA expression data from PiZZ skin fibroblasts profiled at T24.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix GeneChip miRNA 2.0 Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: The data were analyzed with the Robust Multiarray Average (RMA) using the Affymetrix Expression Console.

label: biotin

source_name: PiZZ skin fibroblasts

label_protocol: Biotin labeling was performed using the Affymetrix FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: iPSC and ESC lines were maintained in “hiPSC Media” composed of DMEM/F12 (Sigma-Aldrich, www.sigma.com) with 20% KnockOut Serum Replacement (Invitrogen, www.invitrogen.com), 1mM nonanimal  L-glutamine (Sigma-Aldrich), 0.1mM Β-mercaptoethanol, and 10 ng/ml FGF2 (R&D Systems, Minneapolis, MN) on 0.1% gelatin (Sigma-Aldrich) coated plates preseeded with mitomycin C-inactivated or irradiated mouse embryonic fibroblast (MEF) feeder cells.  Cells were maintained in a 5% CO2 air environment. For endodermal differentiation, cells were passed onto matrigel-coated dishes at 80% confluency.  On the following day, designated “T0”, differentiation was induced by culture in media containing growth factors listed below.  From T0-T6, differentiation media included 2mM l-glutamine, and 4.5x10-4 M monothioglycerol (MTG).  Cells were grown in T0 media, consisting of RPMI-based serum-free medium with Chir 99021 (2ug/ml) and Activin A (100 ng/ml), for one day. On days “T1-2”, medium was changed to RPMI with BMP4 (0.5 ng/ml), FGF2 (10ng/ml), Activin A (100 ng/ml), and VEGF (10 ng/ml).  On days “T3-4”, cells were cultured in SFD media(Gouon-Evans et al., 2006) with BMP4 (0.5 ng/ml), FGF2 (10ng/ml), Activin A (100 ng/ml), and VEGF (10 ng/ml). For hepatic differentiation, PSCs were differentiated as monolayer cultures as outlined above to generate definitive endoderm and then further differentiated for an additional 3 weeks in SFD-based media with ascorbic acid (50mcg/ml), monothioglycerol (4.5x10-4 M ), and the following supplements: T7-12: BMP4 (50 ng/ml), FGF2 (10 ng/ml), VEGF (10 ng/ml), EGF (10ng/ml), TGFa (20 ng/ml), HGF (100 ng/ml), and 0.1 uM Dexamethasone; T13-18: FGF2 (10 ng/ml), VEGF (10 ng/ml), EGF (10 ng/ml), HGF (100 ng/ml), Oncostatin M (20 ng/ml), Vitamin K (6 ug/ml), 1.5 uM gamma secretase inhibitor, 0.1 uM Dexamethasone, and 1% DMSO; T19-24: HGF (100 ng/ml), Oncostatin M (20 ng/ml), Vitamin K (6 ug/ml), and 0.1 uM Dexamethasone. Differentiating human PSCs were maintained in a 5% CO2, 5% O2, 90% N2 environment.

extract_protocol: Total RNA and miRNA were isolated from cells using an miRNeasy kit (Qiagen) with the optional column RNAse-free DNase treatment, according to the manufacturer’s instructions. 200 nanograms to one microgram of RNA was reverse transcribed into cDNA using random hexamers with Superscript III Reverse Transcriptase (Invitrogen). RNA was extracted at each stage, biotin labeled, and hybridized to either Affymetrix GeneChip Human Gene 1.0 ST or miRNA 2.0 arrays. For methylation analysis, gDNA was extracted from the same 27 samples before undergoing bisulfite conversion. Bisulfite converted DNA was then amplified and purified prior to overnight hybridization to Illumina’s Infinium HumanMethylation 450 BeadChips.  Next day staining of hybridized arrays produced methylation-dependent differential fluorescence that was detected via an Illumina iScan array scanner.

treatment_protocol: Aside from differentiation and sorting as described above, cells were not treated in any specific manner prior to DNA/RNA extraction.

value: iPSC

tag: Stage

tag: group

value: iPSC PiZZ


title: 24h - Cisplatin Ctrl Pool - 24 μg/ml - Pool 1

description: Sample 23

source_name: TK6_24h_Cisplatin Ctrl Pool_24 μg/ml_Pool 1

tag: cell type

value: 24 µg/ml Cisplatin


title: 24h - Aflatoxin B1 - 0.025 μM - Replicate 1

description: Sample 20


title: iPSC PiZZ T24 3

description:
Sample name: 103 T24
microRNA expression data from PiZZ skin fibroblasts profiled at T24.


title: 8h - Aflatoxin B1 - 0.075 μM - Replicate 3

description: Sample 19

source_name: TK6_8h_Aflatoxin B1_0.075 μM

value: 0.075 µM Aflatoxin B1 for 4 hrs

value: after 4h recovery in fresh media


title: 4h - Benzo[a]pyrene - 10 μg/ml - Replicate 1

description:
Sample 2
Co-hybridized with negative vehicle control pool (DMSO +S9)

value: human lymphoblastoid cells


title: 24h - Aflatoxin B1 - 0.075 μM - Replicate 1

description: Sample 21

value: after 20h recovery in fresh media


title: 8h - Aflatoxin B1 - 0.025 μM - Replicate 3

description: Sample 18

source_name: TK6_8h_Aflatoxin B1_0.025 μM


title: iPSC PiZZ T24 1

description:
Sample name: 100 T24
microRNA expression data from PiZZ skin fibroblasts profiled at T24.


title: iPSC PiZZ T5 1

description:
Sample name: 100 T5
microRNA expression data from PiZZ skin fibroblasts profiled at T5.


title: 24h - Aflatoxin B1 - 0.1 μM - Replicate 1

description: Sample 22


title: iPSC PiZZ T5 3

description:
Sample name: 103 T5
microRNA expression data from PiZZ skin fibroblasts profiled at T5.


title: 8h - Aflatoxin B1 - 0.1 μM - Replicate 3

description: Sample 16

source_name: TK6_8h_Aflatoxin B1_0.1 μM


title: iPSC PiZZ T0 3

description:
Sample name: 103 T0
microRNA expression data from PiZZ skin fibroblasts profiled at T0.


title: 8h - Aflatoxin B1 - 0.1 μM - Replicate 2

description: Sample 15


title: 8h - Aflatoxin B1 - 0.075 μM - Replicate 1

description: Sample 13


title: iPSC PiZZ T0 2

description:
Sample name: 102 T0
microRNA expression data from PiZZ skin fibroblasts profiled at T0.


title: iPSC wild-type T24 1

description:
Sample name: BMC1 T24
microRNA expression data from wild-type skin fibroblasts profiled at T24.

source_name: wild-type skin fibroblasts

value: iPSC wild-type


title: iPSC wild-type T5 3

description:
Sample name: HRII3 T5
microRNA expression data from wild-type skin fibroblasts profiled at T5.


title: iPSC wild-type T24 2

description:
Sample name: CHOPWT3.1 T24
microRNA expression data from wild-type skin fibroblasts profiled at T24.


title: 8h - Aflatoxin B1 - 0.025 μM - Replicate 2

description: Sample 14


title: iPSC PiZZ T5 2

description:
Sample name: 102 T5
microRNA expression data from PiZZ skin fibroblasts profiled at T5.


title: Patient 1 NCCRI_2012-054_13

source_name: non-responder_primary lung cancer

value: non-responder

value: primary lung cancer

value: adenocarcinoma (AD)

value: IB


title: 8h - Cisplatin Ctrl Pool - 24 μg/ml - Pool 1

description: Sample 12

source_name: TK6_8h_Cisplatin Ctrl Pool_24 μg/ml_Pool 1

source_name: TK6_negative vehicle control pool (DMSO -S9)


title: 4h - Aflatoxin B1 - 0.075 μM - Replicate 2

description: Sample 5

source_name: TK6_4h_Aflatoxin B1_0.075 μM

value: immediate sample collection (after chemical exposure)

source_name: TK6_negative vehicle control pool (DMSO +S9)


title: iPSC PiZZ T0 1

description:
Sample name: 100 T0
microRNA expression data from PiZZ skin fibroblasts profiled at T0.


title: iPSC wild-type T0 2

description:
Sample name: CHOPWT3.1 T0
microRNA expression data from wild-type skin fibroblasts profiled at T0.


title: iPSC wild-type T0 3

description:
Sample name: HRII3 T0
microRNA expression data from wild-type skin fibroblasts profiled at T0.


title: iPSC wild-type T24 3

description:
Sample name: HRII3 T24
microRNA expression data from wild-type skin fibroblasts profiled at T24.


title: iPSC wild-type T0 1

description:
Sample name: BMC1 T0
microRNA expression data from wild-type skin fibroblasts profiled at T0.


title: iPSC wild-type T5 1

description:
Sample name: BMC1 T5
microRNA expression data from wild-type skin fibroblasts profiled at T5.


title: iPSC wild-type T5 2

description:
Sample name: CHOPWT3.1 T5
microRNA expression data from wild-type skin fibroblasts profiled at T5.


title: 4h - Aflatoxin B1 - 0.075 μM - Replicate 1

description: Sample 2


title: 4h - Aflatoxin B1 - 0.025 μM - Replicate 3

description: Sample 8

source_name: TK6_4h_Aflatoxin B1_0.025 μM


title: ESC T24 1

description:
Sample name: H1 T24
microRNA expression data from the H1 embryonic stem cell line profiled at T24.

source_name: H1 embryonic stem cell line

value: ESC H1

value: ESC


title: 8h - Aflatoxin B1 - 0.1 μM - Replicate 1

description: Sample 11

value: 0.1 µM Aflatoxin B1 for 4 hrs


title: 8h - Aflatoxin B1 - 0.025 μM - Replicate 1

description: Sample 10

value: 0.025 µM Aflatoxin B1 for 4 hrs

value: negative vehicle control pool (DMSO +S9)


title: ESC T24 2

description:
Sample name: H9 T24
microRNA expression data from the H9 embryonic stem cell line profiled at T24.

source_name: H9 embryonic stem cell line

value: ESC H9


title: 4h - Cisplatin Ctrl Pool - 24 μg/ml - Pool 1

description: Sample 3

source_name: TK6_4h_Cisplatin Ctrl Pool_24 μg/ml_Pool 1

value: 24 µg/ml Cisplatin

value: negative vehicle control pool (DMSO -S9)


title: 4h - Aflatoxin B1 - 0.075 μM - Replicate 3

description: Sample 9

value: 0.075 µM Aflatoxin B1 for 4 hrs


title: ESC T5 2

description:
Sample name: H9 T5
microRNA expression data from the H9 embryonic stem cell line profiled at T5.


title: ESC T5 3

description:
Sample name: CHB8 T5
microRNA expression data from the CHB-8 embryonic stem cell line profiled at T5.

source_name: CHB-8 embryonic stem cell line

value: ESC CHB-8


title: 4h - Aflatoxin B1 - 0.025 μM - Replicate 1

description: Sample 1

value: human lymphoblastoid cells


title: ESC T24 3

description:
Sample name: CHB8 T24
microRNA expression data from the CHB-8 embryonic stem cell line profiled at T24.


title: ESC T0 3

description:
Sample name: CHB8 T0
microRNA expression data from the CHB-8 embryonic stem cell line profiled at T0.


title: BJ fibroblast_Trt4_4

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: transcript turnover rates measured at 4 h after actinomycin D addition from arsenite-treated BJ fibroblasts

hyb_protocol: 12.5 μg of the pooled amplified biotin-cRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the Affymetrix GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: sodium arsenite 24 h, 4 h actinomycin D

label_protocol: One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.

extract_protocol: Total cellular RNA was isolated using the illustra RNAspin MiniRNA Isolation Kit according to the manufacturer’s instructions (GE Healthcare).

treatment_protocol: Cells were treated with vehicle (water) or sodium arsenite at 1 µM for 24 h followed by addition of actinomycin D at a final of 5 µg/ml for 0, 1, 2, 3, and 4 h.

value: BJ fribroblast


title: 4h - Aflatoxin B1 - 0.1 μM - Replicate 2

description: Sample 6

source_name: TK6_4h_Aflatoxin B1_0.1 μM


title: ESC T0 2

description:
Sample name: H9 T0
microRNA expression data from the H9 embryonic stem cell line profiled at T0.


title: ESC T0 1

description:
Sample name: H1 T0
microRNA expression data from the H1 embryonic stem cell line profiled at T0.


title: 4h - Aflatoxin B1 - 0.025 μM - Replicate 2

description: Sample 4


title: VCaP-PRMT5 shRNA 1; rep#1

city: Cambridge

first: Joshua

middle: M

last: Korn

address: 250 Mass Ave

institute: Novartis

description: Cells were treated with 100ng/ml doxycycline for 3 days

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

source_name: VCaP cells

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: All lines were cultured in DMEM supplemented with 20% FCS and non-essential amino acids

extract_protocol: RNA was extracted with RNeasy extraction kits (Qiagen) with on-column DNA digestion.  The initial lysis step was performed directly on the cell culture plates.

tag: treatment

value: PRMT5 knockdown

value: VCaP

tag: prmt5 expression

value: Low

value: 100ng/ml Dox


title: VCaP-PRMT5 shRNA 1; rep#2

treatment_protocol: Cells were treated with 100ng/ml doxycycline for 3 days


title: 4h - Aflatoxin B1 - 0.1 μM - Replicate 3

description: Sample 7

tag: exposed to

value: immediate sample collection (after chemical exposure)


title: VCaP-NTC shRNA; rep#1

value: control

value: High


title: BJ fibroblast_Trt4_1


title: 8h - Aflatoxin B1 - 0.075 μM - Replicate 2

description: Sample 17

source_name: TK6_8h_Aflatoxin B1_0.075 μM

tag: harvest time

value: after 4h recovery in fresh media


title: VCaP-PRMT5 shRNA 2; rep#2


title: VCaP-PRMT5 shRNA 2; rep#1


title: BJ fibroblast_Trt3_4

description: transcript turnover rates measured at 3 h after actinomycin D addition from arsenite-treated BJ fibroblasts

source_name: sodium arsenite 24 h, 3 h actinomycin D


title: ESC T5 1

description:
Sample name: H1 T5
microRNA expression data from the H1 embryonic stem cell line profiled at T5.

value: ESC H1

value: ESC


title: BJ fibroblast_Trt4_2


title: BJ fibroblast_Trt4_3


title: BJ fibroblast_Trt3_1


title: BJ fibroblast_Trt2_4

description: transcript turnover rates measured at 2 h after actinomycin D addition from arsenite-treated BJ fibroblasts

source_name: sodium arsenite 24 h, 2 h actinomycin D


title: BJ fibroblast_Trt3_3


title: BJ fibroblast_Trt3_2


title: VCaP-NTC shRNA; rep#2


title: BJ fibroblast_Trt2_2


title: BJ fibroblast_Trt2_3


title: BJ fibroblast_Trt1_4

description: transcript turnover rates measured at 1 h after actinomycin D addition from arsenite-treated BJ fibroblasts

source_name: sodium arsenite 24 h, 1 h actinomycin D


title: BJ fibroblast_Trt0_3

description: steady state mRNA levels at time 0 of actinomycin D addition from arsenite-treated BJ fibroblasts

source_name: sodium arsenite 24 h, 0 h actinomycin D


title: BJ fibroblast_Ctrl3_3

description: transcript turnover rates measured at 3 h after actinomycin D addition from vehicle-treated BJ fibroblasts

source_name: vehicle 24 h, 3 h actinomycin D


title: BJ fibroblast_Trt1_2


title: BJ fibroblast_Ctrl2_3

description: transcript turnover rates measured at 2 h after actinomycin D addition from vehicle-treated BJ fibroblasts

source_name: vehicle 24 h, 2 h actinomycin D


title: BJ fibroblast_Ctrl4_3

description: transcript turnover rates measured at 4 h after actinomycin D additon from vehicle-treated BJ fibroblasts

source_name: vehicle 24 h, 4 h actinomycin D


title: BJ fibroblast_Ctrl3_2


title: BJ fibroblast_Trt0_2


title: BJ fibroblast_Trt0_1


title: TESTES_KO_rep4

first: Joseph

middle: Jorge

last: Loureiro

address: 250 Massachusetts Ave 6A-144

hyb_protocol: reconcentrated before labelling // ivt incubation: 12h.

scan_protocol: AffyScannerGCS3000 - Affymetrix GCAS One-Cycle protocol

data_processing: R/BioConductor/LIMMA package using rma normalized data; Relative fluorescence units (RFU)

organism: Mus musculus

source_name: Tmem203 null_testes_24WKS

label_protocol: standard affymetrix protocol

growth_protocol: Testes were  harvested from control and Tmem203 null C57BL/6J mice at 24 weeks of age.

extract_protocol: A QIAGEN Rneasy Mini Kit was employed to isolate total RNA, employing the manufacturer's recommended protocol

treatment_protocol: Harvested tissue was not treated

tag: strain background

tag: genotype/variation

value: Tmem203 null

tag: age

value: 24 weeks

value: Testes


title: TESTES_WT_rep4

source_name: wild type_testes_24WKS

value: wild type

tag: tissue


title: BJ fibroblast_Trt1_1


title: BJ fibroblast_Ctrl2_4


title: BJ fibroblast_Ctrl3_1


title: BJ fibroblast_Trt2_1


title: TESTES_KO_rep3


title: BJ fibroblast_Ctrl4_2


title: BJ fibroblast_Trt0_4


title: BJ fibroblast_Ctrl3_4


title: BJ fibroblast_Ctrl4_1


title: TESTES_WT_rep3


title: TESTES_KO_rep5


title: TESTES_KO_rep2


title: BJ fibroblast_Trt1_3


title: TESTES_WT_rep2


title: 3d2 + m.cat rep2

city: Toronto

first: Scott

middle: D.

last: Gray-Owen

address: 1 King's College Circle

department: Molecular Genetics

institute: University of Toronto

description:
M. catarrhalis treatment (-HBP) rep2
3d2unt2

hyb_protocol: Standard Illumina hybridization with 750 ng of cRNA (58°C, with rotation speed 5 for 18 hrs for hybridization)

scan_protocol: The BeadChip was washed and stained as per Illumina protocol and scanned on the iScan (Illumina).

data_processing: Data was imported in Genespring v11.0.1 for analysis.  During import, the data was normalized using a quantile normalization function. All data analysis was performed on log2 transformed data. The data was first filtered to remove the confounding effect probes that show no signal at all in either group may have on subsequent analysis. Only probes that were in the upper 80th percentile of the distribution of intensities in 100% of either of the categories were allowed to pass through this filtering.

source_name: Jurkat T cell clone 3d2 + m.cat

label_protocol: 250 ng RNA labeled usingTotalPrep RNA Amplification kit Lot # 1107026 (Ambion)

growth_protocol: Cell lines were cultured in RPMI 10% FCS

extract_protocol: Qiagen RNEASy, Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cell lines were treated with a 1:1 dilution of conditioned medium prepared from N. gonorrhoeae, or M. catarrhalis for 2 hours.

value: Jurkat T cell line clone

tag: cell number

tag: passage number

tag: treated with

value: culture supernatants prepared from M. catarrhalis


title: Mouse cochlea of 12 weeks of age with L-methionine and valproic acid #6

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

institute: Keio University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were digitalized using GeneChip Operating Software (GCOS) v.1.3 (Affymetrix).
Gene expression array data were normalized using MAS5 algorithm (Affymetrix). Then, to correct for bias between chips, quantile normalization (Bolstad, B. M. et al. Bioinformatics 19, 185-193 (2003)) was applied to all array data using R software.
The intensities were converted to a logarithmic scale (base 2). Signal reliability of each probe was determined based on the MAS5 Call algorithm (Affymetrix), and each probe was assigned to one of three flags (P: present, M: marginal, and A: absent).

source_name: Mouse cochlea of 12 weeks of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Rev. 3, 2009, Affymetrix).

growth_protocol: Mice were housed in plastic cages with metallic lid in a room with a 12-h light/dark cycle and 55% humidity at 23 C and had free access to food and water.

extract_protocol: Total RNA was extracted from mouse whole cochlea using TRIzol regent (LifeTechnologies). Additionally, total RNA was purified using Rneasy Mini Kit (Qiagen).

treatment_protocol: DBA/2J mice (4 weeks old) were injected subcutaneously once daily for 8 weeks with  L-methionine (500 mg/kg) and valproic acid (300 mg/kg) in 0.1M sodium bicarbonate.

value: 12 weeks of age

tag: Sex

value: male

value: cochlea

tag: strain


title: TESTES_WT_rep1


title: 3d2 + HBP rep2

description:
HBP treatment rep2
3d2treat2

source_name: Jurkat T cell clone 3d2 + HBP

tag: cell line

value: culture supernatants prepared from N. gonorrhoeae


title: Mouse cochlea of 12 weeks of age with L-methionine and valproic acid #3


title: 3e3 + m.cat rep2

description:
M. catarrhalis treatment (-HBP) rep2
3e3unt2

source_name: Jurkat T cell clone 3e3 + m.cat


title: TESTES_KO_rep1


title: 3e3 + m.cat rep1

description:
M. catarrhalis treatment (-HBP) rep1
3e3unt1


title: 3d2 + HBP rep1

description:
HBP treatment rep1
3d2treat1


title: Mouse cochlea of 12 weeks of age with L-methionine and valproic acid #5


title: 3e3 + m.cat rep3

description:
M. catarrhalis treatment (-HBP) rep3
3e3unt3


title: ED107

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

hyb_protocol: standard Affymetrix protocol

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

data_processing: The data were analyzed with Affymetrix expression console 1.2.0 using Affymetrix default analysis settings and plier as normalization method.

source_name: breast cancer_pretreatment

label_protocol: Two-cycle target labeling was carried out on 50 ng total RNA according to Affymetrix's published protocols

growth_protocol: N/A; pretreatment surgical specimens from estrogen receptor positive breast tumors

extract_protocol: Total RNA was extracted from frozen tumor samples using TRIzol, cleaned using the QIAGEN Rneasy Mini Kit, and its quality confirmed using an Agilent 2100 Bioanalyzer and RNA 6000 LabChips

treatment_protocol: Tamoxifen

value: estrogen receptor positive breast tumor

tag: breast cancer recurrence

value: Late


title: Mouse cochlea of 12 weeks of age with control vehicle #5


title: 3e3 + HBP rep2

description:
HBP treatment rep2
3e3treat2

source_name: Jurkat T cell clone 3e3 + HBP


title: 3d2 + m.cat rep1

description:
M. catarrhalis treatment (-HBP) rep1
3d2unt1


title: Mouse cochlea of 12 weeks of age with L-methionine and valproic acid #4


title: Mouse cochlea of 12 weeks of age with L-methionine and valproic acid #1


title: Mouse cochlea of 12 weeks of age with control vehicle #3


title: 3-42BM


title: Mouse cochlea of 12 weeks of age with control vehicle #2


title: 3e3 + HBP rep3

description:
HBP treatment rep3
3e3treat3


title: ED049


title: Mouse cochlea of 4 weeks of age #5

source_name: Mouse cochlea of 4 weeks of age

value: 4 weeks of age


title: NCCIT differentiation for 21days

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

description: Gene expression data of NCCIT differentiation for 21days

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: human embryonic carcinoma cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: The cells were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS), 100 IU ml–1 penicillin and 10 µg ml–1 streptomycin at 37 °C in the CO2 incubator

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

treatment_protocol: For EB formation, 1 × 10^6 NCCIT cells were plated in absence or presence of ethanol (50 mM) in the 90-mm bacterial culture dishes (non-adherent culture conditions) for 7 days. We changed culture media every day to ensure treated ethanol concentration during the course of the study

value: human embryonic carcinoma cells

value: NCCIT


title: ED022


title: ED090


title: NCCIT differentiation for 7days

description: Gene expression data of NCCIT differentiation for 7days


title: ED016


title: NCCIT with FA for 21days

description: Gene expression data of NCCIT with FA for 21days


title: NCCIT with FA for 7days

description: Gene expression data of NCCIT with FA for 7days


title: Mouse cochlea of 12 weeks of age with L-methionine and valproic acid #2


title: ED069


title: Mouse cochlea of 4 weeks of age #2


title: 3-49BC


title: NCCIT with EtOH+FA for 21days

description: Gene expression data of NCCIT with EtOH+FA for 21days


title: Mouse cochlea of 12 weeks of age with control vehicle #1


title: Mouse cochlea of 4 weeks of age #3


title: ED057


title: 3-61YA


title: 3e3 + HBP rep1

description:
HBP treatment rep1
3e3treat1


title: Mouse cochlea of 4 weeks of age #4


title: ED091


title: 3d2 + HBP rep3

description:
HBP treatment rep3
3d2treat3


title: Sample6 POST

city: Barcelona

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

country: Spain

institute: VHIO

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions

data_processing: Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalized using 5 HK genes.  Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system

source_name: Breast tumor

label_protocol: RNA was not labeled; instead, RNA (100 ng/ul) was pre-processed following the NanoString manufacturer's protocol by VHIO´s Translational Genomics Group

extract_protocol: Total RNA was isolated from macrodissected FFPE tissue using ROCHE High Pure FFPE Kit

value: breast cancer

tag: before or after therapy

value: POST


title: 3d2 + m.cat rep3

description:
M. catarrhalis treatment (-HBP) rep3
3d2unt3

tag: cell type


title: 3-56SA


title: Mouse cochlea of 12 weeks of age with control vehicle #4


title: NCCIT with EtOH for 7days

description: Gene expression data of NCCIT with EtOH for 7days


title: ED013


title: Mouse cochlea of 4 weeks of age #1


title: NCCIT with EtOH for 21days

description: Gene expression data of NCCIT with EtOH for 21days


title: iBAT D8 ISO 2hr

first: Royhan

last: Rozqie

address: Komaba, Meguro-ku

institute: The University of Tokyo

description: Gene expression data of BAT

hyb_protocol: Labeled cRNA probes were hybridized to Mouse Genome 430 2.0 array

scan_protocol: Affymetrix GeneChIP scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. The minimum score is 100.

label: streptavidin phycoerythrin

source_name: iBAT

label_protocol: stained with streptavidin phycoerythrin

growth_protocol: iBAT cells were maintained in medium DMEM+FBS 10%+P/S 1%

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

treatment_protocol: For differentiation, cells were induced with Insulin and Indomethacin, and Isoproterenol was added for chatecholamines stimulation.

tag: differentiation

value: Day 8

tag: stimulation


title: 3-26KH


title: Sample6 PRE

value: PRE


title: Sample5 PRE


title: iBAT D8 ISO 1hr

description: Gene expression data of BAT


title: Sample5 POST


title: NCCIT with EtOH+FA for 7days

description: Gene expression data of NCCIT with EtOH+FA for 7days


title: Sample4 PRE


title: iBAT D8 ISO 0hr

description: Gene expression data of BAT


title: Sample3 PRE


title: Sample4 POST


title: 3-87CI

value: Intermediate


title: NCCIT cells

description: Gene expression data of NCCIT cells


title: 3-139MH


title: 3-117CM


title: Sample3 POST


title: BJ fibroblast_Ctrl2_2

value: BJ fribroblast


title: iPSC PiZZ T5 3

description:
Sample name: 103 T5
Gene expression data from PiZZ skin fibroblasts profiled at T5.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

source_name: PiZZ skin fibroblasts

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

value: iPSC

tag: Stage

tag: group

value: iPSC PiZZ


title: BJ fibroblast_Ctrl2_1

description: transcript turnover rates measured at 2 h after actinomycin D addition from vehicle-treated BJ fibroblasts


title: ED033


title: Sample2 POST


title: BJ fibroblast_Ctrl1_4

description: transcript turnover rates measured at 1 h after actinomycin D addition from vehicle-treated BJ fibroblasts

source_name: vehicle 24 h, 1 h actinomycin D


title: BJ fibroblast_Ctrl1_1


title: BJ fibroblast_Ctrl4_4

description: transcript turnover rates measured at 4 h after actinomycin D additon from vehicle-treated BJ fibroblasts


title: BJ fibroblast_Ctrl0_1

description: steady state mRNA levels at time 0 of actinomycin D addition from vehicle-treated BJ fibroblasts

source_name: vehicle 24 h, 0 h actinomycin D


title: Sample2 PRE


title: 3-37CE


title: 3-47QD


title: Sample1 POST


title: Sample1 PRE


title: 3-84HL


title: iPSC PiZZ T24 2

description:
Sample name: 102 T24
Gene expression data from PiZZ skin fibroblasts profiled at T24.


title: BJ fibroblast_Ctrl0_4


title: BJ fibroblast_Ctrl1_3


title: BJ fibroblast_Ctrl0_2


title: BJ fibroblast_Ctrl0_3


title: iPSC PiZZ T5 2

description:
Sample name: 102 T5
Gene expression data from PiZZ skin fibroblasts profiled at T5.


title: 3-107BD


title: BJ fibroblast_Ctrl1_2


title: iPSC PiZZ T24 1

description:
Sample name: 100 T24
Gene expression data from PiZZ skin fibroblasts profiled at T24.


title: iPSC PiZZ T0 2

description:
Sample name: 102 T0
Gene expression data from PiZZ skin fibroblasts profiled at T0.


title: 3-72JI


title: iPSC PiZZ T0 1

description:
Sample name: 100 T0
Gene expression data from PiZZ skin fibroblasts profiled at T0.


title: 3-15PH

value: Early


title: iPSC wild-type T5 1

description:
Sample name: BMC1 T5
Gene expression data from wild-type skin fibroblasts profiled at T5.

source_name: wild-type skin fibroblasts

value: iPSC wild-type


title: iPSC wild-type T5 2

description:
Sample name: CHOPWT3.1 T5
Gene expression data from wild-type skin fibroblasts profiled at T5.


title: iPSC PiZZ T24 3

description:
Sample name: 103 T24
Gene expression data from PiZZ skin fibroblasts profiled at T24.


title: iPSC wild-type T24 3

description:
Sample name: HRII3 T24
Gene expression data from wild-type skin fibroblasts profiled at T24.


title: iPSC wild-type T24 1

description:
Sample name: BMC1 T24
Gene expression data from wild-type skin fibroblasts profiled at T24.


title: iPSC PiZZ T0 3

description:
Sample name: 103 T0
Gene expression data from PiZZ skin fibroblasts profiled at T0.


title: iPSC PiZZ T5 1

description:
Sample name: 100 T5
Gene expression data from PiZZ skin fibroblasts profiled at T5.


title: 3-68RL


title: 3-64HJ


title: 3-149BD


title: iPSC wild-type T5 3

description:
Sample name: HRII3 T5
Gene expression data from wild-type skin fibroblasts profiled at T5.


title: 3-17GE


title: iPSC wild-type T0 3

description:
Sample name: HRII3 T0
Gene expression data from wild-type skin fibroblasts profiled at T0.


title: 3-112DM


title: iPSC wild-type T24 2

description:
Sample name: CHOPWT3.1 T24
Gene expression data from wild-type skin fibroblasts profiled at T24.


title: 3-29BG


title: 3-66SC


title: iPSC wild-type T0 1

description:
Sample name: BMC1 T0
Gene expression data from wild-type skin fibroblasts profiled at T0.


title: ESC T24 2

description:
Sample name: H9 T24
Gene expression data from the H9 embryonic stem cell line profiled at T24.

source_name: H9 embryonic stem cell line

value: ESC H9

value: ESC


title: iPSC wild-type T0 2

description:
Sample name: CHOPWT3.1 T0
Gene expression data from wild-type skin fibroblasts profiled at T0.


title: 3-138MA

value: estrogen receptor positive breast tumor


title: 3-52BC


title: ESC T24 3

description:
Sample name: CHB8 T24
Gene expression data from the CHB-8 embryonic stem cell line profiled at T24.

source_name: CHB-8 embryonic stem cell line

value: ESC CHB-8


title: ESC T5 2

description:
Sample name: H9 T5
Gene expression data from the H9 embryonic stem cell line profiled at T5.


title: ESC T5 1

description:
Sample name: H1 T5
Gene expression data from the H1 embryonic stem cell line profiled at T5.

source_name: H1 embryonic stem cell line

value: ESC H1


title: 3-57AJ


title: 3-60FH


title: ESC T0 3

description:
Sample name: CHB8 T0
Gene expression data from the CHB-8 embryonic stem cell line profiled at T0.


title: 3-131HJ


title: 3-33ME


title: ESC T5 3

description:
Sample name: CHB8 T5
Gene expression data from the CHB-8 embryonic stem cell line profiled at T5.


title: 3-73SM


title: 3-140LC


title: orthoxenograft passage 1, from NF1 associated MPNST cell line S462

city: Badalona

first: Bernat

last: Gel Moreno

state: Barcelona

address: Ctra. de Can Ruti, camí de les escoles, s/n

department: Hereditary Cancer Program

institute: Institut de Medicina Predictiva i Personalitzada del Càncer

hyb_protocol: Labeled cDNA was hybridized to Human GEneCHip Gene 1.0 ST microarray (Affymetrix, Santa Clara, CA)

scan_protocol: The array were scanned using the Affymetrix Model 3000 Scanner.

data_processing: The data were processed using R/Bioconductor using the packages “gcrma” and “hugene10stv1cdf”. The rma function was used to normalize the data.

source_name: S462 - MPNST derived cell line orthoxenograft

label_protocol: The Ambion WT Expression Kit and the Affymetrix GeneChip WT terminal labeling

extract_protocol: Total RNA was isolated from frozen samples using miRCURY RNA (Exiqon). RNA integrity number (RIN) was verified for each sample using a RNA Nano Chip Kit (Agilent Technologies, Germany) in Agilent Bioanalyzer 2100.

tag: sample type

value: orthoxenograft

tag: host organism

value: nude mouse

value: Yes

tag: original tumor

tag: passage


title: ESC T0 1

description:
Sample name: H1 T0
Gene expression data from the H1 embryonic stem cell line profiled at T0.


title: 3-13FS

tag: tissue


title: ESC T24 1

description:
Sample name: H1 T24
Gene expression data from the H1 embryonic stem cell line profiled at T24.


title: orthoxenograft passage 4, from sporadic MPNST number 2

source_name: MPNST orthoxenograft

value: No


title: cell line, from NF1 associated MPNST cell line S462

source_name: S462 - MPNST derived cell line

value: cell line


title: ESC T0 2

description:
Sample name: H9 T0
Gene expression data from the H9 embryonic stem cell line profiled at T0.


title: 3-136YS


title: primary tumor, from sporadic MPNST number 2

source_name: MPNST primary tumor

value: primary tumor


title: 3-102BD

source_name: breast cancer_pretreatment


title: ED031


title: 3-9BA


title: b6_air_t=01h

first: Sallie

middle: W

last: Chisholm

address: 15 Vassar St., Bldg. 48-419

institute: MIT

description: Gene expression of MED4 after resuspension in air-bubbled medium (control)

hyb_protocol: Hybridization and staining were performed by the MIT BioMicro Center.  All reagents were supplied by Affymetrix.  12.5 μg aRNA was hybridized to the MD4-9313 custom Affymetrix array in aqueous hybridization mix during a 16-h incubation at 45°C with rotation at 60 rpm in a GeneChip Hybridization Oven 640.  Hybridized arrays were washed with buffers A (non-stringent) and B (stringent), stained with streptavidin in stain buffer, and washed again with buffer A according to protocol ProkGE_WS2_450 in a GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G.

data_processing: Data processing was performed in R.  Chip images were processed using the package Harshlight prior to robust multi-chip average (RMA) normalization using the package affy.  The Affymetrix chip-definition file used (MD4-9313a520062.2014-06-27.cdf) was updated in June 2014 to reflect recently discovered non-coding RNAs.  Following RMA normalization, the dataset was filtered include only strain-specific probes and to exclude intergenic regions.

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

source_name: MED4 culture 70 mins after resuspension in medium bubbled with air (control condition), biological rep 2

label_protocol: RNA amplification and biotin labeling were performed by the MIT BioMicro Center using the MessageAmp II - Bacteria kit (Ambion) according to the manufacturer's protocol, using 200 ng input RNA.

growth_protocol: Axenic Prochlorococcus MED4 was grown in Sargasso seawater-based Pro99 medium [Moore et al., 2007] amended with 20-mM Na-HEPES pH 8.1.  Cultures were grown in 25-mm glass tubes at 21 degrees C with continuous illumination at ~60 micromol photons per m^2 per s for >30 generations prior to inoculation of experimental cultures.  1.2-L experimental cultures were grown to mid-log phase in clear 2-L bottles sparged with air.

extract_protocol: Cell suspensions were thawed in small batches and processed with the Zymo Research Mini RNA Isolation II kit.  The manufacturer's protocol was followed except that cell lysis was allowed to continue for 20 min on ice.  DNA was removed by treating 1 µg total nucleic acids with 2 µL Turbo DNAfree (Ambion) in a 50-µL reaction for 1 h, followed by DNase inactivation according to the manufacturer’s protocol.  RNA was concentrated by ethanol precipitation and yields were quantified with Ribogreen (Molecular Probes).

treatment_protocol: Experimental cultures were pelleted and resuspended.  Suspensions were split among four 500-mL bottles, each containing medium pre-equilibrated with a different gas (40_0: 0.004% CO2, 0% O2, balance N2; 40_21: 0.004% CO2, 21% O2, balance N2; 360_0: 0.036% CO2, 0% O2, balance N2; air (control): ambient air) by vigorous sparging for 24 h.  Bottles were swirled to mix and immediately sampled for the t = 0 timepoint.  Sparging continued throughout the 24-h timecourse.  At each timepoint, 20-mL samples were collected and pelleted (12500 rpm, 10 minutes, 4 degrees C, JA-25.50 rotor).  Supernatants were immediately discarded and each pellet resuspended in 500 µL resuspension buffer (200 mM sucrose, 10 mM NaOAc pH 5.2, 5 mM EDTA).  Cell suspensions were transferred to 1.5-mL tubes and flash-frozen in liquid nitrogen.  Sampling for each timepoint was completed within 20 min (from withdrawal of samples to flash-freezing).

tag: genbank synonym

value: Prochlorococcus marinus MED4

value: ambient

tag: time


title: primary tumor, from sporadic MPNST number 1


title: 3-147BM


title: b6_air_t=0

source_name: MED4 culture just after resuspension in medium bubbled with air (control condition), biological rep 2


title: primary tumor, from NF1-associated MPNST number 2


title: orthoxenograft passage 4, from NF1-associated MPNST number 1


title: b6_360_0_t=24h

description: Gene expression of MED4 after resuspension in O2-limited medium

source_name: MED4 culture 24 h after resuspension in medium bubbled with 0.036% CO2 and 0% O2, biological rep 2


title: orthoxenograft passage 1, from sporadic MPNST number 1


title: ED042


title: 3-67SL


title: 3-156BD


title: orthoxenograft passage 4, from NF1-associated MPNST number 2


title: b6_air_t=24h

source_name: MED4 culture 24 h after resuspension in medium bubbled with air (control condition), biological rep 2


title: b6_air_t=12h

source_name: MED4 culture 12 h after resuspension in medium bubbled with air (control condition), biological rep 2


title: orthoxenograft passage 1, from NF1-associated MPNST number 2


title: orthoxenograft passage 1, from sporadic MPNST number 2


title: b6_360_0_t=12h

source_name: MED4 culture 12 h after resuspension in medium bubbled with 0.036% CO2 and 0% O2, biological rep 2


title: b6_air_t=06h

source_name: MED4 culture 6 h after resuspension in medium bubbled with air (control condition), biological rep 2

value: 6 h


title: 3-54SL


title: C01_12166

city: BETHESDA

first: Vincent

middle: J.

last: Hearing

state: MD

address: BG 37 RM 2132B 37 CONVENT DR

institute: National Cancer Institute

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing  protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: control from subject C01_12166

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA  InputLinear Amp Kit (Agilent Technologies) following the manufac-turer’s protocol.

extract_protocol: RNA was prepared from each biopsy using standard RNA extraction protocols (Trizol, Sigma, St Louis, MO), and were quality-checked using an Agilent 2100 Bioanalyzer platform (Agilent Technologies,Waldbronn, Germany).

treatment_protocol: 4mm human skin punch biopsies were taken from subjects

value: whole skin

tag: phototype

value: II

tag: hybridization


title: C01_199

source_name: control from subject C01_199


title: b6_360_0_t=06h

source_name: MED4 culture 6 h after resuspension in medium bubbled with 0.036% CO2 and 0% O2, biological rep 2


title: C01_5112

source_name: control from subject C01_5112

value: I-II


title: C01_371

source_name: control from subject C01_371


title: orthoxenograft passage 1, from NF1-associated MPNST number 1


title: b6_360_0_t=01h

source_name: MED4 culture 70 mins after resuspension in medium bubbled with 0.036% CO2 and 0% O2, biological rep 2


title: b6_360_0_t=0

source_name: MED4 culture just after resuspension in medium bubbled with 0.036% CO2 and 0% O2, biological rep 2


title: b6_40_21_t=24h

description: Gene expression of MED4 after resuspension in CO2-limited medium

source_name: MED4 culture 24 h after resuspension in medium bubbled with 0.004% CO2 and 21% O2, biological rep 2


title: C01_5711

source_name: control from subject C01_5711


title: b6_40_21_t=12h

source_name: MED4 culture 12 h after resuspension in medium bubbled with 0.004% CO2 and 21% O2, biological rep 2


title: C01_8188

source_name: control from subject C01_8188


title: C01_3296

source_name: control from subject C01_3296


title: C01_1735

source_name: control from subject C01_1735

value: I


title: b6_40_21_t=06h

source_name: MED4 culture 6 h after resuspension in medium bubbled with 0.004% CO2 and 21% O2, biological rep 2


title: C01_4236

source_name: control from subject C01_4236


title: b6_40_21_t=01h

source_name: MED4 culture 70 mins after resuspension in medium bubbled with 0.004% CO2 and 21% O2, biological rep 2


title: gDNA-VMA16_2-vs-PMA

type: genomic

city: Albuquerque

first: Ulfar

last: Bergthorsson

state: New Mexico

address: 219 Yale Blvd NE

department: Biology

institute: University of New Mexico

hyb_protocol: The sample was rehydrated in 40 μl of NimbleGen Hybridization Buffer (NimbleGen Systems, Inc.), denatured at 95 °C for 5 min, and then cooled to 42 °C. Hybridizations were carried out for 18 hr at 42 °C in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) and immediately dried down by centrifugation. See Selzer,R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44:305-319 (PMID 16075461).

scan_protocol: The scanner used was an Axon Scanner (Model # 40008). See Selzer,R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44:305-319 (PMID 16075461).

data_processing: The raw log2 intensity ratios were normalized with the LOESS regression.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: PMA gDNA from populations

label_protocol: Cy3/Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 μl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 μl/ml β-Mercaptoethanol. 1 μg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 °C and then chilled on ice in 0.2 ml PCR tubes. 10 μl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP, and dTTP), 8 μl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixede well with a pipet. Samples were centrifuged and incubated at 37 °C for 2 hours. 10 μl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precpitated by adding 11.5 μl 0.5 M NaCl and 110 μl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrfuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 μl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 μl DI water. DNA concentration was measured using a spectrophotometer. See Maydan JS, Lorch A, Edgley ML, Flibotte S, and Moerman DG. 2010. Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. BMC Genomics Jan 25;11:62 (PMID: 20100350)

growth_protocol: Large populations maintained on agar plates and fed E coli bacteria prior to freezing and DNA extraction.

extract_protocol: DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using solid tissue protocol.

treatment_protocol: No mutation accumulation, maintained in large populations.

tag: subline

value: PMA Ancestral

source_name: VMA16 gDNA from populations.

treatment_protocol: Mutation accumulation via Msh-2 knockdown and population bottlenecking


title: gDNA-VMA19-vs-PMA

source_name: VMA19 gDNA from populations.


title: AS01_12166

source_name: age spot from subject AS01_12166


title: gDNA-C2-vs-PMA

source_name: C2 gDNA from populations.


title: gDNA-VMA50-vs-PMA

source_name: VMA50 gDNA from populations.


title: b6_40_21_t=0

source_name: MED4 culture just after resuspension in medium bubbled with 0.004% CO2 and 21% O2, biological rep 2


title: AS01_199

source_name: age spot from subject AS01_199


title: b6_40_0_t=24h

description: Gene expression of MED4 after resuspension in CO2- and O2-limited medium

source_name: MED4 culture 24 h after resuspension in medium bubbled with 0.004% CO2 and 0% O2, biological rep 2


title: gDNA-VMA7_2-vs-PMA

source_name: VMA7 gDNA from populations.


title: AS01_5112

source_name: age spot from subject AS01_5112


title: gDNA-C4_2-vs-PMA

source_name: C4 gDNA from populations.


title: b6_40_0_t=12h

source_name: MED4 culture 12 h after resuspension in medium bubbled with 0.004% CO2 and 0% O2, biological rep 2


title: AS01_371

source_name: age spot from subject AS01_371


title: iPSC PiZZ T24 2

description:
Sample name: 102 T24
Gene methylation data from PiZZ skin fibroblasts profiled at T24.

hyb_protocol: Overnight hybridization to BeadChip arrays.

scan_protocol: Next day staining of hybridized arrays produced methylation-dependent differential fluorescence that was detected via an Illumina iScan array scanner.

data_processing: Arrays were visualized and processed using the GenomeStudio software package, which produced IDAT files that were read into a MethyLumiSet using the methylumIDAT function in the methylumi R package (version 2.4.0).  This object was then coerced to a MethyLumiM object and quantile-normalized by sequentially applying the lumiMethyC and lumiMethyN functions from the lumi R package (version 2.10.0).  All methylation analyses were performed using the R environment for statistical computing (version 2.15.1).

label: Cy5 and Cy3

source_name: PiZZ skin fibroblasts

label_protocol: 500ng gDNA underwent bisulfite conversion of unmethylated cytosine bases to uracil, and bisulfite converted DNA was then amplified and purified

extract_protocol: According to Illumina protocol

tag: cell line

value: iPSC

value: iPSC PiZZ


title: iPSC PiZZ T24 3

description:
Sample name: 103 T24
Gene methylation data from PiZZ skin fibroblasts profiled at T24.


title: gDNA-C1-vs-PMA

source_name: C1 gDNA from populations

source_name: PMA gDNA from populations.

value: PMA


title: gDNA-50E-vs-VMA50

source_name: VMA50 gDNA from populations

value: VMA50 ancestral

source_name: 50E gDNA from populations.

treatment_protocol: Fitness recovery from mutation accumulation in large populations.


title: b6_40_0_t=06h

source_name: MED4 culture 6 h after resuspension in medium bubbled with 0.004% CO2 and 0% O2, biological rep 2


title: AS01_8188

source_name: age spot from subject AS01_8188


title: gDNA-50D-vs-VMA50

source_name: 50D gDNA from populations.


title: iPSC PiZZ T24 1

description:
Sample name: 100 T24
Gene methylation data from PiZZ skin fibroblasts profiled at T24.


title: gDNA-C5-vs-PMA

source_name: C5 gDNA from populations


title: gDNA-50B-vs-VMA50

source_name: 50B gDNA from populations.


title: iPSC PiZZ T0 3

description:
Sample name: 103 T0
Gene methylation data from PiZZ skin fibroblasts profiled at T0.


title: iPSC PiZZ T5 3

description:
Sample name: 103 T5
Gene methylation data from PiZZ skin fibroblasts profiled at T5.


title: AS01_5711

source_name: age spot from subject AS01_5711


title: gDNA-50C-vs-VMA50

source_name: 50C gDNA from populations

source_name: VMA50 gDNA from populations.


title: iPSC PiZZ T5 1

description:
Sample name: 100 T5
Gene methylation data from PiZZ skin fibroblasts profiled at T5.


title: b6_40_0_t=01h

source_name: MED4 culture 70 mins after resuspension in medium bubbled with 0.004% CO2 and 0% O2, biological rep 2


title: gDNA-19E-vs-VMA19

source_name: VMA19 gDNA from populations

value: VMA19 ancestral

source_name: 19E gDNA from populations.


title: b6_40_0_t=0

source_name: MED4 culture just after resuspension in medium bubbled with 0.004% CO2 and 0% O2, biological rep 2


title: gDNA-VMA16-vs-PMA

source_name: PMA gDNA from populations

source_name: VMA16 gDNA from populations.


title: iPSC PiZZ T0 1

description:
Sample name: 100 T0
Gene methylation data from PiZZ skin fibroblasts profiled at T0.

source_name: PiZZ skin fibroblasts


title: gDNA-19D-vs-VMA19

source_name: 19D gDNA from populations.


title: gDNA-19C-vs-VMA19

source_name: 19C gDNA from populations.


title: gDNA-19B-vs-VMA19

source_name: 19B gDNA from populations.


title: gDNA-VMA66-vs-PMA

source_name: VMA66 gDNA from populations.


title: b5_air_t=24h

source_name: MED4 culture 24 h after resuspension in medium bubbled with air (control condition), biological rep 1


title: gDNA-50A-vs-VMA50

source_name: VMA50 gDNA from populations

source_name: 50A gDNA from populations.


title: iPSC PiZZ T5 2

description:
Sample name: 102 T5
Gene methylation data from PiZZ skin fibroblasts profiled at T5.


title: iPSC PiZZ T0 2

description:
Sample name: 102 T0
Gene methylation data from PiZZ skin fibroblasts profiled at T0.


title: AS01_3296

source_name: age spot from subject AS01_3296


title: AS01_4236

source_name: age spot from subject AS01_4236


title: b5_air_t=06h

source_name: MED4 culture 6 h after resuspension in medium bubbled with air (control condition), biological rep 1


title: b5_air_t=12h

source_name: MED4 culture 12 h after resuspension in medium bubbled with air (control condition), biological rep 1


title: AS01_1735

source_name: age spot from subject AS01_1735


title: gDNA-19A-vs-VMA19

source_name: VMA19 gDNA from populations

source_name: 19A gDNA from populations.


title: b5_air_t=0

source_name: MED4 culture just after resuspension in medium bubbled with air (control condition), biological rep 1


title: gDNA-C4-vs-PMA

source_name: PMA gDNA from populations

source_name: C4 gDNA from populations.


title: b5_air_t=01h

source_name: MED4 culture 70 mins after resuspension in medium bubbled with air (control condition), biological rep 1


title: gDNA-VMA7-vs-PMA

source_name: VMA7 gDNA from populations.


title: iPSC wild-type T24 2

description:
Sample name: BMC1 T24
Gene methylation data from wild-type skin fibroblasts profiled at T24.

source_name: wild-type skin fibroblasts

value: iPSC wild-type


title: b5_360_0_t=24h

source_name: MED4 culture 24 h after resuspension in medium bubbled with 0.036% CO2 and 0% O2, biological rep 1


title: b5_360_0_t=12h

source_name: MED4 culture 12 h after resuspension in medium bubbled with 0.036% CO2 and 0% O2, biological rep 1


title: b5_360_0_t=06h

source_name: MED4 culture 6 h after resuspension in medium bubbled with 0.036% CO2 and 0% O2, biological rep 1


title: gDNA-C3-vs-PMA

source_name: C3 gDNA from populations.


title: b5_360_0_t=0

source_name: MED4 culture just after resuspension in medium bubbled with 0.036% CO2 and 0% O2, biological rep 1


title: b5_360_0_t=01h

source_name: MED4 culture 70 mins after resuspension in medium bubbled with 0.036% CO2 and 0% O2, biological rep 1


title: iPSC wild-type T24 1

description:
Sample name: CHOPWT3.1 T24
Gene methylation data from wild-type skin fibroblasts profiled at T24.


title: gDNA-66E-vs-VMA66

source_name: VMA66 gDNA from populations

value: VMA66 ancestral

source_name: 66E gDNA from populations.


title: gDNA-66C_3-vs-VMA66

source_name: 66C gDNA from populations.


title: b5_40_21_t=24h

source_name: MED4 culture 24 h after resuspension in medium bubbled with 0.004% CO2 and 21% O2, biological rep 1


title: iPSC wild-type T24 3

description:
Sample name: HRII3 T24
Gene methylation data from wild-type skin fibroblasts profiled at T24.


title: gDNA-66C-vs-VMA66


title: b5_40_21_t=12h

source_name: MED4 culture 12 h after resuspension in medium bubbled with 0.004% CO2 and 21% O2, biological rep 1


title: gDNA-66D-vs-VMA66

source_name: 66D gDNA from populations.


title: gDNA-66A-vs-VMA66

source_name: 66A gDNA from populations.


title: iPSC wild-type T0 1

description:
Sample name: BMC1 T0
Gene methylation data from wild-type skin fibroblasts profiled at T0.


title: iPSC wild-type T5 3

description:
Sample name: HRII3 T5
Gene methylation data from wild-type skin fibroblasts profiled at T5.


title: b5_40_21_t=06h

source_name: MED4 culture 6 h after resuspension in medium bubbled with 0.004% CO2 and 21% O2, biological rep 1


title: gDNA-66B_2-vs-VMA66

source_name: 66B gDNA from populations.


title: gDNA-66B-vs-VMA66


title: b5_40_21_t=01h

source_name: MED4 culture 70 mins after resuspension in medium bubbled with 0.004% CO2 and 21% O2, biological rep 1


title: b5_40_21_t=0

source_name: MED4 culture just after resuspension in medium bubbled with 0.004% CO2 and 21% O2, biological rep 1


title: iPSC wild-type T5 1

description:
Sample name: CHOPWT3.1 T5
Gene methylation data from wild-type skin fibroblasts profiled at T5.

source_name: wild-type skin fibroblasts


title: iPSC wild-type T5 2

description:
Sample name: BMC1 T5
Gene methylation data from wild-type skin fibroblasts profiled at T5.


title: iPSC wild-type T0 2

description:
Sample name: CHOPWT3.1 T0
Gene methylation data from wild-type skin fibroblasts profiled at T0.


title: iPSC wild-type T0 3

description:
Sample name: HRII3 T0
Gene methylation data from wild-type skin fibroblasts profiled at T0.


title: ESC T24 2

description:
Sample name: H9 T24
Gene methylation data from the H9 embryonic stem cell line profiled at T24.

source_name: H9 embryonic stem cell line

value: ESC H9

value: ESC


title: wildtype rep 4

city: Daegue

first: Jieon

last: Lee

address: 333. Techno Jungang-daero Hyeongpung-myeon, Dalseong-gun

department: Chemical Engineering

institute: POSTECH

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization

source_name: Mouse liver

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was isolated with Qiagen RNeasy Mini Kit in accordance with prescribed protocal provided with kit. Quality control was performed with Agilent 2100 Bioanalyzer

tag: strain

tag: age

value: 18 day

value: liver

tag: genotype

value: wildtype


title: ESC T24 3

description:
Sample name: CHB8 T24
Gene methylation data from the CHB-8 embryonic stem cell line profiled at T24.

source_name: CHB-8 embryonic stem cell line

value: ESC CHB-8


title: gDNA-66A_2-vs-VMA66


title: b5_40_0_t=12h

description: Gene expression of MED4 after resuspension in CO2- and O2-limited medium

source_name: MED4 culture 12 h after resuspension in medium bubbled with 0.004% CO2 and 0% O2, biological rep 1

value: Prochlorococcus marinus MED4


title: gDNA-66C_2-vs-VMA66


title: gDNA-16D-vs-VMA16

source_name: VMA16 gDNA from populations

value: VMA16 ancestral

source_name: 16D gDNA from populations.


title: wildtype rep 2

description: replicate 2


title: wildtype rep 1

description: replicate 1


title: ESC T5 2

description:
Sample name: H9 T5
Gene methylation data from the H9 embryonic stem cell line profiled at T5.


title: wildtype rep 3

description: replicate 3


title: b5_40_0_t=01h

source_name: MED4 culture 70 mins after resuspension in medium bubbled with 0.004% CO2 and 0% O2, biological rep 1


title: ESC T0 3

description:
Sample name: CHB8 T0
Gene methylation data from the CHB-8 embryonic stem cell line profiled at T0.


title: gDNA-16C_2-vs-VMA16

source_name: 16C gDNA from populations.


title: b5_40_0_t=0

source_name: MED4 culture just after resuspension in medium bubbled with 0.004% CO2 and 0% O2, biological rep 1


title: gDNA-16C-vs-VMA16


title: ESC T24 1

description:
Sample name: H1 T24
Gene methylation data from the H1 embryonic stem cell line profiled at T24.

source_name: H1 embryonic stem cell line

value: ESC H1


title: gDNA-16E-vs-VMA16

source_name: 16E gDNA from populations.


title: gDNA-16A-vs-VMA16

source_name: 16A gDNA from populations.


title: SHR

first: Sabine

last: Gouraud

address: 3-10-2  Osawa, Mitaka

institute: International Christian University

description: pooled RNA from the NTS of 6 hypertensive rats (SHR)

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization we used the average of 2 housekeeping genes HKG: HPRT1 and ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (SAMPLE 1/SAMPLE 2=SHR/WKY) ratios.

label: SYBR Green

organism: Rattus norvegicus

source_name: NTS from brain

label_protocol: PCRs were performed using the Neurotrophin and Receptors RT²  profiler arrays (SABiosciences) following the Manufacturer’s instructions. Reverse transcription was performed from 1 ug total RNA using the RT²  First Strand Kit (SA Biosciences Qiagen). Quantitative real-time PCR were performed (iCycler iQ thermal cycler Biorad) by using RT²  SYBR Green qPCR Master Mix (SABioscience, Qiagen) with 45 cycles at 94°C for 15 seconds and 60°C for 60 seconds.

extract_protocol: Total RNA was extracted from the 6 NTS by using the Trizol method according to the manufacturer's instruction. 2 ug of the RNA from each NTS were pooled together. The RNA was treated with DNase I and cleaned up with RNeasy Mini Kit (Qiagen).

treatment_protocol: Rats (n=6) were killed by ether inhalation followed by decapitation. The brain was rapidly removed from the cranium and the NTS, located between 1.0 mm rostral and 0.5 mm caudal to the calamus scriptorius (CS), was dissected from the medulla oblongata

value: Spontaneaously hypertensive rat

tag: gender

value: male

value: 10 weeks old

value: Nucleus of Solitary Tract


title: Cic-L-/- rep 2

description: replicate 2

value: Cic-L-/-


title: WKY

description: pooled RNA from the NTS of 6 normotensive rats (WKY)

value: Wistar Kyoto


title: gDNA-16C_3-vs-VMA16


title: ESC T5 3

description:
Sample name: CHB8 T5
Gene methylation data from the CHB-8 embryonic stem cell line profiled at T5.

tag: Stage


title: b5_40_0_t=06h

source_name: MED4 culture 6 h after resuspension in medium bubbled with 0.004% CO2 and 0% O2, biological rep 1

value: 6 h


title: Cic-L-/- rep 3

description: replicate 3


title: ESC T5 1

description:
Sample name: H1 T5
Gene methylation data from the H1 embryonic stem cell line profiled at T5.

tag: group


title: gDNA-16B-vs-VMA16

source_name: 16B gDNA from populations.


title: Cic-L-/- rep 1

description: replicate 1