title: HepaRG-AFB control-72h rep2

description: Control (AFL10)

value: AFB control


title: HCV-associated cirrhosis without HCC - patient 4 - specimen 2

status: Public on Feb 20 2013

type: RNA

city: Bethesda

first: Patrizia

last: Farci

state: MD

address: 50 South Drive

department: National Institute of Allergy and Infectious Diseases

country: USA

institute: National Institutes of Health

description:
CIR-4-2
microRNA

hyb_protocol: Hybridization was performed on Affymetrix GeneChip miRNA 2.0 arrays using standard protocols available at www.affymetrix.com. Standard Affymetrix protocols were also used for staining and washing of the arrays.

scan_protocol: Standard Affymetrix protocols was used for scanning of the arrays (available at www.affymetrix.com).

data_processing:
Affymetrix probeset summaries were computed using the RMA algorithm. Data were then imported to BRB-ArrayTools (Version 4.2.1 - Stable Release (January 2012)) and subsequent data filtering, median normalization and statistical analyses were performed using this software.
Filtering: A first quantile normalization is included in the RMA method. After RMA, miRNAs with a percent of missing data exceeding 50% were excluded. The Sample data table contains only human miRNAs, which were included in the analysis.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: specimen obtained from explanted liver, CIR

label_protocol: 500ng of total RNA, including microRNA, was poly(A) tailed and then directly ligated to a fluorescent dendrimer (a branched single- and double-stranded DNA molecule conjugated to biotin) using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix).

growth_protocol: Not applicable.

extract_protocol: Total RNA, including microRNA, was extracted from frozen liver specimens using the miRNeasy Mini Kit (Qiagen).

treatment_protocol: Not applicable.

tag: disease state

value: HCV-associated cirrhosis without HCC

tag: tissue

value: liver

tag: gender

value: male

tag: age

value: 55 years

tag: patient identifier


title: HepaRG-WYE control-72h rep4

city: Brussels

first: Tatyana

last: Doktorova

state: Belgium

address: Laarbeeklaan 103, building G

department: FAFY

country: Belgium

institute: VUB

description: Control (PRN 10)

hyb_protocol: We used standard Affymetrix hybridisation rotocols

scan_protocol: We used standard Affymetrix scanning parameters

data_processing: The Affymetrix IDs were alternatively remapped to the alternative IDs from Brainarray  (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp), thus the ensemb version 61 was used (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/ensg.download/HGU133Plus2_Hs_ENSG_14.1.0.zip).  All samples were  further normalized by GC-RMA algorithm. In the hES-Heps 2NF, BaP, MAN, MPH, NIF, PIPB, SDF and SPB shared one control whereas AFB, CND, TPA, TOL, WYE and CYCLO shared another control. In the HepaRG system several compounds shared also one control. The groups were divided as follows: 1) 2NF, BaP, MPH, NIF, PIPB and SPB; 2) WYE, AFB, CND, CYCLO, TPA and TOL; 3) MAN and SDF; 4) NNK.  In the HepG2 system there were shared control among several compounds also. 2NF, BaP, NIF, PIPB and SPB shared one control, AFB, CND, CYCLO, TPA, TOL and WYE shared another control. The third group was MAN, MPH and SDF which had their own control whereas NNK had its own control. In the HepsC and the HepsT systems there were also several groups of compounds having the same control.The compounds were separated as follows: 1)2NF, NIF and PIPB sharing one control; 2)NNK, MAN, SDF and SPB sharing one control; 3)AFB, CND, CYCLO, TPA, TOL and WYE sharing one control; 4) BaP and MPH sharing one control.

label: biotin

source_name: HepaRG cell line

label_protocol: We used standard Affymetrix labeling protocols

growth_protocol: Hepatocytes were isolated by using a two-step collagenase perfusion technique . The viability was assessed by trypan blue exclusion and the cells (≥85% viability) were cultured as a monolayer at a density of 0.57x105 cells/cm2 in William’s E medium supplemented with 10%v/v fetal bovine serum, 292mg/ml L-glutamine, 7ng/ml glucagon and antibiotics (7.33IU/ml benzylpenicillin sodium, 50µg/ml kanamycin monosulphate, 50µg/ml streptomycin sulphate, and 10µg/ml ampicillin sodium) in an incubator at 37°C (5% CO2 and 95% air, 100% humidity). After 4 hours, the medium was renewed with serum-free culture medium, supplemented with 25µg/ml hydrocortisone hemisuccinate and 1mg/ml bovine insulin. The hES-Hep cells were derived, cultured and characterized from the human embryonic stem cell (hESC) line SA002 (Cellartis AB, Sweden), as previously described, with an additional step of enzymatic passaging for further expansion before the onset of hepatic differentiation (Heins et al. 2006). The differentiation of SA002 cells into hepatocyte-like cells was achieved by the sequential exposure to growth factors, such as human growth factor and differentiation-promoting factors, including hydrocortisone and insulin (Brolen et al. 2010). The hepatocellular carcinoma-derived HepG2 cell line (Rockville, USA) was cultured and handled as previously described (Tolosa et al. 2011). Human hepatoma HepaRG cells (Biopredic International, France) were cultivated as previously described (Gripon et al. 2002; Guillouzo et al. 2007). At day 13 of cultivation, low DMSO-containing medium was added for a period of 7 days.

extract_protocol: Samples for RNA isolation were collected after 72 hours of exposure. Minimum three independent biological experiments were conducted for each compound. The total RNA extraction (RNA extraction kit, Qiagen), including a DNase digestion step, was done according to the manufacturer’s instructions.

treatment_protocol: The exposure to the selected chemicals was done for a period of 72h at IC10 concentrations.

tag: replicate

tag: cell line

value: HepaRG

tag: treatment

value: WYE control


title: HCV-associated cirrhosis without HCC - patient 3 - specimen 1

description:
CIR-3-1
microRNA

value: 47 years


title: HepaRG-WYE control-72h rep5

description: Control (PRN 10)


title: HepaRG-AFB-72h rep2

description: Treatment with Aflatoxin B2

value: AFB


title: HCV-associated cirrhosis without HCC - patient 2 - specimen 2

description:
CIR-2-2
microRNA

value: 42 years


title: HepaRG-WYE control-72h rep6

description: Control (PRN 10)


title: HepaRG-AFB-72h rep1

description: Treatment with Aflatoxin B1


title: HepaRG-WYE-72h rep2

description: Treatment with Wy 14644

value: WYE


title: HepaRG-WYE control-72h rep3

description: Control (PRN 10)


title: HCV-associated cirrhosis without HCC - patient 2 - specimen 1

description:
CIR-2-1
microRNA


title: HepaRG-WYE control-72h rep1

description: Control (PRN 10)


title: HCV-associated cirrhosis without HCC - patient 3 - specimen 2

description:
CIR-3-2
microRNA


title: HepaRG-WYE-72h rep3

description: Treatment with Wy 14645


title: HepaRG-WYE control-72h rep2

description: Control (PRN 10)


title: HepaRG-WYE-72h rep1

description: Treatment with Wy 14643


title: HCV-associated cirrhosis without HCC - patient 1 - specimen 2

description:
CIR-1-2
microRNA

value: 43 years


title: HepaRG-NNK control-72h rep3

description: Control (NNK10)

value: NNK control


title: HCV-associated cirrhosis without HCC - patient 1 - specimen 1

description:
CIR-1-1
microRNA


title: HepaRG-NNK control-72h rep2

description: Control (NNK10)


title: HepaRG-NNK control-72h rep1

description: Control (NNK10)


title: Liver donor - patient 12 - specimen 1

description:
LD-12-1
microRNA

source_name: specimen obtained from explanted liver, LD

value: donor

tag: tissue type

value: normal

value: 22 years


title: Liver donor - patient 11 - specimen 1

description:
LD-11-1
microRNA

value: female

value: 36 years


title: Liver donor - patient 10 - specimen 1

description:
LD-10-1
microRNA

value: 18 years


title: Liver donor - patient 9 - specimen 1

description:
LD-9-1
microRNA

value: liver

value: 74 years


title: Liver donor - patient 6 - specimen 1

description:
LD-6-1
microRNA

value: 35 years


title: Liver donor - patient 4 - specimen 1

description:
LD-4-1
microRNA

value: male

value: 26 years


title: Liver donor - patient 5 - specimen 1

description:
LD-5-1
microRNA

value: 12 years


title: Liver donor - patient 8 - specimen 1

description:
LD-8-1
microRNA

value: 25 years


title: HepaRG-2NF control-72h rep3

description: Control (2NF10)

value: HepaRG

value: 2NF control


title: Liver donor - patient 3 - specimen 1

description:
LD-3-1
microRNA

value: 66 years


title: Liver donor - patient 7 - specimen 1

description:
LD-7-1
microRNA

value: 32 years


title: HepaRG-2NF-72h rep1

description: Treatment with 2-Nitrofluorene


title: HepaRG-2NF control-72h rep2

description: Control (2NF10)


title: hES-Heps-WYE control-72h rep2

description: Control (WYE1)

source_name: human embryonic stem cell derived hepatocyte like cells

tag: cell type

value: human embryonic stem cell-derived hepatocyte-like cells (hES-Hep)

value: WYE control


title: hES-Heps-WYE control-72h rep1

description: Control (WYE1)


title: hES-Heps-TOL control-72h rep1

description: Control (TOL1)

value: TOL control


title: Normal liver - patient 7 - specimen 1

description:
NL-7-1
microRNA

source_name: specimen obtained from explanted liver, NL

value: liver angioma

value: normal hepatic resection

value: female


title: Liver donor - patient 1 - specimen 1

description:
LD-1-1
microRNA

value: donor

value: liver

value: normal

value: 44 years


title: Liver donor - patient 2 - specimen 1

description:
LD-2-1
microRNA

value: male

value: 47 years


title: HepaRG-NNK-72h rep3

description: Treatment with NNK

value: NNK


title: hES-Heps-WYE -72h rep1

description: Treatment with Wy 14643

value: WYE


title: Normal liver - patient 6 - specimen 1

description:
NL-6-1
microRNA

value: 49 years


title: hES-Heps-TOL control-72h rep2

description: Control (TOL1)


title: Normal liver - patient 4 - specimen 1

description:
NL-4-1
microRNA

value: 48 years


title: Normal liver - patient 3 - specimen 1

description:
NL-3-1
microRNA

value: 59 years


title: HepaRG-2NF control-72h rep1

description: Control (2NF10)

value: HepaRG

value: 2NF control


title: Normal liver - patient 2 - specimen 1

description:
NL-2-1
microRNA

value: 27 years


title: hES-Heps-WYE control-72h rep3

description: Control (WYE1)

value: human embryonic stem cell-derived hepatocyte-like cells (hES-Hep)

value: WYE control


title: Normal liver - patient 1 - specimen 1

description:
NL-1-1
microRNA

value: liver angioma

value: normal hepatic resection

value: female

value: 61 years


title: HepaRG-2NF-72h rep3

description: Treatment with 2-Nitrofluorene


title: hES-Heps-WYE -72h rep3

description: Treatment with Wy 14645


title: HepaRG-NNK-72h rep2

description: Treatment with NNK


title: HepaRG-NNK-72h rep1

description: Treatment with NNK


title: Normal liver - patient 5 - specimen 1

description:
NL-5-1
microRNA

value: liver

value: 44 years


title: HepaRG-2NF-72h rep2

description: Treatment with 2-Nitrofluorene


title: hES-Heps-TOL control-72h rep3

description: Control (TOL1)

value: TOL control


title: hES-Heps-WYE -72h rep2

description: Treatment with Wy 14644


title: hES-Heps-TOL -72h rep3

description: Treatment with Tolbutamide

value: TOL


title: HepsT-WYE control-72h rep5

description: Control (WYE10)

organism: Rattus norvegicus

source_name: TSA-stabilized primary rat hepatocytes

value: TSA-stabilized primary rat hepatocytes


title: HepsT-WYE control-72h rep4

description: Control (WYE10)


title: HepsT-WYE control-72h rep3

description: Control (WYE10)


title: HepsT-WYE control-72h rep6

description: Control (WYE10)


title: HepsT-WYE-72h rep2

description: Treatment with Wy 14644

value: WYE


title: HepsT-TOL control-72h rep6

description: Control (TBT10)


title: hES-Heps-TPA control-72h rep2

description: Control (TPA1)

value: TPA control


title: hES-Heps-TOL -72h rep1

description: Treatment with Tolbutamide


title: hES-Heps-CYCLO control-72h rep2

description: Control (CYC1)

value: CYCLO control


title: HepsT-WYE-72h rep1

description: Treatment with Wy 14643


title: HepsT-WYE control-72h rep1

description: Control (WYE10)


title: hES-Heps-TPA -72h rep1

description: Treatment with Tetraphorbolacetate

value: TPA


title: HepsT-WYE control-72h rep2

description: Control (WYE10)


title: HepsT-TOL control-72h rep5

description: Control (TBT10)


title: HepsT-WYE-72h rep3

description: Treatment with Wy 14645


title: hES-Heps-CYCLO control-72h rep3

description: Control (CYC1)


title: hES-Heps-CND control-72h rep2

description: Control (CLO1)

value: CND control


title: hES-Heps-TPA control-72h rep1

description: Control (TPA1)


title: hES-Heps-CYCLO control-72h rep1

description: Control (CYC1)


title: hES-Heps-CYCLO -72h rep2

description: Treatment with Cyclophosphamide

value: CYCLO


title: hES-Heps-CYCLO -72h rep1

description: Treatment with Cyclophosphamide

value: human embryonic stem cell-derived hepatocyte-like cells (hES-Hep)


title: hES-Heps-TPA -72h rep3

description: Treatment with Tetraphorbolacetate


title: hES-Heps-TOL -72h rep2

description: Treatment with Tolbutamide


title: hES-Heps-TPA -72h rep2

description: Treatment with Tetraphorbolacetate


title: hES-Heps-CND control-72h rep1

description: Control (CLO1)


title: hES-Heps-CYCLO -72h rep3

description: Treatment with Cyclophosphamide


title: HepsT-TOL control-72h rep3

description: Control (TBT10)


title: HepsT-TOL control-72h rep1

description: Control (TBT10)


title: HepsT-TOL control-72h rep2

description: Control (TBT10)


title: HepsT-TOL control-72h rep4

description: Control (TBT10)


title: hES-Heps-CND control-72h rep3

description: Control (CLO1)


title: HepsT-TOL-72h rep3

description: Treatment with Tolbutamide


title: hES-Heps-CND -72h rep1

description: Treatment with Clonidine

value: CND


title: HepsT-TPA control-72h rep3

description: Control (TPA10)


title: HepsT-TPA control-72h rep6

description: Control (TPA10)


title: HepsT-TPA control-72h rep2

description: Control (TPA10)


title: HepsT-TPA-72h rep3

description: Treatment with Tetraphorbolacetate


title: HepsT-TOL-72h rep2

description: Treatment with Tolbutamide


title: hES-Heps-CND -72h rep3

description: Treatment with Clonidine


title: HepsT-TPA-72h rep2

description: Treatment with Tetraphorbolacetate


title: HepsT-TOL-72h rep1

description: Treatment with Tolbutamide


title: HepsT-TPA-72h rep1

description: Treatment with Tetraphorbolacetate


title: hES-Heps-AFB control-72h rep2

description: Control (AFL1)

value: AFB control


title: HepsT-TPA control-72h rep4

description: Control (TPA10)


title: hES-Heps-AFB -72h rep1

description: Treatment with Aflatoxin B1

value: AFB


title: hES-Heps-SPB control-72h rep1

description: Control (SPB1)

value: SPB control


title: hES-Heps-AFB control-72h rep3

description: Control (AFL1)


title: HepsT-TPA control-72h rep5

description: Control (TPA10)


title: hES-Heps-SPB control-72h rep3

description: Control (SPB1)


title: hES-Heps-SPB -72h rep3

description: Treatment with Phenobarbital sodum

value: SPB


title: hES-Heps-SPB control-72h rep2

description: Control (SPB1)


title: hES-Heps-AFB control-72h rep1

description: Control (AFL1)


title: hES-Heps-AFB -72h rep3

description: Treatment with Aflatoxin B3


title: hES-Heps-AFB -72h rep2

description: Treatment with Aflatoxin B2


title: HepsT-SPB control-72h rep4

description: Control (SPB10)


title: hES-Heps-CND -72h rep2

description: Treatment with Clonidine


title: HepsT-TPA control-72h rep1

description: Control (TPA10)


title: hES-Heps-SPB -72h rep2

description: Treatment with Phenobarbital sodum


title: HepsT-SPB control-72h rep3

description: Control (SPB10)


title: HepsT-SPB control-72h rep2

description: Control (SPB10)


title: HepsT-SPB-72h rep3

description: Treatment with Phenobarbital sodum


title: HepsT-SPB control-72h rep1

description: Control (SPB10)


title: hES-Heps-PIPB control-72h rep1

description: Control (PPX1)

value: PIPB control


title: HepsT-SDF control-72h rep3

description: Control (SDF10)

value: SDF control


title: HepsT-SDF control-72h rep4

description: Control (SDF10)


title: hES-Heps-SDF control-72h rep1

description: Control (DIC1)


title: HepsT-SPB-72h rep1

description: Treatment with Phenobarbital sodum


title: HepsT-SDF-72h rep3

description: Treatment with Diclofenac sodium

value: SDF


title: HepsT-SDF control-72h rep2

description: Control (SDF10)


title: hES-Heps-SPB -72h rep1

description: Treatment with Phenobarbital sodum


title: hES-Heps-SDF -72h rep3

description: Treatment with Diclofenac sodium


title: HepsT-SPB-72h rep2

description: Treatment with Phenobarbital sodum


title: hES-Heps-SDF -72h rep2

description: Treatment with Diclofenac sodium


title: hES-Heps-SDF -72h rep1

description: Treatment with Diclofenac sodium


title: HepsT-SDF control-72h rep1

description: Control (SDF10)


title: hES-Heps-PIPB -72h rep3

description: Treatment with Piperonyl butoxide

value: PIPB


title: hES-Heps-SDF control-72h rep2

description: Control (DIC1)


title: hES-Heps-PIPB -72h rep1

description: Treatment with Piperonyl butoxide


title: hES-Heps-SDF control-72h rep3

description: Control (DIC1)


title: HepsT-PIPB control-72h rep3

description: Control (PPX10)

value: TSA-stabilized primary rat hepatocytes


title: HepsT-SDF-72h rep1

description: Treatment with Diclofenac sodium


title: HepsT-SDF-72h rep2

description: Treatment with Diclofenac sodium


title: HepsT-PIPB control-72h rep2

description: Control (PPX10)


title: hES-Heps-PIPB -72h rep2

description: Treatment with Piperonyl butoxide


title: hES-Heps-PIPB control-72h rep2

description: Control (PPX1)


title: hES-Heps-PIPB control-72h rep3

description: Control (PPX1)


title: HepsT-PIPB-72h rep3

description: Treatment with Piperonyl butoxide


title: HepsT-PIPB control-72h rep1

description: Control (PPX10)


title: hES-Heps-NNK control-72h rep2

description: Control (NNK1)

value: NNK control


title: hES-Heps-NNK control-72h rep3

description: Control (NNK1)


title: hES-Heps-NNK -72h rep3

description: Treatment with NNK

value: NNK


title: hES-Heps-NNK -72h rep2

description: Treatment with NNK


title: hES-Heps-TPA control-72h rep3

description: Control (TPA1)

value: TPA control


title: HepsT-NIF control-72h rep3

description: Control (NFE10)

value: NIF control


title: HepsT-NIF control-72h rep2

description: Control (NFE10)


title: hES-Heps-NNK control-72h rep1

description: Control (NNK1)


title: hES-Heps-NIF control-72h rep1

description: Control (NFE1)


title: hES-Heps-NIF-72h rep3

description: Treatment with Nifedipine

value: NIF


title: HepsT-PIPB-72h rep1

description: Treatment with Piperonyl butoxide


title: hES-Heps-NNK -72h rep1

description: Treatment with NNK


title: hES-Heps-NIF control-72h rep3

description: Control (NFE1)


title: HepsT-NIF-72h rep2

description: Treatment with Nifedipine


title: hES-Heps-NIF-72h rep2

description: Treatment with Nifedipine


title: HepsT-NIF-72h rep3

description: Treatment with Nifedipine


title: HepsT-NIF control-72h rep1

description: Control (NFE10)


title: HepsT-NIF-72h rep1

description: Treatment with Nifedipine


title: HepsT-MPH control-72h rep1

description: Control (MPH10)

value: MPH control


title: hES-Heps-NIF control-72h rep2

description: Control (NFE1)

value: human embryonic stem cell-derived hepatocyte-like cells (hES-Hep)


title: HepsT-MPH control-72h rep2

description: Control (MPH10)


title: hES-Heps-MPH control-72h rep2

description: Control (MPH1)


title: HepsT-PIPB-72h rep2

description: Treatment with Piperonyl butoxide


title: hES-Heps-MPH control-72h rep3

description: Control (MPH1)


title: hES-Heps-MPH control-72h rep1

description: Control (MPH1)


title: HepsT-MPH-72h rep3

description: Treatment with Methapyrilene hydrochloride

value: MPH


title: HepsT-MPH-72h rep1


title: HepsT-MPH-72h rep2


title: HepsT-MPH control-72h rep3

description: Control (MPH10)


title: HepsT-MAN control-72h rep4

description: Control (DMT10)

value: MAN control


title: hES-Heps-NIF-72h rep1

description: Treatment with Nifedipine


title: hES-Heps-MPH-72h rep2


title: hES-Heps-MPH-72h rep1


title: hES-Heps-MPH-72h rep3


title: HepsT-MAN-72h rep3

description: Treatment with D-Manitol

value: MAN


title: HepsT-CYCLO control-72h rep6

description: Control (CYC10)

value: CYCLO control


title: hES-Heps-MAN control-72h rep3

description: Control (DMT1)


title: HepsT-CYCLO control-72h rep5

description: Control (CYC10)


title: hES-Heps-MAN-72h rep3

description: Treatment with D-Manitol


title: HepsT-MAN-72h rep1

description: Treatment with D-Manitol


title: hES-Heps-MPH control-72h rep4

description: Control (MPH1)


title: hES-Heps-MAN-72h rep2

description: Treatment with D-Manitol


title: HepsT-MAN control-72h rep3

description: Control (DMT10)


title: hES-Heps-BaP control-72h rep2

description: Control (BaP1)

value: BaP control


title: HepsT-MAN control-72h rep2

description: Control (DMT10)


title: HepsT-MAN control-72h rep1

description: Control (DMT10)


title: HepsT-CYCLO control-72h rep4

description: Control (CYC10)


title: HepsT-MAN-72h rep2

description: Treatment with D-Manitol


title: hES-Heps-MAN-72h rep1

description: Treatment with D-Manitol


title: hES-Heps-MPH-72h rep4


title: hES-Heps-MAN control-72h rep1

description: Control (DMT1)


title: hES-Heps-BaP-72h rep3

description: Treatment with Benzo a pyrene

value: BaP


title: HepsT-CYCLO control-72h rep3

description: Control (CYC10)


title: hES-Heps-BaP control-72h rep1

description: Control (BaP1)


title: hES-Heps-MAN control-72h rep2

description: Control (DMT1)


title: HepsT-CYCLO control-72h rep1

description: Control (CYC10)


title: HepsT-CYCLO control-72h rep2

description: Control (CYC10)


title: hES-Heps-BaP-72h rep1

description: Treatment with Benzo a pyrene


title: hES-Heps-BaP control-72h rep3

description: Control (BaP1)


title: HepsT-CYCLO-72h rep3

description: Treatment with Cyclophosphamide

value: CYCLO


title: HepsT-CYCLO-72h rep2

description: Treatment with Cyclophosphamide


title: HepsT-CND control-72h rep4

description: Control (CND10)

value: CND control


title: hES-Heps-BaP-72h rep2

description: Treatment with Benzo a pyrene


title: HepsT-CND control-72h rep3

description: Control (CND10)


title: HepsT-CND control-72h rep1

description: Control (CND10)


title: HepsT-CND control-72h rep2

description: Control (CND10)


title: HepsT-CND control-72h rep5

description: Control (CND10)


title: hES-Heps-2NF-72h rep2

description: Treatment with 2-Nitrofluorene


title: HepsT-CND control-72h rep6

description: Control (CND10)


title: hES-Heps-2NF control-72h rep2

description: Control (2NF)

value: 2NF control


title: hES-Heps-2NF-72h rep3

description: Treatment with 2-Nitrofluorene


title: HepsT-CYCLO-72h rep1

description: Treatment with Cyclophosphamide

value: TSA-stabilized primary rat hepatocytes


title: 6 weeks heart 48_young microRNA

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Agilent Feature Extraction Software

organism: Mus musculus

source_name: heart

label_protocol: standard Agilent protocol

extract_protocol: RNA was extracted with Trizol

value: heart

tag: genetic background

value: 6 weeks


title: 6 weeks heart 47_young microRNA


title: HepsT-CND-72h rep3

description: Treatment with Clonidine

value: CND


title: 18 months heart 38_old microRNA

value: 18 months


title: 6 weeks heart 46_young microRNA


title: 6 weeks heart 45_young microRNA


title: HepsT-BaP control-72h rep2

description: Control (BaP10)


title: HepsT-BaP control-72h rep1

description: Control (BaP10)


title: HepsT-CND-72h rep1

description: Treatment with Clonidine


title: 18 months heart 36_old microRNA


title: HepsT-BaP control-72h rep3

description: Control (BaP10)


title: hES-Heps-2NF control-72h rep1

description: Control (2NF)


title: hES-Heps-2NF-72h rep1

description: Treatment with 2-Nitrofluorene


title: hES-Heps-2NF control-72h rep3

description: Control (2NF)


title: 18 months heart 37_old microRNA


title: HepsT-BaP-72h rep1

description: Treatment with Benzo a pyrene


title: HepsT-BaP-72h rep3

description: Treatment with Benzo a pyrene


title: HepsT-BaP-72h rep2

description: Treatment with Benzo a pyrene


title: HepsT-CND-72h rep2

description: Treatment with Clonidine


title: HepsT-AFB control-72h rep6

description: Control (AFB10)

value: AFB control


title: HepsT-AFB control-72h rep4

description: Control (AFB10)


title: HepsT-AFB-72h rep3

description: Treatment with Aflatoxin B3

value: AFB


title: HepsT-AFB control-72h rep1

description: Control (AFB10)


title: HepsT-AFB control-72h rep2

description: Control (AFB10)


title: HepsT-NNK-72h rep2

description: Treatment with NNK

value: NNK


title: HepsT-NNK control-72h rep4

description: Control (NNK10)

value: NNK control


title: HepsT-NNK-72h rep3

description: Treatment with NNK


title: HepsT-AFB control-72h rep3

description: Control (AFB10)


title: HepsT-NNK control-72h rep2

description: Control (NNK10)


title: HepsT-NNK control-72h rep1

description: Control (NNK10)


title: HepsT-NNK control-72h rep3

description: Control (NNK10)


title: HepsT-AFB control-72h rep5

description: Control (AFB10)


title: HepsT-2NF-72h rep2

description: Treatment with 2-Nitrofluorene


title: HepsT-2NF-72h rep1

description: Treatment with 2-Nitrofluorene


title: HepsT-AFB-72h rep1

description: Treatment with Aflatoxin B1


title: HepsT-NNK-72h rep1

description: Treatment with NNK


title: HepsT-2NF-72h rep3

description: Treatment with 2-Nitrofluorene


title: HepsT-AFB-72h rep2

description: Treatment with Aflatoxin B2


title: HepsT-2NF control-72h rep2

description: Control (2NF10)


title: HepsC-WYE control-72h rep3

description: Control (WYE10)

source_name: Primary rat hepatocytes

value: Primary rat hepatocytes

value: WYE control


title: HepsC-WYE control-72h rep6

description: Control (WYE10)


title: HepsC-WYE control-72h rep4

description: Control (WYE10)


title: HepsC-WYE-72h rep2

description: Treatment with Wy 14644

value: WYE


title: HepsC-WYE control-72h rep5

description: Control (WYE10)


title: HepsT-2NF control-72h rep1

description: Control (2NF10)


title: HepsC-WYE control-72h rep1

description: Control (WYE10)


title: HepsC-TOL control-72h rep5

description: Control (TBT10)

value: TOL control


title: HepsC-WYE-72h rep3

description: Treatment with Wy 14645


title: HepsT-2NF control-72h rep3

description: Control (2NF10)


title: HepsC-TOL control-72h rep6

description: Control (TBT10)


title: HepsC-TOL control-72h rep4

description: Control (TBT10)


title: HepsC-WYE control-72h rep2

description: Control (WYE10)


title: HepsC-TOL control-72h rep2

description: Control (TBT10)


title: HepsC-WYE-72h rep1

description: Treatment with Wy 14643


title: HepsC-TOL-72h rep1

description: Treatment with Tolbutamide

value: TOL


title: HepsC-TPA-72h rep1

description: Treatment with Tetraphorbolacetate

value: TPA


title: HepsC-TOL-72h rep3

description: Treatment with Tolbutamide


title: HepsC-TOL control-72h rep1

description: Control (TBT10)


title: HepsC-SPB control-72h rep6

description: Control (SPB10)

value: SPB control


title: HepsC-TOL-72h rep2

description: Treatment with Tolbutamide


title: HepsC-SPB control-72h rep5

description: Control (SPB10)


title: HepsC-SPB-72h rep3

description: Treatment with Phenobarbital sodum

value: SPB


title: HepsC-SPB-72h rep2

description: Treatment with Phenobarbital sodum


title: HepsC-TPA control-72h rep1

description: Control (TPA10)

value: TPA control


title: HepsC-SPB control-72h rep4

description: Control (SPB10)


title: HepsC-TPA control-72h rep5

description: Control (TPA10)


title: HepsC-SPB control-72h rep3

description: Control (SPB10)


title: HepsC-SDF control-72h rep5

description: Control (SDF10)

value: SDF control


title: HepsC-SPB-72h rep1

description: Treatment with Phenobarbital sodum


title: HepsC-SPB control-72h rep1

description: Control (SPB10)


title: HepsC-SDF control-72h rep6

description: Control (SDF10)


title: HepsC-TPA control-72h rep2

description: Control (TPA10)


title: HepsC-SPB control-72h rep2

description: Control (SPB10)


title: HepsC-TPA-72h rep2

description: Treatment with Tetraphorbolacetate


title: HepsC-SDF control-72h rep2

description: Control (SDF10)


title: HepsC-SDF-72h rep2

description: Treatment with Diclofenac sodium

value: SDF


title: HepsC-SDF control-72h rep3

description: Control (SDF10)


title: HepsC-TPA control-72h rep4

description: Control (TPA10)


title: HepsC-TOL control-72h rep3

description: Control (TBT10)


title: HepsC-TPA control-72h rep6

description: Control (TPA10)


title: HepsC-SDF-72h rep1

description: Treatment with Diclofenac sodium


title: HepsC-SDF-72h rep3

description: Treatment with Diclofenac sodium


title: HepsC-TPA control-72h rep3

description: Control (TPA10)


title: HepsC-SDF control-72h rep1

description: Control (SDF10)


title: control E14, rep2

city: Boston

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

description: control E14

hyb_protocol: Hybridization to Affymetrix MoGene-1_0-st-v1 array was carried out by Functional Genomics Core Facility in UNC-CH using standard protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G by Functional Genomics Core Facility in UNC-CH using standard protocol.

data_processing:
Primary analysis was carried out by Functional Genomics Core Facility in UNC-CH using Affymetrix Expression Console software.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: control E14

label_protocol: Biotin labeling was carried out by Functional Genomics Core Facility in UNC-CH using GeneChip WT Sense Target Labeling and Control Reagents and standard protocol.

growth_protocol: E14 mESCs are cultured on the 0.1% gelatin coated plates in the DMEM medium (Sigma) supplemented with 100U/ml penicillin/streptomycin, 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate, 1x GlutaMax, 1x beta-mercaptoethanol (Invitrogen) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore).

extract_protocol: Total RNA was extracted from the control and Kdm2b knockdown mESCs using RNeasy mini kit (QIAGEN) following manufacture's instructions.

treatment_protocol: Around 1x10^5 ES cells/well in 24-well plates are infected with lentiviral vectors at 10 MOI. 48 hours after transduction, puromycin (2ug/ml) is added to the medium for selecting transduced cells.

tag: genotype

value: control

tag: strain

value: inbred 129

value: embryonbic stem cells


title: HepsC-PIPB-72h rep2

description: Treatment with Piperonyl butoxide

value: PIPB


title: HepsC-PIPB control-72h rep1

description: Control (PPX10)

value: PIPB control


title: HepsC-PIPB control-72h rep3

description: Control (PPX10)


title: HepsC-PIPB-72h rep3

description: Treatment with Piperonyl butoxide


title: HepsC-PIPB control-72h rep2

description: Control (PPX10)


title: 96 hpi, resistant cv. rep3

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

country: Australia

institute: La trobe University

description:
GC-RMA.24_rice_96 hpi_Res_r3
Rice_96 hpi_Res_r3

hyb_protocol: Following fragmentation, cRNA was hybridized, washed and stained as per manufacterers' instructions.

scan_protocol: GeneChips were scanned using the approved Affymetrix scanner.

data_processing: Data was first analyzed with Gene expression console (MAS 5.0) to determine presence/absence (i.e. above background) expression. Only probesets present in 2 or more replicates were retained (24,763 probesets). Partek Genomics Suite (v6.5) was used to carry out GC-RMA normalisation of data and this was used for further analysis.

organism: Oryza sativa

source_name: IR24_96 h after infection with Xoo_resistant

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

growth_protocol: Rice seeds were germinated in water for 2 days and then grown for 35-days before inoculation.

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

treatment_protocol: Philippine Xoo race 4 (PR4 - strain PXO71) was used to inoculate the leaves of 35-day old IR24 (resistant cultivar) and IRBB21 (sensitive cultivar) plants, 2-3 leaves were collected per time point. Control plants were (mock) treated and collected in a similar manner.

tag: cultivar

tag: infection susceptibility

value: resistant

value: 35-day old plants

tag: infected with

value: Philippine Xanthomonas oryzae pv oryzae (Xoo) race 4 (PR4) strain PXO71

value: leaf


title: HepsC-NIF control-72h rep3

description: Control (NFE10)

value: Primary rat hepatocytes

value: NIF control


title: HepsC-NIF control-72h rep2

description: Control (NFE10)


title: 96 hmi, susceptible cv. rep3

description:
GC-RMA.15_rice_96 hmi_Sus_r3
Rice_96 hmi_Sus_r3

source_name: IRBB21_96 h after mock infection_susceptible

value: susceptible


title: control E14, rep1

description: control E14


title: 96 hmi, susceptible cv. rep1

description:
GC-RMA.13_rice_96 hmi_Sus_r1
Rice_96 hmi_Sus_r1


title: HepsC-NIF control-72h rep1

description: Control (NFE10)


title: 96 hpi, resistant cv. rep1

description:
GC-RMA.22_rice_96 hpi_Res_r1
Rice_96 hpi_Res_r1


title: Kdm2b KD E14, rep1

description: Kdm2b KD E14

source_name: Kdm2b KD E14

value: Kdm2b knockdown


title: 96 hmi, susceptible cv. rep2

description:
GC-RMA.14_rice_96 hmi_Sus_r2
Rice_96 hmi_Sus_r2


title: 96 hmi, resistant cv. rep3

description:
GC-RMA.21_rice_96 hmi_Res_r3
Rice_96 hmi_Res_r3

source_name: IR24_96 h after mock infection_resistant


title: 96 hmi, resistant cv. rep2

description:
GC-RMA.20_rice_96 hmi_Res_r2
Rice_96 hmi_Res_r2


title: 96 hpi, resistant cv. rep2

description:
GC-RMA.23_rice_96 hpi_Res_r2
Rice_96 hpi_Res_r2


title: Kdm2b KD E14, rep2

description: Kdm2b KD E14


title: 96 hpi, susceptible cv. rep2

description:
GC-RMA.17_rice_96 hpi_Sus_r2
Rice_96 hpi_Sus_r2

source_name: IRBB21_96 h after infection with Xoo_susceptible


title: 18 months heart 35_old microRNA

value: heart

value: 18 months


title: 96 hmi, resistant cv. rep1

description:
GC-RMA.19_rice_96 hmi_Res_r1
Rice_96 hmi_Res_r1


title: HepsC-NIF-72h rep3

description: Treatment with Nifedipine

value: NIF


title: 96 hpi, susceptible cv. rep1

description:
GC-RMA.16_rice_96 hpi_Sus_r1
Rice_96 hpi_Sus_r1


title: HepsC-NIF-72h rep2

description: Treatment with Nifedipine


title: 24 hpi, resistant cv. rep3

description:
GC-RMA.9_rice_24 hpi_Res_r3
Rice_24 hpi_Res_r3

source_name: IR24_24 h after infection with Xoo_resistant


title: 24 hpi, resistant cv. rep2

description:
GC-RMA.8_rice_24 hpi_Res_r2
Rice_24 hpi_Res_r2


title: HepsC-MPH control-72h rep3

description: Control (MPH10)

value: MPH control


title: HepsC-NIF-72h rep1

description: Treatment with Nifedipine


title: HepsC-MPH control-72h rep2

description: Control (MPH10)


title: HepsC-MPH-72h rep3

value: MPH


title: HepsC-MPH-72h rep2


title: HepsC-MPH control-72h rep1

description: Control (MPH10)


title: 24 hmi, resistant cv. rep3

description:
GC-RMA.12_rice_24 hmi_Res_r3
Rice_24 hmi_Res_r3

source_name: IR24_24 h after mock infection_resistant


title: HepsC-MPH-72h rep1


title: HepsC-MAN control-72h rep7

description: Control (DMT10)

value: MAN control


title: 24 hpi, susceptible cv. rep2

description:
GC-RMA.5_rice_24 hpi_Sus_r2
Rice_24 hpi_Sus_r2

source_name: IRBB21_24 h after infection with Xoo_susceptible


title: 24 hmi, resistant cv. rep1

description:
GC-RMA.10_rice_24 hmi_Res_r1
Rice_24 hmi_Res_r1


title: 24 hpi, susceptible cv. rep3

description:
GC-RMA.6_rice_24 hpi_Sus_r3
Rice_24 hpi_Sus_r3


title: 24 hpi, resistant cv. rep1

description:
GC-RMA.7_rice_24 hpi_Res_r1
Rice_24 hpi_Res_r1


title: HepsC-MAN control-72h rep3

description: Control (DMT10)


title: HepsC-MAN control-72h rep4

description: Control (DMT10)


title: HepsC-MAN control-72h rep6

description: Control (DMT10)


title: HepsC-PIPB-72h rep1

description: Treatment with Piperonyl butoxide


title: HepsC-MAN control-72h rep5

description: Control (DMT10)


title: 96 hpi, susceptible cv. rep3

description:
GC-RMA.18_rice_96 hpi_Sus_r3
Rice_96 hpi_Sus_r3


title: 24 hmi, resistant cv. rep2

description:
GC-RMA.11_rice_24 hmi_Res_r2
Rice_24 hmi_Res_r2


title: HepsC-SDF control-72h rep4

description: Control (SDF10)

value: SDF control


title: HepsC-MAN control-72h rep2

description: Control (DMT10)


title: HepsC-MAN control-72h rep1

description: Control (DMT10)


title: 24 hmi, susceptible cv. rep1

description:
GC-RMA.1_rice_24 hmi_Sus_r1
Rice_24 hmi_Sus_r1

source_name: IRBB21_24 h after mock infection_susceptible


title: 24 hpi, susceptible cv. rep1

description:
GC-RMA.4_rice_24 hpi_Sus_r1
Rice_24 hpi_Sus_r1


title: Jejunum sample, feed G # 11

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: AB1700 Chemiluminescence detection Kit, 12 Rxn, includes (Applied Biosystems, Cat No. 4342142);

scan_protocol: Instrument: 1700-Reader; Software Version  1.1.1, Firmware Version: AB 1700 Plate Reader 1.2.2

data_processing:
Software Version  1.1.1, Firmware Version: AB 1700 Plate Reader 1.2.2 using Applied default analysis settings for generation of txt.files. (Analysis Method: Primary Analysis)
Data Pre-Processing and Filtering (7.3v GeneSpring Software): values from txt-files: Assay_Normalized_Signal;
Filter on Expression Level: “CEM” ;  Filter on Signal to Noise; Filter on Flag = 0
RMA  (background correction, quantile normalization accross all chips in the experiment, median polish summarization); t-test

label: AB Chemiluminescent RT Labeling Kit

source_name: Jejunum sample_feed G

label_protocol: AB Chemiluminescent RT Labeling Kit, includes, 12 Rxn Kits (Applied Biosystems, Cat No. 4359029)

growth_protocol: Mice were housed in macrolon cages III under a 12h/12h light/dark cycle. Feed and water were given ad libidum.

extract_protocol: Mice were sacrificed by vetebral dislocation. The small intestine beginning from the pylorus to the ileocaecal junction was dissected immediately and divided into two fragments of similar length. A 2 cm segment of the jejunum covering the 1 cm proximal and 1 cm distal regions around the angular point was dissected. Tissue samples were shock frozen in 2-methyl-butane (Merck, Darmstadt, Germany) cooled with liquid nitrogen.  Aproximately 50 mg of jejunum were used for RNA isolation with Trizol (Invitrogen) and purification with QIAgen RNeasy Mini Kit (Qiagen). 40 µg of RNA was used for microarray analysis.

treatment_protocol: Mice were fed for three generations with either feed B, K or G. Samples were derived from seven week old male mice of the third generation without randomization regarding the day time of sampling.

value: male

value: 7 wks

value: small intestine; jejunum

tag: diet group

value: feed G


title: 24 hmi, susceptible cv. rep2

description:
GC-RMA.2_rice_24 hmi_Sus_r2
Rice_24 hmi_Sus_r2

value: 35-day old plants


title: HepsC-MAN-72h rep3

description: Treatment with D-Manitol

value: MAN


title: HepsC-TPA-72h rep3

description: Treatment with Tetraphorbolacetate

value: Primary rat hepatocytes

value: TPA


title: HepsC-MAN-72h rep4

description: Treatment with D-Manitol


title: HepsC-MAN-72h rep2

description: Treatment with D-Manitol


title: Jejunum sample, feed K # 1

source_name: Jejunum sample_feed K

value: feed K


title: HepsC-MAN-72h rep1

description: Treatment with D-Manitol


title: Jejunum sample, feed G # 8


title: Jejunum sample, feed K # 4


title: Jejunum sample, feed K # 3


title: HepsC-CYCLO control-72h rep6

description: Control (CYC10)

value: CYCLO control


title: HepsC-CYCLO control-72h rep5

description: Control (CYC10)


title: HepsC-CYCLO control-72h rep4

description: Control (CYC10)


title: 24 hmi, susceptible cv. rep3

description:
GC-RMA.3_rice_24 hmi_Sus_r3
Rice_24 hmi_Sus_r3

value: susceptible

value: leaf


title: Jejunum sample, feed G # 4


title: HepsC-CYCLO control-72h rep3

description: Control (CYC10)


title: Jejunum sample, feed B # 10

source_name: Jejunum sample_feed B

value: feed B


title: HepsC-CYCLO control-72h rep2

description: Control (CYC10)


title: Jejunum sample, feed B # 7


title: HepsC-CYCLO control-72h rep1

description: Control (CYC10)


title: HepsC-CYCLO-72h rep2

description: Treatment with Cyclophosphamide

value: CYCLO


title: HepsC-CYCLO-72h rep1

description: Treatment with Cyclophosphamide


title: HepsC-CYCLO-72h rep3

description: Treatment with Cyclophosphamide


title: Jejunum sample, feed B # 8


title: HepsC-CND control-72h rep6

description: Control (CND10)

value: CND control


title: HepsC-CND control-72h rep4

description: Control (CND10)


title: HepsC-CND control-72h rep3

description: Control (CND10)


title: HepsC-CND control-72h rep2

description: Control (CND10)


title: HepsC-CND-72h rep3

description: Treatment with Clonidine

value: CND


title: HepsC-CND control-72h rep1

description: Control (CND10)


title: HepsC-CND control-72h rep5

description: Control (CND10)


title: ES2

city: Cambridge

first: Michael

last: Lodato

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression data in wild type ESCs, biological replicate 2

hyb_protocol: 15 µg biotinylated cRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.  GeneChip arrays (Mouse 430) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted and analyzed using GeneChip Operating Software v1.4.

data_processing: Arrays were normalized by RMA normalization using customed CDF file (mouse4302mmensgcdf) from University of Michigan BrainArray site (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/). Ensembl gene IDs were remapped to Gene Symbol by biomart (http://www.biomart.org/). Probes targeting the same gene were collapsed into one mean expression value.

source_name: RNA from Embryonic Stem Cells

label_protocol: 5 µg total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix One Cycle cDNA Synthesis Kit)

growth_protocol: ESCs were grown in under standard conditions in DMEM supplemented with 10% fetal bovine serum, LIF, glutamine, pen-strep, and betamercaptoethanol. NPCs were derived from these ESCs using an established protocol (PMID:8892235), then grown in N3 medium (see manuscript methods section).

extract_protocol: Trizol

tag: strain (genetic background)

value: 129SvJae/C57B6 F1

tag: source

value: blastocyst derived cell line V6.5


title: HepsC-CND-72h rep1

description: Treatment with Clonidine


title: OVA-treated CD16-/- BMDCs, replicate 3

city: Chicago

first: Melissa

middle: Yuwono

last: Tjota

state: IL

department: Department of Medicine

institute: University of Chicago

description: Gene expression data from CD16-/- BMDCs stimulated overnight with OVA

hyb_protocol: Applied Biosystems Mouse Genome Survey microarrays were hybridized with the cRNA target and treated for chemiluminescence detection.

scan_protocol: An AB1700 Microarray Analyzer was used to image and process the array.

data_processing: AB1700 provided software was used to calculate the normalized signal intensity.

label: Digoxigenin

source_name: BMDCs stimulated overnight with OVA

label_protocol: Digoxigenin-labeled cRNA target was prepared and verified on the Bioanalyzer.

growth_protocol: Bone marrow was flushed from the femurs and tibias of C57Bl/6 or CD16-/- mice. The cells were cultured in 10% complete DMEM plus 20 ng/mL GM-CSF in bacteriological Petri dishes at a concentration of 2×105 cells/mL. On day 3, the media was replenished with 20 ng/mL GM-CSF, and on day 6, the suspension cells were harvested.

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.

treatment_protocol: For the 24 hour stimulation, 5×105 BMDCs were cultured in 24-well plates with OVA or OVA-immune complex at a concentration of 100 μg/mL.

value: bone-marrow derived dendritic cells

value: OVA


title: HepsC-CND-72h rep2

description: Treatment with Clonidine


title: OVA-IC treated CD16-/- BMDCs, replicate 2

description: Gene expression data from CD16-/- BMDCs stimulated overnight with OVA-IC

source_name: BMDCs stimulated overnight with OVA-IC

value: OVA-immune complex


title: OVA-IC treated wildtype BMDCs, replicate 1

description: Gene expression data from wildtype BMDCs stimulated overnight with OVA-IC

value: wild type


title: NP106

description: Gene expression data in wild type NPCs. biological replicate 1

source_name: RNA from Neural Precursor Cells

value: ESC-derived Neural Precursor Cells (NPCs)


title: ES3

description: Gene expression data in wild type ESCs, biological replicate 3


title: NP39

description: Gene expression data in wild type NPCs, biological replicate 3


title: OVA-IC treated CD16-/- BMDCs, replicate 1


title: OVA-treated wildtype BMDCs, replicate 2

description: Gene expression data from wildtype BMDCs stimulated overnight with OVA


title: NP107

description: Gene expression data in wild type NPCs, biological replicate 2


title: OVA-treated CD16-/- BMDCs, replicate 2


title: OVA-treated CD16-/- BMDCs, replicate 1


title: OVA-treated wildtype BMDCs, replicate 3


title: OVA-IC treated wildtype BMDCs, replicate 2


title: OVA-IC treated CD16-/- BMDCs, replicate 3


title: HepsC-BaP control-72h rep7

description: Control (BaP10)

source_name: Primary rat hepatocytes

value: Primary rat hepatocytes

value: BaP control


title: OVA-IC treated wildtype BMDCs, replicate 3


title: HepsC-BaP control-72h rep6

description: Control (BaP10)


title: OVA-treated wildtype BMDCs, replicate 1


title: ES1

description: Gene expression data in wild type ESCs, biological replicate 1


title: HepsC-BaP control-72h rep4

description: Control (BaP10)


title: 20120208 BB120 v STR417 7

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street, Biology Building

department: Biology

institute: Indiana University

description: 20120208 BB120 v STR417 7

hyb_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 5 Scan Date : 2012-02-08 Scan Time : 09:24:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.5.3.1
Datafile type : Agilent result file

organism: Vibrio harveyi

label_protocol:
Type of label : Cy3
Labeling method DOI : doi:10.1128/JB.01998-12

extract_protocol: Extraction method DOI : doi:10.1128/JB.01998-12

tag: strain name

tag: time point

label_protocol:
Type of label : Cy5
Labeling method DOI : doi:10.1128/JB.01998-12


title: 20120208 BB120 v STR417 6

description: 20120208 BB120 v STR417 6


title: HepsC-BaP control-72h rep2

description: Control (BaP10)


title: HepsC-BaP control-72h rep3

description: Control (BaP10)


title: HepsC-BaP-72h rep4

description: Treatment with Benzo a pyrene

value: BaP


title: 20120208 BB120 v STR417 8

description: 20120208 BB120 v STR417 8


title: HepsC-BaP-72h rep3

description: Treatment with Benzo a pyrene


title: HepsC-BaP control-72h rep1

description: Control (BaP10)


title: HepsC-BaP-72h rep2

description: Treatment with Benzo a pyrene


title: HepsC-AFB control-72h rep6

description: Control (AFB10)

value: AFB control


title: 20120208 BB120 v STR417 4

description: 20120208 BB120 v STR417 4


title: 20120208 BB120 v STR417 5

description: 20120208 BB120 v STR417 5


title: 20120208 BB120 v STR417 1

description: 20120208 BB120 v STR417 1


title: 20120208 BB120 v STR417 3

description: 20120208 BB120 v STR417 3


title: HepsC-AFB control-72h rep5

description: Control (AFB10)


title: HepsC-AFB control-72h rep4

description: Control (AFB10)


title: 20120208 BB120 v STR417 2

description: 20120208 BB120 v STR417 2


title: HepsC-AFB control-72h rep3

description: Control (AFB10)


title: HepsC-BaP-72h rep1

description: Treatment with Benzo a pyrene


title: 20120404 luxOaphA v luxOaphAluxR 1

description: 20120404 luxOaphA v luxOaphAluxR 1

scan_protocol: Pixel Size : 5 Scan Date : 2012-04-04 Scan Time : 08:46:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: luxO aphA

tag: genotype/variation

value: luxO aphA

source_name: luxOaphAluxR

value: luxOaphAluxR


title: 20120404 luxOaphA v luxOaphAluxR 2

description: 20120404 luxOaphA v luxOaphAluxR 2


title: Control-rep1

city: Kyoto

first: Tokiro

last: Ishikawa

address: Kitashirakawa-oiwake, Sakyo-ku

department: Biophysics

country: Japan

institute: Graduate School of Science, Kyoto University

hyb_protocol: After pAfter purification through an RNeasy mini kit (QIAGEN), 1.65 μg of the labeled cRNA probes were hybridized separately with a 4×44K Agilent oligo microarray designed by Dr. Minoru Tanaka and his colleagues, on which 44,000 medaka genes were spotted, following the manufacturers instructions, for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.  urification through an RNeasy mini kit (QIAGEN), 1.65 μg of the labeled cRNA probes (two each from ATF6α/β-double hetero and double knockout) were hybridized separately with a 4×44K Agilent oligo microarray designed by Dr. Minoru Tanaka and his colleagues, on which 44,000 medaka genes were spotted.

scan_protocol: Cyanine 3 fluorescence intensity of each spot was determined after subtraction of respective background intensity using an Agilent G2565BA Microarray Scanner.

data_processing: The raw data were normalized (75 percentile normalization) using GeneSpringGX (Agilent Technologies, version 11.5.1)

organism: Oryzias latipes

source_name: Control

label_protocol: One hundred and fifty nanograms of total RNA were converted to cDNA, which was then transcribed with cyanine 3-CTP using a Low Input Quick Amp labeling kit, One-Color (Agilent).

extract_protocol: Total RNA was extracted from embryos at 2 dpf by the acid guanidinium/phenol/ chloroform method using Isogen (Nippon Gene) and samples from four embryos each of ATF6α/β-double hetero and double knockout was mixed, purified through RNeasy MinElute Cleanup Kit (QIAGEN) and checked for quality with a RNA 6000 Nano Assay using an Agilent 2100 Bioanalyser (Agilent Technologies).

value: Kyoto Cab

tag: tissue

value: whole embryo

tag: developmental stage

value: stage 24


title: 20120404 luxOluxR v luxOaphAluxR 3

description: 20120404 luxOluxR v luxOaphAluxR 3

source_name: luxO luxR

value: luxO luxR


title: 20120404 luxOaphA v luxOaphAluxR 4

description: 20120404 luxOaphA v luxOaphAluxR 4


title: 20120404 luxOluxR v luxOaphAluxR 4

description: 20120404 luxOluxR v luxOaphAluxR 4


title: HepsC-AFB control-72h rep2

description: Control (AFB10)

tag: replicate

tag: treatment


title: 20120404 luxOaphA v luxOaphAluxR 3

description: 20120404 luxOaphA v luxOaphAluxR 3


title: Control-rep2


title: HepsC-AFB control-72h rep1

description: Control (AFB10)

tag: cell type


title: HepsC-AFB-72h rep2

description: Treatment with Aflatoxin B2

value: AFB


city: Logan

first: Taylor

middle: S

last: Oberg

state: UT

address: 8700 Old Main

department: NDFS

institute: Utah State University

description: Gene expression data from DSM10140 cells exposed to 1.25mM H2O2 after 20 min, biological rep3

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 55oC on a custom Affymetrix Bifidobacteria Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 according to the Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A according to the Affymetrix protocol..

data_processing: The data were analyzed with Bioconductor in the open statistical platform R version 2.9.0 using the robust multiarray average (RMA) muti-species method.

organism: Bifidobacterium animalis subsp. lactis DSM 10140

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

growth_protocol: Bacterial strain and growth conditions. B. animalis ssp. lactis Bl-04 and B. animalis ssp. lactis DSM10140 strains were maintained in a laboratory collection as a glycerol stock at -80oC and propagated anaeirobically at 37oC in Mp5 broth.  Working cultures were prepared from stock cultures through two successive transfers (0.1% inocula) in MP5 broth at 37oC for 18 h.

extract_protocol: RNA isolation.  Cell pellets were thawed at room temperature, then carefully suspended in 1 ml of lysozyme solution (20 mg/ml in TE buffer) that also contained 20 Units of mutanolysin (Sigma, St. Louis, MO).  This mixture was incubated at 37oC for 30 minutes in a shaker incubator at 240 rpm, then total RNA was isolated from each of the cell samples using the Aurum Total RNA Mini Kit (Bio-Rad Laboratories, Hercules, CA) following procedures recommended by the vendor.

treatment_protocol: Cell treatments for transcriptome studies. Cells were grown to late loge phase at 37oC under anaerobic conditions with pH control at 6.5 after which four 5 ml samples were aseptically harvested into sterile 200 ml centrifuge bottles and immediately suspended in 50 mL pre-warmed 50 mL pre-warmed MP5 media containing 1.25mM H2O2. Cells were harvested for RNA isolation after 5 min (T1) and 20 min (T2). Cells were immediatly suspended in 100 mL of RNAprotect reagent (QIAGEN, Inc., Valencia,, CA) and incubated at room temperature for 10 min then collected by cetrifugation. Control cells were immediatly suspended in 10 mL of RNAprotect and incubated at room temperature for 10 min hen collected by cetrifugation (C1).    Cell pellets were stored at -80oC until RNA isolation.


title: HepsC-AFB-72h rep1

description: Treatment with Aflatoxin B1


title: ATF6DKO-rep2

source_name: ATF6 DKO


title: HepsC-NNK control-72h rep5

description: Control (NNK10)

value: NNK control


title: HepsC-NNK control-72h rep6

description: Control (NNK10)


title: HepsC-NNK control-72h rep4

description: Control (NNK10)


title: HepsC-BaP control-72h rep5

description: Control (BaP10)


title: HepsC-NNK control-72h rep3

description: Control (NNK10)


description: Gene expression data from DSM10140 cells exposed to 1.25mM H2O2 after 20 min, biological rep2


description: Gene expression data from DSM10140 cells exposed to 1.25mM H2O2 after 20 min, biological rep1


title: HepsC-AFB-72h rep3

description: Treatment with Aflatoxin B3


title: HepsC-NNK control-72h rep2

description: Control (NNK10)


title: 20120405 D47EaphA v D47EaphAluxR 4

description: 20120405 D47EaphA v D47EaphAluxR 4

scan_protocol: Pixel Size : 5 Scan Date : 2012-04-05 Scan Time : 09:23:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: D47E aphA

value: D47E aphA

source_name: D47E aphA luxR

value: D47E aphA luxR


title: 20120404 luxOluxR v luxOaphAluxR 1

description: 20120404 luxOluxR v luxOaphAluxR 1


description: Gene expression data from DSM10140 cells exposed to 1.25mM H2O2 after 5 min, biological rep3


title: ATF6DKO-rep1


title: HepsC-NNK control-72h rep1

description: Control (NNK10)


description: Gene expression data from DSM10140 cells exposed to 1.25mM H2O2 after 5 min, biological rep2


title: HepsC-NNK-72h rep3

description: Treatment with NNK

value: NNK


title: 20120405 D47EaphA v D47EaphAluxR 3

description: 20120405 D47EaphA v D47EaphAluxR 3


description: Gene expression data from DSM10140 cells exposed to 1.25mM H2O2 after 5 min, biological rep1


description: Gene expression data from DSM10140 unexposed control cells after 20 min, biological rep2


title: 20120524 D47EluxR v D47EluxRaphA 4

description: 20120524 D47EluxR v D47EluxRaphA 4

scan_protocol: Pixel Size : 5 Scan Date : 2012-05-24 Scan Time : 08:23:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: D47E luxR

value: D47E luxR


title: HepsC-NNK-72h rep2

description: Treatment with NNK


title: HepsC-NNK-72h rep1

description: Treatment with NNK


title: 20120404 luxOluxR v luxOaphAluxR 2

description: 20120404 luxOluxR v luxOaphAluxR 2


description: Gene expression data from DSM10140 unexposed control cells after 20 min, biological rep1


title: 20120405 D47EaphA v D47EaphAluxR 2

description: 20120405 D47EaphA v D47EaphAluxR 2


description: Gene expression data from DSM10140 unexposed control cells after 20 min, biological rep3


title: 20120524 D47EluxR v D47EluxRaphA 1

description: 20120524 D47EluxR v D47EluxRaphA 1


title: 20120524 D47EluxR v D47EluxRaphA 3

description: 20120524 D47EluxR v D47EluxRaphA 3


title: HepsC-2NF control-72h rep3

description: Control (2NF10)

value: 2NF control


title: 20120524 D47EluxR v D47EluxRaphA 2

description: 20120524 D47EluxR v D47EluxRaphA 2


title: HepsC-2NF control-72h rep1

description: Control (2NF10)

value: Primary rat hepatocytes


title: 20120405 D47EaphA v D47EaphAluxR 1

description: 20120405 D47EaphA v D47EaphAluxR 1


title: HepsC-2NF-72h rep3

description: Treatment with 2-Nitrofluorene


description: Gene expression data from DSM10140 unexposed control cells at 0 min, biological rep3


description: Gene expression data from DSM10140 unexposed control cells at 0 min, biological rep2


title: HepsC-2NF control-72h rep2

description: Control (2NF10)


description: Gene expression data from DSM10140 unexposed control cells at 0 min, biological rep1


description: Gene expression data from BL-04 cells exposed to 1.25mM H2O2 after 20 min, biological rep3

organism: Bifidobacterium animalis subsp. lactis Bl-04


title: 20120208 BB120 v JV48 8

description: 20120208 BB120 v JV48 8

scan_protocol: Pixel Size : 5 Scan Date : 2012-02-08 Scan Time : 09:57:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: 20120208 BB120 v JV48 6

description: 20120208 BB120 v JV48 6


title: HepsC-2NF-72h rep2

description: Treatment with 2-Nitrofluorene


title: HepsC-2NF-72h rep1

description: Treatment with 2-Nitrofluorene


title: 20120208 BB120 v JV48 4

description: 20120208 BB120 v JV48 4


title: 20120208 BB120 v JV48 7

description: 20120208 BB120 v JV48 7


description: Gene expression data from BL-04 cells exposed to 1.25mM H2O2 after 5 min, biological rep3


title: 20120208 BB120 v JV48 5

description: 20120208 BB120 v JV48 5


description: Gene expression data from BL-04 cells exposed to 1.25mM H2O2 after 20 min, biological rep2


description: Gene expression data from BL-04 cells exposed to 1.25mM H2O2 after 20 min, biological rep1


title: 20120208 BB120 v JV48 2

description: 20120208 BB120 v JV48 2


description: Gene expression data from BL-04 cells exposed to 1.25mM H2O2 after 5 min, biological rep2


title: Slide 344297

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 3

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genepix 6. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of cellobiose over the glucose were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F532 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown to OD600 of 0.38 (time point T2)

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

value: Wild type

tag: growth medium

source_name: F635 Mean


title: Slide 344296

description: Sample 2


title: 20120208 BB120 v JV48 3

description: 20120208 BB120 v JV48 3


title: 20120208 BB120 v KM669 8

description: 20120208 BB120 v KM669 8

scan_protocol: Pixel Size : 5 Scan Date : 2012-02-08 Scan Time : 09:40:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

tag: timepoint


title: 20120208 BB120 v JV48 1

description: 20120208 BB120 v JV48 1


title: Slide 344295

description: Sample 1


description: Gene expression data from BL-04 cells exposed to 1.25mM H2O2 after 5 min, biological rep1

tag: strain


title: 6 weeks heart 47_young mRNA

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

source_name: heart

label_protocol: standard Affymetrix protocol

value: heart

tag: genetic background

tag: age

value: 6 weeks


title: Slide 344133

description: Sample 3

growth_protocol: Cells were grown to OD600 of 0.2 (at time point T1)


title: 20120208 BB120 v KM669 7

description: 20120208 BB120 v KM669 7


description: Gene expression data from BL-04 unexposed control cells after 20 min, biological rep3


title: 6 weeks heart 48_young mRNA


description: Gene expression data from BL-04 unexposed control cells after 20 min, biological rep2


title: 20120208 BB120 v KM669 6

description: 20120208 BB120 v KM669 6


title: 6 weeks heart 46_young mRNA


description: Gene expression data from BL-04 unexposed control cells after 20 min, biological rep1


title: 6 weeks heart 45_young mRNA


title: Slide 344132

description: Sample 2


title: Slide 344131

description: Sample 1


title: 18 months heart 38_old mRNA

value: 18 months


description: Gene expression data from BL-04 unexposed control cells at 0 min, biological rep3

source_name: BL-04 unexposed control cells at 0 min


title: Slide 185695

description: Sample 3

data_processing: Dual-channel array images were analyzed with Arraypro.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of bguR mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

source_name: Net intensity (tr.mean) {B}

growth_protocol: Cells were grown in GM17 medium and harvested at OD600 of 0.25.

value: bguR mutant

source_name: Net intensity (tr.mean) {A}


title: Slide 185518

description: Sample 2


description: Gene expression data from BL-04 unexposed control cells at 0 min, biological rep2


title: 20120208 BB120 v KM669 4

description: 20120208 BB120 v KM669 4


description: Gene expression data from BL-04 unexposed control cells at 0 min, biological rep1


title: Slide 185709

description: Sample 1


title: 20120208 BB120 v KM669 2

description: 20120208 BB120 v KM669 2


title: 18 months heart 36_old mRNA


title: 20120208 BB120 v KM669 3

description: 20120208 BB120 v KM669 3


title: 18 months heart 37_old mRNA


title: 18 months heart 35_old mRNA


title: 20120208 BB120 v KM669 1

description: 20120208 BB120 v KM669 1


title: B73_k27_seed

type: genomic

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: there are three replicates for each Sample.

hyb_protocol: Samples were hybridized to the custom 1.4 or 2.1 M probe array for 16–20 hrs at 42C.

scan_protocol: Slides were washed and scanned according to NimbleGen’s protocol for the MS200 microarray scanner. Images were aligned and quantified using NimbleScan software (Roche NimbleGen) producing raw data reports for each probe on the array.

data_processing: XYS files exported from NimbleScan were imported into the Bioconductor statistical environment (http://bioconductor.org/). Sample-dependent H3K27me3 enrichments were estimated for each probe by fitting a fixed linear model accounting for array, dye, and sample effects to the data using the limma package (Wettenhall and Smyth, 2004).  Moderated t-statistics and the log-odds score for differential MeDIP enrichment was computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05. Results were visualized using Integrated Genomics Viewer (Robinson et al., 2011)

molecule: genomic DNA

organism: Zea mays

source_name: B73 seed r1 input

label_protocol: Chromatin extractions were performed using EpiQuik™ Plant ChIP Kit (Epigentek, Brooklyn, USA) according to manufacturer’s recommendations.  Extracted chromatin was sheared in 600 μl of the EpiQuick buffer CP3F with 5 10-second pulses on a sonicator.  To test and optimize sonication conditions, cross-linking was reversed in a sample of sheared chromatin and the resulting products were analyzed on agarose gel.  Sonication conditions were optimized to yield predominantly 200 – 500 bp DNA samples.  Chromatin immunoprecipitations, reverse cross-linking, and DNA cleanup were performed using EpiQuik™ Plant ChIP Kit (Epigentek) according to manufacturer’s recommendations.  Antibodies specific for H3K27me3 (#07-449) were purchased from Millipore (Billerica, USA).  For each genotype, antibody, and replicate, 50 – 100 ng of input and immunoprecipitated (IP) DNA was amplified with a whole genome amplification kit (WGA2, Sigma, St. Louis, USA).  The amplification of no antibody control (negative control) was always 5 – 10 fold less efficient confirming specificity of immunoprecipitation.  For each amplified IP and input sample, 3 ug of amplified DNA were labeled using the Dual-Color Labeling Kit (Roche NimbleGen, Cat # 05223547001) according to the array manufacturer’s protocol (Roche NimbleGen Methylation User- Guide v7.0).  Each IP sample was labeled with Cy5 and each input/control sonicated DNA was labeled with Cy3.

extract_protocol: The whole above ground tissue was collected from 12 day old de-etiolated seedlings that were grown in the dark at 30oC in 1:1 mix of autoclaved field soil and MetroMix.  For embryo, immature ear (approximately 5 – 7 cm in length), tassel, and endosperm collection, plants were grown to maturity in the field of the University of Minnesota Saint Paul Agricultural Research station during the summer of 2011.  Endosperm and embryo were harvested from multiple B73 and Mo17 ears 14 days after the self-pollination.  The seeds for each replicate came from a unique, single source (ear).  Each biological replicate was planted at a different time and represents the pooled above ground tissue from eight to ten plants.  Three replicate tissue collections were performed for all B73 and Mo17 tissues.  For each replicate / tissue / genotype combination, 1 g of plant material was harvested on ice, rinsed with water, and crosslinked with 1% formaldehyde for 10 minutes under vacuum infiltration.  Cross-linking was quenched by adding Glycine solution to a final concentration of 0.125M under vacuum infiltration for 5 minutes.  Treated tissue was frozen in liquid nitrogen and stored at -800C until chromatin extraction.

tag: genotype

value: Seedling

tag: ChIP

value: input

source_name: B73 seed IP


title: Rv0081-Atc dilution OE by ATc 10 ng Atc 18 Hours TFOE_8902_0081_10ng

status: Public on Feb 19 2013

city: Seattle

first: Tige

last: Rustad

state: WA

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

institute: Seattle Biomedical Research Institute

description:
TFOE_8902_0081_10ng
Rv0081-Atc dilution OE by ATc
18
Hours
10
ng

hyb_protocol: Hybridization was performed following the standard operating protocol recommended by NimbleGen Systems Inc., Madison, WI, USA . See www.nimblegen.com.

scan_protocol: Scanning was performed using a GenePix 4000B using a single intensity for all 12 arrays on each slide.

data_processing: Data was normalized using RMA normalization with the 'affy' package for R.

organism: Mycobacterium tuberculosis H37Rv

label_protocol: Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).

growth_protocol: H37Rv was grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: TFOE experiments done at indicated concentration of anhydrotetracycline.  Hypoxic experiments conducted as described previously (Rustad et al., 2008)

tag: experiment

value: Rv0081-Atc dilution

tag: time

value: 18 Hours

tag: dose

value: 10 ng Atc

value: Rv0081-Atc dilution OE by ATc


title: Rv3050c OE by ATc 100 ng Atc 18 Hours TFOE_7826_3050c

description:
TFOE_7826_3050c
Rv3050c OE by ATc
18
Hours
100
ng

value: A

value: 100 ng Atc

value: Rv3050c OE by ATc


title: Rv3574 OE by ATc 1 ng Atc 18 Hours TFOE_8870_3574__1.0

description:
TFOE_8870_3574__1.0
Rv3574 OE by ATc
18
Hours
1
ng

value: Rv3574-Atc dilution

value: 1 ng Atc

value: Rv3574 OE by ATc


title: Rv0494 OE by Atc 100 ng Atc 18 Hours TFOE_7435_0494

description:
TFOE_7435_0494
Rv0494 OE by Atc
18
Hours
100
ng

value: Rv0494 OE by Atc


title: Rv0081-Atc dilution OE by ATc 1 ng Atc 18 Hours TFOE_8077_0081_1ng

description:
TFOE_8077_0081_1ng
Rv0081-Atc dilution OE by ATc
18
Hours
1
ng


title: Rv0081-Atc dilution OE by ATc 0.1 ng Atc 18 Hours TFOE_9287_0081_.1ng

description:
TFOE_9287_0081_.1ng
Rv0081-Atc dilution OE by ATc
18
Hours
0.1
ng

value: 0.1 ng Atc


title: Rv0757 OE by ATc 10 ng Atc 18 Hours TFOE_6350_0757_10ng

description:
TFOE_6350_0757_10ng
Rv0757 OE by ATc
18
Hours
10
ng

value: Rv0757-Atc dilution

value: Rv0757 OE by ATc


title: Rv0827c OE by Atc 100 ng Atc 18 Hours TFOE_5624_0827c_B_UNINDUCED

description:
TFOE_5624_0827c_B_UNINDUCED
Rv0827c OE by Atc
18
Hours
100
ng

value: Rv0827c OE by Atc


title: Mo17_k27_endo

source_name: Mo17 endo IP

value: Endosperm

source_name: Mo17 endo input


title: Rv0757-Atc dilution OE by ATc 0.1 ng Atc 18 Hours TFOE_4663_0757_.1ng

description:
TFOE_4663_0757_.1ng
Rv0757-Atc dilution OE by ATc
18
Hours
0.1
ng

value: Rv0757-Atc dilution OE by ATc


title: Rv1027c OE by ATc 100 ng Atc 18 Hours TFOE_3781_1027c 2

description:
TFOE_3781_1027c 2
Rv1027c OE by ATc
18
Hours
100
ng

value: B

value: Rv1027c OE by ATc


title: Rv3133c OE by ATc 10 ng Atc 18 Hours TFOE_2382_3133c__10

description:
TFOE_2382_3133c__10
Rv3133c OE by ATc
18
Hours
10
ng

value: Rv3133c-Atc dilution

value: 18 Hours

value: 10 ng Atc

value: Rv3133c OE by ATc


title: 20120208 BB120 v KM669 5

description: 20120208 BB120 v KM669 5

tag: strain name


title: mez3_m4

source_name: mez3_m4 IP

value: mez3_m4 in B73 background

value: seedling

source_name: mez3_m4 input

value: input


title: Rv3574-Atc dilution OE by ATc 10 ng Atc 18 Hours TFOE_1104_3574_10

description:
TFOE_1104_3574_10
Rv3574-Atc dilution OE by ATc
18
Hours
10
ng

value: Rv3574-Atc dilution

value: Rv3574-Atc dilution OE by ATc


title: Hypoxia  8 days SG7T8C

description:
SG7T8C
Hypoxia
8
days

value: C

value: 8 days

value: Hypoxia


title: Hypoxia  8 days SG7T8D

description:
SG7T8D
Hypoxia
8
days

value: D


title: Mo17_k27_seed

source_name: Mo17 seed IP

value: Seedling

source_name: Mo17 seed input


title: Rv0757 OE by ATc 1 ng Atc 18 Hours TFOE_1064_0757_1ng

description:
TFOE_1064_0757_1ng
Rv0757 OE by ATc
18
Hours
1
ng

value: Rv0757-Atc dilution

value: 1 ng Atc

value: Rv0757 OE by ATc


title: Hypoxia  8 days SG7T8A

description:
SG7T8A
Hypoxia
8
days

value: A


title: Hypoxia  7 days SG7T7D

description:
SG7T7D
Hypoxia
7
days

value: 7 days


title: Hypoxia  7 days SG7T7B

description:
SG7T7B
Hypoxia
7
days

value: B


title: Hypoxia  12 days SG7T12D

description:
SG7T12D
Hypoxia
12
days

value: 12 days


title: Hypoxia  12 days SG7T12C

description:
SG7T12C
Hypoxia
12
days


title: Hypoxia  12 days SG7T12A

description:
SG7T12A
Hypoxia
12
days


title: mez2_m4

source_name: mez2_m4 IP

value: mez2_m4 in B73 background

source_name: mez2_m4 input


title: mez3_m1

source_name: mez3_m1 IP

value: mez3_m1 in B73 background

value: seedling

source_name: mez3_m1 input


title: Mo17_k27_ear

source_name: Mo17 ear IP

value: Ear

source_name: Mo17 ear input

value: input


title: mez3mez2_m4

source_name: mez3mez2_m4 IP

value: mez3mez2_m4 in B73 background

source_name: mez3mez2_m4 input


title: Hypoxia  1 days SG7DT1

description:
SG7DT1
Hypoxia
1
days

value: 1 days


title: Cbfb+/+ peripheral blood, replicate 3

first: R. Katherine

last: Hyde

address: 49 Convent Dr

institute: NHGRI/NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse 4302.0 chips. The chips were washed and stained in an Affymetrix Fluidics Stations using standard Affymetrix protocols.

scan_protocol: Affymetrix standard protocol

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC v.1.0). Data was processed and normalized using Affymetrix Expression Console software (v.1.0) and RMA (Robust Multichip Analysis) and Partek Software (v.6.5).

source_name: Cbfb+/+_peripheral blood

label_protocol: RNA was labeled with One Cycle Target Labeling (Affymetrix) according to manufacturer's instructions

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

treatment_protocol: Peripheral blood from E12.5 embryos was collected and frozen. Blood from 8-10 embryos of the same geneotype was pooled

tag: strain background

value: mixed C57BL6/129SvEv

tag: genotype/variation

value: Cbfb+/+

value: peripheral blood


title: Hypoxia  8 days SG7T8B

description:
SG7T8B
Hypoxia
8
days

value: 8 days

value: Hypoxia


title: Hypoxia  0 days SG7DT0

description:
SG7DT0
Hypoxia
0
days

value: D

value: 0 days


title: Hypoxia  1 days SG7CT1

description:
SG7CT1
Hypoxia
1
days

value: C


title: Hypoxia  0 days SG7CT0

description:
SG7CT0
Hypoxia
0
days


title: Hypoxia  0 days SG7BT0

description:
SG7BT0
Hypoxia
0
days

value: B


title: Hypoxia  1 days SG7BT1

description:
SG7BT1
Hypoxia
1
days


title: Hypoxia  1 days SG7AT1

description:
SG7AT1
Hypoxia
1
days

value: A


title: Hypoxia  0 days SG7AT0

description:
SG7AT0
Hypoxia
0
days


title: Mo17_k27_emb

source_name: Mo17 emb IP

tag: tissue

value: Embryo

source_name: Mo17 emb input


title: B73_k27_endo

source_name: B73 endo r1 IP

value: Endosperm

source_name: B73 endo input


title: Cbfb+/ΔC95 peripheral blood, replicate 2

source_name: Cbfb+/ΔC95_peripheral blood


title: Cbfb+/+ peripheral blood, replicate 1


title: Cbfb+/+ peripheral blood, replicate 2


title: Cbfb+/ΔC95 peripheral blood, replicate 3


title: Hypoxia  0 days SG6H0

description:
SG6H0
Hypoxia
0
days

tag: replicate


title: CbfbΔC95/ΔC95 peripheral blood, replicate 3

source_name: CbfbΔC95/ΔC95_peripheral blood


title: Cbfb+/ΔC95 peripheral blood, replicate 1


title: CbfbΔC95/ΔC95 peripheral blood, replicate 2


title: B73_k27_embryo

source_name: B73 embryo r1 IP

source_name: B73 embryo input


title: Rv3574 OE by ATc 0.1 ng Atc 18 Hours TFOE_5888_3574__0.1

description:
TFOE_5888_3574__0.1
Rv3574 OE by ATc
18
Hours
0.1
ng

value: Rv3574-Atc dilution

value: 18 Hours

value: 0.1 ng Atc

tag: treatment

value: Rv3574 OE by ATc


title: Hypoxia  7 days SG7T7C

description:
SG7T7C
Hypoxia
7
days

value: 7 days


title: Hypoxia  8 days SG6DT8

description:
SG6DT8
Hypoxia
8
days


title: B73_k27_tass

source_name: B73 tass r1 IP

value: Tassel

source_name: B73 tass input

value: input


title: CbfbΔC95/ΔC95 peripheral blood, replicate 1

value: mixed C57BL6/129SvEv

value: peripheral blood


title: Hypoxia  8 days SG6C8

description:
SG6C8
Hypoxia
8
days

value: 8 days

value: Hypoxia


title: Hypoxia  14 days SG6DT14

description:
SG6DT14
Hypoxia
14
days

value: D

value: 14 days


title: Hypoxia  0 days SG6G0

description:
SG6G0
Hypoxia
0
days

value: C

value: 0 days


title: B73_k27_ear

source_name: B73 ear r1 IP

value: Ear

source_name: B73 ear r1 input


title: Hypoxia  7 days SG6DT7

description:
SG6DT7
Hypoxia
7
days


title: Hypoxia  1 days SG6C1

description:
SG6C1
Hypoxia
1
days

value: 1 days


title: Hypoxia  8 days SG6D8

description:
SG6D8
Hypoxia
8
days


title: Hypoxia  14 days SG6C14

description:
SG6C14
Hypoxia
14
days


title: Hypoxia  8 days SG6B8

description:
SG6B8
Hypoxia
8
days

value: B


title: Hypoxia  12 days SG6D12

description:
SG6D12
Hypoxia
12
days

value: 12 days


title: Hypoxia  1 days SG6D1

description:
SG6D1
Hypoxia
1
days


title: Hypoxia  7 days SG6CT7

description:
SG6CT7
Hypoxia
7
days


title: Hypoxia  12 days SG6C12

description:
SG6C12
Hypoxia
12
days


title: Hypoxia  14 days SG6B14

description:
SG6B14
Hypoxia
14
days


title: Hypoxia  12 days SG6A11

description:
SG6A12
Hypoxia
12
days

value: A


title: Hypoxia  14 days SG6A14

description:
SG6A14
Hypoxia
14
days


title: Hypoxia  12 days SG7T12B

description:
SG7T12B
Hypoxia
12
days


title: Hypoxia  8 days SG6A8

description:
SG6A8
Hypoxia
8
days


title: Hypoxia  12 days SG6B11

description:
SG6B12
Hypoxia
12
days


title: Hypoxia  1 days SG6_B1

description:
SG6_B1
Hypoxia
1
days


title: Hypoxia  0 days SG6_B0

description:
SG6_B0
Hypoxia
0
days


title: WT HPCD8, biological rep3

city: Ithaca

first: Weishan

last: Huang

state: New York

address: C5 121, Cornell U.

department: Microbiology & Immunology

institute: Cornell University

description:
Gene expression data from CD8 T cells derived through homeostatic expansion
CD8 HP3.CEL

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

scan_protocol: Slides were scanned immediately after washing on the Affymetrix GeneChip Scanner 7G Plus, according to the array’s wash protocol (EukGE-WS2v5).

data_processing: The scanned images were analyzed within the GeneChip Operating Software, version 1.4. Array data were analyzed in GeneSpring, version 12.0. RMA-normalized probe values were used to generate correlation coefficient matrix, and further converted into gene expression values with Quantile normalization for further analysis ['gene_quantile_data.txt'; available on Series records].

source_name: TCRβ+CD8α+CD44hi cells from spleen of female Rag null mice which received TCRβ+CD8α+CD44lo naïve CD8 T cells from WT female spleens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 30 ng total RNA (MessageAmpTM Premier RNA Amplification Kit (Part Number 4385821, AM1792, 4383452), 2010).

growth_protocol: Itknull female mice were housed in specific-pathogen-free condition and used at the age of 8 weeks; WM chimeric mice were generated by trasferring female WT bone mattow to lethally irradiated female MHCI null recipients and used 8 weeks post transplantation; WT HP CD8 cells were obtained by transferring naive CD8 T cells sorted from female WT mice into Rag1null mice for 8 weeks of in vivo expansion.

extract_protocol: Cells with purity (markers indicated in treatment method) from 90-98% were subjected to total RNA extraction using RNeasy Plus Mini Kit with removal of gDNA following the manufacturer's instruction (Qiagen, cat: 74134).

treatment_protocol: Splenocytes were sujected with red blood cells lysis, staining with antibodies and sorted on Aria II Sorp system. Itk null and HP CD8 T cells are those with TCRβ+CD8α+CD44hi, WM CD8 T cels are those with MHCI+TCRβ+CD8α+CD44hi, and WT HP CD8 T cells are those with TCRβ+CD8α+CD44hi.

value: WT naïve CD8 to Rag1 null

value: 8 weeks post adoptive transfer


title: WM chimeric IMPCD8, biological rep3

description:
Gene expression data from IMP CD8 T cells developed through the selection of hematopoietic MHCI
WM3.CEL

source_name: MHCI+TCRβ+CD8α+CD44hi cells from spleen of chimeric mice, female WT bone marrow into female irradiated MHCI null recipient

value: WT bone marrow to MHCI null

value: 8 weeks post bone marrow transfer


title: Rv3133c-Atc dilution OE by ATc 0.1 ng Atc 18 Hours TFOE_2068_3133c_0.1

description:
TFOE_2068_3133c_0.1
Rv3133c-Atc dilution OE by ATc
18
Hours
0.1
ng

value: Rv3133c-Atc dilution

value: 18 Hours

value: 0.1 ng Atc

value: Rv3133c-Atc dilution OE by ATc


title: WT HPCD8, biological rep1

description:
Gene expression data from CD8 T cells derived through homeostatic expansion
CD8 HP1.CEL


title: single DTC isolated from bone marrow (BM) of PCa patient  2679 (#8)

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Hybridization probes were prepared by combining 6 mg of Alexa Fluor® 3 labeled sample and 1 mg Alexa Fluor® 5 labeled reference and denatured at 95°C and hybridized at 63°C on Agilent Human 4x44K microarrays and processed following the manufacturer’s specifications.

scan_protocol: Fluorescence array images were collected for Alexa Fluor® 3 and Alexa Fluor® 5 using the Agilent DNA microarray scanner G2505B (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Graphical examination of raw array signal indicated a batch effect in C42B data due to experimental processing day. We corrected for this effect by separately estimating mean  Alexa Fluor® 3 and mean Alexa Fluor® 5 signal within single-, 5-, and 10-cell C42B arrays between experimental days and adjusting values on the second day by the estimated difference.  We normalized day-effect-corrected signals for C42B data and raw patient data within arrays using loess and normexp background correction with offset 50, removed control probes, averaged duplicate probes, and assigned a value of null to spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers.  C42B and patient data further normalized (each set seperately) using between-array quantile normalization.  All normalizations were performed using the Limma package in R.

label: Alexa Fluor® 5

label_protocol: Amplified cDNA from each sample was labeled with Alexa Fluor® 3 using the BioPrime® Total Genomic labeling kit (Invitrogen) (reference cDNA was labeled with Alexa Fluor® 5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications. The second round amplified amino-allyl RNA was then converted to first strand cDNA and labeled with Alexa Fluor® 5 using the BioPrime® Total Genomic labeling kit (Invitrogen).

tag: gender

value: male

tag: reference cell lines

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

label: Alexa Fluor® 3

extract_protocol: Total RNA was amplified from each sample using the WT-OviationTM one-direct system (NuGEN) according to the manufacturer’s directions. Amplified cDNA from each sample was labeled with Alexa Fluor® 3 using the BioPrime® Total Genomic labeling kit (Invitrogen).

tag: patient

tag: cell type

value: A single DTC was isolated from bone marrow (BM) samples of PCa patient. Essentially, a two-step selection process was employed, in which anti-CD45 and anti-CD61 conjugated to immunomagnetic beads were used for negative selection, and anti-HEA was used for positive selection.  Cells were then fluorescently stained for BerEP4, counter stained with RPE anti-CD45, and individually selected under fluorescent light using a micropipette system for further analysis.


title: single DTC isolated from bone marrow (BM) of PCa patient  2679 (#9)


title: single DTC isolated from bone marrow (BM) of PCa patient  2679 (#5)


title: single DTC isolated from bone marrow (BM) of PCa patient  2679 (#6)


title: single DTC isolated from bone marrow (BM) of PCa patient  2679 (#1)


title: single DTC isolated from bone marrow (BM) of PCa patient  2679 (#3)


title: Itknull IMPCD8, biological rep3

description:
Gene expression data from IMP CD8 T cells developed in the absence of ITK
Itk3.CEL

source_name: TCRβ+CD8α+CD44hi cells from spleen of Itk null mice, female

value: Itk null

value: 8 weeks


title: single DTC isolated from bone marrow (BM) of PCa patient  2679 (#2)


title: WT HPCD8, biological rep2

description:
Gene expression data from CD8 T cells derived through homeostatic expansion
CD8 HP2.CEL


title: Hypoxia  7 days SG6_A7

description:
SG6_A7
Hypoxia
7
days

value: 7 days

value: Hypoxia


title: single DTC isolated from bone marrow (BM) of PCa patient  2679 (#10)


title: WM chimeric IMPCD8, biological rep2

description:
Gene expression data from IMP CD8 T cells developed through the selection of hematopoietic MHCI
WM2.CEL


title: single DTC isolated from bone marrow (BM) of PCa patient  2679 (#7)


title: Itknull IMPCD8, biological rep2

description:
Gene expression data from IMP CD8 T cells developed in the absence of ITK
Itk2.CEL


title: single DTC isolated from bone marrow (BM) of PCa patient  2679 (#4)


title: Hypoxia  7 days SG6_B7

description:
SG6_B7
Hypoxia
7
days

value: B


title: Itknull IMPCD8, biological rep1

description:
Gene expression data from IMP CD8 T cells developed in the absence of ITK
Itk1.CEL


title: WM chimeric IMPCD8, biological rep1

description:
Gene expression data from IMP CD8 T cells developed through the selection of hematopoietic MHCI
WM1.CEL


title: Hypoxia  1 days SG6_A1

description:
SG6_A1
Hypoxia
1
days

value: A

value: 1 days


title: Hypoxia  0 days SG6_A0

description:
SG6_A0
Hypoxia
0
days

value: 0 days


title: Hypoxia  9 days SG2_D9

description:
SG2_D9
Hypoxia
9
days

value: D

value: 9 days


title: Hypoxia  8 days SG2_D8

description:
SG2_D8
Hypoxia
8
days

value: 8 days


title: Hypoxia  7 days SG2_D7

description:
SG2_D7
Hypoxia
7
days


title: Hypoxia  5 days SG2_D5

description:
SG2_D5
Hypoxia
5
days

value: 5 days


title: single DTC isolated from bone marrow (BM) of PCa patient  2613 (#9)


title: single DTC isolated from bone marrow (BM) of PCa patient  2613 (#5)


title: single DTC isolated from bone marrow (BM) of PCa patient  2613 (#10)


title: single DTC isolated from bone marrow (BM) of PCa patient  2613 (#7)


title: single DTC isolated from bone marrow (BM) of PCa patient  2613 (#6)


title: Skeletal Muscle 20mgkg-1 rep1

city: Glasgow

first: Manikhandan

middle: A V

last: Mudaliar

state: Scotland

address: Room B528, Sir Graeme Davies Building, 120 University Place

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

hyb_protocol: Probe quality and fragmentation were confirmed using Bioanalyser 2100 prior to microarray hybridisation. Fragmented and labelled probes were hybridised for 18 hours onto Affymetrix GeneChip® Mouse Genome 430 2.0 Array (cat. 900496, Affymetrix) using GeneChip Hybridization, Wash, and Stain Kit (cat. 900720-900722, Affymetrix).

scan_protocol: Microarrays were scanned using Genechip Scanner 3000 7G.

data_processing: The data in the matrix table were generated from raw CEL files using RMA normalisation method in Partek GS 6.5 software.

source_name: Skeletal Muscle

label_protocol: 50ng RNA from each sample were used to generate complementary DNA strands using Ovation RNA Amplification System V2 (cat. 3100-12, Nugen) and 3.75ug of each cDNA were fragmented and biotin labelled using Encore™ Biotin Module (cat. 4200-12, Nugen).

extract_protocol: RNA extraction was performed in random batches by polytron homogenisation of tissue in Trizol (cat. 15596-026, Invitrogen) followed by phenol chloroform extraction. RNAs were quantitated and qualified using Nanodrop ND8000 (Thermo Scientific) and 2100 Bioanalyser (Agilent). Prior to cDNA probe generation RNAs were subjected to sample clean up and DNAse I treatment using RNEasy Micro (Qiagen) before repeat quantitation and qualification.

value: Skeletal Muscle

tag: mouse number

tag: dosage

value: 20 mg/kg

tag: ast (u/l)

tag: creatinine (umol/l)

tag: bun (mmol/l)

tag: ldh (u/l)

tag: ck (u/l)

tag: rna integrity number (rin)

tag: strain


title: Skeletal Muscle 20mgkg-1 rep2


title: Skeletal Muscle 20mgkg-1 rep3


title: Hypoxia  3 days SG2_D3

description:
SG2_D3
Hypoxia
3
days

tag: experiment

tag: time

value: 3 days


title: single DTC isolated from bone marrow (BM) of PCa patient 2613 (#3)

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines


title: single DTC isolated from bone marrow (BM) of PCa patient  2613 (#8)

value: A single DTC was isolated from bone marrow (BM) samples of PCa patient. Essentially, a two-step selection process was employed, in which anti-CD45 and anti-CD61 conjugated to immunomagnetic beads were used for negative selection, and anti-HEA was used for positive selection.  Cells were then fluorescently stained for BerEP4, counter stained with RPE anti-CD45, and individually selected under fluorescent light using a micropipette system for further analysis.


title: single DTC isolated from bone marrow (BM) of PCa patient  2613 (#4)


title: single DTC isolated from bone marrow (BM) of PCa patient 2613 (#2)


title: Skeletal Muscle vehicle rep3

tag: tissue

value: Vehicle


title: single DTC isolated from bone marrow (BM) of PCa patient 2613 (#1)


title: Hypoxia  2 days SG2_D2

description:
SG2_D2
Hypoxia
2
days

tag: replicate

value: 2 days

tag: treatment


title: set of ten clonally selected and synchronized C42B cells (#32)

data_processing: Graphical examination of raw array signal indicated a batch effect in C42B data due to experimental processing day. We corrected for this effect by separately estimating mean  Alexa Fluor® 3 and mean Alexa Fluor® 5 signal within single-, 5-, and 10-cell C42B arrays between experimental days and adjusting values on the second day by the estimated difference.  We normalized day-effect-corrected signals for C42B data and raw patient data within arrays using loess and normexp background correction with offset 50, removed control probes, averaged duplicate probes, and assigned a value of "null" to spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers.  C42B and patient data further normalized (each set seperately) using between-array quantile normalization.  All normalizations were performed using the Limma package in R.

tag: gender

tag: reference cell lines

value: Clonally selected and cultured single passage of cell cycle synchronized C4-2B PCa cells.  Sets of ten cells were isolated using a micromanipulator under direct visualization with an inverted microscope.


title: Skeletal Muscle 6mgkg-1 rep2

value: 6 mg/kg


title: set of ten clonally selected and synchronized C42B cells (#29)


title: Skeletal Muscle 6mgkg-1 rep3


title: Skeletal Muscle 6mgkg-1 rep1


title: set of ten clonally selected and synchronized C42B cells (#23)


title: set of ten clonally selected and synchronized C42B cells (#26)


title: set of ten clonally selected and synchronized C42B cells (#20)


title: Hypoxia  1 days SG2_D1

description:
SG2_D1
Hypoxia
1
days

value: Hypoxia


title: Hypoxia  9 days SG2_B9

description:
SG2_B9
Hypoxia
9
days

value: B


title: Hypoxia  0 days SG2_D0

description:
SG2_D0
Hypoxia
0
days

value: 0 days


title: Hypoxia  8 days SG2_B8

description:
SG2_B8
Hypoxia
8
days


title: Skeletal Muscle vehicle rep2


title: set of ten clonally selected and synchronized C42B cells (#14)


title: set of ten clonally selected and synchronized C42B cells (#17)


title: Skeletal Muscle vehicle rep1


title: set of ten clonally selected and synchronized C42B cells (#5)


title: Liver 20mgkg-1 rep2

source_name: Liver

value: Liver


title: Hypoxia  5 days SG2_B5

description:
SG2_B5
Hypoxia
5
days


title: set of ten clonally selected and synchronized C42B cells (#11)


title: Liver 6mgkg-1 rep2


title: set of five clonally selected and synchronized C42B cells (#28)

value: Clonally selected and cultured single passage of cell cycle synchronized C4-2B PCa cells.  Sets of five cells were isolated using a micromanipulator under direct visualization with an inverted microscope.


title: set of five clonally selected and synchronized C42B cells (#19)


title: set of five clonally selected and synchronized C42B cells (#25)


title: set of five clonally selected and synchronized C42B cells (#31)


title: Liver 20mgkg-1 rep3


title: set of five clonally selected and synchronized C42B cells (#16)


title: set of five clonally selected and synchronized C42B cells (#22)


title: set of five clonally selected and synchronized C42B cells (#7)


title: Liver 6mgkg-1 rep3


title: set of five clonally selected and synchronized C42B cells (#4)


title: Liver 20mgkg-1 rep1


title: Liver 6mgkg-1 rep1


title: set of five clonally selected and synchronized C42B cells (#10)


title: single clonally selected and synchronized C42B cell (#30)

value: Clonally selected and cultured single passage of cell cycle synchronized C4-2B PCa cells.  Single cells were isolated using a micromanipulator under direct visualization with an inverted microscope.


title: set of five clonally selected and synchronized C42B cells (#13)


title: single clonally selected and synchronized C42B cell (#24)


title: Hypoxia  2 days SG2_B2

description:
SG2_B2
Hypoxia
2
days


title: Hypoxia  7 days SG2_B7

description:
SG2_B7
Hypoxia
7
days

value: 7 days


title: single clonally selected and synchronized C42B cell (#27)


title: single clonally selected and synchronized C42B cell (#21)


title: Hypoxia  1 days SG2_B1

description:
SG2_B1
Hypoxia
1
days

value: 1 days


title: Hypoxia  3 days SG2_B3

description:
SG2_B3
Hypoxia
3
days


title: Hypoxia  0 days SG2_B0

description:
SG2_B0
Hypoxia
0
days


title: Liver vehicle rep3


title: Liver vehicle rep1


title: Hypoxia  7 days SG2_A7

description:
SG2_A7
Hypoxia
7
days

value: A


title: Hypoxia  9 days SG2_A9

description:
SG2_A9
Hypoxia
9
days

value: 9 days


title: Liver vehicle rep2


title: single clonally selected and synchronized C42B cell (#15)

value: male


title: Hypoxia  3 days SG2_A3

description:
SG2_A3
Hypoxia
3
days

value: 3 days


title: Kidney 20mgkg-1 rep3

source_name: Kidney

value: Kidney

value: 20 mg/kg


title: single clonally selected and synchronized C42B cell (#3)

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines


title: Hypoxia  8 days SG2_A8

description:
SG2_A8
Hypoxia
8
days

value: 8 days