title: breast tumor part_IDC_rep1_5325

tag: cell type

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

tag: lymph node metastasis

tag: lymphovascular invasion

tag: mitotic count

tag: nuclear pleomorphism


title: breast tumor part_IDC_rep1_5327

status: Public on Nov 01 2012

type: RNA

city: Taipei

first: King-Jen

last: Chang

address: No.1, Changde St., Zhongzheng Dist.

department: Department of Surgery

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0

scan_protocol: Agilent scanner and Feature Extraction 6.0.

data_processing: The log2-ratio gene expression data in the microarray dataset were normalized by quantile normalization.

molecule: total RNA

organism: Homo sapiens

source_name: Infiltrating Ductal Carcinoma (IDC), Buffer 1, ER(-), PR(-), HER2(-).

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit, protocol version 2.0

growth_protocol: The breast tumor samples were immediately frozen by liquid nitrogen without any additional growth procedure before RNA extraction.

extract_protocol: Trizol reagent combined with RNAeasy mini kit

treatment_protocol: The breast tumor samples were excised, collected, and snap-frozen in liquid nitrogen immediately before RNA extraction.

tag: tissue type

value: breast tumor

value: Infiltrating Ductal Carcinoma (IDC)

tag: array id

tag: er ihc

tag: age

value: I

tag: grade

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

source_name: Stratagene's human common reference RNA

tag: sample type

value: Commercially-available reference


title: breast tumor part_IDC_rep1_4411

tag: cell type

tag: pr ihc

tag: her-2/neu ihc

value: IIB


title: breast tumor part_IDC_rep1_4403

tag: ajcc stage

tag: lymph node metastasis

tag: lymphovascular invasion


title: DNA11091-109A Whole blood sample, SLE patient 8

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

description:
Whole blood sample, SLE patient
DNA11091-109A

hyb_protocol: Labeled RNA was hybridized to GeneChip® HumanGenome U133 Plus 2.0 Arrays (Affymetrix).

scan_protocol: The slides were washed and stained on a GeneChip® Fluidics Station (Affymetrix) and scanned using a GeneChip® Scanner 3000 (Affymetrix).

data_processing:
One SLE patient was excluded from gene expression analysis because of a missing baseline sample. All the analyses displayed in the manuscript were repeated using extrapolated baseline data for this patient (based on expression data of a day 38 whole blood sample), and delivered the same results. Also, a SLE patient who had a disease flare before receiving a second dose of IFN-K was excluded from the analysis at days 84, 112, and 168. One placebo-treated patient received high-dose oral and intravenous steroids between days 112 and 168, so her day 168 samples were excluded from the analysis. Thus, valid gene expression profiles were obtained for 26 SLE patients at baseline, 26 at day 112, and 26 at day 168. Valid gene expression profiles were also obtained for 46 of the 50 healthy volunteers (4 with a RNA integrity number < 6 were excluded) and for all 18 IFNalpha-stimulated healthy volunteer samples.
Fluorescence intensity data were normalized by robust multiarray analysis (RMA) using GeneSpring® (Agilent Technologies, Santa Clara, CA).

label: Biotin

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, day 112

label_protocol: RNA was labeled using a One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA)

extract_protocol: RNA was extracted from blood samples (controls, IFN-stimulated controls and SLE patients at days 0, 112 and 168) using a Paxgene Blood RNA kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies, Santa Clara, CA). Samples with a RNA integrity number < 6 were discarded.

treatment_protocol: SLE patients were treated with IFN K or an equivalent volume of 0.9% NaCl (placebo), both mixed with an equal volume of ISA-51vg adjuvant (Seppic, Paris, France). IFN-K was prepared by crosslinking recombinant human IFNalpha2b with KLH. Subjects were randomized to treatments using an interactive web response system, and both subjects and investigators were blinded to the treatment type. All treatments were delivered by intramuscular injection. A first group of four subjects was randomized 3:1 to receive 30 microgram IFN K or placebo in a volume of 0.15 ml. The second, third, and fourth groups each included eight subjects each who were randomized 3:1 to receive, respectively, 60 microgram IFN K or placebo in 0.3 ml, 120 microgram IFN K or placebo in 0.6 ml, and 240 microgram IFN K or placebo in two injections of 0.6 ml. Safety data were reviewed by an independent medical safety board after 48 hours and before administering the first dose to the next group. All groups received a second dose of IFN K or placebo on day 7 and a third dose of IFN K or placebo on day 28. On day 84, four subjects in each of the 60-, 120-, or 240- microgram IFN K groups received a fourth dose of IFN K or placebo if the independent medical safety board decided there were no safety issues from the previous dose of IFN K and if human IFNalpha-neutralizing antibodies were not detected at day 56 in at least two of the first four subjects at the specific dose.

tag: disease state

value: SLE

tag: treatment

value: IFN-K 30 micrograms, 3 injections

tag: day

tag: tissue

value: Whole blood

tag: ethnicity

value: Caucasian

tag: gender

value: Female


title: DNA11091-053A Whole blood sample, SLE patient 7

description:
Whole blood sample, SLE patient
DNA11091-053A

source_name: SLE patient, Placebo, day 112

value: placebo

tag: age


title: yolk sac_4

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

country: USA

institute: Johns Hopkins University School of Medicine

description: gene expression profiling HSC/Ps from day 9 yolk sac

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Raw microarray signal intensities were RMA-summarized and quantile normalized using R/BioConductor (Bolstad et al., 2003; Gentleman et al., 2004; Irizarry et al., 2003). To correct for batch effects, we applied the ComBat batch correction algorithm to the normalized data (Johnson et al., 2007).  The result of this process is what is presented in the Sample data table.  For downstream analysis, including gene regulatory network reconstruction, differential gene expression, clustering, etc we used 'averaged data' in which multiple probesets mapping to the same gene were averaged, resulting in 21,308 gene expression measures per sample.  This data set is available at http://hsc.hms.harvard.edu/.  Included in the analysis were the following mESC samples: GSM424475, GSM424476, GSM344757, GSM344758, GSM344759, GSM344760.

label: biotin

organism: Mus musculus

source_name: yolk sac

label_protocol: Standard Affymetrix procedure

growth_protocol: mESC were differentitated to ESC-HSCs as previously described in McKinney-Freeman, Naveiras, and Daley 2008 (PMID:18770632)

extract_protocol: Mouse embryos were dissected as described in McKinney-Freeman et al 2009 (PMID:19420357)

tag: strain background

tag: markers

tag: amplification

value: Nugen

tag: developmental stage

value: embryonic day 9

value: yolk sac

tag: in vivo or in vitro

value: in vivo

tag: hsc stage

value: YS-like


title: breast tumor part_IDC_rep1_4409

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: yolk sac_3

tag: strain background

tag: markers

tag: amplification

tag: developmental stage

tag: tissue

tag: in vivo or in vitro


title: DNA10204-341A Whole blood sample, SLE patient 7

description:
Whole blood sample, SLE patient
DNA10204-341A

source_name: SLE patient, Placebo, baseline

tag: disease state

tag: treatment

tag: day

tag: ethnicity

tag: age

tag: gender


title: DNA10204-335A Whole blood sample, SLE patient 8

description:
Whole blood sample, SLE patient
DNA10204-335A

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, baseline


title: DNA11091-077A Whole blood sample, SLE patient 7

description:
Whole blood sample, SLE patient
DNA11091-077A

source_name: SLE patient, Placebo, day 168


title: breast tumor part_IDC_rep1_4397

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: IIA

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size


title: DNA11091-095A Whole blood sample, SLE patient 6

description:
Whole blood sample, SLE patient
DNA11091-095A

tag: disease state

tag: treatment

tag: day

tag: tissue

tag: ethnicity


title: whole bone marrow_5

description: gene expression profiling HSCs from  bone marrow of the adult

tag: strain background

tag: markers

tag: amplification

tag: developmental stage

value: adult

value: bone marrow

tag: in vivo or in vitro

tag: hsc stage

value: Definitive


title: DNA10204-309A Whole blood sample, SLE patient 6

description:
Whole blood sample, SLE patient
DNA10204-309A

tag: age

tag: gender


title: breast tumor part_IDC_rep1_4395

tag: tissue type

value: breast tumor

tag: cell type

value: Infiltrating Ductal Carcinoma (IDC)

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: I

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type

value: Commercially-available reference


title: breast tumor part_IDC_rep1_4405

tag: age

value: IIB

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size


title: DNA11159-013A Whole blood sample, SLE patient 5

description:
Whole blood sample, SLE patient
DNA11159-013A

tag: disease state

value: SLE

tag: treatment

value: placebo and IV Solumedrol 1g between day 112 and day 168

tag: day

tag: tissue

value: Whole blood

tag: ethnicity

value: Caucasian

tag: gender


title: DNA11091-112A Whole blood sample, SLE patient 6

description:
Whole blood sample, SLE patient
DNA11091-112A

value: placebo

value: Female


title: breast tumor part_IDC_rep1_4399

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: IIIC

tag: lymph node metastasis

tag: lymphovascular invasion


title: breast tumor part_IDC_rep1_4401

tag: age

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: 5W_kl(-/-)_Liver_2

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

country: Japan

institute: National Institute of Neuroscience, NCNP

hyb_protocol: Hybridization was carried out with Genopal®-MICM DNA chips (Mitsubishi Rayon) for detection of mouse miRNAs in 100 µl of hybridization buffer [6 x SSC, 0.2% SDS and 1 µg of heat-denatured labeled RNAs] at 42℃ overnight using a hybridization chamber specific for the Genopal®-DNA chip (Mitsubishi Rayon).

scan_protocol: After hybridization, the DNA chips were washed twice in 2xSSC containing 0.2% SDS at 50℃ for 20 min followed by washing in 2xSSC at 50℃ for 10 min, and then hybridization signals were examined by means of a DNA chip reader adopting multi-beam excitation technology according to the manufacturer’s instructions (Yokogawa Electric Corporation).

data_processing: Hybridization signal intensity of each miRNA was normalized to that of the external control oligonucleotides provided by Mitsubishi Rayon.

source_name: klotho(-/-) Liver

label_protocol: Isolated small-sized RNAs (~1 µg) were subjected to direct labeling with a fluorescent dye using a PlatinumBright 647 Infrared nucleic acid labeling kit (KREATECH), according to the manufacturer’s instructions. After fluorescent labeling, the labeled RNAs were purified from free fluorescent substrates by the KREApure columns (KREATECH) and used in hybridization.

extract_protocol: Total RNAs were extracted from various tissues using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. For preparation of cellular miRNAs, 20 µg of each isolated total RNA was mixed with 5 µl of the external control oligonucleotides provided by Mitsubishi Rayon, and subjected to isolation of small-sized RNAs containing miRNAs using an RNeasy MinElute Cleanup kit (Qiagen).

tag: Sex

value: male

tag: genotype/variation

value: klotho(-/-)

tag: tissue

value: Liver


title: yolk sac_5

tag: strain background

tag: markers

tag: amplification

value: Nugen

tag: developmental stage

value: embryonic day 9

value: yolk sac

tag: in vivo or in vitro

value: in vivo

tag: hsc stage

value: YS-like


title: breast tumor part_IDC_rep1_4407

tag: tissue type

value: breast tumor

tag: cell type

value: Infiltrating Ductal Carcinoma (IDC)

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: age

tag: ajcc stage

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: tumor size

value: Commercially-available reference


title: yolk sac_1

tag: strain background

tag: markers

tag: tissue


title: DNA11091-151A Whole blood sample, SLE patient 5

description:
Whole blood sample, SLE patient
DNA11091-151A

tag: disease state

value: SLE

tag: treatment

tag: day

tag: ethnicity

tag: gender


title: yolk sac_2

tag: amplification

tag: developmental stage

tag: in vivo or in vitro

tag: hsc stage


title: whole bone marrow_4

value: adult

value: bone marrow

value: Definitive


title: whole bone marrow_3


title: whole bone marrow_2


title: breast tumor part_IDC_rep1_4393

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: age

tag: ajcc stage

value: IIA

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: DNA11091-083A Whole blood sample, SLE patient 5

description:
Whole blood sample, SLE patient
DNA11091-083A

tag: disease state

tag: treatment

value: placebo

tag: day

tag: tissue

value: Whole blood

tag: ethnicity

value: Caucasian

tag: gender

value: Female


title: whole bone marrow_1

tag: strain background

tag: markers

tag: amplification

tag: developmental stage

tag: in vivo or in vitro

tag: hsc stage


title: breast tumor part_IDC_rep1_4391

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: age

tag: ajcc stage

value: I

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size


title: breast tumor part_IDC_rep1_4387

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: breast tumor part_IDC_rep1_4385

tag: tissue type

tag: cell type

tag: array id

value: IIIC


title: breast tumor part_IDC_rep1_4383

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc


title: Placenta_5

description: gene expression profiling HSCs from day 12.5 placenta

source_name: placenta

tag: strain background

tag: markers

tag: amplification

value: Nugen

tag: developmental stage

value: embryonic day 12.5

tag: tissue

value: placenta

tag: in vivo or in vitro

tag: hsc stage

value: Specifying


title: DNA11091-073A Whole blood sample, SLE patient 4

description:
Whole blood sample, SLE patient
DNA11091-073A

tag: disease state

tag: treatment

tag: day

tag: ethnicity

tag: age

tag: gender


title: Placenta_6

value: in vivo


title: breast tumor part_IDC_rep1_4389

tag: tissue type

value: breast tumor

tag: cell type

value: Infiltrating Ductal Carcinoma (IDC)

tag: array id

tag: ajcc stage

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type

value: Commercially-available reference


title: Granuloma 7 weeks zone 2 rep2

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

description: Gene expression of the outer zone (zone 2) of granuloma present in the liver infected by Schistosoma japonicum at 7 weeks post infection

hyb_protocol: Synthesized cRNA was hybridised to Illumina mouse Ref-8 v2 expression beadchips according to manufacturer instructions.

scan_protocol: Images on the arrays were scanned using Beadstation 500 at green factor level 2.

data_processing: Feature extraction of the data was generated using GenomeStudio version 1.1.1 and analysed further using GeneSpring GX 11.

source_name: Microdissected granuloma, infected

label_protocol: cRNA was synthesised from total RNA with Illumina Total Prep RNA Amplication kit (Ambion).

growth_protocol: The complete life cycle of schistosoma japonicum was maintained in our laboratory. The cercarial of S. japonicum were shed from Oncomelania hupensis snail to infect the experimental mice.

extract_protocol: Total RNA from microdissected materials was extracted by a combination use of Trizol (Invitrogen) and RNeasy Mini kit (Qiagen).

treatment_protocol: Mice were euthanised and liver tissues were embedded in OCT compound to prepare frozen blocks for laser microdissection.

tag: time

value: 7 wk

tag: strain

tag: age

value: 6 weeks

tag: tissue

value: outer zone (zone 2) of liver granuloma

tag: infection

value: Schistosoma japonicum


title: Placenta_2

tag: strain background

tag: markers

tag: amplification

tag: developmental stage

tag: in vivo or in vitro

tag: hsc stage


title: DNA10204-287A Whole blood sample, SLE patient 4

description:
Whole blood sample, SLE patient
DNA10204-287A

tag: disease state

value: SLE

tag: treatment

value: placebo

tag: day

value: Whole blood

tag: ethnicity

tag: gender


title: Granuloma 7 weeks zone 3 rep1

description: Gene expression of the peripheral zone (zone 3) of granuloma present in the liver infected by Schistosoma japonicum at 7 weeks post infection

value: Female

value: peripheral zone (zone 3) of liver granuloma


title: Placenta_4

value: Nugen


title: DNA11091-149A Whole blood sample, SLE patient 3

description:
Whole blood sample, SLE patient
DNA11091-149A

value: Asian


title: DNA11159-003A Whole blood sample, SLE patient 3

description:
Whole blood sample, SLE patient
DNA11159-003A


title: Granuloma 7 weeks zone 2 rep1


title: breast tumor part_IDC_rep1_4379

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: IIA

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: Fetal liver 14.5_6

description: gene expression profiling HSCs from day 14.5 fetal liver

tag: strain background

tag: markers

tag: amplification

tag: developmental stage

value: embryonic day 14.5

tag: tissue

value: fetal liver

tag: in vivo or in vitro

tag: hsc stage

value: Definitive


title: Placenta_1

value: embryonic day 12.5

value: placenta

value: in vivo

value: Specifying


title: DNA11091-081A Whole blood sample, SLE patient 3

description:
Whole blood sample, SLE patient
DNA11091-081A

tag: disease state

tag: treatment

tag: day

tag: ethnicity

tag: age

tag: gender


title: DNA11091-106A Whole blood sample, SLE patient 2

description:
Whole blood sample, SLE patient
DNA11091-106A

value: Caucasian


title: DNA11091-128A Whole blood sample, SLE patient 4

description:
Whole blood sample, SLE patient
DNA11091-128A


title: Granuloma 7 weeks zone 3 rep2

tag: time

value: 7 wk

tag: strain

value: 6 weeks

tag: infection

value: Schistosoma japonicum


title: breast tumor part_IDC_rep1_4381

tag: tissue type

value: breast tumor

tag: cell type

value: Infiltrating Ductal Carcinoma (IDC)

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type

value: Commercially-available reference


title: Granuloma 7 weeks zone 1 rep2

description: Gene expression of the core (zone 1) of granuloma present in the liver infected by Schistosoma japonicum at 7 weeks post infection

tag: time

tag: strain

tag: gender

value: Female

tag: age

tag: tissue

value: core (zone 1) of liver granuloma

tag: infection


title: DNA11091-119A Whole blood sample, SLE patient 2

description:
Whole blood sample, SLE patient
DNA11091-119A

tag: disease state

value: SLE

tag: treatment

value: placebo

tag: day

value: Whole blood

tag: ethnicity


title: Placenta_3

tag: strain background

tag: markers

tag: amplification

tag: developmental stage

tag: in vivo or in vitro

tag: hsc stage


title: breast tumor part_IDC_rep1_4375

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: IIA

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: Fetal liver 14.5_4

tag: strain background

tag: markers

tag: amplification

value: Nugen

tag: developmental stage

value: embryonic day 14.5

tag: tissue

value: fetal liver

tag: in vivo or in vitro

tag: hsc stage

value: Definitive


title: Granuloma 7 weeks zone 1 rep1

tag: time

tag: strain

tag: gender

tag: age

tag: infection


title: breast tumor part_IDC_rep1_4371

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: I

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size


title: DNA11091-017A Whole blood sample, SLE patient 11

description:
Whole blood sample, SLE patient
DNA11091-017A

source_name: SLE Patient, IFN-K 60 microgram, 3 injections, day 112

tag: disease state

tag: treatment

value: IFN-K 60 microgram, 3 injections

tag: day

tag: tissue

tag: ethnicity

value: Caucasian

tag: gender


title: DNA11091-115A Whole blood sample, SLE patient 1

description:
Whole blood sample, SLE patient
DNA11091-115A

tag: age


title: Granuloma 6 weeks zone 1 rep2

description: Gene expression of the core (zone 1) of granuloma present in the liver infected by Schistosoma japonicum at 6 weeks post infection

tag: time

value: 6 wk

tag: strain

value: 6 weeks

tag: infection

value: Schistosoma japonicum


title: DNA11091-089A Whole blood sample, SLE patient 1

description:
Whole blood sample, SLE patient
DNA11091-089A


title: breast tumor part_IDC_rep1_4369

tag: tissue type

value: breast tumor

tag: cell type

value: Infiltrating Ductal Carcinoma (IDC)

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

tag: lymph node metastasis

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type

value: Commercially-available reference


title: DNA10204-331A Whole blood sample, SLE patient 1

description:
Whole blood sample, SLE patient
DNA10204-331A

tag: disease state

value: SLE

tag: treatment

tag: day

tag: tissue

tag: ethnicity

tag: gender

value: Female


title: Granuloma 6 weeks zone 2 rep2

description: Gene expression of the outer zone (zone 2) of granuloma present in the liver infected by Schistosoma japonicum at 6 weeks post infection

tag: time

tag: strain

tag: age

value: outer zone (zone 2) of liver granuloma

tag: infection


title: breast tumor part_IDC_rep1_4377

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

value: IIA

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size


title: breast tumor part_IDC_rep1_4365

tag: ajcc stage

tag: lymph node metastasis

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: breast tumor part_IDC_rep1_4367

tag: tissue type

tag: cell type

tag: age


title: Fetal liver 14.5_2

tag: strain background

tag: markers

tag: amplification

value: Nugen

tag: developmental stage

tag: tissue

tag: in vivo or in vitro

value: in vivo

tag: hsc stage


title: breast tumor part_IDC_rep1_4373

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

value: IIB

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size


title: Fetal liver 14.5_5

tag: strain background

value: embryonic day 14.5

value: fetal liver

value: Definitive


title: Fetal liver 14.5_1

tag: markers


title: Fetal liver 14.5_3

tag: amplification


title: Surrounding 4 weeks rep2

description: Gene expression of the surrounding cells outside the region of granulomas in the liver infected by Schistosoma japonicum at 4 weeks post infection

source_name: Microdissected surrounding cells, infected

tag: time

value: 4 wk

tag: strain

tag: gender

tag: age

value: surrounding cells outside the region of liver granulomas

tag: infection


title: DNA10204-258A Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)
DNA10204-258A

source_name: Healthy individual (unstimulated = DNA10204-083)

tag: tissue

value: Whole blood

tag: ethnicity

value: Caucasian

tag: disease state

value: healthy

tag: treatment

value: in vitro IFNa-2b stimulation (4H)


title: DNA10204-290A Whole blood sample, SLE patient 2

description:
Whole blood sample, SLE patient
DNA10204-290A

value: placebo

tag: day


title: Granuloma 6 weeks zone 1 rep1

value: 6 wk

value: 6 weeks

value: core (zone 1) of liver granuloma

value: Schistosoma japonicum


title: breast tumor part_IDC_rep1_4363

tag: tissue type

value: breast tumor

tag: cell type

value: Infiltrating Ductal Carcinoma (IDC)

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: I

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type

value: Commercially-available reference


title: breast tumor part_IDC_rep1_4361

tag: age

value: IIIA

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size


title: DNA10204-241A Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)
DNA10204-241A

source_name: Healthy individual (unstimulated = DNA10204-079)

tag: tissue

tag: ethnicity

tag: gender

value: Female

tag: disease state

tag: treatment


title: Surrounding 4 weeks rep1

tag: time

value: 4 wk

tag: strain

tag: infection


title: breast tumor part_IDC_rep1_4359

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: IIA

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count


title: Granuloma 4 weeks rep2

description: Gene expression of the granuloma present in the liver infected by Schistosoma japonicum at 4 weeks post infection

tag: gender

tag: age

tag: tissue

value: liver granuloma


title: Granuloma 6 weeks zone 2 rep1

tag: time

value: outer zone (zone 2) of liver granuloma


title: Fetal liver 13.5_3

description: gene expression profiling HSCs from day 13.5 fetal liver

tag: strain background

tag: markers

tag: amplification

value: Nugen

tag: developmental stage

value: embryonic day 13.5

value: fetal liver

tag: in vivo or in vitro

value: in vivo

tag: hsc stage

value: Definitive


title: DNA10204-235A Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)
DNA10204-235A

value: Whole blood

tag: ethnicity

value: Caucasian

tag: disease state

value: healthy

tag: treatment

value: in vitro IFNa-Mix stimulation (4H)


title: DNA10204-252A Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)
DNA10204-252A


title: breast tumor part_IDC_rep1_2461

tag: tissue type

value: breast tumor

tag: cell type

value: Infiltrating Ductal Carcinoma (IDC)

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

tag: lymph node metastasis

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

tag: sample type


title: DNA10204-224A Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)
DNA10204-224A

source_name: Healthy individual (unstimulated = DNA10204-081)

tag: tissue

tag: ethnicity

tag: age

tag: gender

tag: disease state

value: in vitro IFNa-2b stimulation (4H)


title: Fetal liver 12.5_3

description: gene expression profiling HSCs from day 12.5 fetal liver

tag: strain background

tag: markers

tag: amplification

tag: developmental stage

value: embryonic day 12.5

tag: in vivo or in vitro

tag: hsc stage

value: Specifying


title: DNA10204-218A Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)
DNA10204-218A

value: Female

tag: treatment


title: breast tumor part_IDC_rep1_4355

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: IIB

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

value: Commercially-available reference


title: DNA10204-207A Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)
DNA10204-207A

source_name: Healthy individual (unstimulated = DNA10204-075)

tag: tissue

tag: ethnicity

tag: age

tag: gender

tag: disease state


title: Fetal liver 13.5_4

tag: strain background

tag: markers

tag: amplification

value: Nugen

tag: developmental stage

tag: in vivo or in vitro

tag: hsc stage


title: Liver uninfected control rep1

description: Gene expression in the liver of normal C57BL/6 mice

source_name: Microdissected liver, uninfected

tag: time

value: control

tag: strain

value: 6 weeks

value: normal liver

tag: infection

value: Uninfected


title: Liver uninfected control rep2


title: breast tumor part_IDC_rep1_4353

source_name: Infiltrating Ductal Carcinoma (IDC), Buffer 1, ER(-), PR(-), HER2(-).

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: IIA

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

source_name: Stratagene's human common reference RNA

tag: sample type


title: Fetal liver 12.5_4

tag: strain background

tag: markers

tag: amplification

tag: developmental stage

tag: tissue

value: fetal liver

tag: in vivo or in vitro

value: in vivo

tag: hsc stage

value: Definitive


title: Fetal liver 12.5_6


title: DNA10204-190A Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)
DNA10204-190A

source_name: Healthy individual (unstimulated = DNA10204-077)

value: Whole blood

tag: ethnicity

value: Caucasian

tag: age

tag: gender

tag: disease state

value: healthy

tag: treatment


title: Fetal liver 13.5_1

value: embryonic day 13.5


title: Fetal liver 12.5_5

value: embryonic day 12.5


title: DNA10204-201A Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)
DNA10204-201A

value: Female

value: in vitro IFNa-Mix stimulation (4H)


title: Granuloma 4 weeks rep1

tag: time

value: 4 wk

tag: strain

value: liver granuloma

tag: infection

value: Schistosoma japonicum


title: Fetal liver 13.5_2

value: Nugen


title: breast tumor part_IDC_rep1_1683

tag: tissue type

value: breast tumor

tag: cell type

value: Infiltrating Ductal Carcinoma (IDC)

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: I

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death

value: Commercially-available reference


title: Fetal liver 12.5_2

tag: strain background

tag: markers

tag: amplification

tag: developmental stage

tag: tissue

value: fetal liver

tag: in vivo or in vitro

value: in vivo

tag: hsc stage

value: Specifying


title: Control1-TM2

city: Tehran

first: hassan

last: paylakhi

address: Jalale aleahmad

country: Iran

institute: Tarbiat Modares University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Negative controls consisted of probes having no corresponding targets in the human genome.Values obtained with these were taken to represent background absorbance and subtracted from readings at other probe sites. Low Stringency Hyb Control and High Stringency Hyb Control produced similar values on the arrays. Quality of assessment of gene expression levels was queried using p values reported by Beadstudio for each gene. This p value reflects consistency among readings obtained from different probes of the same gene. Considering the two siRNAs for each transcription factors, the two scrambled siRNA treatments,  and the two TM primary cultures, if three or more of the 12 p values for a gene were >0.05, that gene was removed before further analysis of effect of the respective transcription factor. Then all remaining Beadstudio data were normalized using a quantile based algorithm available in the Beadarray software

source_name: Control 1-TM2

label_protocol: Briefly, ds cDNA was synthesized and reverse transcribed to produce biotin-labeled cRNA.

growth_protocol: trabecular meshwork cells were cultured in Dulbecco’s modified Eagle’s medium and F12 (DMEM/F12) containing 15% newborn calf serum.

extract_protocol: Forty eight hours after exposure to siRNAs, cells were harvested and cells of duplicate wells were combined and placed in RNXTM-plus (Cinnagen, Tehran, Iran). Total RNA was isolated according to the manufacturer’s instructions.

treatment_protocol: Fourth to sixth passage cells were used in all experiments. Each of the four TM cultures was exposed to three siRNA treatments in duplicate wells. Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA) was used for reverse transfection according to the manufacturer’s instructions. All TM cultures had two independent treatments with scrambled siRNA (i.e., two treatments, two wells for each) so as to enable testing of technical replication of the array expression assessments.

value: Trabecular meshwork tissue

tag: gender

value: male

tag: age


title: DNA10204-184A Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)
DNA10204-184A

value: Whole blood

tag: ethnicity

value: Caucasian

tag: disease state

value: healthy

tag: treatment


title: breast tumor part_IDC_rep1_1657

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: her-2/neu ihc

tag: ajcc stage

value: IIIA

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: sample type


title: Fetal liver 12.5_1

tag: strain background

tag: markers

tag: amplification

tag: developmental stage

value: embryonic day 12.5

tag: tissue

tag: in vivo or in vitro

tag: hsc stage

value: Definitive


title: breast tumor part_IDC_rep1_1621

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

tag: age

tag: tumor size

tag: distant metastasis-free (years)

tag: event of distant metastasis

tag: event of death


title: Control2-TM2

source_name: Control 2-TM2

tag: gender


title: breast tumor part_IDC_rep1_1661

tag: her-2/neu ihc

tag: ajcc stage

tag: lymph node metastasis

tag: lymphovascular invasion

tag: grade

tag: mitotic count

tag: nuclear pleomorphism

tag: tubule formation

tag: sample type


title: Control1-TM1

source_name: Control 1-TM1

tag: tissue


title: Control2-TM1

source_name: Control 2-TM1


title: breast tumor part_IDC_rep1_1453

tag: tissue type

tag: cell type

tag: array id

tag: er ihc

tag: pr ihc

value: IIA


title: ESC-HSC_3

description: gene expression profiling ESC-derived HSCs

source_name: HSCs derived from differentiating embryonic stem cells in vitro (ESC-HSC)

tag: strain background

value: C57BL/6 x 129 cross

tag: markers

tag: amplification

tag: developmental stage

value: differentiation day 10-14

tag: in vivo or in vitro

value: in vitro

tag: hsc stage


title: DNA10204-156A Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)
DNA10204-156A

source_name: Healthy individual (unstimulated = DNA10204-073)

tag: ethnicity

tag: age

tag: gender

value: Male

tag: disease state

tag: treatment

value: in vitro IFNa-2b stimulation (4H)


title: siRNA 2 FOXC1-TM2

source_name: siRNA 2 FOXC1-TM2

tag: tissue


title: siRNA 1 FOXC1-TM2

source_name: siRNA 1 FOXC1-TM2


title: ESC-HSC_2


title: DNA10204-139A Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)
DNA10204-139A

source_name: Healthy individual (unstimulated = DNA10204-055)


title: ESC-HSC_1


title: siRNA 2 FOXC1-TM1

source_name: siRNA 2 FOXC1-TM1


title: DNA10204-150A Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)
DNA10204-150A

value: in vitro IFNa-Mix stimulation (4H)


title: EB_KIT_CD41_6

description: gene expression profiles of embryoid body kit/cd41+ population

source_name: Embryoid body KIT CD41

value: Nugen

value: differentiation day 6

value: YS-like


title: DNA10204-122A Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)
DNA10204-122A

source_name: Healthy individual (unstimulated = DNA10204-057)

value: North-African

value: Female


title: EB_KIT_CD41_5


title: RNA from  SU8686  cell line

type: genomic

city: Vancouver

first: Kelsie

middle: L

last: Thu

state: British Columbia

address: 675 West 10th Avenue

country: Canada

institute: BC Cancer Research Centre

description: pancreatic cancer cell line

hyb_protocol: One-Color microarray-based gene expression protocol

scan_protocol: Arrays were imaged using an Axon GenePix 4000B scanner

data_processing: array data were spot-found using GenePix 6.1 and normalized by median array normalization

molecule: genomic DNA

label_protocol: Standard agilent protocol (linear amplificiation to generate cRNA labeled with Cy3)

extract_protocol: RNA was extracted from all cell lines using Trizol reagent

tag: cell line

value: female

tag: sample type

value: pancreatic ductal adenocarcinoma

value: cancer


title: DNA10204-116A Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)
DNA10204-116A

value: Whole blood

value: healthy


title: RNA from  HPDE cell line

description: pancreatic cancer cell line

source_name: HPDE

value: HPDE

value: male

value: immortalized non-malignant human pancreatic duct cells

value: normal


title: EB_KIT_CD41_3

value: C57BL/6 x 129 cross

value: in vitro


title: RNA from  SW1990 cell line

description: pancreatic cancer cell line

value: pancreatic adenocarcinoma


title: HEK-293 miR-218 Experimental Replicate A 1521406093_H

city: Callaghan

first: Adam

last: Carroll

state: NSW

address: Ring Road

institute: University of Newcastle

description: Experimental Replicate A

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Illumina Beadstudio software computed average signal intensities and detection p-values.

label_protocol: Biotinylated cRNA was prepared using the TotalPrep RNA amplification kit (Ambion) for Illumina arrays.

growth_protocol: Cell models were grown as confluent monolayers in standard tissue culture conditions.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with DNase I treatment and the RNeasy MinElute cleanup kit (Qiagen) in accordance with manufacturer's instructions. Quality control was performed with an Experion (BioRad) bioanalyser.

treatment_protocol: Cells were transfected with either synthetic miRNA or anti-miR inhibitor oligonucleotides. Control refers to untransfected cell models; siEGFP control refers to transfection with an siRNA to EGFP as a transfection control.

value: miR-218 overexpression


title: RNA from  PL45  cell line

description: pancreatic cancer cell line


title: HEK-293 control Experimental Replicate B 1521406066_E

description: Experimental Replicate B

value: control


title: HEK-293 anti-miR-218 Experimental Replicate A 1521406066_H

description: Experimental Replicate A


title: EB_KIT_CD41_4

value: Nugen

value: differentiation day 6

value: YS-like


title: DNA10204-133A Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)
DNA10204-133A

value: Caucasian

value: Male

value: in vitro IFNa-Mix stimulation (4H)


title: siRNA 1 FOXC1-TM1

source_name: siRNA 1 FOXC1-TM1

value: Trabecular meshwork tissue


title: DNA10204-105A Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-2b stimulation (4H)
DNA10204-105A

source_name: Healthy individual (unstimulated = DNA10204-059)

value: Whole blood

value: Female

value: healthy

value: in vitro IFNa-2b stimulation (4H)


title: RNA from  Panc10.05 cell line

description: pancreatic cancer cell line

value: male

value: pancreatic ductal adenocarcinoma

value: cancer


title: HEK-293 control Experimental Replicate A 1521406093_G

description: Experimental Replicate A


title: AGM_6

description: gene expression profiling HSC/Ps from day 11.5 AGM

source_name: aorta-gonads-mesonephros (AGM)

value: embryonic day 11.5

value: aorta-gonads-mesonephros

value: in vivo

value: Specifying


title: DNA10204-095A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-095A

source_name: Healthy individual, in the absence of any treatment


title: RNA from  Panc05.04  cell line

description: pancreatic cancer cell line

value: female

value: pancreatic adenocarcinoma


title: EB_KIT_CD41_1

value: C57BL/6 x 129 cross

value: Nugen

value: differentiation day 6

value: in vitro

value: YS-like


title: RNA from  Panc08.13 cell line

description: pancreatic cancer cell line


title: EB_KIT_CD41_2


title: DNA10204-093A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-093A

value: Whole blood

value: Caucasian

value: Female


title: RNA from  PANC-1  cell line

description: pancreatic cancer cell line

value: male

value: pancreatic ductal epithelioid carcinoma


title: AGM_5


title: DNA10204-099A Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)

description:
Whole blood sample, healthy individual, in vitro IFNa-Mix stimulation (4H)
DNA10204-099A

value: healthy

value: in vitro IFNa-Mix stimulation (4H)


title: HEK-293 miR-181b Experimental Replicate B 1521406066_D

description: Experimental Replicate B

value: miR-181b overexpression


title: HEK-293 anti-miR-181b Experimental Replicate A 1521406093_F

description: Experimental Replicate A


title: HEK-293 miR-181b Experimental Replicate A 1521406093_E

description: Experimental Replicate A


title: DNA10204-091A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-091A


title: HEK-293 control Experimental Replicate B 1521406066_C

description: Experimental Replicate B

value: control


title: RNA from  Panc03.27 cell line

description: pancreatic cancer cell line

value: cancer


title: HEK-293 control Experimental Replicate A 1521406093_D

description: Experimental Replicate A


title: AGM_2

value: embryonic day 11.5

value: aorta-gonads-mesonephros

value: in vivo

value: Specifying


title: RNA from  Panc04.03 cell line

description: pancreatic cancer cell line

value: pancreatic adenocarcinoma


title: AGM_4

value: Nugen


title: RNA from  Panc02.03 cell line

description: pancreatic cancer cell line

value: female


title: RNA from  Panc02.13 cell line

description: pancreatic cancer cell line


title: DNA10204-085A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-085A

value: Whole blood

value: Male


title: HEK-293 anti-miR-107 Experimental Replicate A 1521406093_C

description: Experimental Replicate A


title: AGM_3


title: DNA10204-089A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-089A

value: Caucasian

value: Female


title: RNA from  MIAPaCa-2  cell line

description: pancreatic cancer cell line

source_name: MIAPACA

value: MIAPACA

value: male


title: DNA10204-087A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-087A

value: healthy


title: AGM_1


title: RNA from  HPAF-II  cell line

description: pancreatic cancer cell line

source_name: HPAFII

value: HPAFII


title: DNA10204-081A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-081A


title: DNA10204-083A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-083A


title: DNA10204-077A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-077A


title: HEK-293 miR-107 Experimental Replicate B 1521406066_B

description: Experimental Replicate B

value: miR-107 overexpression


title: SHAM JBM940

city: Oslo

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

country: Norway

institute: University of Oslo

description: SHAM

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with the R/Bioconductor package gcrma

source_name: left ventricular myocardium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seven weeks old male C57BL/6 mice were subjected to aortic banding (AB) or sham operation (sAB), with sacrifice 4 weeks after banding. Prior to sacrifice, cardiac function and geometry were evaluated by echocardiography.

extract_protocol: Total RNA was isolated with an RNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: Following saccrifice,  the left ventricle was separated from the right ventricle and the atria and snap frozen in liquid nitrogen and stored in a superfreezer untill processing.

tag: strain

value: left ventricular myocardium

tag: starting left ventricular weight (mg)

tag: right ventricle weight (mg)

tag: lung weight (mg)

tag: tibia length (mm)

tag: ending left ventricular weight (mg)

tag: ltindex

value: SHAM

tag: outcome


title: RNA from  HPAC  cell line

description: pancreatic cancer cell line

source_name: HPAC

value: HPAC

value: pancreatic ductal adenocarcinoma

value: cancer


title: DNA10204-079A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-079A


title: SHAM JBM504

description: SHAM


title: RNA from  Hs766T  cell line

description: pancreatic cancer cell line

value: pancreatic adenocarcinoma


title: HEK-293 control Experimental Replicate A 1521406093_A

description: Experimental Replicate A

value: control


title: DNA10204-075A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-075A


title: SHAM JBM821

description: SHAM


title: RNA from  CFPAC-1  cell line

description: pancreatic cancer cell line


title: HeLa DNAzyme miR-181b Experimental Replicate A 1521406066_G

description: Experimental Replicate A

source_name: HeLa

value: DNAzyme miR-181b inhibition

value: HeLa


title: HEK-293 miR-107 Experimental Replicate A 1521406093_B

description: Experimental Replicate A


title: DNA10204-073A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-073A

value: Whole blood

value: Male


title: HeLa anti-miR-9-3p Experimental Replicate B 1521406066_F

description: Experimental Replicate B


title: HEK-293 control Experimental Replicate B 1521406066_A

description: Experimental Replicate B


title: HeLa anti-miR-9-3p Experimental Replicate A 1521406103_D

description: Experimental Replicate A


title: RNA from  Capan-2  cell line

description: pancreatic cancer cell line


title: DNA10204-071A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-071A

value: Caucasian


title: RNA from  Capan-1  cell line

description: pancreatic cancer cell line


title: SHAM JBM493

description: SHAM


title: RNA from  BxPC-3  cell line

description: pancreatic cancer cell line

value: female


title: SHAM JBM499

description: SHAM


title: DNA10204-069A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-069A

value: Female


title: HeLa miR-9-3p Experimental Replicate A 1521406103_C

description: Experimental Replicate A

value: miR-9-3p overexpression


title: HeLa control Experimental Replicate A 1521406103_B

description: Experimental Replicate A


title: RNA from  AsPC-1 cell line

description: pancreatic cancer cell line


title: Aorta banding - heart failure JBM946

description: Aorta banding - heart failure

value: Aorta banding

value: heart failure


title: Aorta banding - heart failure JBM943

description: Aorta banding - heart failure

value: left ventricular myocardium


title: DNA10204-065A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-065A

value: healthy


title: Aorta banding - heart failure JBM799

description: Aorta banding - heart failure


title: HeLa anti-miR-218 Experimental Replicate A 1521406103_A

description: Experimental Replicate A


title: DNA10204-063A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-063A


title: HeLa miR-218 Experimental Replicate A 1521406091_H

description: Experimental Replicate A

value: miR-218 overexpression


title: Aorta banding - heart failure JBM795

description: Aorta banding - heart failure


title: Aorta banding - heart failure JBM496

description: Aorta banding - heart failure


title: HeLa control Experimental Replicate A 1521406091_G

description: Experimental Replicate A


title: C57BL/6_3

city: Berkeley

first: Antoine

middle: M

last: Snijders

state: CA

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

description:
expt4_C57BL.6_sham_0cGy_10hr_5500144057138060309311_Mouse_HTA_4.1_Image.C08
Gene expression data from cardiac blood of unirradiated mice

hyb_protocol: 1ug of total RNA was reverse transcribed with an oligo-dT primer containing a T7 RNA polymerase using the cDNA synthesis system.  Biotin-labeled cRNA was generated using cDNA as input.  All hybridization, washing and scanning steps were performed according to Affymetrix recommendations.

scan_protocol: An HT Plate Scanner was used following manufacturer's recommendation.

data_processing: Robust multi-array average (RMA) was then used to create an expression matrix from Affymetrix data. The normalized unscaled standard error (NUSE) plot was generated to visualize the chip-wise distribution of standard error estimates obtained for each gene on each array when performing the robust multichip probe-level fit. Any array with the upper quartile NUSE value greater than 1.10 was removed from the analysis. A statistical hypothesis testing method based on moderated t-statistic is used for detecting differential expression, which is implemented through the R limma package.

source_name: Cardiac blood_non-irradiated C57BL/6

label_protocol: Total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.

growth_protocol: Female, virgin C57BL/6 and BALB/c mice (~6 weeks old; Harlan Laboratories, Livermore, CA) were acclimatized for 2 weeks, and the study was carried out in strict accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health.

extract_protocol:
Blood was collected from the heart into a heparinized syringe and immediately transferred to RNA later (Ambion). RNA was isolated using the Blood- Ribopure blood kit (Ambion) followed by Globin clear kit following the manufacturer’s recommendations.
Mammary tissues were snap frozen in liquid nitrogen within 10 minutes of the euthanasia procedure. Total RNA was isolated by homogenizing the frozen tissue in Trizol reagent (Invitrogen) followed by phase separation using chloroform. RNA was further purified by Qiagen’s RNeasy mini kit (74104) and DNA was removed using Qiagen’s DNase free kit (79254).

treatment_protocol: At 8 weeks of age, mice (n=6 per group) were exposed to 4 weekly doses of (a) 7.5 cGy, (b) 1.8 Gy, or (c) sham, using a Pantak 320 kVp X-ray machine, operated at 300 kV (2 mA and 196 mGy/min for low dose, 10 mA and 783 mGy/min for high dose).

tag: strain background

value: 9 wks

value: Caridac blood

tag: sample group

value: non-irradiated


title: C57BL/6_2

description:
expt4_C57BL.6_sham_0cGy_10hr_5500144057138060309311_Mouse_HTA_4.1_Image.B07
Gene expression data from cardiac blood of unirradiated mice

tag: age


title: DNA10204-059A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-059A

tag: ethnicity

tag: gender


title: Aorta banding - heart failure JBM937

description: Aorta banding - heart failure

tag: treatment


title: HeLa miR-181b Experimental Replicate A 1521406091_E

description: Experimental Replicate A

value: miR-181b overexpression


title: BALB/c_3

description:
expt4_BALB.c_sham_0cGy_10hr_5500144057138060309311_Mouse_HTA_4.1_Image.C04
Gene expression data from cardiac blood of unirradiated mice

source_name: Cardiac blood_non-irradiated BALB/c

value: BALB/c

tag: tissue


title: BALB/c_4

description:
expt4_BALB.c_sham_0cGy_10hr_5500144057138060309311_Mouse_HTA_4.1_Image.D05
Gene expression data from cardiac blood of unirradiated mice


title: Aorta banding - heart failure JBM494

description: Aorta banding - heart failure


title: HeLa control Experimental Replicate B 1521406103_G

description: Experimental Replicate B

value: control

tag: cell line

value: HeLa


title: C57BL/6_1

description:
expt4_C57BL.6_sham_0cGy_10hr_5500144057138060309311_Mouse_HTA_4.1_Image.A06
Gene expression data from cardiac blood of unirradiated mice


title: HeLa anti-miR-181b Experimental Replicate A 1521406091_F

description: Experimental Replicate A


title: Aorta banding - no heart failure JBM439

description: Aorta banding - no heart failure

value: no heart failure


title: DNA10204-057A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-057A

tag: disease state

value: Whole blood

value: North-African


title: HeLa miR-181b Experimental Replicate B 1521406103_H

description: Experimental Replicate B


title: Aorta banding - no heart failure JBM442

description: Aorta banding - no heart failure

tag: strain


title: Aorta banding - no heart failure JBM445

description: Aorta banding - no heart failure

tag: starting left ventricular weight (mg)


title: DNA10204-067A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-067A

value: Caucasian

value: Female


title: DNA10204-053A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-053A


title: C57BL/6_4

description:
expt4_C57BL.6_sham_0cGy_10hr_5500144057138060309311_Mouse_HTA_4.1_Image.D09
Gene expression data from cardiac blood of unirradiated mice

value: female


title: DNA10204-055A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-055A

value: Male


title: HeLa control Experimental Replicate A 1521406091_D

description: Experimental Replicate A


title: BALB/c_1

description:
expt4_BALB.c_sham_0cGy_10hr_5500144057138060309311_Mouse_HTA_4.1_Image.A02
Gene expression data from cardiac blood of unirradiated mice


title: Aorta banding - no heart failure JBM939

description: Aorta banding - no heart failure

value: left ventricular myocardium

tag: right ventricle weight (mg)

value: Aorta banding


title: DNA10204-051A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-051A

value: healthy


title: Aorta banding - no heart failure JBM812

description: Aorta banding - no heart failure

tag: lung weight (mg)


title: DNA10204-047A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-047A


title: DNA10204-049A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-049A


title: BALBc_sham_late_3

description:
expt6_BALB.c_sham_late_5500144057138060309308_Task_4504_308.H02
Gene expression data from mammary gland after sham radiation regimen

source_name: Mammary gland_BALB/c_1 month after sham regimen

value: 8 wks at start of radiation regimen

value: mammary gland proper (lymph node removed)

value: unexposed; four weekly sham exposures


title: Aorta banding - no heart failure JBM865

description: Aorta banding - no heart failure

tag: tibia length (mm)


title: BALBc_sham_late_2

description:
expt6_BALB.c_sham_late_5500144057138060309308_Task_4504_308.G01
Gene expression data from mammary gland after sham radiation regimen


title: HeLa miR-107 Experimental Replicate B 1521406103_F

description: Experimental Replicate B

value: miR-107 overexpression


title: BALBc_sham_early_3

description:
expt6_BALB.c_sham_early_5500144057138060309308_Task_4504_308.G04
Gene expression data from mammary gland after sham radiation regimen

source_name: Mammary gland_BALB/c_4hr after sham regimen

value: BALB/c


title: DNA10204-043A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-043A


title: DNA10204-045A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-045A


title: BALBc_sham_early_2

description:
expt6_BALB.c_sham_early_5500144057138060309308_Task_4504_308.F03
Gene expression data from mammary gland after sham radiation regimen


title: DNA10204-061A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-061A


title: HeLa control Experimental Replicate B 1521406103_E

description: Experimental Replicate B

value: control


title: HeLa miR-107 Experimental Replicate A 1521406091_B

description: Experimental Replicate A

value: HeLa


title: BALBc_sham_early_1

description:
expt6_BALB.c_sham_early_5500144057138060309308_Task_4504_308.D01
Gene expression data from mammary gland after sham radiation regimen


title: DNA10204-041A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-041A


title: Control LLC cells at pH 6.4 for 12 hr

city: Tokyo

first: Satoshi

last: Ishii

address: 7-3-1 Hongo, Bunkyo

department: Department of Biochem. & Mol. Biol.

institute: The University of Tokyo

hyb_protocol: 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual.  Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

scan_protocol: Scanning was performed in an Affymetrix GeneChip® Scanner 3000.

data_processing:
Global Normalization and Scaling have been applied by the Affymetrix GeneChip® Operating Software v1.4.
The scan values were normalized to make its average equal to 100.

source_name: Lewis lung carcinoma (LLC) cells

label_protocol: 2 µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5’-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3’ (Affymetrix).  Double-stranded cDNA was cleaned up by using the GeneChip® Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: TDAG8-LLC or control LLC cells were seeded onto 6-cm dishes at 5 × 10e5 cells/dish. On the next day, the medium was replaced with 0.1% BSA/DMEM at pH 7.4.

extract_protocol: Total RNA samples were extracted using RNeasy kit (QIAGEN) according to the manufacturer’s instructions

treatment_protocol: After 12-h serum starvation, cells were treated with 0.1% BSA/DMEM at pH 6.4 or 7.4 for 4 or 12 h.

tag: cell type

value: control LLC

tag: ph

value: at pH 6.4

tag: time point

value: 12 hr


title: D1 11:00 replicate 4b_pre EMF exposure

city: Cambridge

first: James

last: Metcalfe

address: 80 Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
SAMPLE 47
technical replicate-labelled extract (reference sample)

scan_protocol: Standard Illumina scanning protocol using the Beadarray reader.

data_processing: Beadstudio v.2.3.47 was used for processing the raw data and the Average method was used for normalization.  Averaged data were filtered for probes with detection pvalue < 0.01 in at least one sample.

source_name: immediately prior to ELF-EMF exposure

label_protocol: Biotinylated cRNA samples were prepared with the Illumina TotalPrep RNA Amplification kit from Ambion.

extract_protocol: The whole blood samples collected in PAXgene blood tubes were stored a 4C overnight and the RNA was extracted the next day with the PAXgene Blood RNA kit from QIAGEN according to the manufacturer's instructions, including the DNase treatment. A pooling strategy was used to detect significant responses that occur in most or all of the volunteers. Equal amounts of RNA (300 ng/sample) were pooled from the 17 RNA samples samples for each of the 40 time points on study days 1 to 4. The 260/280 nm ratio of all pools was > 2.0. The 40 pooled RNA samples were assayed by Agilent Bioanalyser for RNA Integrity Number (RIN) and all RIN values were >8.0 (38/40>9.0).

treatment_protocol: 17 healthy male subjects age 20 -30 each received an extremely low frequency electromagnetic field exposure (ELF-EMF) on study day 1 repeated on study day 3 (7 days later), a  sham exposure ( using counterwound coils in the 1 M cube exposure frames) on study day 2 (the day after study day 1) and a null exposure (no current through coils) on study day 4 (the day after study day 3). All exposures (ELF-EMF, sham or null) were for 2 h at 11.00 - 13.00. 10 ml blood samples were collected at each time point by cannula at 9.00, 11.00, 11.05, 11.10, 11.20,11.40, 12.20, 13.00, 15.00 and 17.00) and transfered directly into PAXgene blood tubes.

tag: tissue source

value: Healthy volunteers

value: male

value: 20-30 years

value: Peripheral blood

tag: study day

tag: time-point

value: immediately prior to ELF-EMF exposure


title: BALBc_lowdose_late_2

description:
expt6_BALB.c_LowDose_late_5500144057138060309308_Task_4504_308.E08
Gene expression data from mammary gland after low dose radiation regimen

source_name: Mammary gland_BALB/c_1 month after LD regimen

tag: strain background

value: female

tag: age

tag: sample group

value: low dose (LD); four weekly doses of 7.5 cGy


title: DNA10204-037A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-037A

value: healthy

tag: treatment

tag: tissue

value: Whole blood

tag: ethnicity

value: Caucasian

tag: gender

value: Female


title: Control LLC cells at pH 7.4 for 12 hr

tag: strain

value: at pH 7.4


title: Control LLC cells at pH 7.4 for 4 hr

value: 4 hr


title: HeLa control Experimental Replicate A 1521406091_A

description: Experimental Replicate A

value: control

tag: cell line

value: HeLa


title: Aorta banding - no heart failure JBM942

description: Aorta banding - no heart failure

value: left ventricular myocardium

tag: starting left ventricular weight (mg)

tag: right ventricle weight (mg)

tag: lung weight (mg)

tag: ending left ventricular weight (mg)

tag: ltindex

value: Aorta banding

tag: outcome

value: no heart failure


title: DNA10204-039A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-039A

tag: disease state


title: DNA10204-033A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-033A

value: Male


title: BALBc_lowdose_late_1

description:
expt6_BALB.c_LowDose_late_5500144057138060309308_Task_4504_308.E06
Gene expression data from mammary gland after low dose radiation regimen

value: BALB/c

value: 8 wks at start of radiation regimen

value: mammary gland proper (lymph node removed)


title: BALBc_sham_late_1

description:
expt6_BALB.c_sham_late_5500144057138060309308_Task_4504_308.A05
Gene expression data from mammary gland after sham radiation regimen

value: female

value: unexposed; four weekly sham exposures


title: LLC-TDAG8 cells at pH 7.4 for 12 hr

tag: cell type

tag: ph

tag: time point

value: 12 hr


title: BALBc_lowdose_early_4

description:
expt6_BALB.c_LowDose_early_5500144057138060309308_Task_4504_308.F12
Gene expression data from mammary gland after low dose radiation regimen

source_name: Mammary gland_BALB/c_4hr after LD regimen

tag: strain background

tag: age

tag: sample group

value: low dose (LD); four weekly doses of 7.5 cGy


title: D1 11:00 replicate 3a_pre EMF exposure

description:
SAMPLE 44
technical replicate-labelled extract (reference sample)

tag: tissue source

value: Healthy volunteers

value: male

value: 20-30 years

tag: tissue

value: Peripheral blood

tag: study day

tag: time-point

tag: treatment

value: immediately prior to ELF-EMF exposure


title: DNA10204-035A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-035A

value: healthy

value: Whole blood

tag: ethnicity

value: Caucasian

tag: gender

value: Female


title: D1 11:00 replicate 4a_pre EMF exposure

description:
SAMPLE 46
technical replicate-labelled extract (reference sample)


title: Control LLC cells before treatment

tag: strain

value: control LLC


title: DNA10204-031A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-031A


title: D1 11:00 replicate 3b_pre EMF exposure

description:
SAMPLE 45
technical replicate-labelled extract (reference sample)


title: Control LLC cells at pH 6.4 for 4 hr

value: at pH 6.4

value: 4 hr


title: LLC-TDAG8 cells at pH 7.4 for 4 hr

value: at pH 7.4


title: D1 11:00 replicate 2b_pre EMF exposure

description:
SAMPLE 43
technical replicate-labelled extract (reference sample)


title: D1 11:00 replicate 2a_pre EMF exposure

description:
SAMPLE 42
technical replicate-labelled extract (reference sample)


title: D1 11:00 replicate 1a_pre EMF exposure_re-analysis

description:
SAMPLE 2
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: D1 11:00 replicate 1b_pre EMF exposure

description:
SAMPLE 41
technical replicate-labelled extract (reference sample)


title: BALB/c_2

description:
expt4_BALB.c_sham_0cGy_10hr_5500144057138060309311_Mouse_HTA_4.1_Image.B03
Gene expression data from cardiac blood of unirradiated mice

value: BALB/c

value: female

value: 9 wks

value: Caridac blood

value: non-irradiated


title: BALBc_lowdose_early_2

description:
expt6_BALB.c_LowDose_early_5500144057138060309308_Task_4504_308.D10
Gene expression data from mammary gland after low dose radiation regimen

value: 8 wks at start of radiation regimen

value: mammary gland proper (lymph node removed)

value: low dose (LD); four weekly doses of 7.5 cGy


title: BALBc_lowdose_early_3

description:
expt6_BALB.c_LowDose_early_5500144057138060309308_Task_4504_308.E11
Gene expression data from mammary gland after low dose radiation regimen


title: BALBc_highdose_late_4

description:
expt6_BALB.c_HighDose_late_5500144057138060309308_Task_4504_308.G12
Gene expression data from mammary gland after high dose radiation regimen

source_name: Mammary gland_BALB/c_1 month after HD regimen

value: high dose (HD); four weekly doses of 1.8 Gy


title: LLC-TDAG8 cells before treatment


title: BALBc_lowdose_early_1

description:
expt6_BALB.c_LowDose_early_5500144057138060309308_Task_4504_308.C09
Gene expression data from mammary gland after low dose radiation regimen


title: DNA10204-025A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-025A

value: healthy


title: LLC-TDAG8 cells at pH 6.4 for 12 hr

value: 12 hr


title: DNA10204-023A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-023A

value: Whole blood

value: Caucasian


title: DNA10204-021A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-021A

value: Female


title: DNA10204-028A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-028A

value: Male


title: LLC-TDAG8 cells at pH 6.4 for 4 hr

value: at pH 6.4

value: 4 hr


title: D4 17:00_post NULL exposure

description:
SAMPLE 40
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: post NULL exposure

value: Healthy volunteers

value: male

value: 20-30 years

value: Peripheral blood

value: post NULL exposure


title: BALBc_highdose_late_2

description:
expt6_BALB.c_HighDose_late_5500144057138060309308_Task_4504_308.E10
Gene expression data from mammary gland after high dose radiation regimen

value: BALB/c

value: female

value: 8 wks at start of radiation regimen


title: BALBc_highdose_late_3

description:
expt6_BALB.c_HighDose_late_5500144057138060309308_Task_4504_308.F11
Gene expression data from mammary gland after high dose radiation regimen

value: mammary gland proper (lymph node removed)

value: high dose (HD); four weekly doses of 1.8 Gy


title: D4 15:00_post NULL exposure

description:
SAMPLE 39
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: DNA10204-019A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-019A

value: healthy


title: D4 13:00_NULL exposure

description:
SAMPLE 38
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: NULL exposure

value: NULL exposure (50 Hz EMF of 0.085 ± 0.01 μT for 2hr)


title: BALBc_highdose_late_1

description:
expt6_BALB.c_HighDose_late_5500144057138060309308_Task_4504_308.D09
Gene expression data from mammary gland after high dose radiation regimen


title: DNA10204-015A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-015A

source_name: Healthy individual, in the absence of any treatment

value: Whole blood

value: Caucasian


title: BALBc_highdose_early_2

description:
expt6_BALB.c_HighDose_early_5500144057138060309308_Task_4504_308.F08
Gene expression data from mammary gland after high dose radiation regimen

source_name: Mammary gland_BALB/c_4hr after HD regimen


title: D4 11:20_NULL exposure

description:
SAMPLE 35
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: DNA10204-011A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-011A

value: Female


title: DNA10204-007A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-007A


title: BALBc_highdose_early_3

description:
expt6_BALB.c_HighDose_early_5500144057138060309308_Task_4504_308.G06
Gene expression data from mammary gland after high dose radiation regimen


title: D4 12:20_NULL exposure

description:
SAMPLE 37
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: BALBc_highdose_early_4

description:
expt6_BALB.c_HighDose_early_5500144057138060309308_Task_4504_308.H08
Gene expression data from mammary gland after high dose radiation regimen


title: HeLa anti-miR-107 Experimental Replicate A 1521406091_C

description: Experimental Replicate A

tag: cell line

value: HeLa


title: C57BL6_sham_late_2

description:
expt5_C57BL.6_sham_late_5500144057138060309306_Task_4507_306.F02
Gene expression data from mammary gland after sham radiation regimen

source_name: Mammary gland_C57BL/6_1 month after sham regimen

value: unexposed; four weekly sham exposures


title: C57BL6_sham_late_3

description:
expt5_C57BL.6_sham_late_5500144057138060309306_Task_4507_306.G01
Gene expression data from mammary gland after sham radiation regimen


title: D4 11:10_NULL exposure

description:
SAMPLE 34
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: Healthy volunteers


title: C57BL6_sham_late_4

description:
expt5_C57BL.6_sham_late_5500144057138060309306_Task_4507_306.H02
Gene expression data from mammary gland after sham radiation regimen


title: D4 11:40_NULL exposure

description:
SAMPLE 36
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: male


title: DNA10204-013A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-013A


title: DNA10204-017A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-017A


title: DNA10204-003A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-003A


title: DNA10204-005A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-005A


title: BALBc_highdose_early_1

description:
expt6_BALB.c_HighDose_early_5500144057138060309308_Task_4504_308.F07
Gene expression data from mammary gland after high dose radiation regimen


title: D4 09:00_pre NULL exposure

description:
SAMPLE 31
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: pre NULL exposure

value: 20-30 years

value: pre NULL exposure


title: D4 11:00_pre NULL exposure

description:
SAMPLE 32
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: Peripheral blood


title: D4 11:05_NULL exposure

description:
SAMPLE 33
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: C57BL6_sham_late_1

description:
expt5_C57BL.6_sham_late_5500144057138060309306_Task_4507_306.A05
Gene expression data from mammary gland after sham radiation regimen


title: DNA10204-001A Whole blood sample, healthy individual, no treatment

description:
Whole blood sample, healthy individual, no treatment
DNA10204-001A

value: Male


title: D3 17:00_post EMF exposure

description:
SAMPLE 30
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: post ELF-EMF exposure

value: post ELF-EMF exposure


title: CD11b24

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

hyb_protocol: Standard Affymetrix protocol for U133 Plus 2.0 Arrays

data_processing: Affymetrix .cel raw data files were normalized using RMA. All data processing was performed using R and the Bioconductor package. Informative, valid probe sets were determined using FARMS (Tolloen et al., 2007, Bioinformatics 23:2897-2902). FARMS represents an unbiased approach to remove non-informative probe sets based on their intra-probe set correlation.

label_protocol: Nugen Ovation biotin labeling system using manufacturer's protocol

growth_protocol: RNA was extracted immediately following sort. No growth in vitro.

extract_protocol: Total RNA was extracted using RNeasy (Qiagen) and amplified using 3 -biased ribo-SPIA (NuGen Ovation), according to the manufacturer's instructions.

treatment_protocol: All tissue were treated similarly, following dissociation, cells were plated overnight in serum-free media and then sorted the next day for each antigen.

tag: patientid

tag: tissue type

value: adult brain

tag: brain region

value: WM

tag: pathology

value: epilepsy

tag: sortfraction

value: pos


title: CD11b23

scan_protocol: Standard Affymetrix protocol for U133 Plus 2.0 Arrays


title: Mature pollen, biological rep2

city: Ottawa

first: Frances

last: Tran

address: 960 Carling Avenue

institute: Agriculture & Agri-Food Canada

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Pollen_MPG2

hyb_protocol: Chip hybridization for Affymetrix Wheat GeneChips was performed at McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com)

scan_protocol: Wheat GeneChips were scanned by the McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com)

data_processing: The data was normalized using the Robust Multichip Average (RMA) normalization algorithm which include background correction, quantile normalization, and a median polish summarization.  The data was analyzed using ArrayStar4 (DNAstar) software package.

organism: Secale cereale x Triticum turgidum subsp. durum

source_name: Tritcale mature pollen

label_protocol:
Biotinylated  cRNA was synthesized according to standard Affymetrix protocol using the one-cycle  Eukaryotic Target labeling kit from 5ug total RNA
Labelling for Affymetrix Wheat GeneChips was performed at McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com)

growth_protocol: Plants maintained in temperature controlled growht chamber at 20°C (day) and 18°C (night) under photoperiod of 16 h light. Plants held at a constant humidity of 70% and fertilized bi-weekly with 20-20-20 NPK.

extract_protocol: CsCl extraction of total RNA for Anther, Ovary, and Stigma @ (TCP) as well as MPG was performed according to Tran et al.  Rneasy plant minikit extraction of total RNA and subsequent DNA clean up using InviTrap® Spin Cell Plant RNA Mini kit was performed according to manufacturer's protocol for Anther, Ovary, and Stigma @ stage UNM, BCP.PicoPureTM RNA Isolation kit including the DNase treatment was performed according to manufacturer's protocol on Anther, Ovary, and Stigma tissues @ TET stage.

value: Pollen

tag: developmental stage

value: mature pollen grain


title: C57BL6_sham_early_3

description:
expt5_C57BL.6_sham_early_5500144057138060309306_Task_4507_306.F03
Gene expression data from mammary gland after sham radiation regimen

source_name: Mammary gland_C57BL/6_4hr after sham regimen

tag: strain background

value: female

tag: age

value: 8 wks at start of radiation regimen

value: mammary gland proper (lymph node removed)


title: Mature pollen, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Pollen_MPG3


title: C57BL6_sham_early_2

description:
expt5_C57BL.6_sham_early_5500144057138060309306_Task_4507_306.E02
Gene expression data from mammary gland after sham radiation regimen

tag: sample group

value: unexposed; four weekly sham exposures


title: Mature pollen, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Pollen_MPG1

tag: tissue


title: D3 12:20_EMF exposure

description:
SAMPLE 27
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: ELF-EMF exposure

tag: tissue source

value: Healthy volunteers

tag: study day

value: ELF-EMF exposure (50 Hz EMF of 62.0 ± 7.1 μT for 2h)


title: D3 13:00_EMF exposure

description:
SAMPLE 28
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: male

value: 20-30 years

tag: time-point

tag: treatment


title: Stigma tricellular pollen, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_TCP3

source_name: Triticale stigmas at tricellular pollen developmental stage

value: Stigma

value: tri-cellular pollen


title: CTX_unsorted21

source_name: unsorted

value: CTX


title: WM_unsorted19

value: adult brain


title: Stigma tricellular pollen, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_TCP2


title: CTX_A2B5pos22


title: Ovary tricellular pollen, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_TCP2

source_name: Triticale ovaries at tricellular pollen developmental stage

value: Ovary


title: Stigma tricellular pollen, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_TCP1


title: WM_A2B5pos18

value: WM

value: epilepsy


title: C57BL6_lowdose_late_1

description:
expt5_C57BL.6_LowDose_late_5500144057138060309306_Task_4507_306.E06
Gene expression data from mammary gland after low dose radiation regimen

source_name: Mammary gland_C57BL/6_1 month after LD regimen

tag: gender

value: low dose (LD); four weekly doses of 7.5 cGy


title: WM_A2B5pos20

value: pos


title: WM_unsorted17


title: D3 11:40_EMF exposure

description:
SAMPLE 26
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: Peripheral blood


title: D3 15:00_post EMF exposure

description:
SAMPLE 29
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: post ELF-EMF exposure


title: C57BL6_lowdose_late_2

description:
expt5_C57BL.6_LowDose_late_5500144057138060309306_Task_4507_306.E08
Gene expression data from mammary gland after low dose radiation regimen

value: female

value: 8 wks at start of radiation regimen

value: mammary gland proper (lymph node removed)


title: Ovary tricellular pollen, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_TCP1


title: C57BL6_lowdose_late_3

description:
expt5_C57BL.6_LowDose_late_5500144057138060309306_Task_4507_306.F05
Gene expression data from mammary gland after low dose radiation regimen


title: D3 11:20_EMF exposure

description:
SAMPLE 25
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: Healthy volunteers

value: ELF-EMF exposure (50 Hz EMF of 62.0 ± 7.1 μT for 2h)


title: D3 11:10_EMF exposure

description:
SAMPLE 24
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: male

value: 20-30 years


title: Ovary tricellular pollen, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_TCP3

value: tri-cellular pollen


title: C57BL6_sham_early_1

description:
expt5_C57BL.6_sham_early_5500144057138060309306_Task_4507_306.D01
Gene expression data from mammary gland after sham radiation regimen

value: unexposed; four weekly sham exposures


title: C57BL6_lowdose_late_4

description:
expt5_C57BL.6_LowDose_late_5500144057138060309306_Task_4507_306.G07
Gene expression data from mammary gland after low dose radiation regimen


title: D3 11:00_pre EMF exposure

description:
SAMPLE 22
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: pre ELF-EMF exposure

value: pre ELF-EMF exposure


title: CTX_unsorted16

value: adult brain

value: CTX


title: D3 11:05_EMF exposure

description:
SAMPLE 23
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: C57BL6_lowdose_early_3

description:
expt5_C57BL.6_LowDose_early_5500144057138060309306_Task_4507_306.E11
Gene expression data from mammary gland after low dose radiation regimen

source_name: Mammary gland_C57BL/6_4hr after LD regimen


title: WM_unsorted14

value: WM

value: epilepsy


title: Anther tricellular pollen, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_TCP3

source_name: Triticale anthers at tricellular pollen developmental stage

value: Anther


title: D3 09:00_pre EMF exposure

description:
SAMPLE 21
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: Peripheral blood


title: C57BL6_lowdose_early_2

description:
expt5_C57BL.6_LowDose_early_5500144057138060309306_Task_4507_306.D10
Gene expression data from mammary gland after low dose radiation regimen

value: low dose (LD); four weekly doses of 7.5 cGy


title: C57BL6_lowdose_early_4

description:
expt5_C57BL.6_LowDose_early_5500144057138060309306_Task_4507_306.F12
Gene expression data from mammary gland after low dose radiation regimen

value: female


title: CTX_A2B5pos15

value: pos


title: Anther tricellualr pollen, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_TCP2


title: CTX_unsorted12


title: D2 15:00_post SHAM exposure

description:
SAMPLE 19
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: post SHAM exposure

value: post SHAM exposure


title: Stigma bicellular pollen, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_BCP3

source_name: Triticale stigmas at bicelular pollen developmental stage

label_protocol:
Biotinylated  cRNA was synthesized according to standard Affymetrix protocol using the 3'IVT  Express kit from 1ug total RNA
Labelling for Affymetrix Wheat GeneChips was performed at McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com)

value: Stigma

value: bi-cellular pollen


title: Anther tricellular pollen, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_TCP1


title: D2 12:20_SHAM exposure

description:
SAMPLE 17
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: SHAM exposure

value: Healthy volunteers

value: male

value: SHAM exposure (50 Hz EMF of 0.21 ± 0.05 μT for 2h)


title: D2 13:00_SHAM exposure

description:
SAMPLE 18
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: 20-30 years


title: C57BL6_highdose_late_3

description:
expt5_C57BL.6_HighDose_late_5500144057138060309306_Task_4507_306.F11
Gene expression data from mammary gland after high dose radiation

source_name: Mammary gland_C57BL/6_1 month after HD regimen

value: 8 wks at start of radiation regimen

value: mammary gland proper (lymph node removed)

value: high dose (HD); four weekly doses of 1.8 Gy


title: C57BL6_highdose_late_4

description:
expt5_C57BL.6_HighDose_late_5500144057138060309306_Task_4507_306.G12
Gene expression data from mammary gland after high dose radiation


title: D2 17:00_post SHAM exposure

description:
SAMPLE 20
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: CTX_A2B5pos11

value: adult brain

value: CTX


title: D2 11:40_SHAM exposure

description:
SAMPLE 16
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: WM_A2B5pos13

value: WM

value: epilepsy


title: C57BL6_lowdose_early_1

description:
expt5_C57BL.6_LowDose_early_5500144057138060309306_Task_4507_306.C09
Gene expression data from mammary gland after low dose radiation regimen

value: low dose (LD); four weekly doses of 7.5 cGy


title: C57BL6_highdose_late_2

description:
expt5_C57BL.6_HighDose_late_5500144057138060309306_Task_4507_306.E10
Gene expression data from mammary gland after high dose radiation

value: female


title: Stigma bicellular pollen, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_BCP2


title: Stigma bicellular pollen, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_BCP1


title: Ovary bicellular pollen, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_BCP3

source_name: Triticale ovaries at bicellular pollen developmental stage

value: Ovary


title: D2 11:20_SHAM exposure

description:
SAMPLE 15
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: Peripheral blood


title: C57BL6_highdose_early_4

description:
expt5_C57BL.6_HighDose_early_5500144057138060309306_Task_4507_306.H08
Gene expression data from mammary gland after high dose radiation

source_name: Mammary gland_C57BL/6_4hr after HD regimen


title: WM_unsorted10


title: C57BL6_highdose_late_1

description:
expt5_C57BL.6_HighDose_late_5500144057138060309306_Task_4507_306.D09
Gene expression data from mammary gland after high dose radiation


title: D2 11:00_pre SHAM exposure

description:
SAMPLE 12
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: pre SHAM exposure

value: pre SHAM exposure


title: WM_A2B5pos9

value: pos


title: D2 11:05_SHAM exposure

description:
SAMPLE 13
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: Healthy volunteers


title: C57BL6_highdose_early_3

description:
expt5_C57BL.6_HighDose_early_5500144057138060309306_Task_4507_306.G06
Gene expression data from mammary gland after high dose radiation


title: C57BL6_highdose_early_2

description:
expt5_C57BL.6_HighDose_early_5500144057138060309306_Task_4507_306.F08
Gene expression data from mammary gland after high dose radiation


title: GLT1neg5

value: Epilepsy

value: neg


title: Ovary bicellular pollen, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_BCP2

value: bi-cellular pollen


title: Anther bicellular pollen, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_BCP2

source_name: Triticale anthers at bicellular pollen developmental stage

value: Anther


title: Ovary bicellular pollen, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_BCP1


title: C57BL6_highdose_early_1

description:
expt5_C57BL.6_HighDose_early_5500144057138060309306_Task_4507_306.F07
Gene expression data from mammary gland after high dose radiation

value: 8 wks at start of radiation regimen

value: mammary gland proper (lymph node removed)


title: D2 09:00_pre SHAM exposure

description:
SAMPLE 11
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: male

value: 20-30 years


title: Anther bicellular pollen, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_BCP3


title: GLT1pos6

value: adult brain

value: CTX

value: Diffuse Astrocytoma


title: CD11b8

value: WM

value: epilepsy


title: D2 11:10_SHAM exposure

description:
SAMPLE 14
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: Peripheral blood

value: SHAM exposure (50 Hz EMF of 0.21 ± 0.05 μT for 2h)


title: GLT1pos4

value: pos


title: D1 17:00_post EMF exposure

description:
SAMPLE 10
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: post ELF-EMF exposure

value: Healthy volunteers

value: post ELF-EMF exposure


title: Anther bicellular pollen, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_BCP1


title: D1 15:00_post EMF exposure

description:
SAMPLE 9
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: Stigma uninucleate, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_UNM3

source_name: Triticale stigmas at uninucleate microspore developmental stage

value: Stigma

value: uninucleate microspore


title: Stigma uninucleate, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_UNM2


title: L-1236 tGFP/EBF1 rep2

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

description: sorted tGFP-positive cells

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project. Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: L-1236 tGFP/EBF1

label_protocol: Samples were labelled with WT terminal labelling Kit (Affymetrix, Fremont, USA), washed and stained using the HWS Kit (Affymetrix).

growth_protocol: Cell lines were purchased from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal calf serum (Biochrom; Berlin, Germany), 2 mM glutamine (Invitrogen; Groningen, The Netherlands) and 1% penicillin G/streptomycin sulfate (Invitrogen).

extract_protocol: RNA from tGFP-positive cells was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA was amplified with the WT Expression Kit (Ambion, Austin, USA).

treatment_protocol: L-428 and L-1236 cells were transduced with tGPF-IRES-EBF1 or tGFP-only, cultured for eight days, and sorted according to their tGFP positivity.

tag: transduction


title: L-1236 tGFP/EBF1 rep3

description: sorted tGFP-positive cells

tag: cell line


title: D1 13:00_EMF exposure

description:
SAMPLE 8
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: ELF-EMF exposure

value: ELF-EMF exposure (50 Hz EMF of 62.0 ± 7.1 μT for 2h)


title: GLT1neg3

tag: patientid

value: Epilepsy

value: neg


title: GLT1pos2

tag: tissue type


title: D1 11:40_EMF exposure

description:
SAMPLE 6
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: male


title: L-1236 tGFP/EBF1 rep1

description: sorted tGFP-positive cells


title: GLT1neg7

tag: brain region


title: L-1236 tGFP rep2

description: sorted tGFP-positive cells

source_name: L-1236 tGFP

value: tGFP-only


title: D1 11:20_EMF exposure

description:
SAMPLE 5
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

value: 20-30 years


title: CD11b1

value: adult brain

tag: pathology


title: Stigma uninucleate, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_UNM1


title: L-1236 tGFP rep3

description: sorted tGFP-positive cells


title: L-428 tGFP/EBF1 rep3

description: sorted tGFP-positive cells

source_name: L-428 tGFP/EBF1


title: Ovary uninucleate, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_UNM2

source_name: Triticale ovaries at uninucleate microspore developmental stage

value: Ovary


title: D1 11:05_EMF exposure

description:
SAMPLE 3
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: Ovary uninucleate, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_UNM1


title: D1 12:20_EMF exposure

description:
SAMPLE 7
pooled RNA samples using equal amounts of RNA  from the 17 volunteers


title: Ovary uninucleate, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_UNM3