title: Chromosomal distribution of H3me2K9 in cd385-dh2.1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with H3me2K9 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385-dh2.1int.


title: Chromosomal distribution of Mis12 in cd385

status: Public on Nov 03 2013

type: genomic

city: Kami

first: Kojiro

last: Ishii

state: Kochi

address: 185 Miyanokuchi, Tosayamada

country: Japan

institute: Kochi University of Technology

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Mis12-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385.

hyb_protocol: Hybridisation was carried out at 65 °C for 40 h against the KU-LSI Schizosaccharomyces pombe genome tiling array 4x44K_v1.0 (Agilent Technologies) according to the manufacturer's instructions. The slide was then washed with Wash Buffer 1 for 5 min at room temperature and with Wash Buffer 2 for 5 min at 31 ºC, according to the manufacturer's instructions (Agilent Technologies), in ozone-depleted surroundings.

scan_protocol: Microarray slides were scanned using the Agilent Microarray Scanner G2505B and Scan Control Software G2565BA, followed by extraction of information from the probe features using Agilent Feature Extraction Software 9.5.1.1.

data_processing: For each data set, intra-array Lowess (intensity-dependent) normalization was performed using the Agilent ChIP Analytics Software 1.3.1, and the enrichment ratios were calculated by dividing the normalised ChIP (Cy5) signals over corresponding WCE (Cy3) signals.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Mis12-GFP

label_protocol: ChIP-purified DNA was treated with RNase A, flush-ended using T4 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy5-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.

growth_protocol: Cells were fixed with 3% formaldehyde at 18 °C for 35 min. The fixation reaction was terminated by adding 330 mM final concentration of glycine and incubating for 10 min. The cells were collected by centrifugation and washed 3 times with 1x PBS.

extract_protocol: Cell lysates were prepared by glass bead vortexing in FA-lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1x Complete) containing 0.5% SDS. The cross-linked chromatin was then pelleted by centrifuging the lysate, and after a wash with ice-cold FA-lysis buffer containing 0.1% SDS, the chromatin pellet was sonicated to yield soluble fragments with an average size of 500 bp and a range between 300 and 1000 bp. The reaction was clarified by centrifugation, and the chromatin solution was supplemented with 1% Triton X-100. To elute DNA and revert cross-links, the beads were incubated with SDS-TE (1% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA) for 15 h at 65 °C, followed by digestion with proteinase K at 42 °C. After extraction with phenol, DNA was precipitated with isopropanol and resuspended in TE.

treatment_protocol: Exponentially growing fission yeast cells were asynchronously cultured at 33 °C in YES, and transferred to 18 °C for 2 h prior to fixation.

tag: cell type

value: neocentric

tag: strain

value: h- leu1 ura4 cen3D::kanR cd385

tag: genotype

tag: chip antibody

value: GFP

tag: antibody vendor

value: Roche

tag: antibody catalog#

tag: antibody lot#

source_name: Chromatin-input DNA (WCE) for Mis12-GFP

label_protocol: WCE DNA was treated with RNase A, flush-ended using T4 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy3-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.


title: Cholangio tumor sample 824T SNP6

city: Singapore

first: Ioana

last: Cutcutache

state: Singapore

address: 8 College Rd

department: Centre for Computational Biology

country: Singapore

institute: Duke-NUS

description: Hybridized to SNP6 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The data in each tumor raw CEL file was normalized using CRMA-v2 and TumorBoost, and then analyzed with version 2 of the ASCAT algorithm which simultaneously models the aberrant cell fraction, regions of copy number changes and allele counts. The matched non-malignant CEL file is used as a reference in this processing. For each heterozygous position found in the normal tissue, the minor allele frequency (BAF) and the log of the ratio of the total signal intensity in the tumor and matched non-tumor sample (Log R) were calculated for the tumor tissue. ASCAT determined the aberrant cell fraction and mean genomic ploidy that best fits these points.
LRR' = normalized logR value; 'normalized_BAF' = normalized B-allele frequency (after TumorBoost); 'nA' = copy number of allele A; 'nB' = copy number of allele B
**For the non-malignant tissue only the raw BAF value is provided, as this is the only information necessary for processing the tumor using TumorBoost and ASCAT.

label: Biotin

organism: Homo sapiens

source_name: Cholangio tumor sample 824T

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from patient specimens using Qiagen Blood and Cell Culture DNA kit (Qiagen, CA). Genomic DNA yield and quality were determined by Nanodrop ND1000 spectrophotometer (Thermo Scientific, MA) and further visually inspected by agarose gel electrophoresis.

tag: tissue

value: cholangio primary tumor tissue


title: Chromosomal distribution of Mis6 in cd385

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Mis6-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Mis6-GFP

source_name: Chromatin-input DNA (WCE) for Mis6-GFP


title: Mantle cell lymphoma  M022 Normal

status: Public on Nov 04 2013

city: Barcelona

first: Sílvia

last: Beà

state: Barcelona

address: Rossello, 153

department: HematoPathology

country: Spain

institute: Hospital Clinic

description: Hybridized to SNP 6.0

data_processing: Image data were analysed with Genotyping Console 4.0 to obtain the CEL data files, which were also exported to the Nexus Biodiscovery Edition for data analysis and visualization. Quality controls assessed by Genotyping Console included Contrast Quality Control (CQC>0.4) produced by Birdseed and Median of the Absolute values of all Pairwise Differences (MAPD<0.35). Tumour and normal DNA samples were analysed individually with the Nexus Biodiscovery Edition using the SNP-FASST2 segmentation algorithm and using segment reporting tool filters: minimum of 100 Kb minimum genomic size of a segment, as well as by visual inspection.

source_name: Normal

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic B cells obtained from peripheral blood and other tissues using the Qiagen Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

tag: gender

value: Female

tag: sample type

value: Normal genomic DNA

tag: subject

tag: disease state

value: Mantle cell lymphoma


title: Chromosomal distribution of Cnp1 in cd385-dh2.1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385-dh2.1int.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Cnp1

value: h- leu1 ura4 cen3D::kanR cd385-dh2.1

source_name: Chromatin-input DNA (WCE) for Cnp1


title: Mantle cell lymphoma  M010 Normal

description: Hybridized to SNP 6.0

value: Male


title: Fibroblasts-P63+KLF4 Replicate 2 (high calcium)

type: RNA

city: La Jolla

first: George

last: Sen

state: CA

address: 9500 GIlman Drive

department: Dermatology/CMM

country: USA

institute: UCSD

description: Cell transduced with p63+KLF4 expressing retrovirus (high calcium)

hyb_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

scan_protocol: Affymetrix HG-U133 2.0 plus arrays were performed at the UCSD Genechip Microarray Core Facility.

data_processing: PLIER

molecule: total RNA

source_name: FB-PK2 (high calcium)

growth_protocol: Fibroblasts were grown in DMEM with 10% FBS.

extract_protocol: Total RNA from cells was extracted using the RNeasy mini kit according to manufacturer's protocol.

treatment_protocol: Fibroblasts were transduced with LacZ or P63+KLF4. p63+KLF4 expressing cells were also treated +/- 1.2mM calcium.

value: Human Primary Fibroblasts

tag: treatment

value: transduced with p63+KLF4 expressing retrovirus and treated with high calcium


title: Fibroblasts-P63+KLF4 Replicate 1 (high calcium)

source_name: FB-PK1 (high calcium)

label_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)


title: Chromosomal distribution of H3me2K9 in cd385

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with H3me2K9 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for H3me2K9

value: abcam

source_name: Chromatin-input DNA (WCE) for H3me2K9


title: Cholangio tumor sample 77071507T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 77071507T


title: Cholangio tumor sample 23474504T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 23474504T


title: Cholangio tumor sample 2000123T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 2000123T


title: Cholangio non-malignant sample 00990196N SNP6

description: Hybridized to SNP6 array

value: cholangio non-malignant tissue


title: Fibroblasts-P63+KLF4 Replicate 2 (low calcium)

description: Cell transduced with p63+KLF4 expressing retrovirus (low calcium)

source_name: FB-PK2 (low calcium)

value: transduced with p63+KLF4 expressing retrovirus and treated with low calcium


title: Chromosomal distribution of Swi6 in cd385-vector

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Swi6 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385-vecint.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Swi6

value: h- leu1 ura4 cen3D::kanR cd385-vector

source_name: Chromatin-input DNA (WCE) for Swi6


title: Fibroblasts-P63+KLF4 Replicate 1 (low calcium)

source_name: FB-PK1 (low calcium)


title: Cholangio tumor sample 715T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 715T


title: Chromosomal distribution of Cnp1 in cd385

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385.


title: Chromosomal distribution of Cnp20 in cd385

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp20-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Cnp20-GFP

source_name: Chromatin-input DNA (WCE) for Cnp20-GFP


title: Chromosomal distribution of Cnp3 in cd385

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp3-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Cnp3-GFP

source_name: Chromatin-input DNA (WCE) for Cnp3-GFP


title: Fibroblasts-P63+KLF4 Replicate 2

description: Cell transduced with p63+KLF4 expressing retrovirus


title: Fibroblasts-P63+KLF4 Replicate 1

value: transduced with p63+KLF4 expressing retrovirus


title: Control, Fibroblasts-LacZ Replicate 2

description: Cell transduced with LacZ expressing retrovirus


title: Cholangio non-malignant sample 72600277N SNP6

description: Hybridized to SNP6 array


title: Control, Fibroblasts-LacZ Replicate 1

value: transduced with LacZ expressing retrovirus


title: Cholangio tumor sample 00990196T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 00990196T


title: Mantle cell lymphoma M010 Lymph Node

description: Hybridized to SNP 6.0

source_name: Lymph Node

value: Lymph Node

value: mononuclear cell preparations of leukemic B cells


title: Cholangio tumor sample 72600277T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 72600277T


title: Chromosomal distribution of Cnp1 in cd163

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen2 deletion survivor cd163

hyb_protocol: Hybridisation was carried out at 65 °C for 40 h against the LSI Schizosaccharomyces pombe genome tiling array 4x44K_v1.0 (Agilent Technologies) according to the manufacturer's instructions. The slide was then washed with Wash Buffer 1 for 5 min at room temperature and with Wash Buffer 2 for 5 min at 31 ºC, according to the manufacturer's instructions (Agilent Technologies), in ozone-depleted surroundings.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Cnp1

label_protocol: ChIP-purified DNA was treated with RNase A, flush-ended using T7 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy5-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.

growth_protocol: Cells were fixed with 3% formaldehyde at 18 °C for 35 min, and the fixation reaction was terminated by adding 330 mM final concentration of glycine and incubating for 10 min; the cells were collected by centrifugation and washed 3 times with 1x PBS.

extract_protocol: Cell lysates were prepared by glass bead vortexing in FA-lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1x Complete) containing 0.5% SDS. The cross-linked chromatin was then pelleted by centrifuging the lysate, and after a wash with ice-cold FA-lysis buffer containing 0.1% SDS, the chromatin pellet was sonicated to yield soluble fragments with an average size of 500 bp and a range between 300 and 1000 bp. The reaction was clarified by centrifugation, and the chromatin solution was supplemented with 1% Triton X-100 and applied for the immunoprecipitation using anti-Cnp1 (Takayama et al. (2008) Mol. Biol. Cell 19 682-690) and Dynabeads M-280 (Dynal). The beads were subsequently washed 3 times in ice-cold FA-lysis buffer containing 0.1% SDS and 1% Triton X-100; once in the same buffer containing 0.5 M NaCl; once in 10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, and 0.5% sodium deoxycholate; and once in TE (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). To elute DNA and revert cross-links, the beads were incubated with SDS-TE (1% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA) for 15 h at 65 °C, followed by digestion with proteinase K at 42 °C. After extraction with phenol, DNA was precipitated with isopropanol and resuspended in TE.

tag: neocentric cell; h90 leu1 ura4 cen2d

value: :kanR cd163 strain

source_name: Chromatin-input DNA (WCE) for Cnp1

label_protocol: WCE DNA was treated with RNase A, flush-ended using T7 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy3-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.


title: total mRNAs in a clinical sample at normal stage_N30+

status: Public on Nov 02 2013

city: Shanghai

first: Wenjuan

last: Mo

address: No. 220 Handan Road

department: School of Life Science

country: China

institute: Fudan University

description: SAMPLE m_N30+

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the cubic spline normalisation method built-in Illumina Beadchip process software.

label: biotin

source_name: cervix tissue at normal stage during CIN progression

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: For each clinical sample, it was grinded in liquid nitrogen, then the total RNA was extracted and purified using the RNeasy Mini kit following the manufacturer’s instructions. The isolated RNA was stored at -70C for the Illumina microarrays.

value: female

value: cervix

tag: disease stage

value: normal (adjacent tissue of early lesions)


title: total mRNAs in a clinical sample at normal stage_N90

description: SAMPLE m_N90


title: Mantle cell lymphoma M009 Peripheral Blood 5 years after diagnosis

description: Hybridized to SNP 6.0

source_name: Peripheral Blood

value: Female

value: Peripheral Blood

value: Mantle cell lymphoma


title: Mantle cell lymphoma  M009 Normal

description: Hybridized to SNP 6.0

source_name: Normal

value: Normal genomic DNA


title: Chromosomal distribution of Cnp1 in cd166

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen2 deletion survivor cd166

value: :kanR cd166 strain


title: total mRNAs in a clinical sample at normal stage_N23+

description: SAMPLE m_N23+


title: total mRNAs in a clinical sample at normal stage_N24+

description: SAMPLE m_N24+


title: total mRNAs in a clinical sample at normal stage_N180

description: SAMPLE m_N180


title: total mRNAs in a clinical sample at CIN I stage_N48

description: SAMPLE m_N48

source_name: cervix tissue at CIN I stage during CIN progression

value: cervical intraepithelial neoplasia (CIN) I


title: total mRNAs in a clinical sample at CIN I stage_N44

description: SAMPLE m_N44


title: total mRNAs in a clinical sample at normal stage_N50+

description: SAMPLE m_N50+


title: total mRNAs in a clinical sample at CIN I stage_C58

description: SAMPLE m_C58


title: total mRNAs in a clinical sample at CIN I stage_N46

description: SAMPLE m_N46


title: total mRNAs in a clinical sample at CIN I stage_N40

description: SAMPLE m_N40


title: total mRNAs in a clinical sample at CIN III stage_C71

description: SAMPLE m_C71

source_name: cervix tissue at CIN III stage during CIN progression

value: cervical intraepithelial neoplasia (CIN) III


title: Cholangio non-malignant sample 29150572N SNP6

description: Hybridized to SNP6 array

value: cholangio non-malignant tissue


title: total mRNAs in a clinical sample at CIN I stage_C35

description: SAMPLE m_C35


title: total mRNAs in a clinical sample at CIN I stage_N21

description: SAMPLE m_N21


title: total mRNAs in a clinical sample at CIN III stage_C25

description: SAMPLE m_C25


title: total mRNAs in a clinical sample at CIN III stage_C27

description: SAMPLE m_C27


title: total mRNAs in a clinical sample at CIN I stage_C59

description: SAMPLE m_C59


title: total mRNAs in a clinical sample at normal stage_N5+

description: SAMPLE m_N5+


title: Cholangio non-malignant sample 33587479N SNP6

description: Hybridized to SNP6 array


title: total mRNAs in a clinical sample at CIN III stage_C68

description: SAMPLE m_C68


title: Cholangio non-malignant sample 21914187N SNP6

description: Hybridized to SNP6 array


title: Cholangio non-malignant sample 2000861N SNP6

description: Hybridized to SNP6 array

source_name: Cholangio non-malignant sample 2000861N


title: total mRNAs in a clinical sample at CIN III stage_C34

description: SAMPLE m_C34


title: Cholangio tumor sample 29150572T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 29150572T

value: cholangio primary tumor tissue


title: total mRNAs in a clinical sample at CIN III stage_C31

description: SAMPLE m_C31


title: Cholangio non-malignant sample 17231203N SNP6

description: Hybridized to SNP6 array


title: total mRNAs in a clinical sample at CIN III stage_C54

description: SAMPLE m_C54


title: Mantle cell lymphoma M003 Peripheral Blood

description: Hybridized to SNP 6.0

value: Male


title: total mRNAs in a clinical sample at CIN I stage_C57

description: SAMPLE m_C57


title: corresponding adjacent non-neoplastic tissues-7754315072_L

city: beijing

first: Demin

last: Han

address: beijing  100730

institute: Beijing Tongren Hospital ofCapital Medical University

description: SAMPLE 20

data_processing: Illumina’s GenomeStudio v1 software with the default settings was used for Gene Expression analysis

source_name: larynx-corresponding adjacent non-neoplastic tissue

label_protocol: Biotinylated cRNA  was hybridized onto the HumanHT-12 v3 Expression BeadChip

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: male

tag: age

value: 64 years old

value: larynx

tag: tissue subtype

value: corresponding adjacent non-neoplastic tissues of sample 19


title: corresponding adjacent non-neoplastic tissues-7754315072_J

description: SAMPLE 18

value: 74 years old

value: corresponding adjacent non-neoplastic tissues of sample 17


title: cancer-T1N0M0-7754315072_K

description: SAMPLE 19

tag: tissue type

value: glottic type

value: laryngeal squamous cell carcinoma

tag: sample id


title: Cholangio non-malignant sample 2000123N SNP6

description: Hybridized to SNP6 array

source_name: Cholangio non-malignant sample 2000123N


title: corresponding adjacent non-neoplastic tissues-7754315072_D

description: SAMPLE 12

value: 55 years old

value: corresponding adjacent non-neoplastic tissues of sample 11


title: corresponding adjacent non-neoplastic tissues-7754315072_F

description: SAMPLE 14

value: 52 years old

value: corresponding adjacent non-neoplastic tissues of sample 13


title: corresponding adjacent non-neoplastic tissues-7754315072_H

description: SAMPLE 16

value: 56 years old

value: corresponding adjacent non-neoplastic tissues of sample 15


title: cancer-T2N0M0-7754315072_E

description: SAMPLE 13


title: cancer-T4N0M0-7754315072_G

description: SAMPLE 15


title: corresponding adjacent non-neoplastic tissues-7754315072_B

description: SAMPLE 10

value: 53 years old

value: corresponding adjacent non-neoplastic tissues of sample 9


title: cancer-T3N2M0-8104461027_E

description: SAMPLE 5


title: cancer-T2N0M0-7754315072_A

description: SAMPLE 9


title: cancer-T3N2M0-8104461027_G

description: SAMPLE 7

value: 66 years old


title: cancer-T3N0M0-7754315072_I

description: SAMPLE 17

value: male


title: corresponding adjacent non-neoplastic tissues-T4N2M0-8104461027_D

description: SAMPLE 4

value: 58 years old

value: corresponding adjacent non-neoplastic tissues of sample 3


title: cancer-T4N3M0-7754315072_C

description: SAMPLE 11

value: larynx

value: supraglottic type


title: corresponding adjacent non-neoplastic tissues-T4N2M0-8104461027_F

description: SAMPLE 6

value: corresponding adjacent non-neoplastic tissues of sample 5


title: cancer-T4N2M0-8104461027_C

description: SAMPLE 3


title: total microRNAs in a clinical sample at normal stage_N50+

description: SAMPLE mi_N50+

value: female

value: cervix

value: normal (adjacent tissue of early lesions)

tag: molecule subtype

value: miRNA


title: corresponding adjacent non-neoplastic tissues-T3N2M0-8104461027_H

description: SAMPLE 8

value: corresponding adjacent non-neoplastic tissues of sample 7


title: corresponding adjacent non-neoplastic tissues-T4N2M0-8104461027_B

description: SAMPLE 2

value: 71 years old

value: corresponding adjacent non-neoplastic tissues of sample 1


title: Cholangio tumor sample 17231203T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 17231203T

value: cholangio primary tumor tissue


title: Mantle cell lymphoma M016 Peripheral Blood

description: Hybridized to SNP 6.0

value: Female

value: Peripheral Blood

tag: cell type

value: mononuclear cell preparations of leukemic B cells

value: Mantle cell lymphoma


title: cancer-T4N2M0-8104461027_A

description: SAMPLE 1

value: male

value: laryngeal squamous cell carcinoma


title: total microRNAs in a clinical sample at normal stage_N90

description: SAMPLE mi_N90


title: total microRNAs in a clinical sample at normal stage_N23+

description: SAMPLE mi_N23+


title: BE2C_HOXC9_Doxy-_rep2

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

description: RNA expression value

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized, significance determined by ANOVA, and fold change calculated with the Partek Genomics Suite (Partek Inc., St. Louis, MO). Gene annotation enrichment analysis was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 and Ingenuity Pathways Analysis (IPA Ingenuity® Systems) for all significantly changed genes (≥ ±1.5 fold, P < 0.01).

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit

growth_protocol: BE(2)-C/Tet-Off/Myc-HOXC9 cells were cultured in a 1:1 mixture of DMEM and Ham’s nutrient mixture F12 supplemented with 10% fetal bovine serum (Invitrogen) in the presence or absence of doxycycline for 6 days.

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

tag: cell line

tag: tumor cell type

value: Neuroblastoma


title: BE2C_HOXC9_Doxy-_rep1

description: RNA expression value


title: BE2C_HOXC9_Doxy-_rep3

description: RNA expression value


title: total microRNAs in a clinical sample at normal stage_N24+

description: SAMPLE mi_N24+


title: total microRNAs in a clinical sample at normal stage_N180

description: SAMPLE mi_N180


title: Cholangio tumor sample 33587479T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 33587479T


title: total microRNAs in a clinical sample at normal stage_N5+

description: SAMPLE mi_N5+


title: total microRNAs in a clinical sample at CIN I stage_C59

description: SAMPLE mi_C59

value: cervical intraepithelial neoplasia (CIN) I


title: Folate deficient diet

city: Montreal

first: Moshe

last: Szyf

state: Quebec

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

department: Pharmacology

country: Canada

institute: McGill University

hyb_protocol: Array hybridization to the NimbleGen mouse 2.1 deluxe promoter array was carried out by Nimblegen..

scan_protocol: Scanning was performed by Nimblegen.

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

organism: Mus musculus

label_protocol: Both immunoprecipitated DNA and input DNA from MeDIP were amplified with the GenomePlex Complete Whole Genome Amplification Kit (Sigma, WGA2) according to the manufacturerâ€™s instructions. Cy3-dUTP and Cy5-dUTP were used by Nimblegen to label the input and bound factions, respectively.

extract_protocol: Genomic DNA was extracted with a DNeasy Mini Kit (Qiagen, Mississauga, Canada) from mouse sperm.

treatment_protocol: To minimize genetic noise the inbred C57BL/6 strain was used for generation of experimental males and for analysis of the sperm epigenome. Mice were housed under a controlled light/dark cycle and were provided with food and water ad libitum. All animal procedures were approved by the Animal Care and Use Committee of McGill University, Montreal. Dietary exposures began in utero. To generate experimental males, female C57BL/6 were fed either the folate sufficient (FS, 2mg folic acid/kg, n=69) diet (TD.01369, Harlan Laboratories, Madison, WI) or the folate deficient diet (FD, 0.3mg folic acid/kg, n=64) (TD.01546), two weeks prior to breeding with non-experimental C57BL/6 males that were fed regular mouse chow (8640 Rodent diet) (used only for breeding to generate experimental males). To breed C57BL/6 females, C57BL/6 males were brought to the femalesâ€™ cages at night and removed in the morning in order to limit consumption of the experimental diets by the males. Females were maintained on the experimental diets through pregnancy and lactation. From weaning at PND21, male pups were given the same experimental diet as their in utero exposure until sacrifice as adults.

tag: strain

value: sperm

value: 2-3 months

tag: chip antibody

value: 5-methylcytidine (BI-MECY-0100, Eurogentec, 10Âµg per immunoprecipitation tube)

tag: treatment protocol

value: Folate deficient diet


title: total microRNAs in a clinical sample at CIN I stage_N44

description: SAMPLE mi_N44

tag: gender

value: female

tag: tissue

value: cervix

value: miRNA


title: Mantle cell lymphoma M013 Lymph Node

description: Hybridized to SNP 6.0

value: Male

value: Lymph Node

tag: sample type

tag: subject

tag: disease state


title: total microRNAs in a clinical sample at CIN I stage_N40

description: SAMPLE mi_N40

tag: disease stage


title: Conjunctiva patient 4

first: Aihua

last: Hou

address: 11 Third Hospital Avenue, #06-18, SNEC Building

department: Ocular Surface Research Group

institute: Singapore Eye Research Institute

hyb_protocol: Sixty nanograms of labeled cRNA was hybridized onto Agilent SurePrint G3 human GE 8x60K microarray for 17h at 65◦C, 10 rpm in Agilent hybridization oven. After hybridization, the microarray slide is washed using gene expression wash buffer 1 for one minute at room temperature followed by gene expression wash buffer 2 for another minute

scan_protocol: plates were scanned on Agilent High Resolution Microarray scanner (C-model)

data_processing: Raw signal data was extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1). The microarray data was processed in Genespring gene expression. The feature extraction raw data was first summarized by computing the geometric mean, set thredshold raw signal to 1. After Logbase 2 transformation, percentile shift to 75th percentile (per chip normalization), baseline transform to median of all samples (per gene normalization). After that did quality control on probeset both Flag filtering (flag value: detected; entities where at least 100.0 percent of samples in any 1 out of 2 conditions have flags in detected.) and Expression filtering (lower cut-off: 20.0; upper cut-off: maximal value; entities where at least 100 percent of samples in any 1 out of 2 conditions have values within cut-off).

source_name: Conjunctiva patient 4

label_protocol: One-hundred nanograms of total RNA was labeled with Low Input Quick Amp Labeling Kit (One-Colour Microarray-based Gene Expression, Analysis Low Input Quick Amp Labeling). Total RNA was converted to double-stranded cDNA using oligo-dT primers and transcribed by T7 RNA polymerase to produce cyanine 3-CTP labeled cRNA

extract_protocol: Pterygium and conjunctiva tissue were minced using surgical scissors,and ground using pestle and mortar with liquid nitrogen, after that were put into TRIzol (Invitrogen)  and passed through 22G needles (Becton Dickenson). Homogenized tissues were subjected for RNA extraction with the RNeasy RNA extraction kit (Qiagen) according to manufacturer’s protocol.

tag: patient number

value: Conjunctiva


title: total mRNAs in a clinical sample at CIN III stage_C33

description: SAMPLE m_C33

value: cervical intraepithelial neoplasia (CIN) III


title: total microRNAs in a clinical sample at normal stage_N30+

description: SAMPLE mi_N30+

value: normal (adjacent tissue of early lesions)


title: BE2C_HOXC9_Doxy+_rep2

description: RNA expression value


title: BE2C_HOXC9_Doxy+_rep1

description: RNA expression value


title: Conjunctiva patient 5

source_name: Conjunctiva patient 5


title: Conjunctiva patient 1

source_name: Conjunctiva patient 1


title: BE2C_HOXC9_Doxy+_rep3

description: RNA expression value


title: Conjunctiva patient 2

source_name: Conjunctiva patient 2


title: total microRNAs in a clinical sample at CIN I stage_C58

description: SAMPLE mi_C58


title: total microRNAs in a clinical sample at CIN I stage_C57

description: SAMPLE mi_C57


title: Pterygium patient 5

source_name: Pterygium patient 5

value: Pterygium


title: Folate sufficient diet

value: male

tag: age

value: Folate sufficient diet


title: Pterygium patient 4

source_name: Pterygium patient 4


title: total microRNAs in a clinical sample at CIN I stage_N21

description: SAMPLE mi_N21


title: total microRNAs in a clinical sample at CIN I stage_C35

description: SAMPLE mi_C35


title: total microRNAs in a clinical sample at CIN III stage_C71

description: SAMPLE mi_C71


title: Cholangio tumor sample 2000861T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 2000861T

value: cholangio primary tumor tissue


title: Cholangio tumor sample 21914187T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 21914187T


title: total microRNAs in a clinical sample at CIN III stage_C25

description: SAMPLE mi_C25


title: Pterygium patient 2

source_name: Pterygium patient 2


title: total microRNAs in a clinical sample at CIN III stage_C68

description: SAMPLE mi_C68


title: total microRNAs in a clinical sample at CIN III stage_C31

description: SAMPLE mi_C31


title: Chemically treated, biological rep3

city: Gent

first: Pavel

last: Kerchev

address: Technologie Park 927

department: Plant Systems Biology

country: Belgium

institute: VIB

description: Gene expression data from seven-day-old Arabidopsis seedlings treated for 24 h with 5 μM 2-(2,4-dichlorophenoxy)-N-[4-(isobutyrylamino)-3-methoxyphenyl]propanamid

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: standard Affymetrix protocol

data_processing: Raw intensity values from the scanned Arabidopsis ATH1 Genome Arrays were processed using the Robust Multiarray Average (RMA) algorithm implemented in the Bioconductor package 'affy'

organism: Arabidopsis thaliana

source_name: Seven-day-old Arabidopsis seedlings treated for 24 h with 5 μM 2-(2,4-dichlorophenoxy)-N-[4-(isobutyrylamino)-3-methoxyphenyl]propanamid

label_protocol: 3’ IVT express kit (100 ng input)

growth_protocol: Gas sterilized Arabidopsis Col0 seeds were sown in a 96-well plate setup using half-strength Murashige and Skoog medium (0.2% sucrose; 250 μl medium per well; 5 seeds per well). Plants were grown under controlled environmental condition (16h/8h light/dark, 100 μmol m−2 s−1 light intensity, 21ºC, 70% relative humidity).

extract_protocol: Total RNA was extracted with RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 2-(2,4-dichlorophenoxy)-N-[4-(isobutyrylamino)-3-methoxyphenyl]propanamid was added to seven-day-old plants in a final concetration of 5 μM from 20 mM stock solution prepared with DMSO. Control plants were treated with equal amounts of DMSO. Seedlings from 24 wells were pooled in one sample.

tag: ecotype

value: Columbia 0

value: whole seedlings

tag: treatment


title: total microRNAs in a clinical sample at CIN III stage_C54

description: SAMPLE mi_C54

source_name: cervix tissue at CIN III stage during CIN progression

tag: molecule subtype


title: total microRNAs in a clinical sample at CIN III stage_C34

description: SAMPLE mi_C34


title: total microRNAs in a clinical sample at CIN III stage_C33

description: SAMPLE mi_C33


title: total microRNAs in a clinical sample at CIN III stage_C27

description: SAMPLE mi_C27


title: Chemically treated, biological rep1

value: treated for 24 h with 5 μM 2-(2,4-dichlorophenoxy)-N-[4-(isobutyrylamino)-3-methoxyphenyl]propanamid


title: Chemically treated, biological rep2


title: Solvent treated, biological rep1

description: Gene expression data from seven-day-old Arabidopsis seedlings treated for 24 h with DMSO

source_name: Seven-day-old Arabidopsis seedlings treated for 24 h with DMSO

value: treated for 24 h with DMSO


title: Solvent treated, biological rep2


title: Solvent treated, biological rep3


title: Lower Fraser_Pink Salmon_13°C_F_Array3_10390

status: Public on Nov 01 2013

city: Vancouver

first: Ken

last: Jeffries

state: British Columbia

address: 2424 Main Mall

institute: University of British Columbia

description:
raw data file (Ch1): Array3Ongo_09K_10390.txt
raw data file (Ch2): Array3Ongo_09K_10390ref.txt

hyb_protocol: Each fish examined in the array experiments was run on a single slide against a reference control that was a pool of RNA from all of the fish used in the experiment. Data was normalized using the print-tip LOESS method. Microarray data were expressed in terms of normalized (background corrected) log2 ratios between each fish and the reference control.  All slides were processed on Tecan-HS4800 Pro Hybridization Station (Tecan Trading AG, Switzerland). All steps from washing, hybridization, denaturation, and slide drying were carried out automatically.

scan_protocol: Fluorescent images were scanned using a Tecan LS Reloaded Scanner (Tecan Trading AG, Männedorf, Switzerland) and the analysis software Array-Pro Analyzer (Media Cybernetics, Inc., Bethesda, MD). The images were quantified using Imagene.

data_processing: Expression data were managed using a local installation of BASE. BASE was customized slightly to support Imagene two-file formatting. Each slide was normalized in BASE using the print-tip LOESS method. The number of missing values, mean signal-to-noise log-ratio and quality metrics from arrayQualityMetrics and arrayQuality in Bioconductor were used to assess slide quality.  Slides were removed from further experimental analysis if two or more plots were flagged on the arrayQualityMetrics report after data normalization, if more than 40% missing spots were identified by the SNR and missing spots report, if there were more than 30% missing spots and an experimentally low SNR value as identified by the SNR and missing spots report, or if the slide had spatial problems as identified by the plots from the arrayQuality package and substantiated by the spatial plots score of the raw microarray data in the arrayQualityMetrics report. The data for each retained slide was further processed to remove poor-quality spots. Flagged spots were treated as missing, as were spots with a SNR less than 2. In a set of slides considered a single data set, probes with more than 50% missing values were removed prior to statistical analysis. For procedures such as PCA that require matrices without missing values, missing data were imputed using an average of the existing probe intensities. The submitted data includes all probes and imputed data is not included.

label: Alexa 555

organism: Oncorhynchus gorbuscha

source_name: Gill tissue cool treatment

label_protocol: Total RNA (11 microlitres) was  used to make aaRNA and labelled with Alexa dyes using the Invitrogen Indirect Labelling Kit. The aaRNA samples were purified, lyophilized and eluted in 12 μl of DNAse/RNAse-free water prior to the dye coupling reactions. During dye labelling, samples were processed individually: DMSO was added to the Alexa dye tube, followed by aaDNA and incubated for 1h at room temperature. After a 1 h incubation at room temperature, the reactions were quenched using 4M hydroxylamine and the samples were purified, eluted in 35 μl of aaRNA elution buffer and quantified using a NanoDrop Spectrophotometer ND-1000. A standard reference design was used in the microarray experiments where the reference was comprised of a mixture of RNA from all individuals used in the study. All individual samples to be run on the arrays were fluorescently tagged with Alexa 555 and the mixed reference sample was labelled with Alexa 647. Prior to hybridization, dye labelled treatment and reference samples (825 ng each) were combined along with 1.2 μl 25X fragmentation buffer, 6 μl blocking agent and nuclease-free water to bring the final volume to 30 μl. The fragmentation mix was incubated at 60°C for 30 minutes and was stopped by adding 30 μl of 2X GEx hybridization buffer HI-RPM. Samples were briefly centrifuged, placed on ice and 55 μl of the mix was loaded into hybridization chambers in a Tecan-HS4800 Pro Hybridization Station.

extract_protocol: Freshly sampled gill tissues were quickly frozen in liquid nitrogen and stored at -80 degrees C until RNA extractions were performed. At each of the subsequent steps leading up to the hybridization of microarray slides, samples were randomized to minimize the impact of technical artefacts. The -80 degrees C samples were removed and processed immediately by adding 600 ml of TRI-reagent and one stainless steel 3 mm ball and homogenized using a Retsch MM301 mixer mill. RNA was extracted using a Biomek FXP automated liquid-handling instrument with the Ambion MagMax-96 for Microarrays Total RNA Isolation Kit, according to the manufacturer's instructions and robotic scripts. Total RNA  purity and quantity was assessed by measuring the A260/A280 ratio. Total RNA (11 microlitres) was used to make aaRNA using Ambion Amino Allyl MessageAmpTM II-96 kits. The aaRNA was made using two 96-well plates.

treatment_protocol: Lower Fraser pink salmon from the Fraser River, B.C., Canada, were exposed to either a warm (19C) or cool (13C) temperature treatment for 5 days.

tag: year

tag: temperature (c)

tag: run-timing group

value: Late-run

tag: stock

value: Lower Fraser

tag: Sex

value: gill

label: Alexa 647

organism:
Oncorhynchus gorbuscha
Oncorhynchus nerka

value: Reference


title: Lower Fraser_Pink Salmon_13°C_F_Array4_10365

description:
raw data file (Ch1): Array4Ongo_09K_10365.txt
raw data file (Ch2): Array4Ongo_09K_10365ref.txt

value: female

source_name: a pool of RNA from all of the fish used in the experiment


title: Lower Fraser_Pink Salmon_13°C_F_Array3_10374

description:
raw data file (Ch1): Array3Ongo_09K_10374.txt
raw data file (Ch2): Array3Ongo_09K_10374ref.txt


title: Lower Fraser_Pink Salmon_19°C_M_Array3_10391

description:
raw data file (Ch1): Array3Ongo_09K_10391.txt
raw data file (Ch2): Array3Ongo_09K_10391ref.txt

source_name: Gill tissue warm treatment


title: Lower Fraser_Pink Salmon_19°C_F_Array3_10384

description:
raw data file (Ch1): Array3Ongo_09K_10384.txt
raw data file (Ch2): Array3Ongo_09K_10384ref.txt


title: Lower Fraser_Pink Salmon_19°C_M_Array3_10428

description:
raw data file (Ch1): Array3Ongo_09K_10428.txt
raw data file (Ch2): Array3Ongo_09K_10428ref.txt


title: Lower Fraser_Pink Salmon_19°C_F_Array4_10431

description:
raw data file (Ch1): Array4Ongo_09K_10431.txt
raw data file (Ch2): Array4Ongo_09K_10431ref.txt


title: Lower Fraser_Pink Salmon_19°C_M_Array2_10432

description:
raw data file (Ch1): Array2Ongo_09K_10432.txt
raw data file (Ch2): Array2Ongo_09K_10432ref.txt


title: Lower Fraser_Pink Salmon_19°C_M_Array3_10373

description:
raw data file (Ch1): Array3Ongo_09K_10373.txt
raw data file (Ch2): Array3Ongo_09K_10373ref.txt


title: Lower Fraser_Pink Salmon_13°C_M_Array4_10428

description:
raw data file (Ch1): Array4Ongo_09K_10428.txt
raw data file (Ch2): Array4Ongo_09K_10428ref.txt


title: Lower Fraser_Pink Salmon_19°C_F_Array4_10397

description:
raw data file (Ch1): Array4Ongo_09K_10397.txt
raw data file (Ch2): Array4Ongo_09K_10397ref.txt


title: Lower Fraser_Pink Salmon_13°C_M_Array4_10385

description:
raw data file (Ch1): Array4Ongo_09K_10385.txt
raw data file (Ch2): Array4Ongo_09K_10385ref.txt


title: Lower Fraser_Pink Salmon_19°C_F_Array2_10433

description:
raw data file (Ch1): Array2Ongo_09K_10433.txt
raw data file (Ch2): Array2Ongo_09K_10433ref.txt


title: Lower Fraser_Pink Salmon_13°C_M_Array3_10394

description:
raw data file (Ch1): Array3Ongo_09K_10394.txt
raw data file (Ch2): Array3Ongo_09K_10394ref.txt


title: Lower Fraser_Pink Salmon_13°C_F_Array2_10431

description:
raw data file (Ch1): Array2Ongo_09K_10431.txt
raw data file (Ch2): Array2Ongo_09K_10431ref.txt


title: Lower Fraser_Pink Salmon_13°C_M_Array3_10388

description:
raw data file (Ch1): Array3Ongo_09K_10388.txt
raw data file (Ch2): Array3Ongo_09K_10388ref.txt


title: Lower Fraser_Pink Salmon_13°C_M_Array4_10377

description:
raw data file (Ch1): Array4Ongo_09K_10377.txt
raw data file (Ch2): Array4Ongo_09K_10377ref.txt


title: Lower Fraser_Pink Salmon_13°C_F_Array3_10386

description:
raw data file (Ch1): Array3Ongo_09K_10386.txt
raw data file (Ch2): Array3Ongo_09K_10386ref.txt


title: Lower Fraser_Pink Salmon_13°C_M_Array4_10399

description:
raw data file (Ch1): Array4Ongo_09K_10399.txt
raw data file (Ch2): Array4Ongo_09K_10399ref.txt


title: Lower Fraser_Pink Salmon_13°C_M_Array2_10399

description:
raw data file (Ch1): Array2Ongo_09K_10399.txt
raw data file (Ch2): Array2Ongo_09K_10399ref.txt


title: Lower Fraser_Pink Salmon_19°C_F_Array2_10388

description:
raw data file (Ch1): Array2Ongo_09K_10388.txt
raw data file (Ch2): Array2Ongo_09K_10388ref.txt


title: Lower Fraser_Pink Salmon_13°C_M_Array2_10391

description:
raw data file (Ch1): Array2Ongo_09K_10391.txt
raw data file (Ch2): Array2Ongo_09K_10391ref.txt


title: Lower Fraser_Pink Salmon_19°C_F_Array2_10389

description:
raw data file (Ch1): Array2Ongo_09K_10389.txt
raw data file (Ch2): Array2Ongo_09K_10389ref.txt


title: Pterygium patient 1

source_name: Pterygium patient 1


title: total microRNAs in a clinical sample at CIN I stage_N46

description: SAMPLE mi_N46

source_name: cervix tissue at CIN I stage during CIN progression

value: cervix

value: cervical intraepithelial neoplasia (CIN) I

value: miRNA


title: Lower Fraser_Pink Salmon_19°C_M_Array2_10385

description:
raw data file (Ch1): Array2Ongo_09K_10385.txt
raw data file (Ch2): Array2Ongo_09K_10385ref.txt


title: Lower Fraser_Pink Salmon_19°C_F_Array2_10376

description:
raw data file (Ch1): Array2Ongo_09K_10376.txt
raw data file (Ch2): Array2Ongo_09K_10376ref.txt


title: Lower Fraser_Pink Salmon_19°C_F_Array2_10386

description:
raw data file (Ch1): Array2Ongo_09K_10386.txt
raw data file (Ch2): Array2Ongo_09K_10386ref.txt


title: S.melongena_INFECTED_rep3

city: Fiorenzuola D'Arda

first: Paolo

last: Bagnaresi

address: Via S. Protaso 302

department: Genomics

country: Italy

institute: CRA-GPG

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20 min at 95 °C. Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as the following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST wash solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a Perkin Elmer ScanArray 4000XL and the accompanying acquisition software (ScanArray Express Microarray Analysis System v4.0). Multiple scanning at different PMT was provided for each hybridization.

data_processing: Data extraction was carried out using CombiMatrix Microarray Imager software, and a quantile normalization of raw medians and log2 transformation were performed using SPSS v.15.0 software. Further statistical processing was performed using the SAM analysis (T-MEV 4.3)

organism: Solanum virginianum

source_name: S. melongena  infected roots

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with the SuperScript™ Indirect RNA Amplification System Kit (Invitrogen) incorporating Alexa Fluor 647 Reactive Dye according to manufacturer's instructions

growth_protocol: Seeds of Solanum torvum Sw accession TG1 [1] and eggplant (Solanum melongena L.) breeding line 1F5(9) were sown in a seed-plot for germination. Seedlings about 10 cm tall at the second-leaf stage were singly transplanted into 10 cm diameter plastic pots, each containing 500 cc of mixture sterilized sandy soil: 70% sand+ 15% leca + 10% clay (sterilized at 70ｰC for 24 hours) + 5% organic matter. The pots were maintained in controlled chambers at 24ｱ2ｰC, 60% relative humidity, with a 16-h light/8-h dark regimen. Plants were watered with tap water at necessity and fertilized every two weeks with a 20-20-20 NPK fertilizer.

extract_protocol: total RNA samples were extracted   by means of the Nucleospin RNA plant Kit (MACHEREY-NAGEL GmbH & Co., Düren, Germany) at 0 and 14 dpi.

value: roots

tag: infection by nematode

value: infected


title: Lower Fraser_Pink Salmon_19°C_F_Array2_10372

description:
raw data file (Ch1): Array2Ongo_09K_10372.txt
raw data file (Ch2): Array2Ongo_09K_10372ref.txt


title: S.torvum_INFECTED_rep3

organism: Solanum torvum

source_name: S. torvum  infected roots


title: S.melongena_INFECTED_rep2


title: S.melongena_CTRL_rep3

source_name: S. melongena  control roots

value: no infection


title: Lower Fraser_Pink Salmon_13°C_F_Array2_10375

description:
raw data file (Ch1): Array2Ongo_09K_10375.txt
raw data file (Ch2): Array2Ongo_09K_10375ref.txt


title: S.torvum_INFECTED_rep1


title: S.melongena_INFECTED_rep1


title: Lower Fraser_Pink Salmon_13°C_F_Array2_10365

description:
raw data file (Ch1): Array2Ongo_09K_10365.txt
raw data file (Ch2): Array2Ongo_09K_10365ref.txt


title: Lower Fraser_Pink Salmon_13°C_F_Array1_10395

description:
raw data file (Ch1): Array1Ongo_09K_10395.txt
raw data file (Ch2): Array1Ongo_09K_10395ref.txt


title: S.melongena_CTRL_rep2


title: S.melongena_CTRL_rep1


title: Lower Fraser_Pink Salmon_19°C_M_Array2_10368

description:
raw data file (Ch1): Array2Ongo_09K_10368.txt
raw data file (Ch2): Array2Ongo_09K_10368ref.txt

value: male


title: S.torvum_CTRL_rep3

source_name: S. torvum  control roots


title: S.torvum_CTRL_rep1


title: Lower Fraser_Pink Salmon_19°C_F_Array1_10427

description:
raw data file (Ch1): Array1Ongo_09K_10427.txt
raw data file (Ch2): Array1Ongo_09K_10427ref.txt


title: Lower Fraser_Pink Salmon_13°C_F_Array1_10394

description:
raw data file (Ch1): Array1Ongo_09K_10394.txt
raw data file (Ch2): Array1Ongo_09K_10394ref.txt


title: S.torvum_CTRL_rep2


title: Lower Fraser_Pink Salmon_13°C_M_Array1_10393

description:
raw data file (Ch1): Array1Ongo_09K_10393.txt
raw data file (Ch2): Array1Ongo_09K_10393ref.txt


title: S.torvum_INFECTED_rep2


title: Lower Fraser_Pink Salmon_19°C_M_Array1_10397

description:
raw data file (Ch1): Array1Ongo_09K_10397.txt
raw data file (Ch2): Array1Ongo_09K_10397ref.txt


title: Primary Cortical Neurons-2_NanoString

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

description:
miRNA profiling
MG400 custom Nanostring codesets

data_processing: Data was proccessed using nSolver, normalized to positive control,  top 100 highly expressed miRNAs and negative controls

label: NanoString oligonucleotide tag

source_name: Primary Cortical Neurons

extract_protocol: Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol

tag: strain

value: Cortex

tag: cell type

value: Primary Neuron


title: Lower Fraser_Pink Salmon_13°C_F_Array1_10430

description:
raw data file (Ch1): Array1Ongo_09K_10430.txt
raw data file (Ch2): Array1Ongo_09K_10430ref.txt

tag: tissue

tag: sample type


title: Primary Hippocampla Neurons-2_NanoString

hyb_protocol: according to the manufacturer’s protocol

source_name: Primary Hippocampla Neurons

value: Hippocampus


title: total microRNAs in a clinical sample at CIN I stage_N48

description: SAMPLE mi_N48

tag: gender


title: Lower Fraser_Pink Salmon_13°C_M_Array2_10366

description:
raw data file (Ch1): Array2Ongo_09K_10366.txt
raw data file (Ch2): Array2Ongo_09K_10366ref.txt


title: Lower Fraser_Pink Salmon_19°C_M_Array1_10426

description:
raw data file (Ch1): Array1Ongo_09K_10426.txt
raw data file (Ch2): Array1Ongo_09K_10426ref.txt


title: Primary Cortical Neurons-1_NanoString

scan_protocol: according to the manufacturer’s protocol


title: Lower Fraser_Pink Salmon_19°C_M_Array1_10390

description:
raw data file (Ch1): Array1Ongo_09K_10390.txt
raw data file (Ch2): Array1Ongo_09K_10390ref.txt


title: Lower Fraser_Pink Salmon_13°C_F_Array1_10379

description:
raw data file (Ch1): Array1Ongo_09K_10379.txt
raw data file (Ch2): Array1Ongo_09K_10379ref.txt


title: Lower Fraser_Pink Salmon_19°C_F_Array1_10383

description:
raw data file (Ch1): Array1Ongo_09K_10383.txt
raw data file (Ch2): Array1Ongo_09K_10383ref.txt


title: Adult Oligodendrocytes-1_NanoString

source_name: Adult Oligodendrocytes

label_protocol: according to the manufacturer’s protocol

value: adult Oligodendrocytes


title: Adult Astrocytes-2_NanoString

source_name: Adult Astrocytes

value: adult Astrocytes


title: Primary Hippocampla Neurons-1_NanoString


title: Adult Astrocytes-1_NanoString


title: Microglia-2_NanoString

source_name: Microglia

value: microglia


title: Microglia-1_NanoString


title: Spleen red pulp macrophages-2_NanoString

source_name: Spleen red pulp macrophages

value: Spleen

value: red pulp macrophages


title: 24-Adult microglia (Brain)_NanoString

source_name: Adult microglia (Brain)

value: Brain

value: adult microglia


title: Adult Oligodendrocytes-2_NanoString


title: 23-Adult microglia (Cortex)_NanoString

source_name: Adult microglia (Cortex)


title: 22-Adult microglia (Hippocampus)_NanoString

source_name: Adult microglia (Hippocampus)


title: Lower Fraser_Pink Salmon_19°C_M_Array1_10366

description:
raw data file (Ch1): Array1Ongo_09K_10366.txt
raw data file (Ch2): Array1Ongo_09K_10366ref.txt

value: Late-run

value: Lower Fraser

value: gill

source_name: a pool of RNA from all of the fish used in the experiment

value: Reference


title: Late run_Sockeye_13°C_F_Array4_10427

description:
raw data file (Ch1): Array4Ongo_09K_10427.txt
raw data file (Ch2): Array4Ongo_09K_10427ref.txt

organism: Oncorhynchus nerka

source_name: Gill tissue cool treatment

treatment_protocol: Late-run sockeye salmon from the Fraser River, B.C., Canada, were exposed to either a warm (19C) or cool (13C) temperature treatment for 5 days.

value: Harrison Rapids

value: female


title: Late run_Sockeye_13°C_M_Array4_10375

description:
raw data file (Ch1): Array4Ongo_09K_10375.txt
raw data file (Ch2): Array4Ongo_09K_10375ref.txt

value: male


title: 21-Adult microglia (spinal cord)_NanoString

source_name: Adult microglia (spinal cord)

value: Spinal cord


title: Late run_Sockeye_13°C_M_Array4_10376

description:
raw data file (Ch1): Array4Ongo_09K_10376.txt
raw data file (Ch2): Array4Ongo_09K_10376ref.txt


title: Late run_Sockeye_19°C_F_Array4_10384

description:
raw data file (Ch1): Array4Ongo_09K_10384.txt
raw data file (Ch2): Array4Ongo_09K_10384ref.txt

source_name: Gill tissue warm treatment


title: Spleen red pulp macrophages-1_NanoString


title: Lower Fraser_Pink Salmon_13°C_M_Array1_10372

description:
raw data file (Ch1): Array1Ongo_09K_10372.txt
raw data file (Ch2): Array1Ongo_09K_10372ref.txt


title: Late run_Sockeye_19°C_M_Array4_10367

description:
raw data file (Ch1): Array4Ongo_09K_10367.txt
raw data file (Ch2): Array4Ongo_09K_10367ref.txt


title: Late run_Sockeye_19°C_M_Array3_10430

description:
raw data file (Ch1): Array3Ongo_09K_10430.txt
raw data file (Ch2): Array3Ongo_09K_10430ref.txt


title: Late run_Sockeye_13°C_M_Array4_10393

description:
raw data file (Ch1): Array4Ongo_09K_10393.txt
raw data file (Ch2): Array4Ongo_09K_10393ref.txt


title: Late run_Sockeye_19°C_F_Array3_10432

description:
raw data file (Ch1): Array3Ongo_09K_10432.txt
raw data file (Ch2): Array3Ongo_09K_10432ref.txt


title: 20-Adult microglia (Olfactory bulb)_NanoString

description:
miRNA profiling
MG400 custom Nanostring codesets

source_name: Adult microglia (Olfactory bulb)

value: Olfactory bulb


title: 19-Adult microglia (Cerebellum)_NanoString

source_name: Adult microglia (Cerebellum)

value: Cerebellum


title: Late run_Sockeye_13°C_M_Array3_10397

description:
raw data file (Ch1): Array3Ongo_09K_10397.txt
raw data file (Ch2): Array3Ongo_09K_10397ref.txt


title: 18-Adult microglia (eyes)_NanoString

source_name: Adult microglia (eyes)

value: Eye


title: 16-Gut macrophages_NanoString

source_name: Gut macrophages

value: Gut

value: macrophage


title: 17-Spleen macrophages_NanoString

source_name: Spleen macrophages

value: Spleen


title: 15-Heart macrophages_NanoString

source_name: Heart macrophages

value: Heart


title: 14-Liver macrophages_NanoString

source_name: Liver macrophages

value: Liver


title: Late run_Sockeye_19°C_M_Array3_10393

description:
raw data file (Ch1): Array3Ongo_09K_10393.txt
raw data file (Ch2): Array3Ongo_09K_10393ref.txt


title: Late run_Sockeye_13°C_F_Array3_10383

description:
raw data file (Ch1): Array3Ongo_09K_10383.txt
raw data file (Ch2): Array3Ongo_09K_10383ref.txt


title: 10-Lung macrophages_NanoString

source_name: Lung macrophages

value: Lung


title: 8-Bone marrow- CD11b/Ly6c Hi_NanoString

source_name: Bone marrow- CD11b/Ly6c Hi

value: Bone marrow

value: CD11b/Ly6C Hi


title: Late run_Sockeye_13°C_M_Array3_10389

description:
raw data file (Ch1): Array3Ongo_09K_10389.txt
raw data file (Ch2): Array3Ongo_09K_10389ref.txt

value: Late-run

value: gill


title: 9-Kidney macrophages_NanoString

source_name: Kidney macrophages

value: Kidney


title: 13-Muscle macrophages_NanoString

source_name: Muscle macrophages

value: Muscle


title: 7-Spleen- CD11b/Ly6C Hi_NanoString

source_name: Spleen- CD11b/Ly6C Hi


title: Late run_Sockeye_19°C_M_Array3_10376

description:
raw data file (Ch1): Array3Ongo_09K_10376.txt
raw data file (Ch2): Array3Ongo_09K_10376ref.txt

value: Harrison Rapids

value: male

value: Reference


title: 11-Dendritic Cells (spleen) CD11b/CD11c_NanoString

source_name: Dendritic Cells (spleen) CD11b/CD11c

value: Dendritic Cells CD11b/CD11c


title: 12-Neutrophils (PBMCs) Ly6G_NanoString

source_name: Neutrophils (PBMCs) Ly6G

value: Neutrophils (PBMCs) Ly6G


title: Late run_Sockeye_13°C_F_Array3_10379

description:
raw data file (Ch1): Array3Ongo_09K_10379.txt
raw data file (Ch2): Array3Ongo_09K_10379ref.txt

source_name: Gill tissue cool treatment

value: female

source_name: a pool of RNA from all of the fish used in the experiment


title: Lower Fraser_Pink Salmon_19°C_M_Array1_10378

description:
raw data file (Ch1): Array1Ongo_09K_10378.txt
raw data file (Ch2): Array1Ongo_09K_10378ref.txt

source_name: Gill tissue warm treatment

value: Lower Fraser


title: Late run_Sockeye_19°C_M_Array3_10372

description:
raw data file (Ch1): Array3Ongo_09K_10372.txt
raw data file (Ch2): Array3Ongo_09K_10372ref.txt


title: 6-Bone marrow- CD11b/Ly6c low_NanoString

source_name: Bone marrow- CD11b/Ly6c low

value: CD11b/Ly6C low


title: Late run_Sockeye_13°C_M_Array3_10368

description:
raw data file (Ch1): Array3Ongo_09K_10368.txt
raw data file (Ch2): Array3Ongo_09K_10368ref.txt


title: Late run_Sockeye_19°C_M_Array3_10371

description:
raw data file (Ch1): Array3Ongo_09K_10371.txt
raw data file (Ch2): Array3Ongo_09K_10371ref.txt


title: Late run_Sockeye_19°C_M_Array2_10430

description:
raw data file (Ch1): Array2Ongo_09K_10430.txt
raw data file (Ch2): Array2Ongo_09K_10430ref.txt


title: Late run_Sockeye_13°C_F_Array4_10380

description:
raw data file (Ch1): Array4Ongo_09K_10380.txt
raw data file (Ch2): Array4Ongo_09K_10380ref.txt


title: Late run_Sockeye_13°C_F_Array3_10365

description:
raw data file (Ch1): Array3Ongo_09K_10365.txt
raw data file (Ch2): Array3Ongo_09K_10365ref.txt


title: Late run_Sockeye_13°C_M_Array3_10366

description:
raw data file (Ch1): Array3Ongo_09K_10366.txt
raw data file (Ch2): Array3Ongo_09K_10366ref.txt


title: Late run_Sockeye_13°C_F_Array2_10392

description:
raw data file (Ch1): Array2Ongo_09K_10392.txt
raw data file (Ch2): Array2Ongo_09K_10392ref.txt


title: Late run_Sockeye_19°C_M_Array2_10394

description:
raw data file (Ch1): Array2Ongo_09K_10394.txt
raw data file (Ch2): Array2Ongo_09K_10394ref.txt


title: Late run_Sockeye_13°C_M_Array2_10390

description:
raw data file (Ch1): Array2Ongo_09K_10390.txt
raw data file (Ch2): Array2Ongo_09K_10390ref.txt


title: 4-T reg (Foxp3 spleen) CD4_NanoString

description:
miRNA profiling
MG400 custom Nanostring codesets

source_name: T reg (Foxp3 spleen) CD4

value: Spleen (Foxp3)

value: T reg CD4


title: 3-T cells (spleen) CD3/CD4_NanoString

source_name: T cells (spleen) CD3/CD4

value: Spleen

value: T cells CD3/CD4


title: Late run_Sockeye_13°C_F_Array2_10384

description:
raw data file (Ch1): Array2Ongo_09K_10384.txt
raw data file (Ch2): Array2Ongo_09K_10384ref.txt


title: Late run_Sockeye_13°C_M_Array2_10428

description:
raw data file (Ch1): Array2Ongo_09K_10428.txt
raw data file (Ch2): Array2Ongo_09K_10428ref.txt


title: Late run_Sockeye_13°C_M_Array2_10381

description:
raw data file (Ch1): Array2Ongo_09K_10381.txt
raw data file (Ch2): Array2Ongo_09K_10381ref.txt


title: 2-B cells (spleen) B220_NanoString

source_name: B cells (spleen) B220

value: B cells B220


title: 1-NK cells (spleen) NK1.1_NanoString

source_name: NK cells (spleen) NK1.1

value: NK cells NK1.1


title: 5-Spleen-  CD11b/Ly6C low_NanoString

source_name: Spleen-  CD11b/Ly6C low


title: Late run_Sockeye_19°C_M_Array1_10432

description:
raw data file (Ch1): Array1Ongo_09K_10432.txt
raw data file (Ch2): Array1Ongo_09K_10432ref.txt

value: Late-run

value: gill


title: Adult, fadrozole, 30ug, day 8, recovery, replicate 7

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters to obtain signal intensities.

organism: Pimephales promelas

source_name: Ovary tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Fish used in this study were reproductively mature female FHM (5-6 months of age) obtained from an onsite culture facility at the US EPA Mid-Continent Ecology Division (Duluth, MN). All procedures involving animals were reviewed and approved by the Animal Care and Use Committee in accordance with Animal Welfare Act and Interagency Research Animal Committee guidelines.

extract_protocol: Qiagen Rneasy

treatment_protocol: Exposures were conducted in 20L glass aquaria containing 10 L ultraviolet light-treated, membrane filtered, Lake Superior water containing 0 or 3, or 30 μg/L FAD. Treatments were delivered via water at a continuous flow of approximately 45 mL/min without the use of carrier solvents.

value: ovary

value: fadrozole, 30ug, day 8, recovery


title: Summer run_Sockeye_14°C_M_Array4_10368

description:
raw data file (Ch1): Array4Ongo_09K_10368.txt
raw data file (Ch2): Array4Ongo_09K_10368ref.txt

treatment_protocol: Summer-run sockeye salmon from the Fraser River, B.C., Canada, were exposed to either a warm (19C) or cool (14C) temperature treatment for 7 days.

value: Summer-run

value: Chilko

value: male


title: Adult, fadrozole, 30ug, day 8, recovery, replicate 3


title: Adult, fadrozole, 3ug, day 8, recovery, replicate 8

value: fadrozole, 3ug, day 8, recovery


title: Summer run_Sockeye_14°C_F_Array4_10396

description:
raw data file (Ch1): Array4Ongo_09K_10396.txt
raw data file (Ch2): Array4Ongo_09K_10396ref.txt

value: female

value: Reference


title: Adult, fadrozole, 30ug, day 8, recovery, replicate 6


title: Adult, fadrozole, 30ug, day 8, recovery, replicate 4


title: Late run_Sockeye_13°C_M_Array1_10371

description:
raw data file (Ch1): Array1Ongo_09K_10371.txt
raw data file (Ch2): Array1Ongo_09K_10371ref.txt

value: Harrison Rapids


title: Adult, fadrozole, 30ug, day 8, recovery, replicate 5


title: Adult, fadrozole, 3ug, day 8, recovery, replicate 6


title: Summer run_Sockeye_19°C_M_Array4_10391

description:
raw data file (Ch1): Array4Ongo_09K_10391.txt
raw data file (Ch2): Array4Ongo_09K_10391ref.txt


title: Summer run_Sockeye_19°C_M_Array4_10426

description:
raw data file (Ch1): Array4Ongo_09K_10426.txt
raw data file (Ch2): Array4Ongo_09K_10426ref.txt


title: Adult, fadrozole, 3ug, day 8, recovery, replicate 7


title: Late run_Sockeye_13°C_F_Array2_10378

description:
raw data file (Ch1): Array2Ongo_09K_10378.txt
raw data file (Ch2): Array2Ongo_09K_10378ref.txt


title: Late run_Sockeye_19°C_M_Array1_10425

description:
raw data file (Ch1): Array1Ongo_09K_10425.txt
raw data file (Ch2): Array1Ongo_09K_10425ref.txt


title: Adult, fadrozole, 3ug, day 8, recovery, replicate 5


title: Late run_Sockeye_19°C_F_Array2_10370

description:
raw data file (Ch1): Array2Ongo_09K_10370.txt
raw data file (Ch2): Array2Ongo_09K_10370ref.txt


title: Late run_Sockeye_19°C_M_Array1_10389

description:
raw data file (Ch1): Array1Ongo_09K_10389.txt
raw data file (Ch2): Array1Ongo_09K_10389ref.txt


title: Adult, fadrozole, 30ug, day 8, recovery, replicate 2


title: Adult, fadrozole, 30ug, day 8, recovery, replicate 1


title: Summer run_Sockeye_19°C_M_Array3_10396

description:
raw data file (Ch1): Array3Ongo_09K_10396.txt
raw data file (Ch2): Array3Ongo_09K_10396ref.txt

value: Mitchell


title: Summer run_Sockeye_19°C_M_Array3_10385

description:
raw data file (Ch1): Array3Ongo_09K_10385.txt
raw data file (Ch2): Array3Ongo_09K_10385ref.txt


title: Summer run_Sockeye_14°C_M_Array4_10373

description:
raw data file (Ch1): Array4Ongo_09K_10373.txt
raw data file (Ch2): Array4Ongo_09K_10373ref.txt


title: Summer run_Sockeye_14°C_M_Array3_10392

description:
raw data file (Ch1): Array3Ongo_09K_10392.txt
raw data file (Ch2): Array3Ongo_09K_10392ref.txt


title: Adult, fadrozole, 3ug, day 8, recovery, replicate 4


title: Adult, fadrozole, 3ug, day 8, recovery, replicate 3


title: Adult, fadrozole, 3ug, day 8, recovery, replicate 2


title: Summer run_Sockeye_19°C_M_Array3_10367

description:
raw data file (Ch1): Array3Ongo_09K_10367.txt
raw data file (Ch2): Array3Ongo_09K_10367ref.txt


title: Summer run_Sockeye_19°C_F_Array3_10375

description:
raw data file (Ch1): Array3Ongo_09K_10375.txt
raw data file (Ch2): Array3Ongo_09K_10375ref.txt

value: Horsefly


title: Summer run_Sockeye_14°C_F_Array1_10433

description:
raw data file (Ch1): Array1Ongo_09K_10433.txt
raw data file (Ch2): Array1Ongo_09K_10433ref.txt


title: Adult, fadrozole, 30ug, day 4, recovery, replicate 5

value: fadrozole, 30ug, day 4, recovery


title: Summer run_Sockeye_19°C_M_Array2_10380

description:
raw data file (Ch1): Array2Ongo_09K_10380.txt
raw data file (Ch2): Array2Ongo_09K_10380ref.txt


title: Adult, water, day 8, recovery, replicate 7

value: water, day 8, recovery


title: Adult, water, day 8, recovery, replicate 4


title: Summer run_Sockeye_19°C_M_Array2_10374

description:
raw data file (Ch1): Array2Ongo_09K_10374.txt
raw data file (Ch2): Array2Ongo_09K_10374ref.txt


title: Adult, water, day 8, recovery, replicate 6


title: Adult, fadrozole, 30ug, day 4, recovery, replicate 3


title: Adult, fadrozole, 30ug, day 4, recovery, replicate 6


title: Summer run_Sockeye_19°C_F_Array2_10383

description:
raw data file (Ch1): Array2Ongo_09K_10383.txt
raw data file (Ch2): Array2Ongo_09K_10383ref.txt


title: Summer run_Sockeye_14°C_F_Array1_10392

description:
raw data file (Ch1): Array1Ongo_09K_10392.txt
raw data file (Ch2): Array1Ongo_09K_10392ref.txt


title: Adult, water, day 8, recovery, replicate 2


title: Summer run_Sockeye_19°C_M_Array1_10382

description:
raw data file (Ch1): Array1Ongo_09K_10382.txt
raw data file (Ch2): Array1Ongo_09K_10382ref.txt


title: Adult, fadrozole, 3ug, day 8, recovery, replicate 1


title: Adult, water, day 8, recovery, replicate 8


title: Adult, fadrozole, 30ug, day 4, recovery, replicate 4


title: Adult, fadrozole, 3ug, day 4, recovery, replicate 7

value: fadrozole, 3ug, day 4, recovery


title: Adult, fadrozole, 30ug, day 4, recovery, replicate 7


title: Summer run_Sockeye_14°C_F_Array1_10391

description:
raw data file (Ch1): Array1Ongo_09K_10391.txt
raw data file (Ch2): Array1Ongo_09K_10391ref.txt


title: Adult, water, day 8, recovery, replicate 3


title: Adult, fadrozole, 30ug, day 4, recovery, replicate 1


title: Adult, fadrozole, 30ug, day 4, recovery, replicate 2


title: Summer run_Sockeye_14°C_F_Array1_10384

description:
raw data file (Ch1): Array1Ongo_09K_10384.txt
raw data file (Ch2): Array1Ongo_09K_10384ref.txt


title: Summer run_Sockeye_19°C_M_Array1_10381

description:
raw data file (Ch1): Array1Ongo_09K_10381.txt
raw data file (Ch2): Array1Ongo_09K_10381ref.txt


title: Adult, water, day 8, recovery, replicate 5


title: Adult, fadrozole, 3ug, day 4, recovery, replicate 6


title: Adult, fadrozole, 30ug, day 4, recovery, replicate 8


title: Summer run_Sockeye_19°C_F_Array1_10365

description:
raw data file (Ch1): Array1Ongo_09K_10365.txt
raw data file (Ch2): Array1Ongo_09K_10365ref.txt


title: Summer run_Sockeye_19°C_M_Array1_10399

description:
raw data file (Ch1): Array1Ongo_09K_10399.txt
raw data file (Ch2): Array1Ongo_09K_10399ref.txt


title: Adult, water, day 8, recovery, replicate 1


title: Adult, fadrozole, 3ug, day 4, recovery, replicate 5


title: Adult, fadrozole, 3ug, day 4, recovery, replicate 4


title: Adult, fadrozole, 3ug, day 4, recovery, replicate 1


title: Adult, water, day 4, recovery, replicate 5

value: water, day 4, recovery


title: Adult, fadrozole, 3ug, day 4, recovery, replicate 3


title: Adult, water, day 4, recovery, replicate 1


title: Adult, fadrozole, 30ug, day 2, recovery, replicate 6

value: fadrozole, 30ug, day 2, recovery


title: flight vs ground - rep 2

city: Bozeman

first: Sheila

last: Nielsen

state: MT

address: 317 Leon Johnson Hall

department: Immunology and Infectious Disease

institute: Montana State University

description: slide 45

hyb_protocol: Each sample pair (~5ul) is resuspended in Formamide-based  hybridization buffer (vial 7-Genisphere) (26ul), Array 50dT blocker (Genisphere) (2ul), and Rnase/Dnase-free water (19ul).  Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity.  Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 350 kit (Genisphere).  For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere)  (26ul), and Rnase/Dnase-free water (21ul).  The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min.  Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 3 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.  To prevent fluorophore degredation, the arrays are treated with Dyesaver (Genisphere).

scan_protocol: Slides are scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence.  Laser power is kept constant for Cy3/Cy5 scans and PMT is varied for each experiment based on optimal signal intensity with lowest possible background fluorescence. A low pmt setting scan is also performed to recover signal from saturated elements.  Gridding and analysis of images is performed using ScanArray v3.0 (Perkin Elmer).

data_processing:
The median value of each set of replicate spots from each array was used.  Data was log2 transformed and quantile normalized.  The Ch2 N Log Ratio is the normalized log (base2) transformation of the  ratio of the medians.  These log ratios are cy5/cy3, or as listed in the raw data files, ch2/ch1.  However, in the dye-swap samples, the values were inversed so that all sample data values represent flight/ground (test/reference) ratio. Three-way ANOVA analysis was then performed on the data using treatment (flight vs. ground), dye, and experimental data as factors.  Flight to ground linear contrast was performed with ANOVA.  False Discovery Rate was controlled using the Step Up method.  The Candida Genome Database (CGD) gene ontology (GO) Slim Mapper was used to classify differentially expressed genes into functional categories.
Analysis was initially restricted to genes that had high intensity on the array and were differentially expressed by at least 2-fold with a confidence interval of 95%.

organism: Candida albicans

source_name: Ground GAP 10, FPA 4

label_protocol: First strand cDNA is generated by oligo-dT primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array 350 kit (Genisphere).  Modified oligo-dT primers are utilized in which a fluorophore/dendrimer specific oligo sequence is attached to the 5’ end of the dT primer.  For cDNA synthesis, 1ul of fluorophore specific oligo-dT primer is added to 8ug of total RNA and the solution is incubated at 80C for 10 minutes then cooled on ice for 2 minutes.  To each sample are added RNase inhibitor (Superase-In; Ambion) (1ul), 5X first strand buffer (4ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (1ul), 0.1M DTT (2ul), and Superscript II RNase H- Reverse Transcriptase (1ul).  Reverse transcription is carried out at 42C for 2 hours.  The reaction is terminated by adding 0.5M NaOH/ 50mM EDTA (3.5ul) and incubation at 65C for 15 minutes then neutralized with 1M Tris-HCL, pH 7.5 (5ul).  For RNA expression level comparison, samples are paired and concentrated using Microcon YM30 microconcentrators (Millipore) according to the manufacturer’s protocol.

growth_protocol: Prior to flight, 6 x 10^6 cells grown in YPD medium were suspended in 0.5 mL sterile ddH2O and loaded into specialized spaceflight hardware, termed Fluid Processing Apparatuses (FPA.  Briefly, growth was initiated in flight (nine days post launch) by addition of 2 mL YPD to the fungal suspension (termed activation). Cultures were grown in spaceflight conditions or synchronous ground control conditions for 25 hours at ambient temperature (23˚C). Subsequently, cells were fixed for RNA, proteins and morphological imaging by addition of 2.5 mL RNA Later II reagent (Ambion, Austin, TX) (termed termination).)

extract_protocol: Two and a half hours after landing at Kennedy Space Center, the culture samples fixed in RNA Later II were recovered, removed from the FPA, and stored at -80°C.  Yeast cells were disrupted by homogenization in the presence of glass beads in a Mini-Beadbeater-8™ (Biospec Products) and RNA was isolated using the RNeasy Micro kit (Qiagen).  RNA quality and quantity were evaluated using the Nanodrop technology (Thermo Scientific) and an Agilent 2100 bioanalyzer (Agilent Technologies).

tag: growth condition

value: ground-based control condition

source_name: Flight GAP 10, FPA 5

value: spaceflight condition


title: flight vs ground - rep 1

description: slide 43

source_name: Ground GAP 10, FPA 1

source_name: Flight GAP 10, FPA 1


title: Adult, water, day 4, recovery, replicate 3

value: ovary


title: Adult, water, day 4, recovery, replicate 7


title: Adult, water, day 4, recovery, replicate 4


title: Adult, water, day 4, recovery, replicate 2


title: Adult, fadrozole, 30ug, day 2, recovery, replicate 1


title: Adult, fadrozole, 30ug, day 2, recovery, replicate 7


title: Adult, fadrozole, 30ug, day 2, recovery, replicate 4


title: ground vs flight - rep 2 dye swap

description: slide 46


title: flight vs ground - rep 3

description: slide 47

source_name: Ground GAP 11, FPA 1

source_name: Flight GAP 11, FPA 1


title: Adult, fadrozole, 3ug, day 2, recovery, replicate 8

value: fadrozole, 3ug, day 2, recovery


title: Adult, fadrozole, 30ug, day 2, recovery, replicate 2


title: ground vs flight - rep 1 dye swap

description: slide 44


title: flight vs ground - rep 4

description: slide 49

source_name: Ground GAP 11, FPA 4

source_name: Flight GAP 11, FPA 5


title: Adult, fadrozole, 3ug, day 4, recovery, replicate 2


title: Adult, fadrozole, 30ug, day 2, recovery, replicate 3


title: Adult, water, day 4, recovery, replicate 6


title: ground vs flight - rep 3 dye swap

description: slide 48


title: Adult, water, day 4, recovery, replicate 8


title: ground vs flight - rep 4 dye swap

description: slide 50


title: Adult, fadrozole, 30ug, day 2, recovery, replicate 5


title: Adult, fadrozole, 3ug, day 2, recovery, replicate 7


title: Adult, fadrozole, 3ug, day 2, recovery, replicate 6


title: Adult, fadrozole, 3ug, day 2, recovery, replicate 4


title: Adult, fadrozole, 3ug, day 2, recovery, replicate 5


title: TOV_si

city: Nagoya

first: Yoriko

last: Yamashita

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Pathology and Biological Resoponses

institute: Nagoya University Graduate School of Medicine

hyb_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010).

scan_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010, Agilent C Scanner Settings).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: TOV21G transduced by Cbx7 siRNA

growth_protocol: Cells were grown in an RPMI-1640 medium (Sigma-Aldrich) containing 10% fetal bovine serum at 37°C under a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted 48 hours after transfection using RNeasy Plus Mini kit (QIAGEN).

treatment_protocol: Cells were transcfeted with 10nM Cbx7 or control siRNA using Lipofectamine RNAiMAX Kit (Invitrogen).

tag: cell line

value: ovarian clear cell adenocarcinoma


title: Adult, water, day 2, recovery, replicate 7

value: water, day 2, recovery


title: TOV_con

source_name: TOV21G transduced by control siRNA

label_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010).


title: KOC_con

source_name: KOC-7C transduced by control siRNA


title: Adult, water, day 2, recovery, replicate 1


title: KOC_si

source_name: KOC-7C transduced by Cbx7 siRNA


title: Adult, water, day 2, recovery, replicate 4


title: Laser_microdissected_cancer_cells_from_Small_cell_lung_carcinoma_case_06_14419

city: Karachi

first: Muhammad

middle: Furqan

last: Bari

state: Sindh

address: Suparco Road, Ojha campus

department: Department of Pathology

country: Pakistan

institute: Dow University of Health Sciences

description: Gene expression after laser microdissection of tumour cells from tumour sections

hyb_protocol: 1.2 µg of Cy3-labelled cDNA (specific activity 24.899 ± 0.284 pmol Cy3/µg cDNA) was mixed with 10X blocking agent (Agilent) and 2X GEx hybridization buffer HI-RPM (Agilent) and hybridized to Agilent SurePrint 8X60K arrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). The array was slowly removed from wash buffer 2 at an angle to minimize the formation of droplets and briefly allowed to air dry

scan_protocol: Slides with ozone-barrier slide covers were scanned immediately after washing on the Agilent G2565CA Microarray Scanner with AgilentG3_GX_1Color setting (Scan area 61 x 21.6 mm, scan resolution 3 µm, dye channel green and green PMT set to 100%)

data_processing: The scanned images were analysed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and grid: 028004_D_F_20110819) to obtain background subtracted signal intensities

source_name: Lung resection

label_protocol: 13.94ng of RNA was amplified using ovation pico WTA system (NuGEN Technologies, San Carlos, CA, USA) following manufacturer's instruction, followed by purification using QIAquick PCR purification kit (Qiagen) and labelled using Agilent Enzymatic Genomic DNA kit with Cyanine 3-dUT following manufacturer's instruction. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Fresh frozen sample

extract_protocol: RNA was extracted from laser microdissected tumour and background lung samples using the Arcturus PicoPure RNA Isolation Kit (Life Technologies, Paisley, UK) with on column DNase digestion (Qiagen, Crawley, UK) following manufacturer's recommendations. RNA was quantified using a Qubit (Life Technologies) while RNA integrity was determined using Agilent 2100 Bioanalyzer (Agilent, Wokingham, UK).

treatment_protocol: The samples were subjected to laser micro-dissection before extracting RNA

tag: batches

value: Laser microdissected lung tissues

tag: disease status


title: Adult, fadrozole, 3ug, day 2, recovery, replicate 1

tag: treatment


title: Laser_microdissected_cancer_cells_from_Small_cell_lung_carcinoma_case_10_26576


title: Laser_microdissected_cancer_cells_from_Small_cell_lung_carcinoma_case_04_14007


title: Adult, water, day 2, recovery, replicate 3


title: Adult, water, day 2, recovery, replicate 8


title: Laser_microdissected_bronchial_epithelial_cells_from_normal_background_lung_Case_11_4442

description: Gene expression after laser microdissection of bronchial epithelial cells from normal background lung sections


title: Adult, water, day 2, recovery, replicate 2


title: Adult, fadrozole, 3ug, day 2, recovery, replicate 3


title: Laser_microdissected_cancer_cells_from_Large_cell_neuroendocrine_carcinoma_case_08_42221


title: Laser_microdissected_bronchial_epithelial_cells_from_normal_background_lung_Case_11_4621


title: Adult, water, day 2, recovery, replicate 6


title: Laser_microdissected_cancer_cells_from_Large_cell_neuroendocrine_carcinoma_case_10_25642


title: Adult, water, day 2, recovery, replicate 5


title: Adult, fadrozole, 3ug, day 2, recovery, replicate 2


title: Laser_microdissected_bronchial_epithelial_cells_from_normal_background_lung_Case_11_1067


title: Laser_microdissected_cancer_cells_from_Large_cell_neuroendocrine_carcinoma_case_10_21327


title: Laser_microdissected_cancer_cells_from_Large_cell_neuroendocrine_carcinoma_case_06_29517


title: Laser_microdissected_cancer_cells_from_Small_cell_lung_carcinoma_case_S811


title: Laser_microdissected_bronchial_epithelial_cells_from_normal_background_lung_Case_10_26576


title: Adult, fadrozole, 30ug, day 1, recovery, replicate 8

value: fadrozole, 30ug, day 1, recovery


title: Laser_microdissected_bronchial_epithelial_cells_from_normal_background_lung_Case_10_25642


title: Laser_microdissected_bronchial_epithelial_cells_from_normal_background_lung_Case_10_21327


title: Adult, fadrozole, 30ug, day 1, recovery, replicate 7


title: Adult, fadrozole, 30ug, day 1, recovery, replicate 5


title: Adult, fadrozole, 30ug, day 1, recovery, replicate 6


title: Laser_microdissected_bronchial_epithelial_cells_from_normal_background_lung_Case_10_15931


title: Adult, fadrozole, 30ug, day 1, recovery, replicate 4


title: Adult, fadrozole, 30ug, day 1, recovery, replicate 3


title: Nuclear RNA_KO_rep1

city: Athens

first: Olga

last: Papadodima

address: 48, Vasileos Konstantinou av.

country: Greece

institute: National Hellenic Research Foundation

description: nuclear RNA, input RNA of the IP reaction, replicate 1

hyb_protocol: Direct Hybridization

scan_protocol: Data were Scanned with the HiScan Reader of Illumina and image acquisition was performed with a BeadStudio version 3.4.0.30825

data_processing: Quantile Normalization, Log2 transformation

source_name: Nuclear RNA, HuR KO MEFs

label_protocol: Biotyn-labeled cRNA

extract_protocol: RNeasy Mini Kit column (Qiagen)

tag: hur status

value: KO

tag: rna subtype

value: nuclear RNA


title: Adult, fadrozole, 30ug, day 1, recovery, replicate 1


title: Adult, fadrozole, 3ug, day 1, recovery, replicate 4

value: fadrozole, 3ug, day 1, recovery


title: Nuclear RNA_WT_rep2

description: nuclear RNA, input RNA of the IP reaction, replicate 2

source_name: Nuclear RNA, HuR WT MEFs

value: WT


title: Adult, fadrozole, 3ug, day 1, recovery, replicate 8


title: IP RNA_KO_rep2

description: RNA after HnRNPA1 Immunoprecipitation, replicate 2

source_name: RNA from HnRNP A1 IPs, HuR KO MEFs

value: nuclear RNA after HnRNPA1 Immunoprecipitation


title: IP RNA_WT_rep2

source_name: RNA from HnRNP A1 IPs, HuR WT MEFs


title: Nuclear RNA_KO_rep3

description: nuclear RNA, input RNA of the IP reaction, replicate 3


title: Adult, fadrozole, 30ug, day 1, recovery, replicate 2

source_name: Ovary tissue


title: Adult, fadrozole, 3ug, day 1, recovery, replicate 6


title: Adult, fadrozole, 3ug, day 1, recovery, replicate 7


title: Adult, fadrozole, 3ug, day 1, recovery, replicate 5


title: Adult, fadrozole, 3ug, day 1, recovery, replicate 3


title: IP RNA_KO_rep1

description: RNA after HnRNPA1 Immunoprecipitation, replicate 1


title: Adult, fadrozole, 3ug, day 1, recovery, replicate 2


title: IP RNA_KO_rep3

description: RNA after HnRNPA1 Immunoprecipitation, replicate 3


title: IP RNA_WT_rep1


title: Nuclear RNA_KO_rep2


title: Nuclear RNA_WT_rep1


title: IP RNA_WT_rep3


title: Adult, fadrozole, 3ug, day 1, recovery, replicate 1


title: Adult, water, day 1, recovery, replicate 7

value: water, day 1, recovery


title: Adult, water, day 1, recovery, replicate 8


title: Bach2 KO - Thymus - biological repeat 2

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

institute: Sidra Medical and Research Center

hyb_protocol: Affymetrix Hybridization Protocol; Biotinilated cDNA were then hybridized to HumanGene 1.0 ST arrays (Affymetrix) overnight at 450C.

scan_protocol: Affymetrix Scanning Protocol; Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Affymetrix RMA Data Processing
Calculation Method: Expression summary values were calculated using the Partek Genomic Suite (v.6.6. 6.12.0907) implemented version of RMA (Robust Multichip Average).

source_name: Bach2 KO Thymus

label_protocol: Encore Biotin Module (NuGEN) Labeling; 5.5ug of amplified sscDNA from 12-13ug total amplification were used for fragmentation and biotinilation using Encore(TM) Biotin Module (NuGEN) according to manual.

extract_protocol: Sample Extraction Protocol; Total RNA from sorted cells were isolated using the RNAeasy mini kit (Qiagen).

treatment_protocol: In-vivo treatment: Male Rag1 knockout animals at 8 weeks of age were lethally irradiated and reconstituted with 1:1 mixtures of bone marrow cells depleted of mature lineages from 8 week old male Ly5.1- Bach2 knockout and Ly5.1+ wildtype mice. Two months following transfer, Ly5.1- (knockout) and Ly5.1+ (wildtype) CD4 single-positive thymocytes were isolated by FACS from single cell suspensions of thymi from mixed chimeric animals. Total RNA was purified from these cells and global gene expression analysis was performed. Thus we were able to measure Bach2-dependent gene expression in CD4 single-positive thymocytes.

tag: strain background

value: male

value: thymus

value: CD4 single-positive thymocytes

tag: genotype/variation

value: Bach2 knock out


title: Bach2 KO - Thymus - biological repeat 3


title: Adult, water, day 1, recovery, replicate 6


title: Adult, water, day 1, recovery, replicate 5


title: WT - Thymus - biological repeat 2

source_name: WT Thymus


title: Bach2 KO - Thymus - biological repeat 1


title: WT - Thymus - biological repeat 3


title: Adult, water, day 1, recovery, replicate 4


title: Adult, fadrozole, 30ug, day 8, replicate 6

value: fadrozole, 30ug, day 8


title: Adult, fadrozole, 30ug, day 8, replicate 4

value: ovary


title: CaseC (with bortezomib)

city: Be'er Yacob

first: Yossi

last: Cohen

state: Zerifin

address: Assaf Harofhe, Institute of Hematology

department: Hematology

country: Israel

institute: Asaf Harofhe Hospital

description:
SAMPLE 6
Cultured bone marrow cells incubated with bortezomib

hyb_protocol: Biotin-labeled cRNA was hybridized onto 1.0 ST Expression Bead Chips

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed Affymetrix gene expression console (GCOS5)

source_name: BM_bortezomib_in vitro

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

growth_protocol: Cultured bone marrow cells were grown in high cell density imposing cell-cell contact

extract_protocol: Frozen samples were lyzed by adding 300 µl lysis buffer to tubes. RNA was isolated by MagNA Pure LC RNA Isolation procedure using MagNA Pure instrument (Roche). Integrity of RNA was examined by Agilent 2100 Bioanalyzer.

treatment_protocol: PBS was added to the control bone marrow samples and bortezomib (2 µg/ml) was added to the treated bone marrow samples for 6-8 hour incubation.

tag: patient source

value: bortezomib resistant myeloma patient

value: Cultured bone marrow (BM) cells

tag: incubated with

value: 2 µg/ml bortezomib for 6-8hrs


title: CaseD (without bortezomib)

description:
SAMPLE 7
Cultured bone marrow cells incubated without bortezomib

source_name: BM_PBS_in vitro

value: PBS for 6-8hrs


title: Adult, fadrozole, 30ug, day 8, replicate 7


title: Adult, water, day 1, recovery, replicate 2


title: Adult, water, day 1, recovery, replicate 1


title: Adult, fadrozole, 30ug, day 8, replicate 5


title: CaseA (without bortezomib)

description:
SAMPLE 1
Cultured bone marrow cells incubated without bortezomib

value: bortezomib responsive myeloma patient


title: CaseB (with bortezomib)

description:
SAMPLE 4
Cultured bone marrow cells incubated with bortezomib


title: CaseC (without bortezomib)

description:
SAMPLE 5
Cultured bone marrow cells incubated without bortezomib


title: WT - Thymus - biological repeat 1


title: Adult, fadrozole, 30ug, day 8, replicate 2


title: CaseD (after IV bortezomib)

description:
SAMPLE 9
Fresh bone marrow sample taken 75 minutes after IV injection of bortezomib (1.3 mg/m2)

source_name: fresh BM after bortezomib IV injection

value: Fresh bone marrow cells

tag: collected


title: Adult, water, day 1, recovery, replicate 3


title: Adult, fadrozole, 3ug, day 8, replicate 6

value: fadrozole, 3ug, day 8


title: Adult, fadrozole, 3ug, day 8, replicate 8


title: Adult, fadrozole, 30ug, day 8, replicate 3


title: Adult, fadrozole, 3ug, day 8, replicate 5


title: CaseB (without bortezomib)

description:
SAMPLE 3
Cultured bone marrow cells incubated without bortezomib


title: CaseA (with bortezomib)

description:
SAMPLE 2
Cultured bone marrow cells incubated with bortezomib


title: Adult, fadrozole, 3ug, day 8, replicate 7


title: CaseD (with bortezomib)

description:
SAMPLE 8
Cultured bone marrow cells incubated with bortezomib


title: Adult, water, day 8, replicate 6

value: water, day 8


title: Adult, fadrozole, 3ug, day 8, replicate 2


title: Adult, water, day 8, replicate 2


title: Adult, fadrozole, 30ug, day 8, replicate 1


title: Adult, water, day 8, replicate 7


title: Adult, fadrozole, 3ug, day 8, replicate 3


title: Adult, fadrozole, 30ug, day 4, replicate 6

value: fadrozole, 30ug, day 4


title: Adult, water, day 8, replicate 1


title: Adult, water, day 8, replicate 3


title: Adult, fadrozole, 30ug, day 4, replicate 7


title: Adult, fadrozole, 3ug, day 8, replicate 4


title: Adult, fadrozole, 30ug, day 4, replicate 5


title: Adult, water, day 8, replicate 4


title: Adult, water, day 8, replicate 5


title: Adult, fadrozole, 30ug, day 4, replicate 3


title: Adult, fadrozole, 3ug, day 8, replicate 1


title: Adult, fadrozole, 30ug, day 4, replicate 4


title: Adult, fadrozole, 3ug, day 4, replicate 7

value: fadrozole, 3ug, day 4


title: Adult, fadrozole, 30ug, day 4, replicate 1


title: Adult, fadrozole, 3ug, day 4, replicate 4


title: Adult, fadrozole, 30ug, day 4, replicate 2


title: Adult, fadrozole, 3ug, day 4, replicate 6


title: Adult, fadrozole, 3ug, day 4, replicate 8


title: Adult, fadrozole, 3ug, day 4, replicate 5


title: Adult, fadrozole, 3ug, day 4, replicate 3


title: Adult, fadrozole, 3ug, day 4, replicate 2


title: Adult, fadrozole, 3ug, day 4, replicate 1


title: 70 µg/L of PVP-AgNPs, replicate 3 [Liver tissue]

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GEML grid file 036574_D_F_20110917.xml to obtain signal intensities.  GeneSpring GX (Agilent Technologies) was used to normalize data by quantile normalizaton and baseline transformation to the median of all samples.  Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of one-way ANOVA to test for significant differential expression of microarray targets.

source_name: Liver tissue

growth_protocol: FHM were obtained from Aquatic Biosystems (Fort Collins, CO), held in aerated dechlorinated tap water and fed three times daily with Zeigler® AquaTox Feed Gardners, PA, USA).

treatment_protocol: Fish were exposed in triplicate, five females per replicate, at 4 µg/L of silver nitrate (AgNO3) or 70 µg/L of PVP-AgNPs (Luna Innovations, Blackburn, VA) for 96 hours at 24°C ± 1 with a 90% water change at 48 hours.

tag: agent

value: polyvinylpyrrolidone-coated silver nanoparticles (PVP-AgNPs)


title: 70 µg/L of PVP-AgNPs, replicate 5 [Liver tissue]


title: Adult, water, day 4, replicate 7

value: water, day 4


title: Adult, water, day 4, replicate 8


title: 70 µg/L of PVP-AgNPs, replicate 1 [Liver tissue]


title: control, replicate 6 [Liver tissue]

value: control sample


title: control, replicate 5 [Liver tissue]


title: Adult, water, day 4, replicate 3


title: control, replicate 1 [Liver tissue]


title: Adult, water, day 4, replicate 4


title: 70 µg/L of PVP-AgNPs, replicate 2 [Liver tissue]


title: Adult, water, day 4, replicate 5


title: Adult, water, day 4, replicate 2


title: Adult, water, day 4, replicate 1


title: control, replicate 2 [Liver tissue]


title: Adult, water, day 4, replicate 6


title: control, replicate 3 [Liver tissue]


title: 4 µg/L of AgNO3, replicate 5 [Liver tissue]

value: silver nitrate (AgNO3)