title: H522Tr-shSOX4-1 Doxycycline 96h

city: L´Hospitalet de Llobregat

first: Sandra

last: Castillo

address: Avda. Gran Via 199-203

institute: IDIBELL-PEBC

hyb_protocol: The hybridization was performed on the Whole Human Genome Microarray 4x44 following Agilent´s instructions.

scan_protocol: For the scanning we used a G2505B DNA microarray scanner (Agilent, Santa Clara, CA, USA). Images were quantified using Agilent Feature Extraction Software (ver. 9.5).

data_processing:
Cy3 and Cy5 fluorescent signals were quantified using GenePix Pro 5.0 (Axon Instruments Inc.). Substandard spots were manually flagged and discarded for further analysis.
The Cy5/Cy3 ratios were normalized to the median ratio value using the DNMAD tool, based on a print-tip loess method. The conditions for the normalization were: 1) use negative flags, that means that the flagged spots are not used for the normalization and are turned into missing values; 2) do not use background correction.
The normalized and semi-logarithmic transformed data were preprocessed using GEPAS software. Conditions for data pre-processing were: 1) merge replicates (the Cy5/Cy3 ratios of replicated spots were averaged); 2) filter missing values in order to exclude for further analysis any gene with data missing in more than 10% of the samples.

source_name: Total cDNA from H522Tr-shSOX4-1 cells 96h after adding 2.5 ug/ml of doxycycline labeled with Cy5

label_protocol: The labelling was done using the commercial Two-Color Microarray-Based Gene Expression Analysis version 5.5 kit and followed the manufacturer instructions. MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA polymerase catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. Cy3 labelling was used for the reference sample.

growth_protocol: H522 lung cancer cell line and its derived clone H522Tr-shSOX4-1 cells were grown in DMEM medium complemented with 10% fetal bovine serum.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: H522Tr-shSOX4-1 cells were treated with 2.5 µg/ml of doxycycline

value: lung

tag: cell line

value: adenocarcinoma

source_name: Human cDNA pool (Stratagene)

tag: reference

value: Human cDNA pool (Stratagene)


title: H522

status: Public on Nov 18 2011

type: RNA

country: Spain

molecule: total RNA

organism: Homo sapiens

source_name: Total cDNA from H522 cells labeled with Cy5

tag: tissue

tag: histology


title: normal whole brain B

type: genomic

city: Edinburgh

first: Colm

middle: E

last: Nestor

address: Western General Hospital, Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: Univeristy of Edinburgh

description: normal whole brain  genomic DNA

hyb_protocol: Labelled samples were applied to an 'Human DNA Methylation 4x72K ENCODE HG17 Targeted Tiling Array' which tiles the biologically significant ENCODE regions (EN001 - EN014) and hybridised overnight at 42degrees C.

scan_protocol: Arrays were scanned on a NimbleGen MS200 scanner per manufacturer's protocol (http://www.nimblegen.com/).

data_processing: Images  were processed using Nimblegen's standard protocol for Nimblescan DNA methylation DNA extraction.

molecule: genomic DNA

source_name: normal whole brain

label_protocol: Amplified DNA samples were Cy5- (IP) or Cy3- (Input) labelled by random priming using the Dual-Color DNA Labeling Kit (NimbleGen, Iceland).

growth_protocol: normal human tissue

extract_protocol: Genomic DNA (5hmC-IP - 2.5 µg in 450 µl TE), sonicated to yield a fragment distribution of approximately 300-1000 bp, was denatured by incubation at 100 degrees C for 10 min. Samples were rapidly chilled on wet-ice. At this point, 45 µl (10%) of denatured sample was removed and saved as input, and 45 µl of 10X IP buffer (100 mM Na-Phosphate pH 7.0  (mono and dibasic), 1.4 M NaCl, 0.5 % Triton X-100) and 1 µg of 5hmC (ActiveMotif; #39769) antibody were added to the remaining sample. Samples were incubated at 4 degrees C with gentle agitation overnight. Then, 40 µl of magnetic beads (Dynabeads® Protein G, Invitrogen, UK) in 1X IP buffer were added to each sample to allow magnetic separation of the antibody from the unbound DNA using a magnetic tube rack. Samples were incubated at 4 degrees C for 1 hr with gentle agitation. Beads were collected with a magnetic rack and washed with 1000 µl of 1X IP buffer at RT for 10 min with gentle agitation; washing was repeated three times. Beads were collected with a magnetic rack and re-suspended in 250 µl of digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA , 0.5 % SDS) followed by addition of 10 µl of proteinase K  (20 mg/ml; Roche Applied Science, Mannheim, Germany) and incubation at 52degrees C for 1.5 hr with constant shaking (≥800 rpm). Finally, beads were removed using a magnetic rack and DNA was purified from the remaining sample using a QIAquick PCR Purification Kit (QIAGEN,CA, USA), eluting in a final volume of 40 µl dH2O. Inputs were also purified using a QIAquick PCR Purification Kit and eluted in 40 µl dH2O. Subsequently, 10 ng of input and IP DNA was subjected to whole genome amplification (WGA) using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich, UK) as per the manufacturer's instructions. Amplified DNA was run on a 1.2% agarose gel to confirm consistency of fragment size between samples.

treatment_protocol: genomic DNA extracted from normal human tissues, purchased from a commercial supplier

tag: gender

value: M

tag: antibody

tag: antibody manufacturer

value: Active Motif

tag: antibody catalog #

value: normal whole brain

value: input DNA


title: H2373 mesothelioma

city: detroit

first: naimei

last: tang

state: mi

address: 110 E warren ave

department: internal medicine

country: USA

institute: wanye state university

hyb_protocol: HumanHT-12 Expression BeadChip.

scan_protocol: Illumina BeadScan Version 3.5.49.29917

data_processing: The data were analyzed using BeadStudio version 3.1.3.0 using the quantilechip normalization method.

label: Biotin

source_name: H2373 mesothelioma

label_protocol: Bioltinylated cRNA were generated following manufacturer protocols usingnthe Illumina TotalPrep Amplication Kit from Ambion.

growth_protocol: H2714 and H2373 (as a SP-negative control ) cell lines derived from patients with malignant plural mesothelioma was cultured in RPMI 1640 (HyClone) supplemented with 100 units/ml of penicillin, 100 µg/ml streptomycin, and 10% fetal calf serum (HyClone).

extract_protocol: Total RNAs were isolated with Ambion RiboPure™ Kit in accordance with  the prescribed protocol provided with kit. Quality of RNA was analyzed with Agilent Bioanalyser.

treatment_protocol: SP and non-SP cells were isolated from H2714 mesothelioma cell line by a sorter after Hoechst 33342 staining


title: H522Tr-shSOX4-1 Doxycycline 24h

source_name: Total cDNA from H522Tr-shSOX4-1 cells 24h after adding 2.5 ug/ml of doxycycline labeled with Cy5


title: Sorted H2714 non-SP cells

source_name: Sorted H2714 non-SP cells


title: Patient n°19

status: Public on Nov 17 2011

city: Meldola

first: Chiara

last: Molinari

state: FC

address: via Maroncelli 40

department: Bioscience Laboratories

country: Italy

institute: IRST(Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori)

hyb_protocol: DNA was then precipitated with 140 µl of blocking mix, 6 μl of yeast  tRNA 10 mg/ml  0.1 V/V of 3 M sodium acetate pH 5.2 and 2 V/V of absolute ethanol. The DNA pellet was dissolved in 10 μl of distilled water and 30 μl of hybridization solution.  After denaturation at 72°C for 10 min and incubation at 37°C for 30 min, the solution was applied to the array. Hybridization was done at 42°C for 40 hrs.  Finally, the slides were washed according to the supplier’s instructions, dried by spinning in a centrifuge for 5 min at 1000 rpm and scanned.

scan_protocol: Arrays were scanned on VersaArray ChipReader scanner (Biorad). Images were analyzed using BlueFuse version 3.5 software (BlueGnome)

data_processing: In the arrays each clone was spotted in quadruplicate. Spots were excluded when the quality flag was < 1, the confidence value < 0.3 or the standard deviation of quadruplicate > 0.2.  Log2 ratios of spots that were not excluded were normalized using block median or block lowess approaches. Alteration analysis was performed using aCGH-Smooth approach,  implemented in BlueFuse version 3.5 software, and Hidden Markov Model

source_name: rectal tumor tissue from pre-therapy biopsy

label_protocol: Approximately 1.2 μg of DNA was labelled by random priming using 1.4 μl of 1 mmol/L Cy3-dCTP or Cy5-dCTP  according to the manufacturer's instructions. Equal amounts of labelled tumor and reference DNA were mixed and unincorporated fluorochromes were removed using Bioprime Array-CGH Purification Module.

extract_protocol: Genomic DNA was extracted using QIAamp DNA Mini Kit (Qiagen) according to manufacturer's instruction

value: rectal tumor

value: Male

tag: age

tag: ut

tag: un

tag: ypt

tag: ypn

tag: response to therapy according to trg by dworak

tag: response group

value: NR

source_name: blood from a pool of healthy individuals

value: blood


title: pMX-Oct4 and pMX-jhdm1b(jmjc) no vitamin C O+JMJCVc-_1

city: guangzhou

first: Pei

middle: Duan

last: Qing

address: 190,Kaiyuan avenue

country: China

institute: Guangzhou Institute of Biomedicine and Health, CAS

description: Gene expression data from ICR MEF infected  with pMX-Oct4 and pMX-jhdm1b(jmjc) retrovirus

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MoGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software.

label: biotin

organism: Mus musculus

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: oct4 and  jhdm1b infected MEF  were cultured with or without vitamin C treatment. Media were changed everyday.

extract_protocol: Cells were trypsinized and feeder cells were eliminated. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: with or without vitamin C treatment.

tag: treatment

value: no vitamin C

tag: cell type

value: MEF

tag: strain

value: ICR

tag: transfection


title: pMX-Oct4 and pMX-jhdm1b(jmjc) no vitamin C O+JMJCVc-_2

source_name: ICR MEF infected  with pMX-Oct4 and pMX-jhdm1b(jmjc) retrovirus


title: H522Tr-shSOX4-1 Doxycycline 0h

source_name: Total cDNA from H522Tr-shSOX4-1 cells 0h after adding 2.5 ug/ml of doxycycline labeled with Cy5

tag: tissue

tag: cell line

tag: reference


title: Patient n°14

tag: gender

value: R


title: Sorted H2714 SP cells

source_name: Sorted H2714 SP cells


title: Patient n°3


title: normal whole brain A

description: normal whole brain genomic DNA

tag: antibody

tag: antibody manufacturer


title: H2714 mesothelioma cells

source_name: H2714 mesothelioma cells


title: pMX-Oct4 and pMX-jhdm1b(jmjc) vitamin C O+JMJCVc+_2

value: vitamin C

value: pMX-Oct4 and pMX-jhdm1b(jmjc) retrovirus


title: Patient n°8

tag: age


title: Patient n°7

tag: ut


title: Patient n°2

tag: un


title: Patient n°15

tag: ypt


title: Patient n°23

value: Female

tag: ypn


title: Patient n°26

tag: response to therapy according to trg by dworak


title: pMX-Oct4 and pMX-jhdm1b vitamin C O+Jhdm1BVc+_2

description: Gene expression data from ICR MEF infected  with pMX-Oct4 and pMX-jhdm1b retrovirus

value: pMX-Oct4 and pMX-jhdm1b retrovirus


title: pMX-Oct4 and pMX-jhdm1b(jmjc) vitamin C O+JMJCVc+_1


title: pMX-Oct4 and pMX-jhdm1b no vitamin C O+Jhdm1BVc-_1

source_name: ICR MEF infected  with pMX-Oct4 and pMX-jhdm1b retrovirus


title: pMX-Oct4 and pMX-jhdm1b no vitamin C O+Jhdm1BVc-_2


title: pMX-jhdm1b no vitamin C Jhdm1BVc-_2

description: Gene expression data from ICR MEF infected  with pMX-jhdm1b retrovirus

value: pMX-jhdm1b retrovirus


title: pMX-Oct4 no vitamin C Oct4Vc-_2

description: Gene expression data from ICR MEF infected  with pMX-Oct4 retrovirus

value: pMX-Oct4 retrovirus


title: pMX-jhdm1b vitamin C Jhdm1BVc+_2

source_name: ICR MEF infected  with pMX-jhdm1b retrovirus


title: pMX-jhdm1b vitamin C Jhdm1BVc+_1


title: pMX-Oct4 and pMX-jhdm1b vitamin C O+Jhdm1BVc+_1


title: pMX-Oct4 no vitamin C Oct4Vc-_1

source_name: ICR MEF infected  with pMX-Oct4 retrovirus


title: pMX-Oct4 vitamin C Oct4Vc+_2


title: pMX-Oct4 vitamin C Oct4Vc+_1


title: pMX-jhdm1b no vitamin C Jhdm1BVc-_1


title: pMX-GFP no vitamin C GFPVc-_2

description: Gene expression data from ICR MEF infected  with pMX-GFP retrovirus

value: pMX-GFP retrovirus


title: Patient n°10T

tag: response group


title: Patient n°9T


title: Patient n°17T


title: Patient n°11T


title: Patient n°6T


title: pMX-GFP no vitamin C GFPVc-_1

source_name: ICR MEF infected  with pMX-GFP retrovirus

tag: treatment


title: Patient n°32T


title: pMX-GFP vitamin C GFPVc+_2

tag: cell type


title: Patient n°45T


title: Patient n°47T


title: pMX-GFP vitamin C GFPVc+_1

tag: strain


title: EctodermT36_vs_EndodermT36

city: NICE

first: Cecile

last: Sabourault

address: Faculte des Sciences, Parc Valrose, BP 71

department: Biology

country: France

institute: University of Nice

description:
Raw file_Rep1: EctodermT36Sy3_vs_EndodermT36Sy3.gpr
Raw file_Rep1: EndodermT36Sy3_vs_EctodermT36Sy3.gpr
Raw file_Rep2: EctodermT36Sy5_vs_EndodermT36Sy5.gpr
Raw file_Rep2: EndodermT36Sy5_vs_EctodermT36Sy5.gpr
Raw file_Rep3: EctodermT36Sy4_vs_EndodermT36Sy4.gpr
Raw file_Rep3: EndodermT36Sy4_vs_EctodermT36Sy4.gpr

hyb_protocol: 500 ng of each labeled cDNA was diluted in Hi-RPM Gene Expression Hyb buffer (Agilent) and hybridized on the array overnight at 47°C. Dye-swapping hybridizations were performed between endodermal and ectodermal extracts at each time point (T0, T12h and T36h) for each sample (3 biological replicates).

scan_protocol: Slides were scanned using an AXON 4000B scanner (Molecular Devices). Image acquisition and quality control was performed using GenePix ® Pro 6.0 software.

data_processing: Analyses were carried out using the LimmaGUI package for the R system. Normexp + offset (positive offset of 50) method was performed as background correction. Print-tip loess normalization was performed for each slide. Quantile normalization was applied to mean-log intensities in order to make the distributions essentially equivalent across arrays.

organism: Anemonia viridis

label_protocol: 5µg of total RNA was labeled using the ChipShotTM Direct labeling system and further purified using the Clean-up system (Promega), according to the manufacturer's instructions. 5ng of a Lux mRNA exogenous standard was added to each sample before labeling.

extract_protocol: Total RNA from whole tentacles was extracted using Trizol® Reagent (Invitrogen) following Chomczynski and Mackey procedure (BioTechniques, 1995). RNA was subjected to a DNase treatment (RQ1-DNAse, Promega), then resuspended in nuclease-free water. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrophotometer and a Bioanalyzer 2100 (Agilent Technology), respectively.

treatment_protocol: Anemonia viridis specimens were collected from Antibes, France. After 30 days of acclimation, sea anemones were subjected to a temperature increase of +10°C and UV exposure (+1.25 mW.cm-2). A time course sampling were done at T0, T12h and T36h. The ectodermal tissue layer was manually separated from the endodermal one (also containing zooxanthellae cells) immediately after tentacle sampling.

tag: time

tag: stress

value: UV+Thermal stress


title: Patient n°44T

tag: tissue


title: Patient n°40T


title: Patient n°35T


title: EctodermT12_vs_EndodermT12

description:
Raw file_Rep1: EctodermT12Sy3_vs_EndodermT12Sy3.gpr
Raw file_Rep1: EndodermT12Sy3_vs_EctodermT12Sy3.gpr
Raw file_Rep2: EctodermT12Sy5_vs_EndodermT12Sy5.gpr
Raw file_Rep2: EndodermT12Sy5_vs_EctodermT12Sy5.gpr
Raw file_Rep3: EctodermT12Sy4_vs_EndodermT12Sy4.gpr
Raw file_Rep3: EndodermT12Sy4_vs_EctodermT12Sy4.gpr


title: EctodermT0_vs_EndodermT0

description:
Raw file_Rep1: EctodermT0Sy3_vs_EndodermT0Sy3.gpr
Raw file_Rep1: EndodermT0Sy3_vs_EctodermT0Sy3.gpr
Raw file_Rep2: EctodermT0Sy5_vs_EndodermT0Sy5.gpr
Raw file_Rep2: EndodermT0Sy5_vs_EctodermT0Sy5.gpr
Raw file_Rep3: EctodermT0Sy4_vs_EndodermT0Sy4.gpr
Raw file_Rep3: EndodermT0Sy4_vs_EctodermT0Sy4.gpr


title: cervix-abstain-B2

city: Adelaide

first: Sarah

middle: Anne

last: Robertson

state: SA

address: Frome Rd

department: paediatrics and Reproductive Health

country: Australia

institute: University of Adelaide

hyb_protocol: Genechips  were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.

scan_protocol: Genechips were scanned using the Affymetrix GSC3000 scanner.

data_processing: Data was processed with Partek Genomics Suite using RMA background correction and quantile array normalisation.

source_name: participant #1 ectocervix, no coitus, LH+2 - LH+3

label_protocol: Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.

extract_protocol: RNA was recovered from cervical tissue biopsies by disruption in 500 μl of Trizol® solution (Invitrogen, Carlsbad, CA, USA) by homogenisation using a pestle mixer (Scientific Specialties Inc, Randallstown, US) and extraction in 50 μl of chloroform (Sigma-Aldrich). RNA was then precipitated from the aqueous phase in isopropanol (Sigma, Castle Hill, AU) and the pellet was washed in ice cold 75% ethanol, dried and resuspended in 100 μl milli-Q water. RNA was then treated with RNase-free DNase I (500 IU/ml; 60 min/37C) (Roche, Basel, Switzerland), precipitated in ethanol and stored at -80oC. Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.

value: (1) no coitus (control)

tag: coitus

value: no

tag: semen exposure


title: cervix-coitus-B1

source_name: participant #3 ectocervix, unprotected coitus, LH0 - LH+1

value: (3) unprotected coitus (coitus)


title: Patient n°33T

value: rectal tumor

tag: gender

value: Male

value: NR


title: cervix-abstain-B1

source_name: participant #1 ectocervix, no coitus, LH0 - LH+1


title: cervix-condom-B2

source_name: participant #2 ectocervix, coitus with condom, LH0 - LH+1

value: (2) coitus with a condom (condom)

value: yes


title: cervix-coitus-B2


title: cervix-condom-B1


title: D_TempUV120h

description:
Raw file_Rep1: D1t0_D1t120.gpr
Raw file_Rep1: D1t120_D1t0.gpr
Raw file_Rep2: D2t0_D2t120.gpr
Raw file_Rep2: D2t120_D2t0.gpr
Raw file_Rep3: D3t0_D3t120.gpr
Raw file_Rep3: D3t120_D3t0.gpr

hyb_protocol: 500 ng of each labeled cDNA was diluted in Hi-RPM Gene Expression Hyb buffer (Agilent) and hybridized on the array overnight at 47°C. Dye-swapping hybridizations were performed between the reference and each kinetic point (T0-Txh), for each sample (3 biological replicates) and condition (control, T°, UV, T°+UV).

data_processing: Analyses were carried out using the LimmaGUI package for the R system. Normexp + offset (positive offset of 50) method was performed as background correction. Print-tip loess normalization was performed for each slide. Quantile normalisation was applied to mean-log intensities in order to make the distributions essentially equivalent across arrays.

treatment_protocol: Anemonia viridis specimens were collected from Antibes, France. After 30 days of acclimation, sea anemones were subjected to a temperature stress (+10°C) or/and a UV stress (+1.25mW.cm-2) and a time course sampling was done over a 5 days period: T0 (reference), T24h, T48h and T120h.

value: tentacle (ectoderm+endoderm)

value: 0h (reference)


title: Patient n°12T

value: blood


title: D_TempUV48h

description:
Raw file_Rep1: D1t0_D1t48.gpr
Raw file_Rep1: D1t48_D1t0.gpr
Raw file_Rep2: D2t0_D2t48.gpr
Raw file_Rep2: D2t48_D2t0.gpr
Raw file_Rep3: D3t0_D3t48.gpr
Raw file_Rep3: D3t48_D3t0.gpr


title: Gene expression profile of DAP12 knockdown THP-1 cells following exposure to phorbol 12-myristate 13-acetate (I)

city: Tokyo

first: Jun-ichi

last: Satoh

address: 2-522-1 Noshio, Kiyose

department: Bioinformatics

country: Japan

institute: Meiji Pharmaceutical University

hyb_protocol: Hybridization was performed at 45℃ for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software (Affymetrix).

source_name: THP-1 cells, scrambled, DMSO treated

label_protocol: Three hundred ng of total RNA was processed for cRNA synthesis, fragmentation, and terminal labeling with the GeneChip Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix).

growth_protocol: THP-1 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 55 microM 2-mercaptoethanol, 2 mM L-glutamine, 100 U/ml penicillin and 100 microgram/ml streptomycin (feeding medium).

extract_protocol: Total RNA was isolated from the cells by using the TRIZOL Plus RNA Purification kit (Invitrogen). The quality of total RNA was evaluated on Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The clonal SCR4 cells were exposed to DMSO for 24 hours.

value: THP-1 monocyte

tag: clone

tag: vector construct

value: scrambled sequence

tag: agent

value: DMSO


title: D_TempUV24h

description:
Raw file_Rep1: D1t0_D1t24.gpr
Raw file_Rep1: D1t24_D1t0.gpr
Raw file_Rep2: D2t0_D2t24.gpr
Raw file_Rep2: D2t24_D2t0.gpr
Raw file_Rep3: D3t0_D3t24.gpr
Raw file_Rep3: D3t24_D3t0.gpr


title: Gene expression profile of DAP12 knockdown THP-1 cells following exposure to phorbol 12-myristate 13-acetate (III)

source_name: THP-1 cells, siRNA, DMSO-treated

treatment_protocol: The clonal SI17 cells were exposed to DMSO for 24 hours.

value: siRNA vector targeting DAP12


title: C_UV120h

description:
Raw file_Rep1: C1t0_C1t120.gpr
Raw file_Rep1: C1t120_C1t0.gpr
Raw file_Rep2: C2t0_C2t120.gpr
Raw file_Rep2: C2t120_C2t0.gpr
Raw file_Rep3: C3t0_C3t120.gpr
Raw file_Rep3: C3t120_C3t0.gpr

value: UV stress (+1.25 mW.cm-2)


title: C_UV48h

description:
Raw file_Rep1: C1t0_C1t48.gpr
Raw file_Rep1: C1t48_C1t0.gpr
Raw file_Rep2: C2t0_C2t48.gpr
Raw file_Rep2: C2t48_C2t0.gpr
Raw file_Rep3: C3t0_C3t48.gpr
Raw file_Rep3: C3t48_C3t0.gpr


title: Gene expression profile of DAP12 knockdown THP-1 cells following exposure to phorbol 12-myristate 13-acetate (IV)

source_name: THP-1 cells, siRNA, PMA treated

treatment_protocol: The clonal SI17 cells were exposed to 50 nM phorbol 12-myristate 13-acetate (PMA) for 24 hours.

value: PMA


title: Gene expression profile of THP-1 monocytes following knockdown of DAP12, a causative gene for Nasu-Hakola disease (III)

source_name: THP-1 cells, siRNA, untreated

treatment_protocol: The clonal SI17 cells were maintained in an untreated condition.

tag: cell line

value: acute monocytic leukemia

tag: genotype/variation

value: clone named SI17 stably expressing the siRNA vector targeting DAP12


title: Gene expression profile of DAP12 knockdown THP-1 cells following exposure to phorbol 12-myristate 13-acetate (II)

source_name: THP-1 cells, scrambled, PMA treated

treatment_protocol: The clonal SCR4 cells were exposed to 50 nM phorbol 12-myristate 13-acetate (PMA) for 24 hours.


title: C_UV24h

description:
Raw file_Rep1: C1t0_C1t24.gpr
Raw file_Rep1: C1t24_C1t0.gpr
Raw file_Rep2: C2t0_C2t24.gpr
Raw file_Rep2: C2t24_C2t0.gpr
Raw file_Rep3: C3t0_C3t24.gpr
Raw file_Rep3: C3t24_C3t0.gpr


title: Patient n°37T

source_name: rectal tumor tissue from pre-therapy biopsy

tag: age

tag: ut

tag: un

tag: ypt

tag: ypn

source_name: blood from a pool of healthy individuals


title: Patient n°28T

tag: response to therapy according to trg by dworak

tag: response group

value: R


title: Gene expression profile of THP-1 monocytes following knockdown of DAP12, a causative gene for Nasu-Hakola disease (II)

source_name: THP-1 cells, scrambled, untreated

treatment_protocol: The clonal SCR4 cells were maintained in an untreated condition.

tag: cell type

value: clone named SCR4 stably expressing the scrambled sequence


title: E. coli K12 interacted with lettuce rhizosphere rep5

city: st. paul

first: zhe

last: hou

state: MN

address: 1334 Eckles Ave

department: Food Science and nutrition

institute: University of Minnesota

hyb_protocol: Total RNA was converted to cDNA using the Superscript II Reverse transcriptase and directly labeled with Cy3 or Cy5 dyes (invitrogen) prior to hybridization. The labeled cDNA was applied to microarray slides. Following prehybridization, microarrays were hybridized with labeled cDNAs for 48 hours at 42°C in a water bath under dark

scan_protocol: Image analysis was carried out with the corresponding software program using a file that lists the corresponding gene to each spot. Signal intensities for each spot on scanned image files were determined using GenePix® Pro 6.0 software

data_processing: Signal intensities were normalized for spot and slide abnormalities with the spatial Lowess algorithm and analyzed by mixed-effect ANOVA (MAANOVA) (Kerr et al. 2000). Both Lowess and MAANOVA are part of the R/MAANOVA microarray statistical package, available at (http://www.jax.org/staff/churchill/labsite/). The resulting variety-by-gene interaction (VG) values of the control and experimental spot intensities were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Cui. et. al). Duplicate expression values from each array were combined, averaged and values from MAANOVA were subsequently subjected to significance analysis of microarray (SAM) data with the SAM package (Tusher. et.al). Significantly up- and down-regulated genes were identified based on a 1.5 cutoff threshold, a global false discovery rate lower than 5% (p<0.05). Six arrays representing a total of 12 replicates were analyzed between a treatment and a control.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655 cells interacted with the lettuce rhizosphere for 3 days

label_protocol: The total nucleic acid samples was precipitated and treated with DNase I for 30 min to remove contaminating DNA. The concentration of RNA was measured spectrophotometrically and RNA samples were electrophoresed in 0.8% agarose gels prior to use to ensure RNA integrity. The cDNA was synthesized from 10 µg of total RNA template.

growth_protocol: Escherichia coli MG1655 were grown in 10 ml of LB medium until stationary phase, collected by centrifugation at 8,000 ×g for 10 min, and washed twice with sterilized, plant growth medium (Caspersen et al. 1999). The resultant cells were re-suspended in 10 ml of the same plant growth medium to a final concentration of approximately 10E9 cells/ml. Germinated lettuce seedlings  were each aseptically transferred into holes in the growth boxes filled with 300 ml of plant growth medium, and 3 ml washed bacterial suspension was added to provide approximately 10E7 cells/ml of growth medium. Seedling boxes were germinated for a week and  transferred to a plant growth chamber, and the aeration pump (Luft Pump; Oceanic systems Inc. Dallas, TX) was immediately started. Each pump supplied aeration of three growth boxes, at a rate of 1.3 L /min. The seedling boxes were incubated under 80% RH at 25°C with a photoperiod of 16 h for 3 days

extract_protocol: Standard hot-phenol method

treatment_protocol: Following incubation, roots had been gently rinsed to remove loosely attached bacteria and roots were cut directly into 100 ml ice cold stop solution (5 % H2O-saturated phenol, pH 4.3, in 95% ethanol).  Root extracts were filtered using 0.5 µm filters to separate bacteria cells from plant cells in order to prevent interference of the cDNA labeling. Qiagen RNA protect solution was used to stabilize RNA during extraction. Bacteria had been collected by shaking and washing and stored in -80°C until using for RNA isolation.

tag: treatment

value: exposed to the lettuce rhizosphere for 3 days

source_name: Escherichia coli MG1655 cells grown in the hydroponic system without interacting with the lettuce rhizosphere for 3 days

value: control


title: E. coli K12 interacted with lettuce rhizosphere rep6


title: Patient n°21T

tag: tissue

value: rectal tumor

value: Male

value: NR


title: A_Temp24h

description:
Raw file_Rep1: A1t0_A1t24.gpr
Raw file_Rep1: A1t24_A1t0.gpr
Raw file_Rep2: A2t0_A2t24.gpr
Raw file_Rep2: A2t24_A2t0.gpr

value: tentacle (ectoderm+endoderm)

tag: time

value: 0h (reference)

tag: stress

value: thermal stress (+10°C)


title: Patient n°36T

tag: gender

value: blood


title: Patient n°43T

value: Female


title: E. coli K12 interacted with lettuce rhizosphere rep3


title: Patient n°29T


title: E. coli K12 interacted with lettuce rhizosphere rep2


title: E. coli K12 interacted with lettuce rhizosphere rep4


title: Gene expression profile of THP-1 monocytes following knockdown of DAP12, a causative gene for Nasu-Hakola disease (I)

source_name: THP-1 cells, wild type, untreated

treatment_protocol: The wild-type cells were maintained in an untreated condition.

value: wild type

value: hematopoietic origin


title: Patient n°39T


title: B_Control120h

description:
Raw file_Rep1: B1t0_B1t120.gpr
Raw file_Rep1: B1t120_B1t0.gpr
Raw file_Rep2: B2t0_B2t120.gpr
Raw file_Rep2: B2t120_B2t0.gpr
Raw file_Rep3: B3t0_B3t120.gpr
Raw file_Rep3: B3t120_B3t0.gpr


title: A_Temp120h

description:
Raw file_Rep1: A1t0_A1t120.gpr
Raw file_Rep1: A1t120_A1t0.gpr
Raw file_Rep2: A2t0_A2t120.gpr
Raw file_Rep2: A2t120_A2t0.gpr


title: Patient n°42T


title: A_Temp48h

description:
Raw file_Rep1: A1t0_A1t48.gpr
Raw file_Rep1: A1t48_A1t0.gpr
Raw file_Rep2: A2t0_A2t48.gpr
Raw file_Rep2: A2t48_A2t0.gpr
Raw file_Rep3: A3t0_A3t48.gpr
Raw file_Rep3: A3t48_A3t0.gpr


title: E. coli K12 interacted with lettuce rhizosphere rep1


title: Patient n°38T


title: Patient n°22T


title: Patient n°56T


title: Patient n°16T


title: Patient n°5T


title: B_Control48h

description:
Raw file_Rep1: B1t0_B1t48.gpr
Raw file_Rep1: B1t48_B1t0.gpr
Raw file_Rep2: B2t0_B2t48.gpr
Raw file_Rep2: B2t48_B2t0.gpr
Raw file_Rep3: B3t0_B3t48.gpr
Raw file_Rep3: B3t48_B3t0.gpr


title: siXist_Morula_rep3

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

description: Gene expression of Xist-siRNA-injected single cloned embryo derived from Sertoli cell at morula stage

hyb_protocol: Cy3-labeled RNA was hybridized to a whole mouse genome oligo DNA microarray (4 x 44 K, Agilent Technologies, Palo Alto, CA, USA) for 17 h at 65 °C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images of microarray slides were processed using Feature Extraction software (Agilent Technologies). All raw data were loaded into Gene Spring GX 11 (Agilent Technologies) and transformed by quantile normalization.
Signal intensity of each sample was normalized using external scalar derived from the total amount of amplified RNA.

source_name: Sertoli Clone, Xist siRNA, single morula

label_protocol: Amplified RNA was labeled with Cyanine-3 (Cy3) dye (GE Healthcare UK Limited, Amersham, England) according to the manufacturer's instructions.

growth_protocol: In vitro fertilized (IVF) or Sertoli Clone embryos were cultured in potassium modified simplex optimization medium (KSOM) for 72 h from the activation.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) from single embryos. They were subjected to linear amplification using TargetAmp Two-Round Aminoallyl-aRNA Amplification Kits (Epicentre Biotechnologies, Madison, WI, USA).

treatment_protocol: Sertoli Clone embryos were injected with Control- or Xist-siRNA 6–7 h after activation, corresponding to the pronuclear (1-cell) stage.

value: male

tag: strain

value: whole embryo

tag: developmental stage

value: morula


title: siXist_Morula_rep4


title: B_Control24h

description:
Raw file_Rep1: B1t0_B1t24.gpr
Raw file_Rep1: B1t24_B1t0.gpr
Raw file_Rep2: B2t0_B2t24.gpr
Raw file_Rep2: B2t24_B2t0.gpr
Raw file_Rep3: B3t0_B3t24.gpr
Raw file_Rep3: B3t24_B3t0.gpr


title: Patient n°54T


title: Patient n°27T


title: Patient n°25T


title: Patient n°46T

value: R


title: Patient n°41T


title: Patient n°24T


title: Patient n°1T


title: Patient n°31T


title: Patient n°34T


title: siXist_Morula_rep2


title: siCont_Morula_rep4

description: Gene expression of Control-siRNA-injected single cloned embryo derived from Sertoli cell at morula stage

source_name: Sertoli Clone, Control siRNA, single morula


title: Patient n°51T


title: siCont_Morula_rep3


title: Patient n°50T


title: Patient n°48T


title: siCont_Morula_rep1


title: IVF_Morula_rep4

description: Gene expression of IVF-generated single embryo at morula stage

source_name: IVF, non-treated, single morula

value: female


title: siXist_Morula_rep1


title: IVF_Morula_rep2


title: C2C12_cells_untreated

city: Campinas

first: Maria Angélica

middle: Lopes de

last: Souza

state: São Paulo

address: Franscisco Otaviano nº 60 sl 52

country: Brazil

institute: Scylla Bioinformática

hyb_protocol: 25µl of reaction was transferred to another tube containing 78µl of Hybridization Buffer A, 130µl of Hybridization Buffer B and 27µl of water and the  reaction was incubated at 90°C for 5min. Each tube was then placed on ice and then  applied to the Codelink DNA microarray containing around 36,000 genes. The  subsequent stages of hybridization, washing and analysis of each microarray were  carried out as detailed in the Codelink Gene Expression System: Single-Assay Biorray Hybridization and Detection manual.

scan_protocol: Scanner Gene Pix 4000B (Molecular Devices) standard procedure

data_processing: The gene expression date were normalized using the Suport Vector Regression (SVR)           implemented in the GEDI toolbox (http://www.iq.usp.br/wwwdocentes/mcsoga/gedi/) . Identification of these genes was obtained using the ratio of normalized intensities between rhBMP (2 or 7) and control (untreated) samples, considering a fold change of >= 2.5.

source_name: C2C12 cells, control

label_protocol:
The cDNA was purified and 20 µl of each purified cDNA was mixed with 12 µl  Biotin-
NTP,  4µl  of 10X T7 reaction buffer and 4 µl  of 10X Enzyme Mix reaction buffer and incubated at 37°C for 14h. After cRNA synthesis, the cRNA preparation was purified
and 10 µg of biotinylated cRNA was mixed with 5 µl  of Fragmentation Buffer in a  final volume of 25 µl , incubated at 94°C for 20min and then kept on ice for 5min.

extract_protocol:
total RNA was extracted with RNeasy
The cRNA was prepared as recommended in the Amersham CodelinkTM iExpress Assay Reagent Kit manual. Briefy, the sample containing 1.5 µg RNA untreated  was mixed with 7.5 µl of bacterial mRNAs (10pg/µl), 1 µl of oligo dT in a final volume of 12 µl.  The reaction was incubated at 70ºC for 10min and kept on ice by 3min. Subsequently, 2 µl of 10X First Strand Buffer, 4 µl 5mM dNTPs, 1 µl RNase inhibitor, and 1 µl ArrayScript were added to tube, in a final volume of 20 µl. The reaction was incubated at 42°C for 2h. After this period, the tube was placed on ice and 63 µl water, 10 µl of 10X Second Strand Buffer, 4 µl of 5mM dNTPs, 2 µl of DNA polymerase and 1 µl of  RNaseH were added. The reaction is incubating at 16°C for 2h.

treatment_protocol: untreated

value: pre-myoblastic and pre-osteoblastic C2C12 cell line


title: siCont_Morula_rep2


title: Patient n°20T


title: IVF_Morula_rep3


title: C2C12_cells_treated_with_rhBMP2

data_processing: The gene expression date were normalized using the Suport Vector Regression (SVR).             Implemented in the GEDI toolbox (http://www.iq.usp.br/wwwdocentes/mcsoga/gedi/) . Identification of these genes was obtained using the ratio of  normalized intensities between rhBMP2 and control (untreated) samples, considering a fold change of >= 2.5.

source_name: C2C12 cells treated with rhBMP2

extract_protocol:
total RNA was extracted with RNeasy
The cRNA was prepared as recommended in the Amersham CodelinkTM  iExpress Assay Reagent Kit manual. Briefly, the sample containing 1.5 µg RNA of  culture treated for 12h with rhBMP2  was mixed with 7.5 µl of
bacterial mRNAs (10pg/µl), 1 µl of oligo dT in a final volume of 12 µl.  The reaction was incubated at 70ºC for 10min and kept on ice by 3min. Subsequently, 2 µl of 10X First Strand Buffer, 4 µl 5mM dNTPs, 1 µl RNase inhibitor, and 1 µl ArrayScript were added to tube, in a final volume of 20 µl. The reaction was incubated at 42°C for 2h. After this period, the tube was placed on ice and 63 µl water, 10 µl of 10X Second Strand Buffer, 4 µl of 5mM dNTPs, 2 µl of DNA polymerase and 1 µl of RNaseH were added. The reaction is incubating at 16°C for 2h.

treatment_protocol: C2C12 cultures treated for 12h with 200ng/ml rhBMP2


title: C2C12_cells_treated_with_rhBMP7

data_processing: The gene expression date were normalized using the Suport Vector Regression (SVR).             Implemented in the GEDI toolbox (http://www.iq.usp.br/wwwdocentes/mcsoga/gedi/) . Identification of these genes was obtained using the ratio of  normalized intensities between rhBMP7 and control (untreated) samples, considering a fold change of >= 2.5.

source_name: C2C12 cells treated with rhBMP7

extract_protocol:
total RNA was extracted with RNeasy
The cRNA was prepared as recommended in the Amersham CodelinkTM  iExpress Assay Reagent Kit manual. Briefly, the sample containing 1.5 µg RNA of  culture treated for 12h with rhBMP7  was mixed with 7.5 µl of
bacterial mRNAs (10pg/µl), 1 µl of oligo dT in a final volume of 12 µl.  The reaction was incubated at 70ºC for 10min and kept on ice by 3min. Subsequently, 2 µl of 10X First Strand Buffer, 4 µl 5mM dNTPs, 1 µl RNase inhibitor, and 1 µl ArrayScript were added to tube, in a final volume of 20 µl. The reaction was incubated at 42°C for 2h. After this period, the tube was placed on ice and 63 µl water, 10 µl of 10X Second Strand Buffer, 4 µl of 5mM dNTPs, 2 µl of DNA polymerase and 1 µl of RNaseH were added. The reaction is incubating at 16°C for 2h.

treatment_protocol: C2C12 cultures treated for 12h with 200ng/ml rhBMP7


title: IVF_Morula_rep1


title: 7days

status: Public on Nov 16 2011

city: bucheon

first: moo kyun

last: park

state: Gyeonggi-do

address: jung dong 1174

department: otorhinolarynogology

country: South Korea

institute: soonchunhyang univeristy bucheon hosptial

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Rat Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).

organism: Rattus norvegicus

source_name: 7days after labyrinthectomy

label_protocol:
each 1ug total RNA and T7 promoter primer mix and incubated at 65oC for 10 min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 65oC for 15 min. The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was preformed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40oC for 2 hours.
Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: labyrinthectomized in the left ear through a postauricular approach under a surgical microscope

extract_protocol: Total RNA from the vestibular nuclei of rats was extracted using Rneasy Mini Kits (Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions (RNeasy Handbook, June 2001).

treatment_protocol: Adult male Sprague-Dawley rats weighing 200 to 250 g were used. One vestibular nucleus was too small to obtain sufficient RNA for microarray analysis. Therefore, the ipsilateral vestibular nuclei of three rats were removed at 1 and 7 days after the left labyrinthectomy, and the vestibular nuclei of three normal rats were used for controls

value: Sprague-Dawley

tag: protocol

value: labyrinthectomy of left ear

value: ipsilateral vestibular nuclei


title: NL rat

source_name: control with sham operation

value: control (sham operation)

value: control

value: vestibular nuclei


title: LNCaP, 12hr ETOH

city: singapore

first: Peck Yean

last: TAN

address: 60 Biopolis Street #02-01 Genome

country: Singapore

institute: Genome Institute of Singapore (GIS)

description:
Total RNA after 12hr ETOH treatment in LNCaP cells
1688628151_B, 1688628114_B, 1688628153_B

hyb_protocol: standard Illumina protocol

scan_protocol: BeadChips were scanned using the BeadArray Reader (Illumina).

data_processing:
Raw data was analyzed using GeneSpring GX 11.0 software. Dataset was normalized using percentile shift normalization and baseline transformed to median of control samples.
Triplicates were generated for the experiment and analyses were performed using the average of the triplicates (after normalization). Raw data provided as supplementary file (filename: LNCaP_Sample_Probe_Profile.txt)

source_name: LNCaP prostate cancer cells

label_protocol: Biotinylated cRNA were prepared from 500ng total RNA using Illumina TotalPrep-96 RNA Amplification Kit (Ambion).

growth_protocol: Human LNCaP prostate cancer cells were maintained in RPMI Medium 1640 (Gibco) supplemented with 10% fetal bovine serum (FBS), 1 mM sodium pyruvate, 100 units/ml penicillin, 100 µg/ml streptomycin, and 30 µg/ml gentamycin in a 37°C incubator with 5% CO2.

extract_protocol: RNA was isolated using TRI reagent (Sigma) and chloroform before purification according to manufacturer protocol in PureLink RNA Mini Kit (Invitrogen).

treatment_protocol: Prior to vehicle/drug stimulation, ~600, 000 cells were seeded into 150 mm dish and starved with phenol red-free RPMI Medium 1640 containing 5% charcoal-dextran treated FBS (Hyclone) and the same amount of sodium pyruvate, penicillin, streptomycin and gentamycin as mentioned earlier for at least 72 hrs to ~70-80% confluence. Androgen-deprived cells were treated with DHT to a final concentration of 10 nM for 1, 3, 6, 12 or 24hrs before harvesting for RNA.  Cells treated with an equal volume of vehicle, ETOH, for the same duration, served as controls.

value: androgen-dependent prostate cancer cells

tag: cell line

value: LNCaP

value: ETOH


title: LNCaP, 3hr ETOH

description:
Total RNA after 3hr ETOH treatment in LNCaP cells
1688628152_D, 1688628113_D, 1688628111_D

value: 3 h


title: LNCaP, 6hr ETOH

description:
Total RNA after 6hr ETOH treatment in LNCaP cells
1688628152_G, 1688628113_G, 1688628153_A

value: 6 h


title: LNCaP, 12hr DHT

description:
Total RNA after 12hr DHT treatment in LNCaP cells
1688628151_C, 1688628114_C, 1688628153_C

value: DHT


title: MO2-nr3c1-5m injected embryos at 10 hours post fertilization - MO2-nr3c1 injected embryos at 10 hours post fertilization

city: Padua

first: Andrea

last: Celeghin

state: Veneto

address: Via Ugo Bassi 58 B

institute: University of Padua

description:
MO2-nr3c1-5m (10hpf) - MO2-nr3c1 (10hpf)
Danio rerio embryos injected with a specific control morpholino compared to embryos injected with a translation blocking morpholino for glucocorticoid receptor. All the embryos are fixed at 10 hours post fertilization.

hyb_protocol: The samples were mixed with 25X Fragmentation Buffer and 10X Blocking Agent (Agilent Gene Expression Hybridization Kit), and the samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on Agilent Technologies Scanner G2505B US22502723. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Danio rerio

source_name: MO2-nr3c1-5m, 10hpf

label_protocol: 200 ng of total RNA were primed and reversed transcribed using the Agilent Quick-Amp labeling Kit protocol following the manufacturer's instructions.

growth_protocol: Microinjected embryos were raised in fish water at 28.5 C degrees and were fixed at 5 hpf and 10 hpf.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: Danio rerio ovulated oocytes were microinjected with a translation-blocking morpholino for glucocorticoid receptor (nr3c1) (8.3 ng per embryo) or with 5-mismatched morpholino (8.3 ng per embryo).

tag: morphant

value: embryo

tag: age

value: 10 hours post fertilization

source_name: MO2-nr3c1, 10hpf


title: MO2-nr3c1-5m injected embryos at 5 hours post fertilization - MO2-nr3c1 injected embryos at 5 hours post fertilization

description:
MO2-nr3c1-5m (5hpf) - MO2-nr3c1 (5hpf)
Danio rerio embryos injected with a specific control morpholino compared to embryos injected with a translation blocking morpholino for glucocorticoid receptor. All the embryos are fixed at 5 hours post fertilization.

source_name: MO2-nr3c1-5m, 5hpf

value: 5 hours post fertilization

source_name: MO2-nr3c1, 5hpf


title: LNCaP, 6hr DHT

description:
Total RNA after 6hr DHT treatment in LNCaP cells
1688628152_H, 1688628114_A, 1688628111_G


title: LNCaP, 24hr DHT

description:
Total RNA after 24hr DHT treatment in LNCaP cells
1688628151_F, 1688628114_F, 1688628153_F


title: LNCaP, 24hr ETOH

description:
Total RNA after 24hr ETOH treatment in LNCaP cells
1688628151_E, 1688628114_E, 1688628153_E


title: 1day

source_name: 1day after labyrinthectomy


title: LNCaP, 3hr DHT

description:
Total RNA after 3hr DHT treatment in LNCaP cells
1688628152_E, 1688628113_E, 1688628111_E


title: wt, skeletal muscle bio rep 1

city: Hershey

first: Nuno

last: Raimundo

state: PA

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

description: gene expression data from cerebellum of wt mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 60C on mouse chip. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix scanner

data_processing: The data were analyzed with GCOS 4.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.  For statistical analysis, unicaudal t-test p<0.05 was used.

source_name: quadriceps femoris

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: tissue type

value: quadriceps femoris

value: 26 months

tag: genome/variation

value: wild type


title: wt, skeletal muscle bio rep 4

value: 23 months


title: mutant Twinkle overexpressor, skeletal muscle bio rep 1

description: gene expression data from cerebellum of mice overexpressing mutant Twinkle

value: 24 months

value: mutant Twinkle overexpressor


title: Wild type embryos at 10 hours post fertilization - MO2-nr3c1 injected embryos at 10 hours post fertilization

description:
WT(10hpf) - MO2-nr3c1 (10hpf)
Danio rerio wild type embryos compared to embryos injected with a translation blocking morpholino for glucocorticoid receptor. All the embryos are fixed at 10 hours post fertilization.

source_name: WT, 10hpf

tag: genotype


title: Wild type embryos at 5 hours post fertilization - MO2-nr3c1 injected embryos at 5 hours post fertilization

description:
WT(5hpf) - MO2-nr3c1 (5hpf)
Danio rerio wild type embryos compared to embryos injected with a translation blocking morpholino for glucocorticoid receptor. All the embryos are fixed at 5 hours post fertilization.

source_name: WT, 5hpf


title: wt, skeletal muscle bio rep 2


title: mutant Twinkle overexpressor, skeletal muscle bio rep 2


title: wt, skeletal muscle bio rep 3

value: 21 months


title: Cell Line, X5

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

description:
X5
Xenograft model, Algimatrix model, sub-cutaneous injection

scan_protocol: ABI Prism 7900 HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA).

data_processing: SDS files were processed in RQ manager software and raw data were then exported in XLS file.

label: FAM

label_protocol: cDNA was prepared using the High Capacity cDNA kit with RNAse inhibitor (Applied Biosystems, Foster City, CA) as per the manufacturer’s instructions, but no labelling was performed as TaqMan-based qRT-PCR was performed subsequently.

growth_protocol: Clinical samples were fresh frozen. Cell lines were grown either as monolayers or in 3-D (see Gillet et al.)

extract_protocol: Total RNA was prepared using the Trizol method (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: All of the CP-r cells were maintained in the presence of cisplatin, but cisplatin was removed from the medium 3 days prior to preparation of RNA. See Gillet et al.

value: ovarian cancer cells


title: Cell Line, X7

description:
X7
Xenograft model, Geltrex, sub-cutaneous injection


title: Cell Line, X8

description:
X8
Xenograft model, Geltrex, sub-cutaneous injection, (plus one additonal passage in culture)


title: Normal ovarian tissue, N1

description:
N1
Commercially available normal ovarian tissue

source_name: Normal ovarian tissue, Biochain

value: normal ovary


title: Cell Line, X6

description:
X6
Xenograft model, monolayer cells sub-cutaneous injection


title: Cell Line, CL24

description:
CL24
Hanging Drop model


title: Cell Line, CL22

description:
CL22
PEO4, cisplatin resistant cell line


title: Cell Line, CL23

description:
CL23
A2780/CP, cisplatin resistant cell line


title: Cell Line, X2

description:
X2
Xenograft model, LAP, IP (plus one additonal passage in culture)


title: Cell Line, CL28

description:
CL28
Geltrex model


title: Normal ovarian tissue, N4

description:
N4
Commercially available normal ovarian tissue

source_name: Normal ovarian tissue, Stratagene


title: Cell Line, X1

description:
X1
Xenograft model, LAP, IP (intra-peritoneal injection)


title: Normal ovarian tissue, N5

description:
N5
Commercially available normal ovarian tissue

source_name: Normal ovarian tissue, Ambion


title: Cell Line, X4

description:
X4
Xenograft model, Geltrex, IP,  (plus one additonal passage in culture)


title: Cell Line, CL21

description:
CL21
PAT-7, cisplatin resistant cell line


title: Normal ovarian tissue, N2

description:
N2
Commercially available normal ovarian tissue


title: Cell Line, X3

description:
X3
Xenograft model, Geltrex, IP


title: Cell Line, CL26

description:
CL26
Algimatrix model


title: mutant Twinkle overexpressor, skeletal muscle bio rep 3

description: gene expression data from cerebellum of mice overexpressing mutant Twinkle


title: Cell Line, CL27

description:
CL27
Grown in low attachment plate (LAP)


title: Cell Line, CL25

description:
CL25
Monolayer


title: Normal ovarian tissue, N3

description:
N3
Commercially available normal ovarian tissue


title: Cell Line, CL20

description:
CL20
C200, cisplatin resistant cell line


title: Cell Line, CL16

description:
CL16
HOSE, cisplatin resistant cell line

value: HOSE


title: Cell Line, CL18

description:
CL18
C30, cisplatin resistant cell line


title: Cell Line, CL19

description:
CL19
CP70, cisplatin resistant cell line


title: Cell Line, CL17

description:
CL17
PEO1, cisplatin resistant cell line


title: Cell Line, CL13

description:
CL13
Parental drug sensitive cells of KB-CP.5 and -CP20


title: Cell Line, CL7


title: Cell Line, CL10


title: Cell Line, CL8


title: Cell Line, CL5


title: Cell Line, CL4


title: Cell Line, CL12


title: Cell Line, CL2


title: Cell Line, CL15

description:
CL15
Liver carcinoma cell line, resistant to 20ug/ml cisplatin


title: Cell Line, CL3

description:
CL3
Adriamycin-resistant cells


title: Cell Line, CL9

description:
CL9
Cisplatin resistant cells (0.5ug/ml)


title: Cell Line, CL11

description:
CL11
Cisplatin resistant cells (20ug/ml)


title: Cell Line, CL1


title: Cell Line, RE.RXF.393

description:
RE.RXF.393
NCI-60 panel

source_name: Renal cancer

value: renal cancer cells


title: Cell Line, RE.CAKI.1

description:
RE.CAKI.1
NCI-60 panel


title: Cell Line, RE.UO.31

description:
RE.UO.31
NCI-60 panel


title: Cell Line, CL14

description:
CL14
Liver carcinoma cell line

value: liver carcinoma


title: Cell Line, RE.A498

description:
RE.A498
NCI-60 panel


title: Cell Line, RE.SN12C

description:
RE.SN12C
NCI-60 panel


title: Cell Line, RE.TK.10

description:
RE.TK.10
NCI-60 panel


title: Cell Line, RE.786O

description:
RE.786O
NCI-60 panel


title: Cell Line, PR.PC.3

description:
PR.PC.3
NCI-60 panel

source_name: Prostate cancer

value: prostate cancer cells


title: Cell Line, PR.DU.145

description:
PR.DU.145
NCI-60 panel


title: Cell Line, OV.SK.OV.3

description:
OV.SK.OV.3
NCI-60 panel

source_name: Ovarian cancer


title: Cell Line, CL6


title: Cell Line, OV.OVCAR.4

description:
OV.OVCAR.4
NCI-60 panel


title: Cell Line, OV.OVCAR.3

description:
OV.OVCAR.3
NCI-60 panel


title: Cell Line, RE.ACHN

description:
RE.ACHN
NCI-60 panel


title: Cell Line, OV.OVCAR.5

description:
OV.OVCAR.5
NCI-60 panel


title: Cell Line, ME.MDA.MB.435

description:
ME.MDA.MB.435
NCI-60 panel

source_name: Melanoma

value: melanoma cells


title: Cell Line, ME.UACC.257

description:
ME.UACC.257
NCI-60 panel


title: Cell Line, ME.LOXIMVI

description:
ME.LOXIMVI
NCI-60 panel


title: Cell Line, ME.M14

description:
ME.M14
NCI-60 panel


title: Cell Line, LE.SR

description:
LE.SR
NCI-60 panel

source_name: Leukemia

value: leukemia


title: Cell Line, OV.OVCAR.8

description:
OV.OVCAR.8
NCI-60 panel


title: Cell Line, ME.SK.MEL.5

description:
ME.SK.MEL.5
NCI-60 panel


title: Cell Line, OV.NCI.ADR.RES

description:
OV.NCI.ADR.RES
NCI-60 panel


title: Cell Line, ME.SK.MEL.2

description:
ME.SK.MEL.2
NCI-60 panel


title: Cell Line, ME.UACC.62

description:
ME.UACC.62
NCI-60 panel


title: Cell Line, LE.RPMI.8226

description:
LE.RPMI.8226
NCI-60 panel


title: Cell Line, ME.MALME.3M

description:
ME.MALME.3M
NCI-60 panel


title: Cell Line, LE.K.562

description:
LE.K.562
NCI-60 panel


title: Cell Line, OV.IGROV1

description:
OV.IGROV1
NCI-60 panel


title: Cell Line, ME.SK.MEL.28

description:
ME.SK.MEL.28
NCI-60 panel


title: Cell Line, LE.CCRF.CEM

description:
LE.CCRF.CEM
NCI-60 panel


title: Cell Line, LE.HL.60

description:
LE.HL.60
NCI-60 panel


title: Cell Line, LE.MOLT.4

description:
LE.MOLT.4
NCI-60 panel


title: Primary parietal epithelial cells EGM-MV Replicate 1

city: Rostock

first: Gregor

last: Warsow

address: Ernst-Heydemann-Str. 8

department: Medical Department

country: Germany

institute: University of Rostock

description: FACs sorted cells from transgenic mice

hyb_protocol: Samples were diluted 10-fold with RPMI-1640, incubate for 30-60 minutes on ice

scan_protocol: Affymetrix standard scan conditions

data_processing: JMP Genomics 4.0, RMA background correction, quantile normalization

label_protocol: Treating the suspended cells for 1 minute at 37°C with 2mM fluorescein di-ß-Galactopyranoside

growth_protocol: Cultivated capsulated or decapsulated glomeruli for 7-14 days in EGM-MV Medium

extract_protocol: trypsinisation the cells, resuspending the cells in RPMI

treatment_protocol: Changing the medium 1-2 times weekly

value: Primary parietal epithelial cell

tag: media

value: EGM-MV

tag: genetic background

value: mixed 75% Sv129


title: Cell Line, LC.NCI.H460

description:
LC.NCI.H460
NCI-60 panel

source_name: Non-small cell lung cancer

tag: cell type

value: non-small cell lung cancer cells


title: Cell Line, LC.NCI.H522

description:
LC.NCI.H522
NCI-60 panel


title: Primary parietal epithelial cells RPMI Replicate 1

description: FACs sorted cells from transgenic mice

source_name: Primary parietal epithelial cells RPMI

value: RPMI


title: Cell Line, LC.NCI.H322M

description:
LC.NCI.H322M
NCI-60 panel


title: 17WG (case30) fetal melanocyte, abdomen

city: Nagoya

first: Motoki

last: Nakamura

address: 1-Kawasumi, Mizuho-cho, Mizuho-ku

department: Nagoya City University

institute: Department of Geriatric and Environmental Dermatology

description: SAMPLE 7

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16hr at 45C on Affymetrix Human Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) algorithms using Affymetrix default analysis settings.

source_name: fetus

label_protocol: Biotinylated cRNA were prepared with the ambion WT Expression Kit (Ambion) and then fragmented and labeled with the GeneChip WT Terminal Labeling Kit (Affymetrix) from 100 ng total RNA.

growth_protocol: Cells were incubated in Medium 254 with human melanocyte growth supplement-2 (Cascade Biologics, Invitrogen) at 37C in 5% CO2.

extract_protocol: RNA purification was performed using an Rneasy Mini kit (Qiagen, Germany).

value: 17 weeks of gestation

tag: site

value: sole

value: cultured melanocyte


title: Podocyte cells EGM-MV Replicate 1

description: FACs sorted cells from transgenic mice

source_name: Podocyte cells EGM-MV

value: Primary podocyte cell


title: Cell Line, LC.HOP.62

description:
LC.HOP.62
NCI-60 panel


title: Cell Line, LC.HOP.92

description:
LC.HOP.92
NCI-60 panel


title: Cell Line, LC.NCI.H226

description:
LC.NCI.H226
NCI-60 panel


title: Primary parietal epithelial cells EGM-MV Replicate 2

description: FACs sorted cells from transgenic mice


title: Podocyte cells EGM-MV Replicate 2

description: FACs sorted cells from transgenic mice


title: Cell Line, LC.NCI.H23

description:
LC.NCI.H23
NCI-60 panel


title: Podocyte cells RPMI Replicate 2

description: FACs sorted cells from transgenic mice

source_name: Podocyte cells RPMI


title: 17WG (case30) fetal melanocyte, scalp

description: SAMPLE 5

tag: tissue


title: Podocyte cells RPMI Replicate 1

description: FACs sorted cells from transgenic mice


title: Cell Line, LC.EKVX

description:
LC.EKVX
NCI-60 panel


title: 17WG (case30) fetal melanocyte, back

description: SAMPLE 6


title: Primary parietal epithelial cells RPMI Replicate 2

description: FACs sorted cells from transgenic mice


title: Cell Line, LC.A549

description:
LC.A549
NCI-60 panel


title: 17WG (case30) fetal melanocyte, sole

description: SAMPLE 8


title: Cell Line, CO.SW.620

description:
CO.SW.620
NCI-60 panel

source_name: Colon cancer

value: colon cancer cells


title: 13WG (case29) fetal melanocyte, sole

description: SAMPLE 4

value: 13 weeks of gestation


title: 13WG (case29) fetal melanocyte, back

description: SAMPLE 2

value: back


title: Cell Line, CO.KM12

description:
CO.KM12
NCI-60 panel


title: 13WG (case29) fetal melanocyte, abdomen

description: SAMPLE 3

value: abdomen


title: Cell Line, CO.HT29

description:
CO.HT29
NCI-60 panel


title: Cell Line, CO.HCT.15

description:
CO.HCT.15
NCI-60 panel


title: Cell Line, CO.HCT.116

description:
CO.HCT.116
NCI-60 panel


title: Cell Line, CO.HCC.2998

description:
CO.HCC.2998
NCI-60 panel


title: Cell Line, CNS.SNB.75

description:
CNS.SNB.75
NCI-60 panel

source_name: Central nervous system cancer

value: central nervous system cancer


title: WI-38OERAS rep1

city: paris

first: Moussa

last: BENHAMED

address: Institut pasteur

institute: Institut Pasteur

hyb_protocol: Samples were hybridized with GeneChip Human HG-U133A (Affymetrix) and scanned at the Strasbourg Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the HG-133A Array Computational Tool  (Affymetrix) for background correction and normalization (MAS5.0). Data analysis and statistical evaluations were performed with GeneSifter. We defined a probeset as present when it had a P value <0.05 and an Intensity value >300. These criteria were suggested by the results of preliminary experiments.

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Culturing of cells and infection of primary human diploid  fibroblasts strain WI38 by retroviral-mediated gene transfer were performed at physiological oxygen concentration of 3% .

extract_protocol: RNA was isolated from 1000000 cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

tag: cell line background

tag: genotype/variation

value: RASv12 overexpression

value: senescent fibroblast


title: 13WG (case29) fetal melanocyte, scalp

description: SAMPLE 1

value: scalp


title: Cell Line, CNS.SF.539

description:
CNS.SF.539
NCI-60 panel


title: Cell Line, CNS.SNB.19

description:
CNS.SNB.19
NCI-60 panel


title: WI-38OERAS rep3


title: WI-38OERAS rep2


title: WI-38 rep3

source_name: WI-38 control

value: wild type

value: growing fibroblast


title: Cell Line, CNS.SF.268

description:
CNS.SF.268
NCI-60 panel


title: Cell Line, CO.COLO205

description:
CO.COLO205
NCI-60 panel


title: Cell Line, CNS.U251

description:
CNS.U251
NCI-60 panel


title: Cell Line, CNS.SF.295

description:
CNS.SF.295
NCI-60 panel


title: WI-38 rep1


title: Kavya with GMB4M, rep 3

city: Hyderabad

first: Nidhi

last: Rawat

state: Andhra Pradesh

address: Rajendranager

department: entomology

country: India

institute: Directorate of rice research

description: Pooled samples 24, 48, 96, and 120 hr after GMB4M infestation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned using the GeneChip Scanner 3000.

data_processing: MAS5.0 using GCOS 1.x.

organism: Oryza sativa

source_name: stem, GMB4M

label_protocol: The kit supplied with Affymetrix chips was used to label the RNA with biotin.

growth_protocol: Samples were grown under standard glasshouse conditions for 15 days.

extract_protocol: RNA from the Kavya seedlings was extracted after removing the maggots at different time intervals. The Trizol (Invitogen) method for RNA isolation was used for the extractions. RNA was further purified using the Qiagen mini RNA isolation kit.

treatment_protocol: 15-day-old kavya seedlngs were exposed to gall midge biotype GMB1 or GMB4M for 24, 48, 96, and 120 hr. Uninfested seedlings were used as control.

tag: variety

value: Kavya

value: stem

tag: infestation

value: gall midge biotype 4M (GMB4M)


title: WI-38 rep2


title: MBO2

description:
AML39
Megakaryoblastic leukemia cell line

value: megakaryoblastic leukemia cells


title: TF-1

description:
AML36
AML cell line

value: acute myeloid leukemia cells


title: Kasumi-6

description:
AML37
AML cell line


title: MO7e

description:
AML38
Megakaryoblastic leukemia cell line


title: AML19D

description:
AML30
AML sample taken at diagnosis

source_name: Acute myeloid leukemia

value: blood


title: Kasumi 1

description:
AML31
AML cell line

source_name: Kasumi 1

value: Kasumi 1


title: U937

description:
AML35
AML cell line


title: ME-1

description:
AML34
AML cell line


title: UT-7

description:
AML33
AML cell line


title: HEL

description:
AML32
AML cell line

source_name: HEL

value: HEL


title: AML16D

description:
AML27
AML sample taken at diagnosis


title: AML17D

description:
AML28
AML sample taken at diagnosis


title: AML15D

description:
AML26
AML sample taken at diagnosis


title: AML18D

description:
AML29
AML sample taken at diagnosis


title: AML14D

description:
AML25
AML sample taken at diagnosis


title: AML13D

description:
AML24
AML sample taken at diagnosis


title: AML12D

description:
AML23
AML sample taken at diagnosis


title: AML11R

description:
AML22
AML sample taken after relapse


title: Control Kavya, rep 3

description: Uninfested samples.

source_name: stem, control


title: AML11D

description:
AML21
AML sample taken at diagnosis


title: Kavya with GMB4M, rep 1


title: Control Kavya, rep 2

description: Uninfested samples.


title: Kavya with GMB1, rep 3

description: Pooled samples 24, 48, 96, and 120 hr after GMB1 infestation.

source_name: stem, GMB1

value: gall midge biotype 1 (GMB1)


title: LNC Bhsp65-tolerized, medium, biological rep2

city: Baltimore

first: Kamal

middle: D.

last: Moudgil

state: MD

address: 685 W. Baltimore Street

department: Microbiology and Immunology

institute: University of Maryland School of Medicine

description: Gene expression data from LNC of rats 5-6 week-old

hyb_protocol: cRNA was hybridized on affymetrix gene chip using GeneChip Fluidics Station 450.following manufacturer's instructions

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: Affymetrix.cel files were checked for quality and corrected for background using Affymetrix Expression Console™ 1.1. The data were normalized and the median polished using robust multi-array (RMA). Thereafter, Significance Analysis of Microarrays (SAM) was used to compare gene expression levels between two different groups by limiting the false discovery rate (FDR) to below 5%. Further analysis was performed using Uniprot, Gene Ontology (GO) and KEGG databases. The microarray experimental plan and data analysis are in accordance with MIAME guidelines.

source_name: LEW rat Bhsp65-tolerized medium

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA mini-column was used to purify RNA obtained from Trizol isolation

treatment_protocol:
Arthritis induction: Lewis rats, male, 5-6 wk, were immunized subcutaneously with heat-killed Mycobacterium tuberculosis H37Ra (Mtb) following standard procedure for adjuvant arthritis induction as described in our publications. Rats were observed for signs of arthritis..
Tolerance induction: Lewis rats were injected with Bhsp65 intraperitoneally (3 injections on alternate days) before arthritis induction, following standard procedure described in our publication.
LNC harvested from arthritic rats in incubation phase (preclinical arthritis) and those from tolerized rats were cultured in HL-1 medium in the presence or absence of Bhsp65 for 24 h. For ex vivo testing, LNC were not cultured in vitro.

value: Lymph node cell (LNC)

value: adult rats 5-6 week-old

tag: strain

value: Lewis

tag: disease state

value: Bhsp65-tolerized medium


title: Kavya with GMB1, rep 2


title: LNC Bhsp65-tolerized, Bhsp65, biological rep2

source_name: LEW rat Bhsp65-tolerized Bhsp65

value: Bhsp65-tolerized Bhsp65


title: AML10R

description:
AML20
AML sample taken after relapse


title: LNC Bhsp65-tolerized, Bhsp65, biological rep1


title: Kavya with GMB4M, rep 2


title: Control Kavya, rep 1

description: Uninfested samples.


title: LNC Pre-arthritic Bhsp65, biological rep2

source_name: LEW rat Pre-arthritic Bhsp65

value: pre-arthritic Bhsp65


title: T3_Normal_(Eh_Eia520620F_Eh), biological replicate 3

city: Shinjuku-ku

first: Gil

middle: Mallari

last: Penuliar

state: Tokyo

address: Toyama 1-23-1

department: Parasitology

institute: National Institute of Infectious Diseases

description: Gene expression data from trophozoites grown in normal medium

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Eh_Eia520620F_Eh Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000

data_processing: Raw probe intensities were generated by the GeneChip Operating Software (GCOS) and GeneTitan Instrument. Resulting expression values were analyzed by Genespring GX 10.0.2 to identify differentially expressed genes

organism: Entamoeba histolytica

source_name: Entamoeba histolytica

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

growth_protocol: (1) wild-type amoeba were selected for trifluoromethionine and metronidazole resistance by exposure to sublethal and gradual increase in drug concentration. (2) G3 strain that is silenced for the amoeba pore was used to silenced MGL1 and MGL2. (3) wild-type amoeba was grown in cysteine deprived conditions.

treatment_protocol: Cells were treated with either trifluoromethionine, metronidazole, or geneticin.

tag: amoeba

value: wild-type

tag: treatment


title: T2_-Cys24X_(Eh_Eia520620F_Eh), biological replicate 2

description: Gene expression data from trophozoites grown in cysteine deprived medium

value: cultured without cysteine


title: cell line - culture B16

city: Muenster

first: Ruediger

last: Liersch

address: Albert-Schweitzer-Campus 1a

department: Department of Medicine - Hematology and Oncology

institute: University Hospital of Muenster,

description: B16 A

hyb_protocol: Hybridization protocol Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.

scan_protocol: Scan protocol Chemiluminescent Detection Kit (P/N 4339627) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).

data_processing: Data processing The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.

label: Chemiluminescent Digoxigenin-UTP labeled cRNA

source_name: Melanoma B16

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 0.5 µg of total RNA for each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit (P/N 4363105) according to the manufacturer’s protocol.

growth_protocol: B16variants were seeded onto culture dishes (10 µg/ml; BD Biosciences, Bedford, MA) and were cultured in DMEM supplemented with 20% fetal bovine serum (FBS; Invitrogen, Grand Island, NY), 2 mM L glutamine, antibiotic-antimycotic solution  for up to 10 passages.

extract_protocol: B16 and B16 variants were cultured in DMEM supplemented with 20% fetal bovine serum (FBS; Invitrogen, Grand Island, NY) supplemented with antibiotic-antimycotic solution. Every B16 variant was cultured in duplicates. Total cellular RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA) extracted with chloroform, precipitated with isopropanol, washed with 70% ethanol, and dissolved in DNase-free/RNase-free distilled water. The concentration of RNA was measured using NanoDrop ND-1000 spectrophotometer (Witec AG, Littau, Switzerland) and RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: B16F1 and B16-variants were cultured in DMEM (Gibco BRL, Grand Island, NY) supplemented with 20% fetal bovine serum. B16F1 cells (1x106) were injected intradermally in the backskin of C57BL6 mice and the tumor was removed 14-17 days after implantation. Metastatic melanoma cells were isolated from lymph nodes (LN) and cultured in vitro (B16-RI).  Then, B16-RI was again intradermally injected into mice, and primary tumors, LN metastases (B16-RII) and lung metastases (B16-RIIL) were isolated and re-cultured. Funcitonal assays were performed on B16 variants in vitro.

tag: strain background

tag: cell line origin

value: highly metastatic melanoma cell line B16 variants


title: Kavya with GMB1, rep 1

value: Kavya

value: stem


title: T2_Normal_(Eh_Eia520620F_Eh), biological replicate 2


title: T1_-Cys24X_(Eh_Eia520620F_Eh), biological replicate 1


title: LNC Bhsp65-tolerized, medium, biological rep3

tag: age


title: cell line - culture B16-RIIL

description: R2L A

source_name: lung metastases (B16-RIIL)


title: T1_Normal_(Eh_Eia520620F_Eh), biological replicate 1


title: LNC Pre-arthritic Bhsp65, biological rep1

tag: genotype


title: cell line - culture B16-RI

description: R1 A

source_name: lymph nodes (LN) metastases (B16-RI)


title: LNC Pre-arthritic Bhsp65, biological rep3


title: T3_-Cys24X_(Eh_Eia520620F_Eh), biological replicate 3


title: LNC Bhsp65-tolerized, Bhsp65, biological rep3


title: T3_MTZR_(Eh_Eia520620F_Eh), biological replicate 3

description: Gene expression data from metronidazole resistant trophozoites cultured without metronidazole

value: MTZ resistant


title: cell line - culture B16-RII

description: R2 A

source_name: lymph nodes (LN) metastases (B16-RII)


title: AML9D

description:
AML17
AML sample taken at diagnosis


title: AML9R

description:
AML18
AML sample taken after relapse


title: LNC Bhsp65-tolerized, medium, biological rep1


title: AML8R

description:
AML16
AML sample taken after relapse


title: AML8D

description:
AML15
AML sample taken at diagnosis


title: LNC Pre-arthritic medium, biological rep3

source_name: LEW rat Pre-arthritic medium

value: pre-arthritic medium


title: AML10D

description:
AML19
AML sample taken at diagnosis

value: blood


title: AML7R

description:
AML14
AML sample taken after relapse


title: AML7D

description:
AML13
AML sample taken at diagnosis


title: T3_MTZR(plus MTZ)_(Eh_Eia520620F_Eh), biological replicate 3

description: Gene expression data from metronidazole resistant trophozoites cultured with metronidazole

value: cultured with metronidazole


title: AML6D

description:
AML11
AML sample taken at diagnosis


title: AML5R

description:
AML10
AML sample taken after relapse


title: AML5D

description:
AML9
AML sample taken at diagnosis


title: T2_MTZR_(Eh_Eia520620F_Eh), biological replicate 2


title: AML6R

description:
AML12
AML sample taken after relapse


title: LNC Pre-arthritic medium, biological rep1


title: LNC Recovery, biological rep3

source_name: LEW rat Recovery

value: recovery


title: AML1R

description:
AML2
AML sample taken after relapse


title: AML4R

description:
AML8
AML sample taken after relapse


title: AML2D

description:
AML3
AML sample taken at diagnosis


title: AML2R

description:
AML4
AML sample taken after relapse


title: AML3D

description:
AML5
AML sample taken at diagnosis


title: T1_MTZR_(Eh_Eia520620F_Eh), biological replicate 1


title: AML1D

description:
AML1
AML sample taken at diagnosis


title: AML4D

description:
AML7
AML sample taken at diagnosis


title: Clinical sample, T-ALL23

description:
T-ALL23
Heavily pre-treated tumor

source_name: T-acute lymphoblastic leukemia


title: LNC Recovery, biological rep2


title: LNC Recovery, biological rep1


title: T2_Clone6 (no MTZ)_(Eh_Eia520620F_Eh), biological replicate 2

description: Gene expression data from untreated trophozoites


title: T3_pSAP2_(Eh_Eia520620F_Eh), biological replicate 3

description: Gene expression data from G3 strain

value: control for gene silencing

value: cultured with geneticin


title: LNC Pre-arthritic medium, biological rep2

value: Lymph node cell (LNC)

value: adult rats 5-6 week-old


title: T3_Clone6 (no MTZ)_(Eh_Eia520620F_Eh), biological replicate 3


title: Clinical sample, T-ALL22

description:
T-ALL22
Heavily pre-treated tumor


title: T2_pSAP2_(Eh_Eia520620F_Eh), biological replicate 2

description: Gene expression data from G3 strain


title: Clinical sample, T-ALL20

description:
T-ALL20
Heavily pre-treated tumor


title: T1_Clone6 (no MTZ)_(Eh_Eia520620F_Eh), biological replicate 1


title: Clinical sample, T-ALL21

description:
T-ALL21
Heavily pre-treated tumor


title: T2_MTZR(plus MTZ)_(Eh_Eia520620F_Eh), biological replicate 2


title: T1_MTZR(plus MTZ)_(Eh_Eia520620F_Eh), biological replicate 1


title: LNC Incubation, biological rep2

source_name: LEW rat Incubation

value: Lewis

value: incubation


title: Clinical sample, T-ALL19

description:
T-ALL19
Heavily pre-treated tumor


title: LNC Incubation, biological rep3


title: LNC Peak, biological rep1

source_name: LEW rat Peak

value: peak


title: Clinical sample, T-ALL17

description:
T-ALL17
Heavily pre-treated tumor


title: Clinical sample, T-ALL15

description:
T-ALL15
Heavily pre-treated tumor


title: Clinical sample, T-ALL16

description:
T-ALL16
Heavily pre-treated tumor


title: LNC Peak, biological rep3


title: Clinical sample, T-ALL14

description:
T-ALL14
Heavily pre-treated tumor


title: Clinical sample, T-ALL18

description:
T-ALL18
Heavily pre-treated tumor


title: T1_pSAP2_(Eh_Eia520620F_Eh), biological replicate 1

description: Gene expression data from G3 strain


title: T3_MGL2gs_(Eh_Eia520620F_Eh), biological replicate 3

description: Gene expression data from trophozoites gene silenced for MGL2

value: MGL2 gene silenced


title: Clinical sample, T-ALL12

description:
T-ALL12
Untreated tumor


title: Clinical sample, T-ALL13

description:
T-ALL13
Heavily pre-treated tumor


title: LNC Peak, biological rep2


title: Clinical sample, T-ALL11

description:
T-ALL11
Untreated tumor


title: LNC Incubation, biological rep1


title: LNC Naive, biological rep3

source_name: LEW rat Naïve

value: naive


title: Clinical sample, T-ALL10

description:
T-ALL10
Untreated tumor


title: Clinical sample, T-ALL9

description:
T-ALL9
Untreated tumor


title: LNC Naive, biological rep2


title: T1_MGL2gs_(Eh_Eia520620F_Eh), biological replicate 1


title: Clinical sample, T-ALL8

description:
T-ALL8
Untreated tumor


title: T2_MGL2gs_(Eh_Eia520620F_Eh), biological replicate 2


title: T2_MGL1gs_(Eh_Eia520620F_Eh), biological replicate 2

description: Gene expression data from trophozoites gene silenced for MGL1

value: MGL1 gene silenced


title: LNC Naive, biological rep1


title: Clinical sample, T-ALL5

description:
T-ALL5
Untreated tumor


title: Clinical sample, T-ALL7

description:
T-ALL7
Untreated tumor


title: T3_MGL1gs_(Eh_Eia520620F_Eh), biological replicate 3


title: T1_MGL1gs_(Eh_Eia520620F_Eh), biological replicate 1


title: Clinical sample, T-ALL6

description:
T-ALL6
Untreated tumor


title: Clinical sample, T-ALL4

description:
T-ALL4
Untreated tumor


title: Clinical sample, T-ALL3

description:
T-ALL3
Untreated tumor


title: T3_TFMR_(Eh_Eia520620F_Eh), biological replicate 3

description: Gene expression data from trifluoromethionine resistant trophozoites cultured without trifluoromethionine

value: TFMR resistant


title: cultured HSCs_SCF + TPO_2C9.G2_3

city: Shinjuku-Ku

first: Terumasa

last: Umemoto

address: 8-1, Kawada-Cho

institute: Tokyo women's medical university

description: Gene expression after the culture of HSCs with anti integrin beta3 antibody (2C9.G2) in the presence of both SCF and TPO for 5days.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The expression value (signal) and detection call (Present or Absent) for each probe set were calculated using Feature Extraction Ver.9.5.3 (Agilent Technologies).  To analyze the data, we first removed the probe sets that were used for quality control and consistently yielded high negative values, resulting in extraction of 35,791 genes.
The distribution of remaining average intensities for each chip was normalized to the quantile value for all chips, and the signal values for genes were normalized to the median value for all genes. Additionally, all values less than 1 were set to 1 when addressing fold changes.

source_name: Hematopoietic stem cells, cultured with SCF plus TPO, treatment with anti integrin beta3 antibody (2C9.G2), 5 days, sample 3

label_protocol: Using the extracted total RNA, fluorescently-labeled cRNA was prepared with a ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, The Netherlands), after which the cRNA was amplified using an OvationTM Aminoallyl System (NuGEN Technologies, San Carlos, CA).

growth_protocol: CD34-KSL cells were cultured for 5 days in S-Clone SF-03 medium supplemented with 0.5% BSA, 50 ng/ml SCF and/or 50 ng/ml TPO.

extract_protocol: After sorting CD48-KSL cells followting the culture, total RNA was obtained from 5000 cells using ISOGEN (Nippon Gene, Tokyo, Japan), according to the manufacturer’s suggested protocol, followed by treatment with DNase I (Nippon Gene). Using extracted total RNA, mRNA was amplified using an OvationTM Aminoallyl System (NuGEN Technologies, San Carlos, CA).

treatment_protocol: CD34-KSL cells were cultured with 2C9.G2 or control IgG for 5 days in the presence of SCF and/or TPO.

value: hematopoietic stem cells

tag: protocol

value: White blood cells


title: T2_TFMR_(Eh_Eia520620F_Eh), biological replicate 2


title: cultured HSCs_SCF + TPO_2C9.G2_2

source_name: Hematopoietic stem cells, cultured with SCF plus TPO, treatment with anti integrin beta3 antibody (2C9.G2), 5 days, sample 2


title: T3_TFMR (plus TFM)_(Eh_Eia520620F_Eh), biological replicate 3

description: Gene expression data from trifluoromethionine resistant trophozoites treated with trifluoromethionine

value: cultured with trifluoromethionine


title: cultured HSCs_SCF + TPO_2C9.G2_1

source_name: Hematopoietic stem cells, cultured with SCF plus TPO, treatment with anti integrin beta3 antibody (2C9.G2), 5 days, sample 1


title: Clinical sample, T-ALL1

description:
T-ALL1
Untreated tumor

value: blood


title: Clinical sample, T-ALL2

description:
T-ALL2
Untreated tumor


title: Clinical sample, MM6

source_name: Metastatic melanoma

value: melanoma

tag: percentage of tumor cells

value: 100%, microdissected sample


title: Clinical sample, MM7


title: Clinical sample, MM8


title: Clinical sample, MM9


title: cultured HSCs_SCF + TPO_IgG_2

description: Gene expression after the culture of HSCs with control IgG in the presence of both SCF and TPO for 5days.

source_name: Hematopoietic stem cells, cultured with SCF plus TPO, treatment with control IgG, 5 days, sample 2

tag: cell type


title: Clinical sample, MM5


title: cultured HSCs_SCF + TPO_IgG_1

source_name: Hematopoietic stem cells, cultured with SCF plus TPO, treatment with control IgG, 5 days, sample 1


title: cultured HSCs_TPO_2C9.G2_3

description: Gene expression after the culture of HSCs with anti integrin beta3 antibody (2C9.G2) in the presence of TPO for 5days.

source_name: Hematopoietic stem cells, cultured with TPO, treatment with anti integrin beta3 antibody (2C9.G2), 5 days, sample 3


title: Clinical sample, MM3


title: cultured HSCs_TPO_2C9.G2_2

source_name: Hematopoietic stem cells, cultured with TPO, treatment with anti integrin beta3 antibody (2C9.G2), 5 days, sample 2


title: T1_TFMR_(Eh_Eia520620F_Eh), biological replicate 1

source_name: Entamoeba histolytica


title: Clinical sample, MM4


title: Clinical sample, MM2


title: Clinical sample, GBM-M2

description:
GBM-M2
Metastatic tumor

source_name: Glioblastoma

value: glioblastoma tumor


title: T2_Clone 6_(Eh_Eia520620F_Eh), biological replicate 2

value: wild-type


title: Clinical sample, GBM-R3

description:
GBM-R3
Recurrent tumor


title: T1_Clone 6_(Eh_Eia520620F_Eh), biological replicate 1


title: Clinical sample, GBM-M1

description:
GBM-M1
Metastatic tumor


title: Clinical sample, GBM-R2

description:
GBM-R2
Recurrent tumor


title: Clinical sample, GBM-R1

description:
GBM-R1
Recurrent tumor


title: cultured HSCs_SCF + TPO_IgG_3

source_name: Hematopoietic stem cells, cultured with SCF plus TPO, treatment with control IgG, 5 days, sample 3


title: T1_TFMR (plus TFM)_(Eh_Eia520620F_Eh), biological replicate 1


title: cultured HSCs_TPO_2C9.G2_1

source_name: Hematopoietic stem cells, cultured with TPO, treatment with anti integrin beta3 antibody (2C9.G2), 5 days, sample 1


title: cultured HSCs_TPO_IgG_1

description: Gene expression after the culture of HSCs with control IgG in the presence of TPO for 5days.

source_name: Hematopoietic stem cells, cultured with TPO, treatment with control IgG, 5 days, sample 1


title: Clinical sample, GBM-P4

description:
GBM-P4
Primary tumor


title: T2_TFMR (plus TFM)_(Eh_Eia520620F_Eh), biological replicate 2


title: Clinical sample, MM1


title: T2_Clone 6_(Eh_Eia520620F_Eh), biological replicate 3


title: cultured HSCs_TPO_IgG_2

source_name: Hematopoietic stem cells, cultured with TPO, treatment with control IgG, 5 days, sample 2


title: Clinical sample, Colon-T7

source_name: Colon cancer

value: colon cancer tumor


title: Clinical sample, GBM-P2

description:
GBM-P2
Primary tumor


title: Clinical sample, GBM-P3

description:
GBM-P3
Primary tumor


title: cultured HSCs_SCF_2C9.G2_2

description: Gene expression after the culture of HSCs with anti integrin beta3 antibody (2C9.G2) in the presence of SCF for 5days.

source_name: Hematopoietic stem cells, cultured with SCF, treatment with anti integrin beta3 antibody (2C9.G2), 5 days, sample 2


title: Clinical sample, GBM-P1

description:
GBM-P1
Primary tumor


title: cultured HSCs_SCF_2C9.G2_1

source_name: Hematopoietic stem cells, cultured with SCF, treatment with anti integrin beta3 antibody (2C9.G2), 5 days, sample 1


title: cultured HSCs_SCF_IgG_3

description: Gene expression after the culture of HSCs with control IgG in the presence of SCF for 5days.

source_name: Hematopoietic stem cells, cultured with SCF, treatment with control IgG, 5 days, sample 3


title: Clinical sample, Colon-N7

description:
Colon-N7
N7-T7, paired samples

source_name: Normal colon tissue

value: normal colon


title: Clinical sample, Colon-T6


title: Clinical sample, Colon-N5

description:
Colon-N5
N5-T5, paired samples


title: Clinical sample, Colon-N4

description:
Colon-N4
N4-T4, paired samples


title: Clinical sample, Colon-T5


title: cultured HSCs_SCF_IgG_2

source_name: Hematopoietic stem cells, cultured with SCF, treatment with control IgG, 5 days, sample 2


title: Clinical sample, Colon-T3


title: cultured HSCs_SCF_IgG_1

source_name: Hematopoietic stem cells, cultured with SCF, treatment with control IgG, 5 days, sample 1


title: human neural progenitor cell line ZNF804A_siRNA HSS150613 replicate3

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

institute: Cardiff University

description: SAMPLE 11

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Sample probe profile were exported from GenomeStudio. Data were then imported into lumi (bioconductor) and Variance Stabilizing transformation applied, Robust Spline Normalized and log2 transformed.

source_name: CTXOE03 cell line; ZNF804A_siRNA HSS150613

label_protocol: Biotinylated cDNA were prepared using the Custom Illumina® TotalPrep™-96 Kit (Ambion)

growth_protocol: Cells were maintained as described by Pollock K et al, Exp Neurol. 2006 May;199(1):143-55.

extract_protocol: Standard Trizol extraction followed by DNase treatment, RNA dissolved in water.

treatment_protocol: Transfection of Stealth siRNA (Invitrogen), either control or two separate siRNAs targeting ZNF804A (HSS150612 or HSS150613) using the N-Ter transfection system(Sigma). Cells were harvested using acutase 4 days after transfection.

tag: cell line

value: CTXOE03 cell line

value: Neural progenitor

tag: brain region of origin

value: Fetal cortical neuroepithelium

tag: gender

value: Male


title: human neural progenitor cell line ZNF804A_siRNA HSS150613 replicate1

description: SAMPLE 9


title: AML3R

description:
AML6
AML sample taken after relapse

source_name: Acute myeloid leukemia

tag: tissue


title: human neural progenitor cell line ZNF804A_siRNA HSS150613 replicate4

description: SAMPLE 12


title: Clinical sample, Colon-N6

description:
Colon-N6
N6-T6, paired samples


title: Clinical sample, Colon-N3

description:
Colon-N3
N3-T3, paired samples


title: human neural progenitor cell line ZNF804A_siRNA HSS150613 replicate2

description: SAMPLE 10


title: human neural progenitor cell line ZNF804A_siRNA HSS150612 replicate4

description: SAMPLE 8

source_name: CTXOE03 cell line; ZNF804A_siRNA HSS150612


title: Clinical sample, Colon-N2

description:
Colon-N2
N2-T2, paired samples


title: human neural progenitor cell line ZNF804A_siRNA HSS150612 replicate3

description: SAMPLE 7


title: human neural progenitor cell line ZNF804A_siRNA HSS150612 replicate1

description: SAMPLE 5


title: Clinical sample, Colon-T2


title: Clinical sample, Colon-T4


title: low-milk yield vs high-milk yield biological rep 4, tech rep 1

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

description: Biological replicate 4 of 4, technical replicate 1 of 2

hyb_protocol: Standard Agilent hybridization protocol.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Background correction method normexp was used and followed by loess method for within array normalization. Between array normalization was performed with the Aquantile method. Mean values of channels intensities were taken as an input and a median of background signal for background correction calculations.

organism: Bos taurus

source_name: quarter of mammary gland

label_protocol: 1000 ng of total RNA was labeled using Quick Amp Labeling Kit, two color with Cy5 i Cyc 3 (Agilent) according to manufacturer’s protocol.

extract_protocol: Total RNA was isolated using (RNeasy Mini Kit Qiagen, Germany), separately from quarter of mammary gland according to the manufacturer’s protocol. Quantity and quality of each RNA sample was estimated by Nanodrop (Nanodrop, USA) and Bioanalyzer (Agilent, USA).

tag: breed

value: Holstein Friesian

tag: individual/probe/cow number

tag: lactation

value: low-milk yield IV

value: high-milk yield IV


title: Clinical sample, Colon-T1


title: high-milk yield vs low-milk yield biological rep 4, tech rep 2

description: Biological replicate 4 of 4, technical replicate 2 of 2


title: high-milk yield vs low-milk yield biological rep 2, tech rep 2

description: Biological replicate 2 of 4, technical replicate 2 of 2

value: high-milk yield II

value: low-milk yield II


title: human neural progenitor cell line ZNF804A_siRNA HSS150612 replicate2

description: SAMPLE 6


title: human neural progenitor cell line Control_siRNA replicate3

description: SAMPLE 3

source_name: CTXOE03 cell line; Control_siRNA


title: Clinical sample, Colon-N1

description:
Colon-N1
N1-T1, paired samples