title: HHCC104

description: Control


title: HHCC103

status: Public on Jun 27 2014

type: RNA

city: Hamamatsu

first: Mahesh

last: Mundalil Vasu

state: Shizuoka

address: 1-20-1 Handayama, Higashi Ward

department: Department of Psychiatry

country: Japan

institute: Hamamatsu University School of Medicine

description: Control

data_processing: Data Analysis: ΔΔCt method for the relative quantification of miRNAs. Normalization: A randomly chosen control sample was amplified in each plate and used as an inter-plate calibrator to correct for the experimental differences among consecutive PCR runs. The qPCR data was first subjected to inter-plate calibration, followed by C.elegans miR-39 (detection of the spike-in control) calibration. The expression of miR-16, an miRNA highly abundant in the red blood cells, was analyzed in each sample to examine the extent of hemolysis in the serum. Any sample that showed significant hemolysis (the value of Ct invariant miRNA – Ct miR16 was greater than 5) was omitted from further analyses. Finally, the qPCR data was normalized to the average of three invariantly expressed miRNAs, let-7a, miR-191-5p and miR-103a-3p. Among these, miR-191-5p and miR-103a-3p were selected on the basis of their performance as invariant miRNAs in the neurological array and custom array, respectively, while let-7a has been widely reported as an invariant miRNA in blood. The fold change in gene expression between the control and autism groups was determined by the Ct method of relative quantification.

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: Serum, Control

label_protocol: Two microliters of each RNA sample was used for cDNA synthesis using the miScript ІІ RT kit (QIAGEN). The reverse transcription reaction mix (20 μl) was prepared using Hispec buffer (for selective conversion of mature miRNAs into cDNA), nucleics mix, RT mix and RNase free water. The reaction mixture was incubated for 60 min at 37ºC, followed by denaturation for 5 min at 95ºC. Ten microliters of qPCR reaction mixture was prepared with a universal primer, primer assay, Template cDNA and RNase free water. All the qPCR reactions were performed in triplicate with the following cycling conditions: 95ºC →15 min, followed by 40 cycles of 94ºC →15 sec, 55ºC →30 sec and 70ºC → 30 sec.

extract_protocol: Total RNA was extracted from serum samples using MiRNeasy Serum/Plasma Kit (QIAGEN GmbH, Hilden, Germany)

tag: diagnosis

value: Normal

tag: age (yrs)


title: HHCC111

description: Control


title: Dengue Hemorrhagic Fever Patient 39

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

hyb_protocol: Two-round in vitro transcription amplification and labeling was performed starting with 50 ng intact, total RNA per sample, following the Affymetrix protocol. Samples were hybridized on Human U133 Plus 2.0 Arrays (using GeneTitan platform).

scan_protocol: Scanning was performed on a 7th generation GeneChip Scanner 3000, and the Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.

data_processing: RMA normalization was performed using Expression Console software.

label: biotin

source_name: Whole Blood of Dengue infected patient at acute infection time point

label_protocol: Total RNA sample quality was evaluated by spectrophotometer to determine quantity, protein contamination and organic solvent contamination, and an Agilent 2100 Bioanalyzer was used to check for RNA degradation. Two-round in vitro transcription amplification and labeling was performed starting with 50 ng intact, total RNA per sample, following the Affymetrix protocol.

extract_protocol: RNA was isolated using the RiboPure-Blood kit (Ambion) and alpha and beta globin mRNA was depleted by GLOBINclear™ Kit (Ambion) according to the manufacturer’s protocol. All RNA samples were checked for purity using a ND-1000 spectrophotometer (NanoDrop Technologies) and for integrity by electrophoresis on a 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: Blood was collected on CPT tubes (Vacutainer® with Sodium Citrate; BD). Whole blood specimens were preserved on RNALater buffer (Ambion) and stored in -80oC

tag: subject id

tag: infection

value: DENV

tag: status

value: DHF

tag: tissue

value: whole blood


title: Dengue Hemorrhagic Fever Patient 38


title: Dengue Fever Patient 35

value: DF


title: HHCC108

description: Control


title: ASP043-1

description: Test

source_name: Serum, Autism

value: Autism


title: Dengue Fever Patient 41


title: Dengue Hemorrhagic Fever Patient 81


title: cardiac defects 1

type: genomic

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

description:
Hypoplastic right heart syndrome
R01C01

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Data was analyzed using the Illumina Kayostudio software v1.3 (Build 36.1, CNV Plugin V3.0) in the recommended setting

molecule: genomic DNA

source_name: peripheral blood

label_protocol: genomic DNA was whole-genome amplified in an overnight reaction at 37¡C. After incubation the amplified DNA was fragmented with FMS, precipitated with 2-propanol and PM1 and resuspended in hybridization buffer (RA1).

extract_protocol: DNA was extracted from the peripheral blood (anticoagulation with EDTA) using the QIAamp DNA Blood Midi Kit (Qiagen, Duesseldorf, Germany) by following the manufacturer’s instructions. Purified genomic DNA was resuspended in ddH2O for SNP-array analysis

tag: gender

value: Female

tag: disease state

value: Hypoplastic right heart syndrome

value: blood


title: HHCC100

description: Control


title: HHCC098

description: Control


title: Dengue Hemorrhagic Fever Patient 32


title: HHCC102

description: Control


title: Dengue Hemorrhagic Fever Patient 34


title: HHCC095

description: Control


title: Dengue Fever Patient 33


title: Pooled sample 8

description: Control

data_processing: Data Analysis: An Excel-based miRNA PCR Array Data Analysis tool (SAB; http://pcrdataanalysis.sabiosciences.com/mirna) was used for data analysis. SAB makes use of the ΔΔCt method for the relative quantification of miRNAs. Normalization: The data sets were first calibrated using a C.elegans miR-39 assay, which detected the spike-in control that was added to the serum samples during RNA extraction. This calibration would have resolved any differences in recovery that may have occurred during the purification procedure, or any differences in amplification efficiency. Due to the very low expression of snoRNA/snRNA PCR controls in the serum, three alternate normalization strategies, as recommended by the manufacturer, were used for data normalization. These were (i) normalization  to the whole plate Ct mean, (ii) normalization to the plate Ct mean of commonly expressed (Ct<30) miRNAs, and (iii) normalization to the Ct mean of at least four invariant miRNAs with little (<1) Ct variation between samples. In the third strategy, miR-125b-5p, miR-126-5p, miR-140-5p and miR-191-5p were chosen for the data normalization of the neurological array, whereas miR-103a-3p, miR-21-5p, miR-23a-3p, and miR-25-3p were chosen for the custom array. Consistent results were obtained using all three strategies.

value: Male

tag: age range (yrs)

tag: treatment

value: Drug Naïve


title: HHCC097

description: Control


title: Pooled sample 5

description: Control


title: Pooled sample 6

description: Control


title: cardiac defects 2

description:
isolated dextrocardia, crisscross heart, double outlet of right ventricle (DORV), ventricular septal defect (VSD), atrial septal defect (ASD) and pulmonary hypertension (PH)  ,SOX7 duplication,DEFB deletion
R03C01


title: Pooled sample 4

description: Autism


title: HHCC085

description: Control


title: Pooled sample 3

description: Autism


title: HHCC082

description: Control


title: Pooled sample 1

description: Autism


title: Pooled sample 2

description: Autism


title: HHCC094

description: Control


title: Dengue Fever Patient 6


title: HHCC075

description: Control


title: Dengue Fever Patient 7


title: HHCC088

description: Control


title: Dengue Fever Patient 3


title: HHCC069

description: Control


title: HHCC061

description: Control


title: HHCC060

description: Control


title: cardiac defects 3

description:
Completeness of the interatrial septum defect
R02C01


title: HHCC056

description: Control


title: S2_Pol II S5P Psip1 KO

city: London

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

description: ChIP-Chip Pol II S5P ChIP in Psip1 KO  MEFs

hyb_protocol: Samples were hybridized according to standard protocol (http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: The median signal intensity of the 4 replicate probes,on each array was taken. Loess normalization was used within arrays to correct for the dye bias, and scale normalization was used to control for inter array variability.

organism: Mus musculus

source_name: Input DNA from Psip1 KO MEFs

label_protocol: 0.6 to 1.5 µg ChIP DNA or Input DNA was directly labeled by Klenow random priming with Cy3/Cy5 nonamers as per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Passage 4 Cells were used

extract_protocol: MEFs were harvested by trypsinizing and immediately fixed with 1% formaldehyde (25C, 10 min) in PBS, and stopped with 0.125M Glycine. Chromatin immunoprecipitation (ChiP) was performed as described previously(Johnson et al 2007). The nuclei were sonicated using a Diagenode Bioruptor (Liege, full power 30s on, 30s off, in an icebath for 50 min) to produce fragments of < 300bp. An arbitrary concentration of 200 µg chromatin was incubated with 4µg rabit IgG (Santa Cruz, sc-2025) or 4 µg Bmi-1, Ring1B, H3K27me3, Ser2 Pol II, Ser 5 Pol II antibodies and washed and eluted as described in (Johnson et al 2007). Reverse cross-linked DNA was purified as described above.

tag: genotype/variation

tag: cell type

value: mouse embryonic fibroblasts (MEFs)

source_name: Pol II S5P ChIP in WT MEFs


title: cardiac defects 4

description:
serious cardiac abnormalities,asplenia syndrome
R04C01


title: HHCC051

description: Control


title: S1_Pol II S5P Psip1 KO

description: ChIP-Chip Pol II S5P ChIP in WT MEFs


title: S2_Pol II S5P WT

description: ChIP-Chip Pol II S5P ChIP in WT MEFs

source_name: Input DNA from WT MEFs

value: wild type


title: S429-1

city: Iksan

first: Soo-Cheon

last: Chae

state: Cheonbuk

address: Iksandaero

department: Department of Patholgy

country: South Korea

institute: Wonkwang University School of Medicine

description: test 3-1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2

source_name: SW480 transfected with MIR429

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit

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

tag: cell line

value: colon cancer


title: S1_Pol II S5P WT

description: ChIP-Chip Pol II S5P ChIP in WT MEFs


title: S3_Pol II S2P Psip1 KO

description: ChIP-Chip Pol II S2P ChIP in Psip1 KO  MEFs

source_name: Pol II S2P ChIP in Psip1 KO MEFs


title: HHCC049

description: Control


title: S1_Pol II S2P Psip1 KO

source_name: Pol II S2P ChIP in WT MEFs


title: S375-2

description: test 2-2

source_name: SW480 transfected with MIR375


title: C429-2

description: test 3-3

source_name: Caco2 transfected with MIR429


title: S375-1

description: test 2-1


title: S196b-2

description: test 1-2

source_name: SW480 transfected with MIR196B


title: C429-1

description: test 3-2


title: C196b-1

description: test 1-3

source_name: Caco2 transfected with MIR196B


title: S196b-1

description: test 1-1


title: CN2

description: control 2


title: HHCC046

description: Control


title: S3_Pol II S2P WT

description: ChIP-Chip Pol II S2P ChIP in WT MEFs


title: HHCC045

description: Control


title: HHCC032

description: Control


title: HHCC031

description: Control


title: Esophagus CTR replicate 3

city: Madrid

first: Daniela

last: Piazzolla

state: España

address: Calle Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

description: ESOPH 133

hyb_protocol: Labeled samples were hybridized to Whole Mouse Genome 4x44K microarrays (Agilent microarray design ID 014868, P/N G4122F)

scan_protocol: Processed Microarrays were scanned on a G2565C DNA microarray scanner (Agilent) and images were analyzed with Agilent Feature Extraction Software (version 10.1.1), which performed feature quantification and additive detrend correction.

data_processing:
Microarray background subtraction was carried out using normexp method. Normalization was performed using quantiles. Differentially expressed genes were obtained by applying linear models with R limma package (Bioconductor project, http://www.bioconductor.org).
Reference: Smyth, G. K. (2005). Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397-420
To account for multiple hypotheses testing, the estimated significance level (p value) was adjusted using Benjamini & Hochberg False Discovery Rate (FDR) correction.

source_name: control esophagus

label_protocol: Total RNA (1 µg) was labeled with the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit (Agilent) following the manufacturer´s instructions. Labeled samples were purified with silica-based RNeasy spin columns (Qiagen)

extract_protocol: Total cellular RNA was extracted from esophagus using RNeasy Fibrous Tissue Mini Kit (Qiagen), and from liver by combining an initial lysis with Trizol (Invitrogen) with a clean-up with RNeasy Kit (Qiagen). RNA Integrity Numbers (RINs) were in the range 7.3 to 9.5 when assayed on an Agilent 2100 Bioanalyzer

treatment_protocol: Nanog transgene expression was induced in mice by replacing normal drinking water with 7.5% sucrose solution containing doxycycline (0.2 mg/ml) for 48 h.

tag: strain background

value: mixed 129Sv/C57BL6

value: male

tag: age

value: 8 months

value: esophagus


title: S2_Pol II S2P WT

description: ChIP-Chip Pol II S2P ChIP in WT MEFs


title: Esophagus CTR replicate 2

description: ESOPH 132


title: S2_Pol II S2P Psip1 KO


title: S1_Pol II S2P WT

description: ChIP-Chip Pol II S2P ChIP in WT MEFs


title: HHCC021

description: Control

value: Normal


title: Dengue Fever Patient 36

value: DENV


title: S2_H3K27me3 Psip1 KO

description: ChIP-Chip for H3K27me3  in Psip1 KO  MEFs

source_name: H3K27me3 ChIP DNA from Psip1 KO_MEFs


title: CN1

description: control 2


title: Esophagus CTR replicate 1

description: ESOPH 131


title: HHCC017

description: Control


title: SN1

description: control 1


title: Esophagus TG replicate 2

description: ESOPH 122

source_name: Nanog overexpressing esophagus


title: Esophagus TG replicate 3

description: ESOPH 130


title: Pooled sample 7

description: Control

source_name: Serum, Control


title: HHCC016

description: Control


title: S1_H3K27me3 Psip1 KO

description: ChIP-Chip for H3K27me3  in Psip1 KO MEFs


title: S2_H3K27me3 WT

description: ChIP-Chip for H3K27me3  in WT MEFs

source_name: H3K27me3 ChIP DNA from WT_MEFs


title: Liver CTR replicate 3

description: LIV 133

source_name: control liver

value: liver


title: S1_H3K27me3 WT

description: ChIP-Chip for H3K27me3  in WT MEFs


title: Liver CTR replicate 2

description: LIV 132


title: HHCC013

description: Control


title: HHCC012

description: Control


title: Liver CTR replicate 1

description: LIV 131


title: Esophagus TG replicate 1

description: ESOPH 121


title: HHCC006

description: Control


title: S2_Ring1B WT

description: Chip-chip MEFs Rin1B in WT MEFs

source_name: Ring1B ChIP DNA from WT_MEFs


title: Liver TG replicate 3

description: LIV 130

source_name: Nanog overexpressing liver


title: S2_Ring1B Psip1 KO

description: Chip-chip MEFs Ring1B  Psio1 KO MEFs

source_name: Input DNA from Psip1 KO MEFs

source_name: Ring1B ChIP DNA from Psip1 KO_MEFs


title: Pooled sample 8

description: Control


title: SN2

description: control 1


title: Pooled sample 7

description: Control


title: Dengue Fever Patient 4

source_name: Whole Blood of Dengue infected patient at acute infection time point

value: DF

value: whole blood


title: S1_Ring1B WT

description: Chip-chip MEFs Rin1B in WT MEFs

source_name: Input DNA from WT MEFs


title: Liver TG replicate 2

description: LIV 122


title: S2_Bmi-1 Psip1 KO

description: Chip-chip MEFs Bmi-1 Psio1 KO MEFs

source_name: Bmi-1 ChIP DNA from Psip1 KO_MEFs


title: S1_Bmi-1 Psip1 KO

description: Chip-chip MEFs Bmi-1 Psio1 KO MEFs


title: Liver TG replicate 1

description: LIV 121


title: S1_Ring1B Psip1 KO

description: Chip-chip MEFs Ring1B in Psio1 KO MEFs


title: Glycine max at stage2 with Cuscuta parasitization, biological rep3

city: Yokohama

first: Takeshi

last: Furuhashi

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN CSRS

hyb_protocol: Following fragmentation, 12.5µg of cRNA were hybridized for 16 hrs at 45˚C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluids Station.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: Robust Multiarray Average (RMA) was used to normalize and summarize the raw Affymetrix signals using the Affymetrix Power Tools (APT version 1.15.0) software

label: Biotin

organism: Glycine max

source_name: Glycine max seedlings 1 week after Cuscuta attachment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Gene Chip 3`ÌVT Express Kit) from 100ng total RNA

growth_protocol: Glycine max seedlings were incubated in a green house with daily watering at a room temperature of 30˚C and a 12-h light/ dark cycle.

extract_protocol: Total RNA extraction was done using a RNeasy mini kit according to manufacturer instructions

treatment_protocol: Seven-day-old Cuscuta seedlings were attached with surgical tape to 9-day-old Glycine max stems between first difolia leaves and cotyledon (epicotyl part). Sampling was done at stage 1 (One and half days after attachment) and stage 2 (1week after attachment), whereby Cuscuta and the Glycine max stem were excised and collected.

tag: cultivar

value: William 82

value: stem


title: Glycine max at stage2 with Cuscuta parasitization, biological rep2


title: Pooled sample 4

description: Autism

source_name: Serum, Autism

value: Autism


title: Pooled sample 5

description: Control

value: Male


title: Pooled sample 6

description: Control

value: Drug Naïve


title: Glycine max at stage2 with Cuscuta parasitization, biological rep1


title: Pooled sample 3

description: Autism


title: Pooled sample 2

description: Autism


title: S2_Bmi-1 WT

description: Chip-chip MEFs Bmi-1WT MEFs

source_name: Bmi-1 ChIP DNA from WT_MEFs

value: mouse embryonic fibroblasts (MEFs)


title: Glycine max at stage2 negative control, biological rep2

source_name: Glycine max seedlings without Cuscuta (negative control for 1 week after Cuscuta attachment)


title: S1_Bmi-1 WT

description: Chip-chip MEFs Bmi-1WT MEFs

value: wild type


title: Pooled sample 1

description: Autism


title: S2_Menin_Psip1KO

description: Chip-chip MEFs Menin Psio1 KO MEFs

extract_protocol: MEFs were harvested by trypsinizing and immediately fixed with 1% formaldehyde (25C, 10 min) in PBS, and stopped with 0.125M Glycine. Chromatin immunoprecipitation (ChiP) was performed as described previously(Johnson et al 2007). The nuclei were sonicated using a Diagenode Bioruptor (Liege, full power 30s on, 30s off, in an icebath for 50 min) to produce fragments of < 300bp. An arbitrary concentration of 200 µg chromatin was incubated with 4µg rabit IgG (Santa Cruz, sc-2025) or 4 µg Psip1 antibodies (A300-847) and washed and eluted as described in (Johnson et al 2007). Reverse cross-linked DNA was purified as described above.

source_name: Menin ChIP DNA from Psip1 KO_MEFs


title: Glycine max at stage2 negative control, biological rep1


title: S2_Menin_WT

description: Chip-chip MEFs Menin WT MEFs

source_name: Menin ChIP DNA from WT_MEFs


title: Glycine max at stage1 with Cuscuta parasitization, biological rep3

source_name: Glycine max seedlings 1 and half day after Cuscuta attachment


title: S1_Menin_WT

description: Chip-chip MEFs Menin WT MEFs


title: Glycine max at stage1 with Cuscuta parasitization, biological rep2


title: Glycine max at stage2 negative control, biological rep3


title: S1_Menin_Psip1KO

description: Chip-chip MEFs Menin Psio1 KO MEFs


title: S3_Mll1_Psip1KO

description: anti Mll1 (pab Active Motif)

source_name: Mll1 ChIP DNA from WT_MEFs

extract_protocol: MEFs were harvested by trypsinizing and immediately fixed with 1% formaldehyde (25C, 10 min) in PBS, and stopped with 0.125M Glycine. Chromatin immunoprecipitation (ChiP) was performed as described previously(Johnson et al 2007). The nuclei were sonicated using a Diagenode Bioruptor (Liege, full power 30s on, 30s off, in an icebath for 50 min) to produce fragments of < 300bp. An arbitrary concentration of 200 µg chromatin was incubated with 4µg rabit IgG (Santa Cruz, sc-2025) or 4 µg Psip1/p75 and Mll1 antibodies and washed and eluted as described in (Johnson et al 2007). Reverse cross-linked DNA was purified as described above.


title: Glycine max at stage1 with Cuscuta parasitization, biological rep1


title: Glycine max at stage1 negative control, biological rep2

source_name: Glycine max seedlings without Cuscuta (negative control for 1 and half day after Cuscuta attachment)


title: S1_Mll1_WT

description: anti Mll1 (pab Active Motif)


title: Glycine max at stage1 negative control, biological rep1


title: SMP30 control 3

status: Public on Jun 26 2014

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

description: normalized by SuperNORM data service

hyb_protocol: and then hybridized to an Affymetrix Total RNA Affymetrix Mouse Gene 1.0 ST Array (Affymetrix), with three biological repeats per group.

scan_protocol: GeneChip® Scanner 3000 7G（Affymetrix）

data_processing: The perfect match data were normalized by using the SuperNORM data service (Skylight Biotech Inc., Akita, Japan) according to a three-parameter lognormal distribution model.

source_name: control diet

label_protocol: Total RNA was processed to prepare biotinylated cRNA using One-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Male SAMP10/TaSlc (SAMP10) mice were purchased from Japan SLC Co. Ltd. (Shizuoka, Japan) and kept under conventional conditions in a temperature- and humidity-controlled room with a 12-h light/dark cycle (light period, 08.00–20.00 h; temperature, 23 ± 1 ˚C; relative humidity, 55 ± 5%). Five groups were prepared and each group consisted of 12 mice; each six mice were housed together in a cage.

extract_protocol: Total RNA in the hippocampus was prepared using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Mice were fed a normal diet (CE-2; Clea Co. Ltd, Tokyo, Japan) containing 3% soybean extract and water ad libitum. All experimental protocols were approved by the University of Shizuoka Laboratory Animal Care Advisory Committee and were in accordance with the guidelines of the US National Institutes of Health for the care and use of laboratory animals.

tag: strain

value: SAMP10/TaSlc (SAMP10)

value: hippocampus


title: SMP30 green soybean 1

description: normalized by SuperNORM data service

source_name: green diet

value: male


title: SMP30 yellow soybean 3

description: normalized by SuperNORM data service

source_name: yellow diet


title: SMP30 yellow soybean 1

description: normalized by SuperNORM data service


title: S2_Mll1_WT

description: anti Mll1 (pab Active Motif)


title: S1_Mll1_Psip1KO

description: anti Mll1 (pab Active Motif)


title: S2_Mll1_Psip1KO

description: anti Mll1 (pab Active Motif)


title: SMP30 green soybean 2

description: normalized by SuperNORM data service


title: S2_Psip1/p75

description: anti Psip1/p75 (Bethyl lab A300-848)

source_name: Psip1/p75 ChIP DNA from MEFs

source_name: Input DNA from MEFs


title: S3_Mll1_WT

description: anti Mll1 (pab Active Motif)


title: SMP30 control 2

description: normalized by SuperNORM data service


title: SMP30 yellow soybean 2

description: normalized by SuperNORM data service


title: SMP30 control 1

description: normalized by SuperNORM data service


title: SMP30 green soybean 3

description: normalized by SuperNORM data service


title: OPR_in_Basal_Stagnant_Short vs Stagnant_Long_Replicate3

city: Eiheiji

first: Katsuhiro

last: Shiono

state: Fukui

address: 4-1-1 Matsuoka-Kenjyojima

department: Department of Bioscience

institute: Fukui Prefectural University

hyb_protocol: Gene Expression Hybridization kit part No. 5188-5242

scan_protocol: Agilent scanner model G2505B

data_processing: Data was analyzed by Feature Extraction Software (Version 9.5.3.1, Agilent)

organism: Oryza sativa

label_protocol: Total RNAs (10ng) were labelled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Aliquots of Cy5-labelled and Cy3-labelled cRNA (825 ng each) were used for hybridization in a rice 44k oligo-DNA microarray (Agilent Technologies). Three biological replicates and a colour swap for each replicate were analysed. The hybridized slides were scanned using a DNA microarray scanner G2505B (Agilent Technologies) and signal intensities were extracted by Feature Extraction software version 9.5.3.1 (Agilent Technologies).

growth_protocol: Lowland rice (O. sativa L. cv. Nipponbare) was grown in a nutrient solution of the same composition as used in earlier studies of rice (Colmer, 2003a; Shiono et al., 2011). Plants were supported at the stem base in pots (light-shielding pots so roots were in darkness) within a controlled-environment chamber (24-h light, 28 °C, relative humidity over 50%, photosynthetic photon flux density at 214 μmol m–2 s–1).In each experiment, seeds were soaked for 30min in 0.6% (w/v) sodium hypochlorite for surface sterilization. Seeds were then washed thoroughly with deionized water, and then the seeds were placed in Petri dishes containing about 5mm deionized water for 2 d in darkness at 30 °C. After 2 d imbibition, germinated seeds were placed on stainless mesh floating on aerated quarter-strength nutri- ent solution and exposed to light. After 6 d imbibition, each seedling was held with soft sponge floating on aerated full-strength nutrient solution. After 9 d imbibition, seedlings were transferred to 5-l pots (height 250 mm, width 120 mm, breadth 180 mm) containing aerated full-strength nutrient solution. Solutions were renewed every 7 d. In each experiment, pots were arranged in a completely randomized design.

extract_protocol: Adventitious roots of 23-d-old plants were classified as short (65– 85 mm) or long (115–135 mm), based on the length of the main axis at commencement of treatments. Selected short and long adventi- tious roots were marked near the base using small loops of sewing cotton, so these could be recognized over time. After treating the roots of plants in aerated, stagnant, or N2-flushed conditions for 9h, the basal parts (12.5–22.5mm below the root– shoot junction) of the adventitious roots were collected, fixed in 100% acetone, embedded in paraffin, and sectioned at a thickness of 16 μm. Serial sections were placed onto PEN membrane glass slides (Life Technologies, Carlsbad, CA, USA) for laser microdissection. To remove paraffin, slides were immersed in Histoclear II (National Diagnostics, Atlanta, GA, USA) for 5 min, followed by drying in air at room temperature. Cells in the outer part of root (OPR, including exodermis and sclerenchyma), cortical parenchyma (CP, excluding exodermis, sclerenchyma, and endodermis), or central cylinder (CC, including endodermis) were collected from the root tissue sections using a Veritas Laser Microdissection System LCC1704 (Molecular Devices, Toronto, ON, Canada) (Fig. 1B), as described previously (Takahashi et al., 2010). Total RNA was extracted from the laser microdissection-isolated cells of OPR, CP, or CC using a PicoPure RNA isolation kit (Life Technologies) according to the manufac- turer’s instructions. The extracted total RNA was quantified with a Quant-iT RiboGreen RNA reagent and kit (Life Technologies) according to the manufacturer’s instructions. The quality of total RNA was assessed using a RNA 6000 Pico kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: 23-d-old plants were either continued in aerated solution or transplanted into N2-flushed or stagnant deoxygenated solution for 9 h. In N2-flushed nutrient solution, oxygen level was kept hypoxic (dissolved oxygen <1.0 mg l–1). Stagnant solution contained 0.1% (w/v) dissolved agar and was deoxygenated (dissolved oxygen <1.0 mg l–1) prior to use by preflushing with N2 gas. The dilute agar Transcriptional profiling during ROL barrier formation prevents convective movements in solution (‘stagnant’ treatment) so this treatment mimics better than other solution culture meth- ods the changes in gas composition found in waterlogged soils (e.g. decreased oxygen, increased ethylene) (Wiengweera et al., 1997).

value: Nipponbare

value: 23-d old

tag: treated in

value: stagnant deoxygenated solution for 9 h

tag: adventitious roots length

value: short (65-85 mm)

value: outer part of roots (OPR)


title: ColorSwap_OPR_in_Basal_Stagnant_Short vs Stagnant_Long_Replicate1


title: ColorSwap_OPR_in_Basal_Stagnant_Short vs Stagnant_Long_Replicate3


title: S1_Psip1/p75

description: anti Psip1/p75 (Bethyl lab A300-848)


title: ColorSwap_OPR_in_Basal_Stagnant_Short vs Stagnant_Long_Replicate2


title: ColorSwap_OPR_in_Basal_N2-flushed_Long vs Stagnant_Long_Replicate2

value: N2-flushed solution for 9hrs


title: OPR_in_Basal_Stagnant_Short vs Stagnant_Long_Replicate1


title: ColorSwap_OPR_in_Basal_N2-flushed_Long vs Stagnant_Long_Replicate3


title: OPR_in_Basal_N2-flushed_Long vs Stagnant_Long_Replicate3

value: N2-flushed solution


title: ColorSwap_OPR_in_Basal_N2-flushed_Long vs Stagnant_Long_Replicate1


title: OPR_in_Basal_N2-flushed_Long vs Stagnant_Long_Replicate2


title: ColorSwap_OPR_in_Basal_Aerated_Long vs Stagnant_Long_Replicate3

value: aerated solution for 9hr


title: ColorSwap_OPR_in_Basal_Aerated_Long vs Stagnant_Long_Replicate2


title: ColorSwap_OPR_in_Basal_Aerated_Long vs Stagnant_Long_Replicate1


title: OPR_in_Basal_N2-flushed_Long vs Stagnant_Long_Replicate1


title: 2a

city: Chongqing

first: Muhan

last: Lv

address: No.30 Gaotanyan Street, Shapingba District

institute: Southwest Hospital of Third Military Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method. Differentially expressed lncRNAs/mRNAs were identified as those with fold change >= 2; p <= 0.05

source_name: human tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy Mini Kit (Qiagen p/n 74104). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: gastric mucosa

tag: tissue cancer status

value: para cancerous tissue

value: female


title: 1b

value: gastric cancer tissue


title: 1a


title: OPR_in_Basal_Aerated_Long vs Stagnant_Long_Replicate2


title: HFK-16E6E7, bilogical rep1

city: Debrecen

first: György

last: Veress

address: Nagyerdei krt. 98

department: Department of Medical Microbiology

country: Hungary

institute: University of Debrecen

description:
Gene expression data from HPV 16 E6/E7 transduced keratinocytes
16E6E7_1_(HuGene-1_0-st-v1)

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing:
CHP files were generated using Affymetrix Expression Control.
Downstream data analysis was performed in GeneSpring GX 12,  CEL files were imported using RMA algorithm and median normalization was performed.

source_name: HFK transduced by 16E6/E7

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of RNA samples.

growth_protocol: Primary human keratinocytes were cultured in Defined Keratinocyte Serum Free Medium.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Primary human keratinocytes were transduced by LXSN (control) retrovirus vector or vectors expressing HPV 16 E6, E7 or E6E7.

value: foreskin keratinocytes

tag: transduction

value: HPV16 E6E7


title: HFK-16E6E7, bilogical rep3

description:
Gene expression data from HPV 16 E6/E7 transduced keratinocytes
16E6E7_3_(HuGene-1_0-st-v1)


title: HFK-16E6, biological rep3

description:
Gene expression data from HPV 16 E6 transduced keratinocytes
16E6_3_(HuGene-1_0-st-v1)

source_name: HFK transduced by 16E6

value: HPV16 E6


title: 3b


title: 2b


title: HFK-16E7, biological rep3

description:
Gene expression data from HPV 16 E7 transduced keratinocytes
16E7_3_(HuGene-1_0-st-v1)

source_name: HFK transduced by 16E7

value: HPV16 E7


title: HFK-16E6E7, bilogical rep2

description:
Gene expression data from HPV 16 E6/E7 transduced keratinocytes
16E6E7_2_(HuGene-1_0-st-v1)


title: OPR_in_Basal_Aerated_Long vs Stagnant_Long_Replicate3


title: HFK-16E7, biological rep1

description:
Gene expression data from HPV 16 E7 transduced keratinocytes
16E7_1_(HuGene-1_0-st-v1)


title: HFK-16E6, biological rep2

description:
Gene expression data from HPV 16 E6 transduced keratinocytes
16E6_2_(HuGene-1_0-st-v1)


title: HFK-16E6, biological rep1

description:
Gene expression data from HPV 16 E6 transduced keratinocytes
16E6_1_(HuGene-1_0-st-v1)


title: HFK-16E7, biological rep2

description:
Gene expression data from HPV 16 E7 transduced keratinocytes
16E7_2_(HuGene-1_0-st-v1)


title: 3a

value: male


title: HFK-LXSN, biological rep2

description:
Gene expression data from LXSN transduced keratinocytes
LXSN_2_(HuGene-1_0-st-v1)

source_name: HFK transduced by LXSN

value: control


title: HFK-LXSN, biological rep3

description:
Gene expression data from LXSN transduced keratinocytes
LXSN_3_(HuGene-1_0-st-v1)


title: OPR_in_Basal_Stagnant_Short vs Stagnant_Long_Replicate2

value: Nipponbare

value: 23-d old


title: Rex1GFPd2 ES cells siYAP/TAZ#2 in PD-only medium, biological replicate  B

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from YAP/TAZ depleted ES cells, cultured in PD-only medium

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GeneChip Command Console Software (AGCC)

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: Rex1GFPd2 mouse embryonic stem cells , transfected with siRNA YAP/TAZ#2, cultured in PD-only medium

label_protocol: Biotinylated cRNA were prepared using the 3'IVT Kit ( Affymetrix, Santa Clara, USA, CA) according to manufacturer's intructions.

growth_protocol: Rex1GFPd2 embryonic stem (ES) cells were culture in Neurobasal/ DMEMF12 1:1, N2 and B27 supplements, aminoacids, glutamine, antibiotics, with PD and CHIR (2i medium) or with PD only (PD)

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

treatment_protocol: Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following a reverse transfection protocol

value: embryonic stem cells

tag: medium

value: PD-only


title: Rex1GFPd2 ES cells siYAP/TAZ#2 in PD-only medium, biological replicate  A


title: HFK-LXSN, biological rep1

description:
Gene expression data from LXSN transduced keratinocytes
LXSN_1_(HuGene-1_0-st-v1)


title: Rex1GFPd2 ES cells siYAP/TAZ#2 in PD-only medium, biological replicate  D


title: Rex1GFPd2 ES cells siYAP/TAZ#1 in PD-only medium, biological replicate  D

source_name: Rex1GFPd2 mouse embryonic stem cells , transfected with siRNA YAP/TAZ#1, cultured in PD-only medium


title: DU_0.25mg_rep2

city: Oslo

first: You

last: Song

address: Økernveien 94

department: Ecotoxicology and Risk Assessment

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

description: Gene expression after 48 h in 0.25 mg DU/L exposed fish liver

hyb_protocol: Totally 600 ng of Cy3-labeled, linearly amplified cRNA was fragmented and hybridized to 8x60k microarrays and rotationally (10 rpm) incubated at 65 ºC for 17 h.

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (Dye channel: G (green), scan region: Agilent HD (61 × 21.6 mm), Scan resolution: 3 µm, Tiff file dynamic range: 20 bit, Green PMI gain: 100%).

data_processing: The microarray scan images (raw signal intensity) were extracted using Agilent Feature Extraction software v10.7. Raw data were normalization (quantile) and statistical analyses were performed using GeneSpring GX v11.0 (Agilent Technologies). Non-uniform outliers were excluded.

organism: Salmo salar

source_name: 0.25 mg/L DU exposed replicate2

label_protocol: Cyanine 3-CTP (Cy3) labeled cRNA was made from 200 ng total RNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, California, USA). The cRNA dye incorporation and yiled were checked using Agilent Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA was extracted from 20-30 mg snap-frozen liver tissue using RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.The RNA quality (purity and yield) was controlled by photometric analyses (260/230 > 2.0, 260/280>1.8, yield >200 ng/μL) using Nanodrop® spectrophotometer (ND-1000, Nanodrop Technologies, Wilminton, Delaware, USA) and RNA integrity (RIN>8.0) inspected by Bioanalyzer gelelectrophoresis with RNA 6000 Nano chips (Agilent technologies, Santa Clara, California, USA) according to the manufacturer’s instructions.

treatment_protocol: Atlantic salmon parr were transferred to lake water (Maridalsvannet, Norway) for 72 h acclimation prior to being exposed to 0 mg/L (control), 0.25 mg/L, 0.5 mg/L and 1.0 mg/L dissolved uranyl acetate dihydrate in the dark for 48 h. Fish were exposed in a static system supplied with air pumps. No feeding was performed during the acclimation and exposure period.

tag: tissue

value: Liver


title: OPR_in_Basal_Aerated_Long vs Stagnant_Long_Replicate1

value: outer part of roots (OPR)

value: stagnant deoxygenated solution for 9 h


title: Control_rep3

description: Gene expression after 48 h in control fish liver

source_name: Control replicate 3


title: Rex1GFPd2 ES cells siYAP/TAZ#1 in PD-only medium, biological replicate  A


title: Rex1GFPd2 ES cells siYAP/TAZ#1 in PD-only medium, biological replicate  C


title: DU_0.25mg_rep1

source_name: 0.25 mg/L DU exposed replicate1


title: Rex1GFPd2 ES cells siControl#1 in PD-only medium, biological replicate  B

description: Gene expression data from control ES cells, cultured in PD-only medium

source_name: Rex1GFPd2 mouse embryonic stem cells , transfected with siRNA Control#1, cultured in PD-only medium


title: Rex1GFPd2 ES cells siControl#2 in PD-only medium, biological replicate  B

source_name: Rex1GFPd2 mouse embryonic stem cells , transfected with siRNA Control#2, cultured in PD-only medium


title: DU_1.0mg_rep3

description: Gene expression after 48 h in 1.0 mg DU/L exposed fish liver

source_name: 1.0 mg/L DU exposed replicate3


title: darkcd4_rep4

city: Bunkyo-ku

first: Masayuki

last: Miura

state: Tokyo

department: Genetics

institute: the University of Tokyo, Grad. Sch. Pharm. Sci

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent GE blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 custom microarray 8x60K (G4102A, #040871) 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.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner using AgilentG3_GX_1Color_HighSensitivity.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 040871_D_F_20120511) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized by Percentile Shift (at 75 % percentile) and subjected to baseline transformation (baseline to median of all samples) using GeneSpring GX.

organism: Drosophila melanogaster

source_name: whole body, darkcd4 mutant

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000c Spectrophotometer.

growth_protocol: Flies were kept at 25 °C on standard diet containing cornmeal, baker's yeast, and glucose in 60% humidity with light/dark (12h/12h) condition.

extract_protocol: Total RNA was purified from five adults for one sample using TRIzol and purified by RNeasy Plus Micro Kit (Qiagen).

treatment_protocol: After adult eclosion, flies were collected within 1 day and kept them five days with free access to food and mating.

tag: developmental stage

value: day 5 adult

value: whole body


title: Rex1GFPd2 ES cells siControl#2 in PD-only medium, biological replicate  A


title: Rex1GFPd2 ES cells siControl#1 in PD-only medium, biological replicate  C


title: Rex1GFPd2 ES cells siControl#2 in PD-only medium, biological replicate  C


title: darkcd4_rep3


title: Rex1GFPd2 ES cells siYAP/TAZ#1 in PD-only medium, biological replicate  B


title: Control_rep2

source_name: Control replicate 2


title: DU_1.0mg_rep1

source_name: 1.0 mg/L DU exposed replicate1


title: Rex1GFPd2 ES cells siControl#2 in 2i medium, biological replicate  C

description: Gene expression data from control ES cells, cultured in 2i medium

source_name: Rex1GFPd2 mouse embryonic stem cells , transfected with siRNA Control#2, cultured in 2i medium

value: 2i medium


title: Rex1GFPd2 ES cells siControl#1 in PD-only medium, biological replicate  A


title: Rex1GFPd2 ES cells siControl#1 in PD-only medium, biological replicate  D


title: Control_rep1

source_name: Control replicate 1


title: DU_1.0mg_rep2

source_name: 1.0 mg/L DU exposed replicate2


title: Rex1GFPd2 ES cells siYAP/TAZ#2 in PD-only medium, biological replicate  C


title: w1118_rep4

source_name: whole body, w118


title: DU_0.5mg_rep3

description: Gene expression after 48 h in 0.5 mg DU/L exposed fish liver

source_name: 0.5 mg/L DU exposed replicate3


title: Rex1GFPd2 ES cells siControl#2 in 2i medium, biological replicate  B


title: Rex1GFPd2 ES cells siControl#2 in 2i medium, biological replicate  A


title: darkcd4_rep1


title: darkcd4_rep2


title: Rex1GFPd2 ES cells siControl#1 in 2i medium, biological replicate  C

source_name: Rex1GFPd2 mouse embryonic stem cells , transfected with siRNA Control#1, cultured in 2i medium


title: DU_0.5mg_rep1

source_name: 0.5 mg/L DU exposed replicate1


title: DU_0.25mg_rep3

source_name: 0.25 mg/L DU exposed replicate3


title: w1118_rep3


title: DU_0.5mg_rep2

source_name: 0.5 mg/L DU exposed replicate2


title: w1118_rep1


title: w1118_rep2


title: pooled DNA-SCC

city: Taipei

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

country: Taiwan

institute: Taipei Medical University

description: clinical samples

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Cervical squamous cell carcinoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor tissue and scarpping cells using Qiagen DNeasy Kit according to standard instructions

value: tumorous cervical samples


title: Rex1GFPd2 ES cells siControl#1 in 2i medium, biological replicate  B


title: pooled DNA-NormalCx

description: clinical samples

source_name: Normal scrapping cervical cells

value: normal cervical samples


title: Rex1GFPd2 ES cells siControl#1 in 2i medium, biological replicate  A


title: Duodenum tissue from germ free rat mono-colonised with AGR1487, 6 of 6

status: Public on Jun 25 2014

city: Palmerston North

first: Wayne

last: Young

address: Tennent Drive

country: New Zealand

institute: AgResearch

description: Biological replicate 6 of 6, duodenum tissue, AGR1487

hyb_protocol: Samples were hybridized to the microarrays using a reference design, where samples labelled with Cy3 were competitively hybridized with a reference RNA labelled with Cy5.

scan_protocol: Microarrays were scanned using an Agilent Technologies Scanner G2505B

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was using to calculate fluorescence values.  Loess within array and Aquantile between array normalisation was carried out using the limma package in R (3.0.1)

organism: Rattus norvegicus

source_name: Duodenum tissue from germ free rats mono-associated with bacteria

label_protocol: 200 ng of sample RNA was linearly amplified with Cy3 labelled CTP using the Agilent Low Input Linear Amplification kit according to the manufacturers instructions.  500 ng of reference RNA was linearly amplified with Cy5 labelled CTP using the Agilent Low Input Linear Amplification kit according to the manufacturers instructions.

growth_protocol: Germ-free newly weaned male Sprague Dawley rats were house in individual cages within a gnotobiotic isolator.  Different isolators were used for colonisation with each strain

extract_protocol: Tissue samples (duodenum and colon) were homogenized in buffer RLT (Qiagen, California, USA) and total RNA was extracted using a AllPrep DNA/RNA/Protein Mini Kit (Qiagen) as per the manufacturer’s protocol

treatment_protocol: This rodent experiment was approved by the AgResearch Grasslands Animal Ethics Committee (Palmerston North, New Zealand; Approval number 12504) in accordance with the New Zealand Animal Welfare Act 1999. Twelve, female germ-free JCL:Wistar rats between 7 and 8 weeks of age were obtained from Japan SCL Inc (Tokyo, Japan). On arrival the rats were transferred to individual cages in two separate sterile isolators (isolator name, company details) using standard operating procedures (n=6 per isolator). The rats underwent an adaptation period of 7 days prior to inoculation via oral gavage. Each rat was given either 400 µL of the L. fermentum AGR1487 secondary  broth or 700 µL of the L. fermentum AGR1485 secondary broth via oral gavage, which was equivalent to approximately 109 bacterial cells per rat. Throughout the experiment the rats were fed sterile standard rat chow (diet nameAIN-93M, company Research Diets Inc, New Brunswick, NJ, USA) and water ad libitum. All consumables and equipment were sterilized prior to entering the isolators; food and most husbandry items were irradiated and water was autoclaved. Fourteen days after inoculation the rats were euthanized by CO2 asphyxiation and cervical dislocation. Intestinal tissue samples were immediately collected post mortem and rapidly frozen in liquid nitrogen until analysis.

value: Duodenum

value: Sprague Dawley

tag: bacterial colonisation

source_name: Colon tissue reference RNA

tag: sample type

value: Pooled reference RNA from conventional rat


title: Colon tissue from germ free rat mono-colonised with AGR1485, 4 of 6

description: Biological replicate 4 of 6, colon tissue, AGR1485

source_name: Colon tissue from germ free rats mono-associated with bacteria

value: Colon


title: Duodenum tissue from germ free rat mono-colonised with AGR1485, 4 of 6

description: Biological replicate 4 of 6, duodenum tissue, AGR1485


title: Duodenum tissue from germ free rat mono-colonised with AGR1487, 5 of 6

description: Biological replicate 5 of 6, duodenum tissue, AGR1487


title: Colon tissue from germ free rat mono-colonised with AGR1487, 5 of 6

description: Biological replicate 5 of 6, colon tissue, AGR1487


title: Colon tissue from germ free rat mono-colonised with AGR1485, 6 of 6

description: Biological replicate 6 of 6, colon tissue, AGR1485


title: Duodenum tissue from germ free rat mono-colonised with AGR1487, 4 of 6

description: Biological replicate 4 of 6, duodenum tissue, AGR1487


title: Duodenum tissue from germ free rat mono-colonised with AGR1485, 6 of 6

description: Biological replicate 6 of 6, duodenum tissue, AGR1485


title: Colon tissue from germ free rat mono-colonised with AGR1487, 4 of 6

description: Biological replicate 4 of 6, colon tissue, AGR1487


title: CD19-IL10neg4

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

description: Sample name: M1694-11

hyb_protocol: Fragmented cRNAs were hybridized to the standard arrays for 17 hours at 45°C, the arrays were then washed and stained using the fluidics station according to genechip array manufacturer's protocol

scan_protocol: The human exon chips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality controls analyses were carried out according to the instructions provided by Affymetrix.

data_processing: Data was analyzed with RMA/quantile normalization in r v 2.13.0 in bioconductor using the oligo package (HuEx-1_0-st-v2.r2.pgf, HuEx-1_0-st-v2.r2.dt1.hg18.core.mps).

source_name: Human blood

label_protocol: cDNA were prepared according to the Ambion® WT Expression Kit's protocol from 100ng Total RNA.  5.5ug of cDNA were fragmented and labelled according to Affymetrix GeneChip® WT Terminal  Labeling and Hybridization kit's protocol.

growth_protocol: Human B-cells were cultured at a density of 2.5×106 cells/ml in complete medium (RPMI-1640 supplemented with 10% FBS, 2mM L-glutamine, 100U/mL penicillin and 100μg/mL streptomycin; Life Technologies) and were stimulated or not with 3µg/ml CpG-B 2006 (InvivoGen) and 10µg/ml Goat Anti-Human IgA + IgG + IgM (H+L) (anti-Ig; Jackson ImmunoResearch Laboratories) for 48h at 37oC, 5% CO2

extract_protocol: Total RNA was extracted using miRNeasy Mini Kits (Qiagen). RNA Integrity Number (RIN) was assessed by Agilent Bioanalyzer (Agilent Technologies). All RNA samples were RIN≥9.2.

treatment_protocol: IL-10-secreting B-cells were isolated using the MACS IL-10 cytokine secretion assay-detection kit (Miltenyi Biotec) according to the manufacturer’s protocol. B-cells were then re-suspended at 1×107 cells/ml in cold PBS pH 7.2 (containing 0.5% BSA and 2 mM EDTA) buffer and stained with LIVE/DEAD Fixable Aqua Dead Cell Stain (Life Technologies) and anti-CD19 AF700 antibody (Biolegend). CD19+ B-cells were sorted into three separate populations using a BD FACSAria II 4-Laser Cell Sorter (BD Biosciences); (1) un-stimulated IL-10- cells, (2) stimulated IL-10- cells, (3) stimulated IL-10+ cells.

value: IL-10- B-cells


title: Colon tissue from germ free rat mono-colonised with AGR1485, 5 of 6

description: Biological replicate 5 of 6, colon tissue, AGR1485


title: Duodenum tissue from germ free rat mono-colonised with AGR1485, 3 of 6

description: Biological replicate 3 of 6, duodenum tissue, AGR1485


title: Colon tissue from germ free rat mono-colonised with AGR1487, 6 of 6

description: Biological replicate 6 of 6, colon tissue, AGR1487


title: Colon tissue from germ free rat mono-colonised with AGR1485, 3 of 6

description: Biological replicate 3 of 6, colon tissue, AGR1485


title: Duodenum tissue from germ free rat mono-colonised with AGR1485, 5 of 6

description: Biological replicate 5 of 6, duodenum tissue, AGR1485


title: CD19-IL10pos5

description: Sample name: M1699-11

value: IL-10+ B-cells


title: H441 siNTC

city: Tokyo

first: Akira

last: Saito

address: 7-31-, Hongo, Bunkyo

institute: Tokyo University

description: Gene expression data from H441 cells transfected with siNTC

hyb_protocol: Biotin-labeled sense-strand cDNA were hybridized for 16 hours at 45°C on GeneChip Human Gene ST 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip Scanner 3000 7G

data_processing: CEL files were obtained by Affymetrix GeneChip Command Console (AGCC). Data were normalized to a global intensity by GeneSpring GX software (Agilent Technologies) using the RMA (Robust Multi-array Average) procedure.

source_name: human lung cancer cell line H441 transfected with siNTC

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: Standard A549 and H441 growth conditions.

extract_protocol: RNeasy mini kit (Qiagen) was used for total RNA extraction.

treatment_protocol: Cells were transfected with siRNA, using Lipofectamine RNAiMAX (Invitrogen), according to the manufacturer’s instructions.Total RNA was extracted from A549 and H441 cells 48h after transfection.

value: lung cancer


title: CD19-IL10neg3

description: Sample name: M1696-11


title: Duodenum tissue from germ free rat mono-colonised with AGR1487, 3 of 6

description: Biological replicate 3 of 6, duodenum tissue, AGR1487


title: Duodenum tissue from germ free rat mono-colonised with AGR1487, 2 of 6

description: Biological replicate 2 of 6, duodenum tissue, AGR1487


title: CD19-IL10pos4

description: Sample name: M1695-11


title: A549 siNTC

description: Gene expression data from A549 cells transfected with siNTC

source_name: human lung cancer cell line A549 transfected with siNTC


title: CD19-IL10neg5

description: Sample name: M1698-11


title: A549 siTAZ

description: Gene expression data from A549 cells transfected with siTAZ

source_name: human lung cancer cell line A549 transfected with siTAZ


title: CD19-IL10pos3

description: Sample name: M1697-11


title: Colon tissue from germ free rat mono-colonised with AGR1485, 2 of 6

description: Biological replicate 2 of 6, colon tissue, AGR1485


title: Colon tissue from germ free rat mono-colonised with AGR1487, 3 of 6

description: Biological replicate 3 of 6, colon tissue, AGR1487


title: H441 siTAZ

description: Gene expression data from H441 cells transfected with siTAZ

source_name: human lung cancer cell line H441 transfected with siTAZ


title: Colon tissue from germ free rat mono-colonised with AGR1487, 2 of 6

description: Biological replicate 2 of 6, colon tissue, AGR1487


title: Veh 24HR #2

city: Ann Arbor

first: Bradley

middle: S

last: Carter

state: MI

address: 109 Zina PItcher Place

department: Molecular and Behavioral Neuroscience Institute

country: USA

institute: University of Michigan

description: 24 hour vehicle replicate-2

hyb_protocol: Standard Illumina hybridization protocol (MouseWG-6 v2.0 Expression BeadChip)

scan_protocol: Standard Illumina scanning protocol (BeadArray reader)

data_processing: Data normalised using quantile normalization with Illumina GenomeStudio software; for each time point, the dexamethasone data was normlized to the corresponding vehicle control data (e.g. Matrix normalized data is representative for 2 hour data; normalized to 2 hour vehicle data)

source_name: Cortical astrocyte culture

label_protocol: Biotinylated cRNA were prepared with the Ambion's TotalPrep RNA Amplification kit for Illumina arrays

growth_protocol: Primary cultures derived from P0-P2 mouse pups (cortex or hippocampus), plated 250,000-500,000/well in 6-well dishes, grown 9-11 days until ~confluent (grown in 37C incubator with DMEM+10%FBS media; 100% media changed 24 hours post-plating, 50% media replaced every 2-3 days afterward)

treatment_protocol: ~100nM dexamethasone in media for given time period (returned to incubator)

value: Brain

tag: treatment

value: 24 hour vehicle


title: Veh 24HR #1

description: 24 hour vehicle replicate-1


title: CD19-IL10pos1

description: Sample name: M1691-11


title: Dex 24HR #1

description: 24 hour steroid replicate-1

value: 24 hour ~100nM dexamethasone


title: Duodenum tissue from germ free rat mono-colonised with AGR1487, 1 of 6

description: Biological replicate 1 of 6, duodenum tissue, AGR1487


title: Duodenum tissue from germ free rat mono-colonised with AGR1485, 2 of 6

description: Biological replicate 2 of 6, duodenum tissue, AGR1485


title: Veh 18HR #1

description: 18 hour vehicle replicate-1

value: 18 hour vehicle


title: Veh 18HR #2

description: 18 hour vehicle replicate-2


title: CD19-IL10pos2

description: Sample name: M1693-11


title: Veh 12HR #2

description: 12 hour vehicle replicate-2

value: 12 hour vehicle


title: CD19-IL10neg2

description: Sample name: M1692-11


title: Colon tissue from germ free rat mono-colonised with AGR1487, 1 of 6

description: Biological replicate 1 of 6, colon tissue, AGR1487


title: CD19-IL10neg1

description: Sample name: M1690-11


title: Dex 18HR #1

description: 18 hour steroid replicate-1

value: 18 hour ~100nM dexamethasone


title: Dex 12HR #2

description: 12 hour steroid replicate-2

value: 12 hour ~100nM dexamethasone


title: Dex 24HR #2

description: 24 hour steroid replicate-2


title: Colon tissue from germ free rat mono-colonised with AGR1485, 1 of 6

description: Biological replicate 1 of 6, colon tissue, AGR1485


title: Veh 12HR #1

description: 12 hour vehicle replicate-1


title: Duodenum tissue from germ free rat mono-colonised with AGR1485, 1 of 6

description: Biological replicate 1 of 6, duodenum tissue, AGR1485


title: creBC_mutant_caz, biological rep 3

city: Palma de Mallorca

first: Bartolome

middle: Moya

last: Cañellas

state: Islas Baleares

address: Ctra. Valldemossa

department: Microbiology

institute: HUSE

description: Gene expression data from the derivative creBC  P. Aeruginosa mutant strain under ceftazidime incubation

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RMA and quantile normalization.

organism: Pseudomonas aeruginosa

source_name: creBC ceftazidime incubation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Three independent replicates of PAO1 and its creBC  derivative mutant (PAOΔcreBC) were grown in 10 ml of LB broth under basal conditions and with cefoxitin and ceftazidime 3h incubation in a 50-ml baffled flask vigorously shaken at 37°C to an optical density at 600 nm (OD600) of 1.

extract_protocol: The cells were collected by centrifugation (8,000 g for 5 min at 4°C) and total RNA was isolated using the RNeasy minikit (QIAGEN) following the manufacturer's instructions

value: ceftazidime

tag: genotype

value: creBC mutant


title: Dex 12HR #1

description: 12 hour steroid replicate-1

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


title: creBC_mutant_caz, biological rep 2


title: Dex 18HR #2

description: 18 hour steroid replicate-2


title: Veh 6HR #1_2

description: 6 hour vehicle replicate-1

value: 6 hour vehicle


title: creBC_mutant_caz, biological rep 1


title: 12_chick_r5_set_2

city: London

first: David

last: Chambers

state: London

address: Guy's Campus

department: Wolfson CARD

institute: King's College Londonn

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 18 Hours at 45oC on GeneChip Gallus gallus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. as per Nugen Inc Instructions for Nugen Ovation V2

scan_protocol: Affymetrix Scanner 3000 7G

data_processing: Probe set values were generated with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and a user defined scale factor of 1.0

organism: Gallus gallus

source_name: Rhombomere 5

label_protocol: Nugen Ovation V2 and Biotin Module

growth_protocol: Embryos were incubated until they had reached HH10-11

extract_protocol: Absolutely RNA Stratagene

treatment_protocol: Neural tubes were proteolytically-treated (Dispase 1mg/ml) for 15 minutes, stripped of ahherent ectoderm and mesoderm followed by manual dissection into individual segments

value: HH10 Neural Tube

value: Rhombomere 5


title: Dex 6HR #2

description: 6 hour steroid replicate-2

value: 6 hour ~100nM dexamethasone


title: Rex1GFPd2 ES cells siContro#1 in 2i medium, biological replicate  D

description: Gene expression data from control ES cells, cultured in 2i medium

source_name: Rex1GFPd2 mouse embryonic stem cells , transfected with siRNA Control#1, cultured in 2i medium

tag: cell type

value: embryonic stem cells

value: 2i medium


title: PAO1_wildtype_caz, biological rep 3

description: Gene expression data from wild type P. Aeruginosa strain under ceftazidime incubation

source_name: PAO1 ceftazidime incubation

value: wyld type


title: Veh 6HR #2_2

description: 6 hour vehicle replicate-2


title: PAO1_wildtype_caz, biological rep 2


title: 11_chick_r4_set_2

source_name: Rhombomere 4

value: Rhombomere 4


title: 10_chick_r3_set_2

source_name: Rhombomere 3

value: Rhombomere 3


title: Dex 4HR #3

description: 4 hour steroid replicate-3

value: Brain

value: 4 hour ~100nM dexamethasone


title: Veh 4HR #2_2

description: 4 hour vehicle replicate-2

value: 4 hour vehicle


title: Veh 4HR #1_2

description: 4 hour vehicle replicate-1


title: Veh 4HR #3_2

description: 4 hour vehicle replicate-3


title: Dex 4HR #2

description: 4 hour steroid replicate-2


title: Dex 4HR #1

description: 4 hour steroid replicate-1


title: 8_chick_r1_set_2

source_name: Rhombomere 1

value: Rhombomere 1


title: creBC_mutant_fox, biological rep 3

description: Gene expression data from the derivative creBC  P. Aeruginosa mutant strain under cefoxitin induction

source_name: creBC cefoxitin induction

value: cefoxitin


title: PAO1_wildtype_caz, biological rep 1


title: creBC_mutant_fox, biological rep 2


title: creBC_mutant_fox, biological rep 1


title: 9_chick_r2_set_2

source_name: Rhombomere 2

value: Rhombomere 2


title: Veh 2HR #3_2

description: 2 hour vehicle replicate-3

value: 2 hour vehicle


title: 7_chick_m_set_2

source_name: midbrain

value: midbrain


title: Veh 2HR #2_2

description: 2 hour vehicle replicate-2


title: Veh 2HR #1_2

description: 2 hour vehicle replicate-1


title: Dex 2HR #1

description: 2 hour steroid replicate-1

value: 2 hour ~100nM dexamethasone


title: PAO1_wildtype_fox, biological rep 1

description: Gene expression data from wild type P. Aeruginosa strain under cefoxitin induction

source_name: PAO1 cefoxitin induction


title: PAO1_wildtype_fox, biological rep 2


title: Dex 2HR #2

description: 2 hour steroid replicate-2


title: PAO1_wildtype_fox, biological rep 3


title: creBC mutant, biological rep 3

description: Gene expression data from the derivative creBC  P. Aeruginosa mutant strain under basal conditions

source_name: creBC mutant basal condition

value: creBC mutant


title: 4_chick_r3_set_1

value: HH10 Neural Tube


title: 6_chick_r5_set_1

value: Rhombomere 5


title: Veh 1HR #2

description: 1 hour vehicle replicate-2

value: 1 hour vehicle


title: Dex 2HR #3

description: 2 hour steroid replicate-3


title: Dex 1HR #1

description: 1 hour steroid replicate-1

value: 1 hour ~100nM dexamethasone


title: 5_chick_r4_set_1


title: Veh 1HR #1

description: 1 hour vehicle replicate-1


title: Dex 1HR #2

description: 1 hour steroid replicate-2


title: creBC mutant, biological rep 2


title: creBC mutant, biological rep 1


title: 3_chick_r2_set_1


title: Veh 0.25HR #2

description: 15 minute vehicle replicate-2

value: 15 minute vehicle


title: 2_chick_r1_set_1


title: PAO1 WILD TYPE, biological rep 3

description: Gene expression data from wild type P. Aeruginosa strain under basal conditions

source_name: PAO1 basal condition

value: wyld type


title: Dex 0.25HR #2

description: 15 minute steroid replicate-2

value: 15 minute ~100nM dexamethasone


title: Veh 0.25HR #1

description: 15 minute vehicle replicate-1

value: Brain


title: Dex 0.25HR #1

description: 15 minute steroid replicate-1


title: 1_chick_m_set_1


title: PAO1 WILD TYPE, biological rep 2


title: PAO1 WILD TYPE, biological rep 1


title: WT HSC

city: hangzhou

first: Hu

last: Wang

address: wenyixi road 1378

institute: hangzhou normal university

description: Gene expression data from  WT HSC.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Mus musculus wild type HSC

label_protocol: Cy3-cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: 3 months

value: Hematopoietic stem cell

tag: phenotype

value: wild type


title: GBCs P21 biol. repl. 1

status: Public on Jun 24 2014

city: Heidelberg

first: Christoph

last: Koerber

address: Im Neuenheimer Feld 307

department: Institute of Anatomy and Cell Biology

country: Germany

institute: University of Heidelberg

description: Gene expression of P21 GBCs

hyb_protocol: 10µg aRNA were hybridized to Affymetrix Rat Expression 230 2.0 chips. Hybridization and labeling were performed by an authorized Affymetrix service provider (Atlas Biolabs GmbH, Friedrichstr.127, 10117 Berlin, Germany).

scan_protocol: Scanning was performed by an authorized Affymetrix service provider (Atlas Biolabs GmbH, Friedrichstr.127, 10117 Berlin, Germany).

data_processing: The R – Bioconductor open source software platform was used throughout the whole data analysis workflow. Quality of obtained microarray data was assessed using the ‘arrayQualityMetrics’ library. Background correction and normalization of raw expression values were performed using of the ‘gcrma’ algorithm. A moderate t-test based on Bayesian statistics, which allows for the reliable estimation of standard deviation of few replicates, was chosen for primary data analysis, and resulting p-values were corrected for multiple test-ing using the false discovery rate method (FDR) of Benjamini and Hochberg (1995).

source_name: GBCs when calyx is fully mature

label_protocol: Biotin-labelled NTPs were introduced in the second round of RNA amplification.

growth_protocol: Rats were stereotaxically injected with Cholera toxin B and sacrificed 24h later

extract_protocol: RNA was isolated from laser microdissection dissected cells using the RNeasy Micro Kit (Qiagen) according to the manufacturers instructions and precipitated by adding 0.3M Na-acetate and ethanol. Total RNA was linearly amplified over two rounds using MessageAmp II aRNA Amplification Kit (Ambion).

treatment_protocol: Brains were acutely removed and flash frozen on dry ice. Labelled cells were excised from cryosections by laser microdissection.

value: brain

value: Sprague Dawley

value: globular bushy cells when calyx is fully mature


title: anti-TNFalpha rep3

city: Amsterdam

first: Martine

middle: A.

last: Boks

address: Plesmanlaan 125

department: Immunopathology

country: Netherlands

institute: Sanquin Blood Supply

description: T cell donor C

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was log2 transformed and normalized between arrays using robust spline normalization method. Triplicate samples of anti-TNFα-treated T cells were compared to non-treated T cells by LIMMA analysis.

source_name: naive CD4+ T cells

label_protocol: Biotinylated cRNA was prepared following standard Illumina labeling protocol.

extract_protocol: RNA was extracted with Trizol reagent, followed by DNase treatment.

value: PBMC

tag: agent

value: anti-TNFalpha

tag: activation

value: by allogeneic dendritic cells

tag: cell subtype

value: CFSE negative T cells


title: Wip1 HSC

description: Gene expression data from Wip1 KO HSC .

source_name: Mus musculus Wip1 KO HSC

tag: age

value: Wip1 knock-out


title: GBCs P8 biol. repl. 8

description: Gene expression of P08 GBCs

source_name: GBCs when calyx is in juvenile, close to the onset of hearing

tag: strain

value: globular bushy cells when calyx is in juvenile, close to the onset of hearing


title: untreated rep1

description: T cell donor A


title: GBCs P21 biol. repl. 2

description: Gene expression of P21 GBCs


title: GBCs P8 biol. repl. 1

description: Gene expression of P08 GBCs


title: GBCs P21 biol. repl. 3

description: Gene expression of P21 GBCs


title: anti-TNFalpha rep1

description: T cell donor A


title: untreated rep3

description: T cell donor C


title: GBCs P3 biol. repl.6

description: Gene expression of P03 GBCs

source_name: GBCs just after calyx of Helds formation

value: globular bushy cells just after calyx of Helds formation


title: GBCs P8 biol. repl. 9

description: Gene expression of P08 GBCs


title: GBCs P8 biol. repl. 7

description: Gene expression of P08 GBCs


title: untreated rep2

description: T cell donor B


title: GBCs P8 biol. repl. 4

description: Gene expression of P08 GBCs


title: GBCs P8 biol. repl. 5

description: Gene expression of P08 GBCs


title: anti-TNFalpha rep2

description: T cell donor B


title: GBCs P3 biol. repl.5

description: Gene expression of P03 GBCs


title: GBCs P8 biol. repl. 3

description: Gene expression of P08 GBCs


title: GBCs P3 biol. repl.2

description: Gene expression of P03 GBCs


title: GBCs P8 biol. repl. 2

description: Gene expression of P08 GBCs


title: gp140-specific IgG+ B cells, HIV, H6

city: Bethesda

first: Susan

last: Moir

state: Maryland

address: 9000 Rockville Pike

department: NIAID

institute: NIH

description: gp140-specific IgG+ B cells from individuals with strong pro-resting memory profile

data_processing:
Data were normalized to the housekeeping genes POLRIIA and GAPDH by a comparative delta Ct method. The Ct values from a given sample were converted to delta Ct (dCt) values by subtracting the Cts from the number of PCR cycles (n = 45). To normalize across samples, the mean value of the housekeeping genes POLRIIA and GAPDH was subtracted from the Ct values within each sample.
Differential expression analysis of resting memory B cells versus the other two subsets, namely tissue-like memory B cells and activated memory B cells, was performed using two-sample Wilcoxon test. To correct for multiple testing, false discovery rates (FDR) were estimated using the Benjamini and Hochberg method.
Fold Change worksheet reports Wilcoxon test pvalues by comparing gene expression in 1) resting memory B cells (RM) versus the other two subsets (AM and TLM), and 2) gp140-specific IgG+ B cells from patients with strong pro-resting memory profile versus weak pro-resting memory profile.

label: FAM

source_name: PBMC

label_protocol: cDNA was synthesized, then preamplified with pool of interested genes and analyzed by quantitative real-time PCR (Applied Biosystems 7500 system) using TaqMan Gene Expression Assay.

extract_protocol: Total RNA was extracted with using the RNeasy micro kit with on-column DNA digestion (Qiagen), according to manufacturer specifications.

value: gp140-specific IgG+ B cells

tag: gender

value: Female

tag: ethnicity

value: African American


title: gp140-specific IgG+ B cells, HIV, H3


title: GBCs P21 biol. repl. 5

description: Gene expression of P21 GBCs


title: GBCs P21 biol. repl. 4

description: Gene expression of P21 GBCs


title: gp140-specific IgG+ B cells, HIV, H4


title: GBCs P8 biol. repl. 6

description: Gene expression of P08 GBCs


title: GBCs P3 biol. repl.3

description: Gene expression of P03 GBCs


title: GBCs P3 biol. repl.4

description: Gene expression of P03 GBCs


title: gp140-specific IgG+ B cells, HIV, H1

value: Male


title: gp140-specific IgG+ B cells, HIV, L5

description: gp140-specific IgG+ B cells from individuals with weak pro-resting memory profile


title: gp140-specific IgG+ B cells, HIV, L6


title: gp140-specific IgG+ B cells, HIV, L3

value: Caucasian


title: gp140-specific IgG+ B cells, HIV, L1


title: gp140-specific IgG+ B cells, HIV, L2


title: Resting memory B cells, HIV, S5

description: resting memory B cells

value: resting memory B cells


title: Resting memory B cells, HIV, S2

description: resting memory B cells

value: Caucasian-Hispanic mixed


title: gp140-specific IgG+ B cells, HIV, L4


title: Resting memory B cells, HIV, S4

description: resting memory B cells


title: Resting memory B cells, HIV, S6

description: resting memory B cells


title: Resting memory B cells, HIV, S3

description: resting memory B cells


title: Tissue-like memory B cells, HIV, S6

description: tissue-like memory B cells

value: tissue-like memory B cells


title: Tissue-like memory B cells, HIV, S4

description: tissue-like memory B cells


title: gp140-specific IgG+ B cells, HIV, H2


title: GBCs P3 biol. repl.1

description: Gene expression of P03 GBCs

value: brain

value: Sprague Dawley


title: Tissue-like memory B cells, HIV, S5

description: tissue-like memory B cells


title: Resting memory B cells, HIV, S1

description: resting memory B cells


title: gp140-specific IgG+ B cells, HIV, H5


title: Tissue-like memory B cells, HIV, S1

description: tissue-like memory B cells


title: Tissue-like memory B cells, HIV, S2

description: tissue-like memory B cells


title: Activated memory B cells, HIV, S1

description: activated memory B cells

value: activated memory B cells


title: Activated memory B cells, HIV, S2

description: activated memory B cells


title: Activated memory B cells, HIV, S3

description: activated memory B cells


title: Activated memory B cells, HIV, S6

description: activated memory B cells


title: Activated memory B cells, HIV, S4

description: activated memory B cells


title: Dex 6HR #1

description: 6 hour steroid replicate-1

source_name: Cortical astrocyte culture

value: Brain

value: 6 hour ~100nM dexamethasone


title: VUB02 P351 30

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829020B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 140204-829020B_bottom_cy3_female_fused.txt

hyb_protocol: After ethanol precipitation, samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Agilent dual laser DNA microarray scanner G2566AA was used for scanning the arrays, data was stored as .TIFF files

data_processing: .TIFF files were imported in BlueFuse Multi 3.1.

source_name: hESC culture

label_protocol: Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

extract_protocol: Extraction was done following standard 24sure v3 protocol. In brief, 2.5µl extraction buffer and 5µl extraction cocktail were added per sample, followed by 10min incubation at 75°C and 4min at 95°C.

tag: sample

value: Single hESC

tag: assayed molecule

value: Amplified DNA

source_name: female/male reference

value: reference


title: VUB02 P59 pooled

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130805-829047B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130805-829047B_bottom_cy3_female_fused.txt

value: DNA sample hESC

value: Genomic DNA


title: VUB02 P351 31

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829020B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 140204-829020B_bottom_cy5_female_fused.txt


title: VUB02 P351 29

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829020B_top_cy3_male_fused.txt
sample_vs_female_reference: 140204-829020B_top_cy3_female_fused.txt


title: VUB07 P165BBB7 01

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130528-376009B_top_cy5_male_fused.txt
sample_vs_female_reference: 130528-376009B_top_cy5_female_fused.txt


title: VUB02 P351 pooled

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130805-829047B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130805-829047B_bottom_cy5_female_fused.txt


title: VUB07 P165BBB7 pooled

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130724-829044B_top_cy3_male_fused.txt
sample_vs_female_reference: 130724-829044B_top_cy3_female_fused.txt


title: VUB07 P165BBB7 02

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130607-376007B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130607-376007B_bottom_cy3_female_fused.txt


title: VUB07 P165BBB7 03

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130607-376008B_top_cy3_male_fused.txt
sample_vs_female_reference: 130607-376008B_top_cy3_female_fused.txt


title: VUB02 P351 17

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376004B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130429-376004B_bottom_cy5_female_fused.txt


title: VUB02 P351 22

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829055B_top_cy5_male_fused.txt
sample_vs_female_reference: 140204-829055B_top_cy5_female_fused.txt


title: VUB02 P351 21

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829055B_top_cy3_male_fused.txt
sample_vs_female_reference: 140204-829055B_top_cy3_female_fused.txt


title: VUB02 P351 20

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140132-829162B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 140132-829162B_bottom_cy5_female_fused.txt


title: VUB02 P351 23

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829055B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 140204-829055B_bottom_cy3_female_fused.txt


title: VUB02 P351 19

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829054B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 140204-829054B_bottom_cy5_female_fused.txt


title: VUB02 P351 27

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829019B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 140204-829019B_bottom_cy3_female_fused.txt


title: VUB02 P351 25

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829019B_top_cy3_male_fused.txt
sample_vs_female_reference: 140204-829019B_top_cy3_female_fused.txt


title: VUB02 P351 26

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829019B_top_cy5_male_fused.txt
sample_vs_female_reference: 140204-829019B_top_cy5_female_fused.txt


title: VUB02 P351 28

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829019B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 140204-829019B_bottom_cy5_female_fused.txt


title: VUB02 P351 18

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829054B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 140204-829054B_bottom_cy3_female_fused.txt


title: VUB02 P351 16

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376004B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130429-376004B_bottom_cy3_female_fused.txt


title: VUB02 P351 14

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376004B_top_cy3_male_fused.txt
sample_vs_female_reference: 130429-376004B_top_cy3_female_fused.txt


title: VUB02 P351 12

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376003B_top_cy3_male_fused.txt
sample_vs_female_reference: 130429-376003B_top_cy3_female_fused.txt


title: VUB02 P351 24

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829055B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 140204-829055B_bottom_cy5_female_fused.txt


title: VUB02 P351 13

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376003B_top_cy5_male_fused.txt
sample_vs_female_reference: 130429-376003B_top_cy5_female_fused.txt


title: VUB02 P351 15

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376004B_top_cy5_male_fused.txt
sample_vs_female_reference: 130429-376004B_top_cy5_female_fused.txt


title: VUB02 P351 11

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376082B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130429-376082B_bottom_cy5_female_fused.txt


title: Tissue-like memory B cells, HIV, S3

description: tissue-like memory B cells

value: Female


title: VUB02 P351 10

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376082B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130429-376082B_bottom_cy3_female_fused.txt


title: VUB02 P351 08

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376076B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130426-376076B_bottom_cy5_female_fused.txt


title: VUB02 P351 09

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376076B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130426-376076B_bottom_cy3_female_fused.txt


title: VUB02 P351 06

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376076B_top_cy5_male_fused.txt
sample_vs_female_reference: 130426-376076B_top_cy5_female_fused.txt


title: VUB02 P351 07

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376076B_top_cy3_male_fused.txt
sample_vs_female_reference: 130426-376076B_top_cy3_female_fused.txt


title: VUB02 P351 05.1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376075B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130426-376075B_bottom_cy5_female_fused.txt


title: VUB02 P351 01

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376074B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130426-376074B_bottom_cy5_female_fused.txt


title: VUB02 P351 02

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376074B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130426-376074B_bottom_cy3_female_fused.txt


title: VUB02 P351 04

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376075B_top_cy3_male_fused.txt
sample_vs_female_reference: 130426-376075B_top_cy3_female_fused.txt


title: VUB02 P351 05.2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140132-829161B_top_cy3_male_fused.txt
sample_vs_female_reference: 140132-829161B_top_cy3_female_fused.txt


title: VUB02 P59 28

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829054B_top_cy3_male_fused.txt
sample_vs_female_reference: 140204-829054B_top_cy3_female_fused.txt


title: VUB02 P59 26

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829053B_top_cy3_male_fused.txt
sample_vs_female_reference: 140204-829053B_top_cy3_female_fused.txt


title: VUB02 P59 27

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829053B_top_cy5_male_fused.txt
sample_vs_female_reference: 140204-829053B_top_cy5_female_fused.txt


title: VUB02 P351 03

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130426-376075B_top_cy5_male_fused.txt
sample_vs_female_reference: 130426-376075B_top_cy5_female_fused.txt


title: SNSganglia-F1178L-P18.2.Wt

city: paris

first: Alex

last: Cazes

state: Please select...

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions. Samples were hybridized to Affymetrix MOE430.2 array

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the GCRMA procedure using Brainarray annotations (V.14.0.0, ENTREZG)

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

extract_protocol: RNA was collected from tumors using the miRNeasy kit (Qiagen) according to the manufacturer's instructions.

value: Wt

tag: tissue


title: SNSganglia-F1178L-P18.1.Wt

tag: developmental stage


title: SNSganglia-F1178L-P0.11.Hom

value: homozygous


title: SNSganglia-F1178L-P0.12.Hom


title: SNSganglia-F1178L-P18.5.Het

value: heterozygous


title: VUB02 P59 25

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140213-829022B_top_cy5_male_fused.txt
sample_vs_female_reference: 140213-829022B_top_cy5_female_fused.txt


title: SNSganglia-F1178L-P0.10.Hom


title: VUB02 P59 29

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829054B_top_cy5_male_fused.txt
sample_vs_female_reference: 140204-829054B_top_cy5_female_fused.txt


title: SNSganglia-F1178L-P18.3.Wt


title: SNSganglia-F1178L-P0.9.Hom


title: VUB02 P59 24

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140132-829161B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 140132-829161B_bottom_cy5_female_fused.txt


title: SNSganglia-F1178L-P18.4.Het


title: SNSganglia-F1178L-P0.7.Het


title: SNSganglia-F1178L-P0.8.Het


title: SNSganglia-F1178L-P0.5.Het


title: SNSganglia-F1178L-P0.6.Het


title: SNSganglia-F1178L-P0.4.Wt


title: SNSganglia-F1178L-P0.3.Wt


title: VUB02 P59 22

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829052B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 140204-829052B_bottom_cy5_female_fused.txt


title: VUB02 P59 23

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140132-829161B_top_cy5_male_fused.txt
sample_vs_female_reference: 140132-829161B_top_cy5_female_fused.txt


title: SNSganglia-F1178L-P0.1.Wt


title: SNSganglia-F1178L-P0.2.Wt


title: VUB02 P59 19

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376082B_top_cy3_male_fused.txt
sample_vs_female_reference: 130429-376082B_top_cy3_female_fused.txt


title: VUB02 P59 18

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376081B_bottom_cy5_male_fused.txt
sample_vs_female_reference: 130429-376081B_bottom_cy5_female_fused.txt


title: VUB02 P59 20

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376082B_top_cy5_male_fused.txt
sample_vs_female_reference: 130429-376082B_top_cy5_female_fused.txt


title: VUB02 P59 21

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140204-829052B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 140204-829052B_bottom_cy3_female_fused.txt


title: VUB02 P59 17

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376081B_bottom_cy3_male_fused.txt
sample_vs_female_reference: 130429-376081B_bottom_cy3_female_fused.txt


title: N2 early embryo rep 4

city: Santa Cruz

last: Strome

state: CA

address: 1156 High St.

department: Molecular, Cell, and Developmental Biology

institute: UC Santa Cruz

description: expression profiling in N2 (wild-type) early embryo

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA normalization (Irizarry et al. Nucleic Acids Research 31(4):e15) by NimbleGen software. See www.nimblegen.com.

organism: Caenorhabditis elegans

source_name: N2 (wild-type) early embryo

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Embryos were then frozen in liquid nitrogen.

extract_protocol: RNA was isolated from early embryos using Trizol and purified using the RNeasy kit (Qiagen, catalog 74104). Samples were analyzed on an Agilent Bioanalyzer to ensure that rRNAs were not degraded and that RNA was free of protein and DNA contamination. The samples were treated with DNase for 30min at room temperature.

tag: genotype/variation

value: wild type

value: early embryo


title: VUB02 P59 15.2

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 140218-829024B_top_cy3_male_fused.txt
sample_vs_female_reference: 140218-829024B_top_cy3_female_fused.txt


title: N2 early embryo rep 3


title: N2 early embryo rep 2


title: N2 early embryo rep 1


title: VUB02 P59 15.1

description:
Sample assayed against both female and male references ('combined' file represents combined result of both tests)
sample_vs_male_reference: 130429-376081B_top_cy3_male_fused.txt
sample_vs_female_reference: 130429-376081B_top_cy3_female_fused.txt