title: Dazl-GFP+ JuvTestis_rep1

city: Boston

first: Niels

last: Geijsen

state: MA

address: 185 Cambridge St. CPZN 4-4256

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

hyb_protocol: Hybridization was done following the Agilent protocols in Agilent hybridization chambers and incubator.

scan_protocol: Slides were scanned in an Agilent scanner following the manufacturer's protocols.

data_processing:
The data were analyzed with GeneSifter online tools. The background-subtracted signals were uploaded into GeneSifter and normalized to median value.
The data in the Sample tables are from the original files prior to median normalization. The GeneSifter processed data is linked to the Series record as a supplementary file.

source_name: in vivo PGCs, P7-P11 juvenile mouse testes, FACS sorted GFP+

label_protocol: RNA was labeled and amplified following Agilent One-Color protocols.

growth_protocol: Stella-GFP and Dazl-GFP ES cells were grown in standard Lif medium with feeder MEFs. For in vitro differentiation, ES cells were trypsinized and depleted of the feeder cells by incubation on tissue culture plastic. The cells were replated on gelatin-coated plates and fed with Differentiation Medium for 7-16 days before harvest. The differentiated cells were dissociated with trypsin and collagenase IV and FACS sorted for the GFP+ population. The in vivo germ cells were dissociated from the gonads by enzymatic treatment and FACS sorted before RNA extraction.

extract_protocol: Total RNA were extracted with TRIZOL.

value: C57BL/6 129SV mixed

value: male

value: testes

value: in vivo Dazl-GFP+ germ cells


title: Dazl-GFP+ JuvTestis_rep2

status: Public on Dec 31 2013

type: RNA

country: USA

molecule: total RNA

organism: Mus musculus

tag: strain

tag: gender

tag: developmental stage

tag: tissue

tag: cell type


title: Strain SCC2302 replicate 2

type: genomic

city: Seattle

first: Weerayuth

last: Kittichotirat

state: WA - Washington

address: 960 Republican st

department: Microbiology

institute: University of Washington

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain SCC2302

hyb_protocol: 40µl hybridization sample mixture was loaded onto the glass slide and incubated at 65°C for 24 hours with rotation. The arrays were then washed with Agilent CGH wash buffer.

scan_protocol: Arrays were scanned using an Agilent scanner 6000C with the manufacturer’s recommended settings for aCGH arrays (scan area 61 x 21.6mm, 5um resolution, 100% PMT R&G). Data was extracted from the scanner using Agilent Feature Extractor v10.5 software using protocol CGH_105_Dec08.

data_processing: The signal data obtained from the Agilent Feature Extraction Software were processed using the following steps. First the gProcessedSignal value, which is a background subtracted signal, for each probe was extracted. Since the labeling process involved incorporating Cyanine 3-dUTP into the genomic sample, it is possible that probes that are rich in nucleotide A have higher signal relative to probes with lower A content and may not accurately reflect the true abundant of the target sequence. For this reason, the signal values were normalized by dividing them with the total number of A nucleotides in the probe sequence. This value was then transformed using log2. After that, Quantile normalization was applied across all the array data being compared to adjust for differences in the probe intensity distribution using limma package. Finally, the normalized signal values from probes that are targeting the same gene cluster were consolidated into a single value by averaging the signals.

molecule: genomic DNA

organism: Aggregatibacter actinomycetemcomitans

source_name: Strain SCC2302 replicate 2

label_protocol: 0.5µg of genomic DNA was labeled with cyanine3. DNA denaturation and fragmentation was done using a thermocycler by mixing 2.5µl of Random Primers (Agilent) and 13µl of genomic DNA at 94°C for 10 minutes. The mixture was cooled to 4°C degree and 9.5µl of labeling master mix (Agilent) was added to make a total volume of 25µl. DNA labeling was done using a thermocycler following the steps: 37°C for 2 hours, 65°C for 10 minutes, and hold at for 4°C. Labeled genomic DNA was purified using individual Amicon 30kDA filters (Millipore) following manufacturer’s protocol. The yield of labeled DNA was determined by measuring the absorbance at A260nm (DNA) and A550nm (cyanine 3) using Nano-Drop (ND-1000).

growth_protocol: A. actinomycetemcomitans was grown on tryptic soy agar plate with 0.6% yeast extract for two days at 37°C in atmosphere supplemented with 5% CO2, and harvested by washing the bacteria off the plates with PBS buffer.

extract_protocol: Genomic DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA 91355 USA) according the manufacturer’s manual.

tag: serotype

value: c


title: Strain AAS4A replicate 1

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain AAS4A

source_name: Strain AAS4A replicate 1


title: E.albidus_Zn_EC90_rep1

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

description: E.albidus gene expression after exposure to zinc reproduction EC90

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit . 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-030589 Custom Gene Expression Array for Enchytraeus albidus 8x15k, for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm).

data_processing: Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies) using default parameters (protocol GE1_105_Dec08 and Grid: 030589_D_F_20101007) to obtain background subtracted and spatially detrended Processed Signal intensities. Processing of the data and statistical analysis were performed using BRB Array Tools version 4.2.1 Stable Release (http://linus.nci.nih.gov/BRB-ArrayTools.html). After background subtraction, the replicated spots within each array were averaged and the intensities were log2 transformed (spots with a value of intensity bellow 1 were excluded from the analysis).

organism: Enchytraeus albidus

source_name: Enchytraeus albidus, zinc EC90, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Isolation of total RNA from each replicate was performed through the Trizol extraction method (Invitrogen, Belgium). This RNA followed a DNAse treatment (Fermentas, Germany) and further purification steps consisting of phenol/chloroform extractions. The quantity and purity of the isolated RNA were measured spectrophotometrically with nanodrop (NanoDrop ND-1000 Spectrophotometer) and its integrity was checked on a denaturing formaldehyde agarose gel electrophoresis.

treatment_protocol: Ten adult worms with well developed clitellum were introduced in the test vessels, each containing 25 g moist soil (control or spiked soil with Cu, Ni, Cd or Zn). The worms were exposed for 4 days at 20ºC and a 16:8h photoperiod. Three biological replicates per exposure condition and 6 biologcal replicates of control conditions were used. At test end, animals of each replicate were carefully removed, rinsed in deionised water, stored in RNA later (Ambion, USA) containing criotubes and frozen in liquid Nitrogen. All the samples were stored at -80ºC till further analysis.

value: Whole body extracts

value: Adult organisms with well developed clitellum

tag: treatment

value: exposure to zinc at EC90 concentration


title: E.albidus_Ni_EC50_rep3

description: E.albidus gene expression after exposure to nickel reproduction EC50

source_name: Enchytraeus albidus, nickel EC50, replicate 3

value: exposure to nickel at EC50 concentration


title: SHH_2_to_18 biological rep 2_of_3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from day 18 of differentiation from FACS sorted NKX2.1::GFP+ cells

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

label: biotin

organism: Homo sapiens

source_name: treated with Sonic hedgehog (SHH) from differentiation day 2 to 18

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

value: human pluripotent stem cells


title: Dazl-GFP+ E13.5_rep2

source_name: in vivo PGCs, E13.5 embryonic gonads, FACS sorted GFP+

value: embryonic gonads


title: 129S2 naiv vs. 129S2 d14 Mtb

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: total lung RNA, color-swap array polarity +

hyb_protocol: After precipitation, purification and quantification the labeled samples were mixed and hybridized according to the supplier’s protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies)

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies)

source_name: 129S2 day 14 naive

label_protocol: Total RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: Mice were 8-12 weeks of age at the beginning of the experiments and were bred and kept under specific pathogen-free (SPF) conditions at the Max Planck Institute for Infection Biology in Berlin, Germany. To enumerate bacterial burdens, lung tissue was dispersed in water 1% w/v BSA/1% v/v Tween 80 (WTA) and plated on Middlebrook 7H11 agar plates supplemented with ampicillin (10 µg/ml).

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier

treatment_protocol: Low dose M.tuberculosis H37Rv infection was delivered via aerosol using a Glas-Col inhalation exposure system.

value: lung

value: naive

tag: genotype

value: wildtype

source_name: 129S2 day14 M.tuberculosis infected


title: SHH_2_to_18 biological rep 1_of_3


title: E.albidus_Ni_EC50_rep2

source_name: Enchytraeus albidus, nickel EC50, replicate 2


title: Dazl-GFP+ E13.5_rep1


title: E.albidus_Ni_EC90_rep1

description: E.albidus gene expression after exposure to nickel reproduction EC90

source_name: Enchytraeus albidus, nickel EC90, replicate 1

value: exposure to nickel at EC90 concentration


title: Strain SCC4092 replicate 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain SCC4092

source_name: Strain SCC4092 replicate 2

value: b


title: Strain SCC2302 replicate 1

source_name: Strain SCC2302 replicate 1


title: Dazl-GFP+ Day16_rep2

source_name: in vitro PGCs, Dazl-GFP ES cells, day 16 differentiation, FACS sorted GFP+

value: in vitro primordial germ cells generated from differentiated Dazl-GFP ES cells, GFP+

tag: days of differentiation


title: E.albidus_Ni_EC50_rep1

source_name: Enchytraeus albidus, nickel EC50, replicate 1


title: E.albidus_Cu_EC90_rep3

description: E.albidus gene expression after exposure to copper reproduction EC90

source_name: Enchytraeus albidus, copper EC90, replicate 3

value: exposure to copper at EC90 concentration


title: PBMC Latent EBV Subj 5524 (HT12)

city: Minneapolis

first: Samantha

last: Dunmire

state: MN

address: 2101 6th St SE

institute: University of Minnesota

hyb_protocol: Illumina recommended hybridization protocol

scan_protocol: Illumina recommended scanning protocol

data_processing: The data were analyzed with GeneSpring GX11

label: Biotin

source_name: Peripheral blood

label_protocol: Microarray probes were produced with the Illumina TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: RNA was extracted using RNeasy Mini columns (Qiagen)

treatment_protocol: None.  Blood was collected from volunteers in EDTA tubes.  PBMC were isolated and frozen prior to RNA extraction.

tag: sample time

value: following resolution of infectious mononucelosis


title: Strain SCC4092 replicate 1

source_name: Strain SCC4092 replicate 1


title: PBMC Seronegative Subj 5524 (HT12)

value: before EBV acquisition


title: E.albidus_Cu_EC90_rep2

source_name: Enchytraeus albidus, copper EC90, replicate 2


title: Dazl-GFP+ Day12_rep1

source_name: in vitro PGCs, Dazl-GFP ES cells, day 12 differentiation, FACS sorted GFP+

value: C57BL/6 129SV mixed

value: male


title: E.albidus_Cu_EC90_rep1

source_name: Enchytraeus albidus, copper EC90, replicate 1

value: Whole body extracts


title: PBMC Latent EBV Subj 5483 (HT12)


title: PBMC Seronegative Subj 5483 (HT12)


title: Dazl-GFP+ Day16_rep1


title: PBMC Seronegative Subj 5509 (HT12)


title: PBMC Latent EBV Subj 5509 (HT12)


title: Dazl-GFP+ Day12_rep2


title: Strain SCC1398 replicate 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain SCC1398

source_name: Strain SCC1398 replicate 2


title: Strain A160 replicate 1

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain A160

source_name: Strain A160 replicate 1

value: c


title: E.albidus_Cu_EC50_rep2

description: E.albidus gene expression after exposure to copper reproduction EC50

source_name: Enchytraeus albidus, copper EC50, replicate 2

value: Adult organisms with well developed clitellum

value: exposure to copper at EC50 concentration


title: Strain SCC1398 replicate 1

source_name: Strain SCC1398 replicate 1


title: Dazl-GFP ES GFP pos_rep1

source_name: Dazl-GFP ES cells, undifferentiated, FACS sorted GFP+

value: undifferentiated Dazl-GFP ES cells, GFP+


title: E.albidus_Cu_EC50_rep1

source_name: Enchytraeus albidus, copper EC50, replicate 1


title: Stella-GFP+ Day7_rep2

description:
StellaD7_2
The Stella-GFP BAC ES cell line is described in Payer et al., Genesis. 2006 Feb;44(2):75-83 (PMID 16437550).

source_name: in vitro PGCs, Stella-GFP ES cells, day 7 differentiation, FACS sorted GFP+

value: in vitro primordial germ cells generated from differentiated Stella-GFP ES cells, GFP+


title: Stella-GFP+ Day7_rep1

description:
StellaD7_1
The Stella-GFP BAC ES cell line is described in Payer et al., Genesis. 2006 Feb;44(2):75-83 (PMID 16437550).


title: E.albidus_Control_rep6

description: E.albidus gene expression under control conditions

source_name: Enchytraeus albidus, control, replicate 6


title: E.albidus_Cu_EC50_rep3

source_name: Enchytraeus albidus, copper EC50, replicate 3


title: Strain SCC393 replicate 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain SCC393

source_name: Strain SCC393 replicate 2


title: PBMC Latent EBV Subj 5370 (HT12)


title: PBMC Seronegative Subj 5370 (HT12)


title: Strain SCC393 replicate 1

source_name: Strain SCC393 replicate 1


title: Strain A160 replicate 2

source_name: Strain A160 replicate 2


title: PBMC Latent EBV Subj 5342 2 (HT12)

source_name: Peripheral blood


title: E.albidus_Control_rep5

source_name: Enchytraeus albidus, control, replicate 5


title: Dazl-GFP ES GFP pos_rep2


title: PBMC Latent EBV Subj 5342 1 (HT12)


title: PBMC Seronegative Subj 5342 (HT12)


title: Dazl-GFP ES GFP neg_rep2

source_name: Dazl-GFP ES cells, undifferentiated, FACS sorted GFP-

value: undifferentiated Dazl-GFP ES cells, GFP-


title: E.albidus_Control_rep4

source_name: Enchytraeus albidus, control, replicate 4


title: E.albidus_Control_rep3

source_name: Enchytraeus albidus, control, replicate 3


title: Stella-GFP ES GFP pos_rep2

description:
StellaESP_2
The Stella-GFP BAC ES cell line is described in Payer et al., Genesis. 2006 Feb;44(2):75-83 (PMID 16437550).

source_name: Stella-GFP ES cells, undifferentiated, FACS sorted GFP+

value: undifferentiated Stella-GFP ES cells, GFP+


title: PBMC Acute IM Subj 5342 (HT12)

value: during infectious mononucleosis


title: Dazl-GFP ES GFP neg_rep1


title: Stella-GFP ES GFP pos_rep1

description:
StellaESP_1
The Stella-GFP BAC ES cell line is described in Payer et al., Genesis. 2006 Feb;44(2):75-83 (PMID 16437550).


title: Stella-GFP ES GFP neg_rep2

description:
StellaESM_2
The Stella-GFP BAC ES cell line is described in Payer et al., Genesis. 2006 Feb;44(2):75-83 (PMID 16437550).

source_name: Stella-GFP ES cells, undifferentiated, FACS sorted GFP-

value: undifferentiated Stella-GFP ES cells, GFP-


title: Rat_liver_LE_100_TCDD_240_hours_rep_5 [NanoString]

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

description: Treated

data_processing: Raw NanoString data (absolute molecule counts) were loaded into the R statistical environment (v2.12.2). Data was normalized for hybridization efficiency using the positive, spike-in controls, negative controls and reference genes Eef1a1, Gapdh, Hprt1, Ppia and Sdha and log2 transformed. Fold-changes calculated using the mean of the biological replicates (Treated - Control).

label: FAM

organism: Rattus norvegicus

source_name: liver, Long-Evans, 100 TCDD, 240 hour exposure

growth_protocol: Animals were housed in suspended, stainless-steel wire-mesh cages in groups of 4 rats with a 12h/12h light/dark cycle and with pelleted R36 feed and tap water. The temperature was maintained at  21 +/- 1 degree Celcius with relative humidity 50% +/- 10%.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). RNA was quantified using a NanoDrop UV spectrophotometer (Thermo Scientific, Mississauga, ON) and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were treated with either TCDD or corn oil vehicle alone by oral gavage.

value: Male

value: Liver

value: Long-Evans

tag: age

value: 10-12 weeks

value: 100 ug/kg

tag: exposure

value: 240 hours


title: E.albidus_Control_rep2

source_name: Enchytraeus albidus, control, replicate 2


title: Stella-GFP ES GFP neg_rep1

description:
StellaESM_1
The Stella-GFP BAC ES cell line is described in Payer et al., Genesis. 2006 Feb;44(2):75-83 (PMID 16437550).

value: C57BL/6 129SV mixed

value: male


title: JuvTestis_GFPIP_rep2

description:
GFPt_2
RNA-IP

source_name: P14 mouse testis, anti-GFP IP

extract_protocol: Testes were dissociated and lysed and subjected to RNA-IP following standard protocols without UV-crosslinking. Total RNA in the IP was  extracted with TRIZOL reagent.

value: testes

value: juvenile testicular germ cells expressing Dazl-GFP-V5

tag: ip antibody

value: anti-GFP

tag: antibody vendor

value: Abcam

tag: antibody catalog number

tag: antibody lot#


title: Rat_liver_LE_100_TCDD_240_hours_rep_4 [NanoString]

description: Treated


title: PBMC Latent EBV Subj 5324 (HT12)

value: following resolution of infectious mononucelosis


title: Rat_liver_LE_100_TCDD_240_hours_rep_3 [NanoString]

description: Treated


title: E.albidus_Control_rep1

source_name: Enchytraeus albidus, control, replicate 1

value: Whole body extracts

value: Adult organisms with well developed clitellum


title: PBMC Seronegative Subj 5139 (HT12)

value: before EBV acquisition


title: PBMC Latent EBV Subj 5139 1 (HT12)


title: PBMC Latent EBV Subj 5139 2 (HT12)


title: JuvTestis_V5IP_rep2

description:
V5t_2
RNA-IP

source_name: P14 mouse testis, anti-V5 IP

value: Invitrogen


title: Rat_liver_LE_100_TCDD_240_hours_rep_2 [NanoString]

description: Treated

value: Male


title: PBMC Seronegative Subj 5324 (HT12)


title: JuvTestis_V5IP_rep1

description:
V5t_1
Total RNA


title: JuvTestis_GFPIP_rep1

description:
GFPt_1
RNA-IP


title: PBMC Latent EBV Subj 5036 (HT12)


title: JuvTestis_IgGIP_rep2

description:
IgGt_2
RNA-IP

source_name: P14 mouse testis, IgG mock IP

value: normal mouse IgG

value: Santa Cruz


title: PBMC Seronegative Subj 5088 (HT12)


title: PBMC Latent EBV Subj 5088 (HT12)


title: Rat_liver_LE_100_TCDD_240_hours_rep_1 [NanoString]

description: Treated

value: Liver

value: Long-Evans

value: 10-12 weeks


title: H4ac Calu-3 untreated

city: Umeå

first: Joscha

last: Muck

address: Analysvägen 1

department: UCMM

country: Sweden

institute: Umeå University

description:
Raw data files (sectors) used for log2 ratio determination (acetylated histone / histone H3pan):
Calu_H3pan_635_HeLa_H4ac_control_532_REP_3.gpr (H3pan-Cy5 ch only)
Calu_H3pan_635_HeLa_H4ac_control_532_REP_4.gpr (H3pan-Cy5 ch only)
Calu_H4ac_635_HeLa_H4ac_TSA_532_REP_3.gpr (H4ac-Cy5 ch only)
Calu_H4ac_635_HeLa_H4ac_TSA_532_REP_4.gpr (H4ac-Cy5 ch only)
pairwise comparison;  both scans REP_3 (REP_4) from sectors on the same Chip

hyb_protocol: Hybridization was performed according to the manufacturer’s instructions using the Stabilization and Drying kit (Agilent Technologies).

scan_protocol: DNA  microarrays were scanned with an Axon Genepix 4200AL Scanner (Molecular Devices, Sunnyvale, CA, USA) using the software Genepix Pro 6.0.

data_processing: Signals with signal to noise less than 3 were omitted. Maxima of the histograms of log2 enrichments were set to zero, and the standard deviation adjusted for replicates. After transformation the log2 enrichments of the replicates were averaged.

source_name: Histone H3pan ChIP

label_protocol: For labeling the Label IT  μArray Labeling Kit Cy3/Cy5 Mirus Bio LLC, Madison, WI, USA) was applied.

growth_protocol: DMEM + 10% FBS

extract_protocol: For histone X-ChIP the Abcam protocol (http://www.abcam.com/index.html?pageconfig=resource&rid=11698) was applied with the following modifications: cross-linking was performed with 1.7% formaldehyde for 6 minutes. Cells were lysed in RIPA buffer (150 mM NaCl, 0.25% deoxycholate, 1% triton X-100, 50 mM Tris-HCl, pH 8.0) with 2 mM EDTA and freshly added protease inhibitor set (complete mini, Roche, Basel, Switzerland). Chromatin was sonicated with a HTU Soni 130 ultrasonic homogenizer (G. Heinemann, Schwabisch Gmund, Germany). Gel electrophoresis and densitometric analysis revealed that ~60% of the fragments had a length of ~200 bp (~80% < 1000 bp). To reverse cross-links protein A/G Dynabeads (Invitrogen) were resuspended in 100  μl PBS with 10  μl 5 M NaCl-solution and incubated for 6 hours (or overnight) at 65°C. DNA was purified using the Quiaquick PCR Purification kit (Quiagen, Hilden, Germany). Amplification of the ChIP-DNA was performed with the GenomePlex Complete WGA Kit (WGA2) according to the manufacturer’s instructions (Sigma-Aldrich).

treatment_protocol: untreated

tag: antibody

tag: cell line

source_name: Histone H4ac ChIP

value: H4ac (Vendor:Millipore, Cat.#:06-866, lot # 31992)


title: H3ac Calu-3 untreated

description:
Raw data files (sectors) used for log2 ratio determination (acetylated histone / histone H3pan):
Calu_H3pan_635_HeLa_H4ac_control_532_REP_2.gpr (H3pan-Cy5 ch only)
Calu_H3ac_635_HeLa_H4ac_TSA_532_REP_2.gpr (H4ac-Cy5 ch only)
both scans from sectors on the same Chip

source_name: Histone H3ac ChIP

value: H3ac (Vendor:Millipore, Cat.#:06-599, lot# DAM1588236)


title: Rat_liver_LE_Corn_oil_240_hours_rep_11 [NanoString]

description: Control

source_name: liver, Long-Evans, Corn oil treated, 240 hour exposure

tag: gender

tag: strain

value: Corn Oil vehicle

value: 240 hours


title: Rat_liver_LE_Corn_oil_240_hours_rep_10 [NanoString]

description: Control

tag: tissue


title: JuvTestis_TotalRNA_rep2

description:
Testis_2
RNA-IP

source_name: P14 mouse testis, total RNA input

value: C57BL/6 129SV mixed

value: male

tag: developmental stage

value: testes

tag: cell type

value: juvenile testicular germ cells expressing Dazl-GFP-V5


title: H4ac HeLa TSA-treated

description:
Raw data files (sectors) used for log2 ratio determination (acetylated histone / histone H3pan):
HeLa_H3ac_635_H3pan_532_TSA_REP_2.gpr (H3pan-Cy3 ch only)
HeLa_H3ac_635_H3pan_532_TSA_REP_3.gpr (H3pan-Cy3 ch only)
HeLa_H3ac_635_H3pan_532_TSA_REP_4.gpr (H3pan-Cy3 ch only)
Calu_H3ac_635_HeLa_H4ac_TSA_532_REP_2.gpr (H4ac-Cy3 ch only)
Calu_H4ac_635_HeLa_H4ac_TSA_532_REP_3.gpr (H4ac-Cy3 ch only)
Calu_H4ac_635_HeLa_H4ac_TSA_532_REP_4.gpr (H4ac-Cy3 ch only)
pairwise comparison; both REP_2 (REP_3, REP_4) scans from sectors on the same Chip

treatment_protocol: TSA treatment (20min)

value: HeLa S3


title: Rat_liver_LE_Corn_oil_240_hours_rep_9 [NanoString]

description: Control

tag: treatment


title: JuvTestis_IgGIP_rep1

description:
IgGt_1
RNA-IP


title: PBMC Latent EBV Subj 5027 (HT12)

source_name: Peripheral blood

value: following resolution of infectious mononucelosis


title: PBMC Acute IM Subj 5036 (HT12)

value: during infectious mononucleosis


title: H3ac HeLa TSA-treated

description:
Raw data files used for log2 ratio determination (acetylated histone / histone H3pan):
HeLa_H3ac_532_H3pan_635_TSA_REP_1.gpr
HeLa_H3ac_635_H3pan_532_TSA_REP_2.gpr (dyeswap)
HeLa_H3ac_635_H3pan_532_TSA_REP_3.gpr (dyeswap)
HeLa_H3ac_635_H3pan_532_TSA_REP_4.gpr (dyeswap)
Dye swap in REP_2, REP_3 and REP_4


title: HDF_SAHA_rep1

city: Kyoto

first: Junichi

last: Taniguchi

address: Kitashirakawa-Oiwakecho, Sakyo-Ku

department: Department of Chemistry, Graduate School of Science

country: Japan

institute: Kyoto University

description: SAHA-treated HDFs.

hyb_protocol: 600ng of labelled cRNA was fragmented at 60°C for 30 minutes using 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44 v2 (G4845A) 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 at 37°C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.10.1.1).

data_processing: Agilent Feature Extraction Software (version 10.10.1.1) was used for background subtraction and normalization.

source_name: Human Dermal Fibroblasts, SAHA

label_protocol: Cy3- and Cy5-labelled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp labeling kit, two-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 39-year-old female Caucasian HDFs were maintained in Dulbecco's modified eagle medium (DMEM, Life Technologies) containing 10% fetal bovine serum (FBS, Japan Serum).

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a Nanodrop ND1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HDFs within the passage P6 were trypsinized for 5 min at 37 °C, and were resuspended in the fresh medium to a concentration of 1.5 x 10^5 cells/2ml in a 35 mm plate and were grown for 24 hours. The medium was then removed and replaced with 2 ml of fresh medium supplimented with DMSO solusion of SAHA, SAHA-PIP9 (final concentration: 1 μM). The cultures were incubated for 48 hours.

tag: cell source

value: human dermal fibroblasts derived from normal human abdominal skin

value: female

source_name: Human Dermal Fibroblasts, DMSO


title: Rat_liver_LE_Corn_oil_240_hours_rep_8 [NanoString]

description: Control

value: Male


title: H3ac HeLa untreated

description:
Raw data files used for log2 ratio determination (acetylated histone / histone H3pan):
HeLa_H3ac_532_H3pan_635_control_REP_1.gpr
HeLa_H3ac_635_H3pan_532_control_REP_2.gpr (dyeswap)
HeLa_H3ac_635_H3pan_532_control_REP_3.gpr (dyeswap)
HeLa_H3ac_635_H3pan_532_control_REP_4.gpr (dyeswap)
Dye swap in REP_2, REP_3 and REP_4


title: H4ac HeLa untreated

description:
Raw data files (sectors) used for log2 ratio determination (acetylated histone / histone H3pan):
HeLa_H3ac_635_H3pan_532_control_REP_2.gpr (H3pan-Cy3 ch only)
HeLa_H3ac_635_H3pan_532_control_REP_3.gpr (H3pan-Cy3 ch only)
HeLa_H3ac_635_H3pan_532_control_REP_4.gpr (H3pan-Cy3 ch only)
Calu_H3pan_635_HeLa_H4ac_control_532_REP_2.gpr (H4ac-Cy3 ch only)
Calu_H3pan_635_HeLa_H4ac_control_532_REP_3.gpr (H4ac-Cy3 ch only)
Calu_H3pan_635_HeLa_H4ac_control_532_REP_4.gpr (H4ac-Cy3 ch only)
pairwise comparison; both REP_2 (REP_3, REP_4) scans from sectors on the same Chip


title: GFP_Native_IP_2

description:
GFP_2
RNA-IP
The ES cells were derived from the V6.5 cell line.

source_name: in vitro PGCs, anti-GFP RNA-IP

growth_protocol: Dazl-GFP ES cells were trypsinized and depleted of the feeder cells by incubation on tissue culture plastic. The cells were replated on gelatin-coated plates and fed with Differentiation Medium for 12 days before harvest.

extract_protocol: Cells were lysed and subjected to RNA-IP following standard protocols without UV-crosslinking. Total RNA in the IP was extracted with TRIZOL reagent.

value: primordial germ cells (PGCs) generated from differentiated Dazl-GFP-V5 ES cells

value: anti-GFP

value: Abcam


title: V5_Native_IP_2

description:
V5_2
RNA-IP
The ES cells were derived from the V6.5 cell line.

source_name: in vitro PGCs, anti-V5 RNA-IP

value: Invitrogen


title: PBMC Acute IM Subj 5027 (HT12)


title: PBMC Seronegative Subj 5027 (HT12)

value: before EBV acquisition


title: JuvTestis_TotalRNA_rep1

description:
Testis_1
Total RNA


title: HDF_SAHA-PIP9_rep1

description: SAHA-PIP9 (SAHA-PIP I)-treated HDFs.

source_name: Human Dermal Fibroblasts, SAHA-PIP9(SAHA-PIP I)


title: TGFb_24h_matrigel_Normal lung fibroblasts_rep3

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description:
SAM4955476
Normal lung fibroblasts treated with TGFb at 24h

hyb_protocol: cRNA was hybridized on Agilent-026652 Whole Human Genome Microarray 4x44K v2.

scan_protocol: Chips were scanned using the Agilent Surescan Microarray Scanner.

data_processing: The data were processed with Agilent Feature Extraction software, version 10.7.3.1, using default settings, including linear and Lowess normalization.

source_name: Normal lung fibroblasts, TGFb, 24h

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

growth_protocol: Normal lung fibroblasts from three different donors were plated and maintained in 10% serum-containing DME for 16h. Monocytes were isolated from whole blood of 5 different donors using the Monocyte Isolation Kit II (Miltenyi # 130-091-153). Purified monocytes were seeded in TC-treated 10 cm plates at the density of 1.5x10^5 cells /cm2 in 15 ml of RPMI medium supplemented with 20% Fetal Calf Serum, 100 ng/ml M-CSF, Pen/strep, and glutamine. Monocytes were differentiated into macrophages for 6 days. After 6 days, the MDMs were rested in media without M-CSF for 24h. Cells were plated on a bed of growth factor reduced Matrigel (GFR Matrigel, BD Biosciences, Bedford, MA; Catalog No. 354230). Matrigel was thawed overnight on ice and a bed volume of 450 μl/well in a 12-well plate was produced by allowing matrigel to harden at 37°C for 30'. Cells (1-2 x 10^5) were then plated onto the Matrigel bed.

extract_protocol: RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells were treated for 6 or 24 hours with IL-4 (10 ng/ml), IL-13 (10ng/ml), IL-10 (20 ng/ml), TGFb (10 ng/ml), TNFa (10 ng/ml), or dexamethasone (0.5 uM).

value: normal primary lung fibroblasts

value: TGFb

tag: timepoint

extract_protocol: Stratagene Universal Human Reference RNA (catalog number 740000).

tag: sample type

value: reference


title: Normal-4

city: seoul

first: minhee

last: park

address: shinchondong

country: South Korea

institute: student

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization method with beadarray version 1.10 and lumi version 1.8.3 in R/Bioconductor package.

source_name: non-neoplastic pancreas

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

extract_protocol: Total RNA was obtained from each independent tissue of patient and extracted using TRIzol Reagent (Invitrogen). RNA quality control was performed with Bio-Rad Experion.

value: non-neoplastic pancreas


title: Normal-5

description: Total RNA was obtained from each independent tissue of patient


title: Rat_liver_LE_Corn_oil_240_hours_rep_7 [NanoString]

description: Control

value: Liver

value: Long-Evans

tag: age

value: 10-12 weeks

value: Corn Oil vehicle

value: 240 hours


title: Mock_IP_2

description:
IgG_2
RNA-IP
The ES cells were derived from the V6.5 cell line.

source_name: in vitro PGCs, IgG mock IP

value: C57BL/6 129SV mixed

value: normal mouse IgG

value: Santa Cruz


title: Rat_liver_LE_100_TCDD_96_hours_rep_3 [NanoString]

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 96 hour exposure

value: Male

value: 100 ug/kg

tag: exposure

value: 96 hours


title: Rat_liver_LE_100_TCDD_96_hours_rep_4 [NanoString]

description: Treated


title: IL13_24h_matrigel_Normal lung fibroblasts_rep3

description:
SAM4955475
Normal lung fibroblasts treated with IL13 at 24h

source_name: Normal lung fibroblasts, IL13, 24h

source_name: Stratagene Universal Human Reference RNA


title: Rat_liver_LE_100_TCDD_96_hours_rep_2 [NanoString]

description: Treated


title: IL4_24h_matrigel_Normal lung fibroblasts_rep3

description:
SAM4955474
Normal lung fibroblasts treated with IL4 at 24h

source_name: Normal lung fibroblasts, IL4, 24h


title: Total_Input_RNA_2

description:
Total_2
Total RNA
The ES cells were derived from the V6.5 cell line.

source_name: in vitro PGCs, total RNA input

value: primordial germ cells (PGCs) generated from differentiated Dazl-GFP-V5 ES cells

tag: ip antibody


title: Normal-3


title: Normal-2


title: V5_Native_IP_1

description:
V5_1
RNA-IP
The ES cells were derived from the V6.5 cell line.

tag: antibody vendor

value: Invitrogen


title: GFP_Native_IP_1

description:
GFP_1
RNA-IP
The ES cells were derived from the V6.5 cell line.

value: anti-GFP

value: Abcam

tag: antibody catalog number


title: TGFb_24h_matrigel_Normal lung fibroblasts_rep2

description:
SAM4955472
Normal lung fibroblasts treated with TGFb at 24h

value: normal primary lung fibroblasts

value: TGFb

value: reference


title: Rat_liver_LE_100_TCDD_96_hours_rep_1 [NanoString]

description: Treated

value: Liver

value: Long-Evans


title: Normal-1

value: non-neoplastic pancreas


title: unstim_24h_matrigel_Normal lung fibroblasts_rep3

description:
SAM4955473
Normal lung fibroblasts treated with unstim at 24h

source_name: Normal lung fibroblasts, unstimulated, 24h

value: unstimulated


title: Total_Input_RNA_1

description:
Total_1
Total RNA
The ES cells were derived from the V6.5 cell line.

value: C57BL/6 129SV mixed


title: Rat_liver_LE_Corn_oil_96_hours_rep_8 [NanoString]

description: Control

source_name: liver, Long-Evans, Corn oil treated, 96 hour exposure

value: 10-12 weeks

value: Corn Oil vehicle


title: Rat_liver_LE_Corn_oil_96_hours_rep_9 [NanoString]

description: Control

value: Male


title: Mock_IP_1

description:
IgG_1
RNA-IP
The ES cells were derived from the V6.5 cell line.

value: normal mouse IgG

value: Santa Cruz

tag: antibody lot#


title: NET-5

source_name: neuroendocrine tumor

value: male

value: neuroendocrine tumor (NET)


title: NET-6


title: NET-4

value: female


title: IL4_24h_matrigel_Normal lung fibroblasts_rep2

description:
SAM4955470
Normal lung fibroblasts treated with IL4 at 24h


title: Rat_liver_LE_Corn_oil_96_hours_rep_6 [NanoString]

description: Control

value: 96 hours


title: TGFb_24h_matrigel_Normal lung fibroblasts_rep1

description:
SAM4955468
Normal lung fibroblasts treated with TGFb at 24h

value: normal primary lung fibroblasts


title: IL13_24h_matrigel_Normal lung fibroblasts_rep2

description:
SAM4955471
Normal lung fibroblasts treated with IL13 at 24h


title: Rat_liver_LE_Corn_oil_96_hours_rep_5 [NanoString]

description: Control


title: Rat_liver_LE_1000_TCDD_19_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Long-Evans, 1000 TCDD, 19 hour exposure

value: 19 hours


title: IL13_24h_matrigel_Normal lung fibroblasts_rep1

description:
SAM4955467
Normal lung fibroblasts treated with IL13 at 24h

value: reference


title: unstim_24h_matrigel_Normal lung fibroblasts_rep2

description:
SAM4955469
Normal lung fibroblasts treated with unstim at 24h


title: NET-3


title: PABP1_IP_2

description:
UVPABP1_2
RNA-IP
The ES cells were derived from the V6.5 cell line.

source_name: in vitro PGCs, anti-PABP1 IP control

extract_protocol: Cells were lysed and subjected to RNA-IP following standard protocols with UV-crosslinking. Total RNA in the IP was proteinase K treated and then extracted with TRIZOL reagent.

value: primordial germ cells (PGCs) generated from differentiated Dazl-GFP-V5 ES cells

value: Abcam


title: Rat_liver_LE_1000_TCDD_19_hours_rep_2 [NanoString]

description: Treated

value: Liver

value: Long-Evans


title: TotalInput RNA_2

description:
UVInput_2
Total RNA
The ES cells were derived from the V6.5 cell line.

value: C57BL/6 129SV mixed


title: NET-2

description: Total RNA was obtained from each independent tissue of patient


title: unstim_24h_matrigel_Normal lung fibroblasts_rep1

description:
SAM4955465
Normal lung fibroblasts treated with unstim at 24h

value: unstimulated


title: PCA-5

source_name: ductal adenocarcinoma

value: ductal adenocarcinoma (PCA)


title: Rat_liver_LE_1000_TCDD_19_hours_rep_3 [NanoString]

description: Treated

value: Male

value: 10-12 weeks


title: Rat_liver_LE_1000_TCDD_19_hours_rep_1 [NanoString]

description: Treated


title: GFP_IP_1

description:
UVGFP_1
RNA-IP
The ES cells were derived from the V6.5 cell line.

source_name: in vitro PGCs, anti-GFP RNA-IP

value: anti-GFP


title: TotalInput RNA_1

description:
UVInput_1
Total RNA
The ES cells were derived from the V6.5 cell line.


title: Rat_liver_LE_100_TCDD_19_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 19 hour exposure

value: 100 ug/kg


title: PCA-6

value: male


title: PABP1_IP_1

description:
UVPABP1_1
RNA-IP
The ES cells were derived from the V6.5 cell line.


title: SuH giants vs Input rep1

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

hyb_protocol: 34 µg labeled sample DNA and 34 µg labeled control DNA were combined, dried in a speed vac with medium heat and resuspended in 12.3 µl water.  For each hybridisation 29.5µl 2X Hybridization Buffer, 11.8µl Hybridization Component A and 1.2µl Alignment Oligo (NimbleGen Hybridization Kit) were combined and 31.7µl added to each hybridisation sample. Samples were incubated at +95°C for 5 minutes, 42°C for 5 minutes and 41 µl loaded onto the array. The hybridisation was performed to NimbleGen D. melanogaster ChIP-chip 2.1M Whole-Genome Tiling Arrays in the Nimbelegen hybridisation station at 42°C (mix mode B) for 18 hours. Post hybridisation washes were performed according to the NimbleGen Wash Buffer Kit instructions.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains. Signal for Cy3 and Cy5 channels are balanced using the histogram view in the GenePix software. Images are saved as Single-image TIFF.

data_processing: Images are processed with NimbleScan v2.4 software (Roche-Nimblegen) as per manufacturer instructions. Raw data files (*.pair) are created for each channel. The *.pair data files are then loaded into limma (Bioconductor Release v.2.8) and normalised with the vsn package (Bioconductor Release v.2.8). The resulting ratios are log2 ratio of ChIP/Input.

organism: Drosophila melanogaster

source_name: SuH giants_ChIP

label_protocol: In duplicate reactions: 1 μg of amplified DNA with 30 µl 2.5X Random Primers Solution (BioPrime DNA labelling kit, Life Technologies) was incubated at 100°C for 5 minutes and then cooled on ice. The samples were labelled as technical dye-swap replicates using the BioPrime DNA labelling kit (Life Technologies) in the presence of 4.5nmol fluorescently labelled Cy3- or Cy5-dCTP (GE Healthcare) and 72 U of Klenow at 37°C. After 2 hours the reactions were stopped with 7.5 µl Stop Buffer (BioPrime DNA labelling kit, Life Technologies). Duplicate reactions were pooled into single tubes and then precipitated with 165 µl Isopropanol and 0.2M sodium chloride and washed with cold 80% ethanol. The DNA was resuspened in 50 µl water and quantified on a Nanodrop spectrophotometer (Thermo Scientific).

growth_protocol: grown on standard Drosophila corn-meal media at 25C until wandering third instar

extract_protocol: Wing imaginal discs from 30 third instar larvea were dissected per one ChIP experiment, fixed 10 minutes on ice with 1% formaldeyde and lyzed in 30ul of lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, 1x Roche complete inhibitor), diluted 10-fold with the dilution buffer (20mM Tris-HCl pH 8.1, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS, 1x Roche complete inhibitor), sonicated 5 times 30 second (Bioruptor) and incubated with 2ug of Su(H) antibody (Santa Cruz) overnight. Antibody complexes were separated by protein G agarose bead (Santa Cruz), washed, eluted and decrosslinked overnight at 65C. Three ChIPs were pooled for one LM-PCR amplification: ChIP fragment were polished by T4 DNA polymerase and DNA was purified with a Qiagen MinElute PCR purification Kit. DNA linkers were attached using T4 DNA ligase (Invitrogen) and the products were amplified by 21 PCR cycles.

tag: strain/genotype

value: UAS-GFP:Su(H) expressed by the patched[559.1]-Gal4 driver

value: Wing imaginal discs

value: third instar larvea

tag: chip antibody

value: Su(H) antibody

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

source_name: total input


title: Nicd giants vs Input rep2

source_name: Nicd giants_ChIP

value: abxUbxFLPase; Act>y>Gal4, UAS GFP; FRT82B tubGal80 with UAS-Nicd; FRT82B

tag: tissue

source_name: Nicd giants total input


title: Rat_liver_LE_100_TCDD_19_hours_rep_3 [NanoString]

description: Treated

tag: gender

tag: strain

value: 19 hours


title: Dex_24h_matrigel_macrophages_rep2

description:
SAM3676770
macrophages treated with Dex at 24h

source_name: Macrophages, Dex, 24h

tag: cell type

value: monocyte-differentiated macrophages

tag: treatment

value: Dex

value: reference


title: PCA-3


title: Dex_24h_matrigel_macrophages_rep4

description:
SAM3676772
macrophages treated with Dex at 24h

tag: timepoint


title: SuH giants vs Input rep2

tag: developmental stage


title: Rat_liver_LE_100_TCDD_19_hours_rep_2 [NanoString]

description: Treated

value: Liver

value: Long-Evans

tag: age


title: Rat_liver_LE_100_TCDD_19_hours_rep_1 [NanoString]

description: Treated

value: Male

tag: exposure


title: NET-1

value: neuroendocrine tumor (NET)


title: Dex_24h_matrigel_macrophages_rep3

description:
SAM3676771
macrophages treated with Dex at 24h

tag: sample type


title: TGFb_24h_matrigel_macrophages_rep4

description:
SAM3676768
macrophages treated with TGFb at 24h

source_name: Macrophages, TGFb, 24h

value: TGFb


title: IL4_24h_matrigel_Normal lung fibroblasts_rep1

description:
SAM4955466
Normal lung fibroblasts treated with IL4 at 24h

value: normal primary lung fibroblasts

source_name: Stratagene Universal Human Reference RNA


title: PCA-4

value: male

value: ductal adenocarcinoma (PCA)


title: D12PGC_control

source_name: FACS-sorted differentiated GFP+tdTomato+ cells, day 12 differentiation, control

growth_protocol: Oct4-GFP ES cells carrying Dazl knockdown or control vectors with tdTomato fluorescent marker were trypsinized and depleted of the feeder cells by incubation on tissue culture plastic. The cells were replated on gelatin-coated plates and fed with Differentiation Medium for 9 or 12 days before harvest. The differentiated cells were dissociated with trypsin and collagenase IV and FACS sorted for the GFP+tdTomato+ double-positive cells.

extract_protocol: The RNA was extracted by Trizol.

value: C57BL/6 129SV mixed

value: primordial germ cells (PGCs) generated from differentiated Oct4-GFP transgenic ES cells

tag: days of differentiation

tag: shRNA

value: control


title: D12PGC_DazlKD_sh2

description: Oct4GD12_Dazl KD2

source_name: FACS-sorted differentiated GFP+tdTomato+ cells, day 12 differentiation, Dazl knockdown

value: Dazl knockdown


title: D12PGC_DazlKD_sh1

description: Oct4GD12_Dazl KD1


title: TGFb_24h_matrigel_macrophages_rep3

description:
SAM3676767
macrophages treated with TGFb at 24h


title: PCA-2


title: PCA-1

value: female


title: D9PGC_DazlKD_sh1

source_name: FACS-sorted differentiated GFP+tdTomato+ cells, day 9 differentiation, Dazl knockdown


title: Rat_liver_LE_50_TCDD_19_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Long-Evans, 50 TCDD, 19 hour exposure

value: 10-12 weeks

value: 50 ug/kg

value: 19 hours


title: SPN-14


title: Dex_24h_matrigel_macrophages_rep1

description:
SAM3676769
macrophages treated with Dex at 24h

value: monocyte-differentiated macrophages

value: Dex

value: reference


title: SuH giants vs Input rep3

value: UAS-GFP:Su(H) expressed by the patched[559.1]-Gal4 driver

value: Wing imaginal discs

value: third instar larvea

value: Su(H) antibody

value: Santa Cruz


title: D9PGC_control

source_name: FACS-sorted differentiated GFP+tdTomato+ cells, day 9 differentiation, control

value: male


title: Rat_liver_LE_50_TCDD_19_hours_rep_3 [NanoString]

description: Treated

value: Male

value: Liver

value: Long-Evans


title: TGFb_24h_matrigel_macrophages_rep2

description:
SAM3676766
macrophages treated with TGFb at 24h

value: TGFb


title: Rat_liver_LE_50_TCDD_19_hours_rep_2 [NanoString]

description: Treated


title: D9PGC_DazlKD_sh2

value: C57BL/6 129SV mixed

value: primordial germ cells (PGCs) generated from differentiated Oct4-GFP transgenic ES cells

value: Dazl knockdown


title: Rat_liver_LE_10_TCDD_19_hours_rep_3 [NanoString]

description: Treated

source_name: liver, Long-Evans, 10 TCDD, 19 hour exposure

value: 10-12 weeks

value: 10 ug/kg

value: 19 hours


title: IL10_24h_matrigel_macrophages_rep2

description:
SAM3676762
macrophages treated with IL10 at 24h

source_name: Macrophages, IL10, 24h

value: monocyte-differentiated macrophages

value: reference


title: Rat_liver_LE_50_TCDD_19_hours_rep_1 [NanoString]

description: Treated

value: 50 ug/kg


title: SPN-11

source_name: solid-pseudopapillary neoplasm

value: female

value: Solid-pseudopapillary neoplasm of pancreas (SPN)


title: SPN-12


title: Rat_liver_LE_10_TCDD_19_hours_rep_2 [NanoString]

description: Treated


title: IL10_24h_matrigel_macrophages_rep4

description:
SAM3676764
macrophages treated with IL10 at 24h


title: Liver DR6 polluted rep1

city: Córdoba

first: Julia

last: Ruiz-Laguna

address: Campus Rabanales, Edif. Severo Ochoa 2ª pl.

country: Spain

institute: University of Córdoba

description: Gene expression of pooled total RNA (n= 9) of male Mus spretus livers captured in a polluted site

hyb_protocol: Hybridizations were carried out in Whole mouse genome oligonucleotide microarrays, 4x44K (4 arrays/slide), 60-mer (Agilent) using the Agilent gene expression hybridization kit with GEx hybridization buffer HI-RPM, according to the manufacturer´s protocol. The fragmentation step used 1.65 μg of cyanine 3-labeled, linearly amplified cRNA and the hybridization were for 17 h in a rotating hybridization oven. Washes were conducted as recommended by the manufacturer using Agilent gene expression wash buffer kit.

scan_protocol: Slides were dried with helium gas and immediately scanned with the GenePix® 4000B microarray scanner (Axon Instruments Inc. Foster City, CA) with GenePixTM Pro 4.1 software, Molecular Devices using the following parameters: 532 nm, 5 μm of resolution, 100 % laser power at various photomultiplier tube (PMT) gains (or voltage settings). The subsequent analysis was performed with that images that had the highest number of valid spots, that is, PMT of 450 V for SOL arrays and 500 V for  PS , DR1. DR4 and DR6 arrays.

data_processing: Spot intensities and other quality control features were extracted with Agilent's Feature Extraction Software version 9.5.3.1, using defaults for all parameters. To analyze the array data GeneSpring GX v. 9.0.2 (Agilent Technologies, Inc., Santa Clara, CA) was utilized. Briefly, a new experiment was generated after importing data. For preprocessing of input data defaults parameters were used, that is, threshold raw signals: 5 –minimum signal intensity-; normalization algorithms: median shift to percentile 75 of the measurements taken from each chip to reduce chip-wide variation in intensity (per chip normalization) and finally baseline transformation option: baseline to median of all samples –for each probe the median of the log summarized values from all the samples is calculated and subtracted from each of the samples- (per gene normalization). Only data from spots designated as “present” were used. Entities in which at least 75% of the values in any 2 out of 2 or 4 conditions (SOL and PS or SOL and DR1, DR4, DR6) had acceptable values were retained for further analysis. To define a set of statistically significant, differentially expressed genes, a unpaired t-test was applied with Bonferroni FWER (family-wise error rate, type of Error control that allow very few occurrences of false positives) as the multiple testing correction (p= 0.01) (asymptotic p-value computation). Fold changes were calculated as the ratio between the signal averages of polluted  site and control SOL site. The normalized data on the logarithm base 2 scales were used in the proceeding analyses. A filter on the fold change (probes with fold differences ≥ 2 were considered significant) was next applied to the list of  genes and a new list of genes was generated containing genes that exhibited ≥ 2-fold increase  or decrease expression compared with control.

organism: Mus spretus

source_name: Liver, DR6-polluted site, rep1

label_protocol: Agilent low RNA input linear amplification kit PLUS, one-color –cyanine 3-CTP-was used for generating fluorescent complimentary RNA (cRNA) along with Agilent's One-Color RNA Spike-in Kit following the manufacturer's protocols. A total of 1 μg of pooled RNA (n=9) was used for the cDNA synthesis of each four technical replicates. Then, the samples were simultaneously amplified and labeled with cyanine 3-CTP. Qiagen´s RNeasy mini spin columns were used for the purifications of the labeled/amplified cRNA samples. Then, cRNAs were quantified using NanoDrop® ND-1000 spectrophotometer with the Nanodrop 3.0.1 software. The examined yield and specific activity of each reaction were always higher than the recommended values to proceed to the hybridization step.

extract_protocol: Total RNA from individual livers were isolated by TRIzol method (Invitrogen, Carlsbad, CA) couped with the GenEluteTM Mammalian Total kit from SIGMA. RNA integrity was examined by electrophoresis, and concentrations were determined by spectrophotometry. Absence of genomic DNA contaminations was checked by PCR amplification of RNA samples without prior cDNA synthesis.

tag: environmental condition

value: polluted

value: liver

tag: location

value: Domingo Rubio stream upper course (DR6)


title: GFP_IP_2

description:
UVGFP_2
RNA-IP
The ES cells were derived from the V6.5 cell line.

source_name: in vitro PGCs, anti-GFP RNA-IP

value: primordial germ cells (PGCs) generated from differentiated Dazl-GFP-V5 ES cells

tag: ip antibody

value: anti-GFP

tag: antibody vendor

value: Abcam

tag: antibody catalog number

tag: antibody lot#


title: SPN-13

description: Total RNA was obtained from each independent tissue of patient

tag: gender

tag: tissue


title: IL10_24h_matrigel_macrophages_rep1

description:
SAM3676761
macrophages treated with IL10 at 24h

tag: cell type


title: Rat_liver_LE_10_TCDD_19_hours_rep_4 [NanoString]

description: Treated

value: Male

value: Liver

tag: strain

value: Long-Evans

tag: treatment


title: IL10_24h_matrigel_macrophages_rep3

description:
SAM3676763
macrophages treated with IL10 at 24h

tag: timepoint


title: SPN-10

tag: age


title: Liver DR6 polluted rep3

source_name: Liver, DR6-polluted site, rep3


title: Rat_liver_LE_10_TCDD_19_hours_rep_1 [NanoString]

description: Treated

value: 10-12 weeks

tag: exposure


title: Liver DR4 polluted rep4

source_name: Liver, DR4-polluted site, rep4

value: Domingo Rubio stream medium course (DR4)


title: SPN-9


title: Liver DR4 polluted rep3

source_name: Liver, DR4-polluted site, rep3


title: Liver DR6 polluted rep2

source_name: Liver, DR6-polluted site, rep2


title: IL13_24h_matrigel_macrophages_rep4

description:
SAM3676760
macrophages treated with IL13 at 24h

source_name: Macrophages, IL13, 24h

tag: sample type


title: Rat_liver_LE_1_TCDD_19_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Long-Evans, 1 TCDD, 19 hour exposure

value: 1 ug/kg

value: 19 hours


title: Nicd giants vs Input rep1

source_name: Nicd giants_ChIP

tag: strain/genotype

value: abxUbxFLPase; Act>y>Gal4, UAS GFP; FRT82B tubGal80 with UAS-Nicd; FRT82B

value: Wing imaginal discs

tag: developmental stage

value: third instar larvea

tag: chip antibody

value: Su(H) antibody

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

source_name: Nicd giants total input


title: SPN-8

value: female

value: Solid-pseudopapillary neoplasm of pancreas (SPN)


title: Rat_liver_LE_1_TCDD_19_hours_rep_2 [NanoString]

description: Treated


title: Rat_liver_LE_1_TCDD_19_hours_rep_3 [NanoString]

description: Treated


title: Rat_liver_LE_1_TCDD_19_hours_rep_1 [NanoString]

description: Treated


title: TGFb_24h_matrigel_macrophages_rep1

description:
SAM3676765
macrophages treated with TGFb at 24h

source_name: Macrophages, TGFb, 24h

value: monocyte-differentiated macrophages

value: TGFb

source_name: Stratagene Universal Human Reference RNA

value: reference


title: Liver DR4 polluted rep2

source_name: Liver, DR4-polluted site, rep2

tag: environmental condition

value: polluted

value: liver

tag: location


title: SPN-6


title: Liver DR1 polluted rep4

source_name: Liver, DR1-polluted site, rep4

value: Domingo Rubio stream lower course (DR1)


title: SPN-7


title: Rat_liver_LE_0.1_TCDD_19_hours_rep_3 [NanoString]

description: Treated

source_name: liver, Long-Evans, 0.1 TCDD, 19 hour exposure

value: Male

value: Liver

value: Long-Evans

value: 10-12 weeks

value: 0.1 ug/kg


title: SPN-5

value: male


title: IL13_24h_matrigel_macrophages_rep3

description:
SAM3676759
macrophages treated with IL13 at 24h


title: Rat_liver_LE_0.1_TCDD_19_hours_rep_4 [NanoString]

description: Treated

value: 19 hours


title: IL4_24h_matrigel_macrophages_rep4

description:
SAM3676756
macrophages treated with IL4 at 24h

source_name: Macrophages, IL4, 24h


title: SPN-4

source_name: solid-pseudopapillary neoplasm


title: Liver DR1 polluted rep2

source_name: Liver, DR1-polluted site, rep2


title: IL13_24h_matrigel_macrophages_rep2

description:
SAM3676758
macrophages treated with IL13 at 24h


title: Liver DR1 polluted rep3

source_name: Liver, DR1-polluted site, rep3


title: SPN-2


title: Liver DR4 polluted rep1

source_name: Liver, DR4-polluted site, rep1

value: Domingo Rubio stream medium course (DR4)


title: IL4_24h_matrigel_macrophages_rep3

description:
SAM3676755
macrophages treated with IL4 at 24h


title: SPN-3


title: Liver PS polluted rep4

source_name: Liver, PS-polluted site, rep4

value: phosphogypsum stacks (PS)


title: Liver DR1 polluted rep1

source_name: Liver, DR1-polluted site, rep1


title: SPN-1

value: female


title: Rat_liver_LE_0.1_TCDD_19_hours_rep_2 [NanoString]

description: Treated


title: Rat_liver_LE_0.1_TCDD_19_hours_rep_1 [NanoString]

description: Treated


title: IL4_24h_matrigel_macrophages_rep1

description:
SAM3676753
macrophages treated with IL4 at 24h


title: IL4_24h_matrigel_macrophages_rep2

description:
SAM3676754
macrophages treated with IL4 at 24h


title: IL13_24h_matrigel_macrophages_rep1

description:
SAM3676757
macrophages treated with IL13 at 24h


title: unstim_24h_matrigel_macrophages_rep4

description:
SAM3676752
macrophages treated with unstim at 24h

source_name: Macrophages, unstimulated, 24h

value: unstimulated


title: Rat_liver_LE_0.01_TCDD_19_hours_rep_3 [NanoString]

description: Treated

source_name: liver, Long-Evans, 0.01 TCDD, 19 hour exposure


title: Rat_liver_LE_0.01_TCDD_19_hours_rep_2 [NanoString]

description: Treated


title: SK-OV-3 transfected with IRF-1 shRNA and CDDP [3_shIRF-1 CDDP]

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

hyb_protocol: Standard Illumina ibridization protocol

data_processing: Data were analysed using BeadStudio version 2;  rank invariant normalization was performed.

label_protocol: Biotilinated cRNA were prepared with the Ambion messageAmp for Illumina array.

extract_protocol: Total RNA was extracted from SK-OV-3 cells transfected with scrambled or IRF-1 shRNA after 24hours of CDDP.

tag: transfection

value: IRF-1 shRNA CDDP

tag: cell line


title: Rat_liver_LE_0.01_TCDD_19_hours_rep_4 [NanoString]

description: Treated

tag: gender

tag: tissue


title: Liver SOL unpolluted rep4

description: Gene expression of pooled total RNA (n= 9) of male Mus spretus livers captured in an unpolluted site

source_name: Liver, SOL-unpolluted site, rep4

value: unpolluted

value: Santa Olalla lagoon (SOL)


title: unstim_24h_matrigel_macrophages_rep2

description:
SAM3676750
macrophages treated with unstim at 24h

tag: cell type

value: monocyte-differentiated macrophages

value: reference


title: Liver PS polluted rep2

description: Gene expression of pooled total RNA (n= 9) of male Mus spretus livers captured in a polluted site

source_name: Liver, PS-polluted site, rep2

value: polluted

value: liver


title: Liver PS polluted rep3

source_name: Liver, PS-polluted site, rep3


title: Liver SOL unpolluted rep3

source_name: Liver, SOL-unpolluted site, rep3


title: unstim_24h_matrigel_macrophages_rep1

description:
SAM3676749
macrophages treated with unstim at 24h

tag: treatment

source_name: Stratagene Universal Human Reference RNA


title: IL13_24h_matrigel_monocytes_rep5

description:
SAM1321567
monocytes treated with IL13 at 24h

source_name: Monocytes, IL13, 24h

value: monocytes

tag: timepoint


title: Liver PS polluted rep1

source_name: Liver, PS-polluted site, rep1


title: Rat_liver_LE_0.01_TCDD_19_hours_rep_1 [NanoString]

description: Treated

value: Male

value: Liver

tag: strain

value: Long-Evans

tag: age


title: SK-OV-3 transfected with IRF-1 shRNA [3_shIRF-1]

description: SK-OV-3 transfected with IRF-1 shRNA

source_name: SK-OV-3 transfected with IRF-1 shRNA

value: IRF-1 shRNA


title: Liver SOL unpolluted rep2

source_name: Liver, SOL-unpolluted site, rep2


title: Rat_liver_LE_0.001_TCDD_19_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Long-Evans, 0.001 TCDD, 19 hour exposure

value: 10-12 weeks

tag: exposure

value: 19 hours


title: SK-OV-3 transfected with scrambled shRNA and CDDP [3_shCTRL CDDP]

value: scrambled shRNA CDDP


title: SK-OV-3 transfected with scrambled shRNA [3_shCTRL]

value: scrambled shRNA


title: SK-OV-3 transfected with IRF-1 shRNA [2_shIRF-1]

description: SK-OV-3 transfected with IRF-1 shRNA


title: Rat_liver_LE_0.001_TCDD_19_hours_rep_3 [NanoString]

description: Treated


title: unstim_24h_matrigel_monocytes_rep5

description:
SAM1321565
monocytes treated with unstim at 24h

source_name: Monocytes, unstimulated, 24h

value: unstimulated

tag: sample type


title: Rat_liver_LE_Corn_oil_19_hours_rep_7 [NanoString]

description: Control

source_name: liver, Long-Evans, Corn oil treated, 19 hour exposure

value: Corn Oil vehicle


title: Yeast_48h in 0.5% glucose_rep2

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

institute: Korea University

description: Gene expression data from yeast cells which were cultured in 0.5% glucose-containing YPD media and harvested at 48h after inoculation.

hyb_protocol: Following fragmentation, 5 μg of fragmented cRNA were hybridized onto a microarray (GeneChip Yeast Genome 2.0 Array) for 16h at 45 °C. Microarrays were washed and stained in GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned using the GeneChip Scanner 3000.

data_processing: All raw data were generated using Affymetrix software, Command Console. The cel files were imprted into Partek Discovery Suite and further processed using quantile normalization in Partek Discovery Suite.

organism: Saccharomyces cerevisiae BY4741

source_name: Yeast cells which were cultured for 48h in 0.5% glucose-containing YPD media

label_protocol: Biotinylated cRNA were synthesized according to the Affymetrix protocol from 250 ng of total RNA.

growth_protocol: Budding yeast cells were inoculated into liquid YPD media with an initial OD600 = 0.2 containing 2% and 0.5% glucose respectively. All cultures were incubated at 30 °C in a 200 rpm shaking incubator.

extract_protocol: For total RNA isolation, we used TRIzol LS reagent (Invitrogen), according to the manufacturer's instructions.

treatment_protocol: Yeast harvested at indicated time-points was broken in RNA isolation buffer using a Beadbeater (BioSpec).

tag: time point

tag: protocol

value: 0.5% glucose-containing YPD media


title: unstim_24h_matrigel_macrophages_rep3

description:
SAM3676751
macrophages treated with unstim at 24h


title: Yeast_48h in 0.5% glucose_rep3


title: Rat_liver_LE_0.001_TCDD_19_hours_rep_2 [NanoString]

description: Treated


title: IL4_24h_matrigel_monocytes_rep5

description:
SAM1321566
monocytes treated with IL4 at 24h

source_name: Monocytes, IL4, 24h


title: SK-OV-3 transfected with IRF-1 shRNA and CDDP [2_shIRF-1 CDDP]

value: IRF-1 shRNA CDDP


title: SK-OV-3 transfected with scrambled shRNA [2_shCTRL]


title: IL13_6h_matrigel_monocytes_rep5

description:
SAM1321564
monocytes treated with IL13 at 6h

source_name: Monocytes, IL13, 6h


title: SK-OV-3 transfected with scrambled shRNA and CDDP [2_shCTRL CDDP]


title: Yeast_48h in 0.5% glucose_rep1


title: unstim_6h_matrigel_monocytes_rep5

description:
SAM1321562
monocytes treated with unstim at 6h

source_name: Monocytes, unstimulated, 6h


title: Rat_liver_LE_0.001_TCDD_19_hours_rep_1 [NanoString]

description: Treated


title: SK-OV-3 transfected with scrambled shRNA [1_shCTRL]


title: Liver SOL unpolluted rep1

source_name: Liver, SOL-unpolluted site, rep1

value: unpolluted

value: Santa Olalla lagoon (SOL)


title: SK-OV-3 transfected with IRF-1 shRNA and CDDP [1_shIRF-1 CDDP]


title: IL4_6h_matrigel_monocytes_rep4

description:
SAM1321563
monocytes treated with IL4 at 6h

source_name: Monocytes, IL4, 6h

value: reference


title: Rat_liver_LE_Corn_oil_19_hours_rep_6 [NanoString]

description: Control


title: SK-OV-3 transfected with scrambled shRNA and CDDP [1_shCTRL CDDP]


title: SK-OV-3 transfected with IRF-1 shRNA [1_shIRF-1]

description: SK-OV-3 transfected with IRF-1 shRNA


title: Rat_liver_LE_Corn_oil_19_hours_rep_4 [NanoString]

description: Control


title: Rat_liver_LE_Corn_oil_19_hours_rep_5 [NanoString]

description: Control


title: Yeast_24h in 0.5% glucose_rep3

description: Gene expression data from yeast cells which were cultured in 0.5% glucose-containing YPD media and harvested at 24h after inoculation.

source_name: Yeast cells which were cultured for 24h in 0.5% glucose-containing YPD media


title: Yeast_24h in 0.5% glucose_rep2


title: Rat_liver_LE_Corn_oil_19_hours_rep_3 [NanoString]

description: Control


title: unstim_24h_matrigel_monocytes_rep4

description:
SAM1321559
monocytes treated with unstim at 24h


title: IL13_24h_matrigel_monocytes_rep4

description:
SAM1321561
monocytes treated with IL13 at 24h


title: Yeast_24h in 0.5% glucose_rep1


title: Yeast_18h in 0.5% glucose_rep3

description: Gene expression data from yeast cells which were cultured in 0.5% glucose-containing YPD media and harvested at 18h after inoculation.

source_name: Yeast cells which were cultured for 18h in 0.5% glucose-containing YPD media


title: siKLF5_2

city: Houston

first: Yun-Yong

last: Park

state: TX

address: 7435 Fannin St.

department: Systems Biology

institute: UT, MD Anderson Cancer Center

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-Ht12 beadChip ver. were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to a ver. 3 of the Illumina Human-Ht-12 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

source_name: SK-Hep1_hepatocellular carcinoma cell line

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000).

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD).

tag: genotype/variation


title: Yeast_18h in 0.5% glucose_rep1


title: siKLF5_3


title: siKLF5_1


title: Yeast_18h in 0.5% glucose_rep2


title: IL4_24h_matrigel_monocytes_rep4

description:
SAM1321560
monocytes treated with IL4 at 24h

source_name: Stratagene Universal Human Reference RNA


title: Rat_liver_LE_Corn_oil_19_hours_rep_1 [NanoString]

description: Control


title: IL13_6h_matrigel_monocytes_rep4

description:
SAM1321558
monocytes treated with IL13 at 6h


title: Rat_liver_LE_100_TCDD_10_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 10 hour exposure

value: 100 ug/kg

value: 10 hours


title: Rat_liver_LE_Corn_oil_19_hours_rep_2 [NanoString]

description: Control

value: Male


title: Yeast_12h in 0.5% glucose_rep3

description: Gene expression data from yeast cells which were cultured in 0.5% glucose-containing YPD media and harvested at 12h after inoculation.

source_name: Yeast cells which were cultured for 12h in 0.5% glucose-containing YPD media


title: IL4_24h_matrigel_monocytes_rep3

description:
SAM1321554
monocytes treated with IL4 at 24h

value: monocytes


title: IL13_24h_matrigel_monocytes_rep3

description:
SAM1321555
monocytes treated with IL13 at 24h

source_name: Monocytes, IL13, 24h


title: Rat_liver_LE_100_TCDD_10_hours_rep_3 [NanoString]

description: Treated

value: Liver

value: Long-Evans


title: Rat_liver_LE_100_TCDD_10_hours_rep_2 [NanoString]

description: Treated

value: 10-12 weeks


title: unstim_6h_matrigel_monocytes_rep4

description:
SAM1321556
monocytes treated with unstim at 6h


title: Yeast_12h in 0.5% glucose_rep2


title: siTEAD1_1


title: Yeast_12h in 0.5% glucose_rep1


title: siTEAD1_3


title: siTEAD1_2


title: IL4_6h_matrigel_monocytes_rep3

description:
SAM1321557
monocytes treated with IL4 at 6h


title: Rat_liver_LE_100_TCDD_6_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 6 hour exposure

value: 6 hours


title: Rat_liver_LE_100_TCDD_10_hours_rep_1 [NanoString]

description: Treated


title: siYAP1_1


title: Yeast_48h in 2% glucose_rep2

description: Gene expression data from yeast cells which were cultured in 2% glucose-containing YPD media and harvested at 48h after inoculation.

source_name: Yeast cells which were cultured for 48h in 2% glucose-containing YPD media

value: 2% glucose-containing YPD media


title: Yeast_48h in 2% glucose_rep3


title: unstim_24h_matrigel_monocytes_rep3

description:
SAM1321553
monocytes treated with unstim at 24h

source_name: Monocytes, unstimulated, 24h


title: Rat_liver_LE_100_TCDD_6_hours_rep_2 [NanoString]

description: Treated


title: Rat_liver_LE_100_TCDD_6_hours_rep_3 [NanoString]

description: Treated


title: Yeast_48h in 2% glucose_rep1


title: siYAP1_2


title: siYAP1_3


title: Yeast_24h in 2% glucose_rep2

description: Gene expression data from yeast cells which were cultured in 2% glucose-containing YPD media and harvested at 24h after inoculation.

source_name: Yeast cells which were cultured for 24h in 2% glucose-containing YPD media


title: Yeast_24h in 2% glucose_rep3


title: Yeast_24h in 2% glucose_rep1


title: Rat_liver_LE_100_TCDD_6_hours_rep_1 [NanoString]

description: Treated


title: unstim_6h_matrigel_monocytes_rep3

description:
SAM1321550
monocytes treated with unstim at 6h


title: siLuc_2

value: siLuc


title: Rat_liver_LE_100_TCDD_3_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 3 hour exposure

value: 3 hours


title: IL4_24h_matrigel_monocytes_rep2

description:
SAM1321542
monocytes treated with IL4 at 24h

source_name: Monocytes, IL4, 24h


title: IL13_6h_matrigel_monocytes_rep3

description:
SAM1321552
monocytes treated with IL13 at 6h

source_name: Monocytes, IL13, 6h


title: unstim_24h_matrigel_monocytes_rep2

description:
SAM1321541
monocytes treated with unstim at 24h

value: unstimulated


title: Rat_liver_LE_100_TCDD_3_hours_rep_3 [NanoString]

description: Treated


title: siLuc_3


title: Rat_liver_LE_100_TCDD_3_hours_rep_2 [NanoString]

description: Treated


title: IL13_24h_matrigel_monocytes_rep2

description:
SAM1321543
monocytes treated with IL13 at 24h


title: Yeast_18h in 2% glucose_rep2

description: Gene expression data from yeast cells which were cultured in 2% glucose-containing YPD media and harvested at 18h after inoculation.

source_name: Yeast cells which were cultured for 18h in 2% glucose-containing YPD media


title: Atasf1ab_rep2

city: Shanghai

first: Yan

last: Zhu

address: 2005, Songhu Road

department: Biochemistry

country: China

institute: Fudan University, School of life sciences

description: Atasf1ab double mutant, 12-day-old seedling, replication 2

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 4x44K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven at 10 rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan (Scan Area 71x21.6 mm, Scan resolution 5 mm).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 021169_D_F_20090824) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared and purified by RNAeasy Mini Kit (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown on MS medium at 22℃ under a light intensity of about 100 μEm-2s-1 in a 16 hrs-light/8 hrs-dark photoperiod.

extract_protocol: Total RNA was prepared using the TRIzol kit (Invitrogen).

value: whole seedling


title: Rat_liver_LE_100_TCDD_3_hours_rep_1 [NanoString]

description: Treated


title: Yeast_12h in 2% glucose_rep2

description: Gene expression data from yeast cells which were cultured in 2% glucose-containing YPD media and harvested at 12h after inoculation.

source_name: Yeast cells which were cultured for 12h in 2% glucose-containing YPD media


title: Yeast_12h in 2% glucose_rep3


title: Atasf1b_rep1

description: Atasf1b single mutant, 12-day-old seedling, replication 1


title: unstim_6h_matrigel_monocytes_rep2

description:
SAM1321538
monocytes treated with unstim at 6h

source_name: Monocytes, unstimulated, 6h


title: Atasf1ab_rep1

description: Atasf1ab double mutant, 12-day-old seedling, replication 1


title: Atasf1a_rep1

description: Atasf1a single mutant, 12-day-old seedling, replication 1


title: Yeast_18h in 2% glucose_rep1


title: Rat_liver_HW_100_TCDD_384_hours_rep_2 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 384 hour exposure

value: Han/Wistar

value: 384 hours


title: Atasf1a_rep2

description: Atasf1a single mutant, 12-day-old seedling, replication 2


title: Rat_liver_HW_100_TCDD_384_hours_rep_1 [NanoString]

description: Treated


title: Rat_liver_HW_100_TCDD_384_hours_rep_3 [NanoString]

description: Treated


title: Yeast_12h in 2% glucose_rep1


title: IL13_6h_matrigel_monocytes_rep2

description:
SAM1321540
monocytes treated with IL13 at 6h


title: siLuc_1

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 47231 probes on the Human-Ht12 beadChip ver. were used.


title: IL4_24h_matrigel_monocytes_rep1

description:
SAM1321536
monocytes treated with IL4 at 24h


title: IL4_6h_matrigel_monocytes_rep1

description:
SAM1321539
monocytes treated with IL4 at 6h

source_name: Monocytes, IL4, 6h


title: IL13_24h_matrigel_monocytes_rep1

description:
SAM1321537
monocytes treated with IL13 at 24h


title: IL4_6h_matrigel_monocytes_rep2

description:
SAM1321551
monocytes treated with IL4 at 6h


title: Yeast_18h in 2% glucose_rep3


title: Rat_liver_HW_Corn_oil_384_hours_rep_4 [NanoString]

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 384hour exposure

value: Corn Oil vehicle


title: Atasf1b_rep2

description: Atasf1b single mutant, 12-day-old seedling, replication 2


title: Rat_liver_HW_Corn_oil_384_hours_rep_3 [NanoString]

description: Control


title: IL13_6h_matrigel_monocytes_rep1

description:
SAM1321534
monocytes treated with IL13 at 6h

source_name: Stratagene Universal Human Reference RNA

value: reference


title: Rat_liver_HW_Corn_oil_384_hours_rep_2 [NanoString]

description: Control


title: Rat_liver_HW_Corn_oil_384_hours_rep_1 [NanoString]

description: Control


title: WT_rep1

description: wild type, 12-day-old seedling, replication 1


title: unstim_24h_matrigel_monocytes_rep1

description:
SAM1321535
monocytes treated with unstim at 24h


title: Rat_liver_HW_100_TCDD_240_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 240 hour exposure

value: 100 ug/kg

value: 240 hours


title: Rat_liver_HW_100_TCDD_240_hours_rep_5 [NanoString]

description: Treated

value: Male


title: CSF1-Fc treated mouse liver sample replicate 3

city: Roslin

first: Kristin

last: Sauter

address: Easter Bush, Midlothian

institute: Roslin Institute/The University of Edinburgh

description: SAMPLE 5

hyb_protocol: Samples were hybridised according to the Nugen protocol for Affymetrix Gene Titan hybridisation, using the Affymetrix Gene Titan Hybridization Wash & Stain Kit for WT Array Plates (PN 901622)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using the Affymetrix Expression Console software version 1.1
probe group file: MoGene-1_1-st-v1.r4.pgf
meta-probeset file: MoGene-1_1-st-v1.r4.mps

source_name: CSF1-Fc treated mouse liver

label_protocol: Samples were biotin labelled using the Nugen Encore labelling kit using the half volume protocol

growth_protocol: Mouse livers dissected from adult mice

extract_protocol: All livers were dissected and stored in RNA later prior to preparation of RNA with Trizol, cDNA synthesis and amplification was performed using the Nugen Pico SL kit

treatment_protocol: Mice were injected subcut for 4 consecutive days with PBS or CSF1-Fc before cull on day 5

value: adult

tag: injected with

value: CSF1-Fc for 4d

value: liver


title: CSF1-Fc treated mouse liver sample replicate 2

description: SAMPLE 4


title: unstim_6h_matrigel_monocytes_rep1

description:
SAM1321532
monocytes treated with unstim at 6h

value: monocytes


title: Control mouse liver sample replicate 1

description: SAMPLE 1

source_name: Control mouse liver

value: PBS for 4d


title: ILC2_TSLP IL-33 IL-25_24 hour_rep3

description:
SAM3461550
Human ILC2 cells treated with TSLP/IL-33/IL-25 for 24 hours.

scan_protocol: Chips were scanned using the Agilent SureScan Microarray Scanner.

source_name: ILC2 cells, TSLP/IL-33/IL-25, 24 hr

growth_protocol: Purified ILC2s were expanded in vitro in the presence of IL-2, IL-7, IL-33 and IL-25 (each at 50 ng/ml) for 7-10 days and then rested for 2 days in the presence of 1 ng/ml IL-2 and IL-7.

treatment_protocol: Cells were treated in the presence of 1 ng/ml IL-2 and IL-7 with either media control, IL-25 (50 ng/ml), IL-33 (50 ng/ml), and/or TSLP (50 ng/ml) in combination, for 6 or 24 hours.

value: ILC2 (Lineage negative, CRTH2+, CD161+, CD127+)

tag: cytokine treatment

value: TSLP, IL-33, IL-25

value: 24 hours


title: WT_rep2

description: wild type, 12-day-old seedling, replication 2


title: ILC2_TSLP IL-33 IL-25_24 hour_rep2

description:
SAM3461549
Human ILC2 cells treated with TSLP/IL-33/IL-25 for 24 hours.


title: ILC2_TSLP IL-33_24 hour_rep3

description:
SAM3461546
Human ILC2 cells treated with TSLP/IL-33 for 24 hours.

source_name: ILC2 cells, TSLP/IL-33, 24 hr

value: TSLP, IL-33


title: Rat_liver_HW_100_TCDD_240_hours_rep_1 [NanoString]

description: Treated

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). RNA was quantified using a NanoDrop UV spectrophotometer (Thermo Scientific, Mississauga, ON) and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Liver

value: 10-12 weeks


title: Rat_liver_HW_100_TCDD_240_hours_rep_3 [NanoString]

description: Treated

value: Han/Wistar


title: ILC2_TSLP IL-33_24 hour_rep1

description:
SAM3461544
Human ILC2 cells treated with TSLP/IL-33 for 24 hours.


title: ILC2_TSLP IL-33 IL-25_24 hour_rep4

description:
SAM3461551
Human ILC2 cells treated with TSLP/IL-33/IL-25 for 24 hours.


title: Control mouse liver sample replicate 2

description: SAMPLE 2


title: Rat_liver_HW_100_TCDD_240_hours_rep_2 [NanoString]

description: Treated


title: ILC2_TSLP IL-33_24 hour_rep2

description:
SAM3461545
Human ILC2 cells treated with TSLP/IL-33 for 24 hours.


title: ILC2_TSLP IL-33_24 hour_rep4

description:
SAM3461547
Human ILC2 cells treated with TSLP/IL-33 for 24 hours.


title: CD-PYC04-cy5

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Biological replicate 4 of 4.

hyb_protocol: samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix 4200L dual-channel laser scanner

data_processing:
R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.
VALUE column reports loess-normalized, log2 (test/reference) ratios.

organism: Clostridioides difficile

source_name: strain C630E grown in PY with cysteine

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile strain C630E was grown for 10 hours in PY medium with 10 mM of cysteine or in PY corresponding to mild range contration of cysteine (Karolinska institut recipe)

extract_protocol: Total RNA extracted using RNAPro (FastPrep) and following MP manufacturer's instructions

value: C630E Mullany

tag: agent

value: 10 mM of cysteine

source_name: strain JIR8094 in TY 8H of growth (reference)


title: Rat_liver_HW_Corn_oil_240_hours_rep_5 [NanoString]

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 240 hour exposure

value: Corn Oil vehicle


title: CSF1-Fc treated mouse liver sample replicate 1

description: SAMPLE 3


title: Rat_liver_HW_Corn_oil_240_hours_rep_4 [NanoString]

description: Control

value: 240 hours


title: Rat_liver_HW_Corn_oil_240_hours_rep_3 [NanoString]

description: Control

value: Male


title: Rat_liver_HW_Corn_oil_240_hours_rep_2 [NanoString]

description: Control


title: ILC2_TSLP IL-33 IL-25_24 hour_rep1

description:
SAM3461548
Human ILC2 cells treated with TSLP/IL-33/IL-25 for 24 hours.

value: reference


title: CD-PY04-cy5

description: Biological replicate 4 of 4.

source_name: strain C630E grown in PY

value: mild concentration of cysteine (control)


title: ILC2_TSLP IL-25_24 hour_rep3

description:
SAM3461542
Human ILC2 cells treated with TSLP/IL-25 for 24 hours.

source_name: ILC2 cells, TSLP/IL-25, 24 hr

value: TSLP, IL-25


title: CD-PYC01-cy3

description: Biological replicate 1 of 4.


title: CD-PYC02-cy5

description: Biological replicate 2 of 4.


title: DTM with modest core vs DTM with high core replicate 2

city: Taoyuan

first: ML

last: Chang

address: 5 Fu-Shin Str.

country: Taiwan

institute: CGMH

hyb_protocol: 2 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 minutes. Correspondingly fragmented labeled cRNAs and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were then pooled and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 60°C for 17 h. After hybridization, slides were washed and drying.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B scanner. Images were quantified using Agilent Feature Extraction Software.  Data II-1 was analyzed by FE version 8.1.1.1. Other data were analyzed by FE version 9.1.3.1.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.  Data II-1 was processed by FE version 8.1.1.1. Other data were  processed by FE version 9.1.3.1.

source_name: DTM (Modest)

label_protocol: 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process.

extract_protocol: Total RNA was extracted by Trizol® Reagent (Invitrogen, USA), and followed by RNeasy Mini Kit (Qiagen, Germany).

value: female

tag: inflammation

value: yes

tag: steastosis

value: FVB/N

source_name: DTM(High)

value: no

tag: stestosis


title: ILC2_TSLP IL-25_24 hour_rep4

description:
SAM3461543
Human ILC2 cells treated with TSLP/IL-25 for 24 hours.

value: ILC2 (Lineage negative, CRTH2+, CD161+, CD127+)

value: 24 hours


title: CD-PYC03-cy3

description: Biological replicate 3 of 4.


title: Rat_liver_HW_Corn_oil_240_hours_rep_1 [NanoString]

description: Control

tag: gender

tag: tissue

value: Liver


title: DTM with modest core vs DTM with high core replicate 3


title: Rat_liver_HW_100_TCDD_96_hours_rep_5 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 96 hour exposure

value: 10-12 weeks

tag: treatment

value: 100 ug/kg

value: 96 hours


title: CD-PY01-cy3

description: Biological replicate 1 of 4.

value: C630E Mullany


title: Bladder cancer tumor_11

city: Nanjing

first: Wen

last: Cheng

address: 305 Zhong Shan Dong Lu

department: Department of Urology

institute: Jinling Hospital

description: Bladder cancer

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505B)

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed 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 15 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 3/15 samples prior to any data processing (e.g. prior to fold-change filtering). There was a considerable number of probes not detected in this experiment.

source_name: Surgical speciment from a patient with bladder cancer

extract_protocol: Total RNAs were extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following manufacturer’s instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Primary  bladder tumours from patients with bladder cancer who underwent surgical treatment, and normal bladder mucosa were obtained, the samples were immeidately stored in liquid nitroge tank.

value: primary bladder urothelial cell carcinoma tumor

tag: tumor stage

value: muscle invasive I


title: ILC2_TSLP_24 hour_rep4

description:
SAM3461539
Human ILC2 cells treated with TSLP for 24 hours.

source_name: ILC2 cells, TSLP, 24 hr

tag: cell type

value: TSLP


title: ILC2_TSLP IL-25_24 hour_rep2

description:
SAM3461541
Human ILC2 cells treated with TSLP/IL-25 for 24 hours.

value: reference


title: ILC2_TSLP IL-25_24 hour_rep1

description:
SAM3461540
Human ILC2 cells treated with TSLP/IL-25 for 24 hours.


title: Rat_liver_HW_100_TCDD_96_hours_rep_4 [NanoString]

description: Treated

value: Male

tag: strain

value: Han/Wistar

tag: age


title: ILC2_TSLP_24 hour_rep2

description:
SAM3461537
Human ILC2 cells treated with TSLP for 24 hours.

tag: sample type


title: CD-PY02-cy5

description: Biological replicate 2 of 4.

value: mild concentration of cysteine (control)


title: CD-PY03-cy3

description: Biological replicate 3 of 4.


title: Bladder cancer tumor_12

description: Bladder cancer

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

value: muscle non-invasive II


title: Rat_liver_HW_100_TCDD_96_hours_rep_3 [NanoString]

description: Treated

tag: exposure


title: ILC2_TSLP_24 hour_rep3

description:
SAM3461538
Human ILC2 cells treated with TSLP for 24 hours.

tag: time point


title: Rat_liver_HW_100_TCDD_96_hours_rep_2 [NanoString]

description: Treated


title: DTM with high core vs STM replicate 3

value: female

value: yes

value: FVB/N

source_name: STM


title: DTM with high core vs STM replicate 2

value: no


title: Bladder cancer tumor_10

description: Bladder cancer

value: muscle invasive III


title: DTM with high core vs STM replicate 1

value: Liver


title: Liver 12

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from Liver sample of adults

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: stress response

value: high

tag: Sex

value: f

tag: group

value: animals with high agressiveness

tag: breed

value: German Landrace


title: DTM with modest core vs DTM with high core replicate 1

tag: inflammation


title: Bladder cancer tumor_08

description: Bladder cancer

value: primary bladder urothelial cell carcinoma tumor


title: ILC2_IL-33 IL-25_24 hour_rep3

description:
SAM3461534
Human ILC2 cells treated with IL-33/IL-25 for 24 hours.

source_name: ILC2 cells, IL-33/IL-25, 24 hr

extract_protocol: RNeasy Mini Kit (Qiagen).

value: ILC2 (Lineage negative, CRTH2+, CD161+, CD127+)

tag: cytokine treatment

value: 24 hours

source_name: Stratagene Universal Human Reference RNA


title: Bladder cancer tumor_07

description: Bladder cancer

value: Male


title: Rat_liver_HW_100_TCDD_96_hours_rep_1 [NanoString]

description: Treated

value: Han/Wistar

value: 10-12 weeks

value: 100 ug/kg

value: 96 hours


title: Bladder cancer tumor_09

description: Bladder cancer

value: muscle invasive I


title: Rat_liver_HW_100_TCDD_384_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 384 hour exposure

value: 384 hours


title: Rat_liver_HW_Corn_oil_96_hours_rep_4 [NanoString]

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 96 hour exposure

value: Corn Oil vehicle


title: Rat_liver_HW_Corn_oil_96_hours_rep_5 [NanoString]

description: Control


title: Bladder cancer tumor_06

description: Bladder cancer

value: muscle invasive III


title: Liver 11

value: m

value: animals with low agressiveness


title: Liver 9

value: high


title: ILC2_TSLP_24 hour_rep1

description:
SAM3461536
Human ILC2 cells treated with TSLP for 24 hours.

value: TSLP

extract_protocol: Stratagene Universal Human Reference RNA (catalog number 740000).

value: reference


title: ILC2_IL-33 IL-25_24 hour_rep4

description:
SAM3461535
Human ILC2 cells treated with IL-33/IL-25 for 24 hours.


title: Bladder cancer tumor_04

description: Bladder cancer

value: primary bladder urothelial cell carcinoma tumor

value: muscle non-invasive I


title: Liver 10

value: German Landrace


title: Rat_liver_HW_Corn_oil_96_hours_rep_3 [NanoString]

description: Control

value: Male

value: Liver


title: Bladder cancer tumor_05

description: Bladder cancer


title: Bladder cancer tumor_03

description: Bladder cancer

value: muscle non-invasive II


title: ILC2_IL-33 IL-25_24 hour_rep1

description:
SAM3461532
Human ILC2 cells treated with IL-33/IL-25 for 24 hours.

value: ILC2 (Lineage negative, CRTH2+, CD161+, CD127+)

value: 24 hours


title: Bladder cancer tumor_01

description: Bladder cancer


title: Liver 7

value: f


title: Rat_liver_HW_Corn_oil_96_hours_rep_1 [NanoString]

description: Control

value: Han/Wistar

value: 10-12 weeks

value: 96 hours


title: Bladder cancer tumor_02

description: Bladder cancer


title: ILC2_IL-33_24 hour_rep4

description:
SAM3461531
Human ILC2 cells treated with IL-33 for 24 hours.

source_name: ILC2 cells, IL-33, 24 hr


title: ILC2_IL-33 IL-25_24 hour_rep2

description:
SAM3461533
Human ILC2 cells treated with IL-33/IL-25 for 24 hours.


title: Liver 8

value: m

value: animals with high agressiveness


title: ILC2_IL-33_24 hour_rep3

description:
SAM3461530
Human ILC2 cells treated with IL-33 for 24 hours.


title: ILC2_IL-33_24 hour_rep1

description:
SAM3461528
Human ILC2 cells treated with IL-33 for 24 hours.


title: Rat_liver_HW_Corn_oil_96_hours_rep_2 [NanoString]

description: Control

value: Corn Oil vehicle


title: Rat_liver_HW_3000_TCDD_19_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 3000 TCDD, 19 hour exposure

value: 19 hours


title: ILC2_IL-33_24 hour_rep2

description:
SAM3461529
Human ILC2 cells treated with IL-33 for 24 hours.

value: reference


title: Liver 5

value: low

value: animals with low agressiveness


title: Rat_liver_HW_3000_TCDD_19_hours_rep_3 [NanoString]

description: Treated


title: Liver 6

value: German Landrace


title: Rat_liver_HW_3000_TCDD_19_hours_rep_2 [NanoString]

description: Treated

value: Male


title: Liver 2


title: Liver 3


title: Normal bladder mucosa normal_02

description: Normal bladder mucosa

source_name: Biopsy specimen from normal bladder mucosa

value: bladder mucosa

value: Normal bladder mucosa


title: Rat_liver_HW_3000_TCDD_19_hours_rep_1 [NanoString]

description: Treated

value: Liver


title: ILC2_IL-25_24 hour_rep2

description:
SAM3461525
Human ILC2 cells treated with IL-25 for 24 hours.

source_name: ILC2 cells, IL-25, 24 hr

value: ILC2 (Lineage negative, CRTH2+, CD161+, CD127+)

value: 24 hours


title: Normal bladder mucosa normal_01

description: Normal bladder mucosa


title: Liver 4


title: Normal bladder mucosa normal_03

description: Normal bladder mucosa


title: Rat_liver_HW_1000_TCDD_19_hours_rep_3 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 1000 TCDD, 19 hour exposure

value: Han/Wistar


title: ILC2_IL-25_24 hour_rep4

description:
SAM3461527
Human ILC2 cells treated with IL-25 for 24 hours.


title: Rat_liver_HW_1000_TCDD_19_hours_rep_4 [NanoString]

description: Treated

value: 10-12 weeks


title: Liver 1

value: f


title: Rat_liver_HW_1000_TCDD_19_hours_rep_2 [NanoString]

description: Treated


title: Rat_liver_HW_1000_TCDD_19_hours_rep_1 [NanoString]

description: Treated


title: Rat_liver_HW_100_TCDD_19_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 19 hour exposure

value: 100 ug/kg


title: ILC2_IL-25_24 hour_rep1

description:
SAM3461524
Human ILC2 cells treated with IL-25 for 24 hours.


title: ILC2_IL-25_24 hour_rep3

description:
SAM3461526
Human ILC2 cells treated with IL-25 for 24 hours.


title: ILC2_Media_24 hour_rep4

description:
SAM3461523
Human ILC2 cells treated with media for 24 hours.

source_name: ILC2 cells, media, 24 hr

value: media


title: Rat_liver_HW_100_TCDD_19_hours_rep_3 [NanoString]

description: Treated


title: Sabre_PBMC_15

description: Gene expression data from PBMC sample of adults

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Leukocytes

tag: status of aggressiveness

value: m


title: Rat_liver_HW_100_TCDD_19_hours_rep_2 [NanoString]

description: Treated

tag: gender

value: 19 hours


title: Sabre_PBMC_13

value: high


title: ILC2_Media_24 hour_rep3

description:
SAM3461522
Human ILC2 cells treated with media for 24 hours.

value: reference


title: ILC2_IL-33 IL-25_6 hour_rep5

description:
SAM798420
Human ILC2 cells treated with IL-33/IL-25 for 6 hours.

source_name: ILC2 cells, IL-33/IL-25, 6 hr

value: 6 hours


title: Rat_liver_HW_10_TCDD_19_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 10 TCDD, 19 hour exposure

tag: tissue

value: 10 ug/kg