title: culturedpodocyte_PBS

status: Public on May 31 2015

type: RNA

city: Kyoto

first: Kenichi

last: Koga

address: 54 Syogoin Kawahara-cho

department: Department of Nephrology, Kyoto University Graduate School of Medicine

country: Japan

institute: Kyoto University

description: Gene expression at 24hr after PBS treatment

hyb_protocol: The dyied Cy3-labelled cRNA was Resuspended in 18 μL of nuclease-free water, 4.5 μL of the 10X GE Blocking Agent and 22.5 μL of 2x Hi-RPM Hybridization Buffer was added following the manufacturer’s instructions. After the sample was incubated at 100°C for 5 minutes, and immediately transfer to an iceed water bath for 5 minutes, and hybridized to Human miRNA Microarray kit 8x15K V2 (Agilent) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediatelyhuman miRNAs.

scan_protocol: Microarrays were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT is set to XDR Hi 100% and XDR Lo 5%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. GeneView files were generated using Agilent's Feature Extraction software version 10.5.1.1. We excluded microRNAs which were not detected and human viral microRNAs.

molecule: total RNA

organism: Homo sapiens

source_name: cultured podocytes, PBS

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng total RNA using the miRNA Complete Labeling and hyb kit (Agilent) according to the manufacturer's instructions.(Agilent Technologies).

growth_protocol: Cells were cultured under growth-permissive conditions at 33°C in RPMI1640 medium (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS; Biowest, Nuaille, France) and insulin–transferrin–selenite supplement (Life Technologies, Carlsbad, CA). For differentiation, podocytes were maintained under non-permissive conditions at 38°C for 14 days prior to the experiments.

extract_protocol: RNA was prepared using mirVana miRNA Isolation Kit (Life Technologies) according to the manufacturer’s instructions. The RNA concentration was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific), and the integrity was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

treatment_protocol: Cells were made quiescent in serum free RPMI1640 medium for 24 h before stimulation with recombinant human 5ng TGF-β1 (R&D Systems, Minneapolis, MN). Cells were harvested at 24 hours after the TGF-b1 stimulation.

tag: cell type

value: immortalized caltured human podocytes


title: culturedpodocyte_TGF-b1

description: Gene expression at 24hr after TGF-b1 treatment

source_name: cultured podocytes, TGF-b1


title: mESC differentiation exposed to THD for 24h, biological rep2 [re-analysis]

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

country: USA

institute: US FDA

description:
Gene expression data after exposure to THD for 24h
mESC-THD-24h-2

hyb_protocol: Hybridization, wash, and staining were carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit on an Affymetrix Fluidics Station 450 following the manufacturer’s protocols.

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000 7G and the image (.DAT) files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software v.4.0 to generate cell intensity (.CEL) files.

data_processing: The values of individual probes belonging to one probe set in .CEL files were summarized using the robust multi-array average (RMA) algorithm embedded in the Expression Console software v.1.3 (Affymetrix), which comprises of convolution background correction, quantile normalization, and median polish summarization.

label: biotin

organism: Mus musculus

source_name: mESC exposed to THD for 24h

label_protocol: The total RNA samples (50 ng each) were labeled using the GeneChip WT PLUS Reagent Kit (Affymetrix) following the manufacturer’s protocol.

growth_protocol: Pluripotent C57BL/6 mouse ESCs were seeded on 0.1% gelatin-coated flasks, and maintained at 37 °C in a 5% CO2 humidified incubator at standard densities (i.e., between 5×104/cm2 and 5×105/cm2) in ESGRO Complete Plus Clonal Grade Medium (EMD Millipore). The medium contains leukemia inhibitory factor (LIF), bone morphogenic protein 4 (BMP-4), and a glycogen synthase kinase-3b inhibitor (GSK3b-I) to help maintain pluripotency and self-renewal of the ESCs. Cells were passaged every 2-3 days (when reaching 60% confluence) with ESGRO Complete Accutase (EMD Millipore) at about 1:6 ratio.

extract_protocol: EBs were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: ESC differentiation cultures were exposed from the EB stage on day 3 for 24, 48 and 72 h to 0.25 mM thalidomide (THD) or vehicle control (0.25% DMSO).

tag: strain

value: embryonic stem cell


title: mESC differentiation exposed to THD for 72h, biological rep2

description:
Gene expression data after exposure to THD for 72h
mESC-THD-72h-2

source_name: mESC exposed to THD for 72h


title: mESC differentiation at 72h, biological rep1 [re-analysis]

description:
Gene expression data during spontaneous differentiation at 72h
mESC-CON-72h-1

source_name: mESC 72h after EB formation


title: mESC differentiation exposed to THD for 72h, biological rep3

description:
Gene expression data after exposure to THD for 72h
mESC-THD-72h-3


title: mESC differentiation exposed to THD for 48h, biological rep1

description:
Gene expression data after exposure to THD for 48h
mESC-THD-48h-1

source_name: mESC exposed to THD for 48h


title: mESC differentiation exposed to THD for 72h, biological rep1

description:
Gene expression data after exposure to THD for 72h
mESC-THD-72h-1


title: mESC differentiation exposed to THD for 48h, biological rep3

description:
Gene expression data after exposure to THD for 48h
mESC-THD-48h-3


title: mESC differentiation exposed to THD for 24h, biological rep3 [re-analysis]

description:
Gene expression data after exposure to THD for 24h
mESC-THD-24h-3


title: mESC differentiation exposed to THD for 48h, biological rep2

description:
Gene expression data after exposure to THD for 48h
mESC-THD-48h-2


title: mESC differentiation at 72h, biological rep2 [re-analysis]

description:
Gene expression data during spontaneous differentiation at 72h
mESC-CON-72h-2


title: mESC differentiation at 48h, biological rep1 [re-analysis]

description:
Gene expression data during spontaneous differentiation at 48h
mESC-CON-48h-1

source_name: mESC 48h after EB formation


title: mESC differentiation exposed to THD for 24h, biological rep1 [re-analysis]

description:
Gene expression data after exposure to THD for 24h
mESC-THD-24h-1


title: mESC differentiation at 72h, biological rep3 [re-analysis]

description:
Gene expression data during spontaneous differentiation at 72h
mESC-CON-72h-3


title: PBMC_OAD15day_Sam3

city: St .Louis

first: Zhongping

last: Xu

state: mo

address: 660s euclide Ave.

department: Surgery

institute: Washington University in St. Louis

hyb_protocol: standard affymetrix protocol

scan_protocol: scanning were performed according to standard protocols provide by Affymetrix

data_processing:
Please note that only mice microRNA were included in the analysis (1033 data rows).  Normalization and statistical analysis were performed with Partek Genomic Suite 6.6 software by means of Multi-Array Analysis (RMA) algorithm and ANOVA test. Fold-change (FC) and p-values were applied to generate miRNA differentially expressed lists
Genes were retained for further analyses if FDR < 5%

label: Cy3, Cy5

label_protocol: standard affymetrix protocol

extract_protocol: PBMC cells were separated from patient blood samples using the Ficoll method (Amersham). Total RNA of PBMC cells was isolated using mirVana miRNA isolation kit according to the manufacturer’s directions (Ambion).

tag: strain background

tag: treated with

value: Anti-H2Kb Abs for 15 days

tag: sample group

value: obliterative airway disease (OAD) mice

value: PBMCs


title: mESC differentiation at 24h, biological rep3 [re-analysis]

description:
Gene expression data during spontaneous differentiation at 24h
mESC-CON-24h-3

source_name: mESC 24h after EB formation


title: GBM8 cells transfected with anti-sense 2'-O-MOE - PO oligonucleotide to microRNA 10b, biological replicate 2

city: Boston

first: Nadiya

middle: M.

last: Teplyuk

state: MA

address: 77 Avenue Louis Pasteur, HIM610

department: Neurology

institute: Brigham and Womens Hospital

description:
Gene expression data from GBM8 cells transfected with anti-sense 2'-MOE - PO oligonucleotide to microRNA 10b
Treatment GBM8 replicate2

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

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

data_processing: Microarray data were background-adjusted, quantile normalized and summarized using the GC Robust Multiarray Average (GCRMA) method using R (www.r-project.org) and the Bioconductor (www.bioconductor.org) package gcrma.

source_name: Glioblastoma stem-like cells neurospheres culture GBM8

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

growth_protocol: Glioblastoma neurospheres were cultured in Neurobasal media supplemented with 3 mmol/L L-Glutamine, 1X B27 serum free supplement (Life Technologies), 0.5X N2 serum free supplement (Life Technologies), 2 ug/ mL heparin, 20 ng/mL recombinant human FGF2 and 20 ng/ mL recombinant human EGF

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

treatment_protocol: Neurospheres were dissociated to single cells using NeuroCult Chemical Dissociation kit (Stem Cell Technologies) and immediately transfected with 50 nM microRNA 10b antisense oligonucleotide (2'-O-MOE, with phosphate backbone), or control (non-specific) oligonucleotide of the same chemistry using Lipofectamine 2000 transfection reagent (Life Technologies). Cells were collected 24h after transfection.

tag: cell culture

tag: genotype

value: PDGFRA and MDM2 amplification, CDKN2A&B deletion

tag: treatment

value: miR-10b antisense oligonucleotide


title: mESC differentiation at 48h, biological rep2 [re-analysis]

description:
Gene expression data during spontaneous differentiation at 48h
mESC-CON-48h-2


title: GBM8 cells transfected with control oligonucleotide biological replicate 2

description:
Gene expression data from GBM8 cells transfected with control oligonucleotide
Control1 GBM8 replicate2

value: non-specific control (control 1)


title: GBM8 cells transfected with anti-sense 2'-O-MOE - PO oligonucleotide to microRNA 10b, biological replicate 1

description:
Gene expression data from GBM8 cells transfected with anti-sense 2'-MOE - PO oligonucleotide to microRNA 10b
Treatment GBM8 replicate1


title: GBM8 cells treated with Lipofectamine 2000, biological replicate 2

description:
Gene expression data from GBM8 cells treated with Lipofectamine 2000
Control2 GBM8 replicate2

value: transfection reagent alone (control 2)


title: mESC differentiation at 48h, biological rep3 [re-analysis]

description:
Gene expression data during spontaneous differentiation at 48h
mESC-CON-48h-3


title: mESC differentiation at 24h, biological rep2 [re-analysis]

description:
Gene expression data during spontaneous differentiation at 24h
mESC-CON-24h-2


title: GBM6 cells transfected with anti-sense 2'-O-MOE - PO oligonucleotide to microRNA 10b, biological replicate 2

description:
Gene expression data from GBM6 cells transfected with anti-sense 2'-MOE - PO oligonucleotide to microRNA 10b
Treatment GBM6 replicate2

source_name: Glioblastoma stem-like cells neurospheres culture GBM6

value: EGFR and MDM4 amplification, CDKN2A&B deletion


title: GBM8 cells transfected with control oligonucleotide biological replicate 1

description:
Gene expression data from GBM8 cells transfected with control oligonucleotide
Control1 GBM8 replicate1


title: GBM8 cells treated with Lipofectamine 2000, biological replicate 1

description:
Gene expression data from GBM8 cells treated with Lipofectamine 2000
Control2 GBM8 replicate1


title: PBMC_OAD15day_Sam2


title: mESC differentiation at 24h, biological rep1 [re-analysis]

description:
Gene expression data during spontaneous differentiation at 24h
mESC-CON-24h-1


title: PBMC_Iso15day_Sam1

value: Isotype Abs for 15 days

value: control mice


title: PBMC_Iso15day_Sam2


title: PBMC_OAD15day_Sam1


title: PBMC_Iso15day_Sam3


title: PBMC_OAD7day_Sam1

value: Anti-H2Kb Abs for 7 days


title: PBMC_OAD7day_Sam3


title: PBMC_OAD7day_Sam2


title: aorta of EC-DicerWT mice Replicate 3

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

description:
Biological replicate 3 of 3. (Dicer wildtype group)
EC-DicerWT 3

data_processing: Taqman low density arrays were run on the 7900 HT Sequence Detection system.  The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software.  Automatic baseline and manual CTs were calculated with the RQ Manager Software for all samples. Statistical analysis: The global data set of miRs from card A and B was used for analysis. Data were calculated using Real Time StatMiner Tools [Integromics. http://www.integromics.com/StatMiner.php].  Input data for analysis consisted of all samples. CT values were normalized to the most stable endogenous controls (snoRNA202, snoRNA135, snoRNA429 and MammU6 for Card A and B) according to the Genorm algorithm.

label: FAM

source_name: aorta, HFD for 4 weeks

extract_protocol: mirVana miRNA Isolation Kit, see http://www.ambion.com/catalog/CatNum.php?1560

tag: age

value: 6-8 weeks

tag: gender

value: male

tag: protocol

value: HFD for 4 weeks

tag: tissue

value: aorta


title: GBM6 cells transfected with control oligonucleotide biological replicate 1

description:
Gene expression data from GBM6 cells transfected with control oligonucleotide
Control1 GBM6 replicate1


title: sample 3 in 1 day group

city: Beijing

first: Jun

last: Tian

address: No.2 Anzhen Road, Chaoyang District

department: Department of Otolaryngology Head & Neck Surgery

country: China

institute: Beijing Anzhen Hospital, Capital Medical University

hyb_protocol: MOA v2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: The arrays were scanned by Agilent G2505C scanner with Agilent 0.1 XDR setting  (635nm power 100; 532nm power 10) and quantify the fluoresence intensity by GenePix Pro 4.1.1.44 (Molecular Device).

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: olfactory mucosa

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion am1753).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: In the study presented here,27 wild-type, 6- to 8-week-old, male C57BL/6 mice were randomly divided into three groups, and were respectively injected with dexamethasone daily for 2 weeks (WK2) (intraperitoneally, 1mg/kg), with saline only for 2 weeks as control group (Ctrl) and with dexamethasone for one day as short term group (D1) (n=9/group).

value: olfactory mucosa

tag: agent

value: dexamethasone

tag: time point

value: 1 day

value: 6- to 8-week-old


title: GBM6 cells treated with Lipofectamine 2000, biological replicate 2

description:
Gene expression data from GBM6 cells treated with Lipofectamine 2000
Control2 GBM6 replicate2


title: PBMC_Iso7day_Sam3

value: Isotype Abs for 7 days

value: PBMCs


title: GBM6 cells transfected with control oligonucleotide biological replicate 2

description:
Gene expression data from GBM6 cells transfected with control oligonucleotide
Control1 GBM6 replicate2


title: sample 1 in 2 week group

value: 2 weeks


title: sample 2 in 1 day group


title: aorta of EC-DicerWT mice Replicate 1

description:
Biological replicate 1 of 3. (Dicer wildtype group)
EC-DicerWT 1


title: aorta of EC-DicerWT mice Replicate 2

description:
Biological replicate 2 of 3.(Dicer wildtype group)
EC-DicerWT 2


title: GBM4 cells treated with Lipofectamine 2000, biological replicate 1

description:
Gene expression data from GBM4 cells treated with Lipofectamine 2000
Control2 GBM4 replicate1

source_name: Glioblastoma stem-like cells neurospheres culture GBM4

value: C-MYC amplification


title: GBM6 cells transfected with anti-sense 2'-O-MOE - PO oligonucleotide to microRNA 10b, biological replicate 1

description:
Gene expression data from GBM6 cells transfected with anti-sense 2'-MOE - PO oligonucleotide to microRNA 10b
Treatment GBM6 replicate1

value: miR-10b antisense oligonucleotide


title: GBM4 cells transfected with anti-sense 2'-O-MOE - PO oligonucleotide to microRNA 10b, biological replicate 2

description:
Gene expression data from GBM4 cells transfected with anti-sense 2'-MOE - PO oligonucleotide to microRNA 10b
Treatment GBM4 replicate2


title: GBM4 cells transfected with anti-sense 2'-O-MOE - PO oligonucleotide to microRNA 10b, biological replicate 1

description:
Gene expression data from GBM4 cells transfected with anti-sense 2'-MOE - PO oligonucleotide to microRNA 10b
Treatment GBM4 replicate1


title: PBMC_Iso7day_Sam2


title: aorta of EC-Dicerflox mice Replicate 2

description:
Biological replicate 2 of 3. (Dicer knockout group)
EC-Dicerflox 2


title: sample 3 in 2 week group


title: sample 1 in control group

value: saline


title: sample 2 in control group


title: sample 1 in 1 day group


title: aorta of EC-Dicerflox mice Replicate 3

description:
Biological replicate 3 of 3. (Dicer knockout group
EC-Dicerflox 3


title: GBM6 cells treated with Lipofectamine 2000, biological replicate 1

description:
Gene expression data from GBM6 cells treated with Lipofectamine 2000
Control2 GBM6 replicate1

value: EGFR and MDM4 amplification, CDKN2A&B deletion

value: transfection reagent alone (control 2)


title: sample 3 in control group


title: GBM4 cells treated with Lipofectamine 2000, biological replicate 2

description:
Gene expression data from GBM4 cells treated with Lipofectamine 2000
Control2 GBM4 replicate2


title: sample 2 in 2 week group


title: aorta of EC-Dicerflox mice Replicate 1

description:
Biological replicate 1 of 3. (Dicer knockout group)
EC-Dicerflox 1


title: PBMC_Iso7day_Sam1

value: control mice


title: aorta of EC-DicerWT mice Replicate 3 (12wks)

source_name: aorta, HFD for 12 weeks

value: 6-8 weeks

value: Female

value: HFD for 12 weeks


title: GBM4 cells transfected with control oligonucleotide biological replicate 1

description:
Gene expression data from GBM4 cells transfected with control oligonucleotide
Control1 GBM4 replicate1

value: non-specific control (control 1)


title: GBM4 cells transfected with control oligonucleotide biological replicate 2

description:
Gene expression data from GBM4 cells transfected with control oligonucleotide
Control1 GBM4 replicate2


title: aorta of EC-Dicerflox mice Replicate 3 (12wks)

value: aorta


title: aorta of EC-DicerWT mice Replicate 1 (12wks)


title: aorta of EC-DicerWT mice Replicate 2 (12wks)

description:
Biological replicate 2 of 3. (Dicer wildtype group)
EC-DicerWT 2


title: ppGpp_R1_OD1

type: mixed

city: Norwich

first: Arthur

last: Thompson

address: Colney Lane

country: United Kingdom

institute: Institute of Food Research

description: Biol. Rep. 1 of 3

hyb_protocol: Hybridisation according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: GenePix 4000A at 10µm resolution

data_processing: Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated usiong BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centering was subsequently performed using the block median

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 1_optical density (600 nm) of 1.0

label_protocol: Labelling according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

growth_protocol: Grown aerobically at 370C with shaking at 250rpm in minimal medium MM5.8 (Erikkson et al., 2006 Inf & Imm., 74:1243) to stationary phase overnight

extract_protocol: RNA extracted according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

treatment_protocol: Where appropriate 1µm cortisol added.

molecule: genomic DNA

source_name: S. Typhimurium SL1344 genomic DNA


title: aorta of EC-Dicerflox mice Replicate 1 (12wks)


title: aorta of EC-Dicerflox mice Replicate 2 (12wks)


title: ppGpp_R2_OD23

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 2_optical density (600 nm) of 2.3


title: ppGpp_R1_OD23

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 1_optical density (600 nm) of 2.3


title: ppGpp_R1_OD30

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 1_optical density (600 nm) of 3.0


title: ppGpp_R2_OD1

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 2_optical density (600 nm) of 1.0


title: ppGpp_R1_OD42

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 1_optical density (600 nm) of 4.2


title: LSP_dksA_PLUS_R2_ChIP

type: genomic

description: Biol. Rep. 2 of 3

hyb_protocol: Hybridisation according to Erikkson et al., 2006 Inf & Immun, 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: GenePix 4000A at 5µm resolution

data_processing: Intensity ratio's of channel 1 (immunoppt labelled DNA fragments) divided by channel 2 (reference gDNA) signals calculated using GenePix 4000A

label: Cy5 dCTP

source_name: SL1344 ΔdksA strain grown to LSP (OD600 = 4.2) and ChIP-chip performed plus antibody.

label_protocol: Labelling according to Erikkson et al., 2006 Inf & Immun, 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

growth_protocol: 25 ml LB cultures in 250 ml flasks 37°C shaking @ 250 rpm

extract_protocol: All cultures grown aerobically at 37°C with shaking at 250 rpm in LB to specified OD's. Crosslinking and immunoppt performed as described in Lucchini et al (2007) PLoS Pathog 2(8):e81.DOI:10.1371

treatment_protocol: Plus antibody to beta subunit of RNA polymerase

tag: antibody

value: RNAP beta subunit (Neoclone, cat # WP023)

label: Cy3 dCTP

source_name: Genomic DNA from S. Typhimurium SL1344

treatment_protocol: gDNA labelled with Cy5 dCTP


title: LSP_dksA_PLUS_R1_ChIP

description: Biol. Rep. 1 of 3


title: Mock_48h

city: Yokohama

first: Juliane

middle: Karine

last: Ishida

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

institute: RIKEN

description: Design number of Microarray slide: 253416810002

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent technologies, Santa Clara CA / US). 0.6 µg Cy3-labeled fragmented cRNA in hybridization buffer were hybridized overnight (65°C) to customized Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven. After hybridization, microarrays were washed with Agilent Gene Expression Wash Buffer 1 (1 min, room temperature) without agilation followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (1 min, 37°C) with agitation.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies)

data_processing: The Agilent Feature Extraction Software (v 10.7.3) was used to read out and process the microarray image files. Normalization of signal intensities from the single-experiment raw data lists were done in GeneSpring version 11  by dividing the intensity values by their median with percentage shift set as 75%.

label: Cyanine 3-labeling

organism: Phtheirospermum japonicum

source_name: Mock-treated roots for 48 h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 µg RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) (5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (Thermo Scientific).

growth_protocol: Sterilized seed coat of Phtheirospermum japonicum was germinated in vitro after a vernalization period of 1 day at 4C (in darkness) and 2 days at 26C (darkness). Seedlings were kept growing vertically under photoperiod of 26C 16 h light/8 h dark for 2 weeks

extract_protocol: Total RNA was extracted using LiCl-based protocol as described in Ishida et al 2015

treatment_protocol: 2-week-old P. japonicum roots were covered with 7 ml solution of Haustorium-inducer 2,6-dimethoxy-p-benzoquinone (DMBQ) with 10 µM and kept horizontally covered with alluminium foil for 0, 0.5, 1, 3, 6, 12, 24 and 48 h. Mock samples were treated with solution with equal amount of DMSO, which was the solvent used to dissolve DMBQ chemical.

value: Root

tag: treatment time-point (h)

value: 2 weeks old


title: LSP_ppGpp0_PLUS_R3_ChIP

description: Biol. Rep. 3 of 3

source_name: SL1344 ΔrelAΔspoT (ppGpp0) strain grown to LSP (OD600 = 4.2) and ChIP-chip performed plus antibody.


title: LSP_dksA_MINUS_R1_ChIP

description: Biol. Rep. 1 of 3

source_name: SL1344 ΔdksA strain grown to LSP (OD600 = 4.2) and ChIP-chip performed minus antibody.

treatment_protocol: Minus antibody to beta subunit of RNA polymerase


title: LSP_ppGpp0_PLUS_R2_ChIP

description: Biol. Rep. 2 of 3


title: Mock_6h

source_name: Mock-treated roots for 6 h


title: LSP_dksA_PLUS_R3_ChIP

description: Biol. Rep. 3 of 3


title: Mock_1h

source_name: Mock-treated roots for 1 h


title: Mock_24h

source_name: Mock-treated roots for 24 h


title: Mock_12h

source_name: Mock-treated roots for 12 h


title: Mock_3h

source_name: Mock-treated roots for 3 h


title: ppGpp_R2_OD42

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 2_optical density (600 nm) of 4.2


title: DMBQ_24h_rep3

source_name: DMBQ-treated roots for 24 h (3rd Biological Replicate)


title: ppGpp_R3_OD1

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 3_optical density (600 nm) of 1.0

source_name: S. Typhimurium SL1344 genomic DNA


title: LSP_ppGpp0_MINUS_R2_ChIP

description: Biol. Rep. 2 of 3

source_name: SL1344 ΔrelAΔspoT (ppGpp0) strain grown to LSP (OD600 = 4.2) and ChIP-chip performed minus antibody.


title: Mock_0h

source_name: Mock-treated roots for 0 h


title: ppGpp_R3_OD23

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 3_optical density (600 nm) of 2.3


title: LSP_ppGpp0_MINUS_R1_ChIP

description: Biol. Rep. 1 of 3


title: DMBQ_12h_rep3

source_name: DMBQ-treated roots for 12 h (3rd Biological Replicate)


title: DMBQ_48h_rep3

source_name: DMBQ-treated roots for 48 h (3rd Biological Replicate)


title: DMBQ_3h_rep3

source_name: DMBQ-treated roots for 3 h (3rd Biological Replicate)


title: ppGpp_R2_OD30

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 2_optical density (600 nm) of 3.0


title: Mock_30min

source_name: Mock-treated roots for 0.5 h


title: LSP_ppGpp0_MINUS_R3_ChIP

description: Biol. Rep. 3 of 3

source_name: Genomic DNA from S. Typhimurium SL1344


title: LSP_ppGpp0_PLUS_R1_ChIP

description: Biol. Rep. 1 of 3

source_name: SL1344 ΔrelAΔspoT (ppGpp0) strain grown to LSP (OD600 = 4.2) and ChIP-chip performed plus antibody.


title: ppGpp_R3_OD30

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 3_optical density (600 nm) of 3.0


title: DMBQ_24h_rep2

description: Design number of Microarray slide: 253261110001

source_name: DMBQ-treated roots for 24 h (2nd Biological Replicate)


title: DMBQ_1h_rep3

source_name: DMBQ-treated roots for 1 h (3rd Biological Replicate)


title: DMBQ_30min_rep3

source_name: DMBQ-treated roots for 0.5 h (3rd Biological Replicate)


title: ppGpp_R3_OD42

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔrelAΔspoT. Biol. Rep. 3_optical density (600 nm) of 4.2


title: DMBQ_6h_rep3

source_name: DMBQ-treated roots for 6 h (3rd Biological Replicate)


title: DMBQ_48h_rep2

source_name: DMBQ-treated roots for 48 h (2nd Biological Replicate)


title: ppGpp_rpoS_R1_OD42

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔrelAΔspoTΔrpoS. Biol. Rep. 1_optical density (600 nm) of 4.2

source_name: S. Typhimurium SL1344 genomic DNA


title: ppGpp_rpoS_R2_OD42

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔrelAΔspoTΔrpoS. Biol. Rep. 2_optical density (600 nm) of 4.2


title: LSP_WT_MINUS_R3_ChIP

description: Biol. Rep. 3 of 3

source_name: SL1344 parent strain grown to LSP (OD600 = 4.2) and ChIP-chip performed minus antibody.


title: LSP_WT_PLUS_R2_ChIP

description: Biol. Rep. 2 of 3

source_name: SL1344 parent strain grown to LSP (OD600 = 4.2) and ChIP-chip performed plus antibody.


title: ppGpp_rpoS_R3_OD42

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔrelAΔspoTΔrpoS. Biol. Rep. 3_optical density (600 nm) of 4.2


title: DMBQ_0h_rep3

source_name: DMBQ-treated roots for 0 h (3rd Biological Replicate)


title: LSP_WT_PLUS_R3_ChIP

description: Biol. Rep. 3 of 3


title: DMBQ_12h_rep2

source_name: DMBQ-treated roots for 12 h (2nd Biological Replicate)


title: rpoS_R1_OD23

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔrpoS. Biol. Rep. 1_optical density (600 nm) of 2.3


title: DMBQ_0h_rep2

source_name: DMBQ-treated roots for 0 h (2nd Biological Replicate)


title: LSP_WT_MINUS_R2_ChIP

description: Biol. Rep. 2 of 3

source_name: Genomic DNA from S. Typhimurium SL1344


title: DMBQ_6h_rep2

source_name: DMBQ-treated roots for 6 h (2nd Biological Replicate)


title: DMBQ_3h_rep2

source_name: DMBQ-treated roots for 3 h (2nd Biological Replicate)


title: LSP_WT_PLUS_R1_ChIP

description: Biol. Rep. 1 of 3


title: rpoS_R1_OD30

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔrpoS. Biol. Rep. 1_optical density (600 nm) of 3.1


title: DMBQ_30min_rep2

source_name: DMBQ-treated roots for 0.5 h (2nd Biological Replicate)


title: LSP_WT_MINUS_R1_ChIP

description: Biol. Rep. 1 of 3


title: DMBQ_1h_rep2

source_name: DMBQ-treated roots for 1 h (2nd Biological Replicate)


title: DMBQ_12h_rep1

source_name: DMBQ-treated roots for 12 h (1st Biological Replicate)


title: ESP_dksA_PLUS_R2_ChIP

description: Biol. Rep. 2 of 3

source_name: SL1344 ΔdksA strain grown to ESP (OD600 = 2.3) and ChIP-chip performed plus antibody.


title: rpoS_R1_OD42

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔrpoS. Biol. Rep. 1_optical density (600 nm) of 4.2

source_name: S. Typhimurium SL1344 genomic DNA


title: rpoS_R2_OD23

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔrpoS. Biol. Rep. 2_optical density (600 nm) of 2.3


title: ArthrospiraPCC8005_P3_1600Gy_CTR_T5H

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

hyb_protocol: cDNA library preparation and amplification were performed from 25 ng total RNA, from three independent irradiated and control samples per test condition (n=3), using the Complete Whole Transcriptome Amplification WTA2 kit (Sigma-Aldrich), according to the instructions of the manufacturer, with 17 cycles of amplification, resulting in microgram quantities of cDNA. Labelling and hybridization of the cDNA onto the microarray, were performed according to Roche-Nimblegen expression guide v5p1. For each sample, 1 µg cDNA was labelled by Cy3 nonamers primers and Klenow polymerization.

scan_protocol: The arrays were washed and scanned in a Roche-Nimblegen MS 200 scanner. Raw data files (Pair and XYS files) were obtained from images using DEVA software (Roche-Nimblegen).

data_processing: Raw data were pre-processed using the “Oligo” package (version 1.24) in BioConductor (version 2.12 / R version 3.0.1) as follows: i) background correction based on the Robust Multichip Aver-age (RMA) convolution model (Irizarry et al., 2003), ii) quantile normalization to make expression values from different arrays more comparable (Bolstad et al., 2003), and iii) summarization of multiple probe intensities for each probe set to one expression value per gene using the median polish approach (Irizarry et al., 2003). To test for differential expression between the different irradiated conditions and the reference conditions (no irradiation) the Bayesian adjusted t-statistics was used as implemented in the “LIMMA” package (version 2.18.0)(Smyth, 2004). P-values were corrected for multiple testing using the Benjamini and Hochberg’s method to control the false discovery rate (Benjamini & Hochberg, 1995). Transcripts were considered significantly differentially expressed when the corresponding adjusted p-value was lower than 0.05 and their absolute FC was equal or larger than 2 for upregulated genes, and equal or miner than 0.5 for the down regulated ones. Gene annotation was curated manually.

organism: Limnospira indica PCC 8005

source_name: Arthrospira sp. PCC8005 control condition non-irradiated - timepoint 5 hour

growth_protocol: The strain of Arthrospira sp. PCC 8005 was obtained from Pasteur Culture Collection. Three independent lab cultures (three biological replicates, n=3) were propagated and used separately for irradiation. They were grown aerobically in 1000 ml Zarrouk medium-UBP in 2000 ml Erlenmeyer on a rotatory shaker 120 rpm in an incubator at 30°C illuminated with a photon flux density of ~ 42 µE m -2 s-1 provided by three Osram daylight tubes (Binder KBW 400), to mid-exponential growth phase corresponding to an optical density of OD750 ~1.

extract_protocol: Thirty ml of all irradiated and control Arthrospira cultures (at OD750 ~1), including three independent biological replicates per test condition, were centrifuged (20 min at 10000 g, at 4°C) (Beckman Coulter (Avanti J- 26XP). Cell pellets were flash frozen in liquid nitrogen then immediately stored at -80°C, until analysis (ca. 5 days). Cells resuspended in 750 µl RNA wiz (Ambion), were disrupted mechanically (bead beaten) using Zirconia Beads for 10 min, at room temperature using a vortex adapter (Mo Bio 13000-V1). Next, the released RNA was separated from the cell debris by centrifugation (Eppendorf 5418R) at (10000 g, 10 min, 4°C). RNA purification was performed using the RiboPure™-Bacteria Kit (Ambion) following the manufacturer's instructions. Ribopure kit doesn’t allow the collection of small RNA (e.g 5S ribosomal RNAs and tRNAs), hence the flow throughout collected form purification with Ribopure kit was further eluted with Directzol RNA mimiprep 2050 (Zymosearch) to recover the small RNAs. The two resulted, RNA (Ripopure kit and Direct-Zol kit) were both combined for microarray analysis. This extraction method was found to yield sufficient quantity and superior quality of RNA, compared to the method based on heat shock lysis and hot Trizol (Invitrogen) extraction and Direct-zol RNA miniprep 2050 (Zymosearch) purification which we used previously (Badri et al). RNA samples (ca. 150 µg per 30ml culture) were then treated with DNAse (TURBO DNA-free™, Ambion) 30 min at 37°C following the manufacturer's instructions to remove DNA. Finally, the RNA was concentrated using RNA Clean & Concentrator™-25 (Zymosearch). RNA quantity and purity was assessed by spectrophotometric analysis using NanoDrop ND-1000 Spectrophotometer (Thermo scientific). The quality and integrity of RNA was assessed using the Bioanalyzer 2100 (Agilent) according to manufacturer's instructions. RNA selected for microarray had integrity number “RIN value” above 7.

treatment_protocol: Each of the 3 separate 1000 ml culture was then divided in three aliquots (ca. 300 ml each) into 3 different flasks (CELLSTAR® Filter Cap Cell; 500 ml Cell Culture Flasks) to be used for the 3 different irradiation experiments (3 doses : 800 Gy, 1600 Gy and 3200 Gy). Each of those 3 flasks (300ml each), were further divided into 2 (ca. 150 ml each), to separate samples for irradiation and for non-irradiated controls. Thus for each irradiation dose, three independent cultures were irradiated, and in parallel of each culture a non-irradiated sample was kept. Irradiation was done on aerobic liquid cultures, containing active planktonic filaments suspended in 144 ml liquid Zarrouk-UBP medium, in plastic culture flasks (CELLSTAR® Filter Cap Cell; 500 ml Cell Culture Flasks). The irradiation was performed using BRIGITTE facility at the Belgian Reactor N°2 (BR2). The irradiation was done inside a closed canister under water, surrounded by 60Co gamma rays sources (Energy of 1.33 Mev and 1.17 Mev). Different doses of gamma rays were given, i.e. 800 Gy, 1600 Gy and 3200 Gy, at a constant dose rate of 20000 Gy h-1. The time required for irradiation was dose-dependent, i.e. 2.4 minutes for 800 Gy, 4.8 minutes for 1600 Gy and 9.6 minutes for 3200 Gy. During irradiation, the cultures were in the dark, and the temperature inside the irradiation canister was automatically monitored and ranged between 26-27°C. In parallel, three other cultures were maintained at the same conditions but outside the irradiation facility, as non-irradiated controls. For each sample, part of the sample was fixed or analysed immediately (i.e. within 1 hour) after irradiation (0H). Another part of the sample was put back into the incubator (at the same conditions as cited above) after irradiation for recovery and were harvested 2H and 5H after irradiation.

tag: dose of gamma rays

tag: time

value: 5 h


title: DMBQ_30min_rep1

source_name: DMBQ-treated roots for 0.5 h (1st Biological Replicate)


title: DMBQ_1h_rep1

source_name: DMBQ-treated roots for 1 h (1st Biological Replicate)


title: DMBQ_48h_rep1

source_name: DMBQ-treated roots for 48 h (1st Biological Replicate)


title: DMBQ_6h_rep1

source_name: DMBQ-treated roots for 6 h (1st Biological Replicate)


title: DMBQ_3h_rep1

source_name: DMBQ-treated roots for 3 h (1st Biological Replicate)


title: ESP_dksA_MINUS_R2_ChIP

description: Biol. Rep. 2 of 3

source_name: SL1344 ΔdksA strain grown to ESP (OD600 = 2.3) and ChIP-chip performed minus antibody.

tag: strain

source_name: Genomic DNA from S. Typhimurium SL1344


title: ESP_dksA_MINUS_R3_ChIP

description: Biol. Rep. 3 of 3


title: DMBQ_24h_rep1

source_name: DMBQ-treated roots for 24 h (1st Biological Replicate)


title: ESP_dksA_PLUS_R3_ChIP

description: Biol. Rep. 3 of 3


title: ArthrospiraPCC8005_P3_3200Gy_IR_T2H

source_name: Arthrospira sp. PCC8005 irradiated with 3200Gy - timepoint 2 hour

label_protocol: cDNA library preparation and amplification were performed from 25 ng total RNA, from three independent irradiated and control samples per test condition (n=3), using the Complete Whole Transcriptome Amplification WTA2 kit (Sigma-Aldrich), according to the instructions of the manufacturer, with 17 cycles of amplification, resulting in microgram quantities of cDNA. Labelling and hybridization of the cDNA onto the microarray, were performed according to Roche-Nimblegen expression guide v5p1. For each sample, 1 µg cDNA was labelled by Cy3 nonamers primers and Klenow polymerization.

value: 2 h


title: rpoS_R3_OD1

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔrpoS. Biol. Rep. 3_optical density (600 nm) of 1.0


title: rpoS_R2_OD42

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔrpoS. Biol. Rep. 2_optical density (600 nm) of 4.2


title: ArthrospiraPCC8005_P3_800Gy_IR_T2H

source_name: Arthrospira sp. PCC8005 irradiated with 800Gy - timepoint 2 hour


title: ArthrospiraPCC8005_P4_1600Gy_IR_T5H

source_name: Arthrospira sp. PCC8005 irradiated with 1600Gy - timepoint 5 hour


title: rpoS_R2_OD30

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔrpoS. Biol. Rep. 2_optical density (600 nm) of 3.0


title: ESP_dksA_PLUS_R1_ChIP

description: Biol. Rep. 1 of 3

source_name: SL1344 ΔdksA strain grown to ESP (OD600 = 2.3) and ChIP-chip performed plus antibody.


title: rpoS_R3_OD30

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔrpoS. Biol. Rep. 3_optical density (600 nm) of 3.0_optical density (600 nm) of 3.0

source_name: S. Typhimurium SL1344 genomic DNA


title: ArthrospiraPCC8005_P3_1600Gy_CTR_T0H

source_name: Arthrospira sp. PCC8005 control condition non-irradiated - timepoint 0 hour

value: 0 h


title: ESP_ppGpp0_PLUS_R4

description: Biol. Rep. 4 of 4

source_name: SL1344 ΔrelAΔspoT (ppGpp0) strain grown to ESP (OD600 = 2.3) and ChIP-chip performed plus antibody.


title: ArthrospiraPCC8005_P3_1600Gy_CTR_T2H

source_name: Arthrospira sp. PCC8005 control condition non-irradiated - timepoint 2 hour


title: ArthrospiraPCC8005_P3_1600Gy_IR_T0H

source_name: Arthrospira sp. PCC8005 irradiated with 1600Gy - timepoint 0 hour


title: ESP_ppGpp0_MINUS_R4

description: Biol. Rep. 4 of 4

source_name: SL1344 ΔrelAΔspoT (ppGpp0) strain grown to ESP (OD600 = 2.3) and ChIP-chip performed minus antibody.


title: rpoS_R3_OD42

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔrpoS. Biol. Rep. 3  optical density (600 nm) of 4.2


title: ArthrospiraPCC8005_P3_800Gy_IR_T5H

source_name: Arthrospira sp. PCC8005 irradiated with 800Gy - timepoint 5 hour


title: ArthrospiraPCC8005_P3_1600Gy_IR_T2H

source_name: Arthrospira sp. PCC8005 irradiated with 1600Gy - timepoint 2 hour


title: ESP_ppGpp0_PLUS_R3_ChIP

description: Biol. Rep. 3 of 4

source_name: Genomic DNA from S. Typhimurium SL1344


title: WT_R1_OD1

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium wt. Biol. Rep. 1 optical density (600 nm) of 1.0


title: ESP_dksA_MINUS_R1_ChIP

description: Biol. Rep. 1 of 3

source_name: SL1344 ΔdksA strain grown to ESP (OD600 = 2.3) and ChIP-chip performed minus antibody.


title: ArthrospiraPCC8005_P3_3200Gy_IR_T5H

source_name: Arthrospira sp. PCC8005 irradiated with 3200Gy - timepoint 5 hour


title: ArthrospiraPCC8005_P2_3200Gy_IR_T2H

source_name: Arthrospira sp. PCC8005 irradiated with 3200Gy - timepoint 2 hour


title: ArthrospiraPCC8005_P2_800Gy_CTR_T2H


title: rpoS_R3_OD23

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔrpoS. Biol. Rep. 3_optical density (600 nm) of 2.3


title: WT_R1_OD23

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium wt. Biol. Rep. 1 optical density (600 nm) of 2.3


title: ESP_ppGpp0_MINUS_R3_ChIP

description: Biol. Rep. 3 of 4


title: ArthrospiraPCC8005_P2_800Gy_CTR_T5H

source_name: Arthrospira sp. PCC8005 control condition non-irradiated - timepoint 5 hour


title: WT_R1_OD30

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium wt. Biol. Rep. 1 optical density (600 nm) of 3.0

source_name: S. Typhimurium SL1344 genomic DNA


title: ArthrospiraPCC8005_P3_800Gy_IR_T0H

source_name: Arthrospira sp. PCC8005 irradiated with 800Gy - timepoint 0 hour


title: ArthrospiraPCC8005_P2_800Gy_CTR_T0H

source_name: Arthrospira sp. PCC8005 control condition non-irradiated - timepoint 0 hour


title: ESP_ppGpp0_PLUS_R2_ChIP

description: Biol. Rep. 2 of 4

source_name: SL1344 ΔrelAΔspoT (ppGpp0) strain grown to ESP (OD600 = 2.3) and ChIP-chip performed plus antibody.


title: ArthrospiraPCC8005_P2_1600Gy_IR_T2H


title: WT_R1_OD42

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium wt. Biol. Rep. 1 optical density (600 nm) of 4.2


title: ArthrospiraPCC8005_P2_800Gy_IR_T2H

source_name: Arthrospira sp. PCC8005 irradiated with 800Gy - timepoint 2 hour


title: Metabolic syndrome subject 6 after exercise training

city: Nijmegen

first: Fleur

last: Poelkens

state: Gelderland

address: PO Box 9101

department: Physiology

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

hyb_protocol: According to the Affymetrix GeneChip whole transcript sense target labelling assay

scan_protocol: According to the Affymetrix GeneChip Expression Wash, Stain and Scan User Manual

data_processing: The Affymetrix CEL files were imported into Genomic Suite software (Version 6.4, Partek, St. Louis, MO, USA). Probe sets were normalised using the Robust Multiarray Analysis (RMA) algorithm including background correction for probe GC content. Transcript summaries were calculated using the mean intensities of the corresponding probe sets, representing the quantitative gene expression levels.

source_name: vastus lateralis muscle, metabolic syndrome, 6 months exercise training

growth_protocol: not applicable

extract_protocol: Frozen muscle biopsy samples were ground using a mortar and pestle, placed in RNA-Bee, which contains phenol and guanidine thiocyanate (Tel-test, Friendswood, TX, USA), and homogenised using an T25 ultra-turrax dispenser (IKA, Staufen, Germany). RNA was isolated using phenol/chloroform extraction, and purified according to the RNeasy mini kit clean-up protocol including an on-column DNase digestion (Qiagen, Hilden, Germany). The RNA concentration and purity were measured with a Nanodrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and RNA integrity was analysed on an Agilent Bioanalyser (Santa Clara, CA, USA).

treatment_protocol: Local aneasthesia with 2% (w/v) lidocaine, incision of the skin and fascia, ~100 mg mucle tissue needle biopsy ~15 cm above the knee according to the Bergström technique, immediately frozen in liquid nitrogen and stored at -80°C

value: female

tag: individual

tag: disease state

value: Metabolic syndrome

tag: intervention

value: 6 month guided endurance exercise training program

tag: timepoint

value: after

value: vastus lateralis muscle


title: WT_R2_OD1

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium wt. Biol. Rep. 2 optical density (600 nm) of 1.0


title: ArthrospiraPCC8005_P2_3200Gy_IR_T5H


title: Metabolic syndrome subject 6 before exercise training

source_name: vastus lateralis muscle, metabolic syndrome, baseline

label_protocol: According to the Affymetrix GeneChip whole transcript sense target labelling assay

value: before


title: DMBQ_0h_rep1

source_name: DMBQ-treated roots for 0 h (1st Biological Replicate)


title: ESP_ppGpp0_MINUS_R2_ChIP

description: Biol. Rep. 2 of 4

source_name: SL1344 ΔrelAΔspoT (ppGpp0) strain grown to ESP (OD600 = 2.3) and ChIP-chip performed minus antibody.

source_name: Genomic DNA from S. Typhimurium SL1344


title: WT_R2_OD30

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium wt. Biol. Rep. 2 optical density (600 nm) of 3.0


title: ESP_ppGpp0_MINUS_R1_ChIP

description: Biol. Rep. 1 of 4


title: ESP_WT_PLUS_R3_ChIP

description: Biol. Rep. 3 of 3

source_name: SL1344 parent strain grown to ESP (OD600 = 2.3) and ChIP-chip performed plus antibody.


title: ESP_ppGpp0_PLUS_R1_ChIP

description: Biol. Rep. 1 of 4


title: ArthrospiraPCC8005_P2_1600Gy_IR_T5H

source_name: Arthrospira sp. PCC8005 irradiated with 1600Gy - timepoint 5 hour


title: Metabolic syndrome subject 4 after exercise training


title: Metabolic syndrome subject 5 after exercise training


title: WT_R3_OD23

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium wt. Biol. Rep. 3 optical density (600 nm) of 2.3


title: ArthrospiraPCC8005_P2_3200Gy_IR_T0H

source_name: Arthrospira sp. PCC8005 irradiated with 3200Gy - timepoint 0 hour


title: ArthrospiraPCC8005_P2_1600Gy_IR_T0H

source_name: Arthrospira sp. PCC8005 irradiated with 1600Gy - timepoint 0 hour


title: WT_R2_OD42

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium wt. Biol. Rep. 2  optical density (600 nm) of 4.2

source_name: S. Typhimurium SL1344 genomic DNA


title: Metabolic syndrome subject 4 before exercise training


title: WT_R3_OD30

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium wt. Biol. Rep. 3 optical density (600 nm) of 3.0


title: ESP_WT_PLUS_R2_ChIP

description: Biol. Rep. 2 of 3


title: dksA_R1_OD1

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 1_optical density (600 nm) of 1.0


title: Metabolic syndrome subject 3 after exercise training


title: ESP_WT_MINUS_R3_ChIP

description: Biol. Rep. 3 of 3

source_name: SL1344 parent strain grown to ESP (OD600 = 2.3) and ChIP-chip performed minus antibody.


title: WT_R3_OD42

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium wt. Biol. Rep. 3 optical density (600 nm) of 4.2


title: ESP_WT_MINUS_R2_ChIP

description: Biol. Rep. 2 of 3


title: Metabolic syndrome subject 2 after exercise training

source_name: vastus lateralis muscle, metabolic syndrome, 6 months exercise training


title: Metabolic syndrome subject 3 before exercise training

source_name: vastus lateralis muscle, metabolic syndrome, baseline


title: ArthrospiraPCC8005_P2_800Gy_IR_T5H

source_name: Arthrospira sp. PCC8005 irradiated with 800Gy - timepoint 5 hour


title: Metabolic syndrome subject 2 before exercise training


title: ArthrospiraPCC8005_P1_3200Gy_IR_T2H

source_name: Arthrospira sp. PCC8005 irradiated with 3200Gy - timepoint 2 hour


title: ArthrospiraPCC8005_P1_3200Gy_CTR_T5H

source_name: Arthrospira sp. PCC8005 control condition non-irradiated - timepoint 5 hour


title: ESP_WT_PLUS_R1_ChIP

description: Biol. Rep. 1 of 3

source_name: Genomic DNA from S. Typhimurium SL1344


title: ArthrospiraPCC8005_P2_800Gy_IR_T0H

source_name: Arthrospira sp. PCC8005 irradiated with 800Gy - timepoint 0 hour


title: Moroberekan_pollinated pistils_drought_heat_day1_rep3

city: Potsdam

first: Xia

last: Li

address: Am Mühlenberg 1

institute: Max-Planck-Institute of Molecular Plant Physiology

description: SAMPLE 35

hyb_protocol: Hybridization solution was prepared according to Affymetrix GeneChip Expression Analysis Technical Manual. The final cRNA concentration was 60 ng/µl. Hybridization was performed for 16-18 h at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix). Washing and staining was performed with a fluidics station (GeneChip Fluidics Station 450, Affymetrix), controlled by GCOS v1.4.

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix), controlled by GCOS v1.4.

data_processing: Data filtering on probe intensity level was done using R software (http://www.r-project.org/). Probes with hybridization intensities [(perfect match (PM) - mismatch (MM)] lower than twice the background value were excluded. Additionally, probe sets were only considered for further analysis when more than 25% of the probes showed sufficiently high hybridization intensity. After the second filtering 259,125 probes in 36,512 probe sets (of the original 57,381) were used for expression analysis. A specific CDF file (custom CDF) containing all selected probes was created using ArrayInitiative, and then imported into the Robin software (version 1.3.1). Quality control and normalization were processed with the default RMA (robust multi-array average) method. All statistical analyses using linear models (R packages limma) with nestdF multiple testing and Benjamini-Hochberg P value correction were performed using the Robin software. Gene-level synonymous probesets were grouped according to corresponding gene ID, based on the Affymetrix Rice Annotation File (Release 29, 07/01/09). The expression values of all synonymous groups were then averaged into an overall value for a dataset. Genes with statistically significant differences in transcript level compared to the controls were identified using a false-discovery corrected P-value <0.05 and a two-fold-change filter as cut-off. Gene locus IDs were obtained from the MSU Rice Genome Annotation Project gene set (release RAGP 7) and the Rice Annotation Project Database (RAP-DB), gene function annotation was according to RGAP 7.

organism: Oryza sativa

source_name: Moroberekan pollinated pistils_drought+heat day 1 (75% RWC + 38/21°C)

label_protocol: Biotinylated cRNA were prepared with the MessageAmp™ II-Biotin Enhanced Kit (Ambion, Austin, TX, USA) following the manufacturer’s instructions.

growth_protocol: Pre-germinated seeds of two rice cultivars N22 and Moroberekan were sown in clay loam soil and transplanted to the pot after 14 days. The growth condition maintained at 29/21°C (day/night) and 75-85% RH under natural sunlight condition.

extract_protocol: Total RNA was extracted by Trizol assay according to the manufacturer's instructions.

treatment_protocol: 30 plants of each rice cultivar were exposed to 6 h (0830–1430) of 38°C for consecutive three days, anthers and pollinated stigmas were collected as heat day 3 samples. For combined drought and heat stress, drought stress was initiated from 5 d before heading by monitoring main-tiller flag-leaf relative water content (RWC). Two sets of plants maintained at 60 to 70% RWC during anthesis were exposed to 38°C for one day or three consecutive days as described above, and floral tissues were collected from both the sets of plants to form drought-heat day 1 and day 3, respectively.

tag: cultivar

value: cv. Moroberekan

tag: growth condition

value: drought+heat day 1 (75% RWC + 38/21°C)

value: Pollinated pistils


title: dksA_R1_OD3

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 1_optical density (600 nm) of 3.0


title: ArthrospiraPCC8005_P1_3200Gy_CTR_T2H

source_name: Arthrospira sp. PCC8005 control condition non-irradiated - timepoint 2 hour


title: Metabolic syndrome subject 1 after exercise training


title: dksA_R1_OD36

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 1_optical density (600 nm) of 3.6


title: Moroberekan_pollinated pistils_drought_heat_day1_rep2

description: SAMPLE 34


title: dksA_R1_OD24

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 1_optical density (600 nm) of 2.4


title: Metabolic syndrome subject 1 before exercise training


title: Moroberekan_pollinated pistils_drought_heat_day1_rep1

description: SAMPLE 33


title: ArthrospiraPCC8005_P1_1600Gy_IR_T2H

source_name: Arthrospira sp. PCC8005 irradiated with 1600Gy - timepoint 2 hour


title: VC1 cells_15 uM DMF 6h rep 3

city: Hanover

first: Karen

middle: T

last: Liby

state: NH

address: Remsen Building, Room 524

institute: Dartmouth Medical School

description: FinalReport_B: 9703559097_F

hyb_protocol: Samples were hybridized using the Illumina hyrbridization protocol.

scan_protocol: Samples were scanned using the Illumina scanning protocol.

data_processing: The data were normalized using Robust Spline Normalization and Variance Stabilizing Transformation

source_name: VC1 lung cancer cells

label_protocol: RNA was labelled using the TargetAmpTM-Nano Labelling Kit for Illumina Expression BeadChip kit.

growth_protocol: VC1 lung cancer cells were grown in DMEM media supplemented with 10% FBS and Penicillin-Streptomycin.

extract_protocol: RNA was extracted by Qiagen RNeasy kit.

treatment_protocol: VC1 lung cancer cells were treated with DMSO, 0.05 uM CDDO-Im, 0.1 uM CDDO-Me and 15 uM DMF for 6 hours before RNA was extracted.

value: A/J

value: Female

value: lung adenocarcinoma


title: ArthrospiraPCC8005_P1_3200Gy_CTR_T0H

source_name: Arthrospira sp. PCC8005 control condition non-irradiated - timepoint 0 hour


title: N22_pollinated pistils_drought_heat_day1_rep2

description: SAMPLE 32

source_name: N22 pollinated pistils_drought+heat day 1 (75% RWC + 38/21°C)

value: cv. N22


title: ArthrospiraPCC8005_P1_800Gy_IR_T2H

source_name: Arthrospira sp. PCC8005 irradiated with 800Gy - timepoint 2 hour


title: dksA_R2_OD3

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 2_optical density (600 nm) of 3.0

source_name: S. Typhimurium SL1344 genomic DNA


title: ArthrospiraPCC8005_P1_3200Gy_IR_T5H

source_name: Arthrospira sp. PCC8005 irradiated with 3200Gy - timepoint 5 hour


title: dksA_R2_OD1

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 2_optical density (600 nm) of 1.0


title: dksA_R2_OD36

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 2_optical density (600 nm) of 3.6


title: dksA_R3_OD1

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 3_optical density (600 nm) of 1.0


title: Moroberekan_pollinated pistils_control_rep3

description: SAMPLE 30

source_name: Moroberekan pollinated pistils_control condition (29/21°C)

value: control condition (29/21°C)


title: Moroberekan_pollinated pistils_control_rep2

description: SAMPLE 29


title: dksA_R2_OD24

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 2_optical density (600 nm) of 2.4


title: VC1 cells_0.1 uM Me 6h rep 3

description: FinalReport_B: 9703559097_E


title: ArthrospiraPCC8005_P1_1600Gy_IR_T0H

source_name: Arthrospira sp. PCC8005 irradiated with 1600Gy - timepoint 0 hour


title: dksA_R3_OD24

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 3_optical density (600 nm) of 2.4


title: dksA_R3_OD3

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 3_optical density (600 nm) of 3.0


title: Moroberekan_pollinated pistils_control_rep1

description: SAMPLE 28


title: ArthrospiraPCC8005_P1_800Gy_IR_T5H

source_name: Arthrospira sp. PCC8005 irradiated with 800Gy - timepoint 5 hour

value: 5 h


title: VC1 cells_15 uM DMF 6h rep 1

description: FinalReport_A: 9703881003_D


title: VC1 cells_0.1 uM Me 6h rep 2

description: FinalReport_B: 9703559097_A


title: N22_pollinated pistils_drought_heat_day1_rep1

description: SAMPLE 31


title: VC1 cells_15 uM DMF 6h rep 2

description: FinalReport_B: 9703559097_B


title: VC1 cells_0.05 uM Im 6h rep 3

description: FinalReport_B: 9703559097_D


title: ArthrospiraPCC8005_P1_3200Gy_IR_T0H

source_name: Arthrospira sp. PCC8005 irradiated with 3200Gy - timepoint 0 hour


title: N22_pollinated pistils_control_rep2

description: SAMPLE 26

source_name: N22 pollinated pistils_control condition (29/21°C)


title: ArthrospiraPCC8005_P1_1600Gy_IR_T5H

source_name: Arthrospira sp. PCC8005 irradiated with 1600Gy - timepoint 5 hour


title: ArthrospiraPCC8005_P3_3200Gy_IR_T0H


title: VC1 cells_0.1 uM Me 6h rep 1

description: FinalReport_A: 9703881003_C

source_name: VC1 lung cancer cells


title: N22_pollinated pistils_control_rep3

description: SAMPLE 27


title: ESP_WT_MINUS_R1_ChIP

description: Biol. Rep. 1 of 3

source_name: SL1344 parent strain grown to ESP (OD600 = 2.3) and ChIP-chip performed minus antibody.

source_name: Genomic DNA from S. Typhimurium SL1344


title: ppGpp_dksA_R1_OD42

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium ΔrelAΔspoTΔdksA. Biol. Rep. 1_optical density (600 nm) of 4.2

source_name: S. Typhimurium SL1344 genomic DNA


title: N22_pollinated pistils_control_rep1

description: SAMPLE 25


title: ArthrospiraPCC8005_P1_800Gy_IR_T0H

source_name: Arthrospira sp. PCC8005 irradiated with 800Gy - timepoint 0 hour


title: Moroberekan_anther_heat_day3_rep3

description: SAMPLE 24

source_name: Moroberekan anthers_heat day 3 (38/21°C)

value: heat day 3 (38/21°C)

value: Anther


title: VC1 cells_0.05 uM Im 6h rep 2

description: FinalReport_A: 9703881003_F


title: dksA_R3_OD36

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 3_optical density (600 nm) of 3.6


title: Moroberekan_anther_heat_day3_rep2

description: SAMPLE 23


title: dksA_R4_OD1

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔdksA. Biol. Rep. 4_optical density (600 nm) of 1.0


title: ppGpp_dksA_R3_OD42

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium ΔrelAΔspoTΔdksA. Biol. Rep. 3_optical density (600 nm) of 4.2


title: WT_R4_OD1_dksA

description: Biol. Rep. 4 of 5

source_name: S. Typhimurium Biol. Rep. 4_optical density (600 nm) of 1.0


title: Adipocyte maturating day 18 replicate 3

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

source_name: D18 adipocytes

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

value: day 18

tag: cell type

value: adipocytes

tag: developmental stage

value: Adipocyte maturating

tag: treatment

value: differentiation medium (IBMX), insulin and dexamethasone, and maturation medium containing insulin

tag: cell line

value: NIH 3T3 L1


title: Adipocyte maturating day 14 replicate 3

description: replicate 3

source_name: D14 adipocytes

value: day 14


title: Adipocyte maturating day 10 replicate 3

description: replicate 3

source_name: D10 adipocytes

value: day 10


title: Adipocyte maturating day 8 replicate 3

description: replicate 3

source_name: D8 adipocytes

value: day 8


title: VC1 cells_0.05 uM Im 6h rep 1

description: FinalReport_A: 9703881003_B

tag: gender

tag: tissue


title: N22_anther_heat_day3_rep3

description: SAMPLE 21

source_name: N22 anthers_heat day 3 (38/21°C)


title: VC1 cells_DMSO 6h rep 2

description: FinalReport_A: 9703881003_E


title: ppGpp_dksA_R2_OD42

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium ΔrelAΔspoTΔdksA. Biol. Rep. 2_optical density (600 nm) of 4.2


title: N22_anther_heat_day3_rep2

description: SAMPLE 20


title: Adipocyte differentiating day 4 replicate 3

description: replicate 3

source_name: D4 adipocytes

tag: time point

value: day 4

value: Adipocyte differentiating

value: differentiation medium (IBMX), insulin and dexamethasone


title: VC1 cells_DMSO 6h rep 3

description: FinalReport_B: 9703559097_C

source_name: VC1 lung cancer cells

value: A/J

value: Female

value: lung adenocarcinoma


title: WT_R1_OD1_dksA

description: Biol. Rep. 1 of 5

source_name: S. Typhimurium wt. Biol. Rep. 1_optical density (600 nm) of 1.0


title: WT_R5_OD1_dksA

description: Biol. Rep. 5 of 5

source_name: S. Typhimurium Biol. Rep. 5_optical density (600 nm) of 1.0


title: Adipocyte maturating day 6 replicate 3

description: replicate 3

source_name: D6 adipocytes

value: day 6


title: WT_R1_OD24_dksA

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium wt. Biol. Rep. 1_optical density (600 nm) of 2.3

source_name: S. Typhimurium SL1344 genomic DNA


title: Moroberekan_anther_heat_day3_rep1

description: SAMPLE 22

source_name: Moroberekan anthers_heat day 3 (38/21°C)

value: cv. Moroberekan

value: heat day 3 (38/21°C)


title: VC1 cells_DMSO 6h rep1

description: FinalReport_A: 9703881003_A


title: Moroberekan_anther_drought_heat_day3_rep3

description: SAMPLE 18

source_name: Moroberekan anthers_drought+heat day 3 (75% RWC + 38/21°C)

value: drought+heat day 3 (75% RWC + 38/21°C)

value: Anther


title: Metabolic syndrome subject 5 before exercise training

source_name: vastus lateralis muscle, metabolic syndrome, baseline

value: female

value: Metabolic syndrome

value: 6 month guided endurance exercise training program

value: before

value: vastus lateralis muscle


title: Moroberekan_anther_drought_heat_day3_rep1

description: SAMPLE 16


title: Adipocyte differentiating day 2 replicate 3

description: replicate 3

source_name: D2 adipocytes

value: day 2

value: adipocytes

value: NIH 3T3 L1


title: N22_anther_heat_day3_rep1

description: SAMPLE 19

value: cv. N22


title: Adipocyte maturating day 18 replicate 2

description: replicate 2

source_name: D18 adipocytes

value: day 18

value: Adipocyte maturating

value: differentiation medium (IBMX), insulin and dexamethasone, and maturation medium containing insulin


title: WT_R1_OD3_dksA

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium wt. Biol. Rep. 1_o optical density (600 nm) of 3


title: WT_R1_OD36_dksA

description: Biol. Rep. 1 of 3

source_name: S. Typhimurium wt. Biol. Rep. 1_optical density (600 nm) of 3.6


title: N22_anther_drought_heat_day3_rep3

description: SAMPLE 15

source_name: N22 anthers_drought+heat day 3 (75% RWC + 38/21°C)


title: N22_anther_drought_heat_day3_rep2

description: SAMPLE 14


title: WT_R2_OD24_dksA

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium wt. Biol. Rep. 2_optical density (600 nm) of 2.3


title: WT_R2_OD1_dksA

description: Biol. Rep. 2 of 5

source_name: S. Typhimurium wt. Biol. Rep. 2_optical density (600 nm) of 1.0


title: Adipocyte maturating day 14 replicate 2

description: replicate 2

source_name: D14 adipocytes

value: day 14


title: Adipocyte undifferentiated day 0 replicate 3

description: replicate 3

source_name: T0 adipocytes

value: day 0

value: Adipocyte undifferentiated

value: differentiation medium (IBMX), insulin and dexamethasone


title: Moroberekan_anther_drought_heat_day3_rep2

description: SAMPLE 17

value: cv. Moroberekan

value: drought+heat day 3 (75% RWC + 38/21°C)

value: Anther


title: N22_anther_drought_heat_day3_rep1

description: SAMPLE 13


title: WT_R2_OD3_dksA

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium wt. Biol. Rep. 2_o optical density (600 nm) of 3


title: WT_R3_OD24_dksA

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium wt. Biol. Rep. 3_optical density (600 nm) of 2.3


title: Moroberekan_anther_drought_heat_day1_rep3

description: SAMPLE 12

source_name: Moroberekan anthers_drought+heat day 1 (75% RWC + 38/21°C)

value: drought+heat day 1 (75% RWC + 38/21°C)


title: Adipocyte maturating day 8 replicate 2

description: replicate 2

source_name: D8 adipocytes

value: day 8


title: WT_R2_OD36_dksA

description: Biol. Rep. 2 of 3

source_name: S. Typhimurium wt. Biol. Rep. 2_optical density (600 nm) of 3.6

source_name: S. Typhimurium SL1344 genomic DNA


title: Adipocyte maturating day 6 replicate 2

description: replicate 2

source_name: D6 adipocytes

value: day 6


title: WT_R3_OD3_dksA

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium wt. Biol. Rep. 3_optical density (600 nm) of 3.0


title: Adipocyte differentiating day 4 replicate 2

description: replicate 2

source_name: D4 adipocytes

value: day 4

value: Adipocyte differentiating


title: Moroberekan_anther_drought_heat_day1_rep1

description: SAMPLE 10


title: N22_anther_drought_heat_day1_rep3

description: SAMPLE 9

source_name: N22 anthers_drought+heat day 1 (75% RWC + 38/21°C)


title: N22_anther_drought_heat_day1_rep2

description: SAMPLE 8


title: Adipocyte maturating day 10 replicate 2

description: replicate 2

source_name: D10 adipocytes

value: day 10

value: adipocytes

value: NIH 3T3 L1


title: Adipocyte maturating day 18 replicate 1

description: replicate 1

source_name: D18 adipocytes

value: day 18

value: Adipocyte maturating


title: Adipocyte differentiating day 2 replicate 2

description: replicate 2

source_name: D2 adipocytes

value: day 2


title: WT_R3_OD36_dksA

description: Biol. Rep. 3 of 3

source_name: S. Typhimurium wt. Biol. Rep. 3_optical density (600 nm) of 3.6


title: SMDCs-passage9-rep3

city: Tehran

first: Seyed Ahmad

last: Mousavi

state: Tehran

address: Bani Hashem sq. - Resalat Hw.

country: Iran

institute: Royan Institute

hyb_protocol: 750 ng of each cRNA sample was hybridized into Illumina’s Sentrix HumanHT-12 v4 Expression Bead Chips at 58 °C overnight according to Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (part # 11322355, rev.A).

scan_protocol: Chips were scanned with Illumina Bead Array Reader (Factor=1.5, PMT=552, Filter=100%)

data_processing: The data were normalised using quantile normalisation with lumi package in R

source_name: human skeletal muscle-derived cells (SMDCs) at passage 9

label_protocol: From 200 ng total RNA, generation of biotin-labeled cRNA was done using Illumina® TotalPrep™ RNA amplification Kit (Applied Biosystems, AMIL1791).

growth_protocol: Cells were cultured in M199, 10% FBS, 1% l-glutamine and 1% penicilin/streptomycin.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer instructions. Briefly, cells were dissolved in 1ml TRIzol reagent. Then they were lysed by vortexing and incubation for 5-10 min, after that 200 µl chloroform was added per 1 ml TRIzol and mixed by inversion. The sample was centrifuged at 12000×g for 15 min at 4°C. The upper layer was carefully removed and stored for RNA isolation. RNA was precipitated by adding 0.5 ml Isopropyl alcohol per 1 ml TRIzol reagent used for the initial homogenization. Samples were incubated at room temperature for 10 minutes and centrifuged at no more than 12,000 x g for 10 minutes at 4°C. Supernatant was carefully removed and the RNA pellet was washed once with 75% ethanol. The sample was vortexed and centrifuged at no more than 7,500 x g for 5 minutes at 4°C. After brief air drying, the RNA pellet was dissolved in RNase-free water and incubated for 10 min at 55°C. The quantity and quality of isolated RNA was evaluated by spectrophotometry.

value: skeletal muscle

tag: passage


title: Adipocyte undifferentiated day 0 replicate 2

description: replicate 2

value: day 0

value: Adipocyte undifferentiated


title: SMDCs-passage12-rep2

source_name: human skeletal muscle-derived cells (SMDCs) at passage 12


title: WT_R3_OD1_dksA

description: Biol. Rep. 3 of 5

source_name: S. Typhimurium wt. Biol. Rep. 3_optical density (600 nm) of 1.0


title: Moroberekan_anther_drought_heat_day1_rep2

description: SAMPLE 11

value: cv. Moroberekan


title: Moroberekan_anther_control_rep3

description: SAMPLE 6

source_name: Moroberekan anthers_control condition (29/21°C)

value: control condition (29/21°C)


title: SMDCs-passage9-rep1


title: SMDCs-passage12-rep1


title: Moroberekan_anther_control_rep2

description: SAMPLE 5

value: Anther


title: SMDCs-passage12-rep3


title: Adipocyte maturating day 14 replicate 1

description: replicate 1

source_name: D14 adipocytes

value: day 14

value: differentiation medium (IBMX), insulin and dexamethasone, and maturation medium containing insulin


title: Adipocyte maturating day 10 replicate 1

description: replicate 1


title: SMDCs-passage9-rep2


title: Adipocyte maturating day 6 replicate 1

description: replicate 1

value: day 6


title: Moroberekan_anther_control_rep1

description: SAMPLE 4


title: siLCN2_2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: This sample is of siLCN2 MDA-MB-231. It is the second of three sicontrol biological replicates used in this experiment, each from separate cultures.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: MDA-MB-231 siLCN2

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

growth_protocol: siRNA LCN2 tranfected MDA-MB-231 breast cancer cells were grown in DMEM low glucose + 10%SVF

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at technical platform of the IUH (Paris).

tag: transfection

value: siRNA LCN2


title: SMDCs-passage6-rep2

source_name: human skeletal muscle-derived cells (SMDCs) at passage 6


title: SMDCs-passage6-rep3


title: Adipocyte differentiating day 4 replicate 1

description: replicate 1

value: day 4

value: Adipocyte differentiating

value: differentiation medium (IBMX), insulin and dexamethasone


title: SMDCs-passage6-rep1


title: N22_anther_control_rep3

description: SAMPLE 3

source_name: N22 anthers_control condition (29/21°C)

value: cv. N22


title: breast cancer patient sample DA070-2

status: Public on May 30 2015

city: Seoul

first: Hee-Jun

last: Kim

address: Heukseok-Ro, Dongjak-gu

country: South Korea

institute: Chung-Ang University Hospital

description: Genomic DNA extracted from mononulcear cells of breast cancer patients was genotyped using Illumina GoldenGate custom 96 SNP microarray.

hyb_protocol: Arrays were hydrated in UB2 for 3 minutes at room temperature, and then preconditioned in 0.1 N NaOH for 30 seconds. Arrays were returned to the UB2 reagent for at least a minute to neutralize the NaOH. The pretreated arrays were exposed to the labeled ssDNA samples described above. Hybridization was conducted under a temperature gradient program from 60 ℃ to 45 ℃ over ~ 12 hours. The hybridization was held at 45 ℃ until the array was processed.

scan_protocol: After hybridization, the arrays were first rinsed twice in UB2 and once with IS1 (IS1l Illumina) at room temperature with mild agitation, and then imaged at a resolution of 0.8 microns using a BeadArray Reader (Illuminal Barker et al. 2003). PMT settings were optimized for dynamic range, channel balance, and signal-to-noise ratio. Cy3 and Cy5 dyes were excited by lasers emitting at 532 nM and 635 nM, respectively

data_processing:
Normalized bead intensity data obtained for each sample were loaded into the Illumina BeadStudio 3.1 software, which converted fluorescence intensities into SNP genotypes. Each SNP is analyzed independently to cluster and identify genotypes
Image data was analyzed using BeadStudio 3.1 software.

source_name: breat cancer blood cell

label_protocol: After extension and ligation, the beads were washed with universal buffer 1 (UB1; Illumina), resuspended in 35ul of elution buffer (IP1; Illumina) and heated at 95℃ for on2 minute to release the ligated products. The supernatant was then used in a 60ul PCR. PCR reactions were thermocycled as follows: 10 minutes at 37℃, 3 minutes at 98℃; 34 cycles of(35 seconds at 95℃, 35 seconds at 56℃, 2 minutes at 72℃); 10minutes at 72℃; and cooled to 4℃ for 5 minutes. The three universal PCR primers (P1, P2, and P3) are labeled with Cy3, Cy5, and biotin, respectively

extract_protocol: Genomic DNA (5ul at 500ng/ul) was mixed with 5ul of photobiotin (MSI; Illumina) and 15ul of mineral oil, and incubated at 95℃ for 30 minutes

value: female

value: breast cancer mononuclear cell

value: carcinoma


title: breast cancer patient sample DA062


title: breast cancer patient sample DA054


title: breast cancer patient sample 45


title: breast cancer patient sample 37


title: breast cancer patient sample 61


title: breast cancer patient sample 53


title: Adipocyte differentiating day 2 replicate 1

description: replicate 1

value: day 2

value: adipocytes

value: NIH 3T3 L1


title: breast cancer patient sample 29


title: siCTRL_2

description: This sample is of sicontrol MDA-MB-231. It is the second of three sicontrol biological replicates used in this experiment, each from separate cultures.

source_name: MDA-MB-231 si control

growth_protocol: siRNA control tranfected MDA-MB-231 breast cancer cells were grown in DMEM low glucose + 10%SVF

value: siRNA control


title: N22_anther_control_rep2

description: SAMPLE 2

value: control condition (29/21°C)


title: breast cancer patient sample 13


title: Adipocyte maturating day 8 replicate 1

description: replicate 1

source_name: D8 adipocytes

value: day 8

value: Adipocyte maturating


title: breast cancer patient sample 21


title: SMDCs-passage3-rep1

source_name: human skeletal muscle-derived cells (SMDCs) at passage 3

value: skeletal muscle


title: SMDCs-passage3-rep3


title: breast cancer patient sample 5


title: siLCN2_3

description: This sample is of siLCN2 MDA-MB-231. It is the third of three sicontrol biological replicates used in this experiment, each from separate cultures.


title: breast cancer patient sample DA069


title: breast cancer patient sample 8265


title: breast cancer patient sample DA061


title: siCTRL_1

description: This sample is of sicontrol MDA-MB-231. It is the first of three sicontrol biological replicates used in this experiment, each from separate cultures.


title: breast cancer patient sample DA053


title: breast cancer patient sample 36


title: breast cancer patient sample 44


title: breast cancer patient sample 60


title: Adipocyte undifferentiated day 0 replicate 1

description: replicate 1

source_name: T0 adipocytes

value: day 0

value: Adipocyte undifferentiated


title: breast cancer patient sample 52


title: breast cancer patient sample 20


title: breast cancer patient sample 12


title: breast cancer patient sample DA060


title: breast cancer patient sample DA068


title: N22_anther_control_rep1

description: SAMPLE 1

value: Anther


title: siLCN2_1

description: This sample is of siLCN2 MDA-MB-231. It is the first of three sicontrol biological replicates used in this experiment, each from separate cultures.

value: siRNA LCN2


title: breast cancer patient sample DA076


title: breast cancer patient sample 4


title: breast cancer patient sample 27


title: breast cancer patient sample 51


title: breast cancer patient sample 59


title: breast cancer patient sample 67


title: breast cancer patient sample 35


title: breast cancer patient sample 19


title: breast cancer patient sample 3


title: N22_anther_drought_heat_day1_rep1

description: SAMPLE 7

source_name: N22 anthers_drought+heat day 1 (75% RWC + 38/21°C)

value: drought+heat day 1 (75% RWC + 38/21°C)


title: breast cancer patient sample 43


title: SMDCs-passage3-rep2


title: breast cancer patient sample 11


title: siCTRL_3

description: This sample is of sicontrol MDA-MB-231. It is the third of three sicontrol biological replicates used in this experiment, each from separate cultures.


title: breast cancer patient sample DA059


title: breast cancer patient sample DA067


title: breast cancer patient sample 50


title: breast cancer patient sample 66


title: breast cancer patient sample 58


title: breast cancer patient sample 18


title: breast cancer patient sample DA075


title: breast cancer patient sample 26


title: breast cancer patient sample 42


title: breast cancer patient sample 34


title: breast cancer patient sample 10


title: breast cancer patient sample 2


title: breast cancer patient sample DA074


title: breast cancer patient sample DA058


title: breast cancer patient sample DA066


title: breast cancer patient sample 65


title: breast cancer patient sample 57


title: breast cancer patient sample 33


title: breast cancer patient sample 25


title: breast cancer patient sample 49


title: breast cancer patient sample 41


title: breast cancer patient sample 17


title: breast cancer patient sample 9


title: breast cancer patient sample DA052


title: breast cancer patient sample DA051


title: breast cancer patient sample 1


title: breast cancer patient sample DA050


title: breast cancer patient sample DA049


title: breast cancer patient sample DA047


title: breast cancer patient sample DA048


title: breast cancer patient sample 28


title: breast cancer patient sample DA044


title: breast cancer patient sample DA043


title: breast cancer patient sample DA045


title: breast cancer patient sample DA042


title: breast cancer patient sample DA037


title: breast cancer patient sample DA039


title: breast cancer patient sample DA040


title: breast cancer patient sample DA038


title: breast cancer patient sample DA046


title: breast cancer patient sample DA033


title: breast cancer patient sample DA034


title: breast cancer patient sample 7299


title: breast cancer patient sample DA035


title: breast cancer patient sample DA036


title: breast cancer patient sample DA032


title: breast cancer patient sample DA031


title: breast cancer patient sample DA028


title: breast cancer patient sample DA030


title: breast cancer patient sample DA027


title: breast cancer patient sample DA026


title: breast cancer patient sample DA025


title: breast cancer patient sample DA029


title: breast cancer patient sample DA024


title: breast cancer patient sample DA022


title: breast cancer patient sample DA021


title: breast cancer patient sample DA023


title: breast cancer patient sample DA020


title: breast cancer patient sample DA019


title: breast cancer patient sample DA017


title: breast cancer patient sample DA016


title: breast cancer patient sample DA018


title: breast cancer patient sample DA015


title: breast cancer patient sample DA013


title: breast cancer patient sample DA011


title: breast cancer patient sample DA012


title: breast cancer patient sample DA007


title: breast cancer patient sample DA008


title: breast cancer patient sample DA010


title: breast cancer patient sample DA006


title: breast cancer patient sample DA009


title: breast cancer patient sample DA005


title: breast cancer patient sample DA003


title: breast cancer patient sample DA002


title: breast cancer patient sample DA001


title: breast cancer patient sample DA004


title: breast cancer patient sample N_DA077


title: breast cancer patient sample N_DA076


title: breast cancer patient sample N_DA075


title: breast cancer patient sample N_DA071


title: breast cancer patient sample N_DA074


title: breast cancer patient sample N_DA063


title: breast cancer patient sample N_DA072


title: breast cancer patient sample N_DA062


title: breast cancer patient sample N_DA061


title: breast cancer patient sample N_DA060


title: breast cancer patient sample N_DA059


title: breast cancer patient sample N_DA058


title: breast cancer patient sample N_DA057


title: breast cancer patient sample N_DA055


title: breast cancer patient sample N_DA056


title: breast cancer patient sample N_DA050


title: breast cancer patient sample N_DA051


title: breast cancer patient sample N_DA047


title: breast cancer patient sample N_DA049


title: breast cancer patient sample N_DA040


title: breast cancer patient sample N_DA044


title: breast cancer patient sample N_DA038


title: breast cancer patient sample N_DA048


title: breast cancer patient sample N_DA037


title: breast cancer patient sample N_DA039


title: breast cancer patient sample N_DA041


title: breast cancer patient sample N_DA032


title: breast cancer patient sample N_DA028


title: breast cancer patient sample N_DA026


title: breast cancer patient sample N_DA023


title: breast cancer patient sample N_DA024


title: breast cancer patient sample N_DA036


title: breast cancer patient sample N_DA011


title: breast cancer patient sample N_DA022


title: breast cancer patient sample N_DA018


title: breast cancer patient sample N_DA020


title: breast cancer patient sample N_DA017


title: breast cancer patient sample N_DA009


title: breast cancer patient sample N_DA013


title: breast cancer patient sample N_DA005


title: breast cancer patient sample N_DA006


title: breast cancer patient sample N_DA004


title: breast cancer patient sample N_DA001


title: breast cancer patient sample N_DA002


title: breast cancer patient sample 40


title: breast cancer patient sample DA065


title: breast cancer patient sample 64


title: breast cancer patient sample DA057


title: breast cancer patient sample 56


title: breast cancer patient sample DA081


title: breast cancer patient sample 48


title: breast cancer patient sample DA073


title: breast cancer patient sample 16


title: breast cancer patient sample 8


title: breast cancer patient sample N_DA010


title: breast cancer patient sample DA080


title: breast cancer patient sample 32


title: breast cancer patient sample 24


title: breast cancer patient sample DA072


title: breast cancer patient sample DA056


title: breast cancer patient sample 55


title: breast cancer patient sample DA064


title: breast cancer patient sample 63


title: breast cancer patient sample 47


title: breast cancer patient sample 39


title: breast cancer patient sample DA079


title: breast cancer patient sample DA071


title: breast cancer patient sample 23


title: breast cancer patient sample 15


title: breast cancer patient sample 31


title: breast cancer patient sample DA063


title: breast cancer patient sample 7


title: breast cancer patient sample 62


title: breast cancer patient sample DA055


title: breast cancer patient sample DA078


title: breast cancer patient sample 22


title: breast cancer patient sample 14


title: breast cancer patient sample 6


title: breast cancer patient sample 46


title: breast cancer patient sample 54


title: breast cancer patient sample 38


title: breast cancer patient sample 30


title: Old_healthy_6

city: Bethesda

first: Nard

last: Kubben

address: 41 Library Drive

institute: NCI, NIH

description: mRNA gene expression data from human skin fibroblasts

hyb_protocol: Fragmentation and hybridization was performed according to standard Affymetric guidelines for the HG-U133_plus_2 arrays

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotinylated

source_name: Human skin fibroblasts from old healthy person 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: All cell lines were grown in vitro using MEM tissue culture medium supplemented with 15%  foetal bovine serum, L-glutamine, non-essential amino acids, pyruvate as well as pen/strep.

extract_protocol: RNA from cells was harvested using the Qiagen RNA isolation kit according to the manufecturers instructions.

treatment_protocol: Cells were not treated

tag: sample type

value: old healthy

value: Primary in vitro culture human skin fibroblasts


title: Young_healthy_1

source_name: Human skin fibroblasts from young healthy person 1

value: young healthy


title: Old_healthy_4

source_name: Human skin fibroblasts from old healthy person 1


title: Vk2 cells_PAM-treated, biol rep 6

city: Norfolk

first: Irina

middle: A

last: Zalenskaya

state: Virginia

address: 601 Colley ave

department: Ob/Gyn

institute: Eastern Virginia Medical School

hyb_protocol: Labeled cRNA was fragmented and hybrized to Affymetrix HG-U133 Plus 2 arrays according to the standard Affymetrix protocol

scan_protocol: The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G

data_processing: A summary of the image signal data, detection calls, and gene annotations for every gene interrogated on the array was generated using the Affymetrix Statistical Algorithm MAS 5.0 (GCOS v1.3) algorithm

source_name: Vk2/E6E7, Pam3CSK4 at 10 μg/ml

label_protocol: Biotinylated cRNA was prepared from 1  μg total RNA using modified MessageAmp™ -based protocols (Ambion Inc., Austin, TX)

extract_protocol: Total RNA was extracted with Trizol, purified using Qiagen Rneasy according to the manufacturer's instructions

treatment_protocol: Vk2/E6E7 cells were treated for 6 h; compounds: non-inflammatory (carboxymethyl cellulose,  hydroxyethyl cellulose at 1mg/ml, growth medium), pro-inflammatory (imiquimod at 30 mg/ml, macrophage activating lipopeptide 2 (MALP2) at 200 ng/ml, nonoxynol 9 (N9) at 12.5 μg/ml, Pam3CSK4 at 10 μg/ml, TNF-alpha at 40 ng/ml)

value: Human vaginal epithelial immortalized cells


title: Young_healthy_2

source_name: Human skin fibroblasts from young healthy person 2


title: Vk2 cells_TNF-a-treated, biol rep 5

source_name: Vk2/E6E7, TNF-alpha at 40 ng/ml


title: HGPS_patient_5

source_name: Human skin fibroblasts from HGPS patient 5

value: HGPS patient


title: HGPS_patient_4

source_name: Human skin fibroblasts from HGPS patient 4


title: Young_healthy_3

source_name: Human skin fibroblasts from young healthy person 3


title: Vk2 cells_PAM-treated, biol rep 3


title: Vk2 cells_N9-treated, biol rep 9

source_name: Vk2/E6E7, nonoxynol 9 (N9) at 12.5 μg/ml


title: Old_healthy_5

source_name: Human skin fibroblasts from old healthy person 2


title: Vk2 cells_TNF-a-treated, biol rep 2


title: HGPS_patient_2

source_name: Human skin fibroblasts from HGPS patient 2


title: Vk2 cells_TNF-a-treated, biol rep 4


title: Vk2 cells_PAM-treated, biol rep 5


title: Vk2 cells_PAM-treated, biol rep 4


title: Vk2 cells_TNF-a-treated, biol rep 3


title: HGPS_patient_6

source_name: Human skin fibroblasts from HGPS patient 6


title: Vk2 cells_TNF-a-treated, biol rep 6


title: HGPS_patient_3

source_name: Human skin fibroblasts from HGPS patient 3


title: Vk2 cells_N9-treated, biol rep 7


title: Vk2 cells_PAM-treated, biol rep 2


title: HGPS_patient_1

source_name: Human skin fibroblasts from HGPS patient 1


title: Vk2 cells_N9-treated, biol rep 8


title: Vk2 cells_MALP-treated, biol rep 5

source_name: Vk2/E6E7, macrophage activating lipopeptide 2 (MALP2) at 200 ng/ml


title: Vk2 cells_N9-treated, biol rep 2


title: Vk2 cells_PAM-treated, biol rep 1


title: Vk2 cells_MALP-treated, biol rep 6


title: Vk2 cells_MALP-treated, biol rep 4


title: Vk2 cells_MALP-treated, biol rep 2


title: Vk2 cells_N9-treated, biol rep 6


title: Vk2 cells_IMQ-treated, biol rep 2

source_name: Vk2/E6E7, imiquimod at 30 mg/ml


title: Vk2 cells_IMQ-treated, biol rep 3


title: Vk2 cells_N9-treated, biol rep 3


title: Vk2 cells_N9-treated, biol rep 1


title: Vk2 cells_TNF-a-treated, biol rep 1


title: Vk2 cells_IMQ-treated, biol rep 6


title: Vk2 cells_MALP-treated, biol rep 3


title: Vk2 cells_MALP-treated, biol rep 1


title: Vk2 cells_IMQ-treated, biol rep 5


title: Vk2 cells_CMC-treated, biol rep 4

source_name: Vk2/E6E7,  carboxymethyl cellulose at 1mg/ml


title: Vk2 cells_CMC-treated, biol rep 2


title: Vk2 cells_CMC-treated, biol rep 1


title: Vk2 cells_CMC-treated, biol rep 6


title: Vk2 cells_HEC-treated, biol rep 9

source_name: Vk2/E6E7,  hydroxyethyl cellulose at 1mg/ml


title: Vk2 cells_IMQ-treated, biol rep 4


title: Vk2 cells_CMC-treated, biol rep 5


title: Vk2 cells_CMC-treated, biol rep 9


title: Vk2 cells_CMC-treated, biol rep 8


title: Vk2 cells_CMC-treated, biol rep 7


title: Vk2 cells_IMQ-treated, biol rep 1


title: Vk2 cells_HEC-treated, biol rep 6


title: Vk2 cells_CMC-treated, biol rep 3


title: Vk2 cells_HEC-treated, biol rep 7


title: Vk2 cells_N9-treated, biol rep 4


title: Vk2 cells_HEC-treated, biol rep 2


title: Vk2 cells_HEC-treated, biol rep 4


title: Vk2 cells_no treatment, biol rep 51

source_name: Vk2/E6E7, no treatment,  growth medium only


title: Vk2 cells_HEC-treated, biol rep 5


title: Vk2 cells_HEC-treated, biol rep 1


title: Vk2 cells_no treatment, biol rep 53


title: Vk2 cells_no treatment, biol rep 48


title: Vk2 cells_HEC-treated, biol rep 8


title: Vk2 cells_HEC-treated, biol rep 3


title: Vk2 cells_no treatment, biol rep 43


title: Vk2 cells_no treatment, biol rep 46


title: Vk2 cells_no treatment, biol rep 41


title: Vk2 cells_no treatment, biol rep 52


title: Vk2 cells_no treatment, biol rep 50


title: Vk2 cells_no treatment, biol rep 42


title: Vk2 cells_no treatment, biol rep 45


title: Vk2 cells_no treatment, biol rep 38


title: Vk2 cells_no treatment, biol rep 54


title: Vk2 cells_no treatment, biol rep 47


title: Vk2 cells_no treatment, biol rep 40


title: Vk2 cells_no treatment, biol rep 44


title: Vk2 cells_no treatment, biol rep 39


title: Vk2 cells_no treatment, biol rep 35


title: Vk2 cells_no treatment, biol rep 36


title: Vk2 cells_no treatment, biol rep 37


title: Vk2 cells_no treatment, biol rep 33


title: Vk2 cells_no treatment, biol rep 34


title: Vk2 cells_no treatment, biol rep 49


title: Vk2 cells_no treatment, biol rep 32


title: Cn_WT pH 4.0 vs WT pH 7.2_replicate 3

city: Stony Brook

first: Maurizio

last: Del Poeta

state: NY

address: 150 Life Science Building

department: Molecular Genetics and Microbiology

institute: Stony Brook University

hyb_protocol: 300ng of each sample to be co-hybridized was fragmented and hybridized to an Agilent custom anti-sense probe 8x15K microarray (AMADID 019465) by manufacturer's specifications with the following exception:  5uL of Kreablock (included in the labeling kit) was added after fragmentation.  Hybridization was carried out in a SureHyb chamber in an Agilent hybridization oven at 65C and 10 rpm for 17 hours.

scan_protocol: Slides were washed using Agilent GE wash buffers and scanned on an Agilent C scanner at 5um.

data_processing: Data was extracted using Agilent Feature Extraction v. 10.7.1 software.  The normalization method used for data extraction was Linear-Lowess. Lowess normalized log2 ratio (test/reference) included in supplementary file processed_data.txt.

organism: Cryptococcus neoformans H99

source_name: Whole cell RNA extract

label_protocol: Total RNA integrity was verified by Agilent 2100 Bioanalyzer.  Concentration and sample purity were determined by Nanodrop ND-1000.  Samples with 260/280 < 1.8, 260/230 < 1.8 were column purified and re-quantitated.  1ug of total RNA was direct labeled using Kreatech ULS aRNA Labeling Kit for dual-color hybridization.  Concentrations and dye incorporation data (Cy3: 100-130 pmol/ug, Cy5:  70-100 pmol/ug) were determined by Nanodrop.

growth_protocol: Cryptococcus strains were routinely grown at 30ºC and 0.04% atmospheric CO2 in YPD broth (2% Peptone, 1% yeast extract, 2% Dextrose, BD). Dulbecco’s modified Eagle mediuma high glucose (DMEM high glucose), buffered with 50 mM HEPES, 10% FBS (Fetal Bovine Serum) and 1M sSorbitol at pH 7.2±0.2 and pH 4, were used as conditioned media for growing C. neoformans strains at 37ºC in presence of 5% CO2.

extract_protocol: Overnight YPD grown cultures of WT, ∆gcs1 and ∆smt1 mutant strain, were pelleted, washed twice with sterile Phosphate Buffer Saline (PBS) and inoculated in DMEM high glucose, buffered with 50 mM HEPES, containing 10% Fetal Bovine Serum, 1M Sorbitol at pH 7.2 and pH 4 and shaken-incubated for 20 hours at 37°C, 5% CO2. The cells were harvested by centrifugation at 5,000 g for 10 minutes and washed twice with PBS. The cell-pellets were flash-frozen in dry-ice/ ethanol bath and stored at -80ºC until ready to use. Total RNA was extracted from Cn strains, as described previously [51]. Briefly, the cells were lyophilized overnight and 100 µl of lyophilized cells were transferred in 2 ml screw cap tubes and 1.25 ml of TRI reagent (Molecular Research Center, Inc.) was added. After homogenization, using Bead Beater 16, the tubes were incubated at room temperature for 10 minutes and centrifuged at 8, 000 g to pellet cell debris and unbroken cells. The supernatants were transferred in fresh tubes along with 60 µl of BAN phase separation reagent (Molecular Research Center, Inc.). After mixing for 20-30 seconds and incubating at room temperature for 5 minutes, samples were centrifuged at 8,000 g. The aqueous phases were placed in fresh tubes along with 70% ethanol, and loaded onto RNeasy isolation columns provided by RNeasy Mini Kit (Qiagen, CA, USA). Total RNA was further purified and eluted according to manufacturer’s instructions. Total RNA integrity was verified by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Concentration and sample purity were determined by Nanodrop ND-1000 (Nanodrop, DE, USA).  Samples with 260/280 < 1.8, 260/230 < 1.8 were column purified and re-quantitated.

treatment_protocol: No treatment

tag: genotype

value: WT

tag: ph


title: Cn_WT pH 4.0 vs WT pH 7.2_replicate 2


title: Wt sham [5511168079_E]

city: Groningen

first: Herman

last: Sillje

address: Hanzeplein 1

institute: University medical center Groningen

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data were normalised (quantile normalization) by using the Illumina GenomeStudio software (version: 2011.1; Expression Module Version: 1.9.0).

source_name: Mouse heart

label_protocol: During the last step of the amplification procedure using the Illumina TotalPrep -96 RNA Amplification kit, purified cDNA was converted to cRNA inclusive biotinylation through an in vitro transcription step.

extract_protocol: RNA was extracted from left ventricular tissue using Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: genotype/variation

value: Wt

tag: protocol

value: sham surgery

tag: strain

tag: age

value: 4 months

value: Left ventricle

value: male


title: Vk2 cells_no treatment, biol rep 30