title: WT_MDP pool 1

description: Gene expression of wildtype myelo-dendritic progenitors

source_name: bone marrow MDPs - lineage-sca1-CD127-CD117+MCSFR+

value: bone marrow

value: myelo-dendritic progenitors - lineage-sca1-CD127-CD117+MCSFR+


title: SS_A3_Comp.1

status: Public on Apr 27 2013

type: RNA

city: Worcester

first: Scarlet

last: Shell

state: MA

address: 60 Prescott St

department: Biology and Biotechnology

country: USA

institute: Worcester Polytechnic Institute

description: Gene expression data from a complemented M. tuberculosis methyltransferase deletion mutant

hyb_protocol: Affymetrix protocol recommended for Pseudomonas aeruginosa

scan_protocol: Microarrays were scanned using Affymetrix GeneArray Scanner 3000 7G Plus according to the manufacturer's protocol.

data_processing: Gene expression estimates were derived from the probe-level hybridization intensities using the RMA algorithm through the Expression Console software package (Affymetrix) using library files obtained from the array manufacturer (Affymetrix).

label: biotin

molecule: total RNA

organism: Mycobacterium tuberculosis H37Rv

source_name: Complemented Rv3263 deletion mutant replicate 1

label_protocol: Standard Affymetrix protocol for prokaryotic microarrays

growth_protocol: Cultures were grown to OD 0.8-0.9 in 7H9 supplemented with OADC, 0.05% Tween-80, and 0.2% glycerol in roller bottles

extract_protocol: Cultures were inactivated with RNAlater, disrupted with bead-beating in the presence of Trizol, and total RNA was extracted according to the manufacturer's instructions. RNA was then treated with Dnase and re-purified with RNeasy.

tag: strain

tag: genotype

value: deltaRv3263 complemented


title: IRF8_PAC_MDP pool 1

city: Berlin

first: Marie

last: Gebhardt

address: Robert-Rössle-Str. 10

department: Cancer

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine

description: Gene expression of myelo-dendritic progenitors from reporter mice with venus expression

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocols by Kompetenzzentrum Fluoreszente Bioanalytik (Regensburg, Germany)

scan_protocol: Scanning was performed according to the standard Affymetrix protocols by Kompetenzzentrum Fluoreszente Bioanalytik (Regensburg, Germany)

data_processing: Primary analysis was performed with the Affymetrix GeneChip® Software (AGCC) and Expression Console Software. The data were analyzed using R/Bioconductor and the RMA normalization method.

organism: Mus musculus

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocols by Kompetenzzentrum Fluoreszente Bioanalytik (Regensburg, Germany)

growth_protocol: Mice of 6-10 weeks of aged were used in this experiment

extract_protocol: Total RNA extraction was performed by Rneasy mini or Rneasy micro kit (Qiagen) according to manufacturers recommendations

treatment_protocol: BM cells from long bones as well as splenice were extracted, RBC lysis was performed, cells were stained with fluorescently labelled antibdies targeted against cell-population specific surface antigens and separated by flow cytometry directly into RNA extraction cell lysis buffer

tag: tissue

tag: cell type

tag: genotype/variation


title: WT_MDP pool 3

value: wild-type


title: IRF8_ko_MDP pool 2

description: Gene expression of myelo-dendritic progenitors with IRF8 knockout


title: WT_DCs pool 3

description: Gene expression of wildtype splenic DCs

source_name: splenic DCs - CD3e-CD19-CD11c+

value: spleen

value: dendritic cells - CD3e-CD19-CD11c+


title: IRF8_ko_MDP pool 3


title: IRF8_neg_MDP pool 1

description: Gene expression of myelo-dendritic progenitors without VENUS expression


title: IRF8_ko_MDP pool 1


title: IRF8_PAC_MDP pool 3


title: LPS (0.05mg/kg), rep 1

city: Callaghan

first: Luba

last: Sominsky

state: NSW

address: University Drive

country: Australia

institute: The University of Newcastle

description: LPS 1

hyb_protocol: Agilent Hybridization Protocol.

scan_protocol: The chips were scanned in the Agilent DNA Microarray Scanner (High Resolution). The scanner operating software, Agilent Scan Control, converts the signal on the array into a TIFF file which can be used for subsequent analysis.

data_processing: The data were normalised using quantile normalisation using BioConductor's lumi package in R statistical software.

organism: Rattus norvegicus

source_name: Neonatal rat ovary (age=PND7), LPS-treated on PNDs 3 and 5

label_protocol: Biotinylated cRNA were prepared according to Agilent protocol.

growth_protocol: Wistar rats were administered intraperitoneally with either LPS (Salmonella enterica, 0.05 mg/kg) or an equivolume of saline on postnatal days 3 and 5. On postnatal day 7, female pups were euthanized by rapid decapitation. Ovaries were collected and frozen on dry ice.

extract_protocol: Total RNA was exctracted using RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA) in accordance with the manufacturer's instructions.

treatment_protocol: Animals were treated with LPS or served as controls and injected with saline. 2 days after the treatment, whole ovaries were extracted and immediately frozen.

tag: strain/background

value: Wistar

value: ovary

tag: treatment

value: LPS

tag: age

value: postnatal day 7


title: IRF8_PAC_MDP pool 2


title: WT_DCs pool 1

description: Gene expression of wildtype splenic DCs


title: WT_MDP pool 2


title: LPS (0.05mg/kg), rep 3

description: LPS 3


title: WT_macrophages pool 3

description: Gene expression of wildtype macrophages

source_name: splenic macrophages - CD11c-CD11b+MCSFR+

value: macrophages - CD11c-CD11b+MCSFR+


title: B6 vis adipocyte 3

city: Schwerzenbach

first: Christian

last: Wolfrum

address: Schorenstrasse 16

country: Switzerland

institute: ETH Zürich

hyb_protocol: Agilent Gene Expression kit for oligo microarrays (Agilent, order number 5188-5242, protocol G4140-90050).

scan_protocol: Agilent Feature Extraction software 9.5.3.1.

data_processing: GeneSpring GX10 default loading and analysis.

source_name: adipocyte fraction of epididymal adipose tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 600 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from cells using Trizol reagent (Invitrogen) and Phase Lock Gel tubes (5prime) according to the manufacturer's instructions. Final RNA samples were re-precipitated with NaOAc and ethanol and washed with 70% ethanol before analysis on a NanoDrop-2000 spectrophotometer and Bioanalyzer 2100 (Agilent).

treatment_protocol: For cellular separation, dissected adipose tissues were minced and incubated in 2.0 ml 0.2% collagenase type II in collagenase buffer (25 mM KHCO3, 12 mM KH2PO4, 1.2 mM MgSO4, 4.8 mM KCl, 120 NaCl, 1.2 mM CaCl2, 5 mM glucose, 2.5% BSA, 1% Pen/Strep, pH 7.4) rocking for 50 min at 37°C with occasional resuspension. 10 ml 90% PBS were added and samples centrifuged 5 min at 200 g. The adipocyte fraction was removed from the top and filtered through 100 µm cell strainers (BD). Filters were washed with 10 ml PBS and sample centrifuged as above. The adipocyte fraction was spun 2 min at 200 g and buffer removed from below the adipocytes with a 40 mm 20 G needle. The SVF pellet from the initial centrifugation was aspirated, resuspended in 2 ml erythrocyte lysis buffer (154 mM NH4lC, 10 mM KHCO3, 0.1 mM EDTA, pH 7.4) and incubated for 4 min. After addition of 2 ml PBS samples were filtered through 40 µm cell strainers. Filters were rinsed with 8 ml buffer and samples centrifuged for 5 min at 200 g.

tag: gender

value: male

tag: developmental stage

value: young adult

value: epididymal adipose

tag: fraction

value: adipocyte


title: B6 vis adipocyte 1


title: B6 vis adipocyte 2


title: B6 vis SVF 3

source_name: stromal-vascular fraction of epididymal adipose tissue

value: stromal-vascular


title: LPS (0.05mg/kg), rep 2

description: LPS 2


title: WT_granulocytes pool 1

description: Gene expression of wildtype granulocytes

source_name: splenic granulocytes - CD11c-CD11b+Ly6C+MCSFR-

value: granulocytes - CD11c-CD11b+Ly6C+MCSFR-


title: WT_macrophages pool 1

description: Gene expression of wildtype macrophages


title: WT_granulocytes pool 3


title: Saline control, rep 3

description: Saline 3

source_name: Neonatal rat ovary (age=PND7), saline-treated on PNDs 3 and 5

value: saline


title: WT_macrophages pool 2

description: Gene expression of wildtype macrophages


title: B6 vis SVF 2


title: IRF8_neg_MDP pool 2

value: bone marrow

value: myelo-dendritic progenitors - lineage-sca1-CD127-CD117+MCSFR+


title: Saline control, rep 2

description: Saline 2


title: NCI-H292 EV-ctrl replicate 3

city: Krakow

first: Klaudia

last: Skrzypek

address: ul. Gronostajowa 7

department: Department of Medical Biotechnology

country: Poland

institute: Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University

description: Biological replicate 3 of 3: NCI-H292 EV-ctrl untreated

hyb_protocol: The Hy3-labeled samples and a Hy5-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA array version 11.0 (Exiqon, Denmark). The hybridization was performed according to the miRCURY LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: The miRCURY LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

organism: Homo sapiens

source_name: NCI-H292 non-small cell lung carcinoma cell line

label_protocol: One µg total RNA from sample and reference was labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: NCI-H292 cells (either EV-ctrl or overexpressing HO-1) were grown grown in RPMI 1640 growth medium with 10% FBS, penicillin (100U/ml) and streptomycin (100 µg/ml) at standrad conditions.

extract_protocol: Total RNA was extracted using miRVana miRNA isolation kit from Ambion following manufacturer's instructions.

treatment_protocol: Confluent NCI-H292 cells (either EV-ctrl or overexpressing HO-1) were either untreated or treated with 10 ng/ml TNF-α for 6 hours before RNA isolation. However, we do not present here the effect of TNF-α, as it is the subject of another studies. The samples are biological triplicates - three independent experiments were performed at different time points for all cell lines.

value: untreated cells

tag: cell line

tag: transfection

value: RV-empty vector

source_name: Total RNA pooled from all samples (untreated and treated with TNF-a)

tag: sample type

value: pooled reference

value: mucoepidermoid non-small cell lung carcinoma NCI-H292

value: combined untreated and 10 ng/ml TNF-α treated


title: NCI-H292 HO-1 replicate 3

description: Biological replicate 3 of 3: NCI-H292 HO-1 untreated

value: mucoepidermoid non-small cell lung carcinoma

value: RV-HO-1 vector


title: B6 subc adipocyte 2

source_name: adipocyte fraction of inguinal adipose tissue

value: inguinal adipose


title: B6 subc adipocyte 1

value: male


title: B6 vis SVF 1

value: young adult


title: 16MΔhfq(CY3)-16M(CY5), rep2

city: Beijing

first: tai

address: Dongdajie

country: China

institute: Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences

description: Biological replicate 4 of 4

hyb_protocol: The slides were pre-hybridized in a buffer containing 5×SSC, 0.1% SDS and 0.1% BSA, and then washed and blown to dry by hot air. The Cy3/Cy5 differentially labeled cDNA samples were resuspended in hybridization solution (50% deionized formamide, 5×SSC, 0.1% SDS, 5×Denhardt's solution, and 0.5μg/μl of sheared salmon sperm DNA), and then hybridized with the slides at 42℃ for 18-20 h. After hybridization, the slides were washed in 1×SSC with 0.06% SDS for 2 min, then in 0.06×SSC for 2 min and finally in ethanol for 2 min.

scan_protocol: The slides were blown to dry by hot air and were scanned by using a GenePix Personal 4100A Microarray Scanner.

data_processing: The scanning images were processed and the data were further analyzed by using GenePix Pro 4.1 software (Axon Instruments) combined with Microsoft Excel software. Spots were analyzed by adaptive quantitation, and the local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels lower than 2-fold of background intensity (median) were rejected from further analysis, and then the remaining data points were normalized by total intensity normalization methods. The normalized log2 ratio of test/reference signal for each spot was recorded. The averaged log2 ratio for each gene with at least four data points was finally calculated.

organism: Brucella melitensis

source_name: 16M cultured in GEM 4.0 for 30min

label_protocol: RNA was reverse transcribed into cDNA in the present of aminoallyl-dUTP, and then labeled with Cy3 or Cy5 monofunctional dye (Amersham).

growth_protocol: 16M and 16MΔhfq strains were grown in TSB at 37℃ to the stationary phase, and then transferred to the stress condition where hfq was greatly activated.

extract_protocol: Total RNA was extracted from liquid cultures of B. melitensis using Trizol reagent (Invitrogen) as recommended by the manufacturer. RNA samples were then treated with DNase I (Promega) to remove any contaminating genomic DNA.

treatment_protocol: Bacteria was transferred from TSB to GEM 4.0 (limited nutrition and acid) for 30min.

value: wild type

source_name: 16MΔhfq cultured in GEM 4.0 for 30min

value: Δhfq


title: Saline control, rep 1

description: Saline 1

value: Wistar

value: ovary

value: postnatal day 7


title: 16MΔhfq(CY3)-16M(CY5), rep1

description: Biological replicate 2 of 4


title: 16MΔhfq(CY5)-16M(CY3), rep2

description: Biological replicate 3 of 4

source_name: Brucella-16MΔhfq-GEM 4.0


title: 16MΔhfq(CY5)-16M(CY3), rep1

description: Biological replicate 1 of 4


title: NCI-H292 HO-1 replicate 1

description: Biological replicate 1 of 3: NCI-H292 HO-1 cells untreated


title: B6 subc adipocyte 3

value: adipocyte


title: B6 subc SVF 2

source_name: stromal-vascular fraction of inguinal adipose tissue

value: stromal-vascular


title: B6 subc SVF 1


title: B6 brown adipocyte 3

source_name: adipocyte fraction of interscapular brown adipose tissue

value: interscapular brown adipose


title: B6 subc SVF 3


title: B6 brown adipocyte 1


title: NCI-H292 HO-1 replicate 2

description: Biological replicate 2 of 3: NCI-H292 HO-1 untreated

value: untreated cells


title: B6 brown SVF 3

source_name: stromal-vascular fraction of interscapular brown adipose tissue


title: B6 brown SVF 2


title: NCI-H292 EV-ctrl replicate 2

description: Biological replicate 2 of 3: NCI-H292 EV-ctrl untreated

value: RV-empty vector

value: pooled reference


title: NCI-H292 EV-ctrl replicate 1

description: Biological replicate 1 of 3: NCI-H292 EV-ctrl cells untreated

value: mucoepidermoid non-small cell lung carcinoma NCI-H292

value: combined untreated and 10 ng/ml TNF-α treated


title: A/J-MyD88 deficient_ssRNA 2

city: DC

first: kitipong

last: Uaesoontrachoon

state: Washington

address: 111 Michigan Ave, NW

institute: Children's national medical center

description: Muscle_ssRNA injected_10days_rep2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with Illumina Genome studio

source_name: A/J-MyD88 deficient_ssRNA

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA amplification kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The tibialis anterior muscle was injected with either saline or ssRNA. Three repeated injections were done over a period of 10 days, with a 3-day recovery period between each injection.

tag: phenotype

value: Dysferlin deficient and MyD88 deficient

value: 2 months

value: tibalis anterior muscle


title: R26R^AC/AC;T-Cre (Mutant), biological replicate #3

city: Baltimore

first: Timothy

middle: Peter

last: Lopez

state: Maryland

address: 3520 San Martin Drive

department: Biology

institute: Johns Hopkins University/Carnegie Institution

description: Gene expression data from mutant PSM.

hyb_protocol: Following fragmentation, 5.5 ug of cRNA was hybridized to Affymetrix Mouse 430 2.0 GeneChips for 16 hours at 45 °C. GeneChips were washed and stained using a fluidics station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.

data_processing: Data was acquired and normalized using Affymetrix Expression Console software under Affymetrix default analysis settings and global scaling as normalization method to generate Microarray Suite version 5.0 (MAS 5.0) files. Data is represented by presence/absence call for each gene using appropriate algorithms and expression data that had an “absent” call was filtered out of data sets using Excel software (Microsoft).

label: Biotin

label_protocol: Biotinylated cRNA was prepared using the 3' IVT Express Kit (Affymetrix) for 1 ug total RNA according to the standard protocol for cRNA synthesis (GeneChip 3’ IVT Express Kit).

growth_protocol: Control and mutant embryos were harvested on Embronic day (E) 8.75 in L-15 media under a dissection light and fluorescent microscope setup.

extract_protocol: The anterior PSM was pipetted into lysis solution and underwent total RNA purification using the PicoPure RNA Isolation Kit (Life Technologies).

treatment_protocol: The anterior 2/3 PSM was dissected from the posterior 1/3 PSM and somites. Anterior PSM was briefly rinsed in 1X PBS (Gibco).

tag: strain background

value: R26R^AC/AC;T-Cre (Mutant)

value: presomitic mesoderm (PSM)


title: R26R^AC/AC;T-Cre (Mutant), biological replicate #1

description: Gene expression data from mutant PSM.


title: B6 brown SVF 1

value: male

value: young adult


title: B6 brown adipocyte 2


title: R26R^AC/AC;T-Cre (Mutant), biological replicate #2

description: Gene expression data from mutant PSM.


title: A/J-MyD88 deficient_ssRNA 1

description: Muscle_ssRNA injected_10days_rep1


title: R26R^AC/AC (Control), biological replicate #3

description: Gene expression data from control PSM.

source_name: Mouse control_PSM

value: R26R^AC/AC (Control)


title: A/J-MyD88 deficient_ssRNA 3

description: Muscle_ssRNA injected_10days_rep3


title: A/J-MyD88 deficient_saline 3

description: Muscle_saline injected_10days_rep3

source_name: A/J-MyD88 deficient_saline


title: A/J-MyD88 deficient_saline 1

description: Muscle_saline injected_10days_rep1


title: A/J-MyD88 deficient_saline 2

description: Muscle_saline injected_10days_rep2


title: R26R^AC/AC (Control), biological replicate #1

description: Gene expression data from control PSM.


title: A/J_ssRNA 2

description: Muscle_ssRNA injected_10days_rep2

value: A/J

value: Dysferlin deficient


title: A/J_ssRNA 3

description: Muscle_ssRNA injected_10days_rep3


title: T23

city: Taipei

first: Yung-Ming

last: Jeng

address: 7 Chung-Shan South Road

department: Department of Pathology

country: Taiwan

institute: National Taiwan University Hospital

description: tumor

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Step 1 Normalize to 75 persentile, Step 2: genes are selected from Control=0. Step 3: Genes from Control=1 with expression raw data higher than 70 (Microsoft Excel 2003)

source_name: tumor

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

extract_protocol: RNA was prepared using the Trizol RNA Purification kit following the manufacturer's recommendations.

tag: specimen id

value: primary hepatocellular carcinomas (HCC)


title: Tbx2/3 DBD at mTb, replicate 2

city: New York

first: Anna

last: Di Gregorio

state: NY

address: 345 E 24th Street, room 804A

department: Basic Science and Craniofacial Biology

institute: NYU College of Dentistry

description: 100-300 fluorescent embryos

hyb_protocol: Hybridization to customized Ciona intestinalis GeneChipTM was performed by the Weill Cornell Genomics Resources Core Facility using standard Affymetrix protocols.

scan_protocol: Standard Affymetrix procedure as performed by the Weill Cornell Genomics Resources Core Facility.

data_processing: Results were RMA summarized from raw data and quantile normalized using GeneSpring GX as carried out by the Weill Cornell Epigenomics Core Facility.

organism: Ciona intestinalis

source_name: whole Bra>Tbx2/3 DBD expressing embryos at mTb

label_protocol: Total RNA was amplified and labeled using the Ambion MessageAmpTM Premier RNA Amplification Kit (Life Technologies #AM1792) by the Weill Cornell Genomics Resources Core Facility.

growth_protocol: Adult Ciona intestinalis were purchased from Marine Research and Educational Products (M-REP; Carlsbad, CA) and kept in an aquarium in recirculating artificial sea water at 18°C.  In vitro fertilization, electroporation and embryo culturing were carried out as previously described (Oda-Ishii I, Di Gregorio A, 2007.  Lineage-independent mosaic expression and regulation of the Ciona multidom gene in the ancestral notochord.  Dev Dyn.  236, 1806–1819 (PMID 17576134).).  Embryos expressing Bra>Tbx2/3DBD::GFP or Bra>Tbx2/3VP16::GFP fusion transgenes or Bra>GFP were grown to two stages:  mid-late neurula (~7 hpf) and mid-tailbud I/II (~10.5 hpf) according to the staging outlined in Hotta, K., Mitsuhara, K., Takahashi, H., Inaba, K., Oka, K., Gojobori, T., Ikeo, K., 2007. A web-based interactive developmental table for the ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva. Dev Dyn. 236 (PMID 17557317).

extract_protocol: Total RNA was extracted using the RNeasy micro kit (Qiagen #74004), following the manufacturer's instructions.  Samples were eluted in 13µl pre-warmed ddH2O.

treatment_protocol: Approximately 100-300 fluorescent Bra>Tbx2/3DBD::GFP, Bra>Tbx2/3VP16::GFP or Bra>GFP embryos were manually selected utilizing a Zeiss SteReo Discovery V12 microscope at neurula and mid-tailbud stages prior to RNA extraction.

tag: electroporated construct

value: Bra>Tbx2/3 DBD::GFP

value: mid-tailbud (mTb):~10.5hpf


title: A/J_ssRNA 1

description: Muscle_ssRNA injected_10days_rep1


title: Tbx2/3 VP16 at mTb, replicate 1

description: 100-300 fluorescent embryos

source_name: whole Bra>Tbx2/3 VP16 expressing embryos at mTb

value: Bra>Tbx2/3 VP16::GFP


title: SS_A1_RV.1

description: Gene expression data from wildtype M. tuberculosis

source_name: Wildtype H37Rv replicate 1

tag: strain

tag: genotype

value: Wildtype


title: Tbx2/3 VP16 at mTb, replicate 3

description: 100-300 fluorescent embryos


title: Tbx2/3 VP16 at mTb, replicate 2

description: 100-300 fluorescent embryos


title: R26R^AC/AC (Control), biological replicate #2

description: Gene expression data from control PSM.

tag: tissue


title: N23

description: normal

source_name: normal

value: non-tumourous liver parenchyma


title: Tbx2/3 DBD at mTb, replicate 3

description: 100-300 fluorescent embryos


title: Tbx2/3 DBD at mTb, replicate 1

description: 100-300 fluorescent embryos


title: control at mTb, replicate 1

description: 100-300 fluorescent embryos

source_name: whole Bra>GFP expressing embryos at mTb

value: Bra>GFP


title: T22

description: tumor


title: control at mTb, replicate 2

description: 100-300 fluorescent embryos


title: N22

description: normal


title: Darwin Pass Varnish

status: Public on Apr 26 2013

type: genomic

city: Madison

first: Andrew

last: Corcoran

state: Wisconsin

address: 1415 Engineering Drive

department: Civil and Environmental

institute: UW-Madison

description: Hybridization of labeled and fragmented 16S rRNA gene from Darwin Pass Varnish

hyb_protocol: 675ng of labeled target was hybridized with the microarray in 10 microliters of custom hybridization buffer (1M Na+, 20 mM Tris [pH=7.2], 0.02% SDS, and variable amounts of formamide) using a Nimblegen mixer matching the arrays used (see www.nimblegen.com).

scan_protocol: Scanning was performed with an Axon 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA).  The wavelength and PMT gain were set at 532 nm and 430, respectively.  Two lines were averaged.  Fluorescence data was saved in TIFF files and processed using Nimblescan software (see www.nimblegen.com).

data_processing: Raw data (.pair files) was analyzed using R . The .ndf file is matched to the .pair file for each sample is the "Match_Index" field. The "probe_sequence" listed in the ndf file are probes targeting one of the entries in the "Target" field in the table containing the processed data. Multiple probes target one consensus sequence which is why there are 481 fields of processed data. The processed data matrix includes background-corrected, averaged probe signal intensities.

molecule: genomic DNA

organism: uncultured prokaryote

source_name: Darwin Pass Varnish

label_protocol: Cloned and purified 16S rRNA genes were Cy3-labeled using random prime amplification with Klenow fragment and a decalabel DNA labeling kit (Fermentas, St Leon-Rot, Germany).  A previously published protocol was followed (Loy, A. et al. 2011. PCR mutation detection protocols. Methods in Molecular Biolology. Vol. 688, pp. 187-206).

extract_protocol: Genomic DNA was extracted using Ultra Clean Soil DNA (MoBio Laboratories, Solana Beach, CA).

tag: sample origin

value: Darwin Pass Varnish


title: Darwin Pass Soil

description: Hybridization of labeled and fragmented 16S rRNA gene from Darwin Pass Soil

source_name: Darwin Pass Soil

value: Darwin Pass Soil


title: WT_granulocytes pool 2

source_name: splenic granulocytes - CD11c-CD11b+Ly6C+MCSFR-

value: spleen

tag: cell type

value: granulocytes - CD11c-CD11b+Ly6C+MCSFR-

tag: genotype/variation

value: wild-type


title: T12

description: tumor


title: Tbx2/3 DBD at N, replicate 2

description: 100-300 fluorescent embryos

source_name: whole Bra>Tbx2/3 DBD expressing embryos at N

value: Neurula (N); ~7hpf


title: T13

description: tumor


title: N17

description: normal


title: N19

description: normal


title: A/J_saline 2

description: Muscle_saline injected_10days_rep2

tag: age

value: 2 months

value: tibalis anterior muscle


title: Tbx2/3 DBD at N, replicate 1

description: 100-300 fluorescent embryos


title: A/J_saline 3

description: Muscle_saline injected_10days_rep3

value: A/J


title: A/JOlaHsd_saline 3

description: Muscle_saline injected_10days_rep3

value: A/JOlaHsd (wild-type)

value: Dysferlin sufficient


title: control at N, replicate 2

description: 100-300 fluorescent embryos

source_name: whole Bra>GFP expressing embryos at N


title: Tbx2/3 VP16 at N, replicate 3

description: 100-300 fluorescent embryos

source_name: whole Bra>Tbx2/3 VP16 expressing embryos at N


title: A/JOlaHsd_ssRNA 2

description: Muscle_ssRNA injected_10days_rep2


title: Tbx2/3 VP16 at N, replicate 2

description: 100-300 fluorescent embryos


title: N12

description: normal


title: T19

description: tumor

value: primary hepatocellular carcinomas (HCC)


title: Tbx2/3 DBD at N, replicate 3

description: 100-300 fluorescent embryos

value: Bra>Tbx2/3 DBD::GFP


title: control at N, replicate 1

description: 100-300 fluorescent embryos


title: A/J_saline 1

description: Muscle_saline injected_10days_rep1

value: Dysferlin deficient


title: Cima Varnish

description: Hybridization of labeled and fragmented 16S rRNA gene from Cima Varnish

source_name: Cima Varnish

value: Cima Varnish


title: Cima Soil

description: Hybridization of labeled and fragmented 16S rRNA gene from Cima Soil

source_name: Cima Soil

value: Cima Soil


title: Tbx2/3 VP16 at N, replicate 1

description: 100-300 fluorescent embryos

value: Bra>Tbx2/3 VP16::GFP


title: A/JOlaHsd_saline 2

description: Muscle_saline injected_10days_rep2


title: N13

description: normal

value: non-tumourous liver parenchyma


title: A/JOlaHsd_ssRNA 3

description: Muscle_ssRNA injected_10days_rep3


title: A/JOlaHsd_ssRNA 1

description: Muscle_ssRNA injected_10days_rep1


title: T17

description: tumor


title: HaCaT_positive H2O2 control_H3

city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

institute: INP Greifswald

description: HaCaT treated positive control

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. MS 200, 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 (Roche NimbleGen, Inc.).

source_name: H2O2-treated HaCat

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

growth_protocol: The HaCaTs cell line (DKFZ), a human adult (low calcium, high temperature) epithelial keratinocyte cell line, was seeded at a density of 1×106 cells in 6 cm dishes in RPMI (Roswell Park Memorial Institute 1640 cell culture media) supplemented with 8 % fetal calf serum (Sigma), 0.1 mg/mL penicillin/streptomycin and 2 mM L-glutamine (Lonza, Basel, Switzerland) and were left to attach for 24 h prior to plasma treatment.

extract_protocol: Total RNAs from each group (n>8) were purified using Total RNA Kit (Bio&Sell, Germany) according to instructions including DNaseI treatment (Qiagen, Germany). RNA integrity was confirmed using the Bioanalyzer2010 (Agilent, Germany). cDNA was synthesized by SuperScript double-stranded cDNA Synthesis Kit (Invitrogen, Germany) from 10 µg of total RNA using oligodT (200 ng/mL) and random hexamer primer (100 ng/mL). Double strand cDNA were end-labeled with fluorescent Cy3 dye using a One-Color DNA Labeling Kit (Roche NimbleGen, Germany).

treatment_protocol: Non-thermal plasma was generated using the experimental setup schematically illustrated in Figure 1. An atmospheric pressure plasma jet kinpen (neoplas GmbH, Greifswald, Germany) ionized a flow of argon gas. A voltage of 2-6 kVpp was applied with a frequency of around 1 MHz. Gas flow was set to 3 sLm (standard liters per minute) which was controlled by a mass flow controller (MKS Instruments, Germany). The treatment efficiency of 300 ms*µL/cell (treatment time equivalents) corresponded to 60 s treatment time in 5 mL RPMI per 1×106 cells (unpublished data). Immediately after RPMI plasma treatment medium was transferred to the cells (indirect treatment). One hour after exposure to treated medium cells were collected, centrifuged, and washed. Alternatively, cells were incubated with fresh media for another 2 h, 5 h, or 23 h. Cells treated with 50 µM H2O2 served as positive controls for oxidative stress. To exclude effects of the carrier gas, cells incubated with argon gas treated medium were used as negative controls. Subsequently, all samples were analyzed and compared in respect to their gene activity.

value: HaCaTs (DKFZ), a human adult (low calcium, high temperature) epithelial keratinocyte cell line

tag: treatment

value: H2O2 (positive control)


title: A/JOlaHsd_saline 1

description: Muscle_saline injected_10days_rep1


title: HaCaT_positive H2O2 control_H4

description: HaCaT treated positive control


title: 293_AMO-CTRL_rep3

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: fragmented and labelled cDNA was hybridized to GeneChip® Human Exon 1.0 ST (Affymetrix,900694) at 45°C for 16 hours, washing and staining was done using GeneChipHybridization Wash and Stain kit (Affymetrix, 900720)

scan_protocol: hybridized microarrays were scanned on GeneChip Scanner 3000 (Affymetrix, P7N 00-00212)

data_processing:
RMA-EXON-CORE-DABG protocol
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Flp-in T-REx 293-PTH-AGO1 AMO-CTRL treated

label_protocol: sense strand cDNA was prepared with Ambion WT Expression Kit (Life Technologies, 4411973), fragmentation and biotin labelling was done with GeneChip WT terminal labelling kit (Affymetrix, 900670)

growth_protocol: Flp-In T-REx 293 cells were stably transfected with a plasmid encoding AGO1 N-terminally tagged with ProteinA-TEV protease cleavage site-Hisx6. Expression of tagged AGO1 is tetracycline inducible. For the purpose of this microarray analysis AGO1 expression was not induced. Cells were grown in Dulbecco’s modified Eagle medium (DMEM) with high glucose, supplemented with 10% fetal bovine serum at 37°C under humidified air with 5% CO2

extract_protocol: total RNA was izolated 48 hours post transfecton with TRIZOL (Life Technologies) according to manufacturers instructions; sample integrity was confirmed on Bioanalyzer and samples were further processed by the Source BioScience UK Limited

treatment_protocol: Flp-In T-REx 293-PTH-AGO1 cells were transfected with Lipofectamine 2000 (Life Technologies) and miR-92a (mA/ZEN/mCmAmGmGmCmCmGmGmGmAmCmAmAmGmUmGmCmA  mAmU/ZEN/mA; IDT; 6.25nM) or control inhibitor (mC/ZEN/mGmCmGmAmCmUmAmUmAmCmGmCmGmCmAmAmUmAmUmGmG/ZEN/mU; IDT; 6.25nM)

value: control inhibitor

value: Flp-in T-REx 293-PTH-AGO1


title: control at N, replicate 3

description: 100-300 fluorescent embryos

value: Bra>GFP

tag: developmental stage

value: Neurula (N); ~7hpf


title: HaCaT_positive H2O2 control_H1

description: HaCaT treated positive control


title: HaCaT_negative argon control

description: HaCaT treated negative control

source_name: Argon gas-treated HaCaT

value: argon (negative control)


title: HaCaT_positive H2O2 control_H2

description: HaCaT treated positive control


title: HaCaT_plasma treated_P4

description: HaCaT treated sample

source_name: plasma-treated HaCaT

value: non-thermal plasma


title: 293_AMO-CTRL_rep5


title: Female WT Hypoxia 704

city: Pittsburgh

first: Jacob

last: Larkin

state: PA

address: 240 Craft Ave.

department: OB/GYN/Reproductive Sciences

institute: University of Pittsburgh

description: Placental gene expression at E15.5

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K mouse mRNA microarrays (GPL10787) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: E15.5 mouse placenta

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: C57Bl6/J mice heterozygous for NDRG1-null allele were bred and separated next day (E0.5), and give ad libitum access to standard chow and water with 12h light:dark cycle. Pregnant dams were sacrificed at E15.5 by cervical dislocation following isoflurane anesthesia. Following sacrifice, embryos and placentas were collected, NDRG1 genotype and sex were determined by PCR of fetal tissue,  and RNA was extracted from placental tissue following removal of membranes.

extract_protocol: RNA was prepared using the Quiagen RNeasy Mini Kit (Quiagen, Valencia, CA) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Hypoxic dams were placed in 12% O2 at E12.5 until sacrifice at E15.5.

tag: Sex

value: Female

tag: ndrg1 genotype

value: Wild Type

tag: oxygen level


title: Female WT Hypoxia 703

description: Placental gene expression at E15.5


title: 293_AMO-miR-92_rep1

source_name: Flp-in T-REx 293-PTH-AGO1 AMO-miR-92a treated

value: miR-92a inhibitor

tag: cell line


title: 293_AMO-miR-92_rep5


title: 293_AMO-miR-92_rep4


title: Female KO Normoxia 603

description: Placental gene expression at E15.5

value: Knock-out

value: Standard


title: Female KO Hypoxia 802

description: Placental gene expression at E15.5


title: 293_AMO-miR-92_rep2


title: 293_AMO-CTRL_rep1


title: Female KO Normoxia 601

description: Placental gene expression at E15.5


title: Female WT Hypoxia 701

description: Placental gene expression at E15.5


title: Female KO Hypoxia 804

description: Placental gene expression at E15.5


title: 293_AMO-CTRL_rep4


title: Female WT Normoxia 502

description: Placental gene expression at E15.5


title: 293_AMO-CTRL_rep2


title: 293_AMO-miR-92_rep3


title: Female KO Hypoxia 803

description: Placental gene expression at E15.5


title: HaCaT_plasma treated_P3

description: HaCaT treated sample


title: HaCaT_plasma treated_P1

description: HaCaT treated sample


title: Female KO Normoxia 602

description: Placental gene expression at E15.5


title: HaCaT_untreated_K2

description: HaCaT untreated control

source_name: HaCaT control

value: untreated control


title: Male KO Hypoxia 402

description: Placental gene expression at E15.5

value: Male


title: 3MC+TPA exposed C3H10T1/2 cultured for 6 weeks_B2

city: Lucknow

first: Dr Sushil

last: Kumar

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

country: India

institute: Indian Institute of Toxicology Research

description:
3MC+TPA exposed C3H10T1/2 cultured for 6 weeks
Sample name: B2

hyb_protocol: The labeled cRNA samples were hybridized on to an Agilent Custom Mouse Whole Genome 8x60k Gene expression designed by Genotypic Technology Private Limited. (AMADID No: 026986).600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: The normalization was done using GeneSpring GX 11.5 Software. 75th Percentile Shift Normalization.

source_name: 3MC+TPA exposed C3H10T1/2 Cell Line

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Mouse embryo fibroblast  cell lines, C3H10T1/2  was  procured  from National Centre For Cell Science (Pune,India).DMEM (GIBCO, Grand Island, NY, USA) media were supplemented with 10% v/v fetal bovine serum (GIBCO, Grand Island, NY, USA), 1.5 g/l NaHCo3, 4.5 g/l Glucose (SRL,India),1X Antibiotic-Antimycotic (GIBCO, Grand Island, NY, USA). The cell lines were maintained in a humidiﬁed, 5% CO2  incubator at 37 0C and sub-cultured twice weekly using 0.25% v/v trypsin/EDTA (GIBCO, Grand Island, NY, USA). All experiments were performed using cells in exponential growth phase .

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit  following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Exponentially growing cells were seeded at a density of 1X 104 cells/25-cm2  .3MC(2.5µg/ml)  was given to each flask after 24  h of seeding for 2 days. Cells were  washed with phosphate  buffered  saline (PBS) and replaced with fresh normal medium for next 4 days .TPA (100ng/ml) exposure was given twice a week and was given to each 3MC treated flask for next two- weeks . After the removal of TPA treatment cells were cultured in normal DMEM media for next 4-weeks. After 6 weeks,flask  were divided into two groups one was used for the gimesa staining and counting and other one was used for the microarray experiment.The methanol fixed, stained with 10% Giemsa solution, rinsed three times with water and observed by light microscopy for foci scoring and classification. Transformed foci were counted and classified . Foci showing deep basophilic, dense multilayering of cells, random cell orientation at any part of the focus edge, invasion into the surrounding contact-inhibited mono- layer, and domination of spindle-shaped cells were scored as positive transformation foci.

value: embryo fibroblast cell line C3H10T1/2

tag: agent


title: Female WT Normoxia 501

description: Placental gene expression at E15.5


title: Male KO Hypoxia 404

description: Placental gene expression at E15.5


title: HaCaT_plasma treated_P2

description: HaCaT treated sample


title: 3MC+TPA exposed C3H10T1/2 cultured for 6 weeks_B1

description:
3MC+TPA exposed C3H10T1/2 cultured for 6 weeks
Sample name: B1


title: HaCaT_untreated_K1

description: HaCaT untreated control


title: C3H10T1/2 cultured for 6 weeks_A2

description:
C3H10T1/2 cultured for 6 weeks
Sample name: A2

source_name: C3H10T1/2 Cell Line

value: control


title: Col 3 Row 2-Array3

city: College Station

first: Maria

middle: Priscila

last: Almario

state: Texas

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

description:
Sample 22
Microarray3.gpr

hyb_protocol: Samples were for hybridization by adding lyophilized 10X Blocking Agent (supplied with Agilent Oligo aCGH Hybridization Kit), following manufacture's protocol.  The samples were hybridazed in a Agilent's Saccharomyces cerevisiae Gene Expression Microarray, 8x15K G4813A

data_processing: The arrays were scanned using the GenePix 4100A Microarray Scanner and GenePix Pro 6.0 software (Molecular Devices) for image analysis.The Microarray Data Analysis System (MIDAS) software was used to normalize the data using LOWESS based normalization algorithm.

organism: Saccharomyces cerevisiae

source_name: liquid culture

label_protocol: 5 µg of  cDNA was labeled using Cy3- and Cy5- mono-Reactive Dye Pack (GE Healthcare)

growth_protocol: Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass. The cells were grown in YNB minimal media (No glucose), and in 1g/mL Hydrolysates biomass

extract_protocol: Total RNA extracted using ZR Fungal/Bacterial RNA MiniPrep™ (Zymo) kit

value: Adaptive Mutant PG-132

value: reference GFP


title: Col 4 Row 1-Array3

description:
Sample 23
Microarray3.gpr

scan_protocol: The arrays were scanned using the GenePix 4100A Microarray Scanner

value: Adaptive Mutant PR-164

value: reference DsRed


title: Sensory neuron Process RNA Sample 4

first: Sergey

last: Kalachikov

address: NWC Bld, 550 West 120th Street Rm 1002

institute: Columbia University

description: array 4 = sCB4_546_sP4_647

hyb_protocol: 825 ng of labeled cRNA for IP and 825 ng of CNS control samples were mixed with oligoarray control targets, degraded and and hybridized (Agilent In Situ Hybridization Kit Plus) overnight in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Arrays were scanned on two channels using Agilent G2565AA scanner.

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (version A.7.5). The values in the Matrix table correspond to background-subtracted, log2-transformed, LOWESS-normalized hybridization probe intensities for each sample. Agilent software and custom R-scripts were used to derive these values.

label: Alexa Fluor 647

organism: Aplysia californica

source_name: Sensory neuron Process

label_protocol: Total RNA samples prepared as described above were amplified in two rounds of IVT-mediated linear amplification using MessageAmp II kits (Ambion) and the resulting amplified cRNA was labeled either with Alexa Fluor 546 or Alex Fluor 647 using ULISES labeling reagents (Invitrogen). The amplification and labeling kits were used in conformity with protocols recommended by their manufacturers.

extract_protocol: Isolated sensory neurons were cultured for four days and proceeded to separate cell bodies and processes. A culture dish contained eight to ten sensory neurons. Glass microelectrodes were prepared from micro-capillaries (AM systems) and used for manual micro-dissection. Under a Zeiss inverted microscope, using these electrodes, cell bodies or processes from the cultured neurons were removed. These dishes were then washed three times with 10 ml of L15 media. Dishes were then briefly kept on ice bath and 100 µl of Trizol were added to each dishes and incubated for 5 minutes. Using a 200 µl pipette tip, the surfaces of these dishes were briefly scrapped and the Trizol-RNA solution was transferred to an RNAse free tube (Ambion) for extraction. A fresh 100 µl of Trizol were added again to each dishes and the extraction was repeated. The dishes were examined under an inverted microscope to confirm extraction. RNA was prepared from TRIZOL extracts (Invitrogen) and precipitated using 5 M ammonium acetate, glycoblue (Ambion) and absolute ethanol.

tag: animal

value: cell culture

value: single sensory neuron


title: Col 3 Row 1-Array3

description:
Sample 21
Microarray3.gpr

value: Adaptive Mutant PG-353


title: Male WT Hypoxia 311

description: Placental gene expression at E15.5


title: Sensory neuron Cell Body RNA Sample 4

description: array 4 = sCB4_546_sP4_647

label: Alexa Fluor 546

source_name: Sensory neuron Cell Body


title: Male WT Hypoxia 302

description: Placental gene expression at E15.5


title: Male KO Hypoxia 401

description: Placental gene expression at E15.5


title: Sensory neuron Process RNA Sample 3

description: array 3 = sCB3_546_sP3_647


title: Col 2 Row 1-Array3

description:
Sample 19
Microarray3.gpr

value: Adaptive Mutant PR-338


title: Col 4 Row 2-Array3

description:
Sample 24
Microarray3.gpr

value: Adaptive Mutant M1


title: E8.5_Head_KO-2

city: Copenhagen

first: Sandra

middle: Ursula

last: Schmitz

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research and Innovation Centre

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing:
Gene Array Analyzer (Gellert et al, NAR, 2012) webtool.
Gene Array Analyzer uses Affymetrix Power Tools (see www.affymetrix.com) to calculate RMA probe set summation values. The Gene Array Analyzer command is:  apt-probeset-summarize -a rma-bg,quant-norm.sketch=-1.bioc=true.lowprecision=false.usepm=true,pm-only,med-polish.expon=true -a pm-only,dabg.chisq=true -p ./affy/MoGene-1_0-st-v1.r4.pgf -c ./affy/MoGene-1_0-st-v1.r4.clf -b ./affy/MoGene-1_0-st-v1.r4.bgp --qc-probesets ./affy/MoGene-1_0-st-v1.r4.qcc -m affy/MoGene-1_0-st-v1.r4.mps upload/e9ccb98b714934751de47d6304ca7f320434/*.CEL -o upload/e9ccb98b714934751de47d6304ca7f320434/apt-result #plus various filtering

source_name: E8.5 head

label_protocol: samples were processed with the Whole Transcript Assay Kit as recommended by the manufacterer (Affymetrix)

growth_protocol: In vivo, E8.5 embryos

extract_protocol: RNAeasy Microkit (Qiagen)

treatment_protocol: no treatment, Heterozygote versus knockout

value: Jarid1b knockout

tag: body part

value: head


title: Male KO Normoxia 203

description: Placental gene expression at E15.5

value: Knock-out


title: Male KO Normoxia 202

description: Placental gene expression at E15.5

value: Standard


title: E8.5_Head_KO-3


title: C3H10T1/2 cultured for 6 weeks_A1

description:
C3H10T1/2 cultured for 6 weeks
Sample name: A1


title: Male WT Hypoxia 301

description: Placental gene expression at E15.5

value: Wild Type


title: Male KO Normoxia 201

description: Placental gene expression at E15.5

value: Male


title: Sensory neuron Cell Body RNA Sample 3

description: array 3 = sCB3_546_sP3_647


title: Sensory neuron Cell Body RNA Sample 2

description: array 2 = sCB2_546_sP2_647


title: Col 1 Row 2-Array3

description:
Sample 18
Microarray3.gpr

value: Adaptive Mutant PR-438


title: Sensory neuron Process RNA Sample 2

description: array 2 = sCB2_546_sP2_647


title: Sensory neuron Process RNA Sample 1

description: array 1 = sCB1_546_sP1_647


title: LIF

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

description: replicate 1

hyb_protocol: Standard Illumina scanning protocol

data_processing: The cut-off: The detection pval of LIF or LIF/2I <0.05

source_name: E3.5 embryo

label_protocol: Standard Illumina hybridization protocol

growth_protocol: B6 mESCs were cutlured in serum medium in thre presence of LIF/2I

extract_protocol: Standard illumina RNA extraction protocol

treatment_protocol: With or without  2I for 24h

value: B6 mouse embryonic stem cells (mESCs)


title: LIF/2I

description: replicate 1


title: Female WT Normoxia 504

description: Placental gene expression at E15.5

value: Female


title: Col 1 Row 1-Array3

description:
Sample 17
Microarray3.gpr

value: Adaptive Mutant PY-231

value: reference YFP


title: E8.5_Head_KO-1


title: Col 2 Row 2-Array2

description:
Sample 12
Microarray2.gpr

value: Adaptive Mutant PG-259

value: reference GFP


title: Col 3 Row 1-Array2

description:
Sample 13
Microarray2.gpr


title: Motor neuron Process RNA Sample 4

description: array 4 = mCB4_546_mP4_647

source_name: Motor neuron Process

extract_protocol: Isolated motor neurons were cultured for four days and proceeded to separate cell bodies and processes. A culture dish contained four motor neurons. Glass microelectrodes were prepared from micro-capillaries (AM systems) and used for manual micro-dissection. Under a Zeiss inverted microscope, using these electrodes, cell bodies or processes from the cultured neurons were removed. These dishes were then washed three times with 10 ml of L15 media. Dishes were then briefly kept on ice bath and 100 µl of Trizol were added to each dishes and incubated for 5 minutes. Using a 200 µl pipette tip, the surfaces of these dishes were briefly scrapped and the Trizol-RNA solution was transferred to an RNAse free tube (Ambion) for RNA extraction. A fresh 100 µl of Trizol were added again to each dishes and repeated extraction. The dishes were examined under an inverted microscope to confirm extraction. RNA was prepared from TRIZOL extracts (Invitrogen) and precipitated using 5 M ammonium acetate, glycoblue (Ambion) and absolute ethanol.

tag: sample type

value: cell culture

value: single motor neuron


title: Motor neuron Process RNA Sample 3

description: array 3 = mCB3_546_mP3_647


title: Motor neuron Cell Body RNA Sample 3

description: array 3 = mCB3_546_mP3_647

source_name: Motor neuron Cell Body


title: Sensory neuron Cell Body RNA Sample 1

description: array 1 = sCB1_546_sP1_647

value: single sensory neuron


title: Motor neuron Process RNA Sample 1

description: array 1 = mCB1_546_mP1_647


title: Male WT Normoxia 101

description: Placental gene expression at E15.5

tag: strain


title: Col 1 Row 2-Array2

description:
Sample 10
Microarray2.gpr

tag: genotype

value: reference DsRed


title: Col 3 Row 2-Array2

description:
Sample 14
Microarray2.gpr

value: Adaptive Mutant PG-132


title: Col 2 Row 1-Array2

description:
Sample 11
Microarray2.gpr

value: Adaptive Mutant PR-338


title: Motor neuron Cell Body RNA Sample 2

description: array 2 = mCB2_546_mP2_647

tag: tissue


title: Male WT Normoxia 102

description: Placental gene expression at E15.5


title: Motor neuron Process RNA Sample 2

description: array 2 = mCB2_546_mP2_647


title: Col 4 Row 2-Array2

description:
Sample 16
Microarray2.gpr

value: Adaptive Mutant M1


title: Motor neuron Cell Body RNA Sample 4

description: array 4 = mCB4_546_mP4_647


title: E8.5_Head_het-1

value: Jarid1b heterozygote

value: head


title: Col 4 Row 1-Array2

description:
Sample 15
Microarray2.gpr

value: Adaptive Mutant PR-164


title: Retina_HAN_rep3

city: Seoul

first: Jeong Hun

last: Kim

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

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

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner (G2565AA) and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

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

source_name: retina, 7 days

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: We intravitreally injected 1 μM of PBS, AAP, or HAN into the right eyes of C57BL/6 male mice. One week later, the mice were sacrificed and the eyes were enucleated.

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

treatment_protocol: Retinal tissues were prepared from the enucleated eyes. Four retinal tissues were pooled into 1 test tube.

value: peptide HAN

tag: gender

value: male

value: retina

value: adult


title: E8.5_Head_het-3


title: Motor neuron Cell Body RNA Sample 1

description: array 1 = mCB1_546_mP1_647


title: Male WT Normoxia 111

description: Placental gene expression at E15.5

value: Male

value: Wild Type

value: Standard


title: Col 1 Row 1-Array2

description:
Sample 9
Microarray2.gpr

value: Adaptive Mutant PY-231

value: reference YFP


title: Retina_HAN_rep2


title: Col 4 Row 2-Array1

description:
Sample 8
Microarray1.gpr


title: Retina_HAN_rep1


title: Col 4 Row 1-Array1

description:
Sample 7
Microarray1.gpr


title: RNA from CNS Sample 4

description: array 4 = IP4_546_T4_647

source_name: RNA from CNS

extract_protocol: All IP experiments were done at 4C in an RNAse-free environment. The antibody incubation buffer contained 50 mM Tris HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM KCl, 0.5 % NP40, 1 mM DTT, 1 % ultra pure BSA (AMBION), 1 % yeast tRNA, and inhibitors of protease (Roche), phosphatase (SIGMA) and RNAse inhibitors (Ambion) Pre-cleared extracts prepared from adult (50-90 gram animals) Aplysia CNS (n=1) were incubated with 20 µg of purified anti-kinesin antibody (Puthanveetil et al., 2008). Following six hours of incubation on a rotator, protein A/G beads (Pierce) were added to the immunoprecipitates and were rotated for another hour.  The immunoprecipitates were washed three times using the same buffer by brief centrifugation (100x g for two minutes). These washes were carried out in separate eppendorf tubes (siliconized RNAse free) to minimize nonspecific binding of RNAs to the plastics. Following the third wash, the beads were incubated with TRIZOL to prepare RNA according to manufacturer’s instructions. Total RNA from the Aplysia CNS that served as a control in these experiments was isolated with TRIZOL following manufacturer’s instructions.

value: 50-90 gram adult animal

value: entire CNS


title: Retina_AAP_rep3

value: peptide AAP


title: RNA from CNS Sample 3

description: array 3 = IP3_546_T3_647


title: Retina_AAP_rep2


title: Col 3 Row 2-Array1

description:
Sample 6
Microarray1.gpr

value: Adaptive Mutant PG-132

value: reference GFP


title: Retina_CON_rep3

value: control


title: RNA from CNS Sample 1

description: array 1 = IP1_546_T1_647


title: Col 2 Row 1-Array1

description:
Sample 3
Microarray1.gpr

value: Adaptive Mutant PR-338

value: reference DsRed


title: Kinesin IP RNA Sample 4

description: array 4 = IP4_546_T4_647

source_name: RNA co-immunoprecipitated with kinesin


title: Col 1 Row 2-Array1

description:
Sample 2
Microarray1.gpr

value: Adaptive Mutant PR-438


title: Col 3 Row 1-Array1

description:
Sample 5
Microarray1.gpr

value: Adaptive Mutant PG-353


title: Retina_CON_rep2

value: male

value: retina


title: Col 2 Row 2-Array1

description:
Sample 4
Microarray1.gpr

value: Adaptive Mutant PG-259


title: Kinesin IP RNA Sample 2

description: array 2 = IP2_546_T2_647


title: Kinesin IP RNA Sample 3

description: array 3 = IP3_546_T3_647


title: Retina_AAP_rep1

value: adult


title: RNA from CNS Sample 2

description: array 2 = IP2_546_T2_647


title: iN-21(shp53)

city: Chengdu

first: chongkui

last: sun

state: Sichuan

address: No.14, Sec. 3, Renmin Road South

department: State key laboratory of oral diseases

institute: Sichuan University

description: induced neurons

hyb_protocol: Standard Illumina hybridization protocol.  Immobilized, biotinylated amplified RNAs were then detected by staining with cy3 Steptavidin (1ug cy3-SA per 1 ml of Illumina “Block E1”) for 10 minutes at room temperature.

scan_protocol: Illumina Scan protocol. Arrays were scanned on an Illumina BeadArray Reader.  Laser power and PMT voltage were kept constant for Cy3 scans.

data_processing: Scanned images were quantitated by Illumina Beadscan, v3. Quantitated data was imported into Illumina GenomeStudio software. The data was normalized by Illumina's quantile method. Average signal of each probe was filtered using 50 as baseline. To each probe of different samples, select differently expressed probes using division of maximum and minimun signal values.

source_name: induced neurons from fibroblasts for 21 days

label_protocol: RNA transcripts were amplified by T7 linear amplification (MessageAmp TotalPrep amplification kit; Life Technologies). Invitro-transcription was carried out by adding 10x T7 reaction buffer (2.5ul), T7 biotin-NTP mix (2.5ul), and T7 RNA polymerase enzyme mix (2.5ul) and incubation at 37C. The Invitro-transcription reaction was carried out for 14 hours.

growth_protocol: Human fibroblast IMR90 grows in DMEM with 10%FBS. Induction process uses special neuron medium.

extract_protocol: Total RNA was extracted using Trizol isolation system (Invitrogen) according to manufacturer’s instructions. Total RNA was treated with DNase I (Qiagen) to prevent DNA contamination. Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm.  Total RNA quality was then determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations.

treatment_protocol: Assemble lentivirus using shRNA plasmids to knockdown p53.

value: culture shRNA-p53 treated cells with induced medium for 21 days

value: culture with induced medium

tag: cell type

value: induced neurons


title: 251983910024_2_2-T5[B(5)/B(3)]

status: Public on Apr 25 2013

city: Cambridge

first: Ilan

last: Wapinski

address: 7 Cambridge Center

institute: Broad Institute

description: Biological replicate B, technical replicate 1

hyb_protocol: Standard Agilent protocols for Agilent 8x15K and 4x44K Oligo Microarrays

scan_protocol: Arrays were scanned using an Agilent scanner and analyzed with Agilent’s feature extraction software version 10.5.1.1.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.  Reported expression values for each gene are median log2 ratios across all probes.

organism: Nakaseomyces glabratus

label_protocol: Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.

growth_protocol: Cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and grown overnight in BMW medium at 30 ° C in a New Brunswick Scientific Edison model TC-7 roller drum on the highest speed until saturated (1-2 days).  These saturated cultures were then used to inoculate 300 ml BMW batch cultures in 2 liter Erlenmeyer flasks at 1 x 106 cells/mL for the glucose depletion and repletion experiments described below.  Flasks were transferred to New Brunswick Scientific Edison water bath model C76 shakers set to 200 rpm.

extract_protocol: Qiagen Yeast RNA extraction

treatment_protocol: Heat Shock: Cultures were grown at 22C to mid-log densities (3x10^7 to 1x10^8 cells/mL) and then vacuum filtered and resuspended in pre-warmed (37C or 42C) media. Samples were harvested at different time intervals (5, 15, 30, 45, 60 mins)

value: heat shock

tag: time point (minutes)


title: Col 2 Row 2-Array3

description:
Sample 20
Microarray3.gpr


title: 251983910024_2_4-T30[B(5)/B(3)]


title: 251983910024_1_4-T45[A(5)/A(3)]

description: Biological replicate A, technical replicate 1


title: 251983910024_1_1-T5[A(5)/A(3)]


title: Col 1 Row 1-Array1

description:
Sample 1
Microarray1.gpr

value: Adaptive Mutant PY-231

value: reference YFP


title: Kinesin IP RNA Sample 1

description: array 1 = IP1_546_T1_647

value: 50-90 gram adult animal

value: entire CNS


title: 251983910024_2_3-T15[B(5)/B(3)]


title: 251983910021_1_2-T60[B(5)/B(3)]


title: 251983910024_1_2-T15[A(5)/A(3)]


title: Retina_CON_rep1

value: control


title: 251983910021_1_1-T45[B(5)/B(3)]


title: 251983910013_2_1-T5[B(5)/B(3)]

treatment_protocol: Salt Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with hydrogen peroxide to a final concentration of 5 mM. Samples were harvested at different time intervals (5, 15, 30, 60 minutes after treatment)

value: hydrogen peroxide


title: 251983910013_2_3-T30[B(5)/B(3)]


title: 251983910013_1_3-T30[A(5)/A(3)]


title: 251983910013_2_2-T15[B(5)/B(3)]


title: 251983910022_2_1-T5[C(5)/C(3)]

description: Biological replicate C, technical replicate 1


title: 251983910028_2_3-T45[A(5)/A(3)]

description: Biological replicate A, technical replicate 2


title: 251983910024_2_1-T60[A(5)/A(3)]


title: 251983910013_1_4-T60[A(5)/A(3)]


title: 251983910013_2_4-T60[B(5)/B(3)]


title: 251983910022_2_2-T15[C(5)/C(3)]


title: 251983910022_2_4-T60[C(5)/C(3)]


title: 251983910013_1_2-T15[A(5)/A(3)]


title: 251983910006_1_1-T5[A(5)/A(3)]

treatment_protocol: Salt Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with NaCl to a final concentration of 0.3M. Samples were harvested at different time intervals (5, 15, 30, 60 minutes after treatment)

value: NaCl


title: 251983910022_2_3-T30[C(5)/C(3)]


title: 251983910013_1_1-T5[A(5)/A(3)]


title: 251983910019_2_1-T5[D(5)/D(3)]

description: Biological replicate D, technical replicate 1


title: 251983910019_1_2-T15[C(5)/C(3)]


title: 251983910006_2_2-T15[B(5)/B(3)]


title: 251983910006_2_3-T30[B(5)/B(3)]


title: 251983910019_2_3-T30[D(5)/D(3)]


title: 251983910019_1_3-T30[C(5)/C(3)]


title: 252035410012_2_4-T45[B(5)/B(3)]

organism: Kluyveromyces lactis


title: 251983910006_2_4-T60[B(5)/B(3)]


title: 251983910019_2_4-T60[D(5)/D(3)]


title: 251983910019_1_4-T60[C(5)/C(3)]


title: 251983910019_1_1-T5[C(5)/C(3)]


title: 251983910006_1_2-T15[A(5)/A(3)]


title: 251983910006_2_1-T5[B(5)/B(3)]


title: 252035410012_2_2-T15[B(5)/B(3)]


title: 251983910019_2_2-T15[D(5)/D(3)]


title: 251983910006_1_3-T30[A(5)/A(3)]


title: 252035410016_2_3-T60[A(5)/A(3)]


title: 251983910006_1_4-T60[A(5)/A(3)]


title: 252035410012_1_2-T15[A(5)/A(3)]


title: 252035410012_2_1-T5[B(5)/B(3)]


title: 252035410012_1_3-T30[A(5)/A(3)]


title: 252035410008_1_2-T15[A(5)/A(3)]


title: 252035410008_1_4-T60[A(5)/A(3)]


title: 252035410008_1_3-T30[A(5)/A(3)]


title: 252035410008_2_3-T30[B(5)/B(3)]


title: 252035410008_1_1-T5[A(5)/A(3)]


title: 252035410012_2_3-T30[B(5)/B(3)]


title: 252035410016_2_4-T60[B(5)/B(3)]


title: 252035410012_1_1-T5[A(5)/A(3)]


title: 252035410012_1_4-T45[A(5)/A(3)]


title: 252035410008_2_4-T60[B(5)/B(3)]


title: 252035410008_2_1-T5[B(5)/B(3)]


title: 252035410008_2_2-T15[B(5)/B(3)]


title: E8.5_Head_het-2

tag: age

tag: genotype/variation

value: Jarid1b heterozygote

value: head


title: 252035410002_1_2-T15[A(5)/A(3)]

organism: Lachancea waltii

tag: treatment


title: 252035410009_2_4-T60[C(5)/C(3)]


title: 252035410009_1_1-T5[B(5)/B(3)]


title: 252035410009_2_3-T30[C(5)/C(3)]


title: 252035410002_1_3-T30[A(5)/A(3)]


title: 252035410002_1_1-T5[A(5)/A(3)]


title: 252035410002_2_4-T60[D(5)/D(3)]


title: 252035410009_2_1-T5[C(5)/C(3)]


title: 252035410002_2_1-T5[D(5)/D(3)]


title: 252035410009_1_3-T30[B(5)/B(3)]


title: 252035410002_1_4-T60[A(5)/A(3)]


title: 252035410009_1_4-T60[B(5)/B(3)]


title: MMA_rep2 [mRNA]

city: Changsha

first: Jia

last: Li

state: Hunan province

address: 110, Xiangya Road

institute: State Key Laboratory of Medical genetics

description: Gene expression in Middle Meningeal Artery

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Middle Meningeal Artery Wall, replicate2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: The total RNA was extracted by Trizol Reagent, and DNase digestion.Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Full-thickness vessel wall samples from ruptured IA domes and MMA were prospectively collected from patients undergoing microsurgical clipping

value: Middle Meningeal Artery Wall

value: female


title: HUVEC/GPR4_pH 6.4-treated_5 h_rep4

city: Greenville

first: Lixue

last: Dong

state: NC

address: 600 Moye Blvd.

institute: East Carolina University

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C US82800149

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.10.7.3.1).
Background subtraction and LOWESS normalization (https://genome.unc.edu/)

source_name: HUVECs with overexpressed GPR4, pH 6.4-treated, 5 h

label_protocol: Agilent Quick Amp Labeling Kits

growth_protocol: HUVECs with endogenous or overexpressed GPR4 level were grown in endothelial growth medium-2 (EGM-2; Lonza, CC-3162) in 10 cm tissue culture plates to reach 80-90% confluency.

extract_protocol: Total RNA was extracted using the RNeasy Plus mini kit (QIAGEN, 74134) following manufacterer's instructions.

treatment_protocol: HUVECs with endogenous or overexpressed GPR4 level were treated  for 5 h with EGM-2 medium that was buffered with 7.5 mM HEPES, 7.5 mM EPSS & 7.5 mM MES and ajusted to pH 8.4 or 6.4.

value: HUVEC

tag: medium

value: EGM-2_HEPES-EPPS-MES-buffered, pH 6.4

source_name: HUVECs with overexpressed GPR4, pH 8.4-treated, 5 h

value: EGM-2_HEPES-EPPS-MES-buffered, pH 8.4


title: HUVEC/Vector_pH 6.4-treated_5 h_rep4

source_name: HUVECs with endogenous GPR4, pH 6.4-treated, 5 h

source_name: HUVECs with endogenous GPR4, pH 8.4-treated, 5 h


title: IA_rep1 [mRNA]

description: Gene expression in Intracranial Aneurysm Wall

source_name: Intracranial Aneurysm Wall, replicate1

value: Intracranial Aneurysm Wall


title: 252035410009_2_2-T15[C(5)/C(3)]


title: 252035410002_2_3-T30[D(5)/D(3)]


title: 252035410009_1_2-T15[B(5)/B(3)]


title: HUVEC/GPR4_pH 6.4-treated_5 h_rep2


title: 252035410002_2_2-T15[D(5)/D(3)]


title: MMA_rep1 [mRNA]

source_name: Middle Meningeal Artery Wall, replicate1


title: HUVEC/Vector_pH 6.4-treated_5 h_rep2


title: MDSL_shIRAK1_rep1

city: Cincinnati

first: Garrett

last: Rhyasen

state: OHIO

address: 3333 Burnet Ave

institute: CCHMC

hyb_protocol: Hybridizations were with the standard Probe Array Cartidge (GeneChip Human Gene 1.0 ST Array; Affymetrix). Create a hybridization cocktail for a single probe array that contains 2.5 µg of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20× Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1× Hybridization Buffer.  Heat hybridization cocktail to 99°C for 2 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 90 µL of 1× Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1× Hybridization Buffer and fill probe array with 90 µL of the hybridization cocktail. Incubate at 45°C for 18 hrs in the Hybridization Oven rotating at 60 rpm.

scan_protocol: Genechips were scanned using the Affymetrix GeneChip Scanner 3000 7G, and data were collected with Genechip Operating Software (Affymetrix)

data_processing:
Use RMA to normalize all arrays (samples) for a project. Average means of replicate samples. Create interpretations to compare different groups. Filter raw data to remove entities (genes) not being expressed. Perform fold change analysis, create list of genes with a  FC  1.5 or higher. Then use a statistical test, T Test unpaired with a p-value cutoff of 0.05 and multiple testing correction using Benjamini-Hochberg.
probe group file: HuGene-1_0-st-v1.pgf
meta-probeset file: HuGene-1_0-st-v1.csv

source_name: MDSL cells, pLKO, IRAK1

label_protocol: A total of 1-20ng of total RNA was reversed transcribed and labeled with the Ovation Pico WTA System (Nugen), the WT-Ovation Exon Module v1.0 (NuGEN), and the Encore Biotin Module (NuGEN)

growth_protocol: MDSL cells were cultured in RPMI1640 supplemented with 10% fetal bovine serum, 100U/mL Penicillin and 100ug/mL Streptomycin, and 10ng/mL hIL-3.

extract_protocol: Total RNA was extracted and purified with Quick-RNA MiniPrep Kit from Zymo Research (Cat#R1054) according to the manufacturer's instructions.

treatment_protocol: Short hairpin RNA targeting human IRAK1 was expressed in pLKO.1-puro lentiviral expression vector, and provided by the Lenti-shRNA library core CCHMC. The clones for TRAF6 is TRCN0000007348. Puromycin resistance gene was replaced by green fluorescent protein (GFP). The vector targeting scramble sequences was used as control. All the plasmids were packaged into pseudo lentivirus for transient and stable knockdown. Lentiviruses were pseudotyped with VSV-G, produced by 293-FT cells, and concentrated through ultracentrifugation at 20,000rpm for 2 hours at 4°C. Cells at 1×10^5/mL were transduced with lentivirus at an multiplicity of infection (MOI) of 0.5~1 and in the presence of 8μg/mL of polybrene (No. TR-1003-G; Millipore). At 2.5 days post-transduction, GFP positive cells were purified via fluorescence-activated cell sorting (FACS).

value: IRAK1 knockdown


title: MDSL_shIRAK1_rep2


title: HUVEC/GPR4_pH 6.4-treated_5 h_rep1


title: 251983910024_1_3-T30[A(5)/A(3)]

value: heat shock


title: MDSL_DMSO_rep1

source_name: MDSL cells, DMSO

value: DMSO control


title: HUVEC/Vector_pH 6.4-treated_5 h_rep1


title: MDSL_shGFP_rep2

source_name: MDSL cells, pLKO, shGFP

value: control knockdown


title: HUVEC/Vector_pH 6.4-treated_5 h_rep3


title: HUVEC/GPR4_pH 6.4-treated_5 h_rep3


title: IA_rep2 [mRNA]

source_name: Intracranial Aneurysm Wall, replicate2


title: MDSL_IRAKinh_rep2

source_name: MDSL cells, IRAKinh

value: IRAK inhibitor


title: MDSL_shGFP_rep1


title: MDSL_IRAKinh_rep1


title: MDSL_DMSO_rep2


title: clock mutant mouse infect night biological rep 2

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description:
Gene expression data from clock mutant mouse infect night cecal tissue
24_CK_IN_2

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 Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with BRB Array Tools version 4.2.1

label_protocol: Biotinylated cRNA were prepared according to the standard protocols described in the Affymetrix Gene Expression Analysis Technical Manual

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

treatment_protocol: Mice were treated with streptomycin intragastrically 24 hours before inoculation with S. Typhimurium. At 72 hours after infection, mice were euthanized

value: Clock mutant

tag: infection

value: Salmonella Typhimurium

tag: circadian time

value: night (10pm)

value: 8 - 14 weeks

value: cecal mucosa


title: clock mutant mouse uninfect night biological rep 1

description:
Gene expression data from clock mutant mouse uninfect night cecal tissue
10_CK_UN_1

value: uninfected


title: clock mutant mouse infect day biological rep 1

description:
Gene expression data from clock mutant mouse infect day cecal tissue
20_CK_ID_1

value: day (10am)


title: wildtype mouse infect day biological rep 4

description:
Gene expression data from wildtype mouse infect day cecal tissue
16_WT_ID_4

source_name: wildtype mouse infect day cecal tissue

value: wild type

value: 8 - 12 weeks


title: wildtype mouse infect night biological rep 1

description:
Gene expression data from wildtype mouse infect night cecal tissue
17_WT_IN_1


title: wildtype mouse uninfect day biological rep 3

description:
Gene expression data from wildtype mouse uninfect day cecal tissue
03_WT_UD_3


title: wildtype mouse infect night biological rep 2

description:
Gene expression data from wildtype mouse infect night cecal tissue
18_WT_IN_2


title: wildtype mouse uninfect day biological rep 2

description:
Gene expression data from wildtype mouse uninfect day cecal tissue
02_WT_UD_2


title: wildtype mouse uninfect night biological rep 2

description:
Gene expression data from wildtype mouse uninfect night cecal tissue
05_WT_UN_2


title: wildtype mouse infect day biological rep 2

description:
Gene expression data from wildtype mouse infect day cecal tissue
14_WT_ID_2


title: clock mutant mouse infect night biological rep 3

description:
Gene expression data from clock mutant mouse infect night cecal tissue
25_CK_IN_3


title: clock mutant mouse uninfect day biological rep 1

description:
Gene expression data from clock mutant mouse uninfect day cecal tissue
07_CK_UD_1


title: clock mutant mouse uninfect night biological rep 2

description:
Gene expression data from clock mutant mouse uninfect night cecal tissue
11_CK_UN_2


title: clock mutant mouse uninfect night biological rep 3

description:
Gene expression data from clock mutant mouse uninfect night cecal tissue
12_CK_UN_3


title: clock mutant mouse infect night biological rep 1

description:
Gene expression data from clock mutant mouse infect night cecal tissue
23_CK_IN_1


title: wildtype mouse uninfect day biological rep 1

description:
Gene expression data from wildtype mouse uninfect day cecal tissue
01_WT_UD_1


title: wildtype mouse uninfect night biological rep 1

description:
Gene expression data from wildtype mouse uninfect night cecal tissue
04_WT_UN_1


title: clock mutant mouse uninfect day biological rep 2

description:
Gene expression data from clock mutant mouse uninfect day cecal tissue
08_CK_UD_2


title: wildtype mouse infect day biological rep 3

description:
Gene expression data from wildtype mouse infect day cecal tissue
15_WT_ID_3


title: wildtype mouse uninfect night biological rep 3

description:
Gene expression data from wildtype mouse uninfect night cecal tissue
06_WT_UN_3


title: clock mutant mouse infect day biological rep 2

description:
Gene expression data from clock mutant mouse infect day cecal tissue
21_CK_ID_2


title: clock mutant mouse infect day biological rep 3

description:
Gene expression data from clock mutant mouse infect day cecal tissue
22_CK_ID_3


title: clock mutant mouse uninfect day biological rep 3

description:
Gene expression data from clock mutant mouse uninfect day cecal tissue
09_CK_UD_3


title: wildtype mouse infect day biological rep 1

description:
Gene expression data from wildtype mouse infect day cecal tissue
13_WT_ID_1


title: wildtype mouse infect night biological rep 3

description:
Gene expression data from wildtype mouse infect night cecal tissue
19_WT_IN_3


title: Pten f/f ;ERG prostate Castrate Rep1

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: The  amplified, biotin-labeled antisense RNA (aRNA) was purified and quality  was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano  kit. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization  reagents and heated at 65C for 10min. After cooled to room temperature,  total 15 ul of the hyb solution was applied to Illumina MouseRef-8 v2  chip. The chip was incubated for about 18 hours at 58C.

scan_protocol: After washing  and staining with streptavidin-Cy3, the chip was scanned using Illumina  BeadArray Reader. The scanning was done using standard DirectHyb Gene  Expression protocol with the following settings: Factor=1, PMT=587,  Filter=100%.

data_processing: The raw data was extracted using Illumina BeadStudio  software without normalization. Raw data was imported into Partek genomic suite.

source_name: Mouse Prostate

label_protocol: ~500 ng of^ total RNA was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Cat# AMIL1791,  Applied Biosystems, Foster City, CA).  Briefly, 500 ng of total RNA was used to synthesize the first strand of  cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer  bearing a T7 promoter. The single-stranded cDNA was then converted into  a double-stranded DNA (dsDNA) by DNA polymerase^ I in the presence of  /E. coli/ RNase H and DNA ligase. After column purification, the dsDNA  was served as a template for in vitro transcription in a reaction  containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase.

extract_protocol: RNA is extracted using Rneasy per protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies Inc., Palo Alto, CA).

treatment_protocol: Mice were either castrated or left intact and RNA was isolated 3 days after castration.

tag: organ

value: Prostate

value: Pten f/f;ERG

tag: androgen

value: Castrate


title: Pten f/f ;ERG prostate Castrate Rep2


title: Pten f/f ;ERG prostate Intact Rep2

value: Intact


title: Pten f/f  prostate Intact Rep2

value: Pten f/f


title: Pten f/f ;ERG prostate Intact Rep1


title: Pten f/f  prostate Intact Rep1


title: Multiple sclerosis serum samples_MS2

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

hyb_protocol: Probing and analysis of microarrays was performed with strict adherence to suggested manufacturer protocols.  (See Invitrogen and Molecular Devices online.)

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters and a pixel size of 5um.

data_processing: The GPR files were imported into Invitrogen's Prospector v5.2 microarray analysis software.  Individual serum results were normalized via the compare-function into disease and control subgroups.   IgG autoantibodies providing a relative immunofluorescence with a Z-factor of greater than or equal to 0.4 were considered significant.

molecule: other

label_protocol: standard Invitrogen protocol

extract_protocol: All serum samples were obtained from public and private biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

value: Female

value: serum

tag: disease state

value: Multiple sclerosis


title: Breast Cancer serum sample_BC20

value: Breast Cancer


title: Breast Cancer serum sample_BC19


title: Breast Cancer serum sample_BC21


title: Breast Cancer serum sample_BC22


title: Breast Cancer serum sample_BC25


title: Pten f/f  prostate Castrate Rep1

city: New York


title: Multiple sclerosis serum samples_MS3


title: Multiple sclerosis serum samples_MS6


title: Multiple sclerosis serum samples_MS4


title: Breast Cancer serum sample_BC18


title: Breast Cancer serum sample_BC17


title: Multiple sclerosis serum samples_MS5


title: Multiple sclerosis serum samples_MS10

value: Male


title: Breast Cancer serum sample_BC15


title: Breast Cancer serum sample_BC10


title: Breast Cancer serum sample_BC11


title: Breast Cancer serum sample_BC13


title: Breast Cancer serum sample_BC14


title: Multiple sclerosis serum samples_MS1


title: Breast Cancer serum sample_BC24


title: Pten f/f  prostate Castrate Rep2


title: Parkinson's Disease Serum Sample_PK24

value: Parkinson's Disease


title: Breast Cancer serum sample_BC1


title: Breast Cancer serum sample_BC16


title: Breast Cancer serum sample_BC12


title: Parkinson's Disease Serum Sample_PK22


title: Breast Cancer serum sample_BC2


title: Parkinson's Disease Serum Sample_PK21


title: Parkinson's Disease Serum Sample_PK23


title: Breast Cancer serum sample_BC23


title: Parkinson's Disease Serum Sample_PK17


title: Parkinson's Disease Serum Sample_PK16

value: UNK


title: Parkinson's Disease Serum Sample_PK15


title: Parkinson's Disease Serum Sample_PK13


title: Parkinson's Disease Serum Sample_PK10


title: Parkinson's Disease Serum Sample_PK11


title: Parkinson's Disease Serum Sample_PK18


title: Parkinson's Disease Serum Sample_PK12


title: Parkinson's Disease Serum Sample_PK2


title: Parkinson's Disease Serum Sample_PK19


title: Parkinson's Disease Serum Sample_PK1


title: Parkinson's Disease Serum Sample_MJFF-PD68L


title: Parkinson's Disease Serum Sample_MJFF-PD67L


title: Parkinson's Disease Serum Sample_MJFF-PD63L


title: Parkinson's Disease Serum Sample_PK20


title: Parkinson's Disease Serum Sample_PK14


title: Parkinson's Disease Serum Sample_MJFF-PD62L


title: Parkinson's Disease Serum Sample_MJFF-PD61L


title: Parkinson's Disease Serum Sample_MJFF-PD66L


title: Parkinson's Disease Serum Sample_MJFF-PD46


title: Parkinson's Disease Serum Sample_MJFF-PD47


title: Parkinson's Disease Serum Sample_MJFF-PD60L


title: Parkinson's Disease Serum Sample_MJFF-PD48


title: Parkinson's Disease Serum Sample_MJFF-PD51L


title: Parkinson's Disease Serum Sample_MJFF-PD50


title: Parkinson's Disease Serum Sample_MJFF-PD44


title: Parkinson's Disease Serum Sample_MJFF-PD59L


title: Parkinson's Disease Serum Sample_MJFF-PD53L


title: Parkinson's Disease Serum Sample_MJFF-PD43


title: Parkinson's Disease Serum Sample_MJFF-PD35


title: Parkinson's Disease Serum Sample_MJFF-PD40


title: Parkinson's Disease Serum Sample_MJFF-PD41


title: Parkinson's Disease Serum Sample_MJFF-PD45


title: Parkinson's Disease Serum Sample_MJFF-PD29


title: Parkinson's Disease Serum Sample_PreM-PD2


title: Parkinson's Disease Serum Sample_PreM-PD3


title: Parkinson's Disease Serum Sample_MJFF-PD38


title: Parkinson's Disease Serum Sample_MJFF-PD11


title: Parkinson's Disease Serum Sample_MJFF-PD18


title: Parkinson's Disease Serum Sample_MJFF-PD14


title: Parkinson's Disease Serum Sample_MJFF-PD31


title: Parkinson's Disease Serum Sample_MJFF-PD33


title: Control serum sample _CY10

value: Control


title: Parkinson's Disease Serum Sample_MJFF-PD30


title: Control serum sample _CY8


title: Control serum sample _CY7


title: Control serum sample _CY6


title: Control serum sample _CY4


title: Control serum sample _CY5


title: Control serum sample _CY3


title: Control serum sample _CY9


title: Parkinson's Disease Serum Sample_PreM-PD1


title: Control serum sample _NJISA-CT53


title: Control serum sample _CY1


title: 252035510015_1_2-T15[A(5)/A(3)]

description: Biological replicate A, technical replicate 1

organism: Candida albicans

value: heat shock


title: Control serum sample _NJISA-CT47


title: Control serum sample _NJISA-CT4


title: 252035510015_2_1-T5[B(5)/B(3)]

description: Biological replicate B, technical replicate 1


title: 252035510015_2_3-T30[B(5)/B(3)]


title: Control serum sample _CY2


title: 252035510015_2_4-T45[B(5)/B(3)]


title: Control serum sample _NJISA-CT3


title: Control serum sample _BioS-CT9


title: Control serum sample _NJISA-CT34


title: 252035510015_1_4-T45[A(5)/A(3)]


title: 252035510007_2_3-T30[C(5)/C(3)]

description: Biological replicate C, technical replicate 1

value: hydrogen peroxide


title: 252035510007_2_4-T60[C(5)/C(3)]


title: 252035510007_2_2-T15[C(5)/C(3)]


title: Control serum sample _BioS-CT8


title: 252035510015_1_1-T5[A(5)/A(3)]


title: Control serum sample _NJISA-CT20


title: 252035510015_1_3-T30[A(5)/A(3)]


title: Control serum sample _BioS-CT7


title: 252035510007_1_3-T30[B(5)/A(3)]

description: Biological replicate B/A, technical replicate 1


title: 252035510007_1_4-T60[B(5)/A(3)]


title: Control serum sample _NJISA-CT45


title: 252035510015_2_2-T15[B(5)/B(3)]


title: 252035510007_1_2-T15[B(5)/A(3)]


title: 252035510023_1_1-T60[A(5)/A(3)]


title: 252035510007_2_1-T5[C(5)/C(3)]


title: 252035510007_1_1-T5[B(5)/A(3)]


title: Control serum sample _BioS-CT4


title: 252035510023_1_2-T60[B(5)/B(3)]


title: Control serum sample _BioS-CT15


title: IA_rep3

description: Gene expression in Intracranial Aneurysm Wall

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)

source_name: Intracranial Aneurysm Wall, replicate3

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: The total RNA was extracted by Trizol Reagent, and DNase digestion.

value: Intracranial Aneurysm Wall

value: male


title: MMA_rep3

description: Gene expression in Middle Meningeal Artery

source_name: Middle Meningeal Artery Wall, replicate3

value: Middle Meningeal Artery Wall


title: MMA_rep2

value: female


title: 252035510008_2_3-T30[B(5)/B(3)]

value: NaCl


title: Control serum sample _BioS-CT3


title: MMA_rep1


title: IA_rep1


title: Control serum sample _BioS-CT14


title: Control serum sample _BioS-CT6


title: Control serum sample _BioS-CT13


title: 252035510008_1_3-T30[A(5)/A(3)]


title: 252035510008_1_1-T5[A(5)/A(3)]


title: 252035510008_2_2-T15[B(5)/B(3)]


title: 252035510008_1_2-T15[A(5)/A(3)]


title: Control serum sample _BioS-CT11


title: IA_rep2


title: 252035510014_1_3-T30[C(5)/C(3)]


title: 252035510014_1_4-T60[C(5)/C(3)]


title: Control serum sample _AST-CT37


title: Control serum sample _AST-CT36


title: Control serum sample _BioS-CT12


title: 252061310013_2_4-T60[B(5)/B(3)]

organism: Schizosaccharomyces pombe


title: 252061310013_1_1-T5[A(5)/A(3)]


title: 252035510008_2_4-T60[B(5)/B(3)]


title: Ser2P_BG3_PhRNAi

city: St Louis

first: Cheri

middle: A

last: Schaaf

state: MO

address: 1100 South Grand Ave

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

description:
Control CEL files: Input_BG3_Repl1.CEL, Input_BG3_Repl2.CEL, and Input_BG3_Repl3.CEL
Ser2P-Pol II ChIP DNA from Ph RNAi-treated Drosophila ML-DmBG3-c2 cells, 5 days RNAi treatment

hyb_protocol: Hybridization cocktails were generated using the labeled DNA fragments (2 μg labeled DNA, 1x MES, 3M TMAC, 40 pM Affymetrix control oligo B2, 100 μg/mL salmon sperm DNA, and 0.02% Triton X-100). Each chip was pre-hybridized with 200 μl of 1X MES-triton for 1 hour in the Affymetrix Hybridization 645 oven at 45 rpm and 45oC.  Samples in hybridization cocktail were heated for 10 minutes at 99oC then incubated to a 45oC for 10 minutes. Samples are spun in a microcentrifuge at maximum speed for 3 min.  200 μl of a sample was injected in to a chip. Hybridization was carry out in the hybridization oven at 45 rpm and 45oC for 18 hours. The arrays were washed and stained on the GeneChip Fluidics Station 450 series.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip® Scanner 3000 7G.

data_processing:
MAT software (Johnson et al. 2006) was used to calculate ChIP enrichment and sites of significant binding across the non-repetitive Drosophila genome.
matscore.bar files contain MATscores for each probe as generated using MAT software (Johnson et al. 2006). .bed files, also generated using MAT software, indicate binding at p-value less than or equal to 10-3.

organism: Drosophila melanogaster

label_protocol: Immunoprecipitated DNA was amplified using the GenomePlex Complete Whole Genome Amplification Kit (Sigma) and fragmented using controlled DNAse I reactions. Fragmented DNA was labeled with bio-11-ddATP (Perkin Elmer) using a Terminal Transferase  labeling kit (Roche).

growth_protocol: BG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin. Drosophila larvae are grown under standard conditions at 25 degrees.

extract_protocol: BG3 cells were grown to a concentration of 5x106/mL, then crosslinked by addition of 36% formaldehyde directly to the cell culture media to a final concentration of 1%, and incubation for 10 minutes at room temperature on a rocking platform. The reaction was stopped by addition of glycine pH 7.0 to a final concentration of 0.125 M. Cells were washed once with 1x PBS and once each with Wash Buffers A (10 mM HEPES pH 7.6; 10 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.25% Triton X100) and B (10 mM HEPES pH 7.6; 200 mM NaCl; 1 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.01% Triton X-100) for 10 minutes each. Cells were resuspended in sonication buffer to a concentration of 1x109/3 mL, and sonicated using a BioRuptor Sonicator for 14-20 cycles of 30 s on, 30 s off. Na-lauroylsarcosine was added to 0.5% and incubated for 10 minutes, rotating. Chromatin was centrifuged at 12,000g for 5 minutes at 4°C to pellet insoluble material, and 200 uL chromatin aliquots, each representing ~50x106 cells, were snap frozen on dry ice. Wing imaginal disc chromatin was prepared similarly, except that larval tissues were fixed in 1.8% formaldehyde for 20 minutes, and sonicated at a concentration of 75 discs per 100 μL buffer with a BioRuptor Sonicator using 20 cycles of 30 s on, 30 s off. Sonicated discs were diluted with 1-2 volumes of sonication buffer before immunoprecipitation. For immunoprecipitation, 200 μL aliquots of chromatin (50 x 106 BG3 cells, 60-75 whole wing imaginal discs, or 100-120 anterior or posterior wing imaginal discs) were adjusted to RIPA buffer in a final volume of 500 μL. Adjusted chromatin was pre-cleared for 2 hours with Protein A agarose beads, then incubated with primary antibody overnight at 4°C. Antibody-chromatin complexes were pulled down by incubation with Protein A/G agarose beads for 4 hours at 4°C, and beads were washed consecutively with RIPA, LiCl buffer, and TE. Samples were treated with RNAse A for 30 minutes at 37°C, then DNA crosslinks were reversed by overnight treatment at 65°C with Proteinase K, and DNA was recovered using Qiagen MinElute columns.

treatment_protocol: For RNAi, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 2 hours. For RNAi of all factors, from 0.7 to 40 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS withSchneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against each target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools. Cohesin RNAi-treated cells were screened for sister chromatid cohesion defects, and none were found, though a mild cell division delay occurred immediately following RNAi treatment.

tag: chip antibody

value: Ser2P-Pol II [Abcam, catalog # ab5095, lot GR5408-1]

value: ML-DmBG3-c2 cells derived from developing Drosophila central nervous system

source_name: Input DNA from Mock RNAi-treated BG3-c2 cells

tag: input


title: 252061310013_2_2-T15[B(5)/B(3)]

state: MA


title: 252035510014_1_2-T15[C(5)/C(3)]


title: 252035510008_2_1-T5[B(5)/B(3)]


title: Control serum sample _AST-CT31

value: Female

tag: sample type


title: Control serum sample _AST-CT29

value: serum


title: 252061310013_1_4-T60[A(5)/A(3)]


title: 252061310013_1_2-T15[A(5)/A(3)]


title: 252061310013_1_3-T30[A(5)/A(3)]


title: 252061310013_2_3-T30[B(5)/B(3)]


title: 252061310013_2_1-T5[B(5)/B(3)]