title: Adult (12-13w old), MC+RW (running wheel), CX (Cortex), biological rep1

description:
AdRW-MCRW-CX-1
Mouse without behavioral test.


title: Adult (12-13w old), MC, CX (Cortex), biological rep3

status: Public on Dec 08 2015

type: RNA

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

country: Japan

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

description:
AdRW-MC-CX-3
Mouse without behavioral test.

hyb_protocol: For hybridization to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol (Fluidics Protocol: EuKGE-WS2v4).

scan_protocol: Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.

data_processing:
Data transformation algorithm and normalization was done by Affymetrix GCOS.
Scaling: All Probe Sets, Target Signal=500
Normalization value: 1
Parameters: default settings

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: MC administered mouse brain cortex at 12-13w old

label_protocol: Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7- (dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG- (dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using the GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.

growth_protocol: Pregnant C57BL/6 mice were individually housed in plastic breeding cages with free access to water and pellet diet in a 12 h light-dark cycle. At three consecutive embryonic days (E) 12.5, E13.5, and E14.5, all mice received an oral administration of the chemicals and were reared in the same condition until being sacrificed for sample preparation. For the analysis of voluntary running effect, the running wheel was put in the cages after mice were weaned.

extract_protocol: Brain samples were prepared from E14.5 (3 h after oral treatment), E18.5, and 12-week-old mice of the MC, VPA, and VPM groups. Samples were homogenized and lysed in 500 ul of RLT buffer (QIAGEN, Valencia, CA), and total RNA was extracted according to the manufacturer's instructions using the RNeasy Kit (QIAGEN) for GeneChip analysis.

treatment_protocol: Three groups were designated as valproic acid (VPA), valpromide (VPM) and methylcellulose (MC) on gestation period. The VPA and VPM groups received an oral administration of 300 mg/kg VPA (Sigma) and VPM (Wako), respectively, once a day on three consecutive embryonic days (E) 12.5, E13.5, and E14.5. The MC group received an oral administration of identical volumes of 0.5% (w/v) MC (Wako) once a day on the same days.

tag: strain

tag: gender

value: male

tag: age

value: 12-13 weeks

tag: tissue

value: cortex

tag: treatment

value: methylcellulose


title: Adult (12-13w old), VPA, HC (Hippocampus), biological rep3

description:
AdRW-VPA-HC-3
Mouse without behavioral test.

source_name: VPA administered mouse brain hippocampus at 12-13w old

value: hippocampus

value: valproic acid


title: Adult (12-13w old), VPA, HC (Hippocampus), biological rep1

description:
AdRW-VPA-HC-1
Mouse without behavioral test.


title: Adult (12-13w old), MC, CX (Cortex), biological rep2

description:
AdRW-MC-CX-2
Mouse without behavioral test.


title: Adult (12-13w old), VPA+RW (running wheel), HC (Hippocampus), biological rep2

description:
AdRW-VPARW-HC-2
Mouse without behavioral test.

source_name: VPA administered + RW mouse brain hippocampus at 12-13w old

value: valproic acid + running wheel


title: Adult (12-13w old), VPA+RW (running wheel), HC (Hippocampus), biological rep1

description:
AdRW-VPARW-HC-1
Mouse without behavioral test.


title: Adult (12-13w old), MC, HC (Hippocampus), biological rep3

description:
AdRW-MC-HC-3
Mouse without behavioral test.

source_name: MC administered mouse brain hippocampus at 12-13w old


title: E18, MC, FB (Forebrain), biological rep2

source_name: MC administered mouse embryonic forebrain at E18.5

value: forebrain


title: E18, VPM, HC (Hippocampus), biological rep3

source_name: VPM administered mouse embryonic brain hippocampus at E18.5

value: valpromide


title: Adult (12-13w old), MC+RW (running wheel), HC (Hippocampus), biological rep2

description:
AdRW-MCRW-HC-2
Mouse without behavioral test.

source_name: MC administered + RW mouse brain hippocampus at 12-13w old

value: methylcellulose + running wheel


title: E18, VPA, FB (Forebrain), biological rep1

source_name: VPA administered mouse embryonic forebrain at E18.5


title: E18, MC, FB (Forebrain), biological rep3


title: E18, VPM, FB (Forebrain), biological rep3

source_name: VPM administered mouse embryonic forebrain at E18.5


title: E18, VPM, FB (Forebrain), biological rep1


title: Adult (12-13w old), VPA, HC (Hippocampus), biological rep2

description:
AdRW-VPA-HC-2
Mouse without behavioral test.


title: Adult (12-13w old), MC+RW (running wheel), HC (Hippocampus), biological rep1

description:
AdRW-MCRW-HC-1
Mouse without behavioral test.


title: E18, VPM, FB (Forebrain), biological rep2


title: E18, VPM, HC (Hippocampus), biological rep1


title: E18, MC, FB (Forebrain), biological rep1


title: E18, VPA, FB (Forebrain), biological rep3


title: Adult (12-13w old), MC, HC (Hippocampus), biological rep1

description:
AdRW-MC-HC-1
Mouse without behavioral test.


title: Adult (12-13w old), MC, HC (Hippocampus), biological rep2

description:
AdRW-MC-HC-2
Mouse without behavioral test.


title: Adult (12-13w old), MC+RW (running wheel), HC (Hippocampus), biological rep3

description:
AdRW-MCRW-HC-3
Mouse without behavioral test.


title: E18, VPA, FB (Forebrain), biological rep2


title: E18, VPM, HC (Hippocampus), biological rep2


title: MSC co-cultured in transwell with activated T cells,  biological repetition 1

city: Genoa

first: Tiziana

last: Vigo

address: Largo Daneo

country: Italy

institute: University of Genoa

description: Gene expression data from MSC exposed to activated Tcell

hyb_protocol: Following fragmentation cRNA were hybridized for 16 hr at 45C on Gene Chip Mouse Genome 430 2.0 array

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

data_processing: Data was normalized using RMA and filtered to keep genes showing at least 1.5-fold difference from the median in at least 20% of the samples

label: biotin

source_name: MSC-Trans-I

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

growth_protocol: Mouse bone marrow derived MSC purified and cultured in vitro in Mesencult medium (Zappia et al., 2005)

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

treatment_protocol: MSC cultured for 48 hrs in a transwell system (Corning) with purified T cells activated in vitro with anti CD3/CD28. MSC:Tcell ratio 1:10

value: bone marrow

tag: cell type

value: primary culture of mouse bone marrow MSC


title: TC-71 JQ1

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

country: Germany

institute: Charité - Universitätsmedizin Berlin

description: cell line: Ewing sarcoma

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: Expression Console, RMA normalization.

organism: Homo sapiens

source_name: Ewing sarcoma_TC71_JQ1

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: cells were grown at 37°C and 5% CO2

extract_protocol: RNA was isolated using TriReagent according to the manufacturer´s instructions.

treatment_protocol: Cell lines were treated for 48 hours with 2mikroM JQ1 or DMSO control

tag: cell line

value: Ewing sarcoma


title: TC-71 DMSO

description: cell line: Ewing sarcoma

source_name: Ewing sarcoma_TC71_DMSO


title: A673 JQ1

description: cell line: Ewing sarcoma

source_name: Ewing sarcoma_A673_JQ1


title: E18, MC, HC (Hippocampus), biological rep3

source_name: MC administered mouse embryonic brain hippocampus at E18.5


title: X18.1.1_Empty Vector_C

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

description: SAMPLE 6

hyb_protocol: Illumina direct hybridisation assay

scan_protocol: Illumina Bead Array Reader

data_processing: Raw data was loaded into R (Version 2.14.0) using the lumi package from  bioconductor (http://bioconductor.org) for comparison and filtering. During the filtering step any non expressed probes were removed using the detection p-value from Illumina: if for a given probe all the detection p-value for the samples are above 0.01 it is removed from the analysis  as it is considered not expressed (not detected in all samples). After the fi ltering step was completed, the data were transformed using the Variance Stabilization Transformation (VST) from lumi which is close to log2 transformation but without bias at low and high intensity. Finally, the data was normalised to remove technical variation between arrays using quantile normalisation.

source_name: X18.1.1_Empty Vector

label_protocol: Illumina IVT generating biotin-labelled cRNA protocol

growth_protocol: Cells were maintained in high glucose RPMI 1640 supplemented with 10% fetal calf serum, 1% penicillin/streptomycin, 300μM asparagine, 2mM L-glutamine and 50µM beta-mercaptoethanol. Cells were partially adherent requiring trypsin treatment for passage, and were maintained between 3-10 x10^5 cells/ml.

extract_protocol: TriReagent (Sigma); DNaseI‐digested RNA was amplified using TotalPrep 96‐RNA amplification kit (Applied Biosystems/Ambion) and hybridised to MouseWG‐6 v2 microarrays (Illumina).

treatment_protocol: 100nM OHT for 2 hours

value: Pu.1-mutated murine AML cell line

tag: transfected with

value: empty vector (EV)


title: 5563-1

city: Raleigh

first: Callie

middle: Virginia

last: Barnwell

address: North Carolina State University

department: Animal Science

country: USA

institute: North Carolina State University

hyb_protocol: Following fragmentation, the aRNA was prepared for hybridization according to the GeneChip 3' IVT Express Kit User Manual. The arrays were washed with the Affymetrix Fluidics Station 450 wash stations.

scan_protocol: The arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader.

data_processing: The data were analyzed using Affymetrix Expression Console software, using the Robust Multi-array Average algorithm.

organism: Bos taurus

source_name: Day 15 bovine conceptus, Grade 1, long length

label_protocol: Biotin-labeled aRNA was prepared according to the standard Affymetrix protocol from 250ng of total RNA

growth_protocol: Synchronized and superovulated donor Holstein cows were artificially inseminated using frozen semen from a single Holstein bull. Embryos were recovered by non-surgical uterine lavage from donor cows at Day 6.5 of gestation and evaluated for stage of development and morphological grade. Embryos were grouped by grade and transferred to recipient Holstein heifers in groups of 2-6 embryos per recipient based. Conceptuses were then non-surgically flushed from the recipients at Day 15 of gestation.

extract_protocol: Total RNA was isolated according to manufacturer's instructions

treatment_protocol: Bovine conceptuses were identified/separated by embryo grade at transfer, then measured for length and width, and snap frozen at -80C.

value: Holstein

tag: grade

value: Grade 1

tag: length

value: Short

value: Male


title: E18, VPA, HC (Hippocampus), biological rep1

source_name: VPA administered mouse embryonic brain hippocampus at E18.5


title: E14, VPM, biological rep1

source_name: VPM administered mouse embryonic brain at E14.5

value: telencephalone


title: E18, VPA, HC (Hippocampus), biological rep3


title: E18, MC, HC (Hippocampus), biological rep2

value: methylcellulose


title: E14, MC, biological rep1

source_name: MC administered mouse embryonic brain at E14.5


title: A673 DMSO

description: cell line: Ewing sarcoma

source_name: Ewing sarcoma_A673_DMSO


title: E14, VPM, biological rep2


title: E18, MC, HC (Hippocampus), biological rep1

value: hippocampus


title: E14, VPA, biological rep3

source_name: VPA administered mouse embryonic brain at E14.5

value: valproic acid


title: E14, VPA, biological rep1


title: X18.1.1_Empty Vector_A

description: SAMPLE 4


title: X18.1.1_Empty Vector_B

description: SAMPLE 5


title: X18.1.1_PuER_B

description: SAMPLE 2

value: inducible Pu.1 (PuER)


title: E14, MC, biological rep2


title: X18.1.1_PuER_A

description: SAMPLE 1


title: E18, VPA, HC (Hippocampus), biological rep2


title: E14, VPM, biological rep3


title: X18.1.1_PuER_C

description: SAMPLE 3


title: E14, MC, biological rep3


title: Lymphoma_IµHABcl6 Msh2-/-_5

city: New Haven

first: Matthew

middle: P.

last: Strout

state: CT

address: 300 George St

department: Yale Cancer Center Section of Hematology

institute: Yale University

hyb_protocol: Hybridization buffer from the BeadChip kit (Illumina) will be mixed with 1.5 ug of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip. The BeadChips are sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.

scan_protocol: The BeadChips are scanned on the Illumina Iscan.

data_processing: Genomestudio software computed normalized signal intensity using quantile normalization.

source_name: lymphoma from IµHABcl6 Msh2-/- mouse 5

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from 5 ug total RNA.

growth_protocol: Mice were monitored weekly and euthanized upon signs of tumor burden.

extract_protocol: Total RNA from tumors was extracted using Trizol reagent and further purified using the RNeasy kit following the manufacturers protocol.

treatment_protocol: Tumor cells from enlarged spleen were isolated with cell strainer and cryoperserved at -80C or in liquid nitrogen.

tag: strain background

value: mixed C57BL/6xSv129

tag: genotype/variation

value: IµHABcl6 Msh2-/-

tag: pathology

value: Diffuse large B-cell lymphoma (DLBCL)


title: E14, VPA, biological rep2


title: Lymphoma_IµHABcl6_3

source_name: lymphoma from IµHABcl6 mouse 3


title: Lymphoma_IµHABcl6 Msh2-/-_4

source_name: lymphoma from IµHABcl6 Msh2-/- mouse 4


title: Lymphoma_IµHABcl6 Ung-/-Msh2-/-_5

hyb_protocol: Hybridization buffer from the BeadChip kit (Illumina) will be mixed with 1.5 ug of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip.  The BeadChips are sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours.

data_processing: The images are analyzed using the Beadstudio software. Quality control and data analysis are carried out according to the instructions provided by Illumina.

source_name: lymphoma from IµHABcl6 Ung-/- Msh2-/-

value: IµHABcl6 Ung-/- Msh2-/-

value: Pre-B lymphoma


title: Lymphoma_IµHABcl6 Ung-/-Msh2-/-_4


title: IAV infected A549 cells at 0.5 h after infection-biological replicate 1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: A human alveolar adenocarcinoma cell line (A549 cells) infected with influenza A/Puerto Rico/8/34 H1N1 (PR8) virus was harvested at 0.5 h infection

hyb_protocol: Refer to Agilent miRNA hybridisation protocol. Probes were hybridized at 55°C for 20 hours with rotation. Then the slides were washed by Gene expression wash buffer 1 at room temperature for 5 minutes and by Gene expression wash buffer 2 at 37°C for 5 minutes.

scan_protocol: After hybridization and washing, the slides were scanned using an Agilent scanner (G2505C). Images were extracted using Agilent Feature Extraction software (ver. 10.5.1.1) and Agilent GeneSpring GX software (ver. 10.0.2).

data_processing: Data were processed by Agilent GeneSpingGX Software.

source_name: Total RNA extracted from IAV infected A549 cells at 0.5 h after infection

label_protocol: One hundred nanograms of aliquots of total RNA was used for making miRNA probes according to the Agilent protocol (ver. 1.6). Briefly, total RNA was dephosphorylated with calf intestine alkaline phosphatase (Takara Bio, Shiga, Japan), denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 using T4 RNA ligase (Takara Bio, Shiga, Japan) using the miRNA Labeling Reagent and Hybridization Kit (5190-0408, Agilent).

extract_protocol: Total RNA was extracted with miRNeasy kit (Qiagen) according to the manufacturer’s instructions. RNA yield and A260/280 ratio were monitored with a NanoDropND-100 spectrometer (Thermo Scientific), and RNA integrity numbers were assessed with the 2100 Bioanalyzer (Agilent Technologies). For the profiling of microRNAs,  All RNA samples with a RNA integrity number >9 were used in microarray analysis.

treatment_protocol: A human alveolar adenocarcinoma (A549) cell line was infected with influenza A/Puerto Rico/8/34 H1N1 (PR8) virus and harvested at 0, 0.5, 1.5 and 4.5 h after infection

value: alveolar adenocarcinoma


title: IAV infected A549 cells at 1.5 h after infection-biological replicate 1

description: A human alveolar adenocarcinoma cell line (A549 cells) infected with influenza A/Puerto Rico/8/34 H1N1 (PR8) virus was harvested at 1.5 h infection

source_name: Total RNA extracted from IAV infected A549 cells at 1.5 h after infection


title: IAV infected A549 cells at 0.5 h after infection-biological replicate 2


title: Lymphoma_IµHABcl6 Ung-/-Msh2-/-_6


title: Lymphoma_IµHABcl6 Msh2-/-_3

source_name: lymphoma from IµHABcl6 Msh2-/-


title: Lymphoma_IµHABcl6_1

source_name: lymphoma from IµHABcl6


title: IAV infected A549 cells at 0 h after infection-biological replicate 2

description: A human alveolar adenocarcinoma cell line (A549 cells) infected with influenza A/Puerto Rico/8/34 H1N1 (PR8) virus was harvested at 0 h infection

source_name: Total RNA extracted from IAV infected A549 cells at 0 h after infection


title: ST701-LMn vs ST701-HMn_rep3

city: Newark

first: G

middle: Marcela

last: Rodriguez

state: NJ

address: 225 Warren St

department: Public Health Research Institute

institute: Rutgers University

description:
Comp 6_ST703-LMn(cy5) vs ST703-HMn(cy3)
Biological replicate 3 of 3

hyb_protocol: Prehybridization  1. Prepare Prehybridization Solution (Fresh Each Time) **this volume is based on a glass dish with a base measurement of 11x8cm. This dish allows for a pre-hyb of 1-4 slides. Adjust volume accordingly based on size of dish and/or number of slides. 106.0ml dH2O 3.0g BSA 1.2ml 10%SDS  2. Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution. Make sure there are no bubbles on the surfaces of the slides.  3. Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42oC.  4. Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water. Wash slides for 2 minutes with constant shaking up and down.  5. Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down.  6. Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly. Spin at 600 RPM in a 50ml conical for 3 minutes to dry. **Complete this step within one hour of hybridization  III. Hybridization  1. Add the following to the 5µl labeled sample. 0.5µl 10 mg/ml tRNA 1.0µl 20X SSC 2.5ul Formamide 1.0µl 1% SDS  2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg. Let cool for 5 min.  3. Pipette cooled 10µl hybridization solution on microarray. Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate).  4. OPTIONAL: Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement. This step is recommended if your waterbath is not perfectly level. 5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization. To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide. Also, clean your coverslips with alcohol and lint-free wipes before placing over probe.  IV. Post Hyb washes (next day)  1. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking.  2. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking.  3. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry. Scan immediately.

scan_protocol: After washing, the arrays were scanned with a GenePix4000B scanner (Molecular Devices, Sunnyvale, CA). The images were processed using GenePix Pro and the resulting text files were exported to Microsoft Excel.

data_processing: The chips were normalized using the global normalization option within Genepix Pro. The data were filtered by removing all spots that were below the background noise or flagged as ‘bad’. Spots were considered to be below the background noise if the sum of the median intensities of the two channels was less than twice the highest average background of the chip.

organism: Mycobacterium tuberculosis

source_name: ST70 (mntR mutant of Mycobacterium tuberculosis)

label_protocol: Synthesis and Labeling of cDNA  1. Bring 1.5µg of RNA to a volume of 11µl (in a PCR tube) with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents).  2. Heat 2 min at 98oC, snap cool on ice.  3. (Keep on ice) and add 11.1µl of the following reaction mix: 5.0µl 5X First-Strand buffer 2.5µl 100 mM DTT 2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock) 1.5ul Cy3 or Cy5 Then add 1.2ul Superscript, vortex to mix and spin to collect contents  4. Incubate 10 min at 25oC followed by 90 min at 42oC in PCR machine. **Can freeze or leave at 4oC overnight if necessary  5. Prime an Amicon Ultra 10K column with 400µl of 25% TE and spin for 5 min at 14,000 Xg.  Empty flow-through from collection tube and return primed column.  Add another 400ul of 25% TE followed by both reactions (cy3 and cy5) to column and centrifuge at 14,000 Xg for 7 min.  Empty flow-through, and add yet another 400ul of 25% TE, centrifuge at 14,000 Xg for 7 min.  Empty flow-through once more, add 400ul of 25% TE and centrifuge at 14,000 Xg for 12 min.  Empty the flow-through.  6. Recover cDNA by inverting Amicon filter into the same collection tube and centrifuge at 1,000 Xg for 2 min.  7. Using a speedvac, concentrate sample to 5ul.  The detailed labeling and hybridization protocol can be obtained at http://www.cag.icph.org/downloads_page.htm#LabelingProtocols.

growth_protocol: Rv (Mycobacterium tuberculosis wild type strain) and ST70 (mntR mutant strain of Mycobacterium tuberculosis) were grown, as three independent biological replicates, in minimal media without manganese or with 50uM manganese upto optical density 0.2 and then the cells were harvested

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

treatment_protocol: Cells were grown in the minimal media supplemented with 50uM manganese or without manganese

value: Low manganese

value: 50uM MnCl2 manganese


title: ST701-LMn vs ST701-HMn_rep2

description:
Comp 5_ST702-LMn(cy3) vs ST702-HMn(cy5)
Biological replicate 2 of 3


title: Lymphoma_IµHABcl6 Ung-/-Msh2-/-_2


title: Lymphoma_IµHABcl6 Ung-/-Msh2-/-_1


title: IAV infected A549 cells at 1.5 h after infection-biological replicate 2


title: Rv1-LMn vs Rv1-HMn_rep3

description:
Comp 3_Rv3-LMn(cy5) vs Rv3-HMn(cy3)
Biological replicate 3 of 3

source_name: Rv (Wild type Mycobacterium tuberculosis)

value: Rv


title: RbpJk KO, Cre positive (CN 109)

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
CN 109
Gene expression data from liver of RbpJk KO mice.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomic Suite.

source_name: Liver of RbpJk KO mice

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix).

treatment_protocol: All mice were sacrificed 5 days after birth, and liver transcriptomes were analyzed using microarrays.

value: RbpJk KO

value: liver

tag: Sex

value: male

value: 5 days


title: Lymphoma_IµHABcl6 Msh2-/-_1


title: Lymphoma_IµHABcl6_2


title: Rv1-LMn vs Rv1-HMn_rep2

description:
Comp 2_Rv2-LMn(cy3) vs Rv2-HMn(cy5)
Biological replicate 2 of 3


title: IAV infected A549 cells at 4.5 h after infection-biological replicate 2

description: A human alveolar adenocarcinoma cell line (A549 cells) infected with influenza A/Puerto Rico/8/34 H1N1 (PR8) virus was harvested at 4.5 h infection

source_name: Total RNA extracted from IAV infected A549 cells at 4.5 h after infection


title: RbpJk WT, Cre negative (CN 106)

description:
CN 106
Gene expression data from liver of WT mice.

source_name: Liver of WT mice

value: WT


title: IAV infected A549 cells at 4.5 h after infection-biological replicate 1


title: Lymphoma_IµHABcl6 Ung-/-Msh2-/-_3


title: IAV infected A549 cells at 0 h after infection-biological replicate 1


title: RbpJk WT, Cre negative (CN 105)

description:
CN 105
Gene expression data from liver of WT mice.


title: RbpJk KO, Cre positive (CN 107)

description:
CN 107
Gene expression data from liver of RbpJk KO mice.


title: ST701-LMn vs ST701-HMn_rep1

description:
Comp 4_ST701-LMn(cy3) vs ST701-HMn(cy5)
Biological replicate 1 of 3


title: Lymphoma_IµHABcl6 Msh2-/-_2


title: RbpJk KO, Cre positive (CN 108)

description:
CN 108
Gene expression data from liver of RbpJk KO mice.


title: RbpJk WT, Cre negative (CN 104)

description:
CN 104
Gene expression data from liver of WT mice.


title: Rv1-LMn vs Rv1-HMn_rep1

description:
Comp 1_Rv1-LMn(cy3) vs Rv1-HMn(cy5)
Biological replicate 1 of 3


title: LKB1 WT, Cre negative  (CLE 100)

description:
CLE 100
Gene expression data from liver of WT mice.


title: LKB1 KO, Cre positive  (CLE 98)

description:
CLE 98
Gene expression data from liver of LKB1 KO mice.

source_name: Liver of LKB1 KO mice

value: LKB1 KO


title: R EtOH rep1 hyb2

city: San Francisco

first: Raga

last: Krishnakumar

state: CA

address: 912E RMB, 35 Medical Center Way

institute: UCSF

hyb_protocol: Standard Illumina protocol - a subset of the RNA was hybed on two separate chips at different times and used as such on Sample Network (see hyb#)

scan_protocol: Standard Illumina protocol

data_processing: Using RGui, the data was processed by Sample Network (ref) and subsequently quantile normalized. Differential gene expression was performed using the limma package, with a cutoff of adjusted p-value < 0.05.

source_name: ESCs

label_protocol: Standard Illumina protocol

growth_protocol: All cells were grown in Knockout DMEM with 15%FBS, Pen/Strep, L-glutamine and Non-essential amino acids. ESCs were also grown in Lif and 2i (GSKi and MEKi).

extract_protocol: RNA was extracted with the standard Trizol protocol

treatment_protocol: Tamoxifen was added at 1uM for 36h to induce knockout

value: EtOH

tag: hyb number


title: R EtOH rep2 hyb2


title: R Tam rep2 hyb2

value: 1uM tamoxifen


title: LKB1 WT, Cre negative  (CLE 95)

description:
CLE 95
Gene expression data from liver of WT mice.


title: R Tam rep1 hyb2


title: R EtOH rep3 hyb2


title: genesPCL.044

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression data from plasma cell leukemia primary tumor.

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 1.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Log2-transformed expression values were extracted from CEL files raw data and normalized using RMA procedure in the affy package for Bioconductor and the Transcript Cluster Annotations included in the cdf definition files version 18 available at the Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/entrezg.asp.

source_name: Plasma cell leukemia patient 044

label_protocol: Biotinylated single-stranded cDNA samples were prepared starting from 100 nanograms of purified total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the RNeasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: disease status

value: plasma cell leukemia (PCL)

tag: pcl type

value: sPCL

value: plasma cells

tag: patient


title: dY Tam rep3 hyb2

source_name: EpiLCs


title: R Tam rep3 hyb1


title: dY EtOH rep1 hyb1


title: genesPCL.046

source_name: Plasma cell leukemia patient 046

value: pPCL


title: dY Tam rep2 hyb2


title: R Tam rep2 hyb1


title: LKB1 WT, Cre negative  (CLE 88)

description:
CLE 88
Gene expression data from liver of WT mice.


title: genesPCL.043

source_name: Plasma cell leukemia patient 043


title: genesPCL.042

source_name: Plasma cell leukemia patient 042


title: R Tam rep3 hyb2


title: genesPCL.038

source_name: Plasma cell leukemia patient 038


title: genesPCL.036

source_name: Plasma cell leukemia patient 036


title: LKB1 KO, Cre positive  (CLE 91)

description:
CLE 91
Gene expression data from liver of LKB1 KO mice.


title: dY Tam rep1 hyb1


title: R EtOH rep2 hyb1


title: genesPCL.037

source_name: Plasma cell leukemia patient 037


title: LKB1 KO, Cre positive  (CLE 92)

description:
CLE 92
Gene expression data from liver of LKB1 KO mice.


title: genesPCL.035

source_name: Plasma cell leukemia patient 035


title: genesPCL.039

source_name: Plasma cell leukemia patient 039


title: R EtOH rep3 hyb1


title: genesPCL.034

source_name: Plasma cell leukemia patient 034


title: Skeletal muscle tissue_P14_rep3

city: Columbus

first: Sandya

last: Liyanarachchi

state: OH

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

description: Gene expression data from postnatal day 14 mouse hindlimb

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

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

data_processing: Gene summary expression estimates were retrieved using Robust multi-array average (RMA) method from probe level data after back ground correction and quantile normalization with Partek software (http://www.r-project.org/)

source_name: Mouse hindlimb at postnatal day 14

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

extract_protocol: RNA were extracted from P2, P7, and P14 mouse hindlimb muscles with Trizol accrording to manufacturere's protocol.

value: Skeletal muscle

tag: strain

value: mixed

tag: developmental stage


title: genesPCL.033

source_name: Plasma cell leukemia patient 033


title: genesPCL.032

source_name: Plasma cell leukemia patient 032


title: genesPCL.031

source_name: Plasma cell leukemia patient 031


title: dY Tam rep3 hyb1


title: Skeletal muscle tissue_P14_rep2

tag: tissue


title: R Tam rep1 hyb1

tag: treatment


title: Skeletal muscle tissue_P14_rep1


title: Skeletal muscle tissue_P7_rep3

description: Gene expression data from postnatal day 7 mouse hindlimb

source_name: Mouse hindlimb at postnatal day 7


title: dY EtOH rep3 hyb1


title: dY Tam rep2 hyb1


title: dY EtOH rep2 hyb1


title: Skeletal muscle tissue_P7_rep2


title: genesPCL.030

source_name: Plasma cell leukemia patient 030

tag: cell type


title: Skeletal muscle tissue_P2_rep3

description: Gene expression data from postnatal day 2 mouse hindlimb

source_name: Mouse hindlimb at postnatal day 2


title: genesPCL.029

source_name: Plasma cell leukemia patient 029


title: genesPCL.021

source_name: Plasma cell leukemia patient 021


title: genesPCL.027

source_name: Plasma cell leukemia patient 027


title: Skeletal muscle tissue_P2_rep1


title: genesPCL.028

source_name: Plasma cell leukemia patient 028


title: genesPCL.026

source_name: Plasma cell leukemia patient 026


title: Skeletal muscle tissue_P2_rep2


title: Skeletal muscle tissue_P7_rep1


title: genesPCL.019

source_name: Plasma cell leukemia patient 019


title: genesPCL.016

source_name: Plasma cell leukemia patient 016


title: genesPCL.020

source_name: Plasma cell leukemia patient 020


title: genesPCL.007

source_name: Plasma cell leukemia patient 007


title: genesPCL.018

source_name: Plasma cell leukemia patient 018


title: genesPCL.006

source_name: Plasma cell leukemia patient 006


title: genesPCL.011

source_name: Plasma cell leukemia patient 011


title: genesPCL.017

source_name: Plasma cell leukemia patient 017


title: genesPCL.013

source_name: Plasma cell leukemia patient 013


title: Omental adipose tissue 210

status: Public on Dec 07 2015

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

country: Australia

institute: the university of Adelaide

hyb_protocol: Hybridized to Illumina HumanHT-12 V4 expression BeadChip following the standard Illumina hybridization protocol.

scan_protocol: Illumina iScan following the standard Illumina scanning protocol.

data_processing: The scanner operating software, GenomeStudio, converts the signal on the array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was carried out in R using the limma package.

source_name: Omental adipose tissue

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

growth_protocol: Non-diabetic women (BMI>40kg.m2) provided tissue during elective gastric band surgery.

extract_protocol: RNA was extracted using QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: adipose

tag: depot

value: omental (VAT)

tag: gender

value: female

tag: phenotype

value: obese

value: insulin-resistant, non-diabetic

tag: patient id


title: genesPCL.005

source_name: Plasma cell leukemia patient 005


title: Omental adipose tissue 203


title: Subcutaneous adipose tissue 203

source_name: Subcutaneous adipose tissue

value: subcutaneous (SC)


title: blood_twin7_2

type: genomic

city: Beijing

first: Bingbing

last: Xie

address: Beicheng west road

country: China

institute: Beijing Istitute of Genomics

description: D22; genomic DNA isolated from a blood of a female who is the second one of twin pair 7 from Chinese Han

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protoco

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

data_processing:
BeadStudio software
The non_normalized data matrix contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from blood samples by QIAamp DNA Blood Midi kit (QIAGEN), according to the manufacturer’s protocol.

tag: pair id number

tag: age

tag: ethnicity

value: Chinese

value: blood


title: Omental adipose tissue 201


title: blood_twin8_1

description: D25; genomic DNA isolated from a blood of a female who is the first one of twin pair 8 from Chinese Han


title: blood_twin6_1

description: D19; genomic DNA isolated from a blood of a female who is the first one of twin pair 6 from Chinese Han


title: Subcutaneous adipose tissue 210


title: Subcutaneous adipose tissue 202


title: Subcutaneous adipose tissue 206


title: Omental adipose tissue 206


title: Subcutaneous adipose tissue 204


title: blood_twin6_2

description: D20; genomic DNA isolated from a blood of a female who is the second one of twin pair 6 from Chinese Han


title: Omental adipose tissue 204


title: GUbs472

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

extract_protocol: RNA was isolated using High Pure RNA Paraffin kit (Roche) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks

tag: 32 gene prediction

value: Good

value: liver

value: obesity with NASH


title: 112111-D4-MM1S.CTRL

city: Chicago

first: Nancy

last: Krett

state: IL

address: 840 South Wood Street, 740 CSB

department: Medicine

institute: University of Illinois Chicago

description:
replicate 4
112111-D4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were imported to the R environment and processed using the Illumina-specific package lumi. Background Correction (bgAdjust), Variance-stabilizing transformation (VST), and quantile normalization were applied.

source_name: human multiple myeloma cell line

label_protocol: Date, followed by replicate (A,B,C or D) and then treatment (1,2,3,4,5,6)

growth_protocol: MM.1S and MM.1RL cells are grown in RPMI1640 with 10% fetal bovine serum, pen/strep, glutamine and seeded to be in log phase growth during drug treatment

extract_protocol: Total RNA is extrated by Qiagen kit

treatment_protocol: MM.1S are treated for 3 hours with either 1 micromolar dexamethasone, 25 micromolar LY249002, combination or DMSO control.  The MM.1RL cells are treated for 3 hours with either 25 micromolar LY249002 or DMSO control.

value: Ctrl


title: Subcutaneous adipose tissue 201


title: GUbs471

scan_protocol: Refer to the NanoString nCounter Assay System Manual


title: GUbs470

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: Poor


title: 112111-D6-MM1RL.PI3K

description:
replicate 4
112111-D6

value: PI3K inhibitor alone (LY249002 - 25 uM)


title: 112111-D5-MM1RL.CTRL

description:
replicate 4
112111-D5


title: GUbs465


title: Omental adipose tissue 202


title: blood_twin5_1

description: D15; genomic DNA isolated from a blood of a female who is the first one of twin pair 5 from Chinese Han


title: GUbs461


title: blood_twin2_1

description: D5; genomic DNA isolated from a blood of a female who is the first one of twin pair 2 from Chinese Han


title: blood_twin7_1

description: D21; genomic DNA isolated from a blood of a female who is the first one of twin pair 7 from Chinese Han


title: blood_twin8_2

description: D26; genomic DNA isolated from a blood of a female who is the second one of twin pair 8 from Chinese Han


title: 112111-D2-MM1S.PI3K

description:
replicate 4
112111-D2


title: 112111-C5-MM1RL.CTRL

description:
replicate 3
112111-C5


title: blood_twin5_2

description: D16; genomic DNA isolated from a blood of a female who is the second one of twin pair 5 from Chinese Han


title: blood_twin3_2

description: D10; genomic DNA isolated from a blood of a female who is the second one of twin pair 3 from Chinese Han


title: GUbs445


title: GUbs447


title: blood_twin4_2

description: D14; genomic DNA isolated from a blood of a female who is the second one of twin pair 4 from Chinese Han


title: 112111-C3-MM1S.COMB

description:
replicate 3
112111-C3

value: Glucocorticoid alone (Dexamethasone - 1 uM) + PI3K inhibitor alone (LY249002 - 25 uM)


title: 112111-C6-MM1RL.PI3K

description:
replicate 3
112111-C6


title: 112111-C4-MM1S.CTRL

description:
replicate 3
112111-C4


title: blood_twin1_2

description: D4; genomic DNA isolated from a blood of a female who is the second one of twin pair 1 from Chinese Han


title: GUbs433


title: GUbs435


title: blood_twin2_2

description: D6; genomic DNA isolated from a blood of a female who is the second one of twin pair 2 from Chinese Han


title: GUbs422


title: GUbs409


title: 112111-D3-MM1S.COMB

description:
replicate 4
112111-D3


title: 112111-C1-MM1S.GC

description:
replicate 3
112111-C1

value: Glucocorticoid alone (Dexamethasone - 1 uM)


title: GUbs399


title: GUbs396


title: 112111-C2-MM1S.PI3K

description:
replicate 3
112111-C2


title: blood_twin4_1

description: D13; genomic DNA isolated from a blood of a female who is the first one of twin pair 4 from Chinese Han


title: 112111-B4-MM1S.CTRL

description:
replicate 2
112111-B4


title: 112111-B6-MM1RL.PI3K

description:
replicate 2
112111-B6


title: blood_twin3_1

description: D9; genomic DNA isolated from a blood of a female who is the first one of twin pair 3 from Chinese Han


title: Muscle.42d.HFD.rep2

city: Camperdown, Sydney

first: Rima

last: Chaudhuri

state: NSW

address: D17 Johns Hopkins Drive

department: Charles Perkins Center

institute: University of Sydney

hyb_protocol: Fifteen micrograms of labeled cRNA was fragmented by incubating at 94°C for 30 min in 40 mM Tris-acetate pH 8.1, 100 mM potassium acetate and 30 mM magnesium acetate. Ten micrograms of fragmented cRNA was then hybridized to Mouse Genome 430 2.0 arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.

scan_protocol: Arrays were washed and stained in the Affymetrix Fluidics station and scanned on GeneChip scanner 3000.

data_processing: Data analysis files were generated using manufacturer’s GeneChip Command Console system (Affymterix). Normalized by RMA

source_name: skeletal muscle_high fat diet fed (42 days)

label_protocol: The methods for preparation of labeled cRNA and array hybridization were provided by Affymetrix (Santa Clara, CA). Briefly, 3 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice (Invitrogen, Carlsbad, CA) and a T7-(dT)24 oligomer primer (Integrated DNA Technologies, Coralville, IO). Double-stranded cDNA was purified using affinity resin Sample Cleanup Module Kit (Affymetrix). Labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotides in an in vitro transcription reaction (Enzo Diagnostics, Farmingdale, NY). The labeled cRNA was purified using Sample Cleanup Module Kit (Affymetrix).

growth_protocol: C57Bl/6 mice were group housed on a 12-h light/dark cycle with free access to food and water.

extract_protocol: Total RNA was isolated using Qiagen Kit.

treatment_protocol: Mice were fed a standard chow (13% of calories from fat) diet until 6 weeks of age and then either continued on standard chow, or fed a high fat diet (HFD, 46% of calories from fat) for 5 days or 42 days.

tag: diet

value: high fat diet fed

tag: time point

value: 42 days

value: skeletal muscle


title: Muscle.42d.HFD.rep1


title: Muscle.42d.HFD.rep3


title: 112111-B3-MM1S.COMB

description:
replicate 2
112111-B3


title: 112111-D1-MM1S.GC

description:
replicate 4
112111-D1


title: 112111-B1-MM1S.GC

description:
replicate 2
112111-B1


title: Muscle.42d.HFD.rep4


title: blood_twin1_1

description: D3; genomic DNA isolated from a blood of a female who is the first one of twin pair 1 from Chinese Han

value: female


title: 112111-B2-MM1S.PI3K

description:
replicate 2
112111-B2


title: GUbs382


title: 112111-B5-MM1RL.CTRL

description:
replicate 2
112111-B5


title: GUbs388


title: GUbs342


title: GUbs335


title: GUbs318


title: GUbs377


title: GUbs299


title: GUbs286


title: GUbs276


title: Muscle.5d.HFD.rep4

source_name: skeletal muscle_high fat diet fed (5 days)

value: 5 days


title: GUbs246


title: GUbs281


title: Muscle.5d.HFD.rep3


title: GUbs235


title: GUbs245


title: GUbs234


title: Muscle.5d.HFD.rep2


title: Muscle.5d.HFD.rep1


title: 112111-A4-MM1S.CTRL

description:
replicate 1
112111-A4


title: GUbs209


title: 112111-A3-MM1S.COMB

description:
replicate 1
112111-A3


title: Muscle.Chow.rep4

source_name: skeletal muscle_Chow fed

value: Chow fed


title: Muscle.Chow.rep3


title: 112111-A1-MM1S.GC

description:
replicate 1
112111-A1

treatment_protocol: MM.1S are treated for 3 hours with either 1 micromolar dexamethasone, 25 micromolar LY249002, combination or DMSO control.  The MM.1RL cells are treated for 3 hours with either 25 micromolar LY249002 or DMSO control


title: GUbs230


title: 112111-A6-MM1RL.PI3K

description:
replicate 1
112111-A6


title: 112111-A2-MM1S.PI3K

description:
replicate 1
112111-A2


title: Muscle.Chow.rep2


title: 112111-A5-MM1RL.CTRL

description:
replicate 1
112111-A5


title: Muscle.Chow.rep1


title: GUbs197


title: GUbs194


title: GUbs188


title: D0KO rep1

city: Baltimore

first: Susan

middle: G

last: Dorsey

address: 655 West Lombard Street

department: Pain and Translational Symptom Science

institute: University of Maryland Baltimore

description: Gene expression data from spinal cord

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station.

scan_protocol: Gene arrays were scanned on Affymetrix platform.

data_processing: The data were normalized using the gcrma R package from Bioconductor.

source_name: SHAM KO

label_protocol: Biotinylated cRNA was prepared according to Affymetrix protocols using 1ug RNA.

growth_protocol: spinal cord tissue from WT or KO mice.

extract_protocol: A standard Trizol extraction was performed per manufacturer instructions.

treatment_protocol: the mice were either SHAM (surgery but spinal cord left intact) or at timepoints following SCI.

tag: genotype

value: knock out

tag: condition

value: sham

value: 0 day

value: spinal cord


title: D0KO rep4

description: Gene expression data from spinal cord


title: GUbs179

value: liver


title: D0WT rep2

description: Gene expression data from spinal cord

source_name: SHAM WT

value: wild type


title: D0WT rep4

description: Gene expression data from spinal cord


title: D0KO rep3

description: Gene expression data from spinal cord


title: GUbs170

value: Good

value: obesity with NASH


title: GUbs168

value: Poor


title: D0KO rep2

description: Gene expression data from spinal cord


title: GUbs166


title: GUbs156


title: GUbs155


title: GUbs140


title: D7KO rep1

description: Gene expression data from spinal cord

source_name: 7D following SCI in KO

value: spinal cord injury

value: 7 days


title: D7WT rep3

description: Gene expression data from spinal cord

source_name: 7D following SCI in WT


title: D7KO rep3

description: Gene expression data from spinal cord


title: D7WT rep2

description: Gene expression data from spinal cord


title: D0WT rep1

description: Gene expression data from spinal cord


title: GUbs122


title: D0WT rep3

description: Gene expression data from spinal cord


title: D7KO rep4

description: Gene expression data from spinal cord


title: D7KO rep2

description: Gene expression data from spinal cord


title: GUbs076


title: D3KO rep4

description: Gene expression data from spinal cord

source_name: 3D following SCI in KO

value: 3 days


title: D7WT rep1

description: Gene expression data from spinal cord


title: GUbs064


title: D7WT rep4

description: Gene expression data from spinal cord


title: GUbs125


title: GUbs023


title: GUbs002


title: GUbs018


title: GUbs045


title: D3KO rep2

description: Gene expression data from spinal cord


title: D3KO rep5

description: Gene expression data from spinal cord


title: D3KO rep1

description: Gene expression data from spinal cord


title: D3WT rep4

description: Gene expression data from spinal cord

source_name: 3D following SCI in WT


title: D3KO rep3

description: Gene expression data from spinal cord


title: D3WT rep2

description: Gene expression data from spinal cord


title: D3WT rep3

description: Gene expression data from spinal cord


title: D3WT rep1

description: Gene expression data from spinal cord


title: D1WT rep5

description: Gene expression data from spinal cord

source_name: 1D following SCI in WT

value: 1 day


title: D1WT rep2

description: Gene expression data from spinal cord


title: D1KO rep2

description: Gene expression data from spinal cord

source_name: 1D following SCI in KO


title: Mcl-1 ko, 12 months (mcl ff 12 702UN)

city: Zürich

first: Yannick

last: Boege

address: Schmelzbergstrasse 12

department: Institute for Surgical Pathology

country: Switzerland

institute: UniversityHospital Zürich

description: mcl ff 12 702UN

hyb_protocol: 300 ng of Cy3-labelled cRNA mixed with 300 ng of Cy5-labelled cRNA (specific activity >6.0 pmol dye/µg 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 manufacturer's 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 Human GE 8x60K 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C), platform: GPL7202

data_processing: Data was normalized with the Bioconductor package limma using the normalizeBetweenArrays method

source_name: liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Animals were scacrificed at 2, 8 or 12 months of age.

extract_protocol: Full liver homogenates were used. RNA isolation by Trizol protocol

treatment_protocol: Mice without any treatment

tag: genotype/variation

value: Mcl-1 ko

value: liver, corresponding non-tumor tissue

value: 12 months


title: D1WT rep4

description: Gene expression data from spinal cord


title: Aortic_MF_Sepsis_bio_rep_03

city: Toronto

first: Clint

last: Robbins

state: Ontario

address: 100 College St

country: Canada

institute: University Health Network

description: Expression Data of Aortic Macrophages 7 days after cecal puncture

hyb_protocol: Arrays were hybridized at 45C for 16-18 hours, washed with Affymetrix fluidic station p450

scan_protocol: Affymetrix 7G scanner

data_processing: Probe set expression levels were calculated using the randomized multi-array procedure (RMA), which is available within the oligo Bioconductor package for the R statistical software project where raw intensity values were background corrected and normalized

source_name: Aortic macrophages isolated 7 days after induction of sepsis by cecal puncture

label_protocol: Encore Biotin Module

growth_protocol: Aortic macrophages (CD11bhighF4/80highCD45+MerTK+CD64+) were isolated from C57/B6 wild-type male mice aged 6-8 weeks before and 7 days after induction of sepsis by cecal puncture.

extract_protocol: PicoPure RNA Isolation Kit (Life Technologies)

treatment_protocol: LPS (50µg) (O55:B5 Sigma-Aldrich) was administered by intra-peritoneal injection. A rodent model of sepsis was induced by opening the peritoneal cavity during isoflurane anesthesia. The distal end of the cecum was then perforated using a 23 G needle, and a small drop of feces was extruded through the puncture. The cecum was relocated into the peritoneal cavity, and the peritoneum was closed

value: male

tag: strain


title: D1KO rep4

description: Gene expression data from spinal cord

value: knock out

tag: tissue


title: Mcl-1 ko, 12 months (mcl ff 12 638UN)

description: mcl ff 12 638UN


title: D1KO rep3

description: Gene expression data from spinal cord


title: D1WT rep3

description: Gene expression data from spinal cord


title: D1WT rep1

description: Gene expression data from spinal cord


title: Mcl-1 ko, 12 months (mcl ff 12 793UN)

description: mcl ff 12 793UN


title: D1KO rep1

description: Gene expression data from spinal cord


title: Mcl-1 ko, 12 months (mcl ff 12 638T)

description: mcl ff 12 638T

value: tumor tissue (HCC), liver


title: Aortic_MF_Sepsis_bio_rep_02


title: Non-operated side lung, minipig with lung I-R

city: Shanghai

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00‐0331‐220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00‐0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer's instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00‐00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Sus scrofa

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer's instructions to obtain biotin labeled cRNA  Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s  instructions to obtain biotin labeled cRNA.

growth_protocol: The minipig were fed in specific pathogen-free conditions

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596‐018，Life technologies,Carlsbad, CA, US) following the manufacturer’s instructions  Carlsbad, CA, US) following the manufacturer’s instructions

treatment_protocol: The minipig surgical model was performed through transient unilateral left pulmonary artery occlusion without bronchial involvement to create ventilated lung I-R injury. Lung tissues from pig of sham and lung ischemia-reperfusion were submitted for gene expression array analysis

value: lung


title: Mcl-1 ko, 12 months (mcl ff 12 793T)

description: mcl ff 12 793T


title: Mcl-1 ko, 12 months (mcl ff 12 1109UN)

description: mcl ff 12 1109UN


title: Lung tissues, sham minipig

source_name: Lung tissues, sham minipig


title: Operated side lung, minipig with lung I-R


title: Mcl-1 ko, 12 months (mcl ff 12 702T)

description: mcl ff 12 702T


title: Mcl-1 ko, 12 months (mcl ff 12 1109T)

description: mcl ff 12 1109T


title: Aortic_MF_Sepsis_bio_rep_01


title: HPD, replicate 5

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description:
high protein diet (HPD)
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus and GEx Hybridization Buffer HI-RPM. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, log2 transformation, and LOWESS normalization.

organism: Rattus norvegicus

source_name: peripheral blood mononuclear cells_HPD

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent linear amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010).

extract_protocol: Total RNA from PBMC samples was extracted using Tripure Reagent (Roche Diagnostics) and purified with Qiagen RNeasy Mini Kit spin columns. RNA yield was quantified on a Nanodrop ND 1000 spectrophotometer and its integrity was measured on an Agilent 2100 Bioanalyzer with RNA 6000 Nano chips.

treatment_protocol: Animals were fed a purified control low-fat diet (LFD; 70% of energy (Kcal) from carbohydrates, 10en% from fat and 20en% from proteins) or high-fat diet (HFD; 20en% from carbohydrates, 60en% from fat (37% saturated and 63% unsaturated fat -46% monounsaturated and 17% polyunsaturated-) and 20en% from proteins), or a high protein diet (HPD; 45en% from carbohydrates, 10en% from fat and 45en% from proteins (mainly casein)). The control group received the diet ad-libitum during 4 months intervention, and food intake was recorded daily. The daily energy intake was used to calculate exact isocaloric amounts of HFD and HPD given to the HFD and HPD groups the next day. Animals were fasted for 14 hr prior sacrification.

value: Wistar

tag: Sex

tag: developmental stage

value: adult

value: peripheral blood mononuclear cells

source_name: peripheral blood mononuclear cells


title: HPD, replicate 4

tag: cell type


title: Aortic_MF_Naive_bio_rep_03

description: Expression Data of Aortic Macrophages before cecal puncture

source_name: Aortic macrophages isolated before sepsis induction

tag: gender


title: Mcl-1 ko, 8 months (mcl ff 08 934UN)

description: mcl ff 08 934UN

value: 8 months


title: HPD, replicate 3


title: HPD, replicate 2


title: Mcl-1 ko, 8 months (mcl ff 08 934T)

description: mcl ff 08 934T


title: Aortic_MF_Naive_bio_rep_02


title: HPD, replicate 1


title: Aortic_MF_Naive_bio_rep_01


title: Mcl-1 ko, 8 months (mcl ff 08 1287UN)

description: mcl ff 08 1287UN


title: Mcl-1 ko, 8 months (mcl ff 08 1347UN)

description: mcl ff 08 1347UN


title: Mcl-1 ko, 8 months (mcl ff 08 1347T)

description: mcl ff 08 1347T


title: HFD, replicate 3

description:
high fat diet (HFD)
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: peripheral blood mononuclear cells_HFD


title: HFD, replicate 5


title: Mcl-1 ko, 2 months (mcl ff 02 69)

description: mcl ff 02 69

value: liver

value: 2 months


title: Mcl-1 ko, 8 months (mcl ff 08 1287T)

description: mcl ff 08 1287T


title: wild type, 12 months (wt 12 641)

description: wt 12 641

value: wild type


title: HFD, replicate 6


title: wild type, 12 months (wt 12 1110)

description: wt 12 1110


title: HFD, replicate 2


title: HFD, replicate 4


title: wild type, 12 months (wt 12 552)

description: wt 12 552


title: HFD, replicate 1


title: HFD, replicate 7


title: Mcl-1 ko, 2 months (mcl ff 02 137)

description: mcl ff 02 137


title: control LFD, replicate 6

description:
low fat diet (LFD)
Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: peripheral blood mononuclear cells_control_LFD


title: control LFD, replicate 5


title: Mcl-1 hemizygous, 2 months (mcl fplus 02 30)

description: mcl fplus 02 30

value: Mcl-1 hemizygous


title: Mcl-1 hemizygous, 2 months (mcl fplus 02 27)

description: mcl fplus 02 27


title: Mcl-1 ko, 2 months (mcl ff 02 64)

description: mcl ff 02 64


title: control LFD, replicate 1


title: Mcl-1 hemizygous, 2 months (mcl fplus 02 28)

description: mcl fplus 02 28


title: C57BL/6 Brain Frontal Cortex WT-CxFold_2

status: Public on Dec 05 2015

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: R packages: lumi, genefilter, mpm

extract_protocol: genomic DNA was extracted and purified from brain samples using phenol-extraction standard protocol.

value: Brain Frontal Cortex


title: C57BL/6 Brain Frontal Cortex WT-CxFold_3


title: control LFD, replicate 3


title: wild type, 2 months (wt 02 34)

description: wt 02 34


title: control LFD, replicate 2


title: C57BL/6 Brain Frontal Cortex WT-CxFold_1


title: C57BL/6 Brain Frontal Cortex WT-CxFold_4


title: C57BL/6 Brain Dentatus Gyrus DG.F8

source_name: C57BL/6 Brain Dentatus Gyrus DG.F8

value: Brain Dentatus Gyrus


title: C57BL/6 Brain Dentatus Gyrus DG.F9

source_name: C57BL/6 Brain Dentatus Gyrus DG.F9


title: C57BL/6 Brain Frontal Cortex CX.F8

source_name: C57BL/6 Brain Frontal Cortex CX.F8


title: C57BL/6 Brain Frontal Cortex CX.F9

source_name: C57BL/6 Brain Frontal Cortex CX.F9


title: C57BL/6 Brain CA1 WT-CA1_3

source_name: C57BL/6 Brain CA1 WT-CA1_3

value: Brain CA1


title: wild type, 2 months (wt 02 31)

description: wt 02 31


title: control LFD, replicate 4


title: C57BL/6 Brain CA1 WT-CA1_2

source_name: C57BL/6 Brain CA1 WT-CA1_2


title: C57BL/6 Brain CA1 CA1.F8

source_name: C57BL/6 Brain CA1 CA1.F8


title: C57BL/6 Brain CA1 CA1.F9

source_name: C57BL/6 Brain CA1 CA1.F9


title: C57BL/6 Brain CA1 CA1.F10

source_name: C57BL/6 Brain CA1 CA1.F10


title: C57BL/6 Brain Dentatus Gyrus DG.F7

source_name: C57BL/6 Brain Dentatus Gyrus DG.F7


title: C57BL/6 Brain CA1 WT_CA1_veh_1

source_name: C57BL/6 Brain CA1 WT_CA1_veh_1


title: C57BL/6 Brain Thalamus TH-M4

source_name: C57BL/6 Brain Thalamus TH-M4

value: Brain Thalamus


title: C57BL/6 Brain Thalamus TH-M3

source_name: C57BL/6 Brain Thalamus TH-M3


title: C57BL/6 Brain Frontal Cortex WT-CxF_1_b

source_name: C57BL/6 Brain Frontal Cortex WT-CxF_1_b


title: C57BL/6 Brain Frontal Cortex CX.F7

source_name: C57BL/6 Brain Frontal Cortex CX.F7


title: C57BL/6 Brain Substantia Nigra  SN-M4

source_name: C57BL/6 Brain Substantia Nigra  SN-M4

value: Brain Substantia Nigra


title: C57BL/6 Brain Thalamus TH-F2

source_name: C57BL/6 Brain Thalamus TH-F2


title: C57BL/6 Brain Substantia Nigra  SN-M3

source_name: C57BL/6 Brain Substantia Nigra  SN-M3


title: C57BL/6 Brain Substantia Nigra  SN-M1

source_name: C57BL/6 Brain Substantia Nigra  SN-M1


title: C57BL/6 Brain Thalamus TH-F4

source_name: C57BL/6 Brain Thalamus TH-F4


title: C57BL/6 Brain Substantia Nigra  SN-F4

source_name: C57BL/6 Brain Substantia Nigra  SN-F4


title: C57BL/6 Brain Substantia Nigra  SN-F1

source_name: C57BL/6 Brain Substantia Nigra  SN-F1


title: C57BL/6 Brain Purkinje Cells PC-M4

source_name: C57BL/6 Brain Purkinje Cells PC-M4

value: Brain Purkinje Cells


title: C57BL/6 Brain Purkinje Cells PC-M3

source_name: C57BL/6 Brain Purkinje Cells PC-M3


title: C57BL/6 Brain Purkinje Cells PC-F1

source_name: C57BL/6 Brain Purkinje Cells PC-F1


title: C57BL/6 Brain Purkinje Cells PC-F4

source_name: C57BL/6 Brain Purkinje Cells PC-F4


title: C57BL/6 Brain Substantia Nigra  SN-F2

source_name: C57BL/6 Brain Substantia Nigra  SN-F2


title: C57BL/6 Brain Purkinje Cells PC-F2

source_name: C57BL/6 Brain Purkinje Cells PC-F2


title: C57BL/6 Brain Globus Pallidus  MGP-M3

source_name: C57BL/6 Brain Globus Pallidus  MGP-M3

value: Brain Globus Pallidus


title: C57BL/6 Brain Globus Pallidus  MGP-M4

source_name: C57BL/6 Brain Globus Pallidus  MGP-M4


title: C57BL/6 Brain Globus Pallidus  MGP-F1

source_name: C57BL/6 Brain Globus Pallidus  MGP-F1


title: C57BL/6 Brain Globus Pallidus  MGP-F2

source_name: C57BL/6 Brain Globus Pallidus  MGP-F2


title: C57BL/6 Brain control Met_75

source_name: C57BL/6 Brain control Met_75

value: whole brain


title: C57BL/6 Brain Globus Pallidus  MFP-F4

source_name: C57BL/6 Brain Globus Pallidus  MFP-F4


title: C57BL/6 Brain control Met_100

source_name: C57BL/6 Brain control Met_100


title: C57BL/6 Brain control Met_50

source_name: C57BL/6 Brain control Met_50


title: C57BL/6 Brain control Met_0

source_name: C57BL/6 Brain control Met_0


title: C57BL/6 Brain Hypothalamus HYP-M3

source_name: C57BL/6 Brain Hypothalamus HYP-M3

value: Brain Hypothalamus


title: C57BL/6 Brain Hypothalamus HYP-M1

source_name: C57BL/6 Brain Hypothalamus HYP-M1


title: C57BL/6 Brain Hypothalamus HYP-F2

source_name: C57BL/6 Brain Hypothalamus HYP-F2


title: C57BL/6 Brain Hypothalamus HYP-F4

source_name: C57BL/6 Brain Hypothalamus HYP-F4


title: C57BL/6 Brain Granular Cell Layer GCL-M4

value: Brain Granular Cell Layer


title: C57BL/6 Brain control Met_25

source_name: C57BL/6 Brain control Met_25


title: C57BL/6 Brain Hypothalamus HYP-F1

source_name: C57BL/6 Brain Hypothalamus HYP-F1


title: C57BL/6 Brain Granular Cell Layer GCL-M1


title: C57BL/6 Brain Granular Cell Layer GCL-F4


title: C57BL/6 Brain Dentatus Gyrus DG-M2

source_name: C57BL/6 Brain Dentatus Gyrus DG-M2


title: C57BL/6 Brain Frontal Cortex FTP-CxF_3

source_name: C57BL/6 Brain Frontal Cortex FTP-CxF_3


title: C57BL/6 Brain Caudate-Putamen  CPU-M3

source_name: C57BL/6 Brain Caudate-Putamen  CPU-M3

value: Brain Caudate-Putamen


title: C57BL/6 Brain Dentatus Gyrus DG-F3

source_name: C57BL/6 Brain Dentatus Gyrus DG-F3


title: C57BL/6 Brain Caudate-Putamen  CPU-M4_a

source_name: C57BL/6 Brain Caudate-Putamen  CPU-M4_a


title: C57BL/6 Brain Frontal Cortex FTP-CxF_2

source_name: C57BL/6 Brain Frontal Cortex FTP-CxF_2


title: C57BL/6 Brain Caudate-Putamen  CPU-M4_b

source_name: C57BL/6 Brain Caudate-Putamen  CPU-M4_b


title: C57BL/6 Brain Caudate-Putamen  CPU-M1

source_name: C57BL/6 Brain Caudate-Putamen  CPU-M1


title: C57BL/6 Brain Frontal Cortex FTP-CxF_5

source_name: C57BL/6 Brain Frontal Cortex FTP-CxF_5


title: C57BL/6 Brain Granular Cell Layer GCL-F2


title: C57BL/6 Brain Caudate-Putamen  CPU-F4

source_name: C57BL/6 Brain Caudate-Putamen  CPU-F4


title: C57BL/6 Brain Caudate-Putamen  CPU-F2

source_name: C57BL/6 Brain Caudate-Putamen  CPU-F2


title: C57BL/6 Brain Caudate-Putamen  CPU-F1

source_name: C57BL/6 Brain Caudate-Putamen  CPU-F1


title: C57BL/6 Brain CA3 CA3-M1

source_name: C57BL/6 Brain CA3 CA3-M1

value: Brain CA3


title: C57BL/6 Brain CA3 CA3-M4

source_name: C57BL/6 Brain CA3 CA3-M4


title: C57BL/6 Brain CA3 CA3-F4

source_name: C57BL/6 Brain CA3 CA3-F4


title: C57BL/6 Brain CA3 CA3-F3

source_name: C57BL/6 Brain CA3 CA3-F3


title: 1550 KO cells

city: Prague

first: Tomas

last: Venit

address: Videnska 1084

department: Depertment of Biology of the cell Nucleus

country: Czech Republic

institute: Institute of Molecular Genetics

hyb_protocol: Following fragmentation, 6.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneTitan HT MG-430 PM 24-array plate. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system with GCOS 1.4 software.

data_processing: Data analysis was carried out in Genomic Suite Software Partek 6.4 (version 6.09.0602), where the Robust Multichip Analysis was used for background correction.

source_name: NM1 knock-out

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

value: skin fibroblast


title: 1593 WT lungs

source_name: NM1 wild type

value: lungs


title: 1584 KO cells


title: C57BL/6 Brain basolateral amygdala  BLA-M4

value: Brain basolateral amygdala


title: C57BL/6 Brain basolateral amygdala  BLA-M3


title: 1623 WT cells


title: 1571 WT cells


title: 1593 WT heart

value: heart


title: 1624 WT heart


title: C57BL/6 Brain basolateral amygdala  BLA-F4


title: 1592 WT heart


title: 1586 KO lungs


title: 1624 WT lungs


title: 1592 WT lungs


title: C57BL/6 Brain basolateral amygdala  BLA-M1


title: 1586 KO heart


title: 1603 KO heart


title: C57BL/6 Brain basolateral amygdala  BLA-F1


title: 1602 KO heart


title: Genomic DNA extracted from whole blood

city: Wuhan, People’s Rep

first: Hao

last: Xu

address: Jiefang Ave.

department: Urology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: cytoscan HD array of II-2

hyb_protocol: Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the fragment DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Cytoscan HD array kit and reagent kit bundle, (Cat#901835, Affymetrix, Santa Clara, CA,US)followed the manufacturer’s instruction Affymetrix CytoScan™ Assay User Manual (Cat#703038 Rev. 3, Affymetrix, Santa Clara, CA, US) to obtain biotin labeled DNA.

scan_protocol: Arrays were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing:
Raw data passed quality control were further analyzed by Affymetrix® Chromosome Analysis Suite (Affymetrix, Santa Clara, CA, US) .
.CEL files were generated from the scanned array image files by the Affymetrix GeneChip Command Console Software and were imported into the Affymetrix Chromosome Analysis Suite v1.2.0 Software.  Copy number data files (.CYCHP files) were generated using the ChAS Analysis Files for the CytoScan HD Array version NA32.1 as a reference。

source_name: Venous whole blood

extract_protocol: Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), following the manufacturer’s instructions. We use Nano Drop (Cat#ND-1000, Thermo Fisher, Waltham, MA, US) and run a 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.

treatment_protocol: Genomic DNA extracted from whole blood

tag: disease

value: Kallmann syndrome and X-linked ichthyosis

value: blood


title: APP/PSEN1 Brain Frontal Cortex APP-PS1-CxF_3

value: Brain Frontal Cortex


title: SKMM2_Bcell_panel_rep1

city: London

first: Dan

last: Frampton

address: Gower Street

department: Infection

institute: UCL

description: Sample used in panel of B-cell lines

hyb_protocol: Hybridization was performed for 17 hrs at 65°C

scan_protocol: Arrays were scanned on an Agilent DNA microarray scanner. Images were analyzed and data were extracted using the standard procedures of Agilent Feature Extraction software (v9.5.3.1).

data_processing: Scale normalisation across arrays (R/BioConductor), with samples 1-6 and 7-20 being normalised separately.

label_protocol: Standard Agilent 4x44k protocol (amplification and labelling of 500 ng of total RNA)

extract_protocol: Trizol purification of total RNA

tag: cell line

tag: hairpin

source_name: Stratagene reference RNA

tag: sample

value: reference RNA


title: JSC1_Bcell_panel_rep1

description: Sample used in panel of B-cell lines


title: RPMI_Bcell_panel_rep1

description: Sample used in panel of B-cell lines

value: RPMI


title: HBL6_Bcell_panel_rep1

description: Sample used in panel of B-cell lines


title: 1603 KO lungs


title: APP/PSEN1 Brain Frontal Cortex APP-PS1-CxF_1


title: APP/PSEN1 Brain CA1 APP-PS1-CA1_3

source_name: APP/PSEN1 Brain CA1 APP-PS1-CA1_3

value: Brain CA1


title: L363_Bcell_panel_rep1

description: Sample used in panel of B-cell lines


title: BC3_Bcell_panel_rep1

description: Sample used in panel of B-cell lines


title: JSC1_Bcell_panel_rep2

description: Sample used in panel of B-cell lines


title: BCP1_Bcell_panel_rep1

description: Sample used in panel of B-cell lines


title: BCP1_Bcell_panel_rep2

description: Sample used in panel of B-cell lines


title: APP/PSEN1 Brain Frontal Cortex APP-PS1-CxF_2


title: 1602 KO lungs


title: RAJI_Bcell_panel_rep1

description: Sample used in panel of B-cell lines

value: RAJI


title: DEL_Bcell_panel_rep1

description: Sample used in panel of B-cell lines

value: DEL


title: APP/PSEN1 Brain CA1 APP-PS1-CA1_2

source_name: APP/PSEN1 Brain CA1 APP-PS1-CA1_2


title: C57BL/6 Brain Thalamus TH-M1

source_name: C57BL/6 Brain Thalamus TH-M1

value: Brain Thalamus


title: AKATA_Bcell_panel_rep1

description: Sample used in panel of B-cell lines

value: AKATA


title: Anthers of large buds-Mock-rep2

city: Fuzhou

first: Zhanjie

last: Li

state: Fujian

address: No.15 Shangxiadian Road

department: College of Crop Science

institute: Fujian Agriculture and Forestry University

description: Gene expression anthers of large buds treated with Mock

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), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT 100%，10%. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) and normalized and log2 transformed using Quantile algorithm using Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Brassica napus

source_name: Anthers of large buds, Mock-treated, rep2

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The rapeseed cultivar “Zhongshuang No. 9”, developed by the Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (Wuhan) and selfed for eight generations, was planted in the experimental field of Northwest A&F University, Yangling, Shaanxi, China (longitude 108°E , latitude 34°15’N), during a natural growth season in 2009 to 2010.

extract_protocol: Total RNAs from four different tissues of Mes-treated and Mock-treated plants were extracted using TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA, US) and purified with QIAGEN RNeasy® Mini Kit (QIAGEN, GmBH, Germany).

treatment_protocol: The experimental plot contained about 2400 plants grown in 120 rows (2 m long each) at a density of 50 cm space between rows and 10 cm between plants within a row. When the rapeseed plants were at the bolting stage with the longest floral bud≤2mm, the plot was divided into two groups, the Mes-treated group and Mock-treated group, each containing 60 rows. Mes-treated group plants were foliar sprayed with 0.1μg mL-1 Mes solution containing 50ppm DMF and 5ppm Tween 80 for about 15 ml per plant (about 1% of the concentration that required for it acting as a herbicide in wheat fields to control broadleaf weeds) to induce male sterility during the entire flowering period without affecting the growth and development of other tissues of rapeseed plants. Meanwhile, Mock-treated group plants were foliar sprayed with the same amount of solution only containing 50ppm DMF and 5ppm Tween 80 as control.

value: anthers of large buds

tag: development stage

value: from the vacuolated-microspore to the mature-pollen stages


title: APP/PSEN1 Brain CA1 APP-PS1-CA1_1

source_name: APP/PSEN1 Brain CA1 APP-PS1-CA1_1


title: JSC1_short_hairpin_K5_rep1

description: Sample used in miR221 experiment


title: DG75_Bcell_panel_rep1

description: Sample used in panel of B-cell lines


title: Anthers of large buds-Mock-rep3

source_name: Anthers of large buds, Mock-treated, rep3


title: JSC1_short_hairpin_K5_rep2

description: Sample used in over-expression of hsa-miR-221 experiment


title: Anthers of large buds-Mes-rep3

description: Gene expression anthers of large buds treated with Mes

source_name: Anthers of large buds, Mes-treated, rep3


title: DAUDI_Bcell_panel_rep1

description: Sample used in panel of B-cell lines

value: DAUDI


title: JSC1_mir221_rep2

description: Sample used in miR221 experiment


title: Anthers of large buds-Mes-rep2

source_name: Anthers of large buds, Mes-treated, rep2


title: Anthers of large buds-Mock-rep1

source_name: Anthers of large buds, Mock-treated, rep1


title: JSC1_rep3

type: other

description: Stratagene enriched for miRNA

hyb_protocol: 100 ng enriched miRNA (or total RNA for the C666 cell line) was added to the labelling reaction, and the entire reaction was hybridized to the array for 20 hours at 55°C.

scan_protocol: Unnormalised data were extracted using Agilent Feature Extraction software (v9.5.3.1).

data_processing: R and BioConductor were used to background subtract and scale normalise the data at the probe level.  Additionally, we applied a filter to reduce the effect of poorly performing probes on overall probeset intensities.  Intensity values were first assembled into specific miRNA probe groups (PGi) and medians calculated for each probe group. The median of the probe group medians was then calculated (PGAll).  Probe groups were included where PGi / PGAll was greater than 0.75.  This intensity filter was empirically derived to minimise false positive miRNA intensities, for example miRs of herpesviruses that are not present in lymphomas. An overall miRNA intensity value was determined as the mean of the remaining PGi’s.

molecule: other

extract_protocol: All miRNA was isolated using the miracleTM miRNA isolation kit (Stratagene, La Jolla, CA).

tag: tumour

value: Primary effusion lymphoma

tag: kshv +/-

tag: ebv +/-


title: APP/PSEN1 Brain Frontal Cortex APP-CxFold_2


title: JSC1_rep2

description: Stratagene enriched for miRNA

label_protocol: 100 ng enriched miRNA (or total RNA for the C666 cell line) was added to the labelling reaction, and the entire reaction was hybridized to the array for 20 hours at 55°C.


title: JSC1_rep2

description: Sample used in miR221 experiment


title: JSC1_rep1

description: Sample used in miR221 experiment


title: C57BL/6-129 Brain Frontal Cortex 3TG-C-CxF_3


title: APP/PSEN1 Brain Frontal Cortex APP-CxFold_1


title: BC3_rep2

description: Stratagene enriched for miRNA


title: JSC1_rep1

description: Stratagene enriched for miRNA


title: C57BL/6-129 Brain Frontal Cortex 3TG-C-CxF_2_b


title: HBL6_rep1

description: Stratagene enriched for miRNA


title: BC3_rep1

description: Stratagene enriched for miRNA


title: BCP1_rep1

description: Stratagene enriched for miRNA


title: BCBL1_rep3

description: Stratagene enriched for miRNA


title: C57BL/6-129 Brain Frontal Cortex CX.F11

source_name: C57BL/6-129 Brain Frontal Cortex CX.F11


title: BCBL1_rep1

description: Stratagene enriched for miRNA


title: JSC1_mir221_rep1

description: Sample used in miR221 experiment


title: SKMM2_rep1

description: Stratagene enriched for miRNA

value: Plasma cell leukemia


title: Anthers of large buds-Mes-rep1

source_name: Anthers of large buds, Mes-treated, rep1


title: Anthers of middle buds-Mock-rep2

description: Gene expression in anthers of middle buds treated with Mock

source_name: Anthers of middle buds, Mock-treated, rep2

value: anthers of middle buds

value: from meiosis to the early-uninucleate-microspore stage


title: C57BL/6-129 Brain Frontal Cortex CX.F10

source_name: C57BL/6-129 Brain Frontal Cortex CX.F10


title: L363_rep1

description: Stratagene enriched for miRNA


title: Anthers of middle buds-Mock-rep3

source_name: Anthers of middle buds, Mock-treated, rep3


title: Anthers of middle buds-Mes-rep2

description: Gene expression in anthers of middle buds treated with Mes

source_name: Anthers of middle buds, Mes-treated, rep2


title: Anthers of middle buds-Mes-rep3

source_name: Anthers of middle buds, Mes-treated, rep3


title: C57BL/6-129 Brain CA1 3TG-C-CA1_3

source_name: C57BL/6-129 Brain CA1 3TG-C-CA1_3


title: C666_rep1

description: total RNA

value: Nasopharyngeal carcinoma


title: RPMI_rep1

description: Stratagene enriched for miRNA

source_name: RPMI

value: Multiple myeloma


title: NCI_rep1

description: Stratagene enriched for miRNA

source_name: NCI

value: NCI


title: C57BL/6-129 Brain CA1 3TG-C-CA1_2

source_name: C57BL/6-129 Brain CA1 3TG-C-CA1_2


title: DEL_rep4

description: Stratagene enriched for miRNA

source_name: DEL

value: Diffuse large B-cell lymphoma


title: BCBL1_rep2

description: Stratagene enriched for miRNA


title: DEL_rep3

description: Stratagene enriched for miRNA


title: C57BL/6-129 Brain CA1 3TG-C-CA1_1

source_name: C57BL/6-129 Brain CA1 3TG-C-CA1_1


title: DEL_rep2

description: Stratagene enriched for miRNA


title: Anthers of middle buds-Mock-rep1

source_name: Anthers of middle buds, Mock-treated, rep1


title: C57BL/6-129 Brain Frontal Cortex 3TG-A-CxF_2

value: Brain Frontal Cortex


title: Anthers of middle buds-Mes-rep1

source_name: Anthers of middle buds, Mes-treated, rep1


title: DEL_rep1

description: Stratagene enriched for miRNA


title: C57BL/6-129 Brain CA1 3TG-A-CA1_3

source_name: C57BL/6-129 Brain CA1 3TG-A-CA1_3

value: Brain CA1


title: Small buds-Mock-rep2

description: Gene expression in small buds treated with Mock

source_name: Small buds, Mock-tretaed, rep2

value: small buds

value: before and during the pollen mother cell (PMC) stage


title: Small buds-Mes-rep3

description: Gene expression in small buds treated with Mes

source_name: Small buds, Mes-tretaed, rep3


title: Small buds-Mes-rep2

source_name: Small buds, Mes-tretaed, rep2


title: Small buds-Mes-rep1

source_name: Small buds, Mes-tretaed, rep1


title: Small buds-Mock-rep3

source_name: Small buds, Mock-tretaed, rep3


title: RAJI_rep3

description: Stratagene enriched for miRNA

source_name: RAJI

value: RAJI

value: Burkitt's lymphoma


title: C57BL/6-129 Brain CA1 3TG-A-CA1_2

source_name: C57BL/6-129 Brain CA1 3TG-A-CA1_2


title: C57BL/6-129 Brain Frontal Cortex 3TG-A-CxF_3


title: RAJI_rep2

description: Stratagene enriched for miRNA


title: C57BL/6-129 Brain CA1 3TG-A-CA1_1

source_name: C57BL/6-129 Brain CA1 3TG-A-CA1_1


title: C57BL/6-129 Brain Frontal Cortex 3TG-A-CxF_1


title: RAMOS_rep1

description: Stratagene enriched for miRNA

source_name: RAMOS

value: RAMOS


title: RAJI_rep1

description: Stratagene enriched for miRNA


title: BL2_rep1

description: Stratagene enriched for miRNA


title: DG75_rep1

description: Stratagene enriched for miRNA


title: Leaves-Mock-rep1

description: Gene expression in young leaves of the main inflorescences treated with Mock

source_name: Leaves, Mock-treated, rep1

value: leaves

value: young leaves of the main inflorescences


title: atc3h17-1_14DAG

city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

country: South Korea

institute: Pusan National University

description: Gene expression in 14-day-old seedlings of atc3h17-1 grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.

hyb_protocol: The Cy3-labeled antisense RNAs (aRNAs) were resuspended in 50 μl of hybridization solution (Agilent technologies, USA). After labeling, aRNAs were placed on an Agilent SurePrint Arabidopsis 4x44k array (Agilent technologies, USA) and covered by a Gasket 4-plex slide (Agilent technologies, USA). The slides were hybridized for 17 h at 65°C in an oven. The hybridized slides were washed in wash buffer 1 for 1 min at room temperature and then washed in buffer 2 for 1 min at 37°C. The slides were centrifuged at 3,000 rpm for 20 sec to dry.

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software v10.7.3.1 (Agilent Technologies, USA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technologies, 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.

organism: Arabidopsis thaliana

source_name: atc3h17-1, whole seedlings, 14 DAG, SD

label_protocol: Cyanine-3 (Cy3) labeled aRNA was prepared from 1 ug RNA using the One-Color Low Input Quick Amp labeling kit (Agilent technologies, USA) according to the manufacturer's instructions.

growth_protocol: Arabidopsis plants were of the Columbia (Col-0) ecotype background. Arabidopsis seeds were surface-sterilized and water-imbibed in the dark for 3 d at 4°C. The seeds were sown on 0.7% (w/v) agar plates containing one-half-strength Murashige and Skoog (MS) media supplemented with B5 vitamins and 1.5% (w/v) sucrose. They were grown at 22°C under SD conditions (8-h-light/16-h-dark cycle).

extract_protocol: Total RNA was isolated using an RNAqueous Kit (Life technologies, USA) with Plant RNA Isolation Aid (Life technologies, USA) according to the manufacturer’s instructions. Plant RNA Isolation Aid reduced common contaminants such as polyphenolics and polysaccharides. RNA was quantified using a NonoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No treatment

tag: ecotype

tag: age

value: 14 days after germination

value: whole seedling


title: Small buds-Mock-rep1

source_name: Small buds, Mock-tretaed, rep1


title: Leaves-Mes-rep1

description: Gene expression in young leaves of the main inflorescences treated with Mes

source_name: Leaves, Mes-treated, rep1


title: Leaves-Mes-rep2

source_name: Leaves, Mes-treated, rep2


title: Leaves-Mock-rep2

source_name: Leaves, Mock-treated, rep2


title: AtC3H17 OX_14DAG_rep2

description: Gene expression in 14-day-old seedlings of AtC3H17 OX grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.

source_name: AtC3H17 OX, whole seedlings, 14 DAG, SD, replicate 2

tag: genotype/variation


title: Leaves-Mock-rep3

source_name: Leaves, Mock-treated, rep3


title: WT_14DAG_control

description: Gene expression in 14-day-old seedlings of WT grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.

source_name: WT, whole seedlings, 14 DAG, SD

value: Wild Type


title: AtC3H17 OX_14DAG_rep1

source_name: AtC3H17 OX, whole seedlings, 14 DAG, SD, replicate 1


title: Leaves-Mes-rep3

source_name: Leaves, Mes-treated, rep3


title: Athal_PNM_14dpi_R2

status: Public on Dec 04 2015

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

description: A. thaliana plants were pre-grown for 14 days prior to mock treatment

hyb_protocol: Hybridization and washing was performed according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (gProcessedSignal).

source_name: A. thaliana grown on 1/10 PNM, 14 days post mock treatment, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA according to Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol (version 6.5) followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-1000 Spectrophotometer (Agilent)

growth_protocol: Piriformospora indica Sav. Verma, Aj. Varma, Rexer, G. Kost & P. Franken (DSM11827, Deutsche Sammlung von Mikroorganismen und Zellkulturen, DSMZ, Braunschweig, Germany) cultures were propagated at 28°C in liquid complete medium (CM) (Pham et al., 2004) supplemented with 2% glucose and 130 rpm shaking or on solid medium supplemented with 1.5% agar. S. vermifera cultures were propagated at 25°C in liquid MYP medium (0.7% w/v malt extract; 0.1% w/v peptone; 0.05% w/v yeast extract) and 120 rpm shaling or on solid medium supplemented with 1.5% agar. For microarray experiments P. indica and S. vermifera were cultivated on 1/10 PNM-agar plates (Basiewicz et al., 2011) for 3 days. Arabidopsis thaliana seeds (Ecotype Columbia-0) were incubated for 5 min in 70 % ethanol, surface sterilized for 5 min with 6 % sodium hypochlorite and washed 6 times for 5 min in sterile water. After stratification for 3 days at 4°C in the dark on 1/10 PNM medium, Arabidopsis seedlings were grown for 14 days under sterile conditions in a phytochamber (Vötsch, Balingen-Frommern, Germany) at long day conditions (day: 16 h, 23°C (350 µmol/m-2s-1); night: 8 h, 18°C; 60% humidity).

extract_protocol: Arabidopsis root material was harvested in liquid nitrogen 3, 7 and 14 dpi. For each time point roots from 45 to 60 plants were pooled. S. vermifera hyphae grown on plate were thoroughly scratched from the agar surface with a sterile scalpel 3 dpi and immediately frozen in liquid nitrogen. All experiments were performed in 3 independent biological replications. Total RNA from 200 mg grounded material was extracted with TRIzol (Invitrogen, Karlsruhe, Germany) following the manufacturer's instructions. Amount and quality of the extracted RNA was estimated by NanoDrop-1000 Spectrophotometer (Agilent) and by a 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: For inoculation of Arabidopsis roots with P. indica or S. vermifera, plants of roughly the same size were first transferred to square petri dishes containing 1/10 PNM. Arabidopsis roots were inoculated directly with either 500.000 P. indica spores per 20 seedlings or 2 plugs S. vermifera mycellium per plant root or mock treated with tween water (0.002% TWEEN20).

value: root


title: Athal_PNM_3dpi_R1

source_name: A. thaliana grown on 1/10 PNM, 3 days post mock treatment, replicate 1


title: Athal_PNM_14dpi_R1

source_name: A. thaliana grown on 1/10 PNM, 14 days post mock treatment, replicate 1


title: Athal_PNM_14dpi_R3

source_name: A. thaliana grown on 1/10 PNM, 14 days post mock treatment, replicate 3


title: Athal_PNM_3dpi_R2

source_name: A. thaliana grown on 1/10 PNM, 3 days post mock treatment, replicate 2


title: adrA_24h_rep2

city: Madison

first: Kimberly

last: Cowles

state: WI

address: 1630 Linden Drive

institute: University of Wisconsin-Madison

hyb_protocol: Hybridization and washes were done following the Agilent Low Input Quick Amp WT protocol (Agilent Technologies)

scan_protocol: The microarrays were scanned using a DNA Microarray Scanner, model G2565CA (Agilent), and data were extracted with Agilent Feature Extraction Software

data_processing: All microarrays passed Agilent quality control standards, and gene expression patterns were analyzed using RMA method (robust multiarray analysis) with a quantile normalization (ArrayStar software, DNASTAR, Inc).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

label_protocol: RNA was treated with Turbo DNA-free (Ambion) using the manufacturer's rigorous protocol, and RNA quality was confirmed with an Agilent Bioanalyzer following the RNA 6000 Pico kit protocol. cDNA synthesis and cRNA labeling were done following the Agilent Low Input Quick Amp WT protocol (Agilent Technologies)

growth_protocol: 10^5 CFU/ml bacterial inoculum was mixed with 0.3 g surface-sanitized alfalfa seeds in 20 ml sterile DI water. This mixture was incubated at 24C on a Stovall Belly dancer with gentle agitation under constant light for 24 hours.

extract_protocol: Bacterial pellets were frozen at -80C for 30 minutes, and total RNA was extracted from samples using the hot phenol method, as described.

treatment_protocol: At 24 hours, the planktonic bacterial population (cells found in the water) were collected in Oakridge tubes with a 1/5 volume of ice-cold 5% phenol in EtOH and pelleted via centrifugation at 10,000 x g for 10 minutes.

value: adrA mutant

value: planktonic cells

tag: time point

value: after 24 hour incubation with alfalfa seeds and water


title: Wildtype_24h_rep1

data_processing: All microarrays passed Agilent quality control standards, and gene expression patterns were analyzed using RMA method (robust multiarray analysis) with a quantile normalization (ArrayStar software, DNASTAR, Inc)

value: wildtype


title: HT-29 treated with TNF-a, biological rep2

city: Sydney

last: Corley

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

institute: UNSW

description: Gene expression data from HT-29 cells treated with TNF-a

hyb_protocol: 10 ug fragmented, biotin labelled aRNA was hybridised to Human Primeview Arrays for 16 hours at 45°C at 60rpm using an Affymetrix hybridization oven. The arrays were washed according to manufacturers instructions on an Affymetrix FS450 fluidics station.

scan_protocol: Arrays were scanned on an Affymetrix Scanner GC3000 7G.

data_processing: The data were analysed using Partek Genomic Solutions (6.13.1224).  RMA background correction was employed with quantile normalisation.

source_name: HT-29 cells

label_protocol: Starting material consisting of 100 ng of total RNA  was amplified using Affymetrix GeneAtlas 3' IVT Express Kit.

growth_protocol: HT-29 cells were seeded in 6-well plates and cultured for approximately 2 weeks unitl 80-90% confluent.

extract_protocol: RNA was isolated from HT-29 cells with TRIzol Total RNA Isolation reagent (Invitrogen).

treatment_protocol: HT-29 cells were treated with 100ng/ml TNF-a in the presence or absence of polymeric formula for 5 hours.

value: HT-29 cells


title: Wildtype_24h_rep2


title: HT-29 treated with TNF-a, biological rep3


title: HT-29 treated with TNF-a, biological rep1


title: adrA_24h_rep1


title: HT-29 treated with TNF-a and PF, biologial rep2

description: Gene expression data from HT-29 cells treated with TNF-a and polymeric formula


title: HT-29 control, biological rep2

description: Gene expression data from HT-29 cells cultured in medium