title: MDS-L_NCD25_48h_rep2

city: Kyoto

first: Masahiro

last: Kawahara

state: State...

address: 54 Shogoin-Kawahara-cho, Sakyo-ku,

department: Hematology Oncology

country: Japan

institute: Kyoto University

description: Gene expression of MDS-L after 48hr incubation with NCD25

hyb_protocol: 600ng Cy3-Labeled cRNA was fragmented using Gene Expression Hybridization Kit (Agilent) according to the manufacturer’s protocol and hybridized to SurePrint G3 Human GE Microarray 8 x 60K Ver2.0 (G4858A) (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with GE Wash Buffer 1 and Buffer 2 (Agilent).

scan_protocol: Microarray slides were scanned immediately after washing on the Microarray Scanner G2565BA (Agilent) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MDS-L, NCD25, 48h, replicate2

label_protocol: 150ng total RNA was labeled with Cyanine-3 (Cy3) using Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer’s protocol, followed by RNAeasy column purification (QIAGEN). Dye incorporation was checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HEL and CMK11-5 were cultured in 10% heat-inactivated fetal bovine serum (FBS) containing RPMI medium. MDS-L was cultured in the same medium with 20ng/ml human IL-3 (PEPRO TECH) and 20M 2-mercaptoethanol (Gibco)

extract_protocol: RNA was extracted using RNA easy mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using the NanoDrop-1000 spectrophotometer. Quality of total RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: NCD38 or NCD25 was dissolved in Dimethyl Sulfoxide (DMSO). 5-7x10^5 Cells were seeded in 6 well plates. 2 micromolar NCD38, NCD25 or DMSO was added and incubated for 48 hours at 37 ºC in the incubator with 5% CO2.

tag: cell line

value: MDS-L

value: leukemia


title: AuditoryNerve_tissue_rep2

status: Public on Apr 29 2015

type: RNA

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

country: USA

institute: MUSC

hyb_protocol: Targets (12.5 ug) were hybridized to Affymetrix Mouse 430 2.0 GeneChips according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: CEL files imported were into Affymetrix Expression Console software and data were normalized by: 1) RMA to obtain probe set expression values, and 2) MAS5 to obtain probe set detection calls.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Auditory nerve tissue

label_protocol: Total RNA (100 ng) was converted into biotin-labeled cRNA and then fragmented using the Affymetrix 3' IVT Express Kit in accordance with manufacturer protocols.

growth_protocol: CBA/CaJ mice were bred in-house in a low-noise environment at the Animal Research Facility of the Medical University of South Carolina (MUSC) with original breeding pairs purchased from The Jackson Laboratory (Bar Harbor, ME).  All mice received food and water ad libitum and were maintained on a 12-hour light/dark cycle.  Mice of both genders were used in the study.  All aspects of the animal research were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee of the MUSC.  Prior to treatment, mice were examined for signs of external ear canal and middle ear obstruction, and mice exhibiting these signs were excluded from the study.

extract_protocol: Total RNA was prepared using the miRNeasy Kit (Qiagen). Total RNA preparations were run on an Agilent 2100 Bioanalyzer to ensure sample quality.

treatment_protocol: Adult Mice (CBA/CaJ, aged 8 to 12 weeks) were euthanized, decapitated under a sterile conditions, and auditory nerves removed from the temporal bones. For cell and neurosphere samples, auditory nerves were incubated with 0.25% trypsin for 5 min at 37oC and then with DNase I (final concentration of 5mg/ml) for 5 min at 37oC.  10% fetal bovine serum (FBS) containing DMEM/F12 medium was added to stop trypsin reaction. Tissues were triturated with pipet tips and centrifuged at 1000 rpm for 5 min.  The pellet was resuspended in DMEM/F12 medium with 10% FBS and B27 supplements and filtered through a 70 µm cell strainer.  Cells were counted, plated on poly-L-ornithine and fibronectin coated plates, and grown to full confluency (5-7 days).  For neurosphere cultures, media was removed and replaced with serum-free proliferation medium (NeuroCultTM proliferation supplement, Stem Cell Technologies) containing 20 ng/ml rh EGF, 10 ng/ml FGF and 2 µg/ml heparin.

tag: strain

value: CBA/CaJ

tag: age

value: 8 to 12 weeks

tag: tissue

value: auditory nerve

tag: treatment


title: Het DMSO rep2

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using Illumina's BeadStudio Data Analysis Software.

organism: Homo sapiens

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

growth_protocol: Esophageal cell lines Het-1A, OE21 and OE33 (European Collection of Cell Cultures, Salisbury, UK) were cultured in GIBCO™ RPMI 1640 medium (Invitrogen, Karlsruhe, Germany) supplemented with 10% FBS and 2 mM GIBCO™ L-Glutamine (Invitrogen) at 37 °C in a 5 % CO2 atmosphere

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

treatment_protocol: Het-1A, OE33 and OE22 were treated independently with the HDAC (histone deacetylase) inhibtor MS-275 (0.5 μM), the DNMT1 inhibtor AZA (Azacytidine, 50 μM) and in the combination of both (MS-275 and AZA) for 24 hours. DMSO were used as the respective control. For ech condition was a triplicate performed. After 24 hours stimulation time  from all treated samples were the total mRNA isolated.

tag: cell ine

tag: tissue origin

value: Esophagus

tag: cell type

value: non-neoplastic esophageal epithlial cells

tag: treated with

value: DMSO for 24 hrs

tag: array id


title: MDS-L_DMSO_48h_rep5

description: Gene expression of MDS-L after 48hr incubation with DMSO

source_name: MDS-L, DMSO, 48h, replicate5


title: MDS-L_NCD25_48h_rep1

source_name: MDS-L, NCD25, 48h, replicate1


title: OE33 MS275 rep1

value: cell line from adenocarcinoma of the lower oesophagus (Barrett′s metaplasia)

value: 0.5 μM MS-275 (histone deacetylase inhibtor) for 24 hrs


title: OE33 AZA rep1

value: 50 μM AZA (Azacytidine) for 24 hrs


title: HEL_NCD25_48h_rep2

description: Gene expression of HEL after 48hr incubation with NCD25

source_name: HEL, NCD25, 48h, replicate2

value: HEL


title: OE33 Combined rep1

value: 50 μM AZA + 0.5 μM MS-275 for 24 hrs


title: OE21 MS275 rep2

value: cell line from squamous carcinoma of mid oesophagus


title: HEL_NCD25_48h_rep1

source_name: HEL, NCD25, 48h, replicate1


title: HEL_DMSO_48h_rep4

description: Gene expression of HEL after 48hr incubation with DMSO

source_name: HEL, DMSO, 48h, replicate4


title: OE33 DMSO rep1


title: OE21 MS275 rep1


title: OE21 Combined rep1


title: CMK11-5_NCD38_48h_rep2

description: Gene expression of CMK11-5 after 48hr incubation with NCD38

source_name: CMK11-5, NCD38, 48h, replicate2


title: HEL_DMSO_48h_rep5

source_name: HEL, DMSO, 48h, replicate5


title: OE21 DMSO rep1


title: CMK11-5_NCD38_48h_rep1

source_name: CMK11-5, NCD38, 48h, replicate1


title: Het Combined rep1


title: MDS-L_DMSO_48h_rep4

source_name: MDS-L, DMSO, 48h, replicate4


title: Het DMSO rep1


title: MDS-L_NCD38_48h_rep3

description: Gene expression of MDS-L after 48hr incubation with NCD38

source_name: MDS-L, NCD38, 48h, replicate3


title: OE21 AZA rep1


title: Het AZA rep1


title: MDS-L_NCD38_48h_rep2

source_name: MDS-L, NCD38, 48h, replicate2


title: prc16-WT16.rep2

city: New York

first: Luke

middle: Mackley

last: Noble

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

hyb_protocol: Samples were competitively hybridized according to protocol M008.

scan_protocol: Microarrays were scanned on an Axon GenePix 4100 or 4000B, with morphological opening feature processing, ensuring total channel ratios were close to 1.

data_processing: Raw data were processed using the R package (http://www.r-project.org/) limma, with background correction and within array normalization (normexp offset = 50), between array quantile normalization, and duplicateCorrelation for replicate probes, normalized to wild-type at 12 hours.

molecule: polyA RNA

organism: Aspergillus nidulans

source_name: prcA WIM27 16h

label_protocol: Poly-A RNA was isolated on oligo-(dT) cellulose (Sigma), reverse transcribed using the Invitrogen Superscript Indirect Labeling Kit with random primers, and cDNA purified using Zymo DNA CLEAN & Concentrator columns according to Pathogen Functional Genomics Resource Center (PFGRC) protocol M007 (http://pfgrc.jcvi.org/index.php/microarray/).

growth_protocol: Mycelium for wild-type and prcA microarrays spanning competence acquisition were from 145 mm diameter petri dishes containing 50 ml YEG inoculated with 100000 conidia ml-1, incubated at 37°C. Between 10 and 50 plates were pooled per time point, harvested by vacuum filtration and immediately frozen in liquid nitrogen.

extract_protocol: Total RNA was prepared in TRIzol (Invitrogen) after disruption by 1 mm zirconia beads (Daintree Scientific) in a FastPrep FP120  (MPBio).

treatment_protocol: Time since inoculation.

tag: genotype

value: prcA

tag: time

source_name: wild-type WIM126 16h

value: wild-type


title: prc16-WT16.rep1


title: CD34+/CD105-, renal ischemia/reperfusion injury (mouse 4)

city: Boston

first: Andrew

middle: Michael

last: Siedlecki

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

description:
experimental
m4e

data_processing:
Initial signal intensity results and normalized cycle time results were analyzed using SymphoniSuite software (Life Technologies, Inc).  Cycle time thresholds were normalized by averaging three endogenous controls including U6 snRNA, RNU44, and RNU48
normalized_mouse.txt reports normalized signal (against housekeeping genes).
Fold Change file worksheet reports 2^ΔΔCt, where ΔΔCt = [average ΔCtcontrol-average ΔCtexperimental]

label: FAM

source_name: renal artery

label_protocol: cDNA was analyzed using the 7900HT Fast Real-Time PCR System  (Life Technologies, Inc) following the manufacturer's instructions

growth_protocol: Renal artery tissue was extracted from animals and digested with collagenase.  Individual CD34+ CD105- cells were then selected by fluorescence assisted cell sorting.

extract_protocol: mirVana miRNA Isolation Kit (Life Technologies, Inc.) was used according to the manufacturer's instructions.

tag: warm ischemia time

value: ischemia/reperfusion


title: prc14-WT14.rep2

source_name: prcA WIM27 14h

source_name: wild-type WIM126 14h


title: WT15-WT16.rep1

source_name: wild-type WIM126 15h


title: prc14-WT14.rep1


title: WT15-WT16.rep2


title: Het MS275 rep1


title: MDS-L_DMSO_48h_rep1

source_name: MDS-L, DMSO, 48h, replicate1

value: MDS-L


title: CD34+/CD105-, renal ischemia/reperfusion injury (mouse 2)

description:
experimental
m2e


title: HEL_NCD38_48h_rep2

description: Gene expression of HEL after 48hr incubation with NCD38

source_name: HEL, NCD38, 48h, replicate2

value: leukemia


title: WT14-WT15.rep1


title: WT14-WT15.rep2


title: CMK11-5_DMSO_48h_rep2

description: Gene expression of CMK11-5 after 48hr incubation with DMSO

source_name: CMK11-5, DMSO, 48h, replicate2


title: prc12-WT12.rep1

source_name: prcA WIM27 12h

source_name: wild-type WIM126 12h


title: HEL_DMSO_48h_rep2

source_name: HEL, DMSO, 48h, replicate2


title: MDS-L_NCD38_48h_rep1

source_name: MDS-L, NCD38, 48h, replicate1


title: CD34+/CD105-, renal ischemia/reperfusion injury (mouse 3)

description:
experimental
m3e


title: MDS-L_DMSO_48h_rep3

source_name: MDS-L, DMSO, 48h, replicate3


title: MDS-L_DMSO_48h_rep2

source_name: MDS-L, DMSO, 48h, replicate2


title: HEL_DMSO_48h_rep3

source_name: HEL, DMSO, 48h, replicate3


title: HEL_NCD38_48h_rep3

source_name: HEL, NCD38, 48h, replicate3


title: HEL_NCD38_48h_rep1

source_name: HEL, NCD38, 48h, replicate1


title: CD34+/CD105-, renal ischemia/reperfusion injury (mouse 1)

description:
experimental
m1e


title: CD34+/CD105-, sham surgery (mouse 4)

description:
control
m4c

value: sham surgery


title: prc12-WT12.rep2


title: CD34+/CD105-, sham surgery (mouse 3)

description:
control
m3c


title: WT12-WT13.rep2

source_name: wild-type WIM126 13h


title: CD34+/CD105-, sham surgery (mouse 2)

description:
control
m2c

source_name: renal artery


title: WT12-WT13.rep1


title: WT14-WT16.rep2

source_name: wild-type WIM126 16h


title: HEL_DMSO_48h_rep1

source_name: HEL, DMSO, 48h, replicate1


title: WT12-WT14.rep1

source_name: wild-type WIM126 14h


title: CD34+/CD105-, sham surgery (mouse 1)

description:
control
m1c


title: WT16-WT12.rep2


title: WT13-WT15.rep2

source_name: wild-type WIM126 15h


title: WT13-WT14.rep2


title: WT16-WT12.rep1


title: WT13-WT14.rep1


title: WT12-WT14.rep2


title: WT13-WT15.rep1


title: Harmine_FACS_2

first: Bernard

last: Khor

address: 185 Cambridge St MCPZN 7106

department: Pathology

institute: Massachusetts General Hospital

data_processing: The data was variance stabilized and normalized using robust splines in R package LUMI

source_name: Harmine treated T cells_FACS

label_protocol: RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit per manufacturer's instructions.

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

value: Foxp3GFP mouse

value: FACS-sorted Tregs generated from FACS-sorted naïve CD4+ T cells

tag: cultured in

value: low TGFb + harmine


title: Harmine_MACS_1

source_name: Harmine treated T cells_MACS

value: FACS-sorted Tregs generated from MACS-sorted naïve CD4+ T cells


title: Harmine_FACS_1


title: Naive_FACS_1

source_name: Naïve T Cells_FACS

value: FACS-sorted naïve CD4+ T cells


title: Naive_MACS_1

source_name: Naïve T Cells_MACS

value: MACS-sorted naïve CD4+ T cells


title: TGFhi_MACS_1

source_name: TGF treated T cells_MACS

value: high TGFb conditions


title: TGFhi_MACS_2


title: Harmine_MACS_2


title: Naive_MACS_2


title: WT14-WT16.rep1


title: Treated-replicate3

status: Public on Apr 28 2015

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

description: sample 6

hyb_protocol: Performed according to the manufacturer’s instructions

scan_protocol: Processed using Genome Studio software

data_processing:
Arrays were QC analyzed using the arrayQualityMetrics package in Bioconductor.
Raw data were transformed using a variance stabilizing transformation (VST) method prior to normalization across all arrays using the robust spline normalization (RSN) method, using the lumi package in Bioconductor.
Array features that were not detected (using the detectionCall function in the lumi Bioconductor package) on all arrays were removed, leaving a total of 19293.
Pairwise group comparisons were undertaken using linear modelling. Subsequently, empirical Bayesian analysis was applied, including vertical (within a given comparison) p value adjustment for multiple testing, which controls for false discovery rate, using the limma Bioconductor package

source_name: Bone marrow-derived dendritic cells

label_protocol: RNA was labeled using the TotalPrep RNA Amplification kit (Life Technologies)

extract_protocol: RNA was extracted from cells using Pure Link RNA Mini Kit and DNase-treated according to the manufacturer’s instructions (Life technologies)

treatment_protocol: Tibias and fibulas of the hind legs of 3 C57BL/6 male mice were collected into ice cold PBS (Sigma), bones were then sterilised in 70% Ethanol (Sigma) for 3 minutes, before washing with PBS (Sigma), to remove all ethanol. Individual bones were selected, the ends of the bone were removed using a scalpel and 5ml of PBS (Sigma) was injected through the bone using a 5ml syringe (BD) and a 21G needle (BD), flushing the bone marrow into a 50 ml falcon tube (BD). Flushed bone marrow samples pooled from all bones collected for each individual mouse were then disrupted by repeatedly passing through a 23G needle (BD). A sample of BM was mixed in a 1:1 dilution with trypan blue and the numbers of HSCs present were counted based on size. 2x10^6 bone marrow cells were seeded per petri dish in 10ml complete medium (RPMI-1640 (Sigma), 10% Fetal Calf Serum (FCS, Hyclone/Sigma), 2mM L-Glutamine (Gibco), 50 U/ml penicillin and 50 μg/ml streptomycin (Invitrogen)) containing 20ng/ml rGM-CSF (Peprotech). 5 petri dishes (10 x 10^6 HSCs) were seeded per mouse. Cells were cultured at 37oC in a humidified atmosphere of 5% CO2. On day 3, 10ml of complete medium was added, on days 6 and 8, 9ml of media was gently (to avoid undesired activation of cells) aspirated and replaced with 10ml of fresh complete medium, cells were harvested gently on day 10. Immature day 10 BMDCs were harvested and re-suspended at 2 x10^6 cells/ml in fresh complete medium containing only 5ng/ml GM-CSF and cultured for 6 hours with and without 20ng/ml rIL-4 (Peprotech).

value: Bone marrow-derived dendritic cells


title: TGFhi_FACS_2

source_name: TGF treated T cells_FACS


title: Treated-replicate2

description: sample 5


title: Treated-replicate1

description: sample 4


title: Control-replicate3

description: sample 3


title: Control-replicate1

description: sample 1


title: Control-replicate2

description: sample 2


title: TGFhi_FACS_1


title: TGMS-Co27 at low temperature,biological rep2

city: Wuhan

first: Yufang

last: Pan

address: bayi road

country: China

institute: Wuhan university

description:
Gene expression data from meiosis-stage inflorescences in TGMS-Co27 at low temperature
F12

hyb_protocol: Affymetrix microarray hybridization was carried out by the ShanghaiBio Corporation using the standard Affymetrix protocol (Affymetrix).

scan_protocol: The signal intensity for each probe_set on the GeneChip microarray was detected with a GeneChip® Scanner 3000 (Affymetrix), and the raw signal value for each probe_set was analyzed with GeneChip Operating Software (GCOS; Affymetrix).

data_processing: Normalization of all arrays was performed by quantile normalization using MAS 5.0, in order to standardize the distribution of probe intensities for each array in a set of arrays.

organism: Oryza sativa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: All experimental materials were transplanted in the field at a spacing of 16.7 cm between plants within rows and 26.7 cm between rows.

extract_protocol: Total RNA was isolated using RNAiso Plus (TARAKA) according to the manufacturer’s protocol.

treatment_protocol: For the high temperature cultivation, TGMS-Co27 and H1493 plants were germinated and transplanted on May 5 and June 3 in an experimental field at Wuhan University Institute of Genetics (Wuhan, China; 30.54°N, 114.36°E). For the low temperature cultivation, TGMS-Co27 and H1493 plants were germinated and transplanted on November 15 and December 12 in a paddy field at Lingshui (18.48°N; 110.02°E), in a region of southern China that is suitable for growing rice in the winter. Meiosis-stage young inflorescences of samples grown at high and low temperatures were harvested in July and January, when the daily average temperatures were 28 and 20 ºC, respectively.

value: inflorescence

tag: developmental stage

value: Meiosis-stage


title: WT_H1493 at low temperature,biological rep1

description:
Gene expression data from meiosis-stage inflorescences in H1493 at low temperature
F5

tag: cultivar

value: Wild-type


title: Naive_FACS_2


title: TGMS-Co27 at low temperature,biological rep1

description:
Gene expression data from meiosis-stage inflorescences in TGMS-Co27 at low temperature
F6


title: TGMS-Co27 at low temperature,biological rep3

description:
Gene expression data from meiosis-stage inflorescences in TGMS-Co27 at low temperature
F16


title: TGMS-Co27 at high temperature,biological rep2

description:
Gene expression data from meiosis-stage inflorescences in TGMS-Co27 at high temperature
F7


title: WT_H1493 at high temperature,biological rep3

description:
Gene expression data from meiosis-stage inflorescences in H1493 at high temperature
F11


title: WT_H1493 at high temperature,biological rep1

description:
Gene expression data from meiosis-stage inflorescences in H1493 at high temperature
F4


title: TGMS-Co27 at high temperature,biological rep3

description:
Gene expression data from meiosis-stage inflorescences in TGMS-Co27 at high temperature
F14


title: TGMS-Co27 at high temperature,biological rep1

description:
Gene expression data from meiosis-stage inflorescences in TGMS-Co27 at high temperature
F3


title: WT_H1493 at low temperature,biological rep2

description:
Gene expression data from meiosis-stage inflorescences in H1493 at low temperature
F8


title: WT_H1493 at low temperature,biological rep3

description:
Gene expression data from meiosis-stage inflorescences in H1493 at low temperature
F15


title: WT_H1493 at high temperature,biological rep2

description:
Gene expression data from meiosis-stage inflorescences in H1493 at high temperature
F9


title: WholeBloodRNA_JR1870_Day0

city: Houston

first: John

middle: W

last: Belmont

state: TX

address: One Baylor Plaza, BCM 320

department: Molecular and Human Genetics

institute: Baylor College of Medicine

scan_protocol: Standard Illumina scanning protocol. Scanning was performed on an Illumina iScan system

data_processing: Raw data underwent background adjustment, variance stabilization transformation, and robust spline normalization using R package lumi (available from Bioconductor)

source_name: Whole blood

label_protocol: Biotinylated cRNA was prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with the QIAGEN PAXgene Blood RNA System, in accordance with the protocol provided with the kit. Quality control was performed on a BioRad Experion microfluidic electrophoresis system

tag: subject id

tag: time point

tag: gender

value: male

tag: infection

value: our tests did not detect one of the viruses sought

tag: baseline anti-a/h1n1 ab titers

tag: spring anti-a/h1n1 ab titers


title: WholeBloodRNA_JR1800_Day6

value: female


title: WholeBloodRNA_JR1870_Day2


title: WholeBloodRNA_JR1870_Day4


title: WholeBloodRNA_JR1870_Day6


title: CMK11-5_DMSO_48h_rep1

source_name: CMK11-5, DMSO, 48h, replicate1

tag: cell line


title: WholeBloodRNA_JR1870_Day21


title: WholeBloodRNA_JR1800_Day21


title: WholeBloodRNA_JR1800_Day2


title: WholeBloodRNA_JR1459_Day6


title: WholeBloodRNA_JR1459_Day2


title: WholeBloodRNA_JR1459_Day4


title: WholeBloodRNA_JR1459_Day21


title: WholeBloodRNA_JR1424_Day4


title: WholeBloodRNA_JR1424_Day21


title: WholeBloodRNA_JR1424_Day0


title: WholeBloodRNA_JR1424_Day6


title: WholeBloodRNA_JR1230_Day0


title: WholeBloodRNA_JR1459_Day0


title: WholeBloodRNA_JR1268_Day2


title: WholeBloodRNA_JR1268_Day6


title: WholeBloodRNA_JR1183_Day21


title: WholeBloodRNA_JR1268_Day0


title: WholeBloodRNA_JR1424_Day2


title: WholeBloodRNA_JR1230_Day2


title: WholeBloodRNA_JR1183_Day6


title: WholeBloodRNA_JR1268_Day4


title: WholeBloodRNA_JR1183_Day0


title: WholeBloodRNA_JR1230_Day6


title: WholeBloodRNA_JR0533_Day6


title: WholeBloodRNA_JR0496_Day6


title: WholeBloodRNA_JR0496_Day21


title: WholeBloodRNA_JR1183_Day4


title: WholeBloodRNA_JR0496_Day4


title: WholeBloodRNA_JR0461_Day21


title: WholeBloodRNA_JR0461_Day0


title: WholeBloodRNA_JR0462_Day6


title: WholeBloodRNA_JR1183_Day2


title: WholeBloodRNA_JR0461_Day6


title: WholeBloodRNA_JR0461_Day4


title: WholeBloodRNA_JR0462_Day21


title: WholeBloodRNA_JR0533_Day21


title: WholeBloodRNA_JR0462_Day0


title: WholeBloodRNA_JR0533_Day0


title: WholeBloodRNA_JR0496_Day0


title: WholeBloodRNA_JR0462_Day2


title: WholeBloodRNA_JR0496_Day2


title: WholeBloodRNA_JR0461_Day2


title: WholeBloodRNA_JR0533_Day4


title: WholeBloodRNA_JR0438_Day4


title: WholeBloodRNA_JR0438_Day21


title: WholeBloodRNA_JR0438_Day6


title: WholeBloodRNA_JR0438_Day0


title: WholeBloodRNA_JR0325_Day6


title: WholeBloodRNA_JR0438_Day2


title: WholeBloodRNA_JR0325_Day21


title: WholeBloodRNA_JR0324_Day4


title: WholeBloodRNA_JR0325_Day4


title: WholeBloodRNA_JR0324_Day6


title: WholeBloodRNA_JR0324_Day2


title: WholeBloodRNA_JR0324_Day21


title: WholeBloodRNA_JR0325_Day2


title: WholeBloodRNA_JR0319_Day21


title: WholeBloodRNA_JR0324_Day0


title: WholeBloodRNA_JR0301_Day0


title: WholeBloodRNA_JR0319_Day4


title: WholeBloodRNA_JR0301_Day21


title: WholeBloodRNA_JR0224_Day6


title: WholeBloodRNA_JR0319_Day2


title: WholeBloodRNA_JR0319_Day6


title: WholeBloodRNA_JR0301_Day4


title: WholeBloodRNA_JR0224_Day21


title: WholeBloodRNA_JR0533_Day2


title: WholeBloodRNA_JR0224_Day2


title: WholeBloodRNA_JR0301_Day2


title: WholeBloodRNA_JR0224_Day0


title: WholeBloodRNA_JR0178_Day6


title: WholeBloodRNA_JR0178_Day21


title: WholeBloodRNA_JR0178_Day4


title: WholeBloodRNA_JR0151_Day21


title: WholeBloodRNA_JR0178_Day2


title: WholeBloodRNA_JR0151_Day6


title: WholeBloodRNA_JR0178_Day0


title: WholeBloodRNA_JR0151_Day2


title: WholeBloodRNA_JR0106_Day21


title: WholeBloodRNA_JR0151_Day0


title: WholeBloodRNA_JR0151_Day4


title: WholeBloodRNA_JR0224_Day4


title: WholeBloodRNA_JR0039_Day2


title: WholeBloodRNA_JR0043_Day2


title: WholeBloodRNA_JR0325_Day0


title: WholeBloodRNA_JR0043_Day4


title: WholeBloodRNA_JR0018_Day21


title: WholeBloodRNA_JR0043_Day6


title: WholeBloodRNA_JR0043_Day21


title: WholeBloodRNA_JR0043_Day0


title: WholeBloodRNA_JR0106_Day2


title: WholeBloodRNA_JR0039_Day21


title: WholeBloodRNA_JR0018_Day2


title: plasma_NPHCon

city: Ottawa

first: Kenny

last: Schlosser

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

description: Non-Pulmonary Hypertension Control (subject was referred for right heart catheterization, but found to have normal hemodynamics)

data_processing:
Matrix non-normalized (raw) Cq values were obtained from the Biorad CFX Manager software.  Manufacturer recommends converting Cq values > 35 to predefined detection limit of 35 prior to analysis.
Matrix MCR subset: Mean-centering restricted (MCR) subset of miRNAs/SNORDs used as an initial pool of candidates for identification of circulating (internal) reference controls. Only miRNAs/SNORDs with Cq<35 in all subjects were included in this initial candidate pool.  Non-normalized Cq or 2-Cq expression units were used as input into the geNorm and NormFinder algorithms as required.

label: SYBR green

source_name: plasma (citrate)

label_protocol: Reverse transcription reactions were performed with a fixed volume of total RNA (5 µL/reaction) according to manufacturer's instructions (miScript II RT kit; Qiagen).  Quantitative real-time PCR was performed with the Human miRNome miScript miRNA PCR arrays (V16.0, 384-well, Qiagen).  The manufacturer's recommended PCR cycling conditions were followed for 40 cycles on a CFX384 real-time PCR machine (Biorad).

extract_protocol: The miRNeasy mini kit (Qiagen) was used to extract total RNA from 200 µL of citrate-plasma according to manufacturer's instructions.  Total RNA was eluted in a final volume of 50 µL of RNase-free water.

tag: tissue

value: plasma

tag: disease status

value: Non-Pulmonary Hypertension

tag: Sex

value: Female

tag: age


title: WholeBloodRNA_JR0039_Day6


title: WholeBloodRNA_JR0106_Day6


title: WholeBloodRNA_JR0018_Day6


title: WholeBloodRNA_JR0018_Day4


title: WholeBloodRNA_JR0039_Day4


title: WholeBloodRNA_JR0039_Day0


title: WholeBloodRNA_JR0017_Spring

value: Spring


title: plasma_HCon3

description: Healthy Control

value: healthy


title: WholeBloodRNA_JR0106_Day0


title: WholeBloodRNA_JR0018_Day0


title: WholeBloodRNA_JR0017_Day21


title: WholeBloodRNA_JR0106_Day4


title: plasma_IPAH4

description: Idiopathic pulmonary arterial hypertension

value: pulmonary arterial hypertension


title: plasma_HCon1

description: Healthy Control

value: Male


title: plasma_HCon2

description: Healthy Control


title: plasma_IPAH3


title: WholeBloodRNA_JR0017_Day6


title: plasma_IPAH2


title: plasma_IPAH1


title: WholeBloodRNA_JR0017_Day4


title: WholeBloodRNA_JR0301_Day6


title: WholeBloodRNA_JR0017_Day2


title: NS40

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

institute: University of Viginia

hyb_protocol: Hybridization reactions were performed according to the manufacturer's instructions (NanoString) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions.

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using quantile normalization.

source_name: colon

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

tag: diagnosis

value: Normal

tag: group

value: colon

tag: sampling

value: Biopsy

tag: location

value: right colon


title: NS47

value: non-dysplastic UC mucosa adjacent to a neoplastic lesion

value: nUCaN

value: left colon


title: NS48


title: NS37


title: NS41


title: NS38


title: NS39


title: NS44

value: ulcerative colitis  associated neoplastic tissues

value: UCN


title: NS42

value: UC patients without neoplasia

value: UC


title: NS45


title: NS46


title: NS36


title: NS33


title: NS32


title: NS31


title: NS43


title: NS30


title: NS35


title: NS24


title: NS28


title: NS27


title: NS25


title: NS26


title: NS29


title: NS23


title: NS22


title: HMECGLI1

city: Nagakute

first: Kenji

last: Kasai

state: Aichi

address: 1-1 Yazakokarimata

department: Department of Pathology

institute: Aichi Medical University School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary culture cells of human mammary epithelium HMEC expressing GLI1.

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

extract_protocol: Not provided.

tag: cell type

value: primary human mammary epithelium cells (HMEC)

tag: genotype/variation

value: expressing GLI1


title: NS21


title: NS20


title: Dye Flip of DTT_3hrs/Control, biological rep2 of 3

city: Chandigarh

first: Ashwani

last: Kumar

state: Chandigarh

address: Sec 39A

department: Molecular Microbiology

country: India

institute: CSIR-Institute of Microbial Technology

description:
Dye Flip of 2 of 3
DTT_3 hrs_2_1

hyb_protocol: II. 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 GenePix4200AL 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 by the print-tip Lowess method (Dudoit, 2000). 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. The ratio of the average median intensity of Cy5 over the average median intensity of Cy3 was determined for each spot.  The data was then processed for statistical significance using Partek Genomics Suite ver 6.5. A false discovery rate (FDR) of 5% was set as cut-off to select for significantly differentially expressed genes from the normalized and processed expression data

organism: Mycobacterium tuberculosis H37Rv

source_name: M.tb in Log phase, DTT

label_protocol: I. 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 a microcon10 column (YM10 from Millipore) with 400µl TE and spin for 10 min at 10,000 Xg. Empty flow-through in collection tube and return primed column. Add both reactions (cy3 and cy5) to column and centrifuge at 10,000 Xg until ~25µl remaining (~20-30 min). Wash with 200µl TE and spin until almost dry (<5µl).  6. Recover cDNA by inverting microcon into new collection 1.5 ml tube and centrifuge at half max speed 1 min.  7. Bring sample to 5µl with TE.  The detailed labeling and hybridization protocol can be obtained at http://www.cag.icph.org/downloads_page.htm#LabelingProtocols.

growth_protocol: M.tb H37 Rv culture was grown upto log pahse.

extract_protocol: Trizol method was used for RNA isolation as per manufactures protocol.

treatment_protocol: To the test sample added 1 mM DTT (reduced) for 3hrs.

tag: treatment

source_name: M.tb in Log phase, untreated

value: Untreated Control


title: NS18


title: NS17


title: DTT_3hrs/Control, biological rep 3 of 3

description:
Biological replicate 3 of 3.
DTT_3 hrs_3_0


title: DTT_3hrs/Control, biological rep 2 of 3

description:
Biological replicate 2 of 3.
DTT_3 hrs_2_0


title: Dye Flip of DTT_3hrs/Control, biological rep3 of 3

description:
Dye Flip of 3 of 3
DTT_3 hrs_3_1


title: HMECLacZ

source_name: primary culture cells of human mammary epithelium HMEC expressing LacZ.

value: expressing LacZ


title: NS13


title: Dye Flip of DTT_3hrs/Control, biological rep1 of 3

description:
Dye Flip of 1 of 3
DTT_3 hrs_1_1


title: DTT_3hrs/Control, biological rep1 of 3

description:
Biological replicate 1 of 3.
DTT_3 hrs_1_0


title: NS9


title: NS19


title: NS6


title: NS16


title: MCF7 shRNA Control rep 2

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

description:
Gene expression data from MCF7 cells transduced with control shRNA
CRTL.2

hyb_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2).

data_processing: The data were analyzed with Partek Genomics Suite using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: MCF7 cells with control shRNA

label_protocol: FL-Ovation cDNA Biotin Module V2 from NuGen Technologies Inc.

growth_protocol: MCF7 cells were cultured and maintained in RPMI medium containing 10% FBS and 2 mM glutamine.

treatment_protocol: Puromycin selection (5 μ/ml) for 5-7 days and wash-out for 2 days.

value: Breast cancer cell line MCF7

value: control


title: NS14

value: Normal


title: NS7

value: colon


title: MCF7 shRNA TSC2 rep 1

description:
Gene expression data from MCF7 cells transduced with TSC2 shRNA
TSC2.1

scan_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2).

source_name: MCF7 cells with TSC2 shRNA

value: tuberin-depleted


title: NS34

value: Biopsy


title: MCF7 shRNA Control rep 1

description:
Gene expression data from MCF7 cells transduced with control shRNA
CRTL.1


title: WholeBloodRNA_JR0319_Day0

tag: subject id

tag: time point

value: female

value: our tests did not detect one of the viruses sought


title: MCF7 shRNA TSC2 rep 2

description:
Gene expression data from MCF7 cells transduced with TSC2 shRNA
TSC2.2


title: Mock_colon

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

hyb_protocol: Fluorescence-labeled RNA targets were hybridized to the Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan), non-specific targets were washed away, and the slides were dried by centrifugation and scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

scan_protocol: The slides were dried by centrifugation and scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA). The Cy3 fluorescent intensity of each spot was analyzed by genepix 4.1 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 0 or control probes. Spots that passed these criteria were normalized by the limma package of the R program using quantile normalization.

source_name: mice colon

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX) and Cy3 dye (Amersham Pharmacia, Piscataway, NJ).

extract_protocol: Total RNAs were extracted from colons using RNeasy Mini kit (Qiagen, Valencia, CA, USA) and quantified using Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: strain

value: BALB/c

tag: gender


title: NS3

value: left colon


title: NS2

value: right colon


title: TNBS_colon

source_name: TNBS colon

value: BALC/c

value: TNBS


title: NS4


title: LowDoseRate_4Gy_rep5

first: Shanaz

middle: Adi

last: Ghandhi

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

description: Gene expression after 24hr in 4Gy-irradiated by low dose rate in human blood

hyb_protocol: 1.6 microgram of cRNA,  >9 pmol Cy3 per microgram cRNA was fragmented and hybridized (17 hours with rotation at 65°C) to Agilent Whole Human Genome Microarrays 4X44K v2 (G4112F), and then washed using the Gene Expression Hybridization Kit and GE Wash Buffers as recommended by Agilent

scan_protocol: Slides were  scanned with the Agilent DNA Microarray Scanner (G2505B), and the images were analyzed (Agilent Feature Extraction Software ver. 10.7) with default parameters for background correction and flagging non-uniform features.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: peripheral blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared with the One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND1000 Spectrophotometer

extract_protocol: RNA was isolated from blood cells using the PerfectPure protocol (5Prime) and RNA quality was checked using a nanodrop spectrophotometer and bioanalyzer.

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: dose

tag: dose rate

value: Low

value: whole blood


title: Acute_2Gy_rep5

description: Gene expression after 24hr in 2Gy-irradiated by acute dose rate  in human blood

value: Acute

tag: tissue


title: Acute_4Gy_rep5

description: Gene expression after 24hr in 4Gy-irradiated by acute dose rate in human blood


title: NS10

value: non-dysplastic UC mucosa adjacent to a neoplastic lesion

value: nUCaN


title: NS11


title: TNBS_zingerone_colon

value: TNBS and zingerone


title: NS12


title: NS1

value: Normal


title: LowDoseRate_0.5Gy_rep5

description: Gene expression after 24hr in 0.5Gy-irradiated by low dose rate in human blood


title: Acute_0.5Gy_rep5

description: Gene expression after 24hr in 0.5Gy-irradiated by acute dose rate in human blood


title: LowDoseRate_4Gy_rep4


title: LowDoseRate_2Gy_rep5

description: Gene expression after 24hr in 2Gy-irradiated by low dose rate  in human blood


title: p38_inhibitor_4h_rep3

city: Taipei

first: Mong-Hsun

last: Tsai

address: 4F, No. 81, Chang-Xing St.

department: Institute of Biotechnology

institute: National Taiwan University

data_processing: Quantile normalization were carried out using commercial microarray analysis software (Partek software).

growth_protocol: The protocol was approved by the Institutional Animal Care and Use Committee of National Taiwan University College of Medicine (IACUC Approval No. 20080220). All surgery was performed under sodium pentobarbital anesthesia, and all efforts were made to minimize suffering. Bone marrow was collected from femurs and tibia of 8-10 week-old mice and used to generate bone marrow-derived macrophages (BMDMs). Briefly, bone marrow cells were collected and cultured in high glucose Dulbecco's modified Eagle's medium (DMEM) (Invitrogen, Carlsbad, CA) containing 20% L929-conditioned media for 7 days with the media replaced after 4 days to differentiate into macrophages.

extract_protocol: Total RNA from the cells were isolated using TRIzol® reagent (Invitrogen, Calsbad, CA) and purified with RNeasy® mini kits (Qiagen)

treatment_protocol: IKK knockout or add p38 inhibitor pretreatment. For the conditional knocked out mice, we conditionally knocked out IKK ] (alias Ikbkb), encoding a catalytic enzyme in IkB kinase (IKK) complex, in C57BL/6 mice. IkbkbF/F (IkkbetaF/F, wild-type) and IkkbetaF/F:Mx1-Cre  mice have been described  in  Hsu, L.C., et al., Nat Immunol, 2011. 12(2): p. 144-50. For inhibition of p38, bone marrow-derived macrophages (BMDMs) from C57BL/6 mice were treated with 10  gM SB202190 (Merck, Germany) for 2 h prior to use.

tag: cell line

tag: genotye/variation

value: p38 inhibitor-treated

tag: time point after lipopolysaccharide stimulus

value: 4 hr


title: TNBS_ginger_colon

value: colon

value: TNBS and ginger extract


title: 0Gy_rep5

description: Gene expression after 24hr in 0Gy-irradiated human blood

value: 0 Gy

value: control


title: LowDoseRate_2Gy_rep4


title: WT_0h_rep3_2

value: wild type

value: 0 hr


title: Human CD14+ HLA-DR-/low isolated from peripheral blood Replicate 3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description: Sample name: mds023

hyb_protocol: Following fragmentation, 5-6 micrograms of biotin-labeled targets were hybridized for 16 hr at 45C on an array using the Affymetrix GeneTitan system. Following hybridization, HT_MG-430_PM and HT_HG-U133_Plus_PM plate arrays were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: HT_MG-430_PM and HT_HG-U133_Plus_PM plate arrays were scanned using the Affymetrix GeneTitan system.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console Software v1.1.

source_name: Human peripheral blood CD14+ HLA-DR-/low cells

label_protocol: Biotinylated cRNA was prepared from 100 ng of toal RNA according to the standard Affymetrix 3’IVT Express protocol (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix).

growth_protocol: Samples mds001-004, 013, 019 and 020 were derived from in vitro myeloid suppressors in IL-6 and GM-CSF according to Marigo et. Immunity 32: 790 (2010). Samples mds010 and 011 are spleen myeloid suppressors where Gr-1+ cells are depleted from the postively-sleceted CD11b+ fraction. The spleen samples originate from mice bearing EL4 flank tumors. Samples 021-023 CD14+ HLA-DR-/low were isolated from freshly obtained peripheral blood with consent from Head & Neck Squamous Cell Carcinoma patients undergoing surgical treatments at Johns Hopkins Hospital and Johns Hopkins Bayview Hospital

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer's protocol

value: peripheral blood

value: Cd14+ HLA-DR-/low cells

tag: sample name


title: LowDoseRate_0.5Gy_rep4

value: Low


title: Acute_4Gy_rep4

value: whole blood


title: p38_inhibitor_0h_rep2


title: WT_4h_rep3_2


title: p38_inhibitor_4h_rep2


title: WT_0h_rep2_2


title: p38_inhibitor_4h_rep1


title: LowDoseRate_4Gy_rep3


title: Acute_2Gy_rep4

value: Acute


title: P4

city: Xi'an

first: Lin

last: Shi

state: Shaanxi

address: Yanta West Road No 76

department: Department of Immunology and Microbiology

institute: Xi'an Jiaotong University Health Science Center

hyb_protocol: not provided

scan_protocol: The arrays were stained with Fluidics Station 450 using fluidics script FS450_0003 (Affymetrix), and then scanned on an GeneChip microarray scanner (Affymetrix)

data_processing:
miRNA probe outliers were defined as per the manufacturer's instructions (Affymetrix) and further analyzed for data summarization, normalization and quality control by using the miRNA QC Tool software (www.affymetrix.com)
To determine the significant differentially expressed genes, Significance Analysis of Microarrays (SAM, version 3.02) were performed

source_name: cumulus cells from PCOS patients

label_protocol: not provided

extract_protocol: Total RNAs were isolated using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA) following manufacturer’s protocol

value: female

tag: diagnosis

value: polycystic ovary syndrome (PCOS)

value: cumulus cells


title: WT_0h_rep1_2


title: P


title: p38_inhibitor_0h_rep1


title: Human CD14+ HLA-DR-/low isolated from peripheral blood Replicate 1

description: Sample name: mds021


title: P5


title: 0Gy_rep4


title: LowDoseRate_0.5Gy_rep3


title: WT_4h_rep1_2


title: N

source_name: cumulus cells from non-PCOS patients

value: non-polycystic ovary syndrome (non-PCOS)


title: IKK_KO_4h_rep3

value: IKK-depleted


title: WT_4h_rep2_2

value: 4 hr


title: N4


title: LowDoseRate_2Gy_rep3


title: Acute_4Gy_rep3


title: Acute_2Gy_rep3


title: IKK_KO_0h_rep3


title: N5


title: WT_4h_rep3


title: WT_0h_rep3


title: p38_inhibitor_0h_rep3

value: p38 inhibitor-treated


title: IKK_KO_4h_rep2


title: 0Gy_rep3


title: Acute_2Gy_rep2


title: WT_4h_rep2


title: WT_4h_rep1


title: LowDoseRate_0.5Gy_rep2


title: IKK_KO_4h_rep1


title: Acute_0.5Gy_rep3


title: IKK_KO_0h_rep1


title: LowDoseRate_4Gy_rep1


title: LowDoseRate_2Gy_rep2


title: WT_0h_rep1


title: LowDoseRate_0.5Gy_rep1


title: Acute_0.5Gy_rep2


title: Acute_4Gy_rep2


title: LowDoseRate_4Gy_rep2


title: LowDoseRate_2Gy_rep1


title: IKK_KO_0h_rep2


title: WT_0h_rep2


title: 0Gy_rep2


title: Exp3_Tyk2-/-

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix Mouse Gene 2.0 ST Array (Cat No. 902118);Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000 7G; AGCC (Command Console Software  AGCC4.1.3)

data_processing:
Affymetrix Genexpression Console (4.1.3) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization);

source_name: Tyk2-/-_splenic NK cells

label_protocol: Affymetrix GeneChip WT PLUS Reagent kit (Cat. No 902280)

growth_protocol: cell suspensions from DX5-MACS-enriched splenic NK cells (pooled from 3-4 mice / genotype / experiment) were cultured for 7 days in the presence of 5000 U/ml rhIL-2 (cells were split on days 4 and 6)

extract_protocol: 3-4 x 10^6 cells were lysed in 1 ml TRIFAST reagent and total RNA isolated according to the manufacturer's protocol; half of the total RNA was purified with the RNeasy minikit (Qiagen)

tag: strain background

value: splenic NK cells

tag: cultured with

value: rhIL-2 (5000 U/ml) for  7 days


title: Exp3_Tyk2K923E

source_name: Tyk2K923E_splenic NK cells

tag: cell type


title: Exp2_Tyk2-/-

tag: genotype/variation


title: Exp2_Tyk2K923E


title: Exp3_WT

source_name: WT_splenic NK cells

value: WT


title: mmr755

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix array per manufacturer's instructions

scan_protocol: Standard HT TITAN scanning protocol

data_processing: The data were analyzed with Partek Genomics suite 6.6 and  in STATA/SE 11.2.

source_name: TUMOR-HGG

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

extract_protocol: Trizol

value: brain

tag: brain region

value: cortex

tag: class gene


title: mmr756

source_name: TUMOR UNKNOWN


title: mmr752

source_name: TUMOR-EPENDYMOMA


title: mmr753


title: Acute_0.5Gy_rep1


title: Acute_4Gy_rep1


title: 0Gy_rep1

value: 0 Gy

value: control


title: mmr746

source_name: TUMOR


title: mmr745


title: Exp1_Tyk2K923E


title: Exp2_WT


title: Acute_2Gy_rep1


title: elw019


title: elw027


title: Exp1_Tyk2-/-


title: TAM population A isolated from EG7 thymoma transplanted in Myd88flox/flox; tie2-Cre recipient rep2

hyb_protocol: Following fragmentation, 5-6 micrograms of biotin-labeled targets were hybridized for 16 hr at 45C on an array. HT_MG-430_PM GeneChips were washed and stained in the Affymetrix GeneTitan system. Mouse Gene 2.0 ST GeneChips were washed and stained using in the Affymetrix Fluidics Station 450.

scan_protocol: HT_MG-430_PM plate arrays were scanned using the Affymetrix GeneTitan system. Mouse Gene 2.0 ST GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console Software v1.1. Sample groups TMQ001-TMQ009, TAT101-TAT110, PJM001-PJM016 were summarized independently.

source_name: CD11b+,Ly6C+,MHCII- tumor associated macrophage cells (TAMs) isolated from thymoma arising in Myd88flox/flox; Tie2-Cre mouse transplanted with EG7 lymphoma cells

label_protocol: For samples analyzed on the Affymetrix HT_MG-430_PM array, biotinylated cRNA was prepared from 100 ng of toal RNA according to the standard Affymetrix 3’IVT Express protocol (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix). For samples analyzed on the Affymetrix Mouse Gene 2.0 ST array, sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).


title: elw024


title: Human CD14+ HLA-DR-/low isolated from peripheral blood Replicate 2

description: Sample name: mds022

value: peripheral blood

value: Cd14+ HLA-DR-/low cells


title: TAM population A isolated from EG7 thymoma transplanted in Myd88flox/flox; tie2-Cre; TNFR1-/- recipient rep2

source_name: CD11b+,Ly6C+,MHCII- tumor associated macrophage cells (TAMs) isolated from thymoma arising in TNFR1-/-; Myd88flox/flox; Tie2-Cre mouse transplanted with EG7 lymphoma cells


title: elw015


title: TAM population A isolated from EG7 thymoma transplanted in Myd88flox/flox; tie2-Cre recipient rep1

source_name: CD11b+,Ly6C+,MHCII- tumor associated macrophage cells (TAMs) isolated from thymoma arising in Myd88flox/flox Tie2-Cre mouse transplanted with EG7 lymphoma cells


title: elw028


title: TAM population A isolated from EG7 thymoma transplanted in TNFR1-/- recipient rep2

source_name: CD11b+,Ly6C+,MHCII- tumor associated macrophage cells (TAMs) isolated from thymoma arising in TNFR1-/- mouse transplanted with EG7 lymphoma cells


title: elw013


title: TAM population A isolated from EG7 thymoma transplanted in Myd88flox/flox; tie2-Cre; TNFR1-/- recipient rep1


title: elw020


title: Exp1_WT


title: TAM population A isolated from EG7 thymoma transplanted in WT recipient rep1

source_name: CD11b+,Ly6C+,MHCII- tumor associated macrophage cells (TAMs) isolated from thymoma arising in WT mouse transplanted with EG7 lymphoma cells


title: TAM population A isolated from EG7 thymoma transplanted in WT recipient rep2


title: elw010


title: elw011


title: elw012


title: elw009


title: elw008


title: soybean-oil_br2_95bp

type: SRA

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

institute: Fraunhofer IGB

description: Cells were grown in a yeast extract medium supplemented with 40 g/l glucose and with 70 g/l soybean oil at 30°C for 114 hours.

library_source: transcriptomic

data_processing:
Basecalls were performed using standard software supplied by Illumina for HiSeq2000 sequencing.
Reads generated with HiSeq2000 were mapped with TOPHAT (version 1.4.1) using default settings and producing bam-files.
Genome_build: P. aphidis DSM70725: GCA_000517465.1 under NCBI accession AWNI01000000
Supplementary_files_format_and_content: TOPHAT automatically outputs bed-files containing junction read positions.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample. RPKM was calculated according to Mortazavi et al.

organism: Moesziomyces aphidis

source_name: soybean oil induced

growth_protocol: Samples "glucose_br1/2/3" and "stranded_glucose_br1" were grown in a yeast extract medium supplemented with 40 g/l glucose at 30°C for 114 hours while samples "soybean-oil_br1/2/3", "stranded_soybean-oil_br1" and "soybean-oil_br2_95bp" were additionally supplemented with 70 g/l soybean oil.

extract_protocol:
After 114h of incubation under the corresponding conditions, cells were harvested by centrifugation and immediately frozen with liquid nitrogen. Disruption was carried out using a Mixer Mill MM 200 (RETSCH) with a shaking frequency of 30/s. The resulting powder was resuspended in lysis buffer RLT plus (QIAGEN, Hilden, Germany) supplemented with 0.01% v/v of ß-mercaptoethanol. The extraction of total RNA was performed according to QIAGEN’s Mechanical Disruption Protocol for the isolation of total RNA from yeast using the RNeasy Plus Mini Kit. Concentration and integrity of total RNA was analyzed using the Agilent 2100 Bioanalyzer using the RNA Nano kit.
The cDNA libraries "glucose_br1/2/3, soybean-oil_br1/2/3 and soybean-oil_br2_95bp" for HiSeq2000-sequencing were performed according Illumina’s TruSeq RNA Sample Prep Kit v2 protocol while the libraries "stranded_glucose_br1 and stranded_soybean-oil_br1" were prepared according to Illumina's TruSeq Stranded RNA Sample Prep Kit. The sequencing run was performed on single-read flow cell with 50bp reads except those for library "soybean-oil_br2_95bp" which was sequenced in paired-end mod with 2 x 95 bp.

tag: treatment

value: soybean oil induced

tag: morphology

value: filaments


title: Acute_0.5Gy_rep4

source_name: peripheral blood

value: Acute

value: whole blood


title: TAM population C isolated from EG7 thymoma transplanted in Myd88flox/flox; tie2-Cre; TNFR1-/- recipient rep2

source_name: CD11b+,Ly6C-,MHCII+ tumor associated macrophage cells (TAMs) isolated from thymoma arising in TNFR1-/-; Myd88flox/flox; Tie2-Cre mouse transplanted with EG7 lymphoma cells


title: elw006


title: TAM population C isolated from EG7 thymoma transplanted in Myd88flox/flox; tie2-Cre; TNFR1-/- recipient rep1


title: stranded_soybean-oil_br1

tag: strain


title: MCF-7_Untreated_for_PL_10uM_6h_1

city: Thuwal

first: Mandeep

last: Kaur

address: Building 2, Level 4

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description: SAMPLE 9

hyb_protocol: Labeled cRNA probes (1.65 µg) were fragmented using fragmentation buffer (Agilent Technologies), and hybridized to the Human Gene Expression 4x44K v2 Microarray Kit, Design ID: 026652 (Agilent Technologies,containing 45220 features and 1377 Agilent control probes) arrays in the presence of the gene expression hybridization buffer HI-RPM & blocking agent (Agilent Technologies) for 17 h at 65° C with a 10 rpm rotation speed in a hybridization oven (Agilent Technologies). The arrays were washed using a low stringent wash buffer 1 (Agilent Technologies) at room temperature for 1 min followed by a high stringent wash using the wash buffer 2 (Agilent Technologies) at 37° C.

scan_protocol: The arrays were air dried and scanned using the high-resolution array scanner (Agilent Technologies) with the appropriate settings for the one color gene expression arrays. The signal intensities were extracted from the scanned images with the Feature extraction software 10.7.1.1 (Agilent Technologies) and subjected to background subtraction and spatial detrending.

data_processing: The outliers and the abnormal features were flagged, and the data was normalized using the intra-array percentile shift normalization (threshold of 75 and above) and median-based inter-array normalization.  The GeneSpring GX (Agilent Technologies) was used to calculate the intensity ratios and fold changes.

label: Cyanine-3 (Cy3)

label_protocol: 150 ng of total RNA was used to prepare Cyanine-3 (Cy3) labeled probe using low RNA input linear amplification/labeling kit (Agilent Technologies).  The Dye incorporation and the cRNA yield were measured using the nanodrop-ND 8000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, United States of America).

growth_protocol: MCF-7 (human breast Adenocarcinoma; HTB-22) cells were cultured in DMEM, supplemented with 10% FCS, penicillin (100U/ml) and streptomycin (100 µg/ml) (Gibco) at 5% CO2 in a 37 °C incubator.

extract_protocol: RNA extraction: The cells were washed twice with 2 ml cold 1 x PBS followed by addition of 0.6 ml of Trizol. Cell lysis was performed by incubating the cells with Trizol for 5 min at room temperature and samples were transferred to 1.5 ml eppendorf tubes and 0.12 ml of chloroform was added. Tubes were then inverted for 15 seconds and incubated on ice for 10 min followed by centrifugation at 8000 rpm for 15 min at 4o C. To the aqueous phase, 0.3 ml of isopropanol was added and RNA was precipitated overnight at -20oC. Samples were centrifuged at 8000 rpm for 30 min at 4o C. The supernatant was removed and the resulting pellet was washed with 0.6 ml of 75% ethanol. Samples were then subjected to centrifugation at 8000 rpm for 20 min at 4oC, the supernatant was discarded and the pellet was air-dried and then resuspended in 30 µl of DEPC water. RNA concentration was determined with a nanodrop (Thermo Scientific, USA) and the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) respectively. Samples with the RNA integrity number (RIN) of 9 and above were chosen for microarray analysis.

treatment_protocol: Cells were grown in 6-well plates for 24 h and treated with PL or AP (10 µM) for 6 hours.

value: estrogen responsive breast cancer cells

tag: treated with

value: none (untreated control for PL treated samples)


title: MCF-7_Untreated_for_PL_10uM_6h_3

description: SAMPLE 11


title: MCF-7_Untreated_for_AP_10uM_6h_3

description: SAMPLE 8

value: none (untreated control for AP treated samples)


title: elw007


title: MCF-7_Untreated_for_PL_10uM_6h_2

description: SAMPLE 10


title: MCF-7_Untreated_for_AP_10uM_6h_2

description: SAMPLE 7


title: elw005


title: elw003


title: TAM population C isolated from EG7 thymoma transplanted in Myd88flox/flox; tie2-Cre recipient rep2

source_name: CD11b+,Ly6C-,MHCII+ tumor associated macrophage cells (TAMs) isolated from thymoma arising in Myd88flox/flox; Tie2-Cre mouse transplanted with EG7 lymphoma cells


title: stranded_glucose_br1

description: Cells were grown in a yeast extract medium supplemented with 40 g/l glucose at 30°C for 114 hours.

source_name: not induced

value: not induced

value: blastospores


title: TAM population C isolated from EG7 thymoma transplanted in Myd88flox/flox; tie2-Cre recipient rep1

source_name: CD11b+,Ly6C-,MHCII+ tumor associated macrophage cells (TAMs) isolated from thymoma arising in Myd88flox/flox Tie2-Cre mouse transplanted with EG7 lymphoma cells


title: MCF-7_AP_10uM_6h_3

description: SAMPLE 5

value: 10uM Acetyl Plumbagin (AP) for 6hrs


title: elw002


title: TAM population C isolated from EG7 thymoma transplanted in TNFR1-/- recipient rep2

source_name: CD11b+,Ly6C-,MHCII+ tumor associated macrophage cells (TAMs) isolated from thymoma arising in TNFR1-/- mouse transplanted with EG7 lymphoma cells


title: elw004


title: soybean-oil_br3


title: MCF-7_AP_10uM_6h_2

description: SAMPLE 4


title: TAM population C isolated from EG7 thymoma transplanted in WT recipient rep1

source_name: CD11b+,Ly6C-,MHCII+ tumor associated macrophage cells (TAMs) isolated from thymoma arising in WT mouse transplanted with EG7 lymphoma cells


title: TAM population C isolated from EG7 thymoma transplanted in TNFR1-/- recipient rep1


title: MCF-7_Untreated_for_AP_10uM_6h_1

description: SAMPLE 6


title: MCF-7_AP_10uM_6h_1

description: SAMPLE 3


title: soybean-oil_br2


title: TAM population C isolated from EG7 thymoma transplanted in WT recipient rep2


title: Bone marrow derived Cd11b+ myeloid suppressors Replicate 7

description: Sample name: mds020

source_name: Mouse bone marrow derived Cd11b+ cells

value: bone marrow

value: Cd11b+ cells


title: glucose_br3


title: 401_mDB::3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression after BRG1 siRNA knockdown

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: embryonic stem cells with BRG1 siRNA knockdown

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: embryonic stem cells in vitro culture

extract_protocol: Trizol exaction, Dnase I treatment,mirVana kit purification

treatment_protocol: siRNA treatment for 48 h

value: BRG1 siRNA knockdown

value: mouse embryonic stem cells

tag: genetic background

value: F1 from 129 and C57BL/6


title: glucose_br2


title: MCF-7_PL_10uM_6h_2

description: SAMPLE 2

value: 10uM Plumbagin (PL) for 6hrs


title: Bone marrow derived Cd11b+ myeloid suppressors Replicate 6

description: Sample name: mds019

tag: tissue


title: 401_mDB::2


title: soybean-oil_br1


title: glucose_br1


title: MCF-7_PL_10uM_6h_1

description: SAMPLE 1

tag: cell line


title: Bone marrow derived Cd11b+ myeloid suppressors Replicate 5

description: Sample name: mds013


title: 401_mDB::1


title: Spleen Cd11b+ Gr1-low myeloid suppressors from tumor bearing mice Replicate 1

description: Sample name: mds010

source_name: Mouse spleen Cd11b+ Gr1-low cells

value: spleen

value: Cd11b+ Gr1-low cells


title: 401_mDC::2

description: Gene expression after control siRNA knockdown

source_name: embryonic stem cells with control siRNA knockdown

value: control siRNA knockdown


title: Slide_49

city: St. Louis

first: Michael

last: Heinz

state: MO

address: 4320 Forest Park Blvd.

department: Genetics

institute: Washington University School of Medicine

description: Brugia pahangi_Infective stage cultured_Cultured Larvae (test) VS Brugia pahangi_Migrating stage_Migrating Larvae (reference) - dye flip

hyb_protocol: 2ug of each aRNA was paired, then fragmented according to manufacturer’s protocol (Fragmentation Reagents; ABI-Ambion).  Each paired, fragmented sample was normalized to 13ul, then suspended in Formamide-based hybridization buffer (vial 7-Genisphere) (26ul) and Kreablock (Kreatech Diagnostics) (13ul).  The hybridization solution was heated to 70C for 5 minutes, then allowed to cool to room temperature.  48ul of hybridization solution was added to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity.  Slides were gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.  To prevent fluorophore degredation, the arrays were treated with Dyesaver (Genisphere).

scan_protocol: Slides were scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence.  Laser power was kept constant for Cy3/Cy5 scans and PMT is varied for each experiment based on optimal signal intensity with lowest possible background fluorescence. Gridding and analysis of images was performed using ScanArray v3.0 (Perkin Elmer).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of Red median signal/Green median signal. ScanArray v3.0 (Perkin Elmer) software was used.

organism: Brugia pahangi

source_name: D-Bp cL3.1a: Larval stage, somatic, embryonic, growth tissue

label_protocol: RNA transcripts were first amplified by T7 linear amplification using MessageAmpII aRNA amplification kit; (ABI-Ambion, cat#AM 1751).   1000ng of RNA (11ul) was primed with an oligo-dT T7 primer (1ul) by heating to 70C for 10 minutes, then cooled on ice for 3 minutes.  For 1st strand cDNA synthesis, each RNA received 10x reaction buffer (2ul), dNTP mix (4ul), Rnase Inhibitor (1ul), and reverse transcriptase (1ul) (Superscript II; Invitrogen).  Reverse transcription was carried out for 2 hours at 42C.  After a three minute incubation on ice, the cDNA underwent 2nd strand synthesis by adding water (63ul), 10x 2nd strand buffer (10ul), dNTP mix (4ul), DNA polymerase (2ul) and Rnase H (1ul).  This cocktail was incubated at 16C for 2 hours.  Following a short column cleanup according to manufacturer’s protocol (DNA Clean and Concentrator 5; Zymo Research), invitro-transcription was carried out by adding non-modified bases (ATP, CTP, GTP, and UTP) (4ul of each), 10x T7 reaction buffer (4ul), and T7 RNA polymerase enzyme mix (4ul).    The IVT reaction was carried out for 14 hours.  Following reaction termination with water (60ul), the aRNAs were cleaned with Rneasy columns (Qiagen) according to manufacturer’s protocol.  aRNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy/DY-ULS (either cy3 or cy5)(2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled aRNAs were purified with Kreapure gel columns (Kreatech Diagnostics) according to manufacturer’s protocol.  The labeled RNAs were then quantitated on a NanoDrop spectrophotometer.

growth_protocol: L3 stage larvae were cultured in vitro for 3 days in complete culture medium

extract_protocol: Total RNA was isolated from two groups of Brugia malayi vector derived L3, B. pahangi vector derived L3, B. pahangi L3 cultured in vitro for 3 days(Bp cL3); Brugia pahangi developing L3  from peritoneal cavity of infected gerbils-3days post inoculation  (Bp ipL3); Brugia pahangi migrating L3 (Bp mL3) from popliteal nodes of subcutaneously infected gerbils using the Trizol (Invitrogen Corporation, Carlsbad, CA) extraction method, following the manufacturer’s protocol with some modifications. RNA was treated with RNAse-free DNAse I (Ambion/Applied Biosystems). Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm. The quality of total RNA was determined by an Agilent 2100 bioanalyzer (Agilent Technologies)

tag: life cycle stage

value: Infective stage cultured

tag: developmental stage

value: Cultured Larvae

source_name: C-Bp mL3.2: Larval stage, somatic, embryonic, growth tissue

growth_protocol: L3 were inoculated into gerbils by subcutaneous route and larvae were recovered from the popliteal nodes 3 days post inoculation

value: Migrating stage

value: Migrating Larvae


title: Spleen Cd11b+ Gr1-low myeloid suppressors from tumor bearing mice Replicate 2

description: Sample name: mds011

tag: sample name


title: Bone marrow derived Cd11b+ myeloid suppressors Replicate 4

description: Sample name: mds004


title: Bone marrow derived Cd11b+ myeloid suppressors Replicate 2

description: Sample name: mds002


title: 401_hEB::3

value: human embryonic stem cells


title: Slide_48

description: Brugia pahangi_Migrating stage_Migrating Larvae (reference) VS Brugia pahangi_Infective stage cultured_Cultured Larvae (test)


title: Slide_75

description: Brugia pahangi_Infective stage cultured_Cultured Larvae (test) VS Brugia pahangi_Developmental stage_Developing Larvae (reference) - dye flip

source_name: B-Bp ipL3.2a: Larval stage, somatic, embryonic, growth tissue

growth_protocol: L3 were inoculated into gerbils by intraperitoneal route and larvae were recovered 3 days post inoculation

value: Developmental stage

value: Developing Larvae


title: Slide_47

source_name: D-Bp cL3.2: Larval stage, somatic, embryonic, growth tissue

source_name: C-Bp mL3.1: Larval stage, somatic, embryonic, growth tissue


title: 401_mDC::1


title: Slide_46


title: Bone marrow derived Cd11b+ myeloid suppressors Replicate 1

description: Sample name: mds001


title: CD11b+ TAM isolated from EG7 thymoma transplanted in Myd88-/- recipient rep5

source_name: CD11b+ tumor associated macrophage cells (TAMs) isolated from thymoma arising in Myd88-/- mouse transplanted with EG7 lymphoma cells


title: 401_mDC::3


title: Slide_44

description: Brugia pahangi_Developmental stage_Developing Larvae (reference) VS Brugia pahangi_Infective stage cultured_Cultured Larvae (test)


title: 401_hEC::3


title: 401_hEB::1


title: 401_hEB::2


title: Slide_43

description: Brugia pahangi_Migrating stage_Migrating Larvae (test) VS Brugia pahangi_Developmental stage_Developing Larvae (reference) - dye flip


title: LF ICR mouse Replicate 7

city: Harbin

first: Qiang

last: Gao

state: Heilongjiang

address: XueFu Road

department: Department of Pharmacology

institute: Harbin Medical University

description: The mouse received humane care under identical condition in a clean environment with a 12:12-hour light/dark cycle and common mouse food and water at will.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed and fixed.

scan_protocol: Scanned on the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 18 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: liver, exposed to CCl4 dissolved in corn oil, 2 times per week for 3 weeks

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

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

tag: gender

value: Male

value: ICR

tag: age

value: liver


title: LF ICR mouse Replicate 6


title: Slide_42

description: Brugia pahangi_Developmental stage_Developing Larvae (reference) VS Brugia pahangi_Migrating stage_Migrating Larvae (test)


title: 401_hEC::2


title: CD11b+ TAM isolated from EG7 thymoma transplanted in Myd88-/- recipient rep4


title: 401_hEC::1


title: CD11b+ TAM isolated from EG7 thymoma transplanted in WT recipient rep4

source_name: CD11b+ tumor associated macrophage cells (TAMs) isolated from thymoma arising in WT mouse transplanted with EG7 lymphoma cells


title: Slide_40

source_name: B-Bp ipL3.1a: Larval stage, somatic, embryonic, growth tissue

growth_protocol: L3 stage larve were cultured in vitro for 3 days in complete culture medium


title: CD11b+ TAM isolated from EG7 thymoma transplanted in Myd88-/- recipient rep3


title: LF ICR mouse Replicate 4


title: LF ICR mouse Replicate 5

description: The mouse received humane care under identical condition in a clean environment with a 12:12-hour light/dark cycle and common mouse food and water at will


title: Lox TR1 +tet

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description:
control v. 1 ug/ml tet stimulation for TR1 knockdown
LOXTR1Tet

hyb_protocol: Agilent two-color GE hyb/wash protocol

scan_protocol: Agilent 5 micron scanning protocol, Agilent Technologies Scanner G2505C US45102802

data_processing: Feature extraction and processing - Agilent FE 10.5.1.1 protocol, lowess normaliztion and background subtracted

source_name: LOX

label_protocol: Agilent two-color LRILAK labeling protocol

growth_protocol: All cells were plated at 6×10^5 cells/well in 6 well plates in 2 ml of Advanced DMEM media (supplemented with 2% FBS, and glutamax) and allowed to begin growing overnight.

extract_protocol: Total RNA was collected using Qiagen RNeasy Mini kits.

treatment_protocol: Cells were allowed to grow overnight, then media was removed and replaced with 2 ml of media with or without 1 ug/ml of tetracycline for 72 hrs prior to collection of RNA.

value: LOX

tag: protocol

value: miRNA TR1 + tetracyline for 72 hrs

value: control


title: CD11b+ TAM isolated from EG7 thymoma transplanted in Myd88-/- recipient rep2

tag: cell type


title: LF ICR mouse Replicate 3


title: Slide_41


title: CD11b+ TAM isolated from EG7 thymoma transplanted in WT recipient rep5


title: TAM population A isolated from EG7 thymoma transplanted in TNFR1-/- recipient rep1

source_name: CD11b+,Ly6C+,MHCII- tumor associated macrophage cells (TAMs) isolated from thymoma arising in TNFR1-/- mouse transplanted with EG7 lymphoma cells


title: Bone marrow derived Cd11b+ myeloid suppressors Replicate 3

description: Sample name: mds003

value: bone marrow

value: Cd11b+ cells


title: Slide_33

description: Brugia pahangi_Developmental stage_Developing Larvae (test) VS Brugia pahangi_Infective stage_Infective Larvae (reference) - dye flip

source_name: A-Bp VL3.1a: Larval stage, somatic, embryonic, growth tissue

growth_protocol: Aedes aegypti were infected with microfilariae positive blood and 14 days after blood meal, larvae were isolated

value: Infective stage

value: Infective Larvae


title: Slide_35

description: Brugia pahangi_Migrating stage_Migrating Larvae (test) VS Brugia pahangi_Infective stage_Infective Larvae (reference) - dye flip


title: LF ICR mouse Replicate 2


title: LF ICR mouse Replicate 1


title: Slide_32

description: Brugia pahangi_Infective stage_Infective Larvae (reference) VS Brugia pahangi_Developmental stage_Developing Larvae (test)


title: CD11b+ TAM isolated from EG7 thymoma transplanted in WT recipient rep3


title: Control ICR mouse liver Replicate 7

source_name: liver, exposed to corn oil only, 2 times per week for 3 weeks


title: Lox neg +tet

description:
control v. 1 ug/ml tet stimulation
LOXTet

value: miRNA Neg control + tetracyline for 72 hr


title: CD11b+ TAM isolated from EG7 thymoma transplanted in WT recipient rep2


title: Control ICR mouse liver Replicate 6


title: SK-Mel TR1 +tet

description:
control v. 1 ug/ml tet stimulation for TR1 knockdown
SKMEl28TR1Tet

source_name: SK Mel-28

value: SK Mel-28


title: CD11b+ TAM isolated from EG7 thymoma transplanted in Myd88-/- recipient rep1


title: Lox TR1 -tet

description:
control v. unstimulated TR1 knockdown
LOXTR1

value: miRNA directed at TR1 no tetracycline


title: Slide_34

description: Brugia pahangi_Infective stage_Infective Larvae (reference) VS Brugia pahangi_Migrating stage_Migrating Larvae (test)

value: Migrating stage

value: Migrating Larvae


title: CD11b+ TAM isolated from glioma rep3

source_name: CD11b+ tumor associated macrophage cells (TAMs) isolated from glioma arising in WT BL/6 mouse transplanted with granule neuron progenitors from cerebellum of Tp53-/-, Cdkn2c-/-, Math1-GFP expressing an HER2/Neu mutant (ERBB2 v695A)

value: CD11b+ TAM isolated from glioma rep3


title: Slide_31

description: Brugia pahangi_Infective stage cultured_Cultured Larvae (test) VS Brugia pahangi_Infective stage_Infective Larvae (reference) - dye flip

value: Infective stage cultured

value: Cultured Larvae

source_name: A-Bp VL3.2: Larval stage, somatic, embryonic, growth tissue


title: CD11b+ TAM isolated from glioma rep2

value: CD11b+ TAM isolated from glioma rep2


title: CD11b+ TAM isolated from EG7 thymoma transplanted in WT recipient rep1


title: SK-Mel TR1 -tet

description:
control v. unstimulated TR1 knockdown
SKMEL28TR1


title: Control ICR mouse liver Replicate 5

value: Male

value: ICR

value: liver


title: Lox neg -tet

description:
control v. control to highlight Cy-dye hyb preference
LOXC

value: LOX

value: uninduced control

value: control


title: SK-Mel neg +tet

description:
control v. 1 ug/ml tet stimulation
SKMEL28Tet


title: Control ICR mouse liver Replicate 4


title: Slide_29

value: Infective stage


title: CD11b+ TAM isolated from glioma rep1

value: CD11b+ TAM isolated from glioma rep1


title: SK-Mel neg -tet

description:
control v. control to highlight Cy-dye hyb preference
SKMEL28C


title: Ovary_theca_rep3

description: Gene expression from cells labeled during neonatal stage

hyb_protocol: 4.6 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 18 hours at 45°C in a rotating hybridization.  Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0004.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: cell, ovary

label_protocol: Four microliters of total RNA (due to varying concentrations among samples) was amplified as directed in the WT-Ovation Pico RNA Amplification System protocol, and labeling with biotin following the Encore Biotin Module.

extract_protocol: Gonadal cells from Gli1-CreERT2; Rosa-LSL-tdTomato ovaries were minced and then enzymatically dissociated in Hank’s balanced salt solution (Sigma) with 1 mg/ml collagenase B (Roche), 1.2 U/ml Dispase II (Roche) and 5 U/ml DNAse I (Sigma) for 20 min at 37 oC. To further aid tissue dissociation, the solution was mixed by repeated pipetting (P1000 pipette). Dissociated cells were rinsed and re-suspended in ice-old PBS, and were subject to fluorescence-activated cell sorting (FACS) for tdTomato+ and tdTomato- cells. Cell counts were also obtained during FACS analysis. FACS was performed using a FACSAria II flow cytometer from Becton Dickinson (San Jose, CA) and FACSDiVa software version 6.1.3.

treatment_protocol: mesonephros-derived theca cells were labeled by tamoxifen treatment at E12.5, E14.5 and E16.5 prior to tissue collection. The ovary-derived theca cells were labeled by tamoxifen administration at P1-3 via lactating dam

value: female

value: 2 months


title: Slide_27

value: Developmental stage

value: Developing Larvae

value: Infective Larvae


title: Slide_30

description: Brugia pahangi_Infective stage_Infective Larvae (reference) VS Brugia pahangi_Infective stage cultured_Cultured Larvae (test)


title: Slide_26


title: Slide_74

description: Brugia pahangi_Infective stage_Infective Larvae (test) VS Brugia malayi_Infective stage_Infective Larvae (reference) - dye flip

organism: Brugia malayi

source_name: E-Bm VL3.2a: Larval stage, somatic, embryonic, growth tissue


title: Ovary_theca_rep2


title: Control ICR mouse liver Replicate 2

description: The mouse received humane care under identical condition in a clean environment with a 12:12-hour light/dark cycle and common mouse food and water at will


title: Ovary_theca_rep1


title: Slide_28

growth_protocol: L3 were inoculated into gerbils by subcutaneous route and larvae were recovered from the poplietal nodes 3 days post inoculation

value: Migrating stage

value: Migrating Larvae


title: CD11b+ TAM isolated from thymoma rep3

value: CD11b+ TAM isolated from thymoma rep3


title: Control ICR mouse liver Replicate 3

description: The mouse received humane care under identical condition in a clean environment with a 12:12-hour light/dark cycle and common mouse food and water at will.


title: CD11b+ TAM isolated from thymoma rep1

value: CD11b+ TAM isolated from thymoma rep1


title: CD11b+ TAM isolated from thymoma rep2

value: CD11b+ TAM isolated from thymoma rep2


title: Control ICR mouse liver Replicate 1

value: Male

value: ICR


title: Slide_73

description: Brugia malayi_Infective stage_Infective Larvae (reference) VS Brugia pahangi_Infective stage_Infective Larvae (test)


title: Mesonephros_theca_rep3

description: Gene expression from cells labeled during fetal stage

source_name: cell, mesonephros


title: Mesonephros_theca_rep2


title: CD11b+ TAM isolated from neuroblastoma rep3

source_name: CD11b+ tumor associated macrophage cells (TAMs) isolated from spontaneous neuroblastom arising in peritoneum of Th-MYCN transgenic mouse


title: Slide_72

source_name: E-Bm VL3.1a: Larval stage, somatic, embryonic, growth tissue


title: CD11b+ TAM isolated from neuroblastoma rep2


title: kh2_60hrs_rep2

status: Public on Apr 27 2015

city: Kansas City

first: Madelaine

last: Gogol

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

hyb_protocol: Labeled aRNA was quantified on the NanoDrop ND-1000 and a 1.5µg mass of cy3 labeled aRNA was hybridized to custom Agilent 2x105K HOX tiling arrays.  Hybridizations were performed at 65 degrees C for 17 hours under standard conditions (1X Agilent blocking agent, and 1X Agilent hybridization buffer) and slides were washed successively with Agilent GE wash buffer 1, at room temperature and with Agilent GE wash buffer 2, at 31oC, prior to scanning.

scan_protocol: Microarray images were acquired with an Agilent High-Resolution DNA Microarray Scanner (G2505C).   Hybridization, array washing, scanning and probe information extraction with Agilent’s Feature Extraction Software (Version 10.5.1.1) were all performed according to Agilent’s One-Color Microarray-Based Gene Expression Analysis Protocol, Version 6.0, December 2009 (Low Input Quick Amp Labeling).

data_processing: Agilent tiling arrays were hybridized in a single-color configuration and data was read into R. Agilent gMeanSignal was used as the measurement (mean green signal for each spot). Data was analyzed using the limma package. Data was normalized between arrays using scale normalization. Replicates were averaged and bedgraph files were created and visualized using IGV and UCSC genome browser.

source_name: KH2 cells, 60 hrs RA

label_protocol: Amplified mRNA, referred to as aRNA, was quantified on a NanoDrop ND-1000 and a mass of 2ug was labeled with cy3 dye using Kreatech’s ULS Fluorescent Labeling Kit, part number EA-023.

growth_protocol: KH2 cells at Passage 12 were cultured on gamma irradiated feeder cells with DMEM containg 15% fetal bovine serum, NAA and β-mercaptoethanol.

extract_protocol: RNA isolation was performed using Trizol and later purified by RNA Easy Kit (Quiagen). Total RNA in the amount of 1ug was amplified according to Ambion’s Message Amp II aRNA Amplification Kit, part number AM1751.  Positive control RNA from Agilent’s One Color RNA Spike-In Kit, part number 5188-5282, was used to monitor sample amplification and labeling as well as array hybridization.

treatment_protocol: ES Cells were differentiated with differentiation media (DMEM + 10% Serum + NAA+ 0.03µM RA) RA supplemented 33nm for requisite length of time.  Feeders were separated by plating freshly trypsinized cells on gelatinized plate for 30 min. After half an hour media was aspirated and centrifuged for 5 min at 1000 rpm.

tag: timepoint

value: 60hrs after RA


title: Mesonephros_theca_rep1


title: kh2_60hrs_rep3


title: kh2_60hrs_rep1


title: kh2_72hrs_rep3

source_name: KH2 cells, 72 hrs RA

value: 72hrs after RA


title: kh2_24hrs_rep6

source_name: KH2 cells, 24 hrs RA

value: 24hrs after RA


title: kh2_72hrs_rep2


title: kh2_24hrs_rep5


title: kh2_36hrs_rep1

source_name: KH2 cells, 36 hrs RA

value: 36hrs after RA


title: Slide_71

source_name: E-Bm VL3.1a: Larval stage, somatic, growth tissue)

value: Infective stage


title: kh2_72hrs_rep1


title: kh2_36hrs_rep3


title: kh2_24hrs_rep4


title: kh2_36hrs_rep2


title: kh2_48hrs_rep3

source_name: KH2 cells, 48 hrs RA

value: 48hrs after RA


title: kh2_48hrs_rep2


title: kh2_24hrs_rep3


title: CD11b+ TAM isolated from neuroblastoma rep1


title: kh2_24hrs_rep2


title: kh2_12hrs_rep5

source_name: KH2 cells, 12 hrs RA

value: 12hrs after RA


title: kh2_12hrs_rep3


title: kh2_16hrs_rep3

source_name: KH2 cells, 16 hrs RA

value: 16hrs after RA


title: kh2_12hrs_rep1


title: kh2_12hrs_rep6


title: kh2_12hrs_rep4


title: kh2_24hrs_rep1


title: kh2_16hrs_rep1


title: kh2_12hrs_rep2


title: kh2_wt_rep2

source_name: KH2 cells, uninduced

treatment_protocol: Feeders were separated by plating freshly trypsinized cells on gelatinized plate for 30 min. After half an hour media was aspirated and centrifuged for 5 min at 1000 rpm.


title: kh2_wt_rep1


title: kh2_48hrs_rep1


title: kh2_wt_rep3


title: kh2_8hrs_rep1

source_name: KH2 cells, 8 hrs RA

value: 8hrs after RA


title: kh2_2hrs_rep1

source_name: KH2 cells, 2 hrs RA

value: 2hrs after RA


title: BAT, technical rep4

city: Mohali

first: Mahendra

last: Bishnoi

state: Punjab

address: C-127, Industrial Area, SAS Nagar, Phase 8

department: Nutrition Science and Technology

institute: National Agri-Food Biotechnology Institute

description:
LACA (Laboratory Animal Centre A-strain) mice
Gene expression data from brown adipose tissue

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on gene chip (mouse 430.2.0 Affymetrix array). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

data_processing: The data were analyzed with GeneSpring GX 12.1 using Affymetrix default analysis settings and RMA as normalization method.

source_name: Murine brown adipose tissue (intrascapular region)

label_protocol: Biotinylated aRNA were prepared as per the protocol and guidelines provided by Affymetrix, Inc. (Santa Clara, CA).

growth_protocol: The mice were fed standard chow (70% carbohydrate, 10% Fat) until sacrifice at the described weight range (25 ± 3g).

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

treatment_protocol: There was no treatment administed to the animals. Tissue samples analyzed are from control animals.

value: Brown adipose tissue (intrascapular region)


title: kh2_2hrs_rep2


title: kh2_6hrs_rep3

source_name: KH2 cells, 6 hrs RA

value: 6hrs after RA


title: kh2_4hrs_rep3

source_name: KH2 cells, 4 hrs RA

value: 4hrs after RA


title: kh2_8hrs_rep2


title: BAT, technical rep3


title: kh2_4hrs_rep1


title: BAT, technical rep2


title: kh2_2hrs_rep3


title: kh2_6hrs_rep2


title: BAT, biological rep4


title: BAT, biological rep3


title: BAT, biological rep2


title: BAT, technical rep1


title: subcuaneous WAT, technical rep4

description:
LACA (Laboratory Animal Centre A-strain) mice
Gene expression data from subcutaneous white adipose tissue

source_name: Murine  white adipose tissue (subcutaneous region)

value: White adipose tissue (subcutaneous region)


title: BAT, biological rep1


title: rxra_24

type: genomic

hyb_protocol: Arrays were hybridized with a mixture of 4µg Cy3 labeled DNA and 4µg Cy5 labeled DNA probes. Hybridizations were performed at 650C for 24 hours under standard conditions (45 mg/mL Human Cot-1 DNA, 1X Agilent blocking agent, and 1X Agilent hybridization buffer) and slides were washed successively with Agilent ChIP wash buffer 1, at room temperature and then Agilent ChIP wash buffer 2, at 31C,  prior to scanning.

scan_protocol: Microarray images were acquired with an Agilent High-Resolution DNA Microarray Scanner (G2505C). For image analysis Agilent Feature Extraction software (Version 10.5.1.1) was used.

data_processing: Agilent tiling arrays were hybridized in a two-color configuration and data was read into R (2.11.1). Data was analyzed using the limma (3.4.3) package. Data was normalized within arrays using loess normalization.

molecule: genomic DNA

source_name: rxra chIP, KH2 cells, 24 hrs RA

label_protocol: Extracts were labeled according to Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).

extract_protocol: 37 degrees C for 11 min. Crosslinking was stopped by 1mL 1.25 M glycine to each 10 mL and by incubating at room temperature for 5 min. Cells were sonicated for 25 min in bioruptor at high setting and 30 sec on-off cycle. Input DNA and IP DNA in the amount of 10ng were amplified according to the Agilent Genomic DNA Labeling Kit PLUS (Agilent, 5188-5309, Agilent publication number G4481-90010).

value: Mouse Embryonic Stem Cells (KH2)

value: 24 hrs after RA

tag: chip antibody

value: rxra

tag: chip antibody vendor

value: Santa Cruz Biotechnology, Inc.

tag: chip antibody catalog

tag: sample type

value: input

value: KH2 cells


title: suz12_un

source_name: suz12 chIP, KH2 cells, uninduced

value: uninduced

value: Abcam


title: suz12_24

source_name: suz12 chIP, KH2 cells, 24 hrs RA


title: rxra_un

source_name: rxra chIP, KH2 cells, uninduced


title: kh2_4hrs_rep2


title: suz12_2

source_name: suz12 chIP, KH2 cells, 2 hrs RA

value: 2 hrs after RA


title: ncor_2

source_name: ncor chIP, KH2 cells, 2 hrs RA

value: ncor


title: rxra_2

source_name: rxra chIP, KH2 cells, 2 hrs RA


title: rara_24_rep3

source_name: rara chIP, KH2 cells, 24 hrs RA

value: rara


title: rarb_24_rep3

source_name: rarb chIP, KH2 cells, 24 hrs RA

value: rarb


title: kh2_16hrs_rep2

source_name: KH2 cells, 16 hrs RA

value: 16hrs after RA


title: ncor_24

source_name: ncor chIP, KH2 cells, 24 hrs RA


title: ncor_un

source_name: ncor chIP, KH2 cells, uninduced


title: rarg_un_rep3

source_name: rarg chIP, KH2 cells, uninduced

value: rarg


title: subcuaneous WAT, biological rep2

value: Male


title: rarg_un_rep2


title: subcuaneous WAT, technical rep3


title: rara_un_rep3

source_name: rara chIP, KH2 cells, uninduced


title: subcuaneous WAT, biological rep1


title: subcuaneous WAT, technical rep1


title: subcuaneous WAT, biological rep3


title: rarb_un_rep3

source_name: rarb chIP, KH2 cells, uninduced


title: rara_24_rep2