title: Aha_gDNA_02

city: La Jolla

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

description:
pooled root and shoot tissue, rep2
Cited publication for protocols: Weber M, Harada E, Vess C, V Roepenack-Lahaye E, Clemens S: Comparative microarray analysis of Arabidopsis thaliana and Arabidopsis halleri roots identifies nicotianamine synthase, a ZIP transporter and other genes as potential metal hyperaccumulation factors. Plant J 2004, 37:269–281.

hyb_protocol: Hybridization was conducted according to the standard protocol for hybridizing fragmented cRNA [Weber et al 2004] using 20 µl of the fragmented and labelled genomic DNA instead of fragmented cRNA

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000.

data_processing: The .CEL files were laoded into R and microarray data for each species was normalized separately using MAS5 background correction and vsn normaliztion using Bioconductor, affy and vsn packages. Prior to normalization, some compact errors in Aha_gDNA_02 sample were corrected using the Harshlight package in Bioconductor. The heterologous species hybridizations (A. halleri and A. lyrata) were scaled to bring the signal strength at par with A. thaliana hybridizations. A probe-level ANOVA test was conducted to test the strangth of differential hybridization signal using the lmfit and ebayes functions in Limma. The average of hybridization signals from all probes of a probeset is reported here as the summarized signal intensity.

organism: Arabidopsis halleri

source_name: A. halleri, 2 parent plants - pool of 10 individuals

label_protocol: The genomic DNA fragments were 3’-end labelled with biotin by adding 40 u terminal deoxynucletidyl transferase (Promega) and 2 µl of 1 mM Bio-N6-ddATP (Enzo Life Sciences, USA) to the remaining 32 µl of the fragmentation reaction and incubating the samples for 1 h at 37°C in the dark

growth_protocol: Arabidopsis halleri ssp. halleri (accession Langelsheim) was obtained from one cloned individual (W 504) and from 10 pooled F1 progeny of controlled, reciprocal crosses between two Langelsheim individuals (Lan3.1 and Lan5) grown from seeds .Arabidopsis lyrata ssp. petraea (accession Kubova Hut, kindly provided by Marc Macnair, University of Exeter) and Arabidopsis thaliana (accession Col-0) were grown from seed.A. thaliana was cultivated on standard soil, and the other two species were cultivated in hydroponics.

extract_protocol: Genomic DNA was isolated, fragmented and end-labeled with Bio-N6-ddATP.  Total genomic DNA was isolated from 4 to 6 g fresh biomass of plant leaf tissue with CTAB buffer (0.8% (w/v) CTAB, 800 mM NaCl, 1% (w/v) N-lauryl sarcosine, 140 mM Sorbitol, 22 mM EDTA, 220 mM Tris pH 8). Frozen plant tissue was ground to a fine powder in liquid N2, transferred to a 50 ml tube containing 30 ml CTAB buffer and incubated at 65°C with occasional vigorous shaking for 20 min. After addition of 12 ml chloroform/isoamylalcohol (24:1) and vigorous mixing, the tubes were placed at RT on an inverter for 20 min. After centrifugation at 4,000 rpm for 5 min in a tabletop centrifuge, the aqueous phase was transferred to a fresh tube, 1 vol. isopropanol was added and nucleic acids were precipitated on ice for 30 min. After centrifugation at 9,500 rpm (rotor: JA25-50), 4°C for 8 min, the supernatant was drained and the pellets were resuspended in 6 ml ddH2O. 1 vol. 4 M LiAc was added, and the samples were incubated on ice for 20 min to precipitate RNA. After centrifugation at 9,500 rpm (rotor: JA25-50), 4°C for 11 min, the supernatant was transferred to a fresh tube, 2 vol. ethanol were added and the samples were placed at RT for a few seconds. To collect the precipitate, samples were centrifuged at 12,000 rpm (rotor: JA25-50), 4°C for 20 min. The pellets were resuspended in 1.35 ml ddH2O, followed by the addition of 150 µl 3 M sodium acetate. Phenol/chloroform (1 vol., composition see above) was added, samples were mixed by shaking, and centrifuged at 14,000 rpm for 5 min to resolve phases. The aqueous phase was collected, 2 vol. ethanol were added and samples were placed on ice for 5 min. The precipitate was collected by centrifugation at 14,000 rpm for 5 min. Each pellet was washed with 80% (v/v) ethanol and dried at 37°C for 10 min. Pellets were resuspended in 300 µl ddH2O by gentle pipetting. Nucleic acid concentration and purity were determined spectrophotometrically by measuring absorption at 260 and 280 nm and by subjecting 4 µg of each sample to agarose gel electrophoresis.

treatment_protocol: plants were grown under normal growth conditions, no treatment applied.

value: pooled root and shoot


title: Ath_gDNA_02

status: Public on Sep 30 2016

type: genomic

country: USA

label: biotin

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: A. thaliana Col-0 inbred line

tag: tissue


title: Col-0 8h unprimed seedlings

type: RNA

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

description:
Seedlings
Gene expression data from Arabidopsis Col-0 seedlings unprimed

hyb_protocol: Labelling, hybridization, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

data_processing: Raw data (CEL files) obtained from RNA hybridization experiments were normalized with the affyPLM package from the Bioconductor software project (Gentleman et al., 2004) using the GCRMA that uses GC content of probes in normalization with RMA (Robust Multiple array Average) and  gives one value for each probe set instead of keeping probe level information (Wu et al., 2004). The transcriptional changes were determined by subtracting the normalized signal intensity of the control samples from that of induced samples.

molecule: total RNA

source_name: Wild-type Col-0 seedling

growth_protocol: Seeds of Arabidopsis thaliana (L.) Heynh., accession Col-0 were surface-sterilized and germinated in Petri dishes containing an equal volume of agar medium (MS medium supplemented with 1% sucrose [w/v]) and were grown under a diurnal cycle of 16 h light (120 µE m-2 s-1) at 22°C and 8 h dark at 22°C.

extract_protocol: RNeasy Plant Mini Kit

treatment_protocol: After 5 days, seedlings were subjected to a heat regime of 1.5 h, 37°C; 1.5 h recovery at 22°C; and 45 min, 44°C. After the priming HS treatment, seedlings were returned to normal growth condition and harvested after 4, 8, 24 and 48 h.

tag: ecotype

tag: genotype/variation

value: Wild-type

tag: age

tag: stress

value: unprimed

tag: time of harvest

value: seedling


title: Aha_gDNA_01

description:
pooled root and shoot tissue, rep1
Cited publication for protocols: Weber M, Harada E, Vess C, V Roepenack-Lahaye E, Clemens S: Comparative microarray analysis of Arabidopsis thaliana and Arabidopsis halleri roots identifies nicotianamine synthase, a ZIP transporter and other genes as potential metal hyperaccumulation factors. Plant J 2004, 37:269–281.

source_name: A. halleri, clone, 1 individual


title: Col-0 4h unprimed seedlings

scan_protocol: Labelling, hybridization, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual


title: S-BC3-A-g126-c2-DNA

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2007-10-03 Scan Time : 10:56:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 0, 0

organism: Saccharomyces cerevisiae

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://dunham.gs.washington.edu/UWyeastDNAprep.pdf

tag: strain name

value: ancestral hybrid strain

value: evolved hybrid strain


title: Aly_gDNA_02

organism: Arabidopsis lyrata

source_name: A. lyrata, pool of 10 individuals


title: Aly_gDNA_01


title: Ath_gDNA_01


title: D35cKit-c

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

description:
replicate 3
D35cKit-c

hyb_protocol: labeled cRNA were hybridized to MouseRef-8v2 Beadchip (Illumina) according to the manufacturer’s protocol

scan_protocol: Arrays were scanned with Beadchip Reader according to standard Illumina scanning protocol

data_processing: The D0 (0dpi) , D4 (4 dpi) , iHP/BM CD45+ and Kit+ microarray chips have undergone quantile normalization using IlluminaNormalizer module on GenePattern platform (http://genepattern.broadinstitute.org/) (http://www.broadinstitute.org/cancer/software/genepattern/). The normalized values were transformed to Log2.

organism: Mus musculus

source_name: SLHR induced kit- D35-3

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

growth_protocol: Mouse embryonic fibroblasts (MEF) were cultured in MEF medium (DMEM (high glucose) with 10% FBS, 1x of L-Glutamine, sodium pyruvate and non-essential amino acid, invitrogen). Infected MEF were cocultured with op9 in the IMDM with FBS and Cytokines

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: MEF were infected with retrovirus for Scl,  Lmo2, Runx1 and HoxB4 overexpression

tag: cell type

value: SLHR induced kit-


title: D35kit+c

description:
replicate 3
D35c

source_name: SLHR induced kit+ D35-3

value: SLHR induced kit+


title: D4a

description:
replicate 1
D4a

source_name: SLHR infected tdTomato MEF  Day 4

value: SLHR infected tdTomato MEF


title: D35cKit-d

description:
replicate 4
D35cKit-d

source_name: SLHR induced kit- D35-4


title: D4d

description:
replicate 4
D4d


title: D35kit+a

description:
replicate 1
D35a

source_name: SLHR induced kit+ D35-1


title: S-BB-2N-B-g557-c3-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2008-01-04 Scan Time : 10:29:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

label_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf

value: evolved S. uvarum strain

value: ancestral S. uvarum strain


title: D35kit+b

description:
replicate 2
D35b

source_name: SLHR induced kit+ D35-2


title: D35cKit-a

description:
replicate 1
D35cKit-a

source_name: SLHR induced kit- D35-1


title: TCDD exposed male, biological rep3

city: Gainesville

first: Tracie

middle: R

last: Baker

state: FL

institute: University of Florida

description: Gene expression data from zebrafish exposed to TCDD

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Zebrafish Gene 1.0 ST Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GC3000 G7.

data_processing: The data was extracted and processed using Affymetrix Command Console version 3.2.4.1515W

organism: Danio rerio

source_name: Zebrafish adult testicular tissue exposed to TCDD during early development

label_protocol: All samples were end-terminus labeled following the guidelines of the Affymetrix GeneChip WT terminal labeling an hybridization user manual tartget (P/N 702808 Rev. 7)

growth_protocol: Zebrafish embryos (AB strain) were kept at 27-30 °C in lightly buffered water with a standard 14-h/10-h light/dark cycle as described by Westerfield (2000).

extract_protocol: Rneasy lipid tissue mini kit extraction of total RNA and was performed according to the manufacturer's instructions.

treatment_protocol: Zebrafish were exposed for 1 hour to waterborne TCDD at 50 pg/ml or vehicle (DMSO) at both 3 and 7 wpf (weeks post fertilization; during sexual differentiation and gonad maturation).

tag: Sex

value: male

value: testes

tag: strain

value: AB

tag: genotype

value: wildtype

value: 1 year old (adult)


title: D4c

description:
replicate 3
D4c


title: D26CD45-c

description:
replicate 3
D26CD45-c

source_name: SLHR induced CD45- Day 26

value: SLHR induced CD45-


title: D4b

description:
replicate 2
D4b


title: D35kit+d

description:
replicate 4
D35d

source_name: SLHR induced kit+ D35-4


title: D35cKit-b

description:
replicate 2
D35cKit-b

source_name: SLHR induced kit- D35-2


title: D26d

description:
replicate 4
D26d

source_name: SLHR induced CD45+ Day 26

value: SLHR induced CD45+


title: D26a

description:
replicate 1
D26a


title: D14d

description:
replicate 4
D14d

source_name: SLHR infected tdTomato MEF  Day 14

value: MEF


title: D26CD45-d

description:
replicate 4
D26CD45-d

source_name: SLHR induiced CD45- Day 26

value: SLHR induiced CD45-


title: D26b

description:
replicate 2
D26b


title: D14c

description:
replicate 3
D14c


title: D14b

description:
replicate 2
D14b


title: D26CD45-a

description:
replicate 1
D26CD45-a


title: D14a

description:
replicate 1
D14a


title: D26c

description:
replicate 3
D26c


title: D0b

description:
replicate 2
D0b

source_name: EV  infected tdTomato MEF-2


title: D0d

description:
replicate 4
D0d

source_name: EV  infected tdTomato MEF-4


title: D0c

description:
replicate 3
D0c

source_name: EV  infected tdTomato MEF-3


title: k9.10 iPS cells

city: Tuebingen

first: Sven

last: Poths

address: Calwerstr. 7

department: Medical Genetics

institute: University hospital Tuebingen

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file HumanCytoSNP-12v2-1_H.egt provided by Illumina. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

organism: Homo sapiens

source_name: induced pluripotent stem cells

label_protocol: Biotin (C, G), Dinitrophenyl (A, T), Standard Illumina labelling protocol

growth_protocol: human pluripotent stem cell medium

extract_protocol: Qiagen DNA extraction kit

value: induced pluripotent stem cells


title: BmcKit-d

description:
replicate 4
BmcKit-d

source_name: Bone marrow (tdTomato)

value: Bone marrow


title: BmcKit-c

description:
replicate 3
BmcKit-c


title: TCDD exposed male, biological rep1


title: BmcKit-a

description:
replicate 1
BmcKit-a


title: BmcKit+c

description:
replicate 3
BmcKit+c


title: BmCD45+d

description:
replicate 4
BMCD45+d


title: BmcKit+d

description:
replicate 4
BmcKit+d


title: BmcKit+b

description:
replicate 2
BmcKit+b


title: BmCD45+a

description:
replicate 1
BMCD45+a


title: BmcKit+a

description:
replicate 1
BmcKit+a


title: CON ASO_28_frontal cortex_rep14

city: Paramus

first: Mary

middle: E

last: Hamby

state: New Jersey

address: 215 College Road

department: Neuroinflammation Disease Biology Unit

institute: Lundbeck Research USA

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, Illumina GenomeStudio, background subtracted and probes with pvalue detection >0.05 were filtered out; Partek, log2 transformed, quantile normalized

source_name: Mouse frontal cortex

label_protocol: Biotin, Illumina protocol

growth_protocol: APP/PS1 mice were group housed before surgery. Post-surgery, animals were single housed.  Animals were supplied with 1/4 block of Nutragel and Bacon Softies prior to and following surgery.  Brain cannulas (Alzet Brain Infusion Kit 3, Durect, Cupertino, CA) were prepared under aseptic conditions with a single spacer attached to the bottom of the pedestal for a 2.5mm cannula length and approximately 1.5 cm of tubing was attached to the cannula for connection to the osmotic pumps (Alzet model 1002). Prior to implantation, the osmotic pumps were filled with either ASO or vehicle and placed into sterile saline at 37°C. Mice were maintained under isoflurane anesthesia during the surgery. Once the osmotic pump was implanted, a small burr hole was drilled above the right lateral ventricle (AP:-0.5, ML: 1.1) and the cannula was slowly inserted into the ventricle.  Osmotic pumps and cannulas were maintained at 37°C during surgery to ensure immediate delivery of the compound. Following the 2 week ASO infusion period, the osmotic pumps were either replaced to extend the infusion window (28 day cohort) or removed to prevent CSF reflux into the pump system (14 day cohort). For both pump replacement and removal, animals were anesthetized with isoflurane.

extract_protocol: Animals were euthanized by cervical dislocation without anesthesia. Forebrains were collected and split into two hemispheres. From left hemispheres, whole hippocampus was dissected and frontal cortex was collected after one single cut at Bregma +1.0 mm. The hippocampus and frontal cortex tissues were left in RNALater (Ambion) at 4°C overnight and then stored at -80°C. Tissue was homogenized in 1ml lysis buffer (Ambion RNAqueous 96 automated kit) and an aliquot used for RNA isolation following the kit protocol. A second DNase digestion was added after the RNA was eluted from the filter plate to eliminate residual genomic DNA.  Purified RNA was stored at  −80 °C .

treatment_protocol: The double transgenic APP/PS1 mouse model of AD (first described by Mathias Jucker’s group) was treated either with a CD33-specific ASO or a non-target Control ASO. Animals were dosed with 40ug/day of ASO (pump delivers 6uL/day) for either 14 days (CD33-specific ASO (N=10) ; non-target Control ASO (N=9)) or 28 days (CD33-specific ASO (N=14) ; non-target Control ASO (N=14)) starting at 18 weeks of age and were sacrificed as described at 22 weeks of age.

tag: age of start of experiment

value: 18 weeks

tag: collection age

value: 22 weeks

tag: treatment

value: CON ASO

tag: trt time (days)

tag: animal number

value: frontal cortex


title: CD33 ASO_28_frontal cortex_rep14

value: CD33 ASO


title: M2 iPS cells


title: CD33 ASO_28_frontal cortex_rep13


title: M1 iPS cells


title: BmCD45+b

description:
replicate 2
BMCD45+b


title: CON ASO_14_frontal cortex_rep8


title: k9.7 iPS cells


title: CON ASO_28_frontal cortex_rep13


title: CON ASO_14_frontal cortex_rep9


title: CD33 ASO_14_frontal cortex_rep9


title: M5 iPS cells


title: CON ASO_14_frontal cortex_rep7


title: K7.3 iPS cells


title: BmcKit-b

description:
replicate 2
BmcKit-b


title: K9.2iPS cells


title: K9 fibroblasts

source_name: fibroblasts

value: fibroblasts


title: CD33 ASO_28_frontal cortex_rep9


title: CD33 ASO_14_frontal cortex_rep5


title: CD33 ASO_14_frontal cortex_rep6


title: D0a

description:
replicate 1
D0a

source_name: EV (empty vector)  infected tdTomato MEF-1


title: CON ASO_14_frontal cortex_rep5


title: K7.6 iPS cells


title: CON ASO_28_frontal cortex_rep11


title: M Fibroblasts


title: CD33 ASO_14_frontal cortex_rep8


title: CON ASO_28_frontal cortex_rep8


title: CON ASO_28_frontal cortex_rep10


title: CD33 ASO_14_frontal cortex_rep4


title: K7.1 iPS cells


title: CD33 ASO_28_frontal cortex_rep12


title: CD33 ASO_28_frontal cortex_rep10


title: CON ASO_14_frontal cortex_rep3


title: CON ASO_28_frontal cortex_rep9


title: D26CD45-b

description:
replicate 2
D26CD45-b


title: CD33 ASO_28_frontal cortex_rep8


title: CD33 ASO_28_frontal cortex_rep7


title: CON ASO_28_frontal cortex_rep7


title: CON ASO_14_frontal cortex_rep6


title: CD33 ASO_14_frontal cortex_rep3


title: K7 fibroblasts


title: CON ASO_28_frontal cortex_rep12


title: CD33 ASO_28_frontal cortex_rep11


title: CON ASO_28_frontal cortex_rep5


title: CON ASO_14_hippocampus_rep9

source_name: Mouse hippocampus

value: hippocampus


title: CD33 ASO_14_frontal cortex_rep2


title: CD33 ASO_28_frontal cortex_rep6


title: CD33 ASO_14_hippocampus_rep9


title: CD33 ASO_28_frontal cortex_rep3


title: CON ASO_28_frontal cortex_rep4


title: CON ASO_28_frontal cortex_rep2


title: CON ASO_14_frontal cortex_rep1


title: CD33 ASO_28_frontal cortex_rep5


title: CD33 ASO_28_frontal cortex_rep1


title: CD33 ASO_14_frontal cortex_rep7


title: CON ASO_28_frontal cortex_rep1


title: CON ASO_28_hippocampus_rep13


title: CD33 ASO_14_hippocampus_rep8


title: CON ASO_28_frontal cortex_rep3


title: CON ASO_14_frontal cortex_rep2


title: CON ASO_28_hippocampus_rep12


title: CD33 ASO_28_frontal cortex_rep4


title: CD33 ASO_28_frontal cortex_rep2


title: CON ASO_28_frontal cortex_rep6


title: CON ASO_14_hippocampus_rep8


title: CD33 ASO_28_hippocampus_rep13


title: CD33 ASO_28_hippocampus_rep12


title: CD33 ASO_14_frontal cortex_rep1


title: CD33 ASO_28_hippocampus_rep11


title: CD33 ASO_28_hippocampus_rep10


title: CON ASO_14_hippocampus_rep7


title: CON ASO_14_hippocampus_rep6


title: CD33 ASO_14_hippocampus_rep7


title: CD33 ASO_14_hippocampus_rep4


title: CON ASO_28_hippocampus_rep11


title: CON ASO_28_hippocampus_rep5


title: CD33 ASO_14_hippocampus_rep5


title: CD33 ASO_28_hippocampus_rep6


title: CON ASO_14_hippocampus_rep3


title: CD33 ASO_28_hippocampus_rep8


title: CON ASO_28_hippocampus_rep7


title: CD33 ASO_14_hippocampus_rep2


title: CON ASO_28_hippocampus_rep9


title: CD33 ASO_14_hippocampus_rep3


title: CD33 ASO_28_hippocampus_rep7


title: CD33 ASO_28_hippocampus_rep5


title: CON ASO_28_hippocampus_rep6


title: CD33 ASO_14_hippocampus_rep6


title: CON ASO_28_hippocampus_rep3


title: CON ASO_14_hippocampus_rep5


title: CON ASO_28_hippocampus_rep10


title: CD33 ASO_28_hippocampus_rep9


title: CON ASO_14_hippocampus_rep2


title: CON ASO_14_hippocampus_rep4


title: BmCD45+c

description:
replicate 3
BMCD45+c


title: CD33 ASO_28_hippocampus_rep4


title: CD33 ASO_28_hippocampus_rep3


title: CON ASO_28_hippocampus_rep4


title: CON ASO_28_hippocampus_rep8


title: CD33 ASO_28_hippocampus_rep2


title: CON ASO_28_hippocampus_rep2


title: SSc EPC-derived endothelial cells - basal - 20

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
YA9
Gene expression from SSc EPC - derived endothelial cells - basal.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix Human Exon 1.0 ST Array. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were RMA normalized with Bioconductor
Core probes were used in the analysis.
Transcript assignments are based on genome build hg19.

label: Biotin

source_name: Endothelial cells derived from circulating progenitors - systemic sclerosis - basal conditions

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

extract_protocol: Total RNA was extracted from cultured cells in RLT RNA extraction buffer (Qiagen RNeasy kit, Qiagen, Courtaboeuf, France) and treated by DNase I to eliminate genomic DNA contamination.

value: endothelial cells

tag: disease state

value: systemic sclerosis without pulmonary arterial hypertension

tag: condition

value: unstimulated


title: CD33 ASO_28_hippocampus_rep1

tag: tissue


title: SSc EPC-derived endothelial cells - hypoxia - 20

description:
YA9H
Gene expression from SSc EPC - derived endothelial cells - hypoxia.

source_name: Endothelial cells derived from circulating progenitors - systemic sclerosis - hypoxic exposure

value: hypoxic exposure


title: CON ASO_14_hippocampus_rep1


title: CON ASO_14_frontal cortex_rep4


title: WT_PBS_Hippocampus_rep12

growth_protocol: APP/PS1 mice and littermate (WT) controls were group housed before surgery. Post-surgery, animals were single housed.  Animals were supplied with 1/4 block of Nutragel and Bacon Softies prior to and following surgery.  Brain cannulas (Alzet Brain Infusion Kit 3, Durect, Cupertino, CA) were prepared under aseptic conditions with a single spacer attached to the bottom of the pedestal for a 2.5mm cannula length and approximately 1.5 cm of tubing was attached to the cannula for connection to the osmotic pumps (Alzet model 1002). Prior to implantation, the osmotic pumps were filled with either ASO or vehicle and placed into sterile saline at 37°C. Mice were maintained under isoflurane anesthesia during the surgery. Once the osmotic pump was implanted, a small burr hole was drilled above the right lateral ventricle (AP:-0.5, ML: 1.1) and the cannula was slowly inserted into the ventricle.  Osmotic pumps and cannulas were maintained at 37°C during surgery to ensure immediate delivery of the compound.

treatment_protocol: The double transgenic APP/PS1 mouse model of AD (first described by Mathias Jucker’s group) was treated either with a CD33-specific ASO (N=14), a non-target Control ASO (N=13), or PBS vehicle (N=8). Wild-type littermates were also treated with PBS vehicle (N=11). Animals were dosed with 50ug/day of ASO (pump delivers 6uL/day) for 14 days starting at 18 weeks of age and were sacrificed as described at 22 weeks of age.

tag: animal #

value: Hippocampus

value: WT

value: PBS

tag: surgery date

tag: collection date


title: CD33 ASO_14_hippocampus_rep1


title: APPPS1_CON ASO_Hippocampus_rep13


title: APPPS1_CD33 ASO_Hippocampus_rep12


title: APPPS1_PBS_Hippocampus_rep9


title: SSc EPC-derived endothelial cells - basal - 19

description:
YA8
Gene expression from SSc EPC - derived endothelial cells - basal.


title: APPPS1_CD33 ASO_Hippocampus_rep11


title: APPPS1_CON ASO_Hippocampus_rep10


title: CON ASO_28_hippocampus_rep1


title: SSc EPC-derived endothelial cells - hypoxia - 19

description:
YA8H
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: SSc EPC-derived endothelial cells - hypoxia - 18

description:
YA7H
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: SSc EPC-derived endothelial cells - hypoxia - 17

description:
YA6H
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: APPPS1_CON ASO_Hippocampus_rep11


title: Control EPC-derived endothelial cells - basal - 7

description:
YA3
Gene expression from control EPC - derived endothelial cells - basal.

source_name: Endothelial cells derived from circulating progenitors - healthy control - basal conditions

value: healthy control


title: Control EPC-derived endothelial cells - basal - 8

description:
YA4
Gene expression from control EPC - derived endothelial cells - basal.


title: APPPS1_CON ASO_Hippocampus_rep12


title: Control EPC-derived endothelial cells - hypoxia - 7

description:
YA3H
Gene expression from control EPC - derived endothelial cells - hypoxia.

source_name: Endothelial cells derived from circulating progenitors - healthy control - hypoxic exposure


title: SSc EPC-derived endothelial cells - basal - 18

description:
YA7
Gene expression from SSc EPC - derived endothelial cells - basal.


title: WT_PBS_Hippocampus_rep11


title: SSc EPC-derived endothelial cells - basal - 17

description:
YA6
Gene expression from SSc EPC - derived endothelial cells - basal.


title: APPPS1_PBS_Hippocampus_rep8


title: Control EPC-derived endothelial cells - hypoxia - 9

description:
YA5H
Gene expression from control EPC - derived endothelial cells - hypoxia.


title: Control EPC-derived endothelial cells - hypoxia - 6

description:
YA2H
Gene expression from control EPC - derived endothelial cells - hypoxia.


title: Control EPC-derived endothelial cells - basal - 9

description:
YA5
Gene expression from control EPC - derived endothelial cells - basal.


title: Control EPC-derived endothelial cells - basal - 6

description:
YA2
Gene expression from control EPC - derived endothelial cells - basal.


title: WT_PBS_Hippocampus_rep10


title: Control EPC-derived endothelial cells - hypoxia - 8

description:
YA4H
Gene expression from control EPC - derived endothelial cells - hypoxia.


title: APPPS1_CD33 ASO_Hippocampus_rep9


title: SSc EPC-derived endothelial cells - hypoxia - 15

description:
YA14H
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: APPPS1_CD33 ASO_Hippocampus_rep10


title: SSc EPC-derived endothelial cells - hypoxia - 16

description:
YA15H
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: WT_PBS_Hippocampus_rep8


title: APPPS1_PBS_Hippocampus_rep7


title: SSc EPC-derived endothelial cells - basal - 16

description:
YA15
Gene expression from SSc EPC - derived endothelial cells - basal.


title: SSc EPC-derived endothelial cells - basal - 14

description:
YA13
Gene expression from SSc EPC - derived endothelial cells - basal.


title: WT_PBS_Hippocampus_rep7


title: Control EPC-derived endothelial cells - hypoxia - 5

description:
YA1H
Gene expression from control EPC - derived endothelial cells - hypoxia.


title: APPPS1_CON ASO_Hippocampus_rep9


title: APPPS1_CD33 ASO_Hippocampus_rep8


title: WT_PBS_Hippocampus_rep9


title: SSc EPC-derived endothelial cells - basal - 15

description:
YA14
Gene expression from SSc EPC - derived endothelial cells - basal.


title: APPPS1_CON ASO_Hippocampus_rep8


title: APPPS1_CON ASO_Hippocampus_rep7


title: APPPS1_CD33 ASO_Hippocampus_rep7


title: SSc EPC-derived endothelial cells - hypoxia - 14

description:
YA13H
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: APPPS1_CD33 ASO_Hippocampus_rep6


title: APPPS1_PBS_Hippocampus_rep6


title: WT_PBS_Hippocampus_rep6


title: SSc EPC-derived endothelial cells - basal - 13

description:
YA12
Gene expression from SSc EPC - derived endothelial cells - basal.


title: WT_PBS_Hippocampus_rep5


title: SSc EPC-derived endothelial cells - hypoxia - 13

description:
YA12H
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: APPPS1_CON ASO_Hippocampus_rep6


title: APPPS1_CON ASO_Hippocampus_rep5


title: SSc EPC-derived endothelial cells - hypoxia - 11

description:
YA35h
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: SSc EPC-derived endothelial cells - hypoxia - 12

description:
YA10H
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: APPPS1_CD33 ASO_Hippocampus_rep5


title: APPPS1_PBS_Hippocampus_rep5


title: SSc PAH EPC-derived endothelial cells - hypoxia - 6

description:
YA11H
Gene expression from SSc PAH EPC - derived endothelial cells - hypoxia.

source_name: Endothelial cells derived from circulating progenitors - pulmonary arterial hypertension associated with systemic sclerosis - hypoxic exposure


title: SSc EPC-derived endothelial cells - hypoxia - 10

description:
YA33h
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: SSc EPC-derived endothelial cells - basal - 10

description:
YA33
Gene expression from SSc EPC - derived endothelial cells - basal.


title: SSc EPC-derived endothelial cells - basal - 12

description:
YA10
Gene expression from SSc EPC - derived endothelial cells - basal.


title: WT_PBS_Hippocampus_rep4


title: APPPS1_CD33 ASO_Hippocampus_rep3


title: APPPS1_PBS_Hippocampus_rep3


title: Control EPC-derived endothelial cells - basal - 5

description:
YA1
Gene expression from control EPC - derived endothelial cells - basal.


title: APPPS1_PBS_Hippocampus_rep4


title: Control EPC-derived endothelial cells - basal - 4

description:
YA34
Gene expression from control EPC - derived endothelial cells - basal.


title: SSc EPC-derived endothelial cells - basal - 11

description:
YA35
Gene expression from SSc EPC - derived endothelial cells - basal.


title: SSc PAH EPC-derived endothelial cells - hypoxia - 5

description:
YA31h
Gene expression from SSc PAH EPC - derived endothelial cells - hypoxia.

value: pulmonary arterial hypertension associated with systemic sclerosis


title: Control EPC-derived endothelial cells - hypoxia - 4

description:
YA34h
Gene expression from control EPC - derived endothelial cells - hypoxia.


title: SSc EPC-derived endothelial cells - basal - 9

description:
YA32
Gene expression from SSc EPC - derived endothelial cells - basal.


title: APPPS1_CD33 ASO_Hippocampus_rep4


title: SSc EPC-derived endothelial cells - hypoxia - 9

description:
YA32h
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: SSc PAH EPC-derived endothelial cells - hypoxia - 4

description:
YA29h
Gene expression from SSc PAH EPC - derived endothelial cells - hypoxia.


title: APPPS1_CON ASO_Hippocampus_rep2


title: APPPS1_CON ASO_Hippocampus_rep4


title: APPPS1_PBS_Hippocampus_rep2


title: WT_PBS_Hippocampus_rep1


title: SSc EPC-derived endothelial cells - hypoxia - 6

description:
YA27h
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: APPPS1_CD33 ASO_Hippocampus_rep1


title: APPPS1_CON ASO_Hippocampus_rep3


title: SSc EPC-derived endothelial cells - basal - 8

description:
YA30
Gene expression from SSc EPC - derived endothelial cells - basal.


title: SSc EPC-derived endothelial cells - hypoxia - 8

description:
YA30h
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: SSc EPC-derived endothelial cells - basal - 7

description:
YA28
Gene expression from SSc EPC - derived endothelial cells - basal.


title: APPPS1_CON ASO_Hippocampus_rep1


title: SSc EPC-derived endothelial cells - hypoxia - 7

description:
YA28h
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: WT_PBS_Hippocampus_rep3


title: APPPS1-PBS_Frontal Cortex_rep9

value: Frontal Cortex


title: SSc PAH EPC-derived endothelial cells - hypoxia - 3

description:
YA26h
Gene expression from SSc PAH EPC - derived endothelial cells - hypoxia.


title: APPPS1_PBS_Hippocampus_rep1


title: SSc PAH EPC-derived endothelial cells - basal - 3

description:
YA26
Gene expression from SSc PAH EPC - derived endothelial cells - basal.

source_name: Endothelial cells derived from circulating progenitors - pulmonary arterial hypertension associated with systemic sclerosis - basal conditions


title: APPPS1-CON ASO_Frontal Cortex_rep13


title: SSc EPC-derived endothelial cells - hypoxia - 5

description:
YA24h
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: SSc PAH EPC-derived endothelial cells - basal - 4

description:
YA29
Gene expression from SSc PAH EPC - derived endothelial cells - basal.


title: SSc PAH EPC-derived endothelial cells - basal - 2

description:
YA25
Gene expression from SSc PAH EPC - derived endothelial cells - basal.


title: APPPS1_CD33 ASO_Hippocampus_rep2


title: SSc EPC-derived endothelial cells - basal - 5

description:
YA24
Gene expression from SSc EPC - derived endothelial cells - basal.


title: WT_PBS_Hippocampus_rep2


title: WT-PBS_Frontal Cortex_rep12


title: SSc PAH EPC-derived endothelial cells - hypoxia - 2

description:
YA25h
Gene expression from SSc PAH EPC - derived endothelial cells - hypoxia.


title: SSc EPC-derived endothelial cells - basal - 6

description:
YA27
Gene expression from SSc EPC - derived endothelial cells - basal.


title: SSc EPC-derived endothelial cells - hypoxia - 4

description:
YA23h
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: APPPS1-CON ASO_Frontal Cortex_rep12


title: WT-PBS_Frontal Cortex_rep11


title: APPPS1-CD33 ASO_Frontal Cortex_rep11


title: SSc PAH EPC-derived endothelial cells - basal - 1

description:
YA22
Gene expression from SSc PAH EPC - derived endothelial cells - basal.


title: APPPS1-PBS_Frontal Cortex_rep8


title: Control EPC-derived endothelial cells - basal - 3

description:
YA21
Gene expression from control EPC - derived endothelial cells - basal.


title: Control EPC-derived endothelial cells - basal - 2

description:
YA20
Gene expression from control EPC - derived endothelial cells - basal.


title: APPPS1-CON ASO_Frontal Cortex_rep10


title: SSc EPC-derived endothelial cells - hypoxia - 2

description:
YA17h
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: WT-PBS_Frontal Cortex_rep9


title: APPPS1-CD33 ASO_Frontal Cortex_rep9


title: SSc EPC-derived endothelial cells - basal - 2

description:
YA17
Gene expression from SSc EPC - derived endothelial cells - basal.


title: Control EPC-derived endothelial cells - hypoxia - 2

description:
YA20h
Gene expression from control EPC - derived endothelial cells - hypoxia.


title: SSc PAH EPC-derived endothelial cells - basal - 6

description:
YA11
Gene expression from SSc PAH EPC - derived endothelial cells - basal.


title: Control EPC-derived endothelial cells - basal - 1

description:
YA19
Gene expression from control EPC - derived endothelial cells - basal.


title: SSc EPC-derived endothelial cells - basal - 4

description:
YA23
Gene expression from SSc EPC - derived endothelial cells - basal.


title: APPPS1-CON ASO_Frontal Cortex_rep9


title: APPPS1-CON ASO_Frontal Cortex_rep11


title: Control EPC-derived endothelial cells - hypoxia - 3

description:
YA21h
Gene expression from control EPC - derived endothelial cells - hypoxia.


title: APPPS1-PBS_Frontal Cortex_rep7


title: APPPS1-CD33 ASO_Frontal Cortex_rep8


title: SSc EPC-derived endothelial cells - hypoxia - 3

description:
YA18h
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: Control EPC-derived endothelial cells - hypoxia - 1

description:
YA19H
Gene expression from control EPC - derived endothelial cells - hypoxia.


title: SSc EPC-derived endothelial cells - basal - 3

description:
YA18
Gene expression from SSc EPC - derived endothelial cells - basal.


title: APPPS1-CON ASO_Frontal Cortex_rep8


title: APPPS1-CD33 ASO_Frontal Cortex_rep10


title: SSc PAH EPC-derived endothelial cells - hypoxia - 1

description:
YA22H
Gene expression from SSc PAH EPC - derived endothelial cells - hypoxia.


title: WT-PBS_Frontal Cortex_rep8


title: SSc EPC-derived endothelial cells - hypoxia - 1

description:
YA16H
Gene expression from SSc EPC - derived endothelial cells - hypoxia.


title: WT-PBS_Frontal Cortex_rep7


title: WT-PBS_Frontal Cortex_rep10


title: APPPS1-CD33 ASO_Frontal Cortex_rep7


title: SSc EPC-derived endothelial cells - basal - 1

description:
YA16
Gene expression from SSc EPC - derived endothelial cells - basal.


title: APPPS1-PBS_Frontal Cortex_rep6


title: PF2

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

institute: Leibniz Institute for Farm Animal Biology

description: Mural granulosa cells from pair-fed cows rep 2

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Data analysis was performed with the Expression Console (Version V1.3.1.187, Affymetrix) using the RMA method for normalization. Further comparative analysis was done with the Transcriptome Analysis Console 3.0 (Affymetrix).

organism: Bos taurus

source_name: Mural granulosa cells, pair-fed

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

extract_protocol: The follicular wall was submersed in Ca2+ and Mg2+-free phosphate buffered saline (PBS, pH 7.4), and cells of the GC layer were gently scraped off with a small scalpel blade. Detached cell clots were collected with a pipette, the cells were isolated by centrifugation from the buffer  Total RNA was prepared using the NucleoSpin RNA Kit including removal of genomic DNA with RNAse free rDNAse (Macherey-Nagel).

treatment_protocol: German Hostein Cows were randomly allocated to two groups: a PF (pair-fed) control (n=4) and an experimental HS group (n=4). Cows received a lactation diet based on corn and grass silage. During the experiment animals were either kept in a respiration chamber under thermoneutral (15°C, 64% relative humidiy, THI = 60) or heat stress conditions (28°C, 52% relative humidiy, THI = 76) for a total of 96 hrs. Cows were treated with 500 µg PGF2α (PGF forte, Veyx Pharma GmbH, Schwarzenborn, Germany) to induce luteolysis of the functional corpus luteum 72 hrs before slaughter. Forty-nine hours later, the animals were injected with 100 µg of a GnRH analog (Depherelin, Gonavet Veyx, Veyx Pharma GmbH) to induce a preovulatory LH surge. 22 hrs after GnRH injection rectal temperatures (RT) were measured and animals were transferred from the respiration chamber directly into the institutional slaughterhouse and slaughtered immediately to obtain ovaries and dissect larg dominant follicles.

tag: breed

value: German Holstein

value: mural granulosa cells


title: APPPS1-CD33 ASO_Frontal Cortex_rep4


title: APPPS1-CON ASO_Frontal Cortex_rep5

value: CON ASO


title: WT-PBS_Frontal Cortex_rep3


title: WT-PBS_Frontal Cortex_rep5


title: APPPS1-PBS_Frontal Cortex_rep4


title: APPPS1-CON ASO_Frontal Cortex_rep4


title: HS4

description: Mural granulosa cells from heat stressed cows rep 4

source_name: Mural granulosa cells, heat stress


title: iPSC-derived astrocytes from HC1

city: Kyoto

first: Haruhisa

last: Inoue

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

description: human iPS cells, originated from skin fibroblast

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST Array in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: We used GeneChip® Scanner 3000 7Gt, according to the manufacturer's instructions.

data_processing: Data were analyzed by default analysis settings and global scaling as normalization method of GeneSpring GX7.3.1 software (Agilent)

source_name: iPSC-derived astrocytes

label_protocol: Not provided

growth_protocol:
Differentiated iPSC-derived astrocytes were cultivated in DMEM/F12 Glutamax (Gibco, Japan) supplemented with 1x N2 supplement, 10 ng/ml EGF (PeproTech, Inc., USA), 12 ng/ml basic FGF (PeproTech, Inc., USA) and 2 μg/ml heparin (Nacalai, Japan)
Differentiated iPSC-derived astrocytes were washed in PBS.

extract_protocol: We used miRneasymicro (Quiagen) extraction kit, according to the manufacturer's instructions.

tag: diagnosis

value: Normal (control)

value: iPSC-derived astrocytes


title: PF3

description: Mural granulosa cells from pair-fed cows rep 3

tag: cell type


title: iPSC-derived astrocytes from HC2


title: HS3

description: Mural granulosa cells from heat stressed cows rep 3


title: WT-PBS_Frontal Cortex_rep6


title: WT-PBS_Frontal Cortex_rep4


title: APPPS1-PBS_Frontal Cortex_rep5


title: HS1

description: Mural granulosa cells from heat stressed cows rep 1


title: APPPS1-CD33 ASO_Frontal Cortex_rep6

value: CD33 ASO


title: PF4

description: Mural granulosa cells from pair-fed cows rep 4


title: iPSC-derived astrocytes from Alex1

value: Alexander disease (AxD)


title: HS2

description: Mural granulosa cells from heat stressed cows rep 2


title: Social defeat - resilient 2

city: Rehovot

first: Alon

last: Chen

address: 234 Herzel St.

department: Neurobiology

country: Israel

institute: The Weizmann Institute of Science

description:
total RNA extracted from the Ago2-amygdala complex following an Ago2 IP
miRNA expression data from mice Ago2-amygdala following social defeat

hyb_protocol: Samples were hybridized to a GeneChip miRNA 2.0 Array (Affymetrix)

scan_protocol: Chips were scanned on a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The data was analyzed with Affymetrix miRNA QC tool and normalized using default parameters

source_name: Ago2-Amygdala IP following social defeat

label_protocol: RNA was labeled using Flashtag RNA labeling kit

growth_protocol: 10-week old C57BL/6J male mice were subjected to a chronic social defeat protocol

extract_protocol: RNA was extracted using the RNeasy kit, miRNA supplementary protocol (QIAGEN, Hilden, Germany).

treatment_protocol: Amygdala samples were collected from social defeat and control mice 8 days after the end of the chronic social defeat protocol

value: Mouse brain amygdala


title: Social defeat - resilient 3


title: APPPS1-CD33 ASO_Frontal Cortex_rep5


title: Social defeat - susceptible 3


title: APPPS1-PBS_Frontal Cortex_rep3


title: Social defeat - susceptible 1


title: APPPS1-CD33 ASO_Frontal Cortex_rep3


title: APPPS1-PBS_Frontal Cortex_rep2


title: iPSC-derived astrocytes from HC3


title: APPPS1-CON ASO_Frontal Cortex_rep3


title: APPPS1-CON ASO_Frontal Cortex_rep2


title: Control - 4

description:
total RNA extracted from the Ago2-amygdala complex following an Ago2 IP
miRNA expression data from mice Ago2-amygdala without social defeat

source_name: Ago2-Amygdala IP without social defeat


title: Control - 2


title: Control - 1


title: Control - 3


title: APPPS1-CON ASO_Frontal Cortex_rep1


title: APPPS1-PBS_Frontal Cortex_rep1


title: APPPS1-CD33 ASO_Frontal Cortex_rep2


title: Social defeat - resilient 1


title: PF1

description: Mural granulosa cells from pair-fed cows rep 1


title: WT-PBS_Frontal Cortex_rep2


title: Social defeat - susceptible 2


title: WT_PBS_frontal cortex_rep11

treatment_protocol: The double transgenic APP/PS1 mouse model of AD (first described by Mathias Jucker’s group) was treated either with a CD33-specific ASO (N=10), a non-target Control ASO (N=10), or PBS vehicle (N=10). Wild-type littermates were also treated with PBS vehicle (N=10). Animals were dosed with 75ug/day of ASO (pump delivers 6uL/day) for 14 days starting at 18 weeks of age and were sacrificed as described at ~20.5 weeks of age (17 days after start of 14 day ASO infusion).

tag: Sex

value: female

value: frontal cortex


title: APPPS1-CD33 ASO_Frontal Cortex_rep1


title: WT-PBS_Frontal Cortex_rep1


title: APPPS1_PBS_frontal cortex_rep8


title: APPPS1_CD33 ASO_frontal cortex_rep10


title: WT_PBS_frontal cortex_rep10


title: APPPS1_CD33 ASO_frontal cortex_rep9


title: WT_PBS_frontal cortex_rep9


title: APPPS1_Ctrl ASO_frontal cortex_rep10

value: Ctrl ASO


title: epithelial brushing_severe_rep63

city: London

first: Chih-hsi

middle: Scott

last: Kuo

address: South Kensington Campus

department: Department of Computing

country: United Kingdom

institute: Imperial College London

description: epithelial brushing_severe_asthma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: The data were quality controlled and pre-processed using R code of Affymetric Analysis QC workflow from ArrayAnalysis.org with Robust Multichip Average (RMA) as normalization method.

source_name: epithelial brushing_severe_asthma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip Expression Analysis Technical Manual, Copyright 2005-2009, Affymetrix)

extract_protocol: column-based extraction of total RNA was performed according to the manufacturer's instructions

value: lung

tag: tissue source

value: epithelial brushing

tag: gender

value: male

tag: age

tag: oral corticosteroid use

value: no


title: epithelial brushing_severe_rep61

description: epithelial brushing_severe_asthma


title: APPPS1_Ctrl ASO_frontal cortex_rep9

tag: genotype

tag: treatment


title: epithelial brushing_severe_rep62

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep34

description: epithelial brushing_moderate_asthma

source_name: epithelial brushing_moderate_asthma


title: APPPS1_Ctrl ASO_frontal cortex_rep8

source_name: Mouse frontal cortex

tag: animal number


title: epithelial brushing_severe_rep57

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep36

description: epithelial brushing_moderate_asthma


title: APPPS1_CD33 ASO_frontal cortex_rep8


title: APPPS1_Ctrl ASO_frontal cortex_rep11


title: epithelial brushing_severe_rep56

description: epithelial brushing_severe_asthma

value: yes


title: epithelial brushing_moderate_rep32

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep58

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep33

description: epithelial brushing_moderate_asthma


title: epithelial brushing_moderate_rep35

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep60

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep59

description: epithelial brushing_severe_asthma


title: APPPS1_PBS_frontal cortex_rep7

value: PBS


title: WT_PBS_frontal cortex_rep8

value: WT


title: epithelial brushing_severe_rep55

description: epithelial brushing_severe_asthma


title: APPPS1_CD33 ASO_frontal cortex_rep7


title: epithelial brushing_moderate_rep31

description: epithelial brushing_moderate_asthma


title: APPPS1-CON ASO_Frontal Cortex_rep7

value: Frontal Cortex


title: APPPS1_Ctrl ASO_frontal cortex_rep7


title: WT_PBS_frontal cortex_rep7


title: epithelial brushing_severe_rep54

description: epithelial brushing_severe_asthma


title: APPPS1_CD33 ASO_frontal cortex_rep6


title: epithelial brushing_severe_rep53

description: epithelial brushing_severe_asthma


title: WT_PBS_frontal cortex_rep6


title: APPPS1_PBS_frontal cortex_rep4


title: epithelial brushing_moderate_rep30

description: epithelial brushing_moderate_asthma


title: APPPS1_PBS_frontal cortex_rep5


title: epithelial brushing_severe_rep51

description: epithelial brushing_severe_asthma


title: APPPS1_PBS_frontal cortex_rep6


title: epithelial brushing_severe_rep50

description: epithelial brushing_severe_asthma


title: WT_PBS_frontal cortex_rep5


title: epithelial brushing_severe_rep52

description: epithelial brushing_severe_asthma


title: APPPS1_CD33 ASO_frontal cortex_rep5


title: APPPS1_Ctrl ASO_frontal cortex_rep6


title: epithelial brushing_severe_rep49

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep29

description: epithelial brushing_moderate_asthma


title: APPPS1_Ctrl ASO_frontal cortex_rep5


title: WT_PBS_frontal cortex_rep3


title: APPPS1_Ctrl ASO_frontal cortex_rep4


title: WT_PBS_frontal cortex_rep4


title: epithelial brushing_severe_rep45

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep47

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep46

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep48

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep44

description: epithelial brushing_severe_asthma


title: APPPS1_Ctrl ASO_frontal cortex_rep3


title: APPPS1-CON ASO_Frontal Cortex_rep6

value: CON ASO


title: APPPS1_PBS_frontal cortex_rep3


title: APPPS1_Ctrl ASO_frontal cortex_rep2


title: epithelial brushing_moderate_rep27

description: epithelial brushing_moderate_asthma


title: epithelial brushing_moderate_rep28

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep43

description: epithelial brushing_severe_asthma


title: WT_PBS_frontal cortex_rep2


title: APPPS1_CD33 ASO_frontal cortex_rep3


title: APPPS1_Ctrl ASO_frontal cortex_rep1


title: WT_PBS_frontal cortex_rep1


title: APPPS1_CD33 ASO_frontal cortex_rep2


title: epithelial brushing_severe_rep39

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep26

description: epithelial brushing_moderate_asthma


title: epithelial brushing_moderate_rep25

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep41

description: epithelial brushing_severe_asthma


title: WT_PBS_hippocampus_rep10

value: hippocampus


title: WT_PBS_hippocampus_rep11


title: APPPS1_CD33 ASO_frontal cortex_rep4


title: APPPS1_PBS_hippocampus_rep8


title: epithelial brushing_severe_rep42

description: epithelial brushing_severe_asthma


title: APPPS1_CD33 ASO_frontal cortex_rep1


title: APPPS1_CD33 ASO_hippocampus_rep9


title: APPPS1_PBS_frontal cortex_rep2


title: epithelial brushing_severe_rep36

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep22

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep40

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep37

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep38

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep35

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep24

description: epithelial brushing_moderate_asthma


title: epithelial brushing_moderate_rep23

description: epithelial brushing_moderate_asthma


title: epithelial brushing_moderate_rep21

description: epithelial brushing_moderate_asthma


title: epithelial brushing_moderate_rep20

description: epithelial brushing_moderate_asthma


title: APPPS1_PBS_frontal cortex_rep1


title: APPPS1_PBS_hippocampus_rep7


title: APPPS1_CON ASO_hippocampus_rep11


title: APPPS1_PBS_hippocampus_rep6


title: APPPS1_CON ASO_hippocampus_rep8


title: APPPS1_CD33 ASO_hippocampus_rep8


title: WT_PBS_hippocampus_rep6


title: WT_PBS_hippocampus_rep8


title: WT_PBS_hippocampus_rep7


title: epithelial brushing_severe_rep32

description: epithelial brushing_severe_asthma


title: APPPS1_CD33 ASO_hippocampus_rep7


title: APPPS1_CON ASO_hippocampus_rep 10


title: epithelial brushing_severe_rep34

description: epithelial brushing_severe_asthma


title: WT_PBS_hippocampus_rep5


title: APPPS1_CON ASO_hippocampus_rep7


title: epithelial brushing_severe_rep33

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep28

description: epithelial brushing_severe_asthma


title: WT_PBS_hippocampus_rep9


title: epithelial brushing_moderate_rep18

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep31

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep17

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep30

description: epithelial brushing_severe_asthma


title: APPPS1_PBS_hippocampus_rep5


title: epithelial brushing_moderate_rep15

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep26

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep27

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep19

description: epithelial brushing_moderate_asthma


title: APPPS1_CON ASO_hippocampus_rep9


title: epithelial brushing_moderate_rep16

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep29

description: epithelial brushing_severe_asthma


title: APPPS1_CD33 ASO_hippocampus_rep6


title: WT_PBS_hippocampus_rep4


title: APPPS1_CON ASO_hippocampus_rep6


title: epithelial brushing_severe_rep25

description: epithelial brushing_severe_asthma


title: APPPS1_CD33 ASO_hippocampus_rep4


title: epithelial brushing_severe_rep19

description: epithelial brushing_severe_asthma


title: APPPS1_CD33 ASO_hippocampus_rep5


title: epithelial brushing_moderate_rep12

description: epithelial brushing_moderate_asthma


title: APPPS1_CD33 ASO_hippocampus_rep2


title: SSc PAH EPC-derived endothelial cells - basal - 5

description:
YA31
Gene expression from SSc PAH EPC - derived endothelial cells - basal.

value: endothelial cells

tag: disease state

value: pulmonary arterial hypertension associated with systemic sclerosis

value: unstimulated


title: APPPS1_CON ASO_hippocampus_rep4


title: epithelial brushing_severe_rep18

description: epithelial brushing_severe_asthma


title: APPPS1_CON ASO_hippocampus_rep5


title: epithelial brushing_severe_rep21

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep13

description: epithelial brushing_moderate_asthma


title: APPPS1_CD33 ASO_hippocampus_rep1

value: CD33 ASO


title: epithelial brushing_severe_rep17

description: epithelial brushing_severe_asthma


title: WT_PBS_hippocampus_rep3

value: female


title: APPPS1_PBS_hippocampus_rep4


title: epithelial brushing_severe_rep22

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep10

description: epithelial brushing_moderate_asthma


title: APPPS1_CON ASO_hippocampus_rep3


title: epithelial brushing_severe_rep24

description: epithelial brushing_severe_asthma


title: APPPS1_CD33 ASO_hippocampus_rep3


title: APPPS1_CON ASO_hippocampus_rep1


title: APPPS1_PBS_hippocampus_rep2


title: epithelial brushing_severe_rep20

description: epithelial brushing_severe_asthma


title: WT_PBS_hippocampus_rep1


title: epithelial brushing_severe_rep15

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep16

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep23

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep9

description: epithelial brushing_moderate_asthma


title: APPPS1_CON ASO_hippocampus_rep2


title: WT_PBS_hippocampus_rep2


title: IL_KA_7_rep3

data_processing: BeadStudio, Illumina GenomeStudio, probes with pvalue detection >0.05 were filtered out; Partek, log2 transformed, quantile normalized

growth_protocol: Experiments were conducted on male C57/BL6J mice 12 weeks of age at the time of surgery (Jackson Laboratory, Bar Harbor, ME, USA). Mice were maintained on a 12:12 light-dark cycle (06:00-18:00) and all experiments were performed during the light cycle between 07:00-16:00. Animals were given access to food and water ad libitum throughout the course of the study.

extract_protocol: Animals were anesthetized with CO2, decapitated, and hippocampi placed into RNA Later (Ambion) and frozen until later. Hippocampus tissue was then homogenized in 1.25ml lysis buffer (Ambion RNAqueous 96 automated kit, AM1812) and an aliquot used for RNA isolation following the kit protocol.

treatment_protocol: Experiments were conducted on male C57/BL6J mice 12 weeks of age at the time of surgery.  A small burr hole was made in the skull above the right dorsal hippocampus (from bregma AP: -1.9, ML: 1.5, DV: -2.0) and a 50nl bolus of 20mM kainic acid (K0250, Sigma-Aldrich, St. Louis, MO, USA) dissolved in 0.9% sterile saline was injected using a Hamilton syringe (Model 7000.5, Hamilton Co., Reno, NV, USA). For sham operated animals a 50nl bolus of saline alone was injected. Animals were sacrificed at 7, 28 or 60 day post-surgery.

tag: strain

tag: animal id

value: KA

tag: treatment time

tag: hemisphere

value: IL

value: 12 weeks-old


title: epithelial brushing_moderate_rep8

description: epithelial brushing_moderate_asthma

tag: tissue

value: lung

value: epithelial brushing


title: epithelial brushing_severe_rep14

description: epithelial brushing_severe_asthma

value: male


title: APPPS1_PBS_hippocampus_rep1

tag: surgery date

tag: collection date


title: epithelial brushing_severe_rep13

description: epithelial brushing_severe_asthma

tag: diagnosis

value: no


title: epithelial brushing_moderate_rep7

description: epithelial brushing_moderate_asthma


title: epithelial brushing_moderate_rep4

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep12

description: epithelial brushing_severe_asthma

value: yes


title: IL_KA_28_rep5

tag: Sex


title: CL_KA_60_rep2

value: CL


title: IL_KA_60_rep9


title: CL_KA_60_rep9


title: CL_KA_7_rep6


title: IL_KA_60_rep3


title: epithelial brushing_severe_rep11

description: epithelial brushing_severe_asthma

tag: tissue source


title: CL_KA_7_rep8


title: IL_KA_60_rep8


title: CL_KA_28_rep9


title: epithelial brushing_moderate_rep5

description: epithelial brushing_moderate_asthma

tag: gender


title: epithelial brushing_severe_rep7

description: epithelial brushing_severe_asthma

tag: age


title: IL_Sham_7_rep2

value: Sham


title: epithelial brushing_severe_rep6

description: epithelial brushing_severe_asthma

tag: oral corticosteroid use


title: IL_KA_7_rep8


title: CL_Sham_60_rep5


title: epithelial brushing_severe_rep9

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep10

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep8

description: epithelial brushing_severe_asthma


title: CL_Sham_7_rep4


title: APPPS1_PBS_hippocampus_rep3

tag: genotype

value: PBS


title: epithelial brushing_moderate_rep3

description: epithelial brushing_moderate_asthma


title: IL_Sham_28_rep5

tag: treatment

value: hippocampus


title: epithelial brushing_moderate_rep11

description: epithelial brushing_moderate_asthma


title: CL_KA_28_rep1


title: epithelial brushing_severe_rep2

description: epithelial brushing_severe_asthma


title: epithelial brushing_moderate_rep2

description: epithelial brushing_moderate_asthma


title: CL_Sham_60_rep4


title: CL_KA_60_rep8


title: IL_KA_60_rep7


title: epithelial brushing_severe_rep5

description: epithelial brushing_severe_asthma


title: IL_Sham_60_rep5


title: IL_Sham_28_rep4


title: epithelial brushing_moderate_rep1

description: epithelial brushing_moderate_asthma


title: epithelial brushing_moderate_rep14

description: epithelial brushing_moderate_asthma


title: epithelial brushing_severe_rep3

description: epithelial brushing_severe_asthma


title: epithelial brushing_severe_rep1

description: epithelial brushing_severe_asthma


title: bronchial biopsy_severe_rep56

description: bronchial biopsy of severe asthma

source_name: bronchial biopsy of severe asthma

value: bronchial biopsy

value: severe asthma


title: bronchial biopsy_moderate_rep34

description: bronchial biopsy of moderate asthma

source_name: bronchial biopsy of moderate asthma


title: CL_KA_60_rep7

source_name: Mouse hippocampus


title: CL_Sham_60_rep3


title: bronchial biopsy_moderate_rep35

description: bronchial biopsy of moderate asthma


title: bronchial biopsy_severe_rep54

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep53

description: bronchial biopsy of severe asthma


title: IL_KA_28_rep9


title: CL_KA_7_rep7


title: CL_KA_28_rep8


title: IL_Sham_60_rep4


title: bronchial biopsy_severe_rep50

description: bronchial biopsy of severe asthma


title: IL_KA_28_rep8


title: IL_KA_60_rep6


title: CL_KA_7_rep5


title: bronchial biopsy_severe_rep47

description: bronchial biopsy of severe asthma


title: IL_Sham_60_rep3


title: bronchial biopsy_severe_rep51

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep49

description: bronchial biopsy of severe asthma


title: IL_KA_7_rep6


title: bronchial biopsy_severe_rep46

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep48

description: bronchial biopsy of severe asthma


title: IL_Sham_7_rep4


title: bronchial biopsy_severe_rep55

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep52

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep45

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep43

description: bronchial biopsy of severe asthma


title: epithelial brushing_moderate_rep6

description: epithelial brushing_moderate_asthma


title: bronchial biopsy_severe_rep42

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep44

description: bronchial biopsy of severe asthma


title: CL_KA_60_rep6


title: CL_KA_60_rep5


title: bronchial biopsy_severe_rep40

description: bronchial biopsy of severe asthma


title: IL_KA_28_rep7


title: IL_KA_28_rep6


title: CL_Sham_28_rep5


title: IL_KA_7_rep5


title: bronchial biopsy_severe_rep36

description: bronchial biopsy of severe asthma


title: IL_KA_60_rep4


title: IL_KA_60_rep5


title: CL_KA_60_rep4


title: IL_Sham_28_rep3


title: bronchial biopsy_severe_rep41

description: bronchial biopsy of severe asthma


title: IL_Sham_7_rep3


title: bronchial biopsy_severe_rep38

description: bronchial biopsy of severe asthma


title: CL_Sham_28_rep4


title: bronchial biopsy_severe_rep35

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep33

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep30

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep31

description: bronchial biopsy of severe asthma


title: CL_KA_28_rep6


title: bronchial biopsy_severe_rep37

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep32

description: bronchial biopsy of severe asthma


title: IL_KA_7_rep4


title: bronchial biopsy_severe_rep39

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep34

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep29

description: bronchial biopsy of severe asthma


title: CL_KA_7_rep4


title: CL_KA_28_rep5


title: IL_Sham_60_rep2


title: IL_KA_7_rep7


title: CL_KA_28_rep4


title: epithelial brushing_severe_rep4

description: epithelial brushing_severe_asthma


title: bronchial biopsy_severe_rep26

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep27

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep21

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep20

description: bronchial biopsy of severe asthma


title: IL_Sham_28_rep2


title: bronchial biopsy_severe_rep25

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep23

description: bronchial biopsy of severe asthma


title: CL_Sham_60_rep2


title: bronchial biopsy_severe_rep28

description: bronchial biopsy of severe asthma


title: CL_KA_60_rep3


title: CL_Sham_7_rep3


title: IL_KA_28_rep4


title: IL_KA_28_rep3


title: CL_KA_28_rep3


title: bronchial biopsy_severe_rep18

description: bronchial biopsy of severe asthma


title: CL_KA_28_rep7


title: bronchial biopsy_severe_rep24

description: bronchial biopsy of severe asthma


title: CL_Sham_28_rep3


title: bronchial biopsy_severe_rep22

description: bronchial biopsy of severe asthma


title: CL_KA_7_rep3


title: CL_KA_28_rep2


title: CL_KA_7_rep2


title: bronchial biopsy_severe_rep17

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep15

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep19

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep16

description: bronchial biopsy of severe asthma


title: IL_KA_60_rep2


title: bronchial biopsy_severe_rep14

description: bronchial biopsy of severe asthma


title: CL_Sham_28_rep2


title: bronchial biopsy_severe_rep13

description: bronchial biopsy of severe asthma


title: IL_KA_7_rep2


title: bronchial biopsy_severe_rep11

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep12

description: bronchial biopsy of severe asthma


title: CL_KA_7_rep1


title: CL_Sham_28_rep1


title: Healthy child, 95

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were processed using RMA summarization algorithm.

source_name: Leukocytes, healthy child

label_protocol: GeneChip Whole Transcript Sense Target Labeling Assay.

extract_protocol: Ambion RiboPure.

tag: disease status

value: Healthy

value: Child

tag: cell type

value: Leukocytes


title: CL_Sham_7_rep1

tag: strain


title: Obese child, 99

source_name: Leukocytes, obese child

value: Obese


title: CL_Sham_7_rep2

tag: animal id


title: bronchial biopsy_severe_rep7

description: bronchial biopsy of severe asthma

value: female


title: Healthy child, 96


title: bronchial biopsy_severe_rep10

description: bronchial biopsy of severe asthma


title: IL_KA_7_rep1

value: KA

tag: treatment time

value: IL

value: 12 weeks-old


title: bronchial biopsy_severe_rep5

description: bronchial biopsy of severe asthma

value: lung


title: IL_KA_28_rep2

tag: hemisphere

value: male


title: CL_Sham_60_rep1

tag: tissue


title: CL_KA_60_rep1


title: Healthy child, 97


title: Obese child, 90


title: Healthy child, 98


title: bronchial biopsy_severe_rep6

description: bronchial biopsy of severe asthma

value: yes


title: Obese child, 91


title: bronchial biopsy_severe_rep3

description: bronchial biopsy of severe asthma

value: no


title: bronchial biopsy_severe_rep4

description: bronchial biopsy of severe asthma


title: Obese child, 89


title: Obese child, 131


title: IL_Sham_60_rep1

value: Sham


title: IL_Sham_7_rep1


title: IL_Sham_28_rep1


title: bronchial biopsy_severe_rep1

description: bronchial biopsy of severe asthma


title: bronchial biopsy_severe_rep9

description: bronchial biopsy of severe asthma


title: IL_KA_60_rep1


title: Obese child, 126


title: bronchial biopsy_moderate_rep32

description: bronchial biopsy of moderate asthma

value: moderate asthma


title: Obese child, 129


title: Obese child, 127_2


title: IL_KA_28_rep1

value: hippocampus


title: Obese child, 130


title: bronchial biopsy_severe_rep2

description: bronchial biopsy of severe asthma

value: bronchial biopsy


title: Healthy child, 124_2


title: Ctrl replicate 3

city: Munich

first: Moritz

middle: J

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

description: analysis of cerebellar granular cell layer isolated by laser capture microdissection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized according to standard procedures by the manufacturer

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner GCS3000

data_processing: Data analysis was performed using Genomics Suite (Partek Inc.). Raw data were normalized using the RMA algorithm and differentially expressed genes were identified with ANOVA according to the workflow suggested by the manufacturer (Partek Inc.).

source_name: Cerebellar granular cell layer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from amplified cRNA

growth_protocol: Adult mice housed under standard conditions

extract_protocol: Trizol extraction of total RNA followed by RNeasy cleanup

treatment_protocol: Genetic modification, granular cell specific PTEN null mutant

tag: genotype/variation

value: wild type

value: cerebellum

value: 3 months


title: bronchial biopsy_moderate_rep33

description: bronchial biopsy of moderate asthma


title: Healthy child, 125

value: Healthy

value: Child

value: Leukocytes


title: bronchial biopsy_moderate_rep28

description: bronchial biopsy of moderate asthma

value: female


title: Obese child, 123

value: Obese


title: Obese child, 120


title: bronchial biopsy_moderate_rep27

description: bronchial biopsy of moderate asthma


title: PTEN cKO replicate 3

value: PTEN cKO


title: bronchial biopsy_moderate_rep31

description: bronchial biopsy of moderate asthma

value: lung


title: Ctrl replicate 2

value: male


title: bronchial biopsy_moderate_rep29

description: bronchial biopsy of moderate asthma


title: Obese child, 122


title: Ctrl replicate 1


title: PTEN cKO replicate 2


title: Healthy child, 119


title: bronchial biopsy_moderate_rep30

description: bronchial biopsy of moderate asthma


title: bronchial biopsy_moderate_rep26

description: bronchial biopsy of moderate asthma


title: PTEN cKO replicate 1


title: Healthy child, 118


title: bronchial biopsy_moderate_rep25

description: bronchial biopsy of moderate asthma


title: bronchial biopsy_moderate_rep24

description: bronchial biopsy of moderate asthma


title: Healthy child, 114


title: bronchial biopsy_moderate_rep22

description: bronchial biopsy of moderate asthma


title: Healthy child, 112


title: Liver, B101_28_L_VC3, replicate 3

city: Kitakatsushika-gun

first: Kyosuke

last: Yamashita

state: Saitama

address: Sugito-machi Shimotakano1600

department: Tokyo

institute: Chemicals Evaluation and Research Institute Japan

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60oC 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 SurePrint G3 Rat GE 8x60K Microarray Toxplus for 17 hours at 65ﾂｰ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ﾂｰ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.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 035170_D_F_20110629) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Liver, B101_28_L_VC3, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear 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.

growth_protocol: 5 week-old male Sprague-Dawley (Crl:CD(SD)) Rat were purchased from Charles River Japan. They were housed in an air-conditioned room at 21 to 25 deg C and 40 to 70% humidity, with a 12 h light, 12 h dark cycle. Rats were maintained on a basal diet (Oriental Yeast Co.), with tap water ad libitum.

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

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated Nitrilotriacetic acid trisodium monohydrate (1000 mg/kg/day) for nine weeks.

value: Liver

value: Purified Water

value: Sprague-Dawley


title: Healthy child, 109


title: Liver, B101_28_L_H1, replicate 1

source_name: Liver, B101_28_L_H1, replicate 1

value: Nitrilotriacetic acid trisodium monohydrate (1000 mg/kg/day)


title: Healthy child, 111


title: Liver, B101_28_L_H3, replicate 3

source_name: Liver, B101_28_L_H3, replicate 3


title: bronchial biopsy_moderate_rep21

description: bronchial biopsy of moderate asthma

value: moderate asthma

value: no


title: bronchial biopsy_moderate_rep23

description: bronchial biopsy of moderate asthma

value: bronchial biopsy


title: bronchial biopsy_moderate_rep20

description: bronchial biopsy of moderate asthma


title: Healthy child, 113


title: Healthy child, 108


title: Liver, B101_28_L_H2, replicate 2

source_name: Liver, B101_28_L_H2, replicate 2


title: Healthy child, 107


title: Healthy child, 106


title: Liver, B100_28_L_H3, replicate 3

source_name: Liver, B100_28_L_H3, replicate 3

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated 2,2-Bis(Bromomethyl)-1,3-Propanediol (1000 mg/kg/day) for nine weeks.


title: Healthy child, 104


title: Liver, B101_28_L_VC1, replicate 1

source_name: Liver, B101_28_L_VC1, replicate 1


title: bronchial biopsy_moderate_rep17

description: bronchial biopsy of moderate asthma


title: bronchial biopsy_moderate_rep19

description: bronchial biopsy of moderate asthma


title: Liver, B101_28_L_VC2, replicate 2

source_name: Liver, B101_28_L_VC2, replicate 2


title: Liver, B100_28_L_VC3, replicate 3

source_name: Liver, B100_28_L_VC3, replicate 3

value: Corn Oil


title: Healthy child, 105


title: Liver, B100_28_L_H1, replicate 1

source_name: Liver, B100_28_L_H1, replicate 1


title: bronchial biopsy_severe_rep8

description: bronchial biopsy of severe asthma

value: severe asthma

value: yes


title: Liver, B100_28_L_H2, replicate 2

source_name: Liver, B100_28_L_H2, replicate 2


title: bronchial biopsy_moderate_rep18

description: bronchial biopsy of moderate asthma


title: bronchial biopsy_moderate_rep16

description: bronchial biopsy of moderate asthma


title: Liver, B100_28_L_VC2, replicate 2

source_name: Liver, B100_28_L_VC2, replicate 2


title: Healthy child, 101

value: Healthy

value: Child


title: bronchial biopsy_moderate_rep15

description: bronchial biopsy of moderate asthma


title: Healthy child, 100

value: Leukocytes


title: bronchial biopsy_moderate_rep14

description: bronchial biopsy of moderate asthma


title: Liver, B99_28_L_H3, replicate 3

source_name: Liver, B99_28_L_H3, replicate 3

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated Tris(2-Chloroethyl) Phosphate (400 mg/kg/day) for nine weeks.


title: CD4+Tcell_clone_L10_unstimulated_replicate3

city: Leiden

first: Martijn

middle: H

last: Brugman

address: Albinusdreef 2

department: IHB

country: Netherlands

institute: LUMC

hyb_protocol: The product was hybridized to Human Gene 1.0 ST arrays (Affymetrix, High Wycombe, UK).

scan_protocol: The product was washed, stained and scanned according to the manufacturer's protocols.

data_processing: The resulting data was processed with R (version 3.0.2), using affy and RankProd Bioconductor packages. The data was normalized and summarized using RMA and differentially regulated genes were identified using the non-parametric rank product method with 100 permutations. Probe sets were considered differentially expressed when the percentage of false positive predictions (pfp), which is a measure  similar to the false discovery rate (FDR), was smaller than 0.05.

label_protocol: cDNA was biotin-labelled with the Encore Biotin Module (NuGEN).

growth_protocol: CD4+ T cell clone L10 was isolated from a duodenal biopsy of a celiac disease patient (Petersen et al., 2014, Nat. Struct. Biol. 21:480-488). It recognizes DQ2-glia-α1, one of the immunodominant T cell epitopes in celiac disease. Cells were restimulated mixed irradiated allogeneic PBMC (feeder cells), 1 μg/ml phytohemagglutinin (PHA), 10 ng/ml IL-15 (R&D systems Europe, Abingdon, UK) and 20 Cetus u/ml IL-2 (Proleukin, Chiron corporation, Emeryville, CA) in IMDM supplemented with 10% human serum (IMDM/HS) approximately every 2 weeks, and maintained in IMDM/HS with IL-15 and IL-2 between restimulations.

extract_protocol: RNA was purified from these cells using the RNAeasy mini kit (Qiagen, Venlo, the Netherlands). cDNA was amplified using the Applause WT-Amp system (NuGEN technologies, Bemmel, the Netherlands).

treatment_protocol: Prior to the addition of cells, CD3- and CD28-specific antibodies (OKT3 and CD28.2, both from Biolegend) were coated onto non-tissue culture treated plates at 2.5 µg/ml (each) in PBS for at least 3h. Control plates were treated identically, but without the addition of antibodies in this step. After a 1h blocking step using 50 µg/ml purified mouse IgG (Innovative Research, Novi, MI, USA) in PBS, unbound antibodies were removed by three washing steps with PBS. After Ficoll purification, L10 cells were stimulated for 3 hours in IMDM with plate-bound CD3/CD28-specific (2.5 µg/ml each) or control antibodies (see above) coated onto 6-well non-tissue culture treated plates. Three independent biological replicates were performed, each time including 6 million Ficoll-purified live cells per condition.

value: CD4+ T clone L10 cells

tag: stimulated with

value: control antibodies (unstimulated control)


title: bronchial biopsy_moderate_rep12

description: bronchial biopsy of moderate asthma

source_name: bronchial biopsy of moderate asthma

value: lung

tag: diagnosis


title: CD4+Tcell_clone_L10_CD3CD28_replicate3

value: duodenal biopsy of a celiac disease patient

value: plate-bound CD3/CD28-specific (2.5 µg/ml each) for 3hrs


title: bronchial biopsy_moderate_rep13

description: bronchial biopsy of moderate asthma

value: female


title: Social defeat - resilient 3

description:
total RNA extracted from the Ago2-amygdala complex following an Ago2 IP
Gene expression data from mice Ago2-amygdala following social defeat

hyb_protocol: 2ug ss cDNA in 80 ul were hybridized to a Mouse Gene 1.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0007 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G     Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G     Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

source_name: Ago2-Amygdala IP following social defeat

label_protocol: 100ng of Total RNA were used. cDNA samples were generated and labeled using Ambion WT Expression Kit and Affymetrix GeneChip WT Terminal Labeling Kit.

value: Mouse brain amygdala


title: CD4+Tcell_clone_L10_unstimulated_replicate1


title: CD4+Tcell_clone_L10_CD3CD28_replicate1


title: Social defeat - resilient 2


title: Liver, B100_28_L_VC1, replicate 1

source_name: Liver, B100_28_L_VC1, replicate 1

value: Liver

value: Sprague-Dawley

value: male


title: Liver, B99_28_L_VC1, replicate 1

source_name: Liver, B99_28_L_VC1, replicate 1


title: bronchial biopsy_moderate_rep11

description: bronchial biopsy of moderate asthma

value: bronchial biopsy

value: moderate asthma

value: no


title: Liver, B97_28_L_H3, replicate 3

source_name: Liver, B97_28_L_H3, replicate 3

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated o-Anthranilic acid (1000 mg/kg/day) for nine weeks.

value: o-Anthranilic acid (1000 mg/kg/day)


title: Liver, B99_28_L_VC3, replicate 3

source_name: Liver, B99_28_L_VC3, replicate 3

value: Corn Oil


title: Liver, B99_28_L_H2, replicate 2

source_name: Liver, B99_28_L_H2, replicate 2

value: Tris(2-Chloroethyl) Phosphate (400 mg/kg/day)


title: CD4+Tcell_clone_L10_unstimulated_replicate2


title: Liver, B97_28_L_H1, replicate 1

source_name: Liver, B97_28_L_H1, replicate 1


title: bronchial biopsy_moderate_rep8

description: bronchial biopsy of moderate asthma


title: CD4+Tcell_clone_L10_CD3CD28_replicate2


title: bronchial biopsy_moderate_rep6

description: bronchial biopsy of moderate asthma


title: bronchial biopsy_moderate_rep5

description: bronchial biopsy of moderate asthma


title: Liver, B99_28_L_VC2, replicate 2

source_name: Liver, B99_28_L_VC2, replicate 2


title: Social defeat - resilient 1


title: Liver, B99_28_L_H1, replicate 1

source_name: Liver, B99_28_L_H1, replicate 1


title: Liver, B97_28_L_H2, replicate 2

source_name: Liver, B97_28_L_H2, replicate 2


title: bronchial biopsy_moderate_rep10

description: bronchial biopsy of moderate asthma


title: bronchial biopsy_moderate_rep7

description: bronchial biopsy of moderate asthma


title: bronchial biopsy_moderate_rep9

description: bronchial biopsy of moderate asthma


title: bronchial biopsy_moderate_rep4

description: bronchial biopsy of moderate asthma


title: Social defeat - susceptible 3


title: bronchial biopsy_moderate_rep3

description: bronchial biopsy of moderate asthma


title: Social defeat - susceptible 2


title: bronchial biopsy_moderate_rep2

description: bronchial biopsy of moderate asthma


title: Liver, B97_28_L_VC3, replicate 3

source_name: Liver, B97_28_L_VC3, replicate 3


title: Control - 2

description:
total RNA extracted from the Ago2-amygdala complex following an Ago2 IP
Gene expression data from mice Ago2-amygdala without social defeat

source_name: Ago2-Amygdala IP without social defeat


title: Control - 1


title: Social defeat - susceptible 1


title: Control - 4


title: Liver, B96_28_L_H3, replicate 3

source_name: Liver, B96_28_L_H3, replicate 3

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated tert-Butyl alcohol (1000 mg/kg/day) for nine weeks.

value: tert-Butyl alcohol (1000 mg/kg/day)


title: Liver, B96_28_L_H1, replicate 1

source_name: Liver, B96_28_L_H1, replicate 1


title: Liver, B97_28_L_VC2, replicate 2

source_name: Liver, B97_28_L_VC2, replicate 2


title: DD6 naïve B cells sort 2

city: Darlinghurst

first: Christopher

middle: Carl

last: Goodnow

state: NSW

address: 384 Victoria Street

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

description:
Gene expression in naïve B cells expressing IgD only
DD6 mouse 54: 252800516797_S01_GE1_107_Sep09_1_4

hyb_protocol: 600 ng Cy3-labelled fragmented cRNA was hybridized for 17 hrs at 65˚C to Agilent Whole Mouse Genome Oligo Microarrays 8x60K according to the Agilent 60-mer microarray processing protoco using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: After washing, the arrays were scanned on an Agilent Microarray Scanner System G2505C.

data_processing: Using Agilent Feature Extraction Software, protocol GE1_107_Sep09, signal intensities from individual features were normalized by dividing by the median signal of all features on the same array, yielding the relative mRNA units shown

source_name: DD6 naïve B cells sort 2

label_protocol: Cy3 labelled cRNA was produced by linear T7-based amplification using the Agilent Low Input Quick Amp Labeling Kit following the manufacturer’s protocol, and yields measured with a Nanodrop ND-1000 Spectrophotometer.

growth_protocol: All mice of C57BL/6 background raised in the same room in specific pathogen free environment in microisolator cages with feed and water ad libitum. Where possible, donors of naïve and anergic B cells were siblings.

extract_protocol: Cell pellets were lysed and RNA isolated on NucleoSpin RNA II kits (Macherey-Nagel) using standard protocols. RNA quality was analyzed on an Agilent 2100 Bioanalyzer and samples with RIN >6.4 were used.

treatment_protocol: CD93- CD23+ B220+ HEL-binding kappa light chain+ B cells were sorted from spleen cell suspensions in RPMI 2%FCS on ice. Aliquots comprising 100,000 selected cells were sorted into 15 ml Falcon tubes containing 2 ml fetal calf serum, on ice. The cells were washed in PBS, resuspended in 1400 ul PBS, transferred to 1.5 ml Eppendorf tubes, centrifuged at 900 g for 6 min at 4˚C, supernatants removed, and tubes with cell pellets snap frozen in liquid N2, stored at -80˚C, and all tubes shipped together on dry ice to Miltenyi Biotec, Germany for processing and microarray hybridization as a single batch.

value: 211 days

value: Spleen mature B cells

tag: sorted cell type

value: naïve B cell

tag: cell expression

value: expressing IgD only


title: DD6 naïve B cells sort 3

description:
Gene expression in naïve B cells expressing IgD only
DD6 mouse  61: 252800516795_S01_GE1_107_Sep09_2_4

source_name: DD6 naïve B cells sort 3

tag: gender

value: 84 days


title: DD6:ML5 anergic B cells pooled sort 1 & 2

description:
Gene expression in anergic B cells expressing IgD only
DD6:ML5 pool from mice 48, 55, 56: 252800516796_S01_GE1_107_Sep09_2_2

tag: age

value: anergic B cell


title: bronchial biopsy_moderate_rep1

description: bronchial biopsy of moderate asthma

source_name: bronchial biopsy of moderate asthma

value: lung

tag: tissue source

value: female

tag: oral corticosteroid use


title: Liver, B96_28_L_VC2, replicate 2

source_name: Liver, B96_28_L_VC2, replicate 2

value: Liver

tag: treatment

value: Purified Water

value: Sprague-Dawley


title: MM4:ML5 anergic B cells sort 3

description:
Gene expression in anergic B cells expressing IgM only
MM4:ML5  mouse 60: 252800516797_S01_GE1_107_Sep09_2_4

source_name: MM4:ML5 anergic B cells sort 3

value: male

value: 153 days

tag: genotype

value: expressing IgM only


title: Liver, B96_28_L_VC3, replicate 3

source_name: Liver, B96_28_L_VC3, replicate 3


title: DD6 naïve B cells sort 1

description:
Gene expression in naïve B cells expressing IgD only
DD6 mouse  47: 252800516796_S01_GE1_107_Sep09_2_1

source_name: DD6 naïve B cells sort 1

value: 149 days

tag: cell type


title: Liver, B96_28_L_H2, replicate 2

source_name: Liver, B96_28_L_H2, replicate 2

tag: strain


title: Lung cDC2s from HDM-treated Irf3-deficient mice, sample 2

city: Liège

first: Thibaut

last: Janss

address: Avenue de l'hopital 1

department: GIGA-R

country: Belgium

institute: Ulg

description:
Irf3 HDM 2
Gene expression data on a pool of lung cDC2s (Cd11c+ Mhc2+ Cd11b+ Ly6c- Cd64- dendritic cells) from 10 HDM-treated Irf3-deficient mice

hyb_protocol: Microarrays were performed following the standard Affymetrix protocol (Mouse Gene 1.0 ST arrays) (Affymetrix Hibridization control kit and Affymetrix Hybridization Wash and Stain Kit)

scan_protocol: Scanner 3000 7G following affymetrix recommandation

data_processing: Microarray raw data was analysed using using Bioconductor in R (version 3.2.1). Data was normalised by RMA using the oligo package from biocLite.

label_protocol: Microarrays were performed following the standard Affymetrix protocol (Mouse Gene 1.0 ST arrays) (Ambion WT expression kit and Affymetrix WT Terminal Labeling kit)

extract_protocol: mRNA was isolated according to the protocol of the Immgen consortium (www.immgen.org)

treatment_protocol: Wild type (WT) or Irf3-deficient mice were treated with 100 µg of house dust mite extract or a saline solution 12 hours before isolation of lung CD11b+ conventional dendritic cells (cDC2s)

tag: strain background

tag: Sex

value: Irf3 deficient

tag: treated with

value: 100 µg House dust mite extract

value: Cd11c+ Mhc2+ Cd11b+ Ly6c- Cd64- cells


title: MM4 naïve B cells sort 2

description:
Gene expression in naïve B cells expressing IgM only
MM4  mouse 52: 252800516797_S01_GE1_107_Sep09_1_2

source_name: MM4 naïve B cells sort 2

value: 158 days

value: Spleen mature B cells


title: MM4:ML5 anergic B cells sort 1

description:
Gene expression in anergic B cells expressing IgM only
MM4:ML5  mouse 46: 252800516796_S01_GE1_107_Sep09_1_4

source_name: MM4:ML5 anergic B cells sort 1

value: 157 days


title: 20-day-old mouse Sertoli cells

city: Nanjing

first: Yabing

address: No. 22 Hankou Rd., Gulou District, Nanjing, Jiangsu

country: China

institute: Nanjing University

description: Gene expression data from 20-day-old mouse Sertoli cells

hyb_protocol: Biotin-labeled cDNA was hybridized to the mouse gene 1.0 ST GenChip (Affymetrix) for 16 hours at 45°C using an Affymetrix-defined protocol.

scan_protocol: Genechips were scanned on the 3000 7G, an Affymetrix GeneChip scanner

data_processing: RMA data

source_name: 20-day-old mouse Sertoli cell

label_protocol: Fragmentation and labeling of the single-stranded cDNA were acquired using GeneChip® WT Terminal Labeling and Control Kit (Invitrogen).

growth_protocol: Sertoli cells were isolated from 20-day mouse testes and cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum.

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

treatment_protocol: After primary culture for 48 hours, Sertoli cells were treated with 500 nm MC-LR. As the control group, the cell were not treated with MC-LR.

value: sertoli cells

tag: tissue

value: testis


description: Gene expression data from 20-day-old mouse Sertoli cells treated with MC-LR


title: MD4:ML5 anergic B cells sort 2 mouse 2

description:
Gene expression in anergic B cells coexpressing IgM and IgD
MD4:ML5  mouse  51: 252800516798_S01_GE1_107_Sep09_1_1

source_name: MD4:ML5 anergic B cells sort 2 mouse 2

value: 135 days

value: anergic B cell

value: coexpressing IgM and IgD


title: Liver, B96_28_L_VC1, replicate 1

source_name: Liver, B96_28_L_VC1, replicate 1

value: Liver

value: Purified Water


title: Lung cDC2s from HDM-treated Irf3-deficient mice, sample 3

description:
Irf3 HDM 3
Gene expression data on a pool of lung cDC2s (Cd11c+ Mhc2+ Cd11b+ Ly6c- Cd64- dendritic cells) from 10 HDM-treated Irf3-deficient mice

value: female

tag: genotype/variation

value: lung CD11b+ conventional dendritic cells (cDC2s)


title: MM4 naïve B cells sort 1

description:
Gene expression in naïve B cells expressing IgM only
MM4  mouse 45: 252800516796_S01_GE1_107_Sep09_1_3

source_name: MM4 naïve B cells sort 1

value: male

value: 195 days

value: naïve B cell

value: expressing IgM only


title: Liver, B93_28_L_VC3, replicate 3

source_name: Liver, B93_28_L_VC3, replicate 3

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated Phenolphthalein (1000 mg/kg/day) for nine weeks.

value: Corn Oil

value: Sprague-Dawley


title: Lung cDC2s from HDM-treated Irf3-deficient mice, sample 1

description:
Irf3 HDM 1
Gene expression data on a pool of lung cDC2s (Cd11c+ Mhc2+ Cd11b+ Ly6c- Cd64- dendritic cells) from 10 HDM-treated Irf3-deficient mice

value: Irf3 deficient

value: 100 µg House dust mite extract

value: Cd11c+ Mhc2+ Cd11b+ Ly6c- Cd64- cells


title: Liver, B93_28_L_H2, replicate 2

source_name: Liver, B93_28_L_H2, replicate 2

value: Phenolphthalein (1000 mg/kg/day)


title: Liver, B93_28_L_H3, replicate 3

source_name: Liver, B93_28_L_H3, replicate 3


title: Liver, B97_28_L_VC1, replicate 1

source_name: Liver, B97_28_L_VC1, replicate 1


title: Liver, B93_28_L_VC1, replicate 1

source_name: Liver, B93_28_L_VC1, replicate 1


title: Liver, B93_28_L_VC2, replicate 2

source_name: Liver, B93_28_L_VC2, replicate 2


title: MD4:ML5 anergic B cells sort 2

description:
Gene expression in anergic B cells coexpressing IgM and IgD
MD4:ML5  mouse  50: 252800516796_S01_GE1_107_Sep09_2_4

source_name: MD4:ML5 anergic B cells sort 2

value: 98 days

value: Spleen mature B cells


title: MD4:ML5 anergic B cells sort 1

description:
Gene expression in anergic B cells coexpressing IgM and IgD
MD4:ML5  mouse 44: 252800516796_S01_GE1_107_Sep09_1_2

source_name: MD4:ML5 anergic B cells sort 1

value: 132 days

value: anergic B cell

value: coexpressing IgM and IgD


title: Liver, B102_28_L_H3, replicate 3

source_name: Liver, B102_28_L_H3, replicate 3

treatment_protocol: Three animals were administrated corn oil for nine weeks, the other three animals were administrated 1-Amino-2,4-Dibromoanthraquinone (1000 mg/kg/day) for nine weeks.

value: Liver


title: Lung cDC2s from HDM-treated WT mice, sample 1

description:
WT HDM 1
Gene expression data on a pool of lung cDC2s (Cd11c+ Mhc2+ Cd11b+ Ly6c- Cd64- dendritic cells) from 10 HDM-treated C57Bl/6 mice

source_name: Lung cDC2s from HDM-treated WT mice

value: female

value: Wild type

value: lung CD11b+ conventional dendritic cells (cDC2s)


title: Lung cDC2s from HDM-treated WT mice, sample 2

description:
WT HDM 2
Gene expression data on a pool of lung cDC2s (Cd11c+ Mhc2+ Cd11b+ Ly6c- Cd64- dendritic cells) from 10 HDM-treated C57Bl/6 mice


title: Lung cDC2s from PBS-treated WT mice, sample 2

description:
WT PBS 2
Gene expression data on a pool of lung cDC2s (Cd11c+ Mhc2+ Cd11b+ Ly6c- Cd64- dendritic cells) from 10 PBS-treated C57Bl/6 mice

source_name: Lung cDC2s from PBS-treated WT mice

value: PBS


title: Lung cDC2s from PBS-treated WT mice, sample 1

description:
WT PBS 1
Gene expression data on a pool of lung cDC2s (Cd11c+ Mhc2+ Cd11b+ Ly6c- Cd64- dendritic cells) from 10 PBS-treated C57Bl/6 mice


title: MD4 naïve B cells sort 2

description:
Gene expression in naïve B cells coexpressing IgM and IgD
MD4  mouse 49: 252800516796_S01_GE1_107_Sep09_2_3

source_name: MD4 naïve B cells sort 2

value: male

value: naïve B cell


title: MD4 naïve B cells sort 1

description:
Gene expression in naïve B cells coexpressing IgM and IgD
MD4  mouse 43: 252800516796_S01_GE1_107_Sep09_1_1

source_name: MD4 naïve B cells sort 1

value: 115 days


title: Liver, B102_28_L_H2, replicate 2

source_name: Liver, B102_28_L_H2, replicate 2

value: Sprague-Dawley


title: Liver, B102_28_L_H1, replicate 1

source_name: Liver, B102_28_L_H1, replicate 1


title: PBS 5

city: Helsinki

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki and Wihuri Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Chipster software (www.chipster.csc.fi)

source_name: Myocardium

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

extract_protocol: Total RNA was isolated from myocardium with TRIsure reagent (Bioline) and further purified with NucleoSpin RNA II (Macherey-Nagel). Quality control was performed with Agilent Bioanalyser.

value: 10 weeks

value: Male

value: injected with PBS


title: Liver, B102_28_L_VC3, replicate 3

source_name: Liver, B102_28_L_VC3, replicate 3

value: Purified Water


title: DOX 4

value: doxorubicin


title: Liver, B102_28_L_VC2, replicate 2

source_name: Liver, B102_28_L_VC2, replicate 2


title: VEGF-B+DOX 5