title: myometrium, progesterone treated (2P4.CEL)

city: Cambridge

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Following fragmentation, 25 ng/uL of fragmented sscDNA were hybridized for 16 hr at 45°C on GeneChip mouse Gene ST1.1 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the FS450_0007 fluidics script.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Raw data normalised using the R package oligo - RMA

source_name: myometrium

label_protocol: Biotinylated cRNA+B44 were prepared according to the standard Ambion and Affymetrix protocol from 200ng total RNA (Ambion WT Expressoin Kit p/n4425209, GeneChip WT Terminal Labelling and Hybridisation User Mannual, Affymetrix p/n702808).

extract_protocol: The uteri were divided longitudinally and fixed in RNAlater for 24 hours at 4˚C. The endometrium was removed from the myometrium using sharp dissection which was stored at -80˚C. Myometrium was homogenized in lysing binding solution concentrate containing b-mercaptoethanol using a bead beater for 20seconds at 6m/s (FastPrep24 tube holder). 100% isopropanol was added to each tube following homogenization to precipitate the RNA. Each tube was inverted for 1 minute to ensure sufficient mixing. The sample lysate was loaded into a 96-well plate and RNA extracted using the MagMAX™ Express Magnetic Particle Processor.

tag: strain

value: myometrium

value: 38-40 weeks

tag: ovariectomy

value: intact

tag: progesterone

value: progesterone implant


title: myometrium, progesterone treated (6P4.CEL)

status: Public on Jul 17 2016

type: RNA

label: Biotin

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: age


title: myometrium, progesterone treated (5P4.CEL)


title: myometrium, progesterone treated (9P4.CEL)


title: myometrium, progesterone treated (7P4.CEL)


title: myometrium, progesterone treated (1P4.CEL)


title: myometrium, progesterone treated (8P4.CEL)


title: myometrium, progesterone treated (3P4.CEL)


title: myometrium, vehicle control (1oil.CEL)

value: vehicle (oil)


title: myometrium, early ovariectomy (7s.CEL)

value: early ovariectomy


title: myometrium, vehicle control (4oil.CEL)


title: myometrium, vehicle control (3oil.CEL)


title: myometrium, vehicle control (5oil.CEL)


title: myometrium, early ovariectomy (5s.CEL)


title: myometrium, late ovariectomy (7o.CEL)

value: late ovariectomy


title: myometrium, early ovariectomy (3s.CEL)


title: Fetal Liver Total RNA, biological rep 3

status: Public on Jul 18 2016

city: Providence

first: Joan

middle: M

last: Boylan

state: RI

address: 593 Eddy Street

department: Pediatrics

country: USA

institute: Rhode Island Hospital

description:
Control Total 3
Fetal rat liver transcriptome.
Biological replicate 3 (control).

hyb_protocol: After fragmentation, 2.475ug cDNA was hybridized for 17 h at 45 C, 60rpm, on a GeneChip Rat Gene 1.0ST Array. Then, washing and staining were done according to manufacturer's instructions using the Fluidics recommended for the arrays and Affymetrix Wash/Stain/ Hyb kit.

scan_protocol: The arrays were scanned with an Affymetrix 3000 7G scanner using manufacturer's instructions.

data_processing: Identification of differentially expressed genes was done in GenePattern (Broad Institute) (Reich M, et al. GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501) using the Expression File Creator module. RMA algorithm.

organism: Rattus norvegicus

source_name: fetal liver total RNA from dam fed ad libitum

label_protocol: Samples (100ng total RNA) were reversed transcribed, turned into ds DNA, IVT transcribed and amplified using the Ambion WT expression kit. The WT labeling kit (Cat#900670) was used to fragment the ssDNA and end label it with a biotinylated nucleotide.

extract_protocol: RNA was extracted from pooled polysome preparations by acid-phenol:chloroform extraction followed by precipitation in ethanol plus ammonium acetate. Total RNA was isolated from frozen liver by homogenization in guanidine thiocyanate followed by cesium chloride density centrifugation. RNA was further purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: For control livers, pregnant dams (n=3) were fed ad libitum until day E19 of gestation. Fetuses were delivered by C-section, and livers were removed and immediately placed in liquid nitrogen. IUGR livers were collected in the same way from pregnant dams (n=3) that were fasted for 48 hr before C-section.

tag: strain/background

value: Sprague Dawley

value: fetal E19

value: liver

tag: treatment

value: dam fed ad libitum (control)

tag: rna fraction

value: total


title: myometrium, early ovariectomy (1s.CEL)


title: myometrium, early ovariectomy (2s.CEL)


title: myometrium, progesterone treated (10P4.CEL)


title: myometrium, late ovariectomy (5o.CEL)


title: myometrium, early ovariectomy (6s.CEL)


title: myometrium, early ovariectomy (4s.CEL)


title: myometrium, late ovariectomy (3o.CEL)


title: myometrium, late ovariectomy (2o.CEL)


title: myometrium, 38-40 weeks (zc.CEL)


title: myometrium, late ovariectomy (1o.CEL)


title: myometrium, 38-40 weeks (za.CEL)


title: myometrium, late ovariectomy (4o.CEL)


title: myometrium, 38-40 weeks (z.CEL)


title: myometrium, late ovariectomy (6o.CEL)


title: myometrium, 38-40 weeks (y.CEL)


title: myometrium, 10-12 weeks (v.CEL)

value: 10-12 weeks


title: myometrium, 38-40 weeks (zb.CEL)


title: myometrium, 10-12 weeks (s.CEL)


title: myometrium, 38-40 weeks (w.CEL)


title: myometrium, 10-12 weeks (u.CEL)


title: myometrium, 38-40 weeks (x.CEL)


title: myometrium, 10-12 weeks (t.CEL)


title: myometrium, 28-30 weeks (l.CEL)

value: 28-30 weeks


title: myometrium, 10-12 weeks (p.CEL)


title: myometrium, 10-12 weeks (o.CEL)


title: myometrium, 28-30 weeks (k.CEL)


title: myometrium, 10-12 weeks (q.CEL)


title: myometrium, 28-30 weeks (m.CEL)


title: myometrium, 10-12 weeks (g.CEL)


title: myometrium, 10-12 weeks (e.CEL)


title: myometrium, 28-30 weeks (h.CEL)


title: myometrium, 28-30 weeks (i.CEL)


title: myometrium, 28-30 weeks (n.CEL)


title: EryBlPB-3

city: Melbourne

first: Jarny

last: Choi

state: Victoria

address: The University of Melbourne

department: Anatomy and Neuroscience

country: Australia

institute: Centre for Stem Cell Systems

description: Polychromatic erythroblasts (some Basophillic erythroblasts)

hyb_protocol: Labelled cRNA was then hybridized to the chips according to the manufacturer’s instructions.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was quantile normalized. We used a curated selection of probes that had been trimmed to find probes that were supported by an ENSEMBL transcript. This collection came from Barbosa-Morais et al.

label: biotin

label_protocol: RNA was amplified according to the manufacturer’s instruction with the Illumina Total Prep RNA Amplification Kit (Ambion). The quality of the labeled product again ascertained using the Agilent Bioanalyzer 2100.

growth_protocol: Except Pre and Pro B cells, which were collected from five to seven week old mice, all cells were purified from wild type C57BL/6 mice, between 7 and 12 weeks of age.

extract_protocol: Total RNA was isolated from purified cell populations using RNeasy Micro / Mini Kits (Qiagen). Each purified RNA sample was assessed for quality and integrity using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Bone marrow was collected from femurs and tibiae, and in some instances, hips. Lymph node cells were collected from the inguinal, axillary, brachial, mesenteric and superficial cervical lymph nodes. Peritoneal cells were isolated by peritoneal lavage. Peripheral blood was collected from the retro-orbital plexus into Microtainer tubes containing EDTA (BD Biosciences). Cells were purified according to the combination of monoclonal antibodies as given in sample information and then isolated on a fluorescence-activated cell sorter.

tag: cell type

value: EryBlPB

value: BM

tag: antibodies

value: Lin- CD44+ Ter119+ FSC Hi

tag: cell lineage

value: Erythrocyte Lineage


title: EryBlPO-2

description: Polychromatic erythroblasts (some Orthochromatic erythroblasts)

value: EryBlPO

value: Lin- CD44+ Ter119+ FSC Int


title: myometrium, 10-12 weeks (d.CEL)

value: myometrium

value: intact


title: myometrium, 10-12 weeks (f.CEL)


title: myometrium, 28-30 weeks (j.CEL)


title: Retic-2

description: Reticulocytes

value: Retic


title: DiFi cells (parental)

city: Houston

first: Zhen

last: Fan

state: TX

address: 1515 Holcombe Blvd.

department: Experimental Therapeutics

institute: UT MD Anderson Cancer Center

description: Gene expression data

hyb_protocol: Hybridization onto an Affymetrix HG-U133A array was performed according to the manufacturer’s instructions. Following fragmentation, 10 µg of cRNA were hybridized for 16 h at 45°C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with DNA-Chip Analyzer (dChip), version 1.3. Gene expression levels were estimated based on Perfect Match (PM) only model using PM probes to calculate all-positive expression values. For normalization an array with median overall intensity is selected as the baseline array against which other arrays are normalized at probe intensity level. The criterion based on Fold Change (F.C.) is that when absolute value of the lower bound of F.C. >1.2.

organism: Homo sapiens

source_name: DiFi cells

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

growth_protocol: DiFi and DiFi5 cells were maintained in a mixture of Dulbecco’s modified Eagle’s medium and Ham’s F-12 medium (1:1, v/v) supplemented with 10% fetal bovine serum in a 37°C humidified atmosphere containing 95% air and 5% CO2 and were split twice a week.

extract_protocol: Total RNA was extracted using Trizol Reagent and then subjected to clean-up and DNase digestion on an RNeasy spin column (QIAGEN).

treatment_protocol: Cells were cultured on 100-mm culture dishes by spliting them every 4-4 days using standard trypsinization method.

value: Colorectal cancer cells

tag: genotype

value: Adenocarcinoma

value: Passage 108


title: myometrium, 10-12 weeks (a.CEL)


title: DiFi5 cells (cetuximab-resistant subline)

description: Gene expression data

source_name: DiFi5 cells

value: Passage 78


title: myometrium, 10-12 weeks (b.CEL)


title: myometrium, progesterone treated (4P4.CEL)

value: 38-40 weeks

value: progesterone implant


title: Retic-3

description: Reticulocytes


title: EryBlPO-3


title: Retic-1

description: Reticulocytes


title: CLP-3

description: Common lymphoid progenitor

value: CLP

value: Lin- c-Kit Lo Sca-1 Lo IL-7Ra Lo Flt3+

value: Restricted Potential Progenitor


title: myometrium, 10-12 weeks (c.CEL)

value: 10-12 weeks


title: EryBlPO-1

value: BM


title: CLP-1

description: Common lymphoid progenitor


title: Mast-1

description: Mast Cells

value: Mast

value: Peritoneal

value: Mast Cell Lineage


title: EryBlPB-1

value: EryBlPB

value: Lin- CD44+ Ter119+ FSC Hi

value: Erythrocyte Lineage


title: Eo-3

description: Naive Eosinophil

value: Eo

value: Siglec-F Med IL-5ra+ c-Kit-

value: Eosinophil Lineage


title: Testis-4

description: Whole organ

value: Testis

value: No sort

value: Non-haematopoietic


title: PreGM1-2

description: PreGranolocyte / macrophage Flt3-

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150- endoglin- Flt3-


title: LSK-8

description: LSK

value: LSK

value: Lin- Sca-1+ c-Kit+

value: Multi Potential Progenitor


title: EryBlPB-2

value: BM


title: NveCD4T-4

description: Naive CD4 T Cell

source_name: C57BL/6-Spleen and LN

value: Spleen and LN

value: T Cell Lineage


title: Mast-2

description: Mast Cells

value: Mast

value: Peritoneal

value: Mast Cell Lineage


title: LSK-9

description: LSK


title: GMP-7

description: Granulocyte Macrophage Progenitor

value: GMP

value: Lin- Sca-1- c-Kit+ CD34+ FcgRII/II+

value: Restricted Potential Progenitor


title: Eo-2

description: Naive Eosinophil

value: Eo

value: Siglec-F Med IL-5ra+ c-Kit-

value: Eosinophil Lineage


title: CD9Hi-2

description: CD9hi bipotential progenitors

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150+ endoglin Lo CD9 Hi


title: PreGM1-3

description: PreGranolocyte / macrophage Flt3-

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150- endoglin- Flt3-


title: CLP-2

description: Common lymphoid progenitor

value: CLP

value: Lin- c-Kit Lo Sca-1 Lo IL-7Ra Lo Flt3+


title: Testis-3

description: Whole organ

value: Testis

value: No sort

value: Non-haematopoietic


title: FcgRBP-3

description: FcgRII/IIIhiCD150+ bipotential progenitors

value: FcgRBP

value: BM

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32+ CD150+ endoglin Lo CD9 Hi


title: FcgRBP-2


title: PreGM2-3

description: PreGranolocyte / macrophage Flt3+

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150- endoglin- Flt3+


title: CFUE-3

description: Colony forming unit - erythroid

value: CFUE

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150- endoglin Hi

value: Erythrocyte Lineage


title: Testis-2

description: Whole organ


title: EmbFib-3

description: Cultured embryonic fibroblasts

value: EmbFib

value: Embryo


title: PreCFUE-3

description: PreColony forming unit - erythroid

value: PreCFUE

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32-CD41- CD150+ endoglin Hi


title: myometrium, vehicle control (2oil.CEL)

value: myometrium

value: 38-40 weeks

value: intact

value: vehicle (oil)


title: CFUE-2

description: Colony forming unit - erythroid


title: GMP-6

description: Granulocyte Macrophage Progenitor

value: GMP

value: Lin- Sca-1- c-Kit+ CD34+ FcgRII/II+

value: Restricted Potential Progenitor


title: BEMP-3

description: Bipotential erythroid megakaryocyte progenitors

value: BEMP

value: BM

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150+ endoglin Lo CD9 Lo


title: FcgRBP-1

value: FcgRBP

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32+ CD150+ endoglin Lo CD9 Hi


title: PreGM1-1

description: PreGranolocyte / macrophage Flt3-

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150- endoglin- Flt3-


title: EmbFib-1

description: Cultured embryonic fibroblasts

value: EmbFib

value: No sort

value: Non-haematopoietic


title: CD9Hi-3

description: CD9hi bipotential progenitors

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150+ endoglin Lo CD9 Hi


title: Meg32N-2

description: 32N Megakaryocytes

value: CD41+ Hoescht3342 ploidy (32N)

value: Megakaryocyte Lineage


title: Meg32N-3

description: 32N Megakaryocytes


title: DblPosT-1

description: Double positive thymocytes

value: DblPosT

value: Thymus

value: CD4+ CD8+ abTCR+

value: T Cell Lineage


title: LSK-7

description: LSK

value: LSK

value: Lin- Sca-1+ c-Kit+

value: Multi Potential Progenitor


title: PreCFUE-2

description: PreColony forming unit - erythroid

value: PreCFUE

value: BM

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32-CD41- CD150+ endoglin Hi

value: Erythrocyte Lineage


title: PreCFUE-1

description: PreColony forming unit - erythroid


title: CFUE-1

description: Colony forming unit - erythroid

value: CFUE

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150- endoglin Hi


title: CD9Hi-1

description: CD9hi bipotential progenitors

value: Restricted Potential Progenitor


title: PreGM2-2

description: PreGranolocyte / macrophage Flt3+

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150- endoglin- Flt3+


title: BEMP-1

value: BEMP

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150+ endoglin Lo CD9 Lo


title: DblPosT-2

description: Double positive thymocytes

value: DblPosT


title: BEMP-2


title: Meg16N-2

description: 16N Megakaryocytes

value: CD41+ Hoescht3342 ploidy (16N)

value: Megakaryocyte Lineage


title: DblPosT-3

description: Double positive thymocytes

value: Thymus

value: CD4+ CD8+ abTCR+

value: T Cell Lineage


title: myometrium, 10-12 weeks (r.CEL)

value: myometrium

value: 10-12 weeks

value: intact


title: Meg16N-3

description: 16N Megakaryocytes

value: BM


title: EmbFib-2

description: Cultured embryonic fibroblasts

value: EmbFib

value: Embryo

value: No sort

value: Non-haematopoietic


title: Meg8N-3

description: 8N Megakaryocytes

value: CD41+ Hoescht3342 ploidy (8N)


title: Meg16N-1

description: 16N Megakaryocytes


title: PreGM2-1

description: PreGranolocyte / macrophage Flt3+

value: Lin- IL-7Ra- c-Kit+ Sca-1- CD16/32- CD150- endoglin- Flt3+

value: Restricted Potential Progenitor


title: Meg32N-1

description: 32N Megakaryocytes

value: CD41+ Hoescht3342 ploidy (32N)


title: GMP-5

description: Granulocyte Macrophage Progenitor

value: GMP

value: Lin- Sca-1- c-Kit+ CD34+ FcgRII/II+


title: Meg8N-1

description: 8N Megakaryocytes

value: Megakaryocyte Lineage


title: Ovary-3

description: Whole organ

value: Ovary


title: Kidney-3

description: Whole organ

value: Kidney


title: Meg8N-2

description: 8N Megakaryocytes


title: Liver-3

description: Whole organ

value: Liver


title: Lung-3

description: Whole organ

value: Lung


title: Ovary-2

description: Whole organ


title: Brain-3

description: Whole organ

value: Brain


title: Brain-2

description: Whole organ


title: Baso-1

description: Basophils

value: Baso

value: Spleen

value: Dx5+ CD123+ IgE+ FceRI+ c-Kit-

value: Basophil Lineage


title: Testis-1

description: Whole organ

value: Testis

value: No sort

value: Non-haematopoietic


title: NeutPt-3

description: Neutrophils from the peritoneum

value: NeutPt

value: Peritoneal

value: Siglec-F- IL-5ra+ Ly6G+

value: Neutrophil Lineage


title: Mac-4

description: Macrophage

value: Mac

value: Macrophage Lineage


title: Liver-1

description: Whole organ


title: Lung-2

description: Whole organ


title: NeutPt-2

description: Neutrophils from the peritoneum


title: Kidney-1

description: Whole organ

value: Kidney


title: Baso-2

description: Basophils


title: ESCell-3

description: Embryonic stem cell

value: ESCell

value: Separated away from GFP pMEF feeder cells as GFP negative cells


title: Lung-1

description: Whole organ

value: Lung


title: Kidney-2

description: Whole organ


title: Liver-2

description: Whole organ

value: Liver


title: Brain-1

description: Whole organ

value: Brain


title: ESCell-2

description: Embryonic stem cell


title: NeutPt-1

description: Neutrophils from the peritoneum


title: Eo-1

description: Naive Eosinophil

value: Eo

value: BM

value: Siglec-F Med IL-5ra+ c-Kit-

value: Eosinophil Lineage


title: Mac-5

description: Macrophage


title: STHSC-6

description: Short term repopulating (ST) LSK

value: STHSC

value: Lin- Sca-1+ c-Kit+ CD34+ Flt3-

value: Multi Potential Progenitor


title: GMP-4

description: Granulocyte Macrophage Progenitor

value: GMP

value: Lin- Sca-1- c-Kit+ CD34+ FcgRII/II+

value: Restricted Potential Progenitor


title: EoP-2

description: Eosinophil Progenitor

value: EoP


title: GMP-2

description: Granulocyte Macrophage Progenitor


title: Ovary-1

description: Whole organ

value: Ovary

value: No sort

value: Non-haematopoietic


title: NK-1

description: Resting NK cells

value: NK

value: LN

value: NK Cell Lineage


title: CMP-2

description: Common Myeloid Progenitor

value: CMP

value: Lin- Sca-1- c-Kit+ CD34+ FcR Lo


title: EoP-1

description: Eosinophil Progenitor

value: BM


title: LTHSC-3

description: Long Term Hematopoietic Stem Cell

value: LTHSC

value: Lin- Sca-1+ c-Kit+ CD34- Flt3-


title: STHSC-4

description: Short term repopulating (ST) LSK

value: STHSC

value: Lin- Sca-1+ c-Kit+ CD34+ Flt3-


title: STHSC-5

description: Short term repopulating (ST) LSK

value: Multi Potential Progenitor


title: GMP-3

description: Granulocyte Macrophage Progenitor

value: GMP

value: Lin- Sca-1- c-Kit+ CD34+ FcgRII/II+


title: EoP-3

description: Eosinophil Progenitor

value: EoP

value: Eosinophil Lineage


title: LTHSC-4

description: Long Term Hematopoietic Stem Cell


title: LTHSC-2

description: Long Term Hematopoietic Stem Cell


title: LSK-4

description: LSK

value: LSK

value: Lin- Sca-1+ c-Kit+


title: MPP-5

description: Multipotent progenitor (MPP) LSK

value: MPP

value: Lin- Sca-1+ c-Kit+ CD34+ Flt3+


title: NeutLN-2

description: Neutrophils from the lymph nodes

value: NeutLN

value: LN

value: Siglec-F- IL-5ra+ Ly6G+

value: Neutrophil Lineage


title: NeutLN-1

description: Neutrophils from the lymph nodes


title: MPP-4

description: Multipotent progenitor (MPP) LSK

value: BM


title: LSK-6

description: LSK


title: LSK-5

description: LSK


title: MonoLN-3

description: Monocytes from the lymph nodes

value: MonoLN

value: Mac-1+ Ly6G- Ly6C+

value: Macrophage Lineage


title: STHSC-7

description: Short term repopulating (ST) LSK

value: STHSC

value: Lin- Sca-1+ c-Kit+ CD34+ Flt3-

value: Multi Potential Progenitor


title: MPP-6

description: Multipotent progenitor (MPP) LSK


title: CMP-3

description: Common Myeloid Progenitor

value: CMP

value: Lin- Sca-1- c-Kit+ CD34+ FcR Lo

value: Restricted Potential Progenitor


title: ESCell-1

description: Embryonic stem cell

value: ESCell

value: Non-haematopoietic

value: Separated away from GFP pMEF feeder cells as GFP negative cells


title: MonoLN-2

description: Monocytes from the lymph nodes


title: CMP-1

description: Common Myeloid Progenitor


title: NK-2

description: Resting NK cells

value: NK

value: NK Cell Lineage


title: MonoLN-1

description: Monocytes from the lymph nodes

value: LN


title: cDC2-3

description: Conventional Dendritic Cell 2

source_name: C57BL/6-Auricular LN

value: Auricular LN

value: Lin- CD11c+ CD8- CD205-

value: Dendritic Cell Lineage


title: cDC1-1

description: Conventional Dendritic Cell 1

value: Lin- CD11c Hi CD8+ CD205+


title: MPP-1

description: Multipotent progenitor (MPP) LSK

value: MPP

value: BM

value: Lin- Sca-1+ c-Kit+ CD34+ Flt3+


title: cDC2-1

description: Conventional Dendritic Cell 2


title: cDC1-3

description: Conventional Dendritic Cell 1


title: cDC2-2

description: Conventional Dendritic Cell 2


title: MigDC-1

description: CD205+ Migratory Dendritic Cell

value: MigDC

value: Lin- CD11c+ CD8- CD205+


title: STHSC-3

description: Short term repopulating (ST) LSK

value: STHSC

value: Lin- Sca-1+ c-Kit+ CD34+ Flt3-

value: Multi Potential Progenitor


title: LSK-1

description: LSK

value: LSK

value: Lin- Sca-1+ c-Kit+


title: MPP-3

description: Multipotent progenitor (MPP) LSK


title: STHSC-2

description: Short term repopulating (ST) LSK


title: B2-2

description: B2 B Cell

value: Peritoneal

value: B Cell Lineage


title: MigDC-3

description: CD205+ Migratory Dendritic Cell


title: MPP-2

description: Multipotent progenitor (MPP) LSK


title: MigDC-2

description: CD205+ Migratory Dendritic Cell


title: B1-2

description: B1 B Cell


title: STHSC-1

description: Short term repopulating (ST) LSK


title: LSK-3

description: LSK


title: B1-1

description: B1 B Cell


title: cDC1-2

description: Conventional Dendritic Cell 1


title: LTHSC-1

description: Long Term Hematopoietic Stem Cell

value: LTHSC

value: Lin- Sca-1+ c-Kit+ CD34- Flt3-


title: TN2-3

description: Triple Negative Thymocyte 2

value: Thymus

value: Lin- c-Kit+ CD25+ CD44+

value: T Cell Lineage


title: TN3-3

description: Triple Negative Thymocyte 3

value: Lin- c-Kit- CD25+ CD44-


title: CDP-3

description: Common DC Precursor

value: CDP

value: BM

value: Lin- FcR Lo CD11c- Flt3+ c-Kit Int CD115+

value: Dendritic Cell Lineage


title: TN2-2

description: Triple Negative Thymocyte 2


title: CD4TThy1lo-2

description: Early Intrathymic CD4lo Precursor

value: Lin- Thy-1.2 Lo c-Kit+


title: LSK-2

description: LSK


title: ProB-3

description: B Cell Progenitor

value: ProB


title: EffCD8T-3

description: Effector CD8 T cells

value: Spleen and LN


title: MonoPB-2

description: Monocytes from the peripheral blood

source_name: C57BL/6-Peripheral Blood

value: MonoPB

value: Peripheral Blood

value: F4/80 Lo Mac-1+ Ly6C.2 Hi Ly6G-

value: Macrophage Lineage


title: ProB-2

description: B Cell Progenitor

value: B Cell Lineage


title: ProB-1

description: B Cell Progenitor


title: TN2-1

description: Triple Negative Thymocyte 2


title: CD4TThy1lo-3

description: Early Intrathymic CD4lo Precursor


title: PreB-3

description: B Cell Precursor

value: PreB


title: MatB-2

description: Mature B Cell

value: MatB

value: B220+ IgM+ IgD+


title: TN4-2

description: Triple Negative Thymocyte 4

value: Thymus

value: Lin- c-Kit- CD25- CD44-

value: T Cell Lineage


title: EffCD8T-2

description: Effector CD8 T cells


title: NveCD8T-2

description: Naive CD8 T Cell


title: EffCD4T-2

description: Effector Memory CD4 T Cells

value: CD4+ CD62L- CD25 Lo or - CD44+


title: TN1-2

description: Triple Negative Thymocyte 1

value: Lin- c-Kit+ CD25- CD44+


title: NveCD8T-3

description: Naive CD8 T Cell


title: EffCD4T-3

description: Effector Memory CD4 T Cells


title: CDP-2

description: Common DC Precursor

value: CDP

value: BM

value: Lin- FcR Lo CD11c- Flt3+ c-Kit Int CD115+

value: Dendritic Cell Lineage


title: EffCD8T-1

description: Effector CD8 T cells

value: Spleen and LN


title: CDP-1

description: Common DC Precursor


title: TN1-3

description: Triple Negative Thymocyte 1


title: TN4-3

description: Triple Negative Thymocyte 4


title: NveCD4T-3

description: Naive CD4 T Cell


title: TN4-1

description: Triple Negative Thymocyte 4


title: NveCD8T-1

description: Naive CD8 T Cell


title: MEP-2

description: Megakaryocyte Erythrocyte Progenitor

value: MEP

value: Lin- Sca-1- c-Kit+ CD34- FcR-

value: Erythrocyte Lineage


title: CD8TLN-3

description: CD8 T Cell

value: LN


title: CD4TThy1lo-1

description: Early Intrathymic CD4lo Precursor

value: Lin- Thy-1.2 Lo c-Kit+


title: ImmB-3

description: Immature B Cell

value: ImmB

value: B220+ IgM+ IgD-

value: B Cell Lineage


title: MonoPB-3

description: Monocytes from the peripheral blood

value: MonoPB

value: Peripheral Blood

value: F4/80 Lo Mac-1+ Ly6C.2 Hi Ly6G-

value: Macrophage Lineage


title: TN1-1

description: Triple Negative Thymocyte 1

value: Thymus

value: Lin- c-Kit+ CD25- CD44+

value: T Cell Lineage


title: TN3-2

description: Triple Negative Thymocyte 3

value: Lin- c-Kit- CD25+ CD44-


title: ImmB-2

description: Immature B Cell

value: BM


title: CD8TLN-2

description: CD8 T Cell


title: TN3-1

description: Triple Negative Thymocyte 3


title: MatB-1

description: Mature B Cell

value: MatB

value: B220+ IgM+ IgD+


title: MonoPB-1

description: Monocytes from the peripheral blood


title: CD8TLN-1

description: CD8 T Cell


title: CD14+ CD163high CD160high cells, rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: CD163high CD160high

hyb_protocol: Before hybridization, 825 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.

scan_protocol: The array was scanned with 5µm resolution using an Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Data were analyzed using the bioinformatics software GeneSpring 13.0 (Agilent).

source_name: Intestinal lamina propria CD14+ CD163high CD160high cells

label_protocol: 50 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from cells using an miRNeasy Mini kit according to the manufacturer’s instructions (Qiagen). The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit on the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Intestinal mucosa samples were obtained from patients who underwent resection of colorectal cancer. Lamina propria cells (LPCs) were obtained by enzymatic digestion, and were analyzed for expression of HLA-DR, lineage markers (Lin), CD14, CD163 and CD160 using flow cytometry.

tag: tissue source

value: intestinal lamina propria

value: CD14+ CD163high CD160high

tag: sample type

value: pooled


title: PreB-2

description: B Cell Precursor

value: PreB


title: Mac-1

description: Macrophage

value: Mac

value: Peritoneal


title: Blood CD14+ monocyte, rep2

source_name: Blood CD14+ monocytes

treatment_protocol: Blood CD14+ monocytes were isolated from peripheral blood mononuclear cells of healthy volunteers using flow cytometry.

value: blood

value: CD14+ monocytes


title: CD14+ CD163low, rep2

source_name: Intestinal lamina propria CD14+ CD163low cells

value: CD14+ CD163low


title: CD14+ CD163high CD160low cells, rep1

description: CD163high CD160low

source_name: Intestinal lamina propria CD14+ CD163high CD160low cells

value: CD14+ CD163high CD160low


title: ImmB-1

description: Immature B Cell

value: ImmB

value: B220+ IgM+ IgD-

value: B Cell Lineage


title: Mac-2

description: Macrophage

value: Macrophage Lineage


title: CX3CR1high cells vs. Ly6c+ CD11b+ monocytes dyeswap

description: Cy3-colon vs Cy5-blood

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.

scan_protocol: The array was scanned with 5µm resolution using an Agilent G2565AA DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization. Data were analyzed using the bioinformatics software GeneSpring 13.0 (Agilent).

source_name: Pooled blood Ly6c+ CD11b+ monocytes derived from C57BL/6J mice

label_protocol: 25 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent). In brief, cDNA was reverse transcribed from 25 ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Murine large intestinal lamina propria cells were isolated from CX3CR1gfp/+ mice as previously described (PMID: 22403066).

value: Ly6c+ CD11b+ monocytes

source_name: Pooled CX3CR1high CD11b+ CD11c+ cells derived from CX3CR1gfp/+ mice

value: CX3CR1high CD11b+ CD11c+ cells


title: RegT-3

description: Regulatory T Cell

value: RegT

value: Spleen and LN

value: CD4+ CD25 Hi

value: T Cell Lineage


title: CD4TLN-3

description: CD4 T Cell

value: LN


title: RegT-2

description: Regulatory T Cell


title: CD4TLN-2

description: CD4 T Cell


title: CD14+ CD163low, rep1

value: intestinal lamina propria

value: pooled


title: Blood CD14+ monocyte, rep1

value: blood


title: MemCD8T-1

description: Memory CD8 T


title: B2-1

description: B2 B Cell

value: Peritoneal


title: NveCD4T-2

description: Naive CD4 T Cell


title: NveCD4T-1

description: Naive CD4 T Cell


title: MemCD8T-3

description: Memory CD8 T


title: CD4TLN-1

description: CD4 T Cell


title: PreB-1

description: B Cell Precursor

value: PreB

value: BM


title: Mac-3

description: Macrophage

value: Mac


title: MemCD8T-2

description: Memory CD8 T


title: CX3CR1high cells vs. Ly6c+ CD11b+ monocytes

description: Cy3-blood vs Cy5-colon


title: MEP-1

description: Megakaryocyte Erythrocyte Progenitor

value: MEP

value: Lin- Sca-1- c-Kit+ CD34- FcR-

value: Erythrocyte Lineage


title: Ileum_IFNgKO_646

status: Public on Jul 16 2016

city: Corvallis

first: Natalia

last: Shulzhenko

state: Oregon

address: 700 SW 30th St, 105 Dryden Hall

institute: Oregon State University

description: Array set 1

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized using lumi package for quantile normalization

source_name: Mouse ileum

label_protocol: Illumina TotalPrep RNA Amplification Kit

growth_protocol: Mice maintained in specific-pathogen free (SPF) conditions, standard chow diet

extract_protocol: Tissue homogenized with 2.8mm ceramic beads in RLT buffer and extracted with Qiagen Rneasy mini kit using QiaCube automated standard protocol.

tag: gender

value: Male

value: 8 weeks

value: ileum

value: IFNgKO


title: UV, rep3

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

country: South Korea

institute: University of Seoul

description: Gene expression data from Caenorhabditis elegans young adults

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C.elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Array scanner 3000 7G.

data_processing: Image data were extracted through Affymetrix GCOS software. Data were subjected to normalization, background correction and data summarization using Affymetrix Expression Console software, using the standard Robust Multi-array Average (RMA) algorithm.

organism: Caenorhabditis elegans

source_name: mRNA isolated from wildtype young adult

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol. 300 ng total RNA from each sample amplified double strated cDNA were labeled with biotin-labeling (Ambion® WT Expression kit)

growth_protocol: C. elegans were grown in Petri dishes on nematode growth medium (NGM) and fed OP50 strain Escherichia coli and young adults (3 days) from an age-synchronized culture were used in all the experiments. To produce age-synchronized cultures, at 2 to 3 days, eggs from mature adults were isolated using a 10% hypochlorite solution, followed by a rinse with M9 buffer, and the eggs allowed to hatch on agar plates with a food source, resulting in synchronized adult worm populations.

extract_protocol: The total RNA prepared from the exposed and control worms according to the standard protocol of the RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: From stock solutions, experimental concentration of TiO2 was prepared in k-media (0.032 M KCl and 0.051M NaCl). For toxicity tests, control and TiO2 group were incubated at 20 °C for 24 hr without a food source and UV and UV+TiO2 group were incubated at 20 °C with UV exposure for 4hr then transferred to same incubator with Control and TiO2 group for next 20 hr without a food source. Then subjected to each type of analysis.

tag: protocol

value: UV

value: wildtype

value: hemaphrodite

value: young adult


title: UV, rep1


title: GMP-1

description: Granulocyte Macrophage Progenitor

value: GMP

value: Lin- Sca-1- c-Kit+ CD34+ FcgRII/II+

value: Restricted Potential Progenitor


title: RegT-1

description: Regulatory T Cell

value: RegT

value: Spleen and LN

value: CD4+ CD25 Hi

value: T Cell Lineage


title: Ileum_IFNgKO_649

description: Array set 2


title: CLAMP 4 zinc finger (ZF) PBM

type: protein

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

description: DNA binding

hyb_protocol: Protein samples were incubated with microarray for 1 hour @ 200 nM protein concention in binding buffer ( 10 mM Tris-HCl, pH 7.4; 0.2 ug/ul bovine serum albumin (BSA) (New England Biolabs #B9001S); 0.3 ng/ul Salmont testes DNA (Sigma #D7656), 2% non-fat dry milk; 1 mM dithiothreitol (DTT); 1 mM ehtylenediaminetetraacetic acid (EDTA); 50 uM zinc acetate dehydrate; 80 mM NaCl).

scan_protocol: Microarray scanning performed using GenePix 4400 A (Moleclar Devices)

data_processing:
Image analysis and data normalization performed using Gene Pix Pro ver 6 and masliner (MicroArray LINear Regression) software
Median fluorescence intensities were calculated over 8 replicate probes for each unique DNA sequence

molecule: protein

organism: Drosophila melanogaster

source_name: IVT sample of GST-tagged CLAMP 4-ZF construct

label_protocol: Microarray-bound protein was labelled by incubation for 20 min with 0.05 mg/ml Alexa488-conjugated anti-GST antibody (Invitrogen, #A11131).

extract_protocol: GST-tagged CLAMP ZF proteins were produced by in vitro transcription translation (IVT) from pDEST15 GST expression plasmics (Invitrogen). IVT was performed using the TnT Quick-coupled Transcription and Translation Systems Kit (Promega) following standard procedure with the one adaption - zinc acetate was added to a final concentration of 50 uM. Proteins were quantified by Western blotting and comparing to a dilution series of GST standard. Concentration of samples used was: CLAMP 4 ZF sample (24.3 nM); CLAMP 6 ZF sample (13.9 nM).

treatment_protocol: Microarray was incubated with GST-tagged CLAMP 4-ZF sample, or GST-tagged CLAMP 6-ZF sample

tag: clamp construct

value: GST-tagged CLAMP 4-ZF protein


title: TiO2, rep2

tag: strain


title: CLAMP 6 zinc finger (ZF) PBM

description: DNA binding

source_name: IVT sample of GST-tagged CLAMP 6-ZF construct

value: GST-tagged CLAMP 6-ZF protein


title: Ileum_IFNgKO_648

description: Array set 2

value: Male


title: UV+TiO2, rep1


title: EffCD4T-1

description: Effector Memory CD4 T Cells

value: CD4+ CD62L- CD25 Lo or - CD44+


title: UV+TiO2, rep3


title: Con, rep1

value: Control


title: Ileum_WT_642

description: Array set 2

value: 8 weeks

value: ileum

value: Wild type


title: Ileum_IFNgKO_647

description: Array set 2

value: IFNgKO


title: UV, rep2

value: UV

value: wildtype

value: hemaphrodite

value: young adult


title: UV+TiO2, rep2


title: TiO2, rep3


title: Con, rep3


title: Ileum_IFNgKO_645

description: Array set 1


title: RHOXF1 48h_3

city: Münster

first: Jennifer

last: Borgmann

address: Albert-Schweitzer Campus 1, Building D11

department: Centre of Reproductive Medicine and Andrology

country: Germany

institute: University Hospital Muenster

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_22

hyb_protocol: Samples were hybridized with  GeneCHip Human Gene 1.0 ST Arrays (Affymetrix) using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) and GeneChip Hybridization Control Kit (Affymetrix).

scan_protocol: Arrays  were  scanned  with  an Affymetrix GCS3000 7G using the AGCC Scan Control software.

data_processing: Normalization, quality control, and output file (CHP format) generation was performed with Affymetrix Gene Expression Console v.3.1 using the Robust Multi-Chip Analysis (RMA) algorithm. Differently expressed genes were identified with Affymetrix transcriptome analysis console (TAC) v.2.0 (Affymetrix). Data were obtained using one-way analysis of variance (ANOVA) and p-value correction according to Benjamini and Hochberg False Discovery Rate (FDR) for multiple testing.

source_name: HEK293, RHOXF1 transfected, 48h

label_protocol: Single-stranded cDNA was generated from the amplified cRNA  using  the  Ambion  WT  Expression  Kit (Thermo Fischer Sientific)  and then fragmented and labeled with the GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Human Embryonic Kidney 293 (HEK293) cells (CLS, Eppelheim, Germany) were culture in DMEM/F12 1:1 (Gibco, Carlsbad, CA, USA) containing 10% (v/v) FCS (PAA Laboratories, Pasching, Austria), 1 % penicillin⁄streptomycin (Gibco) and 2 mM L-Glutamine (Gibco) at 37°C and 5 % CO2 (v/v).Twenty four hours prior to transfection, HEK293 cells were seeded in 24-well plates (9x10^5).

extract_protocol: After 24h and 48h of transfection, cells were washed with PBS and total RNA was isolated using Total RNA Isolation Kit (Agilent). The quality of the RNA was assessed with the Bioanalyzer 2100 (Agilent) and only samples with an RNA integrity number (RIN) > 7 were included in the analysis.

treatment_protocol: For transient transfection, wild type (RHOXF1: RG217618, RHOXF2: RG205957, pCMV6-AC-GFP: PS100010, OriGene, Rockville, MD, USA)  were mixed with Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) in a 1:2,5 ratio. Cells were covered with 475 ml serum-free medium (DMEM/F12) and 25 µl of the prepared DNA-lipofectamine complex was added.

tag: cell line

tag: vector

value: RHOXF1 expression vector

tag: time after transfection


title: Ileum_WT_643

description: Array set 2

tag: age

tag: tissue


title: TiO2, rep1


title: Ileum_WT_644

description: Array set 2


title: control 48h_3

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_24

source_name: HEK293, control vector, 48h

value: empty control vector


title: RHOXF2 48h_3

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_23

source_name: HEK293, RHOXF2 transfected, 48h

value: RHOXF2 expression vector


title: Con, rep2


title: Ileum_WT_641

description: Array set 1


title: control 48h_2

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_21


title: Bovine Granulocytes 2 hrs incubation with IFNT 3

city: Sapporo

first: Noriyuki

last: Toji

state: Hokkaido

address: North10-West8, Kita-ku,

department: Department of Biological Sciences

institute: Hokkaido university

description: Gene expression in Bovine Granulocytes 2hr incubation with 1 mg/mL IFNT treatment

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: Granulocytes with IFNT

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from Granulocytes using TRIzol (Thermo Fisher Scientific) according to the manufacturer's instructions.

treatment_protocol: Granulocytes and BES were treated with PBS or 1 mg/mL IFNT, and  incubated 2 hrs.

value: Granulocytes

tag: study

value: In vivo/In vitro

tag: treatment

value: 1 mg/mL IFNT treatment


title: Bovine Granulocytes 2 hrs incubation with IFNT 4


title: Bovine Granulocytes 2 hrs incubation with IFNT 1


title: Bovine Granulocytes 2 hrs incubation with IFNT 2


title: Ileum_WT_640

description: Array set 1

value: Male


title: control 48h_1

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_18


title: RHOXF1 48h_2

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_19


title: RHOXF2 48h_1

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_17


title: Bovine Granulocytes 2 hrs incubation with PBS 3

description: Gene expression in Bovine Granulocytes 2hr incubation with PBS treatment

source_name: Granulocytes with PBS

value: PBS treatment


title: Spink3-/-XKI/+ rep1

city: Honjo, Chuo-ku

first: Masaki

last: Ohmuraya

state: Kumamoto

department: Institute of Resource Development and

institute: Kumamoto University

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20110722) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Cat. no. 74106, Qiagen, Tokyo, Japan) following the manufacturer's recommendations. DNA was digested byRQ1 RNase-Free DNase (Promega, Madison, WI). RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Yokohama, Japan).

treatment_protocol: The pancreas was harvested at p0.5, and frozen by liquid nitrogen immediately.

tag: strain background

tag: genotype/variation

tag: developmental age

value: whole pancreas


title: Spink3+/+ rep2

source_name: wild type_pancreas_p0.5

value: Wild type; Spink3+/+


title: Spink3-/- rep2


title: Bovine Granulocytes 2 hrs incubation with PBS 4


title: Spink3-/- rep1


title: Bovine Granulocytes 2 hrs incubation with PBS 2


title: BES 2 hrs incubation with IFNT 3

description: Gene expression in BES 2hr incubation with 1 mg/mL IFNT treatment

source_name: BES with IFNT

value: Bovine Endometrial Stromal cells

value: In vitro


title: RHOXF1 48h_1

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_16


title: Bovine Granulocytes 2 hrs incubation with PBS 1


title: BES 2 hrs incubation with IFNT 1


title: RHOXF1 24h_2

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_4

source_name: HEK293, RHOXF1 transfected, 24h


title: control 24h_3

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_9

source_name: HEK293, control vector, 24h


title: RHOXF2 24h_3

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_8

source_name: HEK293, RHOXF2 transfected, 24h


title: RHOXF2 24h_2

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_5


title: control 24h_2

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_6


title: RHOXF1 24h_3

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_7


title: Spink3+/+ rep1


title: Spink3-/-XKI/+ rep2


title: RHOXF2 48h_2

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_20


title: BES 2 hrs incubation with IFNT 2


title: BES 2 hrs incubation with PBS 3

description: Gene expression in BES 2hr incubation with PBS treatment

source_name: BES with PBS


title: control 24h_1

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_3


title: 16

city: Shenyang

first: Funan

last: Liu

address: 155 Nanjing North Street

department: Department of Surgical Oncology

country: China

institute: the First Affiliated Hospital of China Medical University

description: Total RNA was extracted from Gastric cancer BGC823 cells with stable Pak1 knockdown

hyb_protocol: standard CapitalBio Methods: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. The array was hybridized at 42℃ overnight and washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Luxscan 3.0 (CapitalBio)

data_processing: Intensity data was extracted from the TIFF images using LuxScanTM 3.0 software (CapitalBio Corp, Peking, China). The low-intensity spots were removed for which fewer than 30% of the signal pixels exceeded the median background plus two times its standard deviation.

source_name: gastric cancer

growth_protocol: All cells were cultured in a sterile incubator at 37˚C

extract_protocol: total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions, and the low-molecular-weight RNA (LMW-RNA) be isolated using the PEG solution precipitation method

treatment_protocol: Before microarray analysis,the cells were incubated as usual.

tag: transfection

value: stable Pak1 knockdown


title: conU6

description: Total RNA was extracted from Gastric cancer BGC823 cells

value: transfected with U6


title: BES 2 hrs incubation with PBS 1


title: RHOXF2 24h_1

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_2


title: RHOXF1 24h_1

description:
RMA expression value derived from Expression Console software v.3.1
Human_Gene_1_0_ST_20150205_1


title: cc11383-M104

status: Public on Jul 15 2016

city: Rochester

first: Sean

last: Dowdy

state: Minnesota

address: 200 First St. SW

department: Obstetrics and Gynecology

institute: Mayo Clinic

hyb_protocol: 16 hours at 58C

scan_protocol: Illumina BeadArray Reader

data_processing:
Microarray analyses conducted using log-base2 of the gene expression values; programming done in the R statistical language.  Data were normalized using the fastlo algorithm.
Paired t-tests were used to test for significant differences between PAPP-A knock-out and wild-type mice.  False discovery rates were calculated using the Benjamini-Hochberg method.

source_name: wombmate

label_protocol: Illumina Total Prep RNA Amplification kit

growth_protocol: Wild-type and PAPP-A knock-out mice of the same sex and from the same litter were housed together for 18 months with food and water ad libitum

extract_protocol: QIAGEN RNeasy Fibrous Tissue kit

treatment_protocol: no treatment

value: WT

tag: pairing

tag: Sex

value: M


title: BES 2 hrs incubation with PBS 2


title: cc11384-MKO104

value: PAPP-A knock-out


title: ak1139-FWT104

value: F


title: cc11417-FKO78


title: cc11415-FWT78


title: cc16155-MKO78


title: cc16316-MWT78


title: Islets_WT_5

city: Shanghai

first: Qicheng

last: Ni

address: 197 Ruijin 2nd Road

institute: Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa nClara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US).

data_processing: Normalized against other samples in series by log regression on signal obtained with control spots.

source_name: Islets

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip® 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Male C57BL/6 mice aged 8 weeks were fed ad libitum and housed in facility on a 12-h light-dark cycle.  Then mice were sacrificed and total RNAs were isoloated from islets.

extract_protocol: Total RNAs were extracted from islets using RNeasy Micro kit according to the manufacturer’s instructions (Qiagen) .

treatment_protocol: Mice were housed at 21±1°C with a humidity of 55±10% and a 12-hour light–dark cycle.

value: Islets

value: wild type

tag: stain

tag: gender


title: Islets_KO_2

value: knock out


title: cc16153-MWT78


title: Islets_KO_1


title: Islets_WT_2


title: Islets_WT_3


title: Islets_WT_1


title: Islets_KO_3


title: cc16220-MKO78


title: Islets_WT_4


title: Islets_KO_4


title: cc16315-MKO78


title: cc16226-MWT78


title: ak1141-FKO104


title: KO2M2, biological replicate 2

city: Columbus

first: Mireia

last: Guerau

state: OH

address: 453 W 10th Ave

department: HRS-Medical Laboratory Science

institute: The Ohio State University

hyb_protocol: Samples were hybridized to Affymetric 430_2 array using Herring sperm DNA, acetlylated BSA (50 mg/ml) and, Bioarray Eukaryotic Hybridization controls (Enzo Life Sciences), heated 650C 5 minutes, 990C 5 minutes, 450C 5 minutes, centrifuge top speed for 5 minutes, hybridize 16 hours at 450C at 60 rpm; Fluidics script EukGE-WS2v4_450

scan_protocol: Affymetrix Gene ChIP scanner 30007G using Command Console

data_processing: Raw data were normalized with the RMA algorithm implemented in the ‘‘Expression File Creator’’ module from the GenePattern software package. Data were visualized with the Multiplot modules from GenePattern.

source_name: KO2M2, biological replicate 2

label_protocol: Samples were enzymatically labeled using BioArray HighYield RNA Transcript Labeling kit (Enzo)

growth_protocol: To generate BMDM, the bone marrow cells from femurs and tibias from mice were harvested and cultured. Briefly, isolated cells were incubated in Dulbecco’s Modified Eagle Media (DMEM, Mediatech, Herndon, VA) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Life Technologies, Grand Island, NY)), 1% penicillin/streptomycin, 1% glutamine, and 20% L929 cell supernatant (containing macrophage colony stimulating factor).

extract_protocol: To examine miRNA expression, cells were isolated using the miRVana isolation kit (Life Technologies) according to manufacturer specifications.

treatment_protocol: On day 7 in culture the cells were washed, counted and replated in DMEM media (without L929 supernatant) at a density of 6-8^6 cells/well (6-well plate, Falcon polystyrene). Cells were classically activated (M1 condition) with LPS (100 ng/ml, Sigma-Aldrich) + IFN-γ (20ng/mL, E-bioscience, San Diego, CA) or alternatively activated (M2 condition) with IL-4 (20ng/mL, E-bioscience) or received media alone (M0 condition). Cells were harvested at 24 hours post-stimulation, by washing in phosphate buffered saline (PBS) before cell lysis in miRVana Lysis buffer (Life Technologies) for total RNA isolation.

tag: cell type

value: Bone Marrow Derived Macrophages


title: Control rep1

city: Taipei

first: Kung-Hao

last: Liang

address: Tung Hwa North Road

country: Taiwan

institute: Chang Gung Memorial Hospital

description: gene expression data of mice liver sacrificed at 1.5 years old

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr to Affymetrix miRNA 2.0 arrays

scan_protocol: Images scanned using Affymetrix Scanner 3000 7G according to manufacturer's protocols.

data_processing: Data were analyzed using RNAExpress

source_name: Control mice

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

growth_protocol: standard feeding of the mices with normal diet

extract_protocol: RNAs were extracted from liver specimens by use of TRI Reagent RT (Molecular Research Center Inc., Cincinnati, OH) according to the manufacturer's instructions.

treatment_protocol: liver tissue extracted after the sacrifice of mice

value: liver

value: control


title: KO1M1, biological replicate 1

source_name: KO1M1, biological replicate 1

value: classically activated (M1 condition) with LPS (100 ng/ml, Sigma-Aldrich) + IFN-γ (20ng/mL, E-bioscience, San Diego, CA)


title: Control rep2


title: Mutant, low-titer, biological rep1

source_name: Transgenic mice carrying mutant HBsAg with low-titer

value: transgenic mice carrying mutant HBsAg with low-titer


title: KO2M1, biological replicate 2

source_name: KO2M1, biological replicate 2


title: KO1M0, biological replicate 1

source_name: KO1M0, biological replicate 1

value: received media alone (M0 condition)


title: KO1M2, biological replicate 1

source_name: KO1M2, biological replicate 1

value: alternatively activated (M2 condition) with IL-4 (20ng/mL, E-bioscience)


title: Mutant, low-titer, biological rep3


title: Mutant, low-titer, biological rep2


title: Mutant, high-titer, biological rep2

source_name: Transgenic mice carrying mutant HBsAg and with high titer

value: transgenic mice carrying mutant HBsAg and with high titer


title: KO2M0, biological replicate 2

source_name: KO2M0, biological replicate 2


title: Wild type, biological rep2

source_name: Transgenic mice carrying wild-type HBsAg

value: transgenic mice carrying wild-type HBsAg


title: Wild type, biological rep1


title: Control rep3


title: Mutant, high-titer, biological rep3


title: Wild type, biological rep3


title: Mutant, high-titer, biological rep1


title: innervated SOL muscles transfected with shRNA to MRF4, rep1

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

hyb_protocol: The cRNA labeling and hybridizations were performed according to protocols from Affymetrix Inc. (Santa Clara, CA).

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: RMA of .CEL files using affy Bioconductor library and Brainarray custom cdf [CDF: Version 15.1, ENTREZG] for Affymetrix Rat Genome 230 2.0 Array. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: innervated SOL muscles_shRNA to MRF4

label_protocol: The cRNA labeling was performed according to protocols from Affymetrix Inc. (Santa Clara, CA) staring from 250 ng RNA.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) followed by cleanup with the RNeasy Mini Kit (Qiagen). RNA integrity was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and quantified with a NanoVue spectrophotometer (GE Healthcare Life Sciences, Baie d'Urfe, QC).

treatment_protocol: Innervated and denervated rat soleus muscles were transfected with shRNA to Mrf4 or to LacZ as a control. Muscles were dissected and examined afetr 7 days. We screened transfected SOL muscles by GFP fluorescence in order to select  muscles with the highest transfection efficiency and discarded the proximal and distal portions close to the tendons, which are generally poorly transfected.

tag: strain

value: Wistar

value: adult

value: Soleus muscles

tag: muscle innervation

value: innervated

tag: transfected with

value: MRF4 shRNA


title: denervated SOL muscles transfected with shRNA to MRF4, rep2

source_name: denervated SOL muscles_shRNA to MRF4

value: denervated


title: innervated SOL muscles transfected with shRNA to LacZ, rep1

source_name: innervated SOL muscles_shRNA to LacZ

value: LacZ shRNA


title: innervated SOL muscles transfected with shRNA to MRF4, rep2


title: denervated SOL muscles transfected with shRNA to LacZ, rep2

source_name: denervated SOL muscles_shRNA to LacZ


title: innervated SOL muscles transfected with shRNA to LacZ, rep3


title: denervated SOL muscles transfected with shRNA to MRF4, rep3


title: innervated SOL muscles transfected with shRNA to LacZ, rep2


title: innervated SOL muscles transfected with shRNA to MRF4, rep3


title: denervated SOL muscles transfected with shRNA to MRF4, rep1


title: denervated SOL muscles transfected with shRNA to LacZ, rep3


title: denervated SOL muscles transfected with shRNA to LacZ, rep1


title: PEC-control-13

type: genomic

city: Le Plessis Robinson

first: Frédéric

last: Perros

address: 133 Avenue de la Résistance

department: Centre chirurgical Marie Lannelonque

country: France

institute: INSERM U999

description: SAMPLE 33

hyb_protocol: standard Illumina protocol

scan_protocol: Slides were scanned by iScan+.

data_processing: fn normalization

label: cy3, cy5

molecule: genomic DNA

label_protocol: standard Illumina protocol

extract_protocol: Human lung specimen were collected during lung transplantation from patients with pulmonary arterial hypertension (PAH) during lobectomy or pneumonectomy for localized lung cancer from control subjects. Genomic DNA was extracted from cultured PEC by using the phenol/chloroform method including an RNase treatment.

tag: subject status

value: f

value: Pulmonary endothelial cells (PECs)


title: PEC-control-18

description: SAMPLE 39

tag: age

value: m


title: PEC-heritable-9

description: SAMPLE 28

value: heritable Pulmonary arterial hypertension (hPAH)


title: PEC-idiopathic-4

description: SAMPLE 18

value: idiopathic Pulmonary arterial hypertension (iPAH)


title: PEC-idiopathic-5

description: SAMPLE 19


title: PEC-control-14

description: SAMPLE 34

value: control


title: PEC-control-15

description: SAMPLE 35


title: PEC-heritable-6

description: SAMPLE 15


title: PEC-idiopathic-10

description: SAMPLE 32


title: PEC-idiopathic-8

description: SAMPLE 24


title: PEC-control-11

description: SAMPLE 26


title: PEC-control-16

description: SAMPLE 36


title: PEC-idiopathic-11

description: SAMPLE 37


title: PEC-control-6

description: SAMPLE 12


title: PEC-control-10

description: SAMPLE 25


title: PEC-idiopathic-9

description: SAMPLE 30


title: PEC-idiopathic-6

description: SAMPLE 22


title: PEC-heritable-4

description: SAMPLE 10


title: PEC-heritable-10

description: SAMPLE 29


title: PEC-heritable-8

description: SAMPLE 27


title: PEC-control-9

description: SAMPLE 21


title: PEC-heritable-7

description: SAMPLE 20


title: PEC-idiopathic-3

description: SAMPLE 14


title: PEC-control-5

description: SAMPLE 11


title: PEC-idiopathic-7

description: SAMPLE 23


title: PEC-control-17

description: SAMPLE 38


title: PEC-heritable-5

description: SAMPLE 13


title: PEC-control-7

description: SAMPLE 16


title: PEC-control-8

description: SAMPLE 17


title: PEC-control-12

description: SAMPLE 31


title: implantation sites on day 14 in IVT group

city: Beijing

first: Xihui

last: Sheng

address: No.7 Beinong Road, Huilongguan Town, Changping District

institute: Beijing university of agriculture

description: Gene expression data from uterus tissue at implantation sites on day 14 (day 0 = day of estrous beginning) in IVT group

hyb_protocol: 20µg fragmented cRNA was prepared, hybridized to each GeneChip strip, washed, stained with streptavidin phycoerythrinonan (SAPE).

scan_protocol: GeneChips were scanned according to the manufacturer's protocols (Affymetrix GeneAtlas® Instrument).

data_processing: Quantile normalization of microarray data and calculation of gene expression values were conducted by the bioconductor package (http://www.bioconductor.org) using the Robust Multiarray Average (RMA) method.

organism: Ovis aries

label_protocol: 10 ng RNA samples was reverse transcripted and labeled by biotin with GeneChip Pico WT Labeling kit (Affymetrix).

growth_protocol: 21 Ujumqin ewes aged 10 months that were used in this study were housed at Beijing Waddell sheep breeding farm (Beijing, China) under similar environmental and nutritional conditions.

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

treatment_protocol: All uterus samples were frozen in liquid nitrogen for RNA extraction.

tag: breed

value: Ujumqin

tag: tissue

value: uterus tissue

tag: embryo

value: in vitro embryo

tag: day


title: implantation sites on day 14 in IVV group

description: Gene expression data from uterus tissue at implantation sites on day 14 (day 0 = day of estrous beginning) in IVV group

value: in vivo embryo


title: inter-implantation sites on day 10 in IVV group

description: Gene expression data from uterus tissue at inter-implantation sites on day 10 (day 0 = day of estrous beginning) in IVV group


title: OldHag_dominant_vs_brooding_(t2-D2)_b

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

description:
p1.05s90b01ejf040604
replicate of:p1.05s90a01ejf040604.gpr

hyb_protocol: 65 degrees; 12 - 16 hours, standard coverslip in hybe chamber submersed in waterbath

scan_protocol: axon 400B with PMT gain adjusted to match dyes

data_processing:
standard quality flagging and filtering for faing spots (<2SD above background)
M:ratio after loess normalization with minimum background correction

organism: Haplochromis burtoni

label_protocol: direct labeling protocol with amino-alyl-dUTP incorporated with supersript enzyme

extract_protocol: total RNA was trizol extracted

value: female

tag: phenotype

value: dominant from iso-sex tank

value: brooding from mixed-sex tank


title: OldHag_subordinate_vs_brooding_(n3-D2)_b

description:
p1.05s86b03ejf040714
replicate of:p1.05s86a01ejf040714.gpr

value: subordinate from iso-sex tank


title: OldHag_brooding_vs_subordinate_(b3-D2)_b

description:
p1.05s87b01ejf040708
replicate of:p1.05s87a02ejf040708.gpr


title: OldHag_brooding_vs_subordinate_(b2-D2)_a

description:
p1.05s89a01ejf040604
replicate of:p1.05s89b01ejf040604.gpr


title: OldHag_brooding_vs_subordinate_(b2-D2)_b

description:
p1.05s89b01ejf040604
replicate of:p1.05s89a01ejf040604.gpr


title: implantation sites on day 16 in IVV group

description: Gene expression data from uterus tissue at implantation sites on day 16 (day 0 = day of estrous beginning) in IVV group


title: OldHag_brooding_vs_subordinate_(b3-D2)_a

description:
p1.05s87a01ejf040708
replicate of:p1.05s87b01ejf040708.gpr


title: implantation sites on day 16 in IVT group

description: Gene expression data from uterus tissue at implantation sites on day 16 (day 0 = day of estrous beginning) in IVT group


title: implantation sites on day 12 in IVV group

description: Gene expression data from uterus tissue at implantation sites on day 12 (day 0 = day of estrous beginning) in IVV group


title: implantation sites on day 12 in IVT group

description: Gene expression data from uterus tissue at implantation sites on day 12 (day 0 = day of estrous beginning) in IVT group


title: implantation sites on day 10 in IVV group

description: Gene expression data from uterus tissue at implantation sites on day 10 (day 0 = day of estrous beginning) in IVV group


title: OldHag_dominant_vs_brooding_(t1-D2)_b

description:
p1.05s84b03ejf040715
replicate of:p1.05s84a01ejf040715.gpr


title: OldHag_dominant_vs_brooding_(t2-D2)_a

description:
p1.05s90a01ejf040604
replicate of:p1.05s90b01ejf040604.gpr


title: OldHag_subordinate_vs_brooding_(n3-D2)_a

description:
p1.05s86a03ejf040714
replicate of:p1.05s86b03ejf040714.gpr


title: OldHag_dominant_vs_brooding_(t1-D2)_a

description:
p1.05s84a03ejf040715
replicate of:p1.05s84b03ejf040715.gpr


title: OldHag_subordinate_vs_dominant_(n1-D2)_a

description:
p1.05s83a01ejf040715
replicate of:p1.05s83b01ejf040715.gpr


title: OldHag_subordinate_vs_dominant_(n1-D2)_b

description:
p1.05s83b01ejf040715
replicate of:p1.05s83a01ejf040715.gpr


title: OldHag_brooding_vs_subordinate_(b4-D2)_b

description:
p1.05s82b01ejf040716
replicate of:p1.05s82a01ejf040716.gpr


title: OldHag_dominant_vs_brooding_(t4-D2)_b

description:
p1.05s81b01ejf040716
replicate of:p1.05s81a03ejf040716.gpr


title: OldHag_brooding_vs_subordinate_(b4-D2)_a

description:
p1.05s82a01ejf040716
replicate of:p1.05s82b01ejf040716.gpr


title: OldHag_dominant_vs_brooding_(t4-D2)_a

description:
p1.05s81a01ejf040716
replicate of:p1.05s81b01ejf040716.gpr


title: OldHag_brooding_vs_dominant_(b3-D2)_a

description:
p1.05s77a01ejf040721
replicate of:p1.05s77b01ejf040721.gpr


title: OldHag_subordinate_vs_dominant_(n4-D2)_b

description:
p1.05s80b01ejf040720
replicate of:p1.05s80a01ejf040720.gpr


title: OldHag_dominant_vs_subordinate_(t3-D2)_b

description:
p1.05s76b02ejf040721
replicate of:p1.05s76a01ejf040721.gpr


title: OldHag_subordinate_vs_dominant_(n4-D2)_a

description:
p1.05s80a01ejf040720
replicate of:p1.05s80b01ejf040720.gpr


title: OldHag_brooding_vs_dominant_(b2-D2)_b

description:
p1.05s79b02ejf040720
replicate of:p1.05s79a01ejf040720.gpr


title: OldHag_brooding_vs_dominant_(b2-D2)_a

description:
p1.05s79a02ejf040720
replicate of:p1.05s79b02ejf040720.gpr


title: PEC-control-4

description: SAMPLE 7


title: OldHag_dominant_vs_brooding_(t3-D2)_b

description:
p1.05s70b01ejf040722
replicate of:p1.05s70a01ejf040722.gpr


title: OldHag_brooding_vs_dominant_(b3-D2)_b

description:
p1.05s77b01ejf040721
replicate of:p1.05s77a01ejf040721.gpr


title: OldHag_brooding_vs_dominant_(b1-D2)_a

description:
p1.05s68a01ejf040722
replicate of:p1.05s68b01ejf040722.gpr


title: OldHag_brooding_vs_dominant_(b1-D2)_b

description:
p1.05s68b01ejf040722
replicate of:p1.05s68a01ejf040722.gpr


title: OldHag_dominant_vs_brooding_(t3-D2)_a

description:
p1.05s70a01ejf040722
replicate of:p1.05s70b01ejf040722.gpr


title: OldHag_subordinate_vs_dominant_(n3-D2)_a

description:
p1.05s69a01ejf040722
replicate of:p1.05s69b01ejf040722.gpr


title: OldHag_subordinate_vs_dominant_(n3-D2)_b

description:
p1.05s69b01ejf040722
replicate of:p1.05s69a02ejf040722.gpr


title: PEC-control-2

description: SAMPLE 2


title: OldHag_dominant_vs_subordinate_(t4-D2)_a

description:
p1.05s67a01ejf040723
replicate of:p1.05s67b01ejf040723.gpr


title: OldHag_dominant_vs_subordinate_(t3-D2)_a

description:
p1.05s76a02ejf040721
replicate of:p1.05s76b02ejf040721.gpr


title: OldHag_subordinate_vs_brooding_(n4-D2)_b

description:
p1.05s66b01ejf040723
replicate of:p1.05s66a01ejf040723.gpr


title: OldHag_subordinate_vs_brooding_(n4-D2)_a

description:
p1.05s66a01ejf040723
replicate of:p1.05s66b01ejf040723.gpr


title: OldHag_dominant_vs_subordinate_(t4-D2)_b

description:
p1.05s67b01ejf040723
replicate of:p1.05s67a01ejf040723.gpr


title: PEC-heritable-2

description: SAMPLE 4


title: PEC-idiopathic-2

description: SAMPLE 9


title: PEC-idiopathic-1

description: SAMPLE 8


title: PEC-control-3

description: SAMPLE 6


title: PEC-heritable-3

description: SAMPLE 5


title: OldHag_brooding_vs_subordinate_(b1-D2)_b

description:
p1.05s63b03ejf040728
replicate of:p1.05s63a02ejf040728.gpr


title: OldHag_brooding_vs_subordinate_(b1-D2)_a

description:
p1.05s63a03ejf040728
replicate of:p1.05s63b03ejf040728.gpr


title: PEC-heritable-1

description: SAMPLE 3


title: PEC-control-1

description: SAMPLE 1


title: OldHag_brooding_vs_dominant_(b5-D2)_b

description:
p1.05s61b03ejf040729
replicate of:p1.05s61a02ejf040729.gpr


title: OldHag_brooding_vs_dominant_(b5-D2)_a

description:
p1.05s61a03ejf040729
replicate of:p1.05s61b03ejf040729.gpr


title: OldHag_subordinate_vs_brooding_(n5-D2)_a

description:
p1.05s57a01ejf040729
replicate of:p1.05s57b01ejf040729.gpr


title: OldHag_dominant_vs_subordinate_(t5-D2)_b

description:
p1.05s56b01ejf040729
replicate of:p1.05s56a01ejf040729.gpr


title: OldHag_dominant_vs_subordinate_(t5-D2)_a

description:
p1.05s56a01ejf040729
replicate of:p1.05s56b01ejf040729.gpr


title: OldHag_subordinate_vs_brooding_(n1-D2)_b

description:
p1.05s60b02ejf040730
replicate of:p1.05s60a02ejf040730.gpr


title: OldHag_dominant_vs_brooding_(t5-D2)_a

description:
p1.05s64a01ejf040728
replicate of:p1.05s64b01ejf040728.gpr


title: OldHag_subordinate_vs_brooding_(n5-D2)_b

description:
p1.05s57b01ejf040729
replicate of:p1.05s57a02ejf040729.gpr


title: OldHag_subordinate_vs_dominant_(n5-D2)_b

description:
p1.05s55b01ejf040728
replicate of:p1.05s55a01ejf040728.gpr


title: OldHag_dominant_vs_subordinate_(t1-D2)_b

description:
p1.05s65b02ejf040723
replicate of:p1.05s65a01ejf040723.gpr


title: OldHag_subordinate_vs_dominant_(n5-D2)_a

description:
p1.05s55a01ejf040728
replicate of:p1.05s55b01ejf040728.gpr


title: OldHag_subordinate_vs_brooding_(n1-D2)_a

description:
p1.05s60a02ejf040730
replicate of:p1.05s60b02ejf040730.gpr


title: OldHag_dominant_vs_brooding_(t5-D2)_b

description:
p1.05s64b01ejf040728
replicate of:p1.05s64a01ejf040728.gpr


title: OldHag_dominant_vs_subordinate_(t1-D2)_a

description:
p1.05s65a02ejf040723
replicate of:p1.05s65b02ejf040723.gpr


title: OldHag_dominant_vs_subordinate_(t2-D2)_a

description:
p1.05s53a02ejf040730
replicate of:p1.05s53b02ejf040730.gpr


title: OldHag_subordinate_vs_dominant_(n2-D2)_b

description:
p1.05s59b01ejf040730
replicate of:p1.05s59a02ejf040730.gpr


title: OldHag_dominant_vs_subordinate_(t2-D2)_b

description:
p1.05s53b02ejf040730
replicate of:p1.05s53a01ejf040730.gpr


title: OldHag_brooding_vs_subordinate_(b5-D2)_a

description:
p1.05s54a02ejf040728
replicate of:p1.05s54b02ejf040728.gpr


title: OldHag_subordinate_vs_dominant_(n2-D2)_a

description:
p1.05s59a01ejf040730
replicate of:p1.05s59b01ejf040730.gpr


title: OldHag_subordinate_vs_brooding_(n2-D2)_a

description:
p1.05s52a01ejf040828
replicate of:p1.05s52b01ejf040828.gpr


title: OldHag_brooding_vs_subordinate_(b5-D2)_b

description:
p1.05s54b02ejf040728
replicate of:p1.05s54a01ejf040728.gpr


title: OldHag_brooding_vs_dominant_(b4-D2)_a

description:
p1.05s46a01ejf040828
replicate of:p1.05s46b01ejf040828.gpr


title: OldHag_brooding_vs_dominant_(b4-D2)_b

description:
p1.05s46b01ejf040828
replicate of:p1.05s46a01ejf040828.gpr


title: OldHag_subordinate_vs_brooding_(n2-D2)_b

description:
p1.05s52b01ejf040828
replicate of:p1.05s52a02ejf040828.gpr


title: GNS-G362-PNU 96415E-24h

city: Toronto

first: Peter

last: Dirks

state: ON

address: 686 Bay Street

department: Developmental and Stem Cell

country: Canada

institute: Hospital for Sick Children

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C as per standard Affymetrix protocol.

scan_protocol: GeneChip was scanned using Affymetrix GeneChip scanner 3000

data_processing: data were processed using the expresso function of the Bioconductor affy package (affy_1.38.1, R 3.0.1) including RMA background correction, quantile normalization and log 2 transformation.

source_name: Patient derived Glioblastoma neural stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA.

growth_protocol: GNS cells (G362 and G411) are patient derived glioblastoma neural stem cells grown as adherent monolayer culture in serum free medium with  EFG and FGF.

extract_protocol: Total RNA was extracted from the treated cells using RNeasy kit (Qiagen)

treatment_protocol: GNS(G362 and G411) cells were treated with 25μM of PNU 96415E and cells lysed at 0h, 24h and 48h.

value: Glioblastoma neural stem cells


title: GNS-G362-PNU 96415E-48h


title: GNS-G411-Untreated-0h


title: GNS-G362-Untreated-0h


title: GNS-G411-PNU 96415E-24h


title: GNS-G411-PNU 96415E-48h


title: Control rep2

description: gene expression data of mice liver sacrificed at 1.5 years old

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr to Affymetrix Mouse Gene 1.0 ST arrays

value: liver

tag: genotype/variation

value: control mice


title: Wild type, biological rep2

value: transgenic mice carrying wild-type HBsAg


title: Control rep3


title: Mutant, low-titer, biological rep3

value: transgenic mice carrying mutant HBsAg with low-titer


title: Mutant, high-titer, biological rep1

value: transgenic mice carrying mutant HBsAg and with high titer


title: Mutant, low-titer, biological rep1


title: Control rep1


title: AdiposeTissue_after_VANCO_subject_117

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Human Gene 1.1 ST array plates (Santa Clara, CA) according to manufacturer's instructions.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.0).

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 117

label_protocol: One hundred nanogram of total RNA was used for whole transcript cDNA synthesis with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Fifty-seven low active (<3h organized sports activities per week), weight-stable (<2 kg body weight change 3 months prior to inclusion), overweight/obese (BMI 25-35 kg/m2) Caucasian men aged between 35 and 70 years with impaired glucose metabolism (either fasting glucose > 6.1 mmol/l, and/or 2h glucose between 7.8-11 mmol/l) were included in this study. For a period of 3 months before entering the study, subjects did not use antibiotics. Exclusion criteria were known allergic reactions to vancomycin, teicoplanine, amoxicillin or related antibiotics, hearing disorders, cancer, liver malfunction, major illnesses with a life expectancy < 5 years and pulmonary, hepatic, cardiovascular, kidney, and gastrointestinal disease. Participants did not use beta-blockers, lipid and glucose lowering-drugs, antioxidants or chronic corticosteroids. All subjects gave written informed consent for participation in this study, which was reviewed and approved by the local Medical Ethical Committee of Maastricht University Medical Centre+. All procedures were executed according to the declaration of Helsinki.

extract_protocol: Total RNA was prepared from the abdominal subcutaneous adipose biopsies (~500mg) using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 7.0).

treatment_protocol: In this double-blind, randomized controlled, parallel intervention trial, participants received 500 mg/day amoxicillin, vancomycin or placebo for 7 days. All medication (amoxicillin, vancomycin and placebo (microcrystalline cellulose)) was encapsulated equally to blind the content to subjects and investigators (Basic Pharma, Geleen, The Netherlands). After completion of the study, returned capsules were counted for compliance. The randomization was established by the ALEA Randomization Service (www.tenalea.net). Randomization with stratification for BMI, age and 2h-glucose values was used to increase the homogeneity of the three treatment groups. The treatment period started at the day after the last baseline measurement of week 1. All measurements were performed before the antibiotics (week 1) and in the week after the antibiotics (week 3), with a wash out period of 2 days after intervention before performing the measurements. 8 weeks after cessation of the intervention (week 10), a follow-up measurement was planned. In total, subjects were asked to visit the university 7 times (screening, 2x3 clinical investigation days, and one follow-up meeting). Subjects were instructed to maintain their habitual lifestyle pattern throughout the study. In week 1, 3 and 10, subjects were asked to fill in a 3 day food intake record in order to monitor changes in dietary energy and macronutrient intake. Two days prior to the clinical investigation days (CID), participants refrained from intense exercise and alcohol. The evening before an investigation day, a low-fiber and low-fat meal was consumed. After an overnight fast, participants came to the university by car or public transport. All procedures were executed in a resting, half-supine position. At the first investigation day, an abdominal subcutaneous adipose tissue biopsies were taken under local anesthesia under fasted conditions.

value: subcutaneous adipose

value: male

tag: age (yrs)

tag: population

value: Caucasian

value: overweight/obese

tag: disease state

value: prediabetic

tag: treatment

value: vancomycin

tag: time point

value: after 1 wk of intervention


title: Wild type, biological rep1


title: AdiposeTissue_before_intervention_ subject_117

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 117

tag: gender

value: before intervention


title: Testis Lhcgr KO, rep1

city: Kyoto

first: Takashi

last: Tanaka

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

department: Molecular Genetics

institute: Kyoto University

hyb_protocol: Resultant labeled-cDNA were hybridized for 17 hr at 45C on Mouse Gene 1.0 ST Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed with GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Plier normalization. Data analyses were performed using GeneSpring 12.0 software (Agilent Technologies, Inc., Santa Clara, CA). The probeset signals were calculated with the Plier algorithm. The annotation is based on na32 (mm9).

source_name: Testis, Lhcgr KO

label_protocol: For generating whole transcript sense target with label, purified total RNA were converted to sense strand cDNA using The Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript (WT) Expression Arrays (Applied Biosystems). Resultant cDNA samples were labeled using GeneChip WT terminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: All mice were maintained in a controlled environment with 12:12-h light:dark cycles.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by purification with RNeasy Plus Mini kit (Qiagen).

treatment_protocol: Lhcgr KO or control mice were treated with busulfan (44 mg/kg) and sacrificed 4 weeks after treatment.

value: Lhcgr KO

tag: Sex

value: testis


title: Mutant, high-titer, biological rep2


title: AdiposeTissue_before_intervention_ subject_118

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 118


title: Testis Control WT, rep1

source_name: Testis, control WT

value: WT


title: Wild type, biological rep3


title: Mutant, high-titer, biological rep3


title: 4T1-ΔSAP_rep3

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

description: cells grown in 0.03% FCS/DMEM, 48 h

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affzmetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing: Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.10.0 ) / Bioconductor (version 2.4) package affy using annotation from Netaffx (www.netaffx.com).

source_name: 4T1-ΔSAP cell line

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: Cells were grown in 0.03% FCS/DMEM for 48 h before total RNA was extracted.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen).

treatment_protocol: not applicable

tag: cell type

value: mammary epithelial carcinoma

tag: cell line

value: 4T1-ΔSAP cell line

tag: genetic background


title: Testis Control WT, rep2


title: 4T1-ΔSAP_rep1

description: cells grown in 0.03% FCS/DMEM, 48 h


title: Mutant, low-titer, biological rep2

source_name: Transgenic mice carrying mutant HBsAg with low-titer

value: liver


title: Testis Lhcgr KO, rep2


title: Input_Mm

type: SRA

city: Utrecht

first: Jurian

last: Schuijers

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Insitute

library_source: genomic

data_processing:
Sequencing reads were mapped against the reference genome (mm9) using BWA package
Sequencing reads were mapped against the reference genome (hg19) using BWA package
Multiple reads mapping to same location and strand have been collapsed to single read and only uniquely placed reads were used for peak calling.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: [.wig] file reports peaks

source_name: Mouse Crypt

growth_protocol: Mouse intestines were flushed with PBS before being cut open longitudinally. The villi were removed by scraping with a microscope slide. Pieces of approximately 1 cm in length were incubated in 5 mM EDTA/PBS without Ca2+/Mg2+ for 15 min at 4°C per fraction. After incubation, the epithelium was separated by vigorous shaking, and the remaining intestinal tissue was placed in a new tube for collection of the following fraction. Remaining crypts were pelleted and evaluated for purity under the microscope. The two purest fractions were pooled and used as input material for ChIP-seq. All procedures were performed in compliance with local animal welfare laws, guidelines, and policies.

extract_protocol:
human cells or mouse intestinal crypts were crosslinked with 1% formaldehyde for 20 min at room temperature. For β-catenin ChIP-seq, cells were crosslinked for 40 min using ethylene glycol-bis(succinimidylsuccinate) (Thermo Scientific) at 12.5 mM final concentration, with the addition of formaldehyde (1% final concentration) after 20 min of incubation. The reaction was quenched with glycine, and the cells were successively washed with PBS, buffer B (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES, pH 7.6), and buffer C (0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES, pH 7.6). The cells were then resuspended in shearing buffer (0.3% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES, pH 7.6) and sheared using Covaris S2 (Covaris) for 8 min with the following settings: duty cycle, max; intensity, max; cycles per burst, max; mode, power tracking.
Immunoprecipitated chromatin was sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by ligation mediated PCR (LMPCR). After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel, barcoded and sequenced on SOLiD/AB sequencer in multiplexed way to produce 50 base pair long reads.

value: intestinal organoid

tag: chip antibody


title: Tcf4_Mm ChIP-seq

value: goat-anti-Tcf4 (N-20; Santa Cruz Biotechnology, catalog# sc-8631)


title: 4T1-mutB1_rep3

description: cells grown in 0.03% FCS/DMEM, 48 h

source_name: 4T1-mutB1 cell line

value: 4T1-mutB1 cell line


title: B-catenin_Mm ChIP-seq

value: rabbit-anti-β-catenin (H102; Santa Cruz, catalog# sc-7199)


title: Ascl2_Mm ChIP-seq

value: mouse-anti-Ascl2 (7E2; Millipore, catalog# MAB4418)


title: AdiposeTissue_after_VANCO_subject_118

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 118

value: subcutaneous adipose

value: male

value: Caucasian


title: AdiposeTissue_after_PLA_subject_128

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with placebo, subject 128

value: overweight/obese

value: prediabetic

value: placebo


title: AdiposeTissue_after_VANCO_subject_123

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 123

value: vancomycin

value: after 1 wk of intervention


title: 4T1-ΔSAP_rep2

description: cells grown in 0.03% FCS/DMEM, 48 h


title: AdiposeTissue_before_intervention_ subject_123

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 123

value: before intervention


title: 4T1-FL_rep3

description: cells grown in 0.03% FCS/DMEM, 48 h

source_name: 4T1-FL cell line

value: mammary epithelial carcinoma

value: 4T1-FL cell line


title: 4T1-mutB1_rep2

description: cells grown in 0.03% FCS/DMEM, 48 h


title: 4T1-control_rep2

description: cells grown in 0.03% FCS/DMEM, 48 h

source_name: 4T1-control cell line

value: 4T1-control cell line


title: AdiposeTissue_before_intervention_ subject_128

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 128


title: 4T1-control_rep1

description: cells grown in 0.03% FCS/DMEM, 48 h


title: 4T1-FL_rep1

description: cells grown in 0.03% FCS/DMEM, 48 h


title: 4T1-control_rep3

description: cells grown in 0.03% FCS/DMEM, 48 h


title: AdiposeTissue_before_intervention_ subject_127

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 127


title: 4T1-FL_rep2

description: cells grown in 0.03% FCS/DMEM, 48 h


title: AdiposeTissue_after_AMOX_subject_112

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 112

value: amoxicillin


title: AdiposeTissue_after_PLA_subject_127

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with placebo, subject 127


title: 4T1-mutB1_rep1

description: cells grown in 0.03% FCS/DMEM, 48 h


title: AdiposeTissue_after_PLA_subject_9

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with placebo, subject 9


title: AdiposeTissue_after_AMOX_subject_110

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 110


title: AdiposeTissue_before_intervention_ subject_110

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 110


title: AdiposeTissue_before_intervention_ subject_95

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 95


title: AdiposeTissue_after_PLA_subject_95

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with placebo, subject 95


title: AdiposeTissue_after_AMOX_subject_99

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 99


title: AdiposeTissue_before_intervention_ subject_9

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 9


title: AdiposeTissue_after_AMOX_subject_93

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 93


title: AdiposeTissue_after_PLA_subject_78

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with placebo, subject 78


title: AdiposeTissue_before_intervention_ subject_99

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 99


title: AdiposeTissue_before_intervention_ subject_93

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 93


title: AdiposeTissue_before_intervention_ subject_112

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 112


title: AdiposeTissue_after_AMOX_subject_75

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 75


title: AdiposeTissue_after_AMOX_subject_85

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 85


title: AdiposeTissue_before_intervention_ subject_78

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 78


title: AdiposeTissue_before_intervention_ subject_75

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 75


title: AdiposeTissue_before_intervention_ subject_61

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 61


title: AdiposeTissue_before_intervention_ subject_74

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 74


title: AdiposeTissue_before_intervention_ subject_72

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 72


title: AdiposeTissue_after_VANCO_subject_61

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 61


title: AdiposeTissue_before_intervention_ subject_69

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 69


title: AdiposeTissue_after_AMOX_subject_72

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 72


title: AdiposeTissue_after_VANCO_subject_56

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 56


title: AdiposeTissue_before_intervention_ subject_85

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 85


title: AdiposeTissue_before_intervention_ subject_51

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 51


title: AdiposeTissue_after_AMOX_subject_69

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 69


title: AdiposeTissue_after_AMOX_subject_67

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 67


title: AdiposeTissue_after_VANCO_subject_74

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 74


title: AdiposeTissue_before_intervention_ subject_67

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 67


title: AdiposeTissue_before_intervention_ subject_62

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 62


title: AdiposeTissue_before_intervention_ subject_56

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 56


title: AdiposeTissue_after_PLA_subject_62

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with placebo, subject 62


title: AdiposeTissue_after_PLA_subject_51

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with placebo, subject 51


title: AdiposeTissue_after_VANCO_subject_45

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 45


title: AdiposeTissue_before_intervention_ subject_38

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 38


title: AdiposeTissue_after_PLA_subject_38

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with placebo, subject 38


title: AdiposeTissue_after_VANCO_subject_29

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 29


title: AdiposeTissue_before_intervention_ subject_29

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 29


title: AdiposeTissue_after_VANCO_subject_14

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 14


title: AdiposeTissue_after_AMOX_subject_39

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 39


title: AdiposeTissue_before_intervention_ subject_53

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 53


title: AdiposeTissue_before_intervention_ subject_52

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 52


title: AdiposeTissue_before_intervention_ subject_39

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 39


title: AdiposeTissue_before_intervention_ subject_14

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 14


title: AdiposeTissue_after_VANCO_subject_53

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 53


title: AdiposeTissue_before_intervention_ subject_45

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 45


title: AdiposeTissue_after_VANCO_subject_52

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Vancomycin, subject 52


title: AdiposeTissue_after_PLA_subject_15

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with placebo, subject 15


title: AdiposeTissue_after_AMOX_subject_11

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 11


title: AdiposeTissue_before_intervention_ subject_10

source_name: Subcutaneous adipose tissue biopsy, before intervention (baseline measurement), subject 10


title: AdiposeTissue_after_AMOX_subject_6

source_name: Subcutaneous adipose tissue biopsy, after 1 wk of intervention with Amoxicillin, subject 6