title: mDC_CHR_NST_P7

description:
Sample name: mDC_CHR_NST.P7.220.1.3
Gene expression after cell purification


title: rat cochlea - 3 days treated with Roveratrol+N-acetylcysteine 6

status: Public on Jul 29 2016

type: RNA

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: Antioxidant Treated

data_processing: The open source NormFinder v.5 software [44] was used to identify a pair of stable genes, which were used as reference genes for the normalisation of the data. Genes selected from NormFinder were Idh1 and Prnp for the 5-day dataset; Txnip and Idh1 for 23-day dataset; Xirp1 and Txnrd2 for the combined 5 and 23 days dataset. Normalisation was performed using the rank normalisation method and the data subsequently filtered to discard the genes whose expression was undetermined (Ct values > 35) in at least 90 % of the samples in the dataset.

molecule: total RNA

organism: Rattus norvegicus

source_name: Cochlea

label_protocol: Genes involved in oxidation were studied with the “Rat oxidative stress and antioxidant defense RT2 profiler PCR array” (PARN-065, SABiosciences Corp., Frederick, MD, USA). It includes a panel of 84 target genes and 5 housekeeping genes that are listed in Supplementary file 1. First-strand cDNA was synthesised using the RT2 first strand kit (C-03, SABiosciences Corp.) and PCR arrays were then processed on an Applied Biosystems 7900HT Real-Time PCR System, to obtain the Ct values.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Micro Kit after cochleae homogenisation.

treatment_protocol: Two month-old male Wistar rats (n=36) were distributed in two groups, one receiving resveratrol plus NAC (n=20) and the control group receiving vehicle (n=16). Two days after the beginning of the treatment, a gelatin sponge embedded in a concentrated solution of kanamycin and furosemide (200 mg/ml and 50 mg/ml, respectively, in 0.1 M PBS pH 8.5) was located by bullostomy in the middle ear, close to the round window. The contralateral left ears were used as controls for the corresponding experimental conditions.

tag: tissue

value: cochlea

tag: treatment

value: treated with antioxidant drugs

tag: time

value: 3 days


title: Contralateral rat choclea -3 days not treated 1

description: control

value: untreated


title: rat cochlea - 3 days treated with Roveratrol+N-acetylcysteine 5

description: Antioxidant Treated


title: rat cochlea - 3 days treated with Roveratrol+N-acetylcysteine 1

description: Antioxidant Treated


title: rat cochlea - 3 days treated with Roveratrol+N-acetylcysteine 4

description: Antioxidant Treated


title: rat cochlea - 3 days treated with Roveratrol+N-acetylcysteine 2

description: Antioxidant Treated


title: rat cochlea - 3 days post ototoxic treatment 5

description: Ototoxic treated

value: treated with ototoxic drugs


title: rat cochlea - 3 days post ototoxic treatment 4

description: Ototoxic treated


title: rat cochlea - 3 days treated with Roveratrol+N-acetylcysteine 3

description: Antioxidant Treated


title: Rat cochlea - 3 day treated with ototoxic drugs and Antioxidant protection 4

description: Ototoxic treated plus antioxidant

value: treated with antioxidant drugs prior Ototoxic administration


title: rat cochlea - 3 days post ototoxic treatment 3

description: Ototoxic treated


title: mDC_CTRL_ST_P9

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

country: Spain

institute: CIMA

description:
Sample name: mDC_CTRL_ST.P9.239.1.4
Gene expression after 2h stimulation with poly(I:C)

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 8x60K V2  using Agilent’s recommended hybridization chamber and oven. The samples were randomly distributed for the labeling approach and the subsequent  hybridization. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1  for 1 min at room temperature followed by a second wash with preheated Agilent Gene  Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s  Microarray Scanner System (Agilent Technologies).

data_processing: The raw data was extracted with the Agilent Feature Extraction Software and was quantile normalized using R. The limma R package was used for the selection of differentially expressed genes.

organism: Homo sapiens

source_name: Activated myeloid dendritic cells from healthy seronegative individuals

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Peripheral blood dendritic cells were first enriched by incubation with anti-CD304 (BDCA-4/Neuropilin-1)-coated magnetic beads (for pDC), followed by purification of mDC using anti-CD1c (BDCA-1) beads, both from Miltenyi Biotec. To ensure high purity necessary for microarray experiments, enriched cells were further purified by flow cytometry (FACSAria; BD-Biosciences) after staining with CD11c-APC, HLA-DR-PerCP-Cy5.5, Lin-FITC and CD123-PE antibodies (BD-Biosciences). Dead cells were excluded by using the Sytox Blue (Life Technologies) cell death marker and in the Lin-HLA-DR+ gate, pDC were defined as CD11c-CD123+, while mDC were defined as CD11c+CD123-.

extract_protocol: Cell pellets were resuspended in Amplification Buffer (Miltenyi Biotec) before freezing them. Later, samples were sent to Miltenyi Biotec and the SuperAmp technology (Miltenyi Biotec) was used to amplify mRNA before transcriptomic analysis.

treatment_protocol: After purification, a cell aliquot was left un-stimulated while the other was stimulated for 2 hrs at 37 ºC with 1 µg/ml poly(I:C) (Amersham) + 250 µg/ml DEAE-Dextran (Sigma) in case of mDC or 5 µg/ml of Imiquimod (Invivogen) in case of pDC.

tag: individual

value: healthy seronegative individuals

value: peripheral blood

tag: cell type

value: myeloid DC

tag: protocol

value: stimulated with poly(I:C)


title: mDC_ANR_ST_P2

description:
Sample name: mDC_ANR_ST.P2.221.1.2
Gene expression after 2h stimulation with poly(I:C)

source_name: Activated myeloid dendritic cells from patients with hepatitis C virus infection

value: patient with hepatitis C virus infection


title: Rat cochlea - 21day treated with ototoxic drugs and Antioxidant protection 2

description: Ototoxic treated plus antioxidant

value: 21 days


title: mDC_ANR_ST_P4

description:
Sample name: mDC_ANR_ST.P4.220.1.2
Gene expression after 2h stimulation with poly(I:C)


title: mDC_ANR_NST_P4

description:
Sample name: mDC_ANR_NST.P4.220.2.3
Gene expression after cell purification

source_name: Resting myeloid dendritic cells from patients with hepatitis C virus infection

value: non-stimulated


title: Rat cochlea - 21day treated with ototoxic drugs and Antioxidant protection 3

description: Ototoxic treated plus antioxidant


title: rat cochlea - 3 days post ototoxic treatment 2

description: Ototoxic treated


title: mDC_ANR_ST_P3

description:
Sample name: mDC_ANR_ST.P3.222.1.2
Gene expression after 2h stimulation with poly(I:C)


title: mDC_ANR_ST_P1

description:
Sample name: mDC_ANR_ST.P1.220.1.1
Gene expression after 2h stimulation with poly(I:C)


title: mDC_ANR_NST_P1

description:
Sample name: mDC_ANR_NST.P1.220.2.2
Gene expression after cell purification


title: PX 2

city: Singapore

first: Arsen

middle: O

last: Batagov

address: 30 Biopolis St, Matrix, 07-1

country: Singapore

institute: Bioinformatics Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol on BeadArray Reader

data_processing: For normalization, first background correction was performed using the negative control probes present on the chip (Shi). Principal components analysis (using the princomp function of the R stats package with varimax rotation) was then applied to assess the variation across the technical replicates and biological sample types. Across the technical replicates of each sample type (T, ML, PX, and PI), gene expression was normalized, using invariant gene set as follows. Within the technical replicates of each sample type, the coefficient of variation was calculated for each gene individually. Top 400 genes with the lowest coefficients of variation were selected as sample type-specific low-variance genes.

label: biotin

organism: Mus musculus

source_name: Mouse liver

label_protocol: Biotin labeled cRNA was prepared using TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: RNA was isolated using Trizol extraction method (Invitrogen)

value: Liver

tag: sample type

value: Peroxisomal


title: Hamster_Control_Sample

city: Morris Plains

first: David

middle: M

last: Goldenberg

state: NJ

address: 300 The American Road

department: Center for Molecular Medicine and Immunology

country: USA

institute: Garden State Cancer Center

description: ATCC CCL-49 (RPMI 1826)

hyb_protocol: 5.5 ug of fragmented, biotin-labeled cDNA were hybridized for 16 hr at 45 degrees C on GeneChip Human U133_X3P arrays (Affymetrix; catalog no. 900516). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G.

data_processing: Fluorescent signals were collected and processed by AGCC and MAS 5.0 using Affymetrix default analysis settings and global scaling as the normalization method in Expression Colsole. The trimmed mean target intensity (TGT) of each array was set to 250. Following MAS 5.0 normalization and global scaling, unannotated probe sets and probe sets for which no signal value was greater than the median signal for AFFX spike-in controls with all Absent Detection Calls were omitted from further analysis. Subsequently, because an intact hamster cell line (sample IMM006, cell line CCL-49) control RNA sample was used for comparison with the four human-hamster hybrid FFPE samples, all remaining signal values for the hamster cell line sample were multiplied by the ratio of the median signal in all FFPE hybrid samples for AFFX spike-in control probe sets called present in all samples divided by the median signal for the same probe sets in the hamster control sample.

organism: Mesocricetus auratus

source_name: ATCC CCL-49 (RPMI 1826)

label_protocol: Biotinylated cDNA from each sample  weas prepared by conversion of 50 ng total RNA to cDNA by reverse transcription, amplification by the SPIA method, and fragmentation and labeling with biotin using the Ovation Pico WTA System v2 and Encore Biotin Module kits according to the manufacturer’s instructions (NuGEN, San Carlos CA).

growth_protocol: Various human tumors were inidividually grafted to the cheek pouches of adult, unconditioned golden hamsters (Mesocricetus auratus), and the resulting tumor for each was serially passaged in hamsters for multiple years.

extract_protocol: Total RNA was extracted using the RNeasy FFPE Kit (Qiagen, Germantown, MD) according to manufacturer’s instructions (3h incubation at 55 degrees C followed by glass fiber filtration). RNA purity was checked by OD260/280 readings and RNA integrity was checked using Agilent Bioanalyzer capillary electrophoresis profiles.

treatment_protocol: Tissue samples were preserved as formalin-fixed paraffin-embedded (FFPE) tissue blocks for up to 40 years and sectioned to 5-10 um thick for nucleic acid isolation.

tag: hybrid

value: :Mesocricetus auratus

tag: original tumor type

value: Melanoma

value: Cultured monolayer


title: mDC_ANR_NST_P3

description:
Sample name: mDC_ANR_NST.P3.222.2.2
Gene expression after cell purification


title: mDC_ANR_NST_P2

description:
Sample name: mDC_ANR_NST.P2.221.2.2
Gene expression after cell purification


title: TICAM knockout MEFs_ DMSO treated_ rep2

city: Toledo

first: Saurabh

last: Chattopadhyay

state: OH

address: 3000 Arlington Ave

department: MMI

institute: University of Toledo

description: SAMPLE 8

hyb_protocol: Performed by the Lerner Research Institute Genomics Core at the Cleveland Clinic

data_processing: Analyzed by GenomeStudio software V2010.2 with quantile normalization.

source_name: MEF cells_DMSO

growth_protocol: Cells were cultured in DMEM supplement with 10% FBS and Pen/Strep

extract_protocol: extracted by Roche high pure rna isolation kit

treatment_protocol: Cells were transfected with c-di-GMP to final concentration of 8 ug/ml using lipofectamine 2000 or equal amount of DMSO for 30 min. 4 hours post transfection, total RNA was extracted

tag: genotype

value: TICAM knockout

value: MEF


title: rat cochlea -21 days treated with Roveratrol+N-acetylcysteine 3

description: Antioxidant Treated

value: cochlea

value: treated with antioxidant drugs


title: Rat cochlea - 21day treated with ototoxic drugs and Antioxidant protection 1

description: Ototoxic treated plus antioxidant

value: treated with antioxidant drugs prior Ototoxic administration


title: G3341_HumanHodgkinLymphoma-HamsterHybridTumorGW-584_generation 28

description: GW-584: A transplant line established in hamster cheek pouches from the mediastinal Hodgkin lymphoma of a male, also showing HRS cells, and propagated for >5 years. The serial transplants were similar morphologically to the first generation xenograft. The first evidence of metastasis to all major organs and lymph nodes was observed as early as 21 days from the initial grafting, and continued in all subsequent transplant generations, regardless of transplant site.  This sample was obtained from transplant generation 28.

value: :Homo sapiens-Mesocricetus auratus hybrids

value: Hodgkin lymphoma

value: FFPE


title: PX-IP 3

value: immuno-precispitation of the PX fraction with the PMP70-specific antibodies


title: TICAM knockout MEFs_ DMSO treated_ rep1

description: SAMPLE 7

scan_protocol: Performed by the Lerner Research Institute Genomics Core at the Cleveland Clinic


title: PX 3


title: rat cochlea -21 days treated with Roveratrol+N-acetylcysteine 1

description: Antioxidant Treated


title: PX 1


title: rat cochlea -21 days treated with Roveratrol+N-acetylcysteine 2

description: Antioxidant Treated


title: TICAM knockout MEFs_ c-di-GMP treated_ rep2

description: SAMPLE 6

source_name: MEF cells_c-di-GMP treated

label_protocol: Performed by the Lerner Research Institute Genomics Core at the Cleveland Clinic


title: G3272_HumanHodgkinLymphoma-HamsterHybridTumorGW-532_generation 34

description: GW-532: A male’s left axillary Hodgkin lymphoma containing Hodgkin Reed Sternberg (HRS) cells was grafted to the cheek pouches of adult, unconditioned golden hamsters (Mesocricetus auratus), and the resulting tumor was serially passaged in hamsters for >6 years. The transplants were morphologically similar to portions of the original donor specimen, even with HRS cells being identified as early as 17 days after the initial transplantation. This and all subsequent transplant generations showed widespread metastases from the cheek pouch grafts. This sample was obtained from transplant generation 34.


title: WT MEFs_ DMSO treated_ rep2

description: SAMPLE 4

value: wildtype


title: PX-IP 2


title: G4777_HumanGlioblastomaMulltiforme-HamsterHybridTumorGW-532_generation 2

description: GB-749: A glioblastoma multiforme specimen from an adult female was successfully grafted to the cheek pouch of 1 of 9 unconditioned, adult golden hamsters; this tumor appeared in 14 days and killed the recipient due to widespread metastasis by 4 weeks. This aggressive and rapid growth was continued upon serial passage to other hamsters, showing metastases to all major organs regardless of transplant site in the hamster. Morphologically, the transplant was more uniform and anaplastic than the patient’s tumor, but showed the pseudopalisading, lobulated pattern and/or sheets of cells similar to the original patient tumor, even after serial transplantation for >2 years [33,36].

value: Glioblastoma multiforme


title: rat cochlea -21 days post ototoxic treatment 2

description: Ototoxic treated

value: treated with ototoxic drugs

value: 21 days


title: WT MEFs_ DMSO treated_ rep1

description: SAMPLE 3


title: Total cellular RNA 2

value: Liver

value: whole cell extract


title: Total cellular RNA 3


title: Total cellular RNA 1


title: TICAM knockout MEFs_ c-di-GMP treated_ rep1

description: SAMPLE 5


title: WT MEFs_ c-di-GMP treated_ rep2

description: SAMPLE 2


title: rat cochlea -21 days post ototoxic treatment 3

description: Ototoxic treated


title: ML 3

value: Mitochondrial/Lysosomal


title: ML 2


title: Contralateral rat choclea -21 days not treated 1

description: control

value: untreated


title: Contralateral rat choclea -21 days not treated 2

description: control


title: WT MEFs_ c-di-GMP treated_ rep1

description: SAMPLE 1


title: PX-IP 1


title: rat cochlea -21 days post ototoxic treatment 1

description: Ototoxic treated


title: MAP-infected MDMs vs. MAP-infected MDMs treated with bafilomcyin, Replicate 2

city: Saint Paul

first: Elise

last: Lamont

state: MN

address: 1971 Commonwealth Avenue, Veterinary Science, Room 205

institute: University of Minnesota

description:
cDNA
MAP v. bafilomycin R2
Biological replicate 2 of 3.

hyb_protocol: cDNA was hybridized to a 70-mer oligo array (National Animal Disease Center, Ames, IA) overnight at room temperature. Slides were washed in microarray buffer.

scan_protocol: Scanned on a HP ScanArray 5000 (Perkin Elmer). Images were quantified using BlueFuse (BlueGnome) software.

data_processing: Global LOWESS was used to normalize data. GeneSpring GX10 (Agilent) software was used to analyze data.

organism: Mycobacterium avium subsp. paratuberculosis K-10

source_name: MAP-infected MDMs, untreated

label_protocol: RNA was converted to cDNA and labeled with either Cy5 or Cy3 using the SuperScript Direct Plus cDNA labeling system (Invitrogen) per manufacturer's instructions.

extract_protocol: Total RNA was extracted using TriZol. RNA was treated with DNase I and was enriched for microbial RNA using MicrobEnrich by Ambion per manufacturer's instructions. RNA was amplified using MessageAmpII Bacteria kit (Ambion) per manufacturer's instructions.

value: bovine monocyte-derived macrophages (MDMs) infected with Mycobacterium avium subsp. paratuberculosis (MAP)

source_name: MAP-infected MDMs treated with bafilomycin

value: bafilomcyin A1


title: MAP-infected MDMs vs. MAP-infected MDMs treated with bafilomcyin, Replicate 1

description:
cDNA
MAP v. bafilomycin R1
Biological replicate 1 of 3.


title: MAP-infected MDMs vs. MAP-infected MDMs treated with bafilomcyin, Replicate 3

description:
cDNA
MAP v. bafilomycin R3
Biological replicate 3 of 3.


title: ekid_R4_ko3

status: Public on Jul 28 2016

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

description: embryonic kidney F4/80high macrophages Irf8KO rep2

hyb_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.1 ST Arrays , that were stained, washed and scanned following standard procedures.

data_processing: Background correction and normalization was performed using the RMA-Sketch implementation in Affymetrix Expression Console

source_name: embryonic F4/80high macrophages

label_protocol: Total RNA was amplified using the Ovation PicoSL WTA System V2 and further processed using the Encore Biotin Module according to the instructions supplied by the manufacturer (NuGen).

growth_protocol: isolated cells

extract_protocol: RNA isolation was perfomed using Arcturus PicoPure isolation kit according to the manufacturer's instructions.

treatment_protocol: samples from liver, kidney and skin were treated with collagenase. Skin and Liver was additionaly treated with dispase and DNase for digesting the tissue. Brain cells (microglia) were isolated by a percoll-gradient.

value: kidney

tag: celltype

value: macrophages

value: Irf8 knockout


title: ekid_R3_ko2

description: embryonic kidney CD11bhigh macrophages Irf8KO rep1

scan_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.1 ST Arrays , that were stained, washed and scanned following standard procedures.

source_name: embryonic CD11bhigh macrophages


title: A2_ko1

description: yolk sac progenitor population A2 Irf8KO rep1

source_name: yolk sac progenitor population A2

value: yolk sac

value: erythro-myeloid progenitors


title: A2_3_ko

description: yolk sac progenitor population A2 Irf8KO rep3


title: ekid_R3_ko3

description: embryonic kidney CD11bhigh macrophages Irf8KO rep2


title: A1_3_ko

description: yolk sac progenitor population A1 Irf8KO rep3

source_name: yolk sac progenitor population A1


title: ekid_R3_3_ko

description: embryonic kidney CD11bhigh macrophages Irf8KO rep3


title: Contralateral rat choclea -21 days not treated 3

description: control

value: cochlea


title: aLC_KO3

description: adult Langerhans cells Irf8KO rep3

source_name: adulte Langerhans cells

value: skin

value: adult

value: Langerhans cells


title: 11_A2_ko2_2

description: yolk sac progenitor population A2 Irf8KO rep2_2


title: ekid_R4_3_ko

description: embryonic kidney F4/80high macrophages Irf8KO rep3


title: aLC_KO1

description: adult Langerhans cells Irf8KO rep1


title: aLC_GFP+_3_2

description: adult Langerhans cells wildtype rep3

value: wildtype


title: aLC_GFP+_1_2

description: adult Langerhans cells wildtype rep1


title: ekid-wt3-R4

description: embryonic kidney F4/80high macrophages wildtype rep2


title: ekid-wt2-R4

description: embryonic kidney F4/80high macrophages wildtype rep1


title: ekid-wt3-R3

description: embryonic kidney CD11bhigh macrophages wildtype rep3


title: aLC_GFP+_2_2

description: adult Langerhans cells wildtype rep2


title: ekid-wt2-R3_2

description: embryonic kidney CD11bhigh macrophages wildtype rep2


title: ML 1


title: eliv-R5-ko3_2

description: embryonic Kupffer cells Irf8KO rep3

source_name: embryonic Kupffer cells

value: liver

value: Kupffer cells


title: ekid-wt1-R3_2

description: embryonic kidney CD11bhigh macrophages wildtype rep1


title: eliv-R4-ko2

description: embryonic liver CD11bhigh macrophages Irf8KO rep2


title: eliv-R4-ko3_2


title: G2911_HumanHodgkinLymphoma-HamsterHybridTumorGW-532_generation 2

description: GW-532: A male’s left axillary Hodgkin lymphoma containing Hodgkin Reed Sternberg (HRS) cells was grafted to the cheek pouches of adult, unconditioned golden hamsters (Mesocricetus auratus), and the resulting tumor was serially passaged in hamsters for >6 years. The transplants were morphologically similar to portions of the original donor specimen, even with HRS cells being identified as early as 17 days after the initial transplantation. This and all subsequent transplant generations showed widespread metastases from the cheek pouch grafts. This sample was obtained from transplant generation 2.

value: :Homo sapiens-Mesocricetus auratus hybrids

value: Hodgkin lymphoma

value: FFPE


title: eliv-R5-ko1

description: embryonic Kupffer cells Irf8KO rep1


title: Liver_KC_Irf8_ko3

description: adult Kupffer cells Irf8KO rep3

source_name: adult Kupffer cells


title: Liver_KC_Irf8_ko2

description: adult Kupffer cells Irf8KO rep2


title: Liver_KC_Irf8_ko1

description: adult Kupffer cells Irf8KO rep1


title: eliv-R5-ko2

description: embryonic Kupffer cells Irf8KO rep2


title: eMG-KO1

description: embryonic microglia Irf8KO rep1

source_name: embryonic microglia

value: brain

value: microglia


title: eliv-R4-ko1

description: embryonic liver CD11bhigh macrophages Irf8KO rep1


title: subcutaneous inguinal adipose tissue R6/2 - 6

city: Lund

first: Maria

last: Björkqvist

state: Skåne

address: Sölvegatan 17

department: Experimental Medical Sciences

country: Sweden

institute: Lund University

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

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

data_processing: The data were analyzed using expression console software version 1.1.2 using default analysis settings and RMA as normalization method.

source_name: white adipose tissue R6/2 (HD)

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

growth_protocol: Subcutaneous inguinal adipose tissue biospies were obtained from wild type and R6/2 mice, following cervical dislocation.

extract_protocol: Frozen tissues were homogenized using a Fastprep-24 homogenizer (MP Biomedicals) at 4m/s for 60 sec prior to RNA extraction using the Rneasy Lipid Tissue Mini Kit (Qiagen) following manufacturer's protocol.

treatment_protocol: The biopsies were immediately snap frozen in liquid nitrogen and stored at -80°C prior to total RNA extraction.

tag: gender

value: Male

tag: age (weeks)

value: white adipose tissue


title: eMG-KO2

description: embryonic microglia Irf8KO rep2

value: Irf8 knockout


title: subcutaneous inguinal adipose tissue wild type - 6

source_name: white adipose tissue wild type (control)

value: wild type


title: eMG-KO3

description: embryonic microglia Irf8KO rep3


title: subcutaneous inguinal adipose tissue wild type - 3


title: subcutaneous inguinal adipose tissue wild type - 5


title: Liver_non_KC_Irf8ko2

description: adult liver CD11bhigh macrophages Irf8KO rep2

source_name: adult CD11bhigh macrophages

value: macrophages


title: Liver_non_KC_Irf8ko1

description: adult liver CD11bhigh macrophages Irf8KO rep1


title: subcutaneous inguinal adipose tissue wild type - 4


title: subcutaneous inguinal adipose tissue R6/2 - 5


title: subcutaneous inguinal adipose tissue wild type - 2


title: Kidney_F4_80_high_Irf8_ko2_R4

description: adult kidney F4/80high macrophages IrfKO rep2

source_name: adult F4/80high macrophages

value: kidney


title: Kidney_F4_80_high_Irf8_ko3_R4

description: adult kidney F4/80high macrophages IrfKO rep3


title: subcutaneous inguinal adipose tissue wild type - 1


title: Kidney_CD11b_high_Irf8_ko3_R3

description: adult kidney CD11bhigh macrophages Irf8KO rep3


title: subcutaneous inguinal adipose tissue R6/2 - 4


title: subcutaneous inguinal adipose tissue R6/2 - 2


title: Kidney_CD11b_high_Irf8_ko2_R3

description: adult kidney CD11bhigh macrophages Irf8KO rep2


title: Liver_KC2

description: adult Kupffer cells wildtype rep2


title: Kidney_CD11b_high_Irf8_ko1_R3

description: adult kidney CD11bhigh macrophages Irf8KO rep1


title: Kidney_F4_80_high_Irf8_ko1_R4

description: adult kidney F4/80high macrophages IrfKO rep1


title: subcutaneous inguinal adipose tissue R6/2 - 1


title: Liver_KC1

description: adult Kupffer cells wildtype rep1


title: Liver_non_KC1

description: adult liver CD11bhigh macrophages wildtype rep1


title: subcutaneous inguinal adipose tissue R6/2 - 3


title: Liver_KC3

description: adult Kupffer cells wildtype rep3


title: Liver_non_KC3

description: adult liver CD11bhigh macrophages wildtype rep3


title: Liver_non_KC2

description: adult liver CD11bhigh macrophages wildtype rep2


title: Kidney_F4-80_high3_R4

description: adult kidney F4/80high macrophages wildtype rep3


title: Kidney_F4-80_high2_R4

description: adult kidney F4/80high macrophages wildtype rep2


title: Kidney_CD11b_high3_R3

description: adult kidney CD11bhigh macrophages wildtype rep3


title: Liver, Prednisone, 7 day exposure, 9533741092H, 2.5ppm

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

description: Sample name: GRC275_56A.AVG_Signal

scan_protocol: Arrays were scanned and raw data (.idat files) were obtained using Illumina iScan software (v3.3.28)

data_processing: The data were normalized using quantile normalization with GenomeStudio.

label: Biotin

source_name: Liver, Prednisone, 7 day exposure, 2.5ppm

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

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

tag: strain

tag: Sex

tag: chemical

value: Prednisone

tag: vehicle

value: Feed

tag: dose

value: 2.5 ppm

tag: route

tag: dosing duration

value: 7 days

value: Liver


title: Liver, Prednisone, 7 day exposure, 9533741102E, 2.5ppm

description: Sample name: GRC275_9A.AVG_Signal

tag: tissue


title: Liver, Prednisone, 7 day exposure, 9533741099F, 2.5ppm

description: Sample name: GRC275_74A.AVG_Signal


title: Liver, Prednisone, 7 day exposure, 9533741095F, 2.5ppm

description: Sample name: GRC275_40A.AVG_Signal


title: Kidney_CD11b_high2_R3

description: adult kidney CD11bhigh macrophages wildtype rep2

value: adult

value: wildtype


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741099C, 1ppm

description: Sample name: GRC275_48A.AVG_Signal

source_name: Liver, Ethinyl Estradiol, 7 day exposure, 1ppm

value: Ethinyl Estradiol

value: 1 ppm


title: AM_Irf8_ko2

description: adult microglia Irf8KO rep2

source_name: adult microglia

value: brain


title: Kidney_F4-80_high1_R4

description: adult kidney F4/80high macrophages wildtype rep1


title: AM_Irf8_ko3

description: adult microglia Irf8KO rep3

value: microglia


title: AM_Irf8_ko1

description: adult microglia Irf8KO rep1


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741113C, 1ppm

description: Sample name: GRC275_6C.AVG_Signal

value: Male


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741092B, 1ppm

description: Sample name: GRC275_42A.AVG_Signal


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741095H, 1ppm

description: Sample name: GRC275_86A.AVG_Signal


title: Emb_CD11b_high_Liver_3

description: embryonic liver CD11bhigh macrophages wildtype rep1

value: liver


title: Kidney_CD11b_high1_R3

description: adult kidney CD11bhigh macrophages wildtype rep1


title: 10D_HEP

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description:
SAMPLE_11
10D_HEP

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR high 100%, XDR low 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hPSCs, heparin, 10 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human H1 hPSCs were cultured in E8 medium. Cardiomyocyte differentiation was inducted by change to differentiation media when the cells reached 70-90% confluency. Differentiation media was made from E8 basal media alone or with heparin (3ug/ml) and/or IWP2 added.

extract_protocol: RNA was extracted from cultured cells using TRIZOL reagent.

treatment_protocol: 12 RNA samples were collected from cultured hPSCs at different time points and under different culture conditions to evaluate the impact of heparin (HEP) and the WNT inhibitor IWP2 on cardiac differentiation: 1, 0D_Control (hPSCs cultured in E8 medium for < 1 day without HEP or IWP2 added); 2, 0D_HEP (hPSCs cultured in E8 medium for < 1 day with 3ug/ml HEP added); 3, 3D_Control (hPSCs differentiated via E8 basal medium for 3 days without HEP or IWP2 added); 4. 3D_HEP (hPSCs differentiated via E8 basal medium for 3 days with 3ug/ml HEP added days 1-3); 5. 6D_Control (hPSCs differentiated via E8 basal medium for 6 days without HEP or IWP2 added); 6. 6D_IWP2 (hPSCs differentiated via E8 basal medium for 6 days with IWP2 added days 3-6); 7. 6D_HEP (hPSCs differentiated via E8 basal medium for 6 days with 3ug/ml HEP added days 1-6); 8. 6D_HEP_IWP2 (hPSCs differentiated via E8 basal medium for 6 days with 3ug/ml HEP added days 1-6 and IWP2 added days 3-6); 9. 10D_Control (hPSCs differentiated via E8 basal medium for 10 days without HEP or IWP2 added; 10. 10D_IWP2 (hPSCs differentiated via E8 basal medium for 10 days with IWP2 added days 3-6); 11. 10D_HEP (hPSCs differentiated via E8 basal medium for 10 days with 3ug/ml HEP added days 1-6); 12. 10D_HEP_IWP2 (hPSCs differentiated via E8 basal medium for 10 days with 3ug/ml HEP added days 1-6 and IWP2 added days 3-6).

tag: cell line

tag: cell type

value: human pluripotent stem cells (hPSCs)

tag: differentiation conditions

tag: differentiation time

value: 10 days


title: 10D_HEP_IWP2

description:
SAMPLE_12
10D_HEP_IWP2

source_name: hPSCs, heparin + IWP2, 10 days


title: 6D_HEP

description:
SAMPLE_7
6D_HEP

source_name: hPSCs, heparin, 6 days

value: 6 days


title: 10D_Control

description:
SAMPLE_9
10D_Control

source_name: hPSCs, control, 10 days


title: ekid_R4_ko2

description: embryonic kidney F4/80high macrophages Irf8KO rep1

source_name: embryonic F4/80high macrophages

value: kidney

value: macrophages

value: Irf8 knockout


title: 10D_IWP2

description:
SAMPLE_10
10D_IWP2

source_name: hPSCs, IWP2, 10 days


title: 6D_IWP2

description:
SAMPLE_6
6D_IWP2

source_name: hPSCs, IWP2, 6 days


title: 6D_HEP_IWP2

description:
SAMPLE_8
6D_HEP_IWP2

source_name: hPSCs, heparin + IWP2, 6 days


title: A1_ko1

description: yolk sac progenitor population A1 Irf8KO rep1

source_name: yolk sac progenitor population A1

value: yolk sac

value: erythro-myeloid progenitors


title: A1_ko2

description: yolk sac progenitor population A1 Irf8KO rep2


title: Emb_CD11b_high_Liver_2

source_name: embryonic CD11bhigh macrophages


title: 6D_Control

description:
SAMPLE_5
6D_Control

source_name: hPSCs, control, 6 days


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741095C, 5ppm

description: Sample name: GRC275_71B.AVG_Signal

source_name: Liver, Ethinyl Estradiol, 7 day exposure, 5ppm

value: Feed

value: 5 ppm

value: 7 days

value: Liver


title: Emb_CD11b_high_Liver_1

value: wildtype


title: aLC_KO2

description: adult Langerhans cells Irf8KO rep2

source_name: adulte Langerhans cells

value: skin

value: adult

value: Langerhans cells


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741113D, 5ppm

description: Sample name: GRC275_43A.AVG_Signal

value: Male

value: Ethinyl Estradiol


title: Liver, Prednisone, 7 day exposure, 9533741095A, 25ppm

description: Sample name: GRC275_32B.AVG_Signal

source_name: Liver, Prednisone, 7 day exposure, 25ppm

value: Prednisone

value: 25 ppm


title: Liver, Prednisone, 7 day exposure, 9533741039E, 25ppm

description: Sample name: GRC275_85B.AVG_Signal


title: Emb_KC_2

description: embryonic Kupffer cells wildtype rep1

source_name: embryonic Kupffer cells

value: liver

value: Kupffer cells


title: 3D_HEP

description:
SAMPLE_4
3D_HEP

source_name: hPSCs, heparin, 3 days

value: human pluripotent stem cells (hPSCs)

value: 3 days


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741039G, 5ppm

description: Sample name: GRC275_37A.AVG_Signal


title: A2-1

description: yolk sac progenitor population A2 wildtype rep1

source_name: yolk sac progenitor population A2

value: yolk sac

value: erythro-myeloid progenitors


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741113H, 5ppm

description: Sample name: GRC275_59B.AVG_Signal

value: Feed

value: 5 ppm


title: Liver, Ethinyl Estradiol, 28 day exposure, 9533741098F, 10ppm

description: Sample name: GRC275_24A.AVG_Signal

source_name: Liver, Ethinyl Estradiol, 28 day exposure, 10ppm

value: 10 ppm

value: 28 days

value: Liver


title: A1-3

description: yolk sac progenitor population A1 wildtype rep3

value: wildtype


title: Emb_KC_3

description: embryonic Kupffer cells wildtype rep1


title: 11-2_A2_ko2_2

description: yolk sac progenitor population A2 Irf8KO rep2

value: Irf8 knockout


title: 3D_Control

description:
SAMPLE_3
3D_Control

source_name: hPSCs, control, 3 days


title: A2-3

description: yolk sac progenitor population A2 wildtype rep3


title: A1-2

description: yolk sac progenitor population A1 wildtype rep2


title: Emb_KC_1_2

description: embryonic Kupffer cells wildtype rep1


title: 0D_HEP

description:
SAMPLE_2
0D_HEP

source_name: hPSCs, heparin, 0 days

value: 0 days


title: Liver, Ethinyl Estradiol, 28 day exposure, 9533741099H, 10ppm

description: Sample name: GRC275_35B.AVG_Signal

value: Male

value: Ethinyl Estradiol


title: 0D_Control

description:
SAMPLE_1
0D_Control

source_name: hPSCs, control, 0 days


title: Liver, Prednisone, 7 day exposure, 9533741102A, 25ppm

description: Sample name: GRC275_2A.AVG_Signal

value: Prednisone

value: 25 ppm

value: 7 days


title: A2-2

description: yolk sac progenitor population A2 wildtype rep2


title: Liver, Ethinyl Estradiol, 28 day exposure, 9533741092G, 10ppm

description: Sample name: GRC275_50B.AVG_Signal


title: Liver, Prednisone, 7 day exposure, 9533741113A, 25ppm

description: Sample name: GRC275_2D.AVG_Signal


title: V2CD24-CD73+_REP04

city: Copenhagen

first: Terkild

middle: Brink

last: Buus

address: Blegdamsvej 3

department: ISIM

country: Denmark

institute: University of Copenhagen

description: Vgamma2+CD24-CD73+ sorted thymocytes, biological REP04

hyb_protocol: Washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450

scan_protocol: Affymetrix GeneArray® 3000 as described in the Affymetrix GeneChip® protocol; Cell intensity files (CEL files) were generated in the GeneChip® Command Console® Software

data_processing:
R-BioConductor, RMA normalized (oligo package), Batch corrected using ComBat (sva package)
MoEx-1_0-st-v1.r2.pgf
pd.moex.1.0.st.v1 (BioConductor)

source_name: Thymus, gdT, V2CD24-CD73+

label_protocol: Encore-Ovation cDNA Biotin Module (Nugene)

growth_protocol: Mouse thymus was dissected from adult mice after cervical dislocation

extract_protocol: TriReagent (Trizol)

treatment_protocol: not applicable

value: female

tag: age

value: 8 weeks

value: thymus

value: thymocytes

tag: cell population


title: Liver, Ethinyl Estradiol, 28 day exposure, 9533741039C, 10ppm

description: Sample name: GRC275_35D.AVG_Signal

value: Feed


title: A1-1

description: yolk sac progenitor population A1 wildtype rep1

value: yolk sac

tag: celltype

value: erythro-myeloid progenitors

tag: genotype


title: Liver, Androstenedione, 7 day exposure, 9533741098D, 10mg/kg/day

description: Sample name: GRC275_10B.AVG_Signal

source_name: Liver, Androstenedione, 7 day exposure, 10mg/kg/day

value: Androstenedione

value: 0.5% Carboxymethyl Cellulose

value: 10 mg/kg/day

value: Gavage


title: V2CD24+CD73+_REP04

description: Vgamma2+CD24+CD73+ sorted thymocytes, biological REP04

source_name: Thymus, gdT, V2CD24+CD73+

tag: gender


title: Liver, Androstenedione, 7 day exposure, 9533741113G, 10mg/kg/day

description: Sample name: GRC275_34A.AVG_Signal

tag: strain

value: Liver


title: V2CD24-CD73+_REP03

description: Vgamma2+CD24-CD73+ sorted thymocytes, biological REP03


title: EMP1

description: erythro-myeloid progenitors wildtype rep1

source_name: erythro-myeloid progenitors

value: E 8

value: wildtype


title: Liver_non_KC_Irf8ko3

description: adult liver CD11bhigh macrophages Irf8KO rep3

source_name: adult CD11bhigh macrophages

value: liver

value: adult

value: macrophages

value: Irf8 knockout


title: V1CD24+CD73-_REP04

description: Vgamma1.1+CD24+CD73- sorted thymocytes, biological REP04

source_name: Thymus, gdT, V1CD24+CD73-

value: female

value: 8 weeks


title: EM3

description: embryonic microglia wildtype rep3

source_name: embryonic microglia

value: brain

value: microglia


title: EMP3

description: erythro-myeloid progenitors wildtype rep3

value: yolk sac


title: AM3

description: adult microglia wildtype rep3

source_name: adult microglia


title: Liver, Androstenedione, 7 day exposure, 9533741100G, 10mg/kg/day

description: Sample name: GRC275_49A.AVG_Signal

tag: Sex

value: Male

value: 7 days


title: V1CD24-CD73+_REP04

description: Vgamma1.1+CD24-CD73+ sorted thymocytes, biological REP04

source_name: Thymus, gdT, V1CD24-CD73+

value: thymus

value: thymocytes


title: EM1

description: embryonic microglia wildtype rep1


title: EM2

description: embryonic microglia wildtype rep2


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741095G, 2.5ppm

description: Sample name: GRC275_51A.AVG_Signal

source_name: Liver, Ethinyl Estradiol, 7 day exposure, 2.5ppm

tag: chemical

value: Ethinyl Estradiol

value: Feed

value: 2.5 ppm


title: Liver, Androstenedione, 7 day exposure, 9533741099G, 10mg/kg/day

description: Sample name: GRC275_73C.AVG_Signal

value: Androstenedione

tag: vehicle

value: 0.5% Carboxymethyl Cellulose

value: 10 mg/kg/day

value: Gavage

value: Liver


title: V1CD24+CD73+_REP03

description: Vgamma1.1+CD24+CD73+ sorted thymocytes, biological REP03

source_name: Thymus, gdT, V1CD24+CD73+

value: female


title: V2CD24+CD73-_REP03

description: Vgamma2+CD24+CD73- sorted thymocytes, biological REP03

source_name: Thymus, gdT, V2CD24+CD73-

value: 8 weeks


title: V1CD24+CD73-_REP03

description: Vgamma1.1+CD24+CD73- sorted thymocytes, biological REP03


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741115A, 2.5ppm

description: Sample name: GRC275_81B.AVG_Signal

tag: dose


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741039D, 2.5ppm

description: Sample name: GRC275_22A.AVG_Signal

tag: route


title: V2CD24+CD73+_REP03

description: Vgamma2+CD24+CD73+ sorted thymocytes, biological REP03


title: V2CD24+CD73+_REP02

description: Vgamma2+CD24+CD73+ sorted thymocytes, biological REP02


title: V2CD24-CD73+_REP02

description: Vgamma2+CD24-CD73+ sorted thymocytes, biological REP02


title: V1CD24-CD73+_REP03

description: Vgamma1.1+CD24-CD73+ sorted thymocytes, biological REP03


title: Liver, Control, 28 day exposure, 9533741098E, 0 mg/kg/day

description: Sample name: GRC275_29A.AVG_Signal

source_name: Liver,Control, 28 day exposure, 0 mg/kg/day

value: 0 mg/kg/day

tag: dosing duration

value: 28 days


title: AM2

description: adult microglia wildtype rep2

tag: tissue

value: brain

value: adult

value: microglia

value: wildtype


title: EMP2_2

description: erythro-myeloid progenitors wildtype rep2

value: yolk sac

value: E 8

value: erythro-myeloid progenitors


title: AM1

description: adult microglia wildtype rep1


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741100F, 2.5ppm

description: Sample name: GRC275_15C.AVG_Signal

value: Male

value: Ethinyl Estradiol

value: Feed

value: 2.5 ppm

value: 7 days


title: Liver, Control, 28 day exposure, 9533741095E, 0 mg/kg/day

description: Sample name: GRC275_30D.AVG_Signal

source_name: Liver, Control, 28 day exposure, 0 mg/kg/day

value: 0.5% Carboxymethyl Cellulose

value: Gavage

value: Liver


title: V1CD24-CD73+_REP02

description: Vgamma1.1+CD24-CD73+ sorted thymocytes, biological REP02

value: female

value: 8 weeks

value: thymus

value: thymocytes


title: V1CD24+CD73+_REP02

description: Vgamma1.1+CD24+CD73+ sorted thymocytes, biological REP02


title: V2CD24+CD73-_REP02

description: Vgamma2+CD24+CD73- sorted thymocytes, biological REP02


title: V1CD24+CD73-_REP02

description: Vgamma1.1+CD24+CD73- sorted thymocytes, biological REP02


title: Liver, Androstenedione, 7 day exposure, 9533741092E, 2mg/kg/day

description: Sample name: GRC275_41D.AVG_Signal

source_name: Liver, Androstenedione, 7 day exposure, 2ppm

value: Androstenedione

value: 2 mg/kg/day


title: Liver, Androstenedione, 7 day exposure, 9533741102F, 2mg/kg/day

description: Sample name: GRC275_53A.AVG_Signal


title: V2CD24+CD73+_REP01

description: Vgamma2+CD24+CD73+ sorted thymocytes, biological REP01


title: V1CD24+CD73+_REP01

description: Vgamma1.1+CD24+CD73+ sorted thymocytes, biological REP01


title: Liver, Control, 28 day exposure, 9533741098G, 0ppm

description: Sample name: GRC275_67A.AVG_Signal

source_name: Liver, Control, 28 day exposure, 0ppm

value: 0  ppm

value: 28 days


title: Liver, Control, 28 day exposure, 9533741098C, 0 mg/kg/day

description: Sample name: GRC275_29D.AVG_Signal

value: 0 mg/kg/day


title: V1CD24-CD73+_REP01

description: Vgamma1.1+CD24-CD73+ sorted thymocytes, biological REP01


title: Liver, Control, 28 day exposure, 9533741102D, 0ppm

description: Sample name: GRC275_23D.AVG_Signal

value: Male


title: V1CD24+CD73-_REP01

description: Vgamma1.1+CD24+CD73- sorted thymocytes, biological REP01


title: Liver, Control, 28 day exposure, 9533741098A, 0ppm

description: Sample name: GRC275_11A.AVG_Signal


title: V2CD24+CD73-_REP01

description: Vgamma2+CD24+CD73- sorted thymocytes, biological REP01


title: Liver, Control, 28 day exposure, 9533741100B, 0ppm

description: Sample name: GRC275_11C.AVG_Signal


title: Liver, Control, 28 day exposure, 9533741100E, 0 mg/kg/day

description: Sample name: GRC275_88C.AVG_Signal


title: Liver, Androstenedione, 7 day exposure, 9533741098B, 2mg/kg/day

description: Sample name: GRC275_19A.AVG_Signal


title: Liver, Prednisone, 28 day exposure, 9533741115G, 25ppm

description: Sample name: GRC275_28D.AVG_Signal

source_name: Liver, Prednisone, 28 day exposure, 25ppm

value: Prednisone

value: 25 ppm


title: V2CD24-CD73+_REP01

description: Vgamma2+CD24-CD73+ sorted thymocytes, biological REP01

source_name: Thymus, gdT, V2CD24-CD73+


title: Liver, Androstenedione, 7 day exposure, 9533741100D, 2mg/kg/day

description: Sample name: GRC275_53D.AVG_Signal


title: Liver, Control, 28 day exposure, 9533741113E, 0ppm

description: Sample name: GRC275_11D.AVG_Signal

value: Feed


title: Liver, Prednisone, 28 day exposure, 9533741099B, 25ppm

description: Sample name: GRC275_28A.AVG_Signal


title: Liver, Prednisone, 28 day exposure, 9533741102H, 25ppm

description: Sample name: GRC275_77B.AVG_Signal


title: Liver, Prednisone, 28 day exposure, 9533741100A, 25ppm

description: Sample name: GRC275_4C.AVG_Signal


title: Human Adipose Tissue: HAT49

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: Human Adipose Tissue: HAT49 [control subject]

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4)  in R.3.0.1

source_name: control subject_HAT

label_protocol: Standard Affymetrix protocol

extract_protocol: Isolation of total RNA from human adipose tissue (HAT) was performed using the TRIzol reagent. RNA concentration was assessed in a NanoDrop-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE), and its integrity tested with a RNA 6000 Nano Assay in a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

tag: subject status

value: control subject

value: human adipose tissue (HAT)


title: Liver, Androstenedione, 28 day exposure, 9533741102C, 50 mg/kg/day

description: Sample name: GRC275_46B.AVG_Signal

source_name: Liver, Androstenedione, 28 day exposure, 50 mg/kg/day

value: 0.5% Carboxymethyl Cellulose

value: 50 mg/kg/day

value: Gavage


title: Liver, Control, 28 day exposure, 9533741039F, 0ppm

description: Sample name: GRC275_54D.AVG_Signal

value: Liver


title: Human Adipose Tissue: HAT116

description: Human Adipose Tissue: HAT116 [control subject]


title: Liver, Androstenedione, 28 day exposure, 9533741102B, 50 mg/kg/day

description: Sample name: GRC275_45A.AVG_Signal


title: Liver, Androstenedione, 28 day exposure, 9533741105H, 50 mg/kg/day

description: Sample name: GRC275_1A.AVG_Signal


title: Liver, Androstenedione, 28 day exposure, 9533741092F, 50 mg/kg/day

description: Sample name: GRC275_45D.AVG_Signal


title: Human Adipose Tissue: HAT44

description: Human Adipose Tissue: HAT44 [control subject]


title: Human Adipose Tissue: HATCT

description: Human Adipose Tissue: HATCT_pool [control subject]

source_name: control subject_HATCT_pool


title: Human Adipose Tissue: HAT69

description: Human Adipose Tissue: HAT69 [morbid obesity]

source_name: morbid obesity_HAT

value: morbid obesity


title: Liver, Androstenedione, 7 day exposure, 9533741115C, 20/mg/kg/day

description: Sample name: GRC275_33D.AVG_Signal

source_name: Liver, Androstenedione, 7 day exposure, 20/mg/kg/day

value: 20 mg/kg/day

value: 7 days


title: Human Adipose Tissue: HAT52

description: Human Adipose Tissue: HAT52 [morbid obesity]


title: Liver, Androstenedione, 7 day exposure, 9533741102G, 20/mg/kg/day

description: Sample name: GRC275_5A.AVG_Signal

value: Androstenedione


title: Liver, Androstenedione, 7 day exposure, 9533741105G, 20/mg/kg/day

description: Sample name: GRC275_60B.AVG_Signal


title: Liver, Control, 7 day exposure, 9533741105F, 0mg/kg/day

description: Sample name: GRC275_36C.AVG_Signal

source_name: Liver, Control, 7 day exposure, 0mg/kg/day


title: topi mutant testis sample, replicate 1

city: Zurich

first: Christian

middle: F.

last: Lehner

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

description: Gene expression in topi mutant testis

hyb_protocol: After fragmentation, 1.65 microgram of cRNA were mixed with 2.2 microL of 25x hybridization buffer and 11 microL of 10x Blocking Agent (provided by Low input RNA amplification kit) before adjsuting the final volume to 55 microL with RNase-free water. Hybridization was performed during 17 hours at 65°C in a rotating oven (10 rpm).

scan_protocol: After washing, slides were scanned with a Agilent Technologies Scanner G2505C US22502661. Cy3 signals were recorded using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software and R

organism: Drosophila melanogaster

source_name: topi mutant testis sample, replicate 1

label_protocol: Cy3-labeled cRNA probes were generated using the Low RNA Input Linear Amplification kit (Agilent Technologies, Santa Clara, CA 95051, USA). cRNA was purified using the Absolutely RNA Nanoprep Kit (Agilent Technologies). NanoDrop 2000 spectrophotometer (Thermo Scientific) was used for probe quantification and 2100 Bioanalyzer (Agilent Technologies) for quality control.

growth_protocol: Crosses for the generation of males with the desired genotypes were completed on standard Drosophila food at 25°C

extract_protocol: Total RNA was extracted using Trizol

treatment_protocol: Testes were dissected from young adult males (0-2 days after eclosion) in testis buffer (183 mM KCl, 47 mM NaCl, 10 mM Tris-HCl, pH 6.8). After dissection of twenty testes, these were transferred into 5 µl ice-cold testis buffer, snap frozen in liquid nitrogen and stored at -80°C. Eighty testes per genotype were pooled for extraction of a sample of total RNA.

value: testis


title: aly mutant testis sample, replicate 2

description: Gene expression in aly mutant testis

source_name: aly mutant testis sample, replicate 2

value: w*/Y; aly[2] red e/aly[5] red e


title: Human Adipose Tissue: HAT125

description: Human Adipose Tissue: HAT125 [morbid obesity]


title: Liver, Control, 7 day exposure, 9533741100H, 0mg/kg/day

description: Sample name: GRC275_58B.AVG_Signal

value: 0 mg/kg/day


title: Liver, Prednisone, 7 day exposure, 9533741099D, 5ppm

description: Sample name: GRC275_47A.AVG_Signal

source_name: Liver, Prednisone, 7 day exposure, 5ppm

value: Male

value: 5 ppm


title: sa mutant testis sample, replicate 1

description: Gene expression in sa mutant testis

source_name: sa mutant testis sample, replicate 1

value: +/Y;th sa[1] red/ru h sa[2] ca


title: aly mutant testis sample, replicate 1

description: Gene expression in aly mutant testis

source_name: aly mutant testis sample, replicate 1


title: Human Adipose Tissue: HAT105

description: Human Adipose Tissue: HAT105 [morbid obesity]


title: Liver, Prednisone, 7 day exposure, 9533741105E, 5ppm

description: Sample name: GRC275_79C.AVG_Signal

value: Prednisone

value: Feed


title: Liver, Androstenedione, 7 day exposure, 9533741113B, 20/mg/kg/day

description: Sample name: GRC275_66B.AVG_Signal


title: Liver, Prednisone, 7 day exposure, 9533741039A, 5ppm

description: Sample name: GRC275_31B.AVG_Signal


title: Liver, Control, 7 day exposure, 9533741099A, 0ppm

description: Sample name: GRC275_82D.AVG_Signal

source_name: Liver, Control, 7 day exposure, 0ppm

value: 0 ppm


title: Liver, Control, 7 day exposure, 9533741098H, 0ppm

description: Sample name: GRC275_8C.AVG_Signal


title: Liver, Control, 7 day exposure, 9533741115E, 0mg/kg/day

description: Sample name: GRC275_78A.AVG_Signal

value: 0.5% Carboxymethyl Cellulose


title: topi mutant testis sample, replicate 2

description: Gene expression in topi mutant testis

source_name: topi mutant testis sample, replicate 2


title: sa mutant testis sample, replicate 2

description: Gene expression in sa mutant testis

source_name: sa mutant testis sample, replicate 2


title: Control testis sample, replicate 4

description: Gene expression in control testis

source_name: Control testis sample, replicate 3


title: Liver, Prednisone, 7 day exposure, 9533741092A, 5ppm

description: Sample name: GRC275_7A.AVG_Signal


title: dany mutant testis sample, replicate 2

description: Gene expression in dany mutant testis

source_name: dany mutant testis sample, replicate 2


title: Liver, Control, 7 day exposure, 9533741115H, 0mg/kg/day

description: Sample name: GRC275_13C.AVG_Signal


title: Liver, Control, 7 day exposure, 9533741039B, 0ppm

description: Sample name: GRC275_21A.AVG_Signal


title: Liver, Control, 7 day exposure, 9533741113F, 0ppm

description: Sample name: GRC275_23C.AVG_Signal


title: Control testis sample, replicate 3

description: Gene expression in control testis


title: dany mutant testis sample, replicate 1

description: Gene expression in dany mutant testis

source_name: dany mutant testis sample, replicate 1


title: Liver, Control, 7 day exposure, 9533741100C, 0ppm

description: Sample name: GRC275_8A.AVG_Signal


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741115B, 10ppm

description: Sample name: GRC275_12B.AVG_Signal

source_name: Liver, Ethinyl Estradiol, 7 day exposure, 10ppm

value: Ethinyl Estradiol

value: 10 ppm


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741115D, 10ppm

description: Sample name: GRC275_16A.AVG_Signal

value: Liver


title: Liver, Control, 7 day exposure, 9533741105D, 0ppm

description: Sample name: GRC275_90C.AVG_Signal


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741105C, 10ppm

description: Sample name: GRC275_62B.AVG_Signal


title: Liver, Androstenedione, 7 day exposure, 9533741099E, 50mg/kg/day

description: Sample name: GRC275_25A.AVG_Signal

source_name: Liver, Androstenedione, 7 day exposure, 50mg/kg/day

value: 50 mg/kg/day

value: Gavage


title: Control testis sample, replicate 2

description: Gene expression in control testis

source_name: Control testis sample, replicate 2


title: Liver, Ethinyl Estradiol, 7 day exposure, 9533741039H, 10ppm

description: Sample name: GRC275_76A.AVG_Signal

value: 7 days


title: AftPol_1

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Oryza sativa

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

growth_protocol: All seven tissues in this study were prepared from Oryza sativa L. cv. Dongjin.

extract_protocol: Total RNAs were extracted using TriReagent (Molecular Research Center, Inc.).

treatment_protocol: The calli were induced from seeds on 2N6 medium at 37°C for 4 weeks. The regenerating calli were induced from calli for 2 weeks on a MS16 medium and collected when turned green. The seeds were germinated on water-soaked filter paper for 4 days in a dark chamber. Leaves and roots were harvested separately 14 days after sowing in soil. A flower sample was harvested at exact stages following recommendations from previous research. The flowers before pollination were prepared just prior to the opening of the spikelet, and the flowers after pollination were collected followed by anthesis, respectively. The flower before pollination (FBP) was collected prior to the opening of the spikelet, and its pistil length was in the range of 0.5 to 1.5 mm. The flower after pollination (FAP) was collected after the anthesis and maximum opening of the florets.

tag: self-fertile and virulent on host plants

value: Oryza sativa L. cv. Dongjin

tag: cultivar


title: BefPol_2

description: The flower before pollination (FBP) was collected prior to the opening of the spikelet, and its pistil length was in the range of 0.5 to 1.5 mm.


title: Root_1

description: Roots were harvested separately 14 days after sowing in soil.

source_name: Root at 14 days


title: BefPol_1

source_name: The flower before pollination (FBP) was collected prior to the opening of the spikelet, and its pistil length was in the range of 0.5 to 1.5 mm.


title: Liver, Androstenedione, 7 day exposure, 9533741095D, 50mg/kg/day

description: Sample name: GRC275_69A.AVG_Signal

value: Androstenedione


title: Leaf_1

description: Leaves and roots were harvested separately 14 days after sowing in soil.

source_name: Leaf at 14 days


title: Liver, Androstenedione, 7 day exposure, 9533741105B, 50mg/kg/day

description: Sample name: GRC275_38A.AVG_Signal


title: Liver, Prednisone, 7 day exposure, 9533741115F,  1.25ppm

description: Sample name: GRC275_89B.AVG_Signal

source_name: Liver, Prednisone, 7 day exposure, 1.25ppm


title: Liver, Androstenedione, 7 day exposure, 9533741095B, 50mg/kg/day

description: Sample name: GRC275_70A.AVG_Signal


title: GermSeed_2

description: The seeds were germinated on water-soaked filter paper for 4 days in a dark chamber. Leaves and roots were harvested separately 14 days after sowing in soil.


title: Root_2


title: GermSeed_1

source_name: The seeds were germinated on water-soaked filter paper for 4 days in a dark chamber. Leaves and roots were harvested separately 14 days after sowing in soil.


title: RegCal_2

description: The regenerating calli were induced from calli for 2 weeks on a MS16 medium and collected when turned green.


title: AftPol_2

description: The flower after pollination (FAP) was collected after the anthesis and maximum opening of the florets.


title: Liver, Prednisone, 7 day exposure, 9533741092C,  1.25ppm

description: Sample name: GRC275_44C.AVG_Signal


title: Leaf_2


title: Control testis sample, replicate 1

description: Gene expression in control testis

source_name: Control testis sample, replicate 1

value: testis


title: RegCal_1

source_name: The regenerating calli were induced from calli for 2 weeks on a MS16 medium and collected when turned green.


title: Liver, Prednisone, 7 day exposure, 9533741092D,  1.25ppm

description: Sample name: GRC275_3A.AVG_Signal


title: KSHV-infected TCCSUP

type: protein

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

institute: Eulji University School of Medicine

hyb_protocol: Biotin-labeled extract was hybridized with antibody-spotted slide for 2hr at room temperature. After hybridization, slide was washed with 1X wash buffer (Full Moon Bio) and de-ionized water. Detection Buffer including Cy3-Streptavidin (Full Moon Bio) was treated for 20min at room temperature. Slide was washed with 1X wash buffer (Full Moon Bio) and de-ionized water.

scan_protocol: Scanned on an Axon 4000B scanner.

data_processing: GenePix Software (v 6.1) was used for data extraction and Genowiz software (v 4.0.5.6) was used for beta-actin normalization.

molecule: protein

source_name: KSHV-infected TCCSUP

label_protocol: 50ug of Tissue extract was labeled with Biotin and label buffer (Full Moon Bio).

growth_protocol: Both cells were cultured in EMEM with 10% FBS and 1% streptomycin/Penicillin under 5% CO2 and 37C incubator.

extract_protocol: 10~40mg of tissues were washed with cold 1X PBS. Tissue samples were homogenized with Extracting buffer (Full Moon Bio). Debris was removed from tissue extract with centrifuge.

treatment_protocol: Cells were cultured in T75 cell culture flask until confluency was about 80%. Then, protein lysates were collected by extracting buffer.

tag: cell line

value: TCCSUP

tag: cell type

value: bladder cancer cell line

tag: virus

value: KSHV infected


title: Uninfected TCCSUP

source_name: Uninfected TCCSUP

value: uninfected


title: Callus_1

description: The calli were induced from seeds on 2N6 medium at 37°C for 4 weeks.


title: Callus_2

source_name: The calli were induced from seeds on 2N6 medium at 37°C for 4 weeks.


title: MCRC_YidX

status: Public on Jul 27 2016

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

description: Gene expression data from human peripheral blood antigen-specific CD4+T cells from healthy control

data_processing: The data were analyzed with Bioconductor tools in R (version 2.15.0; http://www.r-project.org) using GC-RMA as normalization method. Next we employ a probe-filtering step, excluding those probes that showed a lower coefficient of variation or which were non-informative (not annotated).

source_name: Human peripheral blood CD4+ T cells from healthy control

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

growth_protocol: Antigen-specific CD4+T cells were expanded from CFSE-labelled peripheral blood mononuclear cells (PBMCs), by culturing them in the presence of protein antigen and recombinant IL-2 (for the last 7 days) for 2 weeks. Proliferating cells (CFSE-, CD4+, viable) cells were isolated by FACS sorting, and set in culture for a second round of antigen-specific stimulation in the presence of autologous PBMCs for 10 days. After that time, cells were harvested, washed and resuspended in Trizol for RNA extraction.

extract_protocol: Total RNA was extracted by Rneasy Kit (Qiagen) according to the manufacturer's instructions.

tag: patient

value: MCRC

tag: diagnosis

value: Healthy

tag: antigen

value: YidX

value: female

tag: age (years)

tag: cd evolution time (years)

tag: disease activity


title: ECG_FlaX

value: ECG

value: FlaX

tag: gender


title: MCRC_FlaX


title: Liver, Prednisone, 7 day exposure, 9533741105A, 1.25ppm

description: Sample name: GRC275_52A.AVG_Signal

tag: strain

tag: Sex

value: Male

tag: chemical

value: Prednisone

tag: vehicle

value: Feed

tag: dose

value: Liver


title: LPS_YidX

value: LPS

value: male


title: MMC_YidX

description: Gene expression data from human peripheral blood antigen-specific CD4+T cells from CD patient

source_name: Human peripheral blood CD4+ T cells from CD patient

value: MMC

value: Crohn's Disease (CD)

value: inactive


title: MFF_Fla2

value: MFF

value: active


title: IGC_Fla2

value: IGC


title: AJM_Fla2

value: AJM

value: Healthy


title: ECG_YidX

value: YidX

value: female


title: AMLP_YidX

value: AMLP


title: MMC_FlaX

value: FlaX


title: LPS_FlaX


title: IGC_FlaX


title: IGC_YidX


title: AJM_FlaX


title: LMAB_FlaX

value: LMAB


title: AMLP_Fla2


title: AMLP_FlaX


title: B2(G25R/G25R);P53(Ko/+);P2(Ko/+)-4

type: genomic

city: Frederick

first: Shyam

last: Sharan

address: 1050 Boyles St. Blg 560

department: Mouse Cancer Genetics Program

institute: National Cancer Institute

description:
Mouse tumor DNA vs mouse genomic DNA
LE294

hyb_protocol: 3ug of labeled sample and reference DNA were used for hybridization (at 67C for 40 hour at 20rpm) with Agilent HiRPM hyb buffer. Array wash was done with Agilent protocol and wash buffers.

scan_protocol: Scan was done with Agilent scanner model G2539A.

data_processing: Agilent Feature Extraction 10.7 was uses to extract data from images and data analysis

molecule: genomic DNA

source_name: Mouse  Heterogenous Tumor

label_protocol: 500ng of genomic DNA were used for sample labeling with Enzo CGH kit 42671-10

extract_protocol: DNA Isolated by Qiagen Dneasy Blood and Tissue Kit

treatment_protocol: Frozen Tumor Samples

value: C57Bl6 and 129/SvEv mixed

tag: genotype

value: Male

tag: tumor type

value: NOS Sarcoma

source_name: Mouse Tail DNA

value: Female

value: wildtype


title: dany mutant testis sample, replicate 3

description: Gene expression in dany mutant testis

source_name: dany mutant testis sample, replicate 3

tag: tissue

value: testis


title: B2(G25R/Ko);P53(Ko/+)-3

description:
Mouse tumor DNA vs mouse genomic DNA
PK328

value: Osteosarcoma


title: B2(G25R/G25R);P53(Ko/+);P2(Ko/+)-1

description:
Mouse tumor DNA vs mouse genomic DNA
LE93


title: B2(G25R/G25R);P53(Ko/+);P2(Ko/+)-2

description:
Mouse tumor DNA vs mouse genomic DNA
LE246


title: B2(G25R/G25R);P53(Ko/+)-2

description:
Mouse tumor DNA vs mouse genomic DNA
PK237

value: Lymphoma


title: B2(G25R/G25R);P53(Ko/+)-4

description:
Mouse tumor DNA vs mouse genomic DNA
PK298

value: Lymphoma/Histiocytic Sarcoma


title: CD8a- spDC

city: Shanghai

first: Zhenhong

last: Guo

address: 800 Xiangyin Road

department: Department of Immunology

country: China

institute: Second Milirary Medical University

description: Gene expression data from splenic CD8α- dendritic cells

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

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

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

source_name: Mouse splenic CD8α- dendritic cell

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

growth_protocol: Spleens from C57BL/6J mice were cutted into pieces and digested with Collagenase IV and Dnase.Then mononuclear cell were seperated using density gradient centrifugation with 70% and 30% Percoll(GE Healthcare, Piscataway, NJ, US).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Splenic cell suspension from 30 mice was pooled together, CD3+, B220+, Ter119+ and DX5+ cell were depleted using MACS (Miltenyi Biotec, Bergisch Gladbach, Germany ),  CD11c+ CD8α+ dendritic cellls， or CD11c+ CD8α- DCs were sorted by MoFlo XDP (DakoCytomation, Glostrup, Denmark).

value: Spleen

tag: age

value: 6 week

tag: phenotype

value: CD11c+, CD8α-


title: B2(G25R/Ko);P53(Ko/+)-2

description:
Mouse tumor DNA vs mouse genomic DNA
PK342


title: B2(G25R/G25R);P53(Ko/+);P2(Ko/+)-3

description:
Mouse tumor DNA vs mouse genomic DNA
LE225


title: B2(G25R/Ko);P53(Ko/+)-4

description:
Mouse tumor DNA vs mouse genomic DNA
PK349


title: B2(G25R/+);P53(Ko/+)-4

description:
Mouse tumor DNA vs mouse genomic DNA
PK132


title: CD8a+ spDC

description: Gene expression data from splenic CD8α+ dendritic cells

source_name: Mouse splenic CD8α+ dendritic cell

value: CD11c+, CD8α+


title: B2(G25R/+);P53(Ko/+)-3

description:
Mouse tumor DNA vs mouse genomic DNA
Y101


title: SAL-3068

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description:
8381645025_G.AVG_Signal
Illumina Human HT-12 BeadArray

hyb_protocol: Standard Illumina hybridization protocol for NuGEN target (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing:
Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.  One DBS sample failed amplification and was deleted from the data set (along with corresponding PBMC and saliva samples).
GA_RNAC_Matrix_Raw.txt (linked as a supplementary file on the Series record) has fewer rows than its referenced Platform.  The row-count discrepancy stems from the fact that we did not ask Illumina GenomeStudio software to impute values for probes that were not present on one or more array due to stochastic variations in array synthesis (see Illumina Inc. (2011) Imputing Human HT-12 Expression BeadChip Data. http://res.illumina.com/documents/products/technotes/technote_humanht_12_imputation.pdf)

source_name: Saliva

label_protocol: NuGEN PicoSL target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted using standard QIAgen RNEasy reagents on a QIACube instrument.

tag: individual

tag: biosource

value: SAL

tag: male

tag: race/ethnicity

value: Caucasian

tag: bmi


title: B2(G25R/+);P53(Ko/+)-2

description:
Mouse tumor DNA vs mouse genomic DNA
PK276


title: B2(G25R/G25R);P53(Ko/+)-3

description:
Mouse tumor DNA vs mouse genomic DNA
LE346


title: B2(G25R/Ko);P53(Ko/+)-1

description:
Mouse tumor DNA vs mouse genomic DNA
PK299


title: SAL-3067

description:
8381645025_F.AVG_Signal
Illumina Human HT-12 BeadArray

value: Asian


title: SAL-3066

description:
8381645025_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3065

description:
8381645025_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3070

description:
8381645025_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3069

description:
8381645025_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3062

description:
8381645025_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3064

description:
8381645025_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: B2(G25R/+);P53(Ko/+)-1

description:
Mouse tumor DNA vs mouse genomic DNA
PK275


title: SAL-3060

description:
8381653032_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: B2(G25R/G25R);P53(Ko/+)-1

description:
Mouse tumor DNA vs mouse genomic DNA
Y192


title: SAL-3058

description:
8381653032_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3038

description:
8123460041_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3048

description:
8381653032_C.AVG_Signal
Illumina Human HT-12 BeadArray

value: missing


title: SAL-3051

description:
8381653032_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3037

description:
8123460041_H.AVG_Signal
Illumina Human HT-12 BeadArray

value: AfricanAmerican


title: SAL-3049

description:
8381653032_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3046

description:
8381653032_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3044

description:
8123460041_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3050

description:
8381653032_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3061

description:
8381645025_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3045

description:
8381653032_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3031

description:
8123460041_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3043

description:
8123460041_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3055

description:
8381653032_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3032

description:
8123460041_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3028

description:
8123460035_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3036

description:
8123460041_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3034

description:
8123460041_E.AVG_Signal
Illumina Human HT-12 BeadArray

value: Hispanic


title: SAL-3027

description:
8123460035_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3033

description:
8123460041_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3053

description:
8381653032_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3035

description:
8123460041_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3029

description:
8123460035_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: RefDNA-003

city: Essen

first: Klaus

middle: Georg

last: Griewank

address: Hufelandstr. 55

department: Dermatology

institute: University of Duisburg-Essen

description:
CytoScanHD-Array
Germline DNA of Ma-Mel-86 cell lines.

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions.

scan_protocol: According to manufacturer's instructions.

data_processing:
The array image was acquired using Affymetrix® Chromosome Analysis Suite (ChAS) Software.
Primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

From *.cyhd.cychp file:
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 1.16.0
affymetrix-array-type = CytoScanHD_Array
affymetrix-algorithm-param-ArraySet = CytoScanHD_Array
program-name = apt-copynumber-cyto.exe
program-version = 1.16.0
program-company = Affymetrix
affymetrix-algorithm-param-option-meta-data-info-1 = program-name=Chromosome Analysis Suite
affymetrix-algorithm-param-option-meta-data-info-2 = program-version=2.1.0
affymetrix-algorithm-param-option-cdf-file = CytoScanHD_Array.cdf
affymetrix-algorithm-param-array-type = CytoScanHD_Array
affymetrix-algorithm-param-dbsnp-date = 2011-11-03
affymetrix-algorithm-param-dbsnp-version = 135
affymetrix-algorithm-param-genome-species = Homo sapiens
affymetrix-algorithm-param-genome-version = hg19
affymetrix-algorithm-param-genome-version-ucsc = hg19
affymetrix-algorithm-param-genome-version-ncbi = 37
affymetrix-algorithm-param-genome-version-create-date = 2009-02
affymetrix-algorithm-param-genome-version-ensembl-url-parameter = GRCh37
affymetrix-algorithm-param-netaffx-annotation-date = 2011-11-03
affymetrix-algorithm-param-netaffx-build = 33

source_name: Germline DNA of melanoma patient

label_protocol: DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer's instructions.

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from cell lines and peripheral blood cells using the Qiagen DNA Blood Mini Kit. DNA quality and quantity were assessed using a NanoDrop Spectrophotometer and PicoGreen.

tag: cell type

value: peripheral blood cells

tag: patient id


title: SAL-3030

description:
8123460041_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3039

description:
8123460041_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3025

description:
8123460035_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3017

description:
8123460035_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3059

description:
8381653032_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3021

description:
8123460035_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3012

description:
8123460051_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3014

description:
8123460051_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3015

description:
8123460051_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3024

description:
8123460035_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3018

description:
8123460035_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3020

description:
8123460035_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3022

description:
8123460035_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3016

description:
8123460051_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3009

description:
8123460051_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3010

description:
8123460051_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3008

description:
8123460051_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3007

description:
8123460051_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3023

description:
8123460035_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: Ma-Mel-86b

description: CytoScanHD-Array

source_name: Ma-Mel-86b, cell line from LN metastasis of melanoma patient

value: melanoma cell line from lymph node (LN) metastasis


title: SAL-3013

description:
8123460051_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3006

description:
8123460051_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3019

description:
8123460035_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3011

description:
8123460051_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: Ma-Mel-86f

description: CytoScanHD-Array

source_name: Ma-Mel-86f, cell line from LN metastasis of melanoma patient


title: SAL-3001

description:
8123460046_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: Ma-Mel-86c

description: CytoScanHD-Array

source_name: Ma-Mel-86c, cell line from LN metastasis of melanoma patient


title: Ma-Mel-86a

description: CytoScanHD-Array

source_name: Ma-Mel-86a, cell line from LN metastasis of melanoma patient


title: SAL-3003

description:
8123460046_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3066

description:
8381645035_H.AVG_Signal
Illumina Human HT-12 BeadArray

source_name: Whole blood

value: DBS


title: DBS-3069

description:
8381645035_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3064

description:
8381645035_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3061

description:
8381645059_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3070

description:
8381645035_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3067

description:
8381645035_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3051

description:
8381645059_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: SAL-3005

description:
8123460051_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3045

description:
8381645045_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3065

description:
8381645035_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3050

description:
8381645059_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3059

description:
8381645059_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3068

description:
8381645035_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3053

description:
8381645059_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3062

description:
8381645035_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3060

description:
8381645059_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3055

description:
8381645059_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3039

description:
8381645045_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3049

description:
8381645059_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3037

description:
8381645045_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3048

description:
8381645059_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3035

description:
8381645045_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3044

description:
8381645045_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3046

description:
8381645059_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3033

description:
8381645045_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3030

description:
8381645053_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3029

description:
8381645053_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3036

description:
8381645045_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3038

description:
8381645045_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3025

description:
8381645053_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3043

description:
8381645045_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3058

description:
8381645059_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3022

description:
8381645053_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3023

description:
8381645053_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3027

description:
8381645053_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3031

description:
8381645045_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3017

description:
8381645050_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3019

description:
8381645053_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3032

description:
8381645045_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3021

description:
8381645053_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3028

description:
8381645053_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3018

description:
8381645053_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3034

description:
8381645045_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3020

description:
8381645053_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3016

description:
8381645050_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3024

description:
8381645053_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3007

description:
8381645050_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3015

description:
8381645050_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3014

description:
8381645050_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3012

description:
8381645050_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3065

description:
8123460094_F.AVG_Signal
Illumina Human HT-12 BeadArray

value: PBMC


title: DBS-3006

description:
8381645050_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3060

description:
8123460094_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3010

description:
8381645050_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3055

description:
8123460089_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3005

description:
8381645025_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3001

description:
8381645025_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3011

description:
8381645050_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3070

description:
8123460094_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3013

description:
8381645050_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3067

description:
8123460094_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3068

description:
8123460094_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3061

description:
8123460094_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3069

description:
8123460094_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3009

description:
8381645050_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3008

description:
8381645050_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: DBS-3003

description:
8381645025_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3062

description:
8123460094_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3048

description:
8123460089_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3049

description:
8123460089_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3066

description:
8123460094_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3058

description:
8123460089_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3064

description:
8123460094_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3059

description:
8123460094_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3050

description:
8123460089_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3029

description:
8123460077_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3032

description:
8123460077_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3051

description:
8123460089_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3045

description:
8123460089_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3035

description:
8123460077_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3043

description:
8123460089_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3037

description:
8123460077_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3053

description:
8123460089_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3030

description:
8123460077_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3039

description:
8123460077_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3044

description:
8123460089_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3034

description:
8123460077_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3031

description:
8123460077_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3038

description:
8123460077_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3033

description:
8123460077_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3046

description:
8123460089_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3025

description:
8133182084_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3024

description:
8133182084_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3021

description:
8133182084_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3020

description:
8133182084_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3036

description:
8123460077_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3028

description:
8123460077_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3027

description:
8133182084_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3017

description:
8133182084_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3023

description:
8133182084_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3022

description:
8133182084_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3016

description:
8133182084_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3019

description:
8133182084_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3018

description:
8133182084_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3012

description:
8133182101_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3005

description:
8133182101_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3001

description:
8133182101_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3008

description:
8133182101_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3014

description:
8133182101_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3013

description:
8133182101_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3007

description:
8133182101_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3009

description:
8133182101_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3015

description:
8133182084_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3010

description:
8133182101_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: PBMC-3011

description:
8133182101_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-283

description:
9443362035_E.AVG_Signal
Illumina Human HT-12 BeadArray

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

source_name: Whole blood (PAXgene RNA)

extract_protocol: Total RNA was extracted from primary peripheral blood samples (DBS) using Qiagen RNEasy reagents.

tag: childsoldier

tag: female

tag: ethnicminority

tag: castelow

tag: educationlevel

tag: pts

tag: resilience

value: whole blood


title: NEPAL-DBS-280

description:
9443362035_B.AVG_Signal
Illumina Human HT-12 BeadArray

tag: tissue


title: PBMC-3003

description:
8133182101_B.AVG_Signal
Illumina Human HT-12 BeadArray

tag: age


title: PBMC-3006

description:
8133182101_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-284

description:
9443362035_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-270

description:
9443362110_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-277

description:
9443362110_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-281

description:
9443362035_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-273

description:
9443362110_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-279

description:
9443362035_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-276

description:
9443362110_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-282

description:
9443362035_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-274

description:
9443362110_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-269

description:
9443362110_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-272

description:
9443362110_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-271

description:
9443362110_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-278

description:
9443362110_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-275

description:
9443362110_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-268

description:
9443362110_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-254

description:
9444048004_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-248

description:
9444048004_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-240

description:
9443362108_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-251

description:
9444048004_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-243

description:
9444048004_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-244

description:
9444048004_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-245

description:
9444048004_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-263

description:
9444048013_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-246

description:
9444048004_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-253

description:
9444048004_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-247

description:
9444048004_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-252

description:
9444048004_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-260

description:
9444048013_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-265

description:
9444048013_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-257

description:
9444048013_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-256

description:
9444048013_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-259

description:
9444048013_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-249

description:
9444048004_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-238

description:
9443362108_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-258

description:
9444048013_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-242

description:
9443362108_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-250

description:
9444048004_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-239

description:
9443362108_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-255

description:
9444048013_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-267

description:
9443362110_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-264

description:
9444048013_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-262

description:
9444048013_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-266

description:
9444048013_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-261

description:
9444048013_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-241

description:
9443362108_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-233

description:
9443362108_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-228

description:
9443362069_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-231

description:
9443362108_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-216

description:
9443362062_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-215

description:
9443362062_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-237

description:
9443362108_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-229

description:
9443362069_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-226

description:
9443362069_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-222

description:
9443362069_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-235

description:
9443362108_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-234

description:
9443362108_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-223

description:
9443362069_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-218

description:
9443362062_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-230

description:
9443362069_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-225

description:
9443362069_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-217

description:
9443362062_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-210

description:
9443362062_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-219

description:
9443362069_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-206

description:
9422487045_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-208

description:
9443362062_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-214

description:
9443362062_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-220

description:
9443362069_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-232

description:
9443362108_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-236

description:
9443362108_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-227

description:
9443362069_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-209

description:
9443362062_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-213

description:
9443362062_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-211

description:
9443362062_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-224

description:
9443362069_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-207

description:
9443362062_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-205

description:
9422487045_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-202

description:
9422487045_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-203

description:
9422487045_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-200

description:
9422487045_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-179

description:
9408455003_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-197

description:
9422487045_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-191

description:
9422487018_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-201

description:
9422487045_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-186

description:
9422487018_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-198

description:
9422487045_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-184

description:
9422487018_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-175

description:
9408455003_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-199

description:
9422487045_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-178

description:
9408455003_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-185

description:
9422487018_C.AVG_Signal
Illumina Human HT-12 BeadArray