title: N202 cells adapted to lung, passage 4

description:
H2B-GFP
Gene expression data from N202 cells adapted to lung, passage 4

source_name: N202 cells adapted to lung tissue for 84 days, sorted, and expanded in cell culture.

value: lung


title: B2-NAÏVE-5

status: Public on Jul 14 2014

type: RNA

city: Stanford

first: Robin

last: White

state: CA

address: Grant Building S272, 300 Pasteur Drive

department: Anesthesia

country: USA

institute: Stanford University

hyb_protocol: Standard hybridization for Affymetrix 430_2 arrays was used.

scan_protocol: The Affymetrix GeneChip Scanner 3000 7G was used for scanning. Raw image files were processed using Affymetrix GCOS software.

data_processing: The Significance Analysis of Microarrays (SAM) method was used to determine genes that were significantly expressed between treatments. For SAM analysis, initial chip processing and signal calling was done with R and Bioconductor. The RMA background correction method, quantile normalization and the median polish probeset summary method were employed.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Naive hemisphere, β2KO, 24H

label_protocol: The Affymetrix IVT labeling kit was used according to the manufacturer's protocol.

extract_protocol: Mice were deeply anesthetized with isofluorane and sacrificed. Brains were rapidly removed, divided into hemispheres and RNA was extracted from the ischemic hemisphere or for sham animals the ipsilateral hemisphere using the Qiagen RNeasy Midi Kit.

tag: strain/background

value: FVB

tag: genotype

value: beta2 adrenergic receptor knockout

tag: gender

value: male

tag: tissue

value: naive brain hemisphere


city: San Diego

first: John

last: Welsh

state: California

address: 3030 Bunker Hill Street

institute: Vaccine Research Institute of San Diego

description:
H2B-GFP
Gene expression data from N202 cells adapted to bone marrow, passage 4

hyb_protocol: Arrays were hybridized using the an Affymetrix Genechip hybridization station, and manufacturer's recommended solutions and protocols.

scan_protocol: Chips were scanned using an Affymetrix Genechip Scanner 3000

data_processing: Robust Multiarray Averaging was used according to Laurent Gautier, Leslie Cope, Benjamin M. Bolstad and Rafael A. Irizarry in  affy—analysis of Affymetrix GeneChip data at the probe level (2004) Bioinformatics vol. 20(3), 307-315.

source_name: N202 cells adapted to bone marrow for 84 days, sorted, and expanded in cell culture.

label_protocol: Target was labeled using the Ambion WT expression kit and the Affymetrix WT Terminal and Labeling Control kit according to manufacturer's instructions.

growth_protocol: N202 cells were grown on revascularized, minced brain, bone marrow, or lung tissue in a dorsal skinfold chamber for 21 days for each passage, for up to 4 passages, with intervening growth in cell culture.

extract_protocol: RNA was purified using the Rneasy kit from Qiagen.

treatment_protocol: Between passages, cells were subjected to G418 selection, and before RNA extraction cells containing GFP fluorescence were purified by flow cytometry and placed back into cell culture to increase material for array analysis.

tag: cell line

value: Mouse breast tumor-derived N202

tag: passage

tag: co-implanted tissue

value: bone marrow


description:
H2B-GFP
Gene expression data from N202 cells adapted to breast tissue, passage 1

source_name: N202 cells adapted to breast tissue for 21 days, sorted, and expanded in cell culture.

value: breast


title: FVB-NAÏVE-7

source_name: Naive hemisphere, WT, 24H

value: wild-type


description:
H2B-GFP
Gene expression data from N202 cells adapted to brain, biological replicate, passage 2

source_name: N202 cells adapted to brain tissue for 42 days, sorted, and expanded in cell culture.

value: brain, biological replicate


description:
H2B-GFP
Gene expression data from N202 cells adapted to brain, technical replicate, passage 4

source_name: N202 cells adapted to brain tissue for 84 days, sorted, and expanded in cell culture.

value: brain, technical replicate


title: N202 cells adapted to lung, passage 1

description:
H2B-GFP
Gene expression data from N202 cells adapted to lung, passage 1

source_name: N202 cells adapted to lung tissue for 21 days, sorted, and expanded in cell culture.


title: N202 cells adapted to lung, passage 2

description:
H2B-GFP
Gene expression data from N202 cells adapted to lung, passage 2

source_name: N202 cells adapted to lung tissue for 42 days, sorted, and expanded in cell culture.


title: FVB-NAÏVE-4


title: N202 cells adapted to lung, passage 3

description:
H2B-GFP
Gene expression data from N202 cells adapted to lung, passage 3

source_name: N202 cells adapted to lung tissue for 63 days, sorted, and expanded in cell culture.


title: B2-NAÏVE-2


title: B2-NAÏVE-1


title: B2-NAÏVE-7


description:
H2B-GFP
Gene expression data from N202 cells adapted to bone marrow, passage 2

source_name: N202 cells adapted to bone marrow for 42 days, sorted, and expanded in cell culture.


description:
H2B-GFP
Gene expression data from N202 cells adapted to bone marrow, passage 3

source_name: N202 cells adapted to bone marrow for 63 days, sorted, and expanded in cell culture.


title: FVB-NAÏVE-6


description:
H2B-GFP
Gene expression data from N202 cells adapted to bone marrow, passage 1

source_name: N202 cells adapted to bone marrow for 21 days, sorted, and expanded in cell culture.


title: B2-NAÏVE-3


title: FVB-NAÏVE-8


title: FVB-NAÏVE-5


description:
H2B-GFP
Gene expression data from N202 cells adapted to brain, technical replicate, passage 3

source_name: N202 cells adapted to brain tissue for 63 days, sorted, and expanded in cell culture.


title: B2-NAÏVE-4


description:
H2B-GFP
Gene expression data from N202 cells adapted to brain, technical replicate, passage 1

source_name: N202 cells adapted to brain tissue for 21 days, sorted, and expanded in cell culture.


title: B2-NAÏVE-6


title: FVB-NAIVE-3


title: N202 cells adapted to brain, passage 4

description:
H2B-GFP
Gene expression data from N202 cells adapted to brain, passage 4

value: brain


title: FVB-NAIVE-2


description:
H2B-GFP
Gene expression data from N202 cells adapted to brain, technical replicate, passage 2


title: N202 cells adapted to brain, passage 2

description:
H2B-GFP
Gene expression data from N202 cells adapted to brain, passage 2


title: N202 cells adapted to brain, passage 1

description:
H2B-GFP
Gene expression data from N202 cells adapted to brain, passage 1


title: FVB-NAIVE-1


title: N202 cells adapted to brain, passage 3

description:
H2B-GFP
Gene expression data from N202 cells adapted to brain, passage 3


title: N202 parental cell line 1

description:
H2B-GFP
Gene expression data from N202 parental cell line 1

source_name: Parental N202 cells grown in vitro


title: B2-MCAO-7

source_name: Ischemic hemisphere, β2KO, 24H

extract_protocol: Mice were deeply anesthetized with isofluorane and sacrificed 24h after MCAO or sham surgery.  Brains were rapidly removed, divided into hemispheres and RNA was extracted from the ischemic hemisphere or for sham animals the ipsilateral hemisphere using Qiagen RNeasy Midi Kit.

value: ischemic brain hemisphere


title: B2-MCAO-6


title: B2-MCAO-5


title: Old HSC (22-30m) Rep 3

city: San Francisco

first: Sietske

middle: Tet

last: Bakker

address: 35 Medical Center Way

department: Department of Medicine

institute: University of California San Francisco

hyb_protocol: Biotinylated cRNA were prepared according to the GeneChip Expression Analysis Technical Manual 702232 Rev. 3

scan_protocol: GeneChips were scanned using the Affymetric GCS 3000 Scanner

data_processing: Data was processed by the R package 'affy' version 1.34.0. Normalization was done using RMA as implemented in the 'justRMA' function in the affy package. Statistical analyses were performed using the 'limma' package for R, version 3.12.3

label: Biotin

source_name: HSC

label_protocol: Sense-strand cDNA targets were generated using the Nugen WT-Ovation Exon Module, and then fragmented and biotinylated using the Nugen Encore Biotin Module according to manufacturers’ instructions.

extract_protocol: Total RNA was isolated using the Arcterus PicoPure RNA kit and a modified protocol for Trizol samples according to manufacturers’ instruction. RNA was then amplified using the Nugen Pico WTA kit and amplified products were cleaned using the Qiagen QiaQuick PCR purification kit following Nugen’s protocols.

treatment_protocol: HSCs (Lin-/c-Kit+/Sca-1+/Flk2-/CD48-/CD150+) and GMPs (Lin-/c-Kit+/Sca-1-/CD34+/FcγR+) were isolated from c-Kit-enriched BM, In brief HSC and GMPs were stained with un-conjugated lineage antibodies (Gr-1, Mac1, B220, CD3, CD4, CD5, CD8, Ter-119, goat anti-rat-PE-Cy5, c-Kit-APC-eFluor780, Sca-1-PB, Flk2-Bio CD48-Alexa Fluor 647, CD150-PE, SA-PE-Cy7, FcγR-PerCP-eFluor710 and CD34-FITC. Stained cells were re-suspended for final analysis in Hanks Buffered Salt Solution (HBSS) with 2% heat-inactivated fetal calf serum (FCS) and 1 µg/ml propidium iodide for dead cell exclusion. Cell isolation was performed on a FACS ARIAII (BD), using double sorting to ensure maximum purity.

tag: strain

tag: age

value: Old

value: Male

tag: genotype/variation


title: Young (6-12w) HSC Rep 2

value: Young


title: Young (6-12w) GMP Rep 4

source_name: GMP


title: Young (6-12w) HSC Rep 3


title: N202 parental cell line 2

description:
H2B-GFP
Gene expression data from N202 parental cell line 2


title: Young (6-12w) HSC Rep 1


title: Young (6-12w) GMP Rep 1


title: B2-MCAO-1


title: Young (6-12w) HSC Rep 5


title: Young (6-12w) HSC Rep 4


title: Young (6-12w) GMP Rep 2


title: FVB-MCAO-7

source_name: Ischemic hemisphere, WT, 24H


title: Old HSC (22-30m) Rep 1


title: B2-MCAO-3


title: B2-MCAO-2


title: Old HSC (22-30m) Rep 2


title: Young (6-12w) GMP Rep 3


title: B2-MCAO-4


title: FVB-MCAO-6


title: pcDNA3.0(-) transfected Embryonic kidney(293T) cells Replicate 3

city: Pune

first: Sanjay

last: Mukherjee

state: Maharashtra

address: Ganeshkhind

department: Department of Zoology

country: India

institute: University of Pune

hyb_protocol: Control and Experimental purified labelled aRNA were mixed in equal concentrations in terms of dye labelling and the mixture was dried completely. To the dired mixture 140µl of Hybridization buffer (Pronto Hybridization kit, Corning) was added and denatured at 95˚C for 5 minutes. The denatured mixture was allowed to hybridize onto a pre-soak, pre-hybridized(reagents from Pronto kit[Corning] microarray slide.

scan_protocol: Scanned on Scan array (Perkin Elmer) scanner. Images were quantified using Scan array express Software (version 1.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Homo sapiens

source_name: Control Embyronic kidney(293T) Cells

label_protocol: 1 µg of total RNA were primed with 1 µl of 100 µM T7 Oligo(dT) primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of ArrayScript reverse transcriptase (Aminoallyl MessageAmp II aRNA amplification kit[Ambion]), the first strand cDNA was used for the synthesis of second strand using poly-A T7 primer and DNA polymerase using manufacturer's instruction (Ambion). The purified cDNA was used for in-vitro transcription to synthesize amino-allyl-Modified aRNA using 5-(3-amino allyl)-UTP in a ratio of 1:1 along with unmodified UTPs(25mM) and 25mM of ATP, CTP and GTP.The purified aRNA was used for Dye Coupling reaction using Cy-dyes. The purified dye labelled aRNA was further used for hybridization procedure.

growth_protocol: 293T cells were grown in modified Eagle’s medium (DMEM; Invitrogen Life Technologies, Carlsbad, CA,USA) supplemented with 10% fetal bovine serum (FBS; Invitrogen Life Technologies) serum,100 units/ml penicillin, 100  ug/ml streptomycin in tissue culture flasks (Corning, USA) at 37°C in a CO2 incubator.

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

tag: cell type

value: embryonic cells derived from kidney

treatment_protocol: 293T cells were transfected with pcDNA 3.0(-) vector using TransIT-LT1 (Mirus biosciences) transfection reagent

value: 293T transfected with pcDNA 3.0(-) vector only


title: FVB-MCAO-5

value: FVB


title: Old GMP (22-30m) Rep 3


title: DIPG cell line 2 treated with GSK4 72h post treatment replicate 1

first: Rintaro

last: Hashizume

address: 1450 3rd street

department: Neurosurgery

institute: UCSF

description: Biological replicate 2 of 2. DIPG derived cell line, harboring H3F3A K27M mutation.

hyb_protocol: One hundred ng quantities of corresponding treated – untreated pairs were co-hybridized to SurePrint G3 Human Gene Expression 8x60K Microarrays (Agilent Technologies), in duplicate, for each length of treatment, for 17 hours at 65 °C

scan_protocol: Scanned on an Agilent microarray scanner (model G2505C) Images were quantified using  Agilent’s Feature Extraction 10.5.1 software.

data_processing: Agilent’s Feature Extraction 10.5.1 software with Agilent’s Two Color technology option was used for thresholding of signal values to five, ratio computing (cy3/cy5), and log transformation

source_name: Pediatric, K27M mutated DIPG cells treated with GSKJ4 for 72 h

label_protocol: RNAs from SF8628 K27M DIPG cells, either untreated or treated with GSKJ4 for 24 and 72 hours, were extracted then labeled (Cy3 for treated and Cy5 for untreated).

growth_protocol: Primary pediatric human glioma cells, designated with “SF”, were obtained from surgical biopsy of tumor from patients admitted to UCSF medical center, and in accord with an institutionally approved protocol. Establishment of glioma cell cultures, from surgical specimens, and tumor cell modification for expression of firefly luciferase, for in vivo bioluminescence imaging, have been described inHashizume R et al.,2012 (http://www.ncbi.nlm.nih.gov/pubmed/22983601)

extract_protocol: Briefly, 1×10^6 cells, treated with vehicle or 6 μM GSKJ4 for 24 and 72 hours, were harvested, washed with PBS and fixed with 1% formaldehyde for 5 minutes at room temperature. Cells were then quenched with 125 mM glycine for 5 minutes. After wash, cell extracts were prepared using lysis buffer (50 mM HEPES/KOH at pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton-X100, 0.1% Na-deoxycholate, 1 mM PMSF, 1 mM Pefoblock, 1 mM benzamidine, 1 mg/ml bacitracin) on ice for 10 minutes.

value: year 3

value: Pons

value: female

source_name: Pediatric, untreated, K27M mutated DIPG cells


title: pcDNA3.0(-) transfected Embryonic kidney(293T) cells Replicate 2


title: DIPG cell line 2 treated with GSK4 72h post treatment replicate 2


title: pcDNA3.0(-) transfected Embryonic kidney(293T) cells Replicate 1

growth_protocol: 293T cells were grown in modified Eagle’s medium (DMEM; Invitrogen Life Technologies, Carlsbad, CA,USA) supplemented with 10% fetal bovine serum (FBS; Invitrogen Life Technologies) serum,100 units/ml penicillin, 100 ug/ml streptomycin in tissue culture flasks (Corning, USA) at 37°C in a CO2 incubator.


title: FVB-MCAO-4

value: male


title: DIPG cell line 2 treated with GSK4 24h post treatment replicate 2

source_name: Pediatric, K27M mutated DIPG cells treated with GSKJ4 for 24 h


title: H11N1-NS1-Transfected Embryonic kidney (293T) Cells Replicate 1

treatment_protocol: PCR amplification and standard cloning techniques were used to insert NS1 gene in plasmid pCDNA 3.1-(Invitrogen). The plasmid with insert was transfected into 293T cells using TransIT-LT1 (Mirus biosciences) transfection reagent.

value: 293T transfected with pcDNA 3.0(-)containing H11N1-NS1 gene


title: FVB-MCAO-3


title: Old GMP (22-30m) Rep 2


title: H11N1-NS1-Transfected Embryonic kidney (293T) Cells Replicate 3


title: H11N1-NS1-Transfected Embryonic kidney (293T) Cells Replicate 2


title: H5N1-NS1-Transfected Embryonic kidney (293T) Cells Replicate 3

value: 293T transfected with pcDNA 3.0(-)containing H5N1-NS1 gene


title: Old GMP (22-30m) Rep 1


title: DIPG cell line 2 treated with GSK4 24h post treatment replicate 1


title: H5N1-NS1-Transfected Embryonic kidney (293T) Cells Replicate 2


title: B2-SHAM-2

source_name: Control hemisphere, β2KO, 24H

value: beta2 adrenergic receptor knockout

value: control brain hemisphere


title: B2-SHAM-3


title: FVB-MCAO-2

value: wild-type


title: FVB-SHAM-3

source_name: Control hemisphere, WT, 24H


title: 1 treatment using 0.08ug peptide prime

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

country: United Kingdom

institute: University of Bristol

description: CD4+ T cells isolated from the mice after 1 dose escalation peptide immunotherapy

hyb_protocol: The fragmented, biotinylated cRNA were used for hybridization with Affymetrix Mouse Gene 1.0 ST array.

scan_protocol: An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Raw expression data (.CEL files) were normalized using Robust Multi-array Averaging (RMA) algorithm with the quantile normalization method. The quality control showed that an empirical intensity of 200 or less could not be reliably discriminated, and thus any values below 200 were considered as being technically undetectable.

source_name: CD4+ T cells isolated from mice

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

extract_protocol: RNeasy (Qiagen) column-based extraction of total RNA, with DNase digestion was performed according to the manufacturer's instructions.

treatment_protocol: CD4+ T cells isolated from mice at six stages of dose escalation immunotherapy or a PBS-treated control

value: Tg4 Rag1 deficient TCR-transgenic mice

value: CD4+ T

tag: treatment

value: 0.08ug peptide prime


title: 4 treatment using 0.08ug, 0.8ug, 8ug, 80ug peptide prime

description: CD4+ T cells isolated from the mice after 4 dose escalation peptide immunotherapy

value: 0.08ug, 0.8ug, 8ug, 80ug peptide prime


title: FVB-SHAM-2


title: 6 treatment using 0.08ug, 0.8ug, 8ug, 80ug x 3  peptide prime

description: CD4+ T cells isolated from the mice after 6 dose escalation peptide immunotherapy


title: 10 treatment using 0.08ug, 0.8ug, 8ug, 80ug x 7 peptide prime

description: CD4+ T cells isolated from the mice after 10 dose escalation peptide immunotherapy


title: H5N1-NS1-Transfected Embryonic kidney (293T) Cells Replicate 1


title: PBS-treated control

description: CD4+ T cells isolated from the mice after a PBS-treated control

value: PBS-treated control


title: 3 treatment using 0.08ug, 0.8ug, 8ug peptide prime

description: CD4+ T cells isolated from the mice after 3 dose escalation peptide immunotherapy

value: 0.08ug, 0.8ug, 8ug peptide prime


title: FVB-MCAO-1

value: ischemic brain hemisphere


title: B2-SHAM-1

value: FVB


title: LmOVA Day4 WT, biological rep2

status: Public on Jul 13 2014

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Gene expression data from LmOVA primed WT OT-I cells

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner

data_processing:
Microarray expression data was processed using Command Console (Affymetrix, Inc)  with a custom CDF file and the raw (.CEL) files generated were analyzed using Arraystar version 4 (DNAStar) software with Robust Multichip Analysis ( RMA).
Following gene expression quantitation by RMA normalization, signal intensities were further converted by formula obtained from linear regression of signals for spiked-in control RNA between samples to obtain cell number-normalized gene expression.

source_name: WT OT-I cells

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system

extract_protocol: Total cellular RNA was extracted using Nucleospin RNA XS kit (Macherey-Nagel) according to the manufacturer's instructions.

treatment_protocol: On days 4 and 6 after infection, donor OT-I cells were sorted using FACS AriaII.

value: wildtype OT-I


title: LmOVA Day4 KO, biological rep1

description: Gene expression data from LmOVA primed KO OT-I cells

source_name: Tfap4–/– OT-I cells

value: Tfap4-/- OT-I


title: LLC-subclone-19, biological rep3

city: Boston

first: Serkan

last: KIR

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Inst.

description: Gene expression data

hyb_protocol: Following fragmentation, cRNA were hybridized at 45C to Affymetrix mouse genome 430A v2.0 arrays, according to established methods.

scan_protocol: Labeling, hybridization, and scanning were performed by the Dana-Farber Cancer Institute Microarray Core Facility using established methods.

data_processing: The data were normalized and analyzed using the dChip software.

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

growth_protocol: LLC subclones were derived from parental LLC cells using limiting dilution. Cells were maintained in DMEM with 10% FBS and 1X Pen/Strep.

extract_protocol: Total RNA was isolated with Trizol and purified using Qiagen RNEasy mini columns according to the manufacturer's instructions.

treatment_protocol: LLC subclones were cultered in serum free FreeStyle expression medium (Invitrogen) for 24 hours.

value: Lewis Lung Carcinoma (LLC) cells


title: LmOVA Day6 WT, biological rep1


title: LLC-subclone-24, biological rep1

description: Gene expression data


title: LLC-subclone-24, biological rep3

description: Gene expression data


title: LLC-subclone-23, biological rep2

description: Gene expression data


title: LLC-subclone-19, biological rep1

description: Gene expression data


title: KO+Myc, biological rep1

description: In vitro activated Myc-deficient CD8 T cells transduced with Myc-expressing retrovirus

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Arraystar version 4 (DNAStar) software with Robust Multichip Analysis ( RMA).

source_name: Myc(F/F);CreER CD8 T cells

growth_protocol: Naive CD8 T cells were activated by anti-CD3/CD28 antibodies for 1 day followed by spinoculation of empty, AP4-, or Myc-expressing retrovirus. Deletion of Myc was achieved by culturing the activated CD8 T cells in media containing 500nM 4OHT and IL-7 for 2 days.

treatment_protocol: Transduced (GFP+) cells were sorted using FACS AriaII and re-stimulated with anti-CD3 and anti-CD28 antibodies for 2 days.

value: Myc(F/F);CreER

value: CD8+ T cells


title: LmOVA Day6 WT, biological rep2


title: LmOVA Day6 KO, biological rep1


title: KO+Myc, biological rep2


title: KO+Empty, biological rep1

description: In vitro activated Myc-deficient CD8 T cells transduced with Empty retrovirus


title: LLC-subclone-18, biological rep3

description: Gene expression data


title: LLC-subclone-23, biological rep1

description: Gene expression data


title: LmOVA Day6 KO, biological rep2


title: LmOVA Day4 KO, biological rep2


title: LLC-subclone-23, biological rep3

description: Gene expression data


title: KO+AP4, biological rep1

description: In vitro activated Myc-deficient CD8 T cells transduced with AP4-expressing retrovirus


title: LmOVA Day4 WT, biological rep1


title: LLC-subclone-24, biological rep2

description: Gene expression data


title: 2 treatment using 0.08ug, 0.8ug peptide prime

description: CD4+ T cells isolated from the mice after 2 dose escalation peptide immunotherapy

value: 0.08ug, 0.8ug peptide prime


title: LLC-subclone-19, biological rep2

description: Gene expression data


title: KO+Empty, biological rep2


title: KO+AP4, biological rep2


title: LmOVA d2 KO, biological rep3

description: Adoptively transferred and sorted from LmOVA infected mice using FACS AriaII

source_name: LmOVA primed Tfap4–/– OT-I cells

growth_protocol: Naïve CD103+CD44- CD8 T cells were FACS sorted with AriaII. In vitro activation was done with anti-CD3/CD28 antibodies. For in vivo activation, OT-I cells were adoptively transferred into recipients that were subsequently infected with LmOVA. Two days after infection, OT-I cells were purified with FACS AriaII.

value: Tfap4–/– OT-I


title: LLC-subclone-18, biological rep2

description: Gene expression data


title: FVB-SHAM-1

value: male

value: control brain hemisphere


title: WT+Empty, biological rep1

description: In vitro activated WT CD8 T cells transduced with Empty retrovirus

source_name: Myc(F/F) CD8 T cells

value: Myc(F/F)


title: WT+Empty, biological rep2


title: LmOVA d2 WT, biological rep1

source_name: LmOVA primed WT OT-I cells


title: LmOVA d2 WT, biological rep3


title: LmOVA d2 KO, biological rep2


title: In vitro d3 KO, biological rep2

description: Activated with anti-CD3/CD28

source_name: In vitro activated Tfap4–/– CD8 T cells


title: LLC-subclone-28, biological rep3

description: Gene expression data


title: LmOVA d2 WT, biological rep2


title: LmOVA d2 KO, biological rep1


title: LLC-subclone-28, biological rep2

description: Gene expression data


title: LLC-subclone-18, biological rep1

description: Gene expression data


title: Naïve KO, biological rep2

description: Sorted with FACS AriaII

source_name: CD103+CD44- Tfap4–/– CD8 T cells


title: Naïve WT, biological rep2

description: Sorted with FACS AriaII

source_name: CD103+CD44- WT CD8 T cells

value: wildtype


title: Naïve KO, biological rep1

description: Sorted with FACS AriaII


title: LLC-subclone-28, biological rep1

description: Gene expression data


title: LLC-subclone-6, biological rep1

description: Gene expression data


title: In vitro d3 KO, biological rep1

description: Activated with anti-CD3/CD28


title: Naïve WT, biological rep1

description: Sorted with FACS AriaII


title: plus-IL2, biological rep2

description: Gene expression data from in vitro activated WT CD8 T cells treated IL2

source_name: WT CD8 T cells

growth_protocol: WT CD8 T cells were activated in vitro with anti-CD3/CD28 antibodies for 2 days, followed by culture with 100 U/ml of IL-2 for 1 day.

treatment_protocol: After 1 day resting, CD8 T cells were either maintained in the presence of IL-2 (Plus-IL2) or treated with 2 ug/ml of anti-IL2 antibody (anti-IL2) for 12 hours before harvest.


title: plus-IL2, biological rep3


title: In vitro d3 WT, biological rep2

description: Activated with anti-CD3/CD28

source_name: In vitro activated WT CD8 T cells


title: LLC-subclone-6, biological rep2

description: Gene expression data


title: anti-IL2, biological rep3

description: Gene expression data from in vitro activated WT CD8 T cells treated with anti-IL2 antibody


title: anti-IL2, biological rep1


title: anti-IL2, biological rep2


title: In vitro d3 WT, biological rep1

description: Activated with anti-CD3/CD28


title: LLC-subclone-3, biological rep2

description: Gene expression data


title: LLC-subclone-3, biological rep3

description: Gene expression data


title: IL-13 treated macrophages 1

status: Public on Jul 12 2014

city: Guangzhou

first: Shicheng

last: Su

address: 107 Yanjiang West Road

country: China

institute: Sun-Yat-Sen Memorial Hospital

description:
3'-end-labeled with Hy3TM fluorescent label
miRNAs expression of primary human monocyte-derived macrophages with IL-13 treatment for 48hr-1

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor.
Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering.

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: Peripheral blood monocytes from healthy donors were isolated by Ficoll density gradient centrifugation as previously described. Macrophages were obtained by culturing monocytes in DMEM medium supplemented with 10% heat inactivated human AB serum for 6 days.

extract_protocol: Total RNA from human primary macrophages treated with or without 20 ng/ml IL-4 or 20ng/ml IL-13 for 48 hr was isolated with a mirVana miRNA Isolation kit (Ambion, Foster, CA).

treatment_protocol: Afterward, macrophages were incubated with or without 20ng/ml IL-4 or 20ng/ml IL-13(PeproTech, Rocky Hill, NJ) for 48 hr.

value: buffy coats of peripheral blood

value: macrophage

tag: donors

value: healthy donor 1


title: IL-4 treated macrophages 3

description:
3'-end-labeled with Hy3TM fluorescent label
miRNAs expression of primary human monocyte-derived macrophages with IL-4 treatment for 48hr-3

value: healthy donor 3


title: control macrophages 2

description:
3'-end-labeled with Hy3TM fluorescent label
miRNAs expression of primary human monocyte-derived macrophages-2

value: healthy donor 2


title: IL-13 treated macrophages 3

description:
3'-end-labeled with Hy3TM fluorescent label
miRNAs expression of primary human monocyte-derived macrophages with IL-13 treatment for 48hr-3


title: control macrophages 3

description:
3'-end-labeled with Hy3TM fluorescent label
miRNAs expression of primary human monocyte-derived macrophages-3


title: plus-IL2, biological rep1


title: IL-13 treated macrophages 2

description:
3'-end-labeled with Hy3TM fluorescent label
miRNAs expression of primary human monocyte-derived macrophages with IL-13 treatment for 48hr-2


title: IL-4 treated macrophages 2

description:
3'-end-labeled with Hy3TM fluorescent label
miRNAs expression of primary human monocyte-derived macrophages with IL-4 treatment for 48hr-2


title: LLC-subclone-3, biological rep1

description: Gene expression data


title: LLC-subclone-2, biological rep3

description: Gene expression data


title: IL-4 treated macrophages 1

description:
3'-end-labeled with Hy3TM fluorescent label
miRNAs expression of primary human monocyte-derived macrophages with IL-4 treatment for 48hr-1


title: control macrophages 1

description:
3'-end-labeled with Hy3TM fluorescent label
miRNAs expression of primary human monocyte-derived macrophages-1


title: LLC-subclone-2, biological rep2

description: Gene expression data


title: LLC-subclone-2, biological rep1

description: Gene expression data


title: GE001

city: Kansas City

first: Douglas

middle: C

last: Bittel

address: 2401 Gillham Rd

department: Genetics research

institute: Childrens Mercy Hospital

hyb_protocol: All arrays were run at the Kansas University Medical Center-Microarray Facility (KUMC-MF) according to the manufacturer’s protocols

data_processing:
All statistical analyses were performed using statistical software: SPSS, Partek (Partek, Inc. St Louis, Mo.). Robust Multichip Analysis (RMA) was used for background correction followed by quantile normalization with baseline transformation to the median of the control samples
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: right ventricle

growth_protocol: Tissues samples obtained during patient surgery were immediately de-identified and frozen.

extract_protocol: RNA was extracted from ~10 mg of frozen tissue from right ventricle using a mirVana microRNA isolation kit (Applied Biosystems/Ambion, Austin, TX) according to manufactures instruction

treatment_protocol: All tissue samples removed during surgery were excised by the performing surgeon for clinical indications utilizing standard of care procedures

value: Right ventricular myocardium

tag: group

value: control (normally developing infants)


title: LabCR042

scan_protocol: All arrays were run at the Kansas University Medical Center-Microarray Facility (KUMC-MF) according to the manufacturer’s protocols

value: TOF


title: FH01

label_protocol: All arrays were run at the Kansas University Medical Center-Microarray Facility (KUMC-MF) according to the manufacturer’s protocols

value: fetal heart


title: CR023


title: LabCR025


title: LabCR055


title: FH68


title: CR013


title: CR018


title: LabCR047


title: LabCR020


title: CR003


title: GE002


title: FH46


title: GE003


title: LabCR010


title: LabCR057


title: LabCR012


title: LabCR024


title: LabCR039


title: LabCR022


title: GE004


title: GE008


title: GE005


title: GE009


title: GE007


title: LabCR016


title: term placenta_317

type: genomic

city: Pittsburgh

first: David Peter

middle: G.

last: Peters

state: PA

address: 204 Craft Avenue

department: Department of Obstetrics, Gynecology and Reproductive Sciences

institute: University of Pittsburgh/Magee-Womens Research Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
GenomeStudio software v1.1
Data tables contain normalized log (methylated/unmethylated). Raw data with  Unmethylated and methylated signal intensities are available on the series record.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: term placenta

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the Qiagen Dneasy Blood and Tissue Kit according to standard instructions.

tag: jury

tag: maternal age (years)

tag: gestational age at delivery (weeks)

tag: maternal race

value: White

tag: nulliparous

tag: pre-pregancy bmi

tag: systolic bp <20 weeks (mmhg)

tag: diastolic bp <20 weeks (mmhg)

tag: systolic bp at delivery (mmhg)

tag: diastolic bp at delivery (mmhg)

tag: uric acid (mg/dl)

tag: fetal sex

value: Male

value: placenta


title: term placenta_287

tag: tissue


title: term placenta_310


title: term placenta_313

value: Female


title: term placenta_253


title: term placenta_244


title: term placenta_243


title: term placenta_233


title: term placenta_226


title: term placenta_216


title: term placenta_209


title: term placenta_207


title: term placenta_202


title: C9-without phenylethanol-log phase-rep3

city: TOULOUSE

first: CEREN

last: ALKIM

address: Laboratoire d'Ingénierie des Systèmes Biologiques & des Procédés

country: France

institute: INRA

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) 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 (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321).  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: Phenylethanol-resistant Saccharomyces cerevisiae, log. Phase, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.5 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Precultures of the reference strain and phenylethanol-resistant mutant were prepared in 50 mL yeast minimal medium using 250 mL flasks. They were incubated at 30°C and 150 rpm for about ~ 16 hour. Fresh cultures were inoculated as triplicate with an initial OD600 of 0.1. They were cultivated at 30°C and 150 rpm until they reach the OD600 value of about 1.0. Cells were harvested at this OD600 value.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Yeast cells were not treated with any special agent.

tag: phenotype

value: Phenylethanol-resistant


title: C9-without phenylethanol-log phase-rep2

source_name: Phenylethanol-resistant Saccharomyces cerevisiae, log. Phase, replicate 2


title: Human stomach 28-cancer

city: Goyang

first: Sung-Ho

last: Goh

state: Gyeonggido

address: Research Bldg. 5th Fl., 323 Ilsanro

department: Functional Genomics Branch

country: South Korea

institute: National Cancer Center

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) in a GeneChip Fluidics Station accroding to the manufacturer's protocol.

scan_protocol: Array scanning was performed using GeneChip Scanner 3000 according to the manufacturer's instructions (Affymetrix).

data_processing:
Data were processed with the GeneChip Operating Software (GCOS) to generate CEL files, and then analyzed by Expression Console (Affymetrix) with the RMA algorithm. Further data analysis was performed by the ‘Junction and Exon Array Toolkit for Transcriptome Analysis (JETTA)’ package (http://gluegrant1.stanford.edu/~junhee/JETTA/).
All exon analysis.

source_name: Stomach tissue from cancer lesion

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix), and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Stomach cancer tissues were collected by endoscopic mesenchymal resection and preserved in RNAlater solution (Qiagen, Hilden, Germany) at 4 deg C until they were used for RNA extraction (no more than 24 hours).

extract_protocol: Total RNA was extracted with TRIzol reagent according to the manufacturer’s protocol (Invitrogen), and treated with DNaseI on RNeasy Mini columns (Qiagen) to remove residual genomic DNA. The concentration and A260/280 ratio of the purified RNA were measured with Nanodrop ND-1000 (Thermo Scientific, Wilmington, DE, USA), and the quality was assessed on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA).

tag: Sex

value: female

value: gastric cancer

tag: cancer stage

value: advanced

tag: patient


title: Human stomach 29-cancer


title: Human stomach 27-cancer

value: male

value: early


title: Human stomach 25-cancer


title: Human stomach 26-cancer


title: Human stomach 24-cancer


title: Human stomach 30-cancer


title: term placenta_195

tag: jury

value: Black


title: Wild Type-without phenylethanol-log phase-rep2

source_name: Saccharomyces cerevisiae, log. Phase, replicate 2

value: wild-type


title: Human stomach 15-cancer


title: term placenta_191

tag: maternal age (years)


title: Wild Type-without phenylethanol-log phase-rep1

source_name: Saccharomyces cerevisiae, log. Phase, replicate 1


title: Wild Type-without phenylethanol-log phase-rep3

source_name: Saccharomyces cerevisiae, log. Phase, replicate 3


title: Human stomach 22-cancer


title: Human stomach 23-cancer


title: C9-without phenylethanol-log phase-rep1

source_name: Phenylethanol-resistant Saccharomyces cerevisiae, log. Phase, replicate 1


title: Human stomach 14-cancer


title: Human stomach 18-cancer


title: Human stomach 21-cancer


title: Human stomach 16-cancer


title: Human stomach 19-cancer


title: Human stomach 17-cancer


title: Human stomach 11-cancer


title: term placenta_188

tag: gestational age at delivery (weeks)


title: term placenta_34

tag: maternal race


title: Human stomach 20-cancer


title: term placenta_184

value: Nat Amer

tag: nulliparous


title: Human stomach 05-cancer


title: Human stomach 09-cancer


title: term placenta_28

tag: pre-pregancy bmi


title: term placenta_185

tag: systolic bp <20 weeks (mmhg)


title: term placenta_12

tag: diastolic bp <20 weeks (mmhg)


title: term placenta_17

tag: systolic bp at delivery (mmhg)


title: Human stomach 07-cancer


title: term placenta_329

value: white

tag: diastolic bp at delivery (mmhg)


title: term placenta_161

tag: uric acid (mg/dl)


title: term placenta_307

tag: fetal sex


title: term placenta_85

tag: tissue


title: Testis_Wt(TgMsi2)_rep4

city: Callaghan

first: Jessie

middle: M

last: Sutherland

address: University Drive

country: Australia

institute: University of Newcastle

description: comparison 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: GenomeStudio was used to convert the signal on the array into a TXT file for analysis

source_name: Mouse testis

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

extract_protocol: Total RNA was isolated from samples using a QIAGEN RNeasy Mini Kit (Hilden, Germany). The quality and quantity of mouse total RNA was ascertained on the Agilent Bioanalyser 2100.

tag: strain

tag: age

value: 3 months

value: testis

tag: genotype/variation


title: Human stomach 13-cancer

tag: Sex

tag: cancer stage

tag: patient


title: Human stomach 08-cancer


title: Testis_Wt(TgMsi2)_rep3

description: comparison 2


title: Testis_Wt(TgMsi2)_rep2

description: comparison 2


title: Testis_Wt(TgMsi2)_rep1

description: comparison 2


title: term placenta_305

tag: jury

tag: maternal age (years)

tag: gestational age at delivery (weeks)

value: black


title: Human stomach 12-cancer


title: Testis_TgMsi2_rep4

description: comparison 2


title: Human stomach 03-cancer


title: Human stomach 04-cancer


title: Testis_TgMsi2_rep3

description: comparison 2


title: Human stomach 06-cancer


title: Testis_TgMsi2_rep2

description: comparison 2


title: Testis_Wt(TgMsi1)_rep3

description: comparison 1


title: term placenta_275

tag: maternal race

tag: nulliparous

tag: pre-pregancy bmi


title: Human stomach 02-cancer


title: term placenta_273

tag: systolic bp <20 weeks (mmhg)

tag: diastolic bp <20 weeks (mmhg)

tag: systolic bp at delivery (mmhg)


title: Testis_Wt(TgMsi1)_rep4

description: comparison 1


title: Testis_TgMsi2_rep1

description: comparison 2


title: term placenta_280

tag: diastolic bp at delivery (mmhg)

tag: uric acid (mg/dl)

tag: fetal sex


title: Testis_Wt(TgMsi1)_rep1

description: comparison 1

tag: strain

tag: age

tag: tissue


title: term placenta_298


title: term placenta_249


title: Testis_TgMsi1_rep4

description: comparison 1

tag: genotype/variation


title: Human stomach 29-normal

source_name: Normal stomach tissue from peritumoral region

tag: Sex

value: normal stomach

tag: cancer stage

tag: patient


title: Human stomach 30-normal


title: Human stomach 10-cancer


title: term placenta_199

tag: jury

tag: maternal age (years)

tag: gestational age at delivery (weeks)


title: Testis_TgMsi1_rep2

description: comparison 1


title: term placenta_201

tag: maternal race

tag: nulliparous

tag: pre-pregancy bmi

value: Male


title: Human stomach 25-normal


title: Human stomach 26-normal


title: Testis_Wt(TgMsi1)_rep2

description: comparison 1


title: Testis_TgMsi1_rep1

description: comparison 1


title: Human stomach 28-normal


title: Human stomach 22-normal


title: Human stomach 01-cancer


title: term placenta_108

tag: systolic bp <20 weeks (mmhg)

tag: diastolic bp <20 weeks (mmhg)

tag: systolic bp at delivery (mmhg)

value: placenta


title: Colonized with microbiota from loperamide-treated mouse, , replicate 4

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: raw data were processed using the R/Bioconductor package limma for background correction and quantile normalization

source_name: smooth muscle

label_protocol: standard Illumina protocol

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

tag: group

value: C/+Lop

value: smooth muscle of proximal colon

tag: genotype

value: wild type


title: term placenta_311

tag: diastolic bp at delivery (mmhg)

tag: uric acid (mg/dl)

tag: fetal sex

value: Female


title: Colonized with microbiota from loperamide-treated mouse, replicate 3

tag: tissue

tag: strain


title: term placenta_95


title: Human stomach 24-normal

tag: Sex

tag: cancer stage

tag: patient


title: Colonized with microbiota from loperamide-treated mouse, replicate 2


title: Human stomach 21-normal


title: Testis_TgMsi1_rep3

description: comparison 1

tag: age

tag: genotype/variation


title: Human stomach 19-normal

value: female


title: Human stomach 23-normal

value: male


title: term placenta_117

tag: jury

tag: maternal age (years)

tag: gestational age at delivery (weeks)

tag: maternal race

tag: nulliparous


title: Human stomach 20-normal

value: early


title: Colonized with microbiota from loperamide-treated mouse, replicate 1

tag: group


title: Gfi-1 -/- mouse BMC 3

city: Frederick

first: Jonathan

middle: R

last: Keller

state: MD

address: 1050 Boyles St. P.O. Box B (Building 560, Room 12-03)

department: Mouse Cancer Genetics Program

institute: Center for Cancer Research, National Cancer Institute, NIH

description: Gene expression data from total mouse bone marrow cells

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing:
The data were analyzed with Partek Genomics Suite version 6.6 using Affymetrix default analysis settings and global scaling as normalization method. The genes listed were selected based on the criteria that their expression changed by ≥ 1.5 fold that was statistically significant as indicated by a p-value < 0.05.
RT-PCR data for 12 selected genes from the same genotypes are available on the series level.

source_name: Gfi-1 knockout mouse bone marrow cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: All mice were backcrossed onto C57/Bl6 backgounds. Animals were treated in accordance with the Guidelines of the Frederick National Laboratory for Cancer Research Animal Care and Use Committee (ACUC) in accordance with the Guide for Care and Use of Laboratory Animals.

extract_protocol: Total RNA was purified from whole bone marrow cells using RNeasy kits (QIAGEN Inc., Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: No treatment

value: bone marrow

tag: genotype


title: term placenta_86

tag: pre-pregancy bmi

tag: systolic bp <20 weeks (mmhg)

tag: diastolic bp <20 weeks (mmhg)

tag: systolic bp at delivery (mmhg)

tag: diastolic bp at delivery (mmhg)


title: term placenta_65

tag: uric acid (mg/dl)

tag: fetal sex

tag: tissue


title: Gfi-1 -/- mouse BMC 2

tag: strain


title: Colonized with microbiota from control mouse,, replicate 3

value: C/-Lop


title: Gfi-1 -/- mouse BMC 4


title: term placenta_55


title: Colonized with microbiota from control mouse, replicate 2


title: Human stomach 17-normal

tag: Sex

tag: cancer stage

tag: patient


title: Gfi-1 -/- mouse BMC 1


title: term placenta_52

tag: jury

tag: maternal age (years)

tag: gestational age at delivery (weeks)


title: term placenta_40

tag: maternal race

tag: nulliparous


title: Colonized with microbiota from control mouse, replicate 1

tag: group

tag: genotype


title: Gfi-1 -/-; Id2 +/- mouse BMC 4

source_name: Gfi-1 knockout mouse bone marrow cells with Id2 reduction


title: Specific pathogen free mouse, replicate 4

value: SPF


title: Gfi-1 -/-; Id2 +/- mouse BMC 3


title: Gfi-1 -/-; Id2 +/- mouse BMC 2


title: Gfi-1 -/-; Id2 +/- mouse BMC 1


title: Specific pathogen free mouse, replicate 2


title: term placenta_18

value: white

tag: pre-pregancy bmi

tag: systolic bp <20 weeks (mmhg)

tag: diastolic bp <20 weeks (mmhg)


title: term placenta_96

tag: systolic bp at delivery (mmhg)

tag: diastolic bp at delivery (mmhg)

tag: uric acid (mg/dl)


title: term placenta_11

tag: fetal sex

tag: tissue


title: Specific pathogen free mouse, replicate 13

tag: strain


title: Germ free mouse, replicate 4

value: GF


title: Colonized with microbiota from control mouse, replicate 4


title: term placenta_19


title: term placenta_5


title: Human stomach 15-normal

tag: Sex

tag: cancer stage

tag: patient


title: Germ free mouse, replicate 3


title: Specific pathogen free mouse, replicate 1


title: Human stomach 14-normal


title: Human perirenal adipose tissue PR-AT10

status: Public on Jul 11 2014

city: Gothenburg

first: Per-Arne

last: Svensson

department: Department of molecular and clinical medicine

country: Sweden

institute: institute of medicine

hyb_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were hybridized with biotin labeled sense DNA, washed, stained, and scanned according to the protocol described in WT Sense  Target Labeling Assay Manual at the Uppsala array platform (Sweden)

scan_protocol: Affymetrix GeneChip 3000 7G scanner

data_processing: RMA

source_name: Human perirenal adipose tissue

label_protocol: total RNA was amplified and labelled using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol

extract_protocol: Qiagen RNeasy lipid tissue midi kit

value: Normal perirenal adipose tissue


title: Germ free mouse, replicate 1


title: porcine immune organs_uninfected_rep1

city: Ya’an

first: Xiao

last: Liu

state: Sichuan Province

address: 46# Xinkang Road

department: College of Veterinary Medicine

institute: Sichuan Agricultural University

description: Gene expression of uninfected porcine immune organs

hyb_protocol: Hybridization   Kit and Instruments:  Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):  10X Blocking Agent  25X Fragmentation Buffer  2x GEx Hybridization Buffer HI-RPM  Hybridization Chamber, stainless (Agilent p/n G2534A)  Hybridization Chamber gasket slides (Agilent p/n G2534-60003)  Hybridization oven (Agilent p/n G2545A)  Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029)    Procedure:  1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:  For 1*244K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.5ug  10X Blocking Agent 50ul  Nuclease-free water ×ul  25X Fragmentation Buffer 10ul  Total volume 250ul    For 2*105K array Amount  cyanine 3-labeled, linearly amplified cRNA 1. 5ug  10X Blocking Agent 25ul  Nuclease-free water ×ul  25X Fragmentation Buffer 5ul  Total volume 125ul    For 4*44K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.65ug  10X Blocking Agent 11ul  Nuclease-free water ×ul  25X Fragmentation Buffer 2.2ul  Total volume 55ul    For 8*15K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul    4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  Volumes per hybridization  Components 1*244K 2*105K 4*44K 8*15K  cRNA from Fragmentation Mix 250ul 125ul 55ul 25ul  2* GEx Hybridization Buffer HI-RPM 250ul 125ul 55ul 25ul    7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  Volumes per hybridization  Components 1*244K 2*105K 4*44K 8*15K  Volume Prepared 500ul 250ul 110ul 50ul  Hybridization Sample Volume 490ul 245ul 100ul 40ul    12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.

scan_protocol: Scanning    Instrument:  Agilent Microarray Scanner (Agilent p/n G2565BA)    Procedure:  1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing:
Extract data using Agilent Feature Extraction Software  (Double-click)  Software:  Agilent Feature Extraction    Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt..
Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 2 out of 2 samples have flags in Detected (  All Targets Value  ) were chosen for differentially expressed genes screening.

label: 5×First Strand Buffer, 0.1M DTT, 10mM dNTP mix, MMLV-RT, RNaseOut, Nuclease-free water, 4X Transcription Buffer,0.1 M DTT , NTP mix, 50% PEG, RNaseOUT, Inorganic pyrophosphatase, T7 RNA Polymerase, Cyanine-3-CTP

organism: Sus scrofa

source_name: Normal porcine immune organs

label_protocol: labeling reaction  Kit:  Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)    Procedure:  1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2. Add 1.2 μL of T7 Promoter Primer.   3. Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.   Volume(ul) per reaction  5×First Strand Buffer 4  0.1M DTT 2  10mM dNTP mix 1  MMLV-RT 1  RNaseOut 0.5  Total volume 8.5  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice. Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.   Volume(ul) per reaction  Nuclease-free water 15.3  4X Transcription Buffer 20  0.1 M DTT 6  NTP mix 8  50% PEG 6.4  RNaseOUT 0.5  Inorganic pyrophosphatase 0.6  T7 RNA Polymerase 0.8  Cyanine-3-CTP 2.4  Total volume 60  14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.     Step 4 Purify the labeled/amplified RNA and labeled cRNA QC  Kit and instrument:  RNeasy Mini Kit (Qiagen p/n 74104)  NanoDrop ND-1000    Procedure:  1. Add 20 μL of nuclease-free water to your cRNA sample, for a total volume of 100 μL.  2. Add 350 μL of Buffer RLT and mix well by pipetting.  3. Add 250 μL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge.  4. Transfer the 700 μL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube.  5. Transfer the RNeasy column to a new collection tube and add 500 μL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube.  6. Add another 500 μL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube.  7. Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report ”Labeling Efficiency-QC”) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm.  8. Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column.  9.  Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000( Passed-please see report ”Labeling Efficiency-QC”).   From the main menu, choose MicroArray Measurement. Go to the Sample Type pull-down menu and select DNA-50.   Blank the instrument with 1.5 μL of 1x labeling solution.   Use 1.5 μL of purified labeled genomic DNA for quantitation. Measure the absorbance at A260nm (DNA), A550nm (cyanine 3).   The specific activity (pmol dyes per μg genomic DNA) of the labeled genomic DNA can be obtained by the following calculation:  (Concentration of Cy3)  Specific Activity =——————————————— = pmol Cy3 per μg cRNA  (Concentration of cRNA) * 1000  * If the yield is <1.65 μg and the specific activity is <9.0 pmol Cy3 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

growth_protocol: piglets were divided into two groups of five pigs each, and maintained under controlled temperature and humidity.

extract_protocol: Total RNA was extracted from the immune organs of the PCMV-infected piglets and control piglets using TRIzol Reagent (Invitrogen, Shanghai, China), according to the manufacturer’s instructions. The integrity of the RNA was assessed with electrophoresis on a denaturing agarose gel. A NanoDrop ND-1000 spectrophotometer (NanoDrop Inc., Wilmington, DE, USA) was used to accurately measure the RNA concentrations (optical density at 260 nm, OD260), protein contamination (with the OD260/OD280 ratio), and organic compound contamination (OD260/OD230 ratio).

treatment_protocol: Each pig in the first group was inoculated with 5 ml of 109 PFU/ml PCMV SC strain by intramuscular and intranasal injection, and the other five pigs were injected with 5 ml of RPMI-1640 nutrient solution (Thermo Fisher Scientific, Waltham, UK) as the control. The sera, lymph nodes, spleens, and thymuses of the infected and control pigs were collected at 14 dpi, and all the tissues were immediately frozen in liquid nitrogen and stored at –80 °C until further analysis.

value: Normal porcine immune organs


title: Germ free mouse, replicate 2


title: Human perirenal adipose tissue PR-AT9


title: Human stomach 16-normal

value: normal stomach


title: porcine immune organs_PCMV-infected_rep1

description: Gene expression of PCMV-infected porcine immune organs

source_name: PCMV infected porcine immune organs

value: PCMV infected porcine immune organs


title: Human perirenal adipose tissue PR-AT6


title: Human perirenal adipose tissue PR-AT2


title: Human perirenal adipose tissue PR-AT3


title: Human stomach 12-normal


title: Human perirenal adipose tissue PR-AT4


title: Human perirenal adipose tissue PR-AT5


title: Human stomach 11-normal


title: Human perirenal adipose tissue PR-AT7


title: Human perirenal adipose tissue PR-AT1


title: Human perirenal adipose tissue PR-AT8


title: Human stomach 13-normal


title: Human stomach 08-normal


title: HCC-LM3-fLuc cells were then exposed to AU-SM5-1_rep3

city: Beijing

first: ma

middle: xi

last: bo

address: No.95,Zhongguancun East Road

institute: Chinese Academy of Sciences

description: Gene expression data from HCC-LM3-fLuc cells were then exposed to AU-SM5-1

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

scan_protocol: neChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

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: HCC-LM3-fLuc cells were plated in a 6 well plate(6×105per well) and incubated with 1mLmedium overnight.

treatment_protocol: HCC-LM3-fLuc cells were then exposed to AU-SM5-1 at a concentration of 0.1mg SM5-1 per mL,that is to add 40μL AU-SM5-1 solution  at concentration of 2.5mg/mL.

tag: cell type


title: HCC-LM3-fLuc cells_rep1

description: Gene expression data from HCC-LM3-fLuc cells

source_name: HCC-LM3-fLuc cells


title: Human stomach 10-normal


title: HCC-LM3-fLuc cells_rep3


title: HCC-LM3-fLuc cells were then exposed to AU-SM5-1_rep2


title: Human stomach 07-normal


title: HCC-LM3-fLuc cells_rep2


title: HCC-LM3-fLuc cells were then exposed to AU-SM5-1_rep1


title: Human stomach 09-normal


title: LRH-1 hep-/- liver, biological replicate 2

city: Lausanne

first: Kristina

last: Schoonjans

address: Station 15

department: SV IBI GR-SCH

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne

description: Gene expression data

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. ~16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner

data_processing: Samples were analyzed using Affymetrix Expression Console, Graphpad Prism, and Gene Set Enrichment Analysis (Broad Institute).

source_name: LRH-1 hep-/- liver 2

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (Part Number 4411974) according to manufactures protocols, then 5500ng cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

growth_protocol: Mice are housed 5 per cage in IVC GM500 cages (Tecniplast, 500 cm2) according to the Swiss cantonal rules.

treatment_protocol: Mice were fed ad libitum before beeing sacrificed.

value: liver

value: LRH-1 hep-/-


title: LRH-1 hep-/- liver, biological replicate 6

description: Gene expression data

source_name: LRH-1 hep-/- liver 6


title: LRH-1 hep-/- liver, biological replicate 7

description: Gene expression data

source_name: LRH-1 hep-/- liver 7


title: Wnt+ mouse adrenocortical cells, biological replicate 1

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

description:
Biological replicate 1
008

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized for 20 hr at 48C on Mouse Gene ST 1.1 strip arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the oligo package implemented in the R-statistical environment version 2.15.1. RMA was used to estimate log2 transformed expression values. We analyzed only 28944 probe-sets with category "main", "---", and "flmrna->unmapped" according to Affymetrix annotation.

source_name: Wnt+ mouse adrenocortical cells

label_protocol: cDNA were prepared according to the NuGen WT-Pico V2 kit protocol from 5 ng total RNA (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA were prepared from 3ug of cDNA (Encore Biotin Module P/N 4200-12, 4200-60, 4200-A01).

growth_protocol: TCF/Lef:H2B-GFP transgenic mice were obtained from JAX laboratories. These mice contain an H2B-GFP fusion protein under control of multimerized TCF/LEF binding sites within a minimal Hspa1b heatshock promoter. Sf1:eGFP mice were obtained from the laboratory of the late Keith Parker. These mice contain eGFP expression driven by a BAC fragment containing 50kb of Nr5a1 gene. Both mice are on a C57BL/6J background. GFP-positive cells were obtained from 6-week-old male mouse adrenals.

extract_protocol: RNA was extracted using an RNeasy Micro Kit (Qiagen) from 4 independent sorts per genoytpe.

treatment_protocol: 10 adrenals per genotype per sort were minced and digested by incubation in DMEM/F12 containing 0.1% collagenase/ 0.01% DNaseI solution for 1 h at 37°C. A single cell suspension was obtained following mechanical dispersion, filtration through a 40 micron nylon cell strainer, centrifugation at 1500rpm for 5 min followed by re-suspension in sterile 1X PBS containing 10% cosmic calf serum and 10μg/mL Propidium iodide (PI). 10,000 -50,000 viable GFP-positive cells were isolated via FACS using a BD FACSAria III cell sorter.

tag: strain/background

tag: genotype/variation

tag: age

value: 6 weeks

value: adrenocortical cells

tag: reporter sorted for


title: LRH-1 hep-/- liver, biological replicate 1

description: Gene expression data

source_name: LRH-1 hep-/- liver 1

tag: genotype


title: LRH-1 hep-/- liver, biological replicate 5

description: Gene expression data

source_name: LRH-1 hep-/- liver 5


title: LRH-1 hep-/- liver, biological replicate 4

description: Gene expression data

source_name: LRH-1 hep-/- liver 4


title: Human stomach 06-normal


title: LRH-1 hep-/- liver, biological replicate 3

description: Gene expression data

source_name: LRH-1 hep-/- liver 3


title: SF1+ mouse adrenocortical cells, biological replicate 4

description:
Biological replicate 4
007

source_name: SF1+ mouse adrenocortical cells


title: LRH-1 hep-/- liver, biological replicate 8

description: Gene expression data

source_name: LRH-1 hep-/- liver 8


title: SF1+ mouse adrenocortical cells, biological replicate 2

description:
Biological replicate 2
003


title: BIO-treated adrenocortical cancer cells from pair #4

description:
Replicate 4
004_Bio4

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized for 20 hr at 48C on Mouse Gene 1.1 ST Array Strips using the Affymetrix Gene Atlas system (software version 1.0.4.267).

data_processing: Data was analyzed using the oligo package implemented in the R-statistical environment version 2.15.1. RMA was used to estimate log2 transformed expression values for each probe-set. We analyzed only 28944 probe-sets with category "main", "---", and "flmrna->unmapped" according to Affymetrix annotation.

source_name: mouse adrenocortical tumor cell line ATCL7, BIO treated

label_protocol: Biotinylated cDNA were prepared according to the Ambion WT kit protocol from 250 ng total RNA (GeneAtlas™ WT Expression Kit User Manual P/N 702935 Rev. 3).

growth_protocol: Immortalized mouse adrenocortical ATCL7 cells are grown in a humidified incubator at 37deg C with 5% CO2. Normal growth medium is DMEM:F12 containing 100U/mL pencillin/streptomycin, 1X insulin-transferrin-selenium X, 2.5% fetal bovine serum and 2.5% horse serum. For treatments, cells are grown in a 'low serum' version of the same growth media, containing 0.025% fetal bovine serum and 0.025% horse serum.

extract_protocol: Total RNA was extracted from 250,000 cells using an RNeasy Plus Mini kit (Qiagen).

treatment_protocol: ATCL7 cells were treated with 0.5uM BIO (6-Bromoindirubin-3'-oxime) or 0.01% DMSO (v/v) for 24 hours, in low serum media described in the 'growth protocol'.

tag: cell line

value: adrenocortical tumor cell line

tag: treatment

value: BIO:0.5uM 6-Bromoindirubin-3'-oxime, for 24 h


title: SF1+ mouse adrenocortical cells, biological replicate 3

description:
Biological replicate 3
005

value: male


title: Wnt+ mouse adrenocortical cells, biological replicate 3

description:
Biological replicate 3
013


title: LRH-1 hep +/+ liver, biological replicate 5

description: Gene expression data

source_name: LRH-1 hep +/+ liver 5

value: LRH-1 hep +/+


title: LRH-1 hep +/+ liver, biological replicate 6

description: Gene expression data

source_name: LRH-1 hep +/+ liver 6


title: SF1+ mouse adrenocortical cells, biological replicate 1

description:
Biological replicate 1
001


title: LRH-1 hep +/+ liver, biological replicate 8

description: Gene expression data

source_name: LRH-1 hep +/+ liver 8


title: LRH-1 hep +/+ liver, biological replicate 4

description: Gene expression data

source_name: LRH-1 hep +/+ liver 4


title: Wnt+ mouse adrenocortical cells, biological replicate 2

description:
Biological replicate 2
009


title: Human stomach 05-normal

source_name: Normal stomach tissue from peritumoral region

value: early


title: LRH-1 hep +/+ liver, biological replicate 1

description: Gene expression data

source_name: LRH-1 hep +/+ liver 1


title: LRH-1 hep +/+ liver, biological replicate 3

description: Gene expression data

source_name: LRH-1 hep +/+ liver 3


title: BIO-treated adrenocortical cancer cells from pair #3

description:
Replicate 3
003_Bio3


title: BIO-treated adrenocortical cancer cells from pair #2

description:
Replicate 2
002_Bio2.


title: LRH-1 hep +/+ liver, biological replicate 2

description: Gene expression data

source_name: LRH-1 hep +/+ liver 2


title: LRH-1 hep +/+ liver, biological replicate 7

description: Gene expression data

source_name: LRH-1 hep +/+ liver 7


title: BIO-treated adrenocortical cancer cells from pair #1

description:
Replicate 1
001_Bio1


title: Vehicle-treated adrenocortical cancer cells from pair #4

description:
Replicate 4
008_Vehicle4

source_name: mouse adrenocortical tumor cell line ATCL7, vehicle control treated

value: vehicle control:0.01% DMSO (v/v) for 24 h


title: Vehicle-treated adrenocortical cancer cells from pair #3

description:
Replicate 3
007_Vehicle3


title: LRH-1 K289R liver, biological replicate 6

description: Gene expression data

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

data_processing: Samples were analyzed using Affymetrix Expression Console.

source_name: Mouse liver K289R 6

value: LRH-1 K289R


title: Human stomach 18-normal

value: female


title: Human stomach 27-normal


title: LRH-1 K289R liver, biological replicate 5

description: Gene expression data

source_name: Mouse liver K289R 5


title: Vehicle-treated adrenocortical cancer cells from pair #2

description:
Replicate 2
006_Vehicle2


title: Human stomach 02-normal


title: LRH-1 K289R liver, biological replicate 7

description: Gene expression data

source_name: Mouse liver K289R 7


title: Whole Blood_LPS_6h (7943271037_L)

city: London

first: Simon

last: Blankley

address: The Ridgeway

department: Division of Immunoregulation

institute: MRC - National Insititute for Medical Research

description:
Globin RNA reduced.
7943271037_L

hyb_protocol: Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion)

scan_protocol: Illumina Iscan

data_processing: Background subtraction using Genomestudio

source_name: Whole Blood

growth_protocol: 1ml Human whole blood with 100µl RPMI 1640- with GlutaMAX incubated at 37 degrees celcius and 5% C02

extract_protocol: 1ml added to 2mls Tempus solution. RNA extracted using PerfectPURE RNA Blood kit (5-PRIME), globin RNA reduced using GLOBINclear (Biosystems/Ambion)

treatment_protocol: Treated either with 1ng/ml LPS or 200ng/ml Pam3CSK4 or media alone

value: whole blood

value: LPS 6h

tag: volunteer id


title: LRH-1 K289R liver, biological replicate 2

description: Gene expression data

source_name: Mouse liver K289R 2


title: Whole Blood_LPS_24h (7943271062_H)

description:
Globin RNA reduced.
7943271062_H

label_protocol: Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion)

value: LPS 24h


title: Whole Blood_LPS_3h (7943271084_C)

description:
Globin RNA reduced.
7943271084_C

value: LPS 3h


title: LRH-1 K289R liver, biological replicate 3

description: Gene expression data

source_name: Mouse liver K289R 3


title: LRH-1 K289R liver, biological replicate 4

description: Gene expression data

source_name: Mouse liver K289R 4


title: LRH-1 K289R liver, biological replicate 1

description: Gene expression data

source_name: Mouse liver K289R 1


title: Human stomach 03-normal

value: normal stomach


title: Whole Blood_LPS_0h (7943271062_B)

description:
Globin RNA reduced.
7943271062_B

value: LPS 0h


title: Whole Blood_LPS_12h (7927538083_B)

description:
Globin RNA reduced.
7927538083_B

value: LPS 12h


title: LRH-1 WT liver, biological replicate 6

description: Gene expression data

source_name: Mouse liver WT6

value: liver

value: LRH-1 WT


title: Whole Blood_LPS_12h (7927520084_C)

description:
Globin RNA reduced.
7927520084_C


title: LRH-1 WT liver, biological replicate 4

description: Gene expression data

source_name: Mouse liver WT4


title: Whole Blood_LPS_24h (7943271083_K)

description:
Globin RNA reduced.
7943271083_K


title: Vehicle-treated adrenocortical cancer cells from pair #1

description:
Replicate 1
005_Vehicle1

value: adrenocortical tumor cell line


title: LRH-1 WT liver, biological replicate 5

description: Gene expression data

source_name: Mouse liver WT5


title: Whole Blood_LPS_1h (7943271062_E)

description:
Globin RNA reduced.
7943271062_E

value: LPS 1h


title: LRH-1 WT liver, biological replicate 7

description: Gene expression data

source_name: Mouse liver WT7


title: LRH-1 WT liver, biological replicate 2

description: Gene expression data

source_name: Mouse liver WT2


title: Whole Blood_LPS_6h (8363885086_I)

description:
Globin RNA reduced.
8363885086_I


title: LRH-1 K289R jejunum, biological repliate 6

description: Gene expression data

source_name: Mouse jejunum K289R 6

value: jejunum


title: Whole Blood_LPS_1h (7943271006_D)

description:
Globin RNA reduced.
7943271006_D


title: Whole Blood_LPS_3h (7943271063_H)

description:
Globin RNA reduced.
7943271063_H


title: LRH-1 K289R jejunum, biological repliate 4

description: Gene expression data

source_name: Mouse jejunum K289R 4


title: LRH-1 K289R jejunum, biological repliate 7

description: Gene expression data

source_name: Mouse jejunum K289R 7


title: Whole Blood_LPS_0h (7943271084_B)

description:
Globin RNA reduced.
7943271084_B


title: Whole Blood_LPS_24h (7943271079_F)

description:
Globin RNA reduced.
7943271079_F


title: LRH-1 WT liver, biological replicate 1

description: Gene expression data

source_name: Mouse liver WT1


title: Whole Blood_LPS_12h (7943271037_G)

description:
Globin RNA reduced.
7943271037_G


title: LRH-1 K289R jejunum, biological repliate 2

description: Gene expression data

source_name: Mouse jejunum K289R 2


title: LRH-1 WT jejunum, biological repliate 6

description: Gene expression data

source_name: Mouse jejunum WT6


title: Human stomach 04-normal

source_name: Normal stomach tissue from peritumoral region


title: Whole Blood_LPS_0h (7943271076_B)

description:
Globin RNA reduced.
7943271076_B

source_name: Whole Blood


title: Whole Blood_LPS_12h (7943271062_D)

description:
Globin RNA reduced.
7943271062_D


title: Whole Blood_LPS_24h (7927520097_C)

description:
Globin RNA reduced.
7927520097_C


title: LRH-1 K289R jejunum, biological repliate 3

description: Gene expression data

source_name: Mouse jejunum K289R 3


title: LRH-1 WT jejunum, biological repliate 7

description: Gene expression data

source_name: Mouse jejunum WT7


title: LRH-1 K289R jejunum, biological repliate 1

description: Gene expression data

source_name: Mouse jejunum K289R 1


title: LRH-1 K289R jejunum, biological repliate 5

description: Gene expression data

source_name: Mouse jejunum K289R 5


title: Whole Blood_LPS_1h (8363885086_J)

description:
Globin RNA reduced.
8363885086_J


title: Whole Blood_LPS_3h (7927520044_J)

description:
Globin RNA reduced.
7927520044_J


title: Whole Blood_LPS_6h (7927520033_L)

description:
Globin RNA reduced.
7927520033_L


title: LRH-1 WT jejunum, biological repliate 5

description: Gene expression data

source_name: Mouse jejunum WT5


title: Human stomach 01-normal


title: LRH-1 WT jejunum, biological repliate 4

description: Gene expression data

source_name: Mouse jejunum WT4


title: LRH-1 WT jejunum, biological repliate 3

description: Gene expression data

source_name: Mouse jejunum WT3


title: Whole Blood_LPS_3h (7943271059_G)

description:
Globin RNA reduced.
7943271059_G


title: Whole Blood_LPS_6h (7943271076_I)

description:
Globin RNA reduced.
7943271076_I


title: Whole Blood_LPS_0h (7927538083_H)

description:
Globin RNA reduced.
7927538083_H


title: LRH-1 WT jejunum, biological repliate 2

description: Gene expression data

source_name: Mouse jejunum WT2


title: Whole Blood_LPS_1h (7927520097_B)

description:
Globin RNA reduced.
7927520097_B


title: LRH-1 WT jejunum, biological repliate 1

description: Gene expression data

source_name: Mouse jejunum WT1


title: Whole Blood_Pam3CSK4_24h (7927520030_I)

description:
Globin RNA reduced.
7927520030_I

value: Pam3CSK4 24h


title: Whole Blood_Pam3CSK4_6h (7943271063_G)

description:
Globin RNA reduced.
7943271063_G

value: Pam3CSK4 6h


title: Whole Blood_Pam3CSK4_12h (7943271062_C)

description:
Globin RNA reduced.
7943271062_C

value: Pam3CSK4 12h


title: Whole Blood_Pam3CSK4_3h (7943271063_K)

description:
Globin RNA reduced.
7943271063_K

value: Pam3CSK4 3h


title: ChIP-chip for HA-tagged Cdk11, replicate 3

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description:
biological replicate 1 of 2
cdk11-HA_rep3

hyb_protocol: Samples were hybridized according to standard Agilent protocols.

scan_protocol: Microarrays were scanned using a GenePix 4000B laser scanner (Axon Instrument)

data_processing: Spot quantification was carried out using GenePix (Axon Instruments). Following quantification, the ChIP microarray data was lowess-normalized and a binding ratio (ChIP enrichment) was calculated for each microarray feature by dividing the signal intensity of the immunoprecipitated DNA sample by that of the background control (input DNA).

organism: Schizosaccharomyces pombe

source_name: Cdk11-IP genomic DNA

label_protocol: Fluorophores were resuspended in 9 ul of NaHCO3 0.1 M and incubated with the pelleted DNA for 1 hour. The reaction was stopped by the addition of 4.5 ul of Hydroxylamine 4M and incubation for 15 minutes. The labelled samples were purified using the Qiagen PCR purification kit.

growth_protocol: A culture of 100ml was grown at 32C in YES medium until mid-log phase. Formaldehyde was added to a final concentration of 3% and cells were crosslinked for 10 mins. The crosslink was stopped by adding 20 ml of glycin 2.5 M and cells were further incubated for 5 min in a shaker.

extract_protocol: After formaldehyde crosslinking, cells were lysed using glass beads and chromain extracts were sonicated on a Branson Sonifier 450 to shear the  chromatin to an average size of ~500 bp. A single pulldown was performed with magnetic beads coated with appropriate antibodies and following decrosslinking and LM-PCR amplification of purified IP DNA, the sample was labeled and hybridized on a Agilent 4x44k array.

value: wild-type carrying Cdk11-HA

tag: chip antibody

value: HA.11 Clone 16B12 Monoclonal Antibody

tag: chip antibody vendor

value: Covance

tag: chip antibody cat. #

source_name: Input genomic DNA


title: ChIP-chip for HA-tagged Cdk11, replicate 4

description:
biological replicate 2 of 2
cdk11-HA_rep4


title: Whole Blood_Pam3CSK4_0h (7963862027_K)

description:
Globin RNA reduced.
7963862027_K

tag: tissue

value: whole blood

value: Pam3CSK4 0h


title: ChIP-chip for HA-tagged Cdk11, replicate 2

description:
biological replicate 2 of 2
cdk11-HA_rep2


title: LRH-1 WT liver, biological replicate 3

description: Gene expression data

source_name: Mouse liver WT3


title: Whole Blood_Pam3CSK4_12h (8363885086_G)

description:
Globin RNA reduced.
8363885086_G


title: Whole Blood_Pam3CSK4_3h (7927520084_G)

description:
Globin RNA reduced.
7927520084_G


title: Whole Blood_Pam3CSK4_6h (7943271084_L)

description:
Globin RNA reduced.
7943271084_L


title: Whole Blood_Pam3CSK4_1h (7943271071_C)

description:
Globin RNA reduced.
7943271071_C

value: Pam3CSK4 1h


title: monocytes biological rep 6

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

description: monocytes F

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);  Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.2.)

data_processing:
Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); 1way Anova and 2way Anova

label_protocol: NuGen Ovation Pico WTA System V2, M01224v2 (Cat No. 3302-24); Encore Biotin Module, M01111v6 (Cat No. 4200);

growth_protocol: freshly isolated blood granulocytes/monocytes and in vitro stimulated granulocytes grown in RPMI

extract_protocol: Qiagen Rneasy Micro  Kit

treatment_protocol: Stimulated with pro-inflammatory cytokine mix (GM-CSF / TNFa / IL-1b) for 5 days in vitro

tag: patient id

value: F

value: freshly isolated blood monocytes

tag: cell population

value: FACS sorted for CD14+

tag: stimulated with


title: CD54neg biological rep 2

description: CD54neg B

value: B

value: freshly isolated granulocytes G-CSF mobilized blood

value: FACS sorted for CD15+CD54-


title: granulocytes biological rep 6

description: granulocytes F

value: freshly isolated blood granulocytes


title: CD14pos biological rep 3

description: CD14pos C

value: C

value: G-CSF mobilized neutrophils

value: FACS sorted on day 5 for CD14+

value: pro-inflammatory cytokine mix (GM-CSF/TNFa/IL-1b) for 5 days in vitro


title: Whole Blood_Pam3CSK4_24h (7943271058_G)

description:
Globin RNA reduced.
7943271058_G

value: Pam3CSK4 24h


title: CD54neg biological rep 3

description: CD54neg C


title: ChIP-chip for HA-tagged Cdk11, replicate 1

description:
biological replicate 1 of 2
cdk11-HA_rep1

value: wild-type carrying Cdk11-HA

value: HA.11 Clone 16B12 Monoclonal Antibody


title: Whole Blood_Pam3CSK4_0h (7943271062_J)

description:
Globin RNA reduced.
7943271062_J

value: whole blood


title: Whole Blood_Pam3CSK4_12h (7935440042_G)

description:
Globin RNA reduced.
7935440042_G

value: Pam3CSK4 12h


title: Whole Blood_Pam3CSK4_3h (7935440042_K)

description:
Globin RNA reduced.
7935440042_K

value: Pam3CSK4 3h


title: CD54neg biological rep 1

description: CD54neg A

value: A


title: monocytes biological rep 7

description: monocytes G

value: G

value: freshly isolated blood monocytes


title: monocytes biological rep 5

description: monocytes E

value: E

value: FACS sorted for CD14+


title: Whole Blood_Pam3CSK4_1h (7927520084_J)

description:
Globin RNA reduced.
7927520084_J

value: Pam3CSK4 1h


title: CD54neg biological rep 4

description: CD54neg D

value: D

value: freshly isolated granulocytes G-CSF mobilized blood

value: FACS sorted for CD15+CD54-


title: CD14pos biological rep 4

description: CD14pos D

value: G-CSF mobilized neutrophils

value: FACS sorted on day 5 for CD14+


title: Whole Blood_Pam3CSK4_1h (7927520097_J)

description:
Globin RNA reduced.
7927520097_J


title: CD14pos biological rep 2

description: CD14pos B

value: B

value: pro-inflammatory cytokine mix (GM-CSF/TNFa/IL-1b) for 5 days in vitro


title: granulocytes biological rep 5

description: granulocytes E

value: freshly isolated blood granulocytes


title: granulocytes biological rep 7

description: granulocytes G


title: Whole Blood_Pam3CSK4_6h (7943271079_L)

description:
Globin RNA reduced.
7943271079_L

value: whole blood

value: Pam3CSK4 6h


title: Whole Blood_Pam3CSK4_24h (7963862027_F)

description:
Globin RNA reduced.
7963862027_F

value: Pam3CSK4 24h


title: Whole Blood_Pam3CSK4_24h (7927520044_E)

description:
Globin RNA reduced.
7927520044_E


title: Whole Blood_Pam3CSK4_12h (7963862027_G)

description:
Globin RNA reduced.
7963862027_G

value: Pam3CSK4 12h


title: Whole Blood_Pam3CSK4_3h (7927520044_G)

description:
Globin RNA reduced.
7927520044_G

value: Pam3CSK4 3h


title: Whole Blood_Pam3CSK4_6h (7963862027_C)

description:
Globin RNA reduced.
7963862027_C


title: Whole Blood_Media_3h (7943271059_F)

description:
Globin RNA reduced.
7943271059_F

value: Media 3h


title: Whole Blood_Media_24h (7927520044_D)

description:
Globin RNA reduced.
7927520044_D

value: Media 24h


title: Whole Blood_Media_1h (7943271006_K)

description:
Globin RNA reduced.
7943271006_K

value: Media 1h


title: Whole Blood_Media_24h (7943271037_I)

description:
Globin RNA reduced.
7943271037_I


title: Whole Blood_Media_6h (7963862025_E)

description:
Globin RNA reduced.
7963862025_E

value: Media 6h


title: Whole Blood_Media_1h (7927520030_J)

description:
Globin RNA reduced.
7927520030_J


title: Whole Blood_Media_1h (7927520084_B)

description:
Globin RNA reduced.
7927520084_B


title: Whole Blood_Media_1h (7943271076_H)

description:
Globin RNA reduced.
7943271076_H


title: Whole Blood_Pam3CSK4_0h (7927520030_H)

description:
Globin RNA reduced.
7927520030_H

value: Pam3CSK4 0h


title: Whole Blood_Media_6h (7927520044_F)

description:
Globin RNA reduced.
7927520044_F


title: Whole Blood_Media_12h (7943271083_G)

description:
Globin RNA reduced.
7943271083_G

value: Media 12h


title: CD14pos biological rep 1

description: CD14pos A

value: A


title: Whole Blood_Media_12h (7927520030_B)

description:
Globin RNA reduced.
7927520030_B


title: Whole Blood_Media_12h (7943271076_C)

description:
Globin RNA reduced.
7943271076_C


title: Whole Blood_Media_24h (7963862025_A)

description:
Globin RNA reduced.
7963862025_A


title: Whole Blood_Media_3h (7963862027_I)

description:
Globin RNA reduced.
7963862027_I


title: Whole Blood_Media_0h (7935440042_H)

description:
Globin RNA reduced.
7935440042_H

value: Media 0h


title: Whole Blood_Media_3h (7927538083_F)

description:
Globin RNA reduced.
7927538083_F


title: Whole Blood_Media_6h (7943271058_J)

description:
Globin RNA reduced.
7943271058_J


title: Whole Blood_Media_0h (7943271083_A)

description:
Globin RNA reduced.
7943271083_A


title: Whole Blood_Media_12h (7963862025_L)

description:
Globin RNA reduced.
7963862025_L


title: Whole Blood_Pam3CSK4_1h (7943271059_K)

description:
Globin RNA reduced.
7943271059_K

value: Pam3CSK4 1h


title: Whole Blood_Media_24h (7943271071_D)

description:
Globin RNA reduced.
7943271071_D


title: Akirin2 KO_macrophages stimulated with LPS for 4h

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

country: Japan

institute: Kyoto University

description: Gene expression data from Akirin2 KO macrophages stimulated with LPS for 4h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Gene CHIP scanner 3000.

data_processing: The data were analyzed with RMA using the arrayassist program (Stratagene).

label_protocol: Biotinylated cRNA were prepared by NuGEN Ovation system according to the manufacturer's instructions.

growth_protocol: peritoneal macrophages were preprared from thioglycollate-injected mice.

treatment_protocol: stimulated with 100 ng/ml LPS for indicated periods

value: macrophage

tag: strain


title: med3Δ YEPD replicate 3

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

description: Candida dubliniensis wild type versus med3Δ mutant in YEPD medium

hyb_protocol: Hybridization and washing of the arrays was carried out using the Agilent Gene Expression Hybridization Kit and Gene Expression Wash Pack according the manufacturer’s instructions.

scan_protocol: Slides were scanned using the GenePix personal 4100A scanner (Axon) and data was extracted with GenePix Pro 6.1 (Axon).

data_processing: Spots were flagged absent if the signal was less than background +1 standard deviation in both fluorescent channels. Raw data was exported to GeneSpring GX12 and signals for each replicate spot were background corrected and normalized using Loess normalization. Log2 fluorescence ratios were generated for each replicate spot and averaged. Oligonucleotides were excluded from analysis if >50% of replicates in each condition were flagged absent.

organism: Candida dubliniensis

source_name: Candida dubliniensis YEPD broth, 37˚C, OD600nm 1.0

label_protocol: Total RNA was labelled with Cy5 or Cy3 using the Agilent Quick AmpTwo-Color Labelling Kit

growth_protocol: For YEPD experiments, Candida cells were cultured in standard YEPD broth at 37˚C until they reached OD600nm 0.8. For 10% serum experiments, cultures were growth overnight in YEPD at 30˚C, washed and diluted and 2 x106 cells/ml were added to 10% serum for the indicated time.

extract_protocol: Total RNA was extracted using the Qiagen RNA minikit using a microdismembrator (Braun, Melsungen,Germany) for cell breakage.

treatment_protocol: Cells were spun down at 2,500 x g for 5 min and flash frozen in liquid Nitrogen

value: wild type


title: Whole Blood_Pam3CSK4_0h (7927520097_D)

description:
Globin RNA reduced.
7927520097_D


title: Akirin2 KO_macrophages unstimulated

description: Gene expression data from unstimulated Akirin2 KO macrophages

source_name: Akirin2 KO_macrophages unstimulated

tag: cell type


title: Wild-type_macrophages stimulated with LPS for 4h

description: Gene expression data from wild-type macrophages stimulated with LPS for 4h

value: wildtype


title: med3Δ 1h 10% Serum replicate 4

description: Candida dubliniensis wild type versus med3Δ  mutant in hypha-inducing conditions (10% serum at 37˚C)

source_name: Candida dubliniensis 1h in 10% serum at 37˚C


title: med3Δ 1h 10% Serum replicate 3


title: Akirin2 KO_macrophages stimulated with LPS for 2h

description: Gene expression data from Akirin2 KO macrophages stimulated with LPS for 2h


title: med3Δ 1h 10% Serum replicate 2


title: Quiescent alpha 7

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: QSC

hyb_protocol: For microarray analysis, 100ng of total RNA was amplified and hybridized to the Mouse Gene 1.0 ST array.

scan_protocol: According to the standard Affymetrix protocol using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Expression data was processed using Gene Expression Console (Affymetrix) and RMA expression values were generated.

source_name: Quiescent muscle satellite cells

label_protocol: According to the Affymetrix protocol.

growth_protocol: HAMS's F10 + 20% FBS + bFGF(4ng/ml) for the specified time (0h, 2d, 5d). Quiescent Satellite Cells were process directly from FACS isolation

extract_protocol: For microarray cells were obtained from six week old BALB/c mice. Total RNA was isolated from freshly FACS isolated quiescent satellite cells that were pooled from nine mice, or in triplicates from established mouse primary myoblasts and differentiated myotubes using the RNeasy mini kit (Qiagen).

treatment_protocol: Satellite cells and non-satellite cells were FACS purified from 4 day CTX injured or uninjured muscle of Pax7-zsGreen mice by gating for zsGreen and Hoechst (Bosnakovski et al., 2008). RNA was extracted from 15,000 FACS sorted cells per condition with PicoPure RNA isolation kit (Applied Biosystems) according to manufacturer's recommendations including a DNase (Qiagen) digestion step. cDNA synthesis was performed with SuperScript III reverse transcriptase (Invitrogen) using a mixture of oligodT and random hexamer primers.

value: Balb/c

tag: tissue of origin

value: skeletal muscle

tag: replicate

value: quiescent satellite cells


title: Whole Blood_Media_0h (7943271058_E)

description:
Globin RNA reduced.
7943271058_E

source_name: Whole Blood

value: whole blood


title: med3Δ YEPD replicate 2

tag: genotype/variation


title: Wild-type_macrophages_unstimulated

description: Gene expression data from unstimulated wild-type macrophages


title: Wild-type_macrophages stimulated with LPS for 2h

description: Gene expression data from wild-type macrophages stimulated with LPS for 2h


title: med3Δ 1h 10% Serum replicate 1


title: tlo1Δ/tlo2Δ + TLO2 1h 10% Serum replicate 4

description: Candida dubliniensis tlo1Δ/tlo2Δ versus a TLO2 complemented mutant hypha-inducing conditions (10% serum at 37˚C)

value: tlo1Δ/tlo2Δ + TLO2


title: shMiwi, biological rep2

city: Shanghai

first: Lantao

last: Gou

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology

description: Gene expression data from mouse elongating spermatids transduced with lentiviral Miwi shRNA vector

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.

source_name: Mouse elongating spermatids transduced with lentiviral Miwi shRNA vector

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: Testis transduction was performed in 5-week-old ICR male mice with shMiwi:GFP, shCaf1:GFP, or control pSilencer:GFP vectors.

treatment_protocol: GFP+ elongating spermatids were sorted from isolated total germ cells of transduced mouse testes 1 week post-transduction.

value: elongating spermatids

tag: age

value: adult

value: ICR