title: Namalwa ID3 - 24 hours - mAdbID:117526

description: mAdb experiment ID: 117526

source_name: Namalwa ID3 - 24 hours

value: transduced with retroviral vectors expressing ID3

source_name: Namalwa Empty Vector - 24 hours

value: transduced with empty retroviral vectors


title: Namalwa ID3 - 48 hours - mAdbID:117527

status: Public on Aug 16 2012

type: RNA

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

country: USA

institute: National Cancer Institute

description: mAdb experiment ID: 117527

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

molecule: total RNA

organism: Homo sapiens

source_name: Namalwa ID3 - 48 hours

label_protocol:
Cy5 Labeling Protocol
Other: A 1 ug of total RNA was labeled with Cy5.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing ID3. ID3 expression was induced with doxycycline for 48 hours.

tag: tissue

value: Blood

tag: cell line

value: Namalwa

tag: cell type

value: B cells

tag: disease state

value: Burkitt's Lymphoma

tag: treatment

source_name: Namalwa Empty Vector - 48 hours

label_protocol:
Cy3 Labeling Protocol
Other: A 1 ug of total RNA was labeled with Cy3.

treatment_protocol:
Treatment type: transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with empty retroviral vectors. Doxycycline induction for 48 hours.


title: Luc_shRNA_Jurkat, biological replicate1

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Gene expression data from Jurkat cells transduced with Luciferase shRNA for 72 hrs

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Individual Arrays were normalized using Robust Multichip Averaging (RMA) within the Affytmetrix package from Bioconductor. Probeset definitions for RefSeq genes were derived from CDF version 13.0.0 downloaded from (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) based on improved definitions (Sandberg and Larsson, 2007).

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The Jurkat T-ALL cell line was grown in RPMI-1640 medium supplemented with 10% FBS, L-glutamine and penicillin/streptomycin at 37C in a CO2 incubator.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) followed by a column purification using RNeasy Mini Kit (QIAGEN, Valencia, CA) according to the manufacturers instructions.

treatment_protocol: The Jurkat cells were infected with shRNA lentivirus in the presence of polybrene by centrifugation at 2,500 rpm for 1.5 h followed by a incubation for overnight in a CO2 incubator.  Total RNA was harvested after 3 days of infection.

value: Jurkat E6-1


title: GFP_shRNA1_Jurkat, biological replicate1

description: Gene expression data from Jurkat cells transduced with GFP shRNA for 72 hrs


title: HeLa-normox

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

source_name: Uterine cervical cancer

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

growth_protocol: The cells were incubated in Dulbecco's Modified Eagle medium with GlutaMAX supplemented with 10% fetal calf serum (FCS) and 100 U/ml penicillin/streptomycin (Gibco) under a 5% CO2 atmosphere at 37°C, and subcultured twice a week.

extract_protocol: RNA was extracted using RNeasy MiniKit (Quiagen), according to the manufacturers’ instructions.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were plated out in plastic dishes (3x105 cells for 6 cm dishes, 9x105 for 10 cm dishes) 24 h prior to exposure to hypoxic (0.2% O2, 5% CO2) or normoxic (95% air, 5% Co2) conditions for 24 h at 37°C. The hypoxia treatment was performed in an Invivo2200 chamber (Ruskinn Technology Ltd, Bridgend, UK) with accurate O2 and CO2 controls.

value: HeLa

value: Uterine cervical cancer

tag: histology

value: Squamous cell carcinoma

value: untreated


title: Luc_shRNA_Jurkat, biological replicate2

source_name: Jurkat cells transduced with Luciferase shRNA for 72 hrs


title: HeLa-hypox

description: Hela-hyp

value: hypoxia exposed


title: Subject4_UterusvsLiver(dyeswap)

type: genomic

city: Palo Alto

first: Maeve

last: O'Huallachain

state: CA

address: 1501 S. California Ave. Rm 2204

institute: Stanford University

hyb_protocol: Hybridization and washing was done using NimbleGen hyb and wash buffers per the NImbleGen protocol

scan_protocol: Arrays were scanned using the Roche MS200 scanner per manufacturer's protocol

data_processing: Arrays were processed using NimbleGen's standard protocol for NimbleScan 2.6 aCGH data extraction

molecule: genomic DNA

source_name: Subject4 Uterus

label_protocol: Genomic DNA was labeled using the NimbleGen labeling protocol

extract_protocol:
Tissues were dissected postmortem and flash frozen
DNA was extracted from frozen tissues using the QIAGEN DNeasy Blood & Tissue Kit

value: Uterus

source_name: Subject4 Liver

value: Liver


title: THOMAS shTCF3 - 72 hours - mAdbID:117408

description: mAdb experiment ID: 117408

source_name: THOMAS shControl - 72 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 72 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 72 hours.

value: THOMAS

source_name: THOMAS shTCF3 - 72 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 72 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shTCF3 expression was induced with doxycycline for 72 hours.


title: GFP_shRNA1_Jurkat, biological replicate2

source_name: Jurkat cells transduced with GFP shRNA for 72 hrs


title: THOMAS shTCF3 - 96 hours - mAdbID:117409

description: mAdb experiment ID: 117409

source_name: THOMAS shControl - 96 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 96 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 96 hours.

source_name: THOMAS shTCF3 - 96 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 96 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shTCF3 expression was induced with doxycycline for 96 hours.


title: SiHa-normox

value: SiHa


title: Subject4_UterusvsLiver(regular)


title: Subject4_SIvsLiver(dyeswap)

source_name: Subject4 SI

value: Small Intestine


title: THOMAS shTCF3 - 24 hours - mAdbID:117406

description: mAdb experiment ID: 117406

source_name: THOMAS shControl - 24 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 24 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 24 hours.

source_name: THOMAS shTCF3 - 24 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 24 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shTCF3 expression was induced with doxycycline for 24 hours.


title: THOMAS shTCF3 - 48 hours - mAdbID:117407

description: mAdb experiment ID: 117407

source_name: THOMAS shControl - 48 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 48 hours.

source_name: THOMAS shTCF3 - 48 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shTCF3 expression was induced with doxycycline for 48 hours.


title: FaDu miR-7 rep 3

city: Nedlands

first: Patrick

middle: Aaron

last: Candy

state: Western Australia

address: 6 Verdun St

department: Cancer Medicine

country: Australia

institute: Perkins Institute

description:
biological replicate 3
SAMPLE 6

data_processing: The data were normalised using quantile normalisation with lumiR (v. 1.14.0) in R (v.2.11.0).

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

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

value: FaDu

value: head and neck cancer cells

tag: transfected with


title: FaDu miR-7 rep 2

description:
biological replicate 2
SAMPLE 5


title: TMD8 Lenalidamide -6 hours - mAdbID:108495

description: mAdb experiment ID: 108495

hyb_protocol: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

source_name: TMD8 DMSO (vehicle control)

label_protocol: Cy3 labling protocol : A 1 ug of total RNA was labeled with Cy3.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

value: blood

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: TMD8 Lenalidamide - 6 hours

label_protocol: Cy5 labling protocol : A 1 ug of total RNA was labeled with Cy5.

treatment_protocol:
Treatment type: compound
Agent: lenalidamide
Treatment dose: 10 uM
Treatment time: 6 hours


title: TMD8 Lenalidamide -3 hours - mAdbID:108494

description: mAdb experiment ID: 108494

source_name: TMD8 Lenalidamide - 3 hours

treatment_protocol:
Treatment type: compound
Agent: lenalidamide
Treatment dose: 10 uM
Treatment time: 3 hours


title: FaDu miR-7 rep 1

description:
biological replicate 1
SAMPLE 4


title: Subject4_SIvsLiver(regular)


title: FaDu miR-NC rep 3

description:
biological replicate 3
SAMPLE 3

value: miR-NC (negative control)


title: FaDu miR-NC rep 1

description:
biological replicate 1
SAMPLE 1


title: Subject4_PancreasvsLiver(dyeswap)

source_name: Subject4 Pancreas

value: Pancreas


title: TMD8 Lenalidamide -24 hours - mAdbID:107904

description: mAdb experiment ID: 107904

source_name: TMD8 Lenalidamide - 24 hours

treatment_protocol:
Treatment type: compound
Agent: lenalidamide
Treatment dose: 10 uM
Treatment time: 24 hours


title: OCILY10 Lenalidamide -48 hours - mAdbID:107903

description: mAdb experiment ID: 107903

source_name: OCILY10 DMSO (vehicle control)

source_name: OCILY10 Lenalidamide - 48 hours

treatment_protocol:
Treatment type: compound
Agent: lenalidamide
Treatment dose: 10 uM
Treatment time: 48 hours


title: OCILY10 Lenalidamide -24 hours - mAdbID:107902

description: mAdb experiment ID: 107902

source_name: OCILY10 Lenalidamide - 24 hours


title: MBNL2 KO, biological rep3

city: Santa Cruz

first: Lily

last: Shiue

address: 1156 High Street

department: MCD Biology

institute: UCSC

hyb_protocol: Hybridization was performed as specified, with the GeneChip Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
GPL13185_mjay.pgf
GPL13185_mjay.clf

organism: Mus musculus

source_name: wild-type hippocampus

label_protocol: cDNA synthesis and amplification was performed using the WT Expression Kit (Ambion). Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Hippocampi dissected from MBNL2 deltaE2/deltaE2 mice or WT female mice, 2-3 months of age

extract_protocol: Mice were genotyped and whole brains were dissected from 6 mutant and 6 wild-type animals. Total RNA was extracted using Trizol.

tag: age

value: hippocampus

tag: genotype

value: wild-type

tag: gender

value: Female

tag: genetic background


title: Subject4_PancreasvsLiver(regular)

source_name: Subject4 Liver


title: Subject3_OvaryvsPancreas(regular)

source_name: Subject3 Pancreas

source_name: Subject3 Ovary

value: Ovary


title: TMD8 Lenalidamide -48 hours - mAdbID:107905

description: mAdb experiment ID: 107905

source_name: TMD8 Lenalidamide - 48 hours


title: MBNL2 KO, biological rep1


title: MDA-MB231 cells with shRNA #4 targeting Coco, biological rep3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files.

source_name: MDA-MB231 cells stably transduced with lentiviral vectors encoding a shRNA targeting Coco (shco4)

label_protocol: 200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: 10% fetal bovine serum with DMEM media, 37 degree 5% CO2 incubator

extract_protocol: RNA extraction plus kit was used to isolate RNA, and cDNA was made with invitrogen superscriptase.

treatment_protocol: The lentivirus pLKO vector expression Coco shRNAs (TRCN0000149666 and TRCN0000148148) was used to make stable cell line knocking down Coco.

tag: lentiviral vector transduction

value: shco4 shRNA targeting Coco

tag: genotype/variation

value: Coco knock down


title: MDA-MB231 cells with shRNA #4 targeting Coco, biological rep2


title: MBNL2 KO, biological rep2


title: Subject3_OvaryvsPancreas(dyeswap)


title: WT, biological rep3 (MBNL2 KO)

source_name: MBNL2 deltaE2/deltaE2 hippocampus

value: MBNL2 deltaE2/deltaE2


title: MDA-MB231 cells with shRNA #4 targeting Coco, biological rep1


title: Subject3_SIvsPancreas(dyeswap)

source_name: Subject3 SI


title: Subject3_SIvsPancreas(regular)


title: WT, biological rep2 (MBNL2 KO)


title: Mouse A PyMT mammary epithelium organotypic culture in Collagen I 4 days with FGF2

city: Baltimore

first: Kevin

middle: J

last: Cheung

address: 855 N. Wolfe St, Rangos 452, Center for Cell Dynamics, Johns Hopkins School of Medicine

department: Cell Biology

institute: Center for Cell Dynamics

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent,).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  These intensities were further processed using R and Bioconductor. We performed quantile normalization using the Agi4x44PreProcess package.  No further background subtracted was performed.

source_name: PyMT mammary tumor epithelium_collagen I_Day 4

label_protocol: Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

growth_protocol: We isolated mouse mammary organoids from normal mice using previously described techniques (Fata et al., 2007; Ewald et al., 2008). Briefly, we dissected the #3 and #4 mammary glands and digested this tissue into epithelial fragments by a combination of mechanical and collagenase/trypsin digestion. We then separated these fragments from single cells by differential centrifugation. The final pellet was composed of epithelial fragments, each containing several hundred cells.  Tumors were harvested from mice at 12-16 weeks of age, coinciding with poorly differentiated carcinomas. We surgically isolated the largest tumor in each mouse and processed it as above. Any incompletely digested large tumor fragments were removed prior to differential centrifugation. We also added additional rounds of differential centrifugation as needed to remove single cells.  We embedded organoids derived from normal and tumor epithelium in 3D Matrigel (BD Biosciences 354230) or type I rat tail collagen gels (BD Biosciences 354236). All cultures were set up in 24-well coverslip bottom plates (E&K Scientific EK-42892), or 2-well or 4-well coverslip bottom chambers (Nunc 155383). Acid solubilized rat tail collagen I gels (3 mg/ml collagen I, pH 7-7.5) were prepared as described in the Supplemental Methods. For each matrix, organoids were mixed to yield a suspension of 2-3 organoids/μl. A 100 μl suspension of organoids was plated in each well on the 37C heating block, followed by incubation at 37C for 45 min to allow polymerization. All murine samples were cultured in 1 ml of DMEM/F12 with 1% Penicillin/Streptomycin solution, 1% insulin transferrin solution and supplemented with 2.5 nM of FGF2.

extract_protocol: Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies (http://www.arrays.ucsf.edu and http://www.agilent.com).

treatment_protocol: In total, four unique conditions were profiled (Tumor vs. Normal; Collagen vs. Matrigel), each replicated at least 3 times in independent experiments.  All samples were collected at day 4 in FGF organoid media in the specified ECM microenvironments.

tag: strain

value: MMTV-PyMT

value: tumor-derived mammary organoids

tag: extracellular matrix (ecm) condition

value: collagen l

tag: collected on

value: day 4

tag: batch


title: OCILY10 Lenalidamide -3 hours - mAdbID:107900

description: mAdb experiment ID: 107900

tag: tissue

source_name: OCILY10 Lenalidamide - 3 hours


title: MDA-MB231 cells with shRNA #2 targeting Coco, biological rep3

source_name: MDA-MB231 cells stably transduced with lentiviral vectors encoding a shRNA targeting Coco (shco2)

tag: cell line

value: shco2 shRNA targeting Coco


title: Subject2_KidneyvsLung(regular)

source_name: Subject2 Lung

value: Lung

source_name: Subject2 Kidney

value: Kidney


title: WT, biological rep1 (MBNL2 KO)


title: Mouse A PyMT mammary epithelium organotypic culture in Matrigel 4 days with FGF2

source_name: PyMT mammary tumor epithelium_Matrigel_Day 4

value: Matrigel


title: HBL-1 shspib_2 - 96 hr - mAdbID:99284

description: mAdb experiment ID: 99284

source_name: HBL-1 shspib_2 - 96 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hr
In-vitro treatment: Cells were transduced with retroviral vectors expressing shspib_2. shRNA expression was induced with doxycycline for 96 hours.

value: blood

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: HBL-1 shControl - 96 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 96 hours.


title: MDA-MB231 cells with shRNA #2 targeting Coco, biological rep2


title: Subject2_AmygdalavsLung(regular)

source_name: Subject2 Amygdala

value: Amygdala


title: HBL-1 shspib_2 - 72 hr - mAdbID:99283

description: mAdb experiment ID: 99283

source_name: HBL-1 shspib_2 - 72 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hr
In-vitro treatment: Cells were transduced with retroviral vectors expressing shspib_2. shRNA expression was induced with doxycycline for 72 hours.

source_name: HBL-1 shControl - 72 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 72 hours.


title: Mouse C PyMT mammary epithelium organotypic culture in Matrigel 4 days with FGF2


title: MDA-MB231 cells with shRNA #2 targeting Coco, biological rep1


title: Subject2_LMvsLung(dyeswap)

source_name: Subject2 LM

value: Leptomeningeal tissue


title: MDA-MB231 cells with scramble shRNA, biological rep3

source_name: MDA-MB231 cells stably transduced with lentiviral vectors encoding a control shRNA (shscramble)

value: control shRNA (shscramble)

value: control


title: HBL-1 shspib_2 - 24 hr - mAdbID:99281

description: mAdb experiment ID: 99281

source_name: HBL-1 shspib_2 - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hr
In-vitro treatment: Cells were transduced with retroviral vectors expressing shspib_2. shRNA expression was induced with doxycycline for 24 hours.

source_name: HBL-1 shControl - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 24 hours.


title: Mouse C WT (FVB) mammary epithelium organotypic culture in Collagen I 4 days with FGF2

source_name: Normal mammary epithelium_collagen l_Day 4

value: FVB

value: normal mammary organoids


title: Mouse A WT (FVB) mammary epithelium organotypic culture in Matrigel 4 days with FGF2_batch 2

source_name: Normal mammary epithelium_Matrigel_Day 4


title: Subject2_AmygdalavsLung(dyeswap)


title: FaDu miR-NC rep 2

description:
biological replicate 2
SAMPLE 2

value: FaDu

tag: cell type

value: head and neck cancer cells

value: miR-NC (negative control)


title: M_236300

city: Columbus

first: Peter

last: White

state: OH

address: 700 Children's Drive

department: Microbial Pathogenesis

institute: Nationwide Children's Hospital

hyb_protocol: 16 Hours at 42 degrees Centigrade

scan_protocol: Scan according to manufacturer's protocol in 2-color mode

data_processing:
The FGC analysis script uses the following R packages: Exploratory analysis for two-color spotted microarray data (marray 1.12.0) Linear Models for Microarray Data (limma 2.9.8) SAM: Significance Analysis of Microarrays (samr 1.23) Assessing array quality on spotted arrays (arrayQuality 1.10.0) Convert Microarray Data Objects (convert 1.8.0) Hexagonal Binning Routines (hexbin 1.8.0)
The raw intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process.  The median red (Cy5) and green (Cy3) intensities are used to calculate the ratio of expression for each element on the array, in terms of M (log2(Red/Green)) and A ((log2(Red) + log2(Green))/2)). The M values are then global loess normalized within each array using the LIMMA microarray processing package in “R” (Smyth, 2004). This intensity based normalization approach adjusts the red and green intensities relative to one another so that the red/green ratios are as far as possible an unbiased representation of relative expression.

source_name: Pancreatic Islets Exposed to Pioglitazone and physiological (5.6 mM) glucose concentrations

label_protocol: A direct comparison design was used, generating cDNA from mRNA and labeling such that hybridizations were set up as Test was labeled with (Cy5) vs. Control was labeled with (Cy3). Five biological replicates were used for each condition.

growth_protocol: Islets were isolated from male Wistar rats (220-260g) after perfusion of the pancreatic duct, collagenase (Type V) digestion and purification on Ficoll gradients (Lacy & Kostianovsky 1967) and cultured in RPMI-1640 media with 10% FCS, 5.6 mM glucose, 100 IU/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: mRNA was extracted by Trizol according to manufacturer's recommendations

treatment_protocol: After 24 h of isolation, islets were cultured with 10 µM Pioglitazone (Takeda Pharmaceuticals, Japan) or DMSO (vehicle) for 24 h in either physiological (5.6 mM) or supraphysiological (23 mM) glucose concentrations. Both control and treated culture media contained 0.1% DMSO as a final concentration.

value: Wistar

value: Pancreatic Islets

value: Pio 10 5.6 mM

source_name: DMSO (control) exposed Pancreatic Islets

value: DMSO 5.6 mM


title: Subject2_LMvsLung(regular)

value: Lung


title: Subject1_LivervsKidney(dyeswap)

source_name: Subject1 Liver

value: Liver

source_name: Subject1 Kidney

value: Kidney


title: Mouse C PyMT mammary epithelium organotypic culture in Collagen I 4 days with FGF2

source_name: PyMT mammary tumor epithelium_collagen I_Day 4

value: MMTV-PyMT

value: tumor-derived mammary organoids

value: collagen l

value: day 4


title: MDA-MB231 cells with scramble shRNA, biological rep2

value: control shRNA (shscramble)

value: control


title: OCILY10 Lenalidamide -6 hours - mAdbID:107901

description: mAdb experiment ID: 107901

source_name: OCILY10 DMSO (vehicle control)

value: blood

tag: disease state

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: OCILY10 Lenalidamide - 6 hours


title: M_236310

tag: treatment


title: M_236307


title: Subject1_LivervsKidney(regular)


title: Subject1_PancreasvsKidney(dyeswap)

source_name: Subject1 Pancreas

value: Pancreas


title: HBL-1 shspiB_2_3'UTR 48 hr - mAdbID:99273

description: mAdb experiment ID: 99273

source_name: HBL-1 shspiB_2_3'UTR - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hr
In-vitro treatment: Cells were transduced with retroviral vectors expressing shspiB_2_3'UTR. shRNA expression was induced with doxycycline for 48 hours.

source_name: HBL-1 shControl - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 48 hours.


title: Subject1_PancreasvsKidney(regular)


title: MDA-MB231 cells with scramble shRNA, biological rep1


title: M_236299


title: Treated_8636

city: College Station

first: Qinglei

last: Li

state: TX

address: 4458 TAMU

institute: Texas A&M University

description:
JO1 sample 2
Sample name: 8636

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R. Technical replicates for Control sample 1 were averaged after normalization for subsequent analyses.

source_name: Mouse testis tissue

label_protocol: The total RNA was amplified and purified using Illumina TotalPrep RNA Amplification Kit (Ambion, Cat# IL1791) following kit instructions. Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit.

growth_protocol: Mice were housed in a light-controlled environment, and were fed standard chow ad libitum.

extract_protocol: Total RNA was extracted with Trizol reagent. RNA quality was checked using  a RNA Nano chips on the Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were treated with JQ1 (50 mg/kg) or vehicle daily for 6 weeks (6-12 weeks of age).

value: Male

tag: agent

value: Testis


title: Control_8635

description:
Control sample 2
Sample name: 8635

value: Control


title: HBL-1 shspiB_2_3'UTR 72 hr - mAdbID:99274

description: mAdb experiment ID: 99274

source_name: HBL-1 shspiB_2_3'UTR - 72 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hr
In-vitro treatment: Cells were transduced with retroviral vectors expressing shspiB_2_3'UTR. shRNA expression was induced with doxycycline for 72 hours.

source_name: HBL-1 shControl - 72 hr


title: HBL-1 chimeric repressor - 48 hr - mAdbID:115893

description: mAdb experiment ID: 115893

source_name: HBL-1 chimeric repressor - 48 hr

treatment_protocol:
Treatment type: chimeric repressor
Treatment time: 48 hr
In-vitro treatment: Cells were transduced with retroviral vectors allowing inducible expression of a chimeric repressor consisting of the DNA binding domains of IRF4 and SPIB fused together by an OCT linker (inspired by (Brass et al., 1999)). Chimeric repressor expression was induced with doxycycline for 48 hours.


title: MS_3

source_name: Pancreatic Islets Exposed to Pioglitazone and supraphysiological (23 mM) glucose concentrations

value: Wistar

value: Pancreatic Islets

value: Pio 10 23 mM

value: DMSO 23 mM


title: Treated_8634

description:
JO1 sample 1
Sample name: 8634


title: Mouse B PyMT mammary epithelium organotypic culture in Collagen I 4 days with FGF2


title: Mouse D WT (FVB) mammary epithelium organotypic culture in Matrigel 4 days with FGF2 (previously called D4F)

value: FVB

value: normal mammary organoids

value: Matrigel


title: Subject1_SIvsKidney(dyeswap)

source_name: Subject1 SI

value: Small Intestine

value: Kidney


title: MS_2


title: HBL-1 shspiB_2_3'UTR 96 hr - mAdbID:99275

description: mAdb experiment ID: 99275

source_name: HBL-1 shspiB_2_3'UTR - 96 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hr
In-vitro treatment: Cells were transduced with retroviral vectors expressing shspiB_2_3'UTR. shRNA expression was induced with doxycycline for 96 hours.

source_name: HBL-1 shControl - 96 hr


title: Control (technical replicate for 8633)

description:
Control sample 1 replicate
Sample name: 8633-TR


title: Mouse B WT (FVB) mammary epithelium organotypic culture in Matrigel 4 days with FGF2

description:
B.WMF4.avg
Technical repliates:  the same RNAs hybridizd to different arrays in batch 1 and 2, and data was averaged together.

source_name: Normal mammary epithelium_Matrigel_Day 4

value: day 4


title: Subject1_SIvsKidney(regular)


title: MS_5

source_name: DMSO (control) exposed Pancreatic Islets


title: Control_8633

description:
Control sample 1
Sample name: 8633


title: HBL-1 shspiB_2_3'UTR 24 hr - mAdbID:99272

description: mAdb experiment ID: 99272

source_name: HBL-1 shspiB_2_3'UTR - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hr
In-vitro treatment: Cells were transduced with retroviral vectors expressing shspiB_2_3'UTR. shRNA expression was induced with doxycycline for 24 hours.

source_name: HBL-1 shControl - 24 hr


title: Leiomyoma_FT_rep4

status: Public on Aug 15 2012

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

country: Spain

institute: iGenomix

hyb_protocol: cRNA was fragmented into pieces ranging from 35 to 200 bases which were confirmed using Agilent 2100 Bioanalyzer technology. Fragmented cRNA samples (1.65 μg) were hybridized onto chips through 17 h of incubation at 65 ºC with constant rotation.

scan_protocol: Hybridized microarrays were scanned in an Axon 4100A scanner (Molecular Devices, Sunnyvale, CA, USA) and data were extracted with GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). GenePix Pro 6.0 software was used for array image analysis and the calculation of spot intensity measurements which are considered to be raw data.

data_processing:
Spot intensities (medians) without background subtraction were transformed to log2 scale. Before quantile normalization, data were represented in a box plot to know the data distribution and to subtract abnormal microarray data. The replicates by gene symbol were merged and the data were filtered in order to delete the unknown sequences or probes without gene description.
The R-statistical software system was used as the tool for these purposes and downstream analysis.
Gene expression profiles were determined by comparison of the experimental groups with the control group (2 by 2 comparisons) with non-parametric tests and two criteria were used to define genes that had altered mRNA abundance among the different sample sets: an absolute fold change of 2.0 or more and a corresponding fold change pvalue lower than 0.05.

source_name: Leiomyoma total fraction

label_protocol: In short, first strand cDNA was transcribed from 1 ug of total RNA using the T7-Oligo(dT) Promotor Primer. Samples were in vitro transcribed and Cy-3 labelled, all with the Quick-AMP labelling kit (Agilent technologies, Madrid, Spain). The cRNA synthesis typically yielded between 10 and 15 μg. Following a further clean-up round (QIAGEN, Barcelona, Spain).

extract_protocol: RNA extraction was performed using the Mini RNA Isolation I Kit following the manufacturer’s protocol (Zymo Research).

value: human benign tumour (leiomyoma)

tag: fraction

value: total fraction cells


title: Leiomyoma_FT_rep1


title: HBL-1 chimeric repressor - 24 hr - mAdbID:115892

description: mAdb experiment ID: 115892

source_name: HBL-1 chimeric repressor - 24 hr

treatment_protocol:
Treatment type: chimeric repressor
Treatment time: 24 hr
In-vitro treatment: Cells were transduced with retroviral vectors allowing inducible expression of a chimeric repressor consisting of the DNA binding domains of IRF4 and SPIB fused together by an OCT linker (inspired by (Brass et al., 1999)). Chimeric repressor expression was induced with doxycycline for 24 hours.

value: blood

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)


title: Mouse A WT (FVB) mammary epithelium organotypic culture in Matrigel 4 days with FGF2


title: HBL-1 chimeric repressor - 4 hr - mAdbID:115890

description: mAdb experiment ID: 115890

source_name: HBL-1 shControl - 4 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 4 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 4 hours.

source_name: HBL-1 chimeric repressor - 4 hr

treatment_protocol:
Treatment type: chimeric repressor
Treatment time: 4 hr
In-vitro treatment: Cells were transduced with retroviral vectors allowing inducible expression of a chimeric repressor consisting of the DNA binding domains of IRF4 and SPIB fused together by an OCT linker (inspired by (Brass et al., 1999)). Chimeric repressor expression was induced with doxycycline for 4 hours.


title: Mouse B PyMT mammary epithelium organotypic culture in Matrigel 4 days with FGF2

source_name: PyMT mammary tumor epithelium_Matrigel_Day 4

treatment_protocol: In total, four unique conditions were profiled (Tumor vs. Normal; Collagen vs. Matrigel), each replicated at least 3 times in independent experiments.  All samples were collected at day 4 in FGF organoid media in the specified ECM microenvironments.

value: MMTV-PyMT

value: tumor-derived mammary organoids


title: Leiomyoma_FT_rep2


title: Leiomyoma_SP_rep4

source_name: Leiomyoma side population

value: side population cells


title: HBL-1 shspib_2 - 48 hr - mAdbID:99282

description: mAdb experiment ID: 99282

source_name: HBL-1 shspib_2 - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hr
In-vitro treatment: Cells were transduced with retroviral vectors expressing shspib_2. shRNA expression was induced with doxycycline for 48 hours.

source_name: HBL-1 shControl - 48 hr


title: Subject1_OLvsKidney(regular)

source_name: Subject1 Kidney

source_name: Subject1 OL

value: Occipital lobe


title: Leiomyoma_SP_rep2


title: Subject1_OLvsKidney(dyeswap)


title: MS_1

source_name: Pancreatic Islets Exposed to Pioglitazone and supraphysiological (23 mM) glucose concentrations

value: Wistar

value: Pancreatic Islets


title: Subject1_IPLvsKidney(regular)

source_name: Subject1 IPL

value: Inferior parietal lobe


title: Subject1_IPLvsKidney(dyeswap)


title: Leiomyoma_SP_rep3


title: Leiomyoma_FT_rep3


title: Down syndrome with Atrioventricular Septal Defect  P1094

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

country: France

institute: INSERM U1127-CNRS UMR7225-UPMC

description: replicate 5

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: lymphoblastoid cell line

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

extract_protocol: RNA was extracted with Macherey-Nagel RNAII mini-kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Male

tag: age (y)

tag: karyotype

value: Trisomic 21

value: lymphoblastoid cell line

tag: phenotype

value: Down syndrome Down syndrome with Atrioventricular Septal Defect


title: Down syndrome without congenital heart disease 04-446

description: replicate 17

tag: gender

value: Down syndrome Down syndrome without congenital heart disease


title: Down syndrome without congenital heart disease P1110

description: replicate 21

value: Female


title: Down syndrome without congenital heart disease 10161

description: replicate 15


title: Treated_8637

description:
JO1 sample 3
Sample name: 8637

source_name: Mouse testis tissue

value: Testis


title: HBL-1 chimeric repressor - 8 hr - mAdbID:115891

description: mAdb experiment ID: 115891

source_name: HBL-1 shControl - 8 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 8 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 8 hours.

source_name: HBL-1 chimeric repressor - 8 hr

treatment_protocol:
Treatment type: chimeric repressor
Treatment time: 8 hr
In-vitro treatment: Cells were transduced with retroviral vectors allowing inducible expression of a chimeric repressor consisting of the DNA binding domains of IRF4 and SPIB fused together by an OCT linker (inspired by (Brass et al., 1999)). Chimeric repressor expression was induced with doxycycline for 8 hours.


title: Down syndrome with Atrioventricular Septal Defect  10169

description: replicate 6


title: Down syndrome without congenital heart disease 10118

description: replicate 18


title: Down syndrome with Ventricular Septal Defect 10227

description: replicate 6

value: Down syndrome Down syndrome with Ventricular Septal Defect


title: Down syndrome with Atrial Septal Defect 213GAA

description: replicate 8

value: Down syndrome Down syndrome with Atrial Septal Defect


title: Down syndrome without congenital heart disease P1055

description: replicate 19


title: Down syndrome with Ventricular Septal Defect 10186

description: replicate 5


title: Down syndrome with Atrioventricular Septal Defect  OB 03-375

description: replicate 4


title: Mouse A WT (FVB) mammary epithelium organotypic culture in Collagen I 4 days with FGF2

source_name: Normal mammary epithelium_collagen l_Day 4

value: FVB

value: normal mammary organoids

value: collagen l

value: day 4


title: Subject1_LMvsKidney(dyeswap)

source_name: Subject1 LM

value: Leptomeningeal tissue

value: Kidney


title: Down syndrome with Atrial Septal Defect 10144

description: replicate 7


title: Down syndrome with Atrioventricular Septal Defect  10145

description: replicate 3


title: Down syndrome without congenital heart disease 10213

description: replicate 20


title: Down syndrome without congenital heart disease 10179

description: replicate 12


title: Down syndrome with Atrial Septal Defect 10194

description: replicate 5


title: Down syndrome without congenital heart disease 10204

description: replicate 13


title: Mouse B WT (FVB) mammary epithelium organotypic culture in Collagen I 4 days with FGF2


title: Down syndrome without congenital heart disease 3.31963

description: replicate 14


title: Down syndrome without congenital heart disease 10141

description: replicate 6


title: Down syndrome with Ventricular Septal Defect 10215

description: replicate 3


title: Down syndrome with Atrial Septal Defect 10198

description: replicate 4


title: Down syndrome with Atrial Septal Defect 10264

description: replicate 6


title: Down syndrome with Atrioventricular Septal Defect  10140

description: replicate 1


title: Down syndrome without congenital heart disease 10197

description: replicate 9


title: Down syndrome without congenital heart disease 10133

description: replicate 5


title: Down syndrome without congenital heart disease 10180

description: replicate 10


title: Down syndrome with Atrial Septal Defect 02-247

description: replicate 3


title: Subject2_KidneyvsLung(dyeswap)

source_name: Subject2 Kidney

source_name: Subject2 Lung

value: Lung


title: Down syndrome with Atrioventricular Septal Defect  290BEJ

description: replicate 2


title: Down syndrome with Ventricular Septal Defect 10111

description: replicate 4


title: Down syndrome without congenital heart disease 10143

description: replicate 11


title: Down syndrome without congenital heart disease 10130

description: replicate 7


title: Down syndrome without congenital heart disease 3.32061

description: replicate 8


title: Down syndrome with Atrial Septal Defect 10173

description: replicate 2


title: Down syndrome without congenital heart disease 10115

description: replicate 4


title: Down syndrome with Ventricular Septal Defect 42FAY

description: replicate 2


title: Down syndrome without congenital heart disease 10113

description: replicate 3


title: Down syndrome without congenital heart disease 10112

description: replicate 2


title: Down syndrome without congenital heart disease 117ANM

description: replicate 22


title: Down syndrome without congenital heart disease 3.32064

description: replicate 1


title: Subject1_LMvsKidney(regular)


title: Autism_Cer_AN17678

city: Cleveland

first: Matthew

last: Ginsberg

address: 9500 Euclid Ave

department: Lerner College of Medicine

institute: Cleveland Clinic Foundation

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to the Illumina Infinium Human Methylation27 Beadchip using the standard Illumina protocol.

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

data_processing: BeadStudio software v3.2. Unmethylated and methylated signal intensities were transformed into M-values using the methylumi package in R. Data were color-balanced and quantile-normalized. Please see the documentation for the methylumi package for more details on the M-value derivation (http://www.bioconductor.org/packages/2.9/bioc/html/methylumi.html).

label: Cy5 and Cy3

source_name: Fresh frozen brain tissue, cerebellar, autism

label_protocol: Standard Illumina protocol.

growth_protocol: Fresh frozen brain tissue.

extract_protocol: Genomic DNA was extracted and purified from fresh frozen brain tissue using the Qiagen AllPrep kit according to the manufacturer's instructions. DNA was bisulfite converted with the Zymo EZ DNA methylation kit.

value: brain

tag: brain region

value: cerebellar

value: autism

tag: age (years)

tag: Cause of death

value: other

tag: subject identifier


title: Control_occ_AN10833

source_name: Fresh frozen brain tissue, occipital cortex, control

value: occipital cortex

value: control

tag: postmortem interval (hours)

value: unknown


title: Control_Cer_AN10723

source_name: Fresh frozen brain tissue, cerebellar, control


title: Down syndrome with Ventricular Septal Defect 3.31964

description: replicate 1

value: Female

value: Trisomic 21

value: lymphoblastoid cell line


title: Down syndrome with Atrial Septal Defect 10114

description: replicate 1

value: Down syndrome Down syndrome with Atrial Septal Defect


title: Control_occ_BTB1453


title: Autism_Cer_AN03345

value: hypoxia


title: Leiomyoma_SP_rep1

source_name: Leiomyoma side population

value: human benign tumour (leiomyoma)

value: side population cells


title: Control_Cer_UMB4543


title: Control_occ_UMB1860

value: cardiac


title: Control_Cer_AN05475


title: Control_occ_AN15622


title: Control_Cer_AN15622


title: Autism_Cer_AN09730_rep3

description:
B1a-2
Technical replicate 3 of 3.


title: Down syndrome with Atrioventricular Septal Defect  10176

description: replicate 7

value: Down syndrome Down syndrome with Atrioventricular Septal Defect


title: Control_Cer_AN10833


title: Autism_occ_AN03345

source_name: Fresh frozen brain tissue, occipital cortex, autism


title: Control_occ_UMB4543


title: Autism_Cer_AN09730_rep2

description:
B1a-1
Technical replicate 2 of 3.


title: Control_occ_AN10723


title: Autism_occ_AN11989


title: Control_Cer_UMB4670


title: Autism_occ_AN08873


title: Control_occ_UMB4670


title: Autism_Cer_AN19511

value: cancer


title: Control_Cer_UMB1860

value: brain


title: Down syndrome without congenital heart disease 10172

description: replicate 16

value: Male

value: Down syndrome Down syndrome without congenital heart disease


title: Autism_occ_AN06420

value: autism


title: Autism_Cer_AN09714

value: cerebellar


title: Autism_Cer_AN11989


title: Control_Cer_BTB1453

value: control


title: Autism_occ_AN08166

value: occipital cortex


title: Autism_occ_AN19511


title: Autism_occ_AN09730


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_5,ID=30

city: Kingswood

first: Grant

last: Parnell

state: NSW

address: Nepean Hospital

department: Nepean Clinical School

institute: University of Sydney

hyb_protocol: Hyb protocol as per Illumina Whole-Genome Gene Expression Direct Hybridization Experienced User Guide

scan_protocol: Scanned using default parameters on Illumina BeadArray Reader

data_processing: Data were processed in GenomeStudio. Quantile normalisation was applied without background adjustment

label_protocol: cRNA prepared using Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA extracted using PAXgene blood RNA kit v2 (PreAnalytixs)

value: PAXgene whole blood

tag: sample type

tag: day

tag: ID

value: female


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=32

tag: tissue

value: bacterial pneumonia


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_2,ID=30


title: PAXgene whole blood, bacterial pneumonia,Day_5,ID=29


title: Control_occ_AN05475

tag: disease state


title: Control_Cer_BTB3228

value: other


title: Autism_Cer_AN08166


title: PAXgene whole blood, SIRS,Day_2,ID=27

source_name: PAXgene whole blood, SIRS,Day_2,ID=27

value: systemic inflammatory response

value: male


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=32


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=32


title: PAXgene whole blood, bacterial pneumonia,Day_4,ID=29


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=29


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_1,ID=30


title: Autism_Cer_AN09730_rep1

description:
B1a
Technical replicate 1 of 3.

value: hypoxia


title: PAXgene whole blood, SIRS,Day_1,ID=27

source_name: PAXgene whole blood, SIRS,Day_1,ID=27


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_4,ID=30


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_3,ID=30


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=29


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=38


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_4,ID=37


title: PAXgene whole blood, SIRS,Day_3,ID=21

source_name: PAXgene whole blood, SIRS,Day_3,ID=21


title: PAXgene whole blood, influenza A pneumonia,Day_1,ID=56

value: influenza A pneumonia


title: Autism_Cer_AN06420

value: cardiac


title: Autism_occ_AN09714

value: cancer


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=29


title: PAXgene whole blood, influenza A pneumonia,Day_2,ID=36


title: PAXgene whole blood, SIRS,Day_2,ID=21

source_name: PAXgene whole blood, SIRS,Day_2,ID=21


title: PAXgene whole blood, SIRS,Day_4,ID=21

source_name: PAXgene whole blood, SIRS,Day_4,ID=21


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=22


title: PAXgene whole blood, bacterial pneumonia,Day_5,ID=25


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=22


title: PAXgene whole blood, bacterial pneumonia,Day_4,ID=22


title: PAXgene whole blood, SIRS,Day_1,ID=24

source_name: PAXgene whole blood, SIRS,Day_1,ID=24


title: PAXgene whole blood, bacterial pneumonia,Day_4,ID=39


title: PAXgene whole blood, SIRS,Day_4,ID=28

source_name: PAXgene whole blood, SIRS,Day_4,ID=28


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=25


title: PAXgene whole blood, SIRS,Day_4,ID=24

source_name: PAXgene whole blood, SIRS,Day_4,ID=24


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=31


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=39


title: PAXgene whole blood, bacterial pneumonia,Day_4,ID=25


title: PAXgene whole blood, SIRS,Day_3,ID=24

source_name: PAXgene whole blood, SIRS,Day_3,ID=24


title: PAXgene whole blood, bacterial pneumonia,Day_5,ID=22


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_1,ID=37


title: PAXgene whole blood, SIRS,Day_1,ID=21

source_name: PAXgene whole blood, SIRS,Day_1,ID=21


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_5,ID=37


title: PAXgene whole blood, SIRS,Day_2,ID=24

source_name: PAXgene whole blood, SIRS,Day_2,ID=24


title: PAXgene whole blood, bacterial pneumonia,Day_5,ID=39


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=22


title: PAXgene whole blood, influenza A pneumonia,Day_5,ID=36


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_3,ID=37


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=25


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=39


title: PAXgene whole blood, influenza A pneumonia,Day_4,ID=36


title: PAXgene whole blood, influenza A pneumonia,Day_1,ID=36


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_2,ID=37


title: Autism_Cer_AN08873

value: brain


title: PAXgene whole blood, SIRS,Day_2,ID=26

source_name: PAXgene whole blood, SIRS,Day_2,ID=26


title: PAXgene whole blood, SIRS,Day_5,ID=28

source_name: PAXgene whole blood, SIRS,Day_5,ID=28


title: PAXgene whole blood, SIRS,Day_4,ID=26

source_name: PAXgene whole blood, SIRS,Day_4,ID=26


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=31


title: PAXgene whole blood, SIRS,Day_3,ID=26

source_name: PAXgene whole blood, SIRS,Day_3,ID=26


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=25


title: PAXgene whole blood, SIRS,Day_3,ID=28

source_name: PAXgene whole blood, SIRS,Day_3,ID=28


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=31


title: PAXgene whole blood, influenza A pneumonia,Day_4,ID=55


title: PAXgene whole blood, influenza A pneumonia,Day_5,ID=55


title: PAXgene whole blood, influenza A pneumonia,Day_2,ID=55


title: PAXgene whole blood, SIRS,Day_1,ID=28

source_name: PAXgene whole blood, SIRS,Day_1,ID=28


title: PAXgene whole blood, influenza A pneumonia,Day_5,ID=54


title: PAXgene whole blood, influenza A pneumonia,Day_1,ID=55


title: PAXgene whole blood, influenza A pneumonia,Day_2,ID=54


title: PAXgene whole blood, SIRS,Day_2,ID=28

source_name: PAXgene whole blood, SIRS,Day_2,ID=28


title: PAXgene whole blood, influenza A pneumonia,Day_5,ID=56


title: PAXgene whole blood, influenza A pneumonia,Day_2,ID=56


title: PAXgene whole blood, influenza A pneumonia,Day_3,ID=54


title: PAXgene whole blood, influenza A pneumonia,Day_4,ID=54


title: PAXgene whole blood, influenza A pneumonia,Day_3,ID=55


title: PAXgene whole blood, SIRS,Day_1,ID=16

source_name: PAXgene whole blood, SIRS,Day_1,ID=16


title: PAXgene whole blood, influenza A pneumonia,Day_1,ID=54


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=17


title: PAXgene whole blood, influenza A pneumonia,Day_3,ID=56


title: PAXgene whole blood, bacterial pneumonia,Day_4,ID=17


title: PAXgene whole blood, SIRS,Day_2,ID=16

source_name: PAXgene whole blood, SIRS,Day_2,ID=16


title: PAXgene whole blood, influenza A pneumonia,Day_4,ID=56


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=17


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=13


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=15


title: PAXgene whole blood, bacterial pneumonia,Day_4,ID=15


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=15


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=15


title: PAXgene whole blood, SIRS,Day_2,ID=19

source_name: PAXgene whole blood, SIRS,Day_2,ID=19


title: PAXgene whole blood, SIRS,Day_1,ID=18

source_name: PAXgene whole blood, SIRS,Day_1,ID=18


title: PAXgene whole blood, SIRS,Day_1,ID=19

source_name: PAXgene whole blood, SIRS,Day_1,ID=19


title: PAXgene whole blood, SIRS,Day_3,ID=19

source_name: PAXgene whole blood, SIRS,Day_3,ID=19


title: PAXgene whole blood, SIRS,Day_2,ID=18

source_name: PAXgene whole blood, SIRS,Day_2,ID=18


title: PAXgene whole blood, SIRS,Day_4,ID=20

source_name: PAXgene whole blood, SIRS,Day_4,ID=20


title: PAXgene whole blood, SIRS,Day_2,ID=20

source_name: PAXgene whole blood, SIRS,Day_2,ID=20


title: PAXgene whole blood, SIRS,Day_3,ID=20

source_name: PAXgene whole blood, SIRS,Day_3,ID=20


title: PAXgene whole blood, SIRS,Day_1,ID=20

source_name: PAXgene whole blood, SIRS,Day_1,ID=20


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_1,ID=8


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_2,ID=8


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_4,ID=8


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=39


title: PAXgene whole blood, mixed bacterial and influenza A pneumonia,Day_3,ID=8


title: PAXgene whole blood, influenza A pneumonia,Day_3,ID=36


title: PAXgene whole blood, healthy control,Day_5,ID=42

value: healthy control


title: PAXgene whole blood, healthy control,Day_1,ID=42


title: PAXgene whole blood, healthy control,Day_1,ID=49


title: PAXgene whole blood, healthy control,Day_5,ID=49


title: PAXgene whole blood, healthy control,Day_5,ID=53


title: PAXgene whole blood, healthy control,Day_1,ID=53


title: PAXgene whole blood, healthy control,Day_5,ID=44


title: PAXgene whole blood, healthy control,Day_1,ID=52


title: PAXgene whole blood, healthy control,Day_1,ID=47


title: PAXgene whole blood, healthy control,Day_5,ID=35


title: PAXgene whole blood, healthy control,Day_1,ID=35


title: PAXgene whole blood, healthy control,Day_1,ID=44


title: PAXgene whole blood, healthy control,Day_5,ID=45


title: PAXgene whole blood, healthy control,Day_1,ID=58


title: PAXgene whole blood, healthy control,Day_1,ID=46


title: PAXgene whole blood, healthy control,Day_5,ID=34


title: PAXgene whole blood, healthy control,Day_5,ID=46


title: PAXgene whole blood, healthy control,Day_5,ID=52


title: PAXgene whole blood, healthy control,Day_1,ID=45


title: PAXgene whole blood, healthy control,Day_1,ID=41


title: PAXgene whole blood, healthy control,Day_5,ID=57


title: PAXgene whole blood, healthy control,Day_5,ID=41


title: PAXgene whole blood, healthy control,Day_5,ID=47


title: PAXgene whole blood, healthy control,Day_1,ID=57


title: PAXgene whole blood, healthy control,Day_1,ID=43


title: PAXgene whole blood, healthy control,Day_5,ID=58


title: PAXgene whole blood, healthy control,Day_1,ID=40


title: PAXgene whole blood, healthy control,Day_5,ID=40


title: PAXgene whole blood, healthy control,Day_1,ID=48


title: PAXgene whole blood, healthy control,Day_5,ID=48


title: PAXgene whole blood, healthy control,Day_5,ID=51


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=7


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=7


title: PAXgene whole blood, healthy control,Day_5,ID=50


title: PAXgene whole blood, healthy control,Day_1,ID=51


title: PAXgene whole blood, healthy control,Day_5,ID=43


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=7


title: PAXgene whole blood, SIRS,Day_1,ID=12

source_name: PAXgene whole blood, SIRS,Day_1,ID=12


title: PAXgene whole blood, bacterial pneumonia,Day_5,ID=10


title: PAXgene whole blood, SIRS,Day_1,ID=2

source_name: PAXgene whole blood, SIRS,Day_1,ID=2


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=10


title: PAXgene whole blood, influenza A pneumonia,Day_5,ID=14


title: PAXgene whole blood, influenza A pneumonia,Day_4,ID=14


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=10


title: PAXgene whole blood, influenza A pneumonia,Day_2,ID=11


title: PAXgene whole blood, influenza A pneumonia,Day_4,ID=6


title: PAXgene whole blood, influenza A pneumonia,Day_1,ID=14


title: PAXgene whole blood, influenza A pneumonia,Day_2,ID=6


title: PAXgene whole blood, influenza A pneumonia,Day_3,ID=14


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=10


title: PAXgene whole blood, influenza A pneumonia,Day_4,ID=11


title: PAXgene whole blood, influenza A pneumonia,Day_3,ID=6


title: PAXgene whole blood, influenza A pneumonia,Day_5,ID=9


title: PAXgene whole blood, influenza A pneumonia,Day_5,ID=11


title: PAXgene whole blood, influenza A pneumonia,Day_2,ID=14


title: PAXgene whole blood, bacterial pneumonia,Day_4,ID=10


title: PAXgene whole blood, influenza A pneumonia,Day_3,ID=11


title: PAXgene whole blood, influenza A pneumonia,Day_4,ID=9


title: PAXgene whole blood, influenza A pneumonia,Day_1,ID=6


title: Lgr5-ki-crypts_5+vs3+

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using featuere extraction (V.9.5.3, Agilent Technologies).

source_name: FACS sorted epithelial intestinal cells cells from Lgr5-EGFP-ires-CreERT2 mice

label_protocol: 300 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: Cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice were used, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from five FACS sorted cell populations, with fraction 5+ expressing GFP at highest levels and 1+ expressing GFP at lowest levels.

extract_protocol: RNA was isolated using Trizol (Invitrogen)

tag: lgr5 expression level


title: PAXgene whole blood, influenza A pneumonia,Day_3,ID=9


title: Lgr5-ki-crypts_5+vs4+


title: PAXgene whole blood, influenza A pneumonia,Day_2,ID=9


title: PAXgene whole blood, influenza A pneumonia,Day_1,ID=9


title: PAXgene whole blood, influenza A pneumonia,Day_1,ID=11


title: Lgr5-ki-crypts_5+vs4+_dyeswap


title: Lgr5-ki-crypts_5+vs3+_dyeswap


title: Lgr5-ki-crypts_5+vs2+_dyeswap


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=5


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=5


title: Lgr5-ki-crypts_5+vs2+


title: Lgr5-ki-crypts_5+vs1+


title: Lgr5-ki-crypts_5+vs1+_dyeswap


title: spleen from control group, rep1

city: yangzhou

first: Zenglei

last: Hu

address: 12 East Wenhui Road

country: China

institute: Yangzhou University

description: Gene expression data of spleen from mock-infected chciken

hyb_protocol: Following fragmentation, 12 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: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Log2 transformation was applied to the MAS5 data.

organism: Gallus gallus

source_name: spleen from mock-infected chicken

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

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

tag: breed

value: White Leghorn chickens

value: spleen


title: spleen from JS5/05 group, rep2

description: Gene expression data of spleen from JS5/05-infected chicken

source_name: spleen from JS5/05-infected chicken, day 2 post infection


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=3


title: PAXgene whole blood, bacterial pneumonia,Day_4,ID=5


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=5


title: spleen from JS5/05 group, rep1


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=3


title: spleen from control group, rep3


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=1


title: PAXgene whole blood, bacterial pneumonia,Day_4,ID=3


title: spleen from control group, rep2


title: PAXgene whole blood, bacterial pneumonia,Day_5,ID=5


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=1


title: spleen from Herts/33 group, rep2

description: Gene expression data of spleen from Herts/33-infected chicken

source_name: spleen from Herts/33-infected chicken, day 2 post infection


title: spleen from Herts/33 group, rep1


title: spleen from Herts/33 group, rep3


title: FB elongated embryo replication3

city: Bonn

first: Simret

middle: Betsha

last: Weldenegodguad

address: Endenicher Allee 15

department: ITW

institute: University of Bonn

description: Fibroblasts used as a donor cells for the production of somatic cell nuclear transfer embryos

hyb_protocol: Array hybridization was performed after mixing appropriative amount of hybridization components, fragmented and labelled cRNA, control oligonucleotide B2 (3 nM), 20X eukaryotic hybridization controls (bioB, bioC, bioD, cre), 2X hybridization mix , DMSO and RNAse free water.The hybridization mix was heated to 99°C for 5 min followed by heating at 45°C for 5 min. Following this the samples were hybridized to the GeneChip® Bovine Genome Array (Affymetrix, CA, USA) for 16 h at 45°C. Three biotin labeled cRNA hybridizations were performed for each samples of each category (SCNT, IVP, AI and FB)

scan_protocol: After 16 h of hybridization, the arrays washing and staining was performed using the Fluidics Station 450/250 integrated as recommended in GeneChip® expression wash, stain and scan user manual (P/N 702731 (Affymetrix). The arrays were then scanned using affymetrix®GeneChip™3000 slide scanner (Affymetrix, CA, USA).

data_processing: The microarray data normalization and background correction was performed using guanine cytosine robust multi-array analysis (gcrma) . The quality of the arrays after hybridization was evaluated by assessing the absent and present calls of the control probesets. Differentially expressed genes were generated using linear models for microarray data analysis (LIMMA). For this, we used R software, (www.r-project.org) and bioconductor packages (www.bioconductor.org).

organism: Bos taurus

source_name: FB elongated embryo

label_protocol: The cRNA was biotin labeled using the GeneChip® IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA) according to GeneChip® expression analysis technical manual

extract_protocol:
Total RNA was harvested from 10 mg samples of AI, SCNT or IVP elongated embryos and 2x106 Donor cells (fibroblast cells) using Norgen RNA/DANN/ Protein purification kit (Norgen biotek corporation, Candada).
RNA amplification, cDNA synthesis, labeling was performed using GeneChip®3’ IVT Express Kit following the instructions described in GeneChip®3’ IVT Express Kit user manual [(P/N 702646 Rev. 7) (Affymetrix Inc)].

tag: tissue type

value: elongated embryo


title: PAXgene whole blood, SIRS,Day_1,ID=4

source_name: PAXgene whole blood, SIRS,Day_1,ID=4


title: PAXgene whole blood, bacterial pneumonia,Day_5,ID=3


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=3


title: spleen from JS5/05 group, rep3


title: FB elongated embryo replication2


title: FB elongated embryo replication1


title: PAXgene whole blood, bacterial pneumonia,Day_5,ID=1


title: PAXgene whole blood, SIRS,Day_2,ID=4

source_name: PAXgene whole blood, SIRS,Day_2,ID=4


title: IVP elongated embryo replication1

description: Elongated embryos derived from pregnancies after the transfer of in vitro fertilzed and in vitro culture embryo at day 16 of gestation

source_name: IVP elongated embryo


title: PAXgene whole blood, SIRS,Day_4,ID=23

source_name: PAXgene whole blood, SIRS,Day_4,ID=23


title: IVP elongated embryo replication3


title: SCNT elongated embryo replication3

description: Elongated embryos derived from pregnancies after the transfer of embryos produced by somatic cell nuclear transfer at day 16 of gestation

source_name: SCNT elongated embryo


title: PAXgene whole blood, SIRS,Day_5,ID=23

source_name: PAXgene whole blood, SIRS,Day_5,ID=23


title: AI elongated embryo replication3

description: Elongated embryos derived from pregnancies after the transfer of in vivo produced embryos at day 16 of gestation

source_name: AI elongated embryo


title: PAXgene whole blood, bacterial pneumonia,Day_4,ID=1


title: PAXgene whole blood, SIRS,Day_3,ID=4

source_name: PAXgene whole blood, SIRS,Day_3,ID=4


title: AI elongated embryo replication1


title: PAXgene whole blood, healthy control,Day_1,ID=50


title: AI elongated embryo replication2


title: PAXgene whole blood, bacterial pneumonia,Day_1,ID=33


title: IVP elongated embryo replication2


title: PAXgene whole blood, healthy control,Day_1,ID=34


title: SCNT elongated embryo replication1


title: Euploid 213GAAM

description: replicate 12

source_name: lymphoblastoid cell line

value: Female

tag: age (y)

tag: cell type

value: lymphoblastoid cell line

value: Down syndrome

tag: genetic variation

value: Euploid


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=33

value: PAXgene whole blood

value: bacterial pneumonia

tag: gender

value: female


title: CAR.AH_TCPOBOP_rep2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Human CAR transgenic mice treated with TCPOBOP

hyb_protocol: Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000.  Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)

data_processing: RMA normalization using R version 2.15.0 and affy version 1.34.0

source_name: liver

label_protocol: Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).

growth_protocol: Mice were fed normal chow and housed with a 12 hour light/dark cycle.  AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.

extract_protocol: RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions.  After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide.  Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.

treatment_protocol: Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection.  The injections were given at 24 hour intervals at 10 am.  Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3.  6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.

tag: strain

tag: genotype

value: hCAR transgenic in mCAR knockout background

tag: ligand


title: PAXgene whole blood, SIRS,Day_2,ID=23

source_name: PAXgene whole blood, SIRS,Day_2,ID=23

value: systemic inflammatory response

value: male


title: CAR.AH_TCPOBOP_rep1


title: PAXgene whole blood, SIRS,Day_2,ID=12

source_name: PAXgene whole blood, SIRS,Day_2,ID=12


title: PAXgene whole blood, bacterial pneumonia,Day_3,ID=1


title: CAR.KO_TCPOBOP_rep2

description: CAR knockout mice treated with TCPOBOP

value: mCAR knockout


title: Trisomic 21 10324

description: replicate 11

tag: phenotype

value: Trisomic 21


title: CAR.KO_TCPOBOP_rep1

description: CAR knockout mice treated with TCPOBOP


title: PAXgene whole blood, SIRS,Day_1,ID=23

source_name: PAXgene whole blood, SIRS,Day_1,ID=23


title: PAXgene whole blood, bacterial pneumonia,Day_2,ID=33


title: PAXgene whole blood, SIRS,Day_3,ID=23

source_name: PAXgene whole blood, SIRS,Day_3,ID=23


title: Euploid 10234P

description: replicate 11

value: Male


title: wild-type_TCPOBOP_rep2

description: wild type mice treated with TCPOBOP

value: wild-type


title: wild-type_TCPOBOP_rep1

description: wild type mice treated with TCPOBOP


title: Euploid 10241P

description: replicate 10


title: Trisomic 21 10195

description: replicate 10


title: CAR.AH_corn oil_rep2

description: Human CAR transgenic mice treated with corn oil

value: corn oil


title: V/V-5

city: Ljubljana

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

hyb_protocol: 100 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 1.0 ST Arrays according to manufacturer’s instructions (Genechip® Whole Transcript (wt) Sense Ttarget Labeling Assay Manual – P/N 701880 Rev 4).

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized (w.r.t. core meta-probeset annotations and AFFX control probes, probes grouped to the level of transcripts) and quantile-normalized (background computed from antigenomic probes) using RMA algorithm from XPS package.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: White adipose from adult F2 homozigote mouse for Lean-line allele at FOB3A-QTL

label_protocol: Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA sample were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: From a previous F2 cross (Stylianou, I. M. et al., Microarray gene expression analysis of the Fob3b obesity QTL identifies positional candidate gene Sqle and perturbed cholesterol and glycolysis pathways. Physiol Genomics 20 (3), 224 (2005)), an recombinant individual within Fob3a QTL region was used as a founder for development of subsequent congenic lines also V congenic line used here. A total of 11-12 backcrosses to the Fat line with additional marker-assisted elimination of other QTL regions was performed. Food chow (1324 maintenance diet, Altromin, Germany) and acidified water were offered ad libitum and adipose tissue samples were taken at 14 weeks of age.

extract_protocol: Inguinal-femoral adipose tissue from 14 weeks old females were snap frozen in liquid nitrogen and stored at -80°C for subsequent analysis. Samples were first pulverized and then homogenized in TRIZOL and total RNA was isolated according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop and Agilent 2100 Bioanalyzer instruments, all samples isolated fulfilled the minimum requirements (OD260/280 and OD230/280 > 1.8) and RIN numbers above 8.5 for microarray hybridization.

treatment_protocol: Mice were not treated.

tag: genotype/variation

value: VV

tag: generation

tag: Sex

value: Subcutaneous (femoral) fat depot

tag: animal


title: V/V-2

value: Female

tag: tissue


title: V/V-4


title: V/V-3


title: CAR.AH_corn oil_rep1


title: V/V-1


title: Fat/Fat-5

source_name: White adipose from adult F2 homozigote mouse for Fat-line allele at FOB3A-QTL

value: FF


title: Trisomic 21 10177

description: replicate 9

value: lymphoblastoid cell line

value: Down syndrome


title: wild-type_corn oil_rep2

description: wild type mice treated with corn oil


title: CAR.KO_corn oil_rep1

description: CAR knockout mice treated with corn oil


title: Fat/Fat-4


title: CAR.KO_corn oil_rep2

description: CAR knockout mice treated with corn oil


title: Euploid 213GAAP

description: replicate 8

value: Euploid


title: Fat/Fat-1


title: vacht KD 1 heart

city: London

first: David

middle: E

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

country: Canada

institute: Robarts Research Institute

description: gene expression data from hearts

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomcis Suite using the RMA normalization method

source_name: heart tissue from KD mouse

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

growth_protocol: WT and VAChT KD mice were aged to 3 months of age before hearts were excised for RNA extraction.

extract_protocol: RNA was extracted using the Fatty and Fibrous Tissue RNA Extraction Kit (Bio-rad)

treatment_protocol: No treatments were applied to the animals or tissue.

value: heart

value: KD

tag: age

value: 3 months


title: Fat/Fat-2


title: Trisomic 21 205DER

description: replicate 7


title: CAR.AH_CITCO_rep2

description: Human CAR transgenic mice treated with CITCO

value: female

value: hCAR transgenic in mCAR knockout background


title: wild-type_corn oil_rep1

description: wild type mice treated with corn oil


title: Fat/Fat-3


title: vacht KD 2 heart

description: gene expression data from hearts

value: male


title: wild-type 2 heart

description: gene expression data from hearts

source_name: heart tissue from WT mouse

value: WT


title: vacht KD 3 cardiomyocytes

description: gene expression data from cardiomyocytes

source_name: cardiomyocytes from KD mouse

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Ambion Whole Transcript (WT) Sense Target Labeling Assay Manual and Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual

growth_protocol: WT and VAChT KD mice were aged to 3 months of age before ventricular cardiomyocytes were excised for RNA extraction.

extract_protocol: RNA was extracted using the Fatty and Fibrous Tissue RNA Extraction Kit (Bio-rad).

value: ventricular cardiomyocytes


title: Euploid 10004M

description: replicate 7


title: Euploid 10241M

description: replicate 9


title: vacht KD 2 cardiomyocytes


title: CAR.AH_CITCO_rep1


title: Euploid 10281P

description: replicate 6

value: Male


title: wild-type 1 heart

description: gene expression data from hearts


title: CAR.KO_CITCO_rep2

description: CAR knockout mice treated with CITCO

value: mCAR knockout


title: Trisomic 21 91PES

description: replicate 8

value: Trisomic 21


title: wild-type 3 cardiomyocytes

source_name: cardiomyocytes from WT mouse


title: Trisomic 21 10167

description: replicate 6


title: Euploid 10161M

description: replicate 5


title: wild-type 1 cardiomyocytes


title: wild-type 2 cardiomyocytes


title: vacht KD 1 cardiomyocytes


title: Trisomic 21 10357

description: replicate 5


title: Euploid 10174P

description: replicate 4


title: CAR.KO_CITCO_rep1

description: CAR knockout mice treated with CITCO


title: Infant outflow tract myocardium of TOF 4

city: Shanghai

first: jin

last: zhang

address: 130# Dong'An Road, R307 Ming Dao building

institute: Fudan University

description:
T4
100702-10340A_T11_miRNA-1_0
miRNA expression.

hyb_protocol: 1 ug of labelled cRNA were hybridized for 16 hr at 48C on microRNA microarray Chips. Chips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: To compare the probe intensities across chips, cross-chip variation needs to be addressed, and the values normalized. A very commonly used and accepted normalization method that assures that the distribution of log (probe intensities) is comparable among experiments (see BM Bolstad, RA Irizarry, M Anstrand & TP Speed (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19 (2):185-193 (PMID 12538238)).

source_name: infant outflow tract myocardium of TOF

label_protocol: RNA were labelled by using FlashTag Ligation Mix Biotin after 1 ug of total RNA were added with polyA tail with RNA polyA polymerase.

growth_protocol: Tissue collection: Under the approval by the medical ethics committee of Children's Hospital of Fudan University (reference number 2010094) and parent informed consents, and conforming with the principles outlined in the Declaration of Helsinki for use of human tissue or subjects, the myocardium tissues of right ventricular outflow tracts of children (2- to 24-months-old) with non-syndromic TOF were collected from repair surgery at the Children's Hospital of Shanghai. Normal paired right ventricular tissues were from autopsies in the Department of Forensic Medicine, Fudan University.

value: outflow tract myocardium

tag: developmental stage

value: infant

tag: disease state

value: non-syndromic Tetralogy of Fallot (TOF)


title: wild-type_CITCO_rep2

description: wild type mice treated with CITCO

value: wild-type


title: CAR.AH_phenobarbitol_rep1

description: Human CAR transgenic mice treated with phenobarbitol

value: phenobarbitol


title: CAR.KO_phenobarbitol_rep2

description: CAR knockout mice treated with phenobarbitol


title: 15d Dicer cKO_Pool 12

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

description: 15d Dicer cKO, pool 12

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  Quantile normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

source_name: 15d Dicer cKO

label_protocol: According to Illumina protocol.

extract_protocol: Total RNA was isolated from tissue specimens using the mirVANA Kit (Ambion, Austin, TX). Transcriptional profiles were generated by the Genomics and Proteomics Core Laboratory at Texas Children's Hospital using Human WG-6 (v3) BeadChip (Illumina, San Diego, CA). Prior to profiling, RNA integrity was determined using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

tag: strain background

value: C57BL/6J;129S5/Brd mixed hybrid

value: Cre knockout of Dicer

value: uterine

value: 15 days


title: Euploid 251STMP

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

tag: age (y)

value: lymphoblastoid cell line

value: Down syndrome

value: Euploid


title: Infant outflow tract myocardium of TOF 5

description:
T5
100702-10340A_T33_miRNA-1_0
miRNA expression.


title: wild-type_CITCO_rep1

description: wild type mice treated with CITCO

value: female


title: CAR.AH_phenobarbitol_rep2

value: hCAR transgenic in mCAR knockout background


title: Trisomic 21 226MAR

description: replicate 3

value: Male

tag: cell type


title: SCNT elongated embryo replication2

source_name: SCNT elongated embryo

tag: tissue type

value: elongated embryo


title: CAR.KO_phenobarbitol_rep1

tag: gender

value: mCAR knockout


title: 15d control_Pool 9

description: 15d control, pool 9

source_name: 15d control

value: wild type control


title: 15d control_Pool 11

description: 15d control, pool 11


title: Euploid 10299M

description: replicate 2

value: Female

tag: genetic variation


title: Infant outflow tract myocardium of TOF 3

description:
T3
100702-10340A_T8_miRNA-1_0
miRNA expression.

value: outflow tract myocardium

value: infant

value: non-syndromic Tetralogy of Fallot (TOF)


title: Trisomic 21 209FOJ

description: replicate 4

value: Trisomic 21


title: Trisomic 21 10202

description: replicate 2


title: Infant outflow tract myocardium of TOF 1

description:
T1
100702-10340A_MY_miRNA-1_0
miRNA expression.


title: Normal infant outflow tract myocardium 3

description:
N3
100702-10340B_803-C7_miRNA-1_0
miRNA expression.

source_name: normal infant outflow tract myocardium

value: normal


title: Normal infant outflow tract myocardium 2

description:
N2
100702-10340B_803-C4_miRNA-1_0
miRNA expression.


title: Infant outflow tract myocardium of TOF 2

description:
T2
100702-10340A_T3_miRNA-1_0
miRNA expression.


title: Normal infant outflow tract myocardium 1

description:
N1
100702-10340A_FA48_miRNA-1_0
miRNA expression.


title: 15d control_Pool 7

description: 15d control, pool 7

value: C57BL/6J;129S5/Brd mixed hybrid

value: uterine


title: wild-type_phenobarbitol_rep2

description: wild type mice treated with phenobarbitol

tag: strain

tag: genotype

value: wild-type

value: phenobarbitol


title: 15d Dicer cKO_Pool 10

description: 15d Dicer cKO, pool 10

value: Cre knockout of Dicer

value: 15 days


title: Euploid 10119M

description: replicate 1

source_name: lymphoblastoid cell line

value: lymphoblastoid cell line

tag: phenotype

value: Down syndrome

value: Euploid


title: Trisomic 21 10231

description: replicate 1


title: wild-type_phenobarbitol_rep1

source_name: liver

value: female

tag: ligand


title: TLR4 null sham kidney, biological rep2

city: DALLAS

first: JIANLIN

last: CHEN

state: TEXAS

address: 5323 HARY HINES BLVD.

department: Nephrology/Internal Medicine

institute: University of Texas Southwestern Medical Center at Dallas

description: Gene expression data from TLR4-/- sham kidney at 4hr reperfusion(No.2)

hyb_protocol: Following fragmentation, 15µg of cRNA were hybridized at 45°C  for 16 hr on the GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0(MAS5.0) using Affymetrix default analysis and global scaling as normalization method.

label: Biotin

source_name: TLR4 null sham kidney

label_protocol: Biotinylated cRNA was amplified from 1µg of total RNA using the MessageAmp II-Biotin Enhanced Kit(Ambion) protocol.

growth_protocol: 8 wks old male mice were purchased from the Jackson Laboratory and fed ad libitum in our animal facility before surgery.

extract_protocol: Kidneys were dissected, snap-frozen in liquid nitrogen and stored at -80°C. Samples were homogenized and total RNA was extracted using the the RNeasy Midi Kit(Qiagen) according to the manufacturer's manual. RNA integrity was measured on the Agilent 2100 Bioanalyzer(RIN:9.5).

treatment_protocol: Mice were placed under inhaled isofluorane with body temperature maintained at 37°C. After right nephrectomy, the left pedicle was occluded with a microaneurysm clip for 23min. The clip was then released and buprenorphine was given S.C.. Sham mice underwent the same right nephrectomy except the clip was placed underneath the pedicle. Kidneys were harvested at 4hr reperfusion.

value: Male

value: Kidney

tag: surgery

value: Sham

tag: reperfusion time


title: TLR4 null sham kidney, biological rep3

description: Gene expression data from TLR4-/- sham kidney at 4hr reperfusion(No.3)


title: R13

description: Additional subject data may be obtained from the Autism Tissue Program

data_processing: Data were normalized, variance-stabilized, and filtered for probes with detection p-values less than or equal to 0.01 in R using the lumi Bioconductor package.

extract_protocol: Qiagen AllPrep Kit was used to co-extract DNA and RNA from frozen brain tissue samples of about 40mg each.

tag: brain region

value: occipital

tag: age (years)

tag: postmortem interval (hours)

tag: Cause of death

value: Unknown


title: R4b

value: Cancer


title: R24


title: HPDE

city: Rochester

first: Eric

middle: W

last: Klee

state: MN

address: 200 1st St SW

department: Health Sciences Research

institute: Mayo Clinic -Rochester, MN

description: Transcriptomic profile of the HPDE cell line

hyb_protocol: IVT products were column-purified, fragmented, and hybridized onto Affymetrix U133 Plus 2.0 GeneChips at 45° C for 16 h. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Scanned in an Affymetrix GeneChip Scanner 3000 (Santa Clara, CA).

data_processing: Cel files were analyzed using dChip with invariatn set normalization of PM-only model values.

source_name: Pacreatic Cancer Cell Line

label_protocol: Affymetrix One Cycle Target Labeling and Control Reagnets kit.

growth_protocol: Cells were cultured following the ATCC protocol.

extract_protocol: The mRNA extraction was done using theRNAeasy QIAGEN protocol

tag: cell line

value: HPDE


title: R1X

value: cerebellum

value: Hypoxia


title: R35

value: Other


title: R28

value: Cardiac


title: R30


title: R21


title: HPAF1

description: Transcriptomic profile of the HPAF1 cell line


title: SU86.86

description: Transcriptomic profile of the SU86.86 cell line


title: R14


title: R31


title: L3.6

description: Transcriptomic profile of the L3.6 cell line


title: R6


title: TLR4 null ischemic kidney, biological rep2

description: Gene expression data from TLR4-/- ischemic(23min) kidney at 4hr reperfusion(No.2)

source_name: TLR4 null ischemic kidney

tag: tissue

value: Ischemic


title: PANC1

description: Transcriptomic profile of the PANC1 cell line


title: R12a


title: R9X


title: TLR4 null sham kidney, biological rep1

description: Gene expression data from TLR4-/- sham kidney at 4hr reperfusion(No.1)


title: B10 sham kidney, biological rep3

description: Gene expression data from WT sham kidney at 4hr reperfusion(No.3)

source_name: WT sham kidney

value: WT


title: R25a


title: NA, TS-MG treated, P10, rep2

city: Zhounan, Miaoli

first: Chih-Yeu

last: Fang

address: 35, Keyan Rd.

department: National Cancer Research Institute

country: Taiwan

institute: National Health Research Institutes

description: Gene expression profile of NA cells at passage 10, repeated TS-MG-treated for inducction of recurrrent EBV reaactivation

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: NA cell, passage 10(P10), TPA/SB combined MNNG (TS-MG) treated

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

growth_protocol: NA cells were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum at 37°C with 5% CO2. G418 (400 microg/ml) was added to the medium of NA cells to maintain the EBV genome in the cells.

extract_protocol: RNA was extracted from NPC cells using the Qiagen RNeasy mini kit according to the manufacturer's instructions (Qiagen, Valencia, CA).

treatment_protocol: NA cells were subject to 10 times of repeated chemical exposure by incubating these cells periodically with TPA/SB (10 ng/ml and 1.0 mM) in combination with MNNG (0.1 microg/ml). The NA cells at the beginning of this experiment were defined as passage 0 (P0) cells. 24 h after seeding, the cells were subjected to a 24 h period of mock or chemical treatment. After this 24 hr treatment, the cells were recovered by replacing the medium with fresh (treatment-free) medium and incubation for a further 48 h. The resulting cells were defined as passage 1 (P1) cells. Cells from P1 were trypsinized and transferred and the process repeated again to obtain the P2 cells. A total of ten treatments were applied to the cells in this study. “NA-P10/TS-MG” refers to NA cells with 10 times of combined TPA/SB and MNNG (TS-MG) treatments. NA-P1/mock is mock-treated NA cells with one time of passage that was used as reference in this study.

value: nasopharyngeal carcinoma cells

tag: stress

value: TS-MG

tag: cell passage

value: passage 10


title: B10 sham kidney, biological rep2

description: Gene expression data from WT sham kidney at 4hr reperfusion(No.2)


title: TLR4 null ischemic kidney, biological rep1

description: Gene expression data from TLR4-/- ischemic(23min) kidney at 4hr reperfusion(No.1)


title: TLR4 null ischemic kidney, biological rep3

description: Gene expression data from TLR4-/- ischemic(23min) kidney at 4hr reperfusion(No.3)


title: R5a


title: NA, TS-MG treated, P10, rep1


title: R27


title: R16


title: R29


title: R23


title: R20a


title: R12


title: Brca sera treatment cont vs serum

city: Beijing

first: sp

address: 18 Shuangqing Road, Haidian District

institute: RCEES, CAS

description: compare gene expression profiles of control cells

hyb_protocol: Standard CapitalBio Methods

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio). For individual channel data extract, faint spots were removed for which intensities were below 400 unit after background subtracted in both channels (Cy3 and Cy5).

data_processing: A space- and intensity-dependent normalization based on a LOWESS program was employed. 3 To determine the significant differentially expressed genes, Significance Analysis of Microarrays (SAM, version 3.02) were performed.

source_name: Breast cancer cell-Cont

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, GE Healthcare) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. The amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Cells were cultured in serum-free RPMI 1640 medium (Invitrogen) 12 hours before treatment at 37°C with 5% CO2.

extract_protocol: Sera transfected cells and control cells were harvest, and total RNA was extracted with Trizol Reagent according to the manufacturer's instructions (Invitrogen) and ethanol precipitation.

treatment_protocol: Cells were cultured in serum-free medium with or without addition of 10% human sera from breast cancer patients for 24 hours.

source_name: Breast cancer cell-Serum


title: B10 ischemic kidney, biological rep1

description: Gene expression data from WT ischemic kidney(23min) at 4hr reperfusion(No.1)

source_name: WT ischemic kidney


title: R1a


title: B10 ischemic kidney, biological rep3

description: Gene expression data from WT ischemic kidney(23min) at 4hr reperfusion(No.3)


title: R34


title: R9a


title: huBM_CD10_fresh_rep1

city: los angeles

first: Lisa

last: Kohn

state: ca

address: 650 charles e young drive south

institute: UCLA

description: gene expression from human bone marrow CD10+

hyb_protocol: Hybridized to GeneChip expression arrays, stained with a streptavidin phycoerythrin conjugate

scan_protocol: GeneChip Scanner 3000DX V.2.

data_processing: CEL files were normalised using RMA method using affy package from Bioconductor version 2.8

source_name: CD34 enriched Bone Marrow, Sorted CD34+ CD10+

label_protocol: Affymetrix protocol

growth_protocol: None, freshly isolated human bone marrow

extract_protocol: RNA from BM from 3 different individuals was extracted using Microkit (Qiagen, Valencia California)

treatment_protocol: Freshly isolated human bone marrow was ficoll purified, CD34 enriched with an immunomagnetic column, and then sorted on a FACS Aria

tag: cell type

value: human bone marrow CD10+


title: B10 sham kidney, biological rep1

description: Gene expression data from WT sham kidney at 4hr reperfusion(No.1)

tag: gender

value: Male


title: huBM_CD10_fresh_rep3


title: R29a

description: Additional subject data may be obtained from the Autism Tissue Program

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


title: huBM_CD10_fresh_rep2


title: R5


title: R32


title: huBM_CD62L_fresh_rep3

description: gene expression from human bone marrow CD62Lhi

source_name: CD34 enriched Bone Marrow, Sorted CD34+ CD10- CD62Lhi

value: human bone marrow CD62Lhi


title: NA, mock-treated, P1, rep2

description: Gene expression profile of NA cells at passage 1, mock-treated

source_name: NA cell, passage 1(P1), mock-treated

value: mock

value: passage 1


title: R22


title: huBM_CD62L_fresh_rep1


title: huBM_CD62L_fresh_rep2


title: B10 ischemic kidney, biological rep2

description: Gene expression data from WT ischemic kidney(23min) at 4hr reperfusion(No.2)

value: Kidney


title: R15

value: Cancer


title: R34a


title: R19


title: NA, mock-treated, P1, rep1


title: R10


title: R9


title: Dis XIV 30 Min heatshock

status: Public on Aug 14 2012

city: Cambridge

first: Ana

middle: B

last: Oromendia

address: 500 Main St

institute: MIT- Koch Institute

hyb_protocol: Equal masses of both sample and reference RNA were hybridized for 16-20 hours

scan_protocol: Scanned on a Agilent Technologies Scanner model G2505B

data_processing: Extraction Software: Agilent Feature Extraction, version 10.5.1.1. Opened on puma.db

organism: Saccharomyces cerevisiae

source_name: Dis XIV RNA 30 min 37C

label_protocol: RNA was labeled with Agilent QuickAmp labeling kit.

extract_protocol: Total RNA was extracted via acid-phenol extraction

value: disomic chr. XIV

tag: time

tag: treatment

tag: genetic background

source_name: WT 25 C

value: reference

value: wild type


title: R25

value: cerebellum

value: Hypoxia


title: R1


title: Dis XVI 30 Min heatshock

source_name: Dis XVI RNA 30 min 37C

tag: genotype

value: disomic chr. XVI


title: Dis XVI 5 Min heatshock

source_name: Dis XVI RNA 5 min 37C


title: huBM_CD38_fresh_rep1

description: gene expression from human bone marrow CD38-

source_name: CD34 enriched Bone Marrow, Sorted CD34+ CD38-

value: human bone marrow CD38-