title: stage2 SOX17+, biological rep2

city: Stanford

first: Pei

last: Wang

address: 279 Campus Dr.

department: Dev. Bio.

institute: Stanford University

description: Gene expression data from human embryonic stem cells and FACS purified endodermal progeny

hyb_protocol: Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.

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

data_processing: The data were generated with Affymetrix GeneChip Operating Software (GCOS). Microarray data was normalized and summarized by the Robust Multi-chip Averaging (RMA) algorithm using GeneSpring GX 11 (Agilent).

source_name: hSOX17-2 derived stage 2 endoderm

label_protocol: 100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA

growth_protocol: The human embryonic stem cell lines H9 and modified lin hSOX17-2 were grown on irradiated CD1 mouse embryonic feeder cells in DMEM/F12 supplemented with 20% (vol/vol) knockout serum replacement, FGF2 (8 ng/ml), 3 mM L-glutamine, 0.1 mM nonessential amino acids and 0.1 mM b-mercaptoethanol.

extract_protocol: Total RNA was isolated using PicoPure RNA isolation kit (MDS Analytical Technologies, Cat# KIT0204).

treatment_protocol: For stage 1,  90% confluent hESC were cultured in RPMI with 25ng/ml Wnt3a and 100ng/ml Activin A for one day. then changed to RPMI with 0.2% FBS and 100ng/ml Activin A for two days. To stage 2, the medium was changed to RPMI with 2% FBS, 50 ng/ml human FGF10 and 0.25μM KAAD-cyclopamine for 3 days.

value: hSOX17-2 derived stage 2 endoderm


title: HeLa cells, treated with TNF-alpha 10ng/mL for 2hr, replicate 1 of 2

status: Public on Mar 15 2011

type: RNA

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

country: USA

institute: Case Western Reserve University

description: Gene expression data for HeLa cells treated with TNF-alpha.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: GC-RMA normalization using GCRMA package (version 2.14.1) in R

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Affymetrix protocol

growth_protocol: HeLa and THP-1 cells were obtained from ATCC and cultured under recommended conditions.

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

treatment_protocol: RNA were harvest before or after TNF-alpha treatment (10ng/mL) for 2hr

tag: cell line

value: HeLa


title: BXH6_hippo_totalRNA

city: Los Angeles

first: Christopher

last: Park

state: CA

address: 23-151 CHS, 650 Charles E. Young Drive

department: Molecular and Medical Pharmacology

institute: UCLA

description: RI mouse strain from HMDP

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Data were processed using the Illumina BeadStudio software and rank-invariant normalized

organism: Mus musculus

source_name: whole hippocampus

label_protocol: Illumina TotalPrep RNA, biotin-16-UTP

extract_protocol: total RNA extracted using Trizol (Invitrogen) and prepared using the Qiagen Rneasy kit per manufacturers instructions, Agilent Bioanalyser used for quality control

tag: gender

value: male

tag: strain

tag: tissue

value: whole hippocampus


title: Early EPC 60 adenosine treated 3

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

hyb_protocol: labeled miRNA was hybridized onto Agilent's Human miRNA Microarrays V3, Release 12.0 (P/N G4471A, AMADID 021827) annotated against the Sanger miRBASE 12.0 database of miRNAs. according to the manufacturer's instructions.

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner

data_processing: The scanned images were analyzed with GenePix Pro 6.0 analysis software using default parameters to obtain background subtracted signal intensities. The features flagged Not Found by GenePix as well as with a SNR (Signal to Noise Ratio) less than 3 were removed from the data. The data was normalized with quantile method using R Limma package.

source_name: Early EPC 60 adenosine 6h

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng total RNA using Agilent miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions

extract_protocol: mirVana Ambion

tag: cell type

value: EPC Early primary cells


title: stage2 SOX17+, biological rep3


title: Early EPC 60 adenosine treated 1


title: BXH7_hippo_totalRNA

description: RI mouse strain from HMDP


title: Early EPC 37 notreated 4

source_name: Early EPC 37 DMSO 6h


title: stage2 SOX17+, biological rep1


title: stage1 SOX17+, biological rep2

source_name: hSOX17-2 derived stage 1 endoderm

value: hSOX17-2 derived stage 1 endoderm


title: BXH4_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXH2_hippo_totalRNA

description: RI mouse strain from HMDP


title: stage1 SOX17+, biological rep1


title: stage1 SOX17+, biological rep3


title: hESC, biological rep1

source_name: H9 human embryonic stem cells

value: H9 human embryonic stem cells


title: Early EPC 37 notreated 3


title: hESC, biological rep2


title: hESC, biological rep3


title: Early EPC 37 notreated 2


title: Early EPC 37 adenosine treated 2

source_name: Early EPC 37 adenosine 6h


title: HepG2-NOTUM_RNAi_#2

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: Gene expression analysis to identify downstream genes of NOTUM.

hyb_protocol: According to Affymetrix's instructions.

scan_protocol: According to Affymetrix's instructions.

label: biotin-labelled

source_name: HepG2 with RNAi for NOTUM #2

label_protocol: According to Affymetrix's instructions.

growth_protocol: Standard protocol.

extract_protocol: According to Invitrogen's instructions.

treatment_protocol: Low GC RNAi duplex provided by Invitrogen was added to HepG2 cells. HiPerFect(QIAGEN) was used as transfection reagent.

tag: HepG2 cells with RNAi duplex (NOTUM#2) at 72 hours after transfection.


title: BXH19_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXH20_hippo_totalRNA

description: RI mouse strain from HMDP


title: HepG2-NOTUM_RNAi_#1

source_name: HepG2 with RNAi for NOTUM #1

tag: HepG2 cells with RNAi duplex (NOTUM#1) at 72 hours after transfection.


title: BXD9/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Early EPC 37 notreated 1


title: Early EPC 37 adenosine treated 4


title: Early EPC 37 adenosine treated 3


title: BXD8/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: HepG2-control_RNAi_LowGC

source_name: HepG2 with LowGC control RNAi

tag: HepG2 cells with RNAi duplex (GC-low control) at 72 hours after transfection.


title: Early EPC 01 notreated 4

source_name: Early EPC 01 DMSO 6h


title: BXH22_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXH14_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXD6/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXH10_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXD42/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXD5/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Early EPC 01 notreated 2


title: BXD40/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Early EPC 01 notreated 1


title: Early EPC 01 notreated 3


title: Early EPC 37 adenosine treated 1


title: Early EPC 01 adenosine treated 4

source_name: Early EPC 01 adenosine 6h


title: BXD38/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXD39/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Early EPC 01 adenosine treated 2


title: Early EPC 01 adenosine treated 3


title: BXD36/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXD34/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Early EPC 01 adenosine treated 1


title: BXD33/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXD32/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: p300 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array1of4

type: genomic

description: ChIP-chip mapping of p300 locations in untreated HeLa cells.

hyb_protocol: NimbleGen protocol.

scan_protocol: NimbleGen protocol.

data_processing: Normalization was performed using the Model-based Analysis of 2-Color Arrays (MA2C) software package using default parameters (Robust C=2).

molecule: genomic DNA

source_name: p300 ChIP DNA from untreated HeLa cells

label_protocol: NimbleGen protocol.

growth_protocol: HeLa cells were obtained from ATCC and cultured under recommended conditions.

extract_protocol: Chromatin were isolated from cells crosslinked with 1% formaldehyde, and chromatin immunoprecipitation was performed using specific antibodies. Resulting ChIP DNA and input DNA were isolated and amplified following NimbleGen protocol.

treatment_protocol: No treatment.

tag: chip antibody

tag: treatment

source_name: Input DNA from untreated HeLa cells


title: H3K4me1 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of H3K4me1 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: H3K4me1 ChIP DNA from HeLa with 1hr TNF-alpha treatment

treatment_protocol: Cells were treated with TNF-alpha (10ng/mL) for 1hr.

value: TNF-alpha

tag: treatment duration

source_name: Input DNA from HeLa with 1hr TNF-alpha treatment


title: H3K4me1 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of H3K4me1 locations in untreated HeLa cells.

source_name: H3K4me1 ChIP DNA from untreated HeLa cells


title: BXD31/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: p300 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of p300 locations in untreated THP1 cells.

source_name: p300 ChIP DNA from untreated THP1 cells

growth_protocol: THP1 cells were obtained from ATCC and cultured under recommended conditions.

source_name: Input DNA from untreated THP1 cells


title: p300 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of p300 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: p300 ChIP DNA from HeLa with 1hr TNF-alpha treatment


title: p300 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of p300 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: p300 ChIP DNA from THP1 with 1hr TNF-alpha treatment

source_name: Input DNA from THP1 with 1hr TNF-alpha treatment


title: p65 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of p65 locations in untreated HeLa cells.

source_name: p65 ChIP DNA from untreated HeLa cells


title: H3K4me3 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of H3K4me3 locations in untreated HeLa cells.

source_name: H3K4me3 ChIP DNA from untreated HeLa cells


title: H3K4me3 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of H3K4me3 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: H3K4me3 ChIP DNA from HeLa with 1hr TNF-alpha treatment


title: H3K4me1 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of H3K4me1 locations in untreated THP1 cells.

source_name: H3K4me1 ChIP DNA from untreated THP1 cells


title: BXD29/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP

source_name: whole hippocampus


title: p65 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of p65 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: p65 ChIP DNA from HeLa with 1hr TNF-alpha treatment


title: CEBPA ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of CEBPA locations in untreated THP1 cells.

source_name: CEBPA ChIP DNA from untreated THP1 cells

value: CEBPA


title: H3K4me1 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of H3K4me1 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: H3K4me1 ChIP DNA from THP1 with 1hr TNF-alpha treatment


title: BXD28/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXD27/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: p65 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of p65 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: p65 ChIP DNA from THP1 with 1hr TNF-alpha treatment


title: p65 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array4of4


title: BXD24b/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: PU.1 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of PU.1 locations in untreated THP1 cells.

source_name: PU.1 ChIP DNA from untreated THP1 cells


title: H3K4me1 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array4of4

source_name: Input DNA from untreated HeLa cells


title: M3

city: Irvine

first: Julie

middle: V

last: Harness

address: 845 Health Sciences Rd.

department: Anatomy & Neurobiology

institute: University of California Irvine

description: Methylated control Replicate 4

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

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

data_processing: Genome Studio software v2010.1. Normalization method: Average beta values are range scaled.

label: C-Bio and A-DNP

source_name: Methylated control Replicate 4

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: Methylated control


title: H3K4me1 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array4of4


title: p65 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array4of4


title: p300 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array4of4

source_name: Input DNA from HeLa with 1hr TNF-alpha treatment


title: H3K4me3 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array4of4


title: H3K4me1 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array4of4

source_name: H3K4me1 ChIP DNA from HeLa with 1hr TNF-alpha treatment


title: H3K4me3 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array4of4

description: ChIP-chip mapping of H3K4me3 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: H3K4me3 ChIP DNA from THP1 with 1hr TNF-alpha treatment


title: BXD21/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: p300 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array4of4

source_name: p300 ChIP DNA from THP1 with 1hr TNF-alpha treatment


title: M1

description: Methylated control Replicate 2

source_name: Methylated control Replicate 2


title: BXD24a/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: H3K4me3 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array1of4

source_name: Input DNA from THP1 with 1hr TNF-alpha treatment


title: BXD20/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: M

description: Methylated control Replicate 1

source_name: Methylated control Replicate 1


title: H3

description: Partially methylated control Replicate 4

value: Partially methylated control


title: BXD2/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXD19/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: H2

description: Partially methylated control Replicate 3


title: esophageal squamous cell carcinoma from patient E2644

city: Rockville

first: Robert

middle: J

last: Clifford

state: MD

address: 2115 E Jefferson

department: CCR

institute: NCI

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Arrays were washed and stained in the Genechip Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.  Chips were scanned with the Affymetrix GeneChip Scanner 3000 using GeneChipOperating System 1.4

data_processing: RMA expression values were generated using the R Bioconductor package.

source_name: patient E2644

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: RNA was extracted from micro-dissected tumor and matched normal tissue using the PureLink Micro-to-Midi Total RNA Purification System (Invitrogen, Carlsbad, CA).

value: esophageal squamous cell carcinoma


title: H3K4me3 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of H3K4me3 locations in untreated THP1 cells.

source_name: H3K4me3 ChIP DNA from untreated THP1 cells

source_name: Input DNA from untreated THP1 cells


title: H3K4me3 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array4of4


title: p65 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array4of4


title: BXD18/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP

source_name: whole hippocampus


title: p65 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array1of4

description: ChIP-chip mapping of p65 locations in untreated THP1 cells.

source_name: p65 ChIP DNA from untreated THP1 cells


title: BXD15/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: H3K4me3 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array4of4

source_name: H3K4me3 ChIP DNA from untreated HeLa cells


title: H

description: Partially methylated control Replicate 1


title: H1

description: Partially methylated control Replicate 2


title: U3

description: Unmethylated control Replicate 4

source_name: Unmethylated control Replicate 4

value: Unmethylated control


title: esophageal squamous cell carcinoma from patient E1709

source_name: patient E1709


title: esophageal squamous cell carcinoma from patient E1796

source_name: patient E1796


title: M2

description: Methylated control Replicate 3

source_name: Methylated control Replicate 3


title: esophageal squamous cell carcinoma from patient E1635

source_name: patient E1635


title: H3K4me1 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array4of4

source_name: H3K4me1 ChIP DNA from untreated THP1 cells


title: esophageal squamous cell carcinoma from patient E1614

source_name: patient E1614


title: U1

description: Unmethylated control Replicate 2

source_name: Unmethylated control Replicate 2


title: U2

description: Unmethylated control Replicate 3

source_name: Unmethylated control Replicate 3


title: BXD13/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXD16/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: U

description: Unmethylated control Replicate 1

source_name: Unmethylated control Replicate 1


title: BXD12/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: CEBPA ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array4of4

source_name: CEBPA ChIP DNA from untreated THP1 cells


title: p300 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array4of4

description: ChIP-chip mapping of p300 locations in untreated HeLa cells.

source_name: p300 ChIP DNA from untreated HeLa cells

source_name: Input DNA from untreated HeLa cells


title: p300 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array4of4

description: ChIP-chip mapping of p300 locations in untreated THP1 cells.

source_name: p300 ChIP DNA from untreated THP1 cells

source_name: Input DNA from untreated THP1 cells


title: p65 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array4of4

source_name: p65 ChIP DNA from untreated THP1 cells


title: esophageal squamous cell carcinoma from patient E1610

source_name: patient E1610


title: PU.1 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array4of4

source_name: PU.1 ChIP DNA from untreated THP1 cells


title: H3K4me1 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of H3K4me1 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: H3K4me1 ChIP DNA from HeLa with 1hr TNF-alpha treatment

source_name: Input DNA from HeLa with 1hr TNF-alpha treatment


title: BXD1/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP

source_name: whole hippocampus


title: esophageal squamous cell carcinoma from patient E1603

source_name: patient E1603


title: esophageal squamous cell carcinoma from patient E1589

source_name: patient E1589


title: BXA8/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Breast1

description: Human Tissue Breast

source_name: Human Tissue Breast

value: Human Tissue Breast


title: BXD14/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Colon1

description: Human Tissue Colon

source_name: Human Tissue Colon

value: Human Tissue Colon


title: esophageal squamous cell carcinoma from patient E1584

source_name: patient E1584


title: NuFFP15A

description: human foreskin fibroblasts

source_name: human foreskin fibroblasts

value: human foreskin fibroblasts


title: H3K4me3 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of H3K4me3 locations in untreated HeLa cells.

source_name: H3K4me3 ChIP DNA from untreated HeLa cells


title: HDFA

description: Human dermal fibroblasts, neonatal

source_name: Human dermal fibroblasts, neonatal

value: Human dermal fibroblasts, neonatal


title: BXA4/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXD11/TyJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: esophageal squamous cell carcinoma from patient E1546

source_name: patient E1546


title: H3K4me3 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of H3K4me3 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: H3K4me3 ChIP DNA from HeLa with 1hr TNF-alpha treatment


title: H3K4me1 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of H3K4me1 locations in untreated HeLa cells.

source_name: H3K4me1 ChIP DNA from untreated HeLa cells

source_name: Input DNA from untreated HeLa cells


title: esophageal squamous cell carcinoma from patient E1566

source_name: patient E1566


title: BXA26/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Prostate1

description: Human Tissue Prostate

source_name: Human Tissue Prostate

value: Human Tissue Prostate


title: p300 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of p300 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: p300 ChIP DNA from HeLa with 1hr TNF-alpha treatment

value: HeLa


title: MSCSC31C

description: Bone marrow-derived mesenchymal stem cells, CD105+, CD34-, SC31-MSC


title: GliaSC11B

description: Postmortem-derived primary astrocyte SC11


title: esophageal squamous cell carcinoma from patient E1535

source_name: patient E1535


title: esophageal squamous cell carcinoma from patient E1542

source_name: patient E1542


title: BXA24/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP

source_name: whole hippocampus

value: male


title: esophageal squamous cell carcinoma from patient E1532

source_name: patient E1532


title: GliaSC01C

description: Postmortem-derived primary astrocyte SC01


title: BXA7/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP

value: whole hippocampus


title: BXA25/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Mel1P51D

description: Human embryonic stem cell line MEL1

source_name: Human embryonic stem cell line MEL1

value: Human embryonic stem cell line MEL1

tag: cell passage number


title: BXA2/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: p65 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of p65 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: p65 ChIP DNA from HeLa with 1hr TNF-alpha treatment

source_name: Input DNA from HeLa with 1hr TNF-alpha treatment


title: H3K4me3 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of H3K4me3 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: H3K4me3 ChIP DNA from THP1 with 1hr TNF-alpha treatment

source_name: Input DNA from THP1 with 1hr TNF-alpha treatment


title: esophageal squamous cell carcinoma from patient E1521

source_name: patient E1521


title: p300 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array2of4

source_name: p300 ChIP DNA from untreated HeLa cells


title: HDFP12A

description: Human dermal fibroblasts, neonatal

source_name: Human dermal fibroblasts, neonatal


title: esophageal squamous cell carcinoma from patient E1520

source_name: patient E1520


title: BXA14/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: FibroSC30C

description: Postmortem-derived primary dermal fibroblasts SC30


title: BXA16/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: normal adjacent esophageal tissue from patient E1709

source_name: patient E1709

value: normal adjacent esophageal tissue


title: Ovary1

description: Human Tissue Ovary

source_name: Human Tissue Ovary

value: Human Tissue Ovary


title: esophageal squamous cell carcinoma from patient E1507

source_name: patient E1507


title: normal adjacent esophageal tissue from patient E1796

source_name: patient E1796


title: WA07UNDP95Atech1

description: Human embryonic stem cell line WA07 technical replicate 1

value: Human embryonic stem cell line WA07


title: BXA1/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXA11/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BXA12/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BloodPt5

description: Human blood

source_name: Human blood

value: Human blood


title: normal adjacent esophageal tissue from patient E1635

source_name: patient E1635


title: WA07UNDP95Atech2

description: Human embryonic stem cell line WA07 technical replicate 2


title: normal adjacent esophageal tissue from patient E1614

source_name: patient E1614


title: p65 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of p65 locations in untreated HeLa cells.

source_name: p65 ChIP DNA from untreated HeLa cells

source_name: Input DNA from untreated HeLa cells


title: normal adjacent esophageal tissue from patient E2644

source_name: patient E2644


title: HSF6KSRP61A

description: Human embryonic stem cell line HSF6

source_name: Human embryonic stem cell line HSF6

value: Human embryonic stem cell line HSF6


title: BTBR_hippo_totalRNA

description: RI mouse strain from HMDP

source_name: whole hippocampus

value: BTBR


title: p300 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array2of4

source_name: p300 ChIP DNA from untreated THP1 cells

source_name: Input DNA from untreated THP1 cells


title: p300 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of p300 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: p300 ChIP DNA from THP1 with 1hr TNF-alpha treatment

value: TNF-alpha

source_name: Input DNA from THP1 with 1hr TNF-alpha treatment


title: HES2P105Dtech2

description: Human embryonic stem cell line HES2 technical replicate 2

value: Human embryonic stem cell line HES2


title: H3K4me1 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of H3K4me1 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: H3K4me1 ChIP DNA from THP1 with 1hr TNF-alpha treatment


title: HES2P105Dtech1

description: Human embryonic stem cell line HES2 technical replicate 1


title: normal adjacent esophageal tissue from patient E1589

source_name: patient E1589


title: normal adjacent esophageal tissue from patient E1584

source_name: patient E1584


title: B6Cc3_rep1_hippo_totalRNA

description: RI mouse strain from HMDP


title: normal adjacent esophageal tissue from patient E1566

source_name: patient E1566


title: AXB8/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: H3K4me3 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of H3K4me3 locations in untreated THP1 cells.

source_name: H3K4me3 ChIP DNA from untreated THP1 cells


title: LLC8PP18

description: Human parthenote LLC8

source_name: Human parthenote LLC8

value: Human parthenote LLC8


title: BXA13/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Miz6KSRP27A

description: Human embryonic stem cell line MIZ6

source_name: Human embryonic stem cell line MIZ6

value: Human embryonic stem cell line MIZ6


title: LLC6PP16tech2

description: Human parthenote LLC6 technical replicate 2

value: Human parthenote LLC6


title: LLC7PP16

description: Human parthenote LLC7

source_name: Human parthenote LLC7

value: Human parthenote LLC7


title: AXB6/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: AXB4/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: normal adjacent esophageal tissue from patient E1542

source_name: patient E1542


title: normal adjacent esophageal tissue from patient E1546

source_name: patient E1546


title: AXB5/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: normal adjacent esophageal tissue from patient E1603

source_name: patient E1603


title: BUB_hippo_totalRNA

description: RI mouse strain from HMDP

value: BUB


title: LLC9PP20

description: Human parthenote LLC9

source_name: Human parthenote LLC9

value: Human parthenote LLC9


title: B6Cc3_rep2_hippo_totalRNA

description: RI mouse strain from HMDP

source_name: whole hippocampus

value: male


title: p65 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of p65 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: p65 ChIP DNA from THP1 with 1hr TNF-alpha treatment


title: normal adjacent esophageal tissue from patient E1535

source_name: patient E1535


title: p65 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of p65 locations in untreated THP1 cells.

source_name: p65 ChIP DNA from untreated THP1 cells

source_name: Input DNA from untreated THP1 cells


title: B6_hippo_totalRNA

description: RI mouse strain from HMDP

value: whole hippocampus


title: AXB24/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: normal adjacent esophageal tissue from patient E1610

source_name: patient E1610


title: normal adjacent esophageal tissue from patient E1532

source_name: patient E1532


title: PU.1 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of PU.1 locations in untreated THP1 cells.

source_name: PU.1 ChIP DNA from untreated THP1 cells


title: LLC2PP24tech2

description: Human parthenote LLC2 technical replicate 2

value: Human parthenote LLC2


title: normal adjacent esophageal tissue from patient E1521

source_name: patient E1521

value: normal adjacent esophageal tissue


title: LLC2PP24tech1

description: Human parthenote LLC2 technical replicate 1


title: normal adjacent esophageal tissue from patient E1507

source_name: patient E1507


title: AXB19b/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: AXB13/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: normal adjacent esophageal tissue from patient E1520

source_name: patient E1520


title: three month old TGR, biological rep3

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

description: Gene expression data from retina of 3m old PKD rat

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.

data_processing: The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.

organism: Rattus norvegicus

source_name: retina of three month old TGR

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

growth_protocol: Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.

extract_protocol: Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.

treatment_protocol: The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.

value: retina

tag: age

value: three month old

tag: genotype

value: truncated polycystin-2


title: one month old TGR, biological rep2

description: Gene expression data from retina of 1m old PKD rat

source_name: retina of one month old TGR

value: one month old


title: HUVECBF4P4Btech1

description: Human Umbilical Vein Endothelial Cell Line HUVEC-BF4


title: AXB19a/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: LLC6PP16tech1

description: Human parthenote LLC6 technical replicate 1


title: three month old TGR, biological rep2


title: AXB12/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: three month old TGR, biological rep1


title: AXB15/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: AXB1/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: one month old TGR, biological rep3


title: one month old TGR, biological rep1


title: AKR_hippo_totalRNA

description: RI mouse strain from HMDP

value: AKR


title: three month old SD, biological rep2

description: Gene expression data from retina of 3m old SD rat

source_name: retina of three month old SD

value: Sprague-Dawley

value: wild type


title: one month old SD, biological rep3

description: Gene expression data from retina of 1m old SD rat

source_name: retina of one month old SD


title: AJ_hippo_totalRNA

description: RI mouse strain from HMDP

value: AJ


title: AXB23/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: CEBPA ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of CEBPA locations in untreated THP1 cells.

source_name: CEBPA ChIP DNA from untreated THP1 cells

value: CEBPA


title: three month old SD, biological rep3


title: AXB10/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: AXB19/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: Micro1_PPNL

city: Pune

first: Meera

middle: Vir

last: Singh

state: Maharashtra

address: 73-G, MIDC, Bhosari

department: Immunology

country: India

institute: National AIDS Research Institute

description: US83000164_251633210015_S01_GE1_105_Dec08_2_4

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65°C, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Scanned on an Agilent G2505B US45103024 scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Normalization of the data was done using Per spot per chip intensity dependant lowess normalization. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. One fold and above differentially regulated genes were filtered from the data. Ontology based biological analysis was done using Gene Ontology browser in GeneSpring Gx. Further, pathways that were significantly regulated was done using bio script library in GeneSpring Gx

source_name: 36 hrs infected with ppNL

label_protocol: RNA was labeled using the Agilent Low Input RNA amplification Kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: CD14+ monocytes were isolated from peripheral blood mononuclear cells (PBMCs) from HIV uninfected donors using Dynal magnetic bead isolation system. The Monocytes were cultured in RPMI containing 10% FCS and 100 ng/ml each of IL-4 and GMCSF for 6 days to obtain immature dendritic cells (iDCs).

extract_protocol: Total cellular RNA was extracted using RNEasy protect kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Day 6 iDCs were infected with 2500 TCID50/ml of HIV-1 isolates, pIn (pIndieC, HIV-1 subtype C), ppIn (pIndieC pseudotyped with VSV-g env) and ppNL (pNL4.3, HIV-1 subtype B, pseudotyped with VSV-g env) over night. The cells were washed thrice the following day and incubated further for 24 hours. After 24 hours, the cells were used to isolate genomic RNA. iDCs matured with 250 ng/ml LPS were used as control.

value: dendritic cells

tag: hiv-1 isolate

value: ppNL (pNL4.3, HIV-1 subtype B

tag: donor


title: Micro1_ppln

description: US83000164_251633210015_S01_GE1_105_Dec08_2_3

source_name: 36 hrs infected with ppIn

value: ppIn (pIndieC pseudotyped with VSV-g env)


title: three month old SD, biological rep1


title: Micro1_pln

description: US83000164_251633210015_S01_GE1_105_Dec08_2_2

source_name: 36 hrs infected with pIn

value: pIn (pIndieC, HIV-1 subtype C)


title: one month old SD, biological rep1


title: one month old SD, biological rep2


title: H3K4me1 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array2of4

description: ChIP-chip mapping of H3K4me1 locations in untreated THP1 cells.

source_name: H3K4me1 ChIP DNA from untreated THP1 cells


title: C. albicans CaGAL102 Mutant culture (Biological Replicate 2)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Gene expression of Mutant

hyb_protocol: One color microarrays were performed using the Genotypic deisnged C.albicans gene expression profiling microarray.  Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65°C, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

data_processing: Data was process using GeneSpring GX 7.3 Software. Data was imported using the enhanced Agilent FE Import setting. Spot information in Feature Extraction was used to flag data, and the normalization was done using GeneSpring GX using the recommended Per Chip and Per Gene Normalization: Normalize to specific control sample.

organism: Candida albicans

source_name: C.albicans cultured under aseptic conditions at 30°C

growth_protocol: Strains were cultured under aseptic conditions at 30°C till the OD at 600nm reached 1. Following which total RNA was extracted by hot phenol method.

extract_protocol: 1 OD of cells were pelleted and stored in -80°C until RNA extraction. RNA was extracted using hot phenol method and then purified using the RNeasy kit (Qiagen). RNA quality was assessed using the Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer’s instructions. RNA was amplified, labeled with Cy3 and combined with spike A using the Agilent Low Input RNA amplification Kit (Agilent Technologies). The amplified cRNA was purified using the RNeasy kit (Qiagen), and specific activity was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific).

value: Cagal102 ko

tag: genetic background


title: Micro3_PPNL

description: US83000164_251633210015_S01_GE1_105_Dec08_1_4


title: Micro1_LPS

description: US83000164_251633210015_S01_GE1_105_Dec08_2_1

source_name: 36 hrs treatment with LPS

value: LPS control


title: Arabidosis T1, biological rep1

city: LEXINGTON

first: Mihir

middle: Kumar

last: Mandal

state: KENTUCKY

address: 201 F Plant science Building

department: Plant Pathology

institute: University of Kentucky

description: Gene expression data from Exudate MgCl2+G3P

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: All probe sets on the Genechips were assigned hybridization signal above background using Affymetrix Expression Console Software v1.0 (http://www.affymetrix.com/Auth/support/downloads/manuals  /expression_console_userguide.pdf <http://www.affymetrix.com/Auth/support/downloads/manuals%20/expression_console_userguide.pdf> ). Data was analyzed using the nonparametric Wilcoxen Rank Sum test. Fold changes are reported as ratios of medians. The P values were calculated individually for each probe set.

organism: Arabidopsis thaliana

source_name: Col-0 Treatment1

label_protocol: standard Affymetrix procedures

extract_protocol: Trizol Method

treatment_protocol: Columbia ecotype, 3-4 week old plants, grown in MTPS 144 conviron walk in Chamber at 22 degree C, 65% RH and 14 hr photoperiod. Distal leaves were harvested 24 h after infiltration of Exudate or Exudate+ G3P in the primary leaf

tag: ecotype

value: Columbia

value: 3-4 week old plants

tag: agent

value: distal leaves


title: C. albicans CaGAL102 Mutant culture (Biological Replicate 1)

description: Gene expression of Mutant


title: Micro3_ppln

description: US83000164_251633210015_S01_GE1_105_Dec08_1_2


title: Arabidosis T2, biological rep2

source_name: Col-0 Treatment2

growth_protocol: Columbia ecotype, 3-4 week old plants, grown in MTPS 144 conviron walk in Chamber at 22 degree C, 65% RH and 14 hr photoperiod


title: Micro3_pln

description: US83000164_251633210015_S01_GE1_105_Dec08_1_3


title: Micro3_LPS

description: US83000164_251633210015_S01_GE1_105_Dec08_1_1


title: Arabidosis T3, biological rep3

source_name: Col-0 Treatment3


title: Arabidosis M3, biological rep3

description: Gene expression data from Exudate MgCl2

source_name: Col-0 Mock3

value: control


title: Arabidosis M2, biological rep2

description: Gene expression data from Exudate MgCl2

source_name: Col-0 Mock2


title: Arabidosis M1, biological rep1

description: Gene expression data from Exudate MgCl2

source_name: Col-0 Mock1


title: 129X1_hippo_totalRNA

description: RI mouse strain from HMDP

source_name: whole hippocampus

tag: gender

value: male

tag: strain

value: whole hippocampus


title: BAT_KO_4

city: Boston

first: Marcia

middle: C

last: Haigis

state: MA

address: 77 Ave Louis Pasteur

institute: Harvard Medical School

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array Mouse430_2. 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: The data were analyzed with Robust Multi-array Average (RMA) with PM only models as normalization method.

source_name: Brown adipose tissue, KO

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer instructions (Invitrogen). RNA was cleaned using RNeasy MiniKit from Qiagen.

treatment_protocol: No treatment. Samples are from SIRT3 WT or KO littermate mice of approximately 1 year of age on a 129 background.

value: SIRT3 KO

tag: tissue

value: brown adipose


title: C. albicans wild type culture

description: Gene expression of Wild Type

value: wild type


title: BAT_KO_5


title: AXB2/PgnJ_hippo_totalRNA

description: RI mouse strain from HMDP


title: BAT_KO_3


title: NIH3T3_PP242_18hr_rep4

city: San Francisco

first: Beatrice

address: 600 16th Street MC 2280

institute: Univeristy of California, San Francisco

description: Gene expression in NIH3T3 cells after 18hr treatment with 2 uM PP242

hyb_protocol: Equal amounts of Cy3 labeled target were hybridized to Agilent mouse whole genome 4x44K Ink-jet arrays. Hybridizations were performed for 14 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner.

data_processing: Raw signal intensities were extracted with Feature Extraction v10.1 software.  The dataset was normalized using the quantile normalization method.  No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

source_name: NIH3T3, PP242, 18hr, replicate 4

label_protocol: RNA was amplified using the whole transcriptome amplification kits (Sigma) following the manufacturer’s protocol, and subsequent Cy3-CTP labeling was performed using one-color labeling kits (NimbleGen). The size distribution and quantity of the amplified product was assessed by Nanodrop and Bioanalyzer.

growth_protocol: NIH3T3 cells were cultured in DMEM supplemented with 10% BCS and penicillin/streptomycin.

extract_protocol: Total RNA was isolated using QIAshredder and RNeasy Mini kits (Qiagen).  RNA was quantified by Nanodrop and integrity was assessed on an Agilent 2100 Bioanalyzer.

treatment_protocol: NIH3T3 cells were treated with DMSO, 50 nM rapamycin, or 2 mM PP242 for 18 hours

tag: cell line

value: 2 uM PP242


title: BAT_KO_2


title: NIH3T3_Rapamycin_18hr_rep2

description: Gene expression in NIH3T3 cells after 18hr treatment with 50 nM Rapamycin

source_name: NIH3T3, Rapamycin, 18hr, replicate 2

value: 50 nM Rapamycin


title: NIH3T3_Rapamycin_18hr_rep4

source_name: NIH3T3, Rapamycin, 18hr, replicate 4


title: NIH3T3_PP242_18hr_rep1

source_name: NIH3T3, PP242, 18hr, replicate 1


title: BAT_KO_1


title: NIH3T3_Rapamycin_18hr_rep3

source_name: NIH3T3, Rapamycin, 18hr, replicate 3


title: NIH3T3_DMSO_18hr_rep2

description: Gene expression in NIH3T3 cells after 18hr treatment with DMSO

source_name: NIH3T3, DMSO, 18hr, replicate 2

value: DMSO


title: NIH3T3_Rapamycin_18hr_rep1

source_name: NIH3T3, Rapamycin, 18hr, replicate 1


title: NIH3T3_PP242_18hr_rep2

source_name: NIH3T3, PP242, 18hr, replicate 2


title: BAT_WT_5

source_name: Brown adipose tissue, WT

value: WT


title: NIH3T3_PP242_18hr_rep3

source_name: NIH3T3, PP242, 18hr, replicate 3


title: NIH3T3_DMSO_18hr_rep3

source_name: NIH3T3, DMSO, 18hr, replicate 3


title: NIH3T3_DMSO_18hr_rep4

source_name: NIH3T3, DMSO, 18hr, replicate 4


title: BAT_WT_4


title: NIH3T3_DMSO_18hr_rep1

source_name: NIH3T3, DMSO, 18hr, replicate 1


title: BAT_WT_2


title: Colon_Normal_Adult_4

city: Salt Lake City

first: Mario

middle: R.

last: Capecchi

state: UT

address: 15 North 2030 East

institute: University of Utah

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65Ã,ÂºC for 17 hours with a rotational speed of 10 rpm.  Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; room temperature) for 1 minute each.  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.  The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  Data captured from the scanned microarray image is saved as a TIF file.

data_processing:
TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 10.1.1.1.  The software automatically positions a grid and finds the centroid positions of each feature on the microarray.  This information is used to perform calculations that include feature intensities, background measurements and statistical analyses.  Data generated by the software is recorded as a tab-delimited text file.
Intensity data from Agilent one-color gene expression arrays was log-transformed (to log base 2) and quantile normalized. Data from microarray features flagged as non-uniform by the Agilent Feature Extraction software were removed prior to normalization.

source_name: Normal Colon

label_protocol: The Agilent One-Color Quick Amp Labeling Kit is used to generate fluorescently labeled cRNA for one-color microarray hybridizations.  Agilent RNA spike-in controls are combined with input total RNA samples (50 to 1000 ng).  The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT.  Following cDNA synthesis, T7 RNA polymerase and cyanine 3-CTP nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate cyanine 3-CTP.  Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit.  The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

growth_protocol: For gene expression in tumors, RNA was isolated from the distal 2.5 cm of colon collected from four each of Tcf4HetApcMin and Tcf4WTApcMin littermates.

extract_protocol: RNA was isolated using an RNAqueous RNA isolation kit (Ambion, Foster City, CA).

value: Normal Colon

value: TCF4WT ApcHet


title: Colon_Tumor_Adult_4

source_name: Colon Adenoma

value: Colon Adenoma

value: Tcf4Het ApcHet


title: BAT_WT_3


title: Colon_Tumor_Adult_3


title: Colon_Normal_Adult_2


title: Control macrophages, biological rep2

city: Oslo

first: Alexandre

last: Corthay

address: Rikshospitalet

department: Department of Biosciences

country: Norway

institute: University of Oslo

description: Control macrophages were isolated from Matrigel containing antigen-loss MOPC315 in Idiotype-specific-TCR-transgenic mice at day +8.

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

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

data_processing: The data were analyzed with GeneChip Operating Software 1.3 (Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Mouse macrophages, non-tumoricidal

growth_protocol: Macrophages that had infiltrated subcutaneous Matrigel plugs.

treatment_protocol: Idiotype-specific TCR-transgenic SCID Balb/c mice were injected s.c. with MOPC315 (or antigen-loss MOPC315) myeloma cells in Matrigel. CD11b+ macrophages were isolated by FACSAria sorting.

tag: cell type

value: CD11b+ macrophages

tag: cell phenotype

value: non-tumoricidal

value: Balb/c

value: adult (7-12 weeks)

tag: cell source

value: TCR-transgenic SCID mice injected with Matrigel containing antigen-loss MOPC315


title: Colon_Tumor_Adult_2


title: Control macrophages, biological rep1


title: Tumoricidal macrophages, biological rep2

description: Tumoricidal macrophages were isolated from Matrigel containing MOPC315 in Idiotype-specific-TCR-transgenic mice at day +8.

source_name: Mouse macrophages, tumoricidal

value: tumoricidal

value: Idiotype-specific TCR-transgenic SCID mice injected with MOPC315-containing Matrigel


title: Tumoricidal macrophages, biological rep3


title: Colon_Normal_Adult_3


title: BAT_WT_1

value: brown adipose


title: Colon_Tumor_Adult_1


title: Human Foreskin Keratinocytes 1, 24 hrs stimulated with poly(I:C)

status: Public on Mar 14 2011

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

description:
replicate 1
array: 1825371014_C

hyb_protocol: Standard Illumina hybridization protocol on BeadArrayer 500GX.

scan_protocol: Standard Illumina scanning protocol on BeadArrayer 500GX, BSGX Version 3.2.7.

data_processing: Non-background corrected data were variance stabilizing transformed (vst) followed by robust spline normalization using the lumi v1.6.2 and lumiHumanAll.db v1.2.0 BioConductor v2.2 packages in R v2.7.1

source_name: primary keratinocytes, poly(I:C) 24 hrs

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays on 50-100 ng total RNA according to the manufacturer's protocols.

growth_protocol: Primary cultures of human epidermal keratinocytes were isolated from foreskin, vagina, or cervix of unrelated donors and established in the presence of a layer of lethally 137Cs-irradiated mouse 3T3 fibroblasts. Passage 4-5 of primary keratinocytes - devoid of contaminating cells - were grown in serum-free medium (Defined KSFM, Invitrogen, Breda, The Netherlands). Keratinocyte cultures stably maintaining HPV DNA as episomes were grown in monolayer culture using E medium in the presence of mitomycin C treated 3T3 fibroblasts for passage 6-7 and afterwards were adapted to serum-free medium for one passage before using them for experimentation.

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 RNA 6000 Nano Lab-on-a-Chip in the 2100 Bioanalyzer. All RNA samples used for microarray analysis had RIN scores above 9.6.

treatment_protocol: Where indicated, cells were stimulated with 25 ug/ml poly(I:C) (InvivoGen, San Diego, USA) for 4 or 24 hrs.

value: Human Foreskin Keratinocytes

tag: culture

tag: poly(i

value: C) stimulation time:24

tag: virus

value: male

tag: labeling batch

tag: hyb order

tag: slide number


title: Human Vaginal Keratinocytes p2, 4 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371014_B

source_name: primary keratinocytes, poly(I:C) 4 hrs

value: Human Vaginal Keratinocytes

value: C) stimulation time:4

value: female


title: Human Vaginal Keratinocytes with HPV18, unstimulated

description:
replicate 1
array: 1825371014_E

source_name: primary keratinocytes, unstimulated

tag: hpv subtype

value: C) stimulation time:0


title: Human Foreskin Keratinocytes 1, 4 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371014_D


title: Human Foreskin Keratinocytes with HPV16, 4 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371013_H


title: Human Vaginal Keratinocytes p1, 24 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371013_F


title: Human Foreskin Keratinocytes 2, unstimulated

description:
replicate 1
array: 1825371013_G


title: Tumoricidal macrophages, biological rep1

tag: genetic background

tag: age


title: Human Cervical Keratinocytes with HPV18, 24 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371014_A

value: Human Cervical Keratinocytes


title: Colon_Normal_Adult_1

value: Normal Colon

tag: genotype

value: TCF4WT ApcHet


title: Human Foreskin Keratinocytes 1, unstimulated

description:
replicate 1
array: 1825371013_D

tag: gender


title: Human Vaginal Keratinocytes with HPV16, unstimulated

description:
replicate 1
array: 1825371008_D


title: Human Cervical Keratinocytes with HPV18, 4 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371008_E


title: Human Vaginal Keratinocytes p2, unstimulated

description:
replicate 1
array: 1825371008_H


title: Human Vaginal Keratinocytes with HPV16, 24 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371008_B


title: Human Vaginal Keratinocytes p1, unstimulated

description:
replicate 1
array: 1825371008_C


title: Human Foreskin Keratinocytes 2, 24 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371013_B


title: Human Foreskin Keratinocytes 2, 4 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371013_E


title: H3K4me1 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of H3K4me1 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: H3K4me1 ChIP DNA from HeLa with 1hr TNF-alpha treatment

tag: chip antibody

value: HeLa

tag: treatment

value: TNF-alpha

tag: treatment duration

source_name: Input DNA from HeLa with 1hr TNF-alpha treatment


title: Human Cervical Keratinocytes with HPV18, unstimulated

description:
replicate 1
array: 1825371013_C

tag: cell type


title: H3K4me3 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of H3K4me3 locations in untreated HeLa cells.

source_name: H3K4me3 ChIP DNA from untreated HeLa cells

tag: cell line

source_name: Input DNA from untreated HeLa cells


title: Human Vaginal Keratinocytes p1, 4 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371008_A


title: Human Foreskin Keratinocytes with HPV16, 24 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371008_G


title: Human Vaginal Keratinocytes p2, 24 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371014_G


title: Human Vaginal Keratinocytes with HPV16, 4 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371014_H


title: Patient_033_Never_Smoker

city: Bosotn

first: Xiaoling

last: Zhang

address: 715 Albany Street

department: Pulmonary

institute: Boston University

description: RNA was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER algorithm as implemented in the ExACT software package

hyb_protocol: cDNA was end-labeled with a biotinylated dideoxynucleotide using terminal transferase. Five and a half micrograms of biotinylated cDNA was added to a hybridization cocktail, loaded on a Human Exon 1.0 ST GeneChip and hybridized for 16 hours at 45 ºC and 60 rpm. Following hybridization, the array was washed and stained according to the standard Affymetrix protocol.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.

data_processing: The approximately 230,000 “core” exon probesets on the Exon array were used for transcript level analysis, which map to approximately 17,800 empirically supported transcripts (RefSeq and full-length GenBank mRNAs) with a high degree of confidence. Transcript-level expression values were derived using the model-based iterPLIER algorithm as implemented in the ExACT software package (Affymetrix, Santa Clara, CA). The gene annotations used for each transcript were from the annotation file obtained from Affymetrix (http://www.affymetrix.com).

source_name: epithelial cells from the inferior nasal turbinate

label_protocol: Ribosomal RNA was first removed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, Carlsbad, CA). This treated RNA was then converted to cDNA and subsequently processed and biotin-labeled.

extract_protocol: Nasal epithelial cells were collected by brushing the inferior turbinate  of current and never smoker volunteers. Epithelial cell content yields were generally approximately 90%. 1 ug of RNA was used as starting material for the microarray studies.

tag: sex

value: Female

tag: race

value: Caucasian

tag: pkyrs

tag: smoker

value: Never smoker


title: Patient_029_Never_Smoker


title: Patient_062_Never_Smoker

value: Male


title: Human Vaginal Keratinocytes with HPV18, 24 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371013_A

tag: culture

tag: poly(i

tag: virus

tag: labeling batch


title: Human Foreskin Keratinocytes with HPV16, unstimulated

description:
replicate 1
array: 1825371008_F

tag: hpv subtype

tag: hyb order

tag: slide number


title: Human Vaginal Keratinocytes with HPV18, 4 hrs stimulated with poly(I:C)

description:
replicate 1
array: 1825371014_F

tag: gender


title: p300 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of p300 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: p300 ChIP DNA from HeLa with 1hr TNF-alpha treatment

tag: chip antibody


title: H3K4me3 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of H3K4me3 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: H3K4me3 ChIP DNA from HeLa with 1hr TNF-alpha treatment

tag: treatment


title: Patient_006_Never_Smoker

tag: age


title: Patient_069_Never_Smoker

value: Current smoker


title: Patient_070_Never_Smoker


title: Patient_024_Never_Smoker


title: Patient_047_Current_Smoker


title: Patient_061_Current_Smoker

value: African American


title: Patient_043_Current_Smoker


title: Patient_042_Current_Smoker


title: Patient_031_Current_Smoker


title: Patient_002_Never_Smoker


title: Patient_045_Current_Smoker


title: p300 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of p300 locations in untreated HeLa cells.

source_name: p300 ChIP DNA from untreated HeLa cells


title: Patient_032_Current_Smoker


title: Patient_040_Current_Smoker


title: H3K4me1 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of H3K4me1 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: H3K4me1 ChIP DNA from THP1 with 1hr TNF-alpha treatment

tag: treatment duration

source_name: Input DNA from THP1 with 1hr TNF-alpha treatment


title: p65 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of p65 locations in untreated HeLa cells.

source_name: p65 ChIP DNA from untreated HeLa cells

tag: cell line


title: Patient_081_Never_Smoker

tag: sex


title: p65 ChIP-chip of HeLa cells after 1hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of p65 locations in HeLa cells treated with TNF-alpha for 1hr.

source_name: p65 ChIP DNA from HeLa with 1hr TNF-alpha treatment


title: H3K4me1 ChIP-chip of HeLa cells after 0hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of H3K4me1 locations in untreated HeLa cells.

source_name: H3K4me1 ChIP DNA from untreated HeLa cells


title: p65 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of p65 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: p65 ChIP DNA from THP1 with 1hr TNF-alpha treatment


title: Patient_008_Current_Smoker

tag: race


title: H3K4me3 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of H3K4me3 locations in untreated THP1 cells.

source_name: H3K4me3 ChIP DNA from untreated THP1 cells

source_name: Input DNA from untreated THP1 cells


title: Patient 538 Never Smoker (N525N-temp2)

extract_protocol: Bronchial epithelial cells were obtained from brushing the right mainstem bronchus of current and never smoker volunteers at bronchoscopy. During the same clinic visit, nasal epithelial cells were collected by brushing the inferior turbinate. Epithelial cell content yields were generally approximately 90%. 1 ug of RNA was used as starting material for the microarray studies.

tag: pkyrs

tag: cell type

value: epithelial cells from the inferior nasal turbinate


title: Patient 547 Never Smoker (N547N)

tag: smoker


title: Patient 537 Never Smoker (N538N)


title: Patient 535 Never Smoker (N535N)

value: Hispanic


title: Patient 555 Never Smoker (N555N)


title: Patient 529 Never Smoker (N529N)


title: Patient 544 Never Smoker (N544N)


title: Patient 536 Never Smoker (N537N)


title: Patient 527 Never Smoker (N531N)


title: Patient 142 Never Smoker (N142N)


title: Patient_078_Current_Smoker


title: Patient 525 Never Smoker (N527N-1)


title: p65 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of p65 locations in untreated THP1 cells.

source_name: p65 ChIP DNA from untreated THP1 cells


title: H3K4me1 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of H3K4me1 locations in untreated THP1 cells.

source_name: H3K4me1 ChIP DNA from untreated THP1 cells


title: Patient 556 Current Smoker (N556C)


title: Patient 128 Never Smoker (N128N)


title: Patient_064_Never_Smoker


title: Patient 558 Never Smoker (N558N)


title: PU.1 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of PU.1 locations in untreated THP1 cells.

source_name: PU.1 ChIP DNA from untreated THP1 cells


title: p300 ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of p300 locations in untreated THP1 cells.

source_name: p300 ChIP DNA from untreated THP1 cells


title: H3K4me3 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of H3K4me3 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: H3K4me3 ChIP DNA from THP1 with 1hr TNF-alpha treatment


title: CEBPA ChIP-chip of THP1 cells after 0hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of CEBPA locations in untreated THP1 cells.

source_name: CEBPA ChIP DNA from untreated THP1 cells

value: CEBPA


title: Patient 533 Current Smoker (N528C)

source_name: epithelial cells from the inferior nasal turbinate


title: p300 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array3of4

description: ChIP-chip mapping of p300 locations in THP1 cells treated with TNF-alpha for 1hr.

source_name: p300 ChIP DNA from THP1 with 1hr TNF-alpha treatment


title: Patient 528 Current Smoker (N530C-1)

description: RNA was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER algorithm as implemented in the ExACT software package


title: Patient 530 Current Smoker (N533C)


title: Patient 526 Current Smoker (N526C)


title: Patient 558 Never Smoker (B558N)

source_name: epithelial cells from right mainstem bronchus


title: Patient 462 Current Smoker (N462C)


title: Patient 532 Current Smoker (N534C)


title: Patient 524 Current Smoker (N524C)


title: Patient 539 Current Smoker (N539C)


title: Patient 459 Current Smoker (N459C-1)


title: petri-control-rep2

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: cells control cultivated in petri

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix gene 1ST.Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Affymetrix expression console was used to check the scaned data and RMA on R programm  was used as the normalisation method.

source_name: hepatic human cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Total RNA were extracted using Nucleospin® RNA XS isolation kit system (Macherey-Nagel) after cell trypsination. Samples were freezed at -80°C prior microarray hybridisation

tag: cultivated in

value: petri

tag: dose


title: petri-treated-rep2

description: cells treated cultivated in petri

value: acetaminophen


title: Patient 555 Never Smoker (B555N)

value: epithelial cells from right mainstem bronchus


title: Patient 544 Never Smoker (B544N)


title: petri-treated-rep1

description: cells treated cultivated in petri


title: petri-treated-rep3

description: cells treated cultivated in petri*


title: petri-control-rep3

description: cells control cultivated in petri


title: Patient 534 Current Smoker (N532C)


title: Patient 546 Current Smoker (N546C-1)


title: microsystem-treated-rep2

description: cells treated cultivated in microsytem

value: microsystem


title: petri-control-rep1

description: cells control cultivated in petri


title: microsystem-treated-rep1

description: cells treated cultivated in microsytem


title: microsystem-control-rep3

description: cells control cultivated in microsytem


title: Patient 538 Never Smoker (B538N)


title: Patient 547 Never Smoker (B547N)


title: Patient 537 Never Smoker (B537N)


title: CD34(-)/CD133(-) cells without RBCs of donor A vs. synthetic miRNA pool

type: mixed

city: Bergisch Gladbach

first: Ute

last: Bissels

state: NRW

address: Friedrich-Ebert-Str. 68

department: R&D

institute: Miltenyi Biotec GmbH

description: PMID

hyb_protocol: 1 µg of respective total RNA was mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. Hybridization was performed as described by Bissels et al. (RNA 2009).

scan_protocol: Image capture was done with Agilent DNA-Microarray Scanner (Agilent, Santa Clara, CA)

data_processing:
Signal processing and quantification was done with ImaGene software version 8.0 (BioDiscovery, Los Angeles, CA). For each spot, the local signal was measured inside a fixed circle of 230-280 µm diameter, and background was measured outside the circle within specified rings 30 µm distant to the signal and 100 µm wide. Signal and background was taken to be the average of pixels between defined low and high percentages of maximum intensity with percentage parameter settings for low/high being 2/97% for signal and 0/97% for background. Local background was subtracted from the signal to obtain the net signal intensity and the mean of the net signal intensities of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots) and for which the fluorescent intensity of the miRNAs derived from the samples of interest was one-fold the mean background value in at least four of five donors in the CD133+ and/or CD34+CD133- cell population and where the miRNA was present in the UR. Subsequently,the array data was log2 transformed.
Only the miRNAs detected as present are contained in the data tables, and were used in subsequent data analysis including cluster analysis in TIGR MEV.

source_name: CD34(-)/CD133(-) without RBCs/bone marrow

label_protocol: 1 µg total RNA was labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer

extract_protocol: total RNA was isolated using a commercial kit (miRNeasy Mini kit, Qiagen) following the instructions of the manufacturer

value: female

value: 81 years

tag: tissue

value: bone marrow

molecule: other

organism: synthetic construct

source_name: synthetic miRNA pool

label_protocol: 2.5 fmol of each of 954 synthetic miRNAs were pooled and labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer total RNA was labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer

extract_protocol: synthesized

tag: reference

value: synthetic construct


title: Patient 529 Never Smoker (B531N)

value: Female


title: Patient 531 Never Smoker (N536N)


title: CD133(+) cells of donor E vs. synthetic miRNA pool

description: PMID

source_name: CD133(+)/bone marrow


title: CD34(+)/CD133(-) cells of donor E vs. synthetic miRNA pool

description: PMID

source_name: CD34(+)/CD133(-)/bone marrow


title: CD34(-)/CD133(-) cells without RBCs of donor E vs. synthetic miRNA pool

description: PMID


title: CD133(+) cells of donor A vs. synthetic miRNA pool

description: PMID


title: Patient 533 Current Smoker (B528C)


title: CD34(+)/CD133(-) cells of donor A vs. synthetic miRNA pool

description: PMID


title: CD34(-)/CD133(-) cells with RBCs of donor A vs. synthetic miRNA pool

description: PMID

source_name: CD34(-)/CD133(-) with RBCs/bone marrow


title: Patient 531 Never Smoker (B529N)


title: Patient 546 Current Smoker (B546C)

value: Caucasian


title: microsystem-control-rep2

description: cells control cultivated in microsytem


title: Patient 556 Current Smoker (B556C)


title: microsystem-treated-rep3

description: cells treated cultivated in microsytem


title: CD34(-)/CD133(-) cells without RBCs of donor D vs. synthetic miRNA pool

description: PMID

value: 80 years


title: CD34(-)/CD133(-) cells with RBCs of donor E vs. synthetic miRNA pool

description: PMID


title: Patient 536 Never Smoker (B535N)

value: Male

value: Never smoker


title: microsystem-control-rep1

description: cells control cultivated in microsytem


title: Patient 539 Current Smoker (B539C)

value: African American

value: Current smoker


title: Patient 549 Current Smoker (N549C)

value: epithelial cells from the inferior nasal turbinate


title: Patient 128 Never Smoker (B128N)


title: Neg_14

hyb_protocol: Cy3 labeled cDNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (44K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min followed by a second wash with 0.06x SSPE containing 0.005% N-lauroylsarcosine for 1 min and a final wash step with acetonitrile for 30 sec. All washing steps were performed at room temperature.

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

data_processing: The Agilent Feature Extraction Software (FES) Version 9.1 was used to read out and process the microarray image files. Signal intensity data (w/o control spots) background corrected and normalized to array median and multiplied by median calculated from all values (green_processed_Signal)

label_protocol: 200 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: CD133+ bone marrow cells were enriched with the CliniMACS CD133 Reagent (clone AC133, Miltenyi Biotec Bergisch Gladbach, Germany) using the CliniMACS Cell Separation System (Miltenyi Biotec). CD34+/CD133- cells were isolated by enrichment of  CD34+ cells with the CliniMACS CD34 Reagent (clone QBEND/10, Miltenyi Biotec) using the negative fraction of the first separation.

extract_protocol:
Total RNA was isolated using a commercial kit (miRNeasy Mini kit, Qiagen) and 1-10 ng of RNA were amplified by using the µMACSTM SuperAmpTM Kit (Miltenyi Biotec).
SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol using 1-10 ng total RNA. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

treatment_protocol: Cells were lysed in QIAzol Lysis Reagent (Qiagen) and total RNA was isolated.


title: Patient 526 Current Smoker (B526C)

value: Hispanic


title: Patient 549 Current Smoker (B549C)


title: Neg_11


title: CD34(-)/CD133(-) cells of donor D with RBCs vs. synthetic miRNA pool

description: PMID


title: Patient 524 Current Smoker (B524C)


title: Patient 534 Current Smoker (B532C)


title: Patient 528 Current Smoker (B530C)


title: Patient 535 Never Smoker (B536N-1)


title: CD34(+)/CD133(-) cells of donor D vs. synthetic miRNA pool

description: PMID


title: CD133(+) cells of donor D vs. synthetic miRNA pool

description: PMID


title: Patient 462 Current Smoker (B462C)


title: Patient 459 Current Smoker (B459C-1)


title: CD34(+)/CD133(-) cells of donor C vs. synthetic miRNA pool

description: PMID


title: Neg_15


title: CD34_9

value: 73 years

value: male


title: CD133(+) cells of donor C vs. synthetic miRNA pool

description: PMID


title: CD34_4

extract_protocol:
Total RNA was isolated as described in: Chomczynski P. (1993). A reagent for the single-step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples. Biotechniques. 1993 Sep;15(3):532-4, 536-7. After that, 1-10 ng of RNA were amplified by using the µMACSTM SuperAmpTM Kit (Miltenyi Biotec).
SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol using 1-10 ng total RNA. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

value: 79 years


title: CD34(-)/CD133(-) cells with RBCs of donor C vs. synthetic miRNA pool

description: PMID


title: CD34(-)/CD133(-) cells without RBCs of donor C vs. synthetic miRNA pool

description: PMID


title: CD34(-)/CD133(-) cells with RBCs of donor B vs. synthetic miRNA pool

description: PMID


title: CD34_3

value: 72 years


title: Neg_9


title: GBM_stem_A_control

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

hyb_protocol: Standard Affymetrix protocols

label_protocol: GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 500 ng total RNA.

extract_protocol: RNeasy kits (Qiagen) were used to extract total RNA from brain tumor initiating cells. The integrity and concentration of RNA was determined via microfluidic analysis on an Experion instrument (BioRad).

treatment_protocol: Microarray expression analysis of shTR1- and shTR2-expressing GBM-1 knockdown cells compared to non-targeting shRNA-expressing control cells TRRAP (shTR1, target sequence: CGTGTAAGAAAGGGAGAATAT; shTR2, target sequence: GCCCTGTTCTTTCGCTTTGTA). Total RNA for each sample was obtained after short term puromycin selection (5 ug/mL for 2 days followed by 1 ug/mL for 2 days) from two independent lentiviral infections and pooled prior to RNA preparation.

tag: genotype/variation

value: control


title: Patient 142 Never Smoker (B142N)

value: epithelial cells from right mainstem bronchus


title: GBM_stem_A_BMP_shRNA_B8

value: shTR1-mediated TRRAP knockdown


title: HGPS-iPSC replicate 2

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

hyb_protocol: The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). The amplification and labeling were processed as indicated in Nugen protocol with 25ng starting RNA. For each sample, 3.75ug ssDNA were labeled and hybridized to the Affymetrix HG-U133 Plus 2.0 chips.

scan_protocol: Expression signals were scanned on an Affymetrix GeneChip Scanner (7G upgrade). The data extraction was done by the Affymetrix GCOS software v.1.4.

data_processing: The statistical analysis of the data was performed using ArrayStar 3. Briefly, raw CEL files were imported together with gene annotation from NetAffix (from 11/13/2009) and normalized using RMA algorithm and quantile normalization. As both H9 ESC and HGPS-iPSC originate from female samples, and in order to check for any possible bias introduced by the X and Y chromosome-coded genes, we performed the same analysis with only autosome genes.

label: Biotin

growth_protocol: H9 hESCs (WiCell Research) and iPSCs were maintained on a layer of mitotically inactivated MEFs in DMEM/F12 (Invitrogen) supplemented with 0.1 mM non-essential amino acids (Invitrogen), 1 mM glutamax (Invitrogen), 20% Knockout Serum Replacement (Invitrogen), 55 μM b-mercaptoethanol (Invitrogen) and 10 ng/ml bFGF (Joint Protein Central). hESCs and iPSCs were also cultured in Matrigel (BD Biosciences) with mTeSR medium (Stem Cell Technologies).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) followed by cDNA synthesis using High capability RNA-to-cDNA Mater Mix (Invitrogen).

treatment_protocol: iPSCs Generation. For the generation of human iPSCs, human fibroblasts were seeded in a 6-well plate and spin-infected with a mix of high-quality retroviruses encoding OCT4, SOX2, KLF4, c-MYC, and GFP in the presence of 4 g/ml polybrene. Three infections on consecutive days were performed. 6 days after the first spin-infection, fibroblasts were gently individualized with TrypLE (invitrogen) and seeded onto fresh MEFs in the fibroblast culture medium. After 24 h, the medium was switched to hESC medium. The media was changed every 1–2 days depending on cell density. To establish the iPSC lines, colonies were manually picked and transferred onto MEF feeder cells for several passages before further transfer to Matrigel/mTesR conditions.

value: hgps-ipsc_2:Human HGPS fibroblasts AG01972, AG11498, AG06297, and normal fibroblasts GM00038 (9 year), AG05247 (87 year), AG09602 (92 year) were purchased from Coriell Cell Repository and reprogrammed using the protocol below.


title: CD34_14

value: bone marrow

value: 81 years

value: female


title: HGPS iPSC replicate 1

label_protocol: The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). The amplification and labeling were processed as indicated in Nugen protocol with 25ng starting RNA. For each sample, 3.75ug ssDNA were labeled and hybridized to the Affymetrix HG-U133 Plus 2.0 chips.

value: hgps-ipsc_1:Human HGPS fibroblasts AG01972, AG11498, AG06297, and normal fibroblasts GM00038 (9 year), AG05247 (87 year), AG09602 (92 year) were purchased from Coriell Cell Repository and reprogrammed using the protocol below


title: Patient 527 Never Smoker (B527N)

value: Male

value: Caucasian

value: Never smoker


title: CD133_4

source_name: CD133(+) cells

value: CD133(+) cells


title: Patient 532 Current Smoker (B534C)

value: African American

value: Current smoker


title: CD34_8

value: 70 years

value: male


title: Patient 530 Current Smoker (B533C)

value: Female


title: intestine-EphB2High-R2

first: Eduard

last: Batlle

address: Baldiri i Reixach 10

institute: Institute for Research in Biomedicine

description: Gene expression data from intestinal EphB2 High sorted cells

hyb_protocol: 3.75 µg of cDNA was hybridized per Affymetrix GeneChip® Mouse 430 2.0 Array for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions (http://www.affymetrix.com).

data_processing: Lgr5 samples (samples 1 and 2) and EphB2 samples (samples 3 to 8) were obtained at different dates and pre-processed separately. In both cases quantile normalization and RMA summarization were used. Genespring software was used for samples 1 and 2. Bioconductor software was used for samples 3 to 8. (Bioc version: 2.8.0; Bioc packages: affy, mouse4302cdf)

source_name: EphB2 High Rep2

label_protocol: 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)

growth_protocol: Intestinal epithelial single cell suspensions were obtained from mouse intestines after several rounds of shaking in HBSS containing 8mM EDTA followed by enzyme treatment with 0.4mg/mL Dispase / 0.8U/µL DNAse I.

extract_protocol: RNA from sorted cells was extracted using Trizol Reagent following manufacturer’s instructions.

treatment_protocol: Intestinal single cell suspensions were sorted in a FACS Aria 2.0 (BD) according to high, medium or low EphB2 levels (anti-EphB2 Mab 2H9 -Genentech, 6g/ml detected by secondary anti-mouse IgG-APC -1/500, Jackson) or Lgr5 levels (High or Low expression of the Lgr5-EGFP knock-in allele

value: intestinal crypt cells

tag: strain

tag: group

value: EphB2 High


title: CD133_8


title: CD133_9

value: 73 years


title: H9 ESC - replicate 2

value: h9-esc_2:H9 hESCs (WiCell Research)


title: intestine-EphB2Low-R2

description: Gene expression data from intestinal EphB2 Low sorted cells

scan_protocol: according to the manufacturer’s instructions (http://www.affymetrix.com)

source_name: EphB2 Low Rep2

value: EphB2 Low


title: CD133_3

value: bone marrow

value: 72 years


title: CD34_15

value: 81 years

value: female


title: CD34_11

value: 80 years


title: GBM_stem_F_shRNA_B9

value: shTR2-mediated TRRAP knockdown


title: H9 ESC - replicate 1

value: h9-esc_1:H9 hESCs (WiCell Research)


title: intestine-EphB2Low-R1

source_name: EphB2 Low Rep1


title: BJ-iPSC replicate 1

value: bj-ipsc_1:BJ normal human fibroblasts (CRL-2522) were from ATCC and reprogrammed to iPSC with the protocol defined below


title: intestine-EphB2Medium-R2

description: Gene expression data from intestinal EphB2 Medium sorted cells

source_name: EphB2 Medium Rep2

value: EphB2 Medium


title: BJ-iPSC replicate 2

value: bj-ipsc_2:BJ normal human fibroblasts (CRL-2522) were from ATCC and reprogrammed to iPSC with the protocol defined below


title: CD34(+)/CD133(-) cells of donor B vs. synthetic miRNA pool

description: PMID

value: male

value: synthetic construct


title: CD133(+) cells of donor B vs. synthetic miRNA pool

description: PMID


title: CD34(-)/CD133(-) cells without RBCs of donor B vs. synthetic miRNA pool

description: PMID


title: CD133(+) cells of donor L1 vs. synthetic miRNA pool

description: PMID

source_name: CD133(+)/ moblized leukapheresis

value: 21 years

value: moblized leukapheresis


title: CD133(+) cells of donor L2 vs. synthetic miRNA pool

description: PMID

value: 31 years


title: CD133_11

value: CD133(+) cells


title: CD133_14


title: intestine-EphB2High-R1

source_name: EphB2 High Rep1

value: intestinal crypt cells

value: EphB2 High


title: intestine-Lgr5High-R1

description: Gene expression data from intestinal Lgr5-EGFP high sorted cells

source_name: Lgr5 High

value: Lgr5 High


title: intestine-Lgr5Low-R1

description: Gene expression data from intestinal Lgr5-EGFP low sorted cells

source_name: Lgr5 Low

value: Lgr5 Low


title: HGPS Fibroblast replicate 1

growth_protocol: All fibroblasts were cultured in 5% CO2 and at 37°C in DMEM containing 15% FBS, 2 mM L-glutamine, 0.1 mM non-essential aminoacids, sodium Pyruvate, and 55 μM b-mercaptoethanol.

value: hgps-fib_1:Human HGPS fibroblasts AG01972, AG11498, AG06297, and normal fibroblasts GM00038 (9 year), AG05247 (87 year), AG09602 (92 year) were purchased from Coriell Cell Repository


title: BJ-fib_1

source_name: BJ fibroblasts

value: bj-fib_1:BJ (CRL-2522) fibroblasts were purchased from ATCC.


title: 18 hour EDL, biological rep 4

status: Public on Mar 11 2011

city: Research Triangle Park

first: Michael

middle: Bruce

last: Black

address: 6 Davis Dr., P.O. Box 12137

department: Chemical Safety Sciences

institute: The Hamner Institutes for Health Sciences

description: Gene expression data from adult male rat epididymis - 18 hours EDL

hyb_protocol: Ten micrograms of cRNA were fragmented and hybridized to the RAE230 2.0 array (Affymetrix, Santa Clara, CA), which monitors over 31,000 transcripts. The hybridized arrays were stained in the Fluidics Station 450.

scan_protocol: The hybridized arrays were scanned on the Affymetrix Scanner 3000. All of the array images were visually inspected for defects and quality. Signal values for each array were determined using Gene Chip Operating System 1.0 (GCOS; Affymetrix).

data_processing: Raw signal values were normalized using GCRMA, therefore all subsequent intensity values and odd ratio values are log base 2.  Analyses were performed in R release 2.9 and BioConductor release 2.4

source_name: rat initial segment of epididymis, EDL operation

label_protocol: Five micrograms of total RNA were used to generate biotin-labeled cRNA using an oligo(T7) primer in a reverse transcription reaction, followed by in vitro transcription with biotin-labeled UTP and CTP.

growth_protocol: Normal adult male Sprague-Dawley rats between 275 and 450 grams were maintained on a 12L:12D cycle with free access to food and water in the University of Virginia vivarium.

extract_protocol: The tissue samples stored in RNALater at -20oC were thawed at room temperature and the RNALater was removed. Total RNA was extracted and further purified through RNAeasy columns according to the manufacturer's instructions (Qiagen, Valencia, CA). All samples were treated with DNase on the column and eluted with DEPC-treated water. RNA was quantified by the absorbance at 260 nm and RNA quality was assessed using the Agilent Bioanalyzer (Palo Alto, CA) and spectrophotometric analysis.

treatment_protocol: Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal.  After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out.

tag: time point

tag: gender

value: Sprague-Dawley

value: initial segment of epididymis

value: adult


title: intestine-EphB2Medium-R1

source_name: EphB2 Medium Rep1

value: EphB2 Medium


title: BJ-fib_2

source_name: BJ fibroblast replicate 2

value: bj-fib_2:BJ (CRL-2522) fibroblasts were purchased from ATCC.


title: CD133_15

value: bone marrow

tag: age

value: 81 years

value: female


title: HGPS Fibroblast replicate 2

value: hgps-fib_2:Human HGPS fibroblasts AG01972, AG11498, AG06297, and normal fibroblasts GM00038 (9 year), AG05247 (87 year), AG09602 (92 year) were purchased from Coriell Cell Repository


title: GFP positive 2 (biological replica 2)

status: Public on Mar 13 2011

city: DUNDEE

first: Maria

middle: N

last: Navarro

address: Dow Street

department: Cell Signallig and Immunology

country: United Kingdom

institute: University of Dundee

description: Gene expression data for P14 TCR cytotoxic T cells

data_processing: Expression Console (rma pre-processing) and Multiexperiment Viewer software, comparing GFP positive relative to GFP negative

source_name: P14 TCR cytotoxic T cells

label_protocol: performed by Finnish DNA Microarray Centre at the Centre for Biotechnology, Turku, Finland using GeneChip mouse genome 430_2.0 array (Affimetrix)

growth_protocol: P14 TCR spleens were disaggregated, activated for 24h with gp33 peptide. Cells were retrovirally infected with GFP-HDAC7 phosphorylation deficient mutant and sorted as GFP negative and GFP positive

extract_protocol: Rneasy kit (Qiagen)

value: P14 TCR cytotoxic T cells

value: HDAC7 phosphorylation deficient mutant


title: 12 hour EDL, biological rep 2

description: Gene expression data from adult male rat epididymis - 12 hours EDL

value: male


title: GFP negative 2 (biological replica 2)

hyb_protocol: performed by Finnish DNA Microarray Centre at the Centre for Biotechnology, Turku, Finland

value: control


title: GFP negative 3 (biological replica 3)

scan_protocol: performed by Finnish DNA Microarray Centre at the Centre for Biotechnology, Turku, Finland


title: GFP negative 1 (biological replica 1)


title: GFP positive 1 (biological replica 1)


title: GFP positive 3 (biological replica 3)


title: CD133_12

value: CD133(+) cells


title: 12 hour EDL, biological rep 4


title: 18 hour EDL, biological rep 3


title: 18 hour EDL, biological rep 1


title: 6 hour EDL, biological rep 4

description: Gene expression data from adult male rat epididymis - 6 hours EDL


title: 12 hour EDL, biological rep 3


title: 18 hour EDL, biological rep 2


title: 12 hour EDL, biological rep 1


title: 6 hour EDL, biological rep 3


title: Trophoblast SP

status: Public on Mar 12 2011

city: Fukuoka

first: Tomoka

last: Takao

address: Maidashi3-1-1, Higashi-ku, Fukuoka

institute: Kyushu University

description:
HTR8-SP
Gene expression data from SP cells of the HTR-8/Svneo cell line.

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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 GeneChip Operating Software ver 1.4 (Affymetrix 690036) and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Trophoblast cell line SP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip Expression Analysis Technical Manual, 701021 Rev.5, Affymetrix).

growth_protocol: The parent HTR-8/SVneo cells were cultured in 95% air and 5% CO2 humidified atmosphere at 37 ℃.

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

treatment_protocol: The cells were labeled with 2.5µg/ml Hoechst 33342 dye (Molecular Probes, Eugene, OR) for 120 minutes at 37 ℃, either alone or in combination with 50 µmol/L verapamil (Sigma-Aldrich, ST Louis, MO). The cells were then passed through EPICS ALTRA HyPerSort (Beckman Coulter, Fullerton, CA) using dual wavelength analysis (blue, 424-444 nm; red, 675 nm) after excitation with 350 nm UV light. Sorted cells were cultured for 1 day, then rinsed with PBS and placed on ice in the ISOGEN solution (NIPPONGENE).

value: placenta

value: first trimester (7 weeks)

tag: cell population

value: side population (SP)


title: 6 hour EDL, biological rep 2

value: Sprague-Dawley


title: 6 hour EDL, biological rep 1

value: initial segment of epididymis


title: sham control, biological rep 4

description: Gene expression data from adult male rat epididymis - sham control

source_name: rat initial segment of epididymis, sham operation

value: adult


title: sham control, biological rep 2


title: sham control, biological rep 1


title: asthma severe5

city: Seoul

first: Yoosik

last: Yoon

address: 221 HeukSeok-Dong, DongJak-Gu

country: South Korea

institute: Chung-Ang University

description: Gene expression of RNA

hyb_protocol: Labeled cDNAs were hybridized to Agilent’s Human Oligo Microarray (44K) containing probes for 41 000 genes at 65 °C for 17 hrs and washed with Agilent’s Gene Expression Wash Buffer Kit as suggested by the manufacturer’s protocol.

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction software (Agilent Technology).

data_processing: All data normalization was performed using GeneSpring GX 7.3 software (Agilent Technology). The normalization method was quantile.

source_name: Peripheral Blood

label_protocol: One microgram of RNA was reverse transcribed into cDNA and labeled using Agilent’s Low RNA Input Linear Amplification kit (Agilent Technology, Santa Clara, CA, USA).

growth_protocol: To induce an inflammatory response, for in vitro study, the THP1 cells were seeded in 12-well plates at a density of 1 × 106 cells/well in RPMI 1640 medium containing 0.5% fetal bovine serum, and were incubated for 24hr.

extract_protocol: Ten milliliters of peripheral blood of asthma and normal subjects, for in vivo study, were centrifuged at 4000 rpm for 20 min to collect 0.4 mL of the buffy coat fraction, which is mainly composed of peripheral blood nuclear cells. The buffy coat fraction was then mixed with 1.3 ml RNAlater solution (Ambion, Austin, TX, USA) and stored at 4oC until use. For in vitro study, stimulated THP1 cells by LPS or HDM were harvested using a cell scraper and lysed for total RNA extraction. Total RNA was extracted from the buffy coat fractions using a Ribo-pure blood kit (Ambion, Austin, TX, USA).

treatment_protocol: The THP1 cells stimulated for 24 hrs with LPS or HDM extract, in the in vitro study.

tag: disease state

value: asthma severe

value: whole blood


title: LPS treatment

description: Gene expression of RNA

source_name: THP1 cultured cells

tag: condition

value: LPS treatment

value: monocyte


title: asthma severe4

description: Gene expression of RNA


title: asthma mild2

description: Gene expression of RNA

value: asthma mild


title: normal4

description: Gene expression of RNA

value: normal


title: asthma severe1

description: Gene expression of RNA


title: low con house dust mite treatment

description: Gene expression of RNA

value: low con house dust mite treatment


title: no treatment

description: Gene expression of RNA

value: no treatment


title: asthma severe2

description: Gene expression of RNA

value: male


title: high con house dust mite treatment

description: Gene expression of RNA

value: high con house dust mite treatment


title: asthma mild1

description: Gene expression of RNA


title: normal2

description: Gene expression of RNA


title: asthma mild3

description: Gene expression of RNA


title: normal1

description: Gene expression of RNA


title: Trophoblast NSP

description:
HTR8-NSP
Gene expression data from NSP cells of the HTR-8/Svneo cell line.

source_name: Trophoblast cell line NSP

tag: cell line

value: non-side population (NSP)


title: asthma mild5

description: Gene expression of RNA


title: asthma severe3

description: Gene expression of RNA


title: normal3

description: Gene expression of RNA


title: asthma mild4

description: Gene expression of RNA