title: genomic DNA from Surgical resection GBM-1749

source_name: Surgical resection GBM-1749


title: genomic DNA from Surgical resection GBM-1710

status: Public on Jan 06 2015

type: genomic

city: Acton

first: Sebastian

last: Kurscheid

state: ACT

address: 57 Garran Road

department: JCSMR

country: Australia

institute: Australian National University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2 was used for primary data acqusition. Raw data was imported into R and further processed using R/Bioconductor package “methylumi”. The raw pre-processing (Illumina method) was used for data normalization.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Surgical resection GBM-1710

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA Kit (Qiagen, 80204).

tag: gender

value: M

tag: disease state

value: GBM

tag: geo expression data

tag: age

tag: os

value: U


title: genomic DNA from Surgical resection GBM-1769

source_name: Surgical resection GBM-1769


title: genomic DNA from Surgical resection GBM-1628

source_name: Surgical resection GBM-1628

value: F


title: genomic DNA from Surgical resection GBM-1768

source_name: Surgical resection GBM-1768


title: genomic DNA from Surgical resection GBM-1646

source_name: Surgical resection GBM-1646


title: Unlabeled ADSCs [2]

type: RNA

city: Seoul

first: Min Hwan

last: Kim

address: 75 Nowon-gil, Gongneung-Dong, Nowon-Gu

country: South Korea

institute: Korea Institute of Radiological and Medical Sciences

description:
Sample name: ADSC_2
Unlabeled ADSCs (14 days after culture)

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1.

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat adipose derived stem cells

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Total RNA was isolated from tissue or cell using RNAeasy Mini Kit (Qiagen, Valencia, CA, USA)

tag: strain

value: Sprague Dawley (SD)

value: 13 weeks

tag: cell type

value: ADSCs

tag: treatment

value: unlabeled


title: MDS068

city: Oxford

first: Andrea

last: Pellagatti

address: John Radcliffe Hospital

department: NDCLS, RDM

country: United Kingdom

institute: University of Oxford

description:
MDS patient 68
Gene expression data from bone marrow CD34+ cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix CEL files were pre-processed using GC Robust Multi-array Average (GC-RMA)

label: Biotin

source_name: Bone marrow CD34+ cells

label_protocol: 50 ng of total RNA were amplified and biotin-labelled with the Two-Cycle cDNA Synthesis and the Two-Cycle Target Labelling and Control Reagent packages according to the standard Affymetrix protocol

extract_protocol: Total RNA was extracted using TRIZOL following the manufacturer’s protocol

treatment_protocol: Mononuclear cells were separated using Histopaque density gradient centrifugation, labelled with CD34 MicroBeads, and then CD34+ cells were isolated using MACS magnetic cell separation columns according to the manufacturer’s recommendations.

tag: tissue

value: bone marrow

value: bone marrow CD34+ cells

tag: disease status

value: MDS


title: 124I-HIB-labeled ADSCs transplanted rat infarcted myocardium (MI) (replicate 1) [1]

description:
Sample name: HIB_ADSC_1
124I-HIB-labeled ADSCs transplanted rat infarcted myocardial tissue (MI) (sample labeling number 1)  (21 days after sham operation)

source_name: Myocardial tissue from intramyocardially 124I-HIB-labeled ADSCs injected SD rat

value: Myocardial tissue


title: genomic DNA from Surgical resection GBM-1682

source_name: Surgical resection GBM-1682


title: MDS069

description:
MDS patient 69
Gene expression data from bone marrow CD34+ cells


title: PBS injected MI induced rat myocardium [1]

description:
Sample name: PBS_1
PBS injected MI induced rat myocardial tissue  (21 days after sham operation)

source_name: Myocardial tissue from intramyocardially PBS injected SD rat

value: intramyocardially PBS-injected


title: MDS063

description:
MDS patient 63
Gene expression data from bone marrow CD34+ cells


title: MDS066

description:
MDS patient 66
Gene expression data from bone marrow CD34+ cells


title: MDS067

description:
MDS patient 67
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1612

source_name: Surgical resection GBM-1612


title: MDS062

description:
MDS patient 62
Gene expression data from bone marrow CD34+ cells


title: 124I-HIB-labeled ADSCs transplanted rat infarcted myocardium (MI) (replicate 3) [1]

description:
Sample name: HIB_ADSC_3
124I-HIB-labeled ADSCs transplanted rat infarcted myocardial tissue (MI) (sample labeling number 3)  (21 days after sham operation)


title: Sham operated rat myocardium [1]

description:
Sample name: SHAM_2
Sham operated rat myocardiial tissue (21 days after sham operation)

source_name: Myocardial tissue from sham operated SD rat

value: sham-operated


title: 124I-HIB-labeled ADSCs [2]

description:
Sample name: HIB_ADSC_2
124I-HIB-labeled ADSCs  (14 days after culture)

source_name: 124I-HIB labeled rat adipose derived stem cells


title: genomic DNA from Surgical resection GBM-1766

source_name: Surgical resection GBM-1766


title: genomic DNA from Surgical resection GBM-1709

source_name: Surgical resection GBM-1709


title: genomic DNA from Surgical resection GBM-1617

source_name: Surgical resection GBM-1617


title: KO_22726_422

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

description: Hepatic gene expression from Rev-erb{alpha} -/- mice at ZT10

hyb_protocol: About 2ug cDNA was hybridized at 45°C for 16h to the Mouse Gene 1.0ST array. Arrays were washed and stained using the GeneChIP Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: Array images were captured on a GCS3000 laser scanner (Affymetrix)

data_processing: Raw images were analyzed using Partek Genomics Suite to extract individual probe intensities. Subsequent data analysis was performed using BioConductor. Raw probe signal values were background and quantile normalized and summarized by probe sets using the RMA algorithm. Final differential expression calls were determined using the SAM algorithm with 10% false-discovery rate and an absolute fold-change threshold of 1.3.

label: biotin

organism: Mus musculus

source_name: Rev-erb{alpha} KO Liver

label_protocol: RNA from each liver was individually processed with the Ambion WT expression kit and GeneChIP WT terminal labeling and control kit (Affymetrix) and hybridized to the Mouse Gene 1.0 ST arrays (Affymetrix)

growth_protocol: Wild-type (WT) C57Bl/6 mice were purchased from the Jackson Laboratories. The Rev-erb{alpha} -/- mice were obtained from B. Vennström, and backcrossed at least 7 generations with C57Bl/6 mice. 10-12 weeks old WT and mutant male mice were fed normal chow and housed under standard 12h-light/12h-dark cycles, with lights on (ZT0) at 7AM and lights off (ZT12) at 7PM. All animal care and procedures followed the guidelines of the Institutional Animal Care and Use Committee of the University of Pennsylvania.

extract_protocol: Total RNA was extracted from each mouse liver sample using Trizol extraction followed by QIAGEN Rneasy Kit according to the manufacture's instructions.

treatment_protocol: Mice were euthanized at 5pm (ZT10).

tag: genotype

value: male

tag: time


title: MDS191

description:
MDS patient 191
Gene expression data from bone marrow CD34+ cells


title: MDS059

description:
MDS patient 59
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1764

source_name: Surgical resection GBM-1764


title: genomic DNA from recurrent GBM-1775, originating tumor GBM-1714


title: KO_22728_397


title: MDS076

description:
MDS patient 76
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1584

source_name: Surgical resection GBM-1584


title: genomic DNA from Surgical resection GBM-1601

source_name: Surgical resection GBM-1601


title: KO_22727_420


title: genomic DNA from Surgical resection GBM-1748

source_name: Surgical resection GBM-1748


title: MDS058

description:
MDS patient 58
Gene expression data from bone marrow CD34+ cells


title: KO_22725_442


title: genomic DNA from Surgical resection GBM-1614

source_name: Surgical resection GBM-1614


title: genomic DNA from Surgical resection GBM-1763

source_name: Surgical resection GBM-1763


title: WT_22722_443

description: Hepatic gene expression from WT mice at ZT10

source_name: WT Liver

value: WT


title: KO_22724_444


title: genomic DNA from Surgical resection GBM-1621

source_name: Surgical resection GBM-1621


title: MDS055

description:
MDS patient 55
Gene expression data from bone marrow CD34+ cells

source_name: Bone marrow CD34+ cells


title: WT_22720_399


title: WT_22721_406


title: WT_22723_445


title: MDS054

description:
MDS patient 54
Gene expression data from bone marrow CD34+ cells


title: MDS053

description:
MDS patient 53
Gene expression data from bone marrow CD34+ cells


title: MDS190

description:
MDS patient 190
Gene expression data from bone marrow CD34+ cells


title: MDS057

description:
MDS patient 57
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1603

source_name: Surgical resection GBM-1603


title: WT_22719_382


title: genomic DNA from Surgical resection GBM-1591

source_name: Surgical resection GBM-1591


title: MDS050

description:
MDS patient 50
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1761

source_name: Surgical resection GBM-1761


title: hy5_rep3

city: Yokohama

first: Yukio

last: Kurihara

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

country: Japan

institute: Riken

description: gene expression in hy5 plant

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GE Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Arabidopsis Genome Oligo Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 021169_D_F_20131126) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Arabidopsis thaliana

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds were sown onto MS medium without sucrose. After 3 days growth under white light at 22 ℃, seedlings were harvested.

extract_protocol: Total RNA was extracted using Plant RNeasy mini kit (Qiagen) and digested with DNase I (Takara bio.).

tag: cultivar

value: Col

value: 3 days

tag: light condition

value: continuous white light


title: genomic DNA from Surgical resection GBM-1760

source_name: Surgical resection GBM-1760

value: M

value: GBM

value: U


title: hy5_rep2

description: gene expression in hy5 plant


title: hy5_rep1

description: gene expression in hy5 plant


title: genomic DNA from Surgical resection GBM-1606

source_name: Surgical resection GBM-1606

value: F


title: WT_rep2

description: gene expression in wild type plant

source_name: wild type

value: wild type


title: MDS189

description:
MDS patient 189
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1731

source_name: Surgical resection GBM-1731


title: genomic DNA from Surgical resection GBM-1752

source_name: Surgical resection GBM-1752


title: MDS033

description:
MDS patient 33
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1756

source_name: Surgical resection GBM-1756


title: MDS188

description:
MDS patient 188
Gene expression data from bone marrow CD34+ cells


title: WT_rep1

description: gene expression in wild type plant


title: MDS187

description:
MDS patient 187
Gene expression data from bone marrow CD34+ cells


title: MDS186

description:
MDS patient 186
Gene expression data from bone marrow CD34+ cells


title: WT_rep3

description: gene expression in wild type plant


title: MDS184

description:
MDS patient 184
Gene expression data from bone marrow CD34+ cells


title: MDS061

description:
MDS patient 61
Gene expression data from bone marrow CD34+ cells


title: MDS185

description:
MDS patient 185
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1706

source_name: Surgical resection GBM-1706


title: MDS043

description:
MDS patient 43
Gene expression data from bone marrow CD34+ cells


title: MDS052

description:
MDS patient 52
Gene expression data from bone marrow CD34+ cells


title: MDS025

description:
MDS patient 25
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1589

source_name: Surgical resection GBM-1589


title: genomic DNA from Surgical resection GBM-1707

source_name: Surgical resection GBM-1707


title: MDS029

description:
MDS patient 29
Gene expression data from bone marrow CD34+ cells


title: MDS015

description:
MDS patient 15
Gene expression data from bone marrow CD34+ cells


title: genomic DNA from Surgical resection GBM-1730

source_name: Surgical resection GBM-1730


title: genomic DNA from Surgical resection GBM-1566

source_name: Surgical resection GBM-1566


title: MDS014

description:
MDS patient 14
Gene expression data from bone marrow CD34+ cells


title: 186-day14-control-1

city: London

first: Maciej

last: kaliszczak

address: Du Cane road

department: Surgery and Cancer

institute: Imperial College London

hyb_protocol: Study performed under contract by Alpha Metrix Biotech, Rodermark, Germany. Full details are available upon request.

data_processing: Analysis performed under contract by Alpha Metrix Biotech, Rodermark, Germany. The only processed data available for this study are the differentially expressed genes identified for the comparison of 14d_treated vs 24h_treated. These data are available in the file E10R_039_14dvs24h_treated_05_15_184.txt located on the series record.

source_name: Colon cancer (HCT116 xenograft)

growth_protocol: HCT-116 cells were injected in the flank of Balbc Female mice at 5 x 10^ 6 cells/ 100 uL , treatment started when the size of the tumour reached  50 mm3 (~14 days)

extract_protocol: Tumour were excised and snap frozen in liquid nitrogen, RNA extraction was performed using the RNeasy Kit from Qiagen

treatment_protocol: Mice were treated Intraperitoneally with HDAC6 inhibitor, C1A at 40 mg/day for 14 days

value: Colon cancer (HCT116 xenograft)

tag: cell line

tag: host organism

value: Mus musculus

tag: host strain

value: Balbc


title: MDS012

description:
MDS patient 12
Gene expression data from bone marrow CD34+ cells

value: bone marrow

value: bone marrow CD34+ cells

value: MDS


title: MDS027

description:
MDS patient 27
Gene expression data from bone marrow CD34+ cells


title: MDS011

description:
MDS patient 11
Gene expression data from bone marrow CD34+ cells


title: 48-day14-treated 40mg/kg-3

scan_protocol: Study performed under contract by Alpha Metrix Biotech, Rodermark, Germany. Full details are available upon request.

source_name: Colon cancer (HCT116 xenograft)_C1A


title: genomic DNA from recurrent GBM-1613, originating tumor GBM-1543

tag: gender


title: NN_F3

city: Dallas

first: Alimatou

middle: M

last: Tchafa

state: TEXAS

address: 5323 Harry Hines Blvd, Rm Y4.306

department: Biochemistry

institute: UT Southwestern Medical Center

description:
replicate 3
8556388109_L

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in PARTEK software

source_name: NeuN cell line_flow_IFF

label_protocol: not provided

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

tag: interstitial fluid flow (iff) status

value: flow


title: genomic DNA from Surgical resection GBM-1705

source_name: Surgical resection GBM-1705

tag: disease state

tag: geo expression data


title: genomic DNA from Surgical resection GBM-1774

source_name: Surgical resection GBM-1774

tag: age

tag: os


title: NN_F2

description:
replicate 2
8556388109_K


title: 177-day14-control-3

label_protocol: Study performed under contract by Alpha Metrix Biotech, Rodermark, Germany. Full details are available upon request.


title: 723-24H-control-3


title: NN_F1

description:
replicate 1
8556388109_J


title: genomic DNA from Surgical resection GBM-1545

source_name: Surgical resection GBM-1545


title: genomic DNA from Surgical resection GBM-1732

source_name: Surgical resection GBM-1732


title: genomic DNA from Surgical resection GBM-1543

source_name: Surgical resection GBM-1543


title: 51-day14-treated 40mg/kg-2


title: peripheral airway epithelial cells, smoker 6, rep1

city: new york

first: Jun-Chieh

middle: James

last: Tsay

state: NY

address: 562 First Ave. NBV 7N27

department: Medicine

institute: NYU Langone Medical Center

hyb_protocol: Ten µg of cRNA was hybridized to the array, and was processed with the Affymetrix system, including GeneChip Hybridization Oven 640

scan_protocol: GeneChips scanned with Fluidics Station 450 and Scanner 3000.

data_processing: Normalization of Affymetrix array data was by Robust Multichip Average (RMA) through the RMexpress software package (http://rmaexpress.bmbolstad.com/).

source_name: peripheral airway epithelial cells_smoker

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

extract_protocol: extracted total RNA using Qiagen miRNeasy Mini Kit (Valencia, CA) according to the company protocol

treatment_protocol: The cytology brush was spun down and the cell pellet was collected and stored at -80° C until RNA extraction

tag: subject id

value: smoker 6

value: male

tag: case

value: smoker

tag: cell type

value: peripheral airway epithelial cells


title: 721-24H-control-2

tag: tissue


title: genomic DNA from Surgical resection GBM-1704

source_name: Surgical resection GBM-1704


title: peripheral airway epithelial cells, smoker 5, rep1

value: smoker 5

value: female


title: MDS009

description:
MDS patient 9
Gene expression data from bone marrow CD34+ cells

source_name: Bone marrow CD34+ cells

tag: disease status


title: genomic DNA from Surgical resection GBM-1587

source_name: Surgical resection GBM-1587

value: GBM

value: M


title: 74-day14-control-2


title: genomic DNA from Surgical resection GBM-1759

source_name: Surgical resection GBM-1759


title: NN_S2

description:
replicate 2
8556388109_H

source_name: NeuN cell line_static_IFF

value: static


title: 738-24H-control-1


title: genomic DNA from Surgical resection GBM-1703

source_name: Surgical resection GBM-1703


title: NN_S1

description:
replicate 1
8556388109_G


title: 735-24H-Treated-3


title: NN_S3

description:
replicate 3
8556388109_I


title: 742-24H-Treated-2


title: genomic DNA from Surgical resection GBM-1552

source_name: Surgical resection GBM-1552

value: U


title: peripheral airway epithelial cells, smoker 35, rep1

value: smoker 35


title: 49-day14-treated 40mg/kg-1

value: Colon cancer (HCT116 xenograft)

value: Mus musculus


title: peripheral airway epithelial cells, cancer 33, rep1

source_name: contral-lateral peripheral airway epithelial cells_cancer

value: cancer 33

value: adenocarcinoma


title: genomic DNA from Surgical resection GBM-1729

source_name: Surgical resection GBM-1729


title: peripheral airway epithelial cells, smoker 36, rep1

value: smoker 36


title: NT_F3

description:
replicate 3
7656766044_L

source_name: NeuT cell line_flow_IFF

value: flow


title: H29_Obese_post (Hs)

city: Baltimore

first: Andrew

middle: P

last: Feinberg

state: Maryland

address: 855 N Wolfe St

department: Department of Medicine

institute: Johns Hopkins School of Medicine

description:
processed data file: H_DNAm.txt
DNA methylation

hyb_protocol: as per manufacturer's protocol (NimbleGen Arrays User’s Guide, CGH Arrays v 9.1)

data_processing:
QC scores generated and normalization performed as per CHARM R package (available on Bioconductor)
Processed data description: Methylation beta-values (range from 0-1, differences in beta-values represent relative methylation differences)

extract_protocol: MasterPure DNA Purification Kit (epicentre, WI, USA)

value: Adipose

tag: obesity

value: Obese

tag: pre or post surgery

value: post


title: 722-24H-Treated-1

source_name: Colon cancer (HCT116 xenograft)_C1A

value: Balbc


title: genomic DNA from Surgical resection GBM-1714

source_name: Surgical resection GBM-1714


title: H25_Obese_pre (Hs)

scan_protocol: as per manufacturer's protocol (NimbleGen Arrays User’s Guide, CGH Arrays v 9.1)

value: pre


title: H26_Obese_pre (Hs)

label_protocol: as per manufacturer's protocol (NimbleGen Arrays User’s Guide, CGH Arrays v 9.1)


title: H28_Lean_pre (Hs)

value: Lean


title: genomic DNA from Surgical resection GBM-1755

source_name: Surgical resection GBM-1755

value: F

value: GBM


title: H24_Obese_pre (Hs)


title: H23_Obese_post (Hs)


title: H27_Obese_pre (Hs)


title: H22_Obese_pre (Hs)


title: genomic DNA from Surgical resection GBM-1758

source_name: Surgical resection GBM-1758

value: M


title: NT_F1

description:
replicate 1
7656766044_J


title: H21_Obese_post (Hs)


title: H19_Obese_pre (Hs)


title: peripheral airway epithelial cells, cancer 31, rep1

value: cancer 31

value: male

value: contral-lateral peripheral airway epithelial cells


title: NT_S1

description:
replicate 1
7656766044_G

source_name: NeuT cell line_static_IFF

value: static


title: H18_Obese_post (Hs)


title: peripheral airway epithelial cells, cancer 32, rep1

value: cancer 32


title: H17_Lean_pre (Hs)


title: NT_F2

description:
replicate 2
7656766044_K


title: H16_Obese_pre (Hs)


title: NT_S2

description:
replicate 2
7656766044_H


title: peripheral airway epithelial cells, cancer 21, rep1

value: cancer 21

value: adenocarcinoma


title: peripheral airway epithelial cells, cancer 23, rep1

value: cancer 23


title: NT_S3

description:
replicate 3
7656766044_I


title: peripheral airway epithelial cells, cancer 24, rep1

value: cancer 24


title: H15_Obese_post (Hs)

value: Adipose

value: Obese


title: peripheral airway epithelial cells, cancer 25, rep1

value: cancer 25


title: H14_Lean_pre (Hs)

value: pre


title: peripheral airway epithelial cells, smoker 2, rep1

value: smoker 2

value: smoker

value: peripheral airway epithelial cells


title: H13_Obese_post (Hs)

value: post


title: H12_Obese_pre (Hs)


title: genomic DNA from Surgical resection GBM-1496

source_name: Surgical resection GBM-1496

value: M

value: GBM


title: H11_Obese_pre (Hs)


title: peripheral airway epithelial cells, cancer 22, rep1

value: cancer 22

value: male

value: contral-lateral peripheral airway epithelial cells


title: H9_Lean_pre (Hs)

value: Lean


title: peripheral airway epithelial cells, cancer 18, rep1

value: cancer 18

value: adenocarcinoma


title: peripheral airway epithelial cells, cancer 15, rep1

value: cancer 15

value: female


title: H10_Obese_post (Hs)

value: Adipose

value: Obese


title: H7_Obese_pre (Hs)

value: pre


title: peripheral airway epithelial cells, cancer 14, rep1

value: cancer 14


title: H5_Obese_pre (Hs)


title: H3_Lean_pre (Hs)


title: H8_Lean_pre (Hs)


title: peripheral airway epithelial cells, cancer 19, rep1

value: cancer 19


title: H6_Obese_pre (Hs)


title: H2_Obese_post (Hs)


title: peripheral airway epithelial cells, cancer 12, rep1

value: cancer 12


title: H1_Obese_pre (Hs)


title: peripheral airway epithelial cells, cancer 17, rep1

value: cancer 17


title: peripheral airway epithelial cells, cancer 34, rep1

value: cancer 34


title: peripheral airway epithelial cells, smoker 1, rep1

source_name: peripheral airway epithelial cells_smoker

value: smoker 1

value: smoker

value: peripheral airway epithelial cells


title: peripheral airway epithelial cells, smoker 7, rep1

data_processing:
Five hundred ng of total RNA was used.  The TaqMan Array was processed with an ABI 7900 HT (Applied Biosystems, Foster City, CA). MiRNA Taqman array data was normalized based on comparative CT representation using the global normalization method
Fold Change worksheet reports cancer/control

label: FAM™

label_protocol: per manufacturer's protocol

treatment_protocol: The cytology brush was spun down and the cell pellet was collected and stored at - 80° C until RNA extraction

value: smoker 7

value: male


title: peripheral airway epithelial cells, cancer 11, rep1

value: cancer 11

value: contral-lateral peripheral airway epithelial cells


title: peripheral airway epithelial cells, cancer 13, rep1

value: cancer 13

value: adenocarcinoma


title: H20_Lean_pre (Hs)

value: Adipose

value: Lean


title: peripheral airway epithelial cells, smoker 6, rep1

value: smoker 6


title: peripheral airway epithelial cells, smoker 5, rep1

value: smoker 5

value: female


title: H4_Obese_pre (Hs)

value: Obese

value: pre


title: peripheral airway epithelial cells, smoker 36, rep1

value: smoker 36


title: peripheral airway epithelial cells, cancer 33, rep1

value: cancer 33


title: peripheral airway epithelial cells, cancer 32, rep1

value: cancer 32


title: peripheral airway epithelial cells, smoker 30, rep1

value: smoker 30

value: smoker

value: peripheral airway epithelial cells


title: peripheral airway epithelial cells, smoker 29, rep1

value: smoker 29

value: male


title: peripheral airway epithelial cells, smoker 28, rep1

value: smoker 28


title: peripheral airway epithelial cells, smoker 27, rep1

value: smoker 27


title: peripheral airway epithelial cells, smoker 35, rep1

value: smoker 35


value: cancer 34

value: adenocarcinoma

value: contral-lateral peripheral airway epithelial cells


title: peripheral airway epithelial cells, cancer 25, rep1

value: cancer 25


title: peripheral airway epithelial cells, cancer 31, rep1

value: cancer 31


title: peripheral airway epithelial cells, cancer 23, rep1

value: cancer 23


title: peripheral airway epithelial cells, smoker 3, rep1

value: smoker 3


title: WT dendritic cells treated with LPS and CpG for 6 hours, rep1

city: Rockville

first: Keiko

last: Ozato

address: 9000 Rockville Pike

department: NICHD

institute: National Institutes of Health

description:
WT-Treated1
Gene expression data from mice bone marrow-derived dendritic cells. Treated with LPS and CpG for 6 h.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse 430A 2.0. 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 Affymetrix GeneChip Operating Software (GCOS). Background correction and normalization were done using the RMA method in the R affy package.

source_name: Bone marrow-derived dendritic cells, WT, LPS and CpG

growth_protocol: BM mononuclear cells isolated from mice were differentiated into dendritic cells by incubating the cells in the presence of Flt3L (100 ng/ml) for seven days.

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

treatment_protocol: Differentiated DCs were treated with LPS (100 ng/ml) and CpG (1 ug/ml) for 6 hr.

tag: strain/background

tag: genotype/variation

value: WT

value: mononuclear cells differentiated to dendritic cells

tag: treatment

value: LPS and CpG for 6 h


title: peripheral airway epithelial cells, cancer 24, rep1

value: cancer 24


title: WT dendritic cells with no treatment, rep1

description:
WT-UT1
Gene expression data from mice bone marrow-derived dendritic cells. No treatment.

source_name: Bone marrow-derived dendritic cells, WT, untreated


title: 4_5_3_Murf2_mock_Day 2_1

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse mock treated for 2 Days replicate1
Murf2 _4_5_3_Murf2_mock_Day 2_1

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B).

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and limma packages.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

extract_protocol: Total RNA was isolated according to the manufacturer’s protocol with an RNeasy kit (Qiagen)

value: Lung

tag: strain/genotype


title: 4_4_4_Murf2_10_5_Day 4_1

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse infected with10^5PFU of MA15 for 4 Days replicate1
Murf2 _4_4_4_Murf2_10_5_Day 4_1


title: WT dendritic cells treated with LPS and CpG for 6 hours, rep2

description:
WT-Treated2
Gene expression data from mice bone marrow-derived dendritic cells. Treated with LPS and CpG for 6 h.


title: peripheral airway epithelial cells, smoker 8, rep1

value: smoker 8

tag: gender

value: female

value: smoker

value: peripheral airway epithelial cells


title: 4_5_5_Murf2_mock_Day 2_3

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse mock treated for 2 Days replicate3
Murf2 _4_5_5_Murf2_mock_Day 2_3


title: 4_5_1_Murf2_10_5_Day 4_2

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse infected with10^5PFU of MA15 for 4 Days replicate2
Murf2 _4_5_1_Murf2_10_5_Day 4_2


title: 4_5_2_Murf2_10_5_Day 4_3

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse infected with10^5PFU of MA15 for 4 Days replicate3
Murf2 _4_5_2_Murf2_10_5_Day 4_3


title: WT dendritic cells with no treatment, rep2

description:
WT-UT2
Gene expression data from mice bone marrow-derived dendritic cells. No treatment.


title: 4_6_2_Murf2_mock_Day 4_2

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse mock treated for 4 Days replicate2
Murf2 _4_6_2_Murf2_mock_Day 4_2


title: 4_6_1_Murf2_mock_Day 4_1

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse mock treated for 4 Days replicate1
Murf2 _4_6_1_Murf2_mock_Day 4_1


title: peripheral airway epithelial cells, cancer 22, rep1

value: cancer 22

value: male


title: peripheral airway epithelial cells, cancer 21, rep1

value: cancer 21

value: adenocarcinoma


title: 4_5_4_Murf2_mock_Day 2_2

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse mock treated for 2 Days replicate2
Murf2 _4_5_4_Murf2_mock_Day 2_2


title: peripheral airway epithelial cells, smoker 2, rep1

value: smoker 2


title: peripheral airway epithelial cells, cancer 19, rep1

value: cancer 19

value: contral-lateral peripheral airway epithelial cells


title: peripheral airway epithelial cells, cancer 15, rep1

value: cancer 15


title: peripheral airway epithelial cells, cancer 14, rep1

value: cancer 14


title: peripheral airway epithelial cells, cancer 17, rep1

value: cancer 17


title: peripheral airway epithelial cells, cancer 13, rep1

value: cancer 13


title: peripheral airway epithelial cells, cancer 12, rep1

value: cancer 12


title: 4_4_3_Murf2_10_5_Day 2_3

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse infected with10^5PFU of MA15 for 2 Days replicate3
Murf2 _4_4_3_Murf2_10_5_Day 2_3

value: Lung


title: ZsG plus from C57BL/6 mice rep2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_ZsG plus from C57BL/6 mice rep2

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip mouse 430 2.0 ST arrays according to manufacturer's recommendations

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

data_processing: The data were analyzed with EC 1.1 using Affymetrix default analysis

source_name: ZsG plus from C57BL/6 mice rep2

label_protocol: cDNA was generated from 5ng of total RNA using WT-Ovation™ Pico system (version 1) RNA Amplification System followed by double stranded cDNA synthesis using WT-Ovation™ Exon Module.

growth_protocol: C57BL/6 mice were purchased from Taconic Farms. BAC transgenic mice were bred at and all animals housed at the National Institute of Allergy and Infectious Diseases pathogen-free animal facility, and used between 8-20 weeks of age. All experiments were done under a protocol approved by the National Institutof Allergy and Infectious Diseases Animal Care and Use Committee

extract_protocol: For mRNA analysis, RNA was extracted using RNeasy spin columns (Qiagen) followed by DNAse treatment.

treatment_protocol: Generation of a modified BAC containing the ZsG reporter at the ATG site of the TSLP gene was done using the galK recombineering technique

value: ZsG plus

tag: genetic background

value: keratinocytes


title: 4_4_1_Murf2_10_5_Day 2_1

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse infected with10^5PFU of MA15 for 2 Days replicate1
Murf2 _4_4_1_Murf2_10_5_Day 2_1


title: 4_3_1_B6_mock_Day 2_3

description:
Gene Expression in Lung Tissue after C57BL/6J mouse mock treated for 2 Days replicate3
Murf2 _4_3_1_B6_mock_Day 2_3

value: C57BL/6J wild type


title: Zur 1

city: Jouy-en-Josas

first: Sandrine

last: Auger

address: INRA-Domaine de Vilvert

country: France

institute: INRA

hyb_protocol: Hybridization was done by Roche Nimblegen (Madison, WI, USA) following the standard Nimblegen protocol.

scan_protocol: Scanning was done by Roche Nimblegen (Madison, WI, USA) following the standard Nimblegen protocol.

data_processing: Identification of peaks corresponding to Zur binding sites on the Bacillus subtilis chromosome was done as described previously (Reppas et al., 2006, Mol Cell 24: 747-757 [PMID 17157257]).  Signal intensities were converted as log2 ratio (ChIP-DNA/Control-DNA) and corrected for dye bias using Loess regression on the MA plot.  The signal was smoothed by two rounds of sliding window averaging. The sliding window contained 29 probes (the middle probe and 14 probes on each side) corresponding to approximately 320 bp.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Control DNA replicate 1

label_protocol: Labelling was done by Roche Nimblegen (Madison, WI, USA) using the standard Nimblegen protocol. ChIP DNA was labelled with Cy5 and control DNA was labelled with Cy3.

growth_protocol: Cells were grown in a flask of 2 L LB medium until OD600nm reached 0.6.

extract_protocol: 0.6 % formaldehyde was added in the flasks for 20 min at room temperature before quenching with 125 mM glycine. Cells were harvested by centrifugation at 6000g for 10 min, washed twice with 200 mL of buffer A (10 mM Tris-HCl pH=7.5, 150 mM NaCl), and then lysed in 12 mL of buffer B (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.2 mM EDTA, 0.1 % (v/v) TritonX-100) supplemented with 0.1 mg/mL RNase A and 1 mg/mL lysozyme for 15 min at 37°C. DNA was then sheared by sonication in order to obtain 0.2 to 1 kb fragments. An aliquot of 50 µL of the whole cell extract (WCE) volume was saved for use as control DNA. The rest was used for immuno-precipitation DNA (IP): 400 μL of anti-FLAG M2 agarose beads (Sigma A2220) were incubated 2 h with cell lysates under gentle agitation. Then IP beads were washed 3 times in buffer B before being resuspended into 500 µL of buffer C (100 mM Tris-HCl pH=8, 100 g/L, 1% SDS, 10 mM EDTA) to reverse cross-linking for 18 h at 65°C. WCE and IP DNA fragments were recovered and purified using QIAquick PCR purification kit (Qiagen). Remaining RNA was removed by RNase A treatment followed by a second DNA purification step.

tag: genotype

value: zur::zur-spa strain

tag: sample type

value: whole-cell extract DNA

tag: antibody

source_name: Immunoprecipitated DNA replicate A

value: Immunoprecipitated DNA

value: anti-FLAG M2 (Sigma A2220)


title: 4_2_2_B6_10_5_Day 4_3

description:
Gene Expression in Lung Tissue after C57BL/6J mouse infected with10^5PFU of MA15 for 4 Days replicate3
Murf2 _4_2_2_B6_10_5_Day 4_3


title: ZsG minus cTEC from C57BL/6 mice rep3

description: Gene expression data from_ZsG minus cTEC from C57BL/6 mice rep3

source_name: ZsG minus cTEC from C57BL/6 mice rep3

value: ZsG minus cTEC


title: ZsG minus cTEC from C57BL/6 mice rep2

description: Gene expression data from_ZsG minus cTEC from C57BL/6 mice rep2

source_name: ZsG minus cTEC from C57BL/6 mice rep2


title: ZsG minus mTEC from C57BL/6 mice rep3

description: Gene expression data from_ZsG minus mTEC from C57BL/6 mice rep3

source_name: ZsG minus mTEC from C57BL/6 mice rep3

value: ZsG minus mTEC


title: 4_2_4_B6_mock_Day 2_2

description:
Gene Expression in Lung Tissue after C57BL/6J mouse mock treated for 2 Days replicate2
Murf2 _4_2_4_B6_mock_Day 2_2


title: 4_3_3_B6_mock_Day 4_2

description:
Gene Expression in Lung Tissue after C57BL/6J mouse mock treated for 4 Days replicate2
Murf2 _4_3_3_B6_mock_Day 4_2


title: ZsG minus mTEC from C57BL/6 mice rep1

description: Gene expression data from_ZsG minus mTEC from C57BL/6 mice rep1

source_name: ZsG minus mTEC from C57BL/6 mice rep1


title: ZsG minus cTEC from C57BL/6 mice rep1

description: Gene expression data from_ZsG minus cTEC from C57BL/6 mice rep1

source_name: ZsG minus cTEC from C57BL/6 mice rep1


title: 4_1_3_B6_10_5_Day 2_3

description:
Gene Expression in Lung Tissue after C57BL/6J mouse infected with10^5PFU of MA15 for 2 Days replicate3
Murf2 _4_1_3_B6_10_5_Day 2_3


title: 4_3_2_B6_mock_Day 4_1

description:
Gene Expression in Lung Tissue after C57BL/6J mouse mock treated for 4 Days replicate1
Murf2 _4_3_2_B6_mock_Day 4_1


title: 4_2_3_B6_mock_Day 2_1

description:
Gene Expression in Lung Tissue after C57BL/6J mouse mock treated for 2 Days replicate1
Murf2 _4_2_3_B6_mock_Day 2_1


title: ZsG plus from C57BL/6 mice rep3

description: Gene expression data from_ZsG plus from C57BL/6 mice rep3

source_name: ZsG plus from C57BL/6 mice rep3


title: 4_1_2_B6_10_5_Day 2_2

description:
Gene Expression in Lung Tissue after C57BL/6J mouse infected with10^5PFU of MA15 for 2 Days replicate2
Murf2 _4_1_2_B6_10_5_Day 2_2


title: 4_2_1_B6_10_5_Day 4_2

description:
Gene Expression in Lung Tissue after C57BL/6J mouse infected with10^5PFU of MA15 for 4 Days replicate2
Murf2 _4_2_1_B6_10_5_Day 4_2


title: 4_4_2_Murf2_10_5_Day 2_2

description:
Gene Expression in Lung Tissue after Murf2/Trim55-/- mouse infected with10^5PFU of MA15 for 2 Days replicate2
Murf2 _4_4_2_Murf2_10_5_Day 2_2


title: ZsG minus mTEC from C57BL/6 mice rep2

description: Gene expression data from_ZsG minus mTEC from C57BL/6 mice rep2

source_name: ZsG minus mTEC from C57BL/6 mice rep2


title: Zur 2

source_name: Control DNA replicate 2

source_name: Immunoprecipitated DNA replicate B


title: peripheral airway epithelial cells, smoker 1, rep1

value: smoker 1

tag: age

value: male

value: smoker

value: peripheral airway epithelial cells


title: ZsG plus from C57BL/6 mice rep1

description: Gene expression data from_ZsG plus from C57BL/6 mice rep1

source_name: ZsG plus from C57BL/6 mice rep1


title: Wnt3a-treated myoblasts

city: PALO ALTO

first: Thomas

middle: A

last: Rando

address: 3801 Miranda Ave

institute: STANFORD UNIVERSITY SCHOOL OF MEDICINE

description: Gene expression data from myoblasts culured 4 hours in  DMEM 2%HS in presence of Wnt3a

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized according to the standard Affymetrix protocol on Affymetrix Mouse 430 2.0 Genome Array in a Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The CEL files were used for analysis with limma package from the Bioconductor R packages, and the signal was normalized with the RMA method. The P/M/A calls (P: present, A: absent, M: marginal) were retrieved the code of 'eset' in the Affy package.

source_name: myoblasts from newborn

label_protocol: Biotinylated cRNA were prepared according to the standard protocol by using Affymetrix GeneChip 3' IVT Express Kit.

growth_protocol: Primary myoblasts were isolated from Sv129 (Charles River) newborn mice and were cultured on Laminin/Collagen-coated wells as described in Quach et al (Mol. Biol. Cell 20, 3422-3435 (2009)).

treatment_protocol: Myoblasts were treated for 4 hours in DMEM 2%HS in presence or in absence of Wnt3a (R&D; 100ng/ml).

tag: strain

value: 4 hours in DMEM 2%HS in presence of Wnt3a (R&D; 100ng/ml).


title: 4_1_1_B6_10_5_Day 2_1

description:
Gene Expression in Lung Tissue after C57BL/6J mouse infected with10^5PFU of MA15 for 2 Days replicate1
Murf2 _4_1_1_B6_10_5_Day 2_1


title: Control myoblasts

description: Gene expression data from myoblasts culured 4 hours in  DMEM 2%HS

value: 4 hours in DMEM 2%HS


title: LTL331_Cx_3day_v2

status: Public on Jan 05 2015

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004)

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour GE and 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 11.0.1.1 to produce spatially detrended and background subtracted gProcessedSignal intensities

source_name: Prostate tumor, Patient derived xenograft

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.6.

extract_protocol: Not provided

tag: tumor subtype

value: Adenocarcinoma

tag: time post host castration

value: 3 day


title: LTL331R

value: Neuroendocrine

value: Relapsed


title: LTL331_Cx_12wk

value: 12 week


title: LTL331

value: Pre-castration


title: LTL331_Cx_1wk

value: 1 week


title: LTL331_Cx_8wk

value: 8 week


title: LTL331_Cx_3wk

value: 3 week


title: LTL331_Cx_2day_v1

value: 2 day


title: LTL331_Cx_1day_v1

value: 1 day


title: LTL331_Cx_relapsed


title: LTL331_Cx_2day_v2


title: LTL331_Cx_3day_v1


title: LTL331_Cx_2wk

value: 2 week


title: Cell line_hypoxia exposed DU 145

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

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

source_name: Prostate cancer

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

growth_protocol: The cells were incubated in RPMI-1640 medium supplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin and 1% L-glutamine under a 5% CO2 atmosphere at 37°C.

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

treatment_protocol: Exponentially growing cells were plated and incubated for 2 days, following replacement of cell medium prior to exposure to hypoxic (0.2% O2, 5% CO2) or normoxic (95% air, 5% Co2) conditions for 24 h at 37°C. The hypoxia treatment was performed in an Invivo2200 chamber (Ruskinn Technology Ltd, Bridgend, UK) with accurate O2 and CO2 controls.

tag: cell line

tag: histology

value: Androgen non-responsive

value: hypoxia exposed


title: Cell line_untreated PC-3

value: PC

value: untreated


title: LTL331_Cx_1day_v2


title: Cell line_hypoxia exposed PC-3


title: Cell line_hypoxia exposed LNCaP

value: LNCaP

value: Androgen responsive


title: Cell line_untreated DU 145


title: ANXA1, biological rep3

city: Singapore

first: Peter

last: Nissom

address: 20 Biopolis Way

country: Singapore

institute: Bioprocessing Technology Institute

description: Gene expression data from MCF-7 cells (human breast adenocarcinoma cell line), overexpressing ANXA1

hyb_protocol: MicroRNA microarray analysis was performed using the Affymetrix Solution GeneChip® MicroRNA Version 1.0 array (comprising 46228 probes with 7815 probes sets) according to manufacturer’s (Affymetrix) instructions.   Briefly, a starting material of 1ug of small RNA was used for poly A tailing on the 3’ end of the small RNA followed by ligation of the biotinylated signal molecule to the small RNA samples, according to Affymetrix Flashtag RNA labeling kit (Affymetrix, p/N FT10AFYB). Hybridzation procedure was performed as described in the manufacturer’s protocol.

scan_protocol: The chips were scanned using Affymetrix Genechip Scanner 3000.

data_processing: The data was extracted using Genechip Operating Software (GCOS) and further analysed using BRB-Arraytools

growth_protocol: Human breast cancer cell line MCF7 were obtained from the American Type Culture Collection. The cells were grown as monolayers in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Biowest), 1% L-glutamine (GIBCO) and 1% penicillin-streptomycin (Hyclone) at 37oC in a humid atmosphere containing 5% CO2.  MCF-7_EV and MCF-7_V5 cells were derived as described in Bist et. al, 2013.  (1). Bist P, Shu S, Lee H, Arora S, Nair S, Lim JY, Dayalan J, Gasser S, Biswas SK,  Fairhurst AM, Lim LH. Annexin-A1 regulates TLR-mediated IFN-β production through   an interaction with TANK-binding kinase 1. J Immunol. 2013 Oct 15;191(8):4375-82.  doi: 10.4049/jimmunol.1301504. Epub 2013 Sep 18. PubMed PMID: 24048896.

extract_protocol: Total cellular RNA was isolated with TRIzol (Invitrogen) according to manufacturer’s instructions. Enriched miRNA was isolated from cell pellets using mirPremier miRNA isolation kit (Sigma) according to the manufacturer’s protocol. The enriched miRNA was quantified using a NanoDrop spectrophotometer (NanoDrop Technology) where 1 A260 unit is 33ug/ml of small RNA. The integrity of the miRNA was determined using an Agilent  Bioanaylzer (Agilent Technology).

treatment_protocol: MCF-7_EV and MCF-7_V5 cells were cultured as described in Bist et. al (2013) and harvested after 24hrs of growth.

tag: tissue

value: MCF-7 cells

tag: vector

value: overexpressing ANXA1


title: ANXA1, biological rep2

source_name: MCF-7 cells (human breast adenocarcinoma cell line), overexpressing ANXA1

label_protocol: MicroRNA microarray analysis was performed using the Affymetrix Solution GeneChip® MicroRNA Version 1.0 array (comprising 46228 probes with 7815 probes sets) according to manufacturer’s (Affymetrix) instructions.   Briefly, a starting material of 1ug of small RNA was used for poly A tailing on the 3’ end of the small RNA followed by ligation of the biotinylated signal molecule to the small RNA samples, according to Affymetrix Flashtag RNA labeling kit (Affymetrix, p/N FT10AFYB). Hybridzation procedure was performed as described in the manufacturer’s protocol.


title: Cell line_untreated LNCaP


title: Cell line_hypoxia exposed 22Rv1


title: Control, biological rep2

description: Gene expression data from MCF-7 cells (human breast adenocarcinoma cell line)

value: empty expression vector


title: Control, biological rep3

source_name: MCF-7 cells (human breast adenocarcinoma cell line)


title: ANXA1, biological rep1


title: Cell line_untreated 22Rv1


title: Control, biological rep1


title: peripheral airway epithelial cells, cancer 11, rep1

source_name: contral-lateral peripheral airway epithelial cells_cancer

tag: subject id

value: cancer 11

value: male

tag: case

value: adenocarcinoma

tag: cell type


title: peripheral airway epithelial cells, cancer 18, rep1

value: cancer 18

value: contral-lateral peripheral airway epithelial cells


title: Tumor biopsy FUNC-022

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

source_name: Prostate tumor

growth_protocol: A punch biopsy was collected from each patient at the time of surgery

extract_protocol: RNA was extracted with Rneasy MiniKit (Qiagen). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis. Biopsies with more than 75% malignant glands and less than 50% stroma in HE stained sections from the specimen were used further.

value: prostate tumor biopsy

value: Adeno carcinoma

tag: clinical t-stage (ct)

tag: lymph node metastasis status

tag: cohort

value: Investigation cohort


title: Hu_Mu 73

city: New Haven

first: JOSE

middle: DAVID

last: HERAZO MAYA

state: CT

address: 300 Cedar Street

institute: Yale University

description: Gene expression microarrays of human CD4 T cells transferred into mice

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA High Resolution Microarray Scanner (G2505C US45102918) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 μm, Tiff 20 bit, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (GE1_107_Sep09 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Gene expression data was normalized to the geometric mean of all the  samples using cyclic loess, for the normalization and statistical analysis we used the average gene expression values of the replicated probes, the number of probes after the average and normalization process was 29807.

source_name: CD4 T lymphocytes, blood draw

label_protocol: Labeling reactions were performed for each sample using Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color (5184-3523, Agilent Technologies, Santa Clara, CA). Briefly, with a starting concentration of 200 nanograms of total RNA, an initial cDNA strand was synthesized using a oligo(dT)24 primer containing a T7 RNA polymerase, this cDNA was then used as a template to generate Cy3 labeled cRNA by a reverse transcriptase enzyme. After the cRNA was obtained a purification step was performed using RNeasy Mini Kit (74104, Qiagen, Valencia, CA) followed by measurement of the yield and specific activity of each sample

extract_protocol: Total RNA was extracted using the TRIzol reagent protocol and purified using the miRNeasy Mini Kit (217004, Qiagen, Valencia, CA) under fully automated sample preparation by the assistance of the QIAcube device (9001292, Qiagen, Valencia CA) following the manufacturer’s protocol.After extraction, total RNA yield and quality were evaluated using NanoDrop at 260 nm and the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Blood was drawn by venipuncture in each mice and CD4+CD28 cells were isolated by fluoresence activated cell sorting. After this step 1 ml of TRIzol (15596019, Invitrogen, Carlsbad, CA) was added to each sample and they were snap frozen in -80 celsius.

value: CD4 T cells

tag: cell subtype

value: CD4 CD28 +


title: Hu_Mu 40

value: CD4 CD28 null


title: Hu_Mu 41


title: Hu_Mu 39


title: Hu_Mu 43


title: Bc ATCC 14579 ccpA del vs. wild type with glucose

city: Wageningen

first: Janneke

last: Wijman

address: Bomenweg 2

country: Netherlands

institute: Wageningen UR

description: No extra description.

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.

data_processing: Lowess-normalization, performed in Agilent Feature Extraction Software v8.1.1.1. Subsequently normalized data was processed with the Vampire webbased microarray suite.

organism: Bacillus cereus ATCC 14579

source_name: wild type with glucose

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

growth_protocol: Bc ATCC 14579 wild type strain grown in Y1 with 0.5% glucose, harvested at OD600 0.5

extract_protocol: RNA was extracted as described by van Schaik et al., 2007

tag: genotype/variation

value: wild type

tag: growth protocol

value: with glucose

source_name: ccpA del. with glucose

growth_protocol: Bc ATCC 14579 ccpA deletion strain grown in Y1 with 0.5% glucose, harvested at OD600 0.5

value: ccpA deletion


title: Hu_Mu 44


title: Bc ATCC 14579 wild type vs. ccpA del. without glucose

description: No extra description.

source_name: ccpA del. without glucose

growth_protocol: Bc ATCC 14579 ccpA deletion strain grown in Y1 without glucose, harvested at OD600 0.5

value: without glucose

source_name: wild type without glucose

growth_protocol: Bc ATCC 14579 wild type strain grown in Y1 without glucose, harvested at OD600 0.5


title: Bc ATCC 14579 wild type with vs. without glucose

description: No extra description.


title: Bc ATCC 14579 ccpA del. without vs. with glucose

description: No extra description.

growth_protocol: Bc ATCC 14579 ccpA deletion strain grown in Y1 without 0.5% glucose, harvested at OD600 0.5

growth_protocol: Bc ATCC 14579 ccpA deletion strain grown in Y1 with glucose, harvested at OD600 0.5


title: Bc ATCC 14579 ccpA del. with vs. without glucose

description: No extra description.


title: Bc ATCC 14579 wild type without vs. with glucose

description: No extra description.


title: p53 tau rep1

city: Boston

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

hyb_protocol: standard NimbleGen protocol

scan_protocol: standard NimbleGen protocol

data_processing: normalized the data as described (Peng et al. 2007). For each replicate, we set signal (i.e., log ratio) median to zero and rescaled signals so that their standard deviation is the average standard deviation of the replicates. To identify binding clusters, we took the mean of the replicates and applied running median smoothing with a window size of 500 bp along chromosomal locations.

organism: Drosophila melanogaster

source_name: p53 ChIP DNA

label_protocol: 6.5 mg of purified and amplified chromatin were then submitted to NimbleGen/Roche for the labeling step and the hybridization to a HD2 whole-genome tiling array.

extract_protocol: ChIP-chip was performed on Drosophila tissue. Heads were selected through a sieve from 200 mg of frozen 10-day-old flies (each genotype). Fly heads were then fixed with 1.8% formaldehyde. After two washes in ice-cold PBS they were resuspended in RIPA Buffer plus protease inhibitor. The heads were disrupted by sonication on ice, using a Branson Sonifier 450 and chromatin was sheared into lengths of 400–1000 bp. 1/100 of the clarified sample was stored as input and the remaining sample was incubated with 2 μg of anti-p53 (d-200, Santa Cruz). The samples were then complexed with protein A/salmon sperm DNA. After washing the beads, as per the Millipore ChIP Assay protocol, the DNA was eluted, decrosslinked and then processed with RNase. The chromatin was treated with proteinase K, and DNA was extracted and precipitated. The DNA pellet was then resuspended in water and a whole-genome DNA amplification step was performed with a WGA2 kit (Sigma).

tag: genotype

value: tau

tag: chip antibody

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #

value: head

tag: genetic background

value: Canton S

source_name: Input DNA


title: Bc ATCC 14579 ccpA del vs. wild type without glucose

description: No extra description.


title: Control, biological replicate 3

city: Philadelphia

first: Christopher

last: Lengner

state: PA

address: 3800 Spruce Street, Room 390EA

department: Biomedical Sciences

institute: University of Pennsylvania

description: Gene expression data from control

hyb_protocol: 5.5ug of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA).The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Microarray data was analyzed using Partek® Genomics Suite software. Raw data was normalized using default settings of RMA normalization method.

source_name: Intestinal epithelial cells

label_protocol: All protocols were conducted as described in the Ambion WT Expression Manual and the Affymetrix GeneChip Expression Analysis Technical Manual. 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: No in vitro growth- primary murine intestinal epithelial cells were isolated.

extract_protocol: Total RNA was extracted using a 5-Prime PerfectPure RNA Tissue Kit

treatment_protocol: Mice were treated with doxycycline in the drinking water for 24 hours prior to isolation

value: intestinal epithelial cells


title: p53 tau rep2


title: Transgenic, biological replicate 2

description: Gene expression data from transgenic


title: Transgenic, biological replicate 3

description: Gene expression data from transgenic


title: Transgenic, biological replicate 1

description: Gene expression data from transgenic


title: Control, biological replicate 2

description: Gene expression data from control


title: Control, biological replicate 1

description: Gene expression data from control


title: p53 control rep1

value: elav/+


title: p53 control rep2


title: Uterus female 5

city: Macclesfield

first: Russell

last: Huby

state: Cheshire

address: Alderley Park

institute: AstraZeneca

hyb_protocol: Hybridization mixes including control oligos and biotin-labelled cRNA were prepared following the Affymetrix protocol. Hybridisation to Affymetrix RAE230_2 rat genechips® was carried out overnight at 45oC rotating at 60 rpm. Bound biotinylated probes were revealed with strptavidin-phycoerythrin complex according to the Affymetrix protocol.

scan_protocol: Scanning was carried out with an Affymetric 3000 scanner using the RAE_230_V2 protocol

data_processing: R bioconductor was used for primary analysis, analysis was using GC-RMA-s

source_name: normal uterus

label_protocol: cDNA, biotin-labelled cRNA and fragmented hybridization probes were prepared using the Affymetrix IVT kit (Affymetrix CA.).

growth_protocol: Rats were housed 2-3 per cage

extract_protocol: RNA was purified from lysates using Qiagen RNeasy mini columns according to the manufacturer’s instructions. Nucleic acid (RNA) purity was determined according to the 260/280nM absorbance ratio using a Nanodrop-1000 (Thermo Scientific). Samples were accepted only if the ratio fell between 1.8 and 2.2. Otherwise, RNA was re-extracted from new samples of frozen tissue. RNA integrity was assessed using the 2100 Bioanalyser (Agilent). Samples with an RNA integrity number (RIN) <7 were rejected, and re-processed.

treatment_protocol: Rats were humanely killed at a designated establishment by halothane inhalation, which is an appropriate method under Schedule 1 of the Act.Organs and tissues were removed and cleaned of extraneous tissue by a 5-person necropsy team within 5 min  of death, then frozen in liquid nitrogen. Pancreas was prioritized for rapid freezing, since its mRNA is known to be particularly vulnerable to degredation. Tissue samples from each animal weighing 100-250 mg were taken from frozen samples and homogenized immediately in RNeasy lysis buffer. Care was taken to ensure samples were taken consistently from the same region of tissue for each individual, and that they were representative of the whole organ (e.g. radial segments of kidney were taken from the equator in each case).

value: uterus

tag: Sex

value: female

tag: strain

value: Han Wistar-derived rats (AlpkHsdBrlHan:WIST)


title: Thyroid female 2

source_name: normal thyroid

tag: tissue

value: thyroid


title: Thyroid female 1


title: Thyroid female 3


title: Uterus female 1


title: Uterus female 4


title: Bc ATCC 14579 wild type vs. ccpA del. with glucose

description: No extra description.


title: Epididymis male 2

source_name: normal epididymes

value: epididymes

value: male


title: Uterus female 3


title: Uterus female 2


title: Thyroid male 3


title: Epididymis male 3


title: Epididymis male 5


title: Thyroid female 5


title: Thyroid male 5


title: Thyroid male 1


title: Thyroid male 2


title: Thyroid female 4


title: Thymus female 3

source_name: normal thymus

value: thymus


title: Thymus female 1


title: Thyroid male 4


title: Thymus male 4


title: Thymus female 5


title: Thymus male 2


title: Thymus male 3


title: Thymus male 1


title: Testes male 2

source_name: normal testes

value: testes


title: Testes male 3


title: Thymus female 4


title: Testes male 4


title: Testes male 1


title: Spleen female 5

source_name: normal spleen

value: spleen


title: Spleen female 4


title: Spleen male 2


title: Spleen female 3


title: Skin male 1

source_name: normal skin

value: skin


title: Skin female 5


title: Skin male 5


title: Skin female 2


title: Skin female 1


title: Skin male 3


title: Spleen male 1


title: Skin female 3


title: Skin female 4


title: Spleen female 1


title: Spleen male 3


title: Spleen female 2


title: Skin male 4


title: Prostate male 5

source_name: normal prostate

value: prostate


title: Prostate male 4


title: Pituitary male 2

source_name: normal pituitary

value: pituitary


title: Pituitary male 3


title: Prostate male 2


title: Prostate male 3


title: Pituitary female 5


title: Pituitary male 4


title: Pituitary female 3


title: Pituitary female 4


title: Prostate male 1


title: Pituitary female 2


title: Pancreas female 5

source_name: normal pancreas

value: pancreas


title: Pituitary male 5


title: Pancreas male 2


title: Pancreas female 2


title: Ovary female 5

source_name: normal ovary

value: ovary


title: Pancreas male 3


title: Pancreas male 1


title: Soleus female 3

source_name: normal soleus muscle

value: soleus muscle


title: Ovary female 2


title: Gastroc female 3

source_name: normal gastrocnemius muscle

value: gastrocnemius muscle


title: Soleus female 1


title: Pituitary male 1


title: Mesen LN female 4

source_name: normal mesenteric lymph node

value: mesenteric lymph node


title: Ovary female 3


title: Ovary female 1


title: Soleus female 5


title: Soleus male 3


title: Soleus female 2


title: Gastroc female 1


title: Soleus male 2


title: Pancreas female 4


title: Gastroc male 3


title: Pituitary female 1


title: Gastroc male 2


title: Ovary female 4


title: Soleus female 4


title: Pancreas male 5


title: Gastroc female 5


title: Soleus male 5


title: Mesen LN female 3


title: Gastroc female 2


title: Lung female 2

source_name: normal lung

value: lung


title: Mesen LN male 4


title: Lung male 4


title: Mesen LN female 2

value: female


title: Lung male 2

value: Han Wistar-derived rats (AlpkHsdBrlHan:WIST)


title: Mesen LN male 1


title: Mesen LN female 1


title: Lung female 4


title: Lung female 5


title: Mesen LN male 5


title: Kidney female 4

source_name: normal kidney

value: kidney


title: Lung female 3


title: Kidney female 5


title: Liver male 4

source_name: normal liver

value: liver


title: Liver female 1


title: Lung male 1

value: male


title: Mesen LN male 2


title: Lung male 3


title: Liver male 5


title: Liver female 5


title: Liver female 4


title: Lung female 1


title: Lung male 5


title: Liver male 3


title: Liver female 3


title: Liver male 1


title: Liver female 2


title: Kidney female 1


title: Kidney female 3


title: Kidney female 2


title: Kidney male 4


title: Kidney male 5


title: Stomach male 2

source_name: normal stomach

value: stomach


title: Heart male 5

source_name: normal heart

value: heart


title: Mandib LN female 4

source_name: normal mandibular lymph node

value: mandibular lymph node


title: Stomach male 3


title: Stomach female 4


title: Mandib LN female 2


title: Kidney male 3


title: Stomach female 5


title: Mandib LN male 5


title: Heart male 4


title: Mandib LN female 3


title: Heart female 2


title: Stomach female 2


title: Stomach male 1


title: Kidney male 2


title: Heart male 3


title: Heart female 5


title: Stomach male 5


title: Stomach female 3


title: Mandib LN male 4


title: Stomach female 1


title: Heart male 1


title: Heart female 3


title: Stomach male 4


title: Mandib LN female 1


title: Mandib LN male 3


title: Mandib LN male 1


title: Jejunum female 5

source_name: normal jejunum

value: jejunum


title: Mandib LN male 2


title: Jejunum male 4


title: Jejunum female 3


title: Jejunum female 4


title: Jejunum female 2


title: Jejunum male 5


title: Jejunum male 3


title: Ileum female 2

source_name: normal ileum

value: ileum


title: Jejunum male 1


title: Ileum female 5


title: Treg cells WT replicate 3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six (6) micrograms of cRNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix HT MG-430 PM array. Following hybridization, arrays were washed and stained using the GeneTitan system

scan_protocol: HT MG-430PM arrays were scanned using the Affymetrix GeneTitan system

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5

source_name: Treg cells from WT mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: CD4+CD25+Foxp3-YFP+ Treg cells from WT and Ptenfl/flFoxp3-Cre mice were purified from spleen and peripheral lymph nodes by flow cytometry

extract_protocol: RNA was extracted using Qiagen's RNAeasy kit, with on-column DNase digestion included.

value: C57BL/6 WT


title: Treg cells Ptenfl/flFoxp3-Cre replicate 1

source_name: Treg cells from Ptenfl/flFoxp3-Cre mouse

value: C57BL/6 Ptenfl/flFoxp3-Cre


title: Jejunum female 1


title: AtNIGT1/HRS1 +CHX - DEX + Nitrate rep3

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

department: Biology

institute: CNRS

description: AtNIGT1/HRS1 +CHX - DEX + Nitrate rep3

hyb_protocol: Affymetrix recommendation

scan_protocol: Affymetrix recommendation

data_processing: Mas5 [R]

source_name: Root protoplasts

label_protocol: GeneChip 3'IVT Express Kit (Affymetrix)

growth_protocol: Protoplasts are from NO3- treated roots

extract_protocol: TRIzol reagent

tag: protocol

value: -DEX


title: Ileum female 1


title: Treg cells WT replicate 1


title: Treg cells Ptenfl/flFoxp3-Cre replicate 2


title: Treg cells Ptenfl/flFoxp3-Cre replicate 3


title: AtNIGT1/HRS1 +CHX + DEX + Nitrate rep3

description: AtNIGT1/HRS1 +CHX + DEX + Nitrate rep3

value: +DEX


title: AtNIGT1/HRS1 +CHX + DEX + Nitrate rep2

description: AtNIGT1/HRS1 +CHX + DEX + Nitrate rep2


title: Ileum female 4


title: Treg cells WT replicate 2


title: Ileum male 2


title: Ileum male 5


title: Ileum male 3


title: AtNIGT1/HRS1 +CHX - DEX + Nitrate rep2

description: AtNIGT1/HRS1 +CHX - DEX + Nitrate rep2


title: AtNIGT1/HRS1 +CHX - DEX + Nitrate rep1

description: AtNIGT1/HRS1 +CHX - DEX + Nitrate rep1


title: AtNIGT1/HRS1 +CHX + DEX + Nitrate rep1

description: AtNIGT1/HRS1 +CHX + DEX + Nitrate rep1


title: Ileum female 3


title: Ileum male 4


title: Duodenum female 5

source_name: normal duodenum

value: duodenum


title: Duodenum female 3


title: Duodenum male 3


title: Duodenum female 2


title: Duodenum male 4


title: Duodenum male 5


title: Colon female 4

source_name: normal colon

value: colon


title: Ileum male 1


title: Duodenum male 2


title: Duodenum male 1


title: Duodenum female 1


title: Colon female 1


title: Colon male 1


title: Colon male 3


title: Colon male 4


title: Caecum female 2

source_name: normal caecum

value: caecum


title: Caecum female 5

value: female


title: Colon female 5

value: Han Wistar-derived rats (AlpkHsdBrlHan:WIST)


title: Kidney male 1

value: kidney


title: Caecum male 5


title: Colon male 2


title: Colon female 2


title: Colon female 3


title: Colon male 5


title: Caecum male 2


title: Caecum male 3


title: Caecum female 3


title: Caecum female 4


title: Caecum female 1


title: Caecum male 4


title: MITE_3

city: London

first: Vladimir

last: Zhurov

state: ON

address: 1151 Richmond Street

institute: University of Western Ontario

description: Gene expression of def-1 plants after 24 h of spider mite herbivory.

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 h at 45 °C on GeneChip EUTOM3 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix, Santa Clara, CA).

scan_protocol: Scanning was done following Affymetrix guidelines on a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: CEL files were processed in Bioconductor using RMA workflow with standard settings and GPL16358 platform CDF.

organism: Solanum lycopersicum

source_name: 26 h spider mite treatment, bio rep 1

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual (Affymetrix, Santa Clara, CA).

growth_protocol: Plants were grown under 200-250 µmol m-2 s-1 cool-white fluorescent light at 25 °C with a 16:8 h (light/dark) photoperiod in controlled growth chambers.

extract_protocol: RNA samples were processed in triplicate from pooled samples of two plants per treatment. 3 terminal leaflets of leaf 3 were used. Total RNA was prepared using the RNeasy Plant RNA extraction kit (Qiagen, Venlo, Netherlands).

treatment_protocol: For herbivory response analysis 100 adult female spider mites were applied onto terminal leaflet of leaf 3 per plant and allowed to feed for 24 h. For JA response analysis plants were sprayed with 1 mM JA solution and 3 terminal leaflets of leaf 3 were collected 24 h later.

value: 3 terminal leaflets of leaf 3

tag: cultivar

value: Castlemart

tag: age

value: 1 month old


title: Brain female 5

source_name: normal brain

value: brain


title: MOCK_3

description: Gene expression of def-1 plants 24 h after mock spray application

source_name: Mock spray treatment, bio rep 3


title: Brain female 4


title: Caecum male 1

value: male


title: Brain female 2


title: Brain female 3


title: MITE_1

source_name: 24 h spider mite treatment, bio rep 1


title: MOCK_2

source_name: Mock spray treatment, bio rep 2


title: JA_1

description: Gene expression of def-1 plants 24 h after JA application

source_name: Jasmonic acid treatment samples, bio rep 1


title: Brain female 1


title: NT_3

description: Gene expression of def-1 control plants

source_name: Control plants, bio rep 3


title: MITE_2

source_name: 25 h spider mite treatment, bio rep 1


title: Brain male 3


title: Brain male 5


title: MOCK_1

source_name: Mock spray treatment, bio rep 1


title: Brain male 4


title: JA_3

source_name: Jasmonic acid treatment samples, bio rep 3


title: Bone Marrow female 5

source_name: normal bone marrow

value: bone marrow


title: Brain male 1


title: NT_2

description: Gene expression of def-1 control plants

source_name: Control plants, bio rep 2


title: Brain male 2


title: JA_2

source_name: Jasmonic acid treatment samples, bio rep 2


title: TU_24_1

description: Gene expression of tomato plants after 24 h of spider mite herbivory.

treatment_protocol: In time course scenario 100 adult female spider mites were applied onto terminal leaflet of leaf 3 per plant and allowed to feed for 1, 3, 6, 12 or 24 h. In feeding site scenario leaflets were covered with hundreds of mites that were allowed to feed for 1 h.

value: Heinz 1706


title: Bone Marrow female 4


title: Bone Marrow female 3


title: TU_24_3

source_name: 24 h spider mite treatment, bio rep 3


title: LTL331_Cx_1day

hyb_protocol: 5ug of Cy5-labeled sample was combined with 5ug of Cy3-labeled male reference, and samples were hybridized and washed by following Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol v7.2 on on Agilent SurePrint G3 Human Catalog CGH 8x60K (Design ID 021924)

scan_protocol: scanned at a 3um scan resolution and 20 bit tiff file setting on the Agilent DNA Microarray Scanner G2505C

data_processing:
quantified signal intensities and pre-processed data with Agilent Feature Extraction 11.0.1.1
FE files loaded into Nexus Copy Number Software v.7.5.1  (Biodiscovery Inc.) for analysis.

source_name: prostatic adenocarcinoma, 1 day post-castration

label_protocol: 500ng gDNA labeled by following NimbleGen Arrays User’s Guide: CGH Analysis v5.0, which included a 98C heat fragmentation step and labeling with Cy-labeled random nanomers (TriLink Biotechnologies) and Klenow 3'-5'exo-(New England Biolabs).

extract_protocol: Genomic DNA extracted with Promega Wizard Genomic DNA Extraction Kit

tag: prostate cancer subtype

value: Adenocarcinoma

tag: model

value: Patient Derived Xenograft

source_name: male reference DNA (Promega Corp)

tag: gender


title: Bone Marrow female 2


title: TU_12_2

description: Gene expression of tomato plants after 12 h of spider mite herbivory.

source_name: 12 h spider mite treatment, bio rep 2


title: NT_1

description: Gene expression of def-1 control plants

source_name: Control plants, bio rep 1


title: TU_12_3

source_name: 12 h spider mite treatment, bio rep 3


title: LTL331

source_name: prostatic adenocarcinoma, before host castration


title: LTL331_Cx_8wk

source_name: prostatic adenocarcinoma, 8 weeks post-castration


title: LTL331R

source_name: neuroendocrine prostate cancer, 6 months post-castration

value: Neuroendocrine


title: TU_24_2

source_name: 24 h spider mite treatment, bio rep 2


title: Bone Marrow male 5


title: TU_12_1

source_name: 12 h spider mite treatment, bio rep 1


title: TU_6_3

description: Gene expression of tomato plants after 6 h of spider mite herbivory.

source_name: 6 h spider mite treatment, bio rep 3


title: Bone Marrow male 4


title: seed 48 h

city: Wuhan

first: yongming

last: zhou

state: Hubei

address: No.1,Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

description: Untreated seeds and seeds harvested at 48 h after heat stress.

hyb_protocol: A consistent amount of Cy3-labeled cRNA (1.6 micrograms) were hybridized to the microarray, for 17 hours, prior to washing and scanning.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted from scanned images using Agilent’s Feature Extraction Software (Agilent Technologies). Data were analyzed using a Perl script called BoaoAnalyzer (CapitalBio Corporation, Beijing, China) with LOWESS normalization.

organism: Brassica napus

source_name: heat stressed seeds (48h)

label_protocol: 500 ng of total RNA from each sample was amplified and labeled with a fluorescent dye (Cy3) using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA, USA) following the manufacturer’s protocol. The amount and quality of the fluorescently labeled cRNA was assessed using a NanoDrop ND-1000 spectrophotometer and an Agilent Bioanalyzer.

growth_protocol: Zhongshuang 9, a semi-winter Brassica napus variety, was grown in a greenhouse at 23/18°C (day/night) and a relative humidity of 70% under a 13-h illumination time with a light density of 230-300 µEm-2s-1. At the three-leaf stage, seedlings were vernalized at 4°C for 14 d. Seedlings were then transplanted to a larger pot with one seedling per pot, and continued to grow in the greenhouse until the plants were heat-treated.

extract_protocol: Total RNA was extracted using a cetyltrimethylammonium bromide extraction method as discribed by Wang XM et al. (1998)

treatment_protocol: Plants were heat-treated during pod development. To mimic temperature changes in the field, the temperature was increased linearly from 23°C to 35°C over 4 h, and after heat stress for 5 h at 35°C, the temperature was reduced to 23°C at the same rate; siliques at 20 DAF were randomly sampled after a recovery time of 24 h and 48 h.

tag: variety

value: Zhongshuang 9

tag: developmental stage

value: 20 days after flowering

source_name: controlled seeds (48h)


title: silique wall 48 h

description: Untreated silique walls and silique walls harvested at 48 h after heat stress.

source_name: heat stressed silique walls (48h)

source_name: controlled silique walls (48h)


title: LTL331_Cx_12wk

source_name: prostatic adenocarcinoma, 12 weeks post-castration


title: LTL331_Cx_3wk

source_name: prostatic adenocarcinoma, 3 weeks post-castration


title: Bone Marrow male 2

source_name: normal bone marrow


title: TU_6_2

source_name: 6 h spider mite treatment, bio rep 2


title: seed 24 h

description: Untreated seeds and seeds harvested at 24 h after heat stress.

source_name: heat stressed seeds (24h)

source_name: controlled seeds (24h)


title: Bone Marrow male 1


title: non-treated CCRPKO_rep-2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Gene expression in non-treated CCRPKO mouse liver
251486838172_1_3

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: Liver, fasted

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Mice were kept at 12 h light/dark cycle. Feed and drinking water were supplied ad libtum.

extract_protocol: Total RNA was extracted from livers using Trizol reagent (Invitrogen) and purified with QIAGEN RNAeasy kit (QIAGEN).

treatment_protocol: Mice were fasted for 24 h, and phenobarbital sodium solved in PBS was intraperitoneally injected to mice at a dose of 100 mg/kg body weight.

tag: genotype/variation

value: CCRPKO

tag: treatment

value: non-treated

value: liver


title: TU_6_1

source_name: 6 h spider mite treatment, bio rep 1


title: TU_3_3

description: Gene expression of tomato plants after 3 h of spider mite herbivory.

source_name: 3 h spider mite treatment, bio rep 3


title: Bone Marrow male 3

value: Han Wistar-derived rats (AlpkHsdBrlHan:WIST)


title: non-treated CCRPKO_rep-3

description:
Gene expression in non-treated CCRPKO mouse liver
251486838173_1_3


title: silique wall 24 h

description: Untreated silique walls and silique walls harvested at 24 h after heat stress.

source_name: heat stressed silique walls (24h)

source_name: controlled silique walls (24h)


title: non-treated CCRPKO_rep-1

description:
Gene expression in non-treated CCRPKO mouse liver
251486838171_1_3


title: Bladder female 5

source_name: normal bladder

value: bladder

value: female


title: TU_3_1

source_name: 3 h spider mite treatment, bio rep 1

value: 3 terminal leaflets of leaf 3


title: non-treated WT_rep-3

description:
Gene expression in non-treated WT mouse liver
251486838173_1_1

value: WT


title: TU_3_2

source_name: 3 h spider mite treatment, bio rep 2

value: 1 month old


title: non-treated WT_rep-1

description:
Gene expression in non-treated WT mouse liver
251486838171_1_1

value: male


title: Bladder female 4


title: TU_1_3

description: Gene expression of tomato plants after 1 h of spider mite herbivory.

source_name: 24 h spider mite treatment, bio rep 3


title: CCRPKO-PB_rep-3

description:
Gene expression after 6 h in phenobarbital-treated CCRPKO mouse liver
251486838929_1_4

source_name: Liver, fasted, phenobarbital

value: phenobarbital


title: CCRPKO-PB_rep-2

description:
Gene expression after 6 h in phenobarbital-treated CCRPKO mouse liver
251486838941_1_4


title: Bladder female 2


title: Bladder female 3


title: TU_1_2

source_name: 24 h spider mite treatment, bio rep 2

value: Heinz 1706


title: CCRPKO-PB_rep-1

description:
Gene expression after 6 h in phenobarbital-treated CCRPKO mouse liver
251486838940_1_4


title: non-treated WT_rep-2

description:
Gene expression in non-treated WT mouse liver
251486838172_1_1


title: CCRPKO-PBS_rep-2

description:
Gene expression after 6 h in PBS-treated CCRPKO mouse liver
251486838941_1_3

source_name: Liver, fasted, PBS

value: PBS


title: CCRPKO-PBS_rep-3

description:
Gene expression after 6 h in PBS-treated CCRPKO mouse liver
251486838929_1_3


title: TU_FS_3

description: Gene expression of tomato plants in FS scenario

source_name: Feeding site samples, bio rep 3


title: CCRPKO-PBS_rep-1

description:
Gene expression after 6 h in PBS-treated CCRPKO mouse liver
251486838940_1_3


title: Bladder male 4


title: WT-PBS_rep-3

description:
Gene expression after 6 h in PBS-treated WT mouse liver
251486838932_1_3


title: WT-PBS_rep-1

description:
Gene expression after 6 h in PBS-treated WT mouse liver
251486838940_1_1


title: WT-PBS_rep-2

description:
Gene expression after 6 h in PBS-treated WT mouse liver
251486838941_1_1


title: WT-PB_rep-3

description:
Gene expression after 6 h in phenobarbital-treated WT mouse liver
251486838932_1_4


title: Bladder male 3


title: Bladder male 2


title: WT-PB_rep-1

description:
Gene expression after 6 h in phenobarbital-treated WT mouse liver
251486838940_1_2


title: Bladder male 5


title: TU_1_1

source_name: 24 h spider mite treatment, bio rep 1


title: TU_FS_2

source_name: Feeding site samples, bio rep 2


title: Heart_caAkt_02

city: Birmingham

first: Adam

middle: R

last: Wende

state: AL

address: PBMR Rm 506 901 19th Street South

department: Pathology

institute: University of Alabama at Birmingham

description: Gene expression data from caAkt mouse heart

hyb_protocol: GeneChip Hybridization Oven 640® (Affymetrix, Santa Clara, CA). Washing and staining was performed using an Affymetrix GeneChip Fluidics Station 650

scan_protocol: Affymetrix murine expression U430 2.0 chips were scanned using an Affymetrix GeneChip Scanner 3000® and images interpreted and monitored using GCOS version 1.2.

data_processing: Data from all CEL files was normalized together using R and Bioconductor packages (open source program; http://www.bioconductor.org <http://www.bioconductor.org/>) and statistically analyzed for significant differences (false discovery rate of 0.1) as follows. Briefly, normalization was done by the robust multichip average method (RMA; Irizarry et al. 2003) with the affy package

source_name: Cardiac, ventricular tissue

label_protocol: Affymetrix GeneChip® One-Cycle Target Labeling and Control Kit as described in the Affymetrix Eukaryotic RNA One-cycle cDNA Synthesis and Labeling manual using an MJ Research DNA Engine Tetrad 2 thermocycler® (Bio-Rad Laboratories, Hercules, CA)

extract_protocol: Total RNA was extracted from heart tissue with Trizol reagent (Life Technologies) and purified with the RNEasy Kit (Qiagen Inc., Valencia, CA).

value: Cardiac, ventricular tissue

tag: genotype

value: caAkt

value: 8 weeks-old


title: WT-PB_rep-2

description:
Gene expression after 6 h in phenobarbital-treated WT mouse liver
251486838941_1_2


title: Aorta female 4

source_name: normal aorta

value: aorta


title: TU_CNTRL_24_1

description: Gene expression of tomato control plants

source_name: Control plants, bio rep 1


title: Aorta female 5


title: PerM_Mg2000_exp3

city: New York

first: Sabine

last: Ehrt

state: New York

address: 413 East 69th Street

department: Microbiology & Immunology

institute: Weill Cornell Medical College

description: SAMPLE 12

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent Gene Expression hybridization buffer (Hi-RPM) was added to the fragmentation mixture and hybridized to a custom-designed Mtb microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 019943_D_20080412) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mycobacterium tuberculosis

source_name: Mtb_PerM mutant_2000uM Mg2+

label_protocol: Cy3 labeled RNA was prepared from 100 ng RNA using a Low Input Quick Amp Labeling Kit (Agilent) according to manufacturer's instructions.

growth_protocol: Mtb was grown in standing cultures at 37C for 5 days in Sauton’s media containing 250 or 2000 μM MgCl2 and 0.05% Tween 80. Flasks were shaken for 5 hours prior to harvest.

extract_protocol: Cultures were mixed with an equal volume of GTC buffer containing guanidinium thiocyanate (4 M), sodium lauryl sulfate (0.5%), trisodium citrate (25 mM), and 2-mercaptoethanol (0.1 M) and pelleted by centrifugation. Bacterial RNA was isolated as previously described (Ehrt, S. et al. (2002). Immunology of Infection 169–180).

tag: strain background


title: TU_CNTRL_24_3

source_name: Control plants, bio rep 3


title: BM PC5

city: Cádiz

first: Antonio

last: Campos-Caro

state: Cádiz

address: Avda. Ana de Viya, 21

department: Unidad Investigación

country: Spain

institute: Hospital Universitario Puerta del Mar

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 4x44K V1 using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

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

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: Isolate plasma cells from Bone marrow, donor 5

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

growth_protocol: Tonsils were obtained from patients undergoing tonsillectomy for recurrent tonsillitis. Peripheral blood (PB) samples were obtained from healthy donors 6 days after receiving a conventional booster immunization against tetanus-diphtheria toxoids and acellular pertussis. Bone marrow (BM) specimens showing no abnormalities were collected from discarded BM aspirates obtained for diagnostic purposes. All studies were approved by the Institutional Review Board.

extract_protocol: Cell samples were lysed using SuperAmp™ Lysis Buffer and stored appropriately according to the instructions of the SuperAmp Preparation Kit (Miltenyi Biotec). mRNA was isolated via magnetic bead technology. SuperAmp RNA amplification was performed according to Miltenyi Biotec’s undisclosed procedure, based on a global PCR protocol using mRNA-derived cDNA. The integrity of the cDNA was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

treatment_protocol: Tonsils were mechanically disrupted and the resulting cell suspension was followed by T-cell depletion, as reported previously (Brieva, J.A. 1994. Eur J Immunol 24:362-366.). The resulting cellular fraction was named tonsil non-T cells. Subsequently, CD31+ cells were purified from the tonsil non-T cell fraction by immunomagnetic cell selection to enrich the PCs subset (Medina, F. 2002. Blood 99:2154-2161 and Rodriguez-Bayona, B. 2012. J Immunol 188:1578-1581). PB and BM MCs were isolated by density gradient centrifugation on Hystopaque-1077 (Sigma-Aldrich, St Louis, MO) and PBMCs were T-cell depleted. PB non-T CD27+ and BMMC CD138+ cell fractions containing pre-enriched populations of PCs were next obtained by immunomagnetic cell selection. Finally, tonsil, PB and BM PCs were isolated by sorting in a FACSAria instrument (BD), based on the gating on CD38high cells; post-sort purity was > 97%.

value: Bone Marrow

tag: disease

value: recurrent tonsillitis


title: Heart_caAkt_03


title: BM PC7

source_name: Isolate plasma cells from Bone marrow, donor 7


title: BM PC6

source_name: Isolate plasma cells from Bone marrow, donor 6


title: Aorta female 2


title: Aorta female 3


title: PerM_Mg2000_exp2

description: SAMPLE 11


title: Heart_WT_02

description: Gene expression data from wild-type mouse heart

value: wild-type


title: TU_CNTRL_24_2

source_name: Control plants, bio rep 2


title: Aorta female 1

value: Han Wistar-derived rats (AlpkHsdBrlHan:WIST)


title: Heart_WT_03


title: Aorta male 5


title: Heart_WT_01


title: Heart_caAkt_01


title: PerM_Mg2000_exp1

description: SAMPLE 10


title: PerM_Mg250_exp3

description: SAMPLE 9

source_name: Mtb_PerM mutant_250uM Mg2+


title: Aorta male 4


title: Blood PC6

source_name: Isolate plasma cells from Peripheral Blood, donor 6

value: Peripheral blood

value: none, healthy donor


title: BM PC2

source_name: Isolate plasma cells from Bone marrow, donor 2


title: BM PC4

source_name: Isolate plasma cells from Bone marrow, donor 4


title: Blood PC5

source_name: Isolate plasma cells from Peripheral Blood, donor 5


title: Aorta male 3


title: PerM_Mg250_exp2

description: SAMPLE 8


title: Aorta male 2


title: PerM_Mg250_exp1

description: SAMPLE 7


title: BM PC1

source_name: Isolate plasma cells from Bone marrow, donor 1


title: H37Rv_Mg2000_exp3

description: SAMPLE 6

source_name: Mtb_WT_2000uM Mg2+

value: wild type


title: Tonsil PC7

source_name: Isolate plasma cells from Tonsil, donor 7

value: Tonsil


title: H37Rv_Mg2000_exp2

description: SAMPLE 5


title: Blood PC3

source_name: Isolate plasma cells from Peripheral Blood, donor 3


title: H37Rv_Mg2000_exp1

description: SAMPLE 4


title: Aorta male 1

source_name: normal aorta


title: Blood PC4

source_name: Isolate plasma cells from Peripheral Blood, donor 4


title: Adrenal female 4

source_name: normal adrenal tissue

value: adrenal tissue

value: female


title: Tonsil PC6

source_name: Isolate plasma cells from Tonsil, donor 6


title: Adrenal female 5


title: Tonsil PC1

source_name: Isolate plasma cells from Tonsil, donor 1


title: Tonsil PC3

source_name: Isolate plasma cells from Tonsil, donor 3


title: Blood PC1

source_name: Isolate plasma cells from Peripheral Blood, donor 1


title: BM PC3

source_name: Isolate plasma cells from Bone marrow, donor 3


title: Tonsil PC2

source_name: Isolate plasma cells from Tonsil, donor 2


title: Blood PC2

source_name: Isolate plasma cells from Peripheral Blood, donor 2


title: Tonsil PC4

source_name: Isolate plasma cells from Tonsil, donor 4


title: Tonsil PC5

source_name: Isolate plasma cells from Tonsil, donor 5


title: H37Rv_Mg250_exp3

description: SAMPLE 3

source_name: Mtb_WT_250uM Mg2+


title: H37Rv_Mg250_exp1

description: SAMPLE 1


title: Adrenal female 3


title: Adrenal female 2


title: H37Rv_Mg250_exp2

description: SAMPLE 2


title: Adrenal male 5

value: male


title: Adrenal female 1


title: Adrenal male 2


title: Adipose female 2

source_name: normal adipose tissue

value: adipose tissue


title: Adipose male 3


title: Adipose female 3


title: Adrenal male 1


title: Adipose female 5


title: Adrenal male 4


title: Adipose male 5


title: ihep_j2_day1_replicate2

status: Public on Jan 04 2015

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: R version 2.15.0 (x86_64-pc-linux-gnu), affyPLM_1.32.0, preprocessCore_1.18.0, gcrma_2.28.0, affy_1.34.0, Biobase_2.16.0

source_name: iPS-Hepatocytes cultured alone for 1 day

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA according to the Affymetrix Expression Analysis Technical Manual.

growth_protocol: Induced pluripotent stem cells were plated on matrigel at confluency (1.25e6 cells/6 well plate well) in Rock inhibitor Y27632 10uM), exposed to Activin A, BMP4, FGF, and HGF as described previously (Si-Tayeb, Hepatology ), cultured for 15 days, and replated in Aggrewells in human hepatocyte media (Chen AA, PNAS 2011)

extract_protocol: RNA was purified using the QIAgen Rneasy kit

treatment_protocol: iPS-Hepatocytes were removed from culture and replated into Aggrewells at a ratio of 1:1 with J2 stromal cells for 1 day. As control, post-culture mixing of isolated RNA was done.

tag: cell type

value: iPS-Hepatocytes

tag: j2 fibroblast status

value: No J2 - Day1