title: LGWU702516-1036549WU

source_name: Breast Tumor CALGB 702516


title: LGWU107272-1036540WU

status: Public on Nov 10 2015

type: RNA

city: Saint Louis

first: Sherri

middle: R

last: Davies

state: MO

address: 4950 Parkview Place

country: USA

institute: Washington University

scan_protocol: See manufacturer's website http://www.nanostring.com for procedures.  Digital Analyzer was set to scan at 1155 FOV (fields of view)

data_processing: See manufacturer's website http://www.nanostring.com.  Raw data was background subtracted and normalized to the geometric mean of the housekeepers.

molecule: total RNA

organism: Homo sapiens

source_name: Breast Tumor CALGB 107272

treatment_protocol: The CALGB (Alliance) 9741 adjuvant node-positive breast cancer trial randomized treatment with doxorubicin (A), cyclophosphamide (C), and paclitaxel (T) using a 2x2 factorial design. The two factors were (i) 2-weekly (dose dense; DD) versus 3-weekly administration and (ii) sequential (A→T→C) versus concurrent (AC→T) chemotherapy.

tag: gender

value: female

tag: tissue type

value: Breast Tumor

tag: fixative

value: Formalin-Fixed Paraffin Embedded Tissue


title: LGWU109346-1036535WU

hyb_protocol: See manufacturer's website http://www.nanostring.com for procedures.

source_name: Breast Tumor CALGB 109346


title: LGWU102511-1036539WU

source_name: Breast Tumor CALGB 102511

label_protocol: See manufacturer's website http://www.nanostring.com for procedures


title: LGWU102513-1036537WU

source_name: Breast Tumor CALGB 102513


title: LGWU102491-1036534WU

source_name: Breast Tumor CALGB 102491


title: LGWU107270-1036542WU

source_name: Breast Tumor CALGB 107270


title: LGWU109248-1036527WU

source_name: Breast Tumor CALGB 109248


title: LGWU107284-1036531WU

source_name: Breast Tumor CALGB 107284


title: LGWU103574-1036521WU

source_name: Breast Tumor CALGB 103574


title: LGWU107317-1036520WU

source_name: Breast Tumor CALGB 107317


title: LGWU102762-1036524WU

source_name: Breast Tumor CALGB 102762


title: LGWU102736-1036513WU

source_name: Breast Tumor CALGB 102736


title: LGWU102474-1036533WU

source_name: Breast Tumor CALGB 102474


title: LGWU073456-1036519WU

source_name: Breast Tumor CALGB 073456


title: LGWU073150-1036518WU

source_name: Breast Tumor CALGB 073150


title: LGWU072934-1036515WU

source_name: Breast Tumor CALGB 072934


title: LGWU202109-1036491WU

source_name: Breast Tumor CALGB 202109


title: LGWU107316-1036494WU

source_name: Breast Tumor CALGB 107316


title: LGWU107337-1036506WU

source_name: Breast Tumor CALGB 107337


title: LGWU108958-1036510WU

source_name: Breast Tumor CALGB 108958


title: LGWU109033-1036511WU

source_name: Breast Tumor CALGB 109033


title: LGWU109151-1036504WU

source_name: Breast Tumor CALGB 109151


title: LGWU102596-1036508WU

source_name: Breast Tumor CALGB 102596


title: LGWU073531-1036501WU

source_name: Breast Tumor CALGB 073531


title: LGWU072195-1036496WU

source_name: Breast Tumor CALGB 072195


title: LGWU073196-1036499WU

source_name: Breast Tumor CALGB 073196


title: LGWU102690-1036512WU

source_name: Breast Tumor CALGB 102690


title: LGWU703237-1036484WU

source_name: Breast Tumor CALGB 703237


title: LGWU703392-1036489WU

source_name: Breast Tumor CALGB 703392


title: LGWU072137-1036528WU

source_name: Breast Tumor CALGB 072137


title: LGWU703329-1036487WU

source_name: Breast Tumor CALGB 703329


title: LGWU702575-1036474WU

source_name: Breast Tumor CALGB 702575


title: LGWU702526-1036477WU

source_name: Breast Tumor CALGB 702526


title: LGWU702338-1036485WU

source_name: Breast Tumor CALGB 702338


title: LGWU107371-1036480WU

source_name: Breast Tumor CALGB 107371


title: LGWU702311-1036481WU

source_name: Breast Tumor CALGB 702311


title: LGWU102712-1036476WU

source_name: Breast Tumor CALGB 102712


title: LGWU703433-1036467WU

source_name: Breast Tumor CALGB 703433


title: LGWU203348-1036478WU

source_name: Breast Tumor CALGB 203348


title: LGWU107286-1036505WU

source_name: Breast Tumor CALGB 107286


title: LGWU703327-1036461WU

source_name: Breast Tumor CALGB 703327


title: LGWU702825-1036465WU

source_name: Breast Tumor CALGB 702825


title: LGWU703387-1036466WU

source_name: Breast Tumor CALGB 703387


title: LGWU703333-1036462WU

source_name: Breast Tumor CALGB 703333


title: LGWU702284-1036479WU

source_name: Breast Tumor CALGB 702284


title: LGWU702457-1036472WU

source_name: Breast Tumor CALGB 702457


title: LGWU209164-1036468WU

source_name: Breast Tumor CALGB 209164


title: LGWU702405-1036470WU

source_name: Breast Tumor CALGB 702405


title: LGWU702391-1036469WU

source_name: Breast Tumor CALGB 702391


title: LGWU112099-1036471WU

source_name: Breast Tumor CALGB 112099


title: LGWU109284-1036464WU

source_name: Breast Tumor CALGB 109284


title: LGWU102600-1036473WU

source_name: Breast Tumor CALGB 102600


title: LGWU703188-1036482WU

source_name: Breast Tumor CALGB 703188


title: LGWU703118-1036448WU

source_name: Breast Tumor CALGB 703118


title: LGWU703240-1036458WU

source_name: Breast Tumor CALGB 703240


title: LGWU702731-1036456WU

source_name: Breast Tumor CALGB 702731


title: LGWU702721-1036454WU

source_name: Breast Tumor CALGB 702721


title: LGWU702709-1036452WU

source_name: Breast Tumor CALGB 702709


title: LGWU702667-1036449WU

source_name: Breast Tumor CALGB 702667


title: EWAT YY1aKO_rep1

city: Schlieren

first: Francisco

last: Verdeguer

address: 27a Wagistrasse

country: Switzerland

institute: InSphero

description:
mutant 1
Gene expression data from subcutaneous white adipose tissue of mice exposed to cold.

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution was then removed. The chips were transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, GCS3000, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method RMA quantile normalization yes background correct yes compute present absent calls no normalization method none value to scale to clm file annotate probes yes The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method RMA quantile normalization yes background correct yes compute present absent calls no normalization method none value to scale to clm file annotate probes yes.

label: biotin

organism: Mus musculus

source_name: visceral white adipose tissue

label_protocol: The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) was purified from the IVT reaction mixture using magnetic particles. The cRNA was quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophotometric measurements. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 8-week-old mice (mixed background C57BL6 and 129).

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

treatment_protocol: 4 days cold exposure.

tag: strain

value: mixed background (C57BL6 and 129)

tag: age

value: 8 weeks

tag: genotype/variation

value: Yin Yang 1 adipose-specific knockout mutant

tag: treatment

value: cold exposure (4ºC) for 4 days

tag: tissue

value: visceral white adipose tissue


title: LGWU702313-1036457WU

source_name: Breast Tumor CALGB 702313


title: LGWU702301-1036453WU

source_name: Breast Tumor CALGB 702301


title: EWAT YY1aKO_rep2

description:
mutant 2
Gene expression data from subcutaneous white adipose tissue of mice exposed to cold.


title: EWAT Control_rep3

description:
control 3
Gene expression data from subcutaneous white adipose tissue of mice exposed to cold.

value: control


title: LGWU702276-1036450WU

source_name: Breast Tumor CALGB 702276


title: LGWU703357-1036439WU

source_name: Breast Tumor CALGB 703357


title: LGWU107364-1036451WU

source_name: Breast Tumor CALGB 107364


title: LGWU200443-1036460WU

source_name: Breast Tumor CALGB 200443


title: LGWU702766-1036459WU

source_name: Breast Tumor CALGB 702766


title: EWAT Control_rep2

description:
control 2
Gene expression data from subcutaneous white adipose tissue of mice exposed to cold.


title: EWAT YY1aKO_rep3

description:
mutant 3
Gene expression data from subcutaneous white adipose tissue of mice exposed to cold.


title: LGWU703355-1036438WU

source_name: Breast Tumor CALGB 703355


title: BAT Control_rep1

description: Gene expression data from brown adipose tissue of mice fed a high fat diet

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution was then removed. The chips were transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE

data_processing: The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method RMA quantile normalization yes background correct yes compute present absent calls no normalization method none value to scale to clm file annotate probes yes

source_name: Brown adipose tissue

label_protocol: The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) waas purified from the IVT reaction mixture using magnetic particles. The cRNA was quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 3.5 months old mice (mixed background C57BL6/ and 129)

treatment_protocol: 3 months High fat diet

value: 3.5 months old

value: high fat diet for 3 months

value: brown adipose tissue


title: BAT YY1bKO_rep1

value: Yin Yang 1 brown fat specific knockout mutant


title: LGWU702780-1036436WU

source_name: Breast Tumor CALGB 702780


title: EWAT Control_rep1

description:
control 1
Gene expression data from subcutaneous white adipose tissue of mice exposed to cold.


title: BAT Control_rep3


title: BAT YY1bKO_rep2


title: BAT Control_rep2


title: LGWU702588-1036446WU

source_name: Breast Tumor CALGB 702588


title: KO P20-3

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

description: SAMPLE 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: After exported from BeadStudio, data were normalised using quantile normalisation method

source_name: P20 Testis

label_protocol: Standard Illumina labelled protocol

extract_protocol: Total RNA was extracted with the QIAGEN RNeasy minikit followed by DNAse I treatment in accordance with the manufacturer instructions.

value: testis

tag: genotype

value: Topaz1-/- (KO)


title: LGWU702574-1036445WU

source_name: Breast Tumor CALGB 702574


title: KO P20-2

description: SAMPLE 11


title: BAT YY1bKO_rep3


title: LGWU702527-1036442WU

source_name: Breast Tumor CALGB 702527


title: LGWU702445-1036440WU

source_name: Breast Tumor CALGB 702445


title: LGWU702222-1036443WU

source_name: Breast Tumor CALGB 702222


title: LGWU102677-1036444WU

source_name: Breast Tumor CALGB 102677


title: LGWU102773-1036447WU

source_name: Breast Tumor CALGB 102773


title: IWAT Control_rep2

description: Gene expression data from subcutaneous adipose tissue of mice fed a high fat diet

source_name: subcutaneaous white adipose tissue

growth_protocol: 8 weeks old mice (mixed background C57BL6/ and 129)

treatment_protocol: 2 weeks High fat diet

value: 8 weeks old

value: high fat diet for 2 weeks

value: subcutaneous white adipose tissue


title: IWAT Control_rep3


title: IWAT YY1bKO_rep1


title: IWAT YY1bKO_rep2


title: IWAT YY1bKO_rep3


title: KO P20-1

description: SAMPLE 10


title: LGWU703267-1036420WU

source_name: Breast Tumor CALGB 703267

value: female

value: Breast Tumor


title: IWAT Control_rep1

value: mixed background (C57BL6 and 129)


title: LGWU703254-1036434WU

source_name: Breast Tumor CALGB 703254

value: Formalin-Fixed Paraffin Embedded Tissue


title: LGWU703250-1036419WU

source_name: Breast Tumor CALGB 703250


title: KO P15-3

description: SAMPLE 9

source_name: P15 Testis


title: E15.5 control_4

city: san francisco

first: olga

last: golonzhka

state: CA

address: 1550 4th street

department: psychiatry

institute: UCSF

hyb_protocol: Hybridization were performed for 14 hrs, according to the Agilent protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner

data_processing: Raw signal intensities were extracted with Feature Extraction v10.5 software. We extract the raw signal intensities, log them and quantile normalize the results. Significant changes in gene expression were defined as B value greater than zero. B = log 10 posterior odds ratio, ratio between the probability that a given gene is differentially expressed (DE) over the probability that a given gene is not differentially expressed.B≥0 means equal or greater probability that a gene is DE than non-DE

source_name: whole cortex e15.5

label_protocol: RNA was amplified (labeled with Cy3-CTP)withAgilent low RNA input fluorescent linear amplification kits, and cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE). Equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays, by theUCSF Genomics Core.

growth_protocol: cortex was dissected from mouse embryos at developmental stage E15.5

extract_protocol: corteces were preserved in RNAlater awaiting genotyping; RNA was extracted using Qiagen RNAeasy kit

treatment_protocol: no additional treatment of animals was performed

value: mixed background

tag: developmental stage

value: cortext


title: LGWU703228-1036433WU

source_name: Breast Tumor CALGB 703228


title: LGWU702772-1036421WU

source_name: Breast Tumor CALGB 702772


title: KO P15-1

description: SAMPLE 7


title: E15.5 control_3


title: WT P20-3

description: SAMPLE 6

value: wildtype


title: KO P15-2

description: SAMPLE 8


title: LGWU702440-1036426WU

source_name: Breast Tumor CALGB 702440


title: LGWU702315-1036416WU

source_name: Breast Tumor CALGB 702315


title: E15.5 mutant_3

value: Pbx1 mutant


title: LGWU209166-1036430WU

source_name: Breast Tumor CALGB 209166


title: WT P20-2

description: SAMPLE 5

source_name: P20 Testis


title: LGWU205467-1036425WU

source_name: Breast Tumor CALGB 205467


title: LGWU109057-1036432WU

source_name: Breast Tumor CALGB 109057


title: WT P20-1

description: SAMPLE 4


title: WT P15-3

description: SAMPLE 3


title: E15.5 mutant_2


title: LGWU703407-1036423WU

source_name: Breast Tumor CALGB 703407


title: E15.5 control_2

value: control


title: LGWU703210-1036417WU

source_name: Breast Tumor CALGB 703210


title: LGWU702464-1036407WU

source_name: Breast Tumor CALGB 702464


title: E15.5 control_1


title: LGWU702839-1036401WU

source_name: Breast Tumor CALGB 702839


title: LGWU702611-1036412WU

source_name: Breast Tumor CALGB 702611


title: LGWU702424-1036403WU

source_name: Breast Tumor CALGB 702424


title: LGWU702166-1036402WU

source_name: Breast Tumor CALGB 702166


title: E12.5 mutant_4

source_name: whole cortex e12.5

growth_protocol: cortex was dissected from mouse embryos at developmental stage E12.5

treatment_protocol: no additional treatment were performed


title: WT P15-2

description: SAMPLE 2

source_name: P15 Testis


title: LGWU209165-1036408WU

source_name: Breast Tumor CALGB 209165


title: E12.5 mutant_3


title: LGWU102517-1036404WU

source_name: Breast Tumor CALGB 102517


title: LGWU107382-1036415WU

source_name: Breast Tumor CALGB 107382


title: LGWU109080-1036414WU

source_name: Breast Tumor CALGB 109080


title: E15.5 mutant_4

source_name: whole cortex e15.5


title: WT P15-1

description: SAMPLE 1


title: LGWU702630-1036413WU

source_name: Breast Tumor CALGB 702630


title: LGWU703330-1036399WU

source_name: Breast Tumor CALGB 703330


title: E12.5 mutant_2


title: LGWU200852-1036410WU

source_name: Breast Tumor CALGB 200852


title: LGWU703282-1036397WU

source_name: Breast Tumor CALGB 703282


title: A00024505

city: Orlando

first: Lauren

middle: M.

last: Sparks

state: FL

address: 301 E. Princeton St

department: Translational Research Institute for Metabolism and Diabetes

institute: FLORIDA HOSPITAL

description: obese, T2D

hyb_protocol: Standard  Illumina hybridization protocol

data_processing: Data were normalized by quantile normalization, multiple imputation and log2-transformation, using SAS 9.2. Genes with high background intensity across all samples were filtered.

label: Biotin

source_name: vastus lateralis

label_protocol: Biotinylated cRNA were prepared with the Illumina Total Prep RNA Amplification Kit

extract_protocol: Total RNA was isolated from ~20mg of skeletal muscle tissue using the RNeasy Fibrous Tissue kit (Qiagen)

treatment_protocol: resting skeletal muscle

tag: response to exercise

value: responder

tag: phenotype

value: obese

tag: disease state

value: Type 2 diabetes


title: LGWU702707-1036392WU

source_name: Breast Tumor CALGB 702707


title: A00039616

description: obese, T2D

value: nonresponder


title: A00011211

description: obese, T2D


title: E12.5 control_4


title: LGWU109355-1036389WU

source_name: Breast Tumor CALGB 109355


title: LGWU702272-1036391WU

source_name: Breast Tumor CALGB 702272


title: LGWU703229-1036396WU

source_name: Breast Tumor CALGB 703229


title: LGWU702741-1036395WU

source_name: Breast Tumor CALGB 702741


title: LGWU703193-1036393WU

source_name: Breast Tumor CALGB 703193


title: E12.5 control_3

source_name: whole cortex e12.5


title: LGWU109257-1036400WU

source_name: Breast Tumor CALGB 109257


title: A00024699

description: obese, T2D


title: A00036700

description: obese, T2D


title: LGWU703194-1036394WU

source_name: Breast Tumor CALGB 703194


title: A00031420

description: obese, T2D


title: E12.5 control_1


title: A00034415

description: obese, T2D


title: A00024908

description: obese, T2D


title: A00026868

description: obese, T2D


title: E15.5 mutant_1


title: A00023616

description: obese, T2D


title: LGWU102776-1036390WU

source_name: Breast Tumor CALGB 102776


title: LGWU702589-1036387WU

source_name: Breast Tumor CALGB 702589


title: LGWU702420-1036380WU

source_name: Breast Tumor CALGB 702420


title: LGWU702410-1036379WU

source_name: Breast Tumor CALGB 702410


title: LGWU702568-1036386WU

source_name: Breast Tumor CALGB 702568


title: mEpiSC_686.1930.2.1

city: La Jolla

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

data_processing: The data were filtered for detection pValue > 0.01 and normalised using Robust Spline Normalisation with lumi in R

source_name: epiblast stem cells

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

growth_protocol: TS cells were cultured in RPMI 1640 supplemented with 20% fetal bovine serum, 1 mM sodium pyruvate (Invitrogen), 1X penicillin/streptomycin, 55nM β-mercaptoethanol (Invitrogen), 25 ng/mL  fibroblast growth factor 4(FGF4; Sigma), and 1 μg/mL heparin (Sigma) with 70% of medium being conditioned for 72hrs on inactivated mouse embryonic fibroblasts. ES cells were cultured in DMEM with high glucose supplemented with 15% FBS, GlutaMAX, ß-mercaptoethanol, sodium pyruvate, non-essential amino acids, and 1000U/ml of LIF (Leukaemia inhibitory factor). MEFs were cultured in DMEM supplemented with 10% FBS and non-essential amino acids. Epiblast stem cells were cultured in CDM consisted of Iscove’s modified Dulbecco’s Medium plus Ham’s F12 medium at a 1:1 ratio, both supplemented with Glutamax, bovine serum albumin at a final concentration of 5 mg/ml, 1X chemically defined lipid concentrate, transferrin, insulin at 7 ug/ml.

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion). Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

tag: origin

value: Embryonic

tag: pipeline sample id

tag: background mouse strain


title: mEpiSC_686.1930.4.1


title: A00021704

description: obese, T2D


title: mEpiSC_686.1930.5.1


title: LGWU102731-1036388WU

source_name: Breast Tumor CALGB 102731


title: LGWU107295-1036383WU

source_name: Breast Tumor CALGB 107295


title: LGWU102614-1036385WU

source_name: Breast Tumor CALGB 102614


title: LGWU102569-1036382WU

source_name: Breast Tumor CALGB 102569


title: A00015312

description: obese, T2D

source_name: vastus lateralis


title: FIBRO_605.1641.5.1

source_name: embryo fibroblasts


title: mEpiSC_686.1930.3.1


title: LGWU201357-1036377WU

source_name: Breast Tumor CALGB 201357


title: A00013991

description: obese, T2D


title: FIBRO_605.1641.3.1


title: mEpiSC_686.1930.1.1


title: A00006401

description: obese, T2D


title: FIBRO_605.1641.4.1


title: LGWU102680-1036384WU

source_name: Breast Tumor CALGB 102680


title: A00020739

description: obese, T2D


title: LGWU102547-1036381WU

source_name: Breast Tumor CALGB 102547


title: LGWU101986-1036378WU

source_name: Breast Tumor CALGB 101986


title: FIBRO_605.1641.2.1


title: E12.5 control_2

source_name: whole cortex e12.5


title: A00001835

description: obese, T2D


title: MESC_605.1640.4.1

source_name: embryonic stem cells


title: FIBRO_605.1641.1.1


title: A00000927

description: obese, T2D


title: MESC_605.1640.3.1


title: adjacent normal laryngeal tissue sample C21

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: Labeled RNAs were heat denatured and hybridized to Agilent 8x15k miRNA microarray V19 comprised of 2006 miRNAs from Sanger miRBase (release 19) at 55o C for 20 hr.

scan_protocol: After hybridization, slides were immediately washed and scanned in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA). Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images.

data_processing: Data were normalized by quantile normalization, using Bioconductor 2.10 with R version 2.15.

source_name: adjacent normal laryngeal tissue sample

label_protocol: 100 ng of total RNA from each sample were labeled with Cy3 by using Agilent miRNA labeling kit following manufacturer’s instructions.

extract_protocol: MicroRNA profiling of 4 normal and 12 tumor samples were carried out using Agilent Human miRNA Microarray (V19). Freshly resected tumor tissues were obtained immediately after the surgery and snap frozen, and kept in -80 deg C refrigerators until RNA isolation.

value: adjacent normal laryngeal tissue sample

tag: sample type

value: Normal


title: LSCC tumor tissue specimen C55

source_name: LSCC tumor tissue specimen

value: LSCC tumor tissue specimen

value: Metastatic


title: LSCC tumor tissue specimen C53


title: MESC_605.1640.1.1


title: adjacent normal laryngeal tissue sample C14


title: LSCC tumor tissue specimen E6


title: TSC_605.1639.5.1

source_name: trophoblast stem cell

value: Trophoblast


title: adjacent normal laryngeal tissue sample E6


title: LSCC tumor tissue specimen C14


title: MESC_605.1640.5.1


title: LSCC tumor tissue specimen C21

value: Non-Metastatic


title: TSC_605.1639.3.1


title: TSC_605.1639.4.1


title: adjacent normal laryngeal tissue sample C16


title: LSCC tumor tissue specimen C40


title: LSCC tumor tissue specimen C9


title: MESC_605.1640.2.1


title: LSCC tumor tissue specimen C27


title: LSCC tumor tissue specimen C15


title: LSCC tumor tissue specimen C34


title: LSCC tumor tissue specimen C16


title: TSC_605.1639.2.1


title: exosomal miRNAs from CPT-treated hepatoma Replicate 2

city: New Taipei City

first: Shaochen

last: Lee

address: 510 Zhongzheng Rd., Xinzhuang Dist.

department: School of Medicine

country: Taiwan

institute: FuJen Catholic University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 C, non-speciﬁc binding targets were washed away by three different washing steps (Wash I 42 C 5 mins；Wash II 42 C, 5 mins, 25 C 5 mins; Wash III rinse 20 times)

scan_protocol: The arrays were scanned by GenePix 4200A 01 Autoloader (635nm power 100 PMT 320 ; 532nm power 10, PMT 335) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).
Change in miRNA expression (log2 ratio) in calculated by the value in CPT-treated sample is compared with that in untreated sample.

source_name: Hepatoma cells-derived exosome

label_protocol: 1 µg of small RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Semi-confluent hepatoma Hep3B cells were maintained in exosome-free medium with or without camptothecin for two days.

extract_protocol: The small RNA were extracted by miRNA isolation kit (Geneaid Biotech Ltd., New Taipei City, Taiwan). The small RNAs were characterized by Agilent RNA 6000 Nano assay kit (Angilent Technologies, Santa Clara, CA, USA) to ensure good quality (OD260/OD280 >1.6; OD260/OD230 >1.0; RNA integrity number >5.0) for array analysis.

treatment_protocol: The exosomes were isolated from conditioned medium by Total Exosome Isolation kit (Life Technologies, Grand Island, NY, USA)

tag: cell line

value: 10 uM camptothecin incubation


title: Cartilage_exercise-15d_rep2

city: Columbus

first: Jin

last: Nam

state: OH

address: 305 W. 12th Ave., 4010 Postle Hall

institute: The Ohio State University

hyb_protocol: 2ug of labeled and fragmented DNA was hybridized at 45C for 17 hours at 60rpm. GeneChips were washed and stained on the Affymetrix Fluidics Station 450 according to the manufacturers protocol.

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

data_processing: The data were analyzed by Partek Genomics Suite version 17 using GC-RMA normalization.

organism: Rattus norvegicus

source_name: cartilage, exercised for 15 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng of total RNA according to Affymetrix's protocols.

value: Sprague-Dawley

value: 12-14 weeks old

value: exercised

tag: time

value: 15 days

value: articular cartilage


title: exosomal miRNAs from untreated hepatoma Replicate 1

description: exosomal miRNAs from untreated hepatoma

value: No treatment


title: Cartilage_exercise-15d_rep3


title: exosomal miRNAs from untreated hepatoma Replicate 2

description: exosomal miRNAs from untreated hepatoma


title: Cartilage_exercise-15d_rep1


title: exosomal miRNAs from CPT-treated hepatoma Replicate 1


title: TSC_605.1639.1.1


title: Cartilage_exercise-5d_rep3

source_name: cartilage, exercised for 5 days

value: 5 days


title: Rubrum-25Gy.gamma.irr.in.SPY-rep1

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

country: Belgium

description: Irradiation with 25Gy gamma rays in SPY medium

hyb_protocol: The two differentially labeled cDNAs were resuspended in the universal hybridization buffer (Pronto kit; Corning-Promega, United States), mixed, and added jointly to the surface of the spotted microarray glass slide for overnight hybridization at 42°C using a HS 4800 Pro automated hybridization station (TECAN, Switzerland). The slide was washed according to the Pronto kit’s protocol and then dried in the hybridization station.

scan_protocol: Microarray spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to built-in quality criteria.

data_processing: Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15  as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50. Data were normalized within each array using the printing-tip loess normalization algorithm. The in-slide technical triplicate correlations were calculated using the Duplicate correlation function in the LIMMA package. The log expression values were fit to a linear model and moderated t-statistics were calculated using empirical Bayes method . P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate.

organism: Rhodospirillum rubrum

source_name: non-irradiated culture

label_protocol: Ten micrograms of RNA was reverse transcribed by random priming according to the Pronto kit’s instructions (Corning-Promega, United States) and directly labeled by incorporation of Cy3-dCTP or Cy5-dCTP nucleotides (Amersham Bioscience, United Kingdom) for respectively control and experimental samples.

growth_protocol: The bacterium Rhodospirillum rubrum S1H was obtained from the American Type Culture Collection (ATCC25903) and cultivated in Sistrom medium A containing 2 g/l Na-succinate [20] or Sistrom-peptone-yeast (SPY) [19] containing 30 g/L peptone and 10 g/l yeast extract (BD, USA). Three independent liquid cultures of R. rubrum S1H were allowed to grow to mid-exponential phase in dark aerobic conditions (OD680 of ca. 0.3) at 30 °C in 250 ml vented tissue culture flasks (BD Falcon, USA). About 10*8 colony forming unit (CFU) per ml were harvested by centrifugation (4,000 rpm, 15 min) and resuspended in the appropriate medium, i.e. Sistrom-succinate or SPY prior to irradiation using 50 ml vented tissue culture flasks.

extract_protocol: Ten mL of R. rubrum S1H culture was harvested at OD680 of 0.3 from all test cultures irradiated with gamma rays or not, and 20 mL RNAProtect Bacteria Reagent (QIAGEN) was added to preserve the RNA. The fixed cell suspensions were centrifuged at 3500 rpm for 10 min, the supernatant was removed, and cell pellets were stored at -80°C. The RNA extraction was performed using the RNeasy Midi Kit (QIAGEN), following the manufacturer’s guidelines. RNA quantity and quality was assessed using the Nanodrop ND-1000 and the 2100 Bioanalyzer (Agilent) using the RNA 6000 Nano Chip Kit following the manufacturer’s instructions.

treatment_protocol: Exposure of R. rubrum S1H cultures to various doses of gamma rays was performed in SCK•CEN's Radio Isotope Test Arrangement (RITA) facility. Bacterial cells were exposed for different lengths of time to gamma rays (Cobalt-60 source), to obtain doses ranging from 12.5 to 1,600 Gy using a 1,075 Gy/h dose rate at a constant temperature of 25 °C

tag: treatment group

value: Control

value: 25 Gy SPY


title: Rubrum-25Gy.gamma.irr.in.SPY-rep2

description: Irradiation with 25 Gy gamma rays in SPY medium

tag: strain


title: Cartilage_exercise-2d_rep3

source_name: cartilage, exercised for 2 days

tag: age

value: 2 days


title: Rubrum-12.5Gy.gamma.irr.in.SPY-rep2

description: Irradiation with 12.5 Gy gamma rays in SPY medium

value: 12.5 Gy SPY


title: Rubrum-25Gy.gamma.irr.in.Sis-rep2

description: Irradiation with 25 Gy gamma rays in Sistrom medium

value: 25 Gy Sis


title: Cartilage_control_rep3

source_name: cartilage, control

value: control


title: Rubrum-12.5Gy.gamma.irr.in.SPY-rep3

source_name: Irradiation with 12.5 Gy gamma rays in SPY medium


title: Rubrum-25Gy.gamma.irr.in.Sis-rep1

description: Irradiation with 25Gy gamma rays in Sistrom medium


title: Rubrum-12.5Gy.gamma.irr.in.Sis-rep1

description: Irradiation with 12.5Gy gamma rays in Sistrom medium

value: 12.5 Gy Sis


title: Rubrum-12.5Gy.gamma.irr.in.Sis-rep2

description: Irradiation with 12.5 Gy gamma rays in Sistrom medium


title: Cartilage_control_rep1


title: Cartilage_exercise-5d_rep1


title: Rubrum-12.5Gy.gamma.irr.in.SPY-rep1

description: Irradiation with 12.5Gy gamma rays in SPY medium


title: Cartilage_exercise-2d_rep1


title: Cartilage_exercise-5d_rep2


title: CECT 8666 + Agm (test) compared to CECT 8666 (reference) Replicate 5

status: Public on Nov 09 2015

city: Villaviciosa

first: Beatriz

last: del Rio

state: Asturias

address: Paseo Rio Linares s/n

department: Technology and Biotechnology of Dairy Products

country: Spain

institute: Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

description: Biological replicate 2 of 2.

hyb_protocol: Nine hundred nanograms of DyLight 550- and DyLight 650-labelled cDNA were mixed and hybridized for 17 h at 60°C in the L. lactis subsp. cremoris CECT 8666 DNA microarray using the In situ Hybridization Kit Plus, the Hybridization Gasket Slide and the Agilent G2534A Microarray Hybridization Chamber (Agilent Technologies). After hybridization, slides were washed using appropriate washing buffers as recommended by the manufacturer.

scan_protocol: Slides were scanned using a GenePix 4200A Microarray Scanner (Molecular Devices, Sunnyvale, CA)

data_processing: The images analyzed using GenePix Pro v.6.0 software. Background subtraction and LOWESS (locally weighted scatterplot smoothing) normalization were performed using the standard routines provided by GENOME2D software available at http://server.molgenrug.nl/index.php/analysis-pipeline.

label: DyLight 650

organism: Lactococcus cremoris

source_name: Lactococcus lactis subsp. cremoris CECT 8666 grown with 20 mM agmatine

label_protocol: The synthesis of cDNA was performed using 20 µg of total RNA and the SuperScript® III Reverse Transcriptase kit (Life Technologies, Bleiswijk, Netherlands). After the cDNA was synthesized, the mRNA of the reverse transcription mixture was denaturalized by adding 3 µl of 2.5 mM NaOH for 15 min at 37˚C. The NaOH was neutralized by adding 15 µl of 2 M HEPES free acid. The cDNA was purified using the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nager, Landsmeer, The Netherlands). Briefly, 200 µl of NTC buffer were mixed with the unpurified cDNA, added to a column and centrifuged for 1 min at 11,000 x g. The column was washed first with 600 µl of buffer NT3 and then with 500 µl 80% ethanol. The residual ethanol was completely removed by centrifugation for 2 min at 11,000 x g. To elute the cDNA, 60 µl of 0.1 M sodium bicarbonate pH 9.0 were added to the column and incubated for 1 min at room temperature. Purified cDNA was collected by centrifugation for 1 min at 11,000 x g and was immediately labelled.

growth_protocol: L. lactis CECT 8666 cells were grown in M17 culture medium (Oxoid, UK) supplemented with 1% galactose (w/v) (GalM17) in presence or absence of 20 mM agmatine (Sigma-Aldrich, Barcelona, Spain) for 6h at 30°C without aeration. Cells were harvested by centrifugation at 8,000 x g for 5 min at 4˚C. The supernatants were removed and cell pellets were frozen in liquid nitrogen and stored at -80˚C.

extract_protocol: Cell pellets were resuspended in 500 µl of TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0) and transferred to screw-capped tubes containing 50 µl of 10% SDS, 500 µl of phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma-Aldrich), 500 mg of glass beads (75–150 µm) (Sigma-Aldrich), and 175 µl of Macaloid suspension (Bentone MA, Rheox Inc., Scotland, United Kingdom). Cells were mechanically disrupted in a bead beater at 4˚C. The samples were shaken two times for 45 s. During the shaking intervals the cells were kept on ice for 1 min. The samples were then centrifuged at 8,000 x g for 10 min at 4˚C. The upper phase was transferred to fresh tubes containing 500 µl chloroform: isoamyl alcohol (24:1) and centrifuged for 5 min at 4˚C. 500 µl of the upper phase were transferred to fresh tubes containing 1 ml of lysis/binding buffer of the High Pure RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany). All subsequent steps including the DNaseI treatment were performed following the instructions provided by the manufacturer. The concentration and quality of the RNA was checked on a NanoDrop spectrophotometer (Thermo Scientific, Landsmeer, The Netherlands).

treatment_protocol: Presence or absence of 20 mM agmatine in the culture medium

value: CECT 8666

tag: putrescine producer

value: Yes

tag: growth protocol

value: grown with 20 mM agmatine

label: DyLight 550

source_name: Lactococcus lactis subsp. cremoris CECT 8666 grown without agmatine

value: grown without agmatine


title: CECT 8666 + Agm (test) compared to CECT 8666 (reference) Replicate 2

description: Technical replicate 2 of 3.


title: CECT 8666 + Agm (test) compared to CECT 8666 (reference) Replicate 3

description: Technical replicate 3 of 3.


title: LGWU703286-1036398WU

source_name: Breast Tumor CALGB 703286

tag: gender

value: female

tag: tissue type

value: Breast Tumor

tag: fixative

value: Formalin-Fixed Paraffin Embedded Tissue


title: Cartilage_exercise-2d_rep2

value: Sprague-Dawley

value: 12-14 weeks old

tag: treatment

value: exercised

tag: tissue

value: articular cartilage


title: CECT 8666 + Agm (test) compared to CECT 8666 (reference) Replicate 4

description: Biological replicate 1 of 2.


title: cad_2_mixtox70_Cy3

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

description:
raw data: mixtox70.txt: Cy3
X13
used in analysis: YES

hyb_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red & Green and PMT is set to 100%.

scan_protocol: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 042279_D_F_20120723) to obtain mean Red or Green intensities and median Red or Green background intensities. In limma, edwards method for background correction was used (offset = 30), and global loess normalizing was done.

data_processing: background corrected (edwards method, min. offset at 30) loess normalized, log transformed intensities

organism: Folsomia candida

source_name: total RNA from 30 animals, cad_2

label_protocol: 825 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 4x180k format for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm)  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), washed in acetonitril for 10 seconds, then dried immediately by air.

growth_protocol: Approximately 30 adults individuals were exposed in glass vials containing ~30 g of soil at 50% of the soil WHC. Exposure was done at same conditions as incubation. After exposure the animals were extracted from soil with tap water and snap frozen in liquid N2

extract_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Low Input Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer's guidelines followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Total RNA was extracted from all animals, using the SV Total RNA isolation System (Promega).

tag: developmental stage

value: adult

tag: growth medium

value: LUFA2.2 control soil


title: phe_2_mixtox71_Cy3

description:
raw data: mixtox71.txt: Cy3
X3
used in analysis: YES

source_name: total RNA from 30 animals, phe_2


title: cad_4_mixtox72_Cy3

description:
raw data: mixtox72.txt: Cy3
X25
used in analysis: YES

source_name: total RNA from 30 animals, cad_4


title: cad_1_mixtox65_Cy3

description:
raw data: mixtox65.txt: Cy3
X7
used in analysis: YES

source_name: total RNA from 30 animals, cad_1


title: control_mixtox69_Cy3

description:
raw data: mixtox69.txt: Cy3
X1
used in analysis: YES

source_name: total RNA from 30 animals, control


title: Cartilage_control_rep2


title: phe_3_mixtox64_Cy5

description:
raw data: mixtox64.txt: Cy5
X4
used in analysis: YES

source_name: total RNA from 30 animals, phe_3


title: phe_4_mixtox67_Cy3

description:
raw data: mixtox67.txt: Cy3
X5
used in analysis: YES

source_name: total RNA from 30 animals, phe_4


title: phe_1_mixtox60_Cy3

description:
raw data: mixtox60.txt: Cy3
X2
used in analysis: YES

source_name: total RNA from 30 animals, phe_1


title: cad_2_mixtox55_Cy5

description:
raw data: mixtox55.txt: Cy5
X13
used in analysis: YES


title: cad_3_mixtox58herh_Cy3

description:
raw data: mixtox58herh.txt: Cy3
X19
used in analysis: YES

source_name: total RNA from 30 animals, cad_3


title: phe_2_mixtox56_Cy5

description:
raw data: mixtox56.txt: Cy5
X3
used in analysis: YES


title: E12.5 mutant_1

source_name: whole cortex e12.5

value: mixed background

tag: genotype

value: Pbx1 mutant

value: cortext


title: LSCC tumor tissue specimen C28

source_name: LSCC tumor tissue specimen

value: LSCC tumor tissue specimen


title: CECT 8666 + Agm (test) compared to CECT 8666 (reference) Replicate 1

description: Technical replicate 1 of 3.

value: CECT 8666


title: phe_5_mixtox58herh_Cy5

description:
raw data: mixtox58herh.txt: Cy5
X6
used in analysis: YES

source_name: total RNA from 30 animals, phe_5


title: cad_4_mixtox57_Cy5

description:
raw data: mixtox57.txt: Cy5
X25
used in analysis: YES


title: cad_5_mixtox53_Cy3

description:
raw data: mixtox53.txt: Cy3
X31
used in analysis: YES

source_name: total RNA from 30 animals, cad_5


title: phe_1_mixtox45_Cy5

description:
raw data: mixtox45.txt: Cy5
X2
used in analysis: YES


title: phe_4_mixtox52_Cy5

description:
raw data: mixtox52.txt: Cy5
X5
used in analysis: YES


title: control_mixtox54_Cy5

description:
raw data: mixtox54.txt: Cy5
X1
used in analysis: YES


title: cad_1_mixtox50_Cy5

description:
raw data: mixtox50.txt: Cy5
X7
used in analysis: YES


title: phe_3_mixtox43_Cy3

description:
raw data: mixtox43.txt: Cy3
X4
used in analysis: YES


title: phe_5_mixtox37_Cy3

description:
raw data: mixtox37.txt: Cy3
X6
used in analysis: YES


title: phe_2_mixtox35_Cy3

description:
raw data: mixtox35.txt: Cy3
X3
used in analysis: YES


title: cad_5_mixtox38_Cy5

description:
raw data: mixtox38.txt: Cy5
X31
used in analysis: YES


title: cad_3_mixtox43_Cy5

description:
raw data: mixtox43.txt: Cy5
X19
used in analysis: YES


title: cad_4_mixtox35_Cy5

description:
raw data: mixtox35.txt: Cy5
X25
used in analysis: YES


title: phe_5_mixtox36_Cy5

description:
raw data: mixtox36.txt: Cy5
X6
used in analysis: YES


title: cad_4_mixtox36_Cy3

description:
raw data: mixtox36.txt: Cy3
X25
used in analysis: YES


title: phe_2_mixtox34_Cy5

description:
raw data: mixtox34.txt: Cy5
X3
used in analysis: YES


title: control_mixtox33_Cy3

description:
raw data: mixtox33.txt: Cy3
X1
used in analysis: YES


title: cad_2_mixtox33_Cy5

description:
raw data: mixtox33.txt: Cy5
X13
used in analysis: YES


title: cad_3_mixtox21_Cy5

description:
raw data: mixtox21.txt: Cy5
X19
used in analysis: YES


title: cad_5_mixtox17_Cy3

description:
raw data: mixtox17.txt: Cy3
X31
used in analysis: YES


title: cad_3_mixtox22_Cy3

description:
raw data: mixtox22.txt: Cy3
X19
used in analysis: YES


title: phe_3_mixtox6_Cy5

description:
raw data: mixtox6.txt: Cy5
X4
used in analysis: YES


title: cad_5_mixtox16_Cy5

description:
raw data: mixtox16.txt: Cy5
X31
used in analysis: YES


title: phe_3_mixtox7_Cy3

description:
raw data: mixtox7.txt: Cy3
X4
used in analysis: YES


title: cad_1_mixtox28_Cy5

description:
raw data: mixtox28.txt: Cy5
X7
used in analysis: YES


title: phe_1_mixtox23_Cy5

description:
raw data: mixtox23.txt: Cy5
X2
used in analysis: YES


title: control_mixtox32_Cy5

description:
raw data: mixtox32.txt: Cy5
X1
used in analysis: YES


title: phe_1_mixtox24_Cy3

description:
raw data: mixtox24.txt: Cy3
X2
used in analysis: YES


title: phe_4_mixtox31_Cy3

description:
raw data: mixtox31.txt: Cy3
X5
used in analysis: YES


title: cad_2_mixtox34_Cy3

description:
raw data: mixtox34.txt: Cy3
X13
used in analysis: YES


title: phe_5_mixtox1_Cy3

description:
raw data: mixtox1.txt: Cy3
X6
used in analysis: YES


title: cad_1_mixtox29_Cy3

description:
raw data: mixtox29.txt: Cy3
X7
used in analysis: YES


title: phe_4_mixtox30herh_Cy5

description:
raw data: mixtox30herh.txt: Cy5
X5
used in analysis: YES


title: BT-474-TDM-1-4

city: Charlestown

first: Kamila

last: Naxerova

state: MA

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

hyb_protocol: According to the manufacturer's instructions (Affymetrix)

data_processing: Transcript level normaliztion, RMA, Bioconductor's oligo package (v.1.30.0)

growth_protocol: 8-week old female nude mice were anesthesized with ketamine (90mg/kg BW) and xylazine (9mg/kg BW) and implanted with a 0.36-mg, 60-d or 90-d release 17β-estradiol pellet (Innovative Research of America, Sarasota, FL) 24h before implantation of tumor cells and every 60/90d thereafter. 100,000 BT474-Gluc cells diluted in 1 μL PBS were stereotactically injected in the left frontal lobe of the mice. Mice were randomized prior to treatment initiation when the tumor volume reached 5-6 mm3.

extract_protocol: BT474-Gluc brain tumors were snap-frozen 48h post treatment with trastuzumab or T-DM1 (15mg/kg), then cryopulverized and immediately lysed in Buffer RLT supplemented with beta-mercaptoethanol.  RNA was extracted using the RNeasy Mini kit (Qiagen Valencia, CA) with on-column DNaseI digestion.  After initial quality control, RNA was subjected to in-solution DNaseI treatment and purified using the RNeasy MinElute Kit (Qiagen).  Final determination of RNA quality was performed using the Agilent Bioanalyzer.

treatment_protocol: Tissues were collected 48h after a single treatment with trastuzumab or T-DM1 at the same dose (15mg/kg)

value: Xenograft tissue

tag: host strain info

value: 8-wk-old female nude mice

tag: cell type

value: BT-474 human breast carcinoma cells growing in murine brain

tag: treated with

tag: time point

value: 48h after a single treatment


title: BT-474-Trastuzumab-3

scan_protocol: According to the manufacturer's instructions (Affymetrix)

tag: sample type

value: Trastuzumab


title: BT-474-TDM-1-2

label_protocol: According to the manufacturer's instructions (Affymetrix)


title: BT-474-Trastuzumab-4


title: WHIM12 siZNF165 TGFB Treated Replicate3

city: Dallas

first: Angelique

last: Whitehurst

address: 5323 Harry Hines Blvd.

department: Simmons Cancer Center

institute: UT Southwestern

description: Gene expression data from siZNF165 transfected and TGFB treated WHIM12 cells

hyb_protocol: Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays.

scan_protocol: Hybridization, washing, staining and scanning of the Affymtrix peg plate arrays was carried out using the Affymetrin GeneTitan MC Instrument.

data_processing: Affymetrix Expression Console Software was used for basic data analysis and quality control (RMA normalization).

source_name: WHIM12 cells transfected with ZNF165 siRNA treated with TGFB

label_protocol: The WT Expression HT Kit for Robotics (Ambion) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip HT Terminal Labeling Kit.

growth_protocol: SUM159 and WHIM12 cells were grown in the F12, (Gibco) and MEM (Gibco), respectively, and split 1:3 every two days.

extract_protocol: Total RNA was isolated using Sigma GenElute RNA Isolation Kit

treatment_protocol: SUM159 and WHIM12 cells were reverse transfected with Dharmacon SMART siRNA pools in 6 well dishes. For SUM159 cells, 60 hours post transfection, cells were treated with either vehicle or 10ng/mL TGFB for 3 hours. For WHIM12 cells, 48 hours post transfection, cells were treated with either vehicle or 10ng/mL TGFB for 3 hours.

tag: tumor-derived cell line

tag: transfection

value: ZNF165 siRNA

value: TGFB


title: BT-474-Trastuzumab-1


title: WHIM12 siCNTL Vehicle Treated Replicate2

description: Gene expression data from control transfected and vehicle treated WHIM12 cells

source_name: WHIM12 cells transfected with CNTL siRNA

value: CNTL siRNA

value: vehicle


title: WHIM12 siZNF165 Vehicle Treated Replicate1

description: Gene expression data from siZNF165 transfected and vehicle treated WHIM12 cells

source_name: WHIM12 cells transfected with ZNF165 siRNA


title: BT-474-TDM-1-1


title: WHIM12 siZNF165 Vehicle Treated Replicate2


title: WHIM12 siCNTL Vehicle Treated Replicate3


title: WHIM12 siCNTL TGFB Treated Replicate3

description: Gene expression data from control transfected and TGFB treated WHIM12 cells

source_name: WHIM12 cells transfected with CNTL siRNA treated with TGFB


title: WHIM12 siZNF165 Vehicle Treated Replicate3


title: WHIM12 siZNF165 TGFB Treated Replicate1


title: BT-474-Trastuzumab-2


title: SUM159 siZNF165 Vehicle Treated Replicate3

description: Gene expression data from siZNF165 transfected and vehicle treated SUM159 cells

source_name: SUM159 cells transfected with ZNF165 siRNA

treatment_protocol: SUM159 and WHIM12 cells were reverse transfected with Dharmacon SMART siRNA pools in 6 well dishes. For SUM159 cells, 60 hours post transfection, cells were treated with either vehicle or 10ng/mL TGFB for 3 hours. Total RNA was collected from SUM159 cells sixty three hours post transfection. Total RNA was collected from WHIM12 cells forty eight hours post transfection.


title: WHIM12 siCNTL TGFB Treated Replicate2


title: WHIM12 siZNF165 TGFB Treated Replicate2


title: BT-474-TDM-1-3


title: SUM159 siZNF165 TGFB Treated Replicate2

description: Gene expression data from siZNF165 transfected and TGFB treated SUM159 cells

source_name: SUM159 cells transfected with ZNF165 siRNA treated with TGFB


title: WHIM12 siCNTL TGFB Treated Replicate1


title: SUM159 siZNF165 Vehicle Treated Replicate2


title: SUM159 siCNTL TGFB Treated Replicate3

description: Gene expression data from control transfected and TGFB treated SUM159 cells

source_name: SUM159 cells transfected with CNTL siRNA treated with TGFB


title: WHIM12 siCNTL Vehicle Treated Replicate1


title: SUM159 siCNTL TGFB Treated Replicate2


title: SUM159 siZNF165 TGFB Treated Replicate3


title: SUM159 siCNTL Vehicle Treated Replicate1

description: Gene expression data from control transfected and vehicle treated SUM159 cells

source_name: SUM159 cells transfected with CNTL siRNA


title: SUM159 siCNTL Vehicle Treated Replicate3


title: SUM159 siCNTL TGFB Treated Replicate1


title: SUM159 siCNTL Vehicle Treated Replicate2


title: SUM159 siZNF165 TGFB Treated Replicate1


title: ConditionalKnockOut Ezh2 Replicate3

city: Zurich

first: Martina

last: Zemke

address: Winterthurerstrassse 190

department: Institute of Anatomy

institute: University Zurich

description: ConditionalKnockOut Ezh2 Replicate3

hyb_protocol: 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).

scan_protocol: Standard Affymetrix procedures using a Hewlett-Packard scanner

data_processing: Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the Robust Multichip Average (RMA) method.

source_name: Midbrain

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.

extract_protocol: Tissue dissection followed by RNA isolation with the RNAeasy kit (Qiagen) and RNase-Free DNase Set (79254, Qiagen).

treatment_protocol: wildtype vs genetic knock-out midbrain tissue of E10.5 mouse embryos

tag: strain

value: Conditonal KO Ezh2

value: midbrain


title: FOXC2-KD LEC in static, biological rep2

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: Gene expression data from FOXC2-KD human intestinal LEC grown in static conditions

hyb_protocol: Affymetrix Human Gene 1.0 ST arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 2.7μg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: The data was corrected for batch effect with the COMBAT method, which adjusts for known batches using an empirical Bayes framework , and was normalized using Robust Multichip Average (method Bioconductor package  affy, R version 3.0.1).

source_name: Human intestinal lymphatic endothelial cells isolated from jejunum

label_protocol: For each sample, 100ng of total RNA were amplified using the WT sense strand Target Labelling kit (Affymetrix, Cat.no. 900223); 5.5μg of the resulting sense cDNA was fragmented by UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip® WT Terminal labelling kit (Affymetrix Cat.no. 900671, Santa Clara, USA).

growth_protocol: Human intestinal lymphatic endothelial cells were isolated from jejunum as described (Norrmen et al, 2010, Blood). Cells were grown on plates coated with 0.5 µg/cm2 fibronectin (Roche) in EBM-2 complete medium (Lonza).

extract_protocol: Cells were collected with a 30-min trypsin treatment at 37°C, followed by trypsin inactivation by diluting 7x in complete medium. Cells were lysed in RLT buffer (Qiagen) and total RNA was extracted using the Qiagen RNeasy Micro Kit.

treatment_protocol: Cells were seeded at 30’000 cells/cm2 and transfected 18 hours later with 33 nM siRNA using Lipofectamine RNAiMAX (Invitrogen). Two different sIRNAs were used to knockdown FOXC2: AGGUGGUGAUCAAGAGCGAUU or CAACGUGCGGGAGAUGUUCUU (ThermoScientific). AllStars Negative Control siRNA (Qiagen) was used as a control.  Cells were collected 6 hours post-transfection by trypsin-treatment, and seeded at confluency (50’000 cells/cm2) on microfluidic chamber slides (µ-Slide I-0.8 Luer, ibidi) pre-coated with 3 µg/cm2 fibronectin.  Cells were allowed to attach for 24 hours, and then subjected to oscillatory flow (1 dyn/cm2, 1/4 Hz) in a parallel-plate flow-chamber system (ibidi Pump System, ibidi), or kept under static conditions as a control, for 24 hours.

value: FOXC2 siRNAs

value: static


title: ConditionalKnockOut Ezh2 Replicate2

description: ConditionalKnockOut Ezh2 Replicate2


title: SUM159 siZNF165 Vehicle Treated Replicate1


title: Control Mice Replicate3

description: Control Mice Replicate3

value: WT


title: FOXC2-KD LEC in oscillatory, biological rep2

description: Gene expression data from FOXC2-KD human intestinal LEC grown in oscillatory conditions

value: Human intestinal lymphatic endothelial cells

value: 24-hour oscillatory shear stress (1 dyn/cm2; 1/4 Hz)


title: Control Mice Replicate2

description: Control Mice Replicate2


title: FOXC2-KD LEC in oscillatory, biological rep1


title: control LEC in oscillatory, biological rep1

description: Gene expression data from control human intestinal LEC grown in oscillatory conditions

value: control


title: undifferentiated

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: total RNA (>200 nt)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in a GeneChip 3000 scanner with G7 update.

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

source_name: THP-1 untreated

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

growth_protocol: THP-1 human monocytic leukemia cells were maintained in RPMI-1640 + 10% FBS (foetal bovine serum) supplemented with 1% penicillin and streptomycin. The cells were cultured in a humidified atmosphere with 5% CO2 at 37°C .

extract_protocol: RNA isolation from cell lines was performed using TRI Reagent (Sigma). Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific). RNA integrity was assessed using the Agilent Bioanalyzer nano chip.

treatment_protocol: Undifferentiated cells were seeded in 96-well plates containing medium. For PMA differentiation THP-1 cells were seeded in 96-well plates containing medium with 200 nM PMA. For 3 days differentiation medium was replaced (PMA free) after 24 hours, cells were cultivated for 3 further days. For 8 days differentiation medium was replaced (PMA free) after 72 hours, cells were cultivated for 5 further days. Medium was replaced by medium containing 2 % FBS, 16 hours later RNA was isolated.

tag: cell line

value: undifferentiated


title: FOXC2-KD LEC in static, biological rep1


title: WT EMCV mouse 2

status: Public on Nov 08 2015

city: Rochester

first: Meghan

middle: M

last: Painter

state: MN

address: 200 1st St SW

department: Mayo Graduate School of Medicine

institute: Mayo Clinic

description: Gene expression data from mouse spinal cord

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

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

data_processing:
Raw data from cell intensity files (.cel) were analyzed with Partek GS 6.6 software (St. Louis, MO) using Partek's standard GCRMA normalization algorithm.
Student's unpaired t-test was used to determine statistical significance.

source_name: Mouse spinal cord tissue homogenate

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

growth_protocol: Mice were maintained under standard housing conditions  using a light schedule of 14 h on and 10 h off at a temperature of 28.5°C. Fish were fed  twice daily using a combination of dry food and brine shrimp.

extract_protocol: Spinal cords were removed, flash frozen on dry ice, and RNA was harvested using Qiagen RNeasy mini kit according to the manufacturer's protocol.

treatment_protocol: Mice were euthanized in accordance with animal protocols approved by the Mayo Institutional Animal Care and Use Committee which are consistent with National Institutes of Health guidelines for the care and use of animals.

value: FVB

tag: Sex

value: Male

tag: viral infection status

value: EMCV

tag: age

value: adult >8 weeks


title: control LEC in oscillatory, biological rep2

tag: treatment


title: ConditionalKnockOut Ezh2 Replicate1

description: ConditionalKnockOut Ezh2 Replicate1

tag: tissue


title: Control Mice Replicate1

description: Control Mice Replicate1

tag: developmental stage


title: control LEC in static, biological rep2

description: Gene expression data from control human intestinal LEC grown in static conditions


title: 3 days PMA differentiated

description: total RNA (>200 nt)

source_name: THP-1 differentiated with PMA for 3 days

value: 3 days PMA differentiated


title: 8 days PMA differentiated

description: total RNA (>200 nt)

source_name: THP-1 differentiated with PMA for 8 days

value: 8 days PMA differentiated


title: WT mouse 2

value: No


title: RdRP EMCV mouse 2

value: RdRP

value: Female


title: WT mouse 1


title: WT mouse 3


title: WT EMCV mouse 1


title: WT mouse 2


title: WT mouse 1


title: control LEC in static, biological rep1


title: RdRP mouse 1


title: RdRP mouse 3


title: RdRP mouse 2


title: THP1_Null_2

description: Gene expression data from THP1 monocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 GeneChip Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: THP1 Null

growth_protocol: THP-1 cells (ATCC TIB-202) were cultured in RPMI with glutamine + 10%FBS + 100U/ml Penicillin + 10mM HEPES + 1X MEM-NEAA   using a light schedule of 14 h on and 10 h off at a temperature of 28.5°C. Fish were fed  twice daily using a combination of dry food and brine shrimp.

extract_protocol: Duplicate samples of each cell line were pelleted, flash frozen on dry ice, and RNA was harvested using Qiagen RNeasy mini kit according to the manufacturer's protocol.

treatment_protocol: RT-normalized amounts of lentiviral vector were used to transduce THP-1 cells. Transduced cells were selected in puromycin (3µg/ml) for approximately 2 weeks to produce stable cell lines expressing different mutant forms of the RdRP transgene.

value: THP1 monocytes

tag: genotype/variation

value: Empty vector


title: THP1_Null_1


title: THP1_RdRP∆cat_2

source_name: THP1 RdRP∆cat

value: RdRP∆cat mutant transgene


title: THP1_RdRP∆rna_1

source_name: THP1 RdRP∆rna

value: RdRP∆rna mutant transgene


title: THP1_RdRP∆cat_1


title: THP1_RdRP∆rna_2


title: THP1_RdRP_2

source_name: THP1 RdRP

value: Wildtype RdRP transgene


title: VSMCs in Calcification media for 3 days rep.2 / VSMCs in Growth media rep.2

status: Public on Nov 07 2015

city: Hwasun

first: Nakwon

last: Choe

state: Seoyang-ro 322

address: Baekseo-ro 160

department: Pharmacology

country: South Korea

institute: Chonnam Univ. Med. Sch.

hyb_protocol: Agilent’s Gene Expression Hybridization Kit was used for labeling hybridization.

scan_protocol: Agilent’s DNA microarray scanner and Feature Extraction Software was used for scaning and data acquisition.

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction, and GeneSpringGX v7.3 Software was used for LOWESS normalization.
Reliable genes (flag-out in 2 of 4 arrays ) 18,112 genes selected

source_name: Rat VSMCs in Growth media rep.2

label_protocol: Agilent’s Agilent’s Low RNA Input Linear Amplification kit PLUS was used for labeling.

growth_protocol: VSMCs were grown in 10% FBS in DMEM supplemented with antibiotics at 37C, 5 %CO2, >80 %humidity.

extract_protocol: Total RNA was extracted using Trizol reagent following manufacturer's protocol. Quality was monitored using Agilent 2100 Bioanalyzer.

treatment_protocol: Calcification was induced in VSMCs with inorganic phosphate (2mmole/L).

tag: gender

value: male

value: 6 weeks

value: Aorta

value: Sprague-Dawley 400

source_name: Rat VSMCs in Calcification media for 3 days rep.2


title: VSMCs in Calcification media for 6 days rep.2 / VSMCs in Growth media rep.2

source_name: Rat VSMCs in Calcification media for 6 days rep.2


title: THP1_RdRP_1


title: 25D

city: Nanjing

first: Xiaohong

last: jiang

state: Jiangsu

address: Xianlin Road

country: China

institute: Nanjing university

description: inguinal  adipose tissues from control mice

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

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

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

source_name: ad libitum inguinal adipose tissues

growth_protocol: inguinal adipose from male C57BL/6J mice

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

treatment_protocol: mice were fasted or cold exposure for 24h

value: inguinal adipose


title: VSMCs in Calcification media for 6 days rep.1 / VSMCs in Growth media rep.1

source_name: Rat VSMCs in Growth media rep.1

source_name: Rat VSMCs in Calcification media for 6 days rep.1


title: VSMCs in Calcification media for 3 days rep.1 / VSMCs in Growth media rep.1

source_name: Rat VSMCs in Calcification media for 3 days rep.1


title: 4D

description: inguinal adipose tissues from cold exposure mice

source_name: 24h-cold exposure adipose tissues


title: PAXgene for patient 11-0543

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

data_processing: Agilent Feature Extraction Software (v 11.5) was used for background subtraction

source_name: PAXgene,whole blood

tag: patient id

value: Male

tag: race

value: North Africa

tag: fasting blood

value: yes

tag: patient/control

value: patient

value: whole blood

value: PBMC

value: unstimulated


title: PAXgene for patient 11-0462

value: Europe

tag: cell type


title: PAXgene for patient 11-0669

value: Female


title: PAXgene for patient 11-0581

value: North-East Asia


title: PAXgene for patient 11-0597


title: PAXgene for patient 11-0764


title: PAXgene for patient 11-0365


title: PAXgene for patient 11-0649

value: Other


title: PAXgene for patient 11-0491


title: RdRP EMCV mouse 1

value: FVB

tag: genotype

value: RdRP

value: EMCV

value: adult >8 weeks


title: PAXgene for patient 11-0391


title: PAXgene for patient 11-0497


title: PAXgene for patient 11-0639


title: 25F

description: inguinal adipose tissues from fasted mice

source_name: 24-fasted inguinal adipose tissues

value: male


title: PAXgene for patient 11-0696


title: PAXgene for patient 11-0729


title: PAXgene for patient 11-0646


title: PAXgene for patient 11-0676


title: PAXgene for patient 11-0728


title: PAXgene for patient 11-0648


title: PAXgene for patient 11-0726


title: PAXgene for patient 11-0612


title: _12_120min_0_5pct_F2

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

description: 0.5%ETOH 120min

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing:
Raw data: Probe-level .pair files
Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the standard normalization algorithm (Loess) within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Acetivibrio thermocellus ATCC 27405

growth_protocol: Batch fermentations were conducted in approximately 5 L of MTC medium in 7.5-L BioFlo110 bioreactors (New Brunswick Scientific, Edison, NJ) fitted with agitation, pH, and temperature  probes and controls as described previously (Yang et al., 2008).

extract_protocol: RNA was isolated essentially described previously [26]. Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

tag: agent

value: EtOH

tag: time

tag: array

tag: intensity

value: PM


title: PAXgene for patient 11-0750


title: _13_120min_0_5pct_F4

description: 0.5%ETOH 120min

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: PAXgene for patient 11-0763

value: Male


title: PAXgene for patient 11-0682

value: yes


title: _4_30min_0_5pct_F2

description: 0.5%ETOH 30min

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: PAXgene for patient 11-0656

value: patient


title: PAXgene for patient 11-0711

value: whole blood


title: PAXgene for patient 11-0702

value: PBMC


title: _7_60min_0pct_F3

description: 0.0%ETOH 60min ctl

source_name: Control

value: control


title: PAXgene for patient 11-0508

value: unstimulated


title: PAXgene for patient 11-0603


title: _1_30min_0pct_F1

description: 0%ETOH 30 min


title: _8_60min_0_5pct_F2

description: 0.5%ETOH 60min


title: PAXgene for patient 11-0588

value: Female

value: Europe


title: _9_60min_0_5pct_F4

description: 0.5%ETOH 60min


title: PAXgene for patient 11-0731

value: Other


title: _5_30min_0_5pct_F4

description: 0.5%ETOH 30min


title: _2_30min_0pct_F1

description: 0%ETOH 30 min


title: _11_60min_0_5pct_F2

description: 0.5%ETOH 60min


title: _10_60min_0_5pct_F4

description: 0.5%ETOH 60min


title: PAXgene for patient 11-0565

value: North-East Asia


title: PAXgene for patient 11-0732


title: PAXgene for patient 11-0674


title: PAXgene for patient 11-0476


title: _6_60min_0pct_F1

description: 0.0%ETOH 60min ctl


title: PAXgene for patient 11-0600


title: PAXgene for patient 11-0609


title: yw fly_rep3

city: Stanford

first: Chenggang

last: Lu

address: 279 Campus Drive

institute: Stanford University

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

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

data_processing: Data were background adjusted and normalized using R program (v3.0.2) with the BioConductor package GCRMA.

organism: Drosophila melanogaster

source_name: 1 day old adult testes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~250ng total RNA (GeneChip 3' IVT expression kit)

growth_protocol: Crosses and experimental flies were grown on cornmeal and molasses media at 25 °C

treatment_protocol: testes without seminal vesicle and accessory glands were dissected in PBS for 30 minutes and immediately frozen in liquid nitrogen before transferred to -80°C. Total RNA was extracted using TRIzol (Invitrogen).  RNA quality was assessed by checking rRNA integrity using Bioanalyzer. ~250ngs of total RNA was processed for each replicate.

value: 1 day old adult

value: testis

value: y,w mutant


title: PAXgene for patient 11-0621


title: yw fly_rep2


title: PAXgene for patient 11-0709


title: PAXgene for patient 11-0446


title: sa1/sa2 mutant fly_rep3

value: sa1/sa2 mutant


title: PAXgene for patient 11-0730


title: PAXgene for patient 11-0574


title: yw fly_rep1


title: PAXgene for patient 11-0767


title: PAXgene for patient 11-0605


title: PAXgene for patient 11-0512


title: sa1/sa2 mutant fly_rep2


title: PAXgene for patient 11-0562


title: PAXgene for patient 11-0629


title: PAXgene for patient 11-0654


title: PAXgene for patient 11-0510


title: PAXgene for patient 11-0517


title: PAXgene for patient 11-0756


title: PAXgene for patient 11-0757


title: PAXgene for patient 11-0573


title: PAXgene for patient 11-0736


title: PAXgene for patient 11-0660


title: PAXgene for patient 11-0691


title: PAXgene for patient 11-0480


title: PAXgene for patient 11-0584


title: PAXgene for patient 11-0439


title: PAXgene for patient 11-0490


title: PAXgene for patient 11-0701


title: PAXgene for patient 11-0415


title: PAXgene for patient 11-0738


title: PAXgene for patient 11-0632


title: aly2/aly5P mutant fly_rep2

value: aly2/aly5P mutant


title: aly2/aly5P mutant fly_rep3


title: aly2/aly5P mutant fly_rep1


title: PAXgene for patient 11-0548


title: Med22RNAi_rep1

value: bam-gal4; Med22RNAi


title: sa1/sa2 mutant fly_rep1


title: Med22RNAi_rep3


title: Med22RNAi_rep2


title: PAXgene for patient 11-0741

value: Male


title: PAXgene for patient 11-0529

value: yes


title: PAXgene for patient 11-0607

value: patient


title: NNI-8 [4310479204_F]

city: Singapore

first: Edwin

last: Sandanaraj

address: 11 Jalan Tan Tock Seng

department: Research

country: Singapore

institute: NNI

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation on exonic probesets with lumi packages in R

source_name: Primary neurosphere

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina HumanRef-8 v2 Expression Beadchip

growth_protocol: Graded brain tumor specimens were obtained with informed consent, as part of a study protocol approved by the SingHealth Centralised Institutional Review Board A. GPC lines were described in our previous work. Briefly, cells were seeded as free-floating spheres at a density of 2,500 cells per cm2 in chemically defined serum-free growth medium containing basic fibroblast growth factor (bFGF; 20 ng/ml; PeproTech, New Jersey), epidermal growth factor (EGF; 20 ng/ml; PeproTech), heparin (5 μg/ml; Sigma-Aldrich, St Louis), and serumfree supplement (B27; 1x; Gibco, Grand Island, NY) in a 3:1 mix of Dulbecco’s modified Eagle’s medium (DMEM; Sigma-Aldrich) and Ham’s F-12 Nutrient Mixture (F-12; Gibco). Neurospheres were mechanically triturated with a flame-drawn glass Pasteur pipette twice weekly and re-seeded in fresh culture medium

extract_protocol: Total RNA was isolated from tumor neurospheres using TRI Reagent (Molecular Research Center, Cincinnati, OH). Thereafter, RNA samples were hybridized to Illumina HumanRef-8 v2 Expression Beadchip Array.

tag: pna

tag: histology

value: Anaplastic Oligodendroglioma

tag: grade

value: III

tag: replicate

value: F


title: NNI-8 [4310479204_E]

value: E


title: NNI-8 [4310479110_F]


title: NNI-8 [4310479204_G]

value: G


title: PAXgene for patient 11-0688

tag: age

value: Europe

tag: tissue

value: whole blood

value: PBMC

tag: treatment

value: unstimulated


title: NNI-8 [4310479110_G]


title: NNI-2 [4891461004_G]

value: GBM

value: IV


title: NNI-2 [4891461004_F]


title: NNI-8 [4310479110_E]


title: NNI-2 [4891461004_E]


title: NNI-2 [4891461004_H]

value: H


title: NNI-4 [4891461004_D]

value: D


title: PAXgene for patient 11-0604

tag: patient id

tag: gender

value: Female


title: PAXgene for patient 11-0435

tag: race

tag: fasting blood


title: PAXgene for patient 11-0352

tag: patient/control

tag: cell type


title: NNI-4 [4891461004_C]

value: C


title: NNI-12_35551 [AFG1196-29b]

description: Gene expression data from ST3GAL1 KD Clone(35551) Glioma Propagating Cells(GPCs)

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix scanning protocol

data_processing: The data were processed using mas5 scaled(SF=500) and log2 transformed in R2.14. Probesets with A calls across all samples were trimmed off.

label_protocol: Affymetrix standard labelling protocol

extract_protocol: Total RNA was isolated from tumor neurospheres using TRI Reagent  (Molecular Research Center, Cincinnati, OH). Thereafter, RNA samples were hybridized to  Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array using 3' IVT express kit  (Affymetrix Inc, Santa Clara, California).

treatment_protocol: Total RNA was isolated from glioma neurospheres non-treated and ST3GAL1 knock-down clone(35551)  (Molecular Research Center, Cincinnati, OH). Thereafter, RNA samples were hybridized to  Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array using 3' IVT express kit  (Affymetrix Inc, Santa Clara, California).

value: Glioblastoma multiforme


title: NNI-11_35551 [AFG1196-26b]


title: PAXgene for patient 11-0416

value: Male

value: yes

value: patient


title: NNI-2 [4891461005_H]


title: PAXgene for patient 11-0666


title: NNI-2 [4891461005_G]


title: PAXgene for patient 11-0640


title: NNI-4 [4891461004_B]

value: B


title: NNI-11_35551 [AFG1196-26a]


title: NNI-4 [4891461005_C]


title: NNI-4 [4891461005_B]


title: PAXgene for patient 11-0713


title: NNI-12_35551 [AFG1196-29a]


title: NNI-2 [4891461005_F]

value: F


title: NNI-8_35551 [AFG1196-23b]

value: Anaplastic oligoastrocytoma

value: III


title: NNI-8 [4310479108_H]

value: Anaplastic Oligodendroglioma


title: NNI-4 [4891461005_D]


title: PAXgene for patient 11-0613

value: Europe

value: whole blood

value: PBMC


title: PAXgene for patient 11-0514

value: unstimulated


title: NNI-2 [4891461005_E]

value: GBM

value: IV

value: E


title: NNI-1 [4310479108_D]

value: D


title: PAXgene for patient 11-0753


title: PAXgene for patient 11-0707

value: Female


title: NNI-1 [4310479108_A]

value: A


title: Klrc1_ECTV_biological_rep3

city: Saint Louis

first: Aaron

last: Rapaport

state: Missouri

address: 660 South Euclid Avenue, Box 8118, BJCIH 8107, Colonna Lab

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Gene expression data from virus-specific CD8+ T cells

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

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: Tetramer-positive splenic CD8+ T cells, 6 days post-infection

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 500pg-50 ng total RNA

extract_protocol: All RNA was extracted with RNeasy Plus Micro Kit (Qiagen).

treatment_protocol: For naïve samples, total splenic CD3+CD8+ lymphocytes were sorted by flow cytometry directly into RLT buffer.  For virus-specific samples, B8RH2Kb+CD3+CD8+ lymphocytes were sorted by flow cytometry directly into RLT buffer.

tag: background strain

tag: genotype/variation

tag: cell population

value: Tetramer-positive splenic CD8+ T cells


title: NNI-1 [4310479108_B]


title: PAXgene for patient 11-0461

value: Male

value: North America

value: yes

value: patient


title: NNI-4_35551 [AFG1196-20a]

value: Glioblastoma multiforme


title: PAXgene for patient 11-0678


title: PAXgene for patient 11-0635

value: North-East Asia


title: NNI-1 [4310479116_D]


title: NNI-12_NT [AFG1196-28b]

description: Gene expression data from Non-Treated(NT) Glioma Propagating Cells(GPCs)


title: PAXgene for patient 11-0755

value: Europe


title: NNI-1 [4310479108_C]

value: C


title: NNI-2_35551 [AFG1196-17a]


title: NNI-8_35551 [AFG1196-23a]

value: Anaplastic oligoastrocytoma

value: III


title: Klrc1_ECTV_biological_rep1


title: NNI-11_NT [AFG1196-25b]


title: NNI-2_35551 [AFG1196-17b]


title: NNI-4_35551 [AFG1196-20b]


title: Klrc1_ECTV_biological_rep2


title: NNI-12_NT [AFG1196-28a]


title: Klrc1_ECTV_biological_rep4


title: WT_ECTV_biological_rep3

value: Wild Type


title: NNI-8 [4310479116_H]

value: Anaplastic Oligodendroglioma

value: H


title: WT_ECTV_biological_rep4


title: PAXgene for patient 11-0599

value: whole blood

value: PBMC

value: unstimulated


title: PAXgene for patient 11-0561

value: Other


title: PAXgene for patient 11-0345

value: Male


title: NNI-1 [4310479116_B]

value: GBM

value: IV

value: B


title: NNI-8_NT [AFG1196-22b]


title: NNI-11_NT [AFG1196-25a]

value: Glioblastoma multiforme


title: WT_ECTV_biological_rep2

value: Tetramer-positive splenic CD8+ T cells


title: NNI-1 [4310479116_A]

value: A


title: PAXgene for patient 11-0590

value: Female

value: North-East Asia

value: yes

value: patient


title: female fish liver 1 at 21d high concerntration naphthalene rep 1

city: changchun

first: Hongshan

last: Chen

address: jingyue  street 2555

department: environment

institute: Northeast normal university

description: This sample is of high concerntration of naphthalene treated fish liver. It is the first of two high group biological replicates used in this experiment, each sample from separate 6 fish liver.

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

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

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

organism: Danio rerio

source_name: zebrafish liver

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

growth_protocol: All zebrafish were handled following OECD protocols. Healthy 5-month-old adult zebrafish were acclimatized in 50 L aerated fresh water in glass tanks for 2 weeks, under controlled environmental conditions with the water temperature maintained at 26±0.5℃ for 16-h light and 8-h dark photoperiod.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: Zebrafish were exposed for 21d with naphthalene added at 84 μgL-1 and 840 μgL-1 naphthalene and 0.005% Dimethyl sulfoxide as the solvent control.

tag: strain

value: AB

value: female

tag: agent

value: 840 μg/L naphthalene


title: female fish liver 1 at 21d high concerntration naphthalene rep 2


title: female fish liver 1 at 21d low concerntration naphthalene rep 1

description: This sample is of low concerntration of naphthalene treated fish liver. It is the first of two low group biological replicates used in this experiment, each sample from separate 6 fish liver.

value: 84 μg/L naphthalene


title: NNI-4_NT [AFG1196-19a]

tag: histology


title: NNI-1 [4310479116_C]

tag: pna

tag: grade

value: C


title: female fish liver 1 at 21d low concerntration naphthalene rep 2


title: PAXgene for patient 11-0482

tag: age

value: Europe

value: whole blood

value: PBMC

value: unstimulated


title: PAXgene for patient 11-0445

value: Male

tag: tissue


title: NNI-8_NT [AFG1196-22a]

value: Anaplastic oligoastrocytoma

value: III

tag: replicate


title: WT_ECTV_biological_rep1

value: Wild Type

value: Tetramer-positive splenic CD8+ T cells


title: Klrc1_naïve_biological_rep2

description: Gene expression data from naïve CD8+ T cells

source_name: Total splenic naïve CD8+ T cells

value: Total splenic naïve CD8+ T cells


title: Klrc1_naïve_biological_rep3


title: female fish liver 1 at 21d control rep 2

description: This sample is of control fish liver. It is the first of two control group biological replicates used in this experiment, each sample from separate 5 fish liver.

value: 0.005% Dimethyl sulfoxide


title: WT_naïve_biological_rep4


title: NNI-4_NT [AFG1196-19b]

value: Glioblastoma multiforme

value: IV


title: female fish liver 1 at 21d control rep 1

description: This sample is of control fish liver. It is the first of two control group biological replicates used in this experiment, each sample from separate 4 fish liver.

value: AB

value: female


title: NNI-2_NT [AFG1196-16b]


title: WT_naïve_biological_rep3


title: WT_naïve_biological_rep2


title: PAXgene for patient 11-0578

tag: patient id

value: Female

value: yes

value: patient

tag: treatment


title: Klrc1_naïve_biological_rep1


title: Calvarial osteoblasts_OB-Tsc1 KO_rep1

city: Guangzhou

first: Bin

last: Huang

address: No.1838 North Guangzhou Avenue

institute: Southern Medical University

description: mRNAs expression in calvarial osteoblasts from OB-specific Tsc1 KO mice

hyb_protocol: For hybridization, each slide was hybridized with 1.65 μg Cy3-labeled cRNA using a Gene Expression Hybridization Kit (Cat#5188-5242, Agilent) in a Hybridization Oven (Cat#G2545A, Agilent), according to the manufacturer’s instructions.

scan_protocol: After 17 h of hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with a Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent), following the manufacturer’s instructions. Slides were scanned by an Agilent Microarray Scanner (Cat#G2565CA, Agilent) with the following default settings: dye channel, green; scan resolution, 5 μm; PMT 100%, 10%, 16 bit.

data_processing: For data acquisition, data were extracted with Feature Extraction software 10.7 (Agilent). Raw data were normalized by the Quantile algorithm, Gene Spring Software 11.0 (Agilent).

source_name: Calvarial osteoblasts, OB-specific Tsc1 knockout, replicate 1

label_protocol: For RNA amplification and labeling, total RNA was amplified and labeled using a Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified with an RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Female floxed Tsc1 mice (Tsc1FL/FL) containing LoxP sites flanking exons 17 and 18 of the Tsc1 gene were crossed with male osteocalcin (OC)-Cre mice, whose expression of Cre recombinase is under control of the OC promoter and limited to osteoblasts. The resulting OC-Cre; Tsc1FL/FL (OB-Tsc1 KO) mice are hemizygous for the OC-Cre transgene and homozygous for the floxed Tsc1 allele. All animals were backcrossed for 8 generations onto the C57BL/6 background.

extract_protocol: Total RNA of calvarial osteoblasts from 3 mice were extracted with TRIZOL Reagent and pooled together.

treatment_protocol: Calvariae were dissected from newborn mice (24 hours after birth), rinsed with PBS, and digested in freshly made 0.1mg/ml collagenase Ⅱ(Gibco) in alpha Minimal Essential Eagle’s Medium at 37 ℃ for 20 min; digestion was repeated three times.After digestion, supernatants were combined and centrifuged to pellet cells.

value: Calvarial osteoblasts

tag: genotype

value: OB-specific Tsc1 knockout

tag: developmental stage

value: Newborn (24 hrs)


title: Calvarial osteoblasts_WT_rep1

description: mRNAs expression in calvarial osteoblasts from wild type mice

source_name: Calvarial osteoblasts, wild type, replicate 1

value: wild type


title: NNI-2_NT [AFG1196-16a]


title: BPH-infested KMD2 shoots, biological rep 2

status: Public on Nov 06 2015

city: Hangzhou

first: Gongyin

last: Ye

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

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

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

organism: Oryza sativa

source_name: BPH-infested KMD2 shoots

label_protocol: Double strand cDNA was synthesized from total RNA. After cleanup, biotin-labeled cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Rice seeds were germinated and grown in a controlled chamber at 30°C in the light and 25°C in the dark under a 16:8 h light: dark regime. The relative humidity was maintained at 85%. Three weeks later, rice seedlings of similar sizes were transplanted into glass tubes (38 × 250 mm) covered with nylon mesh, with one tube per seedling. The glass tube was filled with 5 ml nutrient solution, which was renewed every 3 days.

extract_protocol: Frozen rice shoots were homogenized in liquid nitrogen using a mortar and pestle. Total RNA was extracted using Trizol regent according to the supplier‟s recommendation (Invitrogen, Karlsruhe, Germany).

treatment_protocol: For BPH treatment, 10 second-instar nymphs were infested onto each 30-day-old seedling. After 72 h, the BPH nymphs were carefully removed and rice shoots of both BPH-infested and non-infested plants were sampled for microarray analysis. There were four treatments: Xiushui 11-non infested, Xiushui 11-BPH infested, KMD2-non infested, KMD2-BPH infested.

tag: line

value: Bt rice line KMD2

value: BPH-infested 72h

value: shoot


title: non-infested KMD2 shoots, biological rep 3

source_name: non-infested KMD2 shoots

value: non-infested


title: BPH-infested Xiushui 11 shoots, biological rep 2

source_name: BPH-infested Xiushui 11 shoots

value: parental rice line Xiushui 11


title: non-infested KMD2 shoots, biological rep 2


title: WT_naïve_biological_rep1

value: Wild Type

value: Total splenic naïve CD8+ T cells


title: intermediate-state cells-rep3

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

description: Gene expression data from Sox1-GFP-positive cells at day 6 of OKSM-induced astrocyte reprogramming.

hyb_protocol: Fragmented and labelled cDNA was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The probe set signals were calculated with the robust multi-array average (RMA) algorithm implemented in GeneSpring GX 12.6 software (Agilent Technologies).

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) was used according to Affymetrix protocol.

growth_protocol: Astrocytes were maintained in DMEM/F12 with 10% fetal bovine serum (FBS). NSCs were maintained in DMEM/F12 medium supplemented with N2 (25 mg/ml insulin , 100 mg/ml apo-transferrin, 20 nM progesterone, 100 mM putrescine and 30 nM sodium selenite), 20 ng/ml basic FGF (bFGF) and  20 ng/ml EGF. The cells undergoing reprogramming were cultured in standard mouse ESC medium containing 15% ES-FBS and 1000 U/ml LIF. Mature iPSCs were cultured on feeder layers of mitomycin C-treated MEFs in mouse ESC medium containing 15% ES-FBS or 15% KnockOut Serum Replacement (KSR) and 1500 U/ml LIF.

extract_protocol: Total RNAs were extracted using Qiagen RNeasy kit according to the manufacturer’s protocol. On-column DNase digestion was performed.

treatment_protocol: Astocytes (Sox1-GFP-negative cells) were infected with retroviruses encoding the four transcription factors (Oct4, Klf4, Sox2 and c-Myc).

value: Sox1-GFP reporter (Sox1+/-)

tag: cell type


title: non-infested Xiushui 11 shoots, biological rep 3

source_name: non-infested Xiushui 11 shoots


title: intermediate-state cells-rep2

source_name: Sox1-GFP-positive cells at day 6 of OKSM-induced astrocyte reprogramming


title: iPSCs from MEFs-rep2

description: Gene expression data from mature iPSCs established from MEFs (iPS-MEF-Ng-20D-17) that had previously been reported (Okita, K. et al. Nature 448: 313-317 (2007)).

source_name: mature iPSCs establised from MEFs (iPS-MEF-Ng-20D-17)

value: Nanog-GFP-IRES-Puro reproter


title: iPSCs from astrocytes-rep1

description: Gene expression data from mature iPSCs established from Sox1-GFP astrocytes.

source_name: mature iPSCs establised from astrocytes

value: mature iPSCs establised from astrocytes


title: astrocytes-rep2

description: Gene expression data from astrocytes. Astrocytes were prepared from postnatal 3-day Sox1-GFP mouse cortex. Sox1-GFP-negative cells were collected by FACS prior to inducing reprogramming.

source_name: astrocyte cultures from postnatal 3-day mouse cortex


title: astrocytes-rep1

description: Gene expression data from astrocytes. Astrocytes were prepared from postnatal 3-day Sox1-GFP reporter mouse cortex. Sox1-GFP-negative cells were collected by FACS prior to inducing reprogramming.

value: astrocyte cultures from postnatal 3-day mouse cortex


title: NSCs-rep2

description: Gene expression data from NSCs. NSCs were prepared from telencephalons of embryonic (E) 12.5-14.5 embryos of Sox1-GFP reporter mice.

source_name: NSCs prepared from telencephalons of embryonic (E) 12.5-14.5 embryos


title: non-infested Xiushui 11 shoots, biological rep 2


title: astrocytes-rep3


title: iPSCs from MEFs-rep1

value: mature iPSCs establised from MEFs (iPS-MEF-Ng-20D-17)


title: NSCs-rep1

value: NSCs prepared from telencephalons of embryonic (E) 12.5-14.5 embryos