title: Rickettsia rickettsii transcriptome - ch2: G2 replicate 1; ch1: G1 replicate 1

city: São Paulo

first: Maria

middle: Fernanda

last: Galletti

state: São Paulo

address: Av. Prof. Lineu Prestes, 1374 sala 39

department: Department of Parasitology

country: Brazil

institute: Universidade de São Paulo - Instituto de Ciências Biomédicas - Departamento de Parasitologia

description: R. rickettsii under 25oC X R. rickettsii under 35oC, experiment 1

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a High-Resolution C Scanner (Agilent Technologies) using Agilent Settings and image intensity data were extracted with Feature Extraction 10.5 Software using Agilent Settings

data_processing: Raw and background corrected data

organism: Rickettsia rickettsii

source_name: Temperature G1 Cy3

label_protocol: Agilent's Genomic DNA ULS Labeling Kit

growth_protocol: Ticks were mainteined for 3 days at incubator conditons described above

extract_protocol: Total RNA was extracted using Invitrap TwinSpin Cell Mini Kit (Stratec) and reverse transcribed using MessageAmp II  Bacteria RNA Amplification Kit (Ambion)

treatment_protocol: Right after molting to adult, not fed females of A. aureolatum were incubated at 25oC and 93% relative humidity (RH) for 3 days

tag: strain

value: str. Taiaçu

value: Pool of internal organs of 7 Amblyomma aureolatum female infected ticks

value: G1; incubated at 25C for 3 days

source_name: Temperature G2 Cy5

treatment_protocol: Right after molting to adult, not fed females of A. aureolatum were incubated at 35oC and 93% relative humidity (RH) for 3 days

value: G2; incubated at 35C for 3 days


title: Rickettsia rickettsii transcriptome - ch2: G1 replicate 2; ch1: G2 replicate 2

status: Public on Dec 01 2013

type: RNA

description: R. rickettsii under 35oC X R. rickettsii under 25oC, experiment 4

molecule: total RNA

source_name: Temperature G2 Cy3

extract_protocol: Total RNA was extracted using Invitrap TwinSpin Cell Mini Kit (Stratec) and reverse transcribed using MessageAmp II Bacteria RNA Amplification Kit (Ambion)

tag: tissue

tag: group

source_name: Temperature G1 Cy5


title: Rickettsia rickettsii transcriptome - ch2: G2 replicate 2; ch1: G3 replicate 2

description: R. rickettsii under 35C X R. rickettsii exposed to blood feeding condition, experiment 4

source_name: Blood feeding G3 Cy3

growth_protocol: Ticks were mainteined for 3 days inside a cotton chamber attached at the withers of the dog.

treatment_protocol: Right after molting to adult, the females of A. aureolatum fed on a Canis familiares for 3 days

value: G3; fed on Canis familiares for 3 days

source_name: Blood feeding G2 Cy5

value: G2; incubated at 35C for 3 days that were not fed after molting to adults


title: GFP-LYS142

type: genomic

city: San Francisco

first: Jose

middle: Christian

last: Perez

state: CA

department: Microbiology and Immunology

country: USA

institute: University of California, San Francisco

description:
LYS142
Comparison of IP/input in tagged strains to untagged cells immunoprecipitated with the same antibody.

hyb_protocol: The labeled DNA was purified with Zymo columns (Zymo Research). Equal amounts of ChIP and input DNAs (~3 µg each) were mixed and hybridized in a final volume of 500 µl containing Agilent hybridization buffer (Agilent), Agilent blocking agent (Agilent), and 50 µg of human COT1 DNA (Invitrogen). Arrays were hybridized in a hybridization oven for 40 h at 65 degrees C, and then washed with Agilent Oligo aCGH/ChIP-on-chip wash buffers (Agilent) as described by the manufacturer's protocols.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner following manufacturer's protocol.

data_processing: Data normalized using global lowess as implemented in R.

molecule: genomic DNA

organism: Candida albicans

source_name: LYS142 ChIP DNA from GFP-LYS142 cells

label_protocol: Aminoallyl-dUTP (Ambion) was incorporated into 1-2 µg of ChIP and input DNA using Klenow (New England Biolabs) and random DNA nonamers. Dye coupling was carried out by incubating 4-5 µg of aminoallyl-dUTP-labeled ChIP and input DNAs with Cy5 or Cy3, respectively.

growth_protocol: Cells were grown in liquid YPD to logarithmic phase at 30 degrees C.

extract_protocol: Formaldehyde (1% final concentration) was added to 200 ml of Candida albicans cultures at OD600 ~0.5. After crosslinking (15 min), glycine (125 mM final concentration) was added to quench the reaction. Cells were washed twice with 1X TBS and lysed by vortexing for ~2h at 4 degrees C in a suspension containing glass beads. Chromatin was sheared in a Diagenode Bioruptor and immunoprecipitated with the respective antibody.

treatment_protocol: No treatment.

tag: chip antibody

value: GFP (Living Colors Polyclonal antibody raised in rabbit, Clontech, cat no. 632460, lot# 1105002)

source_name: Input DNA from GFP-LYS142 cells


title: 14059747

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

hyb_protocol: The Hy3 and Hy5 labeled RNA samples were mixed, and co-hybridized to miRCURY™ LNA Arrays v.Dx10 and v.11 (Exiqon, Vedbæk, Denmark), which contain Tm normalized capture probes targeting miRNAs from human, mouse and rat , as registered in miRBase v.19.0 at

scan_protocol: After washing and drying, the microarray slides were scanned under ozone free conditions (ozone level < 2.0 ppb to minimize bleaching of the fluorescent dyes) in a G2565BA Microarray Scanner System, (Agilent, Santa Clara, CA). The resulting images were qu

data_processing: All low-level analyses were carried out in the R environment, including importing and pre-processing of the data using the LIMMA package (http://bioconductor.org). Mean pixel intensities were used to calculate signal (foreground) spot intensities, and med

organism: Homo sapiens

source_name: Lung - adenocarcinoma

label_protocol: For microarray analysis, we applied a common reference design, where the reference sample contains a mixture of total RNA representing all tissue types in the study. This allows for both one- and two-channel data analysis, as described in detail by Søkild

extract_protocol: Total RNA was extracted from 20µm FFPE sections with the High Pure miRNA Isolation Kit (Roche Applied Science, Mannheim, Germany) according to the manufacturer’s instructions. After elution in 40µl RNase free water, the RNA concentration (A260 nm) and pur

value: Lung - adenocarcinoma

source_name: Reference

value: mix of all tissues


title: 12974.p1

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

label: biotin nucleotide or dinitrophenyl labeled

source_name: leukocyte

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: sample id

tag: gender

value: Male

tag: sentrix id

tag: sentrix position

value: J

tag: experiment

tag: family

tag: distribution

tag: site

value: pb

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: white

tag: cell type

value: leukocyte


title: GFP-LYS14

description:
LYS14
Comparison of IP/input in tagged strains to untagged cells immunoprecipitated with the same antibody.

source_name: LYS14 ChIP DNA from GFP-LYS14 cells

source_name: Input DNA from GFP-LYS14 cells


title: 12955.p1

hyb_protocol: Followed the manufacturer's (Illumina) specifications

value: F

value: ox


title: Rickettsia rickettsii transcriptome - ch2: G2 replicate 2; ch1: G1 replicate 2

description: R. rickettsii under 25oC X R. rickettsii under 35oC, experiment 3


title: 12964.p1

value: L

value: more-than-one-race


title: 12950.p1

value: K

value: asian


title: Rickettsia rickettsii transcriptome - ch2: G2 replicate 1; ch1: G3 replicate 1

description: R. rickettsii under 35C X R. rickettsii exposed to blood feeding condition, experiment 2

value: str. Taiaçu

value: Pool of internal organs of 7 Amblyomma aureolatum female infected ticks


title: 12958.p1

value: sb


title: Rickettsia rickettsii transcriptome - ch2: G1 replicate 1; ch1: G2 replicate 1

description: R. rickettsii under 35oC X R. rickettsii under 25oC, experiment 2

value: G2; incubated at 35C for 3 days

value: G1; incubated at 25C for 3 days


title: Rickettsia rickettsii transcriptome - ch2: G3 replicate 1; ch1: G2 replicate 1

description: R. rickettsii under 35C X R. rickettsii exposed to blood feeding condition, experiment 1

source_name: Blood feeding G2 Cy3

value: G2; incubated at 35C for 3 days that were not fed after molting to adults

source_name: Blood feeding G3 Cy5

value: G3; fed on Canis familiares for 3 days


title: 12951.p1

value: Male

value: hv


title: 12946.p1

value: G

value: other


title: 12970.p1

value: A

value: xm

value: white

value: leukocyte


title: 354105

city: Houston

first: Anne

middle: Chinenye

last: Katchy

state: Texas

address: 3605 Cullen Blvd, Room 3021

department: CNRCS, Biology and Biochemistry

institute: University of Houston

hyb_protocol: Hybridization was performed at 42 °C for at least 40 hours after pooling of Cy5- and Cy3-labeled samples for each array. Subsequent to hybridization, the slides were washed in three SDS/SSC wash buffers of stepwise lower stringency.

scan_protocol: Slides were scanned using an Axon GenePix 4400A (MDS Analytical Technologies) to obtain TIFF files.

data_processing: Manual processing of data was carried out in GenePix Pro 6.1 to identify possible major issues. Subsequent analysis was carried out in the R environment using the following packages: Bioconductor bundle, Limma, Aroma, KTH. Print-tip lowess was used for normalization and empirical Bayes t-test for statistical analysis. Cut-offs set as described in article.

source_name: MCF7, vehicle control treated

label_protocol: Labeling was carried out with aminoallyl-modified dUTP incorporated during cDNA synthesis using Superscript III (Invitrogen). Incubation with Cy3 or Cy5 monoreactive NHS-ester for 30 min.

extract_protocol: RNA extraction was performed with TRIzol reagent (Invitrogen, Carlsbad, CA) and chloroform extraction according to the manufacturer's protocol.

tag: cell line

tag: treatment

value: vehicle

source_name: MCF7, E2 treated

value: estradiol (E2)


title: Rickettsia rickettsii transcriptome - ch2: G3 replicate 2; ch1: G2 replicate 2

description: R. rickettsii under 35C X R. rickettsii exposed to blood feeding condition, experiment 3

tag: strain

value: str. Taiaçu

tag: tissue


title: 12953.p1

value: H

tag: group


title: 14034232

value: Lung - adenocarcinoma

value: mix of all tissues


title: 12967.p1

tag: sample id

value: B

value: fl


title: 354104


title: 14034231


title: 14059744


title: 12940.p1

tag: gender

value: J

value: lu


title: 14034230


title: 14059739


title: GFP-LYS143

description:
LYS143
Comparison of IP/input in tagged strains to untagged cells immunoprecipitated with the same antibody.

source_name: LYS143 ChIP DNA from GFP-LYS143 cells

tag: chip antibody

value: GFP (Living Colors Polyclonal antibody raised in rabbit, Clontech, cat no. 632460, lot# 1105002)

source_name: Input DNA from GFP-LYS143 cells


title: 12925.p1

value: Male

tag: sentrix id

tag: sentrix position

value: K

value: hv


title: 12942.p1

tag: experiment

tag: family

value: sb


title: 12937.p1

value: G

tag: distribution

tag: site

value: kc

value: other


title: 12930.p1

value: I

value: oi

tag: cpea dx

tag: age at collection (months)

value: white

value: leukocyte


title: 12937.s1

value: E

tag: ethnicity

tag: cell type


title: 14059713

value: Lung - adenocarcinoma

value: mix of all tissues


title: 14059734


title: Inclusion body myositis, biological rep4

city: Barcelona

first: Xavier

last: Suárez-Calvet

address: Sant Antoni Maria Claret, 167

department: Neurology

country: Spain

institute: Institut de Recerca Sant Pau

description: Samples were amplified using NugEn ovation WTA

hyb_protocol: According to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Chips were processed on an Affymetrix GeneChip Fluidics Station 450 using Affymetrix default analysis settings and global scaling as normalization method

label: biotin

source_name: MHC-I-positive microdissected myofibers

label_protocol: ssDNA was fragmented and labelled with the Encore® Biotin Module (NuGEN Technologies)

extract_protocol: Total RNA extraction using Rneasy Micro kit(Qigen). Total RNA from each sample was amplified for ssDNA generation using the Ovation™ Pico WTA System (NuGEN Technologies, San Carlos, CA)

treatment_protocol: Immuno-guided microdissection was performed on muscle biopsies in order to isolate MHC-I-positive myofibers.

value: skeletal muscle

tag: disease status

value: inclusion body myositis


title: 14059736


title: 14059703


title: Inclusion body myositis, biological rep2


title: 12916.p1

value: pb


title: 12923.p1

value: Male

value: J


title: 12905.p1

value: vn


title: 12920.p1

value: F

value: fl


title: 12899.s1

value: L

value: sb


title: Inclusion body myositis, biological rep3


title: 12901.p1

value: H

value: xx

value: more-than-one-race


title: Polymyositis, biological rep5

value: polymyositis


title: 14034018


title: Inclusion body myositis, biological rep1


title: 12902.p1

value: C

value: ox

value: white

value: leukocyte


title: 12857.p1

value: K


title: 12853.p1

value: B


title: Polymyositis, biological rep4

value: skeletal muscle


title: 14034015

value: Lung - adenocarcinoma

value: mix of all tissues


title: 12899.p1

value: Male

value: G


title: 14059698


title: 12938.p1


title: 12859.p1

value: I

value: oi


title: 14059692


title: 14059690


title: 12865.p1

value: E

value: sb


title: Polymyositis, biological rep1


title: 14034010


title: 12843.p1

value: F

value: african-amer


title: 14091250

source_name: Kidney

value: Kidney


title: 12843.s1

value: L


title: Polymyositis, biological rep3

value: polymyositis


title: Polymyositis, biological rep2


title: 12851.p1

value: D

value: vn

value: more-than-one-race

value: leukocyte


title: Dermatomyositis, biological rep4

value: skeletal muscle

value: dermatomyositis


title: 14091247

value: mix of all tissues


title: 12850.p1

value: Male

value: C

value: kc

value: white


title: 14034102

source_name: EG - junction

value: EG - junction


title: 12836.p1

value: J

value: ox


title: 12817.p1

value: I


title: 12803.p1

value: B

value: oi


title: 12766.p1

value: kr


title: 12804.s1

value: K

value: sb


title: 14034076


title: 12804.p1

value: L

value: leukocyte


title: 12852.p1

value: G


title: Dermatomyositis, biological rep5

value: skeletal muscle

value: dermatomyositis


title: 12794.p1

value: Male

value: D

value: lu


title: 12829.p1

value: F

value: fl

value: white


title: 14059878

value: EG - junction

value: mix of all tissues


title: Dermatomyositis, biological rep1


title: Dermatomyositis, biological rep2


title: 12775.p1

value: H


title: 14059877


title: 12799.p1

value: ox


title: Healthy control, biological rep4

source_name: microdissected muscle fibers

value: healthy control


title: 12946.s1

value: C

value: other


title: Dermatomyositis, biological rep3


title: 12786.p1

value: kr

value: leukocyte


title: 12748.p1

value: sb


title: Healthy control, biological rep3

value: skeletal muscle


title: Healthy control, biological rep5


title: 12766.s1

value: Male


title: 12739.p1

value: D


title: 14059876


title: 14059875


title: 12667.s1


title: Healthy control, biological rep2


title: 12676.p1

value: L


title: 14059856


title: 12743.p1

value: E

value: lu


title: 14034105


title: 14059872


title: 12704.p1

value: I

value: white


title: Healthy control, biological rep1


title: 12735.p1

value: G

value: pb


title: 14034103

value: EG - junction

value: mix of all tissues


title: 14059731


title: 12637.p1

value: H


title: 12667.p1

value: A


title: 14091265


title: 12664.p1

value: kr


title: 12622.p1

value: F

value: kc

value: leukocyte


title: 12622.s1

value: Male


title: 12582.p1

value: D

value: other


title: 12651.p1

value: C

value: vn


title: 14059688


title: 12644.p1


title: 14059687


title: 12645.p1

value: fl


title: 14091267


title: 12692.p1

value: E

value: ox

value: white


title: 12592.p1

value: G

value: xm


title: 12605.p1


title: TCHRLBCL 9

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: unsupported Human Gene 1.0 ST Array CDF Files
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: TCHRLBCL

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

extract_protocol: RNA was amplified using the One-direct-Kit from NUGEN applied for 250 microdissected cells

treatment_protocol: Cells were microdissected from HE stained kryosections

value: TCHRLBCL


title: 14035239

source_name: Colorectal

value: Colorectal

value: mix of all tissues


title: 12573.p1

value: kr


title: 12613.p1

value: J


title: TCHRLBCL 10


title: TCHRLBCL 11


title: 14035245

source_name: Cholangiocarcinoma

value: Cholangiocarcinoma


title: 12480.p1

value: Male

value: leukocyte


title: 12469.p1

value: sb


title: 12548.p1

value: L

value: oi


title: 12480.s1

value: I


title: TCHRLBCL 8


title: 12512.p1

value: H


title: 14035244

source_name: Reference


title: TCHRLBCL 6


title: TCHRLBCL 7


title: 12334.p1

source_name: leukocyte


title: 12555.p1

value: A


title: 14091162


title: 14091160


title: 12469.p2

value: white


title: 14091159


title: 12368.p1

value: B


title: TCHRLBCL 5


title: 12325.p1

value: D

value: xm


title: TCHRLBCL 2

value: TCHRLBCL


title: 13364.p1

value: hv


title: TCHRLBCL 4


title: TCHRLBCL 3


title: 12401.p1


title: 12231.p1

value: pb


title: 11601.p1


title: 12219.p1


title: 12108.s1

value: C

value: lu


title: 12460.p1

value: Male

value: K

value: ox


title: 14091156

value: Cholangiocarcinoma

value: mix of all tissues


title: 12076.p1

value: E

value: leukocyte


title: 12116.p1

value: H

value: other


title: 12108.p1

value: F

value: white


title: tumor cells TCHRBCL-like NLPHL 8

description: NLPHL TCHRB-like8

source_name: tumor cells TCHRBCL-like NLPHL

value: tumor cells TCHRBCL-like NLPHL


title: TCHRLBCL 1

value: TCHRLBCL


title: 14091148


title: 14091155


title: 11671.p1

value: J

value: kc

value: not-specified


title: tumor cells TCHRBCL-like NLPHL 7

description: NLPHL TCHRB-like7


title: 14091147


title: 11905.p1

value: hv


title: tumor cells TCHRBCL-like NLPHL 9

description: NLPHL TCHRB-like9


title: 11838.p1

value: Male

value: G

value: xm


title: 14035243

value: Cholangiocarcinoma


title: 14035242

value: mix of all tissues


title: 11892.p1

value: E

value: sb


title: 14091146


title: FT10_3

value: leukocyte


title: 11678.p1

value: B


title: 13095.s1.2

value: L


title: 14035241


title: tumor cells TCHRBCL-like NLPHL 5

description: NLPHL TCHRB-like5


title: tumor cells TCHRBCL-like NLPHL 6

description: NLPHL TCHRB-like6


title: tumor cells TCHRBCL-like NLPHL 4

description: NLPHL TCHRB-like4


title: FT50_3

value: I


title: FT50_1

value: A


title: FT10_1

value: C


title: 12412.p1.2

value: white


title: FT50_2


title: tumor cells TCHRBCL-like NLPHL 1

description: NLPHL TCHRB-like1

value: tumor cells TCHRBCL-like NLPHL


title: 14091149


title: tumor cells TCHRBCL-like NLPHL 3

description: NLPHL TCHRB-like3


title: 12011.p1.2

value: K

value: lu


title: 14035246


title: tumor cells TCHRBCL-like NLPHL 2

description: NLPHL TCHRB-like2


title: tumor cells NLPHL 10

source_name: tumor cells NLPHL

value: tumor cells NLPHL


title: 12096.p1.2

value: Male

value: F


title: FT10_2


title: 12113.s1.3

value: ox


title: tumor cells NLPHL 9


title: 12687.p1

value: J

value: oi


title: 12210.p1.2

value: G

value: xm


title: tumor cells NLPHL 8


title: 12157.p1.2

value: leukocyte


title: 12019.s1.3

value: L

value: hv


title: tumor cells NLPHL 5


title: 11998.p1.3

value: H

value: sb


title: 12006.s1.3

value: xx

value: white


title: tumor cells NLPHL 3


title: tumor cells NLPHL 2


title: tumor cells NLPHL 6


title: tumor cells NLPHL 7


title: 11005.s1.2

value: K


title: 11230.p1.3

value: I

value: fl


title: 11998.p1.2

value: Male


title: tumor cells NLPHL 4

value: tumor cells NLPHL


title: 11104.s1.2


title: 11633.p1.2

value: D


title: 11138.s1.2

value: E


title: 12019.p1.2


title: 12006.s1.2


title: 11491.p1.2

value: vn


title: 11457.p1.2

value: B


title: 11554.s1.2

value: asian


title: 13154.p1

value: J

value: lu

value: leukocyte


title: liver, control, biological rep6

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
Gene expression data of 10 week old healthy rat liver.
SD_144

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of  RaGene10stv1-type from Affymetrix. A Custom CDF Version 15 with entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

organism: Rattus norvegicus

source_name: Healthy liver of 10 week old SD rat

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

growth_protocol: Rats received standard rat diet (containing 19% protein) and tap water ad libitum.

extract_protocol: Total RNA was isolated from frozen liver tissue of 10 week old rats with Trizol reagent (Invitrogen) as described by the manufacturer.

treatment_protocol: Male rats were anesthetized with isoflurane prior to sacrificing by neck fracture at 10 weeks of age. Livers were minced, snap-frozen in liquid nitrogen and stored at - 80 °C until RNA extraction.

tag: strain

value: Sprague Dawley

value: male

tag: disease state

value: control

tag: age

value: 10 weeks old

value: liver


title: 13095.p1

tag: sample id

tag: group

value: hv

value: white


title: 13095.s1.1

tag: gender

value: Male

value: K


title: 11236.p1

tag: sentrix id

value: I


title: liver, control, biological rep5

description:
Gene expression data of 10 week old healthy rat liver.
SD_143

tag: tissue


title: 14091157

value: Cholangiocarcinoma

value: mix of all tissues


title: 13099.p1

tag: sentrix position

value: D

tag: experiment

value: xx


title: tumor cells NLPHL 1

value: tumor cells NLPHL


title: 11236.s1

value: B

tag: family

tag: distribution


title: liver, control, biological rep2

description:
Gene expression data of 10 week old healthy rat liver.
SD_140


title: liver, control, biological rep4

description:
Gene expression data of 10 week old healthy rat liver.
SD_142


title: 13070.p1

value: F

tag: site

tag: cpea dx

value: leukocyte


title: 13082.p1

value: C

value: xm

tag: age at collection (months)

tag: ethnicity


title: 12944.s1.1

value: L

tag: cell type


title: 13053.p1

value: A


title: Ectopic expression of scramble mimic, no 1

first: Yvonne

last: Ceder

address: Medicon Village

department: Laboratory Medicine

institute: Lund University

description: Gene expression data from PC3 cells ectopically expressing scramble mimics

hyb_protocol: Biotinylated cDNA was hybridized to the GeneChip® Human Gene 1.0 ST Arrays (Affymetrix). The arrays were washed and stained on a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software (GCOS, Affymetrix), and in Genepix 4.0 (Axon Instruments, Inverurie, Scotland)

data_processing: The data were normalized, background-corrected, and summarized using the Robust Multichip Average (RMA) algorithm implemented in the Expression Console™ version 1.1.2 software (Affymetrix). The data was analysed using SAM analysis to identify significantly differentially expressed genes between the groups.

source_name: PC3 cells

label_protocol: Single stranded cDNA was generated using the GeneChip® Whole Transcript (WT) cDNA Synthesis and Amplification Kit (Affymetrix Inc, Santa Clara, CA) using 100 ng of total RNA. Amplified cDNA was fragmented and labeled using the GeneChip® WT Terminal Labelling Kit (Affymetrix).

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

tag: treatment

value: Ectopic expression of scramble mimic

tag: cell line

value: aggressive androgen negative prostate cancer


title: liver, diseased, biological rep6

description:
Gene expression data of 10 week old diseased rat liver.
PCK_137

source_name: Cystic liver of 10 week old PCK rat

tag: strain

value: Crj:CD/SD (cesarean derived Sprague Dawley from Charles River Japan)

value: male

tag: disease state

value: PCK

tag: age

value: 10 weeks old

value: liver


title: 12996.p1

tag: sample id

tag: gender

value: Male

value: J

tag: group

value: hv

value: white


title: Ectopic expression of scramble mimic, no 2


title: 12944.p1

tag: sentrix id

tag: sentrix position

value: E


title: Ectopic expression of miR-34c, no 1

description: Gene expression data from PC3 cells ectopically expressing miR-34c

value: Ectopic expression of miR-34c


title: 12784.p1

tag: experiment

tag: family

value: kr

value: leukocyte


title: Ectopic expression of miR-34c, no 3


title: 13010.p1

value: C

tag: distribution

tag: site

value: xx

value: more-than-one-race


title: 12741.p1

value: L

tag: cpea dx

tag: age at collection (months)


title: liver, control, biological rep1

description:
Gene expression data of 10 week old healthy rat liver.
SD_139

value: Sprague Dawley

value: control

tag: tissue


title: liver, control, biological rep3

description:
Gene expression data of 10 week old healthy rat liver.
SD_141

value: male


title: liver, diseased, biological rep4

description:
Gene expression data of 10 week old diseased rat liver.
PCK_135

value: Crj:CD/SD (cesarean derived Sprague Dawley from Charles River Japan)

value: PCK

value: 10 weeks old


title: Ectopic expression of miR-34c, no 2

tag: treatment

tag: cell type

value: aggressive androgen negative prostate cancer


title: 12791.p1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

value: Male

value: B

tag: ethnicity


title: 12773.p1

value: I

value: xm

value: white


title: Astrocytes4

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

country: Italy

institute: University of Milan

description: gene expression in astrocytes before reprogramming

hyb_protocol: fragmentation of 12.5 µg cRNA was performed and hybridized onto the GeneChip according to the Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were processed using the Affymetrix GCOS programme.

source_name: Primary human astrocytes

label_protocol: The GeneChip IVT Express Kit and the GeneChip Hybridization wash and stain kit were used with 100 ng of total RNA that was mixed with 2 µl of 1/500,000 diluted spikes. Synthesis of the first strand and the second strand of cDNA was performed according to the kit instructions at  transcribed, and amplified into cRNA.

growth_protocol: Human cortical astrocytes were cultured in astrocyte medium (Science Cell); HNSC in human NSC medium (Stem Cell Inc.) supplemented with EGF and FGF and heparin, according to manufacturers’ instructions

treatment_protocol: cells were detached from plates and pelleted

value: astrocytes from brain cortex


title: liver, diseased, biological rep5

description:
Gene expression data of 10 week old diseased rat liver.
PCK_136

tag: strain

tag: disease state

value: liver


title: 12780.p1

tag: sample id

value: D

value: xx

value: leukocyte


title: Human Neural Stem Cells (HNSC) derived from astrocytes reprogramming 3

description: gene expression in NSCs reprogrammed from astrocytes

source_name: Reprogrammed NSCs from human astrocytes

value: Human Neural Stem Cells (HNSC) reprogrammed cells from astrocytes


title: 13073.p1

tag: gender

value: hv


title: liver, diseased, biological rep3

description:
Gene expression data of 10 week old diseased rat liver.
PCK_134

value: male

tag: age


title: 12939.p1

tag: sentrix id

value: K

tag: group

value: asian


title: Human Neural Stem Cells (HNSC) derived from astrocytes reprogramming 2


title: 12727.p1

tag: sentrix position

value: H

tag: experiment


title: 12770.p1

value: F

tag: family

tag: distribution

value: fl


title: 12772.p1

value: Male

value: A

tag: site

value: sb

tag: cpea dx


title: 12720.p1

tag: age at collection (months)

value: white


title: Human Neural Stem Cells (HNSC) derived from astrocytes reprogramming 4

tag: tissue


title: 12695.p1

value: L

value: native-hawaiian

tag: cell type


title: 12722.p1

value: B

tag: ethnicity


title: 12705.p1

value: xm


title: Astrocytes3

value: astrocytes from brain cortex


title: Astrocytes2


title: liver, diseased, biological rep2

description:
Gene expression data of 10 week old diseased rat liver.
PCK_133

tag: strain

value: Crj:CD/SD (cesarean derived Sprague Dawley from Charles River Japan)

value: PCK

value: 10 weeks old

value: liver


title: Foxa2 mutant uterus at DOPP3.5, biological rep4

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

description: Gene expression data from whole uterus on day of pseudopregnancy 3.5

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and GeneChip Command Console software (Affymetrix).

data_processing: The data was analyzed with RMA Limma package in Bioconductor (cut-off, p value<0.05, FDR 5% and -1.5> fold change <1.5).

organism: Mus musculus

source_name: day of pseudopregnancy 3.5 female mouse

label_protocol: Biotinylated cRNA were prepared using GeneChip WT Terminal Labeling kitaccording to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. cRNA was generated from a 150 ng of total RNA using Ambion WT Expression Kit according to manufactures recommendations.

treatment_protocol: Control (Pgr+/+Foxa2+/+) and conditional Foxa2 (PgrCre/+Foxa2flox/flox) mutant female mice were bred to wild type vasectomized male. Day of the vaginal plug detection was designated as day of pseudopregnancy (DOPP) 0.5. Mice (n=4/genotype) were sacrificed on DOPP 3.5 and whole uteri snap frozen in liquid nitrogen.

value: whole uterus

tag: genotype

value: PgrCre/+ Foxa2flox/flox


title: 12690.p1

tag: sample id

value: G

value: vn

value: leukocyte


title: 12701.p1

tag: gender

value: Male

value: J

value: xx

value: more-than-one-race


title: liver, diseased, biological rep1

description:
Gene expression data of 10 week old diseased rat liver.
PCK_132

value: male

tag: disease state

tag: age


title: 12688.p1

tag: sentrix id

value: D

tag: group

value: hv

value: white


title: 12673.p1

tag: sentrix position

value: K

tag: experiment


title: Foxa2 mutant uterus at DOPP3.5, biological rep2


title: 12680.p1

value: C

tag: family

tag: distribution

value: xm


title: 12669.p1

value: H

tag: site

tag: cpea dx


title: EKO_HFD_VAT2

city: Worcester

first: Timothy

middle: P

last: Fitzgibbons

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

description: Apolipoprotein E (EKO) mice on C57BL6/J mice fed with Western diet (42% anhydrous milk fat, Harlan diet TD88137) for 24 weeks starting at 8 weeks of age. Second biological replicate

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual)

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software according to manufacturer's protocol (GeneChip Expression Analysis Technical Manual)

data_processing: Probeset signal normalization with RMA

label: Biotin

source_name: Epididymal fat pad

label_protocol: Ambion WT Expression Kit,Affymetrix WT Terminal Labeling Kit

extract_protocol: RNA minilipid kit (Qiagen) using manufacturers protocol

tag: diet

value: HFD

tag: tissue

value: epididymal fat pad

tag: genotype/variation

value: EKO


title: 12655.s1

value: kc

tag: age at collection (months)

tag: ethnicity

value: other

tag: cell type


title: 12646.p1

tag: sample id

tag: gender

value: Male

value: vn

value: leukocyte


title: 12682.p1

value: pb


title: Ectopic expression of scramble mimic, no 3

tag: treatment

value: Ectopic expression of scramble mimic

tag: cell line

value: aggressive androgen negative prostate cancer


title: 12619.p1

tag: sentrix id

tag: group


title: 12621.p1

tag: sentrix position

tag: experiment

value: xx


title: Foxa2 mutant uterus at DOPP3.5, biological rep1

value: whole uterus

tag: genotype

value: PgrCre/+ Foxa2flox/flox


title: 12662.s1

value: J

tag: family

tag: distribution


title: 12679.p1

tag: site

value: oi

tag: cpea dx

value: white


title: 12647.p1

value: B


title: 12618.p1

value: F


title: EKO_HFD_VAT4

description: Apolipoprotein E (EKO) mice on C57BL6/J mice fed with Western diet (42% anhydrous milk fat, Harlan diet TD88137) for 24 weeks starting at 8 weeks of age. Fourth biological replicate

tag: diet

value: HFD

value: male

tag: strain

tag: tissue

value: epididymal fat pad

tag: genotype/variation

value: EKO


title: 12655.p1

tag: sample id

value: Male

value: L

value: kc

tag: age at collection (months)

tag: ethnicity

value: other

tag: cell type


title: Foxa2 mutant uterus at DOPP3.5, biological rep3


title: EKO_ND_VAT4

description: Apolipoprotein E (EKO) mice on C57BL6/J mice fed normal diet for 24 weeks starting at 8 weeks of age. Fourth biological replicate

value: ND

tag: gender


title: 12616.p1

tag: sentrix id

value: K

tag: group

value: xx

value: leukocyte


title: EKO_ND_VAT2

description: Apolipoprotein E (EKO) mice on C57BL6/J mice fed normal diet for 24 weeks starting at 8 weeks of age. Second biological replicate


title: 12683.p1

tag: sentrix position

tag: experiment


title: EKO_HFD_VAT3

description: Apolipoprotein E (EKO) mice on C57BL6/J mice fed with Western diet (42% anhydrous milk fat, Harlan diet TD88137) for 24 weeks starting at 8 weeks of age. Third biological replicate


title: EKO_ND_VAT3

description: Apolipoprotein E (EKO) mice on C57BL6/J mice fed normal diet for 24 weeks starting at 8 weeks of age. Third biological replicate


title: 12662.p1

value: C

tag: family


title: 12623.p1

value: G

tag: distribution


title: 12631.s1

value: D

tag: site

value: hv

value: white


title: 12642.p1

value: kr

tag: cpea dx


title: EKO_ND_VAT1

description: Apolipoprotein E (EKO) mice on C57BL6/J mice fed normal diet for 24 weeks starting at 8 weeks of age. First biological replicate

tag: diet

value: male


title: EKO_HFD_VAT1

description: Apolipoprotein E (EKO) mice on C57BL6/J mice fed with Western diet (42% anhydrous milk fat, Harlan diet TD88137) for 24 weeks starting at 8 weeks of age. First biological replicate

value: HFD

tag: strain

value: epididymal fat pad


title: WT3_HFD

description: Wild type male C57BL6/J mice fed with Western diet(42% anhydrous milk fat, Harlan diet TD88137) for 24 weeks starting at 8 weeks of age. Third biological replicate

tag: tissue

value: WT


title: 12593.s1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

value: Male

value: H


title: 12631.p1

value: B


title: WT2_HFD

description: Wild type male C57BL6/J mice fed with Western diet(42% anhydrous milk fat, Harlan diet TD88137) for 24 weeks starting at 8 weeks of age. Second biological replicate

tag: genotype/variation


title: 12595.p1

tag: sample id

value: fl

value: more-than-one-race


title: 12603.p1

value: xx

tag: age at collection (months)


title: 12588.p1

value: E

tag: ethnicity

value: leukocyte


title: 12656.p1

value: G

value: kc

tag: cell type


title: 12593.p1

tag: gender

value: A


title: WT1_HFD

description: Wild type male C57BL6/J mice fed with Western diet(42% anhydrous milk fat, Harlan diet TD88137) for 24 weeks starting at 8 weeks of age. First biological replicate


title: 12575.s1

tag: sentrix id

value: hv

value: white


title: 12510.p1

value: K

tag: group

value: ox


title: WT2_ND

description: Wild type male C57BL6/J mice fed normal diet for 24 weeks starting at 8 weeks of age. Second biological replicate

value: ND

value: male

value: epididymal fat pad


title: 12575.p1

value: Male

tag: sentrix position

value: D


title: WT1_ND

description: Wild type male C57BL6/J mice fed normal diet for 24 weeks starting at 8 weeks of age. First biological replicate

value: WT


title: WT3_ND

description: Wild type male C57BL6/J mice fed normal diet for 24 weeks starting at 8 weeks of age. Third biological replicate


title: 12563.p1

value: H

tag: experiment


title: 12552.p1

value: C

tag: family

value: lu


title: 12541.p1

value: F

tag: distribution

value: vn

value: leukocyte


title: 12517.p1

value: A

tag: site

value: more-than-one-race


title: C2C12 infected with Ad-GLI1-GFP, biological rep1

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

data_processing:
Data were processed using GeneSpring V11.5 software. Background correction and quantile normalization were performed using Iterative Plier 16. Baseline transformation was to the median of all samples.
Probe group file: Affymetrix.ExonExprChip.MoGene-1_0-st-v1_na31_mm9_2010-08-27

source_name: C2C12 myotubes

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: C2C12 myoblasts (ATCC Number: CRL-1772, Strain: C3H) were grown in DMEM with 10% FBS until 80% confluent, then medium was changed to differentiation medium (DMEM, 2% donor horse serum). Differentiation medium was changed daily after that.

extract_protocol: Total RNA from cultured cells was extracted using miRNeasy Mini kits (Qiagen).

treatment_protocol: Four days after the switch to differentiation medium, >80% of nuclei were contained within syncitial myotubes.  At that time, when >80% of nuclei were incorporated into multi-nucleated syncitial myotubes, we infected the cultures with recombinant adenovirus expressing GFP alone or GFP and a full length human Gli1. Media was changed 12 hours later. Cultures were lysed 60 hours after the initial infection.


title: 12552.s1.1

value: G

tag: cpea dx

value: white


title: 12483.p1

value: ox


title: 12501.p1

value: K

value: hv


title: 12492.p1

value: E

value: sb


title: 12438.p1

value: Male

value: kr


title: 12481.p1

value: B

value: oi

value: native-american


title: 12499.p1

value: fl


title: C2C12 infected with Ad-GLI1-GFP, biological rep3


title: C2C12 infected with Ad-GFP, biological rep3

value: GFP


title: 12457.p1

value: lu

value: leukocyte


title: C2C12 infected with Ad-GFP, biological rep1


title: C2C12 infected with Ad-GFP, biological rep2


title: 12451.p1

value: pb


title: 12478.p1

value: G

value: african-amer


title: 12418.p1

value: F

value: white


title: 12412.p1.1

value: L

value: hv


title: C2C12 infected with Ad-GLI1-GFP, biological rep2


title: R90Wneo/Wneo E

city: SAINT LOUIS

first: Nicholas

middle: M

last: Tran

state: Missouri (MO)

address: 660 S Euclid Ave

department: Ophthalmology

institute: Washington University

description: R90W rep 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data normalized by IlluminaGUI average methods in R.

molecule: polyA RNA

source_name: Mouse retina

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

extract_protocol: Retinas were enucleated from the eye cup and RNA was extracted using the 5 Prime Perfect Pure RNA Tissue Kit

tag: age

tag: genotype

value: retina

value: female and male mixture


title: 12432.p1

value: Male

value: J

value: asian


title: 12437.p1

value: H

value: vn


title: 12445.p1

value: kr


title: 12449.p1

value: ox


title: 12390.p1

value: leukocyte


title: 12346.p1

value: I

value: kc


title: 12361.p1

value: xx


title: 12394.p1

value: C


title: -/- B

description: -/- rep 3

value: Crx -/-

tag: strain

tag: tissue


title: 12314.p1

tag: sample id

value: white


title: E168d2neo/d2neo D

description: E168d2 rep 2


title: 12337.p1

value: L

value: hv

tag: age at collection (months)

value: more-than-one-race


title: -/- C

description: -/- rep 2

value: retina

value: female and male mixture


title: R90Wneo/Wneo A

description: R90W rep 2


title: -/- A

description: -/- rep 1


title: R90Wneo/Wneo D

description: R90W rep 1


title: 12316.p1

value: Male

value: G

value: fl

tag: ethnicity


title: 12363.s1

value: H

value: kr

tag: cell type


title: E168d2neo/d2neo B

description: E168d2 rep 3

tag: gender


title: 12271.s1.1

tag: sentrix id

value: leukocyte


title: 12383.p1

value: E

tag: group

value: xm


title: 12363.p1

tag: sentrix position


title: WT G

description: WT rep 3

value: WT


title: E168d2neo/d2neo A

description: E168d2 rep 1


title: WT B

description: WT rep 1


title: 12382.p1

value: B

tag: experiment

value: pb


title: 12329.p1

tag: family

value: sb

value: white


title: WT F

description: WT rep 2


title: 12295.s1

tag: distribution

value: hv


title: 12289.p1

value: C

tag: site

value: vn


title: 12271.p1

value: D

tag: cpea dx


title: 12304.p1

value: Male

value: oi


title: 12297.p1

value: F


title: sampleN6-pituitary gland-C3

city: BEI JING

first: JIE

last: FENG

address: TIANTAN XILI 6, CHONGWEN DISTRICT

country: China

institute: BEIJING NEUROSURGICAL INSTITUTE

description: Gene expression in human pituitary glands,  non-invasion NFPAs and invasion NFPAs

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: pituitary gland

label_protocol: Total RNA was amplified and labeled by 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 by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The Surgical specimens were frozen at -80℃ in isopentane and stored in liquid nitrogen.

value: pituitary gland

value: male


title: 12225.p1

value: K

value: leukocyte


title: 12296.p1

value: E


title: 12252.p1

value: kr

value: other


title: sampleN1-pituitary gland-C2

value: female


title: 12243.p1

value: J

value: ox


title: 12295.p1

value: B

value: hv

value: white


title: 12257.p1

value: L

value: xm


title: sample856-invasion-IH1217

source_name: tumor samlpe

value: invasion non-functioning pituitary adenomas


title: 12261.p1

value: Male

value: african-amer


title: 12230.p1

value: D

value: sb


title: 12239.p1

value: F

value: leukocyte


title: 12261.s1

value: I

value: kr


title: 12235.p1


title: sampleN-pituitary gland-C1

value: pituitary gland

value: male


title: sample819-invasion-IH1209

value: female


title: sample845 non-invasion NH1214

value: non-invasion non-functioning pituitary adenomas


title: 12255.p1

value: B


title: 12210.p1.1

value: white


title: 12275.p1

value: H

value: vn


title: 12227.p1

value: pb


title: 12210.s1

value: Male

value: G

value: xm


title: sample805 non-invasion NH1211


title: 12201.p1

value: E

value: ox

value: other


title: 12173.p1

value: D

value: hv

value: leukocyte


title: 12224.p1

value: C

value: sb


title: 12206.p1


title: 12157.p1.1

value: L


title: sample809-invasion-IH1207

value: invasion non-functioning pituitary adenomas

value: female


title: 12202.p1

value: A

value: oi

value: more-than-one-race


title: sample735 non-invasion NH1208

value: non-invasion non-functioning pituitary adenomas

value: male


title: 12101.p1

value: Male

value: kr

value: white


title: 12115.s1.1

value: K

value: lu

value: not-specified


title: 12113.s1.1

value: G

value: ox

value: leukocyte


title: 12113.p1

value: D


title: Day12_rep1

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression in 3D culture of MCF-10A cells at day 12

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >11.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4110F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 3D culture at day 12

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were cultured in a 1:1 mix of DME and Ham’s F12 media supplemented with 2% equine serum, 10 ug/ml insulin, 5 ng/ml EGF, 100 ng/ml cholera toxin, 0.5 ug/ml hydrocortisone, and 2% reconstituted basement membrane (Matrigel; BD Bioscuences).

extract_protocol: RNA was prepared using the AllPrep DNA/RNA Mini kit (QIAGEN) following the manufacturer's recommendations.

tag: cell line

value: normal-like human mammary epithelial cells

tag: time point


title: sample733 non-invasion NH1207


title: 12152.p1

value: J


title: 12099.p1

value: F


title: 12068.p1

value: L

value: xx


title: 12096.p1.1

value: A

value: xm


title: 12070.p1

value: Male


title: 12041.p1

value: african-amer


title: 12101.s1.1

value: I

value: kr

value: white


title: Day12_rep2


title: 12051.p1

value: H

value: gv


title: 12115.p1

value: C

value: lu

value: not-specified


title: 12029.s1.1

value: leukocyte


title: Day8_rep1

description: Gene expression in 3D culture of MCF-10A cells at day 8

source_name: 3D culture at day 8

value: normal-like human mammary epithelial cells


title: Day8_rep2


title: 12044.p1

value: vn


title: 3xbhlh + SA Rep3

city: Saarbrücken

first: Petra

last: Bauer

address: Campus A2.4

institute: Saarland University

description: Gene expression in whole 6 day-old 3xbhlh seedlings, -Fe, 100µM SA

hyb_protocol: standard Agilent protocol by ATLAS Biolabs GmbH, Germany

organism: Arabidopsis thaliana

source_name: 3xbhlh+SA Rep3

growth_protocol: 1/2 Hoagland medium without Fe; 6day-old seedlings

extract_protocol: Qiagen RNA purification kit

treatment_protocol: exposed for 6 hours to 100 µM salicylic acid or mock treatment

tag: age

value: 6 day

value: seedling

tag: genotype

value: 3xbhlh KO

tag: treatment

value: minus Fe, plus salicylic acid


title: Day4_rep2

description: Gene expression in 3D culture of MCF-10A cells at day 4

source_name: 3D culture at day 4


title: Day4_rep1


title: 3xbhlh Rep3

description: Gene expression in whole 6 day-old 3xbhlh seedlings, -Fe

scan_protocol: standard Agilent protocol by ATLAS Biolabs GmbH, Germany

source_name: 3xbhlh Rep3

tag: tissue

value: minus Fe


title: 12029.p1

source_name: leukocyte

tag: sample id

value: Male

value: D

value: xx

tag: age at collection (months)

tag: ethnicity


title: 12019.p1.1

tag: gender

tag: sentrix id

value: I

value: hv

value: white

tag: cell type


title: 3xbhlh + SA Rep2

data_processing: standard Agilent protocol by ATLAS Biolabs GmbH, Germany

source_name: 3xbhlh+SA Rep2


title: 12006.s1.1

tag: sentrix position

value: K

tag: experiment

tag: group


title: 12037.p1

value: E

tag: family

tag: distribution

tag: site

value: pb


title: 12014.s1.1

value: G

value: lu

tag: cpea dx

value: leukocyte


title: 11993.s1.1

value: H

value: xm


title: 12056.p1


title: WT + SA Rep2

description: Gene expression in whole 6 day-old wild type seedlings, -Fe,  100µM SA

source_name: WT+SA Rep2

label_protocol: standard Agilent protocol by ATLAS Biolabs GmbH, Germany

tag: age

value: 6 day

value: seedling

value: wild type


title: 12011.p1.1

value: Male

value: J


title: 3xbhlh Rep2

source_name: 3xbhlh Rep2

tag: genotype

value: 3xbhlh KO

value: minus Fe


title: 12006.p1

value: C

value: xx


title: 12020.p1

value: A

value: oi

value: white


title: 12019.s1.1

value: F

value: hv


title: WT Rep3

description: Gene expression in whole 6 day-old wild type seedlings, -Fe

source_name: WT Rep3

tag: treatment


title: 11998.p1.1

value: L

value: sb

value: leukocyte


title: 12033.p1

value: kc

value: asian


title: 12014.p1

value: B

value: lu


title: WT + SA Rep3

source_name: WT+SA Rep3

value: 6 day

tag: tissue

value: seedling

value: wild type

value: minus Fe, plus salicylic acid


title: 3xbhlh + SA Rep1

source_name: 3xbhlh+SA Rep1

value: 3xbhlh KO


title: 12011.s1

tag: sample id

value: Male

value: A


title: WT Rep2

source_name: WT Rep2

value: minus Fe


title: 11969.p1

value: F

value: xm

tag: age at collection (months)

value: white


title: WT + SA Rep1

source_name: WT+SA Rep1


title: 11990.p1

value: D

tag: ethnicity


title: 11998.s1

tag: gender

value: E

value: sb

value: leukocyte


title: WT Rep1

source_name: WT Rep1


title: 11993.p1

tag: sentrix id

value: C


title: 11942.p1

value: J

value: kr

tag: cell type


title: 11966.p1

tag: sentrix position

value: K

value: ox


title: 11939.p1

tag: experiment

value: kc

value: more-than-one-race


title: 11957.p1

value: Male

tag: group

value: lu

value: asian


title: 11897.p1

value: L

tag: family


title: 11949.p1

value: H

tag: distribution


title: 11947.p1

value: I

tag: site

value: xm

value: white


title: 3xbhlh Rep1

source_name: 3xbhlh Rep1

value: 6 day

value: seedling

value: 3xbhlh KO

value: minus Fe


title: 11894.p1

value: F

tag: cpea dx

value: leukocyte


title: 11895.p1

value: A

value: hv


title: 11935.p1

value: B

value: fl


title: 11920.p1

value: Male

value: D

value: kr

value: more-than-one-race


title: 11888.p1

value: I

value: ox


title: 11920.s1

value: C


title: 11835.p1

value: white


title: 11946.p1

value: G


title: 11922.p1

value: J


title: 11933.p1

value: pb


title: 11909.p1

value: sb


title: 11773.p1

value: K

value: oi

value: leukocyte


title: 11824.p1

value: L

value: xm


title: 11834.p1

value: Male

value: E


title: 11860.p1


title: 11800.p1


title: 11788.p1

value: F

value: kc


title: 11740.p1

value: kr


title: 11722.p1

value: vn


title: 11711.p1

value: fl


title: 11716.p1

value: white


title: 11721.p1

value: D


title: 11714.p1

value: J


title: 11792.p1

value: ox


title: 11673.p1


title: 11679.p1

value: hv


title: 11685.p1

value: H


title: 11665.p1

value: I


title: 11634.p1

value: other

value: leukocyte


title: 11491.p1.1

value: L


title: 11630.p1

value: Male

value: not-specified


title: 11633.s1

value: K

value: xm


title: 11691.p1

value: C

value: kr


title: BT_4h

city: Kagoshima

first: Takuro

last: Nishikawa

address: Sakuragaoka 8-35-1

department: Pediatrics

institute: Kagoshima University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8×60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities were normalized by the quantile algorithm with the Bioconductor.

source_name: HL-60 cells, BT exposed, 4h

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: HL-60, a human promyelocytic cell line, was cultured in RPMI-1640 medium (SIGMA-Aldrich, St. Louis, MO) with 10 % of heat-inactivated fetal bovine serum (FBS) (Nichirei Bioscience, Tokyo, Japan) at 37℃ in a humidified atmosphere with 5 % CO2.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: 1, 2, 4-benzenetriol (BT) exposure: For control or BT exposure sample, HL-60 cells suspended in RPMI 1640 supplemented with 10% heat-inactivated FBS at 4×10^5/mL were exposed to BT (0 or 50μM) at 37℃ in 5% CO2 for 1 hour or 4 hours. For 4-aminobenzoic acid hydrazine (ABAH, MPO inhibitor) treatment sample, HL-60 cells suspended in RPMI 1640 supplemented with 10% heat-inactivated FBS at 4×10^5/mL were treated with ABAH (100μM) and preincubated at 37℃ in 5% CO2 for 24 hours. After the pretreatment of ABAH, media was then replaced with new media containing the reagent plus 50μM of BT.

tag: cell line


title: 11666.p1

value: A

value: fl


title: ABAH_4h

source_name: HL-60 cells, ABAH exposed, 4h


title: 11625.p1

value: G

value: xx

value: more-than-one-race


title: 11616.p1

value: vn

value: white


title: 11600.p1

value: F

value: hv


title: BT+ABAH_1h

source_name: HL-60 cells, BT+ABAH exposed, 1h


title: 11638.p1

value: oi

value: leukocyte


title: 11625.s1.1

value: Male

value: I


title: 11633.p1.1


title: Control_4h

source_name: HL-60 cells, 4 h


title: 11628.p1

value: D


title: BT+ABAH_4h

source_name: HL-60 cells, BT+ABAH exposed, 4h


title: 11653.p1


title: 11600.s1

value: B


title: ABAH_1h

source_name: HL-60 cells, ABAH exposed, 1h


title: 11610.p1

source_name: leukocyte

value: xm


title: 11262.p1

value: L

value: ox


title: 11393.p1

value: K


title: Lenti-Fluc-1

city: Dallas

first: John

last: Schoggins

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

data_processing: The raw data were extracted using BeadStudio software (Illumina) without normalization. Data were analysed using GeneSpring software with global normalization. Student’s unpaired t-test was used to determine statistical significance.

source_name: STAT1-/- fibroblasts

growth_protocol: STAT1-/- fibroblasts (an SV40 large T antigen immortalized human skin fibroblast line) were grown in RPMI (Invitrogen) with 10% FCS.

extract_protocol: Total RNA from STAT1-/- fibroblasts transduced with lentiviral vectors was isolated 48 h post-transduction using an RNeasy Mini Kit (Qiagen).

treatment_protocol: For transduction assays, STAT1-/- fibroblasts were seeded into 24-well plates at a density of 70000 cells per well and transduced with lentiviral pseudoparticles by spinoculation at 1,000 x g for 45 min at 37°C in medium containing 3% FBS, 20 mM HEPES and 4 μg/ml polybrene.

value: STAT1-/- fibroblasts

tag: transduced with lentiviruses expressing luciferase


title: Lenti-Fluc-3


title: 11470.p1

value: A


title: BT_1h

source_name: HL-60 cells, BT exposed, 1h


title: 11372.p1

value: kc


title: 11407.p1

value: pb

value: not-specified


title: 11229.p1

value: E

value: fl

value: white


title: Lenti-Fluc-2


title: Control_1h

source_name: HL-60 cells, 1 h


title: 11431.p1

value: H

value: leukocyte


title: Lenti-cGAS-2

tag: transduced with lentiviruses expressing cGAS


title: 11232.p1

value: Male

value: J


title: 11347.p1

value: G

value: kr


title: CS_78P_AS_RNA

city: Linkoping

first: Colm

middle: Eamonn

last: Nestor

address: KEF, Hälsuniversitetet

institute: Linkoping University

description: outside pollen season

data_processing: gene expression microarrays were analyzed using the R statistical programming language, was background corrected and quantile normalized using tusing functions of the gene expression microarray analysis package,he ‘lumi’ package in the R programming environment. Raw probe expression values were background subtracted, variance-stabilizing transformation was used to stabilize the expression variance, and quantile normalization was used to normalize values across all arrays.

source_name: CD4+ T-cells

extract_protocol: RNA extraction was performed using a miRneasy Mini Kit (Qiagen). For each sample, 250 ng of total RNA was amplified and labeled using an Illumina TotalPrep 96 RNA Amplification Kit as per the manufacturer’s instructions. The quantity of the labeled cRNA was measured using a NanoDrop spectrophotometer, and the quality and size distribution of the labeled cRNA assessed using an Agilent 2100 Bioanalyzer.

tag: status

value: patient

tag: season

value: outside pollen season

tag: Sex

value: male


title: 11132.p1

first: Benjamin

last: Barwick

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

institute: Emory University

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

tag: sample id

value: I

value: ox

tag: age at collection (months)

tag: ethnicity


title: 11110.p1

tag: gender

tag: sentrix id

value: vn

value: asian

tag: cell type


title: CS_78P_DS_RNA

description: during pollen season

label_protocol: 250 ng of total RNA was amplified and labeled using an Illumina TotalPrep 96 RNA Amplification Kit as per the manufacturer’s instructions. The quantity of the labeled cRNA was measured using a NanoDrop spectrophotometer, and the quality and size distribution of the labeled cRNA assessed using an Agilent 2100 Bioanalyzer.

value: during pollen season


title: 11177.p1

tag: sentrix position

value: E

tag: experiment

tag: group

value: hv


title: 11167.p1

tag: family

tag: distribution

tag: site

value: kc

value: other


title: 11456.p1

value: F

tag: cpea dx

value: white

value: leukocyte


title: 11158.p1

value: Male

value: H

value: pb

value: african-amer


title: 11167.s1.1

value: A


title: 11241.p1


title: Lenti-cGAS-1

value: STAT1-/- fibroblasts

tag: transduced with lentiviruses expressing cGAS


title: 11074.p1

value: L

value: kr


title: WT, biological rep2

city: Los Angeles

first: Areum

last: Han

address: 6577 MacDonald Research Lab. 675 Charles E. Young Dr. South

institute: UCLA

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

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

source_name: wild-type brain

label_protocol: cDNA synthesis and amplification was performed using the GeneChip® Whole Transcript Sense Target Labeling and Control Reagents kit (Affymetrix).  Targets were enzymatically fragmented and biotinylated using the WT Target Labeling Kit (Affymetrix)

growth_protocol: PTBP2 KO mice were genotyped and whole brains were dissected from 3 mutant and 3 wild-type animals.

extract_protocol: Trizol extracted total RNA from mouse brain was further treated with DnaseI and purified by phenol/chloroform extraction, then treated with Ribominus (Invitrogen).

tag: tissue

value: brain

tag: genotype

value: wild-type


title: 11066.p1

city: Atlanta

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

value: G


title: 11106.p1

value: B

value: hv


title: WT, biological rep3


title: CS_32H_DS_RNA

description: during pollen season

tag: status

value: healthy

tag: season

value: during pollen season

tag: Sex

value: male


title: Embryo_Mismatch.Morpholino_Medium_rep4 Reference

city: Amsterdam

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

country: Netherlands

institute: AMC

description: The  CR (common reference) was composed by combining 1 ug of cRNA from each sample.

hyb_protocol: 825 ng for each channel were combined and made to 55 μl with 10x Blocking Agent and 25x Fragmentation Buffer. 55 μl of 2x Hi-RPM Hybridization Buffer was added (Gene Expression Hybridization Kit, Agilent Technologies). 100 μl of hybridization mixture was loaded onto each array and allowed to hybridize at 65°C (10 RPM) for 17h. The slides were washed with Gene Expression Wash Buffers I and II (Gene Expression Wash Buffer Kit, Agilent Technologies).

scan_protocol: Slides were scanned in an ozone-free room with the Agilent G2565BA scanner as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis guide version 5.5 (G4140-90050, Agilent technologies).

data_processing: Data was extracted with Feature Extraction version 9.5.1.1. (Protocol GE2-v5_95)  for two-color Agilent microarrays.

organism: Danio rerio

source_name: Common Reference

label_protocol: 0,5 μg of total RNA was amplified with the Amino-Allyl MessageAmp II kit (Ambion) according to manufacturer’s instruction. After aRNA synthesis, samples were labeled with Cy3-NHS mono-reactive dye (GE Healthcare) for the test samples and Cy5-NHS (GE Healthcare) mono-reactive dye for the common reference (pooled aRNA).

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Embryos of each treatment group were sampled at the 30% epiboly stage and snap frozen in liquid nitrogen. Total RNA from each sample was extracted using TRIZOL followed by a clean up procedure using the RNeasy Mini Kit (Qiagen) and removal of a residual genomic DNA by an RNase-free DNase treatment (Qiagen). RNA concentration was determined using a Nanodrop ND-1000 (Thermo Fisher Scientific) and RNA quality was assessed on a Agilent 2100 BioAnalyzer (Agilent Technologies). Total RNA samples with an RNA integrity number (RIN) >7 were used for further analysis. All assays were performed according to the manufacturer’s protocols.

treatment_protocol: Translation of traf6 was blocked by either one of two non-overlapping morpholinos (traf6 morpholino-1 and morpholino-2) specifically targeting the 5’UTR region. To be able to control for aspecific morpholino effects, a 5bp mismatch morpholino of traf6 morpholino-1 and a standard control morpholino (Gene Tools) were used. Morpholino oligonucleotides were diluted with Danieu buffer to a concentration of 0.5, 1 and 2 mM and embryos were injected at the one cell stage with 1nl of one of the above mentioned morpholinos. In addition, 1x Danieu’s buffer containing Phenol red was injected to control for the injection effect per se. All injections were performed in random order and the experiment was performed in quintuplicate.

tag: developmental stage

value: 30% epiboly

tag: treatment


title: 11010.p1

hyb_protocol: Followed the manufacturer's (Illumina) specifications

tag: sample id

tag: gender

value: Male

tag: sentrix id

value: F

value: fl

tag: age at collection (months)

tag: ethnicity

value: white

value: leukocyte


title: CS_77P_AS_RNA

description: outside pollen season

value: patient

value: outside pollen season


title: 11027.p1

tag: sentrix position

value: J

tag: experiment

tag: group

tag: family

value: kr

tag: cell type


title: PTBP2 KO, biological rep3

source_name: PTBP2 -/- brain

tag: tissue

value: brain

value: PTBP2 KO


title: CS_77P_DS_RNA

description: during pollen season


title: CS_32H_AS_RNA

description: outside pollen season


title: Embryo_Mismatch.Morpholino_Medium_rep4

description: 1nl of mismatch morpholino (1mM) was injected into 30% epiboly zebrafish embryos

source_name: Mismatch morpholino 1mM injected replicate 4

value: Mismatch morpholino

tag: dose

value: medium


title: WT, biological rep1

tag: genotype

value: wild-type


title: CS_28H_AS_RNA

description: outside pollen season

tag: status

value: healthy

tag: season

value: female


title: Embryo_Mismatch.Morpholino_Medium_rep2

source_name: Mismatch morpholino 1mM injected replicate 2

tag: developmental stage

value: 30% epiboly


title: 11090.p1

value: Male

value: C

tag: distribution

tag: site

value: vn

tag: cpea dx


title: CS_28H_DS_RNA

description: during pollen season

value: during pollen season

tag: Sex


title: 11104.p1

tag: sample id

tag: gender

tag: sentrix id

value: G

value: leukocyte


title: 11285.s1.2

tag: sentrix position

tag: experiment

value: oi

tag: age at collection (months)

tag: ethnicity

value: white


title: 11557.s1.2

value: E

tag: group

tag: family

value: kc

value: more-than-one-race

tag: cell type


title: 11565.p1

value: H

value: fl


title: CS_73P_AS_RNA

description: outside pollen season

tag: status

value: patient

value: outside pollen season

value: male


title: Embryo_Mismatch.Morpholino_Medium_rep1 Reference

value: 30% epiboly

tag: treatment


title: Embryo_Mismatch.Morpholino_Medium_rep1

source_name: Mismatch morpholino 1mM injected replicate 1

tag: developmental stage

value: Mismatch morpholino

tag: dose

value: medium


title: Embryo_Mismatch.Morpholino_Low_rep5 Reference


title: Embryo_Mismatch.Morpholino_Medium_rep2 Reference


title: Embryo_Mismatch.Morpholino_Low_rep5

description: 1nl of mismatch morpholino (0.5mM) was injected into 30% epiboly zebrafish embryos

source_name: Mismatch morpholino 0.5mM injected replicate 5

value: low


title: 11495.p1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

value: Male

value: I

tag: distribution

tag: site

value: pb


title: PTBP2 KO, biological rep2

tag: tissue

value: brain

tag: genotype

value: PTBP2 KO


title: CS_73P_DS_RNA

description: during pollen season

tag: season

value: during pollen season

tag: Sex


title: PTBP2 KO, biological rep1


title: 11350.p1

tag: sample id

tag: gender

tag: sentrix id

tag: sentrix position

value: A

value: kc

tag: cpea dx

value: leukocyte


title: CS_33H_AS_RNA

description: outside pollen season

value: healthy

value: female


title: 11418.p1

value: F

tag: experiment

tag: group

tag: family


title: 11581.p1

value: C

value: xm

tag: age at collection (months)

tag: ethnicity

value: white

tag: cell type


title: Embryo_Mismatch.Morpholino_Low_rep4 Reference

tag: developmental stage

value: 30% epiboly

tag: treatment


title: CS_71P_AS_RNA

description: outside pollen season

tag: status

value: patient

value: outside pollen season

value: male


title: FT50a

value: Male

value: L


title: 11442.p1

value: K

tag: distribution


title: Embryo_Mismatch.Morpholino_Low_rep2 Reference


title: CS_33H_DS_RNA

description: during pollen season

tag: season

value: during pollen season


title: 11426.p1

value: J


title: 11524.p1

value: D

tag: site


title: 11498.p1

tag: sample id

value: H

value: sb

value: leukocyte


title: Embryo_Mismatch.Morpholino_Low_rep4

source_name: Mismatch morpholino 0.5mM injected replicate 4

value: Mismatch morpholino

tag: dose

value: low


title: 11443.p1

tag: gender

tag: sentrix id

value: E


title: CS_27H_AS_RNA

description: outside pollen season

value: healthy

tag: Sex

value: female


title: Embryo_Mismatch.Morpholino_Low_rep1 Reference

value: 30% epiboly


title: 11483.p1

tag: sentrix position

value: B

tag: experiment

value: kc

tag: cpea dx

value: more-than-one-race


title: Lenti-cGAS-3

value: STAT1-/- fibroblasts

tag: transduced with lentiviruses expressing cGAS


title: CS_71P_DS_RNA

description: during pollen season

value: patient

value: male


title: CS_27H_DS_RNA

description: during pollen season

value: during pollen season


title: 11474.s1

value: Male

value: D

tag: group

tag: family

value: kr

tag: age at collection (months)

tag: ethnicity

value: white


title: 11442.s1

value: C

tag: cell type

value: leukocyte


title: CS_80H_AS_RNA

description: outside pollen season

tag: status

value: outside pollen season


title: Embryo_Mismatch.Morpholino_Low_rep2

source_name: Mismatch morpholino 0.5mM injected replicate 2

tag: developmental stage

tag: treatment

value: Mismatch morpholino

value: low


title: 11403.s1

tag: sample id

value: K

tag: distribution


title: PLC/PRF-5

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

description: HCC

hyb_protocol: Microarray hybridization was performed at 42°C for 16-20 hours in NimbleGen Hybridization System.

scan_protocol: After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: Raw data were extracted as pair files by NimbleScan software (version 2.5). NimbleScan software’s implementation of RMA offers quantile normalization and background correction. The Probe level (*_norm_RMA.pair) files and Gene summary (*_RMA.calls) files were produced. The gene summary files were imported into Agilent GeneSpring Software (version 10.0) for further analysis. Differentially expressed non-coding RNA were identified through Fold-change screening. Unsupervised hierarchical clustering was performed using the Agilent GeneSpring GX software (version 10.0).

source_name: malignant hepatocytes

label_protocol: NimbleGen One-Color DNA Labeling Kit

growth_protocol: cells have been culture in 100mm dishes with DMEM medium and 10%FBS until 80% confluent, then collected for RNA extraction

extract_protocol: RNA was extracted with RNeasy mini kit (Qiagen, Valencia, CA)

value: malignant hepatocytes


title: Huh7

description: HCC


title: CS_80H_DS_RNA

description: during pollen season

value: healthy

tag: season


title: HepG2

description: Hepatoma


title: Embryo_Phenol.Re.injected_rep5 Reference

value: 30% epiboly


title: 11461.p1

tag: gender

tag: sentrix id

value: L


title: 11426.s1

tag: sentrix position

value: J


title: CS_75P_AS_RNA

description: outside pollen season

value: patient

tag: Sex

value: female


title: Embryo_Mismatch.Morpholino_Low_rep1

source_name: Mismatch morpholino 0.5mM injected replicate 1

tag: dose


title: 11509.p1

value: Male

value: I

tag: experiment

tag: site

tag: cpea dx


title: CS_75P_DS_RNA

description: during pollen season

value: during pollen season


title: CS_40H_AS_RNA

description: outside pollen season

value: male


title: 11578.p1

value: F

tag: group

tag: family

value: kr

tag: age at collection (months)

value: white


title: HH

description: normal human hepatocytes

source_name: normal human hepatocytes

tag: cell type

value: normal human hepatocytes


title: 11579.p1

source_name: leukocyte

value: D

value: leukocyte


title: 11285.p1.2

value: C

value: oi

tag: ethnicity


title: Embryo_Phenol.Re.injected_rep4

description: 1nl of Phenol Red was injected into 30% epiboly zebrafish embryos

source_name: Phenol red injected replicate 4

tag: developmental stage

value: 30% epiboly

tag: treatment

value: Phenol red


title: Embryo_Phenol.Re.injected_rep5

source_name: Phenol red injected replicate 5


title: Embryo_Phenol.Re.injected_rep2 Reference


title: 11443.s1

tag: sample id

value: B

tag: distribution


title: FT10a

tag: gender

value: H


title: Embryo_Phenol.Re.injected_rep3

source_name: Phenol red injected replicate 3


title: CS_03P_AS_RNA

description: outside pollen season

source_name: CD4+ T-cells

tag: status

value: patient

tag: season

value: outside pollen season

value: female


title: Embryo_Phenol.Re.injected_rep4 Reference


title: Embryo_Phenol.Re.injected_rep3 Reference


title: CS_24H_AS_RNA

description: outside pollen season

value: healthy

tag: Sex


title: Embryo_Phenol.Re.injected_rep1 Reference


title: CS_40H_DS_RNA

description: during pollen season

value: during pollen season

value: male


title: Embryo_Phenol.Re.injected_rep2

source_name: Phenol red injected replicate 2


title: CS_57P_AS_RNA

description: outside pollen season


title: 11403.p1

value: Male

tag: sentrix id

tag: sentrix position

value: A


title: 11416.p1

value: L

tag: experiment


title: Embryo_Phenol.Re.injected_rep1

source_name: Phenol red injected replicate 1


title: 11230.p1.2

tag: site

value: fl

tag: cpea dx

value: white


title: 11461.s1

value: J

tag: group

tag: family

value: leukocyte


title: CS_24H_DS_RNA

description: during pollen season


title: 11474.p1

value: I

value: kr

tag: age at collection (months)

tag: cell type


title: FT10c

value: F


title: CS_03P_DS_RNA

description: during pollen season


title: CS_57P_DS_RNA

description: during pollen season


title: CS_76H_AS_RNA

description: outside pollen season


title: CS_76H_DS_RNA

description: during pollen season


title: CS_74P_AS_RNA

description: outside pollen season


title: Spinal cord_treated_SMA_sample04

description: Gene expression data from ceftriaxone-treated SMA mouse spinal cord

hyb_protocol: Following fragmentation, 15 micrograms of amplified cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix).

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

source_name: Spinal Cord, treated SMA

label_protocol: Biotinylated cRNA were prepared through a single amplification procedure according to the protocol developed by Affymetrix (GeneChip® Eukaryotic Small Sample Target Labeling Assay Version II; Affymetrix, Santa Clara, CA, USA).

growth_protocol: We analyzed whole spinal cords obtained from ceftriaxone-treated SMA mice (n=4), untreated SMA mice (n=4) and wt (n=4). The latter groups were treated with vehicle. Ceftriaxone administration was performed at P5 and the animals were sacrificed at 13 days. Spinal cords (lumbar regions L1–L5) of perfused with PFA mice were rapidly removed, embedded in Tissue-Tek OCT Compound (Zoeterwoude, the Netherlands) and frozen in liquid Nitrogen and stored at -80°C.

extract_protocol: Total RNA from mouse spinal cords was isolated using RNeasy® Mini Kit (Qiagen, Valencia, CA, USA) including DNase treatment to remove potential genomic DNA contamination. The starting RNA was quantified by spectrophotometric analysis (ND-100, NanoDrop technologies).

treatment_protocol: Ceftriaxone was dissolved in saline solution to a final concentration of 600mM. Five days old SMA mice were treated with 200mg/Kg/daily ceftriaxone by an intraperitoneal injection. The total volume injected was 5 µl. Control animals received equal volumes of vehicle alone (wt).

tag: strain

value: SMA mice (line 4299; FVB.Cg-Tg(SMN2*delta7)4299Ahmb Tg(SMN2)89Ahmb Smn1tm1Msd)

tag: genome/variation

tag: tissue

value: spinal cord

tag: treatment group

value: ceftriaxone-treated


title: CS_74P_DS_RNA

description: during pollen season

value: patient


title: Spinal cord_treated_SMA_sample02


title: 11413.p1

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

tag: sample id

tag: gender

value: B

tag: distribution

value: xx

tag: ethnicity


title: 11554.s1.1

tag: sentrix id

value: C

value: hv

value: asian


title: CS_38H_AS_RNA

description: outside pollen season

tag: status

value: healthy

tag: season

value: outside pollen season

tag: Sex

value: male


title: Spinal cord_untreated_SMA_sample03

description: Gene expression data from veichle-treated SMA mouse spinal cord

source_name: Spinal Cord, SMA

value: untreated


title: Spinal cord_untreated_SMA_sample01


title: Spinal cord_untreated_SMA_sample02


title: Spinal cord_treated_SMA_sample03


title: 11533.p1

value: Male

tag: sentrix position

value: D

tag: experiment

value: leukocyte


title: Spinal cord_treated_SMA_sample01


title: 3694T

city: Pittsburgh

first: William

middle: Armand

last: LaFramboise

state: PA

address: 5230 Centre Avenue

department: Pathology

institute: University of Pittsburgh

description: hybridized to SNP6.0

hyb_protocol: Affymetrix 6.0

scan_protocol: Affymetrix 6.0

data_processing:
GCOS to Partek Segmentation
primary data description: SNPs and CNV

label: streptavidin phycoerythrin

source_name: Tumor tissue from patient 3694

label_protocol: Affymetrix 6.0

extract_protocol: QiaAmp DNA FFPE Tissue Kit

value: esophageal adenocarcinoma tumor


title: 3385T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 3385


title: CS_38H_DS_RNA

description: during pollen season

value: during pollen season


title: Spinal cord_untreated_SMA_sample04

value: SMA mice (line 4299; FVB.Cg-Tg(SMN2*delta7)4299Ahmb Tg(SMN2)89Ahmb Smn1tm1Msd)

value: spinal cord


title: Spinal cord_wildtype_sample03

description: Gene expression data from veichle-treated wildtype mouse spinal cord

source_name: Spinal Cord, wildtype


title: 3694N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 3694

value: benign lymph node


title: 3385N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 3385


title: CS_02P_AS_RNA

description: outside pollen season

value: patient

value: female


title: 11489.p1

value: A

tag: group

tag: family

tag: site

value: xm

tag: cpea dx

value: more-than-one-race


title: 11557.p1.2

value: I

value: kc

tag: age at collection (months)

tag: cell type


title: CS_02P_DS_RNA

description: during pollen season


title: CS_11H_DS_RNA

description: during pollen season

value: healthy


title: 11230.s1.2

value: L

value: fl

value: white


title: 11509.s1

value: Male

value: H

value: kr

value: leukocyte


title: 3083N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 3083

tag: tissue


title: CS_11H_AS_RNA

description: outside pollen season

value: outside pollen season


title: 11499.p1

tag: sample id

value: E


title: FT10b

tag: gender

value: G


title: 2967T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2967

value: esophageal adenocarcinoma tumor


title: FT50c

value: A


title: Spinal cord_wildtype_sample04

tag: strain

value: SMA mice (line 4299; FVB.Cg-Tg(SMN2*delta7)4299Ahmb Tg(SMN2)89Ahmb Smn1tm1Msd)

tag: genome/variation

value: spinal cord

tag: treatment group

value: untreated


title: MCF7 45oC rep5

city: El Paso

first: Brad

middle: Allen

last: Bryan

address: 5001 El Paso Drive

department: Biomedical Sciences

institute: Texas Tech University Health Sciences Center

hyb_protocol: 750 ng of biotinylated aRNA was  briefly heat-denatured and loaded onto expression arrays to hybridize overnight.  Following hybridization, arrays were labeled with Cy3-streptavidin.

scan_protocol: The chips were imaged on the Illumina ISCAN.  Intensity values were transferred to GeneSpring GX microarray analysis software (Agilent).

data_processing: GeneSpring GX microarray analysis software (Agilent) was used to filter data based on quality of each call. Statistical relevance was determined using ANOVA with a Benjamini Hochberg FDR multiple testing correction (p-value < 0.05).

source_name: MCF7 45oC

label_protocol: RNA was amplified and biotin-labeled using Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: MCF10A, MCF7, MDA231, and MDA468 cells were maintained at constant 37oC as a control.  For the experimental treatment, prewarmed (45oC) conditioned media was added to each cell line and the cells were incubated for 30 minutes.  The 45oC media was then replaced with 37oC conditioned media.  Cells were allowed to grow for 4 hours and RNA was subsequently extracted.

extract_protocol: Total RNA was collected from each cell line 4 hours after completion of the hyperthermia treatment using the Qiagen RNAeasy mini kit.

tag: cell line

value: breast cancer cells

tag: treatment

value: 45oC hyperthermia shock for 30 minutes

tag: replicate


title: 3083T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 3083


title: MCF7 45oC rep4


title: MCF7 45oC rep6


title: 2967N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2967

value: benign lymph node


title: 11554.p1

source_name: leukocyte

tag: sentrix id

tag: sentrix position

value: L

tag: distribution

value: hv

tag: ethnicity

value: asian


title: Spinal cord_wildtype_sample01

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

institute: University of Milan


title: MCF7 45oC rep2


title: Spinal cord_wildtype_sample02


title: ES_3

city: Bunkyo-ku

first: Jiyoung

last: Lee

state: Tokyo

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University

description: Gene expression of ES cells

hyb_protocol: Cy3-labeled RNA probes were hybridized to a whole mouse genome DNA oligo microarray (4 × 44K, Agilent) for 16 hours at 65°C according to the manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner at a 5 um resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent).

source_name: ES cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using Trizol (Invutrogen) and purified by RNAeasy column (QIAGEN).

treatment_protocol: GS and ES cells were treated with trypsin and collected.

tag: genotype

value: wildtype

value: embryonic stem cells

tag: genetic background


title: 11457.s1

value: Male

value: K

tag: experiment

tag: group

tag: family

value: leukocyte


title: 2964T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2964

tag: tissue


title: 11533.s1

tag: sample id

tag: gender

value: J

tag: cell type


title: ES_2

description: Gene expression of ES cells


title: 11416.s1

value: D


title: MCF7 37oC rep6

source_name: MCF7 37oC

value: 37oC control


title: 2880T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2880

value: esophageal adenocarcinoma tumor


title: MCF7 45oC rep3


title: MCF7 45oC rep1


title: 11104.s1.1

value: G


title: Xist KO GS_2

description: Gene expression of Xist KO GS cells

source_name: GS cells

value: Xist KO

value: germ line stem cells


title: ES_1

description: Gene expression of ES cells


title: FT50b

value: H


title: 2821T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2821


title: MCF7 37oC rep5

value: breast cancer cells


title: 11458.p1

value: F

tag: site

value: xm

tag: cpea dx

tag: age at collection (months)

value: white


title: 2821N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2821

value: benign lymph node


title: Xist KO GS_1

description: Gene expression of Xist KO GS cells


title: Xist KO GS_3

description: Gene expression of Xist KO GS cells


title: 11406.p1

value: kr

value: more-than-one-race


title: 2800T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2800


title: MCF7 37oC rep1

tag: cell line

tag: treatment

tag: replicate


title: wt GS_2

description: Gene expression of wildtype GS cells

value: wildtype


title: 11457.p1.1

value: Male

tag: sentrix id

tag: sentrix position

value: B

tag: distribution

value: leukocyte


title: wt GS_3

description: Gene expression of wildtype GS cells

tag: genotype

tag: genetic background


title: MDA468 45oC rep3

source_name: MDA468 45oC

value: 45oC hyperthermia shock for 30 minutes


title: MCF7 37oC rep3

value: 37oC control


title: MCF7 37oC rep2


title: MCF7 37oC rep4


title: 2800N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2800


title: wt GS_1

description: Gene expression of wildtype GS cells


title: 2738T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2738

value: esophageal adenocarcinoma tumor


title: 2738N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2738


title: SKNDZ-miR-125b2-2

city: Taipei

first: Sheng-Kai

last: Chang

address: NO.1 JEN AI ROAD SECTION 1 TAIPEI 100 TAIWAN R.O.C.

department: Clinical Laboratory Science of Medical Biotechnology

country: Taiwan

institute: NATIONAL TAIWAN UNIVERSITY COLLEGE OF MEDICINE

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArrayR (HOA5.1) with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42℃ 5 mins；Wash Ⅱ 42℃, 5 mins, 25℃, 5 mins; Wash Ⅲ rinse 20 times), and the slides were dried by centrifugation and scanned by an Axon 4000B scanner (Molecular Devices, Sunnyvale, CA, USA).

scan_protocol: The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing:
The technical repeat data was tested by Pearson correlation coefficient calculation to check the reproducibility (R value > 0.975). The signal intensity of each spot was loaded into Rosetta Resolver SystemR (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver SystemR could remove both systematic and random errors. In brief, spots which ﬂag is less than 0 in all arrays were filtered out.
Spots that passed the criteria were normalized by median scaling normalization method. Normalized spot intensities were transformed to gene expression log2 ratios between the control and treatment groups under Rosetta Resolver error model adjustment. The spots with log2 ratio ≥ 1 or log2 ratio ≤ -1 and p-value < 0.05 are tested for further analysis.

label_protocol: Fluorescent aRNA targets were prepared from 2.5 μg total RNA samples using OneArrayR Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: A total of 1 x 10^6 SKNDZ cells treated with either scramble shRNA or miR-125b-2 were harvested, and total RNA were extracted by TRIzol® reagent.

value: Neuroblastoma

value: SKNDZ


title: SKNDZ-miR-125b2-3


title: 11113.p1

department: Hematology and Medical Oncology

value: J

tag: experiment

tag: group

value: hv

tag: ethnicity


title: 11418.s1

tag: sample id

value: E

tag: family


title: 2636T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2636

tag: tissue


title: MDA468 45oC rep2

tag: cell type

value: breast cancer cells


title: SKNDZ-miR-125b2-1


title: SKNDZ-Negative Control-3

source_name: SKNDZ-Negative Control-3

value: Scramble shRNA


title: MDA468 45oC rep1


title: 11149.p1

tag: gender

value: G


title: 2636N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2636

value: benign lymph node


title: 11076.p1

value: H


title: 11138.s1.1

value: L


title: 11005.p1

value: Male

value: F


title: MDA468 37oC rep5

source_name: MDA468 37oC


title: 2634T

description: hybridized to SNP6.0

source_name: Tumor tissue from patient 2634


title: red2∆ 2

city: Tsukuba

first: Tomoyasu

last: Sugiyama

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

description: This sample is of S.pombe that lacks the red3 gene.

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: Schizosaccharomyces pombe

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

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA: 0.5% Yeast extract, 3% glucose, 75mg/L adenine) at 30˚C.

extract_protocol: Total RNA was extracted using mirVana miRNA isolation kit (Applied Biosystems) according manufacturer's instructions.

tag: strain


title: 2634N

description: hybridized to SNP6.0

source_name: Normal tissue from patient 2634


title: SKNDZ-Negative Control-2

source_name: SKNDZ-Negative Control-2

tag: cell line


title: 11113.s1

source_name: leukocyte

tag: site

tag: cpea dx

value: white

value: leukocyte