title: PANC-1 cells 24 hours post GLV-1h153 infection rep1

city: New York

first: Dana

last: Hadadd

state: NY

address: 410 E 69th st 4th floor

department: Surgery

institute: Memorial Sloan-Kettering Cancer Center

description: PANC-1 cells 24 hours after infection with GLV-1h153

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133A Array.

scan_protocol: HG-U133A cDNA microarray chip images were scanned and processed to CEL files using the standard GCOS analysis suite (Affymetrix Inc).

data_processing: CEL files were then normalized and processed to signal intensities using the gcRMA algorithm from the Bioconductor library for the R statistical programming system.

source_name: PANC-1 cells incubated in media

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2002, Affymetrix).

growth_protocol: PANC-1 cells (American type culture collection) were plated at 5 × 105 cells per well in 6-well plates and grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 1% antibiotic-antimycotic solution (Mediatech, Inc., Herndon, VA) and 10% fetal bovine serum (FBS) (Mediatech, Inc.) at 37oC under 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Qiagen Inc., Valencia, CA).

treatment_protocol: Cells were infected with GLV-1h153 at a multiplicity of infection of 5.0 and incubated at for zero, 6 and 24 hours.

value: Pancreas/duct

tag: morphology

value: epithlial

tag: disease

value: epithelioid carcinoma

tag: time


title: 2VD6

status: Public on Jun 20 2013

type: protein

city: Irvine

first: Elisabeth

last: Baum

state: CA

address: Med Surge II

country: USA

institute: University of California Irvine

hyb_protocol: Serum samples were diluted 1:200 in Protein Array Blocking buffer (Whatman Inc, Sanford, ME) supplemented with 10% (vol/vol) DH5α E. coli lysate (MCLAB, San Francisco, CA) and incubated on arrays over night at 4°C.  Microarray slides were incubated in biotin-conjugated anti-IgG Fc fragment secondary antibody (Jackson ImmunoResearch, West Grove, PA) diluted 1:200 in blocking buffer, and detected by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Columbia, MD). The slides were washed and air-dried by brief centrifugation.

scan_protocol: Probed array slides were scanned in a Perkin Elmer ScanArray Express HT at a wavelength of 670 nm, at 95% laser power and 55% PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: For analysis of antibody binding to Pf proteins on the microarray the following steps were taken: (i) the mean background signal of antibody binding to 31 control spots of in vitro transcription/translation reaction without DNA template (no DNA spots) were removed from each sera’s raw values of antibody binding measured as the mean pixel intensity of spots of printed protein; (ii) the average, 95% confidence intervals (CI) and Z-scores of antibody binding intensity for each study and control groups were calculated for each protein target on the array. A Z-score was the number of standard deviations above or below the mean of the control group. Protein targets were considered immunogenic if the following criteria were satisfied: (i) for each sera group, the average pixel intensity to the protein had to be above the group’s upper CI value of pixel intensity of no DNA spots; high reactant proteins were considered for further analysis if at least one study group satisfied this cutoff; (ii) the study group’s lower confidence interval for pixel intensity did not overlap with the control group’s upper confidence interval for each protein; the significant antigens were included in further analysis if this was true for at least one study group.

molecule: protein

organism: Homo sapiens

source_name: serum

tag: serum type

value: Exposed

tag: age group (years)

tag: season

value: DRY

tag: site

value: VALLEY

tag: molecule subtype

value: Total IgG


title: 2VD4


title: 251507210519_1_1-PLAT/LOG[A(3)/A(5)]

type: RNA

city: Cambridge

first: Dawn

last: Thompson

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description:
PLAT
Biological replicate A, technical replicate 1 (dye swap)

hyb_protocol: Standard Agilent protocols for Agilent 8x15K and 4x44K Oligo Microarrays

scan_protocol: Arrays were scanned using an Agilent scanner and analyzed with Agilent’s feature extraction software version 10.5.1.1.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.  Reported expression values for each gene are median log2 ratios across all probes.

molecule: total RNA

organism: Saccharomyces cerevisiae

label_protocol: Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.

growth_protocol: Cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and grown overnight in BMW medium at 30 ° C in a New Brunswick Scientific Edison model TC-7 roller drum on the highest speed until saturated (1-2 days).  These saturated cultures were then used to inoculate 300 ml BMW batch cultures in 2 liter Erlenmeyer flasks at 1 x 106 cells/mL for the glucose depletion and repletion experiments described below.  Flasks were transferred to New Brunswick Scientific Edison water bath model C76 shakers set to 200 rpm.

extract_protocol: Qiagen Yeast RNA extraction

treatment_protocol: Glucose depletion: Samples from the BMW cultures were taken at: Lag, Log, Late log (LL), Diauxic shift (DS), Post shift (PS), and plateau (P) at the appropriate times for each species.  Samples were collected in 50 mL conicals filled with the appropriate amount of 100% methanol in a dry ice-ethanol bath to stop cellular processes and RNase activity at a temperature of – 40 ° C or lower to produce a 60/40 mixture once the sample is added. Cells were pelleted at 3000 rpm at -4°C, flash frozen with liquid N2, and stored at -80°C prior to total RNA extraction.

tag: phase

value: LOG

tag: organism

value: Saccharomyces cerevisiae

value: PLAT


title: PANC-1 cells 6 hours post GLV-1h153 infection rep3

description: PANC-1 cells 6 hours after infection with GLV-1h153

label: biotin

tag: tissue

tag: cell line

value: 6 h

tag: infection


title: 252050510004_2_1-LAG/LOG[Q(5)/Q(3)]

description:
LAG
Biological replicate Q, technical replicate 1

organism: Saccharomyces paradoxus

value: LAG

value: Saccharomyces paradoxus


title: 252050510010_2_1-PLAT/LOG[P(5)/P(3)]

description:
PLAT
Biological replicate P, technical replicate 2


title: 252050510004_1_3-PS/LOG[P(5)/P(3)]

description:
DS
Biological replicate P, technical replicate 1

value: DS


title: PANC-1 cells 24 hours post GLV-1h153 infection rep2


title: Uninfected PANC-1 cells rep3

description: PANC-1 cells cultured in media

value: control


title: PANC-1 cells 6 hours post GLV-1h153 infection rep2


title: Uninfected PANC-1 cells rep2

description: PANC-1 cells cultured in media


title: Fn14_KO_TNBS_6

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

hyb_protocol: The Mouse 430_2 GeneChip probe arrays were pre-hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol. 15 ug of labeled cRNA was fragmented in 30 uL 1X fragmentation buffer 100 mM KOAc, 30 mM MgOAc at 95°C for 35 minutes. The fragmented labeled cRNA was resuspended in 300 uL 1X hybridization buffer containing 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20, 0.5 mg/mL Aceylated BSA, 0.1 mg/mL herring sperm DNA, control oligo B2, and control transcripts bioB 1.5 pM, bioC 5 pM, bioD 25 pM, and cre 100 pM, and hybridized to Genechip probe arrays according to manufacturer’s protocol (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip probe arrays were scanned using GeneArray Scanner (Hewlett Packard, Corvallis, OR).

data_processing: CEL files were subjected to GC-content-based Robust Multi-array Average (GCRMA) normalization.  Expression levels were log (base 2) transformed.  All calculations and analyses were carried out using R and Bioconductor computational tools.  Analyses were applied to discover genes that were differentially expressed between specific sets of tissue.  First, to identify differentially expressed genes between groups of samples, we applied the linear modeling approach (MANOVA) to fit gene expression levels (log2 transformed) according to the defined groups of samples and Bayesian posterior error analysis.  Genes that exhibited a log-odds score greater than zero and fold change greater then 1.5 were considered significantly different.

label: Biotin

organism: Mus musculus

label_protocol: Five ug of purified total RNA was used in a 20 uL first strand reaction with 200U SuperScript II (Invitrogen, Carlsbad,CA) and 0.5ug (dT) T7primer[5’GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(T)24] in 1X first strand buffer (Invitrogen Life Technologies, Carlsbad, CA) with a 42°C incubation for 1 hour. Second strand synthesis was carried out by the addition of 40 U E. coli DNA Polymerase, 2 U E. coli RNase H, 10 U E. coli DNA Ligase in 1X second strand buffer (Invitrogen Life Technologies, Carlsbad, CA) followed by incubation at 16°C for 2 hrs.  The second strand synthesis reaction was purified using the Genechip Sample Cleanup Module according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA). The purified cDNA was amplified using BioArray high yield RNA transcription labeling kit (Enzo Life Sciences, Inc., Parmingdale, NY) according to manufacturer’s protocol to produce 70-120 ?g of biotin labeled cRNA (compliment RNA).

extract_protocol: Mice were sacrificed after colitis induction.  Colons were harvested for total RNA.

treatment_protocol: To induce chronic colitis, under anesthesia with ketamine and xylazine, 0.2% TNBS (Research Organics, Cleveland, OH) in PBS: ethanol =1: 1 was rectally injected with a stainless gavage tube 6 times weekly for 6 consecutive weeks. The dDose of TNBS solution was sequentially ubsequently increased; 1.0, 1.5, 1.5, 1.8, 2.0, 2.0 ul/ g body weight. Tissues and cells were harvested 3 days after the last injection.

tag: strain

value: Balb/c

tag: genotype/variation

value: FN14 KO

value: colon


title: 2VD3


title: 252050510008_2_3-LPS/LOG[R(5)/R(3)]

description:
PS
Biological replicate R, technical replicate 1

value: PS


title: 2VW10

value: WET


title: 2VD2

value: Exposed


title: 252050510010_1_1-LPS/LOG[Q(5)/Q(3)]

description:
PS
Biological replicate Q, technical replicate 2


title: 252050510008_1_1-LPS/LOG[Q(5)/Q(3)]

description:
PS
Biological replicate Q, technical replicate 1


title: 2VW9


title: 252050510004_2_3-DS/LOG[Q(5)/Q(3)]

description:
LL
Biological replicate Q, technical replicate 1

value: LL


title: 252050510010_1_4-DS/LOG[R(5)/R(3)]

description:
LL
Biological replicate R, technical replicate 2


title: Fn14_KO_TNBS_4


title: Fn14_KO_TNBS_7


title: Fn14_KO_TNBS_3


title: PANC-1 cells 24 hours post GLV-1h153 infection rep3

value: Pancreas/duct

value: epithlial

value: epithelioid carcinoma


title: 2VW8

value: VALLEY

value: Total IgG


title: PANC-1 cells 6 hours post GLV-1h153 infection rep1

value: 6 h


title: 2VD1

value: DRY


title: Uninfected PANC-1 cells rep1

description: PANC-1 cells cultured in media


title: Fn14_KO_TNBS_5


title: Brain-fed-4

city: Jena

first: Abu

last: Farhan

state: Thuringia

address: Hans-knol-str 8

department: Evolutionary Neuroethology

country: Germany

institute: MPI for chemical ecology

description: Gene expression after 0hr starvation

hyb_protocol: Labelled amplified cRNA samples were analyzed on a Nanodrop spectrophotometer using the microarray function and used for microarray hybridization at 65°C for 17 hours.

scan_protocol: Slides were scanned using Agilent Microarray Scanner

data_processing: Slides were washed, treated in stabilization and drying solution, scanned with the Agilent Microarray Scanner, and data was extracted with Agilent Feature Extraction software version 9.1. The resulting gene expression profiles were analyzed using GeneSpring GX .software (Silicon Genetics, Redwood City, CA). Raw intensities were normalized using the 75th percentile value and log2 and baseline transformed prior statistical analysis.

organism: Drosophila melanogaster

source_name: Brain fed

label_protocol: RNA was labeled with cyanine 3-CTP dye using the Low RNA Input Linear Amplification kit according to manufacturer instructions (Agilent Technologies).

extract_protocol: Both for starved and fed flies RNA extraction was done four times each with 100 Antennae and 50 brains from 50 flies using the Qiagen RNA extraction kit. RNA concentration was measured photometrically with a NanoDrop ND-1000 and RNA quality and integrity was controlled with the Agilent 2100 Bioanalyzer.

value: Brain

tag: gender

value: Female

tag: age

value: 5-7 days

tag: stress

value: 0hr starvation


title: Brain-fed-2

description: Gene expression after 0hr starvation


title: 2VW7


title: Brain-fed-1

description: Gene expression after 0hr starvation


title: Brain-fed-3

description: Gene expression after 0hr starvation


title: Fn14_KO_TNBS_2

value: Balb/c

value: FN14 KO


title: Fn14_KO_5

value: colon


title: Brain-28 hrs starved-3

description: Gene expression after 28hrs starvation

source_name: Brain starve 28hrs

value: 28hrs starvation


title: Brain-28 hrs starved-4

description: Gene expression after 28hrs starvation


title: Fn14_KO_3


title: 252050510008_1_4-DS/LOG[R(5)/R(3)]

description:
LL
Biological replicate R, technical replicate 1

value: Saccharomyces paradoxus

value: LOG


title: Fn14_KO_4


title: 2VW6

value: Exposed

value: WET


title: 252050510010_2_3-LPS/LOG[P(5)/P(3)]

description:
DS
Biological replicate P, technical replicate 2

value: DS


title: 252050510008_1_3-LAG/LOG[R(5)/R(3)]

description:
LAG
Biological replicate R, technical replicate 1

value: LAG


title: 2VW5

value: VALLEY

value: Total IgG


title: 2VW4


title: 252050510004_2_4-PS/LOG[Q(5)/Q(3)]

description:
DS
Biological replicate Q, technical replicate 1


title: 252050510008_2_2-PS/LOG[R(5)/R(3)]

description:
DS
Biological replicate R, technical replicate 1


title: 252047510017_2_2-sbayuv_PS/LOG[L(5)/L(3)]

description:
PLAT
Biological replicate L, technical replicate 2

organism: Saccharomyces bayanus

value: PLAT

value: S. bayanus uvarum


title: 252047510017_1_1-sbayuv_LL/LOG[E(5)/E(3)]

description:
LL
Biological replicate E, technical replicate 3

value: LL


title: 252047510012_2_1-sbayuv_LPS/LOG[K(5)/K(3)]

description:
PLAT
Biological replicate K, technical replicate 2


title: 2VW3


title: 2VW2


title: 2VW1


title: 1HD2

value: DRY

value: HILLTOP


title: Antennae-fed-4

description: Gene expression after 0hr starvation

source_name: Antennae fed

value: Antennae

value: Female

value: 5-7 days

value: 0hr starvation


title: BALBC_WT_TNBS_5

value: Balb/c

value: Wild Type

value: colon


title: Fn14_KO_TNBS_1

value: FN14 KO


title: Brain-28 hrs starved-1

description: Gene expression after 28hrs starvation

value: Brain

value: 28hrs starvation


title: BALBC_WT_TNBS_3


title: BALBC_WT_TNBS_6


title: Antennae-fed-1

description: Gene expression after 0hr starvation


title: Brain-28 hrs starved-2

description: Gene expression after 28hrs starvation


title: Antennae-28 hrs starved-4

description: Gene expression after 28hrs starvation

source_name: Antennae starve 28hrs


title: BALBC_WT_TNBS_4


title: Antennae-fed-2

description: Gene expression after 0hr starvation


title: 1HD1

value: Exposed


title: Antennae-fed-3

description: Gene expression after 0hr starvation


title: Fn14_KO_1


title: Antennae-28 hrs starved-3

description: Gene expression after 28hrs starvation


title: BALBC_WT_TNBS_1


title: BALBC_WT_TNBS_2


title: BALBC_WT_4


title: 1HW10

value: WET

value: Total IgG


title: 252047510006_1_3-sbayuv_PLAT/LOG[D(5)/D(3)]

description:
PLAT
Biological replicate D, technical replicate 1

value: PLAT

value: S. bayanus uvarum

value: LOG


title: 252047510012_2_2-sbayuv_PLAT/LOG[K(5)/K(3)]

description:
PLAT
Biological replicate K, technical replicate 3


title: 1HW9

value: HILLTOP


title: 252047510017_1_3-sbayuv_LAG/LOG[K(5)/K(3)]

description:
LAG
Biological replicate K, technical replicate 1

value: LAG


title: 1HW8


title: 252047510005_1_4-sbayuv_EPS/LOG[J(5)/J(3)]

description:
PS
Biological replicate J, technical replicate 2

value: PS


title: 252047310007_2_4-PS/LOG[L(5)/L(3)]

description:
PS
Biological replicate L, technical replicate 2

organism: Lachancea waltii

value: Lachancea waltii


title: 252047310003_1_1-LAG/LOG[D(5)/D(3)]

description:
LAG
Biological replicate D, technical replicate 1


title: 252047510006_1_1-sbayuv_LAG/LOG[D(5)/D(3)]


title: 1HW7


title: 252047510006_1_4-sbayuv_LAG/LOG[E(5)/E(3)]

description:
LAG
Biological replicate E, technical replicate 1


title: 252047310004_2_1-EPS/LOG[J(5)/J(3)]

description:
PS
Biological replicate J, technical replicate 1


title: 252047310007_2_2-LL/LOG[L(5)/L(3)]

description:
LL
Biological replicate L, technical replicate 1

value: LL


title: 252047510005_1_2-sbayuv_LL/LOG[J(5)/J(3)]

description:
LL
Biological replicate J, technical replicate 1


title: 252047510005_2_4-sbayuv_LAG/LOG[L(5)/L(3)]

description:
LAG
Biological replicate L, technical replicate 1


title: 1HW5


title: 1HW4


title: 1HW6


title: 252047510005_1_3-sbayuv_DS/LOG[J(5)/J(3)]


title: 1HW3


title: Antennae-28 hrs starved-1

description: Gene expression after 28hrs starvation

value: Antennae

value: Female

value: 5-7 days


title: 252047310005_2_4-PLAT/LOG[L(5)/L(3)]

description:
PLAT
Biological replicate L, technical replicate 1


title: Antennae-28 hrs starved-2

description: Gene expression after 28hrs starvation


title: 1HW2


title: 252047510017_1_2-sbayuv_LPS/LOG[J(5)/J(3)]

description:
PLAT
Biological replicate J, technical replicate 4


title: BALBC_WT_2

value: Balb/c

value: Wild Type

value: colon


title: 252047310003_1_4-LAG/LOG[E(5)/E(3)]


title: BALBC_WT_1


title: 22RV1-ESE1_norm

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

hyb_protocol: Hybridization with dye-swap duplication was performed to compare sample versus reference. The same quantity of differentially labelled sample and reference was put together, fragmented and hybridized to oligonucleotide glass arrays with sequences representing >41K human unique genes and transcripts. All steps were performed using the Gene Expression Hybridization kit (Agilent Technologies) following the 60-mer oligo microarray processing protocol (Agilent Technologies).

scan_protocol: Slides were washed with the Agilent wash procedure and scanned with the dual-laser microarray scanner Agilent G2505B (Agilent Technologies).

data_processing: Images were then analysed using Feature Extraction software (Agilent Technologies) version 9.5. Raw data elaboration was carried out with Bioconductor (Gentleman et al., 2004), using R statistical language. The limma package was used to identify differentially expressed genes, applying a cut-off on the p-value, adjusted for multiple testing by the Benjamini-Hochberg approach (<0.01), followed by filtering on expression level (logFC >1 or ≤1).

source_name: 22Rv1-ESE1 cell line

label_protocol: Labelling was performed using NHS ester Cy3 or Cy5 dyes (GE HealthCare, Buckinghamshire, UK) able to react with the modified RNA.

growth_protocol: ESE1 expressing stable cell lines were generated by transfection of the pESE1 expressing vector using Lipofectamine 2000 (Invitrogen,  Zug, Switzerland) and selection with G418 (Sigma-Aldrich Chemie GmbH, Buchs, Switzerland; 700μg/ml).  Negative control cells were obtained by transfection with pcDNA3.1 and selection in G418.  In both cases, G418 resistant colonies were expanded and expression of ESE1 was determined by RT-PCR and Western blotting.

extract_protocol: Total RNA was extracted with SV Total RNA extraction System (Promega).

value: prostate cancer cell line 22Rv1

value: transfected with ESE1 expression vector

source_name: 22Rv1-pcDNA cell line

value: transfected with pcDNA3.1 empty vector


title: 252047310005_1_3-LL/LOG[K(5)/K(3)]

description:
LL
Biological replicate K, technical replicate 1


title: 22RV1-ESE1_DS


title: 252047510017_2_1-sbayuv_DS/LOG[L(5)/L(3)]

description:
PS
Biological replicate L, technical replicate 1


title: 1VD10

value: Exposed

value: DRY

value: VALLEY

value: Total IgG


title: 252047310005_2_1-EPS/LOG[K(5)/K(3)]

description:
PS
Biological replicate K, technical replicate 1

value: LOG


title: 1VD9


title: BALBC_WT_3


title: 252047510012_1_3-sbayuv_EPS/LOG[K(5)/K(3)]

description:
DS
Biological replicate K, technical replicate 2

value: DS

value: S. bayanus uvarum


title: 252047510001_2_2-sbayuv_DS/LOG[E(3)/E(5)]

description:
LL
Biological replicate E, technical replicate 2 (dye swap)

value: LL


title: 252047310005_1_4-DS/LOG[K(5)/K(3)]

description:
DS
Biological replicate K, technical replicate 1

value: Lachancea waltii


title: 1VD8


title: Nanoparticle - NCAg-10 nm PVP-4_0.5 ppm

city: Durham

first: William

last: Ward

state: NC

address: 109 TW Alexander Dr

department: NHEERL

institute: United States EPA

description:
replicate 4
6116696003_L

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with no background subtraction in Illumina GenomeStudio.

organism: Rattus norvegicus

source_name: rat N27 mesencephalic neurons

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser and quantified by NanoDrop spectrophotometer.

tag: cell type

value: N27 mesencephalic neurons


title: Control - HBSS control-4_0 ppm

description:
replicate 4
6116696003_K


title: 252047510012_2_4-sbayuv_LPS/LOG[L(5)/L(3)]

value: PLAT


title: 252047310001_2_3-DS/LOG[F(3)/F(5)]

description:
LL
Biological replicate F, technical replicate 2 (dye swap)


title: 1HW1

value: WET

value: HILLTOP


title: 1VD6


title: 252047310007_2_3-DS/LOG[L(5)/L(3)]

description:
DS
Biological replicate L, technical replicate 1


title: 252047510001_2_1-sbayuv_DS/LOG[D(3)/D(5)]

description:
DS
Biological replicate D, technical replicate 2 (dye swap)


title: 252047310003_2_4-PLAT/LOG[F(5)/F(3)]

description:
PS
Biological replicate F, technical replicate 1

value: PS


title: 252047510002_2_1-sbayuv_PS/LOG[E(3)/E(5)]

description:
PS
Biological replicate E, technical replicate 2 (dye swap)


title: Nanoparticle - NCAg-10 nm PVP-1_0.5 ppm

description:
replicate 1
6116696003_H


title: 1VD7


title: 1VD5


title: Nanoparticle - NCAg-10 nm citrate-1_0.5 ppm

description:
replicate 1
6116696003_J


title: Control - HBSS control-1_0 ppm

description:
replicate 1
6116696003_G


title: Nanoparticle - NCAg-75 nm citrate-2_0.5 ppm

description:
replicate 2
6116696003_I


title: 252047510002_2_4-sbayuv_DS/LOG[D(5)/D(3)]

description:
DS
Biological replicate D, technical replicate 3


title: Fn14_KO_2

value: Balb/c

value: FN14 KO

value: colon


title: 252047310007_1_1-LAG/LOG[F(5)/F(3)]

description:
LAG
Biological replicate F, technical replicate 1

value: LAG


title: 252047310003_2_2-PLAT/LOG[E(5)/E(3)]

description:
PS
Biological replicate E, technical replicate 1


title: 252047510017_2_4-sbayuv_EPS/LOG[J(5)/J(3)]

description:
PS
Biological replicate J, technical replicate 3


title: 1VD3

value: Exposed

value: DRY


title: 252047510002_1_1-sbayuv_PS/LOG[E(5)/E(3)]


title: Control - HBSS control-3_0 ppm

description:
replicate 3
6116696003_E


title: 252047310005_2_2-PS/LOG[K(5)/K(3)]

description:
PS
Biological replicate K, technical replicate 2


title: 252047510012_2_3-sbayuv_EPS/LOG[L(5)/L(3)]


title: Nanoparticle - NCAg-75 nm PVP-4_0.5 ppm

description:
replicate 4
6116696003_F


title: 252047310002_2_4-DS/LOG[D(5)/D(3)]

description:
LL
Biological replicate D, technical replicate 3


title: 1VD2

value: VALLEY

value: Total IgG


title: 1VD1


title: 252047310004_2_3-PLAT/LOG[J(5)/J(3)]

description:
PLAT
Biological replicate J, technical replicate 1

value: LOG


title: 252047510005_2_3-sbayuv_PLAT/LOG[J(5)/J(3)]

description:
PLAT
Biological replicate J, technical replicate 3

value: S. bayanus uvarum


title: 1VD4


title: Nanoparticle - NCAg-10 nm PVP-3_0.5 ppm

description:
replicate 3
6116696003_B


title: Nanoparticle - NCAg-75 nm citrate-4_0.5 ppm

description:
replicate 4
6116696003_D


title: Nanoparticle - NCAg-10 nm citrate-3_0.5 ppm

description:
replicate 3
6116696002_L


title: Nanoparticle - NCAg-75 nm PVP-1_0.5 ppm

description:
replicate 1
6116696003_C


title: Nanoparticle - NCAg-75 nm PVP-2_0.5 ppm

description:
replicate 2
6116696003_A


title: 252047510005_2_1-sbayuv_PS/LOG[J(5)/J(3)]


title: 1VW10


title: 252047310001_1_1-DS/LOG[D(5)/D(3)]

description:
LL
Biological replicate D, technical replicate 1

value: LL


title: 252047510006_2_2-sbayuv_PLAT/LOG[E(5)/E(3)]

description:
PLAT
Biological replicate E, technical replicate 1


title: 1HD3


title: 252047310005_2_3-PLAT/LOG[K(5)/K(3)]

description:
PLAT
Biological replicate K, technical replicate 1

value: Lachancea waltii


title: 1VW9


title: 252047310007_1_4-LAG/LOG[L(5)/L(3)]

description:
LAG
Biological replicate L, technical replicate 1


title: 252047510001_1_1-sbayuv_DS/LOG[D(5)/D(3)]

description:
DS
Biological replicate D, technical replicate 1

value: DS


title: 252047510012_1_2-sbayuv_DS/LOG[K(5)/K(3)]

description:
DS
Biological replicate K, technical replicate 1


title: 1VW8


title: Nanoparticle - NCAg-75 nm citrate-3_0.5 ppm

description:
replicate 3
6116696002_I

value: N27 mesencephalic neurons


title: 252047510012_1_4-sbayuv_PS/LOG[K(5)/K(3)]

value: PLAT


title: Control - Citrate control-1_0 ppm

description:
replicate 1
6116696002_K


title: 252047310004_1_3-LL/LOG[J(5)/J(3)]

description:
LL
Biological replicate J, technical replicate 1


title: Nanoparticle - NCAg-10 nm citrate-4_0.5 ppm

description:
replicate 4
6116696002_J


title: 1VW7

value: WET


title: 252047310001_2_1-DS/LOG[D(3)/D(5)]

description:
LL
Biological replicate D, technical replicate 2 (dye swap)


title: 1VW6


title: 1VW5


title: 252047510001_1_2-sbayuv_DS/LOG[E(5)/E(3)]

description:
LL
Biological replicate E, technical replicate 1


title: 1VW4


title: 252047510012_1_1-sbayuv_LL/LOG[K(5)/K(3)]

description:
LL
Biological replicate K, technical replicate 1


title: 252047510017_2_3-sbayuv_PLAT/LOG[L(5)/L(3)]

description:
PLAT
Biological replicate L, technical replicate 3


title: Nanoparticle - NCAg-75 nm PVP-3_0.5 ppm

description:
replicate 3
6116696002_H


title: 1VW3


title: 252047310004_2_2-PS/LOG[J(5)/J(3)]

description:
PS
Biological replicate J, technical replicate 2

value: PS


title: 1VW2


title: 252047510005_1_1-sbayuv_LAG/LOG[J(5)/J(3)]

description:
LAG
Biological replicate J, technical replicate 1


title: 252047310001_2_2-DS/LOG[E(3)/E(5)]

description:
LL
Biological replicate E, technical replicate 2 (dye swap)


title: 252047310001_1_2-DS/LOG[E(5)/E(3)]


title: 252047310001_1_3-DS/LOG[F(5)/F(3)]

description:
LL
Biological replicate F, technical replicate 1


title: Nanoparticle - NCAg-75 nm citrate-1_0.5 ppm

description:
replicate 1
6116696002_F


title: 252047510004_1_3-LL/LOG[K(5)/K(3)]

description:
LL
Biological replicate K, technical replicate 2

value: Saccharomyces bayanus


title: Control - Citrate control-4_0 ppm

description:
replicate 4
6116696002_G


title: 1VW1


title: 252047510003_1_1-LAG/LOG[J(5)/J(3)]


title: 252047310003_1_3-PLAT/LOG[D(5)/D(3)]

description:
PS
Biological replicate D, technical replicate 1


title: Nanoparticle - NCAg-10 nm citrate-2_0.5 ppm

description:
replicate 2
6116696002_C


title: 252047310004_2_4-EPS/LOG[L(5)/L(3)]

description:
PS
Biological replicate L, technical replicate 1


title: Control - Citrate control-2_0 ppm

description:
replicate 2
6116696002_E


title: 252047510016_1_4-LAG/LOG[L(5)/L(3)]


title: 252047310004_1_1-LAG/LOG[J(5)/J(3)]


title: Control - Citrate control-3_0 ppm

description:
replicate 3
6116696002_D


title: 252047510017_1_4-sbayuv_LL/LOG[L(5)/L(3)]

description:
LL
Biological replicate L, technical replicate 1


title: Control - HBSS control-2_0 ppm

description:
replicate 2
6116696002_A


title: BALBC_WT_5

value: Balb/c

value: Wild Type


title: 252047510003_2_4-LL/LOG[L(5)/L(3)]

description:
LL
Biological replicate L, technical replicate 2


title: 252047510004_2_3-DS/LOG[L(5)/L(3)]


title: 252047310004_1_4-DS/LOG[J(5)/J(3)]

description:
DS
Biological replicate J, technical replicate 1


title: 252047310007_1_3-LAG/LOG[K(5)/K(3)]

description:
LAG
Biological replicate K, technical replicate 2

value: LAG


title: 252047510003_2_2-PLAT/LOG[J(5)/J(3)]

description:
PLAT
Biological replicate J, technical replicate 2


title: 252035310007_1_2-PLAT/LOG[N(5)/N(3)]

description:
PLAT
Biological replicate N, technical replicate 1

organism: Naumovozyma castellii

value: Naumovozyma castellii


title: Bmpr1a-/- N2B27 sample 2

city: London

first: Tristan

last: Rodriguez

address: Du Cane Road, Hammersmith Hospital Campus

department: National Heart and Lung Institute

country: United Kingdom

institute: NHLI Imperial College London

description:
Gene expression data fromBmpr1a-/- cells in N2B27
Bmpr1a-/- ESCs

hyb_protocol: The hybridisation protocols were performed on GeneChip Fluidics Station 450.

scan_protocol: Samples were scanned using the Affymetrix GeneChip Scanner.

data_processing:
The data was normalised using the RMA normalisation algorithm in Expression Console 1.2. The array QC was performed using Expression Console first and then Bioconductor.
RMA was used as the standard method for probe summarization (i.e. calculating a transcript signal value from multiple independent probes as on Affy arrays) and normalisation of Affymetrix expression array data.  Quality control of Affymetrix expression microarrays involves identifying outlier arrays, rather than setting defined cut-offs for the various quality control metrics that are generated from the various controls and the probe summarization/normalisation. Note that the signal values are all log base 2; this is standard practice for RMA analyzed data. The data was first QC'ed using the Affymetrix Expression console.

source_name: Bmpr1a-/-  ESCs cultured 3 days in N2B27

label_protocol: Biotinylated cRNA were prepared using the Affymetrix GeneChip® WT Terminal Labeling Kit (Ambion, Invitrogen).

growth_protocol: Embryonic stem cells (ESCs) were grown in standard ESC conditions

extract_protocol: Cells were pelleted and total RNA was extracted using the Quiagen RNAeasy Kit and then prepared for analysis with the Ambion WT expression kit (Invitrogen).

treatment_protocol: Wild type ES cells (E14) and Bmpr1a-/- cell lines (C1-6, Fr124 and Fr88) were grown in ES cell culture conditions and in differentiation conditions (N2B27)

value: Embryonic stem cells

tag: genotype

tag: culture condition

value: 3 days in N2B27


title: 252047510004_2_4-PS/LOG[L(5)/L(3)]

description:
PLAT
Biological replicate L, technical replicate 1


title: 252035310007_2_1-DS/LOG[O(5)/O(3)]

description:
DS
Biological replicate O, technical replicate 1


title: 252047510016_2_3-PS/LOG[J(5)/J(3)]

description:
PLAT
Biological replicate J, technical replicate 4


title: 252035310007_2_4-PLAT/LOG[O(5)/O(3)]

description:
PLAT
Biological replicate O, technical replicate 1


title: Bmpr1a-/- N2B27 sample 1


title: Nanoparticle - NCAg-10 nm PVP-2_0.5 ppm

description:
replicate 2
6116696002_B


title: Bmpr1a-/- N2B27 sample 3


title: 252047510004_2_1-PS/LOG[K(5)/K(3)]

description:
PLAT
Biological replicate K, technical replicate 1


title: 252047510016_2_2-DS/LOG[J(5)/J(3)]

description:
PS
Biological replicate J, technical replicate 2


title: 252035310014_1_2-LAG/LOG[Q(5)/Q(3)]

description:
LAG
Biological replicate Q, technical replicate 1


title: 252047510003_2_1-PS/LOG[J(5)/J(3)]

description:
PLAT
Biological replicate J, technical replicate 1


title: 252047510016_1_1-LPS/LOG[J(5)/J(3)]

description:
PLAT
Biological replicate J, technical replicate 3


title: 252047510016_1_3-LPS/LOG[L(5)/L(3)]

description:
PLAT
Biological replicate L, technical replicate 2


title: Control N2B27 sample 3

description:
Gene expression data from E14 cells in N2B27
E14 ESCs

source_name: E14 cell cultured 3 days in N2B27

value: wild type


title: Control N2B27 sample 2


title: 252047510004_1_1-LAG/LOG[K(5)/K(3)]

description:
LAG
Biological replicate K, technical replicate 1

value: LOG


title: 252035310006_2_3-LL/LOG[N(5)/N(3)]

description:
LL
Biological replicate N, technical replicate 1


title: Control ESC media sample 3

description:
Gene expression data from E14 cells in ESC media
E14 ESCs

source_name: E14 cells in ESC media

value: ESC media


title: Bmpr1a-/- ESC media sample 2

description:
Gene expression data from Bmpr1a-/- in ESC media
Bmpr1a-/- ESCs

source_name: Bmpr1a-/- in ESC media


title: Control ESC media sample 2


title: 252035310007_1_1-PS/LOG[N(5)/N(3)]

description:
PS
Biological replicate N, technical replicate 1


title: Control N2B27 sample 1


title: Bmpr1a-/- ESC media sample 3


title: 252035310005_2_3-LL/LOG[M(5)/M(3)]

description:
LL
Biological replicate M, technical replicate 1

value: LL


title: 252035310006_1_3-PS/LOG[M(5)/M(3)]

description:
PS
Biological replicate M, technical replicate 1


title: Control ESC media sample 1


title: 252035310007_1_4-LL/LOG[O(5)/O(3)]

description:
LL
Biological replicate O, technical replicate 1


title: 252047510004_1_2-ELL/LOG[K(5)/K(3)]

description:
LL
Biological replicate K, technical replicate 1


title: 252035310014_1_1-LAG/LOG[P(5)/P(3)]

description:
LAG
Biological replicate P, technical replicate 1


title: 252047510003_1_2-ELL/LOG[J(5)/J(3)]

description:
LL
Biological replicate J, technical replicate 1


title: 252035310006_2_2-LAG/LOG[N(5)/N(3)]

description:
LAG
Biological replicate N, technical replicate 1


title: 252035310006_2_1-PLAT/LOG[M(5)/M(3)]

description:
PLAT
Biological replicate M, technical replicate 1


title: 252035310006_1_2-ELL/LOG[M(5)/M(3)]

description:
LL
Biological replicate M, technical replicate 2


title: 252047510004_1_4-DS/LOG[K(5)/K(3)]

description:
DS
Biological replicate K, technical replicate 1


title: 252047510003_1_3-LL/LOG[J(5)/J(3)]

description:
LL
Biological replicate J, technical replicate 2


title: 252035310014_1_3-PLAT/LOG[P(5)/P(3)]

description:
PLAT
Biological replicate P, technical replicate 1


title: 252047510004_2_2-PLAT/LOG[K(5)/K(3)]

description:
PLAT
Biological replicate K, technical replicate 2


title: 252047510003_1_4-DS/LOG[J(5)/J(3)]

description:
PS
Biological replicate J, technical replicate 1


title: 252047510003_2_3-ELL/LOG[L(5)/L(3)]

description:
LL
Biological replicate L, technical replicate 1


title: 252035310014_1_4-PLAT/LOG[Q(5)/Q(3)]

description:
PLAT
Biological replicate Q, technical replicate 1


title: 252047510016_2_1-PLAT/LOG[L(5)/L(3)]

description:
PLAT
Biological replicate L, technical replicate 3


title: 252047510016_1_2-LPS/LOG[K(5)/K(3)]

description:
PLAT
Biological replicate K, technical replicate 3


title: 252035310006_1_1-LAG/LOG[M(5)/M(3)]

description:
LAG
Biological replicate M, technical replicate 1


title: 252035310007_2_2-PS/LOG[O(5)/O(3)]

description:
PS
Biological replicate O, technical replicate 1


title: 252035510005_2_1-LL/LOG[H(5)/H(3)]

description:
LL
Biological replicate H, technical replicate 1

organism: Candida albicans

value: Candida albicans


title: 252047510016_2_4-DS/LOG[K(5)/K(3)]

description:
DS
Biological replicate K, technical replicate 2

value: DS


title: 252035310006_2_4-DS/LOG[N(5)/N(3)]

description:
DS
Biological replicate N, technical replicate 1


title: 252035510006_1_4-PLAT/LOG[H(5)/H(3)]

description:
PLAT
Biological replicate H, technical replicate 1


title: Ring1B_E14

type: SRA

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

library_source: genomic

data_processing:
High quality reads (Chastity score .= 0.6) were aligned to the mouse genome (mm9) using Eland (Illumina) allowing up to two mismatches within the first 32 bases. Reads not aligning uniquely to the mouse genome were removed.
Aligned datasets were filtered for multiple reads at the same position occurring after PCR amplication. Where more than one read mapped to the same position and at the same strand duplicates were removed.
The reads were extended to 200 bp length, and the number of reads at a given position was counted and saved as a fixedStep wig file with 100 bp resolution.
Peak calling was done in CisGenome 1.2 using IgG samples as negative controls. Lists of peaks and further descriptions can be found here: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002494
Genome_build: mm9
Supplementary_files_format_and_content: aln: list of aligned reads. wig: fixedStep Wiggle file containing densities with 100 bp resolution of aligned and filtered reads.

molecule: genomic DNA

source_name: Mouse embryotic stem cells

growth_protocol: Mouse embryonic stem (mES) cells were cultured on 0.1% (w/v)  gelatin-coated plates in Glasgow medium (Sigma) supplemented  with glutamax-1 (Gibco), non-essential amino acids (Gibco),  50 mM 2-mercaptoethanol–PBS, 15% ES-cell-qualified FBS  (Gibco) in the presence of 1,000 U/ml of LIF (Millipore), and 1% (v/v) pen/strep. In addition, the Rest2/2 and Wt control mES cells were cultured in the presence of feeder cells (Mitomycin C treated primary mouse embryonic fibroblasts). The mES Eed2/2 and Rnf22/2 mES cells were provided by Dr. Anton Wutz. The Rest2/2 and Wt control mES cells were provided by Dr. Zhou-Feng Chen and Dr. Helle Færk Jørgensen.

extract_protocol:
Cells were fixed for 10 min in culture media containing 1% formaldehyde and were processed for ChIP as in Dietrich  et al. (2007) EMBO J 26: 1637–1648.
DNA from three parallel ChIPs were pooled and 10 ng was used for making ChIP-seq libraries. Libraries were generated according to Illumina recommendations and sequencing was done on a Genome Analyzer II (Illumina).

value: wt (ctrl for Eed)

value: mESC

tag: chip antibody

value: rabbit anti-RNF2/Ring1B (NAST; antigen sequence:NASTHSNQEAGPSNKRTKT)

tag: chip antibody manufacturer

value: NAST


title: 252035510005_1_4-PS/LOG[G(5)/G(3)]

description:
PS
Biological replicate G, technical replicate 1

value: PS


title: Ring1B_Eed

value: Eed-/-


title: 252035510002_1_1-PS/LOG[B(5)/B(3)]

description:
DS
Biological replicate B, technical replicate 1


title: 252035310007_1_3-LAG/LOG[O(5)/O(3)]

description:
LAG
Biological replicate O, technical replicate 1


title: 252035510005_1_1-LAG/LOG[G(5)/G(3)]

description:
LAG
Biological replicate G, technical replicate 1


title: Rest_E14

value: rabbit anti-REST (Millipore, 07-579)

value: Millipore

tag: chip antibody catalog #


title: 252035510009_2_3-LAG/LOG[G(5)/G(3)]

description:
LAG
Biological replicate G, technical replicate 2

value: LAG


title: 252035510005_2_3-PLAT/LOG[G(5)/G(3)]

description:
PLAT
Biological replicate G, technical replicate 1

value: PLAT


title: 252035510002_1_2-PS/LOG[C(5)/C(3)]

description:
DS
Biological replicate C, technical replicate 1


title: 252035510004_1_3-PS/LOG[C(3)/C(5)]

description:
DS
Biological replicate C, technical replicate 3 (dye swap)


title: 252035510005_1_2-LL/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 1


title: 252035510002_2_2-PS/LOG[C(3)/C(5)]

description:
DS
Biological replicate C, technical replicate 2 (dye swap)


title: Rest_Eed


title: cardiomyocyte TGF-beta2 treated rep4

city: Umeå

first: Nina

last: Gennebäck

address: NUS 6M

department: Public health and clinical medicin/medicin

country: Sweden

institute: Umeå University

hyb_protocol: Performed according to Illumina protocol

scan_protocol: Illumina Beadstation 500GX according to Illumina protocol

data_processing:
Cubic spline normalization, subtracted background.
Illumina Genomestudio was used

source_name: cardiomyocyte TGF-beta2 treated

label_protocol: Illumina TotalPrep RNA Amplification Kit was used

growth_protocol: HL-1 cells growth in T75 flasks and keept according to protocol (serum was ultrcentrifuged before use.

extract_protocol: RNA was purified with Rneasy Fibrous Tissue Kit (Qiagen)

treatment_protocol: Treated with or without growth factor (10ng/mL TGF-beta2 and 100ng/mL PDGF BB, Invitrogen), incubated in serumfree media for 23h before collection of media.

tag: treatment


title: 252035510006_1_1-DS/LOG[H(5)/H(3)]

description:
LL
Biological replicate H, technical replicate 2

tag: phase


title: cardiomyocyte PDGF BB treated rep3

source_name: cardiomyocyte PDGF BB treated

value: PDGF BB


title: IgG_Eed

value: Rabbit IgG (DAKO)

value: DAKO


title: 252035510002_2_1-PS/LOG[B(3)/B(5)]

description:
DS
Biological replicate B, technical replicate 2 (dye swap)

value: LOG

tag: organism


title: 252035510006_1_2-PS/LOG[H(5)/H(3)]

description:
PS
Biological replicate H, technical replicate 1


title: SOX4_siRNA_TGFbeta_2

city: Basel

first: Neha

last: Tiwari

address: Mattenstrasse 28

country: Switzerland

institute: University of Basel

hyb_protocol: Hybridization was performed according to the standard Affymetrix procedure.

scan_protocol: Scanning was performed with Affymetrix GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Probesets were summarized and probeset-level values normalized with the rma(target=core) function from R/Bioconductor package oligo (version 1.14.0).

source_name: NMuMG, SOX4 siRNA, TGFβ treated

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen).

treatment_protocol: NMuMG cells were transfected with control siRNA (siControl) or siRNA against Sox4 (siSox4) in the presence (2 days) or absence of 2ng/ml TGFβ.

value: NMuMG

tag: sirna

value: TGFβ


title: cardiomyocyte TGF-beta2 treated rep3

tag: cell line


title: cardiomyocyte PDGF BB treated rep1


title: 252035510005_1_3-DS/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 2

value: LL

value: Candida albicans


title: SOX4_siRNA_TGFbeta_1


title: cardiomyocyte PDGF BB treated rep2


title: 252035510009_1_2-LAG/LOG[H(5)/H(3)]

description:
LAG
Biological replicate H, technical replicate 1


title: IgG_E14

value: wt (ctrl for Eed)

value: mESC


title: cardiomyocyte untreated rep4

source_name: cardiomyocte untreated

value: control


title: SOX4_siRNA_1

source_name: NMuMG, SOX4 siRNA, no treatment


title: cardiomyocyte untreated rep2


title: cardiomyocyte untreated rep1


title: SOX4_siRNA_2


title: cardiomyocyte untreated rep3


title: Ecoli_wild-type_repA_Aerobic

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description: This sample is of wild-type Escherichia coli MG1655 K-12, aerobic growth conditions. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridzation was performed following Roche NimbleGen standard opperator protocol.  See www.nimblegen.com.

scan_protocol: Scanning was performed using an Axon GenePix scanner at 5 µM resolution and PMT of 480.

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: Escherichia coli str. K-12 substr. MG1655star

source_name: Escherichia coli MG1655 K-12 WT

label_protocol: Labeling was performed following Roche NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Escherichia coli MG1655 K-12 WT were grown to mid-log phase (O.D.600nm 0.35) aerobically (70% N2, 5% CO2, 25% O2) at 37°C in MOPS +0.2% glucose media (Neidhardt et al, 1974, Lazazzera et al, 1993).

extract_protocol: Total RNA was extracted using a hot phenol method (ref). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer and quantity was determined using a NanoDrop.

treatment_protocol: Cells were treated with a stop solution of Phenol and Ethanol, spun down and flash frozen and stored at -80°C (Khodursky et al, 2003).

value: Wild-type

tag: phenotype

value: normal

tag: accession


title: Ecoli_wild-type_repB_Aerobic

description: This sample is of wild-type Escherichia coli MG1655 K-12, aerobic growth conditions. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.


title: cardiomyocyte TGF-beta2 treated rep2


title: cardiomyocyte TGF-beta2 treated rep1


title: PDGF-BB, rep4

description:
5773660148_F
Exosomal RNA.

hyb_protocol: Performed according to Illumina protocol.

scan_protocol: Illumina BeadStation 500GX according to Illumina protocol.

data_processing: Cubic spline normalization, subtracted background. Illumina GenomeStudio was used.

source_name: exosomes derived from cardiomyocytes, PDGF-BB treated

label_protocol: Illumina TotalPrep RNA Amplification Kit was used.

growth_protocol: HL-1 cells were grown in T75 flasks and kept according to protocol (serum was ultracentrifuged before use).

extract_protocol: Whole exosome RNA was purified with the RNeasy Fibrous Tissue Kit (Qiagen).

treatment_protocol: HL-1 cells were treated with or without growth factor (10ng/mL TGF-beta2 or 100ng/mL PDGF-BB, Invitrogen), and incubated in serum-free media for 23h before collection of media.

value: exosomes derived from HL-1 cardiomyocytes

value: PDGF-BB


title: NK.v2.Foxp3.DTR-.Sp.8hr.081211#3

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

treatment_protocol: BDC2.5/NOD.Foxp3-DTR were injection with DT and NK cells (CD19-CD3-Nkp46+) at various time points were collected. Target organs were harvested and prepared into single cell suspension, stained using fluorescent antibodies and sorted on a MOFLO to high purity (double sorted).  RNA from those sorted cells was analyzed by affymetrix microarray.

value: 7 to 10 weeks

tag: exclusion markers

tag: tissue

value: Spleen

tag: strain

value: NOD

tag: phenotype markers

tag: separation method

value: MoFlo Sorter

tag: Sex

value: female


title: Ecoli_wild-type_rep2_Anaerobic

description: This sample is of wild-type Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.

growth_protocol: Escherichia coli MG1655 K-12 WT and ∆fnr were grown to mid-log phase (O.D.600nm 0.3) anerobically (95% N2, 5% CO2) at 37°C in MOPS +0.2% glucose media (Neidhardt et al, 1974, Lazazzera et al, 1993).

extract_protocol: Total RNA was extracted using a hot phenol method. RNA quality was determined by analysis with an Agilent 2100 bioanalyzer and quantity was determined using a NanoDrop.

tag: genotype


title: NK.v2.Foxp3.DTR-.Sp.8hr.060111#1

tag: age


title: Ecoli_dFNR_rep1_Anaerobic

description: This sample is of ∆fnr Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the first of two ∆fnr biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli MG1655 K-12 ∆fnr

value: dFNR

value: lacking FNR protein


title: PDGF-BB, rep2

description:
5773660151_E
Exosomal RNA.

tag: cell type


title: Ecoli_dFNR_rep2_Anaerobic

description: This sample is of ∆fnr Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the second of two ∆fnr biological replicates used in this experiment, each from separate cultures.


title: NK.v2.Foxp3.DTR-.Sp.8hr.070811#2


title: PDGF-BB, rep1

description:
5773660148_E
Exosomal RNA.


title: NK.v2.Foxp3.DTR-.Sp.24hr.052511#1


title: NK.v2.Foxp3.DTR-.Sp.15hr.081511#3


title: TFG-beta2, rep3

description:
5773660151_D
Exosomal RNA.

source_name: exosomes derived from cardiomyocytes, TGF-beta2 treated


title: NK.v2.Foxp3.DTR-.Sp.24hr.061711#2


title: TFG-beta2, rep2

description:
5773660151_C
Exosomal RNA.


title: NK.v2.Foxp3.DTR-.Pa.8hr.070811#2

value: Pancreas


title: PDGF-BB, rep3

description:
5773660151_F
Exosomal RNA.


title: Ecoli_wild-type_rep1_Anaerobic

description: This sample is of wild-type Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: TFG-beta2, rep4

description:
5773660148_D
Exosomal RNA.


title: H1299 SC_rep 2

city: Hsin-Chu

first: Feng-Mao

last: Lin

state: Taiwan

address: 75 Bo-Ai Street

country: Taiwan

institute: National Chiao Tung University

description: Gene expression data of cells with scramble control

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Images were scanned using an Affymetrix GeneArray Scanner, using default oarameters. The resulting images were analyzed using Affymetrix Genechip Command Console 2.0 software.

data_processing: The data were analyzed with GCRMA with default parameters.

label_protocol: Biotinylated cRNA were prepared from the purified total RNA equivalent to 250ng according to the standard Affymetrix protocol.

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

treatment_protocol: H1299 lung cancer cells were grown in RPMI media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were infected with lentivirus which carry shRNAs specific for RBP2 and harvested for preparation of RNA after 72 hours.

value: H1299 lung cancer cell line

tag: genotype/variation

tag: shRNA

value: scramble


title: H1299 SC_rep 1

growth_protocol: H1299 lung cancer cells were grown in RPMI media supplemented with 10% (v/v) fetal calf serum.


title: NK.v2.Foxp3.DTR-.Pa.24hr.061711#2


title: NK.v2.Foxp3.DTR-.Sp.15hr.061011#1


title: NK.v2.Foxp3.DTR-.Pa.8hr.081211#3


title: 252050410004_1_1-EPS/LOG[H(5)/H(3)]

organism: Yarrowia lipolytica

tag: phase

value: LL

value: Yarrowia lipolytica

value: LOG


title: Control, rep4

description:
5773660151_B
Exosomal RNA.

source_name: exosomes derived from cardiomyocytes, untreated

tag: treatment


title: 252050410001_1_2-DS/LOG[B(5)/B(3)]

description:
LL
Biological replicate B, technical replicate 1

tag: organism


title: 252050410003_2_2-LAG/LOG[H(5)/H(3)]

value: LAG


title: 251983810008_2_4-DS/LOG[F(3)/F(5)]

description:
DS
Biological replicate F, technical replicate 2 (dye swap)

value: Saccharomyces cerevisiae

value: DS


title: 251983810006_1_2-LL/LOG[E(5)/E(3)]

description:
LL
Biological replicate E, technical replicate 1


title: H1299 RBP2 KD2_rep 1

description: Gene expression data of RBP2 depletion cells

tag: cell line

value: RBP2 depletion

value: RBP2 KD2


title: 252050410001_1_1-DS/LOG[A(5)/A(3)]

description:
LL
Biological replicate A, technical replicate 1


title: 252050410002_2_2-PS/LOG[C(3)/C(5)]

description:
LL
Biological replicate C, technical replicate 4 (dye swap)


title: 252050410004_2_2-LL/LOG[I(5)/I(3)]

description:
LL
Biological replicate I, technical replicate 1


title: 251983810007_1_2-LAG/LOG[F(5)/F(3)]

description:
LAG
Biological replicate F, technical replicate 1


title: NK.v2.Foxp3.DTR+.Sp.8hr.060111#1

value: 7 to 10 weeks

value: Spleen


title: 252050410002_1_1-PS/LOG[B(5)/B(3)]

description:
LL
Biological replicate B, technical replicate 3


title: 251983810008_2_2-DS/LOG[E(5)/E(3)]

description:
DS
Biological replicate E, technical replicate 3


title: NK.v2.Foxp3.DTR+.Sp.8hr.070811#2

value: NOD

value: MoFlo Sorter


title: Control, rep3

description:
5773660148_B
Exosomal RNA.

value: exosomes derived from HL-1 cardiomyocytes


title: H1299 RBP2 KD2_rep 2


title: 252050410001_2_3-DS/LOG[C(3)/C(5)]

description:
LL
Biological replicate C, technical replicate 2 (dye swap)


title: 252050410003_1_2-LL/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 1


title: NK.v2.Foxp3.DTR+.Sp.24hr.101211#3

value: female


title: NK.v2.Foxp3.DTR-.Pa.15hr.060811#1

value: Pancreas


title: NK.v2.Foxp3.DTR+.Sp.8hr.081211#3


title: 251983810006_1_4-PS/LOG[E(5)/E(3)]

description:
PS
Biological replicate E, technical replicate 1

value: PS


title: NK.v2.Foxp3.DTR-.Pa.15hr.081511#3


title: NK.v2.Foxp3.DTR+.Sp.15hr.061011#2


title: NK.v2.Foxp3.DTR+.Sp.24hr.101211#4


title: NK.v2.Foxp3.DTR-.Pa.24hr.052511#1


title: Control, rep2

description:
5773660148_A
Exosomal RNA.


title: Control, rep1

description:
5773660151_A
Exosomal RNA.


title: TFG-beta2, rep1

description:
5773660148_C
Exosomal RNA.


title: H1299 RBP2 KD1_rep 1

value: H1299 lung cancer cell line

value: RBP2 KD1


title: NK.v2.Foxp3.DTR+.Sp.24hr.061711#2


title: NK.v2.Foxp3.DTR+.Sp.15hr.081511#3


title: 251983810006_2_4-DS/LOG[D(3)/D(5)]

description:
LL
Biological replicate D, technical replicate 3 (dye swap)

value: LL


title: H1299 RBP2 KD1_rep 2


title: 251983810008_1_3-DS/LOG[E(3)/E(5)]

description:
DS
Biological replicate E, technical replicate 2 (dye swap)

value: LOG


title: 252050410002_2_1-PS/LOG[B(3)/B(5)]

description:
LL
Biological replicate B, technical replicate 4 (dye swap)

value: Yarrowia lipolytica


title: 251983810008_2_3-DS/LOG[F(5)/F(3)]

description:
DS
Biological replicate F, technical replicate 1

value: Saccharomyces cerevisiae


title: 252050410003_1_1-LAG/LOG[G(5)/G(3)]

description:
LAG
Biological replicate G, technical replicate 1

value: LAG


title: 252050410003_2_3-PLAT/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 4


title: NK.v2.Foxp3.DTR+.Pa.8hr.070811#2


title: NK.v2.Foxp3.DTR+.Pa.8hr.081211#3


title: 252050410003_2_4-LPS/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 5


title: 251983810007_2_1-LAG/LOG[D(3)/D(5)]

description:
LAG
Biological replicate D, technical replicate 2 (dye swap)


title: NK.v2.Foxp3.DTR+.Pa.8hr.060111#1


title: 251983810007_1_1-LAG/LOG[D(5)/D(3)]

description:
LAG
Biological replicate D, technical replicate 1


title: 252050410002_1_2-PS/LOG[C(5)/C(3)]

description:
LL
Biological replicate C, technical replicate 3


title: Ecoli_hns-stpA_repB_Aerobic_Tiling

description: This sample is of ∆hns/∆stpA mutant from parent Escherichia coli MG1655 K-12, aerobic growth conditions. It is the second of two mutant biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed following Roche NimbleGen standard operator protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed using an Axon GenePix scanner at 5 µM resolution and PMT for a median background of ~100.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655 K-12 ∆hns/∆stpA, aerobic

label_protocol: Single stranded cDNA was reverse transcribed using SuperScript II, Aminoallyl dUTP and Actinomycin D. Labeling was performed by conjugating Cy3 dyes with dUTP (Cho et al. 2009).

growth_protocol: Escherichia coli MG1655 K-12 WT and ∆hns/∆stpA were grown to mid-log phase (O.D.600nm 0.3) anaerobically (95% N2, 5% CO2) at 37°C in MOPS +0.2% glucose media (Neidhardt et al, 1974, Lazazzera et al, 1993).

extract_protocol: Total RNA was extracted using a hot phenol method (Khodursky et al, 2003). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer and quantity was determined using a NanoDrop.

value: ∆hns/∆stpA

tag: phenotype

value: lacking H-NS and StpA proteins

value: NC_000913 - ∆hns/∆stpA

tag: growth condition

value: aerobic


title: NK.v2.Foxp3.DTR+.Sp.15hr.060811#1

value: 7 to 10 weeks

tag: exclusion markers

value: Spleen

value: NOD


title: 252050410002_2_4-DS/LOG[A(5)/A(3)]

description:
LL
Biological replicate A, technical replicate 5


title: 251983810008_2_1-PLAT/LOG[E(3)/E(5)]

description:
PLAT
Biological replicate E, technical replicate 2 (dye swap)

value: PLAT


title: 251983810008_1_4-PS/LOG[E(3)/E(5)]

description:
PS
Biological replicate E, technical replicate 2 (dye swap)


title: NK.v2.Foxp3.DTR+.Pa.24hr.101211#3

tag: tissue

value: Pancreas

value: MoFlo Sorter

value: female


title: NK.v2.Foxp3.DTR+.Pa.24hr.101211#4

tag: strain


title: 252050410001_1_4-PS/LOG[A(5)/A(3)]

description:
LL
Biological replicate A, technical replicate 2


title: NK.v2.Foxp3.DTR+.Pa.24hr.061711#2

tag: phenotype markers


title: NK.v2.Foxp3.DTR+.Pa.24hr.052511#1

tag: separation method


title: 252050410003_1_4-PS/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 3


title: 251983810006_2_3-DS/LOG[D(5)/D(3)]

description:
LL
Biological replicate D, technical replicate 2


title: HNS - Aerobic B

type: genomic

description: IP and INPUT (reference) for WT HNS from WT Escherichia coli MG1655 K-12 under aerobic growth conditions.

hyb_protocol: Hybridized according to NimbleGen protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: HNS ChIP DNA from WT Escherichia coli MG1655 K-12 Replicate B

label_protocol: Labeled with Cy5 (ChIP) and Cy3 (INPUT) according to NimbleGen protocols (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells were grown aerobically (25% O2, 70% N2 and 5% CO2) until mid-log phase (OD600 of 0.35) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

extract_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

value: anaerobic

tag: antibody

value: Pre-cleared H-NS polyclonal antibody

source_name: INPUT ChIP DNA from WT Escherchia coli MG1655 K-12, no antibody control, Replicate B

treatment_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and no antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

tag: tag


title: Ecoli_hns-stpA_repB_Anaerobic_Tiling

description: This sample is of ∆hns/∆stpA mutant from parent Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the second of two mutant biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli MG1655 K-12 ∆hns/∆stpA, anaerobic

tag: genotype

tag: accession


title: HNS - Anaerobic B

description: IP and INPUT (reference) for WT HNS from WT Escherichia coli MG1655 K-12 under anaerobic growth conditions.

growth_protocol: Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

treatment_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.


title: FNR - ∆hns∆stpA B

description:
IP and INPUT (reference) for  FNR from WT Escherichia coli MG1655 K-12 ∆hns/∆stpA under anaerobic growth conditions.
SAMPLE 2

source_name: FNR ChIP DNA from ∆hns/∆stpA E. coli MG1655

value: Affinity Purified FNR antibody

source_name: INPUT ChIP DNA from ∆hns/∆stpA, no antibody control


title: IHF - Anaerobic B

description: IP and INPUT (reference) for WT IHF from WT Escherichia coli MG1655 K-12 under anaerobic growth conditions.

source_name: IHF ChIP DNA from WT Escherichia coli MG1655 K-12 Replicate B

value: Pre-cleared IHF polyclonal antibody


title: Ecoli_hns-stpA_repA_Anaerobic_Tiling

description: This sample is of ∆hns/∆stpA mutant from parent Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the first of two mutant biological replicates used in this experiment, each from separate cultures.


title: Ecoli_hns-stpA_repA_Aerobic_Tiling

description: This sample is of ∆hns/∆stpA mutant from parent Escherichia coli MG1655 K-12, aerobic growth conditions. It is the first of two mutant biological replicates used in this experiment, each from separate cultures.


title: 251983810008_1_1-LAG/LOG[E(3)/E(5)]

description:
LAG
Biological replicate E, technical replicate 2 (dye swap)

value: LOG

value: Saccharomyces cerevisiae


title: FNR - Anaerobic - Affinity Purified - B

description: IP and INPUT (reference) for WT FNR from WT Escherichia coli MG1655 K-12 under anaerobic growth conditions.

source_name: FNR IP from WT Escherichia coli MG1655 K-12

value: Anaerobic

source_name: FNR INPUT from WT Escherichia coli MG1655 K-12


title: FNR - ∆hns∆stpA A

description:
IP and INPUT (reference) for FNR from WT Escherichia coli MG1655 K-12 ∆hns/∆stpA under anaerobic growth conditions.
SAMPLE 1

value: ∆hns/∆stpA


title: 252050410001_2_4-PS/LOG[A(3)/A(5)]

description:
LL
Biological replicate A, technical replicate 4 (dye swap)

value: Yarrowia lipolytica

value: LL


title: 251983810006_1_1-LAG/LOG[E(5)/E(3)]

description:
LAG
Biological replicate E, technical replicate 1

value: LAG


title: NK.TRCC.Sp.T18.111411#3

tag: age

value: 7 to 10 weeks

value: Spleen

tag: Sex

value: male


title: 251983810006_1_3-DS/LOG[E(5)/E(3)]

description:
DS
Biological replicate E, technical replicate 1

tag: phase

value: DS


title: Ptac::fnr - B - 8 µM IPTG

description: IP and INPUT (reference) for FNR from PK8263 with 8 µM IPTG under anaerobic growth conditions.

source_name: FNR IP from PK8263 with 8 µM IPTG

growth_protocol: Cells were grown with 8 µM IPTG and 300 µL Cm20 anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

value: 8 µM IPTG

source_name: FNR INPUT from PK8263 with 8 µM INPUTTG


title: NK.v2.Foxp3.DTR+.Pa.15hr.060811#1

value: Pancreas

value: NOD

value: MoFlo Sorter

value: female


title: Ptac::fnr - B - 16 µM IPTG

description: IP and INPUT (reference) for FNR from PK8263 with 16 µM IPTG under anaerobic growth conditions.

source_name: FNR IP from PK8263 with 16 µM IPTG

growth_protocol: Cells were grown with 16 µM IPTG and 300 µL Cm20 anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

value: 16 µM IPTG

value: Affinity Purified FNR antibody

source_name: FNR INPUT from PK8263 with 16 µM INPUTTG


title: 252050410004_2_1-LAG/LOG[I(5)/I(3)]

description:
LAG
Biological replicate I, technical replicate 1

value: LOG


title: 252050410004_1_3-LPS/LOG[H(5)/H(3)]

description:
LL
Biological replicate H, technical replicate 4


title: Ptac::fnr - A - 16 µM IPTG


title: 251983810006_2_1-PLAT/LOG[E(5)/E(3)]

description:
PLAT
Biological replicate E, technical replicate 1

value: PLAT

value: Saccharomyces cerevisiae


title: FNR - Anaerobic - Affinity Purified - A

value: Anaerobic


title: Ptac::fnr - A - 8 µM IPTG


title: Ptac::fnr - C - 16 µM IPTG


title: 251983810007_2_2-LAG/LOG[F(3)/F(5)]

description:
LAG
Biological replicate F, technical replicate 2 (dye swap)


title: NK.TRCC.Sp.T18.110811#2


title: 252050410001_1_3-DS/LOG[C(5)/C(3)]

description:
LL
Biological replicate C, technical replicate 1

value: LL

value: Yarrowia lipolytica


title: 252050410001_2_1-DS/LOG[A(3)/A(5)]

description:
LL
Biological replicate A, technical replicate 3 (dye swap)


title: NK.v2.Foxp3.DTR+.Pa.15hr.061011#2

value: 7 to 10 weeks


title: 252050410004_2_3-PS/LOG[I(5)/I(3)]

description:
LL
Biological replicate I, technical replicate 2


title: Ptac::fnr - B - 4 µM IPTG

description: IP and INPUT (reference) for FNR from PK8263 with 4 µM IPTG under anaerobic growth conditions.

source_name: FNR IP from PK8263 with 4 µM IPTG

growth_protocol: Cells were grown with 4 µM IPTG and 300 µL Cm20 anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

value: 4 µM IPTG

source_name: FNR INPUT from PK8263 with 4 µM INPUTTG


title: Ptac::fnr - A - 4 µM IPTG


title: ∆fnr - Anaeroibc

description: IP and INPUT (reference) for dFNR from PK4854 under anaerobic growth conditions.

source_name: ∆fnr ChIP DNA from PK4854

source_name: INPUT ChIP DNA from WTPK4854, no antibody control


title: 252050410004_2_4-PLAT/LOG[I(5)/I(3)]

description:
LL
Biological replicate I, technical replicate 3


title: NK.TRCC.Sp.T0.110811#2

value: Spleen

value: male


title: 251983810007_1_3-PLAT/LOG[D(5)/D(3)]

description:
PLAT
Biological replicate D, technical replicate 1


title: 252050410004_1_2-PS/LOG[H(5)/H(3)]

description:
LL
Biological replicate H, technical replicate 3


title: 252050410001_2_2-DS/LOG[B(3)/B(5)]

description:
LL
Biological replicate B, technical replicate 2 (dye swap)


title: NK.TRCC.Sp.T0.111411#3


title: 251983810007_1_4-PLAT/LOG[F(5)/F(3)]

description:
PLAT
Biological replicate F, technical replicate 1


title: 252050410003_2_1-LL/LOG[H(5)/H(3)]

description:
LL
Biological replicate H, technical replicate 1


title: NK.TRCC.Sp.T18.IL1218TGFb.111411#3

treatment_protocol: NK cells (CD19-CD3-Nkp46+)  were sorted on MOFLO from NOD mice, cultured in cRPMI in a 96 well plate and activated with a combination of IL-12 and IL-18 with or without regulatory TGFb overnight.  Cells were analyzed using intracellular fluorescent staining for IFNg and analyzed on an LSRII machine and analyzed using FlowJo Software.


title: IHF - Anaerobic A

description: IP and INPUT (reference) for WT IHF from WT Escherichia coli MG1655 K-12 under anaerobic growth conditions.

source_name: IHF ChIP DNA from WT Escherichia coli MG1655 K-12

value: Pre-cleared IHF polyclonal antibody

source_name: INPUT ChIP DNA from WT Escherchia coli MG1655 K-12, no antibody control


title: 251983810007_2_3-PLAT/LOG[D(3)/D(5)]

description:
PLAT
Biological replicate D, technical replicate 2 (dye swap)


title: 252050410004_1_4-PLAT/LOG[H(5)/H(3)]

description:
LL
Biological replicate H, technical replicate 5


title: 252050410003_1_3-EPS/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 2


title: HNS - Aerobic A

description: IP and INPUT (reference) for WT HNS from WT Escherichia coli MG1655 K-12 under anaerobic growth conditions.

source_name: HNS ChIP DNA from WT Escherichia coli MG1655 K-12

value: Aerobic

value: Pre-cleared H-NS polyclonal antibody


title: NK.TRCC.Sp.T18.IL1218.110811#2

value: NOD

value: MoFlo Sorter


title: HNS - Anaerobic A


title: NK.TRCC.Sp.T18.IL1218.062211#1


title: NK.TRCC.Sp.T18.IL1218.111411#3


title: 251983810008_1_2-LL/LOG[E(3)/E(5)]

description:
LL
Biological replicate E, technical replicate 2 (dye swap)


title: NK.TRCC.Sp.T18.IL1218TGFb.062211#1


title: NK.v2.Foxp3.DTR+.Pa.15hr.081511#3

value: Pancreas

value: female


title: 251983810007_2_4-PLAT/LOG[F(3)/F(5)]

description:
PLAT
Biological replicate F, technical replicate 2 (dye swap)

value: LOG


title: MC3T3-E1 Cells, SSRI Treated, 7 Day

status: Public on Jun 19 2013

city: Augusta

first: James

last: Cray Jr.

state: GA

institute: Georgia Regents University

description:
ST7
Gene expression data.

hyb_protocol: Following labeling, cDNAs were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6). Differential expressions were calculated using ANOVA of Partek package.

source_name: MC3T3-E1 cell line (C57BL/6 derived), SSRI, 7 days

label_protocol: Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

growth_protocol: MC3T3-E1 cells purchased from ATCC (Manassas, VA) were reconstituted and grown in a T-75 flask until transfer into T-175 flask. Cells were cultured in alpha minimum Eagles medium (αMEM) supplemented with penicillin/streptomycin (pen/strep) and 1% fetal bovine serum (FBS).

treatment_protocol: The experiment was set up in a 6 well plates with 3 wells as control untreated cells, and 3 well SSRI treated cells. Seeding density was 50,000 cells per well.

tag: cell type

tag: treatment

value: citalopram (SSRI)

tag: treatment duration

value: 7 days


title: MC3T3-E1 Cells, SSRI Treated, 3 Day

description:
3S
Gene expression data.

source_name: MC3T3-E1 cell line (C57BL/6 derived), SSRI, 3 days

tag: cell line

value: 3 days


title: MC3T3-E1 Cells, Control, 7 Day

description:
SC7
Gene expression data.

source_name: MC3T3-E1 cell line (C57BL/6 derived), control, 7 days

value: untreated


title: Trisomy 21 sample 08

city: Ljubljana

first: Ales

last: Maver

address: Slajmerjeva 3

country: Slovenia

institute: Clinical institute of medical genetics Ljubljana Slovenia

description:
TS21_08
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.

hyb_protocol: Hybridization of labeled samples was performed according to manufacturer's instructions (Agilent Low Input Quick Amp Labeling protocol).

scan_protocol: Microarray slides were scanned using GenePix 4100A microarray scanner.

data_processing: Post-processing steps included intra-array loess and inter-array quantile normalization to correct for potential bias resulting from differential stability of cyanine dyes (Limma version 2.12 in Bioconductor 2.12 environment).

source_name: Amniotic fluid cells_Trisomy 21

label_protocol: Labeling of RNA samples was performed according to manufacturer's instructions (Agilent Low Input Quick Amp Labeling protocol).

growth_protocol: Amniotic fluid samples were collected between 16th and 18th week of gestation for routine cytogenetic analysis. Primary cell cultures of amniotic fluid were performed according to standard protocols using tissue culture flasks (TPP, Switzerland). Cell cultures were grown in Amnio Max C100 Basal Medium and Amnio Max C100 Supplement (Invitrogen, CA, USA) at 37°C in 5% CO2 environment.

extract_protocol: Isolation of RNA from cultured amniocytes was performed using Fujifilm QuickGene-810 automated isolation system (Fujifilm Life Sciences, Tokyo, Japan), using columns in the Fujifilm RNA Cultured Cell kit to capture purified RNA samples. The purity and yield of isolated RNA samples was determined using NanoDrop 2000c spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

tag: sample group

value: Trisomy 21

value: Amniotic fluid cells

source_name: RNA pool from all samples in the study

tag: sample type

value: Pooled common reference RNA sample


title: ß - Aerobic - B

description: IP and INPUT (reference) for WT ß from WT Escherichia coli MG1655 K-12 under aerobic growth conditions.

source_name: ß ChIP DNA from WT Escherichia coli MG1655 K-12

tag: growth condition

value: RNA Polymerase ß monoclonal antibody from NeoClone (W0002)


title: Trisomy 21 sample 09

description:
TS21_09
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.

tag: tissue


title: ß - Aerobic - A

tag: strain


title: Trisomy 21 sample 05

description:
TS21_05
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: Trisomy 21 sample 02

description:
TS21_02
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: Trisomy 21 sample 03

description:
TS21_03
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: ß - Anaerobic - B

description: IP and INPUT (reference) for WT ß from WT Escherichia coli MG1655 K-12 under anaerobic growth conditions.

value: Anaerobic


title: MC3T3-E1 Cells, Control, 3 Day

description:
3C
Gene expression data.

source_name: MC3T3-E1 cell line (C57BL/6 derived), control, 3 days


title: Euploid sample 09

description:
EU_09
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.

source_name: Amniotic fluid cells_Euploid

value: Euploid


title: Trisomy 21 sample 04

description:
TS21_04
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: Trisomy 21 sample 06

description:
TS21_06
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: Euploid sample 04

description:
EU_04
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: Trisomy 21 sample 07

description:
TS21_07
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: ß - Anaerobic - A


title: Euploid sample 02

description:
EU_02
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: Euploid sample 06

description:
EU_06
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: Euploid sample 01

description:
EU_01
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: Euploid sample 08

description:
EU_08
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: FNR - Anaerobic - A

description: IP and INPUT (reference) for WT FNR from WT Escherichia coli MG1655 K-12 under anaerobic growth conditions.

source_name: FNR ChIP DNA from WT Escherchia coli MG1655 K-12

value: Pre-cleared FNR antibody


title: FNR - Anaerobic - B


title: Euploid sample 07

description:
EU_07
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: FNR - Anaerobic - C


title: Trisomy 21 sample 01

description:
TS21_01
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: Euploid sample 03

description:
EU_03
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.


title: U937_EV+TNF_rep2

city: Budapest

first: Katalin

last: Szabo-Taylor

address: Nagyvárad tér 4.

department: Department of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: Gene expression after 24hr in EV+TNF treated cells

hyb_protocol: Labeled RNA was purified and hybridized to Agilent Whole Human Genome Microarray slides, according to the manufacturer’s protocol.

scan_protocol: After washing, array scanning and feature extraction was performed with default scenario by Agilent DNA Microarray Scanner and Feature Extraction Software 9.5.3.

data_processing: Total gene signal normalization at the 75th percentile of raw signal values and baseline transformation at the median of all samples was performed by GeneSpring software 10.1 following Agilent's recommendation. Genes were filtered by flag values (100% of samples are present or marginal in at least one group) and raw data (expression is higher than 100 in 100% of samples in at least one group).

source_name: U937 cell line, 24h, EV+TNF treated, replicate 2

label_protocol: Total RNA (200 ng) was labeled with Cy3 and amplified using Low Input Quick Amp Labeling Kit according to the instructions of the manufacturer.

growth_protocol: U937 cells were kept in RPMI medium, supplemented with 10% FCS, 1% Penicillin/Streptomycine, 0,5% Ciprofloxacin

extract_protocol: Total RNA extracted using a Qiagen kit, following the manufacturer's instructions

treatment_protocol: U937 cells were treated with CCRF derived EV-containing or EV-depleted supernatant,  with or without the addition of TNF (10 ng/ml)  for 24h

value: EV+TNF treated


title: U937_TNF_rep2

description: Gene expression after 24hr in TNF treated cells

source_name: U937 cell line, 24h, TNF (10 ng/ml) treated, replicate 2

value: TNF (10 ng/ml)


title: U937_EV_rep3

description: Gene expression after 24hr in EV treated cells

source_name: U937 cell line, 24h, EV treated, replicate 3

value: EV treated


title: U937_EV_rep1

source_name: U937 cell line, 24h, EV treated, replicate 1


title: U937_TNF_rep1

source_name: U937 cell line, 24h, TNF (10 ng/ml) treated, replicate 1


title: U937_EV_rep2

source_name: U937 cell line, 24h, EV treated, replicate 2


title: U937_Control_rep3

description: Gene expression after 24hr in control U937 cells

source_name: U937 cell line, 24h, control, replicate 3

value: control


title: U937_Control_rep1

source_name: U937 cell line, 24h, control, replicate 1


title: blood-schizophrenia control sample 65

city: Helsinki

last: Hennah

address: FIMM, PO Box 20

country: Finland

institute: Institute for Molecular Medicine Finland, FIMM

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 65

hyb_protocol: RNA was hybridized to the Illumina Whole-Genome Expression Beadchips (HT12-v4), using the standard Illumina Hybridization Protocol.

scan_protocol: Standard Illumina scanning protocol, using iScan.

data_processing: Missing intensities were removed, raw intensites were quantile normalized and log2 transformed. Poorly variable probe sets were  removed by utilising their inter-quantile range (IQR), cut-off value of 0.7 .

source_name: lymphocytes

label_protocol: The isolated RNAs were amplified and labelled using the Illumina TotalPrep RNA Amplification kit (Ambion)

tag: gender

value: FEMALE

tag: affection status

value: CONTROL

tag: condition

value: lymphocyte


title: blood-schizophrenia control sample 64

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 64

extract_protocol: The isolated RNAs were amplified and labelled using the Illumina TotalPrep RNA Amplification kit (Ambion)

value: MALE


title: blood-schizophrenia case sample 66

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 66

value: CASE

value: schizophrenia


title: blood-schizophrenia control sample 56

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 56


title: blood-schizophrenia control sample 62

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 62


title: blood-schizophrenia case sample 63

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 63


title: blood-schizophrenia case sample 57

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 57


title: blood-schizophrenia control sample 58

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 58


title: blood-schizophrenia control sample 60

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 60


title: U937_EV+TNF_rep1

source_name: U937 cell line, 24h, EV+TNF treated, replicate 1


title: Trisomy 21 sample 10

description:
TS21_10
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.

value: Trisomy 21


title: blood-schizophrenia case sample 55

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 55


title: blood-schizophrenia control sample 53

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 53


title: blood-schizophrenia control sample 61

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 61


title: U937_Control_rep2

source_name: U937 cell line, 24h, control, replicate 2


title: blood-schizophrenia control sample 52

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 52


title: blood-schizophrenia case sample 50

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 50


title: blood-schizophrenia control sample 51

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 51


title: blood-schizophrenia case sample 59

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 59


title: blood-schizophrenia case sample 48

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 48


title: blood-schizophrenia case sample 43

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 43


title: blood-schizophrenia control sample 49

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 49


title: blood-schizophrenia control sample 47

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 47


title: blood-schizophrenia case sample 54

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 54


title: blood-schizophrenia case sample 46

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 46


title: blood-schizophrenia control sample 45

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 45


title: blood-schizophrenia case sample 44

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 44


title: blood-schizophrenia case sample 41

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 41


title: blood-schizophrenia case sample 35

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 35


title: blood-schizophrenia control sample 36

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 36


title: blood-schizophrenia control sample 38

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 38


title: blood-schizophrenia case sample 40

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 40


title: blood-schizophrenia control sample 39

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 39


title: blood-schizophrenia case sample 33

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 33


title: blood-schizophrenia control sample 32

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 32


title: blood-schizophrenia case sample 34

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 34


title: blood-schizophrenia case sample 30

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 30


title: blood-schizophrenia control sample 31

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 31


title: blood-schizophrenia case sample 42

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 42


title: blood-schizophrenia case sample 29

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 29


title: U937_EV+TNF_rep3

description: Gene expression after 24hr in EV+TNF treated cells

source_name: U937 cell line, 24h, EV+TNF treated, replicate 3


title: blood-schizophrenia case sample 37

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 37


title: blood-schizophrenia control sample 28

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 28


title: blood-schizophrenia case sample 27

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 27


title: blood-schizophrenia control sample 24

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 24


title: blood-schizophrenia case sample 25

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 25


title: blood-schizophrenia control sample 26

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 26


title: Euploid sample 05

description:
EU_05
For comparative microarray hybridization, a pooled RNA microarray design was employed, where RNA pool from all samples in the study was labelled with Cy3 and each sample was labelled separately with Cy5, after which both labelled population were co-hybridized on the array.

value: Amniotic fluid cells

source_name: RNA pool from all samples in the study


title: blood-schizophrenia control sample 22

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 22


title: blood-schizophrenia case sample 19

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 19


title: blood-schizophrenia control sample 20

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 20


title: blood-schizophrenia control sample 21

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 21


title: blood-schizophrenia case sample 17

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 17


title: blood-schizophrenia case sample 18

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 18


title: U937_TNF_rep3

description: Gene expression after 24hr in TNF treated cells

source_name: U937 cell line, 24h, TNF (10 ng/ml) treated, replicate 3


title: blood-schizophrenia case sample 15

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 15


title: blood-schizophrenia control sample 13

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 13


title: blood-schizophrenia case sample 14

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 14


title: blood-schizophrenia control sample 23

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 23


title: blood-schizophrenia case sample 7

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 7


title: blood-schizophrenia case sample 5

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 5


title: blood-schizophrenia control sample 12

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 12


title: blood-schizophrenia case sample 6

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 6


title: blood-schizophrenia control sample 3

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 3


title: blood-schizophrenia case sample 4

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 4


title: blood-schizophrenia case sample 11

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 11


title: blood-schizophrenia control sample 8

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 8


title: blood-schizophrenia control sample 10

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 10


title: blood-schizophrenia case sample 2

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 2


title: blood-schizophrenia case sample 1

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 1


title: blood-schizophrenia control sample 9

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 9


title: SL1344_42c_rep3

first: Robert

last: Kingsley

address: Hinxton

institute: The wellcome Trust Sanger Institute

hyb_protocol: standard protocol from Agilent

scan_protocol: standard protocol from Agilent

data_processing: Array Features were calculated using AFE default settings for the GE2-v5_10_Apr08. Using limma, a linear model fite was applied and the top differetnially expressed genes were tabulated for each contrast using the method of Benjamini and Hochberg to correct p-values

organism: Salmonella enterica subsp. enterica serovar Typhimurium

label_protocol: Cy3 standard protocol from agilent

growth_protocol: Culture at OD 0.6 at 600nm in LB broth

extract_protocol: Qiagen mini kit

treatment_protocol: culure at 37c or 42c


title: blood-schizophrenia case sample 16

description:
RNA analysis in Finnish Schizophrenia Families
SAMPLE 16