title: vehicle treated 2

city: Detroit

first: David

middle: H

last: Gorski

state: MI

address: 840.2 HWCRC

department: Surgery

institute: Wayne State University School of Medicine

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: Cells were cultured in RPMI media supplemented with 5% FBS, 50 U/ml penicillin, 50 mg/ml streptomycin and 250 ng/ml amphotericin B

extract_protocol: RNA was extracted  with the QIAGEN Rneasy Plus kit according to manufacturer's instructions and quality assessed using the Agilent 2100 Bioanalyzer

treatment_protocol: Cells were treated with DMSO for 24-hours

value: triple-negative breast cancer cell line

tag: treated with

value: vehicle (DMSO)


title: vehicle treated 3

status: Public on Mar 16 2017

type: RNA

country: USA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: riluzole treated 3

treatment_protocol: Cells were treated with 25 uM riluzole for 24-hours

value: riluzole (25 uM)


title: A3_rep1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using Illumina's BeadStudio Data Analysis Software.

source_name: immortalized cell line from human keratinocytes, ITGA3 mutation

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

growth_protocol: Primary keratinocytes were isolated from skin of the patients and from a normal individual (NHK), and cultivated in serum-free keratinocyte growth medium supplemented with 2 ng/ml EGF and bovine pituitary extract (KGM, Invitrogen) using standard methods. Cell lines were derived from the primary keratinocytes by immortalization with the HPV18-E6E7 genes as described before, and designated as control (Co) and  A3- cells, respectively. The study was approved by the ethics committee of the University of Freiburg and was conducted in accordance to the Helsinki protocols.

extract_protocol: RNA was extracted with the QIAGEN RNeasy Plus Mini Kit from subconfluent cells in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: subject status

value: a patient with an ITGA3 loss-of-function homozygous mutation

tag: tissue

value: Skin

value: Immortalized cell line from primary keratinocytes of patient with ITGA3 mutation

tag: transfected with

value: E6E7 genes of the HPV

tag: mutation

value: ITGA3 loss-of-function (c.1387C>T, p.R463W )

tag: array id


title: riluzole treated 2


title: A3_rep3


title: NHK_rep3

source_name: normal human keratinocytes

value: primary keratinocytes from healthy human donor


title: Co_rep3

source_name: immortalized cell line from human keratinocytes

value: healthy donor (age- and sex-matched)

value: Immortalized cell line from primary keratinocytes from healthy donor


title: OS_3d-3

status: Public on Mar 15 2017

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

description:
hMSCs were treated 3 days with Osteogenic medium replicate 3
SAMPLE 63

data_processing: The data was background subtracted, vst transformation and a quantile normalization was applied. Probes that were detected at least once in the experiments (illumina detection p-value <0.01) were considered to be expressed and further analyzed for differential expression using Limma.

label_protocol: cDNA and Biotinylated cRNA were prepared with the Illumina Totalprep RNA Amplification kit (Ambion)

growth_protocol: aMEM, 20mM HEPES, strep/pen, 1.8 mM CaCl2, 10% HI-FCS. pH7.5 Osteogenic supplement :10 mM beta-glycerophosphate, 100 nM dexamethasone,  Adipogenic supplement :60 uM Indomethasin, 500 uM IBMX, 100 nM dexamethasone

extract_protocol: Total RNA extracted using Trizol (invitrogen)

treatment_protocol: aMEM 10%HI-FCS with Osteogenic differentiation supplement: 10 mM beta-glycerophosphate, 100 nM dexamethasone or Adipogenic differentiation supplement :60 uM Indomethasin, 500 uM IBMX, 100 nM dexamethasone

tag: gender

value: Male

tag: age

value: 19 years

value: Bone Marrow


title: OS_4d-1

description:
hMSCs were treated 4 days with Osteogenic medium replicate 1
SAMPLE 64


title: OS_3d-1

description:
hMSCs were treated 3 days with Osteogenic medium replicate 1
SAMPLE 61


title: riluzole treated 1


title: OS_2d-2

description:
hMSCs were treated 2 days with Osteogenic medium replicate 2
SAMPLE 59


title: OS_2d-3

description:
hMSCs were treated 2 days with Osteogenic medium replicate 3
SAMPLE 60


title: OS_2d-1

description:
hMSCs were treated 2 days with Osteogenic medium replicate 1
SAMPLE 58


title: OS_4d-2

description:
hMSCs were treated 4 days with Osteogenic medium replicate 2
SAMPLE 65


title: A3_rep2


title: OS_4d-3

description:
hMSCs were treated 4 days with Osteogenic medium replicate 3
SAMPLE 66


title: OS_3d-2

description:
hMSCs were treated 3 days with Osteogenic medium replicate 2
SAMPLE 62


title: vehicle treated 1


title: Co_rep2


title: OS_1d-3

description:
hMSCs were treated 1 day with Osteogenic medium replicate 3
SAMPLE 57


title: OS_12hr-3

description:
hMSCs were treated 12 hour with Osteogenic medium replicate 3
SAMPLE 54


title: OS_1d-2

description:
hMSCs were treated 1 day with Osteogenic medium replicate 2
SAMPLE 56


title: OS_1d-1

description:
hMSCs were treated 1 day with Osteogenic medium replicate 1
SAMPLE 55


title: OS_12hr-1

description:
hMSCs were treated 12 hour with Osteogenic medium replicate 1
SAMPLE 52


title: OS_12hr-2

description:
hMSCs were treated 12 hour with Osteogenic medium replicate 2
SAMPLE 53


title: OS_1hr-2

description:
hMSCs were treated 1 hour with Osteogenic medium replicate 2
SAMPLE 41


title: OS_2hr-2

description:
hMSCs were treated 2 hour with Osteogenic medium replicate 2
SAMPLE 44


title: OS_1hr-3

description:
hMSCs were treated 1 hour with Osteogenic medium replicate 3
SAMPLE 42


title: OS_3hr-2

description:
hMSCs were treated 3 hour with Osteogenic medium replicate 2
SAMPLE 47


title: OS_2hr-1

description:
hMSCs were treated 2 hour with Osteogenic medium replicate 1
SAMPLE 43


title: OS_3hr-3

description:
hMSCs were treated 3 hour with Osteogenic medium replicate 3
SAMPLE 48


title: OS_2hr-3

description:
hMSCs were treated 2 hour with Osteogenic medium replicate 3
SAMPLE 45


title: OS_0hr-2

description:
Non differentiated cells at t=0 replicate 5
SAMPLE 35


title: OS_05hr-1

description:
hMSCs were treated 30 min with Osteogenic medium replicate 1
SAMPLE 37


title: OS_3hr-1

description:
hMSCs were treated 3 hour with Osteogenic medium replicate 1
SAMPLE 46


title: AD_3d-2

description:
hMSCs were treated 3 days with Adipogenic medium replicate 2
SAMPLE 29


title: AD_3d-1

description:
hMSCs were treated 3 days with Adipogenic medium replicate 1
SAMPLE 28


title: OS_0hr-1

description:
Non differentiated cells at t=0 replicate 4
SAMPLE 34


title: OS_1hr-1

description:
hMSCs were treated 1 hour with Osteogenic medium replicate 1
SAMPLE 40


title: OS_6hr-2

description:
hMSCs were treated 6 hour with Osteogenic medium replicate 2
SAMPLE 50


title: OS_05hr-3

description:
hMSCs were treated 30 min with Osteogenic medium replicate 3
SAMPLE 39


title: OS_6hr-1

description:
hMSCs were treated 6 hour with Osteogenic medium replicate 1
SAMPLE 49


title: OS_0hr-3

description:
Non differentiated cells at t=0 replicate 6
SAMPLE 36


title: AD_4d-3

description:
hMSCs were treated 4 days with Adipogenic medium replicate 3
SAMPLE 33


title: OS_6hr-3

description:
hMSCs were treated 6 hour with Osteogenic medium replicate 3
SAMPLE 51


title: AD_4d-1

description:
hMSCs were treated 4 days with Adipogenic medium replicate 1
SAMPLE 31


title: AD_3d-3

description:
hMSCs were treated 3 days with Adipogenic medium replicate 3
SAMPLE 30


title: OS_05hr-2

description:
hMSCs were treated 30 min with Osteogenic medium replicate 2
SAMPLE 38


title: AD_4d-2

description:
hMSCs were treated 4 days with Adipogenic medium replicate 2
SAMPLE 32


title: AD_2d-2

description:
hMSCs were treated 2 days with Adipogenic medium replicate 2
SAMPLE 26


title: AD_2d-3

description:
hMSCs were treated 2 days with Adipogenic medium replicate 3
SAMPLE 27


title: AD_1d-3

description:
hMSCs were treated 1 day with Adipogenic medium replicate 3
SAMPLE 24


title: AD_2d-1

description:
hMSCs were treated 2 days with Adipogenic medium replicate 1
SAMPLE 25


title: AD_6hr-2

description:
hMSCs were treated 6 hour with Adipogenic medium replicate 2
SAMPLE 17


title: AD_12hr-1

description:
hMSCs were treated 12 hour with Adipogenic medium replicate 1
SAMPLE 19


title: AD_3hr-3

description:
hMSCs were treated 3 hour with Adipogenic medium replicate 3
SAMPLE 15


title: AD_6hr-1

description:
hMSCs were treated 6 hour with Adipogenic medium replicate 1
SAMPLE 16


title: AD_6hr-3

description:
hMSCs were treated 6 hour with Adipogenic medium replicate 3
SAMPLE 18


title: AD_1d-2

description:
hMSCs were treated 1 day with Adipogenic medium replicate 2
SAMPLE 23


title: AD_1d-1

description:
hMSCs were treated 1 day with Adipogenic medium replicate 1
SAMPLE 22


title: AD_12hr-2

description:
hMSCs were treated 12 hour with Adipogenic medium replicate 2
SAMPLE 20


title: AD_3hr-2

description:
hMSCs were treated 3 hour with Adipogenic medium replicate 2
SAMPLE 14


title: AD_2hr-3

description:
hMSCs were treated 2 hour with Adipogenic medium replicate 3
SAMPLE 12


title: AD_05hr-2

description:
hMSCs were treated 30 min with Adipogenic medium replicate 2
SAMPLE 5


title: CHCC2862_RespirationOD5.6

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

hyb_protocol: According to the Amersham protocol the Cy3 and Cy5 labelled cDNA were combined and lyophilized. Hereafter they were resuspended in 7uL of nuclease free water and, 5uL of hybdridization buffer (4x), and 8uL of formamide was added. This 20uL solution was applied to the array under a 24x24mm LifterSlip (Erie Scientific Company, Portsmouth, NH) and put in an airtight box containing paper towels soaked with NaCl-saturated water. Arrays were hybridized for 16-20h at 42ºC, and then washed using the UltraGAPS protocol (Corning B.V.).

scan_protocol: Arrays were scanned using the GenePix 4100A Personal Scanner with GenePix Pro 6.0 software (Axon Instruments Inc., Union City, CA). The photo multiplier tube (PMT) sensitivity values of the scan were adjusted around 660 for Cy5 and 520 for Cy3 to obtain only few saturated spots on each array and about equal total signal for each dye.

data_processing: A grid with 110um spots was laid over the array and was manually adjusted to fit small irregularities in spotting. Spots clearly covered by for example dust particles were flagged “Bad”. The intensity of all spots was then calculated using the “Analyze” function. Spots with very weak signals in both channels were also flagged “Bad”. These were spots where the signal-to-noise ratio [SNR] < 1 in both channels, or where [% > B + 2SD] < 20 in both channels. All other spots were considered “Found” and had a “Flag” value of >= 0. All data was exported from GenePix Pro in tab-delimited format.  In the further analysis the variables of feature (spot) intensity minus the background intensity around the spot was used, i.e. [F635 median – B635]=Cy5 and [F532 median – B532]=Cy3. The log2(ratio) of this was calculated as log2(Cy5/Cy3). Some spots may have a significant signal in one channel but no signal in the other channel. The latter may result in a negative value due to noise and thus and illegal log2(ratio). To avoid this a macro in Excel 2000 (Microsoft Corporation, Redmond, WA) was used to change [F635 median – B635] and [F532 median – B532] values of <10 to 10 for “Found” spots (the signal scale goes from 0, no signal, to 65535, saturated signal). For these spots the log2(ratio) was re-calculated. The corrected data was exported from Excel and imported into Acuity 4.0 (Axon) where they were ratio-normalized based on the “Found” spots.  In Acuity a dataset was created. For each array only genes were included where 1) at least 3 of the 4 replicate spots were “Found”, 2) the standard deviation was <0.8 among “Found” spots, and 3) <30% of the pixels in “Found” spots, in both channels, were saturated.

organism: Lactococcus lactis subsp. lactis

label_protocol: 10ug of total RNA was lyophilized in a speed-vac. The copying into cDNA and labeling with either Cy3 (reference) or Cy5 (test) was done using the CyScribe Post-Labelling Kit using manufacturer’s protocol (Amersham Biosciences, Hillerød, Denmark). 1uL of random nonamer was used for priming.

growth_protocol: M17 + 0.5% lactose + 5mg/L hemin, agitation at 170rpm

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) except for the following: the 200uL TE buffer contained 15mg/mL of lysozyme, 15uL of proteinase K at 20mg/mL, and 2uL of mutanolysin at 25U/uL with vortexing every 10s at 37ºC for the 2min. The quality and concentration of RNA was determined using the RNA 6000 Nano Kit on the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Routinely, 20-50ug of total RNA was obtained. Only high quality total RNA, as indicated by two sharp rRNA peaks, was used.

treatment_protocol: Samples of 0.67mL were collected in 1.33mL RNAprotect according to protocol (QIAGEN, Valencia, CA).

tag: strain


title: CHCC2862_RespirationOD6.4


title: AD_05hr-1

description:
hMSCs were treated 30 min with Adipogenic medium replicate 1
SAMPLE 4


title: AD_3hr-1

description:
hMSCs were treated 3 hour with Adipogenic medium replicate 1
SAMPLE 13


title: AD_0hr-2

description:
Non differentiated cells at t=0 replicate 2
SAMPLE 2


title: AD_2hr-2

description:
hMSCs were treated 2 hour with Adipogenic medium replicate 2
SAMPLE 11


title: AD_0hr-3

description:
Non differentiated cells at t=0 replicate 3
SAMPLE 3


title: AD_05hr-3

description:
hMSCs were treated 30 min with Adipogenic medium replicate 3
SAMPLE 6


title: AD_0hr-1

description:
Non differentiated cells at t=0 replicate 1
SAMPLE 1


title: AD_12hr-3

description:
hMSCs were treated 12 hour with Adipogenic medium replicate 3
SAMPLE 21


title: AD_2hr-1

description:
hMSCs were treated 2 hour with Adipogenic medium replicate 1
SAMPLE 10


title: AD_1hr-3

description:
hMSCs were treated 1 hour with Adipogenic medium replicate 3
SAMPLE 9


title: AD_1hr-1

description:
hMSCs were treated 1 hour with Adipogenic medium replicate 1
SAMPLE 7


title: control1

city: Osaka-city

first: Risa

last: Uemura

address: 1-4-3 asahimachi, abeno-ku

department: Gastroenterolgy

country: Japan

institute: Osaka city university Graduate School of Medicine

hyb_protocol: Hybridization signals were detected with a　DNA microarray scanner G2539A (Agilent Technology) and the scanned　images were analyzed using Agilent feature extraction software (v10.10.1.1).

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: Data acquisition were used Agilent feature extraction software (v10.10.1.1).

organism: Rattus norvegicus

label_protocol: Expression of miRNAs was assessed by microarray (Agilent Rat microRNA　microarray release 19.0).

extract_protocol: Exosome-rich fractionated RNA was prepared using Exoquick (System Biosciences, CA, USA). Briefly, 900 μl of serum or plasma was mixed with 250 μl of Exoquick and incubated for 12 h at 4°C. The tubes were centrifuged at 1500 g for 30 min at room temperature and then supernatant was discarded. The pellet was dissolved in 200 μl of PBS with vigorous vortex. RNA was extracted using a miRNeasy mini kit (Qiagen, Hilden, Germany).

value: Specific pathogen free Wistar rats

value: male

tag: sample group

value: Shapm operation rats; control

value: serum

tag: molecule subtype

value: exosomal microRNAs


title: RE8

value: acid reflux esophagitis (RE) induced

tag: time point

value: day 21 (chronic phase) after RE induction


title: Co_rep1

value: Skin


title: AD_1hr-2

description:
hMSCs were treated 1 hour with Adipogenic medium replicate 2
SAMPLE 8


title: control2


title: RE5


title: control4


title: control3


title: RE9


title: Ptpn11D61Y treated with 4AP-Bic, bio.rep 3

city: Magdeburg

first: Anna

last: Fejtova

state: Saxony Anhalt

address: Brenneckestrasse, 6

institute: Leibniz Institute for Neurobiology

description: Gene expression data from hippocampal slices (Ptpn11D61Y) treated with 4AP-Bic (biological replicate/animal 3).

hyb_protocol: After the fragmentation and terminal labelling, cRNA samples were hybridized (16-18hat 45oC; 60rpm) on GeneChip Mouse Gene 2.0 ST array plates. Array plates were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChip Mouse Gene 2.0 ST arrays used in this study were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data files (.CEL files) were imported into Expression ConsoleTM 1.4.1.46 software (Affymetrix) for background correction and normalization of fluorescent hybridized signals using the quantile method (PLIER algorithm).

organism: Mus musculus

source_name: 4AP-Bic treated Ptpn11D61Y hippocampal slices

label_protocol: Biotinylated cRNA (Affymetrix proprietary DNA labeling reagent covalently linked to biotin) were prepared from total RNA samples according to the GeneChip® WT Terminal Labeling and Hybridization User Manual and Affymetrix standard protocols.

growth_protocol: Mice heterozygote for a conditional allele Ptpn11floxedD61Y/WT (Chan et al, 2009) and for Emx1IREScre allele (Gorski et al, 2002) were used as model of Noonan syndrom in this study. Control mice had same conditional allele but no Emx1IREScre allele. Brains of adult mice (8-11 weeks) were quickly removed, placed in carbogenated ice-cold artificial cerebrospinal fluid (ACSF),  and hippocampus was dissected. Transverse slices of hippocampus (350 µm thick) were prepared using a McIlwain-type tissue chopper, transferred to small meshed chambers (in ACSF) and incubated for recovery in carbogenated (95% O2/5% CO2) ACSF for 1 h at 37°C. ACSF contained  following (in mM): 125 NaCl, 2.5 KCl, 1.25 NaH2PO4, 25 NaHCO3, 25 D-glucose, 2 CaCl2 and 1 MgCl2.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) as per manufacturer’s protocol. RNA samples with >7 RNA integrity (RINe values determined using RNA Screen tapes and Tape Station) values were used for the microarrays.

treatment_protocol: Hippocampal slices from both control and Ptpn11D61Y groups were treated with 4-AP (2.5 mM) and bicuculline (50 µM) in DMSO for 10 min to increase overall network activity. To  determine the gene expression at basal state, hippocampal slices from both control and Ptpn11D61Y group of slices were treated with DMSO for 10 min. Then slices were placed in ACSF without drugs and incuated for 3 hours. Thereafter slices were immediately placed in RNAlater RNA stabilization reagent (Qiagen) to prevent RNA degradation until total RNA isolation was performed.

value: Hippocampal (HP) slices

tag: condition

value: Noonan syndrom


title: Ptpn11D61Y treated with 4AP-Bic, bio.rep 2

description: Gene expression data from hippocampal slices (Ptpn11D61Y) treated with 4AP-Bic (biological replicate/animal 2).


title: RE10


title: Ptpn11D61Y, bio.rep 1

description: Gene expression data from hippocampal slices (Ptpn11D61Y) treated with DMSO (basal state; biological replicate/animal 1).

source_name: Basal state of Ptpn11D61Y hippocampal slices


title: HC1 CD19high

city: shanghai

first: zhicui

last: liu

address: No. 197 Rui Jin Er Road

department: Department of Dermatology

country: China

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: The data were analyzed with Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by Expression Console.

source_name: B cells

label_protocol: Total RNA were amplified, labeled and purified by using Affymetrix  WT Amplication Kit(Cat#902224， Affymetrix, Santa Clara, CA, US) and GeneChip  WT Terminal Labeling Kit(Cat#900671, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Purified human CD4+ T cells were stimulated in vitro with anti-CD3/CD28 Dynabeads for 24 hrs and co-cultured with autologous B cells for 3 days

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions

treatment_protocol: After 3 days, CD19hi and CD19lo B cells were purified.

value: peripheral blood

value: CD19hi B cells


title: Ptpn11D61Y treated with 4AP-Bic, bio.rep 1

description: Gene expression data from hippocampal slices (Ptpn11D61Y) treated with 4AP-Bic (biological replicate/animal 1).


title: HC1 CD19low

value: CD19lo B cells


title: HC2+3 CD19low


title: Ptpn11D61Y, bio.rep 2

description: Gene expression data from hippocampal slices (Ptpn11D61Y) treated with DMSO (basal state; biological replicate/animal 2).


title: Control, bio.rep 3

description: Gene expression data from hippocampal slices (Control) treated with DMSO (basal state; biological replicate/animal 3).

source_name: Basal state of Control hippocampal slices

value: Control


title: Ptpn11D61Y, bio.rep 3

description: Gene expression data from hippocampal slices (Ptpn11D61Y) treated with DMSO (basal state; biological replicate/animal 3).


title: Control, bio.rep 2

description: Gene expression data from hippocampal slices (Control) treated with DMSO (basal state; biological replicate/animal 2).


title: Control treated with 4AP-Bic, bio. rep 3

description: Gene expression data from hippocampal slices (Control) treated with 4AP-Bic (biological replicate/animal 3).

source_name: 4AP-Bic treated Control hippocampal slices


title: Control treated with 4AP-Bic, bio. rep 1

description: Gene expression data from hippocampal slices (Control) treated with 4AP-Bic (biological replicate/animal 1).


title: Control treated with 4AP-Bic, bio. rep 2

description: Gene expression data from hippocampal slices (Control) treated with 4AP-Bic (biological replicate/animal 2).


title: Control, bio.rep 1

description: Gene expression data from hippocampal slices (Control) treated with DMSO (basal state; biological replicate/animal 1).


title: DMSO UV_rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression of DMSO treated and UV irradiated group, rep 2

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

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

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

source_name: DMSO treated and UV irradiated group

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

growth_protocol: Human primary skin melanocytes extracted from the foreskin were cultured with 254CF medium supplemented with calcium chloride 0.2 M and Human Melanocyte Growth Supplement (HMGS, Gibco, Invitrogen Cell Culture), with the addition of Ampicillin and Streptomycin 100mg/L. After plating, cells were maintained in a humidified incubator at 5% CO2 and 37°C.   We used melanocytes extracted from two unrelated Caucasian donors who were 4- and 6-years of age. Cells were cultured separately and pooled with equal proportions of both donors at the time of assay plating, in an effort to increase genetic diversity.

extract_protocol: Cells were cultured in 100 mm plates, 106 cells/plate. After 6 hours of treatment, total RNA was isolated using the Qiagen RNeasy kit following the manufacturer’s protocol, including the addition of DNase I.

treatment_protocol: Twenty-four hours after plating, cells were at 80% confluency and were subjected to the following experimental treatment groups: Group 1: No treatment; Group 2: Irradiation and no treatment; Group 3: Carbaryl treatment; Group 4: Irradiation and carbaryl treatment; Group 5: Vehicle treatment; Group 6: Irradiation and vehicle treatment. Treatment regimen consisted of melanocyte incubation with carbaryl 100 µM (Sigma-Aldrich, St Louis, USA) for 6 hours after single dose exposure to 375mJ/cm2 of solar radiation using a solar simulator (SS2.5kW, Sciencetech Inc., Ontario, Canada) with a global air mass filter (A.M 1.5G, Sciencetech Inc, Ontario, Canada). For the irradiation assays, culture medium was replaced by PBS buffer without Ca2+ or Mg2+ (PBS-A). All experiments were performed in triplicates.

value: Foreskin

value: Male

value: Melanocytes


title: Control UV_rep3

description: Gene expression of irradiated, non chemical treated control, rep 3


title: DMSO UV_rep3

description: Gene expression of DMSO treated and UV irradiated group, rep 3


title: Control_rep3

description: Gene expression of non treated control, rep 3

source_name: non treated control


title: Carb UV_rep3

description: Gene expression of Carbaryl treated and UV irradiated group, rep 3


title: DMSO_rep3

description: Gene expression of DMSO treated, non irradiated control group, rep 3


title: Carb UV_rep2

description: Gene expression of Carbaryl treated and UV irradiated group, rep 2


title: Carb_rep3

description: Gene expression of Carbaryl treated group, rep 3

source_name: Carbaryl treated group


title: DMSO_rep2

description: Gene expression of DMSO treated, non irradiated control group, rep 2


title: DMSO UV_rep1

description: Gene expression of DMSO treated and UV irradiated group, rep 1


title: Control UV_rep2

description: Gene expression of irradiated, non chemical treated control, rep 2


title: Control_rep2

description: Gene expression of non treated control, rep 2


title: DMSO_rep1

description: Gene expression of DMSO treated, non irradiated control group, rep 1


title: Carb UV_rep1

description: Gene expression of Carbaryl treated and UV irradiated group, rep 1


title: miR-NC 1

city: Nanjing

first: zeng

middle: ai

last: liang

address: No.300, Guangzhou Road

department: Department of Neurosurgery

institute: The First Affiliated Hospital of Nanjing Medical University

description: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000/1997C. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

hyb_protocol: Affymetrix wt labeling protocol  as described in  https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

scan_protocol: Affymetrix wt scanning protocol  as described in  https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

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

source_name: human glioma cells

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000/1995C. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: RNA extracted from miR-151a-overexpressing and miR-NC overexpressing U87 glioma cells.

value: U87 glioma cells.


title: Carb_rep1

description: Gene expression of Carbaryl treated group, rep 1


title: miR-NC 2

description: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000/1998C. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

label_protocol: Affymetrix wt labeling protocol  as described in  https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf


title: miR-NC 3

description: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000/1999C. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.


title: Carb_rep2

description: Gene expression of Carbaryl treated group, rep 2


title: HN-5 Control, 48h

city: Heidelberg

first: Shariq

last: Ansari

address: Im Neuenheimer Feld 581

institute: DKFZ

description:
SAMPLE 9
Replicate 1

hyb_protocol: Standard Illumina Hybridisation Protocol  Part # 11322355 Rev. A (Whole-Genome Gene Expression Direct Hybridization Assay Guide).

scan_protocol: Standard Illumina Scanning Protocol  Part # 11322355 Rev. A (Whole-Genome Gene Expression Direct Hybridization Assay Guide).

data_processing: The data were normalised using quantile normalisation. As test for significance, the student’s t-test was used on the bead expression values of the two groups of interest (control and treated). The average expression value was calculated as mean of the measured expressions of beads together with the standard deviation of the beads.

source_name: HN-5 cell line, untreated control, 48h

label_protocol: Illumina TotalPrep-RNA Amplification (P/N IL1791M Revision C).

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

value: OSCC cell line

tag: treatment

tag: time

value: 48 hours


title: HN-5 IC75, 24h

description:
SAMPLE 8
Replicate 1

source_name: HN-5 cell line, IC75 erufosine, 24h

value: IC75 of erufosine

value: 24 hours


title: Control_rep1

description: Gene expression of non treated control, rep 1


title: miR-151a UP 1

description: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000/1994C. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.


title: miR-151a UP 3

description: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000/1996C. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.


title: HN-5 IC75, 48h

description:
SAMPLE 12
Replicate 1

source_name: HN-5 cell line, IC75 erufosine, 48h


title: miR-151a UP 2

description: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000/1995C. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.


title: HCT8/5Fu-48h-1

city: FuZhou

first: Guo

last: Zheng

state: FuJian

address: No.1 Xue Yuan Road

department: Department of Bioinformatics

institute: Fujian Medical University

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 48 hours .
HCT85481

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.

data_processing: The data were analyzed with Bioconductor using the RMA normalization method.

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: Medium RPMI-1640 which contains 10% FCS, 1% Penicillin-Streptomycin Solution and 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.

tag: genotype

value: 5-FU-induced resistant


title: Control UV_rep1

description: Gene expression of irradiated, non chemical treated control, rep 1


title: HN-5 IC25, 48h

description:
SAMPLE 10
Replicate 1

source_name: HN-5 cell line, IC25 erufosine, 48h

tag: cell line

value: IC25 of erufosine


title: HCT8/5Fu-48h-2

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 48 hours .
HCT85482


title: HCT8/5Fu-48h-3

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 48 hours .
HCT85483


title: HN-5 IC50, 48h

description:
SAMPLE 11
Replicate 1

source_name: HN-5 cell line, IC50 erufosine, 48h

tag: cell type

value: IC50 of erufosine


title: HN-5 IC50, 24h

description:
SAMPLE 7
Replicate 1

source_name: HN-5 cell line, IC50 erufosine, 24h


title: HN-5 IC25, 24h

description:
SAMPLE 6
Replicate 1

source_name: HN-5 cell line, IC25 erufosine, 24h


title: HN-5 IC75, 16h

description:
SAMPLE 4
Replicate 1

source_name: HN-5 cell line, IC75 erufosine, 16h

value: 16 hours


title: HCT8/5Fu-24h-2

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 24 hours .
HCT85242


title: HCT8/5Fu-24h-3

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 24 hours .
HCT85243


title: HN-5 IC50, 16h

description:
SAMPLE 3
Replicate 1

source_name: HN-5 cell line, IC50 erufosine, 16h


title: HCT8/5Fu-0h-3

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 0 hours .
HCT85003


title: HN-5 Control, 24h

description:
SAMPLE 5
Replicate 1

source_name: HN-5 cell line, untreated control, 24h


title: Nr.6

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

description: Freshly isolated BM cells  were purified by removal of T cells and B cells using MACS technology. Then at day 8 DCs were treated with 1 µg/ml cholera toxin for 24h.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and rma followed by quantile-quantile as normalization method

source_name: BM-DC CT 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual,  Affymetrix).

growth_protocol: Freshly isoalted BM cells were purified by removal of T cells and B cells using MACS technology. Then BM-DCs were grown according our standard protocol until d8 in GM-CSF.

extract_protocol: RNeasyKit, according to the manufacturers protocol

treatment_protocol: At day 8  DCs were treated with 500U/ml TNF or 1 µg/ml cholera toxin for 6h or 24h.

value: dendritic cells (DCs)


title: HCT8-48h-3

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 48 hours.
HCT80483

value: wild type


title: Nr.3

description: Freshly isolated BM cells were purified by removal of T cells and B cells using MACS technology. Then at day 8 DCs were treated with 1 µg/ml cholera toxin for 6h.

source_name: BM-DC CT 6h


title: HC2+3 CD19high

source_name: B cells

value: peripheral blood

value: CD19hi B cells


title: HN-5 Control, 16h

description:
SAMPLE 1
Replicate 1

source_name: HN-5 cell line, untreated control, 16h


title: Nr.5

description: Freshly isolated BM cells  were purified by removal of T cells and B cells using MACS technology. Then at day 8 DCs were treated with 500U/ml TNF for 24h.

source_name: BM-DC TNF 24h


title: HCT8/5Fu-0h-2

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 0 hours .
HCT85002


title: HCT8-48h-2

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 48 hours.
HCT80482


title: Nr.1

description: Freshly isolated BM cells were purified by removal of T cells and B cells using MACS technology. Then at day 8 DCs were left untreated  for 6h.

source_name: BM-DC untreated 6h


title: Pregnant HeV Infected

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: PBMC

tag: sample type

value: Pregnant Women With Hev Infection


title: HCT8/5Fu-0h-1

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 0 hours .
HCT85001


title: Nr.4

description: Freshly isolated BM cells  were purified by removal of T cells and B cells using MACS technology. Then at day 8 DCs were left untreated  for 24h.

source_name: BM-DC untreated 24h


title: Non -Pregnant infected

value: Non-Pregnant Women With Hev Infection


title: mus-musculus-bone-marrow-ground-control-2

city: Mountain View

first: NASA

last: GeneLab

address: Mail Stop N211

institute: NASA Ames Research Center

hyb_protocol: Biotin labeled aRNA was fragmented and hybridized to the GeneChip Mouse Genome 430 2.0, 3′ expression array (Affymetrix) according to manufacturer’s instructions. Array washing and staining was conducted using the GeneChip Fluidics Station 450 followed by a 1x scan with the GeneChip 3000 Scanner 7G with Autoloader.

data_processing:
GeneChip processing and data collection was performed using GeneChip Operating System v1.4 (GCOS). Probe intensities were consistent amongst the 4 samples and correlation coefficients among the samples were all greater than 0.95.
ANOVA without Multiple Testing Correction was applied and 1678 significant genes out of 28,972 total genes were selected at a p-value < 0.05 with up or down gene-level fold changes greater than 1.5. To reduce the Type I Error, we performed ANOVA again with the Benjamini Hochberg FDR of Multiple Testing Correction method with cut-off 0.05 on 1678 genes. We obtained 1678 genes with corrected p-values between 0.00165 and 0.04998.

label_protocol: Frozen RNA was sent to the University of Kansas microarray facility at the University of Kansas Medical Center (Kansas City, KS). At the facility, RNA concentrations and qualities were analyzed with an Agilent 2100 Bioanalyzer and RNA 6000 pico assay (Agilent Technologies, Santa Clara, CA). Based on RNA quality, the four best RNA samples were selected (Flight A 21.2 ng, RNA Integrity Value (RIN), 3; Flight D 25 ng, RIN, 3; Ground B 12.5 ng, RIN, 3; Ground D 24.1 ng, RIN, 3). All available RNA was concentrated and processed for target labeling using the 2x IVT labeling protocol. Briefly, the two round RNA amplification and labeling procedure was performed using the Affymetrix Small Sample Labeling Protocol vII (2xIVT) as follows: 50 ng of total RNA was primed with T7-oligo(dT) promoter primer (Affymetrix, Santa Clara, CA) and reverse transcribed using SuperScript Reverse Transcriptase vII kit (Invitrogen). The first round of RNA amplification was performed on the cDNA using the MEGAScript T7 Invitro-Transciption kit (Ambion). Amplified RNA (aRNA) was reverse transcribed using random primers and SuperScript Reverse Transcriptase vII kit. The second round RNA amplification and biotin labeling was conducted using the GeneChip 3′ IVT labeling kit (Affymetrix).

extract_protocol: At KSU, bone marrow cells preserved in GITC were combined in pools of 2 FPAs per sample to provide four independent flight and four ground samples for assessment. RNA was phenol extracted and purified in the aqueous phase using phase-lock tubes (5-prime, Gaithersburg, MD) centrifuged at 10,000 g for 10 min. RNA was ethanol precipitated and DNase treated (Qiagen RNeasy).

treatment_protocol:
The bone marrow cells were loaded into the primary chamber of 48 FPAs (1 × 107 cells per 3 ml DMEM2supplemented with rmM-CSF). A second chamber was formed by sliding a sterile, siliconized septum parallel to the first septum. Excess air was evacuated through a 26GA needle. DMEM2 supplemented rmM-CSF was loaded into the second chamber of all 48 FPAs. A third chamber was formed by adding an additional septum similarly to the second. Thirty-two FPAs were loaded with 8% formalin. Eight FPAs were loaded with 6.0 M guanidinium isothiocyanate (GITC) and 8 FPAs were loaded with DMEM2 plus rmM-CSF (returned as viable cultures). The third chambers were sealed with septa as described above. The FPAs were transported (day-2 of spaceflight) at 4 °C to the National Aeronautics and Space Administration (NASA) Space Life Sciences Laboratory Facility (SLSL) at Kennedy Space Center (KSC). The FPAs were loaded into 6 Group Activation Packs (GAPs), 8 FPAs/GAP. GAPs were placed into the Commercial Generic Bioprocessing Apparatus (CGBA) at 37 °C to start incubation. Parallel temperature and activation profile conditions were maintained on GAPs kept at the SLSL. The incubation was started before the launch of space shuttle (Endeavour) flight Space Transportation System (STS)-126 (day -1 of spaceflight). On day 6 of cell differentiation (day 5 of spaceflight), 1.5 ml of DMEM2supplemented with rmM-CSF was added to the cell suspension by mixing chambers 1 and 2 of the FPAs through the bypass. On day 15 of cell differentiation (day 14 of spaceflight) the content of the FPAs third chamber was mixed with the cell suspension in the previously merged chambers. STS-126 landing occurred in California 17 days after the start of 37 °C cell culture incubation (day 16 of spaceflight). Samples were placed at 4 °C and transported to SLSL in Florida. The FPAs were unloaded from GAPs, inspected, and the cells in medium were collected from 8 FPAs and viable cells (trypan blue exclusion) were counted on a hemacytometer. Cell-free media were collected from these FPA and were frozen and sent to KSU. Glucose content was measured in each sample using a digital glucometer (Home Diagnostics, Inc., Ft. Lauderdale, FL). FPAs prepared to fix cells in formalin or GITC were transported to KSU at 4 °C and were processed 19 days after the cells were place at 37 °C to begin differentiation. Total cell counts were done on formalin-fixed cells.  Fluorescein isothiocyanate conjugated- (FITC-) anti Ly6C (Clone AL-21), FITC-anti IgM (Clone RA-22), Phycoerythrin conjugated- (PE-) anti CD31 (Clone MEC13.3), PE- anti IgG2a (Clone R35-95), PE- anti CD44 (Clone IM7), PE- anti IgG2b (Clone A95-1), Allophycocyanin conjugated- (APC-) anti CD3 (Clone 145-2C11), and APC- anti IgG1 were purchased from BD Pharmingen (San Jose California, CA). Alexa Fluor 647 conjugated-(AF647)– anti Mac2 (Clone eBioM3/38), AF647- anti IgG2a (Clone eBR2a), PE- anti CD11b (Clone M1-70), PE- anti IgG2b (Clone eB149/0H5), PE- anti Ly6G (Clone RB6-8C5), PE- anti IgG2b (Clone eB149/0H5), APC- anti F4/80 (Clone BM8), and APC- anti IgG2a (Clone eBR2a) were purchased from eBioscience Inc. (San Diego, CA). Purifiedanti c-Fms (Clone 20), purified – anti IgG, PE- anti IgG, PE- anti c-Fos (Clone 4) and PE- anti IgG2b (Clone not categorized) were purchased from Santa Cruz Biotechnology Inc. (Santa Cruz, CA).
Bone marrow cells were harvested from humeri, femora, and tibiae of adult C57BL/6 mice (>8-week old; n= 21) originally obtained from the Jackson Laboratory (Bar Harbor, ME) and bred in the animal facility at Kansas State University (KSU. All animal experiments were approved by Kansas State University Institutional Animal Care and Use Committee. Briefly, the bones were recovered and cleaned of all nonosseous tissue. The marrow cavity was flushed with a sterile PBS solution. The red blood cells were lysed by incubating in ammonium chloride lysis buffer (0.15 M NH4Cl, 10 mM KHCO3, and 0.1 mM Na2EDTA, pH 7.3) for 5 min at 4 °C. Pooled cells were centrifuged (300 × g, 5 min) and washed two times with Dulbecco’s Modified Minimal Essentials Medium (Hyclone Laboratories, Inc., Logan, UT) containing 1% fetal bovine serum, 1% Nu serum (BD, Bedford, MA), Glutamine plus (2 mM, Atlanta Biologicals, Atlanta, GA), 0.1 M HEPES and 10% Opti-MEM (Invitrogen, Grand Island, N.Y.)(DMEM2). Primary bone marrow cells were suspended in DMEM2 supplemented with recombinant mouse macrophage colony stimulating factor (rmM-CSF; 1.5 ug/ml, R & D Systems, Minneapolis, MN) in preparation for culture in Fluid Processing Apparatus hardware (FPAs). Briefly, FPAs are 11.70 cm long and 1.35 cm diameter (1.31 mm glass thickness) glass barrels. The FPAs have a bypass which allows for the transfer of media from one chamber to another. The FPAs were siliconized with Rain-X (Blue Coral-Slick 50, Ltd; Cleveland, OH) and fitted with a previously siliconized rubber septum, 1.2 cm from the distal end of the barrel. Bacti-caps (16-mm diam.; Oxford Labware, St. Louis, MO) were placed on the proximal end of the FPAs before sterilization.
The bone marrow cells were loaded into the primary chamber of 48 FPAs (1 × 107 cells per 3 ml DMEM2supplemented with rmM-CSF). A second chamber was formed by sliding a sterile, siliconized septum parallel to the first septum. Excess air was evacuated through a 26GA needle. DMEM2 supplemented rmM-CSF was loaded into the second chamber of all 48 FPAs. A third chamber was formed by adding an additional septum similarly to the second. Thirty-two FPAs were loaded with 8% formalin. Eight FPAs were loaded with 6.0 M guanidinium isothiocyanate (GITC) and 8 FPAs were loaded with DMEM2 plus rmM-CSF (returned as viable cultures). The third chambers were sealed with septa as described above. The FPAs were transported (day-2 of spaceflight) at 4 °C to the National Aeronautics and Space Administration (NASA) Space Life Sciences Laboratory Facility (SLSL) at Kennedy Space Center (KSC). The FPAs were loaded into 6 Group Activation Packs (GAPs), 8 FPAs/GAP. GAPs were placed into the Commercial Generic Bioprocessing Apparatus (CGBA) at 37 °C to start incubation. Parallel temperature and activation profile conditions were maintained on GAPs kept at the SLSL. The incubation was started before the launch of space shuttle (Endeavour) flight Space Transportation System (STS)-126 (day -1 of spaceflight). On day 6 of cell differentiation (day 5 of spaceflight), 1.5 ml of DMEM2supplemented with rmM-CSF was added to the cell suspension by mixing chambers 1 and 2 of the FPAs through the bypass. On day 15 of cell differentiation (day 14 of spaceflight) the content of the FPAs third chamber was mixed with the cell suspension in the previously merged chambers. STS-126 landing occurred in California 17 days after the start of 37 °C cell culture incubation (day 16 of spaceflight). Samples were placed at 4 °C and transported to SLSL in Florida. The FPAs were unloaded from GAPs, inspected, and the cells in medium were collected from 8 FPAs and viable cells (trypan blue exclusion) were counted on a hemacytometer. Cell-free media were collected from these FPA and were frozen and sent to KSU. Glucose content was measured in each sample using a digital glucometer (Home Diagnostics, Inc., Ft. Lauderdale, FL). FPAs prepared to fix cells in formalin or GITC were transported to KSU at 4 °C and were processed 19 days after the cells were place at 37 °C to begin differentiation. Total cell counts were done on formalin-fixed cells.

tag: organism part

value: bone marrow

tag: factor value[space flight,d013026

value: MESH]:Ground Control

tag: organism

value: Mus musculus


title: mus-musculus-bone-marrow-space-flight-1

scan_protocol: 1x scan with the GeneChip 3000 Scanner 7G with Autoloader

growth_protocol: Bone marrow cells were harvested from humeri, femora, and tibiae of adult C57BL/6 mice (>8-week old; n= 21) originally obtained from the Jackson Laboratory (Bar Harbor, ME) and bred in the animal facility at Kansas State University (KSU. All animal experiments were approved by Kansas State University Institutional Animal Care and Use Committee. Briefly, the bones were recovered and cleaned of all nonosseous tissue. The marrow cavity was flushed with a sterile PBS solution. The red blood cells were lysed by incubating in ammonium chloride lysis buffer (0.15 M NH4Cl, 10 mM KHCO3, and 0.1 mM Na2EDTA, pH 7.3) for 5 min at 4 °C. Pooled cells were centrifuged (300 × g, 5 min) and washed two times with Dulbecco’s Modified Minimal Essentials Medium (Hyclone Laboratories, Inc., Logan, UT) containing 1% fetal bovine serum, 1% Nu serum (BD, Bedford, MA), Glutamine plus (2 mM, Atlanta Biologicals, Atlanta, GA), 0.1 M HEPES and 10% Opti-MEM (Invitrogen, Grand Island, N.Y.)(DMEM2). Primary bone marrow cells were suspended in DMEM2 supplemented with recombinant mouse macrophage colony stimulating factor (rmM-CSF; 1.5 ug/ml, R & D Systems, Minneapolis, MN) in preparation for culture in Fluid Processing Apparatus hardware (FPAs). Briefly, FPAs are 11.70 cm long and 1.35 cm diameter (1.31 mm glass thickness) glass barrels. The FPAs have a bypass which allows for the transfer of media from one chamber to another. The FPAs were siliconized with Rain-X (Blue Coral-Slick 50, Ltd; Cleveland, OH) and fitted with a previously siliconized rubber septum, 1.2 cm from the distal end of the barrel. Bacti-caps (16-mm diam.; Oxford Labware, St. Louis, MO) were placed on the proximal end of the FPAs before sterilization.

value: MESH]:Space Flight


title: mus-musculus-bone-marrow-ground-control-1


title: Pregnant Un-infected

value: Pregnant Women (Healthy)


title: mus-musculus-bone-marrow-space-flight-2


title: HN-5 IC25, 16h

description:
SAMPLE 2
Replicate 1

source_name: HN-5 cell line, IC25 erufosine, 16h

value: OSCC cell line


title: Nr.2

description: Freshly isolated BM cells were purified by removal of T cells and B cells using MACS technology. Then at day 8 DCs were treated with 500U/ml TNF for 6h.

source_name: BM-DC TNF 6h


title: HCT8-24h-2

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 24 hours.
HCT80242


title: HCT8-0h-3

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 0 hours.
HCT80003


title: HCT8-24h-1

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 24 hours.
HCT80241


title: HCT8-24h-3

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 24 hours.
HCT80243


title: HCT8-48h-1

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 48 hours.
HCT80481


title: Pregnant Fulminant Liver Failure

value: Pregnant Women With Liver Failure


title: HCT8/5Fu-24h-1

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 24 hours .
HCT85241

value: 5-FU-induced resistant


title: HCT8-0h-1

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 0 hours.
HCT80001


title: HCT8-0h-2

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 0 hours.
HCT80002


title: G00138 PBMC Genomic DNA

type: genomic

city: Toronto

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto Scarborough

description: CFS Genomic DNA

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from Omega EZNA Tissue DNA Kit according to manufacturer's instructions

tag: Sex

value: Female

tag: disease state

value: CFS


title: FMDV-infected RAW264.7 cell_9hr_rep2

city: Lanzhou

first: Xiaoying

last: Zhi

state: Gansu

address: Xujiaping 1,Lanzhou,Gansu,China

institute: Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences

description:
SAMPLE 5
Gene expression after 9hr in FMDV-infected RAW264.7cells

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

organism: Mus

source_name: FMDV-infected RAW264.7 cell_9hr

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The differences gene expression in FMDV-infected and uninfected RAW264.7 cells were measured at 9 hours at MOI of 2. The experiment was divided into two groups (FMDV-infected RAW264.7 and FMDV-uninfected RAW264.7) , each repeated 3 times.All six independent experiments were performed at 9 hours using different cell cultrual samples for each experiment.

value: monocyte macrophage cell line

tag: infected with

value: O type FMDV

value: 9 hours at MOI of 2


title: GA032324 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00181 PBMC Genomic DNA

description: CFS Genomic DNA


title: GA032320 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00232 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00228 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00256 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00190 PBMC Genomic DNA

description: CFS Genomic DNA


title: FMDV-infected RAW264.7 cell_9hr_rep3

description:
SAMPLE 6
Gene expression after 9hr in FMDV-infected RAW264.7cells


title: G00067 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00193 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00238 PBMC Genomic DNA

description: Control Genomic DNA

value: Control


title: G00151 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00118 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00066 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00235 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00114 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00095 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00072 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00210 PBMC Genomic DNA

description: Control Genomic DNA


title: G00170 PBMC Genomic DNA

description: CFS Genomic DNA


title: GA032335 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00110 PBMC Genomic DNA

description: CFS Genomic DNA


title: FMDV-infected RAW264.7 cell_9hr_rep1

description:
SAMPLE 4
Gene expression after 9hr in FMDV-infected RAW264.7cells


title: G00096 PBMC Genomic DNA

description: CFS Genomic DNA


title: FMDV-uninfected RAW264.7 cell_9hr_rep3

description:
SAMPLE 3
Gene expression after 9hr in FMDV-uninfected RAW264.7cells

source_name: FMDV-uninfected RAW264.7 cell_9hr

value: none (uninfected control)

value: 9 hours


title: G00063 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00071 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00247 PBMC Genomic DNA

description: CFS Genomic DNA


title: GA032330 PBMC Genomic DNA

description: CFS Genomic DNA


title: FMDV-uninfected RAW264.7 cell_9hr_rep2

description:
SAMPLE 2
Gene expression after 9hr in FMDV-uninfected RAW264.7cells


title: FMDV-uninfected RAW264.7 cell_9hr_rep1

description:
SAMPLE 1
Gene expression after 9hr in FMDV-uninfected RAW264.7cells


title: BM-LSK_Tet2KD/KDEzh2Δ/Δ -MDS_BMT-2nd_DAC

city: Chiba

first: Motohiko

last: Oshima

state: State...

address: 1-8-1 Inohana

institute: Chiba University

description: Gene expression in Tet2KD/KDEzh2Δ/Δ MDS LSK cells in secondary recipients 10 weeks post-transplantation and 7 weeks after DAC treatment

hyb_protocol: 600 ng of the labeled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray. The process of hybridization and washing was performed using a Hi-RPM Gene Expression Hybridization Kit (Large) (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: GeneChips were scanned using a DNA microarray scanner (Agilent Technologies)

data_processing: Standard Agilent protocol

source_name: bone marrow LSK cells, Tet2KD/KDEzh2Δ/Δ -MDS, 10w post-transplantation, 7w DAC, replicate 1

label_protocol: Total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent), amplified and labeled with Cyanine 3 using a Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, which generated single-color labeled cRNA.

extract_protocol: RNeasy Plus Micro Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Freshly isolated bone marrow cells were stained by appropriate antibodies, and then sorted on FACSAriaII (BD).

tag: strain

tag: tissue

value: HSPCs

tag: cell markers

value: Lineage-Sca-1+c-Kit+ (LSK)

value: Tet2KD/KD; Ezh2delta/delta


title: BM-LSK_Tet2KD/KDEzh2Δ/Δ -MDS_BMT-2nd_PBS

description: Gene expression in Tet2KD/KDEzh2Δ/Δ MDS LSK cells in secondary recipients 10 weeks post-transplantation and 7 weeks after PBS treatment

source_name: bone marrow LSK cells, Tet2KD/KDEzh2Δ/Δ -MDS, 10w post-transplantation, 7w PBS, replicate 1

value: bone marrow


title: G00187 PBMC Genomic DNA

description: Control Genomic DNA


title: G00129 PBMC Genomic DNA

description: Control Genomic DNA


title: Luci_DOX rep2

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: The Cy3-labeled aRNA was hybridized overnight and washed according to the Agilent protocol.

scan_protocol: The dried slides were scanned at 2 µm/pixel resolution using the InnoScan 900 (Innopsys, Carbonne, France). Image analysis was performed with Mapix 6.5.0 software and calculated values for all spots were saved as GenePix files

data_processing: Data was processed using R and limma.

source_name: HEK 292T

label_protocol: total RNA was amplified and Cy3-labeled using the LIRAK kit as described by the provider (Agilent) using 200 ng of total RNA

growth_protocol: HEK-293T cells, its derivatives and U2OS cells were cultured in DMEM medium supplemented with 10% FCS, Glutamine, Penicillin and Streptomycin.

extract_protocol: RNA was extracted using the RNeasy kit from Invitrogen

treatment_protocol: Transfection of adherent cells was done using linear polyethylenimine as described (Milanovic et al., 2014). Briefly, 3 x 107 cells were collected by centrifugation, washed with phosphate-buffered saline (PBS) and resuspended in 300 μl of RPMI medium without serum and antibiotics. 10 µg of DNA were mixed with the cells and transferred to a 4 mm electroporation cuvette. Cells were electroporated using an exponential decay pulse at 250 V and 950 μF. Cells were incubated for 10 min at room temperature and then transferred to a culture flask containing 10 ml of complete RPMI medium.

value: HEK 292T

tag: shRNA

value: control

tag: dox

value: yes


title: Luci_no_DOX rep2


title: CNOT2_DOX rep2


title: CNOT2_no_DOX rep2

value: no


title: CNOT1_DOX


title: G00130 PBMC Genomic DNA

description: Control Genomic DNA


title: CNOT2_DOX rep1


title: G00128 PBMC Genomic DNA

description: Control Genomic DNA


title: G00199_2 PBMC Genomic DNA

description: Control Genomic DNA


title: G00125 PBMC Genomic DNA

description: Control Genomic DNA


title: G00025 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00032 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00248 PBMC Genomic DNA

description: Control Genomic DNA


title: CNOT3_DOX


title: G00154 PBMC Genomic DNA

description: Control Genomic DNA


title: G00056 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00148 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00093 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00017 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00206 PBMC Genomic DNA

description: Control Genomic DNA


title: G00102 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00035 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00155 PBMC Genomic DNA

description: Control Genomic DNA


title: Luci_no_DOX rep1


title: G00164 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00143 PBMC Genomic DNA

description: Control Genomic DNA


title: G00144 PBMC Genomic DNA

description: Control Genomic DNA


title: G00216 PBMC Genomic DNA

description: Control Genomic DNA


title: G00069 PBMC Genomic DNA

description: CFS Genomic DNA


title: CNOT2_no_DOX rep1


title: CNOT1_no_DOX


title: G00049 PBMC Genomic DNA

description: CFS Genomic DNA


title: Luci_DOX rep1


title: heat_rep2

hyb_protocol: Hybridization was performed at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 20 µm/pixel resolution and analyzed with GenePix software V5.2 (MDS).

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47)

source_name: heat-inactivated

label_protocol: Purified total RNA was amplified and Cy-labeled using the dual-color QuickAmp kit (Agilent Technologies, Palo Alto, CA) following the kit instructions.

growth_protocol: 2,5*10^6 Cells were seeded in culture vessels in Dulbecco’s Modified Eagle Medium (DMEM) with 10% Fetal calf serum and 2 mmol/l L-glutamine, 1 mmol/l sodium pyruvate, 100 U/ml penicillin, 100 μg/ml streptomycin GibcoBRL. Afterwards cells were infected with the human coronavirus 229E at 33°C, 5%CO2 - incubation for 24h.

extract_protocol: Macherey Nagel NucleoSpin RNA Kit (with DNAse treatment)

treatment_protocol: For the infection cells were incubated with DMEM containing the virus at a multiplicity of infection (MOI) of 1. Titers were determined by TCID50 assays. The cells were further incubated at 33°C for 24h with either the CoV-229E or with the heat-inactivated virus. Control cells were left untreated, but were also incubated at 33°C. As positive control another sample of cells was treated with IL-1 (10 ng/ml) for 1h.

value: HuH7 cells

tag: treatment

value: heat-inactivated HCoV-229E


title: G00150 PBMC Genomic DNA

description: Control Genomic DNA

value: Female


title: heat_rep1


title: G00163 PBMC Genomic DNA

description: Control Genomic DNA


title: ctrl_rep2

source_name: control


title: G00037 PBMC Genomic DNA

description: CFS Genomic DNA

value: CFS


title: G00208 PBMC Genomic DNA

description: Control Genomic DNA


title: IL1_rep2


title: CoV_rep1

source_name: infected


title: G00162 PBMC Genomic DNA

description: Control Genomic DNA


title: ctrl_rep1


title: IL1_rep1


title: G00113 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00030 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00199 PBMC Genomic DNA

description: Control Genomic DNA


title: HuH7.229E_rep2

source_name: HuH7, infected

growth_protocol: HuH7 cells were seeded in culture vessels in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum, 1% non essential amino acids, 1% Glutamax, 100 U/ml penicillin, 100 μg/ml streptomycin GibcoBRL and incubated at 37°C, 5% CO2 for 24 hours before infection with Human coronavirus 229E.

extract_protocol: QIAgen RNeasy Kit without DNase treatment

treatment_protocol: For the infection, cells were incubated with DMEM (supplemented with 10% fetal calf serum, 1% non essential amino acids, 1% Glutamax, 100 U/ml penicillin, 100 μg/ml streptomycin) containing HCoV-229E at a multiplicity of infection (MOI) of 5  and incubated  at 33°C. Titers were determined by TCID50 assays. 1 hour post inoculation the supernatant was removed and replaced with the according fresh growth medium and incubated at 33°C for 23 hours. Control cells were mock infected and also incubated at 33°C.


title: HuH7.ctrl_rep2

source_name: HuH7, untreated


title: G00054 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00059 PBMC Genomic DNA

description: CFS Genomic DNA


title: A549_IL1

growth_protocol: 700,000 cells were seeded in culture vessels in Dulbecco’s Modified Eagle Medium (DMEM) with 10% Fetal calf serum and 2 mmol/l L-glutamine, 1 mmol/l sodium pyruvate, 100 U/ml penicillin, 100 μg/ml streptomycin GibcoBRL. After 24 hours cells were infected with the human coronavirus 229E at 33°C, 5%CO2 and further incubated for the indicated times.

extract_protocol: Macherey Nagel NucleoSpin RNA Kit

treatment_protocol: For the infection cells were incubated with DMEM containing the virus at a multiplicity of infection (MOI) of 1. The cells were further incubated at 33°C for different times. Control cells were left untreated, but were also incubated at 33°C. As positive control another sample of cells was treated with IL-1alpha (10 ng/ml).

value: A549 cells


title: G00213 PBMC Genomic DNA

description: Control Genomic DNA


title: HuH7.229E_rep1


title: HuH7.ctrl_rep1


title: A549_48h_heat-inactivated

source_name: 48h, heat-inactivated


title: A549_24h_heat-inactivated

source_name: 24h, heat-inactivated


title: A549_16h_heat-inactivated

source_name: 16h, heat-inactivated


title: G00121 PBMC Genomic DNA

description: CFS Genomic DNA

source_name: PBMC


title: CNOT3_no_DOX


title: A549_16h_positive

source_name: 16h, positive


title: G00135 PBMC Genomic DNA

description: Control Genomic DNA


title: A549_24h_positive

source_name: 24h, positive


title: A549_48h_positive

source_name: 48h, positive


title: A549_untreated

source_name: untreated


title: G00212 PBMC Genomic DNA

description: Control Genomic DNA


title: G00140 PBMC Genomic DNA

description: Control Genomic DNA


title: G00158 PBMC Genomic DNA

description: Control Genomic DNA


title: CoV_rep2


title: G00021 PBMC Genomic DNA

description: CFS Genomic DNA


title: 1-month-old spontaneously hypertensive rat vs 3-month-old spontaneously hypertensive rat

city: Estado de México

first: Ronquillo Sánchez

middle: Sánchez

last: María Dolores

state: Tlalnepantla

address: Av. De los Barrios No. 1, Los Reyes, Iztacala

department: Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala

country: Mexico

institute: Universidad Nacional Autónoma de México

description: Tissue from SHR 1-month-old spontaneously hypertensive rat vs SHR 3-month-old spontaneously hypertensive rat

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix from Molecular Devices. All images were captured using 10µm resolution. For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing: Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. Differentially expressed genes were selected using filtering criteria of a change in expression of at least 1.5-fold and a p value of ≤0.05. The associated biological pathways were determined using DAVID Bioinformatics Resources 6.8 software. Functional Analysis by Gene Ontology and Gene Pathways, GeneSpring GX and Database for Annotation, Visualization, and Integrated Discovery (DAVID Bioinformatics database) was used to identify functional related categories of genes.

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: Male, 1 and 3-month-old Wistar Kyoto (WKY) and spontaneously hypertensive rats (SHR) were maintained in a pathogen-free environment with controlled conditions (22 + 2 °C, 40–60% humidity, 12-h/12-h light/dark cycle) and free access to food and water. Animal housing, care and all procedures were conducted in accordance with Mexican Regulations of Animal Care and Use (NOM-062-ZOO-1999, SAGARPA, México) and with the Guide for the Care and Use of Laboratory Animals.

extract_protocol: Rats were sacrificed by cervical dislocation and their liver was rapidly removed and washed in phosphate buffer solution (PBS); the samples were immediately frozen on ice and maintained at -80ºC until analysis. Total RNA was extracted from frozen liver tissues using Trizol reagent (Invitrogen Life Technologies, CA, USA). The RNA concentration was determined by measuring the optical density at 260 nm, and the purity was determined by calculating the OD260/OD280 absorption ratio (all ratios were ensured to be >1.8). RNA integrity was confirmed by electrophoresis on a 1.5% denaturing agarose gel.

treatment_protocol: The gene expression levels in liver samples from WKY and SHR rats were analyzed using rat microarrays. Three independent experiments were performed, microarray number one consist in compare the gene expression profile of 1-month old spontaneously hypertensive rats (SHR) versus age-matched normotensive rats (WKY), the second microarray consist in compare the gene expression profile of 3-month old spontaneously hypertensive rats (SHR) versus age-matched normotensive rats (WKY) and the last compare the gene expression profile of 1-month old spontaneously hypertensive rats (SHR) versus 3-month old spontaneously hypertensive rats (SHR).

value: Liver

tag: age

value: 1 month old

tag: phenotype

value: spontaneously hypertensive

value: 3 month old


title: G00200 PBMC Genomic DNA

description: CFS Genomic DNA


title: pool WKY vs 1-month-old spontaneously hypertensive rat

description: Tissues from WKY 1-month rats were pooled and compared versus SHR age-matched

source_name: pooled liver Wistar Kyoto rat

value: Wistar Kyoto


title: pool WKY vs 3-month-old spontaneously hypertensive rat

description: Tissues from WKY 3-month rats were pooled and compared versus SHR age-matched


title: HCT8/5Fu-72h-3

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 53 hours .
HCT85723

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip

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

data_processing:
GenomeStudio software v2011.1, Methylation module v1.9.0
Unmethylated and methylated signal intensities in Matrix_Signal.txt series supplementary file

source_name: 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 72 hours

extract_protocol: Bisulfite converted DNA was amplified and fragmented

tag: cell line

tag: genotype

value: 5-FU-induced resistant


title: HCT8/5Fu-72h-2

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 52 hours .
HCT85722


title: G00062 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00080 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00061 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00211 PBMC Genomic DNA

description: Control Genomic DNA

value: Control


title: G00055 PBMC Genomic DNA

description: CFS Genomic DNA


title: G00042 PBMC Genomic DNA

description: CFS Genomic DNA


title: platelet_2 day_rep3

city: Guangzhou

last: Li

state: Guangdong

address: Panfu Road No1

department: Blood transfusion Department

institute: Guangzhou First People's Hospital

description:
Gene expression in platelets stored for 2 day
C2.CEL

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by RMA algorithm, Gene Spring Software 13.1 (Agilent technologies, Santa Clara, CA, US).

source_name: apheresis platelet, stored, 2 day

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip WT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was isolated from apheresis platelet using mirVanaTM RNA Isolation Kit in accordance with the manufacturer’s protocol.

treatment_protocol: Apheresis platelets were stored at 22±2 ℃ in storage tank and 10ml sample were collected at 2 day, 5 day, 8 day. The 10 ml platelet product was centrifuged at 1500g for 10 minutes to removal of the plasma. The harvested samples were snap-frozen in liquid nitrogen until being complete frozen , then stored at -80 ℃ until processing.

tag: gender

value: male

value: 30 years

tag: cell type

value: platelet

tag: time

value: stored for 2 days


title: HCT8/5Fu-72h-1

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 51 hours .
HCT85721


title: HCT8/5Fu-0h-3

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 50 hours .
HCT85003

source_name: 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 0 hours


title: adjacent non-neoplastic tissue sample 5NT

first: Zheng

last: Zaosong

address: 107 Yan Jiang West Road, Guangzhou, P.R. China

description:
Gene expression in clear cell renal cell carcinoma tissues surgucally removed tissue samples
5NT

hyb_protocol: The labeled cRNAs were hybridized onto the microarray based on the manufacturer’s standard protocols.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: adjacent non-neoplastic tissue sample

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Trizol reagent(Invitrogen) following the manufacturer's instructions.

treatment_protocol: A total number of 5 pairs of clear cell renal cell carcinoma tissues and adjacent non-neoplastic tissues were surgically removed in Sun Yat-sen Memorial Hospital, Sun Yat-sen University. All tissue samples were stored at -80˚C refrigerator within 10 minutes after the resection.

value: normal


title: HCT8/5Fu-0h-2

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 49 hours .
HCT85002


title: adjacent non-neoplastic tissue sample 2NT

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description:
Gene expression in clear cell renal cell carcinoma tissues surgucally removed tissue samples
2NT


title: platelet_8 day_rep2

description:
Gene expression in platelets stored for 8 day
B8.CEL

source_name: apheresis platelet, stored, 5 day

value: 33 years

value: stored for 8 days


title: adjacent non-neoplastic tissue sample 1NT

description:
Gene expression in clear cell renal cell carcinoma tissues surgucally removed tissue samples
1NT


title: HCT8-0h-1

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 24 hours.
HCT80001

source_name: HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 0 hours

value: wild type


title: platelet_8 day_rep3

description:
Gene expression in platelets stored for 8 day
C8.CEL

source_name: apheresis platelet, stored, 8 day


title: HCT8-72h-3

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 29 hours.
HCT80723

source_name: HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 72 hours


title: platelet_5 day_rep3

description:
Gene expression in platelets stored for 5 day
C5.CEL

value: stored for 5 days


title: platelet_5 day_rep2

description:
Gene expression in platelets stored for 5 day
B5.CEL


title: clear cell renal cell carcinoma sample 5CA

description:
Gene expression in clear cell renal cell carcinoma tissues surgucally removed tissue samples
5CA

source_name: clear cell renal cell carcinoma sample

value: cancer


title: clear cell renal cell carcinoma sample 4CA

description:
Gene expression in clear cell renal cell carcinoma tissues surgucally removed tissue samples
4CA


title: HCT8-0h-3

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 26 hours.
HCT80003


title: adjacent non-neoplastic tissue sample 3NT

description:
Gene expression in clear cell renal cell carcinoma tissues surgucally removed tissue samples
3NT


title: Platelets_thrombin_Ago2-IP_rep2

status: Public on Mar 14 2017

city: Stockholm

first: Xinyan

last: Miao

address: Karolinska University Hospital-Solna

department: Medicine

country: Sweden

institute: Karolinska Institutet

description:
RNA pull down with Ago2
miRNA expression profile

hyb_protocol: Labeled RNA was hybridized onto Agilent miRNA array (G4470B) for 20 hours at 55°C

scan_protocol: Slides were scanned in an Agilent microarray scanner (G2565BA, Agilent Technologies) using default settings for miRNA microarray v2.0. Images obtained after scanning were processed with Feature Extraction Software 10.7.3.1 (Agilent, Santa Clara, CA)

data_processing:
Processing of the intensity values was done using Cluster 3.0 software whereby data were normalized and median centered. Only normalized miRNAs with less than 25% missing values across the samples were included in the further analysis.
Normalized and median centered intensity values.

source_name: washed platelets from venous peripheral blood

label_protocol: 200 ng of total RNA were dephosphorylated and fluorescence-labeled with Cyanine 3-pCp by using T4 RNA Ligase.

growth_protocol: Venous blood was collected using siliconized vacutainers containing 1/10 volume of 3.8% sodium citrate. The blood was centrifuged at 190 ´g for 20 min at room temperature (RT), and the upper two-thirds of platelet-rich plasma (PRP) was collected. After adding PGE1 (final concentration 1 µM), PRP was re-centrifuged at 190 ´g for 10 min at RT. Again, the top two-thirds of PRP was collect to reduce leukocyte contamination. Platelets were further purified by leukocyte depletion using CD45 Dynabeads. Afterwards, PRP was washed with Tyrode’s HEPES buffer containing 0.1 µM PGE1, and centrifuged at 1000 ´g for 10 min at RT. Platelets were then resuspended in DMEM low glucose medium at 109/ml, and kept on bench for 30 min to allow the recovery of platelet responsiveness.

extract_protocol: RNA extraction of the whole cell lysate of platelets and Ago2-IP supernatant was carried out using TRIzol reagent (Invitrogen) and according to manufacture’s instructions.

treatment_protocol: For total RNA, the purified platelets were treated with vehicle or thrombin (0.1 U/ml) at 37℃ for 30 min, then total RNA was extracted; For Ago2-associated RNA, washed platelets were treated with vehicle or thrombin (0.1 U/ml) for 30 min at 37°C, followed by UV crosslinking, and platelet pellets were lysed. The supernatant was then incubated with Dynabeads® Protein G coupled to anti-Ago2 or the isotypic control IgG for 4 hours at 4℃ with rotation, thereafter, the beads were washed 5 times. The washed beads were then treated with proteinase K, and the supernatant was collected for RNA extraction.

tag: stimulation

value: thrombin stimulation

tag: ip

value: Ago2 IP


title: Platelets_resting_Ago2-IP_rep1

value: unstimulation


title: Platelets_thrombin_Ago2-IP_rep1


title: HCT8-72h-2

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 28 hours.
HCT80722


title: HCT8/5Fu-0h-1

description:
Gene expression data from 5-FU-induced resistant cell line (HCT8/5- FU) derived from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT), treated with 5-fluorouracil (5-FU) for 48 hours .
HCT85001


title: platelet_2 day_rep2

description:
Gene expression in platelets stored for 2 day
B2.CEL


title: platelet_5 day_rep1

description:
Gene expression in platelets stored for 5 day
A5.CEL

value: 31 years


title: platelet_8 day_rep1

description:
Gene expression in platelets stored for 8 day
A8.CEL


title: platelet_2 day_rep1

description:
Gene expression in platelets stored for 2 day
A2.CEL


title: Platelets_resting_Ago2-IP_rep2


title: HCT8-0h-2

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 25 hours.
HCT80002


title: clear cell renal cell carcinoma sample 3CA

description:
Gene expression in clear cell renal cell carcinoma tissues surgucally removed tissue samples
3CA


title: clear cell renal cell carcinoma sample 1CA

description:
Gene expression in clear cell renal cell carcinoma tissues surgucally removed tissue samples
1CA


title: adjacent non-neoplastic tissue sample 4NT

description:
Gene expression in clear cell renal cell carcinoma tissues surgucally removed tissue samples
4NT


title: HCT8-72h-4

description:
Gene expression data from HCT-8 human colorectal cancer (CRC) wild type cells (HCT8/WT) treated with 5-fluorouracil (5-FU) for 27 hours.
HCT80724


title: clear cell renal cell carcinoma sample 2CA

description:
Gene expression in clear cell renal cell carcinoma tissues surgucally removed tissue samples
2CA


title: PB1T-3 embryonic stem cells [G-31] (methylation)

city: Shanghai

first: Hongying

last: Sha

state: Shanghai

address: 220 Handan Rd, WuJiaoChang, Yangpu Qu

institute: Fudan University

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

source_name: embryonic stem cells

growth_protocol: In vitro culture at  5% CO2,37℃

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

treatment_protocol: All embryonic stem cells were cultured onto inactived feeder cells  and classical media for humanembryonic stem cells.  Human embryonic fibroblast cells were cultured under 10% fetal  bovine serum  in DMEM/f12.

value: from inner cell mass of PB1T blastocyst


title: PB1T-3 embryonic stem cells [G-32] (methylation)


title: IVF-2 embryonic stem cells [G-42] (methylation)

value: from inner cell mass of IVF blastocyst


title: PB1T-3 embryonic stem cells [G-33] (methylation)


title: IVF-2 embryonic stem cells [G-43] (methylation)


title: PB2T-2 embryonic stem cells [7-1] (methylation)

value: from inner cell mass of PB2T blastocyst


title: IVF embryonic stem cells [10-1] (methylation)


title: PNT-1 embryonic stem cells [8-1] (methylation)

value: from inner cell mass of PNT blastocyst


title: PNT-1 embryonic stem cells [8-2] (methylation)


title: IVF embryonic stem cells [10-2] (methylation)


title: PNT-2 embryonic stem cells [9-1] (methylation)


title: PNT-2 embryonic stem cells [9-2] (methylation)


title: PNT-1 embryonic stem cells [8-3] (methylation)


title: IVF-2 embryonic stem cells [G-41] (methylation)


title: ST-3 embryonic stem cells [5-1] (methylation)

value: from inner cell mass of ST blastocyst


title: ST-2 embryonic stem cells [4-2] (methylation)


title: PB2T-2 embryonic stem cells [7-2] (methylation)


title: human adult fibroblast [G-13] (methylation)

source_name: human adult fibroblast

value: from  head skin of Patients with traumatic brain injury


title: human adult fibroblast [G-11] (methylation)


title: PNT-2 embryonic stem cells [9-3] (methylation)


title: PB2T-1 embryonic stem cells [6-1] (methylation)


title: ST-2 embryonic stem cells [4-1] (methylation)


title: ST-2 embryonic stem cells [4-3] (methylation)


title: ST-3 embryonic stem cells [5-2] (methylation)


title: IVF embryonic stem cells [10-3] (methylation)


title: PB2T-1 embryonic stem cells [6-3] (methylation)


title: human adult fibroblast [G-12] (methylation)


title: PB2T-1 embryonic stem cells [6-2] (methylation)


title: PB2T-2 embryonic stem cells [7-3] (methylation)


title: ST-3 embryonic stem cells [5-3] (methylation)


title: ST-1 embryonic stem cells [3-3] (methylation)


title: Maleic acid (100uM)_H007

city: Kaohsiung

first: Chun-Wei

last: Tung

address: No. 100, Shih-Chuan 1st Rd.

country: Taiwan

institute: Kaohsiung Medical University

description: MA 100uM technical replicate 1

hyb_protocol: Fluorescent aRNA targets were prepared from 1 μg total RNA samples using OneArray® Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA). Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After hybridization at 50℃ for 16 hours, non-speciﬁc binding targets were washed away by three different washing steps.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm power 100 ) and quantify the fluoresence intensity.

data_processing: The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.

source_name: Maleic acid (100uM)

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

growth_protocol: The human neuroblastoma cell line, SH-SY5Y, was purchased from ATCC (Manassas, VA, USA). Cells were cultured in a 1:1 mixture of ATCC-formulated Eagle's Minimum Essential Medium (EMEM) and F12 medium supplemented with 2 mM L-glutamine, 1% of penicillin/streptomycin, and 10% heat-inactivated fetal bovine serum (GIBCO, Gaithersburg, MD, USA) at 37°C in 5% CO2. Cells were seeded at an initial density of 104 cells/cm2 and cultured overnight prior to be treated with various concentration of maleic acid (Sigma-Aldrich, St. Louis, MO).

extract_protocol: Total RNA was extracted from SH-SY5Y cells using the TRizol (Qiagen, CA, USA). The RNA samples were then treated with an RQ1 RNase-free DNase kit (Promega, UK) according to the manufacturer’s instructions to remove contaminated DNA. The RNA concentration and purity were checked by OD260/OD280 (>1.8) and OD260/OD230 (>1.6), and the yield and quality were assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: SH-SY5Y cells were treated with maleic acid (10-100 μM) for 24 h


title: Maleic acid (10uM)_004

description: MA 10uM technical replicate 2

source_name: Maleic acid (10uM)


title: Maleic acid (100uM)_H008

description: MA 100uM technical replicate 2


title: Maleic acid (50uM)_005

description: MA 50uM technical replicate 1

source_name: Maleic acid (50uM)


title: Control_001

description: Control technical replicate 1

source_name: Control


title: Control_002

description: Control technical replicate 2


title: Maleic acid (10uM)_003

description: MA 10uM technical replicate 1


title: PB1T-2 embryonic stem cells [2-3] (methylation)


title: Maleic acid (50uM)_006

description: MA 50uM technical replicate 2


title: KO39M

city: Columbus

first: Bhawana

last: Dikshit

state: OH

address: 500 W 12th Avenue

institute: Ohio State University

description: Gene expression data from liver of Wildtype and Knockout mice

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix) •Heat 650C for 5 minutes, 990C for 5 minutes, 450C for 5 minutes centrifuge top speed for 5 minutes. •Hybridize 16 hours at 450 at 60rpm•Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

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

source_name: Mice liver tissue at 12 weeks of age

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

growth_protocol: Mice liver tissue collected at 12 weeks of age

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

treatment_protocol: Mice were euthanized at 12 weeks of age and liver tissue was snap frozen in liquid nitrogen for RNA extraction

value: Mouse C57BL6/J

value: Liver


title: KO69F


title: KO13F


title: KO40F


title: Subject 29, Meal C (1500 kcal), Postprandial (6h)

city: Bern

first: Doreen

last: Gille

address: Schwarzenburgstrasse 161

country: Switzerland

institute: Agroscope

description: Blood cell transcriptome 6h after ingestion of 1500 kcal of a high fat meal

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16h at 45°C on Human Genome Array HG-U219. Arrays were washed and stained in the Affymetrix Fluidics Station of GeneAtlas™.

scan_protocol: GeneChips were scanned using the GeneAtlas™ Imaging Station.

data_processing: Data was processed by RMA, using the rma() function in the affy package (version 1.38.1) for R (version 3.0.1), to yield log-transformed expression values that were used for all subsequent analysis.

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the GeneAtlas™ 3'IVT Express Kit protocol from Affymetrix.

extract_protocol: Total RNA was extracted using PAXgene Blood RNA Kit (Qiagen AG) according to the manufacturer’s recommendations.Total RNA was purified and concentrated with RNeasy MinElute Cleanup Kit (Qiagen AG). Next step included the depletion of globin mRNA with the GLOBINclear™ hybridization capture technology (Ambion, USA) according to recommendations of manufacturer.

treatment_protocol: Human subjects ingested 500, 1'000, 1'500 kcal of a high-fat meal in a randomized cross-over design. Blood was collected for RNA extraction before ingestion at 0h as well as postprandially at 2h, 4h, and 6h.

value: Whole blood

tag: metabolic status

value: Obese


title: reMAIT_day_0_Start

city: Koto-ku

first: Toutai

last: MITUYAMA

state: Tokyo

department: Artificial Intelligence Research Team

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: DNA methylation from reMAIT at 0 days after the beginning of induction

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol.

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

data_processing: Data normalization was performed using Illumina GenomeStudio Methylation Molude.

source_name: reMAIT, day 0, Start

label_protocol: Extracted genomics DNA (1 micro gram) from each sample was subjected to bisulfite conversion using EZ DNA Methylation Kit (Zymo Research, CA, USA).

growth_protocol: MAIT-derived iPSCs were cultured on OP9, and CD34+ CD43+ cells were isolated. These CD34+ CD43+ precursor cells were furthered cultured on OP9/DL1 for re-differentiation into MAITs.

extract_protocol: Genomic DNA was extracted from each sample using Wizard Genomic DNA Purification Kit (Promega, Tokyo, Japan).

value: cord blood

tag: timecourse

value: 0 day


title: reMAIT_day_4_Early

description: DNA methylation from reMAIT at 4 days after the beginning of induction

source_name: reMAIT, day 4, Early

value: 4 day


title: Subject 29, Meal C (1500 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 1500 kcal of a high fat meal


title: Subject 29, Meal C (1500 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 1500 kcal of a high fat meal


title: PB1T-2 embryonic stem cells [2-2] (methylation)


title: KO18M

tag: strain


title: PB1T-1 embryonic stem cells [1-3] (methylation)

tag: tissue


title: WT27F


title: WT25F


title: Subject 29, Meal C (1500 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 1500 kcal of a high fat meal


title: Immature_T_cells_CD4-_CD8-_day_21_Early

description: DNA methylation from immature T-cells with CD4- and CD8- at 21 days after the beginning of differentiation

source_name: Immature T-cells, CD4-, CD8-, day 21, Early

growth_protocol: CD34+ cells were isolated from CB using CD34 MicroBead Kit (Miltenyi Biotech)

value: 21 day


title: WT33M


title: Immature_T_cells_CD4-_CD8-_day_40_Middle

description: DNA methylation from immature T-cells with CD4- and CD8- at 40 days after the beginning of differentiation

source_name: Immature T-cells, CD4-, CD8-, day 40, Middle

value: 40 day


title: PB1T-1 embryonic stem cells [1-1] (methylation)