title: Sample 28_Time Point 1d Dose 54ug [set 2]

source_name: Time Point 1d Dose 54ug

tag: strain

tag: gender

tag: exposed to


title: staud-00261: LYM161

status: Public on Dec 07 2016

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

molecule: total RNA

organism: Homo sapiens

source_name: diffuse large-B-cell lymphoma

tag: dlbcl sample (lym number)

tag: analysis set

value: Training

tag: follow-up (years)

tag: status at follow-up

value: Alive

tag: subgroup

value: ABC

tag: ipi group

value: Low

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM159

scan_protocol: See mage-tab files linked to series entry for additional details

value: Dead

value: Type III


title: staud-00261: LYM160

data_processing: See mage-tab files linked to series entry for additional details


title: Sample 22_Time Point 1d Dose 0ug [set 2]

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 4x44K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

organism: Mus musculus

source_name: Time Point 1d Dose 0ug

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Five-to-seven week old female C57BL/6 mice (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and heart were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Mice were dosed via single intratracheal instillation of 18 µg (very low), 54 µg (low dose), 162 µg (medium dose), or 486 µg (high dose) of TiO2NPs in a 40 µl suspension   Tissues were collected 24h and 28 days after instillation.

value: female

tag: age

value: 5-7 weeks

value: rutile hydrophilic TiO2NPs of 20 nm diameter

tag: dosage

tag: time point

value: 1d post-exposure

tag: tissue

value: lung

source_name: Universal Mouse Reference RNA

tag: sample type

value: 11 mouse cell lines


title: Sample 24_Time Point 28d Dose 486ug [set 2]

source_name: Time Point 28d Dose 486ug

tag: strain

tag: gender

tag: exposed to

value: 28d post-exposure


title: staud-00261: LYM154

label_protocol: See mage-tab files linked to series entry for additional details

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)

value: Medium


title: Sample 19_Time Point 28d Dose 162ug [set 2]

source_name: Time Point 28d Dose 162ug


title: Sample 25_Time Point 28d Dose 0ug [set 2]

source_name: Time Point 28d Dose 0ug


title: Sample 20_Time Point 1d Dose 486ug [set 2]

source_name: Time Point 1d Dose 486ug


title: staud-00261: LYM151

extract_protocol: See mage-tab files linked to series entry for additional details

tag: status at follow-up

tag: subgroup

tag: ipi group


title: staud-00261: LYM158

value: GCB

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: Sample 18_Time Point 28d Dose 0ug [set 2]

tag: age


title: staud-00261: LYM147

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM152


title: Sample 23_Time Point 1d Dose 162ug [set 2]

source_name: Time Point 1d Dose 162ug

tag: dosage

tag: time point

tag: tissue


title: Sample 17_Time Point 28d Dose 486ug [set 2]

tag: strain

tag: gender

tag: sample type


title: Sample 21_Time Point 1d Dose 54ug [set 2]

tag: exposed to


title: Sample 26_Time Point 28d Dose 54ug [set 2]

source_name: Time Point 28d Dose 54ug


title: staud-00261: LYM164

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)


title: staud-00261: LYM144

tag: status at follow-up

tag: subgroup

tag: ipi group


title: Sample 15_Time Point 1d Dose 162ug [set 2]


title: Sample 13_Time Point 28d Dose 162ug [set 2]


title: Sample 14_Time Point 1d Dose 54ug [set 2]


title: Sample 12_Time Point 28d Dose 54ug [set 2]


title: staud-00261: LYM134

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: staud-00261: LYM136

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM132


title: Sample 7_Time Point 28d Dose 486ug [set 2]

tag: age

tag: dosage

tag: time point


title: Sample 9_Time Point 1d Dose 486ug [set 2]

tag: strain

tag: gender

tag: tissue


title: Sample 16_Time Point 1d Dose 486ug [set 2]

tag: exposed to

tag: sample type


title: Sample 10_Time Point 28d Dose 0ug [set 2]


title: Sample 8_Time Point 1d Dose 54ug [set 2]


title: Sample 11_Time Point 28d Dose 486ug [set 2]


title: Sample 6_Time Point 28d Dose 54ug [set 2]


title: staud-00261: LYM129

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)


title: staud-00261: LYM125

tag: status at follow-up

tag: subgroup

tag: ipi group


title: staud-00261: LYM123

value: High

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: staud-00261: LYM122

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM119


title: Sample 1_Time Point 1d Dose 54ug [set 2]

tag: age

tag: dosage

tag: time point


title: staud-00261: LYM130


title: Sample 3_Time Point 1d Dose 162ug [set 2]

tag: strain

tag: gender

tag: tissue


title: staud-00261: LYM118

tag: dlbcl sample (lym number)


title: staud-00261: LYM124

tag: analysis set


title: staud-00261: LYM116

tag: follow-up (years)


title: staud-00261: LYM110

tag: status at follow-up


title: staud-00261: LYM109

tag: subgroup


title: Sample 33_Time Point 1d Dose 486ug [set 1]

description: Sample 33

tag: exposed to

value: anatase TiO2NPs of 20nm diameter

tag: sample type


title: Sample 2_Time Point 1d Dose 0ug [set 2]


title: Sample 36_Time Point 28d Dose 486ug [set 1]

description: Sample 36


title: staud-00261: LYM121

value: Training

tag: ipi group

tag: germinal center b cell signature

tag: lymph node signature


title: Sample 5_Time Point 28d Dose 162ug [set 2]


title: Sample 34_Time Point 28d Dose 0ug [set 1]

description: Sample 34


title: staud-00261: LYM120

tag: proliferation signature

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM108


title: Sample 32_Time Point 1d Dose 54ug [set 1]

description: Sample 32

tag: age

tag: dosage

tag: time point


title: Sample 37_Time Point 28d Dose 54ug [set 1]

description: Sample 37

tag: strain

tag: gender

tag: tissue


title: Sample 29_Time Point 28d Dose 54ug [set 1]

description: Sample 29


title: Sample 31_Time Point 1d Dose 162ug [set 1]

description: Sample 31


title: Sample 28_Time Point 28d Dose 162ug [set 1]

description: Sample 28


title: Sample 30_Time Point 28d Dose 0ug [set 1]

description: Sample 30


title: staud-00261: LYM104

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)


title: Sample 25_Time Point 1d Dose 54ug [set 1]

description: Sample 25

tag: exposed to


title: staud-00261: LYM117

tag: status at follow-up

tag: subgroup


title: staud-00261: LYM115

tag: ipi group

tag: germinal center b cell signature


title: staud-00261: LYM101

tag: lymph node signature

tag: proliferation signature


title: staud-00261: LYM100

value: Alive

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM098


title: staud-00261: LYM093

value: ABC


title: staud-00261: LYM099

value: Low


title: Sample 26_Time Point 1d Dose 162ug [set 1]

description: Sample 26

tag: age

tag: dosage

tag: sample type


title: Sample 35_Time Point 28d Dose 162ug [set 1]

description: Sample 35

tag: strain

tag: gender

tag: time point


title: staud-00261: LYM092

tag: dlbcl sample (lym number)

tag: analysis set

value: Dead


title: staud-00261: LYM091

tag: follow-up (years)

value: Type III


title: Sample 23_Time Point 1d Dose 0ug [set 1]

description: Sample 23

value: female

tag: exposed to

tag: tissue


title: Sample 24_Time Point 1d Dose 486ug [set 1]

description: Sample 24

value: 5-7 weeks


title: Sample 22_Time Point 28d Dose 162ug [set 1]

description: Sample 22


title: Sample 27_Time Point 28d Dose 486ug [set 1]

description: Sample 27


title: staud-00261: LYM083

tag: status at follow-up

tag: subgroup

tag: ipi group


title: Sample 20_Time Point 28d Dose 0ug [set 1]

description: Sample 20


title: staud-00261: LYM074

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: staud-00261: LYM081

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM069


title: Sample 18_Time Point 1d Dose 162ug [set 1]

description: Sample 18

tag: age

tag: dosage

tag: sample type


title: Sample 16_Time Point 1d Dose 0ug [set 1]

description: Sample 16

tag: strain

tag: gender

tag: time point


title: staud-00261: LYM072

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)


title: Sample 17_Time Point 1d Dose 54ug [set 1]

description: Sample 17

tag: exposed to

tag: tissue


title: staud-00261: LYM066

tag: status at follow-up

tag: subgroup

tag: ipi group


title: staud-00261: LYM062

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: staud-00261: LYM068

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM065


title: staud-00261: LYM076


title: Sample 21_Time Point 28d Dose 486ug [set 1]

description: Sample 21

tag: age

tag: dosage

tag: sample type


title: Sample 13_Time Point 28d Dose 0ug [set 1]

description: Sample 13

tag: strain

tag: gender

tag: time point


title: Sample 14_Time Point 28d Dose 486ug [set 1]

description: Sample 14


title: Sample 12_Time Point 28d Dose 162ug [set 1]

description: Sample 12


title: Sample 11_Time Point 1d Dose 0ug [set 1]

description: Sample 11


title: Sample 15_Time Point 28d Dose 54ug [set 1]

description: Sample 15


title: staud-00261: LYM059

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)


title: staud-00261: LYM061

tag: status at follow-up


title: staud-00261: LYM050

tag: subgroup


title: staud-00261: LYM048

tag: ipi group


title: staud-00261: LYM041

tag: germinal center b cell signature


title: staud-00261: LYM045

tag: lymph node signature


title: staud-00261: LYM044

tag: proliferation signature


title: staud-00261: LYM051

tag: mhc class ii signature


title: staud-00261: LYM034

tag: outcome predictor score


title: staud-00261: LYM030


title: staud-00261: LYM027


title: staud-00261: LYM026


title: staud-00261: LYM025


title: staud-00261: LYM024


title: staud-00261: LYM022


title: Sample 19_Time Point 28d Dose 54ug [set 1]

description: Sample 19

tag: age

tag: exposed to

tag: tissue


title: Sample 7_Time Point 28d Dose 54ug [set 1]

description: Sample 7

tag: strain

tag: dosage

tag: sample type


title: Sample 10_Time Point 1d Dose 54ug [set 1]

description: Sample 10

tag: gender

tag: time point


title: Sample 8_Time Point 1d Dose 486ug [set 1]

description: Sample 8


title: Sample 1_Time Point 1d Dose 0ug [set 1]

description: Sample 1


title: Sample 9_Time Point 1d Dose 162ug [set 1]

description: Sample 9


title: staud-00261: LYM018

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)


title: staud-00261: LYM015

tag: status at follow-up

tag: subgroup

tag: ipi group


title: staud-00261: LYM012

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: staud-00261: LYM011

tag: mhc class ii signature

tag: outcome predictor score


title: Sample 3_Time Point 1d Dose 162ug [set 1]

description: Sample 3

tag: age

tag: exposed to

tag: tissue


title: Sample 4_Time Point 1d Dose 486ug [set 1]

description: Sample 4

tag: strain

tag: dosage

tag: sample type


title: Sample 6_Time Point 28d Dose 0ug [set 1]

description: Sample 6

tag: gender

tag: time point


title: staud-00261: LYM008

tag: dlbcl sample (lym number)

tag: analysis set

tag: follow-up (years)


title: Sample 5_Time Point 28d Dose 486ug [set 1]

description: Sample 5


title: staud-00261: LYM007

tag: status at follow-up

tag: subgroup

tag: ipi group


title: staud-00261: LYM002

tag: germinal center b cell signature

tag: lymph node signature

tag: proliferation signature


title: staud-00261: LYM004

tag: mhc class ii signature

tag: outcome predictor score


title: staud-00261: LYM006


title: Sample 2_Time Point 1d Dose 54ug [set 1]

description: Sample 2

tag: age

tag: exposed to

tag: tissue


title: BCSC1

status: Public on Dec 06 2016

city: Beijing

first: Chong

last: Li

address: NO.15 Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description: The expression profiles of lncRNA and mRNA were compared between bladder cancer stem cells and non-bladder cancer stem cells control group.

hyb_protocol: The Cy3TM-labeled samples were hybridizedaccording to the manufacturer’s protocol (Arraystar Inc).

scan_protocol: The slides were scanned usingthe Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed.

source_name: Bladder cancer cell line

label_protocol: The Arraystar Super RNA Labeling Kit (Arraystar Inc.) was used according to the manufacturer’s guideline for RNA labelling.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including CircRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: sample type

value: Bladder cancer stem cells


title: induction of 35S-PLT2-GR in whole seedlings, biological rep 1

city: Wageningen

first: Luca

last: Santuari

address: Droevendaalsesteeg 1

department: Plant Sciences Group

country: Netherlands

institute: Wageningen University

description: Gene expression data from induction of 35-PLT2-GR in whole seedlings

hyb_protocol: Outsourced at ServiceXS (Leiden, the Netherlands)

data_processing: Analysis with R/Bioconductor. Arrays were RMA normalized and differential gene expression analysis was performed with the limma package version 3.24.15

label: biotin

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: 35S::PLT2-GR seedlings were germinated on 0.5x GM agar and four day old seedlings of each genotype were subsequently divided in 3 batches (representing three biological replicates) of ~50 seedlings into 50 ml liquid 0.5x GM in erlenmeyer flasks. 35S::PLT2-GR line was used as mock sample and for this line an additional 3 erlenmeyer flasks were prepared. Seedlings were cultured overnight under mild shaking (~75 rpm).

extract_protocol: RNA was extracted from the seedlings using the Spectrum Plant Total RNA kit (Sigma-Aldrich) and used for microarray hybridisation.

treatment_protocol: The next day, dex was added to each of the flasks to a final concentration of 10 µM except the mock samples to which an equal amount of DMSO was added. Each genotype was induced with 5 minute intervals which meant that all samples were harvested within half an hour to minimize the effect of time of day on the resulting transcriptome. After 6 hour induction seedlings were quickly harvested through a sieve, transferred briefly onto liquid absorbing paper and flash frozen in liquid nitrogen.

tag: genotype/variation

tag: tissue type

value: whole seedlings

tag: treatment

value: dexamethasone

tag: treatment time

value: 6 hours


title: BCSC3


title: induction of 35S-PLT2-GR in whole seedlings, biological rep 3

scan_protocol: Outsourced at ServiceXS (Leiden, the Netherlands)


title: BCSC2


title: mock treatment of 35S-PLT2-GR, biological rep 1

description: Gene expression data from control

label_protocol: Outsourced at ServiceXS (Leiden, the Netherlands)

value: mock


title: NBCSC3

value: Bladder cancer cells


title: mock treatment of 35S-PLT2-GR, biological rep 3

description: Gene expression data from control


title: NBCSC2


title: induction of 35S-PLT2-GR in whole seedlings, biological rep 2


title: mock treatment of 35S-PLT2-GR, biological rep 2

description: Gene expression data from control


title: NBCSC1


title: embryo as control microRNA, biological rep1

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: embryo as control for 6-120 hpf

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

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

organism: Danio rerio

source_name: Zebrafish (Danio rerio) embryos

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

growth_protocol: Zebrafish embryos treated with PM2.5 for 6-120 hpf

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

treatment_protocol: Newly fertilized zebrafish embryos were treated with PM2.5 for 6-120 hpf, and dead embryos and larvae were removed every day. The dosage without cause mortality was 100 μg/mL of PM2.5 for following microarray analysis.

tag: strain

value: Ablino embryos


title: embryo treated with PM2.5 microRNA, biological rep2

description: embryo treated with PM2.5 for 6-120 hpf


title: embryo treated with PM2.5 mRNA, biological rep3

description: embryo treated with PM2.5 for 6-120 hpf


title: embryo as control mRNA, biological rep3

description: embryo as control for 6-120 hpf


title: embryo treated with PM2.5 mRNA, biological rep1

description: embryo treated with PM2.5 for 6-120 hpf


title: embryo as control microRNA, biological rep2

description: embryo as control for 6-120 hpf


title: embryo treated with PM2.5 microRNA, biological rep3

description: embryo treated with PM2.5 for 6-120 hpf


title: LNCaP_siERRg_vehicle_rep3

city: Québec City

first: Etienne

last: Audet-Walsh

state: QC

address: 2705 boulevard Laurier

department: Molecular Medicine

institute: Université Laval

description: Sample name: sierrbasal3

hyb_protocol: RNA was hybridized to GeneChip® Human Genome U133 Plus 2.0 (Affymetrix) and quantified at Génome Québec Innovation Centre (McGill University)

scan_protocol: Scan of the microarrays was performed by the Génome Québec Innovation Centre (McGill University)

data_processing: FlexArray10 software was using for data normalization and expression comparison between groups.

source_name: LNCaP cells, siRNA targeted against ERRg, 72h vehicle treatment

label_protocol: Labeling was performed using standard Affymetrix protocol at Génome Québec Innovation Centre (McGill University)

growth_protocol: Cells were seeded in RPMI media with no phenol red and containing 2% serum deprived from steroids  and transfected with siRNA controls or against estrogen-related receptor gamma. 48h later, cell were trypsinized and seeded in 6-well plates for treatment with 10nM R1881 or vehicle (EtOH) for 72h, with fresh medium and treatment added after 48h. Triplicate samples were sent for each conditions.

extract_protocol: RNA was purified using RNeasy mini kit from QIAGEN

treatment_protocol: Cells were treated for 72h with R1881 (10nM) or vehicle (EtOH).

tag: cell line

value: LNCaP

value: prostate cancer cells (immortalized cell line)


title: embryo treated with PM2.5 microRNA, biological rep1

description: embryo treated with PM2.5 for 6-120 hpf


title: LNCaP_siERRg_r1881_rep3

description: Sample name: sierrr18813

source_name: LNCaP cells, siRNA targeted against ERRg, 72h R1881 treatment


title: LNCaP_siERRg_vehicle_rep2

description: Sample name: sierrbasal2


title: embryo treated with PM2.5 mRNA, biological rep2

description: embryo treated with PM2.5 for 6-120 hpf


title: embryo as control mRNA, biological rep2

description: embryo as control for 6-120 hpf


title: embryo as control mRNA, biological rep1

description: embryo as control for 6-120 hpf


title: embryo as control microRNA, biological rep3

description: embryo as control for 6-120 hpf


title: LNCaP_siERRg_r1881_rep1

description: Sample name: sierrr18811


title: LNCaP_siERRg_r1881_rep2

description: Sample name: sierrr18812


title: ConDMSO_day8_rep3

city: Maastricht

first: Jarno

last: Wolters

address: Universiteitssingel 40

department: Toxicogenomics

institute: Maastricht University

hyb_protocol: Amplified, biotinylated and fragmented targets were then hybridized on to the BrainArray custom CDF v15.1.0 array.

scan_protocol: After hybridization, arrays were washed and stained using an Affymetrix fluidics station and scanned by use of an Affymetrix GeneArray scanner. A total of 60 RNA samples was prepared and analyzed on GeneChip arrays (treated and control samples from each time point were at least in triplicate). Normalization quality controls, including scaling factors, average intensities, present calls, background intensities, noise, and raw Q values, appeared to be within acceptable limits for all chips. Hybridization controls BioB, BioC, BioD, and CreX were called present on all chips and yielded the expected increases in intensities.

data_processing: The Arrayanalysis.org web service was used for quality control (27) and all microarrays were of high quality. CEL files were imported into R v2.15.3 (http://www.r-project.org) using the “affy” library (28) within BioConductor (v2.9) (29). Probe re-annotation, normalization and data filtering was performed as previously described (30).

label_protocol: High-density oligonucleotide GeneChips from Affymetrix were used to measure gene expression levels (Human Genome U133 Plus 2.0 array (604,258 probes)). Targets for these arrays were prepared, hybridized and scanned according to the Affymetrix protocol (Affymetrix).Normalization quality controls appeared to be within acceptable limits for almost all chips.

growth_protocol: Cryopreserved primary human hepatocytes (PHH) were purchased from Life Technologies. Cells were cultured in pre-coated 24-well plates (2,100,000 cells/sample) in a 2-layer collagen sandwich (A11428-02, Gibco), according to the supplier’s protocol (Invitrogen, 2012). The following culture media were used: Hepatocyte Thawing Medium (HTM) for thawing (CM7500, Gibco), Williams’ Medium E (1x, no phenol red) (A1217601, Gibco) + Cell Maintenance supplement B kit (CM4000, Gibco) for plating and incubation.

extract_protocol: Cells were cultured in triplicate in 24 wells in a collagen sandwich layer. Following 5 days of repetitive daily exposureand thereupon a washout of 3 days, cells lysates were harvested for total RNA isolation after 3, 5 and 8 days. Therefore, medium was removed and PHH were harvested in Qiazol (Qiagen). Total RNA was isolated using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and followed by DNase I (Qiagen) treatment. Upon purification, RNA concentrations were measured by means of a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific) at 260 and 280 nm. RNA quality and integrity were assessed by using automated gel electrophoresis on an Agilent 2100 Bioanalyzer system (Agilent Technologies). Only RNA samples which showed clear 18S and 28S peaks and with an RNA integrity number (RIN) higher than 6, were used. Samples were stored at -80ºC until RNA hybridization.

treatment_protocol: After quick thawing in a water bath at 37°C, viability of the cells was checked by a Trypan blue (CAS no. 72-57-1, Sigma–Aldrich) exclusion test as instructed in the supplier’s protocol (Invitrogen, 2012). All viability scores after thawing were in agreement with those listed by the supplier. Before CsA treatment, cells were allowed to acclimatize for 48 hours. This is needed for the hepatocytes to restore an in vivo like cellular configuration and enzyme expression levels as optimally as possible. PHH were treated with 30 µM CsA for 5 days daily followed by a washout-period (terminating CsA-treatment) of 3 days.

tag: cell type, study type, assay type, strain, compound, dose, dose unit, dose duration, duration unit, dose frequency

value: primary human hepatocytes

tag: assay type

value: in vitro

tag: study type

value: single dose toxicity

tag: dose

value: DMSO 0.5 %

tag: dose duration

value: 8 days


title: ConDMSO_day8_rep1


title: ConDMSO_day8_rep2


title: CsA_day8_rep1

value: CsA 30µM


title: CsA_day8_rep2


title: CsA_day5_rep3

value: 5 days


title: LNCaP_siERRg_vehicle_rep1

description: Sample name: sierrbasal1


title: LNCaP_siCtl_r1881_rep3

description: Sample name: scr18813

source_name: LNCaP cells, control siRNA, 72h R1881 treatment


title: LNCaP_siCtl_vehicle_rep3

description: Sample name: sicbasal3

source_name: LNCaP cells, control siRNA, vehicle treatment


title: CsA_day8_rep3


title: LNCaP_siCtl_vehicle_rep2

description: Sample name: sicbasal2


title: CsA_day5_rep1


title: ConDMSO_day5_rep2


title: LNCaP_siCtl_r1881_rep1

description: Sample name: sicr18811


title: LNCaP_siCtl_r1881_rep2

description: Sample name: sicr18812


title: CsA_day5_rep2


title: LNCaP_siCtl_vehicle_rep1

description: Sample name: sicbasal1


title: ConDMSO_day5_rep3


title: ConDMSO_day5_rep1


title: CsA_day3_rep3

value: 3 days


title: EA_947547A.33_hOKT3_NR

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using the Illumina HiScan and the standard Illumina scanning protocol.

data_processing: Profiles were normalized by robust spline normalization, probes mapped, and collapsed to gene symbols using several R packages. Extreme outlier samples identified by Principal Component Analysis (PCA) were excluded from analyses.

label: Biotin

source_name: Whole Blood

label_protocol: Standard Illumina labeling protocol.

extract_protocol: GLOBINclear (Life Technologies) was used to deplete globin mRNA from total whole blood RNA from the 12-month visit. cRNA was prepared by amplification and labelling using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) and hybridized to Human HT-12 Beadarray Chips (Illumina).

tag: status

value: NR

tag: itn name

tag: barcode

tag: studysiteshortname

value: BRI-VM

tag: gender

value: Male

tag: treatmentgroup

tag: race

value: White

tag: visitnumber

tag: siteandparticipantcode

tag: trunkbarcode

tag: visitmonth


title: EA_947519A.31_hOKT3_R

value: R

value: UCSF

tag: age

value: Female


title: EA_948732A.36_hOKT3_NR

value: YALE


title: EA_948301A.31_hOKT3_R


title: EA_948595A.32_hOKT3_R

value: PNRI

value: Other


title: EA_947641A.37_hOKT3_R

value: White; White


title: EA_947010A.31_Control_NR

value: C

value: Control

value: White; Asian


title: CsA_day3_rep2

tag: cell type, study type, assay type, strain, compound, dose, dose unit, dose duration, duration unit, dose frequency

value: primary human hepatocytes

value: in vitro

value: single dose toxicity

tag: strain

value: CsA 30µM


title: EA_947067A.34_hOKT3_R


title: ConDMSO_day3_rep2

tag: assay type

tag: study type

value: DMSO 0.5 %

value: 3 days


title: ConDMSO_day3_rep3

tag: dose

tag: dose duration


title: ConDMSO_day3_rep1


title: FI_937164A.30_hOKT3_R

tag: status

tag: itn name

value: BRI-VM

value: White


title: CsA_day3_rep1


title: HepG2 cells-control

city: Wuhan

first: Fan

state: HUbei

address: #169, East Lake Road, Wuchang District, Wuhan

institute: Second clinical hospital of Wuhan University

description: Gene expression in HepG2

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（ 8*60K） for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (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: HepG2 cells-control

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: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Human HepG2 cell line was cultured at 37°C in Dulbecco's modified Eagle medium (DMEM; Invitrogen, CA, USA) with 5% CO2, supplemented with 4.5 g/L glucose, 10% fetal calf serum (FBS), 4 mM glutamine, 100 U/mL penicillin, and 0.1 mg/mL streptomycin.

tag: cell line


title: FI_937079A.30_hOKT3_NR

value: NR

tag: barcode

tag: studysiteshortname

tag: gender


title: FI_937163A.30_hOKT3_NR

value: Female

tag: treatmentgroup

tag: race

value: American Indian or Alaska Native; White

tag: visitnumber


title: Muscle_QS-21_6hpost_3

city: Rixensart

first: Margherita

last: Coccia

address: Rue de l'Institut 89

country: Belgium

institute: GSK Vaccines

description: gene expression from gastrocnemius muscle at 6h after immunization

hyb_protocol: RNA samples were processed for hybridization on GeneChip_ Whole Mouse Genome 430 2.0 arrays following standard procedures

scan_protocol: Data acquisition was performed using GeneChip Operating Software (Affymetrix).

data_processing: Data were normalized using gcrma in the Bioconductor suite

source_name: gastrocnemius muscle_QS-21_6hpost_3

extract_protocol: Total RNA was isolated by homogenizing  tissues in Tripure reagent (1 ml/100 mg tissue; Roche Applied Science) and then extracted with chloroform followed by RNeasy™ Minikit (Qiagen) according to the manufacturer’s protocol. A DNAse treatment was applied on the RNeasy column to avoid genomic DNA contamination. RNA was concentrated by ethanol precipitation, and quantified by RiboGreen™ (Life Technologies). 1mgof each RNA sample was used for target preparation, using a one-cycle cDNA synthesis kit.

treatment_protocol: C57BL/6 mice (6-8 weeks old) were immunized in both hind limbs, in the gastrocnemius (gcm) muscles and in a volume of 50 µl/muscle with QS-21 (100mg/ml), formulated in liposomes, or Phosphate Buffer Solution (PBS). Ileac lymph nodes were identified as draining in setup experiments. Tissues were mechanically homogenized prior to RNA extraction.

tag: tissue

value: gastrocnemius muscle


title: EA_936779A.34_hOKT3_NR

value: COLORADO

tag: age

value: Male

tag: siteandparticipantcode

tag: trunkbarcode

tag: visitmonth


title: EA_936735A.31_hOKT3_R

value: R


title: EA_945925A.37_hOKT3_R

value: UCSF


title: Muscle_PBS_6hpost_1

source_name: gastrocnemius muscle_PBS_6hpost_1

label_protocol: RNA samples were processed for hybridization on GeneChip_ Whole Mouse Genome 430 2.0 arrays following standard procedures

tag: strain


title: BLM_3hr_10.0_rep2

city: Houston

first: Tao

last: Lu

state: Texas

address: 2101 E NASA Pkwy

department: Radiation Research

institute: NASA Johnson Space Center

description: Gene expression after 3 hours of 10.0 micrg/mlbleomycin treatment.

hyb_protocol: Followed Agilent protocol for Human Gene Expression 4x44K Microarray Kit (G4112F).

scan_protocol: The slides were scanned with GenePix 4000B Microarray Scanner (Molecular Devices).

data_processing: The scanned images were analyzed with GenePix Pro7 software using default parameters.

label_protocol: Single color labeling with Cy3, using Agilent kit and protocol.

growth_protocol: Human fibroblasts AG01522 were cultured in alpha-MEM supplemented with 10% heat-inactivated fetal bovine serum and Penicillin and Streptomycin to conflence.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini kits. RNA quality was verified by Nanodrop Spectophotometer and Agilent Bioanalyzer.

treatment_protocol: The cells were treated with 0.1, 1.0 and 10 microgram/ml of bleomycin for 3 hours and with no drug control.

tag: cell type

value: fibroblast

tag: treatment

value: 3 hours of 10.0 micrg/mlbleomycin


title: kiaa0101-overexpressing stable HepG2 cells

description: Gene expression after overexpressed kiaa0101


title: EA_945926A.30_hOKT3_R

tag: status


title: EA_936734A.36_hOKT3_NR

tag: itn name


title: FI_937165A.30_Control_NR

value: C

value: Control


title: Muscle_PBS_6hpost_2

source_name: gastrocnemius muscle_PBS_6hpost_2


title: FI_937078A.30_Control_NR

value: YALE


title: Muscle_QS-21_6hpost_1

source_name: gastrocnemius muscle_QS-21_6hpost_1


title: Muscle_PBS_6hpost_3

source_name: gastrocnemius muscle_PBS_6hpost_3


title: Muscle_QS-21_6hpost_2

source_name: gastrocnemius muscle_QS-21_6hpost_2


title: Muscle_PBS_4hpost_3

description: gene expression from gastrocnemius muscle at 4h after immunization

source_name: gastrocnemius muscle_PBS_4hpost_3


title: BLM_3hr_10.0_rep1


title: EA_936733A.36_hOKT3_R


title: FI_934442A.30_hOKT3_NR


title: FI_934443A.30_hOKT3_R


title: BLM_3hr_1.0_rep2

description: Gene expression after 3 hours of 1.0 micrg/mlbleomycin treatment.

value: 3 hours of 1.0 micrg/mlbleomycin


title: BLM_3hr_1.0_rep1


title: Muscle_PBS_4hpost_2

source_name: gastrocnemius muscle_PBS_4hpost_2


title: EA_933829A.35_hOKT3_NR


title: BLM_3hr_0.1_rep2

description: Gene expression after 3 hours of 0.1 micrg/mlbleomycin treatment.

value: 3 hours of 0.1 micrg/mlbleomycin


title: Muscle_PBS_4hpost_1

source_name: gastrocnemius muscle_PBS_4hpost_1


title: Muscle_QS-21_4hpost_3

source_name: gastrocnemius muscle_QS-21_4hpost_3


title: Muscle_QS-21_4hpost_1

source_name: gastrocnemius muscle_QS-21_4hpost_1


title: FI_933800A.30_hOKT3_R


title: Muscle_QS-21_2hpost_3

description: gene expression from gastrocnemius muscle at 2h after immunization

source_name: gastrocnemius muscle_QS-21_2hpost_3


title: BLM_3hr_0.1_rep1


title: BLM_3hr_0_rep2

description: Gene expression after 3 hours of 0.0 micrg/mlbleomycin treatment.

value: 3 hours of 0.0 micrg/mlbleomycin


title: APC TG rep2

city: Stanford

first: Brian

last: Feldman

state: CA

address: 300 Pasteur Drive

department: Pediatrics

institute: Stanford University

description:
expression profiling of adipocyte progenitor cells
TG2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA hybridized following the manufacturers instructions.

scan_protocol: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters

data_processing: Genespring GX v11 software was used to analyze the features. Features flagged as Non-uniform outliers were excluded.

source_name: subcutaneous adipoctye progenitor cells

label_protocol: Total RNA was processed using the Agilent Low Input Quick Amp single color labeling kit

growth_protocol: FACS sorted APCs directly lysed without culture

extract_protocol: Total RNA from the APCs was isolated using RNAeasy micro kit (Qiagen).

treatment_protocol: no treatments

value: FVB

tag: genotype/variation

value: Adamts1 transgenic

value: male

value: adipocyte progenitor cell


title: Muscle_QS-21_2hpost_2

source_name: gastrocnemius muscle_QS-21_2hpost_2

value: gastrocnemius muscle


title: BLM_3hr_0_rep1


title: Muscle_PBS_2hpost_1

source_name: gastrocnemius muscle_PBS_2hpost_1


title: EA_931676B.30_hOKT3_R

source_name: Whole Blood

tag: barcode

value: Female

value: American Indian or Alaska Native; White


title: FI_931982A.30_Control_NR

tag: studysiteshortname

value: Male

value: White


title: Muscle_PBS_2hpost_2

source_name: gastrocnemius muscle_PBS_2hpost_2


title: APC WT rep2

description:
expression profiling of adipocyte progenitor cells
WT2

value: wild-type

tag: gender


title: FI_928954A.30_Control_NR

value: COLORADO

tag: treatmentgroup


title: APC TG rep1

description:
expression profiling of adipocyte progenitor cells
TG1


title: FI_931981A.30_Control_NR

value: C

tag: race

value: White; White


title: EA_931677B.37_Control_NR

value: UCSF

value: Control

tag: visitnumber


title: Draining_lymph_node_PBS_6hpost_2

description: gene expression from draining ileac lymph node at 6h after immunization

tag: tissue

value: ileac lymph node


title: FI_933799A.30_hOKT3_R

value: R

value: YALE

tag: age


title: EA_929107B.36_Control_NR

tag: siteandparticipantcode


title: FI_931307A.30_hOKT3_NR

value: NR

tag: trunkbarcode


title: APC WT rep1

description:
expression profiling of adipocyte progenitor cells
WT1

value: FVB

value: male


title: Draining_lymph_node_PBS_6hpost_3


title: Muscle_QS-21_2hpost_1

source_name: gastrocnemius muscle_QS-21_2hpost_1

value: gastrocnemius muscle


title: FI_924916A.30_Control_NR

value: MC GEORGIA

tag: visitmonth


title: Draining_lymph_node_PBS_6hpost_1

tag: strain


title: Draining_lymph_node_PBS_4hpost_3

description: gene expression from draining ileac lymph node at 4h after immunization


title: Draining_lymph_node_QS-21_6hpost_3


title: Draining_lymph_node_QS-21_6hpost_1


title: Draining_lymph_node_PBS_4hpost_1


title: EA_923974B.35_Control_NR

value: PNRI


title: Draining_lymph_node_PBS_4hpost_2


title: Draining_lymph_node_QS-21_4hpost_3


title: EA_922202B.35_Control_NR

value: Female


title: Draining_lymph_node_QS-21_4hpost_2


title: FI_923359A.30_hOKT3_NR

value: Male

value: White


title: EA_922201A.32_hOKT3_NR

value: Black or African American; White


title: EA_922049A.33_hOKT3_NR

value: COLUMBIA


title: FI_923360A.30_Control_NR

value: C

value: COLORADO


title: Draining_lymph_node_PBS_2hpost_3

description: gene expression from draining ileac lymph node at 2h after immunization


title: Draining_lymph_node_QS-21_6hpost_2


title: EA_922014B.37_Control_NR

value: Control


title: Draining_lymph_node_PBS_2hpost_2

value: ileac lymph node


title: FI_920367A301_Control_NR


title: EA_921847A.37_hOKT3_R

value: R

value: White; American Indian or Alaska Native


title: EA_922070A.31_hOKT3_NR

value: NR


title: EA_924004B.38_hOKT3_R

value: UCSF


title: EA_921900B.38_hOKT3_NR

value: White; Other


title: Draining_lymph_node_PBS_2hpost_1


title: EA_922051B.33_hOKT3_NR


title: P7 Minus

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: Gene expression data from WBC from mice

hyb_protocol: 10ug cDNA were hybridized onto GeneChip® Human Genome U133 Plus 2.0 Array described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized using RMA. Analyzed using BRB array tools

label_protocol: Biotinylated cDNA were prepared using Nugen Ovation Pico WTA V2 kit and labeled and fragmented with the Encore® Biotin Module from total RNA.

growth_protocol: human adenocarcinomas

extract_protocol: Total RNA was isolated from human adenocarcinomas using Qiagen RNEasy kits following manufacturer's instructions

treatment_protocol: Six different sporadic human adenocarcinomas were used. Xenograft tumors from these clones were dissociated and sorted into Aldefluor (high) and Aldefluor (low) groups

tag: patient

value: colon cancer xenografts

tag: Sex

value: M

tag: cell population

value: ALDH-

tag: host

value: mouse


title: Draining_lymph_node_QS-21_4hpost_1


title: Draining_lymph_node_QS-21_2hpost_3


title: Draining_lymph_node_QS-21_2hpost_2


title: Draining_lymph_node_QS-21_2hpost_1


title: P4 Plus

description: Gene expression data from WBC from mice

value: F

value: ALDH+


title: P7 Plus

description: Gene expression data from WBC from mice


title: Kidney marrow_Control-zebrafish_5

city: Padova

first: Chiara

last: Borga

address: Corso Stati Uniti,4

country: Italy

institute: University of Padua

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: Microarray data (.CEL files) were normalized using the justRMA algorithm and analyzed using R-Bioconductor (Version 2.15.3)

source_name: Kidney marrow_Control-zebrafish

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® 3’ IVT Express Kit Technical Manual, 2008, Affymetrix).

tag: genotype/variation

value: control

value: kidney marrow


title: Kidney marrow_Control-zebrafish_4


title: P5 Minus

description: Gene expression data from WBC from mice


title: P4 Minus

description: Gene expression data from WBC from mice


title: P2 Plus

description: Gene expression data from WBC from mice


title: FI_920366A.30_hOKT3_NR

tag: status

tag: itn name

tag: barcode

value: PNRI

value: Male

value: White


title: Kidney marrow_Control-zebrafish_3


title: ConDMSO_day8_rep3

description: microRNA

hyb_protocol: MicroRNA expression profiling was performed using Agilent Sureprint G3 Unrestricted Human miRNA V19 8 × 60 K microarrays. The hybridization was performed following standard protocols, after which the microarray slides were washed and scanned using a DNA microarray scanner (Agilent Technologies).

scan_protocol: DNA microarray scanner

data_processing: The scanned images were converted into TXT files using the Feature Extraction Software v10.7.3.1 from Agilent Technologies, which were imported in R 2.15.3 (http://www.r-project.org) for quality control with an in-house developed pipeline [32]. Filtering and normalization was performed using AgiMicroRna [33], which applies a LIMMA approach for selection of DE-miRs. Total gene signals were log2-transformed and quantile-normalized. DE-miRs with an absolute FC of 1.5 or higher (i.e., average log2 ratio of < −0.58 or > 0.58) and an FDR-corrected p-value < 0.05 were considered statistically significant.

label_protocol: standard Agilent labeling kit

tag: cell type

value: primary human hepatocytes

tag: assay type

value: in vitro

tag: study type

value: single dose toxicity

tag: dose

value: DMSO 0.5 %

tag: dose duration

value: 8 days

tag: dose frequency

value: daily


title: Kidney marrow_Control-zebrafish_2

tag: tissue


title: CsA_day8_rep1

description: microRNA

value: CsA 30µM


title: P5 Plus

description: Gene expression data from WBC from mice

value: colon cancer xenografts


title: P2 Minus

description: Gene expression data from WBC from mice

value: ALDH-


title: P9 Minus

description: Gene expression data from WBC from mice

value: M

value: mouse


title: Kidney marrow_CREB-zebrafish_3

source_name: Kidney marrow_CREB-zebrafish

value: overexpressing the human CREB


title: Kidney marrow_CREB-zebrafish_5


title: Kidney marrow_Control-zebrafish_1

value: control


title: Kidney marrow_CREB-zebrafish_1

value: kidney marrow


title: P9 Plus

description: Gene expression data from WBC from mice

value: ALDH+


title: Kidney marrow_CREB-zebrafish_2


title: IMB-YH-8 replicate2

first: Liyan

last: Yu

address: 1# Tian Tan Xi Li, Chongwen district

department: Institute of Medicinal Biotechnology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

hyb_protocol: The labeled samples where hybridized for 16 hours at 10 rotations per minute.

scan_protocol: Scanned by Agilent scanner and then the image was analyzed by Agilent Feature Extraction v11.5.

data_processing: Data obtained from Feature Extraction were imported to GeneSpring GX version 13.1 (Agilent Technologies, Santa Clara, CA) for 75 percentile shift and baseline to median of all samples normalization. Please note that only 4091 probes which target gene sequence were included in the data processing (excluding the quality control probes designed by Agilent).

organism: Mycobacterium tuberculosis

label_protocol: 100 ng of each RNA sample was amplified to cRNA and labeled with Cy-3 using Agilent Low Input Quick Amp Labeling Kit.

growth_protocol: M. tuberculosis H37Rv was grown at 37°C in Middlebrook 7H9 Broth (Difco Laboratories, USA) supplemented with 0.2% (vol/vol) glycerol, 0.05% (vol/vol) Tween 80, and 10% (vol/vol) oleic acid albumin dextrose catalase (OADC) (BD and Company, USA).

extract_protocol: Total RNAs were isolated by RiboPureTM-Bacteria Kit (Life Technology, AM1925) according to the manufacturer’s instructions.

treatment_protocol: 2.5 μg/ml IMB-YH-8 treated H37Rv as treatment group and equal volume DMSO treated H37Rv as a control for 4 h.

tag: treated with

value: 2.5 μg/ml IMB-YH-8 for 4hrs


title: CsA_day8_rep2

description: microRNA

tag: strain


title: ConDMSO_day8_rep1

description: microRNA


title: ConDMSO_day8_rep2

description: microRNA


title: IMB-YH-8 replicate1


title: CsA_day5_rep3

description: microRNA

value: 5 days


title: CsA_day5_rep2

description: microRNA

value: primary human hepatocytes


title: CsA_day5_rep1

description: microRNA

value: in vitro


title: ConDMSO_day5_rep3

description: microRNA

value: single dose toxicity


title: Control DMSO replicate2

source_name: Control DMSO

value: DMSO for 4hrs


title: Control DMSO replicate1


title: Kidney marrow_CREB-zebrafish_4


title: ConDMSO_day5_rep2

description: microRNA

value: DMSO 0.5 %


title: ConDMSO_day5_rep1

description: microRNA

value: daily


title: P6 Minus

description: Gene expression data from WBC from mice

tag: patient

value: F


title: CsA_day3_rep3

description: microRNA

value: CsA 30µM

value: 3 days


title: dex induction of 35-PLT7-GR, biological rep 1

description: Gene expression data from the induction of 35S-PLT7-GR in whole seedlings

source_name: whole seedlings

growth_protocol: 35S::PLT[1,3,4,5,7]-GR seedlings were germinated on 0.5x GM agar and four day old seedlings of each genotype were subsequently divided in 3 batches (representing three biological replicates) of ~50 seedlings into 50 ml liquid 0.5x GM in erlenmeyer flasks. We chose the 35S::PLT4-GR line to be used as mock sample and for this line an additional 3 erlenmeyer flasks were prepared. Seedlings were cultured overnight under mild shaking (~75 rpm).

treatment_protocol: The next day, dex was added to each of the flasks to a final concentration of 10 µM except the mock samples to which an equal amount of DMSO was added. Each genotype was induced with 5 minute intervals which meant that all samples were harvested within half an hour to minimize the effect of time of day on the resulting transcriptome. After 6 hour induction seedlings were quickly harvested through a sieve, transferred briefly onto liquid absorbing paper and flash frozen in liquid nitrogen. In a separate experiment 35S::PLT2-GR seedlings were treated as described above with dex and, as a mock control, DMSO.

value: whole seedlings

tag: treatment

value: dexamethasone

tag: treatment time

value: 6 hrs


title: dex induction of 35-PLT7-GR, biological rep 2


title: dex induction of 35-PLT5-GR, biological rep 3

description: Gene expression data from the induction of 35S-PLT5-GR in whole seedlings


title: E47_biological replicate 2

city: Freiburg

first: Kristina

last: Schachtrup

address: Breisacher Str. 117

department: Center for Chronic Immunodeficiency

country: Germany

institute: University Medical Center Freiburg

hyb_protocol: cRNA fragments hybridized against MOE430 2.0 Affymetrix gene expression arrays chip according to the manufacturer's instructions

scan_protocol: Chips were scanned using a GeneChip TM Scanner 3000

data_processing: Expression values were acquired using RMA

source_name: in vitro induced Treg cells transduced with E47-ER construct

label_protocol: RNA was labelled and amplified according to Affy,etrix TM GeneChip Expression Analysis Technical Manual 2011

growth_protocol: anti-CD3 (2C11; 2 μg/ml)/anti-CD28 (37.51; 1 μg/ml) coated plates in the presence of IL-2 (200 U/ml) and TGF-β1 (5 ng/ml) for 2 days; retroviral transduction at day 1

extract_protocol: RNEasy Mini Kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: anti-CD3 (2C11; 2 μg/ml)/anti-CD28 (37.51; 1 μg/ml) coated plates in the presence of IL-2 (200 U/ml) and tamoxifen (1 µM) for 6 hours post-sort of transduced cells

tag: age

value: 8 weeks

value: lymph nodes

tag: number of mice per sample

value: MACS isolated CD4+CD25-

tag: post-sort

value: FACS sorted as CD4+Thy1.1+


title: E47_biological replicate 3

value: 9 weeks


title: control_biological replicate 3

source_name: in vitro induced Treg cells transduced with bHLH-ER construct


title: CsA_day8_rep3

type: genomic

hyb_protocol: Labeling and hybridization of arrays were performed according to the manufactures’ protocol. Slides were washed using the NimbleGen wash buffer kit and scanned using the 2 µm high resolution NimbleGen MS 200 microarray scanner.

scan_protocol: Signal intensity data was extracted from the scanned images of each array using NimbleScan v2.6 software and quantile normalized on a per channel basis.

data_processing: Log2 ratios of the intensities were computed (ratio of MeDIP signal / Input signal) and for each array, centering was performed by subtracting the global array bi-weight mean of the log2 ratios such that the computed log2 ratios were centered around 0. Detection of differential methylation was performed using the Probe Sliding Window-ANOVA algorithm (PSW-ANOVA). PSW-ANOVA was implemented in the R statistical programming environment (v2.15.3) (http://www.r-project.org) as a custom script and was provided by Roche NimbleGen as described before [25].  PSW-ANOVA (sliding window of 750 bp comprising 7 probes, and a FDR corrected p- value < 0.01) was used to identify differential methylated regions (DMR) which were statistically significantly different between the different conditions tested in the experiment i.e. exposed versus control. Peaks were identified in the DMR by searching for regions containing at least 8 significant consecutive probes (p<0.01).   Peaks were mapped to genomic features, e.g. transcription start sites (TSS) region (100bp upstream of TSS to 1000bp downstream of TSS), promoter regions (3kb upstream of TSS to 100bp upstream of TSS) or CpG islands, applying a window from 3 kb upstream to 1 kb downstream by using the NimbleScan v2.6 software [26]. A control corrected median log2 ratio was calculated for each peak. Log2 ratio’s > 0 indicate hyper methylation and log2 ratio’s < 0 indicate hypo methylation

molecule: genomic DNA

label_protocol: In order to obtain fragments ranging from 200 bp to 600 bp, genomic DNA was sonicated. Next, the fragments were cleaned up using silica columns (Zymo Research) and eluted in TE buffer. MeDIP was performed using the MagMeDIP kit (Diagenode, Liege, Belgium) according to the manufacturer’s protocol. Briefly, IP incubation mix was added to 1.2 µg sonicated DNA sample and denaturated at 95°C. 10% of this was used as reference samples. The remaining sample was immunoprecipitated overnight using antibody mix containing the 5-methylcytidine antibody and magnetic beads. Following purification using the Ipure kit (Diagenode), reference and MeDIP samples were prepared for microarray analysis by whole genome amplification (WGA) using the WGA2 kit (Sigma-Aldrich) without performing the fragmentation step. Methylation enrichment in the paired samples MeDIP/reference was derived from qPCR data by calculating the ratio positive control/negative control, applying the ΔΔCt method. The Human DNA Methylation 2.1M Deluxe Promoter Array (Roche NimbleGen) was used for analyses of DNA methylation levels.

extract_protocol: PHH were lysed in 500 µl of digestion buffer (containing 1 mM EDTA; 50 mM Tris–HCl, pH 8.0; 0.5% SDS). Next, 25 µl of proteinase K (20mg/ml) (Ambion) was added. After incubation of 1 hour at 55°C, the proteinase K was inactivated for 10 minutes at 80 °C. RNAse A (2 µl; 100mg/ml) (Qiagen) and collagenase (25 µl; 1%) (Sigma) treatment was performed for 1 hour at 37°C. Thereupon, 500 µl of phenol-chloroform-isoamylalcohol (PCI; 25:24:1) (Sigma) was added. The mixture was shaken manually for 5 minutes, and centrifuged for 5 minutes at maximum speed. The upper phase was transferred to a new Eppendorf and the step with PCI was repeated. The upper phase was collected and precipitated using 50 µl of 3M NaAc pH 5.6 and 1250 µl of cold 100% ethanol for 30 min. at -80°C. After centrifugation for 30 min. at maximum speed, the DNA pellet was washed using cold 70% ETOH, dried in a speed-vac and dissolved in 50µl of nuclease free water. The total amount was at least 8 µg DNA, the 260/280 ratio ranged between 1.7-1.9, and the 260/230 ratio appeared higher than 1.6. A total of 18 DNA samples were prepared. DNA was used for MeDIP-Chip analyses.

tag: cell type, sample type

value: primary human hepatocytes, input

value: 30µM CsA

tag: time point

value: day 8

value: primary human hepatocytes, antibody against a monoclonal antibody against 5'-methylcytidine


title: Sample 4_Time Point 28d Dose 0ug [set 2]

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 4x44K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Time Point 28d Dose 0ug

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

tag: gender

value: female

value: 5-7 weeks

tag: exposed to

value: rutile hydrophilic TiO2NPs of 20 nm diameter

tag: dosage

value: 28d post-exposure

value: lung

source_name: Universal Mouse Reference RNA

tag: sample type

value: 11 mouse cell lines


title: dex induction of 35-PLT7-GR, biological rep 3

tag: genotype/variation

value: whole seedlings

value: dexamethasone


title: dex induction of 35-PLT5-GR, biological rep 2

value: 6 hrs


title: Mice DAPP-treated during DSS treatment Biological replicate 2

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

institute: Université de Sherbrooke

description: Biological replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio software.

source_name: Colon

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

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and then purified on QIAgen RNeasy columns.

tag: Sex

value: male

tag: gestional age

value: 7-8 week of age

value: colon

value: DAPP-treated during DSS treatment


title: CsA_day8_rep2

value: primary human hepatocytes, input


title: E47_biological replicate 1

value: 7 weeks

tag: tissue

value: lymph nodes

tag: cell type

value: MACS isolated CD4+CD25-

value: FACS sorted as CD4+Thy1.1+


title: Mice DAPP-treated during DSS treatment Biological replicate 3

description: Biological replicate 3


title: ConDMSO_day3_rep2

description: microRNA

value: primary human hepatocytes

tag: assay type

value: in vitro

tag: study type

value: single dose toxicity

tag: strain

tag: dose

value: DMSO 0.5 %

tag: dose duration

value: 3 days

tag: dose frequency

value: daily


title: control_biological replicate 2

tag: age

value: 8 weeks

tag: number of mice per sample

tag: post-sort


title: CsA_day3_rep2

description: microRNA

value: CsA 30µM


title: CsA_day3_rep1

description: microRNA


title: dex induction of 35-PLT4-GR, biological rep 3

description: Gene expression data from the induction of 35S-PLT4-GR in whole seedlings

hyb_protocol: Outsourced at ServiceXS (Leiden, the Netherlands)

data_processing: Analysis with R/Bioconductor. Arrays were RMA normalized and differential gene expression analysis was performed with the limma package version 3.24.15

value: whole seedlings

tag: treatment

value: dexamethasone

tag: treatment time

value: 6 hrs


title: dex induction of 35-PLT4-GR, biological rep 1

scan_protocol: Outsourced at ServiceXS (Leiden, the Netherlands)


title: Mice DAPP-treated during DSS treatment Biological replicate 1

description: Biological replicate 1

value: male

value: 7-8 week of age

value: colon

value: DAPP-treated during DSS treatment


title: ConDMSO_day8_rep3

tag: cell type, sample type

value: primary human hepatocytes, input

value: DMSO

tag: time point

value: day 8

value: primary human hepatocytes, antibody against a monoclonal antibody against 5'-methylcytidine


title: CsA_day8_rep1

value: 30µM CsA


title: control_biological replicate 1

value: 7 weeks

value: lymph nodes

value: MACS isolated CD4+CD25-

value: FACS sorted as CD4+Thy1.1+


title: Mice DAPP-treated before DSS treatment Biological replicate 3

description: Biological replicate 3

tag: Sex

value: DAPP-treated before DSS treatment


title: ConDMSO_day3_rep1

description: microRNA

value: primary human hepatocytes

value: in vitro

value: single dose toxicity

value: DMSO 0.5 %

value: 3 days

value: daily


title: ConDMSO_day8_rep2


title: Mice DAPP-treated before DSS treatment Biological replicate 2

description: Biological replicate 2

value: male

tag: gestional age

value: 7-8 week of age

value: colon


title: dex induction of 35-PLT5-GR, biological rep 1

label_protocol: Outsourced at ServiceXS (Leiden, the Netherlands)

tag: genotype/variation

tag: tissue

value: whole seedlings

value: dexamethasone

value: 6 hrs


title: dex induction of 35-PLT4-GR, biological rep 2


title: dex induction of 35-PLT3-GR, biological rep 2

description: Gene expression data from the induction of 35S-PLT3-GR in whole seedlings


title: CsA_day5_rep2

value: primary human hepatocytes, input

value: 30µM CsA

value: day 5

value: primary human hepatocytes, antibody against a monoclonal antibody against 5'-methylcytidine


title: CsA_day5_rep3


title: CsA_day5_rep1


title: ConDMSO_day8_rep1

value: DMSO

value: day 8


title: Mice treated with DSS Biological replicate 3

description: Biological replicate 3

value: treated with DSS


title: Mice DAPP-treated before DSS treatment Biological replicate 1

description: Biological replicate 1

value: DAPP-treated before DSS treatment


title: Mice treated with DSS Biological replicate 1

description: Biological replicate 1


title: dex induction of 35-PLT1-GR, biological rep 2

description: Gene expression data from the induction of 35S-PLT1-GR in whole seedlings


title: tumor tongue, biological rep3

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

country: France

institute: Centre Léon Bérard

description: Gene expression data from microdissected cells in murine tongue,tumor

hyb_protocol: Each sample was hybridized onto a GeneChip Mouse Gene ST 2.0 Array (Affymetrix,Santa Clara, CA, USA)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000  (Affymetrix)

data_processing: The data were analyzed with the software Array Studio (Omicsoft Corporation) using quantile normalization and RMA method.

source_name: Mus musculus, 4-NQO group

label_protocol: Following amplification of  2ng of RNA (Ovation Pico WTA System v2, NuGEN Technologies), each amplified sense cDNA product was fragmented and biotinylated, using an Encore Biotin Module according to manufacturer’s instructions (NuGEN Technologies).

growth_protocol: Three mice were from the control group and  9 mice were from the group treated by the 4-NQO.

extract_protocol: Total RNA was performed using the Rneasy Microkit® (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Immediately following death, tongue were excised, longitudinally bisected, each half of the tongue was frozen on dry ice, embedded in OCT and stored at -80°C. Epithelial cells were isolated using an infrared laser microdissection system (Arcturus PixCell II®, Life Technologies, NY, USA). Microdissected cells on the cap were solubilized using a RLT lysis buffer and were subjected to total RNA extraction.

value: tongue

tag: genotype

value: CBA

tag: gender

tag: age (weeks)

tag: tongue section

value: tumor


title: dex induction of 35-PLT1-GR, biological rep 1


title: ConDMSO_day5_rep3


title: dex induction of 35-PLT1-GR, biological rep 3


title: Mice control Biological replicate 2

description: Biological replicate 2

value: male

value: control


title: mock treatment of 35S-PLT4-GR, biological rep 4

description: Gene expression data from whole seedlings for the control

value: mock


title: tumor tongue, biological rep2


title: dysplasia tongue, biological rep3

description: Gene expression data from microdissected cells in murine tongue,dysplasia

value: dysplasia


title: WT HIV-1 Infected_rep3

city: Pune

first: Debashis

last: Mitra

state: Maharashtra

address: Pune university

country: India

institute: National Centre For Cell Science

description: Gene expression after 72 hours of Wild Type HIV-1 infected  CEM-GFP Cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Wild Type HIV-1 Infected CEM-GFP cells replicate 3

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

growth_protocol: CEM-GFP cells were grown in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated  at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the Agilent total RNA isolation Mini kit (Agilent technologies, Wilmington, DE, USA) following the manufacturer's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: CEM-GFP cells were infected with 0.5 Multiplicity of Infection of either Nef deleted HIV-1 or Wild Type HIV-1 and were incubated at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: Human Lymphoblastoid CD4+ T cell

tag: cell line

value: CEM-GFP


title: mock treatment of 35S-PLT4-GR, biological rep 3

value: whole seedlings

value: 6 hrs


title: ConDMSO_day5_rep2

value: primary human hepatocytes, input

value: day 5


title: WT HIV-1 Infected_rep1

source_name: Wild Type HIV-1 Infected CEM-GFP cells replicate 1


title: ∆nef HIV-1 Infected_rep3

description: Gene expression after 72 hours of ∆Nef HIV-1 infected  CEM-GFP Cells

source_name: Nef deleted HIV-1 Infected CEM-GFP cells replicate 3


title: WT HIV-1 Infected_rep2

source_name: Wild Type HIV-1 Infected CEM-GFP cells replicate 2


title: Mice treated with DSS Biological replicate 2

description: Biological replicate 2

value: 7-8 week of age

value: colon


title: Mice control Biological replicate 1

description: Biological replicate 1


title: mock treatment of 35S-PLT4-GR, biological rep 2


title: hyperplasia tongue, biological rep3

description: Gene expression data from microdissected cells in murine tongue,hyperplasia

value: hyperplasia


title: ∆nef HIV-1 Infected_rep2

source_name: Nef deleted HIV-1 Infected CEM-GFP cells replicate 2


title: CsA_day3_rep3

value: 30µM CsA

value: day 3

value: primary human hepatocytes, antibody against a monoclonal antibody against 5'-methylcytidine


title: tumor tongue, biological rep1

value: tongue

value: CBA

value: tumor


title: CsA_day3_rep2


title: CsA_day3_rep1


title: ConDMSO_day5_rep1

value: DMSO


title: dysplasia tongue, biological rep2

value: male

value: dysplasia


title: Uninfected_rep3

description: Gene expression from Uninfected CEM-GFP Cells

source_name: Uninfected CEM-GFP cells replicate 3

value: Human Lymphoblastoid CD4+ T cell

value: CEM-GFP


title: mock treatment of 35S-PLT4-GR, biological rep 1

value: whole seedlings

value: mock

value: 6 hrs


title: hyperplasia tongue, biological rep2


title: dysplasia tongue, biological rep1


title: 1h induction of pPLT2-PLT2-GR in QC cells, biological rep 3

description: Gene expression data from 1h dexamethasone induction of pPLT2-PLT2-GR in the QC

source_name: QC cells sorted by pWOX5-GFP

growth_protocol: To determine the PLT2 regulated transcriptome in the QC we used the plt1;plt2 line harboring the dexamethasone inducible complementing PLT2::PLT2-GR construct and introduced a WOX5::erGFP construct to allow QC cell sorting. Seeds were plated densely in 3 rows on square petri dishes on 0.5x GM agar medium covered with nylon mesh (Sefar Nitex 03-15/10). At 5 days after germination, seedlings were transferred to new 0.5x GM agar plates containing 10 µM dexamethosone (dex) in DMSO and incubated for 1 or 4 hours. The control samples were transferred to new plates containing DMSO only and incubated for 1 hour.

extract_protocol: RNA was extracted from the sorted protoplasts with the RNeasy Micro kit (Qiagen).

treatment_protocol: After treatment root tips were cut and harvested followed by protoplasting as described in Birnbaum, K. et al. Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nature methods 2, 615-619. Briefly: root tips were placed inside cell strainers (70-μm) in petri dishes containing protoplasting solution (50 ml of solution A (21.86 g mannitol, 150 mg KCl, 80 mg MgCl2, 59 mg CaCl2, 0.2 g BSA, 78 mg MES in 200 ml water, set to pH 5.5 with 1 M Tris), 750 mg cellulase, and 50 mg macerozyme) and incubated for 1 hour at room temperature with agitation. Protoplasts were collected by spinning down at 200x gravity. The cells were subsequently washed and filtered through 70-μm and 40-μm cell strainers with 350 µl solution A. Protoplasts expressing GFP were isolated in a fluorescence-activated cell sorter (FACSAria II, BD Biosciences). The nozzle size was 100 μm. Cells were sorted in phosphate-buffered saline (PBS, pH 7.4) as sheath fluid at an event rate of ~5000-10000 events per second and fluid pressure of 20 psi. Upon excitation at 488 nm, GFP expressing protoplasts were selected based on fluorescence emission in the green channel (530 nm with band width of 30 nm) compared to negative controls. Cells were sorted into the RLT lysis buffer (Qiagen) supplemented with β-mercaptoethanol (1%), mixed and flash frozen instantly.

value: plt1plt2 double mutant

tag: tissue type

value: Quiescent Center (QC) cells

value: dexamethasone

value: 1 hour


title: P6 Plus

description: Gene expression data from WBC from mice

tag: patient

value: colon cancer xenografts

value: F

tag: cell population

value: ALDH+

tag: host

value: mouse


title: control, biological rep 3

description: Gene expression data from control

tag: treatment

tag: treatment time


title: 4h induction of pPLT2-PLT2-GR in QC cells, biological rep 3

description: Gene expression data from 4h dexamethasone induction of pPLT2-PLT2-GR in the QC

value: 4 hours


title: normal tongue, biological rep3

description: Gene expression data from microdissected cells in murine tongue,normal

source_name: Mus musculus, control group

value: tongue

value: CBA

value: normal


title: ConDMSO_day3_rep3

tag: cell type, sample type

value: primary human hepatocytes, input

value: DMSO

tag: time point

value: day 3

value: primary human hepatocytes, antibody against a monoclonal antibody against 5'-methylcytidine


title: hyperplasia tongue, biological rep1

value: male

value: hyperplasia


title: Uninfected_rep2

source_name: Uninfected CEM-GFP cells replicate 2

value: Human Lymphoblastoid CD4+ T cell

value: CEM-GFP


title: Mice control Biological replicate 3

description: Biological replicate 3

tag: Sex

tag: gestional age

value: 7-8 week of age

value: colon

value: control


title: ∆nef HIV-1 Infected_rep1

source_name: Nef deleted HIV-1 Infected CEM-GFP cells replicate 1


title: ConDMSO_day3_rep2


title: dex induction of 35-PLT3-GR, biological rep 1

source_name: whole seedlings

extract_protocol: RNA was extracted from the seedlings using the Spectrum Plant Total RNA kit (Sigma-Aldrich) and used for microarray hybridisation.

tag: genotype/variation

tag: tissue

value: whole seedlings

value: dexamethasone

value: 6 hrs


title: Uninfected_rep1

source_name: Uninfected CEM-GFP cells replicate 1


title: ConDMSO_day3_rep3

description: microRNA

value: primary human hepatocytes

tag: assay type

value: in vitro

tag: study type

value: single dose toxicity

tag: strain

tag: dose

value: DMSO 0.5 %

tag: dose duration

value: 3 days

tag: dose frequency

value: daily


title: normal tongue, biological rep2

value: tongue

tag: genotype

value: CBA

tag: gender

tag: age (weeks)

tag: tongue section

value: normal


title: 4h induction of pPLT2-PLT2-GR in QC cells, biological rep 2

value: plt1plt2 double mutant

tag: tissue type

value: Quiescent Center (QC) cells

tag: treatment

tag: treatment time

value: 4 hours


title: ConDMSO_day3_rep1

tag: cell type, sample type

value: primary human hepatocytes, input

value: DMSO

tag: time point

value: day 3

value: primary human hepatocytes, antibody against a monoclonal antibody against 5'-methylcytidine


title: control, biological rep 2

description: Gene expression data from control

tag: genotype/variation

value: mock

value: 1 hour


title: control, biological rep 1

description: Gene expression data from control


title: 1h induction of pPLT2-PLT2-GR in QC cells, biological rep 1

value: dexamethasone


title: 1h induction of pPLT2-PLT2-GR in QC cells, biological rep 2


title: E16 contra RGCs, biological rep3

status: Public on Dec 05 2016

city: New York

first: Qing

last: Wang

state: NY

department: Pathology and Cell Biology

institute: Columbia University

description: RGCs retrogradely labeled from optic tract post-optic chiasm decussation

hyb_protocol: Labeled cDNA was hybridized on Mouse Genome 430 2.0 Array chips Mouse Genome 430 2.0 Array chips

scan_protocol: Arrays were scanned according to the Affymetrix protocol

data_processing: Affymetrix Expression Console (1.1) was used for RMA normalization of all microarray data

source_name: contralateral RGCs isolated from E16 mouse embryos

label_protocol: Amplified cDNA was generated from purified RNA using Ovation Pico WTA System (Nugen) of which 5μg was then labeled and fragmented using the Encore Biotin Module (Nugen) according to the manufacturer's instructions.

growth_protocol: E16.5 were harvested from pregnant females housed in a barrier facility in a timed pregnancy colony. Conception is assumed to take place at approximately midnight, and E0.5 refers to the day on which the vaginal plug was detected.

extract_protocol: RNA purification was performed immediately following FACS using the Absolutely RNA Nanoprep kit (Stratagene) according to the manufacturer's instructions

treatment_protocol: E16.5 embryos were removed from pregnant females under anesthesia and decapitated in DMEM/F12 buffer over ice. The head was immersed in DMEM and hard palate and skull base were removed to expose the optic chiasm and tract. Tetramethylrhodamine-conjugated dextran MW3000 was applied to the severed optic tract. Heads were incubated in pre-oxygenated bubbling ACSF at room temperature for 2 hours followed by immediate harvesting of retinas by dissection. Pooled ipsilateral or contralateral retinas from 2 litters were dissociated using papain. Rhodamine-positive neurons, with exclusion of DAPI-stained dead cells were collected by FACS.

tag: age

value: E16 embryos

tag: tissue

value: embryonic retina


title: 4h induction of pPLT2-PLT2-GR in QC cells, biological rep 1

first: Luca

institute: Wageningen University


title: E16 ipsi RGCs, biological rep3

source_name: ipsilateral RGCs isolated from E16 mouse embryos


title: E16 ipsi RGCs, biological rep1


title: RH needle puncturing 24 h, biological rep2

first: Li

last: Changyan

address: Shizishan Road NO.1

institute: Huazhong Agricultural University

hyb_protocol: Microarray hybridization were conducted by the CapitalBio Corporation (Beijing, China) according to the Affymetrix standard protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: Expression measures for each probe set were obtained by employing the robust multi-array average (RMA) method in R environment with Bioconductor Affy package.

organism: Oryza sativa

source_name: indica rice cultivar Rathu Heenati(RH), widetype

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

growth_protocol: Seeds of RH and TN1 were sown in small pots, and grown under natural conditions. (Wuhan,China).

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

treatment_protocol: Three treatments were implemented to the two week-old RH and TN1 seedlings: untreated (naturally grown), needle puncturing and BPH infestation. For needle puncturing, each plant was pricked with a needle 15 times at the bottom of the seedling, and then grown normally. For BPH infestation, approximately 100 third-instar BPH nymphs were infested per pot (an average of 10 nymphs per seedling). Each pot was placed in a single net cage to prevent escape of nymphs. Two sampling time-points of 6 and 24 h after BPH infestation were used for all treatments. There were three replications for each treatment and sampling time point. All 10 seedlings from each pot were collected together as a replication.

value: seedling shoots

tag: variety

value: RH

tag: collection time point

value: needle puncturing


title: RH BPH infestation 24 h, biological rep3

value: BPH infestation


title: KURC1 sunitinib-sensitive#1

city: Shanghai,

first: Feng

middle: jun

last: lin

state: xvhuiqv

address: 2Institute of Health Sciences

department: Department of Pathophysiology

institute: 1Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education

description: Gene expression data from the rat knee articular cartilage in newborn

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

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

label: total RNA

source_name: renal cancer xenograft tumor of KURC1 treated with vehicle only

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

growth_protocol: The cartilage that was harvested individually from the right knee joint were stored at liquid nitrogen temperatures at once with protected by Rnasin inhibitor.

treatment_protocol: After grinded under the ice, cartilage tissue were collected for further total RNA extraction.

value: xenograft tumor of renal cell carcinoma


title: TN1 needle puncturing 24 h, biological rep3

source_name: indica rice cultivar Taichung Native 1(TN1), widetype


title: RH BPH infestation 24 h, biological rep2


title: E16 ipsi RGCs, biological rep2

tag: strain


title: TN1 BPH infestation 24 h, biological rep2


title: E16 contra RGCs, biological rep2


title: TN1 needle puncturing 24 h, biological rep2


title: E16 contra RGCs, biological rep1


title: RH needle puncturing 24 h, biological rep1


title: KURC1 vehicle#1

source_name: renal cancer xenograft tumor of KURC1 treated with sunitinib and resected at sunitinib-sensitive status


title: RH needle puncturing 24 h, biological rep3


title: RH BPH infestation 24 h, biological rep1


title: TN1 BPH infestation 24 h, biological rep3


title: TN1 needle puncturing 24 h, biological rep1


title: RH widetype 24 h, biological rep3

value: natural growth


title: TN1 BPH infestation 24 h, biological rep1


title: TN1 widetype 24 h, biological rep2


title: RH BPH infestation 6 h, biological rep2

value: 6 h


title: RH widetype 24 h, biological rep1


title: RH needle puncturing 6 h, biological rep3


title: TN1 widetype 24 h, biological rep1


title: RH BPH infestation 6 h, biological rep3


title: TN1 widetype 24 h, biological rep3


title: RH widetype 6 h, biological rep2


title: TN1 needle puncturing 6 h, biological rep3


title: TN1 needle puncturing 6 h, biological rep1


title: TN1 BPH infestation 6 h, biological rep3


title: RH needle puncturing 6 h, biological rep1


title: RH BPH infestation 6 h, biological rep1


title: RH needle puncturing 6 h, biological rep2


title: TN1 needle puncturing 6 h, biological rep2


title: TN1 BPH infestation 6 h, biological rep2


title: RH widetype 6 h, biological rep3


title: RH widetype 6 h, biological rep1


title: TN1 BPH infestation 6 h, biological rep1


title: TN1 widetype 6 h, biological rep3


title: TN1 widetype 6 h, biological rep1


title: CanS, biological rep1

city: Leuven

first: Patrick

last: Callaerts

address: Herestraat 49, bus 602

department: Department of Human Genetics

institute: University of Leuven

description: CanS 1

hyb_protocol: Following fragmentation, 10 µg of cRNA was hybridized for 16 hr at 45°C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: Data was analyzed with the affy package (version 1.36.0) of BioConductor (www.bioconductor.org) to obtain RMA expression values. MAS 5.0 detection calls (Affymetrix) were used to determine if signals were significantly above background.

organism: Drosophila melanogaster

source_name: CanS_whole adult females

label_protocol: Biotinylated cRNA was prepared from total RNA according to the standard Affymetrix protocol.

growth_protocol: Calment1/4 and CanS flies were cultured in standard Drosophila medium in a 25°C incubator

extract_protocol: Total RNA was extracted in TRI-Reagent (Sigma) according to manufacturer's instructions, followed by a second round of RNA precipitation with 10 M ammonium acetate and ethanol before resuspending RNA pellet in water.

treatment_protocol: Adult Calment1/4 and CanS females were collected (30-35 flies per sample) and flash frozen in liquid Nitrogen

value: Canton-S

tag: developmental stage

value: adult

value: female


title: CanS, biological rep2

description: CanS 2


title: TN1 widetype 6 h, biological rep2


title: normal tongue, biological rep1

value: tongue

value: CBA

value: male

value: normal


title: Calment1/4, biological rep3

description: Calment 3

source_name: Calment1/4_whole adult females

value: Calment1/4 mutant (in CS10 background)


title: LIN28A-siRNA/LIN28A-siR_rep2

city: Daejeon

first: Seung-Kyoon

last: Kim

address: 99 Daehak-ro, Yuseong-gu,

department: Convergent Bioscience and Informatics

country: South Korea

institute: Chungnam National University

description: Gene expression in LIN28A depleted and LIN28A overexpressed H9 cells_replicate 2

hyb_protocol: Labeled cRNA was applied microarray (Agilent technologies, 8x60K) using Agilent’s Gene Expression Hybridization Kit. Hybridized microarray was washed using Agilent’s Gene Expression Wash Buffer Kit.

scan_protocol: The microarray chip was scanned using Agilent’s DNA microarray scanner (G2505B) and the raw signal density was acquired from feature Extraction software (Agilent Technology).

data_processing: The raw signal density was processed by using the Limma R package.; quantile normalization was performed, genes with low signal intensity were filtered out, and duplicate probes representing identical genes were merged by taking the average. We selected genes whose expression level differed by threefold or greater between LIN28A or SET7/9 knockdown and EGFP control in both replicates.

source_name: LIN28A-siRNA/ LIN28A-siR, replicate 2

label_protocol: Cyanine 3-labeled cRNA (complementary RNA) was generated from Agilent’s Low RNA Input Linear Amplification kit (Agilent Technology; G4140-90040) with 500ng total RNA. Labeled cRNA was also measured using Nanodrop spectrophotometer.

growth_protocol: H9 cells were cultured in the ESC medium which is Dulbecco modified Eagle medium (DMEM)/F12 medium (Invitrogen, Carlsbad, CA) containing 20% knockout serum replacement, 1% non-essential amino acids, 1% penicillin–streptomycin (Invitrogen), and 4 ng/ml basic fibroblast growth factor (all from Invitrogen, Carlsbad USA), and 0.1 mM β-mercaptoethanol (Sigma, USA) on mitomycin C (Sigma, St Louis, MO)-treated mouse embryonic fibroblast (mct-MEFs) feeders at 37°C and 5% CO2 in air.

extract_protocol: Total RNA from cell was isolated using Trizol Reagent (Molecular Research Center,  Cincinnati, OH, USA), according to the manufacturer’s instructions. Total RNA was quantified by absorbance at 260 nm and the integrity of total RNA was checked by Bioanalyzer2100 (Agilent, CA, USA).

treatment_protocol: H9 cells were washed with PBS and treated with Accutase (STEMCELL Technologies, Vancouver, Canada) as previously described (Bajpai et al., 2008) for 5 - 10 min to dissociate the colonies into single cells in a 37°C incubator. After gentle trituration, the cells were collected by centrifugation (800 rpm for 5 min) and re-plated at ~ 1x105 cells/ml without feeders on matrigel (BD Biosciences, San Diego, CA) coated dishes and cultured in conditioned medium (CM) containing 10 μM ROCK inhibitor (Y-27632; Sigma-Aldrich, USA). 48 h later, single cells were transfected with siRNAs as described above. The cells were analyzed 72 h after transfection by immunoblot or RT-qPCR analysis.

tag: cell line

tag: cell type

value: embryonic stem cell lines


title: Calment1/4, biological rep1

description: Calment 1

tag: gender


title: LIN28A-siRNA/Vector_rep1

description: Gene expression in LIN28A depleted and Vector overexpressed H9 cells_replicate 1

source_name: LIN28A-siRNA/ Vector, replicate 1


title: Calment1/4, biological rep2

description: Calment 2


title: LIN28A-siRNA/LIN28A-K135R-siR_rep1

description: Gene expression in LIN28A depleted and LIN28A-K135R mutant overexpressed H9 cells_replicate 1

source_name: LIN28A-siRNA/ LIN28A-K135R-siR, replicate 1


title: LIN28A-siRNA/LIN28A-siR_rep1

description: Gene expression in LIN28A depleted and LIN28A overexpressed H9 cells_replicate 1

source_name: LIN28A-siRNA/ LIN28A-siR, replicate 1


title: TUT4-siRNA_rep2

description: Gene expression in TUT4 depleted H9 cells_replicate 2

source_name: TUT4-siRNA, replicate 2


title: LIN28A-siRNA/LIN28A-K135R-siR_rep2

description: Gene expression in LIN28A depleted and LIN28A-K135R mutant overexpressed H9 cells_replicate 2

source_name: LIN28A-siRNA/ LIN28A-K135R-siR, replicate 2


title: TUT4-siRNA_rep1

description: Gene expression in TUT4 depleted H9 cells_replicate 1

source_name: TUT4-siRNA, replicate 1


title: control EGFP-siRNA_rep1

description: Gene expression in control EGFP depleted H9 cells_replicate 1

source_name: EGFP-siRNA, replicate 1


title: SET7/9-siRNA_rep1

description: Gene expression in SET7/9 depleted H9 cells_replicate 1

source_name: SET7/9-siRNA, replicate 1


title: LIN28A-siRNA_rep2

description: Gene expression in LIN28A depleted H9 cells_replicate 2

source_name: LIN28A-siRNA, replicate 2


title: LIN28A-siRNA_rep1

description: Gene expression in LIN28A depleted H9 cells_replicate 1

source_name: LIN28A-siRNA, replicate 1


title: DANCR siRNA, biological replicate 3

city: Philadelphia

first: Zhongyi

last: Hu

state: Pennsylvania

address: 421 Curie Blvd

institute: University of Pennsylvania

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Johns Hopkins Medical Institutions Deep Sequencing & Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: Raw data were processed with the Partek Genomics Suite for background correction and normalization. Data analysis and statistical evaluations were performed with Partek Genomics Suite and BRB-Array Tools.

source_name: PC3 Cell Line

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The PC3 cell line was obtained from the American Type Culture Collection (ATCC). Cells were cultured in RPMI 1640 with 10% fetal calf serum (FCS) and 1% penicillin/streptomycin.

extract_protocol: Total RNA was isolated from cells using a RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Cells were seeded in 6-well plates in antibiotic-free media overnight, and then transfections were performed using the Lipofectamine RNAiMAX transfection reagent (Invitrogen).

tag: Sex


title: control EGFP-siRNA_rep2

description: Gene expression in control EGFP depleted H9 cells_replicate 2

source_name: EGFP-siRNA, replicate 2


title: CYSKT_1

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

description: Total RNAs were extracted from muscle tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).

hyb_protocol: Fluorescent targets were hybridized to Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan).

scan_protocol: The slides were scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by Genepix 4.1 software (Molecular Devices, Sunnyvale, CA, USA). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 0 or control probes. Spots that pass aforementioned criteria were normalized by R program in the limma package.

source_name: DM2 mice

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and Cy5 dye (Amersham Pharmacia, Piscataway, NJ, USA).

treatment_protocol: Mice were treated with 200 mg/kg CYSKT.

value: Male

value: Balb/c

value: Muscle


title: CYSKT_2

extract_protocol: Total RNAs were extracted from muscle tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).


title: LIN28A-siRNA/Vector_rep2

description: Gene expression in LIN28A depleted and Vector overexpressed H9 cells_replicate 2

source_name: LIN28A-siRNA/ Vector, replicate 2


title: Mock_3


title: Mock_2


title: CanS, biological rep3

description: CanS 3

source_name: CanS_whole adult females


title: DANCR siRNA, biological replicate 1


title: C-A549-co 3

city: Innsbruck

first: Johanna

middle: M

last: Gostner

address: Innrain 80

department: Medical University Innsbruck

country: Austria

institute: Medical Biochemistry

description:
0 ppm formaldehyde, reference chamber,
condition 2 in comparison 3
raw data file: 7916_3C_20140708.CEL

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays. Fluidics washing was done using the Affymetrix Wash and Stain Kit (#900720), protocol FS450_0004.

scan_protocol: Arrays were scanned with Affymetrix Gene ChIP Scanner 3000 7G and images were processed using the Expression Console.

data_processing: The data were analyzed with R/Bioconductor version 3.0.1 using Affymetrix R-package (affy) with default analysis settings and MAS 5.0 as normalization method. Different normalizations of pair-wise comparisons were used. The number at the end of the title is related to the comparison (1 to 5). Comparison group information is also available in the Description field.

source_name: Control

label_protocol: Applause 3'-Amp System + Encore Biotin Module (NuGEN)

growth_protocol: A549 cells were grown at air liquid interphase (ALI) in transwells (0.4 µM PET membrane, 24-well plate)

extract_protocol: NucleoSpin RNA/Protein isolation kit (Macherey-Nagel, Düren, Germany) according to the manufacturer´s instructions

treatment_protocol: 0.1 ppm, 0.5 ppm and 0 ppm formaldehyde in a humidified atmosphere  (≥ 95%rel humidity), treatment duration 72 h

tag: chamber type

value: Reference Chamber


title: SET7/9-siRNA_rep2

description: Gene expression in SET7/9 depleted H9 cells_replicate 2

source_name: SET7/9-siRNA, replicate 2


title: Mock_1


title: C-A549-co 2

description:
0 ppm formaldehyde, reference chamber,
condition 2 in comparison 3
raw data file: 7916_1C_20140708.CEL


title: B-A549-01FA 2

description:
0.1 ppm formaldehyde, exposure chamber,
condition 1 in comparison 2 and 4
raw data file: 7916_6FA_20140708.CEL

source_name: 0.1 ppm Formaldehyde

value: Exposure Chamber


title: RH widetype 24 h, biological rep2

city: Wuhan

source_name: indica rice cultivar Rathu Heenati(RH), widetype

value: seedling shoots

value: RH


title: Ctl siRNA, biological replicate 3


title: B-A549-co 3

description:
0 ppm formaldehyde, reference chamber,
condition 2 in comparison 2
raw data file: 7916_2C_20140708.CEL


title: Ctl siRNA, biological replicate 2


title: DANCR siRNA, biological replicate 2


title: B-A549-01FA 3

description:
0.1 ppm formaldehyde, exposure chamber,
condition 1 in comparison 2 and 4
raw data file: 7916_2FA_20140708.CEL


title: B-A549-co 2

description:
0 ppm formaldehyde, reference chamber,
condition 2 in comparison 2
raw data file: 7916_6C_20140708.CEL


title: C-A549-05FA 2

description:
0.5 ppm formaldehyde, exposure chamber,
condition 1 in comparison 3 and 5
raw data file: 7916_1FA_20140708.CEL

source_name: 0.5 ppm Formaldehyde


title: A-A549-not 2

description:
0 ppm formaldehyde, exposure chamber,
condition 1 in comparison 1,
condition 2 in comparison 4 and 5
raw data file: 7916_8FA_20140729.CEL

source_name: No treatment


title: C-A549-05FA 1

description:
0.5 ppm formaldehyde, exposure chamber,
condition 1 in comparison 3 and 5
raw data file: 7916_5FA_20140708.CEL


title: A-A549-not 1

description:
0 ppm formaldehyde, exposure chamber,
condition 1 in comparison 1,
condition 2 in comparison 4 and 5
raw data file: 7916_7FA_20140708.CEL


title: B-A549-co 1

description:
0 ppm formaldehyde, reference chamber,
condition 2 in comparison 2
raw data file: 7916_4C_20140708.CEL


title: A-A549-not 3

description:
0 ppm formaldehyde, exposure chamber,
condition 1 in comparison 1,
condition 2 in comparison 4 and 5
raw data file: 7916_9FA_20140708.CEL


title: A-A549-co 1

description:
0 ppm formaldehyde, reference chamber,
condition 2 in comparison 1
raw data file: 7916_7C_20140708.CEL


title: A-A549-co 3

description:
0 ppm formaldehyde, reference chamber,
condition 2 in comparison 1
raw data file: 7916_9C_20140708.CEL


title: Heart_hnRNP A1+/+ (gene)

city: Kaohsiung

first: Ting-Yuan

last: Liu

address: 100 Shih-Chuan 1st Road

department: Graduate Institute of Medicine, College of Medicine

institute: Kaohsiung Medical University

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the KMU Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Expression Console (Affymetrix) for background correction and normalization. These criteria were suggested by the results of preliminary experiments. And RMA expression value derived from transcriptome analysis Console software; gene level differential expression analysis, exon level differential expression analysis.

source_name: knockout mice (wild type)

growth_protocol: Heart tissue was harvested from embryonic 18 days mice and was subjected to RNA extraction.

extract_protocol: Total RNA was isolated from heart tissues by using TRIzol Reagent (Invitrogen).

tag: sample type

value: male, C57BL/6, Heart, embryo

value: heart


title: C-A549-05FA 3

description:
0.5 ppm formaldehyde, exposure chamber,
condition 1 in comparison 3 and 5
raw data file: 7916_3FA_20140708.CEL


title: C-A549-co 1

description:
0 ppm formaldehyde, reference chamber,
condition 2 in comparison 3
raw data file: 7916_5C_20140708.CEL


title: Heart_hnRNP A1+/- (gene)

description: RMA expression value derived from transcriptome analysis Console software; gene level differential expression analysis, exon level differential expression analysis

source_name: knockout mice (heterozygous)


title: Ctl siRNA, biological replicate 1


title: CYSKT_3

description: Total RNAs were extracted from muscle tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).