title: L428 25nM Ixazomib Replicate 2

source_name: L428 Cells with 25nM Ixazomib Treatment

value: 25nM of Ixazomib for 24 Hours


title: iPS-AF-35

status: Public on Jun 08 2015

type: genomic

city: Guangzhou

first: Wenyin

last: HE

state: Guangdong

address: No.63, Duobao road

country: China

institute: The third affiliated hospital of Guangzhou medical university

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Data processing was performed in Chromosome Analysis Suite 2.0 (CHAS2.0) software (Affymetrix), via the standard reference library provided by the manufacturer based on the Hidden Markov Model

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: cell type

value: induced pluripotent stemm cell line

tag: cell line


title: L428 25nM Ixazomib Replicate 3

type: RNA

city: Mountain View

first: Afshin

last: Beheshti

state: CA

address: Moffett Blvd

country: USA

institute: NASA Ames Research Center

description: Gene expression data from L428 Cells with 25nM of Ixazomib treatment for 24 hours

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were corrected with normalization to housekeeping genes and then quantile normalisation with GenePattern Illumina Normalizer Module

label: biotin

molecule: total RNA

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

growth_protocol: L428 cell lines were grown in RPMI 1640 consisting of 10% heat inactivated fetal bovine serum and 200U of penicillin/streptomycin (Mediatech, Manassas, VA) under 5% CO2 and 37C. Ixazomib was kindly provided by Takeda Pharmaceuticals, Inc. Cells were treated with ixazomib for 24 hours at 25nM.

extract_protocol: RNA was isolated using RNeasy Minikit (Qiagen)

treatment_protocol: Cells were treated with ixazomib for 24 hours at 25nM and 71.25nM

value: Hodgkin Lymphoma

tag: treatment


title: iPS-AF-7


title: 5hmCIP_450K (0015-C-HMC)

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

hyb_protocol: As defined by Illumina

scan_protocol: As defined by Illumina

data_processing:
ChAMP pipeline for data filtering, Beta mixed interquantile normalisation (BMIQ) for probe bias correction, SNP filtering, A-Clustering for differential methylation analysis
Processed beta matrix for HM450K and HMeDIP-450K is provided as .txt files; processed_betas_UCB_HM450K.txt and processed_betas_UCB_HMeDIP450K.txt

label: Cy3, Cy5

source_name: Umbilical cord blood (ELEMENT cohort)

label_protocol: As defined by Illumina

growth_protocol: Human Cohort, not applicable

extract_protocol: DNA was isolated from hESCs by using QiagenDNA Easy Kit™.  The “Purification of DNA from Cells” protocol, the EZ1 DNA Cell Card, and the EZ1 DNA Cell 350-μl Kit were used for this study. Approximately 3µg genomic DNA was diluted in 130µl of buffer TE (10mM Tris (pH 8.0), and 1mM EDTA (pH 8.0)) and sheared into ~200-600bp fragment using microcavitation (Covaris, Inc, setting: Duty Cycle = 5%, Intensity = 3, Cycles/burst = 200, Time = 75 seconds run at 6-8°C). 125µl of the sheared DNA samples were mixed with 330µl of buffer TE. The sheared DNA was denatured by boiling it in the Thermomixer at 95°C and 700rpm for ten minutes and left on ice for 10min. 51 µl of 10x immunoprecipitation buffers and 3µl of 5hmC specific antibodies (Active Motif) at a concentration of 1µg/µl was added to the denatured DNA sample and incubated for ≥ 2hours at 4°C with tipping. Then, 25µl protein G beads was added to the samples and incubated overnight at 4°C with tipping. The residual beads were collected with a magnetic rack and washed 3 times with 700µl 1xIP buffer. The bead were then re-suspended in 20mg/ml Proteinase K solution and incubated for 3hours at 50°C and 800rpm. The residual beads where pelleted using a magnetic rack. The supernatant was collected for phenol/chloroform extraction. For extraction, the supernatant was treated with 250µl phenol: chloroform: isoamyl at a ratio of 25:24:1, vortexed and then spun down for 2 minutes at 14,000rpm. Then, the supernatant was treated with 250µl chloroform, vortexed and spun down for 2 minutes. Finally, DNA was precipitated by adding 20µl 5M NaCl, 1µl glycogen and 500µl 100% ethanol and incubated at -20°C for 30 minutes. The samples were then pelleted at 4°C and 14,000rpm for 20 minutes and allowed to dry at room temperature for 10 minutes. The dried out samples are re-suspended in 25-50µl water and readied for the HM450K bead chip array for methylation analysis.

treatment_protocol: The Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) cohort consists of over 4000 mother-infant pairs, belonging to a low income population recruited from 1994 onwards from three hospitals in Mexico City (Mexican Social Security Institute, Manuel Gea Gonzalez Hospital, and National Institute of Perinatology).We used umbilical cord blood (UCB) from the fourth wave of the ELEMENT study (Each of the four waves had approximately 1000 children participants). The blood lead concentrations of umbilical cord blood were determined using atomic absorption spectroscopy (Model 3000; PerkinElmer, Chelmsford, MA, USA) at the metals laboratory of the American British Cowdray Hospital in Mexico City .For our study, we randomly selected UCB from 24 male and 24 female children from the 1st and 4th quartiles of Pb levels. The UCB for male children had a minimum blood lead level (BLL) of 0.59 µg/dl and highest BLL of 7.21µg/dl. The UCB for female children had a minimum BLL of 0.68µg/dl and highest BLL of 10.53 µg/dl. Five male children and seven female children had BLL in UCB ≥ 5µg/dl and classified as high BLL group.

tag: tissue

value: umbilical cord blood

tag: gender

value: Female

tag: socioeconomic score

tag: gestational age

tag: smoke ever

value: Yes

tag: birth weight

tag: pbconc (ng/dl)

tag: sample type

tag: ip antibody

value: 5hmC-specific antibodies (Active Motif)


title: iPS-AF-8


title: 5hmCIP_450K (0144-C-HMC)

value: Male

value: No


title: AF

source_name: AF

value: amnio fluid

value: AF


title: HES29

value: Embryonic stem cells


title: 5hmCIP_450K (0129-C-HMC)


title: HES26


title: L428 Control Replicate 3

description: Gene expression data from L428 Cells as Controls

source_name: L428 Cells

value: Control


title: HES40


title: Chlorhexidine tolerant isolate exposed_rep2

status: Public on Jun 06 2015

type: mixed

city: Dublin 4

first: Séamus

last: Fanning

address: Belfield

department: School of Public Health, Physiotherapy & Sports Science

country: Ireland

institute: University College Dublin

description: 24CHX exp

hyb_protocol: 1)Prepared Cy 5 labelled gDNA (6 µl) was added to Cy3 labelled cDNA (18 µl) for a total volume of 24 µl. 2) To each sample, 6µl of blocking solution (Agilent 5188-5973) and 30 µl of :hybridisation buffer (Agilent 5188-6420) were added. 3) Samples were boiled for 2 min at 95oC and centrifuged for 1 min at 13000 rpm. 4) The gasket slide was placed in hybridization chamber rubber and 50 µl of sample placed directly into centre of gasket slide. 5) When all samples were dispensed the array slide was inserted into the hybridisation chamber, sealed and placed in pre-heated hybridisation over (65˚C) at 10 rpm overnight. 6) Slides were removed from chamber washed according to manufacturer’s instructions (http://www.chem.agilent.com/Library/usermanuals/Public/G2534-90004_HybridizationChamber_User.pdf). 7) Array slides were cleaned with inert gas before measurement.

scan_protocol: Scans were carried out using an Agilent DNA Microarray Scanner, Model G2565, at at 5 µm resolution with Green and Red PMT values set to 100 % and an XDR value of 0.1.  Images generated were saved as multi-image .tiff files.

data_processing: Agilent Feature extraction software was used to process the scanned images of the arrays.  The data generated was then analysed using GeneSpring version 7.3 (Agilent Technologies, Santa Clara, California) based on the log ratio of median Cy3/Cy5 signal normalised to the 50th percentile.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Mutant chlorhexidine tolerant mid-log phase culture

label_protocol: 1)Random priming reactions were set up in 1.5 ml microfuge tubes. Total RNA (10 µg) and 5 µg of random hexamers (Invitrogen, Cat: 48190011) were added to a final volume of 9.4 µl in RNase free water. 2) Samples incubated at 70 ˚C for 5 min and chilled on ice for 10 min. 3) RT reaction mix prepared by using the Stratagene AffinityScript multi-temperature Reverse Transcriptase by adding the following to each tube: 2 µl of 10 X RT buffer; 2 µl of 0.1 M DDT; 0.6 µl of 50 X dNTP’s (25 mM dATP, dGTP, dTTP and 10 mM dCTP[GE Healthcare Lifesciences, Cat: 27-2035-02]); 2 µl of Cy3 dCTP (1 mM stock, GE Healthcare Lifesciences, Cat: PA55321); 4 µl of reverse transcriptase. 4) Samples were vortexed to mix and incubated shaking at 25 ˚C for 10 min. 5) Samples then incubated overnight at 42 ˚C. 6) Freshly prepared 0.1 M NaOH (15 µl) was added and the RNA hydrolysed at 70 ˚C for 10 min. Freshly prepared 0.1 M HCl (15 µl) was added to neutralise the alkali. Samples were placed on ice to cool to room temperature.  7) Qia-quick PCR purification kit (Qiagen, Cat: 28104) was used to remove unincorporated/quenched cy dyes.  Samples eluted into 40 µl RNase free water and dried-down on speed vac to 18 µl.

growth_protocol: Salmonella Typhimurium 24CHX grown to mid-logarithmic phase culture (OD610 nm = 0.6) in Muller-Hinton brothat 37˚C, then exposed to 1 µg/ ml of chlorhexidine for 30 minutes

extract_protocol: RNA was purified from 2 ml of mid-logarithmic phase culture (OD610 nm = 0.6) using an Ambion RiboPure Bacteria Kit (Life Technologies Corporation, Carlsbad, CA). RNA was purified in accordance with the manufacturer’s instructions, with the exception that the final DNase treatment step was carried out twice for each sample.

tag: strain

tag: phenotype

value: chlorhexidine tolerant

tag: growth phase

value: mid-log phase

tag: biological replicate

source_name: Reference genomic DNA

label_protocol: 1) Chromosomal DNA (2 µg) added to sterile microfuge tube and brought to 21 µl with RNase free water (Sigma, W4502-1L). 2) 20 µl each of 2.5 X Random primer/reaction buffer mix from the Invitrogen BioPrime® DNA Labelling System (18094011) was added to sample and boiled for 5 min, then put on ice for 5 min. 3) On ice, 5 µl of 10X dNTP mix (10X dNTP mix: 1.2 mM each dATP, dGTP, dTTP; 0.6 mM dCTP; 10 mM Tris pH 8.0; 1 mM EDTA;); 3 µl of Cy5 dCTP (1 mM stock, GE Helathcare Lifesciences, Cat: PA55321); and 1 µl Klenow enzyme from the kit were added. 4) Samples were spun briefly and the reaction mix incubated at 37 ˚C overnight. 5) A Qia-quick PCR purification kit (Qiagen Cat: 28104) was used to remove unincorporated/quenched Cy dyes.  Samples were eluted into 80 µl of RNase free water.  This protocol supplies sufficient labelled DNA for 9 hybridisations.  Samples adjusted to a volume of 50 µl using speed vac.

growth_protocol: Salmonella enterica serovar Typhimurium 24WT grown to stationary phase at 37˚C

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns).

value: chlorhexidine sensitive


title: Chlorhexidine tolerant isolate exposed_rep3

description: 24CHX exp


title: L428 Control Replicate 1


title: Chlorhexidine tolerant isolate exposed_rep1

description: 24CHX exp


title: PD_Fb_SNCA-ExCont RNAi

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

country: Japan

institute: National Institute of Neuroscience, NCNP

description: PD fibroblasts were treated by SNCA expression-control RNAi.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Reference Web link: http://www.3d-gene.com

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were grown in Minimum Essential Medium (MEM) supplemented with 10% fetal bovine serum at 37ºC in 5% CO2 humidified chamber.

extract_protocol: Total RNAs were extracted from treated fibroblasts using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated by SNCA expression-control RNAi.

tag: Sex

value: female

tag: age

value: fibroblast


title: DN-MCU, Adult, Bio Rep 3

status: Public on Jun 07 2015

city: Iowa City

first: Tyler

middle: Paul

last: Rasmussen

state: IA

address: 285 Newton Rd.

department: Internal Medicine

institute: University of Iowa

description:
Sample name: CC1731DN
Whole, excised heart

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed according to GeneChip 3' IVT Express Kit User Manual.

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

data_processing: Data were analyzed using Partek Genomic Suite.

organism: Mus musculus

source_name: Adult murine heart

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2008, Affymetrix).

extract_protocol: Trizol extraction was performed per manufacturer's protocol.  RNA was purified with Qiagen MinElute RNA Cleanup kit.

value: male

tag: developmental stage

value: adult

value: heart

tag: genotype/variation

value: DN-MCU


title: Chlorhexidine sensitive isolate exposed_rep3

description: 24WT exp

source_name: Wild-type chlorhexidine senstive mid-log phase culture

growth_protocol: Salmonella Typhimurium 24WT grown to mid-logarithmic phase culture (OD610 nm = 0.6) in Muller-Hinton brothat 37˚C, then exposed to 1 µg/ ml of chlorhexidine for 30 minutes


title: WT, Neonate, Bio Rep 2

description:
Sample name: NN6WT
Whole, excised heart

source_name: Neonatal murine heart

value: unknown

value: neonate

value: 1 d

tag: tissue

value: WT


title: WT, Adult, Bio Rep 2

description:
Sample name: CC1736WT
Whole, excised heart

tag: gender


title: DN-MCU, Neonate, Bio Rep 3

description:
Sample name: NN8DN
Whole, excised heart


title: FF

source_name: FF

tag: cell type

value: fetal fibroblast

tag: cell line

value: FF


title: DN-MCU, Adult, Bio Rep 2

description:
Sample name: CC1738DN
Whole, excised heart


title: DN-MCU, Neonate, Bio Rep 2

description:
Sample name: NN4DN
Whole, excised heart


title: WT, Neonate, Bio Rep 3

description:
Sample name: NN9WT
Whole, excised heart


title: WT, Neonate, Bio Rep 1

description:
Sample name: NN2WT
Whole, excised heart


title: WT, Adult, Bio Rep 3

description:
Sample name: CC1737WT
Whole, excised heart


title: DN-MCU, Neonate, Bio Rep 1

description:
Sample name: NN3DN
Whole, excised heart


title: WT, Adult, Bio Rep 1

description:
Sample name: CC1322WT
Whole, excised heart


title: Chlorhexidine tolerant isolate_rep3

growth_protocol: Salmonella Typhimurium 24CHX grown to mid-logarithmic phase culture (OD610 nm = 0.6) in Muller-Hinton broth at 37˚C.


title: Chlorhexidine sensitive isolate exposed_rep2

description: 24WT exp


title: Chlorhexidine sensitive isolate exposed_rep1

description: 24WT exp


title: Chlorhexidine tolerant isolate_rep2


title: DN-MCU, Adults, Bio Rep 1

description:
Sample name: CC1323DN
Whole, excised heart


title: Chlorhexidine sensitive isolate_rep1

growth_protocol: Salmonella Typhimurium 24WT grown to mid-logarithmic phase culture (OD610 nm = 0.6) in Muller-Hinton broth at 37˚C.


title: Chlorhexidine sensitive isolate_rep2


title: L428 Control Replicate 2

value: Hodgkin Lymphoma

tag: treatment


title: Chlorhexidine tolerant isolate_rep1


title: PD_Fb_Non-silencing RNAi

description: PD fibroblasts were treated by a non-silencing siRNA.


title: iPS-FF-c

source_name: iPS-FF-c

value: induced pluripotent stemm cell line

value: iPS-FF-c


title: Chlorhexidine sensitive isolate_rep3

value: mid-log phase


title: Xanthogranuloma Lacrimal gland 2_2AXa

city: Portland

first: James

last: Rosenbaum

state: OR

address: 3181 SW Sam Jackson Park Road

department: Casey Eye Institute

institute: Oregon Health & Science University

description:
2AXa
Gene expression data from biopsies

hyb_protocol: Biotin-labeled cDNA targets were hybridized with a GeneChip Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA) according to standard Affymetrix protocol. Following hybridization, arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays scanned using the GeneChip Scanner 3000 7G system (Affymetrix) and Affymetrix GeneChip Command Console (AGCC) v. 3.1.1

data_processing: Initial quality control analysis was performed using Affymetrix Expression Console v. 1.1 software. Affymetrix CEL files preprocessed by the Robust Multi-array Analysis algorithm for R for expression analysis.

source_name: Lacrimal gland

label_protocol: Approximately 20 to 50 ng of RNA were amplified and  labeled with the SensationPlus FFPE Amplification and 3’ IVT Labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: After deparaffinization, total RNA was extracted from tissue sections with the miRNeasy FFPE kit (Qiagen, Valencia, CA).

treatment_protocol: Biopsies were formalin-fixed and paraffin-embedded

tag: diagnosis

value: Xanthogranuloma

value: Female

value: Lacrimal gland


title: GPA Anterior Orbit 7 Technical replicate 2_7.2AWe

description:
7.2AWe
Gene expression data from biopsies

source_name: Anterior Orbit

value: GPA

value: Anterior Orbit


title: GPA Anterior Orbit 4 Technical replicate 1_4.1AWe

description:
4.1AWe
Gene expression data from biopsies

value: Male


title: GPA Anterior Orbit 4 Technical replicate 2_4.2AWe

description:
4.2AWe
Gene expression data from biopsies


title: GPA Anterior Orbit 7 Technical replicate 1_7.1AWe

description:
7.1AWe
Gene expression data from biopsies


title: HES17

value: Embryonic stem cells


title: GPA Anterior Orbit 3_3AWe

description:
3AWe
Gene expression data from biopsies


title: GPA Lacrimal gland 2_2AWe

description:
2AWe
Gene expression data from biopsies


title: GPA Anterior Orbit 5 Technical replicate 2_5.2AWe

description:
5.2AWe
Gene expression data from biopsies


title: Sarcoidosis Anterior Orbit 13_13ASa

description:
13ASa
Gene expression data from biopsies

value: Sarcoidosis


title: Sarcoidosis Lacrimal gland 12 Technical replicate 2_12.2ASa

description:
12.2ASa
Gene expression data from biopsies


title: GPA Anterior Orbit 1 Technical replicate 2_1.2AWe

description:
1.2AWe
Gene expression data from biopsies


title: GPA Anterior Orbit 5 Technical replicate 1_5.1AWe

description:
5.1AWe
Gene expression data from biopsies


title: GPA Anterior Orbit 1 Technical replicate 1_1.1AWe

description:
1.1AWe
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 8 Technical replicate 2_8.2ASa

description:
8.2ASa
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 12 Technical replicate 1_12.1ASa

description:
12.1ASa
Gene expression data from biopsies


title: Xanthogranuloma Anterior Orbit 1_1AXa

description:
1AXa
Gene expression data from biopsies


title: Sarcoidosis Anterior Orbit 10_10ASa

description:
10ASa
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 11 Technical replicate 2_11.2ASa

description:
11.2ASa
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 4 Technical replicate 2_4.2ASa

description:
4.2ASa
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 3_3DSa

description:
3DSa
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 5_5ASa

description:
5ASa
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 8 Technical replicate 1_8.1ASa

description:
8.1ASa
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 4 Technical replicate 1_4.1ASa

description:
4.1ASa
Gene expression data from biopsies


title: Sarcoidosis Anterior Orbit 7_7ASa

description:
7ASa
Gene expression data from biopsies


title: Sarcoidosis Anterior Orbit 6_6ASa

description:
6ASa
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 3_3CSa

description:
3CSa
Gene expression data from biopsies


title: L428 25nM Ixazomib Replicate 1

description: Gene expression data from L428 Cells with 25nM of Ixazomib treatment for 24 hours

value: 25nM of Ixazomib for 24 Hours


title: Sarcoidosis Lacrimal gland 1_1ASa

description:
1ASa
Gene expression data from biopsies


title: Sarcoidosis Anterior Orbit 2 Technical replicate 2_2.2ASa

description:
2.2ASa
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 3 Technical replicate 2_3.2ASa

description:
3.2ASa
Gene expression data from biopsies


title: NSOI Lacrimal gland 61_61ANS

description:
61ANS
Gene expression data from biopsies

value: NSOI


title: NSOI Anterior Orbit 58_58ANS

description:
58ANS
Gene expression data from biopsies


title: Sarcoidosis Anterior Orbit 3_3BSa

description:
3BSa
Gene expression data from biopsies


title: NSOI Lacrimal gland 59_59ANS

description:
59ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 51_51ANS

description:
51ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 48_48ANS

description:
48ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 49_49ANS

description:
49ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 47_47ANS

description:
47ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 56_56ANS

description:
56ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 54_54ANS

description:
54ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 57_57ANS

description:
57ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 60_60ANS

description:
60ANS
Gene expression data from biopsies


title: Sarcoidosis Anterior Orbit 2 Technical replicate 1_2.1ASa

description:
2.1ASa
Gene expression data from biopsies


title: NSOI Anterior Orbit 45_45ANS

description:
45ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 52_52ANS

description:
52ANS
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 3 Technical replicate 1_3.1ASa

description:
3.1ASa
Gene expression data from biopsies


title: NSOI Anterior Orbit 55_55ANS

description:
55ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 43_43ANS

description:
43ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 53_53ANS

description:
53ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 40 Technical replicate 2_40.2ANS

description:
40.2ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 46_46ANS

description:
46ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 42_42ANS

description:
42ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 50_50ANS

description:
50ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 39_39ANS

description:
39ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 40 Technical replicate 1_40.1ANS

description:
40.1ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 41_41ANS

description:
41ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 35_35ANS

description:
35ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 29_29ANS

description:
29ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 34_34ANS

description:
34ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 26_26ANS

description:
26ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 30_30ANS

description:
30ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 29_29BNS

description:
29BNS
Gene expression data from biopsies


title: NSOI Anterior Orbit 36_36ANS

description:
36ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 37_37ANS

description:
37ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 33_33ANS

description:
33ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 31_31ANS

description:
31ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 38_38ANS

description:
38ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 28_28ANS

description:
28ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 27_27ANS

description:
27ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 25_25ANS

description:
25ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 30_30BNS

description:
30BNS
Gene expression data from biopsies


title: NSOI Anterior Orbit 33_33BNS

description:
33BNS
Gene expression data from biopsies


title: NSOI Lacrimal gland 23 Technical replicate 2_23.2ANS

description:
23.2ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 24_24BNS

description:
24BNS
Gene expression data from biopsies


title: NSOI Anterior Orbit 32_32ANS

description:
32ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 23 Technical replicate 1_23.1ANS

description:
23.1ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 22_22ANS

description:
22ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 18_18BNS

description:
18BNS
Gene expression data from biopsies


title: NSOI Lacrimal gland 16_16ANS

description:
16ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 15_15DNS

description:
15DNS
Gene expression data from biopsies


title: NSOI Anterior Orbit 18_18ANS

description:
18ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 19_19BNS

description:
19BNS
Gene expression data from biopsies


title: NSOI Lacrimal gland 17_17ANS

description:
17ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 21_21ANS

description:
21ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 14_14ANS

description:
14ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 11 Technical replicate 1_11.1ANS

description:
11.1ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 12_12ANS

description:
12ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 13_13ANS

description:
13ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 20_20ANS

description:
20ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 15 Technical replicate 1_15.1ANS

description:
15.1ANS
Gene expression data from biopsies


title: Sarcoidosis Lacrimal gland 11 Technical replicate 1_11.1ASa

description:
11.1ASa
Gene expression data from biopsies


title: NSOI Lacrimal gland 9_9ANS

description:
9ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 12 Technical replicate 2_12.2CNS

description:
12.2CNS
Gene expression data from biopsies


title: Sarcoidosis Anterior Orbit 9_9ASa

description:
9ASa
Gene expression data from biopsies


title: NSOI Lacrimal gland 10_10CNS

description:
10CNS
Gene expression data from biopsies


title: NSOI Anterior Orbit 8 Technical replicate 2_8.2ANS

description:
8.2ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 12 Technical replicate 1_12.1CNS

description:
12.1CNS
Gene expression data from biopsies


title: NSOI Lacrimal gland 11 Technical replicate 2_11.2ANS

description:
11.2ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 8 Technical replicate 2_8.2BNS

description:
8.2BNS
Gene expression data from biopsies


title: NSOI Anterior Orbit 15 Technical replicate 2_15.2ANS

description:
15.2ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 10_10BNS

description:
10BNS
Gene expression data from biopsies


title: NSOI Anterior Orbit 8 Technical replicate 1_8.1ANS

description:
8.1ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 8 Technical replicate 1_8.1BNS

description:
8.1BNS
Gene expression data from biopsies


title: NSOI Anterior Orbit 5_5ANS

description:
5ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 7_7ANS

description:
7ANS
Gene expression data from biopsies


title: blood control rep2

city: Osaka

first: Kohei

last: Kotani

address: 1-4-3, Asahimachi, Abeno-ku

institute: Graduate School of Medicine, Osaka City University

description: SAMPLE 5

hyb_protocol: Human Gene ST 1.0 Array was used according to the standard Affymetrix protocol for hybridization of the sense chain cDNA.

scan_protocol: Gene chips were scanned using the GeneChip 3000 Scanner. The array image data from each sample were converted into files in a format enabling numerical extraction, using the GCOS.

data_processing: The data were analyzed with RMA algorithm using Affymetrix default analysis settings and global scaling as normalization method. The RMA data were divided by the mean signal intensity values for all six samples, and the quotient was converted into a logarithm (Log2).

source_name: healthy_blood at rest

label_protocol: The WT-Ovation Pico RNA Amplification System (NuGEN Technologies, Inc., San Carlos, CA, USA) was employed for cDNA synthesis, conversion into sense chain, fragmentation, and biotin labeling.

extract_protocol: Total RNA was extracted according to the manufacturer's instructions (ISOGEN-LS method, NIPPON GENE Co., Ltd., Tokyo, Japan).

tag: subject status

value: healthy volunteer

value: blood cells


title: blood control rep3

description: SAMPLE 6


title: NSOI Lacrimal gland 3_3ANS

description:
3ANS
Gene expression data from biopsies


title: NSOI Anterior Orbit 2_2ANS

description:
2ANS
Gene expression data from biopsies


title: blood IPH rep3

description: SAMPLE 3

source_name: IPH_blood at rest

value: Idiopathic portal hypertension (IPH) patient


title: NSOI Lacrimal gland 19_19ANS

description:
19ANS
Gene expression data from biopsies


title: blood IPH rep2

description: SAMPLE 2


title: Normal Anterior Orbit 28_28ANo

description:
28ANo
Gene expression data from biopsies

value: Normal


title: blood control rep1

description: SAMPLE 4


title: LH_LNA_56h, biological rep2

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

description: Gene expression data following LNA miR-9 inhibition (56h)

hyb_protocol: Target samples were hybridized to Human HuGene-1_0-st-v1 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Arrays were scanned and labelled according to Affymetrix protocol by external microarray service.

data_processing: All arrays passed standard quality checks. The data was RMA normalised across all arrays simultaneously (R/Bioconductor)  and  log2 fold change (FC) against scramble LNA control was computed. As RMA normalisation assumes approximately equal distributions across samples and can lead to residual non-linear intensity--dependent biases when this does not hold, especially when there is unequal distribution of up-- and down-regulated genes, an additional post-normalisation step was performed to further reduce inter-array technical differences: A loess fit to the mean curve of the M-A plot of a large set of human house--keeping genes was centred by a non-linear correction of fold change (M) depending on mean gene expression (A) (low-expressed genes where loess fit was imprecise i.e. S.E. < 0.02 were not adjusted).

source_name: mir-9, LH, LNA, 56h

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides according to the manufacturer's (Affymetrix) protocols by external microarray service (RH Microarray Center, Copenhagen).

growth_protocol: The HL cell line L428, was grown at standard conditions in 5% CO2 at 37°C in RPMI 1640-glutamax (Gibco, Invitrogen) supplemented with 10% FBS (Hyclone, Thermo Scientific).

extract_protocol: Total RNA was obtained by TRIZOL (invitrogen) extraction.

treatment_protocol: For the array experiments, the L428 were transfected via unassisted uptake (Stein et al., 2010) by adding the LNA-antimiR-9 or LNA scramble control oligonucleotides directly to the culture medium at a final concentration of 10µM. For miR-9 inhibition the following LNA oligonucleotides were used: 5'- AACCAAAG -3' to target miR-9 and 5'- TCATACTA -3' as a negative control. The LNA were checked before the experiment by Luciferase with the perfect match reporter. The oligonucleotides were maintained in the medium throughout the full time course of the experiment, although overall levels would be expected to decrease across the experiment due to uptake by cells. Note that the cells were split 24 hours before the initiation of the experiment to minimise synchronisation, to avoid confounding of the dynamic response by synchronised cell-cycle effects.

value: HL cell line L428

value: LNA miR-9 inhibition

tag: timepoint


title: NSOI Anterior Orbit 1_1ANS

description:
1ANS
Gene expression data from biopsies


title: NSOI Lacrimal gland 6_6ANS

description:
6ANS
Gene expression data from biopsies


title: LH_SC_56h, biological rep2

description: Gene expression data: scramble control (56h)

source_name: mir-9, LH, SC, 56h

value: LNA scramble control


title: LH_SC_80h, biological rep2

description: Gene expression data: scramble control (80h)

source_name: mir-9, LH, SC, 80h


title: GPA Anterior Orbit 6_6AWe

description:
6AWe
Gene expression data from biopsies


title: blood IPH rep1

description: SAMPLE 1


title: LH_LNA_112h, biological rep2

description: Gene expression data following LNA miR-9 inhibition (112h)

source_name: mir-9, LH, LNA, 112h


title: LH_SC_112h, biological rep2

description: Gene expression data: scramble control (112h)

source_name: mir-9, LH, SC, 112h


title: Normal Anterior Orbit 27_27ANo

description:
27ANo
Gene expression data from biopsies


title: LH_LNA_80h, biological rep2

description: Gene expression data following LNA miR-9 inhibition (80h)

source_name: mir-9, LH, LNA, 80h


title: Normal Anterior Orbit 23_23ANo

description:
23ANo
Gene expression data from biopsies


title: LH_LNA_26h, biological rep2

description: Gene expression data following LNA miR-9 inhibition (26h)

source_name: mir-9, LH, LNA, 26h


title: LH_SC_32h, biological rep2

description: Gene expression data: scramble control (32h)

source_name: mir-9, LH, SC, 32h


title: Normal Anterior Orbit 26_26ANo

description:
26ANo
Gene expression data from biopsies


title: Normal Anterior Orbit 21_21ANo

description:
21ANo
Gene expression data from biopsies


title: LH_LNA_40h, biological rep2

description: Gene expression data following LNA miR-9 inhibition (40h)

source_name: mir-9, LH, LNA, 40h


title: LH_SC_26h, biological rep2

description: Gene expression data: scramble control (26h)

source_name: mir-9, LH, SC, 26h


title: LH_SC_40h, biological rep2

description: Gene expression data: scramble control (40h)

source_name: mir-9, LH, SC, 40h


title: Normal Anterior Orbit 16_16ANo

description:
16ANo
Gene expression data from biopsies


title: LH_LNA_32h, biological rep2

description: Gene expression data following LNA miR-9 inhibition (32h)

source_name: mir-9, LH, LNA, 32h


title: Normal Anterior Orbit 14 Technical replicate 2_14.2ANo

description:
14.2ANo
Gene expression data from biopsies


title: Normal Anterior Orbit 24_24ANo

description:
24ANo
Gene expression data from biopsies


title: LH_SC_22h, biological rep2

description: Gene expression data: scramble control (22h)

source_name: mir-9, LH, SC, 22h


title: LH_LNA_22h, biological rep2

description: Gene expression data following LNA miR-9 inhibition (22h)

source_name: mir-9, LH, LNA, 22h


title: Normal Anterior Orbit 14 Technical replicate 1_14.1ANo

description:
14.1ANo
Gene expression data from biopsies

source_name: Anterior Orbit


title: LH_SC_18h, biological rep1

description: Gene expression data: scramble control (18h)

source_name: mir-9, LH, SC, 18h


title: LH_SC_20h, biological rep1

description: Gene expression data: scramble control (20h)

source_name: mir-9, LH, SC, 20h


title: LH_SC_16h, biological rep1

description: Gene expression data: scramble control (16h)

source_name: mir-9, LH, SC, 16h


title: LH_LNA_18h, biological rep1

description: Gene expression data following LNA miR-9 inhibition (18h)

source_name: mir-9, LH, LNA, 18h


title: LH_LNA_20h, biological rep1

description: Gene expression data following LNA miR-9 inhibition (20h)

source_name: mir-9, LH, LNA, 20h


title: Normal Anterior Orbit 13_13ANo

description:
13ANo
Gene expression data from biopsies


title: LH_LNA_16h, biological rep1

description: Gene expression data following LNA miR-9 inhibition (16h)

source_name: mir-9, LH, LNA, 16h


title: Normal Anterior Orbit 9_9ANo

description:
9ANo
Gene expression data from biopsies


title: Normal Anterior Orbit 10_10ANo

description:
10ANo
Gene expression data from biopsies


title: LH_LNA_14h, biological rep1

description: Gene expression data following LNA miR-9 inhibition (14h)

source_name: mir-9, LH, LNA, 14h


title: LH_SC_14h, biological rep1

description: Gene expression data: scramble control (14h)

source_name: mir-9, LH, SC, 14h


title: Normal Anterior Orbit 12_12ANo

description:
12ANo
Gene expression data from biopsies


title: Normal Anterior Orbit 7_7ANo

description:
7ANo
Gene expression data from biopsies


title: LH_SC_10h, biological rep1

description: Gene expression data: scramble control (10h)

source_name: mir-9, LH, SC, 10h


title: Normal Anterior Orbit 5_5ANo

description:
5ANo
Gene expression data from biopsies


title: Normal Anterior Orbit 2_2ANo

description:
2ANo
Gene expression data from biopsies


title: LH_LNA_10h, biological rep1

description: Gene expression data following LNA miR-9 inhibition (10h)

source_name: mir-9, LH, LNA, 10h


title: Normal Anterior Orbit 4_4BNo

description:
4BNo
Gene expression data from biopsies


title: LH_SC_12h, biological rep1

description: Gene expression data: scramble control (12h)

source_name: mir-9, LH, SC, 12h


title: LH_LNA_8h, biological rep1

description: Gene expression data following LNA miR-9 inhibition (8h)

source_name: mir-9, LH, LNA, 8h


title: Normal Anterior Orbit 3_3ANo

description:
3ANo
Gene expression data from biopsies


title: LH_SC_8h, biological rep1

description: Gene expression data: scramble control (8h)

source_name: mir-9, LH, SC, 8h


title: Normal Anterior Orbit 8_8ANo

description:
8ANo
Gene expression data from biopsies


title: Normal Anterior Orbit 6_6ANo

description:
6ANo
Gene expression data from biopsies


title: Lymphoma Anterior Orbit 1_1ALy

description:
1ALy
Gene expression data from biopsies

value: Lymphoma


title: Normal Anterior Orbit 11_11ANo

description:
11ANo
Gene expression data from biopsies

value: Female


title: LH_LNA_12h, biological rep1

description: Gene expression data following LNA miR-9 inhibition (12h)

source_name: mir-9, LH, LNA, 12h


title: Normal Anterior Orbit 1_1ANo

description:
1ANo
Gene expression data from biopsies


title: LH_LNA_6hr, biological rep1

description: Gene expression data following LNA miR-9 inhibition (6h)

source_name: mir-9, LH, LNA, 6h


title: LH_SC_6h, biological rep1

description: Gene expression data: scramble control (6h)

source_name: mir-9, LH, SC, 6h


title: TED Anterior Orbit 28 Technical replicate 1_28.1AGr

description:
28.1AGr
Gene expression data from biopsies

source_name: Anterior Orbit

value: TED


title: TED Anterior Orbit 26 Technical replicate 2_26.2BGr

description:
26.2BGr
Gene expression data from biopsies


title: LH_SC_2h, biological rep1

description: Gene expression data: scramble control (2h)

source_name: mir-9, LH, SC, 2h


title: TED Anterior Orbit 26_26AGr

description:
26AGr
Gene expression data from biopsies


title: LH_LNA_4h, biological rep1

description: Gene expression data following LNA miR-9 inhibition (4h)

source_name: mir-9, LH, LNA, 4h


title: TED Anterior Orbit 25_25AGr

description:
25AGr
Gene expression data from biopsies


title: TED Anterior Orbit 26 Technical replicate 1_26.1BGr

description:
26.1BGr
Gene expression data from biopsies


title: TED Anterior Orbit 28 Technical replicate 2_28.2AGr

description:
28.2AGr
Gene expression data from biopsies


title: TED Anterior Orbit 24_24AGr

description:
24AGr
Gene expression data from biopsies


title: HFD BAT 4

city: Odense

first: Jan-Wilhelm

last: Kornfeld

state: Fyn

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

hyb_protocol: After fragmentation, cDNAs were hybridized for 17h at 45°C on Affymetrix Mouse Gene 1.0 ST Arrays.

scan_protocol: The Arrays were washed and stained in the GeneChip Fluidics Station 450 and scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data intensities were log transformed and normalized with a quantile normalization method using Affymetrix Power Tools. Differentially expressed genes were identified according to statistical evidence indicated by Student's t-test and fold change statistics.

source_name: BAT

label_protocol: Biotin-labeled cDNA was synthesized using GeneChip Whole Transcript Sense Labeling Assay (Affymetrix) according to vendor’s instructions.

extract_protocol: Trizol total RNA extraction

value: male

value: brown adipose


title: HFD BAT 3


title: HFD BAT 2


title: LH_LNA_2h, biological rep1

description: Gene expression data following LNA miR-9 inhibition (2h)

source_name: mir-9, LH, LNA, 2h


title: HFD BAT 1


title: LH_SC_4h, biological rep1

description: Gene expression data: scramble control (4h)

source_name: mir-9, LH, SC, 4h


title: TED Anterior Orbit 22_22BGr

description:
22BGr
Gene expression data from biopsies

value: Male

value: Anterior Orbit


title: TED Anterior Orbit 23_23AGr

description:
23AGr
Gene expression data from biopsies


title: NCD BAT 2


title: NCD BAT 4


title: NCD BAT 3


title: TED Lacrimal gland 19 Technical replicate 1_19.1BGr

description:
19.1BGr
Gene expression data from biopsies

source_name: Lacrimal gland

value: Lacrimal gland


title: NCD BAT 1


title: TED Lacrimal gland 21_21AGr

description:
21AGr
Gene expression data from biopsies


title: TED Lacrimal gland 19 Technical replicate 2_19.2BGr

description:
19.2BGr
Gene expression data from biopsies


title: TED Anterior Orbit 20_20AGr

description:
20AGr
Gene expression data from biopsies


title: TED Anterior Orbit 22_22AGr

description:
22AGr
Gene expression data from biopsies


title: FHH.Pkhd1 at day 30, technical rep3

city: Milwaukee

first: Carol

last: Moreno

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: Gene expression interrogating 31099 transcripts

hyb_protocol: The Affymetrix GeneChip rat genome RD230 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.

organism: Rattus norvegicus

source_name: Congenic Fawn-hooded hypertensive rat that contains the Pkhd1 gene from the PCK rat background

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: All animal procedures including the generation of the SS.Pkhd1 rat model, breeding, and phenotypic characterization were performed at the Medical College of Wisconsin using protocols approved by the Institutional Animal Care and Use Committee. All animal procedures including the generation of the congenic strains, breeding, and phenotypic characterization were performed at the Medical College of Wisconsin using protocols approved by the Institutional Animal Care and Use Committee. Rats were fed 5LOD diet (Purina, Jefferson, WI) for the duration of all experiments. SD and PCK rats were obtained from Charles Rivers. The FHH.Pkhd1 strain was generated as described previously (O'Meara CC, Hoffman M, Sweeney WE, Jr., Tsaih SW, Xiao B, Jacob HJ, Avner ED, Moreno C. Role of genetic modifiers in an orthologous rat model of arpkd. Physiological genomics. 2012;44:741-753). Similar to the development of the FHH.Pkhd1 strain, a SS male was crossed with a PCK female, and the male progeny were backcrossed to SS females for five generations by marker-assisted breeding.

extract_protocol: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: One kidney was harvested from SD, FHH, SS, PCK, FHH.Pkhd1, and SS.Pkhd1 male rats at 30 days-of-age (4 animals for each strain). RNA was extracted from bisected kidneys using TRIzol (Life Technologies, Carlsbad, CA) according to the manufacturer’s instructions. RNA from each strain was pooled, reverse transcribed, and hybridized to three Affymetrix Rat 230 arrays (Affymetrix).

value: FHH.Pkhd1 congenic strain (hypertensive and has ARPKD)

value: Kidney

value: 30 days old


title: TED Lacrimal gland 19_19AGr

description:
19AGr
Gene expression data from biopsies


title: FHH.Pkhd1 at day 30, technical rep2


title: TED Anterior Orbit 18_18AGr

description:
18AGr
Gene expression data from biopsies


title: FHH.Pkhd1 at day 30, technical rep1


title: FHH at day 30, technical rep2

source_name: Fawn-hooded hypertensive rat

value: FHH strain (hypertensive)


title: TED Lacrimal gland 17 Technical replicate 1_17.1AGr

description:
17.1AGr
Gene expression data from biopsies


title: TED Lacrimal gland 17 Technical replicate 2_17.2AGr

description:
17.2AGr
Gene expression data from biopsies


title: FHH at day 30, technical rep3


title: FHH at day 30, technical rep1


title: PCK at day 30, technical rep3

source_name: Polycystic Kidney rat (PCK rat)

value: SD strain (ARPKD rat model)


title: TED Anterior Orbit 16_16AGr

description:
16AGr
Gene expression data from biopsies


title: TED Anterior Orbit 15_15AGr

description:
15AGr
Gene expression data from biopsies


title: TED Lacrimal gland 14 Technical replicate 2_14.2AGr

description:
14.2AGr
Gene expression data from biopsies


title: SD at day 30, technical rep3

source_name: Sprague Dawley rat

value: SD strain


title: PCK at day 30, technical rep2


title: TED Anterior Orbit 13_13AGr

description:
13AGr
Gene expression data from biopsies


title: TED Lacrimal gland 14 Technical replicate 1_14.1AGr

description:
14.1AGr
Gene expression data from biopsies


title: SD at day 30, technical rep1


title: TED Anterior Orbit 8_8AGr

description:
8AGr
Gene expression data from biopsies


title: SUM159_N-Ras_shRNA

city: HOUSTON

first: Eric

middle: C.

last: Chang

state: TX

address: ONE BAYLOR PLZ

department: BREAST CENTER

institute: BAYLOR COLLEGE OF MEDICINE

description: SUM159 cell, N-RAS repressed by shRNA

hyb_protocol: 2 ug labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for over night 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: The arrays were scanned by Axon GenePix 4000B scanner (Axon Instruments)

data_processing: The images were analyzed using Gene Pix Pro 5.0 software (Axon Instruments).  Gene expression values were quantified by the two-based log ratio of red channel intensity (mean) vs. green channel intensity (mean), followed by LOWESS normalization to remove the intensity dependent dye bias.  We used microarray database at University of North Carolina (https://genome.unc.edu/) to perform the filtering and preprocessing.  If the intensity of one probe in one array is less than 10 in either channel, the results from that probe were treated as missing. If a probe has more than 30% expression value missing in all the arrays (due to low intensities or bad flags), the results from that probe were discarded. Data matrix was gene median centered and sample standardized, and missing data were imputed by the 10-nearest-neighbor imputation.

source_name: SUM159 cell, N-RAS repressed by shRNA

label_protocol: Dye labeled cRNA was prepared using the Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification.

growth_protocol: SUM102PT cells were cultured in F12 + Serum Replacement (1 g/L bovine serum albumin, 10 mM HEPES, 5mM ethanolamine, 5 μg/mL transferrin, 10 nM triiodo thyronine, 50 nM sodium selenite) + 5 μg/ml human insulin + 1 μg/ml hydrocortisone + 10 ng/ml EGF; SUM149PT and SUm159PT cells were cultured in F12 + 5% FBS + 5 μg/ml human insulin + 1 μg/ml hydrocortisone

extract_protocol: The RNA was isolated from the rest of the cells by RNeasy kit (Qiagen).

treatment_protocol: Cells were infected with lentiviruses to repress N-RAS (shRNA) or overexpress N-RasG12D. Knock-down and overexpression efficiencies were verified by Western blots.

tag: subtype

value: claudin-low

value: breast cancer

tag: sample type

value: test

source_name: Universal Human Reference RNA (Agilent)

value: reference


title: TED Anterior Orbit 12_12AGr

description:
12AGr
Gene expression data from biopsies


title: SD at day 30, technical rep2

tag: strain


title: TED Anterior Orbit 11_11AGr

description:
11AGr
Gene expression data from biopsies

value: Female


title: TED Anterior Orbit 10_10AGr

description:
10AGr
Gene expression data from biopsies

value: TED


title: SUM159_control

description: SUM159 cell, control

source_name: SUM159 cell, control


title: PCK at day 30, technical rep1


title: SUM159_N-RasOE

description: SUM159 cell, N-RASGD overexpressed

source_name: SUM159 cell, N-RASGD overexpressed


title: SS.Pkhd1 at day 30, technical rep3

source_name: Congenic Dahl Salt-Sensitive rat that contains the Pkhd1 gene from the PCK rat background

value: SS.Pkhd1 congenic strain (salt-sensitive hypertensive and has ARPKD)


title: SUM149_N-RasOE

description: SUM149 cell, N-RASGD overexpressed

source_name: SUM149 cell, N-RASGD overexpressed

value: basal-like


title: mouse immunized, biological rep3

city: Salamanca

first: Jose

last: Rojas-Caraballo

state: Salamanca

address: C/Licenciado Mendez Nieto s/n

department: Molecular Parasitology and Immunology

country: Spain

institute: University of Salamanca

description: Gene expression data from immunized mice

hyb_protocol: Label and hibridization was performed using standardised protocols from Affymetrix using the Ambion Expression Kit

scan_protocol: Washing and scanning were performed using the GeneChip® Instrument System of Affymetrix® (GeneChip® Hybridization Oven 640, GeneChip® Fluidics Station 450 and GeneChip® Scanner 3000 7G).

data_processing: The RMA function provided by the package Affy from R/Bioconductor was applied to the raw expression data. The probes were mapped to GENE LOCi by the CDF built by GATExplorer, which can be found at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php.

source_name: Mice immunized against Fasciola hepatica

extract_protocol: RNA was isolated using the GenElute Mammalian Total RNA Miniprep Kit from Sigma, according to the manufacturer’s instructions

treatment_protocol: Mice from group 1 (n=3) remained untreated along the experiment schedule. Mice from group 2 (n=3) were subcutaneously immunized with a vaccine candidate against Fasciola hepatica infection on day 0 and two booster doses were administered on days 14 and 28, respectively. Two weeks after the last immunization, all animals included in the present study were humanely euthanized and necropsied for spleen isolation.

value: Spleen

value: BALB/c mice

value: immunized against Fasciola hepatica


title: SS.Pkhd1 at day 30, technical rep2


title: mouse immunized, biological rep2

label_protocol: Label and hibridization was performed using standardised protocols from Affymetrix using the Ambion Expression Kit


title: TED Anterior Orbit 5_5AGr

description:
5AGr
Gene expression data from biopsies

source_name: Anterior Orbit

value: Anterior Orbit


title: TED Anterior Orbit 4 Technical replicate 2_4.2AGr

description:
4.2AGr
Gene expression data from biopsies


title: SUM149_N-Ras_shRNA

description: SUM149 cell, N-RAS repressed by shRNA

source_name: SUM149 cell, N-RAS repressed by shRNA


title: TED Anterior Orbit 9_9AGr

description:
9AGr
Gene expression data from biopsies

value: Male


title: TED Anterior Orbit 7_7AGr

description:
7AGr
Gene expression data from biopsies


title: SS at day 30, technical rep3

source_name: Dahl Salt-Sensitive rat

value: SS strain (salt-sensitive hypertensive)

value: Kidney

value: 30 days old


title: SUM149_control

description: SUM149 cell, control

source_name: SUM149 cell, control


title: TED Anterior Orbit 6_6AGr

description:
6AGr
Gene expression data from biopsies


title: mouse untreated, biological rep3

description: Gene expression data from untreated mice

source_name: Healthy untreated mice

value: untreated


title: SS.Pkhd1 at day 30, technical rep1


title: SS at day 30, technical rep2


title: TED Anterior Orbit 3_3AGr

description:
3AGr
Gene expression data from biopsies


title: mouse untreated, biological rep2


title: SUM102_N-RasOE

description: SUM102 cell, N-RASGD overexpressed

source_name: SUM102 cell, N-RASGD overexpressed


title: TED Anterior Orbit 2_2BGr

description:
2BGr
Gene expression data from biopsies


title: SS at day 30, technical rep1


title: mouse immunized, biological rep1


title: SUM102_N-Ras_shRNA

description: SUM102 cell, N-RAS repressed by shRNA

source_name: SUM102 cell, N-RAS repressed by shRNA


title: TED Anterior Orbit 2_2AGr

description:
2AGr
Gene expression data from biopsies


title: mouse untreated, biological rep1


title: Control at 00h replicate 3

status: Public on Jun 05 2015

city: Philadelphia

first: Gao

last: Zhang

state: PA

address: 3601 SPRUCE ST

department: Molecular and Cellular Oncogenesis Program

institute: Wistar Institute

description: Control at 00h replicate 3

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

source_name: human melanoma cells

growth_protocol: Human melanoma cells were grown in Tu2% medium before they reach the 70% confluency.

extract_protocol: Cells were washed again with HBSS and lysed directly in TRI Reagent® RNA Isolation Reagent (Sigma) and stored at -20°C.

treatment_protocol: Human melanoma cells were treated with AZD1152 at 0.5uM and SNS-314 at 0.05uM, respectively.

value: 1205Lu melanoma cells

value: Control

tag: time


title: Control at 00h replicate 4

description: Control at 00h replicate 4


title: Control at 00h replicate 1

description: Control at 00h replicate 1


title: SNS-314 at 48h replicate 2

description: SNS-314 at 48h replicate 2


title: SNS-314 at 48h replicate 3

description: SNS-314 at 48h replicate 3


title: SNS-314 at 24h replicate 3

description: SNS-314 at 24h replicate 3


title: SNS-314 at 24h replicate 1

description: SNS-314 at 24h replicate 1


title: SNS-314 at 18h replicate 1

description: SNS-314 at 18h replicate 1


title: SNS-314 at 18h replicate 3

description: SNS-314 at 18h replicate 3


title: SNS-314 at 18h replicate 4

description: SNS-314 at 18h replicate 4


title: SNS-314 at 12h replicate 4

description: SNS-314 at 12h replicate 4


title: SNS-314 at 18h replicate 2

description: SNS-314 at 18h replicate 2


title: SNS-314 at 48h replicate 4

description: SNS-314 at 48h replicate 4


title: SNS-314 at 24h replicate 2

description: SNS-314 at 24h replicate 2


title: SUM102_control

description: SUM102 cell, control

source_name: SUM102 cell, control

value: breast cancer

value: test


title: SNS-314 at 12h replicate 3

description: SNS-314 at 12h replicate 3


title: SNS-314 at 06h replicate 2

description: SNS-314 at 06h replicate 2


title: AZD1152 at 48h replicate 4

description: AZD1152 at 48h replicate 4


title: SNS-314 at 06h replicate 1

description: SNS-314 at 06h replicate 1


title: SNS-314 at 24h replicate 4

description: SNS-314 at 24h replicate 4


title: SNS-314 at 12h replicate 2

description: SNS-314 at 12h replicate 2


title: AZD1152 at 24h replicate 4

description: AZD1152 at 24h replicate 4


title: AZD1152 at 48h replicate 2

description: AZD1152 at 48h replicate 2


title: SNS-314 at 12h replicate 1

description: SNS-314 at 12h replicate 1


title: SNS-314 at 06h replicate 3

description: SNS-314 at 06h replicate 3


title: AZD1152 at 24h replicate 3

description: AZD1152 at 24h replicate 3


title: AZD1152 at 48h replicate 3

description: AZD1152 at 48h replicate 3


title: AZD1152 at 24h replicate 2

description: AZD1152 at 24h replicate 2


title: AZD1152 at 18h replicate 4

description: AZD1152 at 18h replicate 4


title: SNS-314 at 48h replicate 1

description: SNS-314 at 48h replicate 1


title: AZD1152 at 18h replicate 3

description: AZD1152 at 18h replicate 3


title: AZD1152 at 18h replicate 2

description: AZD1152 at 18h replicate 2


title: AZD1152 at 12h replicate 3

description: AZD1152 at 12h replicate 3


title: AZD1152 at 12h replicate 4

description: AZD1152 at 12h replicate 4


title: AZD1152 at 18h replicate 1

description: AZD1152 at 18h replicate 1


title: AZD1152 at 12h replicate 2

description: AZD1152 at 12h replicate 2


title: AZD1152 at 06h replicate 2

description: AZD1152 at 06h replicate 2


title: Patient 19 - skin-baseline visit

city: Boston

first: Robert

last: Lafyatis

state: MA

address: 72 E Concord St

department: Rheumatology

institute: Boston University School of Medicine

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip HG-U133A 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: human skin

label_protocol: Biotin labeling was performed using the 3' IVT Express Kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: Skin biopseie placed in RNAlater at bedside were stored at -80 degrees C until processing. RNA was exrtacted by homogenization in RNAzol and prifying over Rneasy columns

value: fresolimumab one dose 5 mg/kg


title: Patient 19 - skin-week 24 visit


title: Patient 19 - skin-week 3/4 visit


title: AZD1152 at 12h replicate 1

description: AZD1152 at 12h replicate 1


title: AZD1152 at 24h replicate 1

description: AZD1152 at 24h replicate 1


title: Patient 16 - skin-week 7 visit


title: Patient 17 - skin-week 24 visit


title: Patient 17 - skin-week 3/4 visit


title: AZD1152 at 06h replicate 3

description: AZD1152 at 06h replicate 3


title: AZD1152 at 06h replicate 1

description: AZD1152 at 06h replicate 1


title: Patient 19 - skin-week 7 visit


title: Patient 15 - skin-week 24 visit


title: Patient 16 - skin-week 3/4 visit


title: Patient 16 - skin-baseline visit


title: Patient 17 - skin-baseline visit


title: Patient 13 - skin-week 3/4 visit


title: Patient 12 - skin-week 24 visit


title: Patient 15 - skin-baseline visit


title: Patient 13 - skin-baseline visit


title: Patient 13 - skin-week 7 visit


title: Patient 12 - skin-week 7 visit


title: Patient 11 - skin-week 3/4 visit


title: Patient 15 - skin-week 7 visit


title: mouse heart with Ang II infusion for 7 days, biological rep1

city: Beijing

first: xia

last: wang

address: No.10 Xitoutiao, You An Men

institute: Captial medical university

description: miRNAs expression data from  wide type mouse heart with Ang II infusion 7 days

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: All mice were raised in Pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

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

treatment_protocol: Wide type C57BL/6 mouse were infused saline or Ang II (1500ng/kg/min), and the hearts were taken out after 3 days and 7days.

value: wide type C57BL/6 mouse

value: Ang II infusion for 7 days

value: Heart


title: mouse heart with Ang II infusion for 7 days, biological rep3


title: mouse heart with Ang II infusion for 7 days, biological rep2


title: Patient 15 - skin-week 3/4 visit


title: Patient 11 - skin-week 7 visit


title: Patient 11 - skin-week 24 visit


title: mouse heart with Ang II infusion for 3 days, biological rep3

description: miRNAs expression data from  wide type mouse heart with Ang II infusion 3 days

value: Ang II infusion for 3 days


title: Patient 12 - skin-week 3/4 visit


title: Patient 11 - skin-baseline visit


title: Patient 12 - skin-baseline visit


title: Patient 10 - skin-week 24 visit


title: Patient 10 - skin-baseline visit


title: Patient 17 - skin-week 7 visit


title: Patient 9 - skin-week 7 visit

value: fresolimumab two doses 1 mg/kg at baseline and 3 wks


title: Patient 10 - skin-week 3/4 visit


title: Patient 10 - skin-week 7 visit


title: Control at 00h replicate 2

description: Control at 00h replicate 2


title: SH-SY5Y cells with LSD1+8a shRNA replicate2

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

description: SH-SY5Y cells were induced differentiation with Brain Derived Neural Factor (BDNF) for 3 days

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scaned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Human SH-SY5Y cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

growth_protocol: SH-SY5Y were maintained in Dulbecco's Modified Eagle Medium (DMEM) containing 4,500 mg/L glucose, 10% heat-inactivated fetal bovine serum, 110 mg/L sodium pyruvate, 2 mM L-glutamine and 1% penicillin-streptomycin.

extract_protocol: Total RNA was isolated from cells at indicated time point with RNeasy Mini Kit (Qiagen)

treatment_protocol: SH-SY5Y cells were seeded onto collagen-coated plates at an initial density of 104 cells/cm2. Retinoic acid (RA) (Sigma) was added at a final concentration of 10 μM the next day after plating. After 4 days, the cells were washed three times with PBS and incubated with 50 ng/mL of Brain Derived Neural Factor (BDNF) (Millipore) in serum-free medium for 3 days.

tag: transfection

value: LSD1+8a shRNA


title: SH-SY5Y cells with LSD1+8a shRNA replicate1


title: SH-SY5Y cells with Control shRNA replicate2

value: control shRNA


title: mouse heart with Ang II infusion for 3 days, biological rep2


title: mouse heart with saline infusion, biological rep3

description: miRNAs expression data from  wide type mouse heart with saline infusion

source_name: mouse heart with saline infusion

value: saline infusion


title: mouse heart with saline infusion, biological rep1


title: mouse heart with saline infusion, biological rep2


title: Patient 8 - skin week 3/4 visit


title: Patient 5 - skin-week 7 visit


title: Patient 9 - skin-week 3/4 visit


title: Patient 5 - skin-week 3/4 visit


title: Patient 8 - skin-week 7 visit


title: Patient 9 - skin-baseline visit


title: Patient 4 - skin-week 7 visit


title: Patient 8 - skin-baseline visit


title: Patient 4 - skin-week 24 visit


title: Patient 3 - skin-week 3/4 visit


title: Patient 3 - skin-baseline visit


title: Patient 4 - skin-baseline visit


title: SH-SY5Y cells with Control shRNA replicate1


title: mouse heart with Ang II infusion for 3 days, biological rep1


title: Patient 2 - skin-baseline visit


title: Patient 2 - skin-week 24 visit


title: Patient 2 - skin-week 3/4 visit


title: Patient 2 - skin-week 7 visit


title: Patient 5 - skin-baseline visit


title: Patient 1 - skin-week 7 visit


title: CAD Patient 3

city: chongqing

first: Yue

last: Cai

address: Daping, Yuzhong District, the 10th branch of the Yangtze River

institute: Daping Hospital, Third Military Medical University, Cardiovascular Hospital, Chongqing Institute of Cardiovascular Disease

description: lncRNA  expression of human plasma

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k 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: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization was performed using Expander6 and subsequent data processing was performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After low intensity filtering, LncRNAs that at least 2 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for quantile normalization and further data analysis.

source_name: monocytes

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA was prepared using the RNasey Mini Kit(Qiagen p/n 74104), following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Blood samples collected from radial artery, after insertion of the arterial catheter and before the administration of any anticoagulants, were put into test tube containing EDTA. Freshly drawn plasma was then carefully collected, aliquoted, and stored at -80℃ prior to use.

value: blood

value: monocytes

tag: disease status

value: coronary artery disease

value: male


title: Patient 1 - skin-week 3/4 visit


title: Patient 1 - skin-week 24 visit


title: Patient 1 - skin-baseline visit


title: CAD Patient 2

description: lncRNA  expression of human plasma

tag: age


title: CAD Patient 1

description: lncRNA  expression of human plasma


title: Non-CAD 3

description: lncRNA  expression of human plasma

value: healthy


title: Mtb14_recruit

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

country: Germany

institute: MPIIB

description: M.tuberculosis recruitment whole blood RNA

hyb_protocol: Quantity and labelling efficiency were verified before hybridization to human whole genome microarrays (Agilent Technologies)

scan_protocol: Scanned on an Agilent Scanner G2505B. Image analysis was performed with Feature Extraction software (version 6.1.1, Agilent Technologies).

data_processing: Data were processed and analyzed using Agilents GeneSpring software package (version 12.5)

source_name: Peripheral blood Mtb_recruit

label_protocol: RNA was labeled with the Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer’s instructions.

extract_protocol: RNA was isolated from peripheral blood collected in PAXgene tubes.

treatment_protocol: standard anti-TB chemotherapy

value: Male

value: peripheral blood


title: Mtb12_recruit


title: Mtb11_post

description: M.tuberculosis post-treatment whole blood RNA

source_name: Peripheral blood Mtb_post


title: Mtb06_post


title: Mtb10_post


title: Mtb09_recruit


title: Non-CAD 2

description: lncRNA  expression of human plasma


title: Mtb07_recruit


title: Mtb11_recruit


title: Mtb12_post


title: Mtb08_post


title: Mtb08_recruit


title: Mtb13_recruit


title: Non-CAD 1

description: lncRNA  expression of human plasma


title: Mtb06_recruit


title: Mtb14_post


title: Mtb13_post


title: Mtb05_post


title: Mtb10_recruit


title: Mtb05_recruit


title: Mtb07_post


title: AZD1152 at 48h replicate 1

description: AZD1152 at 48h replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

value: 1205Lu melanoma cells


title: Mtb04_post

value: Female


title: Mtb09_post


title: Mtb04_recruit


title: WAT LCS/LCS Rep1

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: LCS/LCS, perigonadal WAT

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

growth_protocol: Perigonadal white adipose tissue were isolated from 4 month old mice of various genotype

extract_protocol:
Mouse perigonadal white adipose tissue samples were snap-frozen in liquid nitrogen immediately after collection, reduced into powder in a tissue grinder, and dissolved in TRIreagent (Sigma).
After precipitation in alcohol, RNA pellets were washed in cold 75% ethanol and resuspended in nuclease-free water Samples were quantified and evaluated for purity (260-nm/280-nm and 260-nm/230-nm ratio) with a NanoDrop ND-1000 spectrophotometer

treatment_protocol: not applicable

value: 4 months

value: White adipose tissue

tag: genotype

value: LCS/LCS


title: WAT LCS/LCS Rep3


title: WAT LCS/LCS Rep2


title: Patient 16 - skin-week 24 visit

value: fresolimumab one dose 5 mg/kg


title: Mtb03_recruit


title: WAT G609G/G609G Rep2

source_name: G609G/G609G, perigonadal WAT


title: WAT WT Rep2

source_name: wt, perigonadal WAT

value: wt


title: WAT G609G/G609G Rep3


title: WAT G609G/G609G Rep1


title: WAT WT Rep3


title: Maf12_post

description: M.africanum post-treatment whole blood RNA

source_name: Peripheral blood Maf_post


title: Mtb02_post


title: Mtb01_recruit


title: Mtb01_post


title: Mtb03_post


title: PC3_ALKBH3_shRNA_96h

city: Marburg

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in the Hybridization Oven (Agilent). Washing and staining of the arrays were done according to the manufacturer's recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B).

data_processing: Intensity data were extracted using Agilent's Feature Extraction (FE) software (version 10.5.3.1) including a quality control based on internal controls using Agilent's protocol GE1_107_Sep09

source_name: PC3 Cells, ALKBH3 shRNA 96h

label_protocol: 200 ng of total RNA from each sample from PC-3 cells were used as a starting material to prepare cDNA. Microarrays were done using the Low RNA Input linear Amplification Kit Plus, One Color protocol (Agilent Technologies, Cat. N°: 5188-5339) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Cat. N°: 5188-5282) following the manufacturer's standard protocol.

growth_protocol: PC3 cells were cultured in DMEM, supplemented with 10% FCS and Penicillin/Streptavidin.

extract_protocol: Cells were collected after 48h or 96h past selection. RNA was prepared by RNAeasy column.

treatment_protocol: PC3 cells were infected with lentivial ALKBH3 shRNA or Control shRNA for 48 hours.

value: prostate cancer


title: Mtb02_recruit


title: Maf12_recruit

description: M.africanum recruitment whole blood RNA

source_name: Peripheral blood Maf_recruit


title: miR-138 group [qPCR]

first: Jie

last: Li

state: HaiDian Qu

address: Taiping Road 27

department: Biochemistry and Molecular Biology

institute: Institute of Basic Medical Sciences

description: SAMPLE 3; Test

data_processing: Analyze the qPCR results with GeneCopoeia’s online Data Analysis System (www.genecopoeia.com.cn/product/qpcr/analyse/). Relative expression was  calculated using the comparative Ct method. Array genes were normalized to the average value of housekeeping genes (B2M, RPL13A, GAPDH, ACTB).

label: SYBR Green

label_protocol: PCR assays were performed using the Human p53 Signaling Pathway PCR Array (GeneCopoeia, Rockville, MD, USA) following the Manufacturer’s instructions. For cDNA synthesis, 2 µg of RNA was used. The PCR program  was  performed  at  95 °C  for  10 minutes, followed by 40 cycles of 95 °C for 15 seconds and 60 °C for 1 minute by using a Stratagene MX3000P system.

growth_protocol: H1299 cells were cultured in RPMI-1640 Medium (Sigma-Aldrich, Poole, UK), supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated using the TRIZOL reagent (Invitrogen) according to manufacturer’s protocol

treatment_protocol: Cells at 70% confluence were transfected with miRNA mimics using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s recommendations.

value: Human non-small cell lung cancer cell

tag: transfected with


title: WAT WT Rep1

tag: tissue


title: PC3_Control_shRNA_48h

source_name: PC3 Cells, Control shRNA 48h


title: Maf11_recruit

description: M.africanum recruitment whole blood RNA

tag: gender


title: AGO2 siRNA group [qPCR]

description: SAMPLE 2; Test

source_name: H1299_AGO2 siRNA

tag: cell type

value: AGO2 siRNA


title: PC3_Control_shRNA_96h

source_name: PC3 Cells, Control shRNA 96h

tag: cell line


title: Maf08_post


title: Maf10_post


title: Maf07_recruit

description: M.africanum recruitment whole blood RNA


title: Control group [qPCR]

description: SAMPLE 1; Control

value: NC mimics


title: Maf06_recruit

description: M.africanum recruitment whole blood RNA


title: Maf10_recruit

description: M.africanum recruitment whole blood RNA


title: Maf08_recruit

description: M.africanum recruitment whole blood RNA


title: Maf09_post


title: Maf11_post


title: Maf07_post


title: Maf04_post


title: Maf06_post


title: PC3_ALKBH3_shRNA_48h

source_name: PC3 Cells, ALKBH3 shRNA 48h


title: Maf05_recruit

description: M.africanum recruitment whole blood RNA


title: Maf05_post


title: Maf09_recruit

description: M.africanum recruitment whole blood RNA


title: Maf04_recruit

description: M.africanum recruitment whole blood RNA


title: Maf03_post


title: Maf02_post


title: AGS-Mock

city: shanghai

first: jiayan

last: fan

address: No 639 zhi zao ju road

institute: Ninth People’s Hospital, Shanghai JiaoTong

description: AGS-Mock

hyb_protocol: Following fragmentation, 12.5 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: The arrays were scanned by the Affymetrix Scanner 3000(Affymetrix)

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. Next, Genespring software (version 12.5; Agilent Technologies) was employed  to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the RMA algorithm. Differentially expressed genes were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 2.0. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs.intensity of each array was arbitrarily set to 100.

source_name: AGS carrying the empty vector

label_protocol: Biotinylated cRNA were prepared according to the standard GeneChip® IVT Express Kit

growth_protocol: cells were cultured in medium supplemented with 10% (vol/vol) fetal bovine serum, maintained at 37 °C

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

treatment_protocol: LncRNA-ROR depletion cells selection was performed by incubating with 4 μg/ml puromycin for 2 weeks

value: AGS

value: Human gastric cancer cell line

tag: genotype/variation

value: carrying the empty vector


title: Maf01_recruit

description: M.africanum recruitment whole blood RNA


title: AGS

description: AGS

source_name: AGS without treated

value: control (untreated)


title: AGS-shROR

description: AGS-shROR

source_name: AGS knock down lncRNA-ROR

value: knock down lncRNA-ROR


title: Maf01_post

value: peripheral blood


title: Maf02_recruit

description: M.africanum recruitment whole blood RNA


title: Maf03_recruit

description: M.africanum recruitment whole blood RNA


title: HT29-shROR

source_name: HT29 knock down lncRNA-ROR

value: Human colon cancer cell line


title: mouse at T21, biological rep3

description: Gene expression data from mice infected with F. hepatica (21 days)

data_processing: The RMA function provided by the package Affy from R/Bioconductor was applied to the raw expression data.

label: dUTP

source_name: Mice infected with F. hepatica at 21 days

treatment_protocol: Mice were orally infected with 5 metacercariae of Fasciola hepatica on day 0. Mice were then humanely euthanatized on the day of infection (group1), 7 days after infection (group2) and 21 days after infection (group3).

value: BALB/c

value: Liver


title: HT29

source_name: HT29 without treated


title: 5637 vector clone, rep1

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

description: gene expression data from 5637 vector control cells

hyb_protocol: After fragmentation labelled aRNA was hybridized to Affymetrix PrimeViewTM Human Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturers´ protocol

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing: Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by RMA after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability . Input data pre-processing was concluded by baseline transformation to the median of all samples

source_name: 5637 cells, stably transfected with empty vector

label_protocol: Synthesis of cDNA and subsequent biotin labeling of cRNA was performed according to the manufacturers´ protocol (3´ IVT Express Kit; Affymetrix, Inc.). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and biotin labelling of aRNA

growth_protocol: Cells were grown in DMEM supplemented with 10 % FCS.

extract_protocol: Total RNA was extracted by means of RNeasy Mini Kit (Qiagen) according to manufacturer´s instruction. Ectopic overexpression was checked by QRT-PCR.

treatment_protocol: Subsequent to transfection with HOTAIR plasmid or empty vector, stable transfected clones were isolated by treatment with puromycin.

tag: tumor type

value: urothelial cancer


title: HT29-Mock

source_name: HT29 carrying the empty vector


title: mouse at T7, biological rep2

description: Gene expression data from mice infected with F. hepatica (7 days)

source_name: Mice infected with F. hepatica at 7 days


title: VM-CUB1 vector clone, rep2

description: gene expresion data from VM-CUB1 vector control cells

source_name: VM-CUB1 cells, stably transfected with empty vector


title: 5637 vector clone, rep3

source_name: 5639 cells, stably transfected with empty vector


title: mouse at T0, biological rep3

source_name: Healthy untreated mice


title: VM-CUB1 vector clone, rep3


title: mouse at T21, biological rep2


title: mouse at T7, biological rep1


title: mouse at T21, biological rep1


title: mouse at T7, biological rep3


title: mouse at T0, biological rep1


title: Outer4

city: Charlottesville

first: Leen

last: Jamal

email: lj2p@virginia.edu, ljamal@ucsd.edu

state: VA

address: 415 Lane Road, MR5-Rm. 2225

department: Biomedical Engineering

institute: University of Virginia

description: ~50 outer ECM-attached cells.

hyb_protocol: 1 μg Alexa Fluor 555-labeled cDNA (total volume, 5 μl) was mixed with 10 μl GEX hybridization buffer (Illumina). Samples were denatured at 94 °C for 4 min and then added directly to HumanRef-8 v2 Expression BeadChips (Illumina) prewarmed to 58 °C. Slides were incubated at 58 °C for 20 h and washed according to the manufacturer's recommendations.

scan_protocol: Slides were scanned on a BeadArray reader (Illumina) with a scan setting of Direct hybridization 1.

data_processing: Samples were analyzed with normalization using MatLab. Normalization was performed by dividing each sample value by the mean intensity of the sample for all genes.

label: Alexa Fluor 555

source_name: MCF10A-5E cells grown in organotypic culture, outer ECM-attached cells

label_protocol: Samples were purified on a PureLink column (Invitrogen), ethanol-precipitated and labeled with Alexa Fluor 555 amine-reactive dye (Invitrogen) according to the manufacturer's recommendations.

growth_protocol: MCF10A-5E cells diluted to 12,500 cells/ml in assay medium (DMEM/F12, 2% Horse serum, Hydrocortisone 0.5 μg/ml, Cholera toxin 100 ng/ml, Insulin 10 μg/ml, & 1% Pen/Strep) with 5 ng/ml EGF and 2% Matrigel were seeded into a well of a chamber slide coated with 100% Matrigel. Cells were refed every 4 days with assay medium containing 5 ng/ml EGF and 2% Matrigel.

extract_protocol: Day 6 acini were cut into 8 μm sections and fixed onto slides. Microdissection of 50 cells per sample was performed on a Pixcell II instrument (Arcturus) using Capsure HS LCM caps (Arcturus). Samples were eluted from the microdissection caps using digestion buffer (1.25× MMLV reverse transcriptase buffer (Invitrogen), 100 μM dNTPs (Roche), 0.08 OD ml−1 oligo(dT)24 and 250 μg ml−1 proteinase K (Sigma)) and incubated at 42 °C for 1 h. Sample processing was done by using poly(A) PCR.

treatment_protocol: Acini were allowed to grow to day 6.

value: breast epithelial cells

tag: growth stage

value: day 6 of morphogenesis

tag: acini cell type

value: outer ECM-attached cells


title: 5637 vector clone, rep2

source_name: 5638 cells, stably transfected with empty vector


title: Outer3

description: ~50 outer ECM-attached cells.


title: 5637 HOTAIR clone 4, rep1

description: gene expression data from HOTAIR overexpressing 5637 cells

source_name: 5637 cells, stably transfected with HOTAIR


title: 5637 HOTAIR clone 4, rep3

source_name: 5639 cells, stably transfected with HOTAIR


title: mouse at T0, biological rep2


title: Outer1

description: ~50 outer ECM-attached cells.


title: Outer2

description: ~50 outer ECM-attached cells.


title: 5637 HOTAIR clone 4, rep2

source_name: 5638 cells, stably transfected with HOTAIR


title: VM-CUB1 HOTAIR clone 20, rep3

description: gene expression data from HOTAIR overexpressing VM-CUB1 cells

source_name: VM-CUB1 cells, stably transfected with HOTAIR


title: mES_shApela_#2_rep3

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

hyb_protocol: Samples were hybridized to the Affymetrix Mouse Gene ST 1.0 GeneChip.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip scanner 3000.

data_processing:
Data were imported into the Partek Genomics Suite 6.6 using RMA.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: mouse ES cells, transduced with shApela #2

label_protocol: Affymetrix protocol

growth_protocol: R1E cells were grown in mESC growth medium, Knockout DMEM (KO-DMEM), 15% Fetal Bovine Serum, 100mM MEM non-essential amino acids, 0.1mM 2-mercaptoethanol, 2mM L-glutamine and 1X penicillin-streptomycin (All from Invitrogen) plus 1000 units/ml leukemia inhibitory factor (Lif, Life Technologies)

extract_protocol: RNAs were extracted using the GenElute Mammalian total RNA Miniprep kit (Sigma, Cat: RTN350-1kt).

treatment_protocol: No drug treatment


title: VM-CUB1 HOTAIR clone 20, rep2


title: mES_shApela_#2_rep2


title: VM-CUB1 vector clone, rep1


title: miR-138 group [miRNA]

description: micorRNA expression data

hyb_protocol: Hybridization was performed overnight on a Paraflo microfluidic chip using a microcirculation pump (Atactic Technologies, Houston, TX, USA).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Devices, Wokingham, West Berkshire, UK) and digitized using Array-Pro image analysis software (Media Cybernetics, Rockville, MD, USA).

data_processing:
Raw data was digitized by Array-Pro Analyzer v4.5 (Media Cybernetics, Bethesda, MD, USA). Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (locally weighted regression).
Differential detection of mRNA signals was defined as a fold difference (log2 ratio) <﹣1.50 (downregulated) or >1.50 (upregulated) with P values of <0.05.

label_protocol: A sample of total cellular RNA (2–5 µg) was size fractionated using a YM-100 Microcon centrifugal filter (GE Healthcare) and isolated small RNAs (<300 nt) were 3'-extended with a poly(A) tail using poly(A) polymerase (New England Biolabs, Peabody, NB, USA).

treatment_protocol: Cells at 70% confluence were transfected with miRNA mimics or siRNA using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s recommendations.


title: AGO2 siRNA group [miRNA]

description: micorRNA expression data

source_name: H1299_AGO2 siRNA


title: mES_shApela_#2_rep1


title: VM-CUB1 HOTAIR clone 20, rep1


title: mES_shApela_#1_rep3

source_name: mouse ES cells, transduced with shApela #1


title: Inner3

description: ~50 inner non-ECM-attached cells.

source_name: MCF10A-5E cells grown in organotypic culture, inner cells

value: inner non-ECM-attached cells


title: mES_shApela_#1_rep1


title: mES_shApela_#1_rep2


title: MCF7_NRG_24 h_rep3

status: Public on Jun 04 2015

first: Juan

middle: Carlos

last: Montero

address: Campus Miguel de Unamuno

institute: Instituto de Biología Molecular y Celular del Cáncer. CSIC-Universidad de Salamanca.

description: Expression data from MCF7 cells treated with Neuregulin (NRG) at different times

hyb_protocol: hybridizations were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA were amplified and labeled and then hybridized to Human Gene 1.0 ST oligonucleotide arrays (Affymetrix, CA, USA)

scan_protocol: Scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 645, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The data were analyzed with dCHIP software.

source_name: MCF7_NRG_24 h

label_protocol: Double-stranded cDNA and afterwards biotinylated cRNA were synthesized using a T7-polyT primer and the BioArray RNA labeling kit (Enzo, NY, USA), respectively

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10% FBS, 100 mU/ml penicillin, 100 mg/ml streptomycin and 2 mM L-glutamine, in a 95:5 air-CO2 atmosphere at 37º C. Prior to the treatment the cells were serum-starved 24 hours.

extract_protocol: RNA was extracted and purified with the PureLinkTM Micro-to-Midi kit (Invitrogen, Paisley, UK).

treatment_protocol: MCF7 cells were treated with soluble NRG 10 nM at different times

value: mammary gland, breast; derived from metastatic site:pleural effusion

value: 69 years adult

tag: disease

value: adenocarcinoma

tag: treatment

value: NRG


title: mES_shLuc_rep1

source_name: mouse ES cells, transduced with shLuc

tag: strain


title: Inner4

description: ~50 inner non-ECM-attached cells.


title: NC group [miRNA]

description: micorRNA expression data

value: Human non-small cell lung cancer cell

value: NC mimics


title: mES_shLuc_rep2


title: MCF7_NRG_6 h_rep3

source_name: MCF7_NRG_6 h

tag: time

value: 6 h


title: Inner1

description: ~50 inner non-ECM-attached cells.


title: MCF7_NRG_3 h_rep2

source_name: MCF7_NRG_3 h

value: 3 h


title: MCF7_NRG_0 h_rep3

source_name: MCF7_NRG_0 h

value: 0 h


title: MCF7_NRG_12 h_rep2

source_name: MCF7_NRG_12 h


title: MCF7_NRG_0 h_rep1


title: MCF7_NRG_6 h_rep2


title: MCF7_NRG_12 h_rep3


title: MCF7_NRG_24 h_rep1


title: MCF7_NRG_6 h_rep1


title: MCF7_NRG_3 h_rep1


title: Inner2

description: ~50 inner non-ECM-attached cells.


title: mES_shLuc_rep3


title: MCF7_NRG_3 h_rep3


title: MCF7_NRG_12 h_rep1


title: MCF7_NRG_0 h_rep2


title: MCF7_NRG_24 h_rep2


title: Plastic-Cell

city: Morgantown

first: Mary

middle: E

last: Davis

state: WV

address: 1 Medical Center Drive

institute: West Virginia University Health Sciences Center

description: P Cell

hyb_protocol: The entire reaction of fragmented and biotin-labeled cDNA (50 µL) with added hybridization controls was hybridized to the human GeneChip® 1.0 ST Exon Arrays (Affymetrix) at 45°C for 17 h in the GeneChip® Hybridization Oven 640 (Affymetrix).

scan_protocol: Phycoerythrin labeling was detected within the Affymetrix GeneChip Scanner 3000 7G plus using 532 nm light and detected by a photomultiplier tube. Expression Consol software (Affymetrix) was used to check quality controls of hybridized chips.

data_processing: The raw data were uploaded into Partek (St. Louis, MO) and raw intensity was background-subtracted, GC and robust multi-array analysis (GCRMA) normalized, and log2-transformed.

source_name: Plastic expanded cells

label_protocol: cDNA was fragmented and biotin labeled using the Gene Chip WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNAs were isolated from the pellets using Trizol (Invitrogen) followed by additional purification using an RNeasy Mini Kit (Qiagen, Valencia, CA)

tag: expansion media

value: plastic

tag: 30 d growth after expansion

value: no


title: ECM-Pellet

description: E Pellet

source_name: ECM expanded cells, pelleted then grown on chondrogenic media

value: extracellular matrix

value: yes


title: R457ST

city: MEXICO CITY

first: INGRID

last: MEDINA MARTINEZ

state: CUAUHTEMOC

address: DR. BALMIS 148

department: MEDICINA GENOMICA

country: Mexico

institute: HOSPITAL GENERAL DE MEXICO OD

description: Gene expression data from Cervical cancer biopsy

hyb_protocol: Following fragmentation, ssDNA were hybridized for 16 hr at 45C and 60 rpm on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 protocol FS450_0007

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) with GeneChip Scanner 3000

data_processing: Microarrays were normalized using the RMA algorithm (Robust Multichip Average) in the Affymetrix Expression Console. The analysis was done at Gene Level Default: RMA-Sketch

source_name: Cervical cancer biopsy

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

tag: clinic

value: Case

tag: age (years)

tag: histology

value: SCC

tag: tumor stage

value: IIIB


title: R409ST


title: R339ST


title: R411ST

description: re-analysis of GSM732095


title: R336ST

description: re-analysis of GSM732086


title: R268ST

value: IIB


title: R330ST

description: re-analysis of GSM732085


title: R489ST

description: re-analysis of GSM732100


title: R315ST


title: R455ST

value: IIA


title: R426ST


title: R324ST

description: re-analysis of GSM732084


title: R390ST

description: re-analysis of GSM732093


title: R486ST

description: re-analysis of GSM732099


title: R378ST

description: re-analysis of GSM732090


title: R230ST

description: re-analysis of GSM732076


title: R265ST

description: re-analysis of GSM732080


title: R311ST


title: ECM-Cell

description: E Cell

source_name: ECM expanded cells


title: R156ST

description: re-analysis of GSM732067


title: R412ST


title: Plastic-Pellet

description: P Pellet

source_name: Plastic expanded cells, pelleted then grown on chondrogenic media


title: R368ST

description: re-analysis of GSM732088


title: R124ST

description: re-analysis of GSM732065


title: R157ST

description: re-analysis of GSM732068

value: IVB


title: R081ST

description: re-analysis of GSM732059

value: ACC


title: R121ST

description: re-analysis of GSM732062


title: R158ST

description: re-analysis of GSM732069


title: R495ST


title: R102ST


title: R494ST

description: re-analysis of GSM732101


title: R386ST

description: re-analysis of GSM732092


title: R392ST

description: re-analysis of GSM732094


title: R189ST

description: re-analysis of GSM732071


title: R298ST

description: re-analysis of GSM732082

value: ASCC


title: R260ST


title: R221ST

description: re-analysis of GSM732075


title: R208ST

description: re-analysis of GSM732074


title: R322ST

description: re-analysis of GSM732083


title: R244ST

description: re-analysis of GSM732078


title: R194ST

description: re-analysis of GSM732072


title: R183ST

description: re-analysis of GSM732070


title: R478ST

description: re-analysis of GSM732097


title: R154ST

description: re-analysis of GSM732066


title: R198ST

description: re-analysis of GSM732073

value: IVA


title: R496ST

description: re-analysis of GSM732102


title: R075ST

description: re-analysis of GSM732057


title: R380ST

description: re-analysis of GSM732091


title: R072ST

description: re-analysis of GSM732056


title: R483ST

description: re-analysis of GSM732098


title: R240ST

description: re-analysis of GSM732077


title: CEXO-7

description: re-analysis of GSM732054

source_name: Healthy female exocervix

value: Control


title: R476ST

description: re-analysis of GSM732096


title: R035ST

description: re-analysis of GSM732055


title: R444ST


title: R369ST

description: re-analysis of GSM732089


title: R365ST

description: re-analysis of GSM732087


title: R282ST

description: re-analysis of GSM732081


title: CEXO-5

description: re-analysis of GSM732052


title: CEXO-43

description: re-analysis of GSM732050