title: KD_TAL1_HSPC_replicate2

description:
shTal1_12052010
Gene expression data from HSPC KD TAL1.
Hematopoietic immature cells.

source_name: HSPCs, TAL1 knockdown

tag: cell type

value: knockdown


title: LAE_AA-087

status: Public on Oct 23 2015

type: RNA

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

country: USA

institute: Hoffmann-LaRoche

hyb_protocol: Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.

scan_protocol: GeneChips were scanned using the GC 30007G scanner.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure.  Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release.  As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Bronchial epithelial brushing sample from AA-087 (Moderate Asthma)

label_protocol: Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).

extract_protocol: Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.

tag: age

tag: Sex

value: F

tag: disease

value: Asthma

tag: severity

value: Moderate

tag: tissue

value: Lower airway (bronchial)


title: KD_TAL1_HSPC_replicate1

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
shTal1_02102010
Gene expression data from HSPC KD TAL1.
Hematopoietic immature cells.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomic Suite.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay kit).

growth_protocol: HSPCs from cord blood were isolated using MACS and cell sorting. Cells were thereafter incubated with lentiviral vectors allowing to either increase or reduce TAL1 expression. Control cells were transduced with a GFP-encoding lentivector.

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

treatment_protocol: We have used lentiviral vector transduction of human cord blood HSPCs to overexpress (O/E) or knock down (KD) SCL/TAL1. Cells were lysed 24 hours after the end of transduction.

value: CD34+CD38-lowCD34RA-CD90+ HSPCs from cord blood

tag: tal1 expression


title: KD_TAL1_HSPC_replicate3

description:
shTal1_18032010
Gene expression data from HSPC KD TAL1.
Hematopoietic immature cells.


title: LAE_AA-067

source_name: Bronchial epithelial brushing sample from AA-067 (Moderate Asthma)

value: M


title: LAE_AA-066

source_name: Bronchial epithelial brushing sample from AA-066 (Mild Asthma)

value: Mild


title: scramble_3 days_ischemic_G23

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: sample 15 (scramble-ischemic replicate 4)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Summarized signal intensities were generated in BRB ArrayTools using justRMA

label: biotin

organism: Mus musculus

source_name: scramble_3 days_ischemic

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

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy mini kit following standard RNA cleanup protocol

treatment_protocol: In vivo down-modulation of miR-210 was carried out by tail vein injection of Locked Nucleic Acid (LNA) oligonucleotides against miR-210 (anti-miR-210) or scrambled (SCR) control sequence (In vivo LNAmicroRNA Inhibitors, Exiqon).The following 15mers LNA-enhanced sequences with complete phosphothioate backbone were used: anti-miR-210, GCTGTCACACGCACA; SCR, CGTCTAGCCACCTAG. Twelve mg/Kg of anti-miR-210 LNA or scrambled LNA were diluted in 200 µl of saline and injected in the tail vein of 2 different groups of CD1mice, 2 days before femoral artery dissection. Mice were sacrified 3 days later and gastrocnemius muscles were harvested

tag: strain

value: 2 months

tag: injected with

value: scrambled control sequence (SCR)

value: gastrocnemius


title: anti_miR-210_3 days_ischemic_G27

description: sample 19 (anti-miR-210-ischemic replicate 4)

source_name: anti_miR-210_3 days_ischemic

value: miR-210 complementary LNA-oligonucleotide (anti-miR-210)


title: anti_miR-210_3 days_ischemic_G24

description: sample 16 (anti-miR-210-ischemic replicate 1)


title: anti_miR-210_3 days_ischemic_G26

description: sample 18 (anti-miR-210-ischemic replicate 3)


title: LAE_AA-092

source_name: Bronchial epithelial brushing sample from AA-092 (Mild Asthma)


title: NS_R9

source_name: Nasal Scrape sample from R9 (group:Asthma)

value: Male

value: Nasal Scrape

tag: subtype

value: eosino


title: LAE_AA-068

source_name: Bronchial epithelial brushing sample from AA-068 (Healthy Control)

value: Control

value: Healthy


title: NS_R23

source_name: Nasal Scrape sample from R23 (group:Control)

value: Female


title: LAE_AA-096

source_name: Bronchial epithelial brushing sample from AA-096 (Mild Asthma)


title: scramble_3 days_control_G6

description: sample 6 (scramble-non ischemic replicate 3)

source_name: scramble_3 days_control


title: O/E TAL1_HSPC_replicate1

description:
pV81/TAL1_02102010
Gene expression data from HSPC O/E TAL1.
Hematopoietic immature cells.

source_name: HSPCs, TAL1 overexpression

value: overexpression


title: scramble_3 days_ischemic_G20

description: sample 12 (scramble-ischemic replicate 1)


title: LAE_AA-076

source_name: Bronchial epithelial brushing sample from AA-076 (Moderate Asthma)

value: Asthma


title: anti_miR-210_3 days_ischemic_G25

description: sample 17 (anti-miR-210-ischemic replicate 2)


title: LAE_AA-065

source_name: Bronchial epithelial brushing sample from AA-065 (Mild Asthma)


title: scramble_3 days_control_G5

description: sample 5 (scramble-non ischemic replicate 2)


title: untreated_G3

description: sample 3 (untreated replicate 3)

source_name: untreated


title: untreated_G2

description: sample 2 (untreated replicate 2)


title: LAE_AA-064

source_name: Bronchial epithelial brushing sample from AA-064 (Healthy Control)

value: F


title: untreated_G1

description: sample 1 (untreated replicate 1)


title: LAE_AA-063

source_name: Bronchial epithelial brushing sample from AA-063 (Healthy Control)

value: Lower airway (bronchial)


title: LAE_AA-059

source_name: Bronchial epithelial brushing sample from AA-059 (Healthy Control)


title: LAE_AA-062

source_name: Bronchial epithelial brushing sample from AA-062 (Healthy Control)


title: LAE_AA-057

source_name: Bronchial epithelial brushing sample from AA-057 (Healthy Control)


title: LAE_AA-058

source_name: Bronchial epithelial brushing sample from AA-058 (Severe Asthma)

value: Severe


title: Pt061A_1

type: genomic

city: Genova

first: Patrizio

last: Castagnola

state: GE

address: Largo Rosanna Benzi 10

institute: IRCCS AOU San Martino - IST

hyb_protocol: For 2x105k arrays: Hybridization mix was incubated at 37°C for 30 min, and applied to array. Hybridization was carried out for 40 hr at 65°C in a rotating hybridization oven (Agilent Technologies) at 20 rpm. For 4x180k arrays: Cy5-Labeled tumour DNA was combined with an equivalent amount of Cy3-labeled reference DNA. Repetitive sequences were blocked with human Cot-1 DNA (Invitrogen) and samples were hybridised with Oligo aCGH/ChIP-on-chip Hybridization Kit onto SurePrint G3 Human CGH Microarrays, 4x180K (Agilent) according to manufacturer’s instructions. Following hybridization at 65°C for 24 hours in a rotating hybridization oven (Agilent Technologies) at 20rpm. Microarray slides were washed according to manufacturer’s instructions

scan_protocol: For 2x105k arrays: spot fluorescence was measured by the Agilent G2565BA Scanner and images were processed by Feature Extraction software (version 9.5.3.1) (Agilent Technologies). For 4x105k arrays: slides were scanned immediately at 3 microns using the Agilent G2505C Scanner  and images were processed by Feature Extraction software v11.01.1 (Agilent Technologies).

data_processing: Log10 ratios from Agilent feature extraction files were imported in R, averaged over replicates and log2 transformed with the limma package [Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W and Smyth GK (2015). “limma powers differential expression analyses for RNA-sequencing and microarray studies.” Nucleic Acids Research, 43.]. Common probes among the two microarray designs were retained for downstream analysis, and probes mapping on chromosome Y were discarded, resulting in the 87,891 probes reported in the matrix template.

molecule: genomic DNA

source_name: Buccal mucosa

label_protocol: For 2x105k arrays: For each array, 2 μg amplified test and reference DNAs were labeled by Bioprime Labeling Kit (Invitrogen, Paisley, UK) following the manufacture's protocol. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer's protocol. Labeled DNA quality analysis and quantization were performed by NanoDrop ND-1000 Spectrophotometer and parameters that predicted successful hybridization were a specific activity of 25 to 40 and 20 to 35 for cyanine-3 and cyanine-5 labeled sample, respectively. Prior to the denaturation step at 95°C for 3 min, 50 μg Cot-1 DNA (Invitrogen) and control targets (Agilent Technologies) were added to cyanine 5- and cyanine 3-labeled DNA mixture. For 4x180k arrays: 0.8 µg of amplified test and reference (female or male normal genomic DNA: Promega, Madison,WI) were labeled by Sure Tag DNA labeling kit (Agilent Technologies) with Cy5-dUTP and Cy3-dUTP respectively according to CGH Enzymatic Labeling Kit Protocol v.7.2 (Agilent Technologies). Unicorporated nucleotides were  then removed using Centrifugal filters (Amicon Ultra 0.5ml, Millipore) according to manifacturer’s protocol. Quality analysis and quantization of labeled DNA were performed by (Nanodrop ND-1000 Spectrophotometry) measuring A260 (for DNA), A550 (for Cy5) and A649 (for Cy3) to evaluated yield, degree of labeling or specific activity: parameters that predicted successful of hybridisation.

extract_protocol: DNA was extracted using ArchivePure DNA kit (5-Prime Hamburg, Germany) with some modifications: after proteins precipitation the DNA was purified by phenol-chloroform extraction and collected by ethanol precipitation adding 20 μg of glycogen (20 mg/ml) as carrier. DNA quality and quantity were assessed by agarose gel and ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE). A pool of normal male or female DNA (Promega, Madison, WI) was used as reference DNA. A quantity of 50 ng of genomic DNAs (test and reference) was amplified by GenomePlex Whole Genome Amplification Kit (Sigma-Aldrich, St. Louis, MO) that allows to generate a representative amplification of genomic DNA. The kit uses a linker mediated primer PCR amplification technology based upon random fragmentation of genomic DNA and conversion of the resulting small fragments to PCR-amplifiable OmniPlex Library molecules flanked by universal priming sites. The OmniPlex library is then PCR amplified using universal oligonucleotide primers. After purification of PCR products by GenElute PCR Clean-Up Kit (Sigma-Aldrich), amplified DNA was quantified using the ND-1000 Spectrophotometer (Thermo Scientific).

tag: diagnosis

value: ODF

tag: patient id

tag: histology

value: Non dysplastic

value: S

value: SG

tag: gender

value: M

value: Y

tag: sorting

value: N

value: CURETTE

source_name: Commercially available normal genomic DNA, gender matched

tag: manufacturer

value: Promega


title: Pt055B_2

source_name: tongue


title: Pt067B_1

value: OSCC

value: Cancer


title: Pt055B_1

value: BIOPSY


title: Pt059A_2

value: OPML

value: NS


title: Pt062B_1


title: LAE_AA-056

source_name: Bronchial epithelial brushing sample from AA-056 (Severe Asthma)

value: F

value: Asthma


title: LAE_AA-054

source_name: Bronchial epithelial brushing sample from AA-054 (Healthy Control)

value: Control

value: Healthy

value: Lower airway (bronchial)


title: Pt055A_1

value: Non dysplastic

value: S


title: Pt049B_1

value: Dysplastic

value: SG


title: Pt053B_1

value: Y

value: N


title: Pt058A_1

source_name: other

value: M

value: Promega


title: LAE_AA-052

source_name: Bronchial epithelial brushing sample from AA-052 (Mild Asthma)

value: Mild


title: LAE_AA-055

source_name: Bronchial epithelial brushing sample from AA-055 (Moderate Asthma)

value: Moderate


title: Pt065B_1

value: OSCC

value: Cancer

value: BIOPSY


title: Pt043A_1

value: ODF

value: NS

value: F


title: Pt043A_2

value: OPML


title: Pt042A_1

value: Non dysplastic


title: LAE_AA-053

source_name: Bronchial epithelial brushing sample from AA-053 (Healthy Control)

value: Control

value: Healthy

value: Lower airway (bronchial)


title: LAE_AA-051

source_name: Bronchial epithelial brushing sample from AA-051 (Healthy Control)


title: Pt038B_2

value: ONF

value: Y

value: CURETTE


title: Pt056A_2

value: S

value: M

value: N

value: Promega


title: Pt038B_1


title: Pt038A_2

value: SG


title: Pt036B_1

value: BIOPSY


title: LAE_AA-049

source_name: Bronchial epithelial brushing sample from AA-049 (Mild Asthma)

value: Asthma

value: Mild


title: Pt035A_3

value: Dysplastic


title: Pt229B_1

value: OPML


title: LAE_AA-048

source_name: Bronchial epithelial brushing sample from AA-048 (Healthy Control)

value: F


title: Pt204B_1

value: Non dysplastic


title: scramble_3 days_control_G4

description: sample 4 (scramble-non ischemic replicate 1)

source_name: scramble_3 days_control

value: 2 months

value: scrambled control sequence (SCR)

value: gastrocnemius


title: Pt031B_1

value: NS

value: mt

value: Y


title: Pt213B_1

value: CURETTE


title: Pt035A_1

value: ODF

value: S

value: M

value: N


title: Pt051A_2

value: SG

value: Promega


title: Pt029A_2

value: BIOPSY


title: Pt033B_1

value: OPML


title: Pt035A_2

value: Dysplastic


title: Pt252B_1

value: Non dysplastic


title: Pt186B_1

value: F*


title: Pt027B_2

value: OSCC

value: Cancer

value: F


title: Pt244B_1


title: Pt061A_2


title: LAE_AA-045

source_name: Bronchial epithelial brushing sample from AA-045 (Healthy Control)

value: Control

value: Healthy

value: Lower airway (bronchial)


title: Pt027B_5

value: Y

value: CURETTE


title: Pt214B_1

value: S

value: M


title: Pt206B_1

value: mt

value: N


title: Pt027B_3

value: SG

value: Promega


title: Pt029A_1

value: ODF

value: BIOPSY


title: Pt225B_1

value: NS


title: Pt024B_2

value: OPML

value: Dysplastic


title: LAE_AA-047

source_name: Bronchial epithelial brushing sample from AA-047 (Healthy Control)


title: Pt026B_1

value: OSCC

value: Cancer


title: Pt159B_1

value: F


title: LAE_AA-046

source_name: Bronchial epithelial brushing sample from AA-046 (Healthy Control)

value: Control

value: Healthy

value: Lower airway (bronchial)


title: LAE_AA-043

source_name: Bronchial epithelial brushing sample from AA-043 (Healthy Control)


title: LAE_AA-044

source_name: Bronchial epithelial brushing sample from AA-044 (Mild Asthma)

value: Asthma

value: Mild


title: Pt022B_3

source_name: Buccal mucosa

value: mt

value: Y

source_name: Commercially available normal genomic DNA, gender matched


title: LAE_AA-042

source_name: Bronchial epithelial brushing sample from AA-042 (Moderate Asthma)

value: Moderate


title: Pt022C_1

source_name: tongue

value: Non dysplastic

value: S

value: SG

value: CURETTE

value: Promega


title: Pt027B_1

value: N


title: Pt024B_1

value: ODF

value: NS


title: Pt026B_2

value: OSCC

value: Cancer

value: M


title: LAE_AA-041

source_name: Bronchial epithelial brushing sample from AA-041 (Moderate Asthma)

value: Lower airway (bronchial)


title: Pt022B_2

value: OPML

value: Dysplastic

value: F


title: Pt022B_1

value: mt

value: Y


title: LAE_AA-040

source_name: Bronchial epithelial brushing sample from AA-040 (Healthy Control)

value: Control

value: Healthy


title: LAE_AA-038

source_name: Bronchial epithelial brushing sample from AA-038 (Mild Asthma)

value: Asthma

value: Mild


title: LAE_AA-039

source_name: Bronchial epithelial brushing sample from AA-039 (Healthy Control)


title: Pt021A_1

value: Non dysplastic

value: S

value: SG

value: BIOPSY

value: Promega


title: Pt014A_2

value: N


title: Pt205B_1

value: M


title: Pt014A_1

value: ODF


title: Pt195B_1

source_name: other

value: OPML

value: NS

value: CURETTE


title: LAE_AA-035

source_name: Bronchial epithelial brushing sample from AA-035 (Healthy Control)

value: F

value: Lower airway (bronchial)


title: Pt017B_2

value: ONF

value: mt

value: Y


title: Pt013B_1

value: OSCC

value: Cancer


title: LAE_AA-037

source_name: Bronchial epithelial brushing sample from AA-037 (Healthy Control)

value: Control

value: Healthy


title: Pt84B_1

value: S

value: SG


title: Pt150B_1

value: N

value: BIOPSY

value: Promega


title: LAE_AA-034

source_name: Bronchial epithelial brushing sample from AA-034 (Mild Asthma)

value: M

value: Asthma

value: Mild


title: Pt013A_1

value: ODF

value: Non dysplastic

value: NS


title: Pt39B_1

value: OVC


title: Pt013C_1

value: OPML

value: Y


title: Pt021A_2

value: F


title: Pt012A_2

value: Dysplastic


title: Pt37B_1

value: Cancer

value: CURETTE


title: Pt012A_1

value: S


title: Pt190B_1

value: SG

value: N


title: LAE_AA-032

source_name: Bronchial epithelial brushing sample from AA-032 (Healthy Control)

value: Control

value: Healthy

value: Lower airway (bronchial)


title: Pt012B_1

value: M

value: Promega


title: Pt017A_2

value: Non dysplastic

value: BIOPSY


title: Pt008B_1

value: OVC

value: NS


title: Pt008A_1

value: ODF

value: Y


title: Pt008A_2

value: OPML

value: Dysplastic

value: F


title: LAE_AA-030

source_name: Bronchial epithelial brushing sample from AA-030 (Healthy Control)


title: Pt006B_2

value: OSCC

value: Cancer

value: S


title: Pt004B_2

value: SG


title: Pt71A_1

value: N

value: CURETTE


title: LAE_AA-029

source_name: Bronchial epithelial brushing sample from AA-029 (Mild Asthma)

value: Asthma

value: Mild

value: Lower airway (bronchial)


title: LAE_AA-028

source_name: Bronchial epithelial brushing sample from AA-028 (Mild Asthma)


title: Pt002B_3

value: BIOPSY

value: Promega


title: Pt003B_1

value: OVC

value: NS


title: Pt48A_1

value: Non dysplastic

value: M

value: Y


title: Pt002C_1

value: OPML

value: F


title: Pt69B_1

value: Cancer


title: LAE_AA-031

source_name: Bronchial epithelial brushing sample from AA-031 (Healthy Control)

value: Control

value: Healthy


title: Pt70A_1

value: SG

value: N


title: LAE_AA-025

source_name: Bronchial epithelial brushing sample from AA-025 (Mild Asthma)

value: Asthma


title: Pt002B_1

source_name: Commercially available normal genomic DNA, gender matched


title: Pt002B_2


title: Pt92A_1


title: Pt004B_1

value: Dysplastic


title: Pt001B_2

value: OSCC

value: S


title: LAE_AA-026

source_name: Bronchial epithelial brushing sample from AA-026 (Mild Asthma)

value: Mild

value: Lower airway (bronchial)


title: Pt65A_1

source_name: tongue

value: CURETTE

value: Promega


title: LAE_AA-024

source_name: Bronchial epithelial brushing sample from AA-024 (Moderate Asthma)

value: M

value: Moderate


title: Pt112B_2

source_name: Buccal mucosa

value: OPML

value: Non dysplastic

value: NS

value: Y


title: Pt112B_1

value: F


title: Pt18A_1

value: SG

value: BIOPSY


title: Pt46A_1

value: N


title: Pt094B_2

value: ODF


title: LAE_AA-023

source_name: Bronchial epithelial brushing sample from AA-023 (Moderate Asthma)

value: Asthma


title: Pt094B_1

value: OSCC

value: Cancer


title: Pt084A_2

value: mt


title: LAE_AA-021

source_name: Bronchial epithelial brushing sample from AA-021 (Mild Asthma)

value: Mild

value: Lower airway (bronchial)


title: Pt077A_2

value: S

value: M

value: CURETTE

value: Promega


title: Pt4A_1

value: OPML

value: Non dysplastic


title: Pt135B_1

source_name: other

value: NS

value: F

value: Y


title: LAE_AA-022

source_name: Bronchial epithelial brushing sample from AA-022 (Mild Asthma)


title: Pt084A_1

value: N


title: LAE_AA-018

source_name: Bronchial epithelial brushing sample from AA-018 (Severe Asthma)

value: Severe


title: Pt077A_3


title: LAE_AA-020

source_name: Bronchial epithelial brushing sample from AA-020 (Mild Asthma)

value: Asthma


title: Pt076A_2

value: SG

value: BIOPSY


title: Pt076A_3


title: Pt001B_1

value: OSCC

value: Cancer


title: LAE_AA-017

source_name: Bronchial epithelial brushing sample from AA-017 (Moderate Asthma)

value: Moderate

value: Lower airway (bronchial)


title: Pt134B_1


title: Pt66B_1


title: Pt074B_4

value: Dysplastic

value: S

value: M


title: LAE_AA-016

source_name: Bronchial epithelial brushing sample from AA-016 (Healthy Control)

value: Control

value: Healthy


title: Pt086B_2

value: ODF

value: Non dysplastic

value: CURETTE

value: Promega


title: Pt077A_1

value: OPML

value: Y

value: N


title: Pt80B_1

value: F


title: Pt074B_1

value: SG


title: Pt220B_1

value: NS

value: BIOPSY


title: Pt068A_1


title: Pt208B_1


title: Pt201B_1


title: LAE_AA-009

source_name: Bronchial epithelial brushing sample from AA-009 (Healthy Control)

value: Lower airway (bronchial)


title: LAE_AA-012

source_name: Bronchial epithelial brushing sample from AA-012 (Severe Asthma)

value: Asthma

value: Severe


title: Pt108B_4

value: OSCC

value: Cancer


title: Pt111B_2

value: Dysplastic


title: Pt111B_1


title: LAE_AA-005

source_name: Bronchial epithelial brushing sample from AA-005 (Healthy Control)

value: M

value: Control

value: Healthy


title: LAE_AA-010

source_name: Bronchial epithelial brushing sample from AA-010 (Healthy Control)


title: LAE_AA-004

source_name: Bronchial epithelial brushing sample from AA-004 (Mild Asthma)

value: Mild


title: LAE_AA-006

source_name: Bronchial epithelial brushing sample from AA-006 (Healthy Control)


title: Pt111B_3

source_name: tongue

value: ODF

value: Non dysplastic

value: CURETTE

source_name: Commercially available normal genomic DNA, gender matched

value: Promega


title: LAE_AA-008

source_name: Bronchial epithelial brushing sample from AA-008 (Mild Asthma)


title: LAE_AA-014

source_name: Bronchial epithelial brushing sample from AA-014 (Severe Asthma)

value: F


title: Pt074A_1

value: OPML

value: NS

value: Y

value: N


title: Pt108B_2

value: SG

value: BIOPSY


title: LAE_AA-013

source_name: Bronchial epithelial brushing sample from AA-013 (Mild Asthma)

value: Asthma

value: Lower airway (bronchial)


title: LAE_AA-003

source_name: Bronchial epithelial brushing sample from AA-003 (Moderate Asthma)

value: M

value: Moderate


title: Pt108B_1

value: OSCC

value: Cancer


title: Pt090B_3

value: ODF


title: LAE_AA-007

source_name: Bronchial epithelial brushing sample from AA-007 (Healthy Control)

value: Control

value: Healthy


title: Pt108B_3

value: CURETTE

value: Promega


title: Pt108B_5

value: Non dysplastic

value: F


title: Pt090B_2

value: NS

value: Y


title: Pt082B_2

value: OPML

value: SG

value: N


title: LAE_AA-015

source_name: Bronchial epithelial brushing sample from AA-015 (Healthy Control)

value: Lower airway (bronchial)


title: LAE_AA-002

source_name: Bronchial epithelial brushing sample from AA-002 (Mild Asthma)

value: M

value: Asthma

value: Mild


title: Pt081B_3

value: S


title: Pt081B_2


title: NS_AA-095

source_name: Nasal epithelial brushing sample from AA-095 (Moderate Asthma)

value: Moderate

value: Upper airway (Nasal)


title: NS_AA-088

source_name: Nasal epithelial brushing sample from AA-088 (Moderate Asthma)


title: NS_AA-087

source_name: Nasal epithelial brushing sample from AA-087 (Moderate Asthma)


title: NS_AA-096

source_name: Nasal epithelial brushing sample from AA-096 (Mild Asthma)


title: PCBM1655, Passage 3, Technical Replicate 2

city: Silver Spring

first: Raj

middle: K

last: Puri

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

hyb_protocol: Hyper5 and Cy3 labeled samples were mixed and hybridized on he Maui hybridization system for 16 hours at 42C

scan_protocol: Microarray slides were scanned using the 4000B GenePix Axon Scanner.  PMT voltages of both channels were adjusted such that their intensity histograms overlap.

data_processing: LOESS/Linear normalization was performed using ArrayTrack software (FDA) with no background subtraction

source_name: MSC Bone Marrow Derived

label_protocol: Individual RNA material was labeled with Hyper5 and reference material (P3star or P3*) was labeled with Cy3.  5 micrograms RNA used as starting material. See manuscript for more detailed description

growth_protocol: MSCs were grown in alpha minimum essential media with 10% FBS, 1% L-gluatmine & 1% penicillin G and streptomycin under humidified atmosphere of 5% CO2 at 37C

extract_protocol: Total RNA was extracted by the Qiagen Rneasy Mini kit

treatment_protocol: MSCs were passaged after reaching 80% confluency as determined by one sole cell biologist

tag: donor id

value: FEMALE

value: human multipotent stromal cells (MSCs) derived from bone marrow

source_name: Reference Material (P3star): created from equal portions of total RNA from the 6 donors at passage 3

tag: sample type

value: Pooled reference Sample

tag: rna source

value: equal portions of total RNA from 6 donors (PCBM1641 P3, PCBM1632 P3, PCBM1662 P3, 8F3560 P3, 167696 P3, 110877 P3).


title: PCBM1655, Passage 3, Technical Replicate 1

tag: cell type


title: NS_AA-094

source_name: Nasal epithelial brushing sample from AA-094 (Moderate Asthma)

tag: age

tag: Sex

value: F

tag: disease


title: PCBM1655, Passage 3, Technical Replicate 3


title: NS_AA-089

source_name: Nasal epithelial brushing sample from AA-089 (Moderate Asthma)

tag: severity

tag: tissue


title: NS_AA-092

source_name: Nasal epithelial brushing sample from AA-092 (Mild Asthma)


title: 127756, Passage 5, Technical Replicate 2

value: MALE


title: Pt078B_3

source_name: tongue

value: OSCC

value: Cancer

value: Y

value: CURETTE

source_name: Commercially available normal genomic DNA, gender matched

value: Promega


title: NS_AA-090

source_name: Nasal epithelial brushing sample from AA-090 (Moderate Asthma)

value: M


title: NS_AA-093

source_name: Nasal epithelial brushing sample from AA-093 (Moderate Asthma)

value: Asthma


title: Pt192B_1

source_name: Buccal mucosa

value: N

value: BIOPSY


title: Pt082B_1

value: OPML

value: Non dysplastic

value: NS

value: SG


title: Pt078B_2

value: S


title: 127756, Passage 5, Technical Replicate 3

value: human multipotent stromal cells (MSCs) derived from bone marrow

value: Pooled reference Sample

value: equal portions of total RNA from 6 donors (PCBM1641 P3, PCBM1632 P3, PCBM1662 P3, 8F3560 P3, 167696 P3, 110877 P3).


title: Pt077B_3

value: F


title: Pt078B_4

value: ODF


title: Pt077B_1

value: Dysplastic

value: Y


title: NS_AA-086

source_name: Nasal epithelial brushing sample from AA-086 (Moderate Asthma)

value: Moderate

value: Upper airway (Nasal)


title: Pt076A_1

value: CURETTE

value: Promega


title: Pt081B_1

value: M

value: N

value: BIOPSY


title: Pt077B_2

value: OPML

value: NS


title: 127756, Passage 5, Technical Replicate 1

value: MALE


title: 127756, Passage 3, Technical Replicate 3

value: human multipotent stromal cells (MSCs) derived from bone marrow


title: Pt075B_6

value: Non dysplastic

value: SG


title: 127756, Passage 3, Technical Replicate 2

value: Pooled reference Sample

value: equal portions of total RNA from 6 donors (PCBM1641 P3, PCBM1632 P3, PCBM1662 P3, 8F3560 P3, 167696 P3, 110877 P3).


title: 127756, Passage 3, Technical Replicate 1


title: NS_AA-082

source_name: Nasal epithelial brushing sample from AA-082 (Mild Asthma)

value: Asthma

value: Mild


title: NS_AA-083

source_name: Nasal epithelial brushing sample from AA-083 (Mild Asthma)


title: Pt075B_1

value: OSCC

value: Cancer

value: Y


title: Pt075B_2

value: Promega


title: NS_AA-058

source_name: Nasal epithelial brushing sample from AA-058 (Severe Asthma)

value: F

value: Severe

value: Upper airway (Nasal)


title: NS_AA-077

source_name: Nasal epithelial brushing sample from AA-077 (Moderate Asthma)

value: M

value: Moderate


title: Pt068B_2

value: OVC

value: S

value: N

value: CURETTE


title: NS_AA-059

source_name: Nasal epithelial brushing sample from AA-059 (Healthy Control)

value: Control

value: Healthy


title: Pt056B_1

value: NS

value: SG

value: BIOPSY


title: NS_AA-084

source_name: Nasal epithelial brushing sample from AA-084 (Mild Asthma)

value: Asthma

value: Mild


title: Pt075B_4

value: OPML

value: Non dysplastic

value: Y

value: Promega


title: Pt059B_1

value: M

value: M*


title: NS_AA-054

source_name: Nasal epithelial brushing sample from AA-054 (Healthy Control)

value: F

value: Upper airway (Nasal)


title: NS_AA-057

source_name: Nasal epithelial brushing sample from AA-057 (Healthy Control)


title: NS_AA-065

source_name: Nasal epithelial brushing sample from AA-065 (Mild Asthma)


title: NS_AA-064

source_name: Nasal epithelial brushing sample from AA-064 (Healthy Control)


title: NS_AA-074

source_name: Nasal epithelial brushing sample from AA-074 (Mild Asthma)


title: Pt068B_1

source_name: tongue

value: OVC

value: Cancer

value: S

value: N


title: NS_AA-055

source_name: Nasal epithelial brushing sample from AA-055 (Moderate Asthma)

value: Moderate


title: Pt034B_1

value: NS

value: CURETTE

source_name: Commercially available normal genomic DNA, gender matched


title: Pt023B_2

value: SG


title: Pt075B_5


title: Pt023B_3

value: ODF


title: Pt075B_3

value: OSCC

value: BIOPSY


title: NS_AA-056

source_name: Nasal epithelial brushing sample from AA-056 (Severe Asthma)

value: Asthma

value: Severe


title: LAE_AA-019

source_name: Bronchial epithelial brushing sample from AA-019 (Moderate Asthma)

value: Lower airway (bronchial)


title: NS_AA-052

source_name: Nasal epithelial brushing sample from AA-052 (Mild Asthma)

value: M

value: Mild


title: yeast_untreated_240min_rep1

city: Northfield

first: Darlene

middle: M

last: Olsen

state: VT

address: 158 Harmon Drive

department: Mathematics

institute: Norwich University

description: Gene expression data from 2% isopropanol exposure (4 h)

hyb_protocol: Fragmented cRNA was hybridized to Yeast 2.0 GeneChips (Affymetrix) and subsequently stained with streptavidin-phycoerytherin and biotinylated anti-phycoerytherin antibody.

scan_protocol: GeneChips were scanned in a high resolution GS3000 scanner.

data_processing: The robust multi-array analysis (RMA) normalization method was used to preprocess the probe level data using the AffyPLM R/Bioconductor package.

organism: Saccharomyces cerevisiae

source_name: Saturated S. cerevisiae cultures, non-fermentable media

label_protocol: cRNA was prepared using an Enzo bioarray kit and fragmented using the hammerhead cleavage reaction (Tighe et al., J Vis Exp, 2011).

growth_protocol: Cultures of BY4741 yeast were grown in non-fermentable YPGE media at 30°C to saturation.

extract_protocol: Total RNA was isolated from S. cerevisiae using RNeasy Mini Kits (Qiagen) per manufacturer’s instructions.

treatment_protocol: Treated for 1, 2, or 4 hours with 2% isopropanol or 0.05mM TFM.

tag: agent

value: 2% isopropanol

tag: time point

tag: strain


title: NS_AA-047

source_name: Nasal epithelial brushing sample from AA-047 (Healthy Control)

value: Control

value: Healthy

value: Upper airway (Nasal)


title: yeast_untreated_60min_rep1

description: Gene expression data from 2% isopropanol exposure (1 h)


title: Donor172_IVD1_AF

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

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

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G scanner.

data_processing: R/Bioconductor gcrma preprocessing using remapped probesets (CDF:HGU133Plus2_Hs_ENTREZG, version 16.0.0). Batch correction via combat in the bioconductor sva package. Statistical analysis using limma package.

source_name: Isolated cells

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

extract_protocol: Cells were lysed in TRI Reagent (Molecular Research Center, Cincinnati, OH) and RNA was isolated using a modified TriSpin method. Bromo-chloro-propane was added to the lysate, phases were separated, and ethanol added to the aqueous phase. Total RNA was extracted using the SV Total RNA Isolation System (Promega), which includes an on-column DNAse digestion, and eluted in RNase-free water.

treatment_protocol: Intervertebral disc tissue was harvested from spinal segments from levels T12-L1 to L4-L5; NP and AF regions were dissected and separated. Cells were isolated from the tissues using sequential pronase and type II collagenase digestion.

tag: individual

value: donor 172

tag: thompson grade

value: III

value: Annulus fibrosus

tag: batch


title: yeast_untreated_60min_rep2


title: Donor172_IVD1_NP

value: Nucleus pulposus


title: NS_AA-051

source_name: Nasal epithelial brushing sample from AA-051 (Healthy Control)

value: F


title: Pt023B_1

tag: diagnosis

value: OPML

tag: patient id

tag: histology

value: Non dysplastic

value: NS

value: SG

tag: gender

value: Y

tag: sorting

value: N

value: Promega


title: Donor246_IVD1_NP

value: donor 246

value: I-II


title: yeast_untreated_120min_rep1

description: Gene expression data from 2% isopropanol exposure (2 h)

value: 2% isopropanol


title: Donor136_IVD1_AF

value: donor 136


title: yeast_untreated_240min_rep2


title: Donor246_IVD1_AF


title: yeast_TFM_treated_240min_rep1

description: Gene expression data from TFM exposure (4 h)

value: 0.05mM TFM


title: NS_AA-044

source_name: Nasal epithelial brushing sample from AA-044 (Mild Asthma)

value: M

value: Asthma

value: Mild

value: Upper airway (Nasal)


title: Donor106_IVD1_AF

value: donor 106

value: IV

value: Annulus fibrosus


title: yeast_TFM_treated_240min_rep2


title: NS_AA-046

source_name: Nasal epithelial brushing sample from AA-046 (Healthy Control)

value: F

value: Control

value: Healthy


title: NS_AA-042

source_name: Nasal epithelial brushing sample from AA-042 (Moderate Asthma)

value: Moderate


title: Donor100_IVD1_AF

value: donor 100

value: III


title: Donor147_IVD1_NP

value: donor 147

value: I

value: Nucleus pulposus


title: Donor136_IVD1_NP

value: donor 136


title: NS_AA-043

source_name: Nasal epithelial brushing sample from AA-043 (Healthy Control)


title: Donor106_IVD1_NP


title: Donor81_IVD1_AF

value: donor 81


title: yeast_TFM_treated_120min_rep1

description: Gene expression data from TFM exposure (2 h)

value: 0.05mM TFM


title: yeast_TFM_treated_120min_rep2


title: Donor11_IVD1_NP

value: donor 11


title: yeast_TFM_treated_60min_rep2

description: Gene expression data from TFM exposure (1 h)


title: Donor11_IVD1_AF


title: NS_AA-041

source_name: Nasal epithelial brushing sample from AA-041 (Moderate Asthma)

value: M

value: Asthma

value: Upper airway (Nasal)


title: Donor70_IVD1_NP

value: donor 70

value: I-II


title: Donor81_IVD1_NP


title: yeast_untreated_0min_rep2

description: Gene expression data from 2% isopropanol exposure

value: 2% isopropanol


title: Donor70_IVD1_AF

value: Annulus fibrosus


title: NS_AA-040

source_name: Nasal epithelial brushing sample from AA-040 (Healthy Control)

value: F

value: Control

value: Healthy


title: yeast_untreated_0min_rep1


title: Donor8_IVD1_NP

value: donor 8

value: II


title: Donor8_IVD1_AF


title: NS_AA-037

source_name: Nasal epithelial brushing sample from AA-037 (Healthy Control)


title: yeast_TFM_treated_60min_rep1


title: Donor147_IVD1_AF

value: donor 147

value: I


title: Donor6_IVD2_NP

value: donor 6

value: Nucleus pulposus


title: Donor7_IVD1_NP

value: donor 7

value: V


title: NS_AA-035

source_name: Nasal epithelial brushing sample from AA-035 (Healthy Control)


title: Donor9_IVD1_AF

value: donor 9


title: Donor7_IVD1_AF


title: NS_AA-045

source_name: Nasal epithelial brushing sample from AA-045 (Healthy Control)

value: Upper airway (Nasal)


title: NS_AA-038

source_name: Nasal epithelial brushing sample from AA-038 (Mild Asthma)

value: M

value: Asthma

value: Mild


title: Donor100_IVD1_NP

value: donor 100

value: III


title: NS_AA-039

source_name: Nasal epithelial brushing sample from AA-039 (Healthy Control)

value: F

value: Control


title: Donor6_IVD1_AF

value: Annulus fibrosus


title: Donor6_IVD1_NP


title: NS_AA-032

source_name: Nasal epithelial brushing sample from AA-032 (Healthy Control)

value: Healthy


title: NS_AA-031

source_name: Nasal epithelial brushing sample from AA-031 (Healthy Control)


title: Donor9_IVD1_NP


title: Donor5_IVD1_NP

value: donor 5


title: Donor5_IVD2_AF

value: IV


title: Donor6_IVD2_AF

value: donor 6

value: II


title: Donor4_IVD2_AF

value: donor 4


title: Donor4_IVD1_NP

value: Nucleus pulposus


title: NS_AA-029

source_name: Nasal epithelial brushing sample from AA-029 (Mild Asthma)


title: Donor5_IVD1_AF


title: NS_AA-034

source_name: Nasal epithelial brushing sample from AA-034 (Mild Asthma)


title: NS_AA-028

source_name: Nasal epithelial brushing sample from AA-028 (Mild Asthma)


title: Donor5_IVD2_NP

source_name: Isolated cells


title: Donor3_IVD2_NP

value: donor 3

value: V


title: Donor4_IVD2_NP


title: Donor3_IVD2_AF


title: Donor4_IVD1_AF


title: NS_AA-025

source_name: Nasal epithelial brushing sample from AA-025 (Mild Asthma)

value: Upper airway (Nasal)


title: Donor3_IVD1_NP


title: NS_AA-024

source_name: Nasal epithelial brushing sample from AA-024 (Moderate Asthma)

value: M

value: Asthma

value: Moderate


title: Donor2_IVD2_AF

value: donor 2


title: Donor2_IVD1_NP

value: III


title: NS_AA-022

source_name: Nasal epithelial brushing sample from AA-022 (Mild Asthma)

value: F

value: Mild


title: Donor2_IVD2_NP


title: Donor2_IVD1_AF

value: Annulus fibrosus


title: NS_AA-026

source_name: Nasal epithelial brushing sample from AA-026 (Mild Asthma)


title: Donor3_IVD1_AF


title: Donor1_IVD2_NP

value: donor 1


title: NS_AA-021

source_name: Nasal epithelial brushing sample from AA-021 (Mild Asthma)


title: NS_AA-023

source_name: Nasal epithelial brushing sample from AA-023 (Moderate Asthma)


title: NS_AA-020

source_name: Nasal epithelial brushing sample from AA-020 (Mild Asthma)


title: Tobacco(WT)_salt_rep3

city: Lanzhou

first: Yulan

last: Shi

address: Donggang road 320#

country: China

institute: Cold and Arid Regions Environmental and Engineering Research Institution

description: Gene expression in wild-type tobaccos under salt stress condtion

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

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

organism: Nicotiana benthamiana

source_name: wild-type tobacco, salt stress condition, replication 3

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

growth_protocol: WT and transgenic tobacco seeds were sown in soil (30% peat, 70% tuff), and grown at 25℃ under 16 h light/8 h dark.

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

treatment_protocol: Two-week-old seedlings of L2 and WT tobaccos were treated with 200 mM NaCl for 6 h. Leaves from three independent plants of each sample were collected and stored in liquid N2 immediately.

tag: genotype/variation

value: wild-type

tag: condition

value: salt stress condition

value: leaf

value: two weeks old


title: NS_AA-019

source_name: Nasal epithelial brushing sample from AA-019 (Moderate Asthma)

tag: age

tag: Sex


title: Tobacco(L2)_salt_rep3

description: Gene expression in transgenic tobaccos under salt stress condtion

source_name: transgenic tobacco, salt stress condition, replication 3

value: CbFAD3 transgenic


title: Tobacco(L2)_salt_rep2

source_name: transgenic tobacco, salt stress condition, replication 2


title: Tobacco(L2)_salt_rep1

source_name: transgenic tobacco, salt stress condition, replication 1


title: Tobacco(WT)_salt_rep2

source_name: wild-type tobacco, salt stress condition, replication 2


title: Tobacco(WT)_salt_rep1

source_name: wild-type tobacco, salt stress condition, replication 1


title: Donor1_IVD2_AF

value: IV


title: NS_AA-014

source_name: Nasal epithelial brushing sample from AA-014 (Severe Asthma)

tag: disease

tag: severity

value: Severe


title: Donor1_IVD1_NP

tag: tissue

value: Nucleus pulposus


title: NS_AA-018

source_name: Nasal epithelial brushing sample from AA-018 (Severe Asthma)

value: Upper airway (Nasal)


title: Donor1_IVD1_AF

source_name: Isolated cells


title: Tobacco(L2)_normal_rep1

description: Gene expression in transgenic tobaccos under normal condtion

source_name: transgenic tobacco, normal condition, replication 1

value: normal condition


title: NS_AA-010

source_name: Nasal epithelial brushing sample from AA-010 (Healthy Control)

value: M

value: Control

value: Healthy


title: Tobacco(L2)_normal_rep2

source_name: transgenic tobacco, normal condition, replication 2


title: Tobacco(WT)_normal_rep3

description: Gene expression in wild-type tobaccos under normal condtion

source_name: wild-type tobacco, normal condition, replication 3


title: NS_AA-009

source_name: Nasal epithelial brushing sample from AA-009 (Healthy Control)


title: NS_AA-004

source_name: Nasal epithelial brushing sample from AA-004 (Mild Asthma)

value: Asthma


title: ETOH_Liver_6h_rep3

city: Philadelphia

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1020 Locust St

department: Pathology

institute: Thomas Jefferson University

description: ChIP-chip Regenerating rat liver, 6h, NFkB

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

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

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

organism: Rattus norvegicus

source_name: NF-kB ChIP DNA from rattus norvegicus regenerating liver at 0h post PHx, biological replicate 1_ethanol_diet

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: 5x10E^6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

tag: diet

value: Ethanol

tag: genotype

value: Wild-type

value: Male

value: liver

value: Sprague Dawley

value: 8-10 weeks

tag: weight

tag: liver lobe

value: Right median, right lateral, and caudate lobe

tag: chip antibody

value: NF-κB antibody (Cat#ab7970, Rabbit polyclonal NF-κB p65 antibody and negative control IgG antibody from Abcam Inc, Cambridge, MA)

source_name: Input DNA from rattus norvegicus regenerating liver at 0h post PHx, biological replicate 1_ethanol_diet

value: none, input DNA


title: ETOH_Liver_1h_rep2

description: ChIP-chip Regenerating rat liver, 1h, NFkB

tag: strain


title: NS_AA-003

source_name: Nasal epithelial brushing sample from AA-003 (Moderate Asthma)

value: Moderate


title: ETOH_Liver_6h_rep1


title: ETOH_Liver_1h_rep3


title: NS_AA-012

source_name: Nasal epithelial brushing sample from AA-012 (Severe Asthma)

value: F

value: Severe


title: Tobacco(WT)_normal_rep2

source_name: wild-type tobacco, normal condition, replication 2

value: wild-type

value: normal condition

value: leaf

value: two weeks old


title: ALCL - sample 27

status: Public on Oct 22 2015

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

hyb_protocol: Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.

scan_protocol: Scanning was performed according to the Affymetrix protocol.

data_processing: Normalization was performed with the robust multiarray average procedure using the appropriate functions in the affy package for Bioconductor (http://bioconductor.org).

source_name: Human peripheral blood T cells

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

growth_protocol: not applicable

extract_protocol: According to what described for: GSE6338, GSE14879, GSE19069; in other cases, total RNA from cryopreserved samples were extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s protocols and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA), before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA.

treatment_protocol: According to what described for: GSE6338, GSE14879, GSE19069; in other cases, the cryopreserved tissues obtained at the time of diagnosis had been stored in liquid nitrogen or -80 degree C before total RNA extraction.

tag: cell type

value: peripheral blood T cells

tag: sample origin

value: Naples

tag: original name

tag: alk positivity

value: neg


title: wt:Iglambda-rep

city: Yokohama

first: Hisaaki

last: Shinohara

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

description: sorted Ig-lambda positive bone marrow B cell

hyb_protocol: Affymetrix standard procedures

scan_protocol: using GeneChip Scanner 3000

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.

source_name: bone marrow B cell

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

growth_protocol: Ig-lambda/kappa positive bone marrow B cells were sorted on a FACSAria (BD Biosciences ).

extract_protocol: TotalRNA was purified using the Qiagen RNeasy mini kit.

treatment_protocol: no treatment

tag: gender

value: mix

tag: developmental stage

value: 8-12 weeks

tag: genetic modification


title: ETOH_Liver_6h_rep4

value: Ethanol

value: Wild-type

value: Male

value: liver

value: Sprague Dawley

tag: age


title: Tobacco(L2)_normal_rep3

source_name: transgenic tobacco, normal condition, replication 3

tag: genotype/variation

value: CbFAD3 transgenic

tag: condition


title: ALCL - sample 26

value: University Hospitals Leuven


title: ETOH_Liver_0h_rep1

description: ChIP-chip Regenerating rat liver, 0h, NFkB

tag: tissue

value: 8-10 weeks

value: Left lateral and median lobe

value: NF-κB antibody (Cat#ab7970, Rabbit polyclonal NF-κB p65 antibody and negative control IgG antibody from Abcam Inc, Cambridge, MA)

value: none, input DNA


title: CHO_Liver_6h_rep4

source_name: NF-kB ChIP DNA from rattus norvegicus regenerating liver at 0h post PHx, biological replicate 1_carbohydrate_diet

tag: diet

value: Carbohydrate

value: Right median, right lateral, and caudate lobe

source_name: Input DNA from rattus norvegicus regenerating liver at 0h post PHx, biological replicate 1_carbohydrate_diet


title: ETOH_Liver_0h_rep3

tag: genotype


title: tak:Igkappa

description: sorted Ig-kappa positive bone marrow B cell


title: ALCL - sample 23

value: peripheral blood T cells

value: pos


title: CHO_Liver_6h_rep3

tag: weight


title: wt:Igkappa

value: mix

value: sorted Ig-kappa positive bone marrow B cell


title: wt:Iglambda

value: 8-12 weeks

value: sorted Ig-lambda positive bone marrow B cell


title: wt:Igkappa-rep


title: ALCL - sample 22

value: University of Wuerzburg, Germany

value: neg


title: 2640_T3 1ug/ml 4-hydroxytamoxifen

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had a RMA expression value greater than the mean of the negative control probesets, 18,494 probesets were considered expressed.  Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available MeV package ( http://www.tm4.org/mev/).

source_name: Adult lung fibroblasts

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

growth_protocol: Mouse lung was digested into single cell suspension and lung fibroblast was enriched and grown on tissue culture plate in DMEMF12/10%FCS.  Primary fibroblasts were passaged no more than 3 times before discarded.

extract_protocol: RNA was extracted using Rneasy mini kit (Qiagene)

treatment_protocol: Freshly isolated fibroblasts were split into triplicate wells and treated with vehicle or 4OHT for 48 hours before RNA was isolated.

value: lung

value: 2640 UBCCreERT/RSmoM2

value: mixed

value: Adult

tag: treatment

value: treated with 4OHT x48hrs


title: tak:Igkappa-rep


title: ALCL - sample 25

value: University Hospitals Leuven


title: Tobacco(WT)_normal_rep1

source_name: wild-type tobacco, normal condition, replication 1

value: wild-type

value: normal condition

value: leaf

value: two weeks old


title: ALCL - sample 24

value: peripheral blood T cells

value: pos


title: ALCL - sample 21


title: 2640_T1 1ug/ml 4-hydroxytamoxifen


title: CHO_Liver_6h_rep2

value: Carbohydrate

value: Wild-type

value: Male

value: liver

value: Sprague Dawley

value: 8-10 weeks

tag: liver lobe

value: Right median, right lateral, and caudate lobe

tag: chip antibody

value: NF-κB antibody (Cat#ab7970, Rabbit polyclonal NF-κB p65 antibody and negative control IgG antibody from Abcam Inc, Cambridge, MA)

value: none, input DNA


title: 2640_E3 Control

value: lung

value: 2640 UBCCreERT/RSmoM2

tag: strain

value: mixed

value: Adult

value: treated with vehicle


title: CHO_Liver_6h_rep1


title: 2640_T2 1ug/ml 4-hydroxytamoxifen

value: treated with 4OHT x48hrs


title: ALCL - sample 19

tag: cell type

value: peripheral blood T cells

tag: sample origin

value: University of Wuerzburg, Germany


title: ETOH_Liver_1h_rep1

value: Ethanol


title: CHO_Liver_1h_rep3

value: Carbohydrate

value: Wild-type


title: CHO_Liver_0h_rep2

value: Male

value: liver

value: Left lateral and median lobe


title: CHO_Liver_1h_rep2

value: Sprague Dawley

value: 8-10 weeks

value: Right median, right lateral, and caudate lobe


title: ALCL - sample 18

tag: original name

tag: alk positivity

value: pos


title: ALCL - sample 17

value: Turin

value: neg


title: AR7 ABA(+) / WT ABA(+)

city: Setagaya-ku

first: Kenji

last: KOMATSU

state: Tokyo

address: 1-1-1 Sakuragaoka

department: Department of Bioproduction Technology

institute: Tokyo University of Agriculture

description: AS01_high.gpr, AS01_middle.gpr, AS01_low.gpr

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent protocol

organism: Physcomitrium patens

source_name: ABA treated protonemata (AR7)

label_protocol: standard Agilent protocol

growth_protocol: P. patens subspecies patens (Gransden) was the wildtype strain. Protonemal tissue was grown at 25 ºC under continuous light (50 - 80 µmol photons m-2 s-1) on 0.8% (w/v) agar plates of modified BCDAT medium [1.84 mM KH2PO4 (pH 6.5), 10 mM KNO3, 1 mM MgSO4, 1 mM CaCl2, 45 µM FeSO4, 10 µM H3BO3, 2 µM MnCl2, 0.22 µM CuSO4, 0.23 µM CoCl2, 0.19 µM ZnSO4, 0.1 µM Na2MoO4, 5 mM ammonium tartrate]

extract_protocol: Total RNAs were extracted from ABA-treated or non-treated one-week-old protonemal tissues using RNeasy plant mini Kit (QIAGEN)

treatment_protocol: Wildtype and AR7 one-week-old protonemata were transferred to 10 μM ABA contain BCDAT media. The protonemal tissue were incubated for 24 hours at 25 ºC under continuous light.

tag: line

value: 10 mM ABA

source_name: ABA treated protonemata (WT)

value: WT


title: ALCL - sample 9

value: Bologna


title: WT ABA(+) / AR7 ABA(+)


title: ALCL - sample 20

value: peripheral blood T cells


title: ALCL - sample 12

value: HSR


title: 2640_E1 Control

value: lung

value: 2640 UBCCreERT/RSmoM2

value: mixed

value: Adult

value: treated with vehicle


title: 2640_E2 Control


title: AR7 ABA(+) / AR7 ABA(-)

source_name: control protonemata (AR7)

value: without ABA


title: ALCL - sample 10


title: ALCL - sample 6

value: University Hospitals Leuven


title: ALCL - sample 7


title: ALCL - sample 11


title: ALCL - sample 8


title: ALCL - sample 16


title: ETOH_Liver_0h_rep2

value: Ethanol

value: Wild-type

tag: gender

value: Male

value: liver

value: Sprague Dawley

value: 8-10 weeks

value: Left lateral and median lobe

value: NF-κB antibody (Cat#ab7970, Rabbit polyclonal NF-κB p65 antibody and negative control IgG antibody from Abcam Inc, Cambridge, MA)

value: none, input DNA


title: CHO_Liver_0h_rep1

value: Carbohydrate

tag: age


title: sh83_3

city: Cambridge

first: Vijay

middle: G

last: Sankaran

state: MA

address: 7 Cambridge Center

institute: Broad Institute

hyb_protocol: Standard Affymetrix Human Gene ST 2.0 arrays were hybridized with purified RNA samples.

scan_protocol: Signal amplication on Affymetrix Fluidics station 400

data_processing:
Microarrays (GeneChip® Human Gene 2.0 ST Arrays, Affymetrix) were performed on Day 7 cells for SH2B3 KD (sh83 and sh84) and control samples (shLuc).  Raw files were processed and normalized using the RMA algorithm from the oligo package in R 3.2. Differential expression analyses were conducted using limma. A heatmap is displayed for normalized expression values (Z-score) of genes that were significantly up-regulated in SH2B3 KD at a log2 fold change greater than 0.5 and a p-value threshold of 0.001.
probe group file: pd.hugene.2.0.st from Bioconductor

source_name: Day 7 SH2B3 KD

label_protocol: Standard Affymetrix label protocol

growth_protocol: Cells were differentiated into mature RBCs utilizing a three-phase culture protocol. In phase 1 (applicable here, day 0 – 7), cells were cultured at a density of 105 - 106 cells per milliliter (mL) in IMDM supplemented with 2% human AB plasma, 3% human AB serum, 1% penicillin/streptomycin, 3 IU/mL heparin, 10 ug/mL insulin, 200 ug/mL holo-transferrin, 1 IU erythropoietin (Epo), 10 ng/mL stem cell factor (SCF) and 1 ng/mL IL-3.

extract_protocol: Qiagen RNA purification

treatment_protocol: CD34+ cells were lentivirally infected with short hairpin RNAs 7 days before isolation

tag: day

value: CD34+ derived

tag: lentiviral infection


title: CHO_Liver_0h_rep3

tag: tissue


title: sh83_2


title: ALCL - sample 5

value: peripheral blood T cells

value: pos


title: sh84_1


title: AR7 ABA(-) / AR7 ABA(+)

value: 10 mM ABA


title: CHO_Liver_1h_rep1

tag: diet

value: Right median, right lateral, and caudate lobe


title: sh84_3


title: ALCL - sample 4

value: Turin


title: PTCL, nos - sample 6

value: University of Wuerzburg, Germany

value: neg


title: shLuc_1

source_name: Day 7 control

value: shLuc


title: sh83_1


title: FXRKO-PCLS CsA 4

city: Wageningen

first: Ewa

last: Szalowska

address: Akkermaalsbos 2

country: Netherlands

institute: RIKILT-Wageningen UR

description: Gene expression data from precision cut liver slices prepared from livers of FXR knockout mice treated with CsA for 24h.

hyb_protocol: Per sample, 7.5ug cRNA of the obtained biotinylated cRNA samples was fragmented and hybridized in a final concentration of 0.0375 ug /ul on the Affymetrix HT Mouse genome 430 PM array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: After an automated process of washing and staining by the GeneTitan machine (Affymetrix, Santa Clara, CA, USA) using the Affymetrix HWS kit for Gene Titan, absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v 3.2 software.

data_processing: Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v 3.2 software. The data Quality Control was performed in the program Affymetrix Expression Console v 1.1 (Affymetrix, Santa Clara, CA, USA) software to determine if all parameters were within quality specifications. The Probe Logarithmic Intensity Error Estimation (PLIER) algorithm method was used for probe summarisation. Non-normalized data in a form of the Cell Intensity File (*.CEL) were re-annotated (mogene11st_Mm_ENTREZG) and the data were RMA normalized.

label_protocol: Biotin- labelled cRNA was generated from high-quality total RNA with the Affymetrix 3’IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s specifications with an input of 100 ng total RNA.

growth_protocol: 12-weeks old male C57BL/6 mice and 12-weeks old FXRKO mice on a C57BL/6 mice background were bred at the animal facility of University Medical Centre Groningen (UMCG), the Netherlands. After arrival to the animal facility of Wageningen University, animals were kept for 2 weeks at a housing temperature of 22°C and at a relative humidity of 30–70%. The lighting cycle was 12-h light and 12-h dark. At the age of 24 weeks animals were sacrificed by an overdose of isoflurane. The treatment protocol was approved by the Ethical Committee for Animal Experiments of Wageningen University.  Immediately after the animals were killed, the liver was perfused with PBS and placed in ice-cold Krebs–Henseleit buffer (KHB) (pH 7.4, supplemented with 11 mM glucose). Liver tissue was transported to the laboratory within approximately 30 min and cylindrical liver cores were produced using a surgical biopsy punch with diameter of 5 mm (KAI, SynErgo Europe, Romania). Liver cores were placed in a Krumdieck tissue slicer (Alabama Research and Development, Munford, AL, USA) filled with ice-cold KHB aerated with carbogen and supplemented with 11 mM glucose. Slices with a diameter of 5 mm, a thickness of 0.2 mm and a weight of approximately 6 mg were prepared. Immediately after preparation, slices were transferred into culture plates filled with pre-warmed (37⁰C) WEM supplemented with pen/strep. Three liver slices were pre-cultured in one well of the 6-well plate filled with 4 ml of WEM for one hour with continuous agitation (70 rpm). Incubations were performed in an oxygen controlled incubator (Galaxy 48 R, New Brunswick, Nijmegen, the Netherlands) at 80% of oxygen, 5% CO2, and the remaining gas volume was filled up to 95% with N2. After one hour of pre-incubation, media were removed and replaced with fresh media containing test compounds or appropriate solvents. After incubations, samples were snap-frozen in liquid nitrogen and stored in -80 °C for further analysis.

extract_protocol: RNA was extracted from three slices using the RNeasy Tissue Mini Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s instructions.

treatment_protocol: Precision cut liver slices (PCLS) obtained from livers of wild type (WT) and farnesoid X receptor knockout (FXRKO) mice were exposed for 24 hours to 40uM of CyclosporinA (CsA).

tag: background strain

tag: genotype/variation

value: FXR knockout


title: FXRKO-PCLS CsA 5

source_name: precision cut liver slices prepared from livers of FXR knockout mice treated with CsA for 24h.


title: PTCL, nos - sample 7


title: PTCL, nos - sample 8


title: FXRKO-PCLS CsA 3


title: shLuc_3


title: PTCL, nos - sample 5


title: ALCL - sample 2


title: FXRKO-PCLS CsA 2


title: shLuc_2


title: PTCL, nos - sample 4


title: ALCL - sample 3

value: University Hospitals Leuven


title: SKBR3_48 hrs treatment with 5 µM atorvastatin biological replicate 3

city: Lund

first: Siker

last: Kimbung

address: Scheelevägen 2

department: Department of Oncology and Pathology, Clinical Sciences, Lund

country: Sweden

institute: Lund University

scan_protocol: Standard Illumina iScan N240 scanning protocol scan setting file: Direct Hyb

data_processing: The data were normalised using quantile normalisation with BASE (v.3.4)

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

extract_protocol: RNeasy protocol (Qiagen)

tag: cell line

value: Primary breast cancer cell line

tag: treated with

value: 5µM atorvastatin for 48hrs


title: ETOH_Liver_6h_rep2

source_name: NF-kB ChIP DNA from rattus norvegicus regenerating liver at 0h post PHx, biological replicate 1_ethanol_diet

value: Ethanol

tag: genotype

value: Wild-type

value: Male

value: liver

value: Sprague Dawley

value: 8-10 weeks

tag: weight

tag: liver lobe

tag: chip antibody

source_name: Input DNA from rattus norvegicus regenerating liver at 0h post PHx, biological replicate 1_ethanol_diet


title: FXRKO-PCLS CsA 1


title: SKBR3_48 hrs treatment with vehicle (DMSO) biological replicate 3

tag: cell type

value: DMSO (vehicle) for 48hrs


title: SKBR3_48 hrs treatment with vehicle (DMSO) biological replicate 2


title: SKBR3_48 hrs treatment with vehicle (DMSO) biological replicate 1


title: PTCL, nos - sample 3

value: peripheral blood T cells

tag: sample origin

tag: original name

tag: alk positivity


title: PTCL, nos - sample 2


title: FXRKO-PCLS DMSO 4

description: Gene expression data from precision cut liver slices prepared from livers of FXR knockout mice treated with DMSO for 24h.


title: SKBR3_48 hrs treatment with 5 µM atorvastatin biological replicate 2


title: PTCL, nos - sample 1


title: MDA231_48 hrs treatment with vehicle (DMSO) biological replicate 1


title: shRNA_FOXQ1 transfected Human Colorectal Cell DLD1 Replicate 1

city: Kunming

first: Hui

last: Tang

state: Yunnan

address: No.157 Jinbi Street

department: Institute of Clinical and Basic Medical Sciences

institute: The First People’s Hospital of Yunnan Province.

description: Gene expression profile of DLD1 with FOXQ1 expression level has been konckdowned.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug 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 (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: DLD1 colorectal cancer cell transfected by shRNA_FOXQ1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human colorectal cancer cell lines DLD1 was cultured in high glucose DMEM supplemented with 10% fetal bovine serum (FBS, HyClone, Thermo scientific Inc, China) and antibiotics (100 U/mL penicillin and 100 mg/mL streptomycin) at 37°C under an atmosphere containing 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: shRNA_FOXQ1 and shRNA_Control were transfected into the DLD1 cells by using lentiviral virus, at 48 hours after transfection, 12 mg/mL puromycin (Solarbio) was added and the cells were incubated for 20 days to select for transfected cells. The two stable cell lines were named as DLD1 _shRNA_FOXQ1 and DLD1_shRNA_Control.


title: MDA231_48 hrs treatment with vehicle (DMSO) biological replicate 2


title: WT-PCLS CsA 5

description: Gene expression data from precision cut liver slices prepared from livers of wild type mice treated with CsA for 24h.

value: wild type


title: MDA231_48 hrs treatment with 1 µM atorvastatin biological replicate 2

value: 1µM atorvastatin for 48hrs


title: FXRKO-PCLS DMSO 2

source_name: precision cut liver slices prepared from livers of FXR knockout mice treated with DMSO for 24h.


title: MDA231_48 hrs treatment with 1 µM atorvastatin biological replicate 3


title: SKBR3_48 hrs treatment with 5 µM atorvastatin biological replicate 1


title: MDA231_48 hrs treatment with vehicle (DMSO) biological replicate 3


title: shRNA_Control transfected Human Colorectal Cell DLD1 Replicate 2

description: Gene expression profile of DLD1 with normal expression level of FOXQ1

source_name: DLD1 colorectal cancer cell transfected by shRNA_Control


title: MDA231_48 hrs treatment with 1 µM atorvastatin biological replicate 1


title: FXRKO-PCLS DMSO 1


title: MCF7_48 hrs treatment with vehicle (DMSO) biological replicate 2


title: WT-PCLS CsA 4

source_name: precision cut liver slices prepared from livers of wild type mice treated with CsA for 24h.


title: WT-PCLS CsA 3


title: MCF7_48 hrs treatment with 5 µM atorvastatin biological replicate 1


title: MCF7_48 hrs treatment with 5 µM atorvastatin biological replicate 3


title: FXRKO-PCLS DMSO 3


title: shRNA_FOXQ1 transfected Human Colorectal Cell DLD1 Replicate 2


title: MCF7_48 hrs treatment with vehicle (DMSO) biological replicate 1


title: shRNA_Control transfected Human Colorectal Cell DLD1 Replicate 1


title: MCF7_48 hrs treatment with vehicle (DMSO) biological replicate 3


title: MCF7_48 hrs treatment with 5 µM atorvastatin biological replicate 2


title: WT-PCLS CsA 2


title: sh84_2

value: CD34+ derived


title: BT474_48 hrs treatment with vehicle (DMSO) biological replicate 3


title: liver_treatment_HFD_10

city: Clayton

first: Matthew

last: Watt

state: VIC

address: Monash University

department: Department of Physiology

country: Australia

institute: Faculty of Medicine, Nursing and Health Sciences

description: SAMPLE 6

hyb_protocol: The quality and quantity of mouse amplified RNA was ascertained on the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 750 ngs of amplified RNA was then prepared for hybridisation to the Ilumina Mouse WG-6 v2 Expression BeadChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the beadchip). A total hybridisation volume of 15ul was prepared for each sample and 15ul loaded into a single array on the Ilumina Mouse WG-6 v2 Expression BeadChip. A total of 8 different labelled samples were loaded onto two BeadChips.  The chip was then hybridised at 58oC for 16 hours in an oven with a rocking platform.  After hybridisation, the chip was washed using the appropriate protocols as outlined in the Illumina manual.  Upon completion of the washing, the chips were then coupled with Cy3 and scanned in the Illumina iScan Reader.

scan_protocol: The Illumina iScan Reader scanner operating software, GenomeStudio, converts the signal on the array into a TXT file for analysis.

data_processing: Data was pre-processed using the R statistical programming language. Raw signal intensity values were subjected to normalization procedure, including background correction, log2 transformation and variance stabilization using the package lumi from the Bioconductor project. Genes with an expression difference of ≥ 1.20-fold with 95% confidence interval between the conditions were considered to be different.

label_protocol: Standard Illumina protocol

growth_protocol: Isolated primary hepatocytes were plated into tissue culture dishes in filtered M199 medium supplemented with 10% FBS, 1% penicillin-streptomycin (Gibco), 100 nM insulin (Sigma), 400 nM dexamethasone (Sigma) and 1.5 nM EGF (BD Biosciences). After four hours, the media was replaced with the same medium and supplements and 10 nM insulin. RNA was harvested from cells 24 h later.

extract_protocol: Cells were lysed in 500 uL Qiazol and total RNA was extracted using an RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells were washed in ice-cold phosphate buffered saline before RNA extraction.

tag: strain

tag: gender

value: male

tag: fed with

value: high fat diet (HFD)

value: hepatocyte


title: liver_treatment_HFD_12

description: SAMPLE 8

tag: tissue


title: liver_treatment_HFD_11

description: SAMPLE 7


title: Sample674_Schizo

status: Public on Oct 21 2015

city: Baltimore

first: Andrew

last: Jaffe

state: MD

address: 855 N Wolfe St, Ste 300

department: Clinical Sciences

institute: Lieber Institute for Brain Development

description: Human DLPFC DNA methylation sample

hyb_protocol: Following manufacturer's protocol

scan_protocol: Following manufacturer's protocol

data_processing:
idat files were read in using the minfi Bioconductor package and processed using the preprocessQuantile approach
GEO_procData.csv: the resulting Illumina "Beta" matrix (proportion methylation) after stratified quantile normalization.
GEO_rawData.csv: Unmethylated and methylated signal intensities
suppTable9_meQTLs_allPairs.csv: all significant SNP-CpG pairs for meQTLs with FDR < 0.01, with corresponding annotation.

source_name: DLPFC

label_protocol: Following manufacturer's protocol

extract_protocol: Genomic DNA was extracted from 100 mg of pulverized dorsolateral prefrontal cortex (DLPFC) tissue with the phenol-chloroform method.

treatment_protocol: Bisulfite conversion of 600 ng genomic DNA was performed with the EZ DNA methylation kit (Zymo Research).

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

value: FALSE

tag: sex (clinical gender)

value: F

tag: race

value: CAUC

tag: group

value: Schizo

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

value: TRUE

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: WT-PCLS DMSO 5

description: Gene expression data from precision cut liver slices prepared from livers of wild type mice treated with DMSO for 24h.

tag: background strain

tag: genotype/variation


title: WT-PCLS DMSO 4

source_name: precision cut liver slices prepared from livers of wild type mice treated with DMSO for 24h.


title: BT474_48 hrs treatment with vehicle (DMSO) biological replicate 2

tag: cell line

tag: cell type

value: Primary breast cancer cell line

tag: treated with


title: Sample675_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: race

tag: group

tag: age (in years)


title: BT474_48 hrs treatment with vehicle (DMSO) biological replicate 1


title: BT474_48 hrs treatment with 5 µM atorvastatin biological replicate 3

value: 5µM atorvastatin for 48hrs


title: liver_control_chow_3

description: SAMPLE 3

tag: strain

tag: gender

tag: fed with

value: normal diet (chow)

tag: tissue

value: liver


title: Sample673_Control

description: Human DLPFC DNA methylation sample

value: M

value: AA

value: Control

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample671_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: race

tag: group


title: BT474_48 hrs treatment with 5 µM atorvastatin biological replicate 2

tag: cell line

tag: cell type

tag: treated with


title: liver_control_chow_5

description: SAMPLE 4

tag: strain

tag: gender

tag: fed with

tag: tissue


title: Sample670_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample669_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: race

tag: group

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample667_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Sample672_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: WT-PCLS DMSO 3

tag: background strain

tag: genotype/variation

value: wild type


title: WT-PCLS DMSO 1


title: WT-PCLS CsA 1


title: liver_treatment_HFD_8

description: SAMPLE 5

tag: strain

tag: gender

tag: fed with

tag: tissue

tag: cell type


title: WT-PCLS DMSO 2


title: liver_control_chow_1

description: SAMPLE 1


title: liver_control_chow_2

description: SAMPLE 2


title: Sample668_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: BT474_48 hrs treatment with 5 µM atorvastatin biological replicate 1

tag: cell line

tag: treated with


title: Sample663_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample662_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: Sample660_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample659_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample657_Schizo

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)


title: Sample665_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)


title: Sample656_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample666_Schizo

description: Human DLPFC DNA methylation sample

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample654_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample653_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: Sample664_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample652_Schizo

description: Human DLPFC DNA methylation sample

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample649_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample658_Schizo

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)


title: Sample646_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)


title: Sample645_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample644_Control

description: Human DLPFC DNA methylation sample

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample647_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample661_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: BGC823_P16-Dnmt_rep1

city: Beijing

first: Dajun

last: Deng

state: Beijing

address: Fu-Cheng-Lu No.52

department: Dept Aetiology

institute: Peking University Cancer Hospital and Institute

description: This cell line was derived from a surgically resected gastric adenocarcinoma tissue sample from a male Chinese patient at 62 years old, stably transfected with the P16-Dnmt vector and treated with 0.25 microgram/mL doxycycline for 14 days

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

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

data_processing: BeadStudio software v1.8

label: Cy3, Cy5

source_name: BGC823 cells stably transfected with the P16-Dnmt vector and treated with 0.25 microgram/mL doxycycline for 14 days

label_protocol: Processed according to the Illunima HD Methylation450K Assay Manual

growth_protocol: Cultured in RPMI1640 medium supplemented with 10% FBS and maintained at 37°C in humidified air with 5% CO2

extract_protocol: Genomic DNA was isolated and purified with phenol/chloroform extraction, and further treated with sodium bisulfite using ZYMO EZ DNA Methylation kit

treatment_protocol: Stably transfected with the P16-Dnmt or pTRIPZ empty control vector, and treated with 0.25 microgram/mL doxycycline for 7 days

tag: cell line

tag: cell type

value: gastric adenocarcinoma


title: BGC823_Vector_rep2

description: This cell line was derived from a surgically resected gastric adenocarcinoma tissue sample from a male Chinese patient at 62 years old, stably transfected with the pTRIPZ empty control vector and treated with 0.25 microgram/mL doxycycline for 14 days

source_name: BGC823 cells stably transfected with the control vector pTRIPZ and treated with 0.25 microgram/mL doxycycline for 14 days


title: Sample651_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample648_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group

tag: age (in years)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample642_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample640_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample650_Schizo

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: Sample638_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample655_Control

description: Human DLPFC DNA methylation sample

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample637_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: BGC823_Vector_rep1

tag: cell line

tag: cell type


title: BGC823_P16-Dnmt_rep2


title: Sample641_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample643_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample635_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample629_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample630_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample628_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Sample636_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample634_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample633_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample632_Schizo

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: Sample631_Schizo

description: Human DLPFC DNA methylation sample

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample627_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample625_Control

description: Human DLPFC DNA methylation sample

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample622_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample623_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Sample619_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample620_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample615_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample614_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: Sample613_Control

description: Human DLPFC DNA methylation sample

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample612_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample624_Control

description: Human DLPFC DNA methylation sample

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample608_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample606_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Sample616_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample621_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample617_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample626_Schizo

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: Sample618_Schizo

description: Human DLPFC DNA methylation sample

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample611_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample599_Control

description: Human DLPFC DNA methylation sample

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample605_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample598_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Sample596_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample597_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample602_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)