title: LSTGFBR2_TGFB_2

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

hyb_protocol: Hybridization was performed for 16h at 45ºC in hybridization Oven 640 (Affymetrix). Washing and staining were done in Fluidics station 400 (Affymetrix)

scan_protocol: Arrays were scanned in Genechip Scanner 3000

data_processing: RMA normalization using the normqc function of Bioconductor's MDA package

label_protocol: 5 mg total RNA were processed using the One-cycle target labeling and control reagents kit(Affymetrix, Santa Clara, CA) to synthesize dscDNA. Biotin-labeled cRNA was synthesized from dscDNA and fragmented using the IVT labeling kit of Affymetrix.

growth_protocol: Cells were grown under standard culture conditions. Briefly, all cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with L-Glutamine (Invitrogen 41966, Paisley, Scotland) and 10% FBS (Invitrogen 10270) at 37ºC and 5% CO2. Doxycycline (1uM) was used to activate the TGFBR2 inducible contruct (see treatment protocol for more details)

extract_protocol: Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies). Briefly, CRC cell lines were scraped from cell culture dishes (Costar) and homogenized by pipetting in TRIzol solution (Life Technologies, 15596-018). After phase separation with chloroform, the upper aqueous phase was then mixed with 70% ethanol and bound to RNA columns (PureLink™ RNA Mini kit, Life Technologies) according to the protocol provided by the manufacturer. RNA was quantified using a Nanodrop spectrophotometer.

treatment_protocol: TGFBR2 expression was induced in the presence of doxycycline (dox: 1 μg mL-1; Sigma Aldrich) from seeding. 16 hours post seeding, cells were treated with human recombinant TGF-beta1 (Peprotech; 5ng/ml) for another 16 hours.

tag: cell line

value: TGF-β1 for 16 hours.


title: SLRK grown to mid-logarithmic phase in RCV media at 30 degrees C

status: Public on Sep 08 2014

type: RNA

city: St. John's

first: Ryan

middle: G

last: Mercer

state: Newfoundland

address: 232 Elizabeth Avenue

department: Biology

country: Canada

institute: Memorial University

hyb_protocol: as described in the Affymetrix Expression Analysis Technical Manual for prokaryotic samples

scan_protocol: Scanning was completed at the Michael Smith Genome Science Centre

data_processing: Affymetrix Expression Console

label: biotin

molecule: total RNA

organism: Rhodobacter capsulatus

source_name: bacterial cells

growth_protocol: Photoheterotrophic conditions

extract_protocol: RNA was extracted using the RNeasy Kit (Qiagen Inc., Mississauga, Canada) according to the manufacturer’s recommendations

treatment_protocol: Different temperatures (30 or 37 degrees C) in different growth media (RCV or YPS)

tag: strain

value: SLRK

tag: growth phase

value: mid-logarithmic

tag: temperature

tag: growth media

value: RCV


title: Blood_rat Extreme Behavioral Response_rat 44R

city: Belmont

first: Nikolaos

last: Daskalakis

state: MA

address: Oaks Building 328, Mailstop 212, 115 Mill Street

department: Department of Psychiatry

country: USA

institute: McLean Hospital/ Harvard Medical School

description:
replicate 8
SAMPLE 47

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: One array failed. We retained probes for which the majority (>50%) of samples from each group displayed a detection P value lower than <0.05.

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA was prepared with Illumina TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: RNA was extracted from whole blood using the PAXgene Blood RNA Kit (Qiagen) with the addition of on-column DNase digestion. Globin mRNA interference in the total RNA was diminished by GLOBINclear method (Ambion). Quality control was performed with ND-1000 spectrophotometer (NanoDrop Technologies) and 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 2.5 mL whole peripheral blood from each rat was collected into PAXgene Blood RNA Tubes (Qiagen), incubated at room temperature for 4 h for RNA stabilization (PAXgene RNA stabilization system) and then stored at −80 °C

value: Sprague Dawley

tag: age

value: Adult

tag: tissue

value: Blood

tag: gender

value: MALE

tag: group

value: Extreme Behavioral Response

tag: rat i.d.


title: LSTGFBR2_CTRL_2

country: Spain

label: Biotin

organism: Homo sapiens

tag: treatment


title: Amygdala_rat Control_rat F3

description: replicate 3

data_processing: We retained probes for which the majority (>50%) of samples from each group displayed a detection P value lower than <0.05.

source_name: Rat Amygdala

extract_protocol: RNeasy Mini Kits (Qiagen) were used to isolate total RNA with the addition of on-column DNase digestion. Quality control was performed with ND-1000 spectrophotometer (NanoDrop Technologies) and 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Amygdala was dissected on dry ice using established anatomical landmarks. Tissues were immediately submerged in RNA-stabilization solution (RNAlater, Ambion), and stored at −80 °C.

value: Amygdala

value: female

value: Control


title: Blood_rat Extreme Behavioral Response_rat 11R

description:
replicate 4
SAMPLE 43


title: Blood_rat Extreme Behavioral Response_rat 3R

description:
replicate 7
SAMPLE 46


title: Blood_rat Extreme Behavioral Response_rat 5R

description:
replicate 5
SAMPLE 44


title: Genomic DNA of normal colon sample from CRC patient 14

type: genomic

city: Seattle

first: Yanxin

last: Luo

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: normal-C

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: Bio-conductor. Use SWAN for data normalization and Combat for batch-effect corrections.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: colorectal mucosa

label_protocol: Standard Illumina Protocol

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

value: colorectal mucosa

tag: colon region

value: colon

tag: disease status

value: normal-C

value: Female


title: Genomic DNA of normal colon sample from CRC patient 13

description: normal-C


title: LSTGFBR2_TGFB_1


title: SLRK grown to early stationary phase in RCV media at 30 degrees C

label_protocol: as described in the Affymetrix Expression Analysis Technical Manual for prokaryotic samples

value: early stationary


title: LSTGFBR2_CTRL_1


title: Genomic DNA of normal colon sample from CRC patient 12

description: normal-C

value: Male


title: SB1003 grown to mid-logarithmic phase in YPS media at 30 degrees C

value: YPS


title: Blood_rat Extreme Behavioral Response_rat 30R

description:
replicate 2
SAMPLE 41


title: Genomic DNA of normal colon sample from CRC patient 11

description: normal-C


title: K562+ Mesoporphyrin, prep #3

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

description: Set 3

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: K562 treated with 20 uM mesoporphyrin for 20 hours

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

growth_protocol: K562 cells were cultured in RPMI 1640 with 10% FBS and 2 mM Glutamine.

extract_protocol: Active growth cells were treated with DMSO, or mesoporphyrin or Fe(III) mesoporphyrin.

treatment_protocol: Cells were treated for 20 hours.

tag: cell line name

value: K-562 (ATCC® CCL-243™)

tag: cell type

value: chronic myelogenous leukemia (CML)


title: Genomic DNA of normal colon sample from CRC patient 10

description: normal-C


title: K562+ Mesoporphyrin, prep #4

description: Set 4


title: Blood_rat Extreme Behavioral Response_rat 32R

description:
replicate 1
SAMPLE 40

value: Sprague Dawley


title: Genomic DNA of normal colon sample from CRC patient 9

description: normal-C


title: SB1003 grown to transition phase in YPS media at 37 degrees C

value: transition


title: SB1003 grown to early stationary phase in YPS media at 30 degrees C


title: DE442 grown to mid-logarithmic phase in YPS media at 37 degrees C

value: mid-logarithmic


title: Genomic DNA of normal colon sample from CRC patient 6

description: normal-C


title: Blood_rat Minimal Behavioral Response_rat 16R

description:
replicate 7
SAMPLE 38

value: Adult

value: Blood

value: MALE

value: Minimal Behavioral Response


title: K562+ Mesoporphyrin, prep #1

description: Set 1


title: K562+ Mesoporphyrin, prep #2

description: Set 2


title: Genomic DNA of normal colon sample from CRC patient 8

description: normal-C


title: Blood_rat Minimal Behavioral Response_rat 17R

description:
replicate 8
SAMPLE 39


title: Blood_rat Minimal Behavioral Response_rat 14R

description:
replicate 6
SAMPLE 37


title: Genomic DNA of normal colon sample from CRC patient 7

description: normal-C


title: Genomic DNA of normal colon sample from CRC patient 5

description: normal-C


title: K562+Fe(III) Mesoporphyrin, prep #3

description: Set 3

source_name: K562 treated with 20 uM Fe(III) mesoporphyrin for 20 hours


title: K562+Fe(III) Mesoporphyrin, prep #2

description: Set 2


title: DE442 grown to transition phase in YPS media at 37 degrees C


title: cckACKO grown to mid-logarithmic phase in YPS media at 37 degrees C

value: cckACKO


title: Blood_rat Minimal Behavioral Response_rat 10R

description:
replicate 4
SAMPLE 35


title: cckACKO grown to early stationary phase in YPS media at 37 degrees C


title: Blood_rat Minimal Behavioral Response_rat 12R

description:
replicate 5
SAMPLE 36


title: Blood_rat Extreme Behavioral Response_rat 20R

description:
replicate 3
SAMPLE 42

value: Extreme Behavioral Response


title: K562+vehicle(DMSO), prep #3

description: Set 3

source_name: K562 treated with DSMO (0.1%) for 20 hours


title: Blood_rat Minimal Behavioral Response_rat 2R

description:
replicate 1
SAMPLE 32


title: Blood_rat Minimal Behavioral Response_rat 9R

description:
replicate 3
SAMPLE 34


title: Blood_rat Minimal Behavioral Response_rat 8R

description:
replicate 2
SAMPLE 33


title: K562+Fe(III) Mesoporphyrin, prep #1

description: Set 1


title: Genomic DNA of normal colon sample from CRC patient 1

description: normal-C

value: colorectal mucosa

value: colon


title: K562+Fe(III) Mesoporphyrin, prep #4

description: Set 4


title: ALSI grown to transition phase in YPS media at 37 degrees C

value: ALSI


title: Genomic DNA from normal individual 17

description: normal-H

value: normal-H

value: Female


title: K562+vehicle(DMSO), prep #4

description: Set 4


title: Genomic DNA of normal colon sample from CRC patient 4

description: normal-C

value: normal-C

value: Male


title: Genomic DNA from normal individual 15

description: normal-H


title: Genomic DNA from normal individual 16

description: normal-H


title: Blood_rat Control_rat 10R

description:
replicate 8
SAMPLE 31

source_name: Blood_rat Control_rat 10R

value: Control


title: DE442 grown to early stationary phase in YPS media at 37 degrees C

value: early stationary

value: YPS


title: Blood_rat Control_rat 6R

description:
replicate 4
SAMPLE 27

source_name: Blood_rat Control_rat 6R

value: Sprague Dawley


title: Blood_rat Control_rat 7R

description:
replicate 5
SAMPLE 28

source_name: Blood_rat Control_rat 7R

value: Adult


title: A9M-326

city: New York

first: Scott

last: Armstrong

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: According to manufacturer's instructions (Affymetrix)

data_processing: RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).

organism: Mus musculus

source_name: Hoxa9-Meis1 transduced primary leukemias

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were not grown prior to microarray

extract_protocol: Trizol extraction of total RNA and Qiagen RNeasy micro kit was performed according to the manufacturer's instructions.

treatment_protocol: Cells were sorted for dtTomato expression in case of MIT or CRE leukemia cells, Hoxa9-Meis1 leukemia cells were not subject to any treatment prior to RNA preparation.

tag: strain background

value: fresly harvested BM cells


title: Genomic DNA from normal individual 13

description: normal-H


title: Blood_rat Control_rat 9R

description:
replicate 7
SAMPLE 30

source_name: Blood_rat Control_rat 9R

value: Blood

value: MALE


title: Blood_rat Control_rat 8R

description:
replicate 6
SAMPLE 29

source_name: Blood_rat Control_rat 8R


title: Genomic DNA from normal individual 14

description: normal-H


title: MA9-AF10-MIT-6

scan_protocol: According to manufacturer's instructions (Affymetrix)

source_name: Af10 floxed (MIT) leukemias

value: Af10 floxed (MIT) leukemias


title: MA9-AF10-MIT-5


title: K562+vehicle(DMSO), prep #1

description: Set 1

value: K-562 (ATCC® CCL-243™)

value: chronic myelogenous leukemia (CML)


title: A9M-328

value: Hoxa9-Meis1 transduced primary leukemias


title: K562+vehicle(DMSO), prep #2

description: Set 2


title: ALSI grown to early stationary phase in YPS media at 37 degrees C

value: ALSI


title: Genomic DNA from normal individual 11

description: normal-H

value: colorectal mucosa

value: colon

value: normal-H


title: Genomic DNA of normal colon sample from CRC patient 3

description: normal-C

value: normal-C

value: Male


title: Genomic DNA from normal individual 12

description: normal-H


title: Blood_rat Control_rat 5R

description:
replicate 3
SAMPLE 26

source_name: Blood_rat Control_rat 5R

value: Control


title: Genomic DNA from normal individual 10

description: normal-H

value: Female


title: Blood_Extreme Behavioral Response_rat F35

description:
replicate 8
SAMPLE 23

value: Sprague Dawley

value: FEMALE

value: Extreme Behavioral Response


title: MA9-AF10-CRE-6

source_name: Af10 deleted (CRE) leukemias

value: Af10 deleted (CRE) leukemias

value: fresly harvested BM cells


title: Blood_rat Control_rat 4R

description:
replicate 2
SAMPLE 25

source_name: Blood_rat Control_rat 4R

value: Adult

value: Blood

value: MALE


title: MA9-AF10-CRE-5


title: Blood_Extreme Behavioral Response_rat F40

description:
replicate 7
SAMPLE 22


title: Genomic DNA from CRC patients 14

description: cancer

value: Proximal

value: cancer

tag: Stage

value: IV


title: Genomic DNA of normal colon sample from CRC patient 2

description: normal-C

value: colorectal mucosa

value: colon


title: Genomic DNA from normal individual 9

description: normal-H

value: normal-H


title: A9M-327

value: Hoxa9-Meis1 transduced primary leukemias


title: GMP-Dot-K1421

description: Dot1l -/- GMPs

source_name: Dot1l -/- GMPs

treatment_protocol: Cells were sorted on the basis of surface markers for LSKs and GMPs using standard protocols prior to RNA preparation.

tag: genotype/variation

value: Dot1l fl/fl x Mx-Cre; Dot1l -/-

value: Sorted BM cells

tag: cell subtype

value: granulocyte macrophage progenitors (GMPs)


title: MA9-AF10-CRE-4


title: Blood_Extreme Behavioral Response_rat F39

description:
replicate 6
SAMPLE 21

tag: strain

value: Sprague Dawley

value: FEMALE


title: Blood_Extreme Behavioral Response_rat F38

description:
replicate 5
SAMPLE 20

value: Extreme Behavioral Response


title: GMP-Dot-K1359

description: Dot1l -/- GMPs


title: Genomic DNA from CRC patients 12

description: cancer

value: Rectum

value: Male


title: Blood_Extreme Behavioral Response_rat F36

description:
replicate 3
SAMPLE 18

value: Adult

value: Blood


title: Genomic DNA from normal individual 7

description: normal-H


title: Blood_Extreme Behavioral Response_rat F37

description:
replicate 4
SAMPLE 19


title: GMP-Dot-K1190

description: Dot1l -/- GMPs


title: MA9-AF10-MIT-4

value: Af10 floxed (MIT) leukemias

value: fresly harvested BM cells


title: Genomic DNA from CRC patients 10

description: cancer

value: Proximal

value: cancer

value: Female

value: III


title: Genomic DNA from CRC patients 11

description: cancer

value: colorectal mucosa

value: II


title: Blood_Extreme Behavioral Response_rat F45

description:
replicate 1
SAMPLE 16


title: GMP-Control-K1604

description: Wild type GMPs

source_name: Wild type GMPs

value: Dot1 wt/wt x Mx-Cre; wild type

value: Sorted BM cells


title: GMP-Dot-K1272

description: Dot1l -/- GMPs

value: Dot1l fl/fl x Mx-Cre; Dot1l -/-

value: granulocyte macrophage progenitors (GMPs)


title: GMP-Control-K1581

description: Wild type GMPs


title: Blood_Extreme Behavioral Response_rat F44

description:
replicate 2
SAMPLE 17

value: Sprague Dawley

value: FEMALE

value: Extreme Behavioral Response


title: Blood_Minimal Behavioral Response_rat F17

description:
replicate 7
SAMPLE 14

value: Adult

value: Minimal Behavioral Response


title: Blood_Minimal Behavioral Response_rat F20

description:
replicate 5
SAMPLE 12

value: Blood


title: Genomic DNA from normal individual 8

description: normal-H

value: colon

value: normal-H

value: Male


title: GMP-Control-K1603

description: Wild type GMPs


title: GMP-Control-K1602

description: Wild type GMPs


title: Genomic DNA from CRC patients 13

description: cancer

value: Proximal

value: cancer


title: Blood_rat Control_rat 2R

description:
replicate 1
SAMPLE 24

source_name: Blood_rat Control_rat 2R

value: MALE

value: Control


title: Blood_Minimal Behavioral Response_rat F11

description:
replicate 8
SAMPLE 15


title: GMP-Control-K1601

description: Wild type GMPs

value: Dot1 wt/wt x Mx-Cre; wild type


title: LSK-Dot-K1422

description: Dot1l -/- LSKs

source_name: Dot1l -/- LSKs

value: Sorted BM cells

value: Lineage negative Sca-1 positive Kit positive (LSK) cells


title: Genomic DNA from CRC patients 7

description: cancer

source_name: colorectal mucosa

value: colorectal mucosa

value: Transverse

value: II


title: Blood_Minimal Behavioral Response_rat F19

description:
replicate 6
SAMPLE 13

value: Sprague Dawley

value: FEMALE


title: Genomic DNA from CRC patients 9

description: cancer

value: Distal

value: Female

value: III


title: Blood_Minimal Behavioral Response_rat F22

description:
replicate 4
SAMPLE 11

value: Adult

value: Blood

value: Minimal Behavioral Response


title: Genomic DNA from CRC patients 6

description: cancer

value: Proximal

value: cancer

value: Male


title: LSK-Dot-K1359

description: Dot1l -/- LSKs

value: Dot1l fl/fl x Mx-Cre; Dot1l -/-


title: Genomic DNA from CRC patients 5

description: cancer


title: LSK-Dot-K1421

description: Dot1l -/- LSKs

value: Sorted BM cells


title: Blood_Minimal Behavioral Response_rat F24

description:
replicate 3
SAMPLE 10


title: Blood_Minimal Behavioral Response_rat F26

description:
replicate 2
SAMPLE 9


title: Genomic DNA from CRC patients 8

description: cancer

value: IV


title: LSK-Dot-K1190

description: Dot1l -/- LSKs

value: Lineage negative Sca-1 positive Kit positive (LSK) cells


title: Genomic DNA from CRC patients 4

description: cancer

value: colorectal mucosa

value: Transverse


title: LSK-Dot-K1091

description: Dot1l -/- LSKs


title: LSK-Dot-K1272

description: Dot1l -/- LSKs


title: Blood_Minimal Behavioral Response_rat F27

description:
replicate 1
SAMPLE 8

value: Sprague Dawley


title: Genomic DNA from CRC patients 1

description: cancer


title: Blood_Control_rat F9

description:
replicate 6
SAMPLE 6

source_name: Blood_Control_rat F9

value: FEMALE

value: Control


title: Blood_Control_rat F10

description:
replicate 7
SAMPLE 7

source_name: Blood_Control_rat F10


title: Genomic DNA from CRC patients 3

description: cancer

value: Female


title: Genomic DNA from adenoma patient 8

description: adenoma

value: Left

value: adenoma


title: LSK-Control-K1553

description: Wild type LSKs

source_name: Wild type LSKs

value: Dot1 wt/wt x Mx-Cre; wild type


title: Blood_Control_rat F8

description:
replicate 5
SAMPLE 5

source_name: Blood_Control_rat F8

value: Adult

value: Blood


title: Blood_Control_rat F7

description:
replicate 4
SAMPLE 4

source_name: Blood_Control_rat F7


title: Genomic DNA from CRC patients 2

description: cancer

value: Distal

value: cancer

value: I


title: Genomic DNA from adenoma patient 7

description: adenoma

value: Right


title: LSK-Control-K1603

description: Wild type LSKs

value: Sorted BM cells


title: LSK-Control-K1604

description: Wild type LSKs

value: Lineage negative Sca-1 positive Kit positive (LSK) cells


title: LSK-Control-K1581

description: Wild type LSKs


title: Genomic DNA from adenoma patient 6

description: adenoma

value: colorectal mucosa

value: Retum

value: Male


title: Blood_Control_rat F4

description:
replicate 2
SAMPLE 2

source_name: Blood_Control_rat F4

value: Sprague Dawley

value: FEMALE


title: Blood_Control_rat F5

description:
replicate 3
SAMPLE 3

source_name: Blood_Control_rat F5

value: Control


title: Genomic DNA from adenoma patient 5

description: adenoma

value: Female


title: LSK-Control-K1601

description: Wild type LSKs


title: N-Me KO, biological replicate 3

status: Public on Sep 07 2014

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description: gene expression data from N-Me knock-out mouse

hyb_protocol: RNA was hybridized to the MouseRef-8 v2.0 Expression BeadChip (Illumina) using standard procedures

data_processing: Raw gene expression data were log2 transformed and quantile-normalized in MATLAB

source_name: N-Me KO, biological replicate 3

label_protocol: RNA was labeled using standard procedures

extract_protocol: RNA was isolated using standard procedures

treatment_protocol: vehicle only (corn oil, SIGMA) or tamoxifen (3 mg/Kg in corn oil, SIGMA) administered by intraperitoneal injection. Animals were processed at 40 hrs.

value: C57 BL6

value: Tamoxifen


title: Genomic DNA from adenoma patient 3

description: adenoma

value: adenoma


title: Blood_Control_rat F3

description:
replicate 1
SAMPLE 1

source_name: Blood_Control_rat F3

value: Adult

value: Blood


title: N-Me WT, biological replicate 3

description: gene expression data from N-Me wild type mouse

source_name: N-Me WT, biological replicate 3

value: Vehicle


title: LSK-Control-K1602

description: Wild type LSKs

value: Dot1 wt/wt x Mx-Cre; wild type


title: Genomic DNA from adenoma patient 4

description: adenoma

value: Right


title: N-Me KO, biological replicate 1

source_name: N-Me KO, biological replicate 1


title: N-Me WT, biological replicate 1

source_name: N-Me WT, biological replicate 1


title: control shRNA, 3hr KCl, biorep 2

city: Boston

first: Athar

middle: N.

last: Malik

address: 200 Longwood Avenue, Goldenson 405

department: Neurobiology

institute: Harvard Medical School

description: neuronal gene expression with control RNAi after 3 hour of stimulation with neuronal activity via KCl

hyb_protocol: Following fragmentation, cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: The data were analyzed using dCHIP with default parameters.

source_name: DIV7 mCTX neurons infected w control shRNA, stimulated w 3hr KCl, bioreplicate 2

label_protocol: The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.

growth_protocol: Embryonic day 16.5 (E16.5) C57BL/6 embryonic mouse cortices were dissected, dissociated, plated, and subsequently grown in a cell culture incubator that maintained a temperature of 37 degrees C and a CO2 concentration of 5%.

extract_protocol: Total RNA was purified using Trizol and the RNeasy mini kit from Qiagen.

treatment_protocol: On DIV5, lentiviral supernatant containing either a lentivirus expressing a control shRNA targeting firefly luciferase or a lentivirus expressing shRNA targeting FOS was applied to cultures for 6hrs with 6ug/mL polybrene.  At DIV7, mCTX neurons were silenced and stimulated with KCl for either 0, 1, 3, or 6hrs1

value: cultured mouse cortical neurons


title: N-Me KO, biological replicate 2

source_name: N-Me KO, biological replicate 2


title: Genomic DNA from adenoma patient 2

description: adenoma


title: control shRNA, 1hr KCl, biorep 1

description: neuronal gene expression with control RNAi after 1 hour of stimulation with neuronal activity via KCl

source_name: DIV7 mCTX neurons infected w control shRNA, stimulated w 1hr KCl, bioreplicate 1


title: control shRNA, 3hr KCl, biorep 1

source_name: DIV7 mCTX neurons infected w control shRNA, stimulated w 3hr KCl, bioreplicate 1


title: control shRNA, 1hr KCl, biorep 2

source_name: DIV7 mCTX neurons infected w control shRNA, stimulated w 1hr KCl, bioreplicate 2


title: control shRNA, 0hr KCl, biorep 2

description: neuronal gene expression with control RNAi in a silenced (unstimulated) state

source_name: DIV7 mCTX neurons infected w control shRNA, stimulated w 0hr KCl, bioreplicate 2


title: Genomic DNA from normal individual 6

description: normal-H

source_name: colorectal mucosa

value: colon

value: normal-H


title: Genomic DNA from adenoma patient 1

description: adenoma

value: colorectal mucosa


title: c-Fos shRNA, 6hr KCl, biorep 1

description: neuronal gene expression with c-Fos RNAi after 6 hour of stimulation with neuronal activity via KCl

source_name: DIV7 mCTX neurons infected w c-Fos shRNA, stimulated w 6hr KCl, bioreplicate 1


title: control shRNA, 0hr KCl, biorep 1

source_name: DIV7 mCTX neurons infected w control shRNA, stimulated w 0hr KCl, bioreplicate 1


title: Genomic DNA from normal individual 4

description: normal-H

value: Male


title: N-Me WT, biological replicate 2

source_name: N-Me WT, biological replicate 2


title: c-Fos shRNA, 6hr KCl, biorep 2

source_name: DIV7 mCTX neurons infected w c-Fos shRNA, stimulated w 6hr KCl, bioreplicate 2


title: control shRNA, 6hr KCl, biorep 2

description: neuronal gene expression with control RNAi after 6 hour of stimulation with neuronal activity via KCl

source_name: DIV7 mCTX neurons infected w control shRNA, stimulated w 6hr KCl, bioreplicate 2


title: c-Fos shRNA, 3hr KCl, biorep 2

description: neuronal gene expression with c-Fos RNAi after 3 hour of stimulation with neuronal activity via KCl

source_name: DIV7 mCTX neurons infected w c-Fos shRNA, stimulated w 3hr KCl, bioreplicate 2


title: c-Fos shRNA, 1hr KCl, biorep 2

description: neuronal gene expression with c-Fos RNAi after 1 hour of stimulation with neuronal activity via KCl

source_name: DIV7 mCTX neurons infected w c-Fos shRNA, stimulated w 1hr KCl, bioreplicate 2


title: Genomic DNA from normal individual 3

description: normal-H


title: c-Fos shRNA, 1hr KCl, biorep 1

source_name: DIV7 mCTX neurons infected w c-Fos shRNA, stimulated w 1hr KCl, bioreplicate 1


title: c-Fos shRNA, 3hr KCl, biorep 1

source_name: DIV7 mCTX neurons infected w c-Fos shRNA, stimulated w 3hr KCl, bioreplicate 1


title: Genomic DNA from normal individual 2

description: normal-H


title: c-Fos shRNA, 0hr KCl, biorep 1

description: neuronal gene expression with c-Fos RNAi in a silenced (unstimulated) state

source_name: DIV7 mCTX neurons infected w c-Fos shRNA, stimulated w 0hr KCl, bioreplicate 1


title: c-Fos shRNA, 0hr KCl, biorep 2

source_name: DIV7 mCTX neurons infected w c-Fos shRNA, stimulated w 0hr KCl, bioreplicate 2


title: Genomic DNA from normal individual 5

description: normal-H


title: HBPALL NOTCH1 IP

type: SRA

library_source: genomic

data_processing:
SOLiD sofware was used for the primary data processing.
BWA
We used HOMER (Hypergeometric Optimization of Motif EnRichment) software suite48 to call peaks for HBPALL NOTCH1 ChIP-Seq data
Genome_build: hg19
Supplementary_files_format_and_content: processed data file is in bed format it contains peaks coordinates and peak score computed by HOMER software suite

source_name: HBPALL NOTCH1 IP

extract_protocol:
Chromatin was extracted via treatment with a triton and deoxycolate containg lysis buffer and fragmented using a bioruptor sonicator using standard procedures
SOLiD3 standard protocol

treatment_protocol: HPB-ALL cells were fixed for 20 minutes at room temperature with 1% paraformaldehyde, quenched with a glycine containing buffer and recovered by centrifugation

value: Human T Cell Leukemia Cell

tag: cell line

value: HBALL

tag: antibody

value: NOTCH1 IP


title: HBPALL Whole Cell Extract

source_name: HBPALL Whole Cell Extract

value: none, Whole Cell Extract (Control)


title: Genomic DNA from normal individual 1

description: normal-H


title: control shRNA, 6hr KCl, biorep 1

source_name: DIV7 mCTX neurons infected w control shRNA, stimulated w 6hr KCl, bioreplicate 1

tag: age


title: 558 HIV-1 non-progressor

status: Public on Sep 06 2014

city: Cleveland

first: Xuan

last: Xu

state: OH

address: 2109 Adelbert Rd

institute: Case Western Reserve University

description:
the title represents the patient number
non-progressor

data_processing: The data were normalised using cubic spline normalization

source_name: whole blood

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

extract_protocol: RNA was extracted with PAXgene Blood mRNA Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Infinigen SSP3000.

tag: tissue

value: whole blood

tag: disease state

value: HIV-1 non-progressor


title: 561 HIV-1 progressor

description:
the title represents the patient number
progressor

value: HIV-1 progressor


title: 567 HIV-1 progressor


title: 566 HIV-1 progressor


title: 564 HIV-1 non-progressor


title: 556 HIV-1 progressor


title: Dog-MC-403802

first: Deli

last: Liu

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

hyb_protocol: Using NimbleGen Hybridization System (following the NimbleGen official Manual)

scan_protocol: Scanning two-color NimbleGen arrays with GenePix 4000B Scanner and associated software(following the NimbleGen official Manual)

data_processing: Analyzing the data with the segMNT algorithm (following the NimbleGen official Manual), and background correction as implemented in the NimbleScan software package, version 2.6.0.0 (Roche NimbleGen, Inc.).

organism: Canis lupus familiaris

source_name: DNA from mammary tumor tissue of dog 403802

label_protocol: Labeling test samples with Cy3 following the NimbleGen official Manual, see more at NimbleGen website, and labeling reference samples with Cy5 following the NimbleGen official Manual, see more at NimbleGen website.

extract_protocol: Genomic DNA was extracted from the dissected tissues using a Qiagen Tissue DNeasy purification kit (exactly following the kit manual)

tag: strain/breed

value: unknown

tag: sample id

value: canine mammary cancer (MC)

tag: tissue subtype

value: Complex carcinoma

source_name: DNA from mammary normal tissue of dog 403802

tag: dog id

value: mammary normal tissue


title: Dog-MC-518

source_name: DNA from mammary tumor tissue of dog 518

value: dog 518

source_name: DNA from mammary normal tissue of dog 518


title: Dog-MC-402421

source_name: DNA from mammary tumor tissue of dog 402421

source_name: DNA from mammary normal tissue of dog 402421


title: Dog-MC-401188

source_name: DNA from mammary tumor tissue of dog 401188

value: Simple carcinoma

source_name: DNA from mammary normal tissue of dog 401188


title: Dog-MC-5

source_name: DNA from mammary tumor tissue of dog 5

value: dog 5

source_name: DNA from mammary normal tissue of dog 5


title: Dog-MC-401130

source_name: DNA from mammary tumor tissue of dog 401130

source_name: DNA from mammary normal tissue of dog 406434


title: Dog-MC-341400

source_name: DNA from mammary tumor tissue of dog 341400

source_name: DNA from mammary normal tissue of dog 341400


title: 550 HIV-1 progressor


title: Dog-MC-159

source_name: DNA from mammary tumor tissue of dog 159

value: dog 159

source_name: DNA from mammary normal tissue of dog 159


title: 552 HIV-1 progressor

source_name: whole blood


title: Dog-MC-76

source_name: DNA from mammary tumor tissue of dog 76

value: dog 76

source_name: DNA from mammary normal tissue of dog 76


title: Dog-MC-115

source_name: DNA from mammary tumor tissue of dog 115

value: dog 115

value: Simple carcinoma, inflammatory

source_name: DNA from mammary normal tissue of dog 115


title: 547 HIV-1 progressor


title: 545 HIV-1 progressor


title: 551 HIV-1 non-progressor


title: 549 HIV-1 progressor


title: 554 HIV-1 non-progressor


title: Dog-MC-406434

source_name: DNA from mammary tumor tissue of dog 406434


title: 544 HIV-1 progressor


title: Dog-MC-32510

source_name: DNA from mammary tumor tissue of dog 32510

source_name: DNA from mammary normal tissue of dog 32510


title: 519 HIV-1 non-progressor


title: 514 HIV-1 non-progressor


title: 518 HIV-1 non-progressor


title: 531 HIV-1 non-progressor


title: 506 HIV-1 non-progressor


title: 512 HIV-1 non-progressor


title: 504 HIV-1 non-progressor


title: HepG2, siIDE, insulin, rep2

city: Nuthetal

first: Olga

last: Pivovarova

address: Arthur-Scheunert-Allee 114-116

department: Clinical Nutrition

country: Germany

institute: German Institute of Human Nutrition

hyb_protocol: Fragmented cRNA was hybridized to GeneChip Human Gene 1.0 ST Array for 16h at 45° C according to the manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned with an Affymetrix scanner controlled by Affymetrix Microarray Suite software.

data_processing: The raw fluorescence intensity values were normalized applying quantile normalization.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA.

growth_protocol: HepG2 cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: HepG2 cells were transfected with 96nM siRNA for IDE or AllStars Negative Control siRNA (Qiagen) using Lipofectamine 2000 (Invitrogen). 16 h after transfection, cells were treated with 10 nM insulin (Sigma Aldrich) or vehicle for 24 h in serum starvation condition.

tag: transfected with

value: IDE siRNA

tag: treated with

value: insulin 10nM 24h


title: 507 HIV-1 non-progressor


title: 503 HIV-1 non-progressor


title: 511 HIV-1 non-progressor


title: 502 HIV-1 progressor


title: HepG2, siIDE, vehicle, rep3

value: vehicle


title: HepG2, siIDE, insulin, rep1


title: 505 HIV-1 non-progressor

value: whole blood


title: HepG2, siIDE, vehicle, rep1


title: HepG2, siIDE, vehicle, rep2


title: HepG2, siControl, insulin, rep3

value: AllStars Negative Control siRNA


title: HepG2, siControl, insulin, rep1


title: HepG2, siControl, insulin, rep2


title: HepG2, siControl, vehicle, rep3


title: HepG2, siControl, vehicle, rep1


title: HepG2, siControl, vehicle, rep2


title: PHIdTri_25 with array type Brachypodium from Affymetrix

city: evry

first: huguet

last: stephanie

address: rue gaston cremieux

country: France

institute: labo

description:
brachypodium (bd21)  - dev.stage (boyes et al. plant cell 2001): flower development
Fusarium graminearum is the causal agent of Fusarium head blight (FHB) of small-grain cereals, including wheat. Besides direct grain losses, this disease is of major concern because of the production by the pathogen of mycotoxins which are hazardous to animals, thus making the grain unfit for food or feed. Major mycotoxins produced by the fungus are trichothecens, including deoxynivalenol (DON). In our laboratory, we use Brachypodium distachyon as a model plant for cereals because of its amenability (short life cycle, numerous genomic and genetic resources, ...). We have recently shown that F. graminearum does induce head blight symptoms on this species and that DON is produced on infected spikes. We have also evidenced that a F. graminearum strain unable to produce DON exhibits reduced virulence on B. distachyon spikes, as previously shown on wheat. The aim of this project is to analyse and compare the plant response to DON producing and non-producing strains of F. graminearum. This analysis will allow to decipher the mechanisms of detoxification set up by the plant and also more specific responses due to the impact of the mycotoxin on plant metabolism and physiology.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Brachypodium distachyon

label_protocol: labelling Biotin indirect, amplification=yes, total RNA  .

growth_protocol: silique and seed - -2/3 soil, 1/3 perlite -20h/4h photoperiod, 230 uE.m-2.s-1 -23°C day/20°C night -inoculation of plants 32 days after sowing of a single floret of the upper spikelet

treatment_protocol: Name:PHIdTri - nothing - fusarium graminearum delta tri5 mutant strain ,pathogen infection,nothing:time 96hour .

tag: inoculation

value: PHIdTri


title: TWEEN_19 with array type Brachypodium from Affymetrix

treatment_protocol: Name:TWEEN - nothing - mock inoculation tween 0.01%,pathogen infection,nothing:time 96hour .

value: TWEEN


title: PHI_WT_44 with array type Brachypodium from Affymetrix

description:
brachypodium (bd21)  - harvest date: 24-09-11
Fusarium graminearum is the causal agent of Fusarium head blight (FHB) of small-grain cereals, including wheat. Besides direct grain losses, this disease is of major concern because of the production by the pathogen of mycotoxins which are hazardous to animals, thus making the grain unfit for food or feed. Major mycotoxins produced by the fungus are trichothecens, including deoxynivalenol (DON). In our laboratory, we use Brachypodium distachyon as a model plant for cereals because of its amenability (short life cycle, numerous genomic and genetic resources, ...). We have recently shown that F. graminearum does induce head blight symptoms on this species and that DON is produced on infected spikes. We have also evidenced that a F. graminearum strain unable to produce DON exhibits reduced virulence on B. distachyon spikes, as previously shown on wheat. The aim of this project is to analyse and compare the plant response to DON producing and non-producing strains of F. graminearum. This analysis will allow to decipher the mechanisms of detoxification set up by the plant and also more specific responses due to the impact of the mycotoxin on plant metabolism and physiology.

treatment_protocol: Name:PHI_WT - nothing - fusarium graminearum strain ph-1,pathogen infection,nothing:time 96hour .


title: genomic DNA from OAA56

city: TOLEDO

first: Barbara

last: Melendez

address: AVDA. BARBER 30

department: UNIDAD DE INVESTIGACION DE PATOLOGIA MOLECULAR

institute: HOSPITAL VIRGEN DE LA SALUD

description: tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2, Raw data are available in IDAT files on each sample record and on series record in the file: Unmethylated_and_methylated_signal_intensities.txt

extract_protocol: genomic DNA was extracted and purified from samples using phenol-cloroform based methods according to standard conditions

tag: gender

value: Female

value: oligodendroglial tumor

tag: diagnosis

value: AOA

tag: 1p/19q status

value: Intact

tag: idh status

value: WT


title: H2AX_KO_ESC

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

description: ESC_h2ax_KO_vs_ESC_h2ax_Flox CGH

hyb_protocol: Labeled DNA hybridized to CGH array with Nimblegen's standard protocol

scan_protocol: Arrays were scaned with Nimblegen's standard protocol

data_processing: Arrays were processed with Nimblegen's standard protocol

source_name: ES celll (H2A.X -/-) genomic DNA

label_protocol: DNA samples were labled with Nimblegen's standard protocol

growth_protocol: culture on feeder with standard media; just before get DNA, split cells on gelatin coated plates.

extract_protocol: Genomic DNA was extracted with Qiagen Dneasy Blood ans Tissue Kit (Cat No. 69504)

treatment_protocol: No treatment

tag: strain

source_name: ESC (H2A.X f/f) genomic DNA


title: PHIdTri_7 with array type Brachypodium from Affymetrix


title: H2AX_iPSC_4N_positive_TTF1

description: iPSC_TTF1_vs_ESC CGH

source_name: iPS cell (TTF1) genomic DNA

value: 129Sv/C57 mixed background

source_name: ESC (s1b6a) genomic DNA


title: H2AX_iPSC_4N_negative_TTF2

description: iPSC_TTF2_vs_ESC CGH

source_name: iPS cell (TTF2) genomic DNA


title: genomic DNA from OA55

description: tumor

value: OA


title: HepG2, siIDE, insulin, rep3

tag: cell line


title: PHIdTri_39 with array type Brachypodium from Affymetrix


title: H2AX_iPSC_4N_negative_PF2

description: iPSC_PF2_vs_ESC CGH

source_name: iPS cell (PF2) genomic DNA


title: H2AX_iPSC_4N_negative_Bcell2

description: iPSC_Bcell2_vs_ESC CGH

source_name: iPS cell (Bcell2) genomic DNA


title: H2AX_iPSC_4N_negative_Bcell3

description: iPSC_Bcell3_vs_ESC CGH

source_name: iPS cell (Bcell3) genomic DNA


title: genomic DNA from OG54

description: tumor

value: Male

value: OD


title: genomic DNA from OGA36

description: tumor

value: AOD


title: genomic DNA from OGA35

description: tumor


title: genomic DNA from OG53

description: tumor

value: Loss

value: MUT


title: PHI_WT_13 with array type Brachypodium from Affymetrix


title: H2AX_iPSC_4N_negative_Bcell4

description: iPSC_Bcell4_vs_ESC CGH

source_name: iPS cell (Bcell4)) genomic DNA


title: H2AX_iPSC_4N_negative_TTF3

description: iPSC_TTF3_vs_ESC CGH

source_name: iPS cell (TTF3) genomic DNA


title: H2AX_iPSC_4N_positive_PF1

description: iPSC_PF1_vs_ESC CGH

source_name: iPS cell (PF1) genomic DNA


title: TWEEN_1 with array type Brachypodium from Affymetrix


title: genomic DNA from OAA47

description: tumor


title: genomic DNA from OG55

description: tumor


title: genomic DNA from OA41

description: tumor


title: genomic DNA from OG4

description: tumor


title: genomic DNA from OGA30

description: tumor


title: TWEEN_34 with array type Brachypodium from Affymetrix


title: genomic DNA from OGA29

description: tumor


title: genomic DNA from OG19

description: tumor


title: Pancreatitis_tissues_of_PatientC4

city: Guangzhou

first: Wenchao

last: Gao

state: Guangdong

address: N.O. 107, Yuanjiang Road

department: Department of Hepatobiliary Surgery

country: China

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

description: Gene expression of pancreatitis tissues

hyb_protocol: After purification, the labeled RNAs were hybridized with probes on the Hybridization Chamber gasket slides (a slide contained eight microarrays, Agilent,Arraystar Human LncRNA Array v3.0).

scan_protocol: The slides were washed carefully and scanned with Agilent Microarray Scanner G2505C.

data_processing: The raw data was analyzed with the software Agilent Feature Extraction (Agilent Technology,  version 11.0.1.1) and and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies).

source_name: Pancreatic tissues of patient C4 with pancreatitis

label_protocol: mRNA of high quality was fragmented and then labeled with Quick Amp Labeling Kit(One-Color, Cy3, Agilent).

extract_protocol: The total RNA was extracted by Trizol Reagent and cleaned up with Baseline-ZERO DNase(EPICENTR). mRNAs were purified by removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

treatment_protocol: Ethical approval for the study was granted from Sun Yat-sen Memorial Hospital Ethics Committee and written informed consent from each subject was obtained before commencing. Tissue samples were obtained from the surgery of patients. The resected tissues were collected, incubated in the liquid nitrogen immediately after the surgical resection, and stored at -80℃ for use.

value: pancreas

tag: disease status

value: pancreatitis

value: male

tag: fasting blood glucose(mmol/l)


title: genomic DNA from OGA28

description: tumor

tag: tissue


title: Pancreatic_tumors_of_PatientB4

description: Gene expression of pancreatic tumors without PCA-DM

source_name: Pancreatic tumors of patient B4 without PCA-DM

value: pancreatic tumor

tag: age


title: genomic DNA from OGA33

description: tumor


title: Pancreatic_tumors_of_PatientA4

description: Gene expression of pancreatic tumors with PCA-DM

source_name: Pancreatic tumors of patient A4 with PCA-DM


title: genomic DNA from OGA27

description: tumor


title: Pancreatitis_tissues_of_PatientC2

description: Gene expression of pancreatitis tissues

source_name: Pancreatic tissues of patient C2 with pancreatitis


title: Pancreatic_tumors_of_PatientB1

source_name: Pancreatic tumors of patient B1 without PCA-DM

value: female


title: PHI_WT_28 with array type Brachypodium from Affymetrix


title: Pancreatic_tumors_of_PatientB2

source_name: Pancreatic tumors of patient B2 without PCA-DM


title: Pancreatitis_tissues_of_PatientC3

description: Gene expression of pancreatitis tissues

source_name: Pancreatic tissues of patient C3 with pancreatitis


title: Pancreatic_tumors_of_PatientA3

source_name: Pancreatic tumors of patient A3 with PCA-DM


title: genomic DNA from OG16

description: tumor

value: Female


title: Pancreatic_tumors_of_PatientA2

source_name: Pancreatic tumors of patient A2 with PCA-DM


title: genomic DNA from OG18

description: tumor

value: oligodendroglial tumor


title: Pancreatitis_tissues_of_PatientC1

description: Gene expression of pancreatitis tissues

source_name: Pancreatic tissues of patient C1 with pancreatitis


title: genomic DNA from OG17

description: tumor


title: Pancreatic_tumors_of_PatientB3

source_name: Pancreatic tumors of patient B3 without PCA-DM


title: Pancreatic_tumors_of_PatientA1

source_name: Pancreatic tumors of patient A1 with PCA-DM


title: genomic DNA from OG14

description: tumor


title: THP-1-shCtrl

source_name: THP-1 cells engineered to stably expressed scrambled shRNA (control)

growth_protocol: RPMI 1640 supplemented with 10% FBS, penicillin (100 units/ml), streptomycin sulfate (100 mg/ml), β-mercaptoethanol (0.05 mM), L-glutamine (2mM) and puromycin (400ng/ml)

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


title: genomic DNA from OA40

description: tumor


title: Dicer Fx/Fx Experiment 20

city: London

first: Tristan

last: Rodriguez

address: Du Cane Road, Hammersmith Hospital Campus

department: National Heart and Lung Institute

country: United Kingdom

institute: NHLI Imperial College London

description: Expression data of Dicer fx/fx EpiSCs

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

scan_protocol: Samples were scanned using the Affymetrix GeneChip Scanner.

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

source_name: Dicer fx/fx EpiSCs

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

growth_protocol: EpiSCs were grown on FCS coated plates in N2B29 media supplemented with 20ng/ml Activin and 12ng/ml bFGF

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

treatment_protocol: To induce Dicer deletion, Dicer Fx/Fx EpiSCs were treated with 0.3uM 4OH-Tamoxifen for three days and left without tamoxifen for two addicional days prior to RNA extraction. Dicer Fx/Fx EpiSCs used as control were plated and divided at the same time as tamoxifen treated ones and kept in culture without tamoxifen for the duration of the experiment.

tag: cell type

value: Epiblast stem cells

tag: genotype

value: Dicer fx/fx


title: Dicer -/- Experiment 20

description: Expression data of Dicer-/- EpiSCs five days after tamoxifen induction of Dicer deletion

value: Dicer -/-


title: genomic DNA from OAA46

description: tumor

value: AOA

value: Intact

value: WT


title: genomic DNA from OAA43

description: tumor


title: THP-1-shLY6E

source_name: THP-1 cells engineered to stably expressed shRNA specifically targeting LY6E


title: Dicer -/- Experiment 19

source_name: Dicer-/- EpiSCs five days after tamoxifen induction of Dicer deletion


title: Zs-DC-Donor2 Control

city: Toronto

first: Muhammad

middle: Atif

last: Zahoor

state: Ontario

address: 101 College St.

institute: University Health Network

description: [HG-U133A_2 Plus] Affymetrix Human Genome U133A 2.0 Plus Array

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix GeneChip Operating Software (GCOS) were used for processing scanning data. Normalization was performed using the RMA method.

source_name: Healthy Donor 2

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

growth_protocol: Human PBMCs were obtained using a standard Ficoll (Pharmacia ) gradient for heparinized blood extracted from two healthy individuals. CD14+ cells were isolated by positive selection using anti-human CD14+ magnetic beads (Miltenyi). Monocyte derived dendritic cells (MDDCs) were generated by culturing CD14+ cells in RPMI (Sigma) medium supplemented with 10% FBS, 5% human AB serum, antibiotics and GlutaMax (Gibco) in the presence of recombinant human GM-CSF and IL-4  (PeproTech).

extract_protocol: MDDCs were washed three times with ice cold 1 x PBS, and total RNA was extracted using and RNeasy Mini Kit with DNase digestion, according to the manufacturer’s instructions (QIAgen).

treatment_protocol: MDDCs were infected with adenovirus Vpr or ZsGreen1 at an MOI of 100. The cells were harvested for RNA extraction at 48 h post infection.

tag: treatment

value: control

value: Human monocytes-derived dendritic cells (MDDCs)


title: genomic DNA from OAA45

description: tumor


title: genomic DNA from OA39

description: tumor

value: Male

value: OA


title: genomic DNA from OGA32

description: tumor

value: AOD


title: Vpr-DC-Donor2

value: HIV-1 Vpr espression


title: genomic DNA from OAA42

description: tumor

value: MUT


title: Dicer Fx/Fx Experiment 19

description: Expression data of Dicer fx/fx EpiSCs


title: genomic DNA from OG15

description: tumor

value: OD


title: genomic DNA from OA38

description: tumor


title: genomic DNA from OAA44

description: tumor

value: Loss


title: genomic DNA from OG5

description: tumor


title: genomic DNA from OG7

description: tumor


title: Zs-DC-Donor1 Control

source_name: Healthy Donor 1


title: genomic DNA from OG6

description: tumor


title: genomic DNA from OG12

description: tumor


title: AERD967

status: Public on Sep 05 2014

city: Bucheon-si

first: Seung-Woo

last: Shin

state: Gyeonggi-do

address: 1174 Jung-dong, Wonmi-gu

department: Genome research Center for Allergy and Respiratory Diseases

country: South Korea

institute: Soon Chun Hyang University hospital

description: Genomic DNA extracted from breast tumors was genotyped using HumanExome v1.1 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from AERD and ATA subjects was genotyped using Infinium HumanExome Genotyping BeadChips (Illumina).  We used the GenomeStudio (V2011.1) software and GT module (V1.9.4) with default parameter. Genotype values: AA,AB,BB,or NC (no call). Processed data were filtered such that processed data files contain data only for ~52K polymorphic SNPs. Processed data are available on the series record in the tar archive: All-reduced-AsthmaExome_969_processed.tar.gz. Raw data is available in the IDAT files. Raw data are also available on the series record in the tar archive: All-reduced-AsthmaExome_969_matrix_signal.tar.gz All-reduced-AsthmaExome_969_matrix_signal.tar.gz

source_name: AERD

label_protocol: 250ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

value: Female

value: Blood

tag: disease state

value: NC


title: AERD969

source_name: ATA


title: AERD968


title: AERD964


title: Dicer Fx/fx Experiment 18

description: Expression data of Dicer fx/fx EpiSCs

value: Epiblast stem cells

value: Dicer fx/fx


title: AERD962


title: genomic DNA from OGA 25

description: tumor

value: oligodendroglial tumor


title: genomic DNA from OGA 31

description: tumor

value: Intact


title: AERD961


title: Dicer -/- Experiment 18

value: Dicer -/-


title: genomic DNA from OGA 24

description: tumor

value: WT


title: AERD963


title: AERD960


title: genomic DNA from OGA 21

description: tumor


title: genomic DNA from OGA 22

description: tumor


title: AERD959


title: genomic DNA from OG20

description: tumor


title: Vpr-DC-Donor1

value: Human monocytes-derived dendritic cells (MDDCs)


title: AERD957

value: Male


title: AERD956


title: AERD955


title: AERD954


title: AERD952


title: AERD953


title: AERD951


title: AERD950


title: AERD948


title: AERD947


title: AERD946


title: AERD945


title: AERD943


title: AERD942


title: AERD944


title: AERD958


title: AERD938


title: AERD941


title: AERD937

source_name: NC


title: AERD949


title: AERD940


title: AERD934


title: AERD935


title: AERD932


title: AERD931


title: AERD930


title: AERD939


title: AERD928


title: AERD927


title: genomic DNA from OG2

description: tumor


title: AERD926


title: genomic DNA from OG11

description: tumor


title: AERD925


title: AERD966


title: genomic DNA from OG1

description: tumor


title: AERD936


title: AERD924


title: AERD965


title: AERD933


title: AERD923


title: AERD921


title: AERD919


title: AERD916


title: AERD922


title: AERD917


title: genomic DNA from OGA 26

description: tumor


title: AERD918


title: AERD915


title: AERD929


title: AERD920


title: AERD913


title: AERD911


title: AERD912


title: AERD910


title: AERD908


title: AERD906


title: AERD902


title: AERD900


title: AERD903


title: AERD905


title: AERD907


title: AERD904


title: AERD899


title: AERD914


title: AERD895


title: AERD898


title: AERD909


title: AERD891


title: AERD897


title: AERD893


title: AERD889


title: AERD901


title: AERD892


title: AERD894


title: AERD888


title: AERD887


title: AERD884


title: AERD883


title: AERD886


title: genomic DNA from OGA 23

description: tumor


title: AERD878


title: AERD882


title: AERD879


title: AERD876


title: AERD877


title: AERD880


title: AERD873


title: AERD870


title: AERD867


title: AERD871


title: AERD869


title: AERD885


title: AERD896


title: AERD874


title: AERD875


title: AERD868


title: AERD854


title: AERD857


title: AERD860


title: AERD865


title: AERD855


title: AERD845


title: AERD866


title: AERD862


title: AERD859


title: AERD864


title: AERD850


title: AERD853


title: AERD849


title: AERD852


title: AERD846


title: AERD847


title: AERD858


title: AERD863


title: AERD856


title: genomic DNA from OG3

description: tumor


title: AERD844


title: AERD843


title: AERD842


title: AERD851


title: AERD848


title: AERD841


title: AERD839


title: AERD832


title: AERD834


title: AERD835


title: AERD838


title: AERD837


title: AERD833


title: AERD829


title: AERD836


title: AERD830


title: AERD825


title: AERD831


title: AERD821


title: AERD822


title: AERD827


title: AERD823


title: AERD826


title: AERD824


title: AERD820


title: AERD819


title: AERD818


title: AERD817


title: AERD816


title: AERD815


title: AERD840


title: AERD828


title: AERD813


title: AERD811


title: AERD805


title: AERD812


title: AERD807


title: AERD810


title: AERD809


title: AERD806


title: AERD808


title: AERD803


title: AERD804


title: AERD801


title: AERD802


title: AERD800


title: AERD799


title: AERD798


title: AERD797


title: AERD794


title: AERD796


title: AERD793


title: AERD795


title: AERD791


title: AERD790


title: AERD814


title: AERD792


title: AERD789


title: AERD788


title: AERD787


title: AERD785


title: AERD780


title: AERD784


title: AERD783


title: AERD779


title: AERD786


title: AERD777


title: AERD775


title: AERD778


title: AERD782


title: AERD890


title: AERD773


title: AERD774


title: AERD771


title: AERD767


title: AERD772


title: AERD770


title: AERD766


title: AERD769


title: AERD768


title: AERD765


title: AERD763


title: AERD764


title: AERD762


title: AERD760


title: AERD776


title: AERD781


title: AERD759


title: AERD757


title: AERD755


title: AERD758


title: AERD753


title: AERD751


title: AERD752


title: AERD756


title: AERD754


title: AERD748


title: AERD749


title: AERD750


title: AERD746


title: AERD744


title: AERD745


title: AERD743


title: AERD741


title: AERD747


title: AERD742


title: AERD761


title: AERD740


title: AERD737


title: AERD739


title: AERD738


title: AERD736


title: AERD735


title: AERD733


title: AERD734


title: AERD732


title: AERD731


title: AERD729


title: AERD727


title: AERD861


title: AERD726


title: AERD724


title: AERD721


title: AERD720


title: AERD719


title: AERD717


title: AERD718


title: AERD716


title: AERD715


title: AERD872


title: AERD714


title: AERD713


title: AERD712


title: AERD710


title: AERD711


title: AERD708


title: AERD707


title: AERD704


title: AERD702


title: AERD703


title: AERD722


title: AERD723


title: AERD701


title: AERD881


title: AERD705


title: AERD728


title: AERD706


title: AERD700


title: AERD699


title: AERD725


title: AERD696


title: AERD693


title: AERD698


title: AERD692


title: AERD695


title: AERD697


title: AERD694


title: AERD691


title: AERD688


title: AERD709


title: AERD689


title: AERD687


title: AERD690


title: AERD686


title: AERD685


title: AERD683


title: AERD684


title: AERD680


title: AERD679


title: AERD675


title: AERD677


title: AERD674


title: AERD673


title: AERD672


title: AERD671


title: AERD666


title: AERD658


title: AERD668


title: AERD661


title: AERD681


title: AERD663


title: AERD660


title: AERD669


title: AERD667


title: AERD682


title: AERD670


title: AERD665


title: AERD664


title: AERD676


title: AERD659


title: AERD730


title: AERD652


title: AERD657


title: AERD656


title: AERD655


title: AERD653


title: AERD654


title: AERD651


title: AERD649


title: AERD647


title: AERD650


title: AERD662


title: AERD645


title: AERD639


title: AERD646


title: AERD638


title: AERD637


title: AERD643


title: AERD644


title: AERD648


title: AERD635


title: AERD629


title: AERD642


title: AERD633


title: AERD632


title: AERD631


title: AERD630


title: AERD628


title: AERD625


title: AERD627


title: AERD622


title: AERD641


title: AERD636


title: AERD621


title: AERD623


title: AERD617


title: AERD618


title: AERD615

value: ATA


title: AERD640


title: AERD608


title: AERD613


title: AERD614


title: AERD609


title: AERD616


title: AERD607


title: AERD634


title: AERD619


title: AERD624


title: AERD606


title: AERD626


title: AERD678


title: AERD610


title: AERD602


title: AERD603


title: AERD611


title: AERD612


title: AERD605


title: AERD601


title: AERD620


title: AERD599


title: AERD600


title: AERD598


title: AERD597


title: AERD596


title: AERD595


title: AERD592


title: AERD591


title: AERD587


title: AERD589


title: AERD573


title: AERD588


title: AERD583


title: AERD576


title: AERD585


title: AERD582


title: AERD575


title: AERD578


title: AERD581


title: AERD574


title: AERD580


title: AERD586


title: AERD570


title: AERD571


title: AERD577


title: AERD604


title: AERD569


title: AERD567


title: AERD565


title: AERD564


title: AERD584


title: AERD579


title: AERD594


title: AERD572


title: AERD593


title: AERD566


title: AERD590


title: AERD563


title: AERD568


title: AERD553


title: AERD555


title: AERD548


title: AERD558


title: AERD547


title: AERD561


title: AERD551


title: AERD545


title: AERD544


title: AERD543


title: AERD559


title: AERD549


title: AERD554


title: AERD557


title: AERD560


title: AERD539


title: AERD550


title: AERD542


title: AERD537


title: AERD538


title: AERD541


title: AERD536


title: AERD535


title: AERD562


title: AERD556


title: AERD533


title: AERD534


title: AERD552


title: AERD531


title: AERD532


title: AERD540


title: AERD520


title: AERD526


title: AERD529


title: AERD527


title: AERD518


title: AERD525


title: AERD517


title: AERD521


title: AERD519


title: AERD524


title: AERD530


title: AERD522


title: AERD523


title: AERD512


title: AERD513


title: AERD515


title: AERD514


title: AERD509


title: AERD510


title: AERD546


title: AERD508


title: AERD506


title: AERD505


title: AERD507


title: AERD528


title: AERD516


title: AERD504


title: AERD503


title: AERD500


title: AERD491


title: AERD511


title: AERD497


title: AERD492


title: AERD498


title: AERD499


title: AERD493


title: AERD495


title: AERD489


title: AERD490


title: AERD502


title: AERD496


title: AERD494


title: AERD486


title: AERD501


title: AERD487


title: AERD480


title: AERD485


title: AERD481


title: AERD488


title: AERD484


title: AERD479


title: AERD478


title: AERD483


title: AERD476


title: AERD477


title: AERD475


title: AERD474


title: AERD469


title: AERD471


title: AERD467


title: AERD472


title: AERD473


title: AERD470


title: AERD463


title: AERD466


title: AERD464


title: AERD462


title: AERD461


title: AERD465


title: AERD458


title: AERD456


title: AERD459


title: AERD457


title: AERD454


title: AERD451


title: AERD453


title: AERD450


title: AERD452


title: AERD449


title: AERD455


title: AERD447


title: AERD448


title: AERD468


title: AERD445


title: AERD443


title: AERD439


title: AERD442


title: AERD444


title: AERD440


title: AERD437


title: AERD460


title: AERD436


title: AERD435


title: AERD433


title: AERD438


title: AERD429


title: AERD434


title: AERD431


title: AERD428


title: AERD430


title: AERD425


title: AERD432


title: AERD424


title: AERD427


title: AERD422


title: AERD423


title: AERD426


title: AERD446


title: AERD421


title: AERD420


title: AERD419


title: AERD417


title: AERD418


title: AERD415


title: AERD411


title: AERD408


title: AERD412


title: AERD410


title: AERD407


title: AERD405


title: AERD406


title: AERD409


title: AERD392


title: AERD403


title: AERD395


title: AERD396


title: AERD393


title: AERD401


title: AERD397


title: AERD399


title: AERD398


title: AERD394


title: AERD416


title: AERD414


title: AERD387


title: AERD390


title: AERD389


title: AERD391


title: AERD404


title: AERD400


title: AERD386


title: AERD388


title: AERD384


title: AERD383


title: AERD381


title: AERD382


title: AERD402


title: AERD380


title: AERD379


title: AERD378


title: AERD371


title: AERD374


title: AERD376


title: AERD375


title: AERD373


title: AERD370


title: AERD372


title: AERD441


title: AERD369


title: AERD413


title: AERD368


title: AERD363


title: AERD367


title: AERD366


title: AERD361


title: AERD365


title: AERD362


title: AERD364


title: AERD359


title: AERD355


title: AERD356


title: AERD357


title: AERD358


title: AERD360


title: AERD353


title: AERD352


title: AERD354


title: AERD351


title: AERD349


title: AERD350


title: AERD345


title: AERD348

value: AERD


title: AERD347


title: AERD346


title: AERD344


title: AERD343


title: AERD342


title: AERD341


title: AERD340


title: AERD339


title: AERD337


title: AERD336


title: AERD335


title: AERD338


title: AERD331


title: AERD332


title: AERD330


title: AERD329


title: AERD328


title: AERD482


title: AERD327


title: AERD326


city: Nashville

first: Ian

last: Macara

state: TN

address: 465 21st Avenue South U

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
Trypsinized+Mock Sorted, biological rep1
Mock_Sorted_01

hyb_protocol: Samples were hybridized according to the The Ambion® WT Expression Kit protocol

data_processing:
Date processing was facilitated using R-BioConductor packages, mainly Oligo and LIMMA packages, for data normalization, and gene expression differentiation.
MoGene-1_0-st-v1 Transcript Cluster Annotations, from Affymetrix

source_name: Mock Sorted

label_protocol: Samples were labeled using Affymetrix WT genechip WT terminal labeling kit according to manufacturer protocols (GeneChip® WT Terminal Labeling and Hybridization User Manual Rev. 4)

growth_protocol: Mammary epithelial cells harvested from 8-9 week old C3H female mice

extract_protocol: RNA was extracted using the miRVana miRNA Isolation kit (Ambion) according to the “Total RNA” protocol as described by the manufacturer.

treatment_protocol: Cells dissected and released from fat tissue with collagenase prior to digestion with trypsin, following treatment with trypsin, or following treatment with trypsin and a mock FACS sort

value: 8-9 weeks

value: Mammary gland

value: epithelial cells

tag: genotype/variation

value: wild-type

value: Trypsinized+Mock FACS sorted


title: AERD325

value: Female

value: Blood


description:
Trypsinized+Mock Sorted, biological rep3
Mock_Sorted_03


title: Trypsinized, biological rep2

description:
Trypsinized, biological rep2
Trypsinized_02

source_name: Trypsinized

value: Trypsinized


title: Trypsinized, biological rep1

description:
Trypsinized, biological rep1
Trypsinized_01


description:
Trypsinized+Mock Sorted, biological rep2
Mock_Sorted_02


title: AERD324


title: AERD323


title: Untrypsinized, biological rep3

description:
Untrypsinized, biological rep3
Untrypsinized_03

source_name: Untrypsinized

value: Untrypsinized


title: Untrypsinized, biological rep2

description:
Untrypsinized, biological rep2
Untrypsinized_02


title: AERD334

value: NC


title: Untrypsinized, biological rep1

description:
Untrypsinized, biological rep1
Untrypsinized_01


title: AERD322


title: AERD333


title: AERD320


title: AERD321


title: AERD319


title: AERD318


title: AERD316


title: AERD315


title: AERD312


title: AERD314


title: AERD313


title: 10d IL-5-3

city: Cincinnati

first: Patricia

middle: C.

last: Fulkerson

address: 3333 Burnet Ave, ML 7028

institute: Cincinnati Children's Hospital Medical Center

description: ILS  10d  6    M   Gene  1.0   ST.rma-gene-default

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

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

data_processing:
affymetrix-algorithm-name = rma-gene-default (v.1.0); program-name = Expression Console (v.1.1.2637.26569)
Microarray data were further analyzed using the GeneSpring  software (Agilent Technologies, Santa Clara, CA). Statistical significance was determined at P < 0.05 with One-way ANOVA and Benjamini-Hochberg multiple testing correction.

source_name: Pooled LDBM Cells_IL-5_10 days

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

growth_protocol: LDBM cells from pooled Balb/c bone marrow were cultured in media with SCF and FLT3L at 100 ng/mL for 4 days prior to IL-5 stimulation

extract_protocol: RNA was extraced from cultured LDBM cells using TriPure Reagent according to manufacturer's instruction.

tag: strain background

value: Balb/c

value: Low-density bone marrow (LDBM) cells

tag: stimulated with

value: IL-5 for 10 days


title: AERD311

tag: gender


title: Trypsinized, biological rep3

description:
Trypsinized, biological rep3
Trypsinized_03


title: AERD310


title: 4d IL-5-2

description: ILS  4d  2    M   Gene  1.0   ST.rma-gene-default

source_name: Pooled LDBM Cells_IL-5_4 days

value: IL-5 for 4 days


title: AERD309

value: Male


title: AERD317

value: ATA


title: 10d IL-5-2

description: ILS  10d  5    M   Gene  1.0   ST.rma-gene-default


title: 10d IL-5-1

description: ILS  10d  4    M   Gene  1.0   ST.rma-gene-default


title: 4d IL-5-3

description: ILS  4d  3    M   Gene  1.0   ST.rma-gene-default


title: AERD308


title: NO IL-5-3

description: ILS  NO  4  M   Gene  1.0   ST.rma-gene-default

source_name: Pooled LDBM Cells_pre-stimulation

value: none (pre-stimulation control)


title: AERD307


title: 4d IL-5-1

description: ILS  4d  1    M   Gene  1.0   ST.rma-gene-default


title: KDEL-bodipy-biological rep3

city: Naples

first: Jorge

last: Cancino

address: Pietro Castellino 111

department: Life Sciences

country: Italy

institute: IBP

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with the Bioconductor package xps using RMA   method for normalizing and summarizing probe level intensity measurements.

source_name: HeLa treated with KDEL-bodipy peptide for 6 hours

label_protocol: standard Affymetrix protocol

extract_protocol: trizol

value: KDEL-bodipy peptide for 6 hours

value: HeLa


title: KDELR-biological rep3

source_name: HeLa cells transfected with KDELR1 for 72 hours

value: transfected with KDELR1 for 72 hours


title: AERD305

description: Genomic DNA extracted from breast tumors was genotyped using HumanExome v1.1 BeadChip (Illumina).


title: NO IL-5-2

description: ILS  NO  2   M   Gene  1.0   ST.rma-gene-default


title: AERD303


title: KDEL-bodipy-biological rep1


title: NO IL-5-1

description: ILS  NO  1   M   Gene  1.0   ST.rma-gene-default


title: AERD302


title: AERD301


title: AERD299


title: Adult tooth PDL tissue-2

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

institute: Yonsei University College of Dentistry

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: adult tooth PDL

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: The PDL samples were obtained from healthy persons (n=10;from 2 males and 3 females, aged 11-19 years) and the pulp samples were obtained from healthy matured permanent premolar extracted for orthodontic reasons from healthy persons (n=24; from 6 males and 6 females, aged 18-25 years).

extract_protocol: The PDL and the pulp tissues were homogenized using a homogenizer. The Rneasy Fibrous mini kit(Qiagen) was then used to extract total RNA from the PDL and pulp tissues, according to the manufacturer's instructions

treatment_protocol: Extracted teeth were immediately frozen and stored in liguid nitrogen. The PDL tissues were obtained carefully using sterile curetes from the middle-third. Teeth were subsequently crushed with a bolt cutter and pulp tissues were carefully obtained using a sterile tweezers.

value: adult tooth PDL


title: AERD298


title: AERD297


title: AERD304


title: AERD296


title: KDELR-biological rep1


title: KDELR-biological rep2


title: control-biological rep2

source_name: HeLa not treated

value: untreated


title: Adult tooth PDL tissue-1


title: AERD306

value: Female


title: AERD295

value: Blood


title: KDEL-bodipy-biological rep2


title: control-biological rep1


title: AERD377


title: AERD293


title: AERD290


title: AERD292


title: AERD291


title: AERD288

value: AERD


title: AERD287


title: AERD286


title: AERD300


title: control-biological rep3


title: AERD283


title: AERD282


title: AERD280


title: AERD281


title: AERD279


title: AERD294


title: AERD276


title: AERD278


title: AERD277


title: AERD275


title: AERD270


title: AERD271


title: AERD273


title: AERD272


title: AERD269


title: AERD268


title: AERD267


title: AERD284


title: AERD285


title: AERD265


title: AERD274


title: AERD261


title: AERD264


title: AERD263


title: AERD262


title: AERD260


title: AERD258


title: Lymphoblastoid cell line_Individual 5-7_cycle 6_hybridization_batch_4

city: Philadelphia

first: Minal

last: Caliskan

state: PA

address: 415 Curie Blvd., Room 540

institute: University of Pennsylvania

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Raw data across four hybridization batches are included in the file named Matrix non-normalized_batch 1, Matrix non-normalized_batch 2, Matrix non-normalized_batch 3, Matrix non-normalized_batch 4. Among all probes targeted, 24,314 probes passed our probe quality control check (probes that mapped to unique Ensembl gene IDs and probes that did not contain any HapMap SNPs with minor allele frequency > 0.01 in the CEU population). We performed our analyses in 12,972 of the 24,314 probes that were detected as expressed (probes with a detection P value < 0.05 in at least 25% of the 187 samples). Log2-transformed and rank-invariant normalized (using scripts developed in-house by Russell Bainer)  probe intensity data are included in data tables.

source_name: Lymphoblastoid cell line

label_protocol: Standard Illumina label protocol

growth_protocol: A unit of blood was obtained from six unrelated healthy individuals of Caucasian ethnicity by Research Blood Components, LLC. Unpurified buffy coats were prepared from whole blood and shipped to the University of Chicago. At the University of Chicago, peripheral blood mononuclear cells were isolated by further processing of the unpurified buffy coats using ficoll-hypaque protocol. CD20+ B cells are isolated from peripheral blood mononuclear cells using magnetic anti-CD20 mAb-coated microbeads (MACs, Miltenyi Biotec, CA, USA). LCLs are established by EBV-mediated transformation, using the protocol provided by Coriell Cell Repositories.

extract_protocol: Total RNA was extracted using the Rneasy Plus Mini Kit

tag: hybridization batch

value: Lymphoblastoid cell line


title: AERD266


title: AERD257


title: B cell_Individual 2rep_hybridization_batch_4

source_name: B cell

value: B cell


title: Lymphoblastoid cell line_Individual 4-7_cycle 6_hybridization_batch_4


title: AERD256


title: Lymphoblastoid cell line_Individual 6-4_cycle 6_hybridization_batch_4


title: AERD259


title: Lymphoblastoid cell line_Individual 5-5_cycle 2rep_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 6-5_cycle 2rep_hybridization_batch_4


title: AERD385


title: Lymphoblastoid cell line_Individual 4-1_cycle 6_hybridization_batch_4


title: AERD255


title: B cell_Individual 1rep_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 2-1_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 5-1_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 6-2_cycle 6_hybridization_batch_4


title: B cell_Individual 6rep_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 3-5_cycle 6_hybridization_batch_4


title: AERD253


title: Lymphoblastoid cell line_Individual 2-4_cycle 6_hybridization_batch_4


title: AERD254


title: Lymphoblastoid cell line_Individual 5-4_cycle 6_hybridization_batch_4


title: AERD252


title: AERD251


title: AERD250


title: AERD245


title: AERD246


title: AERD248


title: AERD244


title: Lymphoblastoid cell line_Individual 3-1_cycle 6_hybridization_batch_4


title: AERD247


title: Lymphoblastoid cell line_Individual 1-3_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 2-6_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 2-3_cycle 6_hybridization_batch_4


title: AERD243


title: Lymphoblastoid cell line_Individual 5-8_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 3-3_cycle 6_hybridization_batch_4


title: AERD242


title: Lymphoblastoid cell line_Individual 1-6_cycle 4rep_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 1-4_cycle 6_hybridization_batch_4


title: AERD241


title: Lymphoblastoid cell line_Individual 2-1_cycle 4rep_hybridization_batch_4


title: AERD240


title: AERD239


title: AERD249


title: Lymphoblastoid cell line_Individual 4-3_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 3-4_cycle 4rep_hybridization_batch_4


title: AERD238


title: AERD289


title: AERD237


title: Lymphoblastoid cell line_Individual 6-2_cycle 4rep_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 1-3_cycle 2rep_hybridization_batch_4


title: AERD236


title: AERD235


title: Lymphoblastoid cell line_Individual 6-1_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 1-2_cycle 6_hybridization_batch_4


title: AERD234


title: AERD233


title: Lymphoblastoid cell line_Individual 2-4_cycle 2rep_hybridization_batch_4


title: AERD231


title: AERD232


title: Lymphoblastoid cell line_Individual 3-4_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 4-6_cycle 6_hybridization_batch_4


title: AERD229


title: Lymphoblastoid cell line_Individual 2-2_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 3-1_cycle 2rep_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 5-8_cycle 4rep_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 4-7_cycle 4rep_hybridization_batch_4


title: AERD228


title: AERD227


title: AERD225


title: Lymphoblastoid cell line_Individual 4-3_cycle 2rep_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 1-6_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 1-5_cycle 6_hybridization_batch_4


title: AERD224


title: Lymphoblastoid cell line_Individual 5-5_cycle 6_hybridization_batch_4


title: AERD223


title: Lymphoblastoid cell line_Individual 4-8_cycle 6_hybridization_batch_4


title: AERD230


title: Lymphoblastoid cell line_Individual 6-5_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 1-8_cycle 6_hybridization_batch_4


title: AERD222


title: AERD221


title: Lymphoblastoid cell line_Individual 6-6_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 2-5_cycle 6_hybridization_batch_4


title: AERD220


title: AERD226


title: B cell_Individual 5rep_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 6-3_cycle 6_hybridization_batch_4


title: Lymphoblastoid cell line_Individual 1-6_cycle 4_hybridization_batch_3


title: B cell_Individual 4rep_hybridization_batch_4


title: AERD215


title: Lymphoblastoid cell line_Individual 2-5_cycle 4_hybridization_batch_3


title: AERD216


title: AERD218


title: AERD217


title: AERD213


title: AERD214


title: AERD210


title: AERD211


title: AERD212


title: AERD209


title: AERD208


title: AERD219


title: AERD206


title: AERD207


title: Lymphoblastoid cell line_Individual 6-4_cycle 0rep_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 1-5_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 2-3_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 6-6_cycle 2rep_hybridization_batch_3


title: B cell_Individual 5rep_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 2-6_cycle 4_hybridization_batch_3


title: AERD205


title: Lymphoblastoid cell line_Individual 3-5_cycle 2rep_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 5-7_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 5-5_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 3-5_cycle 4_hybridization_batch_3


title: AERD204


title: AERD202


title: AERD203


title: AERD201


title: Lymphoblastoid cell line_Individual 2-1_cycle 2rep_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 3-1_cycle 0rep_hybridization_batch_3


title: AERD199


title: AERD198


title: AERD197


title: AERD196


title: AERD195


title: AERD200


title: Lymphoblastoid cell line_Individual 4-3_cycle 2rep_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 2-2_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 4-7_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 3-4_cycle 4_hybridization_batch_3


title: AERD194


title: AERD189


title: AERD191


title: AERD193


title: AERD190


title: B cell_Individual 4rep_hybridization_batch_3


title: AERD192


title: Lymphoblastoid cell line_Individual 4-6_cycle 0rep_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 6-3_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 1-3_cycle 4_hybridization_batch_3


title: B cell_Individual 1rep_hybridization_batch_3


title: AERD188


title: AERD187


title: Lymphoblastoid cell line_Individual 5-4_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 1-8_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 6-2_cycle 4_hybridization_batch_3


title: B cell_Individual 3rep_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 6-6_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 1-4_cycle 4_hybridization_batch_3


title: AERD186


title: Lymphoblastoid cell line_Individual 4-1_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 3-3_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 1-2_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 6-1_cycle 4_hybridization_batch_3


title: AERD183


title: AERD184


title: AERD181


title: AERD185


title: AERD179


title: Lymphoblastoid cell line_Individual 5-5_cycle 2rep_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 3-1_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 2-4_cycle 4_hybridization_batch_3


title: AERD180


title: AERD178


title: Lymphoblastoid cell line_Individual 4-8_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 2-1_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 4-6_cycle 4_hybridization_batch_3


title: B cell_Individual 6rep_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 6-5_cycle 4_hybridization_batch_3


title: AERD176


title: Lymphoblastoid cell line_Individual 5-5_cycle 0rep_hybridization_batch_3


title: AERD175


title: AERD174


title: AERD182


title: Lymphoblastoid cell line_Individual 1-5_cycle 2rep_hybridization_batch_3


title: AERD173


title: AERD172


title: AERD171


title: AERD177


title: Lymphoblastoid cell line_Individual 5-1_cycle 4_hybridization_batch_3


title: AERD169


title: Lymphoblastoid cell line_Individual 5-8_cycle 4_hybridization_batch_3


title: Lymphoblastoid cell line_Individual 6-4_cycle 4_hybridization_batch_3


title: AERD170


title: B cell_Individual 2rep_hybridization_batch_3


title: AERD168


title: Lymphoblastoid cell line_Individual 1-8_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 3-5_cycle 2_hybridization_batch_2


title: AERD167


title: AERD166


title: AERD164


title: Lymphoblastoid cell line_Individual 1-3_cycle 0rep_hybridization_batch_2


title: AERD163


title: Lymphoblastoid cell line_Individual 6-6_cycle 2_hybridization_batch_2


title: AERD162


title: B cell_Individual 3rep_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 6-3_cycle 0rep_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 2-5_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 4-3_cycle 4_hybridization_batch_3


title: AERD160


title: AERD159


title: AERD157


title: AERD158


title: AERD156


title: Lymphoblastoid cell line_Individual 2-2_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 4-7_cycle 2_hybridization_batch_2


title: AERD165


title: AERD155


title: AERD154


title: Lymphoblastoid cell line_Individual 5-1_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 6-5_cycle 2_hybridization_batch_2


title: AERD161


title: Lymphoblastoid cell line_Individual 4-3_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 4-8_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 1-6_cycle 2_hybridization_batch_2


title: AERD153


title: B cell_Individual 1rep_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 3-3_cycle 2_hybridization_batch_2


title: AERD151


title: Lymphoblastoid cell line_Individual 4-3_cycle 0rep_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 6-1_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 5-2_cycle 2_hybridization_batch_2


title: AERD149


title: AERD148


title: Lymphoblastoid cell line_Individual 2-4_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 2-3_cycle 2_hybridization_batch_2


title: AERD146


title: B cell_Individual 5rep_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 4-1_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 6-2_cycle 2_hybridization_batch_2


title: AERD145


title: Lymphoblastoid cell line_Individual 1-4_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 6-4_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 6-5_cycle 0rep_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 1-3_cycle 2_hybridization_batch_2


title: AERD143


title: AERD144


title: AERD142


title: Lymphoblastoid cell line_Individual 5-4_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 4-7_cycle 0rep_hybridization_batch_2


title: AERD140


title: AERD152


title: AERD147


title: AERD150


title: AERD138


title: AERD137


title: Lymphoblastoid cell line_Individual 3-4_cycle 2_hybridization_batch_2


title: B cell_Individual 2rep_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 1-2_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 4-6_cycle 2_hybridization_batch_2


title: AERD136


title: Lymphoblastoid cell line_Individual 5-2_cycle 0rep_hybridization_batch_2


title: AERD135


title: Lymphoblastoid cell line_Individual 2-6_cycle 2_hybridization_batch_2


title: AERD133


title: AERD132


title: AERD141


title: Lymphoblastoid cell line_Individual 4-4_cycle 2_hybridization_batch_2


title: AERD131


title: AERD130


title: Lymphoblastoid cell line_Individual 1-5_cycle 2_hybridization_batch_2


title: AERD139


title: Lymphoblastoid cell line_Individual 3-1_cycle 2_hybridization_batch_2


title: AERD129


title: Lymphoblastoid cell line_Individual 2-5_cycle 0rep_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 5-7_cycle 2_hybridization_batch_2


title: AERD128


title: Lymphoblastoid cell line_Individual 6-3_cycle 2_hybridization_batch_2


title: AERD127


title: AERD126


title: AERD125


title: Lymphoblastoid cell line_Individual 3-5_cycle 0rep_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 5-5_cycle 2_hybridization_batch_2


title: AERD134


title: Lymphoblastoid cell line_Individual 5-8_cycle 2_hybridization_batch_2


title: Lymphoblastoid cell line_Individual 2-1_cycle 2_hybridization_batch_2


title: B cell_Individual 4rep_hybridization_batch_2


title: AERD122


title: AERD124


title: B cell_Individual 6rep_hybridization_batch_2


title: AERD121


title: AERD120


title: AERD118


title: AERD119


title: AERD117


title: AERD116


title: AERD114


title: AERD123


title: AERD111


title: AERD112


title: AERD106


title: AERD108


title: AERD109


title: AERD107


title: AERD110


title: healthy control NA terminal ileum P18

first: Professor Anthony

middle: W

last: Segal

address: Rayne Building, 5 University Street

department: Division of Medicine

institute: Centre for Molecular Medicine

hyb_protocol: 750 ng of biotin-labelled cRNA (150 ng/μl) was hybridised to Illumina HumanHT-12v4 beadarrays (Illumina, CA, USA) for 16 hours at 58°C.

scan_protocol: Following hybridisation, beadarrays were washed and stained with streptavidin-Cy3 (GE Healthcare, UK), scanned using the Beadarray reader, and processed using Genome Studio software (Illumina).

data_processing: Expression data for Illumina HumanHT-12v4 beadarrays was normalised after Log2 transformation within Genome Studio (Illumina) using cubic spline normalisation followed by ComBat normalisation for chip effects in R.

label: Biotin, Cy3

source_name: TI

extract_protocol: Biopsies (~25 mg) were lysed in a 300 µl RNeasy Fibrous Tissue kit (Qiagen, Hilden, Germany) RLT buffer and 0.14 M β-mercaptoethanol (β-ME) (Sigma-Aldrich, St. Louis, USA), and then homogenised by centrifugation at 10,000 g through a Qiashredder column (Qiagen). Protein was removed by incubation for 10 minutes at 55°C with 10 µl Proteinase K (20 mg/ml) (>600 mAU/ml) (Qiagen).  Total RNA was extracted on RNeasy Mini spin columns and DNA was removed with RNase free DNase digestion (Qiagen). Samples were included in the microarray experiment if they had an optical density ratio reading of 1.8-2.0 OD260/OD280 and >1.8 OD260/OD230 as well as a RNA concentration of greater than 50 ng/μl.  For each biopsy sample, 500 ng of total RNA was amplified and purified using the Illumina TotalPrep-96 RNA Amplification kit (Ambion®, Life Technologies™, CA, USA).

tag: biopsy

value: Pinch biopsy

value: M

value: healthy control

tag: phenotype

value: terminal ileum


title: ulcerative colitis Left terminal ileum P14

label_protocol: 750 ng of biotin-labelled cRNA (150 ng/μl) was hybridised to Illumina HumanHT-12v4 beadarrays (Illumina, CA, USA) for 16 hours at 58°C.

value: F

value: ulcerative colitis

value: Left


title: healthy control NA terminal ileum P19


title: AERD115

value: Male

value: ATA


title: AERD105


title: AERD103


title: AERD104


title: ulcerative colitis Pancolitis terminal ileum P22

value: Pancolitis


title: ulcerative colitis Left terminal ileum P48


title: healthy control NA terminal ileum P41


title: AERD113


title: Crohn's disease Ileal terminal ileum P32

value: Crohn's disease

value: Ileal


title: ulcerative colitis Pancolitis terminal ileum P25


title: healthy control NA terminal ileum P38


title: AERD101


title: healthy control NA terminal ileum P11


title: Crohn's disease Ileal terminal ileum P44


title: AERD099


title: healthy control NA terminal ileum P29


title: ulcerative colitis Pancolitis terminal ileum P33


title: AERD097


title: AERD098

value: Female


title: AERD096

value: Blood


title: ulcerative colitis Left terminal ileum P34


title: healthy control NA terminal ileum P36


title: AERD094


title: ulcerative colitis Pancolitis terminal ileum P56


title: ulcerative colitis Pancolitis terminal ileum P4


title: AERD093


title: AERD091


title: AERD092


title: AERD090


title: AERD102


title: AERD088


title: AERD100


title: AERD089


title: AERD087


title: ulcerative colitis Pancolitis terminal ileum P16


title: healthy control NA terminal ileum P8


title: Crohn's disease Ileal terminal ileum P31


title: AERD095


title: AERD083


title: healthy control NA terminal ileum P37


title: healthy control NA terminal ileum P9


title: AERD082


title: AERD079


title: healthy control NA terminal ileum P28


title: AERD080


title: AERD078


title: healthy control NA terminal ileum P27


title: ulcerative colitis Pancolitis terminal ileum P24


title: AERD075


title: AERD077


title: AERD074

value: AERD


title: AERD084


title: AERD072


title: AERD085


title: AERD086


title: AERD070


title: AERD069


title: AERD071


title: AERD076


title: ulcerative colitis Left terminal ileum P6


title: ulcerative colitis Pancolitis terminal ileum P23


title: AERD068


title: healthy control NA terminal ileum P63


title: AERD067


title: Crohn's disease Ileal terminal ileum P1


title: healthy control NA ascending colon P19

source_name: Ascol

value: ascending colon


title: AERD066

source_name: AERD


title: AERD064


title: AERD065

source_name: ATA


title: healthy control NA ascending colon P41


title: AERD063


title: AERD073


title: AERD061


title: AERD062


title: AERD060


title: healthy control NA ascending colon P38


title: AERD059


title: healthy control NA ascending colon P63


title: ulcerative colitis Left ascending colon P61


title: AERD055


title: AERD057


title: AERD058


title: ulcerative colitis Pancolitis ascending colon P4


title: AERD053


title: AERD054


title: AERD056


title: Crohn's disease Ileal ascending colon P31


title: Crohn's disease Colonic terminal ileum P30

value: Colonic


title: AERD051


title: AERD050

source_name: NC


title: AERD052


title: Crohn's disease Ileocolonic ascending colon P12

value: Pinch biopsy

value: Ileocolonic


title: ulcerative colitis Pancolitis ascending colon P25

value: M


title: AERD045


title: AERD049


title: AERD048


title: AERD044


title: AERD043


title: AERD042


title: ulcerative colitis Left ascending colon P14


title: AERD041


title: healthy control NA ascending colon P50

value: healthy control


title: healthy control NA ascending colon P18


title: healthy control NA ascending colon P37

value: F


title: healthy control NA ascending colon P9


title: healthy control NA ascending colon P29


title: ulcerative colitis Pancolitis ascending colon P24

value: ulcerative colitis


title: AERD036


title: AERD046


title: healthy control NA ascending colon P27


title: AERD040


title: AERD035


title: AERD033


title: AERD038


title: AERD032


title: AERD031


title: AERD039


title: AERD030


title: AERD034


title: AERD047


title: AERD028


title: AERD029


title: AERD037


title: AERD027


title: ulcerative colitis Pancolitis ascending colon P16


title: ulcerative colitis Left ascending colon P6

value: Left


title: AERD025

value: Male


title: ulcerative colitis Left ascending colon P48


title: ulcerative colitis Pancolitis ascending colon P15


title: AERD024

value: ATA


title: AERD023


title: AERD021


title: AERD020


title: AERD022


title: AERD026


title: AERD018


title: AERD017


title: AERD015


title: AERD014


title: AERD016


title: Crohn's disease Ileal ascending colon P3


title: ulcerative colitis Pancolitis ascending colon P22

value: Pancolitis


title: AERD013


title: Crohn's disease Ileal ascending colon P1

value: Crohn's disease