title: SSc-ILD-PH_PAH-49

status: Public on Apr 30 2012

type: RNA

city: baltimore

first: chris

last: cheadle

state: MD

address: 5200 Eastern Ave

department: SOM

country: USA

institute: JHU

description: Interstitial Lung Disease

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction. The  expression values for all the probes for each sample were scaled to have median 256 (28) and then log (base 2) transformed before performing statistical analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

label_protocol: Total RNA was labled with the Ambion TotalPrep RNA Amplification Kit according to manufacturers suggested protocols.

extract_protocol: Venous blood was collected by simple venipuncture under aseptic conditions. All samples were processed within two hours of collection to minimize gene expression variations associated with longer sample incubation times.  PBMCs were separated by Ficoll density gradient, and were immediately lysed in Trizol reagent (Invitrogen, Carlsbad, California). Additional purification was performed on RNeasy columns (Qiagen, Valencia, CA 913555, cat. no. 74104).  The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: disease status

value: Interstitial Lung Disease


title: SSc-ILD-PH_PAH-54

description: Interstitial Lung Disease


title: SSc-ILD-PH_PAH-19

description: Interstitial Lung Disease


title: SSc-ILD-PH_PAH-36

description: Interstitial Lung Disease


title: SSc-ILD-PH_PAH-52

description: Interstitial Lung Disease


title: SSc without PAH_PH5-30

description: Scleroderma only

value: Scleroderma only


title: SSc without PAH_PH5-28

description: Scleroderma only


title: SSc without PAH_PH5-25

description: Scleroderma only


title: SSc without PAH_PH5-29

description: Scleroderma only


title: SSc without PAH_PH5-26

description: Scleroderma only


title: SSc without PAH_PH5-23

description: Scleroderma only


title: SSc-ILD-PH_PAH-62

description: Interstitial Lung Disease


title: SSc-ILD-PH_PAH-80

description: Interstitial Lung Disease


title: SSc-ILD-PH_PAH-132

description: Interstitial Lung Disease


title: SSc without PAH_PH5-24

description: Scleroderma only


title: SSc without PAH_PH5-27

description: Scleroderma only


title: SSc without PAH_PH5-19

description: Scleroderma only


title: SSc without PAH_PH5-20

description: Scleroderma only


title: SSc without PAH_PH5-22

description: Scleroderma only


title: SSc without PAH_PH5-17

description: Scleroderma only


title: SSc without PAH_PH5-18

description: Scleroderma only


title: SSc without PAH_PH5-16

description: Scleroderma only


title: SSc without PAH_PH5-13

description: Scleroderma only


title: SSc without PAH_PH5-14

description: Scleroderma only


title: SSc without PAH_PH5-15

description: Scleroderma only


title: SSc without PAH_PH5-12

description: Scleroderma only


title: SSc with PAH_PH10

description: Scleroderma with Pulmonary Arterial Hypertension


title: SSc with PAH_PH8

value: Scleroderma with Pulmonary Arterial Hypertension


title: SSc with PAH_PAH-86


title: SSc with PAH_PAH-78


title: SSc with PAH_PH5


title: SSc with PAH_PAH-85


title: SSc with PAH_PAH-94


title: SSc with PAH_PAH-82


title: SSc with PAH_PAH-79


title: SSc with PAH_PH9


title: SSc without PAH_PH5-11

description: Scleroderma only


title: SSc with PAH_PAH-96


title: SSc with PAH_PH7


title: SSc with PAH_PAH-65b


title: SSc with PAH_PAH-77


title: SSc with PAH_PAH-73


title: SSc with PAH_PAH-61


title: SSc with PAH_PAH-72


title: SSc with PAH_PAH-64b


title: SSc with PAH_PAH-74


title: SSc with PAH_PAH-44


title: SSc with PAH_PAH-70b


title: SSc with PAH_PAH-55


title: SSc with PAH_PAH-40


title: SSc with PAH_PAH-35


title: SSc with PAH_PAH-38


title: SSc with PAH_PAH-26


title: SSc with PAH_PAH-30


title: SSc with PAH_PAH-21


title: SSc with PAH_PAH-145


title: SSc with PAH_PAH-43


title: SSc with PAH_PAH-34


title: SSc with PAH_PAH-42


title: SSc with PAH_PAH-17


title: SSc with PAH_PAH-144


title: SSc with PAH_PAH-137


title: SSc with PAH_PAH-139


title: SSc with PAH_PAH-138


title: SSc with PAH_PAH-09


title: SSc with PAH_PAH-135


title: SSc with PAH_PAH-24


title: IPAH_PAH-84

description: Idiopathic Pulmonary Arterial Hypertension


title: IPAH_PAH-69

value: Idiopathic Pulmonary Arterial Hypertension


title: IPAH_PAH-76


title: IPAH_PAH-93


title: IPAH_PAH-83


title: IPAH_PAH-67


title: IPAH_PAH-60


title: IPAH_PAH-75


title: SSc with PAH_PAH-08


title: IPAH_PAH-51


title: IPAH_PAH-53


title: IPAH_PAH-59


title: IPAH_PAH-68b


title: IPAH_PAH-48


title: IPAH_PAH-47


title: IPAH_PAH-31


title: IPAH_PAH-33


title: IPAH_PAH-41


title: IPAH_PAH-27


title: IPAH_PAH-14


title: IPAH_PAH-16-2


title: IPAH_PAH-46


title: IPAH_PAH-136


title: Control_PAH-91

description: control

value: control


title: IPAH_PAH-23


title: Control_PAH-92

description: control


title: Control_PAH-90

description: control


title: Control_PAH-98

description: control


title: IPAH_PAH-133


title: IPAH_PAH-18


title: Control_PAH-95

description: control


title: IPAH_PAH-32


title: IPAH_PAH-39


title: IPAH_PAH-25


title: IPAH_PAH-20


title: IPAH_PAH-22


title: Control_PAH-99

description: control


title: Control_PAH-87

description: control


title: Control_PAH-127

description: control


title: Control_PAH-121

description: control


title: Control_PAH-115

description: control


title: Control_PAH-120

description: control


title: Control_PAH-89

description: control


title: Control_PAH-130

description: control


title: Control_PAH-88

description: control


title: Control_PAH-122

description: control


title: Control_PAH-111

description: control


title: Control_PAH-116

description: control


title: Control_PAH-117

description: control


title: Control_PAH-106

description: control


title: Control_PAH-128

description: control


title: Control_PAH-119

description: control


title: Control_PAH-126

description: control


title: Control_PAH-112

description: control


title: Control_PAH-124

description: control


title: Control_PAH-105

description: control


title: Control_PAH-114

description: control


title: Control_PAH-113

description: control


title: Control_PAH-108

description: control


title: Control_PAH-123

description: control


title: Control_PAH-110

description: control


title: Control_PAH-118

description: control


title: Control_PAH-109

description: control


title: Control_PAH-129

description: control


title: Control_PAH-107

description: control


title: Control_PAH-125

description: control


title: SSc with PAH_PAH-134


title: Control_PAH-102

description: control


title: Control_PAH-101

description: control


title: Control_PAH-103

description: control


title: Control_PAH-100

description: control


title: MM-17

city: Chicago

first: Antonia

last: Navarro

state: IL

address: 303 E. Superior st

department: OB/GYN

institute: Northwestern University

description: myometrium sample

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.5.5). It was vst transformed and quantile normalized.

source_name: myometrium

label_protocol: standard as recommended by illumina

extract_protocol: RNeasy kit

tag: tissue

value: myometrium


title: Control_PAH-104

description: control


title: MM-1

description: myometrium sample


title: MM-7

description: myometrium sample


title: LM-11

description: leiomyoma sample

source_name: leiomyoma

value: leiomyoma


title: LM-14

description: leiomyoma sample


title: LM-7

description: leiomyoma sample


title: LM-9

description: leiomyoma sample


title: MM-9

description: myometrium sample


title: MM-13

description: myometrium sample


title: LM-13

description: leiomyoma sample


title: LM-2

description: leiomyoma sample


title: MM-3

description: myometrium sample


title: MM-5

description: myometrium sample


title: MM-2

description: myometrium sample


title: LM-10

description: leiomyoma sample


title: MM-6

description: myometrium sample


title: LM-5

description: leiomyoma sample


title: LM-3

description: leiomyoma sample


title: MM-11

description: myometrium sample


title: MM-10

description: myometrium sample


title: LM-1

description: leiomyoma sample


title: MM-14

description: myometrium sample


title: LM-17

description: leiomyoma sample


title: LM-6

description: leiomyoma sample


title: MM-8

description: myometrium sample


title: LM-8

description: leiomyoma sample


title: MM-15

description: myometrium sample


title: Control_PAH-142

description: control


title: MM-4

description: myometrium sample


title: associated normal breast tissue 4

type: genomic

city: Birmingham

first: Farida

last: Latif

address: Vincent Drive

department: Medical and Molecular Genetics, School of Clinical and Experimental Medicine

country: United Kingdom

institute: University of Birmingham

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

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

data_processing: BeadStudio software v3.2

molecule: genomic DNA

source_name: associated normal tissue 4

label_protocol: Standard illumina protocol

extract_protocol: High-molecular-weight DNA was prepared by standard proteinase K digestion followed by phenol-chloroform extraction

tag: gender

value: Female

tag: disease state

value: normal


title: MM-12

description: myometrium sample


title: associated ductal breast carcinoma 3

source_name: associated breast carcinoma 3

value: carcinoma


title: associated ductal breast carcinoma 4

source_name: associated breast carcinoma 4


title: MAT1-2 mating-type

city: Bunkyo-ku

first: Ryuta

last: Wada

state: Tokyo

address: 1-1-1 Yayoi

department: Biotechnology

country: Japan

institute: University of Tokyo

description:
DPY agar culturing NSPlD-M2 2days
Gene expression data from MAT1-2 strain in Aspergillus oryzae

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

scan_protocol: Genechips were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with GCOS program (version 1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Aspergillus oryzae

source_name: Aspergillus oryzae mycelium growth inducing mating-type gene

label_protocol: Biotinylated cRNA were prepared from 3 mg total RNA using GeneChip 3' IVT Express Kit.

growth_protocol: Approximately 2x10^6 conidia of Aspergillus oryzae RIB40-derived NSPlD1 (Maruyama et al 2008) were inoculated into 100 ml DPY liquid medium supplemented with 0.5% uridine and 0.2% uracil. After 24 h growth(30℃), 200 mg of mycelia were shifted onto DPY agar medium covered with cellulose acetate membrane (Membrane Filter, Advantec Toyo, Tokyo, Japan) and further cultivated for 48 h (30℃).

extract_protocol: Mycelia were immediately frozen in liquid nitrogen and powdered to prepare total RNA using the ISOGEN RNA Extraction Reagent (Nippon Gene) and the RNeasy plant mini kit (Qiagen, Venlo, Netherlands) was used for further purification.

treatment_protocol: Mycelia grown on cellulose acetate membrane for 48 h was subjected to RNA extraction.

tag: strain

value: MAT1-2 mating-type

tag: structure

value: Mycelia


title: MAT1-1 mating-type

description:
DPY agar culturing NSPlD1 2days
Gene expression data from MAT1-1 strain in Aspergillus oryzae

value: MAT1-1 mating-type


title: ductal breast carcinoma 39

source_name: breast carcinoma 39


title: associated ductal breast carcinoma 2

source_name: associated breast carcinoma 2


title: associated normal breast tissue 3

source_name: associated normal tissue 3


title: associated ductal breast carcinoma 1

source_name: assocaited breast carcinoma 1


title: MDA039

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48701 probes on the Human-6 beadChip ver. 2 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-6 V2.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label: Biotin

source_name: gastric tumor tissue

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000).

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD).

value: Male

tag: baseline stage

value: II

tag: grade


title: MDA038

value: IV


title: MDA040


title: ductal breast carcinoma 37

source_name: breast carcinoma 37


title: LM-12

description: leiomyoma sample


title: MDA037

value: IIIA


title: associated normal breast tissue 1

source_name: associated normal tissue 1


title: MDA036


title: ductal breast carcinoma 36

source_name: breast carcinoma 36


title: ductal breast carcinoma 38

source_name: breast carcinoma 38


title: MDA033


title: MDA035


title: ductal breast carcinoma 33

source_name: breast carcinoma 33


title: ductal breast carcinoma 30

source_name: breast carcinoma 30


title: ductal breast carcinoma 32

source_name: breast carcinoma 32


title: ductal breast carcinoma 31

source_name: breast carcinoma 31


title: MDA034

value: IB


title: MDA028


title: ductal breast carcinoma 34

source_name: breast carcinoma 34


title: ductal breast carcinoma 29

source_name: breast carcinoma 29


title: ductal breast carcinoma 35

source_name: breast carcinoma 35


title: MDA032


title: MDA031


title: LM-4

description: leiomyoma sample

source_name: leiomyoma


title: ductal breast carcinoma 28

source_name: breast carcinoma 28


title: MDA030


title: MDA027


title: MDA025


title: ductal breast carcinoma 26

source_name: breast carcinoma 26


title: ductal breast carcinoma 24

source_name: breast carcinoma 24


title: MDA029

value: IIIB


title: MDA024


title: ductal breast carcinoma 23

source_name: breast carcinoma 23


title: MDA023

source_name: gastric tumor tissue


title: MDA022


title: MDA026


title: ductal breast carcinoma 27

source_name: breast carcinoma 27


title: ductal breast carcinoma 22

source_name: breast carcinoma 22


title: MDA021


title: LM-15

description: leiomyoma sample


title: MDA018


title: MDA020


title: ductal breast carcinoma 25

source_name: breast carcinoma 25


title: ductal breast carcinoma 21

source_name: breast carcinoma 21


title: MDA017


title: ductal breast carcinoma 20

source_name: breast carcinoma 20


title: MDA019


title: ductal breast carcinoma 15

source_name: breast carcinoma 15


title: ductal breast carcinoma 16

source_name: breast carcinoma 16


title: ductal breast carcinoma 17

source_name: breast carcinoma 17


title: ductal breast carcinoma 19

source_name: breast carcinoma 19


title: MDA016


title: ductal breast carcinoma 13

source_name: breast carcinoma 13


title: ductal breast carcinoma 18

source_name: breast carcinoma 18


title: MDA011


title: ductal breast carcinoma 11

source_name: breast carcinoma 11


title: ductal breast carcinoma 9

source_name: breast carcinoma 9


title: MDA014


title: MDA012


title: MDA010


title: ductal breast carcinoma 12

source_name: breast carcinoma 12


title: MDA015


title: MDA009


title: ductal breast carcinoma 10

source_name: breast carcinoma 10


title: MDA013


title: MDA007


title: MDA008


title: 12h irradiated and amputated animals

city: Cambridge

first: Danielle

last: Wenemoser

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Biological replica 1 of 3. fragments from irradiated animals harvested 12h following amputation

hyb_protocol: Agilent DNA microarray scanner

scan_protocol: Agilent’s Feature Extraction Image Analysis software with the default two-color gene expression protocol

data_processing: Agilent two-color arrays were within-array normalized by loess, followed by between-array quantile normalization of average intensities across channels (Aquantile). Differential expression analysis was performed using a moderated t-test, as implemented in the limma package of Bioconductor, with P-value correction by false discovery rate.

organism: Schmidtea mediterranea

source_name: regenerating fragments

label_protocol: RNA was labeled using Perkin Elmer's ASAP labeling kit

growth_protocol: Clone W4 Schmidtea mediterranea were kept at 20degree Celsius in Monbijou Salts

extract_protocol: Total RNA was extracted using TRIZOL according to manufacterer's instructions

treatment_protocol: Animals were amputated 7 days following feeding and left to regenerate for indicated time points. Irradiated animals were amputated 5 days following irradiation (Cesium source - 6000rad)

value: regenerating fragments

tag: treatment

value: irradiated and amputated

tag: time

tag: sample type

value: clone W4, asexual

source_name: irradiated and freshly amputated fragments


title: MDA005

source_name: gastric tumor tissue


title: ductal breast carcinoma 14

source_name: breast carcinoma 14


title: ductal breast carcinoma 7

source_name: breast carcinoma 7


title: ductal breast carcinoma 6

source_name: breast carcinoma 6


title: associated normal breast tissue 2

source_name: associated normal tissue 2


title: ductal breast carcinoma 8

source_name: breast carcinoma 8


title: MDA006


title: 1h irradiated and amputated animals

description: Biological replica 1 of 3. fragments from irradiated animals harvested 1h following amputation

value: irradiated and freshly amputated fragments

value: control


title: ductal breast carcinoma 5

source_name: breast carcinoma 5

value: Female


title: 6h irradiated and amputated animals

description: Biological replica 1 of 3. fragments from irradiated animals harvested 6h following amputation


title: 6h amputated animals

description: Biological replica 1 of 3. fragments harvested 6h following amputation

value: amputated

source_name: freshly amputated fragments

value: freshly amputated fragments


title: MDA004


title: 30min irradiated and amputated animals

description: Biological replica 1 of 3. fragments from irradiated animals harvested 30min following amputation


title: ductal breast carcinoma 4

source_name: breast carcinoma 4

value: carcinoma


title: 3h irradiated and amputated animals

description: Biological replica 1 of 3. fragments from irradiated animals harvested 3h following amputation


title: 1h amputated animals

description: Biological replica 1 of 3. fragments harvested 1h following amputation


title: 12h amputated animals

description: Biological replica 1 of 3. fragments harvested 12h following amputation


title: 24h amputated runt-1 RNAi animals (replicates 1-3)

description: Biological replicas 1 - 3 combined for analysis. RNAi animals harvested 24h after amputation

source_name: runt-1(RNAi) animals

label_protocol: RNA was labeled using Agilent's two-color QuickAmp labeling kit

extract_protocol: Total RNA was extracted 5 days following the last feeding using TRIZOL according to manufacterer's instructions

treatment_protocol: Animals were fed respective RNAi food (bacteria expressing dsRNA of gene of interest mixed with homogenized calf liver) every 4 days for 12 days.

tag: tissue type

source_name: unc-22(RNAi) animals


title: MDA001


title: X1 neoblasts, isolated from 9h amputated runt-1 RNAi animals (replicates 1-3)

description: Biological replicas 1 - 3 combined for analysis. X1 cells from RNAi animals harvested 9h after amputation

source_name: X1 cells from runt-1(RNAi) animals

source_name: X1 cells from unc-22(RNAi) animals


title: 5min amputated runt-1 RNAi animals (replicates 1-3)

description: Biological replicas 1 - 3 combined for analysis. RNAi animals harvested right after amputation


title: MDA002


title: ductal breast carcinoma 1

source_name: breast carcinoma 1


title: ductal breast carcinoma 3

source_name: breast carcinoma 3


title: 9h amputated runt-1 RNAi animals (replicates 1-3)

description: Biological replicas 1 - 3 combined for analysis. RNAi animals harvested 9h after amputation


title: MDA003


title: 30min amputated animals

description: Biological replica 1 of 3. fragments harvested 30min following amputation

source_name: regenerating fragments


title: ClockKO_ZT20_pool1

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: Affymetrix Mouse Gene 1.0 ST arrays were hybridized with 5 microgramme of labeled, amplified cDNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each tissues separately.

organism: Mus musculus

source_name: whole kidney from clock KO mice, ZT20

label_protocol: RNA extracted from 2 or 3 mice were combined and 100 ng was used to perform target preparation using the Whole Transcript Sense Target Labeling Protocol procedure (Affymetrix, High Wycombe, UK).

growth_protocol: A colony of the clock deficient mice was established from breeding pairs of clock(+/-) heterozygous mice originally generated by Debruyne et al. (Neuron, 50: 465-477, 2006). All mice were adapted to a 12 hours light, 12 hours dark cycle (LD) for two weeks  and then placed in constant darkness (DD) for 30 hours before sacrifice.

extract_protocol: RNA from whole kidneys of wild-type or clock deficient mice was isolated with the standard method of Chomczynski and Sacchi (Anal Biochem, 162: 156-159, 1987). All RNA quantities were assessed by NanoDrop-ND-1000 spectrophotometer and the quality of RNA was controlled on Aligent 2100 bioanalyzer chips.

treatment_protocol: Animals were sacrificed for microdissection every 4 hours, i.e. at ZT0, ZT4, ZT8, ZT12, ZT16 and ZT20 (ZT – Zeitgeber (circadian) time, indicates time of light-on as ZT0 and time of light-off as ZT12).

value: left kidney

tag: genotype/variation

value: clock(-/-)

tag: zt time


title: LM-1

description: leiomyoma sample

data_processing: Genome Studio output

source_name: leiomyoma

extract_protocol: standard as recommended by illumina

value: leiomyoma


title: hepatopancreas_normoxia_4h_rep1

city: Charleston

first: Karen

last: Burnett

state: SC

address: 205 Fort Johnson Road

department: Biology

institute: College of Charleston

description: Gene expression in hepatopancreas of shrimp exposed to normoxia for 4h

hyb_protocol: Labeled cRNA (1.6 ug) from each animal was purified, fragmented, and hybridized at 65°C for 17 h to an individual, custom-made olignucleotide microarray following the manufacturer’s protocol for One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling, Agilent Technologies, USA).

scan_protocol: Slides were washed then scanned using an Agilent® DNA Microarray Scanner, version B.  This procedure was repeated to obtain individual microarray datasets from seven individuals in each treatment group (H 4 h, H 24 h, HH 4 h, HH 24 h, and N 4 h) and six individual animals from N 24 h.

data_processing: All microarray hybridization data were extracted, quality checked, filtered and normalized according to the recommended pipelines for Agilent platform microarrays in both Agilent Feature Extraction v10.7 (Agilent Technologies, USA) and Rosetta Resolver 7.0 gene expression analysis software.  This process involved preliminary signal processing based on the over 1400 controls printed on every array.  These controls included multiple, replicate positive controls for both L. vannamei and Agilent spike-ins which were used to assess labeling and hybridization efficiency and to generate a standard curve.  Control probes and flagged datapoints with high deviation in pixel intensity were removed, then the processed signal was normalized using a mean value generated by a group dependent, global scaling algorithm inside the Rosetta Resolver environment.  This included an Agilent-specific error-model based forward transformation to stabilize variance.  The transformed data were then detrended, inverse transformed, averaged and subjected to analysis of variance (ANOVA) and ratio building applications.  Data from biological replicate arrays were combined (n=7) for each experimental group.  Combined genes with average signal intensities below or above the detection range as determined by Agilent® spike-ins were not used in subsequent analyses.  Additional details may be found in Weng et al. (2006).

organism: Penaeus vannamei

source_name: hepatopancreas, 4h, normoxia, replicate 1

label_protocol: A 600 ng sample of total RNA from the hepatopancreas of each individual animal (biological replicate) was amplified and labeled fluorescently with cyanine 3-CTP dye in a single step using the Agilent Quick Amp labeling kit.

growth_protocol: Juvenile shrimp were provided by the Waddell Mariculture Center (Bluffton, SC, USA).  All animals were kept in well-aerated, UV-sterilized recirculating seawater systems (30‰ salinity, 22-25°C, pH 7.9-8.0) at the Hollings Marine Laboratory (HML, Charleston, SC, USA) and were fed commercial shrimp pellets (Rangen Inc., Buhl, ID, USA) daily.  Only shrimp 2-5 days post-molt (intermolt shrimp) were used in experiments.  Each animal was confirmed to be in the early stage of anecdysis by histological analysis (Chan et al., 1988)

extract_protocol: Immediately following the applied treatment (H, HH, or N), shrimp were removed from their respective tanks, weighed, and dissected to obtain a posterior portion of hepatopancreas (~ 0.04 g) from each animal.  All dissections were performed at the same time of day, to minimize possible circadian effects.  Tissue samples were preserved in RNAlater® (Qiagen, USA).  RNA was extracted from individual preserved hepatopancreas samples using silica-membrane spin columns, (Qiagen RNeasy® Mini Kits,Qiagen, USA), digested with DNase on-column, and eluted with 50 µl of nuclease-free water.  The eluate was divided into 5 aliquots and stored at −80°C.  RNA yield and quality was determined using a micro-volume spectrophotometer, ND 1000® (Thermo Scientific, Waltham, MA, USA) and an Agilent 2100 bioanalyzer capillary RNA gel (Agilent, Santa Clara, CA, USA).

treatment_protocol: Gas treatments were administered to groups of three animals in a randomized scheme until a total of 9 animals had been exposed to each of the gas conditions (below) for 4 h and 24 h.  Each group of three randomly selected shrimp was transferred from stock tanks into a single 42 l tank containing well-aerated UV-sterilized seawater (20 kPa, 30‰ salinity, 25°C) in a temperature-controlled environmental chamber.  Food was withheld for 24 h after transfer, then one of following gas conditions was applied for 4 or 24 h:  Hypoxia treatment (H) - Po2 = 4.0 kPa, Pco2 < 0.06 kPa, and pH = 7.8-8.0.  Hypercapnic hypoxia treatment (HH) - Po2 = 4.0 kPa, Pco2 = 1.8 kPa, and pH = 6.8-6.9.  Normoxia treatment (N) - Po2 = 20.0 kPa, Pco2 < 0.06 kPa, and pH = 7.8-8.0.  These gas conditions are well-within the normal range of conditions that routinely occur in tidal estuaries (http://dmo.baruch.sc.edu) and aquaculture production ponds of Central and South America (de la Vega, 2010, pers. comm.).  Low oxygen in the H and HH treatments was achieved by gassing the water intermittently with air using a system described previously (Mikulski et al., 2000; Macey et al., 2008b).  Briefly the oxygen demand of the shrimp and a gentle bubbling of the water with pure nitrogen lowered the oxygen pressures to the desired levels.  Initial reductions in oxygen from air saturation occurred over a 20 to 30 min period.  The Po2 of the water was monitored using an oxygen electrode (YSI Model 58, Yellow Springs, OH, USA) and data acquisition system (Sable Systems International, Las Vegas, NV, USA); a small aerator was controlled by the data acquisition system to achieve and maintain the desired Po2.  In the HH treatment, oxygen was controlled as above and hypercapnia was induced by gassing the water continuously with 2% CO2 supplied by a Wösthoff (Bochum, Germany) gas mixing pump.  In the 4 h hypoxia treatment, for example, the 3 shrimp were in the 42 l tank for 24 h, at time zero oxygen pressure was lowered (taking 20 to 30 minutes) and at 4 h shrimp were removed for dissection of the hepatopancreas.

tag: life stage

value: juvenile

tag: molt stage

value: intermolt

value: exposed to normoxia for 4h


title: ductal breast carcinoma 2

source_name: breast carcinoma 2


title: ClockKO_ZT12_pool2

source_name: whole kidney from clock KO mice, ZT12


title: hepatopancreas_hypercapnichypoxia_4h_rep9

description: Gene expression in hepatopancreas of shrimp exposed to hypercapnic hypoxia for 4h

source_name: hepatopancreas, 4h, hypercapnic hypoxia, replicate 9

value: exposed to hypercapnic hypoxia for 4h


title: ClockKO_ZT16_pool1

source_name: whole kidney from clock KO mice, ZT16


title: hepatopancreas_hypercapnichypoxia_4h_rep8

source_name: hepatopancreas, 4h, hypercapnic hypoxia, replicate 8


title: ClockKO_ZT20_pool2


title: MM-1

description: myometrium sample

source_name: myometrium

value: myometrium


title: hepatopancreas_hypercapnichypoxia_4h_rep7

source_name: hepatopancreas, 4h, hypercapnic hypoxia, replicate 7


title: hepatopancreas_hypercapnichypoxia_4h_rep6

source_name: hepatopancreas, 4h, hypercapnic hypoxia, replicate 6


title: MM-13

description: myometrium sample


title: ClockKO_ZT8_pool2

source_name: whole kidney from clock KO mice, ZT8


title: ClockKO_ZT12_pool1


title: LM-13

description: leiomyoma sample


title: ClockKO_ZT0_pool1

source_name: whole kidney from clock KO mice, ZT0


title: ClockKO_ZT8_pool1


title: ClockKO_ZT4_pool2

source_name: whole kidney from clock KO mice, ZT4


title: LM-17

description: leiomyoma sample


title: hepatopancreas_hypercapnichypoxia_4h_rep5

source_name: hepatopancreas, 4h, hypercapnic hypoxia, replicate 5


title: WT_ZT20_pool2

source_name: whole kidney from wild-type mice, ZT20

value: wild type


title: MM-17

description: myometrium sample


title: WT_ZT20_pool1


title: ClockKO_ZT0_pool2


title: MM-7

description: myometrium sample


title: hepatopancreas_hypercapnichypoxia_4h_rep 4

source_name: hepatopancreas, 4h, hypercapnic hypoxia, replicate 4


title: ClockKO_ZT4_pool1


title: WT_ZT16_pool2

source_name: whole kidney from wild-type mice, ZT16


title: hepatopancreas_hypoxia_4h_rep9

description: Gene expression in hepatopancreas of shrimp exposed to hypoxia for 4h

source_name: hepatopancreas, 4h, hypoxia, replicate 9

value: exposed to hypoxia for 4h


title: WT_ZT12_pool1

source_name: whole kidney from wild-type mice, ZT12


title: LM-7

description: leiomyoma sample

source_name: leiomyoma


title: MM-16

description: myometrium sample


title: WT_ZT12_pool2


title: hepatopancreas_hypoxia_4h_rep8

source_name: hepatopancreas, 4h, hypoxia, replicate 8


title: PCNSL_Case G

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13400 E. Shea Blvd, MCCRB-300

institute: Mayo Clinic Arizona

hyb_protocol: Aliquouts of agilent Oligo aCGH hybridization kit were added to the samples as recommended by the manafacture. Samples were heat at 95C for 3 minutes, then 37C for 30 minutes. Samples were dispense in the arrays and hybridized at 65C for 40 hours in a hybrization oven at 20rpm.

scan_protocol: Scanned on DNA Microarray Scanner (Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: DNA tumor sample

label_protocol:
frozen_samples: 1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns
FFPE_samples: 2ug of DNA were labeled with the ULS kit (Agilent) for FFPE tissues according to manufacturer’s recommendation.

extract_protocol:
Frozen samples: Genomic DNA was obtained from frozen tumors using the Puregene Core A kit (Qiagen) according to manufacturer’s recommendations.
FFPE samples: Samples were deparaffinized using heptane at room temperature for 1 hour.  Methanol was added and the sample was pelleted by centrifugation.  DNA was obtained using the AllPrep DNA/RNA FFPE kit (Qiagen) according to manufacturer’s recommendations.

tag: age

tag: pathology

value: DLBCL

tag: subtype

value: Non-GC

tag: ps

value: R-MPV

value: Brain

source_name: Female reference DNA sample

label_protocol:
Frozen samples: 1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns
FFPE samples: 2ug of DNA were labeled with the ULS kit (Agilent) for FFPE tissues according to manufacturer’s recommendation.

value: reference


title: LM-16

description: leiomyoma sample

tag: tissue


title: hepatopancreas_hypoxia_4h_rep7

source_name: hepatopancreas, 4h, hypoxia, replicate 7


title: WT_ZT4_pool1

source_name: whole kidney from wild-type mice, ZT4


title: WT_ZT16_pool1


title: 3h amputated animals

description: Biological replica 1 of 3. fragments harvested 3h following amputation

source_name: regenerating fragments

value: regenerating fragments

value: amputated

value: clone W4, asexual

source_name: freshly amputated fragments

value: freshly amputated fragments

value: control


title: hepatopancreas_hypercapnichypoxia_4h_rep3

source_name: hepatopancreas, 4h, hypercapnic hypoxia, replicate 3

value: juvenile


title: WT_ZT4_pool2

value: left kidney


title: hepatopancreas_hypoxia_4h_rep3

source_name: hepatopancreas, 4h, hypoxia, replicate 3

value: intermolt


title: WT_ZT0_pool1

source_name: whole kidney from wild-type mice, ZT0


title: WT_ZT8_pool1

source_name: whole kidney from wild-type mice, ZT8


title: MM-18

description: myometrium sample

source_name: myometrium


title: WT_ZT0_pool2


title: hepatopancreas_hypoxia_4h_rep10

source_name: hepatopancreas, 4h, hypoxia, replicate 10


title: hepatopancreas_hypoxia_4h_rep11

source_name: hepatopancreas, 4h, hypoxia, replicate 11


title: LM-18

description: leiomyoma sample

value: leiomyoma


title: PCNSL_Case F

tag: gender

value: Male


title: PCNSL_Case D

label_protocol:
Frozen samples: 1ug of tumor and reference DNA were independently labeled with Agilent Genomic DNA labeling Kit PLUS as recommended by the manafacture. Cy5 dye was used to label tumor DNA samples and Cy3 to label reference DNA samples. Next, labeled genomic reactions were cleaned-up with Microcon YM-30 columns
FFPE samples:  2ug of DNA were labeled with the ULS kit (Agilent) for FFPE tissues according to manufacturer’s recommendation.

value: Female


title: hepatopancreas_normoxia_24h_rep9

description: Gene expression in hepatopancreas of shrimp exposed to normoxia for 24h

source_name: hepatopancreas, 24h, normoxia, replicate 9

value: exposed to normoxia for 24h


title: LM-11

description: leiomyoma sample


title: hepatopancreas_hypoxia_4h_rep1

source_name: hepatopancreas, 4h, hypoxia, replicate 1

value: exposed to hypoxia for 4h


title: PCNSL_Case E

value: DLBCL

value: Non-GC


title: tetraploidy (174_3)

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: sample group

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: embryonic fibroblast, tetraploid

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

growth_protocol: Cells were grow in DMEM containing 10% FBS to 80% confluence

extract_protocol: Total RNA was purified with RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. ).  After ribosomal RNA reduction (Invitrogen, Carlsbad, CA) to remove most of the 18S and 28S rRNAs, the GeneChip WT (whole transcript) cDNA Synthesis Kit, WT cDNA Amplification Kit, and WT Terminal Labeling Kit (Affymetrix, Inc., Santa Clara, CA) were used for target preparation. Ten µg of cRNA (antisense RNA) were added to the second-cycle cDNA reaction followed by fragmentation and Terminal Labeling process.

value: abnormal DNA contents


title: LM-9

description: leiomyoma sample

source_name: leiomyoma


title: hepatopancreas_normoxia_24h_rep6

source_name: hepatopancreas, 24h, normoxia, replicate 6


title: P14, normal

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: skin

hyb_protocol: Standard Affymetrix hybridization protocol to Affymetrix Human Gene 1.0 ST arrays (Santa Clara, CA)

scan_protocol: Standard Affymetrix scanning protocol

data_processing: For gene array analysis, RMA algorithm and xps package from Bioconductor was used for preprocessing. After background correction, instead of the default quantile normalization, we used robust quantiles normalization. The reference distribution (to which all chips are normalized) calculated by quantiles normalization has very narrow distribution (small SD), due mainly to 3 chips that had narrow intensity distribution. By using robust quantiles normalization, the reference distribution to which all chips are normalized, is calculated not considering outliers chips. This rendered a normalization in the normal range for this chip series.

source_name: P14, normal

label_protocol: NuGen system (San Carlos, CA)

extract_protocol: Frozen skin biopsies were stored in -800C\. RNA was extracted after homogenization using the RNeasy Micro Kit (for NOMID) or Rneasy Mini Kit (for normal skin) (Qiagen, Valencia, CA, U.S.A.)

tag: patient

tag: disease state

value: normal

tag: disease development

tag: treatment 1

value: Steroids 0mg/kg

value: skin


title: P9, lesional

description: skin

source_name: P9, lesional

value: NOMID

value: lesional

value: Steroids 0.97mg/kg


title: hepatopancreas_normoxia_24h_rep8

source_name: hepatopancreas, 24h, normoxia, replicate 8

value: juvenile

tag: treatment


title: MM-14

description: myometrium sample

value: myometrium


title: P15, normal

description: skin

source_name: P15, normal


title: LM-14

description: leiomyoma sample


title: diploidy (FW_1)

description: control group

source_name: embryonic fibroblast, diploid

value: normal control


title: diploidy (FW_3)

description: control group


title: P6, post-treatment non-lesional

description: skin

source_name: P6, post

value: post-treatment non-lesional

tag: treatment 2

value: anakinra


title: tetraploidy (174_1)

description: sample group


title: P6, pre-treatment non-lesional

description: skin

source_name: P6, nonlesional

value: pre-treatment non-lesional


title: tetraploidy (174_2)

description: sample group


title: P9, post-treatment non-lesional

description: skin

source_name: P9, post

value: Steroids 0.67mg/kg


title: MM-9

description: myometrium sample


title: diploidy (FW_2)

description: control group


title: hepatopancreas_normoxia_24h_rep3

source_name: hepatopancreas, 24h, normoxia, replicate 3

value: intermolt

value: exposed to normoxia for 24h


title: P3, post-treatment non-lesional

description: skin

source_name: P3, post

value: Steroids 0.3mg/kg


title: P3, lesional

description: skin

source_name: P3, lesional

value: Steroids 0.55mg/kg


title: hepatopancreas_normoxia_24h_rep2

source_name: hepatopancreas, 24h, normoxia, replicate 2


title: hepatopancreas_normoxia_24h_rep4

source_name: hepatopancreas, 24h, normoxia, replicate 4


title: MM-10

description: myometrium sample

source_name: myometrium


title: LM-10

description: leiomyoma sample

value: leiomyoma


title: Salmonella_enterica_serovar_Typhimurium_UK1_0.3M NaCl_delta_iacP_mutant_rep2

city: Seoul

first: Yong Keun

last: Park

address: Anam-dong 5Ga, Seoungbuk-Gu

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

description: This sample is of wild-type Salmonella enterica serovar Typhimurium UK1 delta-iacP mutant. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.2

hyb_protocol: Labeled cDNAs were hybridized to a NimbleGen 4-plex array which was designed based on S. Typhimurium strain LT2 (Roche NimbleGen) for 12 h at 42 °C using MAUI system (Biomicro systems).

scan_protocol: Arrays were washed and scanned using an Axon GenePix 4000B scanner (Molecular Devices).

data_processing: Gene expression levels were calculated with NimbleScan software version 2.4 (Roche NimbleGen) using the median polish normalization method and relative signal intensities were generated using the robust multi-array average algorithm. Data analysis was performed using GeneSpring GX 7.3.1 (Agilent Technologies).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1

source_name: Salmonella enterica serovar Typhimurium UK1 wild-type delta-iacP

label_protocol: Each total RNA sample was labeled with Cyanine 3 (Cy3)-conjugated dCTP by a reverse transcription reaction, and then was resuspended in 10 µl of hybridization solution (GenoCheck, Korea).

growth_protocol: Salmonella enterica serovar Typhimurium UK1 and UK1 delta-iacP mutant were grown to mid-log phase (O.D.600nm 0.8) in LB broth containing 0.3M NaCl at 37°C (Kim et al. Infect. Immun. 79(4):1440-1450).

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., USA). RNA quality and concentration was determined by analysis with a Nano drop (School of Life Science and Biotechnology,Korea University,Republic of Korea).

treatment_protocol: Salmonellal enterica serovar Typhimurium UK1 delta-iacP mutant were grown to mid-log phase (O.D.600nm 0.8) in LB broth containing 0.3M NaCl at 37°C (Kim et al. Infect. Immun. 79(4):1440-1450).

tag: genotype

value: deletion mutant delta-iacP

tag: phenotype

value: slightly attenuated

tag: accession


title: Salmonella_enterica_serovar_Typhimurium_UK1_0.3M NaCl_delta_iacP_mutant_rep1

description: This sample is of wild-type Salmonella enterica serovar Typhimurium UK1 delta-iacP mutant. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: Salmonella_enterica_serovar_Typhimurium_UK1_0.3M NaCl_wild-type_rep2

description: This sample is of wild-type Salmonella enterica serovar Typhimurium UK1. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.2

source_name: Salmonella enterica serovar Typhimurium UK1 wild-type

value: Wild-type

value: normal


title: P2, pre-treatment non-lesional

description: skin

source_name: P2, nonlesional

value: NOMID

value: Steroids 0mg/kg

value: skin


title: Salmonella_enterica_serovar_Typhimurium_UK1_0.3M NaCl_wild-type_rep1

description: This sample is of wild-type Salmonella enterica serovar Typhimurium UK1. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.


title: hepatopancreas_hypercapnichypoxia_24h_rep8

description: Gene expression in hepatopancreas of shrimp exposed to hypercapnic hypoxia for 24 h

source_name: hepatopancreas, 24h, hypercapnic hypoxia, replicate 8

tag: life stage

value: juvenile

value: exposed to hypercapnic hypoxia for 24 h


title: P2, post-treatment non-lesional

description: skin

source_name: P2, post

value: post-treatment non-lesional

value: anakinra


title: MM-2

description: myometrium sample

value: myometrium


title: P5, lesional

description: skin

source_name: P5, lesional

value: lesional

value: Steroids 1.04mg/kg


title: LM-3

description: leiomyoma sample

source_name: leiomyoma


title: P13, normal

description: skin

source_name: P13, normal

value: Normal


title: P7, pre-treatment non-lesional

description: skin

source_name: P7, nonlesional

value: pre-treatment non-lesional

value: Steroids 0.83mg/kg


title: MM-3

description: myometrium sample


title: hepatopancreas_hypercapnichypoxia_24h_rep5

source_name: hepatopancreas, 24h, hypercapnic hypoxia, replicate 5

tag: molt stage

value: intermolt


title: MM-5

description: myometrium sample


title: hepatopancreas_hypercapnichypoxia_24h_rep6

source_name: hepatopancreas, 24h, hypercapnic hypoxia, replicate 6


title: P1, post-treatment non-lesional

description: skin

source_name: P1, post


title: P1, pre-treatment non-lesional

description: skin

source_name: P1, nonlesional


title: hepatopancreas_hypercapnichypoxia_24h_rep7

source_name: hepatopancreas, 24h, hypercapnic hypoxia, replicate 7


title: hepatopancreas_hypercapnichypoxia_24h_rep3

source_name: hepatopancreas, 24h, hypercapnic hypoxia, replicate 3


title: LM-2

description: leiomyoma sample

value: leiomyoma


title: hepatopancreas_hypercapnichypoxia_24h_rep4

source_name: hepatopancreas, 24h, hypercapnic hypoxia, replicate 4


title: LM-5

description: leiomyoma sample


title: P8, post-treatment non-lesional

description: skin

source_name: P8, post


title: MM-6

description: myometrium sample

source_name: myometrium


title: hepatopancreas_hypoxia_24h_rep8

description: Gene expression in hepatopancreas of shrimp exposed to hypoxia for 24h

source_name: hepatopancreas, 24h, hypoxia, replicate 8

value: exposed to hypoxia for 24h


title: P8, lesional

description: skin

source_name: P8, lesional


title: hepatopancreas_hypercapnichypoxia_24h_rep2

source_name: hepatopancreas, 24h, hypercapnic hypoxia, replicate 2


title: P12, normal

description: skin

source_name: P12, normal

value: normal


title: AEBP IP1-1

city: Bangalore

first: Jayashree

middle: S

last: Ladha

address: Jakkur

country: India

institute: JNCASR

description: comparison of AEBP1 IP DNA to WCE

hyb_protocol: Hybridization was done on 2X244K using Agilents CoC version 10 protocol

scan_protocol: Agilent Technologies scanner G2505C

data_processing: Median Blanks subtraction, Inter-array median normalization, Dye-bias median normalization

source_name: AEBP1 IP DNA from glial cells

label_protocol: 200 ng ChIP DNA wasblunted, ligated with adaptors and  LMPCR amplified. 1ug of amplified DNA was labeled with Cy3 or Cy5

growth_protocol: U87MG cells were grown in DMEM containing 10%  FBS and antibiotics

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

tag: cell line

source_name: Input DNA from U87MG


title: hepatopancreas_hypoxia_24h_rep6

source_name: hepatopancreas, 24h, hypoxia, replicate 6


title: AEBP IP2-2

description: comparison of AEBP1 IP DNA to WCE


title: hepatopancreas_hypoxia_24h_rep5

source_name: hepatopancreas, 24h, hypoxia, replicate 5


title: MM-8

description: myometrium sample


title: LM-6

description: leiomyoma sample

source_name: leiomyoma


title: AEBP IP1-2

description: comparison of AEBP1 IP DNA to WCE


title: hepatopancreas_hypoxia_24h_rep7

source_name: hepatopancreas, 24h, hypoxia, replicate 7


title: AEBP IP2-1

description: comparison of AEBP1 IP DNA to WCE


title: LM-8

description: leiomyoma sample


title: P10, post-treatment non-lesional

description: skin

source_name: P10, post

value: NOMID

value: Steroids 0.2mg/kg


title: P4, post-treatment non-lesional

description: skin

source_name: P4, post

value: Steroids 0.46mg/kg

value: skin


title: P10, lesional

description: skin

source_name: P10, lesional

value: Steroids 0.29mg/kg


title: MM-15

description: myometrium sample


title: MM-11

description: myometrium sample


title: hepatopancreas_hypoxia_24h_rep3

source_name: hepatopancreas, 24h, hypoxia, replicate 3

value: juvenile


title: hepatopancreas_hypoxia_24h_rep2

source_name: hepatopancreas, 24h, hypoxia, replicate 2


title: PCNSL_Case F_FFPE

source_name: DNA tumor sample

tag: age

value: Male

tag: pathology

value: DLBCL

value: Non-GC

value: Brain

source_name: Female reference DNA sample

tag: sample type

value: reference


title: PCNSL_Case E_FFPE

value: Female

tag: subtype

tag: ps

tag: tissue


title: PCNSL_Case G_FFPE

tag: gender

value: R-MPV


title: P4, lesional

description: skin

source_name: P4, lesional

tag: patient

tag: disease state

tag: disease development

value: post-treatment non-lesional

value: Steroids 0.31mg/kg

value: anakinra


title: PCNSL_Case D_FFPE

tag: treatment


title: LM-15

description: leiomyoma sample

value: leiomyoma


title: MM-4

description: myometrium sample

source_name: myometrium

value: myometrium


title: hepatopancreas_hypoxia_24h_rep1

source_name: hepatopancreas, 24h, hypoxia, replicate 1

value: intermolt

value: exposed to hypoxia for 24h


title: P11, normal

description: skin

source_name: P11, normal

value: normal

tag: treatment 1

value: Steroids 0mg/kg

value: skin


title: hepatopancreas_normoxia_4h_rep8

source_name: hepatopancreas, 4h, normoxia, replicate 8

value: juvenile

value: exposed to normoxia for 4h


title: LM-4

description: leiomyoma sample


title: MM-12

description: myometrium sample


title: SUDHL4

city: Bronx

first: Samir

last: Parekh

address: 1300 Morris Park Ave

department: cancer Center

institute: Albert Einstein College of Medicine

description:
DLBCL_6093
Gene expression data obtained from cells harvested in Log phase

hyb_protocol: Hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 5, using an Affymetrix System consisting of a Scanner 3000 7G with Autoloader, three Fluidics Station 450s and two Hybridization Ovens.

data_processing: Data from Affymetrix GeneChip® Human Gene 1.0 ST Array experiments in the form of .cel files were analyzed using  the Affymetrix® Expression Console™ software. This application uses the RMA-sketch workflow as the default analysis to create CHP files.  Significance Analysis of Microarrays (SAM) was then used to determine those genes that were significantly over-expressed in resistant to Rapamycin cell lines as compared to sensitive cell lines.    (http://www-stat.stanford.edu/~tibs/SAM/) was used to determine those  genes that were significantly over-expressed in resistant to Rapamycin  cell lines as compared to sensitive cell lines.

source_name: DLBCL cell lines

label_protocol: Labeling was performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 5

growth_protocol: The human DLBCL cell lines OCI-Ly1, OCI-Ly4 and OCI-Ly10 were maintained in Iscove's Modified Dulbecco Minimum Essential Medium (Iscov's DMEM) supplemented with 10% heat inactivated Fetal Bovine Serum,  Penicillin/Streptomycin, while the rest of the DLBCL cell lines were grown in RPMI media 1640 supplemented with 10% heat inactivated Fetal Bovine Serum, Penicillin/Streptomycin  and 2 mM L-Glutamine.

extract_protocol: Total RNA was extracted using Qiagen Rneasy Mini kit according to the manufacturer's instructions

value: DLBCL cell line SUDHL4

tag: rapamycin sensitivity

value: resistant


title: SUDHL6

description:
DLBCL_6094
Gene expression data obtained from cells harvested in Log phase

scan_protocol: Hybridization and scanning were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual version 5, using an Affymetrix System consisting of a Scanner 3000 7G with Autoloader, three Fluidics Station 450s and two Hybridization Ovens.

value: DLBCL cell line SUDHL6

value: sensitive


title: hepatopancreas_normoxia_4h_rep2

source_name: hepatopancreas, 4h, normoxia, replicate 2


title: hepatopancreas_normoxia_4h_rep3

source_name: hepatopancreas, 4h, normoxia, replicate 3


title: LM-12

description: leiomyoma sample

source_name: leiomyoma


title: PCNSL_Case B_FFPE

value: Male

value: DLBCL

value: GC

value: Brain

value: reference


title: hepatopancreas_normoxia_4h_rep7

source_name: hepatopancreas, 4h, normoxia, replicate 7


title: Toledo

description:
DLBCL_7561
Gene expression data obtained from cells harvested in Log phase

value: DLBCL cell line Toledo


title: hepatopancreas_normoxia_4h_rep11

source_name: hepatopancreas, 4h, normoxia, replicate 11

value: intermolt


title: PCNSL_Case B


title: iPS-A4-tumor (rep 1)

city: Berlin

first: Ying

last: Wang

address: Ihnestrasse 63

department: Vertebrate Genomics

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: replicate 1

data_processing: The data were normalised using rank invariant normalisation with BeadStudio version 3 (Illumina)

source_name: iPS-A4-derived tumor

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion (RNase-free DNase Set, Quiagen) has been applied on the columns during isolation.

tag: tumor

value: iPS-A4-derived tumor

value: 2 months in mice

tag: cell type

value: iPS-derived tumor


title: iPS-A4-tumor (rep 2)

description: replicate 2


title: NA12864

city: Hsinchu

first: Li-Lan

last: Li

address: 195,Sec. 4, Chung Hsing Rd. Chutung

country: Taiwan

institute: Industrial Technology Research Institute

description: no additional information

hyb_protocol: Ten micrograms of Cy5- labeled aRNA was fragmented (Ambion cat# 8740) and hybridized 16 hrs to Phalanx HOA arrays according to manufacturer’s instructions

scan_protocol: Arrays were scanned using Agilent DNA Microarray Scanner G2565B (Agilent Technologies, Inc. CA, USA) at settings of 60 PMT (for Cy5) and of 10 micron, and the resulting images were quantified using the software ProbeArrayer (an in-house tool developed by ITRI)

data_processing: log2 transformed intensities were normalized across technical replicates for each individual using a ComBat (Johnson et al. 2007) normalization. The normalized replicate values were merged by median as one chip per sample, and then sample-based chips were normalized by median across individuals (n=60 for parent or n=30 for children).

source_name: lymphoblastoid cell line

label_protocol: 1.5 ug of total RNA from each sample was used in cDNA synthesis and IVT reaction using the Amino Allyl MessageAmpTMII aRNA Amplification kit (Ambion, Austin, TX 78744-1832, cat. no.1753). Single stranded aRNA labeled with Cy5 was generated using the Cy5 Mono-Reactive dye pack (Amersham. PA25001)

growth_protocol: RPMI 1640 with Glutamax I medium (Invitrogen Corporation) supplemented with 10% fetal calf serum and 1% penicillin and streptomycin mix (Invitrogen Corporation). Cells lines were harvested at a density of 0.6 ~ 1 x 10^6 cells/ml and at least 80 % viability. Cultures were spun for 5 min at 1000 g, and the resulting pellets were washed once in PBS and lysed by adding 2 ml of micro glass beads (Sigma) and vortexing in 1 ml lysis solution containing beta-mercaptoethanol (Qiagen, RNeasy kit). Cell lysates were stored at -80°C.

extract_protocol: RNAs were extracted using RNeasy mini kits with on-column DNAse I digestion (Qiagen)

value: lymphoblastoid cell line

tag: parent/child

value: HapMap CEU_children

tag: coriell sample


title: PCNSL_Case C

tag: age

value: Female

value: HDMTX


title: PCNSL_Case C_FFPE

tag: pathology


title: hepatopancreas_normoxia_4h_rep10

source_name: hepatopancreas, 4h, normoxia, replicate 10

tag: life stage

value: juvenile

tag: molt stage

value: exposed to normoxia for 4h


title: NA12865

description: no additional information

tag: cell line


title: NA12878

description: no additional information


title: Pfeiffer

description:
DLBCL_7560
Gene expression data obtained from cells harvested in Log phase

value: DLBCL cell line Pfeiffer

value: resistant


title: NA12802

description: no additional information


title: Karpas 422

description:
DLBCL_7559
Gene expression data obtained from cells harvested in Log phase

value: DLBCL cell line Karpas 422


title: iPS-B4-tumor-b (rep 2)

description: replicate 2

source_name: iPS-B4-derived tumor

value: iPS-B4-derived tumor-b


title: B1-tumor-b (rep 2)

description: replicate 2

source_name: B1-derived tumor

value: B1-derived tumor-b

value: B1-derived tumor


title: S2_TopoII_ChIP-B

city: Atlanta

first: Edward

last: Ramos

state: GA

address: 1510 Clifton Rd NE

institute: Emory University

description: ChIP-chip of Topo II

hyb_protocol: Performed by FSU - NimbleGen Microarray Facility

data_processing: Data was processed using NimbleGen's NimbleScan software for ChIP data extraction

organism: Drosophila melanogaster

source_name: Topo II ChIP DNA from S2 cells

label_protocol: DNA was labeld, hybridized and scan using a NimbleGen 2.1 M D.melanogaster Whole-Genome Tilling Array at the Florida State University - NimbleGen Microarray Facility

growth_protocol: S2 cells were grown in HyQ SFX-insect medium (HyClone) with penicilin-streptomycin at 25C

extract_protocol: cells were crosslinked with 1% formaldehyde for 10 min at room temp. Crosslinking was quenced with glycine and nuclear lysates were sonicated to generate 200-1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4C with protein A sepharose beads and then incubated overngith with antibody at 4C.  Chromatin was then precipitated with protein A sepharose beads for 2 hours at 4C. After washing and eluting from beads the crosslinking was reversed and DNA was isolated.

treatment_protocol: cells collected prior to confluency for ChIP

source_name: Input DNA from S2 cells

value: S2 cells


title: iPS-B4-tumor-a (rep 1)

description: replicate 1

value: iPS-B4-derived tumor-a


title: B1-tumor-a (rep 1)

description: replicate 1

value: B1-derived tumor-a


title: NA12752

description: no additional information


title: NA12801

description: no additional information


title: OCI-Ly19

description:
DLBCL_7556
Gene expression data obtained from cells harvested in Log phase

value: DLBCL cell line OCI-Ly19


title: NA12707

description: no additional information


title: H1-tumor (rep 1)

description: replicate 1

source_name: H1-derived tumor

value: H1-derived tumor

value: 2 months in mice

value: hESC-derived tumor


title: OCI-Ly10

description:
DLBCL_7554
Gene expression data obtained from cells harvested in Log phase

value: DLBCL cell line OCI-Ly10

value: sensitive


title: hESCs (rep 1)

description: replicate 1

value: Passage 55

value: hESCs


title: OCI-Ly18

description:
DLBCL_7555
Gene expression data obtained from cells harvested in Log phase

value: DLBCL cell line OCI-Ly18


title: H1-tumor (rep 2)

description: replicate 2


title: NA10863

description: no additional information

value: lymphoblastoid cell line

value: HapMap CEU_children


title: NA12740

description: no additional information


title: OCI-Ly1

description:
DLBCL_7515
Gene expression data obtained from cells harvested in Log phase

value: DLBCL cell line OCI-Ly1


title: OCI-Ly4

description:
DLBCL_7517
Gene expression data obtained from cells harvested in Log phase

value: DLBCL cell line OCI-Ly4


title: SUDHL8

description:
DLBCL_7557
Gene expression data obtained from cells harvested in Log phase

value: DLBCL cell line SUDHL8

value: resistant


title: NA10861

description: no additional information


title: NA10860

description: no additional information


title: S2_TopoII_ChIP-A

description: ChIP-chip of Topo II

scan_protocol: Performed by FSU - NimbleGen Microarray Facility

value: S2 cells


title: NA12743

description: no additional information


title: NA10859

description: no additional information


title: iPS-B4 (rep 1)

description: replicate 1

source_name: iPS-B4 from HFF1

value: Passage 10

value: iPSCs


title: iPS-A4 (rep 2)

description: replicate 2

source_name: iPS-A4 from HFF1


title: iPS-B4 (rep 2)

description: replicate 2


title: NA10856

description: no additional information


title: NA10854

description: no additional information


title: B1 cell line (rep 1)

description: replicate 1

source_name: B1 from HFF1

value: B1 cell line

value: B1 cell line-a


title: WSU-NIH

description:
DLBCL_7562
Gene expression data obtained from cells harvested in Log phase

source_name: DLBCL cell lines

value: DLBCL cell line WSU-NIH


title: iPS-A4 (rep 1)

description: replicate 1


title: OCI-Ly3

description:
DLBCL_7516
Gene expression data obtained from cells harvested in Log phase

value: DLBCL cell line OCI-Ly3


title: B1 cell line (rep 2)

description: replicate 2

value: B1 cell line-b


title: HFF1 (rep 1)

description: replicate 1

value: HFF1 (purchased from ATCC)

value: Passage 8

value: neonatal foreskin fibroblasts


title: NA10847

description: no additional information

value: lymphoblastoid cell line


title: Pollen at anthesis, biological rep 1

city: Norman

first: Scott

middle: D

last: Russell

state: OK

address: 770 Van Vleet Oval

department: Dept of Microbiology and Plant Biology

institute: University of Oklahoma

description: Gene expression data from pollen at anthesis

hyb_protocol: Fifteen ug of fragmented cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rice Genome oligonucleotide array. Subsequent GeneChip washing and staining steps were performed on a GeneChip Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Affymetrix MAS 5.0 default processing, with all chips scaled to the same target value of 500.

organism: Oryza sativa

source_name: Field grown rice, cv Katy

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix GeneChip Two-Cycle cDNA Synthesis Kit for target preparation with signal amplification according to the standard Affymetrix protocol from total RNA of sperm cells and 100 ng total RNA of pollen and seedling, respectively.

growth_protocol: Oryza sativa ssp. japonica, cultivar Katy were grown in fields at Dale Bumpers National Rice Research Center and University of Arkansas Extension Station near Stuttgart, AR, USA under ideal, disease free conditions.

extract_protocol: Total RNA was purified using the RNeasy plant mini kit according to manufacturer’s instructions (Qiagen).

treatment_protocol: Whole anthers were collected from anthesis florets for isolation of sperm cells and pollen as described in Russell et al. (manuscript in preparation) and whole seedlings, developmental stage V3 (collar forms on leaf 3 on main stem), according to Counce et al. (2000).

tag: subspecies

value: japonica

tag: cultivar

value: katy

tag: genetic modification

value: wild type

tag: tissue type

value: pollen

tag: developmental stage

value: anthesis


title: Seedling, V3 stage, biological rep 3

description: Gene expression data from whole seedlings at 3rd collar leaf stage

value: whole seedlings (includes shoots, leaves, roots and apices)

value: 3rd collar leaf stage


title: NA10855

description: no additional information

value: HapMap CEU_children


title: NA10846

description: no additional information


title: HFF1 (rep 2)

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol


title: NA10851

description: no additional information


title: Monocyte RNA 90 days  X4561606069_H_t90

city: Luebeck

first: Heribert

last: Schunkert

address: Ratzeburger Allee 160

department: Medizinische Klinik II

description:
Monocyte RNA 90 days
replicate 1 time point t3 (90 days)

scan_protocol: Standard Illumina hybridization protocol

data_processing: Quality control, background correction, variance stabilization (Lin et al. 2008) and normalization were performed in R statistical environment using the Lumi package (Du et al. 2008). Briefly, output from Illumina’s Bead Studio software (BeadStudio User Guide. San Diego, USA 2004; 2005. http://www.illumina.com) was downloaded into R and a series of quality control and diagnostics were performed to assess the quality of raw and normalized data. Background correction was performed using the Illumina’s default algorithm which uses the signals from negative control bead types to estimates the expected background signal levels. After background correction and filtering out array outliers, variance stabilization transformation (VST) was performed on the intensity data. Data were normalized using quantile normalization method (Bolstad et al. 2003) to make the same overall distribution of expression intensities for all the arrays within the experiment. Control probes as well as transcripts absent (not expressed) in all samples were filtered out (a detection P-value < 0.01 was used as a threshold).

source_name: Monocyte

label_protocol: In vitro transcription reaction of cDNA to cRNA was performed overnight at 37°C including biotin-16-UTP for labelling

extract_protocol: Isolation of monocytes was performed by an immuno-magnetic method using the Miltenyi AutoMacs cell separator using whole-blood CD14+ beads (Miltenyi) according to the manufacturers’ instructions

value: monocyte

tag: stage of mi infection

tag: gender

value: male


title: NA10857

description: no additional information


title: Monocyte RNA 90 days  X4561606069_E_t90


title: Monocyte RNA 90 days  X4561606069_G_t90


title: NA10839

description: no additional information


title: PCNSL_Case A

source_name: DNA tumor sample

value: Female

value: DLBCL

tag: subtype

value: GC

tag: ps

tag: treatment

value: CHOD-BLEO+RT

tag: tissue

value: Brain

source_name: Female reference DNA sample

tag: sample type

value: reference


title: NA10835

description: no additional information

value: lymphoblastoid cell line

tag: parent/child

tag: coriell sample


title: NA10838

description: no additional information


title: Monocyte RNA 90 days  X4561606069_F_t90

tag: cell type

tag: age


title: Farage

description:
DLBCL_7558
Gene expression data obtained from cells harvested in Log phase

tag: cell line

value: DLBCL cell line Farage

tag: rapamycin sensitivity

value: sensitive


title: Sperm at anthesis, biological rep 2

description: Gene expression data from isolated sperm cells at pollen anthesis

tag: subspecies

value: japonica

tag: cultivar

value: katy

value: wild type

value: isolated sperm cells


title: Sperm at anthesis, biological rep 1

tag: genetic modification

tag: tissue type

value: anthesis


title: Pollen at anthesis, biological rep 2

value: pollen

tag: developmental stage


title: NA07348

description: no additional information

value: HapMap CEU_children


title: Follicular lymphoma Grade 3 GN_U133A_2518

first: Elisa

last: Oricchio

address: 1275 York Avenue

institute: MSKCC

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with the R library affy  provided with the Bioconductor software

source_name: Lymphoma

label_protocol: Biotinylated totRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

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

tag: severity

value: Grade 3

value: follicular lymphoma tumor


title: Sperm at anthesis, biological rep 3


title: Monocyte RNA 90 days  X4561606069_D_t90

value: monocyte

tag: stage of mi infection

tag: gender

value: male


title: NA07048

description: no additional information


title: Pollen at anthesis, biological rep 3


title: Seedling, V3 stage, biological rep 2

value: whole seedlings (includes shoots, leaves, roots and apices)

value: 3rd collar leaf stage


title: Monocyte RNA 90 days  X4561606068_G_t90

value: Female


title: Follicular lymphoma Grade 3 GN_U133A_2337


title: Monocyte RNA 90 days  X4561606068_F_t90


title: Follicular lymphoma Grade 2 GN_U133A_2394

value: Grade 2


title: Follicular lymphoma Grade 1 GN_U133A_2343

value: Grade 1


title: Follicular lymphoma Grade 2 GN_U133A_2386


title: Monocyte RNA 90 days  X4561606069_A_t90


title: NA07019

description: no additional information

value: lymphoblastoid cell line


title: NA10830

description: no additional information


title: NA06991

description: no additional information


title: NA10831

description: no additional information


title: Monocyte RNA 90 days  X4561606069_B_t90


title: Monocyte RNA 90 days  X4561606069_C_t90


title: Follicular lymphoma Grade 2 GN_U133A_2328


title: Seedling, V3 stage, biological rep 1

value: japonica


title: Myocardial infarction_rep1

city: Ljubljana

first: Emanuela

last: Boštjančič

address: Korytkova 2

department: Institute of Pathology

country: Slovenia

institute: Faculty of Medicine

description: Expression analysis was performed using hybridization to µParaflo®microfluidics micorarrays (LC Sciences) in the version of the Sanger miRBase database Release 10.1. Each of the microarrays held all 719 predicted mature human miRNA probes (MRA-1001, the latest version of the Sanger miRBase database at the time of analysis, with 100% of experimentally verified miRNA sequences represented on the arrays), as well as spike-in/perfectly matched and mismatched probes for quality control. Each detection probe consisted of a chemically modified nucleotide-coding segment complementary to the target miRNA or other target and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. Each miRNA probe was represented 5 times on a single microarray, and the control probes were spiked into the RNA samples before labelling. The detection probes were made by in situ synthesis using PGR (photogenerated) chemistry, which enable highly sensitive and specific direct detection of miRNAs. The µParaflo® technology enables on-chip synthesis, ensuring high probe quality and tight process control. This platform integrates high throughput parallel synthesis, microfluidics and digital photolithography, which deliver more reliable results than are possible with traditional spotted arrays.

hyb_protocol: Hybridization was performed overnight on a Paraflo microfluidic chip, using a microcirculation pump (Atactic Technologies). The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C.

scan_protocol: After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining. Fluorescence images were collected by using a laser scanner (GenePix4000B; Molecular Devices) and digitized by using Array-Pro image analysis software (Media Cybernetics).

data_processing:
In our analysis with Acuity 4.0 program we used processed data, which are defined as background subtracted, normalized, etc, but not filtered. Normalization was carried out by LC Sciences, which performed microarray analysis. Their description is as follows.
Standard data analysis was performed to detect small amounts of miRNA, including calculation of signal intensities, determination of detectable transcripts and calculation of differential ratios. The signal was amplified and the determined background was subtracted using the local regression method. Cy3/Cy5 channel normalization was carried out using a cyclic LOWESS (locally-weighted regression) method. These transcripts were defined as “processed data”. In addition, detectivity determination was based on the following conditions: (i) signals of the repeating probes should be above the detection level in at least 3 of 5 probes for each miRNA, (ii) signal intensity should be higher than 3 x background standard deviation, (iii) spot CV should be less than 0.5. Transcripts meeting those conditions were determined as “simple detectable or detectable transcripts”.
For the dual colour experiment, the differences between Cy3 and Cy5 signals and p-values of the differences were calculated. When the p-value was less than 0.01, the differentially detected signals were considered to be true and used for data filtering. miRNAs with intensity values below a threshold value were removed; in addition, log2 transformation was used to convert expression values into a linear scale (log2) for statistical comparison.

source_name: heart, remote myocardium

label_protocol: Five to ten μg of RNA from heart samples was used for miRNA microarray. Using size-fractionation, small RNA (<300 nt) enrichment was performed, following extension with a poly(A) tail, to which the an oligonucleotide tag was added for subsequent labelling. The two sets of RNA sequences were labelled with different affinity tags to allow simultaneous detection of both samples using dual colour labelling (Cy3 and Cy5 fluorescent dyes).

extract_protocol: miRNeasy kit (Qiagen)

value: infarcted tissue

value: female

value: 80 yr

source_name: heart, infarcted tissue

value: remote myocardium


title: Follicular lymphoma Grade 3 GN_U133A_2528s2


title: Follicular lymphoma Grade 3 GN_U133A_2363


title: Monocyte RNA 90 days  X4561606068_E_t90


title: Follicular lymphoma Grade 2 GN_U133A_2348


title: NA07029

description: no additional information

source_name: lymphoblastoid cell line


title: NA12156

description: no additional information

value: HapMap CEU_parent


title: Monocyte RNA 90 days  X4561606068_H_t90


title: NA12155

description: no additional information


title: Monocyte RNA 90 days  X4561606068_D_t90


title: Monocyte RNA 90 days  X4561606068_A_t90


title: NA11995

description: no additional information


title: Follicular lymphoma Grade 3 GN_U133A_2326


title: Monocyte RNA 90 days  X4561606068_C_t90


title: Myocardial infarction_rep3

value: 83 yr


title: Follicular lymphoma Grade 3 GN_U133A_2303s2

value: Grade 3


title: Monocyte RNA 90 days  X4561606068_B_t90


title: Follicular lymphoma Grade 3 GN_U133A_2383

value: follicular lymphoma tumor


title: LSL-Kras1-on

first: Sujun

last: Hua

state: Tx

address: 1901 East Rd

institute: MD Anderson Cancer Center

description: Culture of LSL-Kras1.

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Briefly, raw probe intensities were normalized across arrays with quantile normalization using the R package developed by B. Bolstad. The software package LIMMA (Linear Models for Microarray Data) (Smyth, 2004) was applied to detect significantly differentially expressed probes using Benjamini-Hochberg adjusted P-values.

source_name: culture of LSL-Kras1, on dox

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

extract_protocol: Trizol extraction of total RNA followed by RNeasy column cleanup was performed according to the manufacturer's instructions.

treatment_protocol: On doxycycline.

tag: genotype

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+

tag: background strain

value: FVB/B6 mix

value: culture of LSL-Kras1

tag: treatment

value: doxycycline


title: diploidy

description: diploidy cells

hyb_protocol: Following NimbleGen's protocol

scan_protocol: Scanned with Agilent Scanner at 5um resolution

data_processing: The log2 ratio of the input signals for the enriched and input samples that were co-hybridized to the array is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. VALUE is the P value derived from Kolmogorov-Smirnov test using 750bp window size of the Cy5/Cy3 log2 ratio using NimbleScan.

source_name: FW_MIRA, embryonic fibroblast, diploid

label_protocol: Following NimbleGen's protocol

growth_protocol: standard

extract_protocol: Genomic DNA was extracted with Qiagen Blood Tissue kit (Qiagen, Valencia, CA) following the maufacturer's protocol.

tag: fraction

value: methylated DNA-enriched

tag: genotype/variation

value: normal control

source_name: FW_Input, embryonic fibroblast, diploid

value: input


title: NA12154

description: no additional information

value: lymphoblastoid cell line

tag: parent/child

tag: coriell sample


title: NA12236

description: no additional information

tag: cell line


title: LSL-Kras2-off

description: Culture of LSL-Kras2.

source_name: culture of LSL-Kras2, off dox

tag: cell type

value: culture of LSL-Kras2


title: NA11994

description: no additional information


title: Follicular lymphoma Grade 2 GN_U133A_22249

value: Grade 2

tag: tissue


title: LSL-Kras1-off

description: Culture of LSL-Kras1.

source_name: culture of LSL-Kras1, off dox

treatment_protocol: Off doxycycline.

value: off doxycycline


title: tetraploidy

description: tetraploidy cells

source_name: 174_MIRA, embryonic fibroblast, tetraploid

value: abnormal DNA contents

source_name: 174_Input, embryonic fibroblast, tetraploid


title: Myocardial infarction_rep2

value: remote myocardium

value: male

tag: age

value: 84 yr

value: infarcted tissue


title: Monocyte RNA 90 days  X4559291046_F_t90

value: monocyte


title: iKras4-C-off

description: Parental culture of iKras4.

source_name: parental culture of iKras4, off dox

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+

value: parental culture of iKras4


title: NA11992

description: no additional information

value: HapMap CEU_parent


title: Monocyte RNA 90 days  X4559291046_C_t90


title: Monocyte RNA 90 days  X4559291046_D_t90


title: Follicular lymphoma Grade 3 GN_U133A_2257

value: Grade 3

value: follicular lymphoma tumor


title: Follicular lymphoma Grade 3 GN_U133A_2274


title: Monocyte RNA 90 days  X4559291046_E_t90


title: Follicular lymphoma Grade 1 GN_U133A_2297

value: Grade 1


title: NA11882

description: no additional information


title: LSL-Kras2-on

description: Culture of LSL-Kras2.

source_name: culture of LSL-Kras2, on dox

value: FVB/B6 mix

value: doxycycline


title: iKras3-C-off

description: Parental culture of iKras3.

source_name: parental culture of iKras3, off dox

value: parental culture of iKras3


title: iKras2-C-off

description: Parental culture of iKras2.

source_name: parental culture of iKras2, off dox

value: parental culture of iKras2


title: Monocyte RNA 90 days  X4559291046_B_t90

source_name: Monocyte


title: NA11993

description: no additional information

value: lymphoblastoid cell line


title: iKras1-C-off

description: Parental culture of iKras1.

source_name: parental culture of iKras1, off dox

value: parental culture of iKras1

value: off doxycycline


title: Follicular lymphoma Grade 3 GN_U133A_2241s2

source_name: Lymphoma


title: NA12044

description: no additional information


title: NA11881

description: no additional information


title: Monocyte RNA 90 days  X4559291046_A_t90

value: male


title: Follicular lymphoma Grade 3 GN_U133A_2230s2


title: iKras5-C-off

description: Parental culture of iKras5.

source_name: parental culture of iKras5, off dox

value: parental culture of iKras5


title: Follicular lymphoma Grade 2 GN_U133A_2192

value: Grade 2


title: Follicular lymphoma Grade 2 GN_U133A_2188


title: NA12043

description: no additional information


title: Follicular lymphoma Grade 1 GN_U133A_2196


title: Monocyte RNA 72h  X4311471116_D_t3

description:
Monocyte RNA 72h
replicate 1 time point t2 (72h)

value: monocyte

value: Female


title: hESCs (rep 2)

description: replicate 2

value: Passage 55

value: hESCs


title: Monocyte RNA 72h  X4311471115_H_t3


title: iKras2-C-on

description: Parental culture of iKras2.

source_name: parental culture of iKras2, on dox

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+


title: Follicular lymphoma Grade 3 GN_U133A_2164s2

value: Grade 3

value: follicular lymphoma tumor


title: NA07345

description: no additional information

source_name: lymphoblastoid cell line

value: HapMap CEU_parent


title: Monocyte RNA 72h  X4311471115_F_t3


title: NA07357

description: no additional information


title: iKras3-C-on

description: Parental culture of iKras3.

source_name: parental culture of iKras3, on dox

value: FVB/B6 mix

value: doxycycline


title: Follicular lymphoma Grade 3 GN_U133A_2163


title: Monocyte RNA 72h  X4311471115_D_t3


title: Follicular lymphoma Grade 3 GN_U133A_2181


title: Monocyte RNA 72h  X4311471116_B_t3


title: NA07055

description: no additional information


title: Follicular lymphoma Grade 2 GN_U133A_2116s2


title: Monocyte RNA 72h  X4311471115_B_t3


title: Follicular lymphoma Grade 2 GN_U133A_2109


title: NA06993

description: no additional information


title: iKras1-C-on

description: Parental culture of iKras1.

source_name: parental culture of iKras1, on dox


title: NA07034

description: no additional information


title: iKras5-C-on

description: Parental culture of iKras5.

source_name: parental culture of iKras5, on dox


title: iKras4-T-off-2

description: Pancreatic xenograft tumor generated from tetO_LKrasG12D p53L/+ tumor line iKras4.

source_name: xenograft tumor#2 from iKras4 line, off dox

value: pancreatic xenograft tumor generated from iKras4


title: Monocyte RNA 72h  X4311471114_F_t3


title: Monocyte RNA 72h  X4311471114_H_t3


title: Follicular lymphoma Grade 2 GN_U133A_2158


title: Monocyte RNA 72h  X4300799032_A_t3


title: Follicular lymphoma Grade 2 GN_U133A_2123R


title: iKras4-T-off-1

source_name: xenograft tumor#1 from iKras4 line, off dox


title: NA07056

description: no additional information

value: lymphoblastoid cell line


title: iKras4-T-on-2

source_name: xenograft tumor#2 from iKras4 line, on dox


title: NA06985

description: no additional information


title: Follicular lymphoma Grade 1 GN_U133A_2026s2

value: Grade 1


title: Monocyte RNA 72h  X4311471114_D_t3


title: iKras4-T-on-1

source_name: xenograft tumor#1 from iKras4 line, on dox


title: NA07022

description: no additional information


title: iKras3-T-off-2

description: Pancreatic xenograft tumor generated from tetO_LKrasG12D p53L/+ tumor line iKras3.

source_name: xenograft tumor#2 from iKras3 line, off dox

value: pancreatic xenograft tumor generated from iKras3

value: off doxycycline


title: Monocyte RNA 72h  X4300799030_H_t3


title: NA06994

description: no additional information


title: NA12239

description: no additional information


title: NA07000

description: no additional information


title: Follicular lymphoma Grade 3 GN_U133A_2063


title: Monocyte RNA 72h  X4300799018_G_t3

value: male


title: Monocyte RNA 72h  X4300799030_A_t3


title: iKras3-T-off-1

source_name: xenograft tumor#1 from iKras3 line, off dox


title: iKras4-C-on

description: Parental culture of iKras4.

source_name: parental culture of iKras4, on dox

value: parental culture of iKras4


title: Monocyte RNA 72h  X4300799020_B_t3

value: monocyte


title: Follicular lymphoma Grade 3 GN_U133A_1980


title: Follicular lymphoma Grade 3 GN_U133A_1882


title: iKras3-T-on-2

source_name: xenograft tumor#2 from iKras3 line, on dox


title: NA12145

description: no additional information


title: Follicular lymphoma Grade 3 GN_U133A_2013


title: Follicular lymphoma Grade 2 GN_U133A_2007

value: Grade 2


title: iKras2-T-off-2

description: Pancreatic xenograft tumor generated from tetO_LKrasG12D p53L/+ tumor line iKras2.

source_name: xenograft tumor#2 from iKras2 line, off dox

value: pancreatic xenograft tumor generated from iKras2


title: NA12146

description: no additional information


title: Monocyte RNA 72h  X4300799018_E_t3

source_name: Monocyte

value: Female


title: Follicular lymphoma Grade 3 GN_U133A_1879

source_name: Lymphoma


title: iKras3-T-on-1

source_name: xenograft tumor#1 from iKras3 line, on dox

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+


title: Monocyte RNA 72h  X4300799018_D_t3


title: Follicular lymphoma Grade 3 GN_U133A_1550

value: Grade 3


title: NA12144

description: no additional information


title: iKras2-T-off-1

source_name: xenograft tumor#1 from iKras2 line, off dox


title: NA12892

description: no additional information

source_name: lymphoblastoid cell line


title: Follicular lymphoma Grade 1 GN_U133A_1326

value: follicular lymphoma tumor


title: NA12891

description: no additional information

value: HapMap CEU_parent


title: Monocyte RNA 72h  X4300799015_G_t3


title: Monocyte RNA 72h  X4300799018_A_t3


title: NA12875

description: no additional information


title: Monocyte RNA 72h  X4300799018_C_t3


title: Follicular lymphoma Grade 1 GN_U133A_1377


title: iKras2-T-on-1

source_name: xenograft tumor#1 from iKras2 line, on dox

value: FVB/B6 mix


title: iKras1-T-on-1

description: Pancreatic xenograft tumor generated from tetO_LKrasG12D p53L/+ tumor line iKras1.

source_name: xenograft tumor#1 from iKras1 line, on dox

value: pancreatic xenograft tumor generated from iKras1

value: doxycycline


title: iKras2-T-on-2

source_name: xenograft tumor#2 from iKras2 line, on dox


title: Monocyte RNA 72h  X4300799015_D_t3


title: iKras1-T-on-2

source_name: xenograft tumor#2 from iKras1 line, on dox


title: Monocyte RNA 72h  X4300799015_H_t3


title: Follicular lymphoma Grade 1 GN_U133A_1304


title: NA12874

description: no additional information

value: lymphoblastoid cell line


title: iKras1-T-off-1

source_name: xenograft tumor#1 from iKras1 line, off dox


title: NA12872

description: no additional information


title: iKras5-T-off-2

description: Pancreatic xenograft tumor generated from tetO_LKrasG12D p53L/+ tumor line iKras5.

source_name: xenograft tumor#2 from iKras5 line, off dox

value: pancreatic xenograft tumor generated from iKras5


title: Follicular lymphoma Grade 3 GN_U133A_1278


title: Follicular lymphoma Grade 1 GN_U133A_1277

value: Grade 1


title: Follicular lymphoma Grade 3 GN_U133A_1506


title: Follicular lymphoma Grade 2 GN_U133A_1281


title: NA12815

description: no additional information


title: NA12813

description: no additional information


title: iKras5-T-off-1

source_name: xenograft tumor#1 from iKras5 line, off dox

value: off doxycycline


title: Monocyte RNA 72h  X4300799014_F_t3

value: male


title: NA12873

description: no additional information


title: Monocyte RNA 72h  X4300799015_B_t3


title: Follicular lymphoma Grade 3 GN_U133A_1223


title: Monocyte RNA 72h  X4300799015_C_t3


title: iKras5-T-on-1

source_name: xenograft tumor#1 from iKras5 line, on dox


title: Monocyte RNA 72h  X4300799015_A_t3


title: Follicular lymphoma Grade 2 GN_U133A_1171


title: NA12814

description: no additional information


title: Follicular lymphoma Grade 1 GN_U133A_1263


title: Monocyte RNA 72h  X4300799014_H_t3


title: Follicular lymphoma Grade 2 GN_U133A_1172


title: NA12812

description: no additional information


title: Monocyte RNA 72h  X4300799014_D_t3


title: NA12761

description: no additional information


title: iKras5-T-on-2

source_name: xenograft tumor#2 from iKras5 line, on dox


title: mT4

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

institute: University Hospital Essen

description: JoMa1 cells transfected with MYCN (JoMa1-MYCN) are tumorigenic in immunocompromised mice. Expression profiles of four independent tumors induced by JoMa1-MYCN were obtained.

hyb_protocol: Hybridization to Mouse 430 2.0 arrays was performed according to the manufacturer's recommendations (Affymetrix).

scan_protocol: Scanning of chips was performed using a GeneArray scanner (Agilent).

data_processing: Data were RMA normalized using Genomics Suite 6.5 (Partek).

source_name: JoMa1-MYCN-induced tumor

label_protocol: Biotin labelling was performed according to the manufacturer's recommendations (Affymetrix).

growth_protocol: JoMa1 cells were grown as described (Maurer et al. Differentiation, 2007 (PMID 17381545)).

extract_protocol: Cells were harvested when they reached 80% confluency, and lysed using Trizol. RNA was purified using the QIAGEN RNeasy Mini Kit.

value: derived from JoMa1-MYCN-induced tumor


title: NA12763

description: no additional information


title: Monocyte RNA 6h  X4311471116_E_t1

description:
Monocyte RNA 6h
replicate 1 time point t1 (6h)

value: monocyte


title: NA12762

description: no additional information


title: mT6


title: Follicular lymphoma Grade 3 GN_U133A_1139


title: mT5


title: Follicular lymphoma Grade 2 GN_U133A_1188

value: Grade 2


title: NA12760

description: no additional information


title: mT3


title: Monocyte RNA 6h  X4311471115_G_t1


title: Follicular lymphoma Grade 3 GN_U133A_1109


title: Follicular lymphoma Grade 2 GN_U133A_810


title: NA12751

description: no additional information


title: NA12717

description: no additional information


title: Monocyte RNA 6h  X4311471115_C_t1


title: Follicular lymphoma Grade 2 GN_U133A_1033


title: Monocyte RNA 6h  X4311471115_A_t1


title: NA12264

description: no additional information


title: Monocyte RNA 6h  X4311471116_C_t1


title: JoMa1_2

source_name: Parental JoMa1

value: neural crest precursor cells


title: Follicular lymphoma Grade 1 GN_U133A_718


title: Follicular lymphoma Grade 2 GN_U133A_736


title: NA12750

description: no additional information


title: Monocyte RNA 6h  X4311471115_E_t1

value: Female


title: JoMa1_GFP

source_name: GFP-transfected JoMa1

tag: transfectant

value: GFP control


title: NA12716

description: no additional information


title: Monocyte RNA 6h  X4311471114_G_t1

source_name: Monocyte


title: JoMa1_1


title: Monocyte RNA 6h  X4311471114_E_t1


title: NA12249

description: no additional information


title: Monocyte RNA 6h  X4311471114_C_t1


title: Monocyte RNA 6h  X4311471114_A_t1


title: Monocyte RNA 72h  X4300799015_F_t3


title: Follicular lymphoma Grade 3 GN_U133A_1125

source_name: Lymphoma

value: Grade 3


title: Follicular lymphoma Grade 3 GN_U133A_697

value: follicular lymphoma tumor


title: Follicular lymphoma Grade 3 GN_U133A_691


title: NA12057

description: no additional information

value: HapMap CEU_parent


title: Monocyte RNA 6h  X4311471114_B_t1


title: Follicular lymphoma Grade 1 GN_U133A_679


title: Follicular lymphoma Grade 3 GN_U133A_673


title: NA12006

description: no additional information


title: NA12056

description: no additional information


title: Follicular lymphoma Grade 3 GN_U133A_612


title: NA12005

description: no additional information


title: Monocyte RNA 6h  X4300799030_G_t1


title: NA12234

description: no additional information


title: JoMa1_3


title: NA12248

description: no additional information


title: Monocyte RNA 6h  X4300799030_E_t1


title: Healthy control 13

city: Bellaterra, Barcelona

first: Lana

middle: Teixeira

last: Fernandes

state: Catalunya

address: Campus de la UAB, Edifici cresa

department: Virology

country: Spain

institute: CReSA

description: Comparison of PMWS-affected pigs versus a healthy control group to investigate global expression changes in the mediastinal lymph node.

hyb_protocol: Labelled cRNA was fractioned and hybridized with the GeneChip Porcine Genome Array following the manufacturer's instructions. Subsequently, the arrays were washed and stained with a GeneChip Fluidics Station 450 using the standard fluidics protocol.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 by using the GeneChip Operating Software (GCOS) to produce a _.CEL file for further data processing.

data_processing: Data analysis was performed with Bioconductor implemented in R 2.6.0 (http://cran.r-project.org/). Data quality control assessments were performed with affyQCReport implemented in the simpleaffy package. The raw data were background corrected, normalized and converted to expression-level data using the Robust Multichip Average (RMA) algorithm. The Empirical Bayes method implemented in the limma package was used to assess differential expression. The p value cutoff for DE genes was set at 0.05.

organism: Sus scrofa

source_name: Healthy control 13

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug of total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Sections of mediastinal lymph nodes were collected during necropsy and snap-frozen in dry ice for transporting to the laboratory and stored at -80ºC until RNA extraction. Total RNA was isolated from MLN using RiboPure™ kit (Ambion, Austin, USA) according to the manufacturer's instructions and quantified by spectrophotometry (ND-1000 NanoDrop Technologies, Wilmington, DE, USA). RNA quality was assessed by capillary electrophoresis analysis on an Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

value: mediastinal lymph node

value: 13 to 15 week old

tag: disease state

value: control


title: Healthy control 8

source_name: Healthy control 8


title: Monocyte RNA 6h  X4300799030_F_t1


title: Healthy control 9

source_name: Healthy control 9


title: Healthy control 5

source_name: Healthy control 5


title: Healthy control 10

source_name: Healthy control 10


title: Healthy control 4

source_name: Healthy control 4


title: Follicular lymphoma Grade 2 GN_U133A_543


title: Healthy control 6

source_name: Healthy control 6


title: Follicular lymphoma Grade 1 GN_U133A_513


title: Healthy control 11

source_name: Healthy control 11


title: NA11840

description: no additional information

source_name: lymphoblastoid cell line

value: lymphoblastoid cell line


title: NA12003

description: no additional information


title: NA11839

description: no additional information


title: Healthy control 12

source_name: Healthy control 12


title: Monocyte RNA 6h  X4300799030_B_t1


title: Follicular lymphoma Grade 2 GN_U133A_659


title: Healthy control 7

source_name: Healthy control 7


title: Monocyte RNA 6h  X4300799030_D_t1


title: Healthy control 3

source_name: Healthy control 3


title: Healthy control 1

source_name: Healthy control 1


title: Monocyte RNA 6h  X4300799030_C_t1


title: Healthy control 2

source_name: Healthy control 2


title: Monocyte RNA 6h  X4300799020_C_t1


title: Follicular lymphoma Grade 1 GN_U133A_421R


title: Monocyte RNA 6h  X4300799020_A_t1


title: Follicular lymphoma Grade 3 GN_U133A_363


title: NA11832

description: no additional information


title: NA11831

description: no additional information


title: Follicular lymphoma Grade 1 GN_U133A_449R


title: Follicular lymphoma Grade 2 GN_U133A_239


title: NA11830

description: no additional information


title: Monocyte RNA 6h  X4300799018_H_t1