title: 3 month high fat diet mouse 2

city: Los Angeles

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

description: Gene expression after 3 MO in livers of HFD-fed mice

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028282 Whole Rat Genome Microarray 4x44K v3 (G4131F) for 17 hours at 65°C in a rotating SureHyb chamber. After hybridization, microarrays were washed 1minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 3 month high fat diet fed mouse 2

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

growth_protocol: 5-week-old male C57BL/6 mice were purchased from Orient Bio (Seoul, South Korea) and they were housed in a standard animal facility under a 12:12-hr light-dark cycle with the constant room temperature.

extract_protocol: Total RNA was extracted from the liver tissue using a miRNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA quantity and integrity were confirmed with a NanoDrop spectrophotometer.

treatment_protocol: The mice were divided into four weight-matched groups. Mice were fed either normal diet (ND) of overall 3.8kcal/g (ND; 50.21% carbohydrate, 20.78% protein, and 4.8% fat) or high fat diet (HFD: D12231, Research Diets, Inc., New Brunswick, NJ) of overall 5.2kcal/g (25.5% carbohydrate, 16.4% protein and 58% fat) for 3 months or 9 months ad libitum.

tag: strain

tag: diet group

value: 3 month high fat diet


title: 9 month high fat diet mouse 1

status: Public on Jun 22 2015

type: RNA

state: CA

country: USA

description: Gene expression after 9 MO in livers of HFD fed mice

molecule: total RNA

organism: Mus musculus

source_name: 9 month high fat diet fed mouse 1

value: 9 month high fat diet

tag: tissue

value: liver


title: Liver_JNK2_KO_repl1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description:
A186_04_155_JNK2
Replicate 1

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 Fluidics Station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the GeneChip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.28.2).

label: biotin

source_name: liver, global JNK2 knockout

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Mice carrying the loxP-site-flanked NEMO gene under the control of the Alb-cre promoter were generated as previously described (PMID: 19635861). From NEMOΔhepa mice, we generated double-knockout animals by crossing NEMOΔhepa with either constitutive Jnk1-/- or Jnk2-/- in a defined C57BL/6 background.

extract_protocol: Total RNA was isolated using RNeasy Micro Kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice had free acces to standard laboratory chow and water. Mice were killed at the age of 8 wks.

tag: strain/background

tag: genotype/variation

value: global Jnk2-/-

tag: Sex

value: male

tag: age

value: 8 wk

tag: mouseid


title: Bone.Marrow_RA_No_RA12

city: Liverpool

first: Philipp

last: Antczak

state: Merseyside

address: Crown Street

country: United Kingdom

institute: University of Liverpool

hyb_protocol: Hybridization of Chips was performed as per manufacturers instructions.

scan_protocol: SData were scanned as per manufactureres instructions on a GeneArray Scanner.

data_processing: Data was processed and normalized using the RMA methodology. Probes that were called absent in 50% of samples have been removed.

organism: Homo sapiens

source_name: Bone Marrow

label_protocol: 50ng of total RNA was amplified using Nugen Ovation Biotin RNA amplification

growth_protocol: Cells were seeded in duplicate at the required density using 10% FCS. Once attached, the medium was removed and the cells washed in serum free medium before replacing with fibroblast medium, which was identical but contained either 10% or 0.1% FCS.

extract_protocol: Fibroblasts were retrieved from culture by trypsin digestion and washed in fibroblast medium then PBS before resuspending in 200µl of RLT RNA protection buffer (Quiagen) followed by the manufacturer instructions of the RNeasy extraction kit.

value: Bone Marrow

tag: disease

value: RA

tag: serum

value: Low Serum


title: 9 month high fat diet mouse 2

source_name: 9 month high fat diet fed mouse 2


title: Bone.Marrow_RA_No_RA08


title: Bone.Marrow_RA_Yes_RA07

value: High Serum


title: Bone.Marrow_RA_No_RA07


title: Liver_NEMO_/JNK1_DKO_repl1

description:
A186_07_96_NEMOJNK1
Replicate 1

source_name: liver, global JNK1 / hepatocyte-specific NEMO double-knockout

value: global Jnk1-/-/NEMOΔhepa


title: 24-WT-SA-ZT36-3hpi

city: Ames

first: Wei

last: Wang

state: IA

address: 415 Bessey Hall

department: Department of Plant Pathology and Microbiology

institute: Iowa State University

description: 23-day-old soil grown plants

hyb_protocol: aRNA were hybridized to GeneChip®in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: GeneChips were scanned using  Affymetrix GeneChip® Scanner 7G

data_processing: The data were normalized with RMA algorithm using Gene-Spring GX default analysis settings

organism: Arabidopsis thaliana

source_name: true leaves

label_protocol: RNA probes were labelled using the Ambion MessageAmp Premier.

growth_protocol: Arabidopsis seedlings were grown at 21-24°C, 12-hour day length, 60% relative humidity. The seedlings were transfer to constant light condition for 24 hours before treatment and left in constant light condition after treatment

extract_protocol: Total RNA was isolated from the frozen material using Invitrogen TRIzol.

treatment_protocol: 23-day-old wild type treated with water or 1 mM SA at ZT24 or ZT36. Three biological replicates were used.

value: true leaves

tag: genotype

value: WT

tag: treatment

value: 1 mM SA

tag: time of treatment

tag: time after treatment (h)


title: 9 month normal mouse 1

description: Gene expression after 9 MO in livers of ND-fed mice

source_name: 9 month normal diet fed mouse 1

value: 9 month normal diet


title: Liver_JNK1_KO_repl2

description:
A186_02_129_JNK1
Replicate 2

source_name: liver, global JNK1 knockout

value: global Jnk1-/-


title: 9 month normal mouse 2

source_name: 9 month normal diet fed mouse 2


title: 22-WT-CK-ZT36-3hpi

description: 23-day-old soil grown plants

value: Water


title: 23-WT-SA-ZT36-0hpi

description: 23-day-old soil grown plants


title: Liver_JNK1_KO_repl3

description:
A186_03_130_JNK1
Replicate 3


title: Bone.Marrow_RA_Yes_RA04


title: 3 month high fat diet mouse 1

source_name: 3 month high fat diet fed mouse 1

value: 3 month high fat diet


title: 3 month normal mouse 2

description: Gene expression after 3 MO in livers of ND-induced mice

source_name: 3 month normal diet fed mouse 2

value: 3 month normal diet


title: 20-WT-SA-ZT24-3hpi

description: 23-day-old soil grown plants


title: Bone.Marrow_RA_No_RA04


title: Bone.Marrow_RA_Yes_RA03


title: Old Spleen 0.5Gyx3 Protons Replicate 10

city: Mountain View

first: Afshin

last: Beheshti

address: Moffett Blvd

institute: NASA Ames Research Center

description: Old Spleen 0.5Gyx3 Protons Replicate 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were corrected with COMBAT correction and then quantile normalisation with GenePattern Illumina Normalizer Module

source_name: Spleen from LLC tumore bearing mice

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

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

value: C57BL/6 Male Mouse

value: 736 days old

tag: irradation

value: 0.5Gyx3 Protons

value: Spleen


title: 18-WT-CK-ZT24-3hpi

description: 23-day-old soil grown plants


title: 21-WT-CK-ZT36-0hpi

description: 23-day-old soil grown plants


title: 19-WT-SA-ZT24-0hpi

description: 23-day-old soil grown plants


title: 3 month normal mouse 1

description: Gene expression after 3 MO in livers of ND-induced NASH mice

source_name: 3 month normal diet fed mouse 1

value: liver


title: Liver_21days_Control_A10

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

country: France

institute: INSERM

description: Gene expression of liver from rats born to dams fed standard diet.

hyb_protocol: 2.5 ug of Cy3-labelled and Cy5-labelled cRNA (specific activity >6.0 pmol Cy3/ug or Cy5/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µL of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Rat (V3) GE Microarray 4x44K for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Arrays were washed and scanned on the G2505C Agilent scanner.

data_processing: Quantification was using the Agilent Feature Extraction software (version 10.7.1.1; Grid name: 028282_D_F_20110531; Protocol name: GE2_107_Sep09).

organism: Rattus norvegicus

source_name: Liver 21 days

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA were prepared from 0.2 ug RNA using the Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol:
Animal treatments were performed according to the National Institutes of Health guide for the care and use of laboratory animals. The review board of Nancy University approved this study. Adult female Wistar rats (Charles River, Les Oncins, France) were constantly maintained under standard laboratory conditions, on a 12-hour light/dark cycle, with food and water available ad libitum.
One month before pregnancy, adult females were fed either with standard food or diet without vitamin B12 and folates. Diets were maintained until weaning of offsprings.

extract_protocol: RNA was extracted from the liver from Control (n=4) and MDD rats (n=4 animals) using the RNeasy Mini Kit (Qiagen #74104) and the concentration was measured by Nanodrop (Thermo Scientific, Wilmington, DE, USA). Its quality was controlled by 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Genomic DNA was extracted following the phenol-chloroform method.

treatment_protocol: Twenty-one-day old rats were sacrificed by decapitation after exposure to halothane and the liver was rapidly removed. Immediately after sacrifice, intracardiac blood samples were collected and centrifuged for 10 min at 3000 rpm. Aliquots of plasma were stored frozen at -80℃ until analysis. The liver was rapidly collected, washed in Ringer buffered solution, frozen in liquid nitrogen and stored at -80℃ until analysis.

value: female

value: 21 days

value: rats born to dams fed standard diet

value: Wistar


title: Liver_21days_MDD_G7

description: Gene expression of liver from rats born to dams fed MDD diet.

value: male

value: rats born to dams fed MDD diet


title: Old Spleen 0.5Gyx3 Protons Replicate 8

description: Old Spleen 0.5Gyx3 Protons Replicate 8


title: Liver_21days_Control_B6


title: Old Spleen 0.5Gyx3 Protons Replicate 7

description: Old Spleen 0.5Gyx3 Protons Replicate 7


title: 15-WT-SA-ZT36-0hpi

description: 23-day-old soil grown plants

value: true leaves

value: WT

value: 1 mM SA


title: 17-WT-CK-ZT24-0hpi

description: 23-day-old soil grown plants

value: Water


title: Bone.Marrow_RA_No_RA03

value: Bone Marrow

value: RA

value: Low Serum


title: Bone.Marrow_RA_Yes_RA01

value: High Serum


title: Old Spleen 0.5Gyx3 Protons Replicate 6

description: Old Spleen 0.5Gyx3 Protons Replicate 6

value: C57BL/6 Male Mouse

value: 736 days old

value: 0.5Gyx3 Protons


title: Liver_21days_MDD_G8

value: liver


title: Bone.Marrow_RA_No_RA02


title: Bone.Marrow_RA_No_RA01


title: Liver_21days_MDD_E2

value: female

value: 21 days


title: Liver_21days_Control_B2

value: rats born to dams fed standard diet

value: Wistar


title: Old Spleen 0.5Gyx3 Protons Replicate 5

description: Old Spleen 0.5Gyx3 Protons Replicate 5

value: Spleen


title: 16-WT-SA-ZT36-3hpi

description: 23-day-old soil grown plants

value: true leaves


title: Bone.Marrow_RA_Yes_RA02


title: Skin_OA_Yes_ST07

source_name: Skin

value: Skin

value: OA


title: Old Spleen 0.5Gyx3 Protons Replicate 4

description: Old Spleen 0.5Gyx3 Protons Replicate 4


title: Old Spleen 0.5Gyx3 Protons Replicate 3

description: Old Spleen 0.5Gyx3 Protons Replicate 3


title: Skin_OA_No_ST07


title: 12-WT-SA-ZT24-3hpi

description: 23-day-old soil grown plants

value: WT

value: 1 mM SA


title: Old Spleen 0.5Gyx3 Protons Replicate 2

description: Old Spleen 0.5Gyx3 Protons Replicate 2


title: Old Spleen 0.5Gyx3 Protons Replicate 9

description: Old Spleen 0.5Gyx3 Protons Replicate 9


title: 14-WT-CK-ZT36-3hpi

description: 23-day-old soil grown plants

value: Water


title: Old Spleen 0.5Gyx3 Protons Replicate 1

description: Old Spleen 0.5Gyx3 Protons Replicate 1


title: Old Spleen 0Gy Replicate 10

description: Old Spleen 0Gy Replicate 10


title: Old Spleen 0Gy Replicate 9

description: Old Spleen 0Gy Replicate 9


title: 13-WT-CK-ZT36-0hpi

description: 23-day-old soil grown plants


title: 8-WT-SA-ZT36-3hpi

description: 23-day-old soil grown plants


title: Liver_21days_MDD_F5

value: rats born to dams fed MDD diet


title: 7-WT-SA-ZT36-0hpi

description: 23-day-old soil grown plants


title: 6-WT-CK-ZT36-3hpi

description: 23-day-old soil grown plants


title: Old Spleen 0Gy Replicate 7

description: Old Spleen 0Gy Replicate 7


title: Old Spleen 0Gy Replicate 8

description: Old Spleen 0Gy Replicate 8


title: Liver_21days_Control_B7

value: male


title: Skin_OA_Yes_ST02

value: High Serum


title: Skin_OA_Yes_ST06


title: Skin_OA_No_ST04

value: Low Serum


title: 11-WT-SA-ZT24-0hpi

description: 23-day-old soil grown plants


title: Skin_OA_Yes_ST04


title: 5-WT-CK-ZT36-0hpi

description: 23-day-old soil grown plants


title: Skin_OA_No_ST03


title: Skin_OA_Yes_ST03


title: Old Spleen 0Gy Replicate 6

description: Old Spleen 0Gy Replicate 6

value: C57BL/6 Male Mouse

value: 736 days old


title: Old Spleen 0Gy Replicate 2

description: Old Spleen 0Gy Replicate 2


title: 9-WT-CK-ZT24-0hpi

description: 23-day-old soil grown plants


title: Skin_OA_Yes_ST01


title: Old Spleen 0Gy Replicate 5

description: Old Spleen 0Gy Replicate 5


title: Old Spleen 0Gy Replicate 4

description: Old Spleen 0Gy Replicate 4


title: Old Spleen 0Gy Replicate 1

description: Old Spleen 0Gy Replicate 1


title: 2-WT-CK-ZT24-3hpi

description: 23-day-old soil grown plants


title: Skin_OA_No_ST06


title: Skin_OA_No_ST02


title: 10-WT-CK-ZT24-3hpi

description: 23-day-old soil grown plants


title: Skin_RA_Yes_RA17

value: RA


title: Adolescent Spleen 0.5Gyx3 Protons Replicate 10

value: 68 days old

value: 0.5Gyx3 Protons


title: 1-WT-CK-ZT24-0hpi

description: 23-day-old soil grown plants


title: 3-WT-SA-ZT24-0hpi

description: 23-day-old soil grown plants


title: 4-WT-SA-ZT24-3hpi

description: 23-day-old soil grown plants


title: Skin_OA_No_ST01


title: Skin_RA_No_RA17


title: Adolescent Spleen 0.5Gyx3 Protons Replicate 9


title: Adolescent Spleen 0.5Gyx3 Protons Replicate 8


title: Skin_RA_Yes_RA16


title: Skin_RA_No_RA16


title: Adolescent Spleen 0.5Gyx3 Protons Replicate 7


title: Adolescent Spleen 0.5Gyx3 Protons Replicate 6


title: Mice_Lung_IAV_36h

city: Shanghai

first: Meng

last: Guo

address: No. 415, Fengyang Road, Huangpu District

department: Organ transplantation center

country: China

institute: ShangHai Changzheng Hospital

description:
miRNA expression in IAV infection mice at 36h
GM0003

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US).

data_processing:
Data was read by Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings(Scan resolution=5μm, PMT 100%，5% )
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: lung, 36hr

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US). Three mice were performed at each time (24 or 36 hours) and RNA from different donors was mixed before determination.

treatment_protocol: Mice were treated with 50µl of influenza A (50 µl of 10-6 TCID50/µl) via retropharyngeal instillation for 24h or 36h.

tag: gender

tag: infection

value: IAV

tag: time

value: lung


title: Mice_Lung_IAV_24h

description:
miRNA expression in IAV infection mice at 24h
GM0002

source_name: lung, 24hr

tag: strain


title: Liver_JNK1_KO_repl1

description:
A186_01_98_JNK1
Replicate 1

value: global Jnk1-/-

value: 8 wk

tag: tissue

value: liver


title: Mice_Lung_CT

description:
miRNA expression in normal mice
GM0001

source_name: lung, 0hr

value: control


title: Skin_RA_Yes_RA15

value: Skin


title: Skin_RA_No_RA08


title: Skin_RA_Yes_RA12


title: Skin_RA_Yes_RA14


title: Skin_RA_No_RA14


title: Adolescent Spleen 0.5Gyx3 Protons Replicate 3

value: Spleen


title: Adolescent Spleen 0.5Gyx3 Protons Replicate 1


title: Adolescent Spleen 0.5Gyx3 Protons Replicate 4


title: Skin_RA_No_RA12


title: Skin_RA_No_RA07


title: Adolescent Spleen 0.5Gyx3 Protons Replicate 5


title: Skin_RA_No_RA15


title: Adolescent Spleen 0Gy Replicate 7

description: Adolescent Spleen 0Gy Replicate 7


title: Adolescent Spleen 0.5Gyx3 Protons Replicate 2


title: Skin_RA_Yes_RA07


title: Skin_RA_Yes_RA05


title: Adolescent Spleen 0Gy Replicate 4

description: Adolescent Spleen 0Gy Replicate 4


title: Adolescent Spleen 0Gy Replicate 9

description: Adolescent Spleen 0Gy Replicate 9


title: Adolescent Spleen 0Gy Replicate 5

description: Adolescent Spleen 0Gy Replicate 5


title: H1650 PLKO CONTROL replicate 2

city: Isnes Gembloux

first: Roland

last: Hubaux

state: Namur

address: rue Jean Sonet 10

department: R&D

country: Belgium

institute: StratiCELL

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

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

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and RMA normalization method.

source_name: NCI-H1650 pLKO control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA.

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

tag: cell line

tag: cell type

value: Lung cancer cell line

value: empty vector pLKO control


title: H1693 KD replicate 2

source_name: NCI-H1693 Mark2 Knockdown

tag: genotype/variation

value: MARK2 Knockdown


title: Adolescent Spleen 0Gy Replicate 8

description: Adolescent Spleen 0Gy Replicate 8

tag: age


title: Skin_RA_No_RA05

value: Low Serum


title: Adolescent Spleen 0Gy Replicate 6

description: Adolescent Spleen 0Gy Replicate 6

value: C57BL/6 Male Mouse


title: H1993 KD replicate 2

source_name: NCI-H1993 Mark2 Knockdown


title: Skin_RA_No_RA02


title: Skin_RA_Yes_RA04

value: High Serum


title: Skin_RA_No_RA03

value: RA


title: Skin_RA_Yes_RA03


title: Skin_RA_Yes_RA02


title: Adolescent Spleen 0Gy Replicate 3

description: Adolescent Spleen 0Gy Replicate 3

value: 68 days old


title: H1650 KD replicate 2

source_name: NCI-H1650 Mark2 Knockdown


title: Skin_RA_Yes_RA01


title: H1993 PLKO CONTROL replicate 2

source_name: NCI-H1993 pLKO control


title: Skin_RA_Yes_RA08


title: H1693 KD replicate 1


title: H1650 PLKO CONTROL replicate 1


title: H1693 PLKO CONTROL replicate 2

source_name: NCI-H1693 pLKO control


title: H1993 KD replicate 1


title: H1993 PLKO CONTROL replicate 1


title: Skin_RA_No_RA04


title: Synovium_OA_No_ST06

source_name: Synovium

value: Synovium

value: OA


title: H1693 PLKO CONTROL replicate 1


title: Synovium_OA_Yes_ST06


title: Skin_RA_No_RA01


title: H1650 KD replicate 1


title: Synovium_OA_No_ST04


title: Synovium_OA_Yes_ST04


title: Synovium_OA_Yes_ST03


title: Adolescent Spleen 0Gy Replicate 2

description: Adolescent Spleen 0Gy Replicate 2


title: Liver_21days_E2_female

type: genomic

hyb_protocol: Arrays were hybridized in Maui hybridization stations for 16-20 h at 42 °C and gently agitated for 10 - 15 seconds in the shallow dish containing warm Wash I to quickly remove the hybridization buffer. Then they were washed in 42 °C for an additional 2 minutes in Wash I with vigorous, constant agitation. Slides were transferred to Wash III and washed for 15 seconds with vigorous, constant agitation. Then they were spinned dry in a NimbleGen Microarray Dryer or other microarray dryer per the manufacturer’s recommendation.Remove the slide(s) from the NimbleGen Microarray Dryer or other microarray dryer. Blot dry the edges to remove any residual moisture.Proceed immediately to the steps for scanning the array.

scan_protocol: Prepared slides were read with the G2505C Agilent scanner.

data_processing: Array were quantified with the NimbleGen scanControl software.

molecule: genomic DNA

label_protocol: The DNA was sonicated (Bioruptor, Diagenode, Denville, NJ, USA) to obtain fragments between 300 and 1000 bp (with a peak at 500 bp). Then 4 µg of sonicated genomic DNA was denatured for 10 min at 95 °C and immunoprecipitated overnight at 4 °C with an anti5-methylcytidine antibody (Abcam #ab10805). Then dynabeads coupled with a sheep anti-mouse-IgG antibody (Dynal Biotech #11201D) were added to the mixture for 2 h at 4 °C. After washing, proteinase K was added to the beads–DNA complex for 3 h at 50 °C and methylated DNA was isolated by phenolchloroform extraction followed by ethanol precipitation. Immunoprecipitated DNA from MeDIP was amplified with the GenomePlex Complete Whole Genome Amplification Kit (Sigma, #WGA2) according to the manufacturer’s instructions. Quality of the MeDIP assay was performed by qPCR of the promoter of two control genes: the ubiquitously expressed GAPDH gene without promoter methylation, and TSH2B a testis-specific histone highly methylated in all somatic cells. Sample labeling was done with the NimbleGen Dual-Color DNA Labeling Kit.

extract_protocol: Tissue is rapidly frozen and crushed to produce readily digestible pieces. The processed tissue is placed in a solution of proteinase K and SDS and incubated until most of the cellular protein is degraded. The digest is deproteinized by successive phenol/chloroform/  isoamyl alcohol extractions, recovered by ethanol precipitation, and dried and resuspended in buffer.

treatment_protocol: Animal treatments were performed according to the National Institutes of Health guide for the care and use of laboratory animals. The review board of Nancy University approved this study. Adult female Wistar rats (Charles River, Les Oncins, France) were constantly maintained under standard laboratory conditions, on a 12-hour light/dark cycle, with food and water available ad libitum. One month before pregnancy, adult females were fed either with standard food or diet without vitamin B12 and folates. Diets were maintained until weaning of offspring.

value: female

value: Liver

value: Wistar

value: 21 days

tag: diet

value: deficient in B12 and folates

tag: antibody

value: anti5-methylcytidine (Abcam #ab10805)


title: Liver_21days_G8_male

value: male


title: Liver_21days_B7_male

value: standard


title: Synovium_RA_Yes_RA17

tag: disease

tag: serum


title: Liver_21days_G7_male


title: Synovium_OA_No_ST03


title: Synovium_OA_Yes_ST01


title: Synovium_OA_No_ST02


title: Synovium_OA_Yes_ST02


title: Synovium_RA_Yes_RA16


title: Synovium_OA_No_ST01


title: Synovium_RA_No_RA17


title: Liver_21days_B6_female


title: Synovium_RA_No_RA16


title: Synovium_RA_Yes_RA15


title: Synovium_RA_No_RA15


title: Synovium_RA_Yes_RA14


title: Synovium_RA_No_RA14


title: Synovium_RA_Yes_RA12


title: 5935446005_R04C01

city: Baltimore

first: Sarven

last: Sabunciyan

state: MD

address: 600 N. Wolfe Street, Blalock 1146

department: Pediatrics

institute: Johns Hopkins University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing: Bioconductor minfi package

label: Cy5 and Cy3

source_name: human serum DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from serum samples using EpiCenter MasterPure kit according to standard instructions

tag: sample type

value: serum DNA

tag: diagnosis

value: Mania

tag: Sex

value: Male


title: Synovium_RA_No_RA08

value: Low Serum


title: Synovium_RA_No_RA12


title: 5935446005_R06C02


title: 5935403032_R04C01

value: Ctr

value: Female


title: Synovium_RA_No_RA07

value: RA


title: Synovium_RA_Yes_RA08

value: Synovium

value: High Serum


title: 5958091020_R02C02


title: 5958091020_R01C02


title: 5935403032_R03C01


title: Synovium_RA_Yes_RA05


title: 5935446005_R05C02


title: Synovium_RA_No_RA05


title: 5935403032_R02C01


title: 5958091019_R02C02


title: Synovium_RA_Yes_RA04


title: Adolescent Spleen 0Gy Replicate 1

description: Adolescent Spleen 0Gy Replicate 1

value: C57BL/6 Male Mouse

value: 68 days old

tag: irradation

value: Spleen


title: Synovium_RA_No_RA04


title: Synovium_RA_Yes_RA03


title: 5935403032_R01C01


title: Synovium_RA_No_RA03


title: Synovium_RA_No_RA02


title: 5935446005_R04C02


title: Synovium_RA_Yes_RA02


title: 5958091019_R01C02


title: 5958091020_R05C01


title: Synovium_RA_Yes_RA07


title: 5935446005_R03C01


title: 5935403032_R03C02


title: Mixed PCB exposed PBMC cells, biological replicate 6

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

department: Biology

institute: Howard University

description: Gene expression data from PBMC Cells with mixed PCBs treatment after 48 hours.

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Human PBMC cells from healthy donor.

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

growth_protocol: PBMC cells are grown for 48 hours in RPMI 1640 supplemented with 10% FBS and 1X Pennicilllin-Streptromycin with 1.25 mircogram/ml PHA-M and 0.15% (v/v)pokeweed mitogen and 50 microgram Beta-mercaptoethanol.

treatment_protocol: Treated with mixed congeners of PCBs (118, 138, 153, 170, 180) at Slovak median human equivalence level.

tag: gender

value: female

value: 18 years

value: PBMC

tag: treatment


title: 5935446005_R01C01


title: 5935446005_R02C01


title: 5935403032_R02C02


title: Mixed PCB exposed PBMC cells, biological replicate 5


title: Mixed PCB exposed PBMC cells, biological replicate 4


title: WT in glucose, biological rep2

city: Miami

first: Dragana

last: Ajdic

state: Florid

address: 1600 NW 10th Ave, RMSB 2023

department: Dermatology

institute: University of Miami

description: Gene transcription data from planktonic culture OD600=0.65

hyb_protocol: Following fragmentation, 3 μg of cDNA were hybridized for 16 hr at 47℃ on GeneChip S. mutans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a laser scanner 7G (Affymetrix)

data_processing: Data was analyzed with Expression and Transcription Analysis Console software from Affymetrix using default analysis settings and global scaling as normalization method.

organism: Streptococcus mutans UA159

source_name: Streptococcus mutans UA159

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

growth_protocol: Cells were grown in chemically-defined medium supplemented with 0.5% glucose.

extract_protocol: Cells were lysed using beat-beater. Extraction of total RNA was performed using Ambion RiboPure Bacteria kit according to the manufacturers protocol.

treatment_protocol: Cells were grown to the mid-log phase (OD600 = 0.65) and harvested by centrifugation.

tag: culture

value: planktonic cells

tag: genotype

value: wild type


title: 5958091020_R06C01

value: serum DNA


title: Mixed PCB exposed PBMC cells, biological replicate 2


title: 5958091019_R06C01

value: Mania


title: ΔnigR in glucose, biological rep2

value: ΔnigR


title: Mixed PCB exposed PBMC cells, biological replicate 3


title: ΔnigR in glucose, biological rep1


title: 5958091020_R06C02


title: Liver_21days_B2_female

tag: tissue

value: Liver

tag: strain

value: Wistar

value: 21 days

value: standard

value: anti5-methylcytidine (Abcam #ab10805)


title: 5935446005_R02C02

value: Female


title: 5958091020_R03C01

value: Ctr


title: 168_Dhfq_2

city: Jouy-en-Josas

first: Tatiana

last: Rochat

address: Domaine de Vilvert

institute: INRA

description:
hfq mutant replicat 2
DHFQ_2.IFPC_ARN_104_254447310013_532

hyb_protocol: Hybridization was performed by PartnerChip (Evry, France) as described in Nicolas et al (2012) (PMID:22383849).

scan_protocol: Scanning was performed by PartnerChip (Evry, France) as described in Nicolas et al (2012) (PMID:22383849).

data_processing:
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region as described in (Nicolas et al., 2012 PMID: 22383849).
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347). Data were quantile normalized using LIMMA package.
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis cells

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol: B. subtilis strains (wild-type and mutants) were grown in LB medium and harvested by centrifugation 5h after the onset of the stationary phase.

extract_protocol: Total RNA was extracted as described in Nicolas et al (2012) (PMID:22383849)

value: hfq deletion mutant

tag: growth phase

value: stationary phase


title: 5935446005_R03C02

value: Male


title: 5958091020_R04C01


title: 5935446005_R01C02


title: 168_wt_2

description:
wild-type strain replicat 2
WT_2.IFPC_ARN_102_254447310012_532

tag: genotype/variation

value: wild-type


title: 5958091019_R06C02


title: 168_Dhfq_1

description:
hfq mutant replicat 1
DHFQ_1.IFPC_ARN_103_254447310013_532


title: Control PBMC cells for mixed PCB, biological replicate 4

description: Gene expression data from PBMC Cells without PCBs treatment.

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

growth_protocol: Grown for 48 hours in RPMI 1640 supplemented with 10% FBS and 1X Pennicilllin-Streptromycin with 1.25 mircogram/ml PHA-M and 0.15% (v/v)pokeweed mitogen and 50 microgram Beta-mercaptoethanol.

treatment_protocol: Untreated cells

value: female

tag: age

value: 18 years

tag: cell type

value: PBMC

value: control


title: Control PBMC cells for mixed PCB, biological replicate 5


title: Mixed PCB exposed PBMC cells, biological replicate 1


title: Control PBMC cells for mixed PCB, biological replicate 3


title: 168_wt_1

description:
wild-type strain replicat 1
WT_1.IFPC_ARN_101_254447310012_532


title: 5958091019_R04C02

value: serum DNA

value: Mania


title: 5958091019_R05C01


title: Control PBMC cells for mixed PCB, biological replicate 2

description: Gene expression data from PBMC Cells bwithout PCBs treatment.


title: 5958091020_R02C01


title: 5935403032_R01C02


title: Control PBMC cells for mixed PCB, biological replicate 6


title: 5935403032_R06C01


title: WT in glucose, biological rep1

value: planktonic cells

value: wild type


title: Control PBMC cells for mixed PCB, biological replicate 1


title: 5958091020_R04C02


title: 5935446005_R06C01


title: 5958091020_R05C02


title: 5935403032_R05C01


title: 5958091020_R03C02


title: 5958091019_R03C02


title: 5958091020_R01C01


title: 5935446005_R05C01


title: FIST15

status: Public on Jun 21 2015

city: Valencia

first: Patricia

last: Sebastian-Leon

state: Valencia

address: Av Autopista del Saler, 16

department: Bioinformatics and Genomics

country: Spain

institute: CIPF

description: Serrated tumor sample from Finland

hyb_protocol: HumanMethylation450K BeadChip. During hybridization, the amplified and fragmented DNA samples anneal to specific oligomers that are covalently linked to the different bead types. The bead chips were then subjected to a single-base extension reaction. This reaction incorporates labelled nucleotides into the extended primers hybridized to DNA on the BeadChip.

scan_protocol: The fluorescently stained chip was imaged by the Illumina i-SCAN.

data_processing: Illumina's Genome Studio program (Methylation Module) was used to analyze BeadArray data to assign site-specific DNA methylation β-values to each CpG site.

source_name: serrated FIN

label_protocol: Cy3 and Cy5. One or two probes are used to interrogate CpG locus, depending on the probe design for a particular CpG site. The Infinium I assay has two probes per site one “unmethylated” and one “methylated”. The 3' end of each probe is designed to match either the protected cytosine (methylated design) or the thymine base (unmethylated design) resulting from bisulfite conversion and whole-genome amplification. The Infinium II assay has one probe per site. The 3' end of the probe complements the base directly upstream of the query site while single base extension results in the addition of a labeled G or A base, complementary to either the “methylated” C or “unmethylated” T.

extract_protocol: From frozen tissue using QiaAmp DNA Mini Kit (cat nº:51306, Qiagen).

treatment_protocol: Bisulfite convertion with the EZ DNA Methylation Kit (Zymo Research, Orange, CA). DNA was isothermally amplified at 37°C (20-24h) and the DNA product was fragmented by endpoint enzymatic process

tag: type

value: Serrated

value: Tumor

tag: country

value: Finland


title: FICN03

description: Conventional normal sample from Finland

source_name: conventional normal FIN

value: Conventional

value: Normal


title: FIST18

description: Serrated tumor sample from Finland


title: FISN04

description: Serrated normal sample from Finland

source_name: serrated normal FIN


title: FICN04

description: Conventional normal sample from Finland


title: FICT07

description: Conventional tumor sample from Finland

source_name: conventional FIN


title: FICT09

description: Conventional tumor sample from Finland


title: FIST14

description: Serrated tumor sample from Finland


title: FIST17

description: Serrated tumor sample from Finland


title: FICT03

description: Conventional tumor sample from Finland


title: FICT02

description: Conventional tumor sample from Finland


title: FICN01

description: Conventional normal sample from Finland


title: FIST16

description: Serrated tumor sample from Finland


title: FICN02

description: Conventional normal sample from Finland


title: FICT05

description: Conventional tumor sample from Finland


title: FICT06

description: Conventional tumor sample from Finland


title: FICT08

description: Conventional tumor sample from Finland


title: FISN01

description: Serrated normal sample from Finland


title: ESST009

description: Serrated tumor sample from Spain

source_name: serrated ESP

value: Spain


title: FICT04

description: Conventional tumor sample from Finland


title: FIST12

description: Serrated tumor sample from Finland


title: ESCN007

description: Conventional normal sample from Spain

source_name: conventional normal ESP


title: IVD_1

description: Control sample

source_name: control 2

value: IVD


title: ESMSIT007

description: MSI tumos sample from Spain

source_name: MSI ESP

value: MSI


title: FISN03

description: Serrated normal sample from Finland


title: ESCN002

description: Conventional normal sample from Spain


title: FISN02

description: Serrated normal sample from Finland


title: FIST13

description: Serrated tumor sample from Finland


title: ESST019

description: Serrated tumor sample from Spain


title: ESMSIT010

description: MSI tumos sample from Spain


title: ESST011

description: Serrated tumor sample from Spain


title: FIST03

description: Serrated tumor sample from Finland


title: ESCN001

description: Conventional normal sample from Spain


title: ESMSIT005

description: MSI tumos sample from Spain


title: ESSN005

description: Serrated normal sample from Spain

source_name: serrated normal ESP


title: FIST11

description: Serrated tumor sample from Finland


title: ESCT035

description: Conventional tumor sample from Spain

source_name: conventional ESP


title: ESMSIT001

description: MSI tumos sample from Spain


title: ESMSIN005

description: MSI normal sample from Spain

source_name: MSI normal ESP


title: ESCT015

description: Conventional tumor sample from Spain


title: ESSMT002

description: Serrated tumor sample from Spain


title: ESCN009

description: Conventional normal sample from Spain


title: FIST10

description: Serrated tumor sample from Finland


title: ESMSIN002

description: MSI normal sample from Spain


title: ESCT001

description: Conventional tumor sample from Spain


title: ESMSIT006

description: MSI tumos sample from Spain


title: ESST001

description: Serrated tumor sample from Spain


title: ESST038

description: Serrated tumor sample from Spain


title: ESCT027

description: Conventional tumor sample from Spain


title: ESMSIT002

description: MSI tumos sample from Spain


title: ESMSIN003

description: MSI normal sample from Spain


title: FIST02

description: Serrated tumor sample from Finland


title: FIST09

description: Serrated tumor sample from Finland


title: ESCT041

description: Conventional tumor sample from Spain


title: ESSN012

description: Serrated normal sample from Spain


title: FIST01

description: Serrated tumor sample from Finland


title: ESCT042

description: Conventional tumor sample from Spain


title: ESCT036

description: Conventional tumor sample from Spain


title: ESSN004

description: Serrated normal sample from Spain


title: ESCMT003

description: Conventional tumor sample from Spain


title: ESST010

description: Serrated tumor sample from Spain


title: ESST004

description: Serrated tumor sample from Spain


title: FIST08

description: Serrated tumor sample from Finland


title: Slide22 D

city: Edmonton

first: chi

last: zhou

state: Alberta

address: 114 street 90 ave NW.

department: Agriculture Food and Nutritional Science

country: Canada

institute: University of Alberta

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: GenePix 4200 Autoloader by Molecular Devices. Software is GenePix Pro, Acuity 4.0

data_processing: background subtracted, within array global lowess normalization data obtained from log2 of processed Red signal/processed Green signal

organism: Sus scrofa

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol:
This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: developmental stage

tag: time of embryo collection

value: 5.5 dpi (days post-in-vivo insemination)

value: 5 dpi (days post-in-vivo insemination)


title: ESST031

description: Serrated tumor sample from Spain


title: ESCT011

description: Conventional tumor sample from Spain


title: ESST036

description: Serrated tumor sample from Spain


title: ESCPT001

description: Conventional tumor sample from Spain


title: Slide22 B


title: ESCN012

description: Conventional normal sample from Spain


title: ESCN005

description: Conventional normal sample from Spain


title: ESSN002

description: Serrated normal sample from Spain


title: Slide22 C


title: ESST023

description: Serrated tumor sample from Spain


title: Slide22 A


title: ESST008

description: Serrated tumor sample from Spain


title: Slide4 C


title: ESCT021

description: Conventional tumor sample from Spain


title: ESMSIT009

description: MSI tumos sample from Spain


title: ESMSIN001

description: MSI normal sample from Spain


title: ppk_path_5

city: San Francisco

first: Charlie

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

hyb_protocol: 600 ng of each Cy3-labeled aaRNA hybridized to a SurePrint G3 Custom Gene Expression 8x60K microarray (Agilent) as per manufacturer's protocol.

scan_protocol: Arrays were scanned on an Agilent scanner, 3 um resolution, 20-bit tiff.

data_processing: Custom in-house scripts and the Bioconductor Limma package were used for filtering and normalization. Expression values were log2 transformed and quantile normalized.

organism: Drosophila melanogaster

source_name: Sorted class IV da neurons, path mutant

label_protocol: 1.5 ug of aRNA coupled to Cy3 in 0.1 M sodium bicarbonate pH 9 buffer and purified over spin columns.

growth_protocol: Wild type or path mutant Drosophila 3rd instar larvae.

extract_protocol: RNA was isolated from samples (RNAqueous Micro, Life Technologies). Purified RNA was amplified (MessageAmp II, Life Technologies) with minor modifications to manufacturer's instructions to generate amino-allyl incorporated amplified RNA.

treatment_protocol: Total RNA extraction from FACS-isolated class IV da neurons marked with ppk, or whole body wall filets.

value: path mutant

value: 3rd instar larvae

value: purified class IV da neurons


title: ESSN007

description: Serrated normal sample from Spain


title: ESSN009

description: Serrated normal sample from Spain


title: ppk_path_4


title: Slide4 A


title: ppk_path_3


title: ESCN006

description: Conventional normal sample from Spain


title: ESCT033

description: Conventional tumor sample from Spain


title: ESCT030

description: Conventional tumor sample from Spain


title: FIST07

description: Serrated tumor sample from Finland


title: ppk_path_2


title: ESSN001

description: Serrated normal sample from Spain


title: ESMSIN006

description: MSI normal sample from Spain


title: ppk_path_1


title: ppk_wt_3

source_name: Sorted class IV da neurons, wild type


title: ppk_wt_4


title: ESMSIT004

description: MSI tumos sample from Spain


title: ppk_wt_2


title: ESCT026

description: Conventional tumor sample from Spain


title: body_path_df_4

source_name: Body wall filet, path mutation over deficiency

value: path mutation over deficiency

value: body wall filet


title: ESCT002

description: Conventional tumor sample from Spain


title: body_path_df_3


title: ESCT008

description: Conventional tumor sample from Spain


title: body_path_df_2


title: ESCT012

description: Conventional tumor sample from Spain


title: body_path_df_1


title: body_wt_path_2

source_name: Body wall filet, wild type over path mutation

value: wild type over path mutation


title: ESCT010

description: Conventional tumor sample from Spain


title: ESCN010

description: Conventional normal sample from Spain


title: ESSMT001

description: Serrated tumor sample from Spain


title: ESST030

description: Serrated tumor sample from Spain


title: ppk_wt_1

value: wild type


title: ESCN003

description: Conventional normal sample from Spain


title: body_wt_path_3


title: FIST06

description: Serrated tumor sample from Finland

value: Serrated


title: ESSPT001

description: Serrated tumor sample from Spain

value: Tumor


title: body_wt_path_1


title: body_wt_df_2

source_name: Body wall filet, wild type over deficiency

value: wild type over deficiency


title: body_wt_df_3


title: ESMSIT008

description: MSI tumos sample from Spain


title: ESCT013

description: Conventional tumor sample from Spain

value: Conventional


title: ppk_wt_5


title: ESCN008

description: Conventional normal sample from Spain

value: Normal


title: body_wt_df_1


title: ESSMN

description: Serrated normal sample from Spain

value: Spain


title: ESSN010

description: Serrated normal sample from Spain


title: ESSN003

description: Serrated normal sample from Spain


title: Mouse #143 wt/wt

city: Kensington

first: Anthony

middle: John

last: Kee

state: New South Wales

address: University of New South Wales

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

description:
143Wt
fasted for 14-16h

data_processing: Data was normalised to control genes, genes with an Illumina detection score equal to one, and all probes except the genes with an Illumina detection score  equal to one were filtered out to remove probes without adequate expression levels (Gene-Spring GX v7.3.1 software, Agilent)

label: Biotin

source_name: Mouse #143 wt/wt, Epididymal Fat

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer 2100 and RNA integrity scores above 7.8 were present in all samples.

value: FVB/N

value: epididymal adipose tissue


title: Mouse #142 wt/wt

description:
142Wt
fasted for 14-16h

source_name: Mouse #142 wt/wt, Epididymal Fat


title: Mouse #159 wt/wt

description:
159Wt
fasted for 14-16h

source_name: Mouse #159 wt/wt, Epididymal Fat


title: Mouse #141 wt/wt

description:
141Wt
fasted for 14-16h

source_name: Mouse #141 wt/wt, Epididymal Fat


title: Mouse #164 tg/tg

description:
164Tg
fasted for 14-16h

source_name: Mouse #164 tg/tg, Epididymal Fat

value: cytoskleteal tropomyosin Tm5NM1 transgenic


title: Mouse #165 tg/tg

description:
165Tg
fasted for 14-16h

source_name: Mouse #165 tg/tg, Epididymal Fat


title: Mouse #163 tg/tg

description:
163Tg
fasted for 14-16h

source_name: Mouse #163 tg/tg, Epididymal Fat


title: SLIDE20D

value: 5.5 dpi (days post-in-vivo insemination)

source_name: Blastocyst

value: 5 dpi (days post-in-vivo insemination)


title: FIST05

description: Serrated tumor sample from Finland

source_name: serrated FIN

value: Finland


title: ESSN008

description: Serrated normal sample from Spain

source_name: serrated normal ESP


title: Mouse #147 tg/tg

description:
147Tg
fasted for 14-16h

source_name: Mouse #147 tg/tg, Epididymal Fat


title: ESST002

description: Serrated tumor sample from Spain

source_name: serrated ESP


title: SLIDE20C


title: Mouse #152 tg/tg

description:
152Tg
fasted for 14-16h

source_name: Mouse #152 tg/tg, Epididymal Fat


title: green-00030: JG2ME48hD

status: Public on Jun 20 2015

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

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

source_name: SCp2 48h after treatment of 2ME2


title: SLIDE8A


title: SLIDE20A


title: green-00030: JG2ME48hA

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


title: SLIDE8C


title: green-00030: JGCon48hD

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

source_name: SCp2 control at 48h


title: ESST006

description: Serrated tumor sample from Spain


title: green-00030: JGCon48hC

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


title: SLIDE20B


title: green-00030: JGCon48hA

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


title: ESCT043

description: Conventional tumor sample from Spain

source_name: conventional ESP


title: ESCT004

description: Conventional tumor sample from Spain


title: green-00030: JG2ME24hD

source_name: SCp2 24h after treatment of 2ME2


title: green-00030: JG2ME24hC


title: green-00030: JG2ME48hB


title: green-00030: JGCon48hB


title: green-00030: JG2ME24hB


title: ESMSIN004

description: MSI normal sample from Spain

source_name: MSI normal ESP

value: MSI


title: green-00030: JG2ME24hA


title: green-00030: JGCon24hB

source_name: SCp2 control at 24h


title: green-00030: JG2ME6hD

source_name: SCp2 6h after treatment of 2ME2


title: green-00030: JG2ME6hC


title: ESSN006

description: Serrated normal sample from Spain


title: green-00030: JG2ME6hB


title: ESCT034

description: Conventional tumor sample from Spain


title: green-00030: JGCon24hD


title: green-00030: JG2ME6hA


title: green-00030: JGCon6hD

source_name: SCp2 control at 6h


title: green-00030: JGCon24hC


title: green-00030: JGCon6hB


title: green-00030: JGCon6hA


title: green-00030: JG2ME150mgB

source_name: Mammary gland of mice treated by 150 mg 2ME2

value: murine mammary gland


title: green-00030: JG2ME75mgD

source_name: Mammary gland of mice treated by 75 mg 2ME2


title: ESCMT001

description: Conventional tumor sample from Spain


title: green-00030: JG2ME150mgA


title: IVD

description: Control sample

source_name: control 1

value: IVD


title: green-00030: JG2ME75mgC


title: ESSMT003

description: Serrated tumor sample from Spain


title: ESST005_

description: Serrated tumor sample from Spain


title: green-00030: JG2ME75mgB


title: green-00030: JG2ME75mgA


title: green-00030: JG2ME0mgB

source_name: Mammary gland control


title: green-00030: JG2ME0mgA


title: green-00030: JG2ME0mgD


title: green-00160: 18554 wap9

value: FVB Mouse

value: female

value: mammary gland

source_name: Reference RNA

tag: age(weeks)


title: green-00160: 18583 wap11

tag: Sex


title: green-00030: JG2ME0mgC


title: ESST037

description: Serrated tumor sample from Spain

value: Serrated

value: Tumor


title: green-00160: 21333 pmt

source_name: MMTV-polyoma middle T antigen (PyMT)

value: MMTV-polyoma middle T antigen (PyMT)


title: green-00160: 18528 wap3


title: ESCT005

description: Conventional tumor sample from Spain

value: Conventional


title: ESCT022

description: Conventional tumor sample from Spain

value: Spain


title: green-00030: JG2ME150mgD


title: FIST04

description: Serrated tumor sample from Finland

source_name: serrated FIN


title: green-00160: 18800 pmtN5


title: green-00030: JGCon6hC


title: green-00160: 18585 wap10


title: green-00160: 21161 neu10

source_name: MMTV-neu

value: MMTV-neu


title: green-00160: 18555 pmt 96


title: green-00160: 21160 neu9


title: green-00160: 18587 neu12


title: green-00160: 18586 neu11


title: ESST013

description: Serrated tumor sample from Spain

source_name: serrated ESP


title: ESCT007

description: Conventional tumor sample from Spain


title: green-00160: 18581 neu8


title: green-00030: JG2ME48hC

source_name: SCp2 48h after treatment of 2ME2


title: green-00160: 18584 ras9

source_name: MMTV-Ha-ras

value: MMTV-Ha-ras


title: green-00160: 18553 ras4


title: green-00160: 18582 ras5


title: green-00160: 18529 ras6


title: green-00160: 21110 myc55b

source_name: MMTV-c-myc

value: MMTV-c-myc


title: green-00160: 21109 myc2


title: green-00160: 21162 ras7


title: green-00160: 18527 myc1


title: green-00160: 18552 myc3


title: green-00160: 21163 c3-tag 1


title: green-00160: 18799 c3-tag 63


title: green-00160: 18533 c3-tag-37


title: 2200ng_CRNA

city: Ploen

first: Till

last: Czypionka

address: August-Thienemann-Strasse 2

department: Evolutionary Genetics

country: Germany

institute: MPI for Evolutionary Biology

description:
11/3 x recommended amount of cRNA
curve 8

hyb_protocol: The microarray was loaded with labeled cRNA as described in the Agilent protocol for One-Color Microarray-Based Gene Expression Analysis (version 6.5, May 2010).

scan_protocol: Microarrays were scanned with an Agilent DNA Microarray Scanner type C with the standard settings for 8 x 60 k Agilent expression arrays.

data_processing: Feature extraction was carried out using the Agilent Feature Extraction software (version 10.7.3.1) and the “gprocessed signal” was taken in the measure for signal intensity. Based on the changes of raw-signal intensity over different amount of labeled cRNA, we fitted a linear dose response curve for each probe. Information from this probe specific calibration was used to identify non-functional probes and also provides the basis for a new normalization procedure, which relates observed changes in signal intensity to changes in transcript abundance. For a detailed account of this normalization procedure, please refer to the accompanying publication (Czypionka et al. 2015." Ecological transcriptomics – a non-lethal sampling approach for endangered fire salamanders" Methods in Ecology and Evolution).

organism: Salamandra salamandra

source_name: whole body

label_protocol: Labeled cRNA was prepared from total RNA using the Agilent Low Input Quick Amp Labeling kit.

extract_protocol: Total RNA was obtained via Trizol extraction.

tag: sample type

value: calibration pool

value: whole body

tag: crna amount

value: 11/3 x recommended amount of cRNA


title: UTSCC15_pH6.3_5%oxygen

city: Århus C

first: Brita

middle: Singers

last: Sørensen

address: Nørrebrogade 44

department: Dep Experimental Clinical Oncology

country: Denmark

institute: Aarhus Univesity Hospital

description: Cell culture

hyb_protocol: Labeled cRNA was fragmented in fragmentation buffer (5x buffer:200 mM Tris-acetate (pH 8.1)/500nM KOAc/150 mM MgOAc) before hybridization on the array. Fragmented cRNA was hybridized to the nicroarrays in 90ul hybridization solution. GeneTitan Hybridization, Wash and Stain kit for 3`IVT arrays (Affymetrix) was used for preparing hybridization mixes and processing plate array in GeneTitan

scan_protocol: Human Genome U133 Plus 2.0 array plate was processed in GeneTitan according to manufacturer's instructions

data_processing: data was MAS 5.0 global scaled using Affymetrix Expression Console 3.1 Software package

source_name: UTSCC15 pH6.3 5%oxygen

label_protocol: cRNA synthesis was made using 3`IVT Express kit (Affymetrix) following manufacterer's instructions and starting with 150ng of total RNA

extract_protocol: Total RNA from cell pellets was isolated with Rneasy Mini Kit (Qiagen), following the manufacterer's instructon. A fraction was quantitated by spectrophotometric measure.

treatment_protocol: Cell culture, incubated with medie with different pH (6.3 or 7.5) and gassed with different oxygen concentrations for 24 hours prior to harvest

tag: cell line

tag: ph

tag: oxygen level

value: 5% Oxygen


title: UTSCC15_pH6.3_0.1%oxygen

description: Cell culture

source_name: UTSCC15 pH6.3 0.1%oxygen

value: 0.1% Oxygen


title: UTSCC15_pH7.5_0.1%oxygen

description: Cell culture

source_name: UTSCC15 pH7.5 0.1%oxygen


title: UTSCC15_pH7.5_5%oxygen

description: Cell culture

source_name: UTSCC15 pH7.5 5%oxygen


title: UTSCC5_pH7.5_5%oxygen

description: Cell culture

source_name: UTSCC5 pH7.5 5%oxygen


title: UTSCC5_pH6.3_0.1%oxygen

description: Cell culture

source_name: UTSCC5 pH6.3 0.1%oxygen


title: UTSCC5_pH6.3_5%oxygen

description: Cell culture

source_name: UTSCC5 pH6.3 5%oxygen


title: FaDu_pH6.3_0.1%oxygen

description: Cell culture

source_name: FaDu pH6.3 0.1%oxygen

value: FaDuDD


title: UTSCC14_pH6.3_0.1%oxygen

description: Cell culture

source_name: UTSCC14 pH6.3 0.1%oxygen


title: UTSCC14_pH7.5_5%oxygen

description: Cell culture

source_name: UTSCC14 pH7.5 5%oxygen


title: UTSCC14_pH6.3_5%oxygen

description: Cell culture

source_name: UTSCC14 pH6.3 5%oxygen


title: 1800ng_CRNA

description:
3 x recommended amount of cRNA
curve 7

tag: tissue

value: 3 x recommended amount of cRNA


title: FaDu_pH6.3_21%oxygen

description: Cell culture

source_name: FaDu pH6.3 21%oxygen

value: 21% Oxygen


title: FaDu_pH6.3_5%oxygen

description: Cell culture

source_name: FaDu pH6.3 5%oxygen


title: UTSCC5_pH7.5_0.1%oxygen

description: Cell culture

source_name: UTSCC5 pH7.5 0.1%oxygen


title: UTSCC14_pH7.5_0.1%oxygen

description: Cell culture

source_name: UTSCC14 pH7.5 0.1%oxygen


title: green-00030: JG2ME150mgC

source_name: Mammary gland of mice treated by 150 mg 2ME2

value: murine mammary gland


title: 1400ng_cRNA

description:
7/3 x recommended amount of cRNA
curve 6

source_name: whole body

value: 7/3 x recommended amount of cRNA


title: 1000ng_cRNA

description:
5/3 x recommended amount of cRNA
curve 5

value: 5/3 x recommended amount of cRNA


title: green-00160: 18532 c3-tag 28

value: FVB Mouse

value: female

value: mammary gland

source_name: Reference RNA


title: 600ng_cRNA

description:
recommended amount of cRNA
curve 4

value: recommended amount of cRNA


title: FaDu_pH6.3_1%oxygen

description: Cell culture

source_name: FaDu pH6.3 1%oxygen

value: 1% Oxygen


title: 300ng_cRNA

description:
1/2 x recommended amount of cRNA
curve 3

value: 1/2 x recommended amount of cRNA


title: green-00155: NZB_mammary_tumor_mix-A-05-29-02

source_name: Mouse mammary tumor

value: Mouse mammary tumor

tag: strain

value: FVB/Nj

value: Adult

tag: age(days)

value: Mouse mammary gland


title: SiHa_pH6.3_5%oxygen

description: Cell culture

source_name: SiHa pH6.3 5%oxygen

value: SiHa

value: 5% Oxygen


title: green-00155: NZB-Mix-B-4-3-02


title: SiHa_pH6.3_21%oxygen

description: Cell culture

source_name: SiHa pH6.3 21%oxygen


title: SiHa_pH6.3_1%oxygen

description: Cell culture

source_name: SiHa pH6.3 1%oxygen


title: FaDu_pH6.3_0%oxygen

description: Cell culture

source_name: FaDu pH6.3 0%oxygen

value: FaDuDD

value: 0% Oxygen


title: SiHa_pH6.3_0.1%oxygen

description: Cell culture

source_name: SiHa pH6.3 0.1%oxygen

value: 0.1% Oxygen


title: green-00155: MOLF_mammary_tumor_mix-B-05-29-02


title: FaDu_pH7.5_0%oxygen

description: Cell culture

source_name: FaDu pH7.5 0%oxygen


title: green-00030: JGCon24hA

source_name: SCp2 control at 24h


title: 75ng_cRNA

description:
1/8 recommended amount of cRNA
curve 1

value: calibration pool

value: whole body

value: 1/8 recommended amount of cRNA


title: green-00155: MOLF_mammary_tumor_Mix-A-4-25-02

value: female


title: 150ng_cRNA

description:
1/4 x recommended amount of cRNA
curve 2

value: 1/4 x recommended amount of cRNA


title: FaDu_pH7.5_0.1%oxygen

description: Cell culture

source_name: FaDu pH7.5 0.1%oxygen


title: green-00155: LP_mammary_tumor_mix-B-05-29-02


title: green-00155: ILN-Mix-A-4-3-02


title: green-00155: LP_mammary_tumor_Mix-A-4-25-02


title: green-00155: ILn_mammary_tumor_mix-B-05-29-02


title: KOGB_warm_7_T

data_processing: Feature extraction was carried out using the Agilent Feature Extraction software (version 10.7.3.1) and the “gprocessed signal” was taken in the measure for signal intensity. We employed a new normalization procedure, which relates changes in signal intensity to changes in transcript abundance, thereby accounting for observed large differences in probe-binding behavior. This procedure translates measured signal intensities to a percentage of the target transcript’s abundance in a pool previously used for the calibration of the array. Based on this value, new theoretical signal intensity values are calculated based on the same previous calibration. These new theoretical signal intensity values are then normalized for interarray normalization by division by the 75%tile as suggested by Agilent. For a detailed account of the new normalization procedure, please refer to the accompanying publication (Czypionka et al. 2015. Ecological transcriptomics – a non-lethal sampling approach for endangered fire salamanders Methods in Ecology and Evolution)

source_name: warm_tail tip

extract_protocol: Trizol protocol for RNA extraction

value: tail tip

tag: exposed to


title: FaDu_pH7.5_21%oxygen

description: Cell culture

source_name: FaDu pH7.5 21%oxygen

value: 21% Oxygen


title: wholeblood_infected_rep5

city: Montpellier

first: Rodrigues

last: Valérie

address: TA A30/G

department: BIOS

institute: CIRAD

description: Gene expression of animal n°757 at the beginning of the clinical signs in whole blood

hyb_protocol: 1.65 ug of  Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented using the Agilent Gene Expression Hybridization kit, according to the manufacturer's instructions, then  hybridized to Agilent Bovine Gene expression microarray (V2) for 17h.

scan_protocol: Slides were scanned immediately after washing with Agilent Gene Expression wash buffers 1 and 2, according to the manufacturer's instructions. Slides were then scanned on the Agilent C Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 15µm, Dye channel set to Green and Green PMT set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-107_sep09 and Grid: 023647_D_F_20121015) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. We processed paired statistical analyses and compared the differential expression between non-infected and infected status.

organism: Bos taurus

source_name: peripheral blood, at the beginning of clinical signs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Agilent Low Input Quick Amplification Labelling kit according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000 Spectrophotometer.

growth_protocol: whole blood was collected in Tempus tubes

extract_protocol: Total RNA was prepared using the Tempus

treatment_protocol: no treatment was applied on samples. They were stored at -20°C until shipment at the end of the trial. They were transported in refrigerated boxes from Kenya to France, then stored at -°C for several week until RNA extraction.

value: whole blood

tag: infection status

value: infected


title: wholeblood_infected_rep6

description: Gene expression of animal n°767 at the beginning of the clinical signs in whole blood


title: wholeblood_noninfected_rep5

description: Gene expression of animal n°757 before infection in whole blood

source_name: peripheral blood, before contact with infected-animals

value: non-infected


title: KOGB_warm_7_B

source_name: warm_whole body


title: wholeblood_noninfected_rep6

description: Gene expression of animal n°767 before infection in whole blood


title: FaDu_pH7.5_5%oxygen

description: Cell culture

source_name: FaDu pH7.5 5%oxygen


title: SiHa_pH7.5_0%oxygen

description: Cell culture

source_name: SiHa pH7.5 0%oxygen


title: FaDu_pH7.5_1%oxygen

description: Cell culture

source_name: FaDu pH7.5 1%oxygen

value: 1% Oxygen


title: green-00030: JGW30E

source_name: Mammary glands from mice on day 30 after the cessation of lactation

value: murine mammary gland


title: wholeblood_noninfected_rep4

description: Gene expression of animal n°747 before infection in whole blood


title: green-00155: FVBn_mammary_tumor_mix-B-05-29-02

source_name: Mouse mammary tumor

value: Mouse mammary tumor

value: FVB/Nj

value: Adult

value: Mouse mammary gland


title: KOGB_warm_6_T


title: SiHa_pH7.5_0.1%oxygen

description: Cell culture

source_name: SiHa pH7.5 0.1%oxygen

value: SiHa

value: 0.1% Oxygen


title: green-00155: 12Wcombexp_01-07-02


title: green-00030: JGW30D


title: SiHa_pH6.3_0%oxygen

description: Cell culture

source_name: SiHa pH6.3 0%oxygen

value: 0% Oxygen


title: KOGB_warm_6_B

value: whole body


title: KOGB_warm_5_T


title: wholeblood_noninfected_rep3

description: Gene expression of animal n°732 before infection in whole blood


title: SiHa_pH7.5_1%oxygen

description: Cell culture

source_name: SiHa pH7.5 1%oxygen


title: SiHa_pH7.5_5%oxygen

description: Cell culture

source_name: SiHa pH7.5 5%oxygen

value: 5% Oxygen


title: wholeblood_infected_rep4

description: Gene expression of animal n°747 at the beginning of the clinical signs in whole blood


title: wholeblood_infected_rep3

description: Gene expression of animal n°732 at the beginning of the clinical signs in whole blood


title: KOGB_warm_5_B


title: green-00030: JGW30C


title: SiHa_pH7.5_21%oxygen

description: Cell culture

source_name: SiHa pH7.5 21%oxygen


title: green-00030: JGW30B


title: green-00030: JGConWE

source_name: Mammary glands from age matched control mice for W30


title: green-00030: JGW30A


title: KOGB_warm_4_B


title: green-00030: JGConWC


title: wholeblood_infected_rep2

description: Gene expression of animal n°727 at the beginning of the clinical signs in whole blood


title: green-00030: JGConWB


title: KOGB_warm_3_B


title: green-00030: JGConWD


title: KOGB_warm_3_T


title: wholeblood_noninfected_rep1

description: Gene expression of animal n°724 before infection in whole blood


title: KOGB_warm_1_T


title: green-00030: JGConWA


title: HT29 cells treated with RALA-specific siRNA

city: Budapest

first: Balazs

last: Györffy

address: Bókay 53

country: Hungary

institute: Hungarian Academy of Sciences

hyb_protocol: Samples were hybridized according to the manufacturer's protocol using the Hybridization Wash and Stain Kit (Affymetrix). The hybridization was at 45°C and 60 rpm for 16hrs, and the staining and washing were carried out as recommended by Affymetrix (Affymetrix).

scan_protocol: GeneChip Scanner 3000 G7 system (Affymetrix).

data_processing: Raw data was imported into R and was normalized using Bioconductor packages. MAS5.0 normalization. Then removal of probe sets not present on both platforms GPL96 and GPL570. Finally, scaling normalization to have an average expression of 1000 within each chip.

source_name: HT29_BRAF mutated cell line, RALA-specific siRNA

label_protocol: 5.5 μg of the single-strand DNA was enzymatically fragmented with a combination of uracil DNA glucosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) and biotinylated using the WT terminal labeling kit (Affymetrix).

growth_protocol: HCT116, SW480 and HT29 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) (Invitrogen) supplemented with 10% fetal calf serum (FCS) (Sigma-Aldrich), 2 mM Ultraglutamine 1 (Lonza, BioWhittaker), and 100 units/ml penicillin/streptomycin (Biochrom AG) (standard medium). 300,000 cells for HCT116 and SW480 or 150,000 cells for HT29 were plated in 10cm dishes (BD Falcon) in standard medium 24 h prior to transient transfection of siRNA.

extract_protocol: Total RNA extraction was performed using the RNeasy Mini Kit with QIAshredder (Qiagen) according to the manufacturer's instructions. CDNA synthesis was performed using the Ambion® WT Expression Kit (Ambion).

treatment_protocol: Cells were transfected twice with an interval of 24 h using LipofectAMINE RNAiMAX (Invitrogen) for HT29 and HCT116 cell lines and LipofectAMINE 2000 (Invitrogen) for the SW480 cell line according to the manufacturer's specifications and a final siRNA concentration of 1.5 nM according to the manufacturer's specifications in standard medium.

tag: cell type

value: BRAF-mutated colorectal cancer cells

tag: RNAi

value: RALA-specific siRNA


title: KOGB_warm_4_T

source_name: warm_tail tip

value: tail tip


title: wholeblood_infected_rep1

description: Gene expression in whole blood of animal n°724 at the beginning of the clinical signs

value: whole blood


title: KOGB_warm_1_B


title: HT29 cells treated with transfection reagents only

source_name: HT29_BRAF mutated cell line, mock

value: transfection reagents only


title: HT29 cells treated with Scrambled siRNA (nonsense sequence)

source_name: HT29_BRAF mutated cell line, scrambled siRNA

value: scrambled siRNA (nonsense sequence)


title: wholeblood_noninfected_rep2

description: Gene expression of animal n°727 before infection in whole blood

source_name: peripheral blood, before contact with infected-animals

value: non-infected


title: HCT116 cells treated with RALA-specific siRNA

source_name: HCT116_KRAS (codon 13) mutated cell line, RALA-specific siRNA

value: KRAS-mutated colorectal cancer cells


title: Day 18 Ab Treated

city: Singapore

first: Liang

last: Li

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description: Gene expression data from mouse lung tissue infected with PR8, injected with anti-cANGPTL4 monoclonal antibody daily from day 13 post infection onwards and harvested at day 18 post infection

hyb_protocol: 2 ug of cDNA were hybridized for 18 hr at 45°C on GeneChip Mouse Gene 1.0 ST Array inside GeneChip Hybridization Oven 640. GeneChip Fluidics Station 450 was used for the washing and staining of the chips.

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

data_processing: The data were analyzed with Robust Multiarray Average (RMA ) in the Affy bioconductor package (version 1.42) without probe level normalization. The data was later examined for systematic shifts across the samples at the probeset level.

source_name: Mouse lung tissue infected with PR8, injected with anti-cANGPTL4 monoclonal antibody daily from day 13 post infection onwards and harvested at day 18 post infection

label_protocol: This part of work was done according to Applause WT-Amp ST System user guide (NuGEN PART NO. 5500) step by step using Encore Biotin Module.

treatment_protocol:
Mice (C57BL/6J, 8-12 weeks old, female) were infected with a sub-lethal dose of H1N1 PR8 virus (30pfu) through intre-trachea delivery.
Mice were injected with either anti-cANGPTL4 monoclonal antibody or control IgG at a dose of 10mg/kg body weight, daily from day 13 to day 17 post infection. Lungs were harvested and kept in Trizol in -80 degree before RNA extraction. 1 mouse was used for each sample listed above.

tag: gender

value: female

tag: age

value: 8-12 week old

value: lung


title: green-00030: JGL2C

source_name: Mammary glands from mice on day 2 at lactation

value: murine mammary gland


title: HCT116 cells treated with Scrambled siRNA (nonsense sequence)

source_name: HCT116_KRAS (codon 13) mutated cell line, scrambled siRNA


title: Day 14 Ab Treated

description: Gene expression data from mouse lung tissue infected with PR8, injected with anti-cANGPTL4 monoclonal antibody daily from day 13 post infection onwards and harvested at day 14 post infection

source_name: Mouse lung tissue infected with PR8, injected with anti-cANGPTL4 monoclonal antibody daily from day 13 post infection onwards and harvested at day 14 post infection


title: HCT116 cells treated with transfection reagents only

source_name: HCT116_KRAS (codon 13) mutated cell line, mock


title: green-00030: JGL2B


title: KOGB_cold_8_B

source_name: cold_whole body


title: SW480 cells treated with Scrambled siRNA (nonsense sequence)

source_name: SW480_KRAS (codon 12) mutated cell line, scrambled siRNA


title: Day 14 Ctrl IgG

description: Gene expression data from mouse lung tissue infected with PR8, injected with control IgG daily from day 13 post infection onwards and harvested at day 14 post infection

source_name: Mouse lung tissue infected with PR8, injected with control IgG daily from day 13 post infection onwards and harvested at day 14 post infection


title: Day 18 Ctrl IgG

description: Gene expression data from mouse lung tissue infected with PR8, injected with control IgG daily from day 13 post infection onwards and harvested at day 18 post infection

source_name: Mouse lung tissue infected with PR8, injected with control IgG daily from day 13 post infection onwards and harvested at day 18 post infection


title: SW480 cells treated with RALA-specific siRNA

source_name: SW480_KRAS (codon 12) mutated cell line, RALA-specific siRNA


title: KOGB_cold_7_T

source_name: cold_tail tip


title: Day 12 2

description: Gene expression data from mouse lung tissue infected with PR8 and harvested at day 12 post infection

source_name: Mouse lung tissue infected with PR8 and harvested at day 12 post infection


title: green-00030: JGP16C

source_name: Mammary glands from mice on day 16 of pregnancy


title: SW480 cells treated with transfection reagents only

source_name: SW480_KRAS (codon 12) mutated cell line, mock


title: green-00030: JGP16B


title: KOGB_cold_8_T


title: green-00030: JGP16A


title: KOGB_cold_7_B


title: Day 12 1


title: KOGB_cold_6_T


title: SW480 cells treated with LY294002

source_name: SW480_KRAS (codon 12) mutated cell line, LY294002

treatment_protocol: Cells were treated with LY294002 or DMSO.

tag: treatment


title: SW480 cells treated with DMSO

source_name: SW480_KRAS (codon 12) mutated cell line, DMSO

value: DMSO


title: green-00030: JG12wC

source_name: Mammary glands from 12 week virgin mice


title: HT29 cells treated with LY294002

source_name: HT29_BRAF mutated cell line, LY294002


title: green-00030: JGL2A

source_name: Mammary glands from mice on day 2 at lactation


title: green-00030: JG12wB


title: KOGB_cold_6_B


title: Organotypic slices scramble rep_3

city: Milan

first: Nico

last: Mitro

state: MI

address: Via Balzaretti 9

department: Pharmacological and biomolecular sciences

country: Italy

institute: Università degli studi di Milano

description:
Organotypic hippocampal slices lentivirally infected with scramble
Scr_03

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data handling was mainly done using TAC and Partek Genomic Suite software. The Robust MultichipAverage (RMA) method was employed to calculate probe set intensity. RMA is a robustmulti-chip average expression method that estimates the probe-level data from a set of chips:the perfect-match (PM) values are background-corrected, normalized and finally summarizedresulting in a set of expression measures.The identification of differentially expressed genes was addressed using FoldChange (FC) and ANOVA. For each experimental condition the probesets whose fold change are higher or equalthan 1.5 with an ANOVA unadjusted p-value lower than 0,05 are selected as significantlymodulated.

source_name: organotypic slices

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

growth_protocol: Hippocampal organotypic sliceswere prepared from P8 rat pups and grown for 14 days in vitro (DIV). Lentivirus infection was performed at DIV3.

extract_protocol: Organotypic slices from both groups were manually identified as shRNF10 or scramble. Organotypic slices were freshly lyseted. Total RNA was obtained with trizol and nucleospin method

treatment_protocol: Not applicable

value: Sprague-Dawley

value: organotypic hippocampal slice

value: grown for 14 days in vitro (DIV)

tag: infection

value: control at DIV3


title: green-00030: JG12wA


title: Organotypic slices scramble rep_2

description:
Organotypic hippocampal slices lentivirally infected with scramble
Scr_02


title: Organotypic slices scramble rep_1

description:
Organotypic hippocampal slices lentivirally infected with scramble
Scr_01


title: HCT116 cells treated with LY294002

source_name: HCT116_KRAS (codon 13) mutated cell line, LY294002


title: Organotypic slices shRNF10 rep_4

description:
Organotypic hippocampal slices lentivirally infected with shRNF10
Sh_04

value: shRNF10 at DIV3


title: HCT116 cells treated with DMSO

source_name: HCT116_KRAS (codon 13) mutated cell line, DMSO


title: Organotypic slices scramble rep_4

description:
Organotypic hippocampal slices lentivirally infected with scramble
Scr_04


title: KOGB_cold_2_T


title: Organotypic slices shRNF10 rep_1

description:
Organotypic hippocampal slices lentivirally infected with shRNF10
Sh_01


title: Organotypic slices shRNF10 rep_2

description:
Organotypic hippocampal slices lentivirally infected with shRNF10
Sh_02


title: KOGB_cold_5_B

source_name: cold_whole body

value: whole body


title: HT29 cells treated with DMSO

source_name: HT29_BRAF mutated cell line, DMSO

value: BRAF-mutated colorectal cancer cells


title: IPTG concentration of 10 μM

city: Bielefeld

first: Hironori

last: Taniguchi

institute: Bielefeld University

description: EK10 vs EH10 :log2(Cy5/Cy3)

hyb_protocol: DNA microarray hybridization was performed as described previously with modification (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ). Hybridization and washing was performed with HS4800 (Tecan).

scan_protocol: Image was attained with LS200 (Tecan).

data_processing: Normalization and evaluation of the microarray data was done with the software package EMMA 2 (Dondrup, M., Albaum, S. P., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C. K., Küster, H., Linke, B., Mertens, D., et al. (2009). EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10, 50.). Genes which were upregulated in WT(pEKEx3-sigH) under both 10 μM and 15 μM of IPTG concentration were taken into account for further analysis (p-value < 0.05, M value > 1).

organism: Corynebacterium glutamicum ATCC 13032

source_name: pEKEx3-sigH_10 μM of IPTG

label_protocol: cDNA synthesis from total RNA and labeling were performed as described previously (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ).

growth_protocol: C. glutamicum (pEKEx3) and C. glutamicum (pEKEx3-sigH) were cultured in BHI medium for overnight and inoculated into CGXII medium with 222 mM of glucose for adaptation. Cells were cultured overnight and inoculated into 50 mL of CGXII medium with 222 mM of glucose with 10 μM or 15 μM of IPTG at the initial O.D. of 1. Cells were harvested in the early exponential growth phase (O.D. between 6 and 8).

extract_protocol: RNA isolation was performed as described previously with some modification (Wendisch, V. F. (2003). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol. 104, 273–285.). Total RNA was isolated using the RNeasy Mini   Kit(Qiagen). The purified RNA was analyzed by spectrophotometer (NanoDrop) for quantity and gel electrophoresis for quality. The RNA sample was stored at −80 °C until further use.

treatment_protocol: IPTG was added from the beginning of the growth.

tag: genotype/variation

tag: growth phase

value: Early exponential phase

tag: iptg conc.

value: 10 μM of IPTG

source_name: pEKEx3_10 μM of IPTG


title: KOGB_cold_4_T

value: tail tip


title: KOGB_cold_5_T


title: KOGB_cold_2_B


title: Neuroblastoma_13_Tumour_CGH

status: Public on Jun 19 2015

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

institute: University Hospital Essen

description: Tumour

hyb_protocol: Labelled DNA were hybridized to oligonucleotide microarrays (Agilent Technologies) following the manufacture's instructions ("Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, fluorescent-labeled reference and tumor DNA (3 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1(Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Arrays were scanned by using an Agilent G2567AA Scanner follwowing the manufacturer's protocol (Agilent Technologies).

data_processing: The scanned TIFF images were loaded into the Feature Extraction (v9.5 Agilent technologies), Feature Extraction files (LogRatio column) were analyzed by CGH Analytics Software (v. 3.5.14 Agilent Technologies). The circular binary segmentation algorithm was applied. Ref: PMID:17234643.  Background normalization was performed using snapCGH (method "minimum").  The  normalized data  are located on the series record and contain the normalized log2 ratio Cy3/Cy5 values.

source_name: Promega Reference DNA

label_protocol: We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, 2 ug of sample and reference genomic DNAs (for reference were used Human Genomic DNA: male Cat G1471, female Cat G1521, Promega, Madison, WI) were separately digested with AluI/RsaI restriction enzyme mix (Promega). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 ueach), dUTP (60 uM) and Cy3-dUTP (60 uM) or Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by NanoDrop 1000 (ThermoScientific) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: Genomic DNA was isolated using the DNA-Isolation Kit (Gentra) according to the manufacturer's protocol. A pool of normal male or female DNA (Promega) was used as reference.

tag: control type

value: Reference DNA

source_name: Tumour

tag: diagnosis

value: neuroblastoma


title: Neuroblastoma_13_Relapse_CGH

description: Relapse

source_name: Relapse


title: IPTG concentration of 15 μM

description: EK15 vs EH15 :log2(Cy3/Cy5)

source_name: pEKEx3_15 μM of IPTG

value: 15 μM of IPTG

source_name: pEKEx3-sigH_15 μM of IPTG


title: Neuroblastoma_12_Relapse_CGH

description: Relapse


title: Neuroblastoma_12_Tumour_CGH

description: Tumour


title: Organotypic slices shRNF10 rep_3

description:
Organotypic hippocampal slices lentivirally infected with shRNF10
Sh_03


title: Neuroblastoma_8_Relapse_CGH

description: Relapse


title: Neuroblastoma_4_Relapse_CGH

description: Relapse


title: KOGB_cold_4_B


title: Neuroblastoma_4_Tumour_CGH

description: Tumour


title: immune_skin_rep3

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

source_name: flank skin of immune mouse recovered 12 hours post-challenge with Leishmania

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the Illumina TotalPrep RNA Amplification Kit

extract_protocol: Total RNA was isolated using the Qiagen Rneasy Plus Kit

treatment_protocol: Immune mice had been infected with 2x10^6 parasites in the left ear approximately 14 weeks prior to challenge.  Immune mice and aged-matched naive controls were challenged with parasites in a piece of flank skin.  At 12 hours post-challenge, 50mg of skin tissue was harvested from the challenge site of both naive and immune mice, and samples were immediately processed for RNA extraction

tag: Sex

value: Female

value: approximately 50 mg of skin recovered from mouse flank


title: naïve_skin_rep1

source_name: naïve skin from mouse flank

tag: tissue


title: immune_skin_rep2

tag: strain


title: naïve_skin_rep3


title: immune_skin_rep1


title: naïve_skin_rep4


title: naïve_skin_rep2


title: immune_skin_rep4


title: Neuroblastoma_8_Tumour_CGH

description: Tumour


title: Neuroblastoma_17_Tumour_gene_expression

description:
Tumour
cDNA
NB_17_T

hyb_protocol: Hybridization was performed following the manufacturer's protocol. In brief, 1650 ng of Cy3-labeled cRNA was hybridized on 4x44K custom microarrays using Agilent's High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 hours at 65°C in a rotating hyb oven at 10 rpm according the company's recommendations.

scan_protocol: After washing and scanning, resulting TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1.

data_processing: Global gene expression analyses was performed using customized single channel Agilent arrays (4x 44k “NB-custom arrays”, GPL 16876) as described (Kocak et al., Cell Death Dis, 2013). Microarrays   were analysed using R (r-project.org; version 3.1.0) and the following packages: arrayQualityMetrics (version 3.20.0), GEOquery (version 2.30.1), Biobase (version 2.22.0), marray (version 1.42.0) and   limma (version 3.18.13). A gene-wise linear model (limma) was used to identify significantly differentially expressed genes between primary and relapse NB samples.

label_protocol: Labeling was performed according to Agilent's recommentdations. In brief, 1µg total of tumor RNA was linearily amplified and labeled with Cy3 using Agilent's one-color Quick Amp Labeling Kit following the instructions of the protocol.

extract_protocol: Cells were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.


title: Neuroblastoma_17_Relapse_gene_expression

description:
Relapse
cDNA
NB_17_R


title: Neuroblastoma_13_Relapse_gene_expression

description:
Relapse
cDNA
NB_13_R


title: Neuroblastoma_10_Tumour_gene_expression

description:
Tumour
cDNA
NB_10_T


title: Neuroblastoma_11_Tumour_gene_expression

description:
Tumour
cDNA
NB_11_T


title: Neuroblastoma_11_Relapse_gene_expression

description:
Relapse
cDNA
NB_11_R


title: Neuroblastoma_2_Tumour_gene_expression

description:
Tumour
cDNA
NB_2_T


title: Neuroblastoma_8_Tumour_gene_expression

description:
Tumour
cDNA
NB_8_T


title: Neuroblastoma_5_Tumour_gene_expression

description:
Tumour
cDNA
NB_5_T


title: Neuroblastoma_6_Tumour_gene_expression

description:
Tumour
cDNA
NB_6_T


title: Neuroblastoma_7_Tumour_gene_expression

description:
Tumour
cDNA
NB_7_T


title: Neuroblastoma_7_Relapse_gene_expression

description:
Relapse
cDNA
NB_7_R


title: Neuroblastoma_13_Tumour_gene_expression

description:
Tumour
cDNA
NB_13_T


title: Neuroblastoma_4_Relapse_gene_expression

description:
Relapse
cDNA
NB_4_R


title: Neuroblastoma_9_Relapse_gene_expression

description:
Relapse
cDNA
NB_9_R


title: T_93

city: Paris

last: Popova

address: 26, rue d'Ulm

institute: Institute Curie

description: Gene expression data for invasive breast carcinoma

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Data were analyzed using standard AffyCDF or Brainarray HGU133Plus2_Hs_ENTREZG version 13 custom chipset definition file. Data were normalized using  Brainarray.
Gene summarized expression value obtained using Brainarray CDF and software

source_name: Breast tumor sample

label_protocol: Following RNA quality and quantity control, 2 Âµg of total RNA were amplified and labeled according to the Affymetrix one cycle synthesis target preparation protocol to hybridize Affymetrix U133 plus 2.0 chips, as described by the company.

growth_protocol: Tumor samples were obtained from patients treated at the hospital of Institut Curie (Biological Resource Center, Paris, France). Healthy samples were obtained from mammary plastic surgery. Cell lines were grown from the American Type Culture Collection (ATCC),

extract_protocol: Total RNA was extracted and purified from frozen tumor samples using the RNeasy Mini Kit (Qiagen) followed by the RNA clean up kit (Macherey Nagel), according to manufacturer instructions.

treatment_protocol: No

value: female

value: invasive breast carcinoma sample

tag: molecular subtype

value: luminal


title: Neuroblastoma_2_Relapse_gene_expression

description:
Relapse
cDNA
NB_2_R


title: Neuroblastoma_4_Tumour_gene_expression

description:
Tumour
cDNA
NB_4_T


title: T_96


title: T_95


title: Neuroblastoma_9_Tumour_gene_expression

description:
Tumour
cDNA
NB_9_T


title: T_81


title: T_84 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589769


title: T_86 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589771


title: T_92


title: T_82 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589766


title: T_88 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589765


title: T_787


title: T_784


title: T_789


title: T_785


title: T_782


title: T_783


title: T_78 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589763


title: T_777


title: T_775


title: T_778


title: T_776


title: T_85 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589770


title: T_77 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589762


title: T_769


title: T_764


title: T_770


title: T_772


title: T_768


title: T_773


title: T_762


title: T_779


title: T_760


title: T_761


title: T_766


title: T_765


title: T_753


title: T_749


title: T_759


title: T_757


title: T_752


title: T_76 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589761


title: T_755


title: T_748


title: T_758


title: T_75 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589760


title: T_747


title: T_746


title: T_744


title: T_742


title: T_739


title: T_738


title: T_741


title: T_740


title: T_735


title: T_733


title: T_734


title: T_754


title: T_737


title: T_750


title: T_732


title: T_730


title: T_715


title: T_723


title: T_713


title: T_729


title: T_727


title: T_724


title: T_717


title: T_720


title: T_73 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589758


title: T_714


title: T_728


title: T_712


title: T_721


title: T_719


title: T_716


title: T_704


title: T_710


title: T_722


title: T_711


title: T_705


title: T_701


title: T_702


title: T_708


title: T_703


title: T_706


title: T_707


title: T_700


title: T_699


title: T_688


title: T_692


title: T_689


title: T_690


title: T_71 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589756


title: T_687


title: T_685


title: T_682


title: T_674


title: T_676


title: T_681


title: T_675


title: T_693


title: T_697


title: T_673


title: T_69 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589755


title: T_672