title: A5 matched normal tissues_male [B5]

city: wuhan

first: xuegang

last: Wang

address: 1277 Jiefang Avenue

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan

description:
Gene expression array of male A5 matched normal tissues
B5_Log2NormSignal

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°C，20 rpm 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 # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 9.5.3 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 10.0 (Agilent technologies, Santa Clara, CA, US).

source_name: matched normal kidney tissue (NCTs)

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)

treatment_protocol: Fresh tissue samples were snap-frozen in liquid nitrogen after surgery immediately, and then stored in a deep freezer at −80°C for subsequent experiments

value: kidney

tag: tissue type

value: A5 matched normal tissues


title: Liver_CS_rep2

status: Public on Jul 25 2015

type: RNA

city: Nanjing

first: Yong

last: Su

address: Weigang 1#

country: China

institute: Nanjing Agricultural University

description: Gene expression in the liver of pigs fed CS diet

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using a Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, USA) in a hybridization oven.

scan_protocol: After 17 h of hybridization, the slides were washed with a Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. The slides were then scanned on an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: data was extracted using Feature Extraction Software 10.7 (Agilent Technologies, Santa Clara, CA, USA). The raw data was normalized using a quantile algorithm, Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, USA).

molecule: total RNA

organism: Sus scrofa

source_name: Liver, CS group, replicate 2

label_protocol: The total RNA was amplified and labeled using a Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s instructions.

growth_protocol: Pigs in the control group were offered a corn/soybean-based diet, while 230 g/kg purified corn starch (CS) was replaced with purified RPS in the RPS diet group. Diets were formulated according to the nutrient requirements of the National Research Council (1998). When animals reached the age of 120 days, diets were adapted to the nutrient requirements of the animals (finishing diet) and the amount of purified starch increased to 280 g of CS or RPS per kilogram of feed. Pigs had unlimited access to feed and water throughout the experimental period, which consisted of two 50-day trials in which the pigs consumed the growing diet (days 0-50) and finishing diet (days 51-100), respectively.

extract_protocol: The total RNA was extracted using the TRIzol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions and then checked for RNA integrity and purity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). The total qualified RNA was further purified using an RNeasy mini kit (QIAGEN, GmBH, Germany) and an RNase-Free DNase Set (QIAGEN, GmBH, Germany). Only those samples that had an OD260/OD280 ratio of approximately 2.0 and showed no degradation (RNA integrity number ≥ 7.0) were used to generate labeled targets.

treatment_protocol: The liver and colonic mucosa tissues were collected and preserved in liquid nitrogen.

tag: breed

value: Duroc × Landrace × Large White

tag: tissue

value: liver

tag: gender

value: male

tag: age


title: TR.Sp#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

organism: Mus musculus

source_name: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: genetic background

tag: Sex

value: Male

value: 9 Weeks Old

tag: exclusion markers

value: CD11c, CD11b, CD19, B220, DAPI

tag: phenotype markers

value: TCR+ CD4+ GFP+

tag: separation method

value: MoFlo Sorter

tag: source prep description

value: Red blood cells were lysed and spleens were brought to single cell suspension


title: WT roots 1

city: Geneva

first: Teresa

last: Fitzpatrick

address: 30 Quai E. Ansermet

department: Botany and Plant Biology

country: Switzerland

institute: University of Geneva

description:
Gene expression data from WT roots
15

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

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

data_processing: The data were analyzed using MAS 5.0 (Microarray Suite version 5.0) with in its analysis software (GCOS = GeneChip Operating System). The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Arabidopsis thaliana

source_name: 10 days old seedlings

label_protocol: Biotinylated cRNA samples were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown on half strength Murashige&Skoog medium, containing 1% sucrose, without vitamin B6, at long day conditions (16 h light/8 h darkness; 120 uM light; 22°C/18°C day/night temparture) for 10 days after germination.

extract_protocol: Total RNA extraction was performed using a NucleoSpin RNA Plant extraction kit from Macherey Nagel according to the manufacturer's instructions.

treatment_protocol: Leaves and roots were harvested separately, frozen in liquid nitrogen and stored in a freezer (-80 °C) till further processing.

value: roots

tag: genotype/variation

value: pdx1.3 ko

tag: ecotype


title: TR.Sp#2


title: WT roots 2

description:
Gene expression data from WT roots
16


title: WT roots 3

description:
Gene expression data from WT roots
17


title: M0_vs_WT0_rep2_dye_swap

city: Lille

first: Mathias

last: Chamaillard

address: 1, rue Prof A. Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Inserm

description:
Nlrp12-deficient C57BL6J mouse at day 0 (test) versus Wild-type mouse at day 0 both infected by Citrobacter rodentium replicate 2 by dye swap color (reference)
Biological replicate 2 of 3
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.

hyb_protocol: 850 ng of each linearly amplified cRNA per cyanine were cohybridized on microarrays ( Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F) using  Agilent Gene Expression Hybridization Kit , and enclosed in Agilent SureHyb-enabled hybridization chambers during 17 hours at 65°C rotated at 10 rpm . After hybridization, slides were washed sequential

scan_protocol: Scanned on an Innoscan 700 scanner ( Innopsys ) Images were quantified using Mapix Software (version 3.2.1).

data_processing: A specific script on R was used ( limma library ) for LOWESS normalization within slide and between slides.

source_name: caecum

label_protocol: 500 ng of total RNA were labeled using Quick-amp labeling kit 2 colors, following manufacturer's informations

growth_protocol: RNA was isolated from the caecum of Nlrp12-deficient and wild type mice at day 0 and 7 post C. rodentium infection

extract_protocol: Total RNA extracted using Rneasy Mini kit- Qiagen following manufacturer's instructions

treatment_protocol: Nlrp12-deficient and wild type C57BL6/J mice were infected or not with 1x10^9 colony-forming units of C. rodentium

value: caecum

tag: strain

tag: genotype

value: infected Nlrp12-/-

tag: treatment

value: day 0

value: infected wild-type


title: Liver_CS_rep1

source_name: Liver, CS group, replicate 1


title: WT leaves 3

description:
Gene expression data from WT leaves
13

value: leaves


title: renal cell carcinomas_male [A4]

description:
Gene expression array of male renal cell carcinomas
A4_Log2NormSignal

organism: Homo sapiens

source_name: clear cell renal cell carcinomas (ccRCCs)

value: kidney

value: renal cell carcinomas


title: A3 matched normal tissues_female [B3]

description:
Gene expression array of female A3 matched normal tissues
B3_Log2NormSignal

value: female

value: A3 matched normal tissues


title: A4 matched normal tissues_male [B4]

description:
Gene expression array of male A4 matched normal tissues
B4_Log2NormSignal

value: male

value: A4 matched normal tissues


title: A2 matched normal tissues_female [B2]

description:
Gene expression array of female A2 matched normal tissues
B2_Log2NormSignal

value: A2 matched normal tissues


title: renal cell carcinomas_male [A5]

description:
Gene expression array of male renal cell carcinomas
A5_Log2NormSignal


title: Rorc(pos).colonic.Treg#3

source_name: Colon (Lamina Propria)

value: Male

value: 9 Weeks Old

value: CD19, DAPI

value: TCRb+ CD4+ Thy1.1+ GFP+

value: Epithelial layer was removed by EDTA and DTT treatment. Lamina propria was isolated by Collagenase II and Dispase digestion


title: pdx1.3 ko roots 2

description:
Gene expression data from pdx1.3 ko roots
7

value: roots

value: wildtype


title: WT leaves 2

description:
Gene expression data from WT leaves
10

value: pdx1.3 ko


title: Male placenta Biol. Rep. 2

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

hyb_protocol: cRNA was hybridized using Gene Expression Hybridization Kit (Agilent). Hybridized microarrays were washed using standard Washing Buffer kit (Agilent). All procedures were performed according to manufacturer's protocol

scan_protocol: Data were extracted using G2565CA Microarray Scanner (Agilent, USA) and Agilent Feature Extraction Software (Agilent, USA) on default settings (GE2_1010_Sep10).

data_processing: Background correction method normexp was used and followed by loess method for within array normalization. Between array normalization was performed with the Aquantile method. Mean values of channels intensities were taken as an input and a median of background signal for background correction calculations.

label_protocol: RNA was labeled using Two-Color Low Input Quick Amp Labeling Kits (Agilent) according to manufacturer's protocol

growth_protocol: To obtain pregnancies, virgin females aged 3-months-old were mated with either 3-month-old (young paternal age group; 3 pairs) or 15-months-old (advanced paternal age group; 3 pairs) virgin sires. After that pregnancies were detected by the presence of a vaginal plug, males were removed and each dam was singly housed and allowed to deliver spontaneously. If no plug was detected after overnight male–female encountering, the female was removed and replaced by another, to avoid any possible effects of longer contact with the male. The morning, when the plug was detected was designed as Embryonic day 0.5 (E0.5).

extract_protocol: RNA was extracted using column-based Nucleospin miRNA (Machary-Nagel) according to manufacturer protocol

treatment_protocol: Female mice were rapidly sacrificed by cervical dislocation

tag: group

value: APA

value: Swiss Webster

value: Control


title: A1 matched normal tissues_male [B1]

description:
Gene expression array of male A1 matched normal tissues
B1_Log2NormSignal

value: kidney

tag: tissue type

value: A1 matched normal tissues


title: renal cell carcinomas_female [A2]

description:
Gene expression array of female renal cell carcinomas
A2_Log2NormSignal

value: female

value: renal cell carcinomas


title: renal cell carcinomas_female [A3]

description:
Gene expression array of female renal cell carcinomas
A3_Log2NormSignal


title: WT leaves 1

description:
Gene expression data from WT leaves
9

value: leaves


title: Rorc(pos).colonic.Treg#1

value: MoFlo Sorter


title: Male placenta Biol. Rep. 3

value: Male


title: pdx1.3 ko roots 1

description:
Gene expression data from pdx1.3 ko roots
6


title: TR.SPF.CoLP#2

value: 9 Weeks Old

value: CD11c, CD11b, CD19, B220, DAPI

value: TCR+ CD4+ GFP+


title: pdx1.3 ko leaves 2

description:
Gene expression data from pdx1.3 ko leaves
3


title: renal cell carcinomas_male [A1]

description:
Gene expression array of male renal cell carcinomas
A1_Log2NormSignal

value: male


title: TR.SPF.CoLP#1

value: Epithelial layer was removed by EDTA and DTT treatment. Lamina propria was isolated by Collagenase II and Dispase digestion


title: Rorc(pos).colonic.Treg#2

value: CD19, DAPI

value: TCRb+ CD4+ Thy1.1+ GFP+


title: pdx1.3 ko leaves 3

description:
Gene expression data from pdx1.3 ko leaves
4

value: wildtype


title: Male placenta Biol. Rep. 1

value: APA

value: Swiss Webster


title: pdx1.3 ko roots 3

description:
Gene expression data from pdx1.3 ko roots
8

value: roots


title: MD9

status: Public on Jul 24 2015

city: Mississippi State

first: Wen-Hsing

last: Cheng

state: Mississippi

address: 945 Stone Blvd.

department: Food Science, Nutrition and Health promotion

institute: Mississippi state university

description:
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TaqMan OpenArray Rodent MicroRNA Panel (A and B). Quantitative real-time PCR was performed for rodent miRNAs.
For each of two cards per sample (A and B), nine ul of pre-amplified, diluted sample was mixed with TaqMan reaction mix (Applied Biosystems) and loaded into TaqMan OpenArray Rodent MicroRNA Panel (A and B). Cards were sealed, and qRT-PCR was performed with a real-time thermocycler (ABI-7900, Applied Biosystems) per manufacturer's recommendations.

data_processing:
SDS software (Applied Biosystems) was used to collect data.
Threshold intensities were set, visually and individually confirmed, and standardized with RQ Manager (Applied Biosystems). Data were processed using DataAssist (Applied Biosystems) and HTqPCR (R/Bioconductor). In HTqPCR, quantile normalization was employed.

label: FAM

source_name: 18 month_Selenium supplementation

label_protocol: Total RNA per sample was reverse-transcribed using Megaplex primers, sets A and B (Applied Biosystems). cDNA was pre-amplified for fourteen cycles with Mexaplex Pre-Amp primers, sets A and B (Applied Biosystems), then diluted to 30 ul. Manufacturer's protocol was followed throughout.

extract_protocol: Total RNA was extracted from 100 ul plasma with a miRvana isolation kit (Ambion) per the manufacturer's protocol. 5 nM synthetic cel-miR-39  was spiked into each sample to correct for technical differences. RNA was eluted in 100 ul nuclease-free water.

tag: strain background

value: 18 month

value: Terc-/-

tag: diet

value: Selenium supplementation

value: plasma


title: Female placenta Biol. Rep. 3

value: Female

value: Control


title: MD7

tag: tissue


title: MD6

source_name: 12 month_Selenium deprivation

tag: age

value: 12 month

value: Selenium deprivation


title: MD5


title: MD4


title: MD3

source_name: 18 month_Selenium deprivation


title: MD2


title: pdx1.3 ko leaves 1

description:
Gene expression data from pdx1.3 ko leaves
2

value: leaves


title: Rorc(neg).colonic.Treg#4

tag: genetic background

value: Male

value: 9 Weeks Old

value: TCRb+ CD4+ Thy1.1+ GFP-

value: MoFlo Sorter


title: MD10

source_name: 12 month_Selenium supplementation

value: male


title: MD12


title: MD11


title: MD1


title: TR.SPF.CoLP#3

tag: Sex

value: CD11c, CD11b, CD19, B220, DAPI

value: TCR+ CD4+ GFP+

value: Epithelial layer was removed by EDTA and DTT treatment. Lamina propria was isolated by Collagenase II and Dispase digestion


title: Female placenta Biol. Rep. 2

value: APA

value: Swiss Webster


title: Female placenta Biol. Rep. 1


title: Rorc(neg).colonic.Treg#3

tag: exclusion markers

value: CD19, DAPI


title: Rorc(neg).colonic.Treg#1

tag: phenotype markers


title: M7_vs_M0_rep2

description:
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus non-infected Nlrp12-deficient mice replicate 2 (reference)
Biological replicate 2 of 2

value: caecum

value: non-infected Nlrp12-/-

value: day 0

value: infected Nlrp12-/-

value: day 7


title: Leiomyosarcoma_FFPE_21

type: genomic

city: Sheffield

first: Abdulazeez

middle: Temitope

last: Salawu

address: Beech Hill Road

department: Oncology

country: United Kingdom

institute: University of Sheffield Medical School

description: LMS 21

hyb_protocol: Hydridization was done according to Agilent ULS Labeling protocol for FFPE tumour DNA and Agilent Enzymatic Labeling Protocol for fresh tumour DNA

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 10.7.3) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: Leiomyosarcoma tissue, FFPE, 1yr

label_protocol: 500 - 1000ng DNA was labeled using Agilent ULS Labeling protocol for FFPE tissue DNA and Agilent Enzymatic labeling protocol for Fresh tissue DNA

extract_protocol: Genomic DNA extracted using Qiagen DNeasy following manufacturers' instructions for fresh tissue of Agilent protocol for FFPE tissue

tag: gender

value: Female

value: Leiomyosarcoma tissue

tag: tissue status

value: FFPE

tag: archival leiomyosarcoma age

source_name: Reference DNA

tag: sample type

value: Reference DNA


title: TR.Sp#1

value: Male

value: 9 Weeks Old

tag: separation method

value: MoFlo Sorter

tag: source prep description

value: Red blood cells were lysed and spleens were brought to single cell suspension


title: Huh-7_shGFP_Hypoxia (1% O2, 24 h)

city: Daejeon

first: Minho

last: Kang

address: 125 Gwahak-ro, Yuseong-gu

department: Medical Genomics Research Center

country: South Korea

institute: KRIBB

description: Analysis of human Huh-7 cell lines depleted of GFP via RNA interference (RNAi) under hypoxia for 24h

hyb_protocol: Aliquots of amplified and labeled cRNA (700 ng) were hybridized at 58 °C for 16 h to the Illumina HumanHT-12 v3/v4 Expression BeadChips.

scan_protocol: The BeadChips were scanned using an Illumina BeadArray Reader and the Bead Scan Software (Illumina).

data_processing: Standard HumanHT-12 v3/v4 Expression BeadChip (Illumina) procedures

source_name: Huh-7 cells

label_protocol: Total RNA (200 ng) was amplified using the Illumina TotalPrep™ RNA Amplification Kit.

growth_protocol: Huh-7 stable cells were maintained in Dulbecco’s modified Eagle’s medium (Gibco BRL) with 10% fetal bovine serum (Gibco BRL) and 100 U/ml penicillin (Gibco BRL). Hypoxic (1% oxygen) culture conditions were achieved with an O2/CO2 incubator (Sanyo) containing a gas mixture composed of 94% N2, 5% CO2 and 1% O2.

extract_protocol: Total RNA was isolated using a commercially available RNA isolation kit following the procedure recommended by manufacturer (RNeasy midi-prep, Qiagen).

treatment_protocol: Lentiviral particles containing the NDRG3 or HIF-1A-specific shRNA.

tag: cell line

tag: cell type

value: Human hepatoma


title: Leiomyosarcoma_Fresh_10

description: LMS 10 FRESH

source_name: Leiomyosarcoma tissue, Fresh

value: fresh


title: Leiomyosarcoma_FFPE_13

description: LMS 13

source_name: Leiomyosarcoma tissue, FFPE, 8yr


title: Leiomyosarcoma_FFPE_18

description: LMS 18


title: Leiomyosarcoma_Fresh_11

description: LMS 11 FRESH


title: Huh-7_shGFP_Normoxia (24h)

description: Analysis of human Huh-7 cell lines depleted of GFP via RNA interference (RNAi) under normoxia for 24h


title: Leiomyosarcoma_FFPE_22

description: LMS 22

source_name: Leiomyosarcoma tissue, FFPE, 12yr


title: Leiomyosarcoma_FFPE_12

description: LMS 12


title: Huh-7_shNDRG3_Hypoxia (1% O2, 24 h)

description: Analysis of human Huh-7 cell lines depleted of NDRG3 via RNA interference (RNAi) under hypoxia for 24h


title: Leiomyosarcoma_Fresh_9

description: LMS 9 FRESH


title: Leiomyosarcoma_FFPE_20

description: LMS 20

source_name: Leiomyosarcoma tissue, FFPE, 4yr


title: Leiomyosarcoma_FFPE_10

description: LMS 10 FFPE


title: Leiomyosarcoma_FFPE_11

description: LMS 11 FFPE


title: Leiomyosarcoma_FFPE_15

description: LMS 15

source_name: Leiomyosarcoma tissue, FFPE, 15yr


title: F1 21% D90

city: Southampton

first: Samuel

middle: Peter

last: Hoile

state: Hampshire

address: IDS Building, SGH

department: Human Development and Health

institute: University of Southampton

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quintile normalisation by the Genome Centre, Barts and The London

source_name: Mouse liver

label_protocol: Library preparation was carried out by the Genome Centre, Barts and The London

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: amount of dietary fat (corn oil) (w/w)

tag: strain

value: 90 days

value: liver


title: Leiomyosarcoma_FFPE_17

description: LMS 17

source_name: Leiomyosarcoma tissue, FFPE, 14yr


title: F1 21% D456

value: 456 days


title: F3 5% D456


title: Leiomyosarcoma_FFPE_19

description: LMS 19

source_name: Leiomyosarcoma tissue, FFPE, 9yr


title: Leiomyosarcoma_FFPE_16

description: LMS 16


title: F3 21% D456


title: Leiomyosarcoma_FFPE_8

description: LMS 8

source_name: Leiomyosarcoma tissue, FFPE, 13yr


title: Leiomyosarcoma_FFPE_7

description: LMS 7


title: Leiomyosarcoma_FFPE_14

description: LMS 14

source_name: Leiomyosarcoma tissue, FFPE, 17yr


title: F3 21% D90


title: Leiomyosarcoma_FFPE_9

description: LMS 9 FFPE


title: F1 5% D456


title: Leiomyosarcoma_FFPE_6

description: LMS 6


title: TR.SPF.CoLP#5

source_name: Colon (Lamina Propria)

value: CD11c, CD11b, CD19, DAPI, E-Cad, Ep-Cam

value: TCR+ CD4+ GFP+

value: Epithelial layer was removed by EDTA and DTT treatment. Lamina propria was isolated by Collagenase II and Dispase digestion


title: Leiomyosarcoma_FFPE_5

description: LMS 5


title: MKN45_siSET7/9_VS_NC siRNA

city: Tokyo

first: Yoshimitsu

last: Akiyama

address: 1-5-45 Yushima, Bunkyo-ku

department: Molecular Oncology

country: Japan

institute: Tokyo Medical and Dental University

description: 48 hours after transfection

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: Agilent Feature Extraction Software Software version 10.7.3.1. Data are filtered by present (P), absent (A) and marginal (M) flags. The log2 Ratio of Cy5/Cy3 of probe showing “P” flag is calculated.

source_name: Gastric cancer cell line

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: MKN74 and MKN45 cells were grown in RPMI1640 medium containing 10% FBS.

extract_protocol: Total RNAwas extracted by Trizol reagent and then treated with DNA-free.

treatment_protocol: SET7/9 siRNA (SIGMA) or negative control siRNA was transfected at 50nM (final conc.) into gastric cancer cells by using electroporation.

tag: transfection

value: negative control siRNA (SIGMA)

value: SET7/9 siRNA (SIGMA)


title: Leiomyosarcoma_FFPE_4

description: LMS 4

value: Female

tag: tissue

value: Leiomyosarcoma tissue


title: Leiomyosarcoma_FFPE_3

description: LMS 3

value: FFPE

value: Reference DNA


title: F3 5% D90

tag: age


title: Leiomyosarcoma_FFPE_2

description: LMS 2


title: Leiomyosarcoma_FFPE_1

description: LMS 1


title: Huh-7_shNDRG3_Hypoxia (1% O2, 6 h)

description: Analysis of human Huh-7 cell lines depleted of NDRG3 via RNA interference (RNAi) under hypoxia for 6h


title: A. tumefaciens_Manganese_Rep3

city: Bloomington

first: Jason

middle: Eugene

last: Heindl

state: IN

address: 1001 E. 3rd St., Jordan Hall 142

department: Biology

institute: Indiana University

description: Biological replicate 3 of 4

hyb_protocol: Hybridization reactions were performed using Agilent in situ Hybridization Kit Plus, boiled 5 min 95 C, applied to Agilent custom arrays for A. tumefaciens C58, and hybridized overnight at 65 C.  Hybridized arrays were washed with Agilent Wash Solutions 1 and 2, rinsed with acetonitrile, and incubated in Agilent Stabilization and Drying Solution immediately prior to scanning the arrays

scan_protocol: Scanned on an GenePix 4200A 01 scanner. Images were quantified using GenePix Pro (version 6.0.1.25.)

data_processing: Limma Software (version 3.6.9) from Bioconductor (version 2.7) was used for background subtraction, Loess within arrays normalization and Quantile between arrays normalization.

label: Alexa Fluor 555

organism: Agrobacterium tumefaciens

source_name: Whole cell culture, grown without manganese

label_protocol: Labeled cDNA with Invitrogen SuperScript Indirect Labeling Kit, cDNA was purified on Qiagen QIAQuick columns.  cDNA was labeled with AlexaFluor 555 and 647 dyes using Invitrogen SuperScript cDNA Labeling Kit

growth_protocol: Grown w/shaking in ATGN minimal medium without added manganese, then sub-cultured into fresh ATGN minimal medium either with (grown with manganese) or without (grown without manganese) manganese for a second overnight growth, 28 °C, mid-log phase cultures.

extract_protocol: 11 mL of cultures at OD600~0.6. Cells lysed with lysozyme and RNA extracted using Qiagen RNease Kit.

tag: genotype

value: wildtype

label: Alexa Fluor 647

source_name: Whole cell culture, grown with manganese


title: Huh-7_shNDRG3_Hypoxia (1% O2, 12 h)

description: Analysis of human Huh-7 cell lines depleted of NDRG3 via RNA interference (RNAi) under hypoxia for 12h


title: A. tumefaciens_PdhS2_Rep2

description: Biological replicate 2 of 4

source_name: Whole cell culture_C58 delta pdhS2

growth_protocol: Grown w/shaking in ATGN minimal medium, 28 °C, mid-log phase cultures.

value: delta pdhS2

source_name: Whole cell culture


title: A. tumefaciens_Manganese_Rep1

description: Biological replicate 1 of 4


title: A. tumefaciens_PdhS2_Rep3

description: Biological replicate 3 of 4


title: A. tumefaciens_Manganese_Rep2

description: Biological replicate 2 of 4


title: Huh-7_shHIF-1A_Hypoxia (1% O2, 12 h)

description: Analysis of human Huh-7 cell lines depleted of HIF-1A via RNA interference (RNAi) under hypoxia for 12h

source_name: Huh-7 cells


title: MKN74_siSET7/9_VS_NC siRNA

description: 48 hours after transfection


title: A. tumefaciens_PdhS2_Rep1

description: Biological replicate 1 of 4

source_name: Whole cell culture_C58 WT


title: Huh-7_shGFP_Normoxia (6h, 12h)

description: Analysis of human Huh-7 cell lines depleted of GFP via RNA interference (RNAi) under normoxia


title: Huh-7_shGFP_Hypoxia (1% O2, 6 h)

description: Analysis of human Huh-7 cell lines depleted of GFP via RNA interference (RNAi) under hypoxia for 6h


title: HeLa_NDRG3

description: Analysis of human HeLa cell lines overexpressing NDRG3

source_name: HeLa cells

growth_protocol: HeLa stable cells were maintained in Dulbecco’s modified Eagle’s medium (Gibco BRL) with 10% fetal bovine serum (Gibco BRL) and 100 U/ml penicillin (Gibco BRL). Hypoxic (1% oxygen) culture conditions were achieved with an O2/CO2 incubator (Sanyo) containing a gas mixture composed of 94% N2, 5% CO2 and 1% O2.

treatment_protocol: Retroviral particles encoding NDRG3.

value: Human cervical cancer cells


title: HeLa_Hypoxia (1% O2, 24 h)

description: Analysis of human HeLa cell lines under hypoxia for 24h


title: Huh-7_shGFP_Hypoxia (1% O2, 12 h)

description: Analysis of human Huh-7 cell lines depleted of GFP via RNA interference (RNAi) under hypoxia for 12h

value: Human hepatoma


title: HeLa_Normoxia

description: Analysis of human HeLa cell lines under normoxia


title: Huh-7_shNDRG3_Hypoxia_1 (1% O2, 24 h)

hyb_protocol: Aliquots of amplified and labeled cRNA (700 ng) were hybridized at 58 °C for 16 h to the Illumina HumanHT-12 v4 Expression BeadChips.

data_processing: Standard HumanHT-12 v4 Expression BeadChip (Illumina) procedures

tag: treatment

value: depleted of NDRG3 via RNA interference (RNAi) under hypoxia for 24h


title: HeLa_mock

description: Analysis of human HeLa cell lines overexpressing control vector


title: Huh-7_shNDRG3_Hypoxia_2 (1% O2, 24 h)


title: DS 2 Experiment 2

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

description: DS 2 Experiment 2

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

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

data_processing: BeadStudio software v3.2, Minfi

label: Cy5 and Cy3

source_name: HMEC

label_protocol: Standard Illumina Protocol

growth_protocol: Normal finite life span HMECs were obtained from reduction mammoplasty tissue of a 21-year-old individual, specimen 184, and were cultured as previously described (Garbe et al., 2009). Independent cultures were serially passaged from passage 6 (early proliferating, EP cells) through to deep senescence (DS cells). DS cultures underwent no further expansion upon at least two serial passages. The DS cells in our experiments displayed the key characteristics of cellular senescence. All experiments were done on three individual cultures of EP and DS cells, passaged from single progenitor plates.

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

treatment_protocol: HMECs were transfected with 60nM siGLO siRNA (Dharmacon) or p16 siRNA (Qiagen) in 384-well or 6-well plates using Dharmafect3 (Dharmacon).

tag: Sex

value: F

tag: cell stage

value: deep senescence


title: DS 3 Experiment 2

description: DS 3 Experiment 2


title: DS 1 Experiment 2

description: DS 1 Experiment 2


title: WT Tfh, biological rep1

city: Chongqing

first: Xinyuan

last: Zhou

address: 30 Gaotanyan Street

department: Institute of Immunology, PLA

institute: Third Military Medical University

description: SAMPLE 3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Follicular T helper cells from C57BL/6J mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: All mouse experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committees of the Third Military Medical University.

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

treatment_protocol: To isolate Tfh cells, total splenocytes from WT and Tcf7-/- mice at day 8 post LCMV infection were subjected to lineage depletion. The Lin− cells were then surface-stained with CD4, CD44, SLAM, and CXCR5, followed by direct sorting into TRIzol LS reagent by a FACSAriaII cell sorter at the core facility center of Third Military Medical University.

tag: genotype/variation

value: wild type

value: spleen

tag: cell

value: Follicular T helper cells


title: TCF-1-null Tfh, biological rep1

description: SAMPLE 1

source_name: Follicular T helper cells from CD4-Cre-Tcf7fl/fl mouse


title: Huh-7_shHIF-1A_Hypoxia_2 (1% O2, 12 h)

value: depleted of HIF-1A via RNA interference (RNAi) under hypoxia for 12h


title: WT Tfh, biological rep2

description: SAMPLE 4


title: TCF-1-null Tfh, biological rep2

description: SAMPLE 2


title: UAJ 070882

city: Paris

first: Nicolas

last: Dulphy

address: 1, avenue Claude Vellefaux

department: Institut de Recherche Saint-Louis

institute: UNIV PARIS

hyb_protocol: Samples were hybridized to a microarray chip overnight at 45 degree in a solution containg several biotinylated control oligonucleotides.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console

source_name: Blood/bone marrow

label_protocol: Samples were enzymatically fragmented and end-labled with a biotinylated nucleotide analog.

extract_protocol: Trizol

tag: disease state

value: AML

tag: phenotyping group

value: normal AML

tag: sample

value: Sang

value: DMSO


title: A. tumefaciens_Manganese_Rep4

description: Biological replicate 4 of 4


title: COUP-TFII OE ventricles, rep 3

city: Houston

first: San-pin

last: Wu

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Hybridization cocktails containing Affymetrix spike-in controls and 15.0ug of each fragmented, labeled cRNA were loaded onto Affymetrix GeneChipÂ® Mouse 430 2.0 arrays.  The arrays were hybridized for 16 hours at 45Â°C with rotation at 60 rpm in the Affymetrix GeneChipÂ® Hybridization Oven 640. The arrays were washed and stained with a streptavidin, R-phycoerythrin conjugate stain using the Affymetrix GeneChipÂ® Fluidics Station 450 using fluidics protocol FS450_0001. Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: The stained arrays were scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneSpring 12.5 GX using default analysis settings with RMA as the summerization algorithm. Baseline to median of all samples

source_name: COUP-TFII OE ventricles

label_protocol: Samples were labeled using the standard Affymetrix linear amplification protocol using the 3' IVT Express Kit.  250 ng of total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was tested for integrity on the Agilent Bioanalyzer and quantified using the NanoDropÂ® ND-1000 spectrophotometer.  15.0 µg of the labeled cRNA was fragmented and re-checked for concentration and size.

growth_protocol: Mice were grown to 2 months old

extract_protocol: Trizol extraction followed by Qiagen RNeasy purification

treatment_protocol: Tamoxifen of 40 mg/kg/day was administered to all mice for 3 days in a row. Ventricles were harvested 16 days post first Tamoxifen dose.

value: 129SvEv/C57Bl6/J mixed

value: Myh6-MerCreMer; CAG-S-COUP-TFII

value: 2.5 months

tag: treated with

value: 40mg/kg/day Tamoxifen for 3 days

value: Cardiac Ventricles

tag: tissue harvest time

value: 16 days post first dose of Tamoxifen


title: Huh-7_shGFP_Hypoxia_1 (1% O2, 24 h)

tag: cell line

value: depleted of GFP via RNA interference (RNAi) under hypoxia for 24h


title: F1 5% D90

source_name: Mouse liver

tag: amount of dietary fat (corn oil) (w/w)

value: 90 days

value: liver


title: UCL 052571

value: NK deficient AML

value: MO

tag: sample type


title: ULI 061029

value: CS


title: SSA 070690


title: Huh-7_shNDRG3_Hypoxia_2 (1% O2, 12 h)

value: depleted of NDRG3 via RNA interference (RNAi) under hypoxia for 12h


title: Huh-7_shHIF-1A_Hypoxia_1 (1% O2, 12 h)

value: depleted of HIF-1A via RNA interference (RNAi) under hypoxia for 12h


title: Huh-7_shGFP_Hypoxia_2 (1% O2, 24 h)


title: RUE 062886

value: AML


title: DS+p16 D5 3

description: DS+p16 D5 3

data_processing:
BeadStudio software v3.2, Minfi
Raw data files contain unmethylated and methylated signal intensities

value: F

value: deep senescence + p16 siRNA D5


title: EP 1 Experiment 2

description: EP 1 Experiment 2

value: early proliferating


title: EP 2 Experiment 2

description: EP 2 Experiment 2


title: Huh-7_shNDRG3_Hypoxia_1 (1% O2, 12 h)


title: DS+p16 D5 2

description: DS+p16 D5 2


title: DS+p16 D5 1

description: DS+p16 D5 1


title: DS+p16 D2 2

description: DS+p16 D2 2

value: deep senescence + p16 siRNA D2


title: EP 3 Experiment 2

description: EP 3 Experiment 2


title: DS+p16 D2 3

description: DS+p16 D2 3


title: Huh-7_shGFP_Hypoxia_1 (1% O2, 12 h)

value: depleted of GFP via RNA interference (RNAi) under hypoxia for 12h


title: EWF 060935

value: normal AML

value: DMSO


title: Control ventricles, rep 2

source_name: Control ventricles

tag: strain

value: 129SvEv/C57Bl6/J mixed

value: 2.5 months

value: 40mg/kg/day Tamoxifen for 3 days

value: Cardiac Ventricles

value: 16 days post first dose of Tamoxifen


title: DS 3

description: DS 3

value: deep senescence


title: DS+p16 D2 1

description: DS+p16 D2 1


title: GUY 060615

value: NK deficient AML

value: Sang

value: CS


title: Huh-7_shGFP_Hypoxia_2 (1% O2, 12 h)


title: Huh-7_shNDRG3_Hypoxia_2 (1% O2, 6 h)

value: depleted of NDRG3 via RNA interference (RNAi) under hypoxia for 6h


title: liver_1% quercetin diet_rep6

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

institute: Food Research Institute, National Agriculture and Food Research Organization

description: Gene expression data from liver after 20 week feeding of control AIN93G diet containing 1% quercetin

hyb_protocol: Fifteen microgram aliquots of fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method..

source_name: liver, fed control AIN93G diet containing 1% quercetin for 20 weeks

label_protocol: The fragmented biotin-labeled aRNA was synthesized from the total RNA of each mouse using the GeneChip® 3′ IVT Express Kit (Affymetrix Japan KK, Tokyo, Japan).

growth_protocol: Four-week-old male C57BL/6J mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed under conditions of 24± 1°C, 55 ± 5% humidity, and 12 hour light/dark photocycles (dark period from 0800 to 2000) with free access to water and a standard nonpurified diet (NMF, Oriental Yeast Co., Tokyo, Japan) for a week prior to the experiment.

extract_protocol: The mice were killed under anesthesia with pentobarbital, and blood and liver tissue were immediately collected. Total RNA was extracted from liver tissues using an RNeasy Midi Kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: The mice were divided into 3 groups of 12 mice each, housed in groups of 3 per cage and fed one of the following diets for 20 weeks : AIN93G (control), AIN93G containing 0.05% quercetin (0.05% quercetin, (Funakoshi, Tokyo, Japan)) and  AIN93G containing 1% quercetin (1% quercetin).

tag: gender

value: male

tag: tissue

value: liver


title: Control ventricles, rep 1

tag: age


title: Huh-7_shHIF-1A_Hypoxia_1 (1% O2, 6 h)

description: Analysis of human Huh-7 cell lines depleted of HIF-1A via RNA interference (RNAi) under hypoxia for 6h

tag: treatment


title: ENK 060323

value: AML


title: COUP-TFII OE ventricles, rep 2

value: Myh6-MerCreMer; CAG-S-COUP-TFII


title: Control ventricles, rep 3


title: Huh-7_shHIF-1A_Hypoxia_2 (1% O2, 6 h)

value: depleted of HIF-1A via RNA interference (RNAi) under hypoxia for 6h


title: RLO 061320

value: MO


title: LIN 052617

value: DMSO


title: COUP-TFII OE ventricles, rep 1

value: 129SvEv/C57Bl6/J mixed


title: Huh-7_shNDRG3_Hypoxia_1 (1% O2, 6 h)


title: liver_1% quercetin diet_rep5

value: fed control AIN93G diet containing 1% quercetin for 20 weeks


title: AIR 052892

value: normal AML


title: liver_1% quercetin diet_rep4


title: EP p16[+]ve 3

description: EP p16[+]ve 1

tag: Sex

value: F

value: early proliferating + p16[+]ve


title: EP p16[+]ve 2

description: EP p16[+]ve 1

tag: cell stage


title: Huh-7_shGFP_Hypoxia_1 (1% O2, 6 h)

value: depleted of GFP via RNA interference (RNAi) under hypoxia for 6h


title: DS 1

description: DS 1

value: deep senescence


title: EP p16[+]ve 1

description: EP p16[+]ve 1


title: ABR 072336

value: NK deficient AML

value: Sang


title: DS 2

description: DS 2


title: EP other p16[-]ve 3

description: EP other p16[-]ve 3

value: early proliferating + other p16[-]ve


title: EP other p16[-]ve 1

description: EP other p16[-]ve 1


title: liver_1% quercetin diet_rep2

value: male


title: liver_0.05% quercetin diet_rep5

description: Gene expression data from liver after 20 week feeding of control AIN93G diet containing 0.05% quercetin

source_name: liver, fed control AIN93G diet containing 0.05% quercetin for 20 weeks

value: liver


title: Huh-7_shHIF-1A_Hypoxia_2 (1% O2, 3 h)

description: Analysis of human Huh-7 cell lines depleted of HIF-1A via RNA interference (RNAi) under hypoxia for 3h


title: Huh-7_shGFP_Hypoxia_3 (1% O2, 3 h)

description: Analysis of human Huh-7 cell lines depleted of GFP via RNA interference (RNAi) under hypoxia for 3h


title: NK_CD56dim_AMLgroup2_F

hyb_protocol: 10µg of cRNA were hybridized on GeneChip Human Genome U133plus 2.0 arrays provided by Affymetrix

scan_protocol: The arrays were read with a confocal laser (Genechip scanner 3000, Affymetrix).

data_processing:
CEL files were generated using the Affymetrix GeneChip Command Console (AGCC) software 3.0
The obtained data were normalized with Partek Genomic Suite software 6.4 (Partek Inc., St. Louis, MO, US) software using quantile normalization algorithm.

label_protocol: 500pg of total RNA were amplified three times using the ExpressArt mRNA amplification Pico kit (AmpTec Gmbh) and labeled with the BioArray HighYield RNA transcript labeling kit from ENZO Life Sciences

extract_protocol: Total RNA has been extracted from sorted CD56bright NK cells with the RNeasy microkit provided by Qiagen according to manufacturer’s instructions.

value: Natural Killer Cells (NK)

tag: phenotype

value: CD56 dim

tag: group

value: AML group 2

tag: individual


title: EP other p16[-]ve 2

description: EP other p16[-]ve 2


title: NK_CD56dim_HC_C

tag: cell

value: HC

value: C


title: ARI 061698

tag: disease state

value: AML

tag: phenotyping group

tag: sample

value: MO

value: DMSO


title: Huh-7_shGFP_Hypoxia_2 (1% O2, 3 h)

tag: cell line

value: depleted of GFP via RNA interference (RNAi) under hypoxia for 3h


title: NK_CD56dim_AMLgroup1_D

value: AML group 1

value: D


title: Huh-7_shHIF-1A_Hypoxia_1 (1% O2, 3 h)

value: depleted of HIF-1A via RNA interference (RNAi) under hypoxia for 3h


title: NK_CD56dim_AMLgroup2_G

value: G


title: NK_CD56dim_AMLgroup1_E

value: E


title: liver_1% quercetin diet_rep3

value: fed control AIN93G diet containing 1% quercetin for 20 weeks


title: Huh-7_shHIF-1A_Hypoxia_3 (1% O2, 3 h)


title: liver_1% quercetin diet_rep1

value: male


title: liver_0.05% quercetin diet_rep4

value: fed control AIN93G diet containing 0.05% quercetin for 20 weeks

value: liver


title: EP G1 p16[-]ve 2

description: EP G1 p16[-]ve 2

value: F

value: early proliferating + G1 p16[-]ve


title: liver_0.05% quercetin diet_rep6


title: NK_CD56dim_HC_B

value: Natural Killer Cells (NK)

value: CD56 dim

value: HC

value: B


title: EP+p16 3

description: EP+p16 3

value: early proliferating + p16 siRNA


title: EP G1 p16[-]ve 1

description: EP G1 p16[-]ve 1


title: liver_0.05% quercetin diet_rep2


title: Huh-7_shGFP_Normoxia_1

value: depleted of GFP via RNA interference (RNAi) under normoxia


title: NK_CD56bright_AMLgroup2_F

value: CD56bright NK cells presenting defective phenotype and function and profoundly perturbed gene-expression pattern compared to HC and Group 1 patients.

value: CD56 bright

value: AML group 2


title: Huh-7_shGFP_Hypoxia_1 (1% O2, 3 h)

value: depleted of GFP via RNA interference (RNAi) under hypoxia for 3h


title: liver_control diet_rep6  (quercetin)

description: Gene expression data from liver after 20 week feeding of control AIN93G diet

source_name: liver, fed control AIN93G diet for 20 weeks

value: fed control AIN93G diet for 20 weeks


title: EP+p16 2

description: EP+p16 2


title: liver_0.05% quercetin diet_rep1


title: Huh-7_shGFP_Hypoxia_2 (1% O2, 6 h)

value: depleted of GFP via RNA interference (RNAi) under hypoxia for 6h


title: EP+p16 1

description: EP+p16 1


title: NK_CD56bright_AMLgroup1_E

value: CD56bright NK cells presenting similar phenotype and function than HC, but the gene-expression pattern is perturbed compared to HC

value: AML group 1

value: E


title: EP G1 p16[-]ve 3

description: EP G1 p16[-]ve 3

value: F


title: Huh-7_shGFP_Normoxia_2


title: Liver_isoflurane anesthesia_replicate 3

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

institute: Chemicals Evaluation and Research Institute, Japan

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 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 SurePrint G3 Rat GE 8x60K Microarray Toxplus 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: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 035170_D_F_20110629) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Liver, isoflurane anesthesia, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification 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: 9 week-old male Sprague-Dawley (Crl:CD(SD)) Rat were purchased from Charles River Japan. They were housed in an air-conditioned room at 21 to 25 deg C and 40 to 70% humidity, with a 12 h light, 12 h dark cycle. Rats were maintained on a basal diet (Oriental Yeast Co.), with tap water ad libitum.

extract_protocol: RNA was prepared using the miRNA Neasy kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: All animals were administrated corn oil (5ml/kg/day) for nine weeks.

value: isoflurane

value: liver

value: Sprague-Dawley


title: NK_CD56bright_AMLgroup1_D

value: Natural Killer Cells (NK)

value: D


title: liver_0.05% quercetin diet_rep3

value: fed control AIN93G diet containing 0.05% quercetin for 20 weeks

value: male


title: liver_control diet_rep5  (quercetin)


title: liver_control diet_rep3  (quercetin)


title: Liver_isoflurane anesthesia_replicate 2

source_name: Liver, isoflurane anesthesia, replicate 2


title: liver_control diet_rep4  (quercetin)


title: NK_CD56bright_HC_C

value: healthy control

value: HC

value: C


title: liver_control diet_rep2 (quercetin)


title: EP 3

description: EP 3

value: early proliferating


title: Liver_isoflurane anesthesia_replicate 1

source_name: Liver, isoflurane anesthesia, replicate 1


title: NK_CD56bright_HC_B

value: CD56 bright

value: B


title: Liver_CO2/O2 anesthesia_replicate 1

source_name: Liver, CO2/O2 anesthesia, replicate 1


title: EP 2

description: EP 2


title: patients with coronary heart disease, biological rep3

status: Public on Jul 23 2015

city: Changchun

first: Bo

middle: Fan

last: Meng

address: Xiantai Street 126 of Changchun of Jilin Province

institute: the Department of Cardiology, China–Japan Union Hospital, Jilin University,

description: the total RNA was extracted from the leucocyte of peripheral blood

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on HG-U133_Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Genechip Scanner 3000

data_processing: The data were analyzed with robust multichip average method and present or absent calls of each probe set were determined by MAS5 method with affy package in R. The differentially genes between coronary heart disease and healthy groups were identified by performing moderated t-statistic in limma package, and the raw p values were adjusted by the FDR method.

source_name: the peripheral blood of patients with coronary heart disease

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA

growth_protocol: the peripheral blood were stored in 4℃ before extracting the total RNA

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

treatment_protocol: Two milliliter peripheral blood from each subject was collected into BD Vacutainer Single-use Containers for human venous blood specimen collection

value: peripheral blood

tag: ethnicity

value: Chinese

value: 58 years

value: coronary heart disease


title: NK_CD56bright_HC_A

tag: sample type

value: A


title: NK_CD56bright_AMLgroup2_G

value: CD56bright NK cells presenting defective phenotype and function and profoundly perturbed gene-expression pattern compared to HC and Group 1 patients.

value: AML group 2

value: G


title: Control vs CTX3 3 biological replicates

city: valdivia

first: Cristia

middle: Felipe

last: Molina

state: --- Select a state ---

address: Universidad Austral, Isla teja

department: Bioinformatics

country: Chile

institute: AUSTRAL-omics

description: Control vs CTX3. Exponential growing cultures of a transposon library (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.6 and were exposed during 3 h to CTX 0.065 μg/ml.

hyb_protocol: Pre-hybridization buffer (25% formamide, 5X SSC, 0.1%SDS, 0.1 mg/mL BSA). Incubate 45 min at 42 ºC. Hybridization buffer (25% formamide, 5X SSC, 0.1% SDS). Incubate 5 min at 95 ºC. Drop the mixture on the slide and incubate overnight at 42 ºC

scan_protocol: Scanned on an ScanArray Gx scanner (PerkinElmer).

data_processing:
Print-tip LOESS normalized. The data were normalized and analyzed using WebarrayDB [www.webarraydb.org; (Wang et al., 2009)] with quantile normalization.
M ≤ -0.75 (negative selection) or M ≥ 1.5 (improved fitness), A ≥ 8, p ≤ 0.005. Experiments which satisfy these 3 criteria in 2 or 3 replicates were determined to be biologically relevant and were considered as negativelly selected by CTX or with an improved fitness.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Total DNA extracted from CTX exposed transposon library

label_protocol: 4 µg of total DNA was mechanically fragmented, poli adenylated and used as template for 2 sequential PCR reactions (last one is nested). Then, an in vitro transcription was conducted (using T7 promoter inside transposon) and this was used as template for cDNA generation of fluorescent probes as has been shown previously (Santiviago, et al. 2009)

growth_protocol: An overnight culture of a ~60.000 mutants library  in S. Typhimurium 14028s background was inoculated (in a 1:1000 dilution) in fresh LB containing flasks and incubated with vigorous shaking to 37 °C. At an OD600 ~0.4

extract_protocol: Total DNA extracted using GenElute™ Bacterial Genomic DNA Kit following manufacturer's instructions

treatment_protocol: Cultures were exposed to CTX (0.065 µg/ml) during 3 h

tag: strain

source_name: Total DNA extracted from untreated cultures


title: Control vs CTX1 3 biological replicates

description: Control vs CTX1. Exponential growing cultures of a transposon library (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.6 and were exposed during 3 h to CTX 0.065 μg/ml.


title: NK_CD56dim_HC_A

value: Natural Killer Cells (NK)

value: CD56 dim


title: patients with coronary heart disease, biological rep1

value: 53 years


title: Jurkat treated with DMSO 9h_rep2

city: Campinas

first: Jaira

middle: Ferreira de

last: Vasconcellos

state: Sao Paulo

address: Rua Dr. Gabriel Porto, 1270.

country: Brazil

institute: Centro Infantil Boldrini

description: Jurkat cells were treated for 9h with 0.1% DMSO (vehicle control). Affymetrix HAT HG-U133A plate.

hyb_protocol: Biotinylated cRNAs were hybridized to the Affymetrix HAT HG-U133A and HAT HG-U133B Array Plate. Array washing and staining were performed on the GeneChip GCAS Array Station following a robotic protocol according to the manufacturer’s instructions (Affymetrix).

scan_protocol: Arrays were scanned on the GeneChip HT scanner (Affymetrix) following the manufacturer's instructions.

data_processing: Scanned image output files were visually examined for major chip defects and hybridization artifacts and then analyzed with Affymetrix GeneChip Microarray Analysis Suite 5.0 (MAS5) software (Affymetrix).

source_name: Jurkat cells

label_protocol: Antisense biotinylated cRNA was prepared on the Affymetrix GeneChip Array Station using the GeneChip HT One-Cycle cDNA Synthesis and Gene Chip HT IVT Labeling kits (Affymetrix) following the manufacturer's instructions.

growth_protocol: RPMI-1640 medium supplemented with 10% fetal bovine serum, 50 U/ml penicillin and 50 μg/ml of streptomycin. Cells were maintained in a 5% CO2-humidified incubator at 37°C.

extract_protocol: Total RNA was obtained using QIAshredder (Qiagen) and RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: SB225002 was dissolved in dimethyl sulfoxide (DMSO) and cells were treated in RPMI-1640 medium for 6h or 9h. The final concentrations of SB225002 was 12.5 μM. For the control, cells were treated with 0.1% DMSO.

value: Jurkat

tag: cell type

value: T-Acute Lymphoblastic Leukemia cell line


title: patient 8 synovial sarcoma

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

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

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: synovial sarcoma

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

extract_protocol: RNA was extracted from frozen samples using the miRNeasy Mini Kit (Qiagen in Japan, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: All of the sample had not received preoperative treatment.

tag: diagnosis

value: synovial sarcoma

tag: fusion gene

tag: histology

value: poorly defferentiated

value: F


title: patient 6 synovial sarcoma

value: biphasic

tag: Sex

tag: age


title: patient 10 synovial sarcoma

value: monophasic

value: M


title: patient 5 synovial sarcoma


title: patient 11 synovial sarcoma


title: Jurkat treated with SB 9h_rep1

description: Jurkat cells were treated for 9h with SB225002 [12.5 uM]. Affymetrix HAT HG-U133A plate.


title: Jurkat treated with DMSO 6h_rep2

description: Jurkat cells were treated for 6h with 0.1% DMSO (vehicle control). Affymetrix HAT HG-U133A plate.


title: Jurkat treated with DMSO 6h_rep1


title: Liver_CO2/O2 anesthesia_replicate 3

source_name: Liver, CO2/O2 anesthesia, replicate 3

tag: treatment

tag: tissue

value: liver

value: Sprague-Dawley


title: liver_control diet_rep1 (quercetin)

value: fed control AIN93G diet for 20 weeks

tag: gender

value: male


title: patient 9 synovial sarcoma


title: patient 4 synovial sarcoma


title: Jurkat treated with SB 6h_rep2

description: Jurkat cells were treated for 6h with SB225002 [12.5 uM]. Affymetrix HAT HG-U133A plate.


title: patient 3 synovial sarcoma


title: Jurkat treated with DMSO 9h_rep1


title: Control vs CTX2 3 biological replicates

description: Control vs CTX2. Exponential growing cultures of a transposon library (obtained from an ON culture diluted 1:1000 in fresh LB media) were harvested at an OD600 ~0.6 and were exposed during 3 h to CTX 0.065 μg/ml.


title: Jurkat treated with SB 6h_rep1


title: patient 2 synovial sarcoma


title: Jurkat treated with SB 9h_rep2


title: patient 7 synovial sarcoma


title: Whole_blood_ACTH_FR17MAG201313904_24H

city: Castanet-Tolosan

first: Pierre

last: Mormède

address: 24 Chemin de Borde Rouge

institute: INRA

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313904

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 35419 rows each corresponding to a unique ProbeName (provided as data Matrix) and 120 columns (individuals x time). Technical biases were handled by aligning the within-array medians for all genes and by a quantile normalization within animal using the normalize.quantiles function from the preprocessCore library.

source_name: Whole blood, 24 h, individual: FR17MAG201313904

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy purification (QIAGEN). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

extract_protocol: A total RNA isolation and purification was done according to the manufacturer’s instructions using the Nucleospin RNA II kit (MachereyNagel, France) followed by DNase treatment. The quality of each RNA sample was checked through the Bioanalyser Agilent 2100 (Agilent Technologies, Massy, France) and low-quality RNA preparations were discarded (RIN$<8$).

treatment_protocol: At each time, animals were slightly restrained on their back and two blood samples were taken by puncture of a jugular vein in Vacutainer\textregistered~tubes with 20 G needles. After centrifugation (1000 g, 10 min), plasma aliquots were frozen at -80\celsius~until  analysis. One 5-mL tube with EDTA K2 was used for blood cell count and an aliquot (400 $\mu$L) was mixed with the same volume of DL buffer (Machery-Nagel), frozen at -20\celsius~for 4 h and then at -80\celsius~until analysis for gene expression.

tag: agent

value: ACTH injection

tag: individual

tag: time point (h)

value: female


title: Liver_CO2/O2 anesthesia_replicate 2

source_name: Liver, CO2/O2 anesthesia, replicate 2


title: EP 1

description: EP 1

source_name: HMEC

tag: cell stage

value: early proliferating


title: patient 1 synovial sarcoma


title: Whole_blood_ACTH_FR17MAG201313904_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313904

source_name: Whole blood, 4 h, individual: FR17MAG201313904


title: Whole_blood_ACTH_FR17MAG201313904_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313904

source_name: Whole blood, 1 h, individual: FR17MAG201313904


title: Whole_blood_ACTH_FR17MAG201313903_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313903

source_name: Whole blood, 1 h, individual: FR17MAG201313903


title: Whole_blood_ACTH_FR17MAG201313826_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313826

source_name: Whole blood, 0 h, individual: FR17MAG201313826


title: Whole_blood_ACTH_FR17MAG201313903_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313903

source_name: Whole blood, 4 h, individual: FR17MAG201313903


title: Whole_blood_ACTH_FR17MAG201313826_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313826

source_name: Whole blood, 24 h, individual: FR17MAG201313826


title: Whole_blood_ACTH_FR17MAG201313825_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313825

source_name: Whole blood, 0 h, individual: FR17MAG201313825


title: Whole_blood_ACTH_FR17MAG201313826_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313826

source_name: Whole blood, 4 h, individual: FR17MAG201313826


title: Whole_blood_ACTH_FR17MAG201313825_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313825

source_name: Whole blood, 1 h, individual: FR17MAG201313825


title: Whole_blood_ACTH_FR17MAG201313904_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313904

source_name: Whole blood, 0 h, individual: FR17MAG201313904


title: Whole_blood_ACTH_FR17MAG201313903_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313903

source_name: Whole blood, 0 h, individual: FR17MAG201313903


title: Whole_blood_ACTH_FR17MAG201313826_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313826

source_name: Whole blood, 1 h, individual: FR17MAG201313826


title: Whole_blood_ACTH_FR17MAG201313824_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313824

source_name: Whole blood, 1 h, individual: FR17MAG201313824


title: patients with coronary heart disease, biological rep2

description: the total RNA was extracted from the leucocyte of peripheral blood

source_name: the peripheral blood of patients with coronary heart disease

value: peripheral blood

value: Chinese

value: 57 years

tag: disease state

value: coronary heart disease


title: Whole_blood_ACTH_FR17MAG201313824_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313824

source_name: Whole blood, 24 h, individual: FR17MAG201313824


title: Whole_blood_ACTH_FR17MAG201313903_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313903

source_name: Whole blood, 24 h, individual: FR17MAG201313903


title: Whole_blood_ACTH_FR17MAG201313825_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313825

source_name: Whole blood, 24 h, individual: FR17MAG201313825


title: Whole_blood_ACTH_FR17MAG201313788_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313788

source_name: Whole blood, 4 h, individual: FR17MAG201313788


title: Whole_blood_ACTH_FR17MAG201313788_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313788

source_name: Whole blood, 24 h, individual: FR17MAG201313788


title: Whole_blood_ACTH_FR17MAG201313824_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313824

source_name: Whole blood, 0 h, individual: FR17MAG201313824


title: Whole_blood_ACTH_FR17MAG201313825_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313825

source_name: Whole blood, 4 h, individual: FR17MAG201313825


title: Whole_blood_ACTH_FR17MAG201313824_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313824

source_name: Whole blood, 4 h, individual: FR17MAG201313824


title: Whole_blood_ACTH_FR17MAG201313788_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313788

source_name: Whole blood, 0 h, individual: FR17MAG201313788


title: Whole_blood_ACTH_FR17MAG201313787_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313787

source_name: Whole blood, 1 h, individual: FR17MAG201313787


title: Whole_blood_ACTH_FR17MAG201313787_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313787

source_name: Whole blood, 4 h, individual: FR17MAG201313787


title: Whole_blood_ACTH_FR17MAG201313787_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313787

source_name: Whole blood, 0 h, individual: FR17MAG201313787


title: Whole_blood_ACTH_FR17MAG201313664_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313664

source_name: Whole blood, 24 h, individual: FR17MAG201313664


title: Whole_blood_ACTH_FR17MAG201313663_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313663

source_name: Whole blood, 24 h, individual: FR17MAG201313663


title: Whole_blood_ACTH_FR17MAG201313786_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313786

source_name: Whole blood, 0 h, individual: FR17MAG201313786


title: Whole_blood_ACTH_FR17MAG201313663_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313663

source_name: Whole blood, 1 h, individual: FR17MAG201313663


title: Whole_blood_ACTH_FR17MAG201313633_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313633

source_name: Whole blood, 24 h, individual: FR17MAG201313633


title: Whole_blood_ACTH_FR17MAG201313787_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313787

source_name: Whole blood, 24 h, individual: FR17MAG201313787


title: Whole_blood_ACTH_FR17MAG201313664_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313664

source_name: Whole blood, 1 h, individual: FR17MAG201313664


title: Whole_blood_ACTH_FR17MAG201313786_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313786

source_name: Whole blood, 4 h, individual: FR17MAG201313786


title: Whole_blood_ACTH_FR17MAG201313632_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313632

source_name: Whole blood, 24 h, individual: FR17MAG201313632


title: Whole_blood_ACTH_FR17MAG201313664_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313664

source_name: Whole blood, 0 h, individual: FR17MAG201313664


title: Whole_blood_ACTH_FR17MAG201313663_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313663

source_name: Whole blood, 4 h, individual: FR17MAG201313663


title: Whole_blood_ACTH_FR17MAG201313786_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313786

source_name: Whole blood, 24 h, individual: FR17MAG201313786


title: Whole_blood_ACTH_FR17MAG201313788_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313788

source_name: Whole blood, 1 h, individual: FR17MAG201313788


title: Whole_blood_ACTH_FR17MAG201313632_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313632

source_name: Whole blood, 4 h, individual: FR17MAG201313632


title: Whole_blood_ACTH_FR17MAG201313786_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313786

source_name: Whole blood, 1 h, individual: FR17MAG201313786


title: Whole_blood_ACTH_FR17MAG201313664_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313664

source_name: Whole blood, 4 h, individual: FR17MAG201313664


title: Whole_blood_ACTH_FR17MAG201313631_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313631

source_name: Whole blood, 24 h, individual: FR17MAG201313631


title: Whole_blood_ACTH_FR17MAG201313632_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313632

source_name: Whole blood, 1 h, individual: FR17MAG201313632


title: Whole_blood_ACTH_FR17MAG201313631_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313631

source_name: Whole blood, 4 h, individual: FR17MAG201313631


title: Whole_blood_ACTH_FR17MAG201313663_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313663

source_name: Whole blood, 0 h, individual: FR17MAG201313663


title: Whole_blood_ACTH_FR17MAG201313633_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313633

source_name: Whole blood, 4 h, individual: FR17MAG201313633


title: Whole_blood_ACTH_FR17MAG201313631_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313631

source_name: Whole blood, 0 h, individual: FR17MAG201313631


title: Whole_blood_ACTH_FR17MAG201313631_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313631

source_name: Whole blood, 1 h, individual: FR17MAG201313631


title: Whole_blood_ACTH_FR17MAG201313633_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313633

source_name: Whole blood, 1 h, individual: FR17MAG201313633


title: Whole_blood_ACTH_FR17MAG201313633_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313633

source_name: Whole blood, 0 h, individual: FR17MAG201313633


title: Whole_blood_ACTH_FR17MAG201313576_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313576

source_name: Whole blood, 4 h, individual: FR17MAG201313576


title: Whole_blood_ACTH_FR17MAG201313632_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313632

source_name: Whole blood, 0 h, individual: FR17MAG201313632


title: Whole_blood_ACTH_FR17MAG201313576_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313576

source_name: Whole blood, 24 h, individual: FR17MAG201313576


title: Whole_blood_ACTH_FR17MAG201313573_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313573

source_name: Whole blood, 0 h, individual: FR17MAG201313573


title: Whole_blood_ACTH_FR17MAG201313573_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313573

source_name: Whole blood, 4 h, individual: FR17MAG201313573


title: Whole_blood_ACTH_FR17MAG201313548_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313548

source_name: Whole blood, 4 h, individual: FR17MAG201313548


title: Whole_blood_ACTH_FR17MAG201313547_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313547

source_name: Whole blood, 4 h, individual: FR17MAG201313547


title: Whole_blood_ACTH_FR17MAG201313573_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313573

source_name: Whole blood, 24 h, individual: FR17MAG201313573


title: Whole_blood_ACTH_FR17MAG201313576_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313576

source_name: Whole blood, 1 h, individual: FR17MAG201313576


title: Whole_blood_ACTH_FR17MAG201313547_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313547

source_name: Whole blood, 0 h, individual: FR17MAG201313547


title: Whole_blood_ACTH_FR17MAG201313576_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313576

source_name: Whole blood, 0 h, individual: FR17MAG201313576


title: Whole_blood_ACTH_FR17MAG201313547_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313547

source_name: Whole blood, 1 h, individual: FR17MAG201313547


title: Whole_blood_ACTH_FR17MAG201313548_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313548

source_name: Whole blood, 24 h, individual: FR17MAG201313548


title: Whole_blood_ACTH_FR17MAG201313548_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313548

source_name: Whole blood, 0 h, individual: FR17MAG201313548


title: Whole_blood_ACTH_FR17MAG201313546_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313546

source_name: Whole blood, 0 h, individual: FR17MAG201313546


title: Whole_blood_ACTH_FR17MAG201313548_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313548

source_name: Whole blood, 1 h, individual: FR17MAG201313548


title: Whole_blood_ACTH_FR17MAG201313573_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313573

source_name: Whole blood, 1 h, individual: FR17MAG201313573


title: Whole_blood_ACTH_FR17MAG201313546_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313546

source_name: Whole blood, 1 h, individual: FR17MAG201313546


title: Whole_blood_ACTH_FR17MAG201313546_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313546

source_name: Whole blood, 4 h, individual: FR17MAG201313546


title: Whole_blood_ACTH_FR17MAG201313547_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313547

source_name: Whole blood, 24 h, individual: FR17MAG201313547


title: Whole_blood_ACTH_FR17MAG201313545_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313545

source_name: Whole blood, 0 h, individual: FR17MAG201313545


title: Whole_blood_ACTH_FR17MAG201313545_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313545

source_name: Whole blood, 24 h, individual: FR17MAG201313545


title: Whole_blood_ACTH_FR17MAG201313449_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313449

source_name: Whole blood, 4 h, individual: FR17MAG201313449


title: Whole_blood_ACTH_FR17MAG201313546_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313546

source_name: Whole blood, 24 h, individual: FR17MAG201313546


title: Whole_blood_ACTH_FR17MAG201313449_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313449

source_name: Whole blood, 24 h, individual: FR17MAG201313449


title: Whole_blood_ACTH_FR17MAG201313449_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313449

source_name: Whole blood, 1 h, individual: FR17MAG201313449


title: Whole_blood_ACTH_FR17MAG201313449_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313449

source_name: Whole blood, 0 h, individual: FR17MAG201313449


title: Whole_blood_ACTH_FR17MAG201313447_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313447

source_name: Whole blood, 0 h, individual: FR17MAG201313447


title: Whole_blood_ACTH_FR17MAG201313447_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313447

source_name: Whole blood, 4 h, individual: FR17MAG201313447


title: Whole_blood_ACTH_FR17MAG201313390_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313390

source_name: Whole blood, 24 h, individual: FR17MAG201313390


title: Whole_blood_ACTH_FR17MAG201313390_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313390

source_name: Whole blood, 4 h, individual: FR17MAG201313390


title: Whole_blood_ACTH_FR17MAG201313545_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313545

source_name: Whole blood, 1 h, individual: FR17MAG201313545


title: Whole_blood_ACTH_FR17MAG201313447_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313447

source_name: Whole blood, 24 h, individual: FR17MAG201313447


title: Whole_blood_ACTH_FR17MAG201313447_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313447

source_name: Whole blood, 1 h, individual: FR17MAG201313447


title: Whole_blood_ACTH_FR17MAG201313387_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313387

source_name: Whole blood, 4 h, individual: FR17MAG201313387


title: Whole_blood_ACTH_FR17MAG201313389_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313389

source_name: Whole blood, 1 h, individual: FR17MAG201313389


title: Whole_blood_ACTH_FR17MAG201313389_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313389

source_name: Whole blood, 24 h, individual: FR17MAG201313389


title: Whole_blood_ACTH_FR17MAG201313390_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313390

source_name: Whole blood, 0 h, individual: FR17MAG201313390


title: Whole_blood_ACTH_FR17MAG201313389_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313389

source_name: Whole blood, 0 h, individual: FR17MAG201313389


title: Whole_blood_ACTH_FR17MAG201313389_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313389

source_name: Whole blood, 4 h, individual: FR17MAG201313389


title: Whole_blood_ACTH_FR17MAG201313350_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313350

source_name: Whole blood, 24 h, individual: FR17MAG201313350


title: Whole_blood_ACTH_FR17MAG201313387_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313387

source_name: Whole blood, 0 h, individual: FR17MAG201313387


title: Whole_blood_ACTH_FR17MAG201313387_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313387

source_name: Whole blood, 1 h, individual: FR17MAG201313387


title: Whole_blood_ACTH_FR17MAG201313350_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313350

source_name: Whole blood, 1 h, individual: FR17MAG201313350


title: Whole_blood_ACTH_FR17MAG201313350_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313350

source_name: Whole blood, 0 h, individual: FR17MAG201313350


title: Whole_blood_ACTH_FR17MAG201313347_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313347

source_name: Whole blood, 24 h, individual: FR17MAG201313347


title: Whole_blood_ACTH_FR17MAG201313347_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313347

source_name: Whole blood, 1 h, individual: FR17MAG201313347


title: Whole_blood_ACTH_FR17MAG201313350_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313350

source_name: Whole blood, 4 h, individual: FR17MAG201313350


title: Whole_blood_ACTH_FR17MAG201313387_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313387

source_name: Whole blood, 24 h, individual: FR17MAG201313387


title: Whole_blood_ACTH_FR17MAG201313390_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313390

source_name: Whole blood, 1 h, individual: FR17MAG201313390


title: Whole_blood_ACTH_FR17MAG201313347_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313347

source_name: Whole blood, 0 h, individual: FR17MAG201313347


title: Whole_blood_ACTH_FR17MAG201313315_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313315

source_name: Whole blood, 24 h, individual: FR17MAG201313315


title: Whole_blood_ACTH_FR17MAG201313313_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313313

source_name: Whole blood, 24 h, individual: FR17MAG201313313


title: Whole_blood_ACTH_FR17MAG201313313_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313313

source_name: Whole blood, 4 h, individual: FR17MAG201313313


title: Whole_blood_ACTH_FR17MAG201313315_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313315

source_name: Whole blood, 0 h, individual: FR17MAG201313315


title: Whole_blood_ACTH_FR17MAG201313545_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313545

source_name: Whole blood, 4 h, individual: FR17MAG201313545


title: Whole_blood_ACTH_FR17MAG201313315_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313315

source_name: Whole blood, 1 h, individual: FR17MAG201313315


title: Whole_blood_ACTH_FR17MAG201313347_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313347

source_name: Whole blood, 4 h, individual: FR17MAG201313347


title: Whole_blood_ACTH_FR17MAG201313315_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313315

source_name: Whole blood, 4 h, individual: FR17MAG201313315


title: Whole_blood_ACTH_FR17MAG201313286_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313286

source_name: Whole blood, 4 h, individual: FR17MAG201313286


title: Maxillary Mesenchyme E10.5 Control 5

city: New York

first: Juhee

last: Jeong

state: New York

address: 345 E 24th St

department: Basic sciences and Craniofacial development

institute: New York University College of Dentistry

description: Gene expression from control maxillary arches

hyb_protocol: Incubated 10 ng of cRNA at 45 C for 16 hours on Affymetrix GeneChip Mouse Genome 430 2.0 arrays  .RNA samples from three wild-type and three Lhx6−/−;Lhx8−/− mutant embryos, all somite count- and sex-matched (females), were analyzed.

scan_protocol: Genechip was scanned using the Affymetrix Genechip Scanner 3000.

data_processing: Data was processed using Robust Microarray Average (RMA).  The resulting list of 212 genes was used for a gene ontology analysis with DAVID.

source_name: Maxillary Mesenchyme E10.5 control

label_protocol: Amplification of RNA by Ovation Nano Amplification system

growth_protocol: No growth protocol. Embryos were collected from pregnant female mice at embryonic day 10.5 of development.

extract_protocol: The head of E10.5 embryos was collected and embedded in Optimal Cutting Temperature resin (Tissue-Tek) by flash freezing on dry ice. The frozen sections were collected on polyethylene naphthalate membrane slides (Leica). Leica LMD6000 Laser Micro-Dissection System was used to cut out the normal expression domain of Lhx6 and Lhx8 in the maxillary arch mesenchyme, as shown in Figure 3. The tissue was collected from the entire antero-posterior extent of the maxillary arches. Total RNA was extracted using RNeasy Micro Kit.

treatment_protocol: No treatment protocol.

value: mixed genetic background of C57BL/6J, 129 and CD-1 strains

tag: genotype/variation

value: Wild-type

value: maxillary arch mesenchyme


title: Whole_blood_ACTH_FR17MAG201313313_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313313

source_name: Whole blood, 0 h, individual: FR17MAG201313313


title: Whole_blood_ACTH_FR17MAG201313313_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313313

source_name: Whole blood, 1 h, individual: FR17MAG201313313


title: Maxillary Mesenchyme E10.5 Lhx6 KO; Lhx8 KO 1

description: Gene expression from mutant maxillary arches

source_name: Maxillary Mesenchyme E10.5 Lhx6Lhx8 doubleKO


title: Maxillary Mesenchyme E10.5 Lhx6 KO; Lhx8 KO 2

source_name: Maxillary Mesenchyme E10.5 Lhx6Lhx8 double KO


title: Whole_blood_ACTH_FR17MAG201313286_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313286

source_name: Whole blood, 24 h, individual: FR17MAG201313286


title: miR-203_ko, biological rep. 2

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description: Gene Expression Data

hyb_protocol: Standard Affymetrix protocol for Mouse 430 2.0 array

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: Data analysis was performed using the MAS 5.0 normalization scheme with default parameters

source_name: Total Epidermis

label_protocol: Standard 3'IVT reaction accroding to Affymetrix Protocols using .5ug of Total RNA

growth_protocol: Animals were housed in a specific pathogen free barrier facility

extract_protocol: Total epidermal RNAs were isolated by treating skin with Dispase enzyme for 1 hr at 37 degrees C and physcially removing the epidermis from the dermis. The RNA was then extracted using Trizol (Invitrogen) according to the manufacturers instructions

treatment_protocol: Total epidermis was isolated from unperturbed animals

value: skin


title: Whole_blood_ACTH_FR17MAG201313286_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313286

source_name: Whole blood, 1 h, individual: FR17MAG201313286


title: Maxillary Mesenchyme E10.5 Lhx6 KO; Lhx8 KO 4


title: Whole_blood_ACTH_FR17MAG201313286_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313286

source_name: Whole blood, 0 h, individual: FR17MAG201313286


title: Whole_blood_ACTH_FR17MAG201313285_0H

description: Gene expression in blood before ACTH injection for individual: FR17MAG201313285

source_name: Whole blood, 0 h, individual: FR17MAG201313285


title: miR-203 induced, biological rep2

description: Gene Expression Data

source_name: Sorted Hair follicle Outer Root Sheath Cells

extract_protocol: H2BGFP+ cells were isolated by FACS. Total RNA was isolated using Trizol (invitrogen) according to the manufacturer's instructions

treatment_protocol: Hair follicle Outer Root Sheath cells were isolated by FACS from K14-rtTA/pTRE-miR-203/K14-H2BGFP  and pTRE-miR-203/K14-H2BGFP littermates at P4, 24h after administering Doxcycline via IP injection.

value: FVB


title: miR-203_wt, biological rep. 2

description: Gene Expression Data


title: Whole_blood_ACTH_FR17MAG201313285_4H

description: Gene expression in blood 4 h after ACTH injection for individual: FR17MAG201313285

source_name: Whole blood, 4 h, individual: FR17MAG201313285


title: uninduced control, biological rep2

description: Gene Expression Data


title: Whole_blood_ACTH_FR17MAG201313285_1H

description: Gene expression in blood 1 h after ACTH injection for individual: FR17MAG201313285

source_name: Whole blood, 1 h, individual: FR17MAG201313285


title: Maxillary Mesenchyme E10.5 Control 1


title: uninduced control, biological rep1

description: Gene Expression Data


title: CD11b+ cells C26GM_3

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

description: CD11b+ cells from spleen of GM-CSF tumor-bearing mice

hyb_protocol: Accordingly to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004

scan_protocol: Image files from scanning (.dat and .cel files) were generated with Affymetrix Expression Console package.

data_processing: Signal reconstruction was performed using the RMA algorithm as implemented in Bioconductor affy package. Expression Data are expressed as log2 of intensity.

extract_protocol: Trizol extraction of total RNA was performed accordingly to manifacturer guidelines, with minor modifications. Extraction was followed by Qiagen Rneasy column clean-up accordingly to manifacturer instructions.

treatment_protocol: CD11b+ cells were isolated by immuno-sorting using CD11b+ isolation kit (Miltenyi Biotech) and LS columns.

value: Tumour-bearing

tag: source tissue

value: Spleen

value: BALB/c


title: CD11b+ cells C57BL6_1

description: CD11b+ cells from spleen of healthy C57BL/6 mice

label_protocol: Accordingly to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004

value: Healthy

tag: strain


title: CD11b+ cells C26GM_1

tag: cell type


title: CD11b+ cells C26GM_2


title: Whole_blood_ACTH_FR17MAG201313285_24H

description: Gene expression in blood 24 h after ACTH injection for individual: FR17MAG201313285

source_name: Whole blood, 24 h, individual: FR17MAG201313285


title: miR-203_wt, biological rep. 1

description: Gene Expression Data


title: miR-203 induced, biological rep1

description: Gene Expression Data


title: miR-203_ko, biological rep. 1

description: Gene Expression Data


title: CD11b+ cells 4T1_3

description: CD11b+ cells from tumor infiltrate of 4T1 tumor-bearing mice

value: Tumour infiltrate


title: CD11b+ cells BALBc_1

description: CD11b+ cells from spleen of healthy BALB/c mice


title: CD11b+ cells C57BL6_2


title: cell line EL4_2

tag: cell line

tag: tissue:

tag: treatment:


title: Maxillary Mesenchyme E10.5 Control 4


title: CD11b+ cells MCA203_3

description: CD11b+ cells from tumor infiltrate of MCA203 tumor-bearing mice


title: CD11b+ cells MCA203_1


title: CD11b+ cells MCA203_2


title: CD11b+ cells 4T1_1


title: CD11b+ cells BALBc_3


title: CD11b+ cells C26GM_3-mirna

scan_protocol: Creator:GenePix Pro 4.0.1.17 Scanner:GenePix 4000B [84945]

data_processing: BRBArrayTools Calculation Method: Fluorescence intensities generated by Cy5 and Cy3 probes hybridized onto the microarray slides were scanned were scanned on a GenePix 4000 (Axon Instruments, Union City, CA) at variable PMT voltage to obtain maximal signal intensities with < 1% probe saturation. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 100, and spot size less than 10um 2. genes were filtered out if >80% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64.

label_protocol: Cy5 Sample Labeling Protocol. Small RNA was enriched from 10ug total RNA by flashPAGE (Pre-cast Gel,Type A) (Ambion, Austin, TX, USA) and purified using flashPAGE reaction clean-up kit (Ambion, Austin, TX, USA) according to manufacture’s instruction. The same procedures were applied to obtain small RNA from the Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines that was used as the reference for the miRNA expression array assay. Fragmented small RNA were 3’-end tailed with amine-modified nucleotides and chemically coupled to CyDye fluors (Amersham Biosciences, piscatway, NJ, USA), which sample with Cy5 and the reference with Cy3 respectively, using the mirVana miRNA Labeling Kit (Ambion) following the recommended protocol by the manufactures’ instruction. After labeling, the samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).

extract_protocol: Total RNA was extracted from CD11b+ sorted cells by TRIzol (Invitrogen) according to the manufacturer’s instructions. The quality and quantity of RNA samples were determined by Agilent RNA 6000 Nano Chip (Agilent Technologies). Before hybridization, total RNA was size-fractioned to enrich in small RNA (minus than 70 nt in length) with the FlashPAGE purification kit (Ambion), according to the manufacturer’s instructions.


title: Alpha-amylase overproducer versus wild type. REP2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Alpha-amylase overproducer versus wild type. Biological replicate 2 of 3

hyb_protocol: Slides were prehybridized in 6x SSC, 0.5% SDS (w/v), and 1% BSA (w/v) at 42ºC for 30 min, followed by five rinses with milliQ water. Excess water was drained with a 2000-rpm spin for 2 min. 300 pmol of dye of each cDNA labeled with either Cy3 or Cy5 were resuspended in 50% formamide, 3x SSC, 5x Denhardt's, 1% SDS and 5% Dextransulphate. This mix was boiled for 5 min at 95ºC and then added to the prehybridized slide. Hybridization took place overnight at 37ºC in a hybridization chamber. Arrays were then washed for 5 min at 37ºC in 0.5x SSPE, Tween20 0.1%, twice for 5 min at room temperature (21ºC) with 0.5x SSPE, Tween20 0.1%, three times with 0.5x SSPE at room temperature, and 5 min with 0.1x SSPE. The slides were drained with a 2000-rpm spin for 2 min and stored in darknesss until they were scanned.

scan_protocol: The slides were scanned with a GenePix 4000B scanner, and the images were quantified with GenePix Pro 5.1 software (Molecular Devices).

data_processing: Data processing was carried out using the LIMMA package (Smyth, 2003) of the Bioconductor project. Raw intensities were background-subtracted by the NORMEXP method with an offset of 50. Signals (in log2 scale) were then normalized by the LOWESS algorithm (intra-arrays normalization), followed by adjustment of their quantiles (inter-arrays normalization).

organism: Streptomyces lividans

source_name: S. lividans TK21 (wild type)

label_protocol: RNA was labeled with Cy3 or Cy5 by using the SuperScript Indirect cDNA labeling system (Invitrogen) as described in the instruction manual.

growth_protocol: Transcriptomic analyses were performed with cultures grown in liquid NMMP medium. Total RNA was extracted from the cell cultures at the late exponential phase of growth.

extract_protocol: Total RNA was isolated from mycelia harvested and stored from liquid cultures using the RNeasy midi Kit largely from Qiagen, according to the manufacturer’s instructions, with the incorporation of several modifications. Cell pellets were mixed with glass beads (3.5-4.5 mm in diameter), previously freezed with 5 ml of Kirby  (SDS 1%, EDTA 160mM, DEPC-treated H2O). After adding  phenol-chloroform (1ml) samples were vortexed twice, resting on ice for 2 minutes between each vortex. After adding RNeasy RLT buffer (4 ml) samples were vortexed again and extracted twice with phenol-chloroform  (8 ml). Extracts were then treated with ethanol (2.8 ml) and applied to the RNeasy midi columns for purification, according to the manufacturer's protocol.

source_name: S. lividans (TK21) alpha-amylase overproducer


title: CD11b+ cells C57BL6_3