title: BJ_untreated_rep1

source_name: BJ fibroblasts, untreated

value: untreated


title: GRADE II CULTURE

status: Public on Sep 18 2013

type: RNA

city: Messina

first: Alfredo

last: Conti

state: Sicily

address: via La Farina 15

country: Italy

institute: Alfredo

description:
PRIMARY CELL CULTURE FROM GRADE II TUMOR
SAMPLE 5

scan_protocol: Real-time PCR was performed using a standard TaqMan PCR kit procedure on an “Real Time Fast 7900 HT” PCR System (Applied Biosystems). The 100 µl PCR included 50 µl RT product (before diluited 1:60) and 50 µl TaqMan Universal PCR Master Mix (2X) (Applied Biosystems). The total volume were loaded into Card TaqMan Low Density Array Human MicroRNA Panel (Applied Biosystem) including a total of 384 human microRNAs publicated on databases www.sanger.ac.uk. The reaction cards was runned at 50°C for 2 min and 95°C for 10 min, followed by 40 cycles of 97°C for 30s and 59,7°C for 1 min. All reactions were run in triplicate.

data_processing: Analysis of data was performed using the SDS 2.3 software using the 2-∆∆Ct (relative quantitative) method. The ∆Ct of every miRNA was determined in relation to the endogenous control RNA U6 that was invariably expressed in all samples.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: ASTROCYTIC TUMOR

label_protocol: The miRNAs were first converted to cDNA using Multiplex RT for TaqMan Array Human MicroRNA Panel. The RT Master mix included 100 mM each of dNTPs , 50 U/ml MultiScrabe reverse transcriptase (Applied Biosystems), 20 U/µl RNase inhibitor (Applied Biosystems) and 10X RT Buffer. The 10 µl reactions, including 7 µl of RT master mix, 2 µl of purified microRNA and 1 µl of Multiplex RT Human primer pool (Applied Biosystem), were incubated in ice for 5 min and then in a thermal cycler for 30 min at 16°C, 30 min at 42°C, 5 min at 85°C, and then hold at 4°C. miRNA levels were normalized to the expression of small nucleolar RNAs, RNU44, RNU48 and RNU6B. All reverse transcriptase reactions, including no-template controls and RT controls, were run in duplicate.

extract_protocol: Total RNA, including small RNA, was isolated from tissue samples using the mirVanaTM miRNA Isolation Kit (Ambion) following the standard protocol. The quantity and quality of the purified RNA was evaluated by spectrophotometric analysis and electrophoresis on denaturing gel of acrylamide.

tag: grade

value: WHO GRADE 2


title: 7059 - SCC

city: Vancouver

first: Rebecca

middle: M

last: Towle

state: BC

department: Integrative Oncology

country: Canada

institute: British Columbia Cancer Research Centre

description: oral squamous cell carcinoma

hyb_protocol: Performed as per Agilent protocol

scan_protocol: Scanned using Axon GenePix 4000B scanners at 5um resolution.

data_processing: Array images normalized using GenePix Pro 6.1 software and each array was median normalized.

label_protocol: Agilent Low Input Labeling Kit

extract_protocol: Total RNA was extracted using TRIZol protocol, followed by Dnase I treatment

tag: gender

value: Female

tag: tissue

value: tongue

tag: disease state

value: oral squamous cell carcinoma

tag: sample type

value: fresh frozen tissue


title: 7057 - SCC

description: oral squamous cell carcinoma


title: 7057 - Normal

description: normal oral tissue

source_name: 7057 - Normal

value: normal


title: 1858 - Normal

type: genomic

description: normal oral tissue

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 BeadChip using standard Illumina protocol.

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

data_processing: BeadStudio software v3.2.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Normal, 1858

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted using standard phenol chloroform extraction and isopropanol precipitation procedure.

tag: patient identifier

value: male


title: 5266 - SCC

description: oral squamous cell carcinoma


title: 7057 - Dysplasia

description: oral dysplasia

source_name: 7057 - Dysplasia

value: dysplasia


title: 5266 - Normal

description: normal oral tissue

source_name: 5266 - Normal


title: 7059 - Dysplasia

description: oral dysplasia

source_name: 7059 - Dysplasia


title: 7059 - Normal

description: normal oral tissue

source_name: 7059 - Normal


title: 3002 - SCC

description: oral squamous cell carcinoma

value: Male


title: BJ_untreated_rep2

city: Cleveland

first: HyeonJoo

last: Cheon

state: OH

address: 9500 Euclid Ave

department: Molecular Genetics

country: USA

institute: Cleveland Clinic

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

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

growth_protocol: Cells were cultured in DMEM supplemented with 5% FBS, 100 U/ml penicillin, and 100 g/ml streptomycin. Lentiviral vector transfected cells were selected by puromycin treatment.

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

treatment_protocol: Cells were treated with 3 IU/ml of IFN beta for 6 hrs. Cells were transfected with empty lentiviral vector or vector containing Y701F STAT1 cDNA.

tag: cell type

value: normal fibroblasts

tag: treatment


title: 3002 - Dysplasia

description: oral dysplasia

source_name: 3002 - Dysplasia


title: Mcm_cdc6mn_2

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description: Mcm2-7 ChIP in cdc6-mn cells biological replicate 2

hyb_protocol: Samples were co-hybridized to custom Agilent arrays in 1X Agilent hybridization buffer at 65 degrees for 16 hours. Samples were washed according to manufacturer's instructions.

scan_protocol: Agilent scanner using the AgilentHD_CGH protocol (5μM resolution, 100% PMT for each laser). Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing: Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the sma package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).

organism: Saccharomyces cerevisiae

source_name: meiotic budding yeast cells, 3 hours in SPO-medium

label_protocol: Half of the immunoprecipitated DNA or one tenth of the input DNA was labeled with Cy3- or Cy5-dUTP (GE Healthcare) by random priming using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: Cells were pre-grown in presporulation medium (BYTA) and transferred into sporulation medium (SPO) at 0 hours.

extract_protocol: 25 ml of cells were harvested after 30 minutes (Mcm2-7) or 3 hours (all other experiment) in sporulation media. Chromatin immunoprecipitation was performed as described (Aparicio et al., 1997). One tenth of the lysate was removed as an input sample. Proteins were immunoprecipitated with the indicated antibodies in combination with 20 µl GammaBind-Sepharose (GE Healthcare) for 16 hours at 4°C.

tag: strain

tag: chip antibody

value: none (input)

tag: time in spo (hours)

value: 2 µl anti-Mcm2-7  (UM185, S.P. Bell)


title: 1979 - Dysplasia

description: oral dysplasia

source_name: 1979 - Dysplasia

value: front of mouth


title: 5266 - Dysplasia

description: oral dysplasia

source_name: 5266 - Dysplasia


title: 1999 - CIS

description: oral carcinoma in situ

value: carcinoma in situ


title: 1979 - CIS

description: oral carcinoma in situ


title: 1953 - Dysplasia

description: oral dysplasia

source_name: 1953 - Dysplasia


title: 1953 - CIS

description: oral carcinoma in situ


title: Mcm_cdc6mn_1

description: Mcm2-7 ChIP in cdc6-mn cells biological replicate 1


title: 1999 - Normal

description: normal oral tissue

source_name: 1999 - Normal


title: 1896 - Normal

description: normal oral tissue

source_name: Normal, 1896


title: 1953 - Normal

description: normal oral tissue

source_name: 1953 - Normal


title: 1896 - CIS

description: oral carcinoma in situ


title: 1979 - Normal

description: normal oral tissue

source_name: 1979 - Normal


title: Rec114_rad53_HU_2

description: Rec114 ChIP in rad53 cells treated with HU biological replicate 2

value: 2 µg Myc antibody (9E11, Abcam)


title: 3002 - Normal

description: normal oral tissue

source_name: 3002 - Normal


title: Rec114_rad53_HU_1

description: Rec114 ChIP in rad53 cells treated with HU biological replicate 1


title: 1896 - Dysplasia

description: oral dysplasia

source_name: 1896 - Dysplasia


title: 1896 - Normal

description: normal oral tissue

source_name: 1896 - Normal


title: Rec114_mec1_HU_2

description: Rec114 ChIP in mec1 cells treated with HU biological replicate 2


title: 1878 - Dysplasia

description: oral dysplasia

source_name: 1878 - Dysplasia


title: 1858 - Dysplasia

description: oral dysplasia

source_name: 1858 - Dysplasia


title: 1878 - Normal

description: normal oral tissue

source_name: 1878 - Normal


title: 1878 - SCC

description: oral squamous cell carcinoma


title: Rec114_mec1_2

description: Rec114 ChIP in mec1 cells biological replicate 2


title: Rec114_rad53_1

description: Rec114 ChIP in rad53 cells biological replicate 1


title: Rec114_rad53_2

description: Rec114 ChIP inrad53 cells biological replicate 2


title: Rec114_mec1_1

description: Rec114 ChIP in mec1 cells biological replicate 1


title: Mre11_rad53_1

description: Mre11 ChIP in rad53 cells biological replicate 1


title: Mre11_mec1_HU_1

description: Mre11 ChIP in mec1 cells treated with HU biological replicate 1


title: Rec114_mec1_HU_1

description: Rec114 ChIP in mec1 cells treated with HU biological replicate 1


title: Mre11_rad53_HU_2

description: Mre11 ChIP in rad53 cells treated with HU biological replicate 2


title: Mre11_mec1_HU_2

description: Mre11 ChIP in mec1 cells treated with HU biological replicate 2


title: 1999 - Dysplasia

description: oral dysplasia

source_name: 1999 - Dysplasia


title: Mre11_mec1_2

description: Mre11 ChIP in mec1 cells biological replicate 2


title: Mre11_mec1_1

description: Mre11 ChIP in mec1 cells biological replicate 1


title: Mre11_HU_2

description: Mre11 ChIP in wild-type cells treated with HU biological replicate 2


title: 1858 - Normal

description: normal oral tissue

source_name: 1858 - Normal


title: 1858- SCC

description: oral squamous cell carcinoma


title: Rec114_HU_3

description: Rec114 ChIP in wild-type cells treated with HU biological replicate 3


title: Rec114_HU_2

description: Rec114 ChIP in wild-type cells treated with HU biological replicate 2


title: Mre11_HU_1

description: Mre11 ChIP in wild-type cells treated with HU biological replicate 1


title: AF_LAA_12

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2

label: Biotin

source_name: Atrial fibrillation_left atrial appendage_12

label_protocol: Standard Affymetrix protocol

extract_protocol: Cellular RNA Extration with TRIZOL

tag: organ

value: left atrial appendage

tag: age

tag: af duration


title: AF_LAPV_12

source_name: Atrial fibrillation_left atrial junction_12

value: left atrial junction


title: Mre11_rad53_2

description: Mre11 ChIP in rad53 cells biological replicate 2

source_name: meiotic budding yeast cells, 3 hours in SPO-medium


title: Mre11_rad53_HU_1

description: Mre11 ChIP in rad53 cells treated with HU biological replicate 1


title: AF_LAPV_8

source_name: Atrial fibrillation_left atrial junction_8


title: Rec114_HU_1

description: Rec114 ChIP in wild-type cells treated with HU biological replicate 1


title: Mer2_2

description: Mer2 ChIP in wild-type cells biological replicate 2


title: AF_LAA_7

source_name: Atrial fibrillation_left atrial appendage_7

value: female


title: Mer2_HU_1

description: Mer2 ChIP in wild-type cells treated with HU biological replicate 1


title: AF_LAA_15

source_name: Atrial fibrillation_left atrial appendage_15


title: AF_LAPV_4

source_name: Atrial fibrillation_left atrial junction_4


title: AF_LAPV_10

source_name: Atrial fibrillation_left atrial junction_10


title: AF_LAPV_11

source_name: Atrial fibrillation_left atrial junction_11


title: AF_LAA_11

source_name: Atrial fibrillation_left atrial appendage_11


title: Mer2_HU_2

description: Mer2 ChIP in wild-type cells treated with HU biological replicate 2


title: AF_LAA_8

source_name: Atrial fibrillation_left atrial appendage_8


title: AF_LAPV_16

source_name: Atrial fibrillation_left atrial junction_16


title: Mer2_1

description: Mer2 ChIP in wild-type cells biological replicate 1


title: AF_LAA_4

source_name: Atrial fibrillation_left atrial appendage_4


title: AF_LAA_10

source_name: Atrial fibrillation_left atrial appendage_10


title: AF_LAA_16

source_name: Atrial fibrillation_left atrial appendage_16


title: AF_LAA_13

source_name: Atrial fibrillation_left atrial appendage_13


title: AF_LAPV_13

source_name: Atrial fibrillation_left atrial junction_13


title: AF_LAPV_7

source_name: Atrial fibrillation_left atrial junction_7


title: AF_LAPV_3

source_name: Atrial fibrillation_left atrial junction_3


title: AF_LAA_2

source_name: Atrial fibrillation_left atrial appendage_2


title: AF_LAPV_2

source_name: Atrial fibrillation_left atrial junction_2


title: AF_LAA_6

source_name: Atrial fibrillation_left atrial appendage_6


title: AF_LAA_3

source_name: Atrial fibrillation_left atrial appendage_3


title: AF_LAPV_6

source_name: Atrial fibrillation_left atrial junction_6


title: AF_LAA_1

source_name: Atrial fibrillation_left atrial appendage_1


title: AF_LAPV_9

source_name: Atrial fibrillation_left atrial junction_9


title: AF_LAPV_1

source_name: Atrial fibrillation_left atrial junction_1


title: AF_LAA_14

source_name: Atrial fibrillation_left atrial appendage_14


title: Gli1+GFAP+ cells from cerebellum  rep 1

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

description: Gli1+ GFAP+ cells from the cerebellum

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
Quantile normalized gene level expression values from 3' RMA

organism: Mus musculus

source_name: Cerebellum

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

growth_protocol: Mouse brain cells isolated by FACS

extract_protocol: Adult mice (6-8 weeks, male) were treated with Tamoxifen (2 x 10mg), to label Shh-responding Gli1+ cells using tdTomato reporter mice. Three weeks later, SVZ, hippocampus and cerebellum were microdissected, dissociated, and FACS isolated for Gli1+ GFAP+ cells. Each sample contains 10-12 mice pooled.  Total RNA was isolated from each sample using Trizol and the Qiagen RNeasy Micro Kit Appendix C. Samples were then concentrated using Qiagen RNeasy MinElute Cleanup kit. cDNA synthesis and amplification was performed using WT-Ovation™ Pico RNA Amplification System (NuGEN)

treatment_protocol: Tamoxifen treatment for three weeks to lineage label Shh-responding cells

value: 6-8 week old male mice

value: FACS-isolated cells from cerebellum

tag: genotype


title: Gli1+GFAP+ cells from cerebellum  rep 5

description: Gli1+ GFAP+ cells from the cerebellum


title: Gli1+GFAP+ cells from Hippocampus,  rep 5

description: Gli1+ GFAP+ cells from the Hippcampus

source_name: Hippocampus

value: FACS-isolated cells from hippocampus


title: Sinus rhythm_LAA_3

source_name: Sinus rhythm_left atrial appendage_3


title: Gli1+GFAP+ cells from cerebellum  rep 3

description: Gli1+ GFAP+ cells from the cerebellum


title: Sinus rhythm_LAPV_3

source_name: Sinus rhythm_left atrial junction_3


title: Gli1+GFAP+ cells from cerebellum  rep 2

description: Gli1+ GFAP+ cells from the cerebellum


title: Gli1+GFAP+ cells from Hippocampus,  rep 2

description: Gli1+ GFAP+ cells from the Hippcampus


title: Gli1+GFAP+ cells from Hippocampus,  rep 1

description: Gli1+ GFAP+ cells from the Hippcampus


title: AF_LAPV_14

source_name: Atrial fibrillation_left atrial junction_14


title: Gli1+GFAP+ cells from Hippocampus,  rep 3

description: Gli1+ GFAP+ cells from the Hippcampus


title: Sinus rhythm_LAPV_2

source_name: Sinus rhythm_left atrial junction_2


title: Gli1+GFAP+ cells from SVZ, rep 5

description: Gli1+ GFAP+ cells from the SVZ

source_name: SVZ

value: FACS-isolated cells from SVZ


title: Sinus rhythm_LAPV_1

source_name: Sinus rhythm_left atrial junction_1


title: Gli1+GFAP+ cells from SVZ, rep 4

description: Gli1+ GFAP+ cells from the SVZ


title: Gli1+GFAP+ cells from SVZ, rep 3

description: Gli1+ GFAP+ cells from the SVZ


title: AF_LAPV_5

source_name: Atrial fibrillation_left atrial junction_5


title: Sinus rhythm_LAA_2

source_name: Sinus rhythm_left atrial appendage_2


title: Sinus rhythm_LAA_1

source_name: Sinus rhythm_left atrial appendage_1


title: Gli1+GFAP+ cells from SVZ, rep 2

description: Gli1+ GFAP+ cells from the SVZ


title: Gli1+GFAP+ cells from Hippocampus,  rep 4

description: Gli1+ GFAP+ cells from the Hippcampus


title: primary human B-precursor ALL_I1s

status: Public on Sep 17 2013

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: childhood B-precursor ALL

hyb_protocol: Total RNA underwent linear amplification in a two-step procedure, labeled and hybridized to each array according to the manufacturer's instructions using the small sample protocol.

scan_protocol: The Arrays were then washed using Affymetrix Fluidics Station 400, and scanned using a HP GeneArray scanner.

data_processing: The array image was acquired using the Affymetrix GeneChip Microarray Suite Software (v.5.0). The samles were normalized using the MAS5 method and scaled to a target value of 100.

source_name: primary human B-precursor ALL

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: total RNA was isolated from a minimum of 4x10e-3 mononuclear cells. RNA quality and quantity was assessed using a Agilent bioanalyzer.

tag: individual id

value: bone marrow

value: single sorted initial leukemia


title: AF_LAA_9

source_name: Atrial fibrillation_left atrial appendage_9


title: Gli1+GFAP+ cells from SVZ, rep 1

description: Gli1+ GFAP+ cells from the SVZ


title: AF_LAPV_15

source_name: Atrial fibrillation_left atrial junction_15


title: normal B-cell progenitor lymphoblasts_E4s

description: CD10+, CD19+ B-lymphoblasts

source_name: normal B-cell progenitor lymphoblasts

value: single sorted lymphoblasts in complete continuous remission


title: Gli1+GFAP+ cells from cerebellum  rep 4

description: Gli1+ GFAP+ cells from the cerebellum


title: primary human B-precursor ALL_I2s

description: childhood B-precursor ALL


title: primary human B-precursor ALL_I3s

description: childhood B-precursor ALL


title: normal B-cell progenitor lymphoblasts_E1s

description: CD10+, CD19+ B-lymphoblasts


title: normal B-cell progenitor lymphoblasts_E2s

description: CD10+, CD19+ B-lymphoblasts


title: primary human B-precursor ALL_I4

description: childhood B-precursor ALL TEL/AML1

value: Initial, untreated leukemia


title: normal B-cell progenitor lymphoblasts_E3s

description: CD10+, CD19+ B-lymphoblasts


title: primary human B-precursor ALL_I2

description: childhood B-precursor ALL


title: primary human B-precursor ALL_I1

description: childhood B-precursor ALL


title: primary human B-precursor ALL_I3

description: childhood B-precursor ALL


title: TiOblast8 DAY7

city: Chapel Hill

first: Lyndon

last: Cooper

state: NC

address: 330 Brauer Hall, CB#7450

department: Prosthodontics

institute: UNC School of Dentistry

hyb_protocol: The Encore Biotin Module V2-NuGen/Affymetrix Human gene 1.1 ST Array

scan_protocol: Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader

data_processing: The data was analyzed using GeneSpring software v.12.0

source_name: implant adherent cells-alveolar bone-microroughosurface implant-day7

label_protocol: Samples were processed and hybridized to the Affymetrix Human gene 1.1 ST Array at the UNC core facility following the manufacturer’s recommended protocols and reagents (Affymetrix, San Clara,CA). Labeling used Nugen Encore Biotin Module

growth_protocol: 11 Human subjects missing 2 or more teeth were included.Following anesthesia(Lidocaine 2% with epinephrine (1:100,000)), two separate crestal incisions approximately 6mm in length were made and full thickness mucoperiosteal flaps were raised. Each subject received two TIO and two OS implants. Two osteotomies were prepared per site to allow placement of one implant of each surface (1 TiO and 1 Os). This paired surgical design permitted the retrieval of the first 2 implants (1 of each surface) at the earlier time point without disturbing the healing of the other 2 implants. Drilling was completed using a 2.0 mm twist osteotomy drill under profuse irrigation with sterile saline. Single use osteotomy drills were used on each subject. All implants were placed by a self-tapping procedure and primary stability at the time of implant placement was insured. A submerged implant installation technique was used and the mucosal tissues were closed primarily with 4-0 chromic gut sutures.

extract_protocol: At 3 and 7 days following surgery, one surgical site was chosen at random, re-entered and the paired (One TIO and one OS) implants were removed by reverse threading. The implants were then immediately rinsed in cold PBS and then placed into 1000 ul of Tri-reagent (Invitrogen, Carlsbad, CA). Cell lysates were snap frozen, and stored at -80°C until further use.   Total RNA was isolated from the lysates using the standard Tri-reagent protocol and collected by ethanol precipitation. This was followed by purification using RNeasy MinElute Clean up kit (Qiagen, Valencia, CA, USA).  RNA was assessed for quality and quantity using a bioanalyzer (Agilent, Santa Clara, CA, USA) and nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE) respectively.

treatment_protocol: Fourty-four implants (cp titanium) were placed in the alveolar bone of 11 systemically healthy human subjects missing 2 or more teeth.Following anesthesia(Lidocaine 2% with epinephrine (1:100,000)), two separate crestal incisions approximately 6mm in length were made and full thickness mucoperiosteal flaps were raised. Each subject received two TIO and two OS implants. Two osteotomies were prepared per site to allow placement of one implant of each surface (1 TiO and 1 Os). This paired surgical design permitted the retrieval of the first 2 implants (1 of each surface) at the earlier time point without disturbing the healing of the other 2 implants. Drilling was completed using a 2.0 mm twist osteotomy drill under profuse irrigation with sterile saline. Single use osteotomy drills were used on each subject. All implants were placed by a self-tapping procedure and primary stability at the time of implant placement was insured. A submerged implant installation technique was used and the mucosal tissues were closed primarily with 4-0 chromic gut sutures

value: Female


title: TiOblast11 DAY7


title: PDL2-_BMDC_Untreated

city: New Haven

first: Ruoyi

last: Jiang

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale School of Medicine

description: Ex vivo DCs

hyb_protocol: Samples  were hybridized to a GeneChip Mouse Genome 430 Array.

scan_protocol: Samples were scanned at the Yale Center for Genome Analysis (YCGA).

data_processing: Scanned CEL files were background corrected, normalized and summarized using the oligo (2.12, Bioconductor) package.

source_name: WT PDL2- BMDCs Untreated

label_protocol: Samples were labelled at the Yale Center for Genome Analysis (YCGA).

growth_protocol: BMDCs were generated from bone marrow cultures of 1.0 x 106 cells per ml cultured for 5 days in granulocyte-macrophage colony-stimulating factor. BMDC populations were purified by flow cytometry.

extract_protocol: Total RNA from different DC subsets was isolated with RNeasy (QIAGEN).

treatment_protocol: BMDC populations were purified by flow cytometry based on PDL2 expression.

value: Untreated

tag: surface marker


title: TiOblast9 DAY7


title: rat_P2-2

city: Lyon

first: Ingrid

last: Kratzer

address: Rue Guillaume Paradin

country: France

institute: INSERM

description:
Sprague-Dawley rat_P2-2.
Gene expression data from CP of newborn rats.

hyb_protocol: Hybridization was performed according to the Affymetrix protocol (http://www.affymetrix.com). Briefly, 10 µg of labelled cRNA was fragmented and denaturated in hybridization buffer, then hybridized on a chip during 16 hours at 45°C with constant mixing by rotation at 60 rpm in a GeneChip hybridization oven 640 (Affymetrix). After hybridization, arrays were washed and stained with streptavidin-phycoerythrin (GeneChip® Hybridization Wash and Stain Kit) in a Fluidic 450 (Affymetrix) according to the manufacturer's instructions.

scan_protocol: The arrays were read with a confocal laser (GeneChip scanner 3000, Affymetrix). Then, CEL files were generated using the Affymetrix GeneChip Command Console (AGCC) software 3.0.

data_processing: The obtained data were normalized with Affymetrix Expression Console software using the MAS5 statistical algorithm. Two batches of animals were used for each stage and the mean value of both was used for further analysis.

organism: Rattus norvegicus

source_name: LVCP, P2

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated from two batches of 6 to 10 LVCP, sampled from E19, P2, and adult rats, using the RNeasy® Micro Kit (Qiagen, Valencia, CA, USA), and was DNase-treated according to the manufacturer's protocol. Total RNA was quantified using OD 260nm on a NanoDrop 2000c spectrophotometer (ThermoScientific, Baltimore, MA, USA) and quality was assessed with the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA). 100 ng of total RNA were amplified using the GeneChip 3' IVT Express Kit (Affymetrix).

value: Sprague-Dawley

tag: developmental stage

value: postnatal day 2

value: lateral ventricle choroid plexus


title: rat_Ad-2

description:
Sprague-Dawley rat_Ad-2.
Gene expression data from CP of adult rats.

source_name: LVCP, adult

value: adult


title: rat_E19-1

description:
Sprague-Dawley rat_E19-1.
Gene expression data from CP of embryos.

source_name: LVCP, E19

value: embryonic day 19


title: PDL2+_BMDC_Untreated

description: Ex vivo DCs

source_name: WT PDL2+ BMDCs Untreated


title: rat_E19-2

description:
Sprague-Dawley rat_E19-2.
Gene expression data from CP of embryos.


title: rat_P2-1

description:
Sprague-Dawley rat_P2-1.
Gene expression data from CP of newborn rats.


title: TiOblast10 DAY7

tag: gender


title: arcA mutant_CTRL_H2O2_REPLICATE_2

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

hyb_protocol: 42C overnight in standard hybridization buffer (Roche Nimblegen)

scan_protocol: GenePix4000B scanner (Molecular Devices, Sunnyvale, CA) using Acuity 4.0 software.

data_processing:
Signal extraction and quantitation with Roche’s NimbleScan 2.4 package
log base 10 ratios of contributions to total signal (experimental condition / control)
normalized based on total signal for each channel

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

label_protocol: Incorporation of dye using about 1200U Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA), 40ng/ul random hexamer primers, 4nmol Cy dUTP (GE Healthcare, Fairfield, CT), and 80U RNAse Inhibitor (Roche, Indianapolis, IN), in 60ul reactions. Reverse transcription was performed for 2h at 42˚C, and the pH adjusted with 50mM NaOH. After a 10min incubation at 70˚C reactions were neutralized using HCl. Labeled cDNA was purified using the QIAGEN PCR purification kit as suggested by the manufacturer (Qiagen, Valencia, CA).

extract_protocol: High Pure RNA isolation kit (Roche)

tag: genotype/variation

value: arcA mutant

tag: stress

value: CTRL

tag: growth protocol

value: arcA minus salmonella grown to OD600 0.4 in 25 ml LB medium, and treated with 1.5 mM H2O2 for 20 min. replicate 02


title: arcA mutant_CTRL_H2O2_REPLICATE_3

value: arcA minus salmonella grown to OD600 0.4 in 25 ml LB medium, and treated with 1.5 mM H2O2 for 20 min. replicate 03


title: rat_Ad-1

description:
Sprague-Dawley rat_Ad-1.
Gene expression data from CP of adult rats.

tag: tissue


title: PDL2-_BMDC_LPS

description: Ex vivo DCs

source_name: WT PDL2- BMDCs LPS 100 ng/mL

treatment_protocol: BMDC populations were purified by flow cytometry based on PDL2 expression and stimulated with LPS (100 ng/ml).

value: LPS Stimulated


title: AF_LAA_5

source_name: Atrial fibrillation_left atrial appendage_5

value: left atrial appendage

value: female


title: arcA mutant_CTRL_H2O2_REPLICATE_1

value: arcA minus salmonella grown to OD600 0.4 in 25 ml LB medium, and treated with 1.5 mM H2O2 for 20 min. replicate 01


title: WT_CTRL_H2O2_REPLICATE_2

value: WT

value: wt salmonella grown to OD600 0.4 in 25 ml LB medium, and treated with 1.5 mM H2O2 for 20 min. replicate 02


title: TiOblast7 DAY7

value: Female


title: normal_S98_307_expression

city: Cambridge

first: Ian

last: Roberts

address: Hills Road

department: Cancer Cell Unit

country: United Kingdom

institute: Hutchison MRC Research Centre

hyb_protocol: Standard Affymetrix hybridisation protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data analysis was done using Bioconductor R packages. Background correction and normalisation were performed using Robust Microarray Analysis (RMA) provided by the Affy package

source_name: normal uterine cervix

label_protocol: Standard Affymetrix labelling protocol

growth_protocol: Cell lines were cultured in 10% FCS + 90% GMEM + antibiotics, according to standard maintenance procedures

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

value: normal uterine cervix

tag: type

value: Normal


title: normal_S98_308_expression


title: HSIL_S98_66_expression_2

source_name: Squamous cell carcinoma

value: Squamous cell carcinoma

value: HSIL


title: LSIL_M0274_expression

value: LSIL


title: WT_CTRL_H2O2_REPLICATE_3

value: wt salmonella grown to OD600 0.4 in 25 ml LB medium, and treated with 1.5 mM H2O2 for 20 min. replicate 03


title: WT_CTRL_H2O2_REPLICATE_1

value: wt salmonella grown to OD600 0.4 in 25 ml LB medium, and treated with 1.5 mM H2O2 for 20 min. replicate 01


title: normal_S98_286_expression_2


title: normal_S98_306_expression


title: TiOblast4 DAY7

value: Male


title: LSIL_S96_742_expression_2


title: TiOblast3 DAY7


title: TiOblast5 DAY7


title: Salmonella_Typhimurium_ST4/74_yehUT_37c_rep3

city: Hinxton

first: Vanessa

middle: Kuan

last: Wong

state: Cambridgeshire

address: Wellcome Trust Genome Campus

department: Microbial Pathogenesis

institute: Wellcome Trust Sanger Institute

description: no additional information

hyb_protocol: Standard protocol from Agilent

scan_protocol: Standard protocol from Agilent, Agilent DNA High Resolution Microarray Scanner (Agilent, G2505C)

data_processing: Array Features were calculated using AFE default settings for the GE2-v5_10_Apr08. Using limma, a linear model fite was applied and the top differetnially expressed genes were tabulated for each contrast using the method of Benjamini and Hochberg to correct p-values

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: cultures

label_protocol: Cyanine 3-CTP standard protocol from agilent

growth_protocol: Culture at OD 0.6 at 600nm in LB broth

extract_protocol: Qiagen mini kit

treatment_protocol: Culure at 37c

value: ST4/74 yehUT

tag: culture temperature


title: normal_S98_293_expression


title: pancreas

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

description: Sample 10

hyb_protocol: The synthezied cRNA was then purified with RNeasy mini kit (Qiagen). 825ng of the corresponding Cy3 and Cy5 cRNA was fragmentated at 60°C for 30 min in the presence of blocking agent and fragmentation buffer (Agilent), then combined with 55ul 2X hybridization buffer (Agilent) and applied to 4X44k human expression microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an Agilent G2505 DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: pancreas from WT mice

label_protocol: 0.5µg of total RNA were primed with 1.2 µl of T7 promoter primer at 65°C for 10 min together with control spike A/B, then reversed transcribed at 40°C for 2hrs in the presence of MMLV RTase (Agilent), and dNTP mix. It was then followed by the cRNA transcription at 40°C for 2hrs in the presence of T7 RNA polymerase, inorganic pyrophosphatase, NTP mix, DTT, PEG and Cy3/Cy5-labeled-CTP.

growth_protocol: pancreas cultures were grown from single Lgr5 isolated cells (sample 1-2) or isolated pancreatic ducts (sample 3) and cultured as described in Material and Methods (See accompaning material and methods section)

extract_protocol: Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: for samples 4-5, to sort the Sox9+ population, Sox9CreERTxYFP mice were injected with tamoxifen 5x prior to sacrifice, as described in the accompaning Material and Methods.

value: pancreas from WT mice

tag: treatment

value: wildtype mice adult mice (>8weeks old)

tag: strain

source_name: mouse reference RNA (Stratagene)

tag: sample type

value: mouse reference RNA (Stratagene)


title: Salmonella_Typhimurium_ST4/74_yehUT_37c_rep1

description: no additional information


title: Salmonella_Typhimurium_ST4/74_yehUT_37c_rep2

description: no additional information


title: Salmonella_Typhimurium_ST4/74_yehT_37c_rep3

description: no additional information

value: ST4/74 yehT


title: islet_2

description: Sample 7-9 are biological replicates

source_name: pancreatic islets from WT mice

value: pancreatic islets from WT mice


title: normal_S97_277_expression_2


title: TiOblast2 DAY7


title: TiOblast1 DAY7


title: LSIL_M0212_expression


title: Salmonella_Typhimurium_ST4/74_yehT_37c_rep2

description: no additional information


title: LSIL_M0024_expression


title: HSIL_M0236_expression


title: LSIL_S98_154_expression


title: TiOblast6 DAY7


title: HSIL_S99_353_expression


title: Osseospeed11 DAY7

source_name: implant adherent cells-alveolar bone-nanosurface implant-day7


title: Salmonella_Typhimurium_ST4/74_yehU_37c_rep3

description: no additional information

value: ST4/74 yehU


title: Salmonella_Typhimurium_ST4/74_yehU_37c_rep2

description: no additional information


title: Salmonella_Typhimurium_ST4/74_yehT_37c_rep1

description: no additional information


title: islet_1

description: Sample 7-9 are biological replicates


title: Osseospeed10 DAY7


title: acinar cells

description: Sample 6

source_name: pancreatic acinar cells

tag: cell type

value: pancreatic acinar cells


title: normal_S98_303_expression


title: Salmonella_Typhimurium ST4/74_37c_rep2

description: no additional information


title: Salmonella_Typhimurium_ST4/74_37c_rep3

description: no additional information


title: duct  cells_1

description: Sample 4-5 are biological replicates

source_name: pancreas sox9 FACS sorted duct cells

value: pancreas sox9 FACS sorted duct cells

value: Sox9creERT2xRosaYFPinduced adult mice (>8weeks old)


title: duct cells_2

description: Sample 4-5 are biological replicates


title: islet_3

description: Sample 7-9 are biological replicates


title: Osseospeed7 DAY7

value: Female


title: HSIL_M0200_expression

value: Squamous cell carcinoma


title: LSIL_M0176_expression


title: Salmonella_Typhimurium_ST4/74_yehU_37c_rep1

description: no additional information


title: pancreas organoid_3

description: Sample 1-3 are biological replicates

source_name: pancreas organoids from WT mice

value: pancreas organoids from WT mice


title: Osseospeed5 DAY7


title: HSIL_M0159_expression

value: HSIL


title: Osseospeed9 DAY7


title: pancreas organoid_2

description: Sample 1-3 are biological replicates

source_name: pancreas organoids from Lgr5LAcZ mice

value: pancreas organoids from Lgr5LAcZ mice

value: Lgr5LacZ adult mice (>8weeks old)


title: Osseospeed6 DAY7


title: pancreas organoid_1

description: Sample 1-3 are biological replicates


title: HSIL_M0095_expression


title: LSIL_M0080_expression

value: LSIL


title: Osseospeed8 DAY7


title: Osseospeed2 DAY7

value: Male


title: HSIL_S97_703_expression


title: HSIL_M0132_expression


title: Salmonella_Typhimurium_ST4/74_37c_rep1

description: no additional information


title: Osseospeed4 DAY7


title: TiOblast11 DAY3

source_name: implant adherent cells-alveolar bone-microroughosurface implant-day3


title: normal_S98_284_expression

value: normal uterine cervix

value: Normal


title: Tumor-KO-rep4

city: Durham

first: Jian-Liang

last: Li

address: 111 TW Alexander Dr

institute: NIEHS

description:
replicate 4
Tumor-KO-rep4

data_processing: The data were normalized by log2 transformation, background subtraction and quantile normalization approach with Limma in R (v.2.15.0, 2012-03-30).

source_name: Tumor_Pdk1 knock out

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

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

tag: strain background

value: mixed C57BL/6, FVB, 129 background

value: BrafV600E::Pten-/-::Pdk1-/-, Pdk1 knock out

value: tumor


title: normal_S97_318_expression


title: Osseospeed3 DAY7


title: ALL 7293 remission

description: pediatric B-ALL sample after treatment (remission)

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
The array image was acquired using Affymetrix Command Console Software (version 2.0.1). Processing of the raw signals and raw copy-number calculation were performed using the CRMAv2 procedure of the aroma.affymetrix package (version 2.0.0) for R Statistical platform (version 2.12.1) according to the aroma.affymetrix vignette for paired total copy-number analysis. Circular Binary Segmentation (Ohlsen et al., 2004) was then applied using DNAcopy package for R Bioconductor to perform the segmentation. Affymetrix  "GenomeWideSNP_6.na30.annot.csv" annotation (Genome Build version hg18) was used.
Primary data description: Smoothed copy-number signal ratios and detected segments and segment mean values. Genome Build version hg18 was used.

extract_protocol: Genomic DNA was isolated from mononuclear cells from peripheral blood or bone marrow using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: individual

tag: disease

value: B-acute lymphoblastic leukemia

tag: disease status

value: remission


title: Osseospeed1 DAY7


title: Tumor-KO-rep2

description:
replicate 2
Tumor-KO-rep2


title: H1299 cells_pcDNA3.1 transfected

city: Guangzhou

first: Huihua

last: Zhang

address: 601, west Huangpu avenue, Tianhe district

department: Biomedicine Institute & Cell Biology Department

country: China

institute: Jinan University

description: Gene expression data from H1299 cells

hyb_protocol: 2 μg of pooled total RNA was reversed-transcribed, labeled, and hybridized to the chip at 42 °C for 16 h.

scan_protocol: GeneChips were scanned using the GeneArray scanner.

data_processing: RMA

source_name: Human H1299 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2012, Affymetrix).

growth_protocol: Transient recombinant cells were obtained from H1299 cells by the transfection of the recombinant vector or empty vector through the use of Lipofectamine® 2000 reagent

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

treatment_protocol: Cells transfected with an empty vector or with pcDNA-EGR1 plasmid were solubilized and homogenized in TRIzol

value: Lung

tag: cell line

value: control


title: H1299 cells_EGR1 transfected

description: Gene expression data from EGR1-transfected H1299 cells

value: EGR1 transfected


title: TiOblast9 DAY3

value: Female


title: Tumor-KO-rep3

description:
replicate 3
Tumor-KO-rep3


title: LSIL_M0099_expression

value: Squamous cell carcinoma


title: TiOblast10 DAY3


title: HSIL_S99_385C_expression

value: HSIL


title: normal_S98_286_expression


title: Tumor-KO-rep1

description:
replicate 1
Tumor-KO-rep1


title: HSIL_S99_382_expression


title: LSIL_M0045_expression


title: Tumor-WT-rep2

description:
replicate 2
Tumor-WT-rep2

source_name: Tumor_Pdk1 WT


title: ALL 7118 remission


title: TiOblast7 DAY3


title: TiOblast6 DAY3


title: TiOblast8 DAY3


title: TiOblast5 DAY3


title: ALL 6822 remission


title: Tumor-WT-rep3

description:
replicate 3
Tumor-WT-rep3


title: HSIL_S98_23_expression


title: Tumor-WT-rep4

description:
replicate 4
Tumor-WT-rep4


title: Tumor-WT-rep1

description:
replicate 1
Tumor-WT-rep1


title: ALL 6924 remission


title: ALL 7137 remission


title: ALL 6787 remission


title: ALL 6992 remission


title: TiOblast4 DAY3


title: ALL 7523 remission


title: HSIL_M0081_expression


title: TiOblast2 DAY3


title: HSIL_M0034_expression


title: ALL 7503 remission


title: HSIL_S96_660_expression


title: TiOblast3 DAY3


title: ALL 7065 remission


title: ALL 6965 remission


title: normal_S98_296_expression


title: HSIL_S99_386C_expression


title: Osseospeed11 DAY3

source_name: implant adherent cells-alveolar bone-nanosurface implant-day3


title: ALL 7360 remission


title: TiOblast1 DAY3


title: ALL 7115 remission


title: Osseospeed10 DAY3


title: LSIL_M0059_expression


title: ALL 7191 remission


title: ALL 7077 remission


title: HSIL_M0041_expression


title: Osseospeed8 DAY3


title: ALL 6923 remission


title: Osseospeed6 DAY3


title: Osseospeed9 DAY3


title: HSIL_S99_211_C3_expression


title: ALL 7021 remission


title: HSIL_S99_175_expression


title: LSIL_S96_742_expression


title: Osseospeed5 DAY3


title: Osseospeed7 DAY3


title: Osseospeed4 DAY3


title: normal_S97_277_expression


title: HSIL_S98_66_expression


title: ALL 6845 remission


title: Osseospeed2 DAY3


title: ALL 6869 remission


title: HSIL_S99_394_C_expression


title: ALL 7293 initial

description: pediatric B-ALL sample before treatment

value: initial


title: Osseospeed3 DAY3


title: ALL 6646 remission


title: fast HCV fibrosis progression patient 10 group B

city: london

first: siamak

last: salehi

address: denmark hill

department: liver studies

institute: kings college hospital

description: archived formalin fixed histology sample

hyb_protocol: After labeling, 21.5 ug of RNA was hybridized for 16 hr at 48°C on GeneChip miRNA 2.0  Arrays . GeneChips were washed and stained in the Affymetrix Genechip fluidis 450 station.

scan_protocol: Hybridized samples were scanned using Genechip scanner 3000 7G (Affymetrix)

data_processing: miRNA QC Tool v1.0.33.0 ,  algoirthm  Default  was used with the following settings:  Detection ( Background detection), Background adjustment (BC-CG Adjustment),  Normalization (Quantile), Other Process (Add small constant, CVS tab), Other Processes (Threshhold), Summarization ( Median Polish))

source_name: liver biopsy

label_protocol: Total RNA containing miRNA was enriched using microcon YM-100 centrifugal  filter device ( Millipore Cat no: 42413,) according to the manufacturer's protocol. 100 ng of enriched RNA was labeled using Flashtag biotin RNA labeling kit ( Genisphere) according to protocol by Genisphere for labeling RNA for affymetrix Genechip RNA.

extract_protocol: High Pure FFPE RNA Micro Kit ( Roche Applied Sciences) was used to extract  total RNA from FFPE liver sections or slides according  to manufacturers instructions

treatment_protocol: FFPE sections and samples were processed using the FFPE RNA pure kit from Roche, following the manufacturer's protocol.

tag: disease state

value: fast HCV fibrosis progression

value: liver biopsy


title: fast HCV fibrosis progression patient 11 group B


title: ALL 7118 initial

description: pediatric B-ALL sample before treatment


title: Root_serf1_rep3

city: Potsdam

first: Jos

last: Schippers

address: Am Muehlenberg 1

department: Plant Signaling

institute: MPIMP-golm

hyb_protocol: Hybridizations against Affymetrix 57k Rice Genome GeneChip chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 10 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

scan_protocol: GeneChips were scanned by use of the Affymetrix GeneChip Workstation Scanner 3000.

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

organism: Oryza sativa

source_name: 4-week_old root

label_protocol: biotin label. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: Plants were grown for  4 weeks at (day/night) 26/22°C, 75/70% relative humidity with a day-length of 12 h and a light intensity of 700 µmol m-2 s-1.

extract_protocol: Total RNA was isolated with a Qiagen Rnaeasy extraction kit

treatment_protocol: Seeds of serf1 T-DNA lines and Nipponbare wild type were placed on hydroponic boxes with full-strength Yoshida medium (Yoshida et al., 1971) using styrofoam adaptors.

tag: developmental stage

value: vegetative stage

value: roots


title: slow HCV fibrosis progression patient 11 group A

value: slow HCV fibrosis progression


title: slow HCV fibrosis progression patient 10 group A


title: HSIL_M0001_expression

source_name: Squamous cell carcinoma


title: Bcells-Quiescent-B3

city: Baltimore

first: Kasper

middle: Daniel

last: Hansen

address: 615 N Wolfe St. E3527

department: Biostatistics

institute: Johns Hopkins

description:
B3_resting
Resting B-cells from individual B3

hyb_protocol: affymetrix hyb protocol

scan_protocol: affymetrix 7G gene chip scanner

data_processing: data were processed using the frma package from Bioconductor, using the frma method described in McCall MN, Bolstad BM, and Irizarry RA (2010). Frozen Robust Multi-Array Analysis (fRMA), Biostatistics, 11(2):242-253, and the barcode method (used for presence/absence calls) described in McCall MN, Uppal K, Jaffee HA, Zilliox MJ, and Irizarry RA (2011). The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes, Nucleic Acids Research, 39:D1011-5.

source_name: Bcells-Quiescent

label_protocol: 3 prime IVT express

extract_protocol: Qiagen Rneasy

treatment_protocol: Cells were either resting, CD40 activated or EBV transformed

tag: individual/donor id

value: B-cell

tag: sample group

value: Quiescent


title: Bcells-Activation-B3

description:
B3_activation
Activated B-cells from individual B3

source_name: Bcells-Activation

value: CD40 activated


title: Bcells-EBV_Transformed_B3

description:
B3_EBV
EBV transformed B-cells from Individual B3

value: EBV transformed


title: Root_wildtype_rep3

tag: genotype/variation

value: wildtype


title: Root_wildtype_rep2

tag: tissue


title: Root_wildtype_rep1


title: Root_serf1_rep2


title: ALL 6822 initial

description: pediatric B-ALL sample before treatment

value: B-acute lymphoblastic leukemia


title: Root_serf1_rep1


title: Bcells-Quiescent-B2

description:
B2_resting
Resting B-cells from individual B2


title: Osseospeed1 DAY3

tag: gender


title: ALL 7137 initial

description: pediatric B-ALL sample before treatment


title: fast HCV fibrosis progression patient 8 group B


title: slow HCV fibrosis progression patient 8 group A


title: Bcells-EBV_Transformed_B2

description:
B2_EBV
EBV transformed B-cells from Individual B2


title: ALL 6924 initial

description: pediatric B-ALL sample before treatment


title: ALL 6787 initial

description: pediatric B-ALL sample before treatment


title: fast HCV fibrosis progression patient 7 group B


title: ALL 6992 initial

description: pediatric B-ALL sample before treatment


title: Bcells-Activation-B2

description:
B2_activation
Activated B-cells from individual B2


title: 2557

city: Lodnon

first: Xiufen

last: Zheng

state: Ontario

address: 339 windermere Road,LHSC-UC, B4-235

department: Pathology

institute: university of Western Ontario

description:
E1047.CEL
Gene expression data from the I/R injured heart graft 24 h after heart transplantation

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. 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 with Partek Genomcis Suite(v.6.6) using the RMA normalization method

source_name: mouse heart graft tissue with 18h cold ischemia before heart transplantation

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Ambion Whole Transcript (WT) Sense Target Labeling Assay Manual and Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual

growth_protocol: heart grafts were harvested from recipients 24h after heart transplantation

extract_protocol: Total RNA was extracted using miRNEasy mini kit from Qiagen according to manufacturer's instruction

treatment_protocol: Donor hearts were preserved with University of Wisconsin solution for 18h at 4 C degree before being implanted into recipients.

value: 18h cold ischemia reperfusion injured heart

tag: time point

value: 24 h after heart transplantation


title: ALL 7523 initial

description: pediatric B-ALL sample before treatment


title: slow HCV fibrosis progression patient 9 group A


title: 2556

description:
E1046.CEL
Gene expression data from the control heart graft 24 h after heart transplantation

source_name: mouse heart graft tissue without 18h cold ischemia before heart transplantation

value: heart tissue without 18h cold ischemia reperfusion


title: Bcells-Quiescent-B1

description:
B1_resting
Resting B-cells from individual B1


title: Bcells-EBV_Transformed_B1

description:
B1_EBV
EBV transformed B-cells from Individual B1


title: 2555

description:
E1045.CEL
Gene expression data from the I/R injured heart graft 24 h after heart transplantation


title: ALL 7503 initial

description: pediatric B-ALL sample before treatment


title: slow HCV fibrosis progression patient 7 group A


title: slow HCV fibrosis progression patient 6 group A


title: 2553

description:
E1043.CEL
Gene expression data from the I/R injured heart graft 24 h after heart transplantation


title: Bcells-Activation-B1

description:
B1_activation
Activated B-cells from individual B1


title: 2554

description:
E1044.CEL
Gene expression data from the control heart graft 24 h after heart transplantation


title: fast HCV fibrosis progression patient 6 group B


title: HT29 at 10 μM of 5-Aza, biological rep3

city: Stony Brook

first: Xiao

last: Xu

address: Stony Brook University

institute: Stony Brook University BME

description: RNA samples from human colon cancer HT29 cell line

hyb_protocol: The biotinylated cRNA was hybridized on the Affymetrix hgu133 plus2.0 arrays. Gene chips were washed and stained using the Affymetrix GeneChip® Fluidics Station 450

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip® Scanner 3000 7G

data_processing: Gene expression intensities were initially extracted from the CEL files and proceeded with 75% percentile scalling and RMA normalization. Subsequently a filter step was applied to remove probes with one or more absence flags in a given group. The software we used for data normalization are GeneSpring GX (Agilent Inc) and R bioconductor package affy (v 1.14.2).

source_name: HT29 treated with 10 μM of 5-Aza

label_protocol: standard Affymetrix protocol

growth_protocol: HT-29 colon cancer cells were cultured as monolayers in 150 mm dishes in DMEM with 10% fetal bovine serum, 1% kanamycin, streptomycin-penicillin  at 37 CO2 5% .

extract_protocol: Each monolayer was washed with PBS, scraped and centrifuged into a pellet.  RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.

treatment_protocol: Triplicate cultures of HT-29 cells were treated in the following three experimental groups: 1.) Vehicle (DMSO) alone or 0 µM 5-Aza-deoxycytidine (5-Aza); 2.) 5 µM 5-Aza; 3.) 10 µM 5-Aza

value: Human colon cancer cell line

tag: treatment

value: 10 μM of 5-Aza


title: HT29 at 10 μM of 5-Aza, biological rep2


title: Kidney_Biopsy_Liver_Disease_7

city: Bronx

first: Pilib

last: Ó Broin

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description:
L16
Gene expression data from kidney biopsy of liver disease patient

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing: Probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average method from the R/Bioconductor (http://bioconductor.org) oligo package. Array quality control was performed to remove arrays that significantly differed in initial overall probe intensity. Expression values were analyzed on the log base 2 scale. Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and log-posterior odds of differential expression. Gene set analysis was performed using the limma romer method. Gene set used were taken from the Molecular Signatures Database (MSigDB) Pathogenesis Based Transcripts (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets from the University of Alberta, Edmonton. Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeomtric p-values for over or under-representation of each GO term. Biopsy and blood sample were processed separately.

label_protocol: Labelled as per manufacturer's instruction in Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: Biopsy cores were immediately placed into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours and then transferred to -70°C until RNA isolation.  Renal tissue content in all cores was verified using a dissecting microscope and non-renal tissue was removed. Total RNA was isolated using the QIAGEN RNeasy Mini Kit (Catalog Number 74104, Qiagen, USA)

treatment_protocol: A standard percutaneous kidney biopsy was performed under ultrasound guidance using an 18G-biopsy needle. Biopsy specimens prepared for light microscopy (LM) were formalin-fixed, paraffin-embedded and stained with hematoxylin-eosin and Periodic Acid Schiff reagents. Glutaraldehyde-fixed tissue was processed for electron microscopy (EM). Direct immunofluorescence (IF) studies used polyclonal antibodies for IgA, IgG, IgM, and C3 and C1q components of complement. All biopsies were reviewed by a single experienced renal pathologist at our institution.

tag: mortality

value: alive

tag: ethnicity

value: White

value: M

tag: age (yrs)

tag: ld

value: HCV

tag: creatnine

tag: mdrd

tag: gfr

tag: protein

tag: hematuria

tag: rf

value: neg

tag: hcv

value: POS

tag: htn

tag: dm

value: NEG

tag: meld

tag: ana

value: UN

tag: gp

value: ATN, mild IFTA, moderate arterisclerosis

tag: mm (mesangial matrix expansion)

tag: mc (mesangial cell increase)

tag: ii (interstitial inflammation)

tag: podocyte

tag: bm (basement membrane thickening)

tag: ta (tubular atrophy)

tag: if (interstital fibrosis)

tag: as (arteiosclerosis)

tag: igg

tag: iga

tag: igm

tag: c

tag: empe

tag: bmwid

tag: bmd

tag: edd

tag: no of glomeruli

tag: glomerulosclerosis

tag: intact t

tag: arteries

value: moderate intimal fibrois

tag: if

value: IGG+IGA+

tag: mesangium ig

value: A


title: ALL 7065 initial

description: pediatric B-ALL sample before treatment

tag: individual

tag: disease

value: B-acute lymphoblastic leukemia

tag: disease status

value: initial


title: ALL 7360 initial

description: pediatric B-ALL sample before treatment


title: Kidney_Biopsy_Liver_Disease_6

description:
L13
Gene expression data from kidney biopsy of liver disease patient

tag: mortality

tag: ethnicity

value: African American

tag: gender

tag: age (yrs)

tag: ld

tag: creatnine

tag: mdrd

tag: gfr

tag: protein

tag: hematuria

tag: rf

tag: hcv

tag: htn

tag: dm

tag: meld

tag: ana

tag: gp

value: Mild mesangial immune complex glomerulonephritis, Severe tubular atrophy

tag: mm (mesangial matrix expansion)

tag: mc (mesangial cell increase)

tag: ii (interstitial inflammation)

tag: podocyte

tag: bm (basement membrane thickening)

tag: ta (tubular atrophy)

tag: if (interstital fibrosis)

tag: as (arteiosclerosis)

tag: igg

value: intimal duplication

value: MGC

tag: tissue


title: Kidney_Biopsy_Liver_Disease_8

description:
L17
Gene expression data from kidney biopsy of liver disease patient

tag: mortality

value: alive

tag: ethnicity

value: Hispanic

tag: gender

value: F

tag: age (yrs)

tag: ld

tag: creatnine

tag: mdrd

tag: gfr

tag: protein

tag: hematuria

tag: rf

value: MESANGAIL PROLIFEATION,Ig A nephropathy

tag: iga

tag: igm

tag: c

tag: empe

tag: bmwid

tag: bmd

tag: edd

tag: no of glomeruli

tag: glomerulosclerosis

tag: intact t

tag: arteries

value: intimal fibrosis,duplication n widening

tag: if

value: IGG+IGM+IGA+++C1Q+ mesangial only IgG and focal capillary walls

tag: mesangium ig


title: HT29 at 10 μM of 5-Aza, biological rep1

tag: tissue

value: Human colon cancer cell line

tag: cell line

tag: treatment

value: 10 μM of 5-Aza


title: fast HCV fibrosis progression patient 5 group B

description: archived formalin fixed histology sample

tag: disease state

value: fast HCV fibrosis progression

value: liver biopsy


title: acute cellular rejection patient 4 group C

value: acute cellular rejection


title: acute cellular rejection patient 5 group C


title: ALL 6965 initial

description: pediatric B-ALL sample before treatment

tag: individual

tag: disease

value: B-acute lymphoblastic leukemia

tag: disease status


title: ALL 7115 initial

description: pediatric B-ALL sample before treatment

value: initial


title: HT29 at 5 μM of 5-Aza, biological rep3

source_name: HT29 treated with 5 μM of 5-Aza

value: 5 μM of 5-Aza


title: Kidney_Biopsy_Liver_Disease_5

description:
L12
Gene expression data from kidney biopsy of liver disease patient

tag: mortality

tag: ethnicity

tag: gender

value: M

tag: age (yrs)

tag: ld

value: ETOH

tag: creatnine

tag: mdrd

tag: gfr

tag: protein

tag: hematuria

tag: rf

tag: hcv

value: NEG

tag: htn

tag: dm

tag: meld

tag: ana

value: POS

tag: gp

value: Mesangial Immune complex deposit, lupus class II

tag: mm (mesangial matrix expansion)

tag: mc (mesangial cell increase)

tag: ii (interstitial inflammation)

tag: podocyte

tag: bm (basement membrane thickening)

tag: ta (tubular atrophy)

tag: if (interstital fibrosis)

tag: as (arteiosclerosis)

tag: igg

tag: iga

tag: igm

tag: c

tag: empe

value: P

value: intimal fibrosis, thickening

value: ACMG


title: ALL 7191 initial

description: pediatric B-ALL sample before treatment

tag: individual

tag: disease

tag: disease status


title: slow HCV fibrosis progression patient 5 group A

tag: disease state

value: slow HCV fibrosis progression

tag: tissue


title: HCV negative patients patient 4 group D

value: HCV negative patients


title: Kidney_Biopsy_Liver_Disease_4

description:
L3
Gene expression data from kidney biopsy of liver disease patient

tag: mortality

value: dead

tag: ethnicity

value: Hispanic

tag: gender

value: F

tag: age (yrs)

tag: ld

value: HCV

tag: creatnine

tag: mdrd

tag: gfr

tag: protein

tag: hematuria

tag: rf

tag: hcv

tag: htn

tag: dm

tag: meld

tag: ana

tag: gp

value: Nodular glomerulosclerosis, Diabetic Nephropathy

tag: mm (mesangial matrix expansion)

tag: mc (mesangial cell increase)

tag: bmwid

tag: bmd

tag: edd

tag: no of glomeruli

tag: glomerulosclerosis

tag: intact t

tag: arteries

value: duplication

tag: if

value: IGG+IGM++IGA+C3+C1q+ capillary wall linear

tag: mesangium ig

value: O


title: HT29 at 5 μM of 5-Aza, biological rep1

tag: tissue

value: Human colon cancer cell line

tag: cell line

tag: treatment

value: 5 μM of 5-Aza


title: ALL 6923 initial

description: pediatric B-ALL sample before treatment

tag: individual

tag: disease

value: B-acute lymphoblastic leukemia

tag: disease status

value: initial


title: HT29 at 0 μM of 5-Aza, biological rep3

source_name: HT29 treated with 0 μM of 5-Aza

value: 0 μM of 5-Aza


title: Kidney_Biopsy_Liver_Disease_3

description:
L7
Gene expression data from kidney biopsy of liver disease patient

tag: mortality

value: alive

tag: ethnicity

value: African American

tag: gender

value: M

tag: age (yrs)

tag: ld

tag: creatnine

tag: mdrd

tag: gfr

tag: protein

tag: hematuria

tag: rf

tag: hcv

value: POS

tag: htn

tag: dm

tag: meld

tag: ana

value: NEG

tag: gp

value: Mesangial GN+ 2nd FSGS

tag: mm (mesangial matrix expansion)

tag: ii (interstitial inflammation)

tag: podocyte

tag: bm (basement membrane thickening)

tag: ta (tubular atrophy)

tag: if (interstital fibrosis)

tag: as (arteiosclerosis)

tag: igg

tag: iga

tag: igm

tag: c

tag: empe

value: normal

value: IGG+IGM+IGA++C3+ mesangial

value: AMC


title: Kidney_Biopsy_Liver_Disease_2

description:
L8
Gene expression data from kidney biopsy of liver disease patient

tag: mortality

tag: ethnicity

value: White

tag: gender

tag: age (yrs)

tag: ld

value: ETOH

tag: creatnine

tag: mdrd

tag: gfr

tag: protein

tag: hematuria

tag: rf

tag: hcv

tag: htn

value: normal parenchyma by LM and IF, limited sample

tag: mc (mesangial cell increase)

tag: bmwid

tag: bmd

tag: edd

value: P

tag: no of glomeruli

tag: glomerulosclerosis

tag: intact t

tag: arteries

tag: if

value: IGM+ mesangial

tag: mesangium ig

tag: tissue


title: ALL 7077 initial

description: pediatric B-ALL sample before treatment

tag: individual

tag: disease

value: B-acute lymphoblastic leukemia

tag: disease status


title: fast HCV fibrosis progression patient 4 group B

tag: disease state

value: fast HCV fibrosis progression

value: liver biopsy


title: Kidney_Biopsy_Liver_Disease_1

description:
L9
Gene expression data from kidney biopsy of liver disease patient

tag: mortality

value: alive

tag: ethnicity

value: Hispanic

tag: gender

value: F

tag: age (yrs)

tag: ld

value: HCV

tag: creatnine

tag: mdrd

tag: gfr

value: UN

tag: protein

tag: hematuria

tag: rf

value: neg

tag: hcv

tag: dm

tag: meld

tag: ana

tag: gp

value: arterisclerosis, mild mesangial expansion

tag: mm (mesangial matrix expansion)

tag: ii (interstitial inflammation)

tag: podocyte

tag: bm (basement membrane thickening)

tag: ta (tubular atrophy)

tag: if (interstital fibrosis)

tag: as (arteiosclerosis)

tag: igg

tag: iga

tag: igm

tag: c

tag: empe

value: intimal duplication/fibrosis

value: not submitted


title: slow HCV fibrosis progression patient 4 group A

tag: disease state

value: slow HCV fibrosis progression

tag: tissue


title: acute cellular rejection patient 3 group C

value: acute cellular rejection


title: HT29 at 5 μM of 5-Aza, biological rep2

value: Human colon cancer cell line

tag: cell line

tag: treatment

value: 5 μM of 5-Aza


title: ALL 6646 initial

description: pediatric B-ALL sample before treatment

tag: individual

tag: disease

tag: disease status

value: initial


title: HCV negative patients patient 3 group D

value: HCV negative patients


title: HT29 at 0 μM of 5-Aza, biological rep1

value: 0 μM of 5-Aza


title: fast HCV fibrosis progression patient 3 group B

value: fast HCV fibrosis progression

value: liver biopsy


title: ALL 7021 initial

description: pediatric B-ALL sample before treatment

value: B-acute lymphoblastic leukemia


title: Normal_Kidney_Biopsy_9

description:
6V0
Gene expression data from normal kidney biopsy sample

tag: mortality

value: alive

tag: ethnicity

value: African American

tag: gender

value: M

tag: age (yrs)


title: slow HCV fibrosis progression patient 3 group A


title: SCC_N8_expression

value: Squamous cell carcinoma

tag: type

value: SCC


title: Normal_Kidney_Biopsy_8

description:
14V0
Gene expression data from normal kidney biopsy sample

value: White

value: F


title: HT29 at 0 μM of 5-Aza, biological rep2


title: acute cellular rejection patient 2 group C


title: Normal_Kidney_Biopsy_7

description:
18V0
Gene expression data from normal kidney biopsy sample

value: Asian


title: SCC_G22_expression


title: SCC_88_05_expression


title: HCV negative patients patient 2 group D


title: SCC_G11_expression


title: ALL 6845 initial

description: pediatric B-ALL sample before treatment


title: ALL 6869 initial

description: pediatric B-ALL sample before treatment


title: Normal_Kidney_Biopsy_6

description:
20V0
Gene expression data from normal kidney biopsy sample


title: slow HCV fibrosis progression patient 2 group A

value: slow HCV fibrosis progression


title: Normal_Kidney_Biopsy_4

description:
26V0
Gene expression data from normal kidney biopsy sample


title: HCV negative patients patient 1 group D


title: Normal_Kidney_Biopsy_3

description:
29V0
Gene expression data from normal kidney biopsy sample


title: SCC_58a_expression


title: Normal_Kidney_Biopsy_5

description:
23V0
Gene expression data from normal kidney biopsy sample

value: Hispanic


title: acute cellular rejection patient 1 group C

value: acute cellular rejection


title: fast HCV fibrosis progression patient 1 group B


title: SCC_54_05_expression


title: slow HCV fibrosis progression patient 1 group A


title: SCC_72_05_expression


title: muscle Smad4KO 2 denervated 14 days

city: Padua

first: Marco

last: Sandri

address: via Orus,2

institute: VIMM (Venetian Institute of Molecular Biology)

description: Gene expression after 14 days of denervation

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction,  55 μl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) 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 at 37°C with GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Gastrocnemius muscle denervated 14 days, Smad4 KO mouse

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) (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.

extract_protocol: Total RNA was prepared from Gastrocnemius muscles using TRIzol (Life Technologies) following the manufacturer's recommendations.Then a clean-up step and an on-column DNase I treatment were performed using Rneasy Fibrous Tissue Mini Kit (QIAGEN). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: whole Gastrocnemius

value: adult male

tag: strain


title: muscle Smad4KO 2 control

description: Gene expression in control muscle

source_name: Gastrocnemius muscle, Smad4 KO mouse


title: Normal_Kidney_Biopsy_1

description:
32V0
Gene expression data from normal kidney biopsy sample


title: SCC_G23_expression


title: SCC_G14_expression


title: SCC_76_05_expression


title: muscle Smad4KO 3 denervated 14 days


title: CellLine_CaSki_expression

description: CaSki

source_name: metastatic site: small bowel mesentary

value: CaSki

value: CellLine


title: muscle Smad4KO 3 control

description: Gene expression in control muscle


title: ASC_lean_biological rep1

city: Barcelona

first: Lina

last: Badimon

address: St Antoni M Claret, 167

department: ICCC-Cardiovascular Program

country: Spain

institute: Research Institut- HSCSP

description: Gene expression data from ASC isolated from subcutaneous WAT of lean individual 1

hyb_protocol: Labeled and fragmented samples were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0ST Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The raw data (.CEL files) was processed using Robust Multi-array Average (RMA) algorithm, implemented by Expression Console 1.1.1. software (Affymetrix default settings).

source_name: ASC, non-obese individual (ASCn)

label_protocol: After preprocessation of 200 ng of RNA, for each sample, with Ambion WT Expression kit (User Guide  P/N 4425209 Rev.C 09/2009, Ambion), biotinylated DNA were prepared using the Affymetrix GeneChip Terminal Labeling kit from 5,5 ug of ssDNA  (GeneChip WT Terminal, Labeling and Hibridization User Manual , P/N 702808 Rev.7 2009, Affymetrix) according to manufacturers' guidelines.

growth_protocol: Human subcutaneous adipose tissue was washed, minced and digested with collagenase I-A. The digested tissue was sequentially filtered and centrifuged. The pellet was resuspended in culture medium, seeded and incubated overnight under hypoxic (1% O2) conditions. Adherent cells were referred as ASC. Cells were growth under hypoxic conditions, and culture medium was change every 2-3 days, as described previously (Oñate et al., FASEB J, 2012; 26:4327-36).

extract_protocol: Total cell RNA was extracted using silica-membrane columns (RNesasy Mini Kit, Qiagen) according to the manufacturer's instructions.

treatment_protocol: ASC at passage 1 were cryopreserved until subcultivation. Cells were growth under hypoxic conditions. ASC at passage 3 were used for RNA extraction.

tag: cells origin

value: subcutaneous white adipose tissue

tag: individual characteristics

value: Non-obese individual


title: SCC_K7_expression


title: Normal_Kidney_Biopsy_2

description:
31V0
Gene expression data from normal kidney biopsy sample

value: alive


title: muscle Smad4KO 1 denervated 14 days


title: muscle Smad4KO 1 control

description: Gene expression in control muscle


title: E 18 thymic settling progenitors 3

city: Paris

first: Ana

last: Cumano

address: 25 Rue du Dr. Roux

department: Immunology

institute: Pasteur Institute

description: Gene expression of freshly isolated murine E18 thymocytes

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray  processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent  Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was  hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays  8x60K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s  Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the  microarray image files. The software determines feature intensities (including background  subtraction), rejects outliers and calculates statistical confidences. For determination of  differential gene expression FES derived output data files were further analyzed using the  Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware). This  software offers – among other features – the possibility to compare two single intensity  profiles in a ratio experiment (table 4). All samples were labeled with Cy3, here, the ratio  experiments are designated as control versus (vs.) sample experiments (automated data  output of the Resolver system).  Please note, that the ratios are always calculated by dividing sample signal intensity through  control signal intensity.

source_name: thymocytes

label_protocol: The complete amount of each total RNA sample (except 1 μl backup) was used for the T7 based amplification step. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following  the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Freshly isolated thymocytes were depleted of lineage negative cells and thymic settling progenitors were sorted on a MoFlo cell sorted directly to RLT buffer.

extract_protocol: RNA was isoalted using the MicroRNAeasy kit from Quiagen France that included a DNAse treatment according to the manufacture's instructions. RNA quality was checked in an Agilent 2100 Bioanalyzer  platform (Agilent Technologies).

value: Thymocytes

tag: age

value: Embryonic day 18


title: ASC_morbidly-obese_bilogical rep3

description: Gene expression data from ASC isolated from subcutaneous WAT of morbidly obese patient 3

source_name: ASC, obese patient (ASCmo)

value: Morbidly obese patient


title: ASC_lean_biological rep3

description: Gene expression data from ASC isolated from subcutaneous WAT of lean individual 3


title: E 13 thymic settling progenitors 3

description: Gene expression of freshly isolated murine E13 thymocytes

value: Embryonic day 13


title: ASC_lean_biological rep2

description: Gene expression data from ASC isolated from subcutaneous WAT of lean individual 2


title: E 18 thymic settling progenitors 1


title: CellLine_MS751_expression

source_name: metastatic site: lymph node


title: muscle WT 3 denervated 14 days

source_name: Gastrocnemius muscle denervated 14 days, WT mouse


title: muscle WT 2 control

description: Gene expression in control muscle

source_name: Gastrocnemius muscle, WT mouse


title: SCC_87_expression

source_name: Squamous cell carcinoma

value: Squamous cell carcinoma

value: SCC


title: E 13 thymic settling progenitors 2


title: 2557 [miRNA]

hyb_protocol: 1.0 ug of labeled RNA was hybridized for 16 hr at 48C on GeneChip miRNA 3.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

label_protocol: 1.0 ug of total RNA was labeled using the Flash Tag Biotin HSR kit form Genisphere

extract_protocol: Total RNA was extracted using miRNEasy mini kit from Qiagen  according to manufacturer's instruction

treatment_protocol: Donor hearts were preserved  with University of Wisconsin solution for 18h at 4 C degree before being implanted into recipients.

tag: strain background

value: 18h cold ischemia reperfusion injured heart

tag: time point

value: 24h after transplantation


title: E 18 thymic settling progenitors 2

tag: tissue


title: muscle WT 2 denervated 14 days


title: muscle WT 3 control

description: Gene expression in control muscle


title: ASC_morbidly-obese_biological rep1

description: Gene expression data from ASC isolated from subcutaneous WAT of morbidly obese patient 1


title: SCC_71_05_expression


title: En1282_8dpi_BerhcJ_rep2

city: Fuchu

first: Shin

last: OKAZAKI

state: Tokyo

address: 3-5-8 Saiwaicho

country: Japan

institute: Tokyo University of Agriculture and Technology

description: Gene expression in soybean roots after 8 days post inoculation

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized to Agilent G. max (Soybean) Oligo Microarray 4x44K (arrayID:016772) 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: After hybridization, the microarray slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides at two laser power settings (100% and 10%).

data_processing: The scanned images were analyzed with Agilent’s Feature Extraction Software (v 9.5.1) to obtain background subtracted and spatially detrended Processed Signal intensities. The data were then normalized subjected to 75 percentile normalization and log2 transformation using data analysis tools Subio Basic Plug-in (Subio Inc. Tokyo, Japan).

organism: Glycine max

source_name: En1282, 8dpi, BerhcJ inoculation, replicate 2

label_protocol: Each RNA sample (0.5 ug) was labeled with Cyanine-3 (Cy3) fluorescent dye, using Agilent’s Quick Amp Labeling Kit. The cRNA product was purified with RNeasy mini spin columns (QIAGEN, Hilden, Germany).

growth_protocol: Plants were cultivated in a growth chamber at 24°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. RNA was extracted from the roots at 4 days after inoculation for Enrei and 8 days after inoculation for En1282, respectively.

extract_protocol: RNA was prepared using the Qiagen RNeasy plant mini-kit (Qiagen, Hilden, Germany), following the manufacturer's instructions. The protocol includes an on-column DNase digestion. RNA samples were visualized and quantified on Agilent’s Bioanalyzer to check for degradation and to determine the concentration.

treatment_protocol: Seeds of soybeans (Glycine max L. cv. Enrei and its non-nodulating line En1282) were surface-sterilized and germinated at 24 °C for 2 days and were transferred to Magenta GA7 vessels filled with vermiculite and nitrogen-free medium. One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment). Plants were cultivated in a growth chamber at 24°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots at 4 days after inoculation for Enrei and 8 days after inoculation for En1282, respectively.

tag: host soybean genotype

value: nfr

tag: inoculant

value: Bradyrhizobium elkanii BerhcJ

tag: days post inoculation


title: En1282_8dpi_BerhcJ_rep3

source_name: En1282, 8dpi, BerhcJ inoculation, replicate 3


title: 2555 [miRNA]

source_name: mouse heart graft tissue with 18h cold ischemia before heart transplantation


title: 2556 [miRNA]

source_name: mouse heart graft tissue without 18h cold ischemia before heart transplantation

value: heart tissue without 18h cold ischemia reperfusion


title: SCC_N14_expression

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


title: E 13 thymic settling progenitors 1


title: muscle WT 1 control

description: Gene expression in control muscle

value: whole Gastrocnemius

value: adult male


title: ASC_morbidly-obese_biological rep2

description: Gene expression data from ASC isolated from subcutaneous WAT of morbidly obese patient 2


title: muscle WT 1 denervated 14 days


title: SCC_11_04_expression


title: 2554 [miRNA]


title: En1282_8dpi_USDA61_rep3

source_name: En1282, 8dpi, USDA61 inoculation, replicate 3

value: Bradyrhizobium elkanii USDA61


title: En1282_8dpi_BerhcJ_rep1

source_name: En1282, 8dpi, BerhcJ inoculation, replicate 1


title: 2553 [miRNA]


title: FAK Rescue, dense, Experimental Day July12th

city: Zurich

first: Berend

last: Snijder

address: Winterthurerstrasse 190

department: IMLS

country: Switzerland

institute: University of Zurich

hyb_protocol: Cy3-labeled cRNA samples (1.65 μg) were mixed with a Agilent Blocking Solution, subsequently  randomly  fragmented to 100-200 bp at 65°C with Fragmentation Buffer, and resuspended in Hybridization Buffer using a Gene Expression Hybridization Kit (Agilent p/n 5188-5242).  Target cRNA Samples (100μl) were hybridized to  Whole Mouse  Genome 4x44k  OligoMicroarrays (Agilent G4122F) for 17h at 65°C. Arrays were then washed using Agilent GE Wash Buffers 1 and 2 (Agilent p/n 5188-5326), according to the manufacturer instructions (One-Color Microarray-Based Gene Expression Analysis Manual, www.agilent.com)

scan_protocol: An Agilent Microarray Scanner (Agilent p/n G2565BA) was used to measure the fluorescent intensity emitted by the labeled target.

data_processing:
Raw data processing was performed using the Agilent Scan Control and the Agilent Feature Extraction Software Version 10. Quality control measures were considered before performing the statistical analysis. These included, inspection of the array hybridization pattern (absence of scratches, bubbles, areas of non hybridization), proper grid alignment, performance of  the spike in controls (linear dynamic range between 5 orders of magnitude) and number of green feature non uniformity outliers (below 100 for all samples).
Matrix table values are intensities obtained by Agilent feature extraction software, followed by geometric mean normalization. 'null' values indicate measurements below detection backround. To be above background, measurments had to fullfill the default Agilent output gIsWellAboveBG and additional threshold of 25 fluorescence units. Both criteria had to be satisied in at least 2 out of 3 biological replicas for that gene/condition.

source_name: FAK Rescue Mouse Embryonic Fibroblasts

label_protocol: The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies,Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a RNA Integrity Number (RIN) higher than 8 were further processed. Total RNA samples (100ng) were reverse-transcribed into double-stranded cDNA in presence of RNA poly-A controls, RNA Spike-In Kit, One-Color (Agilent p/n 5188-5282). The double-stranded cDNA were in vitro transcribed in presence of Cy3-labelled nucleotides using a Low Input Quick Amp Labeling Kit, one-color (Agilent P/N 5190-2305). The Cy3- cRNA was purified using a RNeasy mini kit, Qiagen (p/n. 74104 or 74106) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100. Only cRNA samples with a total cRNA yield higher than 2 μg  and a  dye incorporation rate between 8 pmol/ μg and 20 pmol/ μg were considered  for hybridization

growth_protocol:
The FAK-Knockout cell line is described here: http://www.nature.com/nature/journal/v377/n6549/pdf/377539a0.pdf (Ilic D et al., Nature, 1995)
The FAK-Rescue cell line is described here: http://jcs.biologists.org/content/112/16/2677.short (Sieg DJ et al., JCS, 1999; clone DA2)
FAK Rescue were cultivated and seeded for experiments in DMEM + Glutamax + 10% FBS + 135ug/ml HygromycinB + non essential amino acids. FAK KO were cultivated and seeded for experimentsin DMEM + Glutamax + 10% FBS (without any further antibiotics). Cells were cultivated in 15cm dishes with 30ml medium ot the respective medium for at least 2 days before the initial seeding for a microarray. Cells were split at at least once within 2 days to keep a constant confluency ~50% for cultivating. For seeding up to three 15cm dishes containing 90% confluent cells were pooled. Cells were harvested with 5ml Trypsin, followed by resuspension in 30ml medium , centrifugation at 250g for 5min, removing of s/n, resuspension in medium. Then cells aggregates were dissolved by pipetting up and down >20 times while pressing the pipet to the bottom of a plate. For dense condition, 8.2 x10^6 cells were seeded into a 10cm dish with 10ml medium. For sparse condition 0.41 x10^6 cells were seeded into a 10cm dish with 10ml medium. Cells were the grown at 37deg for 24+/-1h until being harvested. The position of the plates within the incubator would change for individual samples among replicate days to reduce positional bias. The seeding/harvesting was done on three different experimental days.

extract_protocol: Cells were harvested by trypsinization and frozen at -80deg. RNA preparation was done on the same day for all samples. Sample preparation was done with the Qiagen RNeasy Mini Kit including the optional on column DNAse treatment according to the manufacturer's manual, except: used 0.8mm syringe for homogenization instead of recommended 0.9mm syringe.

treatment_protocol: Cells were grown at a dense or sparse cell density as described in the growth protocol.

tag: seeding condition

value: Seeded densely

tag: cell type

value: Mouse Embryonic Fibroblasts

tag: experimental day


title: En1282_8dpi_USDA61_rep2

source_name: En1282, 8dpi, USDA61 inoculation, replicate 2


title: SCC_73_05_expression

hyb_protocol: Standard Affymetrix hybridisation protocol

data_processing: Data analysis was done using Bioconductor R packages. Background correction and normalisation were performed using Robust Microarray Analysis (RMA) provided by the Affy package

label_protocol: Standard Affymetrix labelling protocol


title: FAK KO, dense, Experimental Day July12th

source_name: FAK KO Mouse Embryonic Fibroblasts


title: normal_S98_306_expression

source_name: normal uterine cervix

value: normal uterine cervix

value: Normal


title: Salmonella_Typhi_BRD948_yehUT_37c_rep1

hyb_protocol: Standard protocol from Agilent

data_processing: Array Features were calculated using AFE default settings for the GE2-v5_10_Apr08. Using limma, a linear model fite was applied and the top differetnially expressed genes were tabulated for each contrast using the method of Benjamini and Hochberg to correct p-values

organism: Salmonella enterica subsp. enterica serovar Typhi

source_name: cultures

label_protocol: Cyanine 3-CTP standard protocol from agilent

extract_protocol: Qiagen mini kit

value: BRD948 yehUT

tag: culture temperature


title: normal_S98_303_expression


title: SCC_81_05_expression


title: Salmonella_Typhi_BRD948_yehT_37c_rep3

value: BRD948 yehT


title: Salmonella_Typhi_BRD948_yehUT_37c_rep2


title: FAK Rescue, sparse, Experimental Day July12th

value: Seeded sparsely


title: Enrei_8dpi_BerhcJ_rep3

source_name: Enrei, 4dpi, BerhcJ inoculation, replicate 3

growth_protocol: Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. RNA was extracted from the roots 8 days after inoculation.

treatment_protocol: Seeds of soybeans (Glycine max L. cv. Enrei and its non-nodulating line En1282) were surface-sterilized and germinated at 25 °C for 2 days and were transferred to Magenta GA7 vessels filled with vermiculite and nitrogen-free medium. One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment). Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 8 days after inoculation.

value: wildtype


title: En1282_8dpi_mock_rep3

source_name: En1282, 8dpi, mock, replicate 3

value: mock


title: Salmonella_Typhi_BRD948_yehUT_37c_rep3


title: SCC_8_04_expression

value: Squamous cell carcinoma

value: SCC


title: En1282_8dpi_mock_rep2

source_name: En1282, 8dpi, mock, replicate 2

value: nfr


title: FAK KO, sparse, Experimental Day July12th


title: SCC_G16_expression


title: SCC_C4I_expression


title: Salmonella_Typhi_BRD948_yehT_37c_rep2


title: En1282_8dpi_mock_rep1

source_name: En1282, 8dpi, mock, replicate 1


title: SCC_N24_expression


title: FAK KO, dense, Experimental Day July11th


title: En1282_8dpi_USDA61_rep1

source_name: En1282, 8dpi, USDA61 inoculation, replicate 1


title: Salmonella_Typhi_BRD948_yehT_37c_rep1


title: FAK KO, sparse, Experimental Day July11th


title: Salmonella_Typhi_BRD948_yehU_37c_rep2

value: BRD948 yehU


title: Salmonella_Typhi_BRD948_yehU_37c_rep3


title: FAK Rescue, dense, Experimental Day July11th


title: Enrei_8dpi_USDA61_rep2

source_name: Enrei, 8dpi, USDA61 inoculation, replicate 2


title: Enrei_8dpi_BerhcJ_rep1

source_name: Enrei, 4dpi, BerhcJ inoculation, replicate 1

value: Bradyrhizobium elkanii BerhcJ


title: Salmonella_Typhi_BRD948_yehU_37c_rep1


title: Enrei_8dpi_BerhcJ_rep2

source_name: Enrei, 4dpi, BerhcJ inoculation, replicate 2


title: FAK Rescue, sparse, Experimental Day July11th


title: Enrei_8dpi_USDA61_rep3

source_name: Enrei, 4dpi, USDA61 inoculation, replicate 3


title: FAK KO, dense, Experimental Day July9th

description: FAK KO, dense, Experimental Day July9th


title: Enrei_8dpi_USDA61_rep1

source_name: Enrei, 8dpi, USDA61 inoculation, replicate 1


title: Salmonella_Typhi_BRD948_37c_rep3


title: FAK Rescue, dense, Experimental Day July9th


title: SCC_22_04_expression

source_name: Squamous cell carcinoma


title: SCC_G1_expression


title: Salmonella_Typhi_BRD948_37c_rep2


title: QM 9414 on glucose

city: Vienna

first: Christian

middle: P.

last: Kubicek

address: Getreidemarkt 9

country: Austria

institute: TU Vienna

description: glucose

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
Microarray scanning, data acquisition and identification of probe sets showing a significant difference (p=0.05) in expression level between the different conditions were performed essentially as described by Metz et al. (2011) Eukaryot Cell 10:1527-1735.

organism: Trichoderma reesei QM9414

source_name: T. reesei growing on glucose for 28 hrs

label_protocol: cDNA synthesis, labelling and hybridization was performed by Roche NimbleGen (Roche-NimbleGen, Inc., Madison, WI, USA) with a high density oligonucleotide (HDO) microarray using 60-mer probes representing the 9.129 genes of T. reesei.

growth_protocol: Cultures were grown in 250ml of Mandels Andreotti (MA) medium (per litre: 1.4g (NH4)2SO4, 2.0g KH2PO4, 0.3g MgSO4*7H2O, 0.3g CaCl2*2H2O, 0.3g urea, 1g peptone (casein), 5mg FeSO4*7H2O, 1.6mg MnSO4*H2O, 1.4mg ZnSO4*7H2O and 2mg CoCl2*2H2O) with 10g/l glucose monohydrate, lactose monohydrate or pretreated wheat straw (dry basis) as the sole carbon source and inoculated with 106 conidia ml-1 of spores. Furthermore, 0.5g l-1 of tween 80 were added in the case of lactose cultures and the pH of wheat straw media was adjusted to 4.8 with 1M KOH. All cultivations were performed in a rotary shaker at 28°C and 250rpm. Biomass samples for total RNA extraction or measurement of biomass were withdrawn at appropriate time points as stated below. Cultures for the qPCR analyses were pregrown for 24h in glycerol containing (10 g l-1) MA medium and equal portions of the harvested and washed mycelium were aseptically replaced into MA medium, again containing either 10 g l-1 glucose monohydrate, lactose monohydrate or pretreated wheat straw (dry basis) as the sole carbon source, but this time devoid of urea or peptone.

extract_protocol: Total RNAs from glucose and lactose cultures were extracted using TRIzol® reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer's instructions, and then purified. For isolation and purification of total RNA from wheat sraw cultures, the RNeasy Plant Mini Kit and the RNeasy MinElute Kit (both Quiagen, Hilden, Germany) respectively were used according to the manufacturer’s instructions.

treatment_protocol: Mycelia were harvested from cultures growing on wheat straw, lactose, and glucose, respectively, for 50 (wheat straw)and 28 hrs (lactose and glucose), respectively.

tag: carbon source

value: glucose

value: mycelia


title: FAK Rescue, sparse, Experimental Day July9th

source_name: FAK Rescue Mouse Embryonic Fibroblasts


title: SCC_N98_expression

city: Cambridge

first: Ian

last: Roberts

address: Hills Road

institute: Hutchison MRC Research Centre

scan_protocol: Standard Affymetrix scanning protocol


title: SCC_G18_expression


title: Enrei_8dpi_mock_rep2

source_name: Enrei, 8dpi, mock, replicate 2


title: FAK KO, sparse, Experimental Day July9th

source_name: FAK KO Mouse Embryonic Fibroblasts


title: Enrei_8dpi_mock_rep3

source_name: Enrei, 8dpi, mock, replicate 3


title: QM 9414 on cellulose

description: cellulose (wheat straw)

source_name: T. reesei growing on cellulose for 50 hrs

value: cellulose


title: QM 9414 on lactose

description: lactose

source_name: T. reesei growing on lactose for 28 hrs

value: lactose


title: Enrei_8dpi_mock_rep1

source_name: Enrei, 8dpi, mock, replicate 1

treatment_protocol: Seeds of soybeans (Glycine max L. cv. Enrei and its non-nodulating line En1282) were surface-sterilized and germinated at 25 °C for 2 days and were transferred to Magenta GA7 vessels filled with vermiculite and nitrogen-free medium. One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment). Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 8 days after inoculation .


title: SCC_K3_expression


title: Salmonella_Typhi_BRD948_37c_rep1

city: Hinxton

first: Vanessa

last: Wong

address: Wellcome Trust Genome Campus

institute: Wellcome Trust Sanger Institute

scan_protocol: Standard protocol from Agilent, Agilent DNA High Resolution Microarray Scanner (Agilent, G2505C)

source_name: cultures