title: 9R1727

status: Public on Nov 30 2012

type: RNA

city: Chapel Hill

first: Jen Jen

last: Yeh

state: NC

address: LCCC, 450 West Drive

department: Surgical Oncology

country: USA

institute: University of North Carolina at Chapel Hill

description: LYMPH NODE

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction (v10.5) software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken using Agilent Feature Extraction (v10.5) software.

molecule: total RNA

organism: Homo sapiens

source_name: Human Reference

extract_protocol: Total RNA isolated by TRIZOL reagent

tag: reference

value: Whole human total RNA

source_name: LYMPH NODE

extract_protocol: Qiagen All-prep Kit

tag: tissue

value: Pancreatic tumor

tag: metastatic lesion

value: lymph node


title: 9R1819

description: LUNG

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

source_name: LUNG

value: lung


title: 9R1821

description: LUNG


title: 6R1278

description: LIVER

source_name: LIVER

value: liver


title: 8R1405

description: PANCREAS

source_name: PANCREAS

value: pancreas


title: 9R1715T

description: LIVER


title: 6R1308

description: MUSCLE

source_name: MUSCLE

value: diaphragm muscle


title: 7R1329

description: LYMPH NODE


title: 7R1347BT

description: LUNG


title: 7R1240

description: LIVER


title: 5R744B2

description: LIVER


title: 9R1701.2P

description: PANCREAS


title: 6R1271

description: FAT

source_name: FAT

value: fat


title: 5RT160

description: LIVER


title: 7R1322N

description: MUSCLE


title: 5R913

description: PANCREAS


title: 9R1701B

description: PANCREAS


title: 7R1327B

description: MUSCLE


title: 6R1273B

description: FAT


title: 9R1632

description: LIVER


title: 7R1353Brpt

description: PANCREAS


title: 5R744B

description: LIVER


title: 5RT160N

description: LIVER


title: 7R1342B

description: LUNG


title: 9R1703

description: PANCREAS


title: 4R687T

description: LYMPH NODE


title: 4R678B2

description: PANCREAS


title: 5R922

description: LYMPH NODE


title: 8R1550

description: LIVER


title: 3R379B

description: LYMPH NODE


title: 16R3333

description: FAT


title: 3R323B

description: LYMPH NODE


title: 13R2778

description: PANCREAS


title: 4R616B

description: MUSCLE


title: 12R2685T

description: PANCREAS


title: 3R261B

description: PANCREAS


title: 4R526B

description: LIVER


title: 2R14B

description: PANCREAS


title: 3R334T

description: LIVER


title: 12R2600.1T

description: LYMPH NODE


title: 12R2600.2T

description: LYMPH NODE


title: 13R2818B N

description: LIVER


title: 13R2713B

description: LIVER


title: 4R510B

description: LIVER


title: 4R617B

description: MUSCLE


title: 3R313T

description: LUNG


title: 4R512

description: LIVER


title: 3R202

description: FAT

value: abdominal wall fat


title: 3R201B

description: FAT


title: 12R2594

description: LIVER


title: 3R324B

description: LYMPH NODE


title: 3R383

description: FAT


title: 3R382

description: FAT


title: RS4;11 treated with VE-465 Replicate 2

city: Tainan

first: Ya-Ping

last: Chen

address: No. 138, Sheng-Li Road

department: Internal Medicine

country: Taiwan

institute: National Cheng Kung University

description: Biological replicate 2 of 3. Gene expression after exposure to  200 nM VE-465 for 48 hours in RS4;11

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, correspondingly fragmented labeled cRNA was pooled and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays (Agilent) at 65°C for 17 hours 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 by nitrogen gun blowing.

scan_protocol: After washing and drying, slides were scanned immediately on the Agilent Microarray Scanner at 535 nm for Cy3.

data_processing: The scanned images were analyzed by Feature Extraction Software 10.5.1.1 (Agilent), an image analysis and normalization software was used to quantify signal and background intensity for each feature.

source_name: RS4;11 treated with VE-465

label_protocol: 0.2 ug of total RNA was amplified by a One-Color Low Input Quick-Amp Labeling kit (Agilent) and labeled with Cyanine-3 (Cy3) during the in vitro transcription process. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RS4;11 cells were cultured in RPMI-1640 (Gibco, Carlsbad, CA) supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted by Trizol Reagent (Invitrogen) according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: RS4;11 cells were plated in appropriate complete media and 0 or 200 nM VE-465 was added to the media. The cultures were incubated for 48 hours at 37 °C in a humidified incubator with 5% CO2.

tag: cell line


title: RS4;11 treated with VE-465 Replicate 1

description: Biological replicate 1 of 3. Gene expression after exposure to  200 nM VE-465 for 48 hours in RS4;11


title: RS4;11 treated with VE-465 Replicate 3

description: Biological replicate 3 of 3. Gene expression after exposure to  200 nM VE-465 for 48 hours in RS4;11


title: 12R2587.1

description: PANCREAS


title: RS4;11 Control Replicate 2

description: Biological replicate 2 of 3. Gene expression after exposure to  0 nM VE-465 for 48 hours in RS4;11

source_name: RS4;11 without VE-465 exposure


title: 13R2872B

description: LYMPH NODE


title: 3R381

description: LYMPH NODE


title: RS4;11 Control Replicate 3

description: Biological replicate 3 of 3. Gene expression after exposure to  0 nM VE-465 for 48 hours in RS4;11


title: 3R382Brpt

description: FAT


title: 12R2585B

description: PANCREAS


title: RS4;11 Control Replicate 1

description: Biological replicate 1 of 3. Gene expression after exposure to  0 nM VE-465 for 48 hours in RS4;11


title: 12R2534B

description: MUSCLE

value: Pelvic Sidewall Muscle


title: 12R2583

description: LUNG


title: 12R2587.2

description: PANCREAS


title: 12R2568

description: FAT


title: vraT +Ox 2

city: CHICAGO

first: Susan

last: Boyle-Vavra

state: IL

address: 900 E 57th Street

institute: University of Chicago

description: vraT mutant Ox treated

hyb_protocol: Four µg of fragmented and biotin-labeled targets were hybridized to the array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640.  Arrays were washed and stained with Streptavidin Phycoerythrin. The fluorescent signals were amplified usin

scan_protocol: The  signals were detected in a GeneChip Scanner 3000 7G.

data_processing: The expression data were extracted using the Gene Chip Operating Software (MicroArray Suite 5.0 software, Affymetrix).  The cel files were imported into GeneSpring version 11.5 (Agilent) to identify differentially expressed genes.

label: biotin

organism: Staphylococcus aureus subsp. aureus USA300

source_name: MRSA USA300

label_protocol: Ten microg of total RNA was processed for biotin labeled target preparation for hybridization to Affymetrix Staphylococcus aureus expression arrays according to Genechip Expression analysis technical manual (Affymetrix, Inc).

growth_protocol: Overnight  cultures were diluted 1:100 in Tryptic Soy Broth, incubated in a 37°C with shaking for 1 hr  (OD600 ~0.2) and treated with water or Oxacillin (1 _g/ml) for 1 hr.

extract_protocol: The pellets were suspended in TE buffer containing lysostaphin (200 _g/ml), incubated at room temperature for 10 min, and then extracted using the Qiagen RNeasy kit with DNase treatment. The RNA purity & concentration were determined using a NanoDrop 1000

tag: genotype/variation

value: vraT mutant

tag: agent

value: oxacillin


title: vraT +Ox 3

description: vraT mutant Ox treated

treatment_protocol: Overnight  cultures were diluted 1:100 in Tryptic Soy Broth, incubated in a 37°C with shaking for 1 hr  (OD600 ~0.2) and treated with water or Oxacillin (1 _g/ml) for 1 hr.


title: 12R2522

description: LIVER


title: vraS +Ox 3

description: vraS mutant Ox treated

value: vraS mutant


title: vraT +Ox 1

description: vraS mutant Ox treated


title: 923 + Ox 2

description: USA300 wildtype  Ox tretaed

value: wildtype


title: 12R2455B

description: MUSCLE


title: 12R2528.2M

description: MUSCLE


title: 923 + Ox 1

description: USA300 wildtype  Ox tretaed


title: 11R2266TB

description: LUNG


title: 12R2528.2

description: MUSCLE


title: Jdp2 WT neutrophil

city: Suita

first: Kenta

last: Maruyama

address: yamada-oka 3-1

country: Japan

institute: Osaka university

description: Gene expression data from WT neutrophils

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: slides were scanned using the Affymetrix GeneChip scanner 3000.

data_processing: Data were analyzed with RMA using the arrayassist program (Stratagene).

organism: Mus musculus

source_name: Bone marrow neutrophls

label_protocol: Biotin

growth_protocol: Bone marrow CD11b+Ly6Clo Ly6G+ neutrophils form wild-type and Jdp2-/-mice were sorted by FACS.

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

value: Bone marrow

tag: cell type

value: neutrophil

tag: strain

value: C57BL/6 /129/J mixed background

value: Jdp2 WT


title: 10R2019B

description: FAT

value: Whole human total RNA

value: Pancreatic tumor

value: fat nerve


title: 11R2157.2

description: LIVER

value: liver


title: 10R2013

description: MUSCLE


title: 11R2266NB

description: LUNG

value: lung


title: 11R2157.2R

description: LIVER


title: vraS +Ox 2

description: vraS mutant Ox treated


title: 923 + Ox 3

description: USA300 wildtype  Ox tretaed


title: 11R2157.1N

description: LIVER


title: vraS +Ox 1

description: vraS mutant Ox treated


title: 923 2

description: USA300 wildtype untretaed


title: vraT 1

description: vraT mutant untretated


title: vraS 2

description: vraS mutant untretaed


title: vraS 3

description: vraS mutant untretaed


title: vraT 2

description: vraT mutant untretated


title: vraS 1

description: vraS mutant untretaed


title: vraT 3

description: vraT mutant untretated


title: TM-3

city: Houston

first: Lei

last: Zhou

address: 6700 Bertner Avenue

institute: Texas Heart Institute

hyb_protocol: Samples were then processed according to Ambion Message Amp II protocol using the kit and 500ng of total RNA. The Bio-11-UTPs were used for the RNA biotinylation and a final reaction volume of 40uL was used. After labeling and amplification, the samples were then fragmented, hybridized, washed, stained, and scanned using the Affymetrix Genechip microarray system. An input amount of 15.0 ¦Ìg of the labeled cRNA was fragmented and re-checked for concentration.  A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto the Mouse 430 2.0 GeneChip array.  The array was hybridized for 16 hours at 45¡ãC with a rotation speed of 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate.  Signal amplification was measured using the biotinylated antistreptavidin.

scan_protocol: The stained array was scanned on the Affymetrix GeneChip Scanner 3000.  The images were analyzed and quality control metrics recorded using Affymetrix GeneChip Command Console 3.0 (AGCC).

data_processing: Samples were compared by using Affymetrix MG 430 2.0 arrays. Expression data were analyzed by using dChip2008 and GenMAPP software programs. Genes with an absolute fold change =2.0 relative to the LacZ group and genes with a signal intensity of 0 in the LacZ group but not in the transcription factor-treated groups (or vice versa) were subjected to GO analysis. GO terms with P<0.05 and a nested gene change number =4 were considered as statistically significant activation or inhibition. Activated and inhibited gene lists were compared by using the GeneVenn web application.

source_name: T+M transfected 10T1/2, 2weeks induction

extract_protocol: Two weeks after doxycline induction, total RNA was isolated from 10T1/2-tTA cells infected with different combinations of Tbx5, Gata4, and Myocardin lentiviruses using Trizol reagent (Invitrogen) followed by DNase I (Qiagen) treatment. RNA was then recovered by using RNeasy MinElute Cleanup Kit (Qiagen).

tag: lentivirus infection

value: TM

value: embryonic 10T1/2 fibroblast cell line


title: 923 1

description: USA300 wildtype untretaed


title: 10R2004B

description: LYMPH NODE

value: lymph node


title: 923 3

description: USA300 wildtype untretaed


title: TGM-3

source_name: T+G+M transfected 10T1/2, 2weeks induction

label_protocol: Samples were then processed according to Ambion Message Amp II protocol using the kit and 500ng of total RNA. The Bio-11-UTPs were used for the RNA biotinylation and a final reaction volume of 40uL was used. After labeling and amplification, the samples were then fragmented, hybridized, washed, stained, and scanned using the Affymetrix Genechip microarray system. An input amount of 15.0 ¦Ìg of the labeled cRNA was fragmented and re-checked for concentration.  A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto the Mouse 430 2.0 GeneChip array.  The array was hybridized for 16 hours at 45¡ãC with a rotation speed of 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate.  Signal amplification was measured using the biotinylated antistreptavidin.

value: TGM


title: TM-2


title: TGM-1


title: Jdp2 KO neutrophil

description: Gene expression data from Jdp2 KO neutrophils

value: Jdp2 KO


title: TM-1


title: TG-3

source_name: T+G transfected 10T1/2, 2weeks induction

value: TG


title: TGM-2


title: TG-1


title: Gata4-1

source_name: Gata4 transfected 10T1/2, 2weeks induction


title: Myocardin-3

source_name: Myocardin transfected 10T1/2, 2weeks induction

value: Myocardin


title: TG-2


title: Gata4-2


title: GM-3

source_name: G+M transfected 10T1/2, 2weeks induction

value: GM


title: GM-1


title: Myocardin-2


title: Myocardin-1


title: LacZ-1

hyb_protocol: Samples were then processed according to Ambion Message Amp II protocol using the kit and 500ng of total RNA. The Bio-11-UTPs were used for the RNA biotinylation and a final reaction volume of 40uL was used. After labeling and amplification, the samples were then fragmented, hybridized, washed, stained, and scanned using the Affymetrix Genechip™ microarray system. An input amount of 15.0 µg of the labeled cRNA was fragmented and re-checked for concentration.  A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto the Mouse 430 2.0 GeneChip® array.  The array was hybridized for 16 hours at 45°C with a rotation speed of 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate.  Signal amplification was measured using the biotinylated antistreptavidin.  The stained array was scanned on the Affymetrix GeneChip® Scanner 3000.  The images were analyzed and quality control metrics recorded using Affymetrix® GeneChip® Command Console® 3.0 (AGCC).

source_name: LacZ transfected 10T1/2, 2weeks induction

value: LacZ


title: GM-2


title: Gata4-3


title: Tbx5-3

source_name: Tbx5 transfected 10T1/2, 2weeks induction


title: Tbx5-2


title: Tbx5-1


title: Control 3 (C3)

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Silurana tropicalis microarrays were manufactured with Agilent Sure Print Technology in Fall 2011.  RNA labeling, microarray hybridization, and microarray analysis were performed according to Agilent’s One-Color Microarray-Gene Based Expression Analysis protocol (May 2010) using an Agilent kit (Agilent, Mississauga, ON, CAN).  After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.

data_processing: Normalized signal intensity provided here is LOESS Normalization

organism: Xenopus tropicalis

source_name: embryos (stage 12 to 46)

label_protocol: Agilent one color protocol for Cy3

extract_protocol: RNA was extracted using the .Z.N.A total RNA kit (VWR International, Mississauga, ON, CA).  RNA quantity was measured using the NanoDrop ND2000 (Thermo Scientific) prior to DNase treatment for real-time PCR and RNA integrity was evaluated according to Agilent 2100 Bioanalyzer protocol (Agilent, Mississauga, ON, CAN).

tag: treatment

tag: development stage

value: embryo stage 12 to 46


title: Treatment 3 (T3)

scan_protocol: After hybridization for 17 hours, microarray slides were washed and scanned using Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology and raw expression data along with tif images were extracted by the Feature Extraction Software 10.7.3.1.

value: 887 ppm Disperse Yellow 7 (DY7)


title: LacZ-2

label_protocol: Samples were then processed according to Ambion Message Amp II protocol using the kit and 500ng of total RNA. The Bio-11-UTPs were used for the RNA biotinylation and a final reaction volume of 40uL was used. After labeling and amplification, the samples were then fragmented, hybridized, washed, stained, and scanned using the Affymetrix Genechip™ microarray system. An input amount of 15.0 µg of the labeled cRNA was fragmented and re-checked for concentration.  A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto the Mouse 430 2.0 GeneChip® array.  The array was hybridized for 16 hours at 45°C with a rotation speed of 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate.  Signal amplification was measured using the biotinylated antistreptavidin.  The stained array was scanned on the Affymetrix GeneChip® Scanner 3000.  The images were analyzed and quality control metrics recorded using Affymetrix® GeneChip® Command Console® 3.0 (AGCC).


title: Treatment 4 (T4)


title: Control 4 (C4)


title: Treatment (T1)


title: Treatment 2 (T2)


title: Control 2 (C2)


title: Control 1 (C1)


title: LacZ-3

hyb_protocol: Samples were then processed according to Ambion Message Amp II protocol using the kit and 500ng of total RNA. The Bio-11-UTPs were used for the RNA biotinylation and a final reaction volume of 40uL was used. After labeling and amplification, the samples were then fragmented, hybridized, washed, stained, and scanned using the Affymetrix Genechip microarray system. An input amount of 15.0 µg of the labeled cRNA was fragmented and re-checked for concentration.  A hybridization cocktail containing Affymetrix spike-in controls and fragmented labeled cRNA was loaded onto the Mouse 430 2.0 GeneChip array.  The array was hybridized for 16 hours at 45°C with a rotation speed of 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate.  Signal amplification was measured using the biotinylated antistreptavidin.


title: Contol3 ZP34 mRNA

city: Taiyuan

first: Ruixia

last: Hou

state: Shanxi

address: 1,Dong San Dao Xiang, Jiefang Road

department: Dermatology

country: China

institute: Taiyuan City Central Hospital

hyb_protocol: 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 4 out of 12 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through volcano plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method

source_name: Contol3 ZP34

label_protocol: 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The Labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA

growth_protocol: The dermises were separated from the epidermis by dispase and monoplast suspension was obtained by pipetting. The MSCs were cultured by adherent assay. Cells of 3rd passage were enrolled in the microarry.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

value: dermal mesenchymal stem cell

tag: age

value: 40 years

tag: gender

value: male

tag: pasi


title: Patient4 Y40 mRNA

scan_protocol: scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

source_name: Patient4 Y40

value: 38 years


title: Patient4 Y36 mRNA

source_name: Patient4 Y36

value: 29 years


title: Contol1 ZP30 mRNA

source_name: Contol1 ZP30

value: 28 yesrs

value: female


title: Patient5 Y41 mRNA

source_name: Patient5 Y41

value: 49 years


title: Contol6 ZP38 mRNA

source_name: Contol6 ZP38

value: 44 years


title: Patient2 Y31 mRNA

source_name: Patient2 Y31

value: 45 years


title: Contol5 ZP36 mRNA

source_name: Contol5 ZP36

value: 21 years


title: Patient3 Y33 mRNA

source_name: Patient3 Y33

value: 16 years


title: Contol2 ZP33 mRNA

source_name: Contol2 ZP33

value: 37 years


title: Contol4 ZP35 mRNA

source_name: Contol4 ZP35

value: 36 years


title: E6 expressing cell line (LV infected UPCI:SCC003) - clone 1A

type: genomic

city: London

first: Matthias

last: Lechner

address: Gower Street

department: UCL Cancer Institute

country: United Kingdom

institute: University College London

description: BS-converted DNA

hyb_protocol: The Infinium HumanMethylation450 BeadChips were processed by the UCL Genomics core facility according to the manufacturer’s recommendation.

data_processing: The scanned data and image output files were managed with the Genomestudio software (version 1.9.0) (Illumina®, Inc., San Diego, CA 92121, USA).

label: Biotin

molecule: genomic DNA

source_name: HNSCC cell line

label_protocol: DNA was prepared in a total volume of 20 µl (1 µg). It was then bisulphite converted using the EZ DNA Methylation kit (Zymo Research Corp, Orange, CA 92867, USA, cat No. D5001) before being hybridized to the array.

growth_protocol: All cell lines were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% foetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol: DNA from HNSCC cell linesn were extracted using the QIAamp DNA Blood Mini Kit (QIAGEN)

treatment_protocol: Clones of SCC003 expressing either empty vector control, HPV-16 E7, HPV-16 E6, or both HPV-16 E6 and E7, respectively: They were generated by infection of the SCC003 cell line with retroviruses and single cell cloning as follows. Viruses were produced by transfecting Human Embryonic Kidney (HEK) 293T cells with pLXSN (empty vector or containing the HPV-16 E6, E7 or E6&E7 cDNAs, kind gifts from Dr. David Beach) together with pHIT- VSVG and MLV-gag/pol (kind gifts from Dr. Juan Martin-Serrano) using polyethylenimine (Polysciences, Inc.). 72 hours post-transfection, viruses were harvested by removal of the medium and filtration through 0.45um surfactant-free filters (Nalgene). The filtered virus stocks were either frozen at -80C or diluted 1:2 in DMEM/10%FBS containing 8ug/ml Polybrene (to give a final conc. of 4ug/ml) and added to SCC003 cells grown to a confluence of 40-50%. Following overnight incubation, the cells were washed to remove virus and medium was replaced with DMEM/10%FBS. At 48-72hrs post-infection cells were passaged at a ratio of 1:5 into selection medium containing 400ug/ml G418. Following death of all mock-infected cells (approx. 1 – 2 weeks), cells were removed from selection and plated at limiting dilution in 96 well plates to generate single cell clones. HPV-16 E6 and E7 qPCR was conducted as described (Wang-Johanning et al. 2002; Zhao et al. 2005). To assess E6 and E7 expression levels in E6-transduced, E7-transduced and E6&E7-transduced SCC003 cell line clones (and empty vector controls), qPCR was performed on cDNA following reverse transcription (Superscript-II, Invitrogen) of total RNA purified from cells using the miRNeasy kit (QIAGEN) as per manufacturers’ recommendations.

tag: transfection

value: E6 expressing  (LV infected UPCI SCC003) - clone 1A

value: UPCI SCC003


title: HPV negative cell line UPCI:SCC036 - replicate 1

description: BS-converted DNA

scan_protocol: The Infinium HumanMethylation450 BeadChips were processed by the UCL Genomics core facility according to the manufacturer’s recommendation.

value: UPCI SCC036


title: Empty vector control (LV infected UPCI:SCC003) - clone 4A

description: BS-converted DNA

value: Empty vector control (LV infected UPCI SCC003) - clone 4A


title: E7 expressing cell line (LV infected UPCI:SCC003) - clone 4A

description: BS-converted DNA

value: E7 expressing  (LV infected UPCI SCC003) - clone 4A


title: exposure to exudates_4h_rep3

city: Bremen

first: Barbara

last: Reinhold-Hurek

department: Microbe-Plant-Interactions

country: Germany

institute: University Bremen

description: 4h_set3. Biological replicate 3 of 3

hyb_protocol: The combined Cy3/Cy5-labelled targets were dried in a speed vac and further dissolved in 60 µl DIG Easy hybridization solution (Roche, Mannheim, Germany).1 µl of sonicated salmon sperm (5 µg/µl) was further added. Before hybridization, the targets were denatured at 65°C for 10 min. The hybridization of fluorescently labelled cDNA targets to oligonucleotide microarrays was performed at 42°C in a hybridization chamber (ArrayIt, Sunnyvale, CA, USA) in a water bath for 14 to 18 hours.

scan_protocol: The Cy3- and Cy5-fluorescence was scanned at 532 nm and 635 nm with the GenePix Scanner 4000A (Molecular Devices, Sunnyvale, CA, USA) with a pixel size of 10 µm.The image analysis was performed with the GenePix 4.1 program and the subsequent analyses were carried out with the open-source software Microarray Data Analysis System (MIDAS v2.19) of TM4 (Saeed et al. 2003, http://www.tm4.org/). After scanning, raw data images of the slides that contain information about gene expression levels were obtained by the GenePix software. These images were analyzed by identifying each spot on the array (with the help of an array layout template) with measurements of its fluorescence intensity and the corresponding background intensity. With the file transformation tool Express Converter v.2.1 (http://www.tm4.org/utilities.html), data files generated from GenePix (.gpr) were converted to TM4 files (.mev) that could be uploaded to the MIDAS platform.

data_processing: Before the intensity values that were measured with GenePix could be compared, normalization with MIDAS was done in order to reduce variability by appropriately adjusting the data. In this study, the LOWESS (locally weighted scattered plot smoothing) normalization was performed using the block mode as set-up parameter as this mode allowed correction of systematic spatial variation between the grids of the array. The normalized data for each spot were exported to Excel and aligned to the corresponding Azoarcus sp. BH72 gene name. In order to reduce the variance in between slides, quantile normalization was done manually according to Bolstad et al., 2003. Overall, three independent experiments were performed. Average expression fold were determined from normalized values of the three sets. Statistical analysis was performed using the log2 of the intensity values in a one tail paired t-test. Genes with an expression factor ≥ 1.5 and P value ≤ 0.05 were considered as differentially expressed.

organism: Azoarcus sp.

source_name: Cells from a bacterial culture grown aerobically in synthetic medium in presence of exudates.

label_protocol: For coupling of fluorescent dyes to the aminoallyl-labelled first strand cDNA, aliquots of Cy3 NHS or Cy5-NHS esters (GE Healthcare) were dissolved in 60 µl of first strand cDNA, mixed and incubated for 90 min at room temperature in the dark. Blocking of all remaining dyes (quenching) was necessary after labelling. This quenching was achieved by adding 4.5 µl hydroxylamine (4 M) to the sample solution, followed by an incubation for 15 min at room temperature. Subsequent cleaning up of labelled cDNA from remaining dyes was performed with the CyScribe GFX Purification Kit (GE Healthcare) according to manufacturer’s instructions. The Cy5- and Cy3-labelled cDNA that was used in one hybridization experiment were cleaned up together. The labelled cDNA (60 µl) was stored at -20°C until microarray hybridization.

growth_protocol: Exponentially growing culture of Azoarcus sp. strain BH72 in SM medium (DL-malic acid, 5.0 g; KOH, 4.5 g; KH2PO4, 0.6 g; K2HPO4, 0.4 g; Mg S04 × 7H20, 0.2 g; NaCl, 0.1 g; CaCl2, 0.02 g; MnSO4 × H20, 0.01 g; Na2MoO4 × 2H20, 0.002 g; Fe(III)-EDTA (0.66% [wt/vol] in water), 0.1 mg; NH4Cl, 0.5 g; yeast extract 0.1 g.) were washed twice in growth medium comprising 3:1 ratio of plant medium (with or without exudates) and modified SM medium (Plant medium: 0.2 g of MgCl2 × 7H2O, 0.1 g of NaCl, 0.026 g of CaCl2 × 2H2O,0.012 g of MnSO4 × H2O, 4 mg of Na2MoO4 × 2H2O, 3 mg of H3BO3, 0.2 mg of ZnSO4 × 7H2O, 0.1 mg of CuSO4 × 5H2O,13 mg of Fe-citrate, 1.5 g each of K2HPO4 and KH2PO4; SM medium with following modifications: 1.25 g DL-malic acid, 25 mg NaCl, 50 mg MgSO4.7H2O, 6.5 mg CaCl2.2H2O, 2.5 mg MnSO4 × H2O, 0.5 mg Na2MoO4 × H2O, Fe(III)-EDTA (0.66% [wt/vol] in water), 0.5g NaCl). The cells were further used for inoculation of growth medium in absence or presence of exudates followed by constant shaking at 200 rpm at 37°C for 1 (initial inoculum OD578: 0.45) and 4 (initial inoculum OD578: 0.15) hours respectively. For obtaining plant medium with exudates, germinated seedlings from surface sterilized grains of Oryza sativa cv. Nipponbare were placed on wire gauze submerged in the plant medium for 14 days and this medium was further harvested and used for growing cells.

extract_protocol: The cell pellets were re-suspended in a 1:1 mixture of pre-warmed phenol-chloroform-isoamylalcohol (25:24:1, pH 4.7) and NAES solution (50 mM sodium acetate, 10 mM EDTA, 1 % SDS, pH 5.1). This suspension was incubated for 5 min at 65°C in a water bath, followed by 10 min incubation on ice. For phase separation, the mixture was centrifuged for 10 min at 12°C and 8000 x g. The upper phase was transferred and mixed with the same volume of phenol-chloroform-isoamylalcohol. This phenol extraction was repeated three times (centrifugation see above), followed by an extraction with equal volume of chloroform isoamylalcohol (24:1). RNA precipitation was performed with the same volume of isopropanol for 45 min on ice. The RNA was pelleted by centrifugation (12900 x g, 10 min at 4°C) and salts were removed with 1 ml of Ethanol (70 %). The dried RNA was dissolved in 100 µl 1 x RNAsecure, frozen in liquid nitrogen and kept at -80°C until further processing.

treatment_protocol: The cells were pelleted by centrifugation (5432 g, 28°C, 5 min), pellets were frozen in liquid nitrogen and stored at -80°C until RNA isolation.

value: grown in synthetic medium with exudates for 4 hour (experiment).

source_name: Cells from a bacterial culture grown aerobically in synthetic medium in absence of exudates.

value: grown in synthetic medium without exudates for 4 hour (control).


title: E7 expressing cell line (LV infected UPCI:SCC003) - clone 5A

description: BS-converted DNA

value: E7 expressing  (LV infected UPCI SCC003) - clone 5A


title: Empty vector control (LV infected UPCI:SCC003) - clone 3B

description: BS-converted DNA

value: Empty vector control (LV infected UPCI SCC003) - clone 3B


title: E6&E7 expressing cell line (LV infected UPCI:SCC003) - clone 2A

description: BS-converted DNA

value: E6 & E7 expressing  (LV infected UPCI SCC003) - clone 2A


title: HPV negative cell line PCI-30 - replicate 1

description: BS-converted DNA


title: exposure to exudates_1h_rep3

description: 1h_set3. Biological replicate 3 of 3.

value: grown in synthetic medium with exudates for 1 hour (experiment).

value: grown in synthetic medium without exudates for 1 hour (control).


title: exposure to exudates_1h_rep2

description: 1h_set2. Biological replicate 2 of 3.


title: exposure to exudates_4h_rep1

description: 4h_set1. Biological replicate 1 of 3.


title: exposure to exudates_4h_rep2

description: 4h_set2. Biological replicate 2 of 3.


title: E6&E7 expressing cell line (LV infected UPCI:SCC003) - clone 1

description: BS-converted DNA

value: E6 & E7 expressing  (LV infected UPCI SCC003) - clone 1


title: E6 expressing cell line (LV infected UPCI:SCC003) - clone 4A

description: BS-converted DNA

value: E6 expressing  (LV infected UPCI SCC003) - clone 4A


title: HPV negative cell line UPCI:SCC003 - replicate 2

description: BS-converted DNA


title: Patient1 Y30 mRNA

source_name: Patient1 Y30

value: dermal mesenchymal stem cell

value: 55 years

value: male


title: Empty vector control (LV infected UPCI:SCC003) - clone 2A

description: BS-converted DNA

value: Empty vector control (LV infected UPCI SCC003) - clone 2A


title: HPV positive cell line 93VU-147T - replicate 2

description: BS-converted DNA


title: HPV negative cell line PCI-30 - replicate 2

description: BS-converted DNA


title: E7 expressing cell line (LV infected UPCI:SCC003) - clone 2A

description: BS-converted DNA

value: E7 expressing  (LV infected UPCI SCC003) - clone 2A

value: UPCI SCC003


title: HPV negative cell line UPCI:SCC036 - replicate 2

description: BS-converted DNA

value: UPCI SCC036


title: HPV negative cell line UPCI:SCC003 - replicate 1

description: BS-converted DNA


title: E6&E7 expressing cell line (LV infected UPCI:SCC003) - clone 5B

description: BS-converted DNA

value: E6 & E7 expressing  (LV infected UPCI SCC003) - clone 5B


title: Contol4 ZP35

hyb_protocol: the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16 – 20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner.  GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: dermal mesenchymal stem cell

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

value: 36 years


title: Contol5 ZP36

value: 21 years

value: female


title: Contol6 ZP38

value: 44 years


title: Contol2 ZP33

value: 37 years


title: Contol1 ZP30

value: 28 yesrs


title: Patient1 Y42

value: 19 years


title: Contol3 ZP34

value: 40 years


title: exposure to exudates_1h_rep1

description: 1h_set1. Biological replicate 1 of 3

value: grown in synthetic medium without exudates for 1 hour (control).

value: grown in synthetic medium with exudates for 1 hour (experiment).


title: E6 expressing cell line (LV infected UPCI:SCC003) - clone 2

description: BS-converted DNA

value: E6 expressing  (LV infected UPCI SCC003) - clone 2


title: Patient5 Y41

value: dermal mesenchymal stem cell

value: 49 years

value: male


title: Patient4 Y40

value: 38 years


title: Patient4 Y36

value: 29 years


title: HPV positive cell line UPCI:SCC47 - replicate 1

description: BS-converted DNA

value: UPCI SCC47


title: HPV positive cell line UPCI:SCC90 - replicate 1

description: BS-converted DNA

value: UPCI SCC90


title: HPV positive cell line UPCI:SCC47 - replicate 2

description: BS-converted DNA


title: Patient2 Y31

value: 45 years


title: HPV positive cell line UPCI:SCC90 - replicate 2

description: BS-converted DNA


title: Patient3 Y33

value: 16 years

value: female


title: HPV positive cell line 93VU-147T - replicate 1

description: BS-converted DNA


title: HPV- HNSCC sample FF 96

description: Ligated BS-converted DNA

source_name: HNSCC

extract_protocol: DNA from fresh-frozen HNSCC patient samples was extracted using the QIAamp DNA Blood Mini Kit (QIAGEN)

tag: tumour site

value: base of tongue

value: HPV- HNSCC tumor


title: HPV+ HNSCC sample FF 39

description: Ligated BS-converted DNA

value: tonsil

value: HPV+ HNSCC tumor


title: HPV+ HNSCC sample FF 105

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 92

description: Ligated BS-converted DNA

label_protocol: DNAs were prepared in a total volume of 20 µl (2 µg for FFPE DNA per sample) using a previously optimized protocol (Thirlwell et al. 2010) in conjunction with the REPLIg FFPE kit (Qiagen GmbH D-40724 Hilden, cat No. 150243) and EZ DNA Methylation kit (Zymo Research Corp, Orange, CA 92867, USA, cat No. D5001). The latter was modified to improve bisulphite conversion efficiency by inclusion of a cyclic denaturation step as described previously (Thirlwell et al. 2010).

extract_protocol: The QIAamp DNA FFPE Tissue Kit (QIAGEN) was used for the DNA extraction of laser dissected FFPE samples.


title: HPV- HNSCC sample FFPE 90

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FFPE 67

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 91

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FFPE 82

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FF 29

description: Ligated BS-converted DNA


title: pineapple_green vs yellow fruit_985_rep3

city: Brisbane

first: Jonni

last: Koia

address: Mansfield Place

department: School of Agriculture and Food Sciences

country: Australia

institute: University of Queensland

description: non-dye swap

hyb_protocol: Labelled cDNA was mixed with  20xSSC (20ul), liquid block (12ul), 2%SDS (4ul) and dH2O (up to 200ul total vol). Denatured labelled target was hybridised in submersible hybridisation cassette chambers (Ambion) at 55°C for 12h. Arrays then washed in 2x SSC (+0.5 % SDS), 1x SSC, 0.5x SSC and 0.05x SSC, each at RT  for 5 min prior to drying and scanning.

scan_protocol: Scanning was undertaken in an ArrayWorx scanner (Applied Precision)

data_processing:
Two raw data files for each slide; The first (*raw.txt) is the original raw data containing everything and the second (*2xSD+new_raw.txt) is an updated version of the first where many are filtered out that don't fall within 2 x standard deviations of the average.  Also, the second raw data files contains a batch of new sequence IDs that were flagged unsequenced (ie. JBW type, not contig # type) in the first original raw data.  Most of the new sequences were actually left out of the microarray, because they were found to be abundant from an earlier pineapple EST cDNA library report.

Spot editing was undertaken using SoftWorx Tracker. Data analysis was carried out using Genespring for biological replicate slides 506, 516 and 985. For each replicate slide, the mean and background intensity values from each channel (W595, W685) were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values.  Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from experimental and biological repeats before all replicates were combined (see Series Data Table). Data was compiled from three hybridisations, including one dye-swap replicate.

organism: Ananas comosus

source_name: pine9 mature yellow fruit_W595

label_protocol: Total RNA labelled with Cy3 and Cy5 using the LabelStar Array Kit (Qiagen) as per manufacturers instructions.

growth_protocol: Field grown

extract_protocol: Trizol

tag: developmental stage

value: pine9 mature yellow pineapple fruit

source_name: pine3 mature green fruit_W685

value: pine3 mature green pineapple fruit


title: HPV+ HNSCC sample FFPE 83

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FF 125

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FFPE 72

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FF 32

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FFPE 79

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 62

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FFPE 60

description: Ligated BS-converted DNA


title: Contol4 ZP35 MeDIP-chip

description: Contol4 ZP35

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc., Madison, WI, USA). For array hybridization, Roche Nimblegen's CpG Promoter array was used, which is a single array design containing all known CpG Islands annotated by UCSC and all well-characterized RefSeq promoter regions (from about -800bp to +200bp of the TSSs) totally covered by ~385, 000 probes

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 MeDIP-chip data extraction.

source_name: ZP35 MeDIP DNA from dermal MSCs

label_protocol: The purified DNA was quantified using a nanodrop ND-1000. For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.

growth_protocol: MSCs were cultured by adherent assay for 14 days

extract_protocol: Genomic DNA (gDNA) was extracted from 12 samples using a DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA). The purified gDNA was then quantified and quality assessed by nanodrop ND-1000. Genomic DNA of each sample was sonicated to ~200 – 1000 bp with a Bioruptor sonicator (Diagenode) on “Low” mode for 10 cycles of 30 seconds “ON” & 30 seconds “OFF”.

value: 36 years

source_name: input DNA from ZP35 dermal MSCs


title: HPV+ HNSCC sample FFPE 74

description: Ligated BS-converted DNA


title: pineapple_green vs yellow fruit_509_rep1

description: non-dye swap


title: HPV+ HNSCC sample FFPE 50

description: Ligated BS-converted DNA

value: tonsil/base of tongue


title: HPV- HNSCC sample FFPE 94

description: Ligated BS-converted DNA


title: Contol2 ZP33 MeDIP-chip

description: Contol2 ZP33

source_name: ZP33 MeDIP DNA from dermal MSCs

value: dermal mesenchymal stem cell

value: 37 years

source_name: input DNA from ZP33 dermal MSCs


title: HPV+ HNSCC sample FFPE 48

description: Ligated BS-converted DNA


title: Contol6 ZP38 MeDIP-chip

description: Contol6 ZP38

source_name: ZP38 MeDIP DNA from dermal MSCs

value: 44 years

value: male

source_name: input DNA from ZP38 dermal MSCs


title: Patient5 Y41 MeDIP-chip

description: Patient5 Y41

source_name: Y41 MeDIP DNA from dermal MSCs

value: 49 years

source_name: input DNA from Y41 dermal MSCs


title: HPV+ HNSCC sample FFPE 43

description: Ligated BS-converted DNA


title: Contol5 ZP36 MeDIP-chip

description: Contol5 ZP36

source_name: ZP36 MeDIP DNA from dermal MSCs

value: 21 years

source_name: input DNA from ZP36 dermal MSCs


title: HPV+ HNSCC sample FFPE 47

description: Ligated BS-converted DNA


title: Contol1 ZP30 MeDIP-chip

description: Contol1 ZP30

source_name: ZP30 MeDIP DNA from dermal MSCs

value: 28 yesrs

source_name: input DNA from ZP30 dermal MSCs


title: pineapple_green vs yellow fruit_516_rep2

description: dye swap

source_name: pine9 mature yellow fruit_W685

source_name: pine3 mature green fruit_W595


title: Contol3 ZP34 MeDIP-chip

description: Contol3 ZP34

source_name: ZP34 MeDIP DNA from dermal MSCs

value: 40 years

source_name: input DNA from ZP34 dermal MSCs


title: HPV- HNSCC sample FFPE 42

description: Ligated BS-converted DNA

source_name: HNSCC


title: HPV- HNSCC sample FFPE 30

description: Ligated BS-converted DNA


title: Gene regulation by FusK (HK) in Enterohemorrhagic E.coli 86-24

city: Dallas

first: Alline

middle: Roberta

last: Pacheco

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data has not been processed other than those protocols within GCOSv1.4

organism: Escherichia coli O157:H7

source_name: E.coli 86-24 fusK mutant

growth_protocol: DMEM logaritmic phase

extract_protocol: Ambion RiboPure RNA Isolation

value: fusK mutant

tag: growth protocol

value: grown to OD600 = 1.0


title: Gene regulation by FusR (RR) in Enterohemorrhagic E.coli 86-24

scan_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

source_name: E.coli 86-24 fusR mutant

value: fusR mutant


title: Patient4 Y40 MeDIP-chip

description: Patient4 Y40

source_name: Y40 MeDIP DNA from dermal MSCs

tag: tissue

value: 38 years

source_name: input DNA from Y40 dermal MSCs


title: HPV- HNSCC sample FFPE 36

description: Ligated BS-converted DNA

value: base of tongue

value: HPV- HNSCC tumor


title: HPV+ HNSCC sample FFPE 38

description: Ligated BS-converted DNA

value: tonsil

value: HPV+ HNSCC tumor


title: 14dCI_rep2

city: Princeton

first: Eric

middle: Jungwoo

last: Suh

state: NJ

address: 14 Washington Rd

department: Molecular Biology

institute: Princeton University

hyb_protocol: Labeled cRNA were hybridized to arrays according to Agilent's manufacturer's protocol

scan_protocol: Scanned using Agilent G2505B array scanner according to manufacturer's protocol.

data_processing: Probes were filtered to eliminate those flagged by Feature Extractor for saturation or no signal above background in any array Replicated signals from identical sequence-probes were averaged. For each array, the ratio of Cy5 to Cy3 (red to green) was log2 transformed and zero-centered.

source_name: 14 day contact inhibited cell line 2

label_protocol: Total RNA extracts were cRNA labeled using the Agilent Low RNA Input Fluorescent Labeling Kit according to the manufacturer's protocol

extract_protocol: Total RNA isolated from fibroblasts 48 hours post-transfection using mirVana total RNA isolation kit and procedure.

treatment_protocol: Fibroblasts were maintained in asynchronously proliferating culture, 7 days of contact inhibition, or 14 days of contact inhibition

value: Male

value: Fibroblast

source_name: Proliferating cell line 2


title: HPV- HNSCC sample FFPE 41

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 25

description: Ligated BS-converted DNA


title: 14dCI_rep1

source_name: 14 day contact inhibited cell line 1

source_name: Proliferating cell line 1


title: HPV- HNSCC sample FFPE 29

description: Ligated BS-converted DNA

value: tonsil/base of tongue


title: HPV+ HNSCC sample FFPE 37

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FFPE 35

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 24

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 14

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 7

description: Ligated BS-converted DNA


title: Meis-nega_TEC_rep2

city: Noda-shi

first: Ryo

last: Goitsuka

state: Chiba

address: 2669 Yamazaki

department: Division of Development & Aging

institute: Research Institute for Biological Sciences

description: gene expression in mouse thymic epithelial cells lacking Meis1 expression

hyb_protocol: 3 ug of Cy3 labeled cDNA (specific activity >15.0 pmol Cy3/ug cDNA) was 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 with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol: GE1-v5_95_Feb07 and Grid: 014868_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized data were analyzed using GeneSpring GX version 11.0.2 software (Agilent Technologies, Santa Clara, CA). Threshold raw signals to 1.0, Normalization algorithm: Percentile Shift, Normalization: Shift to 50 percentile

source_name: Meis-negative

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 10ng RNA using the WT-Ovation™ Pico RNA Amplification System (NuGEN) and Genomic Enzymatic Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Three populations of CD45- EpCAM+ thymic epithelial cells with different EGFP expression levels and cell sizes (EGFPhigh FSClow, EGFPint FSChigh and EGFP- FSClow) was sorted with a FACSAreaTMII (BD Bioscience, San Diego, CA) from 4-week-old Meis1-EGFP BAC-transgenic reporter mice, Tg(Meis1-EGFP)FO156Gsat/Mmcd), that were generated by the GENSAT BAC transgenic project.  RNA was isolated using the Qiagen RNeasy micro kit (Qiagen) following the manufacturer's recommendations. The protocol includes differential lysis of cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: 4 weeks

tag: meis1 expression levels

value: Negative

value: CD45- EpCAM+ thymic epithelial cell (TEC)


title: HPV+ HNSCC sample FFPE 19

description: Ligated BS-converted DNA


title: 7dCI_rep2

source_name: 7 day contact inhibited cell line 2


title: HPV- HNSCC sample FFPE 9

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 3

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FFPE 6

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 17

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 11

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FFPE 16

description: Ligated BS-converted DNA


title: HPV- HNSCC sample FFPE 12

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FFPE 26

description: Ligated BS-converted DNA


title: HPV+ HNSCC sample FFPE 28

description: Ligated BS-converted DNA


title: P_P_control

description: Co-hybridization control of proliferating cell line 1 and proliferating cell line 2


title: 7dCI_rep1

source_name: 7 day contact inhibited cell line 1


title: HPV- HNSCC sample FFPE 40

description: Ligated BS-converted DNA


title: Meis-nega_TEC_rep1


title: Meis-Low_TEC_rep1

description: gene expression in mouse thymic epithelial cells expresing low levels of Meis1

source_name: Meis-Low

value: Low


title: Meis-KO_TEC_rep1

description: gene expression in mouse thymic epithelial cells in the absence of Meis1

source_name: Meis-KO

extract_protocol: Thymic fragments were stirred gently in RPMI-1640 (Wako Pure Chemical Industries) medium for 15 min at 4°C to remove free thymocytes and then transferred to fresh medium containing 1.25 mg/ml collagenase / dispase with 0.01 mg/ml DNase I (Roche Diagnostics, Basel, Switzerland), and incubated for 15 min at 37°C and subjected to vigorous pipetting. The last three steps were repeated twice, discarding the supernatant each time, and incubation was continued until tissue digestion was complete. Released cells were filtered to remove clumps. For enrichment of the TEC populations, an immunomagnetic separation technique was performed using anti-CD45 coated beads and anti-Ter119 coated beads (Miltenyi Biotec) to deplete hematopoietic cells and erythroblasts. Purified TECs were sorted with a FACSAreaTMII or FACSvantage (BD Bioscience, San Diego, CA).  RNA was isolated using the Qiagen RNeasy micro kit (Qiagen) following the manufacturer's recommendations. The protocol includes differential lysis of cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: To induce Meis1 deletion, 3-week-old K14-CreERT2 Meis1fl/fl  (CKO) and K14-CreERT2 Meis1f//+ mice (controls) were injected intraperitoneally on 3 consecutive days with 1 mg of tamoxifen (Final concentration 20 mg/ml, Sigma-Aldrich, St Louis, MO) that was prepared following the manufacturer’s instructions by completely dissolving Tamoxifen into 200 ul of 100% ethanol at 55°C, adding 1800 ul of warmed sunflower oil, and mixing them well by vortexing. Four days after tamoxifen treatment, CD45- EpCAM+ mouse thymic epithelial cells were sorted with a FACSAreaTMII  (BD Bioscience, San Diego, CA).

value: K14-CreER Meis1fl/fl mice

tag: meis1 genotype

value: KO

value: thymic epithelial cells (CD45- EpCAM+)


title: HPV+ HNSCC sample FFPE 13

description: Ligated BS-converted DNA


title: Meis-Low_TEC_rep2

tag: genotype/variation


title: Meis-KO_TEC_rep2


title: Mouse Podocyte rep4

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: 2.47 µg labelled cDNA were hybridized onto the Affymetrix Mouse Gene 1.0 ST Array for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 7G using AGCC.

data_processing:
CEL files were imported and preprocessed with Genedata Refiner (GC background subtraction, RMA Quantile Normalisation, Median Polish summarisation). The resulting .abs-files were further analysed in Genedata Analyst
MoGene-1_0-st-v1.r4.mps.gz

source_name: Mouse Podocyte

label_protocol: Sense target cDNA was prepared from 500 ng total RNA using the Ambion WT Expression kit; the cDNAs were fragmented and labeled with the Affymetrix Terminal labeling and Controls kit according to the manufacturers protocol.

growth_protocol: Glomerula from 8 week old mice of mixed C57Bl6, Sv129/J and ICR background

extract_protocol: Chloroform/Phenol Extraction

treatment_protocol: Mouse kidneys were dissected and transfered into dishes with 37°C  Hank’s buffered salt solution. Each kidney was perfused through the renal artery with 4 ml 37°C warm bead solution and 1 ml bead solution plus enzymatic digestion buffer.  Kidneys were minced and after addition of 3 ml digestion buffer incubated at 37°C for 15 min on a rotator. After incubation all steps were performed at 4 °C or on ice. The digested kidneys were pressed twice through a 100 µm cellstrainer and the flow through washed with HBSS. After spinning down, the supernatant was discarded and the pellet resuspended in 2 ml HBSS. These tubes were inserted into a magnetic particle concentrator and the separated gloms were washed twice. Glomerula were resuspended in 2 ml digestion buffer and incubated for 40 min at 37°C on a thermomixer shaking at 1400/min. During the incubation period the following was done: glomerula were sheered with a 27G needle at 15 min, they were mixed by pipetting twice at 5, 10, 15, 20 and 25 min using a  glass pipette. Podocytes were loosened at 10, 20, 30 min by vortexing once. After 40 min the solution was vortexed three times and the digestion result controlled by fluorescence microscopy. Eppendorfs were put on a magnetic particle concentrator again to get rid of beads and glomerular structures void of podocytes. The supernatant was pooled and the magnetic particles discarded. The cell suspension (2 ml) was sieved through a 40 µm pore size filter on top of a 50 ml Falcon tube, rinsed with 10 ml of HBSS. Cells were collected by centrifugation at 1500 rpm for 5 min at 4°C, re-suspended in 0,5 ml of HBSS supplemented with 0.1% BSA plus DAPI (1µg/ml). To separate GFP-expressing (GFP+) and GFP-negative (GFP-) cells, glomerular cells were sorted with a Mo-Flo cell sorter (Beckman Coulter) with a Laser excitation at 488nm (Power 200 mW) and a sheath pressure of 60 PSI. Only viable (DAPI negative) cells were sorted (laser excitation 380nm, power 80 mW).

value: podocyte cell from kidney glomerulus

tag: genetic background

value: mixed C57Bl6, Sv129/J and ICR


title: Mouse Podocyte rep5

tag: cell type


title: CD103 type medium sheep 11261

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

hyb_protocol: Cy3 labeled cRNA was co-hybridized with the Cy5 reference probe for 17 hrs, at 65°C under 10 rpm

scan_protocol: Images were scanned using an Agilent G2505B Scanner at a 5 µm resolution with a single pass scanning mode and the eXtended Dynamic range selected

data_processing:
Images were quantified using Agilent Feature Extraction version 9.5.3.1 using the GE2-v5-95-Feb 07 protocole; Quantile normalized using median signal of the Red and Green signal.
normalized log2 ratio (Cy3/Cy5) representing test/reference. Data in column LogRatio in the .txt files are in log10 and correspond to the ratio Cy5/Cy3 (reference/test)

organism: Ovis aries

source_name: CD103 type medium sheep 11261

label_protocol: Agilent Low Input Quick Amp Labeling Kit, two-color (Catalog # 5190-2306)

extract_protocol: Total RNA Arcturus

treatment_protocol: cell sorting of CD1b+CD26+ (= CD103 type)  and CD1b+CD26- (= CD11b  type)  lymph DC/ Culture 16h in medium or with CAV2 (50PFU/CELL)

tag: subject

value: CD103 lymph dendritic cell medium sheep 11261

value: medium

tag: breed

value: Prealpes

source_name: Reference

tag: sample type

value: Reference

value: total dendritic cells


title: Meis-High_TEC_rep2

description: gene expression in mouse thymic epithelial cells expresing high levels of Meis1

source_name: Meis-High

tag: strain

value: High


title: Mouse Podocyte rep2


title: Meis-WT_TEC_rep1

description: gene expression in mouse thymic epithelial cells in the presence of Meis1

source_name: Meis-WT

value: K14-CreER Meis1fl/+ mice

value: WT


title: CD103 type CAV sheep 11261

source_name: CD103 type CAV sheep 11261

value: CD103 lymph dendritic cell CAV sheep 11261

tag: treatment

value: Canine Adenovirus serotype 2


title: CD11b type CAV sheep 11261

source_name: CD11b type medium sheep 11261

value: CD11b lymph dendritic cell CAV sheep 11261


title: Meis-High_TEC_rep1

tag: age

value: 4 weeks

value: CD45- EpCAM+ thymic epithelial cell (TEC)


title: CD11b type medium sheep 11261

value: CD11b lymph dendritic cell medium sheep 11261


title: Mouse Podocyte rep3


title: Meis-WT_TEC_rep2

value: thymic epithelial cells (CD45- EpCAM+)


title: CD11b type medium sheep 30066

source_name: CD11b type medium sheep 30066

value: CD11b lymph dendritic cell medium sheep 30066


title: Patient1 Y30 MeDIP-chip

description: Patient1 Y30

source_name: Y30 MeDIP DNA from dermal MSCs

value: dermal mesenchymal stem cell

value: 55 years

tag: gender

value: male

tag: pasi

source_name: input DNA from Y30 dermal MSCs


title: Mouse Podocyte rep1

value: podocyte cell from kidney glomerulus

value: mixed C57Bl6, Sv129/J and ICR


title: 421702A04-KKF527-I

city: San Antonio

first: Xhavit

last: Zogaj

address: One UTSA Circle

department: Biology

institute: UTSA

description: A whole genome NibleGen microarray was developed for multiple Francisella subspecies, using shared probes for common genes as well as unique probes for subspecies-specific genes. Included were probes representing the F. novicida U112 genome, with a maximum of 6 probes/gene. RNA was isolated from bacteria and purified as described above. The double-strand cDNA was generated and labeled with Cy3 according to the NimbleGen Gene Expression Array protocol (www.nimblegen.com), using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and the DNA Labeling Kit (NimbleGen). Microarray results were analyzed using the ArrayStar software (DNASTAR).

hyb_protocol: standard NimbleGen protocols

scan_protocol: standard NimbleGen protocols

data_processing: Microarray results were RMA normalized and analyzed using the ArrayStar software (DNASTAR).

organism: Francisella tularensis subsp. novicida

source_name: log phase culture

extract_protocol: Total RNA was isolated from mid log (OD600 ~0.6) F. novicida cultures grown at 37°C in CDM, using TRIzol Reagent (Ambion), and further purified using the RNeasy Mini Kit (Qiagen). RNA concentrations were determined using the Nano Drop 1000 Spectrophotometer (Thermo Scientific). The isolated RNA was treated with DNase I (Turbo DNA-free kit, Ambion) and reverse-transcribed using random primers to produce cDNA (Invitrogen). cDNA was amplified with the Applied Biosystems ABI 7500 real-time PCR system, using Sybr-Green PCR-Master Mix (Applied Biosystems).

tag: growth phase

value: mid log (OD:0.6)


title: CD103 type CAV sheep 30066

source_name: CD103 type CAV sheep 30066

value: CD103 lymph dendritic cell CAV sheep 30066

value: Prealpes

value: Reference

value: total dendritic cells


title: Mouse Non Podocyte rep4

source_name: Mouse Non Podocyte

value: non-podocyte cell from kidney glomerulus


title: CD11b type CAV sheep 30066

source_name: CD11b type CAV sheep 30066

value: CD11b lymph dendritic cell CAV sheep 30066

value: Canine Adenovirus serotype 2


title: 421702A03-KKF526-II

label_protocol: The double-strand cDNA was generated and labeled with Cy3 according to the NimbleGen Gene Expression Array protocol (www.nimblegen.com), using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and the DNA Labeling Kit (NimbleGen).

growth_protocol: Total RNA was isolated from mid log (OD600 ~0.6) F. novicida cultures grown at 37°C in CDM


title: Patient4 Y36 MeDIP-chip

description: Patient4 Y36

source_name: Y36 MeDIP DNA from dermal MSCs

value: 29 years

source_name: input DNA from Y36 dermal MSCs


title: Mouse Non Podocyte rep5


title: 421702A01-KKF527-II


title: CD103 type CAV sheep 50274

source_name: CD103 type CAV sheep 50274

value: CD103 lymph dendritic cell CAV sheep 50274


title: Mouse Non Podocyte rep3


title: CD103 type medium sheep 30066

source_name: CD103 type medium sheep 30066

value: CD103 lymph dendritic cell medium sheep 30066

value: medium


title: Patient2 Y31 MeDIP-chip

description: Patient2 Y31

source_name: Y31 MeDIP DNA from dermal MSCs

value: dermal mesenchymal stem cell

value: 45 years

value: female

source_name: input DNA from Y31 dermal MSCs


title: Mouse Non Podocyte rep2


title: 421702A02-KKF526-I


title: Patient3 Y33 MeDIP-chip

description: Patient3 Y33

source_name: Y33 MeDIP DNA from dermal MSCs

value: 16 years

source_name: input DNA from Y33 dermal MSCs


title: CD11b type medium sheep 50274

source_name: CD11b type medium sheep 50274

value: CD11b lymph dendritic cell medium sheep 50274

source_name: Reference


title: HPV- HNSCC sample FFPE 10

description: Ligated BS-converted DNA

source_name: HNSCC

tag: tumour site

value: tonsil

value: HPV- HNSCC tumor


title: 126KD 22A n

city: Toronto

first: John

middle: E

last: Dick

address: 101 College St. Toronto

country: Canada

institute: Ontario Cancer Institute

description:
replicate 3
22A n

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanned with Illumina’s BeadArray Reader using standard protocols

data_processing: The data were normalised using quantile normalisation (GeneSpring GX10.0.2)

label_protocol: cRNA was prepared using Ambion - Illumina TotalPrep-96 RNA Amplification Kit

extract_protocol: RNA was extracted using Trizol reagent

tag: source tissue

value: umbilical cord blood

value: CD34+/CD38- Lin- cells

value: mir126 knockdown


title: 126OE 24A n

description:
replicate 3
24A n

value: overexpression control


title: CD11b type CAV sheep 50274

source_name: CD11b type CAV sheep 50274

value: CD11b lymph dendritic cell CAVsheep 50274

value: Prealpes

value: Reference

value: total dendritic cells


title: CD11b type CAV sheep 70958

source_name: CD11b type CAV sheep 70958

value: CD11b lymph dendritic cell CAV sheep 70958

value: Canine Adenovirus serotype 2


title: OE control 23A n

description:
replicate 3
23A n

value: mir126 overexpression


title: HPV+ HNSCC sample FFPE 8

description: Ligated BS-converted DNA

tag: tissue

value: HPV+ HNSCC tumor


title: KD control 21A n

description:
replicate 3
21A n

value: knockdown control


title: 126OE 20A n

description:
replicate 2
20A n


title: A. aceti glyoxylate pathway mutant #2

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

department: Department of Biotechnology

institute: The University of Tokyo

description: This sample is of A. aceti aceA glucB mutant strain GP cells during growth on ethanol and glucose at exponential phase. It is the second of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed with Hybridization System 4 according to the NimbleGen Arrays User´s Guide for Gene Expression Analysis (Roche NimbleGen).

scan_protocol: Array scanning was performed with MS200 Microarray Scanner according to the NimbleGen Arrays User´s Guide for Gene Expression Analysis (Roche NimbleGen).

data_processing: The raw data (.pair file) was subjected to RMA, quantile normalization, and background correction as implemented in the NimbleScan software 2.5 (Roche NimbleGen).

organism: Acetobacter aceti NBRC 14818

source_name: A. aceti, glyoxylate pathway mutant replicate 2

label_protocol: Labeling of double stranded cDNA synthesized with the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) was performed according to the instructions for NimbleGen Arrays User’s Guide for Gene Expression Analysis by Roche NimbleGen using One-Color DNA Labeling Kit (Roche NimbleGen).

growth_protocol: A. aceti strains were cultivated in mixed medium consisting of 1% yeast extract, 200 mM ethanol, and 200 mM glucose in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.3.

extract_protocol: Total RNA was extracted by a hot-phenol method. After contaminated DNA was eliminated by RQ1 DNase (Promega) treatment, RNA was purified by RNeasy mini columns (Qiagen).

treatment_protocol: The culture was mixed with 2 volumes of RNAprotect Bacterial Reagent (Qiagen) before RNA purification.

tag: genotype

value: aceA glcB


title: A. aceti glyoxylate pathway mutant #1

description: This sample is of A. aceti aceA glucB mutant strain GP cells during growth on ethanol and glucose at exponential phase. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, glyoxylate pathway mutant replicate 1


title: A. aceti wild type #2

description: This sample is of A. aceti NBRC14818 cells during growth on ethanol and glucose at exponential phase. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, wild type replicate 2

value: wild type


title: CD103 type medium sheep 70958

source_name: CD103 type medium sheep 70958

value: CD103 lymph dendritic cell medium sheep 70958

value: medium


title: CD103 type CAV sheep 70958

source_name: CD103 type CAV sheep 70958

value: CD103 lymph dendritic cell CAV sheep 70958


title: 126OE 16A

description:
replicate 1
16A

value: umbilical cord blood

value: CD34+/CD38- Lin- cells


title: OE control 19A n

description:
replicate 2
19A n


title: KD control 17A n

description:
replicate 2
17A n


title: CD11b type medium sheep 70958

source_name: CD11b type medium sheep 70958

value: CD11b lymph dendritic cell medium sheep 70958


title: Sample 8 - AML evolution of sample 7

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from acute myeloid leukemia  samples at evolution post MDS

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450dx.

scan_protocol: GeneChips were scanned using the Scan GCS3000dx

data_processing: MAS 5.0

source_name: stored, frozen Bone Marrow cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA purification using selective binding columns

treatment_protocol: stored, frozen Bone Marrow

tag: disease state

value: AML

value: Bone Marrow

tag: individual

value: patient 4


title: A. aceti wild type #1

description: This sample is of A. aceti NBRC14818 cells during growth on ethanol and glucose at exponential phase. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, wild type replicate 1


title: 126KD 18A n

description:
replicate 2
18A n

value: mir126 knockdown


title: OE control 15A

description:
replicate 1
15A


title: Sample 3 - MDs at diagnosis

description: Gene expression data from myelodysplastic sindrome samples at diagnosis

value: MDS

value: patient 2


title: Sample 2 -AML evolution of sample 1

value: patient 1


title: Sample 5 - MDS at diagnosis

value: patient 3


title: Sample 6 - AML evolution of sample 5


title: 126KD 14A n

description:
replicate 1
14A n


title: Sample 4 -AML evolution of sample 3


title: Sample 1 - MDS at diagnosis


title: CD103 type medium sheep 50274

source_name: CD103 type medium sheep 50274

value: CD103 lymph dendritic cell medium sheep 50274

value: Prealpes

value: Reference

value: total dendritic cells


title: Sample 7 - MDS at diagnosis


title: Mouse Non Podocyte rep1

source_name: Mouse Non Podocyte

value: non-podocyte cell from kidney glomerulus

tag: genetic background

value: mixed C57Bl6, Sv129/J and ICR


title: KD control 13A

description:
replicate 1
13A

value: umbilical cord blood

tag: cell type

value: knockdown control


title: N_H16_I5_a1486_M

status: Public on Nov 29 2012

city: Bethesda

first: Luis Fernando

last: Menezes

state: MD

address: Room 8D12A, Building 10, 10 Center Dr

department: NIDDK

institute: National Institutes of Health

description:
Array name: X4165582020_F
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4

hyb_protocol: 0.75 ugs of biotin-labeled cRNA was hybridized according to standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: The data were normalized using VST transformation with lummi in R.

source_name: Kidney

label_protocol: cRNA was generated and labeled by incorporating biotin-16-UTP.

extract_protocol: RNA was isolated using Trizol (Invitrogen), followed by RNeasy plus kit (Qiagen)

tag: genotype (n

value: Control; P:Mutant):N

tag: age induced (days)

tag: age harvested (days)

tag: gender (m

value: Male; F:Female; U:Unknown):M

tag: litter

tag: batch


title: N_H16_I5_a1487_M

description:
Array name: X4165582020_G
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: N_H24_I8_a1334_F

description:
Array name: X4165582020_C
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4

value: Male; F:Female; U:Unknown):F


title: N_H16_I9_a1467_M

description:
Array name: X4160651012_F
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: P_H16_I9_a1468_M

description:
Array name: X4160651012_G
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4

value: Control; P:Mutant):P


title: P_H16_I5_a1484_M

description:
Array name: X4165582020_E
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: P_H24_I8_a1337_F

description:
Array name: X4165582020_D
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: P_H16_I5_a1488_M

description:
Array name: X4165582020_H
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: P_H17_I8_a1335_M

description:
Array name: X4160651012_C
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: P_H17_I8_a1336_M

description:
Array name: X4160651012_D
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: N_H16_I9_a1469_M

description:
Array name: X4160651012_H
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: N_H17_I8_a1332_F

description:
Array name: X4160651012_B
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: RUNX1(41-214), biological replicate 2

city: La Jolla

first: Dong-Er

last: Zhang

state: CA

address: 3855 Health Sciences Drive

department: Moores UCSD Cancer Center

institute: University of California San Diego

description:
RUNX1(41-214)_2
Gene expression data from KSL cells from RUNX1(41-214)-expressing mice

hyb_protocol: Arrays were hybridized using standard Affymetrix protocol as described in Lockhart et al, 1996. (http://affymetrix.com)

scan_protocol: The chips were scanned using the Affymetrix GeneChip Scanner 3000 using defalt settings and a target intensity of 250 for scaling.

data_processing: Microarray analysis was performed in dChip. There was information available on 22,690 genes for each array. Normalization was performed using the invariant set method by Wong and Li (2001). ANOVA filtering criterion was used, with a cutoff of p<=0.02. Groups were compared using the following criteria: ratio greater than 2.0, p-value for testing Experimental=Baseline less than 0.05, P call of either Baseline or Experimental greater than 20%.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling protocol  (Affymetrix P/N 900494).

extract_protocol: Total RNA was extracted from cell pellets using Qiagen microcolumns

tag: strain background

tag: genotype/variation

value: RUNX1(41-214)-expressing mice

tag: transduced with

value: bone marrow

value: sorted c-Kit+/Sca-1+/Lin-/IL7Ra- (KSL) cells

tag: experimental procedure

value: 4 months after transduction/transplantation with RUNX1(41-214)-expressing retroviral vector


title: RUNX1(41-214), biological replicate 3

description:
RUNX1(41-214)_3
Gene expression data from KSL cells from RUNX1(41-214)-expressing mice


title: Runx1KO, biological replicate 3

description:
Runx1KO_3
Gene expression data from KSL cells from Runx1-knockout mice

source_name: KSL cells from Runx1-knockout mice (Runx1floxed/floxedMxCre+/-)

value: 3 months after poly IC treatment


title: N_H17_I8_a1331_M

description:
Array name: X4160651012_A
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: Control, biological replicate 3

description:
Control_3
Gene expression data from KSL cells from control mice

source_name: KSL cells from control mice (Runx1floxed/floxedMxCre-/-)


title: RUNX1(41-214), biological replicate 1

description:
RUNX1(41-214)_1
Gene expression data from KSL cells from RUNX1(41-214)-expressing mice


title: P_H16_I9_a1466_F

description:
Array name: X4160651012_E
Title format: Genotype_AgeHarvested_AgeInduced_AnimalNumber_Gender
Label of raw data matrix: LM4


title: nucleus pulposus, Control  rep4

city: Philadelphia

first: Dessislava

middle: Z

last: Markova

state: PA

address: 1015 Walnut

department: Orthopaedic Surgery

institute: Thomas Jefferson University

description: Gene expression data from nucleus pulposus no treated with TNF-alpha, IL-1beta

hyb_protocol: Each Affymetrix Rat Gene array (RaGene 1.0 ST v1) was hybridized with fragmented and biotin-labeled target for 18h. Arrays were then washed and stained using Gene-chip Fluidic Station 450.

scan_protocol: GeneChips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Background correction and normalization were done using Robust Multichip Average (RMA) with Gene-spring V 11.5 software (Agilent, Palo Alto, CA, USA). A volcano plot was used to identify differentially expressed genes using the unpaired two-sample Student’s t-test, assuming significance for p-values less than or equal to 0.05, and fold changes more than or equal to 1.5.  A heat map was generated by Gene-spring software V 11.5.  The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA-8.8) software (http://www.ingenuity.com)

organism: Rattus norvegicus

source_name: Intervertebral disc no treated with TNF-alpha, IL-1beta

label_protocol: RNA amplification and labeling was performed from 50 ng total RNA by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)

growth_protocol: Wistar rats (250–300 g, Charles River Laboratories, Wilmington, MA) were euthanized with CO2 and the spinal columns were removed en bloc under aseptic conditions. Soft tissues and posterior elements were removed and lumbar discs were rinsed in saline solution before being placed in 48-well culture plates.

extract_protocol: The discs were collected and the annulus fibrosus (AF) was separated from the nucleus pulposus (NP). The tissues were stabilized in RNA later following manufacturer’s instructions and stored at -80°C.  Total RNA was extracted using the RNeasy Micro kit according to the manufacturer’s instructions. The DNA template from the RNA preparation was removed using the DNase I digestion.

treatment_protocol: All experimental lumbar disc specimens (n = 6 discs/animal) were cultured  in Dulbecco’s modified Eagle medium (DMEM) containing 1% fetal bovine serum (FBS), 100 ng/ml tumor necrosis factor alpha (TNF-α), 10 ng/ml interleukin-1beta (IL-1β) , 50 µg/ml L-ascorbate, 40 mM NaCl, antibiotics. Control group discs were cultured in DMEM containing 10% FBS, 50 µg/ml L-ascorbate, 40 mM NaCl and antibiotics.  The discs were maintained in culture 10 days.

tag: strain

value: Wistar

tag: gender

value: male

tag: age

tag: treatment

value: control

value: nucleus pulposus


title: nucleus pulposus, Experimental rep3

description: Gene expression data from nucleus pulposus treated with TNF-alpha, IL-1beta

source_name: Intervertebral disc treated with TNF-alpha, IL-1beta

value: TNF-alpha, IL-1beta

tag: tissue


title: Mycobacterium tuberculosis-Spheroplast induced

city: Amherst

first: Andrea

last: Cossu

state: MA

address: 102 Holdsworth way

department: Department of Food Science

institute: University of Massachusetts, Amherst

description: 5 Technical (spot) replicates. Mycobacterium tuberculosis, spheroplast induced.

hyb_protocol: Hybridization was performed following the Recommended Sample Preparation and Hybridization Protocol drawn-up by the MYcroarrays® Company (Biodiscovery LLC) with some modifications. 220µl of hybridization solution (66µl of 20X SSPE (3M NaCl, 20mM EDTA, 118.2mM NaH2PO4, 81.8mM Na2HPO4), 10% formamide, 0.01mg/ml BSA, 0.01% Tween-20, 1mM DTT, 1% manufacturer control oligos, 10µg of each target coupled-aRNA, RNAse-free water to final volume) was prepared and pre-warmed at 56°C. Hybridizations were carried out in a water bath at 55°C for 18h with OneArray Sealed Hybridization Chambers (PhalanxBio Inc., Palo Alto, CA, USA). After incubation, slides were washed twice with SSPE 1X- 0.1mM DTT for 2 min followed by a 30 sec final wash with 0.25 X SSPE – 0.1mM DTT, dried with air-spray and immediately scanned.

scan_protocol: Scans were carried out with the Gene Pix AXON 4200A instrument (Axon Instruments) at 5-um resolution with full dynamic range of signal intensities at 1 – 65.000 in two-colour red/green mode (635nm and 532 nm filters).

data_processing:
The intensities of the two dyes for each spot were quantified using the Gene Pix 6.0 Software and calculated as the mean of median intensity of each replicate spot for each gene. Total array intensity was used to normalize spot signal intensities with the ratio-mean based algorithm option. Subtraction of local feature background median was achieved as default. Negative corrected intensities were set to 10 .
A change of 2-fold in the intensities with a p-value < 0.05 was considered significant for a differential gene expression. Data were trasnformed in normalized log2 ratio (Alexa Fluor dye 555/647) representing MTB-exp/MTBk-.

label: Alexa Fluor 555

organism: Mycobacterium tuberculosis H37Rv

source_name: M. tuberculosis spheroplast induced

label_protocol: Forty µg samples of amplified RNA (aRNA)  were labelled with either Alexa Fluor dye 647 or 555  purchased from Invitrogen, USA, following manufacturer's protocol. Purification of coupled aRNA was performed by RNeasy purification system (Qiagen) and incorporation of dye was evaluated using the Nanodrop spectrophotometer. Before hybridization, coupled aRNA was fragmented using the RNA fragmentation reagents (Ambion, Inc) following the manufacturer's protocol.

growth_protocol: MTB H37Rv (ATCC 25618)  was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA) and 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA) in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C before lysozyme treatement.

extract_protocol: tot-RNA extracted with the RiboPure-Bacteria Kit (Ambion, Inc). Mycobacterial cells were re-suspended in 350µl of RNAwiz solution and transferred to a 0.5ml RNAse-free skirted screw-cap microcentrifuge tube containing 250µl of 0.1mm ice-cold Zirconia Beads. Tubes were immediately processed in the RiboLyser RNA Lysing Machine (RiboLyser FP120-HY-230, Hybaid) for 2 cycles (30s at speed 6.5 with 1 min of cooling interval between each bead beating step). Remaining steps were performed according to the manufacturer’s instructions. All RNA samples were treated with Dnase I (Ambion, Inc)  and  purified by RNeasy column (Qiagen). RNA yield and purity was evaluated with the Nanodrop spectrophotometer (NanoDrop1000, Thermo Scientific) and RNA quality was examined by Denaturing Gel Electrophoresis. We carried out three independent experiments on three different flasks. Good quality RNA samples obtained from each pellet were then pooled together and used for microarray experiments to get an average of three separate experiments. mRNA was obtained by using the MICROBExpress Bacterial mRNA Purification Kit (Ambion) and was lineary amplified bu using the MessageAmp II Bacterial Kit (Ambion, Inc)

treatment_protocol: Mid log-phase cells were treated with a 1% glycine solution in 7H9/ADC/Tw80 medium for 72h at 37°C. Pre-spheroplasts were harvested by centrifugation at 5800 x g for 15min at RTand washed 2 times with a sucrose – MgCl2 (SM) solution (0.5M sucrose, 20mM MgCl2). The cell pellet was re-suspended in the original volume of 7H9/ADC/Tw80-SM (60:40) solution supplemented with 25μg/ml lysozyme (Sigma-Aldrich, MO, USA) and 1.2% glycine. Conversion from the bacillary form to the CWD state was completed after 5 days at 37°C.

tag: bacterial cells

value: Mycobacterium tuberculosis

label: Alexa Fluor 647

source_name: M. tuberculosis control untreated

growth_protocol: MTB H37Rv (ATCC 25618)  was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA) and 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA) in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C until mid-log phase.

treatment_protocol: Mid log-phase cells were grown in 7H9/ADC/Tw80 medium for 72h at 37°C. Cells were harvested by centrifugation at 5800 x g for 15min at RTand washed 2 times with PBS/Tw80. The cell pellet was re-suspended in the original volume of 7H9/ADC/Tw80 and incubated  5 days  at 37°C.


title: nucleus pulposus, Experimental rep4


title: nucleus pulposus, Experimental rep2


title: Runx1KO, biological replicate 1

description:
Runx1KO_1
Gene expression data from KSL cells from Runx1-knockout mice

tag: cell type


title: Runx1KO, biological replicate 2

description:
Runx1KO_2
Gene expression data from KSL cells from Runx1-knockout mice


title: nucleus pulposus, Control  rep3


title: Control, biological replicate 1

description:
Control_1
Gene expression data from KSL cells from control mice


title: HBEC6 4Gy 7 days

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: 5mC profile in HBEC6 sample

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: Loess normalization was applied excluding top 5% probes with the largest original Cy5/Cy3 log2 ratio

source_name: HBEC6 4Gy-7days 5mC (MIRA) enriched samples

label_protocol: According to standard NimbleGen Protocol

extract_protocol: MinElute PCR Purification Kit (Qiagen; Valencia, CA). Genomic DNA was fragmented by sonication to an average size of ~400 bp using a Sonifier cell disruptor 350 (Branson; Danbury, CT).

treatment_protocol: 4 Gy; 7 days recovery time after harvest

value: Normal human bronchial epithelial cells

tag: enrichment procedure

value: 5mC (MIRA)

tag: antibody

value: In Lab purified His-MBD3L1 & GST-MBD2b

source_name: HBEC6 input DNA

tag: sample type

value: input DNA


title: nucleus pulposus, Control  rep2


title: Control, biological replicate 2

description:
Control_2
Gene expression data from KSL cells from control mice


title: UNC93b-/- iPS-derived neurons CD44- EGFR- biological rep 1-1

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
Gene expression data from UNC93B-/- iPS derived neurons
FL7

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX ref8 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina BeadArray Reader scanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. Quantile normalization is performed.

source_name: Neurons CD44- EGFR- from UNC93B-/-

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

tag: cell line

value: UNC93b-/- iPS

value: neurons CD44- EGFR-


title: H9-derived oligodendrocytes technical rep 1-2-2

description:
Gene expression data from H9 oligos
M2-bis

source_name: Oligos O4+ from H9

value: oligodendrocytes


title: H9-derived astrocytes technical rep 1-1-2

description:
Gene expression data from H9 astrocytes
N1-bis

source_name: Astrocytes from H9

value: astrocytes


title: UNC93b-/- iPS-derived astrocytes biological rep 1-2

description:
Gene expression data from UNC93B-/- iPS derived astrocytes
FL11

source_name: Astrocytes from UNC93B-/-


title: H9-derived neurons CD44- EGFR- biological rep 1-2

description:
Gene expression data from H9 neurons
FL2

source_name: Neurons CD44- EGFR- from H9


title: H9-derived astrocytes biological rep 1-2

description:
Gene expression data from H9 astrocytes
N3


title: UNC93b-/- iPS-derived astrocytes biological rep 1-1

description:
Gene expression data from UNC93B-/- iPS derived astrocytes
FL10


title: nucleus pulposus, Experimental rep1


title: HFB2 0Gy 7 days

description: 5mC profile in HFB2 sample

source_name: HFB2 0Gy-7days 5mC (MIRA) enriched samples

treatment_protocol: 0 Gy; 7 days recovery time before harvest

value: Normal human diploid fibroblasts

source_name: HFB2 input DNA


title: H9-derived neurons CD44- EGFR- biological rep 1-3

description:
Gene expression data from H9 neurons
FL3


title: HFB6 10Gy 7 days

description: 5mC profile in HFB6 sample

source_name: HFB6 10Gy-7days 5mC (MIRA) enriched samples

treatment_protocol: 10 Gy; 7 days recovery time before harvest

source_name: HFB6 input DNA


title: UNC93b-/- iPS-derived neurons CD44- EGFR- biological rep 1-2

description:
Gene expression data from UNC93B-/- iPS derived neurons
FL8


title: H9-derived neurons CD44- EGFR- biological rep 1-1

description:
Gene expression data from H9 neurons
FL1


title: H9-derived astrocytes biological rep 1-1-1

description:
Gene expression data from H9 astrocytes
N1


title: H9-derived oligodendrocytes biological rep 1-2-1

description:
Gene expression data from H9 oligos
M2


title: HBEC1 0Gy 0 days

description: 5mC profile in HBEC1 sample

source_name: HBEC1 0Gy-0days 5mC (MIRA) enriched samples

treatment_protocol: 0 Gy; no recovery time before harvest

value: 0 Gy; no recovery time before harvest

source_name: HBEC1 input DNA


title: HBEC3 0Gy 7 days

description: 5mC profile in HBEC3 sample

source_name: HBEC3 0Gy-7days 5mC (MIRA) enriched samples

treatment_protocol: 0 Gy;7 days recovery time before harvest

source_name: HBEC3 input DNA


title: HBEC4 0.1Gy 7 days

description: 5mC profile in HBEC4 sample

source_name: HBEC4 0.1Gy-7days 5mC (MIRA) enriched samples

treatment_protocol: 0.1 Gy; 7 days recovery time before harvest

source_name: HBEC4 input DNA


title: Monoculture C26_mono

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

description: Monoculture C26_mono

hyb_protocol: standard Nimblegen protocol

scan_protocol: standard Nimblegen protocol

data_processing: quantile normalized the probe intensities to match the G20 mono culture  sample and averaged the log2 values for each gene and set the median log2 expression level in each sample to zero

label: Alexa fluor 555

organism: Oleidesulfovibrio alaskensis G20

source_name: Desulfovibrio alaskensis str. G20 in sulfate-limited monoculture (chemostat dilution rate 0.047h-1)

label_protocol: prepared first-strand labeled cDNA with SuperScript Plus Indirect cDNA Labeling Module (Invitrogen)

growth_protocol: We collected expression data for 2 growth conditions: syntrophic or respiratory growth of Desulfovibrio alaskensis str. G20 on lactate. Desulfovibrio alaskensis str. G20 was grown in monoculture under sulfate-limited conditions and in syntrophic coculture with the methanogen Methanococcus maripaludis. The basal salt solution of the media is described in Walker et. al. (2009) and contained 30 mM sodium DL-lactate or sodium pyruvate, resazurin as redox indicator, and 10 mM Na2SO4 (chemostat monoculture media) or 30 mM Na2SO4 (batch monoculture media). The media were prepared in bioreactor glass vessels (2 liters), medium reservoir bottles (10 liters) and Widdel flasks (1 and 2 liters) anoxically under a N2-CO2 (80:20, v/ v) gas atmosphere according to Widdel and Bak (1992). The media were buffered using 1.1 mM KH2PO4 and 30 mM NaHCO3. Nonchelated trace element mixture 1 and selenite-tungstate solution as well as vitamin mixture, riboflavin, vitamin B1 and B12 solutions and [1M] Na2S solution (79) were added aseptically in 1 ml aliquots per liter of medium. All stock solutions were prepared under anoxic conditions. For batch culture cultivation, the media were dispensed anoxically in sterile N2-CO2 (80:20, v/ v) pre-gassed 250 ml serum bottles or 25 ml Balch tubes in 130 and 13 ml aliquots, repectively. After preparation, the bioreactor and medium reservoir bottles were connected to a N2-CO2 (90:10, v/ v) gas mixture tank.  Cells were harvested from triplicate mono- and coculture chemostat runs after at least 3 volume turnovers at steady state in the chemostat at constant dilution rate of 0.047h-1.  The effect of time for harvesting on transcription results was examined for two reactor studies by collecting biomass at two time points separated by 15 min. at the end of the chemostat run (named E as early harvest  and L as late harvest) giving a total of five coculture and three monoculture gene expression data set.

extract_protocol: Isolated total RNA with RNAeasy mini kit (Qiagen)

treatment_protocol: Varying growth conditions: syntrophy versus sulfate respiration on substrate lactate

tag: carbon source

value: lactate (30 mM)

tag: electron acceptor

value: sulfate (10 mM)

tag: stressor

value: growth rate 0.047h-1 (chemostat growth)


title: HBEC5 1Gy 7 days

description: 5mC profile in HBEC5 sample

source_name: HBEC5 1Gy-7days 5mC (MIRA) enriched samples

treatment_protocol: 1 Gy; 7 days recovery time after harvest

source_name: HBEC5 input DNA


title: HBEC2 4Gy 0 days

description: 5mC profile in HBEC2 sample

source_name: HBEC2 4Gy-0days 5mC (MIRA) enriched samples

treatment_protocol: 4 Gy; no recovery time before harvest

value: 4 Gy; no recovery time before harvest

source_name: HBEC2 input DNA


title: HFB4 1Gy 7 days

description: 5mC profile in HFB4 sample

source_name: HFB4 1Gy-7days 5mC (MIRA) enriched samples

treatment_protocol: 1 Gy; 7 days recovery time before harvest

source_name: HFB4 input DNA


title: Coculture C20_co

description: Coculture C20_co

source_name: Desulfovibrio alaskensis str. G20 in syntrophic coculture with Methanococcus maripaludis (chemostat dilution rate 0.047h-1)


title: HFB5 4Gy 7 days

description: 5mC profile in HFB5 sample

source_name: HFB5 4Gy-7days 5mC (MIRA) enriched samples

treatment_protocol: 4 Gy; 7 days recovery time before harvest

source_name: HFB5 input DNA


title: Coculture C22L_co

description: Coculture C22L_co


title: Coculture C22E_co

description: Coculture C22E_co


title: H9-derived neural rosettes biological rep 1-2

description:
Gene expression data from neural rosettes
B2

source_name: neural rosettes manually purified

value: neural rosettes


title: Coculture C18L_co

description: Coculture C18L_co


title: Monoculture C19L_mono

description: Monoculture C19L_mono


title: H9 hESCs biological rep 1-3

description:
Gene expression data from H9 hESC line
A3

source_name: hESCs

value: undifferentiated hESC


title: nucleus pulposus, Control  rep1

description: Gene expression data from nucleus pulposus no treated with TNF-alpha, IL-1beta

source_name: Intervertebral disc no treated with TNF-alpha, IL-1beta

value: Wistar

value: male

value: control

value: nucleus pulposus


title: Coculture C18E_co

description: Coculture C18E_co


title: H9 hESCs biological rep 1-1

description:
Gene expression data from H9 hESC line
A1