title: Recurrent melanoma patient A, 3rd recurrence, 1st synchronous lesion

description: Recurrent melanoma isolated from patient A, 3rd recurrence, 1st synchronous lesion

value: melanoma cells

value: Recurrent

tag: origin


title: Dorsal Dentate Control #6

status: Public on Dec 31 2013

type: RNA

city: Philadelphia

first: mark

last: alter

state: PA

address: 125 S. 31st Street

department: Center for Neurobiology and Behvior

country: USA

institute: University of Pennsylvania

description: Dorsal untreated

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Robust Multiarray Analysis in Affymetrix Expression Console

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Dorsal dentate gyrus

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

tag: tissue

value: Dorsal dentate gyrus

tag: strain

tag: gender

value: male

tag: age

value: 7-8 wks

tag: treatment

value: untreated

tag: response

value: control


title: Dorsal Dentate Control #5

description: Dorsal untreated


title: Dorsal Dentate Control #4

description: Dorsal untreated


title: 7420044_PBS d15

city: Liège

first: Claire

last: Josse

state: Liège

address: rue de l'hopital, 1

department: Medical Oncology

country: Belgium

institute: CHU Liege

description:
0007420044_raw
biological replicate 3 of 5. Control mice. First point of 2 time points

hyb_protocol: Hy3 and Hy5 labeled (sample_ch1 and sample_ch2) RNA were combined and hybridized overnight to miRXplore™ microarrays (Miltenyi Biotec GmbH) using the a-Hyb™ Hybridization Station (Miltenyi Biotec)

scan_protocol: Image capture and signal quantification of hybridized miRXplore™ microarrays microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification was done using ImaGene software version 8.0.1 (BioDiscovery, Los Angeles, MA). Median normalization was performed using the calibration oligos

organism: synthetic construct

label_protocol: 2 µg of respective total RNA as well as 2 fmol of the Universal Reference (Miltenyi Biotec GmbH) were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labeled using a commercial kit (miRCury™ LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix was hybridized in a dual colour approach to miRXplore™ microarrays (Miltenyi Biotec GmbH).

extract_protocol: RNA were extracted from the whole colon with 8 mL Tripur according to the manufacturer's instructions.

treatment_protocol: AOM 12 mg/kg in PBS, one intraperitoneal injection at day 1. DSS 2% in drinkable water, 3 cycles administration of 5 days followed by 16 days recovery. Fisrt day of first DSS cycle at day 7.

tag: reference

value: syntethic miRNA pool of 954 synthetic miRNAs in equimolar concentrations  from human, mouse, rat, and virus

source_name: PBS d15

value: Whole colonic tissue

value: PBS treated-mice for 15 days


title: 7420043_PBS d15

description:
0007420043_raw
biological replicate 2 of 5. Control mice. First point of 2 time points

source_name: Universal Reference (Miltenyi Biotec GmbH)


title: KP_MGH_capsule_WT_rep1

city: Zhunan

first: Tzu-Wen

last: Huang

address: 35 Keyan Road

department: Institute of Molecular and Genomic Medicine

country: Taiwan

institute: National Health Research Institutes

description: This sample is of wild-type K. pneumoniae MGH 78578. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

source_name: K. pneumoniae MGH 78578 wild-type

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

growth_protocol:
K. pneumoniae MGH 78578 wild-type was grown to mid-log phase (O.D.600nm 0.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose.
K. pneumoniae MGH 78578 capsule deletion mutant was grown to mid-log phase (O.D.600nm 0.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA) and an Agilent 2100 bioanalyzer at the GeneChip Microarray Core (UCSD, San Diego, CA USA).

tag: genotype

value: Wild-type

tag: phenotype

value: normal


title: Recurrent melanoma patient A, 1st recurrence

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: Recurrent melanoma isolated from patient A, 1st recurrence

hyb_protocol: Samples were prepared for hybridization using the GeneChip Hyb Wash and Stain Kit (Affymetrix); mixed with Control Oligonucleotide B2, Eukaryotic Hybridization Controls and Hybridization Mix from and loaded to Human Gene ST 1.0 Arrays (Affymetrix). Hybridization was done in a GeneChip Hybridization Oven 640 (Affymetrix) for 17 hours, at +45°C, 60 rpm. Arrays were washed and PE-labeled on a GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G with autoloader (Affymetrix). Raw data were generated with Affymetrix GeneChip Command Console

data_processing: Raw data from the generated .CEL files were imported into Partek Genomincs Suite using the RMA method. Sample batches scanned at different time points were adjusted by the Distance Weighted Discrimination method

label: biotin

organism: Homo sapiens

source_name: Melanoma cells in culture

label_protocol: 250 ng total RNA per sample was amplified using a WT expression kit (Ambion).  Samples were subjected to reverse transcription for cDNA synthesis, subsequent in vitro transcription for cRNA synthesis, and magnetic bead-associated cRNA purification. The cRNA obtained was random primed, a second round of cDNA synthesis was carried out, and single stranded cDNA was isolated by RNase H treatment followed by magnetic bead isolation. Next, cDNA was labeled with help of a GeneChip WT Terminal Label and Control Reactions kit (Affymetrix). Samples were fragmented in the presence of Ung1 and Ape1, fragment length confirmed by E-Gel® Agarose Gel Electrophoresis (Invitrogen), fragments extended with TdT and thereby biotin-labeled.

growth_protocol: After surgical removal, stable cell cultures were established and maintained in IMDM (Gibco) supplemented by 10% Human Serum AB (Gemini)

extract_protocol: Total RNA was isolated using Qiagen’s RNEasy Mini Kit, following standard protocol. Sample purity and integrity was confirmed by A260/A280 spectrophotometry and capillary gel electrophoresis on a Nanodrop spectrophotometer (Nanodrop) and using RNA 6000 Nano Kits (Agilent) on a 2100 Bioanalyzer (Agilent), respectively.

tag: cell type

tag: sample type

tag: patient id

value: A

tag: lesion id

tag: date of isolation

value: Surgery Branch, NIH, Bethesda, USA

tag: originator's sample label


title: 7420042_PBS d15

description:
0007420042_raw
biological replicate 1 of 5. Control mice. First point of 2 time points


title: 7420068_AOM/DSS d65

description:
0007420068_raw
biological replicate 5 of 5. Fourth point of 4 time points. Tumours present

source_name: AOM/DSS d65

value: AOM/DSS treated-mice for 65 days


title: Dorsal Dentate Control #2

description: Dorsal untreated


title: Dorsal Dentate Control #3

description: Dorsal untreated


title: KP_MGH_capsule_WT_rep2

description: This sample is of wild-type K. pneumoniae MGH 78578. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Recurrent melanoma patient A, 2nd recurrence, 1st synchronous lesion

description: Recurrent melanoma isolated from patient A, 2nd recurrence, 1st synchronous lesion


title: 7420067_AOM/DSS d65

description:
0007420067_raw
biological replicate 4 of 5. Fourth point of 4 time points. Tumours present


title: 7420003_AOM/DSS d65

description:
0007420003_raw
biological replicate 3 of 5. Fourth point of 4 time points. Tumours present


title: Dorsal Dentate Control #1

description: Dorsal untreated


title: NPTX1 shRNA Day 7, biological rep3

city: Rensselaer

first: Nathan

middle: C

last: Boles

address: one Discovery Drive

institute: Neural Stem Cell Institute

description: Gene expression data

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with R and Bioconductor packages. Normalization was performed with the RMA package.

source_name: Human Embryonic Stem Cells

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

growth_protocol: Standard hESC culturing methods.

extract_protocol: Total RNA was extracted with the Rneasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Neural induction was carried out in hESC according to the protocol developed by Chambers et al. (2009).

tag: cell line

tag: passage

tag: induction

value: NPTX1 shRNA

tag: time point

value: Day 7


title: NPTX1 shRNA Day 5, biological rep3

description: Gene expression data

value: Day 5


title: Neonates_Ep200-3_rep1

city: Okazaki

first: Kenji

last: Toyota

address: 5-1 Higashiyama

country: Japan

institute: National Institute for Basic Biology

description:
Gene expression after 48hr  in Ep200 treated neonate
Ep_200_3

hyb_protocol: 165 µg of Cyanine3-labeled cRNA were hybridized to the custom 4x44k D. magna microarray using the protocols of Agilent Technologies. After 17 h incubation with rotation, the microarrays were washed with Gene Expression Wash Buffer Kit (Agilent Technologies) according to the manufacturer’s protocols.

scan_protocol: DNA microarrays were scanned using a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) at 5 µm resolution. The signal intensity of the spots was digitized using the microarray imager software (Combimatrix Molecular Diagnostics, Irvine, CA, USA).

data_processing: Data files generated by Agilent Feature Extraction Software were imported into Subio Platform (Subio Inc., Tokyo) for further data processing.

organism: Daphnia magna

source_name: Neonates, Ep-200-3, replicate 1

label_protocol: 500 ng of total RNA were prepared for microarray hybridization using the Quick Amp Labeling Kit and One-color RNA Spike-in kit (Agilent Technologies), and purified using the RNeasy Micro Kit (Qiagen) following the manufacturer’s protocol. The quality of Cyanine3-labeled complementary RNA (cRNA) was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: At least 20 individuals were used for one set of samples for each chemical concentration and controls. Harvested daphnids were briefly washed and homogenized using the physcotron NS-310E (Nichion, Tokyo, Japan). Total RNA was purified with TRIZOL reagent (Invitrogen, Tokyo, Japan), and purified using the RNeasy Micro Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocols. The quality of total RNA was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Three experiments were conducted independently (biological triplicates).

tag: developmental stage

value: neonate

tag: agent

value: Ep

tag: dose (ppb)

tag: tissue

value: whole body


title: NPTX1 shRNA Day 7, biological rep1

description: Gene expression data


title: Neonates_Ep200-2_rep1

description:
Gene expression after 48hr  in Ep200 treated neonate
Ep_200_2

source_name: Neonates, Ep-200-2, replicate 1


title: Recurrent melanoma patient E, 1st recurrence

description: Recurrent melanoma isolated from patient E, 1st recurrence

value: melanoma cells

value: Recurrent

value: E

tag: origin

value: CRO, Aviano, Italy


title: 7420001_AOM/DSS d65

description:
0007420001_raw
biological replicate 1 of 5. Fourth point of 4 time points. Tumours present

tag: reference

value: syntethic miRNA pool of 954 synthetic miRNAs in equimolar concentrations  from human, mouse, rat, and virus

tag: strain

value: Whole colonic tissue

tag: treatment


title: Mutc-Met_2

city: LOS ANGELES

first: Hanna

last: Mikkola

state: CA

address: 621, Charles E. Young Drive South

department: MCDB

institute: UCLA

description: c-Met KO CD9+ trophoblasts biological rep2

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CEL files were normalised using RMA method using affy package from Bioconductor version 2.8

source_name: c-Met KO CD9+ trophoblasts

label_protocol: Affymetrix standard protocol

growth_protocol: None, freshly isolated mouse placental trophoblast

extract_protocol: RNA from BM from 4 different individuals was extracted using Minikit (Qiagen, Valencia California)

treatment_protocol: Freshly isolated mouse placental trophoblast was CD9 enriched with an immunomagnetic column

tag: cell type

value: placental trophoblast

tag: genotype/variation

value: c-Met KO


title: NPTX1 shRNA Day 7, biological rep2

description: Gene expression data


title: Neonates_Ep200-1_rep1

description:
Gene expression after 48hr  in Ep200 treated neonate
Ep_200_1

source_name: Neonates, Ep-200-1, replicate 1


title: Dorsal Dentate Responder #2

description: Dorsal Fluoxetine Responder

value: Dorsal dentate gyrus

tag: gender

value: male

tag: age

value: 7-8 wks

value: Fluoxetine

tag: response

value: Responder


title: 7420022_AOM/DSS d50

description:
0007420022_raw
biological replicate 5 of 5. Third point of 4 time points. No tumours

source_name: AOM/DSS d50

value: AOM/DSS treated-mice for 50 days


title: Neonates_Ep100-3_rep1

description:
Gene expression after 48hr  in Ep100 treated neonate
Ep_100_3

source_name: Neonates, Ep-100-3, replicate 1

value: neonate


title: NPTX1 shRNA Day 5, biological rep2

description: Gene expression data

tag: cell line

value: NPTX1 shRNA

value: Day 5


title: 7420021_AOM/DSS d50

description:
0007420021_raw
biological replicate 4 of 5. Third point of 4 time points. No tumours


title: 7420018_AOM/DSS d50

description:
0007420018_raw
biological replicate 3 of 5. Third point of 4 time points. No tumours


title: Neonates_Ep100-2_rep1

description:
Gene expression after 48hr  in Ep100 treated neonate
Ep_100_2

source_name: Neonates, Ep-100-2, replicate 1

value: Ep

value: whole body


title: 7420002_AOM/DSS d65

description:
0007420002_raw
biological replicate 2 of 5. Fourth point of 4 time points. Tumours present

value: AOM/DSS treated-mice for 65 days


title: Mutc-Met_1

description: c-Met KO CD9+ trophoblasts biological rep1


title: Wtc-Met_2

description: Wt CD9+ trophoblasts biological rep2

source_name: Wt CD9+ trophoblasts

value: wild type


title: NPTX1 shRNA Day 3, biological rep2

description: Gene expression data

tag: passage

value: Day 3


title: NPTX1 shRNA Day 3, biological rep3

description: Gene expression data

tag: induction


title: NPTX1 shRNA Day 5, biological rep1

description: Gene expression data

tag: time point


title: Neonates_Ep100-1_rep1

description:
Gene expression after 48hr  in Ep100 treated neonate
Ep_100_1

source_name: Neonates, Ep-100-1, replicate 1

tag: developmental stage


title: 3T3-L1 siLSD1 48h, biological rep 3

city: Barcelona

first: Marcelina

last: Parrizas

address: CEK, Rosello, 153, pl.5

department: Endocrinology

country: Spain

institute: IDIBAPS

hyb_protocol: cRNA hybridization was done according to standard Affymetrix protocols.

scan_protocol: Chip scan was done according to standard Affymetrix protocols.

data_processing: Array normalization, modeling and statistical analysis of gene expression was perform using Dchip software.

source_name: 3T3-L1 Day 0 (passage 21) 48h after siLSD1 transfection

label_protocol: cRNA labelling was done according to standard Affymetrix protocols.

growth_protocol: Mouse 3T3-L1 preadipocytes were maintained in Dulbecco's modified Eagle's Medium (DMEM) supplemented with 10% calf serum (all products from Sigma). Cells (1x10^6) were trypsinized 1h before transfection and seeded into 60 mm dishes.

extract_protocol: Total RNA was extracted and purified with the RNeasy Mini Kit (Qiagen GMbH, Hilden, Germany) according to the instructions of the manufacturer.

treatment_protocol: Cells were transfected with 60 nM of the corresponding double-stranded siRNAs (siC or siLsd1; Applied Biosystems, Foster City, CA) using Metafectene Pro (Biontex, Martinsried, Germany) at a 1:3 w:v ratio with the siRNA. RNA was extracted at 24h and 48h after transfection, without any media changes.

value: preadipocytes

tag: cell passage number

tag: sirna

tag: transfection time


title: 7420017_AOM/DSS d50

description:
0007420017_raw
biological replicate 2 of 5. Third point of 4 time points. No tumours

value: syntethic miRNA pool of 954 synthetic miRNAs in equimolar concentrations  from human, mouse, rat, and virus

tag: tissue

value: Whole colonic tissue


title: Wtc-Met_1

description: Wt CD9+ trophoblasts biological rep1

value: placental trophoblast


title: 3T3-L1 siControl 48h, biological rep 3

source_name: 3T3-L1 Day 0 (passage 21) 48h after siControl transfection

value: scrambled


title: NPTX1 shRNA Day 2, biological rep3

description: Gene expression data

value: Day 2


title: Neonates_Ep50-2_rep1

description:
Gene expression after 48hr  in Ep50 treated neonate
Ep_50_2

source_name: Neonates, Ep-50-2, replicate 1

tag: agent

tag: dose (ppb)


title: Neonates_Ep50-3_rep1

description:
Gene expression after 48hr  in Ep50 treated neonate
Ep_50_3

source_name: Neonates, Ep-50-3, replicate 1


title: NPTX1 shRNA Day 3, biological rep1

description: Gene expression data


title: NPTX1 shRNA Day 2, biological rep2

description: Gene expression data


title: 3T3-L1 siControl 48h, biological rep 2


title: 7420057_AOM/DSS d50

description:
0007420057_raw
biological replicate 1 of 5. Third point of 4 time points. No tumours

source_name: Universal Reference (Miltenyi Biotec GmbH)

tag: reference

tag: strain

tag: treatment


title: 3T3-L1 siLSD1 48h, biological rep 2

tag: cell type


title: Neonates_Ep50-1_rep1

description:
Gene expression after 48hr  in Ep50 treated neonate
Ep_50_1

source_name: Neonates, Ep-50-1, replicate 1


title: 7420073_AOM/DSS d29

description:
0007420073_raw
biological replicate 5 of 5. Second point of 4 time points. No tumours

source_name: AOM/DSS d29

value: AOM/DSS treated-mice for 29 days


title: 3T3-L1 siLSD1 48h, biological rep 1


title: 3T3-L1 siControl 48h, biological rep 1


title: Neonates_Fx2.0-3_rep1

description:
Gene expression after 48hr  in Fx2.0 treated neonate
Fx_2.0_3

source_name: Neonates, Fx-2.0-3, replicate 1

value: Fx


title: NPTX1 shRNA Day 2, biological rep1

description: Gene expression data

source_name: Human Embryonic Stem Cells


title: 7420010_AOM/DSS d29

description:
0007420010_raw
biological replicate 4 of 5. Second point of 4 time points. No tumours


title: NPTX1 shRNA Day 0, biological rep1

description: Gene expression data

value: Day 0


title: NPTX1 shRNA Day 0, biological rep2

description: Gene expression data


title: 7420009_AOM/DSS d29

description:
0007420009_raw
biological replicate 3 of 5. Second point of 4 time points. No tumours


title: NPTX1 shRNA Day 0, biological rep3

description: Gene expression data


title: 3T3-L1 siLSD1 24h, biological rep 1

source_name: 3T3-L1 Day 0 (passage 19) 24h after siLSD1 transfection


title: 7420006_AOM/DSS d29

description:
0007420006_raw
biological replicate 1 of 5. Second point of 4 time points. No tumours


title: Neonates_Fx2.0-2_rep1

description:
Gene expression after 48hr  in Fx2.0 treated neonate
Fx_2.0_2

source_name: Neonates, Fx-2.0-2, replicate 1

value: neonate


title: 7420008_AOM/DSS d29

description:
0007420008_raw
biological replicate 2 of 5. Second point of 4 time points. No tumours


title: 3T3-L1 siControl 24h, biological rep 2

source_name: 3T3-L1 Day 0 (passage 19) 24h after siControl transfection


title: Control Day 7, biological rep3

description: Gene expression data

value: Control

value: Day 7


title: 7420023_AOM/DSS d15

description:
0007420023_raw
biological replicate 4 of 5. First point of 4 time points. No tumours

source_name: AOM/DSS d15

value: AOM/DSS treated-mice for 15 days


title: 3T3-L1 siControl 24h, biological rep 1


title: Control Day 7, biological rep2

description: Gene expression data


title: 3T3-L1 siLSD1 24h, biological rep 2


title: 7420020_AOM/DSS d15

description:
0007420020_raw
biological replicate 3 of 5. First point of 4 time points. No tumours


title: HDF_SAHA-PIP32_rep1

city: Kyoto

first: Junichi

last: Taniguchi

address: Kitashirakawa-Oiwakecho, Sakyo-Ku

department: Department of Chemistry, Graduate School of Science

institute: Kyoto University

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP32 (SAHA-PIP φ)

hyb_protocol: 600ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes using 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE Microarray kit 8x60 Ver2.0 (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner (G2539A) using one color scan setting for AgilentG3 GX array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol: GE1_1010_Sep10 and Grid: 039494_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Human Dermal Fibroblasts, SAHA-PIP32(SAHA-PIP φ), replicate 1

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp labeling kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 54-year-old female Caucasian HDFs were maintained in Dulbecco's modified eagle medium (DMEM, Life Technologies) containing 10% fetal bovine serum (FBS, Japan Serum).

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a Nanodrop ND1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HDFs within the passage P6 were trypsinized for 5 min at 37 °C, and were resuspended in the fresh medium to a concentration of 1.5 x 10^5 cells/2ml in a 35 mm plate and were grown for 24 hours. The medium was then removed and replaced with 2 ml of fresh medium supplimented with DMSO solusion of SAHA, SAHA-PIPs 1-32 (final concentration: 1 μM). The cultures were incubated for 48 hours.

tag: cell source

value: human dermal fibroblasts derived from normal human breast skin

tag: gender

value: female

tag: age


title: Control Day 5, biological rep3

description: Gene expression data

tag: cell line

tag: passage

value: Day 5


title: Control Day 7, biological rep1

description: Gene expression data

tag: induction

tag: time point


title: 7420056_AOM/DSS d15

description:
0007420056_raw
biological replicate 2 of 5. First point of 4 time points. No tumours


title: 7420075_AOM/DSS d15

description:
0007420075_raw
biological replicate 5 of 5. First point of 4 time points. No tumours


title: HDF_SAHA-PIP30_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP30 (SAHA-PIP δ)

source_name: Human Dermal Fibroblasts, SAHA-PIP30(SAHA-PIP δ), replicate 1


title: HDF_DMSO2_rep1

description: Gene expression in HDFs after 48hr treatment with DMSO

source_name: Human Dermal Fibroblasts, DMSO, replicate 1

value: 48hr treatment with DMSO


title: Control Day 5, biological rep2

description: Gene expression data


title: 7420013_AOM/DSS d15

description:
0007420013_raw
biological replicate 1 of 5. First point of 4 time points. No tumours


title: HDF_SAHA-PIP31_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP31 (SAHA-PIP ε)

source_name: Human Dermal Fibroblasts, SAHA-PIP31(SAHA-PIP ε), replicate 1


title: Control Day 5, biological rep1

description: Gene expression data


title: cell with GW501516 treatment for 48h replicate 1

city: Bethesda

first: Qihuang

last: Jin

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description: Gene expression data from MEF cell treated with GW501516 for 48h

hyb_protocol: standard Affymetrix hyb protocol

scan_protocol: standard Affymetrix scan protocol

data_processing: The data were normalized by the  methods Microarray Suite version 5.0 (MAS 5.0)

source_name: immortalized mouse embryonic fibroblast

label_protocol: standard Affymetrix label protocol

growth_protocol: All cells were routinely cultured in DMEM plus 10% FBS (Hyclone). For selection, count cells and plate 5x105/10cm, add 2.5ug/ml puromycin for 2~3days. Repeat the selection one more time.

extract_protocol: Trizol extraction of total RNA followed by Qiagen RNeasy mini kit purification was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 100nM of GW501516

value: MEF


title: cell with GW501516 treatment for 8h replicate 3

description: Gene expression data from MEF cell treated with GW501516 for 8h


title: CMT-W2 co-cultured with mq

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: Biological replicate of examined conditions: cancer cell lines grown with macrophages.

hyb_protocol: The hybridization was performed with custom AMADID microarrays (Agilent, USA) using the miRNA Complete Labeling and Hyb Kit (Agilent, USA) according to the manufacturer's protocol.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: CMT-W2, co-culture

label_protocol: The miRNA Complete Labeling and Hyb Kit (Agilent, USA) was used according to the manufacturer's recommendations.

growth_protocol: Cells were cultured in optimal conditions: a medium (RPMI-1640) enriched with 10% (v/v) heat-inactivated fetal bovine serum (FBS), penicillin-streptomycin (50 iU mL-1), and fungizone (2.5 mg mL-1) (reagents obtained from Sigma Aldrich, USA) in an atmosphere of 5% CO2 and 95% humidified air at 37°C, and were routinely subcultured every second day.

extract_protocol: The total RNA from the samples was isolated using a Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer's protocol.

treatment_protocol: Cancer cells were grown, and sorted monocytes were then layered on the top of each cell line. CMTMR was used to stain the cancer cell population prior to addition of the sorted monocyte population. The co-culture was maintained for at least 72 hrs. After the 72 hrs of co-culture, the cells were harvested by trypsinization and sorted using FACS Aria II (Becton Dickinson, USA) into two tubes: not-stained macrophages and stained cancer cells.

value: mammary cancer cell line

tag: culture type

value: co-culture with macrophages


title: Control Day 3, biological rep2

description: Gene expression data

value: Day 3


title: Control Day 3, biological rep3

description: Gene expression data


title: HDF_SAHA-PIP27_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP27 (SAHA-PIP α)

source_name: Human Dermal Fibroblasts, SAHA-PIP27(SAHA-PIP α), replicate 1


title: cell with GW501516 treatment for 48h replicate 3


title: CMT-W2 ctrl

description: Biological replicate of control: cancer cell lines grown as a mono-culture.

source_name: CMT-W2, single culture

value: mono-culture


title: cell with GW501516 treatment for 2h replicate 2

description: Gene expression data from MEF cell treated with GW501516 for 2h


title: HDF_SAHA-PIP26_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP26 (SAHA-PIP Z)

source_name: Human Dermal Fibroblasts, SAHA-PIP26(SAHA-PIP Z), replicate 1


title: cell with GW501516 treatment for 48h replicate 2


title: Mq co-cultured with CMT-W2

description: Biological replicate: macrophages grown with cancer cells as a co-culture.

source_name: macrophages, co-culture

value: macrophages

value: co-culture with CMT-W2


title: cell with GW501516 treatment for 2h replicate 3


title: Control Day 3, biological rep1

description: Gene expression data


title: cell with GW501516 treatment for 8h replicate 1


title: HDF_SAHA-PIP29_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP29 (SAHA-PIP γ)

source_name: Human Dermal Fibroblasts, SAHA-PIP29(SAHA-PIP γ), replicate 1


title: cell with GW501516 treatment for 8h replicate 2


title: Mq co-cultured with CMT-W1

value: co-culture with CMT-W1


title: Control Day 2, biological rep2

description: Gene expression data

value: Day 2


title: Mq co-cultured with CMT-U309

value: co-culture with CMT-U309


title: cell without GW501516 treatment replicate 3

description: Gene expression data from MEF cell without GW501516 treatment


title: HDF_SAHA-PIP28_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP28 (SAHA-PIP β)

source_name: Human Dermal Fibroblasts, SAHA-PIP28(SAHA-PIP β), replicate 1


title: Control Day 2, biological rep3

description: Gene expression data

source_name: Human Embryonic Stem Cells

value: Control


title: HDF_SAHA-PIP23_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP23 (SAHA-PIP W)

source_name: Human Dermal Fibroblasts, SAHA-PIP23(SAHA-PIP W), replicate 1


title: Mq co-cultured with P114

value: co-culture with P114


title: HDF_SAHA-PIP25_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP25 (SAHA-PIP Y)

source_name: Human Dermal Fibroblasts, SAHA-PIP25(SAHA-PIP Y), replicate 1


title: cell with GW501516 treatment for 2h replicate 1


title: Mq ctrl

description: Control macrophages.

source_name: macrophages, single culture


title: HDF_SAHA-PIP24_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP24 (SAHA-PIP X)

source_name: Human Dermal Fibroblasts, SAHA-PIP24(SAHA-PIP X), replicate 1


title: HDF_SAHA-PIP22_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP22 (SAHA-PIP V)

source_name: Human Dermal Fibroblasts, SAHA-PIP22(SAHA-PIP V), replicate 1


title: Control Day 2, biological rep1

description: Gene expression data


title: CMT-W1 co-cultured with mq

source_name: CMT-W1, co-culture


title: Control Day 0, biological rep2

description: Gene expression data

value: Day 0


title: Control Day 0, biological rep1

description: Gene expression data


title: cell without GW501516 treatment replicate 2


title: P114 co-cultured with mq

source_name: P114, co-culture


title: Mq co-cultured with CMT-U27

value: co-culture with CMT-U27


title: cell without GW501516 treatment replicate 1


title: CMT-U27 co-cultured with mq

source_name: CMT-U27, co-culture


title: HDF_SAHA-PIP18_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP18 (SAHA-PIP R)

source_name: Human Dermal Fibroblasts, SAHA-PIP18(SAHA-PIP R), replicate 1

value: human dermal fibroblasts derived from normal human breast skin

value: female


title: HDF_SAHA-PIP20_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP20 (SAHA-PIP T)

source_name: Human Dermal Fibroblasts, SAHA-PIP20(SAHA-PIP T), replicate 1


title: CMT-U309 co-cultured with mq

source_name: CMT-U309, co-culture


title: CMT-W1 ctrl

source_name: CMT-W1, single culture


title: HDF_SAHA-PIP21_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP21 (SAHA-PIP U)

source_name: Human Dermal Fibroblasts, SAHA-PIP21(SAHA-PIP U), replicate 1


title: SUM149-EN1-R3

city: CHAPEL HILL

first: PILAR

last: BLANCAFORT

state: NORTH CAROLINA

address: 4009 MASON FARM RD

department: PHARMACOLOGY

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

description: C_RMF:SUM149PT human mammary breast cancer cell transduced with Engrailed 1

hyb_protocol: Agilent

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 GenePix Pro 5.1 analysis software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

extract_protocol: Total RNA isolated by Stratagene

value: Human Reference B

extract_protocol: Qiagen Rneasy Kit

value: breast cancer cells

tag: transduction

value: Engrailed 1


title: mouse-MEF-PA1 -/- replicate2

first: Ji-Eun

last: Lee

address: 9000 Rockville pike

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

description: Gene expression data from MEF PA1 -/- cell

hyb_protocol: According to standard Affymetrix protocol.

data_processing: The data were normalized by the methods Microarray Suite version 5.0 (MAS 5.0)

source_name: immortalized mouse embryonic fibroblast, infected with retrovirus expressing Cre recombinase

growth_protocol: All cells were routinely cultured in DMEM plus 10% FBS. For antibiotics selection, cells were counted and plated 5x105/10cm, add 2.0ug/ml puromycin for 3days. Repeat the selection one more time.

value: MEF

tag: genotype/variation


title: HDF_SAHA-PIP17_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP17 (SAHA-PIP Q)

source_name: Human Dermal Fibroblasts, SAHA-PIP17(SAHA-PIP Q), replicate 1


title: HDF_SAHA-PIP16_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP16 (SAHA-PIP P)

source_name: Human Dermal Fibroblasts, SAHA-PIP16(SAHA-PIP P), replicate 1


title: SUM149-EN1-R2


title: P114 ctrl

description: Biological replicate of control: cancer cell lines grown as a mono-culture.

source_name: P114, single culture

value: mammary cancer cell line


title: SUM149-EN1 cDNA

source_name: SUM149-EN1 cDNA


title: SUM149-EGFP

description: C_RMF:SUM149PT human mammary breast cancer cell transduced with a EGFP

value: EGFP


title: HDF_DMSO1_rep1

description: Gene expression in HDFs after 48hr treatment with DMSO

source_name: Human Dermal Fibroblasts, DMSO, replicate 1

value: 48hr treatment with DMSO


title: CMT-U27 ctrl

source_name: CMT-U27, single culture

value: mono-culture


title: mouse-MEF-PA1 +/+ replicate2

description: Gene expression data from MEF PA1 +/+ cell

scan_protocol: According to standard Affymetrix protocol.

source_name: immortalized mouse embryonic fibroblast, infected with retrovirus vector alone


title: HDF_SAHA_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA

source_name: Human Dermal Fibroblasts, SAHA, replicate 1

value: 48hr treatment with SAHA


title: CMT-U309 ctrl

source_name: CMT-U309, single culture


title: mouse-MEF-PA1 +/+ replicate1

label_protocol: According to standard Affymetrix protocol.


title: HDF_SAHA-PIP14_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP14 (SAHA-PIP N)

source_name: Human Dermal Fibroblasts, SAHA-PIP14(SAHA-PIP N), replicate 1


title: SUM149-EGFP-R2


title: HDF_SAHA-PIP15_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP15 (SAHA-PIP O)

source_name: Human Dermal Fibroblasts, SAHA-PIP15(SAHA-PIP O), replicate 1


title: Treatment-24h-Rep 3

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

description:
Exiqon array ID 14223128
Replicate 3
Hy5: 0_Exiqon_14223128_S01.txt
Hy3: 1_Exiqon_14223128_S01.txt

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 5th Generation (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 15.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing:
Normalized Hy3/Hy5 ratios (log2 transformed) from all hybridizations. The ratios are transferred from the excel-sheets named SXX.xls, and shown is the median of replicated measurements of the same miRNA from each slide.
The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
All capture probes with both Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide are excluded as indicated by null.

organism: Rattus norvegicus

source_name: Right cortex, Treatment-24h-Rep 3

label_protocol: The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 1000 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: All procedures performed in this study were approved by the Institutional Animal Care and Use Committee of the National University of Singapore.

extract_protocol: RNA was extracted using the conventional Trizol method and cleaned up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.

treatment_protocol: Cerebral ischemia was induced by permanent occlusion of the left middle cerebral artery (MCA) using a subtemporal approach (Qu et al., 2006). Male Wistar rats (250 - 300 g) were anesthetized with ketamine (75mg/kg, intraperitoneal) and xylazine (10mg/kg, intraperitoneal). The MCA was exposed through a subtemporal craniectomy and cauterized from the point proximal to its origin to the point where it intersects the inferior cerebral vein. Sham group was operated in the same way as the experimental group without the occlusion of MCA.

tag: rat id

value: Rat 55

value: Wistar

value: Male

tag: weight

tag: injury

value: ischemia

value: ZM447439 Treatment

tag: treatment time-point

source_name: Common sample reference pool

tag: reference composition

value: equal amounts of the total RNAs of all 24 samples used in the miRNA profiling study


title: Treatment-24h-Rep 4

description:
Exiqon array ID 14223129
Replicate 4
Hy5: 0_Exiqon_14223129_S01.txt
Hy3: 1_Exiqon_14223129_S01.txt

source_name: Right cortex, Treatment-24h-Rep 4

value: Rat 56

tag: strain

tag: agent


title: HDF_SAHA-PIP13_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP13 (SAHA-PIP M)

source_name: Human Dermal Fibroblasts, SAHA-PIP13(SAHA-PIP M), replicate 1

tag: cell source

value: human dermal fibroblasts derived from normal human breast skin

value: female

tag: treatment


title: HDF_SAHA-PIP11_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP11 (SAHA-PIP K)

source_name: Human Dermal Fibroblasts, SAHA-PIP11(SAHA-PIP K), replicate 1

tag: gender

tag: age


title: HDF_SAHA-PIP12_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP12 (SAHA-PIP L)

source_name: Human Dermal Fibroblasts, SAHA-PIP12(SAHA-PIP L), replicate 1


title: Treatment-24h-Rep 1

description:
Exiqon array ID 14223126
Replicate 1
Hy5: 0_Exiqon_14223126_S01.txt
Hy3: 1_Exiqon_14223126_S01.txt

source_name: Right cortex, Treatment-24h-Rep 1

value: Rat 30


title: mouse-MEF-PCAF-/-;GCN5-/- #A rep2

description: Gene expression data from MEF PCAF-/-;GCN5-/- cell

data_processing: The data were normalized by the methods Microarray Suite version 5.0 (MAS 5.0).

treatment_protocol: no treatment

tag: cell type

value: immortalized mouse embryonic fibroblast (MEF)


title: Treatment-24h-Rep 2

description:
Exiqon array ID 14223127
Replicate 2
Hy5: 0_Exiqon_14223127_S01.txt
Hy3: 1_Exiqon_14223127_S01.txt

source_name: Right cortex, Treatment-24h-Rep 2

value: Rat 54


title: Vehicle-24h-Rep 4

description:
Exiqon array ID 14223125
Replicate 4
Hy5: 0_Exiqon_14223125_S01.txt
Hy3: 1_Exiqon_14223125_S01.txt

source_name: Right cortex, Vehicle-24h-Rep 4

value: Rat 59

value: Vehicle


title: HDF_SAHA-PIP8_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP8 (SAHA-PIP H)

source_name: Human Dermal Fibroblasts, SAHA-PIP8(SAHA-PIP H), replicate 1


title: r0 no glucose biol rep3

city: Edmonton

first: Michael

middle: C.

last: Schultz

state: Alberta

department: Biochemistry

country: Canada

institute: University of Alberta

description: Harvested after 4 hours culture in medium without glucose

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized to the Yeast Genome S98 GeneChip Array for 16 hours at 45C in the GeneChip Hybridization Oven.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Saccharomyces cerevisiae

source_name: r0 yeast cells shifted to medium wiothout glucose following preculture to early log phase in glucose-rich medium

label_protocol: Double-stranded cDNA was used to synthesize biotin-labeled cRNA as recommended (Affymetrix GeneChip Expression Analysis Technical Manual).  The biotin-labeled cRNA was fragmented to maximize hybridization efficiency and assay sensitivity.  Sample cleanup was performed at each step using the GeneChip Sample Cleanup Module.  RNA and DNA concentration and purity were evaluated throughout the procedure from A260 and A280 measurements.

growth_protocol: Cells were cultured at room temperature (22C) to early log phase (OD600 = 1) in CM medium with 2% glucose.

extract_protocol: Total RNA was obtained from an equal number of cells using hot phenol extraction (Schmitt et al., 1990.  NAR 18: 3091), except that the 65°C incubation was extended to 10 minutes.  Poly (A)+ RNA isolated using a Qiagen Oligotex mRNA kit was used for the synthesis of double stranded cDNA.

treatment_protocol: Half of each master culture was harvested for isolation of total RNA; these are the glucose-replete samples. The remaining half of each master culture was collected by centrifugation, washed once in CM, then resuspended at 1 OD600 in CM and incubated with constant shaking for 4 hours. After 4 hours each glucose-limited culture was harvested for preparation of total RNA.

tag: condition

value: mtDNA absent, glucose starved


title: HDF_SAHA-PIP10_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP10 (SAHA-PIP J)

source_name: Human Dermal Fibroblasts, SAHA-PIP10(SAHA-PIP J), replicate 1


title: Vehicle-24h-Rep 3

description:
Exiqon array ID 14223124
Replicate 3
Hy5: 0_Exiqon_14223124_S01.txt
Hy3: 1_Exiqon_14223124_S01.txt

source_name: Right cortex, Vehicle-24h-Rep 3

value: Rat 58


title: mouse-MEF-PCAF-/-;GCN5-/- #A rep1


title: HDF_SAHA-PIP9_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP9 (SAHA-PIP I)

source_name: Human Dermal Fibroblasts, SAHA-PIP9(SAHA-PIP I), replicate 1


title: r0 no glucose biol rep2


title: mouse-MEF-PCAF-/-;GCN5+/- #A rep2

description: Gene expression data from MEF PCAF-/-;GCN5+/- cell


title: mouse-MEF-PCAF-/-;GCN5+/- #B

data_processing: The data were normalized by the methods Microarray Suite version 5.0 (MAS 5.0) using Partek software.


title: r0 2%glucose biol rep3

description: Harvested directly from glucose-rich medium

source_name: r0 yeast cells undergoing active proliferation in glucose-rich medium

value: mtDNA absent, glucose replete


title: HDF_SAHA-PIP7_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP7 (SAHA-PIP G)

source_name: Human Dermal Fibroblasts, SAHA-PIP7(SAHA-PIP G), replicate 1


title: r0 no glucose biol rep1


title: mouse-MEF-PCAF-/-;GCN5-/- #B


title: Vehicle-24h-Rep 1

description:
Exiqon array ID 14223120
Replicate 1
Hy5: 0_Exiqon_14223120_S01.txt
Hy3: 1_Exiqon_14223120_S01.txt

source_name: Right cortex, Vehicle-24h-Rep 1

value: Rat 31


title: DTM with modest core vs STM replicate 1

city: Taoyuan

first: ML

last: Chang

address: 5 Fu-Shin Str.

institute: CGMH

hyb_protocol: 2 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 minutes. Correspondingly fragmented labeled cRNAs and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were then pooled and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 60°C for 17 h. After hybridization, slides were washed and drying.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B scanner. Images were quantified using Agilent Feature Extraction Software.  Data II-1 was analyzed by FE version 8.1.1.1. Other data were analyzed by FE version 9.1.3.1.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.  Data II-1 was processed by FE version 8.1.1.1. Other data were  processed by FE version 9.1.3.1.

source_name: DTM (Modest)

label_protocol: 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process.

extract_protocol: Total RNA was extracted by Trizol® Reagent (Invitrogen, USA), and followed by RNeasy Mini Kit (Qiagen, Germany).

tag: tissue

value: Liver

tag: inflammation

value: yes

tag: steastosis

value: FVB/N

source_name: STM

value: no

tag: stestosis


title: mouse-MEF-PCAF-/-;GCN5+/- #A rep1


title: DTM with modest core vs STM replicate 3


title: HDF_SAHA-PIP5_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP5 (SAHA-PIP E)

source_name: Human Dermal Fibroblasts, SAHA-PIP5(SAHA-PIP E), replicate 1


title: DTM with modest core vs STM replicate 2


title: Vehicle-24h-Rep 2

description:
Exiqon array ID 14223123
Replicate 2
Hy5: 0_Exiqon_14223123_S01.txt
Hy3: 1_Exiqon_14223123_S01.txt

source_name: Right cortex, Vehicle-24h-Rep 2

tag: rat id

value: Rat 35

value: Wistar

value: Male

value: ischemia

source_name: Common sample reference pool

value: equal amounts of the total RNAs of all 24 samples used in the miRNA profiling study


title: r0 2%glucose biol rep2


title: Sham-24h-Rep 4

description:
Exiqon array ID 14223119
Replicate 4
Hy5: 0_Exiqon_14223119_S01.txt
Hy3: 1_Exiqon_14223119_S01.txt

source_name: Right cortex, Sham-24h-Rep 4

value: Rat 46

tag: weight

value: Sham


title: HDF_SAHA-PIP6_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP6 (SAHA-PIP F)

source_name: Human Dermal Fibroblasts, SAHA-PIP6(SAHA-PIP F), replicate 1

value: human dermal fibroblasts derived from normal human breast skin

value: female


title: Sham-24h-Rep 3

description:
Exiqon array ID 14223118
Replicate 3
Hy5: 0_Exiqon_14223118_S01.txt
Hy3: 1_Exiqon_14223118_S01.txt

source_name: Right cortex, Sham-24h-Rep 3

value: Rat 44

tag: injury


title: r0 2%glucose biol rep1


title: Col-0, root, nickel stress

type: SRA

city: NEWARK

first: Dong-Hoon

last: Jeong

state: DE

address: 15 Innovation Way

institute: University of Delaware

description:
Small RNA
C0RNi

library_source: transcriptomic

data_processing:
The raw sequencing data was converted to SCARF format, trimmed of adapters, and matched to the Arabidopsis genome (TAIR9) by custom Perl scripts.
Genome_build: TAIR9
Supplementary_files_format_and_content: Text file containing distinct small RNAs with their raw abundance after removing the adapter sequences.

organism: Arabidopsis thaliana

source_name: Root, wild type, nickel stress

growth_protocol: For flowers, seeds were sown directly onto soil and grown at 21°C in a growth chamber with 16 hours of light for six weeks.  For seedlings, surface-sterilized seeds were plated onto Murashige and Skooge (MS) media and grown in a chamber at 21°C with 16 hours of light for two weeks.

extract_protocol:
RNA was extracted using Trizol reagent.
Small RNA libraries were constructed as previously described (Lu et al. 2007 (PMID 17889797)) and sequenced on an llumina Genome Analyzer II. Sequencing was performed at Illumina or the Delaware Biotechnology Institute.

treatment_protocol: For flowers, submergence stress was applied by submerging plants under sterile water for four hours prior to harvesting. For salt stress, 0.1 M NaCl or 0.3 M NaCl solutions were added to plants for 24 hours before harvesting. Cold stress was carried out by transferring plants to a 4°C cold room with continuous light for 24 hours. For seedlings, salt and submergence stresses were carried out by pouring 40 mL of sterile water with 0.3 M NaCl (salt) or without (submergence) eight hours before harvesting. Phosphate starvation stress was carried out by plating onto MS containing one tenth the normal amount of phosphate. For roots, 40 plants each of four-day-old Col-0 plants germinated on MS (with 3% sucrose) media were transferred to magenta boxes containing a mesh for separating roots and shoots with 100 mL each of MS liquid medium (with 1% sucrose). Further, the boxes were incubated on a rotary shaker set at 90 RPM illuminated with cool white fluorescent light at 25 ± 2 °C. The treatment flasks received 50 µM NiNO3 and control plants did not receive any NiNO3. Both the treatment and control flasks were incubated for 15 days, and the roots were harvested on the 15th day and the RNA was isolated for preparing the library.

tag: background

tag: genotype

value: wild type

value: root

value: nickel stress


title: B31 vs rrp1 mutant replicate 3

city: Dallas

first: zhiming

last: ouyang

state: TX

address: 6000 Harry Hines Blvd

department: Department of Microbiology

institute: UT Southwestern Medical Center

description: B31 vs rrp1 mutant replicate 3

hyb_protocol: After loading probes, slides were covered with lifter coverslips (Erie Scientific Company, Portsmouth, NH), placed into a humidified hybridization chamber (Ambion, Austin, TX), and the chamber was placed into a hybridization oven set at 50oC.

scan_protocol: Hybridized slides were scanned on an Axon 4000B microarray scanner using GenePix Pro 6.1 (Molecular Devices, Sunnyvale, CA).

data_processing: Data then were analyzed with Acuity 4.0 (Molecular Devices), using ratio-based normalization method and a cutoff value of a 2-fold change.  Statistical analyses were performed using the one and two-sample significance test (p<0.05) in the Acuity program.

organism: Borreliella burgdorferi

source_name: mutant

label_protocol: cDNA was synthesized from extracted RNA and labeled with Cy3 or Cy5 using the Amersham post-labeling kit according to the manufacturer’s instructions

growth_protocol: Borrelia were grown in BSK medium until late-log phase.

extract_protocol: RNA was extracted from three biological replicates of wild-type parental strain B. burgdorferi B31 and the  rrp1 mutant using the Trizol reagent (Invitrogen) according to the manufacturer’s protocol.

treatment_protocol: Borrelia were collected by using centrifuging.

tag: genotype/variation

value: rrp1 mutant

source_name: parental strain


title: HDF_SAHA-PIP3_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP3 (SAHA-PIP C)

source_name: Human Dermal Fibroblasts, SAHA-PIP3(SAHA-PIP C), replicate 1


title: HDF_SAHA-PIP2_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP2 (SAHA-PIP B)

source_name: Human Dermal Fibroblasts, SAHA-PIP2(SAHA-PIP B), replicate 1


title: Sham-24h-Rep 1

description:
Exiqon array ID 14223116
Replicate 1
Hy5: 0_Exiqon_14223116_S01.txt
Hy3: 1_Exiqon_14223116_S01.txt

source_name: Right cortex, Sham-24h-Rep 1

value: Rat 36

tag: strain

tag: agent

tag: treatment time-point

tag: reference composition


title: r+ no glucose biol rep2

source_name: r+ yeast cells shifted to medium wiothout glucose following preculture to early log phase in glucose-rich medium

value: mtDNA present, glucose starved


title: Treatment-8h-Rep 4

description:
Exiqon array ID 14223113
Replicate 4
Hy5: 0_Exiqon_14223113_S01.txt
Hy3: 1_Exiqon_14223113_S01.txt

source_name: Right cortex, Treatment-8h-Rep 4

value: Rat 50

tag: gender

value: ZM447439 Treatment


title: B31 vs rrp1 mutant replicate 1

description: B31 vs rrp1 mutant replicate 1


title: HDF_SAHA-PIP1_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP1 (SAHA-PIP A)

source_name: Human Dermal Fibroblasts, SAHA-PIP1(SAHA-PIP A), replicate 1

tag: cell source

tag: age

tag: treatment


title: B31 vs rrp1 mutant replicate 2

description: B31 vs rrp1 mutant replicate 2


title: rdr2, seedling, phosphate starvation

description:
Small RNA
r2SP

source_name: Seedling, rdr2 mutant, phosphate starvation

value: rdr2 mutant

tag: tissue

value: seedling

value: phosphate starvation


title: r+ no glucose biol rep1

description: Harvested after 4 hours culture in medium without glucose

tag: condition


title: r+ no glucose biol rep3


title: B31 vs rrp1 mutant replicate 2 (dye swap)

source_name: rrp1 mutant


title: r+ 2%glucose biol rep3

source_name: r+ yeast cells undergoing active proliferation in glucose-rich medium

value: mtDNA present, glucose replete


title: B31 vs rrp1 mutant replicate 1 (dye swap)


title: HDF_SAHA-PIP4_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP4 (SAHA-PIP D)

source_name: Human Dermal Fibroblasts, SAHA-PIP4(SAHA-PIP D), replicate 1


title: Col-0, root, control for nickel stress

description:
Small RNA
C0RC1

source_name: Root, wild type, untreated


title: rdr2, seedling, control of phosphate starvation

description:
Small RNA
r2SC2

source_name: Seedling, rdr2 mutant, untreated


title: B31 vs rrp1 mutant replicate 3 (dye swap)


title: r+ 2%glucose biol rep2


title: HDF_SAHA-PIP19_rep1

description: Gene expression in HDFs after 48hr treatment with SAHA-PIP19 (SAHA-PIP S)

source_name: Human Dermal Fibroblasts, SAHA-PIP19(SAHA-PIP S), replicate 1


title: r+ 2%glucose biol rep1


title: Sham-24h-Rep 2

description:
Exiqon array ID 14223117
Replicate 2
Hy5: 0_Exiqon_14223117_S01.txt
Hy3: 1_Exiqon_14223117_S01.txt

source_name: Right cortex, Sham-24h-Rep 2

value: Wistar

value: Male

source_name: Common sample reference pool

value: equal amounts of the total RNAs of all 24 samples used in the miRNA profiling study


title: mouse-MEF-PA1 -/- replicate1

description: Gene expression data from MEF PA1 -/- cell

source_name: immortalized mouse embryonic fibroblast, infected with retrovirus expressing Cre recombinase

tag: cell line

value: MEF


title: A673/TR/LOX-PP_replicate_3

city: MAJADAHONDA

first: Javier

last: Alonso

state: MADRID

address: CTRA. MAJADAHONDA-POZUELO KM 2

department: AREA DE GENÉTICA HUMANA

institute: INSTITUTO DE SALUD CARLOS III - IIER

description: LOX-PP 3

hyb_protocol: According to Agilent instructions (One-Color Microarray-based gene expression analysis v6.5)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters.

source_name: A673/TR/LOX-PP, doxycycline stimulated, 72 hours

growth_protocol: Cells were grown in DMEM supplemented with 10% serum and antibiotics.

extract_protocol: Total RNA was isolated using Qiagen RNeasy mini kit. Quality and integrity of the RNA was determined with a Bioanalyzer.

treatment_protocol: Cells were stimulated with doxycycline (1 uM) for 72 hours to induce the expression of LOX-PP

value: A673 cell line (Ewing sarcoma)

value: LOX-PP induced expression


title: A673/TR/LOX-PP_replicate_2

description: LOX-PP 2

scan_protocol: According to Agilent instructions (One-Color Microarray-based gene expression analysis v6.5)


title: Treatment-8h-Rep 1

description:
Exiqon array ID 14223110
Replicate 1
Hy5: 0_Exiqon_14223110_S01.txt
Hy3: 1_Exiqon_14223110_S01.txt

source_name: Right cortex, Treatment-8h-Rep 1

tag: rat id

value: Rat 34

value: ischemia


title: Vehicle-8h-Rep 4

description:
Exiqon array ID 14223109
Replicate 4
Hy5: 0_Exiqon_14223109_S01.txt
Hy3: 1_Exiqon_14223109_S01.txt

source_name: Right cortex, Vehicle-8h-Rep 4

value: Rat 48

tag: weight

value: Vehicle


title: Treatment-8h-Rep 3

description:
Exiqon array ID 14223112
Replicate 3
Hy5: 0_Exiqon_14223112_S01.txt
Hy3: 1_Exiqon_14223112_S01.txt

source_name: Right cortex, Treatment-8h-Rep 3

value: Rat 49

tag: injury


title: Vehicle-8h-Rep 2

description:
Exiqon array ID 14223104
Replicate 2
Hy5: 0_Exiqon_14223104_S01.txt
Hy3: 1_Exiqon_14223104_S01.txt

source_name: Right cortex, Vehicle-8h-Rep 2

value: Rat 40


title: rdr2, seedling, salt #1

description:
Small RNA
r2SNa1

source_name: Seedling, rdr2 mutant, salt

tag: background

value: salt


title: Treatment-8h-Rep 2

description:
Exiqon array ID 14223111
Replicate 2
Hy5: 0_Exiqon_14223111_S01.txt
Hy3: 1_Exiqon_14223111_S01.txt

source_name: Right cortex, Treatment-8h-Rep 2

value: Rat 39

value: ZM447439 Treatment


title: A673/TR/empy_replicate_3

source_name: A673/TR/empty, control

label_protocol: According to Agilent instructions (One-Color Microarray-based gene expression analysis v6.5)

value: control


title: Vehicle-8h-Rep 1

description:
Exiqon array ID 14223103
Replicate 1
Hy5: 0_Exiqon_14223103_S01.txt
Hy3: 1_Exiqon_14223103_S01.txt

source_name: Right cortex, Vehicle-8h-Rep 1

value: Rat 33


title: Vehicle-8h-Rep 3

description:
Exiqon array ID 14223108
Replicate 3
Hy5: 0_Exiqon_14223108_S01.txt
Hy3: 1_Exiqon_14223108_S01.txt

source_name: Right cortex, Vehicle-8h-Rep 3

value: Rat 41

value: Wistar


title: 10824A_E5-3

city: Chengdu

first: Mingxiong

last: He

state: Sichuan

address: Section 4-13, Renming Nanlu

department: Biomass Energy Technology Research Centre

country: China

institute: Biogas Institute of Ministry of Agriculture

data_processing: Hierarchical clustering with the average linkage method was performed with Cluster 3.0 software and the cluster result was visualized through with the Treeview software. In a comparison analysis, two class unpaired method in the Significant Analysis of Microarray software (SAM, version 3.02) was performed to identify significantly differentially expressed genes

organism: Zymomonas mobilis

source_name: Zymomonas mobilis ATCC31821 treated with 5% ethanol

label_protocol: The purified RNA from each sample was used as the template to generate cDNAs while labeled with Cy3-dUTP (CapitalBio).

growth_protocol: Z. mobilis ZM4 (ATCC31821) was cultured in Rich media (RM)  at 30°C without shaking (Goodman, Rogers, and Skotnicki, 1982).

extract_protocol: Two samples from Z. mobilis 24 h culture were harvested by centrifugation and the TRIzol reagent (Invitrogen) was used to extract total cellular RNA. Each total RNA preparation was further purified using NucleoSpin® RNA clean-up (MACHEREY-NAGEL, Germany) according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and quantitated at OD260 and OD280 by spectrophotometer, respectively.

treatment_protocol: Z. mobilis ZM4 (ATCC31821) was cultured in Rich media (RM) with 5% ethanol added at 30°C without shaking (Goodman, Rogers, and Skotnicki, 1982).

tag: protocol

value: treated with 5% ethanol


title: A673/TR/LOX-PP_replicate_1

description: LOX-PP 1

tag: genotype/variation


title: 10824A_E5-2


title: A673/TR/empty_replicate_2


title: Sham-8h-Rep 4

description:
Exiqon array ID 14223102
Replicate 4
Hy5: 0_Exiqon_14223102_S01.txt
Hy3: 1_Exiqon_14223102_S01.txt

source_name: Right cortex, Sham-8h-Rep 4

value: Rat 53

tag: strain

value: Male

value: Sham

value: equal amounts of the total RNAs of all 24 samples used in the miRNA profiling study


title: rdr2, seedling, control for heat and salt

description:
Small RNA
r2SC1

source_name: Seedling, rdr2 mutant, untreated

tag: genotype

value: rdr2 mutant

value: seedling


title: rdr2, seedling, heat

description:
Small RNA
r2SH

source_name: Seedling, rdr2 mutant, heat

value: heat


title: cch rep3

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

description: Gene expression of a hemiparkinsonian model animal with intraperitoneal L-DOPA injection, lesioned side

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner G2505A with the Scan Control software (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014879_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hippocampus, cch, 3

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

extract_protocol: Total RNA was then extracted from the tissues by using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). RNA was treated with DNase 1 (Qiagen) and purified using an RNeasy Mini Kit (Qiagen). The purity and integrity of the isolated total RNA were analyzed with both ultraviolet spectrophotometry and the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). All RNA samples exhibited a 260/280 ratio between 2.0 and 2.2 and a 28S/18S ratio of >1.6; the RNA integrity number was >9.0.

value: hippocampus

value: male

value: coral calcium hydride


title: cch rep4

source_name: hippocampus, cch, 4


title: cch rep1

description: Gene expression of a hemiparkinsonian model animal with intraperitoneal normal saline injection, lesioned side

source_name: hippocampus, cch, 1


title: Sham-8h-Rep 3

description:
Exiqon array ID 14223101
Replicate 3
Hy5: 0_Exiqon_14223101_S01.txt
Hy3: 1_Exiqon_14223101_S01.txt

source_name: Right cortex, Sham-8h-Rep 3

value: Rat 51

tag: agent

tag: treatment time-point

source_name: Common sample reference pool


title: 10824A_C-3

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

source_name: Zymomonas mobilis ATCC31821 wild type

value: untreated


title: 10824A_C-2


title: Sham-8h-Rep 2

description:
Exiqon array ID 14223100
Replicate 2
Hy5: 0_Exiqon_14223100_S01.txt
Hy3: 1_Exiqon_14223100_S01.txt

source_name: Right cortex, Sham-8h-Rep 2

value: Rat 43

tag: gender

tag: reference composition


title: 10824A_E5-1


title: cch rep2

source_name: hippocampus, cch, 2


title: Control rep4

source_name: hippocampus, control, 4

value: control


title: 10824A_C-1


title: Control rep3

description: Gene expression of a hemiparkinsonian model animal with intraperitoneal normal saline injection, non-lesioned side

source_name: hippocampus, control, 3


title: Cd Replicate3 96 Hour Male

city: Singapore

first: Choong Yong

last: UNG

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

description: Biological replicate 2 of 3: Cadmium-treated at 96 Hr

hyb_protocol: Reference RNA (labelled with Cy3) is co-hybridized with RNA samples extracted either from treated or control fish (labelled with Cy5) on a glass array spotted with Zf_16.5K_oligo_COMP_v3Apx zebrafish oligo probes.

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).

data_processing: The data were global median normalized. Normalized ratio of means defined by CH1/CH2

organism: Danio rerio

source_name: Male zebrafish liver tissue

label_protocol: For fluorescence labeling of cDNAs, 10 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

growth_protocol: Zebrafish were maintained at room temperature (26°C + 1°C)

extract_protocol: Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.

treatment_protocol: Male zebrafish were exposed to 30 µg/L Cadmium for 8, 24, 48, and 96 hours at room temperature.

value: cadmium

value: liver

tag: time

value: Singapore wild-type

tag: sample type

value: male and female


title: Control rep2

source_name: hippocampus, control, 2

tag: tissue

value: Wistar

tag: treatment


title: rdr2, flower, untreated #2

description:
Small RNA
r2F2

source_name: Flower, rdr2 mutant, untreated

value: flower


title: Cd Replicate1 48 Hour Male

description: Biological replicate 1 of 3: Cadmium-treated at 48 Hr

source_name: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Sham-8h-Rep 1

description:
Exiqon array ID 14223099
Replicate 1
Hy5: 0_Exiqon_14223099_S01.txt
Hy3: 1_Exiqon_14223099_S01.txt

source_name: Right cortex, Sham-8h-Rep 1

value: Rat 42

value: Male

value: Sham

value: equal amounts of the total RNAs of all 24 samples used in the miRNA profiling study


title: Control rep1

source_name: hippocampus, control, 1

value: hippocampus


title: Cd Replicate1 24 Hour Male

description: Biological replicate 1 of 3: Cadmium-treated at 24 Hr

value: male

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Cd Replicate2 24 Hour Male

description: Biological replicate 2 of 3: Cadmium-treated at 24 Hr


title: Cd Replicate1 96 Hour Male

description: Biological replicate 1 of 3: Cadmium-treated at 96 Hr


title: Cd Replicate2 48 Hour Male

description: Biological replicate 2 of 3: Cadmium-treated at 48 Hr


title: Flank tumor-normal diet-3

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

country: Germany

institute: Saarland University

description: Sample Normal Diet 3

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Array-chips were scanned in a high resolution microarray scanner from Agilent Technologies using Scan Control 8.5.1 software, 3 microns resolution in double path mode.

data_processing: Signal intensity values were extracted from the raw data file using feature extraction software (Agilent Technologies). The gTotalProbeSignals were summed up to calculate the total expression value for each miRNA per sample. Quantile normalization was applied to normalize expression values across the arrays using the preprocessCore package of the programming language R. After that we log2-transformed the expression values.

source_name: flank tumor-normal diet

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit

extract_protocol: Total RNA was isolated after phenol/guanidine-based lysis of 50µg samples from flank tumors by silicamembrane-based purification with the miRNeasy Mini Kit (Quiagen) following the manufacturer’s instructions.

treatment_protocol: Male C57BL/6 mice were used for the study.The diet consisted of either standard mouse chow (control group) or chow enriched with 4% of curcumin (treatment group) prepared from the same batch. The dietary intervention started 14 days before tumor induction and continued until the end of the in vivo experiments. For measurements of tumor size over 28 days, 1 x 10^5 B78H1 cells were injected subcutaneously in each flank of male C57BL/6 mice.

tag: injected with

value: 1x10^5 B78H1 cells

tag: diet group

value: standard mouse chow (control)

value: flank tumor

tag: molecule subtype

value: miRNA


title: Flank tumor-normal diet-4

description: Sample Normal Diet 4


title: Flank tumor-normal diet-6

description: Sample Normal Diet 6


title: Flank tumor-normal diet-5

description: Sample Normal Diet 5


title: Flank tumor-normal diet-2

description: Sample Normal Diet 2


title: Cd Replicate3 48 Hour Male

description: Biological replicate 3 of 3: Cadmium-treated at 48 Hr

value: cadmium


title: Cd Replicate2 8 Hour Male

description: Biological replicate 2 of 2: Cadmium-treated at 8 Hr

value: liver

value: 8 h


title: Flank tumor-normal diet-1

description: Sample Normal Diet 1


title: Resting B cells stimulated with anti-CD86 sample 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression after 4 hr of stimulation

hyb_protocol: 800ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: The normalization was done using GeneSpring GX 11 Software.

source_name: Resting B cells from spleen

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: Then cells were harvested and total RNA isolated  using Qiagen Rneasy Minikit as per the manufacturer’s instructions

treatment_protocol: Resting B cells stimulated with anti-CD86 and cultured for 4hr in RPMI 1640 (10% FCS).

value: BALB/c

value: female

tag: age

value: 6 weeks old

value: stimulated with anti-CD86


title: Flank tumor-Curcumin Diet-7

description: Sample Curcumin Diet 7

source_name: flank tumor-Curcumin Diet

value: chow enriched with 4% of curcumin (treatment)


title: Resting B cells unstimulated sample 2


title: Resting B cells stimulated with anti-CD86 and Pam2csk4 sample 2

treatment_protocol: Resting B cells stimulated with anti-CD86 in presence of Pam2csk4 and cultured for 4hr in RPMI 1640 (10% FCS).

value: stimulated with anti-CD86 and Pam2csk4


title: Cd Replicate2 96 Hour Male

value: Singapore wild-type

value: male and female


title: Cd Replicate3 96 Hour Female

source_name: Female zebrafish liver tissue

treatment_protocol: Female zebrafish were exposed to 30 µg/L Cadmium for 8, 24, 48, and 96 hours at room temperature.


title: Flank tumor-Curcumin Diet-6

description: Sample Curcumin Diet 6

value: male


title: Resting B cells stimulated with anti-CD40 sample 2

treatment_protocol: Resting B cells stimulated with anti-CD40 and cultured for 4hr in RPMI 1640 (10% FCS).

value: stimulated with anti-CD40


title: Cd Replicate1 96 Hour Female

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Cd Replicate1 8 Hour Male

description: Biological replicate 1 of 3: Cadmium-treated at 8 Hr


title: Resting B cells stimulated with Pam2csk4 sample 2

treatment_protocol: Resting B cells stimulated with Pam2csk4 and cultured for 4hr in RPMI 1640 (10% FCS).

value: stimulated with Pam2csk4


title: Cd Replicate2 96 Hour Female


title: Resting B cells stimulated with anti-CD40 and Pam2csk4 sample 2

treatment_protocol: Resting B cells stimulated with anti-CD40 in presence of Pam2csk4 and cultured for 4hr in RPMI 1640 (10% FCS).

value: stimulated with anti-CD40 and Pam2csk4


title: Flank tumor-Curcumin Diet-2

description: Sample Curcumin Diet 2

value: 1x10^5 B78H1 cells

value: flank tumor

value: miRNA


title: Flank tumor-Curcumin Diet-5

description: Sample Curcumin Diet 5


title: Flank tumor-Curcumin Diet-4

description: Sample Curcumin Diet 4


title: Flank tumor-Curcumin Diet-3

description: Sample Curcumin Diet 3


title: Cd Replicate1 24 Hour Female

value: cadmium

value: liver


title: Flank tumor-Curcumin Diet-1

description: Sample Curcumin Diet 1


title: Cd Replicate1 48 Hour Female

value: female


title: Cd Replicate2 24 Hour Female


title: Resting B cells stimulated with anti-CD86 and Pam2csk4 sample 1

value: BALB/c

value: 6 weeks old


title: Resting B cells stimulated with anti-CD86 sample 1

value: stimulated with anti-CD86


title: Cd Replicate2 8 Hour Female

value: 8 h


title: Resting B cells stimulated with anti-CD40 sample 1


title: Cd Replicate2 48 Hour Female

value: Singapore wild-type


title: Strain SCC4092_rep 3

city: Seattle

first: Weerayuth

last: Kittichotirat

state: WA - Washington

address: 960 Republican st

department: Microbiology

institute: University of Washington

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain SCC4092
SCC4092_3

hyb_protocol: The labeled samples were hybridized to the custom Agilent slides following the recommended protocol. A change to the protocol was made to use a nitrogen gun for drying the arrays after washing (instead of centrifugation or drying solution).

scan_protocol: Scans were done using the Agilent Scanner 6000C using manufacturer’s recommended settings for 1-color gene expression (scan area 61 x 21.6mm, 5um resolution, single pass, Green channel only, XDR selected, XDR Hi 100%, XDR Lo 10%). For the 8 x 15K custom arrays we had run, we scanned at 5um resolution, dual pass at 100% and 10% PMT in one channel only (green, or cy-3)

data_processing: The data was then Feature extracted using Agilent's Feature Extractor software v10.5 running the extraction protocol GE1_105_Dec08. Expression data obtained from the Agilent Feature Extraction Software were processed using the following steps. First the gProcessedSignal value for all arrays, which is a background subtracted signal, for each probe was extracted. Quantile normalization was then applied across all the array data being compared to adjust for differences in the probe intensity distribution using limma package. The normalized signal values from probes that are targeting the same gene cluster were finally consolidated into a single value by using median.

organism: Aggregatibacter actinomycetemcomitans

source_name: Total RNA

label_protocol: MessageAmp II-Bacteria kit was used for labeling of the RNA (500 ng for each sample) following the protocol recommended by the manufacturer, with a slight modification in the IVT reaction, in which a combination of 2.6uL T7 CTP and 1.4uL of cy-3 labeled CTP were used for the master mix.

growth_protocol: A starter culture was prepared by inoculating the bacteria in tryptic soy broth with 0.6% yeast extract and incubated overnight at 37°C in atmosphere supplemented with 5% CO2. The starter culture (OD650 of 0.06-0.6) was then diluted with fresh broth to ~OD650=0.1 and incubated further for 4 hours. The OD650 was determined again to assure the continued growth of the bacteria (OD650 in the range of 0.12-0.3). Aliquots of the bacterial cultures were also used to determine colony forming unit/ml and checked for contamination.

extract_protocol: The bacterial RNA was isolated using RiboPure™-Bacteria Kit (Life technology). The resultant RNAs were checked for DNA contamination using the 16S-F and 16S-R as primers and Taq polymerase. The RNAs were then stored at -70o until use.

tag: serotype

value: b


title: Resting B cells stimulated with Pam2csk4 sample 1


title: Strain SCC4092_rep 1

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain SCC4092
SCC4092_1


title: Strain SCC1398_rep 3

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain SCC1398
SCC1398_3


title: Strain SCC4092_rep 2

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain SCC4092
SCC4092_2


title: Retroviral, System Bioscience SBI

city: Horsholm

first: Christian

last: Clausen

address: Kogle Alle 2

department: Mammalian Cell Technology

country: Denmark

institute: Bioneer

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Skin biopsy

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays, incorporating biotinylated UTPs

growth_protocol: All iPS cell lines in this study were cultured in feeder-free conditions using mTeSR1 growth medium and ESC grade Matrigel as cell culture substrate

extract_protocol: Total RNA (1x10^6 cells per sample) was extracted by using RNeasy Kit (Qiagen)t. Quality control was evaluated using NanoDrop Spectrophotometer

treatment_protocol: Three iPS cell clones were derived from fibroblast cultures reprogrammed using episomal plasmids hOSKUL containing OCT4 (Addgene, 27076) in combination with SOX2 and KLF4, (Addgene, 27078) and L-MYC and LIN28 (Addgene, 27080). Three iPS cell clones were derived from fibroblast cultures reprogrammed using episomal plasmids hOSKUL+ shP53 containing OCT4 with a short hairpin to P53 (shP53; Addgene, 27077) in combination with SOX2 and KLF4, (Addgene, 27078) and L-MYC and LIN28 (Addgene, 27080). As a reference human iPS cells (derived with retrovius) were used as control. Normal human dermal fibroblasts were used as controls for the starting material.

value: Skin

tag: reprogramming technology

value: Retroviral, System Bioscience

tag: culture system

value: Feeder-free. mTeSR1/Matrigel system

tag: passage number

tag: cell type

value: iPS cell line


title: Cd Replicate1 8 Hour Female

tag: strain

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.

value: male and female


title: Fibroblast control - not reprogrammed NHDF

value: 18 years

value: Male

value: Fibroblast control - not reprogrammed

value: fibroblast


title: episomal plasmids hOSKUL + shP53 , AddGene K3P53


title: E.albidus_Zn_EC90_rep3

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

description: E.albidus gene expression after exposure to zinc reproduction EC90

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit . 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-030589 Custom Gene Expression Array for Enchytraeus albidus 8x15k, 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 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm).

data_processing: Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies) using default parameters (protocol GE1_105_Dec08 and Grid: 030589_D_F_20101007) to obtain background subtracted and spatially detrended Processed Signal intensities. Processing of the data and statistical analysis were performed using BRB Array Tools version 4.2.1 Stable Release (http://linus.nci.nih.gov/BRB-ArrayTools.html). After background subtraction, the replicated spots within each array were averaged and the intensities were log2 transformed (spots with a value of intensity bellow 1 were excluded from the analysis).

organism: Enchytraeus albidus

source_name: Enchytraeus albidus, zinc EC90, replicate 3

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

extract_protocol: Isolation of total RNA from each replicate was performed through the Trizol extraction method (Invitrogen, Belgium). This RNA followed a DNAse treatment (Fermentas, Germany) and further purification steps consisting of phenol/chloroform extractions. The quantity and purity of the isolated RNA were measured spectrophotometrically with nanodrop (NanoDrop ND-1000 Spectrophotometer) and its integrity was checked on a denaturing formaldehyde agarose gel electrophoresis.

treatment_protocol: Ten adult worms with well developed clitellum were introduced in the test vessels, each containing 25 g moist soil (control or spiked soil with Cu, Ni, Cd or Zn). The worms were exposed for 4 days at 20ºC and a 16:8h photoperiod. Three biological replicates per exposure condition and 6 biologcal replicates of control conditions were used. At test end, animals of each replicate were carefully removed, rinsed in deionised water, stored in RNA later (Ambion, USA) containing criotubes and frozen in liquid Nitrogen. All the samples were stored at -80ºC till further analysis.

value: Whole body extracts

tag: developmental stage

value: Adult organisms with well developed clitellum

value: exposure to zinc at EC90 concentration


title: E.albidus_Zn_EC90_rep2

source_name: Enchytraeus albidus, zinc EC90, replicate 2


title: episomal plasmids hOSKUL + shP53 , AddGene K1P53

tag: gender


title: Resting B cells stimulated with anti-CD40 and Pam2csk4 sample 1

value: BALB/c

value: female

value: 6 weeks old

value: stimulated with anti-CD40 and Pam2csk4


title: Strain SCC393_rep 2

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain SCC393
SCC393_2

value: c


title: Cd Replicate3 48 Hour Female

value: cadmium

value: liver

value: Singapore wild-type


title: Strain A160_rep 1

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain A160
A160_1


title: Strain SCC1398_rep 1

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain SCC1398
SCC1398_1

value: b


title: Strain SCC1398_rep 2

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain SCC1398
SCC1398_2


title: Strain A160_rep 2

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain A160
A160_2


title: 129S2 IFNaR1 KO d14 Mtb CD45+ vs. 129S2 IFNaR1 KO naive CD45+

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: lung CD45 cells  RNA, color-swap array polarity -

hyb_protocol: After precipitation, purification and quantification the labeled samples were mixed and hybridized according to the supplier’s protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies)

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies)

source_name: 129S2 IFNaR1 KO day14 M.tuberculosis infected  CD45+ cells

label_protocol: Total RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: Mice were 8-12 weeks of age at the beginning of the experiments and were bred and kept under specific pathogen-free (SPF) conditions at the Max Planck Institute for Infection Biology in Berlin, Germany. To enumerate bacterial burdens, lung tissue was dispersed in water 1% w/v BSA/1% v/v Tween 80 (WTA) and plated on Middlebrook 7H11 agar plates supplemented with ampicillin (10 µg/ml).

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier

treatment_protocol: Low dose M.tuberculosis H37Rv infection was delivered via aerosol using a Glas-Col inhalation exposure system.

value: lung

value: CD45+ cells

tag: genotype

value: type I interferon receptor (IFNAR1) gene knock-out

source_name: 129S2 IFNaR1 KO day14  naive CD45+ cells


title: 129S2 IFNaR1 KO naive CD45+ vs. 129S2 IFNaR1 KO d14 Mtb CD45+

description: lung CD45 cells  RNA, color-swap array polarity +


title: 129S2 IFNaR1 KO d14 Mtb CD45- vs. 129S2 IFNaR1 KO naive CD45-

source_name: 129S2 IFNaR1 KO day14 M.tuberculosis infected  CD45- cells

value: CD45- cells

source_name: 129S2 IFNaR1 KO day14  naive CD45- cells


title: episomal plasmids hOSKUL, AddGene K3

value: 18 years

value: Male

value: Skin

value: episomal plasmids hOSKUL, AddGene

value: Feeder-free. mTeSR1/Matrigel system

value: iPS cell line


title: Resting B cells unstimulated sample 1

value: BALB/c

value: female

value: 6 weeks old


title: Strain SCC393_rep 1

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain SCC393
SCC393_1

value: c


title: Strain I23C_rep 3

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain I23C
I23C_3

value: nonserotypeable


title: Strain I23C_rep 2

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain I23C
I23C_2


title: episomal plasmids hOSKUL + shP53 , AddGene K2P53


title: A673/TR/empty_replicate_1

source_name: A673/TR/empty, control

tag: cell line

value: A673 cell line (Ewing sarcoma)

tag: genotype/variation

value: control


title: Strain I23C_rep 1

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain I23C
I23C_1


title: 129S2 d14 Mtb CD45+ vs. 129S2 naive CD45+

source_name: 129S2 day14 M.tuberculosis infected CD45+ cells

tag: tissue

value: lung

value: wildtype

source_name: 129S2 day 14 naive CD45+ cells


title: Strain S23A_rep 3

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain S23A
S23A_3

value: b


title: episomal plasmids hOSKUL, AddGene K2


title: 129S2 IFNaR1 KO naive CD45- vs. 129S2 IFNaR1 KO d14 Mtb CD45-

value: CD45- cells

value: type I interferon receptor (IFNAR1) gene knock-out


title: E.albidus_Zn_EC50_rep2

description: E.albidus gene expression after exposure to zinc reproduction EC50

source_name: Enchytraeus albidus, zinc EC50, replicate 2

value: Whole body extracts

value: Adult organisms with well developed clitellum

tag: treatment

value: exposure to zinc at EC50 concentration


title: E.albidus_Zn_EC50_rep1

source_name: Enchytraeus albidus, zinc EC50, replicate 1


title: No_SHH unsorted biological rep 3_of_3

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 day 18 of differentiation from unsorted cells

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

source_name: No sonic hedgehog treatment

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.

value: human pluripotent stem cells


title: No_SHH unsorted biological rep 1_of_3


title: Strain S23A_rep 2

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain S23A
S23A_2


title: No_SHH unsorted biological rep 2_of_3


title: E.albidus_Zn_EC50_rep3

source_name: Enchytraeus albidus, zinc EC50, replicate 3


title: E.albidus_Cd_EC90_rep3

description: E.albidus gene expression after exposure to cadmium reproduction EC90

source_name: Enchytraeus albidus, cadmium EC90, replicate 3

value: exposure to cadmium at EC90 concentration


title: episomal plasmids hOSKUL, AddGene K1

value: 18 years

value: Male

value: Skin

value: episomal plasmids hOSKUL, AddGene

value: Feeder-free. mTeSR1/Matrigel system

value: iPS cell line


title: SHH_10_to_18 biological rep 3_of_3

description: Gene expression data from day 18 of differentiation from FACS sorted NKX2.1::GFP+ cells

source_name: treated with Sonic hedgehog (SHH) from differentiation day 10 to 18


title: SHH_10_to_18 biological rep 2_of_3


title: 129S2 naive CD45+ vs. 129S2 d14 Mtb CD45+

value: CD45+ cells


title: 129S2 d14 Mtb CD45- vs. 129S2 naive CD45-

source_name: 129S2 day14 M.tuberculosis infected CD45- cells

value: lung

source_name: 129S2 day 14 naive CD45- cells


title: SHH_10_to_18 biological rep 1_of_3


title: E.albidus_Cd_EC90_rep2

source_name: Enchytraeus albidus, cadmium EC90, replicate 2


title: E.albidus_Cd_EC90_rep1

source_name: Enchytraeus albidus, cadmium EC90, replicate 1


title: Strain S23A_rep 1

description:
Gene expression of Aggregatibacter actinomycetemcomitans strain S23A
S23A_1

source_name: Total RNA


title: E.albidus_Cd_EC50_rep3

description: E.albidus gene expression after exposure to cadmium reproduction EC50

source_name: Enchytraeus albidus, cadmium EC50, replicate 3

value: exposure to cadmium at EC50 concentration


title: SHH_6_to_18 biological rep 3_of_3

source_name: treated with Sonic hedgehog (SHH) from differentiation day 6 to 18


title: Strain S23A replicate 2

type: genomic

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain S23A

hyb_protocol: 40µl hybridization sample mixture was loaded onto the glass slide and incubated at 65°C for 24 hours with rotation. The arrays were then washed with Agilent CGH wash buffer.

scan_protocol: Arrays were scanned using an Agilent scanner 6000C with the manufacturer’s recommended settings for aCGH arrays (scan area 61 x 21.6mm, 5um resolution, 100% PMT R&G). Data was extracted from the scanner using Agilent Feature Extractor v10.5 software using protocol CGH_105_Dec08.

data_processing: The signal data obtained from the Agilent Feature Extraction Software were processed using the following steps. First the gProcessedSignal value, which is a background subtracted signal, for each probe was extracted. Since the labeling process involved incorporating Cyanine 3-dUTP into the genomic sample, it is possible that probes that are rich in nucleotide A have higher signal relative to probes with lower A content and may not accurately reflect the true abundant of the target sequence. For this reason, the signal values were normalized by dividing them with the total number of A nucleotides in the probe sequence. This value was then transformed using log2. After that, Quantile normalization was applied across all the array data being compared to adjust for differences in the probe intensity distribution using limma package. Finally, the normalized signal values from probes that are targeting the same gene cluster were consolidated into a single value by averaging the signals.

molecule: genomic DNA

source_name: Strain S23A replicate 2

label_protocol: 0.5µg of genomic DNA was labeled with cyanine3. DNA denaturation and fragmentation was done using a thermocycler by mixing 2.5µl of Random Primers (Agilent) and 13µl of genomic DNA at 94°C for 10 minutes. The mixture was cooled to 4°C degree and 9.5µl of labeling master mix (Agilent) was added to make a total volume of 25µl. DNA labeling was done using a thermocycler following the steps: 37°C for 2 hours, 65°C for 10 minutes, and hold at for 4°C. Labeled genomic DNA was purified using individual Amicon 30kDA filters (Millipore) following manufacturer’s protocol. The yield of labeled DNA was determined by measuring the absorbance at A260nm (DNA) and A550nm (cyanine 3) using Nano-Drop (ND-1000).

growth_protocol: A. actinomycetemcomitans was grown on tryptic soy agar plate with 0.6% yeast extract for two days at 37°C in atmosphere supplemented with 5% CO2, and harvested by washing the bacteria off the plates with PBS buffer.

extract_protocol: Genomic DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA 91355 USA) according the manufacturer’s manual.

value: b


title: 129S2 naive CD45- vs. 129S2 d14 Mtb CD45-

value: CD45- cells

value: wildtype


title: Strain S23A replicate 1

source_name: Strain S23A replicate 1


title: 129S2 IFNaR1 KO naiv vs. 129S2 IFNaR1 KO d14 Mtb

description: total lung RNA, color-swap array polarity +

source_name: 129S2 IFNaR1 KO day14  naive CD45- cells

value: naive

value: type I interferon receptor (IFNAR1) gene knock-out

source_name: 129S2 IFNaR1 KO day14 M.tuberculosis infected


title: 129S2 d14 Mtb vs. 129S2 naiv

description: total lung RNA, color-swap array polarity -

source_name: 129S2 day14 M.tuberculosis infected

source_name: 129S2 day 14 naive


title: E.albidus_Cd_EC50_rep1

source_name: Enchytraeus albidus, cadmium EC50, replicate 1

value: Whole body extracts

value: Adult organisms with well developed clitellum


title: E.albidus_Ni_EC90_rep3

description: E.albidus gene expression after exposure to nickel reproduction EC90

source_name: Enchytraeus albidus, nickel EC90, replicate 3

value: exposure to nickel at EC90 concentration


title: Strain I23C replicate 1

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain I23C

source_name: Strain I23C replicate 1

value: non-serotypable


title: Strain I23C replicate 2

source_name: Strain I23C replicate 2


title: E.albidus_Cd_EC50_rep2

source_name: Enchytraeus albidus, cadmium EC50, replicate 2


title: 129S2 IFNaR1 KO d14 M.tb vs. 129S2 IFNaR1 KO naiv

source_name: 129S2 IFNaR1 KO day14  naiv


title: Strain AAS4A replicate 2

description: Comparative genomic hybridization of Aggregatibacter actinomycetemcomitans strain AAS4A

source_name: Strain AAS4A replicate 2

value: c


title: E.albidus_Ni_EC90_rep2

source_name: Enchytraeus albidus, nickel EC90, replicate 2


title: SHH_2_to_18 biological rep 3_of_3

source_name: treated with Sonic hedgehog (SHH) from differentiation day 2 to 18

value: human pluripotent stem cells


title: SHH_6_to_18 biological rep 2_of_3


title: SHH_6_to_18 biological rep 1_of_3