title: skeletal muscle biopsy from subject#18 at day 0, biological replicate 10

description: MU 18A


title: anti-CD40L antibody treated, at week8, biological replicate4

status: Public on Aug 29 2016

type: RNA

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 medimmune way

department: Respiratory, Inflammation and Autoimmunity

country: USA

institute: Medimmune

description: Gene expression from total salivary gland from mouse at the age of week 8, treated with anti-CD40L antibody at the age of week 4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: Data was proprocessed and normalized using frma method, and group comparison was performed using the Limma package

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Total salivary gland from NOD.H-2h4 mice

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

growth_protocol: NOD.H-2h4 mice were obtained from Jackson Laboratories and were housed in pathogen-free conditions.

extract_protocol: Salivary glands were isolated and immersed in All-Tissue Protect reagent (Qiagen) and RNA was extracted using RNeasy kit according to manufacturer’s protocol (Qiagen)

treatment_protocol: NOD.H-2h4 female mice were treated intra-peritoneally at the age of 4 weeks with a single injection of anti-CD40L or human IgG1 isotype control mAb at 20 mg/kg

tag: treatment

value: anti-CD40L antibody


title: Control IgG treated, at week8, biological replicate3

description: Gene expression from total salivary gland from mouse at the age of week 8, treated with control IgG at the age of week 4

value: Control antibody


title: CTL_P14-3

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Gene expression data from kidney of KSP_CRE mouse

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430A_2 Array

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: kidney of KSP_CRE mouse

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

growth_protocol: The kidney from three KSP_CRE/KSP_Tcfeb mice at P14 was isolated, while the kidney from other three KSP_CRE mice at P14 was used as control.

extract_protocol: Total RNAs from either KSP_CRE/KSP_Tcfeb and control kidneys were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

tag: tissue

value: kidney

tag: genotype

tag: strain

tag: developmental stage


title: skeletal muscle biopsy from subject#16 at day 56, biological replicate 8

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description: MU 16C

hyb_protocol: Following fragmentation, 15µg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133 Plus 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner GCS3000.

data_processing: The dataset was analyzed inside the R environment using packages from the BioConductor project. Normalization was performed with RMA algorithm

organism: Homo sapiens

source_name: human SM biopsy after 56 days of  high fat diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol adapted for small amounts of RNA from 100ng total RNA

extract_protocol: Extraction of total RNA was performed with mirVana™ miRNA Isolation Kit  according to the manufacturer's instructions and were further purified using RNeasy kit Qiagen

tag: individual

value: subject #16

tag: bmi

value: Overweight

value: high fat diet

value: skeletal muscle biopsy


title: skeletal muscle biopsy from subject#11 at day 56, biological replicate 7

description: MU 11C

value: subject #11

value: Lean


title: skeletal muscle biopsy from subject#17 at day 0, biological replicate 9

description: MU 17A

source_name: human SM biopsy before the diet

value: subject #17

value: control


title: KSP_P14_TFEB-2

description: Gene expression data from kidney of KSP_CRE/KSP_Tcfeb mouse

source_name: kidney of KSP_CRE/KSP_Tcfeb 14 days old  mouse

treatment_protocol: The kidney from three KSP_CRE/KSP_Tcfeb mice at P14 was isolated, while the kidney from other three KSP_CRE mice at P14 was used as control.


title: KSP_P14_TFEB-1


title: CTL_P14-2


title: Control IgG treated, at week8, biological replicate2


title: skeletal muscle biopsy from subject#11 at day 0, biological replicate 7

description: MU 11A


title: skeletal muscle biopsy from subject#9 at day 56, biological replicate 6

description: MU 9C

value: subject #9


title: skeletal muscle biopsy from subject#16 at day 0, biological replicate 8

description: MU 16A


title: skeletal muscle biopsy from subject#9 at day 0, biological replicate 6

description: MU 9A


title: Control IgG treated, at week8, biological replicate4


title: KSP_P0, biological replicate 1

description:
Gene expression data from kidney of KSP_CRE/KSP_Tcfeb mouse
SAMPLE 3

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

source_name: kidney of KSP_CRE/KSP_Tcfeb mouse

treatment_protocol: The kidney from three KSP_CRE/KSP_Tcfeb mice at P0 was isolated, while the kidney from other two KSP_CRE mice at P0 was used as control.


title: Control_KSP_CRE, biological replicate 2

description:
Gene expression data from kidney of KSP_CRE mouse
SAMPLE 2


title: Control IgG treated, at week8, biological replicate1


title: KSP_P0, biological replicate 2

description:
Gene expression data from kidney of KSP_CRE/KSP_Tcfeb mouse
SAMPLE 4


title: skeletal muscle biopsy from subject#6 at day 56, biological replicate 4

description: MU 6C

value: subject #6


title: KSP_P0, biological replicate 3

description:
Gene expression data from kidney of KSP_CRE/KSP_Tcfeb mouse
SAMPLE 5


title: CTL_P14-1


title: skeletal muscle biopsy from subject#8 at day 56, biological replicate 5

description: MU 8C

value: subject #8


title: skeletal muscle biopsy from subject#8 at day 0, biological replicate 5

description: MU 8A


title: skeletal muscle biopsy from subject#6 at day 0, biological replicate 4

description: MU 6A


title: skeletal muscle biopsy from subject#5 at day 56, biological replicate 3

description: MU 5C

value: subject #5


title: Control_KSP_CRE, biological replicate 1

description:
Gene expression data from kidney of KSP_CRE mouse
SAMPLE 1


title: B2_HAP1_CDK12_C1039S_THZ531_300nM

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Samples were prepared for hybridization using 10 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human PrimeView, Affymetrix 901837) were hybridized in a GeneChip Hybridization Oven at 45C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console. A Primeview CDF that included probe information for the ERCC controls (GPL16043), provided by Affymetrix, was used to generate .CEL files.

data_processing: A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf. The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized per batch (B1/B2) to the external spike-ins. See Loven, Orlando et al., Cell, 2012 for additional details.

label_protocol: For microarray analysis, 100 ng of total RNA containing ERCC RNA Spike-In Mix (see above) was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (30 IVT Express Kit, Affymetrix 901228).  Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: Jurkat cells were grown in RPMI medium supplemented with 1% glutamine and 10% FBS.  Cells were cultured at 37 degrees C in a humidified chamber in the presence of 5% CO2, unless otherwise noted.

extract_protocol: Total RNA from biological replicates (equivalent to 5 million cells per replicate) was subsequently isolated using RNeasy Plus Mini kit (Qiagen, cat#74134) following the manufacturer’s instructions and re-suspended in 50 μL nuclease-free water (Ambion, AM9938). Total RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, 4456740) and analyzed on Agilent 2100 Bioanalyzer for integrity.

treatment_protocol: Jurkat cells were plated at 500,000 cells/ mL and incubated in media containing THZ531, THZ532, or THZ531R at the indicated concentrations or with DMSO for 6hrs.  At the end of the experiment cells were collected by centrifugation and cell numbers were determined by manually counting cells using C-Chip disposable hemocytometers (Digital Bio, DHC-N01).  5,000,000 cells were isolated from each treatment condition.

tag: cell line

value: Cells were treated with 300 nM THZ531 for 6 hours


title: B2_HAP1_CDK12_C1039S_THZ531_900nM

value: Cells were treated with 900 nM THZ531 for 6 hours


title: skeletal muscle biopsy from subject#5 at day 0, biological replicate 3

description: MU 5A


title: B1_Jurkat_THZ531R_500nM_1

source_name: Jurkat T-ALL

value: Jurkat

value: wildtype

value: Cells were treated with 500 nM THZ531R (warhead replaced) for 6 hours


title: B2_HAP1_CDK12_C1039S_DMSO

value: Cells were treated with 0.1% DMSO for 6 hours


title: B1_Jurkat_THZ532_500nM_2

value: Cells were treated with 500 nM THZ532 (inactive enantiomer) for 6 hours


title: skeletal muscle biopsy from subject#3 at day 56, biological replicate 2

description: MU 3C

value: subject #3

value: high fat diet


title: skeletal muscle biopsy from subject#3 at day 0, biological replicate 2

description: MU 3A

value: skeletal muscle biopsy


title: B1_Jurkat_THZ532_500nM_1


title: B1_Jurkat_THZ531_500nM_2

value: Cells were treated with 500 nM THZ531 for 6 hours


title: B1_Jurkat_THZ531_350nM_2

value: Cells were treated with 350 nM THZ531 for 6 hours


title: S. typhimurium kanamycin treated 2

status: Public on Aug 28 2016

city: Flagstaff

first: Andrew

last: Koppisch

state: AZ

address: PO Box 5698

department: Chemistry

institute: Northern Arizona University

hyb_protocol: cRNA derived from all samples was coupled to Alexa Fluor 555. Ten micrograms of each target was hybridized separately to one array. Hybridization was performed for 19hrs at 50oC in a proprietary hybridization buffer. The arrays were washed as follows. The wash stock solution was 20X SSPE (3M NaCl, 20mM EDTA, 118.2mM NaH2PO4 and 81.8mM Na2HPO4). Each array was removed from the hybridization cassette in while submerged in 6X SSPE (22C), transferred to fresh 6X SSPE (22C) and stored briefly while the rest of the arrays were liberated from their cassettes (estimated storage time was <2min). Arrays were washed in batches of 5. Arrays were washed in 1X SSPE at 22C for 3 min (2 rounds) followed by 1X SSPE at 50C for 3 min, 1X SSPE at 22 C for 3 min and finally in 0.5 X SSPE at 22 C for 30 seconds.  All washes were performed in baths while the wash solution was gently circulated by stir bar.  Following the final wash, arrays were spun dry in a microarray centrifuge.

scan_protocol: The arrays were scanned in an Axon 4000B Scanner (Molecular Devices) set at 5μm per pixel resolution and 100% laser power. The PMT setting was adjusted to appreciate the maximum dynamic range of signal (0 to 65,000). This was accomplished by increasing the PMT (gain) until a few spots had some saturated pixels. The average number of spots with greater than 10% saturated pixels was 19.2 (out of a possible 26,346 SE spots).

data_processing:
Data was extracted from the scanned images using GenePix Pro Software (version 6.1.0.4). The gal file (“Load Array List” in GenePix) grid was positioned over the array image. For signal extraction, circular feature indicators (30m diameter) were centered over each spot. Median feature pixel intensity was extracted. Due to the manufacturing process, the area immediately surrounding a spot is not used to estimate background levels. MYcroarray INC states that when probes do not bind target, the residual signal is almost always lower compared with the surrounding area. To use local background values would over-estimate the contribution of background signal in the extracted signal intensity of each probe. Therefore, a global background correction algorithm within each array was used instead of a local background correction factor. The background value was determined by the 5th percentile darkest spot from the distribution of median signal intensities for all SE spots for each array (i.e., control spots and empty spots were ignored). Background corrected signal = Max (signal – background, 0.1). In other words, if background subtraction produces a value less than zero, 0.1 was used instead (i.e., the background corrected signal distribution is truncated slightly above zero to avoid having a zero or negative signal value). To adjust for differences in dye behavior, a scale factor was created to equalize signal across all arrays. Only probes that met the following criteria were used to calculate the scale factor: only SE spots were used; spots must have less than 10% saturated pixels; median signal had to be more than 3 fold local background; and all examined arrays had to have the spot qualify as a normalization spot. There were 11,789 qualifying spots.
Absent call (0=absent; 1=present)

label: Alexa Fluor 555

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Cells in early stage logarithmic growth

label_protocol: Ten micrograms of total RNA was converted to enriched mRNA using Applied Biosystem's (Ambion) MicrobExpressTm Kit using the manufacturers protocol.  Enriched mRNA (200 ng) was converted to cRNA using Applied Biosystem's (Ambion) MessageAmp II-Bacteria RNA Amplification Kit.  Amino-allyl-UTP was incorporated into the cRNA during the IVT reaction.  The manufacturer's protocol was followed.  AlexaFluor 555 (Invitrogen) was coupled to cRNA following the manufacturer's instructions and unincorporated dye was removed using RNeasy Mini Columns (Qiagen).  cRNA coupled to fluorescent dye was fragmented using heat and zinc (2+) cations.  The expected mean fragment length is 100-125 nucleotides.  Fragmented cRNA is considered sufficent for use on MYcroarray custom arrays if the mean fragment length is less than 200 nucleotides.

growth_protocol: S. typhimurium cells were inoculated from a confluent culture and grown at 37 C with shaking (200 rpm) in Luria-Bertani medium and monitored by optical density.

extract_protocol: RNA from all treatments was isolated using the Qiagen Rneasy RNA isolation kit according to the manufacturers protocol.

treatment_protocol: At early logarithmic growth (OD600 = 0.4) cells were exposed to subinhibitory concentrations of fosmidomycin or kanamycin and culture was continued for 20 minutes.  A control sample of cells that were not exposed to antibiotics was also grown.  After 20 minutes, the cells were collected by centrifugation, decanted, washed and flash frozen in the presence of an RNA preservative.

value: kanamycin treated


title: B1_Jurkat_THZ531_50nM_2

value: Cells were treated with 50 nM THZ531 for 6 hours


title: B2_HAP1_WT_THZ531_300nM


title: skeletal muscle biopsy from subject#1 at day 0, biological replicate 1

description: MU 1A

value: subject #1

value: Lean

value: control


title: B2_HAP1_WT_DMSO


title: B1_Jurkat_THZ531_350nM_1


title: B2_HAP1_WT_THZ531_900nM


title: B1_Jurkat_THZ531R_500nM_2


title: B1_Jurkat_THZ531_500nM_1


title: B1_Jurkat_THZ531_200nM_2

value: Cells were treated with 200 nM THZ531 for 6 hours


title: B1_Jurkat_THZ531_200nM_1


title: B1_Jurkat_THZ531_50nM_1


title: Ad/NICD replicate 4

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

description: Biological replicate 4 of 4. Ad/NICD White adipose tissue

hyb_protocol: 300 ng of cRNA from the control and test samples were combined and 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 Agilent hybridization buffer was added to the fragmentation mixture and hybridized on an Agilent SurePrint G3 mouse 8x60K microarray (028005) 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).

scan_protocol: Scanned on an Agilent SureScan Microarray scanner following manufacturer's protocol.

data_processing: Array image data was extracted using Agilent Feature Extraction Software 11.5 (Agilent Technologies, Santa Clara, CA). Array image data was then uploaded to GeneSpring 12.5 (Agilent Technologies, Santa Clara, CA) for statistical analysis. Microarray analysis was completed with an ANOVA and a Tukey's post-hoc test when a significant ANOVA was observed. In addition, a mean absolute log2 expression ratio of at least 0.585 (50% increase or decrease in expression) must be satisfied.

source_name: Whtie adipose tissue

label_protocol: Cy3 (control samples) and Cy5 (test samples) labeled cRNA was prepared using the Agilent LowInput QuickAmp Labeling Kit according to 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 extracted using Trizol following manufacturer's instructions

treatment_protocol: Mice were all fed on regular chow diet

value: Ad/NICD

tag: age

value: 5-Week old


title: B1_Jurkat_DMSO_1

value: Jurkat

value: wildtype


title: Ad/NICD replicate 3

description: Biological replicate 3 of 4. Ad/NICD White adipose tissue


title: S. typhimurium kanamycin treated 1


title: B1_Jurkat_DMSO_2

value: Cells were treated with 0.1% DMSO for 6 hours


title: skeletal muscle biopsy from subject#1 at day 56, biological replicate 1

description: MU 1C


title: S. typhimurium kanamycin treated 3


title: Tumor_H13_1352_hybridized_against_blood_CCLG14

type: genomic

city: Oxford

first: Bass

last: Hassan

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology, Oxford Molecular Pathology Institute

country: United Kingdom

institute: University of Oxford

description:
Blood (germline) DNA hybridized against MNTI DNA
H13_1352 vs CCLG14

hyb_protocol: Aliquots of genomic DNA from the tumor and blood were hybridized to a ‘Cytosure Cancer+’ small nucleotide polymorphism array (Oxford Gene Technology, Begbroke, UK). The array was a 4 x 180k custom design, comprising a whole genome backbone with a greater density of probes for 1500 cancer-associated genes.

scan_protocol: Scanned on an Agilent SureScan scanner.

data_processing: Data were analyzed using CytoSure Interpret software, version 4.3.2 (Oxford Gene Technology).

molecule: genomic DNA

source_name: [TEST] Blood

label_protocol: Genomic DNA was labelled with Cy5 or Cy3 using a CytoSure Genomic DNA Labelling Kit (Oxford Gene Technology, Ltd) according to the manufacturer’s instructions.

growth_protocol: Not applicable

extract_protocol:
Genomic DNA was extracted from tumor using a DNeasy Blood & Tissue kit (Qiagen).
Genomic DNA from blood was obtained from the Children’s Cancer and Leukaemia Group Tissue Bank, Newcastle, UK.

treatment_protocol: Tumor was flash frozen in liquid nitrogen.

value: 2 months

tag: gender

value: Female

source_name: [REF] MNTI from fibula


title: B-2

city: Wuhan

first: Jihong

last: Hu

state: Hubei

address: Ba-Yi Road

department: Department of Genetics

country: China

institute: College of life sciences, Wuhan University

description: Gene expression data from young panicles

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 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: Oryza sativa

source_name: young panicle of Meixiang B

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: All the rice materials were grown in the field of Wuhan University, Wuhan, Hubei province (30°54'  N, 114°36' E) .Young panicles of the three CMS lines and MB were harvested at the uninucleate microspore stage, frozen in liquid nitrogen, and then kept at -80°C for use.

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

tag: line

value: Meixiang B

value: young panicle

tag: tissue type

value: fertile


title: S. typhimurium fosmidomycin treated 2

value: fosmidomycin treated


title: S. typhimurium untreated 2

value: untreated


title: S. typhimurium untreated 1


title: S. typhimurium fosmidomycin treated 1


title: A3-1

source_name: young panicle of XQZ-A (DA type).

value: XQZ-A

value: male-sterile


title: WT WAT replicate 4

description: Biological replicate 4 of 4. Wildtype White adipose tissue

value: Wild-type


title: S. typhimurium untreated 3


title: A1-2

source_name: young panicle of D62A (D type)


title: B-1


title: A3-2


title: WT WAT replicate 1

description: Biological replicate 1 of 4. Wildtype White adipose tissue


title: WT WAT replicate 3

description: Biological replicate 3 of 4. Wildtype White adipose tissue


title: WT WAT replicate 2

description: Biological replicate 2 of 4. Wildtype White adipose tissue


title: Ad/NICD replicate 2

description: Biological replicate 2of 4. Ad/NICD White adipose tissue


title: Tumor_H13_1352_and_blood_CCLG14_hybridized_against_hg19_human_reference

description:
Patient DNA (blood and MNTI) hybridized against human reference
H13_1352 + CCLG14

source_name: [TEST] MNTI from fibula and blood (pooled DNA)

source_name: [REF] Hg19 human reference

value: Not applicable – pooled reference

value: Male


title: Ad/NICD replicate 1

description: Biological replicate 1 of 4. Ad/NICD White adipose tissue

value: Ad/NICD


title: hUCBCD34+_DMSO_394_Biological replicate 2

status: Public on Aug 27 2016

city: Boston

first: Trista

middle: E

last: North

state: Massachusetts

address: 3 Blackfan Circle

department: Pathology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

description: DMSO_Treated CD34+_394

hyb_protocol: Hybridization was performed for 16 hrs @ 45 degrees (GeneChip WT PLUS Reagent Kit)

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Arrays were processed using the 'oligo' BioConductor package (Carvalho and Irizarry,2010),normalized with RMA (Irizarry et al 2003), and differentially expressed genes were identified using limma (Smyth et. al. 2005).
HTA-2_0.r1.pgf
HTA-2_0.r1Psrs.mps

label: Biotin

source_name: Umbilical Cord CD34+

label_protocol: Enzymatic fragmentation and labeling was done using Affymetrix GeneChip WT Terminal Labeling Kit (GeneChip WT PLUS Reagent Kit)

growth_protocol: 37 degrees with 5%CO2

extract_protocol: Total RNA was extracted using ThermoFisher RNAqueous-Micro Total RNA isolation kit, followed by Turbo DNAse-I treatment. RNA quality was determined using a Agilent Bionalyzer

treatment_protocol: 4 hr treatment in STEM SPAN SFEM with 1mM 1,25(OH)D3

tag: umbilical cord blood

value: DMSO


title: Nlrp3KO_bladder_7days_exp4_rep3

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

description: experiment 4

hyb_protocol: 6 μg of fragmented and labeled aRNA was hybridized onto Mouse Genome 430 PM array strips for 16 hours at 45°C, washed, stained and scanned using the Geneatlas system (all Affymetrix).

scan_protocol: The arrays were scanned using a GeneAtlas Personal Microarray Systems.

data_processing: The data was normalized using Robust Multi Average (RMA) implemented in the Partek® Genomics Suite™.

source_name: Nlrp3KO, bladder, 7days infected, exp2

label_protocol: 100 ng of total RNA was amplified and biotin-labelled using the GeneChip 3´IVT Express Kit,

growth_protocol: Mice were bred and housed in the specific pathogen-free MIG animal facilities (Lund, Sweden) with free access to food and water. Female mice aged 9-15 weeks were used for experimental infection.

extract_protocol: Total RNA was extracted in RLT buffer with 1% β-Mercaptoethanol after disruption in a tissue homogenizer (TissueLyser LT, Qiagen) using Precellys Lysing kits (Bertin Technologies), with the RNeasy Mini Kit (Qiagen).

treatment_protocol: Overnight static cultures of E. coli CFT073 in Luria-Bertani (LB) broth were used for experimental infection of mice. Mice were intravesically infected under Isofluorane anesthesia with 10^8 CFU in 0.1 ml PBS, through a soft polyethylene catheter (outer diameter 0.61 mm; Clay Adams).

tag: bacterial strain

value: Escherichia coli CFT073

tag: infection time

value: 7 days

value: bladder

tag: mouse strain

value: female


title: Mmp7KO_bladder_0day_exp3_rep2

description: experiment 3

source_name: Mmp7KO, bladder, uninfected

value: 0 day


title: AscKO_bladder_0day_exp4_rep1

description: experiment 4

source_name: AscKO, bladder, uninfected, exp2

value: Asc-/-


title: Casp1KO_bladder_0day_exp3_rep2

description: experiment 3

source_name: Casp1KO, bladder, uninfected


title: A2-2

source_name: young panicle of ZhenShan97A (WA type)

value: young panicle


title: uninfectednormalmucosatissues_normal_rep6

city: xinjiang

first: he

last: ying

state: State...

address: urlumuqi

institute: xinjiang medical university

hyb_protocol: Six cervical cancer tissues infected with HPV16 were randomly selected along with six normal mucosa tissues. Total RNA was isolated using the Trizol Reagent (Invitrogen, USA) according to the manufacturer’s instructions. RNA concentrations were determined using a NanoDrop 2000 spectrophotometer (Thermo Fisher scientific, USA). RNA quality and integrity were examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). All RNA samples used for miRNA microarrays exhibited a 2100RIN (RNA integrity number) of ≥ 6.0, and ratios of 28S/18S ≥ 0.7. Subsequently, reverse transcription (RT) was performed on these samples using 1.0 mg of total RNA to generate cDNA using the miScript II RT kit (QIAGEN, Germany)

scan_protocol: After purification the labeled RNAs were hybridized onto the microarray. After washing, the arrays were scanned with the Agilent Scanner G2505C(Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 12.5; Agilent Technologies) was employed  to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 75 percent of samples in any 1 condition out of 2 conditions have flags in Detected were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05. Target genes of differentially expressed miRNAs were the intersection predicted with 3 databases (Targetscan，microRNAorg，pita). GO analysis and KEGG analysis were applied to determine the roles of these target genes. Hierarchical Clustering was performed to show the distinguishable miRNAs  expression pattern among samples.

source_name: uninfected normal mucosa tissues

label_protocol: Labeling and hybridization were performed by the Urumqi OE Biotech Company, according to the protocols of the Agilent miRNA microarray system. Scanning of microarrays was completed using the Agilent Scan Control software, and all analyses were performed using the Agilent Feature Extraction software (version 10.7.1.1, Agilent Technologies). Raw data were standardized using the Quantile algorithm, Gene Spring Software (Agilent technologies, US).

extract_protocol: Cervical cancer tissues and uninfected normal mucosa tissues were obtained from the Obstetrics and Gynecology Department of Xinjiang Medical University Cancer Hospital. All tissues were obtained between June 2012 and June 2013 as fresh specimens from surgical resection, and stored at -80°C until use. There were 30 cervical cancer tissues and 26 normal mucosa tissues. All patients were from the Uyghur population of Xinjiang, China. All cervical specimens were confirmed as squamous cell carcinoma through pathological examination. Prior to tissue sampling, patients had not received any chemotherapy treatment. Samples from the control group were determined to be normal by ThinPrep cytologic tests. This study was approved by the Ethics Committee of Xinjiang Medical University Cancer Hospital (K-201343), and informed consent was obtained from all patients.

value: uninfected normal mucosa tissues

tag: tissue status

value: normal


title: Cervicalcancertissues_HR-HPV_rep6

source_name: Cervical cancer tissues,HR-HPV

value: Cervical cancer tissues

value: infected with  HR-HPV


title: AscKO_bladder_7days_exp4_rep1

description: experiment 4

source_name: AscKO, bladder, 7days infected, exp2


title: Nlrp3KO_bladder_0day_exp4_rep1

description: experiment 4

source_name: Nlrp3KO, bladder, uninfected, exp2


title: Nlrp3KO_bladder_7days_exp4_rep1

description: experiment 4


title: Cervicalcancertissues_HR-HPV_rep5


title: Casp1KO_bladder_7days_exp3_rep1

description: experiment 3

source_name: Casp1KO, bladder, 7days infected


title: hUCBCD34+_1,25(OH)D3_444_Biological replicate 1

description: 1,25(OH)D3 Treated CD34+_444

tag: treatment


title: uninfectednormalmucosatissues_normal_rep5

tag: tissue


title: Mmp7KO_bladder_0day_exp3_rep1

description: experiment 3

tag: genotype


title: hUCBCD34+_DMSO_444_Biological replicate 1

description: DMSO_Treated CD34+_444


title: Nlrp3KO_bladder_7days_exp4_rep2

description: experiment 4


title: AscKO_bladder_7days_exp4_rep3

description: experiment 4


title: Mmp7KO_bladder_7days_exp3_rep2

description: experiment 3

source_name: Mmp7KO, bladder, 7days infected


title: A1-1

value: male-sterile


title: Mmp7KO_bladder_7days_exp3_rep1

description: experiment 3


title: Casp1KO_bladder_7days_exp3_rep2

description: experiment 3


title: hUCBCD34+_1,25(OH)D3_394_Biological replicate 2

description: 1,25(OH)D3 Treated CD34+_394


title: AscKO_bladder_0day_exp3_rep2

description: experiment 3

source_name: AscKO, bladder, uninfected, exp3


title: Casp1KO_bladder_0day_exp3_rep1

description: experiment 3


title: uninfectednormalmucosatissues_normal_rep2


title: AscKO_bladder_7days_exp3_rep2

description: experiment 3

source_name: AscKO, bladder, 7days infected, exp3


title: AscKO_bladder_7days_exp3_rep1

description: experiment 3


title: uninfectednormalmucosatissues_normal_rep3


title: S. typhimurium fosmidomycin treated 3

source_name: Cells in early stage logarithmic growth

value: fosmidomycin treated


title: Cervicalcancertissues_HR-HPV_rep4


title: AscKO_bladder_0day_exp3_rep1

description: experiment 3


title: Cervicalcancertissues_HR-HPV_rep3


title: Slug KO, no UVR, (rep 1)

city: Albuquerque

first: Donna

middle: Frances

last: Kuseiwtt

state: NM

address: Reginald Heber Fitz Hall, Room 335;  915 Camino de Salud

institute: University of New Mexico School of Medicine

description: Test

data_processing:
For the normalization it uses the average of five housekeeping genes: Gusb, Hprt1, Hsp90ab1, Gapdh, Actb
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Analyses of each plate was performed using the SDS 2.3 program from Applied Biosciences, using the same threshold and baseline for all samples.
Fold Change worksheet reports test value/average control value (i.e., wild type, UVR (rep 1)/Average Wild type, no UVR) ratios

label: SYBR Green

source_name: epidermis, Slug KO, no UVR, (rep 1)

label_protocol: A total of 1000 ng of RNA was used to synthesize cDNA using the High Capacity cDNA RT Kit from Applied Biosystems (Foster City, CA). Equal amounts of cDNA were added to each well, cDNA was mixed with iTAQ SYBR Green Supermix with ROX from Bio-Rad Laboratories (Hercules, CA), and each plate was run using the Applied Biosystems Prism 7900 HT qPCR protocol (Foster City, CA) as follows: one cycle at 95° C for 10 minutes; 40 cycles at 95° C for 0.15 seconds and at 60° C for 60 seconds; and a final cycle of 15 seconds each at 95° C, 60° C, and 95° C.

growth_protocol: Slug knockout and wild type littermates were maintained under standard housing conditions in an animal facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC), in accordance with all applicable state and federal animal welfare regulations and with the NIH Guide for the Care and Use of Laboratory Animals, using protocols approved by the MD Anderson Cancer Center (MDACC) Institutional Animal Care and Use Committee.

extract_protocol: Strips of skin were frozen on a liquid nitrogen-cooled aluminum block and stored at -80° C. To obtain RNA from mouse skin, frozen strips of skin were placed, epidermis side down, on 500 µL of cold TRIzol (Life Technologies, Carlsbad, CA, USA) for one minute. Epidermis was then scraped from the surface, briefly homogenized in a total of 1 ml TRIzol, and frozen in liquid nitrogen for storage at -80° C.    RNA isolation was completed as recommended by the TRIzol supplier and RNA quality was assessed using Agilent’s RNA 6000 Nano kit (Santa Clara, CA). No RNA was used if the RIN value was less than 7.5.

treatment_protocol: Three to four days prior to UVR exposure, mice were shaved (Oster Technique, McMinnville, TN). The next day, mice were treated with Nair (Church and Dwight, Ewing, NJ) for complete hair removal. Two to three days later, mice were exposed to UVR from Westinghouse FS20 sunlamps (80% UVB, 20% UVA). UVR was filtered through UVT cast acrylic (Polycast Technology, Stamford, CT) to exclude wavelengths below 280 nm. The UV dose was assessed with a radiometer-dosimeter (UV-1360, UB-IR Tech, Dietzenbach, Germany). Cpntrol mice were not irradiated. Twenty-four hours later, Mice were euthanized with CO2 and skin collected 24 hours later, mice were euthanized with CO2 and skin was collected.

tag: strain

value: Slug knockout


title: uninfectednormalmucosatissues_normal_rep4


title: Cervicalcancertissues_HR-HPV_rep1


title: Slug KO, no UVR, (rep 3)

description: Test

source_name: epidermis, Slug KO, no UVR, (rep 3)


title: Slug KO, no UVR, (rep 2)

description: Test

source_name: epidermis, Slug KO, no UVR, (rep 2)


title: Wild type, no UVR (rep 3)

description: Control

source_name: epidermis, Wild type, no UVR (rep 3)

value: Wild type


title: Nlrp3KO_bladder_7days_exp2_rep2

description: experiment 2

source_name: Nlrp3KO, bladder, 7days infected, exp1


title: Il1bKO_bladder_7days_exp2_rep2

description: experiment 2

source_name: Il1bKO, bladder, 7days infected


title: WT_bladder_7days_exp2_rep2

description: experiment 2

source_name: WT, bladder, 7days infected

value: WT


title: WT_bladder_7days_exp2_rep1

description: experiment 2


title: uninfectednormalmucosatissues_normal_rep1


title: KHOS PmiR-1

first: Zhenfeng

last: Duan

address: 55 Fruit Street Jackson Building

institute: Massachusetts General Hospital

description: Osteosarcoma cell line with pmiR-1.

hyb_protocol: Total RNA was processed and hybridized to Affymetrix Gene Chip U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu).

scan_protocol: GeneChip Scanner 3000 7G.

data_processing: The average expression value for each gene across the arrays was used to normalize the mRNA intensities. The CEL files were transformed into intensity information using the RMA normalization of Qlucore 3.2. Qlucore were used to analyze the microarray data (http://www.qlucore.com). Fold change in expression between miR-1 treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A 1.2 fold change or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

source_name: KHOS osteosarcoma cells, miR-1

label_protocol: Labeled with biotin.

growth_protocol: The U-2OS and KHOS osteosarcoma cell lines were seeded onto the 100mm cell culture plate.

extract_protocol: Total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis.

treatment_protocol: Cells were transfected with miRSelect pEP-miR-1 or miRSelect pEP-miR-Null using Lipofectamine LTX and Plus Reagent (Invitrogen) for 48 hours.

value: KHOS

tag: cell type

value: osteosarcoma cell line

tag: miRNA


title: Nlrp3KO_bladder_7days_exp2_rep1

description: experiment 2

value: Escherichia coli CFT073

value: 7 days


title: Il1bKO_bladder_7days_exp2_rep1

description: experiment 2

value: bladder

value: female


title: Wild type, no UVR (rep 2)

description: Control

source_name: epidermis, Wild type, no UVR (rep 2)


title: AscKO_bladder_7days_exp2_rep1

description: experiment 2

source_name: AscKO, bladder, 7days infected, exp1

value: Asc-/-


title: Slug KO, UVR (rep 4)

description: Test

source_name: epidermis, Slug KO, UVR (rep 4)

value: UVR


title: U-2OS pmiR-1

description: Osteosarcoma cell line with pmiR-1.

source_name: U-2OS osteosarcoma cells, miR-1


title: Nlrp3KO_bladder_0day_exp2_rep2

description: experiment 2

source_name: Nlrp3KO, bladder, uninfected, exp1

value: 0 day


title: [MI/WO]-[array2]

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: Pooled Merritt Island (MI) Alligator samples are compared to pooled Lake Woodruff (WO) Alligator samples on array 2

hyb_protocol: The array used for the differential methylation analysis was a DNA methylated custom array by Roche Nimblegen that consisted of a Whole Genome Tiling Array of the American Alligator (Alligator mississippiensis) made of two chip set arrays with a 200bp resolution (121211-allmis-ms-meth-ux1). Probe sizes were 50-75mer in length and median probe spacing was 200bp. Two different comparative (MeDIP vs. MeDIP) hybridization experiments were performed (2 sub-arrays) for each contaminated lake collection (AP and MI) versus the non-contaminated WO lake, with each sub-array including hybridizations from MeDIP DNA from DNA pools from these different collections. For one sub-array of each comparison, MeDIP DNA samples from the experimental groups (AP or MI) were labeled with Cy3 and MeDIP DNA samples from the non-contaminated WO were labeled with Cy5.

scan_protocol: Scanning and image acquisition was performed in-house by Nimblegen Inc.

data_processing:
For each competitive hybridization experiment raw data from both the Cy3 and Cy5 channels were imported into R, checked for quality and converted into MA values. The normalization procedure was preformed as follows: within each array, probes were separated into groups by GC content and each group was separately normalized using the loess normalization procedure. After each array was normalized within array, the arrays were then normalized across arrays using the A-quantile normalization procedure.  Following normalization each adjacent ≥3 probe set value represents the median intensity difference between AP or MI and control WO of a 600bp window. Significance was assigned to probe differences between experimental comparisons AP or MI and reference WO samples by calculating the median value of the intensity differences as compared to a normal distribution scaled to the experimental mean and standard deviation of the normalized data. A Z-score and P-value were computed for each probe from that distribution. The statistically significant differential DNA methylation regions (DMR) were identified and p-values associated with each region represented.
The DMR sequence homology search used the Gene NCBI database and correlated the epimutations associated (overlapped) with the  genes. The three adjacent probes constituted approximately a 200bp homology search. The KEGG pathway associations were identified.
Value definitions for processed data files: #ClusterID = an general ID number, #Chromosome = Chromosome number, #cSTART = Cluster start site, #cSTOP = Cluster stop site, #meanM = mean log2 intensity ratio (treated vs. control) across all microarray chips for this treatment/control group, #meanA = mean log2 hybridization intensity (both red and green channel) across all microarray chips for this treatment/control group, #minP = p-value for difference between treated and control intensity as calculated by indicated R-code from raw data files.  P-value must be p<1.0E-5 or less for inclusion, #nProbes = number of consecutive probes with p<1.0E-5 included in cluster.  The analysis at p<1.0E-5 and p<1.0E-4 was identical for the AP/WO chips.

organism: Alligator mississippiensis

source_name: Genomic DNA from alligator blood taken from Merritt Island (MI)_contaminated

growth_protocol: Blood and red blood cells were collected from 30 adult male alligators during a 10 day period in April of 2010. Samples were obtained 10 alligators from three research areas: Lake Apopka (AP), Lake Woodruff National Wildlife Refuge (WO), and one lagoon population located in Merritt Island National Wildlife Refuge, Lake NASA (MI) (Figure 1).  The RBC samples were stored in RNA later and kept under −25 °C until extractions were performed.

extract_protocol: Erythrocyte DNA was isolated with DNAeasy Blood and Tissue Kit (Qiagen, Valencia, CA) and then stored at -80°C prior to analysis.  DNA was sonicated and then purified using a series of washes and centrifugations from a number of animals per collection analyzed. The same concentrations of DNA from individual RBC samples were then used to produce pools of DNA material. Two DNA pools were produced in total per site collection, each one containing the same amount of DNA from different animals.  The number of individuals used per pool was 5. These DNA pools were fragmented by sonication and used for methylated DNA immunoprecipitation (MeDIP). MeDIP was performed as follows: 6 μg of genomic DNA was subjected to a series of three 20 pulse sonications at 20% amplitude and the appropriate fragment size (200-1000 bp) was verified through 2% agarose gels; the sonicated genomic DNA was resuspended in 350 μl TE buffer and denatured for 10 min at 95°C and then immediately placed on ice for 5 min; 100 μl of 5X IP buffer (50 mM Na-phosphate pH 7, 700 mM NaCl, 0.25% Triton X-100) was added to the sonicated and denatured DNA. An overnight incubation of the DNA was performed with 5 μg of antibody anti-5-methylCytidine monoclonal from Diagenode (Denville, NJ) at 4°C on a rotating platform.  Protein A/G beads from Santa Cruz were prewashed on PBS-BSA 0.1% and resuspended in 40 μl 1X IP buffer. Beads were then added to the DNA-antibody complex and incubated 2 h at 4°C on a rotating platform. Beads bound to DNA-antibody complex were washed 3 times with 1 ml 1X IP buffer; washes included incubation for 5 min at 4°C on a rotating platform and then centrifugation at 6000 rpm for 2 min.  Beads DNA-antibody complex were then resuspended in 250 μl digestion buffer (50 mM Tris HCl pH 8, 10 mM EDTA, 0.5% SDS) and 3.5 μl of proteinase K (20 mg/ml) was added to each sample and then incubated overnight at 55°C on a rotating platform.  DNA purification was performed first with phenol and then with chloroform:isoamyl alcohol. Two washes were then performed with 70% ethanol, 1 M NaCl and glycogen. MeDIP selected DNA was then resuspended in 30 μl TE buffer.

treatment_protocol: Expiremental

value: blood

value: male

tag: location

value: Merritt Island (MI)

source_name: Genomic DNA from alligator blood taken from Lake Woodruff (WO)_reference

treatment_protocol: Control

value: Lake Woodruff (WO)


title: Slug KO, UVR (rep 3)

description: Test

source_name: epidermis, Slug KO, UVR (rep 3)


title: Slug KO, UVR (rep 1)

description: Test

source_name: epidermis, Slug KO, UVR (rep 1)


title: Slug KO, UVR (rep 2)

description: Test

source_name: epidermis, Slug KO, UVR (rep 2)


title: AscKO_bladder_7days_exp2_rep2

description: experiment 2


title: WT_bladder_0day_exp2_rep2

description: experiment 2

source_name: WT, bladder, uninfected


title: Nlrp3KO_bladder_0day_exp2_rep1

description: experiment 2


title: Il1bKO_bladder_0day_exp2_rep2

description: experiment 2

source_name: Il1bKO, bladder, uninfected


title: wild type, UVR (rep 3)

description: Test

source_name: epidermis, wild type, UVR (rep 3)


title: [MI/WO]-[array1]

description: Pooled Merritt Island (MI) Alligator samples are compared to pooled Lake Woodruff (WO) Alligator samples on array 1

label_protocol: MeDIP DNA samples from the experimental groups (AP or MI) were labeled with Cy3 and MeDIP DNA samples from the non-contaminated WO were labeled with Cy5


title: Il1bKO_bladder_0day_exp2_rep1

description: experiment 2


title: AscKO_bladder_0day_exp2_rep2

description: experiment 2

source_name: AscKO, bladder, uninfected, exp1


title: WT_kidney_0day_exp1_rep2

description: experiment 1

source_name: WT, kidney, uninfected

value: kidney


title: WT_bladder_0day_exp2_rep1

description: experiment 2


title: Wild type, no UVR (rep 1)

description: Control

source_name: epidermis, Wild type, no UVR (rep 1)


title: AscKO_bladder_0day_exp2_rep1

description: experiment 2


title: wild type, UVR (rep 2)

description: Test

source_name: epidermis, wild type, UVR (rep 2)


title: [AP/WO]-[array2]

description: Pooled Lake Apopka (AP) Alligator samples are compared to pooled Lake Woodruff Alligator samples on array 2

source_name: Genomic DNA from alligator blood taken from Lake Apopka (AP)_contaminated

value: Lake Apopka (AP)


title: WT_kidney_0day_exp1_rep1

description: experiment 1


title: brain cortex_sea level altitude_rep1 [miRNA]

status: Public on Aug 26 2016

city: tianjin

first: hongsheng

last: gao

address: dongli

institute: university

description: gene expression in cases

hyb_protocol: The pre-hybridization of HmiOA3.0  arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled small RNA was hybridize on HmiOA3.0 in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 520-550 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: Among the probe triplicates, the median value were selected into signal normalization processed by R program (2.12.1).  We ﬁltered out probes that ﬂag <0 in all samples. Porbes that passed the criteria were normalized by 75% media scaling normalization method.

organism: Rattus norvegicus

source_name: brain cortex, sea level altitude,  replicate 1

label_protocol: Small RNA population were enriched by (Nanosep100k, Pall Corp.) from 2.5 µg of total RNA. NHS-CyDye (Cy5, Amershan) were direct labeled to Guanine (G) by chemical labeling method using ULS™ microRNA Labeling Kit (EA-038, Kreatech).

extract_protocol: RNA extraction by TRIzol reagent (Invitrogen Cat# 15596-026) RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.6, A260/A230≧ 1, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧5).

value: brain cortex

tag: altitude

value: sea level


title: brain cortex_3km altitude_rep1 [miRNA]

description: gene expression in cases

source_name: brain cortex, 3km altitude,  replicate 1


title: brain cortex_7km altitude_rep1 [miRNA]

description: gene expression in cases

source_name: brain cortex, 7km altitude,  replicate 1


title: WT_kidney_7days_exp1_rep2

description: experiment 1

source_name: WT, kidney, 7days infected

value: WT


title: A2-1

source_name: young panicle of ZhenShan97A (WA type)

value: young panicle

value: male-sterile


title: AscKO_bladder_7days_exp4_rep2

description: experiment 4

source_name: AscKO, bladder, 7days infected, exp2

value: Escherichia coli CFT073

value: 7 days


title: [AP/WO]-[array1]

description: Pooled Lake Apopka (AP) Alligator samples are compared to pooled Lake Woodruff Alligator samples on array 1

source_name: Genomic DNA from alligator blood taken from Lake Woodruff (WO)_reference


title: wild type, UVR (rep 1)

description: Test

source_name: epidermis, wild type, UVR (rep 1)

value: Wild type


title: colorectal adenoma, patient 15 (exon)

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description:
colorectal adenoma, patient 15
colorectal adenoma biopsy

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: colorectal adenoma

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

growth_protocol: not applicable

extract_protocol: Colon or rectum biopsy samples were obtained after surgical removal and informed patient consent. The tissue fragments were stored in RNAlater (Ambion, France). DNA and total RNA were extracted with the AllPrep DNA/RNA Mini kit (Qiagen, Courtabœuf, France) from homogenized tissue samples (20 mg), according to the manufacturer’s instructions. RNA purity and integrity were determined by measuring the optical density ratio (A260/A280) and the RNA integrity number (RIN) using the RNA 6000 Nano LabChip (Agilent, Massy, France) and the 2100 Bioanalyzer (AgilentTM). Only RNA samples with a 28S/18S ratio > 1.0 and RIN ≥ 7.0 were used for microarray analyses.

treatment_protocol: not applicable

value: adenoma

tag: localisation

value: transversal colon


title: colorectal adenoma, patient 24 (exon)

description:
colorectal adenoma, patient 24
colorectal adenoma biopsy

value: left colon


title: colorectal adenoma, patient 22 (exon)

description:
colorectal adenoma, patient 22
colorectal adenoma biopsy

value: cecum


title: BMEC heat stressed 24h

city: Karnal

first: Manishi

last: Mukesh

state: Haryana

address: Po Box 129, GT Road By Pass

department: Animal Biotechnology

country: India

institute: ICAR-National Bureau of Animal Genetic Resources

description:
Gene expression of buffalo MEC after 24h of heat stress
BMEC heat stressed 24h_GE1-v5_95_8

hyb_protocol: For hybridization, 1.65 μg of linearly amplified and cyanine 3-labeled cRNA were fragmented using fragmentation mix (10X Blocking Agent and 25X Fragmentation Buffer) and incubated at 60°C for exactly 30 min. The fragmented RNA samples were immediately transferred on ice for one minute and 55μl of 2x GEx Hybridization Buffer HI-RPM was added to stop the fragmentation reaction. The fragmented samples (110μl volume) were loaded to the array placed in slide chamber. The assembled slide chamber placed in rotisserie was put in a hybridization oven set to rotate at 10 rpm and 65°C. The hybridization was allowed for 17 hours. Followed by hybridization, microarray slide was disassembled in GE wash buffer 1 (pre warm overnight at 37°C) containing Triton X-102 (0.005%), washed with fresh GE wash buffer 1 for 1 min followed by second wash with GE Wash Buffer 2 for 5 min at room temperature. The slide was dried and scanned immediately.

scan_protocol: Immediately after washing, the slides were scanned on GenePix-4000B (Molecular Device) microarray scanner using one color scan setting with 5μm resolution at wavelength of 532 nm (Cy3). After scanning, the images were collected as 16 bit images and finally stored as tif image files.

data_processing: These files were further subjected to feature extraction using Agilent Feature Extractor Software Version 9.5 (Agilent Technologies) software. The data was normalized to the 75th percentile using GeneSpring GX 11.5 (Agilent Technologies). Genespring GX 12.6 (Agilent technologies) was used to perform the analysis of raw data obtained from feature extraction software.

organism: Bubalus bubalis

source_name: MEC heat stressed, 24h, replicate 1

label_protocol: For One-Color Microarray-Based Gene Expression Analysis using Low Input Quick Amp Labelling kit (Agilent Technologies, Santa Clara, CA), the RNA samples (CTR, 30 m, 2h, 4h, 8h, 12h, 16h, 24 h) were labelled with T7 promoter primer (65°C for 10 min followed by incubation in ice for 5 min). cDNA was constructed from labelled RNA samples after adding cDNA master mix (5X First Strand Buffer, 0.1 M DTT, 10 MmdNTP mix and AffinityScriptRNase Block Mix) followed by incubation at 40°C for 2 h, 70°C for 15 min and final incubation on ice for 5 min. The cRNA synthesis and amplification was performed by adding transcription master mix (5X Transcription Buffer, 0.1 M DTT, NTP mix, T7 RNA Polymerase Blend and Cyanine 3-CTP) followed by incubation at 40°C for 2 h. The amplified labelled cRNA was purified (RNeasy mini column kit, Qiagen, Germany), quantified [μgcRNA yield = (Concentration of cRNA) x 30 µL (elution volume)/ 1000] and checked for specific activity [pmol Cy3 per µg cRNA = (Concentration of Cy3/ Concentration of cRNA) x 1000]. All the samples exhibited yield and specific activity values higher than the minimum value of 1.65 and 6, respectively using four pack microarray format.

growth_protocol: The primary MECs derived from buffalo mammary gland were cultured using DMEM/F12 and supplements. After 10th passages, 80% confluent buffalo MECs were distributed in collagen treated 12-wellplates in two sets with one plate assigned as control (kept at 37ºC all the time) and other plate as treated (exposed to 42ºC).

extract_protocol: Total RNA was extracted from MEC using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol. After extraction, RNA was purified using RNeasy Mini kit (Qiagen, Germany) and followed by on-column digestion with the RNase-free DNase (Qiagen, Germany). RNA was quantified using Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA integrity was confirmed by denaturing agarose gel electrophoresis and experion bioanalyzer (BioRad, USA,).

treatment_protocol: Initially, cells were incubated at 37ºC with 5% CO2 to stabilize the culture. Subsequently, the plate marked as treated was exposed to 42ºC for one hour to simulate heat stress  condition. After 1h, the cells were allowed to recover at 37ºC, 5% CO2 and harvested by trypsinization at different time points (30m, 2h, 4h, 8h, 12h, 16h, and 24h).

tag: stress

value: heat stress

tag: time

tag: cells

value: Mammary epithelial cells

tag: gender

value: Female


title: colorectal adenoma, patient 12 (exon)

description:
colorectal adenoma, patient 12
colorectal adenoma biopsy

tag: tissue type

value: rectosigmoid junction


title: WT_kidney_7days_exp1_rep1

description: experiment 1

tag: bacterial strain

tag: infection time

value: kidney

value: female


title: colorectal adenoma, patient 20 (exon)

description:
colorectal adenoma, patient 20
colorectal adenoma biopsy

value: rectum


title: BMEC heat stressed 16h

description:
Gene expression of buffalo MEC after 16h of heat stress
BMEC heat stressed 16 h_GE1-v5_95_7

source_name: MEC heat stressed, 16h, replicate 1


title: colorectal adenoma, patient 19 (exon)

description:
colorectal adenoma, patient 19
colorectal adenoma biopsy

value: right colon


title: colorectal adenoma, patient 14 (exon)

description:
colorectal adenoma, patient 14
colorectal adenoma biopsy


title: colorectal adenoma, patient 8 (exon)

description:
colorectal adenoma, patient 8
colorectal adenoma biopsy


title: pool of colorectal normal mucosae, rep2 (exon)

description:
pool of colorectal normal mucosae, rep2
pool of colorectal normal mucosa biopsies

source_name: colorectal normal mucosae

value: normal mucosa


title: BMEC heat stressed 12h

description:
Gene expression of buffalo MEC after 12h of heat stress
BMEC heat stressed 12h_GE1-v5_95_6

source_name: MEC heat stressed, 12h, replicate 1


title: colorectal adenoma, patient 7 (exon)

description:
colorectal adenoma, patient 7
colorectal adenoma biopsy

value: sigmoid colon


title: BMEC heat stressed 8h

description:
Gene expression of buffalo MEC after 8h min of heat stress
BMEC heat stressed 8h_GE1-v5_95_5

source_name: MEC heat stressed, 8h, replicate 1


title: colorectal adenoma, patient 23 (exon)

description:
colorectal adenoma, patient 23
colorectal adenoma biopsy


title: colorectal adenoma, patient 18 (exon)

description:
colorectal adenoma, patient 18
colorectal adenoma biopsy


title: colorectal adenoma, patient 10 (exon)

description:
colorectal adenoma, patient 10
colorectal adenoma biopsy


title: colorectal adenoma, patient 21 (exon)

description:
colorectal adenoma, patient 21
colorectal adenoma biopsy


title: pool of colorectal normal mucosae, rep1 (exon)

description:
pool of colorectal normal mucosae, rep1
pool of colorectal normal mucosa biopsies


title: colorectal adenoma, patient 13 (exon)

description:
colorectal adenoma, patient 13
colorectal adenoma biopsy


title: colorectal adenoma, patient 16 (exon)

description:
colorectal adenoma, patient 16
colorectal adenoma biopsy


title: colorectal adenoma, patient 17 (exon)

description:
colorectal adenoma, patient 17
colorectal adenoma biopsy


title: colorectal adenoma, patient 6 (exon)

description:
colorectal adenoma, patient 6
colorectal adenoma biopsy


title: colorectal adenoma, patient 9 (exon)

description:
colorectal adenoma, patient 9
colorectal adenoma biopsy


title: colorectal adenoma, patient 11 (exon)

description:
colorectal adenoma, patient 11
colorectal adenoma biopsy


title: colorectal adenoma, patient 4 (exon)

description:
colorectal adenoma, patient 4
colorectal adenoma biopsy


title: colorectal adenoma, patient 5 (exon)

description:
colorectal adenoma, patient 5
colorectal adenoma biopsy


title: BMEC heat stressed 30m

description:
Gene expression of buffalo MEC after 30 min of heat stress
BMEC heat stressed 30m_GE1-v5_95_2

source_name: MEC heat stressed, 30min, replicate 1


title: colorectal adenoma, patient 2 (exon)

description:
colorectal adenoma, patient 2
colorectal adenoma biopsy


title: H2O_56d_1

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: cRNA synthesis, target hybridization, washing, staining and subsequent probe array scanning was done according to the manufacturer's instructions (3'IVT Express Kit User Manual Affymetrix)

scan_protocol: Scanner 3000 7G; Software AGCC (Affymetrix GeneChip Command Console) version 4.0

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

source_name: liver, Water, 0 % (w/v), 56 days

label_protocol: Labeling according to 3'IVT Express Kit User Manual Affymetrix

growth_protocol: Adult male mice (mus muculus) on a C57BL/6J background were treated with phenobarbital (0.05%w/v, drinking water) for 28 or 56d; CITCO for 28d (daily, 10mg/kg, intraperitoneal); WY14,643 for 28d (daily, 100mg/kg, oral gavage); piperonyl butoxide for 28d (daily, 600mg/kg, intraperitoneal); pioglitazone for 28d (daily, 100mg/kg, oral gavage); methapyrilene for 28d (1000ppm, in food); 1,4-Dichlorobenzene for 28d (daily, 600mg/kg, oral gavage); cyproterone acetate for 28d (daily, 16omg/kg, oral gavage).

extract_protocol: Liver tissue was homogenized and RNA isolation was performed with Qiazol extraction (Qiagen, Hilden,Germany).

treatment_protocol: After 28 (or 56) days treatment, mice were sacrificed by a rising concentration of carbon dioxide, and subject to necropsy to remove the liver, which was rinsed in sterile phosphate-buffered saline, snap-frozen in liquid nitrogen and stored at -80oC.

value: male

value: liver

tag: treatment short name

tag: treatment full name

value: Water

tag: treatment duration [days]

tag: treatment dose

tag: group

value: H2O 56d


title: Cervicalcancertissues_HR-HPV_rep2

source_name: Cervical cancer tissues,HR-HPV

tag: tissue

value: Cervical cancer tissues

tag: tissue status

value: infected with  HR-HPV


title: CO_28d_3

source_name: liver, Corn oil, 0 mg/kg, 28 days

tag: strain

value: CO

value: Corn oil

value: 0 mg/kg

value: CO 28d


title: H2O_28d_5

source_name: liver, Water, 0 % (w/v), 28 days

value: H2O 28d


title: CO_28d_4


title: CO_28d_2


title: H2O_56d_2


title: H2O_28d_1


title: H2O_28d_3


title: CO_28d_1


title: CMC_Co5_28d_1

source_name: liver, Carboxymethylcellulose, 0 mg/kg, 28 days

value: CMC

value: Carboxymethylcellulose

value: CMC Co5 28d


title: H2O_28d_4


title: CO_28d_5


title: BMEC heat stressed 4h

description:
Gene expression of buffalo MEC after 4h min of heat stress
BMEC heat stressed 4h_GE1-v5_95_4

source_name: MEC heat stressed, 4h, replicate 1

value: heat stress

value: Mammary epithelial cells

value: Female


title: H2O_56d_4

value: male


title: H2O_56d_5

value: liver


title: H2O_28d_2

value: Water


title: BMEC heat stressed 2h

description:
Gene expression of buffalo MEC after 2h min of heat stress
BMEC heat stressed 2h _GE1-v5_95_3

source_name: MEC heat stressed, 2h, replicate 1


title: CMC_Co5_28d_4


title: CMC_Co5_28d_2


title: CMC_Co4_28d_5

value: CMC Co4 28d


title: colorectal adenoma, patient 3 (exon)

description:
colorectal adenoma, patient 3
colorectal adenoma biopsy

value: adenoma

value: sigmoid colon


title: H2O_56d_3

value: H2O 56d


title: CMC_Co4_28d_4


title: CMC_Co4_28d_3


title: CMC_Co4_28d_2


title: CMC_Co5_28d_3


title: CMC_Co3_28d_4

value: CMC Co3 28d


title: CMC_Co3_28d_2

value: 0 mg/kg


title: CMC_Co2_28d_1

value: CMC Co2 28d


title: CMC_Co2_28d_4


title: CMC_Co2_28d_5


title: CMC_Co3_28d_1


title: CMC_Co4_28d_1


title: CMC_Co2_28d_2


title: CMC_Co1_28d_3

value: CMC Co1 28d


title: WY_28d_5

source_name: liver, Wy-14643, 100 mg/kg, 28 days

value: WY

value: 100 mg/kg

value: WY 28d

tag: corresponding control


title: WY_28d_2


title: CMC_Co2_28d_3

value: CMC

value: Carboxymethylcellulose


title: CMC_Co3_28d_3


title: CMC_Co1_28d_1


title: CMC_Co1_28d_4


title: CMC_Co1_28d_2


title: WY_28d_4


title: WY_28d_1


title: WY_28d_3


title: Pio_28d_4

source_name: liver, Pioglitazone, 100 mg/kg, 28 days

value: Pio

value: Pioglitazone

value: Pio 28d

value: CMC Co5 28d


title: Pio_28d_5

value: male

value: liver


title: PB_28d_4 (2)

source_name: liver, Phenobarbital, 0.05 % (w/v), 28 days

value: PB

value: Phenobarbital

value: PB 28d

value: H2O 28d


title: PB_28d_1 (2)


title: Pio_28d_2


title: PB_56d_2

source_name: liver, Phenobarbital, 0.05 % (w/v), 56 days

value: PB 56d

value: H2O 56d


title: colorectal adenoma, patient 1 (exon)

description:
colorectal adenoma, patient 1
colorectal adenoma biopsy

source_name: colorectal adenoma

value: adenoma

tag: localisation

value: transversal colon


title: PBO_28d_3

source_name: liver, Piperonyl-butoxide, 600 mg/kg, 28 days

value: PBO

value: Piperonyl-butoxide

value: 600 mg/kg

value: PBO 28d

value: CMC Co2 28d


title: Pio_28d_1

value: Pio

value: Pioglitazone

value: 100 mg/kg

value: Pio 28d


title: BMEC control unstressed

description:
Gene expression of control/unstressed buffalo MEC
BMEC control unstressed _GE1-v5_95_1

source_name: MEC unstressed, replicate 1

tag: stress

value: control

value: Mammary epithelial cells

value: Female


title: PBO_28d_2

value: male

value: liver


title: MePy_28d_2

source_name: liver, Methapyrilene HCl, 1000 ppm, 28 days

value: MePy

value: Methapyrilene HCl

value: MePy 28d

value: CMC Co3 28d


title: PB_56d_5

value: PB

value: Phenobarbital

value: PB 56d

value: H2O 56d


title: MePy_28d_5


title: DCB_28d_4

source_name: liver, 1,4-Dichlorobenzene, 600 mg/kg, 28 days

value: DCB

value: 600 mg/kg

value: DCB 28d

value: CO 28d


title: PB_56d_4


title: PB_56d_1


title: PB_28d_3 (2)

value: PB 28d

value: H2O 28d


title: PB_28d_5 (2)


title: Pio_28d_3

value: Pio

value: Pioglitazone

value: 100 mg/kg

value: Pio 28d

value: CMC Co5 28d


title: PB_56d_3

value: male

value: liver


title: PBO_28d_4

value: PBO

value: Piperonyl-butoxide

value: PBO 28d

value: CMC Co2 28d


title: MePy_28d_1

value: MePy

value: Methapyrilene HCl

value: MePy 28d

value: CMC Co3 28d


title: PB_28d_2 (2)

value: PB

value: Phenobarbital

value: PB 28d


title: PBO_28d_1

value: 600 mg/kg


title: MePy_28d_4


title: MePy_28d_3


title: DCB_28d_5

value: DCB

value: DCB 28d

value: CO 28d


title: pool of colorectal normal mucosae, rep1 (gene)

source_name: colorectal normal mucosae

value: normal mucosa


title: colorectal adenoma, patient 22 (gene)

description:
colorectal adenoma, patient 22
colorectal adenoma biopsy

value: adenoma

value: cecum


title: DCB_28d_2

value: male

value: liver


title: colorectal adenoma, patient 24 (gene)

description:
colorectal adenoma, patient 24
colorectal adenoma biopsy

value: left colon


title: colorectal adenoma, patient 23 (gene)

description:
colorectal adenoma, patient 23
colorectal adenoma biopsy

value: rectum


title: DCB_28d_3


title: CPA_28d_5

source_name: liver, Cyproterone acetate, 160 mg/kg, 28 days

value: CPA

value: Cyproterone acetate

value: 160 mg/kg

value: CPA 28d


title: CITCO_28d_4

source_name: liver, CITCO, 10 mg/kg, 28 days

value: CITCO

value: 10 mg/kg

value: CITCO 28d

value: CMC Co4 28d


title: colorectal adenoma, patient 16 (gene)

description:
colorectal adenoma, patient 16
colorectal adenoma biopsy

value: sigmoid colon


title: colorectal adenoma, patient 17 (gene)

description:
colorectal adenoma, patient 17
colorectal adenoma biopsy

value: right colon


title: colorectal adenoma, patient 20 (gene)

description:
colorectal adenoma, patient 20
colorectal adenoma biopsy


title: CPA_28d_3

value: CO 28d


title: colorectal adenoma, patient 19 (gene)

description:
colorectal adenoma, patient 19
colorectal adenoma biopsy

value: adenoma


title: CPA_28d_2


title: colorectal adenoma, patient 21 (gene)

description:
colorectal adenoma, patient 21
colorectal adenoma biopsy

value: rectosigmoid junction


title: pool of colorectal normal mucosae, rep2 (gene)

description:
pool of colorectal normal mucosae, rep2
pool of colorectal normal mucosa biopsies

value: normal mucosa


title: CITCO_28d_1

value: male

value: liver


title: DCB_28d_1

value: DCB

value: 600 mg/kg

value: DCB 28d


title: CITCO_28d_5


title: colorectal adenoma, patient 13 (gene)

description:
colorectal adenoma, patient 13
colorectal adenoma biopsy


title: CPA_28d_4

value: CPA

value: Cyproterone acetate

value: 160 mg/kg


title: CMC_hCAR/hPXR_28d_5

value: CMC

value: Carboxymethylcellulose

value: 0 mg/kg

value: CMC hCAR/hPXR 28d


title: CPA_28d_1

value: CPA 28d


title: CMC_hCAR/hPXR_28d_4


title: CITCO_28d_2

value: CITCO

value: 10 mg/kg

value: CITCO 28d

value: CMC Co4 28d


title: CMC_hCAR/hPXR_28d_3

value: male


title: colorectal adenoma, patient 14 (gene)

description:
colorectal adenoma, patient 14
colorectal adenoma biopsy

value: adenoma

value: rectosigmoid junction


title: colorectal adenoma, patient 18 (gene)

description:
colorectal adenoma, patient 18
colorectal adenoma biopsy

value: sigmoid colon


title: CITCO_28d_3

value: liver


title: colorectal adenoma, patient 15 (gene)

description:
colorectal adenoma, patient 15
colorectal adenoma biopsy

value: transversal colon


title: colorectal adenoma, patient 12 (gene)

description:
colorectal adenoma, patient 12
colorectal adenoma biopsy


title: colorectal adenoma, patient 11 (gene)

description:
colorectal adenoma, patient 11
colorectal adenoma biopsy


title: CMC_hCAR/hPXR_28d_1


title: colorectal adenoma, patient 10 (gene)

description:
colorectal adenoma, patient 10
colorectal adenoma biopsy


title: colorectal adenoma, patient 2 (gene)

description:
colorectal adenoma, patient 2
colorectal adenoma biopsy

value: rectum


title: colorectal adenoma, patient 7 (gene)

description:
colorectal adenoma, patient 7
colorectal adenoma biopsy


title: colorectal adenoma, patient 3 (gene)

description:
colorectal adenoma, patient 3
colorectal adenoma biopsy


title: colorectal adenoma, patient 4 (gene)

description:
colorectal adenoma, patient 4
colorectal adenoma biopsy

value: right colon


title: colorectal adenoma, patient 1 (gene)

description:
colorectal adenoma, patient 1
colorectal adenoma biopsy


title: CITCO_hCAR/hPXR_28d_5

value: CITCO hCAR/hPXR 28d


title: colorectal adenoma, patient 6 (gene)

description:
colorectal adenoma, patient 6
colorectal adenoma biopsy


title: colorectal adenoma, patient 8 (gene)

description:
colorectal adenoma, patient 8
colorectal adenoma biopsy


title: colorectal adenoma, patient 5 (gene)

description:
colorectal adenoma, patient 5
colorectal adenoma biopsy


title: colorectal adenoma, patient 9 (gene)

description:
colorectal adenoma, patient 9
colorectal adenoma biopsy


title: CITCO_hCAR/hPXR_28d_1


title: CITCO_hCAR/hPXR_28d_2


title: CMC_hCAR/hPXR_28d_2

value: CMC

value: Carboxymethylcellulose


title: All Spinal Neurons - 27 hpf - Replicate 4

city: Syracuse

first: Samantha

middle: Jane

last: England

state: NY

address: 107 College Place

department: Biology

institute: Syracuse University

hyb_protocol: Cyanine 3-labelled cRNA was fragmented and hybridised as per the Agilent One-Color Microarray-Based Gene Expression Analysis manual. Hybridisation was performed using our custom-designed Agilent-027382 4x44K arrays.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner (G2505C) using one color scan setting and an x and y scan resolution of 5 microns per pixel.

data_processing:
The scanned images were analyzed with Agilent Feature Extraction software using protocol GE1_105_Dec08 and Grid: 027382_D_F_20100223, to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Quantile normalisation was performed using the Agi4x44PreProcess package in R (https://www.bioconductor.org/).

organism: Danio rerio

source_name: all spinal neurons, 27 hpf

label_protocol: cDNA was first synthesized using the Ovation Pico WTA System V2 (Pico, 3302) and a minimum of 500 pg of input total RNA. The resulting cDNA was converted in to Cyanine 3-labelled cRNA using the Agilent Genomic DNA Enzymatic Labelling Kit (Agilent, 5190-0449).

growth_protocol: Embryos were raised at 28.5oC until 10 hours post fertilisation (hpf), and then incubated at 32oC until they reached 27 hpf. Developmental stage was confirmed by prim-staging.

extract_protocol: Total RNA was extracted from FAC-sorted cells using the Qiagen RNeasy Micro Kit (Qiagen, 74004), following the manufacturer's instructions. The extraction process incorporates an on-column DNase-digestion step to remove any contaminating genomic DNA. Extracted total RNA was eluted in 14 µl of nuclease-free water. RNA integrity was analysed using the Agilent RNA 6000 Pico Kit (Agilent, 5067-1513) on the Agilent 2100 Bioanalyser.

treatment_protocol: Prior to fluorescence activated cell sorting (FACS), prim-staged embryos were manually deyolked by gently pipetting them up and down in ice-cold Ringer's Solution (116 mM NaCl, 2.9 mM KCl, 1.8 mM CaCl2, 5 mM HEPES, pH7.2). Using a glass pipette coated with foetal bovine serum, deyolked embryos were transferred to a petri dish containing fresh ice-cold Ringer's Solution. The spinal cord immediately above the yolk extension was dissected and then dissociated using the Worthington Papain Dissociation System (Worthington Biochemical Corporation, LK003150). Dissociated cells were resuspended in 0.5 ml Leibovitz's L-15 Medium (Invitrogen, 11415064) + 0.5% foetal bovine serum. For additional information, please see Cerda et al., (2009) Dev Dyn 238: 150-161. All FAC-sorting was performed within four hours of commencing the spinal cord dissections. Cell suspensions were filtered to remove cellular aggregates using 35µm Cell Strainer Cap Tubes (BD Falcon, 352235) and then FAC-sorted using a Beckman Coulter 3-laser MoFlo cytometer. Cells were sorted directly in to 100 µl of lysis buffer from the Qiagen RNeasy Micro Kit (Qiagen, 74004) and immediately stored at -80oC.

tag: cell type

value: All spinal neurons

tag: transgenic line

tag: age

value: 27 hpf


title: V0v - 27 hpf - Replicate 3

source_name: V0v interneurons, 27 hpf

value: V0v spinal interneurons


title: CITCO_hCAR/hPXR_28d_3

tag: gender

value: CITCO

value: 10 mg/kg

value: CMC hCAR/hPXR 28d


title: V0v - 27 hpf - Replicate 4


title: All Spinal Neurons - 27 hpf - Replicate 3


title: V0v - 27 hpf - Replicate 2


title: brain cortex_sea level altitude_rep1

description:
replicate 1
SAMPLE 7

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: brain cortex, sea level altitude,  replicate 1

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

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

value: brain cortex

tag: altitude

value: sea level altitude


title: V0v - 27 hpf - Replicate 5


title: brain cortex_sea level altitude_rep3

description:
replicate 3
SAMPLE 9

source_name: brain cortex, sea level altitude,  replicate 3


title: CITCO_hCAR/hPXR_28d_4

value: male


title: All Spinal Neurons - 27 hpf - Replicate 2


title: brain cortex_sea level altitude_rep2

description:
replicate 2
SAMPLE 8

source_name: brain cortex, sea level altitude,  replicate 2


title: brain cortex_3km altitude_rep3

description:
replicate 3
SAMPLE 6

source_name: brain cortex, 3km altitude,  replicate 3


title: UMSCC1_CTL_GFP

status: Public on Aug 25 2016

type: SRA

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

library_source: transcriptomic

data_processing:
Clean paired end fastq files were aligned to human reference (hg19) using STAR aligner.
expression was estimated in terms of FPKM using cufflinks against ensemble version 75 gene model (GTF)
Genome_build: hg19
Supplementary_files_format_and_content: Output from cufflinks (genes.fpkm.tracking file)

molecule: polyA RNA

source_name: cell line

extract_protocol: Libraries were generated using the TruSeq RNA Sample Preparation kit (Illumina)

tag: cell line

tag: condition

value: GFP overexpression


title: brain cortex_3km altitude_rep2

description:
replicate 2
SAMPLE 5

source_name: brain cortex, 3km altitude,  replicate 2


title: Trunk - 27 hpf - Replicate 4

source_name: all trunk cells, 27 hpf

value: Trunk cells (spinal cord and other tissues)


title: Trunk - 27 hpf - Replicate 2


title: brain cortex_7km altitude_rep3

description:
replicate 3
SAMPLE 3

source_name: brain cortex, 7km altitude,  replicate 3


title: HSPC_control rep3

city: New York

first: Beatriz

last: Aranda-Orgilles

address: 522 First Avenue

institute: NYU School of Medicine

description: Gene expression data from Control Lineage negative, c-Kit and Sca1 (HSPCs) positive expressing bone marrow progenitors-repeat3

hyb_protocol: 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using geneChip program. No further adjustments were made to the data in the table.

source_name: Total RNA control HSPCs 4 days after pI:pC

label_protocol: 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation, cDNA Biotin Module V2

growth_protocol: Cells were directly isolated by FACS from mice

extract_protocol: Qiagen RNEasy Plus Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

treatment_protocol: Cells were FACS sorted from control and Med12Flox;MxCre mice 4 days after induction of Med12 deltion via pI:pC injection

tag: background strain


title: brain cortex_3km altitude_rep1

description:
replicate 1
SAMPLE 4

source_name: brain cortex, 3km altitude,  replicate 1


title: Trunk - 27 hpf - Replicate 1


title: All Spinal Neurons - 27 hpf - Replicate 1


title: Trunk - 27 hpf - Replicate 3


title: HSPC_Med12 KO rep2

description: Gene expression data from Med12 KO Lineage negative, c-Kit and Sca1 (HSPCs) positive expressing bone marrow progenitors-repeat2

source_name: Total RNA Med12 KO HSPCs 4 days after pI:pC


title: HSPC_control rep1

description: Gene expression data from Control Lineage negative, c-Kit and Sca1 (HSPCs) positive expressing bone marrow progenitors-repeat1


title: HSPC_Med12 KO rep1

description: Gene expression data from Med12 KO Lineage negative, c-Kit and Sca1 (HSPCs) positive expressing bone marrow progenitors-repeat1


title: brain cortex_7km altitude_rep2

description:
replicate 2
SAMPLE 2

source_name: brain cortex, 7km altitude,  replicate 2


title: brain cortex_7km altitude_rep1

description:
replicate 1
SAMPLE 1

source_name: brain cortex, 7km altitude,  replicate 1


title: SIN KO 1

city: Piscataway

first: Estela

last: Jacinto

state: NJ

address: 683 Hoes Lane

department: Biochemistry and Molecular Biology

institute: Rutgers-Robert Wood Johnson Med School

description: SIN1 KO MEFs (Altered metabolism)

hyb_protocol: As directed in the Genechip WT Terminal Labeling and Hybridization User Manual

scan_protocol: As directed in the GeneChip Hybridization, Wash and Stain Kit : Affymetrix, P/N 900720

data_processing: Genesifter using RMA analysis

source_name: SIN1 KO Murine Epithelial Fibroblast

label_protocol: NuGEN Encore biotin module

growth_protocol: Cells were grown in DMEM using standard tissue culture methods

extract_protocol: Guanidine Isothiocyanate / Acid Phenol standard protocol

treatment_protocol: Cells were either wild type or SIN1 gene ablated

tag: genotype

value: SIN1 KO

value: murine epithelial fibroblasts


title: HSPC_Med12 KO rep3

description: Gene expression data from Med12 KO Lineage negative, c-Kit and Sca1 (HSPCs) positive expressing bone marrow progenitors-repeat3


title: wild type 2

description: Wild type MEFs

source_name: Wild type Murine Epithelial Fibroblast

value: Wild type


title: CaSki_GFP_rep2

data_processing: CEL files were read using ReadAffy command into R and normalized using RMA.

source_name: Cell Line

growth_protocol: CaSki cells either with extopic expression of  GFP or ZNF750 were maintained in DMEM containing 0% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin/streptomycin (P/S), at 37 ºC, 5% CO2 in a humidified atmosphere.

extract_protocol: Qiagen RNeasy kits were used to isolate total RNA

treatment_protocol: Lenti-virus mediated overexpression

value: CaSki

value: GFP over expression


title: CaSki_GFP_rep1


title: CaSki_ZNF750_rep2

value: ZNF750 over expression


title: SIN KO 2

description: SIN1 KO MEFs (Altered metabolism)


title: wild type 1

description: Wild type MEFs


title: CL1-5 HOXA5-overexpressing cells, biological rep1

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: CH_HOXA5 mix 1.CEL

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were processed by GeneSpring GX software version 11 GC-RMA preprocessor to use on the CEL files

source_name: CL1-5 HOXA5-overexpressing cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: Cells were cultured in RPMI-1640 medium  with 10% fetal bovine serum (FBS), 100 u/ml penicillin and 100 mg/ml streptomycin at 37 °C in a humidified atmosphere of 5% CO2.

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

treatment_protocol: The stably pooled HOXA5-overexpressing and mock cells were selected with 2 mg/ml G418 (geneticin; Life Technologies) for one month.

tag: cell line source

value: 64-year-old male Taiwanese patient

tag: tissue source

value: lung

value: human lung adenocarcinoma cells

tag: genotype/variation

value: HOXA5-overexpressing cells


title: CL1-5 HOXA5-overexpressing cells, biological rep2

description: CH_HOXA5 mix 2.CEL


title: CL1-0 PARVA-overexpressing cells, biological rep1

description: AY_PARVA mix 1

hyb_protocol: Following fragmentation, 20 ug of cRNAs were hybridized for 16 hr at 45 oC on Affymetrix Human Genome U133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

data_processing: The expression data were analyzed by the SAS JMP Genomics software (Version 5.1; SAS Institute Inc., Cary, NC). Affymetrix CEL files were transformed by GC-RMA algorithm, imported at the probe level and log2 transformed, and each probe set was summarized using the median of the corresponding probes. Each array was normalized by Quantile Normalization.

source_name: stably pooled PARVA-overexpressing cells

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

treatment_protocol: The stably pooled PARVA-overexpressing and mock cells were selected with 1mg/ml G418 (geneticin; Life Technologies) for one month.

value: PARVA-overexpressing cells


title: CL1-5 HOXA5-overexpressing cells, biological rep3

description: CH_HOXA5 mix 3.CEL


title: Lung tissue_COPD15

city: Barcelona

first: Ricardo

last: Bastos

address: Rosellón  149-153

department: Cell Biology, Neurosciences and Immunology

country: Spain

institute: IDIBAPS/University of Barcelona

hyb_protocol: Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc)

data_processing: Expression measures were normalized and summarized using the GC content adjusted-Robust Multiarray Analysis (GC-RMA) methodology

source_name: Peripheral lung tissue, COPD

label_protocol: cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)

extract_protocol: RNA was prepared from grossly homogenous pieces of tissue (100-200 mg) with an RNeasy Midi kit (Qiagen, Valencia, CA)  according to the manufactures instructions

tag: tissue

value: Peripheral lung tissue

tag: phenotype

value: moderate COPD


title: CL1-5 Mock cells, biological rep1

description: CH_H-MOCK mix 1.CEL

source_name: CL1-5 Mock cells

value: mock control cells


title: CL1-5 Mock cells, biological rep3

description: CH_H-MOCK mix 3.CEL


title: CL1-0 PARVA-overexpressing cells, biological rep2

description: AY_PARVA mix 2


title: Lung tissue_COPD16


title: CL1-0 Mock cells, biological rep2

description: AY_P-MOCK mix 2

source_name: stably pooled Mock-overexpressing cells


title: Lung tissue_COPD14


title: Lung tissue_COPD18


title: Lung tissue_COPD9


title: Lung tissue_COPD11


title: Lung tissue_COPD4


title: Lung tissue_COPD6


title: HSPC_control rep2

description: Gene expression data from Control Lineage negative, c-Kit and Sca1 (HSPCs) positive expressing bone marrow progenitors-repeat2


title: Lung tissue_COPD8


title: Lung tissue_COPD13


title: CL1-0 Mock cells, biological rep1

description: AY_P-MOCK mix 1


title: Lung tissue_COPD3


title: Lung tissue_COPD7


title: CL1-5 Mock cells, biological rep2

description: CH_H-MOCK mix 2.CEL


title: CaSki_ZNF750_rep1

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.

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


title: Lung tissue_COPD2


title: Lung tissue_COPD17


title: Lung tissue_COPD10


title: Lung tissue_COPD12


title: Lung tissue_COPD5


title: Raji_JQ1_rep2

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

institute: fondazione Istituto italiano di tecnologia

description: Gene expression data from Raji cells after 24h JQ1 treatment

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. Targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes  and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Human Gene 1.0 ST Array was then hybridized with each biotin-labeled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip®  cartridges were washed and stained with GeneChip®  Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0002 standard protocol.

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis with proprietary software. Partek Genomics Suite v 6.4 was used for analysis of microarray data.

data_processing:
The data were analyzed with Genespring GX 11 with RMA with probe level summarization. Raw data were normalized for the median of the expression between the six samples. P values were calculated with a t-test and adjusted with BH (Benjamini-Hochberg) multiple testing correction
RMA raw signals, log2FC, adjusted pvalues, expression values in Dmso or JQ1

source_name: Raji cells treated with 100 nM JQ1

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip® WT Plus Kit (Affymetrix, Santa Clara, CA). With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled. All steps of the labeling protocol were performed as suggested by Affymetrix.

growth_protocol: RAJI cells (250000 cells/mL) were cultured in RPMI supplemented with 10% Fetal Bovine Serum, 2mM L-Glutammine and 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted from 107 RAJI cells using TRizol (Invitrogen) according to manufacturer’s instructions. TurboDNase (Ambion) was used to digest genomic DNA

treatment_protocol: RAJI cells were treated with 100 nM of JQ1 or vehicle (DMSO) for 24h. JQ1 or DMSO were added to the culture 24h after the initial plating

tag: treatment


title: Raji_JQ1_rep3


title: Raji_JQ1_rep1


title: Lung tissue_S7

source_name: Peripheral lung tissue,  smoker

value: healthy smoker


title: Lung tissue_COPD1


title: Raji_Dmso_rep1

description: Gene expression data from Raji cells after 24h Dmso treatment

label: DMSO

source_name: Raji cells treated with Dmso

value: DMSO


title: Lung tissue_S10


title: Raji_Dmso_rep2


title: Raji_Dmso_rep3


title: Lung tissue_S11


title: Lung tissue_S8


title: infected_with_K98_1

city: Buenos Aires

first: Natalia

middle: Anahí

last: Juiz

address: 2490, Vuelta de Obligado

country: Argentina

institute: INGEBI-CONICET

description: Replicate 1

hyb_protocol: 1500 ng of labeled cRNA samples were hybridized to each Mouse WG-6 v2.0 Expression Beadchip for 17h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)).   Array probes transformed by logarithm and normalized by quantile method.  Statistical significance of the expression data was determined using LPE test and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm. For a DEG set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity.   Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp).  All data analysis and visualization of differentially expressed genes was conducted using R 3.1.2 (www.r-project.org).

source_name: Mouse Placenta

label_protocol: 500 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP.

growth_protocol: Adult C57BL/6J female mice and pregnant. Animals were maintained in rooms at 24°C with 40% humidity and a 12 hour light/dark cycle and were provided food and water adlibitum until used.

extract_protocol: Total RNA was extracted from placentas using the TRIzol® reagent (Invitrogen, Carlsbad, CA) according to manufacturer's instructions, treated with RQ1 RNase-Free DNase (Promega, Madison, USA) and stored at −80°C until used.

treatment_protocol: To obtain chronically infected mice, 4 inbred females between 6 and 8 weeks old were inoculated by the intradermoplantar (idp) route with 500 bloodstream trypomastigotes of K98 or with 50 bloodstream trypomastigotes of VD, because higher inocula of VD are lethal for this mouse strain by the intraperitoneal route. Parasitemia was measured weekly by counting in a Neubauer chamber the number of parasites obtained from the tail vein blood diluted (1/10) in red blood cell lysis solution (Tris–NH4 Cl 0.83% pH 7.2). Chronic phase was considered when no parasites were detected in chamber (around 3 weeks post-infection). At day 30 post-infection two females were housed with 1 uninfected male per cage. To assess the day of fertilization, the vaginal plug was macroscopically searched [14], being the day of vaginal plug appearance considered as day 0.5 of pregnancy. A third group of 4 uninfected females of the same age and weight were used as control. On day 18.5±1 of pregnancy, dams were euthanized and samples of maternal blood were taken by cardiac puncture and stored in EDTA solution until processed. Finally, entire placentas from the naturally mated crosses were removed and placed in RNAlater® solution (Applied Biosystems, Foster City, CA).

tag: strain

value: female

value: placenta

tag: agent

value: Trypanosoma cruzi K98


title: infected_with_VD_1

description: Replicate 1

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions

value: Trypanosoma cruzi VD