title: fV Q+ LPS

description: Heterozygous Leiden mice, 16h post LPS challenge, CD11c-POS splenocytes

source_name: spleen dendritic cells-heterozygous Leiden mice-16 hours after LPS


title: RAW control normal plasma

status: Public on Jun 10 2014

type: RNA

city: Milwaukee

first: Hartmut

last: Weiler

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

country: USA

institute: BloodCenter of Wisconsin

description: untreated RAW264.7 cells cultured for 3h with 10% v/v plasma prepared from wildtype mice

hyb_protocol: fragmented, biotin-labelled cRNA was hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix,  Santa Clara,  CA)

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/)  to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: RAW264.7 cell-normal plasma-no LPS/aPC

label_protocol: 100 ng RNA was amplified using an Affymetrix two-cycle cDNA synthesis kit.   cRNA was synthesized, labeled with biotin, and fragmented in accordance with the Affymetrix GeneChip expression analysis technical manual.

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

tag: background strain

value: Balb/c

tag: genotype/variation

value: wildtype


title: BAM8-DNA_Ox, untreated, biological rep1

city: Tuebingen

first: Dierk

last: Wanke

address: Auf der Morgenstelle 32

department: Plant Physiology

country: Germany

institute: University of Tuebingen

description:
BAM8-DNA_Ox_A
Gene expression data from 3-week-old shoots; untreated plants.

hyb_protocol: After fragmentation of cRNA using the RNA Fragmentation Reagents (Ambion), 13.5 µg of cRNA was hybridized to Affymetrix Arabidopsis ATH1 Genome Array (ATH1-121501) according to manufacturer's manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the protocol 'EukGE-WS2V4'.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® scanner GS3000 7G according to manufacturer's manual.

data_processing: The data was analysed with GeneSpring GX (vers. 7.3) from Agilent. Preprocessing was performed with included RMA Plugin.

organism: Arabidopsis thaliana

source_name: shoots, BAM8-DNA_Ox, untreated

label_protocol: 1µg of total RNA were used to synthesize amplified labeled cRNA (MessageAmp™ II aRNA Biotin Amplification Kit; Ambion).

growth_protocol: Arabidopsis thaliana (accession Columbia) were grown in a nutrient-rich, medium-grade, peat-based compost in Percival AR95 growth chambers (CLF Plant Climatics) at a constant temperature of 20°C, 70% humidity and a 12-h light period with constant, uniform light intensity of 150 μmol•m-2•s-1.

extract_protocol: For RNA extraction, RNeasy Plant Mini kit was used (according to instructions from Qiagen). Extracted RNA was precipitated ?ul RNA;  8 µl 3 M Sodium acetate (pH 5.2); 2 µl Glycogen(5mg/ml); -80°C? how long? than 30 min 13000 rpm 4°C. 2 times washing with 70% ethanol. resuspended in DEPC water. RNA quantity and integrity were assessed using RNA 6000 Nano LabChip Kit and the BioAnalyzer software (Agilent).

treatment_protocol: No treatment was applied.

tag: ecotype

tag: tissue

value: shoot

tag: age

value: 3 weeks

tag: treatment


title: BAM7-DNA_Ox, untreated, biological rep2

description:
BAM7-DNA_Ox_B
Gene expression data from 3-week-old shoots; untreated plants.

source_name: shoots, BAM7-DNA_Ox, untreated


title: BAM7-DNA_Ox, untreated, biological rep1

description:
BAM7-DNA_Ox_A
Gene expression data from 3-week-old shoots; untreated plants.


title: wildtype control

description: unchallenged wildtype mice, CD11c-POS splenocytes

source_name: spleen dendritic cells-wildtype mice-no LPS/aPC


title: cobalt_high_rep4

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 uL of 2x Agilent GEx hybridization buffer HI-RPM was added to the fragmentation mixture to stop the reaction. For each reaction 100 uL was hybridized to an Agilent Zebrafish custom Genome Oligo Microarrays (G2517A001, design 017662) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 seconds with acetonitrile, and 30 seconds with Stabilization and Drying solution (Agilent) then scanned immediately.

scan_protocol: Slides were scanned immediately after washing using a GenePix 4200 AL with a scan resolution of 5 um, standard green filter, PMT gain set at 400 and scan power set to 45%.

data_processing: Scanned images were analyzed with GenePix Pro 6.1.0.4 using GalFile 017662_D_20070905_update8. Instrument default setting settings were used with the following exceptions: Background Subtraction: width of background = 2 feature diameters; Resize Features: minimum diameter = 80%, maximum diameter = 110%; Feature Movement: maximum translation = 20 um; CPI threshold = 0 with local background subtraction.

organism: Danio rerio

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug pooled RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were verified with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Exposures were conducted in 5-gallon glass aquaria adapted for flow-through use (60 mL/min; 5.4 turnovers/day) and maintained at 25°C with a 12h:12h (light:dark) photoperiod.

extract_protocol: Whole frozen fish were pulverized under liquid nitrogen using a SPEX 6750 freezer mill (SPEX Sample Prep, Metuchen, NJ). Total RNA was isolated from the pulverized material using Trizol (Invitrogen, Carlsbad, CA) with an extra clarification centrifugation step to remove bone, scales, lipid and other debris, followed by column purification with RNeasy Mini kits (Qiagen, GmbH, Germany) to remove residual salt and organic solvents. Total RNA quality and quantity were evaluated using an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA) and verified using the NanoDrop ND-1000 Spectrophotometer (NanoDrop, Wilmington, DE).

treatment_protocol: Exposures were conducted for 24 h using control (no toxicant) plus the high, mid, and low concentrations of each metal in the flow-through aquaria with metal concentrations maintained for the duration of the exposure.

value: adult (6 - 9 months)

tag: chemical group

value: Co

tag: dose

value: high

tag: chemical concentration (measured)

value: whole organism


title: bam7 bam8, untreated, biological rep1

description:
bam7_bam8_A
Gene expression data from 3-week-old shoots; untreated plants.

source_name: shoots, bam7 bam8, untreated

value: bam7 bam8


title: bam7 bam8, untreated, biological rep2

description:
bam7_bam8_B
Gene expression data from 3-week-old shoots; untreated plants.


title: bam8, untreated, biological rep2

description:
bam8_B
Gene expression data from 3-week-old shoots; untreated plants.

source_name: shoots, bam8, untreated


title: bam8, untreated, biological rep1

description:
bam8_A
Gene expression data from 3-week-old shoots; untreated plants.


title: bam7, untreated, biological rep1

description:
bam7_A
Gene expression data from 3-week-old shoots; untreated plants.

source_name: shoots, bam7, untreated


title: bam7, untreated, biological rep2

description:
bam7_B
Gene expression data from 3-week-old shoots; untreated plants.


title: cobalt_high_rep3


title: wildtype, untreated, biological rep2

description:
Wt_B
Gene expression data from 3-week-old shoots; untreated plants.

source_name: shoots, wildtype, untreated


title: cobalt_high_rep2


title: cobalt_high_rep1


title: wildtype, untreated, biological rep1

description:
Wt_A
Gene expression data from 3-week-old shoots; untreated plants.


title: cobalt_low_rep4

value: low


title: cobalt_low_rep1


title: cobalt_low_rep3


title: cobalt_mid_rep2

value: mid


title: cobalt_mid_rep4


title: cobalt_mid_rep1


title: cobalt_mid_rep3


title: normal saline 4

city: Moscow

first: Anastasia

last: Shindyapina

state: Moscow

address: Mosfilmovskaya 76

department: Biengineering

country: Russia

institute: MSU Lomonosov

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: normal saline 4

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.

treatment_protocol: 120 mg/kg methanol (350 mcL) and 350 mcL of normal saline solution

tag: gender

value: male

value: brain


title: cobalt_control_rep2

value: control

value: 0 mg/L


title: cobalt_control_rep4


title: cobalt_control_rep3


title: cobalt_low_rep2


title: BAM8-Cat_Ox, untreated, biological rep2

description:
BAM8-Cat_Ox_B
Gene expression data from 3-week-old shoots; untreated plants.

source_name: shoots, BAM8-Cat_Ox, untreated


title: cobalt_control_rep1


title: nickel_high_rep4

value: Ni


title: normal saline 1

source_name: normal saline 1


title: methanol-treated 4

source_name: methanol-treated 4


title: methanol-treated 3

source_name: methanol-treated 3


title: normal saline 2

source_name: normal saline 2


title: nickel_high_rep2


title: nickel_high_rep3


title: methanol-treated 2

source_name: methanol-treated 2


title: nickel_mid_rep2


title: nickel_high_rep1


title: nickel_mid_rep3


title: nickel_mid_rep4


title: nickel_mid_rep1


title: nickel_low_rep4


title: J82 p12, Sandalwood 1:11,000x dilution, 1h treatment

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

hyb_protocol: After purification, RNA concentrations were determined with a scanning spectrophotometer (Nanodrop, Wilmington), and qualitatively assessed for degradation by capillary gel electrophoresis (Agilent 2100 Bionalalyzer, Agilent Technologies). Biotinylated, amplified RNA was produced from 150 ng total RNA per sample using a modification of the Eberwine protocol14 as described in the Illumina® TotalPrep RNA Amplification Kit (Ambion, Inc., Austin). Briefly, RNA was reverse-transcribed with oligo(dT) primers containing a T7 promoter and amplified by in vitro transcription to generate anti-sense RNA containing biotin-UTP ribonucleotides.

scan_protocol: This RNA was hybridized overnight at 58C to mouse WG-6_v2 Expression BeadChip™ microarrays (Illumina Corp., San Diego), washed under high stringency conditions, labeled with streptavidin-Cy3, and scanned with an Illumina iSCAN scanner.

data_processing: The images and raw data from each chip were transferred automatically to the microarray database using one of the specified microarray core servers. Non-normalized - Raw signal intensity, background-subtracted using Illumina BeadStudio software. Normalized - log10 values processed using two-step normalization (Dozmorov I, Lefkovits I., Nucleic Acids Res. 2009 Oct;37(19):6323-39).

organism: Homo sapiens

source_name: J28 cells

growth_protocol: Human bladder cancer J82 cells were grown in MEM supplemented with 10% FBS.

extract_protocol: Total RNA was extracted at 0.5, 1, and 3 hours following treatment using the Rneasy Mini total RNA isolation kit.

treatment_protocol: J82 cells (500,000) were seeded in 60 mm culture plates for adherence and treated with 1:1,100 dilution of frankincense essential oil or 1:11,000 dilution of sandalwood essential oil.

tag: cell line

value: sandalwood 1:11,000x dilution

tag: time course


title: methanol-treated 1

source_name: methanol-treated 1


title: J82 p12, Sandalwood 1:11,000x dilution, 4h treatment

label_protocol: After purification, RNA concentrations were determined with a scanning spectrophotometer (Nanodrop, Wilmington), and qualitatively assessed for degradation by capillary gel electrophoresis (Agilent 2100 Bionalalyzer, Agilent Technologies). Biotinylated, amplified RNA was produced from 150 ng total RNA per sample using a modification of the Eberwine protocol14 as described in the Illumina® TotalPrep RNA Amplification Kit (Ambion, Inc., Austin). Briefly, RNA was reverse-transcribed with oligo(dT) primers containing a T7 promoter and amplified by in vitro transcription to generate anti-sense RNA containing biotin-UTP ribonucleotides.


title: J82 p12, Sandalwood 1:11,000x dilution, 2h treatment


title: J82 p12, no treatment, Rep 2

description: J82 p12, no treatment, Rep 2

value: no treatment


title: J82 p12, Sandalwood 1:11,000x dilution, 5h treatment


title: nickel_low_rep2


title: Ni/Cr-shared_control_rep4a


title: J82 p12, Frankincense 1:1,100x dilution, 2h treatment

value: frankincense 1:1,100x dilution


title: J82 p12, Frankincense 1:1,100x dilution, 3h treatment


title: nickel_low_rep3


title: Ni/Cr-shared_control_rep4b

value: Cr


title: J82 p12, Sandalwood 1:11,000x dilution, 0.5h treatment


title: J82 p12, Sandalwood 1:11,000x dilution, 3h treatment


title: Melanoma cell line UACC647_rep3

city: Bethesda

first: Laura

middle: L

last: Baxter

address: 35A Convent Drive

department: NHGRI

institute: NIH

hyb_protocol: Total RNA was reverse transcribed to obtain labeled cDNA. Labeled cDNA was hybridized to the chips. Chips were washed and stained using standard protocols for the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Affymetrix Gene Chip Scanner 3000 and gene expression intensities were calculated using the Affymetrix GeneChip Command Console software (AGCC)

data_processing: Affymetrix .CEL files were normalized using the RMA (Robust Multi-Array Analysis) algorithm within Partek Genomics Suite software (Partek Inc., St. Louis, MO).

source_name: Human metastatic melanoma cell line

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were grown to 90% confluency in 6-well dishes for each biological replicate.

extract_protocol: Trizol extraction was performed for an entire 6-well dish for each biological replicate per manufacturer's instructions, with the addition of heating to 65°C for 5 minutes during the Trizol step. Rna was subsequently purified with Qiagen RNeasy Mini columns (Qiagen). RNA quality and quantity was assessed using both a Bioanalyzer (Agilent Inc.) and NanoDrop (Thermo Scientiﬁc Inc.)

tag: tumor stage

value: metastatic


title: Melanoma cell line UACC647_rep2


title: nickel_low_rep1

value: adult (6 - 9 months)


title: J82 p12, Frankincense 1:1,100x dilution, 1h treatment


title: J82 p12, Frankincense 1:1,100x dilution, 0.5h treatment


title: Melanoma cell line UACC647_rep1


title: FUL1/FOR1_2 (MeDip)

type: genomic

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: G. fuliginosa-FUL (experimental) sample 1 is compared to Geospiza fortis-FOR (control) sample 1

hyb_protocol: A DNA methylated custom array by Roche Nimblegen that consisted of a Whole Genome Tiling Array of Zebra finch (Taeniopygia guttata) made of four 2.1M and one 3x720k array with 8,539,570 probes per array. Probe sizes were 50-75mer in length and median probe spacing was 200bp. Two different comparative (MeDIP vs MeDIP) hybridizations experiment were performed (2 sub-arrays) for each experimental species (FUL, SCA, PAR, CRA) versus control FOR, with each sub-array including hybridizations from MeDIP DNA from DNA pools from these different species.

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

data_processing:
For each comparative hybridization experiment raw data from both the Cy3 and Cy5 channels were imported into R, checked for quality and converted into MA values. Within each array, probes were separated into groups by GC content and each group was separately normalized using the loess normalization procedure. This allowed for groups with optimal GC content, which exhibited a reduced quality issue, to receive a normalization curve specific to that group. After each array was normalized within array, the arrays were then normalized across arrays using the A-quantile normalization procedure (Guerrero-Bosagna et al. 2010).  Following normalization each adjacent ≥3 probe set value represents the median intensity difference between FUL, SCA, PAR and CRA and control FOR of a 600bp window. Significance was assigned to probe differences between experimental species samples and reference FOR 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. Each region of interest was then annotated for gene and CpG content. Regions chosen for validation were then described as overlapping regions of interest between the 2 hybridization experiments. This list was further reduced to those overlapping regions with an average intensity value exceeding 9.5 (log scale), at least one 100 bp region with two CpGs or a CpG density>1.  (Guerrero-Bosagna et al. 2010). The July 2008 assembly of the Zebra Finch genome (taeGut1, WUSTL v3.2.4) produced by the Genome Sequencing Center at the Washington University in St. Louis (WUSTL) School of Medicine was retrieved (WUSTL 2008). A seed file was constructed and a BSgenome package was forged for using the Finch DNA sequence in the R code (Herve Pages BSgenome: Infrastructure for Biostrings-based genome data packages. R package version 1.24.0). This sequence was used to design the custom tiling arrays and to perform the bioinformatics.The chromosomal location of CNV and DMR clusters used an R-code developed to find chromosomal locations of clusters (M. K. Skinner et al. 2012).  A 2 Mb sliding window with 50,000 base intervals was used to find the associated CNV and DMR in each window.  A Z-test statistical analysis with p<0.05 was used on these windows to find the ones with over-represented CNV and DMR were merged together to form clusters.  A typical cluster region averaged approximately 3 megabases in size. The DMR and CNV association with specific zebra finch genes and genome locations used the Gene NCBI database for zebra finch gene locations 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 by using the KEGG website 'Search Pathway' tool (M. K. Skinner et al. 2012). Statistically significant over-representation uses a Fisher’s exact analysis.  All DMR and CNV genomic data obtained in the current study have been deposited in the NCBI public GEO database. Spearman Rank correlation coefficients were used to test for a relationship between phylogenetic distance and epigenetic and genetic changes. Spearman Rank correlation coefficients were used to test for a relationship between phylogenetic distance and epigenetic and genetic changes (Whitlock and Schluter 2009).
R-code data processing of raw data as described was used as the basis for conclusions in this study. Value definitions for processed data files:  #ClusterID = ID and chromosomal location for cluster of probes showing a significant difference (p<1.0E-5) between red and green channel hybridization (treated vs. control), #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, #GC = GC content of cluster, #CpG = CpG content of cluster, #CpGdensity = number of CpGs per hundred base pairs, and #Seq = probe sequence of cluster.

molecule: genomic DNA

organism: Geospiza fuliginosa

source_name: MeDIP ChIP DNA from G. fuliginosa (FUL) erythrocytes

label_protocol: For one sub-array of each species, MeDIP DNA samples from the experimental groups were labeled with Cy5 and MeDIP DNA samples from the control lineage were labeled with Cy3. For the other sub-array of each species a dye swap was performed so that MeDIP DNA samples from the experimental groups were labeled with Cy3 and MeDIP DNA samples from the control lineage were labeled with Cy5.

growth_protocol: Birds were captured from January-April 2009 at El Garrapatero, a lowland arid site on Santa Cruz Island, Galapagos Archipelago, Ecuador, with mist nests and banded with numbered Monel bands to track recaptures.  Birds were identified, aged and sexed using size and plumage characteristics.

extract_protocol: A small blood sample (90 µl) from each bird was collected in a microcapillary tube via brachial venipuncture.  Samples were stored on wet ice in the field, then erythrocytes purified by centrifugation and cells stored in a -20°C freezer at a field station.  Following the field season, samples were placed in a -80°C freezer for longer term storage.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 as following: DNA suspension was centrifuged at 500  g for 5 min. The DNA was then resuspended in 5 ml NIM free of EDTA, PMSF, and leupeptin and centrifuged again. A small amount of DNA suspension (1 µl) was finally suspended in 5 µl of EDTA- and protease inhibitor-free NIM medium containing 12% polyvinyl pyrrolidone (PVP; Mr 360 000) (without protease inhibitors) (Tateno et al. 2000) and then purified using a series of washes and centrifugations (Ward et al. 1999) from variable number of animals per species analyzed. The same concentrations of DNA from individual blood samples were then used to produce pools of DNA material. Two DNA pools were produced in total per species, each one containing the same amount of DNA from different animals.  The number of individuals used per pool is shown in the manuscript's Supplemental Table S6. These DNA pools were then used for chromatin immunoprecipitation of methylated DNA fragments (MeDIP). MeDIP was performed as follows: 6 µg of genomic DNA was subjected to series of three 20 pulse sonications at 20% amplitude and the appropriate fragment size (200-1000 ng) 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: Experimental

tag: species (symbol)

value: G. fuliginosa (FUL)

value: blood

tag: cell type

value: erythrocytes

tag: antibody

tag: antibody manufacturer

value: Diagenode

organism: Geospiza fortis

source_name: MeDIP ChIP DNA from Geospiza fortis (FOR) erythrocytes

treatment_protocol: Control

value: Geospiza fortis (FOR)


title: SCA2/FOR2_2 (MeDip)

description: G. scandens-SCA (experimental) sample 2 is comapred to Geospiza fortis-FOR (control) sample 2

organism: Geospiza scandens

source_name: MeDIP ChIP DNA from G. scandens (SCA) erythrocytes

value: G. scandens (SCA)


title: Melanoma cell line 0620LNA_rep3


title: BAM8-DNA_Ox, untreated, biological rep2

description:
BAM8-DNA_Ox_B
Gene expression data from 3-week-old shoots; untreated plants.

source_name: shoots, BAM8-DNA_Ox, untreated

value: shoot

value: 3 weeks


title: Ni/Cr-shared_control_rep3a

value: control

value: whole organism


title: SCA1/FOR1_1 (MeDip)

description: G. scandens-SCA (experimental) sample 1 is compared to Geospiza fortis-FOR (control) sample 1


title: PAR2/FOR2_2 (MeDip)

description: Camarhynchus parvulus-PAR (experimental) sample 2 is comapred to Geospiza fortis-FOR (control) sample 2

organism: Camarhynchus parvulus

source_name: MeDIP ChIP DNA from Camarhynchus parvulus (PAR) erythrocytes

value: Camarhynchus parvulus (PAR)


title: PAR2/FOR2_1 (MeDip)


title: TSA-2 p13, Frankincense 1:800x dilution, 5h treatment

source_name: TSA-2 cells

value: frankincense 1:800x dilution


title: TSA-2 p13, Frankincense 1:800x dilution, 4h treatment


title: Melanoma cell line 0620LNA_rep1


title: J82 p12, no treatment, Rep 1

description: J82 p12, no treatment, Rep 1

value: no treatment


title: SCA1/FOR1_2 (MeDip)


title: Ni/Cr-shared_control_rep2b

value: 0 mg/L


title: Melanoma cell line 0620LNA_rep2


title: Ni/Cr-shared_control_rep3b

value: Cr


title: TSA-2 p13, Frankincense 1:800x dilution, 1h treatment


title: Ni/Cr-shared_control_rep2a

value: Ni


title: Ni/Cr-shared_control_rep1a

value: adult (6 - 9 months)


title: PAR1/FOR1_2 (MeDip)

description: Camarhynchus parvulus-PAR (experimental) sample 1 is compared to Geospiza fortis-FOR (control) sample 1


title: TSA-2 p13, Frankincense 1:800x dilution, 0.5h treatment


title: Melanoma cell line 0708LND_rep3

value: metastatic


title: PAR1/FOR1_1 (MeDip)

value: blood


title: TSA-2 p13, Frankincense 1:800x dilution, 3h treatment


title: Ni/Cr-shared_control_rep1b


title: Melanoma cell line UACC3093_rep3


title: FUL2/FOR2_2 (MeDip)

description: G. fuliginosa-FUL (experiemental) sample 2 is comapred to Geospiza fortis-FOR (control) sample 2

value: G. fuliginosa (FUL)

value: erythrocytes


title: normal saline 3

source_name: normal saline 3

value: male

value: brain


title: TSA-2 p13, Frankincense 1:800x dilution, 2h treatment


title: TSA-2 p13, no treatment

description: TSA-2 p13, no treatment


title: Melanoma cell line 0708LND_rep1


title: Melanoma cell line 0708LND_rep2


title: Melanoma cell line UACC3093_rep2


title: chromium_high_rep3

value: high


title: CRA2/FOR2_2 (MeDip)

description: Platyspiza crassirostris-CRA (experimental) sample 2 is comapred to Geospiza fortis-FOR (control) sample 2

organism: Platyspiza crassirostris

source_name: MeDIP ChIP DNA from Platyspiza crassirostris (CRA) erythrocytes

value: Platyspiza crassirostris (CRA)

value: Diagenode

value: Geospiza fortis (FOR)


title: chromium_high_rep2

value: whole organism


title: MCF7 blackcurrant

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

country: Japan

institute: Aomori University of Health and Welfare

description: MCF7 BCE.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x 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 to Agilent SurePrint G3 Rat GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MCF7 blackcurrant

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MCF-7 cells were seeded in culture dishes in DMEM with 10% FBS  and incubated at 37°C with 5% CO2 until confluent.

extract_protocol: Total RNA was extracted by using the RNeasy mini kit (Qiagen, Tokyo, Japan).

treatment_protocol: The medium was then replaced with phenol red- and serum-free DMEM, with or without BCE (50 μg/ml). After the cells were incubated for 24 h at 37°C with 5% CO2, they were washed twice with phosphate-buffered saline (PBS).

value: Human mammary tumor cells

tag: culture media

value: phenol red- and serum-free DMEM with BCE (50 μg/ml)


title: chromium_high_rep4


title: MCF7 control

description: MCF7 cont.

source_name: MCF7 control

value: phenol red- and serum-free DMEM (without BCE)


title: Melanoma cell line UACC3093_rep1


title: CRA1/FOR1_2 (MeDip)

description: Platyspiza crassirostris-CRA (experimental) sample 1 is compared to Geospiza fortis-FOR (control) sample 1


title: Melanoma cell line 0380MMU_rep2


title: SCA2/FOR2_1 (MeDip)

value: G. scandens (SCA)


title: chromium_mid_rep4

value: Cr

value: mid


title: chromium_mid_rep3

value: adult (6 - 9 months)


title: FUL1/FOR1_1 (MeDip)

value: blood


title: CRA2/FOR2_1 (MeDip)


title: FUL2/FOR2 _1 (MeDip)

value: G. fuliginosa (FUL)


title: CRA1/FOR1_1 (MeDip)

value: erythrocytes


title: Melanoma cell line 0380MMU_rep1

value: metastatic


title: chromium_mid_rep2


title: Melanoma cell line 0380MMU_rep3


title: chromium_low_rep2

value: low


title: chromium_low_rep1


title: chromium_low_rep3


title: chromium_high_rep1

value: high


title: chromium_low_rep4


title: Placenta_3.3_RL_M120_Piece_3

status: Public on Jun 09 2014

city: La Jolla

first: Rathi

middle: D

last: Thiagarajan

state: CA

address: 2880 Torrey Pines Scenic Drive

department: Reproductive Medicine

institute: UCSD

description: SAMPLE 72

data_processing: The data were filtered for detection pValue ≤ 0.01 and normalised using robust spline normalisation with lumi in R and batch corrected using ComBat.

label: Biotin

extract_protocol: Tissue was lysed in mirVana (Ambion) lysis buffer, using a Mini-Beadbeater-16 (Biospec), with agitation for one minute in the presence of 1 mm zirconia beads. Samples were then centrifuged at maximum speed for one minute and the lysed solution was transferred to a fresh microfuge tube. The remainder of the extraction was per the manufacturer’s protocol for the mirVana kit (Ambion). After extraction, RNA was quantified using the Quant-iT Kit (Life Technologies).  RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent).

tag: tissue id

value: Placenta 3.3

tag: pregnancy stage

value: Third trimester

tag: tissue collection method

value: RNAlater

tag: time after removal from the uterus

value: 0 minutes

tag: tissue type

value: Piece


title: Placenta_3.3_RL_M0_Piece_2

description: SAMPLE 68


title: chromium_mid_rep1

tag: age

tag: chemical group

tag: tissue

value: whole organism


title: Placenta_3.3_RL_M120_Piece_1

description: SAMPLE 70


title: Placenta_3.2_RL_M120_Piece_2

description: SAMPLE 65

value: Placenta 3.2

value: 120 minutes


title: BJAB_control_rep3

city: Boston

first: Rajeev

last: Malhotra

state: MA

address: Yawkey 5700, 55 Fruit St

department: Medicine

institute: MGH

description: Gene expression data from BJAB human B lymphocyte cell line treated with control lentivirus

hyb_protocol: cDNA was hybridized overnight at 45°C on the Affymetrix GeneChip Human Gene 1.0 ST array (GPL18401).  Bound cDNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE).

scan_protocol: GeneChips were scanned using a confocal laser scanner.

data_processing: The data were analyzed using the Affymetrix Expression Console and processed with the PLIER method.

source_name: BJAB cell, control

label_protocol: Biotin-labeled, fragmented cDNA

growth_protocol: Cells were cultured in RPMI containing 10% fetal calf serum, L-glutamine (2 mM), penicillin (200 U/ml) and streptomycin (20 mg/ml)

extract_protocol: Total RNA was extracted from cell lines using Rneasy extraction kit.

treatment_protocol: Cells were treated with either lentivirus containing a miRNA directed against LMKB or control (red fluorescent protein)

value: BJAB

value: B lymphocyte


title: BJAB_control_rep2


title: BJAB_LMKB-KD_rep1

description: Gene expression data from BJAB human B lymphocyte cell line treated with a lentivirus containing LMKB siRNA.

source_name: BJAB cell, LMKB siRNA


title: Placenta_3.3_RL_M0_Piece_1

description: SAMPLE 67


title: Placenta_3.2_RL_M120_Piece_3

description: SAMPLE 66


title: Placenta_3.2_RL_M60_Piece_3

description: SAMPLE 63

value: 60 minutes


title: Placenta_3.3_RL_M0_Piece_3

description: SAMPLE 69


title: Placenta_3.2_RL_M0_Piece_1

description: SAMPLE 58


title: Placenta_3.2_RL_M0_Piece_3

description: SAMPLE 60


title: Placenta_3.3_RL_M120_Piece_2

description: SAMPLE 71


title: Placenta_3.2_RL_M120_Piece_1

description: SAMPLE 64


title: Placenta_3.2_RL_M0_Piece_2

description: SAMPLE 59


title: BJAB_LMKB-KD_rep2


title: BJAB_control_rep1


title: Placenta_3.1_RL_M60_Chunk_1

description: SAMPLE 55

value: Placenta 3.1

value: Chunk


title: Placenta_3.1_RL_M60_Chunk_2

description: SAMPLE 56


title: BJAB_LMKB-KD_rep3


title: Placenta_3.1_RL_M60_Chunk_3

description: SAMPLE 57


title: Placenta_3.1_RL_M0_Chunk_2

description: SAMPLE 53


title: 14028s/pIDT-RyhB-2 replicate1

city: Irvine

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

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

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

data_processing: Signal extraction and quantitation with Roche’s NimbleScan 2.4 package

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

source_name: Replicate 1

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

growth_protocol: Cells were grown under aerobic conditions with skaking (250 rpm) in LB medium (25mL) to an OD600 of 0.4. At this point, 50 µm IPTG was added, and RNA was extracted after 20 min.

extract_protocol: High Pure RNA isolation kit (Roche)

treatment_protocol: 50 µm IPTG was added to the cultures at an OD600 of 0.4

tag: protocol

value: RyhB-2 overexpression was induced by adding 50 µM IPTG, and RNA was harvested after 20 min.


title: Placenta_3.2_RL_M60_Piece_2

description: SAMPLE 62


title: Placenta_3.1_RL_M0_Chunk_3

description: SAMPLE 54


title: Placenta_3.1_RL_M0_Chunk_1

description: SAMPLE 52


title: 14028s/pIDT-RyhB-2 replicate2

source_name: Replicate 2


title: Placenta_3.1_RL_M0_Piece_3

description: SAMPLE 45


title: Placenta_3.2_RL_M60_Piece_1

description: SAMPLE 61


title: Placenta_3.1_RL_M120_Piece_3

description: SAMPLE 51


title: Placenta_3.1_RL_M120_Piece_2

description: SAMPLE 50


title: Placenta_3.1_RL_M60_Piece_1

description: SAMPLE 46


title: Placenta_3.1_RL_M120_Piece_1

description: SAMPLE 49


title: Placenta_3.1_RL_M60_Piece_3

description: SAMPLE 48


title: Placenta_3.1_RL_M0_Piece_2

description: SAMPLE 44


title: Placenta_3.1_SF_M120_Piece_3

description: SAMPLE 42

value: Snap Frozen


title: Placenta_3.1_RL_M0_Piece_1

description: SAMPLE 43


title: Placenta_3.1_SF_M120_Piece_2

description: SAMPLE 41


title: Placenta_3.1_SF_M0_Piece_2

description: SAMPLE 35


title: Placenta_3.1_SF_M60_Piece_2

description: SAMPLE 38


title: Placenta_3.1_SF_M60_Piece_1

description: SAMPLE 37


title: Placenta_3.1_SF_M120_Piece_1

description: SAMPLE 40


title: Placenta_3.1_RL_M60_Piece_2

description: SAMPLE 47


title: Placenta_3.1_SF_M0_Piece_3

description: SAMPLE 36


title: Placenta_1.3_RL_M120_Piece_2

description: SAMPLE 32

value: Placenta 1.3

value: First trimester


title: Placenta_1.3_RL_M120_Piece_3

description: SAMPLE 33


title: Placenta_1.3_RL_M0_Piece_3

description: SAMPLE 30


title: Placenta_1.3_RL_M120_Piece_1

description: SAMPLE 31


title: Placenta_3.1_SF_M60_Piece_3

description: SAMPLE 39


title: Placenta_3.1_SF_M0_Piece_1

description: SAMPLE 34


title: Placenta_1.2_RL_M120_Piece_2

description: SAMPLE 26

value: Placenta 1.2


title: Placenta_1.3_RL_M0_Piece_2

description: SAMPLE 29


title: Placenta_1.2_RL_M120_Piece_3

description: SAMPLE 27


title: Placenta_1.3_RL_M0_Piece_1

description: SAMPLE 28


title: Placenta_1.2_RL_M120_Piece_1

description: SAMPLE 25


title: Placenta_1.2_RL_M60_Piece_2

description: SAMPLE 23


title: Placenta_1.2_RL_M60_Piece_3

description: SAMPLE 24


title: Placenta_1.2_RL_M0_Piece_2

description: SAMPLE 20


title: Placenta_1.1_RL_M120_Piece_2

description: SAMPLE 17

value: Placenta 1.1


title: Placenta_1.2_RL_M0_Piece_3

description: SAMPLE 21

value: RNAlater


title: Placenta_1.2_RL_M60_Piece_1

description: SAMPLE 22


title: Placenta_1.1_RL_M120_Piece_1

description: SAMPLE 16


title: Placenta_1.2_RL_M0_Piece_1

description: SAMPLE 19

value: 0 minutes


title: Placenta_1.1_RL_M120_Piece_3

description: SAMPLE 18

value: Piece


title: Placenta_1.1_RL_M60_Piece_3

description: SAMPLE 15


title: Placenta_1.1_RL_M60_Piece_1

description: SAMPLE 13


title: Placenta_1.1_RL_M0_Piece_3

description: SAMPLE 12


title: Placenta_1.1_RL_M60_Piece_2

description: SAMPLE 14


title: Placenta_1.1_RL_M0_Piece_2

description: SAMPLE 11


title: Placenta_1.1_SF_M120_Piece_2

description: SAMPLE 8


title: Placenta_1.2_DG_M0_1

description: SAMPLE 43

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting

data_processing:
We performed preprocessing and normalization utilizing the statistical programming language R (http://www.r-project.org/) (version 3.0.1) and the R package minfi (v.1.6.0). Briefly, IDATs files were control normalized and probes with detection p-values > 0.01 in at least one sample were discarded. The samples were then normalized using the SWAN normalization option in the minfi package and M-values were exported.
The non_normalized.txt contains Signal A, Signal B, Signal Intensity, and Detection P-value.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Samples were lysed in ATL Buffer (DNeasy Blood and Tissue DNA Isolation kit, Qiagen), using a Mini-Beadbeater-16 (Biospec), with agitation for one minute in the presence of 1 mm zirconia beads. Samples were then centrifuged at maximum speed for one minute and the lysed solution was transferred to a new tube.  The remainder of the extraction was followed per the DNeasy handbook using the animal tissue (spin column) protocol, without the optional RNase treatment.  DNA was quantified using the Quant- iT kit (Life Technologies).

value: DNAgard


title: Placenta_1.1_SF_M120_Piece_3

description: SAMPLE 9


title: Placenta_1.2_DG_M120_1

description: SAMPLE 46


title: Placenta_1.1_SF_M60_Piece_3

description: SAMPLE 6


title: Placenta_1.2_DG_M0_2

description: SAMPLE 44


title: Placenta_1.2_DG_M0_3

description: SAMPLE 45


title: Placenta_1.1_RL_M0_Piece_1

description: SAMPLE 10


title: Placenta_1.1_SF_M60_Piece_2

description: SAMPLE 5


title: Kidney_RapKD_rep5

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: 15 µg labelled cRNA were hybridized onto Mouse 4302 arrays (Affymetrix, CA, USA) for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor using Single-Channel Array Normalization (SCAN), (Picolo et al., Genomics 2012).

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: Raptor fl/fl*KspCre and Raptor fl/fl animals were sacrificed at P14 before the development of an overt functional phenotype

extract_protocol: RNeasy Mini Plus Kit (Qiagen, Hilden, Germany)

treatment_protocol: Kidneys were split in half and immediately snap frozen in liquid nitrogen.

tag: strain background

value: C57BL/6 N

tag: genotype/variation

value: Raptor fl/fl*KspCre

tag: developmental stage

value: Kidney


title: Placenta_3.2_SF_M120_2

description: SAMPLE 35

value: Third trimester

value: 120 minutes


title: Placenta_3.2_SF_M120_1

description: SAMPLE 34


title: Placenta_3.2_DG_M120_2

description: SAMPLE 41


title: Placenta_3.2_DG_M0_1

description: SAMPLE 37


title: Placenta_3.2_DG_M0_2

description: SAMPLE 38


title: Placenta_1.1_SF_M0_Piece_3

description: SAMPLE 3


title: Placenta_1.1_SF_M60_Piece_1

description: SAMPLE 4

value: 60 minutes


title: Placenta_1.2_DG_M120_3

description: SAMPLE 48


title: Kidney_RapKD_rep4


title: Kidney_RapKD_rep3


title: Kidney_RapKD_rep2


title: Kidney_WT_rep5

value: Raptor fl/fl


title: Placenta_1.1_SF_M120_Piece_1

description: SAMPLE 7


title: Placenta_1.2_DG_M120_2

description: SAMPLE 47


title: Kidney_RapKD_rep1


title: Placenta_3.2_DG_M120_3

description: SAMPLE 42


title: Placenta_3.2_DG_M120_1

description: SAMPLE 40


title: Placenta_3.2_SF_M120_3

description: SAMPLE 36


title: Placenta_3.2_DG_M0_3

description: SAMPLE 39


title: Placenta_3.2_SF_M0_1

description: SAMPLE 31


title: Placenta_3.2_SF_M0_3

description: SAMPLE 33


title: Placenta_1.1_SF_M0_Piece_2

description: SAMPLE 2


title: Kidney_WT_rep4


title: Kidney_WT_rep1


title: Placenta_1.1_DG_M120_3

description: SAMPLE 30


title: Placenta_3.2_SF_M0_2

description: SAMPLE 32


title: Placenta_1.1_DG_M120_2

description: SAMPLE 29


title: Placenta_1.1_SF_M0_Piece_1

description: SAMPLE 1


title: Kidney_WT_rep2


title: Kidney_WT_rep3


title: Surviving cells after Kras re-expression for 24hs #4

city: Houston

first: Sahil

last: Seth

state: TX

address: 1801 East Road

institute: MD Anderson

description: Surviving cells after 24hs of Kras re-expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip Mouse 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: Raw data were pre-processed using a robust multi-array analysis

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

extract_protocol: Trizol extraction of total RNA followed by RNeasy column cleanup was performed according to the manufacturer's instructions.

treatment_protocol: Doxycycline (Kras expression)

tag: tumor

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+

tag: kras expression

value: Yes

value: Surviving cells


title: Surviving cells #4

description: Surviving cells derived from tumor spheres after 8 days of Kras ablation

source_name: Surviving cells after 8 days of Kras ablation

value: No

tag: cell type


title: Placenta_1.1_DG_M120_1

description: SAMPLE 28

value: First trimester


title: Bulk Tumor #5

description: Pancreatic tumor generated in p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+ mouse

source_name: Pancreatic Tumor tissue

value: Pancreatic Tumor cells


title: Surviving cells after Kras re-expression for 24hs #2


title: Surviving cells after Kras re-expression for 24hs #5


title: Kras expressing spheres #5

description: Tumor spheres derived from the same tumor

source_name: Tumor spheres at 8 days of culture

value: Tumor spheres


title: Kras expressing spheres #4


title: Bulk Tumor #2


title: Placenta_1.1_DG_M0_3

description: SAMPLE 27

value: 0 minutes


title: Surviving cells #3


title: Kras expressing spheres #2


title: Surviving cells #2


title: Bulk Tumor #4


title: Bulk Tumor #3


title: Kras expressing spheres #3


title: Placenta_1.1_DG_M0_2

description: SAMPLE 26


title: Surviving cells after Kras re-expression for 24hs #1


title: Surviving cells #5


title: Placenta_3.1_DG_M120_3

description: SAMPLE 24


title: Placenta_1.1_DG_M0_1

description: SAMPLE 25


title: Kras expressing spheres #1


title: Surviving cells after Kras re-expression for 24hs #3


title: Placenta_3.1_DG_M120_2

description: SAMPLE 23


title: Tgfbeta inhibitor_rep3

city: Portland

first: Jared

middle: Michael

last: Fischer

state: OR

address: 3181 SW Sam Jackson Park Road

department: Molecular and Medical Genetics

institute: Oregon Health and Science University

hyb_protocol: Each sample was hybirdized to Affymetrix Mouse Genome 430 2.0 GeneChip array

scan_protocol: Image processing with Affymetrix GeneChip Command Console v 3.1.1 Expression analysis with Affymetrix Expression Console v 1.1

data_processing: Data were analyzed with Microarray Suite version 5.0.  The absolute analyses were rerun using global scaling to an average target intensity of 350.  The parameters alpha1 = 0.05 and alpha2 = 0.065.

source_name: Intestinal organoid

label_protocol: RNA samples were amplified and labeled with MessageAmp Premier (Ambion) for the 3' IVT assay

growth_protocol: Organoids were grown for 6 days

extract_protocol: RNA was extracted with miRNeasy Mini Kit from Qiagen

treatment_protocol: Organoids were continuously treated with either nothing, TgfbR1/2 inhibitor or Tgfb1 ligand starting at day 1 in triplicate

value: small intestine

tag: treatment

value: Tgfbeta inhibitor (20uM)


title: Tgfbeta1 ligand_rep1

value: Tgfbeta 1 ligand (0.04ng/mL


title: Surviving cells #1


title: Tgfbeta1 ligand_rep3


title: Placenta_3.1_DG_M120_1

description: SAMPLE 22

value: DNAgard


title: Bulk Tumor #1


title: Tgfbeta inhibitor_rep1


title: no treatment_rep1

value: no treatment


title: Tgfbeta inhibitor_rep2


title: Placenta_3.1_DG_M0_3

description: SAMPLE 21

value: Third trimester


title: no treatment_rep3


title: Placenta_3.1_DG_M0_2

description: SAMPLE 20


title: Placenta_3.1_DG_M0_1

description: SAMPLE 19


title: Placenta_1.1_RL_M120_1

description: SAMPLE 16

value: RNAlater

value: 120 minutes


title: Placenta_1.1_RL_M120_3

description: SAMPLE 18


title: no treatment_rep2


title: Placenta_1.1_RL_M120_2

description: SAMPLE 17


title: Placenta_1.1_RL_M0_3

description: SAMPLE 15


title: Klotho-treated MO3.13 human oligodendroglioma cell line  Replicate 3

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description: Gene expression data obtained from MO3.13 human oligodendroglioma cell line

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix Human Exon 1.0 ST Array  for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: MO3.13 cells were grown in DMEM containing 10 % fetal bovine serum (FBS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM of L-glutamine andSodium pyruvate. Cells were treated with 0.4 ug/mL of recombinant mouse Klotho in serum free DMEM for 3.5 hours and total RNA was collected for microarray

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

tag: cell line

value: oligodendroglioma cell line

value: Klotho-treated


title: MO3.13 human oligodendroglioma cell line Replicate 2

growth_protocol: MO3.13 cells were grown in DMEM containing 10 % fetal bovine serum (FBS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM of L-glutamine andSodium pyruvate. Total RNA was collected for microarray

value: control


title: MO3.13 human oligodendroglioma cell line Replicate 3


title: Klotho-treated MO3.13 human oligodendroglioma cell line  Replicate 1


title: Papilloma_tumour_epithelial_cells_CTRL_rep3

status: Public on Jun 08 2014

city: Bruxelles

first: Cédric

last: BLANPAIN

address: 808, route de Lennik

country: Belgium

institute: ULB

description: Gene expression data from alpha6+ TECs from skin papillomas

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix Mouse430 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: The data were analyzed with R (version 2.14.0) Bioconductor fRMA (version 1.6) package with default analysis settings.

source_name: Chemically-induced skin papillomas in control mice treated with tamoxifen for 1 week

label_protocol: Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: Mouse colonies were maintained in a certified animal facility in accordance with the European guidelines.

extract_protocol: RNA extraction was performed using the RNeasy micro kit (Qiagen) according to the manufacturer’s recommendations and DNAase treatment.

treatment_protocol: Tumours were digested in collagenase I (Sigma) for 2 h at 37°C on a rocking plate. Collagenase I activity was blocked by addition of EDTA (5mM) and then rinsed in PBS supplemented with 2% FCS. After tumour digestion, cells were blocked for 15 min at room temperature in PBS supplemented with 30% FCS. Immunostaining was performed  by incubation for 30 min on ice. Living tumour cells were selected by forward scatter, side scatter, doublet discrimination and by Hoechst dye exclusion. Tumour epithelial cells (TECs) were selected based on the expression of Epcam (Epcam+) and exclusion of CD45, CD31, CD140a (Lin-). Sorted cells were collected into lysis buffer for RNA extraction.

tag: tumour stage

value: Benign tumour


title: Klotho-treated MO3.13 human oligodendroglioma cell line  Replicate 2


title: Placenta_3.1_RL_M120_1

description: SAMPLE 10

tag: pregnancy stage


title: Placenta_1.1_RL_M0_1

description: SAMPLE 13

tag: tissue collection method


title: Papilloma_tumour_epithelial_cells_Sox2cKO_rep2

source_name: Chemically-induced skin papillomas in K14CREER:SOX2fl/fl mice treated with tamoxifen for 1 week


title: Carcinoma_tumour_epithelial_cells_Sox2_GFP-_rep2

description: Gene expression data from Sox2-GFP- TECs from primary SCC

source_name: Chemically-induced SCC

value: Malignant tumour


title: Papilloma_tumour_epithelial_cells_CTRL_rep1

value: control mice treated with tamoxifen for 1 week


title: Tgfbeta1 ligand_rep2


title: Carcinoma_tumour_epithelial_cells_Sox2_GFP+_rep2

description: Gene expression data from Sox2-GFP+ TECs from primary SCC


title: Papilloma_tumour_epithelial_cells_Sox2cKO_rep3

value: K14CREER:SOX2fl/fl mice treated with tamoxifen for 1 week


title: Papilloma_tumour_epithelial_cells_CTRL_rep2


title: Papilloma_tumour_epithelial_cells_Sox2cKO_rep1


title: Placenta_3.1_RL_M120_3

description: SAMPLE 12

tag: time after removal from the uterus


title: Carcinoma_tumour_epithelial_cells_Sox2_GFP+_rep1


title: Placenta_3.1_RL_M120_2

description: SAMPLE 11


title: Placenta_3.1_RL_M0_2

description: SAMPLE 8


title: hepG2

city: Oakland

last: Jung

address: PO Box 22688

institute: University of California Davis

description: cancer cells

data_processing: The data were normalised to the mean

source_name: liver

extract_protocol: Total RNA extracted using Qiagen RNeasy kit.


title: MO3.13 human oligodendroglioma cell line Replicate 1


title: Placenta_3.1_RL_M0_1

description: SAMPLE 7


title: primary hepatocytes 1

description: differentiated cells

value: primary hepatocyte


title: Placenta_3.1_SF_M120_3

description: SAMPLE 6

value: Snap Frozen


title: induced pluripotent stem cells

description: stem cells

source_name: fibroblast

value: fibroblast

value: human induced pluripotent stem cells


title: primary hepatocytes 2

description: differentiated cells


title: embryonic stem cells H9

description: stem cells

source_name: blastocyst


title: HepG2 cells_SW 3.5μg/μl_24h_rep1

city: Beijing

first: tiantian

last: she

address: 52 Fucheng Road

department: Biochemistry and Molecular Biology

country: China

institute: Peking University Cancer Hospital & Institute

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data was RMA normalised using  Expression Console software; transcript analysis

source_name: HepG2_SW 3.5μg/μl for 24h

label_protocol: Total RNA were amplified, labeled and purified by using Ambion  WT Expression Kit(Cat#411973， Ambion, US) and GeneChip  WT Terminal Labeling Kit (Cat#900671, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Cells were treated by solvent or SW for 24h before the RNA extraction

tag: cell line source

value: male liver tissue

value: hepatocellular carcinoma

tag: treated with

value: Smilax Glabra rhizome extract (SW) for 24hrs


title: embryonic stem cells H1

description: stem cells


title: Placenta_3.1_SF_M120_1

description: SAMPLE 4

value: Third trimester


title: CLS14_T1_PN_day0_055

status: Public on Jun 07 2014

first: William

middle: R

last: Swindell

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Human Genome Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: Robust Multichip Average (RMA)

source_name: non-lesional skin biopsy obtained from patient at baseline

extract_protocol: RNA was extracted using QIAGEN RNEasy mini kits

treatment_protocol: At baseline, two biopsies were taken from each patient; one 6mm punch biopsy was obtained from lesional skin of each patient (involved sample) and the other from non-lesional skin (uninvolved sample). Non-lesional biopsies were taken from the buttocks or upper thighs. For each patient, lesional biopsies were then taken on days 1, 3, 7 and 14 following etanercept treatment. Biopsies were snap-frozen in liquid nitrogen, stored at -80°C. At processing the biopsy samples were homogenized while still frozen and total RNA isolation was performed using RNeasy kit protocol (Qiagen, Chatsworth, Ca, USA).

tag: patient

tag: diagnosis

value: chronic plaque psoriasis

tag: tissue type

value: skin

tag: phenotype

value: non-lesional


title: CLS14_T6_PP_day14_060

source_name: lesional skin bioposy obtained from patient after 14 days of treatment

value: lesional


title: HepG2 cells_solvent_24h_rep1

source_name: HepG2_solvent for 24h

value: solvent (control) for 24hrs


title: KPW13_T6_PP_day14_054


title: CLS14_T2_PP_day0_056

source_name: lesional skin bioposy obtained from patient at baseline


title: CLS14_T3_PP_day1_057

source_name: lesional skin bioposy obtained from patient after 1 day of treatment


title: Placenta_3.1_RL_M0_3

description: SAMPLE 9

value: RNAlater

value: 0 minutes


title: CLS14_T4_PP_day3_058

source_name: lesional skin bioposy obtained from patient after 3 days of treatment


title: Placenta_1.1_RL_M0_2

description: SAMPLE 14

value: First trimester


title: KPW13_T5_PP_day7_053

source_name: lesional skin bioposy obtained from patient after 7 days of treatment


title: Placenta_3.1_SF_M120_2

description: SAMPLE 5

value: 120 minutes


title: KPW13_T3_PP_day1_051


title: hep3B

description: cancer cells


title: Placenta_3.1_SF_M0_2

description: SAMPLE 2


title: Placenta_3.1_SF_M0_1

description: SAMPLE 1


title: Placenta_3.1_SF_M0_3

description: SAMPLE 3


title: KPW13_T2_PP_day0_050


title: KPW13_T1_PN_day0_049


title: EUR12_T1_PN_day0_043


title: CEM11_T3_PP_day1_039


title: CAB10_T6_PP_day14_036


title: EUR12_T6_PP_day14_048


title: EUR12_T5_PP_day7_047


title: EUR12_T2_PP_day0_044


title: CEM11_T6_PP_day14_042


title: CEM11_T5_PP_day7_041


title: EUR12_T4_PP_day3_046


title: CLS14_T5_PP_day7_059


title: Carcinoma_tumour_epithelial_cells_Sox2_GFP-_rep1

value: Malignant tumour


title: CEM11_T2_PP_day0_038


title: CAB10_T1_PN_day0_031


title: CAB10_T2_PP_day0_032


title: CAB10_T3_PP_day1_033


title: CEM11_T4_PP_day3_040


title: CAB10_T5_PP_day7_035


title: TLW18_T3_PP_day1_015


title: TLW18_T4_PP_day3_016


title: T10-167

city: Fort Detrick

first: Meskerem

last: Jibitu

address: 568 Doughten Drive

department: Integrative Systems Biology

institute: US Army Center for Environmental Health Research

description:
Transcriptional profiling of liver tissue from 10d SS+ 4wk rest: C57BL6/J
Biological replicate 6 of 6.  Liver tissue, 10 day Stressed, harvested after 4 week rest period.

hyb_protocol: cRNA was hybridized to a whole mouse genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: pooled whole mouse tissue cell lines

label_protocol: Total RNA (200 ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Social Stressed (SS) mice were housed 6h box-in-box for 1-12 days sans food/liquid inside an aggressor home cage and 3x exposed at random timepoints. C mice had same schedule without aggressor proximity

tag: vender name and catalog number

value: Stratagene’s Universal Mouse Reference RNA,Catalog #740100

tag: strain

value: liver


title: C10-148

description:
Transcriptional profiling of liver tissue from 10d C+ 4wk rest: C57BL6/J
Biological replicate 5 of 6. Control Liver tissue, 10 days untreated, harvested after 4 week rest period.


title: TLW18_T1_PN_day0_014


title: C10-149

description:
Transcriptional profiling of liver tissue from 10d C+ 4wk rest: C57BL6/J
Biological replicate 6 of 6. Control Liver tissue, 10 days untreated, harvested after 4 week rest period.


title: C10-145

description:
Transcriptional profiling of liver tissue from 10d C+ 4wk rest: C57BL6/J
Biological replicate 2 of 6. Control Liver tissue, 10 days untreated, harvested after 4 week rest period.


title: C10-146

description:
Transcriptional profiling of liver tissue from 10d C+ 4wk rest: C57BL6/J
Biological replicate 3 of 6. Control Liver tissue, 10 days untreated, harvested after 4 week rest period.


title: HC10-125

description:
Transcriptional profiling of liver tissue from 5d C+ 1.5wk rest: C57BL6/J
Biological replicate 4 of 4. Control Liver tissue, 5 days untreated, harvested after 1.5 week rest period.


title: T10-166

description:
Transcriptional profiling of liver tissue from 10d SS+ 4wk rest: C57BL6/J
Biological replicate 5 of 6.  Liver tissue, 10 day Stressed, harvested after 4 week rest period.


title: CAB10_T4_PP_day3_034


title: TLW18_T2_PP_day0_013


title: T10-165

description:
Transcriptional profiling of liver tissue from 10d SS+ 4wk rest: C57BL6/J
Biological replicate 4 of 6.  Liver tissue, 10 day Stressed, harvested after 4 week rest period.


title: CEM11_T1_PN_day0_037


title: EUR12_T3_PP_day1_045


title: C10-147

description:
Transcriptional profiling of liver tissue from 10d C+ 4wk rest: C57BL6/J
Biological replicate 4 of 6. Control Liver tissue, 10 days untreated, harvested after 4 week rest period.


title: TLW18_T5_PP_day7_017


title: T10-164

description:
Transcriptional profiling of liver tissue from 10d SS+ 4wk rest: C57BL6/J
Biological replicate 3 of 6.  Liver tissue, 10 day Stressed, harvested after 4 week rest period.


title: C10-144

description:
Transcriptional profiling of liver tissue from 10d C+ 4wk rest: C57BL6/J
Biological replicate 1 of 6. Control Liver tissue, 10 days untreated, harvested after 4 week rest period.


title: C5-132

description:
Transcriptional profiling of liver tissue from 5d C+ 1.5wk rest: C57BL6/J
Biological replicate 1 of 4. Control Liver tissue, 5 days untreated, harvested after 1.5 week rest period.


title: T10-116

description:
Transcriptional profiling of liver tissue from 5d SS+ 1.5wk rest: C57BL6/J
Biological replicate 5 of 5.  Liver tissue, 5 day Stressed, harvested after 1.5 week rest period.


title: T10-115

description:
Transcriptional profiling of liver tissue from 5d SS+ 1.5wk rest: C57BL6/J
Biological replicate 4 of 5.  Liver tissue, 5 day Stressed, harvested after 1.5 week rest period.


title: T10-113

description:
Transcriptional profiling of liver tissue from 5d SS+ 1.5wk rest: C57BL6/J
Biological replicate 2 of 5.  Liver tissue, 5 day Stressed, harvested after 1.5 week rest period.


title: C5-134

description:
Transcriptional profiling of liver tissue from 5d C+ 1.5wk rest: C57BL6/J
Biological replicate 3 of 4. Control Liver tissue, 5 days untreated, harvested after 1.5 week rest period.


title: C5-133

description:
Transcriptional profiling of liver tissue from 5d C+ 1.5wk rest: C57BL6/J
Biological replicate 2 of 4. Control Liver tissue, 5 days untreated, harvested after 1.5 week rest period.


title: T10-719

description:
Transcriptional profiling of liver tissue from 10d SS+ 1d rest: C57BL6/J
Biological replicate 5 of 5.  Liver tissue, 10 day Stressed, harvested after 1 day rest period.


title: T10-715

description:
Transcriptional profiling of liver tissue from 10d SS+ 1d rest: C57BL6/J
Biological replicate 1 of 5.  Liver tissue, 10 day Stressed, harvested after 1 day rest period.


title: T10-717

description:
Transcriptional profiling of liver tissue from 10d SS+ 1d rest: C57BL6/J
Biological replicate 3 of 5.  Liver tissue, 10 day Stressed, harvested after 1 day rest period.


title: T10-112

description:
Transcriptional profiling of liver tissue from 5d SS+ 1.5wk rest: C57BL6/J
Biological replicate 1 of 5.  Liver tissue, 5 day Stressed, harvested after 1.5 week rest period.


title: T5-750

description:
Transcriptional profiling of liver tissue from 1d SS+ 1d rest: C57BL6/J
Biological replicate 3 of 5.  Liver tissue, 5 day Stressed, harvested after 1 day rest period.


title: ∆spxA2_rep3

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

institute: Yangzhou University

description: Gene expression of ∆spxA2 strain

hyb_protocol: After fragmentation, microarray slides were hybridized with 600ng Cy3-labeled cRNA. Hybridization was performed at 65ºC for 17 h with rotation at 10 rpm.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0.

organism: Streptococcus suis

source_name: ∆spxA2, replicate 3

label_protocol: Total RNA was  were amplified and labeled with Cy3-CTP. Labeled cRNA was purified using the RNeasy mini kit (Qiagen).

growth_protocol: S. suis strains were grown in TSB with 10% (vol/vol) newborn bovine serum at 37ºC under static conditions.

extract_protocol: Total RNA was isolated using an SV total RNA isolation system (Promega), according to the manufacturer’s recommended protocol.

value: spxA2 deletion strain

tag: phase

value: mid-exponential phase


title: T10-718

description:
Transcriptional profiling of liver tissue from 10d SS+ 1d rest: C57BL6/J
Biological replicate 4 of 5.  Liver tissue, 10 day Stressed, harvested after 1 day rest period.


title: T5-751

description:
Transcriptional profiling of liver tissue from 1d SS+ 1d rest: C57BL6/J
Biological replicate 4 of 5.  Liver tissue, 5 day Stressed, harvested after 1 day rest period.


title: T5-749

description:
Transcriptional profiling of liver tissue from 1d SS+ 1d rest: C57BL6/J
Biological replicate 2 of 5.  Liver tissue, 5 day Stressed, harvested after 1 day rest period.


title: C5-744

description:
Transcriptional profiling of liver tissue from 5d C+ 1d rest: C57BL6/J
Biological replicate 1 of 4. Control Liver tissue, 5 day untreated, harvested after 1 day rest period.


title: T10-716

description:
Transcriptional profiling of liver tissue from 10d SS+ 1d rest: C57BL6/J
Biological replicate 2 of 5.  Liver tissue, 10 day Stressed, harvested after 1 day rest period.


title: ∆spxA2_rep2

description: Gene expression of ∆spxA2 strain

source_name: ∆spxA2, replicate 2


title: C5-747

description:
Transcriptional profiling of liver tissue from 5d C+ 1d rest: C57BL6/J
Biological replicate 4 of 4. Control Liver tissue, 5 day untreated, harvested after 1 day rest period.


title: C10-713

description:
Transcriptional profiling of liver tissue from 10d C+ 1d rest: C57BL6/J
Biological replicate 3 of 4. Control Liver tissue, 10 day untreated, harvested after 1 day rest period.


title: C5-746

description:
Transcriptional profiling of liver tissue from 5d C+ 1d rest: C57BL6/J
Biological replicate 3 of 4. Control Liver tissue, 5 day untreated, harvested after 1 day rest period.


title: ∆spxA2_rep1

description: Gene expression of ∆spxA2 strain

source_name: ∆spxA2, replicate 1


title: C10-714

description:
Transcriptional profiling of liver tissue from 10d C+ 1d rest: C57BL6/J
Biological replicate 4 of 4. Control Liver tissue, 10 day untreated, harvested after 1 day rest period.


title: ∆spxA1_rep2

description: Gene expression of ∆spxA1 strain

source_name: ∆spxA1, replicate 2

value: spxA1 deletion strain


title: C10-711

description:
Transcriptional profiling of liver tissue from 10d C+ 1d rest: C57BL6/J
Biological replicate 1 of 4. Control Liver tissue, 10 day untreated, harvested after 1 day rest period.


title: C5-745

description:
Transcriptional profiling of liver tissue from 5d C+ 1d rest: C57BL6/J
Biological replicate 2 of 4. Control Liver tissue, 5 day untreated, harvested after 1 day rest period.


title: T5-748

description:
Transcriptional profiling of liver tissue from 1d SS+ 1d rest: C57BL6/J
Biological replicate 1 of 5.  Liver tissue, 5 day Stressed, harvested after 1 day rest period.


title: ∆spxA1_rep1

description: Gene expression of ∆spxA1 strain

source_name: ∆spxA1, replicate 1


title: ∆spxA1_rep3

description: Gene expression of ∆spxA1 strain

source_name: ∆spxA1, replicate 3


title: WT_rep2

description: Gene expression of WT strain

source_name: WT strain, replicate 2

value: WT strain SC19


title: YY1sc281 in NT2 cells

city: Umeå

first: Yuri

middle: B

last: Schwartz

address: Byggnad 6L, NUS

country: Sweden

institute: Umeå University

description: YY1 (sc281) ChIP in  NTERA-2 cl.D1 cells, Biological Rep 1-2

hyb_protocol: Hybridization of labeled DNA was done in 200ul of solution containing 12xMES, 5M TMAC (Sigma, Cat# T3411), 3nM control oligo B2 (Affymetrix Cat# 900301), 1mg/ml Human Cot-1 DNA (Invitrogen Cat# 15279-011), 10mg/ml sonicated herring sperm DNA and 1% Triton X100. for 18 hours at 45C with 45rpm rotation. Staining and washing was done using EukGE-WS2v4 protocol

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
The data was median scaled to 100 and the ratio of average ChIP to average Input was computed and smoothed by taking trimmed mean over sliding 675bp window. All operations were performed with TiMAT v2.8.3
The .sgr files were produced with TiMAT v2.8.3 and contain average ChIP/ average Input values smoothed by taking trimmed mean over sliding 675bp window. The coordinates were further converted to Hg19 (2009) genomic release using liftOver script

source_name: Anti YY1 (sc281) ChIP from  NTERA-2 cl.D1 chromatin

label_protocol: 8ug of amplified ChIP product was fragmented with DNAse I and labeled with TdT by biotin-11-ddATP incorporation

growth_protocol: NTERA-2 cl.D1 embryonic carcinoma cells (ATCC #CRL-1973, lot#4742175) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, ATCC #30-2002) supplemented with 10% of FBS (ATCC #30-2020) at 37C in 5% CO2 atmosphere.

extract_protocol: Live cells were crosslinked with 1.8% formaldehyde for 10 min at 37C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP and sample amplification was done as described in Schwartz et al., 2006.

tag: chip antibody

value: NTERA-2 cl.D1

source_name: DNA isolated from matching input NTERA-2 cl.D1 chromatin


title: YY1sc7341 in NT2 cells

description: YY1 (sc7341) ChIP in  NTERA-2 cl.D1 cells, Biological Rep 1-2

source_name: Anti YY1 (sc7341) ChIP from  NTERA-2 cl.D1 chromatin


title: WT_rep1

description: Gene expression of WT strain

source_name: WT strain, replicate 1


title: MEL18 in NT2 cells

description: MEL18 ChIP in  NTERA-2 cl.D1 cells, Biological Rep 1-2

source_name: Anti MEL18 ChIP from  NTERA-2 cl.D1 chromatin


title: BMI1 in NT2 cells

description: BMI1 ChIP in  NTERA-2 cl.D1 cells, Biological Rep 1-2

source_name: Anti BMI1 ChIP from  NTERA-2 cl.D1 chromatin


title: H3K27me3 in NT2 cells

description: H3K27me3 ChIP in  NTERA-2 cl.D1 cells, Biological Rep 1-2

source_name: Anti H3K27me3 ChIP from  NTERA-2 cl.D1 chromatin


title: T10-163

description:
Transcriptional profiling of liver tissue from 10d SS+ 4wk rest: C57BL6/J
Biological replicate 2 of 6.  Liver tissue, 10 day Stressed, harvested after 4 week rest period.


title: EZH2 in NT2 cells

description: EZH2 ChIP in  NTERA-2 cl.D1 cells, Biological Rep 1-2

source_name: Anti EZH2 ChIP from  NTERA-2 cl.D1 chromatin


title: SFMBT in Sg4 cells

description: SFMBT ChIP in Sg4 cells, Biological Rep 1-2

hyb_protocol: Hybridization of labeled DNA was done in 200ul of solution containing 1xMES, 3M TMAC, 40pM oligo B2, 100u/ml sonicated salmon sperm DNA, 0.02% Triton X100 for 18 hours at 45C with 45rpm rotation. Staining and washing was done using EukGE-WS2v4 protocol

data_processing:
The data was median scaled to 100 and the ratio of average ChIP to average Input was computed and smoothed by taking trimmed mean over sliding 675bp window. All operations were performed with TiMAT v2.8.3
The .sgr files were produced with TiMAT v2.8.3 and contain average ChIP/ average Input values smoothed by taking trimmed mean over sliding 675bp window. The coordinates were further converted to Dm3 (2006) genomic release using liftOver script

organism: Drosophila melanogaster

source_name: Anti SFMBT ChIP from Sg4 chromatin

label_protocol: 2ug of amplified ChIP product was fragmented with DNAse I and labeled with TdT by biotin-11-ddATP incorporation

growth_protocol: Sg4 cells were grown to a density of 5x10^6 cells/ml in Schneider's medium (Gibco) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate and 292 ug/ml of L-glutamine

extract_protocol: Live cells were crosslinked with 1.8% formaldehyde for 10 min at 25C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP and sample amplification was done as described in Schwartz et al., 2006.

value: SFMBT

source_name: DNA isolated from matching input Sg4 chromatin


title: PHO in ML-DmBG3-c2  cells

description: PHO ChIP in ML-DmBG3-c2  cells, Biological Rep 1-2

source_name: Anti PHO ChIP from ML-DmBG3-c2  chromatin

value: PHO

source_name: DNA isolated from matching input ML-DmBG3-c2  chromatin


title: C10-712

description:
Transcriptional profiling of liver tissue from 10d C+ 1d rest: C57BL6/J
Biological replicate 2 of 4. Control Liver tissue, 10 day untreated, harvested after 1 day rest period.

source_name: pooled whole mouse tissue cell lines


title: PHOL in Sg4 cells

description: PHOL ChIP in Sg4 cells, Biological Rep 1-2

source_name: Anti PHOL ChIP from Sg4 chromatin

value: PHOL


title: Oil-Mice_T12-1

city: Nagoya

first: Yoshihisa

last: Uenoyama

address: Furo-cho, Chikusa-ku

institute: Nagoya University

description: mice treated with oil after 12 hour, biological rep1

hyb_protocol: Following fragmentation, 500 ng of biotinylated cRNAs were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 array.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 (Affimetrix).

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.

source_name: hypothalamus, 12 h after oil treatment

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

growth_protocol: C57BL/6J (B6) mice were housed under a 14:10 h light/dark cycle (lights on 05.00 h) at 23 C ± 2 C and were fed with standard rodent chow (OA-2 for CLEA, Tokyo, Japan) and water ad lib.

extract_protocol: Total RNA was extracted from the whole hypothalamus with RNeasy mini kit according to the manufacturer’s instructions (QIAGEN, Hilden, Germany).

treatment_protocol: Neonatal B6 female mice (approximately 1.4 g BW, n=3 in each group) were subcutaneouly injected with either estradiol benzoate (EB, 7.5 μg/20 μl dissolved in peanut oil) or vehicle (oil) on the D0, and the whole hypothalamus was collected at either 1, 3, 6, 12 or 24 h after the EB injection

tag: gender

value: female

value: hypothalamus


title: EB-Mice_T24-1

description: mice treated with EB after 24 hour, biological rep1

source_name: hypothalamus, 24 h after estradiol benzoate treatment


title: EB-Mice_T12-2

description: mice treated with EB after 12 hour, biological rep2

source_name: hypothalamus, 12 h after estradiol benzoate treatment


title: EB-Mice_T12-3

description: mice treated with EB after 12 hour, biological rep3


title: EB-Mice_T24-3

description: mice treated with EB after 24 hour, biological rep3


title: EB-Mice_T24-2

description: mice treated with EB after 24 hour, biological rep2


title: PHO in Sg4 cells

description: PHO ChIP in Sg4 cells, Biological Rep 1-2

source_name: Anti PHO ChIP from Sg4 chromatin


title: EB-Mice_T6-1

description: mice treated with EB after 6 hour, biological rep1

source_name: hypothalamus, 6 h after estradiol benzoate treatment


title: Oil-Mice_T24-2

description: mice treated with oil after 24 hour, biological rep2

source_name: hypothalamus, 24 h after oil treatment


title: Oil-Mice_T24-1

description: mice treated with oil after 24 hour, biological rep1


title: T10-114

description:
Transcriptional profiling of liver tissue from 5d SS+ 1.5wk rest: C57BL6/J
Biological replicate 3 of 5.  Liver tissue, 5 day Stressed, harvested after 1.5 week rest period.


title: Oil-Mice_T12-3

description: mice treated with oil after 12 hour, biological rep3


title: Oil-Mice_T12-2

description: mice treated with oil after 12 hour, biological rep2


title: EB-Mice_T6-2

description: mice treated with EB after 6 hour, biological rep2


title: Oil-Mice_T24-3

description: mice treated with oil after 24 hour, biological rep3


title: EB-Mice_T12-1

description: mice treated with EB after 12 hour, biological rep1


title: Oil-Mice_T6-2

description: mice treated with oil after 6 hour, biological rep2

source_name: hypothalamus, 6 h after oil treatment


title: EB-Mice_T3-3

description: mice treated with EB after 3 hour, biological rep3

source_name: hypothalamus, 3 h after estradiol benzoate treatment


title: T10-162

description:
Transcriptional profiling of liver tissue from 10d SS+ 4wk rest: C57BL6/J
Biological replicate 1 of 6.  Liver tissue, 10 day Stressed, harvested after 4 week rest period.


title: EB-Mice_T6-3

description: mice treated with EB after 6 hour, biological rep3


title: Oil-Mice_T6-1

description: mice treated with oil after 6 hour, biological rep1


title: EB-Mice_T3-2

description: mice treated with EB after 3 hour, biological rep2


title: EB-Mice_T3-1

description: mice treated with EB after 3 hour, biological rep1


title: Oil-Mice_T6-3

description: mice treated with oil after 6 hour, biological rep3


title: Cancer tissue from patient 1

city: Changzhou

first: Yilin

last: Yang

state: Jiangsu

address: 185#, Juqian Road

department: Modern Medical Research Center

institute: Third Affiliated Hospital of Soochow University

description: Cancer tissue from patient 1

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cancer tissue from patient 1

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

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: disease state

value: astrocytoma

tag: tissue

value: astrocytoma brain tumor

tag: tumor stage

value: WHO grade II


title: normal adjacent tissue from patient 2

description: normal adjacent tissue from patient 2

source_name: normal adjacent tissue from patient 2

value: normal adjacent brain tissue

value: normal adjacent tissue


title: normal adjacent tissue from patient 1

description: normal adjacent tissue from patient 1

source_name: normal adjacent tissue from patient 1


title: 23mM_ClAc_R3

status: Public on Jun 06 2014

city: Berkeley

first: Yvette

middle: M

last: Piceno

address: 1 Cyclotron Rd., MS 70A-3317

department: Ecology

institute: LBNL

hyb_protocol: Arrays were hybridized overnight at 48degC and 60 rpm and then washed and stained using standard Affymetrix buffers/reagents.

scan_protocol: Images were captured on an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
CEL files were converted to CELa files and then processed using proprietary software (PhyCA).
Data are provided as intensity values scaled to internal standards.

organism: mixed sample

source_name: Reactor

label_protocol: TDT enzyme (P/N PM1875; Promega; Madison, WI) and GeneChip Labeling Reagent (P/N 90042; Affymetrix; Santa Clara, CA) were used to label fragmented amplicons.

growth_protocol: see publication

extract_protocol: DNA was extracted using a DNA-EZ RW03 Kit (GeneRite; North Brunswick, NJ)

treatment_protocol: see publication

value: Chloroacetate

value: 23 mM

value: Sterivex filter

tag: replicate


title: normal adjacent tissue from patient 3

description: normal adjacent tissue from patient 3

source_name: normal adjacent tissue from patient 3


title: 11mM_ClAc_R1

value: 11 mM


title: 11mM_ClAc_R3


title: 11mM_ClAc_R2


title: D-threonine_R1

value: D-threonine


title: Glucose_R3

value: Glucose


title: Glucose_R2


title: Cancer tissue from patient 3

description: Cancer tissue from patient 3

source_name: Cancer tissue from patient 3

value: WHO grade IV


title: 23mM_ClAc_R1


title: No-Carbon_R2

value: No-carbon


title: 23mM_ClAc_R2


title: Oil-Mice_T3-2

description: mice treated with oil after 3 hour, biological rep2

source_name: hypothalamus, 3 h after oil treatment


title: Oil-Mice_T3-3

description: mice treated with oil after 3 hour, biological rep3


title: Glucose_R1


title: D-threonine_R3


title: D-threonine_R2


title: EB-Mice_T1-3

description: mice treated with EB after 1 hour, biological rep3

source_name: hypothalamus, 1 h after estradiol benzoate treatment


title: EB-Mice_T1-1

description: mice treated with EB after 1 hour, biological rep1


title: Oil-Mice_T3-1

description: mice treated with oil after 3 hour, biological rep1


title: Oil-Mice_T1-3

description: mice treated with oil after 1 hour, biological rep3

source_name: hypothalamus, 1 h after oil treatment


title: Oil-Mice_T1-2

description: mice treated with oil after 1 hour, biological rep2


title: No-Carbon_R1


title: EB-Mice_T1-2

description: mice treated with EB after 1 hour, biological rep2


title: T5-752

description:
Transcriptional profiling of liver tissue from 1d SS+ 1d rest: C57BL6/J
Biological replicate 5 of 5.  Liver tissue, 5 day Stressed, harvested after 1 day rest period.

source_name: pooled whole mouse tissue cell lines

value: Stratagene’s Universal Mouse Reference RNA,Catalog #740100

value: liver


title: Cancer tissue from patient 2

description: Cancer tissue from patient 2

source_name: Cancer tissue from patient 2

value: WHO grade III


title: Oil-Mice_T1-1

description: mice treated with oil after 1 hour, biological rep1

value: female

value: hypothalamus


title: No-Carbon_F

source_name: Flask


title: [C2mim]Cl_F

value: 1-ethyl-3-methylimidazolium chloride


title: D-threonine_F1


title: 50mM_ClAc_F3

value: 50 mM


title: D-threonine_F3


title: Glucose_F2


title: 50mM_ClAc_F2


title: Inoc_No-Carbon_R1

source_name: Aeration basin of a wastewater treatment plant, Washed Apr_2012 preserved samples

value: 75 mL stock bag


title: D-threonine_F2


title: 11mM_ClAc_F2


title: Glucose_F3


title: Jul_2011-3

source_name: Aeration basin of a wastewater treatment plant

value: 4.5 mL vial


title: Jul_2011-2


title: Jul_2011-1


title: Glucose_F1


title: Inoc_No-Carbon_F1

value: 4.5 ml vial, pooled 5


title: 50mM_ClAc_F1

value: Chloroacetate


title: 23mM_ClAc_F2

value: 23 mM

value: Sterivex filter


title: Inoc_No-Carbon_F2


title: 23mM_ClAc_F1


title: Inoc_No-Carbon_F3


title: Inoc_No-Carbon_R2


title: 11mM_ClAc_F3

value: 11 mM


title: Inoc_No-Carbon_R3


title: Apr_2012-3


title: Oct_2011-3


title: Oct_2011-2


title: 23mM_ClAc_F3


title: 11mM_ClAc_F1


title: Oct_2011-1


title: Apr_2012-2


title: Apr_2012-1


title: sea cucumber 5 DA_002

city: QINGDAO

first: Muyan

last: Chen

address: 5 YUSHAN ROAD

institute: Ocean University of China

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

organism: Apostichopus japonicus

source_name: Apostihopus japonicus intestine

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA from each tissue sample was extracted using miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.

value: degenerated intestine


title: sea cucumber 4 DA_001


title: sea cucumber 6 DA_003


title: sea cucumber 1 NA_001

value: normal intestine


title: Salmonella infected Reg3g-/- KO C57Bl/6 mice, RNA pooled from 3 mice

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

hyb_protocol: Labelled samples were hybridised on Affymetrix GeneChip Mouse Gene 1.1 ST arrays, provided in plate format. Hybridisation, washing and scanning of the array plates was performed on an Affymetrix GeneTitan Instrument, according to the manufacturer’s recommendations. Detailed protocols can be found in the Affymetrix WT Terminal Labelling and Hybridisation User Manual (part no. 702808 revision 4), and are also available upon request.

scan_protocol: The Mouse Gene 1.1 ST array was scanned on an Affymetrix GeneChip 3000 7G scanner. Detailed methods are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix

data_processing: Packages from the Bioconductor project, integrated in an in-house developed on-line management and analysis database for multiplatform microarray experiments, were used for analysing the scanned Affymetrix arrays (Gentleman et al., 2004; Gavai et al, submitted).

source_name: ileal tissue

label_protocol: The Ambion WT Expression kit (Life Technologies, cat. no. 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labelling kit (Affymetrix, Santa Clara, CA; cat. no. 900671) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction.

growth_protocol: Mice (C57Bl/6 strain and corresponding Reg3g-/- mutant strain) were housed individually from one week before the start of the infection and fed a modified diet, to reflect the calcium levels and the high fat content in the Western human diet

extract_protocol: Total RNA was isolated from ileal tissue using the RNeasy kit (Qiagen, Venlo, the Netherlands) with a DNase digestion step according to the manufacturer's protocol. RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only if samples showed intact bands corresponding to the 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RIN (RNA integrity number) above 8.0.

treatment_protocol:
Mice were orally infected by gavage with 0.2 ml saline containing 10exp8 colony forming units (CFU) of Salmonella enterica serovar enteritidis or Listeria monocytogenes (strain EGD-e).
After 4 days of infection, mice were killed, ileal tissues were isolated and incubated with TriZol reagens until lysis was complete, then RNA extraction and purification were performed

tag: infection agent

value: Salmonella

tag: genotype/variation

value: Reg3g-/- KO


title: uninfected wt C57Bl/6 mice, RNA pooled from 3 mice

treatment_protocol:
Mice were orally infected by gavage with 0.2 ml saline containing 10exp8 colony forming units (CFU) of Salmonella enterica serovar enteritidis or Listeria monocytogenes (strain EGD-e).
After 3 days of infection, mice were killed, ileal tissues were isolated and incubated with TriZol reagens until lysis was complete, then RNA extraction and purification were performed

value: wild type


title: Listeria infected wt C57Bl/6 mice, RNA pooled from 3 mice

treatment_protocol:
Mice were orally infected by gavage with 0.2 ml saline containing 10exp8 colony forming units (CFU) of Salmonella enterica serovar enteritidis or Listeria monocytogenes (strain EGD-e).
After 2 days of infection, mice were killed, ileal tissues were isolated and incubated with TriZol reagens until lysis was complete, then RNA extraction and purification were performed

value: Listeria


title: sea cucumber 2 NA_002


title: sea cucumber 3 NA_003


title: uninfected Reg3g-/- KO C57Bl/6 mice, RNA pooled from 3 mice


title: Listeria infected Reg3g-/- KO C57Bl/6 mice, RNA pooled from 3 mice


title: Salmonella infected wt C57Bl/6 mice, RNA pooled from 3 mice


title: AG_AK534

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

description: Methylation data from anaplastic glioma tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 2.0) package minifi (Version 1.10) using function 'preprocessIllumina'
Unmethylated and methylated signal intensities are available on series level

label: biotin/DNP

source_name: Primary brain tumor tissue

label_protocol: Illumina protocol.

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: 1p/19q status

value: codel

tag: idh status

value: mut

tag: molecular classification

value: CIMP-O

value: brain


title: AG_GR_10


title: AG_AK520


title: AG_GR_24


title: AG_AK542


title: AG_GR_6


title: AG_GR_3


title: AG_AK532


title: AG_AK524


title: AG_AK538


title: AG_AK512


title: AG_AK555


title: AG_AK513


title: AG_AK504


title: AG_AK543


title: AG_AK506


title: AG_57142


title: AG_57152


title: AG_64924


title: AG_GR_1


title: AG_58462


title: AG_63314


title: AG_56604


title: AG_57250


title: AG_AK531


title: AG_GR_2


title: AG_AK519


title: AG_62352


title: AG_55576


title: AG_55292


title: AG_55338


title: AG_43920


title: AG_43908


title: AG_49074


title: AG_53286


title: AG_48460


title: AG_43934


title: AG_43884

value: intact


title: AG_43910


title: AG_43882


title: AG_50060


title: AG_43880


title: AG_43710


title: AG_43814


title: AG_43696


title: AG_43708


title: AG_43816


title: AG_43722


title: AG_44826


title: AG_43760


title: AG_43794


title: AG_43688


title: AG_43648


title: AG_43638


title: AG_AK540


title: AG_43654


title: AG_43750


title: AG_43728


title: AG_43612


title: AG_43578


title: AG_43576


title: AG_43630


title: AG_43490


title: AG_43574


title: AG_43802


title: AG_43542


title: AG_43446


title: AG_43566


title: AG_43482


title: AG_43572


title: AG_43614


title: AG_43442


title: AG_43422


title: AG_42626


title: AG_43438


title: AG_43528


title: AG_AK505

value: wt

value: CIMPneg


title: AG_43406


title: AG_GR_21


title: AG_64774


title: AG_AK547


title: AG_AK558


title: AG_GR_28


title: AG_41486


title: AG_GR_16


title: AG_43460


title: AG_22982


title: AG_61050


title: AG_64082


title: AG_58286


title: AG_43564


title: AG_56590


title: AG_56182


title: AG_58450


title: AG_56688


title: AG_56966


title: AG_60608


title: AG_47762


title: AG_57104


title: AG_54794


title: AG_51136


title: AG_57248


title: AG_43918


title: AG_43878


title: AG_44814


title: AG_51086


title: AG_51592


title: AG_43748_1


title: AG_43892


title: AG_43830


title: AG_43868


title: AG_43900


title: AG_43842


title: AG_53266


title: AG_43712


title: AG_43730


title: AG_43726


title: AG_43736


title: AG_43844


title: AG_43496


title: AG_43448


title: AG_43550


title: AG_43636


title: AG_43462


title: AG_27920


title: AG_43690


title: AG_41496


title: AG_AK552

value: CIMP-A


title: AG_AK539


title: AG_GR_12


title: AG_GR_4


title: AG_43642


title: AG_43494


title: AG_AK561


title: AG_AK514


title: AG_AK526


title: AG_43388


title: AG_AK517


title: AG_AK525


title: AG_AK522


title: AG_43916


title: AG_AK530


title: AG_AK518


title: AG_AK533


title: AG_41252


title: AG_AK502


title: AG_60298


title: AG_AK516


title: AG_64768


title: AG_AK511


title: AG_59252


title: AG_64010


title: AG_28166


title: AG_AK529


title: AG_57706


title: AG_60346


title: AG_52102


title: AG_53022


title: AG_48326


title: AG_AK527


title: AG_48336


title: AG_50568


title: AG_51058


title: AG_AK562


title: AG_48324


title: AG_48302


title: AG_48332


title: AG_43926


title: AG_43914


title: AG_43890


title: AG_45128


title: AG_47302


title: AG_43906


title: AG_43912