title: Ml_V2 [Meth450]

city: Atlanta

first: Greg

last: Gibson

state: Georgia

address: North Ave NW

department: School of Biology

institute: Georgia Institute of Technology

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Human Methylation450 Beadchip using standard Illumina protocol.

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

data_processing: Genome Studio software

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol:
Peripheral blood samples (10ml) were collected into EDTA tubes that were frozen for DNA preservation, and Tempus RNA tubes (Life Technologies, Grand Island NY) for preservation of RNA.
Genomic DNA was extracted using Qiagen Flexigene DNA kit following manufacturer's protocols.

tag: tissue

value: Whole blood

tag: ethnicity

value: Caucasian


title: K56ac Kc egta vs Input rep2

status: Public on Jul 01 2015

type: genomic

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

hyb_protocol: 34 µg labeled sample DNA and 34 µg labeled control DNA were combined, dried in a speed vac with medium heat and resuspended in 12.3 µl water.  For each hybridisation 29.5µl 2X Hybridization Buffer, 11.8µl Hybridization Component A and 1.2µl Alignment Oligo (NimbleGen Hybridization Kit) were combined and 31.7µl added to each hybridisation sample. Samples were incubated at +95°C for 5 minutes, 42°C for 5 minutes and 41 µl loaded onto the array. The hybridisation was performed to NimbleGen D. melanogaster ChIP-chip 2.1M Whole-Genome Tiling Arrays in the Nimbelegen hybridisation station at 42°C (mix mode B) for 18 hours. Post hybridisation washes were performed according to the NimbleGen Wash Buffer Kit instructions.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains. Signal for Cy3 and Cy5 channels are balanced using the histogram view in the GenePix software. Images are saved as Single-image TIFF.

data_processing:
Images are processed with NimbleScan software (Roche-Nimblegen) as per manufacturer instructions. Raw data files (*.pair) are created for each channel. Loess spatial correction was performed using the NimbleScan software, followed by quantile normalise between the arrays. For the K56ac Kc pbs experiment the quantile normalisation was perfromed across the sample and control channels separate and then the log ratio calculated. The *.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package. The bed files were created assuming a normalNull distribution centred around the mode and the resulting p-values were adjusted for multiple testing using the fdr method.
Kcr12_e_k56ac.sm_quant-sep_Ringo_hw300v5.sgr, Kcr12_h_k56ac.sm_quant-sep_Ringo_hw300v5.sgr, Kcr1_e_k56ac_quant-sep_normalNullmode_hw300v5g200FDR1.bed, Kcr1_h_k56ac_quant-sep_normalNullmode_hw300v5g200FDR1.bed, Kc_EGTA-Pbs-quantNorm.wig, Kc_EGTA-Pbs-2kb-peaks-FDR1.bed
The *Ringo_hw300v5.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package (Bioconductor 2.14). The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method. The difference between wildtype and N-activation H3K56ac signal was calculated as the subtraction of quantile normalised ChIP signal files (*quantNorm.wig). The *-2kb-peaks-FDR1.bed files were calculated as follows. All ChIP signal files were averaged over a 2kb window (in 200bp increments), and the noise distribution based on two replicates estimated. This noise distribution is used to call differentially enriched 2kb regions at 1% FDR, with overlapping 2kb regions merged together.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: K56ac Kc egta replicate 2

label_protocol: Amplify 10ng of ChIP and input by GenomePlex® Complete Whole Genome Amplification Kit (WGA2, Sigma) using 14 cycles. In PCR tubes take 1 µg double stranded DNA, add 40 diluted Cy3 or Cy5-Random Nonamers (Nimblegen Dual Colour Kit) and make up to a volume of 80 µl with Nuclease-free Water (Nimblegen Dual Colour Kit). Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quickchill on ice for 10 minutes. Add 10 µl 10mM dNTP Mix (Nimblegen Dual Colour Kit), 8 Nuclease-free Water (Nimblegen Dual Colour Kit) and 2 µl 50U/μl Klenow Fragment (3’->5’ exo-) (Nimblegen Dual Colour Kit), mix gently by pipetting. Incubate at 37°C for 3 hours in thermocycler. Stop the reaction by adding 21.5 µl Stop Solution (Nimblegen Dual Colour Kit). Transfer samples to 1.5 ml tubes and add 110 µl Isopropanol, mix and incubate for 10 minutes at room temperature in the dark. Centrifuge at 13,000rpm for 10 minutes and discard supernatant. Add 500 µl ice-cold 80% ethanol and centrifuge at 13,000rpm for 2 minutes. Discard supernatant and dry pellet for 5 minutes in the dark. Resuspend labeled DNA in 50 µl Nuclease-free Water (Nimblegen) and measure the concentration on the Nanodrop. Combine 34 µg of sample with 34 µg control and dry samples in a speed vac with medium heat.

growth_protocol: Kc cells were cultured at 25 OC in Shields and Sang M3 insect medium (Sigma, S3652), supplemented with 5% FBS (Sigma, F9665), 1 g/L yeast extract (Oxoid, LP0021), 2.5 g/L bacto-peptone (BD Biosciences, 211677) and 1x Antibiotic-Antimycotic (Gibco, 15240-062).

extract_protocol: 5x10^6 cells treated with 4mM EGTA in PBS (egta) or PBS only (pbs) for 30min were fixed with 1% formaldehyde in culture medium for 12 min at 25C followed by quenching with 0.125 M glycine for 2 min. The cells were washed twice with ice-cold PBS and lysed in 500ul of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by 20 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 150mM NaCl, Roche Complete inhibitor) and pre-cleared with 25 µl protein A agarose beads (pre-absorbed with BSA) and 2ug IgG for 2 h at 4C. The chromatin supernatant was then incubated overnight with 2 µg of purified antibody at 4C. After incubation with protein A agarose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed for 5min at 4C with the following buffers: dilution buffer, IP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 50mM NaCl) (two washes), IP wash buffer 2 (1% NP-40 substitute, 1% deoxycholic acid, 1mM EDTA, 10mM Tris pH8.0, 250mM LiCl) (two washes) and TE (10mM Tris pH8.0, 1mM EDTA). The protein-DNA complexes were eluted from the beads in 200 µl of fresh elution buffer (1% SDS, 100 mM NaHCO3) at 65C for 2 h with rotation and de-crosslinked by overnight incubation at 65C with addition of 10 ul 5M NaCl. Following the treatment with 1ul RNase A (10mg/ml) for 2h at 37C and 5ul proteinase K (10mg/ml) for 4h at 45C, genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/10 of the material used for ChIP) by QiaQuick PCR purification (Qiagen).

treatment_protocol: Kc cells treated with 4mM EGTA in PBS for 30min

tag: cell type

tag: chip antibody

value: anti-H3K56ac (Active Motif, 39281)

source_name: Totoal Input K56ac Kc egta replicate 2

value: none, input DNA


title: NA19732 Replicate 1

city: Farmington

first: Charles

last: Lee

state: CT

address: 10 Discovery Dr.

country: USA

institute: Jackson Laboratory for Genomic Medicine

hyb_protocol: Labeled samples were purified using Agilent SureTag Purification columns. Test and reference samples were combined with Agilent Oligo aCGH/ChIP-on-Chip Blocking Agent, Agilent Hi-RPM Hybridization Buffer and Cot-1 DNA and applied to microarrays enclosed in Agilent Hybridization Chamber. After 40 hour incubation at 67 °C, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 and 2.

scan_protocol: Slides were scanned on an Agilent G2505C scanner (version A.8.5.1).

data_processing: Images were processed using Agilent Feature Extraction Software (version 10.5.1.1)

organism: Homo sapiens

label_protocol: 1 to 1.5 ug of genomic DNA was digested using AluI and RsaI for 2 hours at 37 °C followed by a 20 minute enzyme-inactivation step at 65 °C. DNA was then labeled with Cyanine-3-dUTP (Reference samples) or Cyanine-5-dUTP (Test samples) at 37 °C for 2 hours followed by a 10 minute enzyme-inactivation step at 65 °C.

growth_protocol: We did not perform the growth in house. We received DNA samples from Coriell. This is the information available on their website for the cell culture of NA10851: Split ratio 1:2, Temperature: 37C, Percent CO2: 5%, Percent O2: Ambient, Medium: Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent, Serum: 15% fetal bovine serum Not Inactivated

extract_protocol: We did not perform the extraction in house. We received DNA samples from Coriell. This is the information available on their website for DNA extraction: gDNA is purified from fresh blood, immortalized lymphocyctes or fibroblasts using the Qiagen Autopure LS instrument according to the manufacturer’s instructions or manually by modified Miller’s Salting out procedures.

treatment_protocol: We, nor Coriell, did not perform any treatment on the samples. We received DNA samples from Coriell.

tag: coriell cell line


title: K56ac Kc pbs vs Input rep1

source_name: K56ac Kc pbs replicate 1

treatment_protocol: Kc cells treated with  PBS for 30min

source_name: Total Input K56ac Kc pbs replicate 1


title: Patient12_Normal

type: RNA

city: Kaohsiung

first: Chun-Wei

last: Tung

address: No. 100, Shih-Chuan 1st Rd.

country: Taiwan

institute: Kaohsiung Medical University

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm power 100 ) and quantify the fluoresence intensity.

data_processing: The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.

molecule: total RNA

source_name: adjacent normal tissues

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (GE, Piscataway, NJ, USA).

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

tag: disease state

value: normal

tag: gender

value: Male


title: Patient11_Tumor

source_name: esophageal squamous cell carcinoma

value: esophageal squamous cell carcinoma


title: NA19731 Replicate 1


title: Su(H) BG3 hbss vs Input rep3

data_processing:
Images are processed with NimbleScan software (Roche-Nimblegen) as per manufacturer instructions. Raw data files (*.pair) are created for each channel. Loess spatial correction was performed using the NimbleScan software, followed by quantile normalise between the arrays. The *.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package. The bed files were created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.
BG3_Ectrl_loess_quant-all_Ringo_hw300v5.sgr, BG3_Hctrl_loess_quant-all_Ringo_hw300v5.sgr, BG3_Ectrl_loess_quant-all_Ringo_normalNullzero_hw300v5g200FDR1_filtered.bed, BG3_Hctrl_loess_quant-all_Ringo_normalNullzero_hw300v5g200FDR1_filtered.bed
The *Ringo_hw300v5.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package (Bioconductor 2.14). The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method.

source_name: Su(H) BG3 hbss replicate 3

label_protocol: Amplify the entire yield of ChIP and 10ng input by GenomePlex® Complete Whole Genome Amplification Kit (WGA2, Sigma) using two rounds of amplification (14 and 6 cycles). In PCR tubes take 1 µg double stranded DNA, add 40 diluted Cy3 or Cy5-Random Nonamers (Nimblegen Dual Colour Kit) and make up to a volume of 80 µl with Nuclease-free Water (Nimblegen Dual Colour Kit). Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quickchill on ice for 10 minutes. Add 10 µl 10mM dNTP Mix (Nimblegen Dual Colour Kit), 8 Nuclease-free Water (Nimblegen Dual Colour Kit) and 2 µl 50U/μl Klenow Fragment (3’->5’ exo-) (Nimblegen Dual Colour Kit), mix gently by pipetting. Incubate at 37°C for 3 hours in thermocycler. Stop the reaction by adding 21.5 µl Stop Solution (Nimblegen Dual Colour Kit). Transfer samples to 1.5 ml tubes and add 110 µl Isopropanol, mix and incubate for 10 minutes at room temperature in the dark. Centrifuge at 13,000rpm for 10 minutes and discard supernatant. Add 500 µl ice-cold 80% ethanol and centrifuge at 13,000rpm for 2 minutes. Discard supernatant and dry pellet for 5 minutes in the dark. Resuspend labeled DNA in 50 µl Nuclease-free Water (Nimblegen) and measure the concentration on the Nanodrop. Combine 34 µg of sample with 34 µg control and dry samples in a speed vac with medium heat.

growth_protocol: BG3 cells were cultured at 25 OC in Shields and Sang M3 insect medium, supplemented with 10% FBS (Sigma, F4135), 10 mg/L insulin (Sigma, I9278), and also 1x Antibiotic-Antimycotic.

extract_protocol: 1x10^7 cells treated with 4mM EGTA in HBSS (egta) or HBSS only (hbss) for 30min were fixed with 1% formaldehyde in culture medium for 12 min at 25C followed by quenching with 0.125 M glycine for 2 min. The cells were washed twice with ice-cold PBS and lysed in 500ul of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by 20 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 150mM NaCl, Roche Complete inhibitor) and pre-cleared with 25 µl protein G agarose beads (pre-absorbed with BSA) and 2ug IgG for 2h at 4C. Protein G agarose beads (50 µl) were pre-bound with 2 µg of purified antibody for 6h at 4C. The chromatin supernatant with beads/antibody was then incubated overnight at 4C, the immune complexes were collected by centrifugation and washed for 5min at 4C with the following buffers: dilution buffer, IP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 50mM NaCl) (two washes), IP wash buffer 2 (1% NP-40 substitute, 1% deoxycholic acid, 1mM EDTA, 10mM Tris pH8.0, 250mM LiCl) (two washes) and TE (10mM Tris pH8.0, 1mM EDTA). The protein-DNA complexes were eluted from the beads in 200 µl of fresh elution buffer (1% SDS, 100 mM NaHCO3) at 65C for 2 h with rotation and de-crosslinked by overnight incubation at 65C with addition of 10 ul 5M NaCl. Following the treatment with 1ul RNase A (10mg/ml) for 2h at 37C and 5ul proteinase K (10mg/ml) for 4h at 45C, genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/10 of the material used for ChIP) by QiaQuick PCR purification (Qiagen).

treatment_protocol: BG3 cells were treated with HBSS for 30min

value: anti-Su(H) (Santa Cruz, sc-15813)

source_name: Total Input Su(H) BG3 hbss replicate 3


title: NA19729 Replicate 1


title: Su(H) BG3 hbss vs Input rep4

source_name: Su(H) BG3 hbss replicate 4

source_name: Total Input Su(H) BG3 hbss replicate 4


title: K56ac BG3 egta vs Input rep1

data_processing:
Images are processed with NimbleScan software (Roche-Nimblegen) as per manufacturer instructions. Raw data files (*.pair) are created for each channel. Loess spatial correction was performed using the NimbleScan software, followed by quantile normalise between the arrays. The *.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package. The bed files were created assuming a normalNull distribution centred around the mode and the resulting p-values were adjusted for multiple testing using the fdr method.
BG3r12_e56.sm_quant-all_Ringo_hw300v5.sgr, BG3r12_h56.sm_quant-all_Ringo_hw300v5.sgr, BG3r12_h56_quant-all_normalNullmode_hw300v5g200FDR1.bed, BG3r12_e56_quant-all_normalNullmode_hw300v5g200FDR1.bed, BG3_EGTA-Hbss-quantNorm.wig, BG3_EGTA-Hbss-2kb-peaks-FDR1.bed
The *Ringo_hw300v5.sgr files contain the median of replicate ratios smoothed into window scores using a sliding window of 600bp and 5 minimum Probes in window with the Bioconductor Ringo package (Bioconductor 2.14). The bed file was created assuming a normalNull distribution centred around zero and the resulting p-values were adjusted for multiple testing using the fdr method. The difference between wildtype and N-activation H3K56ac signal was calculated as the subtraction of quantile normalised ChIP signal files (*quantNorm.wig). The *-2kb-peaks-FDR1.bed files were calculated as follows. All ChIP signal files were averaged over a 2kb window (in 200bp increments), and the noise distribution based on two replicates estimated. This noise distribution is used to call differentially enriched 2kb regions at 1% FDR, with overlapping 2kb regions merged together.

source_name: K56ac BG3 egta replicate 1

extract_protocol: 5x10^6 cells treated with 4mM EGTA in HBSS (egta) or HBSS only (hbss) for 30min were fixed with 1% formaldehyde in culture medium for 12 min at 25C followed by quenching with 0.125 M glycine for 2 min. The cells were washed twice with ice-cold PBS and lysed in 500ul of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by 20 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 150mM NaCl, Roche Complete inhibitor) and pre-cleared with 25 µl protein A agarose beads (pre-absorbed with BSA) and 2ug IgG for 2 h at 4C. The chromatin supernatant was then incubated overnight with 2 µg of purified antibody at 4C. After incubation with protein A agarose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed for 5min at 4C with the following buffers: dilution buffer, IP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH8.0, 50mM NaCl) (two washes), IP wash buffer 2 (1% NP-40 substitute, 1% deoxycholic acid, 1mM EDTA, 10mM Tris pH8.0, 250mM LiCl) (two washes) and TE (10mM Tris pH8.0, 1mM EDTA). The protein-DNA complexes were eluted from the beads in 200 µl of fresh elution buffer (1% SDS, 100 mM NaHCO3) at 65C for 2 h with rotation and de-crosslinked by overnight incubation at 65C with addition of 10 ul 5M NaCl. Following the treatment with 1ul RNase A (10mg/ml) for 2h at 37C and 5ul proteinase K (10mg/ml) for 4h at 45C, genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/10 of the material used for ChIP) by QiaQuick PCR purification (Qiagen).

treatment_protocol: BG3 cells were treated with 4mM EGTA in HBSS for 30min

source_name: Total input K56ac BG3 egta replicate 1


title: Mk_V3 [Meth450]

label: Cy5 and Cy3


title: Patient11_Normal


title: Patient12_Tumor


title: NA19726 Replicate 1


title: NA19728 Replicate 1


title: Patient10_Normal


title: K56ac BG3 egta vs Input rep2

source_name: K56ac BG3 egta replicate 2

source_name: Total input K56ac BG3 egta replicate 2


title: NA19725 Replicate 1


title: Mk_V2 [Meth450]


title: K56ac BG3 hbss vs Input rep2

source_name: K56ac BG3 hbss replicate 2

source_name: Total input K56ac BG3 hbss replicate 2


title: Patient9_Normal


title: Patient9_Tumor


title: Patient10_Tumor


title: Mk_V1 [Meth450]

source_name: Whole blood


title: NA19723 Replicate 1


title: K56ac Kc pbs vs Input rep2

source_name: K56ac Kc pbs replicate 2

source_name: Total Input K56ac Kc pbs replicate 2


title: NA19722 Replicate 1


title: Patient8_Normal


title: NA19719 Replicate 1


title: Mj_V3 [Meth450]


title: Su(H) BG3 egta vs Input rep4

source_name: Su(H) BG3 egta replicate 4

source_name: Total Input Su(H) BG3 egta replicate 4


title: NA19720 Replicate 1


title: Patient8_Tumor


title: Patient7_Tumor


title: Ml_V3 [Meth450]


title: Ml_V1 [Meth450]


title: NA19716 Replicate 1


title: NA19717 Replicate 1


title: NA19713 Replicate 1


title: Patient7_Normal

source_name: adjacent normal tissues


title: NA19712 Replicate 1


title: Patient5_Tumor

source_name: esophageal squamous cell carcinoma


title: Mi_V3 [Meth450]


title: Mi_V2 [Meth450]


title: Patient6_Normal


title: NA19711 Replicate 1


title: NA19704 Replicate 1


title: Patient5_Normal


title: NA19707 Replicate 1


title: Patient6_Tumor


title: Patient4_Normal


title: Mj_V1 [Meth450]


title: Patient4_Tumor


title: NA19703 Replicate 1


title: Patient3_Normal


title: NA19701 Replicate 1


title: Patient3_Tumor


title: Mi_V1 [Meth450]


title: Patient2_Tumor


title: Cg_V1 [Meth450]

value: Female


title: NA19685 Replicate 1


title: Ch_V3 [Meth450]


title: Patient1_Tumor


title: Ch_V1 [Meth450]


title: Patient2_Normal


title: NA19684 Replicate 1


title: Cg_V3 [Meth450]


title: NA19682 Replicate 1


title: Cg_V2 [Meth450]


title: Patient1_Normal


title: Cf_V3 [Meth450]


title: NA19681 Replicate 1


title: NA19679 Replicate 1


title: SGC-7901_Mock

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of empty vector

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) 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, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: SGC-7901 stably transfected with empty vector

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Human gastric cancer cell line SGC-7901 was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

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 integration 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: The ITLN1 expression or empty vectors were transfected into cancer cells, and stable cell lines were screened by administration of neomycin.

tag: treatment

value: Mock

value: gastric cancer

tag: cell line


title: SGC-7901_ITLN1

description: Gene expression after stable transfection of ITLN1 expression vector

source_name: SGC-7901 stably transfected with ITLN1 expression vector


title: Mj_V2 [Meth450]


title: Ce_V2 [Meth450]


title: Ce_V1 [Meth450]


title: Cf_V1 [Meth450]


title: NA19676 Replicate 1


title: NA19678 Replicate 1


title: NA19675 Replicate 1


title: Cf_V2 [Meth450]


title: NA19670 Replicate 1


title: Ad_V1 [Meth450]

value: African American


title: TS2 A

city: Brussels

first: Lorraine

last: Springuel

address: 74, Avenue Hippocrate

department: Brussels Branch

country: Belgium

institute: Ludwig Institute for Cancer Research

hyb_protocol: Affymetrix hybridization control and hybridization wash and stain kit.

scan_protocol: The wash and stain protocols were runned on an Affy 450 station. The chips were scanned according to the Affymetrix standard procedure.

data_processing:
Affymetrix Gene Expression Console and APT suite tool. Normalization: RMA-sketch procedure; signal detection p-values: DABG procedure.
CEL files unavailable due to system failure

label: biotin

organism: Mus musculus

source_name: T-lymphocyte CD4+ derived cell line

label_protocol: Biotinylated cRNAs were prepared according to the standard Ambion WT expression kit from 250ng of total RNA  followed by Affymetrix WT terminal labeling kit.

growth_protocol: Cells were cultured in Iscove-Dulbecco's medium in the presence of murine interleukin-9 in duplicates

extract_protocol: RNA extraction was performed using Tripure (Roche). RNA quality of samples was evaluated using Bioanalyzer .

value: lymphocytes


title: TS1 B


title: Ab_V3 [Meth450]


title: TS1 A


title: NA19669 Replicate 1


title: NA19700 Replicate 1


title: Ac_V2 [Meth450]


title: Ad_V2 [Meth450]


title: Ac_V3 [Meth450]


title: NOD_DCIR2-BDC_biological rep2

city: Bethesda

first: Kristin

middle: V.

last: Tarbell

state: MD

address: Bldg.10, CRC, 5W-5940, 10 Center Drive

department: Diabetes, Endocrinology, and Obesity Branch

institute: National Institute of Diabetes and Digestive and Kidney Diseases

description: Gene expression data from BDC2.5 CD4T cells in NOD mice stimulated with in vivo anti-DCIR2-BDC Ab injetion

hyb_protocol: cDNA samples were mixed with hybridization cocktail and hybridized to Affymetrix Mouse Gene 1.0 ST array for 16 hrs using Affymetrix hybridization oven at 45˚C rotating at 60 rpm. Gene chips were washed and stained with Affymetrix HWS regents using Affymetrix Fluidic Station 450 and FS450_0007 scripts followed by manufactures guidelines.

scan_protocol: Arrays were scanned using Affymetrix GCS 3000 7G operating with GCOS 1.4 software to generate .cel files.

data_processing: Data were background corrected with RMA normalized with Partek Genome Suite 6.6.

source_name: NOD BDCT cells from NOD mice, anti-DCIR2-BDC Ab i.v., 14h

label_protocol: cDNA targets were prepared from 5 ng of total RNA using NuGen Ovation pico WTA system V2. The amplified 2.5 µg of cDNA was fragmented and labeled using the Encore Biotin Module.

extract_protocol: PicoPure® RNA Isolation Kit (Life Technologies) was used according to manufacturer's guide.

tag: strain

value: NOD

value: female

tag: age

value: 7 week

value: spleen

value: Thy1.1+CD4+ cells of MACS negative sorted T cells


title: TS2 B


title: NOD_DCIR2-BDC_biological rep1


title: NA19663 Replicate 1


title: NA19664 Replicate 1


title: NOD_DEC-BDC_biological rep2

description: Gene expression data from BDC2.5 CD4T cells in NOD mice stimulated with in vivo anti-DEC205-BDC Ab injetion

source_name: NOD BDCT cells from NOD mice, anti-DEC205-BDC Ab i.v., 14h


title: NA19661 Replicate 1


title: Ac_V1 [Meth450]

value: Whole blood


title: NA19658 Replicate 1


title: NA19660 Replicate 1


title: NA19657 Replicate 1


title: NA19655 Replicate 1


title: Ch_V2 [Meth450]

value: Caucasian


title: NOD_PBS_biological rep1

description: Gene expression data from BDC2.5 CD4T cells in NOD mice as a control

source_name: NOD BDCT cells from NOD mice, PBS control, 14h


title: NA19654 Replicate 1


title: NOD_DEC-BDC_biological rep1


title: NOD_PBS_biological rep2


title: Transformed Eif4e+/-#1, polysomal RNA, biological rep1

city: San Francisco

first: Davide

last: Ruggero

state: CA

address: 1450 3rd St. Room HD-319

department: Helen Diller Cancer Center

institute: UCSF

description:
polsyomal RNA
Expression data from early passage transformed MEFs in exponential growth phase

hyb_protocol: cRNA was fragmented and then hybridized on Affymetrix Mouse Gene 1.0 ST Arrays according to the GeneChip Expression Analysis Technical Manual 702232 Rev. 3.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Array data was preprocessed by RMA using the aroma.affymetrix R package with default settings. Total RNA and polysomal RNA datasets were quantile normalized separately. Probe sets annotated as being in the main design and not cross-hybridizing were retained (Affymetrix NetAffx version 30).

source_name: Polysomal RNA of Ras and Myc transformed MEFs isolated from Eif4e+/- Embryo #1

label_protocol: Biotinylated cRNA were prepared using the NuGEN Applause WT Amp Plus System & NuGEN Encore Biotin Module.

growth_protocol: Early passage primary untransformed and matched transformed MEFs derived from E13.5 embyros were grown in DMEM, 10% FBS, Pen/Strep and harvested for analysis during the exponential growth phase.

extract_protocol: Total cellular RNA and polysomal RNA were isolated using TRIzol Reagent (Invitrogen) and the Pure Link RNA mini kit (Invitrogen) with on column Dnase digestions by Pure Link Dnase (Invitrogen).

treatment_protocol: For polysomal RNA, cytoplasmic extracts from cells treated with 100μg/ml cyclohexamide (Sigma) were separated on a 10-50% sucrose gradient by ultracentrifugation and fractionated to isolate high MW polysomes.

value: mouse embryonic fibroblasts

tag: genotype

value: isolated from E13.5 embryos


title: Ab_V1 [Meth450]


title: Transformed Eif4e+/-#3, polysomal RNA, biological rep1

source_name: Polysomal RNA of Ras and Myc transformed MEFs isolated from Eif4e+/- Embryo #3


title: Ab_V2 [Meth450]


title: Transformed Eif4e+/-#2, polysomal RNA, biological rep1

source_name: Polysomal RNA of Ras and Myc transformed MEFs isolated from Eif4e+/- Embryo #2


title: NA19652 Replicate 1


title: Aa_V2 [Meth450]


title: Aa_V3 [Meth450]


title: Ad_V3 [Meth450]


title: NA19651 Replicate 1


title: NA19649 Replicate 1


title: Inflammation 24

city: Toronto

first: Daniel

last: De Carvalho

state: ON

address: 101 College Street, room 9-302

country: Canada

institute: Ontario Cancer Institute

description: inflammated oral sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software

source_name: oral swab

extract_protocol: genomic DNA was extracted and purified from oral samples using Qiagen DNeasy Kit according to standard instructions

value: periodontitis


title: NA19648 Replicate 1


title: NA19625 Replicate 1


title: Transformed WT#1, polysomal RNA, biological rep1

source_name: Polysomal RNA of Ras and Myc transformed MEFs isolated from WT Embryo #1

value: WT


title: Transformed WT#2, polysomal RNA, biological rep2

source_name: Polysomal RNA of Ras and Myc transformed MEFs isolated from WT Embryo #2


title: Aa_V1 [Meth450]

source_name: Whole blood


title: NA19475 Replicate 1


title: NA19474 Replicate 1


title: Transformed Eif4e+/-#1, total RNA, biological rep1

description:
total RNA
Expression data from early passage transformed MEFs in exponential growth phase

source_name: Total RNA of Ras and Myc transformed MEFs isolated from Eif4e+/- Embryo #1


title: Transformed WT#3, total RNA, biological rep3

source_name: Total RNA of Ras and Myc transformed MEFs isolated from WT Embryo #3


title: Inflammation 22

description: inflammated oral sample


title: Transformed Eif4e+/-#3, total RNA, biological rep1

source_name: Total RNA of Ras and Myc transformed MEFs isolated from Eif4e+/- Embryo #3


title: Transformed Eif4e+/-#2, total RNA, biological rep1

source_name: Total RNA of Ras and Myc transformed MEFs isolated from Eif4e+/- Embryo #2


title: Transformed WT#2, total RNA, biological rep2

source_name: Total RNA of Ras and Myc transformed MEFs isolated from WT Embryo #2


title: Inflammation 23

description: inflammated oral sample


title: Transformed WT#1, total RNA, biological rep1

source_name: Total RNA of Ras and Myc transformed MEFs isolated from WT Embryo #1


title: Transformed WT#3, polysomal RNA, biological rep3

source_name: Polysomal RNA of Ras and Myc transformed MEFs isolated from WT Embryo #3


title: Inflammation 21

description: inflammated oral sample


title: NA19473 Replicate 1


title: Inflammation 19

description: inflammated oral sample


title: NA19471 Replicate 1


title: NA19472 Replicate 1


title: Inflammation 20

description: inflammated oral sample


city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

country: Japan

institute: Yokohama City University

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 High-Resolution Microarray Scanner using one color scan setting for 4x44k v2 array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
The raw signal intensities of samples were log2-transformed and normalised by the quantile algorithm.

source_name: 04_Kidney bud Tx_4wk

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

extract_protocol: RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Tissue after kidney bud transplantation for 4wk.


title: Inflammation 15

description: inflammated oral sample


title: Untransformed Eif4e+/-#2, polysomal RNA, biological rep1

description:
polsyomal RNA
Expression data from early passage untransformed MEFs in exponential growth phase

source_name: Polysomal RNA of untransformed primary MEFs isolated from Eif4e+/- Embryo #2


title: Inflammation 16

description: inflammated oral sample


title: Untransformed Eif4e+/-#3, polysomal RNA, biological rep1

source_name: Polysomal RNA of untransformed primary MEFs isolated from Eif4e+/- Embryo #3


title: Inflammation 13

description: inflammated oral sample


title: Ce_V3 [Meth450]

value: Female


title: NA19467 Replicate 1


title: 8weeks Kidney

value: Adult Kidney isolated from 8weeks old mice.


title: NA19466 Replicate 1


title: E13.5 kidney

value: Kidney isolated from E13.5 mice.


title: Inflammation 17

description: inflammated oral sample


title: P0 kidney

value: Kidney isolated from P0 mice.


title: Inflammation 18

description: inflammated oral sample


title: Healthy Control 10

description: normal oral sample

value: Normal


title: NA19462 Replicate 1


title: Untransformed Eif4e+/-#1, polysomal RNA, biological rep1

source_name: Polysomal RNA of untransformed primary MEFs isolated from Eif4e+/- Embryo #1


title: NA19463 Replicate 1


title: Untransformed WT#2, polysomal RNA, biological rep2

source_name: Polysomal RNA of untransformed primary MEFs isolated from WT Embryo #2


title: Untransformed WT#1, polysomal RNA, biological rep1

source_name: Polysomal RNA of untransformed primary MEFs isolated from WT Embryo #1


title: Untransformed Eif4e+/-#2, total RNA, biological rep1

description:
total RNA
Expression data from early passage untransformed MEFs in exponential growth phase

source_name: Total RNA of untransformed primary MEFs isolated from Eif4e+/- Embryo #2


title: Healthy Control 8

description: normal oral sample

source_name: oral swab


title: Healthy Control 12

description: normal oral sample


title: Untransformed WT#3, polysomal RNA, biological rep3

source_name: Polysomal RNA of untransformed primary MEFs isolated from WT Embryo #3


title: Untransformed Eif4e+/-#3, total RNA, biological rep1

source_name: Total RNA of untransformed primary MEFs isolated from Eif4e+/- Embryo #3


title: NA19457 Replicate 1


title: NA19456 Replicate 1


title: NA19455 Replicate 1


title: NA19452 Replicate 1


title: NA19454 Replicate 1


title: NA19461 Replicate 1


title: Untransformed Eif4e+/-#1, total RNA, biological rep1

source_name: Total RNA of untransformed primary MEFs isolated from Eif4e+/- Embryo #1


title: NA19449 Replicate 1


title: Healthy Control 11

description: normal oral sample


title: NA19448 Replicate 1


title: Untransformed WT#2, total RNA, biological rep2

source_name: Total RNA of untransformed primary MEFs isolated from WT Embryo #2


title: Untransformed WT#3, total RNA, biological rep3

source_name: Total RNA of untransformed primary MEFs isolated from WT Embryo #3


title: Untransformed WT#1, total RNA, biological rep1

source_name: Total RNA of untransformed primary MEFs isolated from WT Embryo #1


title: NA19451 Replicate 1


title: NA19445 Replicate 1


title: NA19443 Replicate 1


title: Healthy Control 7

description: normal oral sample


title: Healthy Control 5

description: normal oral sample


title: NA19440 Replicate 1


title: NA19439 Replicate 1


title: NA19446 Replicate 1


title: NA19438 Replicate 1


title: NA19437 Replicate 1


title: NA19436 Replicate 1


title: Healthy Control 4

description: normal oral sample


title: Healthy Control 6

description: normal oral sample


title: Healthy Control 2

description: normal oral sample


title: NA19431 Replicate 1


title: NA19434 Replicate 1


title: NA19430 Replicate 1


title: NA19435 Replicate 1


title: Healthy Control 1

description: normal oral sample


title: Healthy Control 3

description: normal oral sample


title: NA19468 Replicate 1


title: NA19429 Replicate 1


title: Male, Liver, 30 mg/kg-d, Replicate 2

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: 1.0 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array 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), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4200AL scanner at PMT gain level 420 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software, version 9.5.1 (Agilent Technologies).  Microarray analysis was performed using a HDArray library of functions available at the R software website (http://www.r-project.org/) which utilizes a Bayesian probabilistic framework-based t-test to test for differences in gene expression (Baldi and Long 2001). Background subtracted, adjusted median signal intensities were normalized on a per-chip basis using R software that transforms the signal intensity by dividing signal intensity for all the genes with the mean intensity in each array (Rawat and Deng 2008). The normalized data was imported into HDArray using Bioconductor (www.bioconductor.org) to measure the confidence value associated with fold change for each gene.  The HDArray output was imported into MySQL (www.mysql.co) and the overlap between log transformed Bayes p (p < 0.05, unless stated otherwise) and present signal flag for all replicates was taken.  As described in Rawat et al 2010a, the microarray for Northern bobwhite includes 8,454 non-redundant sequences with positive-frame orientations in addition to 3,272 sense-antisense probe-pairs representing transcripts for which the frame-orientation was not known.   For the sense-antisense probe pairs, one probe represents a nonsense sequence and our expectation was that no target should have specific binding to it.  All probes for which expression was observed in both the forward- and reverse-sequence were considered non-specific and were removed from the expression analysis.  REFERENCES:  Baldi P, Long AD. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509–519, 2001.  Rawat A, Deng YP. Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data. BMC Bioinformatics 9: S7, 2008.

organism: Colinus virginianus

source_name: Liver tissue from male

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 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.

growth_protocol: The growth protocol is described in Quinn et al (2010).  Northern bobwhite approximately 12 weeks of age were obtained from Trace Pheasantry (Douglassville, PA, USA). Blood samples from a subset of randomly chosen individuals were evaluated through the testing of 15 common bacteriological, fungal, and viral pathogens to assess the health of the population. Birds were then acclimated/ quarantined for more than 14 days and determined to be in good health by the attending veterinarian before being released for use in the present study. On arrival, birds were randomly assigned to and housed individually in cage units 28 cm in width, 30.5 cm in height, and 38 cm in depth and constructed of 1.3- 9 2.5-cm polychlorinated vinyl–coated wire. Each unit contained two adjustable-height, automatic nipple drinkers and individual 18-gauge, stainless steel feeding troughs. Each enclosure had a 15-cm section of sisal rope for environmental enrichment. Birds were kept in a constant 16:8-h light:dark photoperiod, with relative humidity maintained between 30 and 70% and temperature between 64 and 79 F. Birds were uniquely identified by cage card and subcutaneous transponder. Water was provided ad libitum by an automated watering system that was checked daily. Birds were provided with certified feed (Nutrena  Premium Gamebird Feed; Cargill, Minneapolis, MN, USA) weekly, which were weighed along with any spillage.  All animal exposure protocols were conducted consistent with Good Laboratory Practices, conducted at their AAALAC accredited facility and were approved by the Institutional Animal Care and Use Committee at the U.S. Army Public Health Command.  REFERENCE:  Quinn Jr. MJ, McFarland CA, LaFiandra EM, Bazar MA, Johnson MS (2010) Acute, subacute, and subchronic exposure to 2A-DNT (2-amino-4,6-dinitrotoluene) in the northern bobwhite (Colinus virginianus) Ecotoxicology 19:945-952.

extract_protocol: Immediately following euthanasia by CO2 asphyxiation, liver and kidney tissues were collected from each sex and a portion of each tissue was flash frozen for proteomics analyses and another portion fixed in RNA Later™ (Qiagen Inc., Valencia, CA) following manufacturer’s recommendations for transcriptomics analyses.  Tissues were stored at -80ºC until needed for analysis.  RNA extraction was conducted as described in Gust et al (2009).  Briefly, RNA extraction was conducted using RNeasy Mini RNA extraction kits (Qiagen Inc.).  RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) with RNA 6000 Nano LabChips® and a NanoDrop ND-1000 Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). Only samples with a 28s/18s ratio ≥2.0 and RNA integrity number ≥7.0 were used for downstream applications.  REFERENCE:  Gust KA, Pirooznia M, Quinn Jr. MJ, Johnson MS, Escalon, BL, Indest KJ, Guan X, Clarke J, Deng Y, Gong P, Perkins EJ (2009) Neurotoxicogenomic Investigations to Assess Mechanisms of Action of the Munitions Constituents RDX and 2,6-DNT in Northern Bobwhite (Colinus virginianus) Toxicol Sci 110(1):168–180.

treatment_protocol: The treatment (2A-DNT dosing) protocol is described in Quinn et al (2010).  Five treatment groups consisting of 12 male and 12 female bobwhites each were administered 2A-DNT at 0, 0.5, 3, 14, or 30 mg/kg/day via oral gavage. Controls received a volume of corn oil equivalent to the mean volume given to birds in the highest dose group without compound. Body and feed weights were weighed on days 0, 4, then weekly thereafter. Following 60 days of exposure, birds were bled via the jugular vein, anesthetized and killed by CO2 asphyxiation, and evaluated by gross necropsy.  REFERENCE:  Quinn Jr. MJ, McFarland CA, LaFiandra EM, Bazar MA, Johnson MS (2010) Acute, subacute, and subchronic exposure to 2A-DNT (2-amino-4,6-dinitrotoluene) in the northern bobwhite (Colinus virginianus) Ecotoxicology 19:945-952.

value: liver

value: male


title: Male, Liver, 30 mg/kg-d, Replicate 3


title: Male, Liver, 14 mg/kg-d, Replicate 3


title: NA19428 Replicate 1


title: Male, Liver, 14 mg/kg-d, Replicate 2


title: Male, Liver, 30 mg/kg-d, Replicate 1


title: Male, Liver, 30 mg/kg-d, Replicate 4


title: Male, Liver, 14 mg/kg-d, Replicate 4


title: Male, Liver, 14 mg/kg-d, Replicate 1


title: Male, Liver, 3 mg/kg-d, Replicate 2


title: Male, Liver, 3 mg/kg-d, Replicate 4


title: Male, Liver, 3 mg/kg-d, Replicate 3


title: Male, Liver, 3 mg/kg-d, Replicate 1


title: NA19404 Replicate 1


source_name: 03_Kidney bud Tx_2wk

value: Tissue after kidney bud transplantation for 2wk.


title: NA19403 Replicate 1


title: NA19399 Replicate 1


title: Male, Liver, 0 mg/kg-d, Replicate 3


title: NA19397 Replicate 1


title: Male, Liver, 0 mg/kg-d, Replicate 2


title: NA19393 Replicate 1


title: NA19395 Replicate 1


title: NA19394 Replicate 1


title: Male, Liver, 0 mg/kg-d, Replicate 1


title: Male, Liver, 0 mg/kg-d, Replicate 4


title: NA19391 Replicate 1


title: Male, Kidney, 30 mg/kg-d, Replicate 4

source_name: Kidney tissue from male

value: kidney


title: CaMKIIN, aorta, Angiotensin-II, biological rep 2

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

description: Gene expression from thoracic aorta of Angiotensin-II infused TG SM-CaMKIIN mice

hyb_protocol: 1.5 ug of this product were hybridized onto Illumina MouseWG-6 v2 bead chips for 17 h at 58 C.

scan_protocol: GeneChips were scanned using the Illumina iScan system.

data_processing: The data were exported with GenomeStudio software version2011.1. and normalized and tested for differential expression using limma 3.22.1

source_name: thoracic aorta of Angiotensin-II-infused TG SM-CaMKIIN mice

label_protocol: Biotin-aRNA was prepared using the Epicentre TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip according to the manufacturer's instructions.

growth_protocol: 12-week old WT littermate (C57 Bl/6 background) and TG SM-CaMKIIN were implanted with osmotic minipumps to deliver 0.9% normal saline or 1.25 ug/kg/min Angiotensin-II in 0.9% normal saline for 14 days. 5 WT mice were treated with normal saline, 5 WT mice with Angiotensin-II, 5 TG SM-CAMKIIN with saline. 5 TG SM-CaMKIIN mice with Angiotensin-II.

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

treatment_protocol: Thoracic aortas were dissected, rinced in PBS, placed in Trizol solution on ice.

tag: background strain

value: thoracic aorta

value: TG SM-CaMKIIN

value: Angiotensin-II


title: NA19401 Replicate 1


title: Male, Kidney, 30 mg/kg-d, Replicate 3


title: CaMKIIN, aorta, Angiotensin-II, biological rep 1


title: Male, Kidney, 14 mg/kg-d, Replicate 4


title: Male, Kidney, 30 mg/kg-d, Replicate 2


title: Male, Kidney, 30 mg/kg-d, Replicate 1


title: WT, aorta, Angiotensin-II, biological rep 2

description: Gene expression from thoracic aorta of Angiotensin-II infused WT mice

source_name: thoracic aorta of Angiotensin-II-infused WT mice


title: Male, Kidney, 14 mg/kg-d, Replicate 2


title: Male, Kidney, 14 mg/kg-d, Replicate 3


title: TG SM-CaMKIIN, aorta, saline

description: Gene expression from thoracic aorta of saline-infused TG SM-CaMKIIN mice

value: saline


title: High fat diet, rep1

city: Daegu

first: Un Ju

last: Jung

address: 1370, Sankyuk-dong, Buk-gu

department: Center for Food & Nutritional Genomics

country: South Korea

institute: Kyungpook National University

description:
Sample name: HFD1
replicate 1

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each mouse-6 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4).

data_processing:
The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)).
Array probes that have detection p-value > 0.05 (similar to signal to noise) in over 50% samples were filtered out. (We applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05) Selected gene signal value was transformed by logarithm and normalized by quantile method.
All probe signal value was transformed by logarithm and normalized by quantile method. The 1-way anova test, tukey HSD test and fold change were applied. Statistical significance was adjusted by the Benjamini-Hocbherg multiple-testing correction with false discovery rate(FDR). All data analysis was conducted using R statistical language v. 2.4.1.

source_name: Mouse Epididymal adipose tissue, High fat diet

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: Eighteen male C57BL/6J mice were obtained from the Jackson Laboratory (Bar Harbor, ME) at 4 weeks of age. All the mice were individually housed under a constant temperature (24°C) and 12-hour light/dark cycle, fed the chow diet for a one-week acclimation period after arrival

extract_protocol: Total RNA was extracted from the adipose tissue using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The mice were fed a low fat diet (LFD, n=9) or high fat diet (HFD, n=9) for 16 weeks

value: 21 weeks

value: High fat diet

value: epididymal adipose tissue


title: High fat diet, rep2

description:
Sample name: HFD2
replicate 2


title: WT, aorta, saline

description: Gene expression from thoracic aorta of saline-infused WT mice

value: WT


title: WT, aorta, Angiotensin-II, biological rep 1


title: NA19385 Replicate 1


title: Low fat diet, rep3

description:
Sample name: LFD3
replicate 3

source_name: Mouse Epididymal adipose tissue, Low fat diet

value: Low fat diet


title: Male, Kidney, 14 mg/kg-d, Replicate 1


title: NA19390 Replicate 1


title: NA19383 Replicate 1


title: High fat diet, rep3

description:
Sample name: HFD3
replicate 3


title: NA19384 Replicate 1


title: NA19380 Replicate 1


title: Male, Kidney, 3 mg/kg-d, Replicate 4


title: NA19378 Replicate 1


title: Male, Kidney, 3 mg/kg-d, Replicate 3


title: Male, Kidney, 3 mg/kg-d, Replicate 2


title: NA19377 Replicate 1


title: NA19376 Replicate 1


title: heart-KO.TAC.733

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University

description: Gene expression after 3 days of  TAC operation

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 h, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent).

data_processing:
Microarray data were log-transformed before differential expression analysis using the limma package. The 4th replicate in Cre-TAC group did not pass quality control, thus was removed from final data analysis.
Probes with a p value of less than 0.05 after adjusting for false discovery rate using Benjamini and Hochberg method were considered significant in differential expression. Enrichment in biological processes was analyzed using the DAVID bioinformatics suite.

source_name: heart, KO, TAC 3 days, replicate 3

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

extract_protocol: Total ventricular RNA was extracted from A-Cre and A-cKO mice with Sham or TAC at 3 days post surgery (n = 4 in each group) using TRIzol reagent and purified using Qiagen RNA purification kit. Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer.

treatment_protocol: young adult male mice, Cre and KO, on C57BL6 background, were subjected to TAC or sham operation for 3 days. Hearts then were removed, washed in cold PBS, weighted and apex was stored in liquid nitrogen for RNA isolation.

value: heart, apex


title: heart-KO.TAC.732

description: Gene expression after 3 days of  sham operation

source_name: heart, KO, TAC 3 days, replicate 2


title: NA19379 Replicate 1


title: Male, Kidney, 0 mg/kg-d, Replicate 3


title: Low fat diet, rep1

description:
Sample name: LFD1
replicate 1


title: heart-KO.TAC.734

source_name: heart, KO, TAC 3 days, replicate 4


title: HIV-infected Patient - repeat 2 - mAdbID:129080

city: Baltimore

first: Maria

middle: Libera

last: Ascierto

address: 5500 Orleans Street

department: Oncology

institute: Johns Hopkins

description: mAdb experiment ID: 129080

hyb_protocol: Affymetrix Hybridization Protocol Biotinylated cDNA was hybridized to GeneChip Human Gene 1.0 ST Arrays (Affymetrix, Santa Clara, CA) and washed and stained on a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA), according to the manufacturer's instructions.

scan_protocol: Affymetrix Scanning Protocol Arrays were scanned by GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: Calculation Method: The global gene expression profiling was analyzed using Partek Genomics Suite (St Louis, MO). RMA (Robust Multiarray Average) normalization was used for intensity calculations.

source_name: HIV-infected Patient

label_protocol: RNA quality and quantity was estimated using Nanodrop (Thermo Scientific, Pittsburgh, PA)) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). First- and second-strand cDNA were synthesized from 30 ng of total RNA according to manufacturer's instructions (Nugen Ovation Pico WTA System V2, San Carlos, CA). cDNAs were fragmented and biotinylated (Nugen Encore Biotin Module, San Carlos, CA) using WT Terminal Labeling Kit (Affymetrix WT Terminal Labeling Kit, Santa Clara, CA).

extract_protocol:
miRNeasy Minikit
Total RNA was extracted using miRNeasy minikit (Qiagen, Valencia, CA) according to the manufacture's protocol.

value: blood

value: CD34+ hematopoietic stem cells

value: HIV Infection


title: Male, Kidney, 0 mg/kg-d, Replicate 4


title: HIV-infected Patient - repeat 1 - mAdbID:129079

description: mAdb experiment ID: 129079


title: HL60, 72h control, sucrose density gradient Fraction 10

city: Rome

first: Giulia

last: Fontemaggi

address: Via Elio Chianesi, 53

country: Italy

institute: Italian National Cancer Institute Regina Elena

description:
Gene expression from control proliferating HL60 cells
CTR_F10

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Scanned image files (.CEL) were processed, normalized (RMA-SketchQuantile) and Log2-transformed by Expression Console Software (Affymetrix website).Transcripts presenting values higher than 6 in at least 3 out of the 18 fractions were considered.

source_name: Fraction 10 from ribo/polysomal fractionation of proliferating cells

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

growth_protocol: HL-60 cell line was maintained in RPMI 1640 medium supplemented with 1 x penicillin/streptomycin solution, 1 x L-glutamine and 10% Fetal Bovine Serum.

extract_protocol: Total RNA for microarray analyses was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) from fractions obtained by sucrose density gradient centrifugation. Genomic DNA contamination was eliminated through a DNase I (Qiagen, Chatsworth, CA) digestion step. RNA was further purified on Qiagen RNeasy columns for gene expression profiling (Qiagen, Chatsworth, CA). The concentration and purity of total RNA were assessed using a Nanodrop TM 1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Not applicable

value: HL60 cells, promyeloblasts

value: control

tag: sucrose density gradient fraction


title: HL60, 72h control, sucrose density gradient Fraction 11

description:
Gene expression from control proliferating HL60 cells
CTR_F11

source_name: Fraction 11 from ribo/polysomal fractionation of proliferating cells


title: Healthy Donor - repeat 2 - mAdbID:129078

description: mAdb experiment ID: 129078

source_name: Healthy Donor

value: bone marrow


title: Male, Kidney, 3 mg/kg-d, Replicate 1

value: kidney

value: male


title: Healthy Donor - repeat 1 - mAdbID:129077

description: mAdb experiment ID: 129077


title: HL60, 72h control, sucrose density gradient Fraction 9

description:
Gene expression from control proliferating HL60 cells
CTR_F9

source_name: Fraction 9 from ribo/polysomal fractionation of proliferating cells


title: NA19375 Replicate 1


title: Male, Kidney, 0 mg/kg-d, Replicate 2


title: heart-KO.Control.735

source_name: heart, KO, sham, replicate 2


title: heart-KO.Control.737

source_name: heart, KO, sham, replicate 3


title: Male, Kidney, 0 mg/kg-d, Replicate 1


title: heart-KO.Control.929

source_name: heart, KO, sham, replicate 4


title: heart-KO.TAC.729

source_name: heart, KO, TAC 3 days, replicate 1


title: heart-KO.Control.937

source_name: heart, KO, sham, replicate 1


title: heart-Cre.TAC.768

source_name: heart, Cre, TAC 3 days, replicate 3

value: MHC-cre


title: NA19374 Replicate 1


title: HL60, 72h control, sucrose density gradient Fraction 8

description:
Gene expression from control proliferating HL60 cells
CTR_F8

source_name: Fraction 8 from ribo/polysomal fractionation of proliferating cells


title: NA19372 Replicate 1


title: Female, Liver, 30 mg/kg-d, Replicate 4

source_name: Liver tissue from female

value: liver

value: female


title: NA19360 Replicate 1


title: NA19355 Replicate 1


title: HL60, 72h control, sucrose density gradient Fraction 7

description:
Gene expression from control proliferating HL60 cells
CTR_F7

source_name: Fraction 7 from ribo/polysomal fractionation of proliferating cells


title: NA19351 Replicate 1


title: HL60, 72h control, sucrose density gradient Fraction 6

description:
Gene expression from control proliferating HL60 cells
CTR_F6

source_name: Fraction 6 from ribo/polysomal fractionation of proliferating cells


title: NA19350 Replicate 1


title: heart-Cre.TAC.762

source_name: heart, Cre, TAC 3 days, replicate 1


title: HL60, 72h control, sucrose density gradient Fraction 5

description:
Gene expression from control proliferating HL60 cells
CTR_F5

source_name: Fraction 5 from ribo/polysomal fractionation of proliferating cells


title: Female, Liver, 14 mg/kg-d, Replicate 4


title: Female, Liver, 30 mg/kg-d, Replicate 3


title: Female, Liver, 30 mg/kg-d, Replicate 1


title: heart-Cre.TAC.765

source_name: heart, Cre, TAC 3 days, replicate 2


title: NA19347 Replicate 1


title: Female, Liver, 30 mg/kg-d, Replicate 2


title: HL60, 72h control, sucrose density gradient Fraction 4

description:
Gene expression from control proliferating HL60 cells
CTR_F4

source_name: Fraction 4 from ribo/polysomal fractionation of proliferating cells


title: Female, Liver, 14 mg/kg-d, Replicate 3


title: HL60, 72h control, sucrose density gradient Fraction 3

description:
Gene expression from control proliferating HL60 cells
CTR_F3

source_name: Fraction 3 from ribo/polysomal fractionation of proliferating cells


title: Female, Liver, 14 mg/kg-d, Replicate 2


title: heart-Cre.Control.881

source_name: heart, Cre, sham replicate 3


title: heart-Cre.Control.882

source_name: heart, Cre, sham replicate 4


title: heart-Cre.Control.763

source_name: heart, Cre, sham replicate 1


title: heart-Cre.Control.771

source_name: heart, Cre, sham replicate 2


title: HL60, 72h VitD3, sucrose density gradient Fraction 10

description:
Gene expression in VitD3-treated HL60 cells
VitD3_F10

source_name: Fraction 10 from ribo/polysomal fractionation of differentiated cells


title: Female, Liver, 14 mg/kg-d, Replicate 1


title: NA19338 Replicate 1


title: HL60, 72h VitD3, sucrose density gradient Fraction 9

description:
Gene expression in VitD3-treated HL60 cells
VitD3_F9

source_name: Fraction 9 from ribo/polysomal fractionation of differentiated cells


title: Female, Liver, 3 mg/kg-d, Replicate 4


title: NA19334 Replicate 1


title: NA19346 Replicate 1


title: NA19332 Replicate 1


title: HL60, 72h VitD3, sucrose density gradient Fraction 11

description:
Gene expression in VitD3-treated HL60 cells
VitD3_F11

source_name: Fraction 11 from ribo/polysomal fractionation of differentiated cells


title: Female, Liver, 3 mg/kg-d, Replicate 3


title: HL60, 72h VitD3, sucrose density gradient Fraction 8

description:
Gene expression in VitD3-treated HL60 cells
VitD3_F8

source_name: Fraction 8 from ribo/polysomal fractionation of differentiated cells


title: D3-5

city: Ottawa

last: Labib

state: Ontario

address: 204b-50 Colombine

institute: Health Canada

description:
4h BaP Dose Group 3 (50mg/kg BW/day) Liver Replicate 4
Slide Barcode: 251486824088
Array Number (Postion): 1_3
Group: D3T1_50mg_4h

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (825ng) were co-hybridized to Agilent G4122F Whole Mouse Genome (4×44K)  oligonucleotide microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Version 5.7, March 2008).  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Microarray slides were scanned using an Agilent DNA Microarray Scanner (G2505C) using the AgilentHD_GX_2Color scanning profile.  Data was extracted from the scanned images using Feature Extraction Version 10.1.1.1.

data_processing: The log2 of the ratio (sample (Cy5)/reference (Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.

source_name: Liver

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Male B6C3F1 mice, aged 27-30 days old, were obtained from Charles River Laboratories (St-Constant, Quebec, Canada).  Animals were acclimatised for 7 days prior to commencement of the dosing regime.  Animals were housed in individual cages and fed Purina rodent chow and water ad libitum, under a 12h light/12h dark lighting schedule. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine livers were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections of the right medial lobe of the liver (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 8.0.

treatment_protocol: Mice were dosed via oral gavage (10 ml/kg body weight) daily for three consecutive days. Four different doses of BaP dissolved in corn oil were selected to dose the animals: 5mg/kg BW, 50 mg/kg BW, 150 mg/kg BW and 300 mg/kg BW.  Control animals were gavaged with corn oil only.   Tissues were collected 4 hours and 24 hours following the final dose.

tag: dose

tag: time

value: 4 hour

value: Male

source_name: Universal Mouse Reference RNA

tag: sample type

value: Universal Mouse Reference RNA [11 mouse cell lines]


title: D4-1

description:
4h BaP Dose Group 4 (5mg/kg BW/day) Liver Replicate 1
Slide Barcode: 251486824088
Array Number (Postion): 1_4
Group: D4T1_5mg_4h

tag: tissue


title: NA19331 Replicate 1

data_processing: Images were processed using Agilent Feature Extraction Software (version 10.5.1.1)

extract_protocol: We did not perform the extraction in house. We received DNA samples from Coriell. This is the information available on their website for DNA extraction: gDNA is purified from fresh blood, immortalized lymphocyctes or fibroblasts using the Qiagen Autopure LS instrument according to the manufacturer’s instructions or manually by modified Miller’s Salting out procedures.


title: Female, Liver, 3 mg/kg-d, Replicate 2

source_name: Liver tissue from female


title: HL60, 72h VitD3, sucrose density gradient Fraction 7

description:
Gene expression in VitD3-treated HL60 cells
VitD3_F7

source_name: Fraction 7 from ribo/polysomal fractionation of differentiated cells


title: D1-3

description:
4h BaP Dose Group 1 (300mg/kg BW/day) Liver Replicate 3
Slide Barcode: 251486824088
Array Number (Postion): 1_2
Group: D1T1_300mg_4h


title: NA19328 Replicate 1


title: D0-5

description:
4h BaP Control Group (0mg/kg BW/day) Liver Replicate 4
Slide Barcode: 251486824088
Array Number (Postion): 1_1
Group: D0T1_Control_4h


title: NA19327 Replicate 1


title: HL60, 72h VitD3, sucrose density gradient Fraction 6

description:
Gene expression in VitD3-treated HL60 cells
VitD3_F6

source_name: Fraction 6 from ribo/polysomal fractionation of differentiated cells


title: HL60, 72h VitD3, sucrose density gradient Fraction 5

description:
Gene expression in VitD3-treated HL60 cells
VitD3_F5

source_name: Fraction 5 from ribo/polysomal fractionation of differentiated cells


title: HL60, 72h VitD3, sucrose density gradient Fraction 4

description:
Gene expression in VitD3-treated HL60 cells
VitD3_F4

source_name: Fraction 4 from ribo/polysomal fractionation of differentiated cells


title: NA19324 Replicate 1


title: Female, Liver, 0 mg/kg-d, Replicate 4


title: HL60, 72h VitD3, sucrose density gradient Fraction 3

description:
Gene expression in VitD3-treated HL60 cells
VitD3_F3

source_name: Fraction 3 from ribo/polysomal fractionation of differentiated cells


title: Female, Liver, 0 mg/kg-d, Replicate 3


title: Female, Liver, 3 mg/kg-d, Replicate 1


title: Female, Liver, 0 mg/kg-d, Replicate 2


title: D4-11

description:
24h BaP Dose Group 4 (5mg/kg BW/day) Liver Replicate 3
Slide Barcode: 251486824087
Array Number (Postion): 1_2
Group: D4T2_5mg_24h

value: 24 hour


title: NA19323 Replicate 1


title: D4-2

description:
4h BaP Dose Group 4 (5mg/kg BW/day) Liver Replicate 2
Slide Barcode: 251486824087
Array Number (Postion): 1_1
Group: D4T1_5mg_4h


title: NaS NGPS-NII MSCs

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Human Gene 1.0 ST Array according to the protocols recommended by the manufacturer (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix, Inc.).

data_processing: After scanning, raw data (Affymetrix CEL files) were processed with RMAExpress using default settings.

source_name: NaS-treated NGPS MSCs

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

growth_protocol: Mesenchymal stem cells were grown at 37 ºC, 5% CO2, under standard conditions.

treatment_protocol: Cells were treated with 0.2 mM sodium salicylate during the differentiation process.

value: Nestor-Guillermo Progeria Syndrome (NGPS)

value: mesenchymal stem cells (MSCs)

value: sodium salicylate

tag: identifier

value: NII


title: Female, Liver, 0 mg/kg-d, Replicate 1


title: NA19321 Replicate 1


title: D3-6

description:
4h BaP Dose Group 3 (50mg/kg BW/day) Liver Replicate 5
Slide Barcode: 251486824086
Array Number (Postion): 1_4
Group: D3T1_50mg_4h


title: D2-5

description:
4h BaP Dose Group 2 (150mg/kg BW/day) Liver Replicate 4
Slide Barcode: 251486824086
Array Number (Postion): 1_3
Group: D2T1_150mg_4h


title: D0-10

description:
24h BaP Control Group (0mg/kg BW/day) Liver Replicate 2
Slide Barcode: 251486824087
Array Number (Postion): 1_3
Group: D0T2_Control_24h


title: NA19320 Replicate 1


title: NA19319 Replicate 1


title: NGPS-NII MSCs

source_name: NGPS MSCs

tag: cell type


title: NA19317 Replicate 1


title: Female, Kidney, 30 mg/kg-d, Replicate 4

source_name: Kidney tissue from female


title: NA19315 Replicate 1


title: NGPS-NI MSCs

value: NI


title: NaS NGPS-NI MSCs


title: NA19316 Replicate 1


title: NaS Control MSCs

source_name: NaS-treated control MSCs


title: Female, Kidney, 14 mg/kg-d, Replicate 4


title: Female, Kidney, 30 mg/kg-d, Replicate 1


title: Control MSCs

source_name: Control MSCs


title: Female, Kidney, 30 mg/kg-d, Replicate 3


title: Female, Kidney, 30 mg/kg-d, Replicate 2


title: NA19318 Replicate 1


title: D3-14

description:
24h BaP Dose Group 3 (50mg/kg BW/day) Liver Replicate 4
Slide Barcode: 251486824085
Array Number (Postion): 1_4
Group: D3T2_50mg_24h


title: Female, Kidney, 14 mg/kg-d, Replicate 3


title: Female, Kidney, 14 mg/kg-d, Replicate 1


title: Low fat diet, rep2

description:
Sample name: LFD2
replicate 2

source_name: Mouse Epididymal adipose tissue, Low fat diet

value: 21 weeks

value: Low fat diet

value: epididymal adipose tissue


title: NA19314 Replicate 1


title: Female, Kidney, 14 mg/kg-d, Replicate 2

value: kidney


title: NA19313 Replicate 1


title: IST5-002-3

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

description: K562 cells treated with IST5-002 (5 µM) for 48 h

hyb_protocol: Affymetrix gene chips, Human gene 1.0 ST array (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (2.5 μg) in 110 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h.

scan_protocol: Chips (Human gene 1.0 ST array) were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Raw intensity files from the Affymetrix Human Exon 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.2.1. Gene-level expression measurements were computed using the iterPLIER algorithm on the “core” probesets.

source_name: K562 cell line

label_protocol: Amplified cDNA was synthesized from 50 ng of total RNA using NuGen Ovation Pico WTA systems V2 (NuGen Technologies, Inc.). 2.5 μg cDNA was fragmented and chemically labeled with biotin to generate biotinylated cDNA using Encore biotin module (NuGen Technologies, Inc.).

growth_protocol: K562 cells were maintained in IMDM medium supplemented with 1% penicillin/streptomycin and L-glutamine and 10% FBS.

extract_protocol: K562 cells were harvested and total RNA was prepared using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA). A DNase I digestion step was included to eliminate DNA contamination.

treatment_protocol: K562 cells were treated with IST5-002 (5 µM) or vehicle (DMSO) for 48 h.  For Stat5 knockdown, K562 cells were infected with Stat5-shRNA lentivirus or scramble-shRNA lentivirus (as control) for 48 h followed by puromycin (2ug/ml) selection for 6 days to enrich for cells expressing Stat5 or scramble shRNA.

tag: cell ine

tag: shRNA


title: NA19312 Replicate 1

city: Farmington

last: Lee

address: 10 Discovery Dr.

institute: Jackson Laboratory for Genomic Medicine

hyb_protocol: Labeled samples were purified using Agilent SureTag Purification columns. Test and reference samples were combined with Agilent Oligo aCGH/ChIP-on-Chip Blocking Agent, Agilent Hi-RPM Hybridization Buffer and Cot-1 DNA and applied to microarrays enclosed in Agilent Hybridization Chamber. After 40 hour incubation at 67 °C, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 and 2.

scan_protocol: Slides were scanned on an Agilent G2505C scanner (version A.8.5.1).

label_protocol: 1 to 1.5 ug of genomic DNA was digested using AluI and RsaI for 2 hours at 37 °C followed by a 20 minute enzyme-inactivation step at 65 °C. DNA was then labeled with Cyanine-3-dUTP (Reference samples) or Cyanine-5-dUTP (Test samples) at 37 °C for 2 hours followed by a 10 minute enzyme-inactivation step at 65 °C.

tag: coriell cell line


title: D0-2

first: Sarah

description:
4h BaP Control Group (0mg/kg BW/day) Liver Replicate 2
Slide Barcode: 251486824086
Array Number (Postion): 1_1
Group: D0T1_Control_4h

tag: gender


title: D2-2

description:
4h BaP Dose Group 2 (150mg/kg BW/day) Liver Replicate 2
Slide Barcode: 251486824085
Array Number (Postion): 1_1
Group: D2T1_150mg_4h


title: D1-14

description:
24h BaP Dose Group 1 (300mg/kg BW/day) Liver Replicate 4
Slide Barcode: 251486824084
Array Number (Postion): 1_4
Group: D1T2_300mg_24h


title: D3-3

description:
4h BaP Dose Group 3 (50mg/kg BW/day) Liver Replicate 3
Slide Barcode: 251486824085
Array Number (Postion): 1_3
Group: D3T1_50mg_4h


title: NA19311 Replicate 1

first: Charles


title: D1-6

description:
4h BaP Dose Group 1 (300mg/kg BW/day) Liver Replicate 5
Slide Barcode: 251486824084
Array Number (Postion): 1_3
Group: D1T1_300mg_4h


title: D2-12

description:
24h BaP Dose Group 2 (150mg/kg BW/day) Liver Replicate 3
Slide Barcode: 251486824085
Array Number (Postion): 1_2
Group: D2T2_150mg_24h


title: NA19310 Replicate 1


title: Female, Kidney, 3 mg/kg-d, Replicate 4


title: Female, Kidney, 3 mg/kg-d, Replicate 2


title: Female, Kidney, 3 mg/kg-d, Replicate 3


title: IST5-002-2

tag: treatment


title: Female, Kidney, 3 mg/kg-d, Replicate 1


title: Female, Kidney, 0 mg/kg-d, Replicate 4


title: D0-14

description:
24h BaP Control Group (0mg/kg BW/day) Liver Replicate 5
Slide Barcode: 251486824084
Array Number (Postion): 1_2
Group: D0T2_Control_24h


title: CTRL-5

description: Control K562 cells treated with vehicle (DMSO) for 48 h

value: DMSO


title: IST5-002-1


title: D1-2

description:
4h BaP Dose Group 1 (300mg/kg BW/day) Liver Replicate 2
Slide Barcode: 251486824086
Array Number (Postion): 1_2
Group: D1T1_300mg_4h


title: D0-6

description:
4h BaP Control Group (0mg/kg BW/day) Liver Replicate 5
Slide Barcode: 251486824084
Array Number (Postion): 1_1
Group: D0T1_Control_4h


title: D3-1

description:
4h BaP Dose Group 3 (50mg/kg BW/day) Liver Replicate 1
Slide Barcode: 251486824064
Array Number (Postion): 1_3
Group: D3T1_50mg_4h


title: NA19308 Replicate 1


title: D2-3

description:
4h BaP Dose Group 2 (150mg/kg BW/day) Liver Replicate 3
Slide Barcode: 251486824064
Array Number (Postion): 1_2
Group: D2T1_150mg_4h


title: D4-3

description:
4h BaP Dose Group 4 (5mg/kg BW/day) Liver Replicate 3
Slide Barcode: 251486824064
Array Number (Postion): 1_4
Group: D4T1_5mg_4h


title: CTRL-3


title: CTRL-2


title: NA19307 Replicate 1


title: NA19309 Replicate 1


title: NA19257 Replicate 1


title: SHSTAT5-1

description: Stat5 knockdown K562 cells, infected with Stat5-shRNA lentivirus


title: NA19248 Replicate 1


title: NA19247 Replicate 1


title: Female, Kidney, 0 mg/kg-d, Replicate 2


title: D3-11

description:
24h BaP Dose Group 3 (50mg/kg BW/day) Liver Replicate 2
Slide Barcode: 251486824063
Array Number (Postion): 1_3
Group: D3T2_50mg_24h


title: SHSTAT5-3


title: SCRB-3

description: Stat5 control K562 cells, infected with scramble-shRNA lentivirus

value: scramble


title: Female, Kidney, 0 mg/kg-d, Replicate 3


title: SCRB-2


title: D1-11

description:
24h BaP Dose Group 1 (300mg/kg BW/day) Liver Replicate 3
Slide Barcode: 251486824063
Array Number (Postion): 1_2
Group: D1T2_300mg_24h

value: liver


title: D0-3

description:
4h BaP Control Group (0mg/kg BW/day) Liver Replicate 3
Slide Barcode: 251486824064
Array Number (Postion): 1_1
Group: D0T1_Control_4h


title: Female, Kidney, 0 mg/kg-d, Replicate 1

value: female


title: NA19240 Replicate 1


title: PCNSL#22

type: other

city: Cologne

first: Manuel

last: Montesinos-Rongen

state: NRW

address: Kerpenerstr. 62

department: Institute for Neuropathology

country: Germany

institute: University Hospital Cologne

hyb_protocol: standard manufacturer's protocol

scan_protocol: standard manufacturer's protocol

data_processing:
Prospector 5.2.1
Hit (see supplementary file): duplicates of the respective protein with an average Z-score > 3 and a coefficient of variation for the signals from the duplicates < 0.5.

molecule: other

source_name: PCNSL

label_protocol: standard manufacturer's protocol

extract_protocol: standard manufacturer's protocol

value: Primary lymphoma of the central nervous system


title: PCNSL#23


title: SHSTAT5-2


title: PCNSL#21


title: SCRB-1


title: control RNAi, luciferase siRNA, replicate 2

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description: SKmel147, control RNAi

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: R/bioconductor, RMA normalzation, default parameters

source_name: SKmel147 melanoma cell line

label_protocol: standard Affymetrix protocol

growth_protocol: SK-mel147 were grown in 15cm^2 cell culture dishes on DMEM media with 10%FBS and antibiotics. Melanocytes were cultured in Melanocyte Growth Media 254 supplemented with Human Melanocyte Growth Supplement (Life Technologies)

extract_protocol: RNA was isolated using RNAeasy kit (Qiagen).

treatment_protocol: Lentiviral plasmids encoding shRNAs against H2A.Z.1 and H2A.Z.2. sh_scrambled and sh_luciferase–expressing cells were used as controls.  Infections were performed using standard procedures (Kapoor et al., 2010).

tag: cell line

tag: RNAi

value: control (luciferase)


title: D0-12

description:
24h BaP Control Group (0mg/kg BW/day) Liver Replicate 4
Slide Barcode: 251486824063
Array Number (Postion): 1_1
Group: D0T2_Control_24h

source_name: Liver

tag: strain

value: Male

value: Universal Mouse Reference RNA [11 mouse cell lines]


title: D4-15

description:
24h BaP Dose Group 4 (5mg/kg BW/day) Liver Replicate 4
Slide Barcode: 251486824063
Array Number (Postion): 1_4
Group: D4T2_5mg_24h

value: 24 hour

source_name: Universal Mouse Reference RNA


title: Inflammation 14

description: inflammated oral sample

source_name: oral swab

label_protocol: Standard Illumina Protocol

tag: disease state

value: periodontitis


title: NA19239 Replicate 1


title: D2-1

description:
4h BaP Dose Group 2 (150mg/kg BW/day) Liver Replicate 1
Slide Barcode: 251486824062
Array Number (Postion): 1_2
Group: D2T1_150mg_4h

value: 4 hour


title: NA19238 Replicate 1


title: NA19236 Replicate 1


title: NA19225 Replicate 1


title: PCNSL#20


title: PCNSL#19


title: PCNSL#18


title: control RNAi, luciferase siRNA, replicate 1

description: SKmel147, control RNAi


title: D1-1

description:
4h BaP Dose Group 1 (300mg/kg BW/day) Liver Replicate 1
Slide Barcode: 251486824062
Array Number (Postion): 1_1
Group: D1T1_300mg_4h


title: D3-2

description:
4h BaP Dose Group 3 (50mg/kg BW/day) Liver Replicate 2
Slide Barcode: 251486824062
Array Number (Postion): 1_3
Group: D3T1_50mg_4h


title: D4-6

description:
4h BaP Dose Group 4 (5mg/kg BW/day) Liver Replicate 5
Slide Barcode: 251486824062
Array Number (Postion): 1_4
Group: D4T1_5mg_4h


title: D4-10

description:
24h BaP Dose Group 4 (5mg/kg BW/day) Liver Replicate 2
Slide Barcode: 251486824094
Array Number (Postion): 1_4
Group: D4T2_5mg_24h


title: H2AZ1 RNAi, sh_84 siRNA, replicate 2

description: SKmel147, H2AZ1 RNAi


title: NA19223 Replicate 1


title: H2AZ1 RNAi, sh_83 siRNA, replicate 2

description: SKmel147, H2AZ1 RNAi


title: PCNSL#14


title: D3-12

description:
24h BaP Dose Group 3 (50mg/kg BW/day) Liver Replicate 3
Slide Barcode: 251486824094
Array Number (Postion): 1_3
Group: D3T2_50mg_24h


title: PCNSL#15


title: PCNSL#17


title: NA19235 Replicate 1


title: PCNSL#16


title: H2AZ1 RNAi, sh_83 siRNA, replicate 1

description: SKmel147, H2AZ1 RNAi


title: H2AZ1 RNAi, sh_84 siRNA, replicate 1

description: SKmel147, H2AZ1 RNAi


title: D2-11

description:
24h BaP Dose Group 2 (150mg/kg BW/day) Liver Replicate 2
Slide Barcode: 251486824094
Array Number (Postion): 1_2
Group: D2T2_150mg_24h


title: H2AZ2 RNAi, sh_38 siRNA, replicate 1

description: SKmel147, H2AZ2 RNAi


title: NA19222 Replicate 1


title: D0-9

description:
24h BaP Control Group (0mg/kg BW/day) Liver Replicate 1
Slide Barcode: 251486824094
Array Number (Postion): 1_1
Group: D0T2_Control_24h


title: H2AZ2 RNAi, sh_38 siRNA, replicate 2

description: SKmel147, H2AZ2 RNAi


title: PCNSL#13


title: D4-9

description:
24h BaP Dose Group 4 (5mg/kg BW/day) Liver Replicate 1
Slide Barcode: 251486824074
Array Number (Postion): 1_4
Group: D4T2_5mg_24h


title: NA19214 Replicate 1


title: D2-14

description:
24h BaP Dose Group 2 (150mg/kg BW/day) Liver Replicate 4
Slide Barcode: 251486824074
Array Number (Postion): 1_3
Group: D2T2_150mg_24h


title: H2AZ2 RNAi, sh_37 siRNA, replicate 1

description: SKmel147, H2AZ2 RNAi


title: NA19256 Replicate 1


title: H2AZ2 RNAi, sh_37 siRNA, replicate 2

description: SKmel147, H2AZ2 RNAi


title: NA19210 Replicate 1


title: NA19209 Replicate 1


title: NA19213 Replicate 1


title: NA19207 Replicate 1


title: PCNSL#11


title: NA19206 Replicate 1


title: PCNSL#12


title: D1-9

description:
24h BaP Dose Group 1 (300mg/kg BW/day) Liver Replicate 1
Slide Barcode: 251486824074
Array Number (Postion): 1_2
Group: D1T2_300mg_24h


title: D4-5

description:
4h BaP Dose Group 4 (5mg/kg BW/day) Liver Replicate 4
Slide Barcode: 251486824073
Array Number (Postion): 1_4
Group: D4T1_5mg_4h


title: PCNSL#10


title: D2-6

description:
4h BaP Dose Group 2 (150mg/kg BW/day) Liver Replicate 5
Slide Barcode: 251486824073
Array Number (Postion): 1_3
Group: D2T1_150mg_4h


title: PCNSL#07


title: NA19204 Replicate 1


title: PCNSL#09


title: 8HR_novirus_Silymarin_2

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Array Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/members/core-services.html).

data_processing: RMA normalization log2 at the transcript level using the oligo package of Bioconductor.

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Human Gene 1.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit (#74104) following the manufacturer's instructions.

treatment_protocol: Human hepatoma Huh7.5.1 cells were treated with silymarin or DMSO solvent for varying times (4hr, 8hr, 24hr).

value: hepatoma cells

value: silymarin

tag: time point


title: control RNAi, scrambled siRNA, replicate 2

description: SKmel147, control RNAi

value: control (scrambled)


title: control RNAi, scrambled siRNA, replicate 1

description: SKmel147, control RNAi


title: 8HR_novirus_Silymarin_3


title: D0-1

description:
4h BaP Control Group (0mg/kg BW/day) Liver Replicate 1
Slide Barcode: 251486824073
Array Number (Postion): 1_1
Group: D0T1_Control_4h


title: D1-5

description:
4h BaP Dose Group 1 (300mg/kg BW/day) Liver Replicate 4
Slide Barcode: 251486824073
Array Number (Postion): 1_2
Group: D1T1_300mg_4h


title: 8HR_novirus_DMSO_2


title: D3-10

description:
24h BaP Dose Group 3 (50mg/kg BW/day) Liver Replicate 1
Slide Barcode: 251486824072
Array Number (Postion): 1_4
Group: D3T2_50mg_24h


title: NA19200 Replicate 1


title: 4HR_novirus_DMSO_4


title: PCNSL#06


title: PCNSL#05


title: D2-10

description:
24h BaP Dose Group 2 (150mg/kg BW/day) Liver Replicate 1
Slide Barcode: 251486824072
Array Number (Postion): 1_3
Group: D2T2_150mg_24h


title: PCNSL#08


title: PCNSL#04


title: PCNSL#03


title: 4HR_novirus_DMSO_3


title: D1-10

description:
24h BaP Dose Group 1 (300mg/kg BW/day) Liver Replicate 2
Slide Barcode: 251486824072
Array Number (Postion): 1_2
Group: D1T2_300mg_24h


title: 24HR_novirus_Silymarin_1


title: 8HR_novirus_DMSO_1


title: NA19190 Replicate 1


title: NA19201 Replicate 1


title: NA19185 Replicate 1


title: 8HR_novirus_Silymarin_1


title: 24HR_novirus_DMSO_5


title: PCNSL#02


title: D0-11

description:
24h BaP Control Group (0mg/kg BW/day) Liver Replicate 3
Slide Barcode: 251486824072
Array Number (Postion): 1_1
Group: D0T2_Control_24h


title: PCNSL#01


title: NA19189 Replicate 1


title: NA19175 Replicate 1


title: NA19198 Replicate 1


title: 4HR_novirus_DMSO_1


title: NA19172 Replicate 1


title: 8HR_novirus_DMSO_5


title: 24HR_novirus_DMSO_4


title: 4HR_novirus_Silymarin_4


title: NA19160 Replicate 1


title: NA19184 Replicate 1


title: NA19159 Replicate 1


title: NA19197 Replicate 1


title: NA19153 Replicate 1


title: Water avoidance stres rep 4

city: Los Angeles

first: Sylvie

last: Bradesi

address: 10833 Le Conte Avenue

department: Digestive Diseases

institute: UCLA

hyb_protocol: miRCURY standard protocol

scan_protocol: miRCURY standard protocol

data_processing: miRCURY standard protocol

organism: Rattus norvegicus

source_name: spinal cord, control

label_protocol: miRCURY standard protocol

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN) following the manufacturer's recommendations.. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: spinal cord

value: control

value: male

tag: age

value: 12 weeks old


title: Water avoidance stress rep2


title: NA19152 Replicate 1


title: NA19171 Replicate 1


title: SHR_E16.0_kidney2 [gene-level]

city: Berlin

first: Reinhold

last: Kreutz

address: Charitéplatz 1

institute: Charité

description: LEO-MWF-18-Leo_301-220212-RatGe-St1-0.CEL

hyb_protocol: Arrays were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G using GeneChip® Operating Software (GCOS) for image processing

data_processing:
After normalization the arrays have been checked for outliers by principal component analysis (PCA), using a correlation dispersion matrix and normalized Eigenvector scaling. The analysis of differential expression of summarized gene level expression has been performed with Partek Genomic Suite version 6.5
RaGene-1_0-st-v1.r4.pgf
RaGene-1_0-st-v1.r4.mps

source_name: SHR-E16.0 kidney

label_protocol: Terminal labeling kits (Ambion, New-York, USA)

growth_protocol: Rat embryonic kidney dissected at day E15.5/E16.0 respectively

extract_protocol: embryonic kidneys were harvested, snap-frozen in liquid nitrogen and stored at -80°C. Total RNA preparations of male kidney tissues were performed for MWF rats at developmental stage E15.5 and SHRs at E16.0 (n=4) using the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The quality and concentration of the purified total RNA were confirmed by spectroscopy.

treatment_protocol: not applicable

value: SHR

value: kidney


title: SHR_E16.0_kidney4 [gene-level]

description: LEO-MWF-20-SHR_E16_022-220212-RatGe-St1-0.CEL


title: SHR_E16.0_kidney1 [gene-level]

description: LEO-MWF-17-Leo_264-220212-RatGe-St1-0.CEL


title: NA19149 Replicate 1

treatment_protocol: We, nor Coriell, did not perform any treatment on the samples. We received DNA samples from Coriell.


title: Water avoidance stress rep1


title: 4HR_novirus_DMSO_2

value: DMSO


title: MWF_E15.5_kidney4 [gene-level]

description: LEO-MWF-04-Leo_363-220212-RatGe-St1-0.CEL

source_name: MWF-E15.5 kidney

value: MWF


title: 24HR_novirus_DMSO_3


title: MWF_E15.5_kidney1 [gene-level]

description: LEO-MWF-01-Leo_58-220212-RatGe-St1-0.CEL


title: MWF_E15.5_kidney3 [gene-level]

description: LEO-MWF-03-Leo_242-220212-RatGe-St1-0.CEL


title: 4HR_novirus_Silymarin_2


title: NA19147 Replicate 1


title: 8HR_novirus_DMSO_3


title: NA19146 Replicate 1


title: 24HR_novirus_Silymarin_3


title: 8HR_novirus_DMSO_4


title: NA19144 Replicate 1


title: Control rep4

source_name: spinal cord, stress

value: stress


title: 4HR_novirus_Silymarin_3


title: MWF_E15.5_kidney2 [gene-level]

description: LEO-MWF-02-Leo_160-220212-RatGe-St1-0.CEL


title: Control rep3


title: Control rep2


title: Control rep1


title: 24HR_novirus_DMSO_2


title: 4HR_novirus_Silymarin_1


title: 24HR_novirus_DMSO_1


title: Mesenchymal stromal cell, healthy donor, sample MH

status: Public on Jun 30 2015

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing: Microarray data were normalized using the Cubic Spline normalization method with the Illumina BeadStudio Gene Expression Module (Illumina). Statistical analysis of microarray was performed using Significance Analysis for Microarrays (SAM)

source_name: Healthy donor MSC

label_protocol: As per manufacturer's instructions.

growth_protocol: Bone marrow derived mononuclear cells were obtained from 5 to 15 ml of heparinized bone marrow aspirate by density gradient centrifugation on Ficoll. Cells were plated on non-coated 75 cm2 polystyrene flasks at a cell density of 160000/cm2 in complete culture medium (LG-DMEM [Invitrogen, Paisley, United Kingdom] supplemented with penicillin and streptomycin [merk] and 10% fetal bovine serum [FBS; HyClone, Verviers, Belgium]). We used a characterized and defined FBS batch preselected for its potential to support MSC expansion and continued to use this specific batch throughout the culture period.

extract_protocol: RNA was isolated from frozen cell pellets of at least 1*10e6 undifferentiated mesenchymal stem cells at passage 2 to 5 using TRIzol reagent (Invitrogen). Cells were lysed in TRIzol, followed by phase separation in chloroform (merk), precipitation using 2-propanolol (merk) and washing in 75% ethanol. RNA clean-up was performed using the Qiagen Rneasy mini kit with on-column DNAse treatment. RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer and Nanodrop ND-1000, respectively.

value: Mesenchymal stromal cells


title: Mesenchymal stromal cell, healthy donor, sample HD5


title: Mesenchymal stromal cell, healthy donor, sample TD001

value: female


title: Mesenchymal stromal cell, osteosarcoma patient, sample 008

source_name: Osteosarcoma patient MSC


title: Mesenchymal stromal cell, osteosarcoma patient, sample 009


title: Mesenchymal stromal cell, osteosarcoma patient, sample 003


title: Mesenchymal stromal cell, healthy donor, sample HD3


title: Mesenchymal stromal cell, osteosarcoma patient, sample 004


title: Mesenchymal stromal cell, osteosarcoma patient, sample 001


title: Mesenchymal stromal cell, osteosarcoma patient, sample 002


title: 24HR_novirus_Silymarin_2