title: CON19

value: 34 yr


title: SZ5

status: Public on Oct 11 2014

type: RNA

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

hyb_protocol: Agilent Technologies' manufacturer procedures.

scan_protocol: Slides were scanned with the Agilent Bundle Microarray Scanner System (Agilent Technologies) and data were processed using the Feature Extraction 10.7.3.1 software (Agilent Technologies).

data_processing: Among the 45,015 spots present in each array, only those with none flag for quality control (i.e., low intensity, saturation, controls, etc.) were selected for analysis. For analysis of replicate spots, the average intensity after background correction was calculated, normalization was performed using locally weighted linear regression (LOWESS) with α=0.2 within slides using the R software version 2.11.1 (R Development Core Team, 2010) and Linear Models for Microarray (LIMMA) from Bioconductor.

molecule: total RNA

organism: Homo sapiens

source_name: frontal cortex, schizophrenia

growth_protocol: Frozen tissue.

extract_protocol:
Total RNA was isolated using TRIzol (Sigma) according to the manufacturer's instructions.
RNA concentration was determined by spectrophotometry (NanoDrop, Thermo Scientific, US), and integrity was assessed using the 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: tissue

value: brain (frontal cortex)

tag: disease state

value: schizophrenia

tag: age

value: 47 yr

tag: population

value: white

tag: dsm-iv

tag: age of onset

value: 20 yr

source_name: Reference

tag: sample type

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: CON20

source_name: frontal cortex, healthy control

label_protocol: Agilent Technologies' manufacturer procedures.

value: healthy control

value: 42 yr


title: CON25

value: 49 yr


title: CON29

value: 48 yr


title: CON31

value: 55 yr


title: SZ6

value: 24 yr


title: CON26

value: 35 yr


title: CON22

value: 41 yr


title: CON30


title: SZ2

value: 44 yr

value: 16 yr


title: SZ1

value: 40 yr

value: 21 yr


title: SZ3

value: brain (frontal cortex)

value: schizophrenia

value: 31 yr

value: 22 yr


title: SZ4

value: 38 yr

value: Hispanic

value: 17 yr

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: CON27

value: healthy control

value: 47 yr

value: white


title: CON18


title: CON16

value: 45 yr


title: CON9

value: 39 yr


title: CON14

value: 60 yr


title: Schiz29

value: 59 yr

value: 14 yr

tag: gender

value: male


title: CON13

value: brain (frontal cortex)


title: BP27

source_name: frontal cortex, bipolar disorder

value: bipolar disorder

value: 48 yr


title: CON4

value: 51 yr


title: CON17

value: 35 yr


title: CON15


title: CON11

value: 53 yr


title: CON8

value: 31 yr


title: CON12

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: BP28

value: 21 yr


title: CON5

value: healthy control

value: 33 yr


title: BP26

value: 29 yr

value: white

value: 17 yr


title: CON7

value: 40 yr


title: CON3

value: 46 yr


title: BP24

value: 50 yr

value: 25 yr


title: BP23

value: brain (frontal cortex)

value: bipolar disorder

value: 43 yr


title: BP29

value: 15 yr


title: BP25

value: 56 yr

value: 28 yr


title: CON1

value: 34 yr

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: BP22

value: 44 yr

value: 26 yr


title: BP19

value: 35 yr

value: 19 yr


title: BP18

value: 42 yr

value: white

value: 18 yr


title: BP21

value: 38 yr


title: BP20

value: 14 yr


title: CON2

value: brain (frontal cortex)

value: healthy control


title: CON6

value: 48 yr


title: BP17

value: bipolar disorder

value: 33 yr


title: BP15

value: 29 yr


title: BP16


title: BP14

value: 41 yr

value: Native American

value: 22 yr


title: BP12

value: 47 yr

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: BP13

value: 45 yr

value: 35 yr


title: BP7

value: 59 yr

value: white

value: 25 yr


title: BP11

value: 31 yr


title: BP8

value: brain (frontal cortex)

value: 51 yr

value: 23 yr


title: TAp73-/- untreated_rep1

city: Singapore

first: Kanaga

last: Sabapathy

state: Singapore

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

description: TA-KO-Hyp 0h 1.AVG_Signal

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Partek Genomic Suites Version 6.6

label: biotin

organism: Mus musculus

source_name: MEF_TAp73-/- untreated

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

growth_protocol: Cells were grown in 10% serum containing DMEM medium in 5%CO2 and 21% oxygen

extract_protocol: All samples were snap frozen in liquid N2. Total RNA was extracted from all samples using Trizol and further purified by RNeasy RNA extraction kit (Qiagen)

treatment_protocol: 1% oxygen (hypoxia) for 4 or 8 hrs

tag: cell type

value: mouse embryo fibroblast (MEF)

tag: genotype/variation

tag: culture condition

value: untreated (normal condition)

tag: time point

value: 0 hr


title: TAp73-/- hypoxia_8hr_rep2

description: TA-KO-Hyp 8h 2.AVG_Signal

source_name: MEF_TAp73-/- hypoxia_8hr

value: hypoxia (incubated in 1% O2)

value: 8 hr


title: TAp73-/- hypoxia_4hr_rep1

description: TA-KO-Hyp 4h 1.AVG_Signal

source_name: MEF_TAp73-/- hypoxia_4hr

value: 4 hr


title: TAp73-/- hypoxia_4hr_rep2

description: TA-KO-Hyp 4h 2.AVG_Signal


title: T3 leg disc CTCF-ChIP Rep 2

type: genomic

city: Cambridge

first: Robert

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

description:
T3_CTCF.txt
T_3CTPRE.window_scores.sgr

hyb_protocol: Resuspend samples in 12.3 µl water.  For each hybridisation, combine 29.5µl 2X Hybridization Buffer, 11.8µl Hybridization Component A and 1.2µl Alignment Oligo (NimbleGen Hybridization Kit) and add 31.7µl to each hybridisation sample. Incubate samples at 95°C for 5 minutes, 42°C for 5 minutes and load 41 µl onto the array. The hybridisation is 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 16 hours. Perform post hybridisation washes 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:
The scanned images were processed using NimbleScan software to generate pair files which were then converted to chromatin enrichment profiles using the TiMAT pipeline (http://bdtnp.lbl.gov/TiMAT/). Samples were median scaled at 500, quantile normalised (ChIP and Pre-immune ChIP samples together), window smoothed using a window size of 500 bp and a minimum number of oligos per window of 4.
quantile normalised log2 ratio (sample/control)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Leg 3 CTCF Rep 2

label_protocol: 5 µl each of CTCF-ChIP and control ChIP DNA from T1 and T3 leg discs obtained from Oregon R larvae were amplified using GenomePlex Single Cell Whole Genome Amplification Kit (Sigma-Aldrich WGA4) according to manufacturer’s instructions. The samples were amplified for 21 cycles and the amplified DNA purified using the QIAquick PCR Purification Kit. In duplicate reactions: 1 μg of amplified DNA with 30 µl 2.5X Random Primers Solution (BioPrime DNA labelling kit, Life Technologies) was incubated at 100°C for 5 minutes and then cooled on ice. The samples were labelled as technical dye-swap replicates using the BioPrime DNA labelling kit (Life Technologies) in the presence of 4.5nmol fluorescently labelled Cy3- or Cy5-dCTP (GE Healthcare) and 72 U of Klenow at 37°C. After 2 hours the reactions were stopped with 7.5 µl Stop Buffer (BioPrime DNA labelling kit, Life Technologies). Duplicate reactions were pooled into single tubes and then precipitated with 165 µl Isopropanol and 0.2M sodium chloride and washed with cold 80% ethanol. The DNA was resuspened in 50 µl water and quantified on a Nanodrop spectrophotometer (Thermo Scientific).

growth_protocol: Flies were grown on standard medium at 18°C.

extract_protocol: Chromatin immunopurification was performed as described by Birch-Machin (2005). 100 µl aliquots of chromatin were pre-cleared with 13 µl blocked S. aureus cells (SAC) and mixed with 200 µl of IP dilution buffer (16.7mM Tris.HCl pH 8, 167mM NaCl, 1% EDTA, 1.1% Triton X-100, 0.01% SDS) with protease inhibitors. 2 µl of antibody was added and incubated on a roller overnight at 4°C. Then 13 µl of SAC was added to each IP reaction and the samples were incubated for 35 min at 4°C on a roller. The mixture was centrifuged in a microfuge at 13,200 rpm at room temperature and the pellets were washed successively with 1 ml each of Low Salt Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA. Na2 pH 8.0, 20 mM Tris.HCl pH 8, 150 mM NaCl), High Salt Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA.Na2 pH8, 20 mM Tris.HCl pH 8, 500mM NaCl), LiCl Buffer (0.25 M LiCl, 1% NP40, 1% NaDeoxycholate, 1 mM EDTA. Na2 pH 8.0, 10 mM Tris.HCl pH 8.0) and twice with TE buffer pH 8.0, for 5 min at 4°C on roller for each solution. The immune-precipitated chromatin was then eluted twice from the SAC pellet with 300 μl of IP elution buffer (50 mM NaHCO3, 1% SDS) by vigorously vortexing for 15 min at room temperature. One μl of RNase A (Sigma, R4642) and 24.3 μl of 4M NaCl (0.3 M final concentration) were then added to the eluate and the mixture was incubated for 4h at 65°C, to reverse the cross-linking. The DNA was then precipitated by adding 812 μl of 100% ethanol and incubating overnight at -20°C. The samples were centrifuged in a microfuge at 4°C for 20 min and the pellets were air dried for 1 h at room temperature. The pellets were resuspended in 100 μl TE buffer followed by the addition of 25 μl of 5X PK buffer (50 mM Tris HCl pH 7.5, 25 mM EDTA.Na2 pH 8, 1.25% SDS) and 1.5 μl of 20 mg/mL Proteinase K, incubated at 45°C for 2 h and purified using the QIAquick PCR Purification Kit (Qiagen, 28104). The DNA was eluted in 30 μl of buffer EB and stored at -20°C until use.

treatment_protocol: Dissected head segments of late 3rd instar larvae were inverted and fixed with 2% formaldehyde in PBS for 20 min at room temperature. These were washed with twice with PBS/125 mM Glycine/0.01% Triton X-100 followed by a single wash with PBS and then with PBS containing 1% protease inhibitor cocktail (Sigma, P8340). The T1 and T3 leg imaginal discs were then dissected, snap frozen in liquid nitrogen and stored at -80°C prior to use. Approximately 150 leg discs were combined in PBS/0.01% Triton X-100 and centrifuged in a microfuge at 1200 rpm for 1 min. The discs were resuspended in 20 μl cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) containing 1% protease inhibitor cocktail and homogenised using a motorised pestle at 2 min intervals for 8 min. After a brief microfuge centrifugation (13,200 rpm, 10 sec), the pellet was resuspended in 300 µl Nuclear Lysis Buffer (50 mM Tris.HCl pH 8.1, 10 mM EDTA.Na2, 1% SDS) with protease inhibitors and incubated for 20 min at room temperature. The extracts were sonicated in a Bioruptor (Diagenode) at high setting for 4 min 15 sec (30 sec “ON”, 30 sec “OFF” cycle), producing 0.5 to 3.0 kb sized fragments. 100 μl aliquots of chromatin extracts were flash frozen in liquid nitrogen and then stored at -80°C prior to use.

tag: Stage

value: late 3rd instar larva

tag: strain

value: Oregon-R

tag: chip antibody

value: anti-CTCF-C1 (Holohan et al., 2007 Plos Genet 3:e112. doi:10.1371/journal.pgen.0030112.)

source_name: Leg 3 Preimmune Rep 2

value: pre-immune serum  (Holohan et al., 2007 Plos Genet 3:e112. doi:10.1371/journal.pgen.0030112.)


title: BP10

value: bipolar disorder

value: 41 yr

value: 14 yr

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: TAp73-/- untreated_rep2

description: TA-KO-Hyp 0h 2.AVG_Signal


title: TAp73+/+ hypoxia_8hr_rep1

description: TA-WT-Hyp 8h 1.AVG_Signal

source_name: MEF_TAp73+/+ hypoxia_8hr


title: BP5

value: brain (frontal cortex)

value: 63 yr

value: white

value: 43 yr


title: TAp73-/- hypoxia_8hr_rep1

description: TA-KO-Hyp 8h 1.AVG_Signal

value: mouse embryo fibroblast (MEF)


title: BP6

value: 64 yr

value: 19 yr


title: T3 leg disc CTCF-ChIP Rep 1

description:
T3_CTCF.txt
T_3CTPRE.window_scores.sgr

source_name: Leg 3 Preimmune Rep 1

source_name: Leg 3 CTCF Rep 1


title: TAp73+/+ hypoxia_4hr_rep1

description: TA-WT-Hyp 4h 1.AVG_Signal

source_name: MEF_TAp73+/+ hypoxia_4hr

value: hypoxia (incubated in 1% O2)


title: PFR40_EEmb_HPL2

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St.

department: Molecular, Cell, and Developmental Biology

country: USA

institute: UC Santa Cruz

description: ChIP-chip of HPL-2 in PFR40 early embryos

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays Users Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing: The log2-ratio ratio of intensity from sample/reference channel was standardized to obtain z-scores.   Signal was lifted from ce4 to ce10 using the liftOver tool found at the UCSC Genome Browser website (http://hgdownload.cse.ucsc.edu/admin/exe/).

organism: Caenorhabditis elegans

source_name: HPL-2 ChIP DNA for PFR40 EEmb

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays Users Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

growth_protocol: Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Embryos were then frozen in liquid nitrogen.

extract_protocol: Worm_popcorn_chromatin_extract_protocol_vSS1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in a Diagenode Bioruptor (40 pulses of 30 seconds with 1 minute rests in between at full power). Extracts are then spun down and the soluble fraction is stored for quality tests and future ChIP.  Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 μl of protein A dynabeads (Dyna), and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 μL elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Qiagen PCR purification columns.

tag: developmental stage

value: Early Embryo

tag: genotype

value: HPL-2 SDI Q2324

tag: Sex

value: population predominantly Hermaphrodites perhaps with some Males

source_name: Input DNA for PFR40 EEmb

value: input DNA


title: N2_EEmb_HPL2_rep3

description: ChIP-chip of HPL-2 in N2 early embryos

data_processing: The log2-ratio ratio of intensity from sample/reference channel was standardized to obtain z-scores for each replicate; the average z-score in regions not bound by HPL-2 (determined using MA2C with an FDR of 1%) in either wild-type or GW638 extracts was used to center the z-scores, and the variance of these z-scores was used to scale the z-scores.   Signal was lifted from ce4 to ce10 using the liftOver tool found at the UCSC Genome Browser website (http://hgdownload.cse.ucsc.edu/admin/exe/).

source_name: HPL-2 ChIP DNA for N2 EEmb

value: wild type

source_name: Input DNA for N2 EEmb

value: none, Input DNA


title: BP3

tag: tissue

tag: disease state

value: bipolar disorder

value: 54 yr

value: 45 yr


title: BP9

value: brain (frontal cortex)

tag: age

value: 49 yr

tag: population

value: 20 yr

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: BP4

value: 42 yr

value: white

tag: dsm-iv

tag: age of onset


title: T1 leg disc CTCF-ChIP Rep_1

description:
T1_CTCF.txt
T_1CTPRE.window_scores.sgr

source_name: Leg 1 Preimmune Rep 1

value: late 3rd instar larva

value: Oregon-R

value: pre-immune serum  (Holohan et al., 2007 Plos Genet 3:e112. doi:10.1371/journal.pgen.0030112.)

source_name: Leg 1 CTCF Rep 1

value: anti-CTCF-C1 (Holohan et al., 2007 Plos Genet 3:e112. doi:10.1371/journal.pgen.0030112.)


title: TAp73+/+ hypoxia_8hr_rep2

description: TA-WT-Hyp 8h 2.AVG_Signal

value: mouse embryo fibroblast (MEF)

value: hypoxia (incubated in 1% O2)

value: 8 hr


title: TAp73+/+ untreated_rep2

description: TA-WT-Hyp 0h 2.AVG_Signal

source_name: MEF_TAp73+/+ untreated

value: untreated (normal condition)

value: 0 hr


title: N2_EEmb_HPL2_rep2

description: ChIP-chip of HPL-2 in N2 early embryos

value: Early Embryo

value: wild type

value: HPL-2 SDI Q2324

value: population predominantly Hermaphrodites perhaps with some Males

tag: sample type

value: none, Input DNA


title: N2_EEmb_HPL2_rep1

description: ChIP-chip of HPL-2 in N2 early embryos


title: GW638_MxEmb_HPL2_rep1

description: ChIP-chip of HPL-2 in met-2 set-25 mixed-stage embryos

data_processing: The log2-ratio ratio of intensity from sample/reference channel was standardized to obtain z-scores for each replicate; the average z-score in regions not bound by HPL-2 (determined using MA2C with an FDR of 1%) in either wild-type or GW638 extracts was used to center the z-scores, and the variance of these z-scores was used to scale the z-scores.  Signal was lifted from ce4 to ce10 using the liftOver tool found at the UCSC Genome Browser website (http://hgdownload.cse.ucsc.edu/admin/exe/)

source_name: HPL-2 ChIP DNA for met-2 set-25 MxEmb

extract_protocol: Worm_popcorn_chromatin_extract_protocol_vSS1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in a Diagenode Bioruptor (40 pulses of 30 seconds with 1 minute rests in between at full power). Extracts are then spun down and the soluble fraction is stored for quality tests and future ChIP.  Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4C) with 50 μl of protein A dynabeads (Dyna), and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 μL elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Qiagen PCR purification columns.

value: Mixed-stage Embryo

source_name: Input DNA for met-2 set-25 MxEmb

value: input DNA


title: BP1

source_name: frontal cortex, bipolar disorder

value: brain (frontal cortex)

value: bipolar disorder

value: 29 yr

value: white

value: 22 yr

source_name: Reference

value: pool of total RNAs extracted from 15 distinct human cell lines (in-house)


title: BP2

value: 58 yr

value: 27 yr


title: TAp73+/+ hypoxia_4hr_rep2

description: TA-WT-Hyp 4h 2.AVG_Signal

tag: cell type

value: mouse embryo fibroblast (MEF)

value: hypoxia (incubated in 1% O2)

value: 4 hr


title: TAp73+/+ untreated_rep1

description: TA-WT-Hyp 0h 1.AVG_Signal

tag: genotype/variation

value: untreated (normal condition)

value: 0 hr


title: PFR40 early embryo rep 3

description: expression profiling in PFR40 (hpl-2) mutant early embryo

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

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

data_processing: The raw data (.pair file) was subjected to quantile normalization (Bolstad et al. Bioinformatics 19(2):185).

source_name: PFR40 hpl-2(tm1489) early embryo

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

extract_protocol: RNA was isolated from early embryos using Trizol and purified using the RNeasy kit (Qiagen, catalog 74104). Samples were analyzed on an Agilent Bioanalyzer to ensure that rRNAs were not degraded and that RNA was free of protein and DNA contamination. The samples were treated with DNase for 30min at room temperature.

tag: gender

value: hermaphrodites, with a small percentage of males

value: PFR40 hpl-2(tm1489) mutant

value: early embryo


title: T1 leg disc CTCF-ChIP Rep_2

description:
T1_CTCF.txt
T_1CTPRE.window_scores.sgr

source_name: Leg 1 CTCF Rep 2

value: late 3rd instar larva

value: Oregon-R

value: anti-CTCF-C1 (Holohan et al., 2007 Plos Genet 3:e112. doi:10.1371/journal.pgen.0030112.)

source_name: Leg 1 Preimmune Rep 2

value: pre-immune serum  (Holohan et al., 2007 Plos Genet 3:e112. doi:10.1371/journal.pgen.0030112.)


title: GW638_MxEmb_HPL2_rep2

value: Mixed-stage Embryo

value: HPL-2 SDI Q2324

value: population predominantly Hermaphrodites perhaps with some Males

value: input DNA


title: PFR40 early embryo rep 4


title: MEFs_FL-NELF-B_rep1

city: San Antonio

first: Haihui

last: Pan

state: Texas

address: 8403 Floyd Curl Dr.

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

hyb_protocol: standard Illumina protocol for MouseRef-8 version 2.0, Illumina

scan_protocol: BeadChips were scanned on a BeadArrayTM Reader (Illumina) using BeadScan software (version 3.2, Illumina)

data_processing: the scanned data were uploaded into GenomeStudio® software (version 1.1, Illumina) via the gene expression module (Direct Hyb).

label: Biotin

label_protocol: TotalPrepTM RNA amplification kit (Ambion, Cat. #AMIL1791)

growth_protocol: 10% FBS in DMEM, 50% confluence, routine cell culture condition

extract_protocol: miRNeasy mini kit (Qiagen, Cat. #217004)

tag: condition

value: 10% FBS, 50% confluence

value: MEF

value: full length NELF-B

tag: genetic background


title: PFR40 early embryo rep 1


title: KO-naive

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

description: gene expression profiles in CD8+ T cells from nonimmunized spleens (0 day) of TCRgag miR-150−/−

hyb_protocol: cRNAs were fragmented and then applied directly onto an assembled SurePrint G3 Mouse GE 8x60K Microarray (G4852A; 028005). The arrays were hybridized at 65°C for 17 h in an Agilent hybridization oven.

scan_protocol: The hybridized microarrays were washed as per the manufacturer’s protocol (Agilent Technology), and hybridization images were analyzed with an Agilent DNA Microarray Scanner.

data_processing: The mean fluorescence intensity for each spot was calculated, and the local background was subtracted using the Agilent Feature Extraction software package. All data normalization and the selection of up- and downregulated genes were performed using GeneSpring GX 7.3 (Agilent Technology).

label_protocol: The synthesis of fluorescent target cRNAs and hybridizations were performed using the Low RNA Input Linear Amplification Kit PLUS (Agilent Technology), according to the manufacturer’s instructions.

growth_protocol: Thy1.1+ CD8+ T cells were purified from spleens of TCRgag miR-150+/+ and TCRgag miR-150−/−. Equivalent numbers of each type of donor cell were transferred into Thy1.2+ B6 recipients, followed by i.p. infection one day later with Listeria monocytogenes for immunization. In details, Listeria monocytogenes strains expressing the FMuLV GAG epitope (CCLCLTVFL) (LM-GAG) or a control vector (LM-Ø).

extract_protocol: Total RNA from the T cells was extracted using the TRIZOL reagent (Gibco BRL, Rockville, MD, USA), according to the manufacturer’s instructions. RNA was treated with RNase-free DNase I (Promega, Madison, WI, USA) to reduce DNA contamination.

treatment_protocol: Naïve CD8 T cells were prepared from nonimmunized spleen and other cells were harvested at the times (5 days for effector cells; 60 days for memory cells) after immunization and finally analyzed by microarray.

tag: type

value: T cells

value: mir-150 knockout

tag: day

value: 0 day


title: MEFs_FL-NELF-B_rep2


title: PFR40 early embryo rep 2

value: hermaphrodites, with a small percentage of males


title: Maxillary process ectoderm at E12.5, biological rep 1

status: Public on Oct 10 2014

city: Aurora

first: Joan

last: Hooper

state: CO

department: Cell and Developmental Biology

institute: University of Colorado School of Medicine

description:
fxe1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos

hyb_protocol: Hybridization occurs at 45 °C for 17 hours using a GeneChip® Hybridization Oven 640 (Affymetrix). After hybridization, the hybridization solutions are removed and the arrays are washed and stained with Streptavidin-phycoerythrin using a GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays are read at a resolution of 2.5 to 3 microns using the GeneChip Scanner 3000 (Affymetrix).

data_processing:
Data were processed using Affymetrix Power Tools (apt-probeset-summarize, v 1.91) to normalize (Robust Multi-array Average; RMA) and summarize probeset expression levels (log2), and for DABG (detected above background at p > 0.05), and used MoGene-1_0-st-v1.na31.mm9.transcript.csv annotation file.
MoGene-1_0-st-v1.na32.mm9.probeset.csv
MoGene-1_0-st-v1.na31.mm9.transcript.csv

source_name: C57BL6/J, maxillary process ectoderm

label_protocol: Per Affymetrixsrecommended protocol, 100 to 150ng of starting total RNA was converted to cDNA with the Ambion WT Expression kit, following the manufacturer’s protocol. In vitro transcription is than performed using the same kit to generate cRNA. The cRNA was again converted to first-strand cDNA in secong cycle.  The cDNA was then fragmented and end-labeled with biotin using GeneChip® WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Facial prominences dissected from indicated age mouse embryos.

extract_protocol: Ectoderm was separated from mesenchyme by 'peeling' following Disapse II digestion (15 min @ 37oC).  Dissected tissue was frozen, then pooled. Total RNA was extracted withTrizol and purified with the RNAeasy MiniKit.

tag: strain

value: maxillary process ectoderm

value: inbred wild-type


title: KO-memory_1

description: gene expression profiles in CD8+ T cells from spleens (harvested times, 60 days for memory cells) of TCRgag miR-150−/−

tag: genotype

value: 60 days


title: WT-naive

description: gene expression profiles in CD8+ T cells from nonimmunized spleens (0 day) of TCRgag miR-150+/+

value: wild type


title: MEFs_FL-NELF-B_rep3


title: MEFs_ATG-NELF-B_rep2

value: truncated NELF-B


title: MEFs_ATG-NELF-B_rep3


title: 10 µM AlCl3 pH5.0_6hrs vs. noAlCl3 pH5.0_6hrs_rep2

city: Gifu

first: Mutsutomo

last: Tokizawa

address: yanagido 1-1

department: Faculty of Applied Biological Sciences

country: Japan

institute: Gifu University

description: Biological replicate 2 of 2.

hyb_protocol: 0.825 micro g of Cy3- and Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5 per micro g cRNA) were fragmented with Gene Expression Hybridization Kit (5188-5242, Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 micro litter of 2x GE hybridization buffer HI-PRM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis 3 Oligo Microarray (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Scanned on the Agilent G2508B scanner

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: 10 µM AlCl3 pH5.0　6hrs

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA were prepared from 1 micro g of total RNA using the Two-Color Quick Amp Labeling kit (5190-0444, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: Arabidopsis were grown hydroponically in the 2% modified MGRL solution  (0 µM AlCl3, pH 5.5, 2% MGRL containing 200 µM CaCl2)  for 10 days. All seedlings were kept under 12 h illuminations per day (30 µmol m–2 s–1) at 23°C .

extract_protocol: Total RNA was isolated by Sepasol®-RNA I Super G following manufactures instruction (Nacalai Tesque, Kyoto, Japana).

treatment_protocol: Root of the seedlings were exposed to toxic solutions containing 10 µM Al (pH5.0) or　Control (no Al at pH 5.0) for 6 hrs at growth conditions.

tag: ecotype

value: root

source_name: noAl pH5.0　6hrs


title: KO-memory_2

source_name: CD8+ T cells from spleens (harvested times, 60 days for memory cells) of TCRgag miR-150−/−


title: Maxillary process mesenchyme at E12.5, biological rep 3

description:
fxm3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos

source_name: C57BL6/J, maxillary process mesenchyme

tag: tissue

value: maxillary process mesenchyme


title: MEFs_ATG-NELF-B_rep1


title: Maxillary process ectoderm at E12.5, biological rep 2

description:
fxe2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: WT-effector

description: gene expression profiles in CD8+ T cells from spleens (harvested times, 5 days for effector cells) of TCRgag miR-150+/+

value: 5 days


title: Maxillary process ectoderm at E12.5, biological rep 3

description:
fxe3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: 10 µM AlCl3 pH5.0_6hrs vs. noAlCl3 pH5.0_6hrs_rep1

description: Biological replicate 1 of 2.


title: WT-memory_2

description: gene expression profiles in CD8+ T cells from spleens (harvested times, 60 days for memory cells) of TCRgag miR-150+/+


title: Mandibular process mesenchyme at E12.5, biological rep 2

description:
fpm2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos

source_name: C57BL6/J, mandibular process mesenchynme

value: mandibular process mesenchynme


title: Mandibular process ectoderm at E12.5, biological rep 3

description:
fpe3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos

source_name: C57BL6/J, mandibular process ectoderm

value: mandibular process ectoderm


title: Mandibular process mesenchyme at E12.5, biological rep 1

description:
fpm1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process mesenchyme at E12.5, biological rep 3

description:
fpm3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: KO-effector

description: gene expression profiles in CD8+ T cells from spleens (harvested times, 5 days for effector cells) of TCRgag miR-150−/−


title: Maxillary process mesenchyme at E12.5, biological rep 1

description:
fxm1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Maxillary process mesenchyme at E12.5, biological rep 2

description:
fxm2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: WT-memory_1

source_name: CD8+ T cells from spleens (harvested times, 60 days for memory cells) of TCRgag miR-150+/+


title: Mandibular process ectoderm at E12.5, biological rep 2

description:
fpe2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process ectoderm at E12.5, biological rep 1

description:
fpe1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process mesenchyme at E12.5, biological rep 3

description:
fnm3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos

source_name: C57BL6/J, fronto-nasal process mesenchyme

value: fronto-nasal process mesenchyme


title: Fronto-nasal process mesenchyme at E12.5, biological rep 2

description:
fnm2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Maxillary process mesenchyme at E11.5, biological rep 1

description:
dxm1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process mesenchyme at E11.5, biological rep 2

description:
dpm2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process ectoderm at E11.5, biological rep 3

description:
dpe3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process mesenchyme at E12.5, biological rep 1

description:
fnm1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Maxillary process mesenchyme at E11.5, biological rep 3

description:
dxm3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process ectoderm at E12.5, biological rep 1

description:
fne1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos

source_name: C57BL6/J, fronto-nasal process ectoderm

value: fronto-nasal process ectoderm


title: Mandibular process mesenchyme at E11.5, biological rep 3

description:
dpm3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Maxillary process mesenchyme at E11.5, biological rep 2

description:
dxm2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process mesenchyme at E11.5, biological rep 1

description:
dnm1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Maxillary process ectoderm at E11.5, biological rep 3

description:
dxe3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process mesenchyme at E11.5, biological rep 2

description:
dnm2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process ectoderm at E11.5, biological rep 2

description:
dpe2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process ectoderm at E12.5, biological rep 2

description:
fne2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process mesenchyme at E11.5, biological rep 1

description:
dpm1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process ectoderm at E12.5, biological rep 3

description:
fne3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process ectoderm at E11.5, biological rep 1

description:
dpe1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Maxillary process ectoderm at E11.5, biological rep 1

description:
dxe1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process ectoderm at E11.5, biological rep 1

description:
dne1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process mesenchyme at E10.5, biological rep 3

description:
bpm3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process ectoderm at E10.5, biological rep 3

description:
bpe3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process mesenchyme at E11.5, biological rep 3

description:
dnm3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process ectoderm at E11.5, biological rep 2

description:
dne2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Maxillary process ectoderm at E11.5, biological rep 2

description:
dxe2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process ectoderm at E11.5, biological rep 3

description:
dne3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process mesenchyme at E10.5, biological rep 1

description:
bpm1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process mesenchyme at E10.5, biological rep 2

description:
bpm2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process ectoderm at E10.5, biological rep 2

description:
bpe2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Mandibular process ectoderm at E10.5, biological rep 1

description:
bpe1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process mesenchyme at E10.5, biological rep 3

description:
bnm3
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: Fronto-nasal process mesenchyme at E10.5, biological rep 2

description:
bnm2
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: NT;p62-_-, biological rep 2

city: Tokyo

first: Yoshihiro

last: Kino

address: 2-522-1 Noshio, Kiyose

institute: Meiji Pharmaceutical University

description: Gene expression data from the striatum of non-transgenic mice with genetic depletion of  p62

hyb_protocol: 2 ug of Fragmented ssDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed by the RMA algorithm using  AltAnalyze software at the default setting.

source_name: Striatum at 8 weeks

label_protocol: 100ng of total RNA was used to prepare biotinilated DNA, according Affymetrix recomandations (http://media.affymetrix.com/support/downloads/manuals/wt_expressionkit_manual.pdf). Whole transcript targets were produced using the Ambion WT kit and the Affymetrix kit (The Affymetrix GeneChip® WT Terminal Labeling Kit) to fragment and labelled DNA.

extract_protocol: Samples were dissected and snap-frozen in liquid nitrogen. RNA extraction with Trizol and purification with RNeasy mini kit (Qiagen)


title: HD;p62-_-, biological rep 1

description: Gene expression data from the striatum of HD transgenic mice with genetic depletion of p62


title: NT;p62-_-, biological rep 3


title: NT;p62-_-, biological rep 1


title: NT;p62+_+, biological rep 3

description: Gene expression data from the striatum of non-transgenic mice with normal gene dosage of  p62


title: HD;p62+_+, biological rep 2

description: Gene expression data from the striatum of HD transgenic mice with normal gene dosage of p62


title: Fronto-nasal process mesenchyme at E10.5, biological rep 1

description:
bnm1
microdissected prominences, separated ectoderm and mesenchyme, pooled from several embryos


title: HD;p62+_+, biological rep 3


title: Islets-cafeteria diet 30 days-rep3

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

description: Gene expression data from the pancreatic islets of Wistar rats fed with cafeteria diet for 30 days, biological replicate 3

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: Raw data was background adjusted, normalized and summarized by MAS5.0 algorithm using the SimpleAffy package from Bioconductor on R language.

organism: Rattus norvegicus

source_name: Islets from rats fed cafeteria diet for 30 days

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

growth_protocol: Adult male Wistar rats (Charles River Laboratories, Wilmington, MA), 7 wk old (weighing 225–250 g), were caged individually in a 12-h light, 12-h dark cycle in a temperature- and humidity-controlled environment.

extract_protocol: Rneasy minikit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Animals were divided into two dietary sets for 30 days. One group was fed with standard chow diet (supplying 8% of calories as fat; type AO4 from Panlab, Barcelona, Spain). The second group was fed with a cafeteria diet (66% of calories as fat), as previously described (Endocrinology 2012;153:177-87).

value: Wistar

tag: biological replicate

value: Pancreatic islets

tag: diet

value: Standard diet

tag: length of diet

value: 30 days


title: NT;p62+_+, biological rep 1


title: HD;p62+_+, biological rep 1


title: NT;p62+_+, biological rep 2


title: Islets-cafeteria diet 30 days-rep5

description: Gene expression data from the pancreatic islets of Wistar rats fed with cafeteria diet for 30 days, biological replicate 5


title: HD;p62-_-, biological rep 3


title: Islets-cafeteria diet 30 days-rep1

description: Gene expression data from the pancreatic islets of Wistar rats fed with cafeteria diet for 30 days, biological replicate 1


title: HD;p62-_-, biological rep 2


title: Islets-cafeteria diet 30 days-rep2

description: Gene expression data from the pancreatic islets of Wistar rats fed with cafeteria diet for 30 days, biological replicate 2


title: Islets-standard diet 30 days-rep2

description: Gene expression data from the pancreatic islets of Wistar rats fed with standard diet for 30 days, biological replicate 2

source_name: Islets from rats fed standard diet for 30 days

value: Cafeteria diet


title: Islets-cafeteria diet 30 days-rep4

description: Gene expression data from the pancreatic islets of Wistar rats fed with cafeteria diet for 30 days, biological replicate 4


title: Islets-cafeteria diet 10 days-rep5

description: Gene expression data from the pancreatic islets of Wistar rats fed with cafeteria diet for 10 days, biological replicate 5

source_name: Islets from rats fed cafeteria diet for 10 days

treatment_protocol: Animals were divided into two dietary sets for 10 days. One group was fed with standard chow diet (supplying 8% of calories as fat; type AO4 from Panlab, Barcelona, Spain). The second group was fed with a cafeteria diet (66% of calories as fat), as previously described (Endocrinology 2012;153:177-87).

value: 10 days


title: Islets-standard diet 30 days-rep4

description: Gene expression data from the pancreatic islets of Wistar rats fed with standard diet for 30 days, biological replicate 4


title: Islets-cafeteria diet 10 days-rep2

description: Gene expression data from the pancreatic islets of Wistar rats fed with cafeteria diet for 10 days, biological replicate 2


title: Islets-standard diet 30 days-rep3

description: Gene expression data from the pancreatic islets of Wistar rats fed with standard diet for 30 days, biological replicate 3


title: Islets-cafeteria diet 10 days-rep4

description: Gene expression data from the pancreatic islets of Wistar rats fed with cafeteria diet for 10 days, biological replicate 4


title: Islets-standard diet 30 days-rep1

description: Gene expression data from the pancreatic islets of Wistar rats fed with standard diet for 30 days, biological replicate 1


title: Islets-cafeteria diet 10 days-rep3

description: Gene expression data from the pancreatic islets of Wistar rats fed with cafeteria diet for 10 days, biological replicate 3


title: Islets-standard diet 10 days-rep5

description: Gene expression data from the pancreatic islets of Wistar rats fed with standard diet for 10 days, biological replicate 5

source_name: Islets from rats fed standard diet for 10 days


title: Islets-standard diet 10 days-rep3

description: Gene expression data from the pancreatic islets of Wistar rats fed with standard diet for 10 days, biological replicate 3


title: Islets-cafeteria diet 10 days-rep1

description: Gene expression data from the pancreatic islets of Wistar rats fed with cafeteria diet for 10 days, biological replicate 1


title: Islets-standard diet 10 days-rep1

description: Gene expression data from the pancreatic islets of Wistar rats fed with standard diet for 10 days, biological replicate 1


title: Islets-standard diet 10 days-rep4

description: Gene expression data from the pancreatic islets of Wistar rats fed with standard diet for 10 days, biological replicate 4


title: SCAT_HF6_085

city: Nuthetal

first: Martin

middle: A

last: Osterhoff

address: Arthur-Scheunert-Allee 155

department: Clinical Nutrition

country: Germany

institute: German Institute of Human Nutrition

description: Gene expression after 6 weeks of high fat diet (HF6) in human subcutaneous adipose tissue

hyb_protocol: According to Agilents protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 028004_D_F_20111107) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: sc adipose tissue, HF6, replicate63

label_protocol: RNA was transcribed into cDNA which was processed with Agilent One Color Spike Mix Stock Solution and hybridized to a total number of 208 Agilent SurePrint G3 Human GE 8x60K Microarray single-color DNA microarrays according to the manufacturer’s protocol (Agilent Technologies, Germany).

extract_protocol: Total subcutaneous adipose tissue RNA was extracted from homogenates of 300mg frozen sample in Quiazol™ followed by use of Lipid Tissue RNA-Kit™ (Qiagen, Germany) according to the manufacturer’s protocol. The RNA concentration measure and quality control was performed using an ND-1000 spectrophotometer (Nanodrop, PeqLab, Erlangen, Germany) and 2100 Bioanalyser and RNA Nano Chips (Agilent Technologies, Germany).

treatment_protocol: From each participant three adipose tissue biopsies were taken at LF, HF1 and HF6 in starved state, from contralateral sites, at the level of the umbilicus. The skin was anesthetized with 1% lidocaine (10-15 mL). A small incision was made and 1 g of adipose tissue was removed under sterile conditions by using a cutting needle biopsy handy. After removal, the tissue samples were stored in an RNA protecting buffer (RNA later™, Qiagen, Germany) at 4°C until the procedure was finished, then snap-frozen in liquid nitrogen and finally stored at –80°C until total RNA isolation.

value: subcutaneous adipose tissue

tag: zygosity

value: mono


title: SCAT_HF6_075

source_name: sc adipose tissue, HF6, replicate55

value: di


title: Islets-standard diet 10 days-rep2

description: Gene expression data from the pancreatic islets of Wistar rats fed with standard diet for 10 days, biological replicate 2


title: SCAT_HF6_086

source_name: sc adipose tissue, HF6, replicate64


title: SCAT_HF6_090

source_name: sc adipose tissue, HF6, replicate68


title: SCAT_HF6_088

source_name: sc adipose tissue, HF6, replicate66


title: SCAT_HF6_082

source_name: sc adipose tissue, HF6, replicate60


title: SCAT_HF6_080

source_name: sc adipose tissue, HF6, replicate58


title: SCAT_HF6_071

source_name: sc adipose tissue, HF6, replicate51


title: SCAT_HF6_084

source_name: sc adipose tissue, HF6, replicate62


title: SCAT_HF6_069

source_name: sc adipose tissue, HF6, replicate49


title: SCAT_HF6_073

source_name: sc adipose tissue, HF6, replicate53


title: SCAT_HF6_083

source_name: sc adipose tissue, HF6, replicate61


title: SCAT_HF6_081

source_name: sc adipose tissue, HF6, replicate59


title: SCAT_HF6_089

source_name: sc adipose tissue, HF6, replicate67


title: SCAT_HF6_074

source_name: sc adipose tissue, HF6, replicate54


title: SCAT_HF6_065

source_name: sc adipose tissue, HF6, replicate45


title: SCAT_HF6_079

source_name: sc adipose tissue, HF6, replicate57


title: SCAT_HF6_068

source_name: sc adipose tissue, HF6, replicate48


title: SCAT_HF6_064

source_name: sc adipose tissue, HF6, replicate44


title: SCAT_HF6_070

source_name: sc adipose tissue, HF6, replicate50


title: SCAT_HF6_076

source_name: sc adipose tissue, HF6, replicate56


title: SCAT_HF6_063

source_name: sc adipose tissue, HF6, replicate43


title: SCAT_HF6_067

source_name: sc adipose tissue, HF6, replicate47


title: SCAT_HF6_062

source_name: sc adipose tissue, HF6, replicate42


title: SCAT_HF6_058

source_name: sc adipose tissue, HF6, replicate40


title: SCAT_HF6_061

source_name: sc adipose tissue, HF6, replicate41


title: SCAT_HF6_057

source_name: sc adipose tissue, HF6, replicate39


title: SCAT_HF6_056

source_name: sc adipose tissue, HF6, replicate38


title: SCAT_HF6_053

source_name: sc adipose tissue, HF6, replicate35


title: SCAT_HF6_054

source_name: sc adipose tissue, HF6, replicate36


title: SCAT_HF6_051

source_name: sc adipose tissue, HF6, replicate33


title: SCAT_HF6_042

source_name: sc adipose tissue, HF6, replicate28


title: SCAT_HF6_041

source_name: sc adipose tissue, HF6, replicate27


title: SCAT_HF6_034

source_name: sc adipose tissue, HF6, replicate24


title: SCAT_HF6_043

source_name: sc adipose tissue, HF6, replicate29


title: SCAT_HF6_035

source_name: sc adipose tissue, HF6, replicate25


title: SCAT_HF6_055

source_name: sc adipose tissue, HF6, replicate37


title: SCAT_HF6_046

source_name: sc adipose tissue, HF6, replicate32


title: SCAT_HF6_036

source_name: sc adipose tissue, HF6, replicate26


title: SCAT_HF6_023

source_name: sc adipose tissue, HF6, replicate19


title: SCAT_HF6_019

source_name: sc adipose tissue, HF6, replicate15


title: SCAT_HF6_045

source_name: sc adipose tissue, HF6, replicate31


title: SCAT_HF6_022

source_name: sc adipose tissue, HF6, replicate18


title: SCAT_HF6_016

source_name: sc adipose tissue, HF6, replicate12


title: SCAT_HF6_052

source_name: sc adipose tissue, HF6, replicate34


title: SCAT_HF6_033

source_name: sc adipose tissue, HF6, replicate23


title: SCAT_HF6_017

source_name: sc adipose tissue, HF6, replicate13


title: SCAT_HF6_020

source_name: sc adipose tissue, HF6, replicate16


title: SCAT_HF6_044

source_name: sc adipose tissue, HF6, replicate30


title: SCAT_HF6_015

source_name: sc adipose tissue, HF6, replicate11


title: SCAT_HF6_030

source_name: sc adipose tissue, HF6, replicate22


title: SCAT_HF6_010

source_name: sc adipose tissue, HF6, replicate 8


title: SCAT_HF6_014

source_name: sc adipose tissue, HF6, replicate10


title: SCAT_HF6_003

source_name: sc adipose tissue, HF6, replicate 3


title: SCAT_HF6_021

source_name: sc adipose tissue, HF6, replicate17


title: SCAT_HF6_002

source_name: sc adipose tissue, HF6, replicate 2


title: SCAT_HF1_087

description: Gene expression after 1 week of high fat diet (HF1) in human subcutaneous adipose tissue

source_name: sc adipose tissue, HF1, replicate67


title: SCAT_HF6_018

source_name: sc adipose tissue, HF6, replicate14


title: SCAT_HF6_008

source_name: sc adipose tissue, HF6, replicate 6


title: SCAT_HF6_004

source_name: sc adipose tissue, HF6, replicate 4


title: SCAT_HF6_013

source_name: sc adipose tissue, HF6, replicate 9


title: SCAT_HF6_024

source_name: sc adipose tissue, HF6, replicate20


title: SCAT_HF6_009

source_name: sc adipose tissue, HF6, replicate 7


title: SCAT_HF1_089

source_name: sc adipose tissue, HF1, replicate69


title: SCAT_HF1_088

source_name: sc adipose tissue, HF1, replicate68


title: SCAT_HF6_001

source_name: sc adipose tissue, HF6, replicate 1


title: SCAT_HF1_081

source_name: sc adipose tissue, HF1, replicate61


title: SCAT_HF1_082

source_name: sc adipose tissue, HF1, replicate62


title: SCAT_HF1_083

source_name: sc adipose tissue, HF1, replicate63


title: SCAT_HF1_080

source_name: sc adipose tissue, HF1, replicate60


title: SCAT_HF1_085

source_name: sc adipose tissue, HF1, replicate65


title: SCAT_HF1_084

source_name: sc adipose tissue, HF1, replicate64


title: SCAT_HF1_090

source_name: sc adipose tissue, HF1, replicate70


title: SCAT_HF1_086

source_name: sc adipose tissue, HF1, replicate66


title: SCAT_HF1_075

source_name: sc adipose tissue, HF1, replicate57


title: SCAT_HF1_076

source_name: sc adipose tissue, HF1, replicate58


title: SCAT_HF1_074

source_name: sc adipose tissue, HF1, replicate56


title: SCAT_HF1_079

source_name: sc adipose tissue, HF1, replicate59


title: SCAT_HF1_073

source_name: sc adipose tissue, HF1, replicate55


title: SCAT_HF1_068

source_name: sc adipose tissue, HF1, replicate50


title: SCAT_HF1_064

source_name: sc adipose tissue, HF1, replicate46


title: SCAT_HF1_069

source_name: sc adipose tissue, HF1, replicate51


title: SCAT_HF1_061

source_name: sc adipose tissue, HF1, replicate43


title: SCAT_HF1_072

source_name: sc adipose tissue, HF1, replicate54


title: SCAT_HF1_065

source_name: sc adipose tissue, HF1, replicate47


title: SCAT_HF1_066

source_name: sc adipose tissue, HF1, replicate48


title: SCAT_HF1_062

source_name: sc adipose tissue, HF1, replicate44


title: SCAT_HF1_063

source_name: sc adipose tissue, HF1, replicate45


title: SCAT_HF1_071

source_name: sc adipose tissue, HF1, replicate53


title: SCAT_HF1_060

source_name: sc adipose tissue, HF1, replicate42


title: SCAT_HF1_059

source_name: sc adipose tissue, HF1, replicate41


title: SCAT_HF1_070

source_name: sc adipose tissue, HF1, replicate52


title: SCAT_HF1_058

source_name: sc adipose tissue, HF1, replicate40


title: SCAT_HF1_067

source_name: sc adipose tissue, HF1, replicate49


title: SCAT_HF1_055

source_name: sc adipose tissue, HF1, replicate37


title: SCAT_HF1_051

source_name: sc adipose tissue, HF1, replicate33


title: SCAT_HF1_057

source_name: sc adipose tissue, HF1, replicate39


title: SCAT_HF1_056

source_name: sc adipose tissue, HF1, replicate38


title: SCAT_HF1_054

source_name: sc adipose tissue, HF1, replicate36


title: SCAT_HF1_046

source_name: sc adipose tissue, HF1, replicate32


title: SCAT_HF1_053

source_name: sc adipose tissue, HF1, replicate35


title: SCAT_HF1_052

source_name: sc adipose tissue, HF1, replicate34


title: SCAT_HF1_045

source_name: sc adipose tissue, HF1, replicate31


title: SCAT_HF1_043

source_name: sc adipose tissue, HF1, replicate29


title: SCAT_HF1_042

source_name: sc adipose tissue, HF1, replicate28


title: SCAT_HF1_044

source_name: sc adipose tissue, HF1, replicate30


title: SCAT_HF1_036

source_name: sc adipose tissue, HF1, replicate26


title: SCAT_HF1_035

source_name: sc adipose tissue, HF1, replicate25


title: SCAT_HF1_034

source_name: sc adipose tissue, HF1, replicate24


title: SCAT_HF1_019

source_name: sc adipose tissue, HF1, replicate15


title: SCAT_HF1_023

source_name: sc adipose tissue, HF1, replicate19


title: SCAT_HF1_017

source_name: sc adipose tissue, HF1, replicate13


title: SCAT_HF1_030

source_name: sc adipose tissue, HF1, replicate22


title: SCAT_HF1_024

source_name: sc adipose tissue, HF1, replicate20


title: SCAT_HF1_020

source_name: sc adipose tissue, HF1, replicate16


title: SCAT_HF1_022

source_name: sc adipose tissue, HF1, replicate18


title: SCAT_HF1_007

source_name: sc adipose tissue, HF1, replicate 5


title: SCAT_HF1_041

source_name: sc adipose tissue, HF1, replicate27


title: SCAT_HF1_033

source_name: sc adipose tissue, HF1, replicate23


title: SCAT_HF1_018

source_name: sc adipose tissue, HF1, replicate14


title: SCAT_HF1_016

source_name: sc adipose tissue, HF1, replicate12


title: SCAT_HF1_010

source_name: sc adipose tissue, HF1, replicate 8


title: SCAT_HF1_015

source_name: sc adipose tissue, HF1, replicate11


title: SCAT_HF1_008

source_name: sc adipose tissue, HF1, replicate 6


title: SCAT_HF1_013

source_name: sc adipose tissue, HF1, replicate 9


title: SCAT_HF1_009

source_name: sc adipose tissue, HF1, replicate 7


title: SCAT_HF1_003

source_name: sc adipose tissue, HF1, replicate 3


title: SCAT_LF_088

description: Gene expression after 6 weeks of low fat diet (LF) in human subcutaneous adipose tissue

source_name: sc adipose tissue, LF, replicate68


title: SCAT_LF_087

source_name: sc adipose tissue, LF, replicate67


title: SCAT_HF1_001

source_name: sc adipose tissue, HF1, replicate 1


title: SCAT_LF_083

source_name: sc adipose tissue, LF, replicate63


title: SCAT_HF1_004

source_name: sc adipose tissue, HF1, replicate 4


title: SCAT_LF_082

source_name: sc adipose tissue, LF, replicate62


title: SCAT_LF_090

source_name: sc adipose tissue, LF, replicate70


title: SCAT_LF_085

source_name: sc adipose tissue, LF, replicate65


title: SCAT_LF_076

source_name: sc adipose tissue, LF, replicate58


title: SCAT_HF1_014

source_name: sc adipose tissue, HF1, replicate10


title: SCAT_LF_081

source_name: sc adipose tissue, LF, replicate61


title: SCAT_LF_089

source_name: sc adipose tissue, LF, replicate69


title: SCAT_LF_086

source_name: sc adipose tissue, LF, replicate66


title: SCAT_LF_075

source_name: sc adipose tissue, LF, replicate57


title: SCAT_LF_079

source_name: sc adipose tissue, LF, replicate59


title: SCAT_LF_073

source_name: sc adipose tissue, LF, replicate55


title: SCAT_LF_069

source_name: sc adipose tissue, LF, replicate51


title: SCAT_LF_068

source_name: sc adipose tissue, LF, replicate50


title: SCAT_LF_067

source_name: sc adipose tissue, LF, replicate49


title: SCAT_LF_070

source_name: sc adipose tissue, LF, replicate52


title: SCAT_LF_074

source_name: sc adipose tissue, LF, replicate56


title: SCAT_LF_071

source_name: sc adipose tissue, LF, replicate53


title: SCAT_LF_072

source_name: sc adipose tissue, LF, replicate54


title: SCAT_LF_066

source_name: sc adipose tissue, LF, replicate48


title: SCAT_LF_059

source_name: sc adipose tissue, LF, replicate41


title: SCAT_LF_063

source_name: sc adipose tissue, LF, replicate45


title: SCAT_LF_065

source_name: sc adipose tissue, LF, replicate47


title: SCAT_LF_061

source_name: sc adipose tissue, LF, replicate43


title: SCAT_LF_064

source_name: sc adipose tissue, LF, replicate46


title: SCAT_LF_053

source_name: sc adipose tissue, LF, replicate35


title: SCAT_LF_055

source_name: sc adipose tissue, LF, replicate37


title: SCAT_LF_051

source_name: sc adipose tissue, LF, replicate33


title: SCAT_LF_056

source_name: sc adipose tissue, LF, replicate38


title: SCAT_LF_058

source_name: sc adipose tissue, LF, replicate40


title: SCAT_LF_046

source_name: sc adipose tissue, LF, replicate32


title: SCAT_LF_057

source_name: sc adipose tissue, LF, replicate39


title: SCAT_LF_060

source_name: sc adipose tissue, LF, replicate42


title: SCAT_LF_044

source_name: sc adipose tissue, LF, replicate30


title: SCAT_LF_080

source_name: sc adipose tissue, LF, replicate60


title: SCAT_LF_042

source_name: sc adipose tissue, LF, replicate28


title: SCAT_LF_045

source_name: sc adipose tissue, LF, replicate31


title: SCAT_LF_043

source_name: sc adipose tissue, LF, replicate29


title: SCAT_LF_062

source_name: sc adipose tissue, LF, replicate44


title: SCAT_LF_041

source_name: sc adipose tissue, LF, replicate27


title: IRP1-OE-Fe-rep2-shoot

city: Taipei

first: Wolfgang

last: Schmidt

address: No. 128, Sec 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: gene expression data from transgenic arabidopsis shoots under iron deficiency medium

hyb_protocol: Ten microgram labeled samples were hybridized to the ATH1 Genome Array at 45℃ for 16.5 h. Washing and staining involved Fluidic Station-450 and the ATH1 Genome

scan_protocol: Array was scanned with the Affymetrix GeneChip Scanner 7G

data_processing: The results were quantified and analyzed by use of Genespring ver10.

source_name: Arabidopsis OE in iron minus medium

label_protocol: Ten microgram of total RNA was used for cDNA synthesis, labeled by in vitro transcription, followed by fragmentation according to the manufacturer's suggestion (GeneChip Expression Analysis Technical Manual rev5, Affymetrix

growth_protocol: 10-day old seedlings were transferred to ES (+Fe) and ES without addition of FeEDTA (–Fe) medium and grown for 3 days, respectively. Tissues were harvested and immediately frozen in liquid nitrogen transfer.

extract_protocol: Total RNA was extracted with Qiagen RNeasy mini kit

value: shoot


title: SCAT_HF6_007

source_name: sc adipose tissue, HF6, replicate 5


title: IRP1-OE-Ctrl-rep2-shoot

description: gene expression data from transgenic arabidopsis shoots under iron efficiency medium

source_name: Arabidopsis OE in iron plus medium


title: SCAT_LF_052

source_name: sc adipose tissue, LF, replicate34


title: 9455-4: Mouse Hippocampi ASX0.5% n=4

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Dye-swap (Cy3/Cy5) ASX 0.5% x Control

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

source_name: Hippocampus ASX0.5% Cy3

label_protocol: Manual:  Low Input Quick Amp Labeling Kit, Two-Color  (Agilent)

growth_protocol: Male C57BL/6J mice (26-28 g; SLC, Co., Ltd., Shizuoka, Japan), 11 weeks old, were housed individually at one per cage with a 12-h light/dark schedule (light on at 7:00 AM). The mice were fed standard powdered chow (Oriental Yeast Co., Ltd., Tokyo, Japan) during 1 week of acclimatization, and randomly divided into four groups according to varying consistency of ASX; 0% (Control) and 0.5%. All the experimental procedures were performed in accordance with protocols approved by the University of Tsukuba Animal Experiment Committee guidelines for the Care and Use of Laboratory Animals.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: After 1 week of acclimatization rearing, all mice were fed different consistency of dietary supplementation containing ASX for 4 weeks. Briefly, all mice were fed ASX or its placebo powder (AstaReal powder based on 2% content of astaxanthin form Haematococcus pluvialis, Fuji Chemical Industry, Toyama, Japan) in standard powder diet at final consistency of 0.5% and 0% (CON) ASX powder (W/W), respectively, which was formulated to provide mice befor stored at 4°C in dark. Individual food intake and body weight were measured two times a week, and given fresh feed.

value: Hippocampus

source_name: Hippocampus Control Cy5


title: SCAT_LF_036

source_name: sc adipose tissue, LF, replicate26


title: SCAT_LF_034

source_name: sc adipose tissue, LF, replicate24


title: IRP1-OE-Ctrl-rep1-shoot


title: IRP1-OE-Fe-rep1-shoot


title: SCAT_LF_033

source_name: sc adipose tissue, LF, replicate23


title: gf2

city: zhengzhou

first: ruili

last: han

address: 95 wenhua road

country: China

institute: henan agriculture university

description: 385K probes in total

hyb_protocol: Chicken CGH 385k whole-genome Tiling Array

data_processing:
spatial correction and data normalization, segmentation were performed using the DEVA 1.2 software (Roche-NimbleGen).
two criteria, i.e., mean log2 ratio ≥ |0.5| and at least 5 consecutive probes0.5 log2 shift and 5 neighboring probes, were used to filter CNVs.

organism: Gallus gallus

source_name: blood

label_protocol: Test DNA and reference DNA samples were independently labeled with either Cy3 or Cy5 dyes.

extract_protocol: Genomic DNA for each  individuals was extracted from the blood using DNeasy Blood and Tissue Kit

value: blood

tag: breed

value: Guifei chicken

tag: Sex

value: female

value: anka chicken


title: SCAT_LF_035

source_name: sc adipose tissue, LF, replicate25


title: 9455-3: Mouse Hippocampi ASX0.5% n=4

description: Dye-swap (Cy3/Cy5) Control x ASX 0.5%

source_name: Hippocampus Control Cy3

source_name: Hippocampus ASX0.5% Cy5


title: SCAT_LF_030

source_name: sc adipose tissue, LF, replicate22


title: SCAT_LF_054

source_name: sc adipose tissue, LF, replicate36


title: COL-0-Fe-rep2-shoot

description: gene expression data from arabidopsis shoots under iron deficiency medium

source_name: Arabidopsis Col-0 in iron minus medium


title: gf1

description: 385K probes in total

scan_protocol: Chicken CGH 385k whole-genome Tiling Array


title: COL-0-Fe-rep1-shoot


title: SCAT_HF1_002

source_name: sc adipose tissue, HF1, replicate 2


title: cx_15w_R6/2::HDAC4het_rep8

city: Lausanne

first: Tamara

last: Seredenin

address: AI2135 Station 15 EPFL

institute: EPFL

description: Gene expression data

hyb_protocol: cRNA (15 ug) was hybridized to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) at  45°C for 17 hours, washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Microarray quality control was performed using the software package provided on RACE (http://race.unil.ch). Chips with a median normalized unscaled standard error  > 1.05 were excluded. Affymetrix annotations (version 30) were used for probeset-to-gene assignments. T-test was performed to assess the differences in gene expression between groups for each genotype.

source_name: cortex_15w_Double R6/2::HDAC4het

label_protocol: Biotinylated cRNAs were prepared from 200ng of total RNA using the GeneChip® 3’ IVT Express Kit (Affymetrix) following the instructions of the manufacturer.

growth_protocol: Hemizygous R6/2 mice were bred by backcrossing R6/2 males to (CBA x C57BL/6) F1 females (B6CBAF1/OlaHsd, Harlan Olac, Bicester, UK). All animals had unlimited access to food and water, were subject to a 12-h light/dark cycle and housing conditions and environmental enrichment were as previously described (Hockly et al., 2003b). The R6/2 colony was kept on breeding chow (Special Diet Services, Witham, UK).

extract_protocol: Total RNA was extracted with the mini-RNA kit accordingly to manufacturer instructions (Qiagen).

value: male

value: CBA X C57Bl/6

value: cortex

tag: age

value: 15 weeks


title: COL-0-Ctrl-rep2-shoot

description: gene expression data from arabidopsis shoots under iron efficiency medium

source_name: Arabidopsis Col-0 in iron plus medium

tag: genotype/variation


title: sk1

description: 385K probes in total

value: Silkie


title: gs2

description: 385K probes in total

value: Gushi chicken


title: cx_15w_R6/2::HDAC4het_rep9

description: Gene expression data

tag: gender


title: COL-0-Ctrl-rep1-shoot


title: ls1

description: 385K probes in total

value: Lushi chicken


title: SCAT_LF_029

source_name: sc adipose tissue, LF, replicate21


title: xc2

description: 385K probes in total

value: Xichuan Black-bone chicken


title: xc1

description: 385K probes in total


title: SCAT_LF_023

source_name: sc adipose tissue, LF, replicate19

value: subcutaneous adipose tissue


title: cx_15w_R6/2::HDAC4het_rep6

description: Gene expression data


title: cx_15w_R6/2::HDAC4het_rep5

description: Gene expression data


title: sk2

description: 385K probes in total


title: cx_15w_R6/2::HDAC4het_rep1

description: Gene expression data


title: cx_15w_R6/2_rep9

description: Gene expression data


title: SCAT_LF_024

source_name: sc adipose tissue, LF, replicate20

value: mono


title: cx_15w_R6/2::HDAC4het_rep4

description: Gene expression data


title: cx_15w_R6/2::HDAC4het_rep3

description: Gene expression data


title: IRP1-OE-Fe-rep2-root

description: gene expression data from transgenic arabidopsis roots under iron deficiency medium

source_name: Arabidopsis OE in iron minus medium

value: root


title: SCAT_LF_022

source_name: sc adipose tissue, LF, replicate18


title: cx_15w_R6/2::HDAC4het_rep2

description: Gene expression data


title: SCAT_LF_021

source_name: sc adipose tissue, LF, replicate17


title: cx_15w_R6/2_rep7

description: Gene expression data


title: IRP1-OE-Fe-rep1-root


title: cx_15w_R6/2_rep8

description: Gene expression data


title: cx_15w_R6/2_rep5

description: Gene expression data


title: cx_15w_R6/2_rep4

description: Gene expression data


title: IRP1-OE-Ctrl-rep1-root

description: gene expression data from transgenic arabidopsis roots under iron efficiency medium

source_name: Arabidopsis OE in iron plus medium


title: COL-0-Fe-rep1-root

description: gene expression data from arabidopsis roots under iron deficiency medium


title: cx_15w_R6/2::HDAC4het_rep7

description: Gene expression data


title: IRP1-OE-Ctrl-rep2-root


title: COL-0-Fe-rep2-root


title: cx_15w_R6/2_rep1

description: Gene expression data


title: SCAT_LF_018

source_name: sc adipose tissue, LF, replicate14


title: cx_15w_HDAC4het_rep8

description: Gene expression data


title: cx_15w_R6/2_rep6

description: Gene expression data


title: SCAT_LF_020

source_name: sc adipose tissue, LF, replicate16


title: COL-0-Ctrl-rep1-root

description: gene expression data from arabidopsis roots under iron efficiency medium


title: COL-0-Ctrl-rep2-root


title: cx_15w_R6/2_rep2

description: Gene expression data


title: gs1

description: 385K probes in total

source_name: blood


title: SCAT_LF_015

source_name: sc adipose tissue, LF, replicate11


title: cx_15w_R6/2_rep3

description: Gene expression data


title: cx_15w_HDAC4het_rep4

description: Gene expression data


title: SCAT_LF_016

source_name: sc adipose tissue, LF, replicate12


title: cx_15w_HDAC4het_rep7

description: Gene expression data


title: SCAT_LF_017

source_name: sc adipose tissue, LF, replicate13


title: cx_15w_HDAC4het_rep3

description: Gene expression data


title: cx_15w_HDAC4het_rep5

description: Gene expression data


title: SCAT_LF_014

source_name: sc adipose tissue, LF, replicate10


title: SCAT_LF_013

source_name: sc adipose tissue, LF, replicate 9


title: d5G infected animal, 1 wpi, 05

city: Shinjuku

first: Kazuyasu

last: Mori

state: Tokyo

address: 1-23-1 Toyama

department: AIDS Research Center

institute: National Institute of Infectious Diseases

description: Gene expression of PBMCs from rhesus macaque infected with ∆5G

hyb_protocol: After the purification of labeled cRNA, 1.65 mg labeled samples were fragmented by the incubation with Fragmentation Buffer (Agilent) at 60°C for 30 min.  These samples were hybridized onto the Rhesus macaque Microarray version 2, 44k probes × 4 arrays/ slide (Agilent) at 65°C for 16 h in a rotating hyb oven at a speed of 10 rounds per min (RPM).  Microarrays slides were washed in the order of Wash Solution 1 (Agilent), Wash Solution 2 (Agilent) and acetonitrile (Wako).

scan_protocol: Microarrays slides were scanned at 5 micrometer resolution on a microarray scanner (Agilent) with excitation of the fluorophores Cy3.

data_processing: The image files were analyzed by using Feature Extraction software (Agilent) and automatically exported with flag information.

organism: Macaca mulatta

source_name: PBMCs

label_protocol: Twenty five nanogram of total RNA and spike-in control was amplified and labeled using Low RNA Input Linear Amplification Kit (Agilent). RNA was denatured and reverse transcribed to cDNA. cDNA was transcribed from 25 ng of total RNA using a poly-T nucleotide primer containing a T7 RNA polymerase promoter.  cRNA was subsequently synthesized and labeled with cyanine-3 (Cy3) by T7 RNA polymerase.

extract_protocol: Total RNA was purified from the samples using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol. The concentrations and qualities of total RNA were measured by Spectrophotometer ND-100 (Nanodrop Technologies) and Agilent 2100 bioanalyzer (Agilent), respectively.

treatment_protocol: PBMCs isolated from blood samples were stored at -150°C until use.

tag: cell type

value: PBMC

tag: infection status

value: nonpathogenic infection


title: cx_15w_HDAC4het_rep1

description: Gene expression data


title: cx_15w_WT_rep8

description: Gene expression data


title: d5G infected animal, 1 wpi, 04

value: blood


title: cx_15w_WT_rep6

description: Gene expression data


title: SCAT_LF_009

source_name: sc adipose tissue, LF, replicate 7


title: d5G infected animal, 1 wpi, 01


title: SCAT_LF_007

source_name: sc adipose tissue, LF, replicate 5


title: SCAT_LF_010

source_name: sc adipose tissue, LF, replicate 8


title: d5G infected animal, 1 wpi, 02


title: cx_15w_WT_rep7

description: Gene expression data


title: cx_15w_HDAC4het_rep2

description: Gene expression data


title: ls2

description: 385K probes in total


title: cx_15w_WT_rep5

description: Gene expression data


title: SCAT_LF_008

source_name: sc adipose tissue, LF, replicate 6


title: SCAT_LF_002

source_name: sc adipose tissue, LF, replicate 2


title: SCAT_LF_004

source_name: sc adipose tissue, LF, replicate 4


title: d5G infected animal, 1 wpi, 03


title: cx_15w_WT_rep4

description: Gene expression data


title: SCAT_LF_003

source_name: sc adipose tissue, LF, replicate 3


title: cx_15w_WT_rep3

description: Gene expression data


title: SIV239 infected animal, 1 wpi, 02

description: Gene expression of PBMCs from rhesus macaque infected with SIVmac239

value: pathogenic infection


title: SCAT_LF_001

source_name: sc adipose tissue, LF, replicate 1


title: cx_15w_WT_rep2

description: Gene expression data

value: female


title: SIV239 infected animal, 1 wpi, 04


title: SIV239 infected animal, 1 wpi, 03


title: cx_9w_R6/2::HDAC4het_rep10

description: Gene expression data

source_name: cortex_9w_Double R6/2::HDAC4het

value: 9 weeks


title: SIV239 infected animal, 1 wpi, 01


title: cx_15w_WT_rep1

description: Gene expression data

value: male


title: MLL-AF9_shEED_1

city: Chapel Hill

first: Bowen

last: Xu

state: NC

address: 450 West Drive, CB7295, Lineberger Cancer Center, GREG WANG Lab, RM 31-331

department: Biochemistry and Biophysics

institute: UNC-Chapel Hill

hyb_protocol: Samples were hybridized with Affymetrix Mouse Gene 2.1 ST Array Strip (Affymetrix) according to the manifacture's instruction.

scan_protocol: Standard Affymetrix protocol

data_processing:
Hybridization signals were retrieved and normalized, followed by differential expression analysis and statistical analysis using GeneSpring Analysis Platform GX 12.6 (Agilent Technologies).
probe group file: MoGene-2_1-st.pgf
meta-probeset file: MoGene-2_1-st.mps

label_protocol: The cDNA was fragmented and terminally labeled with biotin, using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA)

growth_protocol: Transformed murine leukemia progenitor cell lines were cultured in Opti-MEM base medium supplemented with 10% FBS, 1% antibiotics, 50 μM mercaptoethanol and stem cell factor

extract_protocol: Total RNA was isolated with the Rneasy Plus Miniprep Kit (Qiagen).

treatment_protocol: Treatment with 3μM of the indicated compounds for 4-5 days, or induction of gene-specific shRNAs (with an inducible TRMPVIR system) for 6 days, followed by total RNA preparation for microarray.

tag: strain background

value: Balb/c

tag: cell line

value: transformed murine leukemia progenitor cell line

tag: treated with

value: shEED


title: MLL-AF9_shEED_2


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  18

city: new york

first: Mary Helen

last: Barcellos-Hoff

state: New York

address: 450 29th street

department: Radiation

institute: New York University

hyb_protocol: The labeled cDNA is added to the hybridization cocktail that is prepared according to the protocol included in the Affymetrix GeneTitan Hybridization Wash, and Stain kit.  The samples are then put onto a hybridization tray and loaded into the Affymetrix GeneTitan MC for hybridization, washing, and scanning. The samples are hybridized for 60 degrees C for 16 hours once all plates are loaded

scan_protocol: Arrays are scanned in the  Affymetrix GeneTitan MC using a xenon light bulb and the image is captured using a camera.

data_processing: Background subtraction and normalization was performed using the Robust Multichip Average algorithm from the Bioconductor package oligo

source_name: Total RNA of Trp53-null mammary tumor, Sham-irradiated host

label_protocol: 250 ng of total RNA is first amplified into cRNA and then made into cDNA using the Ambion WT Expression Kit. 5.5 ug of the cDNA is then fragmented using the Affymetrix GeneChip WT Terminal Labeling kit.  Fragmentation is confirmed by running each sample on the Agilent Bioanalyzer using the RNA 6000 kit.  The fragmented cDNA is then labeled using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: Trp53-null mammary fragments were orthotoically transplanted into the inguinal mammary fat pads of 10 week-old wild-type BALB/c  female host mice that had their endogenous epithelium removed at 3wks of age. The development of Trp-null mammary tumors were monitored for 600 days.  Survival surgery were performed to remove the tumors once they reach the size of 1cm3.  Tumor then were frozen in liquid nitrogen for RNA extraction.

extract_protocol: Total RNA was extracted using Trizol Reaget (Invitrogen), according to manufacturer's instructions.

treatment_protocol: Host mice were either irradiated or not, three days before transplantation.

tag: strain (donor)

value: BALB/c

tag: tissue (donor)

value: Trp53-null mammary fragments

tag: strain (host)

tag: protocol (host)

value: Sham-irradiated

tag: disease state (host)

value: Trp53-null mammary tumors


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  17


title: Uninfected animal, 04

description: Gene expression of PBMCs from rhesus macaque

tag: tissue

value: uninfected


title: MLL-AF9_shRen_3

value: shRNA control


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  16


title: MLL-AF9_shEED_3


title: cx_9w_R6/2::HDAC4het_rep9

description: Gene expression data

tag: strain

value: CBA X C57Bl/6

value: cortex


title: MLL-AF9_shRen_2


title: Uninfected animal, 03

value: PBMC


title: Uninfected animal, 05

value: blood


title: MLL-AF9_shRen_1


title: SCAT_LF_019

source_name: sc adipose tissue, LF, replicate15

value: subcutaneous adipose tissue

tag: zygosity

value: mono


title: cx_9w_R6/2::HDAC4het_rep7

description: Gene expression data

value: female

value: 9 weeks


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  14


title: cx_9w_R6/2::HDAC4het_rep6

description: Gene expression data

value: male


title: MLL-AF9-GFP_3μM_UNC1999_D5_6

value: Balb/c

value: transformed murine leukemia progenitor cell line


title: Uninfected animal, 01


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  15

value: BALB/c


title: Uninfected animal, 02


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  13

value: Trp53-null mammary fragments


title: MLL-AF9-GFP_3μM_UNC1999_D5_5


title: cx_9w_R6/2::HDAC4het_rep5

description: Gene expression data


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  10

value: Sham-irradiated


title: MLL-AF9-puro_3μM_UNC1999_D5_3


title: MLL-AF9-GFP_3μM_UNC1999_D5_4


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  12

value: Trp53-null mammary tumors


title: MLL-AF9-GFP_3μM_UNC2400_D5_5

value: UNC2400 (inactive analog of UNC1999)


title: cx_9w_R6/2::HDAC4het_rep3

description: Gene expression data


title: cx_9w_R6/2::HDAC4het_rep8

description: Gene expression data


title: cx_9w_R6/2::HDAC4het_rep4

description: Gene expression data


title: cx_9w_R6/2_rep9

description: Gene expression data


title: MLL-AF9-puro_3μM_UNC1999_D5_2


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  9


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  11


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  7


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  8


title: cx_9w_R6/2::HDAC4het_rep2

description: Gene expression data


title: MLL-AF9-puro_3μM_UNC1999_D5_1


title: cx_9w_R6/2_rep8

description: Gene expression data


title: cx_9w_R6/2_rep7

description: Gene expression data


title: cx_9w_R6/2_rep6

description: Gene expression data


title: MLL-AF9-GFP_3μM_UNC2400_D5_4


title: cx_9w_R6/2::HDAC4het_rep1

description: Gene expression data


title: MLL-AF9-puro_3μM_UNC2400_D5_2


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  6


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  4


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  5


title: cx_15w_HDAC4het_rep6

description: Gene expression data

value: 15 weeks


title: MLL-AF9-puro_3μM_UNC2400_D5_1


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  1


title: cx_9w_R6/2_rep4

description: Gene expression data

value: CBA X C57Bl/6


title: MLL-AF9-GFP_DMSO_D5_5

value: DMSO


title: SIV239 infected animal, 1 wpi, 05

value: PBMC

value: pathogenic infection


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  2


title: MLL-AF9-puro_3μM_UNC2400_D5_3


title: Trp53-null-mammary-tumor, 10 cGy Si-irradiated host repeat  9

source_name: Total RNA of Trp53-null mammary tumor, Si-irradiated host

value: Irradiated with 10 cGy Si


title: cx_9w_R6/2_rep3

description: Gene expression data

value: cortex


title: MLL-AF9-puro_DMSO_D5_2


title: cx_9w_R6/2_rep5

description: Gene expression data

value: female


title: cx_9w_HDAC4het_rep9

description: Gene expression data

value: 9 weeks


title: MLL-AF9-puro_DMSO_D5_1


title: MLL-AF9-GFP_DMSO_D5_4


title: MLL-AF9-puro_DMSO_D5_3


title: cx_9w_HDAC4het_rep8

description: Gene expression data


title: Trp53-null-mammary-tumor, 10 cGy Si-irradiated host repeat  6


title: Trp53-null-mammary-tumor, 10 cGy Si-irradiated host repeat  7


title: Trp53-null-mammary-tumor, sham-irradiated host repeat  3


title: NF4204_52 Glucose - Endothelin - Cortisol

city: Basel

first: Laura

last: Badi

address: Grenzacherstrasse

institute: Hoffmann La Roche LTD

description: Gene expression data from human cardiomyocyte derived from iPS, stressed

hyb_protocol: Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400

scan_protocol: Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA). Log2 probe set signal intensities were calculated by RMA.

source_name: iPS Cardiomyocytes Cell treated 2 days

label_protocol: Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)

extract_protocol: Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)

value: iPS Cardiomyocytes

tag: treatment

value: Glucose - Endothelin - Cortisol

tag: time point

value: 2 days


title: Trp53-null-mammary-tumor, 10 cGy Si-irradiated host repeat  8

value: BALB/c


title: cx_9w_R6/2_rep2

description: Gene expression data

value: male

tag: age


title: Trp53-null-mammary-tumor, 10 cGy Si-irradiated host repeat  5

value: Trp53-null mammary fragments


title: cx_9w_HDAC4het_rep7

description: Gene expression data

tag: gender


title: cx_9w_R6/2_rep1

description: Gene expression data


title: Trp53-null-mammary-tumor, 10 cGy Si-irradiated host repeat  4

value: Trp53-null mammary tumors


title: NF4159_7 Glucose - Endothelin - Cortisol

tag: cell type


title: NF4189_37 Glucose - Endothelin - Cortisol


title: NF4174_22 Glucose - Endothelin - Cortisol


title: NF4201_49 UNTREATED

description: Gene expression data from human cardiomyocyte derived from iPS, untreated

source_name: iPS Cardiomyocytes Cell untreated 2 days

value: UNTREATED


title: cx_9w_HDAC4het_rep4

description: Gene expression data


title: Trp53-null-mammary-tumor, 10 cGy Si-irradiated host repeat  2


title: Trp53-null-mammary-tumor, 10 cGy Si-irradiated host repeat  3


title: cx_9w_HDAC4het_rep6

description: Gene expression data


title: cx_9w_HDAC4het_rep1

description: Gene expression data


title: cx_9w_HDAC4het_rep2

description: Gene expression data


title: cx_9w_HDAC4het_rep5

description: Gene expression data


title: Trp53-null-mammary-tumor, 10 cGy Si-irradiated host repeat  1


title: NF4186_34 UNTREATED


title: NF4156_4 UNTREATED


title: Trp53-null-mammary-tumor, 30 cGy Si-irradiated host repeat  8

value: Irradiated with 30 cGy Si


title: cx_9w_HDAC4het_rep3

description: Gene expression data

value: CBA X C57Bl/6


title: cx_9w_WT_rep9

description: Gene expression data


title: Trp53-null-mammary-tumor, 30 cGy Si-irradiated host repeat  10


title: NF4171_19 UNTREATED


title: cx_9w_WT_rep8

description: Gene expression data


title: Trp53-null-mammary-tumor, 30 cGy Si-irradiated host repeat  9


title: Trp53-null-mammary-tumor, 30 cGy Si-irradiated host repeat  7


title: cx_9w_WT_rep6

description: Gene expression data


title: cx_9w_WT_rep7

description: Gene expression data


title: Trp53-null-mammary-tumor, 30 cGy Si-irradiated host repeat  2


title: Trp53-null-mammary-tumor, 30 cGy Si-irradiated host repeat  6


title: cx_9w_WT_rep3

description: Gene expression data


title: Trp53-null-mammary-tumor, 30 cGy Si-irradiated host repeat  4


title: Trp53-null-mammary-tumor, 30 cGy Si-irradiated host repeat  5


title: Trp53-null-mammary-tumor, 30 cGy Si-irradiated host repeat  1


title: Trp53-null-mammary-tumor, 80 cGy Si-irradiated host repeat  8

value: Irradiated with 80 cGy Si


title: cx_9w_WT_rep2

description: Gene expression data


title: cx_9w_WT_rep1

description: Gene expression data


title: Trp53-null-mammary-tumor, 80 cGy Si-irradiated host repeat  6


title: Trp53-null-mammary-tumor, 80 cGy Si-irradiated host repeat  7


title: Trp53-null-mammary-tumor, 30 cGy Si-irradiated host repeat  3


title: cx_9w_WT_rep5

description: Gene expression data


title: cx_9w_WT_rep4

description: Gene expression data


title: Trp53-null-mammary-tumor, 80 cGy Si-irradiated host repeat  5


title: MOCK-infected NA 24hpi, bio rep2

city: Changchun

first: Pingsen

last: Zhao

state: Jilin

address: No. 666 Liuying Xilu

department: The research centre for canine diseases

institute: Institute of Military Veterinary Academy of Military Medical Sciences

description:
X-N-M-2
Second of two biological replicates.

hyb_protocol: Hybridization was performed by LC Sciences, Texas, USA, following their standard operating protocol. See http://www.LCsciences.com.

scan_protocol: Scanning was performed by LC Sciences, Texas, USA, following their standard operating protocol. See http://www.LCsciences.com.

data_processing: For the raw dataset, hybridization images were collected using a  laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).  The expression data were normalized using a variance stabilizing method VSN (Huber et al. Bioinformatics 18 Suppl 1: S96-104) in Bioconductor (http://www.bioconductor.org).

source_name: NA mock-infected 24hpi

label_protocol: Labeling was performed by LC Sciences, Texas, USA, following their standard operating protocol. See http://www.LCsciences.com.

extract_protocol: RNA was extracted with the mirVana™ miRNA Isolation Kit (Cat. No. 1561, Ambion, USA). We performed procedure FⅠin the Total RNA Isolation Procedure. RNA was quantified using a NanoDrop-2000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, CA).

value: neuroblastoma (NA) cells

value: mock infection

tag: time

value: 24 hpi

tag: mouse strain

value: A/J


title: RABV-infected BV-2 48hpi, bio rep1

description:
X-B-C-48-1
First of two biological replicates.

source_name: Microglia infected CVS-11 48hpi

tag: cell line

value: cultured microglial cells

value: infection with rabies virus CVS-11

value: 48 hpi


title: MOCK-infected BV-2 48hpi, bio rep1

description:
X-B-M-48-1
First of two biological replicates.

source_name: Microglia mock-infected 48hpi


title: MOCK-infected BV-2 24hpi, bio rep2

description:
X-B-M-24-2
Second of two biological replicates.

source_name: Microglia mock-infected 24hpi


title: RABV-infected NA 24hpi, bio rep1

description:
X-N-C-1
First of two biological replicates.

source_name: NA infected CVS-11 24hpi


title: RABV-infected NA 24hpi, bio rep2

description:
X-N-C-2
Second of two biological replicates.


title: RABV-infected BV-2 48hpi, bio rep2

description:
X-B-C-48-2
Second of two biological replicates.


title: MOCK-infected BV-2 48hpi, bio rep2

description:
X-B-M-48-2
Second of two biological replicates.


title: MOCK-infected NA 24hpi, bio rep1

description:
X-N-M-1
First of two biological replicates.


title: RABV-infected BV-2 24hpi, bio rep2

description:
X-B-C-24-2
Second of two biological replicates.

source_name: Microglia infected CVS-11 24hpi


title: RABV-infected BV-2 24hpi, bio rep1

description:
X-B-C-24-1
First of two biological replicates.


title: Trp53-null-mammary-tumor, 80 cGy Si-irradiated host repeat  3


title: MOCK-infected BV-2 12hpi, bio rep2

description:
X-B-M-12-2
Second of two biological replicates.

source_name: Microglia mock-infected 12hpi

value: 12 hpi


title: MOCK-infected BV-2 12hpi, bio rep1

description:
X-B-M-12-1
First of two biological replicates.


title: Trp53-null-mammary-tumor, 80 cGy Si-irradiated host repeat  2


title: MOCK-infected BV-2 24hpi, bio rep1

description:
X-B-M-24-1
First of two biological replicates.


title: RABV-infected BV-2 12hpi, bio rep1

description:
X-B-C-12-1
First of two biological replicates.

source_name: Microglia infected CVS-11 12hpi


title: RABV-infected BV-2 12hpi, bio rep2

description:
X-B-C-12-2
Second of two biological replicates.


title: Trp53-null-mammary-tumor, 80 cGy Si-irradiated host repeat  1


title: SQ20B-resistant 0.01% dmso 48hr replicate 2

city: Iowa City

first: Aditya

last: Stanam

state: Iowa

address: 500 Newton Road

department: Pathology

institute: University of Iowa

description:
Erlotinib-resistant SQ20B larynx squamous cell carcinoma 200,000 cells cultured for 48 hr + 0.01% DMSO (veh) sample 2
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was quantile normalized in GenomeStudio.

source_name: erlotinib-resistant larynx squamous cell carcinoma cultured 48 hr in 0.01% DMSO (veh)

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays.

growth_protocol: Sensitive (i.e., parental) FaDu and SQ20B cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 4 mM L-glutamine, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate and 4.5 g/L glucose with 10% Fetal Bovine Serum (FBS; Hyclone, Logan, UT). However, both types of resistant cells were cultured in their relevant culture media supplemented with erlotinib.

extract_protocol: RNA was extracted using RNeasy® Plus Mini Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: To the cell lines, 0.01% DMSO (vehicle) was added 48 hours prior to RNA harvest.


title: SQ20B-resistant 0.01% dmso 48hr replicate 3

description:
Erlotinib-resistant SQ20B larynx squamous cell carcinoma 200,000 cells cultured for 48 hr + 0.01% DMSO (veh) sample 3
Replicate 3


title: SQ20B-resistant 0.01% dmso 48hr replicate 1

description:
Erlotinib-resistant SQ20B larynx squamous cell carcinoma 200,000 cells cultured for 48 hr + 0.01% DMSO (veh) sample 1
Replicate 1


title: Trp53-null-mammary-tumor, 80 cGy Si-irradiated host repeat  4


title: FaDu-resistant 0.01% dmso 48hr replicate 2

description:
Erlotinib-resistant FaDu pharynx squamous cell carcinoma 200,000 cells (developed from ATCC #HTB-43) cultured for 48 hr + 0.01% DMSO (veh) sample 2
Replicate 2

source_name: erlotinib-resistant pharynx squamous cell carcinoma cultured 48 hr in 0.01% DMSO (veh)


title: SQ20B-sensitive 0.01% dmso 48 hr-replicate 2

description:
SQ20B a gift from Dr. Anjali Gupta (Department of Radiation Oncology, The University of Iowa), erlotinib-sensitive SQ20B larynx squamous cell carcinoma 200,000 cells cultured for 48 hr + 0.01% DMSO (veh) sample 2
Replicate 2

source_name: erlotinib-sensitive larynx squamous cell carcinoma cultured 48 hr in 0.01% DMSO (veh)

value: Erlotinib-sensitive SQ20B larynx squamous cell carcinoma 200,000 cells


title: FaDu-sensitive 0.01% dmso 48 hr-replicate 2

description:
ATCC #HTB-43 erlotinib-sensitive FaDu pharynx squamous cell carcinoma 200,000 cells cultured for 48 hr + 0.01% DMSO (veh) sample 2
Replicate 2

source_name: erlotinib-sensitive pharynx squamous cell carcinoma cultured 48 hr in 0.01% DMSO (veh)


title: FaDu-sensitive 0.01% dmso 48 hr-replicate 3

description:
ATCC #HTB-43 erlotinib-sensitive FaDu pharynx squamous cell carcinoma 200,000 cells cultured for 48 hr + 0.01% DMSO (veh) sample 3
Replicate 3


title: FaDu-sensitive 0.01% dmso 48 hr-replicate 1

description:
ATCC #HTB-43 erlotinib-sensitive FaDu pharynx squamous cell carcinoma 200,000 cells cultured for 48 hr + 0.01% DMSO (veh) sample 1
Replicate 1


title: SQ20B-sensitive 0.01% dmso 48 hr-replicate 1

description:
SQ20B a gift from Dr. Anjali Gupta (Department of Radiation Oncology, The University of Iowa), erlotinib-sensitive SQ20B larynx squamous cell carcinoma 200,000 cells cultured for 48 hr + 0.01% DMSO (veh) sample 1
Replicate 1


title: FaDu-resistant 0.01% dmso 48hr replicate 3

description:
Erlotinib-resistant FaDu pharynx squamous cell carcinoma 200,000 cells (developed from ATCC #HTB-43) cultured for 48 hr + 0.01% DMSO (veh) sample 3
Replicate 3