title: reference male mouse4/ 0GyA3


title: reference male mouse2/ 0GyG3

status: Public on Jan 27 2017

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

molecule: genomic DNA

organism: Mus musculus

source_name: reference male mouse2

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

tag: strain

tag: tissue

value: tail


title: 0GyE3/ reference male mouse1

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

source_name: reference male mouse1


title: reference male mouse1/ 0GyE3


title: 0GyA3/ reference male mouse4

source_name: reference male mouse4


title: ss 93 H9 TKI.P0

type: RNA

city: Lund

first: Mikael

middle: Nils Erik

last: Sommarin

state: skåne

address: klinikgatan 26, BMC B12

department: Department of molecular hematology

country: Sweden

institute: Lund university

description:
CML_Plate2_PatNr.7_TKI
All patients included in this dataset responded well to TKI, but leukemic cells (Ph+) can still be detected in patient bone marrow.

data_processing: Ct values calculated and exported using Fluidigm Biomark software. Data normalized by subtraction of the median Ct per cell followed by z-score scaling.

label: FAM-MGB

molecule: total RNA

organism: Homo sapiens

source_name: CML Bone Marrow HSC

label_protocol: cDNA synthesis and amplification was performed by adding a mix of 96 Taqman assays with a final concentration of 0.025x and Taq/SSIII enzyme reaction mix (CellsDirect One-Step RT-qPCR kit, Invitrogen) and PCR cycling was performed as follows, cDNA synthesis: 60min at 50oC and 2 min at 95oC, amplification:  15sec at 95oC and 4 min at 60oC repeated 25 times.  The cDNA was diluted 5 times with water prior to qPCR on the BioMark HD (Fluidigm Corporation, San Francisco, CA). All primers were used at 12.5x in the final reaction and Taqman universal master mix (Applied Biosystems, Foster City, CA) was used for detection of the qPCR products. The qPCR was performed using the 96.96 Dynamic Array Integrated Fluidic Circuits (IFC) (Fluidigm Corporation, San Francisco, CA) chip in combination with the BioMark HD with the following thermal cycler program: thermal mix 50°C for 2 minutes followed by 70°C for 30 minutes and 25°C for 10 minutes, UNG at 50°C for 2 minutes, hot start 96.5°C for 10 minutes, PCR cycle 40x (96°C 15 seconds, 60°C for 60 seconds).

extract_protocol: Cells were sorted into 96 well plates with 4µl lysis buffer (Neuclease free water, RNAsout (Invitrogen), 0.1M DTT, 10mM dNTP, 10% NP40)  and immediately frozen at -80°C.

treatment_protocol: Single cell suspension of cells were FACS sorted to obtain HSC cells

tag: disease state

value: CML

tag: clinical phase

value: after TKI treatment (TKI)

tag: therapy-response

value: Ph+ detected in BM (but all cells are not Ph+)

tag: cell type

value: CML Bone Marrow HSC

tag: cell subtype


title: SS4 A4 D.P0

description:
CML_Plate2_PatNr.7_Dx
All patients included in this dataset responded well to TKI, but leukemic cells (Ph+) can still be detected in patient bone marrow.

value: at diagnosis (Dx)


title: 0GyA2/ reference male mouse4


title: 0GyG2/ reference male mouse2


title: ss94 H10 TKI.P0


title: 0GyG1/ reference male mouse2


title: 0GyE2/ reference male mouse1


title: reference male mouse4/ 0GyA2


title: 0GyE1/ reference male mouse1


title: reference male mouse1/ 0GyE2


title: reference male mouse4/ 0GyA1


title: SS5 A5 D.P0


title: ss95 H11 TKI.P0


title: reference male mouse2/ 0GyG2


title: 0GyA1/ reference male mouse4


title: reference male mouse2/ 0GyG1


title: reference male mouse1/ 0GyEF


title: 0GyAF/ reference male mouse4


title: 0GyGF/ reference male mouse2


title: 0GyEF/ reference male mouse1


title: reference male mouse2/ 0GyGF


title: Fom 8 hpi rep 3

status: Public on Jan 26 2017

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

description: 4021688_500_33_100_9hybe.txt subarray 3

hyb_protocol: Pre-hybridization, hybridization, washing and imaging were performed according to the manufacturer's protocols (CustomArray, Mulkiteo, USA).

scan_protocol: The array was scanned with a GenePix 4400A scanner. PMT gain was set in order to obtain about 1e-5 normalized counts at 65.000 intensity level for both channels.

data_processing: Raw data were extracted from TIFF images using GenePix Pro 7 software and were quantile normalized using the LIMMA package. The median was calculated between replicated probes.

organism: Solanum virginianum

source_name: Fom inoculated roots 8 hours post infection

label_protocol: Reverse transcription, amplification and labelling was performed with RNA AmpULSe amplification and labelling kit according to manufacturer’s instructions (Kreatech Diagnostics, The Netherlands).

growth_protocol: IL All 96-6 x 1F5(9) plants were grown under greenhouse conditions

extract_protocol: Total RNA was purified from tissue samples using the RNeasy® plant RNA extraction kit (Qiagen).

treatment_protocol: Plants were artificially inoculated at the 2-3th true leaf stage according to the dip-root method reported by Cappelli et al., (1995). Both single and combined inoculations were carried out using a Fom  conidial concentration of 1.5x106/ml, and/or a Vd conidial concentration of 1.0x106/ml while water was employed for mock inoculations as control. Samples of inoculated and mock-inoculated (dipping in water) roots were harvested at 0, 4 (T0+4h) and 8 hours (T0+8h). Three biological replicates were realized for each inoculation treatment and timing. Root samples were subsequently frozen in liquid nitrogen and stored at -80°C.

value: roots

tag: treatment

value: Fusarium oxysporum f. sp. Melongenae inoculation

tag: hours post infection


title: SS6 A6 D.P0


title: reference male mouse4/ 0GyAF


title: Vd+Fom 8 hpi rep 1

description: 4021684_470_33_100_3hybe.txt subarray 4

source_name: Vd+Fom inoculated roots 8 hours post infection

value: Verticillium dahliae + Fusarium oxysporum f. sp. Melongenae inoculation


title: 0GyAM/ reference male mouse4


title: Fom 8 hpi rep 2

description: 4021688_490_33_100_6hybe.txt subarray 3


title: Vd+Fom 8 hpi rep 3

description: 4021688_500_33_100_9hybe.txt subarray 4


title: Fom 8 hpi rep 1

description: 4021684_470_33_100_3hybe.txt subarray 3


title: Vd 8 hpi rep 2

description: 4021688_490_33_100_6hybe.txt subarray 2

source_name: Vd inoculated roots 8 hours post infection

value: Verticillium dahliae inoculation


title: reference male mouse1/ 0GyEM


title: Vd 8 hpi rep 3

description: 4021688_500_33_100_9hybe.txt subarray 2


title: control 8 hpi rep 3

description: 4021688_500_33_100_9hybe.txt subarray 1

source_name: Mock inoculated roots 8 hours post infection

value: Mock inoculation


title: reference male mouse4/ 0GyAM


title: control 8 hpi rep 2

description: 4021688_490_33_100_6hybe.txt subarray 1


title: 0GyGM/ reference male mouse2


title: reference male mouse1/ 0GyE1


title: reference male mouse2/ 0GyGM


title: 0GyEM/ reference male mouse1


title: Vd+Fom 4 hpi rep 2

description: 4021688_520_33_100_5hybe.txt subarray 4

source_name: Vd+Fom inoculated roots 4 hours post infection


title: Vd 8 hpi rep 1

description: 4021684_470_33_100_3hybe.txt subarray 2


title: Vd+Fom 4 hpi rep 1

description: 4021684_510_33_100_2hybe.txt subarray 4


title: Vd+Fom 4 hpi rep 3

description: 4021688_490_33_100_8hybe.txt subarray 4


title: control 4 hpi rep 2

description: 4021688_520_33_100_5hybe.txt subarray 1

source_name: Mock inoculated roots 4 hours post infection


title: control 4 hpi rep 3

description: 4021688_490_33_100_8hybe.txt subarray 1


title: Vd 4 hpi rep 1

description: 4021684_510_33_100_2hybe.txt subarray 3

source_name: Vd inoculated roots 4 hours post infection


title: Vd 4 hpi rep 3

description: 4021688_490_33_100_8hybe.txt subarray 3


title: Vd 4 hpi rep 2

description: 4021688_520_33_100_5hybe.txt subarray 3


title: Fom 4 hpi rep 1

description: 4021684_510_33_100_2hybe.txt subarray 2

source_name: Fom inoculated roots 4 hours post infection


title: Fom 4 hpi rep 3

description: 4021688_490_33_100_8hybe.txt subarray 2


title: Fom 4 hpi rep 2

description: 4021688_520_33_100_5hybe.txt subarray 2


title: control 4 hpi rep 1

description: 4021684_510_33_100_2hybe.txt subarray 1


title: Vd+Fom 0 hpi rep 2

description: 4021684_500_33_100_4hybe.txt subarray 4

source_name: Vd+Fom inoculated roots 0 hours post infection


title: Fom 0 hpi rep 3

description: 4021684_500_33_100_Ihybe.txt subarray 3

source_name: Fom inoculated roots 0 hours post infection


title: Vd+Fom 0 hpi rep 3

description: 4021688_470_33_100_7hybe.txt subarray 4


title: Fom 0 hpi rep 2

description: 4021684_500_33_100_10hybe.txt subarray 1


title: Vd 0 hpi rep 3

description: 4021688_470_33_100_7hybe.txt subarray 2

source_name: Vd inoculated roots 0 hours post infection


title: Fom 0 hpi rep 1

description: 4021688_470_33_100_7hybe.txt subarray 3


title: Vd 0 hpi rep 2

description: 4021684_500_33_100_4hybe.txt subarray 2


title: Tailbud_MeDIP_rep1

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

description: ChIP-chip tailbud 5-methyl-cytosine

hyb_protocol: 10 ug of the labelled DNA was hybridized to each Nimblegen array.

scan_protocol: The arrays were scanned on a Molecular Devices GenePix Axon 4400A at 2.5 uM resolution.

data_processing: The scanned array data was converted into pair files using the NimbleScan software package. Pre-processing was done using Bioconductor R package Ringo. Raw probe intensities were normalized by computing log2(Cy3sample/Cy5input) and subtracting the Tukey's biweight mean, computed across each sample's log2 ratios. To reduce noise the normalized log2 ratios were smoothened using a running median across a 150 bp window.

organism: Oikopleura dioica

source_name: 5-methyl-cytosine ChIP DNA from Oikopleura dioica tailbud

label_protocol: For each sample, ChIPped DNA was labeled and amplified using the Roche NimbleGen protocol

extract_protocol: Day 6 Oikopleura gonads were dissected and nuclei were digested with MNaseI. ChIP was performed according to (Cuddapah et al. 2009) with minor modifications, using 10 male or 40 female gonads in 300 μl buffer per ChIP. We used 10 μg antibody per ChIP. Antibodies were bound to 50 μl Dynabeads® Protein G (Invitrogen) and incubated with chromatin overnight. Immunoprecipitated DNA was purified by phenol-chloroform-isoamylalcohol extraction and EtOH precipitation followed by Min Elute PCR purification (Qiagen). Resulting DNA was amplified using Whole Genome Amplification kit 2 or 4 (Sigma) according to manufacturer’s instructions (the chemical fragmentation step was omitted). For closslink ChIP, the animals were fixed in 1% formaldehyde in PBS for 12 min. Crosslinking was stopped by adding glycine to 0.13 M final concentration for 5 min followed by 3 washes with cold PBS. Fixed animals were kept in PBS containing 0.5 mM PMSF, 1x protease inhibitor, and phosphatase inhibitor for dissection of gonads. Gonads were lysed in RIPA buffer (150 mM NaCl, 1% NP-40, 0.5% Na deoxycholate, 0.1% SDS, 50 mM Tris pH 8, 5 mM EDTA), supplemented with fresh PMSF, protease and phosphatase inhibitor for 15 min. Chromatin was then fragmented to a size range of 200 to 600 bp using a Bioruptor UCD-200 (Diagenode) for 8 x 30 s on/1 min off.

tag: chip antibody

value: Whole tailbud animals

source_name: Input DNA from Oikopleura dioica tailbud

value: none, input DNA


title: control 0 hpi rep 3

description: 4021688_470_33_100_7hybe.txt subarray 1

source_name: Mock inoculated roots 0 hours post infection


title: Vd+Fom 0 hpi rep 1

description: 4021684_500_33_100_Ihybe.txt subarray 4


title: control 0 hpi rep 2

description: 4021684_500_33_100_4hybe.txt subarray 1


title: control 0 hpi rep 1

description: 4021684_500_33_100_Ihybe.txt subarray 1


title: Male_MeDIP_rep2

description: ChIP-chip males 5-methyl-cytosine

source_name: 5-methyl-cytosine ChIP DNA from Oikopleura dioica males

value: Whole day 6 male animal

source_name: Input DNA from Oikopleura dioica males


title: Slide 185700

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

institute: Karolinska Institutet

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: Net intensity (tr.mean) {A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown CDM  + 55mM galactose and harvested at Mid-exponential phase.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: genotype/variation

value: plfB mutant

source_name: Net intensity (tr.mean) {B}

value: Wild type


title: Slide 185708


title: Vd 0 hpi rep 1

description: 4021684_500_33_100_Ihybe.txt subarray 2


title: Testis_CTCF_rep2

description: ChIP-chip testis CTCF

source_name: CTCF ChIP DNA from Oikopleura dioica testis

value: CTCF

value: Testis

source_name: Input DNA from Oikopleura dioica testis


title: Testis_IgG

description: ChIP-chip testis IgG

source_name: IgG ChIP DNA from Oikoplerua dioica testis

value: IgG


title: Testis_E2F7_rep1

description: ChIP-chip testis E2F7

source_name: E2F7 ChIP DNA from Oikoplrua dioica testis


title: Testis_CTCF_rep1

description: ChIP-chip testis CTCF


title: Male_MeDIP_rep1

description: ChIP-chip males 5-methyl-cytosine


title: Testis_p300_rep3

description: ChIP-chip testis p300

source_name: p300 ChIP DNA from Oikopleura dioica testis


title: Testis_p300_rep2

description: ChIP-chip testis p300


title: Testis_p300_rep1

description: ChIP-chip testis p300


title: Testis_RNAP_S2P_rep2

description: ChIP-chip testis RNA polII S2P

source_name: RNA polII S2P ChIP DNA from Oikopleura dioica testis

value: RNA polII S2P


title: 12m_HP_WT_rep1

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

description: hippocampus of 12 months old WT mouse

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole mouse genome oligonucleotide microarray (Agilent grid ID 028005), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction ver 10.7 software using the standard Agilent one-color gene expression extraction protocol (GE1_107_Sep09).

data_processing: The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using Microsoft Excel, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, which is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale. Then differential gene lists were obtained from filtered data using Microsoft Excel. Differentially expressed genes were identified by a combination of Limma test (R-Bionconductor, p-value<0.05 threshold) and foldchange (2.0 threshold in linear scale).

source_name: hippocampus of 12 months old WT mouse

label_protocol: 200ng of Poly A+RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns.

growth_protocol: The pre-proNGF cDNA, obtained by reverse - transcription from total RNA of mouse submandibulary glands,  was mutagenized at the furin cleavage site. The Stratagene site-directed mutagenesis kit was used for mutagenesis, in order to change residues RSKR to RSAA (corresponding to the sequences aa - 4 to - 1 of proNGF, positions 118 - 121 from Uniprot entry P01139). The furin-resistant pre-proNGF cDNA, plus IRES sequence and EGFP, were  cloned into the Thy1.2 promoter vector, containing 6.5kb of the murine thy1.2 gene, driving brain - specific expression in adult transgenic mice. Transgenic mice were generated by pronuclear DNA injection of zygotes C57Bl/6xDBA/2 F2 generation using standard procedures. Microinjected zygotes were reimplanted into pseudopregnant C57Bl/6xDBA/2 F1 foster mothers to complete their development. For genotyping genomic DNA was extracted from tail biopsies. Four founder lines were derived (TgproNGF#3, #17, #36 and #72) and further expanded, bred and analyzed. (Tiveron C, Fasulo L, et al, Cell Death Differ. 2013 Aug;20(8):1017-30). TgproNGF#3 was used for this microarray study.

extract_protocol: Total RNA was extracted from hippocampus  using Trizol (Invitrogen) and DNAse treated by Qiagen columns. Quality and integrity of each sample was checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): samples with a RNA Integrity Number (RIN) index lower than 8.0 were discarded. All the experimental steps involving the labelling, hybridization and washing of the samples were done following the one-color Agilent protocol.

treatment_protocol: Hippocampus (HP) of the right hemisphere were dissected from the brains of freshly sacrificed TgproNGF#3 mice and control of corresponding WT mice, using RNAlater (Qiagen). Mice did not receive any prior treatment.

tag: gender

value: female

tag: genotype

value: wildtype

value: hippocampus

tag: age

value: 12 months


title: Testis_RNAP_S2P_rep1

description: ChIP-chip testis RNA polII S2P


title: 12m_HP_WT_rep3

description: hippocampus of 12 months old WT mouse


title: 12m_HP_WT_rep2

description: hippocampus of 12 months old WT mouse


title: 3m_HP_WT_rep4

description: hippocampus of 3 months old WT mouse

source_name: hippocampus of 3 months old WT mouse

value: male

value: 3 months


title: Testis_RNAP_S5P_rep2

description: ChIP-chip testis RNA polII S5P

source_name: RNA polII S5P ChIP DNA from Oikopleura dioica testis

value: RNA polII S5P


title: Testis_E2F1_rep1

description: ChIP-chip testis E2F1

source_name: E2F1 ChIP DNA from Oikopleura dioica testis


title: Testis_RNAP_S5P_rep1

description: ChIP-chip testis RNA polII S5P


title: Testis_RNAP-CTD_rep1

description: ChIP-chip testis RNA polII CTD

source_name: RNA polII CTD ChIP DNA from Oikopleura dioica testis

value: RNA polII CTD


title: 3m_HP_TgproNGF_rep4

description: hippocampus of 3 months old TgproNGF#3 mouse


title: Testis_H3S28P_rep2

description: ChIP-chip testis H3S28P

source_name: H3S28P ChIP DNA from Oikopleura dioica testis


title: 12m_HP_TgproNGF_rep1

description: hippocampus of 12 months old TgproNGF#3 mouse


title: 3m_HP_WT_rep1

description: hippocampus of 3 months old WT mouse


title: Testis_H3S28P_rep1

description: ChIP-chip testis H3S28P


title: 12m_HP_TgproNGF_rep3

source_name: hippocampus of 12 months old TgproNGF#3 mouse


title: Testis_H3K9me2_rep1

description: ChIP-chip testis H3K9me2

source_name: H3K9me2 ChIP DNA from Oikopleura dioica testis


title: 3m_HP_WT_rep3

description: hippocampus of 3 months old WT mouse


title: Testis_H3K4me2_rep1

description: ChIP-chip testis H3K4me2

source_name: H3K4me2 ChIP DNA from Oikopleura dioica testis


title: 12m_HP_TgproNGF_rep2


title: 1m_HP_WT_rep4

description: hippocampus of 1 month old WT mouse

source_name: hippocampus of 1 month old WT mouse

value: 1 month


title: 3m_HP_TgproNGF_rep2

source_name: hippocampus of 3 months old TgproNGF#3 mouse


title: Testis_RNAP-CTD_rep2

description: ChIP-chip testis RNA polII CTD

value: none, input DNA


title: 1m_HP_WT_rep3

description: hippocampus of 1 month old WT mouse


title: 3m_HP_TgproNGF_rep3


title: 3m_HP_WT_rep2

description: hippocampus of 3 months old WT mouse


title: control 8 hpi rep 1

description: 4021684_500_33_100_10hybe.txt subarray 2

source_name: Mock inoculated roots 8 hours post infection

value: roots

value: Mock inoculation


title: Testis_H3K36me2_rep2

description: ChIP-chip testis H3K36me2

source_name: H3K36me2 ChIP DNA from Oikopleura dioica testis

source_name: Input DNA from Oikopleura dioica testis


title: Testis_H4ac_rep2

description: ChIP-chip testis H4ac

source_name: H4ac ChIP DNA from Oikopleura dioica testis


title: Testis_H3K36me2_rep1

description: ChIP-chip testis H3K36me2


title: Testis_H4ac_rep1

description: ChIP-chip testis H4ac


title: 1m_HP_WT_rep2

description: hippocampus of 1 month old WT mouse


title: Testis_H4ac_rep3

description: ChIP-chip testis H4ac


title: Testis_H3K36me1_rep1

description: ChIP-chip testis H3K36me1

source_name: H3K36me1 ChIP DNA from Oikopleura dioica testis


title: Testis_H3K18ac_rep2

description: ChIP-chip testis H3K18ac

source_name: H3K18ac ChIP DNA from Oikopleura dioica testis


title: Testis_H3K36me1_rep2

description: ChIP-chip testis H3K36me1


title: Testis_H3K18ac_rep1

description: ChIP-chip testis H3K18ac


title: 1m_HP_TgproNGF_rep4

description: hippocampus of 1 month old TgproNGF#3 mouse


title: 1m_HP_WT_rep1

description: hippocampus of 1 month old WT mouse


title: 3m_HP_TgproNGF_rep1


title: 1m_HP_TgproNGF_rep3

source_name: hippocampus of 1 month old TgproNGF#3 mouse


title: Testis_H3K79me3_rep2

description: ChIP-chip testis H3K79me3

source_name: H3K79me3 ChIP DNA from Oikopleura dioica testis


title: Testis_H3K79me3_rep1

description: ChIP-chip testis H3K79me3


title: 1m_HP_TgproNGF_rep1


title: Testis_H3K9me3_rep2

description: ChIP-chip testis H3K9me3

source_name: H3K9me3 ChIP DNA from Oikopleura dioica testis


title: Testis_H3K9me3_rep1

description: ChIP-chip testis H3K9me3


title: Testis_H3K9me1_rep2

description: ChIP-chip testis H3K9me1

source_name: H3K9me1 ChIP DNA from Oikopleura dioica testis


title: 1m_HP_TgproNGF_rep2


title: Testis_H3K9me1_rep1

description: ChIP-chip testis H3K9me1


title: Testis_H3K79me1_rep2

description: ChIP-chip testis H3K79me1

source_name: H3K79me1 ChIP DNA from Oikopleura dioica testis


title: Testis_H3K27me3_rep3

description: ChIP-chip testis H3K27me3

source_name: H3K27me3 ChIP DNA from Oikopleura dioica testis


title: Testis_H3K79me1_rep1

description: ChIP-chip testis H3K79me1


title: Testis_H3K4me1_rep1

description: ChIP-chip testis H3K4me1

source_name: H3K4me1 ChIP DNA from Oikopleura dioica testis


title: Testis_H3K4me1_rep2

description: ChIP-chip testis H3K4me1


title: Testis_H3K27me3_rep4

description: ChIP-chip testis H3K27me3


title: Testis_H3K27me3_rep2

description: ChIP-chip testis H3K27me3


title: Testis_H3K27me1_rep2

description: ChIP-chip testis H3K27me1

source_name: H3K27me1 ChIP DNA from Oikopleura dioica testis


title: Testis_H3K27me1_rep1

description: ChIP-chip testis H3K27me1


title: Testis_H3K4me3_rep2

description: ChIP-chip testis H3K4me3

source_name: H3K4me3 ChIP DNA from Oikopleura dioica testis


title: Vd+Fom 8 hpi rep 2

description: 4021688_490_33_100_6hybe.txt subarray 4

source_name: Vd+Fom inoculated roots 8 hours post infection

value: Verticillium dahliae + Fusarium oxysporum f. sp. Melongenae inoculation


title: Testis_H4K20me1_rep2

description: ChIP-chip testis H4K20me1

source_name: H4K20me1 ChIP DNA from Oikopleura dioica testis


title: Testis_H4K20me3_rep1

description: ChIP-chip testis H4K20me3

source_name: H4K20me3 ChIP DNA from Oikopleura dioica testis


title: Testis_H3K4me3_rep1

description: ChIP-chip testis H3K4me3


title: Testis_H4K20me1_rep1

description: ChIP-chip testis H4K20me1


title: Testis_H3K36me3_rep2

description: ChIP-chip testis H3K36me3

source_name: H3K36me3 ChIP DNA from Oikopleura dioica testis


title: Testis_H3K27me3_rep1

description: ChIP-chip testis H3K27me3

source_name: Input DNA from Oikopleura dioica testis


title: Testis_H3_rep1

description: ChIP-chip testis H3

source_name: H3 ChIP DNA from Oikopleura dioica testis


title: Testis_H3K27ac_rep1

description: ChIP-chip testis H3K27ac

source_name: H3K27ac ChIP DNA from Oikopleura dioica testis


title: Female_MeDIP_rep2

description: ChIP-chip female 5-methyl-cytosine

source_name: 5-methyl-cytosine ChIP DNA from Oikopleura dioica females

value: Whole day 6 female animal

source_name: Input DNA from Oikopleura dioica females


title: Testis_H3K27ac_rep2

description: ChIP-chip testis H3K27ac

value: Testis


title: Testis_H3K36me3_rep1

description: ChIP-chip testis H3K36me3


title: Female_MeDIP_rep1

description: ChIP-chip female 5-methyl-cytosine


title: Ovary_E2F7_rep1

description: ChIP-chip ovary E2F7

source_name: E2F7 ChIP DNA from Oikoplrua dioica ovary

value: Ovary

source_name: Input DNA from Oikopleura dioica ovary


title: Ovary_CTCF_rep2

description: Chip-chip ovary CTCF

source_name: CTCF ChIP DNA from Oikopleura dioica ovary

value: CTCF


title: Ovary_E2F1_rep1

description: Chip-chip ovary E2F1

source_name: E2F1 ChIP DNA from Oikopleura dioica ovary


title: Testis_H4K20me3_rep2

description: ChIP-chip testis H4K20me3


title: Ovary_p300_rep2

description: Chip-chip ovary p300

source_name: p300 ChIP DNA from Oikopleura dioica ovary


title: Ovary_RNAP_S2P_rep2

description: Chip-chip ovary RNA polII S2P

source_name: RNA polII S2P ChIP DNA from Oikopleura dioica ovary

value: RNA polII S2P


title: Ovary_RNAP_S2P_rep1

description: Chip-chip ovary RNA polII S2P


title: Ovary_RNAP_S5P_rep2

description: Chip-chip ovary RNA polII S5P

source_name: RNA polII S5P ChIP DNA from Oikopleura dioica ovary


title: Ovary_RNAP_S5P_rep1

description: Chip-chip ovary RNA polII S5P


title: Ovary_RNAP_CTD_rep2

description: Chip-chip ovary RNA polII CTD

source_name: RNA polII CTD ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3S28P_rep2

description: Chip-chip ovary H3S28P

source_name: H3S28P ChIP DNA from Oikopleura dioica ovary


title: Testis_H3_rep2

description: ChIP-chip testis H3


title: Ovary_H3S28P_rep1

description: Chip-chip ovary H3S28P


title: Ovary_H3K4me2_rep1

description: Chip-chip ovary H3K4me2

source_name: H3K4me2 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K9me2_rep1

description: Chip-chip ovary H3K9me2

source_name: H3K9me2 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K36me2_rep2

description: Chip-chip ovary H3K36me2

source_name: H3K36me2 ChIP DNA from Oikopleura dioica ovary


title: Ovary_RNAP_CTD_rep1

description: Chip-chip ovary RNA polII CTD


title: Ovary_H3K36me2_rep1

description: Chip-chip ovary H3K36me2


title: Ovary_H4ac_rep1

description: Chip-chip ovary H4ac

source_name: H4ac ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K18ac_rep1

description: Chip-chip ovary H3K18ac

source_name: H3K18ac ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K9me3_rep3

description: Chip-chip ovary H3K9me3

source_name: H3K9me3 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K9me3_rep1

description: Chip-chip ovary H3K9me3


title: Ovary_CTCF_rep1

description: Chip-chip ovary CTCF


title: Ovary_H3K9me3_rep2

description: Chip-chip ovary H3K9me3


title: Ovary_H3K36me1_rep1

description: Chip-chip ovary H3K36me1

source_name: H3K36me1 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K18ac_rep2

description: Chip-chip ovary H3K18ac


title: Ovary_p300_rep3

description: Chip-chip ovary p300


title: Ovary_H4ac_rep2

description: Chip-chip ovary H4ac


title: Ovary_p300_rep1

description: Chip-chip ovary p300


title: Ovary_H3K9me1_rep3

description: Chip-chip ovary H3K9me1

source_name: H3K9me1 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K9me1_rep2

description: Chip-chip ovary H3K9me1


title: Ovary_H3K79me3_rep1

description: Chip-chip ovary H3K79me3

source_name: H3K79me3 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K36me1_rep2

description: Chip-chip ovary H3K36me1

source_name: Input DNA from Oikopleura dioica ovary


title: Ovary_H3K9me1_rep1

description: Chip-chip ovary H3K9me1


title: Ovary_H3K79me1_rep2

description: Chip-chip ovary H3K79me1

source_name: H3K79me1 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K79me1_rep1

description: Chip-chip ovary H3K79me1


title: Ovary_H3K4me1_rep3

description: Chip-chip ovary H3K4me1

source_name: H3K4me1 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K4me1_rep2

description: Chip-chip ovary H3K4me1


title: Ovary_H3K4me1_rep1

description: Chip-chip ovary H3K4me1


title: Ovary_H3K27me3_rep3

description: Chip-chip ovary H3K27me3

source_name: H3K27me3 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K27me3_rep1

description: Chip-chip ovary H3K27me3


title: Ovary_H3K4me3_rep2

description: Chip-chip ovary H3K4me3

source_name: H3K4me3 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K27me3_rep2

description: Chip-chip ovary H3K27me3


title: Ovary_H4K20me3_rep2

description: Chip-chip ovary H4K20me3

source_name: H4K20me3 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H4K20me3_rep1

description: Chip-chip ovary H4K20me3


title: Ovary_H4K20me1_rep1

description: Chip-chip ovary H4K20me1

source_name: H4K20me1 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K4me3_rep1

description: Chip-chip ovary H3K4me3


title: Ovary_H3K27me1_rep2

description: Chip-chip ovary H3K27me1

source_name: H3K27me1 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H4K20me1_rep2

description: Chip-chip ovary H4K20me1


title: Ovary_H3K27ac_rep2

description: Chip-chip ovary H3K27ac

source_name: H3K27ac ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K27me1_rep1

description: Chip-chip ovary H3K27me1


title: Ovary_H3K27ac_rep1

description: Chip-chip ovary H3K27ac


title: Ovary_H3K36me3_rep2

description: Chip-chip ovary H3K36me3

source_name: H3K36me3 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3_rep3

description: Chip-chip ovary H3

source_name: H3 ChIP DNA from Oikopleura dioica ovary


title: Ovary_H3K36me3_rep1

description: Chip-chip ovary H3K36me3


title: Ovary_H3_rep2

description: Chip-chip ovary H3


title: Ovary_H3_rep1

description: Chip-chip ovary H3


title: CL_PGF_4h_rep3

city: Beaverton

first: Heather

last: Talbott

state: OR

address: L584 ONPRC (Room 2128), 505 NW 185th Ave

department: Division of Reproductive & Developmental Sciences

country: USA

institute: OHSU, ONPRC

description: Bovine corpus luteum 4h post-PGF

hyb_protocol: Gene expression was analyzed by hybridization of 500 ng cDNA using Affymetrix (Santa Clara, CA) bovine whole-transcript microarrays  at the University of Nebraska Medical Center Microarray Core Facility. Hybridized 16 h to Affymetrix Bovine Gene 1.0 ST Array chip using the GeneChip hybridization oven 645 per suggested recommendations using the Hyb solution from the Hyb, Stain, Wash kit from Affymetrix. Washing and staining was performed using Affymetrix Fluidics station 450.

scan_protocol: Arrays were scanned using an Affymetrix Gene Chip Scanner 7000G to generate the .cel files.

data_processing:
The microarray data were preprocessed using the RMA method from Affymetrix expression console software (Affymetrix Inc., Santa Clara, CA) to normalize data at the exon level. The mean intensities of multiple probe sets (exons) of the same gene were calculated under each array to obtain the corresponding gene expression intensities.  The data was filtered to keep the genes with a raw expression value after preprocessing to be 10 or more for at least three samples. Linear Models for Microarray Analysis in the BioConducter suite under the statistical program R was applied to compare the log ratio between each of the PGF2α time points and the saline control after adjusting for the box effect.  Genes with a fold-change of at least 1.5 and a Benjamini-Hochberg adjusted P-value of no more than 0.05 for each treatment condition versus control were identified as differentially expressed genes.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = BovGene-1_0-v1
program-name = Expression Console
program-version = 1.1.2800.28061

label: biotin

organism: Bos taurus

source_name: Corpus luteum 4h post-PGF

label_protocol: Kit used for preparing the sample for hybridization: 3’ IVT Express  (Affymetrix, Santa  Clara, CA). Samples were reverse transcribed to cDNA and subjected to in vitro transcription per manufactures suggestion to generate biotinylated amplified RNA (aRNA).

growth_protocol: Estrous cycle of treatment animals were synchronized with two intramuscular injections of PGF2α 11 days apart.

extract_protocol: RNA was isolated from the CL of each cow using a Stratagene RNA Isolation Kit (Santa Clara, CA) following manufacturer’s instructions.

treatment_protocol: Postpubertal multiparous female cattle (n = 15) of composite breeding breeding (½ Red Angus, Pinsgauer, Red Poll, Herford and ½ Red Angus and Gelbvich) were treated at midcycle (days 9-10) with saline (n = 3) or PGF2α (n = 12) by intramuscular injection of 5 mL of the PGF2α analog (Lutalyse, 25 mg/mL; Pharmacia & Upjohn Company, Division of Pfizer Inc., New York, NY) or saline.  At each of four time points post-injection (0.5, 1, 2, and 4 h) three cows per treatment were subjected to a bilateral ovariectomy through a right flank approach under local anesthesia.  The CL was removed from the ovary, weighed and < 5 mm sections were snap-frozen in liquid N2 for subsequent protein and RNA analysis.  All animal procedures were completed under an IACUC-approved protocol  and performed at the University of Nebraska—Lincoln, Animal Sciences Department.

tag: breed

value: crossbreed

tag: treated with

tag: time post-treatment

value: 4 h

value: Corpus luteum


title: CL_PGF_4h_rep2

description: Bovine corpus luteum 4h post-PGF


title: CL_PGF_2h_rep3

description: Bovine corpus luteum 2h post-PGF

source_name: Corpus luteum 2h post-PGF

value: 2 h


title: CL_PGF_1h_rep3

description: Bovine corpus luteum 1h post-PGF

source_name: Corpus luteum 1h post-PGF

value: 1 h


title: CL_PGF_0.5h_rep2

description: Bovine corpus luteum 0.5h post-PGF

source_name: Corpus luteum 0.5h post-PGF


title: CL_PGF_2h_rep1

description: Bovine corpus luteum 2h post-PGF


title: CL_PGF_0.5h_rep3

description: Bovine corpus luteum 0.5h post-PGF


title: CL_PGF_1h_rep1

description: Bovine corpus luteum 1h post-PGF


title: CL_PGF_2h_rep2

description: Bovine corpus luteum 2h post-PGF


title: CL_PGF_4h_rep1

description: Bovine corpus luteum 4h post-PGF


title: CL_PGF_1h_rep2

description: Bovine corpus luteum 1h post-PGF


title: CL_PGF_0.5h_rep1

description: Bovine corpus luteum 0.5h post-PGF


title: CL_Saline_rep1

description: Bovine corpus luteum after saline treatment

source_name: Corpus luteum after saline treatment

value: saline

value: 0 h


title: MDA-MB-231_residual_rep3

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: cDNAs were generated and hybridized on Affymetrix HumanGenome 2.0 ST chips according to the Affymetrix protocol.

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 7G using AGCC.

data_processing: Raw data from CEL files were RMA normalized and summariezd to transcript clusters using the R Bioconductor 'oligo' package

label: Biotin

source_name: MDA-MB-231 cell line

label_protocol: cDNA synthesis and amplification for microarray analysis was performed according to Affymetrix (Santa Clara, CA, USA) protocols at the Weizmann Institute of Science Microarray core facility.

growth_protocol: MDA-MB-231 cells were grown in DMEM (Gibco BRL, Grand Island, NY, USA). SUM159T were grown in 1:1 DMEM:F12 medium supplemented with 5% FBS, 10 μg/ml insulin and 0.5 μg ml-1 hydrocortisone. Growth media were supplemented with 10% fetal bovine serum (FBS), 2 mm Glutamine, and penicillin/streptomycin. Cells were cultured at 37°C in a humidified incubator in the presence of 5% CO2.

extract_protocol: Total RNA for microarray analysis was extracted  from naive, resistant and residual MDA-MB-231 cells using the TRI Reagent. RNA purity and integrity were checked on Agilent Bioanalyzer 2100.

treatment_protocol: Paclitaxel was obtained from Calbiochem (Merck Millipore, Billerica, MA, USA). Paclitaxel-resistant cell lines were developed by sequential cycles of drug pulse followed by recovery in drug-free medium. In detail, 4x10^3 MDA-MB-231 cells were seeded at Day 0 in 384-well white opaque TC plates in 40μl of growth medium. On Day 1 paclitaxel at 5x concentration (final concentration, 8.5nM) was added  followed by incubation for 96h. At day 5 the cells recovered in drug-free medium for 96h. These cells are then called residual   MDA-MB-231 cells. To establish Paclitaxel resistant MDA-MB-231 cells, we employed 4-6 repeated pulses of increasing concentrations of paclitaxel followed by recovery cycles.

tag: cell line

value: mammary gland/Breast

tag: replicate

value: replicate 3

value: 51 years adult

value: Female

value: one round of Paclitaxel

tag: condition

value: residual


title: complemented AP2IX-4 knockout, 48h pH 8.2, replicate 1

city: St. Louis

first: Joshua

middle: B

last: Radke

state: Missouri

address: 660 Euclid Ave, CB8230

department: Molecular Microbiology

institute: Washington University School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45 oC to the affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using the Affymetrix GCS3000 scanner.

data_processing: Genespring GX v12.6.1 (Agilent)

organism: Toxoplasma gondii

source_name: bradyzoite induced (pH 8.2)

label_protocol: Ambion messageAmp premier

growth_protocol: parasites were grown in T150cm flasks in human foreskin fibroblasts

extract_protocol: Qiagen RNA easy, double DNAse digestion

treatment_protocol: in vitro growth as tachyzoites (pH 7.0) or induced to bradyzoite differentiation for 48h (pH8.2)

tag: Stage

value: bradyzoite


title: MDA-MB-231_residual_rep1

tag: tissue

value: replicate 1


title: AP2IX-4 knockout, 48h pH 8.2, replicate 2


title: CL_Saline_rep2


title: DEP_pub_23

city: New York

first: Kalpana

last: Gopalakrishnan

state: NY

address: 1428 Madison Avenue, Atran Building 03-02

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from rat mammary tissues at postnatal day 63 following treatment with diethyl phthalate from postnatal day 42 to postnatal day 62

hyb_protocol: Following fragmentation, 5.2 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0 St arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.

data_processing: The data was preprocessed in Expression Console software (Affymetrix) using RMA-sketch worflow and default settings. Transcriptome results from DEP, MPB and TCS treatment during three short term windows – perinatal, prepubertal and pubertal windows – were pre-processed independently to generate three  datasets (DEP and control - table 1, MPB and control - table 2, TCS and control - table 3).  Transcriptome data from chronically exposed TCS animals and corresponding controls were pre-processed separately from short term data (Chronic TCS and control - table 4).  Batch effects were removed using the ComBat package in R (Leek J. T. et al, 2012) for datasets in table 1, 2 and 3 (no batch covariate in table 4). Data submitted here have not been corrected for batch effects. Batch information is provided in the sample datasheet.

organism: Rattus norvegicus

source_name: Rats treated with diethyl phthalate from postnatal day 42 to 62

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays, Affymetrix 2015).

growth_protocol: The breeder animals (F0) were weighed weekly to determine treatment dose, starting from gestation for the perinatal group and during lactation for prepubertal, pubertal, and adult groups and the dose to be administered was calculated on the basis of the weekly weight.  For the perinatal group, all the F1 pups were housed with their dams until sacrifice (postnatal (PND) 21).  F1 pups from all the other groups were housed with their dams (F0) until weaning (PND 28) then separated from the dam, identified by ear punch, weighed individually every week and dosed by gavage following the protocol, based on the weekly mean body weight of each group.  Animals were randomized into different treatment groups in order to have minimal differences in body weight among them, with a standard deviation of no more than 10% from the average.

extract_protocol: The 5th left and right caudal mammary glands were used for transciptome profiling.  Mammary tissues were pulverized in liquid nitrogen and total RNA was extracted using the Maxwell 16 LEV simplyRNA Blood kit (Promega, WI) or the Direct-zol RNA MiniPrep kit (Zymo Research, CA).  Total RNA concentration was determined using Nanodrop (Thermo Scientific, MA), and RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies, CA); only samples with RNA Integrity Number ≥ 7 were used for microarrays.

treatment_protocol: Perinatal animals: five animals were treated in utero daily through oral gavage of their pregnant dams (F0) from gestation day (GD) 1 to GD 20; another five animals were treated daily from post natal day (PND)1 to PND 20 through milk of lactating dams (F0) exposed by oral gavage.  One female pup per litter was randomly selected and sacrificed at PND 21.  Prepubertal animals: treated daily from PND 21 through breast milk, then by oral gavage from PND 28 to PND 41, and sacrificed at PND 42.  Pubertal animals: treated daily by oral gavage from PND 42 to PND 62, and sacrificed at PND 63.  Chronic treatment group: animals were treated daily from PND 1 through milk of dams (F0) exposed from parturition.  After weaning, the female offspring (F1) were treated through oral gavage 3 times a week.  Animals were mated (outbred) at PND 97 and treatments were continued through pregnancy, delivery of pups (F2) and lactation.  At the end of lactation at lactating day 28 (PND 146), F1 animals were sacrificed.

tag: strain

value: Sprague-Dawley

tag: Sex

value: female

value: Caudal mammary tissue

tag: exposure/treatment condition

value: Diethyl phthalate

tag: window of exposure

value: Pubertal

tag: age at sacrifice

value: Rats sacrificed at postnatal day 63

tag: batch

value: Two

tag: rna extraction kit

value: Promega


title: MDA-MB-231_resistant_rep3

tag: gender

tag: treatment

value: 4-6 rounds of Paclitaxel

value: resistant


title: AP2IX-4 knockout, 48h pH 8.2, replicate 1


title: MDA-MB-231_residual_rep2

value: mammary gland/Breast

value: replicate 2

tag: age


title: DEP_pub_22


title: DEP_pub_21

value: One


title: complemented AP2IX-4 knockout, 48h pH 8.2, replicate 2


title: Parent, 48h pH 8.2, replicate 2


title: CL_Saline_rep3

tag: breed

value: crossbreed

tag: treated with

value: saline

value: 0 h

value: Corpus luteum


title: DEP_pub_20

value: Sprague-Dawley


title: AP2IX-4 knockout replicate 2

source_name: tachyzoite (pH 7.0)

value: tachyzoite


title: Parent, 48h pH 8.2, replicate 1

value: bradyzoite


title: AP2IX-4 knockout replicate 1


title: complemented AP2IX-4 knockout, 48h pH 8.2, replicate 3


title: DEP_prep_15

description: Gene expression data from rat mammary tissues at postnatal day 42 following treatment with diethyl phthalate from postnatal day 21 to postnatal day 41

source_name: Rats treated with diethyl phthalate from postnatal day 21 to 41

value: female

value: Caudal mammary tissue

value: Diethyl phthalate

value: Prepubertal

value: Rats sacrificed at postnatal day 42


title: MDA-MB-231_resistant_rep2

tag: cell line

value: 51 years adult

value: Female

value: 4-6 rounds of Paclitaxel


title: DEP_prep_14

value: Two

value: Promega


title: Parent replicate 1


title: DEP_pub_19

value: Pubertal

value: Rats sacrificed at postnatal day 63

value: One


title: K9 iMSC bio rep 2

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

hyb_protocol: Hybridization was performed according to Affymetrix Cartridge Array Hybridization on the GeneChip® Instrument protocol with wash protocol FS450_0002

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner

data_processing: Image files were converted to log2 expression values with RMA (Robust Multiarray Average) background correction and quantile normalization, as implemented by a statistical/visualization package (Partek Genomics Suite v6.6; St Louis, MO

label: WT Plus

organism: Canis lupus familiaris

source_name: canine iPS derived Mesenchymal Stem Cells

label_protocol: cDNA was prepared according to Affymetrix Genechip WT Plus Reagent Kit  protocol

growth_protocol: Canine skin fibroblast were collected following protocols approved by the IACUC. iPS cells were generated using the CytoTune iPS Reprograming kit. iMSC were generated from iPS by small molecule inhibition of TGFb signalling for 10 days. iMSC were then passaged, and processed along side parent iPS cells for microarray.

extract_protocol: RNA extracted using Qiagen RNeasy mini kit

treatment_protocol: iMSC were generated by tratment with 10uM TGFb inhibitor SB431542 for 10 days.

tag: cell type

value: iPS derived mesenchymal stem cells (iMSC)


title: Parent replicate 2


title: MDA-MB-231_naive_rep2

value: mammary gland/Breast

tag: replicate

value: replicate 2

tag: condition

value: naive


title: Testis_H3K4me1_rep3

description: ChIP-chip testis H3K4me1

source_name: H3K4me1 ChIP DNA from Oikopleura dioica testis

tag: chip antibody

tag: tissue

value: Testis

source_name: Input DNA from Oikopleura dioica testis

value: none, input DNA


title: MDA-MB-231_resistant_rep1

value: replicate 1

value: resistant


title: K9 iMSC bio rep 1


title: MDA-MB-231_naive_rep1


title: DEP_prep_13

tag: strain

value: Sprague-Dawley

tag: Sex

value: female

value: Caudal mammary tissue

value: Diethyl phthalate

value: Prepubertal

value: Rats sacrificed at postnatal day 42


title: K9 iMSC bio rep 3


title: DEP_prep_11

tag: exposure/treatment condition

tag: window of exposure

value: Promega


title: DEP_prep_12

tag: age at sacrifice

tag: batch


title: K9 iPSC bio rep3

source_name: canine induced pluripotent stem cells

value: induced pluripotent stem cells (iPSC)


title: K9 iPSC bio rep2


title: DEP_peri_10

description: Gene expression data from rat mammary tissues at postnatal day 21 following treatment with diethyl phthalate from postnatal day 1 to postnatal day 20

source_name: Rats treated with diethyl phthalate from postnatal day 1 to 20

value: Perinatal

value: Rats sacrificed at postnatal day 21

value: Two

tag: rna extraction kit


title: DEP_peri_5

description: Gene expression data from rat mammary tissues at postnatal day 21 following treatment with diethyl phthalate from gestation day 1 to gestation day 20

source_name: Rats treated with diethyl phthalate from gestation day 1 to 20


title: DEP_peri_4


title: DEP_peri_9


title: DEP_peri_6

value: One


title: DEP_peri_7


title: DEP_peri_1


title: DEP_peri_2


title: DEP_peri_8


title: DEP_peri_3


title: K9 iPSC bio rep1


title: Female_STV48_rep9

status: Public on Jan 25 2017

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

hyb_protocol: Samples were hybridized to oligonucleotide microarrays as per manufacturers' instructions for Low-Input Quick Amp kits (Agilent; v6.5). Arrays were designed using previously annotated ESTs from both Pacific and Atlantic L. salmonis (Yasuike et al. 2012; eArray design ID 024389; Agilent).

scan_protocol: Scanned at 5 micrometer resolution on a ScanArray Express (Perkin Elmer) and quantified on Imagene (v8.1; BioDiscovery).

data_processing: For each probe on the microarray, the background median was subtracted from the foreground median. Data analysis was performed in GeneSpring GX11 (Agilent). Each array was normalized using an intensity-dependent Lowess normalization. All entities on the array are presented in the attached matrix file here, however, for the analysis, quality control filters for each of the ttreatments retained probes that pass the following criteria in at least 65% of the samples in any one condition: raw signal ≥ 500 in both channels and no poor quality flags.

organism: Lepeophtheirus salmonis

source_name: adult lice (Pacific Canada)

label_protocol: Labeled cRNA was generated from 825ng total RNA using Low-Input Quick Amp kits (Agilent; v6.5). A Cy3-cRNA reference pool to hybridize alongside samples was created for each of the above experiments, ensuring each experimental condition was included in the pool.

growth_protocol: Adult female lice were obtained from  Atlantic salmon in a salmon farm near Broughton Archipegalo, British Columbia (BC) in 2011, and brought back to the Pacific Biological Station, Nanaimo, BC, Canada for exposure experiments. Time from the farms to the start of the experiments was > 24 hours.

extract_protocol: Lice were flash frozen individually and kept at -80 degrees Celcius until RNA extraction. Total RNA was extracted from frozen tissue using TRIzol reagent® (Life Technologies), on-column DNase digestion (QIAGEN) followed by RNEasy column purification as per manufacturers’ instructions (QIAGEN). Purified total RNA was tested by agarose gel and automated electrophoresis (Experion; Bio-Rad) and spec.

treatment_protocol: There was no treatment applied to the lice during the experiment.

value: Female

tag: feeding group

value: Starved

tag: time (h)

source_name: all condition pool

tag: sample type

value: reference


title: Female_STV48_rep7


title: Female_STV0_rep14


title: Female_STV48_rep6


title: Female_STV0_rep11


title: Female_STV0_rep13


title: Female_CO48_rep12

value: Coho


title: Female_CO24_rep9


title: Female_AT48_rep5

value: Atl


title: Female_SK24_rep10

value: Sox


title: Female_STV0_rep12


title: Female_SK24_rep9


title: Female_STV0_rep10


title: Female_STV48_rep10


title: Female_STV48_rep5


title: Female_STV0_rep9


title: Female_SK24_rep8


title: Female_STV48_rep8


title: Female_STV24_rep10


title: Female_STV24_rep9


title: Female_AT48_rep4


title: Female_CO24_rep7


title: Female_CO24_rep5


title: Female_SK48_rep9


title: Female_CO24_rep6


title: Female_SK24_rep6


title: Female_CO24_rep8


title: Female_AT24_rep4


title: Female_STV24_rep8


title: Female_STV24_rep7


title: Female_STV48_rep4


title: Female_SK24_rep5


title: Female_AT48_rep3


title: Female_SK48_rep8


title: Female_STV0_rep8


title: Female_SK24_rep7


title: Female_CO24_rep4


title: Female_CO48_rep11


title: Female_STV24_rep6


title: Female_AT24_rep3


title: Female_SK24_rep4


title: Female_SK48_rep7


title: AsPC-1_control_siSREBP2_2

city: Tokyo

first: Tsuyoshi

last: Osawa

address: 4-6-1 Komaba, Meguro-ku

department: RCAST

institute: The University of Tokyo

hyb_protocol: 10 micrograms of fragmented cRNA were hybridized (45 deg C, 16 hours). Hybridization was controlled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

scan_protocol: Scanning was performed in an Affymetrix GeneChip Scanner 3000 7G.

data_processing: GeneChip analysis was performed using the Affymetrix GeneChip Operating Software v1.4. Signal value was calculated using MAS5 algorithm with target intensity=100.

source_name: AsPC-1 control siSREBP2_2

label_protocol: In vitro transcription was performed on all of cDNA using the GeneChip IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by metal-induced hydrolysis.

growth_protocol: Human pancreatic carcinoma, epithelial-like cell line PANC-1 and adenocarcinoma ascites metastasis AsPC-1 were maintained in RPMI1640 or Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% fetal bovine serum (FBS) at 37 °C in a 5% CO2 atmosphere, respectively.

extract_protocol: Total RNA was extracted from cells using the Isogen reagent (Nippon Gene, Toyama, Japan), converted to cDNA by using the Prime Script reverse transcriptase (Takara, Shiga, Japan) as per the manufacturer’s instructions.The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix). Double-stranded cDNA was cleaned by Sample Cleanup Module (Affymetrix).

treatment_protocol: Cells were transfected with SREBP siRNAs or negative (scramble) control siRNA using Lipofectamine RNAi MAX transfection reagent according to the instructions of the manufacturer (Invitrogen Life Technologies, Massachusetts, USA). The ability of the siRNA to inhibit target gene expression was accessed 48 h posttransfection and then cultured either low pH culture medium (pH 6.8) or control medium (pH 7.4) for 24 h.

tag: culture condition

value: Control (pH 7.4)

tag: sirna

value: siSREBP2 #2


title: PANC-1_control_siSREBP2_1

source_name: PANC-1 control siSREBP2_1

value: siSREBP2 #1


title: AsPC-1_low_pH_siSREBP2_2

source_name: AsPC-1 low pH siSREBP2_2

value: low pH (pH 6.8)


title: PANC-1_low_pH_siSREBP2_1

source_name: PANC-1 low pH siSREBP2_1


title: AsPC-1_control_siSREBP2_1

source_name: AsPC-1 control siSREBP2_1


title: PANC-1_low_pH_siControl

source_name: PANC-1 low pH siControl

value: siControl


title: PANC-1_control_siSREBP2_2

source_name: PANC-1 control siSREBP2_2


title: AsPC-1_control_siControl

source_name: AsPC-1 control siControl


title: PANC-1_control_siControl

source_name: PANC-1 control siControl


title: Female_CO48_rep10


title: Neutrophils from sJIA sample 53 before treatment

city: London

first: Ebun

last: Omoyinmi

address: 30 Guilford Street

department: Infection, Inflammation and Rheumatology

country: United Kingdom

institute: UCL, Institute of Child Health

description: Gene expression data from Neutrophils (sJIA sample 53) before treatment

hyb_protocol: Samples were hybridized to Affymetrix U133 Plus 2.0 arrays.

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

data_processing: Processing of Affymetrix data was performed in  GeneSpring GX11.0 (Agilent) using GCRMA (RMA; Robust Multi-array Analysis that accounts for the probes GC content) method for normalizing and summarizing probe-level intensity measurements. The CHD file was generated in Affymetrix Expression console build 1.4.1.46 using RMA.

label_protocol: Samples were prepared using the GeneChip eukaryotic small sample target labeling assay, version II, with 100 ng of RNA and an Affymetrix GeneChip IVT labeling kit (Affymetrix, Santa Clara, CA)

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

tag: cell type

value: Neutrophils

tag: disease state

value: sJIA


title: PANC-1_low_pH_siSREBP2_2

source_name: PANC-1 low pH siSREBP2_2


title: AsPC-1_low_pH_siSREBP2_1

source_name: AsPC-1 low pH siSREBP2_1


title: AsPC-1_low_pH_siControl

source_name: AsPC-1 low pH siControl


title: Neutrophils from sJIA sample 53 after treatment

description: Gene expression data from Neutrophils (sJIA sample 53) after treatment


title: Female_SK48_rep6


title: Neutrophils from sJIA sample 51 before treatment

description: Gene expression data from Neutrophils (sJIA sample 51) before treatment


title: Female_AT48_rep2


title: Female_STV24_rep5


title: Female_STV48_rep3


title: Neutrophils from sJIA sample 50 after treatment

description: Gene expression data from Neutrophils (sJIA sample 50) after treatment


title: Female_AT24_rep2


title: Neutrophils from sJIA sample 51 after treatment

description: Gene expression data from Neutrophils (sJIA sample 51) after treatment


title: Neutrophils from sJIA sample 50 before treatment

description: Gene expression data from Neutrophils (sJIA sample 50) before treatment


title: Female_AT24_rep1


title: Female_CO24_rep3


title: Female_STV48_rep2


title: PBMC from sJIA sample 51 before treatment

description: Gene expression data from PBMC (sJIA sample 51) before treatment

value: PBMC


title: Female_CO24_rep2


title: PBMC from sJIA sample 53  after treatment

description: Gene expression data from PBMC (sJIA sample 53) after treatment


title: Neutrophils from sJIA sample 37 after treatment

description: Gene expression data from Neutrophils (sJIA sample 37) after treatment


title: PBMC from sJIA sample 50  after treatment

description: Gene expression data from PBMC (sJIA sample 50) after treatment


title: PBMC from sJIA sample 53 before treatment

description: Gene expression data from PBMC (sJIA sample 53) before treatment


title: Female_CO48_rep8


title: Female_SK48_rep3


title: Female_CO48_rep7


title: K562 KLF3-Repeat

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

country: China

institute: Beijing Institute of Genomics

description:
Gene expression data from K562 cells with KLF3 shRNA knockdown (Repeat)
K562 KLF3 shRNA KD - R

hyb_protocol: 1500 ng of cRNA were hybridized for 16 hr at 58C on HumanHT-12 V4.0 chip. The chip were washed and stained with Streptavidin-Cy3.

scan_protocol: GeneChips were scanned using the iScan Scanner.

data_processing: Bead Studio software

source_name: K562 cells with KLF3 shRNA knockdown

label_protocol: 250 µg of total RNA was used for microarray assay, using illumina Total Prep RNA Amplification Kit.

growth_protocol: K562 cells were purchased from ATCC and grown in culture flasks containing RPMI1640 medium supplied with 10% fetal bovine serum and penicillin (100 U/ml)-streptomycin (0.1 mg/ml). Cells were maintained at 37°C in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted from each cell culture dish with Trizol reagent.

treatment_protocol: Normally cultured K562 cells with KLF3 deficiency and shRNA control.

tag: cell line

tag: genotype/variation

value: KLF3 knockdown


title: Female_STV48_rep1


title: Neutrophils from sJIA sample 37 before treatment

description: Gene expression data from Neutrophils (sJIA sample 37) before treatment


title: Female_CO48_rep9


title: PBMC from sJIA sample 51  after treatment

description: Gene expression data from PBMC (sJIA sample 51) after treatment


title: PBMC from sJIA sample 50 before treatment

description: Gene expression data from PBMC (sJIA sample 50) before treatment


title: Female_STV0_rep6


title: 253949416326-2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis in R / Bioconductor.

molecule: polyA RNA

label_protocol: Agilent - Low RNA input QuickAmp

growth_protocol: A549 (human lung adenocarcinoma epithelial cell line, ATCC, number CCL-185) were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% featal bovine serum (FBS), 50U/ml penicillin, and 50µg/ml streptomycin (Life Technologies).

extract_protocol: Trizol+RNeasy+Minelute

treatment_protocol: Total RNA of A549 cells transfected for 48h with either mirVana miRNA mimic Control or miR-223-3p.

tag: tissue

value: lung

tag: amount in (ug)

tag: rin number


title: Female_SK48_rep5

tag: Sex


title: Female_STV24_rep4


title: Female_SK48_rep2


title: Female_STV24_rep3


title: 253949416326-4


title: 253949416326-3


title: Female_STV0_rep5


title: Female_SK48_rep4


title: 253949416326-1


title: Female_STV24_rep2


title: 253949416326-6


title: K562 CT

description:
Gene expression data from K562 cells with shRNA control
K562 Control

source_name: K562 cells with shRNA control

value: control


title: Female_CO48_rep6

value: Female


title: Female_SK48_rep10


title: K562 CT-Repeat

description:
Gene expression data from K562 cells with shRNA control (Repeat)
K562 Control - R


title: MG1655 galR::kana (with galactose)

city: Bethesda

first: Andrei

middle: Nikolai

last: Trostel

state: Maryland

address: 9000 Rockville Pike, Building 37, Room 5138

department: Laboratory of Molecular Biology

institute: National Institutes of Health

hyb_protocol: Labeled cDNA fragments (3 ug) were hybridized at 45 °C at 60 rpm for 16 h to the tiling array chips (coli_Tab520346F) purchased from Affymetrix. The chips were then washed with wash buffer A: nonstringent wash buffer (6X SSPE, 0.01% Tween-20); wash buffer B: (100 mM Mes, 0.1M [Na+], 0.01% Tween-20) and stained with streptavidin phycoerythrin (Invitrogen, S-866) and antistreptavidin goat antibody biotinylated (Vector Laboratories, BA-0500) on a Genechip Fluidics Station 450 (Affymetrix) according to washing and staining protocol (ProkGE-WS2 450).

scan_protocol: Arrays were scanned on an GeneChip© Scanner 3000 per manufacturer’s protocol.

data_processing:
Standardized signals, for each probe in the arrays, were generated using the MAT software (Johnson WE et al. 2006), which provides a model-based, sequence-specific, background correction for each sample. A gene-specific score was then calculated for each gene by averaging all MAT scores (natural log) for all probes under the annotated gene coordinates. Gene annotation was from the ASAP database (Glasner JD et al. 2003) at the University of Wisconsin-Madison, for E. coli K-12 MG1655 version m56. Differences of two log scale values in the absence of D-galactose were calculated in galR mutant cells.  Finally, the transcriptome results (log scale values) without D-galactose were compared graphically [References: Johnson WE, et al. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 103:12457–12462; Glasner JD, et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 31:147–151]
The MAT software provides analysis capabilities specifically for the GeneChip® Tiling Arrays. MAT analyzes feature intensity data stored in GCOS output .CEL files and produces:
The program used to generate the bed/bar files is “Affymetrix Tiling Analysis Software.” Standardized signals, for each probe in the arrays, were generated using the MAT software (Johnson WE et al. 2006), which provides a model-based, sequence-specific, background correction for each sample. A gene-specific score was then calculated for each gene by averaging all MAT scores (natural log) for all probes under the annotated gene coordinates. Gene annotation was from the ASAP database (Glasner JD et al. 2003) at the University of Wisconsin-Madison, for E. coli K-12 MG1655 version m56. Differences of two log scale values in the absence of D-galactose were calculated in galR mutant cells.  Finally, the transcriptome results (log scale values) without D-galactose were compared graphically [References: Johnson WE, et al. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 103:12457–12462; Glasner JD, et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 31:147–151]
pvalue.bar files also provided
.bar files are generated using Affymetrix Tiling Analysis Software.
The TAS software provides analysis capabilities specifically for the GeneChip® Tiling Arrays. TAS analyzes feature intensity data stored in GCOS output .CEL files and produces:
Signal and p-values for each genomic position interrogated.
Computation of genomic intervals based on computed signal and p-values
Computation of summary statistics
Visualizations for assessing the quality of the array data

label: phycoerythrine

organism: Escherichia coli

source_name: Test

label_protocol: Fragmented cDNA was then 3' termini biotin-labeled using the GeneChip DNA labeling reagent, 900542 (Affymetrix) and 60 U of terminal deoxynucleotidyl transferase, M1875 (Promega) at 37 °C for 1 h. The labeling reaction was then stopped by the addition of 0.5M EDTA.

growth_protocol: E. coli wildtype and GalR mutant cells were cultivated in 125-mL corning flasks containing 30 mL of M63 minimal medium plus glycerol (final 0.3%) at 37 °C.

extract_protocol: Cells were then placed on ice and RNAprotect™ bacteria reagent (Qiagen) was added to stabilize the RNA. Total RNAs of cells were purified by RNeasy mini kit (Qiagen). Isolated RNA (10 ug) was used for random primer cDNA synthesis using SuperScript II reverse transcriptase, 18064–071 (Invitrogen). The reaction mixture was then subsequently treated with 1 N NaOH to degrade any remaining RNA and treated with 1 N HCl to neutralize the NaOH. Synthesized cDNA was then purified using MiniElute PCR purification columns, 28004 (Qiagen). Purified cDNA (3 ug) was fragmented to between 50 and 200 bps by 0.6 U/ g of DNase I, 27–0514-01 (Amersham Biosciences) for 10 min at 37 °C in 1  One-Phor-All buffer, 27–0901-02 (Amersham Biosciences). Heat inactivation of the DNase I enzyme was performed at 98 °C for 10 min.

treatment_protocol: At OD600 of 0.5, cell cultures were separated into two flasks. D-galactose (final 0.3%) or water were added and cells were grown for 1.5 h further.

value: galR mutant

tag: treatment

value: with D-galactose


title: Female_AT48_rep1

source_name: adult lice (Pacific Canada)

value: reference


title: MG1655 galR minus w/o galactose

data_processing:
Standardized signals, for each probe in the arrays, were generated using the MAT software (Johnson WE et al. 2006), which provides a model-based, sequence-specific, background correction for each sample. A gene-specific score was then calculated for each gene by averaging all MAT scores (natural log) for all probes under the annotated gene coordinates. Gene annotation was from the ASAP database (Glasner JD et al. 2003) at the University of Wisconsin-Madison, for E. coli K-12 MG1655 version m56. Differences of two log scale values in the absence of D-galactose were calculated in galR mutant cells.  Finally, the transcriptome results (log scale values) without D-galactose were compared graphically [References: Johnson WE, et al. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 103:12457–12462; Glasner JD, et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 31:147–151]
The MAT software provides analysis capabilities specifically for the GeneChip® Tiling Arrays. MAT analyzes feature intensity data stored in GCOS output .CEL files and produces:
The program used to generate the bed/bar files is “Affymetrix Tiling Analysis Software.” Standardized signals, for each probe in the arrays, were generated using the MAT software (Johnson WE et al. 2006), which provides a model-based, sequence-specific, background correction for each sample. A gene-specific score was then calculated for each gene by averaging all MAT scores (natural log) for all probes under the annotated gene coordinates. Gene annotation was from the ASAP database (Glasner JD et al. 2003) at the University of Wisconsin-Madison, for E. coli K-12 MG1655 version m56. Differences of two log scale values in the absence of D-galactose were calculated in galR mutant cells.  Finally, the transcriptome results (log scale values) without D-galactose were compared graphically [References: Johnson WE, et al. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 103:12457–12462; Glasner JD, et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 31:147–151]
pvalue.bar files also provided
.bar files are generated using Affymetrix Tiling Analysis Software.
The TAS software provides analysis capabilities specifically for the GeneChip® Tiling Arrays. TAS analyzes feature intensity data stored in GCOS output .CEL files and produces:

treatment_protocol: At OD600 of 0.5, cell cultures were separated into two flasks. D-galactose (final 0.3%) or water were added and cells were grown for 1.5 h further. These were the ones with water.

value: no galactose


title: MG1655 w/o galactose

source_name: Control

value: wild type


title: 253949416326-5


title: Female_STV24_rep1

value: Starved

source_name: all condition pool


title: 253949416326-7


title: OS-si-MSX1-3

city: Hiroshima

first: katsumi

last: Fujimoto

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University

hyb_protocol: cRNA fragmentation and hybridization were preformed using the Gene Expression Hybridization Kit (Agilent) according to the manufacturer's instructions. 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes. The fragmentation mixture was hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash buffer 2 (Agilent) according to the manufacturer's instructions.

scan_protocol: The arrays were then scanned using the Agilent DNA Microarray Scanner (G2565CA).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: dental pulp cell, MSX1 siRNA, osteogenic induction

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp Labeling Kit, one color (Agilent) according to the manufacturer's instructions.

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

value: mandibular left deciduous canine

tag: gender

value: male

tag: age


title: B6_female_astrocyte_clone#3(3)_Wild type

city: Frederick

first: Karlyne

middle: M

last: Reilly

state: MD

address: West 7th St at Fort Detrick, PO Box B

department: Mouse Cancer Genetics Program

institute: National Cancer Institute, Center for Cancer Research

description: cells cultured in DMEM + 20% FBS + antibiotics, untransfected

hyb_protocol: Labeled cDNA of each sample were hybridized to Affymetrix mouse Gene ST 2.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.  Wash and stain were performed on Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000 and data were collected using Affymetrix AGCC software.

data_processing: Data was normalized in Partek Genomics Suite v6.5 using RMA normalization algorithm, correcting for GC probe content. Scrambled shRNA control samples and primary astrocytes were selected for M vs F comparison.

source_name: C57BL/6J female astrocyte, Wild type

label_protocol: RNA (100 ng) was reverse transcribed and amplified using Ambion WT expression kit following manufacturer’s suggested protocol. Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

growth_protocol: Mouse male and female astrocytoma cells, established from C57BL/6J (B6) mice with astrocytoma , were cultured in DMEM + 10% FBS + antibiotics. Primary astrocytes cultured from P0-P1C57BL/6J neonates were grown in DMEM + 20% FBS + antibiotics.

extract_protocol: Total RNA was extracted from mouse astrocytoma cells using RNeasy Mini Kit (Qiagen) and treated with TURBO DNAfree (Ambion). RNA quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: Mouse male and female astrocytoma cells were transfected using the Lipofectamine 2000 transfection protocol (Invitrogen). Each well of a 6-well plate received 3.5 μg of total DNA for two days. Cells were seeded in 6-well plates with 3 X 10^5 cells per well and transduced with pLKO.1-puro Cdca7l-shRNA or pLKO.1-puro non-target shRNA the following day. After 8 hrs of incubation, the supernatant was removed, and 2 ml of DMEM complete medium was added. After 16 hrs, the transfection was repeated a second time and medium was not changed. 48 hrs post-transfection, puromycin selection was initiated to make the Cdca7l-depleted stable cell lines.

value: female

tag: strain

tag: cdca7l expression

value: Wild type


title: B6_female_astrocyte_clone#1(3)_Wild type


title: B6_female_astrocyte_clone#1(4)_Wild type


title: Female_CO24_rep1

tag: feeding group

value: Coho

tag: time (h)


title: OS-si-cont-2

source_name: dental pulp cell, control siRNA, osteogenic induction


title: MG1655 (with galactose)


title: Female_STV0_rep4

tag: sample type


title: OS-si-cont-3


title: Female_SK24_rep3

value: Sox


title: OS-si-MSX1-2


title: Female_SK24_rep2


title: Female_STV0_rep1


title: Female_STV0_rep2


title: Female_CO48_rep4


title: B6_male_astrocyte_clone#1(2)_Wild type

source_name: C57BL/6J male astrocyte, Wild type


title: OS-si-cont-1


title: B6_male_astrocyte_clone#4(3)_Wild type


title: B6_male_astrocyte_clone#5(3)_Wild type


title: Female_STV0_rep7


title: Female_CO48_rep3


title: B6_female_astrocytoma_K5001_clone#1_shRNA/Cdca7l(2)

description: cells cultured in DMEM + 10%FBS +antibiotics, and stably transfected

source_name: C57BL/6J female astrocytoma, Cdca7l depleted

value: CDCA7L depletion


title: B6_female_astrocytoma_K5001_clone#1_scrambled shRNA

source_name: C57BL/6J female astrocytoma, non-targeting scrambled shRNA

value: Scrambled shRNA contorl


title: B6_female_astrocytoma_K2797_clone#4_scrambled shRNA


title: B6_female_astrocytoma_K2797_clone#2_shRNA/Cdca7l(2)


title: B6_female_astrocytoma_K2797_clone#3_shRNA/Cdca7l(2)


title: B6_female_astrocytoma_K2797_clone#3_scrambled shRNA


title: B6_male_astrocytoma_K1861_clone#4_shRNA/Cdca7l(2)

source_name: C57BL/6J male astrocytoma, Cdca7l depleted


title: B6_male_astrocytoma_K1861_clone#3_scrambled shRNA

source_name: C57BL/6J male astrocytoma, non-targeting scrambled shRNA


title: B6_male_astrocytoma_K1861_clone#1_scrambled shRNA


title: OS-si-MSX1-4


title: B6_male_astrocytoma_K1861_clone#1_shRNA/Cdca7l(2)


title: Female_SK48_rep1

value: Sockeye


title: B6_male_astrocytoma_K4820_clone#2_scrambled shRNA


title: Female_CO48_rep1


title: Female_SK24_rep1


title: B6_male_astrocytoma_K4820_clone#2_shRNA/Cdca7l(2)


title: B6_male_astrocytoma_K4820_clone#1_scrambled shRNA


title: B6_male_astrocytoma_K4820_clone#3_shRNA/Cdca7l(2)


title: Female_CO48_rep2


title: Post ibrutinib 29 days Pool 2

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

description: Relapse/ Refractory Chronic Lymphocytic leukemia patients

hyb_protocol: 100ng of total RNA was annealed with multiplexed DNA tags (miR-tag) and bridges target specifics. Mature microRNAs were bond to specific miR-tags using a Ligase enzyme and all the tags in excess were removed by enzyme clean-up step. The tagged microRNAs product was diluted 1 to 5 and 5 ul was combined with 20 ul of Reported Probes in hybridization buffer and 5 ul of Capture probes. The overnight hybridization (16 to 20 hours) at 65°C allowed to complex probes sequence specific with targets. Probes excess were removed using two-step magnetic beads based purification on an automated fluidic handling system (nCounter Prep Station) and target/probe complexes were immobilized on the cartridge for data collection.

scan_protocol: The nCounter Digital Analyzer collected the data by taking images of immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. For each cartridge, a high-density scan encompassing 600 fields of view (FIV) has been performed. RLF file, conteing all the key info about the ProbeSet used (such as barcodes info for each specific target miR, Positives controls, Negatives Controls and Housekeeping genes) was uploaded to the Scanner. A CDF file with the experiment informations (sample ID, Data, RLF file needed to be used, FOVs) was uploaded to the Digital Analyzer before to scan the cartridge. RCC files (Reporter Code Count) were collected once the scan was done.

data_processing: miRNA counts were normalized for hybridization efficiency using the 6 positive controls in each sample, then quantile normalization was used to biologically normalize across samples.

source_name: Perpherial Blood lymphocytes

growth_protocol: Perpherial blood CLL cells were isolated using ficoll gradient. Cells were cyropreserved. Cells were thawed and put into trizol. The RNA was isolated using Trizol and purified using the miRVana kit.

treatment_protocol: CLL patients received 420mg/day ibrutinib treatment on clinical trial OSU-10053 (NCT01217749).

tag: tissue type

value: Perpherial Blood lymphocytes

tag: collection time

value: 29 days


title: Post ibrutinib 8 days Pool 2

extract_protocol: Cells were thawed and put into trizol. The RNA was isolated using Trizol and purified using the miRVana kit.

value: 8 days


title: Post ibrutinib 2hr Pool 2

value: 2 hrs


title: Post ibrutinib 24hr Pool 2

value: 24 hrs


title: kidney of db/db mice with Tang-shen formula treatment,biological rep1

first: Hailing

last: Zhao

address: Yinghua DongLu Hepingli Chaoyang District

institute: China–Japan Friendship Hospital

description: Gene expression data from kidney of 20-week-old male db/db mice with TSF-treatment

hyb_protocol: 15µg  fragmented  cRNA,  Control  Oligo  B2  and eukaryotic hybridization controls was hybridized  to  Affymetrix Mouse Genome 430 2.0 Array at 45° C for 16 h in Affymetrix GeneChip  Hybridization Oven 640

scan_protocol: The GeneChip  arrays  were  then  washed  and  stained  with  streptavidin  phycoerythrinonan  with Affymetrix GeneChip FluidicsStation 450, followed by scanning with Affymetrix GeneChip Scanner 3000 7G

data_processing: Data  were  analyzed  using  Affymetrix  Expression  Console  and  Transcriptome  Analysis Console  software

label_protocol: 100ng of total RNA was used  for cDNA synthesis, biotin-tagged cRNA was produced using the GeneChip IVT  Labeling  Kit  (Affymetrix).

growth_protocol: Mice were housed using controlled humidity (55 ± 15%) and temperature (23 ±  3° C), with a 12-h light-dark cycle.  The mice were allowed access to standard laboratory food and water ad libitum.

treatment_protocol: The db/db mice were divided into 2 groups (n = 9 for each group): one was given TSF by intra-gastric gavage (2.4 g/kg/day), whereas the other was administered saline.  After 12 weeks  of  TSF  treatment, kidney tissues  were  collected  for  further  analysis

value: 20-week-old male db/db mice

tag: genotype

value: C57BLKS/J db/db mice


title: kidney of db/m mice ,biological rep3

description: Gene expression data from kidney of 20-week-old male db/m mice

source_name: kidney of 20-week-old male db/m mice

value: 20-week-old male db/m mice

value: C57BLKS/J db/m mice


title: Pre-ibrutinib Peripheral blood Pool 2


title: kidney of db/db mice ,biological rep1

description: Gene expression data from kidney of 20-week-old male db/db mice

source_name: kidney of 20-week-old male db/db mice


title: kidney of db/db mice ,biological rep3


title: Post ibrutinib 29 days Pool 1


title: kidney of db/db mice ,biological rep2


title: kidney of db/m mice ,biological rep1


title: kidney of db/db mice with Tang-shen formula treatment,biological rep3

source_name: kidney of 20-week-old male db/db mice with TSF-treatment


title: Post ibrutinib 8 days Pool 1


title: kidney of db/db mice with Tang-shen formula treatment,biological rep2


title: Post ibrutinib 24hr Pool 1


title: kidney of db/m mice ,biological rep2


title: Post ibrutinib 2hr Pool 1


title: Pre-ibrutinib Peripheral blood Pool 1


title: Pre-Ibrutinib Bone marrow Pool 1

source_name: Bone marrow lymphocytes

value: Bone marrow lymphocytes


title: additional molar germs at E70, biological rep3

status: Public on Jan 24 2017

first: Fu

last: Wang

address: Tian Tan Xi Li No.4, P. R. China

institute: Capital Medical University

description:
Gene expression data from additional molar germs at E70.
E70-3_(Porcine)

hyb_protocol: Array hybridization and washes were performed as detailed in the manufacturer’s instructions.

scan_protocol: The arrays were scanned using the GeneChip® scanner 3000 (Affymetrix, CA, US) and Command Console software 3.1 (Affymetrix, CA, US) with default settings.

data_processing: Raw data were normalized using the MAS 5.0 algorithm of Gene Spring software 11.0 (Agilent technologies, CA, US).

organism: Sus scrofa

source_name: additional molar germs at E70

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

growth_protocol: The staged miniature pig embryos and fetuses were obtained by cesarean section at E50, E60, and E70, and part of it subjected to histological analysis to determine the developmental stage.

extract_protocol: Total RNA was extracted from samples at specific stages using TRIZOL Reagent (Life technologies, CA, US) following the manufacturer’s instructions, and then checked for integrity using an Agilent Bioanalyzer 2100 (Agilent technologies, CA US).  Total RNA was further purified using the RNeasy mini kit and RNase-Free DNase Set (QIAGEN, GmBH, Germany)

treatment_protocol: The additional molar germs, attached the dental lamina from the mandibles of the staged miniature pig embryos were isolated and immerged in 5–10 volumes of RNAlater solution (Ambion, USA) overnight at 4°C, and then stored at –20°C until needed for total RNA extraction.

tag: breed

value: Wuzhishan miniature pig

tag: developmetaal stage

value: E70 when M1 progresses to late bell but M2 changes little

value: additional molar germs


title: additional molar germs at E70, biological rep1

description:
Gene expression data from additional molar germs at E70.
E70-1_(Porcine)

tag: tissue


title: K562 KLF3

description:
Gene expression data from K562 cells with KLF3 shRNA knockdown
K562 KLF3 shRNA KD

source_name: K562 cells with KLF3 shRNA knockdown

tag: cell line

tag: genotype/variation

value: KLF3 knockdown


title: additional molar germs at E60, biological rep3

description:
Gene expression data from additional molar germs at E60.
E60-3_(Porcine)

source_name: additional molar germs at E60

value: E60 targeting M1 at bell followed by M2 initiation


title: additional molar germs at E60, biological rep2

description:
Gene expression data from additional molar germs at E60.
E60-2_(Porcine)


title: additional molar germs at E60, biological rep1

description:
Gene expression data from additional molar germs at E60.
E60-1_(Porcine)


title: additional molar germs at E50, biological rep3

description:
Gene expression data from additional molar germs at E50.
E50-3_(Porcine)

source_name: additional molar germs at E50

value: E50 corresponding to M1 at cap without M2 initiation


title: additional molar germs at E50, biological rep2

description:
Gene expression data from additional molar germs at E50.
E50-2_(Porcine)


title: additional molar germs at E70, biological rep2

description:
Gene expression data from additional molar germs at E70.
E70-2_(Porcine)


title: additional molar germs at E50, biological rep1

description:
Gene expression data from additional molar germs at E50.
E50-1_(Porcine)


title: Noninfected preterm birth endovascular cytotrophoblasts 2

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

hyb_protocol: Sample processing and hybridization were done according to protocols that were devised by the UCSF Gladstone (NHLBI) Genomics Core Facility.

scan_protocol: GeneChips were scanned using a GeneArray Scanner

data_processing: Gene level expression data quality was confirmed, normalized (RMA) and summarized (Affymetrix Expression Console Software). The Sample data tables include transcripts that were annotated and categorized as coding or non-coding (with the non-coding RNAs further broken down into the respective classes lncRNA, microRNA, NATs, pseudogenes, and snoRNA). A coding/noncoding column and an RNA class column are included in the further processed data on the Series record.  Significant differential expression was determined by ANOVA (p < 0.05) and absolute linear fold change >1.5 (Affymetrix Transcriptome Analysis Console Software).

source_name: human placenta, noninfected preterm birth

label_protocol: Samples were prepared using the Ambion Whole-Transcript (WT) Expression kit, used in conjunction with the Affymetrix GeneChip  WT Terminal Labeling and Controls Reagent kit

extract_protocol: Total RNA was extracted using Qiagen RNeasy Plus Micro

treatment_protocol: Laser microdissection enabled the isolation of samples that were enriched for syncytiotrophoblasts, invasive cytotrophoblasts or endovascular cytotrophoblasts.

tag: disease state

value: noninfected preterm birth

value: endovascular cytotrophoblasts


title: Noninfected preterm birth endovascular cytotrophoblasts 3


title: Noninfected preterm birth endovascular cytotrophoblasts 1


title: IM2

city: Bejing

first: Jing

last: Dai

address: No.2 Yuanmingyuan West Road, Haidian District

institute: College of Resources & Environmental Sciences, China Agricultural University

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The probe cell intensity data were generated using GeneChip Operating software (GCOS 1.4) and the data were normalized using dChip. The differential expressed genes were screened with SAM software.

organism: Zea mays

source_name: maize

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

growth_protocol: Peanut (Arachis hypogaea L. cv. Luhua14) and maize (Zea mays L. cv. Nongda108) seeds were grown in calcareous sandy soil in a greenhouse. The soil was enhanced with basal fertilizers [composition (mg·kg−1 soil): N, 100 (Ca (NO3)2·4H2O); P, 150 (KH2PO4); K, 100 (KCl); Mg, 50 (MgSO4·7H2O); Cu, 5 (CuSO4·5H2O); and Zn, 5 (ZnSO4·7H2O)]. The plants were grown in a greenhouse under natural light conditions (28–32 °C).

extract_protocol: Total RNA was extracted from roots using TRIzol reagent (Invitrogen, the United States of America).

treatment_protocol: The experiment consisted of three cropping treatments: peanut monocropping, maize monocropping and intercropping of peanut and maize.

tag: treatment

value: intercropped

value: root

tag: developmental stage

value: reproductive stage


title: Noninfected preterm birth invasive cytotrophoblasts 4

value: invasive cytotrophoblasts


title: IM1


title: IM3


title: M3

value: monocropped


title: Noninfected preterm birth syncytium 4

value: syncytium


title: Noninfected preterm birth endovascular cytotrophoblasts 4


title: Noninfected preterm birth invasive cytotrophoblasts 1


title: M1


title: Noninfected preterm birth invasive cytotrophoblasts 3


title: corneal_endothelium_control_A62

city: Leuven

first: Joost

middle: J

last: van den Oord

address: Minderbroedersstraat 12, block q, box 1032

department: Department of Imaging & Pathology

country: Belgium

institute: KU Leuven

description:
Control
total RNA (> 200 nucleotides)

data_processing: Data analysis was done through the web portal of Qiagen, according to the manufacturers instructions: http://qiagen.com/geneglobe. The web-based software automatically performed all ΔΔCt based fold-change calculations from the uploaded raw threshold cycle data. For normalization it used the average arithmetic mean of Ct values from three reference genes: RPL13A, RPL19 and RPS5. To calculate p-values it used a two-sided t-statistic. Sample table reports normalized signal (against housekeeping genes). Fold Change file reports FECD/Control ratios.

label: SYBR Green

source_name: corneal endothelium control

label_protocol: PCR assays were performed using two complementary Custom RT² Profiler PCR Arrays (CAPH10409 and CAPH104010, Qiagen) following the manufacturer's instructions. Reverse transcription was performed from 100 ng of total RNA per sample for each 96-well plate, using the RT² First Strand Kit (Qiagen). Quantitative real-time PCR was performed (7900 HT Fast Real-Time PCR System; Applied Biosystems, Carlsbad, California) with 40 cycles at 95°C for 15 seconds and 60°C for 60 seconds, using RT² SYBR Green ROX qPCR Mastermix (Qiagen).

extract_protocol: The samples were collected in RNAlater. Tissues were disrupted and homogenized manually with a Disposable Pestle (VWRTM International, Radnor, Pennsylvania). RNA extraction was performed with RNeasy® Micro Kit (Qiagen, Hilden, Germany), without DNase treatment.

tag: gender

value: Female

tag: age

value: corneal endothelium with Descemet's membrane

tag: group

value: donor cornea as normal control

tag: phakic or pseudophakic

value: unknown

tag: Cause of death

value: edema ascites decompensation

tag: number of cells per mm²


title: Noninfected preterm birth invasive cytotrophoblasts 2


title: corneal_endothelium_control_A32

description:
Control
total RNA (> 200 nucleotides)

value: Male

value: traffic accident


title: Severe preeclampsia endovascular cytotrophoblasts 4

source_name: human placenta, severe preeclampsia

value: severe preeclampsia


title: Severe preeclampsia endovascular cytotrophoblasts 2


title: corneal_endothelium_control_A59

description:
Control
total RNA (> 200 nucleotides)

value: cerebral aneurysm


title: M2


title: corneal_endothelium_control_B37

description:
Control
total RNA (> 200 nucleotides)

value: cerebral hemorrhage


title: corneal_endothelium_FECD_A57

description:
FECD
total RNA (> 200 nucleotides)

source_name: corneal endothelium FECD

value: Fuchs' endothelial corneal dystrophy

tag: inheritance

value: not known

tag: type of surgery

value: Descemet's stripping automated endothelial keratoplasty

value: pseudophakic

tag: time between cataract surgery and keratoplasty (in months)


title: Severe preeclampsia endovascular cytotrophoblasts 3

value: endovascular cytotrophoblasts


title: corneal_endothelium_control_A12

description:
Control
total RNA (> 200 nucleotides)

value: trauma


title: corneal_endothelium_control_A54

description:
Control
total RNA (> 200 nucleotides)

value: cerebrovascular accident


title: Severe preeclampsia endovascular cytotrophoblasts 1


title: Noninfected preterm birth syncytium 1

value: noninfected preterm birth

value: syncytium


title: Female_STV0_rep3

source_name: adult lice (Pacific Canada)

tag: Sex

value: Female

tag: feeding group

value: Starved

tag: time (h)

source_name: all condition pool

tag: sample type

value: reference


title: GIST48b_rep1-3

city: Erlangen

first: Evgeny

middle: A.

last: Moskalev

address: Ktankenhausstr. 8-10

department: Institute of Pathology

institute: University of Erlangen-Nuremberg

description:
This Sample represents 3 replicates.
GIST48b_1, GIST48b_2, GIST48b_3

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

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

data_processing: RnBeads version 1.2.

label: Cy5 and Cy3

source_name: Cell line GIST48b

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from GIST cell lines using Qiagen DNeasy Kit according to standard instructions.

tag: cell line

tag: cell type

value: gastrointestinal stromal tumour (GIST) cell line

tag: anatomic site of tumour origin

value: small intestine


title: Female_CO48_rep5

value: Coho


title: Noninfected preterm birth syncytium 3

tag: disease state

tag: tissue


title: Severe preeclampsia invasive cytotrophoblasts 1

value: severe preeclampsia

value: invasive cytotrophoblasts


title: Severe preeclampsia invasive cytotrophoblasts 3


title: Noninfected preterm birth syncytium 2


title: GIST882_rep1-3

description:
This Sample represents 3 replicates.
GIST882_1, GIST882_2, GIST882_3

source_name: Cell line GIST882


title: Severe preeclampsia syncytium 4


title: Severe preeclampsia invasive cytotrophoblasts 2


title: corneal_endothelium_control_A70

description:
Control
total RNA (> 200 nucleotides)

tag: gender

value: Male

tag: age

value: corneal endothelium with Descemet's membrane

value: donor cornea as normal control

value: unknown

value: acute myocardial infarction


title: corneal_endothelium_control_A20

description:
Control
total RNA (> 200 nucleotides)

tag: group

tag: phakic or pseudophakic


title: Severe preeclampsia syncytium 2


title: corneal_endothelium_FECD_A11

description:
FECD
total RNA (> 200 nucleotides)

value: Fuchs' endothelial corneal dystrophy

value: not known

value: Descemet's stripping automated endothelial keratoplasty

value: pseudophakic

tag: Cause of death

tag: number of cells per mm²


title: corneal_endothelium_FECD_A52

description:
FECD
total RNA (> 200 nucleotides)

tag: inheritance

tag: type of surgery


title: corneal_endothelium_FECD_A61

description:
FECD
total RNA (> 200 nucleotides)

value: Female

tag: time between cataract surgery and keratoplasty (in months)


title: corneal_endothelium_FECD_B18

description:
FECD
total RNA (> 200 nucleotides)


title: Severe preeclampsia syncytium 3

value: syncytium