title: MA_Q6

description:
replicate 6
t24.E2.AP20187 rep6

source_name: MCF-7 cell line treated with estrogen and AP20187


title: MA_U1

status: Public on Jul 17 2013

type: RNA

city: Cambridge

first: Mauro

middle: Antonio

last: Alves Castro

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

description:
replicate 1
t6.E2.AP20187.PD rep1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw image files were processed and analysed using the Beadarray R package. The data was corrected for spatial artifacts, log (base 2) transformed, and quantile normalised. Note: detection p-values are not available

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF-7 cell line treated with estrogen, AP20187 and PD173074

label_protocol: Standard Illumina label protocol

growth_protocol: MCF7 human breast cancer cells were cultured in DMEM supplemented with 10% HI-FCS and antibiotics. Cell synchronisation via estrogen deprivation was carried out for at least 3 days in phenol red-free DMEM (Invitrogen) supplemented with 5% charcoal dextran-treated HI-FBS (Hyclone) and 1% penicillin-streptomycin. All cells were grown at 37oC in 5% CO2

extract_protocol: RNA was extracted using the miRNeasy spin column kit (Qiagen) and quality checked using an RNA 6000 Nano chip on a 2100 Bioanalyser (Agilent). 250ng RNA (RIN>7) was used for cRNA amplification and labelling using the Illumina TotalPrep-96 kit (Ambion 4397949)

treatment_protocol: Estrogen deprived cells were stimulated with 1nM estradiol (Sigma); 100ng/mL FGF10 (Invitrogen); 100ng/mL PD173074 (Sigma-Aldrich). iF2 was activated with 100nM AP20187 (Takara Biosciences)

tag: cell line

tag: treatment duration (hs)


title: MA_U2

description:
replicate 2
t6.E2.AP20187.PD rep2


title: MA_Q5_rep

description:
technical replicate 5
t24.E2.AP20187 rep5 (technical replicate of sample MA_Q5)


title: MA_Q2

description:
replicate 2
t24.E2.AP20187 rep2


title: MA_U5

description:
replicate 5
t6.E2.AP20187.PD rep5


title: MA_Q3_rep

description:
technical replicate 3
t24.E2.AP20187 rep3 (technical replicate of sample MA_Q3)


title: MA_Q3

description:
replicate 3
t24.E2.AP20187 rep3


title: MA_V5

description:
replicate 5
t6.E2.AP20187 rep5


title: MA_V2

description:
replicate 2
t6.E2.AP20187 rep2


title: MA_V6

description:
replicate 6
t6.E2.AP20187 rep6


title: MA_Q1

description:
replicate 1
t24.E2.AP20187 rep1


title: MA_V3

description:
replicate 3
t6.E2.AP20187 rep3


title: MA_S4_rep

description:
technical replicate 4
t24.E2 rep4 (technical replicate of sample MA_S4)

source_name: MCF-7 cell line treated with estrogen


title: MA_S1_rep

description:
technical replicate 1
t24.E2 rep1 (technical replicate of sample MA_S1)


title: MA_S2

description:
replicate 2
t24.E2 rep2


title: MA_S3

description:
replicate 3
t24.E2 rep3


title: MA_V1

description:
replicate 1
t6.E2.AP20187 rep1


title: MA_S6

description:
replicate 6
t24.E2 rep6


title: MA_S5

description:
replicate 5
t24.E2 rep5


title: MA_S6_rep

description:
technical replicate 6
t24.E2 rep6 (technical replicate of sample MA_S6)


title: MA_S4

description:
replicate 4
t24.E2 rep4


title: MA_S1

description:
replicate 1
t24.E2 rep1


title: MA_X6

description:
replicate 6
t6.E2 rep6


title: MA_X4

description:
replicate 4
t6.E2 rep4


title: MA_X5

description:
replicate 5
t6.E2 rep5


title: MA_T2

description:
replicate 2
t24.UT rep2

source_name: MCF-7 cell line treated with vehicle


title: MA_X2

description:
replicate 2
t6.E2 rep2


title: MA_X1

description:
replicate 1
t6.E2 rep1


title: MA_Q5

description:
replicate 5
t24.E2.AP20187 rep5


title: MA_T5

description:
replicate 5
t24.UT rep5


title: MinusTet.PlusE2.3h rep1

description:
replicate 1
E1

source_name: MCF-7 cell line treated with estrogen (minus tetracycline)

growth_protocol: MCF7 human breast cancer cells were cultured in DMEM supplemented with 10% HI-FCS and antibiotics. Cell synchronisation via estrogen deprivation was carried out for at least 3 days in phenol red-free DMEM (Invitrogen) supplemented with 5% charcoal dextran-treated HI-FBS (Hyclone) and 1% penicillin-streptomycin. All cells were grown at 37oC in 5% CO2. The FGFR2b tetracycline-inducible over-expression MCF7 line was established by double-transfection of FspI-linearised F2b-pcDNA4/TO and pcDNA6/TR in a 1:5 ratio by DNA weight. Single cell clones were expanded under selection using 500μg/mL Zeocin and 3μg/mL blasticidin. Tetracycline induction of FGFR2b expression was confirmed by Western blot

treatment_protocol: Estrogen deprived cells were stimulated with 1nM estradiol (Sigma); 100ng/mL FGF10 (Invitrogen). FGFR2b over-expression was induced by tetracycline (final concentration of 1mg/mL)

tag: group

value: MinusTet


title: MA_Y3

description:
replicate 3
t6.UT rep3


title: MA_Z6

description:
replicate 6
t0.UT rep6


title: MA_T6

description:
replicate 6
t24.UT rep6


title: MA_Y5

description:
replicate 5
t6.UT rep5


title: MA_Q4

description:
replicate 4
t24.E2.AP20187 rep4


title: MA_Z3

description:
replicate 3
t0.UT rep3


title: MA_T3

description:
replicate 3
t24.UT rep3


title: MA_T1

description:
replicate 1
t24.UT rep1


title: MA_Z5

description:
replicate 5
t0.UT rep5


title: MI2

description:
replicate 2
t24.E2FGF10PD rep2

source_name: MCF-7 cell line treated with estrogen, FGF10 and PD173074

treatment_protocol: Estrogen deprived cells were stimulated with 1nM estradiol (Sigma); 100ng/mL FGF10 (Invitrogen); 100ng/mL PD173074 (Sigma-Aldrich)


title: MI4

description:
replicate 4
t24.E2FGF10PD rep4


title: MA_Y4

description:
replicate 4
t6.UT rep4


title: MA_Y1

description:
replicate 1
t6.UT rep1


title: MA_Y2

description:
replicate 2
t6.UT rep2


title: MI6

description:
replicate 5
t24.E2FGF10PD rep5


title: MA_T4

description:
replicate 4
t24.UT rep4


title: MA_Z4

description:
replicate 4
t0.UT rep4


title: MA_V4

description:
replicate 4
t6.E2.AP20187 rep4


title: MA_X3

description:
replicate 3
t6.E2 rep3


title: MA_Z1

description:
replicate 1
t0.UT rep1


title: MI3

description:
replicate 3
t24.E2FGF10PD rep3


title: ME2

description:
replicate 2
t6.E2FGF10PD rep2


title: ME5

description:
replicate 5
t6.E2FGF10PD rep5


title: ME4

description:
replicate 4
t6.E2FGF10PD rep4


title: MH3

description:
replicate 3
t24.E2FGF10 rep3

source_name: MCF-7 cell line treated with estrogen and FGF10


title: MD2

description:
replicate 2
t6.E2FGF10 rep2


title: MH6

description:
replicate 4
t24.E2FGF10 rep4


title: MH2

description:
replicate 2
t24.E2FGF10 rep2


title: MD1

description:
replicate 1
t6.E2FGF10 rep1


title: MG5

description:
replicate 5
t24.E2 rep5


title: MC2

description:
replicate 2
t6.E2 rep2


title: MD5

description:
replicate 5
t6.E2FGF10 rep5


title: MA_Z2

description:
replicate 2
t0.UT rep2


title: MG2

description:
replicate 2
t24.E2 rep2


title: MI1

description:
replicate 1
t24.E2FGF10PD rep1


title: ME3

description:
replicate 3
t6.E2FGF10PD rep3


title: MD4

description:
replicate 4
t6.E2FGF10 rep4


title: ME1

description:
replicate 1
t6.E2FGF10PD rep1


title: MC3

description:
replicate 3
t6.E2 rep3


title: MG3

description:
replicate 3
t24.E2 rep3


title: MA_T1_rep

description:
technical replicate 1
t24.UT rep1 (technical replicate of sample MA_T1)


title: MG1

description:
replicate 1
t24.E2 rep1


title: MC6

description:
replicate 6
t6.E2 rep6


title: MC1

description:
replicate 1
t6.E2 rep1


title: MG4

description:
replicate 4
t24.E2 rep4


title: MC5

description:
replicate 5
t6.E2 rep5


title: MC4

description:
replicate 4
t6.E2 rep4


title: MH1

description:
replicate 1
t24.E2FGF10 rep1


title: MF6

description:
replicate 6
t24.UT rep6


title: MF3

description:
replicate 3
t24.UT rep3


title: MD3

description:
replicate 3
t6.E2FGF10 rep3


title: MF5

description:
replicate 5
t24.UT rep5


title: MF2

description:
replicate 2
t24.UT rep2


title: MB5

description:
replicate 5
t6.UT rep5


title: MF4

description:
replicate 4
t24.UT rep4


title: MB3

description:
replicate 3
t6.UT rep3


title: MB4

description:
replicate 4
t6.UT rep4


title: MF1

description:
replicate 1
t24.UT rep1


title: MA1

description:
replicate 1
t0.UT rep1


title: MA4

description:
replicate 4
t0.UT rep4


title: MA2

description:
replicate 2
t0.UT rep2


title: SKBR3_Control3

city: Houston

first: Trang

last: Vu

state: TX

address: 3605 Cullen Blvd., SERC Bldg 545

department: The Center for Nuclear Receptors and Cell Signaling

country: USA

institute: The University of Houston

description: Untreated control, replicate 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was normalized and background-corrected using the R Program, lumi package. Comparisons were done with the R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set.

source_name: mammary gland, breast, adenocarcinoma

label_protocol: cRNA were prepared and labeled with Cy3 dye using the Illumina TotalPrep-96RNA Amplification Kit and Illumina Whole-Genome Gene Expression Direct Hybridisation Kit.

growth_protocol: Breast cancer cell lines were grown in respective media with 5-10% FBS.

extract_protocol: RNA was extracted using the EZNA Total RNA Kit I from Omega.

treatment_protocol: Cells were treated with 10 uM synthetic LXR agonist GW3965 for 48 hours prior to harvest and RNA isolation.

tag: cell type

value: breast adenocarcinoma cells

tag: estrogen receptor

value: negative

tag: treatment


title: MB1

description:
replicate 1
t6.UT rep1


title: MB2

description:
replicate 2
t6.UT rep2


title: T47D_Control3

description: Untreated control, replicate 3.

source_name: mammary gland, breast, ductal carcinoma

value: ductal breast carcinoma cells

value: positive


title: SKBR3_GW1

description: GW3965-treated, 48 hours, replicate 1.


title: MDAMB231_Control3

description: Untreated control, replicate 3.

source_name: mammary gland, breast, adenocarcinoma, epithelial


title: T47D_GW3

description: GW3965-treated, 48 hours, replicate 3.


title: MDAMB231_GW3

description: GW3965-treated, 48 hours, replicate 3.


title: MA3

description:
replicate 3
t0.UT rep3


title: MA6

description:
replicate 5
t0.UT rep5


title: T47D_GW1

description: GW3965-treated, 48 hours, replicate 1.


title: MDAMB231_Control1

description: Untreated control, replicate 1.


title: SKBR3_Control1

description: Untreated control, replicate 1.


title: MDAMB231_GW2

description: GW3965-treated, 48 hours, replicate 2.


title: MDAMB231_GW1

description: GW3965-treated, 48 hours, replicate 1.


title: MCF7_GW3

description: GW3965-treated, 48 hours, replicate 3.


title: SKBR3_Control2

description: Untreated control, replicate 2.


title: SKBR3_GW2

description: GW3965-treated, 48 hours, replicate 2.


title: T47D_GW2

description: GW3965-treated, 48 hours, replicate 2.


title: MA_Y6

description:
replicate 6
t6.UT rep6


title: MDAMB231_Control2

description: Untreated control, replicate 2.


title: SKBR3_GW3

description: GW3965-treated, 48 hours, replicate 3.


title: T47D_Control2

description: Untreated control, replicate 2.


title: T47D_Control1

description: Untreated control, replicate 1.


title: MCF7_GW2

description: GW3965-treated, 48 hours, replicate 2.


title: M_g_005_3

type: genomic

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description: s7-6_Mmass_isolate / M. abscessus type strain (ATCC 19977)

hyb_protocol: Agilent Oligo aCGH Hybridization Kit

scan_protocol: Agilent microarray scanner at 3 micron resolution using XDR of 100% and 10% PMT. Agilent Feature Extraction software version 10.7.3.1, protocol CGH_107_Sep09

data_processing: Signal distributions were median normalized between arrays, then the ratios (Cy3/Cy5) from the duplicate tiling probes were averaged

molecule: genomic DNA

organism: Mycobacteroides abscessus subsp. bolletii

source_name: clinical isolate from patient D assigned as M. massiliense

label_protocol: Direct labeling using Agilent Genomic DNA Enzymatic Labeling Kit

extract_protocol: Lysozyme, CTAB/NaCL, SDS/proteinase K/ chloroform isoamyl alcohol/isopropanol/70% ethanol wash/dry pellet/dissolve in TE

tag: source

value: clinical isolate

tag: clathromycin resistance

value: sensitive

tag: isolation date

organism: Mycobacteroides abscessus

source_name: M. abscessus type strain (ATCC 19977)

value: type strain

value: resistant


title: MCF7_Control3

description: Untreated control, replicate 3.


title: gDNA control (for cDNA samples)

first: Desiree

last: Tillo

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: hCMV genomic DNA control reps1-10

hyb_protocol: Arrays were hybridized and imaged at the City of Hope Functional Genomics Core or the UCLA Research Services Clinical Microarray Core exactly following the manufacturer’s instructions.

data_processing: For transcript data, signal intensities from replicate test and control (randomly fragmented DNA) channels were averaged, log-transformed, quantile-normalized, and averaged on the probe level. The ratio between test and control values was calculated resulting in normalized values per probe. Then, the data were scaled by subtracting the biweight mean of the subarray from each probe signal.

label: Cy3, Cy5

organism: Human betaherpesvirus 5

source_name: Sonicated genomic DNA from hCMV TB40E (control)

label_protocol: cDNA was subjected to random-primed labeling with either Cy3- or Cy5-conjugated oligonucleotides using the Dual-Color DNA labeling Kit from Roche/NimbleGen. The labeling was performed in an ozone-free environment at the City of Hope Functional Genomics Core (Duarte/CA, USA) exactly following the manufacturer’s instructions.

extract_protocol: Total RNA was purified using TRIzol reagent (Life Technologies) and Phase Lock Gel Heavy tubes (Eppendorf) according to the manufacturers’ instructions. This RNA was subjected to further clean-up with on-column DNase digestion using the RNeasy Mini Kit from Qiagen. Newly transcribed RNA was purified following exactly the protocols published in Dölken et al., 2008 RNA 14(9):1959-1972. Briefly, nascent RNA was metabolically labeled for 1h with 1µM 4-thiouridine (Sigma-Aldrich), purified using TRIzol and the RNeasy Mini Kit, in vitro-biotinylated (EZ-Link Biotin-HPDP, Thermo Scientific/Pierce), and separated from preexisting RNA using streptavidin-coated magnetic beads (Miltenyi Biotec). After that, the RNA was further purified and concentrated using the RNeasy MinElute Cleanup Kit (Qiagen).  Nascent (10ng) or total (100ng) RNA was used for single-stranded cDNA synthesis using the Ambion WT Expression Kit (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with either the WT human cytomegalovirus TB40E strain (WT) or dlIE1 strain at a multiplicity of infection of 3 pfu/cell.  Infections were carried out for 8-96 h before extraction of viral RNA (total and nascent) .

tag: strain

tag: genotype/variation

value: WT

value: sonication


title: M_g_003_2

description: s1-1_Mmass_isolate / M. abscessus type strain (ATCC 19977)

source_name: clinical isolate from patient A assigned as M. massiliense


title: MCF7_Control1

description: Untreated control, replicate 1.


title: WT Nascent cDNA 96h

type: other

description: hCMV WT Nascent RNA 96h reps1and2

scan_protocol: Arrays were hybridized and imaged at the City of Hope Functional Genomics Core or the UCLA Research Services Clinical Microarray Core exactly following the manufacturer’s instructions.

molecule: other

source_name: Nascent cDNA from hCMV TB40E at 96h postinfection of MRC-5 cells

tag: time

value: 96h postinfection

tag: rna type

value: Nascent RNA


title: dIE1 Nascent cDNA 8h

description: hCMV dlIE1 Nascent RNA 8h reps1and2

source_name: Nascent cDNA from hCMV TB40E dlIE1 at 8h postinfection of MRC-5 cells

value: 8h postinfection


title: siPTTG1_3

description:
replicate 3
t6.E2 rep5

source_name: Transfected MCF-7 cell line (siRNA targeting PTTG1)

growth_protocol: MCF7 human breast cancer cells were cultured in DMEM supplemented with 10% HI-FCS and antibiotics. Cell synchronisation via estrogen deprivation was carried out for at least 3 days in phenol red-free DMEM (Invitrogen) supplemented with 5% charcoal dextran-treated HI-FBS (Hyclone) and 1% penicillin-streptomycin. All cells were grown at 37oC in 5% CO2. siRNA SMARTpools (Dharmacon) targeting PTTG1 (L-004309) and SPDEF (L-020199) and a control non-targeting pool (D-001810) were transfected into MCF7 cells using Lipofectamine RNAiMAX (Invitrogen). RNA was collected after 72 hours and processed for microarray analysis.

tag: sirna


title: siSPDEF_5

description:
replicate 5
t6.E2FGF10 rep2

source_name: Transfected MCF-7 cell line (siRNA targeting SPDEF)

value: SPDEF


title: siPTTG1_6

description:
replicate 6
t24.E2 rep2


title: siSPDEF_2

description:
replicate 2
t24.E2 rep4


title: dIE1 Nascent cDNA 96h

description: hCMV dlIE1 Nascent RNA 96h reps1and2

source_name: Nascent cDNA from hCMV TB40E dlIE1 at 96h postinfection of MRC-5 cells


title: M_g_003_4

description: s7-9_Mabscess_isolate / M. abscessus type strain (ATCC 19977)

source_name: clinical isolate from patient C assigned as M. abscessus


title: MCF7_Control2

description: Untreated control, replicate 2.


title: siPTTG1_4

description:
replicate 4
t6.E2 rep6


title: dIE1 Total cDNA 8h

description: hCMV dlIE1 Total RNA 8h reps1and2

source_name: Total cDNA from hCMV TB40E dlIE1 at 8h postinfection of MRC-5 cells

value: Total RNA


title: WT Total cDNA 8h

description: hCMV WT Total RNA 8h reps1and2

source_name: Total cDNA from hCMV TB40E at 8h postinfection of MRC-5 cells


title: siSPDEF_4

description:
replicate 4
t6.E2FGF10 rep1


title: dIE1 Total cDNA 96h

description: hCMV dlIE1 Total RNA 96h reps1and2

source_name: Total cDNA from hCMV TB40E dlIE1 at 96h postinfection of MRC-5 cells


title: M_g_004_4

description: s8-1_Mmass_type / M. abscessus type strain (ATCC 19977)

source_name: M. massiliense type strain (CCUG 48898)


title: siSPDEF_6

description:
replicate 6
t6.E2FGF10 rep3


title: siSPDEF_3

description:
replicate 3
t24.E2 rep5


title: siSPDEF_1

description:
replicate 1
t24.E2 rep3


title: siPTTG1_5

description:
replicate 5
t24.E2 rep1


title: MCF7_GW1

description: GW3965-treated, 48 hours, replicate 1.


title: WT Total cDNA 96h

description: hCMV WT Total RNA 96h reps1and2

source_name: Total cDNA from hCMV TB40E at 96h postinfection of MRC-5 cells


title: siPTTG1_1

description:
replicate 1
t6.E2 rep3


title: dIE1 MNase 96h rep1

description: hCMV dlIE1 MNase-chip 96h

data_processing: Signal intensities from all tiling arrays were extracted using NimbleScan 2.5–2.6 software (Roche/NimbleGen).  log2 ratios between nucleosomal DNA and sonicated DNA (input) signal intensities, were calculated and scaled around zero by subtracting the biweight mean from each probe signal

source_name: MNase-treated nucleosomal DNA from hCMV TB40E dlIE1 at 96h postinfection of MRC-5 cells

label_protocol: Sonicated DNA (Input) and MNase-treated DNA (1 µg each) was subjected to random-primed labeling with either Cy3- or Cy5-conjugated oligonucleotides using the Dual-Color DNA labeling Kit from Roche/NimbleGen. The labeling was performed in an ozone-free environment at the City of Hope Functional Genomics Core (Duarte/CA, USA) exactly following the manufacturer’s instructions.

extract_protocol: All steps were performed at 4°C or on ice with ice-cold buffers and solutions. Two 15cm-plates of mock- or hCMV-infected MRC-5 cells (3×10^7) were trypsinized, mixed with 10ml ice-cold culture medium (Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum), and centrifuged (5min, 500×g, 4°C). Nuclei were prepared by consecutively resuspending the cell pellet in 1ml lysis buffer (10mM Tris/HCl [pH 7.4], 10mM NaCl, 3mM MgCl2, 0.15mM spermine, 0.5mM spermidine, 0.5% Igepal CA-630) and adding 4ml lysis buffer while simultaneously vortexing the sample. Following a 5min incubation, nuclei were centrifuged (5min, 300×g), and the pellet was consecutively washed in 5ml lysis buffer and 5ml reaction buffer (10mM Tris/HCl [pH 7.4], 15mM NaCl, 60mM KCl, 0.15mM spermine, 0.5mM spermidine). The sample was resuspended in 500µl reaction buffer with 1mM CaCl2, divided into five 100µl-aliquots, and each aliquot was pre-warmed to 30°C for 4min 45s. After that, four aliquots were each reacted with 75U Nuclease S7 MNase (Roche) in 5µl dilution buffer (5mM Tris/HCl [pH 7.4], 0.01M CaCl2) for 5min at 30°C. This treatment produced 80–90% mononucleosomal fragments, with a minimal (undetectable) proportion of subnucleosomal fragments, as determined by agarose gel electrophoresis of purified DNA (data not shown). One aliquot was reacted with 5µl dilution buffer only. The reactions were stopped by adding 100µl reaction buffer with 20mM EDTA, 2mM EGTA, and 10µl 20% sodium dodecyl sulfate. Finally, samples were briefly vortexed, shock-frozen in liquid nitrogen, and stored at -80°C.  DNA from samples not treated with MNase was purified using the DNeasy Blood & Tissue Kit from Qiagen according to the manufacturer’s instructions. This DNA was subsequently subjected to a shearing protocol using a Bioruptor UCD-200 (Diagenode) that generated ?90% of 150–200bp fragments as determined by agarose gel electrophoresis.   DNA from MNase-treated samples was purified by a phenol-chloroform-isoamyl alcohol extraction protocol including consecutive proteinase K (Roche) and RNase A (Promega) digestion steps. This DNA was subsequently separated in 4% MetaPhor (Lonza) agarose gels. From these gels, the ~150bp band was precisely excised, and mononucleosomal DNA was purified using the QIAquick Gel Extraction Kit (Qiagen) following a protocol optimized for recovery of short DNA fragments

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with dlIE1 virus  at a  multiplicity of infection of 3 pfu/cell.  Infections were carried out for  96h before extraction of viral chromatin.

value: MNase

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with dlIE1 virus  at a  multiplicity of infection of 3 pfu/cell.  Infections were carried out for  96h before extraction of genomic DNA.


title: dIE1 MNase 96h rep2

description: hCMV dlIE1 MNase-chip 96h


title: siControl_4

description:
replicate 4
t0.UT rep4

source_name: Transfected MCF-7 cell line (control non-targeting pool)

value: control non-targeting pool


title: dIE1 MNase 8h rep2

description: hCMV dlIE1 MNase-chip 8h

source_name: MNase-treated nucleosomal DNA from hCMV TB40E dlIE1 at 8h postinfection of MRC-5 cells

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with dlIE1 virus  at a  multiplicity of infection of 3 pfu/cell.  Infections were carried out for 8h before extraction of viral chromatin.

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with dlIE1 virus  at a  multiplicity of infection of 3 pfu/cell.  Infections were carried out for 8h before extraction of genomic DNA.


title: siControl_6

description:
replicate 6
t6.UT rep1


title: siControl_2

description:
replicate 2
t0.UT rep2


title: siControl_5

description:
replicate 5
t0.UT rep5


title: siControl_3

description:
replicate 3
t0.UT rep3


title: WT MNase 96h rep1

description: hCMV WT MNase-chip 96h

source_name: MNase-treated nucleosomal DNA from hCMV TB40E at 96h postinfection of MRC-5 cells

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with the  WT human cytomegalovirus TB40E strain at a  multiplicity of infection of 3 pfu/cell.  Infections were carried out for 96h before extraction of viral chromatin.

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with the  WT human cytomegalovirus TB40E strain at a  multiplicity of infection of 3 pfu/cell.  Infections were carried out for 96h before extraction of genomic DNA.


title: WT MNase 48h rep3

description: hCMV WT MNase-chip 48h

source_name: MNase-treated nucleosomal DNA from hCMV TB40E at 48h postinfection of MRC-5 cells

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with the  WT human cytomegalovirus TB40E strain at a  multiplicity of infection of 3 pfu/cell.  Infections were carried out for 48h before extraction of viral chromatin.

value: 48h postinfection

source_name: Sonicated genomic DNA from hCMV TB40E (control)

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with the  WT human cytomegalovirus TB40E strain at a  multiplicity of infection of 3 pfu/cell.  Infections were carried out for 48h before extraction of genomic DNA.


title: PlusTet.PlusE2PlusFGF10.12h rep4

description:
replicate 4
T5

source_name: MCF-7 cell line treated with estrogen and FGF10 (plus tetracycline)

value: PlusTet


title: siPTTG1_2

description:
replicate 2
t6.E2 rep4


title: siControl_1

description:
replicate 1
t0.UT rep1


title: WT MNase 48h rep4

description: hCMV WT MNase-chip 48h


title: PlusTet.PlusE2PlusFGF10.24h rep4

description:
replicate 4
Z4


title: WT MNase 48h rep6

description: hCMV WT MNase-chip 48h


title: PlusTet.PlusE2PlusFGF10.24h rep1

description:
replicate 1
Z1


title: PlusTet.PlusE2PlusFGF10.24h rep3

description:
replicate 3
Z3


title: WT MNase 8h rep6

description: hCMV WT MNase-chip 8h

source_name: MNase-treated nucleosomal DNA from hCMV TB40E at 8h postinfection of MRC-5 cells

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with the  WT human cytomegalovirus TB40E strain at a  multiplicity of infection of 3 pfu/cell.  Infections were carried out for 8h before extraction of viral chromatin.

treatment_protocol: Human fetal lung fibroblasts (MRC-5) were maintaned and growth arrested as described in Nitzsche et al. (2012) J. Virol 86(18):9817-9827.   Cells were infected with the  WT human cytomegalovirus TB40E strain at a  multiplicity of infection of 3 pfu/cell.  Infections were carried out for 8h before extraction of genomic DNA.


title: PlusTet.PlusE2PlusFGF10.24h rep5

description:
replicate 5
Z5


title: PlusTet.PlusE2PlusFGF10.24h rep2

description:
replicate 2
Z2


title: WT Nascent cDNA 8h

description: hCMV WT Nascent RNA 8h reps1and2

source_name: Nascent cDNA from hCMV TB40E at 8h postinfection of MRC-5 cells


title: WT MNase 48h rep1

description: hCMV WT MNase-chip 48h


title: WT MNase 48h rep5

description: hCMV WT MNase-chip 48h


title: WT MNase 48h rep2

description: hCMV WT MNase-chip 48h


title: WT MNase 96h rep2

description: hCMV WT MNase-chip 96h


title: PlusTet.PlusE2PlusFGF10.12h rep3

description:
replicate 3
T4


title: PlusTet.PlusE2PlusFGF10.6h rep5

description:
replicate 5
N5


title: WT MNase 8h rep3

description: hCMV WT MNase-chip 8h


title: WT H3 ChIP 48h rep2

description: hCMV WT H3 ChIP-chip 48h

scan_protocol: Signal intensities from all tiling arrays were extracted using NimbleScan 2.5–2.6 software (Roche/NimbleGen).

data_processing: log2 ratios between the output (H3-ChIP) and the input (IgG) signal intensities, were calculated and scaled around zero by subtracting the biweight mean from each probe signal

source_name: H3 ChIP DNA from hCMV TB40E at 48h postinfection of MRC-5 cells

label_protocol: Input and H3-ChIP DNA (1 µg each) from H3-specific ChIP reactions was subjected to random-primed labeling with either Cy3- or Cy5-conjugated oligonucleotides using the Dual-Color DNA labeling Kit from Roche/NimbleGen. The labeling was performed in an ozone-free environment at the City of Hope Functional Genomics Core (Duarte/CA, USA) exactly following the manufacturer’s instructions.

extract_protocol: Chromatin (H3-ChIP and control IgG) was purified from growth-arrested human fibroblasts (MRC-5) infected at high multiplicity (3 PFU/cell with the hCMV clinical isolate TB40E as described in Nitzsche et al., 2008, Journal of virology 82, 11167-11180, and Knoblach et al., 2011, PLoS pathogens 7, e1002016.

tag: chip antibody

source_name: Non-specific (mock-IgG) ChIP DNA from hCMV TB40E at 48h postinfection of MRC-5 cells

value: IgG


title: WT MNase 8h rep4

description: hCMV WT MNase-chip 8h


title: PlusTet.PlusE2PlusFGF10.6h rep2

description:
replicate 2
N2


title: PlusTet.PlusE2PlusFGF10.6h rep3

description:
replicate 3
N3


title: WT MNase 8h rep5

description: hCMV WT MNase-chip 8h


title: PlusTet.PlusE2PlusFGF10.12h rep1

description:
replicate 1
T1


title: M_g_003_3

description: 15-4_Mmass_isolate / M. abscessus type strain (ATCC 19977)

source_name: clinical isolate from patient B assigned as M. massiliense

source_name: M. abscessus type strain (ATCC 19977)


title: PlusTet.PlusE2PlusFGF10.6h rep4

description:
replicate 4
N4


title: PlusTet.PlusE2PlusFGF10.3h rep5

description:
replicate 5
H5


title: PlusTet.PlusE2PlusFGF10.12h rep2

description:
replicate 2
T3


title: WT MNase 8h rep2

description: hCMV WT MNase-chip 8h


title: PlusTet.PlusE2.24h rep5

description:
replicate 5
X5

source_name: MCF-7 cell line treated with estrogen (plus tetracycline)


title: PlusTet.PlusE2PlusFGF10.6h rep1

description:
replicate 1
N1


title: WT H3 ChIP 8h rep3

description: hCMV WT H3 ChIP-chip 8h

source_name: H3 ChIP DNA from hCMV TB40E at 8h postinfection of MRC-5 cells

source_name: Non-specific (mock-IgG) ChIP DNA from hCMV TB40E at 8h postinfection of MRC-5 cells


title: PlusTet.PlusE2PlusFGF10.3h rep4

description:
replicate 4
H4


title: WT H3 ChIP 8h rep1

description: hCMV WT H3 ChIP-chip 8h


title: WT H3 ChIP 48h rep3

description: hCMV WT H3 ChIP-chip 48h


title: WT H3 ChIP 8h rep2

description: hCMV WT H3 ChIP-chip 8h


title: vtc2 mature somatic embryo, bio rep2

city: Winnipeg

first: Mark

middle: Findlay

last: Belmonte

state: Manitoba

address: 50 Sifton Road

department: Biological Sciences

country: Canada

institute: University of Manitoba

description: gene expression data from mature somatic embryos in a vtc2 mutant

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Arabidopsis ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method.  The mean target intensity of each array was set to 500.

organism: Arabidopsis thaliana

source_name: vtc2 mutant mature somatic embryos at day 14

label_protocol: Amplification and labeling was performed using 3 μg RNA into the Enzo Single-Round RNA Amplification and Biotin Labeling system (Life Technologies).

growth_protocol: plants were grown in a Conviron growth cabinet under long day conditions (16 hour light, 8 hours dark) with fluorescent lamps at 22°C and 50% - 70% relative humidity.

extract_protocol: Total RNA was extracted using Plant RNA reagent (Invitrogen). DNA contamination was removed with the Ambion Turbo DNA-free kit (Life Technologies)

treatment_protocol: bent cotyledon embryos were cultured on modified MS media supplemented with the phytohormone 2,4-D for 14 days to promote callus development. Explants that formed callus were then transferred to MS media lacking 2,4-D for embryos to develop.

tag: ecotype/cultivar

tag: genotype

tag: developmental stage

value: mature somatic embryo


title: PlusTet.PlusE2PlusFGF10.3h rep1

description:
replicate 1
H1

tag: cell line

tag: treatment duration (hs)


title: vtc2 day 14 induction, bio rep1

description: gene expression data from late induction phase in vtc2 mutant of somatic embryogenesis

source_name: vtc2 mutant day 14 induction +2,4-D

value: day 14 induction


title: PlusTet.PlusE2.24h rep4

description:
replicate 4
X4

tag: group


title: PlusTet.PlusE2.24h rep1

description:
replicate 1
X1


title: vtc2 day 14 induction, bio rep2


title: wild type mature somatic embryo, bio rep1

description: gene expression data from mature somatic embryos

source_name: wild type mature somatic embryos at day 14

value: wild type


title: PlusTet.PlusE2.24h rep3

description:
replicate 3
X3


title: wild type day 14 induction, bio rep1

description: gene expression data from late induction phase of somatic embryogenesis

source_name: wild type day 14 induction +2,4-D


title: PlusTet.PlusE2.12h rep4

description:
replicate 4
R4


title: wild type day 14 induction, bio rep2


title: vtc2 zygotic embryo, bio rep1

description: gene expression data from vtc2 mutant zygotic embryos

source_name: vtc2 mutant bent cotyledon zygotic embryo

value: bent cotyledon zygotic embryo


title: PlusTet.PlusE2.6h rep5

description:
replicate 5
L5


title: PlusTet.PlusE2.12h rep3

description:
replicate 3
R3


title: PlusTet.PlusE2.6h rep4

description:
replicate 4
L4


title: dIE1 MNase 8h rep1

description: hCMV dlIE1 MNase-chip 8h

source_name: MNase-treated nucleosomal DNA from hCMV TB40E dlIE1 at 8h postinfection of MRC-5 cells


title: PlusTet.PlusE2PlusFGF10.3h rep2

description:
replicate 2
H2


title: PlusTet.PlusE2.12h rep1

description:
replicate 1
R1


title: PlusTet.PlusE2.24h rep2

description:
replicate 2
X2


title: vtc2 day 7 induction, bio rep2

description: gene expression data from early induction phase in vtc2 mutants of somatic embryogenesis

source_name: vtc2 mutant day 7 induction +2,4-D

value: day 7 induction


title: PlusTet.PlusE2.6h rep3

description:
replicate 3
L3


title: rag2 RMS_RAG2-9

city: New York

first: Richard

middle: Mark

last: White

state: NY

address: 1275 York Avenue MB 424

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Affymetrix zebrafish array protocol

scan_protocol: Affymetrix zebrafish array protocol

data_processing: Affymetrix Gene Console, followed by GenePattern analysis

organism: Danio rerio

source_name: rhabdomyosarcoma

label_protocol: Affymetrix zebrafish array protocol

growth_protocol: Transgenic F0 animals grown until tumor visible, tumor or muscle dissected from adult

extract_protocol: Trizol RNA prep

value: AB

tag: transgene

tag: tissue type

value: rhabdomyosarcoma


title: PlusTet.PlusE2.6h rep1

description:
replicate 1
L1


title: rag2 RMS_RAG2-8


title: rag2 RMS_RAG2-7


title: wild type day 7 induction, bio rep2

description: gene expression data from early induction phase of somatic embryogenesis

source_name: wild type day 7 induction +2,4-D


title: rag2 RMS_RAG2-5


title: PlusTet.PlusE2.6h rep2

description:
replicate 2
L2


title: PlusTet.PlusE2.3h rep3

description:
replicate 3
F4


title: PlusTet.VEH.24h rep5

description:
replicate 5
V5

source_name: MCF-7 cell line treated with vehicle  (plus tetracycline)


title: mylz RMS_MYLZ2-7a


title: mylz RMS_MYLZ2-8a


title: PlusTet.VEH.24h rep3

description:
replicate 3
V3


title: PlusTet.PlusE2.3h rep2

description:
replicate 2
F3


title: rag2 RMS_RAG2-10


title: rag2 RMS_RAG2-2


title: PlusTet.PlusE2.3h rep1

description:
replicate 1
F2


title: mylz RMS_MYLZ2-9


title: PlusTet.VEH.24h rep1

description:
replicate 1
V1


title: PlusTet.VEH.24h rep2

description:
replicate 2
V2


title: rag2 RMS_RAG2-4


title: mylz RMS_MYLZ2-8


title: PlusTet.PlusE2.3h rep4

description:
replicate 4
F5


title: PlusTet.VEH.24h rep4

description:
replicate 4
V4


title: PlusTet.VEH.12h rep5

description:
replicate 5
P5


title: PlusTet.PlusE2PlusFGF10.3h rep3

description:
replicate 3
H3

source_name: MCF-7 cell line treated with estrogen and FGF10 (plus tetracycline)


title: mylz RMS_MYLZ2-7


title: PlusTet.VEH.12h rep4

description:
replicate 4
P4


title: WT MNase 8h rep1

description: hCMV WT MNase-chip 8h

source_name: MNase-treated nucleosomal DNA from hCMV TB40E at 8h postinfection of MRC-5 cells

value: WT

tag: treatment

source_name: Sonicated genomic DNA from hCMV TB40E (control)

value: sonication


title: mylz RMS_MYLZ2-4


title: mylz RMS_MYLZ2-6


title: mylz RMS_MYLZ2-3


title: cdh15 RMS_CDH15-8


title: WT H3 ChIP 48h rep1

description: hCMV WT H3 ChIP-chip 48h

source_name: H3 ChIP DNA from hCMV TB40E at 48h postinfection of MRC-5 cells

source_name: Non-specific (mock-IgG) ChIP DNA from hCMV TB40E at 48h postinfection of MRC-5 cells


title: cdh15 RMS_CDH15-8a


title: cdh15 RMS_CDH15-7a


title: cdh15 RMS_CDH15-6


title: PlusTet.VEH.6h rep2

description:
replicate 2
J2


title: PlusTet.VEH.12h rep3

description:
replicate 3
P3


title: cdh15 RMS_CDH15-5


title: mylz RMS_MYLZ2-1


title: cdh15 RMS_CDH15-7


title: PlusTet.VEH.6h rep5

description:
replicate 5
J5


title: PlusTet.VEH.6h rep4

description:
replicate 4
J4


title: PlusTet.VEH.12h rep1

description:
replicate 1
P1


title: PlusTet.VEH.3h rep4

description:
replicate 4
D4


title: PlusTet.VEH.12h rep2

description:
replicate 2
P2


title: PlusTet.VEH.6h rep1

description:
replicate 1
J1


title: PlusTet.VEH.3h rep5

description:
replicate 5
D5


title: PlusTet.VEH.6h rep3

description:
replicate 3
J3


title: PlusTet.PlusE2.12h rep2

description:
replicate 2
R2

source_name: MCF-7 cell line treated with estrogen (plus tetracycline)


title: PlusTet.VEH.3h rep3

description:
replicate 3
D3


title: wild-type muscle_AB5

source_name: wild-type muscle

value: muscle


title: PlusTet.VEH.0h rep4

description:
replicate 4
B4


title: wild-type muscle_AB8


title: PlusTet.PlusE2.12h rep5

description:
replicate 5
R5


title: cdh15 RMS_CDH15-9


title: wild-type muscle_AB7


title: cdh15 RMS_CDH15-4


title: PlusTet.VEH.3h rep2

description:
replicate 2
D2


title: PlusTet.VEH.0h rep5

description:
replicate 5
B5


title: PlusTet.VEH.0h rep3

description:
replicate 3
B3


title: PlusTet.VEH.0h rep2

description:
replicate 2
B2


title: MinusTet.PlusE2PlusFGF10.24h rep3

description:
replicate 3
Y4

source_name: MCF-7 cell line treated with estrogen and FGF10 (minus tetracycline)

value: MinusTet


title: wild-type muscle_AB6


title: 504h-Low_N-2

city: Houghton

first: Victor

last: Busov

state: MI

address: 1400 Townsend Drive

department: Forest Resources and Environmental Science

institute: Michigan Technological University

description:
Gene expression data from roots
Populus tremula x Populus alba INRA 717-IB4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the  Affymetrix GeneChip® Fluidics Station 450

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570nm. The Affymetrix eukaryotic hybridization control kit and Poly-A RNA control kit were used to ensure efficiency of hybridization and cRNA amplification. All cRNA was synthesized at the same time. Hybridizations were conducted with one replicate of all times and treatments concurrently. Each array image was visually screened to discount for signal artifacts, scratches or debris.

data_processing: Microarray data were normalized with Robust Multichip Average (RMA). Rank Product (RP) (Breitling, Armengaud et al. 2004) was used for identifying differentially expressed genes (DEGs) and  Benjamini and Hochberg False Discovery Rate (Benjamini and Hochberg 1995) was used to defined those genes that have the corrected p-values (< 0.05) as differentially expressed genes.

organism: Populus tremula x Populus alba

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

growth_protocol: In vitro conditions

extract_protocol: We isolated RNA from about 0.3g tissue. RNA was extracted as previously described (Busov VB,at al, 2003, Plant Physiol 132: 1283-1291) using QIAGEN kits.

treatment_protocol: For low nitrogen treatments the three top internodes of in vitro propagated plants (leaves removed) were placed on filter paper bridges in glass tubes filled with 15 ml liquid ½ MS media for 4 weeks to allow development of root system. Only uniformly developed plants were used in the subsequent experiments. For control (normal nitrogen) treatment we used freshly added ½ MS media containing 20 mM KNO3. For low nitrogen treatment we used ½ MS formulation with 0.05 mM KNO3 (only source of N) and accordingly adjusted the K+ concentration by addition of K2SO4. To maintain constant concentration of the nitrogen in the solution, the media was changed after 2, 5 and 15 days. Roots were sampled at 6, 12, 24, 48, and 408h after transfer to control and low nitrogen media and stored at -80oC until further processed. Total RNA from the roots was extracted as previously described (Busov et al., 2003) and on-column DNaseI-treated (Qiagen).

tag: time point

value: low nitrogen

tag: tissue

value: Roots


title: MinusTet.PlusE2PlusFGF10.12h rep5

description:
replicate 5
S5


title: 96h-Low_N-2


title: wild-type muscle_AB9

tag: strain


title: wild-type muscle_AB12


title: vtc2 day 7 induction, bio rep1


title: PlusTet.VEH.0h rep1

description:
replicate 1
B1


title: cdh15 RMS_CDH15-1


title: wild-type muscle_AB2


title: MinusTet.PlusE2PlusFGF10.24h rep2

description:
replicate 2
Y3


title: MinusTet.PlusE2PlusFGF10.24h rep1

description:
replicate 1
Y1


title: 504h-Control-1

value: control (normal nitrogen)


title: PlusTet.VEH.3h rep1

description:
replicate 1
D1


title: MinusTet.PlusE2PlusFGF10.6h rep5

description:
replicate 5
M5


title: MinusTet.PlusE2PlusFGF10.12h rep1

description:
replicate 1
S1


title: 504h-Control-2


title: MinusTet.PlusE2PlusFGF10.12h rep2

description:
replicate 2
S2


title: 504h-Low_N-1


title: 48h-Low_N-2


title: MinusTet.PlusE2PlusFGF10.6h rep2

description:
replicate 2
M2


title: MinusTet.PlusE2PlusFGF10.6h rep4

description:
replicate 4
M4


title: MinusTet.PlusE2PlusFGF10.6h rep3

description:
replicate 3
M3


title: MinusTet.PlusE2PlusFGF10.6h rep1

description:
replicate 1
M1


title: MinusTet.PlusE2PlusFGF10.24h rep4

description:
replicate 4
Y5


title: MinusTet.PlusE2PlusFGF10.3h rep4

description:
replicate 4
G5


title: 96h-Low_N-1


title: MinusTet.PlusE2PlusFGF10.12h rep3

description:
replicate 3
S3


title: MinusTet.PlusE2PlusFGF10.12h rep4

description:
replicate 4
S4


title: 96h-Control-2


title: 96h-Control-1


title: 24h-Low_N-2


title: MinusTet.PlusE2PlusFGF10.3h rep3

description:
replicate 3
G4


title: 48h-Control-1


title: MinusTet.PlusE2PlusFGF10.3h rep1

description:
replicate 1
G2


title: 48h-Low_N-1


title: MinusTet.PlusE2.24h rep5

description:
replicate 5
W5

source_name: MCF-7 cell line treated with estrogen (minus tetracycline)


title: MinusTet.PlusE2.24h rep4

description:
replicate 4
W4


title: 24h-Control-2


title: MinusTet.PlusE2PlusFGF10.3h rep2

description:
replicate 2
G3


title: 24h-Low_N-1


title: 24h-Control-1


title: MinusTet.PlusE2.24h rep2

description:
replicate 2
W2


title: MinusTet.PlusE2.24h rep3

description:
replicate 3
W3


title: C33.3

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

description: Gene expression fromm  C33A

hyb_protocol: Labelled ssDNA was hybridized to the GeneChip® human Gene 1.0 ST array oligonucleotide microarray using standard protocols of Affymetrix.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix), using standard parameters.

data_processing: Raw data were extracted from the scanned images and analyzed with the Affymetrix GeneChip Command Console Software (Affymetrix). The raw array data were preprocessed and normalized using the Robust Multichip Average (RMA) method. Data were further processed using oneChannelGUI.

source_name: Exponentially growing C33A cells

label_protocol: RNA (100 ng) was used for production of end-labelled biotinylated ssDNA

growth_protocol: Cells  were maintained in Dulbecco's modified Eagle's medium (DMEM). Medium was supplemented with 7% fetal bovine serum , 100 units/ml penicillin and 100 µg/ml streptomycin, and cells were cultivated in a 37°C incubator with 5% CO2.

extract_protocol: Total RNA was isolated in triplicate from exponentially growing C33A cells using RNeasy Mini Kit (Qiagen)

treatment_protocol: No specific treatment was applied.


title: C33.2

description: Gene expression fromm  C33A


title: 12h-Low_N-2


title: C33.1

description: Gene expression fromm  C33A


title: 12h-Control-2


title: 6h-Low_N-2


title: 6h-Low_N-1


title: 12h-Low_N-1


title: 6h-Control-2


title: 6h-Control-1


title: 12h-Control-1


title: 0h-Control-1


title: H929 CD138+ population, 2

city: Singapore

first: Renji

last: Reghunathan

address: KentRidge Road

country: Singapore

institute: National University Hospital

hyb_protocol: Biotinylated samples were hybridized onto the array for 16hrs and 60rpm in a GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.

data_processing: The data were analyzed with Genespring GX.

source_name: multiple myeloma cell line

label_protocol: 200ng of total RNA were amplified and labeled using Affymetrix Whole Transcript Sense Target Labeling and control reagents kit (Affymetrix).

growth_protocol: Cells were grown in RPMI-1640 complete medium (10% FBS+1% Penicilliin and Streptomycin+1%L-Glutamine), in 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy plus mini kit (Qiagen).

tag: cell type


title: 8226 CD138- population, 1


title: 8226 CD138+ population, 1


title: H929 CD138+ population, 1


title: H929 CD138- population, 2


title: 8226 CD138- population, 2


title: heart knock out replicate3

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HT MG-430 PM Array Plates. Plates were hybridized, washed and stained in the Affymetrix Gene Titan.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Titan instrument  with AGCC 3.0 software.

data_processing: The data were analysed using Bioconductor package 'oligo' under R-2.14.0. Background correction, normalization and probe summarization was performed with RMA.

organism: Mus musculus

source_name: heart, knock out

label_protocol: Biotinylated cRNA were prepared using the 3'IVT Express Kit (Ambion) from 100ng total RNA according to the manufacturer.

growth_protocol: Mice were housed in Type II L cages (365x207x140 mm, floor area 530 cm2; IVC-based)at an environmental temperature 20-24°C, humidity: 55±10%and under 12/12 h light/dark cycle with food and water ad libitum.

extract_protocol: RNA  was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for animal tissues.

value: heart

value: ClpP KO

tag: genetic background


title: brain wild type replicate1

source_name: brain, wild type

value: brain


title: 0h-Control-2


title: heart knock out replicate2


title: LT-HSCs/CreER

city: Tsu

first: Tetsuya

last: Nosaka

address: 2-174 Edobashi

department: Department of Microbiology and Molecular Genetics

country: Japan

institute: Mie University Graduate School of Medicine

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were labeled and hybridized for 16 hr at 45C on Affymetrix GeneChip® Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values (gene-level).
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

source_name: LT-HSCs transduced with CreER

label_protocol: RNA amplification and labeling using Ambion® WT Expression Kit (Life Technologies, California, US) and GeneChip® WT Terminal Labeling and Controls Kit (Affymetrix, California , US).

growth_protocol: Colony assays in methylcellulose medium supplemented with 20% FBS, SCF, IL-3, IL-6, and GM-CSF.

extract_protocol: Total RNA samples were extracted from colony-forming cells with Trizol (Invitrogen), followed by purification using RNeasy Mini Kit (QIAGEN).

treatment_protocol: Not applicable.

tag: strain/background

value: LT-HSCs

tag: transduction

value: CreER


title: heart wild type replicate2

source_name: heart, wild type


title: heart wild type replicate3


title: brain knock out replicate3

source_name: brain, knock out


title: heart knock out replicate1


title: heart wild type replicate1


title: brain wild type replicate3


title: brain wild type replicate2


title: H929 CD138- population, 1

growth_protocol: Cells were grown in RPMI-1640 complete medium (10% FBS+1% Penicillin and Streptomycin+1%L-Glutamine), in 37°C with 5% CO2.


title: LT-HSCs/mock

source_name: LT-HSCs transduced with mock

value: mock


title: brain knock out replicate2


title: ST-HSCs/mock

source_name: ST-HSCs transduced with mock

value: ST-HSCs


title: ST-HSCs/CreER

source_name: ST-HSCs transduced with CreER


title: brain knock out replicate1


title: H1437_vector_rep1

city: Los Angeles

first: Steven

middle: M

last: Dubinett

state: CA

address: 10833 Le Conte Avenue

department: Medicine-Pulmonary

institute: University of California, Los Angeles

hyb_protocol: labeled targets were combined per hyb order instructions, then mixed with 2x Hyb Buffer, heat denatured at 95C for 2 minutes and quick-chilled on ice. The targets were loaded on an Agilent 1plex coverslip in an Agilent hyb chamber. The targets were then covered with the Exiqon arrays (Item # 20-1122; Lot#34001.03, 6th generation (product#208401-A Lot#6000) and the hybridization chamber was sealed. The hybridizations were performed per protocol specifications, for ~16 - 18 hours (17), 56C, 20rpm in an Agilent Hybridizaiton oven

scan_protocol: Scanned using Axon GenePix 4000B scanner

data_processing: GenePix Pro 6.0 software

source_name: H1437 cell line, vector control

label_protocol: Exiqon miRCURY LNA microRNA Hi-power Labeling Kit (#208035)

growth_protocol: Cells grown in RPMI with 10% FBS

extract_protocol: Total RNA isolated using Qiagen miRNAeasy miRNA kit

treatment_protocol: No treatment

value: control


title: GC_exposed_170ng/L_rep4

city: Boston

first: Helen

middle: C

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

hyb_protocol: Labeled cDNA was hybridized to the 135k microarray using a Nimblegen hybridization station and a hybridization temperature of 42C. Microarrays were hybridized for 17 hours and washed using Nimblegen wash buffers.  Labeling and hybridization proceeded according to the protocols of NimbleGen Arrays User's Guide: Gene Expression Arrays (Version 6.0).

scan_protocol: Washed and dried microarrays were scanned within two days of completing the hybrization at the University of Massachusetts Medical School Genomics Facility.  They were scanned on an Agilent DNA microarray scanner C with SureScan High-Resolution Technology at 3 µm resolution.  Images were processed using Nimblescan software (Roche) which produced “pair” files with raw intensity values for each spot.

data_processing: Raw intensity values were normalized across the set of twenty different microarrays using quantile normalization with median polish in Arraystar (DNASTAR).  Normalized Log2 intensity values were uploaded into MultiExperiment Viewer (Mev 4.5) (part of TM4 microarray software suite; www.tm4.org) and Statistical Analysis for Microarrays (SAM) was used to detect differentially expressed genes between the exposed samples and unexposed samples using a FDR cut-off of 15% (Tusher et al., 2001).

organism: Hyalella azteca

source_name: whole animal

label_protocol: RNA samples were reverse transcribed using Sigma TransPlex Whole Transcriptome Amplification (WTA) Kit, which produces amplified cDNA through two steps. First strand cDNA is produced by reverse transcription and cDNA is then amplified by PCR. Amplified cDNA was labeled using Nimblegen’s one-color DNA labeling kit (cy3 only). This kit is based on Cy3-random priming and uses a high concentration of exo- Klenow, to incorporate dNTPs while replicating the cDNA.

growth_protocol: Hyalella azteca were maintained following standard EPA protocols: USEPA. 2000. Methods for Measuring the Toxicity and Bioaccumulation of Sediment-Associated Contaminants with Freshwater Invertebrates. EPA Publication 600/R-99/064. U.S. Environmental Protection Agency, Washington, D.C.  GC animals were held in the laboratory for two days under standard conditions until toxicity test was initiated.

extract_protocol: Total RNA was extracted from RNAlater preserved whole animals using TriReagent and standard protocols.  Tissue was homogenized using a Qiagen Tissue lyser.  Total RNA was treated with Dnase I by on-column digestion and washed using a Qiagen Rneasy kit.

treatment_protocol: Testing was done in lab water, purified through a Milli-Q system (Millipore, Billerica, MA, USA), and then made moderately hard by addition of salts (USEPA, 2000). Pyrethroids were added to the water in an acetone carrier, with acetone concentrations kept below 30 µl/L and verified to have no toxic effect in solvent control tests.  Exposures were done in glass beakers containing 80 ml of water, and a 1 cm2 square of nylon screen on which the animals cling. Beakers were held at 23 degrees C under a 16 h light:8 h dark cycle. After 48 h, 1 ml of yeast-cerophyll-trout food was added to each beaker, and after allowing approximately 6 h for feeding, 80% of the water was removed and replaced with fresh solution. At 96 h, the test was terminated and animals were preserved in RNAlater (Ambion).

tag: size

value: 500-600 microns

tag: cyfluthrin concentration

tag: population/ species group

value: GC wild population/D


title: muscle wild type replicate3

source_name: muscle, wild type

tag: genotype

value: WT


title: GC_exposed_170ng/L_rep3


title: GC_exposed_170ng/L_rep2


title: H441_vector_rep1

source_name: H441 cell line, vector control

tag: cell line


title: H358_snail_rep1

source_name: H358 cell line, snail overexpressing

value: snail overexpression


title: H1437_snail_rep1

source_name: H1437 cell line, snail overexpressing


title: H292_snail_rep1

source_name: H292 cell line, snail overexpressing


title: H358_vector_rep1

source_name: H358 cell line, vector control


title: H441_snail_rep1

source_name: H441 cell line, snail overexpressing


title: H292_vector_rep1

source_name: H292 cell line, vector control


title: muscle knock out replicate3

source_name: muscle, knock out

value: muscle


title: 48h-Control-2

value: wild type


title: GC_exposed_0.4ng/L_rep4


title: muscle knock out replicate2


title: muscle wild type replicate1


title: liver wild type replicate1

source_name: liver, wild type

value: liver


title: liver wild type replicate2


title: Pten-/-Dicer-/+, sample 2

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Mouse Genome arrays and rotating over night at 65 degC.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software (v.2.11) was used.

label: Alexa Fluor 647

source_name: Dicer HET

label_protocol: Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

growth_protocol: The ARR2PB-Cre transgenic mice were from Dr. Fen Wang at the Institute of Bioscience and Technology, Texas A&M Health Science Center. The Ptenfl/fl mice were from Dr. Hong Wu at the University of California Los Angeles. ARR2PB-Cre;Ptenfl/fl;Dicerfl/wt female mice and Ptenfl/fl;Dicerfl/wt male mice were mated to generated ARR2PB-Cre;Ptenfl/fl, ARR2PB-Cre;Ptenfl/fl;Dicerfl/wt, and ARR2PB-Cre;Ptenfl/fl;Dicerfl/fl mice.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Microarray analysis was performed using 2.5 micrograms of total RNA.

tag: strain background

tag: genotype/variation

value: Pten-/-Dicer-/+; Dicer HET

value: Cancerous urogenital tissues

label: Alexa Fluor 555

source_name: mouse, universal reference RNA

tag: sample type

value: Stratagene, Universal Mouse Reference RNA Catalog #740100


title: Pten-/-Dicer-/+, sample 4


title: GC_exposed_0.4ng/L_rep3


title: Pten-/-Dicer-/+, sample 3


title: liver wild type replicate3


title: GC_exposed_170ng/L_rep1


title: GC_exposed_0.4ng/L_rep1


title: Pten-/-Dicer-/+, sample 1


title: liver knock out replicate2

source_name: liver, knock out

value: ClpP KO


title: muscle knock out replicate1


title: Pten-/-Dicer-/-, sample 4

source_name: Dicer KO

value: Pten-/-Dicer-/-; Dicer KO


title: GC_exposed_0.4ng/L_rep2


title: GC_unexposed,_rep1

value: 0 ng/L


title: GC_unexposed,_rep4


title: Pten-/-Dicer-/-, sample 3


title: liver knock out replicate1


title: GC_unexposed,_rep3


title: GC_unexposed,_rep2


title: 8226 CD138+ population, 2

source_name: multiple myeloma cell line


title: UCB_exposed_0.4ng/L_rep4

value: UCB lab population/ C


title: UCB_exposed_0.4ng/L_rep3


title: liver knock out replicate3


title: Pten-/-Dicer-/-, sample 2


title: testis wild type replicate3

source_name: testis, wild type

value: testis


title: UCB_exposed_0.4ng/L_rep2

source_name: whole animal


title: ssa_1972-null mutant mixed with wild type SK36 Replicate 3

city: Tianjin

first: Lei

last: Chen

address: Weijin 92

department: School of Chemical Engineering

country: China

institute: Tianjin University

description: Biological replicate 3 of RNA mixture from streptococcus sangunis Δssa_1972 and the wild type SK36

hyb_protocol: Hybridization was performed following the protocol at http://pfgrc.jcvi.org/index.php/microarray/protocols.html

scan_protocol: Scanned on an GenePix 4000A scanner. Images were analyzed using the programs Spotfinder (v321win) and Midas (v2.20).

data_processing: LOWESS normalized, background subtracted data obtained from processed Red signal/processed Green signal.

organism: Streptococcus sanguinis SK36

source_name: Streptococcus sanguinis

label_protocol: Microbial RNA Aminoallyl Labeling was performed following the protocol at http://pfgrc.jcvi.org/index.php/microarray/protocols.html

growth_protocol: S. sanguinis SK36 was grown in brain heart infusion broth (BHI; Difco Inc., Detroit, MI) under microaerobic condition at 37 °C. Over night culture was diluted into fresh BHI broth by 1% inoculation and cultured further for 5 hours.

extract_protocol: Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions

growth_protocol: S. sanguinis Δssa_1972 was grown in brain heart infusion broth (BHI; Difco Inc., Detroit, MI) under microaerobic condition at 37 °C. Over night culture was diluted into fresh BHI broth by 1% inoculation and cultured further for 5 hours.


title: ssa_1972-null mutant mixed with wild type SK36 Replicate 2

description: Biological replicate 2 of RNA mixture from streptococcus sangunis Δssa_1972 and the wild type SK36


title: Pten-/-;Dicer wild-type, sample 4

source_name: Dicer wild-type

value: Pten-/-; Dicer wild-type


title: UCB_unexposed,_rep 4


title: Pten-/-Dicer-/-, sample 1


title: testis knock out replicate3

source_name: testis, knock out


title: UCB_exposed_0.4ng/L_rep1


title: testis wild type replicate1


title: testis wild type replicate2


title: Pten-/-;Dicer wild-type, sample 2


title: Pten-/-;Dicer wild-type, sample 3


title: Seed_RAD_7h_rep3

status: Public on Jul 16 2013

city: Sutton Bonington

first: Simon

middle: Peter

last: Pearce

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

institute: University of Nottingham

description:
RAD7.3
Sample redone for QC reasons

hyb_protocol: Fragmented cRNA at a final concentration of 0.0375ng/μl was used for hybridization. The GeneChip (#900720) HWS Kit was used for hybridization, washing and staining.

scan_protocol: The scanning was performed using the Affymetrix 3000G scanner

data_processing: The data was analysed using RMA in the affy Bioconductor package in R, using the v14.0.0 Arabidopsis CustomCDF from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF

source_name: Excised Radicle and Embryonic Axis, 7h after sowing

label_protocol: The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin-labeled cRNA. For each sample 100 ng was used as input.

growth_protocol: Seeds of Arabidopsis accession Columbia-0 (Col-0, N60000) were sown on 0.7% water agarose (Eurogentec) and incubated in a germination cabinet at 22°C with continuous light.

extract_protocol: For RNA extraction a Stratagene kit was used (Agilent Technologies, Absolutely RNA Nanoprep kit, 50 preps, cat# 400753).

treatment_protocol: At eleven stages after sowing seeds were dissected into four parts (as detailed above) using a stereo microscoop, pair of pincers and a scalpel knife.

tag: accession

value: Columbia-0 (Col-0, N60000)

value: Embryo

tag: seed part

value: RAD

tag: time


title: UCB_unexposed,_rep 3

value: 500-600 microns


title: ssa_1972-null mutant mixed with wild type SK36 Replicate 1

description: Biological replicate 1 of RNA mixture from streptococcus sangunis Δssa_1972 and the wild type SK36


title: Seed_MCE_12h_rep2

description:
MCE12.2
Sample redone for QC reasons

source_name: Excised Micropylar & Chalazal Endosperms, 12h after sowing

tag: tissue

value: Endosperm

value: MCE


title: Seed_COT_3h_rep2

description:
COT3.2
Sample redone for QC reasons

source_name: Excised Cotyledons, 3h after sowing

value: COT


title: testis knock out replicate2


title: Seed_MCE_7h_rep2

description:
MCE7.2
Sample redone for QC reasons

source_name: Excised Micropylar & Chalazal Endosperms, 7h after sowing


title: testis knock out replicate1


title: Pten-/-;Dicer wild-type, sample 1


title: Seed_MCE_25h_noTR_rep1

description:
MCE25N.1
Sample redone for QC reasons

source_name: Excised Micropylar & Chalazal Endosperms, 25h after sowing, without testa rupture

tag: testa/endosperm rupture status

value: without testa rupture


title: Seed_COT_16h_rep4

source_name: Excised Cotyledons, 16h after sowing


title: UCB_unexposed,_rep 2


title: Seed_MCE_31h_rep4

description:
MCE31.4
Sample redone for QC reasons

source_name: Excised Micropylar & Chalazal Endosperms, 31h after sowing


title: UCB_unexposed,_rep 1


title: Seed_COT_31h_rep4

source_name: Excised Cotyledons, 31h after sowing


title: Seed_COT_31h_rep1


title: Seed_COT_31h_rep2


title: Seed_COT_31h_rep3


title: Seed_PE_31h_rep2

source_name: Excised Periphial Endosperm, 31h after sowing

value: PE


title: Seed_PE_31h_rep1


title: Seed_COT_16h_rep1


title: Seed_Dry_rep4

source_name: Whole dry seeds

value: Seed

value: Whole dry seed


title: Seed_PE_3h_rep3

source_name: Excised Periphial Endosperm, 3h after sowing


title: Seed_PE_16h_rep1

source_name: Excised Periphial Endosperm, 16h after sowing


title: Seed_RAD_31h_rep4

source_name: Excised Radicle and Embryonic Axis, 31h after sowing


title: Seed_RAD_20h_rep4

source_name: Excised Radicle and Embryonic Axis, 20h after sowing


title: Seed_COT_3h_rep3


title: Seed_COT_3h_rep4


title: Seed_COT_3h_rep1


title: Seed_Dry_rep3


title: Seed_PE_16h_rep4


title: Seed_COT_16h_rep2


title: Seed_RAD_25h_noTR_rep4

source_name: Excised Radicle and Embryonic Axis, 25h after sowing, without testa rupture


title: Seed_RAD_38h_ER_rep4

source_name: Excised Radicle and Embryonic Axis, 38h after sowing, with endosperm rupture

value: with endosperm rupture


title: Seed_RAD_25h_TR_rep4

source_name: Excised Radicle and Embryonic Axis, 25h after sowing, with testa rupture

value: with testa rupture


title: Seed_PE_31h_rep4


title: Seed_PE_16h_rep2


title: Seed_RAD_12h_rep4

source_name: Excised Radicle and Embryonic Axis, 12h after sowing


title: Seed_RAD_16h_rep4

source_name: Excised Radicle and Embryonic Axis, 16h after sowing


title: Seed_RAD_38h_noER_rep4

source_name: Excised Radicle and Embryonic Axis, 38h after sowing, without endosperm rupture

value: without endosperm rupture


title: Seed_RAD_7h_rep4

source_name: Excised Radicle and Embryonic Axis, 7h after sowing


title: Seed_RAD_1h_rep4

source_name: Excised Radicle and Embryonic Axis, 1h after sowing


title: Seed_MCE_38h_ER_rep4

source_name: Excised Micropylar & Chalazal Endosperms, 38h after sowing, with endosperm rupture


title: Seed_MCE_12h_rep4

source_name: Excised Micropylar & Chalazal Endosperms, 12h after sowing


title: Seed_MCE_25h_noTR_rep4

source_name: Excised Micropylar & Chalazal Endosperms, 25h after sowing, without testa rupture


title: Seed_MCE_25h_TR_rep4

source_name: Excised Micropylar & Chalazal Endosperms, 25h after sowing, with testa rupture


title: Seed_MCE_16h_rep4

source_name: Excised Micropylar & Chalazal Endosperms, 16h after sowing


title: Seed_MCE_20h_rep4

source_name: Excised Micropylar & Chalazal Endosperms, 20h after sowing


title: Seed_MCE_7h_rep4

source_name: Excised Micropylar & Chalazal Endosperms, 7h after sowing


title: Seed_RAD_31h_rep3

source_name: Excised Radicle and Embryonic Axis, 31h after sowing


title: Seed_MCE_38h_noER_rep4

source_name: Excised Micropylar & Chalazal Endosperms, 38h after sowing, without endosperm rupture


title: Seed_MCE_3h_rep4

source_name: Excised Micropylar & Chalazal Endosperms, 3h after sowing


title: Seed_RAD_38h_ER_rep3

source_name: Excised Radicle and Embryonic Axis, 38h after sowing, with endosperm rupture


title: Seed_RAD_25h_TR_rep3

source_name: Excised Radicle and Embryonic Axis, 25h after sowing, with testa rupture


title: Seed_PE_31h_rep3

source_name: Excised Periphial Endosperm, 31h after sowing


title: Seed_MCE_1h_rep4

source_name: Excised Micropylar & Chalazal Endosperms, 1h after sowing


title: Seed_RAD_25h_noTR_rep3

source_name: Excised Radicle and Embryonic Axis, 25h after sowing, without testa rupture


title: Seed_RAD_20h_rep3

source_name: Excised Radicle and Embryonic Axis, 20h after sowing


title: Seed_RAD_12h_rep3

source_name: Excised Radicle and Embryonic Axis, 12h after sowing


title: Seed_RAD_16h_rep3

source_name: Excised Radicle and Embryonic Axis, 16h after sowing


title: Seed_RAD_3h_rep3

source_name: Excised Radicle and Embryonic Axis, 3h after sowing


title: muscle wild type replicate2

source_name: muscle, wild type

value: muscle

value: WT


title: L5

city: Bellaterra

first: Yuliaxis

last: Ramayo-Caldas

state: Barcelona

address: Centre for Research in Agricultural Genomics

department: Animal Genetics

hyb_protocol: Microrarrays were hybridized and scanned at the Institut de Recerca Hospital Universitari Vall d'Hebron (Barcelona, Spain). Approximately 10μg of fragmented cRNA was hybridzed per array using the Affymetrix hybridization kit.Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

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

data_processing: Expression data were generated with Gene-Chip Operating Software (GCOS). Probes were adjusted for background noises and normalized using the GCRMA R package RMA algorithm was used to normalize the arrays and summarized the probes.

organism: Sus scrofa

source_name: low intramuscular fatty acid composition

label_protocol: Samples (12μg of cRNA with biotin-conjugated nucleotide) were chemically fragmented and labeled using the Fragmentation Buffer included in the IVT Express kit (Affymetrix)

extract_protocol: From the 10 selected animals, total RNA was isolated from liver using the RiboPureTM Isolation of High Quality Total RNA (Ambion®, Austin, TX) following the manufacturer’s recommendations. RNA was quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop products, Wilmington, USA) and checked for purity and integrity in a Bioanalyzer-2100 (Agilent Technologies, Inc., Santa Clara CA, USA).

value: Liver

tag: gender

value: Female

tag: intramuscular fatty acid composition

value: low (L)


title: L4

institute: Centre for Research in Agricultural Genomics


title: L3


title: Seed_RAD_1h_rep3

source_name: Excised Radicle and Embryonic Axis, 1h after sowing

value: Columbia-0 (Col-0, N60000)

value: Embryo

value: RAD


title: Seed_RAD_3h_rep4


title: Seed_MCE_38h_ER_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 38h after sowing, with endosperm rupture

value: Endosperm

value: MCE


title: L2


title: Seed_MCE_25h_TR_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 25h after sowing, with testa rupture


title: Seed_MCE_31h_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 31h after sowing


title: Seed_RAD_38h_noER_rep3

source_name: Excised Radicle and Embryonic Axis, 38h after sowing, without endosperm rupture


title: H3

source_name: high intramuscular fatty acid composition

value: high (H)


title: H1


title: Seed_MCE_38h_noER_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 38h after sowing, without endosperm rupture


title: H4


title: Seed_MCE_25h_noTR_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 25h after sowing, without testa rupture

value: without testa rupture


title: Seed_PE_16h_rep3

source_name: Excised Periphial Endosperm, 16h after sowing

value: PE


title: L1


title: Seed_MCE_20h_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 20h after sowing


title: H2


title: H5


title: Seed_MCE_3h_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 3h after sowing


title: Seed_MCE_7h_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 7h after sowing


title: Seed_MCE_16h_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 16h after sowing


title: Seed_COT_16h_rep3

source_name: Excised Cotyledons, 16h after sowing

value: COT


title: Seed_MCE_1h_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 1h after sowing


title: Seed_MCE_12h_rep3

source_name: Excised Micropylar & Chalazal Endosperms, 12h after sowing


title: Mouse mammary gland Ccnd1-/- E2 Rep2

first: Mathew

middle: Casimiro

last: Casimiro

state: United States

address: 233 South 10th St, Rm 1035

department: 233 South 10th St, Rm 1035

institute: Thomas Jefferson University

hyb_protocol: 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).

label: Biotin

source_name: mammary gland_Ccnd1-/-_E2

label_protocol: The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)

growth_protocol: No specific growth protocol

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.

treatment_protocol: Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.

tag: treated with

value: estradiol releasing pellets

value: mouse mammary gland


title: Seed_RAD_38h_noER_rep2

value: without endosperm rupture


title: Seed_PE_3h_rep2

source_name: Excised Periphial Endosperm, 3h after sowing


title: Mouse mammary gland Ccnd1-/- Vehicle Rep1

source_name: mammary gland_Ccnd1-/-_Vehicle

value: placebo control


title: Mouse mammary gland Ccnd1-/- E2 Rep1


title: Mouse mammary gland Ccnd1-/- Vehicle Rep2


title: ∆snfA_CMvsAvicel_24h_A

city: Ribeirao Preto

first: Neil

last: Brown

address: Av. do Cafe

country: Brazil

institute: USP

description: Biological rep 1 of 2.

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent's instruction.

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After, data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus nidulans

source_name: ∆snfA, CM, 24h

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for CM samples) or Cyanine-5 (for avicel samples) for 2 hours at 40 oC.

growth_protocol: All A. nidulans strains were grown in CM for 24h, washed twice with dH2O and then transferred to MM plus avicel as a sole carbon source for 8 or 24 h.

extract_protocol: Total RNA was extracted with RNeasy® Plant Mini Kit (Qiagen) following manufacturer's instructions, followed by DNase treatment and purification using RNeasy® Mini Kit (Qiagen).

tag: strain

value: ∆snfA

tag: treatment

value: complete media

tag: time point

source_name: ∆snfA, Avicel, 24h

value: avicel


title: Seed_RAD_31h_rep2

source_name: Excised Radicle and Embryonic Axis, 31h after sowing


title: ∆schA_CMvsAvicel_24h_B

description: Biological rep 2 of 3.

source_name: ∆schA, CM, 24h

value: ∆schA

source_name: ∆schA, Avicel, 24h


title: Mouse mammary gland Ccnd1+/+ E2 Rep1

source_name: mammary gland_Ccnd1+/+_E2


title: Seed_RAD_38h_ER_rep2

source_name: Excised Radicle and Embryonic Axis, 38h after sowing, with endosperm rupture

value: Columbia-0 (Col-0, N60000)

value: with endosperm rupture


title: ∆schA_CMvsAvicel_8h_B

description: Biological rep 2 of 3.

source_name: ∆schA, Avicel, 8h


title: ∆snfA_CMvsAvicel_24h_B

description: Biological rep 2 of 2.


title: Mouse mammary gland Ccnd1-/- Vehicle Rep3


title: ∆schA_CMvsAvicel_24h_C

description: Biological rep 3 of 3.


title: Mouse mammary gland Ccnd1+/+ E2 Rep3


title: Mouse mammary gland Ccnd1+/+ E2 Rep2


title: Seed_RAD_25h_TR_rep2

source_name: Excised Radicle and Embryonic Axis, 25h after sowing, with testa rupture

value: Embryo

value: RAD

value: with testa rupture


title: ∆schA_CMvsAvicel_24h_A

description: Biological rep 1 of 3.


title: Mouse mammary gland Ccnd1-/- E2 Rep3


title: Mouse mammary gland Ccnd1+/+ Vehicle Rep3

source_name: mammary gland_Ccnd1+/+_Vehicle


title: Seed_RAD_25h_noTR_rep2

source_name: Excised Radicle and Embryonic Axis, 25h after sowing, without testa rupture


title: Seed_PE_3h_rep4

value: Endosperm


title: ∆snfA_CMvsAvicel_8h_B

description: Biological rep 2 of 2.

source_name: ∆snfA, Avicel, 8h


title: Seed_RAD_20h_rep2

source_name: Excised Radicle and Embryonic Axis, 20h after sowing


title: TNO_CMvsAvicel_24h_C

description: Biological rep 3 of 3.

source_name: TNO, CM, 24h

source_name: TNO, Avicel, 24h


title: ∆schA_CMvsAvicel_8h_A

description: Biological rep 1 of 3.


title: ∆schA_CMvsAvicel_8h_C

description: Biological rep 3 of 3.


title: Mouse mammary gland Ccnd1+/+ Vehicle Rep2


title: Mouse mammary gland Ccnd1+/+ Vehicle Rep1


title: TNO_CMvsAvicel_24h_A

description: Biological rep 1 of 3.


title: TNO_CMvsAvicel_8h_A

description: Biological rep 1 of 3.

source_name: TNO, Avicel, 8h


title: Seed_RAD_12h_rep2

source_name: Excised Radicle and Embryonic Axis, 12h after sowing


title: TNO_CMvsAvicel_8h_C

description: Biological rep 3 of 3.


title: Seed_RAD_7h_rep2

source_name: Excised Radicle and Embryonic Axis, 7h after sowing


title: Seed_RAD_16h_rep2

source_name: Excised Radicle and Embryonic Axis, 16h after sowing


title: C3H10-BMP9-1

city: Chicago

first: Tong-Chuan

last: He

state: IL

address: 5841 South Maryland Avenue, MC 3079

department: Department of Orthopaedic Surgery

institute: The University of Chicago Medical Center

description: Treatment

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: C3H10 stimulated with BMP9

label_protocol: Affymetrix standard protocol.

growth_protocol: Cultured in 0.5% FCS DMEM medium for 30h.

extract_protocol: Qiagen RNA isolation kit.

treatment_protocol: Adenovirus expressing BMP9 or GFP.

tag: cell type

value: mesenchymal stem cell (MSC) line

tag: transduction


title: Schisto-PH Mouse #3

city: Aurora

first: Brian

last: Graham

state: CO

department: Medicine

institute: University of Colorado Denver

description: Schisto-PH 3

hyb_protocol: Affymetrix Hybridization/Wash/Stain Kit #900720

scan_protocol: Affymetrix GCS3000

data_processing: CEL files pre-processed using GC-RMA algorithm in Affymetrix Expression Console.

source_name: Schistosoma-PH mice

label_protocol: Affymetrix Genechip WT Terminal Label and Control Kit #901524

extract_protocol: Qiagen RNAeasy kit, Ambion WT Expression Kit #4411974

treatment_protocol: Control group: none. Schisto-PH group: 240 S. mansoni eggs IP/gram body weight, followed 2 weeks later by 240 S. mansoni eggs IV/gram body weight (tail vein injection), followed 1 week later by tissue harvest.

value: female

tag: disease state

value: experimental Schistosoma-induced pulmonary hypertension

value: whole lung


title: C3H10-BMP9-2

description: Treatment

tag: cell line


title: Seed_MCE_38h_ER_rep2

source_name: Excised Micropylar & Chalazal Endosperms, 38h after sowing, with endosperm rupture

value: MCE


title: Seed_RAD_3h_rep2

source_name: Excised Radicle and Embryonic Axis, 3h after sowing


title: Seed_RAD_1h_rep2

source_name: Excised Radicle and Embryonic Axis, 1h after sowing


title: TNO_CMvsAvicel_24h_B

description: Biological rep 2 of 3.


title: Control Mouse #2

description: Control 2

source_name: Control mice

value: Control


title: TNO_CMvsAvicel_8h_B

description: Biological rep 2 of 3.


title: C3H10-BMP9-3

description: Treatment


title: Seed_MCE_38h_noER_rep2

source_name: Excised Micropylar & Chalazal Endosperms, 38h after sowing, without endosperm rupture

value: without endosperm rupture


title: Control Mouse #3

description: Control 3


title: Schisto-PH Mouse #2

description: Schisto-PH 2


title: Schisto-PH Mouse #1

description: Schisto-PH 1


title: C3H10-GFP1

description: Control

source_name: C3H10 stimulated with GFP

value: GFP


title: C3H10-GFP3

description: Control


title: Control Mouse #1

description: Control 1


title: C3H10-GFP2

description: Control


title: Seed_MCE_31h_rep2

source_name: Excised Micropylar & Chalazal Endosperms, 31h after sowing


title: WT: VN1203: 4.0 Days: 10XLD50: Animal C

city: Seattle

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: Microarray slide hybridization was performed with Agilent-013326 human microarrays according to the manufacturer's instructions. Each microarray experiment was done with two technical replicates by reverse dye hybridization for experimental and reference samples.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B). Raw images were analyzed using the Agilent Feature Extraction software (version 8.1.1.1) and the GE2-v5_95_Feb07 extraction protocol.

data_processing: Processing was done in R, and background correction (bg=0, none) and loess normalization were performed using the LIMMA package.

label_protocol: Cy3- and Cy5-labeled cRNA probes were generated by using an Agilent Low RNA Input Linear Amplification kit.

extract_protocol:
Lungs were homogenized in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5 % sarcosyl, 0.1 M β-mercaptoethanol) and kept at -80 degrees C prior to RNA isolation.
Lysates were phase-separated, and RNA was isolated from the aqueous phase.

treatment_protocol: Animals were infected with highly pathogenic A/Vietnam/1203 or fully reconstructed 1918 influenza virus. Lungs were harvested at 1, 3, and 4 days post-infection for microarray.

tag: strain/background

tag: genotype/variation

value: wild-type

value: lung

tag: infection status

value: mock

value: influenza

tag: influenza virus strain

tag: time post-infection

value: day 4

tag: animal

value: C


title: WT: VN1203: 4.0 Days: 10XLD50: Animal B, dye-swap

tag: tissue

value: B


title: WT: VN1203: 4.0 Days: 10XLD50: Animal C, dye-swap

tag: gender


title: Seed_MCE_25h_noTR_rep2

source_name: Excised Micropylar & Chalazal Endosperms, 20h after sowing

tag: accession

value: Columbia-0 (Col-0, N60000)

tag: seed part

tag: time


title: Seed_MCE_20h_rep2

source_name: Excised Micropylar & Chalazal Endosperms, 16h after sowing

value: Endosperm


title: Seed_MCE_25h_TR_rep2

source_name: Excised Micropylar & Chalazal Endosperms, 25h after sowing, with testa rupture

tag: testa/endosperm rupture status

value: with testa rupture


title: WT: VN1203: 4.0 Days: 10XLD50: Animal B

value: female


title: Matrigel 3

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

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

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

data_processing: The data were analyzed with Affymetrix Power Tools (APT) using RMA normalization method.

source_name: D2.OR cell

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

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

value: D2.OR mammary tumor cell line

tag: growth protocol

value: cultured in non-fibrillar collagen I in 3D cell culture


title: Non-Fibrillar collagen 3

description: Gene expression data


title: Non-Fibrillar collagen 2

description: Gene expression data


title: Matrigel 2


title: WT: VN1203: 4.0 Days: 10XLD50: Animal A

value: A


title: WT: VN1203: 4.0 Days: 10XLD50: Animal A, dye-swap


title: Matrigel 1


title: Seed_MCE_16h_rep2

source_name: Excised Micropylar & Chalazal Endosperms, 12h after sowing

value: MCE


title: PfNFYB_IP/Input Replicate2

city: Sao Paulo

first: Wania

middle: Rezende

last: Lima

state: Sao Paulo

address: Rua Matão, travessa 14, n 321

department: Physiology

institute: University of São Paulo

description: Chip-chip schizont stage

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Plasmodium falciparum

source_name: PfNF-YB ChIP DNA from red blood cells infected by schizont form

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: For syncronization, P. falciparum strain 3D7 parasites  were cultured in flasks at 37°C and 5% hematocrit in RPMI 1640 medium supplemented with 10% human plasma, gassed with 90% N2, 5% O2 and 5% CO2. High concentration of ring stage parasites culture was centrifuged for 5 min, 1,200 rpm at room temperature. The supernatant was discarded and the parasitized erythrocytes were incubated for 5 min with 8% sorbitol solution. After incubation, the erythrocytes were centrifuged again, washed twice with complete RMPI medium and added back to the normal culture. Finally, schizont parasites (44 h) were collected for Chromatin immunoprecipitation assay.

extract_protocol: Schizont-stage parasites were isolated from cultured P. falciparum. The samples were lysed according to the protocol for protein extraction in lysis buffer (0.01% saponin, 1x PBS, 1 mM PMSF), and the crosslink was performed in red blood cell-free parasites  fixed in 2% formaldehyde at 37°C for 10 minutes. The excess formaldehyde was quenched by addition of glycine for 5 minutes at room temperature, with agitation. The parasites were lysed in a buffered saline for 15 minutes (5 mM HEPES pH 8.0, 85 mM KCl, 0.5% Triton X-100, plus protease inhibitors). Following centrifugation at 3000 rpm the nuclear pellet was incubated with 500 µl of nuclear lysis buffer (50 mM Tris-HCl, 10 mM EDTA pH 8.0, 1% SDS, and protease inhibitors). The DNA was fragmented into 1000 to 200 bp by sonication (10 times for 10 seconds) and the fractionated chromatin was visualized on an agarose gel stained with ethidium bromide. One milliliter of the supernatant was pre-cleared with 100 µl of protein Sepharose A, by incubation overnight at 4 °C with agitation, then the mixture was centrifuged and the pellet discarded. The clarified fragmented chromatin was incubated with 20 µg anti-PfNF-YB attached to beads, and control beads (no antibody attached) overnight at 40C. The mixture was centrifuged at 300 rpm for 3 minutes and a 1/10 part of the supernatant was saved as input and the pellet was also retained. The pellet was washed three times with immunoprecipitation buffer (50 mM HEPES pH 7.5, 500 mM NaCl, 1% TritonX-100, 0.1% sodium deoxycholate, 1 mM EDTA) and then 6 times with wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA). The samples were uncoupled from the Sepharose by reversing the crosslinking at 65°C overnight. The DNA was purified using the phenol extraction method, then redissolved in 30 µl of sterile distilled water. The DNA was amplified to obtain a greater number of DNA copies to be hybridized with the microarray platform. Thus, the ChIP DNA was amplified using the Genomeplex WGA kit from Sigma. The quantity and quality of DNA were verified using the Nanodrop and Bioanalyzer apparatus. A high-density microarray platform of 720,000 features with 3 characters (3 x 720k) covering the whole genome of P. falciparum was produced by NimbleGen-Roche (USA). The ChIP samples were hybridized with this full genome of P. falciparum and the microarray results were analyzed using the Deva program from Roche. The ChIP-on-chip data was normalized by Tukey bi-weight function because used to account for differences in the dyes on the array and was used. Roche NimbleGen scaled the ratios in the .gff files by subtracting the bi-weight mean for the probe log2-ratios values for all features on the array from each log2-ratio value.

tag: genotype

value: schizont form (44 hpi)

tag: cell type

value: red blood cells

tag: strain

tag: chip antibody

value: PfNF-YB

source_name: Input DNA from schizont

growth_protocol: For syncronization, P. falciparum strain 3D7 parasites  were cultured in flasks at 37oC and 5% hematocrit in RPMI 1640 medium supplemented with 10% human plasma, gassed with 90% N2, 5% O2 and 5% CO2. High concentration of ring stage parasites culture was centrifuged for 5 min, 1,200 rpm at room temperature. The supernatant was discarded and the parasitized erythrocytes were incubated for 5 min with 8% sorbitol solution. After incubation, the erythrocytes were centrifuged again, washed twice with complete RMPI medium and added back to the normal culture. Finally, schizont parasites (44 h) were collected for Chromatin immunoprecipitation assay.

value: none, input DNA


title: WT: VN1203: 3.0 Days: 10XLD50: Animal C, dye-swap

tag: strain/background

value: wild-type

value: lung

value: day 3

value: mock


title: Seed_MCE_3h_rep2

source_name: Excised Micropylar & Chalazal Endosperms, 3h after sowing


title: ∆snfA_CMvsAvicel_8h_A

description: Biological rep 1 of 2.

source_name: ∆snfA, CM, 24h

value: ∆snfA

tag: treatment

value: complete media

tag: time point

source_name: ∆snfA, Avicel, 8h

value: avicel


title: WT: VN1203: 3.0 Days: 10XLD50: Animal B, dye-swap

tag: genotype/variation

tag: infection status

value: influenza

tag: influenza virus strain

value: B


title: Seed_Dry_rep2

source_name: Whole dry seeds

value: Columbia-0 (Col-0, N60000)

tag: tissue

value: Seed

value: Whole dry seed


title: WT: VN1203: 3.0 Days: 10XLD50: Animal C

tag: gender

value: female

tag: time post-infection

tag: animal

value: C


title: Seed_MCE_1h_rep2

source_name: Excised Micropylar & Chalazal Endosperms, 1h after sowing

tag: accession

value: Endosperm

tag: seed part

value: MCE

tag: time


title: Non-Fibrillar collagen 1

description: Gene expression data

tag: cell line

value: D2.OR mammary tumor cell line

tag: growth protocol

value: cultured in non-fibrillar collagen I in 3D cell culture


title: Fibrillar collagen 3

description: Gene expression data

value: cultured in fibrillar collagen I in 3D cell culture


title: Seed_PE_3h_rep1

source_name: Excised Periphial Endosperm, 3h after sowing

value: PE


title: Fibrillar collagen 2

description: Gene expression data


title: Fibrillar collagen 1

description: Gene expression data


title: WT: VN1203: 3.0 Days: 10XLD50: Animal B

value: wild-type

value: lung

value: mock

value: day 3


title: genomic DNA from whole 2h sperm 18

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

description:
normal sperm sample
EPI18_2h.20

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

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

data_processing: Genome studio

label: Cy5 and Cy3

source_name: sperm

label_protocol: Standard Illumina Protocol

extract_protocol: Sperm DNA was extracted with an user-developed version of the QIAamp® DNeasy&Tissue Kit purification protocol according to manufacturer instructions.

value: male

tag: disease state

value: Normal donor


title: genomic DNA from whole 2h sperm 1

description:
normal sperm sample
EPI01_2h.20


title: genomic DNA from whole 2h sperm 10

description:
normal sperm sample
EPI10_2h.20


title: WT: VN1203: 3.0 Days: 10XLD50: Animal A, dye-swap

value: influenza

value: A


title: Seed_RAD_38h_ER_rep1

source_name: Excised Radicle and Embryonic Axis, 38h after sowing, with endosperm rupture

value: Columbia-0 (Col-0, N60000)

value: Embryo

value: RAD

tag: testa/endosperm rupture status

value: with endosperm rupture


title: PfNFYB_IP/Input Replicate1

description: Chip-chip schizont stage

tag: genotype

value: schizont form (44 hpi)

tag: cell type

value: red blood cells

tag: strain

tag: chip antibody

value: PfNF-YB

value: none, input DNA


title: WT: VN1203: 1.0 Days: 10XLD50: Animal C, dye-swap

tag: strain/background

tag: genotype/variation

value: female

tag: infection status

value: day 1

value: C


title: Seed_RAD_31h_rep1

source_name: Excised Radicle and Embryonic Axis, 31h after sowing

tag: tissue


title: WT: VN1203: 3.0 Days: 10XLD50: Animal A

value: wild-type

tag: gender

value: lung

value: mock

tag: influenza virus strain

tag: time post-infection


title: Seed_RAD_38h_noER_rep1

source_name: Excised Radicle and Embryonic Axis, 38h after sowing, without endosperm rupture

tag: accession

tag: seed part

value: without endosperm rupture


title: Seed_RAD_25h_TR_rep1

source_name: Excised Radicle and Embryonic Axis, 25h after sowing, with testa rupture

tag: time

value: with testa rupture


title: DIS t+ FL_14

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Agilent DNA Microarray scanner G2505B (Agilent Technologies).

data_processing: Median normalization and dewaving as described in van de Wiel et al. Briefings in Bioinformatics 2011 (PMID 20172948). NimbleScan software version 2.5.16 (Roche NimbleGen).

source_name: DNA isolated from disseminated t+ FL

label_protocol: Standard NimbleGen protocol.

extract_protocol: The DNA isolation protocol is described in Buffart et al., J Pathol. 2007 Jan;211(1):45-51 (PMID 17117405).

value: disseminated t+ follicular lymphoma

value: follicular lymphoma (FL)

source_name: DNA isolated from a pool of 100 healthy individuals

value: healthy

value: blood

tag: sample type

value: reference


title: genomic DNA from whole 1h sperm 18

description:
normal sperm sample
EPI18_1h.20

value: male

tag: disease state

value: Normal donor


title: Seed_RAD_25h_noTR_rep1

source_name: Excised Radicle and Embryonic Axis, 25h after sowing, without testa rupture

value: Columbia-0 (Col-0, N60000)

value: Embryo

value: RAD

tag: testa/endosperm rupture status

value: without testa rupture


title: DIS t+ FL_13


title: DIS t+ FL_12


title: genomic DNA from whole 1h sperm 16

description:
normal sperm sample
EPI16_1h.20


title: genomic DNA from whole 1h sperm 12

description:
normal sperm sample
EPI12_1h.20


title: WT: VN1203: 1.0 Days: 10XLD50: Animal B, dye-swap

value: female

value: influenza

value: day 1

tag: animal

value: B


title: genomic DNA from whole 1h sperm 14

description:
normal sperm sample
EPI14_1h.20


title: DIS t+ FL_11


title: B cells [CD19_Javi]

description: somatic cells sample

source_name: Whole blood


title: Seed_RAD_20h_rep1

source_name: Excised Radicle and Embryonic Axis, 20h after sowing


title: DIS t+ FL_10


title: WT: VN1203: 1.0 Days: 10XLD50: Animal C

value: wild-type

value: lung

value: mock

value: C


title: WT: VN1203: 1.0 Days: 10XLD50: Animal A, dye-swap

value: A


title: Seed_RAD_16h_rep1

source_name: Excised Radicle and Embryonic Axis, 16h after sowing


title: Seed_RAD_12h_rep1

source_name: Excised Radicle and Embryonic Axis, 12h after sowing


title: genomic DNA from whole 1h sperm 20

description:
normal sperm sample
EPI.20_1h.20


title: B cells [CD19_Fer]

description: somatic cells sample


title: genomic DNA from whole 1h sperm 1

description:
normal sperm sample
EPI01_1h.20


title: genomic DNA from whole 1h sperm 7

description:
normal sperm sample
EPI07_1h.20


title: WT: VN1203: 1.0 Days: 10XLD50: Animal A


title: genomic DNA from swim up sperm 16

description:
normal sperm sample
EPI16_Up.20


title: Seed_RAD_7h_rep1

source_name: Excised Radicle and Embryonic Axis, 7h after sowing


title: genomic DNA from whole 1h sperm 10

description:
normal sperm sample
EPI10_1h.20


title: genomic DNA from swim up sperm 20

description:
normal sperm sample
EPI20_Up.20


title: DIS t+ FL_7

value: disseminated t+ follicular lymphoma

value: follicular lymphoma (FL)

value: healthy

value: blood


title: genomic DNA from swim up sperm 18

description:
normal sperm sample
EPI18_Up.20

value: male

value: Normal donor


title: DIS t+ FL_9

value: reference


title: Seed_RAD_3h_rep1

source_name: Excised Radicle and Embryonic Axis, 3h after sowing

value: Columbia-0 (Col-0, N60000)

value: Embryo

value: RAD


title: genomic DNA from swim up sperm 14

description:
normal sperm sample
EPI14_Up.20


title: WT: r1918: 4.0 Days: 10XLD50: Animal B, dye-swap

value: female

value: influenza

value: day 4