title: 9QSA03192010A_14189449_923_90min_Cy3_vs_923agr_90min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus USA300/ late log phase (90 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 90 min after inoculation.

source_name: Staphylococcus aureus USA300 "agr knockout"/ late log phase (90 min)


title: 9QSA03192010A_14189476_1422_90min_Cy3_vs_Q2798_90min_Cy5_MDS.mev.refIsIA.out

status: Public on Apr 08 2011

type: RNA

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

country: USA

institute: The J. Craig Venter Institute

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).

molecule: total RNA

organism: Staphylococcus aureus

source_name: Staphylococcus aureus 1422/late log phase (90 min)

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: Cells were grown in TSA media containing no OXACILLIN. Samples were collected at 90 min after inoculation.

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manusfacturer.

tag: strain

value: 1422; growth phase:late log phase

source_name: Staphylococcus aureus 2798/late log phase (90 min)

value: 2798; growth phase:late log phase


title: normal_lung_fibroblast_cell_line971

type: genomic

city: Toronto

first: Ming-Sound

last: Tsao

country: Canada

institute: Ontario Cancer Institute/ Princess Margaret Hospital

description:
NF971
Genome wide DNA Methylation profiling

hyb_protocol: Standard Illumina protocol 48C, 17.5 Hours

scan_protocol: Standard Illumina protocol on iScan (Illumina)

data_processing: Standard Illumina protocol for Human Methylation 27K Beadchip quantificatin and processing in GenomeStudio v2010.2

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Normal lung

label_protocol: Standard Illumina protocol; Illumina Infinium II methylation kit

extract_protocol: Genomic DNA was extracted using DNeasy blood and tissue kit (Qiagen, cat# 69504) following DNeasy 96 protocol.

tag: age

tag: Sex

value: M

tag: cell line

value: normal lung fibroblast cell line (NF)

tag: histology

value: Normal lung parenchyma

tag: Stage


title: primary_NSCLC_fibroblast_cell_line746

description:
CAF746
Genome wide DNA Methylation profiling

source_name: primary lung cancer

value: primary NSCLC fibroblast cell line (CAF)

value: Adenocarcinoma

value: II


title: primary_NSCLC_fibroblast_cell_line727

description:
CAF727
Genome wide DNA Methylation profiling

value: Squamous cell carcinoma

value: I


title: primary_NSCLC_fibroblast_cell_line549

description:
CAF549
Genome wide DNA Methylation profiling

value: F

value: III


title: 6QSA09032008A_923.MOCK.CY3_V3.MOCK.CY5_13917789_MDS.mev.refIsIA.out

first: Vasily

middle: A

last: Sharov

address: 9704 Medical Center Drive

department: PFGRC

institute: JCVI

source_name: Staphylococcus aureus USA300/Mock (Reference)

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manufacturer.

source_name: Staphylococcus aureus V3/Mock (Query)

growth_protocol: Strains were grown in TSA media containing no oxacillin.


title: 9QSA03192010A_14189464_923_90min_Cy3_vs_649_90min_Cy5_MDS.mev.refIsIA.out

first: PFGRC

last: JCVI

institute: J. Craig Venter Institute

data_processing:
Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html)
USA300 = reference and USA400 = query.

source_name: Staphylococcus aureus strain 923/late log phase (90 min)

growth_protocol: Strains were grown in TSA media. Samples were collected at 90 min after inoculation. Experiments were conducted in 3 technical replicates.

tag: pulsotype

tag: time

value: late log phase

source_name: Staphylococcus aureus strain 649/late log phase (90 min)

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manusfacturer


title: 6QSA09032008A_923.MOCK.CY3_923.OXA.CY5_13917791_MDS.mev.refIsIA.out

description: This is a self-self hybridization (query/reference does not apply).

growth_protocol: Strains were grown in TSA media containing no oxacillin

source_name: Staphylococcus aureus USA300/Oxacilin (Query)

growth_protocol: Strains were grown in TSA media containing oxacillin.

treatment_protocol: Oxacilin


title: 9QSA03192010A_14189473_1422_120min_Cy3_vs_Q2798_120min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 1422/early stationary phase (120 min)

growth_protocol: Cells were grown in TSA media containing no OXACILLIN. Samples were collected at 120 min after inoculation.

value: 1422; growth phase:early stationary phase

source_name: Staphylococcus aureus 2798/early stationary phase (120 min)

growth_protocol: Cells were grown in TSA media containing NO OXACILLIN. Samples were collected at 120 min after inoculation.

value: 2798; growth phase:early stationary phase


title: MCF7VP cell line, biological rep1

city: Frederick

first: Kate

middle: McGee

last: Im

address: 1050 Boyles Street

institute: National Cancer Institute at Frederick

description: Gene expression data from etoposide resistant breast cancer cell line, MCF7VP

hyb_protocol: 11 µg of labeled cRNA, washed, stained, and scanned according to the protocol described in Affymetrix GeneChip Expression Analysis Manual (Fluidics protocol FS450_0001).

scan_protocol: Affymetrix GeneChip scanner 7G

data_processing: The data were analyzed using Partek Genomic Suite with  robust mutlichip averaging (RMA) as the normalization method.  Normalized intensities less than 5 were set to 5.

source_name: etoposide resistant MCF7 breast cancer cell line

label_protocol: 100 ng of total RNA were amplified and labeled using the message amp II-biotin enhanced reagents (Ambion) according to the protocol provided by the supplier.

growth_protocol: Cell lines were cultured for at least 8 passages in 4µM etoposide in IMEM with 10% FBS and 1% Pen-Strep

extract_protocol: RNA was isolated from the cells using the mirVana kit from ABI as per manufacturers instructions

tag: tissue

value: breast

value: MCF7VP (etoposide-resistant)


title: MCF7 cell line, technical rep 3

description: Gene expression data from etoposide sensitive breast cancer cell line, MCF7

source_name: MCF7 breast cancer cell line

value: MCF7 (etoposide-sensitive)


title: 9QSA31910A_14190385_1422_OXA_60min_Cy3_vs_Q2798_OXA_60min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 1422/mid log phase (60 min)

growth_protocol: Cells were grown in TSA media containing OXACILLIN. Samples were collected at 60 min after inoculation.

treatment_protocol: Oxacilin Treated

value: 1422; growth phase:mid log phase

source_name: Staphylococcus aureus 2798/mid log phase (60 min)

value: 2798; growth phase:mid log phase


title: MCF7VP cell line, biological rep3


title: MCF7 cell line, technical rep 1


title: MCF7VP cell line, RUNX2 knockdown

description: Gene expression data from etoposide resistant breast cancer cell line

hyb_protocol: 11 µg of labeled cRNA, washed, stained, and scanned according to the protocol described in Affymetrix GeneChip Expression Analysis Manual (Fluidics protocol FS450_0001)

data_processing: The data were analyzed using Partek Genomic Suite with  robust mutlichip averaging (RMA) as the normalization method.  Normalized intensities less than 3 were set to 3.

label_protocol: 100 ng of total RNA were amplified and labeled using the message amp II-biotin enhanced reagents (Ambion) according to the protocol provided by the supplier


title: MCF7VP cell line, biological rep2


title: 9QSA31910A_14190387_1422_OXA_120min_Cy3_vs_Q2798_OXA_120min_Cy5_MDS.mev.refIsIA.out

growth_protocol: Cells were grown in TSA media containing OXACILLIN. Samples were collected at 120 min after inoculation.


title: MCF7VP cell line


title: Rescue Clone Minus Dox replicate 2

city: New York

first: Jonathan

last: Monk

state: NY

address: One Gustave L. Levy Place

department: Gene and Cell Medicine

institute: Mt. Sinai School of Medicine

description: Wdr5 KD through shRNA expression

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was VST normalized in R using LUMI and LIMMA packages

organism: Mus musculus

source_name: Rescue Clone Minus Dox replicate 2

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

growth_protocol: rtTA-expressing ES cells Aniv15 were used for derivation of rescue clones and were maintained on primary mouse embryonic fibroblasts with DMEM media supplemented with 15% FBS, 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM l-glutamine and 103 U ml-1 of LIF (Chemicon) and doxycycline (1ug/ml)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: Embryonic Stem Cell

tag: transfection

value: Wdr5R4 -dox


title: Rescue Clone Minus Dox replicate 3

description: Wdr5 KD through shRNA expression

source_name: Rescue Clone Minus Dox replicate 3


title: BIO588368

city: South San Francisco

first: Jinfeng

last: Liu

state: CA

address: 1 DNA Way, MS93

department: Bioinformatics and Computational Biology

institute: Genentech Inc.

hyb_protocol: HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol

scan_protocol: HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol

data_processing: Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.

source_name: siRNA COP1.JUN scanned on 11/03/10

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

growth_protocol: LNCap cells were cultured overnight in serum-free medium.

extract_protocol: Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.

treatment_protocol: siRNA oligonucleotides (Dharmacon) were transfected with Lipofectamine2000 and LipofectamineRNAiMax (Invitrogen) into LNCaP cells.  Cell lysates were prepared 48h after siRNA transfection.

value: LNCap

tag: sirna transfection

value: siRNA COP1.JUN


title: BIO588365

source_name: siRNA COP1.JUN.ETV1 scanned on 11/03/10

value: siRNA COP1.JUN.ETV1


title: BIO588362


title: MCF7 cell line, technical rep 2


title: BIO586224

source_name: siRNA COP1 scanned on 07/21/10

value: siRNA COP1


title: Luciferase replicate 2

description: Luciferase replicate 2

source_name: Luciferase replicate 2

value: LucR +dox


title: 9QSA31910A_14190277_1422_OXA_90min_Cy3_vs_Q2798_OXA_90min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 1422/late log phase (90 min)

growth_protocol: Cells were grown in TSA media containing OXACILLIN. Samples were collected at 90 min after inoculation.

value: 1422; growth phase:late log phase

source_name: Staphylococcus aureus 2798/late log phase (90 min)

value: 2798; growth phase:late log phase


title: BIO586233

source_name: siRNA COP1.ETV1 scanned on 07/21/10

value: siRNA COP1.ETV1


title: BIO586221

source_name: siRNA Control1 scanned on 07/21/10

value: siRNA Control1


title: 9QSA31910A_14190383_1422_OXA_120min_Cy3_vs_Q2798_OXA_120min_Cy5_MDS.mev.refIsIA.out

value: 1422; growth phase:early stationary phase

value: 2798; growth phase:early stationary phase


title: 9QSA31910A_14190384_1422_OXA_30min_Cy3_vs_Q2798_OXA_30min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 1422/early log phase(30 min)

growth_protocol: Cells were grown in TSA media containing OXACILLIN. Samples were collected at 30 min after inoculation.

value: 1422; growth phase:early log phase

source_name: Staphylococcus aureus 2798/early log phase(30 min)

value: 2798; growth phase:early log phase


title: BIO588357

source_name: siRNA Control2 scanned on 11/03/10

value: siRNA Control2


title: 9QSA31910A_14190386_1422_OXA_90min_Cy3_vs_Q2798_OXA_90min_Cy5_MDS.mev.refIsIA.out


title: BIO588358


title: Luciferase replicate 1

description: Luciferase replicate 1

source_name: Luciferase replicate 1


title: Rescue Clone Minus Dox replicate 1

description: Wdr5 KD through shRNA expression

source_name: Rescue Clone Minus Dox replicate 1


title: 9QSA31910A_14190275_1422_OXA_60min_Cy3_vs_Q2798_OXA_60min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 1422/mid log phase (60 min)

value: 1422; growth phase:mid log phase

value: 2798; growth phase:mid log phase


title: BIO586220


title: GFP shRNA replicate 2

description: Expressing GFP shRNA

source_name: GFP shRNA replicate 2

growth_protocol: Mouse CCE or E14T stem cells were maintained on primary mouse embryonic fibroblasts with DMEM media supplemented with 15% FBS, 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM l-glutamine and 103 U ml-1 of LIF (Chemicon) and doxycycline (1ug/ml)

value: Embryonic Stem Cell

value: GFP shRNA


title: BIO586228

value: LNCap


title: GFP shRNA replicate 1

description: Expressing GFP shRNA

source_name: GFP shRNA replicate 1


title: BIO588364

value: siRNA COP1.JUN.ETV1


title: BIO586223

value: siRNA COP1


title: BIO588366

value: siRNA COP1.JUN


title: Oct4 shRNA replicate 1

description: Expressing Oct4 shRNA

source_name: Oct4 shRNA replicate 1

value: Oct4 shRNA


title: BIO588356


title: BIO586226


title: Oct4 shRNA replicate 2

description: Expressing Oct4 shRNA

source_name: Oct4 shRNA replicate 2


title: BIO586218


title: BIO588367

source_name: siRNA COP1.JUN scanned on 11/03/10


title: BIO586231


title: 9QSA31910A_14190274_1422_OXA_30min_Cy3_vs_Q2798_OXA_30min_Cy5_MDS.mev.refIsIA.out


title: 9QSA31910A_14190269_1422_OXA_60min_Cy3_vs_Q2798_OXA_60min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 2798/mid log phase (60 min)


title: BIO588361


title: 9QSA31910A_14190272_1422_OXA_120min_Cy3_vs_Q2798_OXA_120min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 1422/early stationary phase (120 min)

source_name: Staphylococcus aureus 2798/early stationary phase (120 min)


title: 9QSA31910A_14190268_1422_OXA_30min_Cy3_vs_Q2798_OXA_30min_Cy5_MDS.mev.refIsIA.out


title: 9QSA31910A_14190271_1422_OXA_90min_Cy3_vs_Q2798_OXA_90min_Cy5_MDS.mev.refIsIA.out

source_name: Staphylococcus aureus 1422/late log phase (90 min)

value: 1422; growth phase:late log phase

source_name: Staphylococcus aureus 2798/late log phase (90 min)

value: 2798; growth phase:late log phase


title: BIO586225

source_name: siRNA COP1 scanned on 07/21/10


title: BIO588371

source_name: siRNA COP1.JUN.ETV1 scanned on 11/03/10


title: BIO586230

source_name: siRNA COP1.ETV1 scanned on 07/21/10

value: siRNA COP1.ETV1


title: BIO586222


title: BIO588359

source_name: siRNA Control2 scanned on 11/03/10


title: control hepatocytes, biological rep3

city: Cologne

first: Jens

middle: Claus

last: Bruening

address: Zuelpicher Str.47

department: Mouse Genetics and Metabolism

country: Germany

institute: Institute for Genetics, University of Cologne

description:
CBE_WUN2_265_WT
Wildtype littermate control.
Gene expression data from isolated mouse hepatocytes.

hyb_protocol: Following fragmentation, cDNAs were hybridized for 17 hr at 45°C on Affymetrix Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

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

data_processing: The data were analyzed with Partek Genomics Suite using Affymetrix default analysis settings and quantile normalization. Full exons were included in the analysis.

source_name: hepatocytes isolated from doxycycline-treated control mice

label_protocol: Biotinylated cDNAs were prepared according to the GeneChip Whole Transcript Sense Target Labeling protocol (Affymetrix).

growth_protocol: Adult mice were treated with drinking water containing 4mg/ml doxycycline/ 10% sucrose for 8 days to induce miR-143 overexpression in miR-143DOX mice.

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

treatment_protocol: Hepatocytes were isolated after liver perfusion with EBSS, 0.5mM EGTA and EBSS, 10mM Hepes, collagenase, trypsin inhibitor, snap-frozen and stored at -80°C until RNA extraction.

tag: strain/background

tag: developmental stage

value: adult

value: primary hepatocytes

tag: genotype

value: wildtype

tag: treatment

value: doxycycline in drinking water

tag: treatment duration

value: 8 days


title: miR-143DOX hepatocytes, biological rep3

description:
CBE_WUN2_266_TG
Gene expression data from isolated mouse hepatocytes.

source_name: hepatocytes isolated from doxycycline-treated miR-143 transgenic mice

value: transgenic for doxycycline-inducible miR-143 allele


title: BIO588370


title: BIO586219

source_name: siRNA Control1 scanned on 07/21/10

value: siRNA Control1


title: BIO586227


title: Skeletal muscle, RXR-gamma TG

city: Tokyo

first: Takako

last: Takai

address: 1-5-45 Yushima, Bunkyo-Ku

department: Bioinformatics

country: Japan

institute: Tokyo Medical and Dental University

hyb_protocol: 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000. Chip analysis was performed using the Affymetrix GeneChip Operating Software v1.3.

data_processing: Fluorescence intensity in the transgenic groups was normalized to that in the non-transgenic group by equating the overall fluorescence intensity for the entire chip of each group. The average values were scaled to 100 so that all chips could be directly compared.

source_name: Skeletal muscle of transgenic mice overexpressing RXR

label_protocol: 5µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix).  Double-stranded cDNA was cleaned up by using Phase Lock Gels (Eppendorf)-Phenol/Chloroform Extraction (Ambion). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: RXR-gamma mice, under the control of the human alpha-actin promoter, were allowed free access to food (CRF-1; Charles River) and water.

extract_protocol: Total RNA was extracted from the three animals using Trizol (WAKO).

treatment_protocol: RXR-gamma was transgenically overexpressed in the skeletal muscle of mice.

tag: gender

value: female

tag: strain

value: 4 months

tag: genotype/variation

value: RXR-gamma


title: BIO588363

tag: cell line

value: LNCap

value: siRNA COP1.JUN.ETV1


title: BIO588360

value: siRNA COP1.JUN


title: BIO586229


title: miR-143DOX hepatocytes, biological rep2

description:
CBE_WUN2_264_TG
Gene expression data from isolated mouse hepatocytes.


title: miR-143DOX hepatocytes, biological rep1

description:
CBE_WUN2_260_TG
Gene expression data from isolated mouse hepatocytes.


title: control hepatocytes, biological rep2

description:
CBE_WUN2_262_WT
Wildtype littermate control.
Gene expression data from isolated mouse hepatocytes.


title: specific growth rate 0.4h-1 2h

status: Public on Apr 07 2011

city: New Delhi

first: Krishna

middle: Jyoti

last: Mukherjee

email: anuradha.bharara@gmail.com, ashishji101@gmail.com, shubhashreemahalik@gmail.com, kjmukherjee@mail.jnu.ac.in

state: delhi

address: New Mehrauli Road

department: School Of Biotechnology

country: India

institute: Jawaharlal Nehru University

description: We are studying the transcriptomic profiling at different specific growth rates while expressing the rhIFN-beta in fed batch cultures with complex media.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Average Normalization using GeneChip Operating Software Version 1.4

label: Biotin

organism: Escherichia coli

source_name: cell culture

label_protocol: Affymetrix protocol

growth_protocol: Fed batch high cell density cultivation

extract_protocol: Qiagen RNA extraction kit

treatment_protocol: Culture samples frozen in liquid methanol

tag: specific growth rate

tag: time post-induction


title: specific growth rate 0.4h-1 0h


title: control hepatocytes, biological rep1

description:
CBE_WUN2_261_WT
Wildtype littermate control.
Gene expression data from isolated mouse hepatocytes.


title: specific growth rate 0.4h-1 4h


title: BIO586232


title: specific growth rate 0.4h-1 6h


title: specific growth rate 0.3h-1 4h


title: specific growth rate 0.3h-1 0h


title: specific growth rate 0.3h-1 6h


title: specific growth rate 0.2h-1 6h


title: specific growth rate 0.2h-1 0h


title: specific growth rate 0.3h-1 2h


title: specific growth rate 0.2h-1 4h


title: Root_inoculated_-N2_7d_rep2

city: MONTPELLIER CDX 5

first: Valérie

last: HOCHER

address: 911 av. Agropolis BP64501

department: DIADE

country: France

institute: IRD

description:
CG-RI 7J_2
Gene expression in inoculated roots cultivated without nitrogen and sampled 7 days after inoculation with the bacteria Frankia.

hyb_protocol: The Agilent Hybridization Kit (catalog no. 5188-5242) was used . 600 ng of the labeled sample RNA was used for hybridization according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol. The hybridization was performed for 17 h at 65°C. Slides were them washed for 1 min at room temperature in Wash Solution 1 (catalog no. 5188-5325) and 1 min at room temperature in Wash Solution 2, prewarmed to 37°C (catalog no. 5188-5326).

scan_protocol: Scanning  was performed with the Agilent scanner (G2505B) using default parameters for 8 x 15 K formats and the one-color protocol. (scan area 61 X 21.6 mm; scan resolution 5µm; single pass; dye channel is set to green and green PMT is set to 100%).

data_processing: Data were extracted with Feature Extraction 9.1 software (Agilent Technologies) according to the 1-color Agilent protocol (GE1-v5_95_Feb protocol). This software reads and processes microarray image files to prepare them for analysis. Feature Extraction automatically assigns a grid template and a protocol, based on the barcode of the slide. It determines feature intensities, rejects outliers and calculates statistical confidence intervals. Genespring sofware was then used for data processing. Normalization was done as follows: data transformation (Set measurements less than 5.0 to 5.0), per chip : normalized to 50th percentile (probes with presence flags only), per gene : normalized to median. Data were then filtered using flag parameter (Flags (Absent, Marginal, Present) : All control -> Absent, Saturated spot -> Marginal, Spot not uniform -> Marginal, Spot not positive and not significant -> Absent, Spot not above background -> Absent, Population outlier -> Marginal) and each probe must be present for 2/3 of the tested conditions.

organism: Casuarina glauca

source_name: Root, inoculated, no N2, 7d post inoculation

label_protocol: Five hundred nanograms of RNA and Agilent One-Color RNA Spike-In RNA were labeled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to the manufacturer's instructions as follows: 1.2 µl of T7 Promoter Primer was added to 500 ng of RNA and 5 µl of spike-in control (in a 11.5-µl volume) and denatured at 65°C. First-Strand Buffer (to 1x), DTT (to 10 mM), dNTP (to 0.5 mM), Moloney murine leukemia virus (MMLV) reverse transcriptase (1 µl of stock provided in the kit in a 20-µl reaction), and RNaseOut (0.5 µl of stock provided in the kit in a 20-µl reaction) were added. The cDNA was synthesized during the following incubation step (2 h at 40°C). After 10-min denaturation at 65°C and the addition of Cy3-labeled CTP (to 0.3 mM), Transcription Buffer (to 1x), DTT (to 10 mM), NTP (8 µl of stock provided in the kit in a 80-µl reaction), RNaseOUT (0.5 µl of stock provided in the kit in a 80-µl reaction), inorganic phosphatase (0.6 µl of stock provided in the kit in a 80-µl reaction), and T7 RNA polymerase (0.8 µl of stock provided in the kit in a 80-µl reaction), the synthesis of the fluorescent labeled cRNA was performed during the second incubation step (2 h at 40°C). The labeled cRNA was purified with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.

growth_protocol: Seeds were grown for one month in a soil/vermiculite substrate (1:1, vol/vol) in a greenhouse. Plantlets were transferred to a Broughton and Dilworth's modified medium with nitrogen in plastic pots and grown for 3 weeks under these hydroponic conditions. Then they were grown for one week without nitrogen. After this starvation step which is necessary for optimal induction of symbiosis,  plants were sub-divided according to the different sampling times and conditions.

extract_protocol: Total RNA was purified from roots and nodules by ultracentrifugation  (Chirgwin et al., 1979).Residual DNA was removed from RNA samples using the Turbo DNA free kit (Ambion, USA), quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Courtaboeuf, France) and qualitatively assessed using a Bioanalyser 2100 (Agilent p/n G2938A) according to the manufacturer’s instructions (Agilent, Santa Clara, CA, USA).

treatment_protocol: The starting point of the experiment was the day of inoculation of plant with the bacteria (0d). At 0d, a set of plants was inoculated  with the bacteria in the medium without nitrogen and two sets of plants were non-inoculated, one in the medium without nitrogen and one in the medium with nitrogen. Sampling was as follows : at 0d, sampling of one control (non-inoculated roots); at 7 days after inoculation, sampling of 2 controls ( non-inoculated roots cultivated with noitrogen, non-inoculated roots cultivated without nitrogen) and of one symbiosis condition (inoculated roots); at 21 days after inoculation, sampling of nodules (specific organs that develop in symbiosis). All samples were frozen in liquid nitrogen and conserved at -80°C before RNA extraction

value: Root

tag: culture condition

value: Cultivated without nitrogen

value: Inoculated with symbiotic Frankia bacteria

value: 7 days (relative to inoculation time)


title: specific growth rate 0.2h-1 2h


title: Root_inoculated_-N2_7d_rep1

description:
CG-RI 7J_1
Gene expression in inoculated roots cultivated without nitrogen and sampled 7 days after inoculation with the bacteria Frankia.

tag: time


title: Root_inoculated_-N2_7d_rep3

description:
CG-RI 7J_3
Gene expression in inoculated roots cultivated without nitrogen and sampled 7 days after inoculation with the bacteria Frankia.

tag: tissue


title: Root_non-inoculated_-N2_7d_rep1

description:
CG-RnI -N 7j_1
Gene expression in non-inoculated roots cultivated without nitrogen and sampled 7 days post inoculation (control)

source_name: Root, non-inoculated, no N2, 7d post inoculation

value: No inoculation


title: Root_non-inoculated_-N2_7d_rep2

description:
CG-RnI -N 7j_2
Gene expression in non-inoculated roots cultivated without nitrogen and sampled 7 days post inoculation (control)


title: Root_non-inoculated_-N2_7d_rep3

description:
CG-RnI -N 7j_3
Gene expression in non-inoculated roots cultivated without nitrogen and sampled 7 days post inoculation (control)


title: Nodule_-N2_21d_rep2

description:
CG-NOD_2
Gene expression in nodules sampled 21 days  after inoculation with the bacteria Frankia on plants cultivated without nitrogen

source_name: Nodule, inoculated, no N2, 21d post inoculation

value: Nodule

value: 21 days (relative to inoculation time)


title: Root_non-inoculated_+N2_7d_rep2

description:
CG-RnI +N 7j_2
Gene expression in non-inoculated roots cultivated with nitrogen and sampled 7 days post inoculation (control)

source_name: Root, non-inoculated, N2, 7d post inoculation

value: Cultivated with nitrogen


title: Root_non-inoculated_+N2_7d_rep3

description:
CG-RnI +N 7j_3
Gene expression in non-inoculated roots cultivated with nitrogen and sampled 7 days post inoculation (control)


title: Nodule_-N2_21d_rep1

description:
CG-NOD_1
Gene expression in nodules sampled 21 days  after inoculation with the bacteria Frankia on plants cultivated without nitrogen


title: Root_non-inoculated_+N2_7d_rep1

description:
CG-RnI +N 7j_1
Gene expression in non-inoculated roots cultivated with nitrogen and sampled 7 days post inoculation (control)


title: Root_non-inoculated_-N2_0d_rep2

description:
CG-RnI T0_2
Gene expression in non-inoculated roots cultivated without nitrogen and sampled the day of inoculation (control)

source_name: Root, non-inoculated, no N2, 0d post inoculation (reference time)

value: 0 day (relative to inoculation time)


title: Root_non-inoculated_-N2_0d_rep3

description:
CG-RnI T0_3
Gene expression in non-inoculated roots cultivated without nitrogen and sampled the day of inoculation (control)


title: FGG vs. U87 fgg_red_u87_green_slide_2

city: San Antonio

middle: Adam

last: Gelfond

state: TX

address: Mail Code 7933, 7703 Floyd Curl

department: Epidemiology & Biostatistics

institute: UT Health Science Ctr San Antonio

hyb_protocol: Per manufacturer protocol

scan_protocol: Agilent Microarray Scanner G2565AA was used

data_processing: Quantile normalization after loess

label_protocol: Cy3/Cy5 dye using Agilent Low RNA Input Linear   Amplification kit as per manufacturer’s protocols.

growth_protocol: All cells were cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10\% fetal bovine serum (Atlanta Biologicals, Inc., Lawrenceville, GA).

extract_protocol: 200ng of each RNA sample was extracted

tag: phenotype

value: More aggressive tumor

source_name: fgg

value: Normal Glial Cells

value: fgg


title: Skeletal muscle, WT

source_name: Skeletal muscle of control non-transgenic mice

value: female

tag: age

value: 4 months

value: wildtype


title: Nodule_-N2_21d_rep3

description:
CG-NOD_3
Gene expression in nodules sampled 21 days  after inoculation with the bacteria Frankia on plants cultivated without nitrogen


title: FGG vs. U87 fgg_red_u87_green_slide_4


title: Root_non-inoculated_-N2_0d_rep1

description:
CG-RnI T0_1
Gene expression in non-inoculated roots cultivated without nitrogen and sampled the day of inoculation (control)


title: FGG vs. T98G fgg_red_t98g_green_slide_4

value: Less aggressive tumor


title: FGG vs. A172 fgg_red_a172_green_slide_4


title: U87 vs. FGG fgg_green_u87_red_slide_1


title: FGG vs. A172 fgg_red_a172_green_slide_2


title: FGG vs. U118 fgg_red_u118_green_slide_2


title: U118 vs. FGG fgg_green_u118_red_slide_1


title: FGG vs. U118 fgg_red_u118_green_slide_4


title: FGG vs. T98G fgg_red_t98g_green_slide_2


title: T98G vs. FGG fgg_green_t98g_red_slide_1


title: A172 vs. FGG fgg_green_a172_red_slide_1


title: normal_lung_fibroblast_cell_line927

description:
NF927
Genome variation profiling by SNP array

data_processing: Standard Illumina protocol for Infinium Human Genotyping beadchips Beadchip quantificatin and processing in GenomeStudio v2010.2

source_name: Normal lung

label_protocol: Standard Illumina protocol; Illumina Infinium Genotyping multi use kit

tag: Sex

value: F

value: normal lung fibroblast cell line (NF)

tag: histology

value: Normal lung parenchyma

tag: Stage


title: U118 vs. FGG fgg_green_u118_red_slide_3


title: U87 vs. FGG fgg_green_u87_red_slide_3


title: T98G vs. FGG fgg_green_t98g_red_slide_3


title: normal_lung_fibroblast_cell_line971

description:
NF971
Genome variation profiling by SNP array

value: M


title: primary_NSCLC_fibroblast_cell_line971

description:
CAF971
Genome variation profiling by SNP array

source_name: primary lung cancer

value: primary NSCLC fibroblast cell line (CAF)

value: Adenocarcinoma

value: II


title: MAA/T+MAA

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: RNA expression profile for MAA treated vs. testosterone+MAA treated  mouse TM3 cells infected by  retrovirus containing AR cDNA.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).

data_processing: Linear and LOWESS normalization as determined using Agilent's Feature Extraction software

label: Alexa 647

source_name: RNA prepared using Trizol from mouse TM3 cells infected by retrovirus encoding Androgen Receptor (AR) cDNA.

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

growth_protocol: TM3 and TM3-AR cells (see below) were grown in DMEM-F12 medium containing 5% horse serum and 2.5% FBS.

extract_protocol: Trizol extraction of RNA

treatment_protocol: TM3-AR cells were treated for 24 hr with either testosterone (T, 10 nM) or MAA (5 mM), or with testosterone in combination with MAA (T+MAA), or were untreated (UT).

value: TM3 Leydig cell infected by retrovirus encoding Androgen Recetor (AR) cDNA.

value: 24h-MAA-5 mM

label: Alexa 555

source_name: TM3-AR Leydig cell RNA prepared using Trizol

value: TM3-AR Leydig cell

value: 24h-testosterone-10 nM and MAA-5mM


title: A172 vs. FGG fgg_green_a172_red_slide_3

value: Normal Glial Cells


title: normal_lung_fibroblast_cell_line727

description:
NF727
Genome variation profiling by SNP array


title: primary_NSCLC_fibroblast_cell_line927

description:
CAF927
Genome variation profiling by SNP array

value: I


title: normal_lung_fibroblast_cell_line746

description:
NF746
Genome variation profiling by SNP array


title: T/T+MAA

description: RNA expression profile for testosterone treated vs. testosterone+MAA treated  mouse TM3 cells infected by  retrovirus containing AR cDNA.

value: 24h-testosterone-10 nM


title: UT/T

description: RNA expression profile for untreated vs. testosterone treated mouse TM3 cells infected by  retrovirus containing AR cDNA.


title: T+MAA/UT

description: RNA expression profile for testosterone+MAA treated vs. testosterone treated mouse TM3 cells infected by  retrovirus containing AR cDNA.


title: UT/MAA

description: RNA expression profile for untreated vs. MAA treated mouse TM3 cells infected by  retrovirus containing AR cDNA.


title: primary_NSCLC_fibroblast_cell_line746

description:
CAF746
Genome variation profiling by SNP array


title: T+MAA/MAA

description: RNA expression profile for testosterone+MAA treated vs. MAA treated mouse TM3 cells infected by  retrovirus containing AR cDNA.


title: primary_NSCLC_fibroblast_cell_line727

description:
CAF727
Genome variation profiling by SNP array

value: Squamous cell carcinoma


title: MM1

city: Vienna

first: Mario

last: Mikula

address: Waehringergürtel 18-20

department: General Dermatology

country: Austria

institute: Medical University Vienna

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions, and the arrays were washed using Affymetrix fluidics stations.

scan_protocol: The arrays were scanned using the appropriate Gene Chip Scanner.

data_processing: CEL files were processed via the genotyping console 3.0.1 using default parameters. CHP files were generated via the genotyping console 3.0.1 using default parameters. Normalization was performed using the birdseed v2 algorithm.

source_name: MM1 cell line

label_protocol: DNA was restriction digested, PCR amplified, fragmented, and labeled as per manufacturer's instructions (Affymetrix).

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted using the Qiagen All Prep DNA Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: Cells were either untreated (MM1, PM1) or passaged through SCID mice (PM1xt).

tag: cell type

value: melanoma

value: untreated


title: MAA/UT

description: RNA expression profile for MAA treated vs. untreated mouse TM3 cells infected by  retrovirus containing AR cDNA.

tag: treatment


title: Pig_DonorCell_rep1

city: Kyoto

first: Kei

last: Miyamoto

address: Oiwakecho, Kitasirakawa, Sakyo-ku

department: Agriculture

institute: Kyoto university

description: The same cells that were used for nuclear transfer

hyb_protocol: Fifteen ug of cRNA were hybridized for 16 hr on Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Sample values [(αDJ1-NT_1, NT_1, DonorCell_1) or αDJ1-NT_2] were divided by values of control samples (IgG-NT_1 or IgG-NT_2, respectively).

organism: Sus scrofa

source_name: Donor cells used for nuclear transfer

label_protocol: Biotinylated cRNA were prepared from 50 ng total RNA by Two-Cycle Target Labeling (Affymetrix) with the following minor modification: the conditions for reverse transcription were 30 min at 42 °C followed by 30 min at 45 °C to increase the reaction efficiency in GC rich regions of mRNA.

growth_protocol: Embryos were incubated in PZM-3 at 38.5C in 5% CO2 in air for 28 h. Cells were cultured in DMEM and 10%FBS at 38.5C in 5% CO2.

extract_protocol: Picopure RNA Extraction Kit, ARCTURUS. Protocol according to manufacturer specification.

treatment_protocol: Embryos and cells were washed 3 times with PBS.

tag: sample type

value: Cultured fibroblast cells

tag: developmental stage

value: not appreciable

tag: source

value: Established from an adult Meishan pig


title: Pig_NT_rep1

source_name: Nuclear transfer embryos at 28 h after nuclear transfer

value: Embryos

value: two cell stage

value: Recipient oocytes were derived from slaughter house


title: LAU-Me275 melanoma cells vs matched PBL_technical replicate #3 (Agilent-014693)

city: Lausanne

first: Armand

last: Valsesia

address: Bâtiment Génopode

country: Switzerland

institute: Ludwig Institute for Cancer Research

description: melanoma cell line hybridized vs its matched control cell (derived from the same patient)

hyb_protocol: Hybridization was done according to the manufacturer's instructions. Following the labeling reaction the individually labeled test and reference samples were concentrated using Microcon YM-30 filters (Millipore, Billerica, MA) and then combined. Following probe denaturation and pre-annealing with Cot-1 DNA, hybridization was performed at 65°C with rotation for 40 hr. Four steps were done with Agilent Oligo CGH washes: Wash buffer 1 at room temperature for 5 min, wash buffer 2 at 37°C for 1 min, an acetonitrile rinse at room temperature for 1 min and a 30 sec wash at room temperature in Agilent's Stabilization and Drying Solution.

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (v.9.5.3.1).

data_processing: Agilent Feature Extraction Software (v.9.5.3.1) was used for background subtraction and to extract signal intensities. Normalization was performed with the framework proposed by Chen et al. (Bioinformatics 2008)

source_name: Low-passage culture of lymph node metastasis from cutaneous melanoma

label_protocol: Labeling was done according to the manufacturer's instructions. Test DNA (1 µg) and reference DNA (1 µg were labeled by random priming with either Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit Plus.

growth_protocol: Melanoma cell lines were cultured in RPMI-1640 medium supplemented with 10% FCS. EBV immortalized B cells were cultured in IMDM /10% FCS medium.

extract_protocol: Genomic DNA was extracted using the Gentra Puregene kit (Qiagen) according to manufacturer's instructions and further purified according to Agilent's protocols; the test and reference DNAs are digested with Alu I and Rsa I (Promega, Madison, WI), and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown, MD)

value: cells derived from metastatic melanoma

tag: source tissue

value: lymph node

source_name: control PBL cell

value: control PBL cell


title: LAU-Me275 melanoma cells vs matched PBL_technical replicate #4 dyeswap (Agilent-014693)

tag: cell line


title: Pig_IgG-NT_rep2

description: Control sample of second experiment samples (αDJ1-NT_2 and IgG-NT_2)

source_name: Nuclear transfer embryos injected with IgG at 28 h after nuclear transfer


title: PM1

source_name: PM1 cell line


title: Pig_IgG-NT_rep1

description: Control sample of first experiment samples (αDJ1-NT_1, IgG-NT_1, NT_1 and DonorCell_1)


title: Pig_αDJ1-NT_rep2

source_name: Nuclear transfer embryos injected with anti-DJ1 antibody at 28 h after nuclear transfer


title: Blood Patient DNA

hyb_protocol: According to manufacturer protocol

scan_protocol: According to manufacturer protocol

source_name: Patient Blood

label_protocol: According to manufacturer protocol Affymetrix dsDNA terminal label

extract_protocol: DNA was isolated by using the All Prep DNA Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

tag: gender

value: female

value: blood


title: PM1xt

source_name: PM1xt cell line

value: passaged through SCID mice


title: LAU-Me275 melanoma cells (GenomeWideSNP_6)

description: metastatic melanoma from lymph node, assayed on Affymetrix 6.0 array for CNV analysis

hyb_protocol: in accordance to manufacturer's instructions

data_processing:
CEL file was parsed to extract raw intensities, then normalization and copy number analysis was performed using the PICNIC algorithm from Greenman et al. (Biostatistics 2009)
The file called Me275.features_intensity.raw.csv was generated using the CEL parser provided in the PICNIC package. This file contains raw intensities for each features at each SNP. The file called output_Me275.feature_intensity.csv was generated by PICNIC and contains normalized intensities, copy number and LOH prediction at each SNP

growth_protocol: Melanoma cell lines were cultured in RPMI-1640 medium supplemented with 10% FCS.

value: male


title: Patient derived melanoma metastasis

source_name: melanoma metastasis

value: axilla melanoma metastasis


title: LAU-Me275 melanoma cells vs matched PBL_technical replicate #1 (Agilent-014693)


title: T/UT

description: RNA expression profile for testosterone treated vs. untreated mouse TM3 cells infected by retrovirus containing AR cDNA.

value: TM3 Leydig cell infected by retrovirus encoding Androgen Recetor (AR) cDNA.

value: 24h-testosterone-10 nM

value: TM3-AR Leydig cell


title: wild type vs mutant_rep3_color swap

first: Hirokazu

last: Takahashi

address: 1-1-1 Yayoi, Bunkyo

department: Graduate school of agricultural and life Science

institute: University of Tokyo

description: Gene expression in the rice coleoptile between wild type and mutant

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent).  cRNA was hybridized to microarray using hybridization oven G2531A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2505B  according to manufacturer's instructions.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 8.5.1.1 (Agilent). We used the linear & lowess methods for normalization.

organism: Oryza sativa Japonica Group

source_name: Coleoptile of mutant seeds germinated under submergence

label_protocol: Cy3and Cy5-labeled cRNA were prepared from total RNA using Low RNA Input Linear Amplification Kit (Agilent) in accordance with the manufacturer's protocol with slight modification.

growth_protocol: 15 seeds were sowed in 1 L glass bottle filed with 1 L deionized water.

extract_protocol: Total RNA was extracted from each cell type and tissue with a PicoPure™ RNA isolation kit (Molecular Devices, Ontario, Canada) following the manufacturer's recommendations. The qualities of the RNA samples were assessed using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Seedling were fixed with ethanol : acetic acid (3:1). Then, seedlings, which were embedded in RNase-free water, were frozen in hexane cooled with dry ice and stored at -80℃.  We cut frozen section of 8 µm thickness.  Coleoptiles were isolated from sections by laser microdissection.

tag: genotype/variation

value: rad mutant

tag: cultivars

value: Kinmaze

source_name: Coleoptile of wild type seeds germinated under submergence

value: wild type


title: Patient derived melanoma primum

source_name: melanoma primum

value: melanoma primum from patients back


title: wild type vs mutant_rep3


title: ABA,rep3

city: La Jolla

first: Maik

last: Boehmer

address: 9500 Gilman Dr 0116

department: Biology

institute: University of Caifornia, San Diego

hyb_protocol: Arabidopsis ATH1 oligonucleotide-based genome arrays were used, and hybridization and washing were performed by using the standard Affymetrix protocol for RNA analyses (www.affymetrix.com/products/arrays/specific/arab.affx).

scan_protocol: Affymetrix 7G scanner

data_processing: RMA (Limma)

organism: Arabidopsis thaliana

source_name: T87 suspension cells

label_protocol: Affymetrix 3' IVT labeling kit

growth_protocol: Arabidopsis thaliana (Columbia ecotype) T87 suspension cells were obtained from RIKEN BioResource Center (Tsukuba, Japan) and were cultured at 20 °C under 16 h light, 8h dark illumination (24 μE s−1 m−2) with shaking at 120 rpm. Cells were subcultured every 7 days by adding 10 ml of the cell suspension to a 500 ml flask containing 90 ml of Gamborg B5 medium with 3% sucrose and 0.5 µM 1-naphthaleneacetic acid (NAA). Experiments were carried out in the exponential phase of growth at about 120 h of cell cultivation.

extract_protocol: RNA was isolated with the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: ABA and DMTU were added to the medium containing the suspension cells to the final required concentrations of 50 µM and 5mM, respectively. Treatments were continued for 20 h before RNA extraction

value: suspension cells

value: 5 days

tag: time

value: 20 hours

tag: hormone

value: abscisic acid (ABA)

tag: genetic background


title: Pig_αDJ1-NT_rep1

value: Embryos

value: two cell stage

value: Recipient oocytes were derived from slaughter house


title: LAU-T618A melanoma cells vs matched PBL (Agilent-014693)

source_name: Low-passage culture of cutaneous metastasis from cutaneous melanoma

value: cells derived from metastatic melanoma

value: skin

value: control PBL cell


title: LAU-T50B melanoma cells vs matched PBL (Agilent-014693)


title: LAU-Me275 melanoma cells vs matched PBL_technical replicate #2 (Agilent-014693)

value: lymph node


title: wild type vs mutant_rep2


title: PBL patient LAU108 (Human1M-Duov3_B)

description: Genomic DNA  was hybridized on Illumina Human 1M-Duov3 DNA Analysis BeadChips for subsequent copy number analysis.

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, vacuum dried for 1 hour and scanned on a iScan System (Illumina).

data_processing: Ratio were normalized in BeadStudio (Illumina), then ploidy was corrected using the OverUnder plugin (Attiyeh et al. Genome Res. 2009). Copy number values were obtained using Overunder with a window size of 201 SNPs.

label: C-Bio and A-DNP

source_name: Peripheral blood lymphocytes

label_protocol: 500ng of genomic DNA was whole-genome amplified in a 20 hours reaction at 37ºC using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

growth_protocol: Melanoma cell lines were cultured in RPMI-1640 medium supplemented with 10% FCS. Normal human melanocytes were grown in HAM-F10 medium supplemented with 2% FCS, 5% MelanoMax supplement (Gentaur, Belgium) and 6 mM HEPES. EBV immortalized B cells were cultured in IMDM /10% FCS medium.

extract_protocol: Genomic DNA was extracted using a salting out method (Gentra Puregene kit, Qiagen) following manufacturer's instructions. In case of pigmented samples, 1% beta-mercaptoethanol and 2% polyvinylpyrrolidone were added to the lysis buffer and the amount of saturated salt solution to precipitate proteins increased

value: Peripheral blood lymphocytes

value: female

value: blood


title: LAU-Me246.M1 melanoma cells vs matched PBL (Agilent-014693)


title: LAU-Me275 melanoma cells patient LAU50 (Human1M-Duov3_B)

value: Low-passage culture of lymph node metastasis from cutaneous melanoma


title: LAU-T149D melanoma cells vs matched PBL (Agilent-014693)

source_name: Low-passage culture of visceral metastasis from cutaneous melanoma

value: visceral tissue


title: Shoot of MIT Knockdown Plant vs. WT, Replicate 2

city: Miyagi

first: Yasuhiro

last: Ishimaru

address: 6-3 Aramakiaza-aoba, Aoba-ku, Sendai

institute: Tohoku University

description: Replicate 2 of 2. Shoot of WT vs. shoot of MIT knockdown plant.

hyb_protocol: Cy3-labelled cRNA and Cy5-labelled cRNA (825ng each) were mixed, fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) for 17 hours at 65°C using the Agilent Gene Expression Hybridization kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.

source_name: MIT knockdown plant, shoot

label_protocol: Labeled cRNA was prepared from 400 ng RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Rice plants were grown in hydroponic solution for 5 weeks under control conditions.

extract_protocol: RNA was prepared using the RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cultivar

value: Dongjing

tag: genotype

value: MIT knockdown

tag: age

value: day 35

tag: tissue

value: shoot

source_name: WT, shoot

value: WT


title: LAU-T50B melanoma cells patient LAU50 (Human1M-Duov3_B)

value: Low-passage culture of cutaneous metastasis from cutaneous melanoma

value: male


title: Shoot of WT vs. MIT Knockdown Plant, Replicate 1

description: Replicate 1 of 2. Shoot of WT vs. shoot of MIT knockdown plant.


title: PBL patient LAU618 (Human1M-Duov3_B)

tag: cell type


title: wild type vs mutant_rep1

value: wild type

value: Kinmaze

value: rad mutant


title: Root of WT vs. MIT Knockdown Plant, Replicate 1

description: Replicate 1 of 2. Root of WT vs. root of MIT knockdown plant.

source_name: WT, root

value: root

source_name: MIT knockdown plant, root


title: LAU-Me235 melanoma cells patient LAU63 (Human1M-Duov3_B)

source_name: Low-passage culture of lymph node metastasis from cutaneous melanoma

value: lymph node


title: LAU-Me280.R.LN melanoma cells patient LAU165 (Human1M-Duov3_B)


title: LAU-Me246.M1melanoma cells patient LAU108  (Human1M-Duov3_B)

value: skin


title: normal melanocyte 1 (Human1M-Duov3_B)

source_name: Culture of epidermal melanocytes

value: cultured epidermal melanocytes


title: control,rep1

value: suspension cells

value: 5 days

value: 20 hours

value: ethanol (control)


title: wild type vs mutant_rep1_color swap


title: wild type vs mutant_rep2_color swap


title: OT-2 tcr transgenic, peptide-injected 3

status: Public on Apr 06 2011

city: Novato

first: Eric

last: Verdin

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

hyb_protocol: In accordance with manufacturer's reccomendation for Gene 1.0ST arrays

scan_protocol: Affymetrix GCS3000 scanner and the GCOS 1.4 data acquisition software

data_processing:
.cel files were normalized using Exppression Console RMA
Matrix values represent log2 normalized scalar expression values for the indicated Affy probe sets

source_name: Flow-sorted CD4/CD8 DP thymocytes, TCR transgenic, activated in vivo

label_protocol: Labeling was in accordance with Affymetrix WT labeling kit

growth_protocol: Mice were all between 3 and 6 weeks of age

extract_protocol: total RNA was extracted using Qiagen Rneasy Mini kit, with on-column DNAse digestion

value: thymus

tag: strain

value: OT-2 TCR transgenic

tag: treatment

value: activation by i.p. injection of agonist peptide for OT-2 TCR, 3 hours prior to harvest.


title: Aire knock out 1

city: Melbourne

first: Francois-Xavier

last: Hubert

state: Victoria

address: 1G Royal Parade

department: Immunology

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Un-normalized summary probe profiles were output from BeadStudio for two Illumina Mouse-6 Expression Beadchip (v1.1). The raw intensities were background corrected using the negative controls, a variance stabilising transformation (vst) was applied and the data quantile normalised using all the arrays on the two beadchips using the lumi package of the Bioconductor open-source software project (http://www.bioconductor.org).

source_name: MHCIIhi mTECs

label_protocol: Standard Illumina protocol

extract_protocol: RNA was isolated using a Qiagen RNeasy mini kit including an on column DNase digest as per manufacturer's instructions.

value: ako

tag: beadchip

tag: Sex

tag: date


title: OT-2 tcr transgenic, peptide-injected 2


title: Root of MIT Knockdown Plant vs. WT, Replicate 2

description: Replicate 2 of 2. Root of WT vs. root of MIT knockdown plant.

value: Dongjing

value: MIT knockdown

value: day 35

value: WT


title: Wildtype 2

value: wt

value: male


title: LAU-Me280.R.LN melanoma cells vs matched EBV transformed lymphoblastoid cells (Agilent-014693)

tag: cell line

value: cells derived from metastatic melanoma

tag: source tissue

value: lymph node

source_name: control EBV cell line

value: control EBV cell line


title: Aire knock out 2

value: female


title: Wildtype 1


title: LAU-T618A melanoma cells patient LAU618 (Human1M-Duov3_B)

tag: sample type

value: Low-passage culture of cutaneous metastasis from cutaneous melanoma

tag: gender

value: skin


title: normal melanocyte 2 (Human1M-Duov3_B)

value: cultured epidermal melanocytes


title: Aire knock out 3


title: EBV transformed lymphoblastoid cells patient LAU108 (Human1M-Duov3_B)

source_name: EBV transformed lymphoblastoid cells

value: EBV transformed lymphoblastoid cells

value: blood


title: LAU-Me235 melanoma cells vs matched PBL (Agilent-014693)

source_name: control PBL cell

value: control PBL cell


title: diploid male patient LAU63 vs pool of diploid males PROMEGA (Agilent-014693)

source_name: pooled diploid male (PROMEGA)

value: diploid pool of DNA used routinely in clinical diagnosis


title: PBL patient LAU149 (Human1M-Duov3_B)

value: Peripheral blood lymphocytes


title: Wildtype 3


title: PBL patient LAU63 (Human1M-Duov3_B)


title: EBV transformed lymphoblastoid cells patient LAU165 (Human1M-Duov3_B)


title: 20913_RA8h_2

city: Baltimore

first: Shuli

last: Xia

institute: Kennedy-Krieger Institute

description:
RNA expression value
Sxia_GBM-SC-20913-RA8h_2a_Huexon.CEL

hyb_protocol: Hybridization to Affymetrix GeneChip Human Exon 1.0ST. Arrays was carried out in Affymetrix hybridization Oven 640 following Affymetrix Whole Transcript sense Target Labeling Assay Manual (Rev. 5).

scan_protocol: Array was scanned using Affymetrix GeneChip Scanner 3000 with G7 upgrade according to the manufacturer's recommendation.  Array was scanned using Affymetrix GeneChip Scanner 3000   with G7 upgrade according to the manufacturer's recommendation.

data_processing:
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and quantile normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.
The probe group report file (SXio032409_Report.txt) and processed data file with full header (rma-gene-extended.summary.txt) are available as supplementary files on the Series record.

source_name: Cultured cells

label_protocol: Single-strand cDNA was generated from the amplified cRNA, fragmented and labeled following Affymetrix Whole Transcript Sense Target Labeling Assay Manual (Rev. 5). Sample labeling, hybridization, and scanning was carried out in JHMI microarray core facility.

growth_protocol: The human glioblastoma neurosphere lines HSR-GBM1A (20913) and HSR-GBM 1B (10627) were originally derived by Vescovi and colleagues and maintained in serum-free medium supplemented with EGF and FGF. Cells were incubated in a humidified incubator containing 5% CO2/95% air at 37°C, and passaged every 4-5 days.

extract_protocol: RNAeasy kit from Qiagen

treatment_protocol: All-trans retinoic acid (RA) was prepared as stock solutions in DMSO and diluted in cell culture medium to the final concentration of 10 uM. In all the experiments, the final DMSO concentration was < 0.1%.

value: glioblastoma neurospheres

tag: treatment group

value: retinoic acid for 8h


title: 20913_RA48h_2

description:
RNA expression value
Sxia_GBM-SC-20913-RA48h_2a_Huexon.CEL

value: retinoic acid for 48h


title: OT-2 tcr transgenic 3

source_name: Flow-sorted CD4/CD8 DP thymocytes, TCR transgenic

value: thymus

value: OT-2 TCR transgenic


title: OT-2 tcr transgenic, peptide-injected 1

value: activation by i.p. injection of agonist peptide for OT-2 TCR, 3 hours prior to harvest.


title: OT-2 tcr transgenic 1


title: 20913_RA8h_1

description:
RNA expression value
Sxia_GBM-SC-20913-RA8h_1a_Huexon.CEL


title: PBL patient LAU50 (Human1M-Duov3_B)

value: male


title: LAU-T149D melanoma cells patient LAU149D (Human1M-Duov3_B)

value: Low-passage culture of visceral metastasis from cutaneous melanoma

value: visceral tissue


title: OT-2 tcr transgenic 2


title: HDAC7-VP16 transgenic 3

source_name: Flow-sorted CD4/CD8 DP thymocytes, HDAC7-VP16 transgenic

value: HDAC7-VP16 transgenic


title: 20913_control_1

description:
RNA expression value
Sxia_GBM-SC-20913-1a_Huexon.CEL

value: control


title: 20913_control_2

description:
RNA expression value
Sxia_GBM-SC-20913-2a_Huexon.CEL


title: 10627_RA48h_1

description:
RNA expression value
Sxia_GBM-SC-10627-RA48h_1a_Huexon.CEL


title: 10627_RA8h_2

description:
RNA expression value
Sxia_GBM-SC-10627-RA8h_2a_Huexon.CEL


title: HDAC7 Knockout 3

source_name: Flow-sorted CD4/CD8 DP thymocytes, HDAC7 knockout

value: HDAC7 knockout


title: 10627_RA48h_2

description:
RNA expression value
Sxia_GBM-SC-10627-RA48h_2a_Huexon.CEL


title: HDAC7-VP16 transgenic1


title: HDAC7 Knockout 1


title: 10627_RA8h_1

description:
RNA expression value
Sxia_GBM-SC-10627-RA8h_1a_Huexon.CEL


title: 20913_RA48h_1

description:
RNA expression value
Sxia_GBM-SC-20913-RA48h_1a_Huexon.CEL


title: HDAC7-VP16 transgenic 2


title: 10627_control_2

description:
RNA expression value
Sxia_GBM-SC-10627-2a_Huexon.CEL


title: 10627_control_1

description:
RNA expression value
Sxia_GBM-SC-10627-1a_Huexon.CEL


title: wild-type 5

source_name: Flow-sorted CD4/CD8 DP thymocytes

value: wild-type


title: HDAC7 Knockout 2


title: wild-type 6


title: Healthy volunteer

city: Houston

first: John

last: Redell

institute: University of Texas Health Science Center at Houston

description: pooled samples

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Cy3 dyes were circulated through the microfluidic chip for dye staining.

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

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression)

source_name: plasma

label_protocol: Equal volumes of total RNA from each group (HV and TBI) was size fractionated using a YM-100 Microcon centrifugal filter (Millipore), and the recovered small RNAs (< 300 nt) were 3′-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was ligated to the poly(A) tail for later fluorescent dye staining with Cy3.

extract_protocol: 20 µl plasma from each of 10 HV or severe TBI patients was pooled (200ul/group), and total RNA was isolated using the Total RNA Isolation kit from Norgen Biotek according to the manufacturer's protocol.

value: plasma

tag: age range

tag: gender composition

value: of the 10 in the pool, 2 were women, 8 were men

tag: race composition

value: of the 10 in the pool, 9 were white, 1 was asian


title: Traumatic brain injury

description: pooled samples


title: wild-type 4

tag: genotype


title: wild-type 2


title: wild-type 3


title: wild-type 1


title: γδ IEL, conventional, rep 1

city: Dallas

first: Lora

middle: V

last: Hooper

address: 5323 Harry Hines Blvd.

institute: The University of Texas Southwestern Medical Center at Dallas

description: gene expression data from purified small intestinal γδ IEL (flow cytometry-purified IELs)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 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 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 500.

source_name: pooled small intestinal γδ IEL from conventionally-raised mice

label_protocol: mRNAs were amplified using the Arcturus RiboAmp HS kit. Biotinylated cRNAs were generated by substituting the Enzo T7 BioArray Transcript kit during the last step.

growth_protocol: Mice were raised under germ-free conditions (microorganism-free) or conventional conditions (having intestinal bacteria).

extract_protocol: Total RNA was extracted and purified using the Arcturus PicoPure RNA isolation kit

treatment_protocol: Total IEL were isolated from mouse small intestines. γδ IEL were labeled with PE-labeled anti-TCRd. γδ IEL were purified by sorting on a BD moFlo cell sorter.

tag: mouse strain

value: small intestine

value: γδ intraepithelial lymphocytes (IEL)

tag: age

value: >8 weeks

tag: intestinal colonization

value: conventionally-colonized


title: Dendritic cells rep3 (miRNA)

status: Public on Apr 05 2011

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

description: miRNA expression data from mouse dendritic cells

hyb_protocol: Following RNA labeling and purifying, the labeled RNAs were hybridized for 16 hr at 56C on miRCURY LNATM microRNA Array ( Exiqon). Arrays were washed according to the manufactaturer's instruction.

scan_protocol: Platforms were scanned using a GenePix 4000 microarray scanner.

data_processing: The images were captured and analyzed by GAL-file (Exiqon Inc, Woburn, MA) which covers miRNA ID annotated by version 10.0 of miRBase (http://microrna.sanger.ac.uk)

source_name: Mouse dendritic cells

label_protocol: RNA molecules were labeled with a single fluorophor Hy5tm or Hy3TM according to the standard Exiqon labeling protocol.

growth_protocol: To obtain mouse dendritic cells, bone marrows were extracted from at leaset 3 mice ( C57BL/6) for each experiment, and were cultured with murine recombinant GM-CSF (10 ng/ml; BDPharmingen) and IL-4 (10 ng/ml; Peprotech) for 7 days, then harvested and positively selected by the autoMACS® Pro Separator (Miltenyi Biotec) for CD11c+ cells. The purity was confirmed by FACS staining ( 96~98%).

extract_protocol: Total RNA was extracted using miRNeasy Mini kit ( Qiagen) according to the manufacturer's instructions.

tag: genetic background

tag: cell type

value: CD11c+ dendritic cells


title: Dendritic cells rep4 (miRNA)


title: γδ IEL, conventional, rep 2

tag: tissue


title: γδ IEL, germ-free, rep 2

source_name: pooled small intestinal γδ IEL from germ-free mice

value: germ-free


title: Dendritic cells rep2 (miRNA)


title: [E-MTAB-368] Mouse developmental stage E12.5 1

city: Kobe

first: Naoki

last: Irie

state: Hyogo

address: 2-2-3 Minatojima-minami Chuo-ku

institute: RIKEN Center for Developmental Biology

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: MAS5, default settings

source_name: whole embryo except amnion, developmental stage E12.5

label_protocol: One-cycle Target Labeling.

extract_protocol: Total RNA extraction by RNeasy Lipid Tissue Mini Kit.

tag: developmental stage

value: wild type

tag: disease state

value: specific-pathogen free (SPF)

tag: organism part

value: whole embryo except amnion

tag: Sex

value: mixed sex

tag: strain or line


title: γδ IEL, germ-free, rep 1


title: [E-MTAB-368] Mouse developmental stage E10.5 3

source_name: whole embryo except amnion, developmental stage E10.5


title: [E-MTAB-368] Mouse developmental stage E18.5 1

source_name: whole embryo except amnion, developmental stage E18.5


title: [E-MTAB-368] Mouse developmental stage E14.5 1

source_name: whole embryo except amnion, developmental stage E14.5


title: [E-MTAB-368] Mouse developmental stage E10.5 2


title: [E-MTAB-368] Mouse developmental stage E18.5 2


title: [E-MTAB-368] Mouse developmental stage E16.5 1

source_name: whole embryo except amnion, developmental stage E16.5


title: [E-MTAB-368] Mouse developmental stage E9.5 3

source_name: whole embryo except amnion, developmental stage E9.5


title: [E-MTAB-369] Xenopus developmental stage 43 2

organism: Xenopus laevis

source_name: whole embryo, developmental stage 43

value: whole embryo


title: [E-MTAB-368] Mouse developmental stage E14.5 2


title: [E-MTAB-369] Xenopus developmental stage 48 1

source_name: whole embryo, developmental stage 48


title: [E-MTAB-369] Xenopus developmental stage 43 1


title: DAF-12 TAP DAF-12 ab IP#3

city: Pittsburgh

first: Alfred

middle: L

last: Fisher

state: PA

address: 3471 5th Ave., Suite 500

department: Medicine

institute: University of Pittsburgh

description: DAF-12 TAP IP #3

hyb_protocol: Labelled DNA was hybridized to Affymetrix GeneChip Caenorhabditis elegans Tiling 1.0R arrays at 45C overnight. Arrays were washed using a GeneChip Fluidics station from Affymetrix.

scan_protocol: Arrays were scanned using a GeneChip scanner.

data_processing:
CEL files were normalized and analyzed using TAS software from Affymetrix
BED files were generated by TAS software and have comparisons of AA86 vs input and then 3 DAF-12:TAP precipitations vs input. Genomic annotation is based on WS170 (Wormbase)

organism: Caenorhabditis elegans

source_name: anti-DAF-12 chIP DNA

label_protocol: DNA was amplified using the Genomeplex WGA kit from Sigma-Aldrich. The amplified DNA was labelled using the DNA terminal labeling kit from Affymetrix

growth_protocol: Worms were grown in liquid culture using OP50-1 as food

extract_protocol: L2 larvae and adult worms were collected by floatation, briefly frozen, and then sonicated in PBS + 1% formaldehyde. Samples were fixed for a total of 30 minutes before being quenched with 0.125 M glycine.

value: L2 Larval + Young Adult (50:50 mix)

source_name: Input genomic DNA


title: [E-MTAB-369] Xenopus developmental stage 48 2


title: [E-MTAB-368] Mouse developmental stage E16.5 2


title: [E-MTAB-369] Xenopus developmental stage 37-38 2

source_name: whole embryo, developmental stage 37-38


title: [E-MTAB-368] Mouse developmental stage E12.5 2


title: [E-MTAB-368] Mouse developmental stage E9.5 2


title: DAF-12 TAP DAF-12 ab IP#2

description: DAF-12 TAP IP #2


title: [E-MTAB-369] Xenopus developmental stage 37-38 1


title: Dendritic cells rep1 (miRNA)


title: [E-MTAB-368] Mouse developmental stage E10.5 1


title: DAF-12 TAP DAF-12 ab IP#1

description: DAF-12 TAP IP #1


title: AA86 DAF-12 ab IP

description: AA86 (daf-12(0)) control


title: [E-MTAB-369] Xenopus developmental stage 31 2

source_name: whole embryo, developmental stage 31


title: [E-MTAB-369] Xenopus developmental stage 31 1


title: [E-MTAB-369] Xenopus developmental stage 28 2

source_name: whole embryo, developmental stage 28


title: [E-MTAB-369] Xenopus developmental stage 26 2

source_name: whole embryo, developmental stage 26


title: [E-MTAB-369] Xenopus developmental stage 23 2

source_name: whole embryo, developmental stage 23


title: [E-MTAB-369] Xenopus developmental stage 23 1


title: [E-MTAB-368] Mouse developmental stage E8.5 3

source_name: whole embryo except amnion, developmental stage E8.5


title: [E-MTAB-368] Mouse developmental stage E9.5 1


title: [E-MTAB-368] Mouse developmental stage E7.5 3

source_name: whole embryo except amnion, developmental stage E7.5


title: [E-MTAB-369] Xenopus developmental stage 28 1


title: [E-MTAB-369] Xenopus developmental stage 19 2

source_name: whole embryo, developmental stage 19


title: [E-MTAB-368] Mouse developmental stage E7.5 2


title: [E-MTAB-368] Mouse developmental stage E8.5 2


title: [E-MTAB-369] Xenopus developmental stage 21 2

source_name: whole embryo, developmental stage 21


title: HdIV3_13627906

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

institute: INRA

description:
FB-HdIV3_Cy3 vs FB-PBS3_Cy5
Date:2007/10/10

hyb_protocol: Corning Pronto : 500.0 ng at 42 degree_C during 12 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : none, Intraslide norm. : loess, Background norm. : subtract, Software used : rscript --> VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Spodoptera frugiperda

label_protocol: Promega Chipshot labeling

extract_protocol: Qiagen

tag: label

tag: extract

tag: sample

value: fat body


title: [E-MTAB-369] Xenopus developmental stage 17 2

source_name: whole embryo, developmental stage 17


title: HdIV3_13619765

description:
FB-PBS3_Cy3 vs FB-HdIV3_Cy5
Date:2007/10/10


title: [E-MTAB-369] Xenopus developmental stage 17 1


title: [E-MTAB-368] Mouse developmental stage E7.5 1


title: HdIV2_13619764

description:
FB-HdIV2_Cy3 vs FB-PBS2_Cy5
Date:2007/10/10


title: [E-MTAB-369] Xenopus developmental stage 19 1


title: [E-MTAB-369] Xenopus developmental stage 21 1


title: [E-MTAB-369] Xenopus developmental stage 13 2

source_name: whole embryo, developmental stage 13


title: MdBV1_13627907

description:
FB-PBS1_Cy3 vs FB-MdBV1_Cy5
Date:2007/10/10


title: [E-MTAB-369] Xenopus developmental stage 11 1

source_name: whole embryo, developmental stage 11


title: [E-MTAB-368] Mouse developmental stage E8.5 1


title: MdBV1_13627908

description:
FB-MdBV1_Cy3 vs FB-PBS1_Cy5
Date:2007/10/10


title: MdBV2_13627909

description:
FB-PBS2_Cy3 vs FB-MdBV2_Cy5
Date:2007/10/10


title: [E-MTAB-369] Xenopus developmental stage 11 2


title: [E-MTAB-369] Xenopus developmental stage 13 1


title: [E-MTAB-369] Xenopus developmental stage 05 1

source_name: whole embryo, developmental stage 05


title: Dendritic cells LPS biological rep 2 (mRNA)

description: Gene expression data from mouse dendritic cells treated with LPS

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 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:
Affymetrix microarray data were published and analyzed using R statistical environment ( version 2.7) (http://cran.r-project.org/) provided by Bioconductor (http://www.bioconductor.org/). The probesets were selected based on a two-fold difference with the added constraint that at least one sample had to have an expression value of 26 or greater. This protects us from choosing probesets with a large fold change that is based on two small numbers.
The expression values after log2 transformed for each gene were calculated using a robust multi-array average (RMA), which is a modeling strategy that converts the PM probe values into an expression value for each gene.

source_name: Mouse dendritic cells treated with LPS

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

growth_protocol: To obtain mouse dendritic cells, bone marrows were extracted from at leaset 3 mice for each experiment, and were cultured with murine recombinant GM-CSF (10 ng/ml; BDPharmingen) and IL-4 (10 ng/ml; Peprotech) for 7 days, then harvested and positively selected by the autoMACS® Pro Separator (Miltenyi Biotec) for CD11c+ cells. The purity was confirmed by FACS staining ( 96~98%).

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

treatment_protocol: Mouse DCs were  treated with LPS (500 ng/ml) or diluent for 12 hours

tag: treatment

value: LPS


title: [E-MTAB-369] Xenopus developmental stage 05 2


title: Dendritic cells control biological rep 1 (mRNA)

description: Gene expression data from mouse dendritic cells treated with control diluent

source_name: Mouse dendritic cells treated with diluent

value: control


title: Dendritic cells LPS biological rep 1 (mRNA)


title: [E-MTAB-369] Xenopus developmental stage 09 1

source_name: whole embryo, developmental stage 09


title: [E-MTAB-369] Xenopus developmental stage 09 2


title: [E-MTAB-369] Xenopus developmental stage 02 1

source_name: whole embryo, developmental stage 02


title: [E-MTAB-366] Chicken developmental stage HH38 2

organism: Gallus gallus

source_name: whole embryo except yolk and amnion, developmental stage HH38

label_protocol: 3' IVT Labeling

growth_protocol: Parent chickens grown by Post Harvest  Free Corn. Incubation at 37.5 degrees celsius.

tag: biosource provider

value: local farmer (Shiroyama Keien)  in Japan

value: whole embryo except yolk and amnion

value: Nera


title: [E-MTAB-369] Xenopus developmental stage 02 2

tag: genotype


title: [E-MTAB-366] Chicken developmental stage HH38 1


title: MdBV3_13627911

description:
FB-PBS3_Cy3 vs FB-MdBV3_Cy5
Date:2007/10/10


title: [E-MTAB-366] Chicken developmental stage HH34 2

source_name: whole embryo except yolk and amnion, developmental stage HH34


title: HdIV1_13619762

description:
FB-HdIV1_Cy3 vs FB-PBS1_Cy5
Date:2007/10/10


title: MdBV2_13627910

description:
FB-MdBV2_Cy3 vs FB-PBS2_Cy5
Date:2007/10/10


title: MdBV3_13619760

description:
FB-MdBV3_Cy3 vs FB-PBS3_Cy5
Date:2007/10/10


title: Dendritic cells control biological rep 2 (mRNA)


title: HdIV1_13619761

description:
FB-PBS1_Cy3 vs FB-HdIV1_Cy5
Date:2007/10/10


title: [E-MTAB-366] Chicken developmental stage HH34 1


title: [E-MTAB-366] Chicken developmental stage HH32 1

source_name: whole embryo except yolk and amnion, developmental stage HH32


title: [E-MTAB-366] Chicken developmental stage HH27 2

source_name: whole embryo except yolk and amnion, developmental stage HH27


title: Normal human mammary epithelial cells genotype 48 (H3K9me2)

city: Tucson

first: Lukas

last: Vrba

state: AZ

address: 1515 N Campbell Ave

department: Arizona Cancer Center

institute: University of Arizona

description: Biological replicate 2 of 3. Human mammary epithelial cells.

hyb_protocol: Combined Cy3 and Cy5 labeled samples were vaccum concentrated to volume of 91.5 µl.  12.5 µl of human Cot-1 DNA (1µg/µl, Invitrogen Cat. No. 15279-011), 26 µl of Agilent blocking agent (10x) and 130 µl of Agilent hybridization buffer (2x) were added.  Samples were heated for 3 min at 95 oC, transferred to 37 oC, incubated for 30 min, and then used for microarray hybridization for 28h at 65 oC.  After hybridization, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 for 5 min at room temperature, then in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 2 for 5 min at 37 oC, washed in acetronitrile for 10 s at room temperature and finally in stabilization and drying solution for 30 s at room temperature.

scan_protocol: Slides were scanned using an Axon GenePix 4000B microarray scanner (Axon Instruments, Inc., Foster City, CA, USA) and GenePix 6.0 software at 5 µm resolution and PMT settings 750 (635nm) and 600 (532nm)

data_processing: Output from GenePix (*.gpr files) were imported to R using the limma package.  Individual channels were first spatially normalized within arrays using ma2D function from the package marray and then loess normalized between arrays using the function normalize.loess from package affy.  The RG object was transformed to an MA object and M values were again loess normalized between arrays.

source_name: Human mammary epithelial cells

label_protocol: DNA amplification was based on random prime synthesis using the BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA). The DNA sample or equivalent amount of input in a total volume of 21 ul was mixed with 20 ul of 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min. 5 ul of 10x dUTP Nucleotide Mix, 3 ul of 1 mM dTTP and 1 ul of Exo-Klenow Fragment, were added and incubated at 37 C for 20 h. Amplified DNA was purified using a QIAquick PCR purification kit (Qiagen, Valencia, CA) and quantified on a ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). The typical yield was 4-5 ug of amplified DNA per 50 ul reaction.  Equal amounts (2 ug) of amplified immunoprecipitated and input DNA were labeled using the BioPrime DNA Labeling System (Invitrogen) with Cy3 or Cy5 dyes respectively. DNA in a volume of 42 ul was mixed with 40 ul 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min.  10 ul of 10x dUTP Nucleotide Mix, 4 ul of 1 mM dTTP, 2 ul of Cy3- or Cy5-dUTP (1mM) (GE healthcare, Piscataway, NJ, USA) and 2 ul of Exo-Klenow Fragment were added and the mixture was incubated for 20 h at 37 C.  Labeled targets were purified using the QIAquick PCR purification kit (Qiagen).  The efficiency of labeling was determined using ND-1000 spectrophotometer (Nanodrop Technologies).  The typical yield was 200 - 300 pmol of dye incorporated in 7 - 8 ug of DNA per sample.

growth_protocol: HMEC were maintained in M87A medium supplemented with oxytocin and cholera toxin at 0.5 ng/ml, HMF were grown in DMEM/F12 with 10% FBS.

extract_protocol:
Wash ~2x107 cells in a tissue culture dishes with 10 ml of HBSS (Hanks Balanced Salt Solution) with 2.5mM EDTA. Add 15 ml of HBSS with 2.5mM EDTA, with 400 ul of 37% formaldehyde added (final conc 1%).  Incubate at 37 C for 10 minutes. Aspirate off formaldehyde solution and add 5 ml of ice cold HBSS, 2.5mM EDTA with protease inhibitors (PIs) at a final concentration of 1 mM PMSF, 1 ug/ml Pepstatin A, 1 ug/ml Aprotinin. Gently detach cells with a cell scraper and transfer the cells to a conical tube.  Wash remaining cells out of flask with 5 ml of HBSS with PIs. Spin cells down ~700 g for 5 min at 4 C. After spin, aspirate HBSS then add PIPES buffer (5 mM PIPES buffer pH 8.0, 85mM KCl, 0.5% NP40) with protease inhibitors 400 ul/sample, transfer sample to microfuge tube, then incubate on ice for 10 min. After incubation, pellet cells at 700 g for 5 min at 4 C. Remove PIPES buffer and add SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) with protease inhibitors. Again 10 min on ice. Store at -80 C. Thaw samples on ice. Sonicate samples 6 x for 10 seconds on setting 7-8 watts until the majority of chromatin is between 500-1000 bp in length when checked on 1% agarose gel. After sonication spin samples at max speed at 4 C for 10 min to remove any cellular debris.  Dilute supernatant fraction 10 fold with ChIPs dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl) with PIs.  Set aside 10 % of sample into a fresh microfuge tube - Input sample.
immunoprecipitation protocol: Pre-clear the diluted sample by adding 120 ul of protein-A sepharose slurry (Pharmacia).  Rotate for 1hr at 4 C. Spin down samples at 400 g at 4 C for 2 min to pellet beads. Divide samples equally into microfuge tubes for each Ab sample and add Abs. Rotate tubes overnight at 4 C. Next day add 90 ul of Pro-A sepharose slurry to each Ab tube. Rotate at 4 C for 1hr.  Spin samples in picofuge for 10 s, discard all but 400 ul of supernatant, resuspend sepahrose beads in remaining volume and transfer to Handee spin cup columns (Pierce), spin in picofuge for 10 s, discard flow through. Wash beads for 5 min at 4 C with 400 ul each of the following buffers:  low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA with 250 ul of elution buffer (1% SDS, 0.1M NaHCO3).  Mix well and rotate for 15 min at room temp.  Spin down, save flow through to a new microfuge tube. Repeat elution and combine eluates.  Total volume ~ 500 ul. Bring the Input sample volume up to 500 ul using the elution buffer. To reverse the cross-links add 40 ul of 5M NaCl to eluate or diluted input and incubate at 65 C for 4 hr. After incubation add 100 ul of 0.1M EDTA, 40 ul of 1M Tris-Cl pH 7.5, and 2 ul of 20 mg/ml proteinase K to each sample and incubate at 45 C for 1 hr. Purify samples using QIAquick PCR purification kit (Qiagen, Valencia, CA): Transfer samples to 10 ml tubes. Add 5 volumes of PB buffer, mix well, apply to Qiagen columns under vacuum, wash 2x with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

tag: cell line

value: HMEC 48RT

value: mammary gland

tag: sample type

value: Immunoprecipitated DNA

tag: antibody

value: anti-histone H3 dimethylated at lysine 9

tag: vendor

value: Millipore

tag: catalog#

value: Input DNA


title: Normal human mammary fibroblast cells genotype 184 (H3K4me3)

description: Biological replicate 1 of 3. Human mammary fibroblast cells.

source_name: Human mammary fibroblast cells

value: HMF 184

tag: tissue

value: anti-histone H3 trimethylated at lysine 4

value: Upstate


title: [E-MTAB-366] Chicken developmental stage HH32 2

tag: developmental stage

value: wild type

value: mixed sex


title: Normal human mammary epithelial cells genotype 240 (H3K9me2)

description: Biological replicate 3 of 3. Human mammary epithelial cells.

value: HMEC 240LB


title: HdIV2_13619763

description:
FB-PBS2_Cy3 vs FB-HdIV2_Cy5
Date:2007/10/10

value: fat body


title: Normal human mammary epithelial cells genotype 48 (H3K4me3)


title: Normal human mammary epithelial cells genotype 184 (H3K9me2)

description: Biological replicate 1 of 3. Human mammary epithelial cells.

value: HMEC 184D


title: Normal human mammary fibroblast cells genotype 48 (H3K9me2)

description: Biological replicate 2 of 3. Human mammary fibroblast cells.

value: HMF 48


title: WT_SK1_t=11hr_B

city: Santa Cruz

first: Lily

last: Shiue

address: 1156 High Street

department: MCD Biology

institute: UCSC

description: Analysis used Reference Pool WT SK1 RNA as control for comparison to the mer1D_SK1 samples taken at 0h, 0.5h, 2h, 5h, 7h, 9h, 11h during the meiotic time course.

hyb_protocol: Two color hybridization mixes were applied to the microarray under a LifterSlip and incubated in aluminum hybridization chambers overnight in a 63 degree water bath.  Hybridized slides were washed in SSC/SDS containing buffers.

scan_protocol: Arrays were scanned using an Axon 4000B Data was quantitated using GenePix Pro 6.1 (Axon)

data_processing: Log2 ratios were calculated from background subtracted median intensities and were LOESS normalized and summarized using Bioconductor

organism: Saccharomyces cerevisiae

label_protocol: Amino-allyl dUTP labeled first strand cDNA was reverse transcribed from 10ug of total RNA primed with oligo dT and random primers.  cDNA was then coupled to Cy3 or Cy5 esters (GE Healthcare).  Dye swapped hybridizations were performed for each sample pair.

growth_protocol: To prepare cells for synchronous meiosis, cells are streaked from frozen stocks to YP-glycerol (3%) plates, and then single colonies from glycerol are streaked to YPD plates. After two days on YPD, a single colony is inoculated into 5mL of YPD, and 30 hours later, 50mL of YPA (1% potassium acetate, 1% yeast extract, 2% peptone) is inoculated to OD600 = 0.25 and shaken for 14 hours. After growth in YPA, cells are washed with water and suspended in SPM (1% potassium acetate, 0.02% raffinose), defining time zero of meiosis.

extract_protocol: Meitoic RNA is exracted according to protocol described in Rio DC, Ares MJr, Hannon GJ, Nilsen TW. 2010. RNA: A laboratory manual. Cold Spring Harbor Laboratory Press.

treatment_protocol: Aliquots are taken at 0h, 30min, 2h, 5h, 7h, 9h, and 11h for RNA preparation, spun down at room temperature, flash frozen in liquid nitrogen and stored at -80°C.

tag: strain

tag: meiotic time point

source_name: REFERENCE POOL

tag: reference

value: Reference pool WT RNA comprised of 50% time zero RNA plus 10% each of time 2 hours, 5, hours, 7 hours, 9 hours and 11 hours


title: Normal human mammary fibroblast cells genotype 240 (H3K4me3)

description: Biological replicate 3 of 3. Human mammary fibroblast cells.

value: HMF 240L


title: [E-MTAB-366] Chicken developmental stage HH24 2

source_name: whole embryo except yolk and amnion, developmental stage HH24

value: local farmer (Shiroyama Keien)  in Japan

tag: organism part

value: whole embryo except yolk and amnion

tag: Sex

tag: strain or line

value: Nera


title: Normal human mammary fibroblast cells genotype 240 (H3K27me3)

value: mammary gland

value: Immunoprecipitated DNA

value: anti-histone H3 trimethylated at lysine 27

value: Millipor


title: Normal human mammary fibroblast cells genotype 184 (H3K9me2)

value: HMF 184

value: anti-histone H3 dimethylated at lysine 9

value: Millipore

value: Input DNA


title: [E-MTAB-366] Chicken developmental stage HH27 1

value: wild type

value: mixed sex


title: Normal human mammary epithelial cells genotype 240 (H3K4me3)

value: HMEC 240LB

value: anti-histone H3 trimethylated at lysine 4

value: Upstate


title: Normal human mammary fibroblast cells genotype 240 (H3K9me2)

value: HMF 240L


title: Normal human mammary fibroblast cells genotype 48 (H3K4me3)

value: HMF 48


title: Normal human mammary fibroblast cells genotype 48 (H3K27me3)


title: Normal human mammary fibroblast cells genotype 184 (H3K27me3)


title: Normal human mammary epithelial cells genotype 184 (H3K4me3)

value: HMEC 184D


title: Normal human mammary epithelial cells genotype 240 (H3K27me3)


title: [E-MTAB-366] Chicken developmental stage HH24 1

value: local farmer (Shiroyama Keien)  in Japan

value: whole embryo except yolk and amnion

value: Nera


title: WT_SK1_t=7hr_B

value: Reference pool WT RNA comprised of 50% time zero RNA plus 10% each of time 2 hours, 5, hours, 7 hours, 9 hours and 11 hours


title: [E-MTAB-366] Chicken developmental stage HH19 2

source_name: whole embryo except yolk and amnion, developmental stage HH19


title: WT_SK1_t=9hr_B


title: WT_SK1_t=5hr_B


title: [E-MTAB-366] Chicken developmental stage HH16 2

source_name: whole embryo except yolk and amnion, developmental stage HH16


title: [E-MTAB-369] Xenopus developmental stage 26 1

source_name: whole embryo, developmental stage 26

value: whole embryo


title: [E-MTAB-366] Chicken developmental stage HH14 1

source_name: whole embryo except yolk and amnion, developmental stage HH14


title: [E-MTAB-366] Chicken developmental stage HH16 1


title: WT_SK1_t=2hr_B


title: WT_SK1_t=0.5hr_B


title: [E-MTAB-366] Chicken developmental stage HH19 1


title: [E-MTAB-366] Chicken developmental stage HH14 2


title: WT_SK1_t=0hr_B


title: WT_SK1_t=9hr_A


title: WT_SK1_t=11hr_A


title: WT_SK1_t=7hr_A


title: [E-MTAB-366] Chicken developmental stage HH11 1

source_name: whole embryo except yolk and amnion, developmental stage HH11


title: Normal human mammary epithelial cells genotype 48 (H3K27me3)

value: HMEC 48RT

value: mammary gland

value: Immunoprecipitated DNA

value: anti-histone H3 trimethylated at lysine 27

value: Millipor


title: Normal human mammary fibroblast cells genotype 184 (H3Acet)

value: HMF 184

value: anti-acetylated histone H3

value: Input DNA


title: Normal human mammary epithelial cells genotype 184 (H3K27me3)


title: Normal human mammary fibroblast cells genotype 240 (H3Acet)


title: Normal human mammary epithelial cells genotype 240 (H3Acet)

value: HMEC 240LB


title: [E-MTAB-366] Chicken developmental stage HH11 2

value: wild type

value: mixed sex


title: Normal human mammary epithelial cells genotype 48 (H3Acet)


title: Normal human mammary epithelial cells genotype 184 (H3Acet)

value: HMEC 184D


title: WT_SK1_t=5hr_A


title: [E-MTAB-366] Chicken developmental stage HH9 2

source_name: whole embryo except yolk and amnion, developmental stage HH9

value: local farmer (Shiroyama Keien)  in Japan


title: WT_SK1_t=2hr_A


title: [E-MTAB-366] Chicken developmental stage HH9 1

value: whole embryo except yolk and amnion


title: WT_SK1_t=0.5hr_A


title: WT_SK1_t=0hr_A


title: [E-MTAB-366] Chicken developmental stage HH8 2

source_name: whole embryo except yolk and amnion, developmental stage HH8

value: Nera


title: Normal human mammary fibroblast cells genotype 48 (MeDIP)

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen). 5 μg of RNase treated DNA was dried under vacuum and resuspended with 50 μl SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and 450 μl of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl).  Vortex for ~20 minutes to fully resuspend the DNA. Sonicate the samples 5x for 10 seconds (5 times total) at 8 watts.  Make sure that most of the DNA is between 300-600 bp long.  Set aside 50 μl of sample in a new microfuge tube - Input DNA.
immunoprecipitation protocol: Denature both the sample and input DNA in a heatblock set at 100 °C for 10 minutes. Cool down on ice.  When cold, add 2 μl of anti-Methylcytosine (5MeC) antibody to sample DNA. Rotate tubes overnight at 4°C. Next day add 90 ul of Pro-A sepharose slurry (Pharmacia) to each tube. Rotate at 4 C for 1hr.  Transfer samples and beads to a Handee spin cup column with paper filter (Pierce).  Spin samples for ~10 seconds in a picofuge to remove the buffer.  Wash beads for 5 min at 4 C with 400 ul each of the following buffers:  low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA from the beads by adding 250 ul of pre-warmed (60°C) QG buffer (Qiagen Quick Spin Kit). Incubate the spin column with the QG buffer in a heat block set at 100oC for 5 min. Gently vortex the samples for 5 min at RT.  Spin the sample for ~10 seconds in a picofuge and transfer the eluate to a clean 1.5 ml microfuge tube.  Repeat the elution step. Add 450 μl of prewarmed QG buffer to the input DNA, incubate for 5 minutes at 100 °C, shake for 5 min. at RT, and spin in a picofuge. Add 150 μl of isopropanol to 500 μl of eluate or diluted input. Put the samples in a QIAquick column and spin for 1 minute at maximum speed. Wash with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

value: HMF 48

value: anti-Methylcytosine


title: ume6D_BY4741_veg

description: Analysis used vegetative WT_BY4741 RNA as control for comparison to the ume6D_BY4741 RNA sample.

growth_protocol: cells were grown to OD600=0.5 in YPD

extract_protocol: Vegetative RNA is exracted according to protocol described in Rio DC, Ares MJr, Hannon GJ, Nilsen TW. 2010. RNA: A laboratory manual. Cold Spring Harbor Laboratory Press.

treatment_protocol: Aliquots are taken for RNA preparation, spun down at room temperature, flash frozen in liquid nitrogen and stored at -80°C.

tag: genotype/variation

value: ume6D mutant

tag: growth protocol

value: vegetatively grown