title: Mes-4_N2_rep2

description: ChIP-chip of Mes-4 in N2 EEMB; channel ch1 is ChIP DNA; Antibody information: SDQ0791-Mes-4;target name: Mes-4;host: Rabbit;antigen: GTASKKSEISPSKPSTSSASSTSFVQQASWPISQNKKNLKKNSNQPVADTGSTLSTSTELNFHEKPQELLSPVSSRSRAASSSTPRAQKSKSRRDDVESE ;clonal: polyclonal;purified: Protein A;company: SDI;catalog: SDQ0791;short description: An affinity pruified rabbit polyclonal antibody to MES-4 obtained from SDI (MES4-Q0791); channel ch2 is Input DNA

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

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

data_processing: The log2-ratio ratio of intensity from IP/Input channels for H3K36me3 and MES-4 was centered so the log2-ratio data had genome-wide zero mean. The H3K36me3 and MES-4 log2-ratio data were scaled so the log2-ratio data  had standard deviation one genome-wide. H3K27me3 is a broad histone mark covering more than half the genome and typically absent from expressed genes. H3K27me3 log2-ratio data was standardized so probes mapping to the 50% top expressed genes had mean zero and standard deviation one. The normalization was performed using cutom scripts. See the associated reference for further details.

source_name: Mes-4 ChIP DNA for N2 EEMB

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

growth_protocol: Worm_embryo_growth_and_harvest_vSS3. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85 % formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5  and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl).  Pellets were frozen at -80C

extract_protocol:
Worm_embryo_extraction_vSS2. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 9 times on ice at the following settings: 30 sec; power output 3; 70% duty cycle. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 um filter units (cat. UFC30HV0S) at 13,000 rpm, 4ºC for 1 minute to remove lipids.  Protein concentration was determined, and extracts were aliquoted and stored at -80ºC.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn:  http://www.flychip.org.uk/protocols/chip/lm_pcr.php.
Worm_chromatin_immunoprecipitation_vSS1. Protein A or G-coupled Dynal magnetic beads from 20 ul of slurry were washed 3 times in 1ml of 5mg/ml IgG-Free BSA in PBS (wash buffer). Beads were resuspended in 100ml of the wash buffer and rotated with 5mg of the appropriate antibody overnight at 4°C. Beads were further washed 2 times in the wash buffer and resuspended in 30ml of the wash buffer. Before beginning IP, 5% of starting material of protein (3-6mg) was saved as input at -20°C. The antibody-conjugated Dynal beads were mixed with 3-6mg of protein and nutated for 2hrs at 4°C. After washing the beads, captured proteins were eluted by incubating beads in 300 ml of TE with 1% SDS and 250mM NaCl for 2 times 15 minutes at 65°C. Samples were treated with proteinase K and reverse-crosslinked at 65°C overnight. DNA was purified using Zymo DNA purification column and eluted in in 43ml dH2O. RNA was digest for 1 hour at 37°C with RNase One (Promega).

value: Early Embryo

tag: chip antibody

tag: Sex

value: population predominantly Hermaphrodites perhaps with some Males

source_name: Input DNA for N2 EEMB

value: none, Input DNA


title: liver 1.0% quercetin diet rep3

status: Public on May 30 2012

type: RNA

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

country: Japan

institute: Food Research Institute, National Agriculture and Food Research Organization

description: Gene expression data from liver after 14 day feeding of 1.0% quercetin diet

hyb_protocol: Fifteen microgram aliquots of fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.3 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.3) using Affymetrix default analysis settings and global scaling as normalization method..

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: liver, fed 1% quercetin diet for 14 days

label_protocol: Double-stranded cDNA was synthesized from the total RNA of each mouse using the One-Cycle cDNA Synthesis Kit (Affymetrix Japan KK, Tokyo, Japan) with a T7-(dT)24 primer. Biotin-labeled cRNA was then synthesized using an IVT Labeling Kit (Affymetrix). The biotin-labeled cRNA was further purified and fragmented using the Sample Cleanup Module (Affymetrix).

growth_protocol: Six-week-old male BALB/c mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed under conditions of 24± 1°C, 55 ± 5% humidity, and 12 hour light/dark photocycles (dark period from 0800 to 2000) with free access to water and a standard nonpurified diet (NMF, Oriental Yeast Co., Tokyo, Japan) for a week prior to the experiment.

extract_protocol: The mice were killed under anesthesia with pentobarbital, and blood and liver tissue were immediately collected. Total RNA was extracted from liver tissues using an RNeasy Midi Kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: The mice were then fed for 2 weeks with AIN93G (control group) or AIN93G containing 0.1%, 0.5% or 1% quercetin.

tag: gender

value: male

tag: strain

value: BALB/c

tag: tissue

value: liver

tag: diet

value: AIN93G with 1.0% quercetin diet for 14 days


title: liver 1.0% quercetin diet rep4


title: non STZ liver control diet rep5

description: Gene expression data from liver after 14 day feeding of control AIN93G diet

source_name: liver, fed control AIN93G diet for 14 days

treatment_protocol: The mice were then intraperitoneally injected with STZ (Wako Pure Chemical Industries, Osaka, Japan, 185 mg/kg in 0.05M citrate buffer, pH 4.5).  Mice (n=6) in the untreated control group did not receive any treatment.  Tail vein blood was sampled weekly and the blood glucose levels of the samples were immediately measured using a blood glucose test meter (Glucocard, Arkray, Kyoto, Japan).  After 1 week, 18 mice showing non-fasting blood glucose levels of 330-590 mg/dL were divided into 3 groups: one group was fed with AIN93G only (control group), the others with an AIN93G diet containing 0.1% or 0.5% phloridzin (Funakoshi, Tokyo, Japan) for 2 weeks. All mice had access to food and water ad libitum during the experimental period.

value: AIN93G diet for 14 days


title: liver 1.0% quercetin diet rep1


title: liver STZ treated diabetic rep1

description: Gene expression data from STZ-treated mouse liver after 14 day feeding of control AIN93G diet

source_name: liver, STZ-treated fed AIN93G diet for 14 days

value: STZ-treated fed AIN93G diet for 14 days


title: H3K27me3_mes-4 RNAi_rep1

type: genomic

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

country: USA

institute: UC Santa Cruz

description: ChIP-chip of H3K27me3 in mes-4 (RNAi) EEMB; channel ch1 is ChIP DNA; Antibody information: HK00013 H3K27me3:1E7;target name: H3K27me3;host: Mouse;antigen:KQLATKAAR(me3-K)SAPATGGVKC ;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: 1E7;short description: A protein G purified mouse monoclonal antibody to H3K27me3 (clone 1E7) obtained from Hiroshi Kimura.; channel ch2 is Input DNA

data_processing: The log2-ratio ratio of intensity from IP/Input channels for H3K36me3 and MES-4 was centered so the log2-ratio data for the X chromosome have the same mean as the respective normalized wt data on the X chromosome (see wt data in GSE38180). The H3K36me3 and MES-4 log2-ratio data were scaled so the log2-ratio data on the X chromosome have the same standard deviation as the respective normalized wt log2-ratio data on the X chromosome. H3K27me3 is a broad histone mark covering more than half the genome and typically absent from expressed genes. H3K27me3 log2-ratio data was standardized so probes mapping to the 50% top expressed genes had mean zero and standard deviation one. The normalization was performed using cutom scripts. See the associated reference for further details.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: H3K27me3 ChIP DNA for mes-4 (RNAi) EEMB

growth_protocol: Worm_embryo_growth_and_harvest_vSS9. Embryos were prepared by bleaching from  N2 adults grown in standard S-basal media liquid culture with RNAi bacteria at 24 C. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5  and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol: Worm_embryo_extraction_vSS5. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated in ice water bath using a Diagenode Bioruptor at the highest setting for 14 pulses 30 seconds long with 1 minute pauses. Cell debris was removed by centrifuging at 13,000 rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 um filter units (cat. UFC30HV0S) at 13,000 rpm, 4°C for 1 minute to remove lipids. Protein concentration was determined, and extracts were aliquoted and stored at -80ºC.   Worm_chromatin_immunoprecipitation_vSS4. 0.3-3 mg extract + 1% sarkosyl was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl). Antibody was added to each IP sample and incubated overnight at 4ºC. Immune complexes were incubated (2 hrs at 4ºC) with 50 ul of IgG dynabeads (Dyna), and washed 5 minutes with 1.5 mL of each of the following solutions: ChIP Buffer, ChIP Buffer + 1 M NaCl, ChIP Buffer + 500 mM NaCl, TEL Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and 2X TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Samples were eluted twice with 150 uL elution buffer for 15 minutes at 65ºC. Samples were treated with RNAse for 30 minutes at 37ºC. Samples were treated with proteinase K at 55ºC for 1-2 hrs then transfer to 65ºC overnight to reverse crosslinks. DNA was cleaned up using Zymo kit.   Worm_LM-PCR_Amplification_for_ChIP-chip_vSS2. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn: http://www.flychip.org.uk/protocols/chip/lm_pcr.php.  For more details see www.modencode.org

tag: developmental stage

tag: genotype

value: mes-4 (RNAi)

source_name: Input DNA for mes-4 (RNAi) EEMB


title: liver 0.5% quercetin diet rep3

description: Gene expression data from liver after 14 day feeding of 0.5% quercetin diet

source_name: liver, fed 0.5% quercetin diet for 14 days

value: AIN93G with 0.5% quercetin diet for 14 days


title: liver 0.5% quercetin diet rep4


title: liver 1.0% quercetin diet rep6


title: H3K27me3_mes-4 RNAi_rep2


title: liver 0.5% quercetin diet rep6


title: MES-4

description: ChIP-chip of Mes-4 in mes-4 (RNAi) EEMB; channel ch1 is ChIP DNA; Antibody information: SDQ0791-Mes-4;target name: Mes-4;host: Rabbit;antigen: GTASKKSEISPSKPSTSSASSTSFVQQASWPISQNKKNLKKNSNQPVADTGSTLSTSTELNFHEKPQELLSPVSSRSRAASSSTPRAQKSKSRRDDVESE ;clonal: polyclonal;purified: Protein A;company: SDI;catalog: SDQ0791;short description: An affinity pruified rabbit polyclonal antibody to MES-4 obtained from SDI (MES4-Q0791); channel ch2 is Input DNA

source_name: Mes-4 ChIP DNA for mes-4 (RNAi)  EEMB


title: T15-2_erlotinib_12h rep3

city: NEW YORK

first: Zhenfeng

last: Zhang

state: NY

address: 1130 ST.NICHOLAS AVENUE R1001

department: Cancer center

institute: Columbia University Medical Center

description:
SAMPLE 18
Triplicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analyzed by Illumina BeadStudio Gene Expression Module v3.2.

organism: Homo sapiens

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

growth_protocol: Cells were grown in RPMI-1640 supplemented with 10% FBS and 1X Antibiotic/Antimycotic (Invitrogen).

extract_protocol: Total RNA was extracted with PureLink Micro-to-Midi Total RNA Purification Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with RAN gel electrophoresis.

treatment_protocol: Cells were starved overnight and then treated with 1uM erlotinib or DMSO as a control for 12 hours.

tag: cell line

value: erlotinib-resistant HCC827-originated sublines T15-2

tag: cell type

value: non-small cell lung cancers

tag: treated with

value: 1uM erlotinib for 12 hr


title: H3K36me3_N2_rep1

description: ChIP-chip of H3K36me3 in N2 EEMB; channel ch1 is ChIP DNA; Antibody information: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura.; channel ch2 is Input DNA

source_name: H3K36me3 ChIP DNA for N2 EEMB


title: mes-2 v wt 1

description: Biological replicate 1 of 4.  Mutant and wild type dissected germ lines grown at 20 deg.

hyb_protocol: Hybridization buffer (Genisphere 2X fromamide hyb buffer) and KREAblock were added, and samples were applied to microarrays enclosed in Die-Tech hyb chambers. After hybridization, slides were washed sequential with 2X SSC/0.2% SDS, 2X SSC and 0.2X SSC.

scan_protocol: Scanned on an GenePix 4000B scanner.

data_processing: Signal from each channel was background subtracted and log2 of test (mt) sample signal over reference (wt) sample signal was obtained. log 2 ratios were print-tip LOWESS normalized, then global scale normalized using median absolut deviation. Bioconductor package marray was used for all processing.

molecule: polyA RNA

source_name: mes-2 mutant dissected germ lines

label_protocol: aRNA was labeled using Kreatech ULS-Cy 3/5 aRNA Labeling Kit (Open Biosystems) and then fragmented using  Ambion Fragmentation Reagents

growth_protocol: Worms were grown to the adult stage. For wild type, mes-2, and mes-4, germ lines were dissected from adults containing no more than a few fertilized embryos. For mes-2; mes-4, well proliferated germ lines with oocytes were collected.

extract_protocol: Total RNA was extracted using Trizol reagent, then amplified poly-A RNA was made using the MessageAmp II aRNA Amplification Kit (Ambion)

tag: Stage

value: adult germ lines

tag: temperature

value: 20 degrees

source_name: wild type dissected germ lines


title: V6.5 ESC Utx KO

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data of the indicated cell line

hyb_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.

data_processing: The data were analyzed with Affy Expression Console software, using RMA method. Probes were further filtered to include only probes that have at least one call > 6 (in log2-scale)

label: Biotin

source_name: V6.5 ESC Utx -/Y

label_protocol: 250 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: N2B27 2i/LIF mouse ESC media

extract_protocol: mRNA was extracted byTRIZOL reagent (invitogene) according to manufacturer's instructions

treatment_protocol: Cells were washed with PBS and then harvested by trypsinization for RNA extraction

value: Mouse Embryonic Stem Cell (ESC)

tag: genotype/variation

value: UTX-/Y (KO)


title: liver 0.5% quercetin diet rep1


title: Mes-4_N2_rep1

growth_protocol: Worm_embryo_growth_and_harvest_vSS2. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl).  Pellets were frozen at –80C.

value: Early Embryo

value: population predominantly Hermaphrodites perhaps with some Males

growth_protocol: Worm_embryo_growth_and_harvest_vSS2. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl).  Pellets were frozen at –80°C.


title: liver 0.5% quercetin diet rep2

value: male


title: liver 0.5% quercetin diet rep5

value: BALB/c


title: liver 0.1% quercetin diet rep6

description: Gene expression data from liver after 14 day feeding of 0.1% quercetin diet

source_name: liver, fed 0.1% quercetin diet for 14 days

value: liver

value: AIN93G with 0.1% quercetin diet for 14 days


title: H3K36me3_N2_rep2

growth_protocol: Worm_embryo_growth_and_harvest_vSS4. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100 mM Tris-HCl pH 7.5 and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl).  Pellets were frozen at -80C.

value: none, Input DNA


title: H3K36me3_N2_rep3


title: liver 0.1% quercetin diet rep2


title: liver 0.1% quercetin diet rep4


title: H3K27me3_N2_rep2

description: ChIP-chip of H3K27me3 in N2 EEMB; channel ch1 is ChIP DNA; Antibody information: HK00013 H3K27me3:1E7;target name: H3K27me3;host: Mouse;antigen:KQLATKAAR(me3-K)SAPATGGVKC ;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: 1E7;short description: A protein G purified mouse monoclonal antibody to H3K27me3 (clone 1E7) obtained from Hiroshi Kimura.; channel ch2 is Input DNA

source_name: H3K27me3 ChIP DNA for N2 EEMB


title: T15-2_DMSO_12h rep1

description:
SAMPLE 13
Triplicate 1

value: DMSO for 12 hr


title: T15-2_erlotinib_12h rep2

description:
SAMPLE 17
Triplicate 2


title: ER3_erlotinib_12h rep2

description:
SAMPLE 11
Triplicate 2

value: erlotinib-resistant HCC827-originated sublines ER3


title: liver 0.1% quercetin diet rep3


title: liver control diet rep6

value: AIN93G diet for 14 days


title: ER3_DMSO_12h rep3

description:
SAMPLE 9
Triplicate 3


title: T15-2_erlotinib_12h rep1

description:
SAMPLE 16
Triplicate 1

value: erlotinib-resistant HCC827-originated sublines T15-2


title: T15-2_DMSO_12h rep3

description:
SAMPLE 15
Triplicate 3

value: non-small cell lung cancers


title: liver 0.1% quercetin diet rep1


title: liver 0.1% quercetin diet rep5


title: liver control diet rep5


title: ER3_erlotinib_12h rep3

description:
SAMPLE 12
Triplicate 3

value: 1uM erlotinib for 12 hr


title: ER3_erlotinib_12h rep1

description:
SAMPLE 10
Triplicate 1


title: T15-2_DMSO_12h rep2

description:
SAMPLE 14
Triplicate 2


title: H3K27me3_N2_rep1


title: liver control diet rep4


title: H3K36me3_mes-4 RNAi_rep2

description: ChIP-chip of H3K36me3 in mes-4 (RNAi) EEMB; channel ch1 is ChIP DNA; Antibody information: HK00001 H3K36me3:13C9;target name: H3K36me3;host: Mouse;antigen: KSAPATGGV(me3-K)KPHRYRPGTC;clonal: Monoclonal;purified: Protein A/G;company: Other;catalog: HK00001;short description: A protein G purified mouse monoclonal antibody to H3K36me3 (clone 13C9) obtained from Hiroshi Kimura.; channel ch2 is Input DNA

source_name: H3K36me3 ChIP DNA for mes-4 (RNAi) EEMB

value: mes-4 (RNAi)


title: ER3_DMSO_12h rep2

description:
SAMPLE 8
Triplicate 2


title: liver control diet rep2


title: liver control diet rep3


title: HCC827_erlotinib_12h rep3

description:
SAMPLE 6
Triplicate 3

value: parental HCC827


title: ER3_DMSO_12h rep1

description:
SAMPLE 7
Triplicate 1


title: HCC827_erlotinib_12h rep2

description:
SAMPLE 5
Triplicate 2


title: liver control diet rep1


title: HCC827_erlotinib_12h rep1

description:
SAMPLE 4
Triplicate 1


title: mES GFP KD hairpin1 rep1

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (Mouse 430 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the  manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console.

data_processing: The data were analyzed with the mas5 function of Bioconductor in R using default settings.

source_name: Embryonic stem cells

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: Mouse embryonic stem cells were grown in standard ESC media for 3 days and then split.  The following day cells were infected with virus and grown in standard ESC media with 8ug/ml polybrene.  The following day media was changed to standard ESC media with 4ug/ml puromycin for 4 days.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up with a Qiagen RNeasy kit and quality control was performed with an Agilent 2100 Bioanalyzer.

treatment_protocol: Mouse embryonic stem cells were rinsed twice with 1x PBS and placed on ice in the Trizol solution (GibcoBRL).

value: V6.5 embryonic stem cells

tag: knockdown

value: GFP


title: HeLa 360A 48 hrs Replicate 3

city: Konstanz

first: Joerg

last: Hartig

address: Universitätsstr. 10

department: Dept. of Chemistry

country: Germany

institute: University of Konstanz

description: G4 specific molecule

scan_protocol: Standard Illumina scan protocol

data_processing: Data normalization using Genome Studio

source_name: HeLa 360A 48hrs

label_protocol: standard Illumina protocol

growth_protocol: Cells were cultured in DMEM high glucose medium with 10 % Fetal Calf Serum

extract_protocol: Qiagen RNeasy plus mini kit

treatment_protocol: Cells were treated with 10 µM of small molecule (in DMSO) for 48 hrs

value: HeLa S3 cells

tag: treatment


title: mES SMC2 KD hairpin1


title: Mes-4_N2_rep3

source_name: Mes-4 ChIP DNA for N2 EEMB

value: Early Embryo

value: population predominantly Hermaphrodites perhaps with some Males

source_name: Input DNA for N2 EEMB


title: mES CapH2 KD hairpin4


title: HCC827_DMSO_12h rep2

description:
SAMPLE 2
Triplicate 2


title: FO-D_t1 vs. t12

city: Hannover

first: Simone

last: Schmidt

address: Am kleinen Felde 30

department: Institute of Food Science and Human Nutrition

institute: Leibniz University of Hannover

description: The human OneArray™ DNA microarray is made of sense-strand 60-mer polynucleotide probes spotted onto a proprietary chemical layer-coated microarray glass slide. Each probe is spotted onto the array using a non-contact spotting technology. Each microarray contains 30,968 human genome probes (Phalanx Biotech Group, Palo Alto, CA 94304-1124, USA).

hyb_protocol: Slides were incubated at 42°C for 120 min in the following preheated (42°C) solution: 5xSSPE, SDS 0.1%, BSA 1%. Slides were washed for 2 minutes in deionized water followed by a centrifugation for drying. Equal amounts of biotin-labeled cDNA and fluorescein-labeled cDNA were hybridized simultaneously in one experiment to the human whole genome OneArray™ Microarray (Phalanx Biotech Group; Belmont, CA, USA). Hybridizations were carried out overnight at 42 °C in hybridization chambers (Eppendorf AG, Hamburg, Germany). After hybridization of the samples on the microarray slides overnight, slides were washed for 5 minutes with 2xSSCP, 5 minutes with 1xSSCP and 5 minutes with 0,5xSSCP at room temperature.

scan_protocol: The hybridized chips were scanned at least six times with an Axon 4000 B™ scanner at different settings, both changing the PMT and the laser power settings. Expression levels were quantified using GenePix Pro 6.0™ image analysis software (Axon Instruments, CA, USA). Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing:
A ratio-based normalization method was carried out. A locally weighted linear regression (Lowess) was employed as a normalization method to account for intensity-dependent effects. The mean of the data for differently labelled targets for each gene on respectively two microarrays was taken. A standard two-state pooled-variance t-test (5% probability of error) was applied to detect differentially expressed genes. VALUE is the normalized Log (base 2) ratio of the median of Channel 1 to Channel 2.

The multiple gpr files per Sample represent the multiple scans using different settings.

label: fluorescien

label_protocol: During reverse transcription, 6 µg of purified total RNA was converted into fluorescein (Fl) and Biotin (B) labeled cDNA and hybridized simultaneously in one experiment to the same array. After hybridisation, FL- and B-labeled cDNAs were sequentially detected with a series of conjugate reporter molecules according to the TSA process, ultimately with Tyramide-Cy3 and Tyramide-Cy5, respectively.

extract_protocol: Total RNA from whole blood was isolated using the PAXgene Blood RNA Kit (Qiagen, Hilden, Germany) according to the manufacturer's recommended procedures. Afterwards, total RNA was purified with the Globin Clear Kit (Ambion, Applied Biosystems, Darmstadt, Germany) according to the manufacturer's instructions. Equal amounts of purified RNA samples from each member of the respective group were pooled together. This was done for all different time points (t0, t4h, t1 and t12). Therefore, four pool-samples were generated by this process for each group, which results in a total of sixteen pool-samples for the microarray experiments. This approach was chosen to reduce biological inter-individual variability, which is frequent due to the variations in relative proportions of specific blood cell subsets, gender, age, and disease state.

treatment_protocol: Venous blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX, Hombrechtikon, Switzerland) at baseline (t0), 4 hours (t4h) after the first intake of the study products, after one week (t1), and after twelve weeks (t12) of supplementation. The collected whole blood samples were incubated for 24 hours in the PAXgene Blood RNA Tubes at room temperature. The patients gave informed consent.

value: whole blood

tag: time point

value: after one week (t1) of supplementation

tag: race

value: Caucasian

value: male

tag: age

value: between 29 and 51 years

tag: condition

value: dyslipidemic (TC > 200 mg/dl; LDL > 130 mg/dl; TG > 150 mg /dl)

tag: supplementation

value: fish oil capsules (2.7 g omega-3 fatty acids per day (1.14 g DHA and 1.56 g EPA))


title: FO-D_t12 vs. t1

tag: tissue

value: after twelve weeks (t12) of supplementation

tag: gender


title: mES SMC1 KD hairpin1 rep1


title: FO-D_t0 vs t4h

value: baseline (t0)

value: 4 hours (t4h) after the first intake of the study products


title: mES GFP KD hairpin1 rep2


title: mES SMC1 KD hairpin1 rep2


title: mES SMC2 KD hairpin2


title: HCC827_DMSO_12h rep1

description:
SAMPLE 1
Triplicate 1

value: non-small cell lung cancers

value: DMSO for 12 hr


title: CO-D_t12 vs. t0

value: corn oil capsules (3.05 g linoleic acid per day)


title: FO-D_t4h vs. t0


title: H3K36me3_mes-4 RNAi_rep1

tag: strain

tag: developmental stage

value: mes-4 (RNAi)

tag: chip antibody

tag: Sex

value: none, Input DNA


title: HeLa 360A 48 hrs Replicate 1

description: G4 specific molecule

tag: cell line

value: HeLa S3 cells


title: CO-D_t1 vs. t12


title: HCC827_DMSO_12h rep3

description:
SAMPLE 3
Triplicate 3

value: parental HCC827

tag: cell type

tag: treated with


title: mES CapH2 KD hairpin3

value: V6.5 embryonic stem cells


title: Mouse_NormalLung_biorep2

city: New York

first: Venkata

middle: J

last: Thodima

department: Cell Biology

institute: Memorial Sloan-Kettering Cancer Center

description: Expression data from RCC cell lines to study tumor-stroma interaction in xenograft model

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MouseGenome 430 Plus 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Scanner GSC3000 M10 type.

data_processing: The data were analyzed with Partek Genomic Suite 6.5 using default analysis settings and RMA as normalization method.

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

extract_protocol: Extraction of total RNA was performed using Qiagen miRNeasy kit according to the manufacturer's instructions.

tag: RCC cell line type

value: normal mouse lung (reference)


title: Mouse_NormalLung_biorep3


title: CO-D_t4h vs. t1

value: whole blood

value: Caucasian

value: after one week (t1) of supplementation


title: HeLa PhenDC3 48 hrs Replicate 3

description: G4 specific molecule

source_name: HeLa PhenDC3 48hrs


title: Mouse_NormalLung_biorep4


title: LM2_xenograft_biorep4

value: Metastatic RCC cell line


title: CO-D_t0 vs t4h

value: male

value: between 29 and 51 years

value: dyslipidemic (TC > 200 mg/dl; LDL > 130 mg/dl; TG > 150 mg /dl)


title: CO-N_t4h vs. t1

value: 4 hours (t4h) after the first intake of the study products

value: normolipidemic (TC < 200 mg/dl; LDL > 130 mg/dl; TG < 150 mg /dl)


title: HeLa 8979A 48 hrs Replicate 3

description: control molecule

source_name: HeLa 8979A 48hrs


title: Mouse_NormalLung_biorep1


title: LM2_xenograft_biorep2


title: Aurka_R_-Dox_rep2

city: san francisco

first: Yen-Sin

last: Ang

state: CALIFORNIA

address: 1650 Owens Street

institute: Gladstone Institute, UCSF

data_processing: Data was VST transformed, RSN normalized in R using LUMI package

source_name: Embryonic Stem Cell

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: total 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.

treatment_protocol: Each rescue ES clone was grown in +Dox (1ug/ml) media; Dox withdrawal was performed for 5days

tag: strain background

tag: genotype/variation

value: Aurka

value: -Dox


title: Aurka_R_-Dox_rep1


title: HeLa PhenDC3 48 hrs Replicate 2

description: G4 specific molecule

tag: treatment


title: VMH_7thECS6h

city: Tokyo

first: Eri

last: Segi-Nishida

state: Tokyo

address: Niijuku 6-3-1

institute: Tokyo University of Science

description: Gene expression data from mouse PVN at 6 h after ECS

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000.

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

source_name: mouse  ventromedial hypothalamus, ECS, 6h, 7th ECS

label_protocol: RNA amplification reaction was carried out using 2 ng of total RNA by Ovation Pico WTA System (NuGEN Technologies, San Carlos, CA), and amplified cDNA products were fragmented and labeled to generate biotinylated cDNA targets by Ovation biotylation kit. Then 5 µg of labeled cDNA was used for subsequent microarray analysis.

extract_protocol: Cryocut sections (7 μm thickness) were placed non-coated glass slides (Jung CM3000 cryostat; Leica Microsystems, Wetzlar, Germany), fixed, stained and dehydrated using the following protocol: 75% of ethanol for 30 sec, RNase-free water for 30 sec, staining using Histogene (Applied Biosystems, Carlsbad, CA) for 20 sec, RNase-free water for 30 sec, 75% of ethanol for 30 sec, 95% of ethanol for 30 sec, 100% of ethanol for 30 sec twice, xylene for 5 min; then sections were vacuumed for 15 min to dry. Laser microdissection was carried out on the Pixell Ile Laser Capture Microdissection System (Applied Biosystems). Immediately after microdissection, samples were dissolved in denaturing buffer and total RNA was isolated using an RNeasy Micro Kit (Qiagen).

treatment_protocol: Bilateral ECS was administered via moistened spring-loaded ear clip electrodes to isoflurane-anesthetized mice using a pulse generator (ECT Unit; Ugo Basile, Comeria, Italy) (current, 25 mA; shock duration, 1 sec; frequency, 100 pulse/sec; pulse width, 0.5 msec). ECS-treated animals received one or 7 times shock and tissue was collected at 2 or 6 h after shock. Sham-treated animals were handled the same fashion as ECS-treated animals, but no shock was delivered. Tissue of sham-treated animals was collected at 2 h after treatment. For microdissection from brain sections, the whole brains were quickly removed and rapidly frozen on dry ice, then stored at -20°C until microdissection.

value: hypothalamus

value: 7 shocks and brain collected after 6hrs


title: Aurka_R_+Dox_rep3

value: +Dox


title: Aurka_R_-Dox_rep3


title: HeLa PhenDC3 48 hrs Replicate 1

description: G4 specific molecule

value: HeLa S3 cells


title: Aurka_R_+Dox_rep2


title: CO-N_t1 vs. t12

tag: time point

tag: race

value: corn oil capsules (3.05 g linoleic acid per day)

value: after twelve weeks (t12) of supplementation


title: Aurka_R_+Dox_rep1

tag: condition


title: LM2_xenograft_biorep3


title: VMH_7thECS2h

description: Gene expression data from mouse PVN at 2 h after ECS

source_name: mouse  ventromedial hypothalamus, ECS, 2h, 7th ECS

value: 7 shocks and brain collected after 2hrs


title: LM2_xenograft_biorep1


title: HeLa 8979A 48 hrs Replicate 2

description: control molecule


title: CO-N_t12 vs. t0

value: whole blood

value: Caucasian

tag: age

tag: supplementation

value: baseline (t0)


title: SN12C_xenograft_biorep4

value: Primary RCC cell line


title: CO-N_t0 vs t4h

tag: tissue

tag: gender

value: male

value: between 29 and 51 years


title: HeLa 8979A 48 hrs Replicate 1

description: control molecule


title: VMH_1stECS6h

source_name: mouse  ventromedial hypothalamus, ECS, 6h, 1st ECS

tag: strain

value: 1 shock and brain collected after 6hrs


title: SN12C_xenograft_biorep3


title: VMH_1stECS2h

source_name: mouse  ventromedial hypothalamus, ECS, 2h, 1st ECS

value: 1 shock and brain collected after 2hrs


title: HeLa no-molecule 48 hrs Replicate 3

description: control

source_name: HeLa no-molecule 48hrs

value: DMSO


title: SN12C_xenograft_biorep2


title: FO-N_t12 vs. t0

value: normolipidemic (TC < 200 mg/dl; LDL > 130 mg/dl; TG < 150 mg /dl)

value: fish oil capsules (2.7 g omega-3 fatty acids per day (1.14 g DHA and 1.56 g EPA))


title: FO-N_t1 vs. t12

value: after one week (t1) of supplementation


title: FO-N_t4h vs. t1

value: 4 hours (t4h) after the first intake of the study products


title: HeLa no-molecule 48 hrs Replicate 2

description: control

value: HeLa S3 cells


title: SN12C_xenograft_biorep1


title: 252800411761-3

status: Public on May 29 2012

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: si-Paaf1 (A)

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

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

data_processing: Feature extraction data processing. log2(signal) normalized with quantile method (R bioconductor).

source_name: si-Paaf1 (A)

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Qiagen

tag: amount in (µg)

value: HeLa-LTR-luc

tag: rin number


title: 252800411761-6

description: si-Neg (B)

source_name: si-Neg (B)

tag: cell line


title: FPV-infected macrophages, biological rep2

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

description: Gene expression data from FPV-infected macrophages

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix U133 Plus 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 3000.

data_processing: The data were analyzed with (GCOS) version 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: cRNA were prepared and biotin-labeled according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA from 5 ug total RNA.

extract_protocol: RNeasy kit (Qiagen) was used to extract total RNA

tag: cell type

value: primary human macrophages


title: 252800411761-4

description: si-Spt6 (A)

source_name: si-Spt6 (A)


title: H5N1-infected macrophages, biological rep3

description: Gene expression data from H5N1-infected macrophages


title: 252800411761-7

description: si-Paaf1 (B)

source_name: si-Paaf1 (B)


title: H5N1-infected macrophages, biological rep2


title: PR8-infected macrophages, biological rep2

description: Gene expression data from PR8-infected macrophages


title: 252800411761-8

description: si-Spt6 (B)

source_name: si-Spt6 (B)


title: VMH_sham

description: Gene expression data from sham-treated mouse PVN

source_name: mouse ventromedial hypothalamus, sham, 2h

value: hypothalamus

value: no shock, brain collected after 2hrs


title: PR8-infected macrophages, biological rep3


title: FPV-infected macrophages, biological rep1


title: FPV-infected macrophages, biological rep3


title: H5N1-infected macrophages, biological rep1


title: Brachyury targets in differentiating mouse embryonic stem cells (2 of 2)

first: Amanda

middle: Lisabeth

last: Evans

state: Cambridgeshire

address: Tennis Court Road

department: Cancer Research UK Gurdon Institute

country: United Kingdom

institute: Wellcome Trust

description: Processed file of design 2 replicates 1,2,and 3 derived from Chip analytics analysis of raw files  AE_251471710182, AE_251471710724, AE_251471710725

hyb_protocol: Hybridisation using 5µg Cy5 and 5µg Cy3 labeled samples for 244K format using Agilent Oligo aCGH/ChiP -on- Chip Hybridisation Kit (5188-5220). Mouse Promoter arrays G44990A 244K format 1 set = 2 slides  of design 1 + design 2 per replicate

scan_protocol: Slides were scanned using the Agilent Microarray scanner and feature extraction software.

data_processing: Raw files were analysed using Agilent G4477AA chip analytics 1.3 as combined sets of 3 replicates using the whitehead error model 2 as described in Evans et al (in preparation)

source_name: Immunoprecipitated chromatin

label_protocol: As described by Agilent Technologies http://www.agilent.com with the exception that immunoprecipitated samples and corresponding inputs were amplified using the Whoile Genome Amplification Kit (Sigma) before Cy5 labeling with the Bioprime Kit (Invitrogen).

growth_protocol: ES cells were differentiated in spinner flasks to produce large numbers of embryoid bodies (EBs) undergoing synchronized differentiation. The Cellspin culture system (Integra Biosciences) was used. Fulls details as described (Evans et al Angiogenesis 2007 10:217-226 and Evans et al in preparation)

extract_protocol: Chromatin Immunoprecipitation assay

treatment_protocol: EBs (1.5 x 109 cells) were cross-linked intact at the peak of brachyury expression using 1M formaldehyde for 20 minutes followed by quenching and nuclei isolation. Nuclei were sonicated using a Misonix 3000 ultrasonicator (Misonix Inc.,N.Y.,U.S.A.) to 500bp, checked by agarose gel electrophoresis and Agilent Technologies 2100 bioanalyser DNA1000 chips, prior to IP using polyclonal goat anti-Brachyury C-19 (Santa Cruz Biotechnology sc-17745)

tag: EScell line derived embryoid bodies

source_name: Whole cell chromatin

label_protocol: As described by Agilent Technologies http://www.agilent.com with the exception that immunoprecipitated samples and corresponding inputs were amplified using the Whoile Genome Amplification Kit (Sigma) before Cy3 labeling with the Bioprime Kit (Invitrogen).

tag: ES Cell Line R1 derived embryoid bodies


title: PR8-infected macrophages, biological rep1


title: 252800411761-2

description: si-Neg (A)

source_name: si-Neg (A)


title: control macrophages, biological rep3

description: Gene expression data from control macrophages

source_name: control macrophages, biological rep3


title: HeLa no-molecule 48 hrs Replicate 1

description: control


title: FO-N_t0 vs. t4h

value: whole blood

value: Caucasian


title: HeLa 360A 48 hrs Replicate 2

description: G4 specific molecule

source_name: HeLa 360A 48hrs


title: Isotype control chip for Brachyury ES cell data design 2 (2of 2)

description:
Isotype control chip chip 2 of 2 (design 2 chip)
raw file AE_251471710722

hyb_protocol: Hybrisation using 5µg Cy5 and 5µg Cy3 labeled samples for 244K format using Agilent Oligo aCGH/CHIP-on-chip Hybridisation Kit (5188-5220). Mouse promoter arrays G4490A 244K format 1set = 2 slides of design 1 + design 2

data_processing: Raw files were analysed using Agilent G4477AA Chip analytics 1.3 using the whitehead error model 2 as described in Evans et al (in preparation).

label_protocol: As described by Agilent Technologies http://www.agilent.com with the exception that immunoprecipitated samples and corresponding inputs were amplified using the Whole Genome Amplification Kit (Sigma) before Cy5 labeling with the Bioprime Kit (invitrogen)

growth_protocol: ES cells were differentiated in spinner flasks to produce large numbers of embryoid bodies (EBs) undergoing synchronized differentiation.  The Cellspin culture system (Integra Biosciences) was used. Full details as desribed (Evans et al Angiogenesis 2007 10 217-226 and Evans et al in preparation).

extract_protocol: Chromatin immunoprecipitation assay

treatment_protocol: EBs (1.5 x 109 cells) were cross-linked intact at the peak of brachyury expression using 1M formaldehyde for 20 minutes followed by quenching and nuclei isolation. Nuclei were sonicated using a Misonix 3000 ultrasonicator (Misonix Inc.,N.Y.,U.S.A.) to 500bp, checked by agarose gel electrophoresis and Agilent Technologies 2100 bioanalyser DNA1000 chips, prior to IP with normal goat IgG (Santa Cruz Biotechnology sc-2028) isotype control

label_protocol: As described by Agilent Technologies http://www.agilent.com with the exception that immunoprecipitated samples and corresponding inputs were amplified using the Whole Genome Amplification Kit (Sigma) before Cy3 labeling with the Bioprime Kit (invitrogen)

treatment_protocol: EBs (1.5 x 109 cells) were cross-linked intact at the peak of brachyury expression using 1M formaldehyde for 20 minutes followed by quenching and nuclei isolation. Nuclei were sonicated using a Misonix 3000 ultrasonicator (Misonix Inc.,N.Y.,U.S.A.) to 500bp, checked by agarose gel electrophoresis and Agilent Technologies 2100 bioanalyser DNA1000 chips.

tag: ES cell line derived embryoid bodies


title: control macrophages, biological rep2

source_name: control macrophages, biological rep2


title: C4d negative biopsies w/o evidence of glomerular disease  186 V0 Group7

first: Bin

last: Ye

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer

scan_protocol: Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing:
Probe intensities were extracted from Affymetrix CEL files and normalized using RMA and summarized at the transcript cluster level using the R/Bioconductor (http://bioconductor.org) oligo package.  Array quality control was performed to remove arrays that significantly differed in performance.  Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package.  Significance testing was performed using a moderated t-test, and comparisons of pre- (V0) and post-treatment (V1) individuals were performed using a moderated paired t-test.  Gene set analysis was performed using the MSigDB (http://www.pnas.org/content/102/43/15545.abstract) and libraries generated from the Halloran labs Pathogenesis Based Transcript (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets.  The PBTs represent the major biologic events in cellular graft rejection and were derived from experimental mouse kidney transplants, cultured cells and human kidney biopsies.  Gene sets were converted to HUGO gene symbols and analysis was executed using the limma romer function.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: G7, C4d negative biopsies without evidence of glomerular disease

label_protocol: Follow protocols of Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: Total RNA was isolated using the QIAGEN RNeasy Mini Kit (Catalog Number 74104, Qiagen, USA) and was quantified using the NanoDrop 2000 (Thermo Scientific, Wilmington, Delaware). To further assess RNA quality, samples were assessed by the Agilent 2100 Bioanalyzer (Agilent Technology, Santa Clara, CA,) and samples with an RNA Integrity Number score cut off  >7 were deemed suitable for Gene Chip Microarray Hybridization.

treatment_protocol: One biopsy core from all patient biopsies studied, as well as 10 pre-implantation biopsies, was collected into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours, then transferred to -70°C until RNA isolation.  Renal tissue content in all cores was verified by Pathology Department personnel using a dissecting microscope.

tag: histochemistry

value: renal biopsy


title: control macrophages, biological rep1

source_name: control macrophages, biological rep1


title: C4d negative biopsies w/o evidence of glomerular disease  133 V0 Group7

value: C4d negative biopsies without evidence of glomerular disease


title: C4d negative biopsies w/o evidence of glomerular disease  144 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  104 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  168 Vex Group7


title: C4d negative biopsies w/o evidence of glomerular disease  160 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  157 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  167 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  115 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  90 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  165 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  141 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  80 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  102 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  128 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  103 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  88 Vex Group7


title: C4d negative biopsies w/o evidence of glomerular disease  37 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  26 Vex Group7


title: C4d negative biopsies w/o evidence of glomerular disease  34 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  1 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  15 V0 Group7


title: C4d negative biopsies w/o evidence of glomerular disease  5 V0 Group7


title: C4d negative with glomerular disease  181 V0 Group6

source_name: G6, C4d negative with glomerular disease

value: C4d negative with glomerular disease


title: C4d negative with glomerular disease  178 V0 Group6


title: C4d negative biopsies w/o evidence of glomerular disease  8 V0 Group7


title: C4d negative with glomerular disease  155 V0 Group6


title: C4d negative with glomerular disease  85 V0 Group6


title: C4d negative biopsies w/o evidence of glomerular disease  13 V0 Group7


title: C4d negative with glomerular disease  83 V0 Group6


title: C4d negative with glomerular disease  49 V0 Group6


title: C4d negative with glomerular disease  73 V0 Group6


title: C4d negative with glomerular disease  54 V0 Group6


title: C4d negative with glomerular disease  27 V0 Group6


title: Isolated glomerular C4d+ staining w/o glomerular disease 166 V0 Group5

source_name: G5, Isolated glomerular C4d+ staining without glomerular disease


title: C4d negative with glomerular disease  114 V0 Group6


title: Isolated glomerular C4d+ staining w/o glomerular disease 175 V0 Group5

value: Isolated glomerular C4d+ staining without glomerular disease


title: Isolated glomerular C4d+ staining w/o glomerular disease 132 V0 Group5


title: C4d negative with glomerular disease  93 V0 Group6


title: Isolated glomerular C4d+ staining w/o glomerular disease 125 V0 Group5


title: Isolated glomerular C4d+ staining w/o glomerular disease 96 V0 Group5


title: Isolated glomerular C4d+ staining w/o glomerular disease 105 V0 Group5


title: C4d negative with glomerular disease  52 V0 Group6


title: Isolated glomerular C4d+ staining w/o glomerular disease 48 V0 Group5


title: Isolated glomerular C4d+ staining w/o glomerular disease 77 Vex Group5


title: Isolated glomerular C4d+ staining w/o glomerular disease 10 V0 Group5


title: Isolated glomerular C4d+ staining w/o glomerular disease 156 V0 Group5


title: Isolated glomerular C4d+ with glomerular disease  154 V0 Group4

source_name: G4, Isolated glomerular C4d+ with glomerular disease


title: Isolated glomerular C4d+ staining w/o glomerular disease 2 V0 Group5


title: Isolated glomerular C4d+ staining w/o glomerular disease 16 V0 Group5


title: Isolated glomerular C4d+ with glomerular disease  169 V0 Group4


title: Isolated glomerular C4d+ staining w/o glomerular disease 159 V0 Group5


title: Isolated glomerular C4d+ staining w/o glomerular disease 99 V0 Group5


title: Isolated glomerular C4d+ staining w/o glomerular disease 42 V0 Group5


title: Isolated glomerular C4d+ with glomerular disease  143 V0 Group4


title: Isolated glomerular C4d+ with glomerular disease  89 V0 Group4


title: Focal or diffuse PTC C4d+  188 V0 Group2

source_name: G2, Focal or diffuse PTC C4d+

value: Focal or diffuse PTC C4d+


title: Minimal PTC C4d+  135 V0 Group3

source_name: G3, Minimal PTC C4d+

value: Minimal PTC C4d+


title: Isolated glomerular C4d+ with glomerular disease  116 V0 Group4


title: Minimal PTC C4d+  161 V0 Group3


title: Isolated glomerular C4d+ with glomerular disease  153 V0 Group4


title: Focal or diffuse PTC C4d+  183 V0 Group2


title: Minimal PTC C4d+  174 V0 Group3


title: Focal or diffuse PTC C4d+  172 V0 Group2


title: Isolated glomerular C4d+ with glomerular disease  3 V0 Group4


title: Isolated glomerular C4d+ with glomerular disease  180 V0 Group4


title: Focal or diffuse PTC C4d+  151 V0 Group2


title: Focal or diffuse PTC C4d+  179 V0 Group2


title: Isolated glomerular C4d+ with glomerular disease  101 V0 Group4


title: Focal or diffuse PTC C4d+  39 V0 Group2


title: Focal or diffuse PTC C4d+  148 V0 Group2


title: Isolated glomerular C4d+ with glomerular disease  130 V1 Group4


title: Focal or diffuse PTC C4d+  140 V0 Group2


title: Focal or diffuse PTC C4d+  120 V0 Group2


title: Focal or diffuse PTC C4d+  33 V0 Group2


title: Native pre-implantation biopsies 81 V0 Group1

source_name: G1, Native pre-implantation biopsies

value: Native pre-implantation biopsies


title: Focal or diffuse PTC C4d+  72 Vex Group2


title: Isolated glomerular C4d+ with glomerular disease  87 V0 Group4


title: Focal or diffuse PTC C4d+  21 V0 Group2


title: Focal or diffuse PTC C4d+  176 V0 Group2


title: Minimal PTC C4d+  142 V0 Group3


title: Native pre-implantation biopsies 76 V0 Group1


title: Native pre-implantation biopsies 20 V0 Group1


title: Native pre-implantation biopsies 26 V0 Group1


title: Isolated glomerular C4d+ with glomerular disease  45 V0 Group4


title: Native pre-implantation biopsies 31 V0 Group1


title: immature Macrophages_rep6

city: Bonn

first: Andrea

last: Nino Castro

state: NRW

address: Carl Troll str. 31

institute: Life and Medical Sciences institute

description: Immature macrophages

data_processing: The data were normalised using quantile normalization

source_name: monocyte derived macrophages

label_protocol: Biotinylated cRNA was prepared with the TargetAmp Nano-g Biotin aRNA Labeling Kit (Biozym Scientific GmbH, Hessisch Oldendorf, Germany).

extract_protocol: RNA was extracted with QIAzol Lysis Reagent using the miRNeasy Mini Kit  according to the manufacturer´s protocol (Qiagen, Hilden, Germany). Quality control was performed with denaturing gel electrophoresis and UV measurement.

value: blood

value: macrophages

tag: infection

value: noninfected


title: Brachyury targets in differentiating mouse embryonic stem cells (1 of 2)

description:
raw file AE_251471610189 Brachyury design 1 replicate 1
 raw file AE_251471610716 Brachyury design 1 replicate 2
 raw file AE_251471610717 Brachyury design 1 replicate 3
processed file is the combined analysis derived from chip analytics with n=3 raw design 1 files

hyb_protocol: Hybridisation using 5µg Cy5 and 5µg Cy3 labeled samples for 244K format using Agilent Oligo aCGH/ChIP -on-Chip Hybridisation Kit (5188-5220). Mouse Promoter arrays G4490A 244K format I set = 2 slides of  design 1 + design 2 per replicate

scan_protocol: Slides were scanned using the Agilent Microarray scanner and feature extraction software

data_processing: Raw files were analysed using Agilent G4477AA ChIP Analytics 1.3 as combined sets of 3 replicates using the whitehead error model 2 as described in Evans et al (in preparation)

label_protocol: As described by Agilent Technologies http://www.agilent.com with the exception that immunoprecipitated samples and corresponding inputs were amplified using the Whole Genome Amplification Kit (Sigma) before Cy5 labeling with the Bioprime  Kit (Invitrogen).

growth_protocol: ES cells were differentiated in spinner flasks to produce large numbers of embryoid bodies (EBs) undergoing synchronized differentiation. The Cellspin culture system (Integra Biosciences) was used. Full details as described (Evans et al Angiogenesis 2007 10:217–226 and Evans et al in preparation)

treatment_protocol: EBs (1.5 x 109 cells) were cross-linked intact at the peak of brachyury expression in 1M formaldehyde for 20 minutes followed by quenching and nuclei isolation. Nuclei were sonicated using a Misonix 3000 ultrasonicator. Chromatin IP  used polyclonal goat anti-Brachyury C-19 (Santa Cruz Biotechnology sc-17745) to generate Cy5 labeled probes.

label_protocol: As described by Agilent Technologies http://www.agilent.com with the exception that immunoprecipitated samples and corresponding inputs were amplified using the Whole Genome Amplification Kit (Sigma) before Cy3 input DNA labeling with the Bioprime  Kit (Invitrogen).


title: immature Macrophages_rep5

description: Immature macrophages


title: immature Macrophages_rep7

description: Immature macrophages


title: immature Macrophages_rep4

description: Immature macrophages


title: immature Macrophages_rep2

description: Immature macrophages


title: Native pre-implantation biopsies 32 V0 Group1


title: immature Macrophages_rep1

description: Immature macrophages


title: Native pre-implantation biopsies 23 V0 Group1


title: Runx1+/VE-cadherin-/CD41+, expression

first: Anagha

middle: M

last: Joshi

address: Wellcome trust/MRC building, Hills road

department: Dept. of haematology, CIMR

institute: University of cambridge

description:
Gene expression data from FACs-sorted day 6 differentiated ES cells.

Runx1(Venus/+) ES cell line: The Venus gene was placed in the P2-5'UTR under the control of the Runx1 proximal promoter P2. Parental ES cells are CCE ES cells.

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to the manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were processed using MAS5.0 (Affymetrix GCOS Ver.1.3).

source_name: FACS-sorted day 6 differentiated ES cells, Runx1+/VE-cadherin-/CD41+

label_protocol: The 3'IVT Express Kit was used for biotin labeling according to the manufacturer's instructions (Affymetrix).

growth_protocol: 1 x 10^5 undifferentiated ES cells were cultured on confluent OP9 cell layers in 10-cm dishes to induce differentiation. After 6 days of ES cell differentiation, cultured cells were harvested for FACS analysis and sorting.

extract_protocol: Extraction of total RNA was performed by using the QIAGEN RNeasy Micro kit according to the manufacturer's instructions.

treatment_protocol: No treatment beyond the normal growth protocol was used.

value: Runx1(Venus/+) ES cell line

value: differentiated ES cells

tag: days of differentiation

tag: cell subpopulation


title: immature Macrophages_rep3

description: Immature macrophages


title: Native pre-implantation biopsies 14 V0 Group1


title: Native pre-implantation biopsies 18 V0 Group1


title: Runx1+/VE-cadherin+/CD41-, expression

source_name: FACS-sorted day 6 differentiated ES cells, Runx1+/VE-cadherin+/CD41-


title: Macrophages 24 hours post-infection_rep3

description: Macrophages 24 hours post  Listeria monocytogenes infection

value: Listeria monocytogenes


title: Runx1+/VE-cadherin+/CD41+, expression

source_name: FACS-sorted day 6 differentiated ES cells, Runx1+/VE-cadherin+/CD41+


title: Isotype control chip for Brachyury ES cell data design1 (1of 2)

description:
Isotype control chip chip 1 of 2 (design 1 chip)
raw file AE_251471610714

source_name: Immunoprecipitated chromatin

source_name: whole cell chromatin


title: Runx1-/VE-cadherin+/Flk1+, expression

source_name: FACS-sorted day 6 differentiated ES cells, Runx1-/VE-cadherin+/Flk1+


title: Macrophages 24 hours post-infection_rep2


title: Macrophages 24 hours post-infection_rep1


title: E.albidus_carbendazim_EC90_rep1

status: Public on May 28 2012

city: Aveiro

first: Sara

last: Novais

address: Campus de Santiago, Department of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

description:
SAMPLE 40
E.albidus gene expression after exposure to carbendazim reproduction EC90

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit . 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-030589 Custom Gene Expression Array for Enchytraeus albidus 8x15k, for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies) using default parameters (protocol GE1_105_Dec08 and Grid: 030589_D_F_20101007) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Enchytraeus albidus

source_name: E. albidus_carbendazim_EC90

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Isolation of total RNA from each replicate was performed through the Trizol extraction method (Invitrogen, Belgium). This RNA followed a DNAse treatment (Fermentas, Germany) and further purification steps consisting of phenol/chloroform extractions. The quantity and purity of the isolated RNA were measured spectrophotometrically with nanodrop (NanoDrop ND-1000 Spectrophotometer) and its integrity was checked on a denaturing formaldehyde agarose gel electrophoresis.

treatment_protocol: Fifteen adult worms with well developed clitellum were introduced in the test vessels, each containing 25 g moist soil (water control, solvent control or spiked soil with pesticides). The worms were exposed for 2 days at 20C and a 16:8h photoperiod. Three biological replicates per treatment  were used. At test end, animals of each replicate were carefully removed, rinsed in deionised water, stored in RNA later (Ambion, USA) containing criotubes and frozen in liquid Nitrogen. All the samples were stored at -80C till further analysis.

value: Whole body extracts

tag: developmental stage

value: Adult organisms with well developed clitellum


title: E.albidus_carbendazim_EC50_rep1

description:
SAMPLE 37
E.albidus gene expression after exposure to carbendazim reproduction EC50

source_name: E. albidus_carbendazim_EC50


title: E.albidus_carbendazim_EC50_rep3

description:
SAMPLE 39
E.albidus gene expression after exposure to carbendazim reproduction EC50


title: Native pre-implantation biopsies 6 V0 Group1


title: E.albidus_carbendazim_EC90_rep2

description:
SAMPLE 41
E.albidus gene expression after exposure to carbendazim reproduction EC90


title: E.albidus_carbendazim_EC20_rep2

description:
SAMPLE 35
E.albidus gene expression after exposure to carbendazim reproduction EC20

source_name: E. albidus_carbendazim_EC20


title: E.albidus_carbendazim_EC20_rep3

description:
SAMPLE 36
E.albidus gene expression after exposure to carbendazim reproduction EC20


title: E.albidus_carbendazim_EC90_rep3

description:
SAMPLE 42
E.albidus gene expression after exposure to carbendazim reproduction EC90


title: E.albidus_carbendazim_EC10_rep2

description:
SAMPLE 32
E.albidus gene expression after exposure to carbendazim reproduction EC10

source_name: E. albidus_carbendazim_EC10


title: E.albidus_carbendazim_EC50_rep2

description:
SAMPLE 38
E.albidus gene expression after exposure to carbendazim reproduction EC50


title: E.albidus_carbendazim_EC10_rep1

description:
SAMPLE 31
E.albidus gene expression after exposure to carbendazim reproduction EC10


title: E.albidus_carbendazim_EC20_rep1

description:
SAMPLE 34
E.albidus gene expression after exposure to carbendazim reproduction EC20


title: E.albidus_carbendazim_EC10_rep3

description:
SAMPLE 33
E.albidus gene expression after exposure to carbendazim reproduction EC10


title: E.albidus_atrazine_EC90_rep3

description:
SAMPLE 30
E.albidus gene expression after exposure to atrazine reproduction EC90

source_name: E. albidus_atrazine_EC90


title: E.albidus_atrazine_EC90_rep1

description:
SAMPLE 28
E.albidus gene expression after exposure to atrazine reproduction EC90


title: Macrophages from Gl261, Rep 3

first: Yujie

last: Huang

address: 510E 70st Street

department: Neurological Surgery

institute: Weill Cornell Medicine

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.

source_name: Macrophages isolated from D21 Gl261 tumor

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

growth_protocol: Gl261 tumor were intracranially injected to C57/Bl6 mice transplanted with GFP bone marrow, and grew for 21 days.

extract_protocol: total RNA was xtracted by microRNAeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Brain with/without Gl261 tumor were choped off and subjected to PAPIN digestion, and then macrophages were isolated  by GFP and F4/80 markers.

value: Gl261 tumor


title: Macrophages from normal brain, Rep 1

source_name: Macrophages isolated from 8 wks old mice

value: normal brain


title: Macrophages from Gl261, Rep 4


title: E.albidus_atrazine_EC50_rep3

description:
SAMPLE 27
E.albidus gene expression after exposure to atrazine reproduction EC50

source_name: E. albidus_atrazine_EC50


title: Macrophages from Gl261, Rep 2


title: Macrophages from normal brain, Rep 3


title: Macrophages from Gl261, Rep 1


title: E.albidus_atrazine_EC20_rep2

description:
SAMPLE 23
E.albidus gene expression after exposure to atrazine reproduction EC20

source_name: E. albidus_atrazine_EC20


title: E.albidus_atrazine_EC20_rep1

description:
SAMPLE 22
E.albidus gene expression after exposure to atrazine reproduction EC20


title: E.albidus_atrazine_EC10_rep3

description:
SAMPLE 21
E.albidus gene expression after exposure to atrazine reproduction EC10

source_name: E. albidus_atrazine_EC10


title: Isolated glomerular C4d+ with glomerular disease  100 V0 Group4

source_name: G4, Isolated glomerular C4d+ with glomerular disease

value: renal biopsy


title: E.albidus_atrazine_EC50_rep2

description:
SAMPLE 26
E.albidus gene expression after exposure to atrazine reproduction EC50


title: E.albidus_atrazine_EC50_rep1

description:
SAMPLE 25
E.albidus gene expression after exposure to atrazine reproduction EC50


title: Macrophages from normal brain, Rep 2


title: E.albidus_atrazine_EC90_rep2

description:
SAMPLE 29
E.albidus gene expression after exposure to atrazine reproduction EC90


title: E.albidus_atrazine_EC20_rep3

description:
SAMPLE 24
E.albidus gene expression after exposure to atrazine reproduction EC20


title: E.albidus_atrazine_EC10_rep1

description:
SAMPLE 19
E.albidus gene expression after exposure to atrazine reproduction EC10


title: JmjD2d knock-down DCs, 4h LPS-stimulated, biological rep 3

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

description: Dendritic cells differentiated for 8d in vitro from bone marrow-derived progenitor cells  using GM-CSF

hyb_protocol: according to Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling manual (version 4)

data_processing: RMA algorithm

source_name: JmjD2d-knockdown dendritic cells, 4h after stimulation with 100ng/ml LPS

label_protocol: Affymetrix GeneChip Whole Transcript (WT) Sense Target labeling

growth_protocol: Bone marrow-derived progenitor cells were cultured in 20ng/ml each of SCF, IL-3 and IL-6, retrovirally infected using the pSir-delta U6CHisD vector carrying a hairpin directed against the JmjD2d coding sequence, and selected using 2mM histidinol.  Dendritic cells were differentiated from progenitor cells in GM-CSF (4% X63-GMCSF supernatant) + 5ng/ml SCF for 4 days, followed by GM-CSF alone for 4 days.

extract_protocol: Cells were lysed using a Qiashredder (Qiagen) and total RNA was extracted using the RNeasy mini kit (Qiagen) with on-column Dnase digestion, following the manufacturer's instructions.

treatment_protocol: Dendritic cells were stimulated with 100ng/ml LPS for 4 hours

tag: transduction

value: transduced with shRNA targeting JmjD2d in pSir-delta U6CHisD

tag: stimulation

value: stimulated for 4h with 100ng/ml LPS


title: E.albidus_atrazine_EC10_rep2

description:
SAMPLE 20
E.albidus gene expression after exposure to atrazine reproduction EC10

tag: tissue


title: E.albidus_dimethoate_EC90_rep2

description:
SAMPLE 17
E.albidus gene expression after exposure to dimethoate reproduction EC90

source_name: E. albidus_dimethoate_EC90


title: WT DCs, 4h LPS-stimulated, biological rep 3

scan_protocol: according to Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling manual (version 4)

source_name: wild-type dendritic cells, 4h after stimulation with 100ng/ml LPS

value: untransduced


title: E.albidus_dimethoate_EC90_rep3

description:
SAMPLE 18
E.albidus gene expression after exposure to dimethoate reproduction EC90


title: JmjD2d knock-down DCs, 4h LPS-stimulated, biological rep 2


title: U87_APN_L243P_EGFP Rep2

city: Greifswald

last: Mostertz

address: F.-L.-Jahnstr 15

department: Competence Center Functional Genomics

institute: Greifswald University

hyb_protocol: Affymetrix Whole-Transcript Expression Analysis & Profiling

data_processing: For each probe set the corresponding values of the gene expression analysis of two replicates for both conditions were performed [APT-RMA_normalized signal intensities, averaged signal intensity, comparison analysis, rank prodit test; processed_data_complete.txt] . Data for the control probe sets are excluded.  Analysis performed with Rosetta Resolver system for gene expression data analysis; Entrez_gene_summary.txt (Rosetta Biosoftware v.7.2.2.0.SP2.12)

growth_protocol: cell culture

extract_protocol: RNA was prepared from cultured cells using the TRIzol reagent (Invitrogen/Life Technologies, Karlsruhe, Germany). The RNA was further purified using the Norgen’s RNA Clean-Up and Concentration Micro Kit (Norgen Biotek, Thorold, Canada).

treatment_protocol: comparable growth for wild type and mutant

tag: cell line background

value: malignant glioma cells

tag: genotype/variation

value: inactive CD13/APN clone


title: U87_APN_L243P_EGFP Rep1

scan_protocol: Affymetrix Whole-Transcript Expression Analysis & Profiling


title: WT DCs, 4h LPS-stimulated, biological rep 2


title: U87_APN_wt_EGFP Rep1

data_processing: For each probe set the corresponding values of the gene expression analysis of two replicates for both conditions were performed [APT-RMA_normalized signal intensities, averaged signal intensity, comparison analysis, rank prodit test; processed_data_complete.txt]. Data for the control probe sets are excluded.  Analysis performed with Rosetta Resolver system for gene expression data analysis; Entrez_gene_summary.txt (Rosetta Biosoftware v.7.2.2.0.SP2.12)

label_protocol: Affymetrix Whole-Transcript Expression Analysis & Profiling

value: wild type


title: U87_APN_wt_EGFP Rep2


title: WT DCs, 4h LPS-stimulated, biological rep 1


title: WT DCs, unstimulated, biological rep 2

source_name: wild-type dendritic cells, unstimulated

value: unstimulated


title: WT DCs, unstimulated, biological rep 3


title: ATMfibHomo rep2

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

description: ATM homozygote;fibroblast;ATMfibHomo rep2

hyb_protocol: Total RNA (100ng) was subjected to reverse transcription, second-strand cDNA synthesis and in-vitro transcription using the TotalPrep RNA Amplification Kit (Illumina). cRNA was hybridized to Illumina HT12 v4 BeadChip microarrays.

scan_protocol: Bead array (Illumina)

data_processing: The raw expression data were normalized using quantile normalisation and without background correction, using the lumi R/Bioconductor package (version 2.4.0) (Du et al., 2008). Only probes passing the Illumina detection threshold were included in the expression analysis; a probe passed the Illumina detection score if it had a detection P-value ≤ 0.01 in at least 75% of cell lines in the same group; this criterion resulted in 20,593 probes being retained. All statistical analyses were performed using R version 2.13.2. All probes were mapped using the annotation package illuminaHumanv4.db (version 1.10.0) available from Bioconductor.

source_name: ATMfibHomo rep2

label_protocol: Samples were labelled using Illumina TotalPrep RNA Amplification Kit (AMIL1791), following manufacturer's instructions.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen).

value: fibroblast

tag: disease state

value: ATM homozygote

tag: cell surface marker expression

value: unsorted


title: ATMfibHomo rep3

description: ATM homozygote;fibroblast;ATMfibHomo rep3

source_name: ATMfibHomo rep3


title: E.albidus_dimethoate_EC50_rep3

description:
SAMPLE 15
E.albidus gene expression after exposure to dimethoate reproduction EC50

source_name: E. albidus_dimethoate_EC50


title: JmjD2d knock-down DCs, 4h LPS-stimulated, biological rep 1


title: E.albidus_dimethoate_EC90_rep1

description:
SAMPLE 16
E.albidus gene expression after exposure to dimethoate reproduction EC90


title: ATMfibHomo rep1

description: ATM homozygote;fibroblast;ATMfibHomo rep1

source_name: ATMfibHomo rep1


title: ATMfibHet rep3

description: ATM heterozygote;fibroblast;ATMfibHet rep3

source_name: ATMfibHet rep3

value: ATM heterozygote


title: ATMfibHet rep1

description: ATM heterozygote;fibroblast;ATMfibHet rep1

source_name: ATMfibHet rep1


title: ATMiPShomo rep2

description: ATM homozygote;induced pluripotent stem cell;ATMiPShomo rep2

source_name: ATMiPShomo rep2

value: induced pluripotent stem cell

value: Tra-1-60 positive


title: ATMfibHet rep2

description: ATM heterozygote;fibroblast;ATMfibHet rep2

source_name: ATMfibHet rep2


title: E.albidus_dimethoate_EC50_rep1

description:
SAMPLE 13
E.albidus gene expression after exposure to dimethoate reproduction EC50

value: Whole body extracts

value: Adult organisms with well developed clitellum


title: ATMiPShomo rep3

description: ATM homozygote;induced pluripotent stem cell;ATMiPShomo rep3

source_name: ATMiPShomo rep3


title: WT DCs, unstimulated, biological rep 1


title: E.albidus_dimethoate_EC20_rep3

description:
SAMPLE 12
E.albidus gene expression after exposure to dimethoate reproduction EC20

source_name: E. albidus_dimethoate_EC20


title: E.albidus_dimethoate_EC10_rep3

description:
SAMPLE 9
E.albidus gene expression after exposure to dimethoate reproduction EC10

source_name: E. albidus_dimethoate_EC10


title: E.albidus_dimethoate_EC50_rep2

description:
SAMPLE 14
E.albidus gene expression after exposure to dimethoate reproduction EC50


title: E.albidus_dimethoate_EC10_rep2

description:
SAMPLE 8
E.albidus gene expression after exposure to dimethoate reproduction EC10


title: E.albidus_dimethoate_EC20_rep1

description:
SAMPLE 10
E.albidus gene expression after exposure to dimethoate reproduction EC20


title: E.albidus_dimethoate_EC10_rep1

description:
SAMPLE 7
E.albidus gene expression after exposure to dimethoate reproduction EC10


title: ATMiPShet rep2

description: ATM heterozygote;induced pluripotent stem cell;ATMiPShet rep2

source_name: ATMiPShet rep2


title: ATMiPShomo rep1

description: ATM homozygote;induced pluripotent stem cell;ATMiPShomo rep1

source_name: ATMiPShomo rep1


title: ATMiPShet rep3

description: ATM heterozygote;induced pluripotent stem cell;ATMiPShet rep3

source_name: ATMiPShet rep3


title: E.albidus_dimethoate_EC20_rep2

description:
SAMPLE 11
E.albidus gene expression after exposure to dimethoate reproduction EC20


title: ATMiPShet rep1

description: ATM heterozygote;induced pluripotent stem cell;ATMiPShet rep1

source_name: ATMiPShet rep1


title: fib2 rep2

description: normal;fibroblast;fib2 rep2

source_name: fib2 rep2

value: normal


title: fib1 rep3

description: normal;fibroblast;fib1 rep3

source_name: fib1 rep3


title: fib1 rep1

description: normal;fibroblast;fib1 rep1

source_name: fib1 rep1


title: iPS2 rep5

description: normal;induced pluripotent stem cell;iPS2 rep5

source_name: iPS2 rep5


title: fib2 rep1

description: normal;fibroblast;fib2 rep1

source_name: fib2 rep1


title: iPS2 rep6

description: normal;induced pluripotent stem cell;iPS2 rep6

source_name: iPS2 rep6


title: fib2 rep3

description: normal;fibroblast;fib2 rep3

source_name: fib2 rep3


title: E.albidus_Solvent Control_rep1

description:
SAMPLE 4
E.albidus gene expression after exposure to acetone

source_name: E. albidus_solvent control


title: E.albidus_Solvent Control_rep2

description:
SAMPLE 5
E.albidus gene expression after exposure to acetone


title: iPS2 rep4

description: normal;induced pluripotent stem cell;iPS2 rep4

source_name: iPS2 rep4


title: fib1 rep2

description: normal;fibroblast;fib1 rep2

source_name: fib1 rep2


title: hES rep1

description: normal;human embyronic stem cell;hES rep1

source_name: hES rep1

value: human embyronic stem cell


title: E.albidus_Control_rep3

description:
SAMPLE 3
E.albidus gene expression under control conditions

source_name: E. albidus_control


title: hES rep3

description: normal;human embyronic stem cell;hES rep3

source_name: hES rep3


title: iPS2 rep1

description: normal;induced pluripotent stem cell;iPS2 rep1

source_name: iPS2 rep1


title: iPS2 rep2

description: normal;induced pluripotent stem cell;iPS2 rep2

source_name: iPS2 rep2


title: hES rep2

description: normal;human embyronic stem cell;hES rep2

source_name: hES rep2


title: iPS2 rep3

description: normal;induced pluripotent stem cell;iPS2 rep3

source_name: iPS2 rep3


title: iPS1 rep3

description: normal;induced pluripotent stem cell;iPS1 rep3

source_name: iPS1 rep3


title: E.albidus_Control_rep2

description:
SAMPLE 2
E.albidus gene expression under control conditions


title: iPS1 rep6

description: normal;induced pluripotent stem cell;iPS1 rep6

source_name: iPS1 rep6


title: iPS1 rep5

description: normal;induced pluripotent stem cell;iPS1 rep5

source_name: iPS1 rep5


title: iPS1 rep4

description: normal;induced pluripotent stem cell;iPS1 rep4

source_name: iPS1 rep4


title: E.albidus_Control_rep1

description:
SAMPLE 1
E.albidus gene expression under control conditions


title: iPS1 rep1

description: normal;induced pluripotent stem cell;iPS1 rep1

source_name: iPS1 rep1


title: Lung control_2

status: Public on May 27 2012

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

hyb_protocol: Hibridization was performed according to the manufacture conditions (arrays: Affymetrix Mouse Genome 430 Plus 2.0 GeneChip)

scan_protocol: GeneChip arrays were canned using a GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis technical Manual.

data_processing: Analysis technical Manual. Affymetrix GeneChip Operating Software was used for image acquisition. The target signal intensity from each chip was scaled to 500. Triplicate samples from each exosome-treated and control lung samples were analyzed to identify differentially expressed genes.

source_name: Lung control, biological replicate 2

label_protocol: The biotin labeled cRNA was fragmented and hybridized to the Affymetrix Mouse Genome 430 Plus 2.0 GeneChip arrays (Santa Clara, CA) for analysis of over 39,000 transcripts on a single array.

growth_protocol: For analyzing the genes modified in lungs by B16-exosomes, a total of 10 μg of exosome protein was injected by tail vein, 24 and 48 h after mice were sacrificed and lungs were kept in RNA-later solution (Ambion) until RNA extraction. A total of 3 mice were used per time point and the experiment was performed in triplicate.

extract_protocol: Total RNA from cells was isolated using RNeasy mini kit (Qiagen) and the Affymetrix a one-round in vitro transcription (IVT) RNA Amplification Kit was used to amplify 1.5 mg amounts of total RNA. The cDNA was synthesized with a primer containing oligo (dT) and T7 RNA polymerase promoter sequences. Double-stranded cDNA was then purified and used as a template to generate biotinylated cRNA. The quantity and quality of the amplified cRNA was assessed using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE) and Agilent Bioanalyzer (Santa Clara CA).

tag: strain

value: lung


title: Aerial parts of 14-day-old GFP-TIE1-15 seedlings

city: Beijing

first: qing

last: tao

address: 5th,Yi he yuan road, hai dian district,Beijing,China

department: Biotechnology

country: China

institute: Peking University

description: Gene expression data from aerial parts of 14-day-old GFP-TIE1-15 seedlings.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis ATH1 Genome Arrays. The standard wash and double-stain protocols (EukGE-WS2v5-450) were applied using an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned on an Affymetrix GeneChip scanner 3000.

data_processing: The scanned arrays were analyzed first with Affymetrix GCOS 1.0 (MAS 5.0) software to generate detection calls. Both data sets were normalized using Affymetrix GCOS software, and the TGT value was set to 100.

organism: Arabidopsis thaliana

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis seeds from wild-type and GFP-TIE1-15 were placed on half-strength Murashige and Skoog (1/2 MS) medium. The plates were put in 4 °C refrigerator for 3 days to complete synchronization before being placed at 22±2 °C under long day conditions (16-h light and 8-h dark) for 14 days.

extract_protocol: The QIAgen RNeasy Total RNA Extraction Kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Aerial parts of the 14-day-old seedlings were excised from the seedlings and collected for total RNA extraction.

tag: genotype

value: GFP-TIE1 transgenic line

tag: age

value: 14 days

value: aerial parts of seedlings


title: F10exo-24 hour_1 lung 24 hours after B16-F10 exosome tail vein injection:Biological replicate 2

source_name: lungs 24  hours after B16-F10 exosome tail vein injection, biological replicate 2


title: iPS1 rep2

description: normal;induced pluripotent stem cell;iPS1 rep2

source_name: iPS1 rep2

tag: cell type


title: Lung control_1

source_name: Lung control, biological replicate 1


title: F10exo-24 hour_1 lung 24 hours after B16-F10 exosome tail vein injection:Biological replicate 3

source_name: lungs 24  hours after B16-F10 exosome tail vein injection, biological replicate 3


title: E.albidus_Solvent Control_rep3

description:
SAMPLE 6
E.albidus gene expression after exposure to acetone

source_name: E. albidus_solvent control


title: Aerial parts of 14-day-old wild-type seedlings

description: Gene expression data from aerial parts of 14-day-old wildtype seedlings.

source_name: Aerial parts of 14-day-old wildtype seedlings

value: Columbia-0 wild-type


title: F10exo-24 hour_1 lung 48 hours after B16-F10 exosome tail vein injection:Biological replicate 3

source_name: lungs 48  hours after B16-F10 exosome tail vein injection, biological replicate 3


title: F10exo-24 hour_1 lung 24 hours after B16-F10 exosome tail vein injection:Biological replicate 1

source_name: lungs 24  hours after B16-F10 exosome tail vein injection, biological replicate 1


title: Lung control_3

source_name: Lung control, biological replicate 3


title: F10exo-24 hour_1 lung 48 hours after B16-F10 exosome tail vein injection:Biological replicate 2

source_name: lungs 48  hours after B16-F10 exosome tail vein injection, biological replicate 2


title: F10exo-24 hour_1 lung 48 hours after B16-F10 exosome tail vein injection:Biological replicate 1

source_name: lungs 48  hours after B16-F10 exosome tail vein injection, biological replicate 1


title: Normal human mammary fibroblast cells genotype 240

status: Public on May 26 2012

city: Tucson

first: Lukas

last: Vrba

state: AZ

address: 1515 N Campbell Ave

department: Arizona Cancer Center

institute: University of Arizona

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 fibroblast 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: Flash-frozen breast specimens derived from non-tumor or cancerous breast tissue were obtained from patients who underwent surgery for breast cancer, either lumpectomy or mastectomy, at the University Medical Center in Tucson from 2003 to 2005.  MCF7, MDA-MB-231, MDA-MB-453, MDA-MB-468 and BT549 were grown in RPMI 1640 medium supplemented with 5% FBS, 100 units/ml penicillin and 50 μg/ml streptomycin. MDA-MB-157 and UACC1179 were grown in M15 medium supplemented with 5% FBS. 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:
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.
IP 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 l 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.

tag: cell line

value: HMF 240L

value: mammary gland

tag: tumor stage

tag: dna fraction

value: Immunoprecipitated DNA

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.
The antibody used was from Diagenode, Catalog#: MAb-006-100, Lot#: DA-0017.  The concentration is 1 ug/ul, so the amount used in the immunoprecipitation protocol was 2 ug.
IP 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 l 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: Input DNA


title: Normal human mammary epithelial cells genotype 184

source_name: Human mammary epithelial cells

value: HMEC 184D


title: Normal human mammary fibroblast cells genotype 184

value: HMF 184


title: Normal human mammary epithelial cells genotype 48

value: HMEC 48RT


title: Normal human mammary fibroblast cells genotype 48

value: HMF 48


title: breast carcinoma cell line MDA-MB-157

description: breast carcinoma cell line MDA-MB-157

source_name: breast carcinoma cell line

value: tumor


title: breast carcinoma cell line MDA-MB-468

description: breast carcinoma cell line MDA-MB-468


title: breast carcinoma cell line MDA-MB-231

description: breast carcinoma cell line MDA-MB-231


title: breast carcinoma cell line MCF7

description: breast carcinoma cell line MCF7


title: breast non-tumor specimen N6333

description: breast non-tumor specimen N6333

source_name: breast non-tumor specimen

value: tissue specimen N6333


title: breast carcinoma cell line UACC1179

description: breast carcinoma cell line UACC1179


title: breast carcinoma cell line BT549

description: breast carcinoma cell line BT549


title: breast carcinoma cell line MDA-MB-453

description: breast carcinoma cell line MDA-MB-453


title: Normal human mammary epithelial cells genotype 240

value: HMEC 240LB

value: normal


title: breast non-tumor specimen N5343-2

description: breast non-tumor specimen N5343-2

value: tissue specimen N5343-2


title: breast tumor specimen T4392

description: breast tumor specimen T4392

source_name: breast tumor specimen

value: tissue specimen T4392


title: breast non-tumor specimen N8964

description: breast non-tumor specimen N8964

value: tissue specimen N8964


title: breast non-tumor specimen N7732

description: breast non-tumor specimen N7732

value: tissue specimen N7732