title: TamR#1 Tamoxifen 0h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR1.Tam.00h


title: TamR HRG+Tamoxifen 48h

status: Public on Nov 03 2010

type: RNA

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN RCAI

description:
Gene expression in HRG+Tamoxifen-stimulated TamR cells.
TamR.HRG_Tam.48h

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocol can be found on the manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, 2.2.p3-8 & 2.3.p3-14).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameters.

data_processing: The data were preprocessed with RMA. Signal intensity was calculated for RefSeq mRNA by using a CustomCDF (HGU133Plus2_Hs_REFSEQ ver.11).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 48h

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocol can be found on the manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, chapter1-p13-18, & 2.1.p32-33,p36-40).

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free RPMI medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using the QIAGEN Rneasy kit.

treatment_protocol: Following the incubation in serum-free medium, the ligand was added and incubated for the indicated time.

tag: cell line

tag: tissue origination

value: mammary gland, breast

tag: cell type

value: epithelial

tag: disease

value: adenocarcinoma

tag: age

tag: gender

value: female

tag: ethnicity

value: Caucasian

tag: tamoxifen phenotype

value: resistant

tag: treatment

value: HRG, tamoxifen

tag: time


title: TamR HRG+Tamoxifen 2h

description:
Gene expression in HRG+Tamoxifen-stimulated TamR cells.
TamR.HRG_Tam.02h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 2h


title: TamR HRG+Tamoxifen 1h

description:
Gene expression in HRG+Tamoxifen-stimulated TamR cells.
TamR.HRG_Tam.01h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 1h


title: TamR Tamoxifen 12h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR.Tam.12h

source_name: breast epithelial cell, adherent, Tamoxifen, 12h

value: tamoxifen


title: TamR HRG 2h

description:
Gene expression in HRG-stimulated TamR cells.
TamR.HRG.02h

source_name: breast epithelial cell, adherent, HRG, 2h

value: HRG


title: TamR HRG 48h

description:
Gene expression in HRG-stimulated TamR cells.
TamR.HRG.48h

source_name: breast epithelial cell, adherent, HRG, 48h


title: TamR Tamoxifen 0h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR.Tam.00h

source_name: breast epithelial cell, adherent, Tamoxifen, 0h


title: TamR HRG+Tamoxifen 3h

description:
Gene expression in HRG+Tamoxifen-stimulated TamR cells.
TamR.HRG_Tam.03h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 3h


title: TamR HRG 1h

description:
Gene expression in HRG-stimulated TamR cells.
TamR.HRG.01h

source_name: breast epithelial cell, adherent, HRG, 1h


title: TamR Tamoxifen 24h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR.Tam.24h

source_name: breast epithelial cell, adherent, Tamoxifen, 24h


title: WT HRG 6h rep1

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.06h.r1

source_name: breast epithelial cell, adherent, HRG, 6h

value: sensitive


title: TamR HRG+Tamoxifen 24h

description:
Gene expression in HRG+Tamoxifen-stimulated TamR cells.
TamR.HRG_Tam.24h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 24h


title: TamR E2+Tamoxifen 12h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR.E2_Tam.12h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 12h

value: E2, tamoxifen


title: TamR HRG 12h

description:
Gene expression in HRG-stimulated TamR cells.
TamR.HRG.12h

source_name: breast epithelial cell, adherent, HRG, 12h


title: TamR HRG 3h

description:
Gene expression in HRG-stimulated TamR cells.
TamR.HRG.03h

source_name: breast epithelial cell, adherent, HRG, 3h


title: TamR E2+Tamoxifen 24h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR.E2_Tam.24h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 24h


title: TamR E2 48h

description:
Gene expression in E2-stimulated TamR cells.
TamR.E2.48h

source_name: breast epithelial cell, adherent, E2, 48h


title: TamR E2 24h

description:
Gene expression in E2-stimulated TamR cells.
TamR.E2.24h

source_name: breast epithelial cell, adherent, E2, 24h


title: TamR HRG 24h

description:
Gene expression in HRG-stimulated TamR cells.
TamR.HRG.24h

source_name: breast epithelial cell, adherent, HRG, 24h


title: TamR E2+Tamoxifen 3h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR.E2_Tam.03h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 3h


title: TamR E2+Tamoxifen 1h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR.E2_Tam.01h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 1h


title: TamR E2 6h

description:
Gene expression in E2-stimulated TamR cells.
TamR.E2.06h

source_name: breast epithelial cell, adherent, E2, 6h


title: TamR HRG+Tamoxifen 6h

description:
Gene expression in HRG+Tamoxifen-stimulated TamR cells.
TamR.HRG_Tam.06h

source_name: breast epithelial cell, adherent, HRG+Tamoxifen, 6h


title: TamR Control 48h

description:
Gene expression in unstimulated TamR cells.
TamR.Ctrl.48h

source_name: breast epithelial cell, adherent, without stimulus, 48h

value: untreated


title: TamR E2 12h

description:
Gene expression in E2-stimulated TamR cells.
TamR.E2.12h

source_name: breast epithelial cell, adherent, E2, 12h


title: Ai20 Cells (Ai)

city: Seoul

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

country: South Korea

institute: East-West Medical Research Institute, Kyung Hee University

description: Gene expression data from LPS- and Ai20-treated human gingival fibroblast

hyb_protocol: Following labeling, each cDNA was hybridized for 17 hr at 45℃ at 60 rpm on Affymetrix HumanGene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0007.

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

data_processing: The quality control was estimated by confirming the order of the signal intensities of the Poly-A controls and Hybridization controls using Expression Console Software (Affymetrix, USA). The microarray data was analyzed using a GenPlex V3.0 (ISTECH, Korea). The data were analyzed with Robust Multichip Analysis (RMA) quantification method as a probe set summarization algorithm for log transformation with base 2 (log2) and Quantile normalization method as a normalization method in the Preprocessing module of GenPlex V3.0. The signal intensities of all genes (33,297 probes (28,869 genes) in a platform) were obtained from one chip of each experimental group.

label_protocol: Fragmented and biotinylated cDNA were prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual from 300 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual, Affymetrix).

growth_protocol: 5-passaged human gingival fibroblasts were cultured.

extract_protocol: The total RNA in the human gingival fibroblast of each group was extracted using an RNeasy Mini kit (QIAGEN, USA) according to the manufacturer’s instruction.

treatment_protocol: Human gingival fibroblasts were divided into four experimental groups: CTL (no treatment control), LPS (LPS treatment only), Ai20 (LPS and Ai20 extract treatments) and Ai40 (LPS and Ai40 extract treatments). The cells were stimulated with 1 µg/ml of LPS (from Escherichia coli serotype 0111:B4) in DMEM (low glucose and serum free) for 24 hr. The Ai extract (20 or 40 µg/ml) was treated at 1 hr before the LPS stimulation.

value: gingival fibroblast

tag: passage

value: passage 5

tag: developmental stage

value: Adult

value: LPS and 20 ug Ai


title: TamR E2 3h

description:
Gene expression in E2-stimulated TamR cells.
TamR.E2.03h

source_name: breast epithelial cell, adherent, E2, 3h


title: TamR E2+Tamoxifen 2h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR.E2_Tam.02h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 2h


title: TamR HRG 6h

description:
Gene expression in HRG-stimulated TamR cells.
TamR.HRG.06h

source_name: breast epithelial cell, adherent, HRG, 6h


title: TamR E2 1h

description:
Gene expression in E2-stimulated TamR cells.
TamR.E2.01h

source_name: breast epithelial cell, adherent, E2, 1h


title: TamR Control 24h

description:
Gene expression in unstimulated TamR cells.
TamR.Ctrl.24h

source_name: breast epithelial cell, adherent, without stimulus, 24h


title: Ej20 Cells

description: Gene expression data from LPS- and Ej20-treated human gingival fibroblast

treatment_protocol: Human gingival fibroblasts were divided into four experimental groups: CTL (no treatment control), LPS (LPS treatment only), Ej20 (LPS and Ej leaves' extract 20 µg/ml treatments) and Ej40 (LPS and Ej leaves' extract 40 µg/ml treatments). The cells were stimulated with 1 µg/ml of LPS (from Escherichia coli serotype 0111:B4) in DMEM (low glucose and serum free) for 24 hr. The Ej extract (20 or 40 µg/ml) was treated at 1 hr before the LPS stimulation.

value: LPS and 20 ug Ej


title: TamR Control 6h

description:
Gene expression in unstimulated TamR cells.
TamR.Ctrl.06h

source_name: breast epithelial cell, adherent, without stimulus, 6h

value: mammary gland, breast


title: TamR E2+Tamoxifen 48h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR.E2_Tam.48h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 48h

value: epithelial


title: TamR Control 2h

description:
Gene expression in unstimulated TamR cells.
TamR.Ctrl.02h

source_name: breast epithelial cell, adherent, without stimulus, 2h

value: adenocarcinoma


title: TamR Control 0h

description:
Gene expression in unstimulated TamR cells.
TamR.Ctrl.00h

source_name: breast epithelial cell, adherent, without stimulus

value: female


title: TamR Control 3h

description:
Gene expression in unstimulated TamR cells.
TamR.Ctrl.03h

source_name: breast epithelial cell, adherent, without stimulus, 3h

value: Caucasian


title: TamR Control 12h

description:
Gene expression in unstimulated TamR cells.
TamR.Ctrl.12h

source_name: breast epithelial cell, adherent, without stimulus, 12h

value: resistant


title: TamR Control 1h

description:
Gene expression in unstimulated TamR cells.
TamR.Ctrl.01h

source_name: breast epithelial cell, adherent, without stimulus, 1h


title: LV-T350A&si-EZH2-3

status: Public on Nov 02 2010

city: Minneapolis

first: Shuai

last: Chen

state: MN

address: MMC 806, 420 Delaware Street S.E.

department: Cancer Center

country: USA

institute: University of Minnesota

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

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

growth_protocol: BJ cells were grown in DMEM medium supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen Inc).

treatment_protocol: Cells were transducted by lentivirus for 72h, followed by si-RNA transfection for 60 h.

value: BJ

tag: transfection

value: si-EZH2 plus RNAi resistant lentivirus expressed T350A mutant


title: LV-EZH2&si-EZH2-3

description: replicate 3

value: si-EZH2 plus RNAi resistant lentivirus expressed EZH2


title: iPS_4A cells

city: Kobe

first: Shin

last: Kawamata

state: Hyogo

department: The Basic Reserch Group for Regenerative Medicine

institute: Foundation for Biomedical and Innovation

description: Gene expression data from cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45oC, 60 rpm on Gene Chip Human Genome U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: human iPS cells

label_protocol: Biotinylated cRNA were prepared using GeneChip 3’ IVT Express Kit according to manufacturer’s instructions from 250 ng total RNA.

growth_protocol: On SNL76/7 feeder cells in human embryonic stem cell medium (DMEM/F-12 containing 20% KSR, 2mM L-glutamine, 1% NEAA, 0.1 mM 2-ME, and 4 ng/mL bFGF

extract_protocol: Total RNA was extracted with the RNeasy Mini kit, according to manufacturer’s instructions.

treatment_protocol: hES and iPS cells with a cell scraper and break up the clonies, add 10mL human ES medium. Centrifuge at 170G for 5min and discard the supernatant and then wash the cell clump twice with PBS. After centrifuge, remove PBS completely.

value: human iPS cells


title: hES_03 cells

description: Gene expression data from cells

source_name: human ES cells

value: human ES cells


title: LV-EZH2&si-EZH2-1

description: replicate 1


title: LV-C&si-EZH2-3

description: replicate 3


title: LV-C&si-EZH2-2

description: replicate 2


title: LV-T350A&si-EZH2-2

description: replicate 2


title: LV-C&si-Control-3

description: replicate 3

value: si-Control


title: LV-C&si-EZH2-1

description: replicate 1


title: male rainbow trout gonads, 10 pooled rep 8

city: Moscow

first: Tim

last: Cavileer

state: ID

address: BioSci LSS 252

department: Biological Sciences

institute: Tim Cavileer

hyb_protocol: Hybridizations were performed according to standard Affymetrix protocols. Briefly, 5.5 μg of fragmented biotinylated second-cycle, first-strand cDNA were hybridized for 16 h at 45 °C with constant rotation (45 rpm). Microarrays were processed using the Affymetrix GeneChip Fluidic Station 450 (Affymetrix). Staining was carried out with streptavidin-conjugated phycoerythrin (SAPE) followed by an amplification with a biotinylated anti-streptavidin antibody and by a second round of SAPE before scanning using a GeneChip Scanner 3000-7G (Affymetrix).

scan_protocol: GeneChip Scanner 3000-7G (Affymetrix)

data_processing:
Scanned images were analyzed with Affymetrix GCOS v1.1 software. Data were analyzed using mas for background correction, invariantset for normalization, mas for perfect match/ mismatch correction and liwong method for summarization. Data assessment combined with measures of RNA quality before hybridization identified the female 550 degree-days microarray as potentially problematic, so further analysis was carried out with and without this time point.
Signal was calculated in R using Bioconductor packages as described by Harr and Schlotterer 2004. http://nar.oxfordjournals.org/content/34/2/e8.full-text-lowres.pdf

organism: Oncorhynchus mykiss

source_name: gonadal ridge, excised at 700 degree-days

label_protocol: The total RNA samples were labeled using Affymetrix’s GeneChip Whole Transcript Sense Target Labeling Assay kit according to manufacturer’s recommendations with the exception of eliminating the ribosomal RNA reduction and concentration steps and following the 100ng total RNA Labeling Protocol listed in appendix A.

growth_protocol: Fish were maintained in incubators containing flowing freshwater (10°C) at the Ooizumi Research Station, Yamanashi, Japan.

extract_protocol: Ten female or male transgenic rainbow trout were randomly selected every 5 days, beginning at 30 days (i.e., 300 degree days = incubation temperature in °C x number of days) post fertilization through until 70 days (i.e., 700 degree days) post fertilization. The gonads from each sex, at each sampling time, were pooled and immediately frozen for subsequent total RNA isolation. Total RNA was isolated from each gonad pool obtained from the 10 individuals sampled, for each sex, at each timepoint.

value: male

tag: degree days (incubation temperature in °c x number of days)

tag: tissue

value: gonadal ridge


title: male rainbow trout gonads, 10 pooled rep 6

source_name: gonadal ridge, excised at 600 degree-days


title: male rainbow trout gonads, 10 pooled rep 7

source_name: gonadal ridge, excised at 650 degree-days


title: male rainbow trout gonads, 10 pooled rep 5

source_name: gonadal ridge, excised at 500 degree-days


title: LV-EZH2&si-EZH2-2

description: replicate 2


title: male rainbow trout gonads, 10 pooled rep 3

source_name: gonadal ridge, excised at 400 degree-days


title: male rainbow trout gonads, 10 pooled rep 2

source_name: gonadal ridge, excised at 350 degree-days


title: TamR E2 2h

description:
Gene expression in E2-stimulated TamR cells.
TamR.E2.02h

source_name: breast epithelial cell, adherent, E2, 2h


title: female rainbow trout gonads, 10 pooled rep 8


title: male rainbow trout gonads, 10 pooled rep 4

source_name: gonadal ridge, excised at 450 degree-days


title: male rainbow trout gonads, 10 pooled rep 1

source_name: gonadal ridge, excised at 300 degree-days


title: female rainbow trout gonads, 10 pooled rep 7


title: CD34+ cells

description: Gene expression data from cells

source_name: CD34 positive cells from cord blood cells

growth_protocol: In hematopoietic medium (X-Vivo10 containing 50 ng/mL IL-6, 50 ng/mL soluble IL-6 R, 50 ng/mL SCF, 10 ng/mL TPO, and 20 ng/mL Flt3-ligand)


title: LV-C&si-Control-1

description: replicate 1


title: female rainbow trout gonads, 10 pooled rep 6


title: si-EZH2&T350Asr-2

description: Gene expression data from LNCaP cells transfected with si-EZH2&T350Asr for 60 h.

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).

data_processing: Normalized by dChip software.

source_name: LNCaP, si-EZH2&T350Asr

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen Inc.).

value: LNCaP

tag: drug treatment


title: LV-C&si-Control-2

description: replicate 2


title: TRIM5KD-rep1

city: Lausanne

first: Federico

last: Santoni

address: rue du Bugnon, 7

country: Switzerland

institute: CHUV

description: TRIM5 KD rep1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data were processed using the Bioconductor R package, lumi, default values fore background correction, variance stabilization and quantile normalization

source_name: THP1 cells

label_protocol: Illumina Total Prep RNA amplification kit

extract_protocol: RNA was extracted with Qiagen columns

treatment_protocol: THP1 cells transduced with a lentivius targeting Luciferase by RNAi and PMA differentiated

value: TRIM5 KD


title: LV-T350A&si-EZH2-1

description: replicate 1


title: TRIM5KD-rep3

description: TRIM5 KD rep3


title: LucKD-rep1

description: Luciferase KD rep1

value: Luciferase KD


title: LucKD-rep2

description: Luciferase KD rep2


title: TRIM5KD-rep2

description: TRIM5 KD rep2


title: TamR#5 Tamoxifen 0h

description:
Gene expression in Tamoxifen-stimulated TamR cells.
TamR5.Tam.00h

source_name: breast epithelial cell, adherent, Tamoxifen, 0h

value: mammary gland, breast

value: tamoxifen


title: female rainbow trout gonads, 10 pooled rep 4


title: WT HRG 12h rep1

description:
Gene expression in HRG-stimulated WT cells.
wt1.HRG.12h.r1

source_name: breast epithelial cell, adherent, HRG, 12h

value: epithelial

value: adenocarcinoma

value: sensitive

value: HRG


title: female rainbow trout gonads, 10 pooled rep 2

value: female


title: ATRX_ChIP_H300_Fibro

type: genomic

city: Oxford

first: Richard

middle: J

last: Gibbons

state: Oxon

address: John Radcliffe Hospital,

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

hyb_protocol: Hybridisation of labelled ChIP DNA onto Microarrays  1. Prepare in 2μl eppendorf tube the hybridisation DNA mixtures for precipitation as follows:  a. 160 μl Cy3 labelled DNA  b. 160 μl Cy labelled DNA  c. 135 μl Human Cot-1 DNA (Invitrogen 15279-011)  d. 55  μl 3M NaAc ph 5.2  e. 6 μl yeast tRNA (Invitrogen 15401-011)  f. 1000 μl  100% EtOH    2. Mix the tube gently, keep in dark and precipitate for 30 min – 1 h at –70^C  3. Pre heat hybridisation buffer in a 65^C heat block  Hybridisation buffer (50 ml): 20X SSC 5 ml      Deionised formamide 25 ml      100mM Tris-Hcl ph7.4 5 ml      Dextran sulphate 2.5 g      Tween 20 50 mcl      HPLC water 15 ml  4. Spin the precipitated DNA for 20 min at 14000 rpm at 4^C  5. Wash the pellet in EtOH 70% 500 mcl and spin 5 min at 14000 rpm at 4^C  6. Leave the pellet drying  7. Resuspend pellet in 120-150 μl of hybridisation buffer (dependant on chamber size) and leave dissolving on 65^C heat block for 1+ hour  8. When the pellet is fully dissolved denature for 10 min at 100^C in darkness  9. Snap freeze on ice, spin down and leave on ice until loading in the liquid station.

scan_protocol: Slides were scanned with a Perkin Elmer Scanarray scanner using scanarray express software.

data_processing: The Easy Quant (Perkin Elmer, Scan Array) analysis program with 'Adaptive circle' quantitation method with lowess normalization was used. log2 ChIP / Input ratios reported

molecule: genomic DNA

source_name: Cultured Primary Fibroblasts

label_protocol: Random Labelling DNA for array CGH    Equipment and reagents  • BioPrime Labelling Kit (Invitrogen 18094-011)  • 10X dNTP mix (Amersham 27-2035-01)  • 1mM Cy3-dCTP (Amersham PA53021)  • 1mM Cy5-dCTP (Amersham PA55021)  • HPLC water BDH 152736D  • Micro-spin G50 columns (Amersham, 275330-01)    Method  1. Random label 450 ng of DNA in a final reaction volume of 150 μl by mixing the DNA with 60 μl 2.5X Random Primers Solution (from BioPrime Labelling Kit) and make up to 130 μl with HPLC water. Make 1 reaction for ChIP DNA and 1 reaction for input DNA.  2. Denature DNA in a heat block for 10 min at 100°C, and immediately cool on ice.   3. The following reagents are added on ice:  15 μl  10X dNTP mix (so prepared: dNTPs Amersham 27-2035-01 4x25umol C 1μl , A 2 μl, G 2 μl , T 2 μl , HPLC water 93 μl)  1.5 μl Cy3 (for ChIP DNA) or Cy5 (for input DNA) labelled dCTP (1 mM) from Amersham PA53021 and PA55021  3 μl  Klenow Fragment from Biopreime Labelling Kit   Mix gently but thoroughly.   4. Incubate the reaction @ 37°C overnight in darkness and then stop it by adding 15 μl of stop buffer (from BioPrime Labelling kit).     Removal of Labelled Nucleotides from DNA Labelling Reactions   (The recommended volume for application to a single column is 50 μl, you therefore have to use 3 columns per 150 µl labelling reaction)    Column Preparation  1. Resuspend the resin in the columns by gentle vortexing.  2. Loosen the cap one-fourth turn and snap off the bottom closure.  3. Place the columns in a 1.5 ml screw-cap microcentrifuge tube for support. Alternatively, cut the cap from a flip-top tube and use this tube for support.  4. Pre-spin the columns for 1 minute at 2700 rpm. DO NOT pulse as this will override the variable speed setting. Wash columns applying 50 mcl of HPLC water to the resin and spin 1 min at 2700 rpm. Use columns immediately after preparation to avoid the resin drying out.    Sample Application  1. Place the columns in a new 1.5 ml tube and slowly apply 50 μl to the centre of the angled surface of the compacted resin bed of each of the columns, being careful not to disturb the resin bed. Careful application of the sample to the centre of the bed is essential for good separation. Do not allow any of the samples to flow around the sides of the bed.  2. Spin the columns for 2 minutes at 2700 rpm. The purified samples are collected in the bottom of the support tube.  3. Discard the columns and retain the flow-through samples.  4. Combine the three samples and run 5 μl on a 1% agarose gel

growth_protocol: RPMI medium with 10% Foetal Bovine Serum

extract_protocol: Protocol:  Chromatin Immunoprecipitation coupled with Microarray Analysis (ChIP-chIP):    I. Dynabead Preparation    -Make PBS/BSA   -For each ChIP reaction. Wash 100ul of beads 3-4 times with PBS BSA (5mg/ml)  -Transfer beads to a 500ul PCR tube.  -For ATRX antibody binding, Add 200ul ATRX H300, 22ul 50mg/ml BSA, 4ul ssDNA (Invitrogen 10mg/ml)  -For NoAb Rxn. Add 222ul PBS BSA 4ul ssDNA  -Incubate 3-4 hrs on roller at 4 oC  -Wash 4 times in PBS BSA  -Resuspend in 100ul PBSBSA and add 4ul (40ug) ssDNA      For each preclear reaction    -Take 100ul of Dynabeads  -Wash 3-4 times with 1ml PBS BSA (5mg/ml freshly prepared)  -Add 100ul of PBS BSA(5ug/ul)  -Add 4ul ssDNA (10ug/ul)  -Incubate at 4oC on roller with antibody binding reactions  -Use 100ul for each preclearing reaction  II. Cell cross-linking:     Need 4oC PBS, Formaldehyde, EGS 1M glycine, Trypan blue, gilsons, timer 1.5ml tubes, calculator,  A. Suspension Cells:    1. Make up EGS (Pierce 21565) stock fresh: 0.046g EGS in 200ul DMSO for 500mM stock  2. Chill PBS  3. Wash twice in PBS and resuspend in 20mls PBS (Important as FCS inhibits EGS)  4. Count cells  5. Use 3x107 – 5x107 cells for each ChIP reaction  6. Add EGS (it will form a white PPT which disperses afer a second) to 2mM and incubate at room temperature of 45 mins with occasional mixing. (80ul per 20mls of PBS).  7. Add formaldehyde solution to 1% for 20mins (526ul /20mls. 4 x 131.5ul)  8. Add 1/8 volume of 1M glycine to tubes to quench formaldehyde.(2.5ml glycine / 20ml PBS).  9. Spin cells at 1k for 5 min at 4oC. Make up protease inhibitors and add to lysis buffers.  10.Wash twice with 20ml 4oC PBS    III. Cell sonication (keep all steps on ice):  Note: Add protease inhibitors to all lysis buffers before use. If using a protease inhibitor cocktail tablet from Complete, dissolve one tablet in 2 ml water for 25X solution. Store aliquots at -20oC.    1. Resuspend each tube of cells in 10 ml of lysis buffer I. Rock at 4oC for 10 min, and then spin at 2k in a table-top centrifuge for 2 min at 4oC.   2. Resuspend each tube of cells in 5-10 ml of lysis buffer 2. Pellet nuclei in table-top centrifuge by spinning at 2.5k for 2 min at 4oC.  3. Resuspend the pellet in each tube in 3 ml lysis buffer 3. (Retain the buffer for step 6)  4. Sonicate the suspension in 15ml corning blue top tubes. 2mls per tube. Use the Bioruptor at high power for 20mins (4x5mins). After each 5 minute pulse, replenish the ice.  5. Add 1/10 volume of 10% Triton X-100. Transfer to 1.5 ml centrifuge tubes. Spin out debris at 14k for 10 min at 4oC. The lysate contains the fragmented DNA.  6. Save pellet for western analysis and take 50ul lysate for western analysis  7. Transfer lysate to 15 ml conical tube, adjusting the volume to 3 ml using lysis buffer 3.  8. Save 50µl of cell lysate from each sample as input. Save 50ul to assess sonication efficiency.    IV. Chromatin immunoprecipitation:   -Add 100ul of the preclearing beads from step I to the 3mls of chromatin lysate  -Preclear on roller at 4 oC for 1 hour  -Precipitate beads from chromatin using magnet and remove chromatin to new 3ml tubes  -Add the washed antibody bound beads from step 1  -Incubate overnight on roller at 4 oC    V. Washing, eluting, and reverse cross-linking:  Note: Carry steps 1-3 in the cold room and all wash solution must be ice cold.  1. Transfer lysates from the 3 ml tubes to a 1.5ml tube.  2. Wash the IPs 5 times with 1 ml wash buffer (be sure to add protease inhibitors to the wash buffer). Use the magnetic stand to precipitate the beads.   3. Wash once with 1 ml cold PBS. Aspirate residual PBS.  4. Add 250µl of elution buffer. Elute on a roller at room temperature for 15 minutes.  5. Add 250ul more of elution buffer to beads, vortex, precipitate and combine with previous round of elution.  6. Take 50ul of eluate for western blot analysis  7. PPT beads and remove eluate to a new tube. Add 20ul 5M NaCl and incubate at 65oC for 4 hours.  Thaw input, make up to 500ul with elution buffer, add 20ul 5M NaCl and incubate for 4hrs at 65oC.      VI. RNase, Proteinase K, Phenol/Chloroform, EtOH PPT:  Remove beads. Then add 20ul of 1M Tris pH6.5, 10ul 0.5M EDTA, 2ul 10mg/mg Proteinase K. Incubate for 1hrs at 45°C.    Phenol chloroform and EtOH PPT with 20ug of carrier glycogen. Resuspend in 21ul sigma water. Use low volume to give the option of labelling for ChIP on Chip. For real time PCR, use 1/12 ul per reaction    Solutions    PBS BSA 5mg/ml  For 50mls: 5mls 10XPBS, 250mg BSA Fraction V, Filter sterilise. Make up fresh every time.    Lysis Buffer 1 (100 ml):        100mM HEPES  140mM NaCl  1mM EDTA  10% Glycerol  0.5% NP40  0.25% Triton X    Lysis Buffer 2 (100 ml):   200mM NaCl  1mM EDTA  0.5mM EGTA  10mM Tris pH 8    Lysis Buffer 3 (100 ml):   1mM EDTA  0.5mM EGTA  1mMTris-HCl pH8  100mM NaCl  0.1% Na DOC  0.5% N-lauroyl Sarcosine    Wash buffer (RIPA Buffer, 100 ml):   50mM Hepes, pH 7.6  1mM EDTA  0.7% Na DOC  1% NP40  500mM LiCl

value: Cultured Primary Fibroblasts

tag: antibody

value: ATRX H300 (Santa Cruz Biotechnology, batch G0105)


title: female rainbow trout gonads, 10 pooled rep 5


title: female rainbow trout gonads, 10 pooled rep 1


title: ATRX_ChIP_H300_Hep3b

source_name: Heb3b cell line

value: Heb3b cell line


title: si-EZH2&T350Asr-1

scan_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).

treatment_protocol: LNCaP cells transfected with si-EZH2&T350Asr for 60 h.

tag: cell line


title: si-EZH2&EZH2sr-1

description: Gene expression data from LNCaP cells transfected with si-EZH2&EZH2sr for 60 h.

source_name: LNCaP, si-EZH2&EZH2sr

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).


title: FigS4-H300d

source_name: Cultured Primary Human Erythroblasts

growth_protocol: Basic Protocol 1: Preparation of Peripheral Blood Mononuclear Cells for Erythroid Cultures    Cultures can be initiated with cells derived from a whole unit of blood obtained from normal donors (or polycythemic patients undergoing phlebotomy). The starting material, i.e., the “buffy-coat” fraction, is readily available, since it is routinely separated and discarded by the blood bank during preparation of packed red blood cells (RBC) and platelet-rich plasma. Anemic patients commonly show high frequencies of erythroid progenitors; cultures from anemic patients (e.g., thalassemia, sickle cell anemia) are usually initiated with cells derived from ~20 ml peripheral blood.   Materials        *        Peripheral blood or buffy coat fraction      *        Phosphate-buffered saline (PBS), pH 7.4 (appendix 2A)      *        Ficoll-Hypaque (density = 1.077 g/ml)        *        15- or 50-ml centrifuge tubes      *        Centrifuge       1.     Dilute peripheral blood or the buffy coat fraction 1:1 (v/v) with PBS. Gently layer on top of a layer of Ficoll-Hypaque such that the Ficoll-Hypaque layer constitutes one-third of the total volume.    Depending on the blood volume, use either 15- or 50-ml tubes.    For convenience, tubes (available from Sigma) containing a special grid that separates the blood from the Ficoll can be used.   2.     Centrifuge 20 min at 400 × g, at room temperature. Do not apply the brake.   3.     Aspirate off the top layer (consisting of plasma and platelets), collect the interphase layer of mononuclear cells with a pipet, and transfer to a 50-ml tube.   4.     Add 40 ml PBS, mix, then centrifuge 5 min at 160 × g, room temperature. Aspirate the supernatant, then resuspend the pellet in the residual buffer by tapping.   5.     Add 40 ml PBS, mix, then centrifuge 5 min at 100 × g, room temperature, and aspirate the supernatant. Repeat this procedure for an additional wash.    Use low-speed centrifugation in order to remove residual platelets.    All procedures should be performed at room temperature. If the blood cannot be processed on the same day, leave overnight at room temperature.    In experiments where Hb content is measured, special care has to be taken to avoid contamination by mature RBC that originated from the processed blood. This does not usually present a problem when normal blood is processed, but may occur with blood derived from patients, e.g., with thalassemia. The contaminating RBCs can be of patient origin and/or derived from transfused blood. In both cases, they may interfere with measurement of the Hb produced in vitro. When the interphase layer is heavily contaminated with RBC, the latter cells should be removed by osmotic hemolysis (see Support Protocol 6) prior to culturing. When only slightly contaminated, the mononuclear cells may be cultured without hemolysis; RBC tend to lyse and disappear during culture. Alternatively, they may be removed by Percoll separation at the second phase of the culture (see Support Protocol 7).  [Top of Page]     Basic Protocol 2: Erythroid Cell Culture Procedure    The culture procedure is divided into two phases. The first is an EPO-independent phase in which peripheral blood mononuclear cells are isolated (described in Basic Protocol 1) and cultured in the presence of a combination of growth factors, but in the absence of EPO. During this phase, early erythroid-committed progenitors, called burst-forming units erythroid (BFUe), proliferate and differentiate into colony-forming unit erythroid (CFUe)–like progenitors. In the second phase, these cells, cultured in an EPO-supplemented medium, continue to proliferate and mature into orthochromatic normoblasts and enucleated erythrocytes.   Materials        *        Complete MEM medium (see recipe)      *        Preselected FBS (see recipe); do not heat-inactivate      *        50 mg/ml cyclosporin A (Sandoz)      *        Conditioned medium from 5637 human bladder carcinoma cell line (see recipe)      *        Mononuclear cells, washed (see Basic Protocol 1)      *        10% (w/v) deionized BSA (see recipe)      *        2-mercaptoethanol (Sigma)      *        4 mg/ml dexamethasone sodium phosphate (Elkin-Sinn Pharmaceuticals, Cherry Hill N.J.)      *        Human holo-transferrin (Sigma)      *        Human recombinant stem cell factor (CytoLab Ltd.; http://www.cytolab.com/)      *        Human recombinant erythropoietin (EPO; Ortho Pharmaceutical)        *        25- or 75-cm2 tissue culture flasks       1.     Prepare Phase I medium by adding the following ingredients to complete MEM medium:        *        10% (v/v) preselected FBS (not heat-inactivated)      *        1 µg/ml cyclosporin A (add from 50 mg/ml stock)      *        10% (v/v) conditioned medium from 5637 human bladder carcinoma cell line.     2a.     For cells obtained from peripheral blood (10 to 20 ml): Plate the washed mononuclear cells in Phase I medium in 25-cm2 flasks at a culture volume equivalent to the original volume of blood.   2b.     In the case of cells obtained from a whole blood unit (400 to 500 ml): Plate the washed mononuclear cells in Phase I medium in two 75-cm2 flasks at a culture volume of 80 to 100 ml.   3.     Incubate the cultures at 37°C in a humidified, 5% CO2 incubator for 5 to 7 days.    Full humidification is achieved by leaving a tray with water standing at the bottom of the incubator.   4.     After the 5- to 7-day incubation in phase I, shake the cultures and harvest the nonadherent cells (do not trypsinize).   5.     Centrifuge the cells 5 min at 160 × g, room temperature, and aspirate the supernatant. Fill the tube with complete MEM, centrifuge 5 min at 160 × g, room temperature, and aspirate the supernatant. Repeat for a second wash.   6.     Prepare Phase II medium by adding the following ingredients to complete MEM medium:        *        30% (v/v) preselected FBS (not heat-inactivated)      *        1% (w/v) deionized BSA (add from 10% w/v stock)      *        10–5 M 2-mercaptoethanol      *        10–6 dexamethasone (add from 4 mg/ml stock)      *        0.3 mg/ml human holo-transferrin      *        10 ng/ml human recombinant stem cell factor      *        1 U/ml human erythropoietin (EPO).     7.     Plate cells in the original volume of phase II medium (as in step 2a or 2b according to the original blood volume) and incubate up to 14 days at 37°C in a humidified, 5% CO2, incubator.

value: Cultured Primary Human Erythroblasts


title: TamR E2+Tamoxifen 6h

description:
Gene expression in E2+Tamoxifen-stimulated TamR cells.
TamR.E2_Tam.06h

source_name: breast epithelial cell, adherent, E2+Tamoxifen, 6h

tag: tissue origination

value: Caucasian

value: resistant

value: E2, tamoxifen


title: figS4_H300a

tag: cell type


title: si-EZH2-2

description: Gene expression data from LNCaP cells transfected with si-EZH2 for 60 h.

source_name: LNCaP, si-EZH2

value: LNCaP


title: si-Control-2

description: Gene expression data from LNCaP cells transfected with control si-RNA for 60 h.

source_name: LNCaP, si-Control

value: si-Control


title: ATRX_29-1-7_rep1


title: FigS4_H300b

data_processing: The Easy Quant (Perkin Elmer, Scan Array) analysis program with 'Adaptive circle' quantitation method with lowess normalization was used. log2 ChIP / Input ratios reported in data table.


title: si-EZH2&EZH2sr-2

treatment_protocol: LNCaP cells transfected with si-EZH2&EZH2sr for 60 h.


title: si-Control-1

treatment_protocol: LNCaP cells transfected with control si-RNA for 60 h.


title: si-EZH2-1

treatment_protocol: LNCaP cells transfected with si-EZH2 for 60 h.


title: Roscovitine-1

description: Gene expression data from LNCaP cells treated with 10 uM Roscovitine for 24 h.

source_name: LNCaP, Roscovitine

value: Roscovitine


title: Roscovitine-2

treatment_protocol: LNCaP cells treated with 10 uM Roscovitine for 24 h.


title: TSA-2

description: Gene expression data from LNCaP cells treated with 5 uM TSA for 24 h.

source_name: LNCaP, TSA

value: TSA


title: female rainbow trout gonads, 10 pooled rep 3

source_name: gonadal ridge, excised at 400 degree-days

value: gonadal ridge


title: TSA-1

treatment_protocol: LNCaP cells treated with 5 uM TSA for 24 h.


title: DMSO-2

description: Gene expression data from LNCaP cells treated with 0.1% DMSO for 24 h.

source_name: LNCaP, DMSO

value: DMSO


title: DMSO-1

treatment_protocol: LNCaP cells treated with 0.1% DMSO for 24 h.


title: skeletal muscle Crhr2-/- replicate2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: A pool of skeletal muscle RNA from 2 Crhr2-/- mice

hyb_protocol: Standard Affymetrix hybridization protocol employed by the UCSD Medical Center core facility

scan_protocol: Hybridized arrays were scanned using equipment in the UCSD Medical Center core facility

data_processing: Probe intensity was sumarized and normalized using Affymetrix Microarray Analysis Suite 5.1. The trimmed mean target intensity of each array was set to 200.

organism: Mus musculus

source_name: Gastrocnemius and Soleus muscles

label_protocol: Standard Affymetrix biotin labeling protocol employed by the UCSD Medical Center core facility

growth_protocol: All animals were fed with mice chow diet and water ad libitum.

extract_protocol: Total RNA from 4 KO and 4 WT animals was extracted using Tri-reagent according to the manufactorer's recommendations. RNA was analyzed by electrophoresis on agarose gel.  The 4 KO and 4 WT samples were combined into 2 KO and 2 WT pools. 100µg were cleaned using QiageneRNA purification kit and analyzed by gel electrophoresis.

treatment_protocol: Skeletal muscle tissue was taken at basal conditions without  prior treatment.

value: male

tag: genetic background

value: 6.5 months

tag: genotype

value: Gastrocnemius and Soleus muscles


title: CTRL-R4_VN_4037

city: Louisville

last: Lamont

state: KY

address: 570 South Preston Street

department: Oral Biology

institute: University of Louisville

description: Gene expression data from human trophoblasts mock inected negative controls

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 scanner

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: CTRL

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HTR8 Cells grown in RPMI 1640 medium (Sigma-Aldrich, St Louis, MO) supplemented with 5% fetal bovine serum at 37°C in 5% CO2.

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

treatment_protocol: Cells were exposed to Porphyromonas gingivalis resuspended in RPMI media at a MOI of 200:1 or mock infected for 2 hours and lysed with Trizol reagent for RNA extraction

value: Cultured trophoblast cell monolayers


title: skeletal muscle Crhr2+/+ replicate1

description: A pool of skeletal muscle RNA from 2 Crhr2+/+ mice

tag: gender

tag: age


title: SC versus nOEC, replicate 2

city: Amsterdam

first: Kasper

middle: Cornelis Dammes

last: Roet

address: Meibergdreef 47

department: Neuroregeneration

country: Netherlands

institute: Netherlands Institute for Neuroscience

description: Biological replicate 2 of 3. Acutely dissected OEC versus cultured SC.

hyb_protocol: For the microarray experiment, a factorial design was used consisting of direct comparisons between the three cell types (Glonek and Solomon, 2004 (PMID 14744830). Three biological replicates were used for each cell type. These three biological replicates encompassed three RNA samples prepared from independent OEC or SC cultures or three independent pools of ONLs. Each comparison thus comprised three microarrays including one dye swap pair. Agilent Rat 60-mer Oligo Microarrays (G4130A, Agilent Technologies) interrogating 20,493 genes were used. Hybridization of arrays was performed according to the manufacturer’s guidelines and using Agilent solutions and buffers. In brief, target solution was prepared containing Cy3- and Cy5-labeled cRNA (500 ng of each) and control targets. cRNA was hydrolyzed for 30 min at 60C. Probes were hybridized in hybridization solution for 17 h at 60C in a hybridization rotator. Arrays were washed in wash solution 1 (63 SSPE, 0.005% N-Lauroylsarcosine) for 5 min, followed by wash solution 2 (0.063 SSPE, 0.005% N-Lauroylsarcosine) for exactly 1 min. Arrays were transferred to acetonitrile for 1 min and then dried quickly under pressurized nitrogen gas.

scan_protocol: Microarrays were scanned with the Agilent microarray scanner G2565AA.

data_processing: Red and green intensity data were acquired using Feature Extraction software V7.5.1 (Agilent). Analysis of the microarray data was performed in R (http://www.rproject. org) (Ihaka and Gentleman, 1996). Feature extraction data were imported into Bioconductor using the limma package. Intra-array normalization was performed using the loess algorithm. Signiﬁcant genes were determined by ﬁtting a linear model to the normalized ratios and determining the contrast between OEG and native OEG, or OEG and SC. Uncorrected P-values were corrected for multiple testing using the Benjamini-Hochberg correction algorithm. Genes with a Pvalue smaller than 0.001 were considered significant.

organism: Rattus norvegicus

source_name: cultured Schwann cells

label_protocol: From the total RNA samples, mRNA was labeled with Cy3-CTP and Cy5-CTP using the Agilent Low RNA Input Fluorescent Linear Amplification kit (5184-3523) according to the manufacturer’s guidelines using 500 ng RNA from each sample. In short, cDNA was synthesized using a T7 promoter primer and the reverse transcriptase MMLV-RT. cRNA is synthesized using T7 RNA polymerase. During this reaction, cRNA is labeled by the incorporation of Cy3-CTP or Cy5-CTP.

growth_protocol: cOEC were harvested after 3.5 weeks in culture (Rubio et al., 2008). cSCs were harvested at 2 weeks after dissociation of the sciatic nerve explants. Cultures were harvested by trypsinization and resuspended in RNeasy lysis buffer (buffer RLT). Olfactory bulbs from adult Fischer rats were dissected and cut into 400 lm thick sagittal sections using a tissue chopper (McIlwain). ONLs were manually dissected from the sections under a dissection microscope using a scalpel and homogenized in buffer RLT.

extract_protocol: Total RNA was isolated from the cultures and from the ONLs using the RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol. RNA was quantified by photospectrometry and the quality was determined on an Agilent 2100 Bioanalyzer (Agilent Technologies). Each RNA sample was obtained from one culture prepared from a pool of four rats, or from a pool of ONLs dissected from four rats.

treatment_protocol: Not applicable.

tag: strain

value: Fischer F344

tag: tissue origin

value: sciatic nerve

value: cultured primary Schwann cells

tag: culture time (after dissociation)

value: 2 weeks

tag: weight of animal

value: adult

value: female

tag: biological replicate

source_name: OEC from ONL

value: olfactory nerve layer

value: acutely dissected primary olfactory ensheathing cells

value: direct


title: cOEC versus nOEC, replicate 1

description: Biological replicate 1 of 3. Cultured OEC versus acutely dissected OEC.

source_name: cultured OEC

value: cultured primary olfactory ensheathing cells

value: 3.5 weeks

tag: developmental stage


title: Pg-R4_VN_4036

description: Gene expression data from human trophoblasts in response to Porphyromonas gingivalis

source_name: pg infected


title: SC versus nOEC, replicate 3

description: Biological replicate 3 of 3. Acutely dissected OEC versus cultured SC.


title: cOEC versus nOEC, replicate 2

description: Biological replicate 2 of 3. Cultured OEC versus acutely dissected OEC.


title: CTRL-R3_VN_4029


title: CTRL-R2_VN_4035


title: skeletal muscle Crhr2+/+ replicate2


title: SC versus nOEC, replicate 1

description: Biological replicate 1 of 3. Acutely dissected OEC versus cultured SC.


title: Pg-R3_VN_4028


title: Pg-R2_VN_4027


title: CTRL-R1_VN_4034


title: Pg-R1_VN_4026


title: cOEC versus SC, replicate 2

description: Biological replicate 2 of 3. Cultured OEC versus cultured SC.


title: cOEC versus SC, replicate 1

description: Biological replicate 1 of 3. Cultured OEC versus cultured SC.


title: cOEC versus SC, replicate 3

description: Biological replicate 3 of 3. Cultured OEC versus cultured SC.


title: ShamLiv48h1

status: Public on Nov 01 2010

city: New York

first: Bisen

last: Ding

state: NY

address: 1300 York Avenue

institute: Cornell Medical College

hyb_protocol: Fragmented cRNA was hybridized to the gene chips, washed, and stained with streptavidin phycoerythrin.

scan_protocol: The probe arrays were scanned with the Genechip System confocal scanner.

data_processing: Affymetrix Microarray suite 4.0 (GCOS ver 1.4) was used to analyze the data

label: Biotin

source_name: liver, 48 hours after sham operation

label_protocol: The Superscript choice kit (Invitrogen, Carlsbad, CA) was used to make cDNA with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. The biotin labeled cRNA was made by in vitro transcription (Enzo Diagnostics).

extract_protocol: The protocol used to extract RNA was according to Manufacturers specifications QIAGEN Rneasy kit.

value: mature liver


title: ShamLiv48h2


title: PHLiv48h2

source_name: liver, 48 hours after partial hepatectomy


title: PHLiv48h1


title: cOEC versus nOEC, replicate 3

description: Biological replicate 3 of 3. Cultured OEC versus acutely dissected OEC.


title: skeletal muscle Crhr2-/- replicate1


title: female reference pool_250kNsp 4

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

institute: Radboud University Nijmegen Medical Centre

description: pool of 10 female individuals

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix scanner 3000.

data_processing: copy number detection using CNAG2.0 software (http://www.genome.umin.jp/)

source_name: Blood from control patients

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix), or from

extract_protocol: QiaAmp purification kit (Qiagen)

tag: reference

value: control sample


title: female reference pool_250kNsp 1

description: pool of 10 female individuals


title: female reference pool_250kNsp 3

description: pool of 10 female individuals


title: male reference pool_250kNsp 4

description: pool of 10 male individuals


title: male reference pool_250kNsp 2

description: pool of 10 male individuals


title: CRC patiënt 31

description: germline DNA from suspected familial microsatellite-stable CRC

source_name: Blood from patients with early-onset colorectal cancer

tag: age at diagnosis

tag: # fisrt degree rel.

tag: tumor location

value: Cecum


title: CRC patiënt 20

value: Rectum


title: CRC patiënt 26


title: female reference pool_250kNsp 2

description: pool of 10 female individuals


title: male reference pool_250kNsp 3

description: pool of 10 male individuals


title: CRC patiënt 32


title: CRC patiënt 25


title: CRC patiënt 35


title: CRC patiënt 17


title: CRC patiënt 15


title: CRC patiënt 19

value: Sigmoid colon


title: CRC patiënt 30

value: Transverse colon


title: CRC patiënt 27


title: CRC patiënt 33


title: CRC patiënt 14


title: CRC patiënt 18

value: Ascending colon


title: CRC patiënt 34


title: CRC patiënt 23


title: male reference pool_250kNsp 1

description: pool of 10 male individuals


title: intestine_rep1

status: Public on Oct 27 2010

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

institute: Okayama University

description: Gene exression in intestine

hyb_protocol: A set of fluorescently labeled cRNA targets (5 µg for each sample) was employed in a hybridization reaction. Hybridization and washing were performed using GE Hybridization Kit and GE Wash Pack (Agilent Technologies). The protocols were according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000B DNA Microarray Scanner (Axon Instruments, Foster City, CA) using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with GenePix Pro4.0 microarray analysis software (Axon Instruments).

organism: Ciona intestinalis

source_name: intestine, replicate 1

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared using the Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Ciona intestinalis were obtained from the National BioResource Project in Japan (Department of Zoology, Kyoto University).

extract_protocol: Total RNA was extracted and purified using RNAeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Each organs from single individual were dissected and dissolved into Trizol (invitrogen).

tag: tissue

value: intestine


title: CRC patiënt 24


title: intestine_rep2

description: Gene exression in intestine

source_name: intestine, replicate 2


title: kidney_iUB_AngII_vs_Media_Sample1

city: new orleans

first: renfang

last: song

state: LA

address: 1430 tulane ave

institute: tulane university

description: AngII vs Media, Sample 1

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Data analysis was performed in R (versions 2.9-2.10).   Independently developed quality-control scripts were used to identify array artifacts and normalize for spatial variation.  Loess and intensity quantile normalization routines from the Bioconductor limma package were applied to adjust for dye bias and variation among arrays, respectively.  A linear model was then fit to the normalized data using the “lmFit” function in the limma package to estimate the average log2 ratios and associated standard errors for each probe.

source_name: AngII treatment

label_protocol: 300ng of total RNA were primed with 1 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Intact Ubs were put in Matrix gel on the top of insert surface, cultured with DMEM/F12 media with 10% FBS with 100ng/ml GDNF and 100ng/ml HGF

extract_protocol: total RNA was extracted with Rnaeasy kit from Qiagen following manufacture's instructions.

treatment_protocol: intact ubs treated with AngII(10-5M) vs. Media for 6 hours

value: kidney intact ureteric buds

source_name: Media treatment

treatment_protocol: intact ubs treated with Media for 6 hours (control)


title: kidney_iUB_AngII_vs_Media_Sample2

description: Biological replicate 2 of 2

treatment_protocol: intact ubs treated with AngII(10-5M) for 6 hours


title: Ai40 Cells (Ai)

status: Public on Oct 23 2010

description: Gene expression data from LPS- and Ai40-treated human gingival fibroblast

treatment_protocol: Human gingival fibroblasts were divided into four experimental groups: CTL (no treatment control), LPS (LPS treatment only), Ai20 (LPS and Ai20 extract treatments) and Ai40 (LPS and Ai40 extract treatments). The cells were stimulated with 1 µg/ml of LPS (from Escherichia coli serotype 0111:B4) in DMEM (low glucose and serum free) for 24 hr. The Ai extract (20 or 40 µg/ml) was treated at 1 hr before the LPS stimulation.

value: gingival fibroblast

tag: passage

value: passage 5

value: Adult

tag: treatment

value: LPS and 40 ug Ai


title: kidney_iUB_Media_vs_AngII_Sample1

description: Dye Swap Replicate for Sample 1


title: CRC patiënt 29


title: LPS Cells (Ai)

description: Gene expression data from LPS-stimulated human gingival fibroblast

source_name: LPS-treated human gingival fibroblast

tag: cell type

value: LPS


title: intestine_rep3

description: Gene exression in intestine

source_name: intestine, replicate 3


title: CRC patiënt 13


title: Ej40 Cells

description: Gene expression data from LPS- and Ej40-treated human gingival fibroblast

treatment_protocol: Human gingival fibroblasts were divided into four experimental groups: CTL (no treatment control), LPS (LPS treatment only), Ej20 (LPS and Ej leaves' extract 20 µg/ml treatments) and Ej40 (LPS and Ej leaves' extract 40 µg/ml treatments). The cells were stimulated with 1 µg/ml of LPS (from Escherichia coli serotype 0111:B4) in DMEM (low glucose and serum free) for 24 hr. The Ej extract (20 or 40 µg/ml) was treated at 1 hr before the LPS stimulation.

value: LPS and 40 ug Ej


title: CRC patiënt 16


title: LPS Cells


title: Control Cells (Ai)

description: Gene expression data from normal human gingival fibroblast

source_name: Control human gingival fibroblast

value: Control


title: CRC patiënt 12

value: Colon


title: Control Cells


title: wild-type_1.0mM_ZnSO4_30min_1

status: Public on Apr 13 2010

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

description: wild-type strain grown on a synthetic medium, 30 min time point after addition of 1.0 mM ZnSO4

hyb_protocol: 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401a520105F GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50°C in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 20 micro g of herring sperm DNA (Promega), 0.1 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The expression levels were summarized by one-step Tukey’s biweight algorithm and normalized by global scaling method using GeneChip Operating Software, version 1.4 (Affymetrix, Santa Clara, CA). The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Thermus thermophilus HB8

source_name: T. thermophilus HB8, wild-type, synthetic medium, 8.5 hrs, 30 min time point after addition of 1.0 mM ZnSO4

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 1.2 units of DNase I (GE Healthcare Bio-Science Corp.) at 37°C for 10 min, and after inactivation at 98°C for 10 min, the cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturerâ€™s instructions (Affymetrix).

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.39).  A 1.0 mM (final) of ZnSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of ZnSO4.  The synthetic medium was made by the same way as described in this section of GSM296605.

extract_protocol: Cells were collected from 200 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: genotype

value: wild-type

tag: agent

tag: time

value: 30 min


title: wild-type_1.0mM_ZnSO4_30min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.43).  A 1.0 mM (final) of ZnSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of ZnSO4.  The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_1.0mM_ZnSO4_30min_3

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.52).  A 1.0 mM (final) of ZnSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of ZnSO4.  The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_1.0mM_ZnSO4_0min_3

description: wild-type strain grown on a synthetic medium, non-addition of ZnSO4

source_name: T. thermophilus HB8, wild-type, synthetic medium, 8 hrs

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.52).  The synthetic medium was made by the same way as described in this section of GSM296605.

extract_protocol: Cells were collected from 50 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

value: control (non-addition of ZnSO4)

value: 0 min


title: wild-type_1.0mM_ZnSO4_0min_2

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.43).  The synthetic medium was made by the same way as described in this section of GSM296605.


title: Tumor_6497

status: Public on Jun 10 2010

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

data_processing:
The data were normalized using quantile normalization with BASE.

The .idat file is not available for this Sample.

source_name: Human breast tumor

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

tag: disease state

value: Human breast tumor


title: (-)csoR_1.25mM_CuSO4_30min_2

description: csoR deficient strain grown on a synthetic medium, 30 min time point after addition of 1.25 mM CuSO4

data_processing: The expression levels were summarized by one-step Tukey’s biweight algorithm using GeneChip Operating Software, version 1.4 (Affymetrix, Santa Clara, CA).

source_name: T. thermophilus HB8, csoR deficient strain, synthetic midium, 8.5 hrs, 30 min time point after addition of 1.25 mM CuSO4

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 1.2 units of DNase I (GE Healthcare Bio-Science Corp.) at 37°C for 10 min, and after inactivation at 98°C for 10 min, the cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturers instructions (Affymetrix).

growth_protocol:
T. thermophilus HB8 csoR deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.44).
A 1.25 mM (final) of CuSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of CuSO4.
The synthetic medium was made by the same way as described in this section of GSM296605.

tag: strain

value: T. thermophilus HB8 csoR deficient

value: addition of 1.25 mM CuSO4


title: CRC patiënt 39

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from two times 250 ng genomic DNA (Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from two times 250 ng genomic DNA ((Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix) using an Affymetrix scanner 3000.

data_processing: Genotyping information obtained using Affymetrix Genotyping Concole software (v2.1)

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from two times 250 ng genomic DNA (Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix).

value: Rectum


title: Tumor_6611


title: (-)csoR_1.25mM_CuSO4_30min_1

growth_protocol:
T. thermophilus HB8 csoR deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.40).
A 1.25 mM (final) of CuSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of CuSO4.
The synthetic medium was made by the same way as described in this section of GSM296605.


title: kidney_iUB_Media_vs_AngII_Sample2

description: Dye swap replicate of Sample 2

value: kidney intact ureteric buds


title: CRC patiënt 9


title: (-)csoR_1.25mM_CuSO4_0min_3

description: csoR deficient strain grown on a synthetic medium, non-addition of CuSO4

source_name: T. thermophilus HB8, (-)csoR strain, synthetic midium, 8 hrs

growth_protocol:
T. thermophilus HB8 csoR deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.53).
The synthetic medium was made by the same way as described in this section of GSM296605.

value: non-addition of CuSO4


title: (-)csoR_1.25mM_CuSO4_0min_1

growth_protocol:
T. thermophilus HB8 csoR deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.40).
The synthetic medium was made by the same way as described in this section of GSM296605.


title: CRC patiënt 11

value: Liver metastasis from CRC


title: (-)csoR_1.25mM_CuSO4_0min_2

growth_protocol:
T. thermophilus HB8 csoR deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.44).
The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_1.0mM_ZnSO4_0min_1

growth_protocol: T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.39).  The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_1.25mM_CuSO4_30min_2

description: wild-type strain grown on a synthetic medium, 30 min time point after addition of 1.25 mM CuSO4

source_name: T. thermophilus HB8, wild-type, synthetic midium, 8.5 hrs, 30 min time point after addition of 1.25 mM CuSO4

growth_protocol:
T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.54).
A 1.25 mM (final) of CuSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of CuSO4.
The synthetic medium was made by the same way as described in this section of GSM296605.

value: wild-type T. thermophilus HB8


title: wild-type_1.25mM_CuSO4_30min_1

growth_protocol:
T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.44).
A 1.25 mM (final) of CuSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of CuSO4.
The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_1.25mM_CuSO4_30min_3

growth_protocol:
T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.48).
A 1.25 mM (final) of CuSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of CuSO4.
The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_1.25mM_CuSO4_0min_3

description: wild-type strain grown on a synthetic medium, non-addition of CuSO4

source_name: T. thermophilus HB8, wild-type, synthetic midium, 8 hrs

growth_protocol:
T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.48).
The synthetic medium was made by the same way as described in this section of GSM296605.


title: wild-type_1.25mM_CuSO4_0min_2

growth_protocol:
T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.54).
The synthetic medium was made by the same way as described in this section of GSM296605.


title: CRC patiënt 4


title: wild-type_1.25mM_CuSO4_0min_1

growth_protocol:
T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.44).
The synthetic medium was made by the same way as described in this section of GSM296605.


title: CL01 cell line RNA polymerase II

status: Public on Jul 06 2010

city: Omaha

first: Himabindu

last: Ramachandrareddy

state: NE

address: 600 South 42nd st

department: Pathology and microbiology

institute: University of Nebraska Medical Center

description: ChIP-chip CL01 RNA polII

hyb_protocol: The labeled ChIP DNA was precipitated and hybridized to the custom arrays by Roche-Nimblegen according to the manufacturers instructions (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: The arrays were scanned using a MS200 Microarray Scanner by Roche-Nimblegen as per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Data processing from the scanned images was performed by Roche-Nimblegen using NimbleScan software (http://www.nimblegen.com/products/lit/lit.html).

source_name: RNA polymerase II ChIP DNA from CL01 cell line

label_protocol: 1µg each of control Input and experimental ChIP DNA were labelled by Roche-Nimblegen using Cy3-random heptamer and Cy5-random heptamer, respectively, according to manufacturer's protocols. (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: cells were grown in RPMI1640 medium with 10%FBS, 1mM L-Glutamine and Penicillin and Streptomycin

extract_protocol: For analysis of Histone modifications, native ChIP without formaldehyde crosslinking was performed followed by micrococcal nuclease digestion of the chromatin to obtain mononucleosomes. Briefly, 20x106 cells were lysed with the buffer (Tris-HCl pH7.6-50mM, CaCl2-1mM, TritonX-100-0.2%, Sodium Butyrate-5mM, PMSF-0.5mM, Protease Inhibitor cocktail (Sigma-Aldrich, St. Louis, MO, USA)-20ul) on ice and digested with micrococcal nuclease 1Unit (Sigma-Aldrich, St. Louis, MO, USA) in the same buffer at 37°C for 6min. The reaction was stopped by addition of Tris-HCl pH7.6 and EDTA to a final concentration of 10mM and 5mM respectively. The cell lysate was then sonicated (Intensity -3, Pulse on-20”, Pulse off- 2’, Number of pulses-6) using Fisher F550 Sonic dismembrator. The chromatin was then dialyzed into RIPA buffer (10mM Tris pH7.6, 1mMEDTA, 0.1%SDS, 0.1% Sodium deoxycholate, 1% TritonX-100) for 2hours at 4°C and proceeded to the immuno precipitation after saving 10% of the dialysate as input. For analysis of PolII binding, 100x106 cells were cross-linked with formaldehyde (1% final concentration) for 10min and then quenched with Glycine (0.125M final concentration).  The cells were washed with ice cold PBS and lysed using 5ml of the lysate buffer (1%SDS, EDTA-10mM, Tris HCl pH8.1-50mM, PMSF-1mM) on ice for 10 min. Chromatin was solubilized by performing sonication (Intensity-5, Pulse on-30”, Pulse off-1’, Number of pulses- 15) to break down the DNA to a size ranging from 200-400bp. The chromatin was then dialyzed overnight into RIPA buffer at 4°C. Chromatin equivalent to 20x106 cells was used for one ChIP experiment and 10% of it was saved as input. Chromatin immunoprecipitation was performed overnight at 4°C using specific antibody (4ug) bound protein A Dynabeads (Dynal Biotech, Oslo, Norway). The antibody- chromatin complexes were washed with RIPA buffer, High salt RIPA buffer (10mM Tris pH7.6, 1mMEDTA, 0.1%SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 300mM NaCl), Lithium chloride buffer (0.25M LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate), TE+0.2% TritonX-100 and TE buffer. The DNA was eluted by incubation of the beads at 65°C in the presence of SDS and simultaneous proteinase K (Roche diagnostics) digestion. The ChIP DNA was validated for enrichment by real time quantitative-PCR amplification (primer sequences shown in the supplementary data) and the enriched input and ChIP DNA samples were later amplified.The ChIP DNA was amplified by using the LMPCR technique as described previously (Oberley et al., Methods Enzymol 376:316, 2004) with a few modifications. The ChIP DNA obtained was repaired using the DNA End Repair Kit (Epicentre Biotechnologies). dATP was added to the 3’ ends of ChIP DNA by incubating with dATP and Taq DNA polymerase (New England Biolabs) at 70°C for 30 min. The ChIP DNA was then ligated to unidirectional adaptors. The sequences of the oligonucleotides used as adaptors are as follows: Adaptor 3a-forward 5’- TCGGTAACGACTCACTTGGGTTCCT-3’ and Reverse 5’- GGAACCCAAGTG-3’, Adaptor 3b-forward 5’-TGGCAATTCCCTCACTAAAGGGCT-3’ and Reverse-5’-GCCCTTTAGTGA. The adaptors were annealed and ligated to the ChIP DNA by incubating ChIP DNA with the adaptors in excess at 16°C overnight using T4 DNA ligase (New England Biolabs). The ChIP DNA was then amplified by PCR using the following protocol: 1 cycle of 55°C 2 min, 72°C 5 min, 95°C 2 min; 30-35 rounds of amplification at 95°C 0.5 min, 55°C 0.5 min and 72°C 1 min; and final extension at 72°C for 4 min. The resulting LMPCR-amplified ChIP DNA was then purified using PCR purification kit (Qiagen) and validated for enrichment by real-time PCR to verify that the enrichment ratios are retained. The ChIP DNA was then hybridized to a custom oligonucleotide chip (NimbleGen Systems, Madison, WI).

value: Burkitt lymphoma cell line reverted back to a phenotype similar to naive B cells

tag: chip antibody

value: RNA PolII

tag: cell line

source_name: Input DNA from CL01 cell line

value: None, Input DNA


title: CRC patiënt 10

source_name: Blood from patients with early-onset colorectal cancer


title: CRC patiënt 6

value: Transverse colon


title: adult_mouse_testis_crem_ChIP_2

status: Public on Oct 13 2010

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

hyb_protocol: Standard protocol by Agilent Co. Ltd.

scan_protocol: Standard protocol by Agilent Co. Ltd.

data_processing: The data were normalized by R 2.10.1 with the command "normalizeWithinArrays method="loess" in library 'limma'.

label_protocol: Standard protocol by Agilent Co. Ltd.

extract_protocol: Protocol for ChIP was modified from Nagamori I et al. (Nagamori, Yomogida et al. 2006). Briefly, germ cells from 5 adult mouse testes were fixed in 5ml of 1% formaldehyde medium for 10 min at 37℃. The fixed germ cells were washed 2 times with PBS, resuspended in PBS and sonicated (power 40%, pulser 60%, ON 60s, OFF 60s, 5 cycles by Ruptor 250, Omni, USA). 200 μl of supernatant were diluted in 1800μl ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA，16.7 mM Tris-HCl，pH 8.1，167 mM NaCl and 1 mM PMSF). Diluted complexes were immune-precipitated by antibody against CREM (sc-440, Santa Cruz) and antibody against goat IgG (negative control) at 4℃ overnight. The immune complexes were precipitated with protein G followed by washes with low salt buffer, high salt buffer, LiCl buffer and TE. The complexes were eluted with elution buffer and cross-linking of DNA and protein was reverted in 5 M NaCl at 65℃ overnight. The solution was digested with proteinase K and the DNA were purified by PheOH/CHCl3 extractions and EtOH precipitations.

tag: antibody

value: goat IgG

tag: gender

value: Male

tag: age

value: adult

value: CREM

tag: antibody catalog

tag: antibody vendor

value: Santa Cruz


title: (-)csoR_1.25mM_CuSO4_30min_3

growth_protocol:
T. thermophilus HB8 csoR deficient strain was pre-cultured at 70°C for 16 h in 3 ml of TT broth. The cells (1 ml) were inoculated into 250 ml of the synthetic medium and then cultivated at 70°C for 8 h (OD600nm = ~ 0.53).
A 1.25 mM (final) of CuSO4 was added into medium and the cultivation was continued. The cells were collected at 30 min time point after addition of CuSO4.
The synthetic medium was made by the same way as described in this section of GSM296605.


title: CRC patiënt 2

tag: age at diagnosis

tag: # fisrt degree rel.

tag: tumor location


title: CRC patiënt 8


title: SUDHL16 cell line RNA polymerase II

description: ChIP-chip SUDHL16 RNA PolII

source_name: RNA polymerase II ChIP DNA from SUDHL16 cell line

value: Diffuse large B cell lymphoma cell line

source_name: Input DNA from SUDHL16 cell line


title: CRC patiënt 7

value: Sigmoid colon


title: Colorectal carcinoma CRC11 [MCIp]

status: Public on Mar 31 2010

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

description: Comparative MCIp-on-Chip for colorectal carcinoma and normal human colon

hyb_protocol: Comparative MCIp hybridizations on CpG island oligonucleotide microarrays (Agilent) were performed using the recommended, stringent protocol (Agilent).

scan_protocol: Scanned on an Agilent scanner at 5 µm resolution. Images were analysed and data extracted using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Linear normalized, background subtracted VALUE data were obtained from log10 transformed, processed Red signal/processed Green signal values derived from image analysis with Agilent Feature Extraction Software (version 9.5.1).  Processed signal intensities were further normalized using GC-dependent regression and imported into Microsoft Office Excel 2007 for further analysis.

label: Alexa Fluor 5–dCTP

source_name: colorectal carcinoma

label_protocol: Enriched methylated DNA fragments of the high-salt MCIp fractions were labeled with Alexa Fluor 5–dCTP (cancer cells) and Alexa Fluor 3–dCTP (normal cells) using the BioPrime Total Genomic Labeling System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

growth_protocol: Colorectal cancer samples were collected from 10 patients who underwent colon resection for biopsy-proven invasive colorectal adenocarcinoma at the University of Regensburg. The study was performed in agreement with the Institutional ethical review board of the University of Regensburg (05/003). DNA from frozen colon tissues was isolated using the PUREGENE™ DNA Purification Kit (Gentra, Minneapolis, USA) according to the supplier’s recommendation. Three normal colon DNAs (male, age 50-63) were purchased from BioChain Institute Inc. (Hayward, CA)

extract_protocol: MCIp enrichment of methylated DNA was performed essentially as described (Gebhard et al. 2006, Cancer Research). In brief, genomic DNA was sonicated to a mean fragment size of 350-400 bp. Two µg of each sample were incubated with 150 µl Protein A-Sepharose 4 Fast Flow beads (GE Healthcare) coated with 60 µg purified MBD-Fc protein in 2 ml Ultrafree-MC centrifugal filter devices (Amicon/Millipore) for 3 h at 4°C in buffer containing 300 mM NaCl. Beads were centrifuged to recover unbound DNA fragments (300 mM fraction) and subsequently washed with buffers containing increasing NaCl concentrations (400, 500, 550 mM). Densely CpG-methylated DNA was eluted with a high-salt buffer (1000 mM NaCl) and all fractions were desalted using the MinElute PCR purification kit (Qiagen). The separation of CpG methylation densities of individual MCIp fractions was controlled by qPCR using primers covering the imprinted SNRPN

value: male

tag: tissue

value: colorectal carcinoma tumor

value: Rectal cancer

tag: protocol

value: MCIp enrichment

label: Alexa Fluor 3–dCTP

source_name: normal colon

tag: sample

value: normal colon; mixture of three samples (age 50-63)

value: colon

value: normal


title: CRC patiënt 1

value: Rectosigmoid colon


title: Colorectal carcinoma CRC09 [MCIp]

value: female


title: CRC patiënt 3


title: Colorectal carcinoma CRC04 [MCIp]


title: Colorectal carcinoma CRC07 [MCIp]

value: Colon cancer


title: Colorectal carcinoma CRC05 [MCIp]


title: Colorectal carcinoma CRC03 [MCIp]


title: Colorectal carcinoma CRC10 [MCIp]


title: adult_mouse_testis_crem_ChIP_1

value: goat IgG


title: Colorectal carcinoma CRC06 [MCIp]


title: Colorectal carcinoma CRC02 [MCIp]

value: Sigma cancer


title: Colorectal carcinoma CRC01 [MCIp]


title: fibroblast 1 input, methyl-depleted [JDM]

status: Public on Oct 20 2010

city: Baltimore

first: Akiko

last: Doi

state: MD

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

description:
DNA methylation data from fibroblasts (input channel)
DNA methylation data from fibroblasts (methyl-depleted channel)

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

source_name: Input fraction from JDM

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

growth_protocol: Fibroblasts were grown in alpha-MEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine.

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

tag: cell type

value: fibroblast

value: GM02416 from Coriell

source_name: Methyl-depleted fraction from JDM


title: iPS 1 input, methyl-depleted [JDM.iPS10]

description:
DNA methylation data from iPS cells (input channel)
DNA methylation data from iPS cells (methyl-depleted channel)

source_name: Input fraction from JDM-iPS10

growth_protocol: iPS cells were cultured in hES medium (80% DMEM/F12, 20% KO Serum Replacement,10 ng/ml bFGF, 1 mM L-glutamine, 100 M nonessential amino acids, 100 M 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin).

value: iPS cells derived from JDM

source_name: Methyl-depleted fraction from JDM-iPS10


title: iPS 2 input, methyl-depleted [ADA-iPS3]

source_name: Input fraction from ADA-iPS3

value: iPS cells derived from ADA

value: GM01390 from Coriell

source_name: Methyl-depleted fraction from ADA-iPS3


title: Tumor_13nsp

status: Public on Mar 18 2010

city: Providence

first: Graham

middle: M

last: Poage

state: RI

address: 70 Ship St

institute: Brown University

description:
Tumor ID 109
Hybridized to 250K_Nsp.

hyb_protocol: As per manufacturer (Affymetrix).

scan_protocol: As per manufacturer (Affymetrix).

data_processing:
Data were collected at the Harvard Partners Microarray Core Facility. Inferred copy number states of each SNP were extracted and converted from .CEL files into signal intensities using GCOS and Affymetrix Copy Number Analysis Tool (CNAT) v4.0.1. We utilized the HMM-based algorithm with defaults for tuning parameters, Gaussian smoothing, transition decay, and median scaling.

The 'GSE20939_tumor_copy_number.txt' file, which is linked to the Series GSE20939 record as a supplementary file, contains the (blood-adjusted) tumor copy number calls used in our final analyses.

source_name: head and neck tumor_13

label_protocol: As per manufacturer (Affymetrix).

growth_protocol: Fresh-frozen human tissue.

extract_protocol: Qiagen Qiamp DNA extraction kit.

treatment_protocol: None.

value: head and neck squamous cell carcinoma

tag: tumor site

value: oral

tag: tumor id


title: Tumor_19nsp

description:
Tumor ID 108
Hybridized to 250K_Nsp.

source_name: head and neck tumor_19


title: Tumor_17nsp

description:
Tumor ID 115
Hybridized to 250K_Nsp.

source_name: head and neck tumor_17


title: Tumor_14nsp

description:
Tumor ID 104
Hybridized to 250K_Nsp.

source_name: head and neck tumor_14

value: larynx


title: Tumor_15nsp

description:
Tumor ID 110
Hybridized to 250K_Nsp.

source_name: head and neck tumor_15

value: pharynx


title: Tumor_16nsp

description:
Tumor ID 103
Hybridized to 250K_Nsp.

source_name: head and neck tumor_16


title: Tumor_18nsp

description:
Tumor ID 105
Hybridized to 250K_Nsp.

source_name: head and neck tumor_18


title: Tumor_11nsp

description:
Tumor ID 116
Hybridized to 250K_Nsp.

source_name: head and neck tumor_11


title: Tumor_12nsp

description:
Tumor ID 102
Hybridized to 250K_Nsp.

source_name: head and neck tumor_12


title: Tumor_10nsp

description:
Tumor ID 118
Hybridized to 250K_Nsp.

source_name: head and neck tumor_10


title: Tumor_9nsp

description:
Tumor ID 106
Hybridized to 250K_Nsp.

source_name: head and neck tumor_9


title: Tumor_7nsp

description:
Tumor ID 114
Hybridized to 250K_Nsp.

source_name: head and neck tumor_7


title: Tumor_19

status: Public on Mar 11 2010

description: Tumor ID 108

hyb_protocol: Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.

data_processing: Illumina BeadStudio Methylation software was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level: beta =(max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. Detection P-values determined poor performing samples (n=2) and CpG loci (n=8), which were removed from analysis. X chromosome loci were also removed, leaving 1413 CpG loci associated with 773 genes. Raw average beta values were used and not subjected to normalization as per manufacturer's recommendations

source_name: head&neck Tumor_19

label_protocol: sodium bisulfite modified using the EZ DNA Methylation Kit (Zymo Research, Orange, CA).

extract_protocol: DNA from fresh frozen tissue was isolated with QIAamp DNA mini kit (Qiagen, Valencia, CA)

tag: state

value: methylated

value: unmethylated


title: Tumor_18

description: Tumor ID 105

scan_protocol: Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.

source_name: head&neck Tumor_18


title: Tumor_17

description: Tumor ID 115

source_name: head&neck Tumor_17


title: Tumor_6nsp

description:
Tumor ID 107
Hybridized to 250K_Nsp.

source_name: head and neck tumor_6


title: Tumor_8nsp

description:
Tumor ID 119
Hybridized to 250K_Nsp.

source_name: head and neck tumor_8


title: Tumor_4nsp

description:
Tumor ID 111
Hybridized to 250K_Nsp.

source_name: head and neck tumor_4


title: Tumor_14

description: Tumor ID 104

source_name: head&neck Tumor_14


title: Tumor_15sty

description:
Tumor ID 110
Hybridized to 250K_Sty.


title: Tumor_13

description: Tumor ID 109

source_name: head&neck Tumor_13


title: Tumor_3nsp

description:
Tumor ID 117
Hybridized to 250K_Nsp.

source_name: head and neck tumor_3


title: Tumor_12

description: Tumor ID 102

source_name: head&neck Tumor_12


title: Tumor_16sty

description:
Tumor ID 103
Hybridized to 250K_Sty.

source_name: head and neck tumor_16


title: Tumor_11sty

description:
Tumor ID 116
Hybridized to 250K_Sty.


title: Tumor_10

description: Tumor ID 118

source_name: head&neck Tumor_10


title: Tumor_7

description: Tumor ID 114

source_name: head&neck Tumor_7


title: Tumor_8

description: Tumor ID 119

source_name: head&neck Tumor_8


title: Tumor_9

description: Tumor ID 106

source_name: head&neck Tumor_9


title: Tumor_17sty

description:
Tumor ID 115
Hybridized to 250K_Sty.

source_name: head and neck tumor_17


title: Tumor_6

description: Tumor ID 107

source_name: head&neck Tumor_6


title: Tumor_14sty

description:
Tumor ID 104
Hybridized to 250K_Sty.

source_name: head and neck tumor_14


title: Tumor_11

description: Tumor ID 116

source_name: head&neck Tumor_11


title: Tumor_2nsp

description:
Tumor ID 113
Hybridized to 250K_Nsp.

source_name: head and neck tumor_2


title: Tumor_18sty

description:
Tumor ID 105
Hybridized to 250K_Sty.

source_name: head and neck tumor_18


title: Tumor_4

description: Tumor ID 111

source_name: head&neck Tumor_4


title: Tumor_5

description: Tumor ID 112

source_name: head&neck Tumor_5


title: Tumor_3

description: Tumor ID 117

source_name: head&neck Tumor_3


title: Tumor_9sty

description:
Tumor ID 106
Hybridized to 250K_Sty.

source_name: head and neck tumor_9


title: Tumor_7sty

description:
Tumor ID 114
Hybridized to 250K_Sty.

source_name: head and neck tumor_7


title: Tumor_15

description: Tumor ID 110

source_name: head&neck Tumor_15


title: Tumor_8sty

description:
Tumor ID 119
Hybridized to 250K_Sty.

source_name: head and neck tumor_8


title: Tumor_2

description: Tumor ID 113

source_name: head&neck Tumor_2


title: Tumor_5sty

description:
Tumor ID 112
Hybridized to 250K_Sty.

source_name: head and neck tumor_5


title: Tumor_1

description: Tumor ID 101

source_name: head&neck Tumor_1


title: Tumor_13sty

description:
Tumor ID 109
Hybridized to 250K_Sty.

source_name: head and neck tumor_13


title: Tumor_1nsp

description:
Tumor ID 101
Hybridized to 250K_Nsp.

source_name: head and neck tumor_1


title: Tumor_10sty

description:
Tumor ID 118
Hybridized to 250K_Sty.

source_name: head and neck tumor_10


title: Tumor_6sty

description:
Tumor ID 107
Hybridized to 250K_Sty.

source_name: head and neck tumor_6


title: Tumor_19sty

description:
Hybridized to 250K_Sty.
Tumor ID 108

source_name: head and neck tumor_19


title: Tumor_16

description: Tumor ID 103

source_name: head&neck Tumor_16


title: Tumor_2sty

description:
Tumor ID 113
Hybridized to 250K_Sty.

source_name: head and neck tumor_2


title: HF-18996 15212_Hind

status: Public on Feb 18 2010

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description:
Dissociation protocol: Mechanical
Enrichment protocol: FACS

hyb_protocol: Affymetrix 100K protocol

scan_protocol: Affymetrix 100K protocol

data_processing: Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization.  Ninety normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=100k) and analyzed at the same time.  One CEL file for each set (Xba and Hind) with the median signal intensity across the set was selected as the reference array.   The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows.  For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set.  The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.

source_name: Pancreatic Adenocarcinoma Tissue

label_protocol: Affymetrix 100K protocol

extract_protocol: Qiagen DNA extraction kit was used according to the manufacturer's instructions

tag: Somatic


title: Tumor_5nsp

description:
Tumor ID 112
Hybridized to 250K_Nsp.


title: Tumor_4sty

description:
Tumor ID 111
Hybridized to 250K_Sty.

source_name: head and neck tumor_4


title: HF-19000 15226_Hind

tag: Tumor


title: HF-17241 16442_Hind


title: HF-16345 15228_Hind


title: HF-18996 15222_Hind


title: HF-18411 15230_Hind


title: HF-18411 15218_Hind


title: HF-18998 15224_Hind


title: HF-16345 15216_Hind


title: HF-18998 15214_Hind


title: HF-17267 16452_Hind


title: HF-17203 16448_Hind


title: HF-17241 16450_Hind


title: HF-17267 16458_Hind

tag: Nonsorted


title: HF-17241 16456_Hind


title: HF-17203 16454_Hind


title: HF-18998 15215_Xba


title: HF-18996 15213_Xba


title: HF-16345 15217_Xba


title: Tumor_12sty

description:
Tumor ID 102
Hybridized to 250K_Sty.

source_name: head and neck tumor_12


title: HF-16980 15210_Hind


title: HF-18411 15219_Xba


title: Tumor_3sty

description:
Tumor ID 117
Hybridized to 250K_Sty.

source_name: head and neck tumor_3


title: HF-18996 15223_Xba


title: HF-16345 15229_Xba


title: HF-16980 15211_Xba


title: HF-17241 16443_Xba


title: HF-19000 15227_Xba


title: HF-17203 16449_Xba


title: FAK transfected rat soleus muscle 436, unloaded + 5 days reloaded

status: Public on Dec 31 2009

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

institute: University of Berne

description: CMV-driven FAK expression construct was electro-transferred into a soleus muscle of an anesthetized rat. 2 days after transfection, the soleus muscles were unloaded for 7 days by hindlimb suspension. Subsequent reloading was provoked by allowing the animals to return to normal cage activity for 5 days. The muscle was isolated, snap frozen and total RNA extracted

hyb_protocol: ATLAS ARRAY-BD Clontech 16h at 68degC in ExpressHyb, Washing: 4x in (2xSSC, 1% SDS) at68degC for 1h. 1x in (0.1xSSC, 0.5% SDS) at68degC for ? h, 1x in (2x SSC) atroom temperature for 5min

scan_protocol: Phosphoimager screen, 4-10 days

data_processing: raw data

label: reverse transcription of 3 microgram total RNA with gene specific primers at 50degC using Superscript II RT (Invitrogen)

source_name: Martin Flueck, Institute of Anatomy, University of Berne

label_protocol: alpha-32P]dATP, and modified dCTP (Ambion (Europe)

extract_protocol: Modified RNeasy mini kit (Qiagen)

value: soleus muscle

value: 3 month

tag: gender

tag: strain

value: Wistar


title: HF-18998 15225_Xba


title: HF-16980 15221_Xba


title: HF-17241 16457_Xba


title: HF-17203 16447_Xba


title: HF-18411 15231_Xba


title: HF-17267 16445_Xba


title: empty transfected rat soleus muscle 436, unloaded + 5 days reloaded

description: CMV-driven empty expression construct was electro-transferred into a soleus muscle of an anesthetized rat. 2 days after transfection, the soleus muscles were unloaded for 7 days by hindlimb suspension. Subsequent reloading was provoked by allowing the animals to return to normal cage activity for 5 days. The muscle was isolated, snap frozen and total RNA extracted

tag: age

value: female


title: FAK transfected rat soleus muscle 435, unloaded + 5 days reloaded


title: empty transfected rat soleus muscle 435, unloaded + 5 days reloaded


title: HF-17241 16451_Xba


title: FAK transfected rat soleus muscle 434, unloaded + 5 days reloaded


title: FAK transfected rat soleus muscle 426, unloaded + 5 days reloaded


title: empty transfected rat soleus muscle 424, unloaded + 5 days reloaded


title: empty transfected rat soleus muscle 425, unloaded + 5 days reloaded


title: empty transfected rat soleus muscle 434, unloaded + 5 days reloaded