title: COLON APCmin/+/VP16LXRa 7

description:
COLON APCmin/+/VP16LXRa 7
replicate 1

source_name: Intestinal (colon) Tumor

value: Intestinal (colon) Tumor


title: COLON APCmin/+/VP16LXRa 8

status: Public on Feb 05 2013

type: RNA

city: Santa Maria Imbaro

first: Antonio

last: Moschetta

address: Via Nazionale 8A

country: Italy

institute: University of Bari & Consorzio Mario Negri Sud

description:
COLON APCmin/+/VP16LXRa 8
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with Illumina Genome Studio Software; items with detection p values >0.001 or AVG Signal <100 in both groups were excluded.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina® TotalPrepTM RNA  Amplification Kit

extract_protocol: RNA was extracted with QIAzol reagent, following manufacturer's instructions. Quality control was performed with Biorad Experion.

tag: strain

value: C57BL/6J-FVBN Mixed Strain

tag: age

value: 8 months

tag: tissue

tag: genotype/variation


title: Liver HF replicate 11

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.5.1.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: liver tissue, high fat diet

label_protocol: 1 µg of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al., (Anal Biochem 2007;363:315-7).

extract_protocol: Total RNA was isolated from liver tissue using TRIzol reagent according to the manufacturer’s instruction, followed by purification with RNeasy Mini columns (Qiagen), quantified using Nanodrop (IsoGen Life Science) and qualified using Experion Automated Electrophoresis System (BioRad).

treatment_protocol: All mice started with a three week adaptation phase, in which they were fed a mild-high-fat diet (30 en% fat). Twelve mice were sacrificed immediately after the adaptation phase (t=0). The other 24 mice received the same mild-high-fat diet without (HF) or with supplementation of 0.33% (w/w) quercetin (HF-Q) for 12 weeks. Animals were fasted for minimal 2 hr prior anaestetization and sacrification.

tag: treatment

value: high fat diet

tag: gender

value: male

tag: development stage

value: adult

value: liver

source_name: liver, reference pool of all samples


title: BDK_donor15 (array B)

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

country: Japan

institute: Hyogo College of Medicine

description: bulge–derived keratinocytes

hyb_protocol: hybridization buffer : 50% formamide-6 x SSC-0.2% SDS-5 x denhardt’s-0.2 mg/ml denatured salmon sperm, hybridization : at 70°C for 16 h, washing : three times with 2× SSC, 0.2% SDS at 65°C for 10 min, and rinsed once with 0.05 × SSC at room temperature

scan_protocol: Scanned on an Affymetrix 428 Array Scanner Images were quantified using ImaGene version 6.0  (Biodiscovery Inc., CA, USA)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Probes with poor-quality signals (S/N <1.2) and having null data at the frequency of more than 35% in all samples were filtered out using the microarray data analysis software, Expressionist (GeneData AG, Basel, Switzerland).

organism: Homo sapiens

source_name: donor 15

label_protocol: 4 µg of total RNA were labeled with Cy3 or Cy5 monoreactive dyes (Amersham, Buckinghamshire, UK) using RNA Transcript SureLABEL™ Core Kit (TaKaRa Bio) according to the manufacture’s instructions

growth_protocol: cultured in Defined Keratinocyte-SFM medium （DK-SFM, GIBCO/Invitrogen Co., CA） at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol: Total RNA extracted using Trizol (Invitrogen, CA) and purified using RNeasy kit (QIAGEN, Hilden, Germany) following manufacturer's instructions

treatment_protocol: third or fourth passaged cells in log phase cultures

tag: disease

value: atopic dermatitis

source_name: Reference RNA

tag: sample type

value: a mixture of NHEK total RNA and Universal Human Reference RNA (Stratagene Corporation, CA, USA)


title: ILEUM APCmin/+/VP16 (CTRL) 1

description:
ILEUM APCmin/+/VP16 (CTRL) 1
replicate 1

source_name: Intestinal (ileal) Tumor

value: Intestinal (ileal) Tumor

value: APCmin/+/VP16 (control)


title: BDK_donor14 (array B)

description: bulge–derived keratinocytes

source_name: donor 14

value: female


title: BDK_donor13 (array B)

description: bulge–derived keratinocytes

source_name: donor 13


title: Liver HF replicate 10


title: BDK_donor12 (array B)

description: bulge–derived keratinocytes

source_name: donor 12


title: BDK_donor11 (array B)

description: bulge–derived keratinocytes

source_name: donor 11


title: D0_1

type: genomic

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

country: USA

institute: Albert Einstein College of Medicine

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing:
Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background.PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.)
ratio_matrix.txt: normalized log2 (HpaII/MspI) ratio

molecule: genomic DNA

source_name: CD34+ early stem/hematopoietic cell culture on day 0

label_protocol: Random 9-mers pre-labeled with either Cy5 or Cy3

growth_protocol: CD34+ early stem/hematopoietic cells were purified from growth factor mobilized peripheral blood of healthy donors purchased from All Cells Inc. Purified stem/progenitor cells were cultured in media containing 15% fetal calf serum, 15% human serum Iscove¡¯s modified Dulbecco¡¯s medium (IMDM), 10 ng/ml IL-3, 2 U/ml EPO and 50 ng/ml SCF. During the initial 7 days of culture cells were fed on days 3 and 6 by adding equal volume of fresh culture media supplemented with growth factors. However, no new IL-3 was added after the initial addition on day 0 and the amount of SCF added to the fresh media was gradually decreased at each feeding (day 3, 25 ng/ml; day 6, 10 ng/ml; day 8, 2 ng/ml). The amount of EPO added was 2 U/ml during each feeding. On day 7 of culture cells were flow cytometry sorted for CD71 positive (transferrin receptor) cells using a MoFlo high-speed flow cytometer. The purity of the population isolated by this method was 98-99%. Sorted cells were cultured in the same media as before with EPO and SCF except the concentration of SCF was reduced to 2 ng/ml. Cells were fed one more time on day 10 of culture by adding equal volume of fresh media with only EPO (2 U/ml) during this final feeding. Cells were collected for DNA and RNA isolation on days 0, 3, 7, 10, 13 and 16 days of culture.

extract_protocol: Genomic DNA from neutrophils isolated from peripheral blood via Ficoll-gradient density separation was prepared using Qiagen reagents.

tag: cell type

value: CD34+ early stem/hematopoietic cell

tag: restriction enzyme

value: MspI representation of genomic DNA

value: HpaII representation of genomic DNA


title: Liver HF replicate 09


title: BDK_donor10 (array B)

description: bulge–derived keratinocytes

source_name: donor 10


title: COLON APCmin/+/VP16LXRa 5

description:
COLON APCmin/+/VP16LXRa 5
replicate 1


title: COLON APCmin/+/VP16LXRa 6

description:
COLON APCmin/+/VP16LXRa 6
replicate 1


title: COLON APCmin/+/VP16 (CTRL) 3

description:
COLON APCmin/+/VP16 (CTRL) 3
replicate 1


title: COLON APCmin/+/VP16 (CTRL) 2

description:
COLON APCmin/+/VP16 (CTRL) 2
replicate 1


title: Liver HF replicate 07


title: BDK_donor8 (array B)

description: bulge–derived keratinocytes

source_name: donor 8


title: Liver HF replicate 06


title: BDK_donor9 (array B)

description: bulge–derived keratinocytes

source_name: donor 9


title: XENO AdVP16hLXRa (LXRa) 12

description:
XENO AdVP16hLXRa (LXRa) 12
replicate 1
human HT29 cells grown in Nu/Nu mice infected with LXRa (VP16hLXRa) Adenovirus

source_name: Xenograft Tumors (human HT29 cells) grown in Nu/Nu Athymic Female Mice

tag: cell type (human)

value: Xenograft Tumors (HT29 cells)

tag: strain (mouse)

value: Nu/Nu

tag: age (mouse)

value: 4 months

tag: infection (mouse)

value: LXRa (VP16hLXRa) Adenovirus


title: XENO AdVP16hLXRa (LXRa) 10

description:
XENO AdVP16hLXRa (LXRa) 10
replicate 1
human HT29 cells grown in Nu/Nu mice infected with LXRa (VP16hLXRa) Adenovirus


title: NHEK_6 (array A)

description: neonatal human epidermal keratinocytes

source_name: Cascade Biologics HEKn　Cat No: C-001-5C，Lot No: 5C0579


title: XENO AdVP16hLXRa (LXRa) 11

description:
XENO AdVP16hLXRa (LXRa) 11
replicate 1
human HT29 cells grown in Nu/Nu mice infected with LXRa (VP16hLXRa) Adenovirus


title: BDK_donor7 (array B)

description: bulge–derived keratinocytes

source_name: donor 7

value: non-atopic control


title: Liver HF replicate 05

value: high fat diet


title: NHEK_5 (array A)

description: neonatal human epidermal keratinocytes

source_name: Cascade Biologics HEKn　Cat No: C-001-5C，Lot No: 3C1272

value: male


title: NHEK_4 (array A)

description: neonatal human epidermal keratinocytes

source_name: Cascade Biologics HEKn　Cat No: C-001-5C，Lot No: 5C0571


title: COLON APCmin/+/VP16 (CTRL) 4

description:
COLON APCmin/+/VP16 (CTRL) 4
replicate 1

source_name: Intestinal (colon) Tumor

value: C57BL/6J-FVBN Mixed Strain

value: 8 months

value: Intestinal (colon) Tumor


title: Liver HF replicate 03

source_name: liver tissue, high fat diet

value: adult

value: liver

source_name: liver, reference pool of all samples


title: Liver HF replicate 08


title: XENO AdVP16hLXRa (LXRa) 9

description:
XENO AdVP16hLXRa (LXRa) 9
replicate 1
human HT29 cells grown in Nu/Nu mice infected with LXRa (VP16hLXRa) Adenovirus


title: XENO AdVP16hLXRa (LXRa) 8

description:
XENO AdVP16hLXRa (LXRa) 8
replicate 1
human HT29 cells grown in Nu/Nu mice infected with LXRa (VP16hLXRa) Adenovirus


title: Liver HF replicate 04


title: BDK_donor6 (array B)

description: bulge–derived keratinocytes

source_name: donor 6

source_name: Reference RNA

value: a mixture of NHEK total RNA and Universal Human Reference RNA (Stratagene Corporation, CA, USA)


title: XENO AdVP16hLXRa (LXRa) 7

description:
XENO AdVP16hLXRa (LXRa) 7
replicate 1
human HT29 cells grown in Nu/Nu mice infected with LXRa (VP16hLXRa) Adenovirus


title: NHEK_3 (array A)

description: neonatal human epidermal keratinocytes

source_name: Cambrex；NHEK-Neo　Cat No: CC2503，Lot No: 4F1363


title: COLON APCmin/+/VP16 (CTRL) 1

description:
COLON APCmin/+/VP16 (CTRL) 1
replicate 1

value: APCmin/+/VP16 (control)


title: Liver HF replicate 02


title: BDK_donor5 (array B)

description: bulge–derived keratinocytes

source_name: donor 5

value: female


title: NHEK_2 (array A)

description: neonatal human epidermal keratinocytes

source_name: Kurabo; NHEK(F)　Lot No.4C1163


title: NHEK_1 (array A)

description: neonatal human epidermal keratinocytes

source_name: Kurabo; NHEK(F)　Lot No.3C1272


title: XENO AdVP16hLXRa (LXRa) 6

description:
XENO AdVP16hLXRa (LXRa) 6
replicate 1
human HT29 cells grown in Nu/Nu mice infected with LXRa (VP16hLXRa) Adenovirus


title: BDK_donor3 (array B)

description: bulge–derived keratinocytes

source_name: donor 3


title: BDK_donor4 (array B)

description: bulge–derived keratinocytes

source_name: donor 4


title: Liver HF replicate 01


title: BDK_donor2 (array B)

description: bulge–derived keratinocytes

source_name: donor 2


title: BDK_donor1 (array B)

description: bulge–derived keratinocytes

source_name: donor 1


title: liver t=0 replicate 12

source_name: liver tissue, high fat diet, sacrificed after adaptation phase


title: liver t=0 replicate 11

value: high fat diet, sacrificed after adaptation phase


title: XENO AdVP16 (CTRL) 4

description:
XENO AdVP16 (CTRL) 4
replicate 1
human HT29 cells grown in Nu/Nu mice infected with Control (Ad-VP16) Adenovirus

source_name: Xenograft Tumors (human HT29 cells) grown in Nu/Nu Athymic Female Mice

value: Control (Ad-VP16) Adenovirus


title: BDK_donor16 (array A)

description: bulge–derived keratinocytes

source_name: donor 16

value: atopic dermatitis


title: liver t=0 replicate 09


title: BDK_donor15 (array A)

description: bulge–derived keratinocytes

source_name: donor 15


title: liver t=0 replicate 10


title: liver t=0 replicate 08


title: XENO AdVP16 (CTRL) 2

description:
XENO AdVP16 (CTRL) 2
replicate 1
human HT29 cells grown in Nu/Nu mice infected with Control (Ad-VP16) Adenovirus

value: Xenograft Tumors (HT29 cells)

value: Nu/Nu


title: BDK_donor17 (array A)

description: bulge–derived keratinocytes

source_name: donor 17


title: BDK_donor18 (array A)

description: bulge–derived keratinocytes

source_name: donor 18


title: XENO AdVP16 (CTRL) 1

description:
XENO AdVP16 (CTRL) 1
replicate 1
human HT29 cells grown in Nu/Nu mice infected with Control (Ad-VP16) Adenovirus

value: 4 months


title: XENO AdVP16 (CTRL) 5

description:
XENO AdVP16 (CTRL) 5
replicate 1
human HT29 cells grown in Nu/Nu mice infected with Control (Ad-VP16) Adenovirus


title: liver t=0 replicate 06

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: liver, reference pool of all samples


title: BDK_donor14 (array A)

description: bulge–derived keratinocytes

source_name: donor 14


title: XENO AdVP16 (CTRL) 3

description:
XENO AdVP16 (CTRL) 3
replicate 1
human HT29 cells grown in Nu/Nu mice infected with Control (Ad-VP16) Adenovirus


title: liver t=0 replicate 07


title: RU486 rep 2

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki

description:
replicate 2 treated with RU486 for 24 hours
5298416024_J

data_processing: The data were normalised using quantile normalisation with BeadStudio Program from Illumina.

source_name: LNCaP-1F5 cell line

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

growth_protocol: LNCaP-1F5 cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 10 mM HEPES supplemented with antibiotics (penicillin and streptomycin).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kitwith DNaseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: LNCaP-1F5 cells were grown in charcoal stripped medium for 3 days followed by treated with vehicle or 100 nM DHT or 100 nM Dex or 1000 nM CPA or 1000 nM (RU486) or combination of 100 nM DHT+Dex for 24 hours followed by RNA isolation.

tag: cell line


title: LNCaP cells treated with miR-NC 2

city: New York

first: Pei-Chun

last: Lin

address: 1300 York Ave

department: Pathology and Laboratory Medicine

institute: Cornell Weill Medical College

description: cell ine LNCaP treated with miR-NC as control, repeat 2

data_processing: The background subtracted and normalized (by Illumina Beadstudio) data was used for the analysis.

source_name: LNCaP cells grown in 10% FBS subjected to miR-NC

label_protocol: Biotinylated cRNA were prepared with Ambion messageAmp kit for llumina arrays

growth_protocol: LNCaP cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: TRIzol according to the manufacturer's protocol

treatment_protocol: Cells were transfected with 50 nM miR-NC or miR-31 for 48 hours

value: LNCaP

value: overexpression miR-NC


title: RU486 rep 1

description:
replicate 1 treated with RU486 for 24 hours
5298416024_I


title: LNCaP cells treated with miR-31 2

description: cell ine LNCaP treated with miR-31, repeat 2

source_name: LNCaP cells grown in 10% FBS subjected to miR-31

value: overexpression miR-31


title: BDK_donor13 (array A)

description: bulge–derived keratinocytes

source_name: donor 13

value: male

source_name: Reference RNA


title: BDK_donor12 (array A)

description: bulge–derived keratinocytes

source_name: donor 12


title: LNCaP cells treated with miR-31 1

description: cell ine LNCaP treated with miR-31, repeat 1


title: CPA rep 2

description:
replicate 2 treated with CPA for 24 hours
5298416024_L

value: CPA


title: BDK_donor11 (array A)

description: bulge–derived keratinocytes

source_name: donor 11


title: BDK_donor10 (array A)

description: bulge–derived keratinocytes

source_name: donor 10


title: liver t=0 replicate 05


title: LNCaP cells treated with miR-NC 1

description: cell ine LNCaP treated with miR-NC as control, repeat 1


title: liver t=0 replicate 04


title: liver t=0 replicate 02


title: CPA rep 1

description:
replicate 1 treated with CPA for 24 hours
5298416024_K


title: BDK_donor9 (array A)

description: bulge–derived keratinocytes

source_name: donor 9


title: liver t=0 replicate 01

source_name: liver tissue, high fat diet, sacrificed after adaptation phase


title: BDK_donor7 (array A)

description: bulge–derived keratinocytes

source_name: donor 7

value: non-atopic control


title: BDK_donor8 (array A)

description: bulge–derived keratinocytes

source_name: donor 8


title: liver t=0 replicate 03

value: adult


title: BDK_donor6 (array A)

description: bulge–derived keratinocytes

source_name: donor 6


title: BDK_donor5 (array A)

description: bulge–derived keratinocytes

source_name: donor 5


title: DHT+Dex rep 3

description:
replicate 3 treated with DHT+Dex for 24 hours
5298416049_L

value: DHT+Dex


title: DHT+Dex rep 2

description:
replicate 2 treated with DHT+Dex for 24 hours
5298416049_K


title: Dex rep 3

description:
replicate 3 treated with Dex for 24 hours
5298416049_I

value: Dex


title: DHT+Dex rep 1

description:
replicate 1 treated with DHT+Dex for 24 hours
5298416049_J


title: BDK_donor4 (array A)

description: bulge–derived keratinocytes

source_name: donor 4

value: a mixture of NHEK total RNA and Universal Human Reference RNA (Stratagene Corporation, CA, USA)


title: BDK_donor2 (array A)

description: bulge–derived keratinocytes

source_name: donor 2


title: BDK_donor3 (array A)

description: bulge–derived keratinocytes

source_name: donor 3


title: DHT rep 2

description:
replicate 2 treated with DHT for 24 hours
5298416049_E

source_name: LNCaP-1F5 cell line

value: DHT


title: DHT rep 3

description:
replicate 3 treated with DHT for 24 hours
5298416049_F


title: BDK_donor1 (array A)

description: bulge–derived keratinocytes

source_name: donor 1

value: female


title: Dex rep 1

description:
replicate 1 treated with Dex for 24 hours
5298416049_G


title: Vehicle rep 3

description:
replicate 3 treated with vehicle for 24 hours
5298416049_C

value: Vehicle


title: Dex rep 2

description:
replicate 2 treated with Dex for 24 hours
5298416049_H


title: Control sample 4 Total Input

status: Public on Feb 04 2013

city: Charlestown

first: Martin

last: Aryee

state: MA

address: 149 13th Street

department: Pathology

institute: Massachusetts General Hospital

hyb_protocol: Samples were hybridized to the Affy6 chip for 18 hrs. We washed and stained the arrays using an Affymetrix fluidics Station 450 and scanned the arrays using a GeneChip Scanner 3000 7G (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: The Affymetrix GeneChip® Operating Software (GCOS) was used to collect and extract feature data from Affymetrix GeneChip® Scanners.

data_processing: Data was normalized using the 'asm' R package.  Due to the sensitivity profile of the MBD enrichment assay, probes in regions with a CpG density of less than 2.5% were discarded (leaving about 50k probes for analysis).

source_name: Control

label_protocol: In the MBD-SNP assay described here, we use the MBD2-MBD polypeptide to isolate methylated DNA fragments from genomic DNA samples followed by analysis with Affymetrix SNP 6.0 high density oligonucleotide microarrays. Comparison with an unenriched total input fraction then allows genome-scale determination of total and allele-specific methylation and copy number in an integrated fashion for each specimen. Briefly, each genomic DNA specimen was divided into two fractions: i) an enriched methylated fraction (EM) and, ii) a total input fraction (TI). Each of these fractions was digested with the NspI and StyI restriction enzymes in separate reactions. The resulting genomic DNA fragments were then ligated with Affymetrix SNP 6.0 assay adaptors. These restriction digest and adaptor ligation steps were carried out following the Affymetrix SNP 6.0 assay protocols. After adaptor ligation, the EM fraction was subject to enrichment for methylated DNA fragments using MBD2-MBD polypeptides immobilized on magnetic beads as previously described (Yegnasubramanian et al., Nucl Acids Res, 2006; Yegnasubramanian et al., BMC Genomics, 2011) except that the final DNA was eluted in 30 uL of EB1 buffer (0.2X NEBuffer 1 (New England Biolabs, Ipswich, MA), 0.2X BSA (NEB), 0.25X T4 DNA ligase Buffer (NEB)) for the NspI reaction and EB2 buffer (0.2X NEBuffer3, 0.2X BSA (NEB), 0.25X T4 DNA ligase buffer (NEB)) for the StyI reaction. The resulting EM and TI fractions were then subjected to one primer amplification, fragmentation, and labeling according to the Affymetrix SNP 6.0 manufacturer’s protocol.

growth_protocol: DNA was obtained from metastatic prostate cancer tissues from the PELICAN rapid autopsy program at Johns Hopkins University, and from normal prostate tissues from organ donors.

extract_protocol: DNA was extracted using the manufacturer's recommended protocol

treatment_protocol: For MBD-SNP, samples were enriched for methylated DNA using magnetic-bead immobilized methyl-binding domain polypeptides as described previously (Yegnasubramanian et al., Nucl Acids Res, 2006; Yegnasubramanian et al., BMC Genomics, 2011). A unenriched total input sample that was otherwise treated the same, was used as a reference for each sample and was used to derive copy number estimates.

tag: dna fraction

value: Total Input

tag: subject type

value: Control

tag: subject id

tag: tissue site

tag: sample id (short form for plotting)


title: Control sample 3 Enriched

value: Enriched


title: Control sample 2 Enriched


title: Control sample 1 Total Input


title: Control sample 2 Total Input


title: Control sample 3 Total Input


title: Control sample 4 Enriched


title: Normal prostate NP_489 Enriched

source_name: Normal prostate

value: Normal

value: BPH

value: Prostate


title: Normal prostate NP_489 Total Input


title: Normal prostate NP_468 Enriched


title: Control sample 1 Enriched


title: Normal prostate NP_387 Total Input


title: DHT rep 1

description:
replicate 1 treated with DHT for 24 hours
5298416049_D

tag: treatment


title: Normal prostate NP_468 Total Input


title: Vehicle rep 2

description:
replicate 2 treated with vehicle for 24 hours
5298416049_B


title: Normal prostate NP_366 Total Input


title: Liver-SG

city: Viterbo

first: Alessio

last: Valentini

address: via San Camillo de Lellis

department: IBAF

institute: University of Tuscia

hyb_protocol: The labelled and fragmented mRNA was then hybridized onto the slide according to CombiMatrix instructions

scan_protocol: Images were obtained by a ScanArray Lite (Perkin Elmer) laser scanner and Microarray Imager 5.8.0 software was used to extract feature data from microarray fluorescence images

data_processing: Saturated spots were flagged by the Microarray Imager software, and then eliminated by the following analysis. For each channel the mean of no oligo spots intensity (E) was calculated. All the spots with signal to E ratio below 1.5 were eliminated in subsequent analyses. We removed systematic bias in the data by applying the dye-swap normalization (Fang, Y.; Brass, A.; Hoyle, D.C.; Hayes, A.; Bashein, A.; Oliver, S.G.; Waddingtong, D.; Rattray, M. A model-based analysis of microarray experimental error and normalisation. Nucleic Acids Res. 2003, 31, e96), that makes use of the reverse labelling in the two microarray replicates, and the lowess normalization. To establish the significance of the observed regulation for each gene we used the t-test and corrected the p-value for multiple comparisons with the Benjamini and Hochberg False Discovery Rate (Benjamini Y, Hochberg Y (1995) Controlling the false-discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57:289-300.).

organism: Ovis aries

source_name: Liver stage 02 Sarda

label_protocol: RNA was amplified and Cy3 and Cy5 labelled using the ULS technology (Kreatech Diagnostics)

extract_protocol: RNA was extracted using the RNeasy midi kit (Qiagen)

tag: breed

value: Sarda

tag: tissue

value: liver

tag: Stage

value: 44 days after lambing (stage 02)

source_name: Liver stage 02 Gentile di Puglia

value: Gentile di Puglia


title: Normal prostate NP_367 Total Input


title: Normal prostate NP_376 Enriched


title: Normal prostate NP_376 Total Input


title: Normal prostate NP_387 Enriched


title: Normal prostate NP_367 Enriched


title: Normal prostate NP_366 Enriched


title: Normal prostate NP_345 Enriched


title: Normal prostate NP_343 Total Input


title: Vehicle rep 1

description:
replicate 1 treated with vehicle for 24 hours
5298416049_A


title: Normal prostate NP_343 Enriched


title: Normal prostate NP_324 Total Input


title: Normal prostate NP_317 Total Input


title: Normal prostate NP_324 Enriched


title: Normal prostate NP_317 Enriched


title: Normal prostate NP_316 Total Input


title: Normal prostate NP_345 Total Input


title: Normal prostate NP_331 Enriched


title: Normal prostate NP_331 Total Input


title: Normal prostate NP_262 Total Input


title: Normal prostate NP_261 Total Input


title: Normal prostate NP_263 Total Input


title: Normal prostate NP_316 Enriched


title: Normal prostate NP_263 Enriched


title: Normal prostate NP_241 Total Input


title: Normal prostate NP_261 Enriched


title: Normal prostate NP_241 Enriched


title: Normal prostate NP_262 Enriched


title: Normal prostate NP_221 Total Input


title: Normal prostate NP_221 Enriched


title: Normal prostate NP_219 Total Input


title: Normal prostate NP_219 Enriched


title: Normal prostate NP_200 Total Input


title: Normal prostate NP_198 Total Input


title: Normal prostate NP_198 Enriched


title: Normal prostate NP_200 Enriched


title: Normal prostate NP_174 Total Input


title: Normal prostate NP_174 Enriched


title: Normal prostate NP_130 Total Input


title: Normal prostate NP_130 Enriched


title: Normal prostate NP_118 Total Input


title: Normal prostate NP_106 Total Input


title: Normal prostate NP_106 Enriched


title: Prostate cancer metastasis 16111 Enriched

source_name: Prostate cancer metastasis

value: Patient

value: Tumor

value: Liver

tag: description

value: Liver Met 3


title: Prostate cancer metastasis 16110 Total Input

tag: cell type

value: Liver Met 12


title: Prostate cancer metastasis 16111 Total Input


title: Prostate cancer metastasis 16110 Enriched


title: Prostate cancer metastasis 16109 Total Input

value: Liver Met 1


title: Prostate cancer metastasis 16090 Enriched

value: Soft tissue

value: SC Comp Met 391T


title: Prostate cancer metastasis 16108 Total Input

value: Total Input

value: Spleen

value: Spleen NL


title: Prostate cancer metastasis 16108 Enriched

value: Enriched

value: Normal


title: Prostate cancer metastasis 16109 Enriched


title: Prostate cancer metastasis 16091 Total Input

value: Blood

value: Blood 391B NL


title: Prostate cancer metastasis 16090 Total Input


title: Prostate cancer metastasis 16091 Enriched


title: Normal prostate NP_317

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium Human Methylation450k Beadchip using the standard Illumina protocol

scan_protocol: Arrays were imaged using a BeadArray Reader

data_processing: Data was normalized using the 'minfi' R package (Scale normalization, No background subtraction).

label: Cy3 and Cy5

source_name: Normal Prostate

label_protocol: Standard Illumina protocol for Human Methylation450k DNA Analysis bead chip

value: Prostate

tag: tissue type

value: Normal prostate


title: Prostate cancer metastasis 16036 Total Input

value: Patient

value: Subdural

value: L Subdural Met


title: Prostate cancer metastasis 16036 Enriched

value: Tumor


title: Prostate cancer metastasis 16035 Total Input

value: L Periadrenal Met


title: Prostate cancer metastasis 16031 Total Input

value: Bone

value: T12-1 Met


title: Prostate cancer metastasis 16030 Total Input

value: R Rib7 met


title: Prostate cancer metastasis 16030 Enriched


title: Normal prostate NP_331


title: Prostate cancer metastasis 16029 Enriched

value: Lymph node

value: Paratracheal LN Met


title: Prostate cancer metastasis 16029 Total Input

value: Total Input


title: Prostate cancer metastasis 16025


title: Prostate cancer metastasis 16035 Enriched

value: Enriched

value: Soft tissue


title: Prostate cancer metastasis 16010 Total Input

value: L Axillary LN Met


title: Prostate cancer metastasis 16028

value: R Hum Met 1-12


title: Prostate cancer metastasis 16026

value: Prostate


title: Prostate cancer metastasis 16032

value: Xiphoid Met


title: Prostate cancer metastasis 16089 Enriched

value: Patient

value: Normal

value: Liver

value: Liver NL


title: Prostate cancer metastasis 16010 Enriched

value: Tumor


title: Prostate cancer metastasis 16089 Total Input


title: Prostate cancer metastasis 16034 Total Input

value: Bone

value: R Rib8 met 1-11


title: Prostate cancer metastasis 16034 Enriched


title: Prostate cancer metastasis 16033 Total Input

value: L Subclavicular LN Met 1-5


title: Normal prostate NP_130

value: Normal prostate


title: Prostate cancer metastasis 16022

value: Lymph node

value: L Superficial ing. LN Met


title: Prostate cancer metastasis 16028 Enriched

value: Enriched


title: Normal prostate NP_262


title: Prostate cancer metastasis 16028 Total Input

value: Total Input


title: Prostate cancer metastasis 16033 Enriched


title: Prostate cancer metastasis 16027 Enriched

value: L Cervical LN Met 1-2


title: Prostate cancer metastasis 16010

value: L Axillary LN Met


title: Prostate cancer metastasis 16027 Total Input


title: Prostate cancer metastasis 16026 Total Input

value: Prostate


title: Prostate cancer metastasis 16037 Enriched

value: Spleen

value: Spleen NL


title: Prostate cancer metastasis 16026 Enriched

value: Patient


title: Prostate cancer metastasis 16086 Total Input

value: Subdural

value: R Subdural Met


title: Prostate cancer metastasis 16086 Enriched

value: Tumor


title: Prostate cancer metastasis 16023


title: Prostate cancer metastasis 16037 Total Input

value: Normal


title: Prostate cancer metastasis 16035

value: Soft tissue

value: L Periadrenal Met


title: Prostate cancer metastasis 16085 Total Input

value: Adrenal

value: L Adrenal Met


title: Prostate cancer metastasis 16085 Enriched


title: Prostate cancer metastasis 16025 Total Input

value: Bone

value: R Rib7 met


title: Prostate cancer metastasis 16025 Enriched

value: Enriched


title: Prostate cancer metastasis 16088 Total Input

value: Total Input

value: Liver

value: Liver NL


title: Prostate cancer metastasis 16024 Enriched

value: Lymph node

value: R Ing. LN Met


title: Prostate cancer metastasis 16088 Enriched

value: Patient


title: Prostate cancer metastasis 16087 Total Input

value: Spleen

value: Spleen NL


title: Prostate cancer metastasis 16087 Enriched


title: Prostate cancer metastasis 16083 Total Input

value: Tumor

value: L Liv Sing.Met 2


title: Prostate cancer metastasis 16017 Total Input

value: R Humerus Marrow Met


title: Prostate cancer metastasis 16082 Enriched

value: L Liv Sing.Met 1


title: Prostate cancer metastasis 16017 Enriched


title: Prostate cancer metastasis 16082 Total Input


title: Prostate cancer metastasis 16016 Enriched

value: R Femur Marrow Met


title: Prostate cancer metastasis 16083 Enriched


title: Prostate cancer metastasis 16016 Total Input


title: Prostate cancer metastasis 16084 Total Input

value: Normal


title: Prostate cancer metastasis 16084 Enriched


title: Prostate cancer metastasis 16021 Total Input

value: Lung

value: R lung Met


title: Prostate cancer metastasis 16022 Enriched

value: Enriched

value: L Superficial ing. LN Met


title: Prostate cancer metastasis 16022 Total Input

value: Total Input


title: Prostate cancer metastasis 16020 Total Input

value: Bladder

value: posterior bladder polypoid Met


title: Prostate cancer metastasis 16024 Total Input

value: Lymph node

value: R Ing. LN Met


title: Prostate cancer metastasis 16079 Enriched

value: Patient

value: Anterior Mediastinal LN Met


title: Prostate cancer metastasis 16023 Enriched

value: Tumor

value: Prostate


title: Prostate cancer metastasis 16023 Total Input


title: Prostate cancer metastasis 16080 Enriched

value: Spleen

value: Spleen NL


title: Prostate cancer metastasis 16020 Enriched


title: Prostate cancer metastasis 16075 Enriched

value: Soft tissue

value: R Diaphragmatic Met


title: Prostate cancer metastasis 16075 Total Input


title: Prostate cancer metastasis 16032 Total Input

value: Bone

value: Xiphoid Met


title: Prostate cancer metastasis 16032 Enriched

value: Enriched


title: Prostate cancer metastasis 16013 Enriched

value: R Rib7 Met


title: Normal prostate NP_118 Enriched

value: Normal

value: BPH


title: Prostate cancer metastasis 16072 Total Input

value: Total Input

value: Apical Prostate CA


title: Prostate cancer metastasis 16008 Enriched

value: Lymph node

value: R Axillary LN Met


title: Prostate cancer metastasis 16072 Enriched

value: Patient


title: Prostate cancer metastasis 16076 Enriched


title: Prostate cancer metastasis 16076 Total Input


title: Prostate cancer metastasis 16079 Total Input

value: Tumor

value: Anterior Mediastinal LN Met


title: Prostate cancer metastasis 16071 Total Input

value: Adrenal

value: L Adrenal Met


title: Prostate cancer metastasis 16021 Enriched

value: Lung

value: R lung Met


title: Prostate cancer metastasis 16071 Enriched


title: Prostate cancer metastasis 16003 Total Input

value: L Pelvic LN7 Met


title: Prostate cancer metastasis 16080 Total Input

value: Spleen

value: Spleen NL


title: Prostate cancer metastasis 16003 Enriched

value: Enriched


title: Prostate cancer metastasis 16002 Total Input

value: Bone

value: L Humerus Bone Marrow Met


title: Prostate cancer metastasis 16013 Total Input

value: Total Input

value: R Rib7 Met


title: Prostate cancer metastasis 16073 Total Input

value: Normal

value: Liver

value: Liver NL


title: Prostate cancer metastasis 16008 Total Input

value: Patient

value: Tumor

value: Lymph node

value: R Axillary LN Met


title: Prostate cancer metastasis 16073 Enriched


title: ventral_Dentate_Gyrus_ES_rep4

first: Miklos

last: Toth

address: 1300 York Ave. Room W-506

department: Department of Pharmacology

institute: Weill Cornell Medical College

hyb_protocol: Hybridizations were carried out for 18hr at 42C in the NimbleGen Service Laboratory. See Roche nimblegen website and PMID 16075461 (Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005)

scan_protocol: Scanning was carried out using a GenePix 4000B scanner (Axon Instuments, Sunnyvale, CA)

data_processing: Data was preprocessed and normalized using the HELP data analysis package (Thompson et al, Bioinformatics 2008) implemented in R.

source_name: embryonic stem cell, MspI

label_protocol: Random 9-mers pre-labels with either Cy3 or Cy5

extract_protocol: DNA extraction as carried out with the QIAGEN Puregene Gentra cell kit.  DNA was dissolved in 10mM Tris(tris[hydroxymethyl]aminomethane)-HCL, pH 8.0.

tag: strain

value: Swiss-Webster

value: embryonic stem cell

tag: restriction enzyme

value: MspI

source_name: embryonic stem cell, HpaII

value: HpaII


title: ventral_Dentate_Gyrus_KOKO_rep2

source_name: ventral Dentate Gyrus, 5HT1A knockout offspring of a 5HT1A knockout mother, MspI

value: ventral Dentate Gyrus

tag: offspring genotype

value: 5HT1A knockout

tag: maternal genotype

source_name: ventral Dentate Gyrus, 5HT1A knockout offspring of a 5HT1A knockout mother, HpaII


title: ventral_Dentate_Gyrus_KOKO_rep3


title: Prostate cancer metastasis 16068 Total Input

value: Single Liver Met #4


title: Prostate cancer metastasis 16069 Enriched

value: Enriched

value: Single Liver Met #8


title: ventral_Dentate_Gyrus_ES_rep2


title: ventral_Dentate_Gyrus_ES_rep3


title: Prostate cancer metastasis 16002 Enriched

value: Bone

value: L Humerus Bone Marrow Met


title: ventral_Dentate_Gyrus_KOH_rep4

source_name: ventral Dentate Gyrus, 5HT1A knockout offspring of a 5HT1A heterozygote mother, MspI

value: 5HT1A heterozygote

source_name: ventral Dentate Gyrus, 5HT1A knockout offspring of a 5HT1A heterozygote mother, HpaII


title: ventral_Dentate_Gyrus_KOKO_rep1


title: ventral_Dentate_Gyrus_KOH_rep3


title: ventral_Dentate_Gyrus_ES_rep1


title: Prostate cancer metastasis 16068 Enriched

value: Liver


title: Prostate cancer metastasis 16069 Total Input

value: Total Input

value: Patient


title: ventral_Dentate_Gyrus_KOH_rep2


title: Prostate cancer metastasis 15999 Total Input

value: Tumor

value: Single Liver Met #5


title: ventral_Dentate_Gyrus_WTH_rep5

source_name: ventral Dentate Gyrus, 5HT1A wildtype offspring of a 5HT1A heterozygote mother, MspI

value: Swiss-Webster

value: wild type

source_name: ventral Dentate Gyrus, 5HT1A wildtype offspring of a 5HT1A heterozygote mother, HpaII


title: ventral_Dentate_Gyrus_WTH_rep3

value: MspI


title: ventral_Dentate_Gyrus_WTH_rep1

value: HpaII


title: Prostate cancer metastasis 15999 Enriched


title: ventral_Dentate_Gyrus_WTWT_rep2

source_name: ventral Dentate Gyrus, 5HT1A wildtype offspring of a 5HT1A wildtype mother, MspI

value: ventral Dentate Gyrus

source_name: ventral Dentate Gyrus, 5HT1A wildtype offspring of a 5HT1A wildtype mother, HpaII


title: ventral_Dentate_Gyrus_WTWT_rep5


title: ventral_Dentate_Gyrus_WTWT_rep4


title: Prostate cancer metastasis 15997 Total Input

value: R Rib Nodular Met


title: Prostate cancer metastasis 15997 Enriched


title: ventral_Dentate_Gyrus_WTH_rep4


title: ventral_Dentate_Gyrus_WTWT_rep1


title: ventral_Dentate_Gyrus_WTH_rep2


title: Prostate cancer metastasis 15996 Total Input

value: Adrenal

value: L Adrenal Met


title: Prostate cancer metastasis 16031 Enriched

value: Enriched

value: T12-1 Met


title: Prostate cancer metastasis 15996 Enriched


title: Prostate cancer metastasis 16070 Total Input

value: Normal

value: Kidney

value: L Kidney NL


title: NormalProstate_489

hyb_protocol: Agilent Gene Expression Hybridization Kit using the manufacturer's protocol.

scan_protocol: Microarrays are scanned with the Agilent G2565BA microarray scanner

data_processing: The Bioconductor limma (v 3.10.3) was used to background correct (normexp model), loess and quantile normalize the data

label_protocol: Agilent low RNA input linear amplification kit

extract_protocol: TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment

tag: sample id

value: Normal Prostate

source_name: pooled reference

tag: sample type

value: pooled reference


title: Prostate cancer metastasis 16070 Enriched

tag: dna fraction

tag: subject type

value: Patient


title: ventral_Dentate_Gyrus_WTWT_rep3


title: ventral_Dentate_Gyrus_KOH_rep1

value: 5HT1A knockout

value: 5HT1A heterozygote


title: NormalProstate_367

tag: subject id


title: NormalProstate_468


title: NormalProstate_387


title: Gene expression data from Sw480 cell line treated with shRNA against gankyrin for 4 days-replicate3

city: Beijing

first: Bai

middle: Zhao

last: Fang

state: Beijing

address: 27 Tai-Ping Road

country: China

institute: National Center of Biomedical Analysis

description: Gene expression data from SW480/shgankyrin cells

hyb_protocol: Standard Affymetrix protocol

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

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software (Agilent technologies, Santa Clara, CA, US).

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

growth_protocol: Human colon cancer cell line SW480 were maintained in   DMEM containing 1% penicillin/streptomycin and supplemented with 10% fetal bovine serum   (FBS)

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

treatment_protocol: no treatment

value: colon

tag: cell line

value: colon cancer cell line SW480

tag: genotype/variation

value: knockdown of Gankyrin


title: Gene expression data from SW480 cell line treated with non targeting shRNA for 4 days - replicate3

description: Gene expression data from SW480/shcontrol cells

value: control


title: Gene expression data from SW480 cell line treated with non targeting shRNA for 4 days - replicate2


title: NormalProstate_376


title: Gene expression data from Sw480 cell line treated with shRNA against gankyrin for 4 days-replicate2


title: NormalProstate_331


title: NormalProstate_366


title: Prostate cancer metastasis 16066 Enriched

value: Tumor

tag: tissue site

value: Lymph node

value: Paraaortic LN Met

tag: sample id (short form for plotting)


title: Prostate cancer metastasis 15994 Total Input

value: Total Input

value: Bone

value: Sternum Soft Met


title: Prostate cancer metastasis 15994 Enriched

value: Enriched


title: Prostate cancer metastasis 16066 Total Input


title: NormalProstate_324


title: NormalProstate_317


title: Prostate cancer metastasis 16065 Total Input

value: Subdural

value: Subdural Met


title: NormalProstate_345

value: Normal Prostate

value: pooled reference


title: NormalProstate_343


title: Gene expression data from SW480 cell line treated with non targeting shRNA for 4 days - replicate1

tag: tissue


title: 9_after PP_rep10

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description: Gene Expression after 8 weeks of  PP diet

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 2x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters  to obtain background subtracted median normalized Signal intensities.

source_name: after 8 wks of polyphenol rich extract supplemented (PP) diet

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 µg RNA using the One-Color Low Input Quick Amp labeling (Agilent) according to the manufacturer's instructions, followed by purification with Absolutely RNA Nanoprep kit (Stratagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the mirVanaTM miRNA Isolation Kit (Applied Biosystems) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: diet group

value: PP

value: skeletal muscle


title: 9_after fructose load_rep10

description: Gene Expression after 7 days of fructose load

source_name: after 7 days of fructose load


title: 9_before PP_rep10

description: Gene Expression in basal state before PP diet

source_name: basal state before polyphenol rich extract supplemented (PP) diet


title: 7_after fructose load_rep9


title: 7_after PP_rep9


title: 7_before PP_rep9


title: 17_after fructose load_rep9

value: PCB


title: NormalProstate_262


title: NormalProstate_263


title: Prostate cancer metastasis 16065 Enriched

value: Patient

tag: cell type

tag: description


title: NormalProstate_261

tag: tissue type


title: Prostate cancer metastasis 16067 Enriched

value: Normal

value: Liver

value: Liver NL


title: Prostate cancer metastasis 16061 Total Input

value: Tumor

value: Lymph node

value: R Supraclavicular LN Met


title: NormalProstate_219


title: Prostate cancer metastasis 16060 Enriched

value: Abd Paraaortic LN Met


title: Prostate cancer metastasis 16061 Enriched


title: 15_after fructose load_rep8


title: Gene expression data from Sw480 cell line treated with shRNA against gankyrin for 4 days-replicate1

value: colon

value: colon cancer cell line SW480

value: knockdown of Gankyrin


title: 17_before PCB_rep9

description: Gene Expression in basal state before PCB diet

source_name: basal state before placebo (PCB) diet


title: 17_after PCB_rep9

description: Gene Expression after 8 weeks of  PCB diet

source_name: after 8 wks of placebo (PCB) diet


title: NormalProstate_316

source_name: Normal Prostate


title: Prostate cancer metastasis 15986 Total Input

source_name: Prostate cancer metastasis

value: Total Input

value: L Axillary LN #2 Met


title: Prostate cancer metastasis 15983 Total Input

value: Bone

value: R Femur marrow Met


title: NormalProstate_198

value: Normal Prostate

value: pooled reference


title: Prostate cancer metastasis 15986 Enriched

value: Enriched

value: Patient


title: NormalProstate_130


title: Prostate cancer metastasis 16060 Total Input


title: Patient-30-2b

value: Prostate cancer metastasis


title: 122_after fructose load_rep7

value: PP

value: skeletal muscle


title: 121_after fructose load_rep6


title: 122_before PP_rep7


title: Patient-30-6b


title: NormalProstate_174


title: NormalProstate_106


title: Patient-30-2a


title: NormalProstate_118


title: 15_after PP_rep8


title: 122_after PP_rep7


title: 15_before PP_rep8


title: Prostate cancer metastasis 15982 Enriched

value: Tumor

value: Subdural

value: Subdural Met Fossa C


title: Prostate cancer metastasis 16062 Enriched

value: Normal

value: Kidney

value: Kidney NL


title: Prostate cancer metastasis 16062 Total Input

value: Total Input


title: Prostate cancer metastasis 15983 Enriched


title: 121_before PP_rep6


title: Patient-22-7


title: Patient-22-3


title: 121_after PP_rep6


title: Patient-30-6a


title: 11_after PP_rep5


title: Prostate cancer metastasis 15990 Total Input

value: R Temporal Subdural Met


title: 11_before PP_rep5


title: 118_after fructose load_rep4


title: 11_after fructose load_rep5


title: Prostate cancer metastasis 15979 Total Input

value: Lymph node

value: L Pulm Hilar LN Met


title: Prostate cancer metastasis 15979 Enriched


title: Prostate cancer metastasis 15982 Total Input


title: Patient-22-6


title: Prostate cancer metastasis 15954 Total Input

value: Soft tissue

value: Pericardial Mets


title: Prostate cancer metastasis 15954 Enriched

value: Enriched


title: 114_after fructose load_rep8

value: PCB


title: Patient-22-5

value: Prostate cancer metastasis

value: pooled reference


title: Patient-21-2c


title: 118_before PP_rep4

value: PP

value: skeletal muscle


title: Prostate cancer metastasis 15990 Enriched

value: Patient

value: Tumor

value: Subdural


title: 114_before PCB_rep8


title: Patient-21-2b


title: Patient-17-5c


title: 118_after PP_rep4


title: Prostate cancer metastasis 16059 Total Input

value: Normal

value: Liver

value: Liver NL


title: Patient-21-2a


title: Patient-21-6


title: 114_after PCB_rep8


title: 112_after fructose load_rep7


title: Prostate cancer metastasis 16128 Total Input

value: Total Input

value: Pericardial Mass Met 1A


title: Prostate cancer metastasis 16059 Enriched


title: Prostate cancer metastasis 16067 Total Input


title: Patient-17-5a


title: Prostate cancer metastasis 16128 Enriched


title: Patient-17-6


title: Prostate cancer metastasis 15963 Total Input

value: Peritoneal nodule pc1 Met


title: Patient-16-5


title: 112_after PCB_rep7


title: Patient-16-1


title: Prostate cancer metastasis 16040 Total Input

value: Kidney

value: Kidney NL


title: Prostate cancer metastasis 15963 Enriched

value: Enriched

value: Soft tissue


title: Prostate cancer metastasis 16040 Enriched


title: Prostate cancer metastasis 16007 Total Input

value: Lymph node

value: Lymphs NL


title: Prostate cancer metastasis 15953 Enriched

value: Pelvic Paraaortic LN Met


title: Prostate cancer metastasis 16007 Enriched


title: Prostate cancer metastasis 15953 Total Input


title: 111_after PP_rep3

value: PP

value: skeletal muscle


title: Patient-16-4

value: Prostate cancer metastasis

value: pooled reference


title: 111_before PP_rep3


title: 10_before PCB_rep6

value: PCB


title: 112_before PCB_rep7


title: 10_after fructose load_rep6


title: 111_after fructose load_rep3


title: E12.5 mouse MCs

city: Los Angeles

first: Kinji

last: Asahina

state: CA

address: 1333 San Pablo Street

institute: University of Southern California

description:
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
Pdpn

hyb_protocol: Following fragmentation, 3.75 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array in the GeneChip Hybridization Oven 640. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymerix GeneArray® Scanner.

data_processing: We analyzed the data by RMA algorithm using Partek Genomics Suite Software.

source_name: E12.5 mouse mesothelial cells

label_protocol: Biotinylated probes were synthesized from 20 ng total RNA using the Ovation RNA amplification system V2 and FL-Ovation cDNA Biotin module V2 (Nugen).

extract_protocol: Total RNA was extracted with RNAqueous Micro (Ambion).

value: Liver

tag: genotype

value: wild type

tag: strain

tag: age

value: E12.5 embryo


title: GADD45a+ING1bΔPHD_rep2

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: SAMPLE 12

hyb_protocol: Microarrays were hybridized following Illumina's standard hybridization protocol.

scan_protocol: Processed arrays were scanned on Illumina iScan System array reader according to the manufacturer's instructions.

data_processing: Raw array data were imported and preprocessed in GenomeStudio V2011.1 software (Illumina) using background subtraction and cubic spline normalization. Subsequent differential expression analysis of the grouped replicate samples was performed within GenomeStudio on the probe level utilizing the Illumina custom error model with FDR multiple-testing correction.

source_name: HEK293T cells cotransfected with GADD45a and ING1bΔPHD expression constructs

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep kit for Illumina arrays.

growth_protocol: HEK293T cells were cultured at 37°C with 10% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM), 10% fetal calf serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 ug/ml streptomycin.

extract_protocol: Total RNA was isolated using the RNeasy mini kit with on-column DNase digest (Qiagen) following the supplied protocol, quantified with a Thermo NanoDrop and quality tested on Agilent Bioanalyzer.

treatment_protocol: Plasmid DNA constructs were transfected using X-tremeGENE 9 (Roche) according to the manufacturer's protocol 48 h before cell harvesting.

value: combined overexpression of human GADD45a and  ING1bΔPHD proteins


title: 109_after fructose load_rep5


title: GADD45a+ING1bΔPHD_rep1

description: SAMPLE 11


title: 108_after fructose load_rep4


title: 108_after PCB_rep4


title: ING1bΔPHD_rep2

description: SAMPLE 10

source_name: HEK293T cells transfected with ING1bΔPHD expression construct

value: human ING1bΔPHD protein overexpression


title: 109_before PCB_rep5


title: 10_after PCB_rep6


title: 109_after PCB_rep5


title: NSN rep2

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Not Surrounded Nucleolus(NSN) 44 oocytes

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) The arrays are scanned twice. gDyeNormSignal,rDyeNormSignal are extracted from both scans and are log-transformed with: log10(max(x,1)). The values are then averaged over both scans, and will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 6 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
The normalized values can be further improved with error correction as described in http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

label_protocol: 2-round linear amplification was used with Agilent Low RNA Input Fluorescent Linear Amplification Kit.

extract_protocol: Total RNA was extracted by TRizol Reagent (Invitrogen, 15596-018) according to manufacturers recommendation.

treatment_protocol: Antral oocytes from both wild type and Matertm/tm mouse (39weeks old; kind gift of Prof. Dean, NIDDK) were collected by puncturing ovaries surface with a sterile needle were then washed in M2 medium and stained with the fluorocrome Hoechst33342 to distinguish chromatin organization in NSN (Non Surrounded Nucleolus) and SN (Surrounded Nucleolus) types28. Isolated oocytes in groups of 50 were then collected in 0.5ul of M2 and stored in liquid nitrogen until further utilization for microarray analysis and proteomics.

value: Embryonic Stem Cells

tag: development stage

value: embryo

tag: individual identifier

source_name: Universal Mouse Reference 129ES Cell

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: Universale Mouse Reference


title: GADD45a+ING1b_rep2

description: SAMPLE 8

source_name: HEK293T cells cotransfected with GADD45a and ING1b expression constructs

value: combined overexpression of human GADD45a and ING1b proteins


title: NSN rep1

description: Not Surrounded Nucleolus(NSN) 41 oocytes


title: ING1bΔPHD_rep1

description: SAMPLE 9


title: 108_before PCB_rep4


title: GADD45a+ING1b_rep1

description: SAMPLE 7


title: ING1b_rep2

description: SAMPLE 6

source_name: HEK293T cells transfected with ING1b expression construct

value: human ING1b protein overexpression


title: ING1b_rep1

description: SAMPLE 5


title: GADD45a_rep2

description: SAMPLE 4

source_name: HEK293T cells transfected with GADD45a expression construct

value: human GADD45a protein overexpression


title: SN rep2

description: Surrounded Nucleolus(SN) 50 oocytes

source_name: Surrounded Nucleolus(SN) 50 oocytes


title: SN rep1

description: Surrounded Nucleolus(SN) 50 oocytes


title: 107_after fructose load_rep2


title: 107_after PP_rep2


title: oocyte rep2

description: 10 Oocytes were used in this sample

data_processing:
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 6 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: 10 oocytes used in this sample


title: DKO_MEF_rep2

description: SAMPLE 8

data_processing: Raw array data were imported and preprocessed in GenomeStudio V2011.1 software (Illumina) using background subtraction and cubic spline normalization. Subsequent differential expression analysis of the grouped replicate samples was performed within GenomeStudio on the probe level utilising the Illumina custom error model with FDR multiple-testing correction.

source_name: double Gadd45a/Ing1 knockout (DKO) embryo MEF cells

growth_protocol: MEF cells were isolated from embryonic day E15.5 male embryos and cultured as described in “Manipulating the mouse embryo: a laboratory manual (2003, CSHL Press)”.

treatment_protocol: Passage P3 confluent MEF culture was collected for microarray profiling.

tag: gender

value: male

tag: develpmental stage

value: embryonic day E15.5

value: mouse embryonic fibroblasts (MEF cells)


title: GADD45a_rep1

description: SAMPLE 3


title: oocyte rep1

description: 10 Oocytes were used in this sample


title: Control_rep1

description: SAMPLE 1

source_name: HEK293T cells transfected with empty vector (control)

value: control (reference)


title: 106_before PCB_rep3

value: skeletal muscle


title: 106_after fructose load_rep3

source_name: after 7 days of fructose load

value: PCB


title: 105_before PP_rep1

source_name: basal state before polyphenol rich extract supplemented (PP) diet

value: PP


title: Ing1-/-_MEF_rep2

description: SAMPLE 6

source_name: Ing1 knockout embryo MEF cells


title: 106_after PCB_rep3

source_name: after 8 wks of placebo (PCB) diet


title: LNCaP_EtOH_3D_rep3

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

description: RNA from LNCaP cells cultured in hydrogel (3D) and treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.

hyb_protocol: 1650 ng of the labeled cRNA were loaded into the array chambers and allowed to hybridize at 65⁰C for 17 hours.

scan_protocol: The arrays were scanned using an Agilent scanner (G2565CA) and feature extraction was performed using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: The raw data were normalized using quantile between array normalization method in the bioconductor package, LIMMA.

molecule: polyA RNA

source_name: LNCaP prostate cancer cell line

label_protocol: 200 ng of total RNA was amplified and labelled using Agilent Low Input Quick Amp Labeling Kit.

growth_protocol: LNCaP cells are cultured in RPMI +10% FCS

extract_protocol: Cells were trypsinized and RNA was extracted using Trizol reagent followed by RNA clean up (Qiagen Rneasy Mini Kit)

treatment_protocol: Cells were cultured in RPMI+% charcoal stripped serum (androgen-starved) for 48 hours prior to R1881 treatment. The treatment consists of RPMI+5% charcoal stripped and final R1881 concentration of 1 nM.

value: LNCaP

tag: treatment

value: EtOH vehicle control

tag: culture condition

value: hydrogel (3D)


title: Gadd45a-/-_MEF_rep2

description: SAMPLE 4

source_name: Gadd45a knockout embryo MEF cells

tag: genotype/variation


title: DKO_MEF_rep1

description: SAMPLE 7


title: Control_rep2

description: SAMPLE 2

tag: cell line


title: 104_after PCB_rep2


title: 104_after fructose load_rep2


title: 107_before PP_rep2


title: 105_after fructose load_rep1


title: LNCaP_EtOH_3D_rep2


title: 105_after PP_rep1

source_name: after 8 wks of polyphenol rich extract supplemented (PP) diet


title: WT_MEF_rep2

description: SAMPLE 2

source_name: wild type embryo MEF cells

value: wild type


title: LNCaP_EtOH_2D_rep2

description: RNA from LNCaP cells cultured in tissue culture plastic (2D) and treated with an ethanol vehicle control for 48 hours was hybridized to a custom 180K Agilent microarray.

value: tissue culture plastic (2D)


title: 104_before PCB_rep2

source_name: basal state before placebo (PCB) diet


title: LNCaP_R1881_3D_rep2

description: RNA from LNCaP cells cultured in hydrogel (3D) and treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: Gadd45a-/-_MEF_rep1

description: SAMPLE 3


title: Ing1-/-_MEF_rep1

description: SAMPLE 5


title: LNCaP_R1881_3D_rep3


title: LNCaP_EtOH_2D_rep3


title: LNCaP_R1881_2D_rep3

description: RNA from LNCaP cells cultured in tissue culture plastic (2D) and treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: WT_MEF_rep1

description: SAMPLE 1


title: LD_Wagyu_3m

status: Public on Feb 03 2013

first: Nicholas

middle: James

last: Hudson

address: 306 Carmody Road

department: Animal, Food and Health Sciences

institute: CSIRO

description:
Sample: W03M
Sample replicates: W03M_1, W03M_2, W03M_3, W03M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Further, a mixed model normalisation method was applied and the BLUP solution for the gene by condition interaction was used as the normalized mean expression of each gene in each experimental condition.
We used a loop experimental design, and in these cases computing red/green ratios are not optimal. Instead we computed the intensity of the red and the intensity of the green signals.

label: Cy3, Cy5

organism: Bos taurus

source_name: Wagyu by Hereford LD muscle, 3 months postnatal

label_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

extract_protocol: Total RNA extracted using Trizol following the manufacturer's instructions

tag: cross

value: Wagyu by Hereford

value: 3 months postnatal

value: LD muscle


title: LD_Wagyu_20m

description:
Sample: W20M
Sample replicates: W20M_1, W20M_2, W20M_3, W20M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Wagyu by Hereford LD muscle, 20 months postnatal

value: 20 months postnatal

tag: tissue


title: LD_Wagyu_25m

description:
Sample: W25M
Sample replicates: W25M_1, W25M_2, W25M_3, W25M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Wagyu by Hereford LD muscle, 25 months postnatal

value: 25 months postnatal


title: LD_Wagyu_195d

description:
Sample: W195
Sample replicates: W195_1, W195_2, W195_3
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Wagyu by Hereford LD muscle, 195 days gestation

value: 195 days gestation


title: LNCaP_R1881_2D_rep2


title: LD_Wagyu_280d

description:
Sample: W280
Sample replicates: W280_1, W280_2, W280_3
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Wagyu by Hereford LD muscle, 280 days gestation

value: 280 days gestation


title: LD_Wagyu_60d

description:
Sample: W060
Sample replicates: W060_1, W060_2, W060_3
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Wagyu by Hereford LD muscle, 60 days gestation

value: 60 days gestation


title: LD_Wagyu_135d

description:
Sample: W135
Sample replicates: W135_1, W135_2, W135_3
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Wagyu by Hereford LD muscle, 135 days gestation

value: 135 days gestation


title: LD_Wagyu_30m

description:
Sample: W30M
Sample replicates: W30M_1, W30M_2, W30M_3, W30M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Wagyu by Hereford LD muscle, 30 months postnatal

value: 30 months postnatal


title: 101_after fructose load_rep1

description: Gene Expression after 7 days of fructose load

source_name: after 7 days of fructose load

tag: diet group

value: PCB

value: skeletal muscle


title: 101_after PCB_rep1

description: Gene Expression after 8 weeks of  PCB diet


title: LD_Piedmontese_30m

description:
Sample: P30M
Sample replicates: P30M_1, P30M_2, P30M_3, P30M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Piedmontese by Hereford LD muscle, 30 months postnatal

value: Piedmontese by Hereford


title: LD_Wagyu_12m

description:
Sample: W12M
Sample replicates: W12M_1, W12M_2, W12M_3, W12M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Wagyu by Hereford LD muscle, 12 months postnatal

value: 12 months postnatal


title: LNCaP_EtOH_3D_rep1

value: LNCaP

value: EtOH vehicle control

value: hydrogel (3D)


title: LD_Piedmontese_25m

description:
Sample: P25M
Sample replicates: P25M_1, P25M_2, P25M_3, P25M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Piedmontese by Hereford LD muscle, 25 months postnatal


title: LNCaP_EtOH_2D_rep1

source_name: LNCaP prostate cancer cell line

value: tissue culture plastic (2D)


title: LNCaP_R1881_3D_rep1


title: LD_Wagyu_7m

description:
Sample: W07M
Sample replicates: W07M_1, W07M_2, W07M_3, W07M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Wagyu by Hereford LD muscle, 7 months postnatal

value: Wagyu by Hereford

value: 7 months postnatal


title: 101_before PCB_rep1

description: Gene Expression in basal state before PCB diet


title: LD_Piedmontese_280d

description:
Sample: P280
Sample replicates: P280_1, P280_2, P280_3
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Piedmontese by Hereford LD muscle, 280 days gestation

value: LD muscle


title: LNCaP_R1881_2D_rep1

description: RNA from LNCaP cells cultured in tissue culture plastic (2D) and treated with 1 nM R1881 for 48 hours was hybridized to a custom 180K Agilent microarray.


title: LD_Piedmontese_12m

description:
Sample: P12M
Sample replicates: P12M_1, P12M_2, P12M_3, P12M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Piedmontese by Hereford LD muscle, 12 months postnatal


title: LD_Piedmontese_7m

description:
Sample: P07M
Sample replicates: P07M_1, P07M_2, P07M_3, P07M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Piedmontese by Hereford LD muscle, 7 months postnatal


title: LD_Piedmontese_3m

description:
Sample: P03M
Sample replicates: P03M_1, P03M_2, P03M_3, P03M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Piedmontese by Hereford LD muscle, 3 months postnatal

value: 3 months postnatal


title: LD_Piedmontese_195d

description:
Sample: P195
Sample replicates: P195_1, P195_2, P195_3
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Piedmontese by Hereford LD muscle, 195 days gestation

value: 195 days gestation


title: LD_Piedmontese_20m

description:
Sample: P20M
Sample replicates: P20M_1, P20M_2, P20M_3, P20M_4
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Piedmontese by Hereford LD muscle, 20 months postnatal

value: 20 months postnatal


title: PC Blimp1 int-2

city: Parkville

first: David

middle: M

last: Tarlinton

state: Vic

address: 1G Royal Pde

institute: WEHI

data_processing: The data were variance stabilised using lumiT and then quantile normalised using lumi package

source_name: follicualr B cells

growth_protocol: Isolated ex vivo. No growth.

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

treatment_protocol: FACS sorted, no external treatments.

tag: background strain

tag: cell type

value: follicualr B cells

tag: cell population

value: CD138+ Blimp1 intermediate


title: LD_Piedmontese_135d

description:
Sample: P135
Sample replicates: P135_1, P135_2, P135_3
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Piedmontese by Hereford LD muscle, 135 days gestation

value: 135 days gestation


title: Naïve follicular B cells

source_name: Naïve follicular B cells

value: Naïve follicular B cells


title: PC Blimp1-int-1


title: LD_Piedmontese_60d

description:
Sample: P060
Sample replicates: P060_1, P060_2, P060_3
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.

source_name: Piedmontese by Hereford LD muscle, 60 days gestation

value: 60 days gestation


title: PC Blimp1-hi

value: CD138+ Blimp1 high


title: GFP- B cell blasts - 1

source_name: B cell blasts

growth_protocol: CD40ligand, IL4 (10U/mL) and IL5 (10U/mL)

treatment_protocol: FACS sorted on day 4 of culture based on GFP expression

value: B cell blasts

value: GFP-


title: GFP+ B cell blasts - 2

source_name: pre-plasmablasts

value: pre-plasmablasts

value: GFP+


title: GFP- B cell blasts - 2


title: GFP+ B cell blasts - 1


title: H37F_rep2_Array3

status: Public on Feb 02 2013

city: college park

first: Carlos Alberto

last: Machado

department: department of biology

institute: University of Maryland

description: Hybrids of Drosophila pseudoobscura (maternal) and Drosophila pseudoobscura bogotana (paternal)

hyb_protocol: Agilent’s protocols

scan_protocol: Agilent’s protocols

data_processing: Performed in HDBStat: data is normalized by flagging out bad spots, filtering unexpressed genes (average raw intensity across all the samples <50), negative and positive Agilent controls, and then normalized with Chip Mean and log2 transformation.

organism: Drosophila pseudoobscura pseudoobscura x Drosophila pseudoobscura bogotana

source_name: whole body, 7-day-old adult, male

label_protocol: Fluorescent cRNA was synthesized from 200 ng of total RNA using Agilent’s low-RNA input fluorescent linear amplification kit following manufacturer's protocols (Agilent Technologies). Labelled RNAs were cleaned with RNeasy columns (Qiagen), and cRNA yields were quantified on a NanoDrop spectrophotometer. Two separate labeling reactions per sample were pooled and hybridized to the arrays following Agilent’s protocols.

growth_protocol: Flies were reared on cornmeal/yeast medium and maintained at 20°C with a 12:12-h light/dark cycle.

extract_protocol: Flies were instantly frozen in liquid nitrogen and stored in TRIZOL (Invitrogen) at -80°C. RNA was isolated using TRIZOL from at least 100 individuals. RNA quantity and quality were separately measured on a NanoDrop spectrophotometer (Thermo Scientific) and a Bioanalyzer 2100 (Agilent Technologies). High-quality samples (260/280>1.85; 260/230>1.7)  further purified using the RNeasy kit (Qiagen).

value: whole body

value: Female


title: H27F_rep3_Array2

description: Hybrids of Drosophila pseudoobscura (paternal) and Drosophila persimilis (maternal)

organism: Drosophila persimilis x Drosophila pseudoobscura

source_name: whole body, 7-day-old adult, female


title: H17M_rep1_Array1

description: Hybrids of Drosophila pseudoobscura (maternal) and Drosophila persimilis (paternal)

organism: Drosophila pseudoobscura x Drosophila persimilis

value: Male


title: H37M_rep2_Array4


title: H47F_rep1_Array2

description: Hybrids of Drosophila pseudoobscura (paternal) and Drosophila pseudoobscura bogotana (maternal)

organism: Drosophila pseudoobscura bogotana x Drosophila pseudoobscura pseudoobscura


title: H47M_rep1_Array4


title: H27M_rep1_Array2


title: H47F_rep3_Array2


title: H27M_rep3_Array3


title: H27F_rep1_Array4


title: H47M_rep3_Array3


title: H37M_rep3_Array4


title: H37F_rep1_Array1


title: H47M_rep2_Array2


title: H27F_rep2_Array1


title: H37F_rep3_Array3


title: H17F_rep3_Array1


title: H17M_rep2_Array4


title: H37M_rep1_Array3


title: H27M_rep2_Array2


title: H17M_rep3_Array2


title: H17F_rep2_Array3


title: SubQ_Adipocyte_Lean_SUBJECT6

city: Houston

first: Zheng

last: Yin

state: TX

address: 6670 Bertner Street R6-414

department: Systems Medicine and Bioengineering

institute: The Methodist Hospital Research Institute

hyb_protocol: Cy3-labeled aRNA concentration and dye incoporation was determined by Nanodrop (Microarray protocol); and 1.65ug of Cy3-labeled aRNA (10-13 pmol/ug specific activity) was fragmented in the presence of GE blocking agent at 60C for 30 minutes and hybridized to an Agilent Whole Human Genome, 4x44K microarray (AMADID 014850) using the Agilent Gene Expression Hybridization Kit (Agilent Ref. 5190-0404).

scan_protocol: Chips were scanned using the Agilent Technologies G2505C Microarray Scanner System with the extended dynamic range option.

data_processing: Image analysis and data collection were carried out using the Agilent Feature Extraction (AFE) 10.7.3.1. Additional details for pre-processing procedures, the corresponding R code and the target file used to set-up the pre-processing are provided in the 'data_processing_details.txt' file available on Series records.

label_protocol: Total RNA integrity was determined using a Bioanalyzer 2100 RNA6000 Nano chip (Eukaryotic total RNA protocol). Total RNA (200ng, 260/280 > 1.8, 260/230 > 2.0) was amplified and labeled using Agilent Low Input Quick Amp Labeling Kit, One Color (Agilent Ref. 5190-2305).

extract_protocol: Subcutaneous adipose tissue was fractionated to isolate adipocytes that were subsequently immunoprecipitated with biotinylated human anti-CD45 antibody and streptavidin-coated Dynabeads to remove contaminating leukocytes and generate highly-purified adiopocyte samples that were then processed for RNA using RNeasy Lipid Tissue Mini kits (Qiagen).

tag: bmi

value: subcutaneous adipose tissue


title: H47F_rep2_Array1


title: SubQ_Adipocyte_Lean_SUBJECT7


title: H17F_rep1_Array3


title: MSC_Li_rep3

city: Delhi

first: Gurudutta

middle: U

last: Gangenahalli

state: Delhi

address: Brig. S. K. Mazumdar Marg, Timarpur

department: Stem Cell Research Division

country: India

institute: Institute of Nuclear Medicine & Allied Sciences

description: Gene expression after 7 days in lithium treated MSCs

hyb_protocol: The labeled cRNA samples were hybridized on to a Custom Whole Genome Human 4x44k designed by Genotypic Technology Pvt. Ltd. (AMADID: 025085) . 1650ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Data extraction from Images was done using Feature Extraction software and Normalization of the data was done in GeneSpring GX V 11 75th Percentile Normalization

source_name: BM-MSC, LiCl, replicate3

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Mononuclear cells isolated from BM aspirates using Histopaque density gradient were plated at 0.1-0.5x106 cells/cm2 in α-MEM containing 16.5% FBS, 1% Streptomycin/Penicillin/amphoterecin  and 2mM L-Glutamine. Medium was changed after 48h to remove non-adherent cells and thereafter every 3-4 days. MSCs were expanded at low plating density (50-500 cells/cm2) and used between passage 3-5 for array experiments.

extract_protocol: RNA was prepared using  using Qiagen Rneasy Minikit following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Culture expanded human MSCs from 3 donors were plated at 5,000 cells/cm2 in PD100 or T75 flasks. LiCl was added after 2 days to a final concentration of 5mM. Lithium stimulation was continued for 7 days with medium change every alternate day. On 7th day, cells were harvested by trypsinisation, washed in PBS and stored in RNAlater.

value: MSC

tag: agent

value: LiCl

value: Bone marrow

value: female


title: SubQ_Adipocyte_Lean_SUBJECT4


title: SubQ_Adipocyte_Lean_SUBJECT5


title: MSC_Li_rep2

source_name: BM-MSC, LiCl, replicate2

value: male


title: SubQ_Adipocyte_Lean_SUBJECT1


title: MSC_Li_rep1

source_name: BM-MSC, LiCl, replicate1


title: SubQ_Adipocyte_Lean_SUBJECT2


title: SubQ_Adipocyte_Obese_SUBJECT5


title: MSC_Ctrl_rep2

description: Gene expression after 7 days in untreated MSCs

source_name: BM-MSC, control, replicate2


title: MSC_Ctrl_rep3

source_name: BM-MSC, control, replicate3


title: c-Myc

city: Shanghai

first: Yongzhong

last: Liu

address: Xietu Road 2200, 25

institute: Shanghai Cancer Institute

description: Gene expression data from the liver progenitor cells transformed with c-Myc

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0 Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

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: p53-/- mouse fetal liver progenitor cells transformed with c-Myc

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Liver progenitor cells were cultured in a maintenance medium containing 1:1 DMEM:F12 (GIBCO, Grand Island, NY) with 10% fetal bovine serum (GIBCO) and the following additives: dexamethasone (1×10−7 M; Sigma-Aldrich, St. Louis, MO), nicotinic acid (0.01 M; Sigma-Aldrich), 2-mercaptoethanol (50 mM; Sigma-Aldrich), 1× ITS liquid media supplement (Sigma-Aldrich), EGF (20 ng/ml; R&D Systems, Minneapolis, MN), HGF (50 ng/ml; R&D Systems), and penicillin/streptomycin (1% [v/v]; GIBCO).

tag: cell

tag: transformation

value: c-Myc


title: H-RasV12

description: Gene expression data from the liver progenitor cells transformed with H-RasV12

source_name: p53-/- mouse fetal liver progenitor cells  transformed with H-RasV12


title: myr-Akt

description: Gene expression data from the liver progenitor cells transformed with myr-Akt

source_name: p53-/- mouse fetal liver progenitor cells transformed with myr-Akt

value: myr-Akt


title: SubQ_Adipocyte_Lean_SUBJECT3


title: SubQ_Adipocyte_Obese_SUBJECT7


title: SubQ_Adipocyte_Obese_SUBJECT6


title: non-transformed

description: Gene expression data from the liver progenitor cells

source_name: p53-/- mouse fetal liver progenitor cells

value: non-transformed


title: SubQ_Adipocyte_Obese_SUBJECT3


title: SubQ_Adipocyte_Obese_SUBJECT4


title: SubQ_Adipocyte_Obese_SUBJECT1


title: MSC_Ctrl_rep1

source_name: BM-MSC, control, replicate1


title: Colorectal cancer tissue patient 08/14630 T2 A CL089

status: Public on Feb 01 2013

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: Colorectal cancer tissue from patient_14_timepoint_T2_replicate_A

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalised using RSN normalisation with IlluminaGUI in R

source_name: colorectal cancer

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

value: Colorectal cancer tissue

tag: patient

tag: time point

tag: replicate

value: A

tag: rin (rna integrity number)

tag: disease state

value: colorectal cancer


title: Colorectal cancer tissue patient 08/14630 T3 A CL090

description: Colorectal cancer tissue from patient_14_timepoint_T3_replicate_A


title: SubQ_Adipocyte_Obese_SUBJECT2


title: Day16 Gata5-induced cardiac cells

first: Todd

last: Evans

state: New York

address: 1300 York Avenue  Box 282

institute: Weill Medical College of Cornell University

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Mouse Genome 430 Plus 2.0 GeneChip arrays (Santa Clara, CA).

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

data_processing: Affymetrix GeneChip Operating Software was used for image acquisition. The data normalization and statistical analysis were performed with Array Star 2 (DNASTAR, Inc,Madison, WI).

source_name: Embryonic Stem Cell

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

growth_protocol: rtTA-expressing ES cells Aniv18 were used for derivation and validation line that allow conditional expression of Gata5 and were maintained without feeders on gelatin in serum-free conditions (2% LIF, 3 mM CHIR 99021 (STEMGENT), 1 mM PD0325901 (STEMGENT),and doxycycline (1ug/ml))

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: The iGata5 ESC line was used to generate embryoid bodies, which were induced with doxycycline (1ug/ml) at day 4 for 48 hr, after which the embryoid bodies were plated for differentiation.


title: Colorectal cancer tissue patient 08/14630 T0 C CL087

description: Colorectal cancer tissue from patient_14_timepoint_T0_replicate_C

value: C


title: Colorectal cancer tissue patient 08/14630 T1 A CL088

description: Colorectal cancer tissue from patient_14_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 08/14630 T0 A CL085

description: Colorectal cancer tissue from patient_14_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/15000 T3 A CL077

description: Colorectal cancer tissue from patient_13_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 08/15161 T0 C CL039

description: Colorectal cancer tissue from patient_12_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 08/15161 T0 A CL037

description: Colorectal cancer tissue from patient_12_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/15000 T0 C CL075

description: Colorectal cancer tissue from patient_13_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 08/14623 T3 A CL030

description: Colorectal cancer tissue from patient_11_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 08/15161 T0 B CL038

description: Colorectal cancer tissue from patient_12_timepoint_T0_replicate_B

value: B


title: Colorectal cancer tissue patient 08/15000 T1 A CL076

description: Colorectal cancer tissue from patient_13_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 08/14623 T2 A CL029

description: Colorectal cancer tissue from patient_11_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 08/14630 T0 B CL086

description: Colorectal cancer tissue from patient_14_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 08/15161 T3 A CL041

description: Colorectal cancer tissue from patient_12_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 08/15000 T0 A CL073

description: Colorectal cancer tissue from patient_13_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/15000 T0 B CL074

description: Colorectal cancer tissue from patient_13_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 08/15161 T1 A CL042

description: Colorectal cancer tissue from patient_12_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 08/15161 T2 A CL040

description: Colorectal cancer tissue from patient_12_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 08/15000 T2 A CL078

description: Colorectal cancer tissue from patient_13_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 08/14856 T3 A CL018

description: Colorectal cancer tissue from patient_10_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 08/14623 T0 A CL025

description: Colorectal cancer tissue from patient_11_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/14623 T1 A CL028

description: Colorectal cancer tissue from patient_11_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 08/14856 T2 A CL017

description: Colorectal cancer tissue from patient_10_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 08/14623 T0 B CL026

description: Colorectal cancer tissue from patient_11_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 08/14623 T0 C CL027

description: Colorectal cancer tissue from patient_11_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 08/14856 T0 C CL015

description: Colorectal cancer tissue from patient_10_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 08/14856 T0 B CL014

description: Colorectal cancer tissue from patient_10_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 08/14856 T1 A CL016

description: Colorectal cancer tissue from patient_10_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 08/15607 T3 A CL006

description: Colorectal cancer tissue from patient_9_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 08/15607 T1 A CL005

description: Colorectal cancer tissue from patient_9_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 08/15607 T0 C CL003

description: Colorectal cancer tissue from patient_9_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 08/15607 T0 A CL001

description: Colorectal cancer tissue from patient_9_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/14856 T0 A CL013

description: Colorectal cancer tissue from patient_10_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/15824 T0 C CL063

description: Colorectal cancer tissue from patient_8_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 08/15824 T0 A CL061

description: Colorectal cancer tissue from patient_8_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/15824 T1 A CL066

description: Colorectal cancer tissue from patient_8_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 08/15824 T3 A CL065

description: Colorectal cancer tissue from patient_8_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 08/15827 T1 A CL053

description: Colorectal cancer tissue from patient_7_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 08/15827 T0 B CL050

description: Colorectal cancer tissue from patient_7_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 08/15827 T3 A CL054

description: Colorectal cancer tissue from patient_7_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 08/15824 T0 B CL062

description: Colorectal cancer tissue from patient_8_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 08/15233 T1 A CL100

description: Colorectal cancer tissue from patient_6_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 08/15607 T2 A CL004

description: Colorectal cancer tissue from patient_9_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 08/15233 T0 B CL098

description: Colorectal cancer tissue from patient_6_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 08/15233 T2 A CL102

description: Colorectal cancer tissue from patient_6_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 08/15827 T0 A CL049

description: Colorectal cancer tissue from patient_7_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/15827 T0 C CL051

description: Colorectal cancer tissue from patient_7_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 08/16477 T3 A CL136

description: Colorectal cancer tissue from patient_5_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 08/15824 T2 A CL064

description: Colorectal cancer tissue from patient_8_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 08/16477 T1 A CL138

description: Colorectal cancer tissue from patient_5_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 08/15827 T2 A CL052

description: Colorectal cancer tissue from patient_7_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 08/15233 T3 A CL101

description: Colorectal cancer tissue from patient_6_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 08/15233 T0 C CL099

description: Colorectal cancer tissue from patient_6_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 08/15233 T0 A CL097

description: Colorectal cancer tissue from patient_6_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/16477 T0 A CL133

description: Colorectal cancer tissue from patient_5_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/16477 T2 A CL137

description: Colorectal cancer tissue from patient_5_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 08/15607 T0 B CL002

description: Colorectal cancer tissue from patient_9_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 09/1056 T0 C CL123

description: Colorectal cancer tissue from patient_4_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 08/16477 T0 C CL135

description: Colorectal cancer tissue from patient_5_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 09/1056 T0 A CL121

description: Colorectal cancer tissue from patient_4_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 09/1056 T1 A CL125

description: Colorectal cancer tissue from patient_4_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 09/1825 T1 A CL161

description: Colorectal cancer tissue from patient_3_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 09/1056 T3 A CL124

description: Colorectal cancer tissue from patient_4_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 09/1825 T0 A CL157

description: Colorectal cancer tissue from patient_3_timepoint_T0_replicate_A


title: Colorectal cancer tissue patient 08/16477 T0 B CL134

description: Colorectal cancer tissue from patient_5_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 09/1825 T0 C CL159

description: Colorectal cancer tissue from patient_3_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 09/1056 T0 B CL122

description: Colorectal cancer tissue from patient_4_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 09/1825 T3 A CL162

description: Colorectal cancer tissue from patient_3_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 09/1056 T2 A CL126

description: Colorectal cancer tissue from patient_4_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 09/1066 T3 A CL113

description: Colorectal cancer tissue from patient_2_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 09/1066 T0 C CL111

description: Colorectal cancer tissue from patient_2_timepoint_T0_replicate_C


title: Colorectal cancer tissue patient 09/1825 T2 A CL160

description: Colorectal cancer tissue from patient_3_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 09/1825 T0 B CL158

description: Colorectal cancer tissue from patient_3_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 09/1601 T3 A CL149

description: Colorectal cancer tissue from patient_1_timepoint_T3_replicate_A


title: Colorectal cancer tissue patient 09/1066 T0 B CL110

description: Colorectal cancer tissue from patient_2_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 09/1066 T2 A CL114

description: Colorectal cancer tissue from patient_2_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 09/1066 T1 A CL112

description: Colorectal cancer tissue from patient_2_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 09/1601 T0 B CL146

description: Colorectal cancer tissue from patient_1_timepoint_T0_replicate_B


title: Colorectal cancer tissue patient 09/1601 T2 A CL150

description: Colorectal cancer tissue from patient_1_timepoint_T2_replicate_A


title: Colorectal cancer tissue patient 09/1601 T1 A CL148

description: Colorectal cancer tissue from patient_1_timepoint_T1_replicate_A


title: Colorectal cancer tissue patient 09/1066 T0 A CL109

description: Colorectal cancer tissue from patient_2_timepoint_T0_replicate_A


title: Normal colon tissue patient 08/14630 T0 C CL093

source_name: normal colon mucosa

value: Normal colon tissue

value: colon cancer


title: Colorectal cancer tissue patient 09/1601 T0 C CL147

description: Colorectal cancer tissue from patient_1_timepoint_T0_replicate_C