title: Sample C, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
C1


title: Sample D, replicate 3

status: Public on Aug 12 2010

type: RNA

city: Durham

first: Dawn

last: Kernagis

state: NC

address: 2100 Erwin Rd

department: Pathology

country: USA

institute: Duke University Medical Center

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
D3

hyb_protocol: Hybridization targets were prepared from 2ug tRNA and hybridized according to standard Affymetric protocol.

scan_protocol: Arrays were scanned on the Affyemtrix GeneChip scanner. Probe set expression values, percent present, and 3'/5' probe set ratios for actin and GAPDH were calculated using the Affymetrix Microarray Analysis Suite v5.0.

data_processing: Expression data is RMA normalized (log2 transformed). The RMA normalization was conducted using Affymetrix Expression Console software.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Breast tumor core needle biopsy

label_protocol: Biotin labeled according to standard Affymetrix protocol

extract_protocol: Total RNA was extracted using a kit-based method (Rneasy, Qiagen, Valencia, CA)

treatment_protocol: Core needle biopsies ontained from breast cancer excisions following patient consent.

tag: patient

value: D

tag: disease state

value: Breast tumor

tag: tumor grade

tag: er status

value: ER Positive

tag: pr status

value: PR Positive


title: Sample B, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
B3

value: B


title: liver_feno_WT_rep3

city: Boston

first: hyewon

last: kang

state: MA

address: 75 Fransis street

institute: Brigham & Women's Hospital

hyb_protocol: 20ug of cRNA was used for hybridization according to the Affymetrix GeneChip Manual,  45℃, overnight.

scan_protocol: GeneChips were scanned on an Affymetrix Model 3000 7G scanner with autoloader.

data_processing: CEL files were loaded and analyzed in dChip.  It was first normalized using an invariant normalization function. Normalized intensity values for individual genes expression were filtered out if a strong signal for the gene was not detected on greater than 30% of the GeneChips.  Fold changes (Pctp-/- vs wild type) of at least 1.2 were considered to be significant for P < 0.05 by two-tailed Student’s t-Test.

label: Biotin

organism: Mus musculus

source_name: Liver, 0.2% fenofibrate (wt/wt) supplemented diet, wild type, 7 days

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix GeneChip Manual (rev 4.0) from 8ug total RNA.

growth_protocol: Mice lacking phosphatidylcholine transfer protein (PC-TP) and wild type littermate controls on FVB/NJ background were maintained in a standard rodent diet 5001 (LabDiets) until 8 weeks of age.

extract_protocol: Total RNA was extracted from liver using Trizol according to the manufacturer's instructions.

treatment_protocol: At 8 weeks of age, a diet including 0.2% fenofibrate (wt/wt) was provided to mice for 7days.  Then, mice were sacrified at age 9 weeks.

tag: genotype

value: Wild type FVB

tag: tissue

value: Liver

tag: age

value: 9 weeks old

tag: gender

value: Male


title: miRNA profile in esophageal squamous cell carcinoma (ESCC) 6

city: shantou

first: Enmin

last: Li

state: guangdong

address: 22 Xinling Road

country: China

institute: Shantou university, medical college

description: Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. After having passed RNA measurement on the Nanodrop instrument, the samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.11.0). The samples were hybridized on a hybridization station following the scheme you outlined in the sample submission. Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

hyb_protocol: the labled RNA were hybridized on the miRCURY™ LNA Array (v.11.0)according to manufacturer’s instructions.

data_processing: The ratio of red signal to green signal (green signal to red signal for Dye Swap) was calculated after background subtraction and normalization using the global Lowess (Locally Weighted Scatter plot Smoothing) regression algorithm (MIDAS, TIGR Microarray Data Analysis System), which we have found produces the best within-slide normalization to minimize the intensity-dependent differences between the dyes. Median ratios were calculated from Lowess normalized capture probe replicates then log2 median ratios were calculated.

source_name: cancerous tissue from ESCC clinical patient

label_protocol: After having passed RNA measurement on the Nanodrop instrument, the samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit according to manufacturer’s instructions.

value: cancerous esophagus

source_name: normal tissue from ESCC clinical patient

value: normal esophagus


title: miRNA profile in esophageal squamous cell carcinoma (ESCC) 5

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

extract_protocol: Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.


title: miRNA profile in esophageal squamous cell carcinoma (ESCC) 3


title: miRNA profile in esophageal squamous cell carcinoma (ESCC) 4


title: IgG control CHIP in CaCo2 array G Rep 3

status: Public on Aug 11 2010

type: genomic

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

hyb_protocol: labeling, hybridization, and scanning were done using manufacturer's instructions (Affymetrix)

data_processing:
Model Based analysis of tiling arrays (MAT) was used to process the data as described previously:  Johnson, et al, 2006, PMID: 16895995
.bar files were generated as the output of default MAT analysis and can be visualized using the publically available Affymetrix Ingtegrated Genome Browser

molecule: genomic DNA

source_name: IgG control CHIP in CaCo2 array G

growth_protocol: Cells were grown in 10% FBS DMEM and grown until 1 day post confluent on 15 cm plates

extract_protocol: Cells were fixed in 1% formaldehyde for 10 minutes at 37 degrees, then washed with cold PBS and scraped into PBS, and resuspended in ChIP lysis buffer and immunoprecipitated and processed as described by Carroll, et al, 2005, PMID: 16009131 and as described in our current work.

tag: cell type

value: Caco-2 colon cancer cells, 1 day post confluent


title: Sample B, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
B1


title: liver_feno_KO_rep6

source_name: Liver, 0.2% fenofibrate (wt/wt) supplemented diet, Pctp-/-, 7 days

value: Pctp-/-, FVB background


title: IgG control CHIP in CaCo2 array G Rep 2

scan_protocol: labeling, hybridization, and scanning were done using manufacturer's instructions (Affymetrix)


title: liver_feno_KO_rep5


title: IgG control CHIP in CaCo2 array E Rep 3

source_name: IgG control CHIP in CaCo2 array E

label_protocol: labeling, hybridization, and scanning were done using manufacturer's instructions (Affymetrix)


title: IgG control CHIP in CaCo2 array G Rep 1


title: Sample A, replicate 3

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
A3

value: A


title: IgG control CHIP in CaCo2 array E Rep 1


title: IgG control CHIP in CaCo2 array E Rep 2


title: CDX2 ChIP-chip in CaCo2 Array G Rep 1

source_name: CDX2 ChIP-chip CaCo2 Array G


title: miRNA profile in esophageal squamous cell carcinoma (ESCC) 2


title: CDX2 ChIP-chip in CaCo2 Array E Rep 3

source_name: CDX2 ChIP-chip CaCo2 Array E


title: CDX2 ChIP-chip in CaCo2 Array G Rep 2


title: miRNA profile in esophageal squamous cell carcinoma (ESCC)


title: CDX2 ChIP-chip in CaCo2 Array G Rep 3


title: liver_feno_KO_rep2


title: liver_feno_KO_rep4


title: CDX2 ChIP-chip in CaCo2 Array E Rep 1


title: CDX2 ChIP-chip in CaCo2 Array E Rep 2


title: liver_feno_KO_rep3


title: liver_feno_KO_rep1


title: Sample A, replicate 1

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
A1


title: Sample B, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
B2


title: Sample A, replicate 2

description:
Following patient consent, samples were obtained from breast cancer excisions as part of a Duke University Health System (DUHS) institutional review board–approved tissue banking and research protocol for the Duke University Medical Center (DUMC) Breast Cancer Specialized Program of Research Excellence (SPORE). Immediately after surgical excision, lumpectomy specimens were sampled by 14-gauge needle core biopsy using an imaging device, as previously described.  The core biopsies were embedded in ornithine carbamoyltransferase and frozen in liquid nitrogen. One 5-um frozen section was prepared from each sample, stained with hematoxylin and eosin, and evaluated by an expert breast pathologist. Routine pathologic evaluation of the corresponding clinical specimens by the DUHS laboratories included determination of ER and PR status by IHC. Samples with an Allred score of 0 or 2 were classified as negative. HER2 status was determined by IHC and fluorescent in situ hybridization. This study included only HER2-negative patients with at least two frozen core biopsies containing neoplastic cells.
A2


title: U937 cells treated with heat stress at 44°C for 6 h

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite. MAS5.0.

source_name: Human lymphoma U937 cells, 44°C, 6 h

label_protocol: Label protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K. K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

treatment_protocol: U937 cells, a human lymphoma cell line, were cultured at 37°C. The cells were treated with heat stress at 44°C for 15 min, followed by incubation for 6 h at 37°C.

tag: cell line

value: human lymphoma cells

tag: treatment

value: heat stress at 44°C for 15 min, 37°C for 6 h


title: U937 cells treated with heat stress at 44°C for 3 h

source_name: Human lymphoma U937 cells, 44°C, 3 h

treatment_protocol: U937 cells, a human lymphoma cell line, were cultured at 37°C. The cells were treated with heat stress at 44°C for 15 min, followed by incubation for 3 h at 37°C.

value: heat stress at 44°C for 15 min, 37°C for 3 h


title: U937 cells treated with heat stress at 42°C for 6 h

source_name: Human lymphoma U937 cells, 42°C, 6 h

treatment_protocol: U937 cells, a human lymphoma cell line, were cultured at 37°C. The cells were treated with heat stress at 42°C for 15 min, followed by incubation for 6 h at 37°C.

value: heat stress at 42°C for 15 min, 37°C for 6 h


title: U937 cells treated with heat stress at 44°C for 1 h

source_name: Human lymphoma U937 cells, 44°C, 1 h

treatment_protocol: U937 cells, a human lymphoma cell line, were cultured at 37°C. The cells were treated with heat stress at 44°C for 15 min, followed by incubation for 1 h at 37°C.

value: heat stress at 44°C for 15 min, 37°C for 1 h


title: U937 cells treated with heat stress at 44°C for 0 h

source_name: Human lymphoma U937 cells, 44°C, 0 h

treatment_protocol: U937 cells, a human lymphoma cell line, were cultured at 37°C. The cells were treated with heat stress at 44°C for 15 min, followed by incubation for 0 h at 37°C.

value: heat stress at 44°C for 15 min, 37°C for 0 h


title: WB-H-7254

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: Whole blood was collected in Tempus tube

hyb_protocol: Hybridized 12-Sample Beadchip according to manufacturer protocol

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analyzed using BeadStudio version 1.5.1.3 using the average chip normalization method.

source_name: Human whole blood

label_protocol: Biotynlated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

extract_protocol: Ambion Temput Isolation kit

value: Female

tag: ethnicity

value: Hispanic

tag: healthy control

value: pSLE


title: WB-H-2817

value: Afican American


title: WB-H-1358-2


title: WB-H-2846

value: Caucasian


title: WB-H-1137

value: Male


title: U937 cells treated with heat stress at 42°C for 0 h

source_name: Human lymphoma U937 cells, 42°C, 0 h

treatment_protocol: U937 cells, a human lymphoma cell line, were cultured at 37°C. The cells were treated with heat stress at 42°C for 15 min, followed by incubation for 0 h at 37°C.

value: heat stress at 42°C for 15 min, 37°C for 0 h


title: WB-H-2811-2


title: WB-H-1149

value: Asian


title: shGFP2

hyb_protocol: Labeling, hybridization and scanning were done according to Affymetrix protocols

data_processing:
Data were processed using dChip 2006 software using default Affymetrix normalization settings.
The results file of comparison of shCDX2/shGFP contains dChip processed data with less stringent cutoffs to allow for larger selection of potentially regulated targets and is provided as a supplementary file on the Series record.

source_name: shGFP control

growth_protocol: Caco-2 cells were grown in 10% FBS DMEM and grown until 1 day post confluent on 6 well plates

extract_protocol: Trizol was used to extract RNA according to manufacturer's instructions

treatment_protocol: Cells were treated with lentivirus containing shCDX2 (MISSION TRCN13684 or shGFP (control)) when about 25% confluent and selected in 2ug/ml Puromycin until 1 day post confluent. Cells at this state are a heterogeneous population of dividing and differentiated CaCo2 cells.

value: colon cancer cell line


title: shGFP1

scan_protocol: Labeling, hybridization and scanning were done according to Affymetrix protocols


title: WB-H-5679


title: U937 cells treated with heat stress at 42°C for 1 h

source_name: Human lymphoma U937 cells, 42°C, 1 h

treatment_protocol: U937 cells, a human lymphoma cell line, were cultured at 37°C. The cells were treated with heat stress at 42°C for 15 min, followed by incubation for 1 h at 37°C.

value: heat stress at 42°C for 15 min, 37°C for 1 h


title: WB-H-4276

value: Strep and Staph


title: WB-H-1254


title: U937 cells treated with heat stress (control)

source_name: Human lymphoma U937 cells, control

treatment_protocol: U937 cells, a human lymphoma cell line, were cultured at 37°C (non-treatment; control).

value: human lymphoma cells


title: WB-H-2804


title: WB-H-4637


title: U937 cells treated with heat stress at 42°C for 3 h

source_name: Human lymphoma U937 cells, 42°C, 3 h

treatment_protocol: U937 cells, a human lymphoma cell line, were cultured at 37°C. The cells were treated with heat stress at 42°C for 15 min, followed by incubation for 3 h at 37°C.

value: heat stress at 42°C for 15 min, 37°C for 3 h


title: WB-H-2819


title: WB-H-5683

value: Still


title: WB-H-1136


title: shCDX2-4

source_name: CDX2 knockdown in Caco-2 cells

label_protocol: Labeling, hybridization and scanning were done according to Affymetrix protocols


title: shCDX2-2b


title: shCDX2-2


title: WB-H-0537

value: Caucasian/Asian


title: WB-H-1946


title: WB-H-8550


title: WB-H-5851


title: WB-H-1134


title: WB-H-9371


title: WB-H-9369


title: WB-H-9355


title: WB-H-1358


title: WB-H-9357


title: WB-H-9363


title: WB-H-2811


title: WB-H-2704


title: WB-H-0545


title: WB-H-9868


title: WB-H-9361


title: WB-H-0565


title: WB-H-2812


title: WB-H-9128


title: WB-H-1359


title: WB-H-2804-2


title: WB-H-0853


title: WB-H-2818


title: WB-H-6035


title: WB-H-1595


title: WB-H-6411


title: WB-H-5679-2


title: WB-H-7837

value: ASLE


title: WB-H-7836


title: WB-H-7835


title: WB-H-7832


title: WB-H-7831


title: WB-H-3339


title: WB-H-7833


title: WB-H-7975


title: WB-H-1074


title: WB-H-4259


title: WB-H-5682


title: WB-H-7466


title: WB-H-6680


title: WB-H-6635


title: WB-H-4260


title: WB-H-6724


title: WB-H-1052


title: WB-H-5556


title: WB-H-5684


title: WB-H-4556


title: WB-H-6726


title: WB-H-6725


title: WB-H-6639


title: WB-H-1055


title: WB-H-1081


title: WB-H-2864


title: WB-H-2289


title: WB-H-1051


title: WB-H-6393


title: WB-H-2290


title: WB-H-6422


title: WB-H-5685


title: WB-H-2865


title: WB-H-2292


title: WB-H-2293


title: WB-H-2863


title: WB-H-6459


title: WB-H-2862


title: WB-H-2806


title: WB-PSLE-0582

value: African American

tag: illness

value: PSLE


title: WB-PSLE-9632

value: Female


title: WB-PSLE-2416

value: Hispanic


title: WB-PSLE-1515


title: WB-PSLE-5951


title: WB-PSLE-2420


title: WB-PSLE-0581


title: WB-PSLE-2919


title: WB-PSLE-2938


title: WB-PSLE-8411


title: WB-PSLE-6165


title: WB-PSLE-6029


title: WB-PSLE-6055


title: WB-PSLE-6298


title: WB-PSLE-8956


title: WB-PSLE-7469


title: WB-PSLE-1916


title: WB-PSLE-7384


title: WB-PSLE-8144


title: WB-PSLE-5622


title: WB-PSLE-2408


title: WB-PSLE-5583


title: WB-PSLE-5657


title: WB-PSLE-8965


title: WB-PSLE-2418


title: WB-PSLE-7474


title: WB-PSLE-8955


title: WB-PSLE-0683


title: WB-PSLE-6166


title: WB-PSLE-9872


title: WB-PSLE-2552


title: WB-PSLE-5587


title: WB-PSLE-2925


title: WB-PSLE-8148


title: WB-PSLE-2546


title: WB-PSLE-8074


title: WB-PSLE-0481


title: WB-PSLE-0067


title: WB-PSLE-3193


title: WB-PSLE-2610


title: WB-PSLE-9870


title: WB-Still-5986


title: WB-PSLE-2526


title: WB-PSLE-5982


title: WB-PSLE-8152


title: WB-PSLE-6156


title: WB-PSLE-1914


title: WB-PSLE-8943


title: WB-PSLE-7393


title: WB-PSLE-2145


title: WB-Still-5985


title: WB-Staph-5069

value: Staph


title: WB-Staph-2745


title: WB-Staph-9549


title: WB-Staph-9557


title: WB-Staph-9565

value: Caucasian


title: WB-Staph-9562

value: Male


title: WB-Staph-2741


title: WB-Staph-9561


title: WB-Staph-5037


title: WB-Staph-5046


title: WB-Staph-9558


title: WB-Staph-9559


title: WB-Staph-9560


title: WB-Staph-5064


title: WB-Staph-9556


title: WB-Staph-9552


title: WB-Staph-9555


title: WB-Staph-9548


title: WB-Staph-5068


title: WB-Staph-9569


title: WB-Staph-9553


title: WB-Staph-5040


title: WB-Strep-5074

value: Strep


title: WB-Staph-9601


title: WB-Staph-2707


title: WB-Staph-9598


title: WB-Staph-2388


title: WB-Strep-8869


title: WB-Strep-6549


title: WB-Strep-9484


title: WB-Strep-2736


title: WB-Staph-1338


title: WB-Strep-5800


title: WB-Strep-5813

value: Asian


title: WB-Strep-5781


title: WB-Strep-9483


title: WB-Staph-5839


title: WB-Staph-5825


title: WB-Staph-1346


title: WB-Strep-5808


title: WB-Strep-8854


title: WB-Strep-5838


title: WB-Staph-5840


title: WB-Staph-1339


title: WB-Staph-1345


title: WB-Staph-1347


title: WB-Staph-1402


title: WB-Staph-1343


title: WB-Staph-1340


title: WB-Staph-1344


title: WB-PSLE-5954


title: WB-PSLE-5615


title: WB-PSLE-8933


title: WB-PSLE-5608


title: WB-PSLE-5613


title: WB-Staph-5827


title: WB-Staph-1342


title: WB-Still-9686


title: WB-PSLE-7465


title: WB-PSLE-7466


title: WB-PSLE-5945


title: WB-PSLE-5618


title: WB-Still-9678


title: WB-PSLE-5600


title: WB-PSLE-5614


title: WB-PSLE-5952


title: WB-PSLE-7471


title: WB-PSLE-7486


title: WB-PSLE-5944


title: WB-PSLE-5623


title: WB-PSLE-5932


title: WB-PSLE-5626


title: WB-PSLE-5627


title: WB-PSLE-5933


title: WB-PSLE-5624


title: WB-PSLE-5611


title: WB-PSLE-7459


title: WB-PSLE-7457


title: WB-PSLE-5980


title: WB-PSLE-5612


title: WB-PSLE-7458


title: WB-PSLE-5610


title: WB-ASLE-8178


title: WB-PSLE-5949


title: WB-PSLE-5947


title: WB-PSLE-7456


title: WB-ASLE-8174


title: WB-PSLE-5970


title: WB-ASLE-7989


title: WB-ASLE-2773


title: WB-ASLE-7995


title: WB-ASLE-7990


title: WB-PSLE-5953


title: WB-ASLE-7987


title: WB-ASLE-7988


title: WB-ASLE-6647


title: WB-ASLE-6645


title: WB-ASLE-7985


title: WB-ASLE-6646


title: WB-ASLE-7984


title: WB-ASLE-6650


title: WB-ASLE-6641


title: WB-ASLE-6644


title: WB-ASLE-6642


title: WB-ASLE-6070


title: WB-ASLE-6069


title: WB-ASLE-6068


title: WB-ASLE-6643


title: WB-ASLE-6071


title: WB-ASLE-5320


title: WB-Still-6168


title: WB-Still-8059


title: WB-ASLE-6066


title: WB-ASLE-5670


title: WB-Still-7759


title: WB-ASLE-6067


title: WB-Still-7760


title: WB-Still-8560


title: WB-Still-6653


title: WB-ASLE-5321


title: WB-Still-6652


title: WB-Still-5871


title: WB-ASLE-5671


title: WB-Still-8980


title: WB-Still-2362


title: WB-Still-6038


title: WB-Still-6037


title: WB-Still-5870


title: WB-Still-2166


title: WB-Still-2358

value: Native American


title: WB-Still-1936


title: WB-Still-1935


title: WB-Still-1934


title: WB-Still-6167


title: WB-Still-5872


title: WB-Still-1102


title: WB-Still-5667


title: WB-Still-1281


title: WB-Still-5163


title: WB-Still-5161


title: WB-Still-5666


title: WB-Still-4639


title: PTB_LON_test049_sep_CD8_055

description: CD8+ cells from patient with active TB recruited in London. The subject was infected with Mycobacterium tuberculosis and confirmed as culture positive.

hyb_protocol: Hybridize 12-Sample Beadchip

source_name: CD8+ cells from patient with Active TB

extract_protocol: Qiagen RNeasy Mini Kit following manufacturer's protocol

value: South Asian

value: PTB

tag: geographical region

value: London

tag: bcg vaccinated

value: Yes

tag: region of birth

tag: tst

tag: smear of index case

tag: modal x-ray grade

value: Advanced

value: tuberculosis


title: PTB_LON_test049_sep_Mono_053

description: Monocytes from patient with active TB recruited in London. The subject was infected with Mycobacterium tuberculosis and confirmed as culture positive.

source_name: Monocytes from patient with Active TB


title: CON_LON_test038_sep_Mono_048

description: Monocytes from healthy control recruited in London. The subject was negative for skin test and IGRA test.

source_name: Monocytes from healthy control

value: Control (BCG+)

tag: modal x-ray grade:


title: CON_LON_test037_sep_Mono_043


title: CON_LON_test038_sep_CD4_049

description: CD4+ cellsd from healthy control recruited in London. The subject was negative for skin test and IGRA test.

source_name: CD4+ cells from healthy control


title: CON_LON_test037_sep_CD4_044

description: CD4+ cells from healthy control recruited in London. The subject was negative for skin test and IGRA test.


title: PTB_LON_test032_sep_Mono_028

value: Black

value: Moderate


title: CON_LON_test038_sep_Neut_047

description: Neutrophils from healthy control recruited in London. The subject was negative for skin test and IGRA test.

source_name: Neutrophils from healthy control

value: Female


title: CON_LON_test036_sep_CD8_040

description: CD8+ cells from healthy control recruited in London. The subject was negative for skin test and IGRA test.

source_name: CD8+ cells from healthy control

value: White


title: CON_LON_test037_sep_Neut_042


title: CON_LON_test038_sep_CD8_050


title: PTB_LON_test032_sep_CD8_030

description: Whole Blood from patient with active TB recruited in London. The subject was infected with Mycobacterium tuberculosis and confirmed as culture positive.


title: PTB_LON_test049_sep_CD4_054

description: CD4+ cells from patient with active TB recruited in London. The subject was infected with Mycobacterium tuberculosis and confirmed as culture positive.

source_name: CD4+ cells from patient with Active TB


title: PTB_LON_test027_sep_Neut_017

description: Neutrophils from patient with active TB recruited in London. The subject was infected with Mycobacterium tuberculosis and confirmed as culture positive.

source_name: Neutrophils from patient with Active TB


title: PTB_LON_test032_sep_CD4_029


title: CON_LON_test036_sep_Mono_038


title: PTB_LON_test027_sep_Mono_018


title: CON_LON_test037_sep_CD8_045


title: PTB_LON_test049_sep_Neut_052


title: PTB_LON_test027_sep_CD8_020


title: CON_LON_test036_sep_Neut_037


title: CON_LON_test036_sep_CD4_039


title: CON_LON_test035_sep_CD4_034


title: PTB_LON_test032_sep_Neut_027


title: PTB_LON_test027_sep_CD4_019


title: CON_LON_test035_sep_CD8_035

description: Whole Blood from healthy control recruited in London. The subject was negative for skin test and IGRA test.


title: CON_LON_test035_sep_Mono_033


title: CON_LON_test035_sep_Neut_032


title: PTB_LON_test023_sep_CD8_015

value: unknown


title: PTB_LON_test023_sep_Mono_013


title: PTB_LON_test023_sep_Neut_012


title: PTB_LON_test007_sep_Neut_007

value: Resistant Streptomycin, Ethio


title: PTB_LON_test007_sep_CD4_009

value: Male


title: PTB_LON_test028_sep_Neut_022

value: Asian other

value: Resistant Isoniazid + Ethambu


title: PTB_LON_test005_sep_CD4_004

tag: smear of index case:

value: Minimal


title: PTB_LON_test023_sep_CD4_014

value: South Asian


title: PTB_LON_test028_sep_Mono_023

value: PTB


title: PTB_SA_val013

description: Whole Blood from patient with active TB recruited in South Africa. The subject was infected with Mycobacterium tuberculosis and confirmed as culture positive.

data_processing: The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

source_name: Whole Blood from patient with Active TB

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

value: South Africa

value: No

value: Scanty Positive


title: PTB_LON_test007_sep_CD8_010

value: London

value: Yes

value: tuberculosis


title: PTB_LON_test005_sep_Mono_003


title: PTB_LON_test028_sep_CD8_025

value: Advanced


title: PTB_LON_test007_sep_Mono_008

value: Moderate


title: PTB_LON_test028_sep_CD4_024


title: LDmuscle_12_G

city: East Lansing

first: juan

middle: p

last: steibel

state: MI

address: 1205 I Anthony Hall

institute: Michigan State University

description: LD MUSCLE EXPRESSION PRP title indicates litter (number) and sex (G=female, B=male)

hyb_protocol: Labeled aRNAs were purified and combined with 65 µl of Slide Hyb #1 solution (Ambion, Inc.) and denatured at 70C for 5 min. Hybridizations were performed in sealed hybridization cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA, USA) for 18 h at a humid 54C. Following hybridization, slides were washed in 2X SSC/0.5% SDS and 0.1X SSC/0.1% SDS solutions for 10 min each. The slides were rinsed in a 0.1X SSC solution and nuclease-free water and dried by centrifugation.

scan_protocol: Fluorescent images were detected by a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) and fluorescence intensity data were collected using GenePix software (Molecular Devices) after spot alignment. Median intensity values for each dye channel were stored as comma-separated values data files.

data_processing: Bioconductor package Marray was used for pre-processing. Values are log2 ratio Cy3/Cy5.

organism: Sus scrofa

label_protocol: Five µg of total RNA were reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, aRNAs were labeled with N-hydroxysuccinate (NHS) ester Cy3 or Cy5 (GE Healthcare, UK).

growth_protocol: detailed growth protocol can be found in J. Anim Sci. 2008. 86:241-253.

extract_protocol: Total RNA from 1.0 g of tissue was extracted using TRIzol reagent (Invitrogen Corp., Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA concentration and quality were determined with an RNA 6000 Pico LabChip® kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA, USA).

tag: litter number

value: female

tag: phenotype

value: loin muscle area


title: PTB_LON_test005_sep_CD8_005

tag: age

tag: gender

value: White


title: LDmuscle_88_G

value: back fat depth at the 10th rib


title: PTB_SA_val006

value: Male

value: Black


title: PTB_SA_val008


title: PTB_LON_test005_sep_Neut_002

extract_protocol: Qiagen RNeasy Mini Kit following manufacturer's protocols

value: Minimal


title: LDmuscle_122_G


title: LDmuscle_93_B

value: male


title: LTB_SA_val050

description: Whole Blood from patient with Latent TB recruited in South Africa.  The subject tested positive for IGRA test.

source_name: Whole Blood from patient with Latent TB

value: Female

value: LATENT TB


title: LDmuscle_88_B


title: LDmuscle_93_G


title: LDmuscle_100_B


title: LDmuscle_19_G


title: PTB_SA_val009

value: PTB

value: South Africa


title: LDmuscle_100_G


title: PTB_SA_val007


title: LDmuscle_122_B


title: LDmuscle_79_B


title: LDmuscle_19_B


title: LTB_SA_val041

value: No


title: LDmuscle_42_G


title: LDmuscle_56_G


title: LDmuscle_64_G


title: LDmuscle_56_B


title: PTB_SA_val004

value: Yes

value: Negative


title: LDmuscle_131_G


title: LTB_LON_tr005

description: Whole Blood from patient with Latent TB recruited in London. The subject was an asymptomatic household contact of an active patient or a new entrant from an endemic country and tested positive by both IGRA and tuberculin skin test.

label_protocol: Biotynlated cRNA were generated following manufacturer protocols from 200 - 250ng of the globin-reduced RNA using the Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion, Austin, TX, USA)

extract_protocol: PerfectPure RNA Blood kit (5 PRIME Inc, Gaithersburg, MD, USA)

value: Latent

value: London

value: pulm

value: Sm+

value: No disease


title: LDmuscle_97_B

value: back fat depth at the 10th rib


title: LDmuscle_42_B

value: loin muscle area


title: LDmuscle_97_G

value: female


title: LDmuscle_64_B


title: LDmuscle_131_B


title: LDmuscle_32_B


title: LDmuscle_13_B


title: LTB_LON_tr024

value: Male

value: Asian Other


title: LDmuscle_92_B

value: male


title: LDmuscle_78_G


title: LTB_LON_tr036

description: Whole Blood from patient with Latent TB  recruited in London .  The subject was an asymptomatic household contact of an active patient or a new entrant from an endemic country and tested positive by both IGRA and tuberculin skin test.

value: Female

value: South Asian


title: LTB_LON-tr004

value: Black

value: Sm-


title: CON_LON_tr016

source_name: Whole Blood from healthy control

value: White

value: Control (BCG-)

value: No


title: CON_LON_tr017

value: London


title: LDmuscle_78_B


title: LDmuscle_121_B


title: LDmuscle_112_B


title: LTB_LON_tr034

value: Latent

value: extrapulm


title: LDmuscle_112_G


title: LDmuscle_13_G


title: LDmuscle_92_G


title: PTB_LON_tr021

description: Whole Blood from patient with Active TB recruited in London. The subject was infected with Mycobacterium tuberculosis and confirmed as culture positive.

value: PTB

value: Minimal

value: tuberculosis

value: scanty


title: CON_LON_tr041

value: Control (BCG+)

value: Yes


title: LDmuscle_123_G

value: female

value: back fat depth at the 10th rib


title: CON_LON_tr033

value: Male


title: LDmuscle_139_B

value: male


title: LDmuscle_73_G

value: loin muscle area


title: CON_LON_tr028

value: Female

value: White


title: CON_LON_tr042


title: LDmuscle_123_B


title: LDmuscle_71_G


title: LDmuscle_140_B


title: LDmuscle_10_B


title: LDmuscle_139_G


title: PTB_LON_tr022

value: Moderate


title: LDmuscle_27_G


title: LDmuscle_116_B


title: LDmuscle_60_B


title: PTB_LON_tr037

value: Other

value: London


title: LDmuscle_27_B


title: LTB_LON_tr009

value: South Asian

value: Latent

value: No

value: pulm

value: unknown


title: PTB_LON_tr038

value: PTB

value: tuberculosis

value: Resistant Isoniazid


title: LDmuscle_116_G

value: female

value: back fat depth at the 10th rib


title: LDmuscle_10_G


title: LTB_LON_tr014

value: Sm+

value: Minimal


title: LDmuscle_65_G

value: loin muscle area


title: LDmuscle_65_B

value: male


title: LDmuscle_121_G


title: LDmuscle_16_G


title: LDmuscle_16_B


title: PTB_LON_tr026

value: Female

value: Black

value: Advanced


title: LTB_LON_tr035

description: Whole Blood from patient with Latent TB recruited in London.   The subject was an asymptomatic household contact of an active patient or a new entrant from an endemic country and tested positive by both IGRA and tuberculin skin test.

value: Asian Other

value: London

value: Yes

value: No disease


title: LDmuscle_79_G


title: LDmuscle_5_B


title: LDmuscle_23_G


title: LDmuscle_60_G


title: LDmuscle_5_G


title: LDmuscle_22_G


title: LTB_LON_tr027

value: Male

value: South Asian

value: Latent

value: extrapulm


title: LDmuscle_23_B


title: LDmuscle_38_G

value: female


title: LTB_LON_tr006

description: Whole Blood from patient with Latent TB recruited in London.The subject was an asymptomatic household contact of an active patient or a new entrant from an endemic country and tested positive by both IGRA and tuberculin skin test.

value: pulm

value: unknown


title: LDmuscle_63_G


title: LDmuscle_22_B


title: PTB_LON_tr012

value: White

value: PTB

value: Moderate

value: tuberculosis

value: scanty


title: PTB_LON_tr019

value: Female

value: Advanced


title: LDmuscle_38_B

value: male

value: loin muscle area


title: LDmuscle_63_B


title: LDmuscle_54_B


title: PTB_LON_tr018

description: Whole Blood from patient with Active TB recruited in London The subject was infected with Mycobacterium tuberculosis and confirmed as culture positive.

value: London

value: Yes

value: Minimal


title: CON_LON_tr039

value: Control (BCG-)

value: No


title: LDmuscle_128_G

value: female

value: back fat depth at the 10th rib


title: LDmuscle_134_G


title: LDmuscle_128_B


title: LDmuscle_90_B


title: LDmuscle_54_G


title: LDmuscle_90_G


title: LTB_LON_tr011

value: Asian Other

value: Latent

value: pulm

value: Sm+

value: No disease


title: LDmuscle_134_B


title: PTB_LON_tr031

value: Male

value: Black

value: PTB

value: Moderate

value: scanty

value: tuberculosis

value: Resistant Streptomycin


title: CON_LON_tr040

value: White

value: Control (BCG+)

value: London

value: Yes


title: LTB_LON_tr029

value: Female

value: No

value: unknown


title: LDmuscle_96_G

value: female

value: back fat depth at the 10th rib


title: LDmuscle_96_B

value: male


title: LDmuscle_110_B


title: LDmuscle_77_B

value: loin muscle area


title: LDmuscle_106_G


title: LDmuscle_77_G


title: PTB_LON_tr002

value: Asian Other


title: LDmuscle_106_B


title: CON_LON_tr025

value: Control (BCG-)


title: LDmuscle_110_G


title: LDmuscle_53_G


title: LDmuscle_53_B


title: LTB_LON_tr003

value: Male

value: Latent

value: pulm

value: Sm+

value: No disease


title: LTB_LON_tr008

value: Black

value: extrapulm

value: Minimal


title: LDmuscle_109_B


title: PTB_LON_tr015

value: White

value: PTB

value: London

value: Yes

value: Advanced

value: tuberculosis


title: LDmuscle_140_G

value: female

value: back fat depth at the 10th rib


title: CON_LON_tr030

value: Control (BCG+)


title: PTB_LON_tr007

description: Whole Blood from patient with Active TB recruited in London. The subject was an asymptomatic household contact of an active patient or a new entrant from an endemic country and tested positive by both IGRA and tuberculin skin test.

value: Male

value: South Asian

value: Moderate

value: scanty


title: LTB_LON_tr010

value: Latent

value: No disease


title: CON_LON_tr023

value: Female

value: Control (BCG-)

value: No


title: LTB_LON_tr013

value: Asian Other

value: pulm

value: unknown


title: CON_LON_tr032

value: White

value: London

value: Yes


title: PTB_LON_tr020

value: Black

value: PTB

value: Minimal

value: tuberculosis


title: LDmuscle_109_G

value: female

value: back fat depth at the 10th rib


title: LDmuscle_32_G

value: loin muscle area


title: LDmuscle_71_B

value: male


title: LDmuscle_73_B


title: LTB_LON_tr001

value: Male

value: Latent

value: Sm+


title: IgG control CHIP in CaCo2 array D Rep 3

source_name: IgG control CHIP in CaCo2 array D

tag: cell type

value: Caco-2 colon cancer cells, 1 day post confluent


title: LDmuscle_12_B


title: PTB_LON_tr026_long_2_017

description: Whole blood from patient with active TB 2 months after treatment started. The patient had been recruited in London. The subject was found to be infected with Mycobacterium tuberculosis that was confirmed as culture positive.

value: 21years, when baseline sample taken

value: Female

tag: time post initiation of treatment

tag: sputum smear status

value: Positive

tag: isolate sensitivity

value: No


title: PTB_LON_tr037_long_0_019

description: Whole blood from patient with active TB before treatment and recruited in London. The subject was infected with Mycobacterium tuberculosis and confirmed as culture positive.

value: 29years, when baseline sample taken

tag: ethnicity

value: South Asian

tag: illness

value: Resistant Isoniazid


title: PTB_LON_tr020_long_12_015

description: Whole blood from patient with active TB 12 months after treatment started (i.e. after treatment completed). The patient had been recruited in London. The subject was found to be infected with Mycobacterium tuberculosis that was confirmed as culture positi

value: 48years, when baseline sample taken

value: Black

value: PTB

tag: bcg vaccinated

value: Yes


title: PTB_LON_tr012_long_12_009

source_name: Whole blood from patient with active TB 12 months after treatment started (i.e. after treatment completed)

value: White


title: PTB_LON_tr037_long_12_021


title: IgG control CHIP in CaCo2 array D Rep 1


title: IgG control CHIP in CaCo2 array D Rep 2


title: PTB_LON_tr026_long_0_016

source_name: Whole blood from patient with active TB before treatment


title: PTB_LON_tr015_long_2_011

source_name: Whole blood from patient with active TB 2 months after treatment started

value: 51years, when baseline sample taken


title: PTB_LON_tr012_long_2_008

value: Male


title: CDX2 ChIP-chip in CaCo2 Array D Rep 2

source_name: CDX2 ChIP-chip CaCo2 Array D


title: PTB_LON_tr037_long_2_020

value: Negative


title: CDX2 ChIP-chip in CaCo2 Array D Rep 3


title: PTB_LON_tr015_long_0_010


title: macrophage_hIAPP15uM_12h_rep4

city: Vancouver

first: Clara

last: Westwell-Roper

state: BC

address: 950 West 28th Ave

department: Pathology and Laboratory Medicine

country: Canada

institute: Child and Family Research Institute, University of British Columbia

description: Human IAPP, Replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized by the rank-invariant method in Bead Studio

source_name: mouse bone marrow-derived macrophage

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

growth_protocol: BMDMs were propagated from bone marrow in complete DMEM containing 15% L929-conditioned media for 7 days. Cells were seeded in 24-well plates and starved of L929-containing media for 12 hours prior to the experiment.

extract_protocol: RNA was extracted with Buffer RLT provided in a QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with an Agilent Bioanalyser.

treatment_protocol: Cells were treated with 15 mM rat or human IAPP dissolved in media, and incubated for 12 hours at 37 degrees C.

tag: strain

tag: media

value: DMEM with 10% FBS

tag: treatment

value: human IAPP

value: bone marrow-derived macrophage


title: PTB_LON_tr026_long_12_018

value: 21years, when baseline sample taken

value: Female


title: PTB_LON_tr015_long_12_012


title: macrophage_hIAPP15uM_12h_rep1

description: Human IAPP, Replicate 1


title: macrophage_rIAPP15uM_12h_rep2

description: Rat IAPP, Replicate 2

value: rat IAPP


title: PTB_LON_tr020_long_2_014


title: macrophage_hIAPP15uM_12h_rep3

description: Human IAPP, Replicate 3


title: CDX2 ChIP-chip in CaCo2 Array D Rep 1

value: Caco-2 colon cancer cells, 1 day post confluent


title: PTB_LON_tr020_long_0_013


title: uninfected RAW macrophage, log bacteria

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression in uninfected RAW macrophages and stationary phase LB grown S.aureus

hyb_protocol: 600ng 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: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)  and gProcessedSignal intensity was used for further analysis.

organism:
Staphylococcus aureus
Mus musculus

source_name: uninfected RAW macrophage, log bacteria

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. The cleaned up 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: infected and uninfected RAW cells were grown in DMEM wiht 10%FCS. S. aureus was grown in LB prior to infecting the RAW264.7 cells

extract_protocol: Cells were briefly fixed in ice cold 1:1 acetone:methanol, treated with lysostaphin and RNA was isolated using TRIzol

treatment_protocol: RAW 264.7 cells were infected with S.aureus ATCC 25923

tag: cell line

value: RAW264.7 cells

tag: infection

value: uninfected, + log-phase S. aureus


title: PTB_LON_tr012_long_0_007

value: 29years, when baseline sample taken

value: Positive


title: IgG control CHIP in CaCo2 array C Rep 3

source_name: IgG control CHIP in CaCo2 array C


title: PTB_LON_tr007_long_12_006

value: 31years, when baseline sample taken

value: South Asian

value: PTB


title: PTB_LON_tr007_long_0_004

value: Yes


title: IgG control CHIP in CaCo2 array C Rep 2


title: macrophage_hIAPP15uM_12h_rep2

description: Human IAPP, Replicate 2


title: RAW macrophage, 18h p.i, replicate 2

description: Gene expression in macrophage and S. aureus 18h after infection of RAW cells with S.aureus

source_name: RAW macrophage, 18h p.i, replicate 2

value: S.aureus ATCC25923 18h p.i.


title: macrophage_rIAPP15uM_12h_rep3

description: Rat IAPP, Replicate 3


title: IgG control CHIP in CaCo2 array C Rep 1


title: RAW macrophage, 7h p.i, replicate 2

description: Gene expression in macrophage and S. aureus 7h after infection of RAW cells with S.aureus

source_name: RAW macrophage, 7h p.i, replicate 2

value: S.aureus ATCC25923 7h p.i.


title: Input Ls174t array F Rep 3

source_name: Input Ls174t array F

value: Ls174t colon cancer cells


title: PTB_LON_tr007_long_2_005

value: Male


title: RAW macrophage, 2h p.i, replicate 2

description: Gene expression in macrophage and S. aureus 2h after infection of RAW cells with S.aureus

source_name: RAW macrophage, 2h p.i, replicate 2

value: S.aureus ATCC25923 2h p.i.


title: RAW macrophage, 18h p.i, replicate 1

source_name: RAW macrophage, 18h p.i, replicate 1


title: uninfected RAW macrophage, stat bacteria

description: Gene expression in uninfected RAW macrophages and log phase LB grown S.aureus

value: uninfected, + stationary S. aureus


title: PTB_LON_tr002_long_12_003

value: 33years, when baseline sample taken

value: Female

value: Asian Other


title: macrophage_rIAPP15uM_12h_rep4

description: Rat IAPP, Replicate 4

value: DMEM with 10% FBS

value: rat IAPP

value: bone marrow-derived macrophage


title: Input Ls174t array F Rep 2


title: macrophage_rIAPP15uM_12h_rep1

description: Rat IAPP, Replicate 1


title: CDX2 ChIP-chip in CaCo2 Array C Rep 2

source_name: CDX2 ChIP-chip CaCo2 Array C

value: Caco-2 colon cancer cells, 1 day post confluent


title: CDX2 ChIP-chip in CaCo2 Array C Rep 3


title: Input Ls174t array F Rep 1


title: Hepatocyte_Cold_72h_Rep2

city: Logy Bay

first: Jennifer

middle: Rejeanne

last: Hall

state: NL

address: 1 Marine Lab Rd.

department: Ocean Sciences Centre

institute: Memorial University of Newfoundland

hyb_protocol: Stock solutions [10% SDS and 20X SSC (Ambion)] used in microarray slide preparation and/or post-hybridization washes were diluted to working concentrations using DNase-free, RNase-free ultraPURE distilled water (Invitrogen). Microarray preparation and post-hybridization washes and centrifugations were performed in 50 ml conical tubes (BD Biosciences). Microarrays were prepared for hybridization by washing at room temperature for 2X5 min in 0.1% SDS and 5X1 min in DNase-free, RNase-free ultraPURE distilled water (Invitrogen), immersing for 3 min in 95°C DNase-free, RNase-free ultraPURE distilled water (Invitrogen) and drying by centrifugation at 1000 rpm for 5 min at room temperature, in loosely-capped 50 ml tubes.     The smelt hepatocyte cDNAs (cold and warm for a given incubation time, each containing an anchor for one of the Cy Dye labeled Capture Reagents, e.g. cold hepatocyte 24 h pool with Cy5 anchor and warm hepatocyte 24 h pool with Cy3 anchor, were pooled and hybridized with 3 μl of Cy5 labeled GFP spike and 2 µl of LNA dT blocker to the array in 2X formamide-based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt’s solution) (Genisphere). Microarray hybridizations were performed in the dark under Hybri-slips hybridization covers (Sigma-Aldrich) in slide hybridization chambers (Corning Life Sciences) placed in a 48°C water bath for 16 h.     Hybri-slips were floated off in 48°C 2X SSC, 0.2% SDS for 5 min and the arrays were washed at room temperature 1X15 min in (2X SSC, 0.2% SDS), 1X15min in 2X SSC, and 1X15min in 0.2X SSC, and dried by centrifugation at 1000 rpm for 5 min at room temperature. The Cy3 and Cy5 three dimensional fluorescent molecules (3DNA Capture Reagent, Genisphere) were hybridized to the bound cDNA on the microarray in 2X formamide-based buffer (Genisphere) for 4 h at 48°C and then washed and dried as previously described.

scan_protocol: Fluorescent images of hybridized arrays were acquired immediately at 10 μm resolution using a ScanArray GX PLUS microarray scanner and ScanArray Express software (PerkinElmer). The Cy3 and Cy5 cyanine fluorophores were excited at 543 nm and 633 nm, respectively. The laser power was set at 90% and the photomultiplier tube (PMT) settings were 79 (Cy3) and 75 (Cy5) for all of the microarrays in this study.

data_processing: For each microarray, fluorescent intensity data were extracted from TIFF images using ImaGene 7.5 software (BioDiscovery). Briefly, microarray elements were gridded manually and then spot sizes were adjusted automatically. Spatial effects were manually flagged and then fluorescent intensity measurements were made. ImaGene files were imported into GeneSpring GX 7.3.1 (Agilent Technologies). Data transformation (background correction and setting background corrected values less than 0.01 to 0.01) and per spot and per chip intensity dependent (Lowess) normalization were performed to generate Background Corrected Lowess Normalized (BCLN) data.    Fluorescent threshold levels for determining if genes were present were calculated by analyzing raw (i.e. not transformed or normalized) signal median levels from Arabidopsis control spots present on the 16K chip (6 Arabidopsis cDNAs X 16 replicates) for each channel (Cy5, Cy3) in each array. BCLN signal strength was considered above threshold (i.e. the transcript was deemed “present”) if it was equal to or greater than the average Arabidopsis raw signal plus two standard deviations in the dominant channel (i.e. the channel with the highest signal in a given comparison).

organism: Osmerus mordax

source_name: Hepatocytes, cold, 72h

label_protocol: Microarray targets were synthesized using the 3DNA Array 900 Expression Array Detection Kit for Microarrays (Cy3 and Cy5) (Genisphere) and SuperScript II (Invitrogen) with the manufacturer’s instructions. Briefly, 2 μg of total RNA was reverse transcribed for 2.5 h at 42°C using 200 U of SuperScript II and the manufacturer’s 5X SuperScript II buffer and oligo d(T) primers with unique 5-prime sequence overhangs for the Cy3 or Cy5 Capture Reagent Anchors (Genisphere).

growth_protocol: Each liver was perfused with medium containing collagenase and yielded approximately 300 million cells per individual. Initial or “pre-incubation” samples were collected and the remaining cell suspension was divided into 20 ml glass scintillation vials (6 x106 cells per vial) containing 2 ml of incubation medium [perfusion medium (in mM): 76 NaCl, 5.4 KCl, 0.81 MgSO4, 0.44 KH2PO4, 0.35 Na2HPO4, 5 NaHCO3, 10 HEPES, and 1 EGTA, adjusted to pH 7.63, supplemented with 2% bovine serum albumin (BSA), 1.5 mM CaCl2 and 5 mM glucose] and incubated at either 0.4°C (cold incubation) or 8°C (warm incubation).

extract_protocol: For total RNA isolation, for each individual fish, duplicate vials from each temperature were sampled at 24, 48 and 72 h incubation times. The cells were resuspended in their incubation medium by gentle pipetting, transferred to a 1.5 ml microcentrifuge tube and centrifuged at 1000 x g for 10 min at 4ºC. The supernatant was discarded and the cell pellet was immediately homogenized in 400 µl of TRIzol Reagent (Invitrogen) using a motorized Kontes RNase-Free Pellet Pestle Grinder (Kimble Chase). Duplicate vials were combined and topped up to 1 ml with 200 µl of TRIzol. The samples were stored at -80°C for a maximum of two weeks before completion of the total RNA isolation, with the manufacturer's instructions. Total RNA was then treated with 6.8 Kunitz units DNaseI (RNase-Free DNase Set, QIAGEN) at room temperature for 10 min and column purified using the RNeasy MinElute Cleanup Kit (QIAGEN) with the manufacturer’s instructions.

tag: tissue

value: Liver

value: Hepatocytes

source_name: Hepatocytes, warm, 72h


title: IgG control CHIP in CaCo2 array F Rep 3

source_name: IgG control CHIP in CaCo2 array F


title: PTB_LON_tr002_long_2_002

value: PTB

value: Negative


title: RAW macrophage, 7h p.i, replicate 1

source_name: RAW macrophage, 7h p.i, replicate 1

value: RAW264.7 cells


title: Hepatocyte_Cold_72h_Rep3


title: IgG control CHIP in CaCo2 array B Rep 3

source_name: IgG control CHIP in CaCo2 array B


title: IgG control CHIP in CaCo2 array F Rep 2


title: IgG control CHIP in CaCo2 array F Rep 1


title: IgG control CHIP in CaCo2 array B Rep 2


title: CDX2 ChIP-chip in CaCo2 Array C Rep 1


title: RAW macrophage, 2h p.i, replicate 1

source_name: RAW macrophage, 2h p.i, replicate 1


title: Hepatocyte_Cold_48h_Rep4

source_name: Hepatocytes, cold, 48h

source_name: Hepatocytes, warm, 48h


title: Hepatocyte_Cold_72h_Rep1


title: IgG control CHIP in CaCo2 array B Rep 1


title: Hepatocyte_Cold_72h_Rep4


title: CDX2 ChIP-chip in CaCo2 Array B Rep 3

source_name: CDX2 ChIP-chip CaCo2 Array B


title: Hepatocyte_Cold_48h_Rep1


title: CDX2 ChIP-chip in Ls174t Array F Rep 2

source_name: CDX2 ChIP-chip in LS174t cells Array F


title: CON_LON_test047_long_0_032

description: Whole blood from healthy control recruited in London. The subject was negative for skin test and IGRA test.

source_name: Whole blood from healthy control

value: 23years, when baseline sample taken

value: South Asian

value: Control

value: Yes


title: PTB_LON_tr002_long_0_001

source_name: Whole blood from patient with active TB before treatment

value: Positive


title: CON_LON_test048_long_0_033

value: 32years, when baseline sample taken

value: Male

value: Asian other


title: CON_LON_test045_long_0_030

value: 43years, when baseline sample taken

value: Black


title: TCF4 ChIP-chip in Ls174t Array F Rep 2

source_name: TCF4 ChIP-chip in LS174t cells Array F

value: Ls174t colon cancer cells


title: Hepatocyte_Cold_24h_Rep4

source_name: Hepatocytes, cold, 24h

source_name: Hepatocytes, warm, 24h


title: Hepatocyte_Cold_48h_Rep3


title: CDX2 ChIP-chip in CaCo2 Array B Rep 1

value: Caco-2 colon cancer cells, 1 day post confluent


title: CDX2 ChIP-chip in CaCo2 Array B Rep 2


title: TCF4 ChIP-chip in Ls174t Array F Rep 1


title: CON_LON_test046_long_0_031

description: Whole blood from healthy contro1 recruited in London. The subject was negative for skin test and IGRA test.

value: 22years, when baseline sample taken

value: Female


title: Hepatocyte_Cold_48h_Rep2

value: Liver

value: Hepatocytes


title: IgG control CHIP in CaCo2 array A Rep 3

source_name: IgG control CHIP in CaCo2 array A


title: CDX2 ChIP-chip in Ls174t Array F Rep 1


title: Hepatocyte_Cold_24h_Rep1


title: TCF4 ChIP-chip in CaCo2 Array F Rep 2

source_name: TCF4 ChIP-chip in CaCo2 Array F


title: Hepatocyte_Cold_24h_Rep3


title: Hepatocyte_Cold_24h_Rep2


title: IgG control CHIP in CaCo2 array A Rep 1


title: CON_LON_test040_long_0_027

value: 28years, when baseline sample taken


title: CDX2 ChIP-chip in CaCo2 Array F Rep 3

source_name: CDX2 ChIP-chip CaCo2 Array F


title: CON_LON_test044_long_0_029

value: 29years, when baseline sample taken

value: Other


title: CDX2 ChIP-chip in CaCo2 Array A Rep 2

source_name: CDX2 ChIP-chip CaCo2 Array A


title: CDX2 ChIP-chip in CaCo2 Array F Rep 2


title: CDX2 ChIP-chip in CaCo2 Array F Rep 1


title: IgG control CHIP in CaCo2 array A Rep 2


status: Public on Aug 10 2010

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

organism: Drosophila melanogaster

source_name: Cell Line S2-DRSC;Antibody mod2.2-VC (target is MOD(MDG4)67.2) extraction4_array1 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: embryo-derived cell-line

tag: developmental stage

value: late embryonic stage

tag: sex


title: TCF4 ChIP-chip in CaCo2 Array F Rep 1


title: CEM Cells_Cluvenone-Treated_4.5 h_Replicate 4

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description: 4.5h cluvenone-treated CEM cells biological replicate 4 of 4 vs. Control CEM cells (untreated, 4 pooled).

hyb_protocol: Labeled RNA samples were hybridized to the Agilent Whole Human Genome 4 x 44K arrays using the Gene Expression Hybridization Kit (Agilent) and using the Agilent’s hybridization platform following manufacturer's instructions. After hybridization, arrays were washed with Agilent’s washing buffers and then shortly immersed in Agilent Stabilization and Drying solution following manufacturer's instructions.

scan_protocol: Scanned on an Perkin Elmer ScanArray Express HT scanner. Images were quantified using ImageGene Software (version 8.0.1) from BioDiscovery, Inc.

data_processing: Using Limma/limmaGUI software from Bioconductor data was background corrected with the Normexp algorithm (offset=50), LOESS normalized, and M and A values calculated.

source_name: CEM cells, cluvenone-treated, 4.5h

label_protocol: 1.4 µg of total RNA was amplified and labeled with the Quick Amp Labeling Kit from Agilent following manufacturer's instructions.

growth_protocol: CEM cells we grown in RPMI medium containing 10% fetal bovine serum, 2 mM glutamine, 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using the ArrayGrade Total RNA Isolation Kit (SuperArray Bioscience Corp.) following manufacturer's instructions. RNA quality was evaluated with the 2100 Agilent Bioanalyzer.

treatment_protocol: CEM cells were treated with 0.3 μM cluvenone for 2 or 4.5 hours. Control CEM cells were treated with 0.1 % DMSO.

value: CCRF-CEM (CCL-119)

value: T lymphoblast

tag: disease

value: acute lymphoblastic leukemia

tag: organ

value: peripheral blood

value: female

value: Caucasian

source_name: CEM cells, untreated


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody mod2.2-VC (target is MOD(MDG4)67.2) extraction2_array1 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

value: Male


title: CDX2 ChIP-chip in CaCo2 Array A Rep 3

tag: cell type

value: Caco-2 colon cancer cells, 1 day post confluent


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody Su(var)3-9 (target is Su(var)3-9) extraction6_array1 channel_1


title: CON_LON_test038_long_0_025

tag: age

value: 41years, when baseline sample taken

tag: gender

value: South Asian

value: Control

tag: time post initiation of treatment

value: Yes


title: CON_LON_test036_long_0_023

value: 21years, when baseline sample taken

tag: ethnicity

value: White

tag: sputum smear status

tag: isolate sensitivity


title: CEM Cells_Cluvenone-Treated_4.5 h_Replicate 1

description: 4.5h cluvenone-treated CEM cells biological replicate 1 of 4 vs. Control CEM cells (untreated, 4 pooled).


title: CDX2 ChIP-chip in CaCo2 Array A Rep 1


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody Su(var)3-9 (target is Su(var)3-9) extraction4_array1 channel_1


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody Su(var)3-9 (target is Su(var)3-9) extraction2_array1 channel_1


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody Su(var)3-7-Q3448 (target is Su(var)3-7) extraction4_array1 channel_1


title: CEM Cells_Cluvenone-Treated_2 h_Replicate 4

description: 2h cluvenone-treated CEM cells biological replicate 4 of 4 vs. Control CEM cells (untreated, 4 pooled).

source_name: CEM cells, cluvenone-treated, 2h


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody Su(var)3-7-Q3448 (target is Su(var)3-7) extraction2_array1 channel_1


title: CEM Cells_Cluvenone-Treated_4.5 h_Replicate 2

description: 4.5h cluvenone-treated CEM cells biological replicate 2 of 4 vs. Control CEM cells (untreated, 4 pooled).


title: CEM Cells_Cluvenone-Treated_2 h_Replicate 2

description: 2h cluvenone-treated CEM cells biological replicate 2 of 4 vs. Control CEM cells (untreated, 4 pooled).


description: channel ch1 is input DNA

source_name: Cell Line CME-W1-Cl.8+;Antibody HP1c (MO 462) (target is HP1c) extraction2_array1 channel_1

value: dorsal mesothoracic disc

value: third instar larval stage


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody Su(var)3-7-Q3448 (target is Su(var)3-7) extraction4_array1 channel_1

value: CNS-derived cell-line

tag: genotype

value: y v f mal

value: Unknown


description: channel ch1 is input DNA

source_name: Cell Line Kc167;Antibody HP1c (MO 462) (target is HP1c) extraction2_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage

value: se/e

value: Female


description: channel ch1 is input DNA

source_name: Cell Line CME-W1-Cl.8+;Antibody HP1c (MO 462) (target is HP1c) extraction4_array1 channel_1

value: Male


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody Su(var)3-7-Q3448 (target is Su(var)3-7) extraction2_array1 channel_1


title: CON_LON_test037_long_0_024

source_name: Whole blood from healthy control

value: 49years, when baseline sample taken

tag: illness

tag: bcg vaccinated


title: CEM Cells_Cluvenone-Treated_2 h_Replicate 1

description: 2h cluvenone-treated CEM cells biological replicate 1 of 4 vs. Control CEM cells (untreated, 4 pooled).

tag: cell line

value: CCRF-CEM (CCL-119)

value: T lymphoblast

value: acute lymphoblastic leukemia

value: peripheral blood

value: female

value: Caucasian


title: CON_LON_test039_long_0_026

value: 33years, when baseline sample taken

value: Black

value: Control

value: Yes


title: CON_LON_test041_long_0_028

value: 23years, when baseline sample taken

value: White


description: channel ch1 is input DNA

source_name: Cell Line Kc167;Antibody HP1c (MO 462) (target is HP1c) extraction4_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage


description: channel ch1 is input DNA

source_name: Cell Line CME-W1-Cl.8+;Antibody HP1 wa191 (target is HP1a) extraction5_array1 channel_1

value: dorsal mesothoracic disc

value: third instar larval stage


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody HP1a wa184 (target is HP1a) extraction2_array1 channel_1

value: Male


description: channel ch1 is input DNA

source_name: Cell Line CME-W1-Cl.8+;Antibody HP1 wa191 (target is HP1a) extraction2_array1 channel_1


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody HP1a wa184 (target is HP1a) extraction4_array1 channel_1


title: CEM Cells_Cluvenone-Treated_2 h_Replicate 3

description: 2h cluvenone-treated CEM cells biological replicate 3 of 4 vs. Control CEM cells (untreated, 4 pooled).

value: CCRF-CEM (CCL-119)

source_name: CEM cells, untreated


title: HP1_wa191.2-4_hr_OR_embryo extraction4_array1

description: channel ch1 is input DNA

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: strain

value: Oregon-R

value: Embryo 2-4hr OR

value: wild type


title: expt.487 extraction2_array1

description: channel ch1 is input DNA

source_name: expt.487 extraction2_array1 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Collection of fly heads from whole adults using sieves of varying sizes.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Mixed Adult


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody HP1 wa191 (target is HP1a) extraction4_array1 channel_1

tag: tissue

value: CNS-derived cell-line

value: y v f mal

value: Unknown


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody HP1 wa191 (target is HP1a) extraction6_array1 channel_1

tag: developmental stage


title: expt.488 extraction4_array1

description: channel ch1 is input DNA

source_name: expt.488 extraction4_array1 channel_1


title: H3K9me3_(new_lot).14-16_hr_OR_embryo extraction2_array1

description: channel ch1 is input DNA

value: Embryo 14-16hr OR


title: H3K9me2-Ab2_(new_lot).2-4_hr_OR_embryo extraction8_array1

description: channel ch1 is input DNA


title: HP1_wa191.2-4_hr_OR_embryo extraction2_array1

description: channel ch1 is input DNA


title: H3K9me3_(new_lot).14-16_hr_OR_embryo extraction4_array1

description: channel ch1 is input DNA


title: H3K9me2-Ab2_(new_lot).2-4_hr_OR_embryo extraction6_array1

description: channel ch1 is input DNA


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody HP1 wa191 (target is HP1a) extraction2_array1 channel_1

tag: sex


title: H3K9me3_(new_lot).14-16_hr_OR_embryo extraction6_array1

description: channel ch1 is input DNA


title: CEM Cells_Cluvenone-Treated_4.5 h_Replicate 3

description: 4.5h cluvenone-treated CEM cells biological replicate 3 of 4 vs. Control CEM cells (untreated, 4 pooled).

source_name: CEM cells, cluvenone-treated, 4.5h

value: T lymphoblast

tag: disease

value: acute lymphoblastic leukemia

value: peripheral blood

value: female

value: Caucasian


title: H3K9me2-Ab2_(new_lot).2-4_hr_OR_embryo extraction4_array1

description: channel ch1 is input DNA


title: H3K9me2-Ab2_(new_lot).2-4_hr_OR_embryo extraction2_array1

description: channel ch1 is input DNA


title: H3K9me2-Ab2_(new_lot).14-16_hr_OR_embryo extraction6_array1

description: channel ch1 is input DNA


title: H3K9me2-Ab2_(new_lot).14-16_hr_OR_embryo extraction4_array1

description: channel ch1 is input DNA


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) extraction6_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage


title: H3K9me2-Ab2_(new_lot).14-16_hr_OR_embryo extraction2_array1

description: channel ch1 is input DNA


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) extraction4_array1 channel_1

value: Male


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) extraction2_array1 channel_1


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) extraction2_array1 channel_1

value: third instar larval stage


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody H3K79Me1 (target is H3K79me1) extraction4_array1 channel_1


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody H3K9acS10P (new lot) (target is H3K9acS10P) extraction4_array1 channel_1


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody H3K79Me1 (target is H3K79me1) extraction2_array1 channel_1


description: channel ch1 is input DNA

source_name: Strain Oregon-R;Antibody H3K4me2 (target is H3K4me2);Developmental Stage 3rd Instar Larvae extraction2_array1 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Oregon-R

value: 3rd Instar Larvae


description: channel ch1 is input DNA

source_name: Strain Oregon-R;Antibody H3K4me2 (target is H3K4me2);Developmental Stage 3rd Instar Larvae extraction4_array1 channel_1

value: wild type


title: Gastric Cancer-56-aCGH

city: Sapporo

first: Nobumoto

last: Tomioka

state: Hokkaido

address: Nishi 7 chome, Kita 15 jo, Kita-ku

department: General Surgery

institute: Hokkaido University

description: The array CGH target slide consists of 4015 BAC clones printed in duplicate (MAC Array TM Karyo4K: Macrogen Inc.; http://www.macrogen.com) on aminosilane-coated slide (CMT-GAPS2 Coated Slides, Corning Inc., USA). The Macrogen BAC library is an original library based on the genome of Koreans established in 2000 by Seo of Seoul National University. The average length of insertion is about 100 Kb. Genomic loci of all BAC clones have been verified by end-sequencing and compared to the NCBI public genome map, http://www.ncbi.nlm.nih.gov/mapview/. The genomic positions of all BAC clones were also confirmed by FISH.

hyb_protocol: The pellet was resuspended in 40 μl hybridization solution containing 50% formamide, 10% dextran sulfate, 2x SSC, 4% SDS, and 200 μg yeast tRNA. The hybridization solution was denatured for 10 min at 72 °C and was subsequently incubated for 1 hour at 37 °C to allow blocking of repetitive sequences. Hybridization was performed in slide chambers for 48 hours at 37 °C. After post-hybridization washes, arrays were rinsed, spin-dried.

scan_protocol: Two 16-bit TIFF image files were scanned using a GenePix 4200A two-color fluorescent scanner (Axon Instruments), and individual spots were analyzed with GenePix Pro 3.0 imaging software (Axon Instruments).

data_processing: Data analysis was performed using MacViewer (Macrogen). The log2-transformed fluorescent ratios were calculated from background-subtracted mean intensity values, and these ratios were used to perform normalization according to intensity normalization methods. LOWESS normalization was applied, a smoothing adjustment that removes intensity-dependent variation in dye bias.

source_name: Human gastric cancer tissue

label_protocol: The labeling and hybridization protocols described by Pinkel et al. were used with some modification to the labeling procedure. Briefly, 21 μl solution containing 500 ng normal DNA (reference DNA) or tumor DNA (test DNA), 20 μl BioPrime DNA Labeling System random primers solution (Invitrogen, Carlsbad, CA, USA), and water were combined and incubated for 5 min at 95 °C, and subsequently cooled on ice. After the addition of 5 μl 10x dNTPs labeling mix (1 mM dCTP, 2 mM dATP, 2 mM dGTP, 2 mM dTTP), 3 μl 1 mM Cy-3 or Cy-5 dCTP (GeneChem Inc., Daejeon, Korea), and 40 U BioPrime DNA Labeling System Klenow fragment (Invitrogen), the mixture was gently mixed and incubated overnight at 37 °C. The addition of 5 μl BioPrime DNA Labeling System Stop Buffer (Invitrogen) ended the reaction. After labeling, unincorporated fluorescent nucleotides were removed using QIAquick Spin columns (Qiagen, Germany). In one tube, Cy3-labeled sample and Cy5-labeled reference DNAs were mixed together, and 50 μg human Cot I DNA (Invitrogen), 20 μl 3M sodium acetate, and 600 μl cold 100% ethanol were added for DNA precipitation.

extract_protocol: DNA was extracted from each cancer tissue sample using the PureGene kit (Gentra Systems Inc., Minneapolis, MN, USA).

value: gastric cancer tumor

value: male

tag: depth of tumor invasion

value: se

tag: lymph node metastasis

value: positive

tag: pathological stage

value: IV

source_name: Normal human muscle tissue

tag: sample

value: Sex-matched reference normal human muscle DNA


title: Gastric Cancer-53-aCGH

tag: gender

value: si

value: negative

value: IIIA


title: H3K4me2.14-16_hr_OR_embryo extraction2_array1

description: channel ch1 is input DNA

value: Embryo 14-16hr OR


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody H3K4me2-Millipore (target is H3K4me2) extraction2_array1 channel_1

value: embryo-derived cell-line


title: H3K4me2.14-16_hr_OR_embryo extraction4_array1

description: channel ch1 is input DNA


description: channel ch1 is input DNA

source_name: Cell Line S2-DRSC;Antibody H3K4me2-Millipore (target is H3K4me2) extraction4_array1 channel_1

value: late embryonic stage


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me2-Millipore (target is H3K4me2) extraction4_array1 channel_1

value: CNS-derived cell-line

value: y v f mal

value: Unknown


title: Gastric Cancer-55-aCGH

value: female


title: Gastric Cancer-54-aCGH

value: IIIB


description: channel ch1 is input DNA

source_name: Strain Oregon-R;Antibody H3K4me2 (target is H3K4me2);Developmental Stage 3rd Instar Larvae extraction6_array1 channel_1

value: Oregon-R

value: 3rd Instar Larvae

value: wild type


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me2-Millipore (target is H3K4me2) extraction2_array1 channel_1

value: third instar larval stage


title: Gastric Cancer-51-aCGH

value: gastric cancer tumor

value: male

value: se

value: positive


title: Gastric Cancer-52-aCGH

value: si

value: IV

value: Sex-matched reference normal human muscle DNA


title: H3K18Ac_(new_lot).2-4_hr_OR_embryo extraction4_array1

description: channel ch1 is input DNA

value: Embryo 2-4hr OR


title: Gastric Cancer-47-aCGH

value: ss

value: IIIA


title: Gastric Cancer-46-aCGH


title: Gastric Cancer-45-aCGH


title: Gastric Cancer-44-aCGH


title: Gastric Cancer-43-aCGH


title: CON_LON_test035_long_0_022

source_name: Whole blood from healthy control

tag: age

value: 28years, when baseline sample taken

value: Male

tag: ethnicity

value: White

value: Control

tag: time post initiation of treatment

value: Yes


title: Gastric Cancer-42-aCGH

value: m

value: negative

value: IA


title: Gastric Cancer-50-aCGH

value: gastric cancer tumor

value: male


title: Gastric Cancer-48-aCGH

value: female

value: se

value: positive

value: IIIB


title: Gastric Cancer-49-aCGH

value: IV

value: Sex-matched reference normal human muscle DNA


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me1 (new lot) (target is H3K4me1) extraction4_array1 channel_1

value: CNS-derived cell-line

value: third instar larval stage

tag: genotype

value: y v f mal

value: Unknown


title: H3K18Ac_(new_lot).2-4_hr_OR_embryo extraction2_array1

description: channel ch1 is input DNA

value: Oregon-R

value: Embryo 2-4hr OR

value: wild type


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody H3K4me1 (new lot) (target is H3K4me1) extraction2_array1 channel_1


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody GAF (target is GAF) extraction4_array1 channel_1


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody Ez (target is Ez) extraction4_array1 channel_1


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody GAF (target is GAF) extraction2_array1 channel_1


description: channel ch1 is input DNA

source_name: Cell Line ML-DmBG3-c2;Antibody Ez (target is Ez) extraction2_array1 channel_1


title: Gastric Cancer-41-aCGH

value: m

value: negative


title: Gastric Cancer-40-aCGH

value: gastric cancer tumor

value: si


title: Chro(Chriz)BR.14-16_hr_OR_embryo extraction8_array1

description: channel ch1 is input DNA

value: Embryo 14-16hr OR


title: Gastric Cancer-39-aCGH

value: male

value: se


title: Chro(Chriz)BR.14-16_hr_OR_embryo extraction6_array1

description: channel ch1 is input DNA


title: Gastric Cancer-33-aCGH

value: ss

value: positive


title: Chro(Chriz)BR.14-16_hr_OR_embryo extraction4_array1

description: channel ch1 is input DNA


title: Gastric Cancer-32-aCGH

value: female

value: IV

value: Sex-matched reference normal human muscle DNA


title: Gastric Cancer-29-aCGH

value: IB


title: Chro(Chriz)BR.14-16_hr_OR_embryo extraction2_array1

description: channel ch1 is input DNA


title: Gastric Cancer-38-aCGH

value: IIIB


title: Gastric Cancer-37-aCGH

value: mp


title: Gastric Cancer-35-aCGH


description: channel ch1 is input DNA

source_name: Developmental Stage Embryo 2-4hr OR;Antibody H3K4Me3(LP) (target is H3K4me3);Strain Oregon-R extraction2_array1 channel_1

value: Oregon-R

value: Embryo 2-4hr OR


description: channel ch1 is input DNA

source_name: Developmental Stage 3rd Instar Larvae;Antibody H3K9me3 (new lot) (target is H3K9me3);Strain Oregon-R extraction4_array1 channel_1

value: 3rd Instar Larvae

value: wild type


title: Gastric Cancer-36-aCGH

value: gastric cancer tumor


title: Gastric Cancer-31-aCGH

value: negative


title: Gastric Cancer-30-aCGH

value: m

value: IA


title: Gastric Cancer-23-aCGH

value: male

value: se


description: channel ch1 is input DNA

source_name: Developmental Stage 3rd Instar Larvae;Antibody H3K9me3 (new lot) (target is H3K9me3);Strain Oregon-R extraction2_array1 channel_1


title: Gastric Cancer-25-aCGH

source_name: Human gastric cancer tissue


title: Gastric Cancer-20-aCGH

source_name: Normal human muscle tissue


title: Gastric Cancer-21-aCGH

value: positive


title: Gastric Cancer-22-aCGH

value: female

value: si


title: Gastric Cancer-34-aCGH

value: ss

value: II

value: Sex-matched reference normal human muscle DNA


title: Gastric Cancer-26-aCGH

value: IIIA


title: Gastric Cancer-19-aCGH

value: IV


title: Gastric Cancer-27-aCGH


title: Gastric Cancer-28-aCGH

value: mp

value: IB


title: expt.493 extraction2_array1

description: channel ch1 is input DNA

source_name: expt.493 extraction2_array1 channel_1

value: Oregon-R

value: Mixed Adult

value: wild type


title: expt.138 extraction4_array1

description: channel ch1 is input DNA

source_name: expt.138 extraction4_array1 channel_1


description: channel ch1 is input DNA

source_name: Developmental Stage 3rd Instar Larvae;Antibody HP1 wa191 (target is HP1a);Strain Oregon-R extraction4_array1 channel_1

value: 3rd Instar Larvae


title: expt.494 extraction4_array1

description: channel ch1 is input DNA

source_name: expt.494 extraction4_array1 channel_1


title: Gastric Cancer-18-aCGH

value: gastric cancer tumor


title: Gastric Cancer-17-aCGH

value: male


description: channel ch1 is input DNA

source_name: Developmental Stage 3rd Instar Larvae;Antibody HP1 wa191 (target is HP1a);Strain Oregon-R extraction2_array1 channel_1


title: Gastric Cancer-16-aCGH


title: expt.197 extraction2_array1

description: channel ch1 is input DNA

source_name: expt.197 extraction2_array1 channel_1


description: channel ch1 is input DNA

source_name: Developmental Stage Embryo 2-4hr OR;Antibody H3K36me3 (target is H3K36me3);Strain Oregon-R extraction4_array1 channel_1

value: Embryo 2-4hr OR


title: Gastric Cancer-15-aCGH

value: positive