title: PDC_control_day4_rep1


title: ESCC with metastasis 1

status: Public on Dec 21 2010

type: genomic

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

description: Replicate 1 of 2. MeDIP-CGI microarray analysis of esophageal squamous cell carcinoma samples with lymph node metastasis.

hyb_protocol: Labelled DNA mixed with Cot-1 DNA and Agilent blocking solution was hybridized to arrays for 40 hours at 67C and 10rpm. Arrays were washed as per Agilent protocol.

scan_protocol: Arrays were washed and scanned immediately with Agilent microarray scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Arrays were processed using Agilent Feature Extraction software and normalized (Background subtraction) using Agilent Chip Analytics software with default settings.

molecule: genomic DNA

organism: Homo sapiens

source_name: MeDIP of ESCC with metastasis 1

label_protocol: Sonicated DNA was labelled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309).

growth_protocol: Esophageal squamous cell carcinoma and metastatic lymph node were obtained from patients who underwent esophagectomy with informed consents.  Samples were stored at -80 ˚C.

extract_protocol: High molecular weight DNA was extracted by the phenol/chloroform method.

treatment_protocol: Five µg of genomic DNA fragmented by sonication was immunoprecipitated with five µg of anti-5-methyl cytidine antibody (Diagnode, Liége, Belgium) in 1 x IP buffer [10 mM Na-phosphate, pH 7.0, 140 mM NaCl, 0.05 % (w/v) Triton X-100]. (Yamashita et al. DNA Res 2009;16:275-86.)

tag: tissue

value: esophageal squamous cell carcinoma (pool of four)

tag: disease status

value: ESCC with metastasis

tag: dna treatment

value: Sonicated and immunoprecipitated with anti-5-methyl cytidine antibody (Diagnode, Liége, Belgium)

source_name: ESCC with metastasis 1

value: Sonicated


title: Metastatic lymph node 1

description: Replicate 1 of 3. MeDIP-CGI microarray analysis of metastatic lymph node from esophageal squamous cell carcinoma patient.

source_name: MeDIP of Metastatic lymph node 1

value: Metastatic lymph node

source_name: Metastatic lymph node 1


title: ESCC without metastasis

description: MeDIP-CGI microarray analysis of esophageal squamous cell carcinoma samples without lymph node metastasis.

source_name: MeDIP of ESCC without metastasis

value: ESCC without metastasis

source_name: ESCC without metastasis


title: ESCC with metastasis 2

description: Replicate 2 of 2. MeDIP-CGI microarray analysis of esophageal squamous cell carcinoma samples with lymph node metastasis.

source_name: MeDIP of ESCC with metastasis 2

source_name: ESCC with metastasis 2


title: Metastatic lymph node 3

description: Replicate 3 of 3. MeDIP-CGI microarray analysis of metastatic lymph node from esophageal squamous cell carcinoma patient.

source_name: MeDIP of Metastatic lymph node 3

source_name: Metastatic lymph node 3


title: Mutant Testis, 16dpc, biol rep 3

status: Public on Dec 20 2010

type: RNA

city: St Lucia

first: Antoine

middle: Dominique

last: ROLLAND

state: QLD, Brisbane

address: 306 Carmody Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

description: Gene expression data from 16dpc Wv/Wv mouse testis

hyb_protocol: Purified labeled cRNAs (20µg) were fragmented and hybridized (16 hours at 45°C) to MG 430 Plus 2.0 GeneChip® arrays (Affymetrix).

scan_protocol: Microarrays were scanned with a GeneChip® scanner 3000 7G (Affymetrix). Raw image files (DAT) as well as feature-level data files (CEL) were finally generated using the Affymetrix GeneChip® Command Console (AGCC).

data_processing: Raw data were normalised using the RMA (Robust Multi-array Analysis; Irizari et al., 2003) in the AMEN (Annotation, Mapping, Expression, Network; Chalmel and Primig, 2008) suite of tools.

label: Biotin

molecule: total RNA

organism: Mus musculus

label_protocol: 50ng of total RNA were used for the synthsis of biotynilated cRNA (GeneChip® 3’ IVT Express Kit User Manual).

extract_protocol: Total RNA was extracted using  a QIAGEN RNeasy Micro column.

tag: sex

value: Male

tag: age

value: 16 days post coitum

tag: genotype

value: Wv/Wv mutant

value: testis


title: Wild-type Testis, 14dpc, biol rep 2

description: Gene expression data from 14dpc wild-type mouse testis

value: 14 days post coitum

value: Wild-type


title: Mutant Testis, 12dpc, biol rep 2

description: Gene expression data from 12dpc Wv/Wv mouse testis

value: 12 days post coitum


title: Mutant Testis, 12dpc, biol rep 3


title: Mutant Testis, 14dpc, biol rep 2

description: Gene expression data from 14dpc Wv/Wv mouse testis


title: Wild-type Ovary, 12dpc, biol rep 2

description: Gene expression data from 12dpc wild-type mouse ovary

value: Female

value: ovary


title: Wild-type Testis, 12dpc, biol rep 1

description: Gene expression data from 12dpc wild-type mouse testis


title: Mutant Testis, 14dpc, biol rep 1


title: Wild-type Testis, 16dpc, biol rep 1

description: Gene expression data from 16dpc wild-type mouse testis


title: Mutant Ovary, 12dpc, biol rep 2

description: Gene expression data from 12dpc Wv/Wv mouse ovary


title: Wild-type Testis, 14dpc, biol rep 1


title: Mutant Testis, 12dpc, biol rep 1


title: Mutant Testis, 16dpc, biol rep 1


title: Mutant Ovary, 12dpc, biol rep 1


title: Wild-type Ovary, 12dpc, biol rep 1


title: Endometrium-prog C (01b9515-2)

city: Brussel

first: Inge

last: Van Vaerenbergh

address: Laarbeeklaan 103

department: EXPA

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Hybridized overnight to the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix).

scan_protocol: Scanned on a 2-µm Affymetrix 3000 GeneScanner.

data_processing: Affymetrix GeneChip Operating (GCOS) 1.4 was used to analyze the resulting image files. The global scaling technique was used to scale the fluorescence intensity of each chip to a target signal of 150.

label: biotin

source_name: Endometrium on day of oocyte retrieval, prog group C

label_protocol: Labeled with biotin using the IVT labeling kit (Affymetrix).

extract_protocol: RNA isolation with RNeasy Mini kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: GnRH-antagonist/rec-FSH stimulated IVF cycle

value: Endometrial biopsy tissue

tag: developmental stage

value: Endometrial dating d4

tag: pregnancy status

value: non-pregnant

tag: progesterone serum level

value: group C (> 1.5ng/ml)


title: Mutant Testis, 16dpc, biol rep 2


title: Wild-type Testis, 16dpc, biol rep 2


title: Wild-type Testis, 16dpc, biol rep 3


title: Wild-type Ovary, 14dpc, biol rep 1

description: Gene expression data from 14dpc wild-type mouse ovary


title: Mutant Ovary, 14dpc, biol rep 2

description: Gene expression data from 14dpc Wv/Wv mouse ovary


title: Mutant Ovary, 14dpc, biol rep 3


title: Mutant Ovary, 14dpc, biol rep 1


title: Wild-type Ovary, 14dpc, biol rep 3


title: Wild-type Testis, 14dpc, biol rep 3


title: Mutant Ovary, 16dpc, biol rep 3

description: Gene expression data from 16dpc Wv/Wv mouse ovary


title: Wild-type Ovary, 14dpc, biol rep 2


title: Mutant Ovary, 16dpc, biol rep 1


title: c088 Extract A Replicate 2

city: Rochester

first: Keith

last: Anderson

state: MN

address: 200 First Street SW

country: USA

institute: Mayo Clinic

description:
c088 Extract A Replicate 2
x88AR2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The software R was used along with bioconductor.  The log 2 tranformation of probe expressions were normalized using the R-package fastlo.

source_name: Breast cancer tumor

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

extract_protocol: RNA was extracted using the Roche Hi-Pure RNA extraction kit in accordance with the prescribed protocol provided with the kit. Quality control was performed using a NanoDrop ND-100 spectrophotometer and an Agilent Bioanalyser.

value: neg

tag: subject id

tag: extract code

value: A

tag: replicate number


title: c088 Extract A Replicate 3

description:
c088 Extract A Replicate 3
x88AR3


title: c088 Extract A Replicate 1

description:
c088 Extract A Replicate 1
x88AR1


title: c096 Extract A Replicate 1

description:
c096 Extract A Replicate 1
x96AR1


title: c096 Extract B Replicate 2

description:
c096 Extract B Replicate 2
x96BR2

value: B


title: c097 Extract A Replicate 1

description:
c097 Extract A Replicate 1
x97AR1


title: c097 Extract A Replicate 3

description:
c097 Extract A Replicate 3
x97AR3


title: c096 Extract B Replicate 1

description:
c096 Extract B Replicate 1
x96BR1


title: Mutant Ovary, 16dpc, biol rep 2


title: c097 Extract A Replicate 2

description:
c097 Extract A Replicate 2
x97AR2


title: c076 Extract B Replicate 2

description:
c076 Extract B Replicate 2
x76BR2

value: pos


title: c076 Extract B Replicate 1

description:
c076 Extract B Replicate 1
x76BR1


title: c076 Extract A Replicate 2

description:
c076 Extract A Replicate 2
x76AR2


title: Wild-type Ovary, 16dpc, biol rep 1

description: Gene expression data from 16dpc wild-type mouse ovary


title: Wild-type Ovary, 16dpc, biol rep 2


title: Wild-type Ovary, 16dpc, biol rep 3


title: c072 Extract A Replicate 3

description:
c072 Extract A Replicate 3
x72AR3


title: Gata1-3

city: Minneapolis

first: Michael

last: Kyba

address: 312 Church St. SE

institute: University of Minnesota

hyb_protocol: Cy3-labeled cDNAs were hybridized overnight (17 hours, 65 C) to Agilent Whole Mouse Genome Oligo Microarrays 4 x 44K.

scan_protocol: Fluorescence signals were detected using Agilent's Microarray Scanner System

data_processing: Raw files were analyzed in genespring11.2 by using the following parameters: Normalization - shift to 75 percentile, Baseline transformation - median of all samples

source_name: Endothelial cells, co-cultured on OP9, 5 days,Doxycycline treatment,Gata1 transduced

label_protocol: 250 ng of each cDNA were used as template for Cy3 labeling which was performed by Miltenyi.

growth_protocol: endothelial cells derived from day 6 Ebs cultured on OP9 stroma for 5 days.

extract_protocol: 5000 cells were sorted into SuperAmp Lysis Buffer and shipped to Miltenyi.

treatment_protocol: Samples were transduced with the appropriate virus and treated with Doxycycline for 5 days, except for the control.

tag: strain

value: 129P2 (also referred to as 129/Ola)

tag: cell type

value: EBs derived endothelial progenitors

tag: transduction protocol

value: HoxA3 + Gata1 upregulation

tag: doxycycline

value: yes


title: Runx1-1

source_name: Endothelial cells, co-cultured on OP9, 5 days,Doxycycline treatment,Runx1 transduced

value: HoxA3 + Runx1 upregulation


title: c006 Extract A Replicate 1

description:
c006 Extract A Replicate 1
x6AR1


title: HoxA3-2

source_name: Endothelial cells, co-cultured on OP9, 5 days,Doxycycline treatment,control transduced

value: HoxA3 upregulation


title: c006 Extract A Replicate 2

description:
c006 Extract A Replicate 2
x6AR2


title: Runx1-3


title: c068 Extract A Replicate 2

description:
c068 Extract A Replicate 2
x68AR2


title: c068 Extract A Replicate 3

description:
c068 Extract A Replicate 3
x68AR3


title: c072 Extract A Replicate 2

description:
c072 Extract A Replicate 2
x72AR2


title: Gata1-1


title: c076 Extract A Replicate 1

description:
c076 Extract A Replicate 1
x76AR1


title: Gata1-2


title: c072 Extract A Replicate 1

description:
c072 Extract A Replicate 1
x72AR1


title: c068 Extract A Replicate 1

description:
c068 Extract A Replicate 1
x68AR1


title: Runx1-2


title: c058 Extract B Replicate 2

description:
c058 Extract B Replicate 2
x58BR2


title: HoxA3-1


title: HoxA3-3


title: Control-2

source_name: Endothelial cells, co-cultured on OP9, 5 days,No Doxycycline treatment,control transduced

value: Control

value: no


title: Endometrium-prog B (01B03931b)

source_name: Endometrium on day of oocyte retrieval, prog group B

value: Endometrial dating d2-3

value: group B (1-1.5 ng/ml)


title: c058 Extract A Replicate 1

description:
c058 Extract A Replicate 1
x58AR1


title: PDC_null_day4_rep2

city: New York

first: Boris

last: Reizis

state: NY

department: Microbiology and Immunology

institute: Columbia University Medical Center

hyb_protocol: Labeled RNA samples (10 ug/array) were hybridized at the HICCC Genomics Facility of the Columbia University according to the manufacturer's instructions.

scan_protocol: Array scanning and raw data processing were done using GCOS 1.4 software (Affymetrix).

source_name: Ex vivo sorted plasmacytoid dendritic cells (PDC)

label_protocol: The aRNA was amplified without labeling in the first round, and then labeled with Biotin-16-UTP and Biotin-11-CTP in the second round. Labeled aRNA was fragmented in RNA Fragmentation Buffer (QIAGEN) prior to hybridization.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen).

treatment_protocol: Inducible deletion of E2-2 (Tcf4) has been performed by administering tamoxifen to conditional E2-2flox/flox Rosa26-CreER+ mice or to E2-2flox/flox Rosa26-CreER- control littermates. Six days later total splenocytes were isolated, pooled from 2-3 mice and enriched for lineage (CD3/CD19)-negative cells by magnetic selection. PDC (CD11b- B220+ CD11clow Bst2+) were isolated using BD FACSAria II flow sorter directly into Trizol reagent.

tag: genotype/varation

value: E2-2-deficient (null)

tag: time point

value: spleen

value: PDC

tag: agent

value: tamoxifen


title: c058 Extract A Replicate 2

description:
c058 Extract A Replicate 2
x58AR2

value: A


title: c051 Extract B Replicate 2

description:
c051 Extract B Replicate 2
x51BR2

value: B


title: c049 Extract A Replicate 3

description:
c049 Extract A Replicate 3
x49AR3

value: pos


title: c058 Extract B Replicate 1

description:
c058 Extract B Replicate 1
x58BR1


title: c051 Extract B Replicate 1

description:
c051 Extract B Replicate 1
x51BR1


title: c049 Extract A Replicate 2

description:
c049 Extract A Replicate 2
x49AR2


title: c051 Extract A Replicate 1

description:
c051 Extract A Replicate 1
x51AR1


title: c051 Extract A Replicate 2

description:
c051 Extract A Replicate 2
x51AR2


title: Control-1

value: 129P2 (also referred to as 129/Ola)


title: c046 Extract A Replicate 2

description:
c046 Extract A Replicate 2
x46AR2


title: c046 Extract A Replicate 3

description:
c046 Extract A Replicate 3
x46AR3


title: c042 Extract B Replicate 1

description:
c042 Extract B Replicate 1
x42BR1


title: c046 Extract A Replicate 1

description:
c046 Extract A Replicate 1
x46AR1


title: c042 Extract A Replicate 2

description:
c042 Extract A Replicate 2
x42AR2


title: Control-3

value: EBs derived endothelial progenitors


title: c042 Extract A Replicate 1

description:
c042 Extract A Replicate 1
x42AR1


title: c042 Extract B Replicate 2

description:
c042 Extract B Replicate 2
x42BR2


title: c035 Extract A Replicate 2

description:
c035 Extract A Replicate 2
x35AR2


title: c035 Extract A Replicate 3

description:
c035 Extract A Replicate 3
x35AR3


title: c035 Extract A Replicate 1

description:
c035 Extract A Replicate 1
x35AR1


title: c030 Extract A Replicate 2

description:
c030 Extract A Replicate 2
x30AR2


title: c030 Extract A Replicate 1

description:
c030 Extract A Replicate 1
x30AR1


title: c030 Extract A Replicate 3

description:
c030 Extract A Replicate 3
x30AR3


title: c027 Extract A Replicate 3

description:
c027 Extract A Replicate 3
x27AR3


title: c027 Extract A Replicate 2

description:
c027 Extract A Replicate 2
x27AR2


title: c027 Extract A Replicate 1

description:
c027 Extract A Replicate 1
x27AR1


title: Coriell_gm13114

city: Morristown

first: Nathan

last: Treff

address: 111 Madison Ave

institute: RMA of New Jersey

description: Three of our reference samples (1-3) were taken from the RMA of New Jersey  patient DNA bank with patient consent and IRB approval.  Eleven of the reference samples (4-14) were generated from karyotipically normal female lymphocyte cell lines purchased from the Coriell Cell Repository (Camden, NJ).

hyb_protocol: DNA was digested with the NspI restriction enzyme, ligated to an adapter molecule, PCR amplified, fragmented with DNase I, labeled and hybridized to each array according to the manufacturer's instructions (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

scan_protocol: Each array was washed using Affymetrix fluidics station 640, and scanned using the Gene Chip Scanner 7G as recommended (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

data_processing: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls.  Copy number and loss of heterozygosity were calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual)  analysis against a reference set consisting of three normal females from in house gDNA  bank, 11 normal females from Coriel cell lines and 16 normal females from the HapMap database (www.hapmap.org).

source_name: Lymphocyte Cell Line

label_protocol: Fragmented DNA was biotinylated using the manufacturers recommendations (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930)

growth_protocol: Four experimental and eleven reference human fibroblast cell lines were cultured as suggested by Coriell Cell BioRepository(Camden, NJ).

extract_protocol: cells underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).

tag: cell line karyotype

value: lymphocyte cell line

tag: cell line


title: Coriell_gm13118


title: c026 Extract A Replicate 2

description:
c026 Extract A Replicate 2
x26AR2


title: c026 Extract A Replicate 3

description:
c026 Extract A Replicate 3
x26AR3


title: c026 Extract A Replicate 1

description:
c026 Extract A Replicate 1
x26AR1


title: Coriell_gm10859


title: DNAbank_1M

source_name: gDNA

tag: sample type

value: gDNA


title: Coriell_gm13119


title: Coriell_gm11870


title: Coriell_gm07441


title: Lymphocyte, Cell Line 3, Sample 2 [GenomePlex]

description: Hybridized to 250K_Nsp

data_processing:
CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls. Copy number and loss of heterozygosity were calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual) analysis against a reference set of 30 normal females from the HapMap database (www.hapmap.org).
Copy number data not provided by submitter.

growth_protocol: Four human fibroblast cell lines were cultured as suggested by Coriell Cell Repository

extract_protocol: Single fibroblast cells underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).

value: Lymphocyte Cell Line

value: lymphocyte single cell sample, cell line 3


title: DNAbank_6M


title: Coriell_gm11875


title: Coriell_gm07555


title: c018 Extract A Replicate 2

description:
c018 Extract A Replicate 2
x18AR2


title: Lymphocyte, Cell Line 3, Sample 3 [GenomePlex]

description: Hybridized to 250K_Nsp


title: Coriell_gm07439


title: DNAbank_9M


title: Lymphoctye, Cell Line 4, Sample 3 [GenomePlex]

description: Hybridized to 250K_Nsp

value: lymphocyte single cell sample, cell line 4


title: c018 Extract B Replicate 2

description:
c018 Extract B Replicate 2
x18BR2


title: Lymphoctye, Cell Line 4, Sample 1 [GenomePlex]

description: Hybridized to 250K_Nsp


title: Lymphoctye, Cell Line 4, Sample 2 [GenomePlex]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 1, Sample 2 [GenomePlex]

description: Hybridized to 250K_Nsp

value: lymphocyte single cell sample, cell line 1


title: c165 Extract B Replicate 2

description:
c165 Extract B Replicate 2
x165BR2

value: neg


title: c165 Extract B Replicate 1

description:
c165 Extract B Replicate 1
x165BR1


title: Lymphocyte, Cell Line 3, Sample 1 [GenomePlex]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 2, Sample 3 [GenomePlex]

description: Hybridized to 250K_Nsp

value: lymphocyte single cell sample, cell line 2


title: Lymphocyte, Cell Line 1, Sample 1 [GenomePlex]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 2, Sample 2 [GenomePlex]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 1, Sample 3 [GenomePlex]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 2, Sample 1 [GenomePlex]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 4, Sample 3 [REPLI-g]

description: Hybridized to 250K_Nsp


title: c165 Extract A Replicate 1

description:
c165 Extract A Replicate 1
x165AR1


title: c163 Extract A Replicate 3

description:
c163 Extract A Replicate 3
x163AR3


title: Lymphocyte, Cell Line 4, Sample 4 [REPLI-g]

description: Hybridized to 250K_Nsp


title: c163 Extract A Replicate 1

description:
c163 Extract A Replicate 1
x163AR1


title: c163 Extract A Replicate 2

description:
c163 Extract A Replicate 2
x163AR2


title: c165 Extract A Replicate 2

description:
c165 Extract A Replicate 2
x165AR2


title: c162 Extract A Replicate 2

description:
c162 Extract A Replicate 2
x162AR2


title: c162 Extract A Replicate 3

description:
c162 Extract A Replicate 3
x162AR3


title: c162 Extract A Replicate 1

description:
c162 Extract A Replicate 1
x162AR1


title: c158 Extract A Replicate 3

description:
c158 Extract A Replicate 3
x158AR3


title: c018 Extract A Replicate 1

description:
c018 Extract A Replicate 1
x18AR1


title: c158 Extract A Replicate 1

description:
c158 Extract A Replicate 1
x158AR1


title: Lymphocyte, Cell Line 3, Sample 1 [REPLI-g]

description: Hybridized to 250K_Nsp


title: c145 Extract A Replicate 3

description:
c145 Extract A Replicate 3
x145AR3


title: c145 Extract A Replicate 2

description:
c145 Extract A Replicate 2
x145AR2


title: Lymphocyte, Cell Line 3, Sample 2 [REPLI-g]

description: Hybridized to 250K_Nsp


title: c145 Extract A Replicate 1

description:
c145 Extract A Replicate 1
x145AR1


title: Lymphocyte, Cell Line 4, Sample 2 [REPLI-g]

description: Hybridized to 250K_Nsp


title: c158 Extract A Replicate 2

description:
c158 Extract A Replicate 2
x158AR2


title: c143 Extract A Replicate 3

description:
c143 Extract A Replicate 3
x143AR3


title: c143 Extract A Replicate 2

description:
c143 Extract A Replicate 2
x143AR2


title: Lymphocyte, Cell Line 3, Sample 3 [REPLI-g]

description: Hybridized to 250K_Nsp


title: c018 Extract B Replicate 1

description:
c018 Extract B Replicate 1
x18BR1


title: c139 Extract B Replicate 2

description:
c139 Extract B Replicate 2
x139BR2


title: Lymphocyte, Cell Line 2, Sample 2 [REPLI-g]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 2, Sample 3 [REPLI-g]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 2, Sample 1 [REPLI-g]

description: Hybridized to 250K_Nsp


title: c139 Extract A Replicate 2

description:
c139 Extract A Replicate 2
x139AR2


title: c139 Extract B Replicate 1

description:
c139 Extract B Replicate 1
x139BR1


title: Lymphocyte, Cell Line 4, Sample 3 [GenomePhi]

description: Hybridized to 250K_Nsp


title: c139 Extract A Replicate 1

description:
c139 Extract A Replicate 1
x139AR1


title: c120 Extract B Replicate 2

description:
c120 Extract B Replicate 2
x120BR2


title: Lymphoctye, Cell Line 3, Sample 2 [GenomePhi]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 4, Sample 2 [GenomePhi]

description: Hybridized to 250K_Nsp


title: c120 Extract A Replicate 2

description:
c120 Extract A Replicate 2
x120AR2


title: c120 Extract B Replicate 1

description:
c120 Extract B Replicate 1
x120BR1


title: Lymphoctye, Cell Line 3, Sample 3 [GenomePhi]

description: Hybridized to 250K_Nsp


title: K41 NoDox-3

description: K41 NoDox-3

data_processing: The data were normalised using cubic spline normalisation with BeadStudio then median normalisation with GeneSpring

source_name: differentiated mouse ES cells 4155448007 E

label_protocol: Standard Illumina label protocol

growth_protocol: EBs were differentiated until day 6. Endothelial (FV) or Hematopoietic (K41) progenitors cells were sorted by facs

extract_protocol: RNA was isolated using the Trizol protocol

treatment_protocol: Doxycycline treatment was performed for 6 hours on day 6

value: no


title: Lymphoctye, Cell Line 3, Sample 1 [GenomePhi]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 2, Sample 2 [GenomePhi]

description: Hybridized to 250K_Nsp


title: K41 Dox-2

description: K41 Dox-2

source_name: differentiated mouse ES cells 4155448007 D

value: yes


title: Lymphocyte, Cell Line 1, Sample 3 [REPLI-g]

description: Hybridized to 250K_Nsp


title: Lymphocyte, Cell Line 2, Sample 3 [GenomePhi]

description: Hybridized to 250K_Nsp


title: c143 Extract A Replicate 1

description:
c143 Extract A Replicate 1
x143AR1


title: Lymphocyte, Cell Line 1, Sample 2 [REPLI-g]

description: Hybridized to 250K_Nsp


title: c120 Extract A Replicate 1

description:
c120 Extract A Replicate 1
x120AR1


title: Lymphocyte, Cell Line 1, Sample 1 [REPLI-g]

description: Hybridized to 250K_Nsp


title: K41 Dox-3

description: K41 Dox-3

source_name: differentiated mouse ES cells 4155448007 F


title: Lymphocyte, Cell Line 4, Sample 1 [GenomePhi]

description: Hybridized to 250K_Nsp


title: ago4-1, biological rep2

city: Toledo

first: Scott

last: Leisner

state: OH

address: 2801 West Bancroft Street

department: Biological Sciences

institute: University of Toledo

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with GCOS and data mining tool.

organism: Arabidopsis thaliana

source_name: ago4 mutant 5 week plant

label_protocol: standard Affymetrix protocol

growth_protocol: Arabidopsis were grown in hydroponics under 16h light

extract_protocol: Trizol extraction of total RNA was performed according to the manufacture's insturctions

tag: tissue

value: whole plants

tag: genotype

tag: age

value: Five weeks


title: Lymphocyte, Cell Line 2, Sample 1 [GenomePhi]

description: Hybridized to 250K_Nsp


title: c118 Extract A Replicate 3

description:
c118 Extract A Replicate 3
x118AR3

value: A


title: Lymphoctye, Cell Line 1, Sample 3 [GenomePhi]

description: Hybridized to 250K_Nsp


title: c118 Extract A Replicate 2

description:
c118 Extract A Replicate 2
x118AR2


title: FV Dox-3

description: FV Dox-3

source_name: differentiated mouse ES cells 4155448007 B

value: FV


title: wild-type La-er, biological rep2

source_name: wild type 5 week plants

value: La-er


title: c118 Extract A Replicate 1

description:
c118 Extract A Replicate 1
x118AR1


title: FV NoDox- 2

description: FV NoDox- 2

source_name: differentiated mouse ES cells 1880222045 C

value: 129P2 (also referred to as 129/Ola)


title: K41 NoDox-2

description: K41 NoDox-2

source_name: differentiated mouse ES cells 4155448007 C


title: gDNA, Cell Line 4, Sample 2

description: Hybridized to 250K_Nsp


title: FV Dox- 2

description: FV Dox- 2

source_name: differentiated mouse ES cells 1880222045 D


title: FV NoDox-3

description: FV NoDox-3

source_name: differentiated mouse ES cells 4155448007 A


title: K41 NoDox-1

description: K41 NoDox-1

source_name: differentiated mouse ES cells 1880222045 E


title: Lymphoctye, Cell Line 1, Sample 1 [GenomePhi]

description: Hybridized to 250K_Nsp


title: Lymphoctye, Cell Line 1, Sample 2 [GenomePhi]

description: Hybridized to 250K_Nsp


title: c114 Extract A Replicate 3

description:
c114 Extract A Replicate 3
x114AR3

source_name: Breast cancer tumor


title: Tumor_II72

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

institute: Dartmouth Medical School

description:
DNA (bisulfite modified).
II72

hyb_protocol: Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93 (PMID 16449502). Bisulfite-converted DNAs are biotinylated and hybridized to query oligos, and washed. The hybridized oligos are then extended and ligated to create amplifiable templates with methylation-specific primers. The PCR that follows uses fluorescently labeled universal PCR primers.

scan_protocol: Arrays were imaged using a BeadArray Reader scanner (Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93).

data_processing: Illumina BeadStudio 3.1.3 with methylation module version 3.2 was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level (β) = (max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. Detection P-values determined poor performing samples (n=2) and CpG loci (n=8), which were removed from analysis. X chromosome loci were also removed, leaving 1413 CpG loci associated with 773 genes. Raw average beta values were used and not subjected to normalization as per manufacturer's recommendations.

source_name: Tumor DNA

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

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

value: brain tumor

tag: histology

value: OD II

tag: idh1 mutation


title: gDNA,Cell Line 3, Sample 1

description: Hybridized to 250K_Nsp

value: gDNA


title: Tumor_90A71

description:
DNA (bisulfite modified).
90A71


title: Normal_99A30

description:
DNA (bisulfite modified).
99A30

source_name: Normal DNA

value: brain

value: Normal


title: wild-type La-er, biological rep1


title: FV NoDox-1

description: FV NoDox-1

source_name: differentiated mouse ES cells 1880222045 A


title: Tumor_86A71

description:
DNA (bisulfite modified).
86A71

value: OA II


title: FV Dox-1

description: FV Dox-1

source_name: differentiated mouse ES cells 1880222045 B


title: gDNA, Cell Line 4, Sample 1

description: Hybridized to 250K_Nsp

source_name: Lymphocyte Cell Line

value: Lymphocyte Cell Line


title: c114 Extract A Replicate 2

description:
c114 Extract A Replicate 2
x114AR2

value: neg

tag: subject id

tag: extract code


title: Tumor_56A87

description:
DNA (bisulfite modified).
56A87

value: GBM

value: Yes


title: Tumor_53A39

description:
DNA (bisulfite modified).
53A39


title: Tumor_81A39

description:
DNA (bisulfite modified).
81A39


title: Tumor_71A

description:
DNA (bisulfite modified).
71A

value: OA III


title: c096 Extract A Replicate 1

description:
c096 Extract A Replicate 1
x96AR1

source_name: Breast cancer Tumor

extract_protocol: RNA was extracted using the Roche Hi-Pure RNA extraction kit in accordance with the prescribed protocol provided with the kit.Quality control was performed using a  NanoDrop ND-100 spectrophotometer and an Agilent Bioanalyzer.

tag: replicate number


title: Tumor_61A1

description:
DNA (bisulfite modified).
61A1


title: gDNA, Cell Line 3, Sample 2

description: Hybridized to 250K_Nsp

tag: cell type


title: Tumor_35A92

description:
DNA (bisulfite modified).
35A92


title: Tumor_39A84

description:
DNA (bisulfite modified).
39A84

value: No


title: Tumor_31A64

description:
DNA (bisulfite modified).
31A64

value: AS II


title: c114 Extract A Replicate 1

description:
c114 Extract A Replicate 1
x114AR1

value: A


title: c105 Extract B Replicate 1

description:
c105 Extract B Replicate 1
x105BR1

value: B


title: c096 Extract B Replicate 1

description:
c096 Extract B Replicate 1
x96BR1


title: gDNA, Cell Line 1, Sample 2 (Coriell_gm00321_2)

description: Hybridized to 250K_Nsp

source_name: Fibroblast Cell Line

value: Fibroblast Cell Line


title: c105 Extract B Replicate 2

description:
c105 Extract B Replicate 2
x105BR2


title: c105 Extract A Replicate 2

description:
c105 Extract A Replicate 2
x105AR2


title: Tumor_46A26

description:
DNA (bisulfite modified).
46A26

value: AS III


title: K41 Dox-1

description: K41 Dox-1

source_name: differentiated mouse ES cells 1880222045 F

tag: strain

value: 129P2 (also referred to as 129/Ola)

value: yes


title: Tumor_25A27

description:
DNA (bisulfite modified).
25A27

value: brain tumor


title: c105 Extract A Replicate 1

description:
c105 Extract A Replicate 1
x105AR1


title: Tumor_16A71

description:
DNA (bisulfite modified).
16A71


title: c076 Extract A Replicate 2

description:
c076 Extract A Replicate 2
x76AR2

value: pos


title: c076 Extract B Replicate 1

description:
c076 Extract B Replicate 1
x76BR1


title: Normal_85A37

description:
DNA (bisulfite modified).
85A37

value: brain

value: Normal


title: Tumor_86A15

description:
DNA (bisulfite modified).
86A15


title: Tumor_8B

description:
DNA (bisulfite modified).
8B

value: OA II


title: Tumor_9A32

description:
DNA (bisulfite modified).
9A32


title: ago4-1, biological rep1

source_name: ago4 mutant 5 week plant

value: whole plants

value: Five weeks


title: Tumor_11A50

description:
DNA (bisulfite modified).
11A50

value: EP


title: Tumor_69V

description:
DNA (bisulfite modified).
69V

value: Yes


title: Tumor_56A10

description:
DNA (bisulfite modified).
56A10


title: Tumor_5A39

description:
DNA (bisulfite modified).
5A39

value: No


title: Tumor_52A8

description:
DNA (bisulfite modified).
52A8

value: GBM


title: c076 Extract A Replicate 1

description:
c076 Extract A Replicate 1
x76AR1

value: A


title: Tumor_79A17

description:
DNA (bisulfite modified).
79A17


title: gDNA, Cell Line 2, Sample 1

description: Hybridized to 250K_Nsp

value: gDNA


title: c076 Extract B Replicate 2

description:
c076 Extract B Replicate 2
x76BR2

value: B


title: c072 Extract A Replicate 1

description:
c072 Extract A Replicate 1
x72AR1


title: Tumor_45A43

description:
DNA (bisulfite modified).
45A43

value: AS II


title: Tumor_38A84

description:
DNA (bisulfite modified).
38A84


title: c058 Extract A Replicate 2

description:
c058 Extract A Replicate 2
x58AR2

value: neg


title: c068 Extract A Replicate 1

description:
c068 Extract A Replicate 1
x68AR1


title: c058 Extract A Replicate 1

description:
c058 Extract A Replicate 1
x58AR1


title: Tumor_24A44

description:
DNA (bisulfite modified).
24A44


title: Tumor_2A42

description:
DNA (bisulfite modified).
2A42

value: OD II


title: Tumor_16A30

description:
DNA (bisulfite modified).
16A30

value: brain tumor


title: Tumor_10C

description:
DNA (bisulfite modified).
10C


title: Tumor_35A77

description:
DNA (bisulfite modified).
35A77


title: c051 Extract B Replicate 2

description:
c051 Extract B Replicate 2
x51BR2

value: pos


title: c058 Extract B Replicate 2

description:
c058 Extract B Replicate 2
x58BR2


title: Tumor_II81

description:
DNA (bisulfite modified).
II81


title: c051 Extract B Replicate 1

description:
c051 Extract B Replicate 1
x51BR1


title: Tumor_87A78

description:
DNA (bisulfite modified).
87A78


title: Tumor_95A32

description:
DNA (bisulfite modified).
95A32

value: AS III


title: Tumor_48A42

description:
DNA (bisulfite modified).
48A42


title: Tumor_61A51

description:
DNA (bisulfite modified).
61A51


title: Tumor_57A83

description:
DNA (bisulfite modified).
57A83


title: Tumor_72A56

description:
DNA (bisulfite modified).
72A56


title: Tumor_81Q

description:
DNA (bisulfite modified).
81Q

value: OA III


title: Tumor_40A58

description:
DNA (bisulfite modified).
40A58


title: c049 Extract A Replicate 2

description:
c049 Extract A Replicate 2
x49AR2


title: c051 Extract A Replicate 2

description:
c051 Extract A Replicate 2
x51AR2


title: c058 Extract B Replicate 1

description:
c058 Extract B Replicate 1
x58BR1


title: c051 Extract A Replicate 1

description:
c051 Extract A Replicate 1
x51AR1


title: Tumor_3282

description:
DNA (bisulfite modified).
3282


title: c049 Extract A Replicate 1

description:
c049 Extract A Replicate 1
x49AR1


title: Tumor_3656

description:
DNA (bisulfite modified).
3656

value: PA


title: Tumor_53A65

description:
DNA (bisulfite modified).
53A65


title: c042 Extract B Replicate 1

description:
c042 Extract B Replicate 1
x42BR1


title: c046 Extract A Replicate 2

description:
c046 Extract A Replicate 2
x46AR2


title: Tumor_25A33

description:
DNA (bisulfite modified).
25A33


title: Normal_36A30

description:
DNA (bisulfite modified).
36A30

value: brain

value: Normal


title: Tumor_16B9

description:
DNA (bisulfite modified).
16B9

value: OA II


title: Tumor_97A49

description:
DNA (bisulfite modified).
97A49


title: gDNA, Cell Line 1, Sample 1 (Coriell_gm00321_1)

description: Hybridized to 250K_Nsp

value: Fibroblast Cell Line


title: c046 Extract A Replicate 1

description:
c046 Extract A Replicate 1
x46AR1


title: c035 Extract A Replicate 1

description:
c035 Extract A Replicate 1
x35AR1


title: Tumor_75A12

description:
DNA (bisulfite modified).
75A12


title: Tumor_88A83

description:
DNA (bisulfite modified).
88A83

value: No


title: Tumor_84A42

description:
DNA (bisulfite modified).
84A42


title: gDNA, Cell Line 2, Sample 2

description: Hybridized to 250K_Nsp


title: Tumor_49A88

description:
DNA (bisulfite modified).
49A88

value: GBM


title: Tumor_59A47

description:
DNA (bisulfite modified).
59A47


title: Tumor_53A9

description:
DNA (bisulfite modified).
53A9


title: Tumor_64A90

description:
DNA (bisulfite modified).
64A90

value: EP


title: c042 Extract A Replicate 1

description:
c042 Extract A Replicate 1
x42AR1

value: A


title: Tumor_13A4

description:
DNA (bisulfite modified).
13A4

value: Yes


title: Tumor_42A54

description:
DNA (bisulfite modified).
42A54


title: Tumor_36A9

description:
DNA (bisulfite modified).
36A9


title: Tumor_33A32

description:
DNA (bisulfite modified).
33A32


title: Tumor_26A5

description:
DNA (bisulfite modified).
26A5


title: c027 Extract A Replicate 1

description:
c027 Extract A Replicate 1
x27AR1


title: c026 Extract A Replicate 1

description:
c026 Extract A Replicate 1
x26AR1


title: Tumor_18A83

description:
DNA (bisulfite modified).
18A83

value: AS II


title: Tumor_14A47

description:
DNA (bisulfite modified).
14A47


title: c018 Extract B Replicate 1

description:
c018 Extract B Replicate 1
x18BR1

value: neg

value: B


title: c030 Extract A Replicate 1

description:
c030 Extract A Replicate 1
x30AR1


title: c018 Extract A Replicate 1

description:
c018 Extract A Replicate 1
x18AR1


title: Normal_73A30

description:
DNA (bisulfite modified).
73A30


title: Tumor_98A77

description:
DNA (bisulfite modified).
98A77

value: brain tumor


title: Tumor_8A21

description:
DNA (bisulfite modified).
8A21


title: Tumor_84A74

description:
DNA (bisulfite modified).
84A74


title: Tumor_76A30

description:
DNA (bisulfite modified).
76A30


title: c165 Extract B Replicate 2

description:
c165 Extract B Replicate 2
x165BR2


title: Tumor_65A32

description:
DNA (bisulfite modified).
65A32


title: Tumor_53Y

description:
DNA (bisulfite modified).
53Y


title: Tumor_59H

description:
DNA (bisulfite modified).
59H


title: c165 Extract B Replicate 1

description:
c165 Extract B Replicate 1
x165BR1


title: c165 Extract A Replicate 1

description:
c165 Extract A Replicate 1
x165AR1


title: c163 Extract A Replicate 1

description:
c163 Extract A Replicate 1
x163AR1


title: Tumor_44A30

description:
DNA (bisulfite modified).
44A30


title: Tumor_51A37

description:
DNA (bisulfite modified).
51A37


title: c165 Extract A Replicate 2

description:
c165 Extract A Replicate 2
x165AR2


title: Tumor_34A32

description:
DNA (bisulfite modified).
34A32


title: Tumor_26T

description:
DNA (bisulfite modified).
26T


title: c163 Extract A Replicate 2

description:
c163 Extract A Replicate 2
x163AR2


title: Lung 23.75-1

city: Buffalo

first: Siddharth

last: Sukumaran

address: 109 Cooke Hall, University at Buffalo, North/Amherst Campus

department: Dept of Biological Sciences

institute: State University of New York at Buffalo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChips Rat Genome 230-2. S450_001 Fluidics Script was used for Staining.

scan_protocol: The array chips were scanned using GeneChip scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0)

organism: Rattus norvegicus

source_name: Wistar rat lungs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from the purified total RNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and was further purified using RNeasy mini-column

tag: circadian time

value: Wistar

value: lung


title: Lung 23.75-2


title: c162 Extract A Replicate 1

description:
c162 Extract A Replicate 1
x162AR1


title: Tumor_15A39

description:
DNA (bisulfite modified).
15A39

value: OD II


title: c158 Extract A Replicate 1

description:
c158 Extract A Replicate 1
x158AR1


title: Tumor_102

description:
DNA (bisulfite modified).
102


title: Lung 23.75-3


title: Lung 23-3


title: Normal_79A23

description:
DNA (bisulfite modified).
79A23


title: c145 Extract A Replicate 1

description:
c145 Extract A Replicate 1
x145AR1


title: Tumor_99A52

description:
DNA (bisulfite modified).
99A52


title: Tumor_3785

description:
DNA (bisulfite modified).
3785

value: PA


title: Tumor_85A55

description:
DNA (bisulfite modified).
85A55


title: Tumor_76A51

description:
DNA (bisulfite modified).
76A51


title: Lung 23-1


title: Tumor_20A46

description:
DNA (bisulfite modified).
20A46


title: Tumor_8A81

description:
DNA (bisulfite modified).
8A81


title: c145 Extract A Replicate 2

description:
c145 Extract A Replicate 2
x145AR2


title: c139 Extract B Replicate 1

description:
c139 Extract B Replicate 1
x139BR1


title: Tumor_59Z

description:
DNA (bisulfite modified).
59Z


title: Tumor_67A47

description:
DNA (bisulfite modified).
67A47


title: Tumor_528

description:
DNA (bisulfite modified).
528


title: Tumor_54A7

description:
DNA (bisulfite modified).
54A7


title: Lung 22-2


title: Lung 22-1


title: c139 Extract A Replicate 1

description:
c139 Extract A Replicate 1
x139AR1


title: LD muscle_Ujumqin_135d(dpc)_rep 3

city: Beijing

first: Lixin

last: Du

address: 2 # Yuanmingyuan West Rd

department: Institute of Animal Sciences

country: China

institute: Chinese Academy of Agricultural Sciences

description: Gene expression in fetal LD muscle at 135d(dpc) in Ujumqin sheep

hyb_protocol: The generated targets were mixed and subjected to hybridization to the Sheep Gene Expression Microarray (Agilent) according to the manufacturer's protocol.

scan_protocol: Scanning of the microarrays was done by a DNA microarray scanner (Agilent). Some important scanning parameters were: 5μm of scan resolution, PMT with 100% and10% one time respectively. All probe sets whose signals were reported “absent” flag call on all 31arrays were filtered out, and those from probe sets called “present” on at least one chip were used for further analysis.

data_processing: Scanner output image files were normalized and filtered using Feature Extraction Software v10.5 (Agilent) and the quantile method was used for data normalization.

organism: Ovis aries

source_name: LD muscle,Ujumqin,135 day(dpc),replicate 3

label_protocol: Target preparation was performed using a Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's protocol. The total RNA extracted from longissimus dosi muscles from each individual were labeled with Cy3 fluorescence.

growth_protocol: All purebred female animals involved were selected based on their age (3-5 years old), body weight (50-55kg) and body size. These selected animals were subjected to pre-feeding for 45 days. Seventy eight Ujumqin and fifty four Texel ewes were prepared for the study. All ewes were synchronized for estrus by implanted CIDR (Pharmacia & Upjohn Pty Limited, NSW, and AU) and intramuscular injection PMSG (Ningbo Renjian Pharmaceutical Co., Ltd, CN) disposal according to the manufacturer’s protocol, followed by artificial insemination using the corresponding breed sires’ sperm. Three pregnant ewes were subject to caesarean section to collect fetuses from Texel and Ujumqin sheep at five fetal development stages (70, 85, 100, 120, 135d of gestation) and eight development stages (70, 85, 100, 120, 135d of gestation, birth, 1 month and 2 month), respectively.

extract_protocol: Total RNA was extracted from the frozen longissimus dorsi using an RNeasy Mini Kit with DNase treatment (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol. The RNA quantity and quality were measured by ND-1000 (Nanodrop, Wilmington, DE, USA) and 2100 Bioanalyzer (Agilent, Santa Clara, CA,USA), respectively.

treatment_protocol: The longissimus dorsi from every fetus were dissected and weighed.The first sample (3 g) was dissected and frozen rapidly whole in isopentane chilled over liquid nitrogen for histology and immunohistochemistry examination. The second sample (5 g) was snap frozen in liquid nitrogen for gene expression analysis.

value: skeletal muscle

tag: development stage

value: 135 day(dpc)

tag: breed

value: Ujumqin

tag: gender

value: female


title: Tumor_35A29

description:
DNA (bisulfite modified).
35A29


title: LD muscle_Ujumqin_2 month(postnatal)_rep 3

description: Gene expression in fetal LD muscle at 2 month(postnatal) in Ujumqin sheep

source_name: LD muscle,Ujumqin,2 month(posnatal),replicate 3

value: 2 month(postnatal)


title: Tumor_2972

description:
DNA (bisulfite modified).
2972

value: AS III


title: Lung 22-3


title: Tumor_21A37

description:
DNA (bisulfite modified).
21A37

value: No


title: Tumor_15A45

description:
DNA (bisulfite modified).
15A45


title: LD muscle_Ujumqin_135d(dpc)_rep 2

source_name: LD muscle,Ujumqin,135 day(dpc),replicate 2


title: Lung 20-3


title: Lung 23-2


title: Lung 20-2


title: Tumor_10A86

description:
DNA (bisulfite modified).
10A86

value: GBM


title: Lung 18-3


title: Lung 20-1


title: Normal_28A24

description:
DNA (bisulfite modified).
28A24

value: brain

value: Normal


title: LD muscle_Ujumqin_2 month(postnatal)_rep 1

source_name: LD muscle,Ujumqin,2 month(posnatal),replicate 1


title: Lung 18-2


title: Tumor_88A46

description:
DNA (bisulfite modified).
88A46

value: AS II

value: Yes


title: Tumor_97A1

description:
DNA (bisulfite modified).
97A1

value: brain tumor

value: OA II


title: Tumor_38A36

description:
DNA (bisulfite modified).
38A36

value: EP


title: Tumor_44A55

description:
DNA (bisulfite modified).
44A55


title: LD muscle_Texel_135d(dpc)_rep 3

description: Gene expression in fetal LD muscle at 135d(dpc) in Texel sheep

source_name: LD muscle,Texel,135 day(dpc),replicate 3

value: Texel

value: male


title: Tumor_83A87

description:
DNA (bisulfite modified).
83A87


title: Lung 18-1

value: Wistar

value: lung


title: Tumor_72A82

description:
DNA (bisulfite modified).
72A82


title: Tumor_6413

description:
DNA (bisulfite modified).
6413

value: PA


title: LD muscle_Ujumqin_135d(dpc)_rep 1

source_name: LD muscle,Ujumqin,135 day(dpc),replicate 1

value: skeletal muscle

value: 135 day(dpc)

value: Ujumqin

value: female


title: Tumor_58C

description:
DNA (bisulfite modified).
58C

value: OA III


title: Tumor_4291

description:
DNA (bisulfite modified).
4291


title: LD muscle_Ujumqin_2 month(postnatal)_rep 2

source_name: LD muscle,Ujumqin,2 month(posnatal),replicate 2

value: 2 month(postnatal)


title: Tumor_49A87

description:
DNA (bisulfite modified).
49A87

source_name: Tumor DNA

value: GBM


title: LD muscle_Texel_135d(dpc)_rep 2

source_name: LD muscle,Texel,135 day(dpc),replicate 2


title: Tumor_32A83

description:
DNA (bisulfite modified).
32A83

value: AS II


title: Tumor_36A8

description:
DNA (bisulfite modified).
36A8


title: Tumor_26A1

description:
DNA (bisulfite modified).
26A1

value: No


title: Tumor_18A55

description:
DNA (bisulfite modified).
18A55

value: brain tumor

value: Yes


title: LD muscle_Texel_120d(dpc)_rep 3

description: Gene expression in fetal LD muscle at 120d(dpc) in Texel sheep

source_name: LD muscle,Texel,120 day(dpc),replicate 3

value: 120 day(dpc)


title: LD muscle_Texel_120d(dpc)_rep 2

source_name: LD muscle,Texel,120 day(dpc),replicate 2

value: Texel


title: Tumor_53A84

description:
DNA (bisulfite modified).
53A84


title: LD muscle_Ujumqin_120d(dpc)_rep 2

description: Gene expression in fetal LD muscle at 120d(dpc) in Ujumqin sheep

source_name: LD muscle,Ujumqin,120 day(dpc),replicate 2


title: Lung 16-1


title: LD muscle_Ujumqin_100d(dpc)_rep 3

description: Gene expression in fetal LD muscle at 100d(dpc) in Ujumqin sheep

source_name: LD muscle,Ujumqin,100 day(dpc),replicate 3

value: 100 day(dpc)

value: male


title: LD muscle_Ujumqin_120d(dpc)_rep 3

source_name: LD muscle,Ujumqin,120 day(dpc),replicate 3


title: Lung 16-3

value: Wistar

value: lung


title: Lung 14-3


title: Tumor_98A33

description:
DNA (bisulfite modified).
98A33

value: EP


title: Lung 14-2


title: Tumor_89R

description:
DNA (bisulfite modified).
89R

value: OA II


title: Lung 13-3


title: Lung 16-2


title: Lung 13-2


title: LD muscle_Ujumqin_100d(dpc)_rep 2

source_name: LD muscle,Ujumqin,100 day(dpc),replicate 2

value: skeletal muscle

value: Ujumqin


title: LD muscle_Ujumqin_120d(dpc)_rep 1

source_name: LD muscle,Ujumqin,120 day(dpc),replicate 1

value: female


title: Tumor_75A73

description:
DNA (bisulfite modified).
75A73


title: Tumor_14A30

description:
DNA (bisulfite modified).
14A30


title: Lung 14-1

source_name: Wistar rat lungs


title: Tumor_59A82

description:
DNA (bisulfite modified).
59A82


title: Normal_45A5

description:
DNA (bisulfite modified).
45A5

source_name: Normal DNA

value: brain

value: Normal


title: Lung 13-1


title: Tumor_84A46

description:
DNA (bisulfite modified).
84A46


title: Lung 12.25-3


title: Tumor_53D

description:
DNA (bisulfite modified).
53D


title: Tumor_4A27

description:
DNA (bisulfite modified).
4A27

value: OD II


title: Tumor_3783

description:
DNA (bisulfite modified).
3783

value: OA III


title: LD muscle_Ujumqin_100d(dpc)_rep 1

source_name: LD muscle,Ujumqin,100 day(dpc),replicate 1


title: Tumor_65A14

description:
DNA (bisulfite modified).
65A14

value: brain tumor


title: Tumor_42A77

description:
DNA (bisulfite modified).
42A77

value: AS II

value: Yes


title: Tumor_26A87

description:
DNA (bisulfite modified).
26A87


title: Tumor_19A

description:
DNA (bisulfite modified).
19A


title: LD muscle_Texel_100d(dpc)_rep 4

description: Gene expression in fetal LD muscle at 100d(dpc) in Texel sheep

source_name: LD muscle,Texel,100 day(dpc),replicate 4

value: Texel


title: Lung 12.25-2


title: Tumor_14G

description:
DNA (bisulfite modified).
14G

value: GBM


title: LD muscle_Texel_120d(dpc)_rep 1

source_name: LD muscle,Texel,120 day(dpc),replicate 1

value: 120 day(dpc)

value: male


title: LD muscle_Texel_135d(dpc)_rep 1

source_name: LD muscle,Texel,135 day(dpc),replicate 1

value: 135 day(dpc)


title: LD muscle_Ujumqin_1 month(postnatal)_rep 3

description: Gene expression in fetal LD muscle at 1 month(postnatal) in Ujumqin sheep

source_name: LD muscle,Ujumqin,1 month(posnatal),replicate 3

value: 1 month(postnatal)


title: Tumor_II85

description:
DNA (bisulfite modified).
II85


title: Lung 12.25-1

value: Wistar

value: lung


title: Tumor_95A70

description:
DNA (bisulfite modified).
95A70

value: No


title: LD muscle_Ujumqin_1 month(postnatal)_rep 2

source_name: LD muscle,Ujumqin,1 month(posnatal),replicate 2

value: skeletal muscle

value: Ujumqin

value: female


title: LD muscle_Ujumqin_1 month(postnatal)_rep 1

source_name: LD muscle,Ujumqin,1 month(posnatal),replicate 1


title: Tumor_87A95

description:
DNA (bisulfite modified).
87A95

source_name: Tumor DNA

value: EP


title: Lung 11.75-3


title: Tumor_82A70

description:
DNA (bisulfite modified).
82A70


title: Lung 11.75-2


title: LD muscle_Texel_100d(dpc)_rep 2

source_name: LD muscle,Texel,100 day(dpc),replicate 2

value: 100 day(dpc)


title: Tumor_72A79

description:
DNA (bisulfite modified).
72A79

value: brain tumor


title: Lung 11-3


title: LD muscle_Texel_100d(dpc)_rep 1

source_name: LD muscle,Texel,100 day(dpc),replicate 1


title: Lung 11.75-1


title: ssdp[neo48]/ssdp]BG1663 vs. mwh red ssdp[neo48] e l(3)?/+ biorep 3

city: Tel-Aviv

first: Revital

last: Bronstein

address: Ramat Aviv

department: Molecular microbiology and biotechnology

country: Israel

institute: Tel-Aviv University

description: In the matrix file the data from slide A and B are combined, A is on top.

hyb_protocol: Hybridization was performed in custom-made chambers allowing simultaneous exposure of the probe solution to both slides representing the entire Drosophila transcriptome. Spots (1 μl each) of a 40% suspension (v/v) of 30 μm ceramic microspheres in water were placed at four locations along each side of one slide and allowed to dry. The second slide was placed over the first slide such that the spotted parts of the slides were facing each other and the beads maintained proper spacing between the slides. Hybridization solution was applied at one end and covered the array surfaces by capillary action. Hybridization of labeled cDNA probes was performed in 50 μl 5x SSC, 0.1% SDS, and 1 mM DTT at 60°C for 6 h. The microarrays were washed after hybridization in 1x SSC, 0.1% SDS, 1 mM DTT at 45°C for 10 min, and then in 0.1x SSC, 0.2% SDS, 1 mM DTT at room temperature for 3 min. Microarrays were dried by centrifugation.

scan_protocol: Arrays were scanned using an Axon GenePix 3000A fluorescence reader (Molecular Devices Corporation, Union City, USA). GenePix v.4.1 image acquisition software (Molecular Devices Corporation) was used to extract signal for each target element.

data_processing: The array data was analyzed using R. The raw intensity data normalized within-arrays using the PrintTipLoess algorithm, and next between-arrays, using Quantile. Array elements whose intensity was lower than the median intensity in both channels were discarded. No other background correction method was used. Duplicated elements were not averaged.

organism: Drosophila melanogaster

source_name: Whole third instar male larvae

label_protocol: Purified mRNA (600 ng) was converted to either Cy3- or Cy5-labeled cDNA probes. Each reaction contains 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 6 μg Cy3 or Cy5 random 9-mer (Trilink, San Diego, CA), 60 U RNase inhibitor (Ambion, Austin, TX), 600 U MMLV RT RNase (H-) (Promega, Madison, WI) in 75 μl. Labeled Cy3 or Cy5 cDNA products were combined and subsequently de-pooled into three aliquots and purified with ChromaSpin+ TE-30 gel-filtration spin column (Clontech). The probes were then re-pooled, concentrated by ethanol precipitation and resuspended in hybridization buffer.

growth_protocol: Larvae were grown in small vials containing colored medium: 7.5g/l agar, 35g/l flour, 50g/l yeast, 55g/l glucose, 2.5ml/l p-Hydroxybenzoic Acid, 4ml/l Propionic Acid and 0.5ml/l Bromophenol.  The colored medium allows for more precise staging of the larvae. Towards the end of the third larval stage the larvae cease to feed and the gut clears out. The colored medium can be seen through the live whole larvae. Larvae were collected when the gut was two thirds full and selected or the desired genotype using the GFP marker.

extract_protocol: Total RNA was extracted using Trizol (Life Technologies, Carlsbad, USA), followed by mRNA isolation using an Oligotex poly(A) extraction kit (Qiagen, Valencia, USA).

value: w[*]/+; ssdp[BG1663]/mwh red ssdp[neo48] e l(3)?

value: Whole third instar male larvae

value: mwh red ssdp[neo48] e l(3)?/+


title: Lung 11-2


title: Lung 11-1


title: Tumor_6339

description:
DNA (bisulfite modified).
6339

value: Yes


title: LD muscle_Texel_100d(dpc)_rep 3

source_name: LD muscle,Texel,100 day(dpc),replicate 3

value: Texel


title: ssdp[neo48]/ssdp]BG1663 vs. mwh red ssdp[neo48] e l(3)?/+ biorep 3 dye-swap


title: ssdp[31]/ssdp[BG1663] vs. Su(Mrt)[31] e[5] ca/+ biorep 3 dye-swap


title: LD muscle_Ujumqin_70d(dpc)_rep 3

description: Gene expression in fetal LD muscle at 70d(dpc) in Ujumqin sheep

source_name: LD muscle,Ujumqin,70 day(dpc),replicate 3

value: 70 day(dpc)


title: Tumor_58A84

description:
DNA (bisulfite modified).
58A84


title: LD muscle_Ujumqin_85d(dpc)_rep 3

description: Gene expression in fetal LD muscle at 85d(dpc) in Ujumqin sheep

source_name: LD muscle,Ujumqin,85 day(dpc),replicate 3

value: 85 day(dpc)


title: ssdp[31]/ssdp[BG1663] vs. Su(Mrt)[31] e[5] ca/+ biorep 3


title: Tumor_53A79

description:
DNA (bisulfite modified).
53A79

value: GBM


title: LD muscle_Ujumqin_85d(dpc)_rep 2

source_name: LD muscle,Ujumqin,85 day(dpc),replicate 2

value: male


title: LD muscle_Ujumqin_70d(dpc)_rep 2

source_name: LD muscle,Ujumqin,70 day(dpc),replicate 2


title: Lung 10-3

source_name: Wistar rat lungs

value: Wistar

value: lung


title: LD muscle_Ujumqin_70d(dpc)_rep 1

source_name: LD muscle,Ujumqin,70 day(dpc),replicate 1

value: skeletal muscle


title: Tumor_49A55

description:
DNA (bisulfite modified).
49A55

value: AS II


title: Lung 10-1


title: ssdp[31]/ssdp[BG1663] vs. w[*]/+; ssdp[BG1663]/+ biorep 3 dye-swap


title: ssdp[31]/ssdp[BG1663] vs. w[*]/+; ssdp[BG1663]/+ biorep 2 dye-swap


title: Lung 10-2


title: Lung 8-3


title: LD muscle_Ujumqin_85d(dpc)_rep 1

source_name: LD muscle,Ujumqin,85 day(dpc),replicate 1

value: Ujumqin


title: Lung 8-2


title: Tumor_4220

description:
DNA (bisulfite modified).
4220

value: PA


title: ssdp[31]/ssdp[BG1663] vs. w[*]/+; ssdp[BG1663]/+ biorep 3


title: Tumor_36A62

description:
DNA (bisulfite modified).
36A62

value: AS III


title: Lung 6-3


title: Lung 8-1


title: ssdp[31]/ssdp[BG1663] vs. w[*]/+; ssdp[BG1663]/+ biorep 2


title: Tumor_32A79

description:
DNA (bisulfite modified).
32A79

value: brain tumor


title: LD muscle_Texel_85d(dpc)_rep 3

description: Gene expression in fetal LD muscle at 85d(dpc) in Texel sheep

source_name: LD muscle,Texel,85 day(dpc),replicate 3


title: ssdp[neo48]/ssdp]BG1663 vs. mwh red ssdp[neo48] e l(3)?/+ biorep 2 dye-swap

value: w[*]/+; ssdp[BG1663]/mwh red ssdp[neo48] e l(3)?


title: Tumor_25A75

description:
DNA (bisulfite modified).
25A75

value: No


title: Lung 6-2


title: Tumor_16H

description:
DNA (bisulfite modified).
16H

value: OA III


title: ssdp[neo48]/ssdp]BG1663 vs. mwh red ssdp[neo48] e l(3)?/+ biorep 2

value: Whole third instar male larvae

value: mwh red ssdp[neo48] e l(3)?/+


title: LD muscle_Texel_70d(dpc)_rep 3

description: Gene expression in fetal LD muscle at 70d(dpc) in Texel sheep

source_name: LD muscle,Texel,70 day(dpc),replicate 3

value: 70 day(dpc)

value: Texel

value: female


title: ssdp[neo48]/ssdp]BG1663 vs. mwh red ssdp[neo48] e l(3)?/+ biorep 1 dye-swap


title: Lung 4-3


title: ssdp[neo48]/ssdp]BG1663 vs. mwh red ssdp[neo48] e l(3)?/+ biorep 1


title: Lung 6-1


title: LD muscle_Texel_70d(dpc)_rep 2

source_name: LD muscle,Texel,70 day(dpc),replicate 2

value: male


title: Lung 4-2

value: Wistar


title: Lung 4-1

value: lung


title: LD muscle_Texel_85d(dpc)_rep 1

source_name: LD muscle,Texel,85 day(dpc),replicate 1

value: skeletal muscle

value: 85 day(dpc)


title: ssdp[neo48]/ssdp]BG1663 vs. w[*]/+; ssdp[BG1663]/mwh red e l(3)? biorep 2


title: LD muscle_Ujumqin_0d(postnatal)_rep 2

description: Gene expression in fetal LD muscle at birth in Ujumqin sheep

value: at birth

value: Ujumqin


title: LD muscle_Ujumqin_0d(postnatal)_rep 3


title: ssdp[31]/ssdp[BG1663] vs. Su(Mrt)[31] e[5] ca/+ biorep 2 dye-swap


title: ssdp[31]/ssdp[BG1663] vs. Su(Mrt)[31] e[5] ca/+ biorep 2


title: LD muscle_Ujumqin_0d(postnatal)_rep 1


title: ssdp[neo48]/ssdp]BG1663 vs. w[*]/+; ssdp[BG1663]/mwh red  e l(3)? biorep 2 dye-swap


title: Lung 2-1


title: Dying rep2

city: Northbrook

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

description: Gene expression of LCM samples sectioned 24hr post-injury

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Rat Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: Hippocampal neuron, fluid percussion injury, Fluoro-Jade-positive, rep2

label_protocol: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using Arcturus RiboAmp HS reagents (Molecular Devices, Sunnyvale, CA).  Alternatively, MessageAMP II (Applied Biosystems, Foster City, CA) was used.  After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: Dying and surviving rat hippocampal neurons from the CA3 subfield were individually obtained from 10 micron frozen coronal sections of rat brain (fixed in 75% ethanol for one minute, stained with Fluoro-Jade, counterstained with cresyl violot and completed dehydrated in graded ethanols and xylene) using laser capture microdissection.

treatment_protocol: Rats were subjected to experimental moderate fluid percussion brain injury, sham injury or were sacrificed with no treatment (naïve) and brains were removed 24 hours later, frozen on dry ice and stored at -80 C.

value: Sprague-Dawley

value: hippocampal neuron


title: LD muscle_Texel_70d(dpc)_rep 1

source_name: LD muscle,Texel,70 day(dpc),replicate 1


title: Lung 2-2


title: LD muscle_Texel_85d(dpc)_rep 2

source_name: LD muscle,Texel,85 day(dpc),replicate 2


title: Lung 2-3


title: Dying rep1

source_name: Hippocampal neuron, fluid percussion injury, Fluoro-Jade-positive, rep1


title: ssdp[31]/ssdp[BG1663] vs. w[*]/+; ssdp[BG1663]/+ biorep 1 dye-swap

source_name: Whole third instar male larvae


title: Lung 1-3


title: Surviving rep2

source_name: Hippocampal neuron, fluid percussion injury, Fluoro-Jade-negative, rep2


title: Sham rep2

source_name: Hippocampal neuron, Sham injury, rep2


title: ssdp[31]/ssdp[BG1663] vs. Su(Mrt)[31] e[5] ca/+ biorep 1


title: Lung .25-3


title: ssdp[31]/ssdp[BG1663] vs. Su(Mrt)[31] e[5] ca/+ biorep 1  dye-swap


title: ssdp[31]/ssdp[BG1663] vs. w[*]/+; ssdp[BG1663]/+ biorep 1


title: ssdp[neo48]/ssdp]BG1663 vs. w[*]/+; ssdp[BG1663]/mwh red e l(3)? biorep 1

value: w[*]/+; ssdp[BG1663]/mwh red ssdp[neo48] e l(3)?


title: Lung 1-2


title: Sham rep1

source_name: Hippocampal neuron, Sham injury, rep1


title: Lung .25-2


title: Naïve rep2

source_name: Hippocampal neuron, no treatment, rep2


title: Surviving rep1

source_name: Hippocampal neuron, fluid percussion injury, Fluoro-Jade-negative, rep1


title: Lung 1-1

source_name: Wistar rat lungs


title: Naïve rep1

source_name: Hippocampal neuron, no treatment, rep1


title: Germ-free rat Resistant starch diet  replicate 5

status: Public on Dec 18 2010

city: Palmerston North

first: Wayne

last: Young

state: Manawatu

address: Tennent Drive

department: Food Nutrition Genomics Team

country: New Zealand

institute: AgResearch Ltd

description: Biological replicate 5 of 6, colon tissue

hyb_protocol: 825 ng of Cy3 labelled cRNA transcribed from the sample RNA and 825 ng of Cy5 labelled cRNA transcribed from the reference RNA was hybridised onto Agilent Whole Rat Genome 4x44K microarrays (G4131F).  Microarrays were hybridised at 65C for 17.5 hours, after which they were washed according to the manufacturers instructions.

scan_protocol: Microarrays were scanned using an Agilent Technologies Scanner G2505B

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was using to calculate fluorescence values.  Loess within array and Aquantile between array normalisation was carried out using the limma (3.4.4) package in R (2.11.1)

source_name: Colony rats

label_protocol: 200 ng of sample RNA was linearly amplified with Cy3 labelled CTP using the Agilent Low Input Linear Amplification kit according to the manufacturers instructions.  500 ng of reference RNA was linearly amplified with Cy5 labelled CTP using the Agilent Low Input Linear Amplification kit according to the manufacturers instructions.

growth_protocol: Conventionally raised newly weaned male Sprague-Dawley rats were house individually in hanging cages.  Germ-free newly weaned male Sprague Dawley rats were house in individual cages within a gnotobiotic isolator.

extract_protocol: RNA was extracted using Trizol (Invitrogen) following manufacturers instructions.  RNA was further purified using Rneasy spin columns (Qiagen) following manufacturers instructions.

treatment_protocol: Rats were fed diets and provided water ad lib for 28 days, after which the animals were sacrificed and colon tissue collected and snap frozen in liquid nitrogen.

value: colon

value: Sprague Dawley

tag: treatment

value: reference colony rats

value: Germ-free rat Resistant starch diet


title: Lung .25-1


title: Germ-free rat Resistant starch diet  replicate 6

description: Biological replicate 6 of 6, colon tissue


title: Germ-free rat Basal diet  replicate 3

description: Biological replicate 3 of 6, colon tissue

source_name: Germ-free rat Basal diet  replicate 3

value: Germ-free rat Basal diet


title: PDL  stimulated by mechanical stress loading for 0h

city: Fukuoka

first: Hiroshi

last: Kajiya

address: 2-15-1 Tamura, Sawara-ku

department: Physiological Science and Molecular Biology

institute: Fukuoka Dental College

description: Gene expression data from human periodontal ligament cells, i.e.

hyb_protocol: GeneChips were washed, stained with streptavidin-phycoerythrin

scan_protocol: GeneChips were scanned using the affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console and  Affymetrix Expression Console softwares using Affymetrix default analysis settings and global scaling as normalization.

source_name: human periodontal ligament cells

label_protocol: Biotinylated cRNA were prepared according to manufacturer's instructions from 15 ug total RNA using an Rneasy mini kit (QIAGEN K.K, Tokyo, Japan).

growth_protocol: Human periodontal ligament cells were obtained from third molars extracted from healthy donors. PDL cells were scraped off with a surgiical knife from the mid-third of each root.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: PDL cells were cultured in α-minimal essential medium containg 10% fetal bovine serum. after 4-8 passages, PDL were cultured in silicon rubber chmbers. Stimulated by intermittent mechanical stretch (Conditions:60 s/returns;resting time:29 s; stretch length: 1.6 mm; stretch ratio: 105%)

value: human periodontal ligament cells

value: 20 years old


title: Germ-free rat Konjac flour diet  replicate 5

value: Germ-free rat Konjac flour diet


title: Germ-free rat Resistant starch diet  replicate 3


title: Germ-free rat Konjac flour diet  replicate 3


title: cultured human vascular adventitial fibroblasts, biological rep1

city: Kashiwa

first: Ayuko

last: Hoshino

state: Chiba

address: 6-5-1 Kashiwanoha

institute: The University of Tokyo

hyb_protocol: The procedures for target hybridization, washing, and staining with signal amplification were conducted according to the supplier's protocols.

scan_protocol: The arrays were scanned with a GeneChip Scanner 3000 (Affymetrix)

data_processing: Intensity of each feature of the array was calculated using GeneChip Operating Software, version 1.1.1 (Affymetrix). The average intensity was standardized to the target intensity, which was set equal to 1,000, to reliably compare various multiple arrays. The values were log-transformed and median-centered. The programs GeneSpring (Agilent Technologies, Santa Clara, CA, http://www.agilent.com) and Excel (Microsoft, Redmond, WA, http://www.microsoft.com) were used to perform the numerical analysis to permit gene selection.

source_name: human lung cancer patient resected lung

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix 3' IVT Express Kit protocol from 100ng of total RNA

growth_protocol: cells were plated at the density of 1x104 cells/cm2 and harvested at semi-confluence

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

value: tissue-derived fibroblasts


title: Germ-free rat Basal diet  replicate 6

source_name: Germ-free rat Basal diet  replicate 6


title: cultured human vascular adventitial fibroblasts, biological rep2

value: lung


title: Germ-free rat Konjac flour diet  replicate replicate 4

description: Biological replicate 4 of 6, colon tissue


title: cultured human lung tissue-derived fibroblasts, biological rep2


title: Germ-free rat Basal diet  replicate replicate 4


title: Germ-free rat Konjac flour diet  replicate 2

description: Biological replicate 2 of 6, colon tissue


title: Germ-free rat Konjac flour diet  replicate 1

description: Biological replicate 1 of 6, colon tissue


title: Germ-free rat Basal diet  replicate 5

source_name: Germ-free rat Basal diet  replicate 5


title: Germ-free rat Konjac flour diet  replicate 6


title: Germ-free rat Resistant starch diet  replicate replicate 4


title: cultured human lung tissue-derived fibroblasts, biological rep1


title: Germ-free rat Resistant starch diet  replicate 2


title: T2D 5 (rat)_liver

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description: replicate 5

hyb_protocol: hybridized on miRCURY LNA™ Arrays, using MAUI® hybridization system

scan_protocol: Chips were scanned on Innopsys Scan 700, microarray scanner at 532 nm

data_processing: miRNA microarray data were analyzed (usingMapix ver 4.5 software) by subtracting the mean background signal (B532nm) from the test signal (F532nm)

source_name: T2D rat liver

label_protocol: LNA-modified oligonucleotide (Exiqon) probes for human, mouse and rat miRNAs annotated in miRBase version 11.0 were used in the microarray. Total RNA (1 μg) was 3’-end –labeled with Cy3 dye using the miRCURY LNA ™ Power Labeling Kit (Exiqon)

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

value: Wistar

tag: disease state

value: type 2 diabetes mellitus

value: liver

tag: replicate


title: Germ-free rat Resistant starch diet  replicate 1

tag: tissue


title: control 5 (rat)_liver

description: replicate 5

source_name: rat control liver

value: control


title: T2D 2 (rat)_adipose

description: replicate 2

source_name: T2D rat adipose

value: adipose tissue


title: T2D 3 (rat)_pancreas

description: replicate 3

source_name: T2D rat pancreas

value: pancreas


title: T2D 1 (rat)_blood

description: replicate 1

source_name: T2D rat blood

value: total blood


title: Germ-free rat Basal diet  replicate 2

value: colon

source_name: Germ-free rat Basal diet  replicate 2


title: T2D 4 (rat)_skeletal muscle

description: replicate 4

source_name: T2D rat skeletal muscle

value: skeletal muscle


title: Germ-free rat Basal diet  replicate 1

value: Sprague Dawley

value: reference colony rats

source_name: Germ-free rat Basal diet  replicate 1


title: control 2 (rat)_adipose

description: replicate 2

source_name: rat control adipose


title: control 1 (rat)_blood

description: replicate 1

source_name: rat control blood


title: control 4 (rat)_skeletal mucsle

description: replicate 4

source_name: rat control skeletal muscle


title: Conventionally raised rat Konjac flour diet  replicate 6

source_name: Colony rats


title: Conventionally raised rat Resistant starch diet  replicate 6


title: Tumor_13X

description:
DNA (bisulfite modified).
13X

source_name: Tumor DNA

value: brain tumor

value: GBM

value: No


title: Conventionally raised rat Inulin diet replicate 5

description: Biological replicate 5 0f 5, colon tissue

value: Conventionally raised rat Inulin diet


title: control 3 (rat)_pancreas

description: replicate 3

source_name: rat control pancreas


title: Conventionally raised rat Basal diet  replicate 5

value: Conventionally raised rat Basal diet


title: ssdp[neo48]/ssdp]BG1663 vs. w[*]/+; ssdp[BG1663]/mwh red  e l(3)? biorep 1 dye-swap

source_name: Whole third instar male larvae

tag: genotype

value: Whole third instar male larvae

value: w[*]/+; ssdp[BG1663]/mwh red ssdp[neo48] e l(3)?


title: Conventionally raised rat Konjac flour diet  replicate 5


title: Conventionally raised rat Basal diet  replicate 6


title: Regenerating liver at 2h after SPH, technical rep3

city: Xinxiang

first: Cunshuan

last: Xu

address: No. 46, Construction East Road

institute: Henan Normal University

description: Gene expression data from liver at priming phase of liver regeneration after sympathectomy combining partial hepatectomy.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Rat Genome 230 2.0 array. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).

data_processing:
The data were analyzed with Affymetrix GCOS 2.0 software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
When P value is < 0.05, it means that the gene is present (P), when < 0.065, means marginal (M), and when > 0.065, means marked absent (A). On the other hand, the normalized signal values in PH to that in control were used to calculate the relative value, that is, ratio value of gene expression abundance. When ratio value is ≥ 3, it means that gene expression change was significantly up-regulated, when ≤ 0.33, means significantly down-regulated, and when 0.33-2.99, means biologically insignificant. To minimize the technical errors from microarray analysis, each sample was tested at least three times using Rat Genome 230 2.0 microarray, and the average value was considered as a reliable value (Wang and Xu, 2010).

source_name: Regenerating liver at 2h after SPH

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip In Vitro Transcript Labeling Kit, ENZO Biochemical, New York, USA).

extract_protocol: Total RNA was extracted according to the manual of Trizol reagent (Invitrogen Corporation, Carlsbad, California, USA) and purified following the RNeasy mini protocol (Qiagen, Inc, Valencia, CA, USA).

treatment_protocol: After the operations were done, the rats at corresponding recovery time points were anaesthetized, and the intrahepatic blood was removed by hepatic portal vein infusion firstly, then the liver tissues from the middle part of the right lobe of the liver were collected in RNase-free tubes and stored at﹣80℃ until use.

value: Sprague-Dawley

value: Liver

tag: age


title: Regenerating liver at 2h after TDPH, technical rep3

description: Gene expression data from liver at priming phase of liver regeneration after total liver denervation combining partial hepatectomy.

source_name: Regenerating liver at 2h after TDPH


title: Regenerating liver at 2h after VPH, technical rep3

description: Gene expression data from liver at priming phase of liver regeneration after vagotomy combining partial hepatectomy.

source_name: Regenerating liver at 2h after VPH


title: Regenerating liver at 2h after TDPH, technical rep2


title: Regenerating liver at 2h after VPH, technical rep2


title: Regenerating liver at 2h after TDPH, technical rep1


title: Regenerating liver at 2h after SPH, technical rep2


title: Conventionally raised rat Resistant starch diet  replicate 5


title: Conventionally raised rat Resistant starch diet  replicate replicate 4


title: Regenerating liver at 2h after PH, technical rep2

description: Gene expression data from liver at priming phase of liver regeneration after partial hepatectomy.

source_name: Regenerating liver at 2h after PH


title: Liver at 2h after sham operation, technical rep2

description: Gene expression data from liver at priming phase after sham operation

source_name: Liver at 2h after sham operation


title: Conventionally raised rat Basal diet  replicate 3


title: Conventionally raised rat Basal diet  replicate replicate 4


title: Conventionally raised rat Inulin diet replicate replicate 4

description: Biological replicate 4 of 5, colon tissue


title: Regenerating liver at 2h after SPH, technical rep1


title: Regenerating liver at 2h after PH, technical rep3


title: Regenerating liver at 2h after PH, technical rep1


title: Regenerating liver at 2h after VPH, technical rep1


title: Liver at 2h after sham operation, technical rep3


title: Regenerating liver at 0h after PH, technical rep3

description: Gene expression data from normal liver.

source_name: Regenerating liver at 0h after PH


title: Conventionally raised rat Resistant starch diet  replicate 3


title: Conventionally raised rat Konjac flour diet  replicate replicate 4


title: Liver at 2h after sham operation, technical rep1


title: Conventionally raised rat Konjac flour diet  replicate 3


title: Endothelial cells from coronary artery rep 4 p4

city: Durham

first: Kelley

last: Burridge

state: NC

address: Rm 136 Hudson Hall

department: Biomedical Engineering

institute: Duke University

description: Endothelial cells from coronary and iliac arteries were harvested from four pigs and grown in culture out to passage 4.

hyb_protocol: • Make hybridization buffer fresh each time. • Add 38 ul hybridization buffer to 12 ul fragmented Cy Dye labeled aa-aRNA. • Add 1ul each poly dA and appropriate Cot-1 DNA. • Heat at 95ºC for 2 minutes and put on ice to cool down. • Mix well and load sample to the array slide with lifter cover slip. • Hybridize overnight in 42ºC water bath.

scan_protocol: Scanned by GenePix 4000B and quantified using GenePix software

data_processing: LOWESS normalized. Agilent GeneSpring GX was used.

organism: Sus scrofa

source_name: coronary endothelial cells

label_protocol: Messenger RNA was amplified using a MessageAmp II aRNA amplification kit (Ambion). Two rounds of amplification were performed, and aminoallyl-UTP was used in the final round to provide reactive groups for dye incorporation. The RNA samples were labeled with Cy5 dyes and reference RNA sample was labeled with Cy3 dyes.

growth_protocol: Endothelial cells were grown in EGM-2MV media.

extract_protocol: Qiagen RNeasy Micro kit following manufacturer's protocol

treatment_protocol: passage 4

tag: animal

value: coronary endothelial cells

source_name: reference RNA

value: aortic endothelial cells (passage 3)


title: Endothelial cells from left and right iliac arteries rep 4 p4

source_name: iliac endothelial cells

value: iliac endothelial cells


title: Endothelial cells from left and right iliac arteries rep 4 p3

treatment_protocol: passage 3


title: Regenerating liver at 0h after PH, technical rep2

description: Gene expression data from normal liver.


title: Endothelial cells from coronary artery rep 4 p3


title: Endothelial cells from coronary artery rep 4 p1

treatment_protocol: passage 1


title: Conventionally raised rat Inulin diet replicate 3

description: Biological replicate 3 of 5, colon tissue


title: Endothelial cells from coronary artery rep 3 p4


title: Regenerating liver at 0h after PH, technical rep1

description: Gene expression data from normal liver.


title: Endothelial cells from left and right iliac arteries rep 4 p1


title: Endothelial cells from left and right iliac arteries rep 3 p3


title: Endothelial cells from left and right iliac arteries rep 3 p4


title: Endothelial cells from left and right iliac arteries rep 3 p1


title: Endothelial cells from coronary artery rep 4 p2

treatment_protocol: passage 2


title: Endothelial cells from coronary artery rep 3 p3


title: Endothelial cells from coronary artery rep 3 p1


title: Conventionally raised rat Resistant starch diet  replicate 2


title: Endothelial cells from coronary artery rep 2 p4


title: Conventionally raised rat Basal diet  replicate 1


title: Conventionally raised rat Konjac flour diet  replicate 2


title: Endothelial cells from left and right iliac arteries rep 2 p4


title: Conventionally raised rat Basal diet  replicate 2


title: Endothelial cells from left and right iliac arteries rep 4 p2


title: Conventionally raised rat Resistant starch diet  replicate 1


title: Endothelial cells from left and right iliac arteries rep 2 p3


title: Conventionally raised rat Inulin diet replicate 1

description: Biological replicate 1 of 5, colon tissue


title: Endothelial cells from coronary artery rep 3 p2


title: Endothelial cells from coronary artery rep 2 p2

data_processing: LOWESS normalized.  Agilent GeneSpring GX was used.


title: HGMDFN090_untreated

city: Ann Arbor

first: Thomas

middle: E.

last: Wilson

state: MI

address: 2065 BSRB, 109 Zina Pitcher

department: Department of Pathology

institute: University of Michigan

hyb_protocol: Labeling, hybridization and scanning were performed by the University of Michigan DNA Sequencing Core according to the manufacturer instructions (Illumina).

data_processing: Data were processed using Illumina BeadStudio (BSGT 3.3.7) according to the manufacturer's instructions.

label: unknown

source_name: human fibroblast cell line HGMDFN090

extract_protocol: Genomic DNA was prepared from cell lines using the Blood & Cell Culture DNA Mini Kit (Qiagen)

value: female

value: fibroblast

tag: cell line


title: Endothelial cells from left and right iliac arteries rep 2 p1


title: Endothelial cells from left and right iliac arteries rep 2 p2


title: Conventionally raised rat Inulin diet replicate 2

description: Biological replicate 2 of 5, colon tissue

value: colon


title: mammary stoma-4w-wt-rep2

city: Montréal

first: Xingxing

last: LIU

state: QC

address: 1160 Pine Ave

department: Biochemistry, GCC

country: Canada

institute: McGill University

description: Gene expression data from young mice with ErbB2.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with FlexArray software developed by Genome Quebec Center at McGill University and RMA as normalization method.

source_name: wild type mammary stroma

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

tag: tisue

value: cleared mammary fat pad

value: Rarb +/+

value: four weeks


title: Endothelial cells from left and right iliac arteries rep 1 p4


title: Endothelial cells from coronary artery rep 1 p4


title: Endothelial cells from left and right iliac arteries rep 1 p3


title: Endothelial cells from coronary artery rep 2 p3


title: HGMDFN090_aphidicolin_treated_subclone

scan_protocol: Labeling, hybridization and scanning were performed by the University of Michigan DNA Sequencing Core according to the manufacturer instructions (Illumina).

source_name: human fibroblast cell line HGMDFN090, aphidicolin-treated subclone A3A2

value: aphidicolin


title: Endothelial cells from left and right iliac arteries rep 1 p2


title: Endothelial cells from coronary artery rep 1 p3


title: mammary stoma-4w-wt-rep3


title: Conventionally raised rat Konjac flour diet  replicate 1

value: Sprague Dawley

value: reference colony rats


title: Endothelial cells from coronary artery rep 1 p2


title: mammary stoma-4w-wt-rep1


title: mammary stoma-4w-KO-rep1

source_name: Rarb null mammary stroma

value: Rarb -/-


title: mammary stoma-4w-KO-rep2


title: CD8 SP thymocytes from CIITAtgpIV-/- mouse

city: Seoul

first: Hye Sook

last: Min

address: Chongnogu Yongondong 28

department: Pathology

country: South Korea

institute: Seoul National University College of Medicine

description: CD8 SP thymocytes pooled litter

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were extracted using Affymetrix GCOS software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized using RMA(Robust Multi-array Average) Normalization.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: CIITAtgpIV-/-

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse thymus dissected from 8 week-old mice and CD8 SP thymocytes were selectively sorted by Magnetic Activated Cell Sorting.

extract_protocol: CIITAtgpIV-/- phenotype were manually identified by flow cytometry as wild-type or mutants. All samples of equivalent genotyped samples (2-4 thymuses) were immediately prepared using Trizol. RNA Samples were then treated with the RiobMinusâ„¢ rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

value: 8 weeks

value: CD8 SP thymocytes

value: CIITAtgpIV-/-

tag: genetic background


title: YPS163 msn2D 30 min vs T0 - 5% EtOH #2

status: Public on Dec 17 2010

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

institute: University of Arkansas

description: 30 min EtOH shock in YPS163  msn2D

hyb_protocol: As indicated in Gasch AP Methods in Enzymology 350: 393-414

scan_protocol: Arrays were scanned on an Axon 4000B scanner

data_processing: Data were extracted using GenePix 6.0.  Data were normalized by regional mean-centering as described by Lyne et al. 2003 BMC Genomics

label: Oyster 550 cyanine dye

organism: Saccharomyces cerevisiae

source_name: YPS163 msn2D 30 min after 5% EtOH shock

label_protocol: Indirect labeling using amino-allyl-dUTP and cyanine dyes from Flownamics (Madison, Wi) as described in Gasch AP Methods in Enzymology 350: 393-414

growth_protocol: All cells were grown for at least 8 doublings in log phase in YPD medium at 30C.

extract_protocol: Hot-phenol RNA extraction as described in Gasch AP Methods in Enzymology 350: 393-414

treatment_protocol: For ethanol-shocked cells, ethanol was added to a final concentration of 5% (v/v).

value: YPS163 MATa msn2D

tag: protocol

value: YPS163 msn2D 30 min after 5% EtOH shock

label: Oyster cyanine 650 dye

source_name: YPS163 msn2D log growth

value: YPS163 msn2D log growth


title: mammary stoma-4w-KO-rep3


title: Fetal Naïve CD4+ T cells 2

city: San Francisco

first: Jeff

last: Mold

state: CA

address: UCSF Box 1234, SFGH Bldg 3

department: Division of Experimental Medicine

institute: University of California San Francisco

description: Gene Expression

hyb_protocol: Arrays were hybridized using Affymetrix GeneChip Fluidics Station 450 according to manufacturer's protocol

scan_protocol: Arrays were scanned with an Affymetrix Model 3000 scanner

data_processing: Data were analyzed using the Bioconductor package affyPLM. Preprocessing followed the following procedures: (1) background correction; (2) normalization using the quantile method; (3) summarization of probe set values using the RMA (Robust Multi-Array Average) method.

source_name: Sort Purified Fetal CD3+CD4+CD45RA+CCR7+CD27+ Naïve T cells

label_protocol: RNA was converted to cDNA and amplified (NuGEN WT-Ovation kit) and then fragmented (WT-Ovation kit) and labeled with biotin (FL-Ovation cDNA biotin module, NuGEN)

growth_protocol: Cells were isolated from fetal mesenteric lymph nodes (mechanical dispersion) and adult peripheral blood (Ficoll-Hypaque)

extract_protocol: Immediately after sorting cell pellets were lysed in RNA lysis buffer (Stratagene) and RNA was obtained using the Absolutely RNA microprep kit (Stratagene) in accordance with manufacturer’s protocol

treatment_protocol: After isolation total cells were cultured overnight (12 hours) in low-serum media (RPMI with 2% FBS) to attempt to normalize differences associated with tissue of origin (blood vs lymph node)

tag: cell type

value: Sort Purified T cells

tag: phenotype


title: CD8 SP thymocytes from B6 WT mouse

description: CD8 SP thymocytes pooled litter

source_name: wild-type B6

value: wild-type


title: Fetal CD4+CD25+ Treg 3

description: Gene Expression

source_name: Sort Purified Fetal CD3+CD4+CD25bright Treg cells


title: Adult BM SP4 thymic implant #2

description: Gene Expression

source_name: CD3+CD4+ Thymocytes derived from Adult BM HSC

growth_protocol: Cells were isolated from human fetal thymic implants (implanted under kidney capsule of SCID mouse) by FACS (Live Marker, HLA-A2+CD3+CD4+CD8-CD25-)

value: Sort Purifed Thymocytes

tag: original cells

value: adult bone marrow HSC


title: Adult BM SP4 thymic implant #3

description: Gene Expression


title: YPS163 msn2D 30 min vs T0 - 5% EtOH #1

description: 30 min EtOH shock in YPS163  msn2D


title: Fetal CD4+CD25+ Treg 1

description: Gene Expression


title: YPS163 MATa hap1D 30 min vs T0 - 5% EtOH #3

description: 30 min EtOH shock in YPS163 MATa hap1D

source_name: YPS163 MATa hap1D log growth

value: YPS163 MATa hap1D

value: YPS163 MATa hap1D log growth

source_name: YPS163 MATa hap1D 30 min after 5% EtOH shock


title: Fetal CD4+CD25+ Treg 2

description: Gene Expression


title: Fetal Naïve CD4+ T cells 1

description: Gene Expression


title: Fetal Naïve CD4+ T cells 3

description: Gene Expression


title: Adult BM SP4 thymic implant #1

description: Gene Expression


title: Fetal BM SP4 thymic implant #3

description: Gene Expression

source_name: CD3+CD4+ Thymocytes derived from Fetal BM HSC

value: fetal bone marrow HSC


title: YPS163 msn2D 30 min vs T0 - 5% EtOH #3

description: 30 min EtOH shock in YPS163  msn2D


title: Fetal BM SP4 thymic implant #1

description: Gene Expression


title: YPS163 MATa hap1D 30 min vs T0 - 5% EtOH #2

description: 30 min EtOH shock in YPS163 MATa hap1D

value: YPS163 MATa hap1D 30 min after 5% EtOH shock


title: Fetal Liver SP4 thymic implant #3

description: Gene Expression

source_name: CD3+CD4+ Thymocytes derived from Fetal Liver HSC

value: fetal liver HSC


title: YPS163 MATa 30 min vs T0 - 5% EtOH #2

description: 30 min EtOH shock in YPS163 MATa

source_name: YPS163 MATa 30 min after 5% EtOH shock

value: YPS163 MATa

value: YPS163 MATa 30 min after 5% EtOH shock

source_name: YPS163 MATa log growth

value: YPS163 MATa log growth


title: YPS163 MATa hap1D 30 min vs T0 - 5% EtOH #1

description: 30 min EtOH shock in YPS163 MATa hap1D


title: YPS163 MATa 30 min vs T0 - 5% EtOH #3

description: 30 min EtOH shock in YPS163 MATa


title: YPS163 MATa 30 min vs T0 - 5% EtOH #1

description: 30 min EtOH shock in YPS163 MATa


title: Fetal Liver SP4 thymic implant #1

description: Gene Expression


title: Fetal Liver SP4 thymic implant #2

description: Gene Expression


title: Fetal BM SP4 thymic implant #2

description: Gene Expression


title: M22 30 min vs T0 - 5% EtOH #3

description: 30 min EtOH shock in M22

source_name: M22 log growth

value: M22 log growth

source_name: M22  30 min after 5% EtOH shock

value: M22  30 min after 5% EtOH shock


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-43H

city: Bethesda

first: Delong

last: Liu

state: MD

address: 10 Center Drive

institute: NHLBI/NIH

description:
CD133+ cells sorted from PB.
SG-43H

hyb_protocol: Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix HG-U133 Plus 2.0 chips for 16 hours.

scan_protocol: Affymetrix GeneChip scanner.

data_processing: Intensities were pre-processed with MAS5.0, and further processed with variance stablization transformation ('S10').  26,123 probesets present in at least 2 out of 14 chips (4 healthy controls and 10 CAD baselines) were S10 transformed and analyzed.

source_name: healthy subject

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

growth_protocol: CAD patients enrolled in a cardiac rehabilitation program consisting of 36 sessions of 60 minutes each, spaced over 3 months. Medical management was stable for at least a month prior to program participation and all patients were maintained on medications throughout the study as prescribed without change in preparation or dose.

extract_protocol: 32 ml of PB was used for isolation of CD133+ cells using fluorescence-actived cell sorting. Total RNA was extracted from CD133+ cells with an RNAqueous micro RNA isolation kit (Ambion, Austin, TX).  Cells were lysed in buffer containing guanidinium thiocyanate.

treatment_protocol: Cardivovascular examination and baseline testing were performed after an overnight fast (except for water). Symptom-limited treadmill exercise was performed using the modified Bruce protocal.  Healthy subjects of similar age and sex distribution were recruited for the study to serve as controls for baseline analysis.

value: peripheral blood

value: CD133+ cells

tag: disease

value: healthy


title: YPS163 30 min vs T0 - 5% EtOH #3

description: 30 min EtOH shock in YPS163

source_name: YPS163 log growth

value: YPS163 log growth

source_name: YPS163  30 min after 5% EtOH shock

value: YPS163  30 min after 5% EtOH shock


title: M22 30 min vs T0 - 5% EtOH #2

description: 30 min EtOH shock in M22


title: YPS163 30 min vs T0 - 5% EtOH #2

description: 30 min EtOH shock in YPS163


title: YPS163 MATa  T0 vs YPS163 MATa hap1D T0 #2

description: Comparison of YPS163 MATa and YPS163 MATa hap1D during log phase growth


title: YPS163 MATa  T0 vs YPS163 MATa hap1D T0 #3


title: YPS163 MATa T0 vs YPS163 MATa hap1D T0 #1


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-42H

description:
CD133+ cells sorted from PB.
SG-42H


title: YPS163 30 min vs T0 - 5% EtOH #1

description: 5% EtOH Time-course in YPS163


title: YPS163 15 min vs T0 - 5% EtOH

description: 5% EtOH Time-course in YPS163

source_name: YPS163 15 min after 5% EtOH shock

value: YPS163 15 min after 5% EtOH shock


title: YPS163 45 min vs T0 - 5% EtOH

description: 5% EtOH Time-course in YPS163

source_name: YPS163 45 min after 5% EtOH shock

value: YPS163 45 min after 5% EtOH shock


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-44B

description:
CD133+ cells sorted from PB.
SG-44B

source_name: CAD patient, after 3 months of exercise

value: coronary artery disease

value: 3 months of exercise


title: YPS163 60 min vs T0 - 5% EtOH

description: 5% EtOH Time-course in YPS163

source_name: YPS163 60 min after 5% EtOH shock

value: YPS163 60 min after 5% EtOH shock


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-25H

description:
CD133+ cells sorted from PB.
SG-25H


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-25B

description:
CD133+ cells sorted from PB.
SG-25B


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-44A

description:
CD133+ cells sorted from PB.
SG-44A

source_name: CAD patient, baseline

value: baseline


title: DBY8268 30 min vs T0 - 5% EtOH #2

description: 30 min EtOH shock in DBY8268

source_name: DBY8268 30 min after 5% EtOH shock

value: DBY8268 30 min after 5% EtOH shock

source_name: DBY8268 log growth

value: DBY8268 log growth


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-24H

description:
CD133+ cells sorted from PB.
SG-24H


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-25A

description:
CD133+ cells sorted from PB.
SG-25A


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-43B

description:
CD133+ cells sorted from PB.
SG-43B


title: M22 60 min vs T0 - 5% EtOH

description: 5% EtOH Time-course in M22

source_name: M22  60 min after 5% EtOH shock

value: M22  60 min after 5% EtOH shock


title: DBY8268 30 min vs T0 - 5% EtOH #3

description: 30 min EtOH shock in DBY8268


title: M22 45 min vs T0 - 5% EtOH

description: 5% EtOH Time-course in M22

source_name: M22 45 min after 5% EtOH shock

value: M22 45 min after 5% EtOH shock


title: M22 15 min vs T0 - 5% EtOH

description: 5% EtOH Time-course in M22

value: M22 log growth

source_name: M22 15 min after 5% EtOH shock

value: M22 15 min after 5% EtOH shock


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-43A

description:
CD133+ cells sorted from PB.
SG-43A

value: peripheral blood


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-22A

description:
CD133+ cells sorted from PB.
SG-22A

value: CD133+ cells


title: DBY8268 60 min vs T0 - 5% EtOH

description: 5% EtOH Time-course in DBY8268

source_name: DBY8268 60 min after 5% EtOH shock

value: DBY8268 60 min after 5% EtOH shock


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-22B

description:
CD133+ cells sorted from PB.
SG-22B


title: transcriptional profiling of CD133+ cells in coronary artery disease, SG-17A

description:
CD133+ cells sorted from PB.
SG-17A