title: Human Lung antisense 2 (exon)

source_name: Human Lung antisense 2 (exon)


title: Human Ovary antisense 1 (exon)

status: Public on Oct 10 2012

type: RNA

city: Brookings

first: Maurice

last: Ling

department: Mathematics and Statistics

country: USA

institute: South Dakota State University

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Array hybridization was performed according to the manufacturer's instruction (Affymetrix) at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) at the UCLA Microarray Core Facility.

data_processing:
probeset group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
CEL files were processed using Affymetrix Expression Console

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Ovary antisense 1 (exon)

label_protocol: Sense transcript detection labeled using standard Affymetrix labeling protocol. Antisense transcript detection labeled using ATE protocol (Ge et al., 2008; PMID 18211689)

extract_protocol: Tissue total RNA purchased from Ambion

tag: tissue

value: ovary

tag: transcript type

value: Antisense transcript (exon)

tag: ambion catalog number


title: Mouse Brain antisense 1 (exon)

data_processing:
probeset group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps
CEL files were processed using Affymetrix Expression Console

organism: Mus musculus

source_name: Mouse Brain antisense 1 (exon)

value: brain


title: Human Ovary sense 1 (gene)

source_name: Human Ovary sense 1 (gene)

value: Sense transcript (gene)


title: Human Liver antisense 2 (exon)

source_name: Human Liver antisense 2 (exon)

value: liver


title: Human Spleen antisense 1 (exon)

source_name: Human Spleen antisense 1 (exon)

value: spleen


title: Human Lung antisense 1 (exon)

source_name: Human Lung antisense 1 (exon)

value: lung


title: Human Ovary sense 2 (gene)

source_name: Human Ovary sense 2 (gene)


title: Human Liver antisense 1 (exon)

source_name: Human Liver antisense 1 (exon)


title: Human Liver sense 1 (gene)

source_name: Human Liver sense 1 (gene)


title: Human Kidney sense 2 (gene)

source_name: Human Kidney sense 2 (gene)

value: kidney


title: Human Lung sense 2 (gene)

source_name: Human Lung sense 2 (gene)


title: Human Liver sense 2 (gene)

source_name: Human Liver sense 2 (gene)


title: Human Kidney sense 1 (gene)

source_name: Human Kidney sense 1 (gene)


title: Human Heart sense 2 (gene)

source_name: Human Heart sense 2 (gene)

value: heart


title: Human Kidney antisense 2 (exon)

source_name: Human Kidney antisense 2 (exon)


title: Human Heart sense 1 (gene)

source_name: Human Heart sense 1 (gene)


title: Human Heart antisense 1 (exon)

source_name: Human Heart antisense 1 (exon)


title: Human Brain sense 2 (gene)

source_name: Human Brain sense 2 (gene)


title: Human Kidney antisense 1 (exon)

source_name: Human Kidney antisense 1 (exon)


title: Human Heart antisense 2 (exon)

source_name: Human Heart antisense 2 (exon)


title: Human Lung sense 1 (gene)

source_name: Human Lung sense 1 (gene)


title: Human Testes antisense 2 (gene)

source_name: Human Testes antisense 2 (gene)

value: testes

value: Antisense transcript (gene)


title: Human Thymus antisense 1 (gene)

source_name: Human Thymus antisense 1 (gene)

value: thymus


title: Human Colon antisense 1 (exon)

source_name: Human Colon antisense 1 (exon)

value: colon


title: Human Thymus antisense 2 (gene)

source_name: Human Thymus antisense 2 (gene)


title: Human Testes antisense 1 (gene)

source_name: Human Testes antisense 1 (gene)


title: Human Colon sense 1 (gene)

source_name: Human Colon sense 1 (gene)


title: Human Spleen antisense 2 (gene)

source_name: Human Spleen antisense 2 (gene)


title: Human Brain sense 1 (gene)

source_name: Human Brain sense 1 (gene)


title: Human Colon sense 2 (gene)

source_name: Human Colon sense 2 (gene)


title: Human Spleen antisense 1 (gene)

source_name: Human Spleen antisense 1 (gene)


title: Human Colon antisense 2 (exon)

source_name: Human Colon antisense 2 (exon)


title: Human Lung antisense 1 (gene)

source_name: Human Lung antisense 1 (gene)


title: Human Lung antisense 2 (gene)

source_name: Human Lung antisense 2 (gene)


title: Human Brain antisense 2 (exon)

source_name: Human Brain antisense 2 (exon)


title: Human Ovary antisense 1 (gene)

source_name: Human Ovary antisense 1 (gene)


title: Human Liver antisense 2 (gene)

source_name: Human Liver antisense 2 (gene)


title: Human Liver antisense 1 (gene)

source_name: Human Liver antisense 1 (gene)


title: Human Brain antisense 1 (exon)

source_name: Human Brain antisense 1 (exon)


title: Human Ovary antisense 2 (gene)

source_name: Human Ovary antisense 2 (gene)


title: Human Kidney antisense 2 (gene)

source_name: Human Kidney antisense 2 (gene)


title: Human Kidney antisense 1 (gene)

source_name: Human Kidney antisense 1 (gene)


title: Human Heart antisense 2 (gene)

source_name: Human Heart antisense 2 (gene)


title: Human Heart antisense 1 (gene)

source_name: Human Heart antisense 1 (gene)


title: Human Brain antisense 1 (gene)

source_name: Human Brain antisense 1 (gene)


title: HudsonAlpha_Genotype_MCF10A-Er-Src

status: Public on Sep 07 2012

type: genomic

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

label: Unknown

molecule: genomic DNA

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: Genotype

tag: datatype description

value: Genotype CNV and SNP

tag: cell

tag: cell organism

value: human

tag: cell description

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: labversion

value: Illumina 1MDuo

tag: obtainedby

value: Stanford

tag: obtainedby description

value: Snyder - Stanford University

tag: replicate


title: HudsonAlpha_Genotype_MCF-7

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_Genotype_SK-N-SH_RA

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)


title: HudsonAlpha_Genotype_AG04449

value: HudsonAlpha

value: fetal buttock/thigh fibroblast

value: normal

value: M


title: HudsonAlpha_Genotype_SAEC

source_name: SAEC

value: Myers - Hudson Alpha Institute for Biotechnology

value: Genotype

value: Genotype CNV and SNP

value: SAEC

value: human

value: small airway epithelial cells

value: endoderm

value: U


title: HudsonAlpha_Genotype_U87

value: ectoderm

value: No special treatment or protocol applies

value: Illumina 1MDuo


title: HudsonAlpha_Genotype_AoSMC

source_name: AoSMC

value: AoSMC

value: aortic smooth muscle cells

value: mesoderm

value: Duke

value: Crawford - Duke University


title: HudsonAlpha_Genotype_NH-A_Duke

source_name: NH-A

value: HudsonAlpha

value: NH-A

value: astrocytes (also called Astrocy)

value: normal


title: HudsonAlpha_Genotype_AG09319

value: Myers - Hudson Alpha Institute for Biotechnology

value: Genotype

value: Genotype CNV and SNP

value: gum tissue fibroblasts from apparently heathly 24 year old

value: F

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_Genotype_SKMC

source_name: SKMC

value: SKMC

value: human

value: skeletal muscle cells

value: U

value: No special treatment or protocol applies

value: Illumina 1MDuo


title: Human Brain antisense 2 (gene)

source_name: Human Brain antisense 2 (gene)

tag: tissue

value: brain

tag: transcript type

value: Antisense transcript (gene)

tag: ambion catalog number


title: HudsonAlpha_Genotype_AG04450

tag: lab

value: HudsonAlpha

tag: lab description

tag: datatype

value: fetal lung fibroblast

value: endoderm

value: M


title: HudsonAlpha_Genotype_AG09309

value: Myers - Hudson Alpha Institute for Biotechnology

value: Genotype

tag: datatype description

value: Genotype CNV and SNP

tag: cell

tag: cell organism

value: adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell


title: HudsonAlpha_Genotype_Myometr

source_name: Myometr

value: Myometr

tag: cell description

value: myometrial cells

value: normal

tag: cell sex

value: F

value: Duke

value: Crawford - Duke University


title: HudsonAlpha_Genotype_PrEC

source_name: PrEC

value: PrEC

value: human

value: prostate epithelial cell line

tag: cell lineage

value: epithelial

value: U

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: Illumina 1MDuo

value: UW

value: Stamatoyannopoulous - University of Washington


title: Human Spleen sense 1 (gene)

source_name: Human Spleen sense 1 (gene)

value: spleen

value: Sense transcript (gene)


title: HudsonAlpha_Genotype_PFSK-1

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: Genotype

value: Genotype CNV and SNP

value: neuroectodermal cell line derived from a cerebral brain tumor, (PMID:1316433)

value: cancer

value: ectoderm

value: M

tag: labversion

tag: obtainedby

tag: obtainedby description


title: HudsonAlpha_Genotype_T-47D

value: human

value: epithelial cell line derived from a mammary ductal carcinoma.

tag: cell karyotype

value: F

tag: replicate


title: Human Colon antisense 1 (gene)

source_name: Human Colon antisense 1 (gene)

tag: tissue

value: colon

tag: transcript type

value: Antisense transcript (gene)

tag: ambion catalog number


title: HudsonAlpha_Genotype_A549

tag: lab

tag: lab description

tag: datatype

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: endoderm

value: No special treatment or protocol applies

value: Illumina 1MDuo


title: Human Colon antisense 2 (gene)

source_name: Human Colon antisense 2 (gene)


title: BM MSC2_late

status: Public on Sep 24 2012

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: BM MSC late

label_protocol: Standard Affymetrix procedures

growth_protocol: Bone marrow fragments from tibia plateau of patients undergoing surgery were flushed with PBS. Cell suspension was filtered through a 100 µm cell strainer and centrifuged for 7 min at 400xg. Cells were seeded into 75 cm2 tissue culture flasks with DMEM-LG (PAA) with 10% FCS (PAA), 2 mM L-glutamine (Sigma-Aldrich) and 100 U/mL penicilline/streptomycine ( Lonza). The first medium exchange was performed after 48 hours to remove erythrocytes and other non-adherent cells. Thereafter, media was exchanged twice per week, and MSC were isolated by their plastic adherence. When reaching 80% confluence, cells were trypsinized, counted in a Neubauer counting chamber (Brand, Wertheim, Germany) and replated at 13,333 cells/cm2.

extract_protocol: mikroRNeasy kit (Quiagen)

tag: cell type

value: Bone marrow derived mesenchymal stromal cells (MSC)

tag: tissue origin

value: bone marrow

tag: passage


title: BM MSC3_late


title: BM MSC2_early

source_name: BM MSC early

extract_protocol: microRNeasy kit (Quiagen)


title: BM MSC1_late


title: HudsonAlpha_Genotype_AG10803

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: Genotype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell

tag: cell sex

value: UW

value: Stamatoyannopoulous - University of Washington


title: BM MSC3_early


title: BM MSC1_early


title: HudsonAlpha_Genotype_HNPCEpiC

source_name: HNPCEpiC

value: Genotype CNV and SNP

value: HNPCEpiC

value: human

value: non-pigment ciliary epithelial cells

value: normal

value: U

tag: treatment

tag: treatment description

tag: labversion

tag: obtainedby

tag: obtainedby description


title: HudsonAlpha_Genotype_NT2-D1

value: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

tag: cell karyotype

value: cancer

tag: cell lineage

value: inner cell mass

value: M

tag: replicate


title: HudsonAlpha_Genotype_HPAEpiC

source_name: HPAEpiC

tag: lab

tag: lab description

tag: datatype

value: HPAEpiC

value: pulmonary alveolar epithelial cells

value: No special treatment or protocol applies

value: Illumina 1MDuo


title: HudsonAlpha_Genotype_MCF10A-Er-Src_4OHTAM_1uM_36hr

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: Genotype

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: ectoderm

value: F

value: (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers)

value: Stanford

value: Snyder - Stanford University


title: HudsonAlpha_Genotype_NHBE

source_name: NHBE

value: Genotype CNV and SNP

value: NHBE

value: human

value: bronchial epithelial cells

value: normal

value: endoderm

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_Genotype_PANC-1

value: HudsonAlpha

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

value: cancer

value: M

value: No special treatment or protocol applies

value: Illumina 1MDuo


title: HudsonAlpha_Genotype_NH-A_UW

value: Myers - Hudson Alpha Institute for Biotechnology

value: Genotype

value: NH-A

value: astrocytes (also called Astrocy)

value: ectoderm

value: U


title: HudsonAlpha_Genotype_NHDF-neo

source_name: NHDF-neo

value: Genotype CNV and SNP

value: NHDF-neo

value: human

value: neonatal dermal fibroblasts

value: mesoderm


title: HudsonAlpha_Genotype_LNCaP

source_name: LNCaP

value: HudsonAlpha

value: LNCaP

value: prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.)

value: endoderm

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_Genotype_HSMM

source_name: HSMM

value: Myers - Hudson Alpha Institute for Biotechnology

value: HSMM

value: skeletal muscle myoblasts

value: normal

value: No special treatment or protocol applies

value: Illumina 1MDuo

value: Duke

value: Crawford - Duke University


title: HudsonAlpha_Genotype_HUVEC

source_name: HUVEC

value: Genotype

value: Genotype CNV and SNP

value: HUVEC

value: human

value: umbilical vein endothelial cells

value: U


title: HudsonAlpha_Genotype_HeLa-S3

value: HudsonAlpha

value: cervical carcinoma

value: cancer

value: ectoderm

value: F


title: HudsonAlpha_Genotype_HTR8svn

value: Myers - Hudson Alpha Institute for Biotechnology

value: trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo


title: HudsonAlpha_Genotype_Melano

source_name: Melano

value: Melano

value: epidermal melanocytes

value: normal

value: No special treatment or protocol applies


title: HudsonAlpha_Genotype_Chorion

source_name: Chorion

value: Genotype

value: Chorion

value: chorion cells (outermost of two fetal membranes), fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes.

value: extraembryonic mesoderm, trophectoderm

value: Illumina 1MDuo

value: Duke

value: Crawford - Duke University


title: HudsonAlpha_Genotype_GM06990

value: HudsonAlpha

value: Genotype CNV and SNP

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment:Epstein-Barr Virus transformed

value: mesoderm

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_Genotype_GM12891

value: Myers - Hudson Alpha Institute for Biotechnology

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: M


title: HudsonAlpha_Genotype_Caco-2

value: Genotype

value: cancer

value: endoderm

value: No special treatment or protocol applies


title: HudsonAlpha_Genotype_Jurkat

source_name: Jurkat

value: Jurkat

value: T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID:68013)

value: Illumina 1MDuo


title: HudsonAlpha_Genotype_BC_Small_Intestine_01-11002

value: HudsonAlpha

value: small intestine, donor 01-11002, age 83, caucasian, DNA and RNA extract

value: normal

value: F


title: HudsonAlpha_Genotype_BC_Jejunum_H12817N

value: Genotype CNV and SNP

value: human

value: jejunum, donor H12817N, age 71, caucasian, DNA and RNA extract


title: HudsonAlpha_Genotype_CMK

source_name: CMK

value: Myers - Hudson Alpha Institute for Biotechnology

value: CMK

value: acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID:3016165)

value: mesoderm

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_Genotype_BJ

source_name: BJ

value: Genotype

value: BJ

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC.  (PMID:9916803)

value: M

value: No special treatment or protocol applies


title: HudsonAlpha_Genotype_GM19239

value: HudsonAlpha

value: B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: Illumina 1MDuo

value: Duke

value: Crawford - Duke University


title: HudsonAlpha_Genotype_NB4

value: Genotype CNV and SNP

value: human

value: acute promyelocytic leukemia cell line. (PMID:1995093)

value: cancer

value: U


title: HudsonAlpha_Genotype_GM12892

value: Myers - Hudson Alpha Institute for Biotechnology

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: mesoderm

value: F


title: HudsonAlpha_Genotype_HSMMtube

source_name: HSMMtube

value: Genotype

value: HSMMtube

value: skeletal muscle myotubes differentiated from the HSMM cell line

value: normal


title: HudsonAlpha_Genotype_ovcar-3

value: HudsonAlpha

value: ovarian adenocarcinoma, "the NIH:OVCAR-3 line was established in 1982 by T.C. Hamilton, et al. from the malignant ascites of a patient with progressive adenocarcinoma of the ovary." - ATCC. (PMID:6604576)

value: No special treatment or protocol applies

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_Genotype_RPTEC

source_name: RPTEC

value: Genotype CNV and SNP

value: RPTEC

value: human

value: renal proximal tubule epithelial cells

value: Illumina 1MDuo


title: HudsonAlpha_Genotype_HL-60

value: Myers - Hudson Alpha Institute for Biotechnology

value: promyelocytic leukemia cells, (PMID:276884)

value: cancer


title: HudsonAlpha_Genotype_K562

value: Genotype

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: mesoderm

value: F


title: HudsonAlpha_Genotype_HepG2

value: HudsonAlpha

value: hepatocellular carcinoma

value: endoderm

value: M


title: HudsonAlpha_Genotype_HCM

source_name: HCM

value: HCM

value: cardiac myocytes

value: normal

value: U

value: No special treatment or protocol applies

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_Genotype_HRE

source_name: HRE

value: Myers - Hudson Alpha Institute for Biotechnology

value: Genotype CNV and SNP

value: HRE

value: human

value: renal epithelial cells

value: Illumina 1MDuo


title: HudsonAlpha_Genotype_GM12878

value: HudsonAlpha

value: Genotype

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: mesoderm

value: F

tag: labexpid

tag: labversion description


title: HudsonAlpha_Genotype_HRCEpiC

source_name: HRCEpiC

tag: datatype description

tag: cell

value: HRCEpiC

value: renal cortical epithelial cells


title: HudsonAlpha_Genotype_IMR90

tag: cell organism

tag: cell description

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: normal

value: endoderm


title: HudsonAlpha_Genotype_HMEC

source_name: HMEC

value: HMEC

value: mammary epithelial cells

value: ectoderm

tag: cell sex

value: U

tag: treatment

value: No special treatment or protocol applies

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_Genotype_H1-hESC

growth_protocol: missing

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: Genotype CNV and SNP

value: human

value: embryonic stem cells

value: inner cell mass

value: M

tag: treatment description

tag: labversion

value: Illumina 1MDuo


title: HudsonAlpha_Genotype_HAEpiC

source_name: HAEpiC

value: Genotype

value: HAEpiC

value: amniotic epithelial cells

value: normal

tag: obtainedby

tag: obtainedby description


title: HudsonAlpha_Genotype_HCF

source_name: HCF

value: HCF

value: cardiac fibroblasts

tag: cell karyotype

tag: cell lineage

value: mesoderm


title: HudsonAlpha_Genotype_HEK293

tag: lab

value: embryonic kidney, cells contain Adenovirus 5 DNA (PMID:11967234)

value: U

value: No special treatment or protocol applies

value: UW

tag: replicate


title: HudsonAlpha_Genotype_HEEpiC

source_name: HEEpiC

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: Genotype CNV and SNP

value: HEEpiC

value: esophageal epithelial cells

value: endoderm

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_AG04449_Methyl27

data_processing:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylArray

Score in the bed files is beta value x 1000

label: Cy3 or Cy5

value: MethylArray

value: DNA Methylation Array

value: human

value: fetal buttock/thigh fibroblast

value: M


title: HudsonAlpha_Genotype_HRPEpiC

source_name: HRPEpiC

value: Genotype

value: HRPEpiC

value: retinal pigment epithelial cells

value: normal

value: ectoderm

value: Illumina 1MDuo


title: Human Spleen sense 2 (gene)

source_name: Human Spleen sense 2 (gene)

tag: tissue

value: spleen

tag: transcript type

value: Sense transcript (gene)

tag: ambion catalog number


title: HudsonAlpha_Genotype_HCPEpiC

source_name: HCPEpiC

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype description

value: Genotype CNV and SNP

tag: cell

value: HCPEpiC

tag: cell organism

value: choroid plexus epithelial cells

value: U

value: No special treatment or protocol applies

value: UW


title: HudsonAlpha_MethylArray_AG04450_Methyl27

value: MethylArray

value: DNA Methylation Array

value: human

tag: cell description

value: fetal lung fibroblast

value: endoderm

tag: cell sex

value: M

tag: treatment

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_Genotype_HIPEpiC

source_name: HIPEpiC

value: Genotype

value: HIPEpiC

value: iris pigment epithelial cells

value: normal

value: ectoderm

tag: treatment description

tag: labversion

value: Illumina 1MDuo

tag: obtainedby


title: HudsonAlpha_MethylArray_BC_Kidney_H12817N_Methyl27

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: kidney, donor H12817N, age 71, caucasian, DNA and RNA extract

tag: cell karyotype

tag: cell lineage

value: mesoderm

value: BioChain

tag: obtainedby description

value: The BioChain subset of HudsonAlpha


title: HudsonAlpha_MethylArray_BC_Left_Ventricle_N41_Methyl27

tag: lab

tag: lab description

value: MethylArray

value: DNA Methylation Array

value: human

value: left ventricle, donor N41, age 26, Asian, DNA extract

value: No special treatment or protocol applies

tag: replicate


title: HudsonAlpha_MethylArray_BC_Kidney_01-11002_Methyl27

tag: datatype

value: kidney, donor 01-11002, age 83, caucasian, DNA and RNA extract

value: F


title: HudsonAlpha_MethylArray_RPTEC_Methyl27

value: RPTEC

value: renal proximal tubule epithelial cells

value: U

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_BC_Skin_01-11002_Methyl27

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: skin, donor 01-11002, age 83, caucasian, DNA extract

value: normal

value: ectoderm, mesoderm


title: HudsonAlpha_MethylArray_BC_Esophagus_01-11002_Methyl27

value: MethylArray

value: esophagus, donor 01-11002, age 83, caucasian, DNA and RNA extract

value: endoderm

value: BioChain

value: The BioChain subset of HudsonAlpha


title: HudsonAlpha_MethylArray_SAEC_Methyl27

source_name: SAEC

value: DNA Methylation Array

value: SAEC

value: human

value: small airway epithelial cells

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_BC_Esophagus_H12817N_Methyl27

value: esophagus, donor H12817N, age 71, caucasian, DNA extract

value: M


title: HudsonAlpha_MethylArray_SK-N-SH_RA_Methyl27

value: HudsonAlpha

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: cancer

value: ectoderm

value: F

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_BC_Lung_01-11002_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

value: lung, donor 01-11002, age 83, caucasian, DNA and RNA extract

value: normal

value: endoderm


title: HudsonAlpha_MethylArray_NH-A_Methyl27

source_name: NH-A

value: DNA Methylation Array

value: NH-A

value: human

value: astrocytes (also called Astrocy)

value: U


title: HudsonAlpha_MethylArray_Jurkat_Methyl27

source_name: Jurkat

value: HudsonAlpha

value: Jurkat

value: T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID:68013)

value: mesoderm

value: M

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_MCF-7_Methyl27

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: cancer

value: ectoderm

value: F

value: Duke

value: Crawford - Duke University


title: HudsonAlpha_MethylArray_HRCEpiC_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

value: DNA Methylation Array

value: HRCEpiC

value: renal cortical epithelial cells

value: normal

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_SKMC_Methyl27

source_name: SKMC

value: HudsonAlpha

value: SKMC

value: human

value: skeletal muscle cells

value: mesoderm

value: U


title: HudsonAlpha_MethylArray_NHBE_Methyl27

source_name: NHBE

value: NHBE

value: bronchial epithelial cells

value: endoderm

value: F

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_HRPEpiC_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

value: DNA Methylation Array

value: HRPEpiC

value: retinal pigment epithelial cells

value: ectoderm


title: HudsonAlpha_MethylArray_HNPCEpiC_Methyl27

source_name: HNPCEpiC

value: HudsonAlpha

value: HNPCEpiC

value: non-pigment ciliary epithelial cells

value: normal

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_NHDF-neo_Methyl27

source_name: NHDF-neo

value: NHDF-neo

value: human

value: neonatal dermal fibroblasts

value: mesoderm

value: U


title: HudsonAlpha_MethylArray_IMR90_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: endoderm

value: F

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_BC_Penis_H12817N_Methyl27

value: MethylArray

value: DNA Methylation Array

value: penis, donor H12817N, age 71, caucasian, DNA extract

value: M

value: BioChain

value: The BioChain subset of HudsonAlpha


title: HudsonAlpha_MethylArray_HPAEpiC_Methyl27

source_name: HPAEpiC

value: HudsonAlpha

value: HPAEpiC

value: pulmonary alveolar epithelial cells

value: normal

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_BC_Colon_H12817N_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: human

value: colon, donor H12817N, age 71, caucasian, DNA and RNA extract


title: HudsonAlpha_MethylArray_BC_Pancreas_H12817N_Methyl27

value: pancreas, donor H12817N, age 71, caucasian, DNA and RNA extract

value: endoderm


title: HudsonAlpha_MethylArray_HMEC_Methyl27

value: MethylArray

value: HMEC

value: mammary epithelial cells

value: ectoderm

value: U

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_BC_Small_Intestine_01-11002_Methyl27

value: HudsonAlpha

value: DNA Methylation Array

value: small intestine, donor 01-11002, age 83, caucasian, DNA and RNA extract

value: F

value: BioChain

value: The BioChain subset of HudsonAlpha


title: HudsonAlpha_MethylArray_HIPEpiC_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: HIPEpiC

value: iris pigment epithelial cells

value: normal

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_BC_Jejunum_H12817N_Methyl27

value: MethylArray

value: human

value: jejunum, donor H12817N, age 71, caucasian, DNA and RNA extract

value: endoderm

value: M


title: HudsonAlpha_MethylArray_BC_Colon_01-11002_Methyl27

value: HudsonAlpha

value: colon, donor 01-11002, age 83, caucasian, DNA and RNA extract

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_BC_Rectum_N29_Methyl27

value: DNA Methylation Array

value: rectum, donor N29, age 29, Asian, DNA extract


title: HudsonAlpha_MethylArray_BC_Prostate_Gland_H12817N_Methyl27

value: prostate gland, donor H12817N, age 71, caucasian, DNA extract

value: BioChain

value: The BioChain subset of HudsonAlpha


title: HudsonAlpha_MethylArray_BC_Skeletal_Muscle_01-11002_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: skeletal muscle, donor 01-11002, age 83, caucasian, DNA and RNA extract

value: mesoderm

value: F


title: HudsonAlpha_MethylArray_AG10803_Methyl27

value: MethylArray

value: abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_AG09319_Methyl27

value: human

value: gum tissue fibroblasts from apparently heathly 24 year old

value: normal


title: HudsonAlpha_MethylArray_BC_Skeletal_Muscle_H12817N_Methyl27

value: HudsonAlpha

value: skeletal muscle, donor H12817N, age 71, caucasian, DNA and RNA extract

value: M

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_BC_Adipose_UHN00001_Methyl27

value: DNA Methylation Array

value: adipose tissue, donor UHN0001, age 35, African American, DNA extract

value: BioChain


title: HudsonAlpha_MethylArray_NB4_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: acute promyelocytic leukemia cell line. (PMID:1995093)

value: cancer

value: U


title: HudsonAlpha_MethylArray_BC_Lung_H12817N_Methyl27

value: MethylArray

value: lung, donor H12817N, age 71, caucasian, DNA and RNA extract

value: endoderm

value: The BioChain subset of HudsonAlpha


title: HudsonAlpha_MethylArray_AG09309_Methyl27

value: human

value: adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell

value: F

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_BC_Breast_02-03015_Methyl27

value: HudsonAlpha

value: breast, donor 02-03015, age 21, caucasian, DNA extract

value: normal

value: ectoderm

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_BC_Brain_H11058N_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: DNA Methylation Array

value: brain, donor H11058N, age 66, Asian, DNA extract

value: M

value: BioChain


title: HudsonAlpha_MethylArray_BC_Bladder_01-11002_Methyl27

value: MethylArray

value: urinary bladder, donor 01-11002, age 83, caucasian, DNA extract

value: endoderm


title: HudsonAlpha_MethylArray_BC_Pericardium_H12529N_Methyl27

value: human

value: pericardium, donor H12529N, age 70, caucasian, DNA extract

value: mesoderm

value: The BioChain subset of HudsonAlpha


title: HudsonAlpha_MethylArray_HCF_Methyl27

value: HudsonAlpha

value: HCF

value: cardiac fibroblasts

value: U

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_HAEpiC_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: DNA Methylation Array

value: HAEpiC

value: amniotic epithelial cells

value: normal

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_HCPEpiC_Methyl27

value: MethylArray

value: HCPEpiC

value: choroid plexus epithelial cells

value: ectoderm


title: HudsonAlpha_MethylArray_CMK_Methyl27

source_name: CMK

value: CMK

value: human

value: acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID:3016165)

value: cancer

value: mesoderm

value: M


title: HudsonAlpha_MethylArray_GM12891_Methyl27

value: HudsonAlpha

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed


title: HudsonAlpha_MethylArray_HEEpiC_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: DNA Methylation Array

value: HEEpiC

value: esophageal epithelial cells

value: endoderm

value: U

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_HRE_Methyl27

source_name: HRE

value: MethylArray

value: HRE

value: renal epithelial cells

value: normal

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_BC_Adrenal_Gland_H12803N_Methyl27

value: human

value: adrenal gland, donor H12803N, age 88, caucasian, DNA extract

value: ectoderm, mesoderm

value: F

value: BioChain

value: The BioChain subset of HudsonAlpha


title: HudsonAlpha_MethylArray_GM12892_Methyl27

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

value: DNA Methylation Array

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: mesoderm


title: HudsonAlpha_MethylArray_HEK293_Methyl27

value: embryonic kidney, cells contain Adenovirus 5 DNA (PMID:11967234)

value: U

value: Yale

value: Snyder - Yale University


title: HudsonAlpha_MethylArray_BC_Placenta_UHN00189_Methyl27

value: MethylArray

value: placenta, donor UHN00189, age 29

value: normal

value: extraembryonic mesoderm, trophectoderm


title: HudsonAlpha_MethylArray_K562_Methyl27

value: human

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: cancer

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_BC_Leukocyte_UHN00204_Methyl27

value: HudsonAlpha

value: peripheral blood mononuclear cell, donor UHN00204, age 54, caucasian, DNA extract

value: M

value: BioChain

value: The BioChain subset of HudsonAlpha


title: HudsonAlpha_MethylArray_BC_Liver_01-11002_Methyl27

value: Myers - Hudson Alpha Institute for Biotechnology

value: DNA Methylation Array

value: liver, donor 01-11002, age 83, caucasian, DNA and RNA extract

value: endoderm

value: F


title: HudsonAlpha_MethylArray_H1-hESC_Methyl27

value: MethylArray

value: embryonic stem cells

value: inner cell mass


title: HudsonAlpha_MethylArray_HepG2_Methyl27

value: human

value: hepatocellular carcinoma


title: HudsonAlpha_MethylArray_GM12878_Methyl27

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal

value: mesoderm


title: HudsonAlpha_MethylArray_HCM_Methyl27

source_name: HCM

value: HudsonAlpha

value: HCM

value: cardiac myocytes

value: U

value: No special treatment or protocol applies

value: UW

value: Stamatoyannopoulous - University of Washington


title: Balb/cJ 12-week-old, Npc1 antisense oligo + NAC treatment, biological replicate 1

status: Public on Jul 12 2012

city: BETHESDA

first: Celine

last: Cluzeau

state: MD

address: 10 Center Drive - room 9D41

department: PDEGEN

institute: NICHD/NIH

description:
Gene expression data
Female Balb/cJ mice were obtained from JAX mice and subsequently had free access to water and normal mouse chow as they were acclimated to our animal facility. Antisense oligo-treated mice were injected with control or antisense oligos for 4 weeks from 8 to 12 weeks of age. A subset of mice simultaneously received treatment with the antioxidant N-acetyl-cysteine (NAC) during the same 4 weeks as antisense oligo treatment. At 12 weeks of age, livers were collected from animals and immediately frozen on dry ice or preserved in RNAlater solution. Livers were collected from 5 biological replicates for each treatment group.

hyb_protocol: 200 ng of total RNA was reverse transcribed to obtain labeled cDNA.  Labeled cDNAs was hybridized to the chips.  Chips were washed and stained using standard protocols for the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Affymetrix Gene Chip Scanner 3000 and gene expression intensities were calculated using the Affymetrix GeneChip Command Console software

data_processing: Affymetrix .CEL files were normalized using the RMA (Robust Multi-Array Analysis) algorithm within Partek Genomics Suite software, version 6.5 (Partek Inc.)

source_name: BALB/c, 12-week-old control mouse

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

extract_protocol: Total RNA was extracted from the liver tissue using TRIzol reagent (Invitrogen), followed by purification with Qiagen RNeasy Mini columns (Qiagen). RNA quality and quantity was assessed using both a Bioanalyzer (Agilent Inc.) and NanoDrop (Thermo Scientiﬁc Inc.).

tag: original sample name

value: DW_72_4wk NPC+4wk NAC 2Xwk

tag: strain

value: BALB/c

tag: gender

value: Female

tag: phenotype

value: symptomatic

tag: genotype/variation

value: injected with Npc1 antisense oligo and treated with NAC

tag: age

tag: tissue

value: Liver


title: Balb/cJ 12-week-old, Npc1 antisense oligo + NAC treatment, biological replicate 4

value: DW_75_4wk NPC+4wk NAC 2Xwk

tag: treatment


title: Balb/cJ 12-week-old, Npc1 antisense oligo + NAC treatment, biological replicate 2

value: DW_73_4wk NPC+4wk NAC 2Xwk


title: Balb/cJ 12-week-old, Control antisense oligo + NAC treatment, biological replicate 4

value: DW_70_4wk ctrl+4wk NAC 2Xwk

value: asymptomatic

value: injected with control antisense oligo and treated with NAC


title: Balb/cJ 12-week-old, Control antisense oligo + NAC treatment, biological replicate 3

value: DW_69_4wk ctrl+4wk NAC 2Xwk


title: Balb/cJ 12-week-old, Npc1 antisense oligo + NAC treatment, biological replicate 3

value: DW_74_4wk NPC+4wk NAC 2Xwk


title: Balb/cJ 12-week-old, Npc1 antisense oligo + NAC treatment, biological replicate 5

value: DW_76_4wk NPC+4wk NAC 2Xwk


title: Balb/cJ 12-week-old, Control antisense oligo + NAC treatment, biological replicate 5

value: DW_71_4wk ctrl+4wk NAC 2Xwk


title: Balb/cJ 12-week-old, Control antisense oligo + NAC treatment, biological replicate 2

value: DW_68_4wk ctrl+4wk NAC 2Xwk


title: Balb/cJ 12-week-old, Control antisense oligo, biological replicate 5

value: DW_61_4wk ctrl no NAC

value: injected with control antisense oligo


title: Balb/cJ 12-week-old, Npc1 antisense oligo, biological replicate 5

value: DW_66_4wk NPC no NAC

value: BALB/c

value: injected with Npc1 antisense oligo


title: Balb/cJ 12-week-old, Control antisense oligo, biological replicate 3

value: DW_59_4wk ctrl no NAC

value: Female


title: Balb/cJ 12-week-old, Control antisense oligo + NAC treatment, biological replicate 1

value: DW_67_4wk ctrl+4wk NAC 2Xwk

value: Liver


title: Balb/cJ 12-week-old control, fasted, biological replicate 1

value: DW_52_12wk Balbc,no t,fst

value: fasted overnight


title: Balb/cJ 12-week-old control, fasted, biological replicate 5

value: DW_56_12wk Balbc,no t,fst

value: asymptomatic


title: Balb/cJ 12-week-old control, fasted, biological replicate 3

value: DW_54_12wk Balbc,no t,fst


title: Balb/cJ 12-week-old, Control antisense oligo, biological replicate 4

value: DW_60_4wk ctrl no NAC


title: Balb/cJ 12-week-old control, fasted, biological replicate 4

value: DW_55_12wk Balbc,no t,fst


title: Balb/cJ 12-week-old control, untreated, biological replicate 4

value: DW_50_12wkBalbc,no t,no f


title: Balb/cJ 12-week-old control, untreated, biological replicate 5

value: DW_51_12wkBalbc,no t,no f


title: Balb/cJ 12-week-old control, untreated, biological replicate 2

value: DW_48_12wkBalbc,no t,no f


title: Balb/cJ 12-week-old control, untreated, biological replicate 3

value: DW_49_12wkBalbc,no t,no f


title: Balb/cJ 12-week-old, Npc1 antisense oligo, biological replicate 4

value: DW_65_4wk NPC no NAC

value: BALB/c

value: symptomatic


title: Balb/cJ 12-week-old control, untreated, biological replicate 1

value: DW_47_12wkBalbc,no t,no f

value: Female


title: Balb/cJ 12-week-old, Npc1 antisense oligo, biological replicate 3

value: DW_64_4wk NPC no NAC

value: injected with Npc1 antisense oligo

value: Liver


title: Balb/cJ 12-week-old, Control antisense oligo, biological replicate 1

value: DW_57_4wk ctrl no NAC

value: injected with control antisense oligo


title: Balb/cJ 12-week-old, Npc1 antisense oligo, biological replicate 1

value: DW_62_4wk NPC no NAC


title: Balb/cJ 12-week-old control, fasted, biological replicate 2

value: DW_53_12wk Balbc,no t,fst

value: asymptomatic

value: fasted overnight


title: Balb/cJ 12-week-old, Control antisense oligo, biological replicate 2

value: DW_58_4wk ctrl no NAC


title: Balb/cJ 12-week-old, Npc1 antisense oligo, biological replicate 2

value: DW_63_4wk NPC no NAC


title: IEC conv. versus IEC GF [M3004]

status: Public on May 17 2012

city: Hannover

first: Mathias

middle: W.

last: Hornef

address: Carl Neuberg Str. 1

department: Inst. of Medical Microbiology

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were performed exactly as recommended by the manufacturer “Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7”.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2505 B at two different PMT settings (100 % and 5 %) to increase the dynamic range of the measurements (extended dynamic range mode).

data_processing: Data extraction and normalization were performed with the “Feature Extraction Software V9.5.3.1” by using the recommended default extraction protocol file: GE2-v5_95_Feb07.xml.

source_name: IEC GF

label_protocol: 1000ng of total RNA per condition were used to prepare Cy3-, or Cy5-labeled cRNA with the “Quick Amp Labeling Kit, Two-Color” (#5190-0444, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: IECs were prepared as described recently (Lotz et al., J. Exp Med. 2006). In brief, mouse intestinal tissue was incubated for 10 min at 37°C in 0.3 M EDTA. shaken vigorously and epithelial cells were separated from the underlying tissue and immune cells by repeated sedimentation at 1 x g at 4°C. Flow cytometric analysis revealed less than 5% and 1% of CD45+ cells in IEC preparations from adult and suckling mice, respectively.

extract_protocol: RNA was isolated using TRIzol (Invitrogen, Darmstadt, Germany) according to the manufacturer’s protocol.

tag: cell type

value: small intestinal epithelial cells

tag: group

value: germ-free

source_name: IEC conv

value: conventionally raised


title: Somatic.Tissue___Lung_Fetal_15wk_Patient30_Male_94.412.1.2

status: Public on May 14 2012

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized by RSN normalization using LUMI package in R. Some probes excluded because of probe failure/poor performance.

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

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion), quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

tag: loring pipeline sample id

tag: loring pipeline stem cell matrix version

value: stem cell matrix version 342

tag: tissue type

value: Lung

tag: fetal vs adult tissue

value: Fetal

tag: gestational age

tag: patient id

value: Male


title: Somatic.Tissue___Skeletal.muscle_Adult__Patient1_Male_97.29.1.1

value: Adult


title: Somatic.Tissue___Ureter_Adult__Patient2_Female_92.30.1.2

value: Ureter

value: Female


title: Somatic.Tissue___Lung_Adult__Patient1_Male_94.29.1.1


title: Somatic.Tissue___Liver_Fetal_14wk_Patient32_Female_147.414.1.2

value: Liver


title: IEC conv. versus IEC GF [M3003]

source_name: IEC conv.


title: Somatic.Tissue___Lymph.Node_Adult__Patient1_Male_100.29.1.1


title: Somatic.Tissue___Ureter_Adult__Patient1_Male_92.29.1.1


title: Somatic.Tissue___Stomach_Fetal_15wk_Patient30_Male_101.412.1.2

value: Stomach


title: Somatic.Tissue___Kidney_Fetal_15wk_Patient30_Male_143.412.1.2

value: Kidney


title: Somatic.Tissue___Stomach_Fetal_14wk_Patient32_Female_101.414.1.2


title: Somatic.Tissue___Kidney_Fetal_14wk_Patient32_Female_143.414.1.2


title: Somatic.Tissue___Diaphragm_Adult__Patient1_Male_93.29.1.1

value: Diaphragm


title: IEC conv. versus IEC GF [M3002]


title: Somatic.Tissue___Adrenal_Adult__Patient1_Male_95.29.1.2

value: Adrenal


title: Somatic.Tissue___Adrenal_Fetal_15wk_Patient30_Male_95.412.1.3


title: Somatic.Tissue___Stomach_Fetal_14wk_Patient26_Female_101.407.1.1


title: Somatic.Tissue___Ovary_Adult__Patient2_Female_106.30.1.3

value: Ovary


title: IEC conv. versus IEC GF [M3001]


title: Somatic.Tissue___Bladder_Adult__Patient1_Male_99.29.1.1

value: Bladder


title: Somatic.Tissue___Adipose_Adult__Patient1_Male_98.29.1.1

value: Adipose


title: Somatic.Tissue___Tongue_Fetal_14wk_Patient26_Female_139.407.1.1

value: Tongue


title: Somatic.Tissue___Stomach_Adult__Patient1_Male_101.29.1.1


title: Somatic.Tissue___Skeletal.muscle_Adult__Patient2_Female_97.30.1.2


title: Somatic.Tissue___Small.intestine_Fetal_15wk_Patient30_Male_146.412.1.2


title: Somatic.Tissue___Gallbladder_Adult__Patient2_Female_105.30.1.2

value: Gallbladder


title: Somatic.Tissue___Lymph.Node_Adult__Patient2_Female_100.30.1.2

value: stem cell matrix version 342


title: Somatic.Tissue___Lung_Fetal_14wk_Patient32_Female_94.414.1.2

value: Lung


title: Somatic.Tissue___Lung_Adult__Patient2_Female_94.30.1.2


title: Somatic.Tissue___Adipose_Adult__Patient2_Female_98.30.1.2


title: Somatic.Tissue___Adrenal_Fetal_14wk_Patient32_Female_95.414.1.2

value: Fetal


title: Somatic.Tissue___Adrenal_Adult__Patient2_Female_95.30.2.2


title: Somatic.Primary_SC23NSC______Male_62.225.1.1

tag: cell line

value: Male


title: Somatic.Primary_HANSE20H______Male_190.295.1.2


title: Somatic.Primary_HANSE21______Male_191.296.1.2


title: Somatic.Tissue___Bladder_Adult__Patient2_Female_99.30.1.2

value: Adult


title: Somatic.Tissue___Diaphragm_Adult__Patient2_Female_93.30.1.2


title: Somatic.Tissue___Duodenum_Adult__Patient2_Female_104.30.1.2

value: Duodenum


title: Somatic.Primary_HMSCad251______Male_219.572.1.2


title: Somatic.Primary_SM3______Male_71.236.1.1


title: Somatic.Primary_SC01GLIA______Male_61.224.1.1


title: Somatic.Primary_SC11GLIA______Male_67.230.4.1


title: Somatic.Primary_HIBEpiC254______Male_213.566.1.2


title: Somatic.Primary_SC41MSC______Female_66.229.2.1

value: Female


title: Somatic.Primary_SC27NSC______Female_125.375.1.1


title: Somatic.Primary_HRCEpiC255______Male_210.563.1.2


title: Somatic.Primary_SC31MSC______Male_64.227.1.1


title: Somatic.Primary_NUFF______Male_6.16.1.3

value: NUFF


title: Somatic.Primary_KERA1______Male_137.400.9.1


title: Somatic.Primary_HREpiC256______Male_211.564.1.2


title: Somatic.Primary_HDF.HSP______Male_40.167.2.1


title: Somatic.Primary_HRPTEpiC257______Male_209.562.1.2


title: Somatic.Primary_KDIB2______Male_251.669.1.1


title: Somatic.Primary_MRC5______Male_312.891.1.1


title: Somatic.Primary_HPLF260______Male_206.559.1.2


title: Somatic.Primary_HDF.HSP______Male_40.164.3.1


title: Somatic.Primary_SM2______Female_72.237.1.1


title: Somatic.Primary_HMSCbm252______Female_218.571.1.2


title: Somatic.Primary_HESMC267______Male_207.560.1.2


title: Somatic.Primary_HBVSMC266______Male_203.556.1.2


title: Somatic.Primary_HUVECBF4______Female_169.250.1.1


title: Somatic.Primary_IMR90______Female_129.382.1.1


title: Somatic.Primary_HCFaa1______Male_216.569.1.2


title: Somatic.Primary_HDK85______Female_257.689.1.4


title: Somatic.Primary_HPAv263______Female_217.570.1.2


title: Somatic.Primary_HUVECBF5______Female_170.251.1.1


title: Somatic.Primary_HBdSMC265______Male_212.565.1.2


title: Somatic.Primary_CCD1079SK______Male_128.380.1.1


title: Somatic.Primary_HCF1______Male_215.568.1.2


title: Somatic.Primary_ASTRO1______Female_253.675.1.1


title: Somatic.Primary_HDF68______Female_200.543.4.2


title: ES.parthenote_LLC7_passage16_____Female_44.173.1.6

value: parthenogentic embryonic stem cell, undifferentiated

tag: passage number


title: Somatic.Primary_HSkMC268______Female_208.561.1.2


title: Somatic.Primary_HDF51______Female_166.411.1.1


title: Somatic.Primary_HDF69______Female_201.544.2.2


title: iPS_HDF51IPS6_passage33_____Female_157.647.1.1

value: induced pluripotent stem cell, undifferentiated


title: iPS_HDF51IPS3_passage34_____Female_155.645.1.1


title: iPS_HDF51IPS7_passage33_____Female_158.648.1.2


title: ES.parthenote_LLC2_passage24_____Female_42.171.1.7


title: ES.parthenote_LLC9_passage20_____Female_46.175.1.6


title: iPS_HDF51IPS2_passage34_____Female_154.644.1.1


title: ES.parthenote_LLC6_passage16_____Female_43.172.1.1


title: ES.parthenote_LLC8_passage18_____Female_45.174.1.7


title: Somatic.Primary_HDF51______Female_166.436.1.1


title: ES.parthenote_LLC15_passage45_____Female_317.905.1.4


title: iPS_HDF51IPS5_passage34_____Female_156.646.1.1


title: Somatic.Primary_HDF258______Female_204.557.1.2


title: iPS_HDF51IPS1_passage25_____Female_153.894.1.1

description: LATE_IPS_F_HDF51IPS1P(37mRNA)(25methy)_21


title: ES.parthenote_LLC6_passage45_____Female_43.904.1.1


title: iPS_HDF51IPS9_passage33_____Female_160.649.1.1


title: iPS_HDF51IPS13_passage34_____Female_164.652.1.3


title: iPS_HDF51IPS12_passage33_____Female_163.651.1.1


title: iPS_NSC253I_passage23_____Male_314.893.1.1


title: iPS_TH152OCT4BTHAL_passage30_____Male_308.887.1.1


title: iPS_TH160OCT4SOX2BTHAL_passage38_____Male_311.890.1.1


title: iPS_HDF51IPS10_passage37_____Female_161.900.1.3


title: iPS_K4AMKIPS4F1_passage15_____Male_138.401.1.1


title: iPS_TH124SOX2BTHAL_passage34_____Male_309.888.2.1


title: iPS_KIPS4F8_passage27_____Male_250.668.1.1


title: iPS_IPS-Foreskin-CL3_passage19_____Male_132.389.2.1


title: iPS_GOTTESFELD3816.5_passage14_____Female_300.780.1.1


title: iPS_IPS-Foreskin-CL4_passage18_____Male_133.390.2.1


title: iPS_HFIB2IPS5_passage69_____Male_85.420.1.1


title: iPS_HDF51IPS11_passage33_____Female_162.650.1.2


title: iPS_IPS-IMR90C2_passage27_____Female_134.392.1.1


title: iPS_IPS-Foreskin-CL1_passage18_____Male_130.384.1.1


title: iPS_HDF51IPS7_passage11_____Female_158.493.2.1


title: iPS_KIPS4F1_passage32_____Female_249.667.1.1


title: iPS_GOTTESFELD4078.1B3_passage20_____Male_301.781.1.1


title: iPS_IPS-IMR90C4_passage27_____Female_135.394.1.1


title: iPS_GOTTESFELD8.2A4R_passage28_____Female_299.779.1.1


title: iPS_HDF51IPS6_passage11_____Female_157.492.2.1


title: iPS_C14_passage32_____Male_310.889.1.1


title: iPS_HDF51IPS9_passage14_____Female_160.500.2.1


title: iPS_HDF51IPS3_passage12_____Female_155.490.2.1


title: iPS_HDF51IPS5_passage12_____Female_156.491.2.1


title: iPS_HDF51IPS2_passage12_____Female_154.489.1.1


title: iPS_GOTTESFELD4078.1A2_passage27_____Male_302.782.1.1


title: iPS_HDF51IPS1_passage12_____Female_153.488.2.1


title: iPS_HDF51IPS12_passage12_____Female_163.497.2.1


title: iPS_HDF51IPS9_passage7_____Female_160.473.1.2


title: iPS_HDF51IPS13_passage14_____Female_164.502.1.1


title: iPS_HDF51IPS10_passage12_____Female_161.495.2.1


title: iPS_HDF51IPS5_passage6_____Female_156.440.1.2


title: iPS_HDF51IPS6_passage5_____Female_157.441.1.2


title: iPS_HDF51IPS7_passage5_____Female_158.442.1.2


title: iPS_IPS-Foreskin-CL2_passage17_____Male_131.387.2.1


title: iPS_HDF51IPS1_passage6_____Female_153.437.2.1


title: iPS_HDF51IPS12_passage6_____Female_163.447.1.2


title: iPS_HDF51IPS10_passage6_____Female_161.445.1.2


title: iPS_HDF51IPS11_passage14_____Female_162.501.2.1


title: iPS_HDF51IPS3_passage6_____Female_155.439.1.2


title: iPS_HDF51IPS11_passage8_____Female_162.475.1.1


title: ES_SIVF050_passage9_____Male_280.750.1.1

value: embryonic stem cell, undifferentiated


title: ES_SIVF048_passage13_____Male_278.748.1.1


title: ES_SIVF045_passage13_____Male_286.756.1.1


title: ES_SIVF044_passage13_____Male_285.755.1.1


title: iPS_HDF51IPS13_passage8_____Female_164.471.1.1


title: iPS_HDF51IPS2_passage6_____Female_154.438.1.1


title: ES_SIVF043_passage12_____Male_284.754.1.1


title: ES_SIVF021_passage19_____Male_120.351.2.1


title: ES_SIVF022_passage48_____Male_121.768.1.1


title: ES_SIVF017_passage67_____Male_292.769.1.1


title: ES_SIVF017_passage43_____Male_116.346.3.1


title: ES_MIZ4_passage62_____Male_37.156.2.1


title: ES_SIVF021_passage49_____Male_120.764.1.1


title: ES_SIVF011_passage28_____Male_273.743.1.3


title: ES_MIZ4_passage65_____Male_37.157.3.1


title: ES_SIVF022_passage19_____Male_121.352.2.1


title: ES_SIVF015_passage18_____Male_274.744.1.1


title: ES_SIVF002_passage50_____Male_290.763.1.1


title: ES_SIVF005_passage44_____Male_123.767.1.1


title: ES_SIVF002_passage17_____Male_136.398.1.1


title: ES_MIZ4_passage63_____Male_37.151.3.1


title: ES_SIVF014_passage42_____Male_295.773.1.2


title: ES_HES4_passage56_____Male_34.116.2.1


title: ES_HES4_passage60_____Male_34.121.2.1


title: ES_FES22_passage44_____Male_23.93.2.1


title: ES_MIZ4_passage53_____Male_37.148.2.1


title: ES_MIZ4_passage53_____Male_37.147.3.1


title: ES_MEL1_passage59_____Male_35.125.2.1


title: ES_FES22_passage44_____Male_23.92.2.1


title: ES_HUES16_passage21_____Male_70.233.1.1


title: ES_MEL1_passage59_____Male_35.128.2.1


title: ES_ESI049_passage38_____Male_28.103.3.1


title: ES_BG02_passage46_____Male_54.215.1.1


title: ES_HES4_passage57_____Male_34.117.2.1


title: ES_MEL1_passage51_____Male_35.122.2.1


title: ES_WA09_passage43_____Female_87.521.1.2


title: ES_WA09_passage44_____Female_87.453.1.2


title: ES_WA09_passage51_____Female_87.302.2.1


title: ES_WA09_passage46_____Female_87.144.2.1


title: ES_WA09_passage41_____Female_87.304.7.4


title: ES_WA09_passage40_____Female_87.137.2.1


title: ES_WA07_passage35_____Female_47.176.1.6


title: ES_WA07_passage56_____Female_47.177.1.6


title: ES_UC06_passage70_____Female_39.156.2.1


title: ES_WA09_passage39_____Female_87.138.2.1


title: ES_UC06_passage71_____Female_39.157.3.1


title: ES_UC06_passage61_____Female_39.159.2.1


title: ES_WA09_passage39_____Female_87.142.2.1


title: ES_SIVF047_passage10_____Female_288.758.1.1


title: ES_SIVF049_passage9_____Female_279.749.1.1


title: ES_SIVF029_passage28_____Female_277.747.1.1


title: ES_SIVF042_passage13_____Female_283.753.1.1


title: ES_UC06_passage61_____Female_39.158.2.1


title: ES_SIVF019_passage81_____Female_118.761.1.1


title: ES_SIVF024_passage15_____Female_294.772.1.2


title: ES_SIVF024_passage28_____Female_294.774.1.2


title: ES_SIVF041_passage17_____Female_282.752.1.1


title: ES_SIVF018_passage44_____Female_117.347.2.1


title: ES_SIVF019_passage67_____Female_118.776.1.2


title: ES_SIVF028_passage28_____Female_276.746.1.1


title: ES_SIVF027_passage31_____Female_297.777.1.2


title: ES_SIVF020_passage82_____Female_289.762.1.1


title: ES_SIVF046_passage11_____Female_287.757.1.1


title: ES_SIVF007_passage23_____Female_115.356.2.1


title: ES_SIVF016_passage19_____Female_275.745.1.1


title: ES_SIVF020_passage52_____Female_119.350.2.1


title: ES_SIVF006_passage22_____Female_114.344.2.1


title: ES_SIVF040_passage17_____Female_281.751.1.1


title: ES_SIVF006_passage24_____Female_114.355.2.1


title: ES_SIVF007_passage21_____Female_115.345.2.1


title: ES_MIZ6_passage27_____Female_38.161.2.1


title: ES_SIVF004_passage43_____Female_291.766.1.1


title: ES_SIVF003_passage22_____Female_113.343.2.1


title: ES_SIVF001_passage18_____Female_112.396.1.1


title: ES_MIZ6_passage27_____Female_38.162.3.1


title: ES_SIVF025_passage35_____Male_296.775.1.3


title: ES_SIVF001_passage45_____Female_112.342.2.1


title: ES_MEL3_passage34_____Female_126.376.1.1


title: ES_HES3_passage54_____Female_33.112.2.1


title: ES_SIVF026_passage30_____Male_298.778.1.3


title: ES_HES3_passage59_____Female_33.118.2.1


title: ES_HES3_passage31_____Female_33.276.2.1


title: ES_MEL2_passage13_____Female_36.131.2.1


title: ES_MEL4_passage36_____Female_127.379.1.1


title: ES_MEL4_passage35_____Female_127.378.1.1


title: ES_MEL2_passage15_____Female_36.133.2.1


title: ES_FES30_passage26_____Female_22.91.2.1


title: ES_ESI053_passage37_____Female_30.105.4.1


title: ES_CM8_passage25_____Female_241.618.1.2


title: ES_HES2_passage105_____Female_32.135.2.1


title: ES_CM7_passage19_____Female_243.621.2.2


title: ES_ESI035_passage35_____Female_27.102.3.1


title: ES_ESI017_passage24_____Female_26.101.2.1


title: ES_ESI051_passage37_____Female_29.104.2.1


title: ES_HES2_passage91_____Female_32.275.2.1


title: ES_HES2_passage92_____Female_32.110.2.1


title: ES_CSC14C1_passage26_____Female_202.550.1.2


title: ES_HES2_passage28_____Female_32.273.3.1


title: ES_HES2_passage55_____Female_32.114.2.1


title: ES_CM8_passage12_____Female_241.619.1.2


title: ES_CM6_passage19_____Female_244.622.1.2


title: Neutrophil - 30 minute - repeat 5 - mAdbID:94604

status: Public on Mar 01 2012

city: Bethesda

first: John

middle: E

last: Bennett

address: Building 10 - Magnuson Clinical Center, 12C103B

department: NIAID

institute: National Institutes of Health

description: mAdb experiment ID: 94604

hyb_protocol: Sample Hybridization Protocol Other: The probes were purified using Vivaspin 500 (Sartorius Stedim Biotech, Edgewood, NY), mixed, heated for 2 min at 98C and hybridized to C. glabrata microarray slides containing 70 mers of 5908 ORFs. Samples were hybridized overnight at 42C and slides were washed and dried for analysis.

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.55;; 3.78 Temperature: 32.98

data_processing:
Data Processing Protocol
Calculation Method: Value: log base 2 expression ratios; Default Ratio: ChanB/ChanA (Cy5/Cy3); Signal calculation: Mean Intensity minus Median Background; Any Features designated Control were excluded; Normalization method: Precalculated 50th Percentile (Median); Spot Filter Options: Target diameter >= 0 um AND Target diameter <= 300 um AND Both Chan A and Chan B Percentage of Target Pixels Saturated <= 50% AND Both Chan A and Chan B Signal/Background Ratios >= 2.000 Override other Chan A & B criteria and Include if Chan A Signal >= 5000 OR Chan B Signal >= 5000; Data was extracted and aligned by the Inventory Well ID; Within array multiple occurrences of Well ID were reduced to a single instance by selecting the one with the strongest signal (Chan A + Chan B).

organism: Nakaseomyces glabratus

source_name: Control - 30 minute - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: Total mRNA was reverse transcribed to cDNA with Cyanine 3 (Cy3) (Amersham, Piscataway, NJ) using Superscript II reverse transcriptase (Invitrogen) .

extract_protocol:
Trizol Extraction Protocol
Other: RNA was prepared from the frozen pellet using Trizol (Invitrogen, Carlsbad, CA), Lysing matrix C with FastPrep-24 (MP Biomedicals) and purified with RNeasy MinElute cleanup kit (Qiagen, Valencia, CA) using the manufacturer’s instruction.

treatment_protocol:
Treatment time: 30 minutes
In-vivo treatment: For control culture, 108 Cg29 cells were incubated in containing RPMI1640 (Gibco, Grand Island, NY) with 25 mM HEPES (Mediatech, Herndon, VA) (PH 7.2) plus 5% donor heparinized plasma without PMN. Tubes were tumbled vertically for 30 min at 8 rpm at 37C in a ProBlot hybridization oven (Labnet, Edison, NJ).

tag: strain

source_name: Neutrophil - 30 minute - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: Total mRNA was reverse transcribed to cDNA with Cyanine 5 (Cy5) (Amersham, Piscataway, NJ) using Superscript II reverse transcriptase (Invitrogen)

treatment_protocol:
Treatment type: stress
Stress: phagocytosis
Treatment time: 30 minutes
In-vivo treatment: A total of 1.0 X 108 Cg29 and 5.0 X 107 PMN were inoculated into 15 ml conical tubes containing RPMI1640 (Gibco, Grand Island, NY) with 25 mM HEPES (Mediatech, Herndon, VA) (PH 7.2) plus 5% donor heparinized plasma, for a total volume of 10 ml. Tubes were tumbled vertically for 30 min at 8 rpm at 37°C in a ProBlot hybridization oven (Labnet, Edison, NJ).


title: Neutrophil - 60 minute - repeat 5 - mAdbID:94606

description: mAdb experiment ID: 94606

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.54;; 3.79 Temperature: 33.13

source_name: Control - 60 minute - Cy3

treatment_protocol:
Treatment time: 60 minutes
In-vivo treatment: For control culture, 108 Cg29 cells were incubated in containing RPMI1640 (Gibco, Grand Island, NY) with 25 mM HEPES (Mediatech, Herndon, VA) (PH 7.2) plus 5% donor heparinized plasma without PMN. Tubes were tumbled vertically for 60 min at 8 rpm at 37C in a ProBlot hybridization oven (Labnet, Edison, NJ).

source_name: Neutrophil - 60 minute - Cy5

treatment_protocol:
Treatment type: stress
Stress: phagocytosis
Treatment time: 60 minutes
In-vivo treatment: A total of 1.0 X 108 Cg29 and 5.0 X 107 PMN were inoculated into 15 ml conical tubes containing RPMI1640 (Gibco, Grand Island, NY) with 25 mM HEPES (Mediatech, Herndon, VA) (PH 7.2) plus 5% donor heparinized plasma, for a total volume of 10 ml. Tubes were tumbled vertically for 60 min at 8 rpm at 37°C in a ProBlot hybridization oven (Labnet, Edison, NJ).


title: ES_CSC14_passage26_____Female_197.524.1.1

tag: gender


title: ES_CM1_passage16_____Female_246.624.2.1


title: Neutrophil - 60 minute - repeat 3 - mAdbID:94602

description: mAdb experiment ID: 94602

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.53;; 3.8 Temperature: 30.81


title: Neutrophil - 60 minute - repeat 4 - rev. fluor. - mAdbID:94603

description: mAdb experiment ID: 94603

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.53;; 3.79 Temperature: 31.21

source_name: Control - 60 minute - Cy5

source_name: Neutrophil - 60 minute - Cy3


title: ES_CM14_passage21_____Female_239.616.1.2


title: Neutrophil - 30 minute - repeat 6 - rev. fluor. - mAdbID:94605

description: mAdb experiment ID: 94605

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.55;; 3.79 Temperature: 33.07

source_name: Control - 30 minute - Cy5

source_name: Neutrophil - 30 minute - Cy3


title: ES_SIVF018_passage72_____Female_293.770.1.1


title: ES_CM11_passage17_____Female_240.617.1.2


title: ES_BG03_passage55_____Female_124.372.1.1


title: ES_CM14_passage87_____Female_239.615.1.2


title: Neutrophil - 60 minute - repeat 6 - rev. fluor. - mAdbID:94607

description: mAdb experiment ID: 94607

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [83871] ScanPower: 100;; 100 LaserPower: 2.54;; 3.79 Temperature: 33.19


title: ES_CM2_passage17_____Female_245.623.1.2


title: Neutrophil - 30 minute - repeat 4 - rev. fluor. - mAdbID:94130

description: mAdb experiment ID: 94130

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.07;; 3.5 Temperature: 28.01


title: Neutrophil - 30 minute - repeat 3 - mAdbID:94129

description: mAdb experiment ID: 94129

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.12;; 3.5 Temperature: 28.46


title: Neutrophil - 60 minute - repeat 1 - mAdbID:94127

description: mAdb experiment ID: 94127

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.07;; 3.51 Temperature: 25.29


title: Neutrophil - 30 minute - repeat 2 - rev. fluor. - mAdbID:94126

description: mAdb experiment ID: 94126

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.08;; 3.51 Temperature: 25.87


title: Neutrophil - 30 minute - repeat 1 - mAdbID:94125

description: mAdb experiment ID: 94125

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.05;; 3.51 Temperature: 26.36


title: Neutrophil - 60 minute - repeat 2 - rev. fluor. - mAdbID:94128

description: mAdb experiment ID: 94128

scan_protocol: Creator: GenePix Pro 6.0.0.45 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 3.04;; 3.51 Temperature: 24.28


title: LY180_w 15 mM furfural

status: Public on Jan 10 2012

city: Gainesville

first: Xuan

last: Wang

state: Florida

address: Bldg. 981 Museum Road

department: Microbiology and Cell Science

institute: University of Florida

description:
Escherichia coli W derivative.
15 mM furfural addition.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Escherichia coli

source_name: E. coli LY180, 15 mM furfural added

label_protocol: Conversion of RNA to cDNA and labeling with Cy3 was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
Cultures were grown in small fermentors. Furfural (15 mM) was added and incubation continued for 15 min prior to harvesting.
Strains were grown in AM1 medium with 14% xylose to OD 550 = 1.5 (0.66 g dcw/liter). 4 replicate 350 ml fermentors per strain.

extract_protocol: Cells were chilled in dry ice/ethanol, centrifuged, and the pellet resuspended in RNA Later (Qiagen) before storing at –80 C. Total RNA was extracted using the RNeasy Mini kit (Qiagen), and DNA was removed by digestion with RNase-Free DNase I. RNA quality and concentration was checked with an Agilent bioanalyzer at the University of Florida Gene Expression core before submitting the RNA to Roche Nimblegen in Iceland for analysis.

tag: genotype

value: frdBC::(Zm frg celYEc)  ldhA::(Zm frg casABKo) adhE::(Zm frg estZPp FRT)  ackA::FRT rrlE::(pdc adhAadhB FRT)  mgsA::FRT

tag: phenotype

value: ethanologenic

tag: accession

value: adapted for xylose fermentation

value: furfural


title: LY180

description:
Escherichia coli W derivative.
No furfural control.

source_name: E. coli LY180, no furfural added


title: HEK293-HIPK2-DN-Mutant-Sample1

status: Public on Feb 01 2012

city: New York

first: Avi

last: Ma'ayan

state: NY

address: One Gustave L. Levy Place Box 1215

department: Pharmacology and Systems Therapeutics

institute: Mount Sinai School of Medicine

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 transfected with HIPK-DN biological rep1

hyb_protocol: Following standard procedures according to the manufacturer's instructions as applied at the MSSM core facility.

data_processing:
Expression Console (1.1.2800.29167), affymetrix-algorithm-name = rma
One-way analysis of variance test (ANOVA) with BH correction at 0.05 FDR was applied to the dataset to identify the genes that were differentially expressed between groups.

growth_protocol: Mice were sacrificed at 8 weeks. Each sample in the Tg and WT mice are from different individual animals. One mice developed significant scarring and since the array results were significantly different this sample was not used for further analysis. HEK 293 and HK2 cells were obtained from ATCC and cultured as described in Rosenstiel, P.E., et al. Kidney Int 74, 1049-1058 (2008).

extract_protocol: Total RNA was extracted from kidney cortices of five Tg26 and five WT for gene expression microarrays. RNA was isolated by using RNAesay kit from Qiagen.

tag: transfection

value: HIPK-DN


title: HEK293-HIPK2-DN-Mutant-Sample3

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 transfected with HIPK-DN biological rep3

scan_protocol: Following standard procedures according to the manufacturer's instructions as applied at the MSSM core facility.


title: HEK293-HIPK2-DN-Mutant-Sample2

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 transfected with HIPK-DN biological rep2

label_protocol: Following standard procedures according to the manufacturer's instructions as applied at the MSSM core facility.


title: iPSC_HDF51iPSC1_p37__153.894.1.1

status: Public on Jan 06 2012

description: Biological Replicate 1

data_processing: The data were filtered for detection pValue > 0.01 and normalised using robust spline normalisation with lumi in R. Some probes excluded because of probe failure/poor performance.

label: Biotin

growth_protocol: Primary fibroblast cultures were established from dermal punch biopsies taken from individuals following informed consent and IRB approval. To generate iPSCs, fibroblasts were transduced with MMLV vectors containing the cDNAs for OCT4, SOX2, KLF4, c-MYC and +EGFP. Differentiation to NPCs and neurons followed Yuan, et al12. 3x105 FACS-purified TRA1-81+ cells were seeded onto 3x10 cm plates that were seeded the previous day with 5x105 PA6 cells36. At day 11, cells were dissociated with Accutase and ~5x105 CD184+CD15+CD44-CD271- NPCs were FACS-purified and plated onto poly-ornithine/laminin-coated plates and cultured with bFGF. At passage 7, NPCs were differentiated with BDNF, GDNF and cAMP. After 3 weeks of differentiation, cells were dissociated with Accutase and CD24+CD184-CD44- cells were purified by FACS, and Aβ, pTau/tTau and aGSK3β measured on purified control and mutant neurons from multiple lines cultured in parallel for an additional 5 days by multi-spot electrochemiluminescence assays (Meso Scale Diagnostics). EEs were analyzed by confocal microscopy on purified neurons co-cultured with human astrocytes (Lonza) for 12 days.

value: hIPSCs Undifferentiated


title: iPSC_HDF51iPSC13_p34__164.652.1.3

description: Biological Replicate 1


title: iPSC_HDF51iPSC10_p37__161.900.1.3

description: Biological Replicate 1


title: Fetal.Lung_8wk__94.416.1.1

description: Biological Replicate 1

value: 8 week fetal lung


title: iPSC_HDF51iPSC6_p33__157.647.1.1

description: Biological Replicate 1


title: iPSC_BJ1iPSC12_pUNK__150.261.1.1

description: Biological Replicate 1


title: iPSC_NSC253I_p23__314.893.1.1

description: Biological Replicate 1


title: iPSC_NDC1.2__681.1911.1.1

description: Biological Replicate 1


title: iPSC_HDF51iPSC5_p34__156.646.1.1

description: Biological Replicate 1


title: iPSC_NDC2.1__680.1908.1.1

description: Biological Replicate 1


title: HEK293-HIPK2-DN-Mutant-Sample4

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 transfected with HIPK-DN biological rep4


title: iPSC_HDF51iPSC7_p33__158.648.1.2

description: Biological Replicate 1


title: iPSC_HDF51iPSC14_p38__165.1029.1.1

description: Biological Replicate 1


title: Fetal.Lung_20wk__94.1440.1.2

description: Biological Replicate 1

value: 20 week fetal lung


title: iPSC_HDF51iPSC2_p34__154.644.1.1

description: Biological Replicate 1


title: iPSC_HDF51iPSC9_p33__160.649.1.1

description: Biological Replicate 1


title: Fetal.Lung_18wk__94.1441.1.2

description: Biological Replicate 1

value: 18 week fetal lung


title: Fetal.Lung_20wk__94.1442.1.2

description: Biological Replicate 1


title: Fetal.Lung_15wk__94.412.1.2

description: Biological Replicate 1

value: 15 week fetal lung


title: Fetal.Lung_10wk__94.409.1.1

description: Biological Replicate 1

value: 10 week fetal lung


title: iPSC_HDF51iPSC12_p33__163.651.1.1

description: Biological Replicate 1


title: Fetal.Liver_20wk__147.1442.1.2

description: Biological Replicate 1

value: 20 week fetal liver


title: iPSC_APPdp2.3__683.1917.1.1

description: Biological Replicate 1

value: Alzheimer's patient derived hIPSC


title: iPSC_HDF51iPSC3_p34__155.645.1.1

description: Biological Replicate 1


title: iPSC_HDF51iPSC11_p33__162.650.1.2

description: Biological Replicate 1


title: Fetal.Lung_14wk__94.414.1.2

description: Biological Replicate 1

value: 14 week fetal lung


title: Fetal.Liver_18wk__147.1441.1.2

description: Biological Replicate 1

value: 18 week fetal liver


title: Fetal.Heart_20wk__111.1442.1.2

description: Biological Replicate 1

value: 20 week fetal heart


title: Fetal.Brain_20wk__21.1440.1.2

description: Biological Replicate 1

value: 20 week fetal brain


title: diff.neuron.NDC1.2_681.1913.1.1

description: Biological Replicate 1

value: hIPSC differentiated into neurons for 56 days


title: diff.neuron.NDC2.1_680.1910.2.1

description: Biological Replicate 2

value: hIPSC differentiated into neurons for 62 days


title: Fetal.Heart_20wk__111.1440.1.2

description: Biological Replicate 1


title: Fetal.Heart_18wk__111.1441.1.2

description: Biological Replicate 1

value: 18 week fetal heart


title: Fetal.Brain_20wk__21.1442.1.2

description: Biological Replicate 1


title: diff.neuron.APPdp2.3_683.1915.2.1

description: Biological Replicate 2

value: Alzheimer's patient derived hIPSC differentiated into neurons for 56 days


title: diff.neuron.NDC2.1_680.1909.1.1

description: Biological Replicate 1


title: Fetal.Liver_20wk__147.1440.1.2

description: Biological Replicate 1


title: HCA37/HCA17 - repeat 2 - mAdbID:110257

status: Public on Jan 01 2012

first: Huei-Fung

last: Tsai

address: 10 Center Dr. Bldg. 10 Rm. 11N228

department: LCID

institute: NIH/NIAID

description: mAdb experiment ID: 110257

hyb_protocol: Hybridization Protocol Other: Microarray hybridization was done at the NIH/NIAID/RTB core facility. The 70-mer oligo arrays were prehybridized at 42°C in prehybridization buffer (5X SSC, 1% BSA, 0.1% SDS) for 30-60 min and then hybridized to the labelled cDNA in 50 ul of hybridization buffer (25% formamide, 5X SSC, 0.2% SDS, 20 ug/ml Poly (dA40-60), 200 ug/ml Cot-1 DNA, 80 ug/ml yeast t-RNA) overnight at 42°C. The microarrays were washed three times in wash buffer A (1X SSC, 0.05% SDS) and washing buffer B (0.1X SSC).

scan_protocol: Creator: GenePix Pro 6.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.94;; 3.67 Temperature: 30.9 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.

data_processing:
mAdb Data Processing
Calculation Method: Background correction was done using median intensity minus median background. Calculations were based on signals greater than 100 in either channels and excluding features designated as controls or flagged as bad or not found. Ratios were normalized using the 50th percentile (median).

organism: Candida albicans

source_name: WT HCA17 Control - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: Ten micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy3-dUTP (GE Health Care).

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was isolated from log-phase culture of C. albicans grown in YPD using Trizole (Invitrogen) and RNeasy MiniElute cleanup kit (Qiagen).

tag: developmental stage

value: log-phase culture

tag: genotype/variation

value: Wild type

source_name: mt HCA37 - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: Ten micrograms of total RNA were used for each labeling. The RNA was reversed transcribed to cDNA to incorporate the fluorescent Cy5-dUTP (GE Health Care).

value: ure2 mutant


title: diff.neuron.NDC1.2_681.1914.1.1

description: Biological Replicate 1

tag: cell type


title: HCA37/HCA17 - repeat 1 - mAdbID:107256

description: mAdb experiment ID: 107256

scan_protocol: Creator: GenePix Pro 6.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.95;; 3.64 Temperature: 26.24 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.


title: HCA40/HCA17 - repeat 2 - mAdbID:110261

description: mAdb experiment ID: 110261

scan_protocol: Creator: GenePix Pro 6.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.9;; 3.67 Temperature: 30.05 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.

source_name: mt HCA40 - Cy5


title: Fetal.Brain_18wk__21.1441.1.2

description: Biological Replicate 1

scan_protocol: Standard Illumina scanning protocol

value: 18 week fetal brain


title: HCA17/HCA40 - repeat 4 - rev. label - mAdbID:110262

description: mAdb experiment ID: 110262

scan_protocol: Creator: GenePix Pro 6.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.92;; 3.67 Temperature: 29.78 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.

source_name: WT HCA17 Control - Cy5

source_name: mt HCA40 - Cy3


title: HCA37/HCA17 - repeat 3 - mAdbID:107254

description: mAdb experiment ID: 107254

scan_protocol: Creator: GenePix Pro 6.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.92;; 3.64 Temperature: 24.98 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.


title: HCA17/HCA37 - repeat 4 - rev. label - mAdbID:110258

description: mAdb experiment ID: 110258

scan_protocol: Creator: GenePix Pro 6.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.96;; 3.67 Temperature: 30.66 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.

source_name: mt HCA37 - Cy3


title: HCA40/HCA17 - repeat 1 - mAdbID:110259

description: mAdb experiment ID: 110259

scan_protocol: Creator: GenePix Pro 6.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.93;; 3.67 Temperature: 30.51 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.


title: t466nsbis_3

status: Public on Nov 25 2011

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: - G protein-coupled receptors (GPCR) are centrally involved in most physiological processes and are a major drug targets. They transduce extracellular signals inside the cells through at least two different mechanisms: i) the classical coupling to heterotrimeric G proteins and ii) a newly discovered -arrestin-dependent pathway. The fundamental issue of the respective impacts that these two transduction mechanisms exert on gene regulation has not been clearly addressed to date. To tackle this question, we have developed two mutants of the follicle stimulating hormone (FSH) receptors which do not couple to G proteins upon FSH activation but continue to recruit -arrestins and signal through them.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: cell culture/primary cell - MEM (PAA Laboratory GmbH) + Fetal Bovin Serum 10% + Penicilin and Streptomycin 1% 37°C, 5% C02

treatment_protocol: no treatment

value: mutant hek293_t466

tag: harvest date

tag: treatment

value: no treatment


title: HCA40/HCA17 - repeat 3 - mAdbID:107255

description: mAdb experiment ID: 107255

scan_protocol: Creator: GenePix Pro 6.1.0.4 Scanner: GenePix 4000B [82425] ScanPower: 100;; 100 LaserPower: 2.98;; 3.64 Temperature: 25.81 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR on an Agilent DNA Microarray Scanner G2505B.


title: t469fsh_1

treatment_protocol: Name:FSH - hormone treatment - fsh stimulation,follicle stimulating hormone (fsh):quantity 3nM time 6hour . 3nM

value: mutant hek_t469

tag: concentration

tag: time

value: 6 hours


title: wtfsh_3

growth_protocol: cell culture/primary cell - MEM (PAA Laboratory GmbH) + Fetal Bovin Serum 10% + Penicilin and Streptomycin 1% 37°C; 5% C02

value: wild type

value: FSH - hormone treatment - fsh stimulation


title: wtns_3


title: t466fsh_2


title: t469fsh_2


title: t469ns_2


title: t466fsh_1


title: wtns_2


title: wtfsh_2


title: t466fsh_3


title: t466nsbis_2


title: t469ns_3


title: wtfsh_1


title: t469fsh_3


title: t469ns_1


title: t466nsbis_1


title: Bone marrow monocyte-1

status: Public on Jun 22 2011

first: Kang

last: Liu

department: Microbiology

institute: Columbia University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE-430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: The data were analyzed with Genespring, using default RMA normalization was used. The normalized values are log2 scaled, where the median is set as zero.

source_name: Bone marrow monocyte

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

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

value: female

tag: age

value: 6-8 weeks

tag: source tissue

value: bone marrow

tag: cell phenotype

value: SSCloCD11bhi CD115+.

value: monocyte


title: wtns_1

tag: cell line


title: Bone marrow monocyte-2

source_name: bone marrow monocyte

tag: strain

value: bone marow

value: SSCloCD11bhi CD115+


title: Spleen CD8+ DC-3

data_processing: The data were analyzed with Genespring, using default RMA normalization. The normalized values are log2 scaled, where the median is set as zero.

source_name: spleen CD8+ DCs

tag: gender

value: Spleen

value: dendritic cell


title: Bone marrow monocyte-3


title: Spleen CD8+ DC-2


title: Brain DC-2

source_name: Brain DC

treatment_protocol: Mice received subcutaneous 1 million B16-Flt3L tumor inoculation 12 days before organ harvest.

value: brain


title: Brain DC-1


title: Spleen CD8+ DC-1


title: Spleen CD8- DC-2

source_name: spleen CD8- DCs


title: GM12865-DS12442

status: Public on Nov 01 2011

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol

scan_protocol: Affymterix Gene Chip Scanner 3000

data_processing:
Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
HuEx-1_0-st-v2.r2.pgf
quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

source_name: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: EBV transformed

label_protocol: A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.

growth_protocol: Followed vendor recommendations for growth protocol/media

extract_protocol: At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: AffyExonArray

tag: datatype description

value: Affymetrix Exon Microarray

tag: cell

tag: cell organism

value: human

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment:Epstein-Barr Virus transformed

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: labexpid

tag: replicate


title: GM12865-DS12436


title: HFF-MyC-DS15073

source_name: Human Foreskin Fibroblast Cells Expressing Canine cMyc

value: HFF-Myc

value: foreskin fibroblast cells expressing canine cMyc

tag: cell karyotype

value: normal

value: fibroblast

value: M


title: HA-h-DS15202

source_name: Human Astrocytes-hippocampal

value: HA-h

value: astrocytes-hippocampal

value: ectoderm

value: U


title: Brain microglia-3

source_name: Brain microglia

value: female

tag: age

value: 6-8 weeks

tag: source tissue

value: brain

tag: cell type

value: microglia


title: Brain microglia-2

tag: strain

tag: cell phenotype


title: HFF-DS15119

source_name: Human Foreskin Fibroblast

tag: lab

value: UW

value: Stamatoyannopoulous - University of Washington

value: AffyExonArray

value: Affymetrix Exon Microarray

value: HFF

value: human

value: foreskin fibroblast


title: HFF-MyC-DS15079

tag: lab description

value: HFF-Myc

value: foreskin fibroblast cells expressing canine cMyc

value: normal

value: fibroblast


title: CD14+-DS16508

description: flow sorted CD14+ primary cells, 32ys,Caucasian female,donor:RO 01746

tag: term


title: Spleen CD8- DC-3

tag: gender

value: Spleen

value: dendritic cell


title: wild type strain 6390 rep 1

status: Public on Mar 29 2011

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

institute: NIH

description: Gene expression data from_wild type strain 6390 rep 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Staphylococcus aureus

source_name: wild type strain 6390 rep 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: standard broth cultures to log phase

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

tag: genotype/variation

value: wild type


title: NTERA-2cl.D1-DS14575

source_name: Malignant pluripotent embryonal carcinoma, NTERA-2 cl.D1 (PMID: 6694356)

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

value: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

value: cancer

value: inner cell mass

value: M


title: wild type strain 6390 rep 3

description: Gene expression data from_wild type strain 6390 rep 3

source_name: wild type strain 6390 rep 3


title: HBVP-DS14834

source_name: Human Brain Vascular Pericytes

value: UW

value: Stamatoyannopoulous - University of Washington

value: HBVP

tag: cell description

value: brain vascular pericytes

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

tag: labexpid


title: SK-N-MC-DS14408

source_name: Neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor

value: AffyExonArray

value: Affymetrix Exon Microarray

value: SK-N-MC

value: human

value: neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

tag: cell karyotype

value: ectoderm

value: F

tag: replicate


title: PrEC-DS12088

source_name: Human Prostate Epithelial Cell line

value: PrEC

value: prostate epithelial cell line

value: normal

value: epithelial


title: GM12864-DS12431

value: UW

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment:Epstein-Barr Virus transformed

value: M


title: HA-h-DS15192

value: Stamatoyannopoulous - University of Washington

value: HA-h

value: astrocytes-hippocampal


title: HPAEC-DS12916

source_name: Human Pulmonary Artery Endothelial Cells

value: AffyExonArray

value: HPAEC

value: pulmonary artery endothelial cells.

value: mesoderm


title: NHBE-DS11959

source_name: Normal Human Bronchial Epithelial Cells w/RA

value: Affymetrix Exon Microarray

value: NHBE

value: human

value: bronchial epithelial cells

value: endoderm


title: HFF-DS15115

value: HFF

value: foreskin fibroblast

value: normal


title: Brain microglia-1

source_name: brain microglia

tag: strain

value: female

tag: age

value: 6-8 weeks

tag: source tissue

value: brain

tag: cell type

value: microglia


title: Spleen CD8- DC-1

source_name: Spleen CD8- DCs

value: Spleen

tag: cell phenotype


title: WERI-Rb-1-DS13674

source_name: retinoblastoma (PMID: 844036)

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

value: AffyExonArray

value: retinoblastoma (PMID:844036)

value: cancer

value: ectoderm

value: F


title: NTERA-2cl.D1-DS14564

tag: datatype

value: Affymetrix Exon Microarray

value: human

value: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

value: inner cell mass

value: M


title: HMVEC-dAd-DS12957

source_name: Adult Human Dermal Microvascular Endothelial Cells, Dermal-Derived.

tag: datatype description

value: HMVEC-dAd

value: adult dermal microvascular endothelial cells.

value: normal


title: PrEC-DS12098

tag: cell

value: PrEC

value: prostate epithelial cell line

value: epithelial

value: U


title: wild type strain 6390 rep 2

description: Gene expression data from_wild type strain 6390 rep 2

source_name: wild type strain 6390 rep 2

tag: genotype/variation

value: wild type


title: HBVSMC-DS14845

source_name: Human Brain Vascular Smooth Muscle Cells

value: UW

value: Stamatoyannopoulous - University of Washington

value: AffyExonArray

value: HBVSMC

tag: cell organism

tag: cell description

value: brain vascular smooth muscle cells.

value: mesoderm


title: HMVEC-dAd-DS12952

value: Affymetrix Exon Microarray

value: human

tag: cell sex

value: F


title: HBVSMC-RS18999

tag: cell lineage

tag: labexpid


title: NHBE-DS11969

value: NHBE

value: bronchial epithelial cells

tag: cell karyotype

value: endoderm

tag: replicate


title: HSMMtube-DS15538

source_name: Normal Human Skeletal Muscle Myoblasts

value: HSMMtube

value: skeletal muscle myotubes differentiated from the HSMM cell line

value: normal


title: 7-day-old seedling of Col-0 at control condition, biological rep2

status: Public on Dec 23 2010

city: Shulin City, Taipei County

first: Hsiang-chin

address: 9F., No.332, Xuefu Rd.

country: Taiwan

institute: Academia sinica

description: Gene expression data from seedling at control condition.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix® GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.

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

organism: Arabidopsis thaliana

growth_protocol: Col-0, Ws and QK were grown at 22°C on 0.5x MS plates containing 1% sucrose for 7 days.

extract_protocol: Total RNA was extracted using RNeasy RNA extraction kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Samples were incubated for 1 h at 37 °C then collected for RNA extraction.

tag: tissue

value: seedling

tag: genotype

tag: age

value: 7 day old

tag: treatment

value: control


title: 7-day-old seedling of Col-0 at HS condition, biological rep2

description: Gene expression data from seedling at heat shock condition.

value: heat shocked