title: CEA_SGF:ALU005

description: RNA sample from transgenic megakaryocytes (c-kit- CD41+)was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.


title: Mouse CBL 29591

status: Public on Dec 01 2004

type: RNA

city: Rockville

first: Jeff

middle: X.

last: Zhou

state: MD

address: 5640 Fishers Lane

department: NIAID

country: USA

institute: NIH

description:
mAdb experiment ID: 34503
Mouse Centroblastic B cell lymphoma Spleen  tissue
Array Print: Mmaa-10

molecule: total RNA

organism: Mus musculus

source_name: mouse hematopoetic tumor cell line common reference 2


title: Mouse SBL 35308

description:
mAdb experiment ID: 34499
Mouse Small B cell B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: CEA_SGF:ALB047

city: Evry

first: Thierry

last: Kortulewski

address: 2 rue Gaston Cremieux

country: France

institute: CEA/DRR/SGF/LGRH

description: RNA sample from transgenic hematopoietic subpopulation (lin- sca1+ c-kit-) was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.

source_name: hematopoietic cells (lin- sca1+ phenotype) sorted by cytometry from 8 MIIb-tk transgenic mice 1 day after ganciclovir withdrawal.

source_name: total bone marrow cells isolated from 50 wild type C57/Bl6 mice.


title: Mouse SBL 35560

description:
mAdb experiment ID: 34500
Mouse Small B cell B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: CEA_SGF:ALB029

description: RNA sample from megakaryocytic cells (c-kit-CD41+) was labeled in Cy5 hybridized against RNA sample from total bone marrow cells labeled in Cy3.

source_name: megakaryocytes (c-kit- CD41+ phenotype) sorted from 15 wild type C57/Bl6 mice by cytometry.


title: CEA_SGF:ALB030

description: RNA sample from megakaryocytic cells (c-kit-CD41+) was labeled in Cy3 hybridized against RNA sample from total bone marrow cells labeled in Cy5.


title: WT Ovule 2 (AtGenome1)

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Microarray Methods: Total RNA was extracted using the Hot Borate Method (ref.).  Fifteen micrograms of biotinylated complementary RNA (cRNA) was prepared as described (Le et. al., 2004, PNAS).  cRNA was subsequently hybridized to Affymetrix ATH1 Arabidopsis GeneChips.  The scanned array images were analyzed using Affymetrix Microarray Suite 4.0 (MAS 4.0) with a global scaling intensity set at 2500.

organism: Arabidopsis thaliana

source_name: Genotype: Ws-0, Wild Type; Stage: Unfertilized Ovule; Technical Replica: 2 of 2


title: Rasagiline_3

city: Haifa

first: Yotam

last: Sagi

address: 2 Efron st.

department: Department of Pharmacology , Faculty of Medicine

country: Israel

institute: Technion - Israel institute of Technology

description: 5 mice (22-24gr) received Rasagiline mesylate (0.1mg/kg in 0.1ml water)for 14 days orally, killed by cervical translocation. Midbrains were punched under dissecting microscope, pooled and total RNA was produced and purified.

source_name: C57/Bl Mouse Midbrain


title: CEA_SGF:ALB027


title: Mouse CBL 30227

description:
mAdb experiment ID: 34504
Mouse Centroblastic B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: Rasagiline_2


title: Mouse SBL 30666

description:
mAdb experiment ID: 34493
Mouse Small B cell B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: CEA_SGF:ALB025

description: RNA sample from myelo/erythro progenitor cells (c-kit+ CD41+) was labeled in Cy3 and hybridized against RNA sample from total bone marrow cells labeled in Cy5.

source_name: myelo/erythro progenitors (c-kit+ CD41+ phenotype) sorted from 15 wild type C57/Bl6 mice by cytometry.


title: Mouse SBL 30746

description:
mAdb experiment ID: 34494
Mouse Small B cell B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: Mouse CBL 29473

description:
mAdb experiment ID: 34501
Mouse Centroblastic B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: CEA_SGF:ALB043

description: RNA sample from transgenic hematopoietic subpopulation (lin- sca1+ c-kit-) was labeled in Cy3 and hybridized against RNA sample from total bone marrow cells labeled in Cy5.


title: Mouse SBL 30769

description:
mAdb experiment ID: 34496
Mouse Small B cell B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: Mouse SBL 34954

description:
mAdb experiment ID: 34498
Mouse Small B cell B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: Mouse SBL 30767

description:
mAdb experiment ID: 34495
Mouse Small B cell B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: CEA_SGF:ALB031


title: Mouse CBL 29477

description:
mAdb experiment ID: 34502
Mouse Centroblastic B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: CEA_SGF:ALU006

description: RNA sample from transgenic megakaryocytes (c-kit- CD41+)was labeled in Cy3 and hybridized against RNA sample from total bone marrow cells labeled in Cy5.

source_name: megakaryocytes (c-kit- CD41+ phenotype) sorted by cytometry from 8 MIIb-tk transgenic mice 3 days after ganciclovir withdrawal.


title: CEA_SGF:ALB026

description: RNA sample from myelo/erythro progenitor cells (c-kit+ CD41+) was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.


title: Mouse SBL 31725

description:
mAdb experiment ID: 34497
Mouse Small B cell B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: Control_4

description: 5 mice (22-24gr) recieved Water for 14 days orally, killed by cervical translocation. Midbrains were punched under dissecting microscope, pooled and total RNA was produced and purified .


title: Rasagiline_1


title: Control_3


title: Control_2


title: Control_1


title: Mouse IBL 30225

description:
mAdb experiment ID: 34518
Mouse Immunoblastic B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: Mouse IBL 29199

description:
mAdb experiment ID: 34558
Mouse Immunoblastic B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: Mouse SBL 30541

description:
mAdb experiment ID: 34492
Mouse Small B cell B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: CEA_SGF:ALB023

description: RNA sample from common myeloid progenitor cells (lin- sca1+ c-kit-) was labeled in Cy3 and hybridized against RNA sample from total bone marrow cells labeled in Cy5.

source_name: common myeloid progenitors(lin- sca1- c-kit+ phenotype) sorted from 50 wild type C57/Bl6 mice by cytometry.


title: CEA_SGF:ALB022

description: RNA sample from common myeloid progenitor cells (lin- sca1+ c-kit-) was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.


title: Mouse FBL 29768

description:
mAdb experiment ID: 34527
Mouse Follicular B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: Mouse FBL 30076

description:
mAdb experiment ID: 34528
Mouse Follicular B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: Mouse B6.nu B cells [#4-1]

description:
mAdb experiment ID: 35635
Mouse Nude B6 Purified resting B cells
Array Print: Mmaa-06

source_name: B6.nu B cells [#4-1]


title: Mouse B6.nu B cells [#3-1]

description:
mAdb experiment ID: 35634
Mouse Nude B6 Purified resting B cells
Array Print: Mmaa-06

source_name: B6.nu B cells [#3-1]


title: Mouse B6.nu B cells [#2-1]

description:
mAdb experiment ID: 35633
Mouse Nude B6 Purified resting B cells
Array Print: Mmaa-06

source_name: B6.nu B cells [#2-1]


title: CEA_SGF:ALB020

description: RNA sample from hematopoietic stem cells (lin- sca1+ c-kit+) was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.

source_name: hematopoietic stem cells (lin- sca1+ c-kit+ phenotype) sorted from 50 wild type C57/Bl6 mice by cytometry.


title: CEA_SGF:ALB019

description: RNA sample from hematopoietic stem cells (lin- sca1+ c-kit+) was labeled in Cy3 and hybridized against RNA sample from total bone marrow cells labeled in Cy5.


title: CEA_SGF:ALB024


title: Mouse B6.nu B cells [#1-1]

description:
mAdb experiment ID: 35632
Mouse Nude B6 Purified resting B cells
Array Print: Mmaa-06

source_name: B6.nu B cells [#1-1]


title: Mouse B6.nu B cells [#5-1]

description:
mAdb experiment ID: 35636
Mouse Nude B6 Purified resting B cells
Array Print: Mmaa-06

source_name: B6.nu B cells [#5-1]


title: Mouse FBL 28874

description:
mAdb experiment ID: 34526
Mouse Follicular B cell lymphoma Spleen  tissue
Array Print: Mmaa-10


title: CEA_SGF:ALB021


title: CEA_SGF:AKI032

description: RNA sample from myelo/erythro progenitor cells (c-kit+ CD41+) was labeled in Cy3 and hybridized against RNA sample from total bone marrow cells labeled in Cy5.


title: Mouse BL 36171 SPL

description:
mAdb experiment ID: 32694
Mouse Burkitt B cell lymphoma Spleen tissue
Array Print: Mmaa-05

source_name: BL 36171 SPL

source_name: mouse hematopoetic tumor cell line common reference 1


title: Mouse BL 36330 SPL

description:
mAdb experiment ID: 32693
Mouse Burkitt B cell lymphoma Spleen tissue
Array Print: Mmaa-05

source_name: BL 36330 SPL


title: CEA_SGF:AKI033

description: RNA sample from myelo/erythro progenitor cells (c-kit+ CD41+) was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.


title: CEA_SGF:AKI034

description: RNA sample from megakaryocytic cells (c-kit-CD41+) was labeled in Cy3 and hybridized against RNA sample from total bone marrow cells labeled in Cy5.


title: CEA_SGF:AKI035

description: RNA sample from megakaryocytic cells (c-kit-CD41+) was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.


title: CEA_SGF:AKI028


title: CEA_SGF:AKI031

description: RNA sample from common myeloid progenitor cells (lin- sca1+ c-kit-) was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.


title: CEA_SGF:AKI027


title: Mouse BL 36723 PLN

description:
mAdb experiment ID: 32687
Mouse Burkitt B cell lymphoma peripheral lymph node tissue
Array Print: Mmaa-05

source_name: BL 36723 PLN


title: Mouse BL 36646 PLN

description:
mAdb experiment ID: 32692
Mouse Burkitt B cell lymphoma peripheral lymph node tissue
Array Print: Mmaa-05

source_name: BL 36646 PLN


title: Mouse BL 36860 MLN

description:
mAdb experiment ID: 32691
Mouse Burkitt B cell lymphoma mesenteric lymph node tissue
Array Print: Mmaa-05

source_name: BL 36860 MLN


title: Mouse BL 36646 MLN

description:
mAdb experiment ID: 32686
Mouse Burkitt B cell lymphoma mesenteric lymph node tissue
Array Print: Mmaa-05

source_name: BL 36646 MLN


title: GG3096 (1) / CEN-PK113-7D (1)

city: Leiden

first: Paul

last: van Heusden

address: Wassenaarseweg 64

country: Netherlands

institute: Institute of Biology

description: GG3096 culture 1

organism: Saccharomyces cerevisiae


title: CEA_SGF:AKI024

source_name: total bone marrow cells isolated from 50 wild type C57/Bl6 mice.


title: CEA_SGF:AKI025

source_name: megakaryocytes (c-kit- CD41+ phenotype) sorted from 15 wild type C57/Bl6 mice by cytometry.


title: pooled day 30 hearts from CxVB3 injected mice

city: Seattle

first: John

last: Gosink

state: WA

address: 1201 Amgen Court West

institute: Amgen

description:
Male, adolescent A/J mice (4-5 week old) were either infected (IP) with coxsackievirus B3 (CVB3; 105 pfu) or PBS.  CVB3 is a cardiotropic virus which leads to cardiac inflammation and fibrosis within 9 days after IP injection.   We wanted to know how the virus would impact long term cardiac function, and whether changes in cardiac function could be associated with cardiac transcriptional regulation.  At days 3, 9 and 30 days post-infection, hearts were imaged with 2D echocardiography (Sonos 5500, Philips).  Briefly, mice were anesthesized subcutaneously with ketamine (0.45mg/kg) and xylazine (0.03mg/kg).  Mice were placed in a dorsal recumbency position and the following systolic and diastolic measurements were taken (N=5 heart beats) using an S-12 (12MHz; Sonos 5000, Philips) probe: parasternal long axis, and short axis at the level of the mitral valve and papillary muscles.  Measurements were utilized for calculation of wall thickness and functional parameters.  Then, heart tissues were flash frozen (N=4 mice/group except CVB3 infected 30 day samples N=2) for hybridization to Affymetrix MG U74Av2 arrays.
This sample is also known as cox868.
Keywords = myocarditis, coxsackievirus B3, microarray, genomics, dilated cardiomyopathy

source_name: heart


title: GG3096 (2) / CEN-PK113-7D (1)

description: GG3096 culture 2


title: pooled day 9 hearts from PBS injected mice

description:
Male, adolescent A/J mice (4-5 week old) were either infected (IP) with coxsackievirus B3 (CVB3; 105 pfu) or PBS.  CVB3 is a cardiotropic virus which leads to cardiac inflammation and fibrosis within 9 days after IP injection.   We wanted to know how the virus would impact long term cardiac function, and whether changes in cardiac function could be associated with cardiac transcriptional regulation.  At days 3, 9 and 30 days post-infection, hearts were imaged with 2D echocardiography (Sonos 5500, Philips).  Briefly, mice were anesthesized subcutaneously with ketamine (0.45mg/kg) and xylazine (0.03mg/kg).  Mice were placed in a dorsal recumbency position and the following systolic and diastolic measurements were taken (N=5 heart beats) using an S-12 (12MHz; Sonos 5000, Philips) probe: parasternal long axis, and short axis at the level of the mitral valve and papillary muscles.  Measurements were utilized for calculation of wall thickness and functional parameters.  Then, heart tissues were flash frozen (N=4 mice/group except CVB3 infected 30 day samples N=2) for hybridization to Affymetrix MG U74Av2 arrays.
This sample is also known as cox862.
Keywords = myocarditis, coxsackievirus B3, microarray, genomics, dilated cardiomyopathy


title: CEN-PK113-7D (1) / GG3096 (1)

description: GG3096 culture 1, dyes reversed.


title: Mouse BL 36904 MLN

description:
mAdb experiment ID: 32690
Mouse Burkitt B cell lymphoma mesenteric lymph node tissue
Array Print: Mmaa-05

source_name: BL 36904 MLN


title: pooled day 3 hearts from CxVB3 injected mice

description:
Male, adolescent A/J mice (4-5 week old) were either infected (IP) with coxsackievirus B3 (CVB3; 105 pfu) or PBS.  CVB3 is a cardiotropic virus which leads to cardiac inflammation and fibrosis within 9 days after IP injection.   We wanted to know how the virus would impact long term cardiac function, and whether changes in cardiac function could be associated with cardiac transcriptional regulation.  At days 3, 9 and 30 days post-infection, hearts were imaged with 2D echocardiography (Sonos 5500, Philips).  Briefly, mice were anesthesized subcutaneously with ketamine (0.45mg/kg) and xylazine (0.03mg/kg).  Mice were placed in a dorsal recumbency position and the following systolic and diastolic measurements were taken (N=5 heart beats) using an S-12 (12MHz; Sonos 5000, Philips) probe: parasternal long axis, and short axis at the level of the mitral valve and papillary muscles.  Measurements were utilized for calculation of wall thickness and functional parameters.  Then, heart tissues were flash frozen (N=4 mice/group except CVB3 infected 30 day samples N=2) for hybridization to Affymetrix MG U74Av2 arrays.
This sample is also known as cox860.
Keywords = myocarditis, coxsackievirus B3, microarray, genomics, dilated cardiomyopathy


title: Mouse BL 36825 MLN

description:
mAdb experiment ID: 32688
Mouse Burkitt B cell lymphoma mesenteric lymph node tissue
Array Print: Mmaa-05

source_name: BL 36825 MLN


title: Mouse BL 36852 CLN

description:
mAdb experiment ID: 32689
Mouse Burkitt B cell lymphoma cercival lymph node tissue
Array Print: Mmaa-05

source_name: BL 36852 CLN


title: CEA_SGF:AKI021

description: RNA sample from common myeloid progenitor cells (lin- sca1+ c-kit-) was labeled in Cy3 and hybridized against RNA sample from total bone marrow cells labeled in Cy5.

source_name: common myeloid progenitors(lin- sca1- c-kit+ phenotype) sorted from 50 wild type C57/Bl6 mice by cytometry.


title: CEA_SGF:AKI023

description: RNA sample from myelo/erythro progenitor cells (c-kit+ CD41+) was labeled in Cy3 and hybridized against RNA sample from total bone marrow cells labeled in Cy5.

source_name: myelo/erythro progenitors (c-kit+ CD41+ phenotype) sorted from 15 wild type C57/Bl6 mice by cytometry.


title: CEA_SGF:AKI020

description: RNA sample from hematopoietic stem cells (lin- sca1+ c-kit+) was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.

source_name: hematopoietic stem cells (lin- sca1+ c-kit+ phenotype) sorted from 50 wild type C57/Bl6 mice by cytometry.


title: Mouse BLL 36481

description:
mAdb experiment ID: 32702
Mouse Burkitt-like B cell lymphoma Spleen tissue
Array Print: Mmaa-02


title: Mouse BLL 36318

description:
mAdb experiment ID: 32701
Mouse Burkitt-like B cell lymphoma Spleen tissue
Array Print: Mmaa-02


title: CEN-PK113-7D (2)/CEN-PK113-7D (1)

description: Wild type control


title: Mouse BLL 35626

description:
mAdb experiment ID: 32695
Mouse Burkitt-like B cell lymphoma Spleen tissue
Array Print: Mmaa-05


title: Mouse BLL 35565

description:
mAdb experiment ID: 32698
Mouse Burkitt-like B cell lymphoma Spleen tissue
Array Print: Mmaa-05


title: Mouse BLL 35632

description:
mAdb experiment ID: 32696
Mouse Burkitt-like B cell lymphoma Spleen tissue
Array Print: Mmaa-05


title: Mouse BLL 30673

description:
mAdb experiment ID: 32697
Mouse Burkitt-like B cell lymphoma Spleen tissue
Array Print: Mmaa-05


title: CEA_SGF:AKI019

description: RNA sample from hematopoietic stem cells (lin- sca1+ c-kit+) was labeled in Cy3 and hybridized against RNA sample from total bone marrow cells labeled in Cy5.


title: pooled day 3 hearts from PBS injected mice

description:
Male, adolescent A/J mice (4-5 week old) were either infected (IP) with coxsackievirus B3 (CVB3; 105 pfu) or PBS.  CVB3 is a cardiotropic virus which leads to cardiac inflammation and fibrosis within 9 days after IP injection.   We wanted to know how the virus would impact long term cardiac function, and whether changes in cardiac function could be associated with cardiac transcriptional regulation.  At days 3, 9 and 30 days post-infection, hearts were imaged with 2D echocardiography (Sonos 5500, Philips).  Briefly, mice were anesthesized subcutaneously with ketamine (0.45mg/kg) and xylazine (0.03mg/kg).  Mice were placed in a dorsal recumbency position and the following systolic and diastolic measurements were taken (N=5 heart beats) using an S-12 (12MHz; Sonos 5000, Philips) probe: parasternal long axis, and short axis at the level of the mitral valve and papillary muscles.  Measurements were utilized for calculation of wall thickness and functional parameters.  Then, heart tissues were flash frozen (N=4 mice/group except CVB3 infected 30 day samples N=2) for hybridization to Affymetrix MG U74Av2 arrays.
This sample is also known as cox858.
Keywords = myocarditis, coxsackievirus B3, microarray, genomics, dilated cardiomyopathy


title: 5 pooled baseline hearts

description:
Male, adolescent A/J mice (4-5 week old) were either infected (IP) with coxsackievirus B3 (CVB3; 105 pfu) or PBS.  CVB3 is a cardiotropic virus which leads to cardiac inflammation and fibrosis within 9 days after IP injection.   We wanted to know how the virus would impact long term cardiac function, and whether changes in cardiac function could be associated with cardiac transcriptional regulation.  At days 3, 9 and 30 days post-infection, hearts were imaged with 2D echocardiography (Sonos 5500, Philips).  Briefly, mice were anesthesized subcutaneously with ketamine (0.45mg/kg) and xylazine (0.03mg/kg).  Mice were placed in a dorsal recumbency position and the following systolic and diastolic measurements were taken (N=5 heart beats) using an S-12 (12MHz; Sonos 5000, Philips) probe: parasternal long axis, and short axis at the level of the mitral valve and papillary muscles.  Measurements were utilized for calculation of wall thickness and functional parameters.  Then, heart tissues were flash frozen (N=4 mice/group except CVB3 infected 30 day samples N=2) for hybridization to Affymetrix MG U74Av2 arrays.
This sample is also known as cox856.
Keywords = myocarditis, coxsackievirus B3, microarray, genomics, dilated cardiomyopathy


title: DNase II- and IFN-IR-double deficient

city: Kyoto

first: Shigekazu

last: Nagata

address: Yoshida. Sakyo-ku

department: Department of Medical Chemistry

country: Japan

institute: Graduate School of Medicine, Kyoto University

description: Total RNA was prepared from the fetal liver using an ISOGEN RNA extraction kit (Nippon Gene), and poly(A) RNA was selected using an mRNA Purification Kit (Amersham Biosciences). The gene array analysis was carried out using a Uniset Mouse 20K Codelink Bioarray (Amersham Biosciences) that displays probe DNAs for about 20,000 mouse genes/ESTs. In brief, double-stranded cDNA was prepared with RNA from the fetal livers of the DNase II-/- and IFN-IR-/- double-deficient mouse embryos (E14.5), and transcribed in vitro using biotin-labeled dUTP as a substrate. The complementary RNA was used as probe for hybridizing the array, and the hybridized RNA was detected with Cy5-conjugated streptavidin. The arrays were scanned using an arrayWoRx Biochip Reader (Applied Precision), and the array image was analyzed using CodeLinkTM System Software (Amersham Biosciences).

source_name: the fetal liver of E14.5 DNase II- and IFN-IR-double deficient mouse embryos


title: pooled day 30 hearts from PBS injected mice

description:
Male, adolescent A/J mice (4-5 week old) were either infected (IP) with coxsackievirus B3 (CVB3; 105 pfu) or PBS.  CVB3 is a cardiotropic virus which leads to cardiac inflammation and fibrosis within 9 days after IP injection.   We wanted to know how the virus would impact long term cardiac function, and whether changes in cardiac function could be associated with cardiac transcriptional regulation.  At days 3, 9 and 30 days post-infection, hearts were imaged with 2D echocardiography (Sonos 5500, Philips).  Briefly, mice were anesthesized subcutaneously with ketamine (0.45mg/kg) and xylazine (0.03mg/kg).  Mice were placed in a dorsal recumbency position and the following systolic and diastolic measurements were taken (N=5 heart beats) using an S-12 (12MHz; Sonos 5000, Philips) probe: parasternal long axis, and short axis at the level of the mitral valve and papillary muscles.  Measurements were utilized for calculation of wall thickness and functional parameters.  Then, heart tissues were flash frozen (N=4 mice/group except CVB3 infected 30 day samples N=2) for hybridization to Affymetrix MG U74Av2 arrays.
This sample is also known as cox01689.
Keywords = myocarditis, coxsackievirus B3, microarray, genomics, dilated cardiomyopathy


title: Mouse BLL 36305

description:
mAdb experiment ID: 32700
Mouse Marginal++/Burkitt-like B cell lymphoma Spleen tissue
Array Print: Mmaa-02


title: pooled day 9 hearts from CxVB3 injected mice

description:
Male, adolescent A/J mice (4-5 week old) were either infected (IP) with coxsackievirus B3 (CVB3; 105 pfu) or PBS.  CVB3 is a cardiotropic virus which leads to cardiac inflammation and fibrosis within 9 days after IP injection.   We wanted to know how the virus would impact long term cardiac function, and whether changes in cardiac function could be associated with cardiac transcriptional regulation.  At days 3, 9 and 30 days post-infection, hearts were imaged with 2D echocardiography (Sonos 5500, Philips).  Briefly, mice were anesthesized subcutaneously with ketamine (0.45mg/kg) and xylazine (0.03mg/kg).  Mice were placed in a dorsal recumbency position and the following systolic and diastolic measurements were taken (N=5 heart beats) using an S-12 (12MHz; Sonos 5000, Philips) probe: parasternal long axis, and short axis at the level of the mitral valve and papillary muscles.  Measurements were utilized for calculation of wall thickness and functional parameters.  Then, heart tissues were flash frozen (N=4 mice/group except CVB3 infected 30 day samples N=2) for hybridization to Affymetrix MG U74Av2 arrays.
This sample is also known as cox864.
Keywords = myocarditis, coxsackievirus B3, microarray, genomics, dilated cardiomyopathy


title: Mouse BLL 36272

description:
mAdb experiment ID: 32699
Mouse Burkitt-like B cell lymphoma Spleen tissue
Array Print: Mmaa-02


title: CEA_SGF:AKI022

description: RNA sample from common myeloid progenitor cells (lin- sca1+ c-kit-) was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.


title: SR4 - Replicate 1

status: Public on Nov 30 2004

city: Basel

first: Michael

last: Primig

state: Basel Stadt

address: Klingelbergstr 50-70

department: Genome Bioinformatics

country: Switzerland

institute: Biozentrum and Swiss Institute of Bioinformatics

description:
Cells were grown to saturation in YPD (YEP + 2% glucose) for 24 hours, diluted into YPA (YEP + 2% potassium acetate) at OD600= 0.3 and grown over night at 30 degree C. Cells were washed with sterilized water the next day and re-suspended in SPO medium (0.3% potassium acetate, pH = 7.0) at OD600= 1.9 at room temperature to induce sporulation. The sample was taken 4 h after induction of sporulation.
Keywords = benomyl sporulation saccharomyces microtubule spindle checkpoint

source_name: Total RNA


title: SR8 - Replicate 2

description:
Cells were grown to saturation in YPD (YEP + 2% glucose) for 24 hours, diluted into YPA (YEP + 2% potassium acetate) at OD600= 0.3 and grown over night at 30 degree C. Cells were washed with sterilized water the next day and re-suspended in SPO medium (0.3% potassium acetate, pH = 7.0) at OD600= 1.9 at room temperature to induce sporulation. 4 h after induction of sporulation cells were filtered and immediately re-suspended in medium. The sample was taken 4 h after filtration.
Keywords = benomyl sporulation saccharomyces microtubule spindle checkpoint


title: Control 2

city: London

first: Kaiping

last: Yang

state: ON

country: Canada

institute: University of Western Ontario

description: Visceral adipose tissue from 130 day old male wistar rat

organism: Rattus norvegicus

source_name: Adipose Tissue


title: SC5 - Replicate 1

description:
Cells were grown to saturation in YPD (YEP + 2% glucose) for 24 hours, diluted into YPA (YEP + 2% potassium acetate) at OD600= 0.3 and grown over night at 30 degree C. Cells were washed with sterilized water the next day and re-suspended in SPO medium (0.3% potassium acetate, pH = 7.0) at OD600= 1.9 at room temperature to induce sporulation. 4 h after induction of sporulation cells were filtered and immediately re-suspended in pre-chilled medium containing DMSO and continued to grow at 10 degree C. The sample was taken 1 h after filtration.
Keywords = benomyl sporulation saccharomyces microtubule spindle checkpoint


title: CEA_SGF:ALB034

description: RNA sample from transgenic hematopoietic subpopulation (lin- sca1+ c-kit-) was labeled in Cy5 and hybridized against RNA sample from total bone marrow cells labeled in Cy3.

source_name: hematopoietic cells (lin- sca1+ phenotype) sorted by cytometry from 8 MIIb-tk transgenic mice 1 day after ganciclovir withdrawal.


title: SR5 - Replicate 2

description:
Cells were grown to saturation in YPD (YEP + 2% glucose) for 24 hours, diluted into YPA (YEP + 2% potassium acetate) at OD600= 0.3 and grown over night at 30 degree C. Cells were washed with sterilized water the next day and re-suspended in SPO medium (0.3% potassium acetate, pH = 7.0) at OD600= 1.9 at room temperature to induce sporulation. 4 h after induction of sporulation cells were filtered and immediately re-suspended in medium. The sample was taken 1 h after filtration.
Keywords = benomyl sporulation saccharomyces microtubule spindle checkpoint


title: SC8 - Replicate 2

description:
Cells were grown to saturation in YPD (YEP + 2% glucose) for 24 hours, diluted into YPA (YEP + 2% potassium acetate) at OD600= 0.3 and grown over night at 30 degree C. Cells were washed with sterilized water the next day and re-suspended in SPO medium (0.3% potassium acetate, pH = 7.0) at OD600= 1.9 at room temperature to induce sporulation. 4 h after induction of sporulation cells were filtered and immediately re-suspended in pre-chilled medium containing DMSO and continued to grow at 10 degree C. The sample was taken 4 h after filtration.
Keywords = benomyl sporulation saccharomyces microtubule spindle checkpoint


title: Obese rat 1

source_name: Adipose tissue


title: Obese 2


title: SR8 - Replicate 1


title: DNAse II-deficient

description: Total RNA was prepared from the fetal liver using an ISOGEN RNA extraction kit (Nippon Gene), and poly(A) RNA was selected using an mRNA Purification Kit (Amersham Biosciences). The gene array analysis was carried out using a Uniset Mouse 20K Codelink Bioarray (Amersham Biosciences) that displays probe DNAs for about 20,000 mouse genes/ESTs. In brief, double-stranded cDNA was prepared with RNA from the fetal livers of the DNase II-deficient mouse embryos (E14.5), and transcribed in vitro using biotin-labeled dUTP as a substrate. The complementary RNA was used as probe for hybridizing the array, and the hybridized RNA was detected with Cy5-conjugated streptavidin. The arrays were scanned using an arrayWoRx Biochip Reader (Applied Precision), and the array image was analyzed using CodeLinkTM System Software (Amersham Biosciences).

source_name: the fetal liver of E14.5 DNase II-deficient mouse embryos


title: Control 1

source_name: Rat Adipose Tissue


title: SC8 - Replicate 1


title: wild-type

description: Total RNA was prepared from the fetal liver using an ISOGEN RNA extraction kit (Nippon Gene), and poly(A) RNA was selected using an mRNA Purification Kit (Amersham Biosciences). The gene array analysis was carried out using a Uniset Mouse 20K Codelink Bioarray (Amersham Biosciences) that displays probe DNAs for about 20,000 mouse genes/ESTs. In brief, double-stranded cDNA was prepared with RNA from the fetal livers of the wild-type mouse embryos (E14.5), and transcribed in vitro using biotin-labeled dUTP as a substrate. The complementary RNA was used as probe for hybridizing the array, and the hybridized RNA was detected with Cy5-conjugated streptavidin. The arrays were scanned using an arrayWoRx Biochip Reader (Applied Precision), and the array image was analyzed using CodeLinkTM System Software (Amersham Biosciences).

source_name: the fetal liver of E14.5 wild-type mouse embryos


title: f2#99 versus pool

status: Public on Nov 25 2004

first: Stephen

middle: W

last: Edwards

department: Research Genetics

institute: Rosetta Inpharmatics (Merck & Co.)

description:
Livers from 111 F2 female mice (all on an atherogenic diet) constructed from C57BL/6J and DBA/2J strains of mice were isolated for expression profiling.
All samples were compared to a common pool created from equal portions of RNA from each of the samples.
See Schadt, et al., Nature , Vol 422(6929):297-302 for details.

source_name: pool


title: SR4 - Replicate 2


title: f2#92 versus pool


title: f2#97 versus pool


title: f2#8 versus pool


title: f2#90 versus pool


title: f2#95 versus pool


title: f2#88 versus pool


title: f2#91 versus pool


title: f2#87 versus pool


title: f2#81 versus pool


title: f2#7 versus pool


title: f2#85 versus pool


title: f2#76 versus pool


title: f2#83 versus pool


title: f2#74 versus pool


title: f2#6 versus pool


title: f2#64 versus pool


title: f2#68 versus pool


title: f2#67 versus pool


title: f2#62 versus pool


title: f2#78 versus pool


title: f2#60 versus pool


title: f2#70 versus pool


title: f2#56 versus pool


title: f2#55 versus pool


title: f2#57 versus pool


title: f2#54 versus pool


title: f2#58 versus pool


title: f2#59 versus pool


title: f2#53 versus pool


title: f2#51 versus pool


title: f2#47 versus pool


title: f2#71 versus pool


title: f2#66 versus pool


title: f2#63 versus pool


title: f2#48 versus pool


title: f2#42 versus pool


title: f2#49 versus pool


title: f2#44 versus pool


title: f2#4 versus pool


title: f2#43 versus pool


title: f2#45 versus pool


title: f2#3 versus pool


title: f2#39 versus pool


title: f2#31 versus pool


title: f2#41 versus pool


title: f2#37 versus pool


title: f2#25 versus pool


title: f2#35 versus pool


title: f2#28 versus pool


title: SR5 - Replicate 1


title: f2#24 versus pool


title: f2#32 versus pool


title: f2#29 versus pool


title: f2#21 versus pool


title: f2#20 versus pool


title: f2#36 versus pool


title: f2#26 versus pool


title: f2#23 versus pool


title: f2#22 versus pool


title: f2#18 versus pool


title: SC5 - Replicate 2


title: f2#157 versus pool


title: f2#16 versus pool


title: f2#15 versus pool


title: f2#9 versus pool


title: f2#149 versus pool


title: f2#155 versus pool


title: f2#151 versus pool


title: f2#156 versus pool


title: f2#17 versus pool


title: f2#134 versus pool


title: f2#150 versus pool


title: f2#14 versus pool


title: f2#147 versus pool


title: f2#140 versus pool


title: f2#143 versus pool


title: f2#130 versus pool


title: f2#144 versus pool


title: f2#142 versus pool


title: f2#127 versus pool


title: f2#129 versus pool


title: f2#137 versus pool


title: f2#128 versus pool


title: f2#13 versus pool


title: f2#138 versus pool


title: f2#126 versus pool


title: f2#123 versus pool


title: f2#120 versus pool


title: f2#124 versus pool


title: f2#117 versus pool


title: f2#116 versus pool


title: f2#122 versus pool


title: f2#114 versus pool


title: f2#113 versus pool


title: Male Placebo-Treated Submandibular Gland Sample C

status: Public on Nov 24 2004

city: Boston

first: Nathaniel

last: Treister

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description: Orchiectomized male BALB/c mice (n = 4/sex/experiment) were treated with either placebo- or testosterone-containing hormone pellets for 21 days.  Glands from five animals (n=10) were pooled and mRNA was isolated to provide a pooled biological replicate. Samples A, B, and C represent three separate pools of five animals each.

source_name: BALB/c Mouse Placebo-Treated Submandibular Gland


title: Male Placebo-Treated Submandibular Gland Sample B

source_name: BLAB/c Mouse Placebo-Treated Submandibular Gland


title: f2#112 versus pool


title: Male Testosterone-Treated Meibomian Gland Sample B

source_name: BALB/c Mouse Testosterone-Treated Meibomian Gland


title: Male Testosterone-Treated Meibomian Gland Sample C


title: Male Testosterone-Treated Submandibular Gland Sample A

source_name: BALB/c Mouse Testosterone-Treated Submandibular Gland


title: f2#106 versus pool


title: Male Testosterone-Treated Submandibular Gland Sample B


title: Male Placebo-Treated Submandibular Gland Sample A


title: f2#109 versus pool


title: f2#100 versus pool


title: Male Testosterone-Treated Submandibular Gland Sample C


title: Male Placebo-Treated Meibomian Gland Sample A

source_name: BALB/c Mouse Placebo-Treated Meibomian Gland


title: Male Testosterone-Treated Meibomian Gland Sample A


title: f2#111 versus pool


title: Male Placebo-Treated Meibomian Gland Sample B


title: f2#10 versus pool


title: f2#102 versus pool


title: Male Placebo-Treated Meibomian Gland Sample C


title: f2#105 versus pool


title: f2#101 versus pool


title: f2#103 versus pool


title: f2#104 versus pool


title: f2#107 versus pool


title: Male Placeo-Treated Lacrimal Gland Sample C

source_name: BALB/c Mouse Placebo-Treated Lacrimal Gland


title: Male Testosterone-Treated Lacrimal Gland Sample A

source_name: BALB/c Mouse Testosterone-Treated Lacrimal Gland


title: Male Testosterone-Treated Lacrimal Gland Sample C


title: Male Meibomian Gland Sample B

description: Glands from five animals (n=10) were pooled and mRNA was isolated to provide a pooled biological replicate. Samples A, B, and C represent three separate pools of five animals each.

source_name: BALB/c Mouse Meibomian Gland


title: Female Meibomian Gland Sample B


title: Male Testosterone-Treated Lacrimal Gland Sample B


title: Male Parotid Gland Sample B

description: Glands from five animals (n=10) were pooled and mRNA was isolated to provide a pooled biological replicate. Samples A and B represent two separate pools of five animals each.

source_name: BALB/c mouse


title: Male Lacrimal Gland Sample B

source_name: BALB/c Mouse Lacrimal Gland


title: Male Meibomian Gland Sample C


title: Male Lacrimal Gland Sample C


title: Male Placebo-Treated Lacrimal Gland Sample A

source_name: BALB/c Placebo-Treated Lacrimal Gland


title: Female Lacrimal Gland Sample B


title: Female Lacrimal Gland Sample A

source_name: BALB/c Lacrimal Glands


title: Male Meibomian Gland Sample A


title: Female Sublingual Gland Sample A


title: Female Lacrimal Gland Sample C


title: Male Parotid Gland Sample A


title: Male Sublingual Gland Sample A


title: Female Meibomian Gland Sample C


title: Male Placebo-Treated Lacrimal Gland Sample B


title: Male Lacrimal Gland Sample A


title: Male Sublingual Gland Sample B


title: Female Parotid Gland Sample A

source_name: BALB/c Mouse


title: Female Meibomian Gland Sample A


title: Male Submandibular Gland Sample C

description: Glands from five animals (n=10) were pooled and mRNA was isolated to provide a pooled biological replicate.  Samples A, B, and C represent three separate pools of five animals each.


title: Female Sublingual Gland Sample B


title: Female Parotid Gland Sample B


title: Male Submandibular Gland Sample B


title: Female Submandibular Gland Sample A

source_name: BALB/c mouse submandibular glands


title: BPL_531432B

city: Tsukuba City

first: Koichi

last: Ushizawa

state: Ibaraki

address: Ikenodai 2

department: Animal Science Department

institute: National Institute of Agrobiological Sciences

description:
Two-microgram of pooled linear amplificated antisence RNA of embryo obtained from pregnant cows was reverse transcribed in the presence of cyanine-5-fluorescent dye (Cy5) & cyanine-3-fluorescent dye (Cy3)-conjugated dUTP (Amersham Pharmacia Biotech) by using Superscript II reverse transcriptase (Life Technologies, Rockville, MD) to yield Cy5 & Cy3 fluorescence-labeled cDNA probe. After a 2-h reverse transcription reaction at 42oC, RNA was degraded by addition of 1.5 micro-l of an alkaline solution (1N NaOH / 20 mM EDTA), and neutralized by addition of 1.5 micro-l 1N HCl.The Cy5 & Cy3 cDNA probe were then mixed and washed by centrifugation with TE (Tris-EDTA, pH 7.0) first and then with TE, 20 micro-g Salmon sperm DNA, 20 micro-g polyA and 20 micro-g yeast RNA in a Microcon YM-30 column (Millipore, Bedford, MA). The concentrated probe mix was adjusted with TE to a volume of 10 micro-l, denatured at 100oC for 2 min, spun for a few min and made to a final hybridization volume of 15 micro-l with 2.55 micro-l 20XSSC and 0.45 micro-l 10% SDS and kept at room temperature until used. Before hybridization, microarray glass slides were immersed in 0.2% SDS for 2 min followed by two washes each 2 min in autoclaved Milli Q water, and subjected to blocking in 180 ml of Methyl Pyrrolidinone (Aldrich) containing 2.7 g Succinic Anhydride (WAKO, Japan) and 15.3 ml 1M Boric acid (pH 8.0) solution for 20 min. Slides were then washed with autoclaved Milli Q water, and the spotted cDNA targets (microarray) were denatured in boiling water for 2 min. The slides were dehydrated in 100% ethanol for 2 min and air dried by spinning at a low speed. The mixture of labeled probes, for example, the Cy3 & Cy5, were then applied to the microarray, placed a cover slip carefully and incubated at 65oC for 14 - 16 h in a custom slide chamber. After incubation for 14 - 16 h at 65oC, the slides were washed in 2 x SSC / 0.01% SDS for 2 min, followed by washing in 0.2 x SSC/0.01% SDS and 0.2 x SSC, each for 2 min with gentle agitation, and air dried by spinning at a low speed.
Keywords = bovine embryo
Keywords = gene expression

organism: Bos taurus

source_name: Fetus day27


title: Male Submandibular Gland Sample A


title: Female Submandibular Gland Sample B


title: BPL_531431A

source_name: Fetus day28


title: BPL_531427A

source_name: Embryo day19


title: Female Submandibular Gland Sample C


title: BPL_540342A

source_name: Embryo day14


title: BPL_531432A

source_name: Fetal membrane day27_1


title: BPL_531416B

source_name: Fetal membrane day27_2


title: BPL_531434A

source_name: Embryo day21


title: BPL_531425B

source_name: Embryo day20


title: BPL_531421A

source_name: Embryo day7


title: BPL_531422B

source_name: Fetal membrane day28


title: BPL_531435A


title: 16C-M4-D

status: Public on Nov 20 2004

city: Jerusalem

first: Noa

last: Shefi

department: Computer Science

institute: Hebrew University

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2001
Keywords = Control
Keywords = M4
Keywords = D

organism: Homo sapiens

source_name: PMBCs


title: 16C-ER-D

description:
Peripheral blood cells taken from survivors few hours after exposure to trauma. date: 2001
Keywords = Control
Keywords = ER
Keywords = D


title: 15C-M4-D

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2002
Keywords = Control
Keywords = M4
Keywords = D


title: 24C-ER

description:
Peripheral blood cells taken from survivors few hours after exposure to trauma. date: 2001
Keywords = Control
Keywords = ER


title: Control (untrained) vs P6h (6 hours after 12 hours running).

city: Pasadena

first: Sangdun

last: Choi

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology

description:
All samples were gathered from mouse skeletal muscle (plantaris). Control total RNAs were extracted from 8 control untrained mice and combined.
All samples were gathered from mouse skeletal muscle (plantaris). Test total RNAs were extracted from 3-5 P6h mice and combined.

source_name: Total RNA from Control was labeled with Cyanine-3 (green).

source_name: Total RNA from P6h was labeled with Cyanine-5 (red).


title: 20C-ER-D


title: Control (untrained) vs P3h (3 hours after 12 hours running).

description:
All samples were gathered from mouse skeletal muscle (plantaris). Control total RNAs were extracted from 8 control untrained mice and combined.
All samples were gathered from mouse skeletal muscle (plantaris). Test total RNAs were extracted from 3-5 P3h mice and combined.

source_name: Total RNA from P3h was labeled with Cyanine-5 (red).


title: 19C-ER

description:
Peripheral blood cells taken from survivors few hours after exposure to trauma. date: 2002
Keywords = Control
Keywords = ER


title: 22C-M4-D


title: 21C-M4-ND

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2002
Keywords = Control
Keywords = M4
Keywords = ND


title: 23C-M4-D


title: 13P-ER-ND

description:
Peripheral blood cells taken from survivors few horus after exposure to trauma. date: 2002
Keywords = PTSD
Keywords = ER
Keywords = ND


title: 24C-M4

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2001
Keywords = Control
Keywords = M4


title: Control (untrained) vs R12h (0 hour after 12 hours running).

description:
All samples were gathered from mouse skeletal muscle (plantaris). Control total RNAs were extracted from 8 control untrained mice and combined.
All samples were gathered from mouse skeletal muscle (plantaris). Test total RNAs were extracted from 3-5 R12h mice and combined.

source_name: Total RNA from R12h was labeled with Cyanine-5 (red).


title: 15C-ER-D

description:
Peripheral blood cells taken from survivors few horus after exposure to trauma. date: 2002
Keywords = Control
Keywords = ER
Keywords = D


title: 17C-M4

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2002
Keywords = Control
Keywords = M4


title: Control (untrained) vs P12h (12 hours after 12 hours running).

description:
All samples were gathered from mouse skeletal muscle (plantaris). Control total RNAs were extracted from 8 control untrained mice and combined.
All samples were gathered from mouse skeletal muscle (plantaris). Test total RNAs were extracted from 3-5 P12h mice and combined.

source_name: Total RNA from P12h was labeled with Cyanine-5 (red).


title: 18C-M4


title: Control (untrained) vs P24h (24 hours after 12 hours running).

description:
All samples were gathered from mouse skeletal muscle (plantaris). Control total RNAs were extracted from 8 control untrained mice and combined.
All samples were gathered from mouse skeletal muscle (plantaris). Test total RNAs were extracted from 3-5 P24h mice and combined.

source_name: Total RNA from P24h was labeled with Cyanine-5 (red).


title: Control (untrained) vs R3h (running for 3 hours and sacrifice immediately).

description:
All samples were gathered from mouse skeletal muscle (plantaris). Control total RNAs were extracted from 8 control untrained mice and combined.
All samples were gathered from mouse skeletal muscle (plantaris). Test total RNAs were extracted from 3-5 R3h mice and combined.

source_name: Total RNA from Contol was labeled with Cyanine-3 (green).

source_name: Total RNA from R3h was labeled with Cyanine-5 (red).


title: Control (untrained) vs R4w (after 4 weeks running).

description:
All samples were gathered from mouse skeletal muscle (plantaris). Control total RNAs were extracted from 8 control untrained mice and combined.
All samples were gathered from mouse skeletal muscle (plantaris). Test total RNAs were extracted from 3-5 R4w mice and combined.

source_name: Total RNA from R4w was labeled with Cyanine-5 (red).


title: 20C-M4-D

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2001
Keywords = Control
Keywords = M4
Keywords = D


title: 18C-ER


title: 12P-ER

description:
Peripheral blood cells taken from survivors few hours after exposure to trauma. date: 2002
Keywords = PTSD
Keywords = ER


title: 9P-M4-ND

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2001
Keywords = PTSD
Keywords = M4
Keywords = ND


title: 6P-M4-ND

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2002
Keywords = PTSD
Keywords = M4
Keywords = ND


title: 6P-ER-ND

description:
Peripheral blood cells taken from survivors few hours after exposure to trauma. date: 2002
Keywords = PTSD
Keywords = ER
Keywords = ND


title: 7P-ER-ND


title: 11P-M4

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2002
Keywords = PTSD
Keywords = M4


title: 12P-M4


title: Spanish soil sample S4, replicate 1

status: Public on Nov 19 2004

type: genomic

city: Vancouver

first: Josh

middle: D

last: Neufeld

state: BC

address: #300-6174 University Blvd.

department: Department of Microbiology & Immunology

institute: University of British Columbia

description:
Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray.

Location	Ansio
Depth	100
alpha-HCH (ppm)	3580
Total HCH (ppm)	3750
Heterotrophic counts	5.14E+05
Fungal counts	3.51E+03
pH	5.9
Organic matter	3.96

molecule: genomic DNA

organism: Bacteria

source_name: Soil sample from Ansio


title: Spanish soil sample S5, replicate 1

description:
Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray.

Location	Portugalete
Depth	10
alpha-HCH (ppm)	4.36
Total HCH (ppm)	8.95
Heterotrophic counts	9.20E+06
Fungal counts	2.20E+04
pH	8.4
Organic matter	3.27

source_name: Soil sample from Portugalete


title: 8P-ER-ND


title: 5P-ER

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2002
Keywords = PTSD
Keywords = ER


title: 3P-M4-ND

description:
Peripheral blood cells taken from survivors 4 months after exposure to trauma.
date: 2001
Keywords = PTSD
Keywords = M4
Keywords = ND


title: Spanish soil sample S4, replicate 2


title: f2#11 versus pool

description:
Livers from 111 F2 female mice (all on an atherogenic diet) constructed from C57BL/6J and DBA/2J strains of mice were isolated for expression profiling.
All samples were compared to a common pool created from equal portions of RNA from each of the samples.
See Schadt, et al., Nature , Vol 422(6929):297-302 for details.

source_name: pool


title: 1P-M4-ND

description:
Peripheral blood cells taken from survivors 4 month after exposure to trauma.
date: 2001

Keywords = PTSD
Keywords = M4
Keywords = ND


title: Spanish soil sample S15, replicate 1

description:
Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray.

Location	Artxanda
Depth	10
alpha-HCH (ppm)	1900
Total HCH (ppm)	21800
Heterotrophic counts	6.61E+06
Fungal counts	4.63E+04
pH	4.4
Organic matter	18.6

source_name: Soil sample from Artxanda


title: 4P-ER-ND

description:
Peripheral blood cells taken from survivors few hours after exposure to trauma.
date: 2001
Keywords = PTSD
Keywords = ER
Keywords = ND


title: Spanish soil sample S5, replicate 2


title: Spanish soil sample S15, replicate 2


title: Spanish soil sample S16, replicate 1

description:
Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray.

Location	Artxanda
Depth	10
alpha-HCH (ppm)	17.7
Total HCH (ppm)	53.3
Heterotrophic counts	4.30E+06
Fungal counts	1.05E+04
pH	7.2
Organic matter	31.9


title: 3P-ER-ND


title: 14C-ER

description:
Peripheral blood cells, taken at ER hours after trauma exposure (Control sample).

Keywords = Control
Keywords = ER


title: Spanish soil sample S16, replicate 2


title: 4P-M4-ND


title: 10P-M4

description:
Peripheral blood cells, taken 4 months after trauma exposure (PTSD sample). date: 2002
Keywords = PTSD
Keywords = M4


title: Spanish soil sample S14, replicate 2

description:
Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray.

Location	Artxanda
Depth	10
alpha-HCH (ppm)	1270
Total HCH (ppm)	13500
Heterotrophic counts	5.43E+05
Fungal counts	4.18E+04
pH	3.6
Organic matter	96.4


title: Spanish soil sample S12, replicate 2

description:
Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray.

Location	Artxanda
Depth	8
alpha-HCH (ppm)	0.17
Total HCH (ppm)	0.4
Heterotrophic counts	4.01E+06
Fungal counts	6.41E+03
pH	7.6
Organic matter	31.8


title: Spanish soil sample S14, replicate 1


title: Spanish soil sample S12, replicate 1


title: Peace River boreal forest soil

type: SARST

description:
Ribosomal sequence tag (RST) data from a composite soil sample from Peace River, Alberta

Sample : Peace River
Date sampled : 030613
Observations : Wet, clay-like, hard to mix composite
Composite # : 10
Depth : 10 cm
Latitude : 56 46' 13'' N
Longitude : 118 22' 28'' W
GPS : NAD83, Zone 11, U E 415994, N 6292657
Location : Alberta (EMEND)
Moisture (% of dry weight) : 27.2
Forest type : Mixedwood boreal
Soil type : SiL
Wet (g) : 262.6
Dry (g) : 206.4
pH : 4.5
C/N ratio : 24.4
Nitrate-N (ppm) : 3.3
Ammonium-N (ppm) : 6
Mineralizable-N  (ppm) : 8.8
DNA (ug/g fresh soil) : 19.3
Organic Matter (%) : 6.3
Total Nitrogen (%) : 0.15
Phosphate (P; ppm) : 45
Potassium (K; ppm) : 210
Calcium (Ca; ppm) : 1300
Magnesium (Mg; ppm) : 225
Sulfate-S (ppm) : 6
Textural class : SiL
Sand (VCS; #10-2.00mm) : 23.8
Silt (#270-0.053 mm) : 50
Clay (2 microns) : 26.2

source_name: Soil sample from Peace River boreal forest


title: Narrow Hills boreal forest soil

description:
Ribosomal sequence tag (RST) data from a composite soil sample from Narrow Hills, Saskatchewan

Sample : Narrow Hills
Date sampled : 030624
Observations : Nice dark soil
Composite # : 10
Depth : 10 cm
Latitude  : 53 54' 58" N
Longitude : 104 41' 19" W
GPS : NAD83, Zone 13, U E 0520453, N 5974249
Location : Saskatchewan
Moisture : (% of dry weight)	7.9
Forest type : Jack Pine boreal
Soil type : Sand
Wet (g) : 416.1
Dry (g) : 385.5
pH : 5.3
C/N ratio : 37.1
Nitrate-N (ppm) : 3.6
Ammonium-N (ppm) : 4
Mineralizable-N  (ppm) : 14
DNA (ug/g fresh soil) : 19.2
Organic Matter (%) : 3.2
Total Nitrogen (%) : 0.05
Phosphate (P; ppm) : 14
Potassium (K; ppm) : 39
Calcium (Ca; ppm) : 400
Magnesium (Mg; ppm) : 28
Sulfate-S (ppm) : 2.6
Textural class : Sand
Sand (VCS; #10-2.00mm) : 91.2
Silt (#270-0.053 mm) : 5.7
Clay (2 microns) : 3.1

source_name: Soil sample from Narrow Hills boreal forest


title: Montmorency boreal forest soil

description:
Ribosomal sequence tag (RST) data from a composite soil sample from Montmorency, Quebec

Sample : Montmorency
Date sampled : 030909
Observations
Composite # : 10
Depth : 10 cm
Latitude : 47 19' 00'' N
Longitude : 71 06' 00'' W
GPS : NAD83, Zone 19, U E 341294, N 5242493
Location : Quebec (Montmorency)
Moisture : (% of dry weight)	24.6
Forest type : Balsam fir boreal
Soil type : Sandy loam
Wet (g) : 534.5
Dry (g) : 428.9
pH : 4.7
C/N ratio : 25.3
Nitrate-N (ppm) : 13
Ammonium-N (ppm) : 6
Mineralizable-N  (ppm) : 21
DNA (ug/g fresh soil) : 26.0
Organic Matter (%) : 6.1
Total Nitrogen (%) : 0.14
Phosphate (P; ppm) : 46
Potassium (K; ppm) : 19
Calcium (Ca; ppm) : 25
Magnesium (Mg; ppm) : 5
Sulfate-S (ppm) : 4.9
Textural class : Sandy loam
Sand (VCS; #10-2.00mm) : 67.4
Silt (#270-0.053 mm) : 21.1
Clay (2 microns) : 11.5

source_name: Soil sample from Montmorency boreal forest


title: Spanish soil sample S11, replicate 2

description:
Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray.

Location	Artxanda
Depth	10
alpha-HCH (ppm)	0
Total HCH (ppm)	0.01
Heterotrophic counts	1.07E+07
Fungal counts	9.31E+03
pH	8.1
Organic matter	9.1


title: Spanish soil sample S11, replicate 1


title: Spanish soil sample S10, replicate 2

description:
Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray.

Location	Artxanda
Depth	15
alpha-HCH (ppm)	0
Total HCH (ppm)	0.03
Heterotrophic counts	2.17E+06
Fungal counts	7.43E+03
pH	5.4
Organic matter	21.2


title: Alert Arctic tundra soil

description:
Ribosomal sequence tag (RST) data from a composite soil sample from Alert, Nunavut

Sample : Alert
Date sampled : 980804
Observations : Dark, dry, and soft (humics)
Composite # : 3
Depth : 10 cm
Latitude : 82 30' N
Longitude : 62 19' W
GPS : NAD83, Zone 20, U E 509957, N 9160702
Location : Arctic
Moisture : (% of dry weight)	19.0
Forest type : Alpine tundra
Soil type : SiL
Wet (g) : 60.3
Dry (g) : 50.68
pH : 7.6
C/N ratio : 31.4
Nitrate-N (ppm) : 1.7
Ammonium-N (ppm) : 12
Mineralizable-N  (ppm) : Insufficient sample
DNA (ug/g fresh soil) : 30.0
Organic Matter (%) : 9.2
Total Nitrogen (%) : 0.17
Phosphate (P; ppm) : 4
Potassium (K; ppm) : 66
Calcium (Ca; ppm) : 2900
Magnesium (Mg; ppm) : 180
Sulfate-S (ppm) : 16.2
Textural class : SiL
Sand (VCS; #10-2.00mm) : 39.9
Silt (#270-0.053 mm) : 49.1
Clay (2 microns) : 11

source_name: Soil Sample Arctic site Alert


title: Spanish soil sample S10, replicate 1


title: Composite, replicate 2

description: Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray.

source_name: Composite Spanish soil sample


title: 2P-M4

description:
Peripheral blood cells taken from survivors 4 month after exposure to trauma.
date: 2002

Keywords = PTSD
Keywords = M4

source_name: PMBCs


title: H295RAII3h017a

city: Jackson

first: Damian

middle: G.

last: Romero

state: MS

address: 2500 N. State St.

department: Biochemistry

institute: University of Mississippi Medical Center

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Lot batch = 12329282

source_name: H295R Control 3h


title: H295RAII3h023b

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12314960


title: Cape Dyer Arctic tundra soil (disturbed soil)

description:
Ribosomal sequence tag (RST) data from a composite soil sample from Cape Dyer, Nunavut

Sample : Cape Dyer
Date sampled : 021104
Observations : Very wet, clay (compacted pad beneath fuel storage tank)
Composite # : 3
Depth : 50-140 cm
Latitude : 66 36' 4'' N
Longitude : 61 34' 33'' W
GPS : NAD83, Zone 20, U E 563108, N 7387634
Location : Arctic
Moisture : (% of dry weight)	11.0
Forest type : disturbed Alpine tundra
Soil type : LS
Wet (g) : 387.1
Dry (g) : 348.6
pH : 6
C/N ratio : 8.7
Nitrate-N (ppm) : <0.1
Ammonium-N (ppm) : 2
Mineralizable-N  (ppm) : 5
DNA (ug/g fresh soil) : 0.4
Organic Matter (%) : 0.3
Total Nitrogen (%) : 0.02
Phosphate (P; ppm) : 10
Potassium (K; ppm) : 60
Calcium (Ca; ppm) : 350
Magnesium (Mg; ppm) : 90
Sulfate-S (ppm) : 4.6
Textural class : LS
Sand (VCS; #10-2.00mm) : 82.9
Silt (#270-0.053 mm) : 12.1
Clay (2 microns) : 5

source_name: soil sample Arctic site Cape Dyer


title: H295RAII3h016a

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12328955


title: H295RAII3h022a

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12280479


title: H295RAII3h018a

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12251411


title: H295RAII3h016b

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Lot batch = 12287800


title: H295RAII3h017b

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Lot batch = 12287672


title: H295RAII3h019a

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12251430


title: H295RAII3h020a

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12319669


title: H295RAII3h021a

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12319649


title: Composite, replicate 1


title: H295RAII3h022b

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12314924


title: 129/BSw het2 heart

city: Cincinnati

first: Amy

last: Moseley

state: OH

address: 231 Albert Sabin Way

department: Molecular Genetics

institute: University of Cincinnati

description: Adult male mice, age 8-16 weeks old, 129/Black Swiss background were used. Mice are heterozygous for the Na,K-ATPase alpha 1 isoform. Hearts were removed and immediatedly homogenized in Trizol using the procedure by Molecular Research Center (Cincinnati, Ohio) with an additional phenol-chloroform step in the total RNA isolation. A pool of 5 hearts was used in the RNA isolation.

source_name: murine whole heart tissue


title: THP-1

type: SAGE

anchor: NlaIII

first: J Max

last: Wilkinson

state: UK

address: Rowland Hill Street

department: Medicine

country: United Kingdom

institute: Royal Free & University College London School of Medicine

description: Library contructed from proliferating THP-1 cells growing in RPMI1640 supplemented with 10%FCS, penecillin/Steptomycin and B-ME.

source_name: Cultured THP-1 cells


title: H295RAII3h020b

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12327537


title: H295RAII3h023a

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12315495


title: H295RAII3h019b

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12251781


title: PMAthp-1

description: Cultured THP-1 cells were stimulated with PMA for 8 days by which time they had differentiated into a macrophage-like phenotype


title: H295RAII3h018b

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12251826


title: 129/BSw het1 heart


title: H295RAII3h021b

description:
H295R human adrenocortical cells treated with or without angiotensin II (100 nM) for 3 hr.
Keywords = adrenal angiotensin aldosterone
Lot batch = 12327552


title: Spanish soil composite

description: Ribosomal sequence tag (RST) data from a composite soil sample from hexachlorocyclohexane (HCH) contaminated and uncontaminated soils.  Sites include Artxanda, Portugalete, and Ansio.  Predominant RST sequences used to design oligonucleotide probes for microarray application.

source_name: Soils from the Basque region of Spain differing in HCH contamination


title: 129/BSw wt1 heart

description: Adult male mice, age 8-16 weeks old, 129/Black Swiss background were used. Mice are wild-type. Hearts were removed and immediatedly homogenized in Trizol using the procedure by Molecular Research Center (Cincinnati, Ohio) with an additional phenol-chloroform step in the total RNA isolation. A pool of 5 hearts was used in the RNA isolation.


title: adenocarcinoma (ADC1)

status: Public on Nov 18 2004

city: Chicago

first: Nikolai

middle: N.

last: Khodarev

state: IL

address: 5841 South Maryland Avenue

department: Radiation and Cellular Oncology

institute: The University of Chicago

description:
RNA was extracted and purified as described in Khodarev et.al., Biotechniques, 2002, 32:316
Keywords = Barrett's esophagus
Keywords = Barrett's-associated adenocarcinomas
Keywords = epidermal differentiation

source_name: Surgical sample


title: adenocarcinoma (ADC4)


title: adenocarcinoma (ADC7)


title: MIP-1a-inj_Mip-1a-KO_rep2

city: Lexington

first: Kevin

last: Kwong

state: KY

department: Physiology

institute: University of Kentucky

description:
Effect of the absence of CCL3 and its injection in response to bilateral bulbectomy in the olfactory mucosa.

CCL3-injected Ccl3-/-, replicate 2

source_name: Olfactory mucosa


title: adenocarcinoma (ADC5)


title: 129/BSw wt2 heart


title: Barrett's esophagus (B7)


title: MIP-1a-inj_Mip-1a-KO_rep1

description:
Effect of the absence of CCL3 and its injection in response to bilateral bulbectomy in the olfactory mucosa.

CCL3-injected Ccl3-/-, replicate 1


title: Barrett's esophagus (B8)


title: Carrier-inj_Mip-1a-KO_rep2

description:
Effect of the absence of CCL3 and its injection in response to bilateral bulbectomy in the olfactory mucosa.

Carrier-injected Ccl3-/-, replicate 2


title: Carrier-inj_Mip-1a-KO_rep1

description:
Effect of the absence of CCL3 and its injection in response to bilateral bulbectomy in the olfactory mucosa.

Carrier-injected Ccl3-/-, replicate 1


title: Barrett's esophagus (B3)


title: Carrier-inj_C57_rep2

description:
Effect of the absence of CCL3 and its injection in response to bilateral bulbectomy in the olfactory mucosa.

Carrier-injected C57BL/6, replicate 2


title: Barrett's esophagus (B5)


title: MIP-1a-inj_C57_rep2

description:
Effect of the absence of CCL3 and its injection in response to bilateral bulbectomy in the olfactory mucosa.

CCL3-injected C57BL/6, replicate 2


title: Normal esophageal epithelium (N6)


title: Normal esophageal epithelium (N3)


title: adenocarcinoma (ADC2)


title: Normal esophageal epithelium (N8)


title: Normal esophageal epithelium (N5)

description: RNA was extracted and purified as described in Khodarev et.al., Biotechniques, 2002, 32:316


title: adenocarcinoma (ADC3)


title: Barrett's esophagus (B2)


title: adenocarcinoma (ADC8)


title: Barrett's esophagus (B6)


title: Normal esophageal epithelium (N4)


title: Barretts esophagus (B1)


title: Carrier-inj_C57_rep1

description:
Effect of the absence of CCL3 and its injection in response to bilateral bulbectomy in the olfactory mucosa.

Carrier-injected C57BL/6, replicate 1


title: Segregant diploid hybrid-1

status: Public on Nov 16 2004

first: James

last: Ronald

institute: University of Washington

description: Diploid hybrid formed by crossing two segregants which were the product of a BY (isogenic to S288C) and RM (wild vineyard strain) cross

source_name: Log phase cells


title: Normal esophageal epithelium (N7)


title: Segregant diploid hybrid-2


title: Barrett's esophagus (B4)


title: RM diploid-2

description: Diploid hybrid formed by crossing RM (wild vineyard strain)


title: Segregant-2

description: Segregant from a cross between BY (isogenic to S288C) and RM (wild vineyard strain)


title: MIP-1a-inj_C57_rep1

description:
Effect of the absence of CCL3 and its injection in response to bilateral bulbectomy in the olfactory mucosa.

CCL3-injected C57BL/6, replicate 1


title: RM diploid-1


title: RM diploid-3


title: normal esophageal epithelium (N2)


title: BY diploid-2

description: Diploid hybrid formed by crossing BY (isogenic to S288C)


title: normal esophageal epithelium (N1)

source_name: surgical specimen


title: BY diploid-3


title: BY-RM mixture-5

description: 1:1 mixture of mRNA from BY (isogenic to S288C) and RM (wild vineyard strain)


title: Segregant-1


title: BY-RM mixture-6


title: BY-RM mixture-4


title: BYxRM diploid-4

description: Diploid hybrids from a cross between BY (isogenic to S288C) and RM (wild vineyard strain)


title: BY-RM mixture-2


title: BYxRM diploid-6


title: BY-RM mixture-3


title: BY-RM mixture-1


title: BYxRM diploid-3


title: BYxRM diploid-5


title: RM haploid-2

description: RM (wild vineyard strain)


title: Bone marrow MP 5

first: Kalliopi

last: Liadaki

institute: Children's Hospital Boston

description: Gene expression of Main Population (MP) cells, isolated from adult murine (C57BL/10SnJ) bone marrow.

source_name: Adult murine bone marrow Main Population cells


title: RM haploid-1

description: RM (wild vineyard strain)


title: Bone marrow MP 4


title: BYxRM diploid-2


title: RM haploid-3

description: RM (wild vineyard strain)


title: Bone marrow SP 5

description: Gene expression of Side Population (SP) cells, isolated from adult murine (C57BL/10SnJ) bone marrow.

source_name: Adult murine bone marrow Side Population cells


title: BYxRM diploid-1


title: Bone marrow SP 2


title: Bone marrow SP 1


title: Bone marrow MP 2


title: BY haploid-3

description: BY (strain isogenic to S288C)


title: Muscle MP 1

description: Gene expression of Main Population (MP) cells, isolated from adult murine (C57BL/10SnJ) skeletal muscle.

source_name: Adult murine muscle Main Population cells


title: Bone marrow SP 3


title: Bone marrow SP 4


title: Bone marrow MP 3


title: BY haploid-2

description: BY (strain isogenic to S288C)


title: Muscle MP 2


title: Muscle SP 4

description: Gene expression of Side Population (SP) cells, isolated from adult murine (C57BL/10SnJ) skeletal muscle.

source_name: Adult murine muscle Side Population cells


title: Muscle SP 3


title: Muscle MP 3


title: Muscle SP 5


title: BY haploid-1

description: BY (strain isogenic to S288C)


title: Muscle SP 2

source_name: Murine muscle Side Population cells


title: E100-/- rescue 10min FBS

status: Public on Nov 15 2004

city: boston

first: Gerhard

last: Schratt

institute: Children's Hospital

description: ES cells of different Srf genotype (E14wt, E100-/-,E100-/-rescue) were stimulated with FBS for 0, 10, 30, 60 and 180 min. RNA was harvested and hybridized to Affymetrix MGU74A arrays.

source_name: ES cells


title: E100-/- 180min FBS


title: E100-/- rescue 30min FBS


title: Bone marrow MP 1


title: E100-/- 60min FBS


title: Muscle SP 1


title: E100-/- 30min FBS


title: E100-/- 0min FBS


title: E100-/- 10min FBS


title: E100-/- rescue 0min FBS


title: E100-/- rescue 180min FBS


title: E100-/- rescue 60min FBS


title: E14wt 60min FBS


title: E14wt 0min FBS


title: Muscle MP 5


title: E14wt 10min FBS


title: E81-/-SRFVP16-1

description: ES cells were transfected with either vector, SRFdM-VP16 control or SRF-VP16 expression plasmids. RNA was harvested 72 hours after transfection. Each experimental condition was performed in duplicate.


title: E14wt 180min FBS


title: E14wt 30min FBS


title: E100-/-SRFVP16-2


title: E14wt-SRFVP16-2


title: E99-/+SRFVP16-1


title: E99-/+SRFVP16-2


title: E81-/-SRFVP16-2


title: E100-/-SRFVP16-1


title: E14wt-SRFVP16-1


title: E100-/-SRFdM-VP16-2


title: E14wt-SRFdM-VP16-2


title: E81-/-SRFdM-VP16-1


title: E81-/-vector-1


title: E14-99+/-vector-1


title: F2- S SLE

status: Public on Nov 13 2004

city: Nashville

first: Zheng

last: Liu

state: TN

institute: Vanderbilt University

description:
Family 2
Son
SLE

source_name: PBMC


title: E14wt-SRFdM-VP16-1


title: E81-/-vector-2


title: F4-GM

description:
Family 4
Grandmother
Unaffected


title: E14-99+/-vector-2


title: F4-M

description:
Family 4
Mother
Unaffected


title: F3-D

description:
Family 3
Daughter
Unaffected


title: F2-M

description:
Family 2
Mother
Unaffected


title: E100-/-vector-2


title: E14wt-vector-2


title: E99-/+SRFdM-VP16-1


title: F2-F

description: Family 1


title: E14wt-vector-1


title: E99-/+SRFdM-VP16-2


title: F1-D SLEb

description:
Family 1
Daughter
SLE b (twin)


title: F1-M

description:
Family 1
Mother
Unaffected


title: E100-/-SRFdM-VP16-1


title: E81-/-SRFdM-VP16-2


title: F1-D SLEa

description:
Family 1
Daughter a (twin)
SLE


title: ERA-025

description: AUTOIMMUNE: ERA


title: F4-D SLE

description:
Family 4
Daughter
SLE


title: Muscle MP 4


title: ERA-020

description: AUTOIMMUNE: ERA


title: ERA-024

description: AUTOIMMUNE: ERA


title: ERA-015

description: AUTOIMMUNE: ERA


title: ERA-016

description: AUTOIMMUNE: ERA


title: ERA-002

description: AUTOIMMUNE: ERA


title: ERA-014

description: AUTOIMMUNE: ERA


title: ERA-006

description: AUTOIMMUNE: ERA


title: ERA-013

description: AUTOIMMUNE: ERA


title: RA-006

description: AUTOIMMUNE: RA


title: ERA-003

description: AUTOIMMUNE: ERA


title: RA-005

description: AUTOIMMUNE: RA


title: ERA-012

description: AUTOIMMUNE: ERA


title: RA-004

description: AUTOIMMUNE: RA


title: RA-007

description: AUTOIMMUNE: RA


title: RA-009

description: AUTOIMMUNE: RA


title: ERA-022

description: AUTOIMMUNE: ERA


title: ERA-021

description: AUTOIMMUNE: ERA


title: ERA-001

description: AUTOIMMUNE: ERA


title: RA-003

description: AUTOIMMUNE: RA


title: RA-002

description: AUTOIMMUNE: RA


title: SLE-019

description: AUTOIMMUNE: SLE


title: SLE-015

description: AUTOIMMUNE: SLE


title: SLE-016

description: AUTOIMMUNE: SLE


title: RA-001

description: AUTOIMMUNE: RA


title: adenocarcinoma (ADC6)

description:
RNA was extracted and purified as described in Khodarev et.al., Biotechniques, 2002, 32:316
Keywords = Barrett's esophagus
Keywords = Barrett's-associated adenocarcinomas
Keywords = epidermal differentiation


title: SLE-017

description: AUTOIMMUNE: SLE


title: SLE-014

description: AUTOIMMUNE: SLE


title: SLE-011

description: AUTOIMMUNE: SLE


title: sle-007

description: AUTOIMMUNE: SLE


title: sle-006

description: AUTOIMMUNE: SLE


title: ERA-004

description: AUTOIMMUNE: ERA


title: sle-004

description: AUTOIMMUNE: SLE


title: sle-008

description: AUTOIMMUNE: SLE


title: sle-009

description: AUTOIMMUNE: SLE


title: sle-003

description: AUTOIMMUNE: SLE


title: sle-002

description: AUTOIMMUNE: SLE


title: cont-018

description: healthy control


title: cont-014

description: healthy control


title: cont-012

description: healthy control


title: cont-013

description: healthy control


title: cont-016

description: healthy control


title: sle-001

description: AUTOIMMUNE: SLE


title: post-017

description: allergy patient post-immunotheray


title: post-015

description: allergy patient post-immunotheray


title: cont-017

description: healthy control


title: cont-021

description: healthy control


title: cont-011

description: healthy control


title: pre-009

description: allergy patient pre-immunotheray


title: post-016

description: allergy patient post-immunotheray


title: post-019

description: allergy patient post-immunotheray


title: pre-002

description: allergy patient pre-immunotheray


title: sle-010

description: AUTOIMMUNE: SLE


title: pre-010

description: allergy patient pre-immunotheray


title: pre-013

description: allergy patient pre-immunotheray


title: pre-006

description: allergy patient pre-immunotheray


title: pre-007

description: allergy patient pre-immunotheray


title: pre-004

description: allergy patient pre-immunotheray


title: pre-001

description: allergy patient pre-immunotheray


title: Connexin43 null neonatal mouse heart3 (K43-3)

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
Cy3-labeled cDNA from a pool of three hearts of neonatal connexin43 null C57BL mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.
Keywords = connexin43 null neonatal mouse heart

source_name: pool of ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, stomach)


title: Connexin43 null neonatal mouse heart4 (K43-4)


title: wildtype neonatal mouse heart4 (W-4)

description:
Cy3-labeled cDNA from a pool of three hearts of neonatal wildtype C57BL mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.
Keywords = wildtype neonatal mouse heart

source_name: wildtype neonatal mouse heart4 (W-4)


title: knockdown Tcof1 [B]

status: Public on Nov 11 2004

city: Richmond

first: Timothy

middle: P

last: York

state: VA

department: Human Genetics

institute: Virginia Commonwealth University

description: NB N1E-115 cell line knockdown mouse Tcof1.

source_name: mouse NB N1E-115 cell line


title: Connexin43 null neonatal mouse heart2 (K43-2)


title: knockdown Tcof1 [A]


title: Connexin43 null neonatal mouse heart1 (K43-1)


title: Connexin32 null mouse brain4 (K32-4)

status: Public on Nov 12 2004

description:
Cy3-labeled cDNA from brains of neonatal C57BL Cx32 null mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.
Keywords = Cx32 null mouse brain

source_name: pool of mouse aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach

source_name: Connexin32 null mouse brain4 (K32-4


title: wildtype Tcof1 [A]

description: NB N1E-115 cell line wildtype mouse Tcof1.

source_name: mouse NB N1-115 cell line


title: Connexin32 null mouse brain1 (K32-1)

source_name: Connexin32 null mouse brain1 (K32-1)


title: wildtype Tcof1 [C]


title: overexpressed Tcof1 [B]

description: NB N1E-115 cell line overexpressing mouse Tcof1.


title: wildtype neonatal mouse heart2 (W-2)

source_name: wildtype neonatal mouse heart2 (W-2)


title: overexpressed Tcof1 [A]


title: knockdown Tcof1 [C]

source_name: mouse NB N1E-115 cell lines


title: overexpressed Tcof1 [C]


title: wildtype Tcof1 [B]


title: Connexin43 heterozygous neonatal mouse brain3 (H43-3)

description:
Cy3-labeled cDNA from brains of neonatal C57BL Cx43 heterozygous mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.
Keywords = Cx43 hetrozygous neonatal mouse brain


title: conidia on non-inductive (7 hr) vs inductive (7 hr) surface

status: Public on Nov 10 2004

city: Raleigh

first: Ralph

last: Dean

state: NC

institute: CIFR, North Carolina State University

description: RNA from conidia germinated on non-inductive (hydrophilic) Gelbond surface (7 hr) vs inductive (hydrophobic) Gelbond surface (7hr)

organism: Pyricularia grisea

source_name: green channel, RNA from conidia on non-inductive surface for 7 hours

source_name: red channel,  RNA from conidia on inductive surface for 7 hours


title: conidia on non-inductive (12 hr) vs inductive (12 hr) surface

description: RNA from conidia germinated on non-inductive (hydrophilic) Gelbond surface (12 hr) vs inductive (hydrophobic) Gelbond surface (12 hr) in Magnaporthe grisea

source_name: green channel, RNA from conidia on inductive surface for 12 hours

source_name: red channel,  RNA from conidia on non-inductive surface 12 hours


title: Connexin43 heterozygous neonatal mouse brain1 (H43-1)


title: wildtype neonatal mouse heart1 (W-1)

source_name: wildtype neonatal mouse heart1 (W-1)


title: wildtype neonatal mouse heart3 (W-3)

source_name: wildtype neonatal mouse heart3 (W-3)


title: conidia on inductive surface (12 hr) vs non-inductive surface (7 hr)

description: RNA from conidia germinated on inductive (hydrophobic) Gelbond surface (12 hr) vs non-inductive (hydrophilic) Gelbond surface (7 hr) in Magnaporthe grisea

source_name: red channel,  RNA from conidia on non-inductive for 7 hours


title: Connexin32 null mouse brain2 (K32-2)

source_name: Connexin32 null mouse brain2 (K32-2)


title: Connexin43 heterozygous neonatal mouse brain2 (H43-2)

source_name: pool of ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, stomach)


title: Connexin32 null mouse brain3 (K32-3

source_name: Connexin32 null mouse brain3 (K32-3


title: Connexin43 heterozygous neonatal mouse brain4 (H43-4)


title: G_Kin_2

city: Columbus

first: David

middle: Lawrence

last: Newsom

department: Human Cancer Genetics

institute: Comprehensive Cancer Center

description:
K562 cell line treated for 24 hours with one micromolar imatinib. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA and included half the standard level of Affymetrix RNA spike in controls.
Keywords = Human, leukemia, mock treated

source_name: K562 Cell line


title: H_Ctrl_2

description:
K562 cell line was mock treated.  RNA was extracted using Trizol plus Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA and included suggested level of Affymetrix RNA spike controls.
Keywords = Human, leukemia, mock treated

source_name: K562 cell line


title: conidia on non-inductive surface, 7 hrs vs 12 hrs

description: RNA from conidia germinated on non-inductive (hydrophilic) Gelbond surface for 7 and 12 hours in Magnaporthe grisea

source_name: green channel, RNA from conidia on non-inductive surface for 12 hours

source_name: red channel,  RNA from conidia on non-inductive surface for 7 hours


title: H_Ctrl_3


title: G_Ctrl_2


title: conidia vs inductive surface (7 hr)

description: RNA from conidia and from conidia germinated on inductive (hydrophobic) surface of Gelbond for 7 hours

source_name: green channel, RNA from conidia on inductive surface for 7 hours

source_name: red channel,  RNA from conidia


title: inductive surface (7 hr) vs non-inductive surface (12 hr)

description: RNA from conidia germinated on inductive (hydrophobic; 7 hr) vs non-inductive (hydrophilic; 12 hr) Gelbond surface in Magnaporthe grisea

source_name: red channel,  RNA from conidia on non-inductive surface for 12 hours


title: F_Ctrl_2


title: G_Kin_3


title: H_Kin_3


title: F_Ctrl_1


title: conidia  vs inductive surface (12 hr)

description: RNA from conidia and from conidia germinated on hydrophobic (inductive) surface of Gelbond for 12 hours

source_name: green channel, RNA from conidia

source_name: red channel,  RNA from conidia on inductive surface for 12 hours


title: G_Ctrl_1


title: F_Kin_2


title: inductive surface 12 hours vs 7 hours

description: RNA from conidia germinated on inductive hydrophobic surface of Gelbond for 7 and 12 hours

source_name: green channel, RNA from conidia on inductive surface for 12 hours

source_name: red channel,  RNA from conidia on inductive surface for 7 hours


title: H_Kin_1


title: P60_TR_1

city: Zurich

first: Ned

last: Mantei

department: Institute for Cell Biology

institute: Swiss Federal Institute of Technology

description:
Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 60 days old (P60) and carrying the Trembler mutation in the Pmp22 gene.
RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22

source_name: sciatic nerve of P60 Trembler mice


title: H_Ctrl_1


title: conidia vs non-inductive surface (12 hr)

description: RNA from conidia and conidia germinated on non-inductive (hydrophilic) surface of Gelbond 12 hours

source_name: red channel,  RNA from conidia on (non-inductive) hydrophilic 12 hours


title: P60_TR_2


title: H_Kin_2


title: BY diploid-1

city: Seattle

description: Diploid hybrid formed by crossing BY (isogenic to S288C)

source_name: Log phase cells


title: F_Kin_1


title: G_Kin_1


title: conidia vs conidia germinated on non-inductive surface for 7 hours

description: RNA from conidia and conidia germinated on non-inductive (hydrophilic) surface of Gelbond for 7 hours

source_name: green channel, RNA from conidia on non-inductive surface for 7 hours


title: F_Kin_3


title: P60_PMP22TG_2

description:
Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 60 days old (P60) and carrying a Pmp22 transgene (Magyar, J.P., et al. Impaired differentiation of Schwann cells in transgenic mice with increased Pmp22 gene dosage. J. Neurosci. 16:5351-5360 (1996)). RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22

source_name: sciatic nerve of P60 Pmp22 transgenic mice


title: E_Kin_2


title: F_Ctrl_3


title: G_Ctrl_3


title: E_Kin_3


title: P4_TR_2

description:
Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 4 days old (P4) and carrying the Trembler mutation in the Pmp22 gene.
RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22

source_name: sciatic nerve of P4 Trembler mice


title: P4_TR_3


title: P60_PMP22KO_1

description:
Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 60 days old (P60) and homozygously null for the Pmp22 gene (Adlkofer, K., et al. Hypermyelination nd demyelinating peripheral neuropathy in Pmp22-deficient mice. Nature Genetics 11, 274-280 (1995)).
RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22

source_name: sciatic nerve of P60 Pmp22 knockout mice


title: E_Ctrl_3

source_name: K562 cell line


title: E_Ctrl_2


title: E_Ctrl_1


title: P60_PMP22TG_1


title: E_Kin_1

source_name: K562 Cell line


title: P4_PMP22TG_3

description:
Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 4 days old (P4) and carrying a Pmp22 transgene (Magyar, J.P., et al., Impaired differentiation of Schwann cells in transgenic mice with increased Pmp22 gene dosage. J. Neurosci. 16, 5351-5360 (1996)).
RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22

source_name: sciatic nerve of P4 Pmp22 transgenic mice


title: D_Ctrl_3


title: P4_PMP22TG_2


title: P4_TR_1


title: D_Kin_3


title: D_Ctrl_1


title: PMI40 deletion strain, 1 g/L initial mannose, repeat 2/3

city: Helsinki

first: Anssi

last: Torma

address: Haartmaninkatu 8

department: Department of Bacteriology and Immunology

country: Finland

institute: Haartman Institute

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 1 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 2 of 3.

source_name: Total RNA from an aerobic batch culture of a pmi40 deletion strain


title: D_Kin_2


title: P4_PMP22KO_3

description:
Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 4 days old (P4) and homozygously null for Pmp22 (Adlkofer,K. et al., "Hypermyelination and demyelinating peripheral neuropathy in Pmp22-deficient mice, Nature Genetics 11, 274-280 (1995)).
RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22

source_name: sciatic nerve of P4 Pmp22 knockout mice


title: P4_PMP22KO_2

source_name: sciatic nerve of Pmp22 knockout mice


title: P60_PMP22KO_2


title: PMI40 deletion strain, 1 g/L initial mannose, repeat 3/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 1 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 3 of 3.


title: PMI40 deletion strain, 1 g/L initial mannose, repeat 1/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 1 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 1 of 3.


title: D_Kin_1

description:
K562 cell line treated for 24 hours with one micromolar imatinib. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA and included half the standard level of Affymetrix RNA spike in controls.
Keywords = Human, leukemia, mock treated


title: PMI40 deletion strain, 1.5 g/L initial mannose, repeat 3/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 1.5 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 3 of 3.


title: P60_WT_3

description:
Origin of sample: Sciatic nerve of 60 day old (P60) wild type mice (mixed background), pooled from 4--7 mice.
RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22

source_name: sciatic nerve of P60 wild type mice


title: P4_PMP22KO_1

source_name: sciatic nerve of PMP22 knockout mice at P4


title: C_Kin_3


title: D_Ctrl_2

description:
K562 cell line was mock treated.  RNA was extracted using Trizol plus Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA and included suggested level of Affymetrix RNA spike controls.
Keywords = Human, leukemia, mock treated


title: PMI40 deletion strain, 5 g/L initial mannose, repeat 3/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 5 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 3 of 3.


title: P4_PMP22TG_1


title: C_Kin_2


title: C_Kin_1


title: PMI40 deletion strain, 5 g/L initial mannose, repeat 2/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 5 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 2 of 3.


title: PMI40 deletion strain, 5 g/L initial mannose, repeat 1/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 5 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 1 of 3.


title: PMI40 deletion strain, 1.5 g/L initial mannose, repeat 2/3

description: A Saccharomyces cerevisiae strain with PMI40 knockout (parent CEN.PK113-7A) was cultivated in an aerated batch with mineral medium initially containing 15 g/L glucose and 1.5 g/L mannose. Samples for gene expression measurement were taken 6 hours after inoculation. Replicate assay 2 of 3.


title: C_Ctrl_3