title: mLSAGE Pancreas normal Theiler Stage 20 MMD SM245

status: Public on Jul 11 2007

first: BCGSC

last: BC Cancer Agency

address: 675 West 10th Avenue

institute: Canada's Michael Smith Genome Sciences Centre

description:
Developmental Stage = Theiler Stage 20
This library is of the MORGEN project.

source_name: Mouse Pancreas TS20 N3N3-GFP-

value: CBA/B6 (n=2 on B6), Age:E12.5, Preparation:Manual microscope dissected


title: current3

status: Public on Aug 08 2007

type: SAGE

anchor: NlaIII

city: Vancouver

first: Raj

last: Chari

state: BC

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

description: Current smoker, BE-12 from Lonergan et al. (2006) PMID: 16809635

molecule: polyA RNA

organism: Homo sapiens

source_name: Bronchial brushings, current smoker

tag: Bronchial brushings, current smoker, Gender

value: F, Age:63


title: Human Naive CD4 T Cells

status: Public on Sep 16 2006

city: Tokyo

first: Shinichi

last: Hashimoto

address: 7-3-1 Hongo, Bunkyo-ku

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

description: Peripheral blood mononuclear cells were isolated from venous blood drawn from normal healthy volunteers. Briefly, PBMC were isolated by centrifugation on a Ficoll-Metrizoate density gradient. CD4+CD45RA+ cells were purified using CD4 multisort.

molecule: total RNA

source_name: CD45RA+ CD4 T cells

tag: healthy donor


title: Bombyx ovary SAGE library #1

status: Public on Nov 01 2006

first: shunsuke

last: funaguma

address: Yayoi 1-1-1, Bunkyo-ku

description: This library was constructed Bombyx ovary (stage1-3) where One cystocyte differentiates into the oocyte in which the meiotic pathway continues, while the remaining cystocytes divert to the endomitotic pathway and become nurse cells.

organism: Bombyx mori

source_name: ovary (stage1-stage3)

tag: 3'long SAGE library


title: Human Mature Dendritic Cells

description: To generate mature dendritic cells, human monocytes were cultured in RPMI 1640 containing 7.5% FCS in the presense of GM-CSF(500 unit/ml), IL-4(100 unit/ml) for 5 days and stimulated with LPS for 2 days.

source_name: monocyte-derived mature dendritic cells


title: Human activated Th1 Cells

description:
Human neonatal leukocytes were isolated from freshly collected, heparinized, neonatal cord blood by a density gradient centrifugation using Lymphoprep . Th1- -polarized cells were generated by stimulating cord blood leukocytes with 1 ug/ml PHA in the presence of 2 ng/ml IL-12 and 200 ng/ml neutralizing anti-IL-4 antibody. Cells were washed on day 3 and expanded in each medium containing 4 ng/ml IL-2. At day 12 to 14, leukocytes were incubated with anti-CD4 monoclonal antibody coated magnetic beads, and CD4+ cells were isolated by passing the cultured cells through a magnetic cell separation system.
Cord blood-derived Th1 were collected after 3 days of CD4 positive cell separation, washed, and restumulated with 50 ng/ml of PMA and 1 ug/ml of ionomycin for 4 h.

source_name: Cord blood-derived Th1


title: Shoot winter 2003

status: Public on Nov 09 2006

city: Auckland

first: Sathish

last: puthigae

address: PO box 109185, Newmarket,

country: New Zealand

institute: Pastoral Genomics, c/o ViaLactia Biosciences (NZ) Ltd

description:
TITLE:
Transcriptome analysis reveals season-specific RbcS gene expression profiles in diploid perennial ryegrass (Lolium  perenne L.)
AUTHORS:
Puthigae Sathish, Nimali Withana, Margaret Biswas, Catherine Bryant, Kerry Templeton, Muhannad Al-Wahb, Claudia Smith-Espinoza, John R. Roche, Kieran M. Elborough and Jonathan R. Phillips
JOURNAL: Plant Biotechnology Journal, in press
YEAR: 2007
http://www.blackwell-synergy.com/doi/abs/10.1111/j.1467-7652.2006.00228.x

organism: Lolium perenne

source_name: shoot, pre- and post-grazed

growth_protocol:
Ryegrass tissue
Perennial ryegrass (Lolium perenne L.) cv. Bronsyn was used throughout this study.  Field grown samples, comprising mainly of viable leaves and pseudostems, were collected at mid-day from livestock-active monocultural paddocks at Dexcel, Hamilton, New Zealand during the peak of each season and frozen immediately in liquid nitrogen.  Samples were transported in dry-ice and stored at -80°C until used. During spring and summer, care was taken so as to not to include any floral stems in the tissue sample. Grass samples were collected from pre-grazed (15-60 days post grazing) and post-grazed (1 day post grazing) ryegrass swards, which were visibly healthy and free of any pests.

extract_protocol:
Construction of SAGE™ libraries
RNA was extracted using TRIZOL® reagent (Invitrogen, CA, USA).  For each SAGE™ library 100 µg each of pre- and post-grazed sample-derived of total RNA was were used and the libraries were created using I-SAGE™ or I-SAGE™ Long kit (Invitrogen, CA, USA) according to the manufacturer’s protocol.  Pre- and post-grazed SAGE™ libraries were sequenced at the Australian Genome Research Facility (Brisbane, Australia) and the tags were extracted using the SAGE2000 software and combined to produce the transcript profile for the season.

tag: Bronsyn monoculture


title: Human GM-CSF-macrophages SAGE

description: SAGE library generated from human monocytes incubated with GM-CSF(500unit/ml) in RPMI 1640 containing 7.5% FCS for 7 days.

source_name: GM-CSF-induced macrophages


title: SAGE_hypothalamus_adrenalectomized male mice 3h after glucocorticoid injection

status: Public on Sep 22 2006

city: Hershey

first: Yuichiro

last: Nishida

state: PA

address: 500 University Drive

department: Department of Anatomy and Physiology

country: USA

institute: Penn State College of Medicine

description: Hypothalamus were dissected from C57BL6 male mice  3h after glucocorticoid injection and pooled together. Total RNA was isolated by Trizol.

organism: Mus musculus

source_name: hypothalamus


title: Human Immature Dendritic Cells

description: To generate immature dendritic cells, monocytes were cultured in RPMI 1640 containing 7.5% FCS in the presense of GM-CSF(500 unit/ml), IL-4(100 unit/ml), and TNF-alpha(50unit/ml) for 5 days.

source_name: monocyte-derived immature dendritic cells


title: SAGE_hypothalamus_adrenalectomized male mice

description: Hypothalamus were dissected from C57BL6 male mice and pooled together. Total RNA was isolated by Trizol.


title: Human monocyte

description: SAGE library generated from CD14+monocytes isolated with the use of anti CD14 monoclonal antbody coated microbeads from PBMC from 7 helthy donors

source_name: CD14+ monocytes isolated from human peripheral blood


title: Human LPS monocytes

description: To prepare LPS-stimulated monocytes, the freshly isolated monocytes were incubated with 1 ug/ml of LPS in RPMI 1640 medium containing 10% FCS for 3 hours.

source_name: LPS-stimulated human CD14+ monocytes


title: Human M-CSF-macrophages SAGE

description: SAGE library generated from human monocytes incubated with M-CSF(100ng/ml) in RPMI 1640 containing 7.5% FCS for 7 days.

source_name: M-CSF-induced macrophages


title: SAGE_skeletal muscle_Detraining training young men

status: Public on Sep 12 2006

description: Muscle biopsies were obtained from vastus lateralis in men 12 weeks after finishing training program and pooled together. Total RNA was isolated by Trizol.

source_name: skeletal muscle

tag: Japanese, men, Detraining


title: SAGE skeletal muscle 12 wk training young men

status: Public on Sep 09 2006

description: Muscle biopsies were obtained from vastus lateralis in men 12 weeks after exercise training and pooled together. Total RNA was isolated by Trizol.

tag: Japanese, men, 12 weeks training


title: SAGE skeletal muscle 6 wk training young men

description: Muscle biopsies were obtained from vastus lateralis in men 6 weeks after exercise training and pooled together. Total RNA was isolated by Trizol.

tag: Japanese, men, 6 weeks training


title: Neuroblastoma_CL_IMR5

status: Public on Sep 06 2006

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Pediatric Oncology

country: Germany

institute: University Children's Hospital

description: SAGE library of neuroblastoma cell line IMR-5

data_processing: SAGE2000 software, version 4.12

source_name: Neuroblastoma, cell line, IMR-5

growth_protocol: Neuroblastoma cell line IMR-5 was cultured in RPMI 1640 (Biochrom KG) supplemented with 20% fetal calf serum (Biochrom KG). Cells were harvested after they were grown to confluent monolayers.

extract_protocol:
RNA extraction: TRIzol reagent (Invitrogen)
SAGE library construction: according to Velculescu et al. 1995, Science 270(5235):484-7

tag: Tissue

value: neuroblastoma cell line IMR-5

tag: MYCN status

value: amplified


title: Neuroblastoma_primary_stage4_NB9

description: SAGE library of a primary stage 4 neuroblastoma without preceding cytotoxic treatment

source_name: Neuroblastoma, primary tumor, stage 4

extract_protocol:
RNA extraction: TRIzol reagent (Invitrogen)
SAGE library construction: I-SAGE kit (Invitrogen)

value: primary neuroblastoma, bulk

tag: Stage

tag: Age at diagnosis

value: 5465 days

tag: Sex

value: female

value: non-amplified

tag: histology (INPC)

value: stroma poor, poorly differentiated


title: Neuroblastoma_primary_stage4_NB7

value: 933 days

value: male

value: stroma poor, differentiating


title: Neuroblastoma_primary_stage4S_NB10

description: SAGE library of a primary stage 4S neuroblastoma without preceding cytotoxic treatment

source_name: Neuroblastoma, primary tumor, stage 4S

value: 49 days


title: SAGE_Drosophila pseudoobscura_Female

status: Public on Jul 27 2006

city: Wien

first: Schlötterer

last: Christian

address: Josef Baumann Gasse 1

department: Institut für Tierzucht und Genetik

country: Austria

institute: Veterinärmedizinische Universität Wien

description: The mRNA was isolated from total RNA using a biotin-labeled Tn oligo and Dynal beads. Double stranded cDNA was generated with Superscript II reverse transcriptase and DNA polymerase I. The resulting cDNA library was digested with NlaIII (anchoring enzyme). 3’ restriction fragments were recovered with Dynal beads and split into two populations. Each aliquot was ligated to one of the two annealed linker pairs. After extensive washing tags were created by digestion with BsmFI (tagging enzyme). Tags were blunted with T4 polymerase and ligated to generate ditags. Ditags were PCR amplified and digested with NlaIII. Restriction fragments were separated on a 12% polyacrylamide gel and the band containing the ditags was isolated from the gel. The purified inserts were concatemerized and ligated into pZero and transformed into EDH5? electromax cells.

organism: Drosophila pseudoobscura

source_name: female flies

tag: virgin female flies aged 3 to 7 days old


title: Day 6 in vivo-produced porcine blastocysts

status: Public on Aug 23 2006

city: Clay Center

first: Jeremy

middle: R

last: Miles

state: NE

address: State Spur 18A

institute: USDA-ARS

description: Comparison of gene expression from in vivo- and in vitro- produced porcine embryos in an attempt to identify compromised gene expression from in vitro-produced embryos.

organism: Sus scrofa

source_name: Porcine Blastocysts (In vivo-produced)

tag: In vivo-produced porcine blastocysts collected at Day 6 of gestation (Day 0, Day of AI)


title: Day 6 in vitro-produced porcine blastocysts

description: Comparison of gene expression from in vivo- and in vitro-produced porcine embryo to identify compromised gene expression from in vitro-produced embryos.

source_name: Porcine Blastocysts (In vitro-produced)

tag: In vitro-produced porcine blastocysts collected at Day 6 of gestation (Day 0, Day of in vitro fertilization)


title: Neuroblastoma_primary_stage4S_NB11

value: 0 days


title: SAGE skeletal muscle pretraining young men

description: Muscle biopsies were obtained from vastus lateralis in men and pooled together. Total RNA was isolated by Trizol.

tag: Japanese, men, pretraining


title: Neuroblastoma_primary_stage4S_NB5

value: 3 days

tag: histology (Shimada)

value: stroma poor, undifferentiated


title: Neuroblastoma_primary_stage4S_NB1

value: 239 days


title: RL-SAGE_MGGW_Vegetative mycelium_Gowda et al., 2004

status: Public on Aug 18 2006

city: Columbus

first: Mohan

middle: B

last: Raghupathy

email: mohanbabu_r@yahoo.com, wang.620@osu.edu

state: OH

address: 201 Kottman Hall, 2021 Coffey Rd

department: Department of Plant Pathology

institute: The Ohio State University

description: An RL-SAGE library was constructed using the same RNA sample that was used for the construction of the mycelium MPSS library (Table 1). The average insert size of the  concatemer in the RL-SAGE clones was approximately 1.1 kb. A total of 245,873 individual tags and 51,925 unique tags were obtained from 7,292 sequence reads.

organism: Pyricularia grisea

source_name: The Ohio State University

growth_protocol: Rice blast fungus (Magnaporthe grisea) strain 70-15 (Mitchell et al., 2003) was grown on a minimum medium (0.2% [w/v] yeast extract and 1% [w/v] Suc) for 3 d (28°C at 200 rpm) and mycelium was harvested for RNA isolation.

extract_protocol: About 50 ng of mRNA isolated from mycelium tissue was used for RL-SAGE library construction as described by Gowda et al [2004].

tag: A total of 7,292 sequence reads from the RL-SAGE library were sequenced at Arizona Genomics Institute. The ditags and unique tags were extracted from these sequences using SAGEspy program developed at the Ohio Supercomputer Center (http://bioinformatics.osc.edu/sagespy). All RL-SAGE tags from mycelium library are available from the MGOS database (http://www.mgosdb.org/cgibin/sage/advTagSearchResult.cgi?lib_include=MG_SGa).


title: BE-16

status: Public on Jul 14 2006

first: Kim

middle: Marie

last: Lonergan

state: British Columbia

institute: British Columbia Cancer Research Centre

description: bronchial brushing

source_name: bronchial epithelium

tag: bronchial epithelium


title: BE-15

description: bronchial brushing


title: SAGE_Drosophila pseudoobscura_Male

source_name: male flies

tag: Unmated male flies aged 3 to 7 days


title: BE-11B

description: bronchial brushing


title: Microvascular endothelial cells cultured on fibronectin and exposed to sustained low shear stress.

status: Public on Aug 01 2006

city: Vienna

first: Gürkan

last: Sengoelge

address: Waehringer Guertel 18-20

department: Medicine/Division of Nephrology

institute: Medical University Vienna

description:
Pulmonary microvascular endothelial cells were cultured on the inner surface of fibers (each 700 µm inner diameter) coated with native-fibronectin in hollow-fiber cartridges (FiberCell Systems, Inc.). Duration of shear stress application was 10 days. Shear stress was steady at 0.7 dyne/cm2.
Keywords = microvascular endothelial cells
Keywords = chronic shear stress

source_name: Pulmonary microvascular endothelial cells in culture.


title: BE-14

description: bronchial brushing


title: SAGE skeletal muscle 5 days training young men

description: Muscle biopsies were obtained from vastus lateralis in men 5 days after exercise training and pooled together. Total RNA was isolated by Trizol.

tag: Japanese, men, 5 days training


title: BE-13

description: bronchial brushing


title: BE-11A

description: bronchial brushing


title: Neuroblastoma_primary_stage4_NB12

value: 3394 days


title: BE-12

description: bronchial brushing


title: BE-10

description: bronchial brushing


title: STAGE tag library for c-myc

status: Public on Nov 23 2006

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description:
ChIP procedure
Human cells were cross-linked by addition of formaldehyde (1% final concentration) directly to tissue culture plates for 7 min at room temperature. Cross-linking was terminated by adding glycine to a final concentration of 125 mM. Cells were washed with cold phosphate-buffered saline (PBS) containing PMSF, scraped off the plates, collected by centrifugation and washed again. After centrifugation, the pellet was resuspended in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-Cl pH 8.1, plus protease inhibitors) and incubated at room temperature for 20 min. Cells were sonicated on ice and fragmented DNA was visualized on an agarose gel (average size 1 kb). The sample was centrifuged at 12000 rpm at 4 °C for 10 min and 10x ChIP dilution buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-Cl pH 8.1, 150 mM NaCl, plus protease inhibitors) was added to the collected supernatant. Sample was pre-cleared with protein A-agarose beads (previously washed with 10x ChIP dilution buffer) at 4 °C for 1 hr. Pre- cleared chromatin was incubated with an antibody against E2F4 (sc-1082x, Santa Cruz) at 4 °C overnight. For the mock IP controls in Figs. 3 and 4, the antibody was left out. Pre-washed protein A-agarose beads were added and protein-DNA complexes were recovered after a 2 hour incubation at 4 °C. Immunoprecipitated complexes were successively washed with Low- salt wash buffer (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 150 mM NaCl), High-salt wash buffer (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), LiCl wash buffer (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). SDS elution buffer was added and incubated at 65 °C for 30 min to recover protein-DNA complexes. Crosslinks were reversed by incubating at 65 °C overnight. The sample was treated with RNase A and Proteinase K, extracted with phenol:chloroform and precipitated. The pellet was resuspended in 25 µl of water. A 5'-biotinylated primer was used for random amplification of immunoprecipitated DNA fragments. The biotinylated amplified ChIP material was used as input for STAGE.

molecule: genomic DNA

source_name: Cultured HeLa cells

extract_protocol: STAGE is based on high-throughput sequencing of concatemerized tags of defined length that are derived from DNA enriched by ChIP. Proteins were cross-linked to their binding sites in vivo with formaldehyde and chromatin was extracted and sheared. The cross-linked protein-DNA complexes were immunoprecipitated, cross-links were reversed and ChIP DNA was amplified by PCR using biotinylated primers. Amplified DNA fragments were digested with NlaIII, which cuts at 5'-CATG sites. Fragments with ends containing the NlaIII site were isolated by binding to streptavidin beads. They were separately ligated to one of two linkers containing a MmeI site, then incubated with MmeI, which cleaves 21 bp away from its recognition site. The 21-bp tags attached to linkers were isolated and ligated to create ditags. Ditags were amplified by PCR using nested primers and trimmed by digesting with NlaIII. Trimmed ditags were gel purified, concatemerized by ligation, cloned and sequenced

tag: HeLa cells were cultured under normal growth conditions (10% Fetal Bovine Serum).


title: BE-7

description: bronchial brushing


title: BE-9

description: bronchial brushing


title: Microvascular endothelial cells cultured on advanced glycated fibronectin and exposed to sustained high shear stress.

description:
Pulmonary microvascular endothelial cells were cultured on the inner surface of fibers (each 700 µm inner diameter) coated with advanced glycation endproduct modified (AGE)-fibronectin in hollow-fiber cartridges (FiberCell Systems, Inc.). Duration of shear stress application was 10 days. Shear stress was gradually increased to 17 dyne/cm2.
Keywords = AGE
Keywords = human microvascular endothelial cell
Keywords = chronic shear stress


title: BE-5

description: bronchial brushing


title: Asthmatic Rat Lung

status: Public on Jul 12 2006

city: Shanghai

first: Yong Qing

last: Yang

address: 650 South Wanping Rd

department: Shanghai Research Institute of Acupuncture

country: China

institute: Shanghai University of Traditional Chinese Medicine

description:
SAGE profile of the asthmatic male rat (Sprague Dawley) lung with linker sequences removed. Rats weighted 250 grams and were 50 days old.
Keywords = asthma
Keywords = Rat
Keywords = Lung

organism: Rattus norvegicus

source_name: Asthmatic Rat Lung


title: BE-6

description: bronchial brushing


title: BE-4B

description: bronchial brushing


title: BE-2

description: bronchial brushing


title: Neuroblastoma_primary_stage4S_NB2

value: 52 days


title: BE-8A

description: bronchial brushing


title: BE-8B

description: bronchial brushing


title: BE-3

description: bronchial brushing


title: Liver stellate cells 15 days

status: Public on Jul 01 2006

city: Amsterdam

first: Willem

last: Boers

address: Meibergdreef 69

department: AMC Liver Center

country: Netherlands

institute: Academic Medical Center

description: Intermediate phase of transformation to myofibroblast

source_name: Liver stellate cells cultured for 15 days

value: liver


title: BE-1

description: bronchial brushing


title: BE-4A

description: bronchial brushing


title: Squamous esophagus long-term primary cell culture

status: Public on Jun 28 2006

city: Utrecht

first: Jantine

middle: Wilhelmina Paula Maria

last: van Baal

address: Heidelberglaan 100

department: Gastroenterology and Hepatology

institute: University Medical Center Utrecht

description: SAGE data of long-term primary cell culture derived from normal squamous esophagus biopsy


title: Liver myofibroblast

description: End stage of transformed stellate cells

source_name: Liver myofibroblast

tag: Transformed stellate cells from liver

tag: Myofibroblast


title: Liver stellate cells 0 days

description: Freshly isolated stellate cells on first day

source_name: Liver stellate cells isolated on first day

tag: Tissue


title: mLSAGE_Large_intestine_normal_TS20_MMD_SM155

status: Public on Jun 08 2006

department: Gene Expression

description:
Developmental stage: Theiler stage TS20
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

data_processing: not normalized

source_name: Large_intestine, normal

tag: Mouse strain

tag: Gender

value: Unknown

tag: Age

tag: Preparation

value: Manual microscope dissected


title: Esophageal adenocarcinoma

description: SAGE data of biopsy taken from esophageal adenocarcinoma patient with known history Barrett's esophagus

source_name: Esophageal adenocarcinoma

tag: Esophageal adenocarcinoma


title: Barrett long-term primary cell culture

description: SAGE data of long-term primary cell culture derived from metaplastic Barrett's esophagus

source_name: Barrett

tag: long-term primary cell culture


title: acidotic mouse OMCD

city: Paris

first: Alain

last: Doucet

country: France

institute: Institut des Cordeliers

description: Library obtained from microdissected kidney outer medullary collecting duct from C57BL6/J mice after 3 days NH4Cl-diet. The library was generated using Sau3AI as anchoring enzyme. Data are provided after removal of linker derived sequences

source_name: microdissected outer medullary collecting duct

tag: male

tag: 10 weeks

tag: NH4Cl-loaded for 3 days


title: SAGE_hypothalamus intact male mice

status: Public on Apr 03 2007

city: Québec

first: Kouamé Ettienne

last: Kouadjo

state: Québec

address: 2705 Bld Laurier

institute: Laval University

description: hypothalamus were dissected from C57BL6 intact male mice and pooled together. Total RNA was isolated by Trizol.

source_name: hypothalamus


title: esophageal squamous cell carcinoma

description: SAGE data of esophageal squamous cell carcinoma biopsy

source_name: esophageal squamous cell carcinoma

tag: esophageal squamous cell carcinoma


title: mLSAGE_Brain_normal_P84-P90_LCM_SM152

first: BCGSC

last: BC Cancer Agency

institute: Canada's Michael Smith Genome Sciences Centre

description:
Other information: P84
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Brain, normal

value: Male

value: Laser microscope dissected


title: mLSAGE_Lung_normal_TS19_MMD_SM127

description:
Developmental stage: Theiler stage TS19
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Lung, normal


title: mLSAGE_Pancreas_normal_P42_MMD_SM114

description:
Other information: P42
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Pancreas, normal


title: mLSAGE_Embryo_normal_TS9_MMD_SM146

description:
Developmental stage: Theiler stage TS9
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Embryo, normal


title: mLSAGE_Neural_tube_normal_TS13_MMD_SM117

description:
Developmental stage: Theiler stage TS13
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Neural_tube, normal


title: mLSAGE_Stomach_normal_TS20_MMD_SM072

source_name: Stomach, normal


title: mLSAGE_Brain_normal_P27_MMD_SM097

description:
Other information: P27
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Pancreas_normal_TS26_MMD_SM016

description:
Developmental stage: Theiler stage TS26
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Brain_normal_P27_MMD_SM073


title: mLSAGE_Lung_normal_TS25_MMD_SM045

description:
Developmental stage: Theiler stage TS25
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Brain_normal_TS15_LCM_SM070

description:
Developmental stage: Theiler stage TS15
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Embryo_normal_TS1_MMD_SM077

description:
Developmental stage: Theiler stage TS1
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Embryo_normal_TS11_MMD_SM106

description:
Developmental stage: Theiler stage TS11
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Urogenital_sinus_normal_TS24_MMD_SM065

description:
Developmental stage: Theiler stage TS24
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Urogenital_sinus, normal


title: mLSAGE_Embryo_normal_TS3_MMD_SM061

description:
Developmental stage: Theiler stage TS3
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Heart_normal_TS19_MMD_SM008

source_name: Heart, normal


title: mLSAGE_Heart_normal_TS13_MMD_SM174

tag: Mutation

value: Foxh1 -/-


title: mLSAGE_Muscle_normal_TS25_MMD_SM042

source_name: Muscle, normal


title: Grass Shrimp Cadmium-exposed Library

status: Public on May 18 2006

city: Ocean SPrings

first: Joe

last: Griffitt

state: MS

address: 703 East BEach Drive

department: Coastal Sciences

institute: University of Southern Mississippi

description: This library was constructed from Cadmium-exposed shrimp in an exposure to identify differentially expressed genes in shrimp following exposure to fipronil, endosulfan, or cadmium.

organism: Palaemon pugio

source_name: Grass shrimp Cadmium-exposed

tag: Adult male grass shrimp were exposed to a 96-hour LC50 concentration of Cadmium.


title: mSAGE_Liver_normal_TS20_MMD_SM001

description:
Developmental stage: Theiler stage TS20
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Liver, normal


title: mLSAGE_Kidney_normal_TS20_MMD_SM169

source_name: Kidney, normal


title: mLSAGE_Liver_normal_TS15_MMD_SM158


title: mLSAGE_Spleen_normal_TS22_MMD_SM011

description:
Developmental stage: Theiler stage TS22
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Spleen, normal


title: Grass Shrimp Endosulfan-exposed Library

description: This library was constructed from Endosulfan-exposed shrimp in an exposure to identify differentially expressed genes in shrimp following exposure to fipronil, endosulfan, or cadmium.

source_name: Grass shrimp Endosulfan-exposed

tag: Adult male grass shrimp were exposed to a 96-hour LC50 concentration of endosulfan


title: mLSAGE_Heart_normal_TS15_MMD_SM007


title: mLSAGE_Embryo_normal_TS9_MMD_SM157


title: mLSAGE_Brain_normal_P84-P90_LCM_SM181

description:
Other information: P84
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: Grass Shrimp Fipronil-exposed Library

description: This library was constructed from Fipronil-exposed shrimp in an exposure to identify differentially expressed genes in shrimp following exposure to fipronil, endosulfan, or cadmium.

source_name: Grass shrimp Fipronil-exposed

tag: Adult male grass shrimp exposed to LC50 concentration of fipronil for 96-hours


title: Rat Limbus Epithelium

status: Public on May 15 2006

city: Bethedsa

first: Hagit

last: Ulanovsky

state: MD

address: 7 Memorial Dr, room 135

institute: NEI

description: Limbal Epithelial region, from the termination of Bowman's layer to approximately 1 mm peripherally on the conjunctival side, was scraped.

source_name: 6-week male Wister rats

extract_protocol: SNAP total RNA isolation kit (Invitrogen, Carlsbad, CA)

tag: 48 eyes, 6-week male Wister rats were used.


title: Rat Central Corneal Epithelium

description: Central region of the cornea was marked with 2.5 mm diameter trephine (Storz), and corneal epithelium was scraped by miniature scalpel.

tag: 16 eyes, 6-week male Wister rats were used.


title: mSAGE_Pancreas_normal_TS24_MMD_SM015

status: Public on Apr 28 2006

city: Vancouver

address: 675 West 10th Avenue

description:
Developmental stage = Theiler Stage 24
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mSAGE_Pancreas_normal_TS22_MMD_SM014

description:
Developmental stage = Theiler Stage 22
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Embryonic_stem_cells_normal_MMD_SM401

status: Public on Apr 27 2006

description:
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Embryonic_stem_cells, normal

value: Unspecified


title: mSAGE_Spleen_normal_TS26_MMD_SM010

description:
Developmental stage = Theiler Stage 26
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mSAGE_Heart_normal_TS20_MMD_SM003

description:
Developmental stage = Theiler Stage 20
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Pancreas_normal_TS22_MMD_SM223

value: WT Tle6


title: mLSAGE_Brain_normal_TS25_LCM_SM230

description:
Developmental stage = Theiler Stage 25
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Brain, normal

value: Tg(Hum)


title: mLSAGE_Pancreas_normal_TS22_MMD_SM224

value: Tle 6


title: mLSAGE_Bone_normal_P84_MMD_SM218

source_name: Bone, normal


title: mLSAGE_Lymph_nodes_normal_P63_MMD_SM222

source_name: Lymph_nodes, normal

value: Mixed

value: PBCrePten(flox/-)


title: mLSAGE_Brain_normal_TS23_LCM_SM301

description:
Developmental stage = Theiler Stage 23
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

value: fierce


title: mLSAGE_Lymph_nodes_normal_P63_MMD_SM221

value: PBCrePten(flox/flox)


title: mLSAGE_Prostate_normal_P63_MMD_SM220

source_name: Prostate, normal

value: Pten +/-


title: mLSAGE_Embryonic_stem_cells_normal_Embryonic_Stem_Cell_MMD_SM302

description:
Other information: Embryonic Stem Cell
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Embryonic_stem_cells_normal_MMD_SM208


title: mLSAGE_Embryo_normal_TS7_MMD_SM203

description:
Developmental stage = Theiler Stage 7
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Embryo, normal


title: mLSAGE_Pituitary_gland_normal_P84_MMD_SM202

source_name: Pituitary_gland, normal


title: mLSAGE_Skin_normal_P84_MMD_SM214

source_name: Skin, normal


title: mLSAGE_Esophagus_normal_TS24_MMD_SM210

source_name: Esophagus, normal


title: mLSAGE_Prostate_normal_P63_MMD_SM219

value: Pten -/-


title: mLSAGE_Brain_normal_TS23_LCM_SM200


title: mLSAGE_Mammary_glands_normal_P84_MMD_SM069

source_name: Mammary_glands, normal

value: Female

value: Adult


title: mLSAGE_Esophagus_normal_TS20_MMD_SM209

value: Unknown


title: mLSAGE_Heart_normal_TS15_MMD_SM206

description:
Developmental stage = Theiler Stage 15
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Heart, normal

value: Manual microscope dissected


title: mLSAGE_Brain_normal_TS21_LCM_SM197

description:
Developmental stage = Theiler Stage 21
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

value: Male


title: mLSAGE_Brain_normal_TS21_LCM_SM199

value: Laser microscope dissected


title: mLSAGE_Brain_normal_P84-P90_LCM_SM196


title: mLSAGE_Brain_normal_P35_LCM_SM190


title: mLSAGE_Brain_normal_P07_LCM_SM185


title: mLSAGE_Brain_normal_P35_LCM_SM191


title: mLSAGE_Brain_normal_P84-P90_LCM_SM195


title: mLSAGE_Brain_normal_P07_LCM_SM189


title: mLSAGE_Brain_normal_P84-P90_LCM_SM194


title: mLSAGE_Brain_normal_P84-P90_LCM_SM180


title: mLSAGE_Brain_normal_P35_LCM_SM186


title: mLSAGE_Brain_normal_P35_LCM_SM192


title: mLSAGE_Brain_normal_P07_LCM_SM188


title: mLSAGE_Brain_normal_P84-P90_LCM_SM184


title: mLSAGE_Brain_normal_P35_LCM_SM187


title: mLSAGE_Brain_normal_TS23_MMD_SM179


title: mLSAGE_Uterus_normal_P0_MMD_SM171

source_name: Uterus, normal


title: mLSAGE_Limb_normal_TS17_MMD_SM172

description:
Developmental stage = Theiler Stage 17
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Limb, normal


title: mLSAGE_Brain_normal_TS23_LCM_SM178


title: mLSAGE_Brain_normal_TS21_LCM_SM167


title: mLSAGE_Brain_normal_P84-P90_LCM_SM182


title: mLSAGE_Brain_normal_P84-P90_LCM_SM183


title: mLSAGE_Limb_normal_TS23_MMD_SM177


title: mLSAGE_Urogenital_sinus_normal_TS24_MMD_SM170

source_name: Urogenital_sinus, normal


title: mLSAGE_Brain_normal_TS21_MMD_SM154


title: mLSAGE_Large_intestine_normal_TS20_MMD_SM156

source_name: Large_intestine, normal


title: mLSAGE_Brain_normal_TS25_LCM_SM175


title: mLSAGE_Pancreas_normal_TS17_MMD_SM161

source_name: Pancreas, normal

value: CBA/B6 (n=2 on B6)

value: PDX1-GFP Tg


title: mLSAGE_Pancreas_normal_TS20_MMD_SM160

value: NGN3-GFP Tg


title: mLSAGE_Liver_normal_TS26_MMD_SM149

source_name: Liver, normal


title: mLSAGE_Pituitary_gland_normal_P0_MMD_SM165


title: mLSAGE_Ovaries_normal_P0_MMD_SM164

source_name: Ovaries, normal


title: mLSAGE_Heart_normal_TS13_MMD_SM145

description:
Developmental stage = Theiler Stage 13
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Small_intestine_normal_TS20_MMD_SM159

source_name: Small_intestine, normal


title: mLSAGE_Brain_normal_P07_LCM_SM144

source_name: Brain, normal


title: mLSAGE_Brain_normal_P84-P90_LCM_SM153


title: mLSAGE_Pancreas_normal_TS20_MMD_SM162


title: mLSAGE_Brain_normal_P84-P90_LCM_SM139


title: mLSAGE_Brain_normal_TS21_LCM_SM142


title: mLSAGE_Urogenital_sinus_normal_TS24_MMD_SM163


title: mLSAGE_Brain_normal_P84-P90_LCM_SM137


title: mLSAGE_Brain_normal_P84-P90_LCM_SM132


title: mLSAGE_Brain_normal_P35_MMD_SM138


title: mLSAGE_Pituitary_gland_normal_P0_MMD_SM166


title: mLSAGE_Skin_normal_TS24_MMD_SM134


title: mLSAGE_Brain_normal_TS25_LCM_SM148


title: mLSAGE_Brain_normal_P84-P90_LCM_SM147


title: Grass Shrimp Control Library

description: This library was constructed from control shrimp in an exposure to identify differentially expressed genes in shrimp following exposure to fipronil, endosulfan, or cadmium.

source_name: Grass shrimp control

extract_protocol: RNA BEE

tag: Adult male grass shrimp exposed to acetone as a carrier control for xenobiotic exposure experiments


title: mLSAGE_Pituitary_gland_normal_TS23_MMD_SM133

tag: Mouse strain


title: mLSAGE_Lymph_nodes_normal_P84_MMD_SM130

source_name: Lymph_nodes, normal

tag: Gender


title: mLSAGE_Small_intestine_normal_TS20_MMD_SM151

tag: Age


title: mLSAGE_Mammary_glands_normal_P84_MMD_SM129

tag: Preparation


title: mLSAGE_Brain_normal_TS20_MMD_SM143


title: mLSAGE_Brain_normal_P07_MMD_SM141


title: mLSAGE_Lung_normal_TS19_MMD_SM135

description:
Developmental stage = Theiler Stage 19
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Lung, normal


title: mLSAGE_Neural_tube_normal_TS13_MMD_SM125

source_name: Neural_tube, normal


title: mLSAGE_Testis_normal_P0_MMD_SM128

source_name: Testis, normal


title: mLSAGE_Brain_normal_TS15_MMD_SM122


title: mLSAGE_Brain_normal_TS19_MMD_SM131


title: mLSAGE_Skin_normal_TS21_MMD_SM119

source_name: Skin, normal


title: mLSAGE_Kidney_normal_TS19_MMD_SM113

source_name: Kidney, normal


title: mLSAGE_Neural_tube_normal_TS13_MMD_SM126


title: mLSAGE_Testis_normal_P84_MMD_SM118


title: mLSAGE_Kidney_normal_TS20_MMD_SM124


title: mLSAGE_Brain_normal_TS25_MMD_SM111


title: mLSAGE_Brain_normal_TS17_MMD_SM121


title: mLSAGE_Skin_normal_TS21_MMD_SM120


title: mLSAGE_Endoderm_normal_TS13_MMD_SM112

source_name: Endoderm, normal


title: mLSAGE_Endoderm_normal_TS12_MMD_SM108

description:
Developmental stage = Theiler Stage 12
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Brain_normal_TS20_LCM_SM109


title: mLSAGE_Brain_normal_P84_LCM_SM110


title: mLSAGE_Embryo_normal_TS11_MMD_SM116

description:
Developmental stage = Theiler Stage 11
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Embryo, normal


title: mLSAGE_Brain_normal_TS25_LCM_SM168


title: mLSAGE_Pancreas_normal_P72_MMD_SM103


title: mLSAGE_Mammary_glands_normal_P84_MMD_SM074

description:
Other information: P84
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Mammary_glands, normal


title: mLSAGE_Liver_normal_P84_MMD_SM100


title: mLSAGE_Kidney_normal_P84_MMD_SM104


title: mLSAGE_Branchial_arch_normal_TS17_MMD_SM105

source_name: Branchial_arch, normal


title: mLSAGE_Endoderm_normal_TS13_MMD_SM107


title: mLSAGE_Embryo_normal_TS11_MMD_SM099


title: mLSAGE_Pancreas_normal_P72_MMD_SM102


title: mLSAGE_Ovaries_normal_TS22_MMD_SM093

description:
Developmental stage = Theiler Stage 22
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Small_intestine_normal_TS25_MMD_SM094


title: mLSAGE_Large_intestine_normal_TS25_MMD_SM096

source_name: Large_intestine, normal


title: mLSAGE_Brain_normal_TS20_LCM_SM092


title: mLSAGE_Embryo_normal_TS11_MMD_SM090


title: mLSAGE_Brain_normal_TS19_LCM_SM087


title: mLSAGE_Brain_normal_TS20_LCM_SM088


title: mLSAGE_Kidney_normal_P0_MMD_SM086

description:
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Stomach_normal_TS25_MMD_SM089

source_name: Stomach, normal


title: mLSAGE_Limb_normal_TS22_MMD_SM085

source_name: Limb, normal


title: mLSAGE_Kidney_normal_TS24_MMD_SM082

description:
Developmental stage = Theiler Stage 24
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Small_intestine_normal_TS20_MMD_SM095

description:
Developmental stage = Theiler Stage 20
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Brain_normal_TS13_MMD_SM081


title: mLSAGE_Testis_normal_P36_MMD_SM091


title: mLSAGE_Brain_normal_TS13_MMD_SM083


title: mLSAGE_Adrenal_glands_normal_TS22_MMD_SM079

source_name: Adrenal_glands, normal


title: mLSAGE_Large_intestine_normal_TS20_MMD_SM078


title: mLSAGE_Limb_normal_TS22_MMD_SM084


title: mLSAGE_Testis_normal_TS22_MMD_SM080


title: mLSAGE_Uterus_normal_P36_MMD_SM075

source_name: Uterus, normal


title: mLSAGE_Mammary_glands_normal_P84_MMD_SM071


title: mLSAGE_Brain_normal_P84-P90_MMD_SM098

source_name: Brain, normal


title: mLSAGE_Thymus_normal_TS23_MMD_SM057

source_name: Thymus, normal


title: mLSAGE_Brain_normal_P84-P90_LCM_SM193


title: mLSAGE_Brain_normal_TS17_LCM_SM067


title: mLSAGE_Embryo_normal_TS5_MMD_SM058

description:
Developmental stage = Theiler Stage 5
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Lung_normal_TS26_MMD_SM066

description:
Developmental stage = Theiler Stage 26
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Ovaries_normal_P36_MMD_SM076

source_name: Ovaries, normal


title: mLSAGE_Placenta_normal_TS11_MMD_SM063

source_name: Placenta, normal


title: mLSAGE_Urogenital_sinus_normal_TS24_MMD_SM054

source_name: Urogenital_sinus, normal


title: mLSAGE_Adrenal_glands_normal_P84_MMD_SM059


title: mLSAGE_Spleen_normal_TS23_MMD_SM055

description:
Developmental stage = Theiler Stage 23
This library is of the Mouse Atlas of Gene Expression Project:  http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Spleen, normal


title: mLSAGE_Placenta_normal_TS15_MMD_SM047


title: mLSAGE_Placenta_normal_TS22_MMD_SM049


title: mLSAGE_Mammary_glands_normal_P60_MMD_SM062


title: mLSAGE_Brain_normal_P84-P90_MMD_SM060


title: mLSAGE_Brain_normal_TS20_LCM_SM064


title: mLSAGE_Brain_normal_TS20_LCM_SM052


title: mLSAGE_Brain_normal_TS20_LCM_SM053


title: mLSAGE_Brain_normal_TS17_MMD_SM056


title: mLSAGE_Brain_normal_P42_MMD_SM050


title: mLSAGE_Heart_normal_TS19_MMD_SM051

source_name: Heart, normal


title: mLSAGE_Brain_normal_P27_MMD_SM040


title: mLSAGE_Bladder_normal_P84_MMD_SM037

source_name: Bladder, normal


title: mLSAGE_Testis_normal_TS24_MMD_SM044

source_name: Testis, normal


title: mLSAGE_Urogenital_sinus_normal_TS24_MMD_SM032


title: mLSAGE_Bladder_normal_TS24_MMD_SM027


title: mLSAGE_Prostate_normal_P0_MMD_SM025

source_name: Prostate, normal


title: mLSAGE_Branchial_arch_normal_TS15_MMD_SM043


title: mLSAGE_Prostate_normal_P72_MMD_SM026


title: mLSAGE_Bladder_normal_TS22_MMD_SM041


title: mLSAGE_Thymus_normal_TS26_MMD_SM022


title: mLSAGE_Spleen_normal_P84_MMD_SM012


title: mLSAGE_Pancreas_normal_P70_MMD_SM017

source_name: Pancreas, normal


title: mLSAGE_Brain_normal_P27_MMD_SM029


title: mLSAGE_Heart_normal_TS15_MMD_SM006


title: mLSAGE_Lung_normal_P0_MMD_SM021

source_name: Lung, normal


title: mLSAGE_Urogenital_sinus_normal_TS24_MMD_SM036


title: mLSAGE_Lung_normal_TS19_MMD_SM018


title: mLSAGE_Heart_normal_TS15_MMD_SM005


title: mLSAGE_Brain_normal_P20_MMD_SM031


title: mLSAGE_Heart_normal_TS20_MMD_SM002


title: mLSAGE_Heart_normal_TS19_MMD_SM004


title: NCSC

status: Public on Apr 18 2006

city: Newcastle upon Tyne

first: Maya

last: Sieber-Blum

address: Central Parkway Road

department: Institute of Human Genetics and

country: United Kingdom

institute: Newcastle University

description: I-SAGE Long kit (Invitrogen, Carlsbad, CA).

source_name: Embryonic neural crest stem cells

tag: Embryonic neural crest stem cells


title: mLSAGE_Thymus_normal_P72_MMD_SM024


title: FVB sciatic nerve

status: Public on Apr 15 2006

first: Anneloor

last: ten Asbroek

address: Meibergdreef 9

description: FVB wild-type sciatic nerves from 10 adult animals (5 male, 5 female) pooled in total RNA extraction

source_name: adult sciatic nerve


title: Rat_Normal_PVCN

status: Public on Jan 01 2006

city: Milwaukee

first: David

last: Friedland

state: WI

address: 8701 Watertown Plank Rd

department: Otolaryngology and Communication Sciences

institute: Medical College of Wisconsin

description: The posterior ventral cochlear nucleus was dissected from 40 normal, female, 45 day old, Brown Norway rat brains and total RNA extracted

data_processing: Sequences were imported into eSAGE for tag extraction and counting

source_name: Posterior Ventral Cochlear Nucleus

extract_protocol: Trizol protocol

tag: Strain

value: Brown Norway

value: 45 days

tag: Tissue

value: Brain

tag: Region

value: Posterior ventral cochlear nucleus


title: Rat_Normal_DCN

description: The dorsal cochlear nucleus was dissected from 40 normal, female, 45 day old, Brown Norway rat brains and total RNA extracted

source_name: Dorsal Cochlear Nucleus

value: Dorsal cochlear nucleus


title: FVB cultured Schwann cells

description: Primary Schwann cells cultured from FVB wild-type sciatic nerve from adult female

source_name: Primary Schwann cells culture FVB wt mouse


title: Rat_Normal_AVCN

description: The anterior ventral cochlear nucleus was dissected from 40 normal, female, 45 day old, Brown Norway rat brains and total RNA extracted

source_name: Anterior Ventral Cochlear Nucleus

extract_protocol: Trizol Protocol

value: Anterior ventral cochlear nucleus


title: D11.5 Tubular pre-implantation embryos

status: Public on Dec 31 2005

city: Beltsville

first: Le Ann

last: Blomberg

address: 10300 Baltimore Ave.

department: ANRI

institute: ARS-USDA

description: Comparison of gene expression in in vivo derived pre-implantation porcine embryos.  An attempt to elucidate mechanism involved during pre-implantation embryo development.

source_name: Porcine conceptus (sus scrofa)

tag: In vivo derived porcine tubular embryos collected at 11.5 days of gestation.  Day of AI being 0.


title: Leishmania donovani promastigotes

status: Public on Dec 20 2005

first: qiaoli

last: li

address: 800 Dongchuan Rd.

department: School of Life Sciences

institute: Shanghai Jiao Tong University

description: L. donovani promastigotes were routinely cultured at 22℃ in M199 medium(pH 7.4) supplemented with 10% heat-inactivated fetal bovine serum

data_processing: SAGE2000 (Version 4.5) software was used to extract the tags

organism: Leishmania donovani

source_name: leishmania donovani

growth_protocol: cultrued in M199 medium,pH 7.4,22℃

extract_protocol: Total RNA was extracted by Trizol RNA isolation reagent (Invitrogen, Carlsbad, California, USA)

treatment_protocol: (no special)

tag: Axenic promastigotes of leishmania donovani


title: Zebrafish ovarian follicles

status: Public on Mar 17 2006

city: Talence

first: Patrick

middle: J.

last: BABIN

address: Avenue des facultés

department: UFR Biologie

institute: Université Bordeaux

description: 50 micrograms of total RNAs were used to generate the SAGE library using the I-SAGE kit (Invitrogen)

data_processing: SAGE-tag extraction, counting and quality control were undertaken by Skuld-Tech (Monpellier, France)

organism: Danio rerio

source_name: full-grown ovarian follicles

extract_protocol: Total RNAs were extracted with Nucleospin RNA II kit (Machery-Nagel, Duren, Germany)

treatment_protocol: About 250 full-grown ovarian follicles were obtained after gentle squeezing the abdomen of five mature zebrafish females.

tag: strain

value: wild type; gender:5 females; age:sexual mature; tissue:full-grown ovarian follicles (diameter superior 0.69 mm)


title: SAGE_cortex_intact female mice

status: Public on Jan 14 2006

city: Hershey

first: Yuichiro

last: Nishida

address: 500 University Drive

institute: Penn State College of Medicine

description:
Parietal cortex were dissected from C57BL6 female mice and pooled together. Total RNA was isolated by Trizol.
Keywords = cortex
Keywords = SAGE

source_name: parietal cortex


title: SAGE_hypothalamus_intact male mice

description:
Hypothalamus were dissected from C57BL6 male mice and pooled together. Total RNA was isolated by Trizol.
Keywords = hypothalamus
Keywords = SAGE

source_name: hypothalamus


title: PAOR3 replicate 1 od 0.8

status: Public on Jan 18 2006

type: RNA

city: Seattle

first: Yannick

last: Lequette

state: WA

address: 1959 NE PACiFiC

department: Microbiology HSB -I420 BOX 357242

institute: University of Washington

description: RNA extracted from culture at optical density at 600 nm of 0.8

data_processing: standard Affymetrix procedures

label: biotin

organism: Pseudomonas aeruginosa

source_name: PAOR3 planktonic culture

tag: PAOR3 qscR knock out


title: NCP

tag: In vitro differentiated neural crest progeny.


title: SAGE_hypothalamus_intact female mice

department: Department of Anatomy and Physiology

description:
Hypothalamus were dissected from C57BL6 female mice and pooled together. Total RNA was isolated by Trizol.
Keywords = hypothalamus
Keywords = SAGE


title: differentiated mammospheres, SAGE

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E227
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=227
SCGP Sample ID:				S356
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=227#SAMPLE_334
Short description:			Differentiated mammosphere RNA extracted from the cells of mouse mammospheres induced to differentiate over a 6-day period. Mammosphere are believed to be comprised of stem/progenitor cells.
Estimated purity:				50% myoepithelial, 50% luminal
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~ 8.8x10E6
Sample volume:				5ul

source_name: Differentiated mammosphere cells, Mammary gland

growth_protocol:
Growth medium:				High glucose DMEM
Media supplements:			5% FBS
Culture conditions:			On collagen coated dishes, 37C, 5%CO2

extract_protocol:
RNA prep method:				Trizol
Amplification method:			none
Cell purification method:			mammospheres cultures induced to differentiate
Contaminating cell type:			none known
Method for estimating purity:		Use of molecular markers

treatment_protocol: Assays to confirm viability:		Undifferentiated antecedants recapitulate mammary gland development.

tag: Strain:					FVB

tag: Gender:					Female

tag: Karyotype:				Not determined


title: SAGE_cortex_intact male mice

description:
Parietal cortex were dissected from C57BL6 male mice and pooled together. Total RNA was isolated by Trizol.
Keywords = cortex
Keywords = SAGE


title: control hippocampus

status: Public on Dec 30 2005

first: Aronica

last: Eleonora

department: Neuropathology

institute: AMC

description:
We used ±5 µg poly(A)+ RNA for production of double-stranded cDNA. After the cDNA was digested with Nla III as anchoring enzyme, the 3’-terminal cDNA fragments were captured using streptavidin-coated magnetic beads (Dynal). SAGE cDNA tags (~10 bp attached to the linker) were generated by ligation of linkers to the Nla III-compatible sticky ends and subsequent BsmF I digestion (site present in linkers). After blunting of the linker-cDNA products, dimerisation and PCR amplification (30 cycles) using primers directed against linker sequences, the linkers were excised by Nla III digestion. The released ditag was purified from the excised linkers by polyacrylamide gel electrophoresis and ligated to long multi-mers of ditags (concatamers) separated by Nla III sites. The concatamers were digested with Sph I. Size separation by polyacrylamide gel electrophoresis was performed after the sample was heated for 10 min at 65 °C. A 400-1000 bp fraction was excised from gel, purified and cloned into the Sph I site of pZero-1 (Invitrogen). The resulting colonies were gridded in 96-well microtiter dishes containing Low Salt LB + Zeozine (100 µg/ml) (LB + 7.5% glycerol), grown overnight at 37°C and stored at 4°C until further use. Sequence analysis was performed using the BigDye Terminator Cycle Sequencing Kit (Perkin Elmer) and a 96-lane ABI 3100 automated sequencer (PE Biosystems).
Primary analysis of the SAGE libraries was performed with the program Usage (van Kampen et al., 2000). This program is able to do initial analyses on raw sequence data, e.g. ditag and tag extraction, tag counting, and tag identification. Tags were identified with the SAGEmap database available through NCBI (http://www.ncbi.nlm.nih.gov/SAGE), to which the program is directly linked (van Ruissen et al., 2002). Secondly, the Z test was used to compare SAGE libraries, and to do statistical analyses on tag count differences (Kal et al., 1999, Ruijter et al., 2002).

source_name: Human Hippocampus

extract_protocol: Total RNA was isolated from control hippocampus (48 years old man without history of seizures or other neurological diseases and no brain abnormalities at autopsy), using the Trizol method according to the manufacturer’s instructions (Invitrogen - Life Technologies, The Netherlands). Part of the anterior hippocampus of control and HS patients (including sectors CA1- CA4 and dentate gyrus, DG) was used.  Poly(A)+ RNA isolation, cDNA synthesis and all subsequent steps of the SAGE procedure were essentially performed as described (Velculescu et al., 1995) with minor modifications given previously (Michiels et al., 1999).

tag: Hippocampus

value: including sectors CA1- CA4 and dentate gyrus.


title: neurospheres, SAGE

status: Public on Dec 09 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Luc Sabourin (lsab@uottawa.ca; 451 Smyth Road) for analysis.
Stembase Experiment ID:			E224
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=224
SCGP Sample ID:				S331
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=224#SAMPLE_331
Short description:			Putative neural stem cells were derived from E12-E14 stiatal tissue and that was cultured for 10-12 dy s in neural stem cell media supplemented with bFGF
RNA concentration:			2 ug/ul

source_name: Neural Stem Cells, Striatal

growth_protocol:
Growth medium:				DMEM-F12
Media supplements:			d-glucose, l-glutamine, pen/strep, insulin, apotransferrin, progesterone, putrescine, selenium, Fungizone, heparin

extract_protocol: RNA prep method:				Qiagen RNEasy

tag: Strain:					C57 BL/6

tag: Gender:					Male

tag: Defining markers:				Nestin


title: undifferentiated mammospheres, SAGE

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Hassell (hassell@mcmaster.ca; Life Science Building, Rm 422; 1280 Main St. W.) for analysis.
Stembase Experiment ID:			E226
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=226
SCGP Sample ID:				S355
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=226#SAMPLE_333
Short description:			Undifferentiated mammosphere RNA. Samples contain RNA extracted from the cells of mouse mammospheres. Mammosphere are believed to be comprised of stem/progenitor cells.
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			~1x10E7
Sample volume:				5ul

source_name: Mammosphere passage 3, Mammary gland

growth_protocol:
Growth medium:				3:1 DMEM: F12
Media supplements:			B-27 supplement, bFGF & EGF, heparin
Culture conditions:			37C, 5%CO2

extract_protocol:
RNA prep method:				Trizol
Amplification method:			none
Cell purification method:			mammospheres comprise stem & progenitor cells
Contaminating cell type:			myoepithelial cells, 10%
Method for estimating purity:		Analysis of cellular markers

treatment_protocol: Assays to confirm viability:		Transplant into cleared fat pad of mice: mammary gland development recapitulated in recipient.


title: ncp, SAGE

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Luc Sabourin (lsab@uottawa.ca; 451 Smyth Road) for analysis.
Stembase Experiment ID:			E225
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=225
SCGP Sample ID:				S332
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=225#SAMPLE_332
RNA concentration:			2ug/ul

source_name: , striatal

growth_protocol:
Growth medium:				DMEM-F12
Media supplements:			d-glucose, 1-glutamine, en/strep, insulin, apotransferrin

extract_protocol: RNA prep method:				RNeasy


title: SAGE_pituitary_intact female mice

description:
Pituitary were dissected from C57BL6 female mice and pooled together. Total RNA was isolated by Trizol.
Keywords = pituitary gland
Keywords = SAGE

source_name: pituitary gland


title: AML_t(15;17)_LIB2

status: Public on Dec 01 2005

city: Evanston

first: San Ming

last: Wang

state: IL

address: 1001 University Place

department: Center for Functional Genomics

institute: ENH Research Institute, Northwestern University

description: SAGE analysis of gene expression in leukemic myeloid progenitor cells isolated from bone marrow

source_name: bone marrow, CD15+ myeloid progenitor cells

tag: Acute Myeoloid Leukemia (AML) patient sample with chromosomal translocation t(15;17)


title: Rat brain microvessel SAGE

status: Public on Dec 03 2005

city: Duluth

first: Les

last: Drewes

state: MN

address: 1035 University Drive

institute: University of Minnesota Duluth

description: Total RNA was prepared from the pooled microvessels and from the minced brain sample using RNAwiz.  The quantity and quality of the RNA was assessed by UV absorption spectrophotometry and by use of a RNA chip assay (RNA 6000 nanochip with Bioanalyzer, Agilent, Palo Alto, CA).

source_name: Rat brain microvessels

tag: Rat brain microvessels were isolated from fifty adult male Long-Evans rats (30 days old).


title: AML_t(15;17)_LIB3


title: Unfertilized eggs

status: Public on Dec 12 2005

city: Isehara City

first: Shohei

last: Horiuchi

state: Kanagawa Pref.

address: Bohseidai

department: School of Medicine

institute: Tokai University

description: LongSAGE library was constructed by standard methods with several modifications. Additional amplification step was not performed.

source_name: 200 of unfertilized eggs (C57BL/6J)


title: AML_t(9;11)_LIB3

tag: Acute Myeoloid Leukemia (AML) patient sample with chromosomal translocation t(9;11)


title: AML_t(9;11)_LIB1


title: AML_t(15;17)_LIB5


title: AML_t(8;21)_LIB5

tag: Acute Myeoloid Leukemia (AML) patient sample with chromosomal translocation t(8;21)


title: AML_t(15;17)_LIB4


title: AML_t(9;11)_LIB5

tag: Acute Myeoloid Leukemia (AML) patient sample with chromosomal translocation t(9;11). This library was constructed from a treatment-related AML cells with t(9;11).


title: AML_t(9;11)_LIB2


title: AML_t(9;11)_LIB4


title: AML_t(9;11)_LIB7


title: AML_t(8;21)_LIB4


title: AML_t(8;21)_LIB3


title: AML_INV(16)_LIB5

tag: Acute Myeoloid Leukemia (AML) patient sample with chromosomal inversion INV(16)


title: AML_t(8;21)_LIB2


title: AML_INV(16)_LIB4


title: AML_t(9;11)_LIB6


title: AML_INV(16)_LIB3


title: SAGE library from ejaculate sperm of one fertile Chinese man

status: Public on Nov 11 2005

city: Shanghai

first: Yangxing

last: Zhao

description:
Producer: Yangxing Zhao, Zhaoxia Wang and Zhongdong Qiao
The same method for spermatozoa separation was used as in that of GSM82243. Five separate ejaculates from the same volunteer were pooled together to get enough total RNA for the SAGE analysis.

data_processing: SAGE2000 (Version 4.5)

source_name: spermatozoa

extract_protocol: Total RNA of purified spermatozoa was extracted by Trizol RNA isolation reagent (Invitrogen, Carlsbad, California, USA)

tag: Human ejaculates were obtained from one healthy volunteers aged 33, who had no special medical record. The volunteer has fathered a healthy child.  And normal semen quality as assessed according to WHO criteria (1999) was applied to the ejaculate samples.


title: AML_t(8;21)_LIB1


title: AML_INV(16)_LIB1

tag: Acute Myeloid Leukemia (AML) patient sample with chromosomal inversion INV(16)


title: SAGE library from ejaculate sperm of 10 fertile Chinese men

description: The ejaculate was purified by swim-up technique to get rid of somatic contaminations (Hargreaves et al., 1998). Briefly, each liquefied semen sample was diluted with 2×volume of EBSS (Earle’s balanced salt solution) supplemented with 10% FBS and then centrifuged at 220 g for 10 min. The supernatant was transferred to another tube. The pellet was resuspended in 2ml of EBSS with 10% FBS. Both supernatant and pellet were centrifuged at 220 g for 10 min and the supernatants discarded. The pellets were combined and resuspended in 0.5 ml of EBSS with 10% FBS. This suspension was layered gently under 1ml of EBSS with 10% FBS. The tube was slanted at 45° angle and incubated at 37°C in a 5% CO2 incubator for 60 min. The swim-up sperm fraction was collected. Microscopy inspection was performed to make certain the reliability and reproducibility of this purification process. The purified spermatozoa from 10 fertile men were combined for RNA extraction.

extract_protocol: Total RNA from purified spermatozoa was extracted by Trizol RNA isolation reagent (Invitrogen, Carlsbad, California, USA)

tag: Human ejaculates were obtained from 10 healthy volunteers ranging in age from 27 to 43. They had no special medical record. All of them have fathered a healthy child.  And normal semen quality as assessed according to WHO criteria (1999) was applied to all the samples.


title: AML_INV(16)_LIB2

tag: Acute Myeoloid Leukemia(AML) patient sample with chromosomal inversion INV(16)


title: Human Pulmonary Artery Endothelial Cell Exposure to 24h Short-Term Chronic Hypoxia

status: Public on Jun 28 2005

city: Pittsburgh

middle: Gerard

last: Peters

department: Medicine

institute: University of Pittsburgh

description: Primary human pulmonary artery endothelial cells exposed to short-term chronic hypoxia for 24h

source_name: David G. Peters Ph.D.


title: Uterus_day 5 of pregnancy_implantation site

status: Public on Jul 13 2005

city: Shantou

first: Zeng-Ming

last: Yang

address: 263 Daxue Road

department: Biology

institute: Shantou University

description: Female mice on day 5 of pregnancy (day 1=day of vaginal plug) were injected with 0.1 ml of 1% Chicago blue (i.v.) and sacrificed 5 min later to collect implantation sites and inter-implantation sites, respectively. SAGE libraries were constructed from 20 microgram of total RNA from implantation sites or interimplantation sites utilizing the I-SAGE kit (Invitrogen, Gaithersburg, MD) according to the manufacturer’s recommendation.

source_name: Uterus, day 5 of pregnancy, implantation site

tag: Strain

value: Kunming White outbred strain

tag: Gender

value: female

tag: Age

value: Sexally mature

tag: Tissue

value: Uterus


title: Human HL-60 cells exposed to 2.45 GHz radiofrequency for 2 hours

status: Public on Jul 30 2005

description:
The biological effect of radiofrequency (RF) fields remains controversial. We address this issue by examining whether RF fields can cause changes in gene expression.  We used the pulsed RF fields at a frequency of 2.45 GHz that is commonly used in telecommunication to expose cultured human HL-60 cells. We used the SAGE (serial analysis of gene expression) method to measure the RF effect on gene expression at the genome level. We observed that 221 genes altered their expression after a 2-hour exposure. The number of affected genes increased to 759 after a 6-hour exposure. Functional classification of the affected genes reveals that apoptosis-related genes were among the up-regulated ones and the cell cycle genes among the down-regulated ones. We observed no significant increase in the expression of heat shock genes. These results indicate that the RF fields at 2.45 GHz can alter gene expression in cultured human cells through non-thermal mechanism.
FEBS LETTERS, 2005 (in press)

source_name: HL-60 cells exposed 2 hours

treatment_protocol: Human HL-60 cells were exposed to 2.45 GHz radiofrequency for 2 hours

tag: 2.45 GHz radiofrequency fields alter gene expression in clutured human cells.


title: Human Pulmonary Artery Endothelial Cell Exposure to 0h Short-Term Chronic Hypoxia (Control)

description: Primary human pulmonary artery endothelial cells exposed to short-term chronic hypoxia for 0h (control)


title: Human Pulmonary Artery Endothelial Cell Exposure to 8h Short-Term Chronic Hypoxia

description: Primary human pulmonary artery endothelial cells exposed to short-term chronic hypoxia for 8h


title: Uterus_day 5 of pregnancy_inter-implantation site

source_name: Uterus, day 5 of pregnancy, inter-implantation site


title: Human HL-60 cells exposed to 2.45 GHz radiofrequency for 6 hours

source_name: HL-60 cells exposed 6 hours

treatment_protocol: Human HL-60 cells were exposed to 2.45 GHz radiofrequency for 6 hours

tag: 2.45 GHz Radiofrequency fields alter gene expression in cultured human cells.


title: Aldosterone Producing Adenoma

status: Public on Oct 06 2005

city: Paris

first: Guillaume

last: Assié

institute: Inserm Institut Cochin

description:
Adrenocortical adenoma producing aldosterone.
Preoperative diagnosis of primary aldosteronism with increased aldosterone, increased aldosterone to renin ratio, lateralisation of aldosterone to cortisol ratio on adrenal venous sampling.
Histology: 10 mm, unique adenoma with no adjacent hyperplasia
Keywords = adrenocortical adenoma aldosterone

source_name: Aldosterone Producing Adenoma


title: R1 EB 9 days, SAGE

status: Public on Jul 28 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E222
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=222
SCGP Sample ID:				S359
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=222#SAMPLE_326
Short description:			9 days of an 11-point time course study of R1 embryonic stem cells and their cognate differentiated embryoid bodies. The cells are differentiating embryonic bodies from murine embryonic stem cells.
Estimated purity:				100%

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06

source_name: R1, Fetal cells

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Culturing
Contaminating cell type:			none

tag: Strain:					129/Sv x 129/Sv-CP

tag: Gender:					Male


title: Mouse R1 ES cell, SAGE

status: Public on Sep 01 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E221
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=221
SCGP Sample ID:				S358
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=221#SAMPLE_325
Short description:			R1ES: Embryonic stem cells (WT)
Estimated purity:				95-99%

source_name: ES cell line, Blastocyst

growth_protocol:
Growth medium:				0.1% gelatin
Media supplements:			high glucose, +15% HyClone FBS, Lif, NaPyruvate, nonessential aa, L-glutamine, B-mercaptoethanol

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			None
Contaminating cell type:			differentiated ES cells may be present
Method for estimating purity:		Visual inspection

treatment_protocol: Assays to confirm viability:		None, grown in normal stem cell conditions

tag: Strain:					129/SV

tag: Defining markers:				Oct4


title: Human HL-60 cells

description:
The biological effect of radiofrequency (RF) fields remains controversial. We address this issue by examining whether RF fields can cause changes in gene expression.  We used the pulsed RF fields at a frequency of 2.45 GHz that is commonly used in telecommunication to expose cultured human HL-60 cells. We used the SAGE (serial analysis of gene expression) method to measure the RF effect on gene expression at the genome level. We observed that 221 genes altered their expression after a 2-hour exposure. The number of affected genes increased to 759 after a 6-hour exposure. Functional classification of the affected genes reveals that apoptosis-related genes were among the up-regulated ones and the cell cycle genes among the down-regulated ones. We observed no significant increase in the expression of heat shock genes. These results indicate that the RF fields at 2.45 GHz can alter gene expression in cultured human cells through non-thermal mechanism.

FEBS LETTERS, 2005 (in press)

source_name: HL-60 cells

treatment_protocol: Sham treatment of 2.45GHz exposure for 2 hours

tag: Human HL-60 cells, used as normal control in studying the effects of 2.45GHz radiofrequency on gene expression.


title: Human Aortic Endothelial Cell Exposure to 0h Short-Term Chronic Hypoxia (Control)

description: Primary human aortic endothelial cells exposed to short-term chronic hypoxia for 0h (control)

tag: Primary human aortic endothelial cells


title: Human Aortic Endothelial Cell Exposure to 8h Short-Term Chronic Hypoxia

description: Primary human aortic endothelial cells exposed to short-term chronic hypoxia for 8h


title: Human Aortic Endothelial Cell Exposure to 24h Short-Term Chronic Hypoxia

description: Primary human aortic endothelial cells exposed to short-term chronic hypoxia for 24h


title: Human Gastric Cardia

status: Public on Jun 20 2005

city: Utrecht

first: Jantine

last: van Baal

address: Heidelberglaan 100

institute: University Medical Center Utrecht

description: gastric cardia biopt is taken from a metaplastic Barrett's esophagus patient

source_name: Gastric Cardia


title: Zona Glomerulosa (adjacent to an APA)

description:
Microdissected zona glomerulosa adjacent to an aldosterone producing adenoma
Preoperative diagnosis of primary hyperaldosteronism by increased aldosterone, increased aldosterone to renin ratio, lateralisation of the aldosterone to cortisol ratio after adrenal venous sampling.
Histological confirmation of a unique 10 mm adenoma; no hyperplasia of the adjacent zona glomerulosa.
Microdissection on fresh tissue with a forceps after fat cleansing: the glomerulosa comes with the adrenal capsule.
Keywords = adrenocortical adenoma aldosterone

source_name: Zona Glomerulosa (adjacent to an APA)


title: Human Squamous Esophagus

description: squamous esophagus biopt is taken from a metaplastic Barrett's esophagus patient

source_name: Squamous esophagus


title: leaf_greenhouse_rep1

status: Public on Jun 15 2005

city: Leuven

first: Bert

last: Coemans

address: Kasteelpark Arenberg 13

department: department of biosystems - division of crop biotechnics

country: Belgium

institute: Katholieke Universiteit Leuven

description:
SuperSAGE protocol was applied;

Matsumura H, Reich S, Ito A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Krüger DH, Terauchi R (2003) Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc Natl Acad Sci USA 100:15718-15723

data_processing: SAGE2000 software (Dr. K.W. Kinzler, Johns Hopkins University, Baltimore, USA)

organism: Musa acuminata

growth_protocol: standard growing conditions in greenhouse

extract_protocol: Eggermont K, Goderis I, Broekaert W (1996) High throughput RNA extraction from samples based on homogenization by reciprokal shaking in the presence of sand and glass beads. Plant Mol Biol Rep 14:273-279

treatment_protocol: no treatment applied to biological material

tag: variety

value: Tuu Gia;

tag: Leaf stage

value: 10 leafs;

value: youngest unfurled leaf;

tag: growing conditions

value: greenhouse


title: Human Barrett's Esophagus

department: Gastroenterology and Hepatology

description: Biopt is taken from a metaplastic Barrett's esophagus patient

source_name: Barrett's Esophagus


title: SAGE library generated from normal Bombyx. mori embryos

first: Huang

last: Jianhua

institute: Shanghai Institute of Plant Physiology ang Ecology

description: It would provide an opportunity to identify additional genes involved in the control of embryonic development.

source_name: mix of the developing embryos


title: AtRoot14DayMSRDX

status: Public on Jun 08 2005

city: Athens

first: Jeffrey

last: Dean

state: GA

department: Warnell School of Forest Resources

institute: University of Georgia

description: Samples run in series in the same month and year as other samples in the GSE560 experimental series.

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Prior to dosing with RDX, 40 seeds in 500mL flasks containing 200 mL MS medium were grown 14 days at 25°C under a 16-hour photoperiod with constant shaking at 85 rpm in a growth chamber.

extract_protocol: Chang, S.; Puryear, J.; Cairney, J. Simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 1993, 11, 113-116. Plants were dipped in water to rinse, roots were dissected from hypocotyls, and flash-frozen in liquid nitrogen.

treatment_protocol: 24 hour exposure to hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) (>98% purity) added to liquid Murashige-Skoog culture medium at a rate of 150 mg/L from a 0.015% (v:v) DMSO stock solution

tag: Roots from (14+1)-day old A. thaliana ecotype Columbia (WT-2) seedlings


title: radiation treated Bombyx Mori developing embryos

description: These results provide valuable information for understanding the mechanisms of radiation-induced changes in gene expression.

source_name: mix of the radiation developing embryos


title: expression profile of human sciatic nerve

status: Public on Apr 16 2005

city: Amsterdam

first: Anneloor

last: ten Asbroek

institute: Academic Medical Center

source_name: sciatic nerve

extract_protocol: Trizol extracted RNA

tag: post-mortem sciatic nerve


title: SAGE_Drosophila_Embryo

status: Public on Jun 03 2005

description:
SAGE tags collected from Drosophila Embryo
Lee S et al. Detecting novel low-abundant transcripts in Drosophila. RNA. 2005 Jun;11(6):939-46.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strain (y: cn bw sp) embryo


title: Normal Rat Lung

status: Public on Mar 18 2005

first: Yong Qing

address: 650 South Wanping Rd

department: Shanghai Research Institute of Acupuncture

institute: Shanghai University of Traditional Chinese Medicine

description:
SAGE profile of the normal male rat (Sprague Dawley) lung with linker sequences removed. Rats weighted 250 grams and were 50 days old.
Keywords = Rat
Keywords = Lung

source_name: Lung


title: Bovine granulosa cells from subordinate follicles

status: Public on Apr 30 2005

city: Glasgow

first: Paul

last: Baker

address: Bearsden Road

department: Faculty of Veterinary Medicine

institute: University of Glasgow

description:
Granulosa cells harvested from largest subordinate follicles belonging to the first follicle wave of the estrous cycle. Follicles were dissected from ovaries following slaughter of 4 Holstein cows at 2.6 days after wave emergence. Total RNA extracted from granulosa cells of the 4 follicles was pooled for generation of the SAGE library..
Keywords = Bovine Reproduction
Keywords = Ovary
Keywords = dominant follicle selection
Keywords = Granulosa cell

organism: Bos taurus

source_name: Bovine granulosa cells


title: SAGE_Drosophila_Pooled_Set

description:
Pooled set - embryo (0 to 24 hour), larvae (2nd and 3rd day), pupae (3rd day), and young and aged adults (10 males and 10 females, up to 10 day)
Lee S et al. Detecting novel low-abundant transcripts in Drosophila. RNA. 2005 Jun;11(6):939-46.

source_name: Drosophila melanogaster strain (y: cn bw sp) pooled set


title: Bovine granulosa cells from cohort follicles

description:
Granulosa cells harvested from largest cohort follicles growing in the first follicle wave of the estrous cycle. Follicles were dissected from ovaries following slaughter of 4 Holstein cows at 1.3 days after wave emergence. Total RNA extracted from granulosa cells of the 4 follicles was pooled for generation of the SAGE library.
Keywords = Bovine Reproduction
Keywords = Ovary
Keywords = dominant follicle selection
Keywords = Granulosa cell


title: expression profile of human Schwann cells cultured from a sural nerve biopsy

description: Primary Schwann cells, cultured from sural nerve

source_name: cultured Schwann cells

extract_protocol: Trizol extracted RNA from cultured cells

tag: Schwann cells cultured in vitro, from a healthy female donor


title: bovine CD8 lymphocytes

status: Public on Feb 04 2005

city: Ames

first: John

middle: D.

last: Neill

state: IA

address: 2300 Dayton Ave.

institute: National Animal Disease Center

description: CD8+ lymphocytes were isolated from bovine blood by positive mAb selection.  This library represents mRNA from lymphocytes pooled from 4 animals

source_name: bovine circulating CD8 lymphocytes


title: SAGE_Drosophila_Testis

description: Testis from testicular tissue of adult males

source_name: Lee S et al. Detecting novel low-abundant transcripts in Drosophila. RNA. 2005 Jun;11(6):939-46.


title: SAGE_Drosophila

description:
Keywords = SAGE
Keywords = novel transcript
Keywords = Drosophila
Keywords = genome
Keywords = EST
Keywords = low abundant
Lee S et al. Detecting novel low-abundant transcripts in Drosophila. RNA. 2005 Jun;11(6):939-46.

source_name: embryo, embryo with radiation, larvae, pupae, male and female adults, and testis


title: Bovine granulosa cells from dominant follicles

description:
Granulosa cells harvested from dominant follicles belonging to the first follicle wave of the estrous cycle. Follicles were dissected from ovaries following slaughter of 4 Holstein cows at 2.6 days after wave emergence. Total RNA from granulosa cells of the 4 follicles was pooled for generation of the SAGE library.
Keywords = Bovine Reproduction
Keywords = Ovary
Keywords = dominant follicle selection
Keywords = Granulosa cell


title: EPI-NCSC

status: Public on Apr 18 2006

city: Newcastle upon Tyne

first: Maya

last: Sieber-Blum

address: Central Parkway Road

department: Institute of Human Genetics and

institute: Newcastle University

description: I-SAGE Long kit (Invitrogen, Carlsbad, CA).

source_name: Epidermal neural crest stem cells

tag: Epidermal neural crest stem cells


title: PBEC_PAO1

status: Public on Feb 03 2005

first: Joost

last: Vos

address: Van der Boechorststraat 7

department: Molecular Cell Biology and Immunology

institute: Vrije Universiteit Medisch Centrum

description:
SAGE library derived from primary human bronchial epithelial cells stimulated with heat-inactivated Pseudomonas aeruginosa (strain PAO1); the RNA used for these libraries was extracted from bronchial epithelial cells derived from 7 donors 6 hours after stimulation. Library was constructed at the department of Medical Pharmacology, LACDR, Leiden University Medical Center.
Keywords = epithelial cells
Keywords = bacterial infection
Keywords = inflammation

source_name: primary bronchial epithelial cells


title: Lentinula edodes - Parent A of strain L54

status: Public on Jan 20 2005

city: Shatin

first: Hoi Shan

last: Kwan

state: Hong Kong SAR

institute: The Chinese University of Hong Kong

description: Gene expression profile at dikaryotic mycelial stage of parent A of L54 grown on sawdust.

organism: Lentinula edodes

source_name: Dikaryotic mycelium of parent A of Lentinula edodes L54 grown on sawdust


title: PBEC_IL1beta/TNFalpha

description:
SAGE library derived from primary human bronchial epithelial cells stimulated with the pro-inflammatory cytokines IL1beta and TNFalpha; the RNA used for these libraries was extracted from bronchial epithelial cells derived from 7 donors 6 hours after stimulation. Library was constructed at the department of Medical Pharmacology, LACDR, Leiden University Medical Center.
Keywords = epithelial cells
Keywords = bacterial infection
Keywords = inflammation

organism: Homo sapiens


title: PBEC_unstimulated

description:
SAGE library derived from primary (unstimulated) human bronchial epithelial cells ; the RNA used for these libraries was extracted from bronchial epithelial cells derived from 7 donors.
Library was constructed at the department of Medical Pharmacology, LACDR, Leiden University Medical Center.
Keywords = epithelial cells
Keywords = bacterial infection
Keywords = inflammation


title: Lentinula edodes - parent B of strain L54

description: Gene expression profile at dikaryotic mycelial stage of parent B of L54 grown on sawdust.

source_name: Parent B of L54 at dikaryotic mycelium grown on sawdust


title: B6_Total_Testis_1

status: Public on Mar 15 2005

city: Prague

first: Petr

last: Divina

address: Videnska 1083

department: Mammalian Molecular Genetics

country: Czech Republic

institute: Institute of Molecular Genetics, Academy of Sciences

description:
Testes from a single 9-weeks-old male of C57BL/6J mouse strain.
Seminiferous tubules were released from tunica and total RNA was isolated with TRIzol.
Library was constructed from total RNA using MicroSAGE protocol.
Linker tags and all 1-bp linker tag variations were removed.
Keywords = testis
Keywords = SAGE

source_name: testis


title: B6_Total_Testis_2

description:
Testes from three 9-weeks-old males of C57BL/6J mouse strain.
Seminiferous tubules were released from tunica, total RNA was isolated with TRIzol and equal weight amounts of total RNA were pooled.
Library was constructed from total RNA using MicroSAGE protocol.
Linker tags and all 1-bp linker tag variations were removed.
Keywords = testis
Keywords = SAGE


title: Lentinula edodes - dikaryotic mycelium L54

description: Gene expression profile at dikaryotic mycelial stage of L. edodes. Dikaryotic mycelium grown on PDA plate have different gene expression profile of that grown on sawdust.

source_name: Dikaryotic mycelium of Lentinula edodes strain L54 grown on potato dextrose agar (PDA) plate


title: SAGE_CD34+

status: Public on Mar 01 2005

first: San Ming

last: Wang

institute: ENH Research Institute, Northwestern University

description:
Human bone marrow CD34+ cells
The pattern of gene expression in human CD34+ stem/progenitor cells. PNAS 98(24):13966-13971, 2001
Keywords = SAGE
Keywords = GLGI
Keywords = gene
Keywords = expression
Keywords = EST
Keywords = UTR
Lot batch =

source_name: Human bone marrow CD34+ cells


title: Lentinula edodes - dikaryotic mycelial stage

description: Gene expression profile at dikaryotic mycelial stage of L. edodes shows cell structure and defence are important for dikaryotic mycelial growth.


title: Diff

status: Public on Nov 30 2004

city: Villeurbanne Cedex

first: Olivier

last: Gandrillon

address: 16 rue Raphael Dubois

institute: Universite' Claude Bernard Lyon I

description: RNA samples from two cell cultures were prepared,  one for self-renewing T2EC cells and one for T2EC cells induced to differentiate for 24 h. Both cultures were originated from the same cell preparation and divided just before the onset of differentiation. The differentiation process was validated by real-time PCR quantification of betaA globin mRNA, before proceeding with the construction of the libraries

organism: Gallus gallus

source_name: erythroid progenitors cells induced to differentiate for 24 hours


title: SR

source_name: erythroid progenitors cells


title: Microvascular endothelial cells cultured on fibronectin and exposed to sustained high shear stress.

status: Public on Jan 14 2005

city: Vienna

first: Gürkan

last: Sengoelge

address: Waehringer Guertel 18-20

department: Medicine/Division of Nephrology

institute: Medical University Vienna

description:
Pulmonary microvascular endothelial cells were cultured on the inner surface of fibers (each 700 µm inner diameter) coated with native-fibronectin in hollow-fiber cartridges (FiberCell Systems, Inc.). Duration of shear stress application was 10 days. Shear stress was gradually increased to 17 dyne/cm2.
Keywords = microvascular endothelial cells
Keywords = chronic shear stress

source_name: Pulmonary microvascular endothelial cells in culture.


title: mouse testis BDF1 (29 mo)

status: Public on Jan 09 2005

anchor: RsaI

city: Matsumoto

first: Junjie

last: Yao

state: Nagano

address: Asahi 3-1-1

department: Aging and Adaptation

institute: Shinshu university

description:
5 male BDF1 mice, aged 29 months, were used in the experiment. RNA from all five animals was pooled and used as input in the SAGE procedure.
Keywords = mouse
Keywords = testis
Keywords = aging

source_name: testis 29-month-old male BDF1 mice


title: Old Mouse Heart

status: Public on Dec 31 2004

city: Baltimore

first: Kenneth

middle: R.

last: Boheler

address: 5600 Nathan Shock Drive

department: GRC

institute: National Institute on Aging, NIH

description:
Male C57Bl/6 Mice, 24 months old.
Total number of 54,236 SAGE tags sequenced. SAGE tags analyzed after clean-up (extraction of poly(A) tags, linker-generated tags, and tags originated from clones producing 4 tags or less).

source_name: Heart


title: Rat - Superior Olivary Complex (SOC)

status: Public on Dec 13 2004

city: Kaiserslautern

first: Hans Gerd

last: Nothwang

institute: University of Kaiserslautern

description:
SAGE profile of the rat superior olivary complex with linker sequences removed. Rats were 60 days old (P60).
Keywords = superior olivary complex
Keywords = SOC

source_name: superior olivary complex


title: SAGE of skeletal muscle of intact mice

status: Public on Jan 06 2005

city: Quebec City

first: Andre

last: Boivin

state: Quebec

address: 2705 Boul. Laurier

department: SAGE Laboratory

institute: Laval University Hospital Center Research Center

description:
Gastrocnemius muscle were dissected from 10 C57BL6 male mice and pooled together. Total RNA was isolated by Trizol.
Keywords = mouse, skeletal muscle
Keywords = skeletal muscle

source_name: skeletal muscle (gastrocnemius)


title: SAGE of skeletal muscle of adrenalectomized mice 24 hours after an IP injection with cortisol (0.1mg)

description:
Ten mice were adrenalectomized, and received an IP injection of cortisol (0.1mg) 24h before experiment.
Gastrocnemius muscle were dissected from 10 C57BL6 male mice and pooled together.
Total RNA was isolated by Trizol.
Keywords = skeletal muscle
Keywords = glucocorticoids


title: mouse testis BDF1 (3 mo)

description:
5 male BDF1 mice, aged 3 months, were used in the experiment. RNA from all five animals was pooled and used as input in the SAGE procedure.
Keywords = mouse
Keywords = testis
Keywords = aging

source_name: testis 3-month-old male BDF1 mice


title: mouse testis SAMP1 (14 mo)

description:
5 male SAMP1 mice, aged 14 months, were used in the experiment. RNA from all five animals was pooled and used as input in the SAGE procedure.
Keywords = mouse
Keywords = testis
Keywords = aging

source_name: testis 14-month-old male SAMP1 mice


title: SAGE of skeletal muscle of adrenalectomized mice 3 hours after an IP injection with cortisol (0.1mg)

description:
Ten mice were adrenalectomized, and received an IP injection of cortisol (0.1mg) 3h before experiment.
Gastrocnemius muscle were dissected from 10 C57BL6 male mice and pooled together.
Total RNA was isolated by Trizol.
Keywords = skeletal muscle
Keywords = glucocorticoids


title: SAGE of skeletal muscle of adrenalectomized mice

description:
Gastrocnemius muscle were dissected from 10 C57BL6 male mice and pooled together. Total RNA was isolated by Trizol.
Keywords = skeletal muscle
Keywords = adrenalectomy


title: LongSAGE of mouse tails

status: Public on Jan 03 2005

city: Neuherberg

first: Matthias

last: Wahl

address: Ingolstaedter Landstrasse 1

department: Institute of Developmental Genetics

institute: GSF - National Research Center for Environment and Health

description: microdissected embryonic mouse tails

source_name: microdissected embryonic mouse tails


title: C22 sciatic nerve (CMT1A model)

status: Public on Nov 13 2004

address: Meibergdreef 9

description:
mRNA samples from transgenic mice overexpressing human PMP22; half from C57Bl/6 and half from FVB mice. Average age 10 weeks, ranging from 6-20 weeks
Lot batch =

source_name: sciatic nerve


title: normal sciatic nerve

description:
mRNA samples were half from C57Bl/6 and half from FVB mice. Average age 10 weeks, ranging from 6-20 weeks
Lot batch =


title: Human Glomerular Endothelial Cell

description:
Tissue from macroscopically healthy parts of nephrectomized kidneys. Endothelial cells were purified from the cell outgrowth of glomeruli twice using CD31 magnetic beads and cultured on fibronectin coated surface. Cells were not passaged more than eight times and stained with vWf, CD31, and after stimulation with TNF alpha also with CD62E/P.
Protocol according to MicroSAGE adaptation of Velculescu, V. E., Zhang,
L.,Vogelstein, B., and Kinzler, K. W. (1995) Serial
Analysis of Gene Expression. Science 270, 484-487.
Anchor enzyme: NlaIII.

source_name: Human glomeruli


title: OSJNGd

status: Public on Nov 08 2004

city: Tucson

first: Carol

last: Soderlund

state: AZ

address: 303, Forbes Building

department: BIO5 Institute

institute: University of Arizona

description:
Library: OSJNGd,
Treatment: C9240-1,
Reaction: Resistant,
Time Point: 24 hr after infection with fungus,
Tissue: 21 days leaf
Tag extraction: Ditags are rejected if they do not start and end with CATG and the length is not between 40-43 bases. Tags are only rejected if they contain one or more N's. View quality of tags at http://www.mgosdb.org/sage.
Keywords = Oryza Sativa
Keywords = LongSAGE
Keywords = Rice blast disease
Keywords = OSJNGd
Keywords = MGOS
Lot batch =

organism: Oryza sativa Japonica Group

source_name: 21 days leaf of Oryza sativa subsp. japonica cultivar Nipponbare


title: OSJNGb

description:
Library: OSJNGb,
Treatment: Che8061,
Reaction: Suceptible,
Time Point: 24 hrs after infection with fungus,
Tissue: 21 days leaf
Tag extraction: Ditags are rejected if they do not start and end with CATG and the length is not between 40-43 bases. Tags are only rejected if they contain one or more N's. View quality of tags at http://www.mgosdb.org/sage.
Keywords = Oryza Sativa
Keywords = LongSAGE
Keywords = Rice blast disease
Keywords = OSJNGb
Keywords = MGOS
Lot batch =


title: OSJNGf

description:
Library: OSJNGf,
Treatment: Water +Tween20 (0.1%),
Reaction: Normal ,
Time point: 24 hr after water spray,
Tissue: 21 days leaf
Tag extraction: Ditags are rejected if they do not start and end with CATG and the length is not between 40-43 bases. Tags are only rejected if they contain one or more N's. View quality of tags at http://www.mgosdb.org/sage.
Keywords = Oryza Sativa
Keywords = LongSAGE
Keywords = Rice blast disease
Keywords = OSJNGf
Keywords = MGOS
Lot batch =


title: MG_SGa

description:
Library: MG_SGa,
Treatment: Fungus grown on a minimum medium [0.2% (w/v) yeast extract, and 1% (w/v) Sucrose at 28°C at 200 rpm],
Reaction: Liquid grown mycelium,
Time point: 3 days,
Tissue: 3 days old mycelia
Tag extraction: Ditags are rejected if they do not start and end with CATG and the length is not between 40-43 bases. Tags are only rejected if they contain one or more N's. View quality of tags at http://www.mgosdb.org/sage.
Keywords = Magnaporthe Grisea
Keywords = LongSAGE
Keywords = Rice blast disease
Keywords = MG_SGa
Keywords = MGOS
Lot batch =

organism: Pyricularia oryzae 70-15

source_name: 3 days old mycelia from Magnaporthe grisea (strain 70-15)


title: OSJNGg

description:
Library: OSJNGg,
Treatment: Che8061,
Reaction: Susceptible,
Time point: 96 hr after infection with fungus,
Tissue: 21 days leaf
Tag extraction: Ditags are rejected if they do not start and end with CATG and the length is not between 40-43 bases. Tags are only rejected if they contain one or more N's. View quality of tags at http://www.mgosdb.org/sage.
Keywords = Oryza Sativa
Keywords = LongSAGE
Keywords = Rice blast disease
Keywords = OSJNGg
Keywords = MGOS
Lot batch =


title: P92 Cerebellum

status: Public on Oct 26 2004

city: Columbus

first: Magdalena

last: Popesco

state: OH

institute: The Ohio State Universiy

description:
C57BL6/J male mouse was sacrificed and the cerebellum was quickly removed. Total RNA was isolated using Trizol. For the creation of the library, 40 micrograms of total RNA was used. cDNA was synthesized on oligo dT beads.
Enzyme: NlaIII
Vector: pZER0-1

organism: Mus musculus

source_name: P92 C57BL6/J male mouse cerebellum


title: P810 cerebellum #2

description:
C57BL6/J male mouse was sacrificed and the cerebellum was quickly removed.  Total RNA was isolated using Trizol.  For the creation of the library, 40 micrograms of total RNA was used. cDNA was synthesized on oligo dT beads.
Enzyme: NlaIII
Vector: pZERO-1

source_name: P810 C57BL6/J male mouse cerebellum


title: Purified blood reticulocytes

status: Public on Oct 23 2004

city: Montpellier

first: David

last: Piquemal

address: 1682, rue de la Valsière

institute: ACOBIOM

description:
Reticulocytes were purified from fresh blood samples obtained from 10 healthy adult volunteers (5 women and 5 men) after informed consent. The donors had normal blood cell counts, blood smears, hemoglobin electrophoresis, red cells membrane resistance tests and no biological evidence of hemolysis.
Whole blood samples were centrifuged, the supernatant and the buffy coat containing white blood cells (WBC) and platelets were removed. The red cells pellet was then purified using the method described by Brun et al.
Purity, assessed by Hematology  Flow Cytometer was 1 leukocyte per 15 millions RBC and efficiency of purification process was 99.8% and 1 platelet per 10 000 RBC.

source_name: Blood reticulocytes from ten healthy adult


title: U937 differentiated cells

description:
U937 cells (ATCC CRL-1593.2 Rockville MD, USA) were grown in RPMI 1640 (Life Technologies, Cergy-Pontoise, France) supplemented with 10% fetal calf serum. Cell cultures were checked for the absence of mycoplasma contaminations (Mycoplasma Detection kit, Boehringer Mannheim, Meylan, France) and performed without antibiotics to avoid masking silent bacterial contaminations.
U937 cells are treated with TTNPB (0.1 µM), LGD1069 (1 µM) and vitamin D (0.1 µM). Cells seeded at a density of 2x105 cells/ml were collected 48 h later. The percentage of G0/G1 cells was near 80% for differentiating cells.

Keywords = U937 cells
Keywords = Vitamin D
Keywords = 9-cis retinoic acid
Keywords = TTNPB
Keywords = 48h treated
Lot batch = ATCC CRL-1593.2

source_name: U937 cell line


title: P810  Cerebellum #1

description:
C57BL6/J male mouse was sacrificed and the cerebellum was quickly removed. Total RNA was isolated using Trizol. For the creation of the library, 40micrograms of total RNA was used. cDNA was synthesized on oligo dT beads.
Enzyme: NlaIII
Vector: pZERO-1


title: P150 Cerebellum

description:
C57BL6/J male mouse was sacrificed and the cerebellum was quickly removed. Total RNA was isolated using Trizol. For the creation of the library, 40 micrograms of total RNA was used. cDNA was synthesized on oligo dT beads.
Enzyme: NlaIII
Vector: pZERO-1

source_name: P150 C57BL6/J male mouse cerebellum


title: Lentinula edodes - primordial stages L54

status: Public on Sep 27 2004

description: Gene expression profile at primordial stage of L. edodes shows that cellular differentiation are important for primordial growth.

source_name: Primordium of Lentinula edodes strain L54 grown on potato dextrose agar (PDA) plate


title: P840 cerebellum

description:
C57BL6/J mice (2 males) were sacrificed and cerebella were quickly removed. Total RNA was isolated using Trizol. For the creation of the library, 40 micrograms of total RNA was used. cDNA was synthesized on oligo dT beads.
Enzyme: NlaIII
Vector: pZERO-1
Restriction sites 1 & 2: Sph1
Library treatment: non-normalized

source_name: P840 C57BL6/J mouse cerebellum