title: ATP1-111/ATP1-111 Cells 27 hours following mtDNA loss compared to ATP1-111/ATP1-111 cells with mtDNA

city: Seattle

first: Daniel

last: Gottschling

address: 1100 Fairview Avenue N., Mailstop A3-025

department: Division of Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: average over 5 samples,  3 and 2 biological replicates

hyb_protocol: Hybridization was carried out for 16 hours at 63 degrees celsius in 0.2% SDS/3X SSC.  Slides were then washed with 1x SSC/0.03% SDS, then 1x SSC, then 0.2x SSC, then 0.05x SSC and then dried.

scan_protocol: Following cohybridization to the chip, a fluorescent image of a microarray was collected at both emission wavelengths using a GenePix 4000 fluorescence scanner (Axon Instruments, Inc., Foster City, Calif.), and image analysis was performed using GenePix Pro microarray acquisition and analysis software

data_processing: LOWESS normalized using agilent software (Genespring 7)

label: Cy5, Cy3

source_name: ATP1-111 cells with intact mtDNA

label_protocol: labeled cDNA targets were prepared by reverse transcription of 2 µg of mRNA using oligo(dT)18 primer in the presence of 0.2 mM 5-(3-aminoallyl)-2'-deoxyuridine 5'-triphosphate (Sigma-Aldrich Company, St. Louis, Mo.), 0.3 mM dTTP, and 0.5 mM each dATP, dCTP, and dGTP. Following cDNA synthesis, either Cy3 or Cy5 monoreactive fluor (Amersham Life Sciences, Arlington Heights, Ill.) was covalently coupled to the cDNA-incorporated aminoallyl linker in the presence of 50 mM sodium bicarbonate (pH 9.0).

growth_protocol: Cells were grown in YEPD medium at or below an OD of 1.0 for the duration of the experiment

extract_protocol: Total RNA was extracted using acid phenol

source_name: ATP1-111 cells 27 hours following loss of the mtDNA by treatment with 30micrograms/ml ethidum bromide for 6 hours


title: Cells 27 hours following repression of NAR1 expression compared to cells expressing NAR1

status: Public on Mar 24 2009

type: RNA

state: WA

country: USA

description: average over 6 samples, 3 biological replicates per dye swap

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Cells expressing NAR1 grown in 50 nanomolar estradiol

tag: strain

label: Cy3, Cy5

source_name: Cells 27 hours following repression of NAR1 by transfer from medium with 50 nanomolar estradiol to medium containing 2 nanomolar estradiol


title: 63T (expression)

city: Boston

first: Rameen

last: Beroukhim

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: Per manufacturer's instructions

scan_protocol: Agilent Microarray Scanner Bundle

data_processing: Signal intensities were determined using J-express, filtered to remove genes with low signal intensity, batch corrected, and mean-centered across the tumor set.

organism: Homo sapiens

source_name: endometrial cancer

label_protocol: Per manufacturer's instructions

extract_protocol: RNA was isolated from tissue or cell pellets using Rneasy kit (Qiagen).

tag: gender

value: F

tag: histologic type

value: endometrioid

tag: metastatic phenotype

value: FIGO I/II and no recurrence

source_name: Stratagene Universal RNA


title: 31T (Xba240)

type: genomic

hyb_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

scan_protocol: Standard Affymetrix protocol

data_processing: Genotyping was performed using Affymetrix Genotyping Tools Version 2.0.  dChip was used to normalize probe-level signal intensities to a baseline array with median intensity using invariant set normalization and obtain SNP-level signal intensities using a model-based (PM/MM) method,

label: biotin

molecule: genomic DNA

label_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

extract_protocol: biotin

treatment_protocol: Genomic DNA was isolated from tissue or cell pellets using SDS/proteinase K followed by phenol/chloroform and isopropanol precipitation, and quantified using Picogreen.

value: FIGO III/IV or recurrence


title: 306T (Xba240)


title: 262T (expression)


title: 4553/4555/4557/4559

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
This sample consists of four replicate RNA extractions performed of each genotype using independent pools of plants.
tfIIs1#1 (Cy5) vs. Col-0#1 (Cy3)
Col-0#2 (Cy5) vs. tfIIs1#2 (Cy3) dye-swap
tfIIs1#3 (Cy5) vs. Col-0#3 (Cy3)
Col-0#5 (Cy5) vs. tfIIs1#4  (Cy3) dye-swap
The data were normalized over all 4 hybridizations to obtain one, single log-ratio(Sample/Reference).

hyb_protocol: For each color 10 pmol incorporated dye was fragmented and resuspended in 500 ml hybridization solution (Agilent).The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 60ºC.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent) using the `extended dynamic range' (scanner control software v7 update) and images were processed with the Feature Extraction Software version 9.5 (Agilent).

data_processing: Empty, control spots, and spots with signals below the background in all arrays and in both channels (according to gIsPosAndSignif and rIsPosAndSignif features obtained from the Agilent Feature Extraction software v9.5.1.1) were removed prior to the analysis.  The Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal from Agilent Feature Extraction v9.5.1.1) were used for the data analysis.  Using Limma (Bioconductor package http://bioconductor.org/packages/2.1/bioc/html/limma.html), a linear model was fitted and based on the resulting coefficients, contrasts Sail versus Col-0 were fitted.

organism: Arabidopsis thaliana

source_name: tfIIs

label_protocol: Probes were prepared from 1 µg total RNA using the Low RNA input Fluorescent Linear Amplification Kit-plus for dual color (Agilent). Probes were verified for amplification yield and incorporation efficiency by measuring the DNA concentration at 280 nm, Cy5 incorporation at 650 nm using a Nanodrop.

extract_protocol: RNA was extracted from 10-day old Col-0 and tfIIs seedlings using the RNeasy Plant Mini Kit (Qiagen).

tag: T-DNA insertion in the Arabidopsis TFIIS gene (ecotype Col-0), confirmed by PCR. RNA was isolated from 10d seedlings.

label_protocol: Probes were prepared from 1 µg total RNA using the Low RNA input Fluorescent Linear Amplification Kit-plus for dual color (Agilent). Probes were verified for amplification yield and incorporation efficiency by measuring the DNA concentration at 280 nm, Cy3 incorporation at 550 nm.

tag: Arabidopsis thaliana (ecotype Col-0) - reference for the T-DNA insertion mutant. RNA was isolated from 10d seedlings.


title: Wild-type Cells 19 hours following mtDNA loss compared to Wild-type cells with mtDNA

source_name: WT cells with intact mtDNA

source_name: WT cells 19 hours following loss of mtDNA by treatment with 30micrograms/ml ethidum bromide for 6 hours


title: Wild-type Cells 27 hours following mtDNA loss compared to Wild-type cells with mtDNA

source_name: WT cells 27 hours following loss of mtDNA by treatment with 30micrograms/ml ethidum bromide for 6 hours


title: Wild-type Cells 11 hours following mtDNA loss compared to Wild-type cells with mtDNA

source_name: WT cells 11 hours following loss of mtDNA by treatment with 30micrograms/ml ethidum bromide for 6 hours


title: 5T (expression)


title: 37T (expression)


title: 32T (expression)

value: non-endometrioid


title: 4T (expression)


title: 290T (Xba240)


title: day6_siRNA_PPARgrep3

city: Singapore

first: Vinsensius

middle: B

last: Vega

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: The standard Illumina protocol was followed

data_processing: rank invariant normalization, background correction

organism: Mus musculus

source_name: 3T3-L1 fibroblasts (ATCC, CL-173)

label_protocol: cRNA was sybthezised using the Ambion's cRNA kit.

extract_protocol: Total RNA was extracted directly from the cells using the Qiagen RNeasy kit (Qiagen).

treatment_protocol: 3T3-L1 cells were transfected using the LipofectAMINE RNAimax reagent (Invitrogen) according to the manufacturerÆs protocol. Final concentration of siRNA was 50nM. SMARTpool siRNA and negative control siRNA (siCONTROL non-targeting pooled, Dharmacon) were used. Transfected 3T3-L1 fibroblasts were differentiated into adipocytes by treating confluent cells with 0.5mM isobutylmethylxanthine (IBMX) and 0.25?M dexamethasone for 48hrs and then with insulin (5?g/ml) and 1?M Rosiglitazone for 48hrs. Media was replaced every 2 days. Cells were cultured and harvested on day -2, 0, 1, 2, 3, 4, 5, 6 days in relation to rosiglitazone treatment.  Three independent biological replicates were collected.

tag: fibroblasts


title: 41T (expression)


title: 288T (Xba240)


title: L1 LMS

city: Lund

first: Mef

last: Nilbert

state: Skåne

address: Barngatan 2B

department: Oncology

country: Sweden

institute: Lund University

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C51

hyb_protocol: Hybridized and washed as described in Jonsson et al. (Oncogene 2007)

scan_protocol: Scanned in Agilent Microarray scanner

data_processing: Image analysis was performed using Genepix v4.0. Resultsfile were uploaded into BASE where they were filtered and pop-lowess normalized

source_name: LMS tumor tissue

label_protocol: Labeling was done with Invitrogens aCGH Bioprime Genomic labeling

extract_protocol: Genomic DNA was extracted using the Wizard« Genomic DNA Purification Kit (Promega, Madison, WI, USA) followed by a phenol-chloroform purification.

tag: pleomorphic subtype

value: leiomyosarcoma

tag: tissue

value: soft tissue sarcoma of the extremity, primary tumor, fresh frozen

source_name: Promega reference male DNA

value: pooled lymphoblastoid genomic DNA from ten male individuals


title: 293T (Xba240)


title: gcn4deletion_3AT_rep#3

status: Public on Mar 01 2010

city: Indianapolis

first: Ron

last: Wek

state: IN

address: 635 Barnhill Dr. MS4065

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description: Gene expression data from yeast.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on HGU133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Affymetrix Gene Chip Operating Software (GCOS) using the MAS 5.0 algorithm using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: gcn4 deletion, 3AT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix, 2004).

growth_protocol: Cells were cultured in synthetic medium (SD) containing 2% dextrose and 0.5% ammonium sulfate and supplemented with all amino acids except histidine (SC).

extract_protocol: Total RNA was purified using the hot phenol method.

treatment_protocol: Microarray analysis was carried out using RNA prepared from cells treated for 1 hour with 10 mM 3-amino-1,2,4-triazole (3-AT), 200 nM rapamycin, or no stress, as indicated.

tag: treatment

tag: genotype

value: gcn4 deletion


title: 31T (expression)


title: 272T (Xba240)


title: Wild-type Cells 3 hours following mtDNA loss compared to Wild-type cells with mtDNA

source_name: WT cells 3 hours following loss of mtDNA by treatment with 30micrograms/ml ethidum bromide for 6 hours


title: 30T (expression)


title: 3657 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C50

source_name: UPS tumor tissue

value: undifferentiated pleomorphic sarcoma


title: day6_siRNA_PPARgrep2

scan_protocol: The standard Illumina protocol was followed


title: 2697 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C49


title: 262T (Xba240)


title: 279T (Xba240)


title: day6_siRNA_PPARgrep1


title: 290T (expression)


title: day6_siRNA_neg_rep3


title: 256T (Xba240)


title: 279T (expression)


title: 247T (Xba240)


title: 244T (Xba240)


title: 234T (Xba240)


title: 306T (expression)


title: day6_siRNA_neg_rep2


title: 1518 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C45


title: 1788 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C46


title: 2201 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C47


title: 2552 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C48


title: day5_siRNA_PPARg_rep2


title: 225T (expression)


title: day6_siRNA_neg_rep1


title: 1118 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C44


title: day5_siRNA_PPARg_rep3


title: 244T (expression)


title: 225T (Xba240)


title: 235T (Xba240)


title: 206T (expression)


title: 214T (Xba240)


title: day5_siRNA_neg_rep2


title: 172T (expression)


title: 1081 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C42


title: 159T (expression)


title: day5_siRNA_PPARg_rep1


title: 1074 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C40


title: 141T (expression)


title: 213T (Xba240)


title: day5_siRNA_neg_rep1


title: 206T (Xba240)


title: 1098 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C43


title: day5_siRNA_neg_rep3


title: 1080 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C41


title: 14T (expression)


title: 1065 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C39


title: 202T (Xba240)


title: day4_siRNA_PPARg_rep3


title: 1058 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C38


title: 128T (expression)


title: 113T (expression)


title: 111T (expression)


title: 201T (Xba240)


title: day4_siRNA_neg_rep3


title: day4_siRNA_PPARg_rep1


title: 129T (expression)


title: 934 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C36


title: day4_siRNA_PPARg_rep2


title: 1030 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C37


title: 110T (expression)


title: 177T (Xba240)


title: 192T (Xba240)


title: day4_siRNA_neg_rep2


title: 920 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C34


title: day4_siRNA_neg_rep1


title: 185T (Xba240)


title: 172T (Xba240)


title: 922 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C35


title: 878 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C33


title: day3_siRNA_PPARg_rep3


title: 108T (expression)


title: 168T (Xba240)


title: 162T (Xba240)


title: 14T (Xba240)


title: day3_siRNA_PPARg_rep2


title: 161T (Xba240)


title: day3_siRNA_PPARg_rep1


title: 104T (expression)


title: 844 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C31


title: 10T2 (expression)


title: 848 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C32


title: day3_siRNA_neg_rep2


title: 839 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C30


title: day3_siRNA_neg_rep1


title: 813 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C29


title: 141T (Xba240)


title: 795 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C28


title: day3_siRNA_neg_rep3


title: 159T (Xba240)


title: 129T (Xba240)


title: day2_siRNA_PPARg_rep3


title: Cancer tissue from patient 209772-1

status: Public on Feb 11 2010

city: beijing

first: wu

last: jp

address: 18 Life Science Parkway

country: China

institute: National Engineering Research Center

description: the microRNA expression in the tissue

hyb_protocol: Hybridization was performed at 42oC under LifterSlipTM (Erie, Portsmouth, NH) in a hybridization chamber which was placed in a 3D-tilting agitator BioMixerTM  II (CapitalBio) to provide continuous mixing of the hybridization buffer that results in more uniform hybridization across the entire slide surface, preventing edge effects and giving improved signal intensity, the efficiency of which has been demonstrated with our genome-wide mRNA expression profiling (Patterson et al., Nat Biotechnol. 2006, 24:1140-1150).The array was then washed with two consecutive washing solutions of 0.2% SDS, 2¡ÁSSC at 42¡ãC for 5 min, and 0.2% SSC for 5 min at room temperature

scan_protocol: Arrays were scanned with a LuxScanTM 10K-A laser confocal scanner and the images obtained were then analyzed using LuxScan 3.0TM software (both from CapitalBio, Beijing, China)

data_processing: After average values of the replicate spots of each miRNA were background subtracted, faint spots were filtered out when expression signal were lower than 800 in all samples.

source_name: human

label_protocol: 4 ug of low-molecular-weight RNA was labeled with 500 ng of 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon, Lafayette, CO) with 2 units T4 RNA ligase (New England Biolabs, Ipswich, MA).  The labeling reaction was performed at 4oC for 2 h.  Labeled RNA was precipitated with 0.3 M sodium acetate and 2.5 volumes ethanol and after washing with ethanol and drying was resuspended in 15 ¦Ìl of hybridization buffer containing 3¡ÁSSC, 0.2% SDS and 15% formamide.

extract_protocol: Total RNA was extracted with TRIZOL reagent (Invitrogen, Carlsbad, CA) and the low-molecular-weight RNA was isolated by using the Ambion miRNA Isolation Kit

value: Cancer tissue from patient 209772-1


title: 772 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C27


title: 128T (Xba240)


title: day2_siRNA_PPARg_rep1


title: 714 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C25


title: 670 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C24


title: day2_siRNA_PPARg_rep2


title: 113T (Xba240)


title: 719 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C26


title: day2_siRNA_neg_rep2


title: day2_siRNA_neg_rep3


title: 590 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C23


title: day2_siRNA_neg_rep1


title: 10T2 (Xba240)


title: 581 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C22


title: 110T (Xba240)


title: 111T (Xba240)


title: 570 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C21


title: 108T (Xba240)


title: day1_siRNA_PPARg_rep3


title: day1_siRNA_PPARg_rep2


title: 104T (Xba240)


title: 101T (Xba240)


title: 543 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C20


title: day1_neg_siRNA_neg_rep3


title: day1_neg_siRNA_neg_rep2


title: 481 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C19


title: day1_neg_siRNA_neg_rep1


title: day0_siRNA_PPARg_rep2


title: 474 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C17


title: day0_siRNA_PPARg_rep3


title: 431 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C15


title: 430 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C14


title: 326 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C11


title: 415 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C13


title: 470 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C16


title: 331 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C12


title: day0_siRNA_neg_rep2


title: 292 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C8


title: day-2_siRNA_PPARg_rep3


title: 313 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C9


title: day-2_siRNA_neg_rep3


title: day0_siRNA_neg_rep1


title: 314 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C10


title: 287 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C7


title: day-2_siRNA_PPARg_rep2


title: day-2_siRNA_PPARg_rep1


title: 259 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C4


title: 265 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C5


title: 286 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C6


title: 199 UPS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C3


title: day-2_siRNA_neg_rep1


title: day-2_siRNA_neg_rep2


title: TNF Sample 24 TNF T24 Control

status: Public on Mar 23 2009

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

hyb_protocol: Agilent Mouse G4121A Microarrays (containing approximately 22,000 probes) were hybridized with 5 µg Cy5-labelled lung RNA and 5 µg Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays.  Arrays were incubated overnight at 60 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned using a ScanArray Express (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada), and data were acquired with ImaGene 5.5 (BioDiscovery, CA, USA).

data_processing: The data were normalized by lowess curve (Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data:. Nucleic Acids Res. 2002; 30: e15.) using SAS/STAT software, Version 8.2 of the SAS System for Windows (1999 2001 SAS Institute Inc., Cary, NC, USA).  Data used to estimate foldchanges were adjusted for variation due to date of hybridization and date of exposure using the least square estimates.

source_name: Total RNA from mouse lungs labeled with Cyanine-5 (red)

label_protocol: Individual 2.5 µg aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

extract_protocol: RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada).  RNA was quantified using the RiboGreen RNA Quantitation Reagent and Kit (Molecular Probes, Eugene, OR, USA), and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

tag: Tissue

value: Whole lung

tag: Gender

value: Male

tag: Age

value: 128 days

tag: Strain

value: SP-C/TNF-α

tag: Date of exposure

tag: Exposure

value: 0 mg/m3 EHC

tag: Time post exposure

tag: Microarray ID

tag: Hybridization Block 6

source_name: universal mouse reference total RNA (Catalog #740100; Stratagene, La Jolla, CA, USA)

tag: Total RNA derived from 11 mouse cell lines

tag: Stratagene, La Jolla, CA, USA

tag: purchased from Stratagene


title: TNF Sample 40 TNF T0 Exposed

value: 126 days

value: 50 mg/m3 EHC

value: 0 h

tag: Hybridization Block 1


title: TNF Sample 30 TNF T0 Control

value: 134 days

tag: Hybridization Block 7


title: TNF Sample 15 TNF T24 Exposed

value: 127 days

tag: Hybridization Block 5


title: TNF Sample 16 TNF T24 Control


title: TNF Sample 12 WT T0 Exposed

value: 136 days

tag: Hybridization Block 4


title: TNF Sample 32 WT T0 Control


title: TNF Sample 36 TNF T0 Control


title: TNF Sample 4 WT T0 Exposed

tag: Hybridization Block 2


title: TNF Sample 39 TNF T24 Control

tag: Tissue

value: 137 days


title: TNF Sample 38 WT T0 Control

tag: Gender


title: TNF Sample 31 TNF T0 Exposed

tag: Age


title: TNF Sample 8 TNF T24 Exposed

tag: Strain

tag: Hybridization Block 3


title: TNF Sample 37 WT T24 Control

tag: Date of exposure

tag: Exposure


title: TNF Sample 29 WT T24 Exposed

tag: Time post exposure

tag: Microarray ID


title: TNF Sample 35 WT T24 Exposed

tag: Total RNA derived from 11 mouse cell lines


title: TNF Sample 22 TNF T0 Exposed

tag: Hybridization Block 6

tag: Stratagene, La Jolla, CA, USA


title: TNF Sample 14 TNF T0 Control

tag: purchased from Stratagene


title: day1_siRNA_PPARg_rep1

tag: fibroblasts


title: 480 LMS

description:
array CGH data for soft tissue tumors of the extremity (UPS and LMS)
STS_DNA_C18

tag: pleomorphic subtype

value: leiomyosarcoma

tag: tissue

value: soft tissue sarcoma of the extremity, primary tumor, fresh frozen


title: TNF Sample 10 WT T24 Control

tag: Hybridization Block 4


title: TNF Sample 21 WT T24 Control

tag: Tissue


title: TNF Sample 33 TNF T24 Exposed

tag: Gender

tag: Hybridization Block 1


title: TNF Sample 7 WT T24 Exposed

tag: Age

tag: Strain


title: TNF Sample 19 WT T24 Exposed

value: 135 days

tag: Date of exposure


title: TNF Sample 11 WT T0 Control

tag: Exposure


title: TNF Sample 9 WT T24 Exposed

tag: Time post exposure


title: TNF Sample 28 TNF T24 Control

tag: Microarray ID

tag: Hybridization Block 7


title: TNF Sample 34 WT T0 Exposed

tag: Total RNA derived from 11 mouse cell lines


title: TNF Sample 13 TNF T0 Exposed

tag: Hybridization Block 5

tag: Stratagene, La Jolla, CA, USA


title: TNF Sample 20 TNF T24 Exposed

tag: Hybridization Block 6

tag: purchased from Stratagene


title: TNF Sample 18 WT T0 Control


title: TNF Sample 26 TNF T24 Exposed


title: TNF Sample 27 WT T0 Exposed


title: TNF Sample 25 WT T24 Control


title: SQ20B Go6976 12hr 3

status: Public on Mar 22 2009

type: other

city: Nashville

first: Christine

middle: H.

last: Chung

state: TN

address: 777 PRB

department: Internal Medicine

institute: Vanderbilt University

description: 6 treated samples across two time points hybridized to paired time 0, untreated controls

hyb_protocol: manufacturer's specification

scan_protocol: scanned using Axon 4000B and image analysis using GenePix Pro 4.0

data_processing: loess normalization (R - Bioconductor 'limma' package)

molecule: other

label_protocol: mirVana miRNA labeling kit (Ambion, Austin, TX)

growth_protocol: SQ20B (5 x 10e6) tumor cells were injected into the right hind limbs of female athymic nude mice

extract_protocol: PureLink miRNA Isolation Kit (Invitrogen, Carlsbad, CA)

treatment_protocol: control, 12 or 24hr 100nm Gö6976 exposure

tag: SQ20B cells 12hr 100nm Gö6976

tag: SQ20B cells control


title: SQ20B Go6976 24hr 1

tag: SQ20B cells 24hr 100nm Gö6976


title: TNF Sample 17 TNF T0 Control

tag: Tissue

tag: Gender


title: SQ20B Go6976 24hr 3


title: SQ20B Go6976 12hr 1


title: SQ20B Go6976 24hr 2


title: SQ20B Go6976 12hr 2


title: TNF Sample 3 TNF T0 Control

tag: Age

tag: Hybridization Block 2


title: TNF Sample 2 TNF T0 Exposed

tag: Strain

tag: Date of exposure


title: TNF Sample 1 WT T0 Control

tag: Exposure

tag: Time post exposure


title: TNF Sample 5 TNF T24 Control

tag: Microarray ID

tag: Hybridization Block 3


title: 300531

description: Gene expression comparisons of head and neck squamous cell carcinoma in humans.

hyb_protocol: manufacturer’s recommendations

scan_protocol: manufacturer’s recommendations

data_processing: GC-RMA (Bioconductor) followed by distance weighted discrimination to eliminate variation due to protocol

label: ENZO BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA)

source_name: HNSCC from FFPE block

extract_protocol: Total RNA was purified from frozen tumors using Qiagen RNeasy Mini Kit according to the manufacturer’s recommendations (Qiagen, Valencia, CA) using approximately 10-20 milligram of wet tissue from each sample

tag: Head and Neck Squamous Cell Carcinoma from FFPE block

tag: recurrence censor

tag: recurrence date

tag: death censor (1 dead_0 alive)


title: TNF Sample 6 WT T24 Control

tag: Total RNA derived from 11 mouse cell lines

tag: Stratagene, La Jolla, CA, USA

tag: purchased from Stratagene


title: 300710

label_protocol: ENZO BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA)


title: 300688


title: 300400


title: 300637


title: 300372


title: P rat - region amyg - animal 15

status: Public on Dec 31 2009

city: Westfield

first: Mark

middle: William

last: Kimpel

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

description: Gene expression data from brain Caudate-Putamen from P rat

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on rat 230.2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

data_processing: The data were analyzed with RMA

organism: Rattus norvegicus

source_name: Caudate-Putamen from P rat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 2-cycle protocol from 25 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: RNA was extracted using Trizol followed by Qiagen RNeasy mini kit.

tag: strain

value: P

tag: tissue

value: Caudate-Putamen


title: day0_siRNA_PPARg_rep1

tag: fibroblasts


title: day0_siRNA_neg_rep3


title: TNF Sample 23 WT T0 Exposed

tag: Tissue

value: Whole lung

tag: Gender

tag: Age

tag: Hybridization Block 6


title: 300383


title: 300430


title: 300423


title: 300142


title: 300663


title: 300520


title: 300249


title: HN02-0502B


title: HN02-0454B


title: 300171


title: HN02-0421B


title: HN02-0486B


title: HN02-0136B


title: HN02-0333


title: HN96-0071B


title: HN97-0108B


title: HN01-0394B


title: HN02-0458B


title: HN01-0291B


title: HN00-0318B


title: HN01-0446B


title: HN96-0671B


title: HN02-0387B


title: 300148


title: HN02-0152B


title: HN02-0323

tag: death censor(1dead_0 alive)

tag: time to death (mos)


title: HN02-0478B


title: UTI89 LB-MES +3 mM ASN, rep2

status: Public on Mar 21 2009

city: Salt Lake City

first: Matthew

middle: A

last: Mulvey

address: 15 N. Medical Drive East

department: Pathology

institute: University of Utah

description: Gene expression data from E. coli UTI89 grown in LB-MES + 3 mM ASN.

hyb_protocol: Fragmented and labeled cDNA (15 μg) was added to 270 μl of hybridization buffer, and hybridized to the Affymetrix GeneChip® E. coli Genome 2.0 Array.  After 20 h of hybridization at 45°C, the GeneChips® were washed, stained, and scanned according to the standard Affymetrix protocol.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000 enabled for High-Resolution Scanning, and the raw images were converted to CEL files using Affymetrix GCOS software.

data_processing: Image processing using the GCRMA method for probe-level data was performed using the Bioconductor Package in the R statistical environment.  The CEL files were analyzed as a group, background corrected using GCRMA, normalized using quantile normalization, and summary measures for probe sets were obtained by median polish.

organism: Escherichia coli UTI89

source_name: UTI89 at OD600=1.5 in LB-MES +3 mM ASN

label_protocol: cDNA was synthesized, fragmented, and labeled according to the protocol recommended by Affymetrix.

growth_protocol: Separate colonies of the UPEC isolate UTI89 grown on LB agar plates from a -80°C freezer stock were used to start overnight shaking cultures in MES-buffered LB broth (MES-LB, pH 5.0).   Each culture was then diluted 1:100 into 7 ml MES-LB with or without 3 mM ASN in loosely capped 20-by-150-mm borosilicate glass tubes and grown with shaking at 37°C.

extract_protocol: RNA was extracted with hot phenol-chloroform and purified by CsCl centrifugation.

treatment_protocol: Bacteria were grown ± ASN.

tag: isolate

tag: pathogenicity

value: uropathogenic

tag: optical density


title: UTI89 LB-MES, rep1

description: Gene expression data from E. coli UTI89 grown in LB-MES.

source_name: UTI89 at OD600=1.5 in LB-MES


title: UTI89 LB-MES, rep2


title: HN03-0079B

tag: Head and Neck Squamous Cell Carcinoma from FFPE block

tag: recurrence censor

tag: recurrence date


title: UTI89 LB-MES +3 mM ASN, rep1


title: mSAGE_Whole_embryo_normal_TS26_CARM_null_B_27

status: Public on Mar 20 2009

type: SAGE

anchor: NlaIII

city: Bethesda

first: Cancer Genome Anatomy Project

last: CGAP

state: MD

department: Cancer Genome Anatomy Project

institute: National Cancer Institute

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 768
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: whole body, late gestation embryo, bulk, des, normal, female, short sage, 129svevtac x c57bl/6j,  carm , ts26

tag: organ/tissue

value: whole body

tag: tissue preparation

value: bulk

tag: age

value: 18.5 days

tag: sex

value: female

tag: cell type

value: 18.5 days, whole mouse embryo

tag: mutations

value: CARM

tag: other information

value: Pool of 2 female Embryos 18.5 days (129/B6), treated with DES 15mg 4h prior to euthanized. Genotype = CARM


title: HN01-0393B


title: HN03-0034B

tag: death censor (1 dead_0 alive)


title: mSAGE_Whole_body_teratocarcinoma_CL_ATDC5_BMP4

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1084
Laboratory: Matthias B. Wahl, Chisa Shukunami, Ulrich Heinzmann ,Kumiko Hamajima, YujiHirak, Kenji Imai

source_name: whole body, teratocarcinoma,  cell line, differentiated, bmp4, short sage

value: cell line

value: unknown


title: mSAGE_Whole_embryo_normal_TS26_CARM_wildtype_B_26

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 767
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: whole body, bulk, des, normal, late gestation embryo, female, short sage, 129svevtac x c57bl/6j, carm wild type, ts26

value: CARM wild type

value: Pool of 2 female embryos 18.5 days (129/B6), treated with DES (diethylbestrol) 15mg, 4h prior to euthanisia. Genotype = CARM wild type


title: mSAGE_Whole_body_teratocarcinoma_CL_P19_U

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1087
Laboratory: Sergey V. Anisimov, Kirill V . Tarasov , Daniel Riordon,  Anna M. Wobus,  Kenneth R. Boheler

source_name: embryonic cell, whole body, teratocarcinoma, cell line, undifferentiated, short sage

value: SAGE identification of differentiation responsive genes in P19 embryonic cells induced to form cardiomyocytes in vitro. Undifferentiated P19 embryonic carcinoma (EC) cells. Total number of 65,677 SAGE tags sequenced. 64,952 SAGE tags analyzed after clean-up (extraction of poly(A) tags, linker-generated tags, and tags originated from clones producing 4 tags or less). (NCBI name:Undifferentiated P19 embryonic carcinoma (EC) cells


title: mSAGE_Whole_body_teratocarcinoma_CL_P19_3+0.5

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1088
Laboratory: Sergey V. Anisimov, Kirill V . Tarasov , Daniel Riordon,  Anna M. Wobus,  Kenneth R. Boheler

source_name: embryonic cell, teratocarcinoma, cell line, whole boday, differentiated, cardiomyocyte, short sage

value: SAGE identification of differentiation responsive genes in P19 embryonic cells induced to form cardiomyocytes in vitro. P19 embryonic carcinoma (EC) cells, induced to form cardiomyocytes in vitro, day 3+0.5 of differentiation protocol. Total number of 51,822 SAGE tags sequenced. 50,983 SAGE tags analyzed after clean-up (extraction of poly(A) tags, linker-generated tags, and tags originated from clones producing 4 tags or less). (NCBI name:P19 embryonic carcinoma (EC) cells, day 3+0.5)


title: mSAGE_Vascular_endothelium_SW620_tumor_associated_AP_SW620TEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2230
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]

source_name: vascular, tumor associated, endothelium, antibody purified, extracted short sage, adult

value: vascular

value: antibody purified


title: mSAGE_Vascular_endothelium_normal_spleen_associated_AP_NSEC1

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2190
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]

source_name: vascular, normal, endothelium, antibody purified, extracted short sage, adult


title: mSAGE_Vascular_endothelium_normal_muscle_associated_AP_NMEC1

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2195
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mSAGE_Whole_body_teratocarcinoma_CL_P19_3+3

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1089
Laboratory: Sergey V. Anisimov, Kirill V . Tarasov , Daniel Riordon,  Anna M. Wobus,  Kenneth R. Boheler

value: SAGE identification of differentiation responsive genes in P19 embryonic cells induced to form cardiomyocytes in vitro. P19 embryonic carcinoma (EC) cells, induced to form cardiomyocytes in vitro, day 3+3.0 of differentiation protocol. Total number of 54,236 SAGE tags sequenced. 53,022 SAGE tags analyzed after clean-up (extraction of poly(A) tags, linker-generated tags, and tags originated from clones producing 4 tags or less). (NCBI name:P19 embryonic carcinoma (EC) cells, day 3+3.0)


title: mSAGE_Whole_body_teratocarcinoma_CL_ATDC5_U

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1083
Laboratory: Matthias B. Wahl, Chisa Shukunami, Ulrich Heinzmann ,Kumiko Hamajima, YujiHirak, Kenji Imai

source_name: whole body, teratocarcinoma, cell line, short sage, undifferentiated


title: mSAGE_Vascular_endothelium_normal_lung_associated_AP_NLgEC1

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2193
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mSAGE_Vascular_endothelium_normal_kidney_associated_AP_NKEC1

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2188
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mSAGE_Vascular_endothelium_KM12SM_tumor_associated_AP_KM12TEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2226
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mSAGE_Vascular_endothelium_normal_heart_associated_AP_NHEC1

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2184
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mSAGE_Vascular_endothelium_CT26_tumor_associated_AP_CT26TEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2205
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mSAGE_Vascular_endothelium_normal_liver_associated_AP_NLiEC1

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2197
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mSAGE_Vascular_endothelium_normal_brain_associated_AP_NBEC1

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2186
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mSAGE_Vascular_endothelium_EMT6_tumor_associated_AP_EMT6TEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2224
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mSAGE_Uterus_normal_P0_MMD_SM171

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1744
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: uterus, normal, microscope dissected, extracted short sage, female, ts27

value: uterus

value: microscope dissected


title: mSAGE_Uterus_normal_P36_MMD_SM075

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1510
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: uterus, normal, microscope dissected, female, 21 days post natal, extracted short sage


title: mSAGE_Vascular_endothelium_LLC_tumor_associated_AP_LLCTEC

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2228
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]


title: mSAGE_Urogenital_sinus_normal_TS24_MMD_SM054

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1235
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, female urogenital sinus, normal, microscope dissected, extracted short sage, late gestation embryo, ts24, female, atlas

value: embryonic tissue

value: Urogenital sinus female


title: mSAGE_Urogenital_sinus_normal_TS24_MMD_SM163

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1740
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, female urogenital sinus epithelium, normal, microscope dissected, extracted short sage, female, ts24, late gestation embryo

value: female


title: mSAGE_Urogenital_sinus_normal_TS24_MMD_SM036

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1230
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, microscope dissected, normal, male urogenital sinus mesenchyme, male, ts24, late gestation embryo, extracted short  sage, atlas

value: male

value: Mesenchyme


title: mSAGE_Urogenital_sinus_normal_TS24_MMD_SM170

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1743
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, female urogenital sinus mesenchyme, normal, microscope dissected, extracted short sage, ts24, late gestation embryo


title: mSAGE_Urogenital_sinus_normal_TS18_MMD_SM065

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1246
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, male urogenital sinus epithelium, microscope dissected, normal, male, extracted short sage, ts24, late gestation embryo, atlas

value: urogenital sinus epithelium


title: mSAGE_Urogenital_sinus_normal_TS24_MMD_SM032

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1273
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, male urogenital sinus, normal, microscope dissected, male, late gestation embryo, extracted short sage, ts24, atlas

value: 16.5 days post coitum. reposition of umbilical hernia. theiler stage 24


title: mSAGE_Thymus_normal_TS26_MD_SMET1

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1272
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: thymus, normal, microscope dissected, late gestation embryo, extracted short sage, ts26, atlas

value: thymus

value: 18.5 days post coitum. long whiskers. theiler stage 26

value: unknown


title: mSAGE_Testis_normal_somatic_cell_TS26_B_Wv/Wv

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1090
Laboratory: Peter J. O'Shaughnessy, Lynne Fleming , Paul J. Baker, Gary Jackson, Heather Johnston

source_name: testis, somatic cell, normal, bulk, short sage, late gestation embryo

value: testis

value: bulk

value: RNA was extracted from testes of Wv/Wv fetuses at day 18 post coitum. These testes are largely devoid of germ cells and SAGE library will represent somatic cells of the fetal testis. (NCBI name:fetal testis somatic cells)


title: mSAGE_Testis_normal_TS24_MMD_SM044

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1241
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: testis, normal, microscope dissected, male, extracted short sage, late gestation embryo, ts24, atlas


title: mSAGE_Thymus_normal_P72_MMD_SM024

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1271
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: thymus, normal, adult, male, microscope dissected, extracted short sage, atlas


title: mSAGE_Testis_normal_P84_MMD_SM118

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1526
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: testis, normal, microscope dissected, male, adult, extracted short sage


title: mSAGE_Thymus_normal_TS23_MMD_SM057

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1242
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: thymus, normal, microscope dissected, late gestation embryo, extracted short sage, ts23, atlas


title: mSAGE_Testis_normal_TS22_MMD_SM080

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1348
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: testis, normal, microscope dissected, male, ts22, mid-gestation embryo, extracted short sage, atlas


title: mSAGE_T_cell_tolerated_skin_graft_normal_CL

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1067
Laboratory: Diana Zelenika,  Elizabeth Adams,  Susan Humm, Luis Graca, Sara Thompson, Steve Cobbold, Herman Waldmann

source_name: t-cell, normal, cell line, pcr directed strategy, cdna template, short sage

value: white blood cells

value: cell line

value: A CD4+ Treg/Tr1-like H-Y + H2Ek specific line grown from the accepted male skin grafts of female A1(M) TCR transgenic mice. mRNA was derived from CD4+ T cells (>99%) 7 days from last stimulation, and contains <0.1% mast cells. cDNA was preamplified (SMART) before SAGE analysis.[SAGEMap name:Treg line SKA from skin graft]


title: mSAGE_T_cell_normal_AP_CD4+CD25+

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1064
Laboratory: Luis Graca, Sara Thompson, Chun-Yen Lin, Elizabeth Adams,  Steve Cobbold,  Herman Waldmann
References: http://sciencepark.mdanderson.org/ggeg/

source_name: t-cell, normal, spleen lymphocyte, short sage, antibody purified, pcr directed strategy, cdna template

value: antibody purified

value: CD4+CD25+ T cells were purified from naive CBA/Ca mouse spleen cells by MACS sorting.  cDNA was preamplified (SMART) before SAGE analysis. [SAGEMap name:CD4+CD25+ spleen]


title: mSAGE_T_cell_normal_anti-CD3_AP_CD4+CD25-

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1063
Laboratory: Luis Graca, Sara Thompson, Chun-Yen Lin, Elizabeth Adams, Steve Cobbold, Herman Waldmann

source_name: t-cell, antibody purified, normal, spleen lymphocyte, pcr directed strategy, cdna template, anti-cd3, short sage

value: CD4+CD25negative spleen cells were purified from naive CBA/Ca mice by MACS sorting.  T cells were activated overnight by solid phase anti-CD3.  cDNA was preamplified (SMART) before SAGE analysis. [SAGEMap name:CD4+CD25neg activated]


title: mSAGE_T_cell_naive_FS_61

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 865
Library_producer: John Shires
Laboratory: Adrian Hayday, Guy's King's St. Thomas' Medical School, London, UK

source_name: white blood cell, t-cell, normal, flow-sorted, adult, short sage

value: flow-sorted

value: LCMV specific CD8 T cells tranferred to uninfected syngeneic animals, then isolated from spleen.


title: mSAGE_T_cell_normal_AP_CD4+CD25-

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1068
Laboratory: Luis Graca, Sara Thompson, Chun-Yen Lin, Elizabeth Adams, Steve Cobbold, Herman Waldmann

source_name: t-cell, normal, antibody purified, short sage, pcr directed strategy, cdna template

value: CD4+CD25negative spleen cells were purified from naive CBA/Ca mice by MACS sorting.  cDNA was preamplified (SMART) before SAGE analysis.[SAGEMap name:CD4+CD25neg spleen]


title: mSAGE_T_cell_memory_FS_62

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 883
Library_producer: John Shires
Laboratory: Adrian Hayday, Guy's King's St. Thomas' Medical School, London, UK

value: LCMV specific CD8 T cells tranferred to LCMV infected syngeneic animals, then isolated from spleen.


title: mSAGE_Testis_normal_P36_MMD_SM091

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1508
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: testis, normal, microscope dissected, male, 21 days post natal, extracted short sage

value: microscope dissected

value: male


title: mSAGE_Testis_normal_P0_MMD_SM128

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1549
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: testis, normal, microscope dissected, short extracted sage, male, 1 day post natal


title: mSAGE_T_cell_spleen_mitomycin_IL10_CL

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1069
Laboratory: Diana Zelenika, Elizabeth Adams,  Susan Humm, Luis Graca,  Sara Thompson, Chun-Yen Lin,  Steve Cobbold,  Herman Waldmann

source_name: white blood cell, normal, cell line, pcr directed strategy, cdna template


title: mSAGE_T_cell_TCR_gamma_delta_normal_FS_60

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 863
Library_producer: John Shires
Laboratory: Adrian Hayday, Guy's King's St. Thomas' Medical School, London, UK

source_name: white blood cell, t-cell, normal, flow-sorted, adult, t-cell receptor gamma/delta, short sage

value: Intra-epithelial lymphocytes from mouse small intestine expressing T cell receptor gamma/delta.


title: mSAGE_Stomach_normal_TS25_MMD_SM089

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1354
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: stomach, normal, microscope dissected, female, male, ts25, late gestation embryo, extracted short sage, atlas

value: stomach

value: male and female


title: mSAGE_T_cell_TCR_alpha_beta_normal_FS_59

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 864
Library_producer: John Shires
Laboratory: Adrian Hayday, Guy's King's St. Thomas' Medical School, London, UK

source_name: white blood cell, t-cell, normal, flow-sorted, adult, short sage, t-cell receptor alpha/beta

value: unknown

value: Intra-epithelial lymphocytes from mouse small intestine expressing T cell receptor alpha/beta.


title: mSAGE_Testis_normal_somatic_cell_adult_busulphan_B

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1091
Laboratory: Peter J. O'Shaughnessy, Lynne Fleming , Paul J. Baker, Gary Jackson, Heather Johnston

source_name: testis, somatic cell, normal, bulk, short sage, adult, busulphan

value: testis

value: bulk

value: Adult mice were treated with busulphan (30mg/Kg). RNA was extracted from testes 60 days later. At this stage the testes were largely devoid of germ-cells. (NCBI name:Adult testis -somatic cells)


title: mSAGE_Spleen_normal_TS26_MMD_SM010

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 636
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: spleen, normal, microscope dissected, short sage, late gestation embryo, ts26, atlas

value: spleen

value: 18.5 days post coitum. long whiskers. theiler stage 26


title: mSAGE_Stomach_normal_TS20_MMD_SM072

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1324
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: stomach, normal, microscope dissected, extracted short sage, ts20, mid-gestation embryo, atlas


title: mSAGE_Small_intestine_normal_TS20_MMD_SM151

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1808
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: small intestine, epithelium, normal, microscope dissected, extracted short sage, ts20, mid-gestation embryo

value: gastrointestinal tract


title: mSAGE_Small_intestine_normal_TS20_MMD_SM159

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2008
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: small_intestine, tissues, normal, microscope dissected, e12, unknown, extracted short  sage

value: tissues

value: normal


title: mSAGE_Spleen_normal_TS22_MMD_SM011

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1266
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: spleen, normal, microscope dissected, extracted short sage, late gestation embryo, ts24, atlas

value: 16.5 days post coitum. reposition of umbilical hernia. theiler stage 22


title: mSAGE_Small_intestine_normal_TS25_MMD_SM094

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1407
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: small intestine, whole small intestine, normal, microscope dissected, ts25, late gestation embryo, extracted short sage, atlas

value: small intestine


title: mSAGE_Spleen_normal_TS23_MMD_SM055

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1236
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: spleen, normal, microscope dissected, extracted short sage, late gestation embryo, ts23, atlas

value: microscope dissected


title: mSAGE_Small_intestine_normal_TS20_MMD_SM095

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1409
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: small intestine, small intestine mesenchyme, microdissected microscope, ts20, extracted short sage, mid-gestation embryo, atlas

value: small intestine - mesenchyme


title: mSAGE_Spleen_normal_P84_MMD_SM012

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1265
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: spleen, normal, microscope dissected, adult, extracted short sage, atlas


title: mSAGE_Skin_normal_TS21_MMD_SM119

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1732
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: skin, normal, microscope dissected, extracted short sage, ts21, mid-gestation embryo

value: skin


title: mSAGE_Skin_normal_TS21_MMD_SM120

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2004
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: skin, normal, microscope dissected, e13.5, unknown, extracted short sage


title: mSAGE_Skin_squamous_cell_carcinoma_B_25

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 784
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: skin, squamous cell, carcinoma, adult, female, short sage, skh-1, uv radiation

value: 30 wk

value: female

value: Skin Squamous Cell Carcinomas, pool

value: Skin Squamous Cell Carcinomas induced in SKH-1 female mice by UV irradiation. Pool of various tumors.


title: mSAGE_Skin_normal_E2F1_wildtype_B_20

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 763
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: skin, epidermis, normal, bulk, adult, female, short sage, skh-1, e2f1 wild type

value: Normal epidermis

value: E2F1 wild type

value: Epidermal scrapes from the dorsal skin of female SKH-1, Genotype = E2F1 Wild type mice, untreated. Pool of various female mice.


title: mSAGE_Skin_normal_TS24_MMD_SM134

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1736
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: skin, normal, microscope dissected, extracted short sage, ts24, late gestation embryo

value: unknown


title: mSAGE_Skin_normal_E2F1_wildtype_UV_B_21

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 764
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: skin, epidermis, bulk, normal, adult, female, short sage, skh-1, e2f1 wild type, uv radiation

value: bulk

value: Epidermal scrapes from the dorsal skin of female SKH-1, Genotype = E2F1 Wild type mice, treated with UV light irradiation (8h post-treatment). Pool of various female mice.


title: mSAGE_Skin_normal_E2F1_null_UV_B_23

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 766
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: skin, epidermis, normal, bulk, adult, female, short sage, skh-1, e2f1 , uv radiation

value: Epidermal scrapes from the dorsal skin of female SKH-1, Genotype = E2F1  mice, treated with UV light irradiation (8h post-treatment). Pool of various female mice.


title: mSAGE_Skin_normal_B_24

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 783
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: skin, epidermis, normal, bulk, adult, female, short sage, skh-1

value: Epidermal scrapes from the dorsal skin of female SKH-1 mice, untreated. Pool of various female mice.


title: mSAGE_Retina_normal_TS22_B_48

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 925
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, bulk, normal, female, male, short sage, c57bl/6, mid-gestation embryo, ts22

value: retina

value: Embryonic day 14.5

value: male and female

value: Wildtype

value: Embryonic 14.5 whole retina (consists of a number of individuals of different sexes). Strain=C57BL/6.


title: mSAGE_Retina_normal_TS26_B_50

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 927
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, bulk, normal, female, male, late gestation embryo, short sage, ts26, c57bl/6

value: Embryonic day 18.5

value: Embryonic 18.5 whole retina (consists of a number of individuals of different sexes). Strain=C57BL/6.


title: mSAGE_Retina_normal_TS24_B_49

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 926
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, normal, bulk, female, male, short sage, c57bl/6, ts24, late gestation embryo

value: Embryonic day 16.5

value: Embryonic 16.5 whole retina (consists of a number of individuals of different sexes). Strain=C57BL/6.


title: mSAGE_Retina_normal_TS20_B_47

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 924
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, normal, bulk, male, female, mid-gestation embryo, ts20, short sage, cl57bl/6

value: Embryonic day 12.5

value: Embryonic 12.5 whole retina (consists of a number of individuals of different sexes). Strain=C57BL/6.


title: mSAGE_Retina_normal_adult_MD_58

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 935
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, normal, microscope dissected, adult, male, c57bl/6, photoreceptor layer, short sage

value: microscope dissected

value: 7 weeks

value: male

value: Postnatal day ~50 adult male microdissected photoreceptor layer of retina. Strain=C57BL/6.


title: mSAGE_Skin_normal_P84_MMD_SM214

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2050
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: skin, normal, mocroscope dissected, p84, male, extracted short sage

value: skin

value: normal


title: mSAGE_Retina_normal_4.5d_B_53

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 930
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, bulk, normal, female, male, short sage, 4.5 days post natal, c57bl/6

value: retina

value: bulk

value: Postnatal day 4.5

value: Postnatal 4.5 whole retina (consists of a number of individuals of different sexes). Strain=C57BL/6.


title: mSAGE_Retina_normal_2.5 d_B_52

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 929
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, bulk, normal, female, male, short sage, 2.5 days post natal, c57bl/6

value: Postnatal day 2.5

value: male and female

value: Wildtype

value: Postnatal 2.5 whole retina (consists of a number of individuals of different sexes). Strain=C57BL/6.


title: mSAGE_Skin_normal_E2F1_null_B_22

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 765
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: skin, epidermis, bulk, normal, adult, female, short sage, skh-1, e2f1

value: female

value: Normal epidermis

value: Epidermal scrapes from the dorsal skin of female SKH-1, Genotype= E2F1  mice, untreated. Pool of various female mice.


title: mSAGE_Retina_normal_0.5d_B_51

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 928
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, bulk, normal, 0.5 days post natal, c57bl/6, short sage, female, male

value: Postnatal day 0.5

value: Postnatal 0.5 whole retina (consists of a number of individuals of different sexes). Strain=C57BL/6.


title: mSAGE_Retina_normal_6.5d_B_54

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 931
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, bulk, normal, female, male, short sage, 6.5 days post natal, c57bl/6

value: Postnatal day 6.5

value: Postnatal 6.5 whole retina (consists of a number of individuals of different sexes). Strain=C57BL/6.


title: mSAGE_Retina_normal_10.5d_CRXnull_B_56

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 933
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, bulk, normal, female, male, short sage, 10.5 days post natal, c57bl/6 x 129/sv, crx

value: Postnatal day 10.5

value: Crx

value: Postnatal 10.5 whole retina of mice homozygous for a mutation in the Crx gene (consists of a number of individuals of different sexes). Strain=C57BL/6 x Sv129.


title: mSAGE_Prostate_normal_P63_MMD_SM220

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2056
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: prostate, normal, mocroscope dissected, p63, male, extracted short sage

value: prostate

value: microscope dissected

value: male

value: normal

value: Pten +/-


title: mSAGE_Retina_normal_adult_B_57

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 934
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, bulk, normal, male, short sage, adult, c57bl/6

value: retina

value: bulk

value: 7 weeks

value: Wildtype

value: Postnatal day ~50 adult male whole retina. Strain=C57BL/6.


title: mSAGE_Placenta_normal_TS15_MMD_SM047

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1226
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: placenta, normal, microscope dissected, ts15, extracted short sage, mid-gestation embryo, atlas

value: placenta

value: unknown


title: mSAGE_Placenta_normal_TS11_MMD_SM063

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1248
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: ectoplacental cone, normal, microscope dissected, extracted short sage, post implantation embryo, ts10, atlas

value: other

value: Embryo - ectoplacental cone


title: mSAGE_Prostate_normal_P63_MMD_SM219

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2054
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: prostate, normal, mocroscope dissected, p63, extracted short sage

value: Pten -/-


title: mSAGE_Placenta_normal_TS22_MMD_SM049

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1227
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: placenta, normal, microscope dissected, ts22, extracted short sage, mid-gestation embryo, atlas


title: mSAGE_Retina_normal_10.5d_B_55

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 932
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: retina, bulk, normal, female, male, short sage, 10.5 days post natal, c57bl/6 x 129/sv

value: Postnatal day 10.5

value: male and female

value: Postnatal 10.5 whole retina (consists of a number of individuals of different sexes). Strain= C57BL/6 x Sv129.


title: mSAGE_Prostate_normal_P72_MMD_SM026

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1263
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: prostate, prostate dorsal lobe, normal, microscope dissected, extracted short sage, adult, male, atlas

value: prostate

value: microscope dissected


title: mSAGE_Pancreas_normal_TS26_MMD_SM016

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1270
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, normal, microscope dissected, late gestation embryo, extracted short sage, ts26, atlas

value: pancreas

value: 18.5 days post coitum. long whiskers. theiler stage 26


title: mSAGE_Pituitary_gland_normal_TS23_MMD_SM133

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1813
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pituitary gland, normal, microscope dissected, extracted short sage, ts23, mid-gestation embryo

value: pituitary


title: mSAGE_Pituitary_gland_normal_P0_MMD_SM165

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1822
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pituitary gland, normal, microscope dissected, extracted short sage, ts27

value: pituitary gland


title: mSAGE_Prostate_normal_P0_MMD_SM025

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1264
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: prostate, whole prostate, normal, microscope dissected, extracted short sage, ts27, male, atlas

value: male


title: mSAGE_Pituitary_gland_normal_P0_MMD_SM166

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2010
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pituitary gland, tissues, normal, microscope dissected, p0, male, extracted short sage

value: tissues

value: normal


title: mSAGE_Pancreas_normal_TS22_MMD_SM223

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2062
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, normal, mocroscope dissected, e14.5, ts16, extracted short sage

value: WT Tle6


title: mSAGE_Pancreas_normal_TS24_MMD_SM015

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 663
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, normal, microscope dissected, late gestation embryo, short sage, ts24, atlas

value: 16.5 days post coitum. reposition of umbilical hernia. theiler stage 24

value: unknown


title: mSAGE_Pancreas_normal_TS20_MMD_SM162

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1739
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, normal, microscope dissected, extracted short sage, sagelite, gfp-, ngn3, ts20, mid-gestation embryo

value: NGN3 Pancreas GFP-,  SAGELite


title: mSAGE_Pancreas_normal_TS21_MMD_SM225

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2066
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, normal, mocroscope dissected, e13.5, ts21, extracted short sage

value: other

value: NGN3 GFP+


title: mSAGE_Pancreas_normal_TS22_MMD_SM014

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 668
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, normal, microscope dissected, mid-gestation embryo, short sage, ts22, atlas

value: 14.5 days post coitum. fingers separate distally. theiler stage 22


title: mSAGE_Pancreas_normal_TS22_MMD_SM224

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2064
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

value: Tle 6


title: mSAGE_Pituitary_gland_normal_P84_MMD_SM202

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1823
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pituitary gland, normal, microscope dissected, extracted short sage, 84 days post natal


title: mSAGE_Pancreas_normal_TS17_MMD_SM161

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1738
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, normal, microscope dissected, extracted short sage, sagelite, gfp+, pdx1, ts10.5, mid-gestation embryo

value: PDX1 Pancreas GFP+,  SAGELite


title: mSAGE_Pancreas_normal_P70_MMD_SM017

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1727
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, islets, normal, microscope dissected, extracted short sage, 70 days post natal

value: microscope dissected

value: 10 weeks


title: mSAGE_Ovaries_normal_TS22_MMD_SM093

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1350
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: ovary, normal, microscope dissected, female, ts22, mid-gestation embryo, extracted short sage, atlas, sagelite

value: ovary

value: female


title: mSAGE_Neural_tube_normal_TS9_MMD_SM117

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1817
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, neuropore, posterior, normal, microscope dissected, extracted short sage, ts13, mid-gestation embryo

value: embryonic tissue


title: mSAGE_Ovaries_normal_P0_MMD_SM164

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1741
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: ovary, normal, microscope dissected, extracted short sage, female, ts27


title: mSAGE_Pancreas_normal_P42_MMD_SM114

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1731
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, islets, regenerating, normal, microscope dissected, extracted short sage, 42 days post natal

value: pancreas

value: 6 weeks


title: mSAGE_Pancreas_normal_P72_MMD_SM102

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1729
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, duct, normal, microscope dissected, extracted short sage, 42 days post natal


title: mSAGE_Pancreas_normal_P72_MMD_SM103

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1730
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, duct, regenerating, normal, microscope dissected, extracted short sage, 42 days post natal


title: mSAGE_Mammary_glands_normal_P84_MMD_SM071

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1250
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: mammary gland, involuting mammary gland, normal, microscope dissected, involuting, adult, extracted short sage, female, atlas

value: mammary gland

value: 6 days post weaning, Inguinal without lymph node (L+R)


title: mSAGE_Mammary_glands_normal_P84_MMD_SM129

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1734
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: mammary gland, normal, microscope dissected, extracted short sage, female, virgin, 84 days post natal


title: mSAGE_Pancreas_normal_TS20_MMD_SM160

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1737
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: pancreas, normal, microscope dissected, extracted short sage, sagelite, gfp+, ngn3, ts20, mid-gestation embryo

value: NGN3 Pancreas GFP+,  SAGELite


title: mSAGE_Mammary_glands_normal_P84_MMD_SM069

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1408
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: mammary gland, normal, lactation, microscope dissected, female, adult, extracted short sage, atlas

value: Mammary gland at 5 days lactation, Inguinal without lymph node (L+R)


title: mSAGE_Mammary_glands_normal_P60_MMD_SM062

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1243
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: mammary gland, pubertal mammary gland, normal, microscope dissected, extracted short sage, female, puberty, 35 days post natal, atlas

value: Inguinal without lymph node (L+R)


title: mSAGE_Neural_tube_normal_TS13_MMD_SM126

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1815
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, neural tube, normal, microscope dissected, extracted short sage, ts13, mid-gestation embryo

value: unknown


title: mSAGE_Ovaries_normal_P36_MMD_SM076

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1253
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: ovary, normal, microscope dissected, female, extracted short sage, 21 days post natal, atlas


title: mSAGE_Mammary_gland_normal_p53_null_pseudopregnant_organoid_B_15

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 744
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: C. M. Aldaz et al., Oncogene 21, 6366-76 (2002) [PUBMED=12214277]

source_name: mammary gland, normal, epithelium, organoid, bulk, short sage, female, adult, balb/c, p53 , pseudopregnant

value: bulk

value: 15 wk

value: Normal mouse mammary epithelium pseudopregnant

value: Balb/c mammary epithelium from transplants grown into cleared fat pads of syngeneic hosts. Genotype = P53   mammary gland transplants, that received hormonal treatment by means of pituitary isografts, harvested 7 wk post-transplatation and 5 wk of hormonal treatment. Ref. Oncogene (2002) 21, 6366-6376


title: mSAGE_Neural_tube_normal_TS13_MMD_SM125

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1816
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, neuropore, anterior, normal, microscope dissected, extracted short sage, ts13, mid-gestation embryo

value: microscope dissected


title: mSAGE_Mammary_gland_normal_p53_null_organoid_B_14

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 745
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: C. M. Aldaz et al., Oncogene 21, 6366-76 (2002) [PUBMED=12214277]

source_name: mammary gland, normal, organoid, epithelium, bulk, female, adult, short sage, balb/c, p53

value: 15 weeks

value: Normal mouse mammary epithelium

value: Balb/c mammary epithelium from transplants grown into cleared fat pads of syngeneic hosts. Genotype = P53   mammary gland transplants, that received no treatment, harvested 7 wks post-transplatation. Ref. Oncogene (2002) 21, 6366-6376


title: mSAGE_Muscle_normal_TS19_MMD_SM042

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1223
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: muscle, skeletal muscle, normal, microscope dissected, late gestation embryo, extracted short sage, ts25, atlas

value: muscle


title: mSAGE_Mammary_glands_normal_P84_MMD_SM074

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1252
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: mammary gland, pregnant mammary gland, normal, microscope dissected, pregnant, female, adult, extracted short sage, atlas

value: female

value: pregnancy stage TS15 (9.5dpc), Inguinal without lymph node (L+R)


title: mSAGE_Mammary_gland_normal_p53_wildtype_pseudopregnant_organoid_B_16

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 746
Library_producer: C. Marcelo Aldaz
Laboratory: C. M. Aldaz et al., Oncogene 21, 6366-76 (2002)
References: C. M. Aldaz et al., Oncogene 21, 6366-76 (2002) [PUBMED=12214277]

source_name: mammary gland, normal, bulk, epithelium, pseudopregnant, female, short sage, adult, balb/c, p53 wild type

value: mammary gland

value: Normal mouse mammary epithelium, pseudopregnant

value: p53 wild type

value: Balb/c mammary epithelium from transplants grown into cleared fat pads of syngeneic hosts. Genotype = P53 wild type  mammary gland transplants, that received hormonal treatment by means of pituitary isografts, harvested 7 wk post-transplatation and 5 wk of hormonal treatment. Ref. Oncogene (2002) 21, 6366-6376


title: mSAGE_Mammary_gland_adenocarcinoma_p53_null_B_19

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 749
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: mammary gland, bulk, adenocarcinoma, adult, female, balb/c, short sage, p53

value: 10 months

value: Mammary adenocarcinoma

value: P53 mammary tumor (T2539) derived from mammary isograft in untreated Balb/C mice.


title: mSAGE_Mammary_gland_normal_C3(1)SV40Tag_B_72

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 824
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center

source_name: mammary gland, bulk, normal, female, short sage, c3-1, sv40tag, fvb, unknown development stage

value: bulk

value: Normal mammary gland

value: C3(1)SV40 Tag

value: Bulk mammary gland from C3(1)SV40 Tag untreated mice. Pool


title: mSAGE_Mammary_gland_normal_p53_wildtype_organoid_B_12

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 743
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: C. M. Aldaz et al., Oncogene 21, 6366-76 (2002) [PUBMED=12214277]

source_name: mammary gland, organoid, normal, bulk, epithelium, adult, short sage, female, balb/c, p53 wild type

value: 15 weeks

value: Balb/c mammary epithelium from transplants grown into cleared fat pads of syngeneic hosts. Genotype = P53wild type mammary gland, transplants that received no treatment, harvested 7 wks post-transplatation. Ref. Oncogene (2002) 21, 6366-6376


title: mSAGE_Mammary_gland_normal_C3(1)SV40Tag_LGD1069_B_73

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 823
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center

source_name: mammary gland, bulk, normal, short sage, female, c3-1, sv40tag, lgd1069, fvb

value: Bulk mammary gland from C3(1)SV40 Tag mice treated with LGD1069 (RXR ligand). Pool


title: mSAGE_MEF_normal_CL_SHE18

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1393
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, fibroblast, normal, cell line, irradiation, extracted short sage

value: embryonic tissue

value: cell line

value: unknown


title: mSAGE_Mammary_gland_adenocarcinoma_p53_null_B_18

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 748
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: mammary gland, bulk, adenocarcinoma, female, adult, balb/c, short sage, p53

value: mammary gland

value: female

value: P53 mammary tumor (T2532 ) derived from mammary isograft in untreated Balb/C mice.


title: mSAGE_Lymph_nodes_normal_P63_MMD_SM221

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2058
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lymph node, normal, mocroscope dissected, p63, male, extracted short sage

value: lymph node

value: microscope dissected

value: male

value: normal

value: PBCrePten(flox/flox)


title: mSAGE_Mammary_gland_adenocarcinoma_p53_null_B_17

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 747
Library_producer: C. Marcelo Aldaz
Laboratory: C. Marcelo Aldaz, M.D. Anderson Cancer Center
References: http://sciencepark.mdanderson.org/ggeg/

source_name: mammary gland, adenocarcinoma, bulk, adult, female, balb/c, short sage, p53

value: bulk

value: 10 months

value: Mammary Adenocarcinoma

value: P53 mammary tumor (TG7) derived from the PNIa transplantable mammary duct outgrowth line, Balb/C mice Medina et al. FASEB J., 2002; 16(8):881-3)


title: mSAGE_Lymph_nodes_normal_P84_MMD_SM130

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1735
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lymph node, normal, microscope dissected, extracted short sage, 84 days post natal

value: lymph nodes, mesenteric


title: mSAGE_Lung_normal_TS19_MMD_SM045

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1233
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lung, normal, microscope dissected, extracted short sage, late gestation embryo, ts25, atlas

value: lung


title: mSAGE_Lymph_nodes_normal_P63_MMD_SM222

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2060
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

value: PBCrePten(flox/-)


title: mSAGE_Lung_normal_TS19_MMD_SM135

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1812
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lung, lung mesenchyme, normal, microscope dissected, extracted short sage, ts19, mid-gestation embryo


title: mSAGE_Lung_normal_P0_MMD_SM021

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1262
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lung, normal, microscope dissected, extracted short sage, ts27, atlas


title: mSAGE_Lung_normal_TS19_MMD_SM018

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1275
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lung, normal, microscope diseccted, extracted short sage, mid-gestation embryo, ts19, atlas


title: mSAGE_Lung_normal_TS13_MMD_SM127

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1814
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lung, lung epithelium, normal, microscope dissected, extracted short sage, ts19, mid-gestation embryo


title: mSAGE_Lung_normal_TS26_MMD_SM066

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1245
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lung, microscope dissected, normal, late gestation embryo, extracted short sage, ts26, atlas


title: mSAGE_Liver_normal_TS26_MMD_SM149

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1809
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: liver, normal, microscope dissected, extracted short sage, ts26, late gestation embryo

value: liver


title: mSAGE_Liver_normal_TS15_MMD_SM158

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1807
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: liver, septum transversum, bud, normal, microscope dissected, extracted short sage, ts14, mid-gestation embryo

value: unknown


title: mSAGE_Liver_normal_TS14_MMD_SM001

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 630
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: liver, normal, microscope dissected, mid-gestation embryo, short sage, ts20, atlas

value: 12.5 days post coitum. earliest signs of fingers. theiler stage 20


title: mSAGE_Lung_normal_P109_MMD_SM212

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2048
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lung, normal, other, p109, male, extracted short sage

value: other


title: mSAGE_Limb_normal_TS23_MMD_SM177

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1707
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: limb, forelimb, normal, microscope dissected, extracted short sagets23, late gestation embryo

value: limb


title: mSAGE_Liver_normal_P84_MMD_SM100

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1820
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: liver, right lobe, normal, microscope dissected, extracted short sage, adult, male

value: adult


title: mSAGE_Large_intestine_normal_TS20_MMD_SM156

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1805
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: large intestine, epithelium, normal, microscope dissected, extracted short sage, ts20, mid-gestation embryo

value: gastrointestinal tract

value: microscope dissected


title: mSAGE_Kidney_normal_TS14_MMD_SM169

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1742
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: kidney,  epithelium, normal, microscope dissected, extracted short sage

value: kidney


title: mSAGE_Limb_normal_TS22_MMD_SM085

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1821
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: limb, forelimb, normal, microscope dissected, extracted short sage, ts22, mid-gestation embryo


title: mSAGE_Large_intestine_normal_TS20_MMD_SM078

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1325
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: intestine, large intestine mesenchyme, microscope dissected, normal, extracted short sage, ts20, mid-gestation embryo, atlas

value: Large intestine - mesoderm


title: mSAGE_Kidney_normal_TS20_MMD_SM124

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1733
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: kidney, kidney mesenchyme, normal, microscope dissected, extracted short sage


title: mSAGE_Large_intestine_normal_TS25_MMD_SM096

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1410
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: large intestine, whole large intestine, normal, microscope dissected, ts25, late gestation embryo, extracted short sage, atlas

value: large intestine


title: mSAGE_Kidney_normal_TS19_MMD_SM113

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1548
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: kidney, normal, microscope dissected, extracted short sage, mid-gestation embryo, ts19


title: mSAGE_Limb_normal_TS22_MMD_SM084

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1352
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: limb, forelimb, paddle, normal, microscope dissected, female, male, ts22, mid-gestation embryo, extracted short sage, atlas

value: male and female


title: mSAGE_Kidney_normal_TS24_MMD_SM082

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1344
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: kidney, normal, microscope dissected, ts24, late gestation embryo, extracted short sage, atlas


title: mSAGE_Limb_normal_TS17_MMD_SM172

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1706
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: limb, forelimb, normal, microscope dissected, extracted short sage, ts17, mid-gestation embryo


title: mSAGE_Hindlimb_bud_normal_TS19_B

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1093
Laboratory: Elliott H. Margulies,  Sharon L. R. Kardia , Jeffrey W. Innis

source_name: hindlimb, normal, bulk, short sage, mid-gestation embryo

value: bulk

value: SAGE expression profile of developing hindlimbs. Used to define unique patterns of transcription between developing forelimbs and hindlimbs. (NCBI name:mouse_hindlimb)


title: mSAGE_Hippocampus_normal_B_SAL

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1086
Laboratory: Dorine Feldker, Nicole Datson, Alexa Veenema,  Erik Meulmeester, E. Ronald de Kloet, Erno Vreugdenhil

source_name: hippocampus, normal, adult, bulk, short attack latency, short sage

value: brain

value: Two wild house mice lines were genetically selected for short and long attack latency. Mice with an attack latency <50s were considered short attack latency mice (SAL). RNA from the hippocampus of 14 SAL mice was pooled and used as input material for the SAGE library. (NCBI nmae:mouse hippocampus:short attack latency (SAL) mice)


title: mSAGE_Hypothalamus_normal_adult_B_46

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 923
Laboratory: Seth Blackshaw, Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute

source_name: brain, hypothalamus, normal, bulk, adult, male, short sage, c57bl/6

value: 7 weeks

value: male

value: Wildtype


title: mSAGE_Heart_normal_TS20_MMD_SM003

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 629
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: heart, ventricle, normal, microscope dissected, mid-gestation embryo, short sage, ts20, atlas

value: heart

value: 12.5 days post coitum. earliest signs of fingers. theiler stage 20

value: unknown


title: mSAGE_Kidney_normal_P84_MMD_SM104

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1728
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: kidney, normal, microscope dissected, extracted short sage, 84 days post natal

value: 12 weeks


title: mSAGE_Hippocampus_normal_B_LAL

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1085
Laboratory: Dorine Feldker, Nicole Datson, Alexa Veenema,  Erik Meulmeester, E. Ronald de Kloet, Erno Vreugdenhil

source_name: hippocampus, normal, bulk, short sage, long attack latency, adult

value: Two wild house mice lines were genetically selected for short and long attack latency. Mice with an attack latency >600s were considered long attack latency mice (LAL). RNA from the hippocampus of 14 LAL mice was pooled and used as input material for a SAGE library. (NCBI name:mouse hippocampus:long attack latency (LAL) mice)


title: mSAGE_Heart_normal_TS9_MMD_SM174

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2027
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: heart, normal, microscope dissected, e8.5, ts9, extracted short sage

value: microscope dissected

value: normal

value: Foxh1 -/-


title: mSAGE_Large_intestine_normal_TS20_MMD_SM155

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2006
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: large_intestine, tissues, normal, microscope dissected, e12, ts20, unknown, extracted short  sage

value: tissues


title: mSAGE_Heart_normal_TS19_MMD_SM004

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1257
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: heart, atrium, normal, microscope dissected, mid-gestation embryo, extracted short sage, ts19, atlas

value: 11.5 days post coitum. lens vesicle completely separated from surface. theiler stage 19


title: mSAGE_Heart_normal_TS19_MMD_SM008

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1259
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: heart, atrioventricular canal, normal, microscope dissected, mid-gestation embryo, extracted short sage, ts19, atlas


title: mSAGE_Heart_normal_TS15_MMD_SM006

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1258
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: heart, atrium, normal, microscope dissected, mid-gestation embryo, extracted short  sage, ts14, atlas


title: mSAGE_Fibroblasts_normal_CL_3T3

description:
Tagging_enzyme: BsmF I
CGAP_Numeric_library_ID: 1585
Library_producer: Velculescu VE
Laboratory: Vogelstein B, and Kinzler KW
References: Veculescu, V., Unpublished.

source_name: fibroblast, uncharacterized tissue, normal, cell line, short sage

value: uncharacterized tissue

value: cell line