title: Rat striatum SAGE of methamphetamine treatment

status: Public on Sep 30 2004

first: Ning-sheng

last: Cai

address: 5500 Nathan Shock Drive

department: Molecular Neuropsychiatry Branch

institute: National Institute on Drug Abuse

description:
SAGE profile from rat striatum treated with 40mg/kg methamphetamine (METH)
Keywords = rat
Keywords = striatum
Keywords = methamphetamine
Keywords = SAGE

source_name: rat striatum (Sprague-Dawley)


title: injured LSEC

status: Public on Oct 01 2004

type: SAGE

anchor: NlaIII

city: Tokyo

first: Hidenori

last: Nonaka

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

department: Institute of Molecular and Cellular Biosciences

country: Japan

institute: University of Tokyo

description: LSECs from injured liver by carbon tetrachloride administration  (8-10 weeks male)

molecule: total RNA

organism: Mus musculus

source_name: C57BL/6J mouse liver sinusoidal endothelial cells


title: normal LSEC

description: LSECs from normal liver (8-10 weeks male)


title: granulosa cells, PMSG-treated

status: Public on Sep 17 2004

city: Glasgow

first: Peter

middle: James

last: O'Shaughnessy

address: Bearsden Rd

department: Veterinary Preclinical Studies

country: United Kingdom

institute: University of Glasgow Veterinary School

description: granulosa cells isolated from immature mice (18-22days) treated 48h earlier with 5IU PMSG

source_name: granulosa cells


title: granulosa cells, PMSG/hCG-treated

description: granulosa cells isolated from immature mice (18-22days) treated with 5IU PMSG followed 48h later with 5IU hCG. Cells were isolated 12h after hCG treatment


title: Rat striatum SAGE

city: Baltimore

state: MD

country: USA

description:
SAGE profile from rat striatum treated with saline
Keywords = rat
Keywords = striatum
Keywords = SAGE

organism: Rattus norvegicus


title: F1477-I14 versus pool

status: Public on Sep 04 2004

type: RNA

city: Seattle

first: Stephen

middle: W

last: Edwards

state: WA

department: Research Genetics

institute: Rosetta Inpharmatics (Merck & Co.)

description:
Lymphoblastoid cell lines were obtained from Coriell Repositories.
Sample identifiers consist of the family identifier and individual identifier for the sample source.
All individuals were compared to a common pool created from equal portions of RNA from all samples.
See Monks, et al., American Journal of Human Genetics (2004) for details.

organism: Homo sapiens

tag: Description

value: CEPH 1477 MATERNALGRANDMOTHER GM12910

source_name: pool

tag: A common pool created from equal portions of RNA from all samples.


title: U937 cell line untreated

status: Public on Oct 23 2004

city: Montpellier

first: David

last: Piquemal

address: 1682, rue de la Valsière

country: France

institute: ACOBIOM

description:
U937 cells (ATCC CRL-1593.2 Rockville MD, USA) were grown in RPMI 1640 (Life Technologies, Cergy-Pontoise, France) supplemented with 10% fetal calf serum. Cell cultures were checked for the absence of mycoplasma contaminations (Mycoplasma Detection kit, Boehringer Mannheim, Meylan, France) and performed without antibiotics to avoid masking silent bacterial contaminations.
Keywords = U937 proliferative cells
Lot batch = ATCC CRL-1593.2

source_name: U937 cell line


title: F1477-I9 versus pool

value: CEPH 1477 SON GM12905


title: F1477-I4 versus pool

value: CEPH 1477 DAUGHTER GM12900


title: F1477-I3 versus pool

value: CEPH 1477 DAUGHTER GM12899


title: F1424-I14 versus pool

value: CEPH 1424 MATERNALGRANDMOTHER GM11933


title: F1477-I5 versus pool

value: CEPH 1477 DAUGHTER GM12901


title: F1477-I7 versus pool

value: CEPH 1477 SON GM12903


title: F1477-I8 versus pool

value: CEPH 1477 DAUGHTER GM12904


title: F1477-I11 versus pool

value: CEPH 1477 DAUGHTER GM12907


title: F1477-I2 versus pool

value: CEPH 1477 MOTHER GM12898


title: F1424-I13 versus pool

value: CEPH 1424 MATERNALGRANDFATHER GM11932


title: F1477-I13 versus pool

value: CEPH 1477 PATERNALGRANDMOTHER GM12909


title: F1424-I12 versus pool

value: CEPH 1424 PATERNALGRANDMOTHER GM11931


title: F1424-I9 versus pool

value: CEPH 1424 SON GM11928


title: F1477-I12 versus pool

value: CEPH 1477 PATERNALGRANDFATHER GM12908


title: F1424-I10 versus pool

value: CEPH 1424 SON GM11929


title: F1424-I4 versus pool

value: CEPH 1424 SON GM11923


title: F1424-I11 versus pool

value: CEPH 1424 PATERNALGRANDFATHER GM11930


title: F1424-I6 versus pool

value: CEPH 1424 SON GM11925


title: F1424-I5 versus pool

value: CEPH 1424 DAUGHTER GM11924


title: F1424-I2 versus pool

value: CEPH 1424 MOTHER GM10844


title: F1424-I7 versus pool

value: CEPH 1424 DAUGHTER GM11926


title: F1477-I1 versus pool

value: CEPH 1477 FATHER GM12897


title: F1424-I8 versus pool

value: CEPH 1424 SON GM11927


title: F1424-I3 versus pool

value: CEPH 1424 SON GM11922


title: F1424-I1 versus pool

value: CEPH 1424 FATHER GM10845


title: F1421-I10 versus pool

value: CEPH 1421 PATERNALGRANDMOTHER GM12283


title: AML_t(15;17)_LIB1

status: Public on Dec 01 2005

city: Evanston

first: San Ming

last: Wang

state: IL

address: 1001 University Place

department: Center for Functional Genomics

institute: ENH Research Institute, Northwestern University

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

source_name: bone marrow, CD15+ myeloid progenitor cells

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


title: F1421-I13 versus pool

value: CEPH 1421 MATERNALGRANDFATHER GM12286


title: F1421-I9 versus pool

value: CEPH 1421 PATERNALGRANDFATHER GM12282


title: F1421-I12 versus pool

value: CEPH 1421 SON GM12285


title: F1418-I12 versus pool

value: CEPH 1418 PATERNALGRANDMOTHER GM12273


title: F1421-I7 versus pool

value: CEPH 1421 DAUGHTER GM12280


title: F1421-I11 versus pool

value: CEPH 1421 SON GM12284


title: F1421-I2 versus pool

value: CEPH 1421 MOTHER GM10840


title: F1418-I9 versus pool

value: CEPH 1418 DAUGHTER GM12270


title: F1421-I8 versus pool

value: CEPH 1421 SON GM12281


title: F1421-I1 versus pool

value: CEPH 1421 FATHER GM10841


title: F1421-I5 versus pool

value: CEPH 1421 DAUGHTER GM12278


title: F1421-I4 versus pool

value: CEPH 1421 DAUGHTER GM12277


title: F1418-I14 versus pool

value: CEPH 1418 MATERNALGRANDMOTHER GM12275


title: F1418-I11 versus pool

value: CEPH 1418 PATERNALGRANDFATHER GM12272


title: F1418-I8 versus pool

value: CEPH 1418 SON GM12269


title: F1418-I10 versus pool

value: CEPH 1418 DAUGHTER GM12271


title: F1418-I7 versus pool

value: CEPH 1418 DAUGHTER GM12268


title: F1418-I5 versus pool

value: CEPH 1418 DAUGHTER GM12266


title: F1418-I6 versus pool

value: CEPH 1418 SON GM12267


title: F1418-I4 versus pool

value: CEPH 1418 DAUGHTER GM12265


title: F1408-I14 versus pool

value: CEPH 1408 DAUGHTER GM12157


title: F1408-I5 versus pool

value: CEPH 1408 DAUGHTER GM12149


title: F1408-I9 versus pool

value: CEPH 1408 SON GM12153


title: F1408-I8 versus pool

value: CEPH 1408 SON GM12152


title: F1408-I10 versus pool

value: CEPH 1408 PATERNALGRANDFATHER GM12154


title: F1408-I7 versus pool

value: CEPH 1408 DAUGHTER GM12151


title: F1377-I10 versus pool

value: CEPH 1377 PATERNALGRANDFATHER GM11891


title: F1408-I2 versus pool

value: CEPH 1408 MOTHER GM10831


title: F1408-I13 versus pool

value: CEPH 1408 MATERNALGRANDMOTHER GM12156


title: F1377-I4 versus pool

value: CEPH 1377 SON GM11885


title: F1377-I5 versus pool

value: CEPH 1377 SON GM11886


title: F1408-I6 versus pool

value: CEPH 1408 DAUGHTER GM12150


title: F1377-I3 versus pool

value: CEPH 1377 SON GM11884


title: F1408-I4 versus pool

value: CEPH 1408 SON GM12148


title: F1408-I3 versus pool

value: CEPH 1408 DAUGHTER GM12147


title: F1377-I8 versus pool

value: CEPH 1377 SON GM11889


title: F1377-I11 versus pool

value: CEPH 1377 PATERNALGRANDMOTHER GM11892


title: F1408-I12 versus pool

value: CEPH 1408 MATERNALGRANDFATHER GM12155


title: F1377-I13 versus pool

value: CEPH 1377 MATERNALGRANDMOTHER GM11894


title: F1377-I12 versus pool

value: CEPH 1377 MATERNALGRANDFATHER GM11893


title: F1421-I14 versus pool

value: CEPH 1421 MATERNALGRANDMOTHER GM12287


title: F1377-I2 versus pool

value: CEPH 1377 MOTHER GM10864


title: F1375-I11 versus pool

value: CEPH 1375 MATERNALGRANDFATHER GM12264


title: F1375-I6 versus pool

value: CEPH 1375 DAUGHTER GM12232


title: F1375-I8 versus pool

value: CEPH 1375 SON GM12263


title: F1375-I13 versus pool

value: CEPH 1375 SON GM12235


title: F1375-I2 versus pool

value: CEPH 1375 MOTHER GM10863


title: F1375-I7 versus pool

value: CEPH 1375 DAUGHTER GM12233


title: F1375-I5 versus pool

value: CEPH 1375 DAUGHTER GM12231


title: F1375-I1 versus pool

value: CEPH 1375 FATHER GM10862


title: F1375-I3 versus pool

value: CEPH 1375 SON GM12229


title: F1362-I16 versus pool

value: CEPH 1362 MATERNALGRANDMOTHER GM11995


title: F1362-I12 versus pool

value: CEPH 1362 DAUGHTER GM11991


title: F1362-I11 versus pool

value: CEPH 1362 SON GM11990


title: F1375-I12 versus pool

value: CEPH 1375 MATERNALGRANDMOTHER GM12234


title: F1362-I17 versus pool

value: CEPH 1362 SON GM11996


title: F1362-I14 versus pool

value: CEPH 1362 PATERNALGRANDMOTHER GM11993


title: F1362-I9 versus pool

value: CEPH 1362 DAUGHTER GM11988


title: F1362-I13 versus pool

value: CEPH 1362 PATERNALGRANDFATHER GM11992


title: F1362-I10 versus pool

value: CEPH 1362 DAUGHTER GM11989


title: F1362-I15 versus pool

value: CEPH 1362 MATERNALGRANDFATHER GM11994


title: F1362-I8 versus pool

value: CEPH 1362 SON GM11987


title: F1362-I7 versus pool

value: CEPH 1362 DAUGHTER GM11986


title: F1362-I3 versus pool

value: CEPH 1362 DAUGHTER GM11982


title: F1362-I6 versus pool

value: CEPH 1362 DAUGHTER GM11985


title: F1362-I1 versus pool

value: CEPH 1362 FATHER GM10860


title: F1358-I14 versus pool

value: CEPH 1358 MATERNALGRANDMOTHER GM12718


title: F1362-I5 versus pool

value: CEPH 1362 SON GM11984


title: F1358-I8 versus pool

value: CEPH 1358 DAUGHTER GM12714


title: F1358-I12 versus pool

value: CEPH 1358 PATERNALGRANDMOTHER GM12717


title: F1358-I11 versus pool

value: CEPH 1358 PATERNALGRANDFATHER GM12716


title: F1358-I7 versus pool

value: CEPH 1358 SON GM12713


title: F1358-I15 versus pool

value: CEPH 1358 SON GM12719


title: F1358-I9 versus pool

value: CEPH 1358 DAUGHTER GM12715


title: F1362-I4 versus pool

value: CEPH 1362 DAUGHTER GM11983


title: F1358-I6 versus pool

value: CEPH 1358 SON GM12712


title: F1358-I1 versus pool

value: CEPH 1358 FATHER GM12707


title: F1358-I3 versus pool

value: CEPH 1358 SON GM12709


title: F1418-I2 versus pool

value: CEPH 1418 MOTHER GM10836


title: F1358-I2 versus pool

value: CEPH 1358 MOTHER GM12708


title: F1350-I13 versus pool

value: CEPH 1350 MATERNALGRANDMOTHER GM11832


title: F1350-I12 versus pool

value: CEPH 1350 MATERNALGRANDFATHER GM11831


title: F1350-I10 versus pool

value: CEPH 1350 PATERNALGRANDFATHER GM11829


title: F1350-I11 versus pool

value: CEPH 1350 PATERNALGRANDMOTHER GM11830


title: F1350-I8 versus pool

value: CEPH 1350 DAUGHTER GM11827


title: F1350-I7 versus pool

value: CEPH 1350 DAUGHTER GM11826


title: F1350-I9 versus pool

value: CEPH 1350 DAUGHTER GM11828


title: F1350-I3 versus pool

value: CEPH 1350 SON GM11822


title: F1350-I2 versus pool

value: CEPH 1350 MOTHER GM10855


title: F1349-I11 versus pool

value: CEPH 1349 PATERNALGRANDFATHER GM11843


title: F1349-I7 versus pool

value: CEPH 1349 DAUGHTER GM11835


title: F1377-I1 versus pool

value: CEPH 1377 FATHER GM10865


title: F1349-I8 versus pool

value: CEPH 1349 DAUGHTER GM11836


title: F1349-I9 versus pool

value: CEPH 1349 DAUGHTER GM11837


title: F1349-I4 versus pool

value: CEPH 1349 SON GM11841


title: F1349-I14 versus pool

value: CEPH 1349 MATERNALGRANDMOTHER GM11840


title: F1350-I5 versus pool

value: CEPH 1350 DAUGHTER GM11824


title: F1349-I3 versus pool

value: CEPH 1349 DAUGHTER GM11833


title: F1346-I11 versus pool

value: CEPH 1346 PATERNALGRANDFATHER GM12043


title: F1349-I2 versus pool

value: CEPH 1349 MOTHER GM10854


title: F1346-I12 versus pool

value: CEPH 1346 PATERNALGRANDMOTHER GM12044


title: F1349-I5 versus pool

value: CEPH 1349 SON GM11834


title: F1349-I1 versus pool

value: CEPH 1349 FATHER GM10853


title: F1349-I10 versus pool

value: CEPH 1349 SON GM11838


title: F1346-I13 versus pool

value: CEPH 1346 MATERNALGRANDFATHER GM12045


title: F1349-I6 versus pool

value: CEPH 1349 DAUGHTER GM11842


title: F1346-I8 versus pool

value: CEPH 1346 DAUGHTER GM12040


title: F1346-I4 versus pool

value: CEPH 1346 SON GM12036


title: F1346-I7 versus pool

value: CEPH 1346 SON GM12039


title: F1345-I8 versus pool

value: CEPH 1345 SON GM07355


title: F1345-I13 versus pool

value: CEPH 1345 MATERNALGRANDMOTHER GM07345


title: F1346-I5 versus pool

value: CEPH 1346 SON GM12037


title: F1345-I12 versus pool

value: CEPH 1345 MATERNALGRANDFATHER GM07357


title: F1345-I7 versus pool

value: CEPH 1345 DAUGHTER GM07354


title: F1346-I10 versus pool

value: CEPH 1346 DAUGHTER GM12042


title: F1345-I9 versus pool

value: CEPH 1345 SON GM07356


title: F1346-I1 versus pool

value: CEPH 1346 FATHER GM10857


title: F1362-I2 versus pool

value: CEPH 1362 MOTHER GM10861


title: F1345-I4 versus pool

value: CEPH 1345 SON GM07351


title: F1345-I5 versus pool

value: CEPH 1345 SON GM07352


title: F1345-I1 versus pool

value: CEPH 1345 FATHER GM07349


title: F1340-I13 versus pool

value: CEPH 1340 SON GM11821


title: F1345-I6 versus pool

value: CEPH 1345 SON GM07353


title: F1340-I10 versus pool

value: CEPH 1340 PATERNALGRANDMOTHER GM07000


title: F1340-I12 versus pool

value: CEPH 1340 MATERNALGRANDMOTHER GM07056


title: F1345-I2 versus pool

value: CEPH 1345 MOTHER GM07348


title: F1340-I8 versus pool

value: CEPH 1340 SON GM07027


title: F1340-I11 versus pool

value: CEPH 1340 MATERNALGRANDFATHER GM07022


title: F1340-I3 versus pool

value: CEPH 1340 DAUGHTER GM07062


title: F1340-I5 versus pool

value: CEPH 1340 SON GM07008


title: F1340-I7 versus pool

value: CEPH 1340 SON GM07342


title: F1334-I13 versus pool

value: CEPH 1334 MATERNALGRANDMOTHER GM12239


title: Adipose tissue of gonadectomized male mice

status: Public on Aug 18 2004

city: Ste-Foy

first: Carl

last: Bolduc

state: Québec

address: 2705 Boul. Laurier

department: Anatomy and physiology

country: Canada

institute: Molecular Endocrinology and Oncology Research Center, Laval University Medical Center (CHUL)

description: This sample correspond to retroperitoneal adipose tissue of gonadectomized C57BL6 male mice.

source_name: Retroperitoneal adipose tissue


title: Bovine circulating CD4 T lymphocytes

status: Public on Aug 28 2004

city: Ames

first: John

middle: D.

last: Neill

state: IA

address: 2300 Dayton Ave.

institute: National Animal Disease Center

description: CD4 lymphocytes were purified from buffy coats from pooled serum of 3 Holsteins by positive monoclonal antibody selection

organism: Bos taurus

source_name: circulating bovine CD4 lymphocytes


title: F1334-I12 versus pool

value: CEPH 1334 MATERNALGRANDFATHER GM12146


title: Adipose tissue of GDX + DHT 3h male mice

description: This sample correspond to retroperitoneal adipose tissue of gonadectomized C57BL6 male mice injected with dihydrotestosterone. The mice were sacrificed 3 hours after the dihydrotestosterone administration.


title: F1340-I2 versus pool

value: CEPH 1340 MOTHER GM07019


title: SAGE_CGAP_GY0 Swarm rat chondrosarcoma tibia tumor

status: Public on Jul 24 2004

city: Iowa City

first: Thomas

middle: L.

last: Casavant

department: Electrical & Computer Department

institute: University of Iowa

description:
This library represents a Cancer Genome Anatomy Project libray, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy project (CGAP:http://cgap.nci.nih.gov) is an interdisplinary program established and administered by the National Cancer Institute (NCI:http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Swarm rat chondrosarcoma tumor line JWS was grown subcutaneously (25 days) in a Spargue-Dawley rats, the tumor was then harvested, and transplanted into the medullar cavity of the tibia of a new set of Sprague Dawley male rats. The tibia tumor was harvested 35-40 days post tumor transplantation.   mRNA was isolated from the rat tibia chondrosarcoma using Trizol, followed by the use of a direct mRNA extraction kit.
Vector: pUC-18
R. Site1:Sma1
R. Site2:Sma1
Keywords = Swarm rat chondrosarcoma tibia tumor

source_name: mRNA Swarm rat chondrosarcoma tibia tumor, tissue line JWS


title: F1334-I3 versus pool

value: CEPH 1334 SON GM12138


title: F1334-I9 versus pool

value: CEPH 1334 SON GM12143


title: SAGE_CGAP_HR0 Swarm rat chondrosarcoma lung tumor

description:
This library represents a Cancer Genome Anatomy Project libray, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy project (CGAP:http://cgap.nci.nih.gov) is an interdisplinary program established and administered by the National Cancer Institute (NCI:http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Swarm rat chondrosarcoma (SRC) tumor line JWS was grown subcutaneously for 21 days in Sprague-Dawely male rats. The subcutaneous Swarm rat chondrosarcoma JWS tumor was then harvested and transplanted into the proximal tibia of 8 week old male Sprague-Dawely rats. Forty-two days post tibia Swarm rat chondrosarcoma transplantation the rats were euthanized, and Swarm rat chondrosarcoma tumor was collected from the lungs. Swarm rat chondrosarcoma JWS lung tumors from five separate rats were pooled for RNA isolation and this RNA was used for the construction of the SAGE library HR0.  Vector: pUC-18
R. Site1:Sma1
R. Site2:Sma1
Keywords = Swarm rat chondrosarcoma tumor

source_name: mRAN from Swarm rat chondrosarcoma tumor line


title: F1334-I8 versus pool

value: CEPH 1334 SON GM12238


title: SAGE_CGAP_HF0 Swarm rat chondrosarcoma

description:
This library represents a Cancer Genome Anatomy Project libray, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy project (CGAP:http://cgap.nci.nih.gov) is an interdisplinary program established and administered by the National Cancer Institute (NCI:http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Swarm rat chondrosarcoma TGO is a subcutaneously grown rat chondrosarcoma that is derived from a subcutaneous transplantation of the Swarm rat chondrosarcoma tissue line TG0 into Sprague-Dawley male rats. The subcutaneously grown Swarm rat chondrosarcoma tissue was harvested 3 weeks after initial tumor transplantation. mRNA was isolated from the rat chondrosarcoma using Trizol, followed by the use of a direct mRNA extraction kit.
Vector: pUC-18
R. Site1:Sma1
R.  Site2:Sma1
Keywords = Subcutaneous Swarm rat chondrosarcoma tibia tumor

source_name: mRNA from subcutaneously grown Swarm rat chondrosarcoma tissue line TGO


title: SAGE_CGAP_GF0 rat articular cartilage

description:
This library represents a Cancer Genome Anatomy Project libray, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy project (CGAP:http://cgap.nci.nih.gov) is an interdisplinary program established and administered by the National Cancer Institute (NCI:http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Femoral head cartilage isolated from 38 day old Outbreed Sprague-Dawley male rats.  Femoral head cartilage was collected from 29 rats.  mRNA was isolated using Trizol, followed by the use of a direct mRNA extraction kit.  Vector used pUC-18 and restriction sites are Site1:Sma1 and site2:Sma1
Keywords = rat femoral cartilage

source_name: mRAN from rat femoral head cartilage


title: FSCHW_ANGII_7DH

status: Public on Jul 22 2004

city: Boston

first: Faina

last: Schwartz

state: MA

address: 700 Albany Street,W508

department: Medicine, Hypertension Section

institute: Boston University School of Medicine

description: C57Bl/6J mice received continuous administration of Angiotensin II via implanted minipumps for 7 days, total RNA prepared from homogenized hearts, SAGE library constructed from heart RNA pooled from 6 mice

source_name: HEART


title: FSCHW_SALINE_7DH

description: C57Bl/6J mice received continuous saline infusion via implanted minipumps for 7 days, total RNA prepared for homogenized hearts, SAGE library constructed from heart RNA pooled from 6 mice


title: F1334-I1 versus pool

value: CEPH 1334 FATHER GM10846


title: F1334-I11 versus pool

value: CEPH 1334 PATERNALGRANDMOTHER GM12145


title: Day 11 pre-implantation embryos

status: Public on Jul 01 2004

city: Beltsville

first: Jane

middle: Garlow

last: McDougal

address: 10300 Baltimore Avenue, BARC-East, Bldg 200, Rm 101A

department: USDA

institute: ANRI

description:
Comparison of gene expression in in vivo derived pre-implantation porcine embryos.  An attempt to elucidate mechanisms involved during pre-implantation embryo development.
Keywords = pre-implantation
Keywords = embryo
Keywords = porcine
Lot batch =

organism: Sus scrofa

source_name: Day 11 Porcine embryos


title: Day 12 pre-implantation embryos

source_name: Day 12 Porcine Embryo


title: C. elegans FACS sorted ciliated neurons

status: Public on Jun 11 2004

city: Vancouver

first: Kim

last: Wong

state: BC

address: 600 West 10th Avenue

institute: British Columbia Cancer Agency

description:
Libraries were constructed from total RNA from FACS sorted embryonic ciliated neurons (bbs-1::GFP); 21 bp tags (LongSAGE).  Tagging enzyme: MmeI.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = ciliated neurons
Keywords = LongSage
Lot batch =

organism: Caenorhabditis elegans


title: C. elegans FACS sorted muscle

description:
Libraries were constructed from total RNA from FACS sorted embryonic muscle cells (myo-3::GFP); 21 bp tags (LongSAGE).  Tagging enzyme: MmeI.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = muscle
Keywords = LongSage
Lot batch =


title: C. elegans whole embryo (LongSAGE)

description:
Libraries were constructed from total RNA from whole embryos, 21 bp. tags (strain N2); 21 bp tags (LongSAGE). Tagging enzyme: MmeI.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = embryo
Keywords = LongSAGE
Lot batch =

source_name: whole embryos (strain N2)


title: C. elegans adult gut (glp-4)

description:
Libraries were constructed from total RNA from manually dissected gut of adult worms (glp-4); 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = gut
Lot batch =

source_name: dissected gut from adult worms (glp-4)


title: C. elegans dauer larvae

description:
Libraries were constructed from total RNA from dauer larvae. 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = dauer
Lot batch =

source_name: dauer larvae


title: C. elegans adult (fer-15, 6 days)

description:
Libraries were constructed from total RNA from 6 day old worms (fer-15); 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = ageing
Lot batch =

source_name: whole adult worms (fer-15, 6 days)


title: C. elegans mixed stage

description:
Libraries were constructed from total RNA from mixed stage larvae/worms.  14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Lot batch =

source_name: mixed stage larvae/worms


title: C. elegans L1 larvae

description:
Libraries were constructed total RNA from whole L1 stage larvae (strain N2); 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = L1 larvae
Lot batch =

source_name: L1 larvae (strain N2)


title: C. elegans L2 larvae

description:
Libraries were constructed from total RNA from whole L2 stage larvae (strain N2); 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = L2 larvae
Lot batch =

source_name: L2 larvae (strain N2)


title: C. elegans FACS sorted gut

description:
Libraries were constructed from total RNA from FACS sorted embryonic gut cells (elt-2::GFP); 21 bp tags (LongSAGE).  Tagging enzyme: MmeI.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = gut
Keywords = LongSAGE
Lot batch =


title: C. elegans adult worms (glp-4)

description:
Libraries were constructed from total RNA from whole adult worms (glp-4); 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Lot batch =

source_name: adult worms (glp-4)


title: bovine gamma/delta T cells

status: Public on Jun 10 2004

description:
bovine circulating gamma/delta T cells isolated and pooled from 4 9 week old holstein calves
Keywords = bovine gamma/delta T cells

source_name: circulating gamma/delta T cells


title: C. elegans L3 larvae

description:
Libraries were constructed from total RNA from whole L3 stage larvae (strain N2); 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = L3 larvae
Lot batch =

source_name: L3 larvae (strain N2)


title: C. elegans L4 larvae

description:
Libraries were constructed from total RNA from whole L4 stage larvae (strain N2); 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = L4 larvae
Lot batch =

source_name: L4 larvae (strain N2)


title: C. elegans adult (fer-15, 1 day)

description:
Libraries were constructed from total RNA from 1 day old worms (fer-15); 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = ageing
Lot batch =

source_name: whole adult worms (fer-15, 1 day)


title: C. elegans young adult worms

description:
Libraries were constructed from total RNA from whole young adult worms (strain N2); 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = young adult whole worms
Lot batch =

source_name: young adult whole worms (strain N2)


title: C. elegans whole embryos

description:
Libraries were constructed from total RNA from whole embryos (strain N2); 14 bp tags.  Tagging enzyme: BsmF1.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = embryo
Lot batch =


title: D3 ES

status: Public on Jun 01 2004

first: Kenneth

middle: R.

last: Boheler

address: 5600 Nathan Shock Drive

department: GRC

institute: National Institute on Aging, NIH

description:
D3 ES Cells

Linker-based, Poly(A) and short clone-generated tags (=<4 tags per clone) are extracted.
Keywords = ES

source_name: D3 ES Cells


title: normal MDBK cells

status: Public on May 31 2004

description: MDBK cells at 90 - 95% confluency

source_name: Madin-Darby bovine kidney cells


title: F1340-I6 versus pool

description:
Lymphoblastoid cell lines were obtained from Coriell Repositories.
Sample identifiers consist of the family identifier and individual identifier for the sample source.
All individuals were compared to a common pool created from equal portions of RNA from all samples.
See Monks, et al., American Journal of Human Genetics (2004) for details.

value: CEPH 1340 SON GM07040

source_name: pool


title: Kidney outer medullary collecting duct: Control

status: Public on May 29 2004

city: Paris

first: Alain

last: Doucet

institute: Institut des Cordeliers

description:
Library obtained from microdissected kidney outer medullary collecting duct from control C57Bl6/J mice .The library was generated using Sau3A I as anchoring enzyme. Data are  provided after removal of linker derived sequences.
Keywords = microdissection
Keywords = nephron
Keywords = SADE

source_name: microdissected outer medullary collecting duct


title: Retroperitoneal adipose tissue

status: Public on Apr 24 2004

description: This SAGE library was produced from intact male mice retroperitoneal adipose tissue

source_name: Retroperitoneal adipose tissue


title: Kidney outer medullary collecting duct

description:
Library obtained from microdissected kidney outer medullary collecting duct from C57Bl6/J mice after 3 days potassium-depleted diet.The library was generated using Sau3A I as anchoring enzyme. Data are  provided after removal of linker derived sequences.
Keywords = microdissection
Keywords = nephron
Keywords = SADE


title: Adipose tissue of GDX + DHT 24h male mice

description: This sample correspond to retroperitoneal adipose tissue of gonadectomized C57BL6 male mice injected with dihydrotestosterone. The mice were sacrificed 24 hours after the dihydrotestosterone administration.


title: bovine immature B cell

status: Public on Feb 01 2004

description:
Immature B cells isolated from ileal Peyer's patch from clinically normal cattle
Keywords = B cell
Keywords = Peyer's patch

source_name: ileal Peyer's patch follicle


title: AT-TERT dermal fibroblasts

status: Public on Jan 14 2004

first: Agnes

last: Baross

description: AT skin primary fibroblasts (AG 04405 strain from the National Institute of Aging Cell Culture Repository) were cultured in Ham's F10 medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 ug/ml streptomycin. The cells were transduced with TERT cDNA at population doubling PD=17. The population doubling of TERT expressing AT cells chosen for SAGE library construction was PD=21. The cells were ~80% confluent at the time of RNA isolation.

source_name: A-T homozygous skin fibroblast cells immortalized by telomerase overexpression


title: BJ dermal fibroblasts

description: BJ neonatal foreskin primary fibroblasts were cultured in Ham's F10 medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 ug/ml streptomycin. The population doubling (PD) of cells chosen for SAGE library construction was PD=37. The cells were ~80% confluent at the time of RNA isolation.

source_name: BJ foreskin primary fibroblast cells


title: post natal day 9 mouse total cornea

status: Public on Jan 02 2004

city: Bethesda

first: Barbara

last: Norman

address: MSC2730, 9000 Rockville Pike

department: National Eye Institute

institute: National Institutes of Health

description:
post natal day 9 C57/Bl6 mouse total cornea
Keywords = cornea

source_name: post natal day 9 mouse total cornea


title: BVDV2-infected MDBK cells

description: Madin-Darby bovine kidney cells were infected at 40% cofluency with MOI of 1.0 of BVDV2 strain 1373.  Cells were collected at 48 hours post-infection when cells were 95% confluent

source_name: BVDV2-infected MDBK cells


title: Undifferentiated HES3 Human Embryonic Stem Cells

status: Public on Jan 19 2004

city: Singapore

first: Mark

last: Richards

country: Singapore

institute: National University of Singapore

description:
Undifferentiated 40P HES3 (XX) human embryonic stem cells grown on mouse embryonic fibroblast feeder layers. HES3 is a proprietary human ES cell line of ES Cell International Pte Ltd. Singapore.
Keywords = undifferentiated, human embryonic stem cell

source_name: Undifferentiated HES3 40P Human Embryonic Stem Cells


title: BJ-TERT dermal fibroblasts

description: BJ neonatal foreskin primary fibroblasts were cultured in Ham's F10 medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 ug/ml streptomycin. The cells were transduced with TERT cDNA at population doubling PD=63. The population doubling of TERT expressing cells chosen for SAGE library construction was PD=110. The cells were ~80% confluent at the time of RNA isolation.

source_name: BJ foreskin fibroblast cells immortalized by telomerase overexpression


title: mouse liver: C57BL/6JIco (B6)

status: Public on Nov 10 2003

city: Leiden

first: Nicole

last: Datson

department: Medical Pharmacology

country: Netherlands

institute: Leiden University

description: 10 female B6 mice, aged 10 weeks, were used in the experiments. Total RNA from the caudate liver lobe was isolated. RNA from all ten animals was pooled and used as input in the SAGE procedure.

source_name: mouse liver


title: 6-week mouse total cornea

description:
6-week C57/Bl6 mouse total cornea
Keywords = cornea

source_name: 6-week C57/Bl6 mouse cornea


title: Undifferentiated HES4 Human Embryonic Stem Cells

description:
Undifferentiated 40P HES4 (XY) human embryonic stem cells grown on mouse embryonic fibroblast feeder layers. HES4 is a proprietary human ES cell line of ES Cell International Singapore Pte Ltd. Singapore.
Keywords = undifferentiated, human embryonic stem cell

source_name: Undifferentiated HES4 40P Human Embryonic Stem Cells


title: AT dermal fibroblasts

description: AT skin primary fibroblasts (AG 04405 strain from the National Institute of Aging Cell Culture Repository) were cultured in Ham's F10 medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 ug/ml streptomycin. The population doubling (PD) of cells chosen for SAGE library construction was PD=21. The cells were ~80% confluent at the time of RNA isolation.

source_name: A-T homozygous skin fibroblast cells


title: Cardiac fibroblast

status: Public on Dec 05 2003

city: Dublin

first: Albert

middle: Peter

last: Smolenski

address: Belfield

department: Conway Institute

country: Ireland

institute: University College Dublin

description:
Cardiac fibroblasts were isolated from 3-month old C57BL/6 mice.
RNA was prepared from quiescent, serum-starved cardiac fibroblasts in passage 15.
A total number of 118654 tags was sequenced. After removal of duplicate ditags and linker-derived sequences 110169 tags remained.
Keywords = cardiac
Keywords = fibroblast
Keywords = mouse
Keywords = heart

molecule: polyA RNA

source_name: cardiac fibroblasts isolated from adult mouse heart

extract_protocol: TRIzol reagent (Invitrogen) followed by oligo(dT) cellulose (Ambion)


title: mouse liver: apoE3L transgenics

description: ApoE3-Leiden(E3L) transgenic mice were used in this SAGE study. E3L mice carry the human apoE3-Leiden and apoC1 gene cluster on an inbred C57BL/6J (B6) background. In humans the apoE3-Leiden mutation is associated with a dominantly inherited form of familial dysbetalipoproteinemia. E3L mice show a profound diet-induced hyperlipidemia and susceptibility to atherosclerosis.


title: Kidney outer medullary collecting duct.

status: Public on Nov 08 2003

city: 91191 Gif/ Yvette Cedex

first: Jean-Marc

last: Elalouf

department: IBITEC-S

institute: CEA Saclay

description:
Library generated from microdissected outer medullary collecting ducts obtained from the healthy pole of cancerous kidneys. Donors were from either sex. The library was generated using Sau3A I as anchoring enzyme. Data are provided after removal of linker derived sequences.
Keywords = microdissection
Keywords = nephron
Keywords = SADE


title: Kidney cortical collecting duct

description:
Library generated from microdissected kidney cortical collecting ducts obtained from the healthy pole of cancerous kidneys. Donors were from either sex. The library was generated using Sau3A I as anchoring enzyme. Data are provided after removal of linker derived sequences.
Keywords = microdissection
Keywords = nephron
Keywords = SADE

source_name: microdissected cortical collecting ducts


title: Kidney distal convoluted tubule

description:
Library generated from microdissected kidney distal convoluted tubules obtained from the healthy pole of cancerous kidneys. Donors were from either sex. The library was generated using Sau3A I as anchoring enzyme. Data are provided after removal of linker derived sequences.
Keywords = microdissection
Keywords = nephron
Keywords = SADE

source_name: microdissected distal convoluted tubules


title: Kidney medullary thick ascending limb

description:
Library generated from microdissected kidney medullary thick ascending limbs obtained from the healthy pole of cancerous kidneys. Donors were from either sex. The library was generated using Sau3A I as anchoring enzyme. Data are provided after removal of linker derived sequences.
Keywords = microdissection
Keywords = nephron
Keywords = SADE

source_name: microdissected medullary thick ascending limbs


title: Kidney cortical thick ascending limb

description:
Library generated from microdissected kidney cortical thick ascending limbs obtained from the healthy pole of cancerous kidneys. Donors were from either sex. The library was generated using Sau3A I as anchoring enzyme. Data are provided after removal of linker derived sequences.
Keywords = microdissection
Keywords = nephron
Keywords = SADE

source_name: microdissected cortical thick ascending limbs


title: Kidney proximal straight tubule

description:
Library generated from microdissected kidney proximal straight tubules obtained from the healthy pole of cancerous kidneys. Donors were from either sex. The library was generated using Sau3A I as anchoring enzyme. Data are provided after removal of linker derived sequences.
Keywords = microdissection
Keywords = nephron
Keywords = SADE

source_name: microdissected proximal straight tubules


title: rat hippocampus: status epilepticus group

status: Public on Oct 31 2003

description: Hippocampus RNA pooled from 6 rats was used as input for the SAGE library. The rats had electrodes implanted into their hippocampus and were electrically stimulated to induce status epilepticus (SE). In order to study changes in gene expression in the period prior to the first spontaneous seizure, all rats were placed under continuous EEG monitoring and only rats that showed no seizure activity for 8 days after SE were used for SAGE analysis.

source_name: rat hippocampus (Sprague Dawley)


title: rat hipocampus: ADX + low CORT

description: Wistar rats were adrenalectomised and implanted with a subcutaneous pellet containing 20 mg corticosterone and 80% cholesterol (ADX + low CORT). Three days after ADX and pellet implantation the rats were sacrificed and their hippocampus was isolated. RNA from 6 ADX + low CORT rats was pooled and used as input material for the SAGE library.

source_name: rat hippocampus (Wistar)


title: Leishmania major TBP ChIP replicate#2

status: Public on Nov 11 2008

type: genomic

first: Sean

last: Thomas

address: WTC East #600, 2211 Elliott Ave

department: Genome Sciences

institute: University of Washington

description: (refer to manuscript)

hyb_protocol: On the Nimblegen hybridization system, the temperature was set to 42C with the cover closed and left alone 3 hours to stabilize. 6ug of labeled sample in 5uL of water was added to 13uL of Nimblegen Hybridization Solution, incubated at 95C for 5 minutes, then placed at 42C for at least 5 minutes until sample loading. The samples were loaded into a NimbleGen X1 Mixer, and hybridized at 42C for 16-20 hours.  The mixers were disassembled in warm Nimblegen Wash Buffer 1, and agitated vigorously for 2 minutes, then washed in Nimblegen Wash Buffer 2 for another minute under vigorous agitation.  After 15 seconds of vigorous agitation in Wash Buffer III, the slides were spun dry for one minute.

scan_protocol: The microarrays were scanned using a with a GenePix 4000B Scanner and associated software.  The arrays were kept in the dark until scanning.  Cy3 was detected using 532nm light and Cy5 was detected using 635nm light. The photomultiplier tube gain settings for each channel were set such that the curves obtained when examining the histograms of Cy3 and Cy5 intensities overlap significantly.

data_processing: The logratio of experimental to control for each microarray probe was taken as the relative enrichment at any given site for the target of the antiserum.

molecule: genomic DNA

organism: Leishmania major

source_name: TBP antiserum precipitated input chromatin

label_protocol: 1ug of ChIP sample was added to 40 uL of Random Priming buffer (0.125M Tris pH 7.4, 0.0125M MgCl2, 0.175% B-ME) containing Cy3 or Cy5 labeled 9mers (1 O.D. per 42uL of random priming buffer). The total volume was raised to 80uL with water and heat denatured at 98C for 10 minutes.  20uL of a dNTP/Klenow Master mix (25xdNTP, Klenow 5U/uL) was added to the Random Priming Buffer solution with labeled 9mers, repipeted and incubated at 37C for 2 hours in the dark, after which the reaction was stopped using 10uL 0.5M EDTA. 11.5uL of 5M NaCl was added to each tube, then the reactions were precipitated with the addition of 110uL of isopropanol for 10 minutes at room temperature in the dark. Labeled sample was pelleted at 12k x g for 10 minutes, rinsed with 500uL of 80% cold ethanol, repelleted at 12k x g for 2 minutes, and dried on low heat in a SpeedVac for 5 minutes. Pellets were rehydrated in 25uL of water.

extract_protocol: For each IP, 2.5 ×109 L. major cells were incubated with 1% formaldehyde at 25 °C for 15 min. Next 2.5 ml of 2.5 M glycine was added and incubation continued at 25 °C for an additional 5 min. The cells were pelleted and washed once with 20 ml 1x phosphate buffered saline (PBS), pelleted again and washed once more with 2 ml PBS. After the final pelleting, the cells were resuspended in 400 ul ChIP lysis buffer (50 mM HEPES (pH 7.5), 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate and Complete Protease Inhibitor Tablets [Roche]) and an equal volume of glass beads were added. The sample was shaken continuously for 30 min on a vortex at 4 °C. The lysate was recovered by piercing the bottom of the tube and collecting drops. The samples were sheared on a Misonix Microson model #XL2007 sonicator with 6?10 s pulses at 12 Watts followed by a 15 s pause after each pulse. The lysate was centrifuged at 10,000 rpm for 10 min at 4°C. The supernatant was taken and its protein concentration determined. One mg of protein was used for each immunoprecipitation reaction. One-fortieth of the amount of lysate that would be used for an immunoprecipitation was reverse-crosslinked (65 °C overnight), and the DNA was purified on a Qiagen QiaQuick® spin column and analysed by agarose gel to determine the average genomic fragment size achieved by sonication (300 bp). Antiserum and 50 ul protein A-agarose (equilibrated in lysis buffer) were added to 1 mg of lysate and incubated overnight at 4 °C. Two washes each of the following were then performed, pelleting beads after each wash: 1 ml ChIP lysis buffer (50 mM HEPES pH7.5, 140 mM NaCl, 1% Triton X100, 0.1% sodium deoxycholate, Complete Protease Inhibitor Tablets [Roche]), 1 ml high salt lysis buffer (same as lysis buffer except 500 mM NaCl),1 ml ChIP wash buffer (10 mM Tris?HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Nadeoxycholate, 1 mM EDTA), and 1 ml TE. The beads were mixed with 75 ul of ChIP elution buffer (50 mM Tris?HCl pH 8.0, 1% SDS, 10 mM EDTA) and the sample incubated at 65 °C for 10 min. After centrifuging, the supernatant was taken and the beads were eluted again with 75 ul elution buffer. The supernatants were combined and incubated at 65 °C overnight to reverse-crosslink and the liberated DNA was purified with a Qia-Quick column. Where PCR is used to assay the chromatin, 1 ul is used for each 10 ul reaction.  Chromatin to be used in microarray experiments was first lyophilized, then using the GenomePlex Whole Genome Amplification Kit (Sigma), the lyophilized chromatin was amplified to obtain 4 ug of material

tag: LmjF promastigotes

source_name: Input chromatin


title: rat hippocampus: (ADX + low CORT)+ acute high CORT

description: Wistar rats were adrenalectomised (ADX) and implanted with a subcutaneous pellet containing 20 mg corticosterone and 80% cholesterol (ADX + low CORT). Three days after ADX and pellet implantation the rats were injected subcutaneously with corticosterone (1 mg/kg bodyweight) ((ADX + low CORT) + acute high CORT). Three hours after this injection the rats were sacrificed and their hippocampus was isolated. RNA from 6 (ADX + low CORT) + acute high CORT rats was pooled and used as input material for the SAGE library.


title: rat hippocampus: control group for SE

description: Hippocampus RNA pooled from 6 rats was used to generate the SAGE library. The rats were control animals for a group of rats in which status epilepticus (SE) was induced by electrical stimulation.The control rats were sham-operated and had electrodes implanted but no electrical stimulation.


title: FSCHW_ANGII7DK

status: Public on Oct 20 2003

description: The genetic background of mice used in this study is mainly C57BL/6J with a small contribution from 129/Sv and DBA/2J strains. Male littermates were received continuous administration of AngII for 7 days at 0.9ug/hour. On day 7 of AngII infusion, the blood pressure of infused mice was (mmHg, mean ± SD) 156 ± 1, while the control littermates remained normotensive (106 ± 9).

source_name: whole kidney


title: Whole kidney

status: Public on Oct 02 2003

description:
Pool of three libraries generated from the mouse kidney (8-10 weeks old male mice). Most of the tags (N = 12,154) originate from a SAGE library generated using the original protocol (Velculescu et al., Science 270: 484-487, 1995). The remaining tags originate from two libraries obtained using the SADE method (Virlon et al., Proc. Natl. Acad. Sci. USA 96: 15286-15291, 1999). Data are provided after removal of linker derived sequences.
Keywords = microsage
Keywords = nephron
Keywords = SADE

source_name: adult (8-10 weeks old) mouse kidneys


title: 6.5 dpc embryo, Otx2 -/-

status: Public on Sep 24 2003

description:
The SAGE library was generated starting from 30 Otx2 -/- embryos of either sex. Sau3A I was used as anchoring enzyme. Data are provided after removal of tags derived from linkers sequences
Keywords = development
Keywords = embryo
Keywords = Otd
Keywords = Otx2
Keywords = SADE

source_name: Otx2 -/- 6.5 dpc embryos of either sex


title: FSCHW_CONTROL

description: The genetic background of mice used in this study is mainly C57BL/6J with a small contribution from 129/Sv and DBA/2J strains.


title: 6.5 dpc embryo, wild type

description:
The SAGE library was generated starting from 30 wild type embryos of either sex. Sau3A I was used as anchoring enzyme. Data are provided after removal of tags derived from linkers sequences.
Keywords = development
Keywords = embryo
Keywords = Otd
Keywords = Otx2
Keywords = SADE

source_name: wild type 6.5 dpc embryos from either sex


title: mouse hippocampus: short attack latency (SAL) mice

description: 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.

source_name: mouse hippocampus


title: mouse hippocampus: long attack latency (LAL) mice

description: 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


title: SAGE_CGAP_FM0 rat chondrosarcoma

status: Public on Jul 24 2004

description:
This library represents a Cancer Genome Anatomy Project libray, which was either produced through CGAP funding, or donated to CGAP.
The Cancer Genome Anatomy project (CGAP:http://cgap.nci.nih.gov) is an interdisplinary program established and administered by the National Cancer Institute (NCI:http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell.
Swarm rat chondrosarcoma JWS is a subcutaneously grown rat chondrosarcoma that is derived from a subcutaneous transplantation of the Swarm rat chondrosarcoma JWS tissue line into Sparque-Dawley rats.
The subacutaneously grown Swarm rat chondrosarcoma tissue was harvested 23 days after initial tumor transplantation.
mRNA was isolated from male rat chondrosarcoma tissue using Trizol, followed by the use of a direct mRNA extraction kit.
Vector:pUC-18
R. Site1:Sma1
R.Site2: Sma1
Keywords = Subcutaneous Swarm Rat chondrosarcoma

source_name: mRNA from subcutaneously grown Swarm rat chondrosarcoma, tissue line JWS


title: mpkCCD, control

description:
mpkCCD stands for Murine Principal Kidney Cortical Collecting Duct. mpkCCD consists of a clonal cell line that displays some of the properties of native principal collecting duct cells, e.g. responsiveness to aldosterone and vasopressin. The current transcriptome corresponds to mpkCCD cells cultured under control conditions. Data are provided after removal of tags derived from linkers sequences.
Keywords = cortical collecting duct
Keywords = kidney
Keywords = SADE


title: mpkCCD, vasopressin 4 h

description:
mpkCCD stands for Murine Principal Kidney Cortical Collecting Duct. mpkCCD consists of a clonal cell line that displays some of the properties of native principal collecting duct cells, e.g. responsiveness to aldosterone and vasopressin. The current transcriptome corresponds to mpkCCD cells incubated with 10 nM vasopressin for 4 hours. Data are provided after removal of tags derived from linkers sequences.
Keywords = cortical collecting duct
Keywords = kidney
Keywords = SADE
Keywords = AVP

source_name: mpkCCDcl4 incubated with 10 nM AVP for 4 hours


title: ATDC5, BMP4 induced

status: Public on Aug 25 2003

city: Neuherberg

first: Matthias

last: Wahl

address: Ingolstaedter Landstrasse 1

department: Institute of Developmental Genetics

country: Germany

institute: GSF - National Research Center for Environment and Health

description: SAGE library made from BMP4-induced ATDC5 cells

source_name: ATDC5 cells


title: Kidney glomerulus

description:
Library generated from microdissected kidney glomeruli obtained from the healthy pole of cancerous kidneys. Donors were from either sex. The library was generated using Sau3A I as anchoring enzyme. Data are provided after removal of linkers derived sequences
Keywords = microdissection
Keywords = nephron
Keywords = SADE

source_name: microdissected glomeruli


title: ATDC5 undifferentiated

description: SAGE library made from undifferentiated ATDC5 cells at confluence


title: mpkCCD, Aldosterone 4h

description:
mpkCCD stands for Murine Principal Kidney Cortical Collecting Duct. mpkCCD consists of a clonal cell line that displays some of the properties of native principal collecting duct cells, e.g. responsiveness to aldosterone and vasopressin. The current transcriptome corresponds to mpkCCD cells incubated with 1µM aldosterone for 4 hours. Data are provided after removal of tags derived from linkers sequences
Keywords = aldosterone
Keywords = cortical collecting duct
Keywords = kidney
Keywords = SADE

source_name: mpkCCDcl4 treated with 1 µM aldosterone


title: Medial striatum

status: Public on Aug 14 2003

city: Gif-sur-Yvette Cedex

first: Michel

last: de Chaldée

department: Département de Biologie Joliot-Curie

description:
Medial striatum from 8- to 12-week-old male C57BL/6 mice.
Data provided after linker removal.

source_name: Control mouse medial striatum


title: Lateral striatum

description:
Lateral striatum from 8- to 12-week-old male C57BL/6 mice.
Data provided after linker removal.

source_name: Control mouse lateral striatum


title: rat hippocampus: adrenalectomised rat (ADX)

description: Wistar rats were adrenalectomised (ADX). Three days after ADX the rats were sacrificed and their hippocampus was isolated. RNA from 6 ADX rats was pooled and used as input material for the SAGE library.


title: Somatosensory cortex

description:
Somatosensory cortex from 8- to 12-week-old male C57BL/6 mice.
Data provided after linker removal.

source_name: Control mouse somatosensory cortex


title: AtRoot14DayMSTNT

status: Public on Jul 30 2003

city: Athens

first: Jeffrey

last: Dean

state: GA

department: Warnell School of Forest Resources

institute: University of Georgia

description:
14-day old seedlings grown submerged in MS medium and exposed 24 h to 0.0015% (v:v) DMSO and 15 mg/L TNT final concentration.
Keywords = phytoremediation, munitions, TNT, RDX, explosives

organism: Arabidopsis thaliana

source_name: Roots


title: PtaedaBaseXylem

status: Public on Aug 11 2003

description:
Lignifying xylem scraped from the lower trunk of a single 10-year old loblolly pine tree.
Keywords = wood, lignin, mature, juvenile, phase change
Lot batch =

organism: Pinus taeda

source_name: Xylem


title: bmDC (Vitamin D3 treated)

status: Public on Jul 05 2003

city: Oxford

first: Steve

last: Cobbold

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

description: CBA/Ca mouse bone marrow cells were culture with GM-CSF for 7 days in the presence of 1 alpha 25 dihydroxyvitamin D3 (10^-7M) from day 3.

source_name: Mouse bone marrow derived dendritic cells (Vitamin D3 treated)


title: Splenic B cells (mouse)

description: CBA/Ca mice were depleted of T cells in vivo using monoclonal antibodies to CD4 and CD8.  Splenic B cells were purified (>93% B220+CD3-) by MACS using negative selection with a cocktail of non-B cell binding antibodies.

source_name: Mouse splenic B cells (unstimulated)


title: Nucleus accumbens

description:
Nucleus accumbens from 8- to 12-week-old male C57BL/6 mice.
Data provided after linker removal.

source_name: Control mouse nucleus accumbens


title: bmDC (mouse)

description: CBA/Ca mouse bone marrow was cultured for 7 days in GM-CSF to generate dendritic cells (>90% CD11c+).

source_name: Mouse bone marrow derived dendritic cells


title: ES derived DCs

description: Dendritic cells were produced by directed differentiation of the CBA/Ca mouse derived embryonic stem cell line ESF 116 (Fairchild et al, Curr. Biol. 10:1515-8 (2000)).

source_name: Dendritic cells derived from ESF 116 stem cell line


title: bmDC (IL-10+LPS)

description: CBA/Ca mouse bone marrow was cultured with GM-CSF for 9 days to generate dendritic cells.  Recombinant mouse IL-10(20ng/ml) was added from day 6 and bacterial derived LPS also added for the last 20 hrs of culture.

source_name: Mouse bone marrow derived dendritic cells (IL-10 plus LPS treated)


title: bmDC (LPS treated)

description: CBA/Ca bone marrow was cultured in the presence of GM-CSF for 6 days to generate dendritic cells, and treated with bacterial derived LPS for overnight.

source_name: Murine bone marrow derived dendritic cells (LPS treated)


title: PtaedaCrownXylem

description:
Lignifying xylem scraped from the upper trunk of a 14-year old loblolly pine tree.
Keywords = wood, lignin, mature, juvenile, phase change
Lot batch =


title: ES derived DCs (LPS treated)

description: Dendritic cells were generated from the CBA/Ca mouse derived embryonic stem cell line ESF 116 (Fairchild P., et al., Curr. Biol. 10:1515-8 (2000)).  These were mature by treatment with bacterial derived LPS overnight (Fairchild et al, Methods in Enzymology, in press (2003)). cDNA was preamplified (SMART) before SAGE analysis.

source_name: Dendritic cells derived from ESF 116 stem cell line treated with LPS


title: ESF 116

description: A pluripotent embryonic stem cell line (ESF 116) derived from CBA/Ca mice.  Normal male karyotype. Initially maintained on embryonic fibroblasts, but passaged 6 times in LIF without feeders before making mRNA.

source_name: Embryonic stem cell line ESF 116 (mouse)


title: Th1 clone R2.2 (CD3 activated)

description: A CD4+ Th1 clone (R2.2) from a primed A1xRAG-1-/- TCR transgenic mouse specific for H-Y + H2Ek.  Purified CD4+ T cells were stimulated overnight with solid phase anti-CD3. cDNA was preamplified (SMART) before SAGE analysis.

source_name: CD4+ Th1 clone R2.2: overnight activation with anti-CD3


title: AtRoot14DayMSControl

description:
14-day old sterile seedlings grown submerged in Murashige and Skoog (MS) medium and dosed 24 h with DMSO at 0.0015% (v:v) final concentration.
Keywords = phytoremediation, munitions, TNT, RDX, explosives

source_name: Seedling roots


title: Skin graft draining nodes (CBA)

status: Public on Jun 15 2003

description: Draining lymph nodes were pooled from normal CBA/Ca mice grafted with B10.BR (multiple minor antigen mismatched) skin on day 7 after grafting.  mRNA was made from total lymph nodes.

source_name: Normal CBA/Ca Lymph nodes draining B10.BR skin graft


title: Treg clone Tr1D1 culture

description: A CD4+ Treg/Tr1-like clone from a naive A1xRAG-1-/- TCR transgenic mouse specific for H-Y + H2Ek.  mRNA was derived from a T cell culture 7 days from last stimulation with male spleen cells, and also contains approx. 5% mast cells.  cDNA was preamplified (SMART) before SAGE analysis.

source_name: CD4+ Tr1-like clone H-Y specific (resting)


title: Whole brain

description:
Whole brain from 8- to 12-week-old male C57BL/6 mice.
Data provided after linker removal.

source_name: Control mouse whole brain


title: CD4+CD25+ spleen

status: Public on Jun 14 2003

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

source_name: CD4+CD25+ spleen cells


title: CD4+CD25neg spleen

description: CD4+CD25negative spleen cells were purified from naive CBA/Ca mice by MACS sorting.  cDNA was preamplified (SMART) before SAGE analysis.

source_name: MACS sorted CD4+CD25- spleen T cells


title: Treg line SKB from skin graft

description: A CD4+ Treg/Tr1-like H-Y + H2Ek specific line grown from the accepted male skin grafts of female A1(M) TCR transgenic mice in the presence of anti-CTLA4. 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.

source_name: CD4+ Tr1-like T cell line H-Y specific (resting)


title: Th2 clone R2.4(CD3 activated)

description: A CD4+ Th2 clone (R2.4) from a primed A1xRAG-1-/- TCR transgenic mouse specific for H-Y + H2Ek.  Purified CD4+ T cells were stimulated overnight with solid phase anti-CD3. cDNA was preamplified (SMART) before SAGE analysis.

source_name: CD4+ Th2 clone (R2.4): overnight with anti-CD3


title: CD4+CD25+ activated

description:
CD4+CD25+ spleen T cells were purified from naive CBA/Ca mice by MACS.  These were activated overnight by solid phase anti-CD3.
cDNA was preamplified (SMART) before SAGE analysis.
Keywords = CD4, CD25, Treg, regulatory T cell, activation

source_name: CD4+CD25+ spleen cells (CD3 X-linked)


title: Treg line SKA from skin graft

description:
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.
Keywords = Treg, Tr1, Tskin, CD4, T cell, skin graft


title: Rat extraocular muscle in dark reared

status: Public on May 12 2003

city: Cleveland

first: Henry

middle: J.

last: Kaminski

state: OH

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

description:
Comprehensive evaluation of the extraocular muscle critical period by expression profiling in the dark reared rat and monocularly deprived monkey
Keywords = Rat extraocular muscle, critical period

source_name: Adult rat extraocular muscle


title: Treg clone Tr1D1 pure

description: A CD4+ Treg/Tr1-like clone from a naive A1xRAG-1-/- TCR transgenic mouse specific for H-Y + H2Ek.  mRNA was derived from >99% CD4+ T cells 7 days from last stimulation, and contains <0.1% mast cells. cDNA was preamplified (SMART) before SAGE analysis.


title: BW5147 thymoma

description: Thymoma line BW 5147 from AKR/J mice.  This is a cloned subline that is negative for TCR alpha/beta expression and is HPRT negative.

source_name: Mouse thymoma line BW (TCR alpha/beta negative)


title: CD4+CD25neg activated

description: 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.

source_name: CD4+CD25- spleen cells (CD3 X-linked)


title: P10 cerebellum

status: Public on Mar 24 2003

city: Columbus

first: Julie

last: Besco

department: Pharmacology

institute: The Ohio State University

description: Cerebellum of P10 mouse; wild type littermate to lurcher.

source_name: cerebellum of P10 mouse; wild type littermate to lurcher


title: P10 Lurcher Cerebellum

description: Cerebellum of postnatal day 10 Lurcher (Lc +/-) mouse.

source_name: cerebellum of P10 mouse


title: Th2 clone R2.4

description:
A CD4+ Th2 clone (R2.4) from a primed A1xRAG-1-/- TCR transgenic mouse specific for H-Y + H2Ek. mRNA was derived from resting T cells 7 days from last stimulation. cDNA was preamplified (SMART) before SAGE analysis.
Keywords = T cell, clone, Th2, CD4, graft rejection, SMART

source_name: CD4+ Th2 clone H-Y specific (resting)


title: Skin graft draining nodes

description:
Draining lymph nodes taken on day 7 from male skin grafted anti-HY TCR transgenic female A1xRAG-1-/- mice.  mRNA was derived from total lymph node pool.
Keywords = CD4, T cell, graft rejection, lymph node

source_name: Lymph nodes draining skin graft


title: SAGEHISL1

status: Public on Feb 05 2003

city: Saint Louis

first: Corentin

last: Cras-Méneur

state: MO

address: 660 S. Euclid

department: Metabolism Division

institute: Washington University School of Medicine

description:
SAGEHISL1, was constructed with pancreatic islets from 3 normal human donors (HR39, HR46, HR50).
Keywords = pancreas, islets, ficol-purified
Lot batch = HR39, HR46, HR50

source_name: pancreatic islets


title: SAGEHEXO1

description:
SAGEHEXO1, was constructed with normal pancreatic exocrine cells, which were obtained during the process of islet purification from 2 donors (HR18, HR27).
Keywords = exocrine pancreas
Lot batch = HR18, HR27

source_name: exocrine pancreas


title: Adult testis - somatic cells

status: Public on May 02 2003

city: Glasgow

first: Peter

last: O'Shaughnessy

department: Veterinary Preclinical Studies

institute: University of Glasgow Veterinary School

description:
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
Keywords = testis, mouse, somatic

source_name: adult mouse testis


title: CD4 T-cells

status: Public on Dec 17 2002

city: Amsterdam

first: Antoinette

last: van der Kuyl

department: Human Retrovirology

institute: Academic Medical Centre, University of Amsterdam

description: SAGE library generated from CD4+ T-cells isolated with the use of CD4-coated immunomagnetic beads from PBMC from a single healthy female donor. Half of the cells have been cultured, half of the cells were directly used for SAGE.

source_name: CD4+ T-cells isolated from a single healthy donor


title: EG

status: Public on Jun 01 2004

city: Baltimore

first: Kenneth

last: Boheler

description:
EG-1 Cells

Linker-based, Poly(A) and short clone-generated tags (=<4 tags per clone) are extracted.
Keywords = EG

source_name: EG-1 Cells


title: SAGEHR96R

description:
Individual islets were isolated using a standard protocol of an intraductal Liberase perfusion, gentle mechanical dissociation, and a continuous gradient of Hypaque Euroficoll on a refrigerated COBE 2991. 300 islets were then hand-selected.
Keywords = pancreas, islets, hand-selected
Lot batch = HR96

source_name: hand-selected pancreatic islet


title: fetal testis somatic cells

description: 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

source_name: testes from Wv/Wv mice


title: KS-48

description: SAGE library generated grom a KS lesion from an AIDS-KS patient. Biopsy was taken 48 hours after chemotherapy with adriamycine, bleomycine, and vincristine.

source_name: AIDS-KS lesion


title: AI SST

city: Beltsville

first: Kurt

middle: A.

last: Zuelke

address: Bldg 200, Barc-EAST

institute: USDA ARS Animal and Natural Resources Institute

description: Sperm storage tubules from mature laying hens.

organism: Meleagris gallopavo

source_name: sperm storage tubules


title: Control SST


title: KS-24

description: SAGE library generated from a KS lesion from an AIDS-KS patient. Biopsy was taken 24 hours after treatment with adriamycine, bleomycine, and vincristine.


title: Thy_N

status: Public on Mar 04 2003

first: Erwin

last: Pauws

address: Meibergdreef 9

institute: Academic Medical Center

description:
This library was generated from normal human thyroid tissue collected at routine autopsy.
Standard SAGE protocol was used (Velculescu et al. Science 1995).
Data from this library was published in: 'Pauws E, Moreno JC, Tijssen M, Baas F, de Vijlder JJ, Ris-Stalpers C. J Clin Endocrinol Metab. 2000 May;85(5):1923-7'
Data was generated and analyzed at the laboratory of Pediatric Endocrinology, Academic Medial Center, Amsterdam, The Netherlands.
Keywords = thyroid, normal, tissue

source_name: normal thyroid tissue


title: SAGE_P23_cerebellum

status: Public on Sep 05 2002

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

source_name: P23 C57BL6/J mouse cerebellum


title: Bovine Renal Glomerular Endothelial Cells

status: Public on Dec 06 2002

city: Bronx

first: Barbara

middle: Jutta

last: Ballermann

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

description:
Endothelial cells were derived from isolated bovine renal glomeruli.  Cells were cloned and shown to uniformly label with acetylated LDL and anti-vWF antibody.  Cells were cultured on gelatin-coated cell culture plastic in RPMI 1640 medium containing 10% fetal bovine serum.  mRNA was isolated from passage 9 cells, at confluence  48 hours after the last medium change.
Keywords = endothelial, glomerular, renal

source_name: Cultured Primary Glomerular Endothelial Cells


title: Bovine Aortic Endothelial Cells

description:
Endothelial cells were derived from  bovine aorta by collagenase digestion.  Cells were cloned and shown to uniformly label with acetylated LDL and anti-vWF antibody.  Cells were cultured on gelatin-coated cell culture plastic in RPMI 1640 medium containing 10% fetal bovine serum.  mRNA was isolated from passage 10 cells, at confluence  48 hours after the last medium change.
Keywords = endothelial, aorta

source_name: Cultured Bovine Aortic Endothelial Cells


title: P19 embryonic carcinoma (EC) cells, day 3+3.0

status: Public on Jul 22 2002

institute: National Institute on Aging, NIH

description:
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).
Keywords = EC cells, P19, differentiation, cardiomyocytes

source_name: P19 EC cells, day 3+3.0


title: AIDS-KSb

description: SAGE library derived from a nodular KS lesion of an AIDS-KS patient. Sample was taken at autopsy (1986). Patient died of AIDS-KS, and received vinblastine therapy till two weeks before death.

source_name: AIDS-KS nodular lesion


title: P19 embryonic carcinoma (EC) cells, day 3+0.5

description:
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).
Keywords = EC cells, P19, differentiation, cardiomyocytes

source_name: P19 EC cells, day 3+0.5


title: AIDS-KSa

description: SAGE library derived from a nodular skin lesion of an AIDS-KS patient taken at autopsy (1986).


description:
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).
Keywords = EC cells, P19, undifferentiated

source_name: Undifferentiated P19 EC cells


title: fce

status: Public on May 03 2002

city: Bethesda

first: Elliott

middle: H

last: Margulies

department: Genome Technology Branch

institute: National Human Genome Research Institute

description: SAGE on Fuchs' corneal endothelium.

source_name: Fuchs' corneal endothelium


title: AKAffected_Epidermis_skin

status: Public on Feb 12 2002

city: Nijmegen

first: Bastiaan

last: Jansen

address: PO Box 9101

department: Tumor Immunology

institute: Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Center Nijmegen

description: SAGE library derived from affected epidermis of kidney transplant recipient suffering from actinic keratosis (AK)

source_name: Affected epidermis from AK patient


title: PC3 AS2

status: Public on Mar 26 2002

city: New Heaven

first: Nikki

last: Holbrook

state: CT

address: 333 Cedar Street

department: Department of Internal Medicine

institute: Yale University School of Medicine

description:
Identification of targets of JNK2 signaling involved in regulation of human tumor cell growth.

PC3 cells, AS2 treatment, total number of 42,236 SAGE tags sequenced. 40,768 SAGE tags analyzed after clean-up (extraction of poly(A) tags, linker-generated tags, and tags originated from clones producing 4 tags or less).


title: rat hippocampus

status: Public on May 18 2002

city: Leiden

first: Nicole

last: Datson

department: Medical Pharmacology

institute: Leiden University

description:
SAGE profile of rat hippocampus mRNA from Wistar rats.
Keywords = rat, hippocampus, SAGE, expression profile, transcriptome

source_name: rat hippocampus (Wistar)


title: PC3 Mock

description:
Identification of targets of JNK2 signaling involved in regulation of human tumor cell growth.

PC3 cells, Mock treatment, total number of 40,655 SAGE tags sequenced. 38,819 SAGE tags analyzed after clean-up (extraction of poly(A) tags, linker-generated tags, and tags originated from clones producing 4 tags or less).


title: nce

description: SAGE on human donor corneal endothelium.

source_name: Normal corneal endothelium


title: AKUnaffected_Epidermis_skin

description: SAGE library from unaffected epidermis of a kidney transplant recipient suffering from pre-malignant actinic keratosis (AK)

source_name: Unaffected epidermis from AK patient


title: TNF_AlphaCultKC

description: SAGE library derived from differentiated human epidermal keratinocytes that have been stimulated with TNF-alpha for 48 hours; keratinocytes are derived from a single male donor

source_name: Cultured human epidermal keratinocytes, stimulated with TNF-alpha


title: NormCultKC_Diff

description: SAGE library derived from cultured human epidermal keratinocytes, differentiated for 48 hrs in KGM medium without growth factors; keratinocytes are derived from a single male donor

source_name: Cultured human epidermal keratinocytes


title: Adult mouse heart

status: Public on Jul 25 2002

department: GRC

description:
A quantitative and validated SAGE transcriptome reference for adult mouse heart.
Adult mouse heart, 3-month old female C57BL/6 mice. Total number of 88,860 SAGE tags sequenced. 84,192 SAGE tags analyzed after clean-up (extraction of poly(A) tags, linker-generated tags, and tags originated from clones producing 4 tags or less).
Keywords = mouse, heart

source_name: Hearts, 3-month old female C57BL/6 mice


title: HumanEpidermis_skin

description: SAGE library derived from isolated human epidermis from a single donor

source_name: Human epidermis (skin)


title: Normal Human Muscle (old)

status: Public on Jan 31 2002

city: Rochester

first: Stephen

last: Welle

address: 601 Elmwood Avenue

institute: University of Rochester

description: RNA was pooled from vastus lateralis biopsies obtained from 8 older (66-77 yr) men. Healthy subjects with no neuromuscular disease.

source_name: Muscle biopsies


title: C. elegans FACS sorted pan neural cells

status: Public on Jun 11 2004

city: Vancouver

first: Kim

last: Wong

institute: British Columbia Cancer Agency

description:
Libraries were constructed from total RNA from FACS sorted embryonic pan neural cells (F25B3.3::GFP); 21 bp tags (LongSAGE).  Tagging enzyme: MmeI.
Linker sequences and duplicate ditags are excluded.
Keywords = SAGE
Keywords = pan neural
Keywords = LongSAGE
Lot batch =


title: HMAC2_SAGE

status: Public on Oct 03 2001

city: Boston

first: Dror

last: Sharon

address: 243 Charles St.

institute: Massachusetts Eye and Ear

description:
Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE).
A normal macula from a 44-year-old male.
Patient had periocular malignancies that required exenteration of a normal eye as part of the clinically indicated surgical therapy. The eye was placed in saline after it was removed from the patient and macular fragments were collected. The retina fragment used for this library was approximately 6 mm in diameter and centered at the foveola. The tissue was frozen within 45 minutes of the surgical removal to ensure minimal degradation of mRNA molecules.

source_name: Human central retina (macula)


title: Normal Human Muscle (young)

status: Public on Feb 01 2002

description: RNA was pooled from vastus lateralis biopsies obtained from 8 younger (21-24 yr) men. Healthy subjects with no neuromuscular disease.


title: Rat_extraocular muscle

status: Public on Dec 03 2001

description: Transcriptional profile of rat extraocular muscle by serial analysis of gene expression.

source_name: Adult rat extraocular muscle


title: R1 Embryonic Stem Cells

status: Public on Oct 25 2001

description: R1 embryonic stem (ES) cells, undifferentiated.

source_name: R1 ES cells, undifferentiated


title: HPR1_SAGE

description:
Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE).
A normal peripheral retina from an 88-year-old female.
Patient had periocular malignancies that required exenteration of a normal eye as part of the clinically indicated surgical therapy. The eye was placed in saline after it was removed from the patient and peripheral retinal fragments were collected from regions outside the central arcades and frozen within 45 minutes of the surgical removal to ensure minimal degradation of mRNA molecules.

source_name: human peripheral retina


title: HRPE1_SAGE

description:
Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE).

A normal retinal pigment epithelium (RPE) from an 88-year-old female.
Patient had periocular malignancies that required exenteration of a normal eye as part of the clinically indicated surgical therapy.  The eye was placed in saline after it was removed from the patient and the RPE from the posterior pole and the periphery was harvested by gentle scraping with a Pasteur pipette. Fragments of RPE were collected by aspiration in sterile 0.9% saline.  Tissue fragments were collected and frozen within 45 minutes of the surgical removal to ensure  minimal degradation of mRNA molecules. The RPE fragments were from the posterior pole and the periphery.

source_name: human retinal pigment epithelium (RPE)


title: Foreskin Fibroblasts

status: Public on Sep 28 2000

city: Bern

first: Marc

last: Kenzelmann

address: Friedbuhlstrasse 51

department: Molecular Genome Analysis

country: Switzerland

institute: Institute of Medical Microbiology, University of Bern

description:
Primary human foreskin fibroblasts at passages 15-18, cultured in Eagles Minimal Essential Medium (MEM) supplemented with penicillin and 10% fetal calf serum (FCS).
Confluent cells serum starved for 3 days with MEM containing 1% FCS. 85% of cells in G0/G1 phase of cell cycle.
mRNA was isolated using a direct mRNA extraction kit.
Keywords = fibroblast, cultured, cell cycle synchronized

source_name: mRNA of untreated foreskin fibroblasts


title: mouse_hindlimb

status: Public on Jul 30 2001

description:
SAGE expression profiles define unique
patterns of transcription between developing
forelimbs and hindlimbs.

source_name: E11.5 intact developing B6C3H hindlimbs


title: mouse_forelimb

source_name: E11.5 intact developing B6C3H forelimb buds


title: HPR2_SAGE

description:
Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE).
A normal peripheral retina from a 44-year-old male. Patient had periocular malignancies that required exenteration of a normal eye as part of the clinically indicated surgical therapy. The eye was placed in saline after it was removed from the patient and peripheral retinal fragments were collected from regions outside the central arcades and frozen within 45 minutes of the surgical removal to ensure minimal degradation of mRNA molecules.
Keywords = retina,44 year old male, macula


title: Kidney proximal convoluted tubule

status: Public on Nov 08 2003

city: 91191 Gif/ Yvette Cedex

first: Jean-Marc

last: Elalouf

department: IBITEC-S

institute: CEA Saclay

description:
Library generated from microdissected kidney proximal convoluted tubules obtained from the healthy pole of cancerous kidneys. Donors were from either sex. The library was generated using Sau3A I as anchoring enzyme. Data are provided after removal of linker derived sequences.
Keywords = microdissection
Keywords = nephron
Keywords = SADE

source_name: microdissected proximal convoluted tubules


title: bmDC (IL-10 treated)

status: Public on Jul 05 2003

city: Oxford

first: Steve

last: Cobbold

institute: University of Oxford

description: CBA/Ca mouse bone marrow was cultured in GM-CSF for 6 days to generate dendritic cells. These were treated for a further 36 hrs with recombinant mouse IL-10.

source_name: Mouse bone marrow derived dendritic cells (IL-10 treated)


title: Th1 clone R2.2

status: Public on Jun 14 2003

description:
A CD4+ Th1 clone (R2.2) from a primed A1xRAG-1-/- TCR transgenic mouse specific for H-Y + H2Ek.  mRNA was derived from resting T cells 7 days from last stimulation.  cDNA was preamplified (SMART) before SAGE analysis.
Keywords = T cell, clone, Th1, CD4, graft rejection, SMART

source_name: CD4+ Th1 clone H-Y specific (resting)


title: NS

status: Public on Dec 17 2002

description: SAGE library generated from pooled normal skin from three different breast reduction patients.

source_name: normal skin pooled from 3 breast reductions


title: 40 ug/mL hATG treated for 6h, biological rep1 (S4)

status: Public on Nov 10 2008

first: Xingmin

last: Feng

address: 9000 Rockville Pike

institute: National Institutes of Health

description: Gene expression data from hATG-treated PBMC.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

label: biotin

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: total RNA was extracted with the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: hATG-treated for 6h


title: pa14 sma6 7/2 4hrs

status: Public on Nov 06 2008

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27362.gif
Measurement: time(absolute) 4 h
Infection: PA14
Strain Name: sma-6(wk7)

hyb_protocol: see Proc Natl Acad Sci U S A. 2006;103:14086-14091

scan_protocol: Scanner Make = Axon Instruments (V1.00); Scanner Model = GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: sma-6 mutants exposed to P. aeruginosa PA14- 4 hours

source_name: Common reference- Mixed stage N2 worm culture


title: Dendritic cell DNA-allergy susceptible d14 mice-rep3

status: Public on Nov 04 2008

first: Alexey

last: Fedulov

address: 75 Francis St.

department: Brigham and Women's Hospital

institute: Harvard Medical School

description: Cy3 labels portion of DNA sample treated with methylation-sensitive nucleases, Cy5 is untreated portion

hyb_protocol: Competitive hybridization to probes, each of which cover 50 bp, results in changes in the ratio of fluorescence depending on methylation-driven nuclease sensitivity: in an unmethylated sample nuclease destroys the DNA in the green-labeled portion, so only red-labeled fragments hybridize; in a methylated sample nuclease does not perform so both portions hybridize returning mixed fluorescence. Therefore demethylation leads to increased binding of the red-labeled fragments. The ratio of untreated (red) versus treated (green) will now be proportionate to hybridization at each probe. Respectively, higher ratios are obtained if hybridization is lower (unmethylated).

scan_protocol: commercial service provided by Switchgear Genomics

data_processing: These ratios are normalized with background adjustment to obtain ‘z-scores’. A z-score is a dimensionless value which represents the number of standard deviations from the background control (which behaves as fully methylated DNA). Z-scores are quantitative log2-transformed data proportionate to the methylation of the interrogated target, which allow comparison of samples from different chips and batches. They are calculated as: [(exp log2 ratio)-(mean log2 ratio of negs)] / (stdev log2 ratio of negs). A typical threshold value of 1.6 or more indicates that the site has a >95% chance of being demethylated. Of notice is the fact that each z-score is a summary of fluorescence ratio for 3 adjacent probes, this ‘frame’ shifts one probe at a time, so each probe is also included into 3 of the z-scores; this should be taken into consideration during validation. For this reason there is also less z-score data raws than fluorescence data raws. Fluorescence reading, normalization, background adjustment and the resulting z-scores are provided by the company’s bioinformatics facility along with the annotation file. Raw values are also provided

source_name: Splenic CD11c+ dendritic cell - allergy susceptible (methylase treated)

label_protocol: The assay relies on sensitivity to restriction endonucleases conferred by the absence of methylation on cytosine residues. A cocktail of methylation-sensitive nucleases (with 99.9% efficiency and specificity for unmethylated DNA) is used to digest half of each genomic DNA sample, prior to differential fluorescent labeling (Cy 5 red for the nuclease-untreated sample; Cy3 green for the treated).

growth_protocol: Maternal sensitization is achieved by initial i.p. injections of 5 μg OVA with 1 mg alum in 0.1 ml PBS into mice at 3 and 7 days of age. After weaning, female mice are exposed to aerosols of allergen (3% (w/v) OVA (grade V, Sigma-Aldrich) in PBS, pH 7.4) for 10 min on 3 consecutive days at 4, 8, and 12 wk of age, and then mated with normal male mice. The aerosol exposure is performed within individual compartments of a mouse pie chamber (Braintree Scientific, Braintree, MA) using a Pari IS2 nebulizer (Sun Medical Supply, Kansas City, KS) connected to air compressor (PulmoAID; DeVilbiss, Somerset, PA). These female mice were shown to consistently have strong allergic airway inflammation and evidence of Th2 polarization.

extract_protocol: Dendritic cells were isolated from splenocyte suspension using magnetic cell separation (Miltenyi). Genomic DNA was isolated using Qiagen procedure.

treatment_protocol: All neonate mice are untreated, genetically and environmentally identical.

tag: Strain

value: BALB/c

tag: Age

value: 14 day old

tag: Mothers

value: allergic asthma

tag: Organ

value: spleen

tag: Cell type

value: dendritic cells

source_name: Splenic CD11c+ dendritic cell - allergy susceptible (untreated)


title: mLSAGE_Brain_normal_TS17_LCM_SM068

status: Public on Apr 27 2006

first: BCGSC

last: BC Cancer Agency

address: 675 West 10th Avenue

department: Gene Expression

institute: Canada's Michael Smith Genome Sciences Centre

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

data_processing: not normalized

source_name: Brain, normal

tag: Mouse strain

tag: Gender

value: Unknown

tag: Preparation

value: Laser microscope dissected


title: mLSAGE_Branchial_arch_normal_TS17_MMD_SM039

source_name: Branchial_arch, normal

value: Manual microscope dissected


title: PAOI replicate 2 od 0.8

status: Public on Jan 18 2006

city: Seattle

first: Yannick

last: Lequette

address: 1959 NE PACiFiC

department: Microbiology HSB -I420 BOX 357242

institute: University of Washington

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

data_processing: standard Affymetrix procedures

organism: Pseudomonas aeruginosa

source_name: PAOI planktonic culture

tag: PAOI wild type