title: Motor cortex

description: Data provided after linker removal.

source_name: Wild-type mouse motor cortex

value: C57BL/6; Gender:male; Age:8-12 weeks; Tissue:brain, motor cortex.


title: Cingulate cortex

status: Public on Feb 05 2008

type: SAGE

city: 91191 Gif/ Yvette Cedex

first: Jean-Marc

last: Elalouf

department: IBITEC-S

country: France

institute: CEA Saclay

description: Data provided after linker removal.

molecule: polyA RNA

organism: Mus musculus

source_name: Wild-type mouse cingulate cortex

extract_protocol: Virlon B, Cheval L, Buhler JM, Billon E, Doucet A, Elalouf JM. 1999. Serial microanalysis of renal transcriptomes. Proc Natl Acad Sci U S A. 96:15286-91.

tag: Strain

value: C57BL/6; Gender:male; Age:8-12 weeks; Tissue:brain, cingulate cortex.


title: N3

status: Public on Feb 19 2008

anchor: NlaIII

city: Vancouver

first: Ashleen

last: Shadeo

address: 675 West 10th Ave

country: Canada

institute: BCCRC

description: The specimens were collected immediately prior to the LEEP (Loop electrosurgical excision procedure) cone biopsy targeting a small portion of the affected epithelium. These specimens were collected with patient consent at the Vancouver General Hospital Women’s Clinic at Vancouver Hospital & Health Science Centre.

organism: Homo sapiens

source_name: LEEP cone biopsy of cervical tissue

extract_protocol: The biopsies were individually homogenised in Lysis Binding buffer (100mM Tris-HCl, pH7.5, 500mM LiCl, 10mM EDTA, pH 8.0, 1% LiDS, 5mM dithiothreitol).  Long SAGE libraries were constructed according to the L-SAGE kit manual (Invitrogen, Ontario, Canada).  Sequencing was performed at the BC Cancer Agency Michael Smith Genome Sciences Centre.

tag: Normal Cervical Tissue


title: Dunel (Landrace X Duroc) age 3 month

status: Public on Feb 01 2008

city: trieste

first: simeone

last: dal monego

address: piazzale valmaura 9

department: biology

country: Italy

institute: university of trieste

description: Muscle development is associated with a modification of mass, composition and function that in productive animals are considered responsible of meat characteristics. In this study, SAGE was employed to describe gene expression in pigs of two commercial lines at the 3 and  9 months og age. The aim was to obtained a full gene expression profile that would assist in identifying genes differentially expressed in the muscle Longissimum dorsi during normal growth. The pattern of expression between lines and ages will help to elucidate the metabolic pathways modulated by these genes during muscle development.

data_processing: we used sageparser.pl script to extract tags

molecule: total RNA

organism: Sus scrofa

source_name: sus scrofa Dunel (Landrace X Duroc) 3 month Longissimum dorsi biopsy

extract_protocol: Samples were homogenised in TRIZOL Reagent (Life Technologies),  mono-phasic solution of phenol and guanidine isothiocyanate, that is an improvement to the single-step RNA isolation method (Chomczynski and Sacchi, 1987)

tag: swine

value: Landrace X Duroc

tag: Gender

value: male

tag: type

value: castrate

tag: Age

value: 3 months

tag: Tissue

value: Longissimum dorsi

tag: level:between the third and fourth last ribs


title: Dunel (Landrace X Duroc) age 9 month

source_name: sus scrofa Dunel (Landrace X Duroc) 9 month Longissimum dorsi biopsy


title: Entorhinal cortex

description: Data provided after linker removal.

source_name: Wild-type mouse entorhinal cortex

value: C57BL/6; Gender:male; Age:8-12 weeks; Tissue:brain, entorhinal cortex.


title: Somatosensory cortex

description: Data provided after linker removal.

source_name: Wild-type mouse somatosensory cortex

value: C57BL/6; Gender:male; Age:8-12 weeks; Tissue:brain, somatosensory cortex


title: large white age 9 month

source_name: sus scrofa large white 9 month Longissimum dorsi biopsy

value: purebred Large White


title: large white age 3 month

source_name: sus scrofa large white 3 month Longissimum dorsi biopsy


title: Hepatocellular carcinoma (HCC), metastasis free, 226A

status: Public on Jan 14 2008

type: RNA

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

country: USA

institute: National Cancer Institute

description: No additional information.

hyb_protocol: Sample Hybridization Protocol Qty. of labeled target: 5 ug of total RNA Other: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.

scan_protocol: Scanning Protocol Other: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.

data_processing:
Data Processing Protocol
Calculation Method: Raw data were normalized and analyzed in GENESPRING software version 6.1.1 (Silicon Genetics, Redwood City, CA). GENESPRING generated an average value of the spot replicates of each miRNA. After data transformation (to convert any negative value to 0.01), normalization was performed by using a per-chip on median normalization and a normalization to specific samples used as common reference for miRNA expression.

label: alexa 647

label_protocol:
Labeling Protocol
Other: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.

extract_protocol:
Tri-Reagent Protocol
Other: Total RNA isolation was performed using the Tri-Reagent Protocol (Molecular Research Center, Cincinnati)

value: liver tissue (tumor)

tag: Disease state

tag: Individual

tag: Clinical info

value: Follow up status:dead


title: Hepatocellular carcinoma (HCC), metastasis free, 102A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, A187A

description: No additional information.


title: Nucleus accumbens

description: Data provided after linker removal.

source_name: Wild-type mouse nucleus accumbens

value: C57BL/6; Gender:male; Age:8-12 weeks; Tissue:brain, nucleus accumbens.


title: Hepatocellular carcinoma (HCC), metastasis free, 430A

description: No additional information.

value: Follow up status:alive


title: Orbital cortex

description: Data provided after linker removal.

source_name: Wild-type mouse orbital cortex

value: C57BL/6; Gender:male; Age:8-12 weeks; Tissue:brain, orbital cortex.


title: Hepatocellular carcinoma (HCC), venous metastasis, 210A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 311A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 364A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-314A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 051A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 317A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 244A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, A023A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 139A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 147A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 395A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 061A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 088A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 280A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 350A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 418A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 265A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 081A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 02-363A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 02-415A

description: No additional information.

value: Follow up status:


title: Acupuncture-treated Asthmatic Rat Lung

status: Public on Apr 07 2008

city: Shanghai

first: Yong Qing

last: Yang

address: 650 South Wanping Rd

department: Shanghai Research Institute of Acupuncture

country: China

institute: Shanghai University of Traditional Chinese Medicine

organism: Rattus norvegicus

source_name: Lung

extract_protocol: The SAGE library was established using the I-SAGE Kit (Cat. No. T5001-01; Invitrogen) according to SAGE protocol v1.0c (http://www.sagenet.org).

tag: SAGE profile of the asthmatic male rat (Sprague Dawley) lung treated by acupuncture with linker sequences removed. Rats weighted 250 grams and were 50 days old.


title: Hepatocellular carcinoma (HCC), venous metastasis, 03-345A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-387A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-284A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 231A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 215A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-342A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 186A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 355A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-342A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 03-313A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 365A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 468A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 464A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 289A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 02-366A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 180A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 230A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 450A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 334A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 423A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 073A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 237A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 343A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 219A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 071A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-269A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 033A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 105A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-366A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 089A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 214A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 054A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-339A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-457A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 228A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 205A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-301A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 322A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 329A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 03-315A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 369A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 409A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 055A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 02-456A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-455A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 271A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 149A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 043A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 211A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-452A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-313A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-375A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 098A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 199A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-424A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-455A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 435A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 057A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-375A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-301A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 251A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 112A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 050A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 454A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 307A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 059A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 220A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 208A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 325A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 182A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-339A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 439A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 070A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 374A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 233A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-416A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 326A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 146A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 162A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 048A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-452A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 062A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 234A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 03-295A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 434A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 429A

description: No additional information.

value: lymph node


title: Hepatocellular carcinoma (HCC), metastasis free, 360A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 349A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 441A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 223A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 200A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 263A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-284A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 195A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-321A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 447A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 405A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 037A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-285A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 333A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-285A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 312A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-404A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-361A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 277A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 458A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 394A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 281A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 448A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-269A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 438A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 306A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-387A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 077A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-354A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-309A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 323A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 064A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 225A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 151A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 421A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 017A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-384A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 03-456A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 381A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 442A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 196A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 197A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 024A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 02-346A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 116A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-335A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 165A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 235A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-315A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 03-314A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 292A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 042A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 356A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 192A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 082A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 02-384A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-398A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 337A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 445A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 358A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 015A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 362A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 047A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 344A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-309A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 02-457A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-415A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 119A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 243A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 049A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 466A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, A396A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 138A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-321A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 298A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 255A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 467A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 256A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 241A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-427A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 347A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 305A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 218A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 286A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 150A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 058A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 03-460A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-424A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 03-291A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 316A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 025A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-361A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 290A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 302A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 422A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 093A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-370A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-345A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-407A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-416A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-398A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 432A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-460A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 262A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 283A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 278A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 318A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 425A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 443A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-291A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 397A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, AN A

description: No additional information.

source_name: AN A

value: AN A


title: Hepatocellular carcinoma (HCC), metastasis free, 02-295A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 227A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 431A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 383A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 273A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 012A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 02-354A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 164A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 287A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 459A

description: No additional information.


title: Hepatocellular carcinoma (HCC), metastasis free, 336A

description: No additional information.


title: LongSAGE of P. chrysosporium, initiated ligninolytic enzyme production

status: Public on Dec 31 2007

city: Hikone-City

first: Masahiko

last: Minami

state: Shiga

address: 2500, Hassaka-cho

department: Department of Biological Resources Management

country: Japan

institute: University of Shiga Prefecture

description:
Day 3 culture was selected as initiated ligninolytic enzyme production SAGE library.
Veratryl alcohol is a secondary metabolite to act as a substrate and a stabilizer of the lignin peroxidase (Cancel et al. 1993). O2 purge is required for optimal lignin degradation culture condition (Kirk and Farrell 1987). Without the veratryl alcohol and/or O2 purge, the enzyme activities were greatly decreased and destabilized but not completely repressed in this strain.

data_processing: Sequence data were analyzed using the SAGE2000 version 4.5 software (http://www.invitrogen.com/sage) to extract, count, and catalogue the tag sequences.

organism: Phanerodontia chrysosporium

source_name: Mycelium grown on defined medium

growth_protocol: Phanerochaete chrysosporium RP78 was grown statically in a liquid medium (1% (v/v) Basal III medium, 1% (w/v) glucose, 20 mM Na-2,2-dimethylsuccinate (pH 4.5), 0.0001% thiamine, and 1.2 mM ammonium tartrate) at 37ºC. After 48 h of incubation under air, 3 mM veratryl alcohol was added, and an O2 purge was initiated at 24-h intervals.

extract_protocol: Total RNA was isolated with NucleoSpin RNA L (MACHEREY-NAGEL).

tag: Mycelium grown on defined medium, day 3 culture


title: Hepatocellular carcinoma (HCC), metastasis free, 319A

description: No additional information.


title: Mammary_biopsy_IMF4_pooled (SAGE)

status: Public on Dec 26 2007

city: Beltsville

first: Erin

middle: E

last: Connor

address: 10300 Baltimore Avenue

department: Animal and Natural Resources Institute

institute: USDA-ARS, BARC

description: This library was constructed to compare to a library constructed from pooled RNA samples obtained from mammary biopsies of dairy cows milked twice daily.

data_processing: SAGE2000, Version 4.5 software (Invitrogen Corp., Carlsbad, CA) was used to compare libraries, using a normalization value of 12000.

organism: Bos taurus

source_name: biopsy of mammary parenchyma, milked 4 times daily beginning at day 4 of lactation, sampled at approx. day 7 of lactation

growth_protocol: Multiparous Holstein dairy cattle were evaluated during the first week of lactation.

extract_protocol: Total RNA was isolated using the RNeasy Midi Kit (Qiagen, Valenica, CA). To remove contaminating genomic DNA, on-column DNase digestion was performed using the RNase-free DNase Set (Qiagen) according to kit instructions. RNA quality was assessed using the BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) and concentrations were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE).

treatment_protocol: Four multiparous Holstein dairy cattle were milked twice daily during the first 3 days of lactation then 4 times daily until day 21 of lactation. Mammary biopsies were performed at approximately day 7 of lactation for extraction of total RNA, RNA pooling and subsequent SAGE library synthesis.

tag: Pooled total RNA isolated from mammary biopsies of 4 multiparous Holstein cows milked twice daily from days 1-3 of lactation and then 4 times daily beginning at day 4 of lactation. Biopsies performed at approximately day 7 of lactation.


title: Mammary_biopsy_control_pooled (SAGE)

description: This library was constructed to compare to a library constructed from pooled RNA samples obtained from mammary biopsies of dairy cows milked 4 times daily beginning at day 4 of lactation.

source_name: biopsy of mammary parenchyma, milked twice daily, approx. day 7 of lactation

treatment_protocol: Three multiparous Holstein dairy cattle were milked twice daily during the first 21 days of lactation. Mammary biopsies were performed at approximately day 7 of lactation for extraction of total RNA, RNA pooling and subsequent SAGE library synthesis.

tag: Pooled total RNA isolated from mammary biopsies of 3 multiparous Holstein cows milked twice daily and biopsied at approximately day 7 of lactation.


title: Hepatocellular carcinoma (HCC), metastasis free, 148A

description: No additional information.


title: Hepatocellular carcinoma (HCC), venous metastasis, 272A

description: No additional information.


title: SAGE_rat_P0_VSU

status: Public on Dec 21 2007

city: Edinburgh

first: Axel

last: Thomson

address: 47 Little France Crescent

country: United Kingdom

institute: MRC Human Reproductive Sciences Unit

description: Library prepared using freshly isolated rat tissue - 100 VSUs

source_name: rat female P0 microdissected urethra, comprising VMP, Smooth muscle and Urethra

extract_protocol: Qiagen RNeasy mini kit

treatment_protocol: Fresh tissue, dissected

tag: Wistar P0 (day of birth) female manually microdissected urethra, proximal to the bladder


title: Hepatocellular carcinoma (HCC), venous metastasis, 087A

description: No additional information.


title: SAGE_rat_P0_VMP

description: Library prepared using freshly isolated rat VMP tissue - 90 VMPs

source_name: rat female P0 microdissected ventral mesenchymal pad

tag: Wistar P0 (day of birth) female manually microdissected vental mesenchymal pad tissue, dissected from the urethra proximal to the bladder


title: Vero cell

status: Public on Nov 05 2007

city: Hangzhou

first: Jiyong

last: Zhou

state: Zhejiang Province

address: 268 Kaixuan road

department: Colege of Animal Science

institute: Zhejiang University

description: as the commercial kit producted by invitrogen company,I-SAGE™ Long Kit,Catalog no. T5000-03

organism: Chlorocebus aethiops

source_name: vero cell

extract_protocol: as the protocol of commercial kit producted by invitrogen company,I-SAGE™ Long Kit,Catalog no. T5000-03

tag: Cercopithecus aethiops kidney cells were incubated in MEM media containing 10%FBS,at 5%CO2,37℃.


title: Vero cell line transformed by the 243 fragment of genome of infectious bursal disease virus

source_name: vero cell,the 243 fragment of genome of infectious bursal disease virus

tag: vero cell line transformed by the 243 fragment of genome of infectious bursal disease virus NB strain


title: Vero cell line transformed by A fragment of genome of infectious bursal disease virus

source_name: vero cell,A fragment of genome of infectious bursal disease virus

extract_protocol: as the protocol commercial kit producted by invitrogen company,I-SAGE™ Long Kit,Catalog no. T5000-03

tag: vero cell line transformed by A fragment of genome of infectious bursal disease virus NB strain


title: Vero cell line transformed by vp5 gene of infectious bursal disease virus

source_name: vero cell,vp5 gene of infectious bursal disease virus

tag: cercopithecus aethiops kidney cells

tag: vp5 gene of infectious bursal disease virus NB strain


title: LongSAGE of Phanerochaete chrysosporium, day 2 culture

description: Day 2 culture was selected as control SAGE library.

growth_protocol: Phanerochaete chrysosporium RP78 was grown statically in a liquid medium (1% (v/v) Basal III medium, 1% (w/v) glucose, 20 mM Na-2,2-dimethylsuccinate (pH 4.5), 0.0001% thiamine, and 1.2 mM ammonium tartrate) at 37ºC.

tag: Strain

tag: Mycelium grown on defined medium, day 2 culture


title: Hepatocellular carcinoma (HCC), metastasis free, 268A

description: No additional information.

tag: Tissue


title: PCCl3_iodide_24h_1

status: Public on Nov 02 2007

city: Sao Paulo

first: Edna

middle: Teruko

last: Kimura

state: SP

address: Av Prof Lineu Prestes 1524 sala 414

department: ICB - Cell and Developmental Biology

country: Brazil

institute: USP - University of Sao Paulo

description: PCCl3 cells were cultured with 10-3M Sodium Iodide (NaI)

source_name: rat thyroid cell PCC3_iodide treated_24h

growth_protocol: Cell were cultured in Ham's F12 medium supplemented with 5% calf serum and the four hormones: 1mU/ml bovine TSH, 10ug/ml insulin, 5ug/ml transferrin and 10nM hydrocortisone.

extract_protocol: RNA poly A tail was isolated in magnetic beads provided by I-SAGE kit (Invitrogen)

tag: Rat thyroid cell

tag: Second passage


title: PCCl3_24h_1

description: PCCl3 cells were cultured without any additional treatment

source_name: PCCl3 thyroid follicular cell, 24h

extract_protocol: Polyadenylated RNA was isolated using magnetic beads provided by I-SAGE Kit (Invitrogen)


title: African endemic Kaposi's sarcoma

status: Public on Nov 01 2007

city: Amsterdam

first: Antoinette

last: van der Kuyl

department: Human Retrovirology

country: Netherlands

institute: Academic Medical Centre, University of Amsterdam

description: The presence of HHV-8 DNA in the endemic KS lesions was tested with a nested HHV-8 PCR before generation of the SAGE library. Subsequently, the absence of HIV-1 RNA in the endemic KS lesions was tested with a HIV-1 specific RT-PCR before generation of the SAGE library.

data_processing:
Primary analysis of the SAGE library was performed with USAGE version2 (van Kampen, A. H., van Schaik, B. D., Pauws, E., Michiels, E. M., Ruijter, J. M., Caron, H. N., Versteeg, R., Heisterkamp, S. H., Leunissen, J. A., Baas, F., & van der Mee, M. (2000). USAGE: a web-based approach towards the analysis of SAGE data. Bioinformatics., 16, 899-905).The program performs initial analyses on raw sequence data, e.g. ditag and tag extraction, tag counting, and tag identification. Tags were identified with the SAGEmap database available through NCBI, to which USAGE is directly linked. Viral tags were identified with a USAGE viral database created by extracting relevant SAGE tags from all viral cDNA sequences present in the NCBI database.
Reference: van der Kuyl AC, van den Burg R, Zorgdrager F, Lebbé C, and Cornelissen M.
Chapter VIII. Analysis of gene family expression in African endemic- and AIDS-related Kaposi’s sarcoma. Pp. 147-173, In: New Topics in Cancer Research (Horizons in Cancer Research, Volume 34). Ed. FG Drabell. 2006. Nova Science Publishers Inc., Hauppauge NY, USA.

source_name: Endemic Kaposi's sarcoma tissue

growth_protocol: All tissues were collected, snap frozen, and stored at -80ºC.

extract_protocol: The SAGE library was constructed from the four pooled tissues using the I-SAGE kit™ from Invitrogen (Carlsbad, CA, USA).

treatment_protocol: The biopsies were cut with a microtome in 10-14 micrometer sections for RNA isolation.

tag: Library constructed from mixed frozen biopsies from nodal Kaposi's sarcoma (KS) lesions from four HIV-1 negative male African endemic KS patients. Two patients were from Zaire, one patient was from Mali, and the fourth patient originated from Cameroon. All four skin biopsies showed a similar histopathological picture of nodular advanced-stage Kaposi’s sarcoma with irregular, dense areas of spindle cell proliferations that were HHV8-LANA positive.


title: Hepatocellular carcinoma (HCC), metastasis free, 133A

description: No additional information.

tag: Disease state

tag: Individual

tag: Clinical info


title: Vero cell infected by infectious bursal disease virus

source_name: vero cell,infectious bursal disease virus

tag: Cercopithecus aethiops kidney cell were incubated in MEM media containing 10%FBS,at 5%CO2,37℃.

tag: IBDV NB strain


title: whole brain_chinook_ocean

status: Public on Oct 10 2007

city: Newport

first: Jeremiah

last: Bernier

state: OR

address: 2030 SE Marine Science Drive

department: Fisheries and Wildlife

institute: Hatfield Marine Science Center, Oregon State University

description: 3 of 3 Chinook salmon SAGE libraries

organism: Oncorhynchus tshawytscha

source_name: whole brain_chinook_ocean

extract_protocol: Trizol RNA extraction of whole brains. SAGE libraries constructed with 10ug total RNA

tag: Sample

value: Caught in Pacific Ocean 5 miles off of Eureka, CA, Summer, 2005

tag: Sex

value: Female

value: whole brain tissue


title: SAGE_pituitary_adrenalectomized male mice

status: Public on Dec 19 2007

city: Hershey

first: Yuichiro

last: Nishida

state: PA

address: 500 University Drive

department: Department of Anatomy and Physiology

institute: Penn State College of Medicine

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

source_name: pituitary


title: whole brain_chinook_fall

description: 1 of 3 Chinook salmon SAGE libraries

source_name: whole brain_chinook_fall

extract_protocol: Trizol RNA extraction of whole brains.  SAGE libraries constructed with 10ug total RNA

value: Caught in the Feather River, CA, Fall, 2004


title: PSA-NCAM-positive neuronal precursor cells from adult mouse brain

status: Public on Sep 22 2007

city: Bergisch Gladbach

first: Sandra

middle: Juliane

last: Pennartz

address: Friedrich-Ebert-Strasse 68

department: Research & Development

country: Germany

institute: Miltenyi Biotec GmbH

description:
No amplification of RNA samples. No cultivation steps, isolated cells were processed immediately.
MicroSAGE Detailed Protocol with minor modifications was performed as described in Pennartz et al., Mol Cell Neurosci. 2004 Apr;25(4):692-706 and PhD thesis "Gene expression analysis of neuronal precursors
from adult mouse brain and differential screen for
neural stem cell markers" , University of Cologne, Germany, http://deposit.ddb.de/cgi-bin/dokserv?idn=973392754

data_processing: SAGE data analysis was carried out using the Memorec SAGE Analysis Package (Memorec Biotec GmbH, Cologne, Germany).

source_name: PSA-NCAM-positive neuronal precursor cells from the adult subventricular zone

extract_protocol: RNeasy Mini Lit (Qiagen, Hilden)

treatment_protocol:
PSA-NCAM positive cells were isolated from dissected subventricular zone (SVZ) tissue using FACS as described in Pennartz et al., Mol Cell Neurosci. 2004 Apr;25(4):692-706 and PhD thesis "Gene expression analysis of neuronal precursors
from adult mouse brain and differential screen for
neural stem cell markers" , University of Cologne, Germany, http://deposit.ddb.de/cgi-bin/dokserv?idn=973392754

tag: strain

value: C57BL/6J mice

tag: age

value: 4-6 week

tag: gender

value: male


title: whole brain_chinook_spring

description: 2 of 3 Chinook salmon SAGE libraries

source_name: whole brain_chinook_spring

value: Caught in the Feather River, CA, Spring, 2005


title: Bruce-4 embryonic stem cells (undifferentiated)

description:
No amplification of RNA samples.
MicroSAGE Detailed Protocol with minor modifications as described in Pennartz et al., Mol Cell Neurosci. 2004 Apr;25(4):692-706.

data_processing: SAGE data analysis was carried out using the Memorec SAGE Analysis Package (Memorec Biotec GmbH, Cologne, Germany)

source_name: Bruce-4 embryonic stem cells

growth_protocol: C57BL/6J derived Bruce-4 ES cells were grown on a layer of embryonic fibroblasts in DMEM containing 10% FCS, 1 mM sodium pyruvate, 1% L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 1% nonessential amino acids, LIF (Leukemia Inhibitory Factor) and 0.01 mM β-mercaptoethanol.

extract_protocol: RNeasy Mini Kit (Qiagen, Hilden)

treatment_protocol: To reduce the contamination of embryonic fibroblasts prior to RNA preparation, ES cells were grown on gelatine-coated plates for 24 h, and then passaged to a new plate for 20 min to allow feeder cells to adhere. The ratio of ES cells to fibroblasts was approximately 60:1 after initial plating. After reduction of contaminating fibroblasts by transient plating the ratio was approximately 80:1 (1.25%).

tag: Bruce-4 ES cells are derived from C57BL/6J mice,

tag: Kontgen et al., 1993


title: SAGE_pituitary_intact male mice

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

source_name: pituitary gland


title: RDE2_X3339_FlightvsGround_G25_LB_7DS520_1

status: Public on Sep 13 2007

type: mixed

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate, Date of Scan Wed Dec 13 10:23:20 2006

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv7S_01_051201

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica

source_name: Salmonella enterica subsp. enterica serovar Typhimurium X3339 total RNA after ground G25

label_protocol: incorporation of Cy3-dCTP with Reverse Transcriptase

extract_protocol: total RNA preparation

tag: Salmonella typhimurium X3339 total RNA harvested after exposure to conditions

molecule: genomic DNA

source_name: Salmonella enterica subsp. enterica serovar Typhimurium X3339 gDNA from overnight cultures in LB

label_protocol: incorporation of Cy5-dCTP with Klenow enzyme

extract_protocol: total gDNA preparation

tag: Salmonella typhimurium X3339 grown O/N in LB at 37C with aeration


title: RDE2_X3339_FlightvsGround_G25_LB_7DS520_3


title: RDE2_X3339_FlightvsGround_G25_LB_7DS520_2


title: RDE2_X3339_FlightvsGround_G123_LB_7DS516_1

description: biological replicate, Date of Scan Tue Dec 12 14:39:50 2006

source_name: Salmonella enterica subsp. enterica serovar Typhimurium X3339 total RNA after ground G123


title: RDE2_X3339_FlightvsGround_G11_LB_7DS519_2

description: biological replicate, Date of Scan Wed Dec 13 09:49:36 2006

source_name: Salmonella enterica subsp. enterica serovar Typhimurium X3339 total RNA after ground G11


title: RDE2_X3339_FlightvsGround_G123_LB_7DS516_3


title: Hepatocellular carcinoma (HCC), metastasis free, 261A

description: No additional information.

tag: Tissue


title: RDE2_X3339_FlightvsGround_G123_LB_7DS516_2


title: RDE2_X3339_FlightvsGround_F25_LB_7DS518_3

description: biological replicate, Date of Scan Wed Dec 13 09:12:30 2006

source_name: Salmonella enterica subsp. enterica serovar Typhimurium X3339 total RNA after flight F25


title: RDE2_X3339_FlightvsGround_F25_LB_7DS518_1


title: Hepatocellular carcinoma (HCC), venous metastasis, 270A

description: No additional information.


title: RDE2_X3339_FlightvsGround_G11_LB_7DS519_3


title: Mouse bmDC treated with TGF-beta

status: Public on Aug 29 2007

city: Oxford

first: Steve

last: Cobbold

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

description: This library was generated to compare treatment with TGF-beta with other mouse bone marrow dendritic cells given other immunomodulatory treatments such as VitD3, IL-10 or LPS.

data_processing: SAGEScreen (Akmaev et al, 2004) was used to correct for non-random sequence errors.

source_name: Mouse bone marrow cultured in 25ng/ml GM-CSF plus 2ng/ml rhTGFbeta1

growth_protocol: Femurs and tibias of 6-10 week old CBA/Ca mice were dissected and single cell bone marrow suspension made.  Red cells were lysed with ammonium chloride. Cells were washed twice and grwon at 4x10^5/ml per 10cm culture plate in RPMI 1640, 10%FCS, 2mM L-glutamine, pennicilin and streptomcyin, 5x10^-5M 2-mercaptoethanol, plus 25ng/ml murine recombinant GM-CSF, plus 2ng/ml rhTGFbeta1.  Medium was replaced at days 3 and 6 wirth removal of non-adherant cells.  Semi-adherent dendritic cells were harvested by gentle pipetting on day 7.

extract_protocol: Total RNA was extracted using RNEasy Midi Kit (Qiagen) including a DNAse digest step. A LongSAGE library was generated using the I-SAGE kit (Invitrogen) with the addition of biotinylated primers for amplification.

treatment_protocol: 2ng/ml rhTGFbeta1 was  included throughout the 7 day culture

tag: Strain

value: CBA/Ca, Gender:male, Tissue:bone marrow, Age:adult:Culture time:7 days, Culture medium:RPMI 1640 10%FCS plus 25ng/ml GN-CSF plus 2ng/ml rhTGFbeta1:Cell type:dendritic cell


title: RDE2_X3339_FlightvsGround_F15_LB_7DS517_3

description: biological replicate, Date of Scan Wed Dec 13 07:57:23 2006

source_name: Salmonella enterica subsp. enterica serovar Typhimurium X3339 total RNA after flight F15


title: RDE2_X3339_FlightvsGround_F15_LB_7DS517_1


title: RDE2_X3339_FlightvsGround__F11_LB_7DS515_3

description: biological replicate, Date of Scan Thu Dec 07 12:26:13 2006

source_name: Salmonella enterica subsp. enterica serovar Typhimurium X3339 total RNA after microgravity in flight F11

tag: Salmonella typhimurium X3339 total RNA harvested after exposure to space flight


title: RDE2_X3339_FlightvsGround_F25_LB_7DS518_2


title: ovarian gene expression innthe absence of FIGLA, an oocyte specific transcription factor

status: Public on Sep 08 2007

city: bethesda

first: saurabh

last: joshi

address: 9000 rockville pk

department: national institute of diabestes digestive and kidney diseases

institute: national institutes of health

description: not applicable

data_processing: eSAGE was used to extract tags and remove duplicate ditags from raw data.

source_name: normal Versus FIGLA null ovary at new born developmental stage

growth_protocol: not applicable

extract_protocol: total RNA was extracted from the normal and homozygous null mice by using RNeasy mini kit (Qiagen, Valencia, CA). homozygous null mouse RNA was confired by one step RT PCR using primers for ZP2 and MSY gene and absence of ZP2 and presence of MSY gene was considered as homozygous null ovary RNA. Poly (A)+ RNA was isolated with oligo d(T)- conjugated magnetic beads (Dynal- Invitrogen, Carlsbad, CA). 5 microgram of this RNA was used for construction of these libraries using the original SAGE protocol of Velculescu et al (Velculescu et al, 1995). Final concatenated ditags were cloned into Bluescript pKS (Stratagene, LA Jolla, CA) using BamHI site for blue white screening. Sequencing was perfomred at NIH Intramural Sequencing Centre (NISC). Low quality sequence data was eliminated by Phred analysis

treatment_protocol: Figla null mouse line was made by targetted disruption of Figla gene in the mouse chromosome by homologous recombination in mouse 129Sv ES cells. The correctly targetted ES cells were injected in the blastocyst of C57BL/6 mice

tag: CF1 normal mice and mixed background Figla null mouse

tag: Gender

value: female

value: newborn

tag: homozygous Null mouse for Figla

tag: Normal CF1

tag: tissue

value: ovary


title: RDE2_X3339_FlightvsGround_F15_LB_7DS517_2


title: Mouse bone marrow derived dendritic cells LPS matured - LongSAGE

description: This combined Long SAGE library was generated to compare and extend data on LPS treated bmDC obtained previously using standard SAGE in GSM3832.  The CBA/Ca library has been submitted independantly GSM269526 (29253 tags)

data_processing: SAGEScreen software (Akmaev et al, Bioinformatics, (2004) 20:1254-63) was used to correct for non-random sequence errors within the ditags and to extract the 17 bp long SAGE tags

source_name: Mouse bone marrow derived dendritic cells LPS matured (CBA/Ca and Balbc mixed library)

growth_protocol: Bone marrow, isolated from the femurs and tibias of CBA/Ca mice, were made into single cell suspension by sieving through a 70 micron nylon mesh. Red cells were lysed using ammonium chloride, washed and plated in 10cm dishes in RPMI 1640, 10% FCS, 2 mM L-glutamine, 50 u/ml Penicillin, 50 microg/ml streptomycin, 5x10^-5M 2-ME, ~25 ng/ml recombinant GM-CSF (supplied as x-63 transfected tissue culture supernatant). Cells in suspension were removed and culture medium replaced on days 3 and 6. On day 6 the medium was supplemented with 1 microg/ml LPS and the cells cultured for a further 18-20 hr, when semi-adherent cells were harvested by gentle pippetting

extract_protocol:
Total RNA was prepared using RNEasy Midi kit (Qiagen) including a DNAse treatment.
CBA/Ca: poly A+ RNA, isolated using (dT)25-coated Dynabeads (Dynal) according to the manufacturer's protocols and a long SAGE library generated essentially according to the original description by Saha et al., Nature Biotechnology, (2002)20:508-512.
Balbc: a long SAGE library was generated using Invitrogen's I-SAGE long kit according to the manufacturer's protocol.
In both cases biotinylated linkers were used biotinylated linkers as described by Powell, NAR (1998)26:3445-6.

treatment_protocol: 1 microg/ml LPS (E.coli) added for the final 18-20 hours of culture

value: CBA/Ca; Gender:female; Tissue:bone marrow; Culture time:7 days; Culture medium:RPMI 10%FCS plus 25ng/ml rmGM-CSF. Treatment:1microg/ml LPS

tag: and

value: Balbc; Tissue:Bone marrow; Culture time:9 days; Treatment:1microg/ml LPS


title: RDE2_X3339_FlightvsGround_F11_LB_7DS515_1


title: LongSAGE_fetal skeletal muscle_Landrace pig_90 dpc

status: Public on Aug 10 2007

city: Beijing

first: Kui

last: Li

address: 2 West Yuanmingyuan Rd

department: Institute of Animal Science

institute: Chinese Academy of Agricultural Sciences

description: fetal skeletal muscle from lean-type pig at 90 dpc, Landrace pigs

source_name: fetal skeletal muscle, 90 dpc, Landrace pigs

tag: In vivo derived porcine skeletal muscle collected at 90 days post coitus.

tag: Pig breed

value: western breed, Landrace pig

value: male and female

tag: Age

value: 90 dpc

value: longissimus dorsi


title: RDE2_X3339_FlightvsGround_G11_LB_7DS519_1


title: LongSAGE_fetal skeletal muscle_Landrace pig_33 dpc

description: fetal skeletal muscle from lean-type pig at 33 dpc, Landrace pigs

source_name: fetal skeletal muscle, 33 dpc, Landrace pigs

tag: In vivo derived porcine skeletal muscle collected at 33 days post coitus.

value: 33 dpc


title: LongSAGE_fetal skeletal muscle_Tongcheng pig_33 dpc

description: fetal skeletal muscle from obese-type pig at 33 dpc, Tongcheng pigs

source_name: fetal skeletal muscle, 33 dpc, Tongcheng pigs.

value: chinese indigenous breed, Tongcheng pig


title: LongSAGE_fetal skeletal muscle_Landrace pig_65 dpc

description: fetal skeletal muscle from lean-type pig at 65 dpc, Landrace pigs

source_name: fetal skeletal muscle, 65 dpc, Landrace pigs

tag: In vivo derived porcine skeletal muscle collected at 65 days post coitus.

value: 65 dpc


title: RDE2_X3339_FlightvsGround__F11_LB_7DS515_2


title: LongSAGE_fetal skeletal muscle_Tongcheng pig_90 dpc

description: fetal skeletal muscle from obese-type pig at 90 dpc, Tongcheng pigs.

source_name: fetal skeletal muscle, 90 dpc, Tongcheng pigs


title: never3

status: Public on Aug 08 2007

city: Vancouver

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

institute: BC Cancer Research Centre

description: Never smoker

source_name: Bronchial brushings, never smoker

tag: Bronchial brushings, never smoker, Gender

value: M, Age:53


title: never2

description: Never smoker

value: F, Age:56


title: former10

description: Former smoker, BE-16 from Lonergan et al. (2006) PMID: 16809635

source_name: Bronchial brushings, former smoker

tag: Bronchial brushings, former smoker, Gender

value: F, Age:71


title: never4

description: Never smoker

value: F, Age:81


title: former9

description: Former smoker, BE-15 from Lonergan et al. (2006) PMID: 16809635

value: M, Age:72


title: former12

description: Former smoker

value: M, Age:69


title: former7

description: Former smoker, BE-11A from Lonergan et al. (2006) PMID: 16809635


title: former8

description: Former smoker, BE-14 from Lonergan et al. (2006) PMID: 16809635

value: F, Age:63


title: former5

description: Former smoker, BE-6 from Lonergan et al. (2006) PMID: 16809635

value: M, Age:67


title: never1

description: Never smoker

value: M, Age:58


title: former11

description: Former smoker, BE-8B from Lonergan et al. (2006) PMID: 16809635


title: former6

description: Former smoker, BE-10 from Lonergan et al. (2006) PMID: 16809635

value: M, Age:65


title: current8

description: Current smoker

source_name: Bronchial brushings, current smoker

tag: Bronchial brushings, current smoker, Gender

value: F, Age:55


title: former1

description: Former smoker, BE-3 from Lonergan et al. (2006) PMID: 16809635

value: M, Age:68


title: former3

description: Former smoker, BE-9 from Lonergan et al. (2006) PMID: 16809635


title: current2

description: Current smoker, BE-7 from Lonergan et al. (2006) PMID: 16809635

value: M, Age:56


title: current7

description: Current smoker

value: M, Age:52


title: current1

description: Current smoker, BE-13 from Lonergan et al. (2006) PMID: 16809635


title: current5

description: Current smoker, BE-2 from Lonergan et al. (2006) PMID: 16809635

value: M, Age:64


title: current4

description: Current smoker, BE-1 from Lonergan et al. (2006) PMID: 16809635


title: former2

description: Former smoker, BE-4A/4B combined from Lonergan et al. (2006) PMID: 16809635


title: current6

description: Current smoker

value: M, Age:66


title: former4

description: Former smoker, BE-5 from Lonergan et al. (2006) PMID: 16809635

value: M, Age:70


title: LongSAGE_fetal skeletal muscle_Tongcheng pig_65dpc

description: fetal skeletal muscle from obese-type pig at 65 dpc, Tongcheng pigs.

source_name: fetal skeletal muscle, 65 dpc, Tongcheng pigs

value: chinese indigenous breed, Tongcheng pig

value: male and female

value: 65 dpc

value: longissimus dorsi


title: mLSAGE Endoderm normal Theiler Stage 13 MMD SM248

status: Public on Jul 11 2007

first: BCGSC

last: BC Cancer Agency

department: Gene Expression

institute: Canada's Michael Smith Genome Sciences Centre

description:
Developmental Stage = Theiler Stage 13
This library is of the MORGEN project.

source_name: Mouse Endoderm Hindgut TS13

tag: Location

value: Endoderm, Sublocation:Hindgut, Strain:C57BL/6J, Age:E8.5, Preparation:Manual microscope dissected


title: mLSAGE Heart normal Theiler Stage 15 MMD SM246

description:
Developmental Stage = Theiler Stage 15
This library is of the MORGEN project.

source_name: Mouse Heart AV Canal TS15

tag: Location:Heart, Sublocation

value: Atrioventricular Canal, Strain:C57BL/6J, Age:E9.5, Preparation:Manual microscope dissected


title: mLSAGE Pancreas normal Theiler Stage 21 MMD SM249

description:
Developmental Stage = Theiler Stage 21
This library is of the MORGEN project.

source_name: Mouse Pancreas TS21

tag: Location:Pancreas, Strain

value: C57BL/6J, Age:E13.5, Preparation:Manual microscope dissected


title: mLSAGE Endoderm normal Theiler Stage 12 MMD SM247

description:
Developmental Stage = Theiler Stage 12
This library is of the MORGEN project.

source_name: Mouse definitive endoderm TS12

value: Endoderm, Sublocation:Definitive, Strain:C57BL/6J, Age:8.0, Preparation:Manual microscope dissected


title: mLSAGE Pancreas normal Theiler Stage 17 MMD SM244

description:
Developmental Stage = Theiler Stage 17
This library is of the MORGEN project.

source_name: Mouse Pancreas TS17 PDX1-GFP+

tag: Location:Pancreas, Sublocation

value: PDX1-GFP+, Strain:CBA/B6(n=2 on B6), Age:E10.5, Preparation:Manual microscope dissected


title: Low phosphate

status: Public on Jul 07 2007

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

description: Recombinant pZero clones produced by SAGE were purified using GeneMachines RevPrep Orbit (San Carlos, CA) and were sequenced on an ABI 3730xl DNA sequencer (Applied Biosystems, Foster City, CA).

data_processing: Sequences collected were analyzed with software created for SAGE analysis.  The SAGE software extracts ditag sequences from the ABI 3730xl results according to the SAGE sequence grammar, parses out individual SAGE tags, excludes tags with sequence ambiguities, and reduces all SAGE tags to a table of unique SAGE tag sequences and their observed frequencies.  Multiple instances of ditag sequences were ignored in the data processing – only a single instance contributed to tag frequencies.

organism: Emiliania huxleyi CCMP1516

source_name: Emiliania huxleyi, low phosphate

growth_protocol: Cultures were grown at 18°C on a 14 h:10 h light:dark cycle.  Nitrogen and phosphate replete (Replete, low nitrogen (-N) and low phosphate (-P) cells were grown in f/50 medium without Si.  Locally collected seawater was filtered (pore size, 0.2 µm) and autoclaved.  Filter-sterilized inorganic nutrients, trace metals and vitamins (thiamin, biotin and B12) were added after autoclaving.  The cells were grown in 8 L batch cultures.  The growth of cultures was monitored daily by cell number counted on a hemacytometer, and by relative fluorescence using a Turner Designs AU Fluorometer.  Replete cells were harvested in mid-log phase while –N and –P cells were harvested at the onset of stationary phase.

extract_protocol: Approximately 20,000,000 cells were harvested (8,000 x g for 10 min at 22 °C) and the RNA extracted using TRI Reagent (Sigma, St. Louis, MO) according to the manufacturer’s instructions.

tag: Strain


title: Low nitrogen

source_name: Emiliania huxleyi, low nitrogen


title: Replete

source_name: Emiliania huxleyi, nitrogen and phosphate replete


title: Control adults

status: Public on Jul 04 2007

description: Recombinant pGEM3Z clones produced by SAGE were purified using GeneMachines RevPrep Orbit (San Carlos, CA) and were sequenced on an ABI 3730xl DNA sequencer (Applied Biosystems, Foster City, CA).

organism: Schistosoma mansoni

source_name: Schistosoma mansoni adults, un-exposed

extract_protocol: RNA was extracted using TRIZOL.

treatment_protocol: Adult S. mansoni perfused from infected Swiss-Webster female mice (obtained from the NIAID Schistosomiasis Resource Center) 42-49 days postinfection were maintained in culture (RPMI medium) overnight and then exposed for 3 hours to either 1 mM sodium nitroprusside (SNP), a well-characterized NO donor, or to RPMI alone.


title: SNP exposed adults

source_name: Schistosoma mansoni adults, SNP exposed


title: mLSAGE Heart normal Theiler Stage 17 MMD SM235

data_processing: not normalized

source_name: Mouse Heart AV Canal TS17

value: Heart, Sublocation:Outflow Tract, Strain:C57BL/6J, Age:E10.5, Preparation:Manual microscope dissected


title: mLSAGE Heart normal Theiler Stage 17 MMD SM234

source_name: Mouse Heart TS17

value: Heart, Sublocation:Atrioventricular Canal, Strain:C57BL/6J, Age:E10.5, Preparation:Manual microscope dissected


title: mLSAGE Heart normal Theiler Stage 20 MMD SM238

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

source_name: Mouse Heart AV Canal TS20

value: Heart, Sublocation:Atrioventicular Canal, Strain:C57BL/6J, Age:E12.5, Preparation:Manual microscope dissected


title: mLSAGE Heart normal Theiler Stage 19 MMD SM241

description:
Developmental Stage = Theiler Stage 19
This library is of the MORGEN project.

source_name: Mouse Heart AV Canal TS19

tag: Location:Heart,Sublocation:Atrioventricular Canal, Strain:C57BL/6J, Age:E11.5, Preparation

value: Manual microscope dissected


title: Trophozoite

status: Public on Jul 03 2007

description: Recombinant pZero1 clones produced by SAGE were purified using GeneMachines RevPrep Orbit (San Carlos, CA) and were sequenced on an ABI 3730xl DNA sequencer (Applied Biosystems, Foster City, CA).

data_processing: Sequences collected were analyzed with software created for SAGE analysis. The SAGE software extracts ditag sequences from the ABI 3730xl results according to the SAGE sequence grammar, parses out individual SAGE tags, excludes tags with sequence ambiguities, and reduces all SAGE tags to a table of unique SAGE tag sequences and their observed frequencies.  Multiple instances of ditag sequences were ignored in the data processing - only a single instance contributed to tag frequencies.

organism: Giardia duodenalis

source_name: Trophozoite cell culture

growth_protocol: A confluent culture of trophozoites was used to inoculate fresh cultures and grown for 21 hr before sampling for SAGE.  These were log phase trophozoites.

tag: Giardia intestinalis isolate WB clone C6 (ATCC 50803)


title: mLSAGE Pancreas normal Theiler Stage 20 MMD SM243

source_name: Mouse Pancreas TS20 N3N3-GFP+

value: N3N-GFP+, Strain:CBA/B6(n=2 on B6), Age:12.5, Preparation:Manual microscope dissected


title: mLSAGE Pancreas normal Theiler Stage 22 MMD SM232

description:
Developmental Stage = Theiler Stage 22
This library is of the MORGEN project.

source_name: Mouse Pancreas TS22

value: Pancreas, Sublocation:N3N3-GFP+, Strain:C57BL/6J, Age:E14.5


title: Bloodstream form T. b. brucei 427-221

organism: Trypanosoma brucei brucei

source_name: Bloodstream form of Lister strain 427 Trypanosoma brucei brucei  (MiTat 1.2),  expressing VSG221

growth_protocol: Cells were cultured in HMI-9 medium with the addition of heat inactivated fetal bovine serum (FBS) (10%) and Serum Plus (10%).

extract_protocol: Total trypanosome RNA was isolated using the Tripure Isolation Reagent (Roche, Mannheim, Germany).

treatment_protocol: At a cell density of approximately 1,000,000 cells/ml, T. b. brucei 427-221 were exposed to various amounts of human HDLs for 24 h in a 6 well plate.  Surviving trypanosomes were counted using a hemocytometer then diluted into fresh HMI-9 medium and allowed to recover for 5-14 days.  Once the cells had grown to a density of approximately 1,000,000  cells/ml, they were once again incubated with human HDLs.  Each round of selection was performed with increasing concentrations of human HDLs and freezer stocks were prepared for each surviving population.  Over nine months we conducted eight rounds of human HDL selection, resulting in a population of T. b. brucei that survived incubation with 800 μl of human HDLs (160 lytic U).

value: Lister strain 427 T. b. brucei  (MiTat 1.2)

tag: Stage

value: bloodstream


title: mLSAGE Heart normal Theiler Stage 15 MMD SM236

source_name: Mouse Heart TS15

value: Heart, Sublocation:Outflow Tract, Strain:C57BL/6J, Age:E9.5, Preparation:Manual microscope dissected


title: Bloodstream form T. b. brucei 427-800

source_name: Bloodstream form of Lister strain 427 Trypanosoma brucei brucei  (MiTat 1.2),  expressing VSG800


title: mLSAGE Pancreas normal Theiler Stage 19 MMD SM231

source_name: Mouse Pancreas TS19

tag: Sublocation

tag: Preparation


title: Bovine BL3 cells under normal culture conditions

status: Public on Jun 30 2007

city: Ames

first: John

middle: D.

last: Neill

state: IA

address: 2300 Dayton Ave.

institute: National Animal Disease Center

description: SAGE library construction was done using the microSAGE protocol.

data_processing: Tag sequences were extracted using SAGE 2000 ver. 4.0 software.

source_name: Bovine BL3 cells

growth_protocol: BL3 cells were grown in Leibovitz MEM with Earles salts medium supplemented with 1.4 mM glutamate.

extract_protocol: Cells were collected by centrifugation and washed once with PBS.  The cell pellet was resuspended and the cells lysed by addition of Trizol Reagent.  The total RNA was prepared according to manufacturer's specifications.

treatment_protocol: Normal cells grown under normal culture conditions.

tag: Bovine BL3 cells - B cell lymphosarcoma cell line, nonadherent.


title: Bovine BL3 cells acutely infected with BVDV2 strain 296c

source_name: Bovine BL3 cells infected with BVDV2 strain 296c

treatment_protocol: BL3 cells were infected with BVDV strain 296c at MOI of 2.  Cells were collected at 18 hours post-infection.

tag: Bovine BL3 cells - B cell lymphosarcoma cell line, nonadherent.  BL3 cells had acute infection with BVDV2 strain 296c.  The cells were collected at 18 hours post-infection before signs of cytopathic effect were visible.  Immunohistochemistry examination of culture showed >90% of the cells were infected.


title: Bovine Macrophage Cells Control

status: Public on Jun 22 2007

first: Richard

last: Zuerner

address: P.O. Box 70

department: BDLRU

institute: USDA, ARS, NADC

description: Standard SAGE protocols were used to generate library, cloned into pZER0-1, and sequenced on an ABI 3700 system.

data_processing: Data were processed using Phred and Sequencher with manual editing then processed by eSAGE software.

source_name: Bovine macrophage

growth_protocol: Cells were propagated in RPMI 1640 medium with 10% fetal calf serum, 100 ug/ml each streptomycin and penicillin, at 37C with 5% C02.

extract_protocol: Cell monolayers were disrupted with RLT+ lysis solution and total cellular RNA isolated with RNeasy kits, treated with DNaseI, followed by a second RNA isolation.  PolyA RNA was enriched from total RNA using PolyATract mRNA isolation kit.

tag: BoMac cell line


title: Bovine Macrophage Cells Tpl Treated

treatment_protocol: Cells were treated with 1 ug/ml of sonicated Treponema phagedenis-like bacterium strain 1A isolated from a papillomatous digital dermatitis lesion. Treatment was for 4 hr at 37C under normal growth conditions before RNA was extracted.


title: Leaf_LYP9_milky-stage

status: Public on Jun 08 2007

first: shuhui

last: song

address: Airport Industrial Zone B-10

department: Genomics & Bioinformatics

institute: Beijing Institute of Genomics, Chinese Academy of Sciences, China

description: Poly(A+) RNA isolation, cDNA synthesis, and SAGE library construction were performed according to a published protocal(Lee et al., 2001). mRNA were purified with the Oligotex mRNA Mini kit (Qiagen USA, Valencia, CA) and double-stranded cDNA were synthesiezed from the fractioned poly(A)-containing mRNA with 5'-biotinylated 3'-anchored oligo(dT) primers (5'-biotin-ATCTAGAGCGGCCGCdT16[A/G/CA/CG/CC]-3'). cDNAs were digested with NlaIII adn collected with Streptavidincoated magenetbeads (Roche Diagnostic, Mannheim, Germany). After ligation with two SAGE linkers, cDNAs were PCR-amplified with primers, digested and purified. Tag-containing cDNA fragment were blunt-ended, ligated, amplified, and redigested with NalIII. Digensted tags were concatemerized at their NalIII overhangs, DNA fragments between 500 and 1000bp in size were extracted and cloned into the SphI site of the pZero-1 vector (Invitrogen, Carlsbad, CA). Sequecing were carried out with the DYEnamic ET terminator Cycle sequencing kit and Magabase 1000 sequencer. Sequence data were anaylsed with SAGE2000.

organism: Oryza sativa

source_name: first leaves at the milky stage of the grain ripening phase

extract_protocol: Total RNAs were prepared according to a LiCl-precipitation protocol (Lobreaux et al., 1992)

value: LYP9 Tissue:leaves Development stage:at the milky stage of the grain ripening phase


title: Root_LYP9_firt-tillering-stage

data_processing: Sequence data were anaylsed with SAGE2000

source_name: roots at the first tillering stage

tag: Strain:LYP9 Tissue:roots Development stage:first tillering stage


title: Panicle_LYP9_Pollen-maturing-stage

source_name: panicles of the top one-third portion at pollen-maturing stage

value: LYP9 Tissue:panicles Development stage:pollen-maturing stage


title: Human Kidney Glomeruli

status: Public on Jun 13 2007

city: Edmonton

first: Barbara

middle: Jutta

last: Ballermann

state: Alberta

address: HMRC 261

department: Medicine

institute: University of Alberta

description: The SAGE library was custom-prepared from mRNA by GENZYME.

data_processing: Data represent raw SAGE tag counts and have not been further processed.

source_name: Glomeruli, Isolated from Kidney Cortex, Sieving Technique

growth_protocol: Not Applicable

extract_protocol: Glomeruli were isolated by differential sieving using ice-cold phosphate buffered saline. Pure glomeruli were placed directly into "RNA-protect" (QIAGEN) and total RNA was isolated with RNeasy (QIAGEN). 4.2 µg total RNA was used for mRNA isolation using oligo-dT affinity support.

treatment_protocol: Kidney was removed surgically. Patient was under general anesthesia at the time of kidney removal.

tag: Gender

value: Male, Age:72, Glomeruli isolated from the unaffected pole of a kidney with renal cell carcinoma. Histological examination (H&E) of the portion of kidney used for sample isolation showed normal glomeruli. Purity of glomeruli was > 95%.


title: Root_PA64s_firt-tillering-stage

tag: Development stage:first tillering stage


title: Root_9311_firt-tillering-stage

growth_protocol: rice seeds were sown in green houses until reaching the seeding stage. The seedlings were transferred subsequently to an outdoor rice paddy and cultivated under typical conditions.


title: Panicle_PA64s_Pollen-maturing-stage

tag: Development stage

value: pollen-maturing stage


title: Leaf_Pa64s_milky-stage

value: PA64s Tissue:leaves Development stage:at the milky stage of the grain ripening phase


title: SAGE_lymphocytes_Down_syndrome_children

status: Public on Apr 25 2007

city: Sao Carlos

first: César

middle: Adolfo

last: Sommer

state: Sao Paulo

address: Rodovia Washington Luis (SP-310), km 235

department: Genetics and Evolution

institute: Universidade Federal de Sao Carlos

description: Lymphocytes were prepared from peripheral blood using Ficoll density centrifugation. Equal quantities of RNA were pooled and used to construct the SAGE library.

source_name: Lymphocytes from Down syndrome children (pooled samples)

extract_protocol: Total RNA was isolated from lymphocytes with TRIzol Reagent  (Invitrogen), according to the manufacturer’s instructions

tag: Lymphocytes from karyotypically confirmed full trisomy 21 children, 1 - 4 years old


title: Panicle_9311_Pollen-maturing-stage


title: SAGE_lymphocytes_normal_children

source_name: Lymphocytes from normal children (pooled samples)

extract_protocol: Total RNA was isolated from lymphocytes with TRIzol Reagent (Invitrogen), according to the manufacturer’s instructions

tag: Lymphocytes from normal children 1-4 years old


title: SAGE_uterus_intact female mice

status: Public on Apr 03 2007

city: Québec

first: Kouamé Ettienne

last: Kouadjo

state: Québec

address: 2705 Bld Laurier

institute: Laval University

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

source_name: uterus

tag: C57BL/6, female, 12-15 wk


title: SAGE_adipose_tissue intact male mice

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

source_name: adipose tissue


title: SAGE_pituitary_ gland intact male mice

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

source_name: pituitary gland


title: SAGE_skin_intact male mice

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

source_name: skin


title: SAGE_mammary gland_intact female mice

description: mammary gland were dissected from C57BL6 intact female mice and pooled together. Total RNA was isolated by Trizol.

source_name: mammary gland


title: SAGE_cerebral_cortex intact male mice

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

source_name: cerebral cortex


title: SAGE of 9-DPA ovule

status: Public on Feb 18 2007

city: Shanghai

first: Xiao-Ya

last: Chen

address: No. 300, Fenglin Road

department: Institute of Plant Physiology and Ecology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: 30 μg total RNA was used to construct the SAGE library by the I-SAGE kit (Invitrogen, Carlsbad, CA) according to the manual.

data_processing: The software SAGE2000 ver4.5 (courtesy of Ken Kinzler and Victor Velculescu, Johns Hopkins University School of Medicine) was applied to analyze the sequence data.

organism: Gossypium hirsutum

source_name: 9-DPA ovule (fiber-detached) of Gossypium hirsutum L. cv. Xu-142

growth_protocol: Plants of Upland Cotton, Gossypium hirsutum L. cv. Xu-142 were grown in field. Bolls were tagged and the flowering day was taken as 0 day post-anthesis (DPA). Ovules at 9 DPA were collected in the morning, and the material was frozen in liquid nitrogen and stored at -70 C before use.

extract_protocol: Total RNA for SAGE library construction was isolated from fiber-detached ovules by a cold-phenol method as previously described (Li et al., 2002).

treatment_protocol: No treatment.

tag: 9-DPA ovule


title: SAGE_lung_intact male mice

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

source_name: lung


title: Leaf_9311_milky-stage

tag: Strain

tag: Development stage:milky stage


title: SAGE of 9-DPA cotton fiber

description: 30 μg total RNA from 9 DPA Gossypium. hirsutum Xu-142 c.v. fiber was used to construct the SAGE library by the I-SAGE kit (Invitrogen, Carlsbad, CA) according to the manual.

source_name: Cotton fiber at 9 DPA

extract_protocol: Total RNA for SAGE library construction was isolated from the 9 DPA fibers by a cold-phenol method as previously described (Li et al. 2002).

tag: 9-DPA cotton fiber


title: SAGE_ovairy_intact female mice

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

source_name: ovary


title: SAGE_liver_intact male mice

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

source_name: liver


title: SAGE_vagina_intact female mice

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

source_name: vagina


title: SAGE of 9-DPA fl mutant ovule

source_name: fuzzless-lintless mutant ovule at 9 DPA

extract_protocol: Total RNA for SAGE library construction was isolated  by a cold-phenol method as previously described (Li et al., 2002).

tag: 9-DPA fl mutant ovule


title: SAGE_bone_intact male mice

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

source_name: bone


title: mLSAGE_Embryo_normal_Theiler Stage 11_MMD_SM204

status: Public on Feb 08 2007

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

source_name: Embryo, normal

tag: Mouse strain

value: Unknown

tag: Age

tag: Mutation

value: Foxh1 -/-


title: Megakaryocyte

status: Public on Feb 03 2007

city: Birmingham

middle: Graham

last: Tomlinson

state: West Midlands

address: Wolfson Drive

department: Division of Medical Sciences

institute: University of Birmingham

description: The SAGE library was generated using the I-SAGE Long Kit (Invitrogen) and sequenced by Agencourt Bioscience Corporation.

data_processing: SAGE tags were identified using SAGE2000 4.5 Analysis Software (Invitrogen) with reference to the SAGEmap_tag_ug-rel database (http://www.ncbi.nlm.nih.gov/SAGE/).

source_name: Megakaryocyte

growth_protocol: The cell depleted population was cultured in serum-free medium supplemented with 2 mM L-glutamine, penicillin/streptomycin and 20 ng/ml murine SCF at 37°C and 5% CO2 for 2 days and 5 more days under the same conditions, in addition to 200 ng/ml recombinant human thrombopoietin.  High density mature megakaryocytes were then isolated in a 0-3% BSA gradient (4 ml 3% BSA/PBS in a 15 ml tube overlaid with 4 ml of 1.5% BSA/PBS and 4 ml of suspension cells in PBS).  After standing for 40 min at room temperature, the cells remaining in the lower 2 ml were collected, washed in PBS and subjected to another 0-3% BSA gradient to obtain a pure population.  DNA content of cells was determined by staining with 50 µg/ml propidium iodide and analyzing cells by flow cytometry.

extract_protocol: RNA was extracted using the RNeasy Miniprep Kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: Mouse bone marrow cells were flushed from femurs and tibias.  Mature erythrocytes were lysed with ammonium chloride potassium buffer (0.15 M NH4Cl, 1 mM KHCO3, 0.1 mM Na2EDTA pH 7.3).  CD16/CD32+Gr1+B220+CD11b+ cells were depleted using immunomagnetic sheep anti-rat IgG beads and rat-anti mouse antibodies.

value: 12 to 16 weeks.

tag: Tissue

value: Megakaryocytes differentiated in vitro from bone marrow progenitors.


title: Alzheimer_Affected_APOE34

status: Public on Jan 13 2007

city: Durham

first: Puting

last: Xu

state: NC

address: 595 LaSalle St

institute: Duke

source_name: Hippocampus; APOE3/4

extract_protocol: As per Trizol Manufacturer Protocol

value: Female

tag: B&B Stage

value: IV

tag: PMD


title: mLSAGE_Embryo_normal_Theiler Stage 9_MMD_SM211

description:
Developmental stage: Theiler Stage 9
This library is of the Mouse Atlas of Gene Expression Project: http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

tag: Gender

tag: Preparation

value: Manual microscope dissected


title: mLSAGE_Embryo_normal_Theiler Stage 11_MMD_SM205

value: Foxa2 -/-


title: Alzheimer_Affected_APOE44

source_name: Hippocampus; APOE4/4

value: Male


title: SAGE_prostate_intact male mice

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

source_name: prostate


title: SAGE_testis_intact male mice

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

source_name: testis


title: mLSAGE_Embryo_normal_Theiler Stage 9_MMD_SM173

description:
Developmental stage: Theiler stage 9
This library is of the Mouse Atlas of Gene Expression Project: http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/


title: mLSAGE_Brain_normal_12 weeks post birth_LCM_SM201

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

source_name: Brain, normal

value: Laser microscope dissected


title: mLSAGE_Pancreas_normal_Theiler Stage 21_MMD_SM225

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

source_name: Pancreas, normal

value: NGN3 GFP+


title: Alzheimer_Affected_APOE33_LongSage

source_name: Hippocampus; APOE3/3


title: mLSAGE_Lung_normal_109 days post birth_MMD_SM212

description:
Developmental stage: 109 days post birth
This library is of the Mouse Atlas of Gene Expression Project: http://www.mouseatlas.org
Also available at CGAP: http://cgap.nci.nih.gov/

source_name: Lung, normal


title: NB4 cell line untreated

status: Public on Dec 22 2006

city: Montpellier

first: Commes

last: Therese

address: 141 rue de la cardionille

department: Groupe d'Etude des Transcriptomes

institute: Institut de Génétique Humaine

description: DSMZ cell line no ACC 207

data_processing: Automatic tag detection and counting was performed with software dedicated to SAGE data mining (Skuld-Tech, France).

source_name: NB4 cell line (Acute Promyelocytic Leukemia model)

growth_protocol: The NB4 promyelocytic cell line (DSMZ) was cultured in RPMI 1640 (Invitrogen), containing 10% decomplemented FBS (Dutscher).

extract_protocol: Libraries were constructed using the SAGE procedure with the Sau3AI anchoring enzyme (GATC). polyA mRNA were extracted from untreated NB4 cells.

treatment_protocol: untreated cells

tag: NB4 is a cell line model of acute promyelocytic leukemia (APL).

tag: DSMZ cell line no ACC 207

tag: The t(15;17) translocation and consequent expression of the PML (Promyelocytic Leukemia Protein)/RARalpha (Retinoic Acid Receptor Alpha) fusion protein blocks differentiation at the promyelocytic stage.


title: Alzheimer_Affected_APOE33


title: SAGE_skeletal_muscle intact male mice

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

source_name: skeletal muscle


title: STAGE tag library for STAT1

status: Public on Nov 23 2006

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description:
ChIP procedure
STAT1 ChIP was performed in HeLa S3 cells that were induced with 5 ng/ml human recombinant IFN-γ for 30 min and then fixed with 1% formaldehyde at room temperature for 10 min. Fixation was quenched with 125 mM glycine and cells were lysed in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, 0.1 mM sodium orthovanadate, and protease inhibitors). Cell lysates were homogenized and nuclear pellets were collected and lysed in RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, 0.1 mM sodium orthovanadate, and protease inhibitors). Clarified lysates were incubated overnight at 4°C with anti-STAT1 alpha p91 (C-24) rabbit polyclonal antibody . Protein-DNA complexes were precipitated by protein A agarose and immunoprecipitates were washed three times in 1x RIPA, once in PBS, and then eluted. Crosslinks were reversed overnight at 65°C, and ChIP DNA was purified by Proteinase K treatment followed by extraction with phenol:chloroform:isoamyl alcohol extraction and precipitation with ethanol. A 5'-biotinylated primer was used for random amplification of immunoprecipitated DNA fragments. The biotinylated amplified ChIP material was used as input for STAGE.

source_name: Cutured HeLa S3 cervical cancer cells

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

treatment_protocol: Cultured HeLa S3 cells were stimulated by 5ng/ml human recombinant interferon-gamma for 30 minutes and then cross-linked with 1% formaldehyde.

tag: Cell line

value: HeLa S3

tag: Type

value: Human cervical cancer


title: Alzheimer_Control_APOE33

value: I


title: NB4 cell line induced to differentiate by a 48h exposure to 1µM ATRA

description: DSMZ cell line No ACC 207

source_name: NB4 cell line (Acute Promyelocytic Leukemia model) expposed to 1µM ATRA for 48hours

growth_protocol:
The NB4 promyelocytic cell line (DSMZ) was cultured in RPMI 1640 (Invitrogen), containing 10% decomplemented FBS (Dutscher).
The chemical agents used for the differentiation were all-trans Retinoic Acid (ATRA; Sigma-Aldrich)
NB4 cells were induced to differentiate by a 48h exposure to 1µM ATRA

extract_protocol: Libraries were constructed using the Sau3AI anchoring enzyme (GATC) on polyA mRNA.

tag: The PML portion of the PML/RARalpha fusion protein has a high affinity for the corepression complex, preventing RARalpha transcriptional activity. To induce complete remission in a high proportion of patients, a pharmacological dose of ATRA is required to destabilize this interaction and re-establish the differentiation program.


title: P300 Ethanol treated mouse cerebellum

status: Public on Nov 22 2006

city: Columbus

first: Magdalena

last: Popesco

state: OH

institute: The Ohio State Universiy

description: The ethanol-treated C57BL/6 male mouse was sacrificed and the cerebellum was quickly removed. Total RNA was isolated using Trizol. For the creation of the library, 40micrograms of total RNA was used. cDNA was synthesized on oligo dt beads

source_name: P300 C57BL6/J male mouse cerebellum

tag: P300 C57BL6/J male mouse was exposed to ethanol vapor (95% w/v) for 3 hours each day for a total of 5 days. The blood alcohol level in the ethanol treated animal was 3.0mg/ml


title: Alzheimer_Control_APOE33_LongSage


title: P720 Ethanol treated mouse cerebellum

source_name: P720 C57BL6/J male mouse cerebellum

tag: P720 C57BL6/J male mouse was exposed to ethanol vapor (95% w/v) for 3 hours each day for a total of 5 days. The blood alcohol level in the ethanol treated animal was 3.0mg/ml.


title: P720 mouse cerebellum

description: The  C57BL/6 male mouse was sacrificed and the cerebellum was quickly removed. Total RNA was isolated using Trizol. For the creation of the library, 40micrograms of total RNA was used. cDNA was synthesized on oligo dt beads

tag: P720 normal C57BL/6 male mouse cerebellum


title: Shoot summer 2004

status: Public on Nov 09 2006

city: Auckland

first: Sathish

last: puthigae

address: PO box 109185, Newmarket,

country: New Zealand

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

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

organism: Lolium perenne

source_name: shoot, pre- and post-grazed

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

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

tag: Bronsyn monoculture


title: Shoot autumn 2003

source_name: post- and pre-grazed

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


title: P300 mouse cerebellum

description:
C57BL/6 male mouse was sacrificed and the cerebellum was quickly removed. Total RNA was isolated using Trizol. For the creation of the library, 40micrograms of total RNA was used. cDNA was synthesized on oligo dt beads
Enzyme: NlaIII
Vector: pZERO-I

tag: P300 C57BL/6 normal male mouse cerebellum


title: Human NK Cells

status: Public on Sep 16 2006

city: Tokyo

first: Shinichi

last: Hashimoto

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

department: Graduate School of Medicine

institute: The University of Tokyo

description: PBMC were incubated with anti-CD56 mAb coated with microbeads and NK were isolated by passing the PBMC through a magnetic cell separation system with column type VR. More than 99% of the cells were positive for CD56 and CD16 in a flow cytometric analysis

source_name: CD56+ NK cells

tag: healthy donor


title: Bombyx ovary SAGE library #2

status: Public on Nov 01 2006

first: shunsuke

last: funaguma

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

description: This library was constucted from Bombyx ovary (stage2-3).

organism: Bombyx mori

source_name: ovary (stage2-3)


title: NLP-1

status: Public on Nov 21 2006

first: Kim

middle: Marie

last: Lonergan

state: British Columbia

institute: British Columbia Cancer Research Centre

description: lung parenchyma pooled from 4 individuals

source_name: lung parenchyma


title: Shoot spring 2003


title: Human CD8 T cells

description: PBMC were incubated with anti-CD8 mAb coated with microbeads and CD8 T cells were isolated by passing the PBMC through a magnetic cell separation system with column type VR.

source_name: Human CD8+ T cells


title: NLP-2

tag: lung parenchyma pooled from 4 individuals


title: Human B cells

description: PBMC were incubated with anti-CD19 mAb coated with microbeads and B cells were isolated by passing the PBMC through a magnetic cell separation system with column type VR.

source_name: Human CD19+ B cells


title: Human activated Th2 Cells

description:
Human neonatal leukocytes were isolated from freshly collected, heparinized, neonatal cord blood by a density gradient centrifugation using Lymphoprep. Th2-polarized cells were generated by stimulating cord blood leukocytes with 200 U/ml IL-4 and 2 ug/ml neutralizing anti-IL-12 antibody for Th2 cultures. Cells were washed on day 3 and expanded in each medium containing 4 ng/ml IL-2. At day 12 to 14, leukocytes were incubated with anti-CD4 monoclonal antibody coated magnetic beads, and CD4+ cells were isolated by passing the cultured cells through a magnetic cell separation system.
Cord blood-derived Th2 cells were collected after 3 days of CD4 positive cell separation, washed, and restumulated with 50 ng/ml of PMA and 1 ug/ml of ionomycin for 4 h.

source_name: Cord blood-derived Th2 cells


title: SAGE_hypothalamus_adrenalectomized male mice 1h after glucocorticoid injection

status: Public on Sep 22 2006

city: Hershey

first: Yuichiro

last: Nishida

address: 500 University Drive

department: Department of Anatomy and Physiology

institute: Penn State College of Medicine

description: Hypothalamus were dissected from C57BL6 male mice 1h after glucocorticoid injectionand pooled together. Total RNA was isolated by Trizol.

organism: Mus musculus

source_name: hypothalamus


title: SAGE_hypothalamus_adrenalectomized male mice 24h after glucocorticoid injection

description: Hypothalamus were dissected from C57BL6 male mice 24h after glucocorticoid injection and pooled together. Total RNA was isolated by Trizol.