title: fetal_liver_hematopoietic_stem_cells

description: Murine fetal liver was harvested and stained as described in Bowie et al. PNAS 2007 and the cells Lin-/Mac1+/CD43+/Sca1+ were sorted on a FACSVantage.  Individual single cell transplantation experiments into sublethally irradiated recipients confirm that the HSC purity is at ~1 in 10.

source_name: fetal liver, FACS sorted Lin-/Mac1+/CD43+/Sca1+

extract_protocol:
Starting RNA: ~10ng (24 cycles of PCR used)
Isolation method: Arcturus PicoPure [total RNA was extracted using the PicoPure kit (Arcturus), a column based method that isolates polyA RNA (http://www.moleculardevices.com/pages/reagents/picopure.html)]
Storage Medium: H2O
DNaseI treatment: Yes
Method of RNA (cDNA) quant: Agilent
SAGE type: PCR-LongSAGE

tag: Strain

value: Fetal Liver


title: Arabidopsis_control

status: Public on Oct 01 2008

type: SAGE

anchor: NlaIII

city: Saskatoon

first: Stephen

middle: James

last: Robinson

state: Saskatchewan

address: 107 Science Place

department: Molecular Genetics

country: Canada

institute: Agriculture and agri-Food Canada

description:
Characterization of the gene expression changes occurring throughout the cold acclimation adaptation.
Control library.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana: control

extract_protocol: Total RNA was extracted from 10 g of Arabidopsis plant tissue using the Total RNA extraction kit and mRNA was purified from total RNA using an mRNA purification kit according to the manufacturer’s protocols (Amersham Biosciences, Baie d’Urfe, Canada).

tag: Aerial tissues collected from 14-day old plants. Grown under axenic conditions at 22 degrees Celsius and 125 uE light with a 16 hour photo-period on 0.5 x MS media.

tag: No exposure at 4 degrees Celsius


title: Arabidopsis_1week_low_temp

description:
Characterization of the gene expression changes occurring throughout the cold acclimation adaptation.
7 days of low temperature treatment library.

source_name: Arabidopsis thaliana: 1 week, low temp

tag: Arabidopsis thaliana (Col-4)

tag: Exposed to 1 week at 4 degrees Celsius


title: Arbidopsis_30_minutes_low_temp

description:
Characterization of the gene expression changes occurring throughout the cold acclimation adaptation.
30 minutes of low temperature library.

source_name: Arabidopsis thaliana: 30 minutes, low temp

tag: Exposed to 4 degrees Celsius for 30 minutes.


title: Arabidopsis_2_hours_low_temp

description:
Characterization of the gene expression changes occurring throughout the cold acclimation adaptation.
120 minutes of low temperature treatment library.

source_name: Arabidopsis thaliana: 2 hours, low temp

tag: Exposed to 2 hours at 4 degrees Celsius.


title: VUB02.2passage252

status: Public on Nov 04 2008

type: genomic

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 101

department: Embryology and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Array-CGH was performed as described by Vermeesch, J.R. et al. J. Histochem. Cytochem. 53, 413–422 (2005). 1500 ng of each labelled DNA were cohybridized. Hybridization time was between 24 and 72 hours

scan_protocol: Slides were scanned either using an Axon GenePix 4000B scanner (raw data files in gpr format) or a Agilent dual laser DNA microarray scanner G2566AA (Raw data files in txt format).

data_processing: All data is lowess normalized. The scan images were processed and data was normalized with using GenePix Pro software or the Agilent Feature Extraction Software v9.5.The final steps of data analysis were performed using Excel (Microsoft). The data obtained from the Agilent software was converted from log10 to log2.

molecule: genomic DNA

organism: Homo sapiens

source_name: VUB02.2 passage 252

label_protocol: Samples were labelled using the BioPrime Array CGH Genomic Labelling System; (Invitrogen, Carlsbad, CA) and Cy5- and Cy3-labelled dCTPs (GE Healthcare, Buckinghamshire, UK ), following the protocol as described by the manufacturer

growth_protocol: Human embryonic stem cells derived and cultured as described by Mateizel, I. et al. Hum. Reprod. 21, 503-511 (2006).

extract_protocol: Standard phenol-clorophorm DNA extraction followed by an ethanol precipitation and resuspended in distilled water

tag: Human embryonic stem cells

source_name: Female reference DNA

tag: 46, XX reference DNA


title: Triticum aestivum cv Scorpion 25 Normal rep 1

status: Public on Sep 20 2008

city: Bristol

first: Gary

last: Barker

address: Woodland Road

department: Biological Sciences

country: United Kingdom

institute: University of Bristol

description:
Libraries were produced for wheat varieties Xi19 and Scorpion 25 each grown under both normal and hot/dry conditions. Full details in:
Rebecca L Poole, Gary LA Barker, Kay Werner, Gaia F Biggi, Jane Coghill, J
George Gibbings, Simon Berry, Jim M Dunwell and Keith J Edwards. Analysis of wheat SAGE tags reveals evidence for widespread antisense
transcription BMC Genomics Accepted.

data_processing: Tags were extracted using invitrogen software, no further manipulations were performed.

molecule: polyA RNA

organism: Triticum aestivum

source_name: Bread Wheat Triticum aestivum, normal and hot/dry growth conditions

growth_protocol: The plants were grown under normal conditions

extract_protocol: As described by Wilson et al. 2004 Plant Biotechnology Journal Volume 2 Issue 6, Pages 495 - 506

tag: Plants of cultivar Scorpion 25 were grown under normal conditions for comparison to Scorpion 25 plants and Xi19 plants grown under normal and hot/dry conditions


title: Arabidopsis_2_days_low_temp

description:
Characterization of the gene expression changes occurring throughout the cold acclimation adaptation.
2 days of low temperature treatment library.

source_name: Arabidopsis thaliana: 2 days, low temp

tag: Exposed to 2 days at 4 degrees Celsius


title: Triticum aestivum cv Xi19 Normal rep 1

source_name: Triticum aestivum cv Xi19 rep 1 normal growth conditions

tag: Triticum aestivum cv Xi19 grown under normal conditions


title: Triticum aestivum cv Xi19 Hot Dry

source_name: Triticum aestivum cv Xi19 hot/dry growth conditions

growth_protocol: The plants were grown under hot/dry conditions

tag: Triticum aestivum cv Xi19 grown under hot/dry conditions


title: CTC_Head&Neck_carcinoma_MD_SJR3T

status: Public on Sep 30 2008

city: Ribeirão Preto

first: Daniel

middle: Guariz

last: Pinheiro

state: São Paulo

address: Rua Tenente Catão Roxo, 2501

department: Departamento de Genética

country: Brazil

institute: Faculdade de Medicina de Ribeirão Preto (Universidade de São Paulo)

description: Larynx cancer sample with no lymph node metastasis

extract_protocol: Total RNA was extracted using TRIzol Reagent and treated with DNase (Invitrogen Corporation, Carlsbad, CA, USA)

tag: Sample from Laryngeal Squamous Cell Carcinoma (LSCC)

value: T3N0M0, male, 69 years old


title: CTC_Head&Neck_carcinoma_MD_SJR2T_AG

description: Larynx cancer sample with lymph node metastasis

tag: Aggressive Laryngeal Squamous Cell Carcinoma (LSCC)

value: T4N2bM0, male, 73 years old


title: Human CD15+ myeloid progenitor cells

status: Public on Oct 03 2008

city: Evanston

first: San Ming

last: Wang

state: IL

address: 1001 University Place

department: Center for Functional Genomics

country: USA

institute: ENH Research Institute, Northwestern University

description:
Lee S, Zhou G, Clark T, Chen J, Rowley JD, Wang SM. The pattern of gene expression in human CD15+ myeloid progenitor cells. Proc Natl Acad Sci U S A. 98(6):3340-5, 2001;
Lee S, Chen J, Zhou G, Shi RZ, Bouffard GG, Kocherginsky M, Ge X, Sun M, Jayathilaka N, Kim YC, Emmanuel N, Bohlander SK, Minden M, Kline J, Ozer O, Larson RA, LeBeau MM, Green ED, Trent J, Karrison T, Liu PP, Wang SM, Rowley JD. Gene expression profiles in acute myeloid leukemia with common translocations using SAGE. Proc Natl Acad Sci U S A. 103(4):1030-5, 2006;
We performed a genome-wide analysis of gene expression in primary human CD151 myeloid progenitor cells. By using the serial analysis of gene expression (SAGE) technique, we obtained quantitativetinformation for the expression of 37,519 unique SAGE-tag sequences. Of these unique tags, (i) 25% were detected at high and intermediate levels, whereas 75% were present as single copies, (ii) 53% of the tags matched known expressed sequences, 34% of which were matched to more than one known expressed sequence, and (iii) 47% of the tags had no matches and represent potentially novel genes. The correct genes were confirmed by application of the generation of longer cDNA fragments from SAGE tags for gene identification (GLGI) technique for high-copy tags with multiple matches. A set of genes known to be important in myeloid differentiation were expressed at various levels and used different spliced forms. This study provides a normal baseline for comparison of gene expression in myeloid diseases. The strategy of using SAGE and GLGI techniques in this study has broad applications to the genome-wide identification of expressed genes.

source_name: Primary human CD15+ myeloid progenitor cells

extract_protocol: Human bone-marrow mononuclear cells were isolated from bone marrow with FicollyPaque solution and stored in liquid nitrogen. Cells from three donors were thawed at 37°C, pooled, and used immediately for the isolation of myeloid progenitor cells with CD15 magnetic beads (Dynal, Oslo, Norway). The cells isolated by CD15 magnetic beads were lysed directly with TRIzol reagent for isolation of total RNA. mRNA was purified from 5 mg of total RNA with oligo(dT)25 beads. cDNA was synthesized with a cDNA synthesis kit, and SAGE was performed according to the SAGE protocol with the exceptions described in the original paper. SAGE-tag sequences were collected with the Big-Dye sequencing kit and ABI377 sequencer, and tag sequences were extracted with SAGE 300 software.

tag: Human bone-marrow mononuclear cells were obtained from the Poietics Company (Gaithersburg, MD).


title: Triticum aestivum cv Xi19 Normal rep 2

source_name: Triticum aestivum cv Xi19 rep 2 normal growth conditions


title: CTC_Head&Neck_normal_MD_SJRPool

description: Normal control library pooled from two matched normal samples

source_name: Margins of laryngeal squamous cell carcinoma (LSCC)

extract_protocol: Total RNA was extracted with TRIZOL Reagent (Invitrogen Corporation, Carlsbad, CA, USA) and treated with DNase

tag: Pooled sample of tumor-free surgical margins of laryngeal squamous cell carcinoma (LSCC)

value: LSCC T4N1M0, male, 52 years old and LSCC T4N0M0, male, 51 years old


source_name: Triticum aestivum cv Scorpion 25 Hot/Dry growth conditions

tag: Triticum aestivum cv Scorpion 25 grown under hot/dry conditions


title: Triticum aestivum cv Scorpion 25 Normal rep 2

source_name: Triticum aestivum cv Scorpion 25 rep 2 normal growth conditions

tag: Triticum aestivum cv Scorpion 25 grown under normal conditions


title: 2002 - mAdbID:79584

status: Public on Sep 04 2008

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 79584

hyb_protocol: NimbleGen Hybridization Protocol Other: Proprietary protocol information available at http://www.nimblegen.com/technology/index.html

scan_protocol: NimbleGen Scanning Protocol Other: Scanning was performed using a GenePix4000B scanner (Axon instruments). NimbleGen proprietary protocol information available at http://www.nimblegen.com/technology/index.html.

data_processing:
NimbleGen Data Processing
Calculation Method: Scaled log2-ratio data GFF file (ratio of control vs. sample for individual probes).

source_name: Normal Lymphocytes

label_protocol:
NimbleGen Cy5 Sample Labeling Protocol
Other: Proprietary protocol information available at http://www.nimblegen.com/technology/index.html

extract_protocol:
Sample DNA Extraction Protocol
Other: The DNA was isolated by Qiagen DNeasy Tissue kit according to the manufacturer's recommendations.

tag: Tissue

value: lymphocytes

label_protocol:
NimbleGen Cy3 Sample Labeling Protocol
Other: Proprietary protocol information available at http://www.nimblegen.com/technology/index.html

tag: Gender

value: female

tag: Age

value: lymph node

tag: Disease state

value: Lymphoma

tag: Individual

tag: Clinical info

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:PMBL

value: Follow up status:ALIVE

value: Follow up years:6.62

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 1005 - mAdbID:79582

description: mAdb experiment ID: 79582

value: male

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:5.77

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:0.61

value: Number of extranodal sites:0


title: VUB03_DM1.2passage102

source_name: VUB03_DM1.2 passage 102

tag: Human embryonic stem cells

tag: 46, XX reference DNA


title: 712 - mAdbID:79583

description: mAdb experiment ID: 79583

value: lymphocytes

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:3.26

value: ECOG performance status:2


title: 1027 - mAdbID:79526

description: mAdb experiment ID: 79526

value: female

value: lymph node

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.25


title: 484 - mAdbID:79528

description: mAdb experiment ID: 79528

value: male

value: Final microarray diagnosis:PMBL

value: Follow up years:1.39

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 1059 - mAdbID:79527

description: mAdb experiment ID: 79527

value: Follow up years:2

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.92

value: Number of extranodal sites:1


title: 2018 - mAdbID:79533

description: mAdb experiment ID: 79533

value: lymphocytes

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:0.16


title: 1008 - mAdbID:79581

description: mAdb experiment ID: 79581

value: lymph node

value: Lymphoma

value: Follow up status:ALIVE

value: Follow up years:6.46

value: ECOG performance status:1

value: LDH ratio:0.48

value: Number of extranodal sites:0


title: 1994 - mAdbID:79531

description: mAdb experiment ID: 79531

value: female

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.20

value: ECOG performance status:NA

value: LDH ratio:NA


title: 1026 - mAdbID:79355

description: mAdb experiment ID: 79355

value: lymphocytes

value: male

value: Follow up years:6.94

value: Chemotherapy:CHOP-Like Regimen


title: 808 - mAdbID:79314

description: mAdb experiment ID: 79314

value: lymph node

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:DEAD

value: Follow up years:0.37

value: ECOG performance status:2

value: LDH ratio:0.05


title: 1039 - mAdbID:79524

description: mAdb experiment ID: 79524

value: Lymphoma

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:2.05

value: Number of extranodal sites:0


title: 1049 - mAdbID:79523

description: mAdb experiment ID: 79523

value: female

value: Submitting diagnosis:DLBCL

value: Follow up years:1.33

value: ECOG performance status:1

value: LDH ratio:1.56

value: Number of extranodal sites:1


title: 1001 - mAdbID:79316

description: mAdb experiment ID: 79316

value: lymphocytes

value: male

value: Follow up years:0.33

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.96


title: 710 - mAdbID:79263

description: mAdb experiment ID: 79263

value: lymph node

value: Follow up status:DEAD

value: Follow up years:1.08

value: LDH ratio:2.78


title: 1041 - mAdbID:79521

description: mAdb experiment ID: 79521

value: Lymphoma

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:3.13


title: 626 - mAdbID:79261

description: mAdb experiment ID: 79261

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:2.49

value: LDH ratio:0.74

value: Number of extranodal sites:0


title: 912 - mAdbID:79315

description: mAdb experiment ID: 79315

value: lymphocytes

value: female

value: Follow up status:ALIVE

value: Follow up years:16.79

value: ECOG performance status:0


title: 674 - mAdbID:79260

description: mAdb experiment ID: 79260

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:7.22

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:0.775


title: 577 - mAdbID:79259

description: mAdb experiment ID: 79259

value: male

value: Lymphoma

value: Follow up years:1.65

value: LDH ratio:0.67


title: 724 - mAdbID:79262

description: mAdb experiment ID: 79262

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:1.4

value: LDH ratio:1.16


title: 546 - mAdbID:79254

description: mAdb experiment ID: 79254

value: lymphocytes

value: female

value: Final microarray diagnosis:PMBL

value: Follow up years:0.77

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 692 - mAdbID:78975

description: mAdb experiment ID: 78975

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:10.53

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:1.37

value: Number of extranodal sites:0


title: 803 - mAdbID:79317

description: mAdb experiment ID: 79317

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:1.45

value: ECOG performance status:2

value: Number of extranodal sites:1


title: 854 - mAdbID:78986

description: mAdb experiment ID: 78986

value: lymphocytes

value: male

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:1.51

value: LDH ratio:0.82


title: 816 - mAdbID:78987

description: mAdb experiment ID: 78987

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.86

value: ECOG performance status:3

value: LDH ratio:10.2


title: 704 - mAdbID:79256

description: mAdb experiment ID: 79256

value: female

value: Lymphoma

value: Follow up status:ALIVE

value: Follow up years:9.67

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: Number of extranodal sites:0


title: 432 - mAdbID:78974

description: mAdb experiment ID: 78974

value: lymphocytes

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:0.38

value: LDH ratio:NA


title: 615 - mAdbID:79255

description: mAdb experiment ID: 79255

value: lymph node

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:4.94

value: ECOG performance status:2

value: LDH ratio:1.24


title: 621 - mAdbID:78984

description: mAdb experiment ID: 78984

value: male

value: Final microarray diagnosis:PMBL

value: Follow up years:8.14

value: ECOG performance status:NA

value: Number of extranodal sites:NA


title: 2001 - mAdbID:78412

description: mAdb experiment ID: 78412

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.31


title: 1021 - mAdbID:78411

description: mAdb experiment ID: 78411

value: lymphocytes

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:14.59

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:2.15

value: Number of extranodal sites:0


title: 439 - mAdbID:78970

description: mAdb experiment ID: 78970

value: male

value: lymph node

value: Follow up status:NA

value: Follow up years:NA

value: LDH ratio:NA


title: 1946 - mAdbID:78414

description: mAdb experiment ID: 78414

value: Lymphoma

value: Follow up status:DEAD

value: Follow up years:0.68

value: ECOG performance status:NA

value: Number of extranodal sites:NA


title: 523 - mAdbID:78410

description: mAdb experiment ID: 78410

value: lymphocytes

value: female

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:8.36

value: ECOG performance status:0


title: 618 - mAdbID:78972

description: mAdb experiment ID: 78972

value: Follow up status:ALIVE

value: Follow up years:5.65

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:0.94

value: Number of extranodal sites:0


title: 874 - mAdbID:78206

description: mAdb experiment ID: 78206

value: male

value: lymph node

value: Lymphoma

value: Follow up years:0.12

value: LDH ratio:1.1


title: 1991 - mAdbID:78312

description: mAdb experiment ID: 78312

value: lymphocytes

value: Follow up status:DEAD

value: Follow up years:1.00

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 995 - mAdbID:78207

description: mAdb experiment ID: 78207

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:6.65

value: LDH ratio:0.76


title: 2095 - mAdbID:78309

description: mAdb experiment ID: 78309

value: Follow up years:0.96


title: 1037 - mAdbID:78182

description: mAdb experiment ID: 78182

value: female

value: Follow up years:0.23

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:3

value: Number of extranodal sites:0


title: 1990 - mAdbID:78314

description: mAdb experiment ID: 78314

value: lymphocytes

value: male

value: lymph node

value: Lymphoma

value: Follow up years:0.06


title: 731 - mAdbID:78100

description: mAdb experiment ID: 78100

value: Follow up years:10.18

value: ECOG performance status:0

value: LDH ratio:0.64


title: 744 - mAdbID:78101

description: mAdb experiment ID: 78101

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:8.86


title: 1051 - mAdbID:78075

description: mAdb experiment ID: 78075

value: female

value: Follow up status:DEAD

value: Follow up years:0.12

value: ECOG performance status:2

value: LDH ratio:10.34


title: 711 - mAdbID:78099

description: mAdb experiment ID: 78099

value: lymphocytes

value: Follow up years:3.93

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:3

value: LDH ratio:0.4

value: Number of extranodal sites:0


title: 1000 - mAdbID:77578

description: mAdb experiment ID: 77578

value: male

value: lymph node

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.69

value: LDH ratio:1.68


title: 1009 - mAdbID:78202

description: mAdb experiment ID: 78202

value: female

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:9.68

value: ECOG performance status:1

value: LDH ratio:0.98

value: Number of extranodal sites:1


title: 1007 - mAdbID:77563

description: mAdb experiment ID: 77563

value: lymphocytes

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:DEAD

value: Follow up years:2.26

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:1.01


title: 831 - mAdbID:77562

description: mAdb experiment ID: 77562

value: male

value: lymph node

value: Lymphoma

value: Follow up years:11.02

value: LDH ratio:1.41

value: Number of extranodal sites:0


title: 1054 - mAdbID:77583

description: mAdb experiment ID: 77583

value: female

value: Submitting diagnosis:DLBCL

value: Follow up status:ALIVE

value: Follow up years:12.34

value: LDH ratio:0.52


title: 742 - mAdbID:78183

description: mAdb experiment ID: 78183

value: lymphocytes

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:4.09

value: ECOG performance status:1

value: LDH ratio:0.5


title: 1018 - mAdbID:77490

description: mAdb experiment ID: 77490

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:DEAD

value: Follow up years:0.03

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:5.68

value: Number of extranodal sites:1


title: 855 - mAdbID:77561

description: mAdb experiment ID: 77561

value: female

value: lymph node

value: Lymphoma

value: Follow up years:1.67

value: LDH ratio:1.2

value: Number of extranodal sites:0


title: 860 - mAdbID:77183

description: mAdb experiment ID: 77183

value: lymphocytes

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:3.03

value: ECOG performance status:0

value: LDH ratio:0.77


title: 832 - mAdbID:77486

description: mAdb experiment ID: 77486

value: male

value: Follow up status:ALIVE

value: Follow up years:4.01

value: ECOG performance status:1

value: LDH ratio:0.64


title: 847 - mAdbID:77182

description: mAdb experiment ID: 77182

value: female

value: Follow up years:4.16

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.8


title: 1004 - mAdbID:77489

description: mAdb experiment ID: 77489

value: lymph node

value: Lymphoma

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:6.72

value: LDH ratio:0.62


title: 840 - mAdbID:77559

description: mAdb experiment ID: 77559

value: lymphocytes

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:3.4

value: LDH ratio:0.6

value: Number of extranodal sites:0


title: 821 - mAdbID:77468

description: mAdb experiment ID: 77468

value: male

value: Follow up status:ALIVE

value: Follow up years:9.47

value: ECOG performance status:1

value: LDH ratio:NA


title: 836 - mAdbID:77487

description: mAdb experiment ID: 77487

value: Follow up years:4.29

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:2


title: 698 - mAdbID:77181

description: mAdb experiment ID: 77181

value: female

value: lymph node

value: Lymphoma

value: Follow up years:3.88

value: LDH ratio:0.74


title: 617 - mAdbID:77180

description: mAdb experiment ID: 77180

value: lymphocytes

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:5.88

value: ECOG performance status:0

value: LDH ratio:0.61


title: 834 - mAdbID:77004

description: mAdb experiment ID: 77004

value: male

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:DEAD

value: Follow up years:1.64

value: ECOG performance status:NA

value: LDH ratio:0.8

value: Number of extranodal sites:0


title: 1023 - mAdbID:77576

description: mAdb experiment ID: 77576

value: female

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:5.57

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1


title: 664 - mAdbID:76913

description: mAdb experiment ID: 76913

value: lymphocytes

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.62

value: ECOG performance status:2

value: LDH ratio:1.05


title: 619 - mAdbID:76957

description: mAdb experiment ID: 76957

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:8.76

value: LDH ratio:1.32

value: Number of extranodal sites:1


title: 751 - mAdbID:76912

description: mAdb experiment ID: 76912

value: male

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:9.99

value: ECOG performance status:0

value: LDH ratio:0.72

value: Number of extranodal sites:0


title: 838 - mAdbID:77000

description: mAdb experiment ID: 77000

value: lymphocytes

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:NA

value: LDH ratio:NA


title: 458 - mAdbID:76915

description: mAdb experiment ID: 76915

value: female

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:1.18

value: ECOG performance status:1


title: 856 - mAdbID:77002

description: mAdb experiment ID: 77002

value: male

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:0.6

value: ECOG performance status:2

value: LDH ratio:1.17


title: 625 - mAdbID:76914

description: mAdb experiment ID: 76914

value: lymphocytes

value: Follow up status:ALIVE

value: Follow up years:5.24

value: ECOG performance status:0

value: LDH ratio:0.88

value: Number of extranodal sites:0


title: 627 - mAdbID:76956

description: mAdb experiment ID: 76956

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:1.27

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.49


title: 572 - mAdbID:76911

description: mAdb experiment ID: 76911

value: female

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:14.24


title: 772 - mAdbID:76910

description: mAdb experiment ID: 76910

value: Follow up years:2.48

value: ECOG performance status:1

value: LDH ratio:NA


title: 688 - mAdbID:76907

description: mAdb experiment ID: 76907

value: lymphocytes

value: Follow up years:0.33

value: LDH ratio:0.78


title: 528 - mAdbID:76803

description: mAdb experiment ID: 76803

value: male

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:ALIVE

value: Follow up years:1.64

value: LDH ratio:0.85

value: Number of extranodal sites:0


title: 491 - mAdbID:76802

description: mAdb experiment ID: 76802

value: lymph node

value: Follow up status:DEAD

value: Follow up years:4.47

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:3


title: 817 - mAdbID:76801

description: mAdb experiment ID: 76801

value: female

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:2.76

value: ECOG performance status:2


title: 1060 - mAdbID:76800

description: mAdb experiment ID: 76800

value: lymphocytes

value: Follow up years:6.45

value: ECOG performance status:1

value: LDH ratio:1.92

value: Number of extranodal sites:1


title: 460 - mAdbID:76805

description: mAdb experiment ID: 76805

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:ALIVE

value: Follow up years:9.02


title: 565 - mAdbID:76909

description: mAdb experiment ID: 76909

value: male

value: lymph node

value: Follow up status:DEAD

value: Follow up years:9.11

value: ECOG performance status:0

value: LDH ratio:1.15

value: Number of extranodal sites:0


title: 747 - mAdbID:76908

description: mAdb experiment ID: 76908

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:15.41

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:NA


title: 553 - mAdbID:76741

description: mAdb experiment ID: 76741

value: lymphocytes

value: Follow up years:0.82

value: LDH ratio:1.12


title: 748 - mAdbID:76691

description: mAdb experiment ID: 76691

value: female

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:1.01

value: ECOG performance status:1

value: LDH ratio:2.38

value: Number of extranodal sites:1


title: 524 - mAdbID:76742

description: mAdb experiment ID: 76742

value: lymph node

value: Follow up status:ALIVE

value: Follow up years:5.88

value: ECOG performance status:0


title: 2092 - mAdbID:76740

description: mAdb experiment ID: 76740

value: male

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:PMBL

value: Follow up years:1.27

value: ECOG performance status:NA

value: Number of extranodal sites:NA


title: 2019 - mAdbID:76575

description: mAdb experiment ID: 76575

value: lymphocytes

value: Follow up status:DEAD

value: Follow up years:0.99

value: LDH ratio:NA


title: 684 - mAdbID:76690

description: mAdb experiment ID: 76690

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:1.92

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:1.19

value: Number of extranodal sites:0


title: 1993 - mAdbID:76689

description: mAdb experiment ID: 76689

value: female

value: lymph node

value: Follow up years:1.32


title: 549 - mAdbID:76656

description: mAdb experiment ID: 76656

value: male

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:2.68

value: ECOG performance status:1


title: 671 - mAdbID:76655

description: mAdb experiment ID: 76655

value: lymphocytes

value: Follow up status:ALIVE

value: Follow up years:3.35

value: LDH ratio:0.74


title: 1948 - mAdbID:76576

description: mAdb experiment ID: 76576

value: Final microarray diagnosis:PMBL

value: Follow up years:7.95

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 1949 - mAdbID:76577

description: mAdb experiment ID: 76577

value: lymph node

value: Follow up years:4.27


title: 1942 - mAdbID:76469

description: mAdb experiment ID: 76469

value: male

value: Follow up years:0.87


title: 682 - mAdbID:76654

description: mAdb experiment ID: 76654

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:DEAD

value: Follow up years:0.11

value: Chemotherapy:CHOP-Like Regimen

value: Number of extranodal sites:0


title: 449 - mAdbID:76594

description: mAdb experiment ID: 76594

value: lymphocytes

value: Follow up status:ALIVE

value: Follow up years:9.16

value: ECOG performance status:0

value: LDH ratio:0.72


title: 1935 - mAdbID:76470

description: mAdb experiment ID: 76470

value: female

value: Final microarray diagnosis:PMBL

value: Follow up years:12.41

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 1943 - mAdbID:76480

description: mAdb experiment ID: 76480

value: lymph node

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:8.96


title: 1921 - mAdbID:76457

description: mAdb experiment ID: 76457

value: Follow up years:4.15


title: 1920 - mAdbID:76416

description: mAdb experiment ID: 76416

value: Follow up years:1.97


title: 1941 - mAdbID:76593

description: mAdb experiment ID: 76593

value: lymphocytes

value: Follow up years:0.70


title: 1923 - mAdbID:76455

description: mAdb experiment ID: 76455

value: Follow up status:ALIVE

value: Follow up years:1.59


title: 1024 - mAdbID:76413

description: mAdb experiment ID: 76413

value: Follow up years:19.83


title: 570 - mAdbID:76415

description: mAdb experiment ID: 76415

value: female

value: Follow up years:14.39


title: 1924 - mAdbID:76456

description: mAdb experiment ID: 76456

value: Final microarray diagnosis:PMBL

value: Follow up years:6.11


title: 1053 - mAdbID:76414

description: mAdb experiment ID: 76414

value: Follow up status:DEAD

value: Follow up years:1.04

value: ECOG performance status:NA

value: LDH ratio:NA


title: 1992 - mAdbID:76379

description: mAdb experiment ID: 76379

value: male

value: lymph node

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.99

value: Number of extranodal sites:NA


title: 1006 - mAdbID:76389

description: mAdb experiment ID: 76389

value: lymphocytes

value: Follow up status:ALIVE

value: Follow up years:7.11


title: 998 - mAdbID:76293

description: mAdb experiment ID: 76293

value: Follow up years:9.10


title: 638 - mAdbID:76222

description: mAdb experiment ID: 76222

value: Follow up years:0.69


title: 824 - mAdbID:76292

description: mAdb experiment ID: 76292

value: Final microarray diagnosis:PMBL

value: Follow up years:12.23


title: 669 - mAdbID:76219

description: mAdb experiment ID: 76219

value: Final microarray diagnosis:GCB DLBCL

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:0.68

value: Number of extranodal sites:0


title: 722 - mAdbID:76251

description: mAdb experiment ID: 76251

value: female

value: lymph node

value: Follow up years:3.32

value: LDH ratio:1.78


title: 681 - mAdbID:76254

description: mAdb experiment ID: 76254

value: male

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:9.7

value: LDH ratio:1.01


title: 2020 - mAdbID:76165

description: mAdb experiment ID: 76165

value: lymphocytes

value: Follow up status:ALIVE

value: Follow up years:2.07

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 695 - mAdbID:76252

description: mAdb experiment ID: 76252

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:0.15

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:0.77


title: 661 - mAdbID:76220

description: mAdb experiment ID: 76220

value: male

value: lymph node

value: Follow up years:0.56

value: LDH ratio:0.66

value: Number of extranodal sites:0


title: 1989 - mAdbID:76378

description: mAdb experiment ID: 76378

value: lymphocytes

value: female

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:PMBL

value: Follow up status:NA

value: Follow up years:NA


title: 994 - mAdbID:76285

description: mAdb experiment ID: 76285

value: Follow up status:ALIVE

value: Follow up years:4.78

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 777 - mAdbID:76391

description: mAdb experiment ID: 76391

value: male

value: Follow up status:DEAD

value: Follow up years:4.27


title: 819 - mAdbID:76164

description: mAdb experiment ID: 76164

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:0.72

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:2.8

value: Number of extranodal sites:1


title: 691 - mAdbID:76166

description: mAdb experiment ID: 76166

value: lymphocytes

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:PMBL

value: Follow up years:0.32


title: 543 - mAdbID:76130

description: mAdb experiment ID: 76130

value: female

value: Follow up status:ALIVE

value: Follow up years:3.47

value: ECOG performance status:1

value: LDH ratio:0.48

value: Number of extranodal sites:0


title: 701 - mAdbID:76253

description: mAdb experiment ID: 76253

value: male

value: lymph node

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:3.9

value: LDH ratio:1.54


title: 479 - mAdbID:76128

description: mAdb experiment ID: 76128

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:7.24

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:0.76


title: 795 - mAdbID:76131

description: mAdb experiment ID: 76131

value: lymphocytes

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:3.43


title: 529 - mAdbID:76126

description: mAdb experiment ID: 76126

value: Follow up status:DEAD

value: Follow up years:1.06

value: ECOG performance status:1

value: LDH ratio:1.37

value: Number of extranodal sites:1


title: 545 - mAdbID:76132

description: mAdb experiment ID: 76132

value: male

value: lymph node

value: Follow up years:1.1

value: LDH ratio:0.68

value: Number of extranodal sites:0


title: 672 - mAdbID:76076

description: mAdb experiment ID: 76076

value: female

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:6.78

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.49


title: 550 - mAdbID:76073

description: mAdb experiment ID: 76073

value: lymphocytes

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:21.78

value: ECOG performance status:0

value: LDH ratio:NA


title: 424 - mAdbID:76071

description: mAdb experiment ID: 76071

value: Follow up status:DEAD

value: Follow up years:10.62

value: ECOG performance status:3

value: LDH ratio:1.54

value: Number of extranodal sites:1


title: 1038 - mAdbID:75915

description: mAdb experiment ID: 75915

value: male

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.71

value: ECOG performance status:1

value: Number of extranodal sites:0


title: 433 - mAdbID:76075

description: mAdb experiment ID: 76075

value: lymphocytes

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:0.76

value: Chemotherapy:CHOP-Like Regimen


title: 438 - mAdbID:75916

description: mAdb experiment ID: 75916

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up status:ALIVE

value: Follow up years:8.15

value: ECOG performance status:0

value: LDH ratio:1.51


title: 791 - mAdbID:75889

description: mAdb experiment ID: 75889

value: female

value: Final microarray diagnosis:PMBL

value: Follow up status:DEAD

value: Follow up years:1.32

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 415 - mAdbID:76072

description: mAdb experiment ID: 76072

value: lymphocytes

value: male

value: lymph node

value: Follow up years:5.38

value: LDH ratio:1.21

value: Number of extranodal sites:0


title: 1055 - mAdbID:75737

description: mAdb experiment ID: 75737

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:7.81

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:0.66


title: 1031 - mAdbID:75735

description: mAdb experiment ID: 75735

value: Follow up status:DEAD

value: Follow up years:6.64

value: ECOG performance status:0


title: 421 - mAdbID:76070

description: mAdb experiment ID: 76070

value: lymphocytes

value: female

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:1.24

value: LDH ratio:0.72


title: 434 - mAdbID:76067

description: mAdb experiment ID: 76067

value: lymph node

value: Follow up years:10.53

value: Number of extranodal sites:0


title: 533 - mAdbID:76129

description: mAdb experiment ID: 76129

value: male

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.71

value: LDH ratio:1.01

value: Number of extranodal sites:1


title: 1043 - mAdbID:75736

description: mAdb experiment ID: 75736

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:2.31

value: Chemotherapy:CHOP-Like Regimen


title: 517 - mAdbID:76127

description: mAdb experiment ID: 76127

value: lymphocytes

value: Follow up years:3.03

value: ECOG performance status:1

value: LDH ratio:NA


title: 459 - mAdbID:75917

description: mAdb experiment ID: 75917

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:9.65

value: ECOG performance status:2


title: 492 - mAdbID:76068

description: mAdb experiment ID: 76068

value: male

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:11.29

value: ECOG performance status:0

value: Number of extranodal sites:0


title: 858 - mAdbID:75522

description: mAdb experiment ID: 75522

value: female

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:3.58

value: LDH ratio:0.85


title: 1045 - mAdbID:75524

description: mAdb experiment ID: 75524

value: lymphocytes

value: Follow up years:2.26

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.98

value: Number of extranodal sites:1


title: 810 - mAdbID:76069

description: mAdb experiment ID: 76069

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:11.72

value: LDH ratio:0.56


title: 678 - mAdbID:75510

description: mAdb experiment ID: 75510

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.06

value: ECOG performance status:1

value: LDH ratio:NA


title: 470 - mAdbID:76074

description: mAdb experiment ID: 76074

value: male

value: Follow up years:11.17

value: ECOG performance status:0

value: LDH ratio:2.09

value: Number of extranodal sites:0


title: 756 - mAdbID:75503

description: mAdb experiment ID: 75503

value: lymphocytes

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:7.21

value: Chemotherapy:CHOP-Like Regimen


title: 771 - mAdbID:75506

description: mAdb experiment ID: 75506

value: female

value: lymph node

value: Follow up status:DEAD

value: Follow up years:6.8

value: ECOG performance status:2


title: 789 - mAdbID:75507

description: mAdb experiment ID: 75507

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up status:NA

value: Follow up years:NA

value: ECOG performance status:NA

value: Number of extranodal sites:NA


title: 809 - mAdbID:75508

description: mAdb experiment ID: 75508

value: Follow up years:0.51

value: ECOG performance status:0

value: LDH ratio:1.31


title: 428 - mAdbID:75500

description: mAdb experiment ID: 75500

value: lymphocytes

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:11.38

value: ECOG performance status:1

value: LDH ratio:5.8

value: Number of extranodal sites:0


title: 996 - mAdbID:75512

description: mAdb experiment ID: 75512

value: lymph node

value: Lymphoma

value: Follow up status:DEAD

value: Follow up years:0.21

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:6


title: 823 - mAdbID:75432

description: mAdb experiment ID: 75432

value: Submitting diagnosis:DLBCL

value: Follow up years:0.16

value: ECOG performance status:3

value: LDH ratio:NA


title: 730 - mAdbID:75509

description: mAdb experiment ID: 75509

value: lymphocytes

value: male

value: Follow up years:1.03

value: LDH ratio:1.89

value: Number of extranodal sites:NA


title: 872 - mAdbID:75436

description: mAdb experiment ID: 75436

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:5

value: ECOG performance status:1

value: LDH ratio:1.7


title: 462 - mAdbID:75434

description: mAdb experiment ID: 75434

value: female

value: lymph node

value: Lymphoma

value: Follow up status:DEAD

value: Follow up years:7.49

value: Number of extranodal sites:0


title: 646 - mAdbID:75511

description: mAdb experiment ID: 75511

value: Submitting diagnosis:DLBCL

value: Follow up years:2.59

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:1.87


title: 726 - mAdbID:75501

description: mAdb experiment ID: 75501

value: lymphocytes

value: Follow up years:7.62

value: LDH ratio:0.82


title: 616 - mAdbID:75502

description: mAdb experiment ID: 75502

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.99

value: LDH ratio:0.466


title: 725 - mAdbID:75494

description: mAdb experiment ID: 75494

value: female

value: Follow up years:0.96

value: ECOG performance status:1

value: LDH ratio:0.74


title: 1057 - mAdbID:75493

description: mAdb experiment ID: 75493

value: lymph node

value: Lymphoma

value: Follow up status:DEAD

value: Follow up years:2.13

value: LDH ratio:NA


title: 481 - mAdbID:75320

description: mAdb experiment ID: 75320

value: male

value: Submitting diagnosis:DLBCL

value: Follow up status:ALIVE

value: Follow up years:10.75

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:2

value: Number of extranodal sites:1


title: 753 - mAdbID:75291

description: mAdb experiment ID: 75291

value: lymphocytes

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.04

value: ECOG performance status:4

value: LDH ratio:1.56

value: Number of extranodal sites:0


title: 482 - mAdbID:75288

description: mAdb experiment ID: 75288

value: lymph node

value: Lymphoma

value: Follow up years:7.72

value: ECOG performance status:0


title: 714 - mAdbID:75496

description: mAdb experiment ID: 75496

value: female

value: Follow up status:DEAD

value: Follow up years:2.45

value: ECOG performance status:1

value: LDH ratio:1


title: 702 - mAdbID:75490

description: mAdb experiment ID: 75490

value: Submitting diagnosis:DLBCL

value: Follow up years:4.13

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.9


title: 446 - mAdbID:75495

description: mAdb experiment ID: 75495

value: lymphocytes

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:2.82

value: LDH ratio:0.68


title: 1061 - mAdbID:75286

description: mAdb experiment ID: 75286

value: lymph node

value: Lymphoma

value: Follow up years:1.04

value: LDH ratio:1.04

value: Number of extranodal sites:0


title: 779 - mAdbID:75290

description: mAdb experiment ID: 75290

value: Follow up status:DEAD

value: Follow up years:0.35


title: 875 - mAdbID:75497

description: mAdb experiment ID: 75497

value: Follow up status:ALIVE

value: Follow up years:8.45

value: ECOG performance status:1

value: LDH ratio:1.42


title: 544 - mAdbID:75282

description: mAdb experiment ID: 75282

value: Submitting diagnosis:DLBCL

value: Follow up years:1.31

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:0.6

value: Number of extranodal sites:1


title: 413 - mAdbID:75283

description: mAdb experiment ID: 75283

value: lymphocytes

value: male

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.6

value: LDH ratio:6.13


title: 538 - mAdbID:75280

description: mAdb experiment ID: 75280

value: female

value: Lymphoma

value: Follow up status:DEAD

value: Follow up years:0.34

value: ECOG performance status:3

value: LDH ratio:NA


title: 839 - mAdbID:75278

description: mAdb experiment ID: 75278

value: Submitting diagnosis:DLBCL

value: Follow up years:0.29

value: LDH ratio:2


title: 835 - mAdbID:75439

description: mAdb experiment ID: 75439

value: Follow up years:1.22

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:1.9


title: 541 - mAdbID:75279

description: mAdb experiment ID: 75279

value: lymphocytes

value: lymph node

value: Follow up status:ALIVE

value: Follow up years:4.11

value: ECOG performance status:1

value: LDH ratio:1.83

value: Number of extranodal sites:0


title: 841 - mAdbID:75277

description: mAdb experiment ID: 75277

value: male

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:10.14

value: LDH ratio:2.56


title: 547 - mAdbID:75274

description: mAdb experiment ID: 75274

value: female

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:0.05

value: LDH ratio:NA

value: Number of extranodal sites:1


title: 694 - mAdbID:75281

description: mAdb experiment ID: 75281

value: lymphocytes

value: lymph node

value: Follow up years:4.83

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.68


title: 700 - mAdbID:75491

description: mAdb experiment ID: 75491

value: Follow up years:5.4

value: ECOG performance status:2

value: LDH ratio:1.68

value: Number of extranodal sites:0


title: 709 - mAdbID:75276

description: mAdb experiment ID: 75276

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.47

value: ECOG performance status:1

value: LDH ratio:1.44


title: 807 - mAdbID:75261

description: mAdb experiment ID: 75261

value: female

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:0.31

value: LDH ratio:1.22


title: 477 - mAdbID:75273

description: mAdb experiment ID: 75273

value: lymphocytes

value: male

value: lymph node

value: Follow up years:1.7

value: ECOG performance status:0

value: LDH ratio:NA


title: Leishmania donovani axenic amastigotes

status: Public on Jul 30 2008

city: Shanghai

first: qiaoli

last: li

address: 800 Dongchuan Rd.

department: School of Life Sciences

country: China

institute: Shanghai Jiao Tong University

description: Amastigotes were cultured in a 95% air:5% CO2 humid atmosphere ratio in Medium 199 supplemented with 20% (V/V) FBS, pH 5.5, 37℃.

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

organism: Leishmania donovani

source_name: Leishmania donovani

growth_protocol: cultured in  in Medium 199 supplemented with 20% (V/V) FBS, pH 5.5, 37℃

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

treatment_protocol: no special

tag: Axenic amastigotes of Leishmania donovani


title: 633 - mAdbID:75262

description: mAdb experiment ID: 75262

value: Follow up status:ALIVE

value: Follow up years:2.02

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:1.11

value: Number of extranodal sites:1


title: Porcine alveolar macrophages infected with PRRSV VR-2332 (6 hours)

status: Public on Sep 01 2008

city: Ames

first: John

middle: D.

last: Neill

state: IA

address: 2300 Dayton Ave.

institute: National Animal Disease Center

description: SAGE library was prepared by pooling equimolar amounts of RNA from the cells from the 3 pigs.

organism: Sus scrofa

source_name: Porcine alveolar macrophages infected with PRRSV (6 hours)

growth_protocol: Cells from lavage from 3 pigs were resuspended in RPMI and placed in T75 flasks.  Cells were allowed to adhere for 2 hours prior to mock infection.  The flasks were placed at 4C for 1 hour then washed twice with medium.  Cells from each pig were maintained separately.

extract_protocol: Total RNA was extracted from PAMs using the Qiagen RNeasy kit.

treatment_protocol: T75 flasks (1 from each pig) were infected with PRRSV strain VR-2332 at an multiplicity of infection of 10 at 4C for 1 hour to synchronize the infection.  The flasks were washed 2X, fresh medium added and incubated at 37C for 6 hours.

tag: Porcine alveolar macrophages (PAMs) from broncho-alveolar lavage of PRRSV- and PCV-free pigs (3 pigs).  These cells were infected with PRRSV for 6 hours.


title: 717 - mAdbID:75265

description: mAdb experiment ID: 75265

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.42

value: ECOG performance status:1

value: LDH ratio:4.15

value: Number of extranodal sites:0


title: 1034 - mAdbID:75267

description: mAdb experiment ID: 75267

value: lymphocytes

value: female

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:2.31


title: Porcine alveolar macrophages infected with PRRSV VR-2332 (12 hours)

source_name: Porcine alveolar macrophages infected with PRRSV (12 hours)

treatment_protocol: T75 flasks (1 from each pig) were infected with PRRSV strain VR-2332 at an multiplicity of infection of 10 at 4C for 1 hour to synchronize the infection.  The flasks were washed 2X, fresh medium added and incubated at 37C for 12 hours.

tag: Porcine alveolar macrophages (PAMs) from broncho-alveolar lavage of PRRSV- and PCV-free pigs (3 pigs).  These cells were infected with PRRSV for 12 hours.


title: Neural crest C13 trunk cultured pass7

status: Public on Aug 07 2008

city: Marseille

first: Heather

middle: C

last: Etchevers

address: 27 boulevard Jean Moulin

department: INSERM U1251

country: France

institute: INSERM/Aix-Marseille Univ

description: For LongSAGE library construction, standard protocols as described by Velculescu et al., Saha, et al. and Basrai and Hieter were used with minor modifications. Briefly, SAGE was performed with 5 μg total RNA prepared from C13 embryo isolated hNCC cultured 7 weeks, using Qiagen total RNA extraction kit. The cDNA were prepared using the SuperscriptIII cDNA synthesis kit (Invitrogen). NlaIII and MmeI restriction enzymes (New England Biolab) were used for tag generation. After a three-hour concatemerization step, the concatemers were heated at 65°C for 10 minutes, followed by two minutes on ice to enhance cloning efficiency. Purified concatemers were subsequently cloned in the SphI site of pZero-1 (Invitrogen) and transformed into competent ElectroMax DH10B cells (Invitrogen). Individual SAGE library clones were selected and sequenced with ABI “3100” capillary sequencer using BigDye chemistry.

data_processing: LongSAGE tags (17 bps) were extracted from raw sequence data using SAGE2000 version 4.5 Analysis Software. LongSAGE tag database was then linked to SAGE Map database (NCBI) for tag to gene mapping.

source_name: migrated neural crest from trunk level of Carnegie stage 13 embryonic neural tube

growth_protocol: 8h clean neural tube in film of medium on collagen I-coated plastic. Add 1ml medium in 35mm dish to promote cell migration for 8-16 subsequent hours. Remove neural tube with fire-rounded glass filament, leaving neural crest cells. Detach with trypsin and reseed all regularly and sparsely in new 35mm dish. Medium: 12% fetal calf serum, 8.5% BGjb medium, 25.5% DMEM, 51% F12 medium, 1x penicillin/streptomycin, 2 mM glutamine, 10 mM HEPES, 0.1 ug/ml hydrocortisone, 10 µg/ml transferrin, 0.4 ng/ml T3 (3,3,5-thio-iodo-thyronine), 10 pg/ml glucagon, 100 pg/ml EGF, 1 ng/ml insulin, 200pg/ml FGF2

extract_protocol: Qiagen RNA mini columns with on-column DNase treatment. RNA integrity number >9.9 on Agilent Bioanalyzer.

treatment_protocol: Dissociate mesoderm (including notochord), ectoderm and endoderm from neural tube segment corresponding to somites 6-18 with brief incubation in PBS-diluted pancreatin. Stop reaction with serum-containing PBS and transfer to clean PBS to finish cleaning neural tube.

value: Female

tag: Karyotype

tag: Developmental stage

value: Carnegie 13 (28-32 dpf) younger end

value: Enriched neural crest cells


title: 689 - mAdbID:75196

description: mAdb experiment ID: 75196

value: lymph node

value: Follow up years:2.54

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:3

value: LDH ratio:1.01


title: 820 - mAdbID:75264

description: mAdb experiment ID: 75264

value: male

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.59

value: ECOG performance status:0

value: LDH ratio:0.91


title: 642 - mAdbID:75270

description: mAdb experiment ID: 75270

value: lymphocytes

value: female

value: Submitting diagnosis:DLBCL

value: Follow up years:0.34

value: ECOG performance status:2

value: LDH ratio:1.32

value: Number of extranodal sites:0


title: 800 - mAdbID:75263

description: mAdb experiment ID: 75263

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0.33

value: ECOG performance status:1


title: Porcine alveolar macrphages infected with PRRSV VR-2332 (16 hours)

source_name: Porcine alveolar macrphages infected with PRRSV (16 hours)

treatment_protocol: T75 flasks (1 from each pig) were infected with PRRSV strain VR-2332 at an multiplicity of infection of 10 at 4C for 1 hour to synchronize the infection.  The flasks were washed 2X, fresh medium added, and incubated at 37C for 16 hours.

tag: Porcine alveolar macrophages (PAMs) from broncho-alveolar lavage of PRRSV- and PCV-free pigs (3 pigs).  These cells were infected with PRRSV for 16 hours.


title: Super-SAGE Data from wild type leaves (Wassilewskija)

status: Public on Aug 08 2008

city: Miyazaki

first: Takehito

last: Inaba

state: Miyazaki

address: 1-1 Gakuenkibanadai-nishi

department: Interdisciplinary Research Organization

country: Japan

institute: University of Miyazaki

description: This sample was used for the comparison with ppi2-1 mutant.

source_name: Wild type (Wassilewskija) leaves

extract_protocol:
Matsumura H, Reich S, Ito A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Kruger DH, Terauchi R.
Gene expression analysis of plant host-pathogen interactions by SuperSAGE.
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15718-23.

tag: Accession

value: Wassilewskija

value: leaf

tag: Growth condition

value: Murashige-Skoog plate


title: Porcine alveolar macrophages infected with PRRSV VR-2332 (24 hours)

source_name: Porcine alveolar macrophages infected with PRRSV (24 hours)

treatment_protocol: T75 flasks (1 from each pig) were infected with PRRSV strain VR-2332 at an multiplicity of infection of 10 at 4C for 1 hour to synchronize the infection.  The flasks were washed 2X, fresh medium added, and incubated at 37C for 24 hours.

tag: Porcine alveolar macrophages (PAMs) from broncho-alveolar lavage of PRRSV- and PCV-free pigs (3 pigs).  These cells were infected with PRRSV for 24 hours.


title: Super-SAGE Data from ppi2-1 mutant leaves (Wassilewskija)

description: This sample was used for the comparison with wild type (Wassilewskija).

source_name: ppi2-1 mutant (Wassilewskija) leaves

tag: Mutant line

value: ppi2-1 (Wassilewskija, CS11072)

tag: Tissue


title: 676 - mAdbID:75194

description: mAdb experiment ID: 75194

tag: Gender

tag: Age

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:1.47


title: AML P 7

status: Public on Jul 01 2008

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

description: Array CGH analysis of a patient with AML

hyb_protocol: Hybridization was done overnight at 42C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned using an Agilent scanner .

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones wereconsidered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Dec 2005)

source_name: DNA isolated from bone marrow

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: DNA was extracted from bone marrow using a standard salting out procedure

tag: DNA isolated from bone marrow of a patient with AML M5a, Age

value: 56 Gender:female

tag: lab code

tag: diagnosis

tag: age

tag: sex

value: f

tag: tissue

value: BM

source_name: DNA isolated from blood

extract_protocol: DNA was extracted from peripheral blood by  a salting out procedure (Blin and Stafford,1976).

tag: DNA isolated from the blood of a healthy female donor


title: 645 - mAdbID:75285

description: mAdb experiment ID: 75285

value: lymphocytes

value: male

tag: Disease state

tag: Individual

tag: Clinical info

value: Submitting diagnosis:DLBCL

value: Follow up years:6.08

value: ECOG performance status:0

value: LDH ratio:1.96

value: Number of extranodal sites:0


title: 663 - mAdbID:75193

description: mAdb experiment ID: 75193

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0.62

value: ECOG performance status:1

value: LDH ratio:0.99


title: 668 - mAdbID:74260

description: mAdb experiment ID: 74260

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:6.44

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:1.68


title: 687 - mAdbID:75195

description: mAdb experiment ID: 75195

value: lymphocytes

value: female

value: Follow up years:0.94

value: LDH ratio:3.99


title: AML P4

extract_protocol: DNA was extracted from bone marrow using the Puregene DNA isolation kit (Gentra)

tag: DNA isolated from bone marrow of a patient with AML, Age

value: 60 Gender:male

value: m

value: BM

tag: DNA isolated from the blood of a healthy male donor


title: 660 - mAdbID:75192

description: mAdb experiment ID: 75192

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:0.2

value: LDH ratio:1

value: Number of extranodal sites:0


title: 644 - mAdbID:75271

description: mAdb experiment ID: 75271

value: male

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.31

value: ECOG performance status:2

value: LDH ratio:1.64


title: 30 min Excystation

status: Public on Jun 29 2008

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

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: Excystation, 30 min

growth_protocol: A confluent culture of trophozoites was used to inoculate fresh cultures and grown for 21 hr.  These were log phase trophozoites.  Encystation cultures were inoculated from the same cultures in encystation medium "GS-4" following Sun et al. (Mol. Microbiol. 2002. 46: 971-84). From the end-point cysts, excystation was carried out by a two-step method as described by Boucher and Gillin (Infect. Immun. 1990. 58: 3516-3522) and RNA isolated at four timepoints (Stage 1, Stage 2, 30 min, 60 min). Stage 1 is an acidic, reducing environment that models the stomach. Stage 2 consists of proteases in a slightly alkaline solution that mimicks the small intestine.

extract_protocol: RNA was extracted using TRIZOL.

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


title: 60 min Excystation

source_name: Excystation, 60 min


title: 652 - mAdbID:75138

description: mAdb experiment ID: 75138

value: lymphocytes

value: female

value: Follow up years:0.01

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:NA


title: AML P2

source_name: DNA isolated from peripheral blood

tag: DNA isolated from peripheral blood of a patient with tMDS RAEB/RAEB-T (mammary carcinoma), Age

value: 65 Gender:female

value: f

value: PB


title: AML P55

source_name: DNA isolated bone marrow

tag: DNA isolated from bone marrow of a patient with AML M5, Age

value: 71 Gender:male

value: AML M5

value: m

value: BM


title: S1 Excystation

source_name: Excystation, stage S1


title: AML P40

extract_protocol: DNA was extracted from bone marrow by  a salting out procedure  (Grimberg et al.,1989).

tag: DNA isolated from bone marrow of a patient with acute myeloid leukemia, Age

value: 69 Gender:female

value: AML


title: AML P1

value: 46 Gender:male

value: AML M1


title: AML P45

extract_protocol: DNA was extracted from bone marrow using the Wizard Genomic DNA exraction kit from Promega

tag: DNA isolated from bone marrow of a patient with AML M1, Age


title: AML P14

tag: DNA isolated from bone marrow of a patient with AML; secondary to MDS, Age

value: 57 Gender:female


title: 12 hr Encystation

source_name: Encysting trophozoites, 12 hr

growth_protocol: A confluent culture of trophozoites was used to inoculate fresh cultures and grown for 21 hr.  These were log phase trophozoites.  Encystation cultures were inoculated from the same cultures in encystation medium "GS-4" following Sun et al. (Mol. Microbiol. 2002. 46: 971-84). Cells were harvested at 12 hr of encystation for total RNA isolation for SAGE.


title: Normal porcine alveolar macrophages

source_name: Normal porcine alveolar macrophages

treatment_protocol: These cells were not infected.

tag: Porcine alveolar macrophages (PAMs) from broncho-alveolar lavage of PRRSV- and PCV-free pigs (3 pigs).


title: 42 hr Encystation

source_name: Encysting trophozoites, 42 hr

growth_protocol: A confluent culture of trophozoites was used to inoculate fresh cultures and grown for 21 hr.  These were log phase trophozoites.  Encystation cultures were inoculated from the same cultures in encystation medium "GS-4" following Sun et al. (Mol. Microbiol. 2002. 46: 971-84). Cells were harvested at 42 hr of encystation for total RNA isolation for SAGE.


title: S2 Excystation

source_name: Excystation, stage S2


title: AML P39

value: 95 Gender:female

tag: lab code

tag: diagnosis


title: 4 hr Encystation

source_name: Encysting trophozoites, 4 hr

growth_protocol: A confluent culture of trophozoites was used to inoculate fresh cultures and grown for 21 hr.  These were log phase trophozoites.  Encystation cultures were inoculated from the same cultures in encystation medium "GS-4" following Sun et al. (Mol. Microbiol. 2002. 46: 971-84). Cells were harvested at 4 hr of encystation for total RNA isolation for SAGE.


title: AML P43

value: 72 Gender:female

value: AML (secondary after PV)

tag: age

tag: sex


title: AML P47

extract_protocol: DNA was extracted from bone marrow using TRIZOL

tag: DNA isolated from bone marrow of a patient with tAML M2 (Hodgkin NS IIIA), Age

value: 74 Gender:female

value: tAML M2 (Hodgkin's NSIIIA)

tag: tissue

tag: DNA isolated from the blood of a healthy female donor


title: 21 hr Encystation

source_name: Encysting trophozoites, 21 hr

growth_protocol: A confluent culture of trophozoites was used to inoculate fresh cultures and grown for 21 hr.  These were log phase trophozoites.  Encystation cultures were inoculated from the same cultures in encystation medium "GS-4" following Sun et al. (Mol. Microbiol. 2002. 46: 971-84). Cells were harvested at 21 hr of encystation for total RNA isolation for SAGE.


title: longSAGE library from NET KO mice

status: Public on Jun 23 2008

city: Newcastle upon Tyne

first: Maya

last: Sieber-Blum

address: Central Parkway Road

department: Institute of Human Genetics and

institute: Newcastle University

description: According to manufacturer's specification

organism: Mus musculus

source_name: neural crest cell cultures from day 9.5 mouse embryos.

growth_protocol: Isolated from 60 neural crest cell cultures at day 7 in culture.

extract_protocol: I-SAGElong kit (Invitrogen, Carlsbad, CA)

tag: C57BL6/J background;

tag: neural tube explants;

tag: deleted norepinephrine transporter gene


title: Cysts

source_name: Cysts

growth_protocol: A confluent culture of trophozoites was used to inoculate fresh cultures and grown for 21 hr.  These were log phase trophozoites.  Encystation cultures were inoculated from the same cultures in encystation medium "GS-4" following Sun et al. (Mol. Microbiol. 2002. 46: 971-84). Endpoint Cysts were harvested for total RNA isolation for SAGE.

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


title: erythro-megakaryocytic_progenitor

status: Public on Jun 18 2008

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

institute: Canada's Michael Smith Genome Sciences Centre

description:
Assays to confirm viability: Colony Forming Cell Assay (CFCs)
No PCR amplification before SAGE

source_name: Human embryonic stem cell-derived erythro-megakaryocytic progenitors

growth_protocol: Growth medium: αMEM (Invitrogen) with 10% FBS (HyClone)

extract_protocol: RiboPureTM Kit (Ambion, Austin, TX)

tag: Cell line

value: Human embryonic stem cell line WA01 (H1)

tag: Gender

value: Male

tag: Karyotype

tag: Culture condition

value: hESC/OP9 coculture day 8 of differentiation

tag: Estimated 10% CFU

tag: Cell purification Method

value: Immuno-magnetic and Fluorescent Activated Cell Sorting (FACS)

tag: Defining markers


title: fetal_liver_stem_or_progenitor_cells

description:
Assays to confirm viability: Colony Forming Cell Assay (CFCs)/ longterm culture-initiating cells (LTC-ICs)
PCR amplification before SAGE

source_name: Human fetal liver cells

extract_protocol: PicoPureTM (Arcturus, Mountain View, CA)

tag: Tissue

value: human fetal liver cells from 5 aborted fetuses of 14-to-21-week gestational age

value: Male/Female

tag: Estimated 31% colony forming cells and 58% longterm culture-initiating cells.

tag: Cell purification method

value: lin-CD34+CD38-CD45RA-CD36-CD71-CD7- (lin = CD2, CD3, CD14, CD16, CD19, CD20, CD24, CD56, CD66b and GlyA)


title: Wildtype FVB/N Embryonic Stem Cells, replicate 3, Chip C

status: Public on Jun 01 2008

type: RNA

city: Zurich

first: Paolo

last: Cinelli

address: Winterthurerstrasse 190

department: Institute of Laboratory Animal Science

country: Switzerland

institute: University of Zurich

description: Wildtype FVB/N Embryonic Stem Cells, replicate 3, Chip B

hyb_protocol: Prior to injection of hybridization cocktail, probes were primed by injection with hybridisation buffer (100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween-20 and placed in oven (45oC) for 10 minutes with rotation (60rpm). Hybridisation was performed by injection of the hybridization cocktail and incubating the probe in oven at 45oC with rotation (60rpm) for 16 hours. Probes were washed at the Fluidics FS-450 station with Buffer A (6X SSPE, 0.01% Tween 20) and B (100mM MES, 0.1M [Na+], 0.01% Tween-20). Staining of the probes was performed with 0.01mg/ml SAPE (Streptavidin Phycoerythrin) and biotinylated antibody (0.06mg/ml).

scan_protocol: standard Affymetrix procedures

data_processing: MAS 5

label: Biotin

source_name: FVB/N derived Embryonic stem cells

label_protocol:
cDNA synthesis 1st round of amplification. RNA was combined with 1ug of T7-dT primer (5â€™-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-(dT)24-3â€™) in a total volume of 12 ul and incubated at 70Â°C for 10 min. The reaction was placed on ice and the following reagents added in a total volume of 20 ul: first strand buffer (1x), DTT (10 mM), dNTP mix (500 uM), and Superscript III (200 units, Invitrogen) and incubated at 42Â°C for 2 h. Second strand synthesis was performed by adding the following reagents in a total volume of 150 ul: second strand buffer (1x), dNTP mix (200 uM), E. coli DNA ligase (10 units), E. coli DNA polymerase (40 units), RNase H (2 units), and incubated at 16Â°C for 2 h. T4 DNA polymerase (10 units) was then added to fill in the ends of the cDNA and incubated at 16Â°C for an additional 15 min. Following phenol:chloroform extraction and ethanol precipitation, the cDNA was resuspended in RNase-free water. Transcription was
 performed using Ambionâ€™s (Austin, USA) MEGAscript reagents. A 20 ul reaction containing cDNA, NTP mix (7.5 mM), reaction buffer (1x), and 2 ul enzyme mix was incubated at 37Â°C for 4 h and the primary cRNA was purified using the RNeasy kit (Qiagen, Chatsworth, CA) per the manufacturerâ€™s specifications. Two hundred nanograms of the purified cRNA were then carried forward in the secondary amplification. Samples with less than 200 ng cRNA were concentrated to a 5 ul volume and the entire sample used for the next round of amplification.
	cDNA synthesis 2nd round of amplification. First-strand cDNA was synthesized by incubating the above cRNA with 1 ug of random primers (Invitrogen, Carlsbad, CA) at 70Â°C for 10 min. The reaction was then placed on ice and the following reagents added in a 20-uL reaction: first-strand buffer (1x), DTT (10 mM), dNTP mix (500 uM), and Superscript III (200 units). The reaction was incubated at 42Â°C for 2 h. RNase H (2 units) was added to the reaction and incubated at 37Â°C for 20 min and then heat-inactivated. The cDNA was combined with 1 ug of the T7-dT primer and incubated at 70Â°C for 10 min. The reaction was then placed on ice and the following reagents added for a final volume of 150ul: second-strand buffer (1x), dNTP mix (200 uM), E. coli DNA Polymerase (40 units), and then incubated at 16Â°C for 2 h. T4 DNA polymerase (10 units) was added to fill in the ends of the cDNA and incubated at 16Â°C for an additional 15 min. The cDNA was purified with phenol:chloroform and prec  ipitated with ethanol.
Biotin secondary IVT. The secondary transcription reaction was performed using the Enzo BioArray HighYield RNA kit (Affymetrix, Santa Clara, CA). The secondary cDNA was incubated at 37Â°C for 4 h in a 40 ul reaction as indicated by in the manufacturer recommendations and the labelled cRNA purified using the RNeasy kit.

extract_protocol: RNA extraction with QIAGEN RNeasy Kit

treatment_protocol: Cells were cultivated in the presence of LIF

tag: Embryonic stem cells derived from the FVB/N mouse strain


title: umbilical_cord_blood_CD38-

description:
Assays to confirm viability: Colony Forming Cell Assay (CFCs) / Longterm Culture-Initiating Cells (LTC-ICs)
PCR amplification before SAGE

source_name: Human umbilical cord blood stem/progenitor cells

value: umbilical cord blood

tag: Estimated 6% colony forming cells and 14% lonterm culture-initiating cells


title: San Roman_OP_untreated

status: Public on May 14 2008

city: Kerrville

first: Leonel

middle: (Leo)

last: Saldivar

state: TX

address: 2700 Fredericksburg Rd.

department: Agriculture

institute: USDA

data_processing:
Sequence data was processed to extract 14 bp tags using a pipeline of Perl scripts.  Duplicate ditags, ditags not of length 28-38 bp, and linker sequences were removed.
For more details see: Insect Molecular Biology (2007) 16(1), 49-60.

organism: Rhipicephalus microplus

source_name: San Roman_f18 generation_12-16 days old larvae

extract_protocol: Total RNA was prepared using the Totally RNA kit (Ambion, Inc., Austin, TX, USA), including a LiCl precipitation step, according to the kit protocol.  SAGE library was synthesized using the I-SAGE kit (Invitrogen, Carlsbad, CA, USA).  For more details see: Insect Molecular Biology (2007) 16(1), 49-60.

treatment_protocol: Placed in larval packet test papers treated with 0.4% coumaphos.  This is approximately a LD25 dosage for each strain.  For more details see: Insect Molecular Biology (2007) 16(1), 49-60.

tag: untreated sample.  For further details see

value: Insect Molecular Biology (2007), 16(1), 49-60.


title: San Roman_OP_treated

extract_protocol: Total RNA was prepared using the Totally RNA kit (Ambion, Inc., Austin, TX, USA), including aaLiCL precipitation step, according to the kit protocol.  SAGE library was synthesized using the I-SAGE kit (Invitrogen, Carlsbad, CA, USA).  For more details see: Insect Molecular Biology (2007) 16(1), 49-60.

tag: Placed in larval packet test papers treated with 0.4% coumaphos.  This is approximately a LD25 dosage for each strain.  For more details see


title: Munoz_OP_treated

source_name: Munoz stratin_f13 generation_12-16d old larvae

extract_protocol: Total RNA was prepared using the Totally RNA kit(Ambion, Inc., Austin, TX, USA), including aa LiCl precipitation step, according to the kit protocol.  SAGE library was snthesized using the I-SAGE kit (Invitrogen, Carlsbad, CA, USA).  For more details see: Insect Molecular Biology (2007) 16(1), 49-60.

treatment_protocol: treatment: placed in larval packet test papers treated with 0.03% coumaphos.  This is approximately a LD25 dosage for each strain.   For more details see: Insect Molecular Biology (2007) 16(1), 49-60.

tag: strain

value: Munoz

tag: generation

tag: material

value: 5 grams

tag: age

value: 12-16 day old

tag: stage

value: larvae

tag: treatment


title: Human Monocyte Derived Macrophage infected with Leshmania major parasites

status: Public on May 22 2008

city: Tunis-Belvedere

first: Dhafer

last: Laouini

address: 13, place Pasteur. BP74

country: Tunisia

institute: Institut Pasteur de Tunis

source_name: Leishmania major infected human derived macrophages

growth_protocol:
In order to obtain macrophages, monocytes were cultured at 37°C, 5% CO2 in endotoxin-free RPMI 1640 medium supplemented with 10% heat-inactivated normal human AB serum and 10% heat-inactivated fetal calf serum (HyClone Laboratories, Logan, UT), 100 U/ml penicillin, 100 µg/ml streptomycin, 2 mM L-glutamine for 7 days at 2 x 106 cells/ml, in 6-well tissue-culture plates.
Obtained MFs were exposed to metacyclic parasites of L. major (MHOM/TN/95/GLC94 strain (ratio parasites:cells 5:1) for 24h and then harvested for RNA preparation.

extract_protocol:
Cells or parasites were collected at the indicated time points by centrifugation, homogenized by Trizol reagent (Gibco BRL) and frozen at -70°C until RNA extraction.
The RNA from each of the 4 donors was extracted independently then pooled, and used for library construction. RNA was purified of contaminating genomic DNA by using standard protocol. Briefly, contaminating DNA was removed from total macrophage or parasite RNA by using DNase I (Invitrogen, Carlsbad, Calif). The RNA samples were then ethanol-precipitated, washed once in 70% ethanol, and re-dissolved in water. RNA was quantified using spectrophotometer.
Examination of purified total RNA by gel electrophoresis revealed prominent 5S, 18S and 28S ribosomal bands for human samples and 18S and 24Sa and 24Sb ribosomal bands for parasitic samples indicating that the RNA was not degraded.

treatment_protocol: Human PBMC were isolated from leukopacks peripheral blood mononuclear cells of four healthy volunteers using Ficoll-Paque density gradient centrifugation. Cells were washed and resuspended at 106 cells/ml in RPMI 1640 medium supplemented with 2 mM L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin and 10% autologous heat inactivated serum. Monocytes were purified by fibronectin-mediated adhesion using gelatin and autologous heat inactivated serum substratum.

tag: Human Derived Macrophages obtained from four healthy donors and individually infected with Leishmania major metacyclic parasites


title: primitive_hematopoietic_cells_enriched_for_multipotent_progenitors

source_name: Human embryonic stem cell-derived primitive hematopoietic cells enriched for multipotent progenitors

tag: Cell line

tag: Gender

tag: Karyotype

tag: Culture condition

tag: Estimated 19% CFU


title: primitive_hematopoietic_cells_enriched_for_multipotent_myeloid-skewed_progenitors

source_name: Human embryonic stem cell-derived primitive hematopoietic cells enriched for multipotent myeloid-skewed progenitors

tag: Estimated 37% CFU

tag: Cell purification Method

tag: Defining markers


title: Munoz_OP_untreated

extract_protocol: Total RNA was prepared using the Totally RNA kit (Ambion, Inc, TX, USA), including aaLiCL precipitation step, according to the kit protocol.  SAGE library was synthesized using the I-SAGE kit (Invitrogen, Carlsbad, CA, USA).  For more details see: Insect Molecular Biology (2007) 16(1), 49-60.

treatment_protocol: treatment: untreated.  For more details see: Insect Molecular Biology (2007) 16(1), 49-60.

tag: untreated Munoz larvea.   For more details see


title: Diff-Basal

status: Public on May 10 2008

description: Highly purified subpopulations of primitive bipotent and committed luminal progenitor cells as well as mature luminal and myoepithelial cells from normal human mammary tissue were isolated and compared their transcriptomes obtained using PCR-LONG-SAGE protocol (Zhao, et al, Stem Cells, 2007)

source_name: Differentiated basal Cells of mammary tissue

growth_protocol: Primary cells extracted from reduction mammoplasty samples were cultured in EpiCult-B medium (StemCell Technologies) with 5% fetal Calf Serum supplementation.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and DNase treated.

treatment_protocol: Epithelial-enriched fraction of reduction mammoplasty samples were made into single cell suspensions and co-cultured with irradiated mouse fibroblasts for 3 days.

tag: Tissue

value: reduction mammoplasty sample

value: Female

tag: Age

value: 26 days


title: Diff-Luminal

source_name: Differentiated luminal Cells of mammary tissue

value: female


title: umbilical_cord_blood_CD38+

description:
Assays to confirm viability: Colony Forming Cell Assay (CFCs) / Longterm Culture-Initiating Cells (LTC-ICs)
PCR Amplification before SAGE

tag: Estimated 15% colony forming cells and 4% longterm culture-initiating cells

tag: Cell purification method:Immuno-magnetic and Fluorescent Activated Cell Sorting (FACS)

tag: Defining Markers

value: lin-CD34+CD38+CD45RA-CD36-CD71-CD7- (lin = CD2, CD3, CD14, CD16, CD19, CD20, CD24, CD56, CD66b and GlyA)


title: Human Monocyte Derived Macrophages

description: Human Monocyte Derived Macrophages

source_name: Resting human derived macrophages

growth_protocol: In order to obtain macrophages, monocytes were cultured at 37°C, 5% CO2 in endotoxin-free RPMI 1640 medium supplemented with 10% heat-inactivated normal human AB serum and 10% heat-inactivated fetal calf serum (HyClone Laboratories, Logan, UT), 100 U/ml penicillin, 100 µg/ml streptomycin, 2 mM L-glutamine for 7 days at 2 x 106 cells/ml, in 6-well tissue-culture plates.

extract_protocol:
Cells or parasites were collected at the indicated time points by centrifugation, homogenized by Trizol reagent (Gibco BRL) and frozen at -70°C until RNA extraction. The RNA from each of the 4 donors was extracted independently then pooled, and used for library construction.
RNA was purified of contaminating genomic DNA by using standard protocol. Briefly, contaminating DNA was removed from total macrophage or parasite RNA by using DNase I (Invitrogen, Carlsbad, Calif). The RNA samples were then ethanol-precipitated, washed once in 70% ethanol, and re-dissolved in water. RNA was quantified using spectrophotometer. Examination of purified total RNA by gel electrophoresis revealed prominent 5S, 18S and 28S ribosomal bands for human samples and 18S and 24SÎ± and 24SÎ² ribosomal bands for parasitic samples indicating that the RNA was not degraded.

tag: Human Derived Macrophages obtained from four healthy donors


title: Pig melanoma cells from lung metastasis

status: Public on May 08 2008

city: Maisons-Alfort

first: Giorgia

last: Egidy

address: 7, ave Gral de Gaulle

institute: INRA-ENVA

description: Library was generated using the SAGE adaptation for downsized extracts (SADE) method (Virlon et al, P.N.A.S. 96:15286-15291, 1999). Cell lysates were centrifugated to discard melanin.

data_processing: SAGE 2002 version 4.5 software

source_name: Primary culture of melanoma cells from a lung metastasis in MeLiM minipigs

growth_protocol: Conditions for primary culture of pig melanocytic cells were described in Julé et al, Pigment Cell Research 16:407-410, 2003.

extract_protocol: Dynabead mRNA direct kit

treatment_protocol: Gentamicine, penicilline, steptomycin and fungizone treatment of the biopsies before and during the primary culture.

tag: Melanoma cells were prepared from the biopsy of a lung metastasis of minipiglet, 2 and a half months old, with spontaneous cutaneous melanoma and metastasis in lymph nodes, lung, spleen, and liver. 48hs culture of tumoral cells resulted in melanocytic bipolar and pigmented cells.


title: Acupuncture-treated Normal Rat Lung

status: Public on Apr 07 2008

first: Yong Qing

last: Yang

address: 650 South Wanping Rd

department: Shanghai Research Institute of Acupuncture

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 normal male rat (Sprague Dawley) lung treated by acupuncture with linker sequences removed. Rats weighted 250 grams and were 50 days old.


title: Bipotent_CFC

source_name: Bipotent progenitor Enriched subpopulation of mammary cells


title: Metacyclic Leishmanaia major parasites

description: Metacyclic Leishmanaia major parasites

organism: Leishmania major

source_name: Metacyclic Leishmania major parasites

growth_protocol: Parasites were cultured at 26°C without CO2 in endotoxin-free RPMI medium supplemented with 10% heat-inactivated fetal calf serum, 100 U/ml penicillin, 100 µg/ml streptomycin, 2 mM L-glutamine. Infective-stage metacyclic promastigotes were isolated from stationary culture (5 to 6 days old) by negative selection using peanut agglutinin.Parasites were then harvested for RNA preparation.

extract_protocol: Parasites were collected homogenized by Trizol reagent (Gibco BRL) and frozen at -70°C until RNA extraction. The RNA was purified of contaminating genomic DNA by using standard protocol. Briefly, contaminating DNA was removed from total parasite RNA by using DNase I (Invitrogen, Carlsbad, Calif). The RNA samples were then ethanol-precipitated, washed once in 70% ethanol, and re-dissolved in water. RNA was quantified using spectrophotometer. Examination of purified total RNA by gel electrophoresis revealed prominent 18S and 24SÎ± and 24SÎ² ribosomal bands indicating that the RNA was not degraded.

tag: Leishmania major isolate obtained from the field (L. major (MHOM/TN/95/GLC94))


title: Luminal-CFC

source_name: Committed luminal progenitor-enriched subpopulation of mammary cells

tag: Gender


title: Pig melanocyte cell line PigMel

description: Library was generated using the SAGE adaptation for downsized extracts (SADE) method (Virlon et al., P.N.A.S. 96:15286-15291, 1999). Cell lysates were centrifugated to discard melanin.

source_name: PigMel P37, normal melanocyte cell line derived from pig skin

growth_protocol: Culture conditions of the PigMel cell line are described by Julé et al., in Pigment Cell Research 16:407-410, 2003.

tag: The non transformed pigmented melanocyte cell line PigMel was used at passage 37 for the SAGE library.


title: AML P37

source_name: DNA isolated bone marrow

extract_protocol: DNA was extracted from bone marrow by  a salting out procedure  (Grimberg et al.,1989).

tag: DNA isolated from bone marrow of a patient with acute myeloid leukemia, Age

value: 59 Gender:female

tag: lab code

tag: diagnosis

value: AML

tag: age

tag: sex

value: f

tag: tissue

value: BM

source_name: DNA isolated from blood

extract_protocol: DNA was extracted from peripheral blood by  a salting out procedure (Blin and Stafford,1976).

tag: DNA isolated from the blood of a healthy female donor


title: Murine CBA/Ca bone marrow dendritic cells LPS matured LongSAGE

status: Public on Feb 28 2008

city: Oxford

first: Kathleen

last: Nolan

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: Oxford University

description: Double stranded cDNA was generated from polyA+ RNA using a cDNA  synthesis kit (Roche), primed using a biotinylated dT20 primer and a long SAGE library generated essentially according to the original description by Saha et al., Nature Biotechnology, (2002)20:508-512, including the use of biotinylated linkers as described by Powell, NAR (1998)26:3445-6.

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: Murine CBA/Ca_bone marrow dendritic cells_LPS matured

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 an RNeasy midi kit (Qiagen), including treatment with DNase I to remove any genomic contamination and poly A+ RNA isolated using (dT)25-coated Dynabeads (Dynal) according to the respective manufacturer's protocols.

treatment_protocol: 1 microg/ml LPS (E. Coli) added on day 6 for the final 18-20 hr of culture

tag: Strain:CBA/Ca; Gender

value: female; Age:~7 weeks; Tissue:cultured bone marrow; Culture time:7 days; Culture medium: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);  Treatment:1 microg/ml LPS added for the final 18-20 hr of culture


title: expression profile of human Schwann cells cultured from a HMSN-Lom patient (NDRG1 R148X mutant)

status: Public on Mar 01 2008

city: Amsterdam

first: Anneloor

last: ten Asbroek

address: Meibergdreef 9

country: Netherlands

institute: Academic Medical Center

description: this sample has also been profiled using Agilent microarrays

source_name: in vitro cultured Schwann cells

extract_protocol: Trizol extracted RNA from cultured cells

tag: Schwann cells cultured in vitro, from HMSN-Lom patient with missense mutation of NDRG1 (R148X)


title: expression profile of human Schwann cells cultured from a CMT1A (PMP22 duplication) patient plantar nerve

tag: Schwann cells cultured in vitro, from plantar nerve, from 52 year old male CMT1A patient with duplication of PMP22


title: M4

status: Public on Feb 19 2008

first: Ashleen

last: Shadeo

address: 675 West 10th Ave

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.

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: CIN II, moderate dysplasia, cervical tissue


title: M3

tag: CIN I, mild dysplasia, cervical tissue


title: M5


title: M2


title: M6


title: N4

tag: Normal Cervical Tissue


title: C5

tag: CIN III, severe dysplasia cervical tissue


title: C3


title: Brassica napus_immature seeds at 5 and 9 days after pollination

status: Public on Feb 26 2008

first: Hong-Wei

last: Xue

state: Shanghai

address: 300 Fenglin Road

department: molecular genetics

institute: Institute of Plant Physiology & Ecology

description: Siliques at 5 and 9 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70℃. Immature seeds were separated from silique coats for RNA extraction.

data_processing: Each sequencing result was proofread according to the map, the transforming to tag sequence files. These files were analysed using SAGE2000 to generate SAGE tag sequences database and related statistic report. The number of effective files is 1344, the sequencing succeed ratio is 93.33%. The anchoring enzyme is NlaIII-CATG. Totally 68,718 tags were obtained after sequencing 1344 clones, of which 23,897 are unique.

organism: Brassica napus

source_name: 5 and 9 day after pollination Brassica Napus immature seed

growth_protocol: Brassica Napus plants (Huyou-15) were grown in field at the last ten-day of September of the first year. And the immature seeds were harvested at April-May of the second year. The average temperature of these months of Shanghai is as fellow: September 23.4℃, October 18℃, November 12.3℃, December 6.2℃, January 3.5℃, February 4.6℃, March 8.3℃, April 14℃, May 18.8℃.

extract_protocol:
1、	Weigh appropriate Brassica Napus immature seeds, grind the tissue in liquid N2 using a mortar and pestle;
2、	Transfer the material into 15ml centrifuge tube, 12000g, 4℃, 10min;
3、	Transfer the top phase to a new 15ml centrifuge tube, incubate for 5min at 15-30℃;
4、	Add chloroform, vortex vigorously, incubate for 3min at 15-30℃;
5、	12000g, 4℃, 15min;
6、	Transfer the top phase to a new 15ml centrifuge tube, add isopropyl alcohol, invert several times, incubate for 10min at 15-30℃;
7、	12000g, 4℃, 10min;
8、	Remove the supernatant by pipet, add 5ml 75% ethanol, invert several times, remove the ethanol;
9、	Add 10ml 75% ethanol, vortex briefly, 8000g, 4℃, 10min;
10、	Remove the supernatant carefully, centrifuge briefly, remove all the supernatant by pipet, air-dry the pellet for 5min;
11、	Resuspend the RNA with RNase-free Milli-Q wate.

tag: Ecotype

tag: Tissue

value: Immature seeds

tag: Stage

value: 5 and 9 day after pollination (DAP)

tag: Siliques at 5 and 9 day after pollination (DAP) of Brassica napus (Huyou15) were frozen in liquid nitrogen after harvesting and stored at -70 ℃. Immature seeds were separated from silique coats for RNA extraction.


title: Cervical Long SAGE Library N2

data_processing: Duplicate ditags have been removed prior to submission to GEO

source_name: tissue biopsy prior to LEEP cone biopsy

extract_protocol: Trizol extraction followed by phenol and precipitation.

tag: Normal Cervical Epithelium


title: C4


title: Cervical Long SAGE Library N1


title: M1


title: C6


title: Cervical Long SAGE Library C2

tag: Severe Dysplasia (CIN III)


title: Cervical Long SAGE Library C1

tag: Severe Dysplasia (CIN III) biopsy


title: Substantia nigra

status: Public on Feb 05 2008

city: 91191 Gif/ Yvette Cedex

first: Jean-Marc

last: Elalouf

department: IBITEC-S

institute: CEA Saclay

description: Data provided after linker removal.

source_name: Wild-type mouse substantia nigra

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, substantia nigra.


title: Caudate-putamen

description: Data provided after linker removal.

source_name: Wild-type mouse caudate-putamen

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


title: Thalamus

description: Data provided after linker removal.

source_name: Wild-type mouse thalamus

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


title: Whole brain

description: Data provided after linker removal.

source_name: Wild-type mouse whole brain

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


title: Prelimbic cortex

description: Data provided after linker removal.

source_name: Wild-type mouse prelimbic cortex

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


title: Ventral tegmental area

description: Data provided after linker removal.

source_name: Wild-type mouse ventral tegmental area

value: C57BL/6; Gender:male; Age:8-12 weeks; Tissue:brain, ventral tegmental area.