title: Hues 62 (sibling of 63)

city: New York

first: Dieter

middle: M

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

description:
sibling of 62-63
Chip # 4256425036; Array F

hyb_protocol: Hybridization according to Illumina protocols on Illumina humanRef-8 v3 BeadArray

scan_protocol: according to Illumina protocols

data_processing: Variance stabilization before normalization using the vst function in the illumina package (http://www.bioconductor.org/packages/bioc/vignettes/lumi/inst/doc/lumi.pdf) Quantile normalization, due to normalization, there is no p value.

label: biotin

source_name: undifferentiated human ES cells

label_protocol: according to Illumina protocols

growth_protocol: Standard human embryonic stem cell media.

extract_protocol: RNAeasy Plus Mini Kit Qiagen

treatment_protocol: Chen et al., Cell Stem Cell 4, February 6, 2009, pp103-106

value: undifferentiated human ES cells

tag: development stage

value: embryonic


title: mLSAGE_Vascular_endothelium_CT26_tumor_associated_AP_CT26TEC

status: Public on Mar 20 2009

type: SAGE

anchor: NlaIII

city: Bethesda

first: Cancer Genome Anatomy Project

last: CGAP

state: MD

department: Cancer Genome Anatomy Project

country: USA

institute: National Cancer Institute

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2204
Library_producer: Brad St. Croix
Laboratory: Brad St. Croix, National Cancer Institute, Tumor Angiogenesis Section
References: Seaman S et al.  Cancer Cell. 2007 Jun;11(6):539-54 [PUBMED=17560335]

molecule: total RNA

organism: Mus musculus

source_name: vascular, tumor associated, endothelium, antibody purified, long sage, adult

tag: organ/tissue

value: vascular

tag: tissue preparation

value: antibody purified

tag: sex

value: unknown


title: mLSAGE_Muscle_normal_TS19_MMD_SM042

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 805
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: muscle, skeletal muscle, normal, microscope dissected, late gestation embryo, long sage, ts25

value: muscle

value: microscope dissected

tag: age


title: Hues 63 (sibling of 62)

type: RNA

description:
sibling of 62-63
Chip # 4256425036; Array G

organism: Homo sapiens

tag: cell type


title: Hues 66

description: Chip # 4256425036; Array H


title: Hues 60

description: Chip # 4256425036; Array E


title: mLSAGE_Lung_normal_TS13_MMD_SM127

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1788
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

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

value: lung


title: mLSAGE_Kidney_normal_TS14_MMD_SM169

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1682
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: kidney,  epithelium, normal, microscope dissected, long sage

value: kidney


title: mLSAGE_Embryonic_stem_cells_normal_TS38_MMD_SM302

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2071
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, normal, microscope dissected, long sage

value: stem cell

value: Unspecified

value: normal


title: mLSAGE_Neural_tube_normal_TS9_MMD_SM117

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1791
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

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

value: embryonic tissue


title: mLSAGE_Lung_normal_TS19_MMD_SM045

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1023
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lung, normal, microscope dissected, long sage, late gestation embryo, ts25


title: Hues 56 (sibling of 55, 58, 59)

description:
sibling of 55-59
Chip # 4256425036; Array B


title: Hues 59 (sibling of 55, 56, 58)

description:
sibling of 55-59
Chip # 4256425036; Array D


title: Hues 51 (sibling of 50)

description: Chip # 4256425034; Array G


title: mLSAGE_Lung_normal_P109_MMD_SM212

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2047
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: lung, normal, other, p109, male, long sage

value: other

value: male


title: mLSAGE_MEF_normal_CL_SHE18

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1392
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, fibroblast, normal, cell line, irradiation, long sage

value: cell line


title: Hues 55 (sibling of 56, 58, 59)

description:
sibling of 55-59
Chip # 4256425036; Array A


title: Hues 52

description: Chip # 4256425034; Array H


title: Hues 58 (sibling of 55, 56, 59)

description:
sibling of 55-59
Chip # 4256425036; Array C


title: mLSAGE_Heart_normal_TS9_MMD_SM174

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2026
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

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

value: heart

tag: mutations

value: Foxh1 -/-


title: Hues 48

description: Chip # 4256425034; Array D

value: undifferentiated human ES cells

value: embryonic


title: mLSAGE_Embryo_normal_TS7_MMD_SM205

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2043
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryo, normal, mocroscope dissected, e7.5, ts7, long sage

value: Foxa2 -/-


title: Hues 12

description: Chip # 4256425034; Array B


title: mLSAGE_Embryo_normal_TS34_MMD_SM211

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2045
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryo, normal, mocroscope dissected, e6.5, ts34, long sage

value: unknown


title: Hues 50 (sibling of 51)

description:
sibling of 50-51
Chip # 4256425034; Array F


title: mLSAGE_Embryo_normal_TS7_MMD_SM204

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2041
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC


title: Hues 49

description: Chip # 4256425034; Array E


title: Hues 31

description: Chip # 4256425034; Array C


title: mLSAGE_Embryo_normal_TS34_MMD_SM173

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2023
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryo, normal, microscope dissected, e6.5, ts34, long sage


title: mLSAGE_Embryo_normal_TS7_MMD_SM106

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1793
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic tissue, posterior, normal, microscope dissected, long sage, ts11, post implantation embryo


title: mLSAGE_Brain_normal_P84-P90_MMD_SM201

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 2039
Library_producer: Gene Expresion Lab, GSC
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: brain, normal, other, p84-p90, male, long sage

value: brain


title: Hues 8

description: Chip # 4256425034; Array A


title: LSAGE_White_Blood_Cells_plaque_macrophage_normal_AP_P1

description:
CGAP_Numeric_library_ID: 1983
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI
References: W.D. Patino et al., Circulation Research (2006, in press)

source_name: white blood cell, plaque macrophage, normal, antibody purified, human, male, adult, long sage

value: white blood cells

value: antibody purified

value: plaque macrophage


title: LSAGE_White_Blood_Cells_monocytes_normal_AP_P2

description:
CGAP_Numeric_library_ID: 1563
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI
References: W. D. Patino et al., Proc Natl Acad Sci U S A 102, 3423-3428 (2005) [PUBMED=15728378]

source_name: white blood cell, monocyte, normal, antibody purified, female, adult, long sage

value: female

value: monocyte


title: LSAGE_White_Blood_Cells_monocytes_normal_AP_A2

description:
CGAP_Numeric_library_ID: 1567
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI
References: W. D. Patino et al., Proc Natl Acad Sci U S A 102, 3423-3428 (2005) [PUBMED=15728378]

source_name: white blood cell, monocyte, normal, antibody purified, male, adult, long sage


title: LSAGE_White_Blood_Cells_plaque_macrophage_normal_AP_P2

description:
CGAP_Numeric_library_ID: 1985
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI
References: W.D. Patino et al., Circulation Research (2006, in press)


title: mLSAGE_Embryo_normal_TS34_MMD_SM146

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1784
Library_producer: David Charest Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: extraembryonic tissue, normal, microscope dissected, long sage, ts8, post implantation embryo

value: microscope dissected

value: 6.5 dpc/TS8


title: LSAGE_White_Blood_Cells_lung_macrophage_normal_AP_L1

description:
CGAP_Numeric_library_ID: 1987
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI
References: W.D. Patino et al., Circulation Research (2006, in press)

source_name: white blood cell, lung macrophage, normal, antibody purified, human, male, adult, long sage

value: lung macrophage


title: LSAGE_Vascular_endothelium_normal_liver_associated_AP_NLEC1

description:
CGAP_Numeric_library_ID: 655
Tagging_enzyme: Mme I
Library_producer: Brad St. Croix
Laboratory: Johns Hopkins Molecular Genetics Laboratory (Victor Velculescu)

source_name: vascular, normal, endothelium, antibody purified, long sage, adult

value: vascular

value: normal liver


title: LSAGE_White_Blood_Cells_breast_carcinoma_associated_CD45+_AP_IDC7

description:
CGAP_Numeric_library_ID: 659
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, M.D., Ph.D.
Laboratory: Polyak lab, Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: white blood cells, antibody purified, adult, female, long sage, tumor associated

value: invasive breast cancer, ER+, PR+, Her2-

tag: other information

value: CD45+ purified tumor  infiltrating leukocytes. Library name in Cancer Cell, 2004, 6(1):17-32 "I-LEU-7-leukocytes"


title: LSAGE_Testis_Embyronal_Carcinoma_B_1

description:
CGAP_Numeric_library_ID: 1863
Tagging_enzyme: Mme I
Library_producer: Jennifer B. Edwards
Laboratory: Dr. Gregory Riggins

source_name: testis, embyronal carcinoma, non-normalized, long sage, bulk

value: testis

value: bulk

value: male

value: Embyronal Carcinoma, Mixed germ cell tumor consisting primarily of embryonal carcinoma with foci of yolk sac tumor and teratoma seen. Size:4.5 x 3.8 x 2.8 cm. Non-neoplastic tissue:Marked hypospermatogenesis with Leydig cell hyperplasia and chronic inflammation.


title: mLSAGE_Embryo_normal_TS2_MMD_SM061

description:
Tagging_enzyme: Mme I
CGAP_Numeric_library_ID: 1203
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: whole body, morula, normal, microscope dissected, long sage, ts3, sagelite

value: whole body

value: unknown

value: Morula


title: LSAGE_White_Blood_Cells_monocytes_normal_AP_C1

description:
CGAP_Numeric_library_ID: 1564
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI
References: W. D. Patino et al., Proc Natl Acad Sci U S A 102, 3423-3428 (2005) [PUBMED=15728378]

value: white blood cells

value: antibody purified


title: LSAGE_White_Blood_Cells_monocyte_normal_AP_A1

description:
CGAP_Numeric_library_ID: 1566
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI
References: W. D. Patino et al., Proc Natl Acad Sci U S A 102, 3423-3428 (2005) [PUBMED=15728378]

value: monocyte


title: LSAGE_Uterus_Normal_B_hs0194

description:
CGAP_Numeric_library_ID: 2303
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: uterus, normal, bulk, long sage, slx-sage, solexa sage, female

value: uterus

value: female

value: SLX-SAGE


title: LSAGE_White_Blood_Cells_monocyte_normal_AP_P1

description:
CGAP_Numeric_library_ID: 1565
Tagging_enzyme: Mme I
Library_producer: Willmar D. Patino, Cardiovascular Branch-NHLBI
Laboratory: Paul M. Hwang, Cardiovascular Branch-NHLBI
References: W. D. Patino et al., Proc Natl Acad Sci U S A 102, 3423-3428 (2005) [PUBMED=15728378]


title: LSAGE_Vein_normal_B_hs0230

description:
CGAP_Numeric_library_ID: 2249
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: vascular, normal, bulk, long sage, slx-sage, solexa sage, female

value: vascular

value: SLX-SAGE, pool of 3 female Umbilical vein endothelial cells.


title: LSAGE_Uterus_normal_B_hs0195

description:
CGAP_Numeric_library_ID: 2243
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada


title: LSAGE_Urothelium_normal_B_hs0239

description:
CGAP_Numeric_library_ID: 2255
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: other, normal, bulk, long sage, slx-sage, solexa sage

value: other


title: LSAGE_Vein_normal_B_hs0237

description:
CGAP_Numeric_library_ID: 2251
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: vascular, normal, bulk, long sage, slx-sage, solexa sage, male

value: SLX-SAGE, pool of 3 male Umbilical vein endothelial cells


title: LSAGE_Skin_Normal_B_hs0281

description:
CGAP_Numeric_library_ID: 2325
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, normal, bulk, benign hyperplasia, long sage, slx-sage, solexa sage, male, seborrheic keratosis

value: skin

value: Seborrheic Keratosis


title: LSAGE_Skin_Normal_B_hs0278

description:
CGAP_Numeric_library_ID: 2275
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: other, normal, bulk, long sage, slx-sage, solexa sage, female

value: bulk

value: Nevus


title: LSAGE_Skin_Normal_B_hs0282

description:
CGAP_Numeric_library_ID: 2313
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, normal, bulk, long sage, slx-sage, solexa sage, female, seborrheic keratosis


title: LSAGE_Rheumatoid_arthritis_synovial_fibroblast_CS

description:
CGAP_Numeric_library_ID: 2349
Tagging_enzyme: Mme I
Library_producer: Min Hu, PhD
Laboratory: Polyak Lab, Dana-Farber Cancer Institute, Boston, MA

source_name: human, other, short term culture, uncharacterized histology, synovial fibroblasts from rheumatoid arthritis, rheumatoid arthritis, long sage

value: short term culture


title: LSAGE_Retina_Retinoblastoma_B_1

description:
CGAP_Numeric_library_ID: 1883
Tagging_enzyme: Mme I
Library_producer: Jennifer B. Edwards
Laboratory: Dr. Gregory Riggins

source_name: retina, bulk, retinoblastoma, long sage, poorly differentiated

value: retina

value: Bilateral retinoblastoma, poorly differentiated, left orbit


title: LSAGE_Skin_Normal_B_hs0277

description:
CGAP_Numeric_library_ID: 2323
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, normal, bulk, long sage, slx-sage, solexa sage, male, nevus

value: male


title: LSAGE_Skin_Melanoma_B_hs0274

description:
CGAP_Numeric_library_ID: 2269
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, cancer, bulk, long sage, slx-sage, solexa sage, male, melanoma

value: stage2 primary melanoma non-pigmented


title: LSAGE_Skin_Cancer_B_hs0283

description:
CGAP_Numeric_library_ID: 2281
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, cancer, bulk, long sage, slx-sage, solexa sage, male, squamous cell carcinoma

value: Squamous cell carcinoma


title: LSAGE_Retina_normal_B_4cRet

description:
CGAP_Numeric_library_ID: 1993
Tagging_enzyme: Mme I
Library_producer: Jessica Ebright
Laboratory: Catherine Bowes Rickman, Duke University Eye Center
References: Bowes Rickman C and Ebright JN, et al. Defining the Human Macula Transcriptome and Candidate Retinal Disease Genes Using EyeSAGE. Invest Ophthalmol Vis Sci. 2006 Jun;47(6):2305-16.  [PUBMED=16723438]

source_name: retina, central retina, normal, bulk, human, male, female, adult, long sage

value: 41-66 year old pool of 7 donors

value: male and female

value: central retina

value: The library was constructed using RNA isolated from pooled 4 mm punches of human macula and central peripheral retina from 7 morphologically normal donor eyes.


title: LSAGE_Skin_Melanoma_B_hs0275

description:
CGAP_Numeric_library_ID: 2271
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

value: stage 4 melanoma

value: SLX-SAGE


title: LSAGE_Skin_Cancer_B_hs0280

description:
CGAP_Numeric_library_ID: 2279
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, cancer, bulk, long sage, slx-sage, solexa sage, female, basal cell carcinoma

value: female

value: basal cell carcinoma


title: LSAGE_Pancreas_normal_B_1

description:
CGAP_Numeric_library_ID: 643
Tagging_enzyme: Mme I
Library_producer: Deric Olschner
Laboratory: Gregory Riggins, Duke University Medical Center

source_name: pancreas, normal, bulk, long SAGE, adult

value: pancreas

value: unknown


title: LSAGE_Muscle_Rhabdomyosarcoma_B_1

description:
CGAP_Numeric_library_ID: 1923
Tagging_enzyme: Mme I
Library_producer: Jennifer B. Edwards
Laboratory: Gregory Riggins, M.D., Ph.D

source_name: long sage, muscle, juvenile, male, rhabdomyosarcoma, bulk

value: muscle

value: bulk

value: rhabdomyosarcoma


title: LSAGE_Skin_Melanoma_B_hs0273

description:
CGAP_Numeric_library_ID: 2267
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

value: skin

value: stage2 primary melanoma pigmented


title: LSAGE_Skin_Normal_B_hs0272

description:
CGAP_Numeric_library_ID: 2265
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, normal, bulk, long sage, slx-sage, solexa sage, female


title: LSAGE_Skin_Cancer_B_hs0284

description:
CGAP_Numeric_library_ID: 2283
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, cancer, bulk, long sage, slx-sage, solexa sage, female, squamous cell carcinoma


title: LSAGE_Skin_Melanoma_B_hs0276

description:
CGAP_Numeric_library_ID: 2273
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

value: male


title: LSAGE_Peripheral_Blood_Cancer_B_hs0429

description:
CGAP_Numeric_library_ID: 2367
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: other, cancer, bulk, long sage, slx-sage, solexa sage, male, peripheral blood from aml patient

value: other

value: Peripheral blood from AML patient


title: LSAGE_Skin_Normal_B_hs0271

description:
CGAP_Numeric_library_ID: 2263
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, normal, bulk, long sage, slx-sage, solexa sage, male


title: LSAGE_Lymph_node_Lymphoma_B_hs0204

description:
CGAP_Numeric_library_ID: 2305
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: lymph node, cancer, bulk, long sage, slx-sage, solexa sage, male, diffuse large b cell lymphoma

value: lymph node

value: Diffuse Large B Cell Lymphoma


title: LSAGE_GallBladder_Normal_B_HN

description:
CGAP_Numeric_library_ID: 2127
Tagging_enzyme: Mme I
Library_producer: Dr. Hector Alvarez
Laboratory: Dr. Gregory Riggins and Dr. Anirban Maitra

source_name: gall bladder, bulk, ventral body wall, normal, adult, female, long sage

value: ventral body wall


title: LSAGE_Lung_adenocarcinoma_B_1

description:
CGAP_Numeric_library_ID: 963
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, M.D. Ph.D
Laboratory: Korenlia Polyak, M.D. , PhD., Dana-Farber Cancer Institute

source_name: lung, bulk, adenocarcinoma, long sage, adult, male, poorly differentiated

value: lung

value: poorly differentiated adenocarcinoma

value: Stage IV lung cancer. Cells isolated from pleural effusions.


title: LSAGE_Testis_Embryonal_Carcinoma_CL_hs0212

description:
CGAP_Numeric_library_ID: 2247
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: testis, cancer, cell line, long sage, slx-sage, solexa sage, adult, male

value: testis

value: cell line

value: 22 years old

value: SLX-SAGE


title: LSAGE_Lymph_Node_Lymphoma_B_1

description:
CGAP_Numeric_library_ID: 1864
Tagging_enzyme: Mme I
Library_producer: Jennifer B. Edwards
Laboratory: Dr. Gregory Riggins

source_name: lymph node, b cell lymphoma, non-normalized, long sage, bulk

value: bulk

value: Large B cell Lymphoma, Malignant, high grade, involving the serosa of the appendix


title: LSAGE_Skin_Cancer_B_hs0279

description:
CGAP_Numeric_library_ID: 2277
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, cancer, bulk, long sage, slx-sage, solexa sage, male, basal cell carcinoma

value: skin

value: basal cell carcinoma


title: LSAGE_Kidney_Glomeruli_Normal_B_bjballer1

description:
CGAP_Numeric_library_ID: 2444
Tagging_enzyme: Mme I
Laboratory: B. Ballermann, M.D., Endothelial Cell Biology Lab, University of Alberta, Edmonton, Canada
References: A. Lal et al., Cancer Res 59, 5403-7 (1999) [PUBMED=10554005]|A. Lal et al., Cancer Res 59, 5403-7 (1999) [PUBMED=10554005]

source_name: kidney, normal, male, adult, long sage, bulk

value: kidney

value: male

value: Glomeruli are from the unaffected pole of a kidney that was surgically removed for renal cell carcinoma. Glomeruli were isolated by sieving to >95% purity. Linker Sequences have been removed from the library.


title: LSAGE_Esophagus_Normal_B_CN01

description:
CGAP_Numeric_library_ID: 2103
Tagging_enzyme: Mme I
Library_producer: Dr. Hector Alvarez
Laboratory: Dr. Gregory Riggins and Dr. Anirban Maitra

source_name: other, bulk, normal, esophagus, long sage, adult, male

value: other


title: LSAGE_Testis_Embryonal_Carcinoma_CL_hs0213

description:
CGAP_Numeric_library_ID: 2307
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: testis, cancer, cell line, long sage, slx-sage, solexa sage, male, embryonal carcinoma

value: Embryonal Carcinoma


title: LSAGE_Peripheral_Blood_Cancer_B_hs0430

description:
CGAP_Numeric_library_ID: 2369
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

value: Peripheral blood from a AML patient


title: LSAGE_Esophagus_Dysplasia_B_LGD01

description:
CGAP_Numeric_library_ID: 2143
Tagging_enzyme: Mme I
Library_producer: Dr. Hector Alvarez
Laboratory: Dr. Gregory Riggins and Dr. Anirban Maitra

source_name: other, bulk, pre-cancer, esophagus, long sage, adult, male

value: low grade dysplasia


title: LSAGE_GallBladder_Adenocarcinoma_B_HAIIb

description:
CGAP_Numeric_library_ID: 2125
Tagging_enzyme: Mme I
Library_producer: Dr. Hector A. Alvarez and Jennifer B. Edwards
Laboratory: Dr. Gregory Riggins

source_name: gall bladder, bulk, adenocarcinoma, tubular, cancer, adult, female, long sage

value: female

value: Adenocarcinoma, tubular, poorly differentiated


title: LSAGE_GallBladder_Adenocarcinoma_B_C01

description:
CGAP_Numeric_library_ID: 2133
Tagging_enzyme: Mme I
Library_producer: Dr. Hector Alvarez
Laboratory: Dr. Gregory Riggins and Dr. Anirban Maitra

source_name: gall bladder, bulk, adenocarcinoma, cancer, adult, male, long sage

value: Adenocarcinoma


title: LSAGE_Embryonic_stem_cell_HES3_normal_p16_CL_SHE10

description:
CGAP_Numeric_library_ID: 1312
Tagging_enzyme: Mme I
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, normal, cell line, hes3, es03, female, long sage

value: stem cell

value: cell line

value: passage 16


title: LSAGE_GallBladder_Adenocarcinoma_B_NAM01

description:
CGAP_Numeric_library_ID: 2131
Tagging_enzyme: Mme I
Library_producer: Dr. Hector Alvarez
Laboratory: Dr. Gregory Riggins and Dr. Anirban Maitra

value: bulk

value: Adenocarcinoma, tubular


title: LSAGE_Embryonic_stem_cell_HSF6_normal_p50_CL_SHES9

description:
CGAP_Numeric_library_ID: 1311
Tagging_enzyme: Mme I
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, normal, cell line, hsf6, uc06, female, long sage

value: passage 50


title: LSAGE_Esophagus_Dysplasia_B_HGD02

description:
CGAP_Numeric_library_ID: 2145
Tagging_enzyme: Mme I
Library_producer: Dr. Hector Alvarez
Laboratory: Dr. Gregory Riggins and Dr. Anirban Maitra

source_name: other, bulk, pre-cancer, high grade dysplasia, esophagus, long sage, adult, male

value: high grade dysplasia


title: LSAGE_Esophagus_Adenocarcinoma_B_CA1D

description:
CGAP_Numeric_library_ID: 2147
Tagging_enzyme: Mme I
Library_producer: Dr. Hector Alvarez
Laboratory: Dr. Gregory Riggins and Dr. Anirban Maitra

source_name: other, bulk, cancer, adenocarcinoma, esophagus, long sage, adult, male

value: adenocarcinoma


title: LSAGE_Embryonic_stem_cell_H9_normal_p38_CL_SHES2

description:
CGAP_Numeric_library_ID: 843
Tagging_enzyme: Mme I
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, normal, cell line, h9, wa09, female, long sage, mef

value: passage 38


title: LSAGE_Embryonic_stem_cell_H13_normal_p22_CL_SHE15

description:
CGAP_Numeric_library_ID: 1385
Tagging_enzyme: Mme I
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, normal, cell line, male, long sage, h13, wa13, mef

value: male


title: LSAGE_Embryonic_stem_cell_H14_normal_p22_CL_SHE14

description:
CGAP_Numeric_library_ID: 1314
Tagging_enzyme: Mme I
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, normal, cell line, h14, wa14, male, long sage

value: passage 22


title: LSAGE_Embryonic_stem_cell_HES4_normal_p36_CL_SHE11

description:
CGAP_Numeric_library_ID: 1383
Tagging_enzyme: Mme I
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, normal, cell line, long sage, male, hes4, es04, mef


title: LSAGE_Embryonic_stem_cell_H7_normal_p33_CL_SHE13

description:
CGAP_Numeric_library_ID: 1313
Tagging_enzyme: Mme I
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, normal, cell line, h7, wa07, female, long sage

value: passage 33


title: LSAGE_Foreskin_normal_B_hs0305

description:
CGAP_Numeric_library_ID: 2285
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: skin, normal, bulk, long sage, slx-sage, solexa sage, male, foreskin, baby

value: skin

value: 9 months old baby

value: foreskin

value: SLX-SAGE


title: LSAGE_Colon_carcinoma_CL_Hct116_p53_knockout_Normal_Oxygen

description:
CGAP_Numeric_library_ID: 652
Tagging_enzyme: Mme I
Library_producer: ANITA LAL
Laboratory: RIGGINS LABORATORY AT DUKE UNIVERSITY MEDICAL CENTER

source_name: colon, carcinoma, cell line, long sage

value: colon

value: unknown


title: LSAGE_Eye_Retinoblastoma_B_hs0389

description:
CGAP_Numeric_library_ID: 2424
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: eye, cancer, bulk, retinoblastoma, long sage, slx-sage, solexa sage, female

value: eye

value: female

value: retinoblastoma


title: LSAGE_Embryonic_stem_cell_H1_normal_p54_CL_SHE16

description:
CGAP_Numeric_library_ID: 1387
Tagging_enzyme: Mme I
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, normal, cell line, matrigel, long sage, male, h1, wa01

value: stem cell

value: cell line


title: LSAGE_Lymph_node_Lymphoma_B_hs0196

description:
CGAP_Numeric_library_ID: 2245
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: lymph node, cancer, bulk, long sage, slx-sage, solexa sage, lymphoma

value: lymph node

value: bulk

value: Burkitt's lymphoma


title: LSAGE_Colon_carcinoma_CL_Hct116_p53_knockout_Anoxia

description:
CGAP_Numeric_library_ID: 654
Tagging_enzyme: Mme I
Library_producer: ANITA LAL
Laboratory: RIGGINS LABORATORY AT DUKEUNIVERSITY MEDICAL CENTER


title: LSAGE_Colon_carcinoma_CL_Hct116_wildtype_p53_Normal_Oxygen

description:
CGAP_Numeric_library_ID: 653
Tagging_enzyme: Mme I
Library_producer: ANITA LAL
Laboratory: RIGGINS LABORATORY AT DUKE UNIVERSITY MEDICAL CENTER

value: cell line derived from colorectal carcinoma


title: LSAGE_Embryonic_stem_cell_BG01_normal_p20_CL_SHE19

description:
CGAP_Numeric_library_ID: 1603
Tagging_enzyme: Mme I
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, cell line, normal, bg01, male, long sage

value: Passage 20 after derivation

value: male


title: LSAGE_Breast_normal_stroma_B_IDC8

description:
CGAP_Numeric_library_ID: 1943
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak
Laboratory: Kornelia Polyak, MD,PhD, Dana-Farber Cancer Institute

source_name: breast, stroma, normal, bulk, long sage, adult, female

value: mammary gland


title: LSAGE_Breast_normal_myoepithelium_CD10+_AP_N15

description:
CGAP_Numeric_library_ID: 2395
Tagging_enzyme: Mme I
Library_producer: Noga Qimron MSc/ MIn Hu PhD, DFCI
Laboratory: Polyak Lab, DFCI

source_name: human, breast/mammary gland, antibody purified, normal, normal breast tissue reduction, cd10+ mammary myoepithelial cells, female, adult, long sage

value: antibody purified

value: Normal breast tissue reduction

value: cells purified using CD10 antibody, these cells are CD10+ mammary myoepithelial cells


title: LSAGE_Embryonic_stem_cell_normal_CL_hs0238

description:
CGAP_Numeric_library_ID: 2253
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: stem cell, normal, antibody purified, long sage, slx-sage, solexa sage, male

value: SLX-SAGE


title: LSAGE_Colon_carcinoma_CL_Hct116_wildtype_p53_Anoxia

description:
CGAP_Numeric_library_ID: 651
Tagging_enzyme: Mme I
Library_producer: ANITA LAL
Laboratory: RIGGINS LABORATORY AT DUKE UNIVERSITY MEDICAL CENTER

value: colon

value: unknown


title: LSAGE_Breast_phyllodes_tumor_fibroblasts_AP_070202

description:
CGAP_Numeric_library_ID: 683
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, MD,PhD
Laboratory: Polyak laboratory Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: breast, neoplasia, high grade, poorly differentiated, bulk, long sage, adult, female

value: female

value: recurrent phyllodes tumor, malignant, high grade, poorly differentiated

value: Library name in Cancer Cell, 2004, 6(1):17-32 "PHY"


title: LSAGE_Breast_normal_epithelium_CD44+_AP_N5

description:
CGAP_Numeric_library_ID: 2391
Tagging_enzyme: Mme I
Library_producer: Noga Qimron MSc/ MIn Hu PhD, DFCI
Laboratory: Polyak Lab, DFCI

source_name: human, breast/mammary gland, antibody purified, normal, normal breast tissue reduction, cd44+ mammary epithelial cells, female, adult, long sage

value: cells purified using CD44 antibody, these cells are CD44+ mammary epithelial stem cells


title: LSAGE_Breast_normal_epithelium_MUC1+_AP_N5

description:
CGAP_Numeric_library_ID: 2385
Tagging_enzyme: Mme I
Library_producer: Noga Qimron MSc/ MIn Hu PhD, DFCI
Laboratory: Polyak Lab, DFCI

source_name: human, breast/mammary gland, antibody purified, normal, normal breast tissue reduction, muc1+ mammary epithelial cells, female, adult, long sage

value: cells purified using MUC1 antibody, these cells are MUC1+ mammary epithelial cells


title: LSAGE_Breast_normal_myoepithelium_CD10+_AP_N5

description:
CGAP_Numeric_library_ID: 2387
Tagging_enzyme: Mme I
Library_producer: Noga Qimron MSc/ MIn Hu PhD, DFCI
Laboratory: Polyak Lab, DFCI

source_name: human, breast/mammary gland, antibody purified, normal, normal breast tissue reduction, cd10+ mammary myoepithelial cells, adult, long sage


title: LSAGE_Breast_normal_myoepithelium_CL_HME50

description:
CGAP_Numeric_library_ID: 2347
Tagging_enzyme: Mme I
Library_producer: Min Hu, PhD
Laboratory: Polyak Lab, Dana-Farber Cancer Institute, Boston, MA

source_name: human, breast/mammary gland, cell line, normal, spontenously immortalized mammary myoepithelial cell line from li-fraumeni patient, female, li-fraumeni patient (heterozygous tp53 mutation), long sage

value: cell line

value: spontenously immortalized mammary myoepithelial cell line from Li-Fraumeni patient

value: Li-Fraumeni patient (heterozygous TP53 mutation)


title: LSAGE_Breast_normal_epithelium_MUC1+_AP_N15

description:
CGAP_Numeric_library_ID: 2393
Tagging_enzyme: Mme I
Library_producer: Noga Qimron MSc/ MIn Hu PhD, DFCI
Laboratory: Polyak Lab, DFCI


title: LSAGE_Embryo_Pre-Cancer_B_hs0324

description:
CGAP_Numeric_library_ID: 2327
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: embryonic tissue, pre-cancer, bulk, long sage, slx-sage, solexa sage, hydatidiform mole

value: embryonic tissue

value: bulk

value: Hydatidiform mole


title: LSAGE_Breast_normal_epithelium_CD44+_AP_N2

description:
CGAP_Numeric_library_ID: 2179
Tagging_enzyme: Mme I
Library_producer: Michail Shipitsin, PhD, DFCI
Laboratory: Polyak Lab, DFCI
References: Shipitsin et al. Cancer Cell 2007 11: 259-273. [PUBMED=17349583]

source_name: human, breast/mammary gland, antibody purified, normal, normal breast tissue reduction, adult, female, long sage

value: mammary gland

value: antibody purified


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 70Gy (g_nrs1_70_1d_2)

city: Chiba

first: Kazunori

last: Nojiri

address: 4-9-1, Anagawa, Inage-ku

country: Japan

institute: National Institute of Radiological Sciences

description: 1day after gamma irradiation at 70Gy

hyb_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection

scan_protocol: Scanning CodeLink Bioarrays on Agilent G2565 microarray scanner

data_processing: global median normalization

source_name: Murine tumor

label_protocol: CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation

tag: Squamous cell carcinoma developed spontaneously in C3H/He mouse etablished by National Institute of Radiological Science, Chiba, Japan


title: LSAGE_Breast_normal_epithelium_CD24+_AP_N2

description:
CGAP_Numeric_library_ID: 2177
Tagging_enzyme: Mme I
Library_producer: Michail Shipitsin, PhD, DFCI
Laboratory: Polyak Lab, DFCI
References: Shipitsin et al. Cancer Cell 2007 11: 259-273. [PUBMED=17349583]

value: Normal breast tissue reduction

value: cells purified using CD24 antibody, these cells are CD24+ differentiated luminal epithelial cells


title: LSAGE_Breast_normal_epithelium_CD24+_AP_N15

description:
CGAP_Numeric_library_ID: 2389
Tagging_enzyme: Mme I
Library_producer: Noga Qimron MSc/ MIn Hu PhD, DFCI
Laboratory: Polyak Lab, DFCI

source_name: human, breast/mammary gland, antibody purified, normal, normal breast tissue reduction, cd24+ mammary epithelial cells, female, adult, long sage

value: cells purified using CD24 antibody, these cells are CD24+ mammary epithelial cells


title: LSAGE_Breast_carcinoma_epithelium_X_MUC1+_AP

description:
CGAP_Numeric_library_ID: 2345
Tagging_enzyme: Mme I
Library_producer: Min Hu, PhD
Laboratory: Polyak Lab, Dana-Farber Cancer Institute, Boston, MA

source_name: human, breast/mammary gland, antibody purified, cancer, muc1 bead purified cells from mcf10dcis xenografts, female, 8q gain, cdkn1a and lrp1b homozygous deletions, long sage

value: MUC1 bead purified cells from MCF10DCIS xenografts

value: 8q gain, CDKN1A and LRP1B homozygous deletions


title: LSAGE_Breast_normal_epithelium_CD24+_AP_N5

description:
CGAP_Numeric_library_ID: 2383
Tagging_enzyme: Mme I
Library_producer: Noga Qimron MSc/ MIn Hu PhD, DFCI
Laboratory: Polyak Lab, DFCI

value: female


title: LSAGE_Breast_carcinoma_epithelium_PROCR+_AP_IDC28

description:
CGAP_Numeric_library_ID: 2166
Tagging_enzyme: Mme I
Library_producer: Michail Shipitsin, PhD, DFCI
Laboratory: Polyak Lab, DFCI
References: Shipitsin et al. Cancer Cell 2007 11: 259-273. [PUBMED=17349583]

source_name: human, breast/mammary gland, antibody purified, cancer, invasive ductal carcinoma, high-grade, er+,pr+,her2-, female, adult, long sage

value: Invasive ductal carcinoma, high-grade, ER+,PR+,HER2-

value: cells purified using PROCR antibody, these cells are CD44+ breast "cancer stem" cells


title: LSAGE_Breast_carcinoma_epithelium_PROCR+_AP_IDC29

description:
CGAP_Numeric_library_ID: 2163
Tagging_enzyme: Mme I
Library_producer: Michail Shipitsin, PhD, DFCI
Laboratory: Polyak lab, DFCI
References: Shipitsin et al. Cancer Cell 2007 11: 259-273. [PUBMED=17349583]

source_name: human, breast/mammary gland, antibody purified, cancer, invasive ductal carcinoma er+,pr+,her2-, female, adult, long sage

value: invasive ductal carcinoma ER+,PR+,HER2-


title: LSAGE_Breast_normal_myoepithelium_CD10+_AP_IDC7

description:
CGAP_Numeric_library_ID: 647
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, M.D., Ph.D.
Laboratory: Polyak lab, Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: breast, normal, myoepithelium, antibody purified, long sage, adult, female

value: normal breast tissue from a breast cancer patient (corresponding to IDC7)

value: CD10 positive purified myoepithelial cells. Library name in Cancer Cell, 2004, 6(1):17-32 "N-MYO-I7"


title: LSAGE_Breast_fibroadenoma_MD

description:
CGAP_Numeric_library_ID: 723
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, MD,PhD
Laboratory: Polyak laboratory Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: breast, benign neoplasia, microscope dissected, juvenile, female, long sage

value: microscope dissected

value: juvenile fibroadenoma

value: Library name in Cancer Cell, 2004, 6(1):17-32 "FA"


title: LSAGE_Breast_carcinoma_epithelium_CD44+_AP_ASC3

description:
CGAP_Numeric_library_ID: 2169
Tagging_enzyme: Mme I
Library_producer: Michail Shipitsin, DFCI
Laboratory: Polyak Lab, DFCI
References: Shipitsin et al. Cancer Cell 2007 11: 259-273. [PUBMED=17349583]

source_name: human, breast/mammary gland, antibody purified, cancer, ascites, mixed lobular/ductal carcinoma, her2-, recurrence of er+ tumor, female, long sage

value: unknown

value: Ascites, mixed lobular/ductal carcinoma, HER2-, recurrence of ER+ tumor

value: cells purified using CD44 antibody, these cells are CD44+ breast "cancer stem" cells


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 70Gy (g_nrs1_70_1d_1)

description: 1day after gamma irradiation at 70Gy


title: LSAGE_Breast_carcinoma_myoepithelium_X_ITGB6+_AP

description:
CGAP_Numeric_library_ID: 2343
Tagging_enzyme: Mme I
Library_producer: Min Hu, PhD
Laboratory: Polyak Lab, Dana-Farber Cancer Institute, Boston, MA

source_name: human, breast/mammary gland, antibody purified, cancer, itgb6 bead purified cells from mcf10dcis xenografts, female, 8q gain, cdkn1a and lrp1b homozygous deletions, long sage

value: mammary gland

value: antibody purified

value: ITGB6 bead purified cells from MCF10DCIS xenografts


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50Gy (g_nrs1_50_1d_2)

description: 1day after gamma irradiation at 50Gy


title: LSAGE_Breast_carcinoma_MD_LCIS

description:
CGAP_Numeric_library_ID: 703
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, MD,PhD
Laboratory: Polyak laboratory Dana-Farber Cancer Institute

source_name: breast, carcinoma, microscope dissected, adult, female, long sage

value: extensive LCIS


title: LSAGE_Embryonic_stem_cell_H1_normal_p31_CL_SHE17

description:
CGAP_Numeric_library_ID: 1390
Tagging_enzyme: Mme I
Library_producer: Jas Khattra, Gene Expression Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, BC

source_name: embryonic stem cell, normal, cell line, male, long sage, h1, wa01, mef

value: stem cell

value: cell line

value: male


title: LSAGE_Breast_carcinoma_epithelium_CD44+_AP_PE2

description:
CGAP_Numeric_library_ID: 2171
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, MD,PhD, DFCI
Laboratory: Polyak Lab, DFCI
References: Shipitsin et al. Cancer Cell 2007 11: 259-273. [PUBMED=17349583]

source_name: human, breast/mammary gland, antibody purified, cancer, pleural effusion, her2-, recurrence of er+ tumor, female, long sage

value: unknowm

value: female

value: Pleural effusion, HER2-, recurrence of ER+ tumor


title: LSAGE_Breast_carcinoma_epithelium_BerEP4+_AP_IDC7

description:
CGAP_Numeric_library_ID: 645
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, M.D., Ph.D.
Laboratory: Polyak lab, Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: breast, carcinoma, epithelium, antibody purified, long sage, adult, female

value: invasive breast cancer, ER+, PR+, Her-, grade II

value: BerEP4 purified epithelial cells. Library name in Cancer Cell, 2004, 6(1):17-32 "I-EPI-7 epithelial cells"


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30Gy (g_nrs1_30_1d_2)

description: 1day after gamma irradiation at 30Gy


title: LSAGE_Breast_carcinoma_epithelium_BerEP4+_AP_IDC8

description:
CGAP_Numeric_library_ID: 673
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, MD,PhD
Laboratory: Polyak laboratory Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: breast, carcinoma, epithelium, antibody purified, long sage, female, adult

value: Grade II, ER+, PR+, Her2- tumor

value: BerEP4 purified epithelial cells from invasive breast cancer. Library name in Cancer Cell, 2004, 6(1):17-32 "I-EPI-8 epithelial cells"


title: LSAGE_Breast_carcinoma_epithelium_BerEP4+AP_IDC9

description:
CGAP_Numeric_library_ID: 675
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, MD,PhD
Laboratory: Polyak laboratory Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: breast, carcinoma, antibody purified, epithelium, long sage, female, adult

value: Grade I, ER+, PR+, Her2- invasive ductal carcinoma

value: BerEP4 purified epithelial cells from invasive breast cancer. Library name in Cancer Cell, 2004, 6(1):17-32 "I-EPI-9 epithelial cells"


title: LSAGE_Breast_carcinoma_epithelium_CD24+_AP_IDC26

description:
CGAP_Numeric_library_ID: 2175
Tagging_enzyme: Mme I
Library_producer: Michail Shipitsin, DFCI
Laboratory: Polyak Lab, DFCI
References: Shipitsin et al. Cancer Cell 2007 11: 259-273. [PUBMED=17349583]

source_name: human, breast/mammary gland, antibody purified, cancer, invasive ductal carcinoma, er+,pr+,her2-, adult, female, long sage

value: Invasive ductal carcinoma, ER+,PR+,HER2-

value: cells purified using CD24 antibody, these cells are CD24+ more differentiated breast cancer cells


title: LSAGE_Breast_carcinoma_epithelium_CD24+_AP_IDC28

description:
CGAP_Numeric_library_ID: 2165
Tagging_enzyme: Mme I
Library_producer: Michail Shipitsin, PhD, DFCI
Laboratory: Polyak Lab, DFCI
References: Shipitsin et al. Cancer Cell 2007 11: 259-273. [PUBMED=17349583]

value: mammary gland

value: antibody purified

value: Invasive ductal carcinoma, high-grade, ER+,PR+,HER2-


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50Gy (g_nrs1_50_1d_1)

description: 1day after gamma irradiation at 50Gy


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 70Gy (g_scc7_70_1d_2)

description: 1day after gamma irradiation at 70Gy

tag: Squamous cell carcinoma developed spontaneously in C3H/He mouse etablished by Dr. L. Milas from the University of Texas, M. D. Anderson Cancer Center, Huston, USA"


title: LSAGE_Breast_carcinoma_associated_stroma_B_IDC7

description:
CGAP_Numeric_library_ID: 646
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, M.D., Ph.D.
Laboratory: Polyak lab, Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: breast, stroma, tumor associated, bulk, long sage, adult, female

value: bulk

value: invasive breast cancer ER+, PR+, Her2-, grade II

value: Library name in Cancer Cell, 2004, 6(1):17-32 "I-STR-7-fibroblast"


title: SCC induced spontaneously in C3H/He mouse, no irradiation (g_nrs1_0_1d_1)

description: no irradiation

source_name: Murine tumor


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30Gy (g_nrs1_30_1d_1)

description: 1day after gamma irradiation at 30Gy


title: SCC induced spontaneously in C3H/He mouse, no irradiation (g_nrs1_0_1d_2)

description: no irradiation


title: LSAGE_Breast_carcinoma_B_CT15_IDC

description:
CGAP_Numeric_library_ID: 649
Tagging_enzyme: Mme I
Library_producer: Anna Merlos-Suarez
Laboratory: Polyak

source_name: breast, carcinoma, ductal, invasive, bulk, long sage, female, adult

value: 71 yrs

value: primary grade III. ductal invasive breast carcinoma


title: LSAGE_Breast_carcinoma_B_BWHT18_DCIS

description:
CGAP_Numeric_library_ID: 657
Tagging_enzyme: Mme I
Library_producer: Anna Merlos-Suarez
Laboratory: Polyak

source_name: breast, bulk, carcinoma, in situ, ductal, long sage, adult, female

value: 44 yrs

value: female

value: primary ductal in situ breast carcinoma, intermediate grade

value: Estrogen and progesteron receptor positive, erbB2 negative, 0/25 lymph nodes (no lymph node metastasis)


title: LSAGE_Breast_carcinoma_epithelium_CD24+_AP_PE2

description:
CGAP_Numeric_library_ID: 2173
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, MD,PhD, DFCI
Laboratory: Polyak Lab, DFCI
References: Shipitsin et al. Cancer Cell 2007 11: 259-273. [PUBMED=17349583]

value: unknown

value: Pleural effusion, HER2-, recurrence of ER+ tumor


title: LSAGE_Breast_carcinoma_associated_myofibroblast_CD10+_AP_IDC8

description:
CGAP_Numeric_library_ID: 674
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, MD,PhD
Laboratory: Polyak laboratory Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: mammary gland, myofibroblast, tumor associated, female, adult, long sage, antibody purified

value: Grade II, ER+, PR+, Her2- tumor

value: CD10+ purified myofibroblasts from invasive breast cancer. Library name in Cancer Cell, 2004, 6(1):17-32 "I-MYOFIB-8 myofibroblasts"


title: LSAGE_Brain_Medulloblastoma_CL_UW228-N

description:
CGAP_Numeric_library_ID: 2123
Tagging_enzyme: Mme I
Library_producer: Jennifer B. Edwards
Laboratory: Dr. Gregory Riggins

source_name: brain, cell line, medulloblastoma, cancer, female, long sage

value: brain

value: cell line

value: Medulloblastoma


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 70Gy (g_scc7_70_1d_1)

description: 1day after gamma irradiation at 70Gy


title: LSAGE_Breast_carcinoma_associated_myofibroblast_CD10+_AP_IDC7

description:
CGAP_Numeric_library_ID: 644
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, M.D., Ph.D.
Laboratory: Polyak lab, Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: mammary gland, myofibroblast, antibody purified, tumor associated, adult, female, long sage

value: mammary gland

value: antibody purified

value: ER+, PR+, HER2-, grade II

value: CD10 positive purified myofibroblasts from invasive breast carcinoma. Library name in Cancer Cell, 2004, 6(1):17-32 "I-MYOFIB-7 myofibroblasts"


title: LSAGE_Breast_carcinoma_associated_myofibroblast_CD10+_AP_IDC9

description:
CGAP_Numeric_library_ID: 676
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, MD,PhD
Laboratory: Polyak laboratory Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: breast, myofibroblast, tumor associated, antibody purified, adult, female, long sage

value: Grade I, ER+, PR+, Her2- invasive ductal carcinoma

value: CD10+ purified myofibroblasts from invasive breast cancer Library name in Cancer Cell, 2004, 6(1):17-32 "I-MYOFIB-9-myofibroblasts"


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50Gy (g_scc7_50_1d_2)

description: 1day after gamma irradiation at 50Gy


title: LSAGE_Brain_Medulloblastoma_CL_UW228-V2

description:
CGAP_Numeric_library_ID: 2083
Tagging_enzyme: Mme I
Library_producer: Jennifer B. Edwards
Laboratory: Dr. Gregory Riggins

source_name: brain, cell line, medulloblastoma, cancer, long sage, female


title: LSAGE_Breast_carcinoma_associated_stroma_B_DCIS6

description:
CGAP_Numeric_library_ID: 650
Tagging_enzyme: Mme I
Library_producer: Kornelia Polyak, M.D., Ph.D.
Laboratory: Polyak lab, Dana-Farber Cancer Institute
References: Allinen et al. Cancer Cell. 2004 Jul;6(1):17-32. [PUBMED=15261139]

source_name: breast, stroma, tumor associated, long sage, adult, female

value: bulk

value: ductal carcinoma in situ, extensive, gradeIII, Her2+

value: Library name in Cancer Cell, 2004, 6(1):17-32 "D-STR-6-fibroblast"


title: LSAGE_Brain_Medulloblastoma_CL_425C2

description:
CGAP_Numeric_library_ID: 2085
Tagging_enzyme: Mme I
Library_producer: Jennifer B. Edwards
Laboratory: Dr. Gregory Riggins

source_name: brain, cell line, medulloblastoma, cancer, long sage, male

value: male

value: Medulloblastoma cell line


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50Gy (g_scc7_50_1d_1)

description: 1day after gamma irradiation at 50Gy


title: LSAGE_Brain_normal_substantia_nigra_B_1

description:
CGAP_Numeric_library_ID: 648
Tagging_enzyme: Mme I
Library_producer: Deric Olschner
Laboratory: RigginsÆ Lab at Duke University Medical Center

source_name: brain, substantia nigra, normal, bulk, long SAGE

value: unknown


title: LSAGE_Brain_Medulloblastoma_CL_425Otx2siRNA

description:
CGAP_Numeric_library_ID: 2129
Tagging_enzyme: Mme I
Library_producer: Jennifer B. Edwards, MS
Laboratory: Dr. Gregory Riggins

source_name: brain, cell line, medulloblastoma, cancer, male, long sage

value: Medulloblastoma cell line treated with Otx2 siRNA


title: LSAGE_Brain_glioblastoma_CL_4d

description:
CGAP_Numeric_library_ID: 1645
Tagging_enzyme: Mme I
Laboratory: Riggins laboratory
References: A. Lal et al., Cancer Res 59, 5403-7 (1999) [PUBMED=10554005]

source_name: brain, glioblastoma multiforme, cell line, long sage


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30Gy (g_scc7_30_1d_1)

description: 1day after gamma irradiation at 30Gy


title: LSAGE_Brain_glioblastoma_CL_28d

description:
CGAP_Numeric_library_ID: 1643
Tagging_enzyme: Mme I
Laboratory: Riggins laboratory
References: A. Lal et al., Cancer Res 59, 5403-7 (1999) [PUBMED=10554005]

source_name: brain, cell line, glioblastoma multiforme, long sage


title: LSAGE_Brain_glioblastoma_CL_stem_cells

description:
CGAP_Numeric_library_ID: 1644
Tagging_enzyme: Mme I
Laboratory: Riggins laboratory
References: A. Lal et al., Cancer Res 59, 5403-7 (1999) [PUBMED=10554005]


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30Gy (g_scc7_30_1d_2)

description: 1day after gamma irradiation at 30Gy


title: SCC induced spontaneously in C3H/He mouse, no irradiation (g_scc7_0_1d_2)

description: no irradiation


title: LSAGE_Bone_marrow_AML_FS_CD34+CD38+

description:
CGAP_Numeric_library_ID: 1483
Tagging_enzyme: Mme I
Library_producer: Jennifer Edwards
Laboratory: Gregory Riggins, Johns Hopkins Department of Neurosurgery

source_name: bone marrow, acute myelogenous leukemia, flow-sorted, long sage

value: bone marrow

value: flow-sorted

value: Acute myelogenous leukemia


title: LSAGE_Bone_Marrow_AML_FS_CD34+CD38+

description:
CGAP_Numeric_library_ID: 1865
Tagging_enzyme: Mme I
Library_producer: Jennifer B. Edwards
Laboratory: Dr. Gregory Riggins

source_name: bone marrow, aml, non-normalized, long sage, flow sorted

value: Stem Proginitor Cells, CD34+, CD38+


status: Public on Mar 19 2009

city: Toronto

first: Philip

last: Sherman

state: Ontario

address: 555 University Ave

country: Canada

institute: Hospital for Sick Children

description: Gene expression profile after E.coli O157:H7 growth in minimal media in 5%CO2 rep 2

hyb_protocol: Following fragmentation, upto 7 ug of cDNA were hybridized for 16 hr at 45C on GeneChip E. coli 2.0 genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned at The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario GeneChip® Scanner 3000 enabled for High-Resolution Scanning

data_processing: The data were analyzed with Partek Genomics Suite version 6.08.0128

organism: Escherichia coli O157:H7

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

growth_protocol: E. coli O157:H7 was grown overnight and then re-grown for a 6 hour period in one of the four growth conditions listed above

extract_protocol: Qiagen Total RNA extraction (Kit #74104)

treatment_protocol: after the 6 hour infection period, total E. coli O157:H7 was collected, centrifuged and cells were lysed using Lysozyme

tag: growth condition

value: 6 hour regrowth in minimal medium in 5%CO2


description: Gene expression profile after E.coli O157:H7 growth in the presence of Hep-2 cells rep 5

value: 6 hour regrowth with HEP-2 cells


title: SCC induced spontaneously in C3H/He mouse, no irradiation (g_scc7_0_1d_1)

description: no irradiation


title: LSAGE_Bone_Marrow_Normal_FS_hs0404

description:
CGAP_Numeric_library_ID: 2363
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: bone marrow, normal, flow-sorted, adult, long sage, slx-sagelite, solexa sagelite, male and female, facs-sorted normal adult bone marrow lin-cd38-rho-cells

value: adult

value: male and female

value: FACS-sorted normal adult bone marrow Lin-CD38-Rho-cells

value: SLX-SAGELite


description: Gene expression profile after E.coli O157:H7 growth in minimal media in 5%CO2 rep 1


description: Gene expression profile after E.coli O157:H7 growth in minimal media in 5%CO2 rep 4


title: LSAGE_Bone_Marrow_Cancer_FS_hs0405

description:
CGAP_Numeric_library_ID: 2365
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: bone marrow, cancer, flow-sorted, long sage, slx-sagelite, solexa sagelite, male, facs-sorted rna from single cml patient lin-cd38-rho-cells

value: FACS-sorted RNA from single CML patient Lin-CD38-Rho-cells


title: LSAGE_Brain_fetal_normal_B_S1

description:
CGAP_Numeric_library_ID: 656
Tagging_enzyme: Mme I
Library_producer: Brad St. Croix
Laboratory: Molecular Genetics Lab at Johns Hopkins Oncology Center

source_name: brain, normal, bulk, fetus, long SAGE

value: brain

value: bulk

value: Spontaneously aborted male/female Caucasian fetuses, ages 20-33 weeks


description: Gene expression profile after E.coli O157:H7 growth in minimal media in 5%CO2 rep 3


description: Gene expression profile afterE.coli O157:H7 growth in minimal media rep 4

value: 6 hour regrowth in minimal medium


title: LSAGE_Bladder_Cancer_B_hs0241

description:
CGAP_Numeric_library_ID: 2257
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: bladder, cancer, bulk, long sage, slx-sage, solexa sage, t1g3, female

value: bladder

value: female

value: SLX-SAGE


title: LSAGE_Bladder_Cancer_B_hs0264

description:
CGAP_Numeric_library_ID: 2311
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: bladder, cancer, bulk, long sage, slx-sage, solexa sage, female, t1g3


title: LSAGE_Bladder_Cancer_B_hs0240

description:
CGAP_Numeric_library_ID: 2309
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: bladder, cancer, bulk, long sage, slx-sage, solexa sage, female, tag2


description: Gene expression profile afterE.coli O157:H7 growth in Penassay broth rep 5

value: 6 hour regrowth in Penassay broth


title: LSAGE_Bladder_Cancer_B_hs0266

description:
CGAP_Numeric_library_ID: 2261
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: bladder, cancer, bulk, long sage, slx-sage, solexa sage, tag2, male

value: male


description: Gene expression profile afterE.coli O157:H7 growth in minimal media rep 3


title: 16m_post-transplantation

type: other

city: Stanford

first: Persis

middle: P

last: Wadia

state: CA

address: 269 W Campus Drive, CCSR 2210

department: Medicine

institute: Stanford University

hyb_protocol: 1. Add 5 ml serum diluted (1:500) in PBST Probing Buffer at the indented numeral end of the 4-chamber incubation tray without touching the array surface. Allow the serum to flow across the array surface. Avoid pipetting serum directly onto the array surface. 2. Incubate the tray for 90 minutes at 4ºC on a shaker set at 50 rpm (circular shaking). 3. Aspirate the serum using vacuum or pipette as described on the previous page (Step 5). 4. Wash each array with 5 ml PBST Probing Buffer with gentle shaking on a shaker set at 50 rpm for 5 minutes at room temperature. Aspirate the PBST Probing Buffer as described on the previous page (Step 5). 5. Repeat Step 4 four more times using fresh PBST Probing Buffer each time to obtain a total of 5 wash steps. 6. During the wash steps, mix 2.5 μl Alexa Fluor® 647 goat anti-human IgG antibody (secondary antibody) with 5 ml PBST Probing Buffer per array to obtain a final antibody concentration of 1 μg/ml. Store on ice until use. 7. Add 5 ml Alexa Fluor® 647 antibody solution from Step 6 to the incubation tray at the indented numeral end of the tray without touching the array surface. Allow the solution to flow across the array surface. Avoid pipetting solution directly onto the array surface. 8. Incubate the tray for 90 minutes at 4ºC on a shaker set at 50 rpm (circular shaking). 9. Aspirate the antibody solution. 10. Wash each array with 5 ml PBST Probing Buffer with gentle shaking on a shaker set at 50 rpm for 5 minutes at room temperature. Aspirate the PBST Probing Buffer. 11. Repeat Step 10 four more times using fresh PBST Probing Buffer each time to obtain a total of 5 wash steps. 12. Proceed immediately to Drying the Microarray.

scan_protocol: The scanning time for each array is ~7-8 minutes. 1. Start the appropriate array acquisition and analysis software on the computer connected to the fluorescence microarray scanner. 2. Open the microarray enclosure on the scanner. 3. Place the ProtoArray® Microarray in the holder such that the nitrocellulosecoated side of the array faces the laser source and barcode on the array is closest to the outside of the instrument. 4. Close the microarray enclosure on the scanner. 5. Set the following settings to image the microarray: • Wavelength: 635 nm • PMT Gain: 600 • Laser Power: 100% • Pixel Size: 10 μm • Lines to Average: 1.0 • Focus Position: 0 μm 6. Preview the microarray. Adjust settings, if needed. Scan the microarray in detail and include the barcode for record 7. Save the image to a suitable location as ‘multi-image TIFF’ file. Remove the microarray from the scanner. 8. Proceed to downloading lot-specific information available on the ProtoArray® Central Portal, 9. Using GenePix® Pro microarray data acquisition software adjust the subarray grid to ensure the grid is in proper location for each subarray. After the grid is properly adjusted and all features are aligned, utilize the automatic spot finding functionalities of the image acquisition software program, if desired. Then, acquire the pixel intensity data for each feature by clicking the Analyze button in GenePix® Pro, and save/export the results as a .GPR (GenePix® Results) file

data_processing: Raw data results in replicates are averaged and log normalized such that the second highest concentration of postitve control "Human IgG" is positioned at log 7 on a scale of upto log 10.

label: Alexa Fluor 647

molecule: other

source_name: serum sample from an AML patient 16 months after bone marrow transplantation

label_protocol: Add 5 ml Alexa Fluor® 647 (secondary) antibody solution to the incubation tray at the indented numeral end of the tray without touching the array surface. Allow the solution to flow across the array surface. Avoid pipetting solution directly onto the array surface

extract_protocol:
1. Draw 4.5 mL of blood into red top tubes
2. Let stand for 30 minutes until clot is formed
3. Centrifuge the tube for 5 minutes at 2000g using a swing-out rotor or other non-desk top centrifuge
4. Transfer (pipette) the clear supernatant (serum) carefully without disturbing the clot, to a 5 mL labeled cryotube

tag: fluid

value: serum from an AML patient 16 months after bone marrow transplantation

tag: gender

value: Female


description: Gene expression profile afterE.coli O157:H7 growth in Penassay broth rep 4


description: Gene expression profile afterE.coli O157:H7 growth in the presence of Hep-2 cells rep 3

value: 6 hour regrowth with HEP-2 cells


description: Gene expression profile afterE.coli O157:H7 growth in Penassay broth rep 3


title: 18m_post-transplantation

source_name: serum sample from an AML patient 18 months after bone marrow transplantation

value: serum from an AML patient 18 months after bone marrow transplantation


description: Gene expression profile afterE.coli O157:H7 growth in the presence of Hep-2 cells rep 2


description: Gene expression profile afterE.coli O157:H7 growth in Penassay broth rep 2


title: 14m_post-transplantation

source_name: serum sample from an AML patient 14 months after bone marrow transplantation

value: serum from an AML patient 14 months after bone marrow transplantation


title: 12m_post-transplantation

source_name: serum sample from an AML patient 12 months after bone marrow transplantation

value: serum from an AML patient 12 months after bone marrow transplantation


description: Gene expression profile afterE.coli O157:H7 growth in minimal media rep 2


title: 2m_post-transplantation

source_name: serum sample from an AML patient 2 months after bone marrow transplantation

value: serum from an AML patient 2 months after bone marrow transplantation


title: 11m_post-transplantation

source_name: serum sample from an AML patient 11 months after bone marrow transplantation

value: serum from an AML patient 11 months after bone marrow transplantation


description: Gene expression profile afterE.coli O157:H7 growth in the presence of Hep-2 cells rep 4


title: Pre_transplantation

source_name: serum sample from an AML patient before bone marrow transplantation

value: serum from an AML patient before bone marrow transplantation


title: Donor_for transplantation

description: Donor_for transplantation

source_name: serum sample from donor before bone marrow transplantation

value: serum from donor before bone marrow transplantation

value: Male


title: 1m_post-transplantation

source_name: serum sample from an AML patient 1 month after bone marrow transplantation

value: serum from an AML patient 1 month after bone marrow transplantation


description: Gene expression profile afterE.coli O157:H7 growth in Penassay broth rep 1


title: LSAGE_Bladder_Cancer_B_hs0265

description:
CGAP_Numeric_library_ID: 2259
Tagging_enzyme: Mme I
Library_producer: Martin Hirst, Functional Genomics Lab
Laboratory: Marco Marra, Genome Sciences Centre, Vancouver, Canada

source_name: bladder, cancer, bulk, long sage, slx-sage, solexa sage, t4ag3, male

value: bladder

value: bulk


description: Gene expression profile afterE.coli O157:H7 growth in minimal media rep 1

value: 6 hour regrowth in minimal medium


title: TGCT_Methylation_hg17_Chip_3

status: Public on Mar 18 2009

type: genomic

first: Hoi Hung

last: Cheung

address: 49 Convent Dr, Rm.2C08 Bldg.49

institute: NICHD

description: TGCT MeDIP-chip technical replicates 1-3, Chip C

hyb_protocol: Biotin-labeled DNA was hybridized to each array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. The hybridization mix was removed from these arrays and reused to hybridize the remaining arrays. Hybridized arrays were washed and stained on the Affymetrix Fluidic Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner GCS3000 7G.

data_processing:
CEL files from tiling arrays were analyzed by Tiling Analysis Software (TAS). Arrays from each group (cancer vs normal) were quantile-normalized and differential methylation between groups of tumor and normal was compared by choosing the “two-sample comparison analysis” option in TAS. A two-sided test was performed to evaluate both hypermethylation and hypomethylation. Transfrags (or DMRs) were generated by Interval Analysis with a p-value cutoff at 20 (p < 0.01) and a bandwidth of 275. Transfrags generated by p-value cutoff with a positive signal difference were defined as hypermethylation while those of negative difference were defined as hypomethylation.

signal.bar files store the signal comparison between normal and tumor cells. Pvalue.bar files store the p-value (-10log10) of each probe. NT2-IP CEL files correspond to Ntera2 DNA hybridizations, and HT-IP CEL files correspond to CRL-7002 DNA hybridizations.

molecule: genomic DNA

source_name: MeDIP DNA from cultured testicular cancer cells

label_protocol: Amplified DNA samples (9 μg) were enzymatically fragmented and biotin-labeled using the WT Labeling Kit (Affymetrix).

extract_protocol: Genomic DNA was extracted from cultured cells using Gentra Puregene Kit (Qiagen) and then sonicated on ice to give random fragments of 100-500 bp.

tag: cell line

tag: tissue

value: testis

tag: antibody

value: mouse anti-5-methylcytidine monoclonal antibody

source_name: MeDIP DNA from cultured normal testis cells


description: Gene expression profile afterE.coli O157:H7 growth in the presence of Hep-2 cells rep 1


title: Set B Squamous cell carcinoma Scc173

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

hyb_protocol: The Cy3/Cy5–labeled targets were hybridized overnight to human promoter array slide at 42jC in the presence of 5  SSC, 0.1% SDS, 25% formamide, and Cot1 blocking solution. Slides were washed following the Corning protocol (Corning, Inc.).

scan_protocol: Arrays were scanned with a Perkin Elmer Scanarray Express Microarray Scanner (Perkin Elmer, Inc., Wellesley, MA).

data_processing: Microarray data were retrieved with a Quantarray Microarray Analysis Software (Perkin Elmer, Inc.).

source_name: Pooled Samples, as reference.

label_protocol: PCR products were purified and 1 mg of DNA was labeled with Cy3 or Cy5 using Ready-To-Go DNA Labeling Beads (Amersham Biosciences).

extract_protocol: QiaGen DNeasy extraction of genomic DNA was performed according to the manufacturer's instructions.

tag: sample

value: Pooled Samples, as reference.

source_name: Cervical Squamous Cell Carcinoma

tag: disease state

value: Cervical Squamous Cell Carcinoma


title: Set B Cervical adenocarcinoma Acc037

source_name: Cervical Adenocarcinoma

value: Cervical Adenocarcinoma


title: Set B Cervical adenocarcinoma Acc166


title: Set B Cervical adenocarcinoma Acc188


title: Set B Cervical adenocarcinoma Acc132


title: Set B Squamous cell carcinoma Scc036


title: Set B Squamous cell carcinoma Scc020


title: TGCT_Methylation_hg17_Chip_2

description: TGCT MeDIP-chip technical replicates 1-3, Chip B

value: male


title: Set A Squamous cell carcinoma Scc036


title: Set B Cervical adenocarcinoma Acc133


title: Set B Squamous cell carcinoma Scc167


title: TGCT_Methylation_hg17_Chip_4

description: TGCT MeDIP-chip technical replicates 1-3, Chip D

data_processing:
CEL files from tiling arrays were analyzed by Tiling Analysis Software (TAS). Arrays from each group (cancer vs normal) were quantile-normalized and differential methylation between groups of tumor and normal was compared by choosing the “two-sample comparison analysis” option in TAS. A two-sided test was performed to evaluate both hypermethylation and hypomethylation. Transfrags (or DMRs) were generated by Interval Analysis with a p-value cutoff at 20 (p < 0.01) and a bandwidth of 275. Transfrags generated by p-value cutoff with a positive signal difference were defined as hypermethylation while those of negative difference were defined as hypomethylation.

signal.bar files store the signal comparison between normal and tumor cells. Pvalue.bar files store the p-value (-10log10) of each probe.


title: Set A Cervical adenocarcinoma Acc188


title: Set B Cervical adenocarcinoma Acc003


title: Set A Squamous cell carcinoma Scc173


title: Set A Squamous cell carcinoma Scc020


title: Rice Control 1

city: Wuhan

first: Kabin

last: Xie

state: Hubei

address: Shizi Shan Street

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agriculture University

description: shoots of Zhonghua11, biological rep1 (WT-1)

hyb_protocol: standard Affymetrix procedures

scan_protocol: GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.

data_processing: Affymetrix ® GeneChip® Operating SoftwareVersion1.0

label: Biotin

organism: Oryza sativa Japonica Group

source_name: Rice Control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Sterilized seeds of transgenic plants and wild type were germinated in MS medium. Positive transgenic plants were selected by adding 50 mM hygromycin for S58S, or 50 mM G418 for S59R into the medium. Ten-day-old uniform seedlings were transferred to hydroponics culture medium and 1-month-old whole plants were collected for microarray analysis. All transgenic plants were prechecked by real time RT-PCR for the expression level of OsSKIPa to confirm overexpression or suppression of the gene.

extract_protocol: TRIzol(Invitrogen, Carlsbad, CA, USA) extraction of total RNA was performed according to the manufacturer's instructions.

tag: wild type


title: TGCT_Methylation_hg17_Chip_1

description: TGCT MeDIP-chip technical replicates 1-3, Chip A


title: TGCT_Methylation_hg17_Chip_7

description: TGCT MeDIP-chip technical replicates 1-3, Chip G


title: Set A Squamous cell carcinoma Scc167


title: TGCT_Methylation_hg17_Chip_6

description: TGCT MeDIP-chip technical replicates 1-3, Chip F


title: TGCT_Methylation_hg17_Chip_5

description: TGCT MeDIP-chip technical replicates 1-3, Chip E


title: Rice Control 2

description: shoots of Zhonghua11, biological rep2 (WT-2)


title: Set A Cervical adenocarcinoma Acc166


title: Set A Cervical adenocarcinoma Acc133


title: Set A Cervical adenocarcinoma Acc132


title: Set A Cervical adenocarcinoma Acc037


title: Rice suppressed OsSKIPa, biological repeat 3

description: shoots of S59R, biological rep3 (S59R-3)

source_name: Rice suppressed OsSKIPa

tag: OsSKIPa suppressed plants


title: Rice overexpressed OsSKIPa, biological repeat 2

description:
shoots of S58S, biological rep2
S58S-2

source_name: Rice overexpressed OsSKIPa

tag: OsSKIPa over-xpressed plants


title: Rice suppressed OsSKIPa, biological repeat 1

description: shoots of S59R, biological rep1 (S59R-1)


title: UCD171

status: Public on Mar 17 2009

city: Madison

first: Hui

last: Cai

address: 1605 Linden Dr

institute: University of Wisconsin

description: Comparative genome hybridization

hyb_protocol: Reactions containing 1 μg labeled DNA were used for hybridization at the Utah State University Center for Integrated Biosystems Affymetrix core facility (Logan, UT).

scan_protocol: Genechips were scanned using Affmetrix GeneChip Scanner 3000.

data_processing: Statistical analysis of microarray data was done by R (www.r-project.org). Array images were reduced to intensity values for each probe and all arrays that met acceptable quality control criteria were used for further analysis. Array pre-processing (background correction, normalization, and summarization) was performed using the Robust Multi-array Average (RMA) method (Bolstad et al. 2003) using Bioconductor (http://www.bioconductor.org). Cutoff values for presence/absence determination were selected empirically based on hybridization signal intensity from negative (Lb. helveticus CNRZ 32) and positive (from hybridization with Lb. casei ATCC 334 DNA) probe controls. The cutoff value set for this dataset is 5.3.

organism: Lacticaseibacillus casei

source_name: Lactobacillus casei UCD171, plant

label_protocol: Five micrograms of genomic DNA was fragmented and labeled according to instructions for labeling mRNA for antisense prokaryotic arrays (Affymetrix Inc.).

growth_protocol: Lactobacillus casei strains were prepared from frozen stock by two transfers in MRS broth (BD Biosciences), without shaking, for 16–18 h at 37 °C.

extract_protocol: Genomic DNA was extracted using a MasterPureTM Gram Positive DNA Purification Kit (Epicentre, Madison, WI).

treatment_protocol: No treatment.

tag: ecological niche of isolation

value: plant materials (wine)

tag: strain


title: Rice overexpressed OsSKIPa, biological repeat 1

description: shoots of S58S, biological rep1 (S58S-1)


title: 12A

description: Comparative genome hybridization

source_name: Lactobacillus casei 12A, plant

value: plant materials (silage)


title: Set A Cervical adenocarcinoma Acc003


title: A2-309

description: Comparative genome hybridization

source_name: Lactobacillus casei A2-309, plant


title: 32G

description: Comparative genome hybridization

source_name: Lactobacillus casei 32G, plant


title: UCD174

description: Comparative genome hybridization

source_name: Lactobacillus casei UCD174, plant


title: USDA-P

description: Comparative genome hybridization

source_name: Lactobacillus casei USDA-P, plant

value: plant materials (pickle)

value: USDA-P


title: 21/1

description: Comparative genome hybridization

source_name: Lactobacillus casei 21/1, plant


title: DMSO treated RH strain, ChIP-on-chip acetylated H4

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

description:
Toxoplasma gondii DMSO-treated parasite.
Immunoprecipitated DNA with the acH4(K5-K8-12-K16) antibody from DMSO treated RH strain.
Input genomic DNA (from DMSO-treated RH strain)

data_processing: After background correction, log base 2 ratios of immunoprecipitated DNA signal over input DNA signal is given in this table. Data not normalized.

organism: Toxoplasma gondii

source_name: Toxoplasma gondii RH strain

extract_protocol: For ChIP-chip experiments freshly released tachyzoites (~5 x 109 at ~12 x 107 parasites/mL) were fixed for 15 min in 1% formaldehyde. Increase in AcH4 signals was verified by immunoblot to verify that FR235222 treatment was effective. To prepare chromatin samples, fixed parasites were lysed in MNase buffer (0.32 M Sucrose, 50 mM Tris-HCl pH7.8, 4 mM MgCl2, 3 mM CaCl2, 100 mM NaCl, 0.25% (v/v) NP40, 5%  (v/v) glycerol, protease inhibitor EDTA-free cocktail (Roche)) and DNA was digested for 4 min at 37°C by MNase (2 units/mL). Digestion was stopped with 20 mM EDTA and chromatin was recovered in the soluble fraction after centrifugation at 10,000 g at 4°C; this constituted the S1 fractions. Pelleted materials were resuspended in dialysis buffer (1mM Tris-HCl pH7.8, 0.2 mM EDTA) containing 1 mM PMSF and protease inhibitor cocktail (Roche®) and dialyzed overnight at 4°C against the same solution. Then dialyzed materials were centrifuged and supernatant were harvested; this constitutes the S2 fractions. For chromatin immunoprecipitations, fractions S1 and S2 were pooled and DNA quality was verified by electrophoresis on 2% agarose gels; oligonucleosome ladder of 100-1000 bp were obtained. The histone-DNA complexes were immunoprecipitated with anti-acetyl histone H4 (Upstate®, catalog # 06-866) antibodies according to NimbleGen’s protocol (http://www.chiponchip.org/index.html). NimbleGen's "Protocols for Chromatin Immunoprecipitation and Amplification" (http://www.vmrf.org/researchcenters/gene-chip/chromatin_immunoprecipitation.pdf).

treatment_protocol: Freshly released tachyzoites were needle-passed, and filtered using a 3-µm nucleopore membrane. Parasites were resuspended into fresh DMEM supplemented with 10% (v/v) FBS and 25 mM HEPES buffer pH7.2. Parasites were incubated in the presence of FR235222 (40 nM) or DMSO (0.1%) for 4 h at 37°C with 5% CO2.

tag: agent

tag: fraction

value: IP

tag: chip antibody

value: anti-acetyl histone H4 [acH4(K5-K8-12-K16)]

value: DMSO

value: input genomic DNA


title: T7136

description: Comparative genome hybridization

source_name: Lactobacillus casei T7136,  human

value: human sources (blood)


title: A2-362

description: Comparative genome hybridization

source_name: Lactobacillus casei A2-362, plant


title: T71499

description: Comparative genome hybridization

source_name: Lactobacillus casei T71499,  human


title: L9

description: Comparative genome hybridization

source_name: Lactobacillus casei L9,  human

value: human sources (feces)


title: FR235222 treated RH strain, ChIP-on-chip acetylated H4

description:
Toxoplasma gondii FR235222-treated parasite.
Immunoprecipitated DNA with the acH4(K5-K8-12-K16) antibody from FR235222 treated RH strain.
Input genomic DNA (from FR235222-treated RH strain)

label_protocol: NimbleGen’s protocol (http://www.chiponchip.org/index.html). NimbleGen's "Protocols for Chromatin Immunoprecipitation and Amplification" (http://www.vmrf.org/researchcenters/gene-chip/chromatin_immunoprecipitation.pdf).


title: CRF28

description: Comparative genome hybridization

source_name: Lactobacillus casei CRF28,  human


title: DN

description: Comparative genome hybridization

source_name: Lactobacillus casei DN,  human

value: DN


title: Cervical Cancer Replicate 4

description: replicate array 4

hyb_protocol: Samples were sent to NimbleGen Inc. for the labeling/hybridizing/scanning services.

data_processing: Tukey bi-weight mean scaling

source_name: Cervical Squamous Cell Carcinoma Pool 2

source_name: Cervical Adenocarcinoma Pool 2


title: 83M4

description: Comparative genome hybridization

source_name: Lactobacillus casei 83M4, cheese

value: cheese (Denmark)


title: 7A1

description: Comparative genome hybridization

source_name: Lactobacillus casei 7A1, cheese


title: L6

description: Comparative genome hybridization

source_name: Lactobacillus casei L6,  human


title: Cervical Cancer Replicate 3

description: replicate array 3

scan_protocol: Samples were sent to NimbleGen Inc. for the labeling/hybridizing/scanning services.


title: UW4

description: Comparative genome hybridization

source_name: Lactobacillus casei UW4, cheese

value: cheese (USA)


title: AR3_Control_CWR_R1

city: Baltimore

first: Hegang

last: Chen

address: 660 West Redwood Street

institute: University of Maryland School of Medicine

description: see manufacturer's web site at http://www.agilent.com/

hyb_protocol: Hybridization was carried out using the conditions specified in the Agilent Human Whole Genome Expression system.

scan_protocol: Scanned images were processed for quality assessment and preprocessing of image data using the Agilent Feature Extraction software (Agilent Technologies)

data_processing: The software quantifies feature signals and their background, performs dye normalization and calculates feature log ratios and error estimates. The error estimates, based on an extensive error model and pixel level statistics calculated from the feature and background for each spot, are used to generate a p-value for each log ratio.

source_name: CWR-R1 cell treated with shAR3-1

tag: CWR-R1 cells treated with shAR3-1

source_name: scrambled shRNA control of CWR-R1 cells

tag: The scrambled shRNA control of CWR-R1 cells


title: AR_Control_CWR_R1

source_name: CWR-R1 cell treated with shARa

label_protocol: see manufacturer's web site at http://www.agilent.com/

tag: CWR-R1 cell treated with shARa


title: Cervical Cancer Replicate 1

description: replicate array 1

source_name: Cervical Squamous Cell Carcinoma Pool 1

label_protocol: Samples were sent to NimbleGen Inc. for the labeling/hybridizing/scanning services.

source_name: Cervical Adenocarcinoma Pool 1


title: ASCC 1087

description: Comparative genome hybridization

source_name: Lactobacillus casei ASCC 1087, cheese

value: cheese (Australia)

value: ASCC 1087


title: Cervical Cancer Replicate 2

description: replicate array 2

value: Cervical Adenocarcinoma

value: Cervical Squamous Cell Carcinoma


title: UW1

description: Comparative genome hybridization

source_name: Lactobacillus casei UW1, cheese


title: M36

description: Comparative genome hybridization

source_name: Lactobacillus casei M36, cheese


title: ATCC 334

description: Comparative genome hybridization

source_name: Lactobacillus casei ATCC 334, cheese

value: ATCC 334


title: S. pombe Mis4 binding pattern, G1 (cdc10-129)

first: Christine

middle: Katrin

last: Schmidt

address: 41 Library Drive, Bldg. 41, C619

department: LRBGE

institute: NCI (NIH)

description: no additional information

hyb_protocol: Labeled DNA was hybridised to microarrays in an Affymterix Gene Chip Hybridisation Oven 640 for 16h at 42°C & 60rpm. For washing and staining the EukGe_WS1_v4_450 fluidics protocol was run on an Affymetrix Gene Chip Fluidics Station (version 450). Staining included one step with SAPE.

scan_protocol: Microarray scanning was performed with an Affymetrix Gene Chip Scanner 3000.

data_processing: The Affymetrix Gene Chip Operating Software GCOS, version 1.4, was used for data processing.

label: biotin-11-ddATP (NEL548)

organism: Schizosaccharomyces pombe

source_name: Chromatin-immunoprecipitated DNA

label_protocol: DNA was labeled with biotin-11-ddATP using terminal transferase TdT (Roche, 400U/µl).

growth_protocol: Cells were arrested for 3.5 h at 37°C in rich medium (YE4S) in G1 using the thermosensitive cdc10-129 mutant.

extract_protocol:
ChIP and microarray analysis were largely performed as described previously (Katou et al., 2003, see below). Essentially, 2 x 10^9 cells were fixed with 1% formaldehyde for 30 min at room temperature. Whole cell extracts were prepared using a multi-beads shocker (Yasui Kikai). Cell extracts were sonicated (Sanyo Soniprep 150) to fragment DNA into 400 - 800 bp long pieces which were processed for ChIP. Anti-Pk antibodies (SV5-Pk1, Serotec), in conjunction with protein-A coupled magnetic Dynabeads were used against the Pk-tagged cohesin loader subunit Mis4. Reversal of the cross-linking was achieved by incubating the eluted immunoprecipitates at 65°C overnight. Genomic DNA was purified and amplified by random PCR.
Reference:
Katou, Y., Kanoh, Y., Bando, M., Noguchi, H., Tanaka, H., Ashikari, T., Sugimoto, K. and Shirahige, K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature, 424, 1078-1083.


title: AR3_Control_22Rv1

hyb_protocol: Hybridization was carried out using the conditions specified in the Agilent Human Whole Genome Expression system. See manufacturer's web site at http://www.agilent.com/

scan_protocol: Scanned images were processed for quality assessment and preprocessing of image data using the Agilent Feature Extraction software. See manufacturer's web site at http://www.agilent.com/

source_name: 22Rv1 cell treated with shAR3-1

extract_protocol: see manufacturer's web site at http://www.agilent.com/

tag: 22Rv1 cells treated with shAR3-1

source_name: scrambled shRNA control of 22Rv1 cells

tag: The scrambled shRNA control of 22Rv1 cells


title: WSU-NHL1

status: Public on Mar 16 2009

city: Boston

first: Cheng

last: Li

state: MA

address: 44 Binney St

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

hyb_protocol: High molecular weight DNA from DLBCLs and sex-matched normal control DNAs (Stratagene) were differentially labeled with Cy3 and Cy5  and co-hybridization to the array CGH platform, as recommended by the manufacturer (Agilent Technologies).

scan_protocol: The arrays were scanned and the intensity of the hybridization signals obtained using the Feature Extraction software (Agilent Technologies).

data_processing: The log10 data of the 44K CGH probes (LogRatio column in the  individual text files) of all array CGH samples were organized into a single data file. The  data were read into to the dChip software (www.dchip.org, version 6/7/08) and the log10  ratios were converted to log2 ratios. The probe chromosome and position information  were used to visualize the data in dChip according to probe genome positions. Data  quality check. We inspected the sample quality visually according the log2 ratio curves  and excluded 13 samples with noisy or very low signals throughout the genome. The 77  remaining samples were used in the following analyses. First, for each probe, we  computed the median log2 ratio across all samples and subtracted this median value from  all samples. This step removed regional systematic gain or loss patterns, which are likely  due to the bias in the hybridization process or the control channel sample. Second, data  quality verification was performed for the each probe included in the array. We observed  the existence of “spike probes”, which showed significantly outlying higher or lower  signals comparing to their neighboring probes in multiple samples (defined as absolute  value of log 2 ratio >= 1 in more than 20% of samples). Thus, we computed a correlation  score across all samples between each probe data vector and the average data vector of all  “spike probes”; a threshold >0.5 was then used to exclude these underperforming probes  (n= 4158) from the downstream analysis. Thus, the actual number of probes in miRTile is  37113 and its resolution (mean probe spacing) in the focally covered areas is 319bp.  Obtaining the miRNA-level data. To obtain the miRNA genes copy number data we first  organized the probes into miRNA regions. Each region extends the positions of the  precursor miRNAs by ~ 17 Kb in the upstream and downstream directions to include all  the CGH probes in that region; two or more such extended areas could be merged into  one miRNA region (due to the common clustering of miRNA genes) containing multiple  miRNA genes. The log2 ratio values of all the probes in a region were averaged to obtain  the miRNA region-level log2 ratios and copy number summary plots displayed the  proportion of the samples that have copy number gain (>=2.5) or loss (<=1.5) for all  miRNA regions.

source_name: DLBCL cell line

growth_protocol: Primary tumors were flash frozen after excision. Cell lines were grown in RPMI 10% serum prior to DNA isolation

extract_protocol: High molecular weight genomic DNA was isolated from the frozen DLBCL samples and DLBCL cell lines using the Blood & Cell Culture DNA Maxi Kit from Qiagen. DNA quality was verified by spectrophotometry and gel electrophoresis.

tag: cell line

value: DLBCL

source_name: sex-matched normal control DNA

tag: tissue

value: normal


title: USC-DHL-1

label_protocol: High molecular weight DNA from DLBCLs and sex-matched normal control DNAs (Stratagene) were differentially labeled with Cy3 and Cy5  and co-hybridization to the array CGH platform, as recommended by the manufacturer (Agilent Technologies).


title: SUDHL6


title: SUDHL10


title: Toledo


title: 7R1

description: Comparative genome hybridization

source_name: Lactobacillus casei 7R1, cheese


title: SUDHL8


title: RC-K8


title: SUDHL16


title: SUDHL9


title: SUDHL5


title: SUDHL4


title: NU-DUL-1


title: Pfeiffer


title: NU-DHL-1


title: normalDNA

source_name: normal genomic DNA


title: normal DNA dyeswap


title: LY8


title: Input Samples for MCF7 Cells (Whole Genome # 1, Replicate # 3)

city: Houston

first: Sujun

last: Hua

state: Tx

address: 1901 East Rd

institute: MD Anderson Cancer Center

description: Input DNA from MCF-7 cells hybridized on Affymetrix whole genome tiling arrays 2.0R.

hyb_protocol: According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).

data_processing: Tiling array data were normalized and analyzed as described (Cawley et al, 2004).  Briefly, raw data were normalized within ChIP and control groups and for each genomic position a local dataset composed of intensities for all adjacent probes within a window of +/-250 bp was generated. A one-tailed Wilcoxon Rank Sum test was then applied to compare control and ChIP experiments and was performed in a sliding window across all tiled genomic regions.  Significantly enriched probes (p < 1e-4) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions.

source_name: Chromatin Immunoprecipitated DNA

label_protocol: ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.

extract_protocol: According to the standard chromatin extraction protocol (Shang et al., 2000).

treatment_protocol: MCF7 Cells were hormone-deprived for 3 days and then were treated with nuclear receptor ligand or vehicle at 80% confluence.

tag: cell type

value: MCF7 cells


title: LY7


title: Input Samples for MCF7 Cells (Whole Genome # 1, Replicate # 1)

scan_protocol: According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).


title: Control for non-specific binding for GFP antibody (Whole Genome # 1, Replicate # 3)

description: Chromatin immunoprecipitation control experiments on Affymetrix whole genome tiling arrays 2.0R with GFP antibodies  in MCF7 cells (ChIP).

treatment_protocol: ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

value: wild type MCF7 cells

tag: antibody

value: Goat anti-eGFP


title: GATA3 localization in MCF7 (Whole Genome # 1, Replicate # 2)

description: Chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R for GATA3 in MCF7 cells (ChIP).

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.  Prior to hormone or vehicle (100% DMSO) treatments, cells were changed to hormone-depleted media for 72 hours by using 10% charcoal-stripped calf serum.

treatment_protocol: MCF7 Cells were hormone-deprived for 3 days and then were treated with vehicle at 80% confluence.  ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

value: transgenic MCF7 cells

tag: transcription factor

tag: tag

value: modified LAP (localization and affinity purification) tag containing green fluorescent protein (GFP)

value: Goat anti-GFP


title: Control for non-specific binding for GFP antibody (Whole Genome # 1, Replicate # 2)


title: Input Samples for MCF7 Cells (Whole Genome # 1, Replicate # 2)


title: Control for non-specific binding for GFP antibody (Whole Genome # 1, Replicate # 1)


title: FoxA1 localization in MCF7 (Whole Genome # 1, Replicate # 3)

description: Chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R for FoxA1 in MCF7 cells (ChIP).

value: goat anti-foxa1 (abcam:ab5089)


title: GATA3 localization in MCF7 (Whole Genome # 1, Replicate # 3)


title: GATA3 localization in MCF7 (Whole Genome # 1, Replicate # 1)


title: AR_Control_22Rv1

source_name: 22Rv1 cell treated with shARa

tag: 22Rv1 cell treated with shARa

tag: The scramled shRNA control of 22Rv1 cells


title: LY1


title: LY4


title: FoxA1 localization in MCF7 (Whole Genome # 1, Replicate # 1)


title: RARA localization in MCF7 (Whole Genome # 1, Replicate # 3)

description: Chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R for RARA in MCF7 cells (ChIP).

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.  Prior to hormone (AM580 at 100 nM) or vehicle (100% DMSO) treatments, cells were changed to hormone-depleted media for 72 hours by using 10% charcoal-stripped calf serum.

treatment_protocol: MCF7 Cells were hormone-deprived for 3 days and then were treated with 100 nM AM580 at 80% confluence.  ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

value: RARA


title: FoxA1 localization in MCF7 (Whole Genome # 1, Replicate # 2)


title: RARG localization in MCF7 (Whole Genome # 1, Replicate # 1)

description: Chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R for RARG in MCF7 cells (ChIP).

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.  Prior to hormone (CD437 at 100 nM) or vehicle (100% DMSO) treatments, cells were changed to hormone-depleted media for 72 hours by using 10% charcoal-stripped calf serum.

treatment_protocol: MCF7 Cells were hormone-deprived for 3 days and then were treated with 100 nM CD437 at 80% confluence.  ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

value: RARG


title: RARG localization in MCF7 (Whole Genome # 1, Replicate # 2)


title: LY3


title: Karpas-422


title: Karpas-1106p

source_name: MLBCL cell line

value: MLBCL


title: FL-318


title: LY19


title: LY18


title: HT


title: Ctrl 1 MCy3 FCy5 1.2


title: 7970

source_name: Frozen DLBCL sample

tag: tumor site

value: Extra-nodal

tag: cell of origin classifiction defined by ihc

value: GCB

tag: infiltrating t-cells


title: Farage


title: RARA localization in MCF7 (Whole Genome # 1, Replicate # 2)


title: Ctrl 1 FCy3 MCy5 1.1


title: 7924

value: Lymph Node

value: Non-GCB


title: 7295


title: Input Samples for MCF7 Cells (Whole Genome # 4, Replicate # 3)


title: SUDHL7


title: Input Samples for MCF7 Cells (Whole Genome # 4, Replicate # 2)


title: RARG localization in MCF7 (Whole Genome # 1, Replicate # 3)


title: RARA localization in MCF7 (Whole Genome # 1, Replicate # 1)