title: Hs 742.T

description: SNP array data from the CCLE


title: Hs 675.T

status: Public on Mar 20 2012

type: genomic

city: Cambridge

first: Nicolas

last: Stransky

state: MA

address: 7 Cambridge center

department: Cancer Program

country: USA

institute: Broad Institute

description: SNP array data from the CCLE

hyb_protocol: After denaturation, 200ul of sample are injected into a Genome-Wide Human SNP 6.0 array. Arrays are loaded in the GeneChip® Hybridization Oven 640 @ 50 °C temp, rotating arrays @ 60 rpm. Samples are hybridized for 16 to 18 hours.

scan_protocol: Genome-Wide Human SNP Array 6.0 are stained using the GeneChip® Fluidics Station 450 and scanned using the GeneChip® Scanner 3000

data_processing: The raw CEL files were normalized to copy number estimates using a GenePattern pipeline, as described in Cancer Genome Atlas Research Network et al, Nature, 2008, and hg18 Affymetrix probe annotations. Normalized copy number estimates (log2 ratios) were segmented using the Circular Binary Segmentation (CBS) algorithm, followed by median centering of the segment values to a value of zero in each sample.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: ATCC

label_protocol: PCR amplification fragments (200 and 1100 bp) are labeled using terminal deoxynucleotidyl transferase following the Affymetrix GenomeWideSNP_6 protocol

growth_protocol: Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached.  Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.

extract_protocol: DNA was extracted from frozen cell pellets, containing an average cell count of 4.5 million cells, using the Qiagen Gentra Puregene method following the manufacturers recommendations. Samples were quantified using picogreen on a ThermoScientific Varioskan Flash instrument.

tag: primary site

tag: histology

value: carcinoma


title: Hs 729

description: SNP array data from the CCLE

value: rhabdomyosarcoma


title: Hs 578T

description: SNP array data from the CCLE

value: breast

tag: histology subtype1


title: Hs 822.T

description: SNP array data from the CCLE

value: bone


title: Hs 821.T

description: SNP array data from the CCLE


title: Hs 746T

description: SNP array data from the CCLE

value: stomach


title: Hs 819.T

description: SNP array data from the CCLE

value: chondrosarcoma


title: Hs 294T

description: SNP array data from the CCLE

value: skin


title: Hs 600.T

description: SNP array data from the CCLE


title: Hs 706.T

description: SNP array data from the CCLE


title: Hs 611.T

description: SNP array data from the CCLE


title: Hs 616.T

description: SNP array data from the CCLE


title: Hs 606.T

description: SNP array data from the CCLE


title: Hs 840.T

description: SNP array data from the CCLE

value: other

value: papilloma


title: Hs 683

description: SNP array data from the CCLE

value: glioma


title: Hs 343.T

description: SNP array data from the CCLE


title: Hs 604.T

description: SNP array data from the CCLE


title: Hs 739.T

description: SNP array data from the CCLE


title: Hs 281.T

description: SNP array data from the CCLE


title: Hs 618.T

description: SNP array data from the CCLE

value: lung

value: adenocarcinoma


title: Hs 229.T

description: SNP array data from the CCLE


title: Hs 274.T

description: SNP array data from the CCLE


title: HOS

description: SNP array data from the CCLE

value: osteosarcoma


title: HPAC

description: SNP array data from the CCLE

value: pancreas


title: HN

description: SNP array data from the CCLE

source_name: DSMZ


title: HPB-ALL

description: SNP array data from the CCLE


title: HLF-a

description: SNP array data from the CCLE


title: HEC-1-B

description: SNP array data from the CCLE

value: endometrium


title: HLE

description: SNP array data from the CCLE

source_name: HSRRB

value: liver


title: HGC-27

description: SNP array data from the CCLE

source_name: ECACC


title: HPAF-II

description: SNP array data from the CCLE


title: HEC-6

description: SNP array data from the CCLE


title: HH

description: SNP array data from the CCLE


title: Hep 3B2.1-7

description: SNP array data from the CCLE


title: HMCB

description: SNP array data from the CCLE


title: Hs 172.T

description: SNP array data from the CCLE


title: HEC-50B

description: SNP array data from the CCLE


title: Hey-A8

description: SNP array data from the CCLE

source_name: Academic Lab

value: ovary


title: HEC-1-A

description: SNP array data from the CCLE

value: carcinoma


title: HEC-265

description: SNP array data from the CCLE


title: HEL

description: SNP array data from the CCLE


title: HEL 92.1.7

description: SNP array data from the CCLE


title: HEC-251

description: SNP array data from the CCLE


title: HL-60

description: SNP array data from the CCLE


title: Hep G2

description: SNP array data from the CCLE


title: HEC-59

description: SNP array data from the CCLE


title: HLF

description: SNP array data from the CCLE


title: HD-MY-Z

description: SNP array data from the CCLE


title: HDLM-2

description: SNP array data from the CCLE


title: HEC-108

description: SNP array data from the CCLE


title: HDQ-P1

description: SNP array data from the CCLE


title: HCT-15

description: SNP array data from the CCLE


title: HCT 116

description: SNP array data from the CCLE


title: HCC-95

description: SNP array data from the CCLE

source_name: KCLB


title: HEC-151

description: SNP array data from the CCLE


title: HCC70

description: SNP array data from the CCLE


title: HCC-33

description: SNP array data from the CCLE


title: HCC-78

description: SNP array data from the CCLE


title: HCC38

description: SNP array data from the CCLE


title: HCC4006

description: SNP array data from the CCLE


title: HCC2935

description: SNP array data from the CCLE


title: HCC1937

description: SNP array data from the CCLE


title: HCC1806

description: SNP array data from the CCLE


title: HCC-366

description: SNP array data from the CCLE


title: HCC-15

description: SNP array data from the CCLE


title: HCC827

description: SNP array data from the CCLE


title: HCC1954

description: SNP array data from the CCLE


title: HCC-2279

description: SNP array data from the CCLE


title: HCC2218

description: SNP array data from the CCLE


title: HCC-44

description: SNP array data from the CCLE


title: HCC1569

description: SNP array data from the CCLE


title: HCC202

description: SNP array data from the CCLE


title: HCC-56

description: SNP array data from the CCLE


title: HARA

description: SNP array data from the CCLE


title: HCC1599

description: SNP array data from the CCLE


title: HCC1500

description: SNP array data from the CCLE


title: HCC1419

description: SNP array data from the CCLE


title: HCC2157

description: SNP array data from the CCLE


title: HCC1428

description: SNP array data from the CCLE


title: HCC1395

description: SNP array data from the CCLE


title: HCC-1195

description: SNP array data from the CCLE


title: HCC1187

description: SNP array data from the CCLE


title: HCC1143

description: SNP array data from the CCLE


title: GSU

description: SNP array data from the CCLE

source_name: RIKEN


title: H4

description: SNP array data from the CCLE


title: GRANTA-519

description: SNP array data from the CCLE


title: GI-1

description: SNP array data from the CCLE

value: gliosarcoma


title: GSS

description: SNP array data from the CCLE


title: GDM-1

description: SNP array data from the CCLE


title: HCC-1171

description: SNP array data from the CCLE


title: GMS-10

description: SNP array data from the CCLE


title: GCIY

description: SNP array data from the CCLE


title: GOS-3

description: SNP array data from the CCLE

value: astrocytoma


title: GCT

description: SNP array data from the CCLE


title: GA-10

description: SNP array data from the CCLE


title: GP2d

description: SNP array data from the CCLE


title: GB-1

description: SNP array data from the CCLE


title: GAMG

description: SNP array data from the CCLE


title: FU97

description: SNP array data from the CCLE


title: G-361

description: SNP array data from the CCLE


title: G-401

description: SNP array data from the CCLE


title: FaDu

description: SNP array data from the CCLE


title: ESS-1

description: SNP array data from the CCLE


title: EPLC-272H

description: SNP array data from the CCLE


title: F-36P

description: SNP array data from the CCLE


title: FU-OV-1

description: SNP array data from the CCLE


title: G-292, clone A141B1

description: SNP array data from the CCLE

value: bone


title: EFO-27

description: SNP array data from the CCLE


title: EN

description: SNP array data from the CCLE


title: EFO-21

description: SNP array data from the CCLE


title: EOL-1

description: SNP array data from the CCLE


title: G-402

description: SNP array data from the CCLE


title: EJM

description: SNP array data from the CCLE


title: EFM-192A

description: SNP array data from the CCLE

value: breast


title: ES-2

description: SNP array data from the CCLE


title: EFM-19

description: SNP array data from the CCLE


title: ECC10

description: SNP array data from the CCLE

value: stomach


title: EM-2

description: SNP array data from the CCLE


title: EFE-184

description: SNP array data from the CCLE


title: ECC12

description: SNP array data from the CCLE


title: EB1

description: SNP array data from the CCLE


title: EHEB

description: SNP array data from the CCLE


title: EBC-1

description: SNP array data from the CCLE


title: DV-90

description: SNP array data from the CCLE


title: EB2

description: SNP array data from the CCLE


title: FTC-133

description: SNP array data from the CCLE

value: thyroid


title: EC-GI-10

description: SNP array data from the CCLE

value: oesophagus


title: DU 145

description: SNP array data from the CCLE

value: prostate


title: DMS 153

description: SNP array data from the CCLE


title: DMS 79

description: SNP array data from the CCLE


title: DEL

description: SNP array data from the CCLE


title: DBTRG-05MG

description: SNP array data from the CCLE

value: glioma


title: DMS 273

description: SNP array data from the CCLE

value: lung


title: DK-MG

description: SNP array data from the CCLE


title: DND-41

description: SNP array data from the CCLE


title: DMS 53

description: SNP array data from the CCLE


title: DMS 454

description: SNP array data from the CCLE


title: DMS 114

description: SNP array data from the CCLE


title: DOHH-2

description: SNP array data from the CCLE


title: Detroit 562

description: SNP array data from the CCLE


title: DB

description: SNP array data from the CCLE


title: COV644

description: SNP array data from the CCLE


title: CPC-N

description: SNP array data from the CCLE


title: DLD-1

description: SNP array data from the CCLE

value: adenocarcinoma


title: DU4475

description: SNP array data from the CCLE


title: CW-2

description: SNP array data from the CCLE


title: D283 Med

description: SNP array data from the CCLE


title: DAN-G

description: SNP array data from the CCLE


title: COV362

description: SNP array data from the CCLE


title: COR-L95

description: SNP array data from the CCLE


title: Daudi

description: SNP array data from the CCLE


title: Daoy

description: SNP array data from the CCLE


title: COV504

description: SNP array data from the CCLE


title: D341 Med

description: SNP array data from the CCLE


title: COR-L88

description: SNP array data from the CCLE


title: COV318

description: SNP array data from the CCLE


title: COV434

description: SNP array data from the CCLE


title: COR-L279

description: SNP array data from the CCLE


title: COLO-849

description: SNP array data from the CCLE

value: skin


title: COR-L311

description: SNP array data from the CCLE


title: COR-L47

description: SNP array data from the CCLE


title: COR-L24

description: SNP array data from the CCLE


title: COLO 829

description: SNP array data from the CCLE


title: COLO-800

description: SNP array data from the CCLE


title: COLO 792

description: SNP array data from the CCLE


title: COLO-818

description: SNP array data from the CCLE


title: COLO 741

description: SNP array data from the CCLE


title: COLO 684

description: SNP array data from the CCLE


title: COLO-680N

description: SNP array data from the CCLE


title: COLO-704

description: SNP array data from the CCLE


title: COLO-679

description: SNP array data from the CCLE


title: COLO 668

description: SNP array data from the CCLE


title: COR-L105

description: SNP array data from the CCLE


title: COLO-699

description: SNP array data from the CCLE


title: COLO-783

description: SNP array data from the CCLE


title: COLO 205

description: SNP array data from the CCLE


title: COLO-320

description: SNP array data from the CCLE


title: CML-T1

description: SNP array data from the CCLE


title: CL-40

description: SNP array data from the CCLE


title: COR-L23

description: SNP array data from the CCLE


title: COLO-678

description: SNP array data from the CCLE


title: CMK-11-5

description: SNP array data from the CCLE


title: CMK-86

description: SNP array data from the CCLE


title: CL-34

description: SNP array data from the CCLE


title: CL-14

description: SNP array data from the CCLE


title: CMK

description: SNP array data from the CCLE


title: CJM

description: SNP array data from the CCLE


title: CCF-STTG1

description: SNP array data from the CCLE


title: CAL-78

description: SNP array data from the CCLE

value: chondrosarcoma

value: dedifferentiated


title: CGTH-W-1

description: SNP array data from the CCLE


title: CAS-1

description: SNP array data from the CCLE

source_name: ICLC


title: Capan-2

description: SNP array data from the CCLE

value: pancreas


title: CAL-85-1

description: SNP array data from the CCLE


title: CAMA-1

description: SNP array data from the CCLE


title: ChaGo-K-1

description: SNP array data from the CCLE


title: CAL-33

description: SNP array data from the CCLE


title: Caov-3

description: SNP array data from the CCLE

value: ovary


title: CCK-81

description: SNP array data from the CCLE

value: carcinoma


title: Caov-4

description: SNP array data from the CCLE


title: CHL-1

description: SNP array data from the CCLE


title: CAL-54

description: SNP array data from the CCLE

value: kidney


title: CAL-51

description: SNP array data from the CCLE


title: CL-11

description: SNP array data from the CCLE


title: CHP-126

description: SNP array data from the CCLE

value: neuroblastoma


title: Calu-1

description: SNP array data from the CCLE


title: CI-1

description: SNP array data from the CCLE


title: CAL-62

description: SNP array data from the CCLE


title: CHP-212

description: SNP array data from the CCLE


title: CAL 27

description: SNP array data from the CCLE


title: CFPAC-1

description: SNP array data from the CCLE


title: Capan-1

description: SNP array data from the CCLE


title: Calu-3

description: SNP array data from the CCLE


title: Calu-6

description: SNP array data from the CCLE


title: CAL-29

description: SNP array data from the CCLE


title: CAL-148

description: SNP array data from the CCLE


title: CAL-12T

description: SNP array data from the CCLE


title: Caki-2

description: SNP array data from the CCLE


title: CAL-120

description: SNP array data from the CCLE


title: BICR 22

description: SNP array data from the CCLE


title: BT-549

description: SNP array data from the CCLE


title: BV-173

description: SNP array data from the CCLE


title: CADO-ES1

description: SNP array data from the CCLE

value: bone


title: Caki-1

description: SNP array data from the CCLE


title: BICR 31

description: SNP array data from the CCLE


title: Becker

description: SNP array data from the CCLE


title: BT-474

description: SNP array data from the CCLE

value: breast


title: BxPC-3

description: SNP array data from the CCLE


title: CA46

description: SNP array data from the CCLE


title: BICR 56

description: SNP array data from the CCLE


title: BICR 6

description: SNP array data from the CCLE


title: BT-483

description: SNP array data from the CCLE


title: C3A

description: SNP array data from the CCLE

value: liver


title: BT-20

description: SNP array data from the CCLE


title: BL-70

description: SNP array data from the CCLE


title: C2BBe1

description: SNP array data from the CCLE


title: BDCM

description: SNP array data from the CCLE


title: BEN

description: SNP array data from the CCLE


title: C32

description: SNP array data from the CCLE


title: BFTC-905

description: SNP array data from the CCLE


title: BICR 18

description: SNP array data from the CCLE


title: BL-41

description: SNP array data from the CCLE


title: BHY

description: SNP array data from the CCLE


title: BHT-101

description: SNP array data from the CCLE

value: thyroid


title: BICR 16

description: SNP array data from the CCLE


title: BFTC-909

description: SNP array data from the CCLE


title: AsPC-1

description: SNP array data from the CCLE


title: BCP-1

description: SNP array data from the CCLE


title: AN3 CA

description: SNP array data from the CCLE

value: endometrium


title: AU565

description: SNP array data from the CCLE


title: BC-3C

description: SNP array data from the CCLE


title: ABC-1

description: SNP array data from the CCLE


title: AGS

description: SNP array data from the CCLE

value: stomach


title: AMO-1

description: SNP array data from the CCLE


title: ACC-MESO-1

description: SNP array data from the CCLE

value: pleura

value: mesothelioma


title: AZ-521

description: SNP array data from the CCLE


title: AML-193

description: SNP array data from the CCLE


title: A-673

description: SNP array data from the CCLE


title: ACHN

description: SNP array data from the CCLE


title: A3/KAW

description: SNP array data from the CCLE


title: A549

description: SNP array data from the CCLE

value: lung


title: A-704

description: SNP array data from the CCLE


title: Alexander cells

description: SNP array data from the CCLE


title: B-CPAP

description: SNP array data from the CCLE


title: A-375

description: SNP array data from the CCLE

value: skin


title: A4/Fuk

description: SNP array data from the CCLE


title: A-498

description: SNP array data from the CCLE


title: AM-38

description: SNP array data from the CCLE

value: glioma


title: A101D

description: SNP array data from the CCLE


title: A-253

description: SNP array data from the CCLE


title: A-204

description: SNP array data from the CCLE

value: rhabdomyosarcoma


title: 639-V

description: SNP array data from the CCLE


title: A172

description: SNP array data from the CCLE


title: 8-MG-BA

description: SNP array data from the CCLE


title: A2058

description: SNP array data from the CCLE


title: 697

description: SNP array data from the CCLE


title: 769-P

description: SNP array data from the CCLE


title: 647-V

description: SNP array data from the CCLE


title: 59M

description: SNP array data from the CCLE


title: 786-O

description: SNP array data from the CCLE


title: 8505C

description: SNP array data from the CCLE


title: 1321N1

description: SNP array data from the CCLE

value: astrocytoma


title: 42-MG-BA

description: SNP array data from the CCLE


title: Patient 10, before first IFN-beta injection

status: Public on Dec 06 2011

type: RNA

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description: Gene expression data from a multiple sclerosis patient treated with IFN-beta

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133 Plus 2.0 arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The raw probe-level signals were converted to expression values using the MAS5.0 algorithm and custom GeneAnnot-based chip definition files (version 2.1.0, available at http://www.xlab.unimo.it/GA_CDF). Data normalization was performed by a loess fit to the data with span=0.05 (using R package affy). Each chip yielded mRNA levels of 18,862 human genes.

molecule: total RNA

source_name: Peripheral blood mononuclear cells

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

growth_protocol: Patient blood samples were taken immediately before first IFN-beta injection as well as two days, one month, one year and two years post therapy initiation.

extract_protocol: Blood was separated using isopycnic centrifugation (Ficoll), and peripheral blood mononuclear cells were lysed using chaotropic buffer and cleaned by RNeasy (Qiagen) according to the manufacturers' protocol.

treatment_protocol: Patients were treated with subcutaneous IFN-beta-1a (Rebif, Merck Serono) at standard doses.

tag: gender

value: male

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 5 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 1-year follow-up

tag: number of relapses during 2-year follow-up

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)

tag: completed years of ifn-beta therapy


title: 143B

description: SNP array data from the CCLE

value: osteosarcoma


title: Patient 8, 24 months after start of IFN-beta therapy

value: female


title: 22Rv1

description: SNP array data from the CCLE

value: prostate

value: carcinoma


title: Patient 8, 12 months after start of IFN-beta therapy


title: Patient 9, before first IFN-beta injection


title: Patient 9, 24 months after start of IFN-beta therapy


title: Patient 9, before second IFN-beta injection


title: CD34_3

status: Public on Jan 10 2012

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place, MS 342

department: Pathology

institute: St. Jude Children's Research Hospital

description: Adult normal bone marrow; CD34(+)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: Adult normal bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix One-Cycle protocol from 1 ug of total RNA

growth_protocol: No growth protocol. Cells were obtained from bone marrow or blood from children with acute lymphoblastic leukemia

extract_protocol: Trizol

tag: cell type

value: sorted CD34(+) cells

tag: subtype


title: Patient 9, 12 months after start of IFN-beta therapy


title: 23132/87

description: SNP array data from the CCLE

tag: primary site

tag: histology

value: adenocarcinoma


title: CD34_4

description: Adult normal bone marrow; CD34(+)


title: A2780

description: SNP array data from the CCLE

value: ovary

tag: histology subtype1


title: Patient 7, 1 month after start of IFN-beta therapy

tag: gender

tag: age at ifn-beta therapy onset (baseline blood sampling)


title: Patient 7, 12 months after start of IFN-beta therapy

tag: duration from ms diagnosis to therapy initiation (in months)

tag: edss at baseline


title: CD34_1

description: Adult normal bone marrow; CD34(+)


title: Patient 8, before first IFN-beta injection

tag: edss after 1 year

tag: edss after 2 years


title: Patient 7, 24 months after start of IFN-beta therapy

tag: edss after 5 years

tag: number of relapses during the year prior to treatment


title: Patient 8, before second IFN-beta injection

tag: number of relapses during 1-year follow-up

tag: number of relapses during 2-year follow-up


title: Patient 7, before first IFN-beta injection

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)


title: CD34_2

description: Adult normal bone marrow; CD34(+)

tag: cell type


title: Patient 9, 1 month after start of IFN-beta therapy

tag: completed years of ifn-beta therapy


title: Patient 6, 12 months after start of IFN-beta therapy


title: Patient 8, 1 month after start of IFN-beta therapy


title: Patient 6, 24 months after start of IFN-beta therapy


title: Patient 6, before first IFN-beta injection


title: Patient 5, 24 months after start of IFN-beta therapy


title: Patient 7, before second IFN-beta injection


title: Patient 6, before second IFN-beta injection


title: Patient 5, 12 months after start of IFN-beta therapy


title: Patient 4, 12 months after start of IFN-beta therapy


title: Patient 4, 1 month after start of IFN-beta therapy


title: Patient 5, before first IFN-beta injection


title: Patient 4, before second IFN-beta injection


title: 8305C

description: SNP array data from the CCLE

tag: primary site

value: thyroid


title: Patient 6, 1 month after start of IFN-beta therapy


title: Patient 5, 1 month after start of IFN-beta therapy


title: Patient 5, before second IFN-beta injection


title: Patient 4, before first IFN-beta injection


title: Patient 4, 24 months after start of IFN-beta therapy


title: Patient 3, before first IFN-beta injection


title: Patient 3, before second IFN-beta injection


title: Patient 3, 12 months after start of IFN-beta therapy


title: Patient 2, 24 months after start of IFN-beta therapy


title: Patient 3, 1 month after start of IFN-beta therapy


title: Patient 2, 12 months after start of IFN-beta therapy


title: Patient 1, 12 months after start of IFN-beta therapy


title: Patient 3, 24 months after start of IFN-beta therapy


title: Patient 2, before first IFN-beta injection


title: Patient 2, before second IFN-beta injection


title: Patient 1, 24 months after start of IFN-beta therapy


title: Patient 2, 1 month after start of IFN-beta therapy


title: Patient 1, before second IFN-beta injection


title: Patient 1, 1 month after start of IFN-beta therapy


title: Patient 12, 12 months after start of IFN-beta therapy


title: Patient 1, before first IFN-beta injection


title: Patient 12, 1 month after start of IFN-beta therapy


title: Patient 12, before first IFN-beta injection


title: Patient 12, 24 months after start of IFN-beta therapy


title: Patient 12, before second IFN-beta injection


title: Patient 11, before first IFN-beta injection


title: Patient 11, 24 months after start of IFN-beta therapy


title: Patient 10, 24 months after start of IFN-beta therapy


title: Patient 11, 1 month after start of IFN-beta therapy


title: Patient 10, before second IFN-beta injection


title: Patient 10, 12 months after start of IFN-beta therapy


title: Patient 11, 12 months after start of IFN-beta therapy


title: Patient 10, 1 month after start of IFN-beta therapy


title: SJTALL078

status: Public on Nov 23 2011

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

description: RNA extracted from tumor cells obtained at diagnosis

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Data were background adjusted, normalized and summarized by the RMA method. The Bioconductor package was used for this analysis.

source_name: RNA extracted from diagnostic leukemic blasts of T-cell precursor acute lymphoblastic leukemia (non-ETP)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from T-ALL cases

value: tumor cells


title: Patient 11, before second IFN-beta injection


title: SJTALL077


title: SJTALL143


title: SJTALL079


title: SJTALL068


title: SJTALL157


title: SJTALL067


title: SJTALL070


title: SJTALL056


title: SJTALL159


title: SJTALL066


title: SJTALL075


title: SJTALL037


title: SJTALL071


title: SJTALL047


title: 5637

description: SNP array data from the CCLE

tag: histology


title: SJTALL041


title: SJTALL072


title: SJTALL032


title: SJTALL050


title: SJTALL044


title: SJTALL069


title: SJTALL048


title: SJTALL038


title: SJTALL036


title: SJTALL033


title: SJTALL028


title: SJTALL029


title: SJTALL020


title: SJTALL031


title: IMR90 AU5

status: Public on May 29 2011

city: Singapore

first: Sherry

last: Wang

address: 21 Lower Kent Ridge Road

department: Biochemistry

country: Singapore

institute: National University of Singapore

description:
1787466010_F
MT-hTer-4U5 introduced into IMR90 cells.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Scanner: Illumina BeadArray Reader Scanning protocol: Scan factor of 1, PMT520 Software: Illumina Beadscan version 3.0

data_processing:
Data was extracted using Illumina GenomeStudio version 2010.2, Expression Module version 1.7.0.
Data were analyzed using Partek GS6.4 Ver 6.09.0922.
Normalization algorithm: RMA
Analysis was performed using ANOVA.

source_name: IMR90, AU5

label_protocol: Standard Illumina label protocol.

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (HIFBS) (Gibco, Invitrogen), 2mM L-glutamine (Gibco, Invitrogen) and 100U/ml penicillin and streptomycin (Gibco, Invitrogen).

extract_protocol: Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen) with modifications. Cells were first washed with PBS twice and then lysed in TRIzol (Invitrogen) before purification using RNA extraction columns and buffers provided in the kit. The RNA concentration was quantified using Nanodrop (Thermo Scientific). 500ng total RNA was used for cRNA amplification using Illumina TotalPrep RNA Amplification kit (Ambion). Steps were carried out by following the instruction manual in the kit.

treatment_protocol: IMR90 and IMR90 WT-hTERT cells were infected with DMEM-diluted virus supernatant with 8µg/ml of polybrene for 24 hours.

tag: cell line

value: IMR-90 (ATCC:CRL-186)

value: lung fibroblast

tag: factors

tag: immortalized

value: no


title: SJTALL026


title: SJTALL027


title: IMR90 WThTERT 47A

description:
1787466010_D
MT-hTer-47A introduced into IMR90 cells immortilized with hTERT.

source_name: IMR90 WT-hTERT, 47A

value: WT-hTERT and MT-hTer-47A

value: yes


title: IMR90 47A

description:
1787466010_G
MT-hTer-47A introduced into IMR90 cells.


title: SJTALL030


title: SJTALL019


title: SJTALL025


title: IMR90 WThTERT AU5

description:
1787466010_E
MT-hTer-4U5 introduced into IMR90 cells immortilized with hTERT.

source_name: IMR90 WT-hTERT, AU5

value: WT-hTERT and MT-hTer-AU5


title: SJTALL016


title: IMR90 WThTERT Vector

description:
1787466010_H
Empty vector introduced into IMR90 cells immortilized with hTERT.

source_name: IMR90 WT-hTERT, vector

value: WT-hTERT and empty vector


title: IMR90 WT

description:
1787466010_C
WT-hTer introduced into IMR90 cells.

source_name: IMR90, WT

value: WT-hTER


title: SJTALL034


title: LCM-9

status: Public on Sep 20 2011

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor). Each platform was preprocess separately, then merged. An extra quantile normalization was needed to normalized across platforms.

source_name: normal skin epidermal cells

label_protocol: GeneChip Affymetrix protocol

growth_protocol: Primary keratinocytes were cultured in Epilife medium (Cascade Biologics, Portland, OR, U.S.A.) with EDGS (Cascade Biologic) and Penicillin Streptomycin (100 IU mL-1 and 0.1 mg mL-1, respectively) (Gibco, Carlsbad, CA, U.S.A.) at 37 °C. Once 80% confluent, the medium was supplemented with or without the following cytokines: recombinant human (rh)-IL-17 (R&D System, Minneapolis, MN, U.S.A.) 200 ng mL-1 and TNF-α (Sigma-Aldrich Corp, St. Louis, MO, USA) (1 ng mL-1 or 10 ng mL-1) for 24 h before harvesting for other analyses.

extract_protocol: Qiagen RNeasy Kit protocol

tag: group

value: KC LCM

tag: type

value: Vivo


title: LCM-2


title: LCM-6


title: LCM-8


title: IMR90 WThTERT WT

description:
1787466010_B
WT-hTer introduced into IMR90 cells immortilized with hTERT.

source_name: IMR90 WT-hTERT, WT

value: WT-hTERT and WT-hTER


title: LCM-4


title: SJTALL024


title: LCM-5


title: LCM-10


title: IMR90 Vector

description:
1787466010_A
Empty vector introduced into IMR90 cells.

source_name: IMR90, vector

value: empty vector


title: LCM-3


title: LCM-7


title: normal colonic mucosa sample AUS2_038_p1961_NM

status: Public on May 19 2011

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: For analysis at the exon level, raw data were processed (using a custom-made cdf-file; HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf) and analyzed for alternative splicing with the FIRMA algorithm (aroma.affymetrix). For gene-level analysis, raw data were processed with the RMA procedure using Expression Console (Affymetrix; gene-core analysis).

source_name: Normal colonic mucosa from colorectal cancer patient

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: For the colorectal cancer samples, total RNA was isolated from <30 mg tissue biopsies using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer's protocol. For the normal colon mucosa samples, total RNA was isolated from <100 mg tissue biopsies using the Ambion RiboPure kit (Life Technologies), according to the manufacturer's protocol.

tag: tissue

value: normal colonic mucosa biopsy

tag: tumor stage

tag: msi-status


title: normal colonic mucosa sample AUS2_053_norm


title: normal colonic mucosa sample AUS2_017_norm


title: normal colonic mucosa sample AUS2_041_norm


title: normal colonic mucosa sample AUS2_054_norm


title: normal colonic mucosa sample AUS2_072_p1965_NM


title: normal colonic mucosa sample AUS2_044_p1962_NM


title: normal colonic mucosa sample AUS2_100_p1840_NM


title: normal colonic mucosa sample AUS2_012_norm


title: normal colonic mucosa sample AUS2_036_norm


title: normal colonic mucosa sample AUS2_029_norm


title: normal colonic mucosa sample AUS2_003_norm


title: normal colonic mucosa sample AUS2_068_p1836_NM


title: LCM-1


title: GF, rep5

status: Public on Mar 15 2011

city: Chapel Hill

first: Wei

last: Sun

state: NC

address: UNC

institute: UNIVERSITY OF NORTH CAROLINA CHAPEL HILL

description:
GF5
Replicate 5

hyb_protocol: Standard Illumina hybridization protocol, hybridizations to the MouseWG-6 v2.0 BeadChip arrays (Illumina, San Diego, CA).

scan_protocol: Standard Illumina scanning protocol, scanning was performed at the University of Tennessee at Memphis Core Facility.

data_processing: Data were log-e transformed, quantile normalized, and analyzed using R/limma. Two batches were used: CONV1-3 and GF1-3 belong to one batch, and CONV4-6 and GF4-6 belong to the other batch. Batch effect was corrected by including batch indicator in the model. Quantile normalized data yielded similar results.

organism: Mus musculus

source_name: Isolated colonocytes, germfree

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: Mice were maintained germfree in isolators or were conventionally raised.

extract_protocol: Total RNA was prepared using Trizol reagent (Invitrogen, Carlsbad, CA), and integrity was assessed using the RNA 6000 Nano-LabChip kit followed by analysis using a Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: Colonocytes were prepared from GF and CONV-R mice (6 biological replicates per experimental group) and flash-frozen.

tag: strain

value: colon

value: colonocytes

tag: condition

value: germfree

tag: batch


title: GF, rep6

description:
GF6
Replicate 6


title: CONV, rep5

description:
CONV5
Replicate 5

source_name: Isolated colonocytes, conventionally raised

value: conventionally raised


title: GF, rep4

description:
GF4
Replicate 4


title: GF, rep1

description:
GF1
Replicate 1


title: CONV, rep6

description:
CONV6
Replicate 6


title: CONV, rep4

description:
CONV4
Replicate 4


title: GF, rep2

description:
GF2
Replicate 2


title: GF, rep3

description:
GF3
Replicate 3


title: p53null-mammary-tumor, TGFb-Het Irradiated host repeat 16

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

description:
Het IR-host_34
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts

hyb_protocol: 12.5 micrograms of fragmented cRNA was hybridized for 16 hr to the Affymetrix MG 430 2.0 arrays using GeneChip Hybridization Oven 640 and Genechip® fluidics station FS 450, following standard Affymetrix protocols.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Agilent GeneSpring GX10 program. No further adjustments were made to the data in the table.

source_name: Total RNA of p53null mammary tumor, TGFb-Het-Irradiated host

label_protocol: 100 ng of total RNA were used to prepare cRNA following the Affymetrix 3’IVT Express Kit labeling protocol

growth_protocol: p53null tumors developed from p53null mammary fragments that were orthotoically transplanted into the inguinal mammary fat pads of wild-type or TGFb1 heterozygous female host mice that had their endogenous epithelium removed at 3wks of age.

extract_protocol: Total RNA was extracted using Trizol Reaget (Invitrogen), according to manufacturer's instructions.

treatment_protocol: Host mice were either irradiated or not, three days before transplantation.

tag: strain (donor)

value: BALB/c

tag: tissue (donor)

value: p53null mammary fragments

tag: strain (host)

tag: genotype/variation (host)

value: TGFb1 heterozygote

tag: protocol (host)

value: irradiated

tag: disease state (host)

value: p53null mammary tumors


title: CONV, rep3

description:
CONV3
Replicate 3

tag: cell type


title: CONV, rep2

description:
CONV2
Replicate 2


title: p53null-mammary-tumor, TGFb-Het Irradiated host repeat 18

description:
Het IR-host_51
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het Irradiated host repeat 15

description:
Het IR-host_33
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het Irradiated host repeat 17

description:
Het IR-host_42
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het Irradiated host repeat 13

description:
Het IR-host_29
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het Irradiated host repeat 14

description:
Het IR-host_32
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het Irradiated host repeat 10

description:
Het IR-host_6
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het Irradiated host repeat 12

description:
Het IR-host_23
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: CONV, rep1

description:
CONV1
Replicate 1


title: p53null-mammary-tumor, TGFb-Het sham-irradiated host repeat 3

description:
Het Sham-IR-host_52
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts

source_name: Total RNA of p53null mammary tumor, TGFb-Het-Sham-irradiated host

value: sham-irradiated


title: p53null-mammary-tumor, wild-type Irradiated host repeat  23

description:
WT IR-host_59
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts

source_name: Total RNA of p53null mammary tumor, WT-Irradiated host

value: wild type


title: p53null-mammary-tumor, TGFb-Het sham-irradiated host repeat 1

description:
Het Sham-IR-host_58
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het Irradiated host repeat 11

description:
Het IR-host_7
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  22

description:
WT IR-host_57
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het sham-irradiated host repeat 4

description:
Het Sham-IR-host_30
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het sham-irradiated host repeat 6

description:
Het Sham-IR-host_15
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  20

description:
WT IR-host_5
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  21

description:
WT IR-host_54
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het sham-irradiated host repeat 5

description:
Het Sham-IR-host_38
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  18

description:
WT IR-host_20
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het sham-irradiated host repeat 2

description:
Het Sham-IR-host_19
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  15

description:
WT IR-host_9
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  11

description:
WT IR-host_43
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  14

description:
WT IR-host_53
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  16

description:
WT IR-host_12
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  13

description:
WT IR-host_48
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  7

description:
WT IR-host_25
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  9

description:
WT IR-host_39
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  6

description:
WT IR-host_24
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  17

description:
WT IR-host_14
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  19

description:
WT IR-host_21
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, TGFb-Het Irradiated host repeat 9

description:
Het IR-host_56
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  12

description:
WT IR-host_44
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  10

description:
WT IR-host_40
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  4

description:
WT IR-host_2
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  2

description:
WT IR-host_11
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type Irradiated host repeat  1

description:
WT IR-host_10
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts

source_name: Total RNA of p53null mammary tumor, WT-Sham-irradiated host


title: p53null-mammary-tumor, wild-type Irradiated host repeat  3

description:
WT IR-host_16
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type sham-irradiated host repeat  9

description:
WT Sham-IR-host_65
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type sham-irradiated host repeat  4

description:
WT Sham-IR-host_31
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: 6682-8 (Trisomic)

status: Public on Nov 02 2010

city: Indianapolis

first: Randall

middle: J.

last: Roper

state: IN

address: 723 W. Michigan Street., SL306

department: Biology

institute: Indiana University-Purdue University Indianapolis

description: Trisomy 12

hyb_protocol: Samples were hybridized on 24 arrays using four MouseWG-6 v2.0 bead chips.

scan_protocol: Standard Illumina scanning protocol

data_processing: Resultant array data (probe level data) were preprocessed by Genomestudio software version 1.0.6 to give non-normalized gene level data. Normalization and analysis of the gene level data was conducted in R 2.7.1 using functions from Bioconductor 2.1. (www.bioconductor.org). The “lumi” Bioconductor package was used to read in the data and complete the normalization procedures.

source_name: E13.5 mandible precursor

label_protocol: RNA was quantified and converted to cDNA using the Ambion Illumina total prep RNA amplification kit.

extract_protocol: RNA from E13.5 mandibular precursors was extracted with TRIzol.

tag: age

value: Mandible precursor


title: p53null-mammary-tumor, wild-type sham-irradiated host repeat  3

description:
WT Sham-IR-host_17
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type sham-irradiated host repeat  6

description:
WT Sham-IR-host_60
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type sham-irradiated host repeat  2

description:
WT Sham-IR-host_8
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type sham-irradiated host repeat  5

description:
WT Sham-IR-host_46
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: 6671-5 (Trisomic)

description: Trisomy 6


title: 6682-5 (Trisomic)

description: Trisomy 11


title: p53null-mammary-tumor, wild-type sham-irradiated host repeat  8

description:
WT Sham-IR-host_64
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: p53null-mammary-tumor, wild-type sham-irradiated host repeat  1

description:
WT Sham-IR-host_3
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: 6649-3 (Trisomic)

description: Trisomy 8


title: 6682-3 (Trisomic)

description: Trisomy 10


title: p53null-mammary-tumor, wild-type sham-irradiated host repeat  7

description:
WT Sham-IR-host_61
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: 6649-2 (Trisomic)

description: Trisomy 7


title: p53null-mammary-tumor, wild-type Irradiated host repeat  5

description:
WT IR-host_22
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts


title: 6671-1 (Trisomic)

description: Trisomy 13


title: 6671-4 (Trisomic)

description: Trisomy 5


title: 6649-1 (Euploid)

description: Euploid 11


title: 6572-8 (Trisomic)

description: Trisomy 3


title: 6649-4 (Trisomic)

description: Trisomy 9


title: 6572-6 (Trisomic)

description: Trisomy 2


title: 6671-2 (Trisomic)

description: Trisomy 4


title: 6572-5 (Trisomic)

description: Trisomy 1


title: 6572-7 (Euploid)

description: Euploid 10


title: 6572-4 (Euploid)

description: Euploid 9


title: 6572-3 (Euploid)

description: Euploid 8


title: 6612-4 (Euploid)

description: Euploid 4


title: 6572-1 (Euploid)

description: Euploid 5


title: sEphB4-Alb treated 1

status: Public on Oct 09 2010

city: Los Angeles

first: ren

last: liu

state: CA

address: 1441 Eastlake Avenue

institute: University of Southern California

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: sEphB4-Alb treated

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: RIP1Tag2 mice of CD1 and C57/BL6 backgrounds

value: 13.5 weeks

value: tumor


title: 6671-6 (Euploid)

description: Euploid 7


title: 6671-3 (Euploid)

description: Euploid 6


title: 6612-1 (Euploid)

description: Euploid 3


title: PBS treated 1

description: replicate 1

source_name: PBS treated


title: PBS treated 2

description: replicate 1


title: sEphB4-Alb treated 2

description: replicate 2


title: 6660-1 (Euploid)

description: Euploid 2


title: 6682-7 (Euploid)

description: Euploid 1


title: hESC_CM_rep3

status: Public on Sep 15 2010

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Illumina HumanHT-12 V3.0 expression beadchip

data_processing: The data were normalised using quantile normalisation in R

source_name: hESC-derived contracting areas

growth_protocol: The human iPS and ES cells were maintained on irradiated (2x26 Gray/6 minutes each) mouse embryonic fibroblasts (MEFs). MEFs were derived from outbred CF-1 mice and plated at a density of 19500 cells/sqcm in 60 mm tissue culture dishes (BD Falcon). Both lines were maintained in DMEM/ F12 culture medium supplemented with Glutamax, 20% knockout serum replacer, 1% nonessential amino acids and 0.1 mmol/L beta-mercaptoethanol. Additionally, the medium was supplemented with 100 ng/ml basic fibroblast growth factor (Peprotech) for iPS cells, and 4 ng/ml for human ES cells. Culture media were changed daily and undifferentiated cells were passaged by manual dissection of cell clusters every five to six days.

extract_protocol: Total RNA from ES and iPS cell samples was isolated using TRIzol Reagent (Invitrogen). Human fetal and adult RNA samples were purchased from Clontech and were prepared by a guanidinium thiocyanate method.

treatment_protocol: Cardiac differentiation of human iPS and ES cells was carried out on the murine visceral endoderm-like cell line END2 as described by Mummery C, et al. Differentiation of human embryonic stem cells to cardiomyocytes: role of coculture with visceral endoderm-like cells. Circulation 107(21):2733-2740, 2003. To initiate co-cultures, human iPS and ES cell colonies were dissociated into clumps by either using collagenase IV (1mg/ml in DMEM/F-12 at 37°C for 5-10 minutes) or by manual cutting. The differentiation was carried out in Knockout-DMEM having 1mM L-glutamine, 1x non-essential amino acids, 0.1 mmol/L beta-mercaptoethanol and Penicillin-Streptomycin (100 U/ml and 100 ug/ml, respectively) but devoid of serum and serum replacement (all reagents were from Invitrogen). Medium change was performed at day 5, 9, 12 and 15 after beginning of the co-culture. Contracting cardiac outgrowths were first observed on day 11 after the initiation of human iPS and ES cell differentiations.

tag: developmental stage

value: enriched hESC-CM, day 18 of in vitro differentiation

tag: passage number

value: passage 97

tag: cell line

tag: origin of a cell line

value: ES Cell International, Singapore


title: hESC_CM_rep2

value: passage 132


title: hiPSC_undiff_rep2

source_name: human induced pluripotent stem cells (hiPSC), undifferentiated

value: undifferentiated human iPS cells

value: passage 23

value: iPS(Foreskin), clone 1

value: James Thomson, University of Wisconsin


title: hESC_undiff_rep3

source_name: human ES cells (hESC), undifferentiated

value: undifferentiated human ES cells


title: hiPSC_undiff_rep3

value: passage 28


title: adult heart_rep1b

source_name: Normal adult heart, pooled from 3 individuals

value: adult, 20-42 years old

value: not applicable

value: human tissue


title: hiPSC_CM_rep2

source_name: hiPSC-derived contracting areas

value: enriched hiPSC-CM, day 18 of in vitro differentiation


title: adult heart_rep1a


title: hESC_undiff_rep2


title: fetal heart_rep1a

source_name: Normal fetal heart, pooled from 34 fetuses

value: fetus, 12-31 weeks of gestation


title: adult heart_rep1c


title: fetal heart_rep1c


title: hESC_undiff_rep1

value: passage 129


title: fetal heart_rep1b


title: hiPSC_CM_rep3


title: hiPSC_undiff_rep1

value: passage 20


title: hiPSC_CM_rep1


title: hESC_CM_rep1

value: enriched hESC-CM, day 18 of in vitro differentiation


title: Adult S. mansoni male head

status: Public on Sep 03 2010

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

description: Tissue specific gene expression

hyb_protocol: 1.4 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul  containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x GEx HI-RPM Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent S.mansoni 44k oligoneucleotide microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (B version) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 024207_D_F_20090609) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Schistosoma mansoni

source_name: Macro-dissected male head

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from LMM samples and manually dissected samples using RNAqueous®-Micro kits (Ambion) using the manufacturer’s protocol for LMM samples and whole tissue samples, respectively

tag: tissue type

value: Macro-dissected male head

tag: gender

value: male


title: Adult S. mansoni whole male control

description: Tissue specific gene expression

source_name: Whole male worm control

value: Whole male worm control


title: Adult S. mansoni vitelline 2

description: Tissue specific gene expression

source_name: Microdissected vitelline tissue 2

value: Microdissected vitelline tissue

value: female


title: Adult S. mansoni ovary

description: Tissue specific gene expression

source_name: Microdissected ovary

value: Microdissected ovary


title: Adult S. mansoni female middle

description: Tissue specific gene expression

source_name: Macro-dissected female middle region

value: Macro-dissected female middle region


title: Adult S. mansoni testis 1

description: Tissue specific gene expression

source_name: Microdissected testes 1

value: Microdissected testes


title: Adult S. mansoni male hind

description: Tissue specific gene expression

source_name: Macro-dissected male hind region

value: Macro-dissected male hind region


title: Adult S. mansoni female gastrodermis

description: Tissue specific gene expression

source_name: Microdissected female gastrodermis

value: Microdissected female gastrodermis


title: Adult S. mansoni vitelline 3

description: Tissue specific gene expression

source_name: Microdissected vitelline tissue 3


title: Adult S. mansoni microdissected female control

description: Tissue specific gene expression

source_name: Microdissected female control

value: Microdissected female control


title: Adult S. mansoni female head

description: Tissue specific gene expression

source_name: Macro-dissected female head

value: Macro-dissected female head


title: Adult S. mansoni microdissected male control

description: Tissue specific gene expression

source_name: Microdissected male control

value: Microdissected male control


title: Adult S. mansoni female hind

description: Tissue specific gene expression

source_name: Macro-dissected female hind region

value: Macro-dissected female hind region


title: Adult S. mansoni vitelline 1

description: Tissue specific gene expression

source_name: Microdissected vitelline tissue 1


title: Adult S. mansoni testis 2

description: Tissue specific gene expression

source_name: Microdissected testes 2


title: Mibi_6_v2

status: Public on May 12 2009

description: whole blood from bacteremia patient

hyb_protocol: cRNA (1.5 µg) was hybridized to Human-6 Expression BeadChips V1 and V2 (Illumina, San Diego, CA), the standard Illumina hybridization protocol

scan_protocol: Arrays were scanned on Illumina BeadStation 500x using the standard Illumina scanning protocol

source_name: whole blood

label_protocol: cDNA and biotin-labeled cRNA synthesis was generated from 100 ng total RNA using the Illumina® TotalPrep™ RNA Amplification Kit (Applied Biosystems, Darmstadt, Germany).

growth_protocol: Blood samples from patients with systemic sclerosis or bacteremia, respectively, were collected in PAXgene blood RNA tubes (BD Biosciences, Heidelberg, Germany)

extract_protocol: RNA from Treg  and Tconv cells lysed in TRIzol (Invitrogen, Karlsruhe, Germany) was isolated according to the manufacturer´s protocol with subsequent column purification using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). Total RNA from PAXgene samples was prepared according to the manufacturer´s recommendations including an optional DNAse digestion step.

treatment_protocol: CD4+ CD127low CD25+ (Treg) and CD4+ CD127+ CD25- (Tconv) T cells were stained with CD4, CD25 and CD127 mAb (all from BD Pharmingen) and sorted on a FACSDiva cell sorter. Cell purity after isolation was assessed by intracellular staining for FOXP3 (e-bioscience) and routinely showed purities >95%.

tag: tissue

value: whole blood

tag: disease state

value: bacteremia


title: M3 MR-

status: Public on Jun 19 2009

description: replicate 1

source_name: bone marrow derived DC

growth_protocol: Freshly isolated bone marrow derived cells were differentiated for 1 week with GM-CSF into bone marrow derived DCs. Afterwards, cells were incubated with Alexa647-labeled OVA to distinguish mannose receptor positive from mannose receptor negative cells by FACS analysis.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with NanoDrop ThermoScientific.

treatment_protocol: Immediately after FACS sort, bone marrow derived DC were lysed in Trizol reagent

value: dendritic cells (DCs)

tag: mannose receptor

value: negative


title: M2 MR+

description: replicate 2

value: positive


title: M1 MR-

description: replicate 1


title: M1 MR+

description: replicate 2


title: Mibi_3_v2

description: whole blood from bacteremia patient


title: Sklero_9_v2

description: whole blood from sclerodermma patient

value: scleroderma


title: Sklero_11_v2

description: whole blood from sclerodermma patient


title: M3 MR+

description: replicate 2


title: M2 MR-

description: replicate 1


title: Mibi_5_v2

description: whole blood from bacteremia patient


title: Sklero_8_v2

description: whole blood from sclerodermma patient


title: Mibi_7_v2

description: whole blood from bacteremia patient


title: Treg_3_v2

description: purified T lymphocyte subset

source_name: T lymphocyte, CD4+CD25+ Treg

value: CD4+CD25+ Treg


title: Sklero_10_v2

description: whole blood from sclerodermma patient


title: Sklero_5_v2

description: whole blood from sclerodermma patient


title: nonTreg_3_v2

description: purified T lymphocyte subset

source_name: T lymphocyte, CD4+CD25- non-Treg

value: CD4+CD25- non-Treg


title: Mibi_4_v2

description: whole blood from bacteremia patient


title: Sklero_1_v2

description: whole blood from sclerodermma patient


title: Adult S. mansoni whole female control

description: Tissue specific gene expression

source_name: Whole female worm control

value: Whole female worm control

value: female


title: Mibi_2_v2

description: whole blood from bacteremia patient


title: Sklero_6_v2

description: whole blood from sclerodermma patient


title: Mibi_1_v2

description: whole blood from bacteremia patient


title: Sklero_7_v2

description: whole blood from sclerodermma patient


title: Sklero_2_v2

description: whole blood from sclerodermma patient


title: nonTreg_2_v2

description: purified T lymphocyte subset


title: Sklero_4_v2

description: whole blood from sclerodermma patient


title: p53null-mammary-tumor, wild-type Irradiated host repeat  8

description:
WT IR-host_36
From frozen mammary tumors
BALB/c wild-type RNA of tumors grown in BALB/c hosts

source_name: Total RNA of p53null mammary tumor, WT-Irradiated host

tag: strain (donor)

value: BALB/c

value: p53null mammary fragments

value: wild type

value: irradiated

value: p53null mammary tumors


title: Sklero_3_v2

description: whole blood from sclerodermma patient


title: nonTreg_1_v2

description: purified T lymphocyte subset


title: Mibi_7_v1

description: whole blood from bacteremia patient


title: Mibi_4_v1

description: whole blood from bacteremia patient


title: Sklero_10_v1

description: whole blood from sclerodermma patient


title: Mibi_2_v1

description: whole blood from bacteremia patient


title: Treg_1_v2

description: purified T lymphocyte subset


title: Mibi_6_v1

description: whole blood from bacteremia patient


title: Mibi_5_v1

description: whole blood from bacteremia patient


title: Sklero_1_v1

description: whole blood from sclerodermma patient


title: Sklero_11_v1

description: whole blood from sclerodermma patient


title: Mibi_3_v1

description: whole blood from bacteremia patient


title: nonTreg_3_v1

description: purified T lymphocyte subset


title: Sklero_4_v1

description: whole blood from sclerodermma patient


title: Mibi_1_v1

description: whole blood from bacteremia patient


title: Sklero_6_v1

description: whole blood from sclerodermma patient


title: Sklero_7_v1

description: whole blood from sclerodermma patient


title: Sklero_8_v1

description: whole blood from sclerodermma patient


title: Sklero_9_v1

description: whole blood from sclerodermma patient


title: Sklero_2_v1

description: whole blood from sclerodermma patient


title: nonTreg_1_v1

description: purified T lymphocyte subset


title: Sklero_5_v1

description: whole blood from sclerodermma patient


title: Treg_1_v1

description: purified T lymphocyte subset


title: Treg_2_v1

description: purified T lymphocyte subset


title: nonTreg_2_v1

description: purified T lymphocyte subset


title: Sklero_3_v1

description: whole blood from sclerodermma patient


title: Treg_3_v1

description: purified T lymphocyte subset


title: Treg_2_v2

description: purified T lymphocyte subset


title: inferior Frontal Cortex promoter array 3

status: Public on Dec 31 2007

first: Daniel

middle: H

last: Geschwind

address: 695 Charles E Young Drive

department: Neurology

institute: UCLA

hyb_protocol: Previous step: LM-PCR and labeling Materials: hyb buffer: 70% formamide/3XSSC/14.3% dextran sulfate Make this a few hours ahead of time to allow the dextran sulfate to go into solution. To make 10 ml: 1.43 grm dextran sulfate 1.5 ml of 20xSSC 7 ml formamide Bring up to 10 ml with water. -2% of BSA: 1 g of BSA in 50 ml of  Mili-Q water -Array Pre-hybridization  Solution  2XSSC/0.05%SDS/0.2%BSA. (to make take premade solution and add 0.16 grm of BSA to 80 ml solution) -DNA: purified from random labeling step. -Cot-1 DNA (from Invitrogen), need to measure DNA concentration for each tube.  Do not trust the concentration of company label. -One water bath at 42 degrees -One water bath at 60 degrees -Heat block at 95 degrees -Incubator at 37 degrees Procedures: A. Array Pre-hybridization 1. Fresh made pre-hybridization  solution:  2X SSC/0.05% SDS/0.2% BSA  (use fresh made BSA). 2. Add 80 ml of pre-hyb solution into a Coplin jar and warm up solution to 42°C in water bath (take about 20-30 min). 3. Soak slides in the Coplin jar (max. 4 slides/jar) and incubate for 40 min, at 42°C.  Then rinse with RO water for 10 sec, then spin at 2k rpm in epperdurf 5840  for 30”). Place in Corning Hyb chamber. B. Preparing the Hybridization Solution   In the meanwhile, Mix 2.0ug Cy3 labeled DNA and 2.0ug of Cy5 labeled DNA, add 36ug of human Cot-1 DNA, and dH2O so that final volume is 130ul.  Add 14ul 3M NaOAc, 280ul EtOH.  Mix by vortexing, freeze in dry ice for 15’, then spin 15’ at 14k in cold room.  Wash 1x, and dry in air. Dissolve the pellet in 22.4 ul of buffer (2.2x ssc, 0.22% SDS), incubate at 37°C for 10 min to dissolve.  Resuspend by pipeting.  Add 20 µl Hybridization buffer.  Denature probe at 95 C for 5 min,  then spin for 30 seconds, Incubate at 42°C for 2 minutes.  Add 4ul yeast tRNA (at 10ug/ul). Add 3.0ul of 2% BSA.  Incubate at 42°C for 5 min.  Spin briefly. C. Hybridization:  spot 47ul to the array in three evenly spaced droplets.  Place cover slip on and incubate at 60°C for overnight. (16 hours at least). Step 10---washing materials: 400ml 2x SSC, 0.1% SDS, preheated to 60°C 300ml 0.1x SSC, 0.1% SDS 1 liter of 0.1X SSC. Procedures: Note: Although the 2X SSC solutions are preheated to 60°C the washes are actually done at room temperature. 1. Fill a Coplin jar with 50ml 2X SSC, 0.1% SDS pre-heated to 60ºC. Gently place the array into the jar, barcode up. Let the Gene Array sit for 1 minute then remove each array slowly from the Coplin jar leaving the cover slip behind. 2. Place the array into a slide rack submersed in 2X SSC, 0.1% SDS pre-heated to 42ºC in a Wheaton glass staining dish. Incubate the array for 5 minutes with gentle agitation (rocking on the rocker platform). 3. Remove the slide rack from the 2X SSC, 0.1% SDS solution and place in 250ml of room temperature 0.1X SSC, 0.1% SDS in a Wheaton glass staining dish. Incubate for 10 minutes with gentle agitation. 4. Remove the slide rack from the 0.1x SSC, 0.1% SDS solution and place in 250ml of room temperature 0.1X SSC in a Wheaton glass staining dish for 15 seconds. Agitate gently by hand. This quick wash removes much of the residual SDS. 5. Remove the slide rack from the 250ml of 0.1X SSC solution and place it in 250ml of 0.1X SSC in a glass staining dish. Incubate for 1 minutes (with gentle agitation if desired). 6. Repeat step 5 two more times (3 total) 7. After 15 seconds remove the array slowly from the slide rack and place into the rack on centrifuge. Balance well.  Spin for 1 minute at 1500rpm in eppendurf 5840.  After spin, store slides in slide boxes.  Protect slides from dust and light until analyzed.

scan_protocol: Arrays were scanned on a GenePix 4000B (Molecular Devices, Sunnyvale, CA) and image analysis was performed with GenePix Pro 6.0.

data_processing:
Normalized ratios were obtained subtracting the log2-transformed
expression value in the control sample from the log2-transformed
expression value in the experimental sample, after median normalization.

source_name: inferior frontal cortex IP

label_protocol: Random prime labeling

growth_protocol: Tissue was frozen and stored at -80 degrees C until crosslinking procedure

extract_protocol:
Hypotonic solution was used to isolate DNA and protein crosslinked material
Prepare chromatin from frozen cell pellets
Materials
Cell: two pellet, each from 0.5x 10^9 cells.
Lysis buffer 1,  100ml, add protease inhibitor tablet before use. (Zheng uses the protease inhibitors at the end of the protocol-he bought the Sigma protease panel)
5ml 1M Hepes-KOH, pH 7.5
2.8ml 5M NaCl
0.2ml 0.5M EDTA
10ml glycerol
5ml 10% NP-40
0.25ml Triton X-100
 add 76.75 ml H2O
buffer 2, 100ml, add protease inhibitor tablet before use
4ml 5M NaCl
0.2ml 0.5M EDTA
0.1ml 0.5M EGTA (add .125 of 0.4M)
0.5ml 2M Tris pH 8
add 95.2 H2O
buffer 3, 100ml and add protease inhibitor tablet before use.
0.2ml 0.5M EDTA
0.1ml 0.5M EGTA
0.5ml 2M Tris-HCl, pH8
Procedures
1.  Resuspend each tube of cells (5x10^8 cells)(zheng only used 2x10^8) in 30ml of Lysis buffer I. Rock at 4°C for 10’.  Then spin at 4000rpm in a table top centrifuge, 10’ at 4°C. -check under scope for complete lysis.
2. Resuspend each tube of cells in 24ml of buffer 2.  Rock gently at room temperature for 10 min.  Pellet nuclei in tabletop centrifuge by spinning at 4K rpm, 10 min at 4°C.
3. Resuspend both pellets from each tube in a total of 4ml buffer 3.  Transfer into two 15ml conical tubes.   Place the tube into a 50-ml tube with ice in it.
4. Sonicate the suspension in 15ml conical tube with a microtip attached to Branson 450 sonifier, setting at 5, constant power.  Sonicate 8-10 times with 25sec, allowing the suspension to cool on ice for 1 min between pulses.  Take 40ul of extracts every two cycles.
5. Pool all the lysate together.  Add 10mg of sarkosyl (Sigma L-5125) and rock for 10min at room temperature.  Transfer to falcon tubes. Spin out debris at 10K, 10min, in a ss34-rotor (13,000 RPM at 4 degrees in microfuge).
6. Proceed to next step (immunoprecipitation) or freeze cell extracts in –80°C as 1ml aliquots.
Step 3.  Chromatin immunoprecipitation
Materials:
Cell extracts prepared from step 2.
Antibody-coupled magnetic beads from step 0
elution buffer: to make 1 ml
50mM Tris pH8	50 ul 1M  Tris
10mM EDTA	20 ul 0.5M EDTA
1% SDS	100 ul
	830 ul H2O
Procedures:
1. set up IP reactions with  crude extract:
take 1 ml cell extract;  add the following:
	material	cconc.		amount added
	----------	---------	----------------
	Triton-x100	0.1%		0.01 ml of 10%
	deoxycholate   0.1%	            0.01ml of 10%
	PMSF		1x		0.01ml of 100x
	Benz		1x		0.01ml of 100x
	Approtenin	1x		0.005ml of 200x
	leup		1x		0.001ml of 1000x

2. Add 100ul of magnetic beads pre-coupled with antibody to the tube. incubate at 4°C overnight in a rotating platform.---Save 40 ul for elution control
3. Use a magnet MPC-E (from Dynal)  to precipitate the beads, discard supernatant. In cold room

4. Wash 5 times with 1ml wash buffer, with 3’ incubation on rotating platform in cold room, and aspiration.
wash buffer, (RIPA buffer)
--------------------                     final 100ml                     10 ml
50mM Hepes, pH 7.6	5ml of 1M Hepes	0.5ml
1mM EDTA	200ul of 0.5M	20 ul
0.7% DOC	7ml of 10%	0.7 ml
1% NP-40 (IPGEL)	10ml of 10%	1.0 ml
0.5M LiCl	2.12g of powder [sigma]	.2 grm
1mM PMSF		1ml of 100x	100 ul
leupeptin	1ml of 100x	100 ul
aprotinin
water	77.8 ml	7.8 ml
Add NP-40 first and then DOC to reduce cloudiness.
Wash once with 1 ml TE (pH 8.0).
 After removing the TE by aspiration, spin the tubes for 3 minutes at 3000 rpm and remove any remaining liquid with a pipette.

 5. Elution from beads and reversal of cross links
  Add 50 µl elution buffer, vortex briefly to resuspend the beads and incubate at 65°C for 12 minutes. Vortex lightly every 2 minutes during the incubation.
6. Spin for 30 seconds at maximum speed and transfer 50 µl of supernatant to a new tube. Discard the rest.
7.  Add 150 µl of TE/SDS to the supernatant in the new tube in order to reverse the crosslinking  reaction.    In the meanwhile, take 40ul of cell extract taken in the step 1, add 120ul of TE/SDS.   Incubate overnight at 65°C in an incubator.

treatment_protocol: Cells were crosslinked and sonicated

tag: 16-20 week human fetal brain IPed with Foxp2 antibody

source_name: control

treatment_protocol: total genome control-no IP

tag: total genome control-no IP


title: Tcell_18h_TGF_rep3

status: Public on Mar 29 2008

hyb_protocol: Biotin labeled cRNA (1.5ug) was hybridized to Sentrix(r) whole genome bead chips 6 x 2 (Illumina, San Diego, CA, USA)

scan_protocol: Scanning was performed on the Illumina(r) BeadStation 500x.

data_processing: BeadStudio raw data were normalized using R

source_name: T cells resting, 18h + 10ng TGF

label_protocol: Biotin labeled cRNA preparation for the Illumina platform was performed using the Ambion(r) Illumina RNA amplification kit (Ambion Europe, Huntington, Cambridgeshire, UK).

extract_protocol: CD4+ T cells were isolated from blood samples by using RosetteSep CD4+ enrichment kit (StemCell Technologies, Meylan, France); purity: > 90% as determined by flow cytometry. RNA was isolated with Trizol(r) method according to the manufacturer's protocol. The RNA was purified with the RNeasy MiniElute Cleanup Kit (Qiagen, Hilden, Germany).

tag: T cells resting, 18h + 10ng TGFs


title: inferior Frontal Cortex promoter array 2

tag: 16-20 week human fetal brain IPed with FOxp2 antibody


title: Lung promoter array 2

source_name: Lung

tag: 16-20 week human fetal lung IPed with Foxp2 antibody


title: Tcell_18h_8h_rep3

status: Public on May 01 2007

source_name: T cells resting, 18h + 8h

tag: T cells resting, 18h + 8h


title: basal ganglia promoter 3

source_name: basal ganglia

tag: 16-20 week huamn fetal brain IPed with Foxp2 antibody


title: Tcell_18h_8h_rep1


title: Tcell_18h_TGF_rep2

tag: T cells resting, 18h + 10ng TGF


title: 1522628110_A

status: Public on Dec 31 2008

description: Skleroderma patient

hyb_protocol: cRNA (1.5 µg) was hybridized to Human-6 Expression BeadChips V1 and V2 (Illumina, San Diego, CA).

source_name: PAXGene, whole blood

extract_protocol: Blood samples from patients with systemic sclerosis or bacteremia, respectively, were collected in PAXgene blood RNA tubes (BD Biosciences, Heidelberg, Germany). Total RNA from PAXgene samples was prepared according to the manufacturer´s recommendations including an optional DNAse digestion step.

tag: Skleroderma patient


title: Tcell_18h_8h_TGF_rep3

source_name: T cells resting, 18h + 8h + 10ng TGF

tag: T cells resting, 18h + 8h + 10ng TGF


title: Inferior Frontal Cortex

source_name: Inferior frontal cortex IP


title: Tcell_18h_1h_TGF_rep1

source_name: T cells resting, 18h + 1h + 10ng TGF

tag: T cells resting, 18h + 1h + 10ng TGF


title: Basal ganglia promoter 2

tag: total genome DNA not IPed


title: Tcell_18h_2h_TGF_rep1

source_name: T cells resting, 18h + 2h + 10ng TGF

tag: T cells resting, 18h + 2h + 10ng TGF


title: 1522628100_E

description: Bacteremia patient

tag: Bacteremia patient


title: Tcell_18h_2h_rep2

source_name: T cells resting, 18h + 2h

tag: T cells resting, 18h + 2h


title: Tcell_18h_2h_TGF_rep3


title: Tcell_18h_2h_rep3


title: Tcell_18h_2h_rep1


title: Tcell_18h_TGF_rep1


title: Tcell_18h_8h_TGF_rep1


title: Tcell_18h_1h_TGF_rep3


title: Tcell_18h_1h_rep3

source_name: T cells resting, 18h + 1h

tag: T cells resting, 18h + 1h


title: Tcell_18h_8h_TGF_rep2


title: Tcell_18h_8h_rep2


title: Lung promoter array 1

source_name: lung

tag: 16-20 week human fetal lung IPed with FOXP2 antibody


title: Tcell_18h_1h_TGF_rep2


title: Basal ganglia promoter 1

source_name: Basal ganglia

tag: Cy5, 16-20 week human fetal brain IPed with FOXP2

tag: 16-20 week human fetal brain


title: Tcell_12h_rep3

source_name: T cells resting, 12h

tag: T cells resting, 12h


title: Tcell_18h_1h_rep1


title: Tcell_18h_rep3

source_name: T cells resting, 18h

tag: T cells resting, 18h


title: Tcell_18h_rep1


title: Tcell_12h_rep4


title: Tcell_12h_rep2


title: Tcell_18h_2h_TGF_rep2


title: Rat fatty liver6

status: Public on Sep 16 2004

first: Julian

last: Griffin

address: Tennis Court Road

country: United Kingdom

institute: University of Cambridge

description:
Rats (Charles River UK Ltd.) were fed either standard laboratory chow, or chow supplemented with 1% orotic acid (Sigma Aldrich, UK) ad libitum. Orotic acid feeding is a well-characterised method for inducing reversible fatty liver disease in rodents. Rats were killed by cervical dislocation and the left lateral lobe of the liver excised. Tissues were snap frozen and stored in liquid nitrogen and/or at –80oC.

Keywords = orotic acid
Lot batch = 1

hyb_protocol: Biotinylated cRNA was fragmented and hybridised to RGU34A Affymetrix GeneChips according to standard Affymetrix protocols.

scan_protocol: Performed according to standard Affymetrix protocols.

data_processing: Data were analysed with the Affymetrix Microarray Suite 5.0 algorithm to generate a “signal” value and a “detection” label. Prior to normalisation, probes that generated an absent call in all cells were removed. Normalisation was calculated using a Global Scaling method based on the entire data set. Globally scaled values <10 were rounded up to 10.

organism: Rattus norvegicus

source_name: Kyoto Rat liver tissue following animal exposure to orotic acid for 14 days

label_protocol: cDNA was generated from total RNA using SuperscriptTM Double-stranded cDNA Synthesis kit (Invitrogen, Life Technologies), cRNA was prepared by in vitro transcription (BioArray High Yield RNA transcript labelling kit Affymetrix, UK), and purified on an affinity resin column (RNeasy, Qiagen Ltd., UK).

extract_protocol: Total RNA was extracted by RNA Isolation Kit (Stratagene) from the livers of Wistar and Kyoto rats at day 0 (Wistar n=3, Kyoto n=2), day 1 and 3 (Wistar n=2, Kyoto n=2), and day 14 (Wistar n=3, Kyoto n=2).

tag: Kyoto rat liver tissue following animal exposure to orotic acid for 3 days


title: Tcell_18h_rep2


title: Tcell_18h_1h_rep2


title: RadS13-IR

status: Public on Sep 06 2004

city: Stanford

first: Wan-Jen

last: Hong

address: 269 Campus Dr., CCSR Room 1140

department: Medicine/Biochemistry

institute: Stanford University School of Medicine

description:
Peripheral blood lymphocytes from a total of 57 patients were immortalized with Epstein-Barr virus.  Fourteen radiation-therapy patients suffered unusual levels of radiation toxicity (RadS).  Thirteen radiation-therapy patients with limited toxicity (RadC) were enrolled as controls.  Fifteen patients diagnosed with skin cancer before age 40 (SkCa) were used as a second group of controls.  Fifteen healthy subjects without any history of cancer (NoCa) were matched to the skin cancer patients and used as a third group of controls.

Cells were exposed to mock treatment (Mock), ultra-violet radiation (UV), or ionizing radiation (IR).  For UV radiation treatment, cells were exposed to 10 J/m^2 and harvested for RNA 24 hours later.  For IR treatment, cells were exposed to 5 Gy of IR and harvested for RNA 4 hours later.  For example, RadS1-Mock refers to cells from radiation sensitive patient 1 exposed to mock treatment.

Data were analyzed with Affymetrix MAS version 4.0.

Normalization – A reference data set was generated by averaging the expression of each gene over all data sets. The data for each hybridization were compared with the reference data set in a cube root scatter plot. A linear least-squares fit to the cube root scatter plot was then used to normalize each hybridization.
Keywords = Gene expression in lymphoid cells of cancer patients

source_name: Lymphoblastoid cells immortalized with Epstein-Barr virus


title: Tcell_12h_rep1