title: TNBS colitis day 23_mouse#1

description: replicate _1

value: day 23


title: GMP_65_fl/BRM2, rep3

status: Public on Jul 08 2013

type: RNA

city: Copenhagen N

first: Anne-Katrine

last: Frank

address: Ole Maaløesvej 5

department: Porse Group

country: Denmark

institute: Finsenlaboratoriet

description: Sorted myeloid progenitor from bone marrow samples, 3w post-conditional gene knockout.

hyb_protocol: Affymetrix EukGE-WS2v4_450 Hybridization protocol, according to manufacturer's specifications.

scan_protocol: Cell intensity files (CEL files) were generated in the GeneChip Command Console Software (AGCC) (Affymetrix, Santa Clara, CA, USA).

data_processing: The data were processed using the Bioconductor affy package. Values are log2 transformed post-RMA processing.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: bone marrow cells, GMPs, cebpa fl/BRM2; Mx1Cre

label_protocol: 2.5ug of amplified cDNA was fragmented and labeled using Encore Biotin Module V2 according to manufacturer's instructions (www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/).

growth_protocol: Murine bone marrow cells were enriched for cKit+ and hematopoietic progenitor cells were sorted by FACS.

extract_protocol: Total RNA from sorted cells were isolated with RNeasy Micro Kit (Qiagen). Samples were prepared in triplicates for each genotype. 20 ng of total RNA was amplified using Ovation Pico WTA system V2 (Nugene) according to manufacturer's instructions (www.nugeninc.com/nugen/index.cfm/products/cs/microarrays-and-qpcr/ovation-pico-wta-system-v2/).

treatment_protocol: Female mice were sacrificed and bones were dissected, bone marrow cells were isolated by crushing and the preGM and GMP populations were sorted by FACS. Immunophenotypes: PreGM: Lin- Sca1- cKit+ CD150- CD41- FcgRII- Endoglin-; GMP: Lin- Sca1- cKit+ CD150- CD41- FcgRII+.

tag: strain

tag: genotype/variation

value: cebpa fl/BRM2; Mx1Cre

tag: tissue

value: bone marrow

tag: cell population

value: GMP:Lin-, Sca1-, cKit+, CD150-, CD41-, FcgRII+

tag: gender

value: female


title: TNBS colitis day 16_mouse#1

city: Leiden

first: Rob

last: Mariman

address: Vestwal 5

country: Netherlands

institute: TNO

description: replicate _1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Image Analysis and extraction of raw and background subsracted expression data were preformed with Genome Studio software. GeneSpring GX 11.0 was used for quantile normalization and converting expression levels to a log2 scale

label: biotin

source_name: distal colon

label_protocol: Biotinylated cRNA were prepared using Illumnia TotalPrep RNA Amplification   Biotinylated cRNA were prepared using Illumnia TotalPrep RNA Amplification  Biotinylated cRNA were prepared using Illumnia TotalPrep RNA Amplification

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: BALB/c

tag: disease status

value: TNBS colitis

tag: time

value: day 16

tag: animal


title: Bsub_prpE_60min_rep3

city: Gdansk

first: Adam

last: Iwanicki

address: Debinki 1

department: Department of Medical Biotechnlogy

country: Poland

institute: Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 60 min upon induction of sporulation. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed using NimbleGen 4x72k B. subtilis subsp. subtilis strain NC_000964 microarray slides following operating protocol (Roche NimbleGen Inc.).

scan_protocol: Scaning was performed using Roche MS 200 Microarray Scanner following operating protocol (Roche).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Bacillus subtilis subsp. subtilis str. 168 delta-prpE

label_protocol: Extracted total RNA was used for synthesis of double-stranded cDNA using Roche cDNA Synthesis System kit (Roche). cDNA was labeled using Roche Dual-Color DNA Labeling kit (Roche), 168 strain – Cy5, delta-prpE – Cy3)

growth_protocol: Bacteria were inoculated into sporulation medium (Sterlini, J.M. and Mandelstam, J. 1969 Biochem. J. 113:29-37) and grown with shaking at 37°C to an optical density at 570 nm (OD570) of 1. Cells were harvested by centrifugation and resuspended in the starvation sporulation medium (Sterlini and Mandelstam 1969), and incubation was continued with shaking at 37°C. Samples of 10 OD570 units were collected at 60, 130, 200, 270, 340 and 410 min upon resuspension in starvation medium (initiation of sporulation).

extract_protocol: Total RNA was extracted using the Universal RNA Purification Kit (Eurx Ltd, Gdańsk, Poland) and DNA was removed by on-column DNase digestion with the RNase-Free DNase (Fermentas, Lithuania). RNA concentration and purity was determined by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA).

treatment_protocol: not applicable

tag: genotype

value: mutant delta-prpE

tag: accession

tag: collection time


title: htz1D

city: Augusta

first: Wei-Hua

last: Wu

state: GA

address: 1462 Laney Walker Blvd

department: Neurology

country: USA

institute: IMMAG/MCG/GRU

description:
Samples 13-18:
htz1D 1 duplicate 1: WT 1_Cy3, htz1D 1_Cy5; raw file: US45102975_251507210188_S01_GE2-v5_95_Feb07_1_3.txt
htz1D 1 duplicate 2: htz1D 1_Cy3, WT 1_Cy5; raw file: US45102975_251507210189_S01_GE2-v5_95_Feb07_1_3.txt
htz1D 2 duplicate 1: WT 2_Cy3, htz1D 2_Cy5; raw file: US45102975_251507210187_S01_GE2-v5_95_Feb07_1_3.txt
htz1D 2 duplicate 2: htz1D 2_Cy3, WT 2_Cy5; raw file: US45102975_251507210200_S01_GE2-v5_95_Feb07_1_3.txt
htz1D 3 duplicate 1: WT 3_Cy3, htz1D 3_Cy5; raw file: US45102975_251507210201_S01_GE2-v5_95_Feb07_1_3.txt
htz1D 3 duplicate 1: htz1D 3_Cy3, WT 3_Cy5; raw file: US45102975_251507210202_S01_GE2-v5_95_Feb07_1_3.txt

Normalized, log2 (htz1/WT) ratios were generated from Samples 13-18 and Samples 1-6 (see WT raw files linked to Series record).

hyb_protocol: The labeled cDNA was hybridized to the Agilent Yeast 4X44k 60-mer oligo microarray according to the manufacturer's protocol

scan_protocol: Slides were scanned using a GenePix 4000 Microarray scanner

data_processing:
Data were extracted using the Agilent Feature Extraction software and analyzed using the LIMMA package in R
We used the normalization method in the LIMMA package - background correction, normalization within and between the arrays, and correlation between duplicates.
Six sets of wt (see supplementary raw files linked to Series record) and six sets of mutant (fun30 or htz1 or fun30htz1; see raw files linked below) altogether were inputted into LIMMA to analyze. The outputted file is (log 2 ratio of normalized mutant signal divided by normalized WT signal).

label: Cy3, Cy5

organism: Saccharomyces cerevisiae

source_name: WT

label_protocol: cDNA was synthesized by reverse transcription of total RNA in the presence of oligo-dT (Superscript II, Invitrogen).  Dye coupling of cDNA was done using Cy3 or Cy5, followed by QIAquick PCR purification Kit (Qiagen)

growth_protocol: Wild type and mutant yeast cells were grow in YPD medium at 30C and harvested at ~ O.D. 0.5

extract_protocol: Total RNA was isolated using the standard hot acid phenol extraction method, followed by purificaiton with RNeasy Kit (Qiagen)

treatment_protocol: Wild type, fun30∆, htz1∆, fun30∆htz1∆

value: WT


title: GMP_63_fl/BRM2, rep2


title: fun30D

description:
Samples 7-12:
fun30D 1 duplicate 1: WT 1_Cy3, fun30D 1_Cy5; raw file: US45102975_251507210188_S01_GE2-v5_95_Feb07_1_2.txt
fun30D 1 duplicate 2: fun30D 1_Cy3, WT 1_Cy5; raw file: US45102975_251507210189_S01_GE2-v5_95_Feb07_1_2.txt
fun30D 2 duplicate 1: WT 2_Cy3, fun30D 2_Cy5; raw file: US45102975_251507210187_S01_GE2-v5_95_Feb07_1_2.txt
fun30D 2 duplicate 2: fun30D 2_Cy3, WT 2_Cy5; raw file: US45102975_251507210200_S01_GE2-v5_95_Feb07_1_2.txt
fun30D 3 duplicate 1: WT 3_Cy3, fun30D 3_Cy5; raw file: US45102975_251507210201_S01_GE2-v5_95_Feb07_1_2.txt
fun30D 3 duplicate 2: fun30D 3_Cy3, WT 3_Cy5; raw file: US45102975_251507210202_S01_GE2-v5_95_Feb07_1_2.txt

Normalized, log2 (fun30/WT) ratios were generated from Samples 7-12 and Samples 1-6 (see WT raw files linked to Series record).


title: fun30Dhtz1D

description:
Samples 19-24:
fun30Dhtz1D 1 duplicate 1: WT 1_Cy3, fun30Dhtz1D 1_Cy5; raw file: US45102975_251507210188_S01_GE2-v5_95_Feb07_1_4.txt
fun30Dhtz1D 1 duplicate 2: fun30Dhtz1D 1_Cy3, WT 1_Cy5; raw file: US45102975_251507210189_S01_GE2-v5_95_Feb07_1_4.txt
fun30Dhtz1D 2 duplicate 1: WT 2_Cy3, fun30Dhtz1D 2_Cy5; raw file: US45102975_251507210187_S01_GE2-v5_95_Feb07_1_4.txt
fun30Dhtz1D 2 duplicate 2: fun30Dhtz1D 2_Cy3, WT 2_Cy5; raw file: US45102975_251507210200_S01_GE2-v5_95_Feb07_1_4.txt
fun30Dhtz1D 3 duplicate 1: WT 3_Cy3, fun30Dhtz1D 3_Cy5; raw file: US45102975_251507210201_S01_GE2-v5_95_Feb07_1_4.txt
fun30Dhtz1D 3 duplicate 2: fun30Dhtz1D 3_Cy3, WT 3_Cy5; raw file: US45102975_251507210202_S01_GE2-v5_95_Feb07_1_4.txt

Normalized, log2 (fun30htz1/WT) ratios were generated from Samples 19-24 and Samples 1-6 (see WT raw files linked to Series record).


title: TNBS colitis day 21_mouse#1

description: replicate _1

value: day 21


title: TNBS colitis day 28_mouse#1

description: replicate _1

value: day 28


title: GMP_213_fl/+, rep1

source_name: bone marrow cells, GMPs, cebpa fl/+; Mx1Cre

value: cebpa fl/+; Mx1Cre


title: GMP_989_fl/+, rep2


title: Bsub_prpE_60min_rep2

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 60 min upon induction of sporulation. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.

organism: Bacillus subtilis subsp. subtilis str. 168


title: preGM_987_+/+, rep3

source_name: bone marrow cells, preGMs, cebpa +/+:Mx1Ce

value: cebpa +/+:Mx1Ce

value: preGM:Lin-, Sca1-, cKit+, CD150-, CD41-, FcgRII-, Endoglin-


title: Bsub_prpE_60min_rep1

description: This sample is of mutant delta-prpE Bacillus subtilis 168 collected 60 min upon induction of sporulation. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: WT Rep 4 vs Ph7 Rsh1

city: Montpellier

first: Stephan

last: Kohler

address: 1919 Route de Mende

country: France

institute: CNRS

description:
Wildtype versus Rsh for pH7 condition
H7-WT2-2009-02-10:URefMerged:H8-Rsh2-2009-02-10
Virtual dual channel design; Channel 1 (Cy3) on each hybridization was a universal reference (Uref) used as a reference point to merge two (2 channel arrays) into a virtual 2 channel array with wild-type versus rsh mutant.

hyb_protocol: Samples were heated at 95°C for 5 min and then kept at 45 °C until hybridization, when 35 μL of 2× formamide-based hybridization buffer (50% formamide; 10× SSC; 0.2% SDS) was added to each sample. Samples were then well-mixed and applied to custom 3.2 K Brucella oligo-arrays. Prior to hybridization, oligo-arrays were pretreated by washing in 0.2% SDS, followed by 3 washes in distilled water, and immersed in pre-hybridization buffer (5 × SSC, 0.1% SDS; 1% BSA in 100 ml of water) at 45°C for at least 45 min. Immediately before hybridization, the slides were washed 4 × in distilled water, dipped in 100% isopropanol for 10 sec and dried by centrifugation at 1,000 × g for 2 min. Four slides for each condition (Wild-type and rsh mutant) were hybridized at 45°C for ~ 20 h in a dark, humid chamber (Corning) and then washed for 10 min at 45°C with low stringency buffer (1× SSC, 0.2% SDS), followed by two 5-min washes in a higher stringency buffer (0.1 × SSC, 0.2% SDS and 0.1 × SSC) at room temperature with agitation.

scan_protocol: Hybridized microarrays were scanned using a GenePix 4000A dual-channel (635 nm and 532 nm) confocal laser scanner (Axon Instruments). The genes represented on the arrays were adjusted for background and normalized to internal controls using image analysis software (GenePixPro 4.0; Axon Instruments Inc.).

data_processing: Global scaling to 200 across all aways, LOWESS normalized, background subtracted data. Channel 1 (Cy3) was a universal reference (Uref) used as a reference point to merge two (2 channel arrays) into a virtual 2 channel array with wild-type versus rsh mutant. Non hybridized probes labeled as  “empty” in the raw data files where excluded from the analysis.

label: Cy5 with Uref on Cy3

organism: Brucella suis 1330

source_name: Brucella liquid culture (minimal medium)

label_protocol: Total RNA (30 µg) was first converted to cDNAs incorporating a chemically reactive nucleotide analog (amino allyl-dUTP) using Superscript III reverse transcriptase and random hexamers (Invitrogen). This cDNA was then post labeled with the reactive forms of fluoroLink Cy3-NHS esters (Amersham), which bind to the modified nucleotides. The labeled cDNAs were then combined with 0.5 µg of labeled gDNA to a final volume of 35 μL.

extract_protocol: Total RNA extracted using Rneasy (Qiagen) following manufacturer's instructions

value: Wild-type

tag: genotype/variaton

value: rsh mutant


title: preGM_986_fl/p30, rep2

source_name: bone marrow cells, preGMs, cebpa fl/p30; Mx1Cre

value: cebpa fl/p30; Mx1Cre


title: preGM_168_fl/p30, rep1


title: WT Rep 2 vs Ph7 Rsh1

description:
Wildtype versus Rsh for pH7 condition
H3-WT2-2009-01-22:URefMerged:H4-Rsh2-2009-01-22
Virtual dual channel design; Channel 1 (Cy3) on each hybridization was a universal reference (Uref) used as a reference point to merge two (2 channel arrays) into a virtual 2 channel array with wild-type versus rsh mutant.


title: WT Rep 1 vs Ph7 Rsh1

description:
Wildtype versus Rsh for pH7 condition
H1-WT1-2009-01-22:UrefMerged:H2-Rsh1-2009-01-22
Virtual dual channel design; Channel 1 (Cy3) on each hybridization was a universal reference (Uref) used as a reference point to merge two (2 channel arrays) into a virtual 2 channel array with wild-type versus rsh mutant.


title: preGM_988_fl/p30, rep3


title: WT Rep 3 vs Ph7 Rsh1

description:
Wildtype versus Rsh for pH7 condition
H5-WT1-2009-02-10:URefMerged:H6-Rsh1-2009-02-10
Virtual dual channel design; Channel 1 (Cy3) on each hybridization was a universal reference (Uref) used as a reference point to merge two (2 channel arrays) into a virtual 2 channel array with wild-type versus rsh mutant.


title: A224_RFP-overexpression_rep2

city: Boston

first: Michael

last: Birrer

state: MA

address: 70 Blossom Street

department: Medicine

institute: MGH

description:
Gene expression data from RFP overexpressing A224 cells
A224 RFP 2

hyb_protocol: A 15 μg aliquot of amplified biotinylated cRNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).

data_processing: JustRMA algorithm and median intensity of entire array were applied for data input and normalization by BRB ArrayTools version 4.1.0 (developed by Dr. Richard Simon et al, NCI, NIH). Differentially regulated genes were identified by a univariate paired t-test (p<0.0001, fold-change>2.0, random-variance model) from probe sets presenting in all arrays and displaying a variance in the top 50th percentile.

organism: Homo sapiens

source_name: A224 cells with RFP overexpression

label_protocol: One-round amplification were completed according to standard Affymetrix One-Cycle Amplification protocol using 2.5μg of total RNA.

growth_protocol: A224 cells were grown in RPMI1640 supplemented with 10% FBS and penicillin/streptomycin (Invitrogen).

extract_protocol: Total RNA samples were extracted from cells at ~70-80% confluence using RNeasy Mini Kit and RNase-Free DNase Set (both from QIAGEN) for on-column gDNA removal during RNA purification.

treatment_protocol: Ectopic overexpression was performed by lentiviral vector mediated delivery of FGF18 cDNA or RFP cDNA (pLoc series, Thermo Scientific). Stably infected cells were maintained in medium containing blasticidin S (15 μg/ml).

tag: cell line

value: A224 human epithelial ovarian cancer cell line

value: stably infected with lentivirus expressing RFP cDNA


title: A224_RFP-overexpression_rep3

description:
Gene expression data from RFP overexpressing A224 cells
A224 RFP 3


title: A224_FGF18-overexpression_rep3

description:
Gene expression data from FGF18 overexpressing A224 cells
A224 FGF18 3

source_name: A224 cells with FGF18 overexpression

value: stably infected with lentivirus expressing human FGF18 cDNA


title: preGM_169_+/+, rep1

value: bone marrow

value: female


title: preGM_210_+/+, rep2


title: A224_RFP-overexpression_rep1

description:
Gene expression data from RFP overexpressing A224 cells
A224 RFP 1


title: A224_FGF18-overexpression_rep2

description:
Gene expression data from FGF18 overexpressing A224 cells
A224 FGF18 2


title: MBMEC, 5 µM LY-317615 treatmen for 8h. [Naive Ly3]

city: Heidelberg

first: Tobias

middle: Volker

last: Lanz

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
repetition ov Naive LY-treated sample
Naive Ly3

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

label_protocol: Cy3-labeled cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: primary cultured mouse brain microvascular endothelial cells (MBMEC) have been prepared from new-born mice and cultured for one week.

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.

treatment_protocol: MBMEC were stimulated 8h with 5 µM LY317615. Two samples had been treated for ghe last 24h with 500 µM TNF-alpha and 500 µM IFN-gamma (inflamed) whereas two samples had been left untreated (naive).


title: Bsub_168_340min_rep3

description: This sample is of wild-type Bacillus subtilis 168 collected 340 min upon induction of sporulation. It is the third of three wild-type strain biological replicates used in this experiment, each from separate cultures.

source_name: Bacillus subtilis subsp. subtilis str. 168

value: wild-type


title: A224_FGF18-overexpression_rep1

description:
Gene expression data from FGF18 overexpressing A224 cells
A224 FGF18 1


title: Metastatic Bladder Cancer 1613

status: Public on Jul 07 2013

type: genomic

first: Markus

last: Riester

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

description: Genomic DNA isolated from metastatic bladder cancer

hyb_protocol: Genomic DNA samples were hybridized to the array using an Agilent microarray hybridization chamber for 40 hours in a Robbins Scientific oven with rotation at 20 rpm at 65°C

scan_protocol: Post-hybridization, the slides were washed and scanned using an Agilent DNA microarray scanner

data_processing:
CGH Analytics software (version 3.4, Agilent Technologies, CA) was used to analyze the aCGH data
Copy numbers were segmented using the GLAD algorithm. The 'spanishaCGH.glad.txt' are the segmented data (like the Level 3 data in TCGA), calculated with the GLAD algorithm: Sample ID, Chromosome, Start, End, Number of Probes in the segment, log2 copy number ratio of the segment (available on a Series records).

molecule: genomic DNA

source_name: Metastatic Bladder Cancer

label_protocol: The Genomic DNA ULS labeling kit for FFPE Samples (Agilent Technologies, Inc., Palo Alto, CA) was used to chemically label 500ng of DNA with either ULS-Cy5 (tumor) or ULS-Cy3 dye (normal/reference DNA) following the manufacturer's protocol

extract_protocol: Genomic DNA was extracted from tumors using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA)

value: tumor

value: radical cystectomy

tag: summarystage

value: invasive

tag: tumor stage

value: n

tag: ecog_ps (eastern cooperative oncology group performance status)

value: y

value: recurrence

value: living


title: Metastatic Bladder Cancer 1617


title: Metastatic Bladder Cancer 1614


title: Metastatic Bladder Cancer 1616


title: Metastatic Bladder Cancer 1610


title: Metastatic Bladder Cancer 1604

value: superficial


title: Metastatic Bladder Cancer 1591


title: Metastatic Bladder Cancer 1600


title: Metastatic Bladder Cancer 1609


title: Metastatic Bladder Cancer 1594

value: deceased


title: Metastatic Bladder Cancer 1605


title: Metastatic Bladder Cancer 1592


title: Metastatic Bladder Cancer 1582


title: Metastatic Bladder Cancer 1599


title: Metastatic Bladder Cancer 1602


title: Metastatic Bladder Cancer 1615


title: Metastatic Bladder Cancer 1601


title: Metastatic Bladder Cancer 1585


title: Metastatic Bladder Cancer 1608


title: Metastatic Bladder Cancer 1603


title: Metastatic Bladder Cancer 1587


title: Metastatic Bladder Cancer 1583


title: Metastatic Bladder Cancer 1598


title: Metastatic Bladder Cancer 1577


title: Metastatic Bladder Cancer 1589


title: Metastatic Bladder Cancer 1579


title: Metastatic Bladder Cancer 1572


title: Metastatic Bladder Cancer 1569


title: Metastatic Bladder Cancer 1574


title: Metastatic Bladder Cancer 1573


title: Metastatic Bladder Cancer 1576


title: Metastatic Bladder Cancer 1570


title: Metastatic Bladder Cancer 1568


title: Metastatic Bladder Cancer 1571


title: Metastatic Bladder Cancer 1567


title: Metastatic Bladder Cancer 1565


title: Metastatic Bladder Cancer 1540


title: Metastatic Bladder Cancer 1564


title: Metastatic Bladder Cancer 1539


title: Metastatic Bladder Cancer 1543


title: Metastatic Bladder Cancer 1533


title: Metastatic Bladder Cancer 1534


title: Metastatic Bladder Cancer 1535


title: Metastatic Bladder Cancer 1538


title: Metastatic Bladder Cancer 1529


title: Metastatic Bladder Cancer 1532


title: Metastatic Bladder Cancer 1530


title: Metastatic Bladder Cancer 1527


title: Metastatic Bladder Cancer 1526


title: Metastatic Bladder Cancer 1531


title: FFPE bladder cancer metastatic tissue 250

description:
X0006263_H01
at_array: a520683-00-811124-050712-4137168-69154.CEL
cg_array: a520683-00-912239-050312-4137158-87854.CEL

hyb_protocol: Hybridization was performed by Affymetrix according to the platform protocol

scan_protocol: Scanning was performed by Affymetrix

data_processing:
Data processing was performed by Affymetrix using the NEXUS software (v.6). Tables contain the following columns as provided by Affymetrix.
CopyNumber: The measured copy number value summed over both alleles of the SNP.
Copy_A: The data in this column corresponds to the measured number of copies of the Major_Allele.  Values of -1 or -0.5 are an indication of untrustworthy data. -0.5 is used as a minimum value for allelic copy values and -1 is an indication of erroneous data.
Copy_B: The measured number of copies of the Minor_Allele.
AlleleRatio: The allele ratio for the two alleles of the SNP. This ratio corresponds to copy_B/copy_A (minor /major) with the caveat that it is  flipped  to be copy_A/copy_B (major / minor) in cases where copy_B is  significantly  larger than copy_A (for the given sample). This  flipping  (mostly) constrains the allele ratio to the range 0 to 1, so that allele ratios can be smoothed over neighboring SNPs (after excluding homozygous cases). For example, for diploid samples the heterozygous SNPs will smooth to an allele ratio value of 1.0. Or consider another example where a sample has 3 total copies in a given region. This will produce  unflipped  allele ratios of approximately 0/3, 1/2, 2/1, 3/0. After flipping these values will be  normalized  to two cases: 0/3 & 1/2. If we then exclude the 0/3 (homozygous) cases and smooth the data across the region the allele ratio will average out to 1/2. A negative allele ratio is due to negative allele copy number. Small negative allele ratios should be treated as zero, while large negative allele ratios are clearly outliers and should be disregarded.
AllelicDifference: The Allelic Difference calculation is based on the formula: (Copy A - Copy B)/(Copy A + Copy B)
Data was segmented using the GLAD algorithm. The 'dfciMIP.glad.txt' are the segmented data (like the Level 3 data in TCGA), calculated with the GLAD algorithm: Sample ID, Chromosome, Start, End, Number of Probes in the segment, log2 copy number ratio of the segment (available on a Series records).

source_name: FFPE bladder cancer metastatic tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: As per manufacturer (Affymetrix)

value: metastatic

tag: tumor stage (t)

tag: tumor grade (g)

tag: node (n)

tag: distant mets (m)

value: ddMVAC


title: Metastatic Bladder Cancer 1541


title: Metastatic Bladder Cancer 1536


title: FFPE bladder cancer metastatic tissue 249

description:
X0006263_D07
at_array: a520683-00-643563-020512-4128466-90848.CEL
cg_array: a520683-00-912235-050212-4137157-87020.CEL

value: Gemzar


title: FFPE bladder cancer tumor tissue 231

description:
X0006263_D03
at_array: a520683-00-643563-020512-4128466-90840.CEL
cg_array: a520683-00-912235-050212-4137157-87039.CEL

source_name: FFPE bladder cancer tumor tissue

value: Carbo-Taxol

value: Gem-Cis


title: Metastatic Bladder Cancer 1537


title: FFPE bladder cancer tumor tissue 240

description:
X0006263_H09
at_array: a520683-00-912238-050312-4137158-87691.CEL
cg_array: a520683-00-912239-050312-4137158-87861.CEL


title: Metastatic Bladder Cancer 1525


title: FFPE bladder cancer tumor tissue 239

description:
X0006263_G11
at_array: a520683-00-912238-050312-4137158-87649.CEL
cg_array: a520683-00-912239-050312-4137158-87856.CEL


title: FFPE bladder cancer tumor tissue 206

description:
X0006263_C09
at_array: a520683-00-643556-020512-4128465-90950.CEL
cg_array: a520683-00-912235-050212-4137157-87031.CEL

value: MVAC


title: FFPE bladder cancer metastatic tissue 218

description:
X0006263_H05
at_array: a520683-00-912237-050312-4137158-87569.CEL
cg_array: a520683-00-912239-050312-4137158-87836.CEL


title: Metastatic Bladder Cancer 1522


title: Metastatic Bladder Cancer 1520


title: FFPE bladder cancer metastatic tissue 198

description:
X0006263_G03
at_array: a520683-00-912235-050212-4137157-87079.CEL
cg_array: a520683-00-912237-050312-4137158-87617.CEL


title: FFPE bladder cancer metastatic tissue 211

description:
X0006263_H04
at_array: a520683-00-912238-050312-4137158-87645.CEL
cg_array: a520683-00-912239-050312-4137158-87800.CEL


title: Metastatic Bladder Cancer 1524


title: Metastatic Bladder Cancer 1521


title: FFPE bladder cancer metastatic tissue 219

description:
X0006263_D02
at_array: a520683-00-643563-020512-4128466-90837.CEL
cg_array: a520683-00-912235-050212-4137157-87019.CEL

value: CT + RT


title: Metastatic Bladder Cancer 1517


title: Metastatic Bladder Cancer 1516


title: FFPE bladder cancer metastatic tissue 255

description:
X0006263_H11
at_array: a520683-00-912238-050312-4137158-87647.CEL
cg_array: a520683-00-912239-050312-4137158-87863.CEL


title: FFPE bladder cancer metastatic tissue 227

description:
X0006263_H06
at_array: a520683-00-912238-050312-4137158-87648.CEL
cg_array: a520683-00-912239-050312-4137158-87834.CEL


title: FFPE bladder cancer metastatic tissue 215

description:
X0006263_C12
at_array: a520683-00-912235-050212-4137157-87076.CEL
cg_array: a520683-00-912237-050312-4137158-87581.CEL

value: Taxol-Gemzar


title: Metastatic Bladder Cancer 1518

value: tumor


title: Metastatic Bladder Cancer 1514

value: radical cystectomy


title: FFPE bladder cancer metastatic tissue 222

description:
X0006263_G08
at_array: a520683-00-912238-050312-4137158-87666.CEL
cg_array: a520683-00-912237-050312-4137158-87561.CEL

value: invasive

value: Adriam Gem Carbo Tax


title: FFPE bladder cancer metastatic tissue 207

description:
X0006263_G04
at_array: a520683-00-912238-050312-4137158-87664.CEL
cg_array: a520683-00-912239-050312-4137158-87841.CEL

value: n

value: y

value: CT-RT


title: FFPE bladder cancer metastatic tissue 203

description:
X0005289_C03
at_array: a520683-00-643563-020512-4128466-90858.CEL
cg_array: a520683-00-912238-050312-4137158-87641.CEL

value: recurrence


title: Metastatic Bladder Cancer 1512

description: Genomic DNA isolated from metastatic bladder cancer

value: living


title: Metastatic Bladder Cancer 1513


title: FFPE bladder cancer metastatic tissue 195

description:
X0006263_C08
at_array: a520683-00-643559-020512-4128465-91391.CEL
cg_array: a520683-00-912235-050212-4137157-87050.CEL

value: metastatic

value: Gem-Carbo

value: RT

value: deceased


title: Metastatic Bladder Cancer 1523


title: FFPE bladder cancer tumor tissue 216

description:
X0006263_G06
at_array: a520683-00-912238-050312-4137158-87705.CEL
cg_array: a520683-00-912239-050312-4137158-87833.CEL

value: Carbo-Taxol


title: FFPE bladder cancer metastatic tissue 176

description:
X0006263_F07
at_array: a520683-00-643559-020512-4128465-91397.CEL
cg_array: a520683-00-912238-050312-4137158-87683.CEL

value: CMV RT

value: CMV


title: Metastatic Bladder Cancer 1509


title: Metastatic Bladder Cancer 1508


title: Metastatic Bladder Cancer 1510


title: FFPE bladder cancer metastatic tissue 188

description:
X0006263_F11
at_array: a520683-00-643559-020512-4128465-91389.CEL
cg_array: a520683-00-912237-050312-4137158-87596.CEL

tag: substage

value: a

value: MVAC

value: Taxol-Gemzar


title: FFPE bladder cancer tumor tissue 186

description:
X0005289_C01
at_array: a520683-00-912240-050312-4137158-87918.CEL
cg_array: a520683-00-912238-050312-4137158-87681.CEL

value: tumor

value: radical cystectomy

value: invasive

value: Gem-Cis


title: FFPE bladder cancer tumor tissue 169

description:
X0006263_C02
at_array: a520683-00-643556-020512-4128465-90994.CEL
cg_array: a520683-00-912237-050312-4137158-87552.CEL

value: n

value: y


title: Metastatic Bladder Cancer 1504

value: recurrence


title: Metastatic Bladder Cancer 1500

value: superficial

value: living


title: Metastatic Bladder Cancer 1503


title: Metastatic Bladder Cancer 1505


title: Metastatic Bladder Cancer 1357


title: FFPE bladder cancer tumor tissue 160

description:
X0006263_F06
at_array: a520683-00-643556-020512-4128465-90980.CEL
cg_array: a520683-00-912238-050312-4137158-87639.CEL

value: Gem-Carbo


title: Metastatic Bladder Cancer 1356


title: Metastatic Bladder Cancer 1350

value: deceased


title: FFPE bladder cancer tumor tissue 181

description:
X0006263_C04
at_array: a520683-00-643556-020512-4128465-90967.CEL
cg_array: a520683-00-912235-050212-4137157-87062.CEL


title: FFPE bladder cancer metastatic tissue 187

description:
X0006263_C06
at_array: a520683-00-643563-020512-4128466-90883.CEL
cg_array: a520683-00-811124-050712-4137168-69179.CEL

value: metastatic


title: Metastatic Bladder Cancer 1355


title: Metastatic Bladder Cancer 1340


title: Metastatic Bladder Cancer 1507


title: FFPE bladder cancer metastatic tissue 150

description:
X0005289_B05
at_array: a520683-00-643563-020512-4128466-90873.CEL
cg_array: a520683-00-912238-050312-4137158-87728.CEL


title: FFPE bladder cancer metastatic tissue 159

description:
X0006263_B09
at_array: a520683-00-811124-050712-4137168-69109.CEL
cg_array: a520683-00-912239-050312-4137158-87802.CEL

value: MCV


title: Metastatic Bladder Cancer 1351


title: Scrambled 168 hours sample 67

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: RNA,  Sample  :  67,  Treatment  :  Scrambled,  Control  :  Control,  Time  :  168,  Expt  :  Scrambled.168

data_processing: log2 Ratio of red/green

tag: RNA,  Sample

source_name: Untreated Cells

tag: Untreated


title: Metastatic Bladder Cancer 1308


title: FFPE bladder cancer tumor tissue 41

description:
X0006263_E10
at_array: a520683-00-643559-020512-4128465-91366.CEL
cg_array: a520683-00-912238-050312-4137158-87682.CEL

value: Docetaxel +/- ZD6474


title: Metastatic Bladder Cancer 1345


title: C3

city: Dublin

first: Shane

middle: P

last: Duggan

address: TCD Health Sciences Building, St James Hospital,

department: Clinical Medicine

country: Ireland

institute: Institute of Molecular Medicine

hyb_protocol: as per instructions by affymetrix

scan_protocol: as per instructions by affymetrix

data_processing: RMA normalized using Expression Console 1.2.0.20

source_name: Colon

label_protocol: as per instructions by affymetrix

extract_protocol: Samples were extracted by homogenisation in Tri reagent followed by clean up with Min-elute RNA purification kit.

tag: tissue

value: Colon

tag: cell type

value: Normal epithelium


title: FFPE bladder cancer tumor tissue 19

description:
X0006263_E06
at_array: a520683-00-643559-020512-4128465-91393.CEL
cg_array: a520683-00-912235-050212-4137157-87053.CEL

value: a


title: FFPE bladder cancer tumor tissue 64

description:
X0006263_F02
at_array: a520683-00-912254-050512-4137164-66226.CEL
cg_array: a520683-00-643559-020512-4128465-91300.CEL

value: tumor

value: MVAC


title: Scrambled 72 hours sample 68

description: RNA,  Sample  :  68,  Treatment  :  Scrambled,  Control  :  Control,  Time  :  72,  Expt  :  Scrambled.72


title: Metastatic Bladder Cancer 1301

description: Genomic DNA isolated from metastatic bladder cancer

value: radical cystectomy

value: invasive


title: FFPE bladder cancer tumor tissue 5

description:
X0006263_A11
at_array: a520683-00-912235-050212-4137157-87095.CEL
cg_array: a520683-00-912237-050312-4137158-87558.CEL

value: b

value: n

value: Cisplatin based


title: Scrambled 72 hours sample 65

description: RNA,  Sample  :  65,  Treatment  :  Scrambled,  Control  :  Control,  Time  :  72,  Expt  :  Scrambled.72


title: DU4

source_name: Duodenum

value: Duodenum


title: Metastatic Bladder Cancer 1347

value: superficial

value: y

value: recurrence

value: living


title: Metastatic Bladder Cancer 1300


title: Metastatic Bladder Cancer 1298


title: FFPE bladder cancer tumor tissue 25

description:
X0005289_B01
at_array: a520683-00-912240-050312-4137158-87880.CEL
cg_array: a520683-00-912234-050212-4137157-86916.CEL

value: deceased


title: SiRNA 168 hours sample 64

description: RNA,  Sample  :  64,  Treatment  :  SiRNA,  Control  :  Control,  Time  :  168,  Expt  :  SiRNA.168


title: Scrambled 168 hours sample 70

description: RNA,  Sample  :  70,  Treatment  :  Scrambled,  Control  :  Control,  Time  :  168,  Expt  :  Scrambled.168


title: Metastatic Bladder Cancer 1305


title: SiRNA 168 hours sample 60

description: RNA,  Sample  :  60,  Treatment  :  SiRNA,  Control  :  Control,  Time  :  168,  Expt  :  SiRNA.168


title: OS4

source_name: Oesophagus

value: Oesophagus


title: SiRNA 96 hours sample 63

description: RNA,  Sample  :  63,  Treatment  :  SiRNA,  Control  :  Control,  Time  :  96,  Expt  :  SiRNA.96


title: Metastatic Bladder Cancer 1294


title: U0126 96 hours sample 50

description: RNA,  Sample  :  50,  Treatment  :  U0126,  Control  :  Control,  Time  :  96,  Expt  :  U0126.96


title: DU1


title: SiRNA 72 hours sample 58

description: RNA,  Sample  :  58,  Treatment  :  SiRNA,  Control  :  Control,  Time  :  72,  Expt  :  SiRNA.72


title: SiRNA 96 hours sample 59

description: RNA,  Sample  :  59,  Treatment  :  SiRNA,  Control  :  Control,  Time  :  96,  Expt  :  SiRNA.96


title: SiRNA 72 hours sample 62

description: RNA,  Sample  :  62,  Treatment  :  SiRNA,  Control  :  Control,  Time  :  72,  Expt  :  SiRNA.72


title: OS3


title: U0126 48 hours sample 49

description: RNA,  Sample  :  49,  Treatment  :  U0126,  Control  :  Control,  Time  :  48,  Expt  :  U0126.48


title: SiRNA 48 hours sample 57

description: RNA,  Sample  :  57,  Treatment  :  SiRNA,  Control  :  Control,  Time  :  48,  Expt  :  SiRNA.48


title: C2

value: Colon


title: SiRNA 48 hours sample 61

description: RNA,  Sample  :  61,  Treatment  :  SiRNA,  Control  :  Control,  Time  :  48,  Expt  :  SiRNA.48


title: Metastatic Bladder Cancer 1291


title: Scrambled 48 hours sample 55

description: RNA,  Sample  :  55,  Treatment  :  Scrambled,  Control  :  Control,  Time  :  48,  Expt  :  Scrambled.48


title: OS1

value: Normal epithelium


title: U0126 10 hours sample 46

description: RNA,  Sample  :  46,  Treatment  :  U0126,  Control  :  Control,  Time  :  10,  Expt  :  U0126.10


title: FFPE bladder cancer tumor tissue 31

description:
X0006263_B04
at_array: a520683-00-912235-050212-4137157-87080.CEL
cg_array: a520683-00-912239-050312-4137158-87830.CEL


title: Metastatic Bladder Cancer 1289

description: Genomic DNA isolated from metastatic bladder cancer


title: Metastatic Bladder Cancer 1287


title: FFPE bladder cancer tumor tissue 63

description:
X0006263_B06
at_array: a520683-00-811124-050712-4137168-69147.CEL
cg_array: a520683-00-912239-050312-4137158-87860.CEL

value: a

value: Gem-Cis MVAC

value: Docetaxel +/- ZD6474


title: DU3


title: Bai_Animal_ID_14352

status: Public on Jul 06 2013

first: Kent

last: Hunter

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

description: Gene expression data of mammary tumors.

hyb_protocol: Hybridization was performed using an Affymetrix Fluidics Station, following the manufacturer's protocol.

scan_protocol: Scanning was performed using an Affymetrix Scanner, following the manufacturer's protocol.

data_processing: Data were processed using RMA.

source_name: PyMT-induced mammary tumors

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100n g total RNA.

growth_protocol: Tumors were permitted to grow until animal neared humane endpoints. Tumors were harvested, snap frozen and stored at -80oC until RNA extraction.

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

treatment_protocol: No treatment was performed.

tag: strain/background

value: Diversity Outcross x PyMT

value: mammary tumor

tag: mouse id


title: Bai_Animal_ID_14312

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14320

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14309

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14358

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14354

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14328

description: Gene expression data of mammary tumors.


title: C4


title: Bai_Animal_ID_14356

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14327

description: Gene expression data of mammary tumors.


title: U0126 24 hours sample 43

description: RNA,  Sample  :  43,  Treatment  :  U0126,  Control  :  Control,  Time  :  24,  Expt  :  U0126.24


title: U0126 48 hours sample 44

description: RNA,  Sample  :  44,  Treatment  :  U0126,  Control  :  Control,  Time  :  48,  Expt  :  U0126.48


title: Bai_Animal_ID_14329

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14306

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14352r

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14322

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14295

description: Gene expression data of mammary tumors.


title: U0126 10 hours sample 42

description: RNA,  Sample  :  42,  Treatment  :  U0126,  Control  :  Control,  Time  :  10,  Expt  :  U0126.10


title: Metastatic Bladder Cancer 1283

value: tumor

value: radical cystectomy

value: invasive


title: Metastatic Bladder Cancer 1280

value: n


title: Bai_Animal_ID_14291

description: Gene expression data of mammary tumors.


title: Scrambled 96 hours sample 69

description: RNA,  Sample  :  69,  Treatment  :  Scrambled,  Control  :  Control,  Time  :  96,  Expt  :  Scrambled.96


title: Bai_Animal_ID_14308

description: Gene expression data of mammary tumors.


title: Metastatic Bladder Cancer 1285


title: U0126 96 hours sample 45

description: RNA,  Sample  :  45,  Treatment  :  U0126,  Control  :  Control,  Time  :  96,  Expt  :  U0126.96


title: Bai_Animal_ID_14286

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14287

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14290

description: Gene expression data of mammary tumors.


title: Metastatic Bladder Cancer 1281


title: Bai_Animal_ID_14311

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14260

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14275

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14272

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14262

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14251

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14252r

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14250

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14280

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14248

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14231

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14224

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14282

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14223

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14200

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14253r

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14190

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14201

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14195

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14187

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14170

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14289

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14148

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14189

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14151

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14126

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14106

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14085

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14099

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14072

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14122

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14043

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14281

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14044

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14033

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14050r

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14124

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14027

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14032

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14058

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14018r

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14050

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14083

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14094

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14037

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14055

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14026

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14022r

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13999

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13986

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14000

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13983

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14002

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13958

description: Gene expression data of mammary tumors.


title: 9_Animal_ID_14021

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13948

description: Gene expression data of mammary tumors.


title: 5_Animal_ID_13976

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13987

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13974

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13981

description: Gene expression data of mammary tumors.


title: 6_Animal_ID_14150

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13973

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13956

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13998

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13975

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14005

description: Gene expression data of mammary tumors.


title: 8_Animal_ID_14185

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13950

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_13951

description: Gene expression data of mammary tumors.


title: 7_Animal_ID_14077

description: Gene expression data of mammary tumors.


title: 4_Animal_ID_14198

description: Gene expression data of mammary tumors.


title: 43_Animal_ID_14128

description: Gene expression data of mammary tumors.


title: 46_Animal_ID_13953

description: Gene expression data of mammary tumors.


title: 47_Animal_ID_14261

description: Gene expression data of mammary tumors.


title: 48_Animal_ID_14028

description: Gene expression data of mammary tumors.


title: 41_Animal_ID_14090

description: Gene expression data of mammary tumors.


title: 40_Animal_ID_14199

description: Gene expression data of mammary tumors.


title: 44_Animal_ID_14125

description: Gene expression data of mammary tumors.


title: 3_Animal_ID_14086

description: Gene expression data of mammary tumors.


title: 45_Animal_ID_14110

description: Gene expression data of mammary tumors.


title: 42_Animal_ID_14052

description: Gene expression data of mammary tumors.


title: 39_Animal_ID_14098

description: Gene expression data of mammary tumors.


title: Bai_Animal_ID_14001

description: Gene expression data of mammary tumors.


title: 38_Animal_ID_14271

description: Gene expression data of mammary tumors.


title: 37_Animal_ID_14118

description: Gene expression data of mammary tumors.


title: 32_Animal_ID_14127

description: Gene expression data of mammary tumors.


title: 35_Animal_ID_14048

description: Gene expression data of mammary tumors.


title: 36_Animal_ID_14024

description: Gene expression data of mammary tumors.


title: 31_Animal_ID_14103

description: Gene expression data of mammary tumors.


title: 33_Animal_ID_14182

description: Gene expression data of mammary tumors.


title: 29_Animal_ID_14078

description: Gene expression data of mammary tumors.


title: 24_Animal_ID_14149

description: Gene expression data of mammary tumors.


title: 26_Animal_ID_14141

description: Gene expression data of mammary tumors.


title: 30_Animal_ID_14089

description: Gene expression data of mammary tumors.


title: 27_Animal_ID_14064

description: Gene expression data of mammary tumors.


title: 28_Animal_ID_14121

description: Gene expression data of mammary tumors.


title: 25_Animal_ID_14061

description: Gene expression data of mammary tumors.


title: 34_Animal_ID_14051

description: Gene expression data of mammary tumors.


title: 2_Animal_ID_13960

description: Gene expression data of mammary tumors.


title: 20_Animal_ID_14247

description: Gene expression data of mammary tumors.


title: 22_Animal_ID_14015

description: Gene expression data of mammary tumors.


title: 21_Animal_ID_14233

description: Gene expression data of mammary tumors.


title: 1_Animal_ID_14266

description: Gene expression data of mammary tumors.


title: 17_Animal_ID_14267

description: Gene expression data of mammary tumors.


title: 16_Animal_ID_13955

description: Gene expression data of mammary tumors.


title: 15_Animal_ID_14056

description: Gene expression data of mammary tumors.


title: 14_Animal_ID_14273

description: Gene expression data of mammary tumors.


title: 23_Animal_ID_14091

description: Gene expression data of mammary tumors.


title: 13_Animal_ID_14176

description: Gene expression data of mammary tumors.


title: 19_Animal_ID_14249

description: Gene expression data of mammary tumors.


title: 18_Animal_ID_14095

description: Gene expression data of mammary tumors.


title: 11_Animal_ID_14264

description: Gene expression data of mammary tumors.


title: 12_Animal_ID_14227

description: Gene expression data of mammary tumors.


title: 10_Animal_ID_14087

description: Gene expression data of mammary tumors.


title: 97_Animal_ID_4534

description: Gene expression data of mammary tumors.

value: MOLF/Ei x PyMT


title: 95_Animal_ID_4532

description: Gene expression data of mammary tumors.


title: 90_Animal_ID_4515

description: Gene expression data of mammary tumors.


title: 87_Animal_ID_4495

description: Gene expression data of mammary tumors.


title: 80_Animal_ID_4451

description: Gene expression data of mammary tumors.


title: 93_Animal_ID_4525

description: Gene expression data of mammary tumors.


title: 85_Animal_ID_4486

description: Gene expression data of mammary tumors.


title: 98_Animal_ID_4537

description: Gene expression data of mammary tumors.


title: 89_Animal_ID_4513

description: Gene expression data of mammary tumors.


title: 88_Animal_ID_4496

description: Gene expression data of mammary tumors.


title: 94_Animal_ID_4529

description: Gene expression data of mammary tumors.


title: 77_Animal_ID_4433

description: Gene expression data of mammary tumors.


title: 99_Animal_ID_4539

description: Gene expression data of mammary tumors.


title: 79_Animal_ID_4435

description: Gene expression data of mammary tumors.


title: 81_Animal_ID_4452

description: Gene expression data of mammary tumors.


title: 82_Animal_ID_4478

description: Gene expression data of mammary tumors.


title: 78_Animal_ID_4434

description: Gene expression data of mammary tumors.


title: 92_Animal_ID_4522

description: Gene expression data of mammary tumors.


title: 84_Animal_ID_4485

description: Gene expression data of mammary tumors.


title: 73_Animal_ID_4386

description: Gene expression data of mammary tumors.


title: 134_Animal_ID_4638

description: Gene expression data of mammary tumors.


title: 96_Animal_ID_4533

description: Gene expression data of mammary tumors.


title: 91_Animal_ID_4517

description: Gene expression data of mammary tumors.


title: 86_Animal_ID_4491

description: Gene expression data of mammary tumors.


title: 75_Animal_ID_4403

description: Gene expression data of mammary tumors.


title: 83_Animal_ID_4482

description: Gene expression data of mammary tumors.


title: 76_Animal_ID_4413

description: Gene expression data of mammary tumors.


title: 133_Animal_ID_4547

description: Gene expression data of mammary tumors.


title: 74_Animal_ID_4392

description: Gene expression data of mammary tumors.


title: 132_Animal_ID_4516

description: Gene expression data of mammary tumors.


title: 129_Animal_ID_4488

description: Gene expression data of mammary tumors.


title: 126_Animal_ID_4438

description: Gene expression data of mammary tumors.


title: 127_Animal_ID_4459

description: Gene expression data of mammary tumors.


title: 121_Animal_ID_4164

description: Gene expression data of mammary tumors.


title: 130_Animal_ID_4492

description: Gene expression data of mammary tumors.


title: 125_Animal_ID_4378

description: Gene expression data of mammary tumors.


title: 122_Animal_ID_4262

description: Gene expression data of mammary tumors.


title: 123_Animal_ID_4315

description: Gene expression data of mammary tumors.


title: 120_Animal_ID_4144

description: Gene expression data of mammary tumors.


title: 110_Animal_ID_3654

description: Gene expression data of mammary tumors.


title: 105_Animal_ID_4614

description: Gene expression data of mammary tumors.


title: 119_Animal_ID_4142

description: Gene expression data of mammary tumors.


title: 131_Animal_ID_4511

description: Gene expression data of mammary tumors.


title: 124_Animal_ID_4357

description: Gene expression data of mammary tumors.


title: 116_Animal_ID_4036

description: Gene expression data of mammary tumors.


title: 115_Animal_ID_4030

description: Gene expression data of mammary tumors.


title: 102_Animal_ID_4567

description: Gene expression data of mammary tumors.


title: 111_Animal_ID_3871

description: Gene expression data of mammary tumors.


title: 113_Animal_ID_4016

description: Gene expression data of mammary tumors.


title: 109_Animal_ID_3540

description: Gene expression data of mammary tumors.


title: 104_Animal_ID_4610

description: Gene expression data of mammary tumors.


title: 117_Animal_ID_4038

description: Gene expression data of mammary tumors.


title: 114_Animal_ID_4020

description: Gene expression data of mammary tumors.


title: 107_Animal_ID_3273

description: Gene expression data of mammary tumors.


title: 112_Animal_ID_3939

description: Gene expression data of mammary tumors.


title: 128_Animal_ID_4461

description: Gene expression data of mammary tumors.


title: 118_Animal_ID_4139

description: Gene expression data of mammary tumors.


title: 108_Animal_ID_3427

description: Gene expression data of mammary tumors.


title: 103_Animal_ID_4569

description: Gene expression data of mammary tumors.


title: 106_Animal_ID_4615

description: Gene expression data of mammary tumors.


title: 101_Animal_ID_4546

description: Gene expression data of mammary tumors.


title: 071_Animal_ID_4382

description: Gene expression data of mammary tumors.


title: 070_Animal_ID_4380

description: Gene expression data of mammary tumors.


title: 068_Animal_ID_4376

description: Gene expression data of mammary tumors.


title: 069_Animal_ID_4379

description: Gene expression data of mammary tumors.


title: 100_Animal_ID_4540

description: Gene expression data of mammary tumors.


title: 072_Animal_ID_4385

description: Gene expression data of mammary tumors.


title: 067_Animal_ID_4375

description: Gene expression data of mammary tumors.


title: 064_Animal_ID_4363

description: Gene expression data of mammary tumors.


title: 063_Animal_ID_4360

description: Gene expression data of mammary tumors.


title: 057_Animal_ID_4345

description: Gene expression data of mammary tumors.


title: 065_Animal_ID_4367

description: Gene expression data of mammary tumors.


title: 066_Animal_ID_4374

description: Gene expression data of mammary tumors.


title: 047_Animal_ID_4310

description: Gene expression data of mammary tumors.


title: 059_Animal_ID_4349

description: Gene expression data of mammary tumors.


title: 049_Animal_ID_4333

description: Gene expression data of mammary tumors.


title: 044_Animal_ID_4278

description: Gene expression data of mammary tumors.


title: 039_Animal_ID_4258

description: Gene expression data of mammary tumors.


title: 055_Animal_ID_4343

description: Gene expression data of mammary tumors.


title: 050_Animal_ID_4334

description: Gene expression data of mammary tumors.


title: 061_Animal_ID_4356

description: Gene expression data of mammary tumors.


title: 058_Animal_ID_4348

description: Gene expression data of mammary tumors.


title: 060_Animal_ID_4352

description: Gene expression data of mammary tumors.


title: 052_Animal_ID_4337

description: Gene expression data of mammary tumors.


title: 051_Animal_ID_4335

description: Gene expression data of mammary tumors.


title: 042_Animal_ID_4275

description: Gene expression data of mammary tumors.


title: 054_Animal_ID_4342

description: Gene expression data of mammary tumors.


title: 046_Animal_ID_4299

description: Gene expression data of mammary tumors.


title: 056_Animal_ID_4344

description: Gene expression data of mammary tumors.


title: 041_Animal_ID_4273

description: Gene expression data of mammary tumors.


title: 048_Animal_ID_4312

description: Gene expression data of mammary tumors.


title: 053_Animal_ID_4341

description: Gene expression data of mammary tumors.


title: 045_Animal_ID_4295

description: Gene expression data of mammary tumors.


title: 038_Animal_ID_4256

description: Gene expression data of mammary tumors.


title: 040_Animal_ID_4263

description: Gene expression data of mammary tumors.


title: 043_Animal_ID_4277

description: Gene expression data of mammary tumors.


title: 037_Animal_ID_4183

description: Gene expression data of mammary tumors.


title: 036_Animal_ID_4180

description: Gene expression data of mammary tumors.


title: 032_Animal_ID_4158

description: Gene expression data of mammary tumors.


title: 034_Animal_ID_4174

description: Gene expression data of mammary tumors.


title: 026_Animal_ID_3947

description: Gene expression data of mammary tumors.


title: 028_Animal_ID_4025

description: Gene expression data of mammary tumors.


title: 031_Animal_ID_4143

description: Gene expression data of mammary tumors.


title: 017_Animal_ID_3792

description: Gene expression data of mammary tumors.


title: 030_Animal_ID_4140

description: Gene expression data of mammary tumors.


title: 029_Animal_ID_4028

description: Gene expression data of mammary tumors.


title: 019_Animal_ID_3832

description: Gene expression data of mammary tumors.


title: 035_Animal_ID_4175

description: Gene expression data of mammary tumors.


title: 012_Animal_ID_3594

description: Gene expression data of mammary tumors.


title: 023_Animal_ID_3942

description: Gene expression data of mammary tumors.


title: 014_Animal_ID_3598

description: Gene expression data of mammary tumors.


title: 025_Animal_ID_3945

description: Gene expression data of mammary tumors.


title: 015_Animal_ID_3790

description: Gene expression data of mammary tumors.


title: 011_Animal_ID_3544

description: Gene expression data of mammary tumors.


title: 027_Animal_ID_4021

description: Gene expression data of mammary tumors.


title: 018_Animal_ID_3807

description: Gene expression data of mammary tumors.


title: 024_Animal_ID_3943

description: Gene expression data of mammary tumors.


title: 016_Animal_ID_3803

description: Gene expression data of mammary tumors.


title: 033_Animal_ID_4161

description: Gene expression data of mammary tumors.


title: 020_Animal_ID_3872

description: Gene expression data of mammary tumors.


title: 010_Animal_ID_3536

description: Gene expression data of mammary tumors.


title: 009_Animal_ID_3533

description: Gene expression data of mammary tumors.


title: 022_Animal_ID_3878

description: Gene expression data of mammary tumors.


title: 062_Animal_ID_4358

description: Gene expression data of mammary tumors.


title: 021_Animal_ID_3874

description: Gene expression data of mammary tumors.


title: 005_Animal_ID_3493

description: Gene expression data of mammary tumors.


title: 008_Animal_ID_3508

description: Gene expression data of mammary tumors.


title: 013_Animal_ID_3595

description: Gene expression data of mammary tumors.


title: 007_Animal_ID_3498

description: Gene expression data of mammary tumors.


title: 003_Animal_ID_3276

description: Gene expression data of mammary tumors.


title: 004_Animal_ID_3402

description: Gene expression data of mammary tumors.


title: 002_Animal_ID_3275

description: Gene expression data of mammary tumors.


title: 001_Animal_ID_1491

description: Gene expression data of mammary tumors.


title: 006_Animal_ID_3497

description: Gene expression data of mammary tumors.


title: Primary T-ALL sample 9

city: Baltimore

first: Yezhou

last: Sun

address: 620 W. Lexington St.

institute: U. of Maryland, Baltimore

description: Gene Expression Data from T ALL Patient

hyb_protocol: Following fragmentation, 5 ug of labled DNA was hybridized for 16 hr at 45C on HuGene-1_0-st-v1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Genechip Scanner 3000 and software AffyMetrix Genechip Command Console .

data_processing: The data were analyzed using the affy R package to load the data before using the quantile method in the limma R package from Bioconductor to normalize all of the data

source_name: T ALL Patient

label_protocol: DNA was labeled by teriminal deoxynucleotidyl transferase (TdT) with the Affymetrix propritary DNA labeling reagent that is covalently linked to biotin. (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All the leukemia cell lines were culture in vitro under appropriate cell cutlure conditions according to the supplier recommondataion. Normal mature hematopoietic cells were purifed from normal healthy donor peripheral blood using Ficoll gradiant centrifugation followed by FACS sorting.

extract_protocol: Cell were lysed in Trizol and total RNA was purifed using miRNAeasy kit  according to the manufacturer's instructions.

tag: phenotype

value: Leukemia


title: Primary B-ALL sample 43-spleen-2

description: Gene Expression Data from B ALL Patient

source_name: B ALL Patient


title: Primary B-ALL sample 47

description: Gene Expression Data from B ALL Patient


title: Primary T-ALL sample 7-bone marrow

description: Gene Expression Data from T ALL Patient


title: Primary T-ALL sample 11

description: Gene Expression Data from T ALL Patient


title: Primary B-ALL sample 48-spleen

description: Gene Expression Data from B ALL Patient


title: Primary T-ALL sample 10

description: Gene Expression Data from T ALL Patient


title: Primary B-ALL sample 41

description: Gene Expression Data from B ALL Patient


title: Primary B-ALL sample 43-spleen-1

description: Gene Expression Data from B ALL Patient


title: Primary AML sample 9-spleen

description: Gene Expression Data from AML Patient

source_name: AML Patient


title: Primary T-ALL sample 10-spleen

description: Gene Expression Data from T ALL Patient


title: Primary AML sample 201

description: Gene Expression Data from AML Patient


title: Primary AML sample 201-bone marrow

description: Gene Expression Data from AML Patient


title: Primary B-ALL sample 42-spleen

description: Gene Expression Data from B ALL Patient


title: Primary B-ALL sample 40

description: Gene Expression Data from B ALL Patient


title: Primary T-ALL sample 12

description: Gene Expression Data from T ALL Patient


title: Primary B-ALL sample 42

description: Gene Expression Data from B ALL Patient


title: Primary B-ALL sample 50-spleen

description: Gene Expression Data from B ALL Patient


title: Primary B-ALL sample 25-2

description: Gene Expression Data from B ALL Patient


title: Primary AML sample 14-bone marrow

description: Gene Expression Data from AML Patient


title: Primary T-ALL sample 8

description: Gene Expression Data from T ALL Patient


title: Primary B-ALL sample 23-spleen-1

description: Gene Expression Data from B ALL Patient


title: Primary T-ALL sample 6-bone marrow

description: Gene Expression Data from T ALL Patient


title: Primary B-ALL sample 46

description: Gene Expression Data from B ALL Patient


title: Primary B-ALL sample 4-spleen

description: Gene Expression Data from B ALL Patient


title: Primary B-ALL sample 5

description: Gene Expression Data from B ALL Patient


title: Primary T-ALL sample 13

description: Gene Expression Data from T ALL Patient


title: MHH-CALL4-3

description: Gene Expression Data from B ALL Cell Line

source_name: B ALL Cell Line


title: Primary AML sample 9

description: Gene Expression Data from AML Patient


title: Primary B-ALL sample 21-spleen-1

description: Gene Expression Data from B ALL Patient


title: Normal CD34+ cell-2

description: Gene Expression Data from CD34+HSPC

value: Normal


title: KG1a-1

description: Gene Expression Data from AML Cell Line

source_name: AML Cell Line


title: KG1a-3

description: Gene Expression Data from AML Cell Line


title: KASUMI1-2

description: Gene Expression Data from AML Cell Line


title: Primary T-ALL sample 4-spleen-2

description: Gene Expression Data from T ALL Patient


title: MOLT3-1

description: Gene Expression Data from T ALL Cell Line

source_name: T ALL Cell Line


title: Primary T-ALL sample 15

description: Gene Expression Data from T ALL Patient


title: MOLT3-3


title: Primary B-ALL sample 16

description: Gene Expression Data from B ALL Patient


title: KOPN8-2


title: REH-2


title: KG1a-2

description: Gene Expression Data from AML Cell Line


title: Normal CD34+ cell-1

description: Gene Expression Data from CD34+HSPC


title: MHH-CALL4-2


title: MOLT3-2


title: HL60-3

description: Gene Expression Data from AML Cell Line


title: REH-3


title: Normal CD34+ cell-3

description: Gene Expression Data from CD34+HSPC


title: HL60-1

description: Gene Expression Data from AML Cell Line


title: KASUMI1-1

description: Gene Expression Data from AML Cell Line


title: K562-2

description: Gene Expression Data from AML Cell Line


title: KOPN8-3


title: Primary B-ALL sample 23-spleen-2

description: Gene Expression Data from B ALL Patient


title: MUTZ5-2


title: REH-1


title: K562-3

description: Gene Expression Data from AML Cell Line


title: Primary B-ALL sample 19-spleen

description: Gene Expression Data from B ALL Patient


title: Primary B-ALL sample 30

description: Gene Expression Data from B ALL Patient


title: Primary T-ALL sample 1-spleen

description: Gene Expression Data from T ALL Patient


title: U937-2

description: Gene Expression Data from AML Cell Line


title: Primary B-ALL sample 21-bone marrow

description: Gene Expression Data from B ALL Patient


title: M07e-3

description: Gene Expression Data from AML Cell Line


title: Primary B-ALL sample 27

description: Gene Expression Data from B ALL Patient


title: KASUMI1-3

description: Gene Expression Data from AML Cell Line


title: U937-3

description: Gene Expression Data from AML Cell Line


title: M07e-1

description: Gene Expression Data from AML Cell Line


title: MHH-CALL4-1


title: ML2-3

description: Gene Expression Data from AML Cell Line


title: MOLT16-2


title: M07e-2

description: Gene Expression Data from AML Cell Line


title: ML2-2

description: Gene Expression Data from AML Cell Line


title: Primary B-ALL sample 22

description: Gene Expression Data from B ALL Patient


title: Primary B-ALL sample 25-1

description: Gene Expression Data from B ALL Patient


title: MOLT16-3


title: MUTZ5-1


title: MOLT16-1


title: KARPAS45-2


title: Primary B-ALL sample 17

description: Gene Expression Data from B ALL Patient


title: ML2-1

description: Gene Expression Data from AML Cell Line


title: JURKAT-1


title: RCHACV-1


title: CEM-1


title: KASUMI2-1


title: NALM6-1


title: JURKAT-3


title: RCHACV-3


title: KARPAS45-3


title: MHH-CALL3-3


title: SUPB15-3


title: KARPAS45-1


title: MHH-CALL3-2


title: RCHACV-2


title: JURKAT-2


title: Primary AML sample 39

description: Gene Expression Data from AML Patient


title: Primary T-ALL sample 1

description: Gene Expression Data from T ALL Patient


title: HL60-2

description: Gene Expression Data from AML Cell Line


title: CEM-2


title: Primary B-ALL sample 21-spleen-2

description: Gene Expression Data from B ALL Patient


title: NALM6-2


title: SUPB15-2


title: KASUMI2-3


title: KOPN8-1


title: MUTZ5-3


title: KASUMI2-2


title: SUPB15-1


title: HEK-PLZF_PLZF_PLZF

status: Public on Jul 05 2013

city: Berlin

first: Daniela

last: Zaade

address: Hessische Straße 3-4

department: Center for Cardiovascular Research

institute: Charité

hyb_protocol: Arrays were hybridized by Imagenes, Berlin, Germany  (www.imagenes-bio.de)

scan_protocol: Arrays were scanned by Imagenes, Berlin, Germany  (www.imagenes-bio.de)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. The data were further analysed using Genome Analyzer, Next Generation Sequencing (NGS) Analyzer and RegionMiner (all Genomatix).

source_name: PLZF ChIP DNA from stably PLZF-overexpressing HEK293T cells

label_protocol: Labeling was done by Imagenes, Berlin, Germany  (www.imagenes-bio.de)

growth_protocol: Cells were cultured in DMEM, 10% FBS and 100 U/ml penicillin and 100 µg/ml streptomycin

extract_protocol: KELLY cells were fixed at a conﬂuence of about 90% using 1% formaldehyde (Merck, Darmstadt, Germany) in PBS (Life Technologies) for 7 min at 37 °C. Subsequently, cells were rinsed twice with ice-cold 1X PBS, scraped off in 1X PBS and centrifuged for 5 min at 660 g. Each pellet was resuspended in 2.5 ml lysis buffer (1% SDS, 50 mM Tris–HCl, 1X complete protease inhibitor cocktail (Roche, Mannheim, Germany), 5 mM EDTA (ﬁnal concentration); pH 8.1), followed by a 20 min incubation on ice. Soniﬁcation, immunoprecipitation and reversal of crosslink were performed according to Bryant and Ptashne using 3 µg of the following antibodies: anti-PLZF (mouse mAb (2A9), Calbiochem/ EMD Millipore, Darmstadt, Germany) and anti-RNA polymerase II (raised against a peptide mapping at the N-terminus; sc-899 X, Santa Cruz Biotechnology, Santa Cruz, USA). Soniﬁcation was carried out using the Sonoplus HD 2070/ UW 2070 soniﬁer with the tip MS 72 (Bandelin Electronic, Berlin, Germany) and a constant duty cycle with output control (power %) of 100 for 20 s (twice) and output control of 30% for 20 s (three times). After reversal of crosslink, DNA was purified using QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). Quantitative genomic PCR was performed applying Go-Taq qPCR Master Mix (Promega) and the following primers located around the transcriptional start site: Human beta-actin promoter: 5´ aatgctgcactgtgcggcga-3´ (sense), 5´-ggcggatcggcaaaggcga-3´ (antisense). Input (total) DNA served as positive controls.

tag: chip antibody

value: anti-PLZF (mouse mAb (2A9), Calbiochem/EMD Millipore, Darmstadt, Germany)

source_name: PLZF ChIP DNA from HEK293T cells stably transfected with insertless pCEP4


title: Kelly-PLZF_PLZF_IgG

source_name: PLZF ChIP DNA from stably PLZF-overexpressing KELLY cells

growth_protocol: Cells were cultured in RPMI1640, 10% FBS and 100 U/ml penicillin and 100 µg/ml streptomycin

tag: cell line

value: KELLY

source_name: IgG ChIP DNA from KELLY cells from stably PLZF-overexpressing KELLY cells

value: IgG


title: Kelly-pCEP4_PLZF_IgG

source_name: PLZF ChIP DNA from KELLY cells stably transfected with insertless pCEP4

source_name: IgG ChIP DNA from KELLY cells stably transfected with insertless pCEP4.


title: U937-1

description: Gene Expression Data from AML Cell Line


title: Kelly-PLZF_PolII_PolII

source_name: RNA polymerase II ChIP DNA from stably PLZF-overexpressing KELLY cells

value: anti-RNA polymerase II (sc-899 X, Santa Cruz Biotechnology, Santa Cruz, USA)

source_name: RNA polymerase II ChIP DNA from KELLY cells stably transfected with insertless pCEP4


title: Kelly-pCEP4_PolII_IgG

source_name: IgG ChIP DNA from KELLY cells stably transfected with insertless pCEP4


title: K562-1

description: Gene Expression Data from AML Cell Line


title: Primary B-ALL sample 29

description: Gene Expression Data from B ALL Patient


title: Kelly-PLZF_PolII_IgG

source_name: IgG ChIP DNA from stably PLZF-overexpressing KELLY cells


title: CEM-3


title: NALM6-3


title: Primary B-ALL sample 23

description: Gene Expression Data from B ALL Patient


title: Primary AML sample 14

description: Gene Expression Data from AML Patient


title: Primary AML sample 1

description: Gene Expression Data from AML Patient


title: RIP140inERabcells

type: SRA

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

library_source: genomic

data_processing:
Sequences generated were mapped uniquely onto the human genome (hg18) by ELAND.
MACS (Model-based Analysis of ChIP-Seq) algorithm (Zhang et al, 2008) was used to identify enriched peak regions (default settings) with a p-value cutoff of 6.0e-7 and FDR of 0.01.
Genome_build: hg18
Supplementary_files_format_and_content: bed files

source_name: MCF-7 cells

growth_protocol: The cells were maintained in phenol red-free MEM plus 5% charcoal-dextran-treated calf serum for at least 3 days and were then seeded at a density of 3 x 10^5 cells per 10 cm tissue culture dish (Corning, Corning, NY) for 2 days before adenovirus infection. Recombinant adenoviruses were constructed and prepared as described (Chang et al, 2006). Adenoviral infection conditions were those described previously (Chang et al, 2006; Charn et al, 2010; Frasor et al, 2006) and were used to generate MCF-7 cells expressing levels of ERβ equal to that of the endogenously expressed ERα. ERβ only cells were generated from these cells by knockdown of ERα in parental cells using the following siERα sequences from Dharmacon: forward, 5’-UCAUCGCAUUCCUUGCAAAdTdT-3’, and reverse, 5’-UUUGCAAGGAAUGCGAUGAdTdT-3’. siRNA experiments were performed as previously described, and resulted in knocknown of ERα mRNA and protein by greater than 95% (Chang et al, 2008). Briefly, cells were transfected with 20 nM siCtrl or siERα for 48 h after infection.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIP DNA was prepared into libraries according to Illumina Solexa ChIP-seq sample processing methods, and single read sequencing was performed using the Illumina Solexa Genomic Analyzer.

treatment_protocol: Cells were treated with 10 nM E2 (Sigma-Aldrich) for 45 minutes.

value: Human breast Adenocarcinoma

tag: infected with

value: adenovirus carrying estrogen receptor beta (AdERb)

tag: transfected with

value: siCtrl

tag: treated with

value: 10 nM E2 (Sigma-Aldrich) for 45 min

value: RIP140 antibody

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #


title: RIP140inERbcells

value: siERα


title: RIP140inERacells

value: adenovirus carrying no insert (Ad)


title: Primary AML sample 27

description: Gene Expression Data from AML Patient


title: SRC3inERbcells

value: SRC3 antibody


title: GM-CSF

city: Montreal

first: mathieu

last: tremblay

state: QC

address: 2950 Chemin de Polytechnique, pav marcelle-coutu 1432

country: Canada

institute: Université de Montréal/IRIC

hyb_protocol: Hybridization to the probe array HG-U133A (Affymetrix) was performed by the Ottawa Genome Center.

scan_protocol: Scanning performed by the Ottawa Genome Center.

data_processing:
Normalization and summarization were performed with GeneChip Robust Multichip Analysis (www.bioconductor.org) and statistical analysis performed in R (www.r-project.org).
Following a false discovery rate multiple test correction, genes that show a significant change (q≤0.1) were classified into up-regulated by ΔbSCL or down regulated. Genes were subsequently selected based on published association with apoptosis.

source_name: TF-1 cells, expressing MSCV-GFP, treated with GM-CSF for 6h

label_protocol: The extract was labelled using the GeneChip Eukaryotic Small Sample Target Labelling protocol (Affymetrix).

growth_protocol: The TF-1 human cell line was maintained in Iscove´s Modified Dulbecco´s Medium (IMDM) supplemented with 10% fetal calf serum (FCS) and 5 ng/ml human GM-CSF.

extract_protocol: RNA was extracted and purified using Qiagen RNeasy Mini Kit (P/N 741104) and resuspended in 5 ml of RNase free water at a concentration of 0.05 mg/ul.

treatment_protocol: TF-1 cells expressing either MSCV-GFP or MSCV-GFP-ΔbSCL were stimulated with GM-CSF (5 ng/mL), SF (20ng/mL) or Epo for 6 hours after over-night growth factor deprivation.

tag: treatment

value: GM-CSF

tag: retroviral vector

value: MSCV-GFP


title: Primary AML sample 41

description: Gene Expression Data from AML Patient

value: Leukemia


title: Primary AML sample 28

description: Gene Expression Data from AML Patient


title: Primary AML sample 40

description: Gene Expression Data from AML Patient


title: Primary AML sample 33

description: Gene Expression Data from AML Patient


title: Primary AML sample 8

description: Gene Expression Data from AML Patient


title: SRC3inERacells


title: ERBetainERbcells

value: ERβ antibodies were a combination with equal parts of CWK-F12 (produced in our lab (Choi et al, 2001)), GTX70182 (GeneTex), GR40 (Calbiochem), and PA1-311 (Affinity Bioreagents)


title: SRC3inERabcells


title: DbSCL/EPO

source_name: TF-1 cells, expressing DbSCL-GFP, treated with Erythropoietin for 6h

value: Erythropoietin

value: MSCV-DbSCL


title: Primary AML sample 44

description: Gene Expression Data from AML Patient

source_name: AML Patient


title: ERalpha inERabcells

value: Eralpha HC-20


title: ERalphainERacells


title: EPO

source_name: TF-1 cells, expressing MSCV-GFP, treated with Erythropoietin for 6h


title: MHH-CALL3-1

source_name: B ALL Cell Line


title: SF

source_name: TF-1 cells, expressing MSCV-GFP, treated with Steel Factor for 6h

value: Steel Factor


title: Primary AML sample 3

description: Gene Expression Data from AML Patient


title: Primary AML sample 42

description: Gene Expression Data from AML Patient


title: Primary AML sample 12

description: Gene Expression Data from AML Patient


title: KELLY, DMSO control, rep 2

hyb_protocol: Samples were hybridized with Genechip Human Gene 1.0 ST Arrays using Affymetrix Hybridization Kit.

scan_protocol: Scanning was performed at the microarray core facility at the Charité, Berlin, Germany (http://lfgc.charite.de/).

data_processing:
Data were processed using Chipinspector software (Genomatix GmbH). Raw data were normalised on the single probe level and subsequent pairwise comparison analyses of the expression values from the experimental condition versus control conditions were performed based on a single-sided permutational t-test analysis.
ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided.

source_name: KELLY, DMSO control

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Sense Target Labeling Assay (Affymetrix).

growth_protocol: KELLY cells cultured in RPMI1640 medium

extract_protocol: RNA extraction using Nucleospin-RNA-II (Macherey-Nagel)

treatment_protocol: KELLY cells were incubated with a final concentration of 10 µM genistein for 48 h or 1 nM of bafilomycin A1 for 48 h. Genistein and bafilomycin were solved in 1% DMSO; 1% DMSO (final) was used as control.

value: KELLY


title: ERBetainERabcells

value: Human breast Adenocarcinoma

value: adenovirus carrying estrogen receptor beta (AdERb)


title: KELLY, DMSO control, rep 3


title: KELLY, DMSO control, rep 1


title: KELLY, bafilomycin incubation, rep 3

source_name: KELLY, bafilomycin incubation


title: KELLY, bafilomycin incubation, rep 2


title: KELLY, bafilomycin incubation, rep 1


title: DbSCL/SF

source_name: TF-1 cells, expressing DbSCL-GFP, treated with Steel Factor for 6h


title: KELLY, genistein incubation, rep 3

source_name: KELLY, genistein incubation


title: KELLY, genistein incubation, rep 1


title: R993_EPC

city: Milan

first: Giuliana

last: Gregato

address: Via ripamonti 435

department: Anatomy pathology

country: Italy

institute: IEO

hyb_protocol: Hybridization mix for target dilution (100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20) was prepared as indicated by Affymetrix, including DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip cartridge. A single GeneChip Human Gene 1.0 ST was then hybridized with each biotin-labelled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip cartridges were washed and stained with GeneChip Hybridization, Wash and Stain Kit in the Affymetrix fluidics station following the FS450_0007 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.

scan_protocol: Images were scanned using an Affymetrix GeneChip Scanner3000 7G, using default parameters. The resulting images were analysed using GeneChip Operating Software v1.2 (GCOS1.2).

data_processing:
The data were preprocessed with RMA using Partek GS software from Partek Inc., St.Louis, Missouri, USA using default settings. All analysis were performed considering only 28829 probesets belonging to the category main
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.na30.1.hg19.probeset.csv

source_name: CD13- cells from 7 Lipotransfer aspirate

label_protocol: Biotin-labelled cDNA targets were synthesized starting from 200 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip WT cDNA Synthesis and Amplification Kit . With the same kit was synthesized the sense strand cDNA before to be fragmented and labelled with GeneChip WT Teminal Labeling Kit.. All steps of the labelling protocol were performed as suggested by Affymetrix (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

extract_protocol: Total RNA extraction  with QiaAmp RNA blood mini kit with DnaseI Rnase-free treatment.

treatment_protocol: digestion with collagenase and sorting of CD34+CD13- and CD34+CD13+ cells from lipotransfer aspirates

tag: gender

value: female


title: R993_ASC

source_name: CD13+ cells from 7 Lipotransfer aspirate


title: Cells obtained from GFP+ CD24+CD29lo sorted mammary epithelial cells [Sample 34]

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

description: Mammary epithelial cell population sorted with the markers GFP+ and CD24+CD29lo using flow cytometry

hyb_protocol: Illumina hybridization protocol at 48 degrees.

scan_protocol: Standard Illumina scanning protocol (Genome Studio Version 2011.1)

data_processing: The data were normalised using standard quantile normalization followed by an empirical Bayes normalization (PMID: 16632515) to account for batch specific differences using R 2.14.1.

source_name: GFP+ CD24+CD29lo mammary epithelial cells

label_protocol: Biotinylated cDNA were prepared with the Nugen WT-Ovation Pico RNA amplification kit (Version 1.0).

extract_protocol: RNA was extracted with Qiagen RNeasy Micro Kit , followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser using RNA Pico Kit (Agilent).

tag: strain

value: CD1 backcrossed to FVB

tag: age

value: 4 weeks

value: Sorted mammary epithelial cell


title: Cells obtained from GFP+ CD24+CD29+ sorted mammary epithelial cells [Sample 32]

description: Mammary epithelial cell population sorted with the markers GFP+ and CD24+CD29+ using flow cytometry

source_name: GFP+ CD24+CD29+ mammary epithelial cells

tag: tissue


title: Cells obtained from GFP- CD24+CD29+ sorted mammary epithelial cells [Sample 29]

description: Mammary epithelial cell population sorted with the markers GFP- and CD24+CD29+ using flow cytometry

source_name: GFP- CD24+CD29+ mammary epithelial cells


title: Cells obtained from GFP- CD24+CD29+ sorted mammary epithelial cells [Sample 25]


title: Cells obtained from GFP+ CD24+CD29+ sorted mammary epithelial cells [Sample 28]


title: Cells obtained from GFP- CD24+CD29+ sorted mammary epithelial cells [Sample 30]


title: Cells obtained from GFP- CD24+CD29lo sorted mammary epithelial cells [Sample 26]

description: Mammary epithelial cell population sorted with the markers GFP- and CD24+CD29lo using flow cytometry

source_name: GFP- CD24+CD29lo mammary epithelial cells


title: Cells obtained from GFP- CD24+CD29+ sorted mammary epithelial cells [Sample 33]


title: Cells obtained from GFP+ CD24+CD29lo sorted mammary epithelial cells [Sample 22]


title: Cells obtained from GFP- CD24+CD29lo sorted mammary epithelial cells [Sample 31]


title: Cells obtained from GFP- CD24+CD29+ sorted mammary epithelial cells [Sample 21]


title: treat_48h_2_Cy5

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

hyb_protocol: Samples were mixed with blocking agent, fragmentation- and hybridization buffer, and were hybridized to Agilent SurePrint G3 Mouse GE 8 x 60K Microarrays for 17 hours at 65°C. Microarrays were washed and scanned with Agilent Scanner, using manufacturer provided protocols.

scan_protocol: scanned on an Agilent Scanner G2505C; Agilent Feature Extraction software 11.0.1.1

data_processing: Raw data files were imported into R v. 2.15 and analyzed with the BioConductor package limma

source_name: Mouse embryonic fibroblasts actinonin (150uM) treated for 48h

label_protocol: 120 ng of total RNA was primed using oligo-dT(T7) promoter primers and converted to cDNA with AffinityScript RNase Block (mix of enzymes, Agilent). Primed cDNA was amplified and labeled using fluorescent dNTP-nucleotides (Cy3 and Cy5) and T7 RNA Polymerase. Clean-up of labelled and amplified samples was performed by using Qiagen´s RNeasy mini spin columns. RNA Spike-In Kit was used to monitor the success of the labelling.

growth_protocol: Mouse embryonic fibroblasts were cultured at 37°C in Dulbecco’s modified Eagle’s medium (Lonza) supplemented with 10% (v/v) foetal bovine serum (FBS), 1x glutamax and 50mg/ml uridine. Cells were collected at 90% confluence.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: For each actinonin treated time point (6, 24, 48, and 72 hours) and control, four independent samples were used (n=4). Each individual sample (n=1) consisted of RNA extracted from cells of four 10 cm plates pooled together. The four independent total RNAs samples (n=4) were labeled with either Cy3 or Cy5.

tag: cell type

value: MEFs

value: Balb/c background

value: actinonin (150uM) treated for 48h


title: treat_24h_2_Cy5

source_name: Mouse embryonic fibroblasts actinonin (150uM) treated for 24h

value: actinonin (150uM) treated for 24h


title: Cells obtained from GFP+ CD24+CD29+ sorted mammary epithelial cells [Sample 24]


title: HEK293T, stable transfection of insertless vector, replica 3

growth_protocol: HEK293T cells were cultured in DMEM medium.

tag: genetic modification


title: Cells obtained from GFP+ CD24+CD29lo sorted mammary epithelial cells [Sample 19]


title: Cells obtained from GFP- CD24+CD29lo sorted mammary epithelial cells [Sample 20]


title: Cells obtained from GFP+ CD24+CD29lo sorted mammary epithelial cells [Sample 23]


title: Cells obtained from GFP- CD24+CD29lo sorted mammary epithelial cells [Sample 27]


title: Cells obtained from GFP+ CD24+CD29+ sorted mammary epithelial cells [Sample 17]


title: treat_24h_1_Cy5


title: treat_6h_2_Cy5

source_name: Mouse embryonic fibroblasts actinonin (150uM) treated for 6h

value: actinonin (150uM) treated for 6h


title: Cells obtained from GFP+ CD24+CD29lo sorted mammary epithelial cells [Sample 16]


title: Cells obtained from GFP- CD24+CD29lo sorted mammary epithelial cells [Sample 18]


title: HEK293T, stable PLZF overexpression, replica 3

source_name: HEK293T, stable PLZF overexpression

value: stable PLZF overexpression


title: HEK293T, stable transfection of insertless vector, replica 2


title: HEK293T, stable PLZF overexpression, replica 2

source_name: HEK293T, stable PLZFoverexpression

value: stable PLZFoverexpression


title: HEK293T, stable transfection of insertless vector, replica 1


title: Cells obtained from GFP+ CD24+CD29+ sorted mammary epithelial cells [Sample 15]


title: ctrl_0h_2_Cy5

source_name: Mouse embryonic fibroblasts carrier EtOH treated 3ul/ml

value: EtOH treated 3ul/ml


title: Cells obtained from GFP+ CD24+CD29lo sorted mammary epithelial cells [Sample 12]


title: Cells obtained from GFP- CD24+CD29+ sorted mammary epithelial cells [Sample 13]


title: HEK293T, stable PLZF overexpression, replica 1


title: Cells obtained from GFP- CD24+CD29lo sorted mammary epithelial cells [Sample 14]


title: Cells obtained from GFP- CD24+CD29lo sorted mammary epithelial cells [Sample 8]


title: Cells obtained from GFP+ CD24+CD29+ sorted mammary epithelial cells [Sample 11]


title: Cells obtained from GFP+ CD24+CD29lo sorted mammary epithelial cells [Sample 10]


title: KELLY, stable transfection of insertless vector, replica 2

hyb_protocol: Samples were hybridized with Genechip Human Exon 1.0 ST Arrays using Affymetrix Hybridization Kit..


title: Cells obtained from GFP- CD24+CD29lo sorted mammary epithelial cells [Sample 6]


title: KELLY, stable PLZF-HA overexpression, replica 2

source_name: KELLY, stable PLZF-HA overexpression

value: stable PLZF-HA overexpression


title: Cells obtained from GFP+ CD24+CD29+ sorted mammary epithelial cells [Sample 9]


title: treat_72h_1_Cy5

source_name: Mouse embryonic fibroblasts actinonin (150uM) treated for 72h

value: actinonin (150uM) treated for 72h


title: KELLY, stable transfection of insertless vector, replica 1

value: KELLY


title: ctrl_0h_1_Cy5


title: treat_48h_1_Cy5


title: Cells obtained from GFP- CD24+CD29lo sorted mammary epithelial cells [Sample 7]


title: treat_72h_2_Cy5


title: KELLY, stable PLZF-HA overexpression, replica 1


title: KELLY, scrambled siRNA, rep 3

hyb_protocol: Samples were hybridized with Genechip Human Exon 1.0 ST Arrays using Affymetrix Hybridization Kit.

data_processing:
Data were processed using Chipinspector software (Genomatix GmbH). Raw data were normalised on the single probe level and subsequent pairwise comparison analyses of the expression values from the experimental condition versus control conditions were performed based on a single-sided permutational t-test analysis
ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided.

source_name: KELLY, scrambled siRNA

treatment_protocol: SiRNA experiments were performed with siRNA against the (P)RR or scrambled control siRNA using Hiperfect (Qiagen, Hilden, Germany) and a final siRNA concentration of 25 nM. SiRNA was transfected twice (48 h and 24 h before harvest).


title: treat_6h_1_Cy5


title: Cells obtained from GFP+ CD24+CD29lo sorted mammary epithelial cells [Sample 4]


title: KELLY, siRNA against (P)RR, rep 3

source_name: KELLY, siRNA against (P)RR


title: KELLY, scrambled siRNA, rep 2


title: Cells obtained from GFP+ CD24+CD29+ sorted mammary epithelial cells [Sample 3]


title: KELLY, siRNA against (P)RR, rep 2


title: ctrl_0h_2_Cy3


title: treat_72h_2_Cy3


title: KELLY, scrambled siRNA, rep 1


title: Cells obtained from GFP- CD24+CD29lo sorted mammary epithelial cells [Sample 5]


title: Cells obtained from GFP+ CD24+CD29+ sorted mammary epithelial cells [Sample 1]


title: KELLY, siRNA against (P)RR, rep 1


title: Wild type with tumor produced by AT-3 cell line 2

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

hyb_protocol: The labeled probes were then mixed with hybridization reagents and hybridized overnight to the MouseWG-6 v2 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio gene expression module (V1.6.0)

source_name: Splenic CD11b+Gr-1 high cell populations

label_protocol: Initially, we converted 250-500 ng total RNA to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA (Illumina TotalPrep RNA Amplification Kit, Ambion Inc., Austin, TX).

extract_protocol: Total RNA from highly purified splenic CD11b+Gr-1high cells from the different experimental groups was quantified by a ND-1000 spectrophotometer (NanoDrop, Thermo Scientific) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples requirements were as follows: RIN >7, an OD 260:280 of 1.9-2.0, and an OD 260/230 >1.8.

tag: source tissue

value: lymphoid

value: Splenic CD11b+Gr-1 cells

tag: disease state

value: tumor bearing

tag: genotype

value: wild type w/ AT-3 tumor

tag: genetic background


title: IRF8 KO 2

value: no tumor

value: IRF8 KO


title: treat_72h_1_Cy3

value: MEFs


title: Cells obtained from GFP+ CD24+CD29lo sorted mammary epithelial cells [Sample 2]

value: CD1 backcrossed to FVB

value: 4 weeks

value: Sorted mammary epithelial cell


title: Wild type with tumor produced by AT-3 cell line 1


title: IRF8 KO 1


title: treat_48h_1_Cy3

value: Balb/c background

value: actinonin (150uM) treated for 48h


title: treat_24h_2_Cy3

value: actinonin (150uM) treated for 24h


title: treat_24h_1_Cy3


title: treat_48h_2_Cy3


title: treat_6h_2_Cy3

value: actinonin (150uM) treated for 6h


title: treat_6h_1_Cy3


title: Wild type no tumor 2

value: wild type


title: ctrl_0h_1_Cy3

value: EtOH treated 3ul/ml


title: Wild type no tumor 1


title: SECONDTMAF_CON_sample_16_

status: Public on Jul 04 2013

city: Medford

first: Heather

middle: C

last: Wick

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

description: gene expression data from  fetus with TTTS

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix 5.0 software, we used the mas5calls function from the Bioconductor affy package.

source_name: AF cell free mRNA from second trimester fetus of lean mother

label_protocol: Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)

extract_protocol: RNA was extracted from 5-30 mL AF supernatant.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.

tag: gestational age

tag: fetal sex

value: F

tag: maternal bmi


title: SECONDTMAF_OB_sample_14_

source_name: AF cell free mRNA from second trimester fetus of obese mother

value: M