title: 5 μM_ETP_Replicate_1

description: quality control: approved

value: B4418 of C57BL/6 background

value: Etoposide

value: ETP

value: 5 μM ETP


title: post-RASP stress samples 41

status: Public on Oct 27 2014

type: RNA

city: Fort Detrick

first: seid

last: muhie

state: MD

address: 568 Doughten Dr

department: Systems Biology Enterprise

country: USA

institute: USACEHR

description: post-RASP stress samples 41  of 43

hyb_protocol: The slides were hybridized at 60ºC for 16 h (for cDNA microarrays and Trizol® isolated RNA)

scan_protocol: Hybridized slides were scanned and recorded using a GenePix® Pro 4000B (Axon Instruments Inc., Union City, CA) optical scanner, and the images were digitized using GenePix® 6.0 software (Axon Instruments Inc, Union City, CA).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

molecule: total RNA

organism: Homo sapiens

source_name: pooled whole human tissue cell line

label_protocol: RNA was reverse transcribed and labeled using Micromax Tyramide Signal Amplification (TSA) Labeling and Detection Kit (Perkin Elmer, Inc., Waltham, MA) following the manufacturer’s protocol.

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

treatment_protocol: RASP trainees underwent extreme stressor condtions which simulated an intense battlefield scenario for more than 8 weeks; and Isolated Leucocytes (~ 106 cells/ml in RPMI 1640 and 10 % human AB serum media) were treated with SEB toxin to a final concentration of 100 ng/ml and SEB treated cells were incubated for 6 hours at 37 ºC and 5% CO2.

tag: reference

value: Strategen universal reference RNA Cat. No. 740000

source_name: leukocytes

tag: cell type

value: WBCs (leukocytes)

tag: protocol

value: post-RASP stress


title: post-RASP stress samples 40

description: post-RASP stress samples 40  of 43


title: USC.DISC.MIBC63

city: vancouver

first: Mohammed

last: Alshalalfa

state: bc

address: water st

country: Canada

institute: GenomeDx

description:
muscle_invasive_bladder_cancer_primary_63
celfile_group_name: Mitra2014-BladderRec-trn

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using fRMA software package (Bioconductor)
probe group file: HuEx-1_0-st-v1.r2.pgf

label: biotin

source_name: primary muscle-invasive bladder cancer FFPE tissue sample

label_protocol: RNA was amplified, fragmented and biotinylated using the Ovation FFPE system v 2.0 (NuGEN)

extract_protocol: not provided

tag: tissue type


title: USC.DISC.MIBC69

description:
muscle_invasive_bladder_cancer_primary_69
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: 5 μM_CSPT_Replicate_1

city: Bilthoven

first: Mirjam

middle: M

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

description: quality control: approved

hyb_protocol: According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit  According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit (#901229)

scan_protocol: According to Affymetrix protocols, using a GeneChip HT Array Plate Scanner (Affymetrix)

data_processing: The raw data were subjected to a set of quality control checks. After passing array quality control, the arrays were annotated according to de Leeuw et al. (2008) and expression values were calculated using the robust multi-array average (RMA) algorithm (Affy package, version 1.22.0; Irizarry et al. 2003) available from the Bioconductor project (http://www.bioconductor.org) for the R statistical language (http://cran.r-project.org)). The normalized data was statistically analyzed for differential gene expression using a mixed linear model with coefficients for block (random) and each experimental group (fixed) (Smyth 2004; Wolfinger et al. 2001). A contrast analysis was applied to compare each exposure with the corresponding vehicle control. For hypothesis testing, a permutation-based Fs test was used (Cui et al. 2005). False discovery rate (FDR) correction was performed globally across all contrasts according to Storey and Tibshirani (2003). Only the annotated genes were used for further analysis.

organism: Mus musculus

source_name: Embryonic stem cells

label_protocol: Biotins labeled cRNA samples were prepared as described in the Affymetrix GeneChip HT 3” IVT Express Technical Manual (Affymetrix) using 200 ng of purified total RNA as template for the reaction.

growth_protocol: Wild type mouse embryonic stem cells (ESC) (B4418 of C57Bl/6 genetic background) were maintained on mitomycin-C treated mouse embryonic fibroblast (MEF) feeders in ES complete medium. Exposure experiments were conducted with ESC cells at passage three (P3), which were cultured on 0.1% (w/v) gelatin-coated plates or wells (Greiner) in ES-BRL medium. To obtain third passage cells, ESC were re-seeded from MEF feeder layers to gelatin-coated plates and subsequently passed twice on gelatin-coated plates or wells. Cultures were incubated at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol: RNA was extracted using QIAzol and purified using the miRNeasy mini kit and the QIAcube (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: Mouse embryonic stem cells were exposed for 8 hours to the chemicals. Control cells were vehicle-treated (DMSO or PBS, 0.5%). After 8 hours of exposure, cells were collected in 1 ml RNAprotect (QIAgen) and stored at -80˚C for RNA isolation.

value: Embryonic stem cells

tag: strain

tag: chemical

value: Cisplatin

tag: abbreviation

value: CSPT

tag: concentration

value: 5 μM CSPT


title: post-RASP stress samples 38

description: post-RASP stress samples 38  of 43


title: post-RASP stress samples 37

description: post-RASP stress samples 37  of 43


title: 2 mM_DIDP_Replicate_1

description: quality control: approved

value: Diisodecyl phtalate

value: DIDP

value: 2 mM DIDP


title: 80 μM_BPA_Replicate_1

description: quality control: approved

value: Bisphenol A

value: BPA

value: 80 μM BPA


title: Male Repeat of Replicate 4

city: South Bend

first: Molly

middle: Duman

last: Scheel

state: IN

address: 1234 Notre Dame Ave.

institute: Indiana University School of Medicine

description:
SAMPLE 11
Gene expression data from male Aedes aegypti 24 hr pupal head replicate

hyb_protocol: Hybridization to the Roche NimbleGen 12-plex Aedes aegypti microarray, design: 090305_Aedes_aegypti_TEfam_expr.ndf, was performed in a GeneChip Hybridization Oven 640 according to the manufacturer’s instructions.  Four unique replicates and two repeat replicates were assessed in the hybridization experiment.

scan_protocol: Microarrays were scanned using a NimbleGen MS 200 Microarray Scanner (Roche NimbleGen).

data_processing:
NimbleScan was used to calculate signal intensities.
Microarray data pre-processing and normalization were performed using the Bioconductor packages in R Version 3.0.1.  Raw gene expression data were log-transformed and normalized using the quantile normalization method.

label: Cy3-Random Nonamer

organism: Aedes aegypti

source_name: LVP-IB12_WT_male_pupal heads

label_protocol: Labeling was performed by the Notre Dame Genomics and Bioinformatics Core Facility according to the NimbleGen Gene Expression Analysis Labeling Protocol v3.2.

growth_protocol: Mosquitoes were maintained in an insectary at 26° C, ~80% humidity, under a 12 hr light and 12 hr dark cycle with 1 hr crepuscular periods at the beginning and end of each light cycle.  Mosquito larvae were fed a suspension of dried beef liver powder, while adults were provided cotton soaked with 10% sugar solution.   An artificial membrane blood feeding system was utilized to deliver a sheep blood meal to females.

extract_protocol: For each of the four replicates, total RNA extraction was performed with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.  Total RNA sample integrity was verified with a 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: Following animal sexing, 20 age-matched male and female heads per replicate for each of four replicates were dissected from 24 hr pupae and immediately stored in RNAeasy (Qiagen) for subsequent RNA extraction.

value: Liverpool-IB12 (LVP-IB12)

tag: genotype/variation

value: wild type

tag: developmental stage

value: 24 hours after pupariaum formation

tag: Sex

value: male

tag: tissue

value: head


title: Female Repeat of Replicate 2

description:
SAMPLE 12
Gene expression data from female Aedes aegypti 24 hr pupal head replicate

source_name: LVP-IB12_WT_female_pupal heads

value: female


title: post-RASP stress samples 36

description: post-RASP stress samples 36  of 43

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)

value: post-RASP stress


title: 2 mM_D-M_Replicate_1

description: quality control: approved

value: Embryonic stem cells

value: B4418 of C57BL/6 background

value: D-mannitol

value: D-M

value: 2 mM D-M


title: USC.DISC.MIBC66

description:
muscle_invasive_bladder_cancer_primary_66
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: pre-RASP control samples 7

description: pre-RASP control samples 7 of 36

value: pre-RASP control


title: USC.DISC.MIBC62

description:
muscle_invasive_bladder_cancer_primary_62
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP stress samples 35

description: post-RASP stress samples 35  of 43


title: Male Repeat of Replicate 1

description:
SAMPLE 10
Gene expression data from male Aedes aegypti 24 hr pupal head replicate


title: USC.DISC.MIBC60

description:
muscle_invasive_bladder_cancer_primary_60
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC57

description:
muscle_invasive_bladder_cancer_primary_57
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP stress samples 39

description: post-RASP stress samples 39  of 43


title: USC.DISC.MIBC64

description:
muscle_invasive_bladder_cancer_primary_64
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC55

description:
muscle_invasive_bladder_cancer_primary_55
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC61

description:
muscle_invasive_bladder_cancer_primary_61
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC58

description:
muscle_invasive_bladder_cancer_primary_58
celfile_group_name: Mitra2014-BladderRec-trn


title: 10 μM_LAC_Replicate_1

description: quality control: approved

value: Lead Acetate

value: LAC

value: 10 μM LAC


title: 0.5 nM_CA_Replicate_1

description: quality control: approved

value: Calyculin A

value: CA

value: 0.5 nM CA


title: USC.DISC.MIBC59

description:
muscle_invasive_bladder_cancer_primary_59
celfile_group_name: Mitra2014-BladderRec-trn


title: 250 nM_TBTO_Replicate_1

description: quality control: approved

value: Tributyltinoxide

value: TBTO

value: 250 nM TBTO


title: USC.DISC.MIBC68

description:
muscle_invasive_bladder_cancer_primary_68
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP stress samples 34

description: post-RASP stress samples 34  of 43

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)

value: post-RASP stress


title: 2 μM_SAR_Replicate_1

description: quality control: approved

value: Embryonic stem cells

value: B4418 of C57BL/6 background

value: Sodium Arsenite

value: SAR

value: 2 μM SAR


title: USC.DISC.MIBC54

description:
muscle_invasive_bladder_cancer_primary_54
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: Female Replicate 3

description:
SAMPLE 7
Gene expression data from female Aedes aegypti 24 hr pupal head replicate

value: Liverpool-IB12 (LVP-IB12)

value: wild type

value: 24 hours after pupariaum formation

value: female

value: head


title: post-RASP stress samples 31

description: post-RASP stress samples 31  of 43


title: Male Replicate 4

description:
SAMPLE 5
Gene expression data from male Aedes aegypti 24 hr pupal head replicate

value: male


title: post-RASP stress samples 33

description: post-RASP stress samples 33  of 43


title: post-RASP stress samples 32

description: post-RASP stress samples 32  of 43


title: USC.DISC.MIBC65

description:
muscle_invasive_bladder_cancer_primary_65
celfile_group_name: Mitra2014-BladderRec-trn


title: Female Replicate 2

description:
SAMPLE 6
Gene expression data from female Aedes aegypti 24 hr head replicate


title: 3 mM_CT_Replicate_1

description: quality control: approved

value: Carbon Tetrachloride

value: CT

value: 3 mM CT


title: Female Replicate 4

description:
SAMPLE 8
Gene expression data from female Aedes aegypti 24 hr pupal head replicate


title: USC.DISC.MIBC53

description:
muscle_invasive_bladder_cancer_primary_53
celfile_group_name: Mitra2014-BladderRec-trn


title: Female Repeat of Replicate 1

description:
SAMPLE 9
Gene expression data from female Aedes aegypti 24 hr pupal head replicate


title: USC.DISC.MIBC52

description:
muscle_invasive_bladder_cancer_primary_52
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP stress samples 30

description: post-RASP stress samples 30  of 43

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)


title: Male Replicate 3

description:
SAMPLE 4
Gene expression data from male Aedes aegypti 24 hr head replicate


title: 4 nM_OA_Replicate_1

description: quality control: approved

value: Embryonic stem cells

value: Okadaic Acid

value: OA

value: 4 nM OA


title: 3 mM_TCE_Replicate_1

description: quality control: approved

value: B4418 of C57BL/6 background

value: TCE

value: 3 mM TCE


title: USC.DISC.MIBC56

description:
muscle_invasive_bladder_cancer_primary_56
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: USC.DISC.MIBC49

description:
muscle_invasive_bladder_cancer_primary_49
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP stress samples 29

description: post-RASP stress samples 29  of 43

value: post-RASP stress


title: Male Replicate 2

description:
SAMPLE 3
Gene expression data from male Aedes aegypti 24 hr pupal head replicate

value: Liverpool-IB12 (LVP-IB12)

value: wild type

value: 24 hours after pupariaum formation


title: USC.DISC.MIBC51

description:
muscle_invasive_bladder_cancer_primary_51
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP stress samples 28

description: post-RASP stress samples 28  of 43


title: Female Replicate 1

description:
SAMPLE 2
Gene expression data from female Aedes aegypti 24 hr head replicate

value: female

value: head


title: USC.DISC.MIBC47

description:
muscle_invasive_bladder_cancer_primary_47
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP stress samples 27

description: post-RASP stress samples 27  of 43


title: 25 μM_ARO_Replicate_1

description: quality control: approved

value: Aroclor 1254

value: ARO

value: 25 μM ARO


title: 5 μM_TCPOBOP_Replicate_1

description: quality control: approved

value: Embryonic stem cells

value: TCPOBOP

value: 5 μM TCPOBOP


title: 100 nM_TCDD_Replicate_1

description: quality control: approved

value: TCDD

value: 100 nM TCDD


title: USC.DISC.MIBC50

description:
muscle_invasive_bladder_cancer_primary_50
celfile_group_name: Mitra2014-BladderRec-trn


title: Male Replicate 1

description:
SAMPLE 1
Gene expression data from male Aedes aegypti 24 hr pupal head replicate

value: male


title: post-RASP stress samples 26

description: post-RASP stress samples 26  of 43

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)


title: post-RASP stress samples 25

description: post-RASP stress samples 25  of 43

value: post-RASP stress


title: E5 hom 4h

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description:
KO homozygous
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol applied for Illumina HiScan

data_processing: The data were normalised using quantile normalisation with Illumina Genomestudio 2011.1

source_name: T cells 4h stimulated

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

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

treatment_protocol: Purification and stimulation of T-cells. Total T-cells were purified by negative selection using magnetic beads (Dynal, Invitrogen) against B cells (B220) and myeloid cells (CD11b). CD4+ T-cells were purified using MACS CD4+ or CD4+CD62L+ T Cell isolation kits (Miltenyi). Cells were stimulated with PMA (Adipogen) and ionomycin (Alexis) or with plate-bound anti-CD3 (145-2C11) and anti-CD28 (37.51, both eBioscience) antibodies after pre-coating with anti-Syrian hamster antibodies (F(ab')2 fragment of IgG H+L, rabbit, Jackson ImmunoResearch) at given concentrations and for indicated time points at 37°C.

tag: genotype

tag: period of stimulation

tag: treatment

value: stimulated

value: T cells


title: E6 hom 4h

description:
KO homozygous
replicate 4


title: post-RASP stress samples 24

description: post-RASP stress samples 24  of 43


title: post-RASP stress samples 23

description: post-RASP stress samples 23  of 43


title: 5 μM_HCE_Replicate_1

description: quality control: approved

value: B4418 of C57BL/6 background

value: Heptachlor epoxide

value: HCE

value: 5 μM HCE


title: post-RASP stress samples 22

description: post-RASP stress samples 22  of 43


title: E4 hom 4h

description:
KO homozygous
replicate 2


title: 100 μM_CF_Replicate_1

description: quality control: approved

value: Clofibrate

value: CF

value: 100 μM CF


title: E3 hom 4h

description:
KO homozygous
replicate 1


title: post-RASP stress samples 21

description: post-RASP stress samples 21  of 43


title: 50 μM_HCH_Replicate_1

description: quality control: approved

value: Embryonic stem cells

value: β-Hexachlorocyclohexane

value: HCH

value: 50 μM HCH


title: 10 μM_CsA_Replicate_1

description: quality control: approved

value: Cyclosporin A

value: CsA

value: 10 μM CsA


title: post-RASP stress samples 20

description: post-RASP stress samples 20  of 43

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)

value: post-RASP stress


title: E6 hom 1h

description:
KO homozygous
replicate 4

source_name: T cells 1h stimulated

value: stimulated

value: T cells


title: E5 hom 1h

description:
KO homozygous
replicate 3


title: 10 μM_FK506_Replicate_1

description: quality control: approved

value: B4418 of C57BL/6 background

value: Tacrolimus


title: 3 mM_PB_Replicate_1

description: quality control: approved

value: Phenobarbital

value: PB

value: 3 mM PB


title: post-RASP stress samples 19

description: post-RASP stress samples 19  of 43


title: PBS_Replicate_2

description: quality control: approved

value: Embryonic stem cells

value: PBS


title: USC.DISC.MIBC46

description:
muscle_invasive_bladder_cancer_primary_46
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: post-RASP stress samples 18

description: post-RASP stress samples 18  of 43


title: USC.DISC.MIBC44

description:
muscle_invasive_bladder_cancer_primary_44
celfile_group_name: Mitra2014-BladderRec-trn


title: E3 hom 1h

description:
KO homozygous
replicate 1


title: 250 μM_WY_Replicate_1

description: quality control: approved

value: WY

value: 250 μM WY


title: E4 hom 1h

description:
KO homozygous
replicate 2


title: PBS_Replicate_1

description: quality control: approved


title: USC.DISC.MIBC45

description:
muscle_invasive_bladder_cancer_primary_45
celfile_group_name: Mitra2014-BladderRec-trn


title: DMSO_Replicate_2

description: quality control: approved

value: DMSO

value: 0,5 % DMSO


title: post-RASP stress samples 17

description: post-RASP stress samples 17  of 43

value: Strategen universal reference RNA Cat. No. 740000


title: E5 hom 0h

description:
KO homozygous
replicate 3

source_name: T cells non-stimulated

value: non-stimulated


title: E6 hom 0h

description:
KO homozygous
replicate 4


title: DMSO_Replicate_1

description: quality control: approved

value: B4418 of C57BL/6 genetic background


title: USC.DISC.MIBC42

description:
muscle_invasive_bladder_cancer_primary_42
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP stress samples 15

description: post-RASP stress samples 15  of 43

value: WBCs (leukocytes)

value: post-RASP stress


title: post-RASP stress samples 16

description: post-RASP stress samples 16  of 43


title: E4 hom 0h

description:
KO homozygous
replicate 2

value: T cells


title: post-RASP stress samples 14

description: post-RASP stress samples 14  of 43


title: USC.DISC.MIBC41

description:
muscle_invasive_bladder_cancer_primary_41
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC43

description:
muscle_invasive_bladder_cancer_primary_43
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC40

description:
muscle_invasive_bladder_cancer_primary_40
celfile_group_name: Mitra2014-BladderRec-trn


title: E6 PM 4h

description:
point mutation heterozygous
replicate 4

value: stimulated


title: USC.DISC.MIBC48

description:
muscle_invasive_bladder_cancer_primary_48
celfile_group_name: Mitra2014-BladderRec-trn


title: Human mesenchymal stem cells_mixed with rat synovium_rep1

city: Tokyo

first: Nobutake

last: Ozeki

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Joint Surgery and Sports Medicine

country: Japan

institute: Tokyo Medical and Dental University

description: Sample name: S4

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

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

data_processing: The data were analyzed with Expression Console Version1.1 (EC1.1) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: human mesenchymal stem cells, mixed samples

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3'IVT Expression Analysis Technical Manual, 2008, Affymetrix)

growth_protocol: Human synovial mesenchymal stem cells were isolated using collagenase and prepared for the injection into the rat knee joint , or for mixing with rat synovium as a control samples

extract_protocol: RNA was extracted using TRIZol solution (Invitrogen) and High Pure RNA Isolation Kit (Roche Applied Sciences)

treatment_protocol: After injection of human synovial mesenchymal stem cells into the rat knee joint, rat synovium was harvested for the extraction of RNA. Human mesenchymal stem cells mixed rat synovium was used as a control.

value: human mesenchymal stem cells mixed with rat synovium

value: human synovial mesenchymal stem cells


title: Human mesenchymal stem cells_injected into rat knee joint_rep1

description: Sample name: S3

source_name: human mesenchymal stem cells, injected samples

value: human mesenchymal stem cells injected into rat knee joint


title: post-RASP stress samples 12

description: post-RASP stress samples 12  of 43


title: post-RASP stress samples 13

description: post-RASP stress samples 13  of 43


title: E5 PM 4h

description:
point mutation heterozygous
replicate 3


title: USC.DISC.MIBC38

description:
muscle_invasive_bladder_cancer_primary_38
celfile_group_name: Mitra2014-BladderRec-trn


title: E4 PM 4h

description:
point mutation heterozygous
replicate 2


title: E3 PM 4h

description:
point mutation heterozygous
replicate 1


title: post-RASP stress samples 10

description: post-RASP stress samples 10  of 43


title: post-RASP stress samples 11

description: post-RASP stress samples 11  of 43


title: E5 PM 1h

description:
point mutation heterozygous
replicate 3


title: post-RASP stress samples 8

description: post-RASP stress samples 8  of 43


title: USC.DISC.MIBC39

description:
muscle_invasive_bladder_cancer_primary_39
celfile_group_name: Mitra2014-BladderRec-trn


title: E4 PM 1h

description:
point mutation heterozygous
replicate 2


title: E3 hom 0h

description:
KO homozygous
replicate 1


title: USC.DISC.MIBC37

description:
muscle_invasive_bladder_cancer_primary_37
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP stress samples 7

description: post-RASP stress samples 7  of 43


title: post-RASP stress samples 9

description: post-RASP stress samples 9  of 43


title: USC.DISC.MIBC36

description:
muscle_invasive_bladder_cancer_primary_36
celfile_group_name: Mitra2014-BladderRec-trn


title: post-RASP stress samples 6

description: post-RASP stress samples 6  of 43


title: post-RASP stress samples 5

description: post-RASP stress samples 5  of 43


title: E3 PM 1h

description:
point mutation heterozygous
replicate 1


title: E6 PM 0h

description:
point mutation heterozygous
replicate 4


title: E6 PM 1h

description:
point mutation heterozygous
replicate 4


title: USC.DISC.MIBC32

description:
muscle_invasive_bladder_cancer_primary_32
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC35

description:
muscle_invasive_bladder_cancer_primary_35
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC34

description:
muscle_invasive_bladder_cancer_primary_34
celfile_group_name: Mitra2014-BladderRec-trn


title: E5 PM 0h

description:
point mutation heterozygous
replicate 3


title: post-RASP stress samples 4

description: post-RASP stress samples 4  of 43


title: post-RASP stress samples 3

description: post-RASP stress samples 3  of 43


title: E4 PM 0h

description:
point mutation heterozygous
replicate 2


title: post-RASP stress samples 2

description: post-RASP stress samples 2  of 43


title: USC.DISC.MIBC31

description:
muscle_invasive_bladder_cancer_primary_31
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC30

description:
muscle_invasive_bladder_cancer_primary_30
celfile_group_name: Mitra2014-BladderRec-trn


title: E3 PM 0h

description:
point mutation heterozygous
replicate 1


title: post-RASP stress samples 1

description: post-RASP stress samples 1  of 43


title: E6 het 4h

description:
KO heterozygous
replicate 4


title: E5 het 4h

description:
KO heterozygous
replicate 3


title: cervix_paired non-tumor_5ad

city: shanghai

first: chen

last: ye

address: Xiangyin road, no.800

country: China

institute: the second military medical university

description: Gene expression data from cervical cacner sample without chemoradiotherapy

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix hGlue3_0 transcriptome array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The arrays were scanned using Affymetrix Fluidics Station FS450 and GeneChip Scanner 30007G.

data_processing: Affymetrix Power Tools (APT) was applied for data processing. Arrays were RMA-background-corrected, quantile-normalized and summarized into exon/gene expression using median-polish approaches. The probe group file is hGlue3_0.r1.pgf, and the meta-probeset file is hGlue3_0.r1.TC.mps

source_name: paired adjacent non-tumor tissues

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneChip WT Terminal Labeling Kit protocol from 100 ng total RNA.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step.

tag: gender

value: female

value: cervix

tag: cancer status

value: non-tumor


title: E4 het 4h

description:
KO heterozygous
replicate 2


title: USC.DISC.MIBC28

description:
muscle_invasive_bladder_cancer_primary_28
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: cervix_paired non-tumor_4ad


title: cervix_cancer_4c

source_name: cervical cancer tissues

value: cancer


title: USC.DISC.MIBC29

description:
muscle_invasive_bladder_cancer_primary_29
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC26

description:
muscle_invasive_bladder_cancer_primary_26
celfile_group_name: Mitra2014-BladderRec-trn


title: E6 het 1h

description:
KO heterozygous
replicate 4


title: USC.DISC.MIBC33

description:
muscle_invasive_bladder_cancer_primary_33
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC27

description:
muscle_invasive_bladder_cancer_primary_27
celfile_group_name: Mitra2014-BladderRec-trn


title: cervix_paired non-tumor_3ad


title: E5 het 1h

description:
KO heterozygous
replicate 3


title: E4 het 1h

description:
KO heterozygous
replicate 2


title: E3 het 4h

description:
KO heterozygous
replicate 1


title: USC.DISC.MIBC25

description:
muscle_invasive_bladder_cancer_primary_25
celfile_group_name: Mitra2014-BladderRec-trn


title: cervix_cancer_5c


title: E3 het 1h

description:
KO heterozygous
replicate 1


title: cervix_paired non-tumor_2ad


title: E6 het 0h

description:
KO heterozygous
replicate 4


title: USC.DISC.MIBC20

description:
muscle_invasive_bladder_cancer_primary_20
celfile_group_name: Mitra2014-BladderRec-trn


title: cervix_cancer_2c


title: cervix_cancer_3c


title: USC.DISC.MIBC23

description:
muscle_invasive_bladder_cancer_primary_23
celfile_group_name: Mitra2014-BladderRec-trn


title: E5 het 0h

description:
KO heterozygous
replicate 3


title: E4 het 0h

description:
KO heterozygous
replicate 2


title: E3 het 0h

description:
KO heterozygous
replicate 1


title: cervix_cancer_1c


title: USC.DISC.MIBC18

description:
muscle_invasive_bladder_cancer_primary_18
celfile_group_name: Mitra2014-BladderRec-trn


title: control3_v1_No stimulation

status: Public on Oct 26 2014

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

hyb_protocol: Hybridization to HumanHT-12 v4 Expression BeadChip

scan_protocol: SentrixScanVersion 2.3.0.13

data_processing: The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

source_name: whole blood from healthy control

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

value: F

tag: race

value: White

tag: illness

value: healthy control

tag: geographic

value: France

tag: age at enrollment

tag: cell population

value: Whole blood

tag: in vitro stimulation condition

value: No stimulation

tag: in vitro stimulation incubation time

tag: in vitro stimulation blood volume per condition

value: 1 ml


title: MYD88 P2_TNFa

source_name: whole blood from MYD88-/- patient

value: M

value: MYD88-/- patient

value: Portugal

value: TNFa


title: MYD88 P2_No stimulation


title: USC.DISC.MIBC24

description:
muscle_invasive_bladder_cancer_primary_24
celfile_group_name: Mitra2014-BladderRec-trn

tag: tissue type


title: control4_v1_poly(I:C)


title: cervix_paired non-tumor_1ad


title: USC.DISC.MIBC19

description:
muscle_invasive_bladder_cancer_primary_19
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC17

description:
muscle_invasive_bladder_cancer_primary_17
celfile_group_name: Mitra2014-BladderRec-trn


title: control3_v1_IL33


title: MYD88 P1_poly(I:C)


title: control2_v1_PAM3


title: USC.DISC.MIBC16

description:
muscle_invasive_bladder_cancer_primary_16
celfile_group_name: Mitra2014-BladderRec-trn


title: control1_v1__3M2


title: control3_v1_PMA/Iono

value: PMA/Iono


title: control4_v1_CpG C

value: CpG C


title: control4_v1_LPS

value: LPS


title: USC.DISC.MIBC15

description:
muscle_invasive_bladder_cancer_primary_15
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC21

description:
muscle_invasive_bladder_cancer_primary_21
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC13

description:
muscle_invasive_bladder_cancer_primary_13
celfile_group_name: Mitra2014-BladderRec-trn


title: IRAK4 P1_PAM2

source_name: whole blood from IRAK4-/- patient

value: IRAK4-/- patient

value: Hungary


title: control2_v1_CpG-D19


title: MYD88 P1_PAM2


title: IRAK4 P1_Flagellin

value: Flagellin


title: control1_v1_PAM2


title: control2_v1_PAM2

value: F


title: USC.DISC.MIBC12

description:
muscle_invasive_bladder_cancer_primary_12
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: MYD88 P2_IL18

value: White


title: control1_v1_LPS

value: healthy control

value: France


title: USC.DISC.MIBC10

description:
muscle_invasive_bladder_cancer_primary_10
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC14

description:
muscle_invasive_bladder_cancer_primary_14
celfile_group_name: Mitra2014-BladderRec-trn


title: control4_v1_PAM2

value: Whole blood


title: control1_v1_poly(I:C)

value: 1 ml


title: USC.DISC.MIBC9

description:
muscle_invasive_bladder_cancer_primary_9
celfile_group_name: Mitra2014-BladderRec-trn


title: MYD88 P1_Flagellin


title: control3_v1_PAM3


title: USC.DISC.MIBC8

description:
muscle_invasive_bladder_cancer_primary_8
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC6

description:
muscle_invasive_bladder_cancer_primary_6
celfile_group_name: Mitra2014-BladderRec-trn


title: MYD88 P2_IL33

value: M


title: MYD88 P1_LPS

value: MYD88-/- patient


title: control2_v1__3M2


title: control2_v1_IL-1b


title: USC.DISC.MIBC11

description:
muscle_invasive_bladder_cancer_primary_11
celfile_group_name: Mitra2014-BladderRec-trn


title: USC.DISC.MIBC22

description:
muscle_invasive_bladder_cancer_primary_22
celfile_group_name: Mitra2014-BladderRec-trn


title: control3_v1_PAM2


title: USC.DISC.MIBC7

description:
muscle_invasive_bladder_cancer_primary_7
celfile_group_name: Mitra2014-BladderRec-trn


title: IRAK4 P1_IL33


title: USC.DISC.MIBC3

description:
muscle_invasive_bladder_cancer_primary_3
celfile_group_name: Mitra2014-BladderRec-trn


title: IRAK4 P2_R848

value: Spain


title: control3_v1_3M13


title: control3_v1_poly(I:C)


title: USC.DISC.MIBC5

description:
muscle_invasive_bladder_cancer_primary_5
celfile_group_name: Mitra2014-BladderRec-trn


title: MYD88 P1_CpG C

value: Portugal


title: control3_v1_LPS


title: control3_v1_Flagellin


title: MYD88 P1_IL-1b


title: control2_v1_IL18


title: IRAK4 P1_R848


title: IRAK4 P1__3M2


title: control3_v1_IL-1b


title: MYD88 P2_Flagellin


title: control4_v1_PAM3


title: USC.DISC.MIBC1

description:
muscle_invasive_bladder_cancer_primary_1
celfile_group_name: Mitra2014-BladderRec-trn


title: MYD88 P2_poly(I:C)


title: control4_v1_IL18


title: MYD88 P1_PMA/Iono

value: PMA/Iono


title: IRAK4 P1_LPS


title: control2_v1_R848


title: MYD88 P1_PAM3


title: control4_v1_TNFa

value: TNFa


title: MYD88 P1_R848


title: MYD88 P1_No stimulation

value: No stimulation


title: control1_v1_3M13


title: IRAK4 P1_PMA/Iono

value: IRAK4-/- patient


title: control4_v1_R848


title: IRAK4 P2_CpG C

value: CpG C


title: control4_v1_IL33


title: IRAK4 P1_No stimulation

value: Hungary


title: control4_v1_IL-1b


title: IRAK4 P1_IL18


title: control4_v1_CpG-D19


title: control2_v1_poly(I:C)

value: F


title: IRAK4 P2_CpG-D19


title: IRAK4 P2_IL18


title: USC.DISC.MIBC4

description:
muscle_invasive_bladder_cancer_primary_4
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: IRAK4 P1_CpG-D19

value: White


title: IRAK4 P2_LPS

value: LPS


title: IRAK4 P1_CpG C


title: MYD88 P2_PAM2


title: control1_v1_TNFa

value: healthy control

value: France


title: control2_v1_TNFa

value: Whole blood

value: 1 ml


title: control3_v1_CpG C


title: IRAK4 P2_poly(I:C)

value: M


title: control1_v1_Flagellin

value: Flagellin


title: control2_v1_CpG C


title: MYD88 P2_PAM3

value: MYD88-/- patient

value: Portugal


title: IRAK4 P2_PAM3

value: Spain


title: control2_v1_PMA/Iono

value: PMA/Iono


title: control4_v1_Flagellin


title: control2_v1_No stimulation

value: No stimulation


title: MYD88 P2_LPS


title: IRAK4 P1_3M13

value: IRAK4-/- patient


title: control2_v1_IL33


title: IRAK4 P2_No stimulation


title: IRAK4 P2_PAM2


title: IRAK4 P2_3M13


title: MYD88 P1_IL33


title: IRAK4 P1_IL-1b

value: Hungary


title: IRAK4 P1_PAM3


title: IRAK4 P2_IL-1b


title: control3_v1__3M2

value: F


title: IRAK4 P2__3M2


title: control3_v1_CpG-D19


title: control3_v1_IL18


title: IRAK4 P1_TNFa

value: TNFa


title: control2_v1_LPS

value: White


title: IRAK4 P2_IL33


title: MYD88 P2__3M2


title: MYD88 P1__3M2


title: MYD88 P1_CpG-D19


title: control1_v1_PMA/Iono


title: control1_v1_No stimulation


title: MYD88 P2_PMA/Iono


title: IRAK4 P2_TNFa


title: USC.DISC.MIBC2

description:
muscle_invasive_bladder_cancer_primary_2
celfile_group_name: Mitra2014-BladderRec-trn

value: primary muscle-invasive bladder cancer FFPE tissue sample


title: MYD88 P2_3M13


title: MYD88 P2_CpG-D19


title: MYD88 P2_IL-1b


title: control3_v1_TNFa

value: healthy control


title: control1_v1_R848

value: France


title: MYD88 P1_IL18

value: Whole blood


title: control1_v1_CpG C

value: CpG C

value: 1 ml


title: MYD88 P1_TNFa


title: control2_v1_Flagellin

value: Flagellin


title: control4_v1_3M13

value: M


title: control1_v1_IL33


title: MYD88 P2_R848

value: MYD88-/- patient

value: Portugal


title: control4_v1_No stimulation


title: MYD88 P2_CpG C


title: control1_v1_IL18


title: MYD88 P1_3M13


title: control1_v1_IL-1b


title: MYD88 P3_CpG C

value: Traveller (Gypsies)


title: IRAK4 P1_poly(I:C)


title: control3_v1_R848


title: control4_v1_PMA/Iono

value: PMA/Iono


title: MYD88 P3_IL18


title: control1_v1_PAM3


title: MYD88 P4__3M2

value: Turkish


title: IRAK4 P2_Flagellin

value: IRAK4-/- patient

value: Spain


title: control 9_CpG-D19


title: MYD88 P4_R6

value: F


title: control 9_PMA/Iono

value: White


title: MYD88 P4_PMA/Iono


title: control 10_R8450


title: control 10__3M2


title: control 8_PMA/Iono


title: control 7_PAM2


title: control1_v1_CpG-D19


title: control 10_IL-1b


title: control 8_IL33


title: control 8_3M13


title: control 8_TNFa

value: TNFa


title: control 10_PAM2

value: healthy control


title: control 7_PAM3

value: France


title: MYD88 P3_IL33

value: Whole blood


title: control 7_3M13


title: control 10_IL18


title: MYD88 P3_R848


title: MYD88 P4_R8450


title: MYD88 P3_LPS

value: LPS


title: control 7_IL18

value: 1 ml


title: MYD88 P4_PAM2


title: control 10_Flagellin

value: Flagellin


title: control 9_SAC

value: M

value: SAC


title: control 9_No stimulation

value: No stimulation


title: control 9_LPS


title: MYD88 P3_PAM3

value: MYD88-/- patient

value: Traveller (Gypsies)


title: control 8_IL18


title: control 10_No stimulation

value: Turkish


title: control 10_IL33


title: MYD88 P3_R6


title: MYD88 P4_PAM3


title: MYD88 P4_poly(I:C)


title: control 9__3M2


title: control 10_LPS


title: control 8_PAM2


title: control 8_R11470


title: control 8_R8450


title: MYD88 P3_PAM2


title: control 9_poly(I:C)


title: control4_v1__3M2


title: control 8_SAC


title: MYD88 P3_CpG-D19


title: control 7_IL-1b


title: control 9_3M13


title: control 8_CpG-D19


title: control 9_R8450


title: MYD88 P4_R848


title: control 9_IL-1b


title: control 7_LPS


title: control 9_CpG C

value: CpG C


title: control 7_IL33


title: control 10_R11470


title: control 10_SAC


title: MYD88 P3_R8450


title: MYD88 P4_IL18


title: control 8_No stimulation


title: control 7_CpG C


title: MYD88 P3_3M13


title: control 10_3M13


title: MYD88 P4_LPS


title: control 8_IL-1b


title: MYD88 P4_3M13


title: control 10_CpG C


title: control 9_IL33


title: control 7_R848


title: control 8_PAM3


title: control 8_R848


title: MYD88 P3_poly(I:C)


title: control 7_poly(I:C)


title: control 9_TNFa


title: control 9_R848


title: control 4_IL33


title: MYD88 P4_IL33


title: control 10_poly(I:C)


title: control 7_SAC


title: control 10_CpG-D19


title: control 9_PAM2


title: control 3_CpG C


title: control 9_IL18


title: control 6_IL33


title: IRAK4 P4_PAM2

value: IRAK4-/- patient

value: UK


title: control 4_LPS

value: White


title: control 3_TNFa

value: F

value: TNFa


title: control 3_CpG-D19

value: healthy control

value: France


title: control 6_IL18

value: Whole blood


title: control 4_3M13

value: 1 ml


title: control 6_R11470


title: IRAK4 P3_R8450

value: Portugal


title: control 4_IL18

value: M


title: control 5_R848


title: control 6_PAM3


title: IRAK4 P4_No stimulation


title: control 5_3M13


title: control 5_IL-1b


title: control 1_PAM2


title: control 4_TNFa


title: control 2_R848


title: control 1_PAM3


title: control 4_PAM3


title: control 4_R848


title: IRAK4 P4_IL18


title: control 6_R6


title: IRAK4 P3_No stimulation


title: control 4_CpG C


title: IRAK4 P3_poly(I:C)


title: control 4_SAC

value: SAC


title: control 5_CpG C


title: IRAK4 P4_LPS

value: LPS


title: control 3_3M13


title: IRAK4 P3_3M13


title: control 5_IL18


title: control 5_Flagellin

value: Flagellin


title: control 1__3M2


title: control 4_PAM2


title: control 4_poly(I:C)


title: control 5__3M2


title: control 5_poly(I:C)


title: control 1_R848


title: control 6_CpG-D19


title: IRAK4 P3_R11470


title: control 6_SAC


title: control 10_R6


title: MYD88 P4_CpG C

value: MYD88-/- patient


title: control 8_CpG C


title: IRAK4 P3_Flagellin


title: MYD88 P4_R11470

value: Turkish


title: control 10_R848


title: control 5_CpG-D19


title: control 7_PMA/Iono

value: PMA/Iono


title: MYD88 P3_PMA/Iono

value: Traveller (Gypsies)


title: control 8__3M2


title: control 10_PAM3


title: control 7_No stimulation

value: No stimulation


title: control 8_LPS

value: White


title: MYD88 P3_Flagellin

value: F


title: MYD88 P4_SAC


title: MYD88 P4_IL-1b


title: MYD88 P3_SAC


title: control 8_poly(I:C)


title: MYD88 P4_No stimulation


title: MYD88 P3_No stimulation


title: control 9_Flagellin


title: control 7_Flagellin


title: MYD88 P4_TNFa

value: TNFa


title: control 8_R6

value: healthy control


title: MYD88 P3_TNFa


title: control 10_TNFa


title: control 10_PMA/Iono


title: control 9_PAM3

value: France


title: control 7_R11470

value: Whole blood


title: control 7_R8450

value: 1 ml


title: MYD88 P4_CpG-D19


title: control 9_R6


title: control 7_CpG-D19


title: MYD88 P3_IL-1b


title: control 8_Flagellin


title: control 5_PAM2


title: control 3_R848


title: IRAK4 P4_3M13

value: IRAK4-/- patient

value: UK


title: MYD88 P4_Flagellin


title: control 2_Flagellin


title: control 6_IL-1b

value: M


title: control 6_R848


title: MYD88 P3__3M2


title: control 5_LPS

value: LPS


title: control 6__3M2


title: control 2__3M2


title: control 4_Flagellin

value: Flagellin


title: control 3_PMA/Iono


title: control 2_LPS


title: control 5_IL33


title: IRAK4 P4_R8450


title: control 2_No stimulation


title: control 5_No stimulation


title: control 5_PMA/Iono


title: control 6_No stimulation


title: control 5_TNFa


title: control 2_PMA/Iono


title: control 6_LPS


title: control 1_No stimulation

value: Portugal


title: control 1_CpG-D19


title: IRAK4 P3_R6


title: IRAK4 P3_IL-1b


title: control 4_R8450


title: MYD88 P3_R11470

value: MYD88-/- patient


title: control 6_TNFa


title: IRAK4 P4_poly(I:C)


title: control 4_CpG-D19


title: IRAK4 P3_R848


title: control 4_PMA/Iono

value: PMA/Iono


title: IRAK4 P4_IL-1b


title: IRAK4 P4_R6


title: control 4_IL-1b


title: control 2_3M13


title: control 3_PAM3


title: control 3_poly(I:C)


title: control 6_CpG C

value: CpG C


title: control 2_CpG-D19


title: IRAK4 P3_IL33


title: control 3_Flagellin


title: control 1_CpG C


title: IRAK4 P4_Flagellin


title: control 3_No stimulation

value: No stimulation


title: IRAK4 P4__3M2

value: White


title: control 2_CpG C

value: F


title: control 3_IL33


title: IRAK4 P3_PAM2


title: IRAK4 P3_CpG C


title: Brain Control:biological rep5

city: Fujisawa

first: Tsukasa

last: Mori

state: Kanagawa

address: Kameino 1866

department: Bioresource Sciences

institute: Nihon University

description: Gene expression data from brain of Rana pirica tadpoles without predators.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Xenopus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data (SF:1.000; NF:1.000) were analyzed with summarization algorithm MAS 5 and using GeneSpringGX11.5.1. Baseline Transformation was set as median of Control Samples

organism: Rana pirica

source_name: Brains from tadpoles without predators for 8days

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

growth_protocol: Tadpoles before growing hind rimb.

extract_protocol: Total RNA was obtained using the Qiagen RNA mini preparation system.  RNA yield was measured by absorbance at 260 nm and the quality was assessed by confirming the integrity of the rRNA bands by electrophoresis.

treatment_protocol: Brain was dissected from each tadpole, and 10 brain tissues were collected together for one sample in a single tube containing RNAlater (QIAGEN RNA stabilization reagent) for subsequent use in producing RNA probes for the functional microarray analysis. The tissues were stored at -80°C until RNA extraction.

value: Brain


title: Brain Larvae salamander treatment: biological rep3

description: Gene expression data from brain of Rana pirica tadpoles exposed by larval salamanders.

source_name: Brains from tadpoles exposed by larvae salamander for 8days


title: Brain Larvae salamander treatment: biological rep1


title: Brain Control:biological rep6


title: Brain Larvae salamander treatment: biological rep2


title: Brain Control:biological rep3


title: IRAK4 P3_PAM3


title: Pilot Study Cthe 4150 Exponential C6

city: Winnipeg

first: Richard

last: Sparling

state: MB

address: 418 Buller Building

department: Microbiology

institute: University of Manitoba

hyb_protocol: Cyanine-3-labeled cDNA was hybridized to custom Agilent 8x15K Clostridium thermocellum gene expression arrays (Design ID 034174) using the Fairplay III kit (Agilent)

scan_protocol: As specified in One-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) Protocol Version 1.3, August 2010 using GenePix 4000B.

data_processing: Signal was processed using Agilent Feature Extraction software (quantitation). GeneSpring 11.5.1, was used for quantile normalization of the data, with no per gene normalization.

organism: Acetivibrio thermocellus

source_name: DSM 4150_exponential

label_protocol: RNA for each sample was converted to Cyanine-3-labeled cDNA using the Fairplay III kit (Agilent)

growth_protocol: The type strains of Clostridium thermocellum, DSM 1237, 2360, and 4150, obtained from the German Type Culture collection, were employed for all growth experiments. Fresh cultures were maintained by routinely transferring 10% (v/v) mid-exponential phase inoculum into complex 1191 medium containing 2.2 g L-1 (11.8 mM) cellobiose. Cultures were grown at 60C and stored anaerobically at 4C. Cells for end-product, microarray, RNAseq, and proteomic analysis were grown in anaerobic Balch tubes (26 mL; Bellco Glass Inc., Vineland, NJ) in 10 mL of 1191 medium (pH 7.2) on 2.2 g L-1 cellobiose. 1191 media preparation and inoculation protocols were followed as described by Islam, Cisek, Sparling &Levin (2006). Samples were taken in exponential and stationary phase (OD600 ~ 0.37 and ~0.80, respectively).

extract_protocol: Cells for end-product, microarray, RNAseq, and proteomic analysis were grown in anaerobic Balch tubes (26 mL; Bellco Glass Inc., Vineland, NJ) in 10 mL of 1191 medium (pH 7.2) on 2.2 g L-1 cellobiose.  1191 media preparation and inoculation protocols were followed as described by Islam et al.  Samples for end-product, cell biomass, and pH measurements were taken throughout growth, while samples for microarray, RNAseq, and proteomic analysis were taken in exponential and stationary phase (OD600 ~ 0.37 and ~0.80, respectively).  Cell pellets were stored at -80 °C in 1 ml RNAlater until ready for processing. Total RNA was extracted from 10 ml mid-exponential and late exponential  (OD600 ~ 0.37 and ~0.80, respectively) Clostridium thermocellum cultures using the RNeasy Mini kit (QIAGEN, Valencia, CA, USA) protocol as described for gram-positive bacteria, but with the following modifications.  Cell pellets were collected by centrifugation and re-suspended in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) containing 20 mg/ml lysozyme and incubated at 37 °C for 30 minutes.  To ensure efficient lysis, a mechanical shearing step was included that involved passing the cell pellets 10 times through a 22G syringe prior to the addition of ethanol.  Total RNA was eluted in 30 μl RNase-free water.  Following the first elution, the entire volume was re-applied to the mini column, incubated for 3 minutes and finally centrifuged at 8000 x g for 1 minute.

tag: stain

tag: growth phase

value: exponential


title: Pilot Study Cthe 2650 Exponential B5

source_name: DSM 2650_exponential


title: control 1_poly(I:C)

value: healthy control


title: Pilot Study Cthe27405 Stationary D12

source_name: ATCC 27405_stationary

value: stationary


title: IRAK4 P4_R11470

value: Whole blood

value: 1 ml


title: IRAK4 P4_CpG-D19

value: IRAK4-/- patient

value: UK


title: Pilot Study Cthe 27405 Exponential A9

source_name: ATCC 27405_exponential


title: Brain Control:biological rep4

tag: tissue


title: Brain Control:biological rep2


title: IRAK4 P3_SAC

value: M

value: SAC


title: IRAK4 P3_CpG-D19

value: Portugal


title: Pilot Study Cthe 27405 Stationary D9


title: IRAK4 P3_TNFa

value: TNFa


title: Pilot Study Cthe 2650 Exponential B3


title: Pilot Study Cthe 27405 Stationary D4


title: Pilot Study Cthe 4150 Exponential C4


title: control 6_3M13

value: France


title: IRAK4 P4_TNFa


title: Pilot Study Cthe 2650 Exponential B6


title: control 4_R11470


title: Pilot Study Cthe 27405 Exponential A8


title: control 4_R6


title: Pilot Study Cthe 27405 Exponential A4


title: Brain Control:biological rep1


title: IRAK4 P4_PMA/Iono

value: PMA/Iono


title: control 6_PMA/Iono


title: control 6_Flagellin

value: Flagellin


title: DbGP33+ CD8 T cells, Atg7flox/floxCre mice, Day 8, biological rep1

city: Atlanta

first: Xiaojin

last: Xu

state: Georgia

address: 1510 Clifton Road

department: Emory Vaccine Center and Department of Microbiology and Immunology

institute: Emory University School of Medicine

description: Gene expression data from antigen-specific CD8 T cells (DbGP33+) from Atg7flox/flox:GranzymeBCre mice at Day 8 post LCMV Armstrong infection

hyb_protocol: Following fragmentation, cDNA were hybridized over-night at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using a high resolution confocal scanner.

data_processing: The data were analyzed with Microarray Suiteusing Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cDNA were prepared from NuGEN Ovation V2 Amplification System according to the standard protocol from total RNA.

extract_protocol: QIAgen RNeasy Plus kit was used to extract total RNAs from the isolated cells according to manufacturer's instruction

value: Spleen

tag: strain

value: Generated in 129 background; backcrossed 9 generations to C57BL/6J

tag: age

value: 6-12 weeks

tag: genotype/variation


title: DbGP33+ CD8 T cells, Atg7flox/flox mice, D8, biological rep4

description: Gene expression data from antigen-specific CD8 T cells (DbGP33+) from Atg7flox/flox mice at Day 8 post LCMV Armstrong infection


title: DbGP33+ CD8 T cells, Atg7flox/floxCre mice, Day 8, biological rep3

source_name: antigen-specific CD8 T cells (DbGP33+) from Atg7flox/flox:GranzymeBCre mice at Day 8 post LCMV Armstrong infection


title: control 6_R8450

tag: gender

value: White


title: DbGP33+ CD8 T cells, Atg7flox/flox mice, D8, biological rep3

source_name: antigen-specific CD8 T cells (DbGP33+) from Atg7flox/flox mice at Day 8 post LCMV Armstrong infection


title: Bach2KO FoB cells IgM stimulated 24h rep2

city: Sendai

first: ari

last: itoh

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

institute: Tohoku univ.

description: Gene expression in FoB of Bach2KO stimulated IgM

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.7-20.7 pmo Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sureprint G3 Mouse GE 8x60k Microarray slides for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Labeled samples were incubated with Sureprint G3 Mouse GE 8x60k Microarray Kit slides for 17 h. The slides were scanned, and the gene expression analysis was performed using the Genespring GX software program version 11.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Bach2KO FoBs

label_protocol: One RNA sample of WT Fo B or Bach2KO Fo B was amplified and labeled with cyanine-3 (Cy3) dye. Agilent Low RNA Input Fluorescent Linear Amplification Kits were used to amplify RNA samples following the manufacturer’s protocol. After amplification and labeling, cRNA yields and dye incorporation efficiencies were determined using a Nanodrop  spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Plus Mini kit (QIAGEN) following the manufacturer's recommendations. RNA quantity and quality were measured with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The RNA samples of WT or Bach2KO FO B cells were cultured with 10ug/ml anti-mouse IgM (Fab') (115-006-020; Jacson ImmunoResearch Laboratories for 24 h.

tag: cell type

value: follicular B cells


title: IRAK4 P4_IL33

value: F

tag: race


title: Bach2KO FoB cells IgM stimulated 24h rep3


title: DbGP33+ CD8 T cells, Atg7flox/floxCre mice, Day 8, biological rep2


title: DbGP33+ CD8 T cells, Atg7flox/floxCre mice, Day 8, biological rep4


title: Pilot Study Cthe 4150 Exponential C1

value: exponential


title: Pilot Study Cthe 2650 Exponential B2


title: Pilot Study Cthe 4150 Exponential C8


title: WT FoB cells IgM stimulated 24h rep2

description: Gene expression in FoB of WT stimulated IgM

source_name: WT FoBs

value: WT


title: IRAK4 P3_IL18

tag: illness

value: IRAK4-/- patient

value: Whole blood

value: 1 ml


title: IRAK4 P4_R848

tag: geographic

value: UK


title: Pilot Study Cthe 27405 Exponential A3


title: control 2_poly(I:C)

value: healthy control

tag: age at enrollment


title: control 5_PAM3

tag: cell population


title: Pilot Study Cthe 4150 Exponential C2


title: Pilot Study Cthe 27405 Stationary D6

value: stationary


title: IRAK4 P3_LPS

value: M

value: Portugal

tag: in vitro stimulation condition

value: LPS


title: MPP Bach2 vector B220+ rep3

description: Gene expression in B220+ cells expressing Bach2-GFP, cultured B cell condition３

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 104-156 pmo Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sureprint G3 Mouse GE 8x60k Microarray slides for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

source_name: WT MPPs B220+

label_protocol: Three RNA samples of CLPs or MPPs were performed in two rounds of amplification using the Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion) and Cy3 labeled with a CyDye post-labeling Reactive Dye Pack (Amersham) following the manufacturer’s protocol. After amplification and labeling, cRNA yields and dye incorporation efficiencies were determined using a Nanodrop spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Plus Micro kit (QIAGEN) following the manufacturer's recommendations. RNA quantity and quality were measured with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The RNA samples of GFP+ WT MPPs (Lin-, c-kit+, Sca-1+ Flt3mid) infected with Bach2 GFP retrocirus vectors. cells were pooled from WT mouse (4 mice per one experiment). MPPs were stimulated overnight with SCF (50ng/ml), IL-3(5ng/ml) and IL-6(10ng/ml), and were spin infected on the nextday. Infected cells were cultured under the Multi-lineage developmental condition 24h, followed by culture for for 6 d under B lineage developmental condition. then sorted for GFP+, B220+ cells.

value: WT infected with Bach2-GFP

value: B220+ multipotent progenitors


title: Pilot Study Cthe 27405 Stationary D11


title: Pilot Study Cthe 27405 Exponential A5


title: WT FoB cells IgM stimulated 24h rep1


title: Pilot Study Cthe 2650 Exponential B7


title: WT FoB cells IgM stimulated 24h rep3


title: MPP Bach2 vector B220+ rep1

description: Gene expression in B220+ cells expressing Bach2-GFP, cultured B cell condition１


title: MPP Bach2 vector rep1

description: Gene expression in MPPs expressing Bach2-GFP1

source_name: WT MPPs

treatment_protocol: The RNA samples of GFP+ WT MPPs (Lin-, c-kit+, Sca-1+ Flt3mid) infected with MSCV-GFP or Bach2 GFP retrocirus vectors. cells were pooled from WT mouse (4 mice per one experiment). MPPs were stimulated overnight with SCF (50ng/ml), IL-3(5ng/ml) and IL-6(10ng/ml), and were spin infected on the nextday. Infected cells were cultured under the Multi-lineage developmental condition 2d.Then sorted by GFP+ expression.

value: WT expressing Bach2-GFP

value: multipotent progenitors


title: MPP Bach2 vector B220+ rep2

description: Gene expression in B220+ cells expressing Bach2-GFP, cultured B cell condition２

treatment_protocol: The RNA samples of GFP+ WT MPPs (Lin-, c-kit+, Sca-1+ Flt3mid) infected with Bach2 GFP retrocirus vectors. cells were pooled from WT mouse (4 mice per one experiment). MPPs were stimulated overnight with SCF (50ng/ml), IL-3(5ng/ml) and IL-6(10ng/ml), and were spin infected on the nextday. Infected cells were cultured under the Multi-lineage developmental condition 24h, followed by culture for for 6 d under B lineage developmental condition. then sorted forGFP+, B220+ cells.


title: control 3_IL-1b

value: White

value: France

tag: in vitro stimulation incubation time


title: Pilot Study Cthe 2650 Exponential B9

value: exponential


title: Pilot Study Cthe 27405 Exponential A7


title: MPP control vector (MSCV) rep2

description: Gene expression in MPPs expressing MSCV-GFP2

value: WT expressing MSCV-GFP


title: MPP Bach2 vector rep3

description: Gene expression in MPPs expressing Bach2-GFP3


title: MPP Bach2 vector rep2

description: Gene expression in MPPs expressing Bach2-GFP2


title: DbGP33+ CD8 T cells, Atg7flox/flox mice, D8, biological rep1

value: Spleen

value: Generated in 129 background; backcrossed 9 generations to C57BL/6J

value: 6-12 weeks


title: Pilot Study Cthe 27405 Stationary D3


title: MPP control vector (MSCV) rep3

description: Gene expression in MPPs expressing MSCV-GFP3


title: DbGP33+ CD8 T cells, Atg7flox/flox mice, D8, biological rep2


title: IRAK4 P4_SAC

value: F

value: IRAK4-/- patient

value: UK

value: Whole blood

value: SAC

tag: in vitro stimulation blood volume per condition

value: 1 ml


title: IRAK4 P4_PAM3


title: control 3__3M2

value: healthy control


title: MPP control vector (MSCV) rep1

description: Gene expression in MPPs expressing MSCV-GFP1


title: WT Bone marrow CLPs rep2

description: Gene expression in CLPs of WT2

source_name: WT CLPs

label_protocol: Three RNA samples of WT or DD CLPs were performed in two rounds of amplification using the Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion) and Cy3 labeled with a CyDye post-labeling Reactive Dye Pack (Amersham) following the manufacturer’s protocol. After amplification and labeling, cRNA yields and dye incorporation efficiencies were determined using a Nanodrop spectrophotometer.

treatment_protocol: The RNA samples of CLPs cells were pooled from WT or DD mouse (rep1=WT8,DD8,rep2=WT7,DD7 and rep3=WT6,DD6). lineage+ cells (CD4, CD8, CD3e, CD11b, Gr-1, Ter119, B220, NK1.1) were partially removed using sheep anti-rat IgG conjugated magnetic beads (Dynabeads M-450, Invitrogen), and the remaining cells were stained with avidin-PerCP-Cy5.5 (BD). The cells were stained with FITC-conjugated anti Sca-1 (D7; BD), PE-conjugated anti CD135 (A2F10; eBioscience), APC-conjugated anti CD117 (2B8; BD) and PE-Cy7-conjugated anti CD127 (A7R34; eBiosciences or TONBO).  Then they were sorted by FACSAria II (BD) into 3% FBS/PBS.

value: WT

value: common lymphoid progenitors


title: DD Bone marrow CLPs rep2

description: Gene expression in CLPs of DD2

source_name: DD CLPs

value: compound Bach1/Bach2-deficient (DD)


title: control 4_No stimulation

source_name: whole blood from healthy control

value: M

value: White

value: No stimulation


title: control 6_poly(I:C)

value: France


title: DD Bone marrow CLPs rep1

description: Gene expression in CLPs of DD1


title: control 4__3M2


title: WT Bone marrow CLPs rep3

description: Gene expression in CLPs of WT3


title: DNA_Sample 32

status: Public on Oct 25 2014

type: genomic

first: Karen

middle: E

last: Hermetz

state: GA

address: 1518 Clifton Rd

department: Human Genetics

description:
037127
EGL601

hyb_protocol: Labeled DNA and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on Agilent high-resolution C scanner.

data_processing:
Signal intensities were evaluated using Feature Extraction software and Genomic Workbench was used to analyze array data and make breakpoint predictions. Algorithm settings as follows:
Genome: hg19
Aberration Algorithm: ADM-1
Threshold: 6.7
Fuzzy Zero: ON
GC Correction: ON
Window Size: 2Kb
Centralization (legacy): OFF
Diploid Peak Centralization: ON
Manually Reassign Peaks: OFF
Combine Replicates (Intra Array): ON
Combine Replicates (Inter Array): OFF
Array Level Filter: NONE
Aberration Filter:  ( Minimum Number of Probes for Amplification >= 3 AND Minimum Size (Kb) of Region for Amplification >= 0.0 AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.25 ) OR ( Minimum Number of Probes for Deletion >= 3 AND Minimum Size (Kb) of Region for Deletion >= 0.0 AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.25 )
Feature Level Filter: gIsSaturated = true OR rIsSaturated = true OR gIsFeatNonUnifOL = true OR rIsFeatNonUnifOL = true OR LogRatio = 0
Design Level Filter: Homology = 0 OR IsPseudoautosomal = 1
Genomic Boundary: OFF
Show Flat Intervals: OFF

molecule: genomic DNA

source_name: patient genomic DNA

label_protocol: Genomic DNA, 0.5-1ug, from patient samples and controls were Cy3/Cy5 labeled with Agilent Genomic DNA Enzymatic Labeling Kit following manufacture's protocol

extract_protocol: Genomic DNA was extracted from peripheral blood or cell lines using Gentra Puregene DNA Extraction kit following manufacturers protocol

value: peripheral blood

value: m

tag: array number

tag: chromosome affected

tag: cnv type

value: duplication

source_name: Normal control DNA

value: f

tag: cell line


title: DNA_Sample 33

description:
037127
EGL602

tag: tissue


title: DNA_Sample 35

description:
037127
EGL605

value: two duplications, same chromosomes


title: DNA_Sample 31

description:
037127
EGL608

value: tandem duplication


title: DNA_Sample 34

description:
037127
EGL600

value: duplication-triplication


title: WT Bone marrow CLPs rep1

description: Gene expression in CLPs of WT1


title: DNA_Sample 20

description:
037118
EGL465


title: DNA_Sample 22

description:
037118
EGL464


title: DNA_Sample 30

description:
037127
EGL603


title: DNA_Sample 19

description:
037118
EGL461


title: DNA_Sample 24

description:
037118
EGL468


title: DNA_Sample 23

description:
037118
EGL475


title: DNA_Sample 18

description:
037118
EGL460


title: DNA_Sample 29

description:
037127
EGL598


title: DNA_Sample 4

description:
036678
EGL406

value: Xq


title: DNA_Sample 3

description:
036678
EGL402


title: DD Bone marrow CLPs rep3

description: Gene expression in CLPs of DD3


title: DNA_Sample 21

description:
037118
EGL472


title: DNA_Sample 2

description:
036678
EGL403


title: DNA_Sample 1

description:
036678
EGL407


title: DNA_Sample 160

description:
037126
EGL594


title: DNA_Sample 77

description:
037133
EGL687

value: Xp


title: DNA_Sample 7

description:
036678
EGL404

value: two duplications, different chromosomes


title: DNA_Sample 157

description:
037126
EGL596


title: DNA_Sample 6

description:
036678
EGL401


title: DNA_Sample 79

description:
037133
EGL701

value: insertional translocation


title: DNA_Sample 159

description:
037126
EGL586

value: two duplications, same chromosome


title: DNA_Sample 5

description:
036678
EGL400


title: DNA_Sample 156

description:
037126
EGL595


title: DNA_Sample 74

description:
037133
EGL697


title: DNA_Sample 78

description:
037133
EGL700


title: DNA_Sample 76

description:
037133
EGL688


title: DNA_Sample 58

description:
037131
EGL655


title: DNA_Sample 72

description:
037133
EGL690


title: DNA_Sample 161

description:
037126
EGL593


title: DNA_Sample 73

description:
037133
EGL691


title: DNA_Sample 158

description:
037126
EGL597


title: DNA_Sample 155

description:
037126
EGL588


title: DNA_Sample 153

description:
037126
EGL592


title: DNA_Sample 154

description:
037126
EGL582


title: DNA_Sample 57

description:
037131
EGL660


title: DNA_Sample 71

description:
037133
EGL695


title: DNA_Sample 52

description:
037130
EGL641


title: DNA_Sample 51

description:
037130
EGL653


title: DNA_Sample 70

description:
037133
EGL692


title: DNA_Sample 75

description:
037133
EGL698


title: DNA_Sample 69

description:
037132
EGL684


title: DNA_Sample 56

description:
037131
EGL662


title: DNA_Sample 47

description:
037130
EGL644


title: DNA_Sample 55

description:
037131
EGL666


title: DNA_Sample 43

description:
037129
EGL626


title: DNA_Sample 46

description:
037130
EGL649


title: DNA_Sample 50

description:
037130
EGL650


title: DNA_Sample 68

description:
037132
EGL686


title: DNA_Sample 53

description:
037131
EGL668


title: DNA_Sample 150

description:
037126
EGL585


title: DNA_Sample 65

description:
037132
EGL672


title: DNA_Sample 45

description:
037130
EGL648


title: DNA_Sample 151

description:
037126
EGL583


title: DNA_Sample 64

description:
037132
EGL685


title: DNA_Sample 148

description:
037125
EGL579


title: DNA_Sample 44

description:
037129
EGL629


title: DNA_Sample 66

description:
037132
EGL680


title: DNA_Sample 48

description:
037130
EGL645


title: DNA_Sample 152

description:
037126
EGL587


title: DNA_Sample 67

description:
037132
EGL677


title: DNA_Sample 42

description:
037129
EGL639


title: DNA_Sample 147

description:
037125
EGL569


title: DNA_Sample 149

description:
037125
EGL573


title: DNA_Sample 49

description:
037130
EGL646


title: DNA_Sample 146

description:
037125
EGL581


title: DNA_Sample 41

description:
037129
EGL627


title: DNA_Sample 63

description:
037132
EGL676


title: Bach2KO FoB cells IgM stimulated 24h rep1

value: follicular B cells


title: DNA_Sample 62

description:
037132
EGL683


title: DNA_Sample 145

description:
037125
EGL580


title: DNA_Sample 36

description:
037128
EGL615


title: DNA_Sample 61

description:
037132
EGL681


title: DNA_Sample 144

description:
037125
EGL578


title: DNA_Sample 40

description:
037129
EGL638


title: DNA_Sample 60

description:
037132
EGL673


title: DNA_Sample 39

description:
037129
EGL625


title: DNA_Sample 37

description:
037128
EGL617


title: DNA_Sample 141

description:
037125
EGL577


title: DNA_Sample 142

description:
037125
EGL572


title: DNA_Sample 126

description:
037123
EGL543


title: DNA_Sample 135

description:
037124
EGL558


title: DNA_Sample 127

description:
037123
EGL544


title: DNA_Sample 136

description:
037124
EGL556


title: DNA_Sample 125

description:
037123
EGL542


title: DNA_Sample 137

description:
037124
EGL557


title: DNA_Sample 138

description:
037124
EGL555


title: DNA_Sample 128

description:
037123
EGL537


title: DNA_Sample 59

description:
037132
EGL671


title: DNA_Sample 129

description:
037123
EGL547


title: DNA_Sample 54

description:
037131
EGL669


title: DNA_Sample 97

description:
037120
EGL499


title: DNA_Sample 98

description:
037120
EGL495


title: DNA_Sample 140

description:
037125
EGL570


title: mutant p53, rep3

city: Chicago

first: Joanna

last: Burdette

state: IL

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

hyb_protocol: Affymetrix's GeneChip Hybridization, Wash and Stain Kit.  GeneChip was washed using the Fluidics Station 450 and Affymetrix GeneChip Command Console (AGCC) v4.0.0.1567 Fluidics Control software.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G and basic data processing was done on the AGCC Scan Control software.

data_processing: AGCC Scan Control software

source_name: R273H mutant p53

label_protocol: Affymetrix's GeneChip WT PLUS Reagent Kit

growth_protocol: Mouse oviductal epithelium was grown in α-modified Eagle’s medium (Mediatech) supplemented with 10% v/v fetal bovine serum (Gibco), 2mM L-glutamine (Gibco), 2 μg/ml epithelial growth factor (Roche), 5 μg/ml insulin (Roche), 5 μg/ml transferrin (Roche), 5ng/ml sodium selenite (Roche), 1mg/ml gentamycin (Mediatech), 50U penicillin (Gibco), 50 μg/ml streptomycin (Gibco), 20ng/ml β-estradiol dissolved in ethanol (Sigma-Aldrich).

extract_protocol: RNeasy kit with spin columns (Qiagen)

treatment_protocol: Parental cells were transfected using TransIT LT1 (Mirus Bio) according to the manufacturer’s instructions with plasmids containing targets of interest. Cells were clonogenically isolated via antibiotic selection and validated via qRT-PCR and western blotting.

value: oviductal epithelium


title: DNA_Sample 139

description:
037124
EGL559


title: mutant p53, rep2


title: DNA_Sample 95

description:
037120
EGL491


title: DNA_Sample 143

description:
037125
EGL568


title: DNA_Sample 99

description:
037120
EGL501


title: DNA_Sample 133

description:
037124
EGL566


title: DNA_Sample 123

description:
037123
EGL550


title: DNA_Sample 124

description:
037123
EGL539


title: DNA_Sample 110

description:
037121
EGL520


title: mutant p53, rep1


title: DNA_Sample 134

description:
037124
EGL554


title: DNA_Sample 130

description:
037124
EGL561


title: DNA_Sample 131

description:
037124
EGL562


title: DNA_Sample 111

description:
037121
EGL515


title: DNA_Sample 121

description:
037122
EGL521


title: DNA_Sample 109

description:
037121
EGL518


title: control rep 3

source_name: empty vector control


title: DNA_Sample 91

description:
037120
EGL492


title: DNA_Sample 107

description:
037121
EGL517


title: DNA_Sample 108

description:
037121
EGL506


title: DNA_Sample 132

description:
037124
EGL565


title: DNA_Sample 93

description:
037120
EGL503


title: DNA_Sample 89

description:
037120
EGL497


title: control, rep 1


title: DNA_Sample 122

description:
037122
EGL526


title: DNA_Sample 94

description:
037120
EGL505


title: OE2

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in dentate gyrus of EB-treated OVX adult female rat

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

organism: Rattus norvegicus

source_name: Overexpression of Prr7_Replicate 2

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Sprague–Dawley rats were killed using CO2 according to the guidelines of the Albert Einstein College of Medicine Institutional Animal Care and Use Committee. Primary hippocampal neuronal cultures from embryonic day (18-19) embryos of either sex were prepared as described (Osten et al., Neuron 27:313-325, 2000).

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: We used pTRIP vectors to generate lentiviral shRNA vectors for knockdown following the methods previously described (Janas et al., Methods Enzymol 406:593-605, 2006). The sequence used to knockdown PRR7 targeted the coding region of PRR7: 413bp [5’- CGGAATCGGACATGTCTAA 3’]. To overexpress PRR7 we subcloned the full length PRR7 into FUGW vector (Dittgen et al., Proc Natl Acad Sci U S A 101:18206-18211, 2004). Viral particles were produced as described previously (Klein et al., Proc Natl Acad Sci U S A 110:3125-3130, 2013). Plasmids encoding human Prr7, Prr7-GFP, and Prr7(1-44)-GFP were generated previously (Hrdinka et al. J Biol Chem 286:19617-19629, 2011). C-terminally tagged Prr7-Myc and Prr7-Flag construct were created by sub-cloning of Prr7 into pRK-Myc and pFLAG-CMV vectors, respectively. The N-terminal deletion mutant Prr7(34-269)-GFP was generated by PCR and inserted into pEGFP-C2 vector (Clontech).

tag: treatment

value: Overexpression of Prr7

tag: strain

value: Sprague-Dawley

value: primary hippocampal neuronal culture

tag: developmental stage

value: embryonic day 18-19


title: DNA_Sample 96

description:
037120
EGL504

value: peripheral blood

tag: gender

value: m


title: OE4

source_name: Overexpression of Prr7_Replicate 4


title: DNA_Sample 106

description:
037121
EGL512

value: f


title: DNA_Sample 120

description:
037122
EGL525

value: duplicaton


title: DNA_Sample 92

description:
037120
EGL500

value: tandem duplication


title: OE3

source_name: Overexpression of Prr7_Replicate 3


title: DNA_Sample 90

description:
037120
EGL498


title: OE1

source_name: Overexpression of Prr7_Replicate 1


title: DNA_Sample 88

description:
037120
EGL496

value: duplication


title: control, rep 2


title: DNA_Sample 119

description:
037122
EGL527


title: DNA_Sample 87

description:
037119
EGL483


title: DNA_Sample 105

description:
037121
EGL514


title: DNA_Sample 38

description:
037128
EGL614


title: KD4

description: Gene expression in dentate gyrus of oil-treated OVX adult female rat

source_name: Knock-down _ Replicate 4

value: PRR7 Knock-down


title: DNA_Sample 104

description:
037121
EGL507


title: DNA_Sample 84

description:
037119
EGL480


title: DNA_Sample 117

description:
037122
EGL530


title: DNA_Sample 102

description:
037121
EGL513


title: KD3

source_name: Knock-down _ Replicate 3


title: DNA_Sample 116

description:
037122
EGL529


title: KD2

source_name: Knock-down _ Replicate 2


title: DNA_Sample 83

description:
037119
EGL479


title: DNA_Sample 82

description:
037119
EGL478


title: DNA_Sample 86

description:
037119
EGL484


title: DNA_Sample 114

description:
037122
EGL535


title: NT4

source_name: Non-targeting shRNA _ Replicate 4

value: Non-targeting shRNA


title: DNA_Sample 115

description:
037122
EGL522


title: DNA_Sample 101

description:
037121
EGL509


title: DNA_Sample 100

description:
037121
EGL519


title: DNA_Sample 13

description:
036677
EGL413

value: 7p; Xq

value: two duplications, different chromosomes


title: DNA_Sample 118

description:
037122
EGL524


title: KD1

source_name: Knock-down _ Replicate 1


title: NT2

source_name: Non-targeting shRNA _ Replicate 2


title: DNA_Sample 113

description:
037122
EGL523


title: DNA_Sample 112

description:
037122
EGL531


title: NT3

source_name: Non-targeting shRNA _ Replicate 3


title: DNA_Sample 80

description:
037119
EGL477


title: DNA_Sample 81

description:
037119
EGL481

value: duplication-triplication


title: DNA_Sample 17

description:
036676
EGL420

value: 3q; Xq


title: DNA_Sample 28

description:
037118
EGL467


title: DNA_Sample 12

description:
036677
EGL408

value: 12p; Xq


title: DNA_Sample 27

description:
037118
EGL463


title: NT1

source_name: Non-targeting shRNA _ Replicate 1


title: DNA_Sample 25

description:
037118
EGL470


title: DNA_Sample 10

description:
036677
EGL410


title: DNA_Sample 85

description:
037119
EGL490


title: NO4

source_name: Not transduced _ Replicate 4

value: Not transduced


title: DNA_Sample 11

description:
036677
EGL415

source_name: patient genomic DNA


title: DNA_Sample 14

description:
036676
EGL418

source_name: Normal control DNA


title: DNA_Sample 26

description:
037118
EGL473


title: Lymphoblastoid cell line Down Syndrome sample435

status: Public on Oct 24 2014

first: Michael

middle: Edward

last: Zwick

address: 615 Michael Street, Suite 301

description: primary data description:  Probe ID, genomic position (Chr and base position), Copy number state and Log2 ratio for each probe.

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were washed using Affymetrix GeneChip 450 fluidics stations, and scanned using the Gene Chip Scanner.

data_processing: Initial QC analysis and generation of log2 files (CNCHP) were done using Affymetrix power tools (APT 1.12.0). To mimimize the issue of false positives, we used 3 algorithms to make the CNV calls from CNCHP files (BEAST, GADA and GLAD).

source_name: Lymphoblastoid cell line sample435

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was isolated using Puregene DNA purification kit from lymphoblastoid cell lines according to manufacturer's instructions. DNA quality and quantity was assessed using Nanodrop ND-1000 spectrophotometer and agarose gel electrophoresis.

tag: cell type

value: lymphoblastoid cell line

tag: phenotype

value: Down Syndrome

tag: ethnicity

value: European Ancestry

tag: status

value: control


title: Lymphoblastoid cell line Down Syndrome sample434

source_name: Lymphoblastoid cell line sample434


title: Lymphoblastoid cell line Down Syndrome sample432

source_name: Lymphoblastoid cell line sample432


title: Lymphoblastoid cell line Down Syndrome sample436

source_name: Lymphoblastoid cell line sample436


title: DNA_Sample 15

description:
036676
EGL421

value: peripheral blood

value: m


title: Lymphoblastoid cell line Down Syndrome sample429

source_name: Lymphoblastoid cell line sample429

value: case


title: Lymphoblastoid cell line Down Syndrome sample430

source_name: Lymphoblastoid cell line sample430


title: Lymphoblastoid cell line Down Syndrome sample431

source_name: Lymphoblastoid cell line sample431


title: Lymphoblastoid cell line Down Syndrome sample437

source_name: Lymphoblastoid cell line sample437


title: DNA_Sample 8

description:
036677
EGL414

value: f


title: NO2

source_name: Not transduced _ Replicate 2

value: Sprague-Dawley

value: primary hippocampal neuronal culture

value: embryonic day 18-19


title: NO1

source_name: Not transduced _ Replicate 1


title: Lymphoblastoid cell line Down Syndrome sample425

source_name: Lymphoblastoid cell line sample425


title: Lymphoblastoid cell line Down Syndrome sample427

source_name: Lymphoblastoid cell line sample427


title: Lymphoblastoid cell line Down Syndrome sample426

source_name: Lymphoblastoid cell line sample426


title: NO3

source_name: Not transduced _ Replicate 3


title: DNA_Sample 16

description:
036676
EGL417


title: DNA_Sample 9

description:
036677
EGL411

value: duplication


title: Lymphoblastoid cell line Down Syndrome sample423

source_name: Lymphoblastoid cell line sample423


title: Lymphoblastoid cell line Down Syndrome sample419

source_name: Lymphoblastoid cell line sample419


title: Lymphoblastoid cell line Down Syndrome sample428

source_name: Lymphoblastoid cell line sample428


title: Lymphoblastoid cell line Down Syndrome sample424

source_name: Lymphoblastoid cell line sample424


title: Lymphoblastoid cell line Down Syndrome sample422

source_name: Lymphoblastoid cell line sample422


title: Lymphoblastoid cell line Down Syndrome sample418

source_name: Lymphoblastoid cell line sample418


title: Lymphoblastoid cell line Down Syndrome sample421

source_name: Lymphoblastoid cell line sample421


title: Lymphoblastoid cell line Down Syndrome sample420

source_name: Lymphoblastoid cell line sample420


title: Lymphoblastoid cell line Down Syndrome sample408

source_name: Lymphoblastoid cell line sample408


title: Lymphoblastoid cell line Down Syndrome sample413

source_name: Lymphoblastoid cell line sample413


title: Lymphoblastoid cell line Down Syndrome sample416

source_name: Lymphoblastoid cell line sample416


title: Lymphoblastoid cell line Down Syndrome sample409

source_name: Lymphoblastoid cell line sample409


title: Lymphoblastoid cell line Down Syndrome sample415

source_name: Lymphoblastoid cell line sample415


title: Lymphoblastoid cell line Down Syndrome sample412

source_name: Lymphoblastoid cell line sample412


title: Lymphoblastoid cell line Down Syndrome sample410

source_name: Lymphoblastoid cell line sample410


title: Lymphoblastoid cell line Down Syndrome sample406

source_name: Lymphoblastoid cell line sample406


title: Lymphoblastoid cell line Down Syndrome sample407

source_name: Lymphoblastoid cell line sample407


title: Lymphoblastoid cell line Down Syndrome sample411

source_name: Lymphoblastoid cell line sample411


title: Lymphoblastoid cell line Down Syndrome sample405

source_name: Lymphoblastoid cell line sample405


title: Lymphoblastoid cell line Down Syndrome sample404

source_name: Lymphoblastoid cell line sample404


title: Lymphoblastoid cell line Down Syndrome sample402

source_name: Lymphoblastoid cell line sample402


title: Lymphoblastoid cell line Down Syndrome sample417

source_name: Lymphoblastoid cell line sample417


title: Lymphoblastoid cell line Down Syndrome sample401

source_name: Lymphoblastoid cell line sample401


title: Lymphoblastoid cell line Down Syndrome sample400

source_name: Lymphoblastoid cell line sample400


title: Lymphoblastoid cell line Down Syndrome sample398

source_name: Lymphoblastoid cell line sample398


title: Lymphoblastoid cell line Down Syndrome sample399

source_name: Lymphoblastoid cell line sample399


title: Lymphoblastoid cell line Down Syndrome sample397

source_name: Lymphoblastoid cell line sample397


title: Lymphoblastoid cell line Down Syndrome sample414

source_name: Lymphoblastoid cell line sample414


title: Lymphoblastoid cell line Down Syndrome sample396

source_name: Lymphoblastoid cell line sample396


title: Lymphoblastoid cell line Down Syndrome sample393

source_name: Lymphoblastoid cell line sample393


title: Lymphoblastoid cell line Down Syndrome sample390

source_name: Lymphoblastoid cell line sample390


title: Lymphoblastoid cell line Down Syndrome sample395

source_name: Lymphoblastoid cell line sample395


title: Lymphoblastoid cell line Down Syndrome sample391

source_name: Lymphoblastoid cell line sample391


title: Lymphoblastoid cell line Down Syndrome sample392

source_name: Lymphoblastoid cell line sample392


title: Lymphoblastoid cell line Down Syndrome sample387

source_name: Lymphoblastoid cell line sample387


title: Lymphoblastoid cell line Down Syndrome sample388

source_name: Lymphoblastoid cell line sample388


title: Lymphoblastoid cell line Down Syndrome sample403

source_name: Lymphoblastoid cell line sample403


title: Lymphoblastoid cell line Down Syndrome sample386

source_name: Lymphoblastoid cell line sample386


title: Lymphoblastoid cell line Down Syndrome sample381

source_name: Lymphoblastoid cell line sample381


title: Lymphoblastoid cell line Down Syndrome sample385

source_name: Lymphoblastoid cell line sample385


title: Lymphoblastoid cell line Down Syndrome sample384

source_name: Lymphoblastoid cell line sample384


title: Lymphoblastoid cell line Down Syndrome sample383

source_name: Lymphoblastoid cell line sample383


title: Lymphoblastoid cell line Down Syndrome sample389

source_name: Lymphoblastoid cell line sample389


title: Lymphoblastoid cell line Down Syndrome sample379

source_name: Lymphoblastoid cell line sample379


title: Lymphoblastoid cell line Down Syndrome sample380

source_name: Lymphoblastoid cell line sample380


title: Lymphoblastoid cell line Down Syndrome sample378

source_name: Lymphoblastoid cell line sample378


title: Lymphoblastoid cell line Down Syndrome sample382

source_name: Lymphoblastoid cell line sample382


title: Lymphoblastoid cell line Down Syndrome sample375

source_name: Lymphoblastoid cell line sample375


title: Lymphoblastoid cell line Down Syndrome sample376

source_name: Lymphoblastoid cell line sample376


title: Lymphoblastoid cell line Down Syndrome sample374

source_name: Lymphoblastoid cell line sample374


title: Lymphoblastoid cell line Down Syndrome sample377

source_name: Lymphoblastoid cell line sample377


title: Lymphoblastoid cell line Down Syndrome sample372

source_name: Lymphoblastoid cell line sample372


title: Lymphoblastoid cell line Down Syndrome sample394

source_name: Lymphoblastoid cell line sample394


title: Lymphoblastoid cell line Down Syndrome sample366

source_name: Lymphoblastoid cell line sample366


title: Lymphoblastoid cell line Down Syndrome sample369

source_name: Lymphoblastoid cell line sample369


title: Lymphoblastoid cell line Down Syndrome sample367

source_name: Lymphoblastoid cell line sample367


title: Lymphoblastoid cell line Down Syndrome sample370

source_name: Lymphoblastoid cell line sample370


title: Lymphoblastoid cell line Down Syndrome sample368

source_name: Lymphoblastoid cell line sample368


title: Lymphoblastoid cell line Down Syndrome sample371

source_name: Lymphoblastoid cell line sample371


title: Lymphoblastoid cell line Down Syndrome sample365

source_name: Lymphoblastoid cell line sample365


title: Lymphoblastoid cell line Down Syndrome sample364

source_name: Lymphoblastoid cell line sample364


title: Lymphoblastoid cell line Down Syndrome sample362

source_name: Lymphoblastoid cell line sample362


title: Lymphoblastoid cell line Down Syndrome sample360

source_name: Lymphoblastoid cell line sample360


title: Lymphoblastoid cell line Down Syndrome sample363

source_name: Lymphoblastoid cell line sample363


title: Lymphoblastoid cell line Down Syndrome sample361

source_name: Lymphoblastoid cell line sample361


title: DNA_Sample 103

description:
037121
EGL511

source_name: patient genomic DNA

source_name: Normal control DNA


title: Lymphoblastoid cell line Down Syndrome sample357

source_name: Lymphoblastoid cell line sample357


title: Lymphoblastoid cell line Down Syndrome sample359

source_name: Lymphoblastoid cell line sample359


title: Lymphoblastoid cell line Down Syndrome sample358

source_name: Lymphoblastoid cell line sample358


title: Lymphoblastoid cell line Down Syndrome sample373

source_name: Lymphoblastoid cell line sample373


title: Lymphoblastoid cell line Down Syndrome sample350

source_name: Lymphoblastoid cell line sample350


title: Lymphoblastoid cell line Down Syndrome sample351

source_name: Lymphoblastoid cell line sample351


title: Lymphoblastoid cell line Down Syndrome sample346

source_name: Lymphoblastoid cell line sample346


title: Lymphoblastoid cell line Down Syndrome sample353

source_name: Lymphoblastoid cell line sample353


title: Lymphoblastoid cell line Down Syndrome sample349

source_name: Lymphoblastoid cell line sample349


title: Lymphoblastoid cell line Down Syndrome sample348

source_name: Lymphoblastoid cell line sample348


title: Lymphoblastoid cell line Down Syndrome sample352

source_name: Lymphoblastoid cell line sample352


title: Lymphoblastoid cell line Down Syndrome sample345

source_name: Lymphoblastoid cell line sample345


title: Lymphoblastoid cell line Down Syndrome sample342

source_name: Lymphoblastoid cell line sample342


title: Lymphoblastoid cell line Down Syndrome sample344

source_name: Lymphoblastoid cell line sample344


title: Lymphoblastoid cell line Down Syndrome sample343

source_name: Lymphoblastoid cell line sample343


title: Lymphoblastoid cell line Down Syndrome sample340

source_name: Lymphoblastoid cell line sample340


title: Lymphoblastoid cell line Down Syndrome sample337

source_name: Lymphoblastoid cell line sample337


title: Lymphoblastoid cell line Down Syndrome sample336

source_name: Lymphoblastoid cell line sample336


title: Lymphoblastoid cell line Down Syndrome sample341

source_name: Lymphoblastoid cell line sample341


title: Lymphoblastoid cell line Down Syndrome sample335

source_name: Lymphoblastoid cell line sample335


title: Lymphoblastoid cell line Down Syndrome sample331

source_name: Lymphoblastoid cell line sample331


title: Lymphoblastoid cell line Down Syndrome sample339

source_name: Lymphoblastoid cell line sample339


title: Lymphoblastoid cell line Down Syndrome sample334

source_name: Lymphoblastoid cell line sample334


title: Lymphoblastoid cell line Down Syndrome sample356

source_name: Lymphoblastoid cell line sample356


title: Lymphoblastoid cell line Down Syndrome sample332

source_name: Lymphoblastoid cell line sample332


title: Lymphoblastoid cell line Down Syndrome sample355

source_name: Lymphoblastoid cell line sample355


title: Lymphoblastoid cell line Down Syndrome sample354

source_name: Lymphoblastoid cell line sample354


title: Lymphoblastoid cell line Down Syndrome sample333

source_name: Lymphoblastoid cell line sample333


title: Lymphoblastoid cell line Down Syndrome sample329

source_name: Lymphoblastoid cell line sample329


title: Lymphoblastoid cell line Down Syndrome sample327

source_name: Lymphoblastoid cell line sample327


title: Lymphoblastoid cell line Down Syndrome sample321

source_name: Lymphoblastoid cell line sample321


title: Lymphoblastoid cell line Down Syndrome sample328

source_name: Lymphoblastoid cell line sample328


title: Lymphoblastoid cell line Down Syndrome sample326

source_name: Lymphoblastoid cell line sample326


title: Lymphoblastoid cell line Down Syndrome sample325

source_name: Lymphoblastoid cell line sample325


title: Lymphoblastoid cell line Down Syndrome sample323

source_name: Lymphoblastoid cell line sample323


title: Lymphoblastoid cell line Down Syndrome sample330

source_name: Lymphoblastoid cell line sample330


title: Lymphoblastoid cell line Down Syndrome sample347

source_name: Lymphoblastoid cell line sample347


title: Lymphoblastoid cell line Down Syndrome sample320

source_name: Lymphoblastoid cell line sample320


title: Lymphoblastoid cell line Down Syndrome sample338

source_name: Lymphoblastoid cell line sample338


title: Lymphoblastoid cell line Down Syndrome sample322

source_name: Lymphoblastoid cell line sample322


title: Lymphoblastoid cell line Down Syndrome sample324

source_name: Lymphoblastoid cell line sample324


title: Lymphoblastoid cell line Down Syndrome sample317

source_name: Lymphoblastoid cell line sample317


title: Lymphoblastoid cell line Down Syndrome sample319

source_name: Lymphoblastoid cell line sample319


title: Lymphoblastoid cell line Down Syndrome sample318

source_name: Lymphoblastoid cell line sample318


title: Lymphoblastoid cell line Down Syndrome sample314

source_name: Lymphoblastoid cell line sample314


title: Lymphoblastoid cell line Down Syndrome sample316

source_name: Lymphoblastoid cell line sample316


title: Lymphoblastoid cell line Down Syndrome sample315

source_name: Lymphoblastoid cell line sample315


title: Lymphoblastoid cell line Down Syndrome sample312

source_name: Lymphoblastoid cell line sample312


title: Lymphoblastoid cell line Down Syndrome sample311

source_name: Lymphoblastoid cell line sample311


title: Lymphoblastoid cell line Down Syndrome sample310

source_name: Lymphoblastoid cell line sample310


title: Lymphoblastoid cell line Down Syndrome sample305

source_name: Lymphoblastoid cell line sample305


title: Lymphoblastoid cell line Down Syndrome sample313

source_name: Lymphoblastoid cell line sample313


title: Lymphoblastoid cell line Down Syndrome sample308

source_name: Lymphoblastoid cell line sample308


title: Lymphoblastoid cell line Down Syndrome sample309

source_name: Lymphoblastoid cell line sample309


title: Lymphoblastoid cell line Down Syndrome sample306

source_name: Lymphoblastoid cell line sample306


title: Lymphoblastoid cell line Down Syndrome sample303

source_name: Lymphoblastoid cell line sample303


title: Lymphoblastoid cell line Down Syndrome sample304

source_name: Lymphoblastoid cell line sample304


title: Lymphoblastoid cell line Down Syndrome sample302

source_name: Lymphoblastoid cell line sample302


title: Lymphoblastoid cell line Down Syndrome sample298

source_name: Lymphoblastoid cell line sample298


title: Lymphoblastoid cell line Down Syndrome sample297

source_name: Lymphoblastoid cell line sample297


title: Lymphoblastoid cell line Down Syndrome sample299

source_name: Lymphoblastoid cell line sample299


title: Lymphoblastoid cell line Down Syndrome sample300

source_name: Lymphoblastoid cell line sample300


title: Lymphoblastoid cell line Down Syndrome sample295

source_name: Lymphoblastoid cell line sample295


title: Lymphoblastoid cell line Down Syndrome sample296

source_name: Lymphoblastoid cell line sample296


title: Lymphoblastoid cell line Down Syndrome sample294

source_name: Lymphoblastoid cell line sample294


title: Lymphoblastoid cell line Down Syndrome sample293

source_name: Lymphoblastoid cell line sample293


title: Lymphoblastoid cell line Down Syndrome sample292

source_name: Lymphoblastoid cell line sample292


title: Lymphoblastoid cell line Down Syndrome sample291

source_name: Lymphoblastoid cell line sample291


title: Lymphoblastoid cell line Down Syndrome sample289

source_name: Lymphoblastoid cell line sample289


title: Lymphoblastoid cell line Down Syndrome sample288

source_name: Lymphoblastoid cell line sample288


title: Lymphoblastoid cell line Down Syndrome sample290

source_name: Lymphoblastoid cell line sample290


title: Lymphoblastoid cell line Down Syndrome sample307

source_name: Lymphoblastoid cell line sample307


title: Lymphoblastoid cell line Down Syndrome sample287

source_name: Lymphoblastoid cell line sample287


title: Lymphoblastoid cell line Down Syndrome sample285

source_name: Lymphoblastoid cell line sample285


title: Lymphoblastoid cell line Down Syndrome sample286

source_name: Lymphoblastoid cell line sample286


title: Lymphoblastoid cell line Down Syndrome sample283

source_name: Lymphoblastoid cell line sample283


title: Lymphoblastoid cell line Down Syndrome sample284

source_name: Lymphoblastoid cell line sample284


title: Lymphoblastoid cell line Down Syndrome sample282

source_name: Lymphoblastoid cell line sample282


title: Lymphoblastoid cell line Down Syndrome sample301

source_name: Lymphoblastoid cell line sample301