title: DMSO-treated (Cy3) vs. 6-NDA-treated (Cy5) Replicate 2

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

description: DMSO-treated sample labeled with Cy3 hybridized to 6-NDA-treated sample labeled with Cy5 - Replicate 2

hyb_protocol: Based on Nantel et al., 2006, Microarrays for Studying Pathogenicity in C. albicans (Wiley Press, Hoboken, NJ).

scan_protocol: Scanned on Axon GenePix 4100A scanner.  Image analysis was performed using Axon GenePix Pro software.

data_processing: Background corrected signal intensities were normalized with Lowess algorithm using BRB Array Tools software.

organism: Candida albicans

source_name: DMSO-treated C. albicans cells Rep2

extract_protocol: Qiagen Rneasy Midi kit was used for total RNA extraction.

source_name: 6-NDA-treated C. albicans cells Rep2


title: SET2_INC424_1600nM_6h_1

status: Public on Feb 08 2012

type: RNA

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

description: SET2 cells exposed to 1600 nM INC424  for 6h (replicate #1)

hyb_protocol: Total labeled RNA was hybridized to the Affymetrix Genechip miRNA array 1.0 using manufacturer's protocols.

scan_protocol: Image files from scanning (.dat and .cel files) were generated with Affymetrix Expression Console package.

data_processing: Signal reconstruction was performed using the RMA algorithm as implemented in Bioconductor affy package. All chip probes were used for background estimation but only human probes were considered for normalization and summarization phases.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: SET2 cell line

label_protocol: Total RNA (500ng for samples) was labeled using the FlashTag Biotin HSR kit (Genisphere)

extract_protocol: Total cellular RNA, including small RNAs, was extracted using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

tag: treatment group

tag: genotype

value: MUTATED FOR JAK2V617F


title: xylem, mature_tree41453

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

country: Canada

institute: Université Laval

description:
JF003-8021.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Microarray Scanner: ScanArray Express (Perkin Elmer, Waltham MA, USA) Image Analysis Program: QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA) Slide scanning was performed at 5 micron resolution.

data_processing: Data analyses were performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background intensities were subtracted from the foreground intensities. Background-subtracted data were log2-transformed and normalized using quantile correction approach.   A filtering step was applied to select positive genes to be used for further analysis. The mean intensity of spots containing buffer only was calculated for each row of sub-grids, and was taken as the minimum intensity of probes for that subgrid. A probe was called positive (detected above background) when its signal intensity was above the buffer intensity on at least 50% of slides within a given sample type. When determining differential expression, positive probes were probes that were detected according to this criterion in at least one of the tissues (e.g. phelloderm and xylem juvenile). Mean probe intensity was determined for genes represented by more than one positive probe.   The average signal intensity was determined from all of the slides available for a sample type. The genes were then ranked based on their average signal intensities within a tissue type and equally divided into 10 separate classes according to their signal intensity. Genes from class 1 or class 10 were the 10% with lowest and highest signal intensities, respectively.

label: Alexa 555

organism: Picea glauca

source_name: xylem, mature

label_protocol: Total RNA (1 µg) or mRNA (10 ng) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 or 647 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: For a complete description of experimental site and sample collection see Beaulieu et al. (Genetics 188 [2011])

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the trees, the seed or tissue culture vessels, and stored at -80°C. Tissues were ground under liquid nitrogen and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008) for all of the sample types, except for megagametophytes where poly A+ RNA was extracted directly by using the Dynabeads mRNA Mikro kit (Dynal/Invitrogen, Oslo, Norway) following manufacturers instructions.

tag: tissue

value: xylem (mature)

tag: age of trees

tag: slide batch


title: DMSO-treated (Cy3) vs. 6-NDA-treated (Cy5) Replicate 3

country: USA

description: DMSO-treated sample labeled with Cy3 hybridized to 6-NDA-treated sample labeled with Cy5 - Replicate 3

source_name: DMSO-treated C. albicans cells Rep3

label_protocol: Based on Nantel et al., 2006, Microarrays for Studying Pathogenicity in C. albicans (Wiley Press, Hoboken, NJ).

tag: strain

source_name: 6-NDA-treated C. albicans cells Rep3


title: xylem, mature_tree11692

description:
JF003-8020.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, mature_tree20714

description:
JF003-8019.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: SET2_INC424_1600nM_6h_2

description: SET2 cells exposed to 1600 nM INC424  for 6h (replicate #2)


title: K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + ctrl, biological replicate 4

city: Cologne

first: Karin

last: Schnetz

address: Zuelpicher Str. 47a

department: Institute for Genetics

country: Germany

institute: University of Cologne

description: Escherichia coli K12 BW30270

hyb_protocol: Hybridization was performed according to Affymetrix GeneChip E. coli Genome 2.0 Array protocol.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were processed using Affymetrix apt-probeset-summarize software version 1.10 and RMA algorithm. Samples were normalized using the standard normalization probes present on the Affymetrix GeneChip.

organism: Escherichia coli K-12

source_name: K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + ctrl

label_protocol: 10 µg of RNA was labelled according to Affymetrix GeneChip E. coli Genome 2.0 Array protocol.

growth_protocol: Exponential cultures of transformants were inoculated from fresh overnight cultures in LB medium supplemented with 25 µg/ml of kanamycin to an optical density at 600 nm (OD) of 0.1 and grown for 30 min at 37°C to an OD of 0.15. Then, IPTG was added to a final concentration of 1 mM for induction of expression. After 60 min of additional growth cells were harvested for RNA isolation.

extract_protocol: Cells were harvested using RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) for stabilization of RNA. Stabilized cultures were used for RNA isolation using the RNeasy MiniKit system (Qiagen, Hilden, Germany). In brief, 1 ml of each culture was used and processed according to the manufacturer's instructions including an on-column DNaseI treatment. RNA quality was assayed by denaturing urea-PAGE and by measuring the ratio of absorption at 260/280 nm in a GeneQuant II spectrophotometer (Amersham). RNA concentration was determined by measuring UV light absorption at 260 nm.

tag: sample id

value: Δ(yjjP-yjjQ-bglJ) ΔleuO

tag: overexpression

tag: plasmid


title: xylem, mature_tree40973

description:
JF003-8017.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: SET2_INC424_160nM_3h_1

description: SET2 cells exposed to 160 nM INC424  for 3h (replicate #1)


title: DMSO-treated (Cy3) vs. 6-NDA-treated (Cy5) Replicate 1

description: DMSO-treated sample labeled with Cy3 hybridized to 6-NDA-treated sample labeled with Cy5 - Replicate 1

source_name: DMSO-treated C. albicans cells Rep1

source_name: 6-NDA-treated C. albicans cells Rep1


title: DMSO-treated (Cy5) vs. 6-NDA-treated (Cy3) Replicate 3

description: DMSO-treated sample labeled with Cy5 hybridized to 6-NDA-treated sample labeled with Cy3 - Replicate 3


title: K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + ctrl, biological replicate 3

description: Escherichia coli K12 BW30270


title: DMSO-treated (Cy5) vs. 6-NDA-treated (Cy3) Replicate 2

description: DMSO-treated sample labeled with Cy5 hybridized to 6-NDA-treated sample labeled with Cy3 - Replicate 2


title: SET2_INC424_160nM_3h_2

description: SET2 cells exposed to 160 nM INC424  for 3h (replicate #2)


title: xylem, mature_tree51832

description:
JF003-8018.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Melanoma cell EDMEL3 xenograft 1 rep1

city: Edinburgh

first: Yan

last: Xu

address: Crewe Road South

department: MRC

country: United Kingdom

institute: The University of Edinburgh

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in R 2.8.1 software.

source_name: Human skin

label_protocol: Biotinylated cDNA  were prepared for the Illumina microRNA microarray (Catalogue # MI 501-1001, Part # 11297743) assay which was carried out on RNA extracted from FFPE and cultured cell samples using the manufacturer’s protocol.

extract_protocol: RNA from mammalian cell lines was isolated using the reagent RNAzolB and RNA from melanocytic tissue samples was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Ambion) with the guidance of protocol.

value: Cell

tag: cell line

tag: developmental stage

value: Metastatic melanoma cell


title: K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + ctrl, biological replicate 2

description: Escherichia coli K12 BW30270


title: xylem, mature_tree51061

description:
JF003-8013.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + ctrl, biological replicate 1

description: Escherichia coli K12 BW30270


title: xylem, mature_tree10103

description:
JF003-8015.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + pBglJ, biological replicate 3

description: Escherichia coli K12 BW30270

source_name: K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + pBglJ

value: BglJ


title: SET2_INC424_160nM_3h_3

description: SET2 cells exposed to 160 nM INC424  for 3h (replicate #3)


title: K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + pBglJ, biological replicate 1

description: Escherichia coli K12 BW30270


title: K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + pBglJ, biological replicate 2

description: Escherichia coli K12 BW30270


title: K12 Δ(yjjP-yjjQ-bglJ) ΔleuO + pBglJ, biological replicate 4

description: Escherichia coli K12 BW30270


title: DMSO-treated (Cy5) vs. 6-NDA-treated (Cy3) Replicate 1

description: DMSO-treated sample labeled with Cy5 hybridized to 6-NDA-treated sample labeled with Cy3 - Replicate 1


title: K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + ctrl, biological replicate 4

description: Escherichia coli K12 BW30270

source_name: K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + ctrl

value: Δ(yjjP-yjjQ-bglJ) ΔrcsB


title: xylem, mature_tree32024

description:
JF003-8007.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: SET2_ctr_3h_3

description: SET2 control cells collected at 3h (replicate #3)


title: xylem, mature_tree41813

description:
JF003-8006.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, mature_tree20915

description:
JF003-8005.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: SET2_ctr_3h_2

description: SET2 control cells collected at 3h (replicate #2)


title: SET2_ctr_3h_1

description: SET2 control cells collected at 3h (replicate #1)


title: xylem, mature_tree41955

description:
JF003-8012.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + ctrl, biological replicate 2

description: Escherichia coli K12 BW30270


title: K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + ctrl, biological replicate 1

description: Escherichia coli K12 BW30270


title: K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + ctrl, biological replicate 3

description: Escherichia coli K12 BW30270


title: K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + pBglJ, biological replicate 3

description: Escherichia coli K12 BW30270

source_name: K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + pBglJ


title: K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + pBglJ, biological replicate 4

description: Escherichia coli K12 BW30270


title: xylem, mature_tree51162

description:
JF003-8001.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: K12 Δ(yjjP-yjjQ-bglJ) + pLeuO, biological replicate 3

description: Escherichia coli K12 BW30270

source_name: K12 Δ(yjjP-yjjQ-bglJ) + pLeuO

value: Δ(yjjP-yjjQ-bglJ)

value: LeuO


title: K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + pBglJ, biological replicate 2

description: Escherichia coli K12 BW30270


title: xylem, mature_tree11484

description:
JF003-8002.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: K12 Δ(yjjP-yjjQ-bglJ) ΔrcsB + pBglJ, biological replicate 1

description: Escherichia coli K12 BW30270


title: xylem, mature_tree50564

description:
JF003-7990.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: K12 Δ(yjjP-yjjQ-bglJ) + pLeuO, biological replicate 2

description: Escherichia coli K12 BW30270


title: xylem, mature_tree30655

description:
JF003-7986.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, mature_tree41093

description:
JF003-7983.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: K12 Δ(yjjP-yjjQ-bglJ) + ctrl, biological replicate 4

description: Escherichia coli K12 BW30270

source_name: K12 Δ(yjjP-yjjQ-bglJ) + ctrl


title: K12 Δ(yjjP-yjjQ-bglJ) + pLeuO, biological replicate 1

description: Escherichia coli K12 BW30270


title: K12 Δ(yjjP-yjjQ-bglJ) + ctrl, biological replicate 1

description: Escherichia coli K12 BW30270


title: K12 Δ(yjjP-yjjQ-bglJ) + ctrl, biological replicate 3

description: Escherichia coli K12 BW30270


title: xylem, mature_tree30252

description:
JF003-7987.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: K12 Δ(yjjP-yjjQ-bglJ) + ctrl, biological replicate 2

description: Escherichia coli K12 BW30270


title: K12 Δ(yjjP-yjjQ-bglJ) + pLeuO, biological replicate 4

description: Escherichia coli K12 BW30270


title: xylem, mature_tree51004

description:
JF003-7981.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, mature_tree10542

description:
JF003-7982.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: K12 Δ(yjjP-yjjQ-bglJ) + pBglJ, biological replicate 4

description: Escherichia coli K12 BW30270

source_name: K12 Δ(yjjP-yjjQ-bglJ) + pBglJ


title: c2_linf at T3

city: Botucatu

first: João Marcelo

middle: Azevedo de Paula

last: Antunes

state: São Paulo

address: FMVZ, Distrito de Rubião Júnior

department: Higiene Veterinária e Saúde Pública

country: Brazil

institute: UNESP

description:
c2_linf.cel
Gene expression data from rams infected with B. ovis.

hyb_protocol: Expression measurements were performed using the Affymetrix GeneChip® Bovine Genome Array (Affymetrix, USA), which interrogates 23,000 genes, following the hybridization protocol recommended by the manufacturer.

scan_protocol: After array scanning, quality control was performed with GCOS software (Affymetrix, USA) according to the manufacturer’s recommendations.

data_processing: The quality control also was verified using Expression Console (http://www.affymetrix.com/browse/level_seven_software_products_only.jsp?productId=131414&categoryId=35623#1_1). The unwanted variables (batch effects) were removed using ComBat methodology (http://jlab.byu.edu/ComBat/Abstract.html) (Johnson et al., 2007). The IQR (Inter-Quartile-Range) filter available at R/Bioconductor (Irizarry et al., 2003) was applied. Gene expression values were obtained using the three-step Robust Multi-array Average (RMA) pre-processing method, implemented in the Affy package from R/Bioconductor (Irizarry et al., 2003). We employed the RankProd method for the selection of differentially expressed genes (DEGs), considering a p-value cut-off of 0.05 adjusted for FDR (False Discovery Rate) (Benjamini & Hochberg, 1995). RankProd is a rank-based nonparametric procedure (Hong et al., 2006). The method used HCL (Hierarchical Clustering) for the grouping of data with the Pearson correlation coefficient for the calculation of within-group distance and complete linkage between groups for the calculation. The method is available in the program Expander (http://acgt.cs.tau.ac.il/expander/index.html) (Shamir et al., 2005). We performed functional annotation analysis of the differentially expressed genes with the IPA (Ingenuity Pathway Analysis, http://www.ingenuity.com) tools. In IPA, we considered the default parameter Molecules per Network=35, Networks per Analysis=25, only direct relationships between genes and the “Ingenuity Expert Information” Data Source, including the new option of “Ingenuity ExpertAssist Findings”, in which the information has been manually reviewed and curated from full-text scientific publications.

organism: Ovis aries

source_name: lymph nodes, biopsied, 60 min, chronic2

label_protocol: RNA labeling was performed as recommended by the manufacturer.

growth_protocol: Twelve 12-month-old healthy Santa Inês rams, previously diagnosed as negative for brucellosis/visna maedi/toxoplasmosis/neosporosis, were selected for the study.

extract_protocol: Total RNA was isolated from tissue samples collected at 0, 60, 120, 240 dpc using the Invisorb® Spin Tissue RNA Mini Kit (Invitek Gmbh, Germany) according to the manufacturer’s instructions, and purified with the RNeasy Mini-kit (Qiagen, Mississauga, ON, Canada). Total RNA was quantified by absorbance at 260 nm. The quality of all RNA preparations was controlled by electrophoresis on agarose gels. They were also evaluated on an Agilent Bioanalyser instrument (Agilent Technologies, Palo Alto, CA, USA). Only samples with a preserved rRNA ratio (28S/18S), no evidence of RNA degradation, and values ≥ 8 at the Bioanalyser were used in the microarray hybridization and qPCR.

treatment_protocol: The rams were kept in an isolated pen and experimentally challenged with a rough (R) virulent B. ovis PA strain (ATCC 25840).

tag: gender

value: male

tag: breed

value: Santa Inês

tag: age

value: 12 months

value: lymph nodes

tag: treatment

value: Brucella ovis ATCC 25840 infection

tag: phase of infection


title: c2_test at T3

description:
c2_test.cel
Gene expression data from rams infected with B. ovis.

source_name: testicles, biopsied, 60 min, chronic2

value: testicles


title: K12 Δ(yjjP-yjjQ-bglJ) + pBglJ, biological replicate 2

description: Escherichia coli K12 BW30270


title: xylem, mature_tree51093

description:
JF003-7979.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: K12 Δ(yjjP-yjjQ-bglJ) + pBglJ, biological replicate 1

description: Escherichia coli K12 BW30270


title: c2_bulb at T3

description:
c2_bulb.cel
Gene expression data from rams infected with B. ovis.

source_name: bulbourethral glands, biopsied, 60 min, chronic2

value: bulbourethral glands


title: c2_vesi at T3

description:
c2_vesi.cel
Gene expression data from rams infected with B. ovis.

source_name: vesicular glands, biopsied, 60 min, chronic2

value: vesicular glands


title: xylem, mature_tree40812

description:
JF003-7980.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

source_name: xylem, mature


title: c2_epid at T3

description:
c2_epid.cel
Gene expression data from rams infected with B. ovis.

source_name: epididymus, biopsied, 60 min, chronic2

value: epididymus


title: xylem, mature_tree10702

description:
JF003-7978.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

value: xylem (mature)


title: K12Δ(yjjP-yjjQ-bglJ) + pBglJ, biological replicate 3

description: Escherichia coli K12 BW30270

source_name: K12Δ(yjjP-yjjQ-bglJ) + pBglJ


title: c2_amp at T3

description:
c2_amp.cel
Gene expression data from rams infected with B. ovis.

source_name: ampolae, biopsied, 60 min, chronic2

value: ampolae


title: Sciatic nerve, acrylamide treated, biological rep1

description:
ACRL_SN__Treated_A
Gene expression data from acrylamide-treated rat pups.

hyb_protocol: Affymetrix GeneChip Hybridization protocol, and GeneChip Fluidics Station 450 default protocol were used. GeneChip Rat Genome 230 2.0 arrays were used.

scan_protocol: Affymetrix GenChip Scanner 3000 default parameters were used.

data_processing: Image analysis, scaling (TGT = 500), and probeset-level data analysis was performed using default parameters in GCOS v1.1.

organism: Rattus norvegicus

source_name: Rat pups treated with acrylamide, sciatic nerve

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: 25-day-old male Wistar rats were housed two per cage and maintained in a 12 h light / 12 h dark cycle with food (Purina 5001) and water provided ad libitum.

extract_protocol: The Qiagen RNeasy Lipid Tissue Midi-kit was used for total RNA extraction.

treatment_protocol: 25-day-old rats were treated with either solvent or acrylamide daily (30 mg/kg) via oral gavage. Tissues (cerebellum, right and left sciatic nerves, and spinal cord) were collected 21 days after treatment.

value: Wistar

value: sciatic nerve

value: acrylamide


title: xylem, mature_tree50152

description:
JF003-7967.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Sciatic nerve, acrylamide treated, biological rep2

description:
ACRL_SN__Treated_B
Gene expression data from acrylamide-treated rat pups.


title: Sciatic nerve, saline control, biological rep1

description:
ACRL_SN__Control_A
Gene expression data from saline-treated rat pups.

source_name: Rat pups treated with saline, sciatic nerve

value: saline


title: ctr_test at T0, chronic2

description:
ctr_test.cel
Gene expression data from uninfected rams.

source_name: testicles, biopsied, 60 min, control

value: control


title: Sciatic nerve, saline control, biological rep2

description:
ACRL_SN__Control_B
Gene expression data from saline-treated rat pups.


title: ctr_vesi at T0, chronic2

description:
ctr_vesi.cel
Gene expression data from uninfected rams.

source_name: vesicular glands, biopsied, 60 min, control


title: xylem, mature_tree50835

description:
JF003-7973.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Spinal cord, acrylamide treated, biological rep1

description:
ACRL_SC__Treated_A
Gene expression data from acrylamide-treated rat pups.

source_name: Rat pups treated with acrylamide, spinal cord

value: spinal cord


title: xylem, mature_tree60023

description:
JF003-7976.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Spinal cord, saline control, biological rep2

description:
ACRL_SC__Control_B
Gene expression data from saline-treated rat pups.

source_name: Rat pups treated with saline, spinal cord

value: male


title: ctr_linf at T0, chronic2

description:
ctr_linf.cel
Gene expression data from uninfected rams.

source_name: lymph nodes, biopsied, 60 min, control

value: Santa Inês


title: Spinal cord, acrylamide treated, biological rep2

description:
ACRL_SC__Treated_B
Gene expression data from acrylamide-treated rat pups.


title: xylem, mature_tree61501

description:
JF003-7964.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: ctr_bulb at T0, chronic2

description:
ctr_bulb.cel
Gene expression data from uninfected rams.

source_name: bulbourethral glands, biopsied, 60 min, control

value: 12 months


title: 14F-HighFat 18%

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

description: Biological replicate 2

data_processing: The data after background substraction were normalized using quantile normalization with BeadStudio Expression Module 3.2.7

label: Biotin

organism: Mus musculus

source_name: Liver

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

extract_protocol: RNA was extracted with TriReagent (Sigma). Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Pregnant females were fed a control diet (18%) or a low protein diet 9%  (90 g casein/kg) during the gestational period, offspring was placed after 6 wks on HF diet (36% SF) or a control diet for 14 wks.

value: C57bl/6J OlaHsd

value: Female

value: Liver

tag: diet

value: HighFat 18%


title: 15F-HighFat 18%

description: Biological replicate 3


title: ctr_amp at T0, chronic2

description:
ctr_amp.cel
Gene expression data from uninfected rams.

source_name: ampolae, biopsied, 60 min, control


title: 13F-HighFat 18%

description: Biological replicate 1


title: xylem, mature_tree10905

description:
JF003-7965.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Spinal cord, saline control, biological rep1

description:
ACRL_SC__Control_A
Gene expression data from saline-treated rat pups.


title: Cerebellum, acrylamide treated, biological rep1

description:
ACRL_CBM__Treated_A
Gene expression data from acrylamide-treated rat pups.

source_name: Rat pups treated with acrylamide, cerebellum

value: cerebellum


title: Cerebellum, acrylamide treated, biological rep2

description:
ACRL_CBM__Treated_B
Gene expression data from acrylamide-treated rat pups.


title: c1_vesi at T2

description:
c1_vesi.cel
Gene expression data from rams infected with B. ovis.

source_name: vesicular glands, biopsied, 60 min, chronic1

value: vesicular glands

value: Brucella ovis ATCC 25840 infection


title: Cerebellum, saline control, biological rep2

description:
ACRL_CBM__Control_B
Gene expression data from saline-treated rat pups.

source_name: Rat pups treated with saline, cerebellum


title: xylem, mature_tree51241

description:
JF003-7962.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

source_name: xylem, mature

value: xylem (mature)


title: ctr_epid at T0, chronic2

description:
ctr_epid.cel
Gene expression data from uninfected rams.

source_name: epididymus, biopsied, 60 min, control

value: epididymus


title: xylem, mature_tree10834

description:
JF003-7961.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: 16F-HighFat 18%

description: Biological replicate 4


title: c1_linf at T2

description:
c1_linf.cel
Gene expression data from rams infected with B. ovis.

source_name: lymph nodes, biopsied, 60 min, chronic1

value: lymph nodes


title: xylem, mature_tree60353

description:
JF003-7963.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, mature_tree11674

description:
JF003-7960.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: c1_test at T2

description:
c1_test.cel
Gene expression data from rams infected with B. ovis.

source_name: testicles, biopsied, 60 min, chronic1

value: testicles


title: 12F-Control18%

description: Biological replicate 4


title: c1_epid at T2

description:
c1_epid.cel
Gene expression data from rams infected with B. ovis.

source_name: epididymus, biopsied, 60 min, chronic1


title: Cerebellum, saline control, biological rep1

description:
ACRL_CBM__Control_A
Gene expression data from saline-treated rat pups.

value: Wistar

value: saline


title: 16M-HighFat 18%

description: Biological replicate 4

value: Male


title: xylem, mature_tree60484

description:
JF003-7959.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: 11F-Control18%

description: Biological replicate 3


title: 10F-Control18%

description: Biological replicate 2


title: 15M-HighFat 18%

description: Biological replicate 3


title: c1_bulb at T2

description:
c1_bulb.cel
Gene expression data from rams infected with B. ovis.

source_name: bulbourethral glands, biopsied, 60 min, chronic1

value: male

value: bulbourethral glands


title: 13M-HighFat 18%

description: Biological replicate 1


title: 9F-Control18%

description: Biological replicate 1


title: 12M-Control18%

description: Biological replicate 4


title: xylem, mature_tree10801

description:
JF003-7955.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, mature_tree61153

description:
JF003-7956.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: 8F-HighFat 9%

description: Biological replicate 4

value: HighFat 9%


title: ctr_vesi at T0, chronic1

description:
ctr_vesi.cel
Gene expression data from uninfected rams.

value: Santa Inês

value: 12 months

value: control


title: xylem, mature_tree42034

description:
JF003-7957.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, mature_tree21722

description:
JF003-7954.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: 11M-Control18%

description: Biological replicate 3

value: C57bl/6J OlaHsd

value: Liver


title: 14M-HighFat 18%

description: Biological replicate 2

value: HighFat 18%


title: 6F-HighFat 9%

description: Biological replicate 2

value: Female


title: xylem, mature_tree20341

description:
JF003-7952.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

value: xylem (mature)


title: 7F-HighFat 9%

description: Biological replicate 3


title: 5F-HighFat 9%

description: Biological replicate 1


title: 10M-Control18%

description: Biological replicate 2


title: c1_amp at T2

description:
c1_amp.cel
Gene expression data from rams infected with B. ovis.

source_name: ampolae, biopsied, 60 min, chronic1

value: ampolae

value: Brucella ovis ATCC 25840 infection


title: ctr_linf at T0, chronic1

description:
ctr_linf.cel
Gene expression data from uninfected rams.

value: lymph nodes


title: 9M-Control18%

description: Biological replicate 1


title: xylem, mature_tree11513

description:
JF003-7951.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: ctr_test at T0, chronic1

description:
ctr_test.cel
Gene expression data from uninfected rams.

source_name: testicles, biopsied, 60 min, control

value: testicles


title: 4F-Control 9%

description: Biological replicate 4

value: Control 9%


title: ctr_bulb at T0, chronic1

description:
ctr_bulb.cel
Gene expression data from uninfected rams.


title: xylem, mature_tree51972

description:
JF003-7949.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: ctr_amp at T0, chronic1

description:
ctr_amp.cel
Gene expression data from uninfected rams.


title: 7M-HighFat 9%

description: Biological replicate 3

value: Male


title: ac_test at T1

description:
ac_test.cel
Gene expression data from rams infected with B. ovis.

source_name: testicles, biopsied, 60 min, acute

value: male

value: acute


title: ctr_epid at T0, chronic1

description:
ctr_epid.cel
Gene expression data from uninfected rams.

value: epididymus


title: 8M-HighFat 9%

description: Biological replicate 4

value: HighFat 9%


title: xylem, mature_tree41473

description:
JF003-7950.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: ac_vesi at T1

description:
ac_vesi.cel
Gene expression data from rams infected with B. ovis.

source_name: vesicular glands, biopsied, 60 min, acute

value: Santa Inês

value: 12 months

value: vesicular glands


title: 2F-Control 9%

description: Biological replicate 2

value: C57bl/6J OlaHsd

value: Liver


title: xylem, mature_tree51541

description:
JF003-7933.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: 6M-HighFat 9%

description: Biological replicate 2


title: 3F-Control 9%

description: Biological replicate 3

value: Female


title: 1F-Control 9%

description: Biological replicate 1


title: 3M-Control 9%

description: Biological replicate 3


title: ac_linf at T1

description:
ac_linf.cel
Gene expression data from rams infected with B. ovis.

source_name: lymph nodes, biopsied, 60 min, acute


title: 4M-Control 9%

description: Biological replicate 4


title: xylem, mature_tree20371

description:
JF003-7948.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

value: xylem (mature)


title: ac_bulb at T1

description:
ac_bulb.cel
Gene expression data from rams infected with B. ovis.

source_name: bulbourethral glands, biopsied, 60 min, acute

value: bulbourethral glands


title: xylem, mature_tree11354

description:
JF003-7929.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: 2M-Control 9%

description: Biological replicate 2

source_name: Liver


title: xylem, mature_tree40161

description:
JF003-7931.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: xylem, mature_tree11552

description:
JF003-7930.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Fetal_Mammary_E15.5_rep2

city: La Jolla

first: Benjamin

middle: T

last: Spike

state: California

address: 10010 N Torrey Pines Rd

department: Gene Expression Laboratory

institute: The Salk Institute

description:
Pooled bilateral, #1-5 mammary rudiments from multiple embryos
Dissected mammary tissue from adult and fetal mice was dissociated according to StemCell technologies' EasySep procedure (product #29008)  with minor modifications.  Briefly, fetal rudiments were dissociated for only 90min in collagenase/hyaluronidase containing media and trypsinization was omitted.
Cells were labeled with Anti-CD49f-FITC, Anti-CD24-PE and a biotinylated antibody cocktail against CD31,CD45 and Ter119 (StemCell Technologies CAT# 19757).Secondary labeling was achieved using Streptavidin conjugated PerCPCy5.5. Cells were sorted  into RNA Lysis solution (Ambion Cat# 8540G12) using a FACS Vantage SE DiVa sorter.

hyb_protocol: Hybridization was performed by the UCSD Gene Chip Microarray Core according to their standard operating protocol and instructions from NimbleGen Systems Inc., Madison, WI for the 12x135k array format. See www.nimblegen.com.

scan_protocol: Scanning was performed by the  UCSD Gene Chip Core  following their standard operating protocol and instructions for NimbleGen arrays.  See www.nimblegen.com.

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

source_name: Dissociated E15.5 fetal mammary cells

label_protocol: Labeling was performed by the Gene Chip Microarray Core through the UCSD: Rebecca and John Moores Cancer Center, following the standard operating protocol described by NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

extract_protocol: Total RNA was isolated using the RNAqueous-Micro kit (Ambion Cat # AM1931) according to the manufacturers' instructions.

tag: cell type

value: Dissociated E15.5 fetal mammary cells

tag: tissue source

value: Mammary gland

tag: Stage

value: Fetal E15.5

tag: processing

value: 2 rounds of  polyA-primed linear T7 amplification of total RNA

tag: quality control notes

value: Fail:low complexity


title: 5M-HighFat 9%

description: Biological replicate 1

tag: strain

value: Male

tag: tissue


title: ac_epid at T1

description:
ac_epid.cel
Gene expression data from rams infected with B. ovis.

source_name: epididymus, biopsied, 60 min, acute

value: male

value: Brucella ovis ATCC 25840 infection

value: acute


title: ac_amp at T1

description:
ac_amp.cel
Gene expression data from rams infected with B. ovis.

source_name: ampolae, biopsied, 60 min, acute

value: Santa Inês

value: ampolae


title: Fetal_Mammary_E18.5_CD24low_rep3

source_name: Flow sorted lineage depleated (CD31, CD45 and Ter119 neg), CD24low E18.5 fetal  mouse mammary cells

value: Fetal E18.5

value: Pass Conditional:Sample Tracking Controls indicate low level mixing with 364014A12


title: Fetal_Mammary_E18.5_CD24high_rep3

source_name: Flow sorted lineage depleated (CD31, CD45 and Ter119 neg), CD24high E18.5 fetal  mouse mammary cells

value: Pass


title: Adult_Mammary_Lineage_depleted_rep1

description:
Four #4 (inguinal) mammaries from two nulliparous females were combined in this sample
Dissected mammary tissue from adult and fetal mice was dissociated according to StemCell technologies' EasySep procedure (product #29008)  with minor modifications.  Briefly, fetal rudiments were dissociated for only 90min in collagenase/hyaluronidase containing media and trypsinization was omitted.
Cells were labeled with Anti-CD49f-FITC, Anti-CD24-PE and a biotinylated antibody cocktail against CD31,CD45 and Ter119 (StemCell Technologies CAT# 19757).Secondary labeling was achieved using Streptavidin conjugated PerCPCy5.5. Cells were sorted  into RNA Lysis solution (Ambion Cat# 8540G12) using a FACS Vantage SE DiVa sorter.

source_name: Flow sorted lineage depleated (CD31, CD45 and Ter119 neg) adult mouse mammary cells

value: Female

value: Adult


title: xylem, mature_tree21721

description:
JF003-7927.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

source_name: xylem, mature

value: xylem (mature)

tag: age of trees

tag: genotype

tag: slide batch


title: TATNR2B9c #3, Right Hemisphere, 6 hour

city: Toronto

first: DJ

last: Cook

state: ON

address: 11-414MCl, 399 Bathurst St

institute: University of Toronto

description: Cortex, Ischemic Hemisphere, 6 Hour After Stroke, TatNR2B9c Treatment

hyb_protocol: Pairs of fluor-labelled cDNA and DIG Easy Hyb solution (Roche cat#1603558) were combined, samples were applied to microarrays enclosed in hybridization chambers (VWR cat#48444-004). After hybridization, slides were washed sequentially and dried (See http://microarray.ca/info/protocols/DirectLabelling.pdf)

scan_protocol: Scanned on an Agilent G2565C scanner. Images were quantified using Agilent Feature Extraction Software (version10.7.3.1).

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and Linear LOWESS

organism: Macaca fascicularis

label_protocol: 20 µg of total RNA were primed with 8.0 µl of 5X First Strand reaction buffer (Invitrogen cat#18064-014) at 65°C for 5 min, then reversed transcribed at 42°C for 2h in the presence of 2µL SuperScript II RTase (Invitrogen cat#18064-014), and 6.67mM each dATP, dTTP, dGTP, with  2mM dCTP, 1mM Cy3 or Cy5 label (See http://microarray.ca/info/protocols/DirectLabelling.pdf)

extract_protocol: Cortical biopsies were flash frozen in liquid nitrogen. Total RNA extraction was undertaken with the Qiagen kit as per manufacturers's instructions.

treatment_protocol: Cynomolgus macaques underwent right sided Middle Cerebral Artery Occlusion (MCAO) and were intravenously administered either placebo or 2.6mg/kg TatNR2B9c 5 minutes after MCAO, cortex sampled from ischemic right side or left non-ischemic side at 1h and 6h after MCAO.  N=3 animals per group.

tag: tissue type

value: Cortex

tag: time post mcao before sample

organism: Macaca mulatta

source_name: Universal Reference RNA

tag: type

value: Universal Reference RNA


title: 1M-Control 9%

description: Biological replicate 1

value: C57bl/6J OlaHsd

tag: gender

tag: age

value: Liver

value: Control 9%


title: xylem, mature_tree10952

description:
JF003-7928.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Adult_Mammary_CD49highCD24med_rep2

source_name: Flow sorted lineage depleated (CD31, CD45 and Ter119 neg), CD49fHigh,CD24Medium adult mouse mammary cells

value: Mammary gland

value: 2 rounds of  polyA-primed linear T7 amplification of total RNA


title: ctr_vesi at T0, acute

description:
ctr_vesi.cel
Gene expression data from uninfected rams.

source_name: vesicular glands, biopsied, 60 min, control

value: male

tag: breed

value: 12 months

value: vesicular glands

tag: treatment

tag: phase of infection

value: control


title: ctr_test at T0, acute

description:
ctr_test.cel
Gene expression data from uninfected rams.

value: Santa Inês

value: testicles


title: ctr_linf at T0, acute

description:
ctr_linf.cel
Gene expression data from uninfected rams.

source_name: lymph nodes, biopsied, 60 min, control

value: lymph nodes


title: xylem, mature_tree10092

description:
JF003-7925.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: Fetal_Mammary_E15.5_rep1

tag: cell type

value: Dissociated E15.5 fetal mammary cells

value: Female

tag: tissue source

value: Fetal E15.5

value: Pass


title: ctr_epid at T0, acute

description:
ctr_epid.cel
Gene expression data from uninfected rams.

source_name: epididymus, biopsied, 60 min, control

value: epididymus


title: TATNR2B9c #3, Left Hemisphere, 6 hour

description: Cortex, Control Hemisphere, 6 Hour After Stroke, TatNR2B9c Treatment

value: Cortex

value: Universal Reference RNA


title: Fetal_Mammary_E18.5_CD24low_rep2

value: Flow sorted lineage depleated (CD31, CD45 and Ter119 neg), CD24low E18.5 fetal  mouse mammary cells

tag: Stage

value: Fetal E18.5

tag: processing


title: TATNR2B9c #2, Right Hemisphere, 6 hour

source_name: Cortex, Ischemic Hemisphere, 6 Hour After Stroke, TatNR2B9c Treatment


title: xylem, mature_tree61415

description:
JF003-7926.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

value: xylem (mature)


title: Adult_Mammary_CD49highCD24med_rep1

value: Flow sorted lineage depleated (CD31, CD45 and Ter119 neg), CD49fHigh,CD24Medium adult mouse mammary cells

tag: strain

value: Mammary gland

value: Adult

value: 2 rounds of  polyA-primed linear T7 amplification of total RNA

tag: quality control notes


title: ctr_bulb at T0, acute

description:
ctr_bulb.cel
Gene expression data from uninfected rams.

source_name: bulbourethral glands, biopsied, 60 min, control

value: male

value: Santa Inês

value: 12 months

tag: tissue

value: bulbourethral glands

value: control


title: xylem, mature_tree10134

description:
JF003-7924.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

tag: age of trees

tag: genotype


title: Fetal_Mammary_E18.5_CD24high_rep2

value: Flow sorted lineage depleated (CD31, CD45 and Ter119 neg), CD24high E18.5 fetal  mouse mammary cells

value: Female


title: ctr_amp at T0, acute

description:
ctr_amp.cel
Gene expression data from uninfected rams.

source_name: ampolae, biopsied, 60 min, control

value: ampolae


title: TATNR2B9c #2, Left Hemisphere, 6 hour

source_name: Cortex, Control Hemisphere, 6 Hour After Stroke, TatNR2B9c Treatment

tag: tissue type

value: Cortex


title: Fetal_Mammary_E18.5_CD24low_rep1

description:
Pooled bilateral, #1-5 mammary rudiments from multiple embryos
Dissected mammary tissue from adult and fetal mice was dissociated according to StemCell technologies' EasySep procedure (product #29008)  with minor modifications.  Briefly, fetal rudiments were dissociated for only 90min in collagenase/hyaluronidase containing media and trypsinization was omitted.
Cells were labeled with Anti-CD49f-FITC, Anti-CD24-PE and a biotinylated antibody cocktail against CD31,CD45 and Ter119 (StemCell Technologies CAT# 19757).Secondary labeling was achieved using Streptavidin conjugated PerCPCy5.5. Cells were sorted  into RNA Lysis solution (Ambion Cat# 8540G12) using a FACS Vantage SE DiVa sorter.

value: Pass


title: xylem, mature_tree50145

description:
JF003-7923.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

tag: slide batch


title: DMSO Control, biological repB1

description: Gene expression data from DMSO-treated yeast cells (repB, hyb1)

hyb_protocol: Affymetrix GeneChip Hybridization protocol, and GeneChip Fluidics Station 450 default protocol were used. GeneChip Yeast Genome 2.0 arrays were used.

data_processing: Image analysis, scaling (TGT = 1000), and probeset-level data analysis was performed using default parameters in GCOS v1.1

organism: Saccharomyces cerevisiae

source_name: Yeast cells treated with DMSO

growth_protocol: All cultures were grown in SD broth (2% dextrose, 0.67% yeast nitrogen base without amino acids, MOPS buffered, pH 7.0) at 30 degrees, with shaking at 200 rpm.

treatment_protocol: Cultures of S. cerevisiae strain S288C were started at OD600 of 0.1, allowed to grow to OD600 of 0.2, then treated with either DMSO (0.25%) or 6-NDA at the IC50 concentration (2.2 ug/ml).  When OD600 of 0.5 was reached, cells were harvested and frozen.  Two biological replicate cultures were grown for each treatment, and RNA from each replicate was hybridized to 2 independent arrays, resulting in 4 hybridizations for each treatment.


title: DMSO Control, biological repB2

description: Gene expression data from DMSO-treated yeast cells (repB, hyb2)


title: xylem, mature_tree11785

description:
JF003-7922.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: TATNR2B9c #1, Left Hemisphere, 6 hour

tag: time post mcao before sample

tag: type

value: Universal Reference RNA


title: TATNR2B9c #3, Left Hemisphere, 1 hour

description: Cortex, Control Hemisphere, 1 Hour After Stroke, TatNR2B9c Treatment


title: xylem, mature_tree60031

description:
JF003-7919.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: TATNR2B9c #1, Right Hemisphere, 6 hour

description: Cortex, Ischemic Hemisphere, 6 Hour After Stroke, TatNR2B9c Treatment


title: xylem, mature_tree31951

description:
JF003-7918.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: TATNR2B9c #3, Right Hemisphere, 1 hour

description: Cortex, Ischemic Hemisphere, 1 Hour After Stroke, TatNR2B9c Treatment


title: 6-NDA-treated, biological repA2

description: Gene expression data from 6-NDA-treated yeast cells (repA, hyb2)

source_name: Yeast cells treated with 6-NDA


title: Fetal_Mammary_E18.5_CD24high_rep1

tag: gender

value: Fetal E18.5

value: Pass Conditional:Sample Tracking Controls indicate some mixing with 364014A01


title: Adult_Mammary_Lineage_Depleted_rep1

description:
Four #4 (inguinal) mammaries from two nulliparous females were combined in this sample
Dissected mammary tissue from adult and fetal mice was dissociated according to StemCell technologies' EasySep procedure (product #29008)  with minor modifications.  Briefly, fetal rudiments were dissociated for only 90min in collagenase/hyaluronidase containing media and trypsinization was omitted.
Cells were labeled with Anti-CD49f-FITC, Anti-CD24-PE and a biotinylated antibody cocktail against CD31,CD45 and Ter119 (StemCell Technologies CAT# 19757).Secondary labeling was achieved using Streptavidin conjugated PerCPCy5.5. Cells were sorted  into RNA Lysis solution (Ambion Cat# 8540G12) using a FACS Vantage SE DiVa sorter.

value: Flow sorted lineage depleated (CD31, CD45 and Ter119 neg) adult mouse mammary cells

value: Fail:Sample Tracking control indicates unacceptable mixing


title: xylem, mature_tree11863

description:
JF003-7917.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.

value: xylem (mature)


title: 6-NDA-treated, biological repB2

description: Gene expression data from 6-NDA-treated yeast cells (repB, hyb2)


title: xylem, mature_tree31402

description:
JF003-7920.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: TATNR2B9c #1, Right Hemisphere, 1 hour

source_name: Cortex, Ischemic Hemisphere, 1 Hour After Stroke, TatNR2B9c Treatment


title: TATNR2B9c #2, Left Hemisphere, 1 hour

source_name: Cortex, Control Hemisphere, 1 Hour After Stroke, TatNR2B9c Treatment


title: 6-NDA-treated, biological repA1

description: Gene expression data from 6-NDA-treated yeast cells (repA, hyb1)


title: TATNR2B9c #2, Right Hemisphere, 1 hour


title: DMSO Control, biological repA1

description: Gene expression data from DMSO-treated yeast cells (repA, hyb1)


title: xylem, mature_tree10142

description:
JF003-7921.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: 6-NDA-treated, biological repB1

description: Gene expression data from 6-NDA-treated yeast cells (repB, hyb1)


title: xylem, mature_tree50574

description:
JF003-7915.txt
Raw data represented in 'ch1' columns of raw file after the Begin Data tag.


title: DMSO Control, biological repA2

description: Gene expression data from DMSO-treated yeast cells (repA, hyb2)


title: Placebo #3, Left Hemisphere, 6 hour

description: Cortex, Control Hemisphere, 6 Hour After Stroke, Placebo Treatment

value: Placebo


title: Placebo #3, Right Hemisphere, 6 hour

description: Cortex, Ischemic Hemisphere, 6 Hour After Stroke, Placebo Treatment


title: Placebo #2, Right Hemisphere, 6 hour

source_name: Cortex, Ischemic Hemisphere, 6 Hour After Stroke, Placebo Treatment


title: TKO CMP1

city: Chiba

first: ATSUSHI

last: IWAMA

address: 1-8-1 Inohana, Chuo-ku

department: Department of Cellular and Molecular Medicine

country: Japan

institute: Graduate School of Medicine, Chiba University

description: Gene expression data of CMP from recipient mouse BM repopulated with Bmi1-/-Ink4a-/-Arf-/- BM cells

hyb_protocol: standard affymetrix protocol

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

data_processing: ExpressionStat 5.0 algorithm using Programmatic identifier: GeneChip.CallGEBaseCall.1

source_name: Bmi1-/-Ink4a-/-Arf-/- CMP

label_protocol: Biotinylated cRNA were prepared  from the purified total RNA equivalent to 10,000 cells according to the standard Affymetrix protocol.

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

value: common myeloid progenitor (CMP)

value: C57BL/6 recipient mice repopulated with Bmi1-/-Ink4a-/-Arf-/- BM cells


title: TATNR2B9c #1, Left Hemisphere, 1 hour

description: Cortex, Control Hemisphere, 1 Hour After Stroke, TatNR2B9c Treatment


title: Placebo #1, Left Hemisphere, 6 hour

source_name: Cortex, Control Hemisphere, 6 Hour After Stroke, Placebo Treatment


title: DKO CMP1

description: Gene expression data of CMP from recipient mouse BM repopulated with Ink4a-/-Arf-/- BM cells

source_name: Ink4a-/-Arf-/- CMP

value: C57BL/6 recipient mice repopulated with Ink4a-/-Arf-/- BM cells


title: Placebo #1, Right Hemisphere, 6 hour

source_name: Universal Reference RNA


title: Placebo #2, Left Hemisphere, 6 hour


title: Sro9 1

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Simple annotation: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76263.gif

hyb_protocol: not provided

scan_protocol: GenePix 4200A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: total RNA SRO9-TAP

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: total RNA SRO9-TAP

source_name: IP RNA SRO9-TAP

tag: experiment

value: IP RNA SRO9-TAP


title: TKO CMP2


title: Fpr1 3

description:
Simple annotation: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78763.gif

source_name: total RNA Fpr1-TAP

value: total RNA Fpr1-TAP

source_name: IP RNA Fpr1-TAP

value: IP RNA Fpr1-TAP


title: Sro9 3

description:
Simple annotation: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77143.gif


title: Epididymal tissue of mice administered Nt8U [10A]

city: Mysore

first: Uma

middle: Venkateswaran

last: Manjappara

state: Karnataka

address: Cheluvamba Mansion

department: Protein Chemistry and Technology

country: India

institute: Central Food Technological Research Institute

hyb_protocol: 825 ng of cy3 labeled sample and 825 ng of cy5 labeled sample were fragmented and hybridized. Fragmentation of labeled aRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner at 5 micron resolution

scan_protocol: Scanned using the Agilent Technologies Scanner G2505C at 5 micron resolution. Images were quantified using Agilent Feature Extraction Software

data_processing: Data was analyzed in GeneSpring GX software from Agilent V.10 using 75th percentile shift Normalization. Probe intensities generated from feature extraction raw data were split based on channel type. •  Probe intensities generated from feature extraction raw data were split based on channel type cy3 and cy5.  [9A (Cy5), 5A (Cy3), 10A (Cy5), 2A (Cy3), 11A (Cy5), 3A (Cy3), 8A (Cy5) and 4A (Cy3)]  •  Data was analyzed in GeneSpring GX software from Agilent using 75th percentile shift Normalization (Intra array normalization) for all 9A (Cy5), 5A (Cy3), 10A (Cy5), 2A (Cy3), 11A (Cy5), 3A (Cy3), 8A (Cy5) and 4A (Cy3)  • Fold calculation was done taking 9A (Cy5), 10A (Cy5), 11A (Cy5) (treated samples) vs. 8A (Cy5)--control sample  • Fold calculation was done taking 5A (Cy3),  2A (Cy3), 3A (Cy3) (treated samples) vs. 4A (Cy3)--control sample  All cy3-labeled test samples were compared to control cy3 sample data and all cy5-labeled test samples were compared to control cy5 sample data to generate fold expression values. Genes showing >One fold change in the test sample compared to the control were compiled as differentially regulated genes. Fold change values log base 2 (test/control).

source_name: mice epididymal fat pad

label_protocol: Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for aRNA generation. aRNA was generated by in vitro transcription and the dyes Cy3 CTP(Agilent) and Cy5 CTP(Agilent) were incorporated during this step.

growth_protocol: Twelve mice of similar weight (20-23g) were placed individually in metabolic cages and acclimatized for a week to feed between 6 PM and 6AM. Water was made available throughout the day. These mice were given intraperitoneal injections of saline for two days to get them used to the trauma of being handled. After this initial preparations, the mice were grouped into four groups of three mice each and each group was injected 80nmol/kg of the specific peptide around 6 PM and fed (pulverized mice feed) 15 minutes after injection. The amount of feed consumed was monitored every hour till five hours after injection and the water consumed was measured before and after this five hour period. This routine was followed for eight days. Mice were weighed every day around 4.30 PM before the experiment. The balance we used for all the weighing during the experiment has an accuracy of 0.1g. After eight days the mice were sacrificed. Their individual epididymal fat was collected and stored in RNA Later solution or frozen in liquid nitrogen and subjected to microarray analysis.

extract_protocol: RNA was extracted using Trizol method from the frozen adipose tissues.

tag: agent

tag: age

value: 5 weeks old

tag: time

value: 8 days treated

value: epididymal

value: CFT Swiss albino


title: Epididymal tissue of mice administered obestatin [11A]

value: obestatin


title: Slf1 3

description:
Simple annotation: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74825.gif

source_name: SLF1-TAP total RNA

value: SLF1-TAP total RNA

source_name: SLF1-TAP IP RNA

value: SLF1-TAP IP RNA


title: DKO CMP2

tag: cell type


title: Slf1 1

description:
Simple annotation: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74823.gif


title: WT CMP2

description: Gene expression data of CMP from recipient mouse BM repopulated with wild-type BM cells

source_name: Wild-type CMP

value: Wild type

value: C57BL/6 recipient mice repopulated with wild-type BM cells


title: Slf1 2

description:
Simple annotation: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2007-06/74824.gif

source_name: total RNA SLF-TAP

value: total RNA SLF-TAP

source_name: IP RNA SLF-TAP

value: IP RNA SLF-TAP


title: Fpr1 2

description:
Simple annotation: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78762.gif


title: Fpr1 1

description:
Simple annotation: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78761.gif


title: Epididymal tissue of mice administered N-terminal peptide [9A]

value: N-terminal peptide


title: Sro9 2

description:
Simple annotation: RNA coimmunoprecipitation, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77142.gif


title: Placebo #3, Left Hemisphere, 1 hour

description: Cortex, Control Hemisphere, 1 Hour After Stroke, Placebo Treatment

value: Cortex

tag: treatment

value: Placebo

value: Universal Reference RNA


title: Control: Epididymal tissue of mice administered saline [8A]

value: saline

tag: strain


title: Placebo #3, Right Hemisphere, 1 hour

description: Cortex, Ischemic Hemisphere, 1 Hour After Stroke, Placebo Treatment


title: Placebo #2, Right Hemisphere, 1 hour

source_name: Cortex, Ischemic Hemisphere, 1 Hour After Stroke, Placebo Treatment


title: WT CMP1

value: common myeloid progenitor (CMP)


title: Epididymal tissue of mice administered N-terminal peptide [5A]

value: 5 weeks old


title: Placebo #2, Left Hemisphere, 1 hour

source_name: Cortex, Control Hemisphere, 1 Hour After Stroke, Placebo Treatment


title: SLF1 overexpression 24h (2)

description:
Simple annotation: Absolute transcript levels, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2011-02/92022.gif

source_name: BY4741 (control vector, pBG1805)

value: BY4741 (control vector, pBG1805)

source_name: SLF1Overexpression (24h-2)

value: SLF1Overexpression (24h-2)


title: Control: Epididymal tissue of mice administered saline [4A]

value: 8 days treated

value: epididymal

value: CFT Swiss albino


title: SLF1 overexpression 6h (1)

description:
Simple annotation: Absolute transcript levels, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2011-02/92020.gif

source_name: SLF1Overexpression (6h-1)

value: SLF1Overexpression (6h-1)


title: Placebo #1, Right Hemisphere, 1 hour


title: SLF1 overexpression 24h (1)

description:
Simple annotation: Absolute transcript levels, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2011-02/92021.gif

source_name: SLF1Overexpression (24h-1)

value: SLF1Overexpression (24h-1)


title: SLF1 overexpression 6h (2)

description:
Simple annotation: Absolute transcript levels, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2011-02/92019.gif

source_name: SLF1Overexpression (6h-2)

value: SLF1Overexpression (6h-2)


title: Tbx1 cKO hair follicle stem cells set #1

status: Public on Feb 07 2012

city: New York

first: Ting

last: Chen

state: NY

institute: Rockefeller University

description: Gene expression data from quiescent hair follicle stem cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA method using Gene Pattern analysis settings and median scaling as normalization method.

source_name: Tbx1 cKO hair follicle stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: HF-SCswere FACS-purifed from the back skins of indicated ages of mice

treatment_protocol: 48hrs prior to harvesting the skin, depilation of mid-dorsal HFs was achieved on anesthetized mice. The mid-dorsum was coated with molten wax, which was peeled off after hardening

value: Mouse back skins

value: Female

tag: sorting markers

value: YFP, integrin α6 and CD34


title: Placebo #1, Left Hemisphere, 1 hour

value: Cortex

source_name: Universal Reference RNA


title: Epididymal tissue of mice administered obestatin [3A]

value: obestatin

tag: tissue


title: Epididymal tissue of mice administered Nt8U [2A]


title: WT hair follicle stem cells set #2

description: Gene expression data from activated hair follicle stem cells

source_name: WT hair follicle stem cells


title: WT hair follicle stem cells set #1


title: Tbx1 cKO hair follicle stem cells set #2


title: i16290rl

type: genomic

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description: Patient i16290 DNA extracted from tumor cells obtained at relapse.

hyb_protocol: 200-270 micrograms of amplified and biotinylated DNA were hybridized for 16-18 hr at 50C on a GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CEL files and birdseed-v2.txt files (generated by Affymetrix GTYPE using the Birdseed v2 algorithm) were processed by dChip and model-based expression was performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St. Jude and described in Pounds et al. Bioinformatics. 2009 Feb 1;25(3):315-21 (PMID 19052058). The Sample data table contains the normalized expression values produced by that algorithm and genotyping calls.

molecule: genomic DNA

source_name: Patient i16231 relapse leukemic cells obtained from bone marrow or blood at relapse, inv(16), adult

label_protocol: 250 nanograms of genomic DNA were digested to completion with NspI or StyI, ligated to adapaters and amplified by PCR. 200-270 micrograms of pooled amplified DNA were fragmented and end-labeled with a biotinylated nucleotide according to the Genome-Wide Human SNP Nsp/Sty 6.0 User Guide 702504 Rev 3, 2008, Affymetrix).

growth_protocol: DNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from AML cases with t(8;21) or inv(16).

extract_protocol: Trizol/AllPrep DNA/RNA Mini Kit (Qiagen).

treatment_protocol: None.

value: bone marrow or blood

value: leukemic cells

tag: disease state

value: core-binding-factor acute myeloid leukemia (CBF-AML)

tag: developmental stage

value: adult

tag: chromosomal abnormality

tag: sampling time

value: at relapse

tag: patient


title: i16241rl

description: Patient i16241 DNA extracted from tumor cells obtained at relapse.


title: i16242rl

description: Patient i16242 DNA extracted from tumor cells obtained at relapse.


title: i16301rl

description: Patient i16301 DNA extracted from tumor cells obtained at relapse.


title: i16295rl

description: Patient i16295 DNA extracted from tumor cells obtained at relapse.


title: i16307rl

description: Patient i16307 DNA extracted from tumor cells obtained at relapse.


title: i16311rl

description: Patient i16311 DNA extracted from tumor cells obtained at relapse.


title: i16008rl

description: Patient i16008 DNA extracted from tumor cells obtained at relapse.

source_name: Patient i16008 relapse leukemic cells obtained from bone marrow or blood at relapse, inv(16), pediatric

value: pediatric


title: i16009rl

description: Patient i16009 DNA extracted from tumor cells obtained at relapse.


title: AE245rl

description: Patient AE245 DNA extracted from tumor cells obtained at relapse.

source_name: Patient AE203 relapse leukemic cells obtained from bone marrow or blood at relapse, t(8;21), adult


title: AE251rl

description: Patient AE251 DNA extracted from tumor cells obtained at relapse.


title: i16251rl

description: Patient i16251 DNA extracted from tumor cells obtained at relapse.


title: i16231rl

description: Patient i16231 DNA extracted from tumor cells obtained at relapse.


title: AE306rl

description: Patient AE306 DNA extracted from tumor cells obtained at relapse.


title: i16233rl

description: Patient i16233 DNA extracted from tumor cells obtained at relapse.


title: AE233rl

description: Patient AE233 DNA extracted from tumor cells obtained at relapse.


title: i16237rl

description: Patient i16237 DNA extracted from tumor cells obtained at relapse.


title: i16235rl

description: Patient i16235 DNA extracted from tumor cells obtained at relapse.


title: AE265rl

description: Patient AE265 DNA extracted from tumor cells obtained at relapse.


title: AE282rl

description: Patient AE282 DNA extracted from tumor cells obtained at relapse.


title: AE228rl

description: Patient AE228 DNA extracted from tumor cells obtained at relapse.


title: AE260rl

description: Patient AE260 DNA extracted from tumor cells obtained at relapse.


title: i16299rl

description: Patient i16299 DNA extracted from tumor cells obtained at relapse.


title: AE299rl

description: Patient AE299 DNA extracted from tumor cells obtained at relapse.


title: i16248rl

description: Patient i16248 DNA extracted from tumor cells obtained at relapse.


title: AE250rl

description: Patient AE250 DNA extracted from tumor cells obtained at relapse.


title: AE286rl

description: Patient AE286 DNA extracted from tumor cells obtained at relapse.


title: AE236rl

description: Patient AE236 DNA extracted from tumor cells obtained at relapse.


title: AE229rl

description: Patient AE229 DNA extracted from tumor cells obtained at relapse.


title: AE235rl

description: Patient AE235 DNA extracted from tumor cells obtained at relapse.


title: AE223rl

description: Patient AE223 DNA extracted from tumor cells obtained at relapse.


title: AE024rl

description: Patient AE024 DNA extracted from tumor cells obtained at relapse.

source_name: Patient AE011 relapse leukemic cells obtained from bone marrow or blood at relapse, t(8;21), pediatric


title: AE019rl

description: Patient AE019 DNA extracted from tumor cells obtained at relapse.


title: AE033rl

description: Patient AE033 DNA extracted from tumor cells obtained at relapse.


title: i16306pn

description: DNA extracted from patient i16306 germline cells.

source_name: Patient i16306 germline cells obtained from bone marrow or blood at remission, adult

value: germline cells

value: at remission

tag: sample type

value: control DNA


title: AE023rl

description: Patient AE023 DNA extracted from tumor cells obtained at relapse.


title: i16296pn

description: DNA extracted from patient i16296 germline cells.

source_name: Patient i16296 germline cells obtained from bone marrow or blood at remission, adult


title: i16293pn

description: DNA extracted from patient i16293 germline cells.

source_name: Patient i16293 germline cells obtained from bone marrow or blood at remission, adult


title: i16247pn

description: DNA extracted from patient i16247 germline cells.

source_name: Patient i16247 germline cells obtained from bone marrow or blood at remission, adult


title: i16290pn

description: DNA extracted from patient i16290 germline cells.

source_name: Patient i16290 germline cells obtained from bone marrow or blood at remission, adult


title: i16305pn

description: DNA extracted from patient i16305 germline cells.

source_name: Patient i16305 germline cells obtained from bone marrow or blood at remission, adult


title: i16245pn

description: DNA extracted from patient i16245 germline cells.

source_name: Patient i16245 germline cells obtained from bone marrow or blood at remission, adult


title: i16243pn

description: DNA extracted from patient i16243 germline cells.

source_name: Patient i16243 germline cells obtained from bone marrow or blood at remission, adult


title: AE013rl

description: Patient AE013 DNA extracted from tumor cells obtained at relapse.


title: i16307pn

description: DNA extracted from patient i16307 germline cells.

source_name: Patient i16307 germline cells obtained from bone marrow or blood at remission, adult


title: i16246pn

description: DNA extracted from patient i16246 germline cells.

source_name: Patient i16246 germline cells obtained from bone marrow or blood at remission, adult


title: AE025rl

description: Patient AE025 DNA extracted from tumor cells obtained at relapse.


title: AE011rl

description: Patient AE011 DNA extracted from tumor cells obtained at relapse.


title: i16249pn

description: DNA extracted from patient i16249 germline cells.

source_name: Patient i16249 germline cells obtained from bone marrow or blood at remission, adult


title: i16288pn

description: DNA extracted from patient i16288 germline cells.

source_name: Patient i16288 germline cells obtained from bone marrow or blood at remission, adult


title: i16241pn

description: DNA extracted from patient i16241 germline cells.

source_name: Patient i16241 germline cells obtained from bone marrow or blood at remission, adult


title: i16302pn

description: DNA extracted from patient i16302 germline cells.

source_name: Patient i16302 germline cells obtained from bone marrow or blood at remission, adult


title: i16248pn

description: DNA extracted from patient i16248 germline cells.

source_name: Patient i16248 germline cells obtained from bone marrow or blood at remission, adult


title: i16250pn

description: DNA extracted from patient i16250 germline cells.

source_name: Patient i16250 germline cells obtained from bone marrow or blood at remission, adult


title: AE203rl

description: Patient AE203 DNA extracted from tumor cells obtained at relapse.

source_name: Patient AE203 relapse leukemic cells obtained from bone marrow or blood at relapse, t(8;21), adult


title: AE018rl

description: Patient AE018 DNA extracted from tumor cells obtained at relapse.

source_name: Patient AE011 relapse leukemic cells obtained from bone marrow or blood at relapse, t(8;21), pediatric


title: AE022rl

description: Patient AE022 DNA extracted from tumor cells obtained at relapse.


title: i16239pn

description: DNA extracted from patient i16239 germline cells.

source_name: Patient i16239 germline cells obtained from bone marrow or blood at remission, adult


title: i16240pn

description: DNA extracted from patient i16240 germline cells.

source_name: Patient i16240 germline cells obtained from bone marrow or blood at remission, adult


title: i16229pn

description: DNA extracted from patient i16229 germline cells.

source_name: Patient i16229 germline cells obtained from bone marrow or blood at remission, adult


title: i16234pn

description: DNA extracted from patient i16234 germline cells.

source_name: Patient i16234 germline cells obtained from bone marrow or blood at remission, adult


title: i16232pn

description: DNA extracted from patient i16232 germline cells.

source_name: Patient i16232 germline cells obtained from bone marrow or blood at remission, adult


title: i16237pn

description: DNA extracted from patient i16237 germline cells.

source_name: Patient i16237 germline cells obtained from bone marrow or blood at remission, adult


title: i16215pn

description: DNA extracted from patient i16215 germline cells.

source_name: Patient i16215 germline cells obtained from bone marrow or blood at remission, adult


title: i16223pn

description: DNA extracted from patient i16223 germline cells.

source_name: Patient i16223 germline cells obtained from bone marrow or blood at remission, adult


title: i16227pn

description: DNA extracted from patient i16227 germline cells.

source_name: Patient i16227 germline cells obtained from bone marrow or blood at remission, adult


title: i16222pn

description: DNA extracted from patient i16222 germline cells.

source_name: Patient i16222 germline cells obtained from bone marrow or blood at remission, adult


title: i16225pn

description: DNA extracted from patient i16225 germline cells.

source_name: Patient i16225 germline cells obtained from bone marrow or blood at remission, adult


title: i16233pn

description: DNA extracted from patient i16233 germline cells.

source_name: Patient i16233 germline cells obtained from bone marrow or blood at remission, adult


title: i16238pn

description: DNA extracted from patient i16238 germline cells.

source_name: Patient i16238 germline cells obtained from bone marrow or blood at remission, adult


title: i16242pn

description: DNA extracted from patient i16242 germline cells.

source_name: Patient i16242 germline cells obtained from bone marrow or blood at remission, adult


title: i16231pn

description: DNA extracted from patient i16231 germline cells.

source_name: Patient i16231 germline cells obtained from bone marrow or blood at remission, adult


title: i16221pn

description: DNA extracted from patient i16221 germline cells.

source_name: Patient i16221 germline cells obtained from bone marrow or blood at remission, adult


title: i16213pn

description: DNA extracted from patient i16213 germline cells.

source_name: Patient i16213 germline cells obtained from bone marrow or blood at remission, adult


title: i16218pn

description: DNA extracted from patient i16218 germline cells.

source_name: Patient i16218 germline cells obtained from bone marrow or blood at remission, adult


title: i16210pn

description: DNA extracted from patient i16210 germline cells.

source_name: Patient i16210 germline cells obtained from bone marrow or blood at remission, adult


title: i16212pn

description: DNA extracted from patient i16212 germline cells.

source_name: Patient i16212 germline cells obtained from bone marrow or blood at remission, adult


title: i16211pn

description: DNA extracted from patient i16211 germline cells.

source_name: Patient i16211 germline cells obtained from bone marrow or blood at remission, adult


title: i16219pn

description: DNA extracted from patient i16219 germline cells.

source_name: Patient i16219 germline cells obtained from bone marrow or blood at remission, adult


title: i16235pn

description: DNA extracted from patient i16235 germline cells.

source_name: Patient i16235 germline cells obtained from bone marrow or blood at remission, adult


title: i16236pn

description: DNA extracted from patient i16236 germline cells.

source_name: Patient i16236 germline cells obtained from bone marrow or blood at remission, adult


title: i16217pn

description: DNA extracted from patient i16217 germline cells.

source_name: Patient i16217 germline cells obtained from bone marrow or blood at remission, adult


title: i16228pn

description: DNA extracted from patient i16228 germline cells.

source_name: Patient i16228 germline cells obtained from bone marrow or blood at remission, adult


title: i16220pn

description: DNA extracted from patient i16220 germline cells.

source_name: Patient i16220 germline cells obtained from bone marrow or blood at remission, adult


title: i16214pn

description: DNA extracted from patient i16214 germline cells.

source_name: Patient i16214 germline cells obtained from bone marrow or blood at remission, adult


title: i16209pn

description: DNA extracted from patient i16209 germline cells.

source_name: Patient i16209 germline cells obtained from bone marrow or blood at remission, adult


title: i16226pn

description: DNA extracted from patient i16226 germline cells.

source_name: Patient i16226 germline cells obtained from bone marrow or blood at remission, adult


title: i16208pn

description: DNA extracted from patient i16208 germline cells.

source_name: Patient i16208 germline cells obtained from bone marrow or blood at remission, adult


title: i16205pn

description: DNA extracted from patient i16205 germline cells.

source_name: Patient i16205 germline cells obtained from bone marrow or blood at remission, adult


title: i16207pn

description: DNA extracted from patient i16207 germline cells.

source_name: Patient i16207 germline cells obtained from bone marrow or blood at remission, adult


title: i16202pn

description: DNA extracted from patient i16202 germline cells.

source_name: Patient i16202 germline cells obtained from bone marrow or blood at remission, adult


title: i16204pn

description: DNA extracted from patient i16204 germline cells.

source_name: Patient i16204 germline cells obtained from bone marrow or blood at remission, adult


title: i16036pn

description: DNA extracted from patient i16036 germline cells.

source_name: Patient i16036 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16037pn

description: DNA extracted from patient i16037 germline cells.

source_name: Patient i16037 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16039pn

description: DNA extracted from patient i16039 germline cells.

source_name: Patient i16039 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16040pn

description: DNA extracted from patient i16040 germline cells.

source_name: Patient i16040 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16032pn

description: DNA extracted from patient i16032 germline cells.

source_name: Patient i16032 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16024pn

description: DNA extracted from patient i16024 germline cells.

source_name: Patient i16024 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16203pn

description: DNA extracted from patient i16203 germline cells.

source_name: Patient i16203 germline cells obtained from bone marrow or blood at remission, adult


title: i16025pn

description: DNA extracted from patient i16025 germline cells.

source_name: Patient i16025 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16038pn

description: DNA extracted from patient i16038 germline cells.

source_name: Patient i16038 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16014pn

description: DNA extracted from patient i16014 germline cells.

source_name: Patient i16014 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16031pn

description: DNA extracted from patient i16031 germline cells.

source_name: Patient i16031 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16029pn

description: DNA extracted from patient i16029 germline cells.

source_name: Patient i16029 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16033pn

description: DNA extracted from patient i16033 germline cells.

source_name: Patient i16033 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16019pnt

description: DNA extracted from patient i16019 germline cells.

source_name: Patient i16019 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16034pn

description: DNA extracted from patient i16034 germline cells.

source_name: Patient i16034 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16026pn

description: DNA extracted from patient i16026 germline cells.

source_name: Patient i16026 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16030pn

description: DNA extracted from patient i16030 germline cells.

source_name: Patient i16030 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16023pn

description: DNA extracted from patient i16023 germline cells.

source_name: Patient i16023 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16017pnt

description: DNA extracted from patient i16017 germline cells.

source_name: Patient i16017 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16022pnt

description: DNA extracted from patient i16022 germline cells.

source_name: Patient i16022 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16035pn

description: DNA extracted from patient i16035 germline cells.

source_name: Patient i16035 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16028pn

description: DNA extracted from patient i16028 germline cells.

source_name: Patient i16028 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16018pnt

description: DNA extracted from patient i16018 germline cells.

source_name: Patient i16018 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16027pn

description: DNA extracted from patient i16027 germline cells.

source_name: Patient i16027 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16003pn

description: DNA extracted from patient i16003 germline cells.

source_name: Patient i16003 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16007pn

description: DNA extracted from patient i16007 germline cells.

source_name: Patient i16007 germline cells obtained from bone marrow or blood at remission, pediatric


title: i16011pn

description: DNA extracted from patient i16011 germline cells.

source_name: Patient i16011 germline cells obtained from bone marrow or blood at remission, pediatric


title: AE295pn

description: DNA extracted from patient AE295 germline cells.

source_name: Patient AE295 germline cells obtained from bone marrow or blood at remission, adult


title: AE285pn

description: DNA extracted from patient AE285 germline cells.

source_name: Patient AE285 germline cells obtained from bone marrow or blood at remission, adult


title: i16206pn

description: DNA extracted from patient i16206 germline cells.

source_name: Patient i16206 germline cells obtained from bone marrow or blood at remission, adult


title: AE283pn

description: DNA extracted from patient AE283 germline cells.

source_name: Patient AE283 germline cells obtained from bone marrow or blood at remission, adult


title: AE253pn

description: DNA extracted from patient AE253 germline cells.

source_name: Patient AE253 germline cells obtained from bone marrow or blood at remission, adult


title: i16001pn

description: DNA extracted from patient i16001 germline cells.

source_name: Patient i16001 germline cells obtained from bone marrow or blood at remission, pediatric


title: AE293pn

description: DNA extracted from patient AE293 germline cells.

source_name: Patient AE293 germline cells obtained from bone marrow or blood at remission, adult


title: AE255pn

description: DNA extracted from patient AE255 germline cells.

source_name: Patient AE255 germline cells obtained from bone marrow or blood at remission, adult


title: AE256pn

description: DNA extracted from patient AE256 germline cells.

source_name: Patient AE256 germline cells obtained from bone marrow or blood at remission, adult


title: AE290pn

description: DNA extracted from patient AE290 germline cells.

source_name: Patient AE290 germline cells obtained from bone marrow or blood at remission, adult


title: AE261pn

description: DNA extracted from patient AE261 germline cells.

source_name: Patient AE261 germline cells obtained from bone marrow or blood at remission, adult


title: AE252pn

description: DNA extracted from patient AE252 germline cells.

source_name: Patient AE252 germline cells obtained from bone marrow or blood at remission, adult


title: AE262pn

description: DNA extracted from patient AE262 germline cells.

source_name: Patient AE262 germline cells obtained from bone marrow or blood at remission, adult


title: AE298pn

description: DNA extracted from patient AE298 germline cells.

source_name: Patient AE298 germline cells obtained from bone marrow or blood at remission, adult


title: AE257pn

description: DNA extracted from patient AE257 germline cells.

source_name: Patient AE257 germline cells obtained from bone marrow or blood at remission, adult


title: AE291pn

description: DNA extracted from patient AE291 germline cells.

source_name: Patient AE291 germline cells obtained from bone marrow or blood at remission, adult


title: AE249pn

description: DNA extracted from patient AE249 germline cells.

source_name: Patient AE249 germline cells obtained from bone marrow or blood at remission, adult


title: AE258pn

description: DNA extracted from patient AE258 germline cells.

source_name: Patient AE258 germline cells obtained from bone marrow or blood at remission, adult


title: AE250pn

description: DNA extracted from patient AE250 germline cells.

source_name: Patient AE250 germline cells obtained from bone marrow or blood at remission, adult


title: AE259pn

description: DNA extracted from patient AE259 germline cells.

source_name: Patient AE259 germline cells obtained from bone marrow or blood at remission, adult


title: AE284pn

description: DNA extracted from patient AE284 germline cells.

source_name: Patient AE284 germline cells obtained from bone marrow or blood at remission, adult


title: AE247pn

description: DNA extracted from patient AE247 germline cells.

source_name: Patient AE247 germline cells obtained from bone marrow or blood at remission, adult


title: AE260pn

description: DNA extracted from patient AE260 germline cells.

source_name: Patient AE260 germline cells obtained from bone marrow or blood at remission, adult


title: AE254pn

description: DNA extracted from patient AE254 germline cells.

source_name: Patient AE254 germline cells obtained from bone marrow or blood at remission, adult


title: AE251pn

description: DNA extracted from patient AE251 germline cells.

source_name: Patient AE251 germline cells obtained from bone marrow or blood at remission, adult


title: AE245pn

description: DNA extracted from patient AE245 germline cells.

source_name: Patient AE245 germline cells obtained from bone marrow or blood at remission, adult


title: AE248pn

description: DNA extracted from patient AE248 germline cells.

source_name: Patient AE248 germline cells obtained from bone marrow or blood at remission, adult


title: AE246pn

description: DNA extracted from patient AE246 germline cells.

source_name: Patient AE246 germline cells obtained from bone marrow or blood at remission, adult


title: AE244pn

description: DNA extracted from patient AE244 germline cells.

source_name: Patient AE244 germline cells obtained from bone marrow or blood at remission, adult


title: AE242pn

description: DNA extracted from patient AE242 germline cells.

source_name: Patient AE242 germline cells obtained from bone marrow or blood at remission, adult


title: AE243pn

description: DNA extracted from patient AE243 germline cells.

source_name: Patient AE243 germline cells obtained from bone marrow or blood at remission, adult


title: AE238pn

description: DNA extracted from patient AE238 germline cells.

source_name: Patient AE238 germline cells obtained from bone marrow or blood at remission, adult


title: AE241pn

description: DNA extracted from patient AE241 germline cells.

source_name: Patient AE241 germline cells obtained from bone marrow or blood at remission, adult


title: AE231pn

description: DNA extracted from patient AE231 germline cells.

source_name: Patient AE231 germline cells obtained from bone marrow or blood at remission, adult


title: AE236pn

description: DNA extracted from patient AE236 germline cells.

source_name: Patient AE236 germline cells obtained from bone marrow or blood at remission, adult


title: AE229pn

description: DNA extracted from patient AE229 germline cells.

source_name: Patient AE229 germline cells obtained from bone marrow or blood at remission, adult


title: AE240pn

description: DNA extracted from patient AE240 germline cells.

source_name: Patient AE240 germline cells obtained from bone marrow or blood at remission, adult


title: AE239pn

description: DNA extracted from patient AE239 germline cells.

source_name: Patient AE239 germline cells obtained from bone marrow or blood at remission, adult


title: AE224pn

description: DNA extracted from patient AE224 germline cells.

source_name: Patient AE224 germline cells obtained from bone marrow or blood at remission, adult


title: AE235pn

description: DNA extracted from patient AE235 germline cells.

source_name: Patient AE235 germline cells obtained from bone marrow or blood at remission, adult


title: AE234pn

description: DNA extracted from patient AE234 germline cells.

source_name: Patient AE234 germline cells obtained from bone marrow or blood at remission, adult


title: AE226pn

description: DNA extracted from patient AE226 germline cells.

source_name: Patient AE226 germline cells obtained from bone marrow or blood at remission, adult


title: AE227pn

description: DNA extracted from patient AE227 germline cells.

source_name: Patient AE227 germline cells obtained from bone marrow or blood at remission, adult


title: AE230pn

description: DNA extracted from patient AE230 germline cells.

source_name: Patient AE230 germline cells obtained from bone marrow or blood at remission, adult


title: AE222pn

description: DNA extracted from patient AE222 germline cells.

source_name: Patient AE222 germline cells obtained from bone marrow or blood at remission, adult


title: AE220pn

description: DNA extracted from patient AE220 germline cells.

source_name: Patient AE220 germline cells obtained from bone marrow or blood at remission, adult


title: AE237pn

description: DNA extracted from patient AE237 germline cells.

source_name: Patient AE237 germline cells obtained from bone marrow or blood at remission, adult


title: AE225pn

description: DNA extracted from patient AE225 germline cells.

source_name: Patient AE225 germline cells obtained from bone marrow or blood at remission, adult


title: AE218pn

description: DNA extracted from patient AE218 germline cells.

source_name: Patient AE218 germline cells obtained from bone marrow or blood at remission, adult


title: AE223pn

description: DNA extracted from patient AE223 germline cells.

source_name: Patient AE223 germline cells obtained from bone marrow or blood at remission, adult


title: AE233pn

description: DNA extracted from patient AE233 germline cells.

source_name: Patient AE233 germline cells obtained from bone marrow or blood at remission, adult


title: AE219pn

description: DNA extracted from patient AE219 germline cells.

source_name: Patient AE219 germline cells obtained from bone marrow or blood at remission, adult


title: AE217pn

description: DNA extracted from patient AE217 germline cells.

source_name: Patient AE217 germline cells obtained from bone marrow or blood at remission, adult


title: AE221pn

description: DNA extracted from patient AE221 germline cells.

source_name: Patient AE221 germline cells obtained from bone marrow or blood at remission, adult


title: AE216pn

description: DNA extracted from patient AE216 germline cells.

source_name: Patient AE216 germline cells obtained from bone marrow or blood at remission, adult


title: AE213pn

description: DNA extracted from patient AE213 germline cells.

source_name: Patient AE213 germline cells obtained from bone marrow or blood at remission, adult


title: AE228pn

description: DNA extracted from patient AE228 germline cells.

source_name: Patient AE228 germline cells obtained from bone marrow or blood at remission, adult


title: AE214pn

description: DNA extracted from patient AE214 germline cells.

source_name: Patient AE214 germline cells obtained from bone marrow or blood at remission, adult


title: AE210pn

description: DNA extracted from patient AE210 germline cells.

source_name: Patient AE210 germline cells obtained from bone marrow or blood at remission, adult


title: AE208pn

description: DNA extracted from patient AE208 germline cells.

source_name: Patient AE208 germline cells obtained from bone marrow or blood at remission, adult


title: AE212pn

description: DNA extracted from patient AE212 germline cells.

source_name: Patient AE212 germline cells obtained from bone marrow or blood at remission, adult


title: AE209pn

description: DNA extracted from patient AE209 germline cells.

source_name: Patient AE209 germline cells obtained from bone marrow or blood at remission, adult


title: AE211pn

description: DNA extracted from patient AE211 germline cells.

source_name: Patient AE211 germline cells obtained from bone marrow or blood at remission, adult


title: AE201pn

description: DNA extracted from patient AE201 germline cells.

source_name: Patient AE201 germline cells obtained from bone marrow or blood at remission, adult


title: AE200pn

description: DNA extracted from patient AE200 germline cells.

source_name: Patient AE200 germline cells obtained from bone marrow or blood at remission, adult


title: AE205pn

description: DNA extracted from patient AE205 germline cells.

source_name: Patient AE205 germline cells obtained from bone marrow or blood at remission, adult


title: AE047pn

description: DNA extracted from patient AE047 germline cells.

source_name: Patient AE047 germline cells obtained from bone marrow or blood at remission, pediatric


title: AE046pn

description: DNA extracted from patient AE046 germline cells.

source_name: Patient AE046 germline cells obtained from bone marrow or blood at remission, pediatric


title: AE204pn

description: DNA extracted from patient AE204 germline cells.

source_name: Patient AE204 germline cells obtained from bone marrow or blood at remission, adult


title: AE040pn

description: DNA extracted from patient AE040 germline cells.

source_name: Patient AE040 germline cells obtained from bone marrow or blood at remission, pediatric


title: AE207pn

description: DNA extracted from patient AE207 germline cells.

source_name: Patient AE207 germline cells obtained from bone marrow or blood at remission, adult


title: AE039pn

description: DNA extracted from patient AE039 germline cells.

source_name: Patient AE039 germline cells obtained from bone marrow or blood at remission, pediatric


title: AE206pn

description: DNA extracted from patient AE206 germline cells.

source_name: Patient AE206 germline cells obtained from bone marrow or blood at remission, adult


title: AE038pn

description: DNA extracted from patient AE038 germline cells.

source_name: Patient AE038 germline cells obtained from bone marrow or blood at remission, pediatric


title: AE036pn

description: DNA extracted from patient AE036 germline cells.

source_name: Patient AE036 germline cells obtained from bone marrow or blood at remission, pediatric


title: AE203pn

description: DNA extracted from patient AE203 germline cells.

source_name: Patient AE203 germline cells obtained from bone marrow or blood at remission, adult


title: AE037pn

description: DNA extracted from patient AE037 germline cells.

source_name: Patient AE037 germline cells obtained from bone marrow or blood at remission, pediatric