title: wild type exposed to Aminocandin 2 hours_1

status: Public on Jan 31 2017

type: RNA

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramón y Cajal, S/N

department: Facultad de Farmacia, Departamento de Microbiologia II

country: Spain

institute: Universidad Complutense de Madrid

description: All the procedure for microarrays experiments was carried out following the instructions of affymetrix for each of the steps

hyb_protocol: Following affymetrix hybridation instructions

scan_protocol: Following affymetrix scanning instructions

data_processing: CEL files from scaner were analyzed using GCRMA algorithm from Bioconductor software

label: biotin

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast

label_protocol: Following affymetrix labelling instructions

growth_protocol: Saccharomyces cerevisiae strain BY4741 was grown overnight and dilluted to 0.2 OD, allowed to grow until 0.5 and then was grown for 2 hours

extract_protocol: Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the RNeasy kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

treatment_protocol: Saccharomyces cerevisiae strain BY4741 was grown overnight and dilluted to 0.2 OD, allowed to grow until 0.5 and then was grown with Caspofungin or Aminocandin for 2 hours

tag: genetic background


title: wild type exposed to Aminocandin 2 hours_2


title: slt2 mutant exposed to Caspofungin 2 hours_3


title: msn2/4 double mutant exposed to Caspofungin 2 hours_1


title: wild type 2 hours_1 (-AMC)


title: slt2 mutant exposed to Caspofungin 2 hours_2


title: wild type 2 hours_2 (-AMC)


title: msn2/4 double mutant 2 hours_3


title: msn2/4 double mutant exposed to Caspofungin 2 hours_3


title: msn2/4 double mutant 2 hours_1


title: msn2/4 double mutant exposed to Caspofungin 2 hours_2


title: slt2 mutant exposed to Caspofungin 2 hours_1


title: msn2/4 double mutant 2 hours_2


title: slt2 mutant 2 hours_1


title: slt2 mutant 2 hours_2


title: rlm1 mutant exposed to Caspofungin 2 hours_3


title: rlm1 mutant exposed to Caspofungin 2 hours_1


title: slt2 mutant 2 hours_3


title: rlm1 mutant exposed to Caspofungin 2 hours_2


title: rlm1 mutant 2 hours_3


title: rlm1 mutant 2 hours_1


title: rlm1 mutant 2 hours_2


title: wild type exposed to Caspofungin 2 hours_6


title: wild type exposed to Caspofungin 2 hours_4


title: wild type exposed to Caspofungin 2 hours_5


title: wild type exposed to Caspofungin 2 hours_2


title: wild type 2 hours_2


title: wild type 2 hours_1


title: wild type 2 hours_6


title: wild type 2 hours_3


title: wild type 2 hours_5


title: wild type exposed to Caspofungin 2 hours_3


title: wild type exposed to Caspofungin 2 hours_1


title: TALL-1

city: Singapore

first: Takaomi

last: Sanda

address: 14 Medical Dr 12-01

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

hyb_protocol: Standard Affymetrix 3' array hybridyzation protocol.

scan_protocol: Standard Affymetrix confocal laser scanner protocol.

data_processing: The data was normalized and analyzed by dChip software.

organism: Homo sapiens

source_name: T-ALL cell line

label_protocol: Standard Affymetrix biotin label protocol.

growth_protocol: T-ALL cells (3 million cells) were cultured in 10 ml RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol: After 24 hours of culture, total RNA was harvested by Trizol followed by a column purification using RNeasy Mini kit (Qiagen) following manufacturer's instruction.

treatment_protocol: Not applicable

tag: cell line

tag: tissue

value: T-cell acute lymphoblastic leukemia (T-ALL)


title: SUP-T13


title: co-culture, biological rep2

city: Kahoku-gun

first: Yasuo

last: Yoshitomi

state: Ishikawa

address: 1-1 Daigaku, Uchinada-machi

department: Biochemistry

country: Japan

institute: Kanazawa Medical University

description: Gene expression data from primary human microvascular endothelial cells co-cultured with primary mouse dorsal root ganglion cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were processed with Affymetrix Expression Console Software and the normalized intensity data were exported

source_name: RNA from human microvascular endothelial cell primary culture co-cultured with mouse dorsal root ganglion cell primary culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HMVECs were cultured in HuMedia-EB2 medium supplemented with 5% FBS, 5 ng/mL bFGF, 10 µg/mL heparin, 10 ng/mL EGF, 1 µg/mL hydrocortisone and 39.3 µg/mL dibutyryl cAMP (Kurabo, Tokyo Japan).

extract_protocol: Cells were extracted by TRI-Reagent and total RNA was purified using Rneasy Mini kits (QIAGEN, CA). RNA quality was assessed according to 28S/18S ratios of rRNA bands on electrophoresis gels under denaturing conditions.

treatment_protocol: HMVECs were co-cultured or separately-cultured with primary mouse dorsal root ganglion cells.

value: primary microvascular endothelial cells

value: primary dorsal root ganglion cells


title: Vehicle control, ip, 6hr, spleen, biological replicate 3

city: Ibaraki

first: Yoshinobu

last: Igarashi

state: Osaka

address: 7-6-8 Asagi-Saito

institute: National Institutes of Biomedical Innovation, Health and Nutrition

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) in Bioconductor/R Affy package. Median normalization was used. The customized PA call for fold change value was applied.

organism: Mus musculus

label_protocol: The total RNA was isolated and purified from the sample homogenates with an RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

growth_protocol: After a 7-day quarantine and acclimatization period, the adjuvants were injected to the C57BL/6J mice (6 week old, male) at 10 AM.

treatment_protocol: After 6 h, the inguinal LNs, liver, and spleen were removed and stored in RNAlater RNA Stabilization Reagent (Life Technologies, CA). Each sample in RNAlater was homogenized in Buffer RLT (Qiagen, Germany) by adding a 5 mm diameter zirconium bead (AS ONE Corporation, Japan) and shaking with a MixerMill 300 (Qiagen GmbH) at 20 Hz for 5 min.

tag: administration route

value: ip

tag: organ

value: Spleen

tag: gender

value: male

tag: age

tag: strain


title: wild type 2 hours_4


title: Vehicle control, ip, 6hr, spleen, biological replicate 2

extract_protocol: The total RNA was isolated and purified from the sample homogenates with an RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.


title: SUP-T11


title: co-culture, biological rep1


title: separate, biological rep2

description: Gene expression data from primry human microvascular endothelial cells (HMVECs) for control. The total RNA from HMVECs were mixed with the total RNA from separatately cultured primary mouse dorsal root ganglion cells

source_name: RNA from human microvascular endothelial cell primary culture mixed with RNA from mouse dorsal root ganglion cell primary culture


title: separate, biological rep1

description: Gene expression data from primary human microvascular endothelial cells (HMVECs) for control. The total RNA from HMVECs were mixed with the total RNA from separatately cultured primary mouse dorsal root ganglion cells


title: Vehicle control, ip, 6hr, spleen, biological replicate 1


title: PF-382


title: MOLT-4


title: Vehicle control, ip, 6hr, liver, biological replicate 3

value: Liver


title: MOLT-16


title: KOPT-K1


title: PEER

value: PEER


title: Advax, ip, 6hr, spleen, biological replicate 2


title: SKW-3


title: Advax, ip, 6hr, spleen, biological replicate 3


title: Vehicle control, ip, 6hr, liver, biological replicate 2


title: Vehicle control, ip, 6hr, liver, biological replicate 1


title: Advax, ip, 6hr, spleen biological replicate 1


title: Advax, ip, 6hr, liver biological replicate 1


title: Advax, ip, 6hr, liver, biological replicate 3


title: LN19_SNB+_PN

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol with Agilent SureScan microarray scanner (G2505C).

data_processing: Scanned images were processed with Agilent Feature Extraction v10.7 with default parameters to obtain raw data. Raw data were imported in R and processed using the limma package. After background correction with the normexp method, raw data were normalized with quantile method and log2 transformed.

source_name: biopsy from sentinel lymph node

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations.

extract_protocol: RNA was extracted with RecoverAll Total Nucleic Acid Isolation Kit (Ambion)  according to the protocol provided by the manufacturer.

value: sentinel lymph node

tag: patient id

tag: disease

value: Melanoma

tag: snb status

value: positive

tag: progression status at 5 years follow up

value: not progressing (PN)

tag: stage after surgery

value: IIIA

tag: primary tumor classification

tag: primary tumor localization

value: Foot

value: female

tag: age (years)


title: Advax, ip, 6hr, liver, biological replicate 2


title: LN7_SNB-_N

value: negative

value: not progressing (N)

value: IB

value: Leg


title: LN21_SNB+_PN

value: progressing (PN)

value: IIIC


title: JURKAT

value: JURKAT

value: T-cell acute lymphoblastic leukemia (T-ALL)


title: LN22_SNB-_N


title: CCRF-CEM

value: CCRF-CEM


title: LN8_SNB-_N

value: male


title: DU528


title: LN6_SNB+_PN

value: sentinel lymph node


title: LN23_SNB+_PN

value: Melanoma

value: IIIB


title: LN49_SNB+_PN

value: positive

value: not progressing (PN)


title: P12-ICHIKAWA


title: Vehicle control, ip, 6hr, lung, biological replicate 2

value: ip

value: Lung


title: Vehicle control, ip, 6hr, kidney, biological replicate 3

value: Kidney


title: LN5_SNB+_PN

value: Foot


title: LN3_SNB+_PN

value: IIIA

value: female


title: LN24_SNB+_PN

value: progressing (PN)

value: Trunk


title: LN1_SNB-_N

value: negative

value: not progressing (N)

value: IIA

value: Leg


title: LN2_SNB+_PN

value: sentinel lymph node

value: IIIC

value: male


title: Vehicle control, ip, 6hr, lung, biological replicate 1


title: Advax, ip, 6hr, lung, biological replicate 2


title: LOUCY

value: LOUCY

value: T-cell acute lymphoblastic leukemia (T-ALL)


title: Vehicle control, ip, 6hr, lung, biological replicate 3

value: ip


title: HSB-2


title: LN4_SNB+_PN

value: Melanoma

value: positive


title: Advax, ip, 6hr, lung biological replicate 1

value: Lung


title: ALL-SIL

value: ALL-SIL


title: Advax, ip, 6hr, lung, biological replicate 3


title: LN14_SNB+_PN

value: not progressing (PN)

value: IIIA

value: female


title: LN13_SNB+_PN

value: Trunk


title: Vehicle control, ip, 6hr, kidney, biological replicate 2

value: Kidney


title: LN16_SNB+_PN

value: progressing (PN)


title: LN17_SNB-_N

value: negative

value: not progressing (N)

value: IB


title: LN15_SNB+_PN

value: sentinel lymph node

value: Foot


title: LN11_SNB-_N

value: Leg

value: male


title: LN18_SNB+_PN

value: Melanoma

value: IIIC


title: Advax, ip, 6hr, kidney, biological replicate 3

value: ip


title: Vehicle control, ip, 6hr, kidney, biological replicate 1


title: LN9_SNB+_PN

value: positive

value: IIIB


title: LN12_SNB-_N

value: IIB


title: Advax, ip, 6hr, kidney, biological replicate 2


title: Advax, ip, 6hr, kidney biological replicate 1


title: Vehicle control, id, 6hr, spleen, biological replicate 3

value: id

value: Spleen


title: LN10_SNB-_N

value: female


title: Vehicle control, id, 6hr, spleen, biological replicate 2


title: Advax, id, 6hr, spleen, biological replicate 3


title: Advax, id, 6hr, spleen, biological replicate 2


title: Vehicle control, id, 6hr, spleen, biological replicate 1


title: Vehicle control, id, 6hr, liver, biological replicate 3

value: Liver


title: Advax, id, 6hr, spleen biological replicate 1


title: Vehicle control, id, 6hr, liver, biological replicate 1


title: Vehicle control, id, 6hr, liver, biological replicate 2


title: Advax, id, 6hr, liver, biological replicate 1


title: Advax, id, 6hr, liver, biological replicate 2


title: Advax, id, 6hr, liver, biological replicate 3


title: Vehicle control, id, 6hr, lymph node, biological replicate 2

value: lymph node


title: Vehicle control, id, 6hr, lymph node, biological replicate 1


title: Advax, id, 6hr, lymph node, biological replicate 2


title: Multiple myeloma. Pair 11. Relapse. [DNA copy number]

type: genomic

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

institute: Centro de Investigación del Cáncer de Salamanca

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
ChAS console from Affymetrix was used to assess genome wide copy number frequencies
The normalized data matrix contains Weighted Log2 Ratios
The *cychp files were generated as following:
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 1.16.0
program-name = apt-copynumber-cyto.exe
program-version = 1.16.0

molecule: genomic DNA

source_name: MM patient_relapse

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix

growth_protocol: Not applicable

extract_protocol: Tumors were extracted and cells were collected. Total RNA from disgregated cells was extracted using Buffer RLT plus (Qiagen, CA, USA) and purified with All prep DNA/RNA mini Kit (Qiagen, CA, USA).

tag: subject condition

value: Multiple myeloma (MM) patient

tag: sample pair id

value: pair 11

value: Male

tag: patient status

value: relapse

value: Bone marrow

tag: cell type

value: CD 138+ plasma cells


title: Multiple myeloma. Pair 20. Relapse. [DNA copy number]

value: pair 20

tag: tissue


title: Multiple myeloma. Pair 16. Diagnosis. [DNA copy number]

source_name: MM patient_diagnosis

value: pair 16

value: diagnosis


title: Multiple myeloma. Pair 13. Diagnosis. [DNA copy number]

value: pair 13

value: Female


title: Multiple myeloma. Pair 12. Relapse. [DNA copy number]

value: pair 12


title: Multiple myeloma. Pair 13. Relapse. [DNA copy number]


title: Multiple myeloma. Pair 20. Diagnosis. [DNA copy number]


title: Multiple myeloma. Pair 17. Diagnosis. [DNA copy number]

value: pair 17


title: Advax, id, 6hr, lymph node, biological replicate 1

tag: administration route

value: id

tag: organ

value: male


title: Multiple myeloma. Pair 19. Diagnosis. [DNA copy number]

value: pair 19

tag: gender

tag: age


title: Multiple myeloma. Pair 14. Relapse. [DNA copy number]

value: pair 14


title: Multiple myeloma. Pair 15. Diagnosis. [DNA copy number]

value: Multiple myeloma (MM) patient

value: pair 15


title: ShhGFPCRE_R26RYFP_E12.5_positive_2219

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description: URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:22949

hyb_protocol: Amplification protocol Target Amplified manufacturer/kit: GeneChip® Mouse Genome 430 2.0 Assay kit (Affymetrix, cat# 902490) Target Amplified protocol: Affymetrix two-cycle (small-sample protocol) Rounds of amplification: 2 Amount labelled  target hybridization to array: 15 µg The GeneChips were washed and stained with a GeneChip Fluidics Station 450 according to the Expression Analysis Technical Manual.

scan_protocol: GeneChip Scanner 3000 was used to collect data into the GeneChip Operating Software using default parameters and global scaling as the normalization protocol.

data_processing: Analysis method: BRB array tools

source_name: ShhGFP, YFP positive urethral epithelium E12.5

label_protocol: IVT Labeling Kit (Affymetrix)

extract_protocol: RNeasy Mini Kit (QIAGEN, Inc., Valencia, CA)

treatment_protocol:
Pooled sample: yes
Pool size: 2 (littermates)
Dissection method: The genital tubercle was dissected at the base of the genital tubercle and fluorescence activated cell sorting for GFP/YFP positive cells.
Experimental design: Pregnant dams were euthanized by cervical dislocation followed by thoracotomy and the embryos were harvested in ice-cold phosphate buffer saline (PBS).  For cell purification experiments, embryos were harvested at embryonic day E12.5 and viewed under a stereomicroscope with epifluorescence in order to detect GFP/eYFP activity.  In all embryos confirmed by PCR to carry the ShhGFPCre allele and at least one copy of R26ReYFP, we detected bright yellow-green fluorescence throughout the urethral plate epithelium of the genital tubercle. The genital tubercle was dissected at the base of the genital tubercle and placed in 0.05% trypsin at 37 degrees for 5 minutes.  A single cell suspension was achieved by trituration using glass pasture pipette.  These cells were centrifuged at 1800 RPM for 2 minutes and re-suspended in 0.5umM EDTA containing 0.5% BSA in PBS for sorting.

tag: gene reported

tag: strain

value: mixed background

tag: Sex

value: pooled male and female

tag: developmental stage

tag: theiler stage

value: YFP positive urethral epithelium


title: Multiple myeloma. Pair 19. Relapse. [DNA copy number]

value: Male

value: relapse

value: Bone marrow

value: CD 138+ plasma cells


title: Multiple myeloma. Pair 7. Diagnosis. [DNA copy number]

value: pair 7

value: diagnosis


title: Multiple myeloma. Pair 8. Relapse. [DNA copy number]

value: pair 8

value: Female


title: Multiple myeloma. Pair 14. Diagnosis. [DNA copy number]


title: Multiple myeloma. Pair 15. Relapse. [DNA copy number]


title: ShhGFPCRE_R26RYFP_E12.5_positive_2217

description: URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:22947

treatment_protocol:
Pooled sample: yes
Pool size: 5 (littermates)
Dissection method: The genital tubercle was dissected at the base of the genital tubercle and fluorescence activated cell sorting for GFP/YFP positive cells.
Experimental design: Pregnant dams were euthanized by cervical dislocation followed by thoracotomy and the embryos were harvested in ice-cold phosphate buffer saline (PBS).  For cell purification experiments, embryos were harvested at embryonic day E12.5 and viewed under a stereomicroscope with epifluorescence in order to detect GFP/eYFP activity.  In all embryos confirmed by PCR to carry the ShhGFPCre allele and at least one copy of R26ReYFP, we detected bright yellow-green fluorescence throughout the urethral plate epithelium of the genital tubercle. The genital tubercle was dissected at the base of the genital tubercle and placed in 0.05% trypsin at 37 degrees for 5 minutes.  A single cell suspension was achieved by trituration using glass pasture pipette.  These cells were centrifuged at 1800 RPM for 2 minutes and re-suspended in 0.5umM EDTA containing 0.5% BSA in PBS for sorting.


title: Multiple myeloma. Pair 16. Relapse. [DNA copy number]

value: pair 16


title: Multiple myeloma. Pair 9. Diagnosis. [DNA copy number]

value: pair 9


title: Multiple myeloma. Pair 11. Diagnosis. [DNA copy number]

value: pair 11


title: Multiple myeloma. Pair 12. Diagnosis. [DNA copy number]

value: pair 12


title: Multiple myeloma. Pair 8. Diagnosis. [DNA copy number]

value: Multiple myeloma (MM) patient


title: ShhGFPCRE_R26RYFP_E12.5_negative_2220

description: URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:22950

source_name: ShhGFP, YFP negative genital tubercle E12.5

treatment_protocol:
Pooled sample: yes
Pool size: 2 (littermates)
Dissection method: The genital tubercle was dissected at the base of the genital tubercle and fluorescence activated cell sorting for GFP/YFP positive cells.
Experimental design: Pregnant dams were euthanized by cervical dislocation followed by thoracotomy and the embryos were harvested in ice-cold phosphate buffer saline (PBS).  For cell purification experiments, embryos were harvested at embryonic day E12.5 and viewed under a stereomicroscope with epifluorescence in order to detect GFP/eYFP activity.  In all embryos confirmed by PCR to carry the ShhGFPCre allele and at least one copy of R26ReYFP, we detected bright yellow-green fluorescence throughout the urethral plate epithelium of the genital tubercle. The genital tubercle was dissected at the base of the genital tubercle and placed in 0.05% trypsin at 37 degrees for 5 minutes.  A single cell suspension was  achieved by trituration using glass pasture pipette.  These cells were centrifuged at 1800 RPM for 2 minutes and re-suspended in 0.5umM EDTA containing 0.5% BSA in PBS for sorting.

value: YFP negative genital tubercle


title: ShhGFPCRE_R26RYFP_E12.5_positive_2215

description: URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:22945

treatment_protocol:
Pooled sample: yes
Pool size: 3 (littermates)
Dissection method: The genital tubercle was dissected at the base of the genital tubercle and fluorescence activated cell sorting for GFP/YFP positive cells.
Experimental design: Pregnant dams were euthanized by cervical dislocation followed by thoracotomy and the embryos were harvested in ice-cold phosphate buffer saline (PBS).  For cell purification experiments, embryos were harvested at embryonic day E12.5 and viewed under a stereomicroscope with epifluorescence in order to detect GFP/eYFP activity.  In all embryos confirmed by PCR to carry the ShhGFPCre allele and at least one copy of R26ReYFP, we detected bright yellow-green fluorescence throughout the urethral plate epithelium of the genital tubercle. The genital tubercle was dissected at the base of the genital tubercle and placed in 0.05% trypsin at 37 degrees for 5 minutes.  A single cell suspension was achieved by trituration using glass pasture pipette.  These cells were centrifuged at 1800 RPM for 2 minutes and re-suspended in 0.5umM EDTA containing 0.5% BSA in PBS for sorting.

value: mixed background


title: Multiple myeloma. Pair 17. Relapse. [DNA copy number]

value: pair 17


title: ShhGFPCRE_R26RYFP_E12.5_negative_2218

description: URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:22948

data_processing: Analysis method: BRB array tools GCOS

treatment_protocol:
Pooled sample: yes
Pool size: 5 (littermates)
Dissection method: The genital tubercle was dissected at the base of the genital tubercle and fluorescence activated cell sorting for GFP/YFP positive cells.
Experimental design: Pregnant dams were euthanized by cervical dislocation followed by thoracotomy and the embryos were harvested in ice-cold phosphate buffer saline (PBS).  For cell purification experiments, embryos were harvested at embryonic day E12.5 and viewed under a stereomicroscope with epifluorescence in order to detect GFP/eYFP activity.  In all embryos confirmed by PCR to carry the ShhGFPCre allele and at least one copy of R26ReYFP, we detected bright yellow-green fluorescence throughout the urethral plate epithelium of the genital tubercle. The genital tubercle was dissected at the base of the genital tubercle and placed in 0.05% trypsin at 37 degrees for 5 minutes.  A single cell suspension was  achieved by trituration using glass pasture pipette.  These cells were centrifuged at 1800 RPM for 2 minutes and re-suspended in 0.5umM EDTA containing 0.5% BSA in PBS for sorting.

value: pooled male and female


title: Multiple myeloma. Pair 10. Diagnosis. [DNA copy number]

value: pair 10


title: Multiple myeloma. Pair 6. Diagnosis. [DNA copy number]

value: pair 6

value: Male


title: Ac2PIM2 treated_8h

city: Kagoshima

first: Kenji

last: TOYONAGA

address: 8-35-1 Sakuragaoka

department: Department of Immunology

institute: Graduate School of Medical and Dental Sciences, Kagoshima University

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 2.0 ST array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Power Tool version 1.15.0 software, and obtained normalized intensity values.

source_name: monocyte-derived dendritic cells, tetra-acylated PIM2 (Ac2PIM2) treated, 8h

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

growth_protocol: Monocyte-derived dendritic cells were obtained from CD14+ monocytes after culture in RPMI1640 supplemented with 10% FBS, non-essential amino acid, anti-biotics, 10 ng/ml human GM-CSF and 10 ng/ml human IL-4 for seven days.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Monocyte-derived dendritic cells were stimulated with plate-coated tri-acylated PIM2 (AcPIM2) or tetra-acylated PIM2 (Ac2PIM2) for 48 hours.

value: dendritic cells


title: ShhGFPCRE_R26RYFP_E12.5_negative_2216

description: URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:22946

label_protocol: IVT Labelling Kit (Affymetrix)

treatment_protocol:
Pooled sample: yes
Pool size: 3 (littermates)
Dissection method: The genital tubercle was dissected at the base of the genital tubercle and fluorescence activated cell sorting for GFP/YFP positive cells.
Experimental design: Pregnant dams were euthanized by cervical dislocation followed by thoracotomy and the embryos were harvested in ice-cold phosphate buffer saline (PBS).  For cell purification experiments, embryos were harvested at embryonic day E12.5 and viewed under a stereomicroscope with epifluorescence in order to detect GFP/eYFP activity.  In all embryos confirmed by PCR to carry the ShhGFPCre allele and at least one copy of R26ReYFP, we detected bright yellow-green fluorescence throughout the urethral plate epithelium of the genital tubercle. The genital tubercle was dissected at the base of the genital tubercle and placed in 0.05% trypsin at 37 degrees for 5 minutes.  A single cell suspension was  achieved by trituration using glass pasture pipette.  These cells were centrifuged at 1800 RPM for 2 minutes and re-suspended in 0.5umM EDTA containing 0.5% BSA in PBS for sorting.


title: Untreated

source_name: monocyte-derived dendritic cells, untreated


title: Multiple myeloma. Pair 9. Relapse. [DNA copy number]

value: relapse

value: Bone marrow

value: CD 138+ plasma cells


title: MLS-1765_SOX11_rep2

city: Heidelberg

first: Marcus

last: Renner

address: Im Neuenheimer Feld 224

department: General Pathology

country: Germany

institute: Institute of Pathology

hyb_protocol: Standard Illumina Hybridisation Protocol Part # 11322355 was used. (Whole-Genome Gene Expression Direct Hybridization Assay Guide). In brief, 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide)

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: Biotin, Cy3-Streptavidin

source_name: MLS-1765_SOX11_late passage

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologie) is used to generate single-stranded cRNA from input amounts of 150ng total RNA

growth_protocol: MLS-1765 cells were grown in RPMI medium with 10% FCS and 1% penicillin/streptomycin

extract_protocol: RNA was isolated from cells using the NucleoSpin® RNA kit (Machery-Nagel, Düren, Germany) according to the manufacturer’s instructions. Quality control and quantification of total RNA were conducted using a RNA 6000 nano LabChip with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Only RNA with a RNA integrity number >7 was used for microarray-based mRNA profiling.

treatment_protocol: codon-optimized SOX11 was stably overexpressed in MLS-1765

tag: cell line

value: myxoid liposarcoma (MLS)

tag: transfected with

value: codon-optimized full-length human SOX11

tag: passage

value: late


title: AcPIM2 treated_8h

source_name: monocyte-derived dendritic cells, tri-acylated PIM2 (AcPIM2) treated, 8h


title: PC-9 Gefitinib resistant, nuclear replicate 1

first: Henry

last: Yang

address: 28 Medical Drive

institute: Cancer Science Institute of Singapore

description:
Gene expression data from PC-9 cells
RN1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HumanHT-12 v4 Beadchip Array.

scan_protocol: Beadchips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Raw data were obtained after background subtraction. The background-subtracted data were normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 20.

source_name: Non-small cell lung cancer

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

growth_protocol: Cells were grown in RPMI supplemented with 10% fetal bovine serum and penicillin/streptomycin.

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

treatment_protocol: PC-GR was generated by continuous exposure to Gefitinib, in increasing concentration ranging from 50nM to 5μM, for a duration of 6 months.

value: Non-small cell lung cancer

tag: gefitinib resistance status

value: resistant

tag: cell compartment

value: nucleus


title: PC-9 Parental, cytosolic replicate 1

description:
Gene expression data from PC-9 cells
PC1

value: non-resistant (parental)

value: cytosol


title: PC-9 Parental, cytosolic replicate 2

description:
Gene expression data from PC-9 cells
PC2


title: PC-9 Parental, nuclear  replicate 2

description:
Gene expression data from PC-9 cells
PN2


title: PC-9 Gefitinib resistant, nuclear replicate 2

description:
Gene expression data from PC-9 cells
RN2


title: PC-9 Gefitinib resistant, cytosolic replicate 1

description:
Gene expression data from PC-9 cells
RC1


title: 05_R17_110892-0614-Capasso-H2

city: Naples

first: Massimo

last: Mallardo

address: Via Sergio Pansini, 5

department: Molecular Medicine and Medical Biotechnology

institute: University of Naples Federico II°

description: miRNa expression profile

hyb_protocol: LCscience

scan_protocol: LCscience

data_processing: Lcscience ArrayPro Software

organism: Rattus norvegicus

source_name: Hypersodic diet  rat (3 pooled animals)

label_protocol: LCscience

extract_protocol: RNA Trizol (Life technology) standard protocol

treatment_protocol: Normal Diet vs hypersodic diet

tag: tag

value: Kidney Thick Ascendig Limb


title: 06_R17_110893-0614-Capasso-H3

description: miRNa expression profile


title: PC-9 Parental, nuclear replicate 1

description:
Gene expression data from PC-9 cells
PN1

tag: cell type


title: MLS-1765_EV_rep2

source_name: MLS-1765_EV_late passage

value: emtpy vector (EV)


title: PC-9 Gefitinib resistant, cytosolic replicate 2

description:
Gene expression data from PC-9 cells
RC2


title: Multiple myeloma. Pair 7. Relapse. [DNA copy number]

tag: subject condition

value: Multiple myeloma (MM) patient

tag: sample pair id

value: pair 7

value: Female

tag: patient status

tag: tissue


title: Multiple myeloma. Pair 5. Relapse. [DNA copy number]

value: pair 5

tag: gender

value: Male

tag: age


title: PC-9 Gefitinib  Resistant, whole cell replicate 1

description:
Gene expression data from PC-9 cells
RT1

value: whole cell


title: 03_R17_110906-0607-Capasso-N3

description: miRNa expression profile

source_name: Normal diet rat (3 pooled animals)


title: Multiple myeloma. Pair 4. Relapse. [DNA copy number]

value: pair 4

value: relapse

value: Bone marrow

value: CD 138+ plasma cells


title: PC-9 Parental, whole cell replicate 1

description:
Gene expression data from PC-9 cells
PT1

value: Non-small cell lung cancer


title: Multiple myeloma. Pair 10. Relapse. [DNA copy number]

value: pair 10


title: HMEC-hTERT_PELP1-WT_2

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

country: USA

institute: University of Minnesota

description:
WT_2
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were filtered and any probes with a detection P value less than 0.05 were removed from the normalized dataset. The data was then normalized using log2 transformation and quantile normalization with R using the lumi Bioconductor package.

label: Biotin

source_name: Human mammary epithelial cell line, PELP1-wild type

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

growth_protocol: Cell lines were cultured in HuMEC Ready Media supplemented with epidermal growth factor, hydrocortisone, isoproterenol, transferrin, insulin, and 25 mg of bovine pituitary extract for 24 hr before total RNA harvest.

treatment_protocol: No treatment.

tag: parental cell line

value: HMEC-hTERT

tag: parental cell type

value: breast epithelial cells, immortalized with hTERT expression

tag: stable vector integration

tag: time point

value: 24 hr


title: MLS-1765_SOX11_rep1

source_name: MLS-1765_SOX11_ealy passage

tag: cell line

value: myxoid liposarcoma (MLS)

value: codon-optimized full-length human SOX11

value: early


title: 02_R17_110790-0607-Capasso-N2

description: miRNa expression profile

value: Kidney Thick Ascendig Limb


title: HMEC-hTERT_PELP1-CYTO_1

description:
CYTO_1
Replicate 1

source_name: Human mammary epithelial cell line, PELP1-cytoplasmic


title: PC-9 Parental, whole cell replicate 2

description:
Gene expression data from PC-9 cells
PT2

value: non-resistant (parental)


title: 01_R17_110789-0607-Capasso-N1

description: miRNa expression profile


title: HMEC-hTERT_PELP1-WT_1

description:
WT_1
Replicate 1


title: PC-9 Gefitinib  resistant, whole cell replicate 2

description:
Gene expression data from PC-9 cells
RT2

value: resistant


title: siRb1_rep3

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.9 was used and cubic spline normalization was applied to the data.

source_name: Ovcar3 cell lines were transfected with Rb1 siRNA

label_protocol: Standard labeling protocol with biotin wirh Cy3-streptavidin

growth_protocol: Human cell lines OVCAR-3 were cultured in RPMI-1640 medium (BioWhittaker, Lonza) supplemented with 20% (v/v) Fetal Bovine Serum (FBS), insulin (10 μg/ml; I9278, Sigma) and 1% (v/v) penicillin/streptomycin (Lonza).

extract_protocol: Total RNA was prepared 72 hours after transfection. RNA was extracted with Qiazol reagent (Qiagen), following the protocol provided by the manufacturer. RNA integrity was checked by formaldehyde agarose gel electrophoresis. Purity and concentration were determined on a Nanodrop spectrophotometer.

treatment_protocol: Transient transfections of siRNAs were performed using Lipofectamine RNAiMAX reagent (Invitrogen).

tag: transfection

value: Rb1 siRNA


title: HMEC-hTERT_LXSN-vector-control_1

description:
LXSN_1
Replicate 1

source_name: Human mammary epithelial cell line, empty vector control pLXSN

value: pLXSN


title: Multiple myeloma. Pair 3. Relapse. [DNA copy number]

source_name: MM patient_relapse

value: Multiple myeloma (MM) patient

value: pair 3

value: Female


title: Ctrl_rep3

source_name: Ovcar3 cell lines were transfected with control siRNA

value: control siRNA


title: 04_R17_110907-0607-Capasso-H1

description: miRNa expression profile


title: siOct4_rep3

source_name: Ovcar3 cell lines were transfected with Oct4 siRNA

value: Oct4 siRNA


title: siCcnf+siNipp1_rep3

source_name: Ovcar3 cell lines were transfected with Ccnf siRNA + Nipp1 siRNA

value: Ccnf siRNA + Nipp1 siRNA


title: Ctrl_rep2


title: siOct4_rep2


title: Multiple myeloma. Pair 4. Diagnosis. [DNA copy number]

source_name: MM patient_diagnosis

value: pair 4

value: Male

value: diagnosis

value: Bone marrow

value: CD 138+ plasma cells


title: siCcnf+siNipp1_rep2


title: HMEC-hTERT_PELP1-CYTO_2

description:
CYTO_2
Replicate 2

value: HMEC-hTERT

value: breast epithelial cells, immortalized with hTERT expression

value: 24 hr


title: Multiple myeloma. Pair 1. Relapse. [DNA copy number]

value: pair 1

value: relapse


title: siOct4_rep1


title: Ctrl_rep1


title: siRb1_rep2

value: Rb1 siRNA


title: siCcnf+siNipp1_rep1


title: HMEC-hTERT_LXSN-vector-control_2

description:
LXSN_2
Replicate 2

value: pLXSN


title: Multiple myeloma. Pair 2. Relapse. [DNA copy number]

value: Multiple myeloma (MM) patient

value: pair 2


title: siRb1_rep1


title: Multiple myeloma. Pair 1. Diagnosis. [DNA copy number]


title: Multiple myeloma. Pair 3. Diagnosis. [DNA copy number]

value: pair 3

value: Female


title: REH_NT_rep2

city: Tokyo

first: Jun

last: Inoue

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

department: Molecular Cytogenetics

institute: Tokyo Medical & dental univ.

description: Gene expression in miR-NC transfected cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: REH, NT, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA fractions were prepared using TRIsure (BIOLINE,London, UK) following the manufacturer's recommendations. The protocol includes clean up step after TURBO DNA-free™ Kit (Ambion, Austin, TX) digestion. RNAs were quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: L-asparaginase were treated with 1U/ml for 2 days.

tag: resource

value: cell line

value: leukemia


title: REH_L-asparaginase_rep2

description: Gene expression in miR-634 transfected cells

source_name: REH, L-asparaginase, replicate2


title: REH_NT_rep1

source_name: REH, NT, replicate1


title: Multiple myeloma. Pair 6. Relapse. [DNA copy number]

value: pair 6

value: Male


title: Multiple myeloma. Pair 2. Diagnosis. [DNA copy number]

value: diagnosis

value: Bone marrow


title: REH_L-asparaginase_rep1

source_name: REH, L-asparaginase, replicate1


title: Multiple myeloma. Pair 20. Relapse. [methylation]

hyb_protocol: Hybridization was performed according to the instructions in the NimbleGen Array User Guide

scan_protocol: Scanning was performed according to the instructions in the NimbleGen Array User Guide

data_processing: Arrays were processed using Nimblegen's standard protocol. Batch-effects were removed using ComBat R package. Quantile normalization was done using the affy R package.

label_protocol: Samples were denatured and labeled in parallel with Cy3 for the test group and Cy5 for the control group, each through a random priming method, using Klenow fragments (NimbleGen Dual-Color DNA Labeling Kit, Roche NimbleGen, Inc., Madison, WI, USA) following the manufacturer protocol

extract_protocol: The genomic DNA was extracted from frozen bone marrow samples with QIAmp DNA Mini Kit (Qiagen, 16 Valencia, CA, USA) following the manufacturer’s instructions

value: pair 20

tag: age (yr)

value: CD 138+ plasma cells

source_name: MM patient_relapse_input

tag: sample type

value: Input


title: Multiple myeloma. Pair 18. Relapse. [methylation]

value: pair 18


title: MLS-1765_EV_rep1

source_name: MLS-1765_EV_ealry passage

value: myxoid liposarcoma (MLS)

tag: transfected with

value: emtpy vector (EV)

tag: passage

value: early


title: Multiple myeloma. Pair 5. Diagnosis. [DNA copy number]

tag: subject condition

value: Multiple myeloma (MM) patient

value: pair 5

tag: cell type


title: Multiple myeloma. Pair 19. Relapse. [methylation]

tag: sample pair id

value: pair 19

tag: patient status

value: relapse


title: Multiple myeloma. Pair 20. Diagnosis. [methylation]

tag: gender

tag: tissue

source_name: MM patient_diagnosis_input


title: Multiple myeloma. Pair 18. Diagnosis. [methylation]

value: Female


title: Multiple myeloma. Pair 20. Relapse. [gene expression]

hyb_protocol: Labeled RNA was hybridized to Human Gene 1.0 ST Array

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Expression value for each probe set was calculated using Affymetrix Expression Console that uses RMA (Robust Multi-Array Average) algorithm.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)

value: CD138+ plasma cells


title: TIME-JunBOE

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

source_name: Immortalized human microvascular endothelial cells (TIME cells) transduced human JunB expression vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using Ambion WT Expression Kit.

growth_protocol: Endothelial cells were cultured in M133 medium supplemented with MVGS

treatment_protocol: Cells were transduced with lentiviruses containing human JunB cDNA or empty vector.

value: Endothelial cell culture

tag: transduced with

value: JunB expression vector


title: TIME-Vec

source_name: Immortalized human microvascular endothelial cells (TIME cells) transduced empty vector

value: control vector


title: Multiple myeloma. Pair 15. Diagnosis. [methylation]

value: pair 15

value: Male

value: diagnosis

value: Bone marrow


title: Multiple myeloma. Pair 12. Diagnosis. [methylation]

value: pair 12

value: CD 138+ plasma cells

value: Input


title: Multiple myeloma. Pair 17. Diagnosis. [methylation]

value: pair 17


title: Multiple myeloma. Pair 17. Relapse. [methylation]

value: Multiple myeloma (MM) patient


title: Multiple myeloma. Pair 11. Relapse. [methylation]

value: pair 11


title: Multiple myeloma. Pair 16. Diagnosis. [methylation]

value: pair 16


title: Multiple myeloma. Pair 16. Relapse. [methylation]

value: relapse


title: Multiple myeloma. Pair 13. Relapse. [methylation]

value: pair 13

value: Female


title: Multiple myeloma. Pair 15. Relapse. [methylation]


title: Multiple myeloma. Pair 10. Relapse. [methylation]

value: pair 10


title: Multiple myeloma. Pair 14. Relapse. [methylation]

value: pair 14


title: Multiple myeloma. Pair 13. Diagnosis. [methylation]


title: Multiple myeloma. Pair 18. Diagnosis. [gene expression]

treatment_protocol: Not applicable

value: pair 18

value: CD138+ plasma cells


title: Multiple myeloma. Pair 12. Relapse. [methylation]


title: Multiple myeloma. Pair 10. Diagnosis. [methylation]


title: Multiple myeloma. Pair 8. Diagnosis. [methylation]

value: pair 8


title: Multiple myeloma. Pair 11. Diagnosis. [methylation]

value: Male

value: diagnosis


title: Multiple myeloma. Pair 14. Diagnosis. [methylation]

value: Bone marrow


title: Multiple myeloma. Pair 15. Diagnosis. [gene expression]

value: pair 15


title: Multiple myeloma. Pair 9. Relapse. [methylation]

value: pair 9

value: CD 138+ plasma cells

value: Input


title: Multiple myeloma. Pair 20. Diagnosis. [gene expression]

value: Multiple myeloma (MM) patient

value: pair 20


title: Multiple myeloma. Pair 15. Relapse. [gene expression]

value: relapse


title: Multiple myeloma. Pair 14. Relapse. [gene expression]


title: Multiple myeloma. Pair 9. Diagnosis. [methylation]


title: Multiple myeloma. Pair 8. Relapse. [methylation]


title: Multiple myeloma. Pair 14. Diagnosis. [gene expression]


title: Multiple myeloma. Pair 7. Relapse. [methylation]

value: pair 7


title: Multiple myeloma. Pair 13. Diagnosis. [gene expression]

value: pair 13

value: Female


title: Multiple myeloma. Pair 19. Diagnosis. [methylation]

value: pair 19


title: Multiple myeloma. Pair 12. Diagnosis. [gene expression]

value: pair 12


title: Multiple myeloma. Pair 11. Diagnosis. [gene expression]

value: pair 11

value: CD138+ plasma cells


title: Multiple myeloma. Pair 13. Relapse. [gene expression]


title: Multiple myeloma. Pair 11. Relapse. [gene expression]

value: Male


title: Multiple myeloma. Pair 12. Relapse. [gene expression]


title: Multiple myeloma. Pair 10. Relapse. [gene expression]

value: pair 10


title: Multiple myeloma. Pair 7. Diagnosis. [methylation]

value: diagnosis

value: Bone marrow


title: Multiple myeloma. Pair 10. Diagnosis. [gene expression]


title: WT, biological rep 3

city: Tuebingen

first: Qifeng

last: Zhou

address: Otfried Mueller str.10

department: Cardiology

institute: University Hospital Tuebingen

description: microRNA expression data from WT left ventricle tissue

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were imported using expression console software from Affymetrix and analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of multispecies miRNA-2_0-type from Affymetrix.The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction.

source_name: Mouse heart, left ventricle

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Mice at age 2-3 months old were infused with Angiotensin II for 3 days. BL6, male.

extract_protocol: RNA was extracted according to the manual of the Qiagen RNeasy Fibrous Tissue Mini Kit.

treatment_protocol: Mice were euthanized and the heart was removed. The apex of the left ventricle was isolated and snap frozen in liquid nitrogen.

tag: strain

value: male

value: heart

tag: tissue compartment

value: left ventricle

tag: genotype

value: WT

tag: age

value: 2-3 months


title: Multiple myeloma. Pair 6. Relapse. [methylation]

value: Multiple myeloma (MM) patient

value: pair 6

value: relapse

value: CD 138+ plasma cells

value: Input


title: WT, biological rep 2


title: stable line control replicate4

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

description:
Replicate 4 of 5
sneg-rep4

hyb_protocol: Samples were prepared with Gene Expression Hybridization Kit (Agilent) and placed in Agilent microarray hybridization chambers and rack. Hybridization occurred for 17 hr. at 65°.

scan_protocol: Scanned on Axon Genepix 4000B scanner. Images were processed with Agilent Feature Extraction Software v9.1.1.

data_processing:
Background substraction and linear LOWESS normalization was used in Feature Extraction software.
All retained VALUEs met Agilent spot quality filters in all arrays.

source_name: Stratagene Universal Reference RNA

label_protocol: 500 ng of total RNA was labeled using Low RNA Input Fluor Linear Amp Kit PLUS (Agilent).

growth_protocol: Cells were split to 2x10^5 cells per ml every 48 hr.

extract_protocol: Cells were harvested with RNA-bee (Tel-test). RNA integrity was assayed using a Bioanalyzer 2100 (Agilent) and quantitated with a ND1000 spectrophotometer (Nanodrop).

treatment_protocol: BJAB and BCBL-1 cells were electroporated with siPORT system (Ambion) at 30 nM for mimics and 100 nM for inhibitors (RNA harvested 48 and 72 hr. after transfection, respectively)

tag: reference

value: Pooled cell line RNA

source_name: stable BJAB line

tag: cell line

value: BJAB

tag: protocol

value: transduced with retrovirus lacking any sequence to encode for a microRNA


title: stable line control replicate5

description:
Replicate 5 of 5
sneg-rep5


title: HET, biological rep 3

description: microRNA expression data from HET left ventricle tissue

value: HET


title: Multiple myeloma. Pair 9. Relapse. [gene expression]

source_name: MM patient_relapse

value: pair 9

value: Male

tag: age (yr)

value: CD138+ plasma cells


title: stable line control replicate3

description:
Replicate 3 of 5
sneg-rep3


title: Multiple myeloma. Pair 9. Diagnosis. [gene expression]

value: diagnosis

value: Bone marrow


title: stable line control replicate2

description:
Replicate 2 of 5
sneg-rep2


title: HET, biological rep 2

value: male

value: heart

value: left ventricle


title: Multiple myeloma. Pair 6. Diagnosis. [methylation]

value: Multiple myeloma (MM) patient

tag: sample type


title: stable line control replicate1

description:
Replicate 1 of 5
sneg-rep1


title: Multiple myeloma. Pair 8. Relapse. [gene expression]

value: pair 8

value: Female


title: Multiple myeloma. Pair 18. Relapse. [gene expression]

value: pair 18

value: relapse


title: Multiple myeloma. Pair 8. Diagnosis. [gene expression]


title: WT, biological rep 1

value: WT

value: 2-3 months


title: HET, biological rep 1


title: Multiple myeloma. Pair 5. Relapse. [methylation]

value: pair 5

value: CD 138+ plasma cells

value: Input


title: stable line miR-K6,11,7 replicate2

description:
Replicate 2 of 2
s6117-rep2

value: Pooled cell line RNA

value: BJAB

value: transduced with a retrovirus expressing one or more KSHV microRNAs


title: stable line miR-K6,11,7 replicate1

description:
Replicate 1 of 2
s6117-rep1


title: Multiple myeloma. Pair 5. Relapse. [gene expression]

value: Male

value: Bone marrow

value: CD138+ plasma cells


title: Multiple myeloma. Pair 6. Relapse. [gene expression]

value: pair 6


title: stable line miR-K1 to -K5 replicate2

description:
Replicate 2 of 2
s15-rep2


title: Multiple myeloma. Pair 6. Diagnosis. [gene expression]

value: Multiple myeloma (MM) patient

value: diagnosis


title: Multiple myeloma. Pair 7. Diagnosis. [gene expression]

value: pair 7

value: Female


title: Multiple myeloma. Pair 5. Diagnosis. [gene expression]


title: Multiple myeloma. Pair 4. Diagnosis. [methylation]

value: pair 4


title: stable line miR-K8 replicate1

description:
Replicate 1 of 2
s8-rep1


title: Multiple myeloma. Pair 4. Relapse. [gene expression]

value: relapse


title: stable line miR-K8 replicate2

description:
Replicate 2 of 2
s8-rep2


title: transfected miR-neg replicate9

description:
Replicate 9 of 12
pneg-rep9

source_name: transfected BJAB cells

value: transiently transfected with miR-neg

tag: time

value: 48 hr post-transfection


title: Multiple myeloma. Pair 4. Diagnosis. [gene expression]

tag: subject condition


title: transfected miR-neg replicate6

description:
Replicate 6 of 12
pneg-rep6


title: transfected miR-neg replicate7

description:
Replicate 7 of 12
pneg-rep7


title: transfected miR-neg replicate8

description:
Replicate 8 of 12
pneg-rep8


title: stable line miR-K1 to -K5 replicate1

description:
Replicate 1 of 2
s15-rep1


title: Multiple myeloma. Pair 3. Diagnosis. [gene expression]

value: pair 3

tag: cell type


title: Multiple myeloma. Pair 3. Relapse. [gene expression]

tag: sample pair id


title: Multiple myeloma. Pair 7. Relapse. [gene expression]

tag: patient status


title: Multiple myeloma. Pair 2. Relapse. [gene expression]

value: pair 2

tag: gender


title: Multiple myeloma. Pair 3. Relapse. [methylation]

tag: tissue

value: CD 138+ plasma cells

value: Input


title: transfected miR-neg replicate5

description:
Replicate 5 of 12
pneg-rep5

value: Pooled cell line RNA

value: BJAB


title: Multiple myeloma. Pair 3. Diagnosis. [methylation]

value: Bone marrow


title: transfected miR-neg replicate4

description:
Replicate 4 of 12
pneg-rep4


title: Multiple myeloma. Pair 4. Relapse. [methylation]

value: Male


title: transfected miR-neg replicate3

description:
Replicate 3 of 12
pneg-rep3


title: transfected miR-neg replicate2

description:
Replicate 2 of 12
pneg-rep2


title: Multiple myeloma. Pair 2. Diagnosis. [gene expression]

value: CD138+ plasma cells


title: Multiple myeloma. Pair 1. Relapse. [gene expression]

value: Multiple myeloma (MM) patient

value: pair 1


title: Multiple myeloma. Pair 1. Diagnosis. [gene expression]

value: diagnosis


title: Multiple myeloma. Pair 1. Diagnosis. [methylation]


title: transfected miR-neg replicate12

description:
Replicate 12 of 12
pneg-rep12


title: DUX4c - Mouse 3

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

institute: King's College London

description: Gene expression data with DUX4c-encoding retrovirus - Mouse 3

hyb_protocol: Biotinylated fragmented cDNA was hybridised to Mouse Gene 1.0- ST arrays (Affymetrix) according to manufacturer's protocols.

scan_protocol: Arrays were processed and scanned according to Affymetrix standard procedures.

data_processing: CEL files were normalised, background corrected and summarised using the RMA sketch algorithm in Expression Console software (Affymetrix).

source_name: myoblasts_DUX4c_mouse 3

label_protocol: RNA (215ng) was labelled using the WT Expression kit from Ambion.

growth_protocol: Primary murine satellite cell-derived myoblasts were derived from 3 mice and then expanded for 6 days.

extract_protocol: RNA was extracted using Trizol according to manufacturer's instructiuons.

treatment_protocol: Myoblasts were then divided into six sister cultures per mouse and each sister culture infected with a different construct and cultured for a further 20 hours.

tag: Sex

value: 6-8 weeks old

value: Satellite cell-derived myoblasts from hindlimb skeletal muscle

tag: mouse id

value: mouse 3

tag: construct


title: Constitutively Active DUX4-VP16 - Mouse 3

description: Gene expression data with constitutively active DUX4-VP16 encoding retrovirus - Mouse 3

source_name: myoblasts_Constitutively Active DUX4-VP16_mouse 3

tag: strain

value: Constitutively Active DUX4-VP16


title: transfected miR-neg replicate1

description:
Replicate 1 of 12
pneg-rep1

value: transiently transfected with miR-neg

value: 48 hr post-transfection


title: transfected miR-neg replicate10

description:
Replicate 10 of 12
pneg-rep10


title: Dominant-negative DUX4-ERD - Mouse 3

description: Gene expression data with Dominant-negative DUX4-ERD encoding retrovirus - Mouse 3

tag: age

value: Dominant-negative DUX4-ERD


title: transfected miR-neg replicate11

description:
Replicate 11 of 12
pneg-rep11

tag: reference


title: transfected miR-K9star replicate1

description:
Replicate 1 of 2
p9s-rep1

tag: cell line

value: transiently transfected with miR-K9star


title: Multiple myeloma. Pair 2. Relapse. [methylation]

value: pair 2

value: relapse

value: CD 138+ plasma cells

value: Input


title: transfected miR-K9star replicate2

description:
Replicate 2 of 2
p9s-rep2

value: Pooled cell line RNA

value: BJAB

tag: protocol


title: Multiple myeloma. Pair 5. Diagnosis. [methylation]

source_name: MM patient_diagnosis

value: Multiple myeloma (MM) patient

value: pair 5

value: Male

tag: age (yr)

value: Bone marrow


title: Truncated DUX4 - Mouse 3

description: Gene expression data with truncated DUX4-encoding retrovirus - Mouse 3

source_name: myoblasts_Truncated DUX4_mouse 3

value: 6-8 weeks old

value: Satellite cell-derived myoblasts from hindlimb skeletal muscle

value: Truncated DUX4


title: DUX4 - Mouse 3

description: Gene expression data with DUX4-encoding retrovirus Mouse 3

source_name: myoblasts_DUX4_mouse 3

value: mouse 3


title: Control RV - Mouse 3

description: Gene expression data with control retrovirus - Mouse 3

source_name: myoblasts_Control RV_mouse 3

value: Control RV


title: transfected miR-K8 replicate1

description:
Replicate 1 of 2
p8-rep1

value: transiently transfected with miR-K8

value: 48 hr post-transfection


title: transfected miR-K8 replicate2

description:
Replicate 2 of 2
p8-rep2


title: transfected miR-K7 replicate1

description:
Replicate 1 of 2
p7-rep1

value: transiently transfected with miR-K7


title: DUX4c - Mouse 2

description: Gene expression data with DUX4c-encoding retrovirus - Mouse 2

source_name: myoblasts_DUX4c_mouse 2

value: mouse 2


title: transfected miR-K7 replicate2

description:
Replicate 2 of 2
p7-rep2


title: Multiple myeloma. Pair 1. Relapse. [methylation]

value: pair 1

value: relapse

value: CD 138+ plasma cells

source_name: MM patient_relapse_input

tag: sample type


title: Constitutively Active DUX4-VP16 - Mouse 2

description: Gene expression data with constitutively active DUX4-VP16 encoding retrovirus - Mouse 2

source_name: myoblasts_Constitutively Active DUX4-VP16_mouse 2

value: Constitutively Active DUX4-VP16


title: Multiple myeloma. Pair 2. Diagnosis. [methylation]

value: Multiple myeloma (MM) patient

value: pair 2

value: diagnosis

source_name: MM patient_diagnosis_input

value: Input


title: transfected miR-K4-5 replicate1

description:
Replicate 1 of 2
p45-rep1

value: Pooled cell line RNA

value: BJAB

value: transiently transfected with miR-K4-5

tag: time


title: Dominant-negative DUX4-ERD - Mouse 2

description: Gene expression data with Dominant-negative DUX4-ERD encoding retrovirus - Mouse 2

value: Male

value: 6-8 weeks old

value: Satellite cell-derived myoblasts from hindlimb skeletal muscle

value: Dominant-negative DUX4-ERD


title: transfected miR-K4-5 replicate2

description:
Replicate 2 of 2
p45-rep2

value: 48 hr post-transfection


title: DUX4 - Mouse 2

description: Gene expression data with DUX4-encoding retrovirus - Mouse 2

source_name: myoblasts_DUX4_mouse 2

value: mouse 2


title: Control RV - Mouse 2

description: Gene expression data with control retrovirus - Mouse 2

source_name: myoblasts_Control RV_mouse 2

value: Control RV


title: Truncated DUX4 - Mouse 2

description: Gene expression data with truncated DUX4-encoding retrovirus - Mouse 2

source_name: myoblasts_Truncated DUX4_mouse 2

value: Truncated DUX4


title: transfected miR-K4-3 replicate1

description:
Replicate 1 of 2
p43-rep1

source_name: Stratagene Universal Reference RNA

value: transiently transfected with miR-K4-3


title: transfected miR-K4-3 replicate2

description:
Replicate 2 of 2
p43-rep2


title: transfected miR-K3star replicate2

description:
Replicate 2 of 2
p3s-rep2

value: transiently transfected with miR-K3star


title: Constitutively Active DUX4-VP16 - Mouse 1

description: Gene expression data with constitutively active DUX4-VP16 encoding retrovirus - Mouse 1

source_name: myoblasts_Constitutively Active DUX4-VP16_mouse 1

value: mouse 1

value: Constitutively Active DUX4-VP16


title: Dominant-negative DUX4-ERD - Mouse 1

description: Gene expression data with Dominant-negative DUX4-ERD encoding retrovirus - Mouse 1


title: transfected miR-K3star replicate1

description:
Replicate 1 of 2
p3s-rep1


title: Truncated DUX4 - Mouse 1

description: Gene expression data with truncated DUX4-encoding retrovirus - Mouse 1

source_name: myoblasts_Truncated DUX4_mouse 1


title: DUX4c - Mouse 1

description: Gene expression data with DUX4c-encoding retrovirus - Mouse 1

source_name: myoblasts_DUX4c_mouse 1


title: transfected miR-K6-3 replicate1

description:
Replicate 1 of 2
p63-rep1

source_name: transfected BJAB cells

value: transiently transfected with miR-K6-3


title: transfected miR-K6-3 replicate2

description:
Replicate 2 of 2
p63-rep2


title: non-segmental Vitiligo 7

city: Buffalo

first: Rama

last: Dey-Rao

state: NY

address: 6086 CTRC Bldg, 875 Ellicott Street

department: Dermatology

institute: University at Buffalo

description: Gene expression data from ns vitiligo patient blood

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Background Correction: GCRMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish, Probe filtering: skip, Probes to Import: Interrogating Probes. CEL files were imported in to Partek Genomic Suite v 6.6 (Partek, St. Louis, MO)

source_name: Vitiligo blood (PBMC)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Whole blood was drawn from vitiligo patients and healthy control subjects. Ficoll gradients (AmershamBiosciences) were used to extract peripheral blood mononuclear cells from collected blood. Specimen were immediately frozen at -80C for subsequent RNA extraction.

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

treatment_protocol: RNA was extracted using Trizol reagent  reagent (Invitrogen).

value: Whole blood

tag: disease state

value: Disease Vitiligo


title: transfected miR-K3 replicate2

description:
Replicate 2 of 2
p3-rep2

value: Pooled cell line RNA

value: BJAB

value: transiently transfected with miR-K3


title: non-segmental Vitiligo 8


title: DUX4 - Mouse 1

description: Gene expression data with DUX4-encoding retrovirus - Mouse 1

source_name: myoblasts_DUX4_mouse 1

value: Male

value: 6-8 weeks old

tag: cell type


title: transfected miR-K11 replicate1

description:
Replicate 1 of 2
p11-rep1

value: transiently transfected with miR-K11


title: non-segmental Vitiligo 5


title: transfected miR-K2 replicate1

description:
Replicate 1 of 2
p2-rep1

value: transiently transfected with miR-K2

value: 48 hr post-transfection


title: Control RV - Mouse 1

description: Gene expression data with control retrovirus - Mouse 1

source_name: myoblasts_Control RV_mouse 1

value: Satellite cell-derived myoblasts from hindlimb skeletal muscle

value: Control RV


title: transfected miR-K11 replicate2

description:
Replicate 2 of 2
p11-rep2


title: transfected miR-K3 replicate1

description:
Replicate 1 of 2
p3-rep1


title: non-segmental Vitiligo 4


title: Metastasis (FFPE) of Case 9

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

institute: Humanitas University

description: Metastasis (FFPE) of Case 9

hyb_protocol: According to manufacturer's instructions

data_processing: Affymetrix OncoScan Console

source_name: Metastasis (FFPE) of Case 9

extract_protocol: Genomic DNA for each sample was extracted using the DNeasy® Blood & Tissue Kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions, and subsequently quantified using the Qubit® 2.0 Fluorometer (Invitrogen, Life Technologies, Grand Island, NY).

tag: disease

value: Metastatic breast cancer


title: non-segmental Vitiligo 2


title: non-segmental Vitiligo 6


title: transfected miR-K10b replicate1

description:
Replicate 1 of 2
p10b-rep1

value: transiently transfected with miR-K10b


title: Primary (FFPE) of Case 9

description: Primary (FFPE) of Case 9

scan_protocol: According to manufacturer's instructions

source_name: Primary (FFPE) of Case 9


title: transfected miR-K2 replicate2

description:
Replicate 2 of 2
p2-rep2


title: Metastasis (FFPE) of Case 8

description: Metastasis (FFPE) of Case 8

source_name: Metastasis (FFPE) of Case 8

label_protocol: According to manufacturer's instructions


title: transfected miR-K1 replicate2

description:
Replicate 2 of 2
p1-rep2

value: transiently transfected with miR-K1


title: non-segmental Vitiligo 3


title: Primary (FFPE) of Case 8

description: Primary (FFPE) of Case 8

source_name: Primary (FFPE) of Case 8


title: Control 6

description: Gene expression data from normal healthy control blood

source_name: Control blood(PBMC)

value: Normal healthy


title: Control 5


title: Primary (FFPE) of Case 7

description: Primary (FFPE) of Case 7

source_name: Primary (FFPE) of Case 7


title: Metastasis (FFPE) of Case 7

description: Metastasis (FFPE) of Case 7

source_name: Metastasis (FFPE) of Case 7


title: Metastasis (FFPE) of Case 6

description: Metastasis (FFPE) of Case 6

source_name: Metastasis (FFPE) of Case 6


title: Control 4


title: transfected miR-K1 replicate1

description:
Replicate 1 of 2
p1-rep1


title: transfected anti-neg replicate3

description:
Replicate 1 of 3
aneg-rep3

source_name: transfected BCBL-1 cells

value: transiently transfected with anti-neg

value: 72 hr post-transfection


title: Control 3

value: Whole blood


title: transfected anti-neg replicate2

description:
Replicate 1 of 3
aneg-rep2

source_name: Stratagene Universal Reference RNA

value: Pooled cell line RNA


title: transfected anti-neg replicate1

description:
Replicate 1 of 3
aneg-rep1


title: transfected miR-K10b replicate2

description:
Replicate 2 of 2
p10b-rep2

value: BJAB


title: transfected anti-miR-K9star replicate1

description:
Replicate 1 of 1
a9s-rep1

value: transiently transfected with anti-miR-K9star


title: transfected anti-miR-K8 replicate1

description:
Replicate 1 of 1
a8-rep1

value: transiently transfected with anti-miR-K8


title: transfected anti-miR-K7 replicate1

description:
Replicate 1 of 1
a7-rep1

value: transiently transfected with anti-miR-K7


title: non-segmental Vitiligo 1

source_name: Vitiligo blood(PBMC)

value: Disease Vitiligo


title: Control 1


title: Metastasis (FFPE) of Case 5

description: Metastasis (FFPE) of Case 5

source_name: Metastasis (FFPE) of Case 5


title: Primary (FFPE) of Case 5

description: Primary (FFPE) of Case 5

source_name: Primary (FFPE) of Case 5


title: Primary (FFPE) of Case 4

description: Primary (FFPE) of Case 4

source_name: Primary (FFPE) of Case 4


title: 0GyM7/ reference male mouse3

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail

source_name: reference male mouse3


title: transfected anti-miR-K6-5 replicate1

description:
Replicate 1 of 1
a65-rep1

value: transiently transfected with anti-miR-K6-5


title: transfected anti-miR-K6-3 replicate1

description:
Replicate 1 of 1
a63-rep1

value: transiently transfected with anti-miR-K6-3


title: reference male mouse3/ 0GyM7

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: Metastasis (FFPE) of Case 1

description: Metastasis (FFPE) of Case 1

source_name: Metastasis (FFPE) of Case 1


title: Control 2


title: Primary (FFPE) of Case 1

description: Primary (FFPE) of Case 1

source_name: Primary (FFPE) of Case 1


title: transfected anti-miR-K4-5 replicate1

description:
Replicate 1 of 1
a45-rep1

value: transiently transfected with anti-miR-K4-5


title: transfected anti-miR-K4-3 replicate1

description:
Replicate 1 of 1
a43-rep1

value: transiently transfected with anti-miR-K4-3


title: transfected anti-miR-K3 replicate1

description:
Replicate 1 of 1
a3-rep1

value: transiently transfected with anti-miR-K3


title: Schistosomula 1 µM TSA 48h replicate 3

city: São Paulo

first: Leticia

last: Anderson

state: SP

address: Av. Vital Brasil, 1500

department: Parasitologia

country: Brazil

institute: Instituto Butantan

description:
Biological replicate 1 of 6
Somula_TSA_48h_rep3

hyb_protocol: Labeled samples (treated and control) were combined and hybridized on one 180K-elements custom oligoarray from a 4 x 180K elements slide produced by Agilent Technologies; hybridization and washing steps were performed according to Agilent instructions

scan_protocol: Slides were scanned with Agilent Scanner G2505C

data_processing: Image data was extracted using Feature Extraction software (Agilent Technologies) with the protocol GE2_107_Sep09. Spots with intensity lower than local background (IsPosAndSignif) were filtered out, and intensities were normalized applying trimmed mean (20% on each side). For each probe, the log2 ratio of treated sample/control sample was calculated and the SAM statistical test was applied.

organism: Schistosoma mansoni

source_name: Schistosomula treated with 1 µM Trichostatin A and kept in culture for 12 h.

label_protocol: All samples were labeled using Agilent Low Input Quick Amp Labeling Kit Two-color according to manufacturer´s instructions.

growth_protocol: Schistosomula were obtained from mechanical transformation of cercariae, released from the intermediate host Biomphalaria glabrata

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to manufacturer´s instructions.

treatment_protocol: Newly transformed schistosomula were exposed to 1 µM Trichostatin A and kept in culture for 12 h. Three independent biological replicates were assayed for each condition.

tag: developmental stage

value: Schistosomula

tag: exposed to

value: 1 µM Trichostatin A for 48h

source_name: Schistosomula treated with ethanol and kept in culture for 12 h.

value: vehicle solution (ethanol) for 48hrs


title: transfected anti-miR-K3star replicate1

description:
Replicate 1 of 1
a3s-rep1

value: transiently transfected with anti-miR-K3star

value: 72 hr post-transfection


title: transfected anti-miR-K2 replicate1

description:
Replicate 1 of 1
a2-rep1

value: Pooled cell line RNA

value: transiently transfected with anti-miR-K2


title: Schistosomula 1 µM TSA 48h replicate 3 swap

description:
Biological replicate 1 of 7
Somula_TSA_48h_rep3_swap


title: hepatocytes_BMP2_biological rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from hepatocytes after 24h BMP2 stimulation

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-1_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: hepatocytes after 24h BMP2 stimulation replicate 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Mouse hepatocytes were plated on collagen coated 6-well-plates at a density of 5 x105 cells/well in Williams' medium E supplemented with 10 % FBS, 2 mmol L-glutamine, 1 % penicillin/streptomycin and 100 nmol dexamethasone. After 4 hrs of incubation in 5 % CO2 at 37 oC to facilitate attachment, medium was replaced with serum-free Williams' medium E supplemented with 1 % penicillin/streptomycin, 2 mmol L-glutamine and 100 nmol dexamethasone. The next day, medium was changed to serum-free Williams' medium E supplemented with 2 mMol L-glutamine and 1% penicillin/streptomycin.

extract_protocol: Mouse hepatocytes from C57BL/6 mice were isolated as described by Ciuclan L et al, 2010.

treatment_protocol: Hepatocytes and LSEC were stimulated for 24 hours with or without 50ng/ml recombinant BMP-2. BMP2 was reconstituted in 4 mM HCL.

tag: tissue

value: primary hepatocytes


title: hepatocytes_control_biological rep3

description: Gene expression data from control hepatocytes

source_name: control hepatocytes replicate 3


title: reference male mouse3/ 0GyM6


title: transfected anti-miR-K10b replicate1

description:
Replicate 1 of 1
a10b-rep1

value: transiently transfected with anti-miR-K10b


title: 0GyM5/ reference male mouse3


title: Schistosomula 1 µM TSA 48h replicate 1 swap

description:
Biological replicate 1 of 3
Somula_TSA_48h_rep1_swap


title: 0GyM6/ reference male mouse3


title: transfected anti-miR-K1 replicate1

description:
Replicate 1 of 1
a1-rep1

value: transiently transfected with anti-miR-K1


title: hepatocytes_control_biological rep2

source_name: control hepatocytes replicate 2


title: Schistosomula 1 µM TSA 48h replicate 1

description:
Biological replicate 1 of 3
Somula_TSA_48h_rep1


title: transfected anti-miR-K11 replicate1

description:
Replicate 1 of 1
a11-rep1

value: transiently transfected with anti-miR-K11


title: Schistosomula 1 µM TSA 48h replicate 2 swap

description:
Biological replicate 2 of 3
Somula_TSA_48h_rep2_swap


title: reference male mouse3/ 0GyM5

value: tail


title: hepatocytes_BMP2_biological rep3

source_name: hepatocytes after 24h BMP2 stimulation replicate 3


title: reference male mouse3/ 0GyM3


title: Schistosomula 1 µM TSA 24h replicate 3 swap

description: Biological replicate 1 of 7

value: 1 µM Trichostatin A for 24h

value: vehicle solution (ethanol) for 24hrs


title: hepatocytes_BMP2_biological rep1

source_name: hepatocytes after 24h BMP2 stimulation replicate 1


title: Schistosomula 1 µM TSA 24h replicate 3

description: Biological replicate 1 of 6


title: 0GyM4/ reference male mouse3


title: reference male mouse3/ 0GyM4


title: Schistosomula 1 µM TSA 48h replicate 2

description:
Biological replicate 2 of 3
Somula_TSA_48h_rep2


title: 0GyM3/ reference male mouse3


title: 0GyM2/ reference male mouse3


title: reference male mouse3/ 0GyM2


title: Elder with Sepsis_2

first: Eduardo

middle: Moraes

last: Reis

address: Av. Prof. Lineu Prestes, 748

institute: University of São Paulo

hyb_protocol: Agilent Gene Expression Hybridization Kit were used and samples were applied to microarrays enclosed in Agilent Microarray Hybridization Chamber. After hybridization, slides were washed sequentially.

scan_protocol: Slides were read on a SureScan Microarray Scanner (Agilent, USA).

data_processing: Images were processed using the Feature Extraction Software v12 (Agilent, USA) for quality control, determination of feature intensities and ratios, and for background correction. The flag IsWellAboveBG in the FE output was used to select probes whose intensity were within a 99% confidence interval of being well above the background levels. 16698 out of 58717 probes with valid Well Above Background flag in both Cy3 and Cy5 channels in at least 5 out of 6 replicates of at least one group (elderly sepsis, elderly healthy, adult sepsis, adult healthy) were further analyzed.

source_name: Elder with Sepsis

label_protocol: 200 ng of total RNA were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit following manufacturer's instructions

growth_protocol: Neutrophils were isolated from blood samples immediately after the collection using a Ficoll gradient and stored at −80°C.

extract_protocol: Total RNA was isolated using Trizol reagent (Life Technologies, Carlsbad, CA, USA) following the manufacturer’s protocol.

value: Sepsis

tag: developmental state

value: elder

value: neutrophil granulocytes

source_name: common reference RNA pool

value: reference (Universal Human Reference RNA, Agilent, cat #740000)


title: hepatocytes_control_biological rep1

source_name: control hepatocytes replicate 1


title: Schistosomula 1 µM TSA 24h replicate 2 swap

description: Biological replicate 2 of 3

value: Schistosomula


title: 0GyM1/ reference male mouse3


title: 0GyN5/ reference male mouse3


title: 0GyN6/ reference male mouse3


title: Healthy Elder_6

source_name: Healthy Elder

value: Healthy


title: Elder with Sepsis_1


title: 0GyN4/ reference male mouse3


title: Schistosomula 1 µM TSA 24h replicate 1

description: Biological replicate 1 of 3


title: reference male mouse3/ 0GyN6


title: Healthy Elder_4


title: Schistosomula 1 µM TSA 12h replicate 3 swap

description:
Biological replicate 1 of 7
Somula_TSA_12h_rep3_swap

value: 1 µM Trichostatin A for 12h

value: vehicle solution (ethanol) for 12hrs


title: Schistosomula 1 µM TSA 24h replicate 1 swap

description: Biological replicate 1 of 3


title: reference male mouse3/ 0GyN5


title: Healthy Elder_1


title: Schistosomula 1 µM TSA 12h replicate 3

description:
Biological replicate 1 of 6
Somula_TSA_12h_rep3


title: Schistosomula 1 µM TSA 24h replicate 2

description: Biological replicate 2 of 3


title: Healthy Elder_5


title: reference male mouse3/ 0GyM1


title: 0GyMM/ reference male mouse3


title: Schistosomula 1 µM TSA 12h replicate 2

description:
Biological replicate 2 of 3
Somula_TSA_12h_rep2


title: Healthy Elder_3


title: reference male mouse3/ 0GyN4


title: Schistosomula 1 µM TSA 12h replicate 2 swap

description:
Biological replicate 2 of 3
Somula_TSA_12h_rep2_swap


title: reference male mouse3/ 0GyMM


title: reference male mouse4/ 0GyK7

source_name: reference male mouse4


title: reference male mouse3/ 0GyMF


title: 0GyMF/ reference male mouse3


title: Adult with Sepsis_6

source_name: Adult with Sepsis

value: adult


title: reference male mouse3/ 0GyN3


title: Adult with Sepsis_5


title: Schistosomula 1 µM TSA 12h replicate 1 swap

description:
Biological replicate 1 of 3
Somula_TSA_12h_rep1_swap


title: 0GyK6/ reference male mouse4


title: 0GyN2/ reference male mouse3


title: 0GyK7/ reference male mouse4


title: Healthy Elder_2


title: Adult with Sepsis_3


title: reference male mouse3/ 0GyN2


title: 0GyN1/ reference male mouse3


title: Adult with Sepsis_4


title: reference male mouse3/ 0GyN1


title: 0GyNF/ reference male mouse3


title: Adult with Sepsis_1


title: Schistosomula 1 µM TSA 12h replicate 1

description:
Biological replicate 1 of 3
Somula_TSA_12h_rep1


title: reference male mouse4/ 0GyK6


title: 0GyJ4/ reference male mouse4


title: reference male mouse4/ 0GyK5


title: 0GyJ5/ reference male mouse4


title: Adult with Sepsis_2


title: 0GyJ3/ reference male mouse4


title: Healthy Adult_5

source_name: Healthy Adult


title: reference male mouse4/ 0GyK4


title: Healthy Adult_6


title: 0GyNM/ reference male mouse3

source_name: reference male mouse3


title: reference male mouse3/ 0GyNF


title: 0GyK4/ reference male mouse4


title: 0GyK3/ reference male mouse4


title: reference male mouse4/ 0GyK3


title: reference male mouse4/ 0GyJ5


title: Healthy Adult_4


title: reference male mouse3/ 0GyNM


title: reference male mouse4/ 0GyJ3


title: Healthy Adult_2


title: Healthy Adult_3


title: 0GyJ2/ reference male mouse4


title: Elder with Sepsis_6


title: 0GyK2/ reference male mouse4


title: Elder with Sepsis_5


title: reference male mouse4/ 0GyJ2


title: 0GyKF/ reference male mouse4


title: reference male mouse4/ 0GyK2


title: 0GyK1/ reference male mouse4


title: 0GyJ1/ reference male mouse4


title: reference male mouse4/ 0GyK1


title: Healthy Adult_1


title: reference male mouse4/ 0GyJ1


title: Elder with Sepsis_4


title: Elder with Sepsis_3


title: 0GyN3/ reference male mouse3


title: 0GyKM/ reference male mouse4


title: 0GyJM/ reference male mouse4


title: 0GyJF/ reference male mouse4


title: reference male mouse4/ 0GyJM


title: reference male mouse4/ 0GyJF


title: reference male mouse4/ 0GyKF


title: Karpas_EED226144hr_1

status: Public on Jan 30 2017

city: Shanghai

first: Vicky

last: Qi

address: No. 4218 Jinke Road

country: China

institute: China Novartis Institutes for BioMedical Research Co., Ltd

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit

scan_protocol: GeneChip Scanner 3000

data_processing: R/Bioconductor, RMA

label_protocol: GeneChip 3'IVT Express Kit

growth_protocol: cultured in RPMI-1640 (Invitrogen, 11875) with 15% (vol/vol) FBS (Invitrogen, 10099-141)

extract_protocol: TRIZOL

treatment_protocol: Karpas422 after 1, 2, 3, and 6 days after DMSO, EI1 or EED226 (5 _M) treatment

value: lymphoma


title: Karpas_EED226144hr_2


title: Karpas_EED22648hr_3


title: Karpas_EED226144hr_3


title: Karpas_EED22624hr_3


title: Karpas_EED22648hr_2


title: Karpas_EED22672hr_3


title: Karpas_EED22648hr_1


title: 0GyK5/ reference male mouse4


title: Karpas_EED22624hr_1


title: Karpas_DMSO144hr_1


title: Karpas_DMSO144hr_2


title: Karpas_EED2268hr_2


title: Karpas_EED22624hr_2


title: Karpas_EED2268hr_3


title: Karpas_EED22672hr_1


title: Karpas_DMSO72hr_1


title: Karpas_EED22672hr_2


title: Karpas_DMSO144hr_3


title: reference male mouse4/ 0GyJ4


title: Karpas_DMSO72hr_3


title: miRNA_TLT-C-092-TT

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

description:
HB
High-quality miRNA samples were profiled using Agilent human miRNA v13 Rev2 (8x15K) arrays

hyb_protocol: Agilent human miRNA v13 Rev2 (8x15K) arrays, Agilent miRNA Microarray System v2.2

scan_protocol: Agilent G2505C Microarray Scanner w/SureScan High Resolution Technology

data_processing: Probes were extracted with Agilent’s Feature Extraction software v10.7 to attain the expression levels of 866 human and 89 human viral miRNAs. Data collected from both of these array profiles was analyzed using the Agilent Genomic Workbench Software and Partek Genomics Suite 6.x

label: As per Agilent

source_name: Hepatoblastoma

label_protocol: As per Agilent miRNA Microarray System

extract_protocol: mirVana miRNA Isolation Kit (Ambion)

value: Hepatoblastoma

tag: age (yrs)

tag: Sex

value: F

tag: race

value: Caucasian

tag: histology

value: Epithelial, embryonal and small cell (minor)


title: miRNA_TLT-C-093-TT

value: Epithelial, embryonal and  small cell (minor)


title: Karpas_DMSO48hr_1


title: Karpas_DMSO72hr_2


title: Karpas_EED2268hr_1


title: Karpas_DMSO24hr_1


title: miRNA_TLT-C-089-TT

value: Hispanic

value: Epithelial hepatoblastoma


title: Karpas_DMSO48hr_2


title: Karpas_DMSO8hr_2


title: Karpas_DMSO48hr_3


title: Karpas_0hr_3


title: Karpas_DMSO24hr_3


title: Karpas_DMSO24hr_2


title: Karpas_DMSO8hr_1


title: Karpas_0hr_2


title: miRNA_TLT-C-085-TT

value: M

tag: Stage


title: miRNA_TLT-C-091-TT

value: Epithelial, embryonal, nesting pattern (small cell)


title: Karpas_DMSO8hr_3

tag: cell line


title: miRNA_TLT-C-087-TT


title: Karpas_0hr_1


title: miRNA_TLT-C-086-TT

value: African American

value: Epithelial hepatoblastoma, fetal


title: miRNA_TLT-C-079-TT

value: Epithelial hepatoblastoma, embryonal and fetal


title: miRNA_TLT-C-083-TT

value: Normal liver


title: miRNA_TLT-C-084-TT

value: Epithelial hepatoblastoma, embryonal


title: miRNA_TLT-C-080-TT

value: Epithelial hepatoblastoma, crowded fetal


title: miRNA_TLT-C-081-TT


title: miRNA_TLT-C-082-TT

value: Epithelial hepatoblastoma, mitotically active fetal


title: miRNA_TLT-C-077-TT

value: Other

value: Epithelial hepatoblastoma, fetal, well differentiated


title: miRNA_TLT-C-075-TT

value: Hepatoblastoma

value: F

value: Asian

value: Epithelial hepatoblastoma, embryonal and fetal


title: miRNA_TLT-C-078-TT

value: Caucasian


title: miRNA_TLT-C-074-TT


title: miRNA_TLT-C-070-TT

value: Hispanic


title: miRNA_TLT-C-066-TT

value: M

value: Epitthelial hepatoblastoma, embryonal and blastemal


title: miRNA_TLT-C-065-TT

value: Epithelial hepatoblastoma, fetal and embryonal


title: miRNA_TLT-C-068-TT

value: Unknown


title: miRNA_TLT-C-063-TT


title: miRNA_TLT-C-064-TT

value: Epithelial hepatoblastoma, fetal


title: miRNA_TLT-C-053-TT

value: Mixed epithelial and mesenchymal, fetal (60%), embryonal (20%), stromal (10%), blastema (5%) and small cell (2%)


title: miRNA_TLT-C-060-TT

value: Epithelial hepatoblastoma, embryonal


title: miRNA_TLT-C-058-TT

value: Epithelial, hepatoblastoma embryonal, fetal, some anaplastia, telangiectatic


title: miRNA_TLT-C-052-LV

description:
NL
High-quality miRNA samples were profiled using Agilent human miRNA v13 Rev2 (8x15K) arrays

value: Normal liver


title: miRNA_TLT-C-048-TT

value: Other

value: Epithelial hepatoblastoma , embryonal


title: miRNA_TLT-C-050-TT

value: Hepatoblastoma

value: Epithelial hepatoblastoma, fetal, embryonal with rare small cell


title: miRNA_TLT-C-049-TT

value: African American

value: Epithelial hepatoblastoma, embryonal, fetal and 15-20% small cell


title: miRNA_TLT-C-047-LV

source_name: Normal liver

value: Caucasian

value: Epithelial hepatoblastoma, fetal (50%) and embryonal (50%)


title: miRNA_TLT-C-048-LV

value: M


title: miRNA_TLT-C-046-TT

value: F

value: Epithelial hepatoblastoma, mostly embryonal, nesting


title: miRNA_TLT-C-042-TT

value: Asian

value: Epithelial hepatoblastoma, embryonal (65%) and fetal (15%)


title: miRNA_TLT-P-038-TT

value: Hispanic

value: Epithelial hepatoblastoma, embryonal and fetal


title: miRNA_TLT-C-043-TT

value: Epithelial hepatoblastoma, pure fetal


title: miRNA_TLT-C-040-TT

value: Epithelial hepatoblastoma, fetal (20%), embryonal (70%) and small cell (10%)


title: miRNA_TLT-C-041-LV

value: Normal liver

value: Epithelial hepatoblastoma, fetal (50%), embryonal (10%) and small cell (5%)


title: miRNA_TLT-P-039-TT

value: Hepatoblastoma


title: miRNA_TLT-P-035-TT

value: Epithelial hepatoblastoma,  fetal and embryonal


title: miRNA_TLT-P-031-TT

value: Epithelial hepatoblastoma, mitotically active fetal


title: miRNA_TLT-P-034-TT

value: Epithelial hepatoblastoma, predominantely embryonal and fetal


title: miRNA_TLT-P-028-TT

value: Caucasian

value: Epithelial hepatoblastoma, predominately embryonal


title: miRNA_TLT-C-052-TT

value: M

value: Epithelial hepatoblastoma, fetal (70%), embryonal (10%), small cell (20%)


title: miRNA_TLT-C-062-TT

value: F

value: Epithelial hepatoblastoma, embryonal


title: miRNA_TLT-P-023-TT


title: miRNA_TLT-C-088-TT

value: Epithelial, embryonal, fetal, minor small cell


title: miRNA_TLT-P-024-TT

value: Mixed epithelial and mesenchymal hepatoblastoma


title: miRNA_TLT-P-027-TT

value: Epithelial hepatoblastoma, mixed fetal and small cell


title: miRNA_TLT-P-020-TT

value: Asian

value: Epithelial hepatoblastoma, fetal


title: miRNA_TLT-D-009-LV

value: Normal liver


title: miRNA_TLT-S-010-TT

value: Epithelial hepatoblastoma, fetal and embryonal


title: miRNA_TLT-P-016-TT

value: Hepatoblastoma

value: Epithelial hepatoblastoma, embryonal, fetal and minor small cell


title: miRNA_TLT-P-013-TT

value: Hispanic

value: Well differentiated pure fetal hepatoblastoma; lack of mitotic activity


title: miRNA_TLT-P-020-LV


title: miRNA_TLT-P-021-TT

value: Other

value: Mixed hepatoblastoma, predominately epithelial (fetal and embryonal), small area of osteoid


title: miRNA_TLT-D-009-TT

value: Caucasian

value: Hepatocellular neoplasm, NOS


title: miRNA_TLT-P-036-TT

value: F

value: Epithelial hepatoblastoma


title: miRNA_TLT-P-004-TT

value: M


title: miRNA_TLT-P-003-LV

value: Epithelial hepatoblastoma mitotically active fetal and embryonal


title: reference male mouse4/ 0GyKM

tag: strain

value: tail


title: miRNA_TLT-P-003-TT


title: miRNA_TLT-D-001-LV


title: miRNA_TLT-D-001-TT

value: Epithelial hepatoblastoma, fetal, embryonal and minor small cell


title: miRNA_TLT-P-011-TT

value: Epithelial hepatoblastoma predominantly fetal and embryonal


title: miRNA_TLT-S-008-TT

value: Epithelial hepatoblastoma, embryonal and small cell


title: 515_lcl-trisomy21

city: Atlanta

first: Benjamin

last: Rambo-Martin

state: Georgia

address: 1600 Clifton Road

institute: Centers for Disease Contol and Prevention

description: Custom Agilent 8x60k targeting chr21

hyb_protocol: Default: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells or Tissues with Covaris sonicated fracturing.  Version 6.3 - October 2010

scan_protocol: Default: Agilent SureScan High-Resolution Microarray Scanner

data_processing: Default: Agilent Feature Extraction Software version 10.7

extract_protocol: Genomic DNA extraction protocol not provided.

value: female

tag: ethnicity

tag: omim

source_name: lcl-trisomy21_reference individual


title: 522_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21

label_protocol: Default: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells or Tissues with Covaris sonicated fracturing.  Version 6.3 - October 2010

value: male


title: 513_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 508_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 510_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 520_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 512_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 514_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 523_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 519_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 524_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 505_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 517_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 506_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 526_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 516_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 518_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 525_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 509_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 504_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 501_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 507_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 502_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 500_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 498_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 503_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 511_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 521_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 499_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 497_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 496_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 495_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 491_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 490_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 486_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 487_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 488_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 485_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 489_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 492_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 494_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 479_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 478_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 480_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 475_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 483_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 481_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 493_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 477_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 482_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 473_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 484_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 470_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 469_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 476_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 474_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 465_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 471_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 472_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 467_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 468_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 466_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 459_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 462_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 458_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 464_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 461_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 454_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 455_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 457_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 463_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 451_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 460_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 446_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 447_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 453_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 452_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 456_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 450_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 442_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 443_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 441_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 435_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 436_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 438_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 448_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 445_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 449_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 440_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 439_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 437_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 444_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 432_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 433_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 429_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 434_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 431_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21


title: 422_lcl-trisomy21

description: Custom Agilent 8x60k targeting chr21