title: LASV_D4_6_Z-132

tag: cell type

value: PBMC

tag: infection

value: LASV Z-132

tag: age


title: Pediatric LGG 115

status: Public on Aug 29 2014

type: RNA

city: Boston

first: Rameen

last: Beroukhim

state: MA

address: 450 Brookline Av

department: Cancer Biology

country: USA

institute: DANA-FARBER CANCER INSTITUTE

hyb_protocol: Refer to the Illumina beadarray Assay System

data_processing: Data were extracted and normalized using cubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern).

label: Cy3 and Cy5

molecule: total RNA

organism: Homo sapiens

source_name: FFPE pediatric low-grade gliomas (PLGG)

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from FFPE blocks

tag: tissue

value: low-grade glioma

value: CHILD

tag: location

value: SUP

tag: histology

value: PA

tag: braf status

value: DUP

tag: primary (p) or recurrent tumor

value: P

tag: primary tumor that further progressed


title: LASV_D7_1_Josiah

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K rhesus macaque array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the using the ‘normalizeBetweenArrays’ normalization method available in the ‘limma’ package of the R suite.

organism: Macaca fascicularis

source_name: virus, day post-infection, replicate, virus strain

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: 3 adult cynomolgus macaques (Macaca fascicularis) aged 3-7 years were infected under anesthesia with 10e4 PFU LASV or LUJV by intramuscular inoculation.  PBMC were collected on days 1, 4, 7, 10, 13 and 29 (for surviving LUJV-infected animals) post-infection.  Additionally, PBMC were collected from 3 uninfected animals for use as a control.

extract_protocol: Samples were thawed and diluted with 2 volumes RLT buffer, and then adjusted to a 1:1 ratio with 70% ethanol.  All extractions were performed using Qiagen RNeasy Micro columns with the manufacturer's recommended protocol.  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the picochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: PBMC were isolated by Ficoll density gradient centrifugation, washed in PBS, preserved in 0.5 mL AVL buffer diluted 1:1 with 70% ethanol, and stored at -80ºC prior to further processing.

value: LASV Josiah

tag: time


title: LASV_D4_9_Soromba

value: LASV Soromba


title: Pediatric LGG 114

scan_protocol: Refer to the Illumina beadarray Assay System

value: ADO

value: DNT

value: WT


title: 98_27_substantia nigra

city: London

first: Mina

last: Ryten

address: Queen Square

department: Department of Molecular Neuroscience

country: United Kingdom

institute: UCL Institute of Neurology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Data were processed using Affymetrix Power Tools 1.14.3. Arrays were pre-processed using RMA quantile normalization with background correction. Gene level summary signals were generated by calculating the Winsorized mean (10% and 90%) of all probe sets annotated to a transcript.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: Core_adapted_from_netaffyx31
Transcript assignments are based on genome build hg19
Core exons only are included in this analysis

label: biotin

source_name: post-mortem brain tissue, individual ID 98_27, substantia nigra

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal labelling kit (Affymetrix).

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, UK). cDNA synthesis and amplification were performed using the Ambion┬«WT Expression Kit (Ambion, UK).

treatment_protocol: Not applicable.

tag: individual id

tag: brain region

value: substantia nigra

tag: disease status

value: neurologically and neuropathologically normal

tag: brain bank

value: Sun Health Research Institute

tag: Cause of death

value: cerebrovascular accident

tag: Sex

value: Male

tag: age at death (in years)

tag: post-mortem interval (in hours)

tag: ancestry

value: European

tag: brain ph

tag: rin


title: LASV_D4_7_Soromba

tag: cell type

value: PBMC

tag: infection

tag: age


title: LASV_D4_4_Z-132

value: LASV Z-132


title: 95_21_substantia nigra

source_name: post-mortem brain tissue, individual ID 95_21, substantia nigra


title: 98_27_temporal cortex

source_name: post-mortem brain tissue, individual ID 98_27, temporal cortex

value: temporal cortex


title: 96_03_temporal cortex

source_name: post-mortem brain tissue, individual ID 96_03, temporal cortex


title: 96_03_substantia nigra

source_name: post-mortem brain tissue, individual ID 96_03, substantia nigra


title: 02_06_putamen

source_name: post-mortem brain tissue, individual ID 02_06, putamen

value: putamen

value: Female


title: LASV_D4_5_Z-132


title: 96_03_putamen

source_name: post-mortem brain tissue, individual ID 96_03, putamen


title: Pediatric LGG 112

label_protocol: Refer to the Illumina beadarray Assay System

tag: tissue

value: low-grade glioma

value: CHILD

tag: location

value: SUP

tag: histology

value: NOS

tag: braf status

value: MUT

tag: primary (p) or recurrent tumor

value: P


title: Pediatric LGG 113

extract_protocol: Refer to the Illumina beadarray Assay System

value: ADO

value: DNT

value: WT

tag: primary tumor that further progressed


title: Pediatric LGG 110

value: GG

value: R


title: Pediatric LGG 107

value: INF

value: PA

value: DUP


title: Pediatric LGG 109


title: LASV_D13_8_Soromba

value: PBMC

value: LASV Soromba

tag: time


title: LASV_D4_2_Josiah

value: LASV Josiah


title: Pediatric LGG 108

value: low-grade glioma


title: LASV_D4_1_Josiah


title: LASV_D13_9_Soromba


title: 98_27_putamen

source_name: post-mortem brain tissue, individual ID 98_27, putamen

tag: individual id

tag: brain region

value: putamen

tag: disease status

value: neurologically and neuropathologically normal

tag: brain bank

value: Sun Health Research Institute

tag: Cause of death

value: cerebrovascular accident

value: Male

value: European


title: Pediatric LGG 106

value: ADO

value: SUP

value: P


title: Pediatric LGG 105


title: LASV_D4_3_Josiah


title: Pediatric LGG 104

value: CHILD


title: 98_27_hippocampus

source_name: post-mortem brain tissue, individual ID 98_27, hippocampus

value: hippocampus

tag: Sex

tag: age at death (in years)

tag: post-mortem interval (in hours)

tag: ancestry

tag: brain ph


title: LASV_D13_6_Z-132

tag: cell type

tag: infection

value: LASV Z-132

tag: age


title: Pediatric LGG 103

tag: tissue

tag: location

tag: histology

value: GG

tag: braf status

value: WT


title: Pediatric LGG 102

value: DNT

tag: primary (p) or recurrent tumor

tag: primary tumor that further progressed


title: 98_27_occipital cortex

source_name: post-mortem brain tissue, individual ID 98_27, occipital cortex

tag: individual id

tag: brain region

value: occipital cortex

tag: disease status

tag: rin


title: 96_03_occipital cortex

source_name: post-mortem brain tissue, individual ID 96_03, occipital cortex

tag: brain bank

tag: Cause of death

tag: Sex

tag: age at death (in years)


title: LASV_D10_9_Soromba

tag: cell type

value: PBMC

value: LASV Soromba

tag: time


title: LASV_D13_7_Soromba

tag: infection

tag: age


title: 02_06_occipital cortex

source_name: post-mortem brain tissue, individual ID 02_06, occipital cortex

value: neurologically and neuropathologically normal

value: Female

tag: post-mortem interval (in hours)

tag: ancestry

tag: brain ph


title: 96_03_medulla

source_name: post-mortem brain tissue, individual ID 96_03, medulla

value: medulla

value: Sun Health Research Institute

value: cerebrovascular accident


title: Pediatric LGG 101

tag: tissue

value: low-grade glioma

tag: location

value: INF

tag: histology

value: NOS

tag: braf status

value: DUP

tag: primary (p) or recurrent tumor


title: 98_27_medulla

source_name: post-mortem brain tissue, individual ID 98_27, medulla

tag: individual id

tag: brain region

tag: disease status

value: Male

value: European

tag: rin


title: Pediatric LGG 100

value: ADO

value: PA

value: P

tag: primary tumor that further progressed


title: LASV_D10_4_Z-132

tag: cell type

value: LASV Z-132


title: Pediatric LGG 99

value: CHILD


title: 95_21_hippocampus

source_name: post-mortem brain tissue, individual ID 95_21, hippocampus

value: hippocampus

tag: brain bank

tag: Cause of death

tag: Sex

tag: age at death (in years)


title: Pediatric LGG 98

source_name: FFPE pediatric low-grade gliomas (PLGG)

tag: age


title: 95_21_frontal cortex

source_name: post-mortem brain tissue, individual ID 95_21, frontal cortex

value: frontal cortex

value: neurologically and neuropathologically normal

tag: post-mortem interval (in hours)

tag: ancestry

tag: brain ph


title: 96_03_frontal cortex

source_name: post-mortem brain tissue, individual ID 96_03, frontal cortex


title: Pediatric LGG 96

tag: tissue

tag: location

tag: histology

value: R


title: Pediatric LGG 97

value: SUP

tag: braf status

tag: primary (p) or recurrent tumor


title: Pediatric LGG 95

value: OD

value: ND


title: LASV_D10_2_Josiah

source_name: virus, day post-infection, replicate, virus strain

value: PBMC

tag: infection

value: LASV Josiah

tag: time


title: LASV_D10_8_Soromba

value: LASV Soromba


title: Pediatric LGG 94

value: low-grade glioma

value: INF

value: WT

tag: primary tumor that further progressed


title: LASV_D1_9_Soromba

tag: cell type


title: LASV_D10_5_Z-132


title: 98_27_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 98_27, cerebellar cortex

tag: individual id

tag: brain region

value: cerebellar cortex

tag: disease status

tag: brain bank

value: Sun Health Research Institute

value: cerebrovascular accident

value: Male

value: European

tag: rin


title: 98_27_frontal cortex

source_name: post-mortem brain tissue, individual ID 98_27, frontal cortex

value: frontal cortex

tag: Cause of death

tag: Sex

tag: age at death (in years)

tag: post-mortem interval (in hours)


title: LASV_D10_3_Josiah

tag: age


title: Pediatric LGG 93

tag: tissue

value: CHILD

tag: location

tag: histology

value: PA

value: DUP

value: P


title: LASV_D10_1_Josiah

tag: infection


title: 02_06_frontal cortex

source_name: post-mortem brain tissue, individual ID 02_06, frontal cortex

value: neurologically and neuropathologically normal

value: Female

tag: ancestry

tag: brain ph


title: 95_21_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 95_21, cerebellar cortex


title: LASV_D1_7_Soromba

tag: cell type

value: PBMC

tag: time


title: LASV_D1_6_Z-132

value: LASV Z-132


title: Pediatric LGG 90

value: low-grade glioma

value: ADO

tag: braf status

tag: primary (p) or recurrent tumor

tag: primary tumor that further progressed


title: Pediatric LGG 92

value: INF


title: Pediatric LGG 91

value: SUP

value: R


title: LASV_D1_8_Soromba

value: LASV Soromba


title: 96_03_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 96_03, cerebellar cortex

tag: individual id

tag: brain region

value: cerebellar cortex

tag: disease status

tag: brain bank

value: Sun Health Research Institute

value: cerebrovascular accident

value: Male

tag: rin


title: Pediatric LGG 86

tag: age

value: CHILD

value: PA

value: WT


title: LASV_D1_5_Z-132


title: Pediatric LGG 89

tag: tissue

value: ND

value: P


title: Pediatric LGG 87

tag: location

value: DA

value: MUT


title: LASV_D1_4_Z-132

value: PBMC

value: LASV Z-132


title: Pediatric LGG 88

value: low-grade glioma

value: INF

tag: histology

value: DUP


title: 02_06_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 02_06, cerebellar cortex

value: neurologically and neuropathologically normal

tag: Cause of death

tag: Sex

value: Female

tag: age at death (in years)

tag: post-mortem interval (in hours)

value: European


title: LASV_D1_3_Josiah

tag: cell type

tag: infection

value: LASV Josiah

tag: time


title: LASV_D1_2_Josiah


title: Pediatric LGG 85

tag: braf status

tag: primary (p) or recurrent tumor

tag: primary tumor that further progressed


title: LASV_D10_6_Z-132


title: Pediatric LGG 84

value: ADO

value: SUP

value: R


title: LASV_D1_1_Josiah


title: Liver_mouse_PB_2500ppm_38

city: Osaka

first: Kayo

last: Sumida

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

department: Environmental Health Science Laboratory

country: Japan

institute: Sumitomo Chemical Co., Ltd.

description: Gene expression after 7 days of administration

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: Liver, 7days, 2500ppm, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling kit, one-color (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-2000 Spectrophotometer.

extract_protocol: Total RNA was prepared using the Isogen solution (Nippon Gene, Tokyo, Japan) and RNeasy Mini Kits (QIAGEN, Valencia, CA) from liver following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).

treatment_protocol: Male CD-1 mice were fed diets containing 0 (control) or 2500 ppm NaPB for 7 days. Liver samples were used for gene expression analysis.

tag: background strain

value: Liver

tag: gender

value: male


title: Control volunteer [87C_81_1_2]

city: Leon

first: Octavio

middle: Miguel

last: Rivero-Lezcano

state: Leon

address: Altos de Nava, s/n

department: Unidad de Investigación

country: Spain

institute: Hospital de Leon

hyb_protocol: 1.65 ng of labeled cRNA was hybridized with Whole Human Genome Microarray 4x44K v2 (Design ID: 026652) containing 41,000+ unique human genes and transcripts.

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol and data extracted using Agilent Feature Extraction Software 10.7.1.1 following the Agilent protocol GE1-107_Sep09.

data_processing: The microarrays data analysis was performed by using GeneSpring GX 11.0 software. The original data was cleansed and normalized using an algorithm consisting in three steps: background correction, p75 normalization and expression calculation. Subsequent to log2 transformation, baseline transformation of the data was performed using the median of control samples. Before statistical analyses all microarrays were subjected to quality analysis, assessed on Principal Component analysis (PCA) plots and BoxWhisker Plot and filtering criteria. Entities were filtered based on their flag values and their signal intensity values.  Student´s t test unpaired was used to identify genes differentially expressed between different groups at the level of significance p < 0.05 applying the Westfall and Young permutation multiple testing corrections post-hoc method.

source_name: Control volunteer_M.tuberculosis infected monocytes

label_protocol: According to the ‘One-Color Microarray-Based Gene Expression Analysis’ protocol Version 5.7 (Agilent p/n 4140-90040), 100 ng of purified total RNA were used to produce Cyanine 3-CTP-labeled cRNA using the Quick Amp Labeling kit (Agilent p/n 5190-0442). Following cRNA was purified with the RNeasy MinElute Cleanup kit (QIAGEN). RNA was eluted with 30 microliter of RNasefree H2O.

growth_protocol: 100,000 CD14+ cells (monocytes) per well were cultivated in 24 wells plates in 400 ml of RPMI-1640 with 10% autologous serum. Cells were incubated at 37C in an humified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from 2 - 4 wells of infected cells with a commercial kit from Biotools B&M Labs (Total RNA Extraction Kit). The protocol includes an on-column DNAse digestion. In the final step RNA was eluted in 100 ml RNAse free water and concentrated with centrifugal filter units AMICON-0.5 ml-30K (Millipore). The evaluation of quantity and quality was performed by spectrometry (NanoDrop ND1000, NanoDrop Technologies) and by the RNA Experion Bioanalyzer (BioRad) assay.

treatment_protocol: Monocytes were infected with 100,000 bacteria (Mycobacterium tuberculosis, Multiplicity of Infection = 1) for 24 hours

tag: subject status

value: Control volunteer

value: female

value: M.tuberculosis infected monocytes


title: Control volunteer [86C_81_1_1]

tag: age


title: Pediatric LGG 111

tag: tissue

value: CHILD

value: PA

value: P


title: Control volunteer [101C_81_1_4]


title: Control volunteer [91C_81_1_3]


title: Liver_mouse_PB_2500ppm_35

source_name: Liver, 7days, 2500ppm, replicate 2


title: Control volunteer [73C_80_1_3]


title: Control volunteer [72C_80_1_2]


title: Liver_mouse_PB_2500ppm_36

source_name: Liver, 7days, 2500ppm, replicate 3


title: Control volunteer [83C_80_1_4]


title: Pediatric LGG 83

value: low-grade glioma

tag: location

value: INF


title: Pediatric LGG 82

tag: histology

value: MUT


title: 95_21_occipital cortex

source_name: post-mortem brain tissue, individual ID 95_21, occipital cortex

tag: individual id

tag: brain region

value: occipital cortex

tag: disease status

value: neurologically and neuropathologically normal

tag: brain bank

value: Sun Health Research Institute

tag: Cause of death

value: cerebrovascular accident

value: Male

tag: ancestry

tag: brain ph

tag: rin


title: Tuberculosis patient [93T_79_1_4]

source_name: Tuberculosis patient_M.tuberculosis infected monocytes

value: Tuberculosis patient

tag: cell type


title: Liver_mouse_PB_control_3

source_name: Liver, 7days, 0ppm, replicate 3

value: Liver


title: Control volunteer [68C_80_1_1]

value: male


title: Liver_mouse_PB_control_2

source_name: Liver, 7days, 0ppm, replicate 2


title: Liver_mouse_PB_2500ppm_33

source_name: Liver, 7days, 2500ppm, replicate 1


title: Tuberculosis patient [60T_79_1_3]


title: Liver_mouse_PB_control_1

source_name: Liver, 7days, 0ppm, replicate 1


title: Liver_mouse_PB_control_4

source_name: Liver, 7days, 0ppm, replicate 4


title: LASV_D10_7_Soromba

source_name: virus, day post-infection, replicate, virus strain

value: PBMC

tag: infection

value: LASV Soromba

tag: time


title: Tuberculosis patient [48T_89_1_4]

tag: gender

value: M.tuberculosis infected monocytes


title: Liver_rat_PB_2500ppm_134

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8x60K Microarrays for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028279_D_F_20110601) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus rattus

treatment_protocol: Male WH rats (4 animals/dose) were fed diets containing 0 (control) or 2500 ppm NaPB for 7 days. Liver samples were used for gene expression analysis.

tag: background strain

value: WH


title: A549_B+F_6h_rep1

city: Shanghai

first: Xiufeng

last: Pang

address: 500 Dongchuan Road

department: School of Life Sciences

country: China

institute: East China Normal University

description: Gene expression data from A549 cells after 4nM BI-2536 and 20μM fasudil combined treat for 6 h.

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

scan_protocol: GeneChips were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: A549 NSCLC cells,4nM BI-2536 and 20μM fasudil combined treat for 6 h

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

growth_protocol: cells were grown at 37°C under a humidified 95:5 (%; v/v) mixture of air and CO2

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

treatment_protocol: A549 cells were treated with BI-2536 (4 nM), fasudil (20 µM), or the combination of BI-2536 and fasudil for 6 h as indicated.

tag: cell line

tag: treatment

value: Lung

value: epithelial cell

tag: genotype

value: KRAS mutation

tag: disease

value: Carcinoma


title: Tuberculosis patient [47T_89_1_3]

tag: subject status

tag: age


title: Liver_rat_PB_2500ppm_135

tag: tissue


title: Tuberculosis patient [28T_89_1_2]


title: A549_f20_6h_rep3

description: Gene expression data from A549 cells after 20μM fasudil treat for 6h.

source_name: A549 NSCLC cells,20μM fasudil treat for 6 h

value: 20μM fasudil treat for 6 h


title: Liver_rat_PB_2500ppm_136


title: A549_B+F_6h_rep3

value: 4nM BI-2536 and 20μM fasudil combined treat for 6 h


title: Liver_rat_PB_2500ppm_133


title: Tuberculosis patient [22T_89_1_1]

value: female


title: A549_B+F_6h_rep2


title: Liver_rat_PB_control_103


title: Liver_rat_PB_control_102


title: A549_f20_6h_rep1


title: A549_BI4_6h_rep3

description: Gene expression data from A549 cells after 4nM BI-2535 treat for 6h.

source_name: A549 NSCLC cells,4nM BI-2536 treat for 6 h

value: 4nM BI-2536 treat for 6 h


title: A549_BI4_6h_rep2


title: A549_control_rep3

description: Gene expression data from A549 cells with no treatment.

source_name: A549 NSCLC cells,no treatment (control)

value: no treatment (control)


title: A549_control_rep1


title: A549_control_rep2


title: Liver_rat_PB_control_101


title: Bos taurus_biceps brachii_F37

status: Public on Aug 28 2014

city: legnaro

first: sara

last: pegolo

address: viale dell'università 16

country: Italy

institute: university of padua

description: Sample of bovine biceps brachii

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using cyclic lowess by R 2.11.1 statistical software

label: Cyanine 3

organism: Bos taurus

source_name: Bovine biceps brachii samples collected at the slaughterhouse

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted using the QiAgen RNeasy Mini Kit protocol for tissue samples

treatment_protocol: F: Finaplix exposure for 92 days; R: Revalor exposure for 89 days; RD:  Revalor exposure for 89 days and dexamethazone (0.7 mg/day/animal) for 40 days per os


title: Bos taurus_biceps brachii_F35

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_F33

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_R16

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_R14

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_R15

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_F40

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_F36

description: Sample of bovine biceps brachii


title: A549_BI4_6h_rep1


title: Bos taurus_biceps brachii_F39

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_F34

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_F38

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_R11

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_R13

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_R10

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_R9

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RD5

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RD6

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_R12

description: Sample of bovine biceps brachii


title: Tuberculosis patient [56T_79_1_1]


title: Bos taurus_biceps brachii_RD1

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RD3

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_K48

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RD2

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RD8

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_K47

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RD4

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_K44

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_K46

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_K45

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_C24

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_K41

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_C20

description: Sample of bovine biceps brachii


title: A549_f20_6h_rep2


title: Bos taurus_biceps brachii_C22

description: Sample of bovine biceps brachii


title: WT J1 ESCs on day 7 #2

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: WT J1 ESCs on day 7

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 94°C for 35 minutes in Fragmentation buffer of the company.

growth_protocol: Murine ESCs (cell lines: Eed KO J1, Eed KO E14, V6.5 WT (Open Biosystems), J1 wt) were expanded in 15% ESC FCS (PAA), non-essential amino acids solution and LIF-conditioned medium on Mitomycin C-inactivated MEFs. Eed KO ESCs were kindly provided by Dr. A. Wutz, Cambridge, UK. Differentiation in hanging drop cultures was done as described. Briefly, 1000 MEF-depleted ESCs were pipetted onto a lid of a petri plate in 30μl of differentiation medium (10% FCS, without LIF). After 2 days, EBs were collected and replated in suspension cultures. Cell number determination was done by counting single cell suspension of pooled and Trypsin-treated EBs under Trypan blue staining and microscopy. To assess CFC frequencies, 1000 undifferentiated ESCs were plated and cultured for 2 days under ESC expansion conditions before numbers of ES cell-type alkaline phosphatase (AP)-active colonies were determined by staining of fixed cultures with the 'leukocyte alkaline phosphatase'-kit (Sigma-Aldrich). To determine frequencies of EB formation, 1000 undifferentiated ESCs were plated under differentiation condition into semisolid methylcellulose cultures. EB numbers were counted at days 5-7 of differentiation. In addition, graded numbers of ESCs (7, 15, 31, 62, 125, 250 cells) were plated into hanging drops in differentiation medium. After 5-7 days, numbers of drops without EBs were scored. Based on drops without EBs, regression analysis was done using Excel software.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen, Hilden, Germany) with DNase digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

tag: genotype/variation

value: WT

value: embryonic stem cells

tag: days of differentiation


title: Eed KO J1 ESCs on day 7 #2

source_name: Eed KO J1 ESCs on day 7

value: Eed KO


title: Bos taurus_biceps brachii_C23

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_C21

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_C17

description: Sample of bovine biceps brachii


title: WT V6.5 ESCs on day 3 #2

source_name: WT V6.5 ESCs on day 3


title: Eed KO J1 ESCs on day 3 #2

source_name: Eed KO J1 ESCs on day 3


title: Eed KO E14 ESCs on day 0 #2

source_name: Eed KO E14 ESCs on day 0


title: WT J1 ESCs on day 3 #2

source_name: WT J1 ESCs on day 3


title: WT V6.5 ESCs on day 7 #2

source_name: WT V6.5 ESCs on day 7


title: WT J1 ESCs on day 0 #2

source_name: WT J1 ESCs on day 0


title: Bos taurus_biceps brachii_RD7

description: Sample of bovine biceps brachii


title: Eed KO E14 ESCs on day 7 #2

source_name: Eed KO E14 ESCs on day 7


title: Eed KO E14 ESCs on day 3 #2

source_name: Eed KO E14 ESCs on day 3


title: WT V6.5 ESCs on day 7 #1


title: WT V6.5 ESCs on day 0 #2

source_name: WT V6.5 ESCs on day 0


title: Eed KO J1 ESCs on day 7 #1


title: Eed KO J1 ESCs on day 0 #2

source_name: Eed KO J1 ESCs on day 0


title: Bos taurus_biceps brachii_C18

description: Sample of bovine biceps brachii


title: Eed KO E14 ESCs on day 7 #1


title: WT V6.5 ESCs on day 3 #1


title: WT J1 ESCs on day 0 #1


title: Eed KO J1 ESCs on day 0 #1


title: Liver_rat_PB_control_105

source_name: Liver, 7days, 0ppm, replicate 4

value: Liver

value: male


title: Eed KO E14 ESCs on day 0 #1


title: WT J1 ESCs on day 7 #1


title: Eed KO E14 ESCs on day 3 #1


title: WT V6.5 ESCs on day 0 #1


title: WT J1 ESCs on day 3 #1


title: Eed KO J1 ESCs on day 3 #1


title: Bone marrow21

city: Oslo

first: Jon-Magnus

last: Tangen

address: Kirkeveien 166

country: Norway

institute: Oslo University Hospital

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix.

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization. Gene array data were filtered to include only those probe sets derived from the core meta-probe list.

source_name: bone marrow

label_protocol: Total RNA (100 ng) from each sample was prepared using the Ambion WT Expression Kit (Ambion Inc., Austin, Texas, USA) according to manufacturer’s instructions.

extract_protocol: RNA from bone marrow samples were extracted by use of PAXgene Blood RNA Kit from Qiagen.

tag: individual

value: patient 32

value: Placebo

value: Before treatment

value: bone marrow


title: Bone marrow20

value: patient 26

value: Agaricus

value: After treatment


title: Bone marrow26

value: patient 13


title: Bone marrow13

value: patient 3


title: Bone marrow19


title: Bone marrow14


title: Bone marrow28

value: patient 35


title: Bone marrow24

value: patient 10


title: Bone marrow22


title: Bone marrow18

value: patient 23


title: Bone marrow25


title: Bone marrow23


title: Bone marrow16

value: patient 4


title: Bone marrow17


title: Bone marrow15


title: Bone marrow27


title: Bone marrow11

value: patient 2


title: Bone marrow12


title: Bone marrow9

value: patient 25


title: Bone marrow6

value: patient 7


title: Bone marrow7

value: patient 22


title: Bone marrow8


title: Bone marrow5


title: Bone marrow4

value: patient 5


title: Bone marrow1

value: patient 1

value: Placebo


title: Bone marow3

value: Before treatment

value: bone marrow


title: Bone marrow10

value: Agaricus


title: Bone marrow2

value: After treatment


title: shTR, biological rep3

city: San Francisco

first: Elizabeth

last: Blackburn

state: CA

address: 600 16th St Genentech Hall S316

institute: UCSF

description: Gene expression data from cultured human primary CD4 T cells with lentivirus containing shRNAs and puromycin resistance

hyb_protocol: Hybridization was performed by the Gladstone Institute Genomics core using a Hybridization Oven 645

scan_protocol: GeneChip Humang Gene ST 1.0 were scanned  by the Gladstone Institute Genomics Core using the GeneChip Scanner 3000 7G System

data_processing: The Gladstone Genomics Core performed RMA analysis using the Affymetrix GeneChip Command Console Software. The three samples for shScramble, shTERT, and shTR were averaged and fold change was calculated using MATLAB.  Fold change of 2 fold or higher with p<0.05 was considetered significant gene chance and was caclulated using MATLAB

source_name: primary human CD4 T cells

label_protocol: Labeling was performed by the Gladstone Institute Genomics Core using the Affymetrix GeneChip WT Terminal Labeling Kit

growth_protocol: PBMCs were isolated from buffy coat by centrifugation with Ficoll-Paque Plus (GE Healthcare 17-1440-02) according to the manufacturer’s instructions.  CD4+ T cells were isolated from PBMCs using either the Untouched CD4+ T cell Isolation Kit II Human (Miltenyi 130-091-155), Naïve CD4+ T Cell Isolation Kit II (Miltenyi 130-094-131), the Dynabeads Untouched Human CD4 T cell Isolation Kit (Life Technologies 11346D), or the Human Dynabeads CD4 Positive Isolation Kit (Life Technologies 11331D) according to the manufacturer’s instructions.  CD4 T cells were cultured in 24 well dishes at 1 million cells/ml.  Cells were stimulated 24 hours after isolation with 50 μl of Dynabeads Human T Cell Activator CD3/CD28 (Life Technologies 111.32D) per 1 million CD4+ T cells and cultured in RPMI with 10% FBS (Hyclone), 1% Penicillin and Streptomycin, and 1% glutamine with 10 ng/ml IL-2 (Sigma 12644-10UG).   Cells were transduced in triplicate with lentivirus containing shRNAs and Ef1a promotor driving puromycin resistance 24 hours after stimulation by centrifuging with titered virus to a volume of 1 ml at 800g for 30 min at 37°C with 8μg/ml polybrene.  Viral supernatant was removed and cells were resuspended in 1ml of fresh media with 10 ng IL-2.  2 μg/ml of Puromycin was added 24 hours after transduction and kept in culture during the course of the experiment.  Cells were split at day 6 and split and restimulated at day 12.  When cells were split, they were resuspended in fresh media, IL-2, and puromycin.  Cells were collected at day 15 for microarray anaylsis.

extract_protocol: RNA was extracted from CD4 T cells using the Qiagen RNA mini kit and given to the Gladstone Institute for processing

treatment_protocol: Cells were collected at day 15 in culture and washed twice with PBS before RNA extraction.

tag: shRNA

value: shTR

tag: apoptosis

value: increased


title: male ethanol socially-enriched amygdala replicate 3

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

hyb_protocol: Affymetrix EukGE-WS2v4 Protocol

scan_protocol: Standard Affymetrix Genechip 7G Scanner

data_processing: Partek Genomics Suite 6.5 to perform RMA normalization;  the data were filtered afterwards to include only rat transcripts since the experiments were done with rat RNA.

organism: Rattus norvegicus

source_name: male ethanol socially-enriched amygdala

label_protocol: 100 ng of total RNA was prepared for hybridization using the WT Expression Kit (Ambion) according to manufacturer protocol

extract_protocol: Qiagen total RNA

tag: strain

value: Long Evans

value: male

value: postnatal day 42

tag: brain region

value: Amygdala

tag: prenatal exposure

value: Ethanol

tag: postnatal social treatment

value: Socially-enriched


title: male ethanol socially-enriched amygdala replicate 2

tag: gender


title: shTR, biological rep2


title: shScramble, biological rep3

value: shScramble

value: normal


title: male saline socially-enriched amygdala replicate 2

source_name: male saline socially-enriched amygdala

value: Saline


title: male ethanol non-enriched amygdala replicate 1

source_name: male ethanol non-enriched amygdala

value: Non-enriched


title: male ethanol non-enriched amygdala replicate 2


title: shTERT, biological rep3

value: shTERT


title: shTR, biological rep1


title: male ethanol non-enriched amygdala replicate 3


title: shTERT, biological rep1


title: shTERT, biological rep2


title: shScramble, biological rep1


title: shScramble, biological rep2


title: male saline non-enriched amygdala replicate 3

source_name: male saline non-enriched amygdala


title: male ethanol socially-enriched amygdala replicate 1


title: male saline non-enriched amygdala replicate 2


title: female ethanol socially-enriched amygdala replicate 3

value: female


title: female ethanol non-enriched amygdala replicate 1

source_name: female ethanol non-enriched amygdala


title: female ethanol non-enriched amygdala replicate 2


title: male saline non-enriched amygdala replicate 1


title: female ethanol non-enriched amygdala replicate 3


title: male saline socially-enriched amygdala replicate 1


title: male saline socially-enriched amygdala replicate 3


title: female ethanol socially-enriched amygdala replicate 2


title: female ethanol socially-enriched amygdala replicate 1


title: female saline socially-enriched amygdala replicate 3


title: female saline non-enriched amygdala replicate 3

source_name: female saline non-enriched amygdala


title: female saline socially-enriched amygdala replicate 2


title: E15.5 UB cells_rep1

city: Charlottesville

first: Jing

last: Yu

state: VA

address: 1340 Jefferson Park Ave.

institute: University of Virginia School of Medicine

description: miRNA expression data in E15.5 UB cells

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: E15.5 UB cells

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3/Cy5 dye staining.

growth_protocol: Kidneys were dissected from E15.5 Rosa26YFP; Hoxb7Cre embryos.

extract_protocol: Total RNAs including miRNAs were purified with Qiagen's miRNeasy mini kit following the manufaturer's protocol

treatment_protocol: Kidneys were trypsinized to get single cell suspension. UB cells were FACS sorted by YFP fluoresence.

tag: cell type

value: UB epithelial cells

value: Rosa26YFP; Hoxb7Cre


title: female saline socially-enriched amygdala replicate 1


title: E15.5 UB cells_rep2

description: miRNA expression data in E15.5 UB cells


title: male saline socially-enriched ventral striatum replicate 1

value: Ventral striatum


title: male ethanol socially-enriched ventral striatum replicate 1


title: male ethanol non-enriched ventral striatum replicate 3


title: male ethanol non-enriched amygdala replicate 2 [miRNA]

label_protocol: 250 ng of total RNA was prepared for hybridization using the using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix)


title: male ethanol non-enriched amygdala replicate 1 [miRNA]


title: male ethanol socially-enriched ventral striatum replicate 2


title: female saline non-enriched amygdala replicate 2


title: male ethanol socially-enriched amygdala replicate 1 [miRNA]


title: male ethanol non-enriched ventral striatum replicate 2


title: male saline socially-enriched ventral striatum replicate 2


title: male ethanol non-enriched amygdala replicate 3 [miRNA]


title: male ethanol socially-enriched amygdala replicate 3 [miRNA]


title: male ethanol socially-enriched amygdala replicate 2 [miRNA]


title: male ethanol non-enriched ventral striatum replicate 1


title: male ethanol socially-enriched ventral striatum replicate 3


title: male saline non-enriched ventral striatum replicate 2


title: male saline socially-enriched ventral striatum replicate 3


title: male saline socially-enriched amygdala replicate 3 [miRNA]


title: female ethanol socially-enriched ventral striatum replicate 1


title: female ethanol socially-enriched ventral striatum replicate 2


title: female ethanol socially-enriched ventral striatum replicate 3


title: female saline non-enriched amygdala replicate 1


title: male saline socially-enriched amygdala replicate 2 [miRNA]


title: female ethanol non-enriched ventral striatum replicate 3


title: male saline non-enriched ventral striatum replicate 1


title: male saline non-enriched ventral striatum replicate 3


title: female ethanol non-enriched ventral striatum replicate 2


title: male saline non-enriched amygdala replicate 3 [miRNA]


title: female ethanol socially-enriched amygdala replicate 3 [miRNA]


title: male saline non-enriched amygdala replicate 2 [miRNA]


title: female ethanol socially-enriched amygdala replicate 1 [miRNA]


title: female ethanol non-enriched amygdala replicate 2 [miRNA]


title: female ethanol non-enriched amygdala replicate 3 [miRNA]


title: female ethanol socially-enriched amygdala replicate 2 [miRNA]


title: male saline socially-enriched amygdala replicate 1 [miRNA]


title: female ethanol non-enriched ventral striatum replicate 1


title: male saline non-enriched amygdala replicate 1 [miRNA]


title: female saline non-enriched amygdala replicate 3 [miRNA]


title: female saline socially-enriched amygdala replicate 3 [miRNA]


title: female saline socially-enriched amygdala replicate 2 [miRNA]


title: female saline non-enriched amygdala replicate 2 [miRNA]


title: female saline socially-enriched amygdala replicate 1 [miRNA]


title: female ethanol non-enriched amygdala replicate 1 [miRNA]


title: female saline non-enriched amygdala replicate 1 [miRNA]


title: female saline socially-enriched ventral striatum replicate 2


title: female saline socially-enriched ventral striatum replicate 1


title: male ethanol socially-enriched ventral striatum replicate 2 [miRNA]


title: GST-overexpression seedlings, control, rep 2

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description:
Gene expression data from control GST overexpression Arabidopsis seedlings
GST_Control_rep2

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 h at 45 degree C on the rice Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChip were scanned using Affymetrix scanner

data_processing: CEL files wer imported into Genespring software and probe summarization and normalization was performed using RMA algorithm

label: Biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

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

growth_protocol: Wild-type and transgenic Arabidopsis seedlings were grown on MS medium for 14-days in a culture room with a daily photoperiodic cycle of 16h light and 8h dark

extract_protocol: Total RNA was extracted using TRI reagent according to the manufacturer's instructions

treatment_protocol: Seedlings were grown under normal control conditions

value: GST-overexpression

tag: ecotype

value: Columbia

value: Seedlings

tag: Stage


title: female saline socially-enriched ventral striatum replicate 3

value: Long Evans


title: GST-overexpression seedlings, control, rep 1

description:
Gene expression data from control GST overexpression Arabidopsis seedlings
GST_Control_rep1


title: female saline non-enriched ventral striatum replicate 2

value: postnatal day 42


title: male ethanol socially-enriched ventral striatum replicate 3 [miRNA]

value: male


title: male ethanol non-enriched ventral striatum replicate 3 [miRNA]

value: Ethanol


title: female saline non-enriched ventral striatum replicate 1


title: male ethanol socially-enriched ventral striatum replicate 1 [miRNA]

value: Socially-enriched


title: female saline non-enriched ventral striatum replicate 3


title: male ethanol non-enriched ventral striatum replicate 2 [miRNA]


title: male ethanol non-enriched ventral striatum replicate 1 [miRNA]


title: Wild-type seedlings, control, rep 2

description:
Gene expression data from control wild-type Arabidopsis seedlings
WT_Control_rep2

value: Wild-type


title: Wild-type seedlings, control, rep 1

description:
Gene expression data from control wild-type Arabidopsis seedlings
WT_Control_rep1


title: male saline socially-enriched ventral striatum replicate 3 [miRNA]


title: Mouse spinal cord, EAE, R-Flurbiprofen treatment, replicate3

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

description: EAE-experimental autoimmune encephalomyelitis; F-R-Flurbiprofen; Veh-Vehicle (i.e. tap water); MS-Multiple sclerosis model; KONT-negative control; s.c.-subcutaneous; p.o.- perorally;  MOG 35-55-peptide of myelin oligodendrocyte glycoprotein used for immunization; CFA-complete Freund adjuvant

hyb_protocol: Hybridization was performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed once in High Temp Wash buffer (Illumina Inc.) at 55°C and then twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes (in between washed with ethanol at room temperature). After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays were dried and scanned.

scan_protocol: Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers were removed when > 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.

data_processing: Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampel’s method). All remaining bead level data points are than quantile normalized [1]. As test for significance the student’s t-test was used on the bead expression values of the groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction [2] was applied to the complete set of p-values of all ProbeIDs on the chip. The average expression value was calculated as mean of the measured expressions of beads together with the standard deviation of the beads.    [1] Probe Level Quantile Normalization of High Density Oligonucleotide   Array Data, Ben Bolstad, Division of Biostatistics,   University of California, Berkeley December 2001    [2] Y. Benjamini and Y. Hochberg (1995). Controlling the false   discovery rate: a practical and powerful approach to multiple   testing. Journal of the Royal Statistical Society B, Vol. 57, 289–300.

source_name: lumbar spinal cord, EAE

label_protocol: The laboratory work was done in the Genomics and Proteomics Core Facility at the German Cancer Research Center, Heidelberg, Germany (DKFZ). Biotin-labeled cRNA samples for hybridization on Illumina Mouse Sentrix-6 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al., 1992). In brief, 100 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies).  Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60 µl of water. (Eberwine J, Yeh H, Miyashiro K, Cao Y, Nair S, Finnell R, Zettel M, Coleman P. Analysis of gene expression in single live neurons. Proc. Natl. Acad. Sci. U. S. A. (1992) 89:3010–3014).

extract_protocol: Total RNA was extracted from homogenized tissue with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit according to the protocol provided in the RNeasy tissue Mini Kit. The quality of total RNA was checked by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). Only samples with RNA index values greater than 8.5 were selected for expression profiling. RNA concentrations were determined using the NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE)

treatment_protocol:
EAE immunization: C57BL6/J mice were immunized with the Hooke Kit™ MOG35-55/CFA emulsion PTX (EK-2110, Hooke Labs, St Lawrence, MA), which contains 200 µg myelin oligodendrocyte glycoprotein (MOG) 35-55 emulsified in 200 µl Complete Freund’s Adjuvant (CFA). The emulsion was injected subcutaneously at two sites followed by two intraperitoneal (i.p.) injections of 200 ng pertussis toxin (PTX) in phosphate buffered saline (PBS), the first 1-2 h after MOG35-55, and the second 24 h after MOG35-55. Sham control mice received a subcutaneous injection of CFA without MOG35-55.
Mice were treated with R-flurbiprofen (10 mg/kg/d) or vehicle. Treatments were continuously administered via the drinking water starting 5 days after immunization. Drinking bottles were exchanged daily with freshly prepared drug or vehicle. Therapy was monitored by weighing water bottles and by analysis of plasma concentrations of R-flurbiprofen.

value: 10-12 weeks

tag: disease

value: EAE

tag: treatment

value: R-Flurbiprofen

value: lumbar spinal cord

tag: sampleID

tag: group label

value: EAE + F


title: Mouse spinal cord, EAE, vehicle treatment, replicate3

value: female

tag: age

value: Vehicle

tag: tissue

value: EAE + Veh


title: Mouse spinal cord, EAE, R-Flurbiprofen treatment, replicate2


title: male saline socially-enriched ventral striatum replicate 1 [miRNA]

value: Ventral striatum

value: Saline


title: male saline non-enriched ventral striatum replicate 3 [miRNA]

value: Non-enriched


title: male saline socially-enriched ventral striatum replicate 2 [miRNA]

value: Long Evans


title: Mouse spinal cord, EAE, vehicle treatment, replicate1


title: Mouse spinal cord, EAE, R-Flurbiprofen treatment, replicate1


title: Mouse spinal cord, sham control without EAE, RFlurbiprofen treatment, replicate1 (negative control)

source_name: lumbar spinal cord, sham

value: sham

value: KONT + F


title: male saline non-enriched ventral striatum replicate 2 [miRNA]

value: male

value: postnatal day 42


title: Mouse spinal cord, EAE, vehicle treatment, replicate2


title: Mouse spinal cord, sham control without EAE, RFlurbiprofen treatment, replicate2 (negative control)


title: male saline non-enriched ventral striatum replicate 1 [miRNA]


title: Mouse spinal cord, sham control without EAE, Vehicle treatment, replicate2 (negative control)

value: KONT + Veh


title: Mouse spinal cord, sham control without EAE, Vehicle treatment, replicate3 (negative control)

value: 10-12 weeks


title: Mouse spinal cord, sham control without EAE, RFlurbiprofen treatment, replicate3 (negative control)


title: female ethanol socially-enriched ventral striatum replicate 3 [miRNA]

value: Ethanol

value: Socially-enriched


title: female ethanol non-enriched ventral striatum replicate 3 [miRNA]


title: female ethanol socially-enriched ventral striatum replicate 1 [miRNA]


title: Mouse spinal cord, sham control without EAE, Vehicle treatment, replicate1 (negative control)

value: lumbar spinal cord


title: female ethanol socially-enriched ventral striatum replicate 2 [miRNA]


title: female ethanol non-enriched ventral striatum replicate 1 [miRNA]


title: female ethanol non-enriched ventral striatum replicate 2 [miRNA]


title: skin_7d_IMQ_rep2

first: Hong

middle: Lin

last: Wang

address: 280 Chongqing South Road

institute: Shanghai Jiao Tong University

description: Gene expression of skin after 7 days exposed to IMQ

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 Whole Human Genome Oligo Microarrays (G4112A) 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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, 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-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: whole skin, 7 days, IMQ, replicate 2

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.

extract_protocol: RNA was prepared using TRIzol (Invitrogen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C57BL/6J mice at 6 to 8 weeks of age were applied to a daily topical dose of 62.5 mg of IMQ cream (5%) on the shaved back for 7 consecutive days. Control mice were treated with a same dose of vehicle cream. After 7 days, the mice were sacrificed and skin on the back were cut off and used to extract total RNA.

value: skin


title: skin_7d_IMQ_rep3

source_name: whole skin, 7 days, IMQ, replicate 3

value: female


title: skin_7d_IMQ_rep1

source_name: whole skin, 7 days, IMQ, replicate 1


title: skin_7d_vehicle cream_rep2

description: Gene expression of skin after 7 days exposed to vehicle cream of IMQ

source_name: whole skin, 7 days, vehicle cream, replicate 2


title: female saline socially-enriched ventral striatum replicate 3 [miRNA]


title: female saline socially-enriched ventral striatum replicate 2 [miRNA]


title: female saline socially-enriched ventral striatum replicate 1 [miRNA]


title: female saline non-enriched ventral striatum replicate 3 [miRNA]


title: skin_7d_vehicle cream_rep3

source_name: whole skin, 7 days, vehicle cream, replicate 3


title: female saline non-enriched ventral striatum replicate 2 [miRNA]


title: skin_7d_vehicle cream_rep1

source_name: whole skin, 7 days, vehicle cream, replicate 1


title: female saline non-enriched ventral striatum replicate 1 [miRNA]


title: VCaP.2217 day7 +dox (B)

status: Public on Aug 27 2014

city: Cambridge

first: Joshua

middle: M

last: Korn

address: 250 Mass Ave

institute: Novartis

description: VCaP cells stably expressing a Doxycycline (dox)-inducible  ERG shRNA (2217), were exposed to 100ng/ml doxycycline for 7 days

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

source_name: VCaP cells

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: All lines were cultured in DMEM supplemented with 10% FCS, NEAA and 100ng/ml Doxycycline for 1, 3, 7 and 10days.

extract_protocol: RNA was extracted with RNeasy extraction kits (Qiagen) with on-column DNA digestion.  The initial lysis step was performed directly on the cell culture plates.

treatment_protocol: Cells were stably transduced with Doxycycline-induced lentiviral vectors (nontargeting=Pak4, ERG=2217) and treated with Doxycycline (Dox) for the noted timepoints, or kept in base media for the same timepoints as control (1, 3, 7, 10 days).

tag: erg expression

value: Low


title: VCaP.Pak4 day10 +dox (B)

description: VCaP cells stably expressing a Doxycycline (dox)-inducible control nontargeting shRNA (Pak4) were exposed to 100ng/ml doxycycline for 10 days

value: High


title: VCaP.2217 day3 +dox (B)

description: VCaP cells stably expressing a Doxycycline (dox)-inducible  ERG shRNA (2217), were exposed to 100ng/ml doxycycline for 3 days


title: VCaP.Pak4 day7 +dox (B)

description: VCaP cells stably expressing a Doxycycline (dox)-inducible control nontargeting shRNA (Pak4) were exposed to 100ng/ml doxycycline for 7 days


title: westGreenland14

type: genomic

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

value: blood

tag: population

value: West Greenlanders

tag: region

value: Greenland


title: VCaP.2217 day10 +dox (B)

description: VCaP cells stably expressing a Doxycycline (dox)-inducible  ERG shRNA (2217), were exposed to 100ng/ml doxycycline for 10 days


title: westGreenland4


title: westGreenland8


title: VCaP.Pak4 day3 +dox (B)

description: VCaP cells stably expressing a Doxycycline (dox)-inducible control nontargeting shRNA (Pak4) were exposed to 100ng/ml doxycycline for 3 days


title: westGreenland15


title: westGreenland19


title: VCaP.2217 day1 +dox (B)

description: VCaP cells stably expressing a Doxycycline (dox)-inducible  ERG shRNA (2217), were exposed to 100ng/ml doxycycline for 1 day


title: eastGreenland8

value: East Greenlanders


title: VCaP.Pak4 day1 +dox (B)

description: VCaP cells stably expressing a Doxycycline (dox)-inducible control nontargeting shRNA (Pak4)  were exposed to 100ng/ml Doxycycline for 1 day


title: VCaP.Pak4 day10 +dox


title: eastGreenland15


title: VCaP.2217 day1 +dox


title: westGreenland7


title: VCaP.Pak4 day7 +dox


title: eastGreenland2


title: westGreenland3


title: westGreenland12


title: VCaP.Pak4 day3 +dox


title: eastGreenland19


title: VCaP.2217 day7 +dox


title: eastGreenland13


title: eastGreenland20


title: westGreenland13


title: VCaP.2217 day10 +dox


title: eastGreenland18


title: eastGreenland11


title: Ostrava winter 2010 4961941026_K

city: Prague

first: Pavel

last: Rossner

address: Videnska 1083

department: Genetic Ecotoxicology

country: Czech Republic

institute: Institute of Experimental Medicine

hyb_protocol: Standard Illumina hybridization protocol was used.

scan_protocol: Standard Illumina scanning protocol was used.

data_processing: The expression values were imported into Genedata Expressionist from the Illumina Inc. BeadStudio file, as average signals. The detection scores were used as quality parameters and expression values were transformed into log values for analysis. Experiments were normalized to a common median of 100. Pearson’s correlation analyses, T-tests and ANOVA were performed with the log transformed and median normalized data.

source_name: leukocytes

label_protocol: Biotinylated cRNA was prepared by reverse transcription of RNA (200 ng) to cDNA and subsequent in vitro transcription using the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: not applicable

extract_protocol: RNA was extracted from frozen leukocytes using the LeukoLOCK system. Quantification was performed using a Nanodrop ND-1000 Spectrophotometer. The integrity of the RNA was assessed with an Agilent 2100 Bioanalyzer and isolated RNA was stored at -80°C until further processing.

treatment_protocol: not applicable

tag: exposure

value: pollution

value: leukocyte


title: Ostrava winter 2010 5447354013_F

value: male


title: Ostrava winter 2010 5447354011_L


title: Ostrava winter 2010 5447338025_D


title: Ostrava winter 2010 5376111020_G


title: Ostrava winter 2010 5447338015_G


title: Ostrava winter 2010 5447354012_J


title: Ostrava winter 2010 4961941026_D


title: Ostrava winter 2010 4961941027_H


title: Ostrava winter 2010 5447338013_H


title: Ostrava winter 2010 4961941026_H


title: Ostrava winter 2010 4961941027_B


title: Ostrava winter 2010 5376111020_E


title: VCaP.2217 day3 +dox


title: eastGreenland4


title: Ostrava winter 2010 5447354013_E


title: Ostrava winter 2010 5447338013_B


title: VCaP.Pak4 day1 +dox


title: Ostrava winter 2010 5376111055_F


title: Ostrava winter 2010 5447338015_A


title: Ostrava winter 2010 5447338027_D


title: eastGreenland12


title: Ostrava winter 2010 5376111055_G


title: Ostrava winter 2010 5447338012_D


title: dSETDB1null HP1_repeat_1

city: Taipei

first: Che-Kun

middle: James

last: Shen

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Chip-chip_ dSETDB1null third instar larvae_HP1

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., following their standard operating protocol.(NG_Chip-chip_Guide_v6p2)

scan_protocol: MS-200 scanner at 2 µm resolution using high-sensitivity and autogain settings. Separate autogain area was defined for each subarray.

data_processing: Images were aligned and quantified using NimbleScan software  (V2.6) (Roche NimbleGen) which produced .pair reports of raw data and converted to ratio of Cy5 vs cy3

organism: Drosophila melanogaster

source_name: HP1 ChIP DNA

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.(NG_Chip-chip_Guide_v6p2)

growth_protocol: The flies were grown on standard medium at 25°C, and homozygous third instar larvae were obtained by identification of no-GFP phenotype

extract_protocol: Third instar larvae (approximately 250-280 mg) were homogenized and cross-linked for 15 min at room temperature in 5ml buffer A1 (60mM KCl, 15mM NaCl, 15mM HEPES, pH 7.6, 10mM Sodium Butyrate, 4mM MgCl2, 0.5mM DTT, 0.5% Triton X-100 and protease inhibitors (complete EDTA-free protease inhibitor cocktail; Roche)) with 1.8% formaldehyde. Cross-linking was stopped by adding 225mM glycine followed by incubation for 5 min. The homogenate was transferred to a 15 ml tube and centrifuged for 5 min at 4000g at 4°C. The supernatant was discarded and the nuclei pellet was washed three times in 3ml A1 buffer and once in 2ml of lysis buffer (140mM NaCl, 15mM HEPES, pH 7.6, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 10mM Sodium Butyrate, and protease inhibitors) at 4°C. After the washes, nuclei were resuspended in lysis buffer containing 0.1% SDS and 0.5% N-lauroylsarcosine and incubated for 10 min at 4°C. Chromatin was sonicated and sheared chromatin had length of 200 bp to 1 kb. After sonication and 10 min high speed centrifugation, fragmented chromatin was recovered in the supernatant. Chromatin was pre-cleared by addition of 100µl of Protein A Sepharose suspension (PAS; GE Healthcare) for 2hours at 4°C. PAS was removed by centrifugation, specific antibodies or purified IgG were added to the supernatant and samples were incubated overnight at 4°C. 40µl of PAS was added and incubated was for 1hour 30 min at 4°C. Samples were washed four times in wash buffer (140mM NaCl, 15mM HEPES, pH 7.6, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.05% SDS and 10mM Sodium Butyrate) and twice in TE buffer (1mM EDTA and 10mM Tris-HCl, pH 8). Chromatin was eluted from PAS twice. First, add 100µl of 10mM EDTA, 1% SDS, 50mM Tris-HCl, pH 8 and incubate at 65°C for 15 min. After centrifugation and recovery of the supernatant, PAS material was re-extracted in 150µl of TE buffer containing 0.67% SDS. The combined supernatants were incubated overnight at 65°C to reverse cross-links and then treated with Proteinase K at 50°C for 2 hours. Add 55µl of 4M LiCl to each sample and extract DNA by phenol/chloroform. The immunoprecipitated DNA was dissolved in 20µl of water.

tag: developmental stage

value: third instar larvae

tag: antibody

tag: antibody company/catalog

tag: genotype/variation

source_name: input DNA


title: w1118 HP1_repeat_2

description: Chip-chip_w1118 third instar larvae_HP1

growth_protocol: The flies were grown on standard medium at 25°C


title: Ostrava winter 2010 5447354011_C

tag: cell type

tag: gender


title: dSETDB1null HP1_repeat_2


title: Ostrava winter 2010 5447338013_F


title: Ostrava winter 2010 5447338013_L


title: Ostrava winter 2010 5447338012_G


title: Ostrava winter 2010 5447354011_K


title: Ostrava winter 2010 5447338027_J


title: Ostrava winter 2010 5447354011_H


title: Ostrava winter 2010 5447354013_G


title: Ostrava winter 2010 5447338012_B


title: Ostrava winter 2010 5376154022_H


title: Ostrava winter 2010 4961941027_E


title: Ostrava winter 2010 4961941027_F


title: Ostrava winter 2010 5376111055_E


title: Ostrava winter 2010 5376111055_C


title: Ostrava winter 2010 5447354012_C


title: w1118 HP1_repeat_1

description: Chip-chip_w1118 third instar larvae_HP1


title: Ostrava winter 2010 5447338012_K


title: Ostrava winter 2010 5447354012_F


title: Ostrava winter 2010 4961941025_F


title: Ostrava winter 2010 5447354013_C


title: w1118 HP1_repeat_3

description: Chip-chip_w1118 third instar larvae_HP1


title: Ostrava winter 2010 4961941027_C


title: Ostrava winter 2010 5447354011_E


title: Ostrava winter 2010 4961941026_G


title: Ostrava winter 2010 5376154022_A


title: Ostrava winter 2010 5447338013_D


title: Ostrava winter 2010 5447338013_J


title: Ostrava winter 2010 5376111020_C


title: Ostrava winter 2010 4961941026_B


title: Ostrava winter 2010 4961941027_G


title: Ostrava winter 2010 5447354013_K


title: Ostrava winter 2010 4961941025_L


title: Ostrava winter 2010 5447354012_I


title: Ostrava winter 2010 5447354013_A


title: Ostrava winter 2010 5447354012_L


title: Ostrava winter 2010 5447338012_C


title: Ostrava winter 2010 5447354013_I


title: Ostrava winter 2010 5447354011_D


title: Ostrava winter 2010 5447338015_D


title: dSETDB1null HP1_repeat_3


title: Ostrava winter 2010 5447338027_K


title: Ostrava winter 2010 5447354011_J


title: Ostrava winter 2010 5447338027_C


title: Ostrava winter 2010 5447338027_I


title: Ostrava winter 2010 5447338027_G


title: Ostrava winter 2010 5376154022_E


title: Ostrava winter 2010 5447338025_B


title: Ostrava winter 2010 5447338025_K


title: Ostrava winter 2010 5447338027_E


title: Ostrava winter 2010 5447338027_H


title: Ostrava winter 2010 5447338015_F


title: Ostrava winter 2010 5376154022_K


title: Ostrava winter 2010 5447338026_J


title: Ostrava winter 2010 5447338015_K


title: Ostrava winter 2010 5447354022_L


title: Ostrava winter 2010 5447338012_I


title: Ostrava winter 2010 5447354022_J


title: Ostrava winter 2010 5376154022_C


title: Ostrava winter 2010 5447354012_B


title: Ostrava winter 2010 5447338015_E


title: Ostrava winter 2010 5447354012_E


title: Ostrava winter 2010 5447338013_G


title: Ostrava winter 2010 5447354011_I


title: Ostrava winter 2010 4961941025_H


title: Ostrava winter 2010 5447338012_F


title: Ostrava winter 2010 5376111020_A


title: Ostrava winter 2010 4961941025_K


title: Ostrava winter 2010 5447338025_J


title: Ostrava winter 2010 5447338027_B


title: Ostrava winter 2010 5447338025_E


title: Ostrava winter 2010 5376111020_B


title: Ostrava winter 2010 5447354013_L


title: Ostrava winter 2010 5447354012_D


title: Ostrava winter 2010 5376111020_D


title: Ostrava winter 2010 5447354011_F


title: Ostrava winter 2010 5376111055_B


title: Ostrava winter 2010 4961941027_K


title: Ostrava winter 2010 5447354011_B


title: Ostrava winter 2010 5447338015_C


title: Ostrava winter 2010 5376111020_J


title: Ostrava winter 2010 4961941026_J


title: Ostrava winter 2010 5376111055_A


title: Ostrava winter 2010 5447354013_D


title: Ostrava winter 2010 5447338026_I


title: Ostrava winter 2010 5447354012_K


title: Ostrava winter 2010 5447354012_G


title: Ostrava winter 2010 5447354022_F


title: Ostrava winter 2010 5447354012_H


title: Ostrava winter 2010 5447338026_G


title: Ostrava winter 2010 4961941026_I


title: Ostrava winter 2010 4961941026_C


title: Ostrava winter 2010 5447354013_J


title: Ostrava winter 2010 4961941027_J


title: Ostrava winter 2010 5447338013_E


title: Ostrava winter 2010 5447354013_H


title: Ostrava winter 2010 5447338025_G


title: Ostrava winter 2010 5447354022_D


title: Ostrava winter 2010 5447338013_A


title: Ostrava winter 2010 5447338025_L


title: Ostrava winter 2010 5376111020_I


title: Ostrava winter 2010 5447338027_A


title: Ostrava winter 2010 5447354022_I


title: Ostrava winter 2010 5447338026_A


title: Ostrava winter 2010 5447354013_B


title: Ostrava winter 2010 5376111055_L


title: Ostrava winter 2010 5447354011_G


title: Ostrava winter 2010 4961941026_E


title: Ostrava winter 2010 5447354012_A


title: Prague winter 2010 4961941025_I

value: control


title: Prague winter 2010 5447354022_G


title: Prague winter 2010 5447338026_F


title: Ostrava winter 2010 5447338025_A


title: Ostrava winter 2010 5447338015_I


title: Prague winter 2010 5447338026_K


title: Prague winter 2010 5447354022_H


title: Prague winter 2010 5376154022_D


title: Prague winter 2010 5447354022_C


title: Ostrava winter 2010 4961941025_C


title: Ostrava winter 2010 5447338025_I


title: Prague winter 2010 5447338027_F


title: Prague winter 2010 5447354022_A


title: Prague winter 2010 4961941027_D


title: Prague winter 2010 5447354022_E


title: Ostrava winter 2010 4961941011_D


title: Ostrava winter 2010 4961941025_A


title: Prague winter 2010 5376111020_H


title: Prague winter 2010 5447338026_D


title: Prague winter 2010 4961941025_E


title: Prague winter 2010 4961941026_F


title: Prague winter 2010 5447338015_J


title: Ostrava winter 2010 4961941026_L


title: Ostrava winter 2010 4961941026_A


title: Prague winter 2010 5447338026_B


title: Prague winter 2010 5376111020_L


title: Prague winter 2010 5447338026_L


title: Prague winter 2010 4961941025_B


title: Prague winter 2010 5376154022_J


title: Prague winter 2010 5447338027_L


title: Prague winter 2010 5376154022_I


title: Prague winter 2010 5447338026_H


title: Prague winter 2010 5447338015_B


title: Prague winter 2010 5447338026_C


title: Prague winter 2010 4961941027_I


title: Prague winter 2010 5447338015_L


title: Prague winter 2010 5447338012_A


title: Prague winter 2010 4961941025_G


title: Prague winter 2010 5447338015_H


title: Prague winter 2010 5447338025_H


title: Prague winter 2010 5447338012_J


title: Prague winter 2010 5447338012_E


title: Prague winter 2010 5376154022_F


title: Prague winter 2010 5447354011_A


title: Prague winter 2010 5447338025_C


title: Prague winter 2010 5376154022_G


title: Prague winter 2010 5447338013_I


title: Prague winter 2010 5447338012_H


title: Prague winter 2010 5376111020_F


title: Prague winter 2010 5447338026_E


title: Prague winter 2010 5447338012_L


title: Prague winter 2010 5447338025_F


title: Prague winter 2010 4961941027_L


title: Prague winter 2010 5447338013_K


title: Prague winter 2010 4961941027_A


title: Ostrava summer 2009 4961941060_A


title: Ostrava summer 2009 4961941060_B


title: Ostrava summer 2009 4961941059_L


title: Ostrava summer 2009 4961941044_J


title: Ostrava summer 2009 4961941031_A


title: Prague winter 2010 5376154022_B


title: Prague winter 2010 5447338013_C


title: Ostrava summer 2009 4961941044_G


title: Ostrava summer 2009 4961941036_G


title: Ostrava summer 2009 4961941031_F


title: Ostrava summer 2009 4961941044_E


title: Ostrava summer 2009 4961941031_H


title: Ostrava summer 2009 4961941053_I


title: Ostrava summer 2009 4961941052_G


title: Ostrava summer 2009 4961941054_L


title: Ostrava summer 2009 4961941045_K


title: Ostrava summer 2009 4868499057_H


title: Ostrava summer 2009 4961941053_E


title: Ostrava summer 2009 4868499049_L


title: Ostrava summer 2009 4961941003_L


title: Ostrava summer 2009 4961941042_E


title: Ostrava summer 2009 4961941054_F


title: Ostrava summer 2009 4961941053_K


title: Ostrava summer 2009 4961941053_D


title: Ostrava summer 2009 4961941036_J


title: Ostrava summer 2009 4868499055_I


title: Ostrava summer 2009 4961941059_J


title: Ostrava summer 2009 4961941042_J


title: Ostrava summer 2009 4868499050_K


title: Ostrava summer 2009 4961941060_I


title: Ostrava summer 2009 5067327057_A


title: Ostrava summer 2009 4961941032_H


title: Ostrava summer 2009 5067327057_I


title: Ostrava summer 2009 4961941044_I


title: Ostrava summer 2009 4961941044_K


title: Ostrava summer 2009 4961941053_L


title: Ostrava summer 2009 4961941060_H


title: Ostrava summer 2009 4961941044_A


title: Ostrava summer 2009 4961941045_L


title: Ostrava summer 2009 4961941042_C


title: Ostrava summer 2009 4961941053_F


title: Ostrava summer 2009 4868499055_G


title: Ostrava summer 2009 4961941044_C


title: Ostrava summer 2009 4961941032_A


title: Ostrava summer 2009 4961941032_G


title: Ostrava summer 2009 4961941045_B


title: Ostrava summer 2009 4961941060_L


title: Ostrava summer 2009 4961941054_D


title: Ostrava summer 2009 4856050027_L


title: Ostrava summer 2009 4961941010_D


title: Ostrava summer 2009 4961941052_L


title: Ostrava summer 2009 4961941053_B


title: Ostrava summer 2009 4961941053_A


title: Ostrava summer 2009 4868499055_D


title: Ostrava summer 2009 4961941052_J


title: Ostrava summer 2009 4961941036_L


title: Ostrava summer 2009 4961941059_G


title: Ostrava summer 2009 4961941052_C


title: Ostrava summer 2009 4961941032_D


title: Ostrava summer 2009 4961941053_J


title: Ostrava summer 2009 4868499055_C


title: Ostrava summer 2009 4961941003_D


title: Ostrava summer 2009 4961941003_B


title: Ostrava summer 2009 5067327057_F


title: Ostrava summer 2009 5067327057_C


title: Ostrava summer 2009 4961941032_L


title: Ostrava summer 2009 4961941032_E


title: Ostrava summer 2009 4961941052_E


title: Ostrava summer 2009 4961941052_I


title: Ostrava summer 2009 4961941054_J


title: Ostrava summer 2009 4961941054_B


title: Ostrava summer 2009 4961941036_C


title: Ostrava summer 2009 4961941031_E


title: Ostrava summer 2009 4856050027_J


title: Ostrava summer 2009 4856050027_K


title: Ostrava summer 2009 4961941045_G


title: Ostrava summer 2009 4961941045_E


title: Ostrava summer 2009 4961941031_J


title: Ostrava summer 2009 4961941060_F


title: Ostrava summer 2009 4961941045_F


title: Ostrava summer 2009 4961941031_C


title: Ostrava summer 2009 4961941052_A


title: Ostrava summer 2009 4961941059_E


title: Ostrava summer 2009 4856050027_I


title: Ostrava summer 2009 4961941042_L


title: Ostrava summer 2009 4961941032_B


title: Ostrava summer 2009 4961941060_E


title: Ostrava summer 2009 4961941045_H


title: Ostrava summer 2009 4961941042_H


title: Ostrava summer 2009 4961941045_A


title: Ostrava summer 2009 4961941032_J


title: Ostrava summer 2009 4961941053_G


title: Ostrava summer 2009 4868499050_A


title: Ostrava summer 2009 4961941042_A


title: Ostrava summer 2009 4961941059_C


title: Prague summer 2009 4961941010_A


title: Prague summer 2009 4961941054_K


title: Prague summer 2009 4961941036_F


title: Prague summer 2009 4961941031_K


title: Prague summer 2009 4961941052_F


title: Ostrava summer 2009 4961941045_C


title: Prague summer 2009 4961941036_B


title: Prague summer 2009 4961941042_K


title: Prague summer 2009 4961941031_I


title: Prague summer 2009 4961941054_C


title: Prague summer 2009 4961941032_C


title: Prague summer 2009 4961941031_L


title: Ostrava summer 2009 4961941010_C


title: Prague summer 2009 4961941042_B


title: Prague summer 2009 4961941052_B


title: Prague summer 2009 4961941052_K


title: Prague summer 2009 4961941010_B


title: Prague summer 2009 4961941044_L


title: Prague summer 2009 4961941042_D


title: Prague summer 2009 4961941054_A


title: Prague summer 2009 4961941031_D


title: Prague summer 2009 4961941042_I


title: Prague summer 2009 4961941052_D


title: Prague summer 2009 4961941054_I


title: Prague summer 2009 4961941032_I


title: Prague summer 2009 4961941044_H


title: Prague summer 2009 4961941054_E


title: Prague summer 2009 4961941042_G


title: Prague summer 2009 4961941045_J


title: Prague summer 2009 4961941059_I


title: Prague summer 2009 4961941060_G


title: Prague summer 2009 4961941045_D


title: Prague summer 2009 4868499057_G


title: Prague summer 2009 4961941053_C


title: Prague summer 2009 4961941060_K


title: Prague summer 2009 4961941031_G


title: Prague summer 2009 4868499049_A


title: Prague summer 2009 4961941003_A


title: Prague summer 2009 4868499055_J


title: Prague summer 2009 4961941011_C


title: Prague summer 2009 4961941003_G


title: Prague summer 2009 4961941032_F


title: Prague summer 2009 4961941044_B


title: Prague summer 2009 5067327057_J


title: Prague summer 2009 4961941031_B


title: Prague summer 2009 4961941011_B


title: Prague summer 2009 4961941054_H


title: Prague summer 2009 4961941044_D


title: Prague summer 2009 4961941044_F


title: Prague summer 2009 4961941045_I


title: Prague summer 2009 4961941011_A


title: Prague summer 2009 4961941036_E


title: Prague summer 2009 4961941052_H


title: Prague summer 2009 4961941053_H


title: Ostrava winter 2009 4868499049_E


title: Ostrava winter 2009 4961941060_C


title: Ostrava winter 2009 5067327057_H


title: Prague summer 2009 4961941003_J


title: Ostrava winter 2009 5067327057_E


title: Prague summer 2009 4961941042_F


title: Ostrava winter 2009 4609518292_J


title: Ostrava winter 2009 4609518292_L


title: Ostrava winter 2009 5067327057_B


title: Prague summer 2009 4868499055_H


title: Ostrava winter 2009 5067327057_K


title: Ostrava winter 2009 4868499049_F


title: Prague summer 2009 4961941036_K


title: Ostrava winter 2009 5067327057_D


title: Prague summer 2009 4961941054_G


title: Ostrava winter 2009 5067327057_G


title: Ostrava winter 2009 4961941003_H


title: Ostrava winter 2009 4609518292_K


title: Ostrava winter 2009 4868499049_G


title: Ostrava winter 2009 4609518292_H


title: Ostrava winter 2009 4868499051_I


title: Ostrava winter 2009 4868499051_J


title: Ostrava winter 2009 4609518292_I


title: Ostrava winter 2009 4961941036_A


title: Ostrava winter 2009 4868499050_F


title: Ostrava winter 2009 4961941059_F


title: Ostrava winter 2009 4609518292_D


title: Ostrava winter 2009 4961941059_A


title: Ostrava winter 2009 4868499051_L


title: Ostrava winter 2009 4609518292_E


title: Ostrava winter 2009 4868499057_L


title: Ostrava winter 2009 4609518292_G


title: Ostrava winter 2009 4868499056_C


title: Ostrava winter 2009 4961941003_K


title: Ostrava winter 2009 4609518292_B


title: Ostrava winter 2009 4609518292_A


title: Ostrava winter 2009 4961941003_F


title: Ostrava winter 2009 4613710042_L


title: Ostrava winter 2009 4961941003_C


title: Ostrava winter 2009 4609518292_C


title: Ostrava winter 2009 4868499056_G


title: Ostrava winter 2009 4868499056_J


title: Ostrava winter 2009 4613710042_K


title: Ostrava winter 2009 4609518293_L


title: Ostrava winter 2009 4868499057_K


title: Ostrava winter 2009 4613710042_J


title: Ostrava winter 2009 4868499051_G


title: Ostrava winter 2009 4609518293_K


title: Ostrava winter 2009 4961941003_I


title: Ostrava winter 2009 4868499057_D


title: Ostrava winter 2009 4961941003_E


title: Ostrava winter 2009 4868499057_B


title: Ostrava winter 2009 4868499057_C


title: Ostrava winter 2009 4613710042_I


title: Ostrava winter 2009 4609518293_J


title: Ostrava winter 2009 4868499050_D


title: Ostrava winter 2009 4613710042_G


title: Ostrava winter 2009 4868499057_A


title: Ostrava winter 2009 4609518293_H


title: Ostrava winter 2009 4613710042_H


title: Ostrava winter 2009 4609518293_I


title: Ostrava winter 2009 4868499050_I


title: Ostrava winter 2009 4868499051_C


title: Ostrava winter 2009 4868499049_C


title: Ostrava winter 2009 4961941036_H


title: Ostrava winter 2009 4868499051_A


title: Ostrava winter 2009 4868499050_C


title: Ostrava winter 2009 4609518293_G


title: Ostrava winter 2009 4868499055_E


title: Ostrava winter 2009 4609518293_E


title: Ostrava winter 2009 4609518293_F


title: Ostrava winter 2009 4868499055_F


title: Ostrava winter 2009 4613710042_D


title: Ostrava winter 2009 4868499055_L


title: Ostrava winter 2009 4613710042_E


title: Ostrava winter 2009 4609518293_D


title: Ostrava winter 2009 4609518241_B


title: Ostrava winter 2009 4609518241_A


title: Ostrava winter 2009 4609518241_D


title: Ostrava winter 2009 4609518293_A


title: Ostrava winter 2009 4609518241_E


title: Ostrava winter 2009 4868499055_K


title: Ostrava winter 2009 4609518241_C


title: Ostrava winter 2009 4609518241_F


title: Ostrava winter 2009 4609518293_C


title: Ostrava winter 2009 4868499055_A


title: Prague winter 2009 4961941059_D


title: Prague winter 2009 4609518241_K


title: Prague winter 2009 4961941059_H


title: Ostrava winter 2009 4868499055_B


title: Prague summer 2009 4961941032_K


title: Ostrava winter 2009 4609518293_B


title: Prague winter 2009 4868499057_E


title: Prague winter 2009 4609518241_L


title: Prague winter 2009 4868499057_J


title: Prague winter 2009 4868499057_I


title: Prague winter 2009 4609518241_I


title: Prague winter 2009 4609518241_J


title: Prague winter 2009 4613710042_A


title: Prague winter 2009 4613710042_B


title: Prague winter 2009 4613710042_C


title: Prague winter 2009 4609518241_G


title: Prague winter 2009 4868499049_D


title: Prague winter 2009 4868499056_H


title: Prague winter 2009 4868499056_L


title: Prague winter 2009 4868499049_K


title: Prague winter 2009 5067327057_L


title: Prague winter 2009 4609518241_H


title: Prague winter 2009 4868499049_J


title: Prague winter 2009 4868499050_L


title: Prague winter 2009 4868499050_G


title: K8 WT variant male bio replicate 4

last: Strnad

address: Pauwelsstraße 30

institute: RWTH Aachen University

description: Gene expression

hyb_protocol: 2µg of total RNA were used for the One-Cycle target labeling assay, further processed and hybridized to the GeneChip® Mouse 430 Plus 2.0 array from Affymetrix according to manufacturer’s instructions.

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

data_processing: Statistical analyses were carried out using BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html). Arrays have been normalized using Robust Multichip Average (RMA)

source_name: Liver from male human wild type K8

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: All animals were housed animal facilty of the Ulm University (Ulm, Germany)

extract_protocol: RNA from livers were extracted by Qiagen Rneasy mini isolation kit (#74106).

treatment_protocol: Animals are untreated

value: liver tissue under basal condition

tag: strain

value: FVB/N backround

value: K8 WT variant


title: Prague winter 2009 4868499051_B


title: Prague winter 2009 4868499056_K


title: K8 WT variant male bio replicate 3

description: Gene expression


title: Prague winter 2009 4868499056_A


title: Prague winter 2009 4868499051_H


title: K8 R341H variant male bio replicate 3

description: Gene expression

source_name: Liver from male human K8 R341H variant

value: K8 R341H variant


title: K8 R341H variant male bio replicate 2

description: Gene expression


title: Prague winter 2009 4961941036_I


title: K8 WT variant female bio replicate 1

description: Gene expression

source_name: Liver from female human wild type K8


title: K8 WT variant female bio replicate 4

description: Gene expression


title: K8 WT variant male bio replicate 2

description: Gene expression


title: K8 R341H variant male bio replicate 1

description: Gene expression


title: K8 R341H variant male bio replicate 4

description: Gene expression


title: K8 WT variant female bio replicate 3

description: Gene expression


title: K8 R341H variant female bio replicate 4

description: Gene expression

source_name: Liver from female human K8 R341H variant


title: K8 WT variant male bio replicate 1

description: Gene expression


title: Prague winter 2009 4868499056_I


title: Prague winter 2009 4961941059_K


title: K8 WT variant female bio replicate 2

description: Gene expression


title: Prague winter 2009 4961941059_B


title: Prague winter 2009 4961941036_D


title: Prague winter 2009 4868499051_K


title: Prague winter 2009 4961941060_J


title: K8 R341H variant female bio replicate 3

description: Gene expression


title: K8 G62C variant_male bio replicate 4

description: Gene expression

source_name: Liver from male human K8 G62C variant

value: K8 G62C variant


title: K8 R341H variant female bio replicate 1

description: Gene expression

value: female


title: Prague winter 2009 4868499049_I


title: Prague winter 2009 4868499049_H


title: Prague winter 2009 4868499056_E


title: Prague winter 2009 4961941060_D


title: Ostrava winter 2009 4868499050_J


title: K8 G62C variant_male bio replicate 3

description: Gene expression


title: Prague winter 2009 4868499049_B


title: K8 R341H variant female bio replicate 2

description: Gene expression


title: K8 G62C variant_male bio replicate 1

description: Gene expression


title: K8 G62C variant_female bio replicate 4

description: Gene expression

source_name: Liver from female human K8 G62C variant


title: K8 G62C variant_female bio replicate 3

description: Gene expression


title: K8 G62C variant_female bio replicate 2

description: Gene expression


title: Prague winter 2009 4868499056_F


title: Prague winter 2009 4868499051_F


title: Prague winter 2009 4868499050_H


title: K8 G62C variant_female bio replicate 1

description: Gene expression


title: Prague winter 2009 4868499051_E


title: Prague winter 2009 4868499056_D


title: K8 G62C variant_male bio replicate 2

description: Gene expression


title: Prague winter 2009 4868499056_B


title: Prague winter 2009 4868499051_D


title: P1CM_rep2

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

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

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

data_processing: All CEL files were normalized by RMA using R.

source_name: neonatal cardiomyocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cardiomyocytes and cardiac fibroblasts freshly obtained from postnatal day 1 and 8-week-old C57BL/6J mice.

treatment_protocol: The cells were all dissociated by trypsin and collagenase. To separate the cardiomyocytes from cardiac fibroblasts, dissociated cells were expanded on a culture dish and checked the absence of cardiomyocytes by TMRM (Nat Methods 2009 Hattori).

tag: Sex

value: male/female

value: day 1, neonatal

value: cardiomyocytes

tag: isolation

value: dissociation and Percoll separation


title: Prague winter 2009 4868499050_B


title: P1CF_rep2

source_name: neonatal cardiac fibroblasts

value: cardiac fibroblasts


title: Prague winter 2009 4868499050_E


title: W8CM_rep2

source_name: adult cardiomyocytes

value: 8 weeks, adult

value: dissociation by Langendorf perfusion


title: Dicer KO Alone_mRNA_1

city: London

first: Mark

middle: Stephen

last: Wilson

address: The Ridgeway

department: Molecular Immunology

institute: MR, NIMR

description: Dicer KO cells cultured alone-mRNA_1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on either mouse whoel genome array or miRNA3  Arraya. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: the data were RMA normalised using Agilent GeneSpring 12.6 GX.

source_name: Dicer KO cells

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

growth_protocol: complete IMDM media was used for all T cell culturs

treatment_protocol: T cells were isolated and stimulated with anti-CD3 (1ug/ml) and anti-CD28 (10ug/ml) for exosome release. Purified exosomes, as described, were harvested and RNA extracted.

tag: strain background

value: Dicer KO cells


title: Dicer KO + Treg_mRNA_1

description: Dicer KO cells cultured with Treg cels-mRNA_1

source_name: co-cultured Dicer KO cells with Treg cells


title: Dicer KO + Treg_mRNA_2

description: Dicer KO cells cultured with Treg cels-mRNA_2

value: co-cultured Dicer KO cells with Treg cells


title: Dicer KO Alone_mRNA_3

description: Dicer KO cells cultured alone-mRNA_3


title: Dicer KO + Treg_mRNA_3

description: Dicer KO cells cultured with Treg cels-mRNA_3