title: tail-1081


title: back-1081

status: Public on May 18 2016

type: RNA

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

country: USA

institute: UCSF

description: Gene expression data from untreated P56 mouse skin

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the MoGene-1_1-st-v1-96 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates.  Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: CEL files were background corrected and normalized with RMA using oligo in R and then log2 transformed

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: dorsal skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Mice were housed in standard conditions with standard chow and water ad libitum

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol: Mice were aged to 8 weeks, untreated

tag: tissue

value: back

tag: Sex

value: F

value: no

tag: batch


title: tail-1079

source_name: tail skin

value: tail


title: tail-1076


title: back-1077


title: tail-1078


title: back-1079


title: tail-1077


title: back-1080

value: yes


title: tail-1082

value: M


title: DBS-084

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

hyb_protocol: Standard Illumina hybridization protocol for NuGEN target (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

organism: Homo sapiens

source_name: Whole blood (PAXgene RNA)

label_protocol: NuGEN PicoSL target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from primary peripheral blood samples (PAXgene RNA collection tubes, PBMC, and DBS) using a QIACube instrument.

tag: sampletype

value: DBS

tag: age

tag: bmi

tag: alcohol

tag: smoke

tag: female

tag: black

tag: asian

tag: otherminority

tag: white

tag: educattain


title: tail-1083


title: tail-1085


title: back-1078


title: back-1083


title: tail-1075


title: back-1076


title: DBS-083


title: back-1074


title: DBS-081


title: DBS-078


title: DBS-080


title: DBS-079


title: back-1075


title: tail-1073


title: tail-1074


title: DBS-082


title: tail-1072


title: DBS-072


title: DBS-073


title: DBS-074


title: DBS-071


title: back-1072


title: DBS-076


title: back-1073


title: DBS-077


title: DBS-069


title: DBS-070


title: tail-1071


title: tail-1069


title: back-1070


title: back-1071


title: back-1069


title: tail-1070


title: DBS-067


title: DBS-063


title: DBS-062


title: back-1068


title: DBS-064


title: back-1067


title: tail-1066


title: tail-1067


title: DBS-066


title: DBS-061


title: back-1066


title: back-1065


title: DBS-065


title: tail-1068


title: DBS-058


title: DBS-060


title: tail-1064


title: back-1064


title: DBS-057


title: DBS-055


title: back-1063


title: tail-1063


title: back-1062


title: DBS-056


title: DBS-059


title: tail-1061


title: tail-1062


title: DBS-053


title: DBS-054


title: back-1061


title: back-1060


title: DBS-049


title: tail-1060


title: DBS-050


title: DBS-051


title: DBS-048


title: DBS-052


title: back-1059


title: tail-1057


title: back-1058


title: DBS-046


title: tail-1059


title: tail-1058


title: DBS-043


title: DBS-047


title: tail-1056


title: DBS-042


title: DBS-045


title: DBS-039


title: DBS-040


title: tail-1055


title: DBS-044


title: back-1055


title: back-1056


title: tail-1054


title: DBS-036


title: back-1054


title: back-1057


title: DBS-038


title: DBS-041


title: back-1053


title: DBS-037


title: tail-1051


title: DBS-032


title: back-1050


title: back-1051


title: tail-1050


title: back-1052


title: DBS-030


title: tail-1053


title: DBS-029


title: DBS-033


title: DBS-035


title: DBS-028


title: back-1049


title: tail-1049


title: DBS-025


title: DBS-026


title: DBS-068


title: DBS-027


title: back-1048


title: DBS-023


title: tail-1046


title: tail-1045


title: back-1046


title: tail-1047


title: DBS-022


title: back-1047


title: back-1045


title: DBS-024


title: back-1043


title: DBS-020


title: tail-1043


title: DBS-017


title: DBS-019


title: DBS-018


title: tail-1044


title: tail-1052


title: back-1044


title: DBS-015


title: DBS-021


title: tail-1042


title: DBS-012

value: missing


title: DBS-014


title: DBS-016


title: tail-1040


title: DBS-009


title: DBS-011


title: tail-1041


title: DBS-013


title: DBS-010


title: tail-1039


title: back-1040


title: back-1039


title: DBS-008


title: back-1041


title: tail-1038


title: back-1037


title: back-1038


title: DBS-004


title: back-1036


title: DBS-007


title: tail-1036


title: tail-1037


title: DBS-002


title: DBS-003


title: tail-1035


title: tail-1034


title: PBMC-083

value: PBMC


title: DBS-034


title: back-1032


title: tail-1032


title: back-1035


title: DBS-001


title: back-1033


title: PBMC-084


title: PBMC-079


title: PBMC-082


title: PBMC-081


title: PBMC-080


title: back-1034


title: DBS-006


title: DBS-005


title: tail-1033


title: PBMC-077


title: PBMC-078


title: PBMC-076


title: tail-1030


title: back-1031


title: tail-1031


title: PBMC-073


title: PBMC-074


title: PBMC-070


title: tail-1029


title: PBMC-071


title: back-1029


title: PBMC-066


title: back-1028


title: PBMC-061


title: DBS-031


title: back-1042


title: back-1027


title: tail-1026


title: tail-1027


title: PBMC-064


title: back-1030


title: back-1023


title: PBMC-069


title: PBMC-072


title: tail-1023


title: PBMC-067


title: PBMC-062


title: back-1026


title: PBMC-060


title: back-1022


title: back-1024


title: tail-1025


title: PBMC-057


title: PBMC-059


title: tail-1022


title: PBMC-068


title: PBMC-063


title: PBMC-058


title: back-1025


title: PBMC-056


title: tail-1024


title: back-1021


title: tail-1021


title: PBMC-055


title: tail-1020


title: back-1020


title: PBMC-052


title: tail-1018


title: tail-1017


title: PBMC-053


title: back-1018


title: tail-1019


title: back-1019


title: PBMC-050


title: PBMC-051


title: PBMC-048


title: PBMC-054


title: tail-1014


title: PBMC-046


title: PBMC-065


title: back-1016


title: PBMC-047


title: back-1014


title: tail-1028


title: PBMC-045


title: PBMC-041


title: PBMC-043


title: tail-1016


title: PBMC-049


title: back-1015


title: PBMC-044


title: tail-1013


title: back-1013


title: PBMC-040


title: PBMC-038


title: PBMC-042


title: tail-1010


title: back-1012


title: back-1011


title: back-1010


title: tail-1009


title: PBMC-035


title: tail-1011


title: PBMC-028


title: PBMC-036


title: PBMC-031


title: PBMC-032


title: PBMC-037


title: PBMC-033


title: PBMC-030


title: tail-1015


title: back-1006


title: back-1008


title: PBMC-039


title: PBMC-034


title: tail-1006


title: tail-1007


title: PBMC-029


title: tail-1008


title: back-1007


title: PBMC-022


title: PBMC-023


title: PBMC-018


title: back-1003


title: back-1001


title: back-1005


title: back-1002


title: tail-1000


title: back-1009


title: tail-1003


title: PBMC-026


title: PBMC-020


title: tail-1002


title: PBMC-021


title: tail-1005


title: tail-1001


title: PBMC-024


title: PBMC-027


title: tail-1004


title: PBMC-019


title: PBMC-025


title: PBMC-014


title: back-1000


title: PBMC-013


title: PBMC-015


title: PBMC-012


title: back-1004


title: PBMC-011


title: PBMC-016


title: PBMC-002


title: PBMC-003


title: PBMC-007


title: PBMC-008


title: PBMC-010


title: PAX-076

value: PAXgene


title: PAX-081


title: PAX-082


title: PBMC-009


title: PBMC-006


title: PBMC-005


title: PAX-077


title: PBMC-004


title: PAX-083


title: PAX-078


title: PAX-084


title: PAX-079


title: PBMC-001


title: PAX-073


title: PAX-071


title: PAX-080


title: PAX-067


title: PAX-074


title: PAX-068


title: PBMC-017


title: PAX-069


title: PAX-065


title: PAX-061


title: PAX-060


title: PAX-070


title: PAX-055


title: PAX-050


title: PAX-064


title: PAX-059


title: PAX-054


title: PAX-063


title: PAX-058


title: PAX-048


title: PAX-066


title: PAX-053


title: PAX-051


title: PAX-072


title: PAX-056


title: PAX-045


title: PAX-046


title: PAX-044


title: PAX-062


title: PAX-057


title: PAX-041


title: PAX-052


title: PAX-047


title: PAX-039


title: PAX-040


title: PAX-042


title: PAX-036


title: PAX-035


title: PAX-049


title: PAX-034


title: PAX-037


title: PAX-043


title: PAX-032


title: PAX-038


title: PAX-030


title: PAX-033


title: PAX-027


title: PAX-031


title: PAX-026


title: PAX-025


title: PAX-028


title: PAX-029


title: PAX-023


title: PAX-024


title: PAX-021


title: PAX-020


title: PAX-018


title: PAX-016


title: PAX-019


title: PAX-022


title: PAX-017


title: PAX-012


title: PAX-015


title: PAX-011


title: PAX-014


title: PAX-013


title: PAX-010


title: PAX-007


title: PAX-003


title: PAX-009


title: PAX-008


title: PAX-004


title: PAX-002


title: PAX-005


title: PAX-001


title: PAX-006


title: Wild Type MEFs Non treated

city: Clayton

first: Michael

middle: Paul

last: Gantier

state: VIC

address: Hudson Institute of Medical Research

department: Centre for Innate Immunity and Infectious Diseases

country: Australia

institute: Hudson Institute of Medical Research

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion, 25 μl of 2x Agilent gene expression hybridisation buffer was added and 43 μl of sample hybridised for 17 hours at 67°C in a rotating Agilent hybridisation oven

scan_protocol: After hybridisation, microarrays were sequentially washed 1 minute with room temperature GE wash buffer 1 (Agilent) and 1 minute with 37°C GE wash buffer 2 (Agilent). Slides were scanned on the Agilent C, DNA microarray scanner using one-color scan settings for 8x60k array slides. Scan area 61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid: 028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.
Analysis were done with Genespring 13.0 (Agilent) - using Threshold of 1, Percentile shift (Target percentile 75), and Baseline median of all parameters to normalize the data.

source_name: Mouse embryonic Fibroblasts

label_protocol: Cy3 labelled cRNA was prepared from 0.1 μg total RNA using the One-Color Low input Quick Amp labelling Kit (Agilent, v6.6 September 2012), followed by RNeasy column purification (Qiagen). 600 ng of Cy3 labeled cRNA was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA containing small RNAs was purified from cultured MEFs using the mirVana miRNA Isolation Kit (samples 1-4) or the ISOLATE II RNA Mini Kit (BIOLINE).

treatment_protocol:
Hydroxytamoxifen was first diluted to 2.5 mM in 100% ethanol before being diluted further to the final concentration of 500 nM in complete DMEM.
Samples 1,2,3,4: C57B/6 MEFs were treated or not with 500 nM OHT for 24h, rinsed, incubated another 72 h before RNA extraction (total time after OHT treatement of 24 h +72 h= 96 h).
Samples 5,6,7,8: C57B/6 MEFs were treated or not with 500 nM OHT for 24h, rinsed, incubated another 24 h before RNA extraction (total time after OHT treatement of 24 h+24 h= 48 h).

tag: strain

tag: genotype/variation

value: Wild Type

tag: cell type

value: embryonic fibroblast

tag: treatment

value: control

tag: time after treatment

tag: sample


title: Prefrontal cortex_BTBR_replicate_3

city: Trento

first: Yuri

last: Bozzi

address: via Sommarive 9

department: CIBIO - Centre for Integrative Biology

country: Italy

institute: University of Trento

hyb_protocol: According to manufacturer's instructions for Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F.

scan_protocol: Slides were scanned immediately after washing using a Agilent High-Resolution C Scanner with one color scan setting for 4x44k array slides, according to manufacturer's instructions.

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. Intensity values were processed with GeneSpring GX software (Agilent) using default parameters to remove low-quality probes. Signals were then normalized by means of the quantile normalization method, and data were statistically filtered by two-way ANOVA imposing a fold change 2 for each gene in at least one of the four experimental data groups. Differentially expressed genes were classified by DAVID software, applying Benjamini-corrected p value cutoff of 0.05. Data are reported as mean values of normalized signal intensity values  (n=3 per group).

source_name: BTBR prefrontal cortex

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent 5190-0442) according to the manufacturer's instructions.

extract_protocol: RNAs from dissected prefrontal cortices (n=3 per experimental group) were purified using standard column purification according to the manufacturer’s protocol (RNAeasy Mini Kit, QIAGEN). RNA quality was analyzed by microfluidic gel electrophoresis on RNA 6000 NanoChips using the Agilent 2100 Bioanalyzer. Only RNA with a high (9) RNA integrity number was selected and used for subsequent retrotranscription, labeling, and array hybridization according to Agilent protocols.

treatment_protocol: Mice were housed in standard cages and received no pharmacological treatment. Prefrontal cortices were freshly dissected and frozen on dry ice.

tag: strain background

value: BTBR T+ Itpr3tf/J

tag: gender

value: male

value: 5 months

tag: tissue

value: whole prefrontal cortex


title: Wild Type MEFs OHT

value: 500 nM OHT


title: Dicer wt/wt x ESRCRE+ Non treated

value: Dicer wt/wt x ESRCRE


title: Dicer wt/wt x ESRCRE+ OHT


title: Dicer fl/fl x ESRCRE+ OHT

value: Dicer fl/fl x ESRCRE


title: Prefrontal cortex_C75Bl6_replicate_3

source_name: C57BL/6J prefrontal cortex

value: wild type

tag: age


title: Prefrontal cortex_BTBR_replicate_2


title: Dicer fl/fl x ESRCRE+ Non treated


title: Dicer fl/wt x ESRCRE+ OHT

value: Dicer fl/wt x ESRCRE


title: Primary Uveal Melanoma, sample08

type: genomic

city: Liverpool

first: Sarah

middle: E

last: Coupland

address: 6th Floor Duncan Building, Daulby Street

department: Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

description:
Genome-Wide Human SNP 6.0 Array
PUM08

hyb_protocol: Hybridised to Affymetrix SNP 6.0 arrays according to manufacturers protocol

scan_protocol: Arrays were scanned using the Affymetrix GeneChip 3000 7G Scanner with the GeneChip Command Console software.

data_processing:
Genotypes and confidence scores were generated by fitting two-dimensional Gaussian functions to the microarray data using a customized expectation-maximization algorithm (Birdseed algorithm v. 2.0, Affymetrix). Subsequent data analysis was performed using Partek® Genomics Suite® software v. 6.6 (Partek, St. Louis, MI, USA) starting from CEL files. Considering the use of FFPE specimens and to increase the signal-to-noise ratio, probe sets from fragments longer than 700 bp were removed from further analysis (as recommended by Partek®). CN values were generated from the allele intensities using the Partek® 380-sample HapMap reference (run by Affymetrix) for unpaired samples. Starting with CN estimates for each marker, a list of regions was identified using genomic segmentation. This algorithm identified breakpoints, which represented changes in CN between adjacent regions. For the identification of different regions, a minimum of 50 genomic markers had to be included within a region and a t-test p-value threshold of 0.001 was applied. After genomic segmentation, the dataset was separated into different groups: (i) MUMs only, (ii) matched PUM-MUM pairs, and (iii) PUMs only, whereby the final dataset of (iii) functioned as a reference for comparisons to the MUMs. These individual worksheets were filtered further to identify regions, which showed either only amplifications or only deletions within the samples for individual regions. This step was included not only to minimize the output amount, but mainly because we hypothesized that only non-contradicting alterations would lead to meaningful data. Genes overlapping the regions were identified and annotated with the NCBI Reference Sequence (RefSeq, released 02.02.2015) database. Venn diagrams were used to identify genes with common aberrations as well as genes specifically amplified or deleted in both primary and metastatic tumors. For the AsCN analysis, the AsCN workflow was used. In brief, the intensity (CEL) and genotype (CHP) files were uploaded and the AsCN was created using the unpaired analysis. AI was calculated and overlapped with the CN regions determined using the CN analysis workflow. Finally, the overlapping genes were identified and annotated with the NCBI RefSeq.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

source_name: Uveal Melanoma, enucleation

label_protocol: Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 Assay following the manufacturers protocol with the exception of doubling the number of PCR reactions to compensate for using FFPE material.

extract_protocol: Qiagen DNeasy blood and tissue kit following FFPE protocol. Final purification using GenElute (Sigma) following the manaufacturer's protocol.

value: Uveal melanoma

tag: paired partner


title: Hippocampus_BTBR_replicate_4

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. Intensity values were processed with GeneSpring GX software (Agilent) using default parameters to remove low-quality probes. Signals were then normalized by means of the quantile normalization method, and data were statistically filtered by two-way ANOVA imposing a fold change 2 for each gene in at least one of the four experimental data groups. Differentially expressed genes were classified by DAVID software, applying Benjamini-corrected p value cutoff of 0.05. Data are reported as mean values of normalized signal intensity values  (n=4 per group).

source_name: BTBR hippocampus

growth_protocol: not applicable

extract_protocol: RNAs from dissected hippocampi (n=4 per experimental group) were purified using standard column purification according to the manufacturer’s protocol (RNAeasy Mini Kit, QIAGEN). RNA quality was analyzed by microfluidic gel electrophoresis on RNA 6000 NanoChips using the Agilent 2100 Bioanalyzer. Only RNA with a high (9) RNA integrity number was selected and used for subsequent retrotranscription, labeling, and array hybridization according to Agilent protocols.

treatment_protocol: Mice were housed in standard cages and received no pharmacological treatment. Hippocampi were freshly dissected and frozen on dry ice.

value: whole hippocampus


title: Prefrontal cortex_C75Bl6_replicate_2


title: Prefrontal cortex_C75Bl6_replicate_1


title: Primary Uveal Melanoma, sample02

description:
Genome-Wide Human SNP 6.0 Array
PUM02


title: 9495_10 Lung

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

country: Germany

institute: Research Center Borstel - Leibniz Lung Center

hyb_protocol: 1650 ng of Cy3-labelled cRNA was fragmented according to Low Input Quick Amp Labelling Kit Protocol (Agilent) with 2xHI-RPM Hybridization Buffer for 30 min at 60°C. Hybridization on Agilent Human Whole Genome 4x44k V2 arrays was performed at 65°C for 17h under constant rotation in a hybidization oven. Washing was performed using the GE Wash buffer 1 (Agilent) at RT and Ge Wash Buffer 2 (Agilent) at 37°C for each 1 min. Washed slides were air-dried and immediately scanned.

scan_protocol: Slides were immediately scannend on an Agilent SureScan Scanner with Dye Channel =Green, 5 µm Resolution and scanning area=61 x 21.6 mm.

data_processing: Agilent Feature Extraction Software V 11.5 was used with default options (GE 1-color protocol) to extract raw data. Txt files were imported into GeneSpring software Version 13 under omission of compromised flags. Flags were accepted if at least 100 percent of samples in any 1 out of 7 conditions were detected.

source_name: Lung

label_protocol: Cy3-labelling of total RNA was conducted with the Low Input Quick Amp Labelling Kit (Agilent) according to manufacturer´s instructions. Dye incorporation rate and specific yield was calculated using an NanoDrop spectrophotometer.

extract_protocol: Hope-fixed, paraffin-embedded tissues were cut on a microtome and transferred into microcentrifuge tubes to retrieve rolls of each specimen. Samples were subsequently deparaffinized by following protocol: 10 min. 1ml 100% xylene on a rotating device followed by centrifugation at 5000 rpm for 5 min. Supernatant was removed and step repeated. After 2nd incubation with xylene, 1ml of 100% EtOH was added and samples rotated for 10 min as well as 5 min. of centrifugation. EtOH was repeated. After xylene and EtOH incubation, the samples were dried using a vacuum centrifuge until totally dry. Deparaffinized samples were then subjected to RNA isolation with Qiagen Rneasy Mini Kit according to manufacturer´s instructions.

tag: individual id

value: Tumor-free lung


title: 9495_10 Tumor

value: NSCLC

tag: tissue type

value: Squamous Cell Carcinoma


title: Primary Uveal Melanoma, sample04

description:
Genome-Wide Human SNP 6.0 Array
PUM04


title: Metastatic Uveal Melanoma, sample21

description:
Genome-Wide Human SNP 6.0 Array
MUM21

source_name: Uveal Melanoma, liver resection


title: Primary Uveal Melanoma, sample09

description:
Genome-Wide Human SNP 6.0 Array
PUM09


title: Hippocampus_C75Bl6_replicate_4

source_name: C57BL/6J hippocampus


title: Hippocampus_BTBR_replicate_1


title: 13230_12 Tumor


title: 13230_12 Lung


title: Primary Uveal Melanoma, sample05

description:
Genome-Wide Human SNP 6.0 Array
PUM05


title: 22024_11 Tumor

value: Adenocarcinoma


title: Metastatic Uveal Melanoma, sample13

description:
Genome-Wide Human SNP 6.0 Array
MUM13


title: Metastatic Uveal Melanoma, sample11

description:
Genome-Wide Human SNP 6.0 Array
MUM11


title: Prefrontal cortex_BTBR_replicate_1


title: Hippocampus_BTBR_replicate_3


title: Metastatic Uveal Melanoma, sample12

description:
Genome-Wide Human SNP 6.0 Array
MUM12


title: Primary Uveal Melanoma, sample18

description:
Genome-Wide Human SNP 6.0 Array
PUM18


title: Hippocampus_BTBR_replicate_2


title: Metastatic Uveal Melanoma, sample18

description:
Genome-Wide Human SNP 6.0 Array
MUM18


title: Metastatic Uveal Melanoma, sample17

description:
Genome-Wide Human SNP 6.0 Array
MUM17


title: Metastatic Uveal Melanoma, sample08

description:
Genome-Wide Human SNP 6.0 Array
MUM08


title: Metastatic Uveal Melanoma, sample05

description:
Genome-Wide Human SNP 6.0 Array
MUM05


title: Metastatic Uveal Melanoma, sample10

description:
Genome-Wide Human SNP 6.0 Array
MUM10


title: 2508_11 Tumor


title: Dicer fl/wt x ESRCRE+ Non treated

value: embryonic fibroblast


title: Hippocampus_C75Bl6_replicate_2


title: 22024_11 Lung


title: IRAK4_EPB07P1_hPBMC_GARD_vehicle_D122_2B

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

hyb_protocol: The Biotin-labeled cRNA was used to probe Human Genome U219 array, comprising of 49,293 probe sets and representing more than 20,000 human genes.

scan_protocol: Biotin-labeled cRNA was generated from cDNA and used to probe Human Genome U219 array, comprising of 49,293 probe sets and representing more than 20,000 human genes, using the Gene Titan MC instrument (Affymetrix, West Sacramento, CA).

data_processing: The data were analyzed with the BMS Xpress functional genomics data warehouse (internal BMS system) and were processed to RMA intensities.

source_name: Human Donor PBMC

label_protocol: Total RNA was treated with DNase I and cleaned up with Qiagen RNeasy MiniElute Cleanup Kit (Cat. # 74204). The RNA concentrations were determined by NanoDrop and RNA quality was evaluated using Experion (Bio-Rad). All target labeling reagents were purchased from Affymetrix (West Sacramento CA). Double-stranded cDNAs were synthesized from 1 ug of total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA.

extract_protocol: Total RNA was isolated from the cells with Qiagen RNeasy Mini Kit (Cat. # 74104).

treatment_protocol: PBMCs from two donors were pretreated with compound for 30 minutes and stimulated with gardiquimod (TLR7 ligand) for 5 hrs.

tag: donor id

value: PBMC

tag: pretreated with

value: DMSO (vehicle) for 30 min at 37C

tag: stimulated with

value: 5ug/ml gardiquimod for 5hrs


title: Metastatic Uveal Melanoma, sample07

description:
Genome-Wide Human SNP 6.0 Array
MUM07


title: 2508_11 Lung


title: IRAK4_EPD01P1_hPBMC_GARD_vehicle_D140_2F


title: 1799_12 Lung


title: Hippocampus_C75Bl6_replicate_3

value: male

value: 5 months


title: 21918_11 Lung


title: Hippocampus_C75Bl6_replicate_1


title: IRAK4_EPC04P1_hPBMC_GARD_BMT087965_D140_5E


title: 21918_11 Tumor


title: Metastatic Uveal Melanoma, sample03

description:
Genome-Wide Human SNP 6.0 Array
MUM03


title: IRAK4_EPB01P1_hPBMC_GARD_vehicle_D122_2D


title: IRAK4_EPC05P1_hPBMC_GARD_BMT087965_D140_5G


title: IRAK4_EPD07P1_hPBMC_unstim_vehicle_D140_1G

value: none (unstimulated)


title: 1799_12 Tumor


title: 12928_12 Lung


title: IRAK4_EPD06P1_hPBMC_GARD_vehicle_D140_2E


title: Metastatic Uveal Melanoma, sample09

description:
Genome-Wide Human SNP 6.0 Array
MUM09


title: 12928_12 Tumor


title: 5622_12 Tumor


title: Liver_PALMdiet_rep09

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

hyb_protocol: 1,65 µg of Cy3-labelled cRNA was fragmented (60°C, 30 min) and hybridized to Agilent Mouse GE 4x44K v2 microarrays (G4846A) following the manufacturer's instructions. Following Hybridization, microarrays were washed sequentially in Wash buffer 1 (1 min), Wash buffer 2 (37°C, 1 min) and Stabilization and Drying Solution (30 sec) as recommended by the manufacturer.

scan_protocol: Slides were scanned immediately after washing on a GenePix™ 4000B array scanner

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and grid 026655_D_F_20100123). All subsequent data analyses were done under R (www.r-project.org) using Bioconductor packages (www.bioconductor.org). Raw data (median of pixels intensity for each spot) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot):  myfunw <- function(x)  {okType < -x$ControlType==0 ; okFoundGreen <- x$gIsFound==1 ; okPos <- x$gIsPosAndSignif==1 ; okWellAbove <- x$gIsWellAboveBG==1 ; as.numeric(okType & okFoundGreen & okPos & okWellAbove)}  We selected the spots with a weight of 1 for 14 out of 18 microarrays or with a weight of 1 in at least 8 microarrays from at least one experimental group. At this step, 18060 spots out of 45018 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median log normalized signal of each set of replicated probes. The resulting matrix has 18060 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver, mouse, PALM diet, replicate 09

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was perpared from 1µg of total RNA using the One-color Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions. Dye incorporation and cRNA yield were controlled on a Nanodrop ND-1000 spectrophotometer.

growth_protocol: Seven-week old male C57BL/6J mice were purchased from Charles River (L’Arbresle, France). They were housed collectively on wood litter, at 23 ± 1°C under 12-h light/dark cycles (light on at 06:00 am) and were fed ad libitum a standard pelleted diet (SAFE A04, Augy, France) during acclimatization for 1 week.

extract_protocol: Immediately following euthanasia, liver was removed and weighted. Liver samples of ~100 mg were snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, USA) following manufacturer's instructions. Total RNA quality was controlled on an Agilent 2100 Bioanalyzer (Agilent Technologies) and concentration was assayed using absorbance at 260nm on a Nanodrop ND-1000 spectrophotometer (Thermo Scientific)

treatment_protocol: At 8 weeks of age, mice were randomly assigned to the experimental groups and fed during 5 weeks one of the two high fat diets containing palm oil (PALM diet; 55.6% SFA, 34.8% MUFA and 8.8% PUFA) or linseed oil  (LIN diet; 9.7% SFA, 22.5% MUFA and 66.7% PUFA (49.7% ALA)). Diets were prepared freshly twice a week, stored at 4°C, and provided daily to mice as soft pellets. The calculated composition (in energy %) of both high fat diets is 16.7% protein, 32.1% carbohydrate, and 51.1% lipid.

value: 13 weeks

value: liver

tag: diet

value: 5 weeks on High fat PALM diet


title: Liver_PALMdiet_rep08

source_name: Liver, mouse, PALM diet, replicate 08

tag: strain


title: Liver_PALMdiet_rep07

source_name: Liver, mouse, PALM diet, replicate 07


title: Liver_PALMdiet_rep06

source_name: Liver, mouse, PALM diet, replicate 06


title: IRAK4_EPE04P1_hPBMC_GARD_BMT087965_D122_5D


title: Metastatic Uveal Melanoma, sample01

description:
Genome-Wide Human SNP 6.0 Array
MUM01


title: 12893_12 Tumor


title: Liver_PALMdiet_rep10

source_name: Liver, mouse, PALM diet, replicate 10


title: 5622_12 Lung


title: 12893_12 Lung


title: Liver_PALMdiet_rep04

source_name: Liver, mouse, PALM diet, replicate 04


title: 3302_12 Lung


title: Liver_PALMdiet_rep01

source_name: Liver, mouse, PALM diet, replicate 01


title: 3302_12 Tumor


title: IRAK4_EPF02P1_hPBMC_GARD_BMT087965_D122_5B


title: Liver_PALMdiet_rep03

source_name: Liver, mouse, PALM diet, replicate 03


title: IRAK4_EPF01P1_hPBMC_unstim_vehicle_D122_1B


title: IRAK4_EPG04P1_hPBMC_unstim_vehicle_D140_1F


title: IRAK4_EPG01P1_hPBMC_unstim_vehicle_D122_1D


title: IRAK4_EPE07P1_hPBMC_unstim_vehicle_D122_1C


title: Liver_PALMdiet_rep05

source_name: Liver, mouse, PALM diet, replicate 05


title: Liver_PALMdiet_rep02

source_name: Liver, mouse, PALM diet, replicate 02


title: Liver_LINdiet_rep8

source_name: Liver, mouse, LIN diet, replicate 8

value: 5 weeks on High fat LIN diet


title: IRAK4_EPG02P1_hPBMC_GARD_vehicle_D140_2G


title: IRAK4_EPA02P1_hPBMC_GARD_BMT087965_D140_5F


title: IRAK4_EPH03P1_hPBMC_GARD_BMT087965_D122_5C


title: 1888_12 Tumor


title: 11560_12 Tumor


title: 11560_12 Lung


title: Liver_LINdiet_rep4

source_name: Liver, mouse, LIN diet, replicate 4


title: 15982_07 Tumor


title: Liver_LINdiet_rep5

source_name: Liver, mouse, LIN diet, replicate 5


title: IRAK4_EPG05P1_hPBMC_unstim_vehicle_D140_1E


title: 15982_07 Lung

source_name: Lung


title: Demeclocycline BT012

city: Calgary

first: Voon

middle: Wee

last: Yong

state: Alberta

address: 3330 Hospital drive NW

department: Clinical Neurosciences

country: Canada

institute: University of Calgary

description: Gene expression data from 6h of Demeclocycline treatment

hyb_protocol: Following fragmantation, hybridized to Affymetrix GeneChip® Human Gene 2.0 ST at 45°C for 16h.

scan_protocol: Scanned with Affymetrix GeneChip Scanner 3000 7G System.

data_processing: For data analysis, array data files were generated with GeneChip® Command Console® Software (AGCC) and statistical analyses were carried out in GeneSpringTM (Agilent Technologies). The fold change between treatment and control was based on the p<0.05 from T-test of unpaired samples.

source_name: BT012 human BTICs

label_protocol: The total of 250 ng of RNA for each sample with RIN higher than 9 was labelled with WT Express Kit (Ambion).

extract_protocol: RNA was extracted using a mirVana miRNA Isolation Kit (Ambion, Austin, USA) according to the manufacturer’s protocol.  Total RNA was purified with RNeasy Plus Micro Kit (Qiagen, Valencia, USA) to remove genomic DNA.  The RNA quality of integrity number (RIN) was measured with Agilent RNA Nano Chips on 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

value: BTIC exposed to Demeclocycline


title: 1888_12 Lung


title: Liver_LINdiet_rep1

source_name: Liver, mouse, LIN diet, replicate 1


title: IRAK4_EPH06P1_hPBMC_GARD_vehicle_D122_2C

source_name: Human Donor PBMC


title: Demeclocycline BT048

source_name: BT048 human BTICs


title: Liver_LINdiet_rep3

source_name: Liver, mouse, LIN diet, replicate 3


title: Demeclocycline BT025

source_name: BT025 human BTICs


title: 12799_12 Tumor


title: Control BT048

description: Gene expression data from 6h of vehicle treatment

value: BTIC exposed to vehicle


title: 6495_08 Tumor


title: 12799_12 Lung

value: Tumor-free lung


title: Control BT025


title: pb treated mouse 2 5mC profile

status: Public on May 17 2016

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

hyb_protocol: Labelled samples were applied commercially to a "Nimblegen 2.1M Deluxe promoter array" by Nimblegen, Iceland

scan_protocol: Arrays were scanned commercially by Nimblegen, Iceland

data_processing: Normalised data after normalised within arrays (loess) and between arrays (sclae normalisation) resulting in log2(IP/input) scores for each probe

source_name: 12 week PB exposed whole liver

label_protocol: Amplification of DNA samples was carried out commercially by NimbleGen, Iceland  (Cy5- (IP) or Cy3- (Input) labelled)

extract_protocol: Genomic DNA (5mC-IP - 2.5 µg in 450 µl TE), sonicated to yield a fragment distribution of approximately 300-1000 bp, was denatured by incubation at 100°C for 10 min. Samples were rapidly chilled on wet-ice. At this point, 45 µl (10%) of denatured sample was removed and saved as input, and 45 µl of 10X IP buffer (100 mM Na-Phosphate pH 7.0  (mono and dibasic), 1.4 M NaCl, 0.5 % Triton X-100) and 1 µg of 5mC (ActiveMotif; #39769) antibody were added to the remaining sample. Samples were incubated at 4C with gentle agitation overnight. Then, 40 µl of magnetic beads (Dynabeads® Protein G, Invitrogen, UK) in 1X IP buffer were added to each sample to allow magnetic separation of the antibody from the unbound DNA using a magnetic tube rack. Samples were incubated at 4C for 1 hr with gentle agitation. Beads were collected with a magnetic rack and washed with 1000 µl of 1X IP buffer at RT for 10 min with gentle agitation; washing was repeated three times. Beads were collected with a magnetic rack and re-suspended in 250 µl of digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA , 0.5 % SDS) followed by addition of 10 µl of proteinase K  (20 mg/ml; Roche Applied Science, Mannheim, Germany) and incubation at 52C for 1.5 hr with constant shaking (≥800 rpm). Finally, beads were removed using a magnetic rack and DNA was purified from the remaining sample using a QIAquick PCR Purification Kit (QIAGEN,CA, USA), eluting in a final volume of 40 µl dH2O. Inputs were also purified using a QIAquick PCR Purification Kit and eluted in 40 µl dH2O. Subsequently, 10 ng of input and IP DNA was subjected to whole genome amplification (WGA) using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich, UK) as per the manufacturer's instructions. Amplified DNA was run on a 1.2% agarose gel to confirm consistency of fragment size between samples.

value: Male

tag: genotype/variation

value: Wild type

value: PB exposed mouse liver tissue

tag: antibody

value: 5-mc - Eurogentec(cat# BI-MECY-1000)

source_name: PB exposed mouse liver tissue_input

value: none (Input)


title: Liver_LINdiet_rep6

source_name: Liver, mouse, LIN diet, replicate 6


title: Liver_LINdiet_rep2

source_name: Liver, mouse, LIN diet, replicate 2


title: 6495_08 Lung


title: pb treated mouse 1 5mC profile


title: control mouse 2 5mC profile

source_name: normal whole liver

value: normal mouse liver tissue

source_name: normal whole liver_input


title: 21577_08 Lung


title: 12097_07 Lung


title: Control BT012

tag: treatment


title: 21577_08 Tumor

value: NSCLC

value: Adenocarcinoma


title: 17962_08 Lung


title: NASH driven tumour mouse 2 5hmc profile

description:
processed data file: hmeDIP_NASH_study.txt
Tum2_5HMC_NASHstudy

hyb_protocol: Labelled samples were applied to Agilent-028383 SurePrint G3 Mouse Promoter Microarray 1x1M

scan_protocol: Arrays were scanned inhouse

data_processing: Normalised data after normalised within arrays (loess) and between arrays (scale normalisation) resulting in log2(IP/input) scores for each probe. Data generated using Agilent Feature extraction software (version 12)

source_name: NASH liver tumour

label_protocol: Amplification of DNA samples was carried out following manufacturers instructions using (Cy5- (IP) or Cy3- (Input) labelled)

treatment_protocol: genomic DNA extracted from STZ + High fat diet exposed mouse liver resulting in liver tumour

value: wild type

tag: exposed to

value: STZ + High fat diet resulting in liver tumour

value: non-acoholic steatohepatitis (NASH) related hepatocellular carcinoma (HCC)

value: 5-hmC - Active Motif (cat# 39769)

source_name: NASH liver tumour_input

value: male


title: control mouse 1 5mC profile


title: 12097_07 Tumor

value: Squamous Cell Carcinoma


title: descending colon cancer_with liver metastasis_original [Exp 1]

city: Hangzhou

first: Dong

last: Chen

address: 79# Qingchun Rd

country: China

institute: First Affiliated Hospital, Zhejiang University

description: lncRNAs and mRNAs expression in the colon cancer tissue of CRC patients with liver metastasis

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.

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 the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37C in a humidified incubator with 5% CO2.

tag: subject status

value: colorectal cancer (CRC) patient with liver metastasis

tag: age (yrs)

value: F

value: peripheral blood


title: descending colon cancer_no metastasis_original [Ctrl 1]

description: lncRNAs and mRNAs expression in the colon cancer tissue of CRC patients without metastasis

source_name: descending colon cancer_no metastasis

value: colorectal cancer (CRC) patient without liver metastasis

tag: gender

value: M


title: ascending colon cancer_no metastasis_original [Ctrl 2]

source_name: ascending colon cancer_no metastasis

tag: tissue


title: rectal cancer_with liver metastasis_original [Exp 4]

description: lncRNAs and mRNAs expression in the rectal cancer tissue of CRC patients with liver metastasis

source_name: rectal cancer_with liver metastasis


title: sigmoid colon cancer_with liver metastasis_original [Exp 6]


title: ascending colon cancer_no metastasis_original [Ctrl 6]


title: 17962_08 Tumor

source_name: Lung


title: descending colon cancer_no metastasis_original [Ctrl 4]


title: control mouse 2 5hmc profile

description:
processed data file: hmeDIP_NASH_study.txt
WT2_5HMC_NASHstudy

treatment_protocol: genomic DNA extracted from normal mouse liver

tag: strain background

value: Male


title: rectal cancer_with liver metastasis_original [Exp 3]


title: control mouse 1 5hmc profile

description:
processed data file: hmeDIP_NASH_study.txt
WT1_5HMC_NASHstudy


title: ascending colon cancer_with liver metastasis_original [Exp 5]


title: NASH driven tumour mouse 1 5mC profile

description:
processed data file: MeDIP_NASH_study.txt
Tum1_MC_NASHstudy

value: 5-mc - Eurogentec(cat# BI-MECY-1000)


title: descending colon cancer_with liver metastasis_original [Exp 2]


title: NASH driven tumour mouse 2 5mC profile

description:
processed data file: MeDIP_NASH_study.txt
Tum2_MC_NASHstudy

value: none (Input)


title: ascending colon cancer_no metastasis_original [Ctrl 5]


title: control mouse 2 5mC profile

description:
processed data file: MeDIP_NASH_study.txt
WT2_MC_NASHstudy

value: normal mouse liver tissue


title: control mouse 1 5mC profile

description:
processed data file: MeDIP_NASH_study.txt
WT1_MC_NASHstudy


title: NASH driven tumour mouse 1 5hmc profile

description:
processed data file: hmeDIP_NASH_study.txt
Tum1_5HMC_NASHstudy


title: ascending colon cancer_no metastasis_original [Ctrl 3]


title: AI837

city: Murcia

first: Pilar

last: Coy

state: Murcia

address: Campus de Espinardo.Facultad de Veterinaria

department: Physiology

country: Spain

institute: University of Murcia

description: Gene expression after insemination

hyb_protocol: Microarrays where hybridized and washed according to manufacturer's protocol

scan_protocol: Scanned on GenePix 4100A 01  [109997]

data_processing: Images were quantified using GenePix Pro 6.0.1.25.

organism: Sus scrofa

source_name: Inseminated

label_protocol: One-color microarray-based GE LowInput QuickAmp Labeling (Agilent)

extract_protocol: Total RNA was extracted using the ‘TRIzol method’ according to the protocol recommended by the manufacturer (Life Technologies Inc., Gaithersburg, MD). The quantity and quality of the RNA samples were analysed with ARN 6.000 NanoLabChip® kit and the Agilent 2100 Bionalyzer (Agilent Technologies, Santa Clara, CA) respectively. Only samples with an RNA integrity number of > 7.0 were used for microarray analysis.

value: oviductal ampullary-isthmic junction

value: female


title: AI993

description: Gene expression after insemination


title: AI992

description: Gene expression whitout insemination

source_name: Not Inseminated


title: AI1059

description: Gene expression after insemination


title: AI792

description: Gene expression after insemination


title: AI696

description: Gene expression whitout insemination


title: patient1258-030 [38764]

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

data_processing: Genespring GX 12.6., RMA normalization

source_name: whole blood transcripts

tag: visit date

tag: Sex

value: Female

tag: age (years)


title: patient1258-343 [39624]


title: AI991

description: Gene expression whitout insemination


title: patient1258-587 [39506]


title: patient1258-343 [39576]


title: AI788

description: Gene expression whitout insemination


title: AI943

description: Gene expression after insemination


title: patient1258-343 [39456]


title: patient1258-587 [39450]


title: patient1258-914 [39583]


title: patient1258-030 [38792]


title: patient1258-343 [39581]


title: patient1258-030 [39105]


title: patient1258-343 [39400]


title: patient1258-587 [39513]


title: patient1258-343 [39428]


title: patient1258-587 [39590]


title: patient1258-343 [39602]


title: patient1258-030 [39011]


title: patient1258-030 [38848]


title: Ctnnb1 mut tumour mouse 3 5mC profile

source_name: Ctnnb1 liver tumour

value: Wild type

tag: tissue type

value: DEN+PB exposed mouse liver resulting in liver tumour

source_name: Ctnnb1 liver tumour_input


title: Ha-Ras mut tumour mouse 1 5mC profile

source_name: Ha-Ras liver tumour

value: DEN only exposed mouse liver resulting in liver tumour

source_name: Ha-Ras liver tumour_input


title: Liver_LINdiet_rep7

source_name: Liver, mouse, LIN diet, replicate 7

value: male

tag: age

value: 13 weeks

value: liver

value: 5 weeks on High fat LIN diet


title: patient1258-914 [39547]


title: Ctnnb1 mut tumour mouse 2 5mC profile


title: Ctnnb1 mut tumour mouse 2 5hmC profile

data_processing: Normalised data after normalised within arrays (loess) and between arrays (sclae normalisation) resulting in log2(IP/input) scores for each probe. Normalisation carried out using R console, version 3.1.2.

extract_protocol: Genomic DNA (5hmC-IP - 2.5 µg in 450 µl TE), sonicated to yield a fragment distribution of approximately 300-1000 bp, was denatured by incubation at 100°C for 10 min. Samples were rapidly chilled on wet-ice. At this point, 45 µl (10%) of denatured sample was removed and saved as input, and 45 µl of 10X IP buffer (100 mM Na-Phosphate pH 7.0  (mono and dibasic), 1.4 M NaCl, 0.5 % Triton X-100) and 1 µg of -5hmC (ActiveMotif; #39769) antibody were added to the remaining sample. Samples were incubated at 4C with gentle agitation overnight. Then, 40 µl of magnetic beads (Dynabeads® Protein G, Invitrogen, UK) in 1X IP buffer were added to each sample to allow magnetic separation of the antibody from the unbound DNA using a magnetic tube rack. Samples were incubated at 4C for 1 hr with gentle agitation. Beads were collected with a magnetic rack and washed with 1000 µl of 1X IP buffer at RT for 10 min with gentle agitation; washing was repeated three times. Beads were collected with a magnetic rack and re-suspended in 250 µl of digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA , 0.5 % SDS) followed by addition of 10 µl of proteinase K  (20 mg/ml; Roche Applied Science, Mannheim, Germany) and incubation at 52C for 1.5 hr with constant shaking (≥800 rpm). Finally, beads were removed using a magnetic rack and DNA was purified from the remaining sample using a QIAquick PCR Purification Kit (QIAGEN,CA, USA), eluting in a final volume of 40 µl dH2O. Inputs were also purified using a QIAquick PCR Purification Kit and eluted in 40 µl dH2O. Subsequently, 10 ng of input and IP DNA was subjected to whole genome amplification (WGA) using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich, UK) as per the manufacturer's instructions. Amplified DNA was run on a 1.2% agarose gel to confirm consistency of fragment size between samples.

value: 5-hmC - Active Motif (cat# 39769)


title: Ha-Ras mut tumour mouse 1 5hmC profile


title: Ctnnb1 mut tumour mouse 1 5mC profile


title: Ctnnb1 mut tumour mouse 3 5hmC profile


title: Ctnnb1 mut tumour mouse 1 5hmC profile


title: pb treated mouse 2 5hmC profile

source_name: 12 week PB exposed whole liver

value: PB exposed mouse liver tissue

source_name: PB exposed mouse liver tissue


title: pb treated mouse 1 5hmC profile


title: control mouse 2 5hmC profile

source_name: normal whole liver


title: patient1258-896 [39288]


title: patient1258-896 [39254]


title: patient1258-914 [39373]


title: patient1258-914 [39345]


title: patient1258-896 [39591]


title: patient1258-896 [39562]


title: patient1258-896 [39623]


title: patient1258-896 [39548]


title: patient1258-896 [39367]


title: patient1258-914 [39457]


title: control mouse 1 5hmC profile


title: patient1258-896 [39226]


title: C-fb-3

city: Guangzhou

first: Tong

last: Wu

state: Guangdong

address: Zhongshaner Road

institute: Sun Yat-sen University

description: Gene expression data from tongue submucosal fibroblasts in squamous cell carcinoma condition

hyb_protocol: Gene expression profile was examined by rat genome oligonuleotide microarray (Affymetrix Gene Chip Rat Genome 230 2.0 Array) at Capitalbiochip Corporation (Beijing, China), where gene chip microarray service is certificated by Affymetrix. Briefly an aliquot of 2 µg of total RNA was used to synthesize double-stranded cDNA, and then produce biotin-tagged cRNA using the MessageAmpTM II-Biotin (Ambion, USA). The resulting bio-tagged cRNA were fragmented to strands of 35–200 bases in length according to the protocols from Affymetrix. The chip measures the expression of over 31,000 probe sets representing over 28,700 well-substantiated mouse genes. The protocol for microarray processing was carried out according to GeneChip® Expression Analysis Technical Manual (Affymetrix, 701021, Rev.5).

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with Expression Console Software using RMA algorithm.

organism: Rattus norvegicus

source_name: fibroblasts

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

extract_protocol: extraction of total RNA was performed using Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Briefly, A 0.05% stock solution of 4-nitroquinoline oxide (4-NQO; Sigma-Aldrich, Saint Louis, MO, USA) was prepared with distilled water and stored at 4℃ in a dark refrigerator. Thirty male SD rats were divided into two groups. In the experimental group (n=20), rats were daily fed with distilled water containing 0.002% 4NQO for 22 weeks, whereas animals in the control group (n=10) were fed with distilled water only. From week14 to week 22, ten experimental rats were sacrificed while visible lesions of tongue leukoplasia or squamous cell carcinoma (SCC) were developed respectively.

value: Sprague Dawley

value: tongue

tag: cell type

value: fibroblasts

tag: disease status

value: carcinoma


title: C-fb-1

tag: strain


title: LOUCY

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

country: Belgium

institute: UGent

description: Gene expression of LOUCY cell line

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating  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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting a 10% higher expression than the negative control probes of the array design in at least one treatment.

source_name: LOUCY

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in RPMI supplemented with 10% or 20% (ALL-SIL)  fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol: Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.

tag: cell line

value: LOUCY

value: IMM


title: D-fb-2

description: Gene expression data from tongue submucosal fibroblasts in dysplasia condition

value: dysplasia


title: PF-382

description: Gene expression of PF-382 cell line

value: TAL


title: KE-37

description: Gene expression of KE-37 cell line


title: ALL-SIL

description: Gene expression of ALL-SIL cell line

source_name: ALL-SIL

value: ALL-SIL

value: TLX


title: KARPAS-45

description: Gene expression of KARPAS-45 cell line

value: other


title: PEER

description: Gene expression of PEER cell line

source_name: PEER

value: PEER


title: D-fb-3


title: N-fb-2

description: Gene expression data from tongue submucosal fibroblasts in normal condition

value: normal control


title: NKB cell

city: Beijing

first: Pengyan

last: Xia

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of biophysics, Chinese Academy of Sciences

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner. Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through fold change. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed using the standard enrichment computation method.

source_name: WT C57/BL6 mouse spleen

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA).

growth_protocol: WT C57/BL6 mice were maintained in SPF conditions.

extract_protocol: Sorted cells were subjected to total RNA extraction with TRIZOL reagent.

treatment_protocol: 8 week-old mice were anesthetized and spleen cells were collected, followed by LT-HSCs sorting through a BD AriaIII sorter.

tag: genotype

value: WT

value: spleen

value: Natural killer B cells

value: 8 weeks


title: HPB-ALL

description: Gene expression of HPB-ALL cell line

source_name: HPB-ALL

value: HPB-ALL


title: N-fb-3

value: Sprague Dawley

value: tongue


title: C-fb-2

value: fibroblasts

value: carcinoma


title: AI1061

description: Gene expression whitout insemination

value: oviductal ampullary-isthmic junction

value: female


title: DND-41

description: Gene expression of DND-41 cell line


title: CCRF-CEM

description: Gene expression of CCRF-CEM cell line

source_name: CCRF-CEM

value: CCRF-CEM

value: TAL


title: C-E-3

description: Gene expression data from tongue epithelia in squamous cell carcinoma condition

source_name: epithelia

value: epithelia


title: B cell

value: B cells


title: D-fb-1

value: dysplasia


title: C-E-2


title: N-fb-1

value: normal control


title: NK cell

value: WT

value: Natural killer cells


title: JURKAT

description: Gene expression of JURKAT cell line

source_name: JURKAT

value: JURKAT


title: HCs in chick utricle rep.5

city: Fukuoka

first: Takahiro

last: Wakasaki

state: Fukuoka

address: 3-1-1 Notame

country: Japan

institute: National Kyushu Cancer Center

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Gallus gallus

source_name: chick 10-12days post hatching chick

label_protocol: Total RNA from each sample was subjected to two rounds of amplification using the MessageAmpTMII aRNA Amplification Kit and biotin-11-UTP (both from Applied Biosystems, Austin, TX, USA) according to the manufacturer’s instruction to obtain biotin-labeled antisense (a)RNA.

growth_protocol: 10–12 days post-hatching chick

extract_protocol: LCM was performed by capturing the cytoplasm and nuclei of HCs and SCs from individual utricle samples into different caps according to the cell type using an Arcturus Pixcell II LCM Microdissection System (Arcturus Engineering, Mountain View, CA, USA). Total RNA was isolated from HC- and SC-enriched samples using the Picopure RNA Isolation Kit (Bucher Biotec AG, Basel, Switzerland) and DNase I (Qiagen, Hilden, Germany), according to the manufacturers’ instructions.

tag: breed

value: White leghorns

tag: developmental stage

value: 10-12 days post-hatching

value: hair cells in chick utricle


title: SCs in chick utricle rep.4

value: supporting cells in chick utricle


title: SCs in chick utricle rep.5


title: D-E-3

description: Gene expression data from tongue epithelia in dysplasia condition

value: Sprague Dawley

value: tongue


title: HCs in chick utricle rep.4


title: SCs in chick utricle rep.3


title: N-E-2

description: Gene expression data from tongue epithelia in normal condition


title: D-E-1


title: SCs in chick utricle rep.2


title: N-E-1


title: HCs in chick utricle rep.2


title: HCs in chick utricle rep.3


title: N-E-3


title: D-E-2


title: Distal_HEY_Control_2

first: Swetha

last: Srinivasan

address: 315 ferst drive

department: Biology

institute: Georgia Institute of technology

description: Gene expression data from HEY Cells stimulated with control exosomes

hyb_protocol: Labeled mRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays in the GeneChip Hybridization oven 640, further processed with the GeneChip Fluidics Station 450 and scanned with the GeneChip Scanner 3000

scan_protocol: as per manufacturer's protocol using GeneChip Scanner 3000.

data_processing: mRNA microarray data were analyzed using Bioconductor tools written in the R statistical programming language (www.rproject.org). Pre-processing of raw signal intensities and normalization was performed using GCRMA (R). Linear modelling of the transformed data was determined by using Limma in R with the Benjamini and Hochberg correction. Differentially expressed probesets were identified using a threshold 5% FDR correction and a fold change ≥ 1.4 was applied.

source_name: RNA from HEY cells exposed to control exosomes

label_protocol: mRNAs were converted to double stranded (ds)-cDNA and amplified using Applause 3’-Amp System (NuGen, San Carlos, CA). This cDNA was then biotin labeled and fragmented by using Encore Biotin Module (NuGen)

growth_protocol: HEY ovarian cancer cell lines were cultured in RPMI 1640 (Mediatech, Manassas, VA) supplemented with 10% v/v Fetal Bovine Serum (Atlanta Biologicals, Lawrenceville, GA) and 1% v/v antibiotic-antimycotic solution (10,000 I.U. Penicillin (per mL), 10,000 µg/mL Streptomycin and 25 µg/mL Amphotericin, Mediatech-Cellgro, Manassas, VA).

extract_protocol: Total RNA was isolated from control and TLR stimulated parental and recipient cells (grown with exosomes) after 48 hours using RNeasy mini RNA isolation kit (QIAGEN, Valencia, CA). The integrity of the RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Ultra-pure E.coli K12 LPS and poly(I:C) ( Invivogen, San Diego, CA) were used to treat local cells at concentrations of 100 ng/mL and 10 µg/mL  respectively  for 6 hours before RNA isolation. Distal cells were incubated with 100ug of (control, pIC or LPS) exosomes for 48 hours before RNA isolation

value: HEY

value: ovarian cancer

tag: treatment

value: control exosome treatment for 48 hours


title: Distal_HEY_LPS_1

description: Gene expression data from HEY Cells stimulated with LPS exosomes

source_name: RNA from HEY cells stimulated with LPS exosomes

value: LPS exosome treatmenf for 48 hours


title: Local_HEY_LPS_2

description: Gene expression data from HEY Cells stimulated with LPS

source_name: RNA from HEY Cells stimulated with LPS for 6 hours

value: LPS treatment for 6 hours


title: Distal_HEY_Control_1


title: Local_HEY_pIC_1

description: Gene expression data from HEY Cells stimulated with pIC

source_name: RNA from HEY Cells stimulated with pIC for 6 hours

value: pIC treatment for 6 hours


title: C-E-1

value: epithelia

value: carcinoma


title: HCs in chick utricle rep.1


title: Distal_HEY_pIC_2

description: Gene expression data from HEY Cells stimulated with pIC exosomes

source_name: RNA from HEY cells exposed to pIC exosomes

value: pIC exosomes treatment for 48 hours


title: Heps_LCM_2

city: San Francisco

first: Milad

last: Rezvani

state: California

address: 35 Medical Center Way

department: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research

institute: University of California San Francisco

hyb_protocol: Labeled cDNA targets were hybridized to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix).

scan_protocol: Images were processed using Affymetrix Command Console v.3.1.1 software and expression analysis for QC was performed using Affymetrix Expression Console v.1.4 software with normalization by Robust Multi-Array Average.

data_processing: For statistical analyses, all array probesets were removed where no experimental groups had an average log2 intensity greater than 3.0. Linear models were fitted for each gene using the bioconductor limma package in R.

source_name: Primary hepatocytes

label_protocol: Total RNA (0.4 to 1.0 ng) was reverse transcribed, amplified and biotin labeled using the Ovation Pico WTA System V2 and the Encore Biotin Module (both NuGEN Technologies).

growth_protocol: Total RNA was extracted immediately after cell isolation.

extract_protocol: RNA was extracted with the Arcturus Pico Pure RNA Isolation Kit (AB Biosystems).

treatment_protocol: Mice were treated with CCl4 and intravenously injected with AAV6 vectors expressing Foxa1, Foxa2, Foxa3, Hnf1a, Hnf4a and Gata4 to generate MF-iHeps in vivo.

value: CCl4, AAV6

value: primary hepatocyte


title: MF-iHeps_LCM_5


title: Heps_LCM_1


title: Distal_HEY_pIC_1


title: SCs in chick utricle rep.1

value: White leghorns


title: patient1258-343 [39540]

source_name: whole blood transcripts

value: Male


title: Local_HEY_pIC_2


title: Heps_LCM_3


title: Local_HEY_LPS_1


title: Distal_HEY_LPS_2


title: patient1258-914 [39571]

value: Female


title: MF-iHeps_LCM_3


title: MF-iHeps_LCM_4


title: shIL-1-3

description: Expression data from oral squamous cell carcinoma cell line Cal27 with lentivirus shIL-1 beta transfection

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

source_name: Cal27 cell with lentivirus shIL-1beta transfection

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: Human tongue squamous cell carcinoma cell line Cal27 (American Type Culture  Collection, Rockville, MD) were maintained in DMEM high glucose culture medium (GIBCO, Grand Island, NY, USA) with 10% fetal bovine serum (FBS; GIBCO) at 37°C in a humidified atmosphere containing 5% CO2.

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

treatment_protocol: MISSION shRNA plasmids for human IL-1β, and lentiviral packaging mix (Forevergen Biosciences, Guangzhou, China) were used. The sequences were shIL-1β forward: 5’-AACTGGAGAGTGTAGATCCCAAATTCAAGAGATTT  GGGATCTACACTCTCCTTTTTTC-3’, reverse: 3’-TTGACCTCTCACATCTA  GGGTTTAAGTTCTCTAAACCCTAGATGTGAGAGGAAAAAAGAGCT-5' and a scrambled shRNA forward: 5’-AACTTTCTCCGAACGTGTCACGTTT  CAAGAGAACGTGACACGTTCGGAGAATTTTTTC-3’,reverse:5’-TCGAGAAAAAATTCTCCGAACGTGTCACGTTCTCTTGAAACGTGACACGTTCGGAGAAAGTT-3'. Lentiviral-mediated transfection of shRNAs was performed according to the manufacturer’s instructions. Briefly, 293T cells were co-transfected with the lentiviral vector and packaging vector and the supernatant was collected after 48 and 72 h. After centrifugation for 15 min at 5000×g, the lentiviruses were recovered and resuspended in PBS before performing the infection with 6μg/mL of polybrene. Stable cells with IL-1β knockdown were selected with 2μg/mL puromycin following transduction for 2 weeks. The transfection efficiency of IL-1β knockdown was examined by Western Blot analysis.

tag: genotype/variation

value: IL-1beta knockdown


title: MFs_FACS_3

source_name: Primary myofibroblasts

value: CCl4, No AAV6

value: primary myofibroblast


title: MF-iHeps_LCM_2


title: shIL-1-1

value: tongue squamous cell carcinoma cell line Cal27


title: MFs_FACS_2


title: Local_HEY_control_1

description: Gene expression data from unstimulated HEY Cells

source_name: RNA from unstimulated HEY Cells

value: HEY

value: ovarian cancer

value: no treatment


title: NC-3

description: Expression data from oral squamous cell carcinoma cell line Cal27 with scramble shRNA

source_name: Cal27 cell with scramble shRNA transfection

value: control


title: MFs_FACS_1


title: mESCs_shCops5_rep1

city: Tianjin

first: Lingyi

address: 94 Weijin Road

institute: Nankai University

description:
Gene expression after shCops5 knockdown in mouse ESCs
C5

hyb_protocol: Cy3-labelled cDNA were hybridized to the array in 2xGEx Hyb Buffer (HI-RPM), 25% formamide, 42 C, overnight.  After hybridization, microarrays were washed 5 minute with 0.2% SDS, 2XSSC at 42°C, and 5 minute with 0.2XSSC at room temperature,and 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.

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

source_name: Mouse ESCs transfected with shCops5 plasmid

label_protocol: Use CbcScript and T7 Oligo (dT) Primer to synthesize 1st-strand cDNA, and then use DNA polymerase to synthesize 2nd-strand cDNA.  cRNA was then synthesized with the double strand cDNA and T7 Enzyme Mix.  cRNA was reverse-transcribed with CbcScript II and random primer.  The resulting DNA were labeled with Cy3-dCTP and KLENOW.

growth_protocol: mouse ESCs were cultured in conventional Serum+LIF condition.

extract_protocol: RNA was prepared using Trizol (Invitrogen, Gaithersburg, MD, USA) and the NucleoSpin RNA clean-up kit (MACHEREY-NAGEL, Germany) following the manufacturer's recommendations.

treatment_protocol: mouse ESCs were transfected with shGFP, shCops2-1, shCops2-3, or shCops5 plasmids with Lipofectamine 2000 (Invitrogen, USA) following the manufacturer's recommendations.

value: embryonic stem cell

tag: gender

value: male

tag: transfection

value: shCops5 plasmid

value: Cops5 knockdown


title: shIL-1-2


title: PD03_24h_rep3

city: xi'an

first: Zhiying

last: Ai

state: shannxi

address: No.3 Taicheng Road, Yangling

institute: Northwest A&F University (NWAFU)

description: Gene expression after 24h in PD03 treated J1 mESCs

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer  Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: J1 mESC, PD03, 24h, replicate 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The J1 mouse embryonic stem cell line purchased from ATCC (Manassas, VA, USA) was gelatin adapted and grown on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF (ESGRO, Millipore, USA).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: J1 mESCs maintained in medium containing 1000 U/mL LIF and treated by 1 μΜ PD0325901 for 24h.

tag: tissue

value: Inner Cell Mass

value: Embryonic Stem Cell


title: mESCs_shCops2_1_rep1

description:
Gene expression after shCops2-1 knockdown in mouse ESCs
C2-1

source_name: Mouse ESCs transfected with shCops2-1 plasmid

value: shCops2-1 plasmid

value: Cops2 knockdown


title: MF-iHeps_LCM_1

value: CCl4, AAV6


title: NC-2


title: mESCs_shCops2_3_rep1

description:
Gene expression after shCops2-3 knockdown in mouse ESCs
C2-3

source_name: Mouse ESCs transfected with shCops2-3 plasmid

value: shCops2-3 plasmid


title: Local_HEY_control_2


title: mESCs_shGFP_rep1

description:
Gene expression after shGFP knockdown in mouse ESCs
G1

source_name: Mouse ESCs transfected with shGFP plasmid

value: shGFP plasmid


title: PD03_24h_rep1

source_name: J1 mESC, PD03, 24h, replicate 1


title: M2-Muscle_Wild Type PUS1_Indiv4

status: Public on May 16 2016

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description:
Gene expression of M2-Muscle tissue
R: US10130359_252800516692_S01_GE2_107_Sep09_1_4.txt

hyb_protocol: 300 ng of Cy3-labelled cRNA and 300 ng of Cy5-labelled cRNA was mixed and fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer 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 Microarray (G4852A-028005) 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 immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channels set to 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software  10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid 028005_D_F_20130207) to obtain background- and dye-corrected (LOWESS) signal intensities.  Data was uploaded into Genespring version 11.5.1 where it was log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filted by flags in a way that at least 75% of the samples in any of the experimental groups had DETECTED flags. Then, differentially expressed genes were determined.

source_name: M2-Muscle, Wild Type PUS1 Individual 4

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

growth_protocol: The tissue samples were from mice that were 14 to 16 weeks old.

extract_protocol: Total RNA was isolated from frozen gastrocnemius muscle (white portion) using the mirVanaTM PARISTM kit.

value: C57BL/6J with backcrosses for 5 generations before experimentation

value: Wild Type PUS1

value: Female


title: PD03_24h_rep2

source_name: J1 mESC, PD03, 24h, replicate 2


title: Mot1_Spt16_mut_RNA

city: Charlottesville

first: David

last: Auble

state: VA

address: Box 800733 Jordan Hall University of Virginia Health System

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: double mutant total RNA

hyb_protocol: Labeled samples were hybridized to Affymetrix GeneChip S.cerevisiae Tiling 1.0R Array according to manufacturer's directions.

scan_protocol: Samples hybridized to Affymetrix GeneChip S.cerevisiae Tiling 1.0R Arrays were scanned according to manuracturer's directions.

data_processing:
Raw data was analyzed using Affymetrix Tiling Analysis Software (TAS).  Signal profiles were smoothed over a 50 bp bandwidth (100 bp sliding window), and differential profiles were smoothed over a 250 bp bandwithc (500 bp sliding window).  Additional TAS parameters:  log2 signal scale, scale to target intensity 100, two-sided test type, plus or minus 0.3 threshold, 100 bp maximum gap, and 50 bp minimum run.  Differential files were generated by dividing the mutant by the WT signal.
The signal BAR files listed were generated from using TAS as described.  The differential BAR files were generated using TAS by dividing the mutant signal over the WT signal.

organism: Saccharomyces cerevisiae

source_name: Total RNA from mot1-42 spt16-197

label_protocol: cDNA was synthesized from 7 μg of total RNA in biological duplicate using Affymetrix GeneChip Eukaryotic Double Strand Whole Transcript Protocols. dsDNA was purified using the USB PrepEase DNA Clean-Up Kit. 7.5 μg of amplified sample was fragmented, and proper fragment length distribution was confirmed on an RNA Nano chip using an Agilent Bioanalyzer. Fragments were labeled with DNA labeling reagent (DLR), and efficient labeling was confirmed by NeutrAvidin gel-shift assay on polyacrylamide gel.

growth_protocol: Yeast cells were grown in YPD media at 30°C to an O.D. of ~1.0, except the double mutant was grown at 25°C to an OD of ~1.0.

extract_protocol: Cells were resuspended in 4 mL lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and 4 mL acid phenol was added to sample and vortexed.  Samples were incubated at 65°C for one hour with vortexing every 10 minutes.  Tubes were placed on ice for 10 minutes then spun down at 4°C for 10 minutes.  The aqueous layer was extracted again with phenol then once more with chloroform.  RNA was precipitated overnight with addition of 0.4 mL 3 M sodium acetate and 8 mL 200 proof ethanol and incubation at -80°C.  Pellets were collected and washed with 70% ethanol and dried.

treatment_protocol: Cells were shifted to 35°C for 45 minutes to induce heat shock then spun down.

value: Heat shocked at 35°C for 45 minutes


title: Spt16_mut_RNA

description: mutant total RNA

source_name: Total RNA from spt16-197


title: M1-Muscle_Wild Type PUS1_Indiv3

description:
Gene expression of M1-Muscle tissue
G: US10130359_252800516691_S01_GE2_107_Sep09_2_3.txt

source_name: M1-Muscle, Wild Type PUS1 Individual 3

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

extract_protocol: Total RNA was isolated from frozen gastrocnemius muscle (red portion) using the mirVanaTM PARISTM kit.


title: M2-Muscle_Wild Type PUS1_Indiv2

description:
Gene expression of M2-Muscle tissue
R: US10130359_252800516692_S01_GE2_107_Sep09_1_2.txt

source_name: M2-Muscle, Wild Type PUS1 Individual 2

value: Male


title: M1-Muscle_Homozygous Mutant PUS1_Indiv1

description:
Gene expression of M1-Muscle tissue
R: US10130359_252800516691_S01_GE2_107_Sep09_2_1.txt

source_name: M1-Muscle, Homozygous Mutant PUS1 Individual 1

value: Homozygous Mutant PUS1


title: NC-1

value: tongue squamous cell carcinoma cell line Cal27

value: control


title: M2-Muscle_Wild Type PUS1_Indiv3

description:
Gene expression of M2-Muscle tissue
G: US10130359_252800516692_S01_GE2_107_Sep09_1_3.txt

source_name: M2-Muscle, Wild Type PUS1 Individual 3


title: WA09-SMC rep1

city: Athens

first: wenjuan

last: zhang

address: 120 Green street, Life Science Building, Room B304B

institute: University of Georgia

description: RNA was purified from approximately 5 million cells per sample using the Qiagen RNeasy Plus Mini kit (Cat. No. 74134).  Then, high quality (a 260/280 absorbance ratio of ~2.0, undegraded, and free of genomic DNA contamination) samples were analyzed.

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data was processed with RMA (robust multichip average) normalization included in 'limma' package (http://www.bioconductor.org).

source_name: Human smooth muscle cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: WA09-hESCs were maintained in StemPro defined media (Invitrogen).  Differentiation to INM and SMCs was achieved by supplementation of defined media with Wnt3a (25 ng/ml) and BMP4 (50 ng/ml) for 4 and 21 days, respectively.

value: Human smooth muscle cells derived from WA09-hESC


title: WA09-hESC rep1

source_name: Human embryonic cells WA09

extract_protocol: RNA was purified from approximately 5 million cells per sample using the Qiagen RNeasy Plus Mini kit (Cat. No. 74134).

value: Human embryonic cells WA09


title: M2-Muscle_Homozygous Mutant PUS1_Indiv4

description:
Gene expression of M2-Muscle tissue
G: US10130359_252800516692_S01_GE2_107_Sep09_1_4.txt

source_name: M2-Muscle, Homozygous Mutant PUS1 Individual 4


title: M2-Muscle_Homozygous Mutant PUS1_Indiv1

description:
Gene expression of M2-Muscle tissue
R: US10130359_252800516692_S01_GE2_107_Sep09_1_1.txt

source_name: M2-Muscle, Homozygous Mutant PUS1 Individual 1


title: M1-Muscle_Wild Type PUS1_Indiv2

description:
Gene expression of M1-Muscle tissue
R: US10130359_252800516691_S01_GE2_107_Sep09_2_2.txt

source_name: M1-Muscle, Wild Type PUS1 Individual 2


title: M2-Muscle_Homozygous Mutant PUS1_Indiv2

description:
Gene expression of M2-Muscle tissue
G: US10130359_252800516692_S01_GE2_107_Sep09_1_2.txt

source_name: M2-Muscle, Homozygous Mutant PUS1 Individual 2


title: WA09-INM rep1

source_name: Human ISL1+ nascent mesoderm cells

value: Human ISL1+ nascent mesoderm cells derived from WA09-hESC


title: M1-Muscle_Wild Type PUS1_Indiv4

description:
Gene expression of M1-Muscle tissue
R: US10130359_252800516691_S01_GE2_107_Sep09_2_4.txt

source_name: M1-Muscle, Wild Type PUS1 Individual 4


title: M2-Muscle_Wild Type PUS1_Indiv1

description:
Gene expression of M2-Muscle tissue
G: US10130359_252800516692_S01_GE2_107_Sep09_1_1.txt

source_name: M2-Muscle, Wild Type PUS1 Individual 1


title: WA09-SMC rep2


title: M1-Muscle_Homozygous Mutant PUS1_Indiv3

description:
Gene expression of M1-Muscle tissue
R: US10130359_252800516691_S01_GE2_107_Sep09_2_3.txt

source_name: M1-Muscle, Homozygous Mutant PUS1 Individual 3


title: M1-Muscle_Homozygous Mutant PUS1_Indiv4

description:
Gene expression of M1-Muscle tissue
G: US10130359_252800516691_S01_GE2_107_Sep09_2_4.txt

source_name: M1-Muscle, Homozygous Mutant PUS1 Individual 4


title: M1-Muscle_Homozygous Mutant PUS1_Indiv2

description:
Gene expression of M1-Muscle tissue
G: US10130359_252800516691_S01_GE2_107_Sep09_2_2.txt

source_name: M1-Muscle, Homozygous Mutant PUS1 Individual 2


title: WA09-hESC rep2


title: M2-Muscle_Homozygous Mutant PUS1_Indiv3

description:
Gene expression of M2-Muscle tissue
R: US10130359_252800516692_S01_GE2_107_Sep09_1_3.txt

source_name: M2-Muscle, Homozygous Mutant PUS1 Individual 3


title: M1-Muscle_Wild Type PUS1_Indiv1

description:
Gene expression of M1-Muscle tissue
G: US10130359_252800516691_S01_GE2_107_Sep09_2_1.txt

source_name: M1-Muscle, Wild Type PUS1 Individual 1


title: WA09-INM rep2


title: Spt16_WT_RNA

description: WT total RNA

source_name: Total RNA from SPT16-WT


title: Liver_Homozygous Mutant PUS1_Indiv3

description:
Gene expression of Liver tissue
R: US10130359_252800516692_S01_GE2_107_Sep09_2_3.txt

source_name: Liver, Homozygous Mutant PUS1 Individual 3

growth_protocol: The tissue samples were from mice that were 14 to 16 weeks old

extract_protocol: Total RNA was isolated from frozen liver tissue using the mirVanaTM PARISTM kit.

value: Liver


title: Liver_Wild Type PUS1_Indiv3

description:
Gene expression of Liver tissue
G: US10130359_252800516692_S01_GE2_107_Sep09_2_3.txt

source_name: Liver, Wild Type PUS1 Individual 3


title: Liver_Wild Type PUS1_Indiv2

description:
Gene expression of Liver tissue
R: US10130359_252800516692_S01_GE2_107_Sep09_2_2.txt

source_name: Liver, Wild Type PUS1 Individual 2


title: Liver_Homozygous Mutant PUS1_Indiv4

description:
Gene expression of Liver tissue
G: US10130359_252800516692_S01_GE2_107_Sep09_2_4.txt

source_name: Liver, Homozygous Mutant PUS1 Individual 4


title: Liver_Wild Type PUS1_Indiv4

description:
Gene expression of Liver tissue
R: US10130359_252800516692_S01_GE2_107_Sep09_2_4.txt

source_name: Liver, Wild Type PUS1 Individual 4


title: Liver_Homozygous Mutant PUS1_Indiv1

description:
Gene expression of Liver tissue
R: US10130359_252800516692_S01_GE2_107_Sep09_2_1.txt

source_name: Liver, Homozygous Mutant PUS1 Individual 1


title: MEFs_WT_rep2

city: Hyderabad

first: Rashna

last: Bhandari

state: Telangana

address: Bldg 7, Gruhakalpa, 5-4-399/B Nampally

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

description:
Gene expression in exponentially growing Ip6k1+/+ MEFs
Control B

hyb_protocol: 600ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method

source_name: Ip6k1+/+ MEFs biological replicate 2

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: RNA was extracted using RNeasy minikit (Qiagen)

treatment_protocol: MEFs were isolated from E14 embryos from a single heterozygous female mouse that had been paired with a heterozygous male, and were genotyped to select two Ip6k1+/+ and Ip6k1-/- embryos each (Ref: Bhandari et al., Proc. Natl. Acad. Sci. USA, 2008, 105, 2349-53). These MEFs were immortalised by the expression of SV40 large T antigen and frozen in liquid nitrogen. Thawed cells were grown at 37°C in a humidified incubator with 5% CO2, passaged twice, harvested by trypsinization, and their genotype was re-confirmed. 10^7 cells were resuspended in 100 µl phosphate buffered saline and 5 volumes of RNAlater (Sigma-Aldrich).

value: Mouse embryonic fibroblasts


title: MEFs_KO_rep1

description:
Gene expression in exponentially growing Ip6k1-/- MEFs
Treated A

source_name: Ip6k1-/- MEFs biological replicate 1


title: Liver_Homozygous Mutant PUS1_Indiv2

description:
Gene expression of Liver tissue
G: US10130359_252800516692_S01_GE2_107_Sep09_2_2.txt

source_name: Liver, Homozygous Mutant PUS1 Individual 2


title: Kidney_Homozygous Mutant PUS1_Indiv2

description:
Gene expression of Kidney tissue
G: US10130359_252800516690_S01_GE2_107_Sep09_2_2.txt

source_name: Kidney, Homozygous Mutant PUS1 Individual 2

extract_protocol: Total RNA was isolated from frozen kidney (cross section of whole kidney) using the mirVanaTM PARISTM kit.

value: Kidney


title: Kidney_Wild Type PUS1_Indiv1

description:
Gene expression of Kidney tissue
G: US10130359_252800516690_S01_GE2_107_Sep09_2_1.txt

source_name: Kidney, Wild Type PUS1 Individual 1


title: Brain_Homozygous Mutant PUS1_Indiv4

description:
Gene expression of Brain tissue
G: US10130359_252800516690_S01_GE2_107_Sep09_1_4.txt

source_name: Brain, Homozygous Mutant PUS1 Individual 4

extract_protocol: Total RNA was isolated from frozen brain tissue (cross section of whole brain) using the mirVanaTM PARISTM kit.

value: Brain


title: Kidney_Wild Type PUS1_Indiv2

description:
Gene expression of Kidney tissue
R: US10130359_252800516690_S01_GE2_107_Sep09_2_2.txt

source_name: Kidney, Wild Type PUS1 Individual 2


title: Kidney_Wild Type PUS1_Indiv3

description:
Gene expression of Kidney tissue
G: US10130359_252800516690_S01_GE2_107_Sep09_2_3.txt

source_name: Kidney, Wild Type PUS1 Individual 3


title: Kidney_Homozygous Mutant PUS1_Indiv4

description:
Gene expression of Kidney tissue
G: US10130359_252800516690_S01_GE2_107_Sep09_2_4.txt

source_name: Kidney, Homozygous Mutant PUS1 Individual 4


title: Heart_Wild Type PUS1_Indiv1

description:
Gene expression of Heart tissue
G: US10130359_252800516691_S01_GE2_107_Sep09_1_1.txt

source_name: Heart, Wild Type PUS1 Individual 1

extract_protocol: Total RNA was isolated from frozen heart tissue (portion of atrium and ventricle) using the mirVanaTM PARISTM kit.

value: Heart


title: MEFs_KO_rep2

description:
Gene expression in exponentially growing Ip6k1-/- MEFs
Treated B

source_name: Ip6k1-/- MEFs biological replicate 2


title: MEFs_WT_rep1

description:
Gene expression in exponentially growing Ip6k1+/+ MEFs
Control A

source_name: Ip6k1+/+ MEFs biological replicate 1


title: Brain_Wild Type PUS1_Indiv4

description:
Gene expression of Brain tissue
R: US10130359_252800516690_S01_GE2_107_Sep09_1_4.txt

source_name: Brain, Wild Type PUS1 Individual 4


title: Liver_Wild Type PUS1_Indiv1

description:
Gene expression of Liver tissue
G: US10130359_252800516692_S01_GE2_107_Sep09_2_1.txt

source_name: Liver, Wild Type PUS1 Individual 1


title: Kidney_Homozygous Mutant PUS1_Indiv1

description:
Gene expression of Kidney tissue
R: US10130359_252800516690_S01_GE2_107_Sep09_2_1.txt

source_name: Kidney, Homozygous Mutant PUS1 Individual 1


title: Brain_Wild Type PUS1_Indiv2

description:
Gene expression of Brain tissue
R: US10130359_252800516690_S01_GE2_107_Sep09_1_2.txt

source_name: Brain, Wild Type PUS1 Individual 2


title: Heart_Wild Type PUS1_Indiv4

description:
Gene expression of Heart tissue
R: US10130359_252800516691_S01_GE2_107_Sep09_1_4.txt

source_name: Heart, Wild Type PUS1 Individual 4


title: Heart_Wild Type PUS1_Indiv3

description:
Gene expression of Heart tissue
G: US10130359_252800516691_S01_GE2_107_Sep09_1_3.txt

source_name: Heart, Wild Type PUS1 Individual 3


title: Kidney_Homozygous Mutant PUS1_Indiv3

description:
Gene expression of Kidney tissue
R: US10130359_252800516690_S01_GE2_107_Sep09_2_3.txt

source_name: Kidney, Homozygous Mutant PUS1 Individual 3


title: Heart_Wild Type PUS1_Indiv2

description:
Gene expression of Heart tissue
R: US10130359_252800516691_S01_GE2_107_Sep09_1_2.txt

source_name: Heart, Wild Type PUS1 Individual 2


title: Heart_Homozygous Mutant PUS1_Indiv3

description:
Gene expression of Heart tissue
R: US10130359_252800516691_S01_GE2_107_Sep09_1_3.txt

source_name: Heart, Homozygous Mutant PUS1 Individual 3


title: Brain_Homozygous Mutant PUS1_Indiv3

description:
Gene expression of Brain tissue
R: US10130359_252800516690_S01_GE2_107_Sep09_1_3.txt

source_name: Brain, Homozygous Mutant PUS1 Individual 3


title: Kidney_Wild Type PUS1_Indiv4

description:
Gene expression of Kidney tissue
R: US10130359_252800516690_S01_GE2_107_Sep09_2_4.txt

source_name: Kidney, Wild Type PUS1 Individual 4


title: Brain_Homozygous Mutant PUS1_Indiv1

description:
Gene expression of Brain tissue
R: US10130359_252800516690_S01_GE2_107_Sep09_1_1.txt

source_name: Brain, Homozygous Mutant PUS1 Individual 1


title: Heart_Homozygous Mutant PUS1_Indiv1

description:
Gene expression of Heart tissue
R: US10130359_252800516691_S01_GE2_107_Sep09_1_1.txt

source_name: Heart, Homozygous Mutant PUS1 Individual 1


title: Brain_Wild Type PUS1_Indiv3

description:
Gene expression of Brain tissue
G: US10130359_252800516690_S01_GE2_107_Sep09_1_3.txt

source_name: Brain, Wild Type PUS1 Individual 3


title: Heart_Homozygous Mutant PUS1_Indiv2

description:
Gene expression of Heart tissue
G: US10130359_252800516691_S01_GE2_107_Sep09_1_2.txt

source_name: Heart, Homozygous Mutant PUS1 Individual 2


title: Heart_Homozygous Mutant PUS1_Indiv4

description:
Gene expression of Heart tissue
G: US10130359_252800516691_S01_GE2_107_Sep09_1_4.txt

source_name: Heart, Homozygous Mutant PUS1 Individual 4


title: Brain_Homozygous Mutant PUS1_Indiv2

description:
Gene expression of Brain tissue
G: US10130359_252800516690_S01_GE2_107_Sep09_1_2.txt

source_name: Brain, Homozygous Mutant PUS1 Individual 2


title: Combined CUL4A  siRNA with IL-6 stimulation treated group 2

city: Changsha

first: Weiguo

last: Ren

state: Hunan

address: No.216, Tongzipo, Yuelu District

institute: hird Xiangya Hospital of Central South University

description: Expression data for xenograft tumor treated with IL-6 combined CUL4A siRNA

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix® Multispecies miRNA 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. Raw data were normalized with the RMA algorithm by Gene Spring Software 13.0 (Agilent）

source_name: colon adenocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: The human colon adenocarcinoma cell lines HCT116 were cultured inDulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 units/m of penicillin and streptomycin. Cultures were incubated at 37°C in a humidified incubator at 5% CO2.

treatment_protocol: Male BALB/c athymic nude mice (4–5 weeks old) were injected in right armpit subcutaneously with 1×107 of HCT116 cells, in a volume of 2ml of PBS, Once the tumor size reached approximately 5 mm in diameter, the mice were randomly divided into groups: 1) PBS control group with tumors untreated; 2) IL-6 stimulation treated group, 3) Combined CUL4A  siRNA with IL-6 stimulation treated group.30 ul siRNA/oligofectamine mixture containing 400 pmol siRNA or/and 600pg IL-6 every four days. After a month, the mice were sacrificed and the tumor tissues were taken.

tag: agent

value: IL-6+ siCUL4A


title: IL-6 stimulation treated group 1

description: Expression data for xenograft tumor treated with IL-6


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1550

status: Public on May 15 2016

city: Duarte

first: Nancy

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned by Illumina iScan machine using standard recommended Illumina scanner setting

data_processing:
Bioconductor R pachage "Minfi" was used to process data including background substraction, control normalization and Subset-quantile Within Array (SWAN) normalization.
GEO.Monos.processed.data.txt: Average beta after data processing
GEO.Monos.signal.intensities.data.txt: unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Case_blood draw

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA extraction and purification method uses sodium dodecylsulfate cell lysis followed by salt precipitation method for protein removal using commercial uregene® reagents (Gentra System, Inc., Minneapolis, MN) in the Molecular Diagnostics Section of the EDIC Central Biochemistry Laboratory.

tag: sample group

value: Case

value: M

value: monocyte

tag: collection time


title: Combined CUL4A  siRNA with IL-6 stimulation treated group 1


title: PBS control group 2 with tumors untreated

description: Expression data for xenograft tumor treated with PBS

value: PBS