title: Hum_CC_OSC20_vitro

first: Yuuichi

last: Soeno

address: 1-9-20 Fujimi, Chiyoda-ku

institute: The Nippon Dental University

description:
NDUP_023
Gene expresson in culture condition

hyb_protocol: Labeled RNA was hybridized to a Whole Human Genome Microarray 4×44K Version 2.0; Agilent) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (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: OSC20, culture, pellet

label_protocol: 500 ng of total RNA was labeled with Cyanine-3 (Cy3) as detailed in the One-Color microarray-based gene expression analysis protocol (ver6.5; www.agilent.com). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: In culture, each cell line was maintained in RPMI1640 medium supplemented with 10% fetal bovine serum and 2 mM L-glutamine at 37°C in 5% CO2 and 95% air. To develop tumors in vivo, nude mice were anesthetized and 25 µl of cell suspension containing 2×10^5 cells in serum-free RPMI1640 medium were injected submucosally into the tongue. Mice were euthanized 12 days after the transplantation, and tumor-bearing tongue tissue was frozen in OCT compound.

extract_protocol: Total RNA was extracted from the sample using RNeasy Mini Kit (QIAGEN) according to the manufacturer's instruction.

treatment_protocol: For in vitro samples, cultured cells were pelleted down by gentle centrifugation in PBS at 4C. For in vivo samples, frozen-specimens were sliced (10 um thick) and microdissected by a laser microdissection system (Leica, Germany). Totally 40 slices were used per cell line.

tag: tissue

value: oral cancer


title: Hum_CC_OSC20_vivo

status: Public on Mar 14 2015

type: RNA

city: Tokyo

department: Pathology

country: Japan

description:
NDUP_025
Gene expression 12 days after transplantation into mouse tongue

molecule: total RNA

organism: Homo sapiens

source_name: OSC20, transplant, 12 days

tag: cell line


title: Granulocytes of primary myelofibrosis - biological replicate 5

city: Belgrade

first: Vladan

middle: Predrag

last: Cokic

address: Dr Subotica 4

country: Serbia

institute: Institute for Medical Research

description:
PMF 5
Primary myelofibrosis JAK2+ 5

hyb_protocol: For hybridization, 36 μl hybridization mixture [26 μl cDNA mixture, 1 μl (10 μg) COT-1 DNA, 1 μl (8-10 μg) poly(dA), 1 μl yeast tRNA (4 μg), 6 μl 20X SSC and 1 μl 10% SDS] was pre-heated at 100oC for 2 minutes and cooled for 1 minute. Total volume of probe was added on the array and covered with cover slip. Slides are placed in hybridization chamber and 20µl water was added to the slide, and incubated overnight at 65oC.  Slides were then washed for 2 minutes each in 2X SSC, 1X SSC and 0.1X SSC and spin-dried.

scan_protocol: Microarray slides were scanned in both Cy3 (532nm) and Cy5 (635nm) channels using Axon GenePix 4000B scanner (Axon Instruments, Inc., Foster City, CA) with a 10-micron resolution. Scanned microarray images were exported as TIFF files to GenePix Pro 3.0 software for image analysis. The raw images were collected at 16-bit/pixel resolutions with 0 to 65,535 count dynamic range.

data_processing:
The area surrounding each spot image was used to calculate a local background and subtracted from each spot before the Cy5:Cy3 ratio calculation. The average of the total Cy3 and Cy5 signal gave a ratio that was used to normalize the signals. Spots with confidence interval of 99 (≥ 2 fold) with at least 150-fluorescence intensity for both channel and 30 μm spot size were considered as good quality spots for analysis. For advanced data analysis, gpr and jpeg files were imported into microarray database, and normalized by mAdb software provided by NIH Center for Information Technology (http://nciarray.nci.nih.gov/).
We have used the normalization method (Linear & Lowess) to normalize the data and then the Welch T test (comparison mean for single group test);
Default Ratio: ChanB/ChanA (Cy5/Cy3) Signal calculation: Mean Intensity minus Median Background Any Features designated Control were excluded.
Normalization method: Local Mean Across Element Signal Intensity (LOESS)
Spot Filter Options: Include Spots not flagged BAD or Not Found AND Target diameter >= 20 um AND Target diameter <= 300 um AND Both Chan A and Chan B Signal >= 200
Data was extracted and aligned by the Inventory Well ID Within array multiple occurrences of Well ID were reduced to a single instance by selecting the one with the strongest signal (Chan A + Chan B) Note: For all GenePix results from Axon scanned arrays Chan A is CY3 and Chan B is CY5.
Then the gene list was analyzed by GOFFA library for functional characterization of the overexpressed genes. The same gene list was copied and analyzed in Ingenuity for functional characterization. Ingenuity Pathways Analysis is a software application that enables identification of the biological mechanisms, pathways and functions most relevant to the genes of interest [www.ingenuity.com].
Each microarray experiment was globally normalized to make the median value of the log2-ratio equal to zero. The normalization process corrects for dye bias, photo multiplier tube voltage imbalance, and variations between channels in the amounts of the labeled cDNA probes hybridized. The data files representing the differentially expressed genes were then created.

source_name: Peripheral blood granulocytes

label_protocol: Labeled cDNA probes were produced: 5 μg of tRNA was incubated at 70oC for 5 minutes along with 1 μl of aminoallyl-oligo dT primer and quickly chilled for 3 minutes. Then, 2 μl 10X first strand buffer, 1.5 μl SSII enzyme (Stratagene, La Jolla, CA), 1.5 μl 20X aminoallyl dUTP and 2 μl of 0.1M DTT were added and incubated for 90 minutes at 42oC. After incubation, volume of the reaction mixture was raised to 60 μl with 40 μl of DEPC water. cDNA was purified by the MinElute column (Qiagen). 300 μl of Binding buffer PB was added to the coupled cDNA, and the mixture applied to the MinElute column, and centrifuged for 1minute at 10.000 rpm.  After discharging the flow-through, 600 μl of washing buffer PE was added to the column, and centrifuged for 1 minute at 10.000 rpm. The flow-through was discharged and the washing repeated. Then the columns were placed into a fresh eppendorf tube and 15 μl elution buffer added to the membrane, incubated for 1 minute at room temperature, centrifuged for 1 minute at 10.000 rpm and probe collected. The probe was dried in speed-vac for 16 minutes. Finally, 5 μl of 2X coupling buffer and 5 μl Cy3 and Cy5 dye (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) were mixed into the control (huURNA) and experimental cDNAs (huES cell-derived) respectively and incubated at room temperature in dark for 90 minutes. After incubation, the volume was raised to 60 μl by 50 μl DEPC water and then cDNA was purified by the MinElute column and eluted with 13 μl elution buffer by centrifugation.

growth_protocol: CD34+ hematopoietic progenitors are isolated from peripheral blood by immunomagnetic separation, while granulocytes are isolated after lymphoprep application

extract_protocol: we used the RNeasy protocol for isolation of total RNA (tRNA) from erythroid progenitor cells (Qiagen, Valencia, CA) according to the manufacturer's instructions

treatment_protocol: Immunomagnetic separation

tag: subject condition

value: Primary myelofibrosis JAK2+

tag: cell type

value: Granulocytes

source_name: Total human universal RNA (HuURNA)

tag: sample type

value: reference

tag: sample source

value: isolated from a collection of adult human tissues to represent a broad range of expressed genes from both male and female donors (BD Biosciences, Palo Alto, CA)


title: Hum_CC_OSC19_vivo

description:
NDUP_024
Gene expression 12 days after transplantation into mouse tongue

source_name: OSC19, transplant, 12 days


title: Nobeokabouzu-komugi 7 DAI treated_rep2

city: Yokohama

first: Alagu

last: Manickavelu

state: Kanagawa

address: Maioka 641-12

institute: Yokohama City University

description: Gene expression wheat florets 7 days after F. graminearum inoculation

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ml containing 25x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55μl of 2x GE Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-015520 Custom wheat 38k array  for 17 hours at 65°C in a 10rpm rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k 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 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 015520_D_F_20061122) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: Nobeokabouzu-komugi florets, treated, 7 days after inoculation_rep2

label_protocol: Total RNA was converted to cRNA labeled using Low Input Quick Amp Labeling kit (Agilent technologies) and fluorophore cy3-CTP. The samples were cleaned using RNeasy MinElute Clean up kit (Qiagen).

growth_protocol: Plants were grown in glass without any stress, the temperature and moisture inside the glass house were maintained 25 °C and 50%respectively

extract_protocol: Total RNA was extracted from the florets by using Nucleo Spin RNA plant kit (Macherey-Nagel, Germany)

treatment_protocol: At the early anthesis time, single floret inoculation with F. graminearum strain H3 was carried out by pipetting 10μl of the fungal suspension (1x105 macroconidia ml-1) between lemma and palea of each floret. Same time control plants (mock) were inoculated with 10 μl of distilled water. The inoculated spikes were covered with a plastic bag for 72 hours.

value: Floret

tag: genotype

value: Nobeokabouzu-komugi

tag: time point

value: 7 day after inoculation

tag: treatment

value: F. graminearum inoculation


title: Nobeokabouzu-komugi 7 DAI control_rep3

description: Gene expression wheat florets 7 days after water inoculation

source_name: Nobeokabouzu-komugi florets, control, 7 days after inoculation_rep3

value: water inoculation


title: Nobeokabouzu-komugi 7 DAI treated_rep1

source_name: Nobeokabouzu-komugi florets, treated, 7 days after inoculation_rep1


title: CD34+ hematopoietic progenitors of primary myelofibrosis - biological replicate 4

description:
PMF 4
Primary myelofibrosis JAK2- 4

source_name: Peripheral blood CD34+

value: Primary myelofibrosis JAK2-

value: CD34+ hematopoietic progenitors


title: Nobeokabouzu-komugi 3 DAI control_rep3

description: Gene expression wheat florets 5 days after water inoculation

source_name: Nobeokabouzu-komugi florets, control, 3 days after inoculation_rep3

value: 3 day after inoculation


title: Nobeokabouzu-komugi 7 DAI treated_rep3

source_name: Nobeokabouzu-komugi florets, treated, 7 days after inoculation_rep3


title: Nobeokabouzu-komugi 7 DAI control_rep2

source_name: Nobeokabouzu-komugi florets, control, 7 days after inoculation_rep2


title: Nobeokabouzu-komugi 3 DAI treated_rep3

description: Gene expression wheat florets 3 days after F. graminearum inoculation

source_name: Nobeokabouzu-komugi florets, treated, 3 days after inoculation_rep3


title: Nobeokabouzu-komugi 7 DAI control_rep1

source_name: Nobeokabouzu-komugi florets, control, 7 days after inoculation_rep1


title: CD34+ hematopoietic progenitors of primary myelofibrosis - biological replicate 3

description:
PMF 3
Primary myelofibrosis JAK2- 3


title: Granulocytes of essential thrombocythemia - biological replicate 9

description:
ET 9
Essential thrombocythemia JAK2- 9

value: Essential thrombocythemia JAK2-


title: Nobeokabouzu-komugi 3 DAI treated_rep2

source_name: Nobeokabouzu-komugi florets, treated, 3 days after inoculation_rep2


title: CD34+ hematopoietic progenitors of primary myelofibrosis - biological replicate 2

description:
PMF 2
Primary myelofibrosis JAK2+ 2


title: Sumai 3 7 DAI treated_rep2

source_name: Sumai 3 florets, treated, 7 days after inoculation_rep2

value: Sumai 3


title: Hum_CC_OSC19_vitro

description:
NDUP_022
Gene expresson in culture condition

source_name: OSC19, culture, pellet


title: control_rep4

city: Hangzhou

first: Angelina

middle: Shuhua

last: Wang

state: Zhejiang

address: Binwen Road No.548

department: the School of Dentistry

country: China

institute: Zhejiang Chinese Medical University

description:
X31
gene expression without internal derangement in condylar cartilage

hyb_protocol: 0.6 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 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-020908 Oryctolagus cuniculus (Rabbit) Oligo  Microarray   (Feature Number version) (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Oryctolagus cuniculus

source_name: control,condylar cartilage

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 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 extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

tag: gender

value: male

tag: age

value: 6 month old

tag: sample group

value: control

value: TMJ condylar cartilage


title: Nobeokabouzu-komugi 3 DAI control_rep1

description: Gene expression wheat florets 3 days after water inoculation

source_name: Nobeokabouzu-komugi florets, control, 3 days after inoculation_rep1


title: Nobeokabouzu-komugi 3 DAI control_rep2

description: Gene expression wheat florets 4 days after water inoculation

source_name: Nobeokabouzu-komugi florets, control, 3 days after inoculation_rep2


title: control_rep3

description:
X30
gene expression without internal derangement in condylar cartilage


title: Granulocytes of essential thrombocythemia - biological replicate 8

description:
ET 8
Essential thrombocythemia JAK2+ 8

source_name: Peripheral blood granulocytes

value: Essential thrombocythemia JAK2+

value: Granulocytes

source_name: Total human universal RNA (HuURNA)


title: Granulocytes of essential thrombocythemia - biological replicate 7

description:
ET 7
Essential thrombocythemia JAK2+ 7

value: reference

value: isolated from a collection of adult human tissues to represent a broad range of expressed genes from both male and female donors (BD Biosciences, Palo Alto, CA)


title: Sumai 3 7 DAI control_rep3

source_name: Sumai 3 florets, control, 7 days after inoculation_rep3

value: Floret


title: Nobeokabouzu-komugi 3 DAI treated_rep1

source_name: Nobeokabouzu-komugi florets, treated, 3 days after inoculation_rep1

value: Nobeokabouzu-komugi


title: Sumai 3 7 DAI treated_rep1

source_name: Sumai 3 florets, treated, 7 days after inoculation_rep1

value: 7 day after inoculation

value: F. graminearum inoculation


title: internal derangement_8week_rep4

description:
W30
gene expression after 8 week TMJ ID in condylar cartilage

source_name: internal derangement condylar cartilage_8 week

value: left joints subjected to TMJ ID

value: after 8 week TMJ ID


title: Sumai 3 7 DAI treated_rep3

source_name: Sumai 3 florets, treated, 7 days after inoculation_rep3


title: CD34+ hematopoietic progenitors of essential thrombocythemia - biological replicate 6

description:
ET 6
Essential thrombocythemia JAK2- 6

source_name: Peripheral blood CD34+

value: CD34+ hematopoietic progenitors


title: control_rep2

description:
X29
gene expression without internal derangement in condylar cartilage


title: control_rep1

description:
X25
gene expression without internal derangement in condylar cartilage


title: internal derangement_8week_rep3

description:
W22
gene expression after 8 week TMJ ID in condylar cartilage


title: Sumai 3 7 DAI control_rep1

source_name: Sumai 3 florets, control, 7 days after inoculation_rep1

value: water inoculation


title: CD34+ hematopoietic progenitors of essential thrombocythemia - biological replicate 5

description:
ET 5
Essential thrombocythemia JAK2- 5

value: Essential thrombocythemia JAK2-


title: Sumai 3 7 DAI control_rep2

source_name: Sumai 3 florets, control, 7 days after inoculation_rep2

value: Sumai 3


title: Sumai 3 3 DAI treated_rep3

source_name: Sumai 3 florets, treated, 3 days after inoculation_rep3

value: 3 day after inoculation


title: Sumai 3 3 DAI control_rep1

source_name: Sumai 3 florets, control, 3 days after inoculation_rep1


title: CD34+ hematopoietic progenitors of essential thrombocythemia - biological replicate 4

description:
ET 4
Essential thrombocythemia JAK2- 4


title: internal derangement_8week_rep2

description:
W21
gene expression after 8 week TMJ ID in condylar cartilage

value: male

value: 6 month old


title: Gamenya 7 DAI treated_rep3

source_name: Gamenya florets, treated, 7 days after inoculation_rep3

value: Gamenya


title: Sumai 3 3 DAI treated_rep1

source_name: Sumai 3 florets, treated, 3 days after inoculation_rep1


title: Sumai 3 3 DAI control_rep2

source_name: Sumai 3 florets, control, 3 days after inoculation_rep2


title: Sumai 3 3 DAI control_rep3

source_name: Sumai 3 florets, control, 3 days after inoculation_rep3


title: internal derangement_4week_rep3

description:
D6
gene expression after 4 week TMJ ID in condylar cartilage

source_name: internal derangement condylar cartilage_4 week

value: after 4 week TMJ ID

value: TMJ condylar cartilage


title: CD34+ hematopoietic progenitors of essential thrombocythemia - biological replicate 1

description:
ET 1
Essential thrombocythemia JAK2+ 1

value: Essential thrombocythemia JAK2+

value: reference

value: isolated from a collection of adult human tissues to represent a broad range of expressed genes from both male and female donors (BD Biosciences, Palo Alto, CA)


title: Sumai 3 3 DAI treated_rep2

source_name: Sumai 3 florets, treated, 3 days after inoculation_rep2

value: Floret


title: Gamenya 7 DAI treated_rep1

source_name: Gamenya florets, treated, 7 days after inoculation_rep1

value: 7 day after inoculation

value: F. graminearum inoculation


title: internal derangement_4week_rep4

description:
D8
gene expression after 4 week TMJ ID in condylar cartilage

value: left joints subjected to TMJ ID


title: internal derangement_8week_rep1

description:
W9
gene expression after 8 week TMJ ID in condylar cartilage

value: after 8 week TMJ ID


title: Gamenya 7 DAI control_rep3

source_name: Gamenya florets, control, 7 days after inoculation_rep3

value: water inoculation


title: internal derangement_4week_rep2

description:
D4
gene expression after 4 week TMJ ID in condylar cartilage


title: internal derangement_4week_rep1

description:
D2
gene expression after 4 week TMJ ID in condylar cartilage


title: CD34+ hematopoietic progenitors of essential thrombocythemia - biological replicate 3

description:
ET 3
Essential thrombocythemia JAK2+ 3

value: CD34+ hematopoietic progenitors

source_name: Total human universal RNA (HuURNA)


title: Gamenya 7 DAI control_rep2

description: Gene expression wheat florets 7 days after water inoculation

source_name: Gamenya florets, control, 7 days after inoculation_rep2


title: Gamenya 7 DAI control_rep1

source_name: Gamenya florets, control, 7 days after inoculation_rep1


title: Granulocytes of polycythemia vera - biological replicate 10

description:
PV 10
Polycythemia vera 10

source_name: Peripheral blood granulocytes

value: Polycythemia vera (PV)

value: Granulocytes


title: Gamenya 3 DAI treated_rep2

description: Gene expression wheat florets 3 days after F. graminearum inoculation

source_name: Gamenya florets, treated, 3 days after inoculation_rep2

value: 3 day after inoculation


title: Gamenya 3 DAI treated_rep3

source_name: Gamenya florets, treated, 3 days after inoculation_rep3


title: Gamenya 3 DAI treated_rep1

source_name: Gamenya florets, treated, 3 days after inoculation_rep1


title: Gamenya 7 DAI treated_rep2

description: Gene expression wheat florets 7 days after F. graminearum inoculation

source_name: Gamenya florets, treated, 7 days after inoculation_rep2


title: Granulocytes of polycythemia vera - biological replicate 8

description:
PV 8
Polycythemia vera 8


title: CD34+ hematopoietic progenitors of essential thrombocythemia - biological replicate 2

description:
ET 2
Essential thrombocythemia JAK2+ 2

source_name: Peripheral blood CD34+


title: CD34+ hematopoietic progenitors of polycythemia vera - biological replicate 6

description:
PV 6
Polycythemia vera 6


title: Granulocytes of polycythemia vera - biological replicate 9

description:
PV 9
Polycythemia vera 9


title: internal derangement_2 week_rep4

description:
C7
gene expression after 2 week TMJ ID in condylar cartilage

source_name: internal derangement condylar cartilage_2 week

value: male

value: 6 month old

value: after 2 week TMJ ID


title: Gamenya 3 DAI control_rep3

description: Gene expression wheat florets 5 days after water inoculation

source_name: Gamenya florets, control, 3 days after inoculation_rep3

value: Gamenya


title: Gamenya 3 DAI control_rep1

description: Gene expression wheat florets 3 days after water inoculation

source_name: Gamenya florets, control, 3 days after inoculation_rep1


title: internal derangement_2 week_rep1

description:
C1
gene expression after 2 week TMJ ID in condylar cartilage

value: TMJ condylar cartilage


title: Gamenya 3 DAI control_rep2

description: Gene expression wheat florets 4 days after water inoculation

source_name: Gamenya florets, control, 3 days after inoculation_rep2


title: CD34+ hematopoietic progenitors of polycythemia vera - biological replicate 3

description:
PV 3
Polycythemia vera 3

value: reference


title: CD34+ hematopoietic progenitors of polycythemia vera - biological replicate 5

description:
PV 5
Polycythemia vera 5

value: isolated from a collection of adult human tissues to represent a broad range of expressed genes from both male and female donors (BD Biosciences, Palo Alto, CA)


title: SW480-R

city: Kunming

first: youguang

last: huang

state: Yunnan Province

address: 519 Kunzhou Road

department: Tumor Institute of Yunnan Province

institute: The Third Affiliated Hospital of Kunming Medical University

description: gene expression data from SW480-R

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by RMA algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label: biotin

source_name: SW-480-R, derived from SW-480 (ATCC CCL-228)

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Cells were routinely cultured in DMEM-F12 (Gibco) supplemented with 10% fetal bovine serum (FBS, Thermo) and 1% Antimycotics/ Antibiotics (Gibco) at 37°C, 5% CO2 in a humidified incubator.

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 integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: No treatment

value: SW480 17-AAG resistance


title: CD34+ hematopoietic progenitors of polycythemia vera - biological replicate 2

description:
PV 2
Polycythemia vera 2


title: internal derangement_2 week_rep3

description:
C5
gene expression after 2 week TMJ ID in condylar cartilage


title: internal derangement_1 week_rep3

description:
B27
gene expression after 1 week TMJ ID in condylar cartilage

source_name: internal derangement condylar cartilage_1 week

value: after 1 week TMJ ID


title: internal derangement_1 week_rep4

description:
B28
gene expression after 1 week TMJ ID in condylar cartilage


title: SW480

description: gene expression data from SW480

value: SW480 parental


title: internal derangement_1 week_rep2

description:
B26
gene expression after 1 week TMJ ID in condylar cartilage

value: left joints subjected to TMJ ID


title: internal derangement_2 week_rep2

description:
C3
gene expression after 2 week TMJ ID in condylar cartilage


title: HL7702-484

city: Shanghai

first: YANG

middle: YING

last: CHENG

address: International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University

institute: EHBH

description: Gene expression data from overexpression miR-484 cells

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by RMA algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

growth_protocol: QSG7701, HL7702 and hHep cells were cultured in 6cm dishes for 24 hr

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 integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: QSG7701, HL7702 and hHep cells were treated with 100nM mimic-NC or mimic-484 for 72 hr

value: human hepatocytes

value: 100nM mimic-484 for 72 hr


title: HL7702-NC

description: Gene expression data from negative control cells

value: 100nM mimic-NC for 72 hrs


title: hiHep-484


title: internal derangement_1 week_rep1

description:
B24
gene expression after 1 week TMJ ID in condylar cartilage


title: QSG7701-484


title: Match normal of fusion positive tumor; biological rep7

status: Public on Mar 13 2015

city: Houston

first: Nicholas

last: Navin

state: tx

address: 6767Bertner AVE

country: USA

institute: UT MD Anderson

description: gene expression array for normal tissue

hyb_protocol: The ligated samples were hybridized onto GeneChip miRNA-1_0 arrays at 48C for 16hrs.

scan_protocol: The miRNA-1_0  GeneChip arrays were washed and stained in a fluidics FS_450 and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data were analyzed with Partek Genomics Suite using RMA algorithm followed by log2 transformation.

source_name: Human salivary gland tumor patient

label_protocol: 500ng total RNA was polyA tailed and then ligated to the biotinylated signal molecule using the FlashTag® Biotin HSR kit from Genisphere according to manufacturer's instructions.

growth_protocol: Samples were collected from fresh frozen tissues

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

treatment_protocol: Samples were excised from human patients under approved IRB protocols

value: Adenoid cystic tumor

value: Match normal of fusion positive tumor


title: QSG7701-NC


title: Fusion positive tumor; biological rep8

description: gene expression array for tumor

value: Fusion positive tumor


title: Match normal of fusion positive tumor; biological rep8

description: gene expression array for normal tissue


title: CD34+ hematopoietic progenitors of polycythemia vera - biological replicate 1

description:
PV 1
Polycythemia vera 1

value: Polycythemia vera (PV)

value: CD34+ hematopoietic progenitors


title: hiHep-NC

source_name: hiHep-NC


title: Match normal of fusion positive tumor; biological rep6

description: gene expression array for normal tissue


title: Fusion positive tumor; biological rep7

description: gene expression array for tumor


title: mst2∆ epe1∆ meu6∆

type: genomic

city: New York

first: Songtao

last: Jia

state: NY

address: 1114, Fairchild center

institute: Columbia University

hyb_protocol: Agilent Yeast ChIP-on-chip Analysis” protocol

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: mst2∆ epe1∆ meu6∆ cells

growth_protocol: 50mL cells grow at 30°C overnight until OD595 is 0.5

treatment_protocol: Paraformaldehyde was added to the cultures at the final concentratin of 3% and incubate 30min

tag: strain

tag: antibody

value: DNA from WCE


title: Fusion positive tumor; biological rep5

description: gene expression array for tumor


title: Match normal of fusion positive tumor; biological rep5

description: gene expression array for normal tissue


title: mst2∆ epe1∆ swi6∆

source_name: mst2∆ epe1∆ swi6∆ cells

label_protocol: Agilent Yeast ChIP-on-chip Analysis” protocol


title: Fusion positive tumor; biological rep6

description: gene expression array for tumor


title: Match normal of fusion negative tumor; biological rep4

description: gene expression array for normal tissue

value: Match normal of fusion negative tumor


title: Fusion negative tumor; biological rep4

description: gene expression array for tumor

value: Fusion negative tumor


title: Fusion positive tumor; biological rep4

description: gene expression array for tumor


title: mst2∆

source_name: mst2∆ cells

extract_protocol: Agilent Yeast ChIP-on-chip Analysis” protocol


title: Match normal of fusion positive tumor; biological rep4

description: gene expression array for normal tissue


title: Match norma of fusion positive tumor; biological rep3

description: gene expression array for normal tissue

value: Match norma of fusion positive tumor


title: Fusion positive tumor; biological rep3

description: gene expression array for tumor


title: Match normal of fusion negative tumor; biological rep3

description: gene expression array for normal tissue


title: epe1∆

source_name: epe1∆ cells


title: mst2∆ epe1∆

source_name: mst2∆ epe1∆ cells


title: Fusion negative tumor; biological rep3

description: gene expression array for tumor


title: WT

source_name: WT cells


title: Fusion negative tumor; biological rep2

description: gene expression array for tumor


title: Fusion negative tumor; biological rep1

description: gene expression array for tumor


title: Mim2-3

city: Jinan

first: Qiji

last: Liu

address: 44# Wenhua Xi Rd

department: Department of Medical Genetics

institute: Shandong University School of Medicine

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

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

organism: Mus musculus

source_name: spleen from mir-155 knockout mice Mim2-3

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted using the trizol (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by od260

value: male

value: spleen

value: mir-155 knockout


title: Match norma lof fusion positive tumor; biological rep2

description: gene expression array for normal tissue

value: Match norma lof fusion positive tumor


title: WT-2

source_name: spleen from wildtype mice WT-2

value: wildtype


title: Mim1-5

source_name: spleen from mir-155 knockout mice Mim1-5

value: female


title: Match normal of fusion positive tumor; biological rep1

description: gene expression array for normal tissue


title: WT-1

source_name: spleen from wildtype mice WT-1


title: Fusion positive tumor; biological rep1

description: gene expression array for tumor


title: Mim1-6

source_name: spleen from mir-155 knockout mice Mim1-6


title: WT-3

source_name: spleen from wildtype mice WT-3


title: Mim2-2

source_name: spleen from mir-155 knockout mice Mim2-2


title: WT-4

source_name: spleen from wildtype mice WT-4


title: Match normal of fusion negative tumor; biological rep2

description: gene expression array for normal tissue


title: Fusion positive tumor; biological rep2

description: gene expression array for tumor


title: primary adult hepatocyte

city: Chuo-ku

first: Tetsuya

last: Ishikawa

state: Tokyo

address: 1-1, Tsukiji 5-chome

department: Research Institute

institute: National Cancer Center

description: Immediately after thawing frozen cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (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-v5_95_Feb07 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hepatic cells

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 RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: No culture

extract_protocol: Using the AllPrep DNA/RNA Mini kit (Qiagen), total RNA was prepared from human primary adult hepatocytes (obtained from the Health Science Research Resources Bank). RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Total RNA was prepared from a frozen vial and subjected to microarray analysis.

value: liver


title: hiHSCs [NGC1-1]

description: Self-renewal culture with MEF in mTeSR1 on gelatin

source_name: stem cells

growth_protocol: The gastric cells (67 years old, Japanese, male) were seeded on collagen-coated dishes with Dulbecco's modified Eagle medium supplemented with 10% fetal bovine serum. One day later, the cells at approximately 5–10% confluency were incubated with the pantropic retrovirus vector solution at 37°C for 24 hr in a 5% CO2 incubator. The replication-incompetent pantropic Moloney murine leukemia virus (MMLV)-derived retrovirus vector pMX solution was used for the ectopic expression of human OCT3/4, SOX2, and KLF4. Mitomycin C-treated mouse embryonic fibroblast (MEF; Millipore) were seeded following the infection. The culture was replaced with the MEF-conditioned medium every three days until proliferating cells reached 100% confluency at a very high density. The confluent culture was further refreshed with mTeSR1 medium (STEMCELL Technologies) every day from day 31. Clone NGC1-1 was isolated at day 41 after the three-gene transduction using forceps under a microscope.

extract_protocol: Using the AllPrep DNA/RNA Mini kit (Qiagen), total RNA was prepared from a hepatocellular carcinoma cell line (HuH-7) and human primary adult hepatocyte (obtained from the Health Science Research Resources Bank) as well as clones AFB1-1, NGC1-1, and NGC1-2 that were cultured on the MEFs (5 X 10^4 cells/cm^2) with mTeSR1 (StemCell Technologies) medium in gelatin-coated 100-mm dishes before long-term serial passage. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The isolated clone NGC1-1 was subcultured in a well of gelatin-coated 24-well plates. After an expansion culture, clone NGC1-1 was further cultured to a well of gelatin-coated 6-well plates and finally cultured in a gelatin-coated 100-mm dish. The expanded clone NGC1-1 was treated with a dissociation solution (0.25% trypsin–EDTA [Gibco] and 1% collagenase [Invitrogen]) or 0.25% trypsin–EDTA and passaged in mTeSR1 supplemented with 10–20 μM Y-27632 (Calbiochem and Wako) to avoid cell death. The clone NGC1-1 was cultured with the MEFs (5 X 10^4 cells/cm^2) mainly in mTeSR1 medium and occasionally in Primate ESC medium (ReproCell) on gelatin-coated dishes. Total RNA was prepared from a 100-mm dish and subjected to microarray analysis.

value: gastric tissue-derived


title: WP3ΔlexA-20MPa and 4℃-rep6

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

description: WP3ΔlexA cDNA was labled with Cy3 and WP3 wild-type cDNA was labled with Cy5

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing:
S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model
In all of the experiments, WP3ΔlexA is the test sample and WP3 wild-type is the reference sample. Microarray spots with P values <0.001 in the F-test and log2 ratio were regarded as differentially expressed genes. In addition, all of the DEGs were confirmed with Significance Analysis of Microarrays (SAM) software

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20MPa and 4°C

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

tag: genotype/variation

value: WP3 wild-type

tag: growth cultured

value: 20MPa and 4℃ in 2216E medium

value: 4℃ in 2216E medium


title: hiHSCs [NGC1-2]

growth_protocol: The gastric cells (67 years old, Japanese, male) were seeded on collagen-coated dishes with Dulbecco's modified Eagle medium supplemented with 10% fetal bovine serum. One day later, the cells at approximately 5–10% confluency were incubated with the pantropic retrovirus vector solution at 37°C for 24 hr in a 5% CO2 incubator. The replication-incompetent pantropic Moloney murine leukemia virus (MMLV)-derived retrovirus vector pMX solution was used for the ectopic expression of human OCT3/4, SOX2, and KLF4. Mitomycin C-treated mouse embryonic fibroblast (MEF; Millipore) were seeded following the infection. The culture was replaced with the MEF-conditioned medium every three days until proliferating cells reached 100% confluency at a very high density. The confluent culture was further refreshed with mTeSR1 medium (STEMCELL Technologies) every day from day 31. Clone NGC1-2 was isolated at day 46 after the three-gene transduction using forceps under a microscope.

treatment_protocol: The isolated clone NGC1-2 was subcultured in a well of gelatin-coated 24-well plates. After an expansion culture, clone NGC1-2 was further cultured to a well of gelatin-coated 6-well plates and finally cultured in a gelatin-coated 100-mm dish. The expanded clone NGC1-2 was treated with a dissociation solution (0.25% trypsin–EDTA [Gibco] and 1% collagenase [Invitrogen]) or 0.25% trypsin–EDTA and passaged in mTeSR1 supplemented with 10–20 μM Y-27632 (Calbiochem and Wako) to avoid cell death. The clone NGC1-2 was cultured with the MEFs (5 X 10^4 cells/cm^2) mainly in mTeSR1 medium and occasionally in Primate ESC medium (ReproCell) on gelatin-coated dishes. Total RNA was prepared from a 100-mm dish and subjected to microarray analysis.


title: WP3ΔlexA-20MPa and 4℃-rep5


title: Klf4 mCherry+ intermediate reprogramming population (day 6)

city: Kyoto

first: Knut

last: Woltjen

address: 53 Kawahara-Cho, Shogoin, Sakyo-ku

department: Reprogramming Science

institute: CiRA, Kyoto University

description:
Klf4S d6 mCherry+
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. FACS sorted on day 6 of dox treatment.

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 TG.

data_processing: Mouse Gene 1.0 ST arrays were normalized using RMA implemented in GeneSpring 12.1.

label: Biotin

source_name: MEFs, Klf4S, reprogramming day 6, FACS sorted

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) was used according to Affymetrix protocol.

growth_protocol: ROSA-rtTA; Nanog-GFP MEFs were transfected with transposons (PB-TAC-OSKM, -OKMS, -OK+9MS, -MKOS, -STEMCCA, -EB-C5, -WTSI, -OKN-HAMS, -Klf4S, -Klf4L, and -lacZ) plus pCyL43 PB transposase plasmid using FugeneHD (Promega). After 24 hr, the media was replaced with ES cell medium with doxycycline (1ug/mL).

extract_protocol: Total RNA was prepared from harvested cells using the RNeasy Mini Kit (QIAGEN). Total RNA was eluted from spin columns using 30 uL RNase-free water. To eliminate contaminating DNA in the RNA solutions, DNase digestion was carried out and the RNA solutions was cleaned up using RNA clean up protocol according to the manufacturer’s instructions.

treatment_protocol: mCherry+ cell population from the PB transfected MEFs on d6 was collected on a BD FACSAria II cell sorter (BD Biosciences).

value: F1 hybrid

tag: female parent

value: ROSA-rtTA homozygous C57Bl6 backcross

tag: male parent

value: Nanog-GFP homozygous BAC transgenic C57Bl6/129SV hybrid intercross

value: ROSA-rtTA; Nanog-GFP

tag: developmental stage

value: mouse embryonic fibroblasts (MEFs)

tag: transgene

value: piggyBac transposon PB-TAC, Klf4S

tag: reprogramming day


title: OKN-HAMS mCherry+ intermediate reprogramming population (day 6)

description:
OKN-HAMS d6 mCherry+
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. FACS sorted on day 6 of dox treatment.

source_name: MEFs, OKN-HAMS, reprogramming day 6, FACS sorted

value: male

tag: cell type

value: piggyBac transposon PB-TAC, OKN-HAMS polycistronic reprogramming vector


title: LacZ population (day 2)

description:
LacZ d2
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. Harvested on day 2 of dox treatment.

source_name: MEFs, lacZ, reprogramming day 2, unsorted

value: piggyBac transposon PB-TAC, lacZ


title: hepatocellular carcinoma cell line

description: Culture in DMEM with 10% FBS

growth_protocol: A human hepatocellular carcinoma cell line, HuH-7, was cultured with DMEM medium supplemented with 10% FBS.

extract_protocol: Using the AllPrep DNA/RNA Mini kit (Qiagen), total RNA was prepared from a hepatocellular carcinoma cell line (HuH-7) in a 100-mm dish. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Total RNA was prepared from a 100-mm dish and subjected to microarray analysis.

tag: tissue

value: hepatocellular carcinoma

tag: cell line


title: EB-C5 mCherry+ intermediate reprogramming population (day 6)

description:
EB-C5 d6 mCherry+
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. FACS sorted on day 6 of dox treatment.

source_name: MEFs, EB-C5, reprogramming day 6, FACS sorted

tag: genotype

value: piggyBac transposon PB-TAC, EB-C5 polycistronic reprogramming vector


title: hiHSCs [AFB1-1]

growth_protocol: Human adult dermal fibroblasts (43 years old, white, female) were obtained from a company (Lonza). The cells were seeded with FGM-2 Bullet kit medium (Lonza) in Matrigel-coated dishes. One day later, the cells at approximately 5–10% confluency were incubated with the pantropic retrovirus vector solution at 37°C for 24 hr in a 5% CO2 incubator. The replication-incompetent pantropic Moloney murine leukemia virus (MMLV)-derived retrovirus vector pMX solution was used for the ectopic expression of human OCT3/4, SOX2, and KLF4. Following gene transduction, the culture was replaced with mitomycin C-treated mouse embryonic fibroblast (MEF; Millipore)-conditioned media every three days until the fibroblasts reached 100% confluency at a very high density. The confluent culture was further refreshed with mTeSR1 medium (STEMCELL Technologies) daily from days 18 to 27, the MEF-conditioned medium daily from days 28 to 33, and mTeSR1 medium daily from days 34 to 38. Clone AFB1-1 was isolated at day 39 after the three-gene transduction using forceps under a microscope.

treatment_protocol: The isolated clone AFB1-1 was subcultured in each well of gelatin-coated 24-well plates. After an expansion culture, clone AFB1-1 was further cultured to each well of gelatin-coated 6-well plates and finally cultured in a gelatin-coated 100-mm dish. The expanded clone AFB1-1 was treated with a dissociation solution (0.25% trypsin–EDTA [Gibco] and 1% collagenase [Invitrogen]) or 0.25% trypsin–EDTA and passaged in mTeSR1 supplemented with 10–20 μM Y-27632 (Calbiochem and Wako) to avoid cell death. The clone was cultured with the MEFs (5 X 10^4 cells/cm^2) mainly in mTeSR1 medium and occasionally in Primate ESC medium (ReproCell) on gelatin-coated dishes. Total RNA was prepared from a 100-mm dish and subjected to microarray analysis.

value: dermal fibroblast-derived

value: female


title: WTSI mCherry+ intermediate reprogramming population (day 6)

description:
WTSI d6 mCherry+
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. FACS sorted on day 6 of dox treatment.

source_name: MEFs, WTSI, reprogramming day 6, FACS sorted

value: piggyBac transposon PB-TAC, WTSI polycistronic reprogramming vector


title: STEMCCA mCherry+ intermediate reprogramming population (day 6)

description:
STEMCCA d6 mCherry+
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. FACS sorted on day 6 of dox treatment.

source_name: MEFs, STEMCCA, reprogramming day 6, FACS sorted

value: piggyBac transposon PB-TAC, STEMCCA polycistronic reprogramming vector


title: WP3ΔlexA-20MPa and 4℃-rep4

value: WP3 wild-type

value: 20MPa and 4℃ in 2216E medium


title: WP3ΔlexA-20MPa and 4℃-rep3

description: WP3ΔlexA cDNA was labled with Cy5 and WP3 wild-type cDNA was labled with Cy3

value: 4℃ in 2216E medium


title: MKOS mCherry+ intermediate reprogramming population (day 6)

description:
MKOS d6 mCherry+
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. FACS sorted on day 6 of dox treatment.

source_name: MEFs, MKOS, reprogramming day 6, FACS sorted

value: F1 hybrid

value: ROSA-rtTA homozygous C57Bl6 backcross

value: piggyBac transposon PB-TAC, MKOS polycistronic reprogramming vector


title: WP3ΔlexA-20MPa and 4℃-rep2


title: OKMS mCherry+ intermediate reprogramming population (day 6)

description:
OKMS d6 mCherry+
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. FACS sorted on day 6 of dox treatment.

source_name: MEFs, OKMS, reprogramming day 6, FACS sorted

value: Nanog-GFP homozygous BAC transgenic C57Bl6/129SV hybrid intercross

value: ROSA-rtTA; Nanog-GFP

value: mouse embryonic fibroblasts (MEFs)

value: piggyBac transposon PB-TAC, OKMS polycistronic reprogramming vector


title: WP3ΔlexA-20MPa and 4℃-rep1


title: Klf4+9 mCherry+ intermediate reprogramming population (day 6)

description:
Klf4L d6 mCherry+
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. FACS sorted on day 6 of dox treatment.

source_name: MEFs, Klf4L, reprogramming day 6, FACS sorted

value: male

value: piggyBac transposon PB-TAC, Klf4L


title: OSKM mCherry+ intermediate reprogramming population (day 6)

description:
OSKM d6 mCherry+
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. FACS sorted on day 6 of dox treatment.

source_name: MEFs, OSKM, reprogramming day 6, FACS sorted

value: piggyBac transposon PB-TAC, OSKM polycistronic reprogramming vector


title: TREM2_APP+_5

city: Saint Louis

first: Marco

last: Colonna

state: MO

address: 660 S Euclid Ave.

department: Pathology and Immunology

institute: Washinton University School of Medicine

description: gene expression from purifed microglia

hyb_protocol: Samples are prepared using a Nugen Ovation Pico SL kit.

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

data_processing: Data were analyzed using GenePattern (Broad Institute)

source_name: microglia from Trem2-/-5XFAD mice

label_protocol: Biotinylated cRNA were prepared using a Nugen Encore Biotin kit from 2 ng total RNA.

growth_protocol: 8.5 month old WT, Trem2-/-, 5XFAD, and Trem2-/- 5XFAD littermates were used.

extract_protocol: Cells were sorted directly into RLT buffer (Qiagen). A Rneasy micro kit (Qiagen) was used for subsquent RNA extraction.

treatment_protocol: Brains were harvested from PBS perfused animal. Single cell suspension was made using a neuronal tissue dissociation kit (Miltenyi). Microglia were then purified using FACS.

value: 8.5 month old

value: microglia


title: TREM2_APP+_6

description: gene expression from purifed microglia


title: TREM2_APP+_3

description: gene expression from purifed microglia


title: TREM2_APP+_2

description: gene expression from purifed microglia


title: TREM2_APP+_1

description: gene expression from purifed microglia


title: TREM2_APP+_4

description: gene expression from purifed microglia


title: WT_APP+_5

description: gene expression from purifed microglia

source_name: microglia from 5XFAD mice


title: WT_APP+_2

description: gene expression from purifed microglia


title: OK+9MS mCherry+ intermediate reprogramming population (day 6)

description:
OK+9MS d6 mCherry+
The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter. FACS sorted on day 6 of dox treatment.

source_name: MEFs, OK+9MS, reprogramming day 6, FACS sorted

value: piggyBac transposon PB-TAC, OK+9MS polycistronic reprogramming vector


title: TREM2_APP-_2

description: gene expression from purifed microglia

source_name: microglia from Trem2-/- mice


title: WT_APP+_4

description: gene expression from purifed microglia


title: TREM2_APP-_1

description: gene expression from purifed microglia


title: TREM2_APP-_3

description: gene expression from purifed microglia


title: WT_APP+_3

description: gene expression from purifed microglia


title: Match normal of fusion positive tumor; biological rep8

description: gene expression array for normal tissue

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on Affymetrix Human Gene ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data were analyzed with Affymetrix Expression Console using RMA algorithm followed by log2 transformation.

source_name: Human salivary gland tumor patient

label_protocol: 200ng total RNA was labeledusing Ambion WT expression Kit following manufacturer's instructions. cDNA was fragmented and labeled using the Affymetrix GeneChip WT terminal labeling kit according to manufacturer's instructions.

value: Adenoid cystic tumor

tag: sample type

value: Match normal of fusion positive tumor


title: WT_APP-_5

description: gene expression from purifed microglia


title: WT_APP-_1

description: gene expression from purifed microglia

source_name: microglia from WT mice

value: WT


title: WT_APP-_3

description: gene expression from purifed microglia


title: TREM2_APP-_4

description: gene expression from purifed microglia


title: Fusion positive tumor; biological rep4

description: gene expression array for tumor

value: Fusion positive tumor


title: WT_APP-_2

description: gene expression from purifed microglia


title: Fusion positive tumor; biological rep7

description: gene expression array for tumor


title: Match normal of fusion positive tumor; biological rep7

description: gene expression array for normal tissue


title: Fusion positive tumor; biological rep8

description: gene expression array for tumor


title: CD34+ hematopoietic progenitors of polycythemia vera - biological replicate 4

description:
PV 4
Polycythemia vera 4

source_name: Peripheral blood CD34+

tag: subject condition

value: Polycythemia vera (PV)

value: CD34+ hematopoietic progenitors

source_name: Total human universal RNA (HuURNA)

value: reference

tag: sample source

value: isolated from a collection of adult human tissues to represent a broad range of expressed genes from both male and female donors (BD Biosciences, Palo Alto, CA)


title: Fusion positive tumor; biological rep5

description: gene expression array for tumor


title: Match normal of fusion negative tumor; biological rep4

description: gene expression array for normal tissue

value: Match normal of fusion negative tumor


title: Match normal of fusion positive tumor; biological rep5

description: gene expression array for normal tissue


title: WT_APP+_1

description: gene expression from purifed microglia

tag: age


title: Match normal of fusion positive tumor; biological rep6

description: gene expression array for normal tissue


title: Match normal of fusion positive tumor; biological rep4

description: gene expression array for normal tissue


title: Fusion negative tumor; biological rep4

description: gene expression array for tumor

value: Fusion negative tumor


title: Match norma of fusion positive tumor; biological rep3

description: gene expression array for normal tissue

value: Match norma of fusion positive tumor


title: WT_APP-_4

description: gene expression from purifed microglia


title: Fusion positive tumor; biological rep3

description: gene expression array for tumor


title: Fusion negative tumor; biological rep2

description: gene expression array for tumor


title: Match normal of fusion negative tumor; biological rep2

description: gene expression array for normal tissue


title: 2860_StromalGFP_Control

city: Stanford

first: CHEN

last: ZHAO

state: CA

address: 265 Campus Dr.

department: Biochemistry

institute: Stanford University

description: Gene expression data in mammary stromal cells of Gli2WT mice

hyb_protocol: Followng fragmentation, 10ug of cRNA were hybridized to Mouse 2.0ST gene array chips

scan_protocol: GeneChips were scanned using GeneArray Scanner

data_processing: Raw data were analyzed by expression analysis console and transcriptome analysis console, differential expressed genes between Gli2WT and Gli2∆S stromal cells were ranked according to fold changes

source_name: FACS-isolated Fsp1-expressing mammary stromal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50 ug total RNA

growth_protocol: Mammary glands were collected from 10 weeks old control or stromal Gli2 ablated littermates

extract_protocol: Total RNAs of FACS-isolated Fsp1-Cre labeled (GFP expressing) stromal population from Gli2WT (2860) and Gli2ΔS (2857) mice were extracted by Trizol and subsequently by RNeasy Plus min kit (Qiagen).

treatment_protocol: Mammary glands were dissected and made as single cell suspension, followed by FACS-isolation of Fsp1Cre labeled GFP expressing cells (Rosa26mTmG).

value: mammary stromal cells


title: 2857_StromalGFP_StromalGl2Ablation

description: Gene expression data in mammary stromal cells of Gli2∆S mice


title: Fusion negative tumor; biological rep1

description: gene expression array for tumor


title: Match normal of fusion negative tumor; biological rep1

description: gene expression array for normal tissue


title: Fusion positive tumor; biological rep2

description: gene expression array for tumor


title: Fusion negative tumor; biological rep3

description: gene expression array for tumor


title: U937_EVI1 DMSO replicate 3

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

hyb_protocol: 12.5 µg of fragmented and labeled aRNA were hybridized to Affymetrix Human Affymetrix GeneChip Human Genome U133 plus 2.0 arrays for 16 h at 45 °C in a GeneChip hybridization oven 640.

scan_protocol: GeneChips were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled the by the Affymetrix GeneChip Command Console software v3.2 (AGCC).

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using the RMA algorithm (Irizarry et al., 2003) in the Affymetrix GeneChip Expression Console v1.3 software.

source_name: U937_EVI1 cells, 24 h DMSO treatment

label_protocol: The Affymetrix GeneChip 3’ IVT Express Protocol was used for the preparation of biotinylated amplified RNA (aRNA) from 250ng of total RNA.

growth_protocol: RPMI 10% FCS 1% Penicillin-Streptomycin-Glutamin

extract_protocol: RNeasy (Qiagen)

treatment_protocol: Logarithmically growing cells were treated with 1µM all-trans retinoic acid (ATRA) or an equivalent amount of solvent (DMSO) for 24 h

tag: protocol

value: EVI1 expression vector

tag: agent

value: DMSO


title: Match normal of fusion positive tumor; biological rep1

description: gene expression array for normal tissue


title: U937_vec ATRA replicate 2

source_name: U937_vec cells, 24 h ATRA treatment

value: empty vector

value: ATRA


title: U937_vec DMSO replicate 2

source_name: U937_vec cells, 24 h DMSO treatment


title: U937_vec DMSO replicate 3


title: U937_vec ATRA replicate 3


description: gene expression array for normal tissue


title: U937_EVI1 ATRA replicate 2

source_name: U937_EVI1 cells, 24 h ATRA treatment


title: Fusion positive tumor; biological rep1

description: gene expression array for tumor


title: U937_vec ATRA replicate 1


title: Match normal of fusion negative tumor; biological rep3

description: gene expression array for normal tissue


title: U937_EVI1 ATRA replicate 3


title: U937_EVI1 ATRA replicate 1


title: Fusion positive tumor; biological rep6

description: gene expression array for tumor


title: Match norma lof fusion positive tumor; biological rep2

description: gene expression array for normal tissue

value: Match norma lof fusion positive tumor


title: U937_EVI1 DMSO replicate 1


title: U937_vec DMSO replicate 1


title: U937_EVI1 DMSO replicate 2


title: HL60_EVI1 ATRA replicate 3

source_name: HL60_EVI1 cells, 24 h ATRA treatment

tag: cell


title: HL60_vec ATRA replicate 3

source_name: HL60_vec cells, 24 h ATRA treatment


title: HL60_vec ATRA replicate 2


title: HL60_EVI1 DMSO replicate 3

source_name: HL60_EVI1 cells, 24 h DMSO treatment


title: HL60_vec DMSO replicate 3

source_name: HL60_vec cells, 24 h DMSO treatment


title: HL60_EVI1 DMSO replicate 2


title: Male Wenchang Chicken DNA vs female Dehong DNA

city: Beijing

first: ming

last: tian

state: Beijing

address: No.2, Yuan Ming Yuan West Road, Haidian District

institute: China Agricultural University

description: Male Wenchang Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

hyb_protocol: Array hybridization was performed using Agilent Oligo aCGH Hybridization Kit (Agilent technologies) for 40 h at 20 rpm in a 65℃ Agilent hybridization oven.

scan_protocol: Arrays were scanned at 3μm resolution using an Agilent Microarray Scanner, and image analysis was performed using Feature Extraction software 10.7  with 90% laser power value and PMT 100%.

data_processing: Agilent Feature Extraction Software 10.7 was used for background subtraction and LOWESS normalization.

organism: Gallus gallus

source_name: Male Wenchang Chicken blood

label_protocol: 1.5µg of genomic DNA was digested with restriction enzymes AluI and RsaI and fluorescently labelled using the Agilent Genomic DNA Labeling Kit PLUS (Agilent technologies).Test samples were labelled with cyanine 5-dUTP and the reference sample with cyanine 3-dUTP.

extract_protocol: DNA was extracted using DNeasy Blood & Tissue kit(QIAGEN No.69504) and  Wizard Genomic DNA purification kit(Promega No.A1125) by the standard protocal for each kit separately.

treatment_protocol: Blood sample were got from adult chicken individuals by syringe and kept in 0.5M EDTA solution in order to avoid error.

value: blood

value: adult

tag: gender

value: Male

tag: breed

value: Wenchang

source_name: Dehong chicken

value: Dehong

value: female


title: Female Wenchang Chicken DNA vs female Dehong DNA

description: Female Wenchang Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Female Wenchang Chicken blood

value: Female


title: Male Shek-Ki Chicken DNA vs female Dehong DNA

description: Male Shek-Ki Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Male Shek-Ki Chicken blood

value: Shek-Ki


title: HL60_EVI1 ATRA replicate 1


title: Female Beijing Fatty Chicken DNA vs female Dehong DNA

description: Female Beijing Fatty Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Female Beijing Fatty Chicken blood

value: Beijing Fatty


title: Male Qingyuan partridge Chicken DNA vs female Dehong DNA

description: Male Qingyuan partridge Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Male Qingyuan partridge Chicken blood

value: Qingyuan partridge


title: Female Shek-Ki Chicken DNA vs female Dehong DNA

description: Female Shek-Ki Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Female Shek-Ki Chicken blood


title: Q31E

city: Philadelphia

first: BAIWEI

last: GU

state: PA

address: 3615 Civic center BLVD

institute: The Children's Hospital of Philadelphia

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Exon 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Probes for each targeted gene were averaged and inter-array normalization performed using the RMA algorithm

source_name: IPS cells with Q31E mutation of DKC1 gene

label_protocol: 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling

growth_protocol: IPS cells were cultured in 10-cm dish coated with mouse embryonic fibroblasts (MEFs) and grown in iPS cell medium (ES medium, DMEM/F12, supplemented with 20% knockout serum replacement, 0.1 mM nonessential amino acids, 1 mM l-glutamine [Invitrogen, Carlsbad, CA USA], 10 ng/ml recombinant human fibroblast like growth factor–basic (Peprotech, NJ, USA.), and 0.1 mM 2-mercaptoethanol (Sigma, St Louis, MO USA).

extract_protocol: Total RNA was extracted by using RNeasy Mini Kit (Qiagen)

value: human IPS cells

value: Q31E mutation


title: Male Beijing Fatty Chicken DNA vs female Dehong DNA

description: Male Beijing Fatty Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Male Beijing Fatty Chicken blood


title: HL60_vec ATRA replicate 1


title: Male Langshan Chicken DNA vs female Dehong DNA

description: Male Langshan Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Male Langshan Chicken blood

value: Langshan


title: Female Anak Chicken DNA vs female Dehong DNA

description: Female Anak Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Female Anak Chicken blood

value: Anak


title: HL60_EVI1 DMSO replicate 1

value: DMSO

value: EVI1 expression vector


title: Del371

source_name: IPS cells with Del37 mutation of DKC1 gene, biological duplication 1

value: Del37 mutation


title: HL60_vec DMSO replicate 1

value: empty vector


title: Female Langshan Chicken DNA vs female Dehong DNA

description: Female Langshan Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Female Langshan Chicken blood

value: blood

value: adult


title: Male Bearded Chicken DNA vs female Dehong DNA

description: Male Bearded Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Male Bearded Chicken blood

value: Male

value: Bearded


title: Female Jinhu Chicken DNA vs female Dehong DNA

description: Female Jinhu Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Female Jinhu Chicken blood

value: Jinhu

value: Dehong

value: female


title: Female Tibetan Chicken DNA vs female Dehong DNA

description: Female Tibetan Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Female Tibetan Chicken blood

value: Female

value: Tibetan


title: Female Qingyuan partridge Chicken DNA vs female Dehong DNA

description: Female Qingyuan partridge Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Female Qingyuan partridge Chicken blood

value: Qingyuan partridge


title: HL60_vec DMSO replicate 2

source_name: HL60_vec cells, 24 h DMSO treatment


title: Male Jinhu Chicken DNA vs female Dehong DNA

description: Male Jinhu Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Male Jinhu Chicken blood

source_name: Dehong chicken


title: WT p65 PNT1a cells 1_4

status: Public on Mar 12 2015

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: After labeling, 2ug of each aRNA was mixed with 2 ug of reference RNA and purified with Qiagen MinElute PCR Purification kit according to manufacturer’s instructions. Eluted sample was mixed with 10× Blocking Solution and 2× HiRPM buffer (Agilent Technologies), incubated for 2 min at 95°C and hybridized on 8× 60K Whole Human Genome Oligo Microarray chip (Agilent Technologies) using SureHyb DNA Microarray Hybridization Chambers in DNA Microarray hybridization oven (Agilent Technologies) at 10 rpm, 65°C for 18 h.

scan_protocol: After hybridization, slides were washed in Gene Expression Wash Buffer 1 and 2 for 1 min. Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent Microarray Scanner–G2565BA, Agilent Technologies) using Agilent-provided parameters (Red and Green photomultiplier tube (PMT) were each set at 100%, and scan resolution was set to 3 μm). The Feature Extraction Software v9.1.3.1 (Agilent Technologies) was used to extract and analyze the signals.

data_processing: Expression arrays were processed and loess-normalized using BioConductor.

source_name: PNT1a cell line

label_protocol: The cDNA reverse transcription and fluorescent labeling reactions were carried out using Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S’-Aminohexylacrylamido-dUTP.Briefly, 2ug of aRNA and Universal Human Reference RNA (Stratagene) were labeled in reverse transcription with Alexa647 and Alexa 555 aha-dUTPs respectively.

growth_protocol: PNT1a cells were maintained in the RPMI with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA samples were extracted with RNeasy Mini Kit (Qiagen) according to the manufacture’s recommendations. RNA quality was assessed with Nanodrop (Invitrogen). The cDNA reverse transcription and fluorescent labeling reactions were carried out using Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S’-Aminohexylacrylamido-dUTP.

tag: genotype/variation

value: p65 wildtype

source_name: human, universal reference RNA

value: reference RNA


title: Male Tibetan Chicken DNA vs female Dehong DNA

description: Male Tibetan Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Male Tibetan Chicken blood


title: Male Anak Chicken DNA vs female Dehong DNA

description: Male Anak Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Male Anak Chicken blood

value: Anak


title: Del372

source_name: IPS cells with Del37 mutation of DKC1 gene, biological duplication 2

value: human IPS cells


title: Female Bearded Chicken DNA vs female Dehong DNA

description: Female Bearded Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Female Bearded Chicken blood


title: Normal_A419_ChipC_5mC_Expt1

city: CUHK, Shatin

first: Hoi-Hung

last: Cheung

address: Rm.708A, LKS Integrated Biomedical Sciences Bldg.

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
A419 C_pvalue_Hs_NCBIv36.BED
Normal

hyb_protocol: Samples were prepared and hybridized to GeneChip Human Tiling 2.0R Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner GCS3000 according to manufacturer's instruction.

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (version 1.1) using parameters: two-sided test, 250 bp bandwidth and perfect match only.
The resulting BED files are generated by the Affymetrix Tiling Analysis Software (version 1.1) using parameters: Threshold = 20 (p < 0.01), Gap = 100.

source_name: Genomic DNA, sonicated, anti-5mC

growth_protocol: Primary tumors and normal tissues without any culture

extract_protocol: Genomic DNA was directly extracted from tissues using column-based purification method

treatment_protocol: Untreated and frozen before DNA extraction

tag: treatment

value: IP

value: normal testicular tissue

tag: source tissue

value: testis

tag: antibody


title: Normal_A090_ChipC_5mC_Expt1

description:
A090 C_pvalue_Hs_NCBIv36.BED
Normal

label_protocol: Samples were prepared and hybridized to GeneChip Human Tiling 2.0R Array according to Affymetrix specifications.


title: EC_2761_ChipC_5mC_Expt2

description:
2761 C_pvalue_Hs_NCBIv36.BED
embryonal carcinoma

value: testicular embryonic carcinoma


title: EC_3256_ChipC_5mC_Expt2

description:
3256 C_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2701_ChipC_5mC_Expt2

description:
2701 C_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: A353V2

source_name: IPS cells with A353V mutation of DKC1 gene, biological duplication 2

tag: cell type

value: A353V mutation


title: Normal_A090_ChipC_5mC_Expt2

description:
A090 C_pvalue_Hs_NCBIv36.BED
Normal

tag: tissue


title: EC_2701_ChipC_5mC_Expt1


title: HL60_EVI1 ATRA replicate 2

source_name: HL60_EVI1 cells, 24 h ATRA treatment

value: ATRA

value: EVI1 expression vector


title: EC_2761_ChipC_5mC_Expt1


title: WT p65 PNT1a cells 2_4

tag: cell line


title: Female Gallus gallus spadiceus DNA vs female Dehong DNA

description: Female Gallus gallus spadiceus DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

organism: Gallus gallus spadiceus

source_name: Female Gallus gallus spadiceus blood

value: blood

value: adult

value: Gallus gallus spadiceus


title: EC_2080_ChipC_5mC_Expt2

description:
2080 C_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: A353V1

source_name: IPS cells with A353V mutation of DKC1 gene, biological duplication 1

tag: genotype


title: EC_3256_ChipC_5mC_Expt1


title: control PNT1a cells 1_3

value: pCDH (control)

tag: sample type


title: p65-S536E PNT1a cells 1_1


title: p65-S536A PNT1a cells 1_2


title: control PNT1a cells 2_3


title: EC_2080_ChipC_5mC_Expt1


title: p65-S536E PNT1a cells 2_1


title: BMC

source_name: Wild type control IPS cells

value: Wild type


title: EC_1703_ChipC_5mC_Expt2

description:
1703 C_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: Male Gallus gallus spadiceus DNA vs female Dehong DNA

description: Male Gallus gallus spadiceus DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Male Gallus gallus spadiceus blood

value: Male

value: Dehong

value: female


title: Female Silkie DNA vs female Dehong DNA

description: Female Silkie DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Female Silkie blood

value: Female

value: Silkie


title: EC_1458_ChipC_5mC_Expt1

description:
1458 C_pvalue_Hs_NCBIv36.BED
embryonal carcinoma

value: IP


title: Normal_A419_ChipC_Input_Expt1

description: Normal

source_name: Genomic DNA, sonicated, input control

value: untreat

value: normal testicular tissue


title: p65-S536A PNT1a cells 2_2

value: reference RNA


title: KC3 (1)

description: KC3 lung cancer cell line, highly metastatic cells (biological replicate 1).

hyb_protocol: According to Affymetrix protocol.

scan_protocol: According to Affymetrix protocol.

data_processing: Gene expression values were processed by Asuragen (Austin, TX) and subjected to quantile normalization.

source_name: KC3 cell line, highly metastatic cells

label_protocol: According to Affymetrix protocol.

growth_protocol: K-rasLA1/+ mice were crossed with Cdkn1a+/+ and Cdkn1a-/- mice to generate K-rasLA1/+; Cdkn1a+/+ and K-rasLA1/+; Cdkn1a-/- mice, respectively. Mice were of 127s background. Murine lung adenocarcinoma cell lines (KC1-KC4) were derived from 6 different primary lung tumors obtained at necropsy from 4 different KC mice using the Cancer Cell Isolation Kit (Affymetrix) and cultured in RPMI 1640 medium supplemented with 10% FBS.

extract_protocol: According to Affymetrix protocol.

tag: strain/background

value: K-rasLA1/+; Cdkn1a-/-

value: lung adenocarcinoma cell line

tag: metastasis level

value: highly metastatic


title: KC3 (2)

description: KC3 lung cancer cell line, highly metastatic cells (biological replicate 2).


title: KC2 (1)

description: KC2 lung cancer cell line, highly metastatic cells (biological replicate 1).

source_name: KC2 cell line, highly metastatic cells


title: KC1 (3)

description: KC1 lung cancer cell line, highly metastatic cells (biological replicate 3).

source_name: KC1 cell line, highly metastatic cells


title: KC4 (2)

description: KC4 lung cancer cell line, poorly metastatic cell (biological replicate 2).

source_name: KC4 cell line, poorly metastatic cells

value: poorly metastatic


title: Male Silkie DNA vs female Dehong DNA

description: Male Silkie DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.

source_name: Male Silkie blood

value: blood

tag: age

value: adult

source_name: Dehong chicken


title: KC4 (1)

description: KC4 lung cancer cell line, poorly metastatic cell (biological replicate 1).


title: Normal_A419_ChipC_5mC_Expt2

description:
A419 C_pvalue_Hs_NCBIv36.BED
Normal

value: testis


title: KC2 (3)

description: KC2 lung cancer cell line, highly metastatic cells (biological replicate 3).


title: Normal_A090_ChipC_Input_Expt1

description: Normal


title: KC2 (2)

description: KC2 lung cancer cell line, highly metastatic cells (biological replicate 2).


title: KC3 (3)

description: KC3 lung cancer cell line, highly metastatic cells (biological replicate 3).


title: Normal_A090_ChipC_Input_Expt2

description: Normal


title: KC1 (1)

description: KC1 lung cancer cell line, highly metastatic cells (biological replicate 1).


title: lung tumors from mice with knock out of SMAD4 and PTEN rep1

description: knockout

hyb_protocol: According to Affymetix protocol.

scan_protocol: According to Affymetix protocol.

data_processing: Processed the CEL files using dChip (PM-MM model, Quantile normalization).

source_name: CCSPi-Cre mice, Ptend/dSmad4d/d lung cancer

label_protocol: According to Affymetix protocol.

growth_protocol: All animal experiments were performed in accordance with an IACUC approved protocol (Baylor College of Medicine, Houston, TX). Generation of CCSPiCre mice was carried out as previously described with some modifications. An iCre-SV40 poly A fragment was amplified from Cyp17iCre plasmid by PCR and subcloned immediately upstream to a Frt-flanked phosphoglycerol kinase neomycin-resistance cassette (PGK-Neo). The iCre-SV40 poly A-PGK-Neo fragment was again subcloned into a pGEM-4Z plasmid harboring a 5.3-kb mouse CCSP genomic sequence to generate the targeting plasmid. The targeting plasmid was then linearized and transfected into R1 ES cells by electroporation. Genomic DNA was isolated from Neomycin-resistant clones and digested with Nde I and Xho I and were screened by southern-blot using a 5’ external probe. Twenty two of ninety eight clones were targeted. Correctly targeted clones were microinjected into blastocysts from C57BL/6 mice. Chimeras were bred to C57BL/6 mice and germ line transmission of the iCre gene to F1 offspring were validated with PCR genotyping.   The CCSPicre mice were crossed with Ptenf/f and Smad4f/f mice to generate Ptend/d,Smad4d/d  and Smad4d/d  Ptend/d mice.

extract_protocol: Twelve-month-old adult mice were used for the microarray analysis.  After sacrifice, lungs were harvested from wild type mice, and lung tumors were macrodissected from Ptend/dSmad4d/d   mice.  These lung tissues were stored at -80°C and total RNA was extracted using the TRIzol method (TRIzol reagent; Invitrogen, Carlsbad, CA) followed by purification using an RNeasy column (Qiagen, Valencia, CA). RNA quality was assessed by using the Agilent Model 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: CCSPi-Cre Ptend/dSmad4d/d

value: lung tumor

tag: disease state

value: Ptend/dSmad4d/d lung cancer

tag: genetic background

value: mixed C57BL/6


title: Normal_A419_ChipC_Input_Expt2

description: Normal


title: EC_3256_ChipC_Input_Expt1

description: embryonal carcinoma

value: testicular embryonic carcinoma


title: lung tumors from mice with knock out of SMAD4 and PTEN rep2

description: knockout


title: KC1 (2)

description: KC1 lung cancer cell line, highly metastatic cells (biological replicate 2).


title: EC_3256_ChipC_Input_Expt2

description: embryonal carcinoma


title: EC_2761_ChipC_Input_Expt2

description: embryonal carcinoma


title: EC_2761_ChipC_Input_Expt1

description: embryonal carcinoma


title: lung from control mice rep3

description: control

source_name: CCSPi-Cre mice, normal lung

value: CCSPi-Cre

value: lung

value: normal lung


title: EC_2701_ChipC_Input_Expt2

description: embryonal carcinoma

value: untreat


title: lung tumors from mice with knock out of SMAD4 and PTEN rep3

description: knockout


title: Metastatic lesion from 4D model day 25, biological replicate #1

hyb_protocol: Ten microgram of dye labeled RNA was further hybridized with OneArray slide in a humidified oven with 2X SSPE buffer at 50C for 14-16 hours.

scan_protocol: The slides were scanned using Axon GenePix 4100 from Molecular Devices at wavelength 635 to 532 nm.

data_processing: The filtered data were log2 transformed and corrected using quantile normalization before their average ratios and significance values were calculated. Technical replicates (there being three technical replicates per biological replicate) were averaged together.

source_name: H1299 cells

label_protocol: Target RNA was labeled with Cye5 dye and OneArray slide is pre-hybridized to reduce the background signals and increase the performance of microarray.

growth_protocol: We created the 4D model as previously described (PMID:23934967).  Briefly, we used decellularized lung matrices from 6-week-old rats using 0.1% SDS and 1% Triton-X100.  The acellular matrices were thoroughly washed with PBS supplemented with antibiotics (100 IU/mL penicillin, 100 ug/mL streptomycin, and 0.25 ug/mL amphotericin; MP Biomedicals, Solon, OH, USA).  Next, we cannulated the trachea and placed 25 million H1299 cells diluted in 50 ml of complete media through the trachea of the 4D model (n=3). We collected the cells with media that passively came out of the model into a 500-mL container, we passed the media again through the trachea three times, and incubated it at 37degC for 2 hours to allow for cell attachment. We then counted the cells in the container and determined the percentage of tumor cells that were seeded on the 4D model.  We placed an additional 200 mL of complete media in the bioreactor previously described and allowed the media to go through the pump at 6 ml per minute and then through the oxygenator and the pulmonary artery of the acellular lung matrix.  Media in bioreactor was replaced with fresh media every day for 25 days. There were live CTC in the media which were counted and stored in Trizol (Iso-RNA Lysis reagent) at -80°C. The primary tumor was isolated on day 2 and day 25. The metastatic lesion was isolated by performing a lobectomy of the right upper lobe on day 10, the right middle lobe on day 20, and the right lower lobe on day 25.

extract_protocol: According to Human OneArray protocol.

value: Metastatic lesion

tag: time point

value: day 25


title: lung from control mice rep1

description: control


title: EC_2080_ChipC_Input_Expt2

description: embryonal carcinoma


title: lung from control mice rep2

description: control


title: Metastatic lesion from 4D model day 10, biological replicate #2

value: day 10


title: Metastatic lesion from 4D model day 25, biological replicate #3


title: Metastatic lesion from 4D model day 10, biological replicate #3


title: CTC from 4D model on day 25, biological replicate #2

value: CTC


title: Metastatic lesion from 4D model day 25, biological replicate #2


title: CTC from 4D model on day 25, biological replicate #1


title: EC_2080_ChipC_Input_Expt1

description: embryonal carcinoma


title: Metastatic lesion from 4D model day 10, biological replicate #1


title: EC_2701_ChipC_Input_Expt1

description: embryonal carcinoma


title: CTC from 4D model on day 10, biological replicate #2


title: H1299 cell grown on 4D model - primary tumor on day 25, biological replicate #3

value: H1299 cell - primary tumor


title: CTC from 4D model on day 10, biological replicate #1


title: EC_1703_ChipC_Input_Expt1

description: embryonal carcinoma


title: EC_1703_ChipC_Input_Expt2

description: embryonal carcinoma


title: EC_1458_ChipC_Input_Expt2

description: embryonal carcinoma


title: CTC from 4D model on day 10, biological replicate #3


title: EC_1458_ChipC_Input_Expt1

description: embryonal carcinoma


title: H1299 cell grown on 4D model - primary tumor on day 2, biological replicate #2

value: day 2


title: Normal_A419_ChipD_5mC_Expt1

description:
A419 D_pvalue_Hs_NCBIv36.BED
Normal

source_name: Genomic DNA, sonicated, anti-5mC

value: IP

value: normal testicular tissue


title: Normal_A090_ChipD_5mC_Expt2

description:
A090 D_pvalue_Hs_NCBIv36.BED
Normal

value: testis


title: Normal_A090_ChipD_5mC_Expt1

description:
A090 D_pvalue_Hs_NCBIv36.BED
Normal


title: EC_3256_ChipD_5mC_Expt2

description:
3256 D_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: M2 macrophages-vehicle-2

city: Manhasset

first: Anthony

middle: John

last: Hesketh

state: New York

address: 350 Community Dr.

institute: Feinstein Institute for Medical Research

description: SAMPLE 9

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensities were cubic spline normalized with background subtraction in GenomeStudio Gene Expression Analysis Module (V. 1.9.0) in GenomeStudio (V. 2011.1)

source_name: M2 macrophages_vehicle

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: CD14+ cells were MACS sorted (Miltenyi monocyte isolation kit II) from peripheral blood, M1 or M2 macrophages were polarized with GM-CSF (25ng/ml) or M-CSF (25ng/ml) for 7 days in complete RPMI, followed by activation with addition of IFN-γ (20ng/ml) and LPS (100ng/ml) or IL-4 (40ng/ml) for 18 hours, respectively

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

treatment_protocol: Macrophages were treated with CNI-1493 (200nM) during activation step

tag: subject id#

value: M2 macrophages

tag: treated with

value: vehicle


title: M1 macrophages-CNI-1493-3

description: SAMPLE 10

source_name: M1 macrophages_CNI-1493

value: M1 macrophages


title: M2 macrophages-vehicle-1

description: SAMPLE 11


title: H1299 cell grown on 4D model - primary tumor on day 2, biological replicate #1


title: H1299 cell grown on 4D model - primary tumor on day 2, biological replicate #3


title: EC_3256_ChipD_5mC_Expt1

value: testicular embryonic carcinoma


title: M2 macrophages-vehicle-3

description: SAMPLE 12


title: M2 macrophages-CNI-1493-2

description: SAMPLE 6

source_name: M2 macrophages_CNI-1493


title: M1 macrophages-vehicle-3

description: SAMPLE 8

source_name: M1 macrophages_vehicle


title: EC_2761_ChipD_5mC_Expt1

description:
2761 D_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: M1 macrophages-CNI-1493-2

description: SAMPLE 7


title: M2 macrophages-CNI-1493-3

description: SAMPLE 3


title: M1 macrophages-CNI-1493-1

description: SAMPLE 2


title: M1 macrophages-vehicle-2

description: SAMPLE 4


title: EC_2761_ChipD_5mC_Expt2


title: Normal_A419_ChipD_5mC_Expt2

description:
A419 D_pvalue_Hs_NCBIv36.BED
Normal


title: EC_2701_ChipD_5mC_Expt1

description:
2701 D_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2701_ChipD_5mC_Expt2


title: M1 macrophages-vehicle-1

description: SAMPLE 1


title: EC_1458_ChipC_5mC_Expt2


title: EC_2080_ChipD_5mC_Expt2

description:
2080 D_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_2080_ChipD_5mC_Expt1


title: EC_1703_ChipC_5mC_Expt1

description:
1703 C_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_1458_ChipD_5mC_Expt2

description:
1458 D_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: EC_1703_ChipD_5mC_Expt1

description:
1703 D_pvalue_Hs_NCBIv36.BED
embryonal carcinoma


title: M2 macrophages-CNI-1493-1

description: SAMPLE 5


title: Normal_A419_ChipD_Input_Expt1

description: Normal


title: EC_1703_ChipD_5mC_Expt2


title: Normal_A090_ChipD_Input_Expt1

description: Normal


title: KC4 (3)

description: KC4 lung cancer cell line, poorly metastatic cell (biological replicate 3).

tag: genotype/variation

value: K-rasLA1/+; Cdkn1a-/-

value: lung adenocarcinoma cell line

value: poorly metastatic


title: Normal_A090_ChipD_Input_Expt2

description: Normal

tag: treatment

value: untreat


title: EC_3256_ChipD_Input_Expt1

description: embryonal carcinoma

tag: source tissue


title: EC_3256_ChipD_Input_Expt2

description: embryonal carcinoma

tag: antibody


title: EC_2761_ChipD_Input_Expt2

description: embryonal carcinoma


title: EC_2761_ChipD_Input_Expt1

description: embryonal carcinoma


title: EC_1458_ChipD_5mC_Expt1


title: EC_2701_ChipD_Input_Expt1

description: embryonal carcinoma


title: Normal_A419_ChipD_Input_Expt2

description: Normal


title: EC_2080_ChipD_Input_Expt2

description: embryonal carcinoma


title: EC_2080_ChipD_Input_Expt1

description: embryonal carcinoma


title: RF-342 Liver

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format (please note that the ID_REF column in raw data files contains 'Array_Address_Id'). The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

source_name: OS liver metastasis_RF-342 specimen

label_protocol: According to Illumina protocol.

growth_protocol: Three genetically engineered mouse lines were used in this study.  Col2.3-Cre mice contain a rat Col1a1 2.3 kb rat promoter driving a Cre transgene (Liu et al., 2004) These mice express Cre  in osteoblast lineages.  These mice were backcrossed into a C57BL/6 background and further crossed to either floxed p53 mice or LSL-p53R172H mice.  Floxed p53 mice were generated by the Berns laboratory (Marino et al., 2000) and obtained from the NCI Mouse Repository. These mice were also backcrossed into a C57BL/6 background and contain a wildtype p53 allele that can be excised by Cre recombinase binding to LoxP sites located in introns 1 and 10 of the p53 gene.  The LSL-p53R172H mice were made by the Jacks laboratory (Olive et al., 2004), obtained from the NCI Mouse Repository and backcrossed into a C57BL/6 background. These mice contain a “hot spot” point-mutant allele of Trp53 frequently observed in human tumors that can be activated by Cre-mediated deletion of the lox-stop-lox (LSL) cassette located in the altered p53 promoter.  All mice were bred and maintained in a specific pathogen-free animal facility at Baylor College of Medicine. All research with mice was conducted in compliance with the Baylor Animal Protocol Committee (Baylor College of Medicine Animal Protocol AN336) and AAALAC recommendations as published in The Guide for the Care and Use of Laboratory Animals (NRC1996).

extract_protocol: Total RNA was extracted from tissue samples, using Trizol. RNA quality were inspected on a 2100 Bioanalyzer (Agilent).

tag: sample group

value: OS liver metastasis

tag: specimen id

value: RF-342 specimen


title: RF-379 Lungs

source_name: OS lung metastasis_RF-379 specimen

value: OS lung metastasis

value: RF-379 specimen


title: CR-147 Lungs

source_name: OS lung metastasis_CR-147 specimen

value: CR-147 specimen


title: EC_1703_ChipD_Input_Expt1

description: embryonal carcinoma

source_name: Genomic DNA, sonicated, input control

tag: tissue


title: EC_1703_ChipD_Input_Expt2

description: embryonal carcinoma


title: EC_1458_ChipD_Input_Expt2

description: embryonal carcinoma


title: CR-147 Liver

source_name: OS liver metastasis_CR-147 specimen


title: CRE-155 Lungs

source_name: OS lung metastasis_CRE-155 specimen

value: CRE-155 specimen


title: RF-229 primary

source_name: primary OS that produced metastatic lesion_RF-229 specimen

value: RF-229 specimen


title: EC_1458_ChipD_Input_Expt1

description: embryonal carcinoma


title: CR-45 primary

source_name: primary OS that produced metastatic lesion_CR-45 specimen

value: CR-45 specimen


title: EC_2701_ChipD_Input_Expt2

description: embryonal carcinoma

value: testis


title: FC-279 Lungs

source_name: OS lung metastasis_FC-279 specimen

value: FC-279 specimen


title: RF-104 primary

source_name: primary OS that produced metastatic lesion_RF-104 specimen

value: RF-104 specimen


title: RF-364 Lungs

source_name: OS lung metastasis_RF-364 specimen

value: RF-364 specimen


title: RF-212 Lungs

source_name: OS lung metastasis_RF-212 specimen

value: RF-212 specimen