title: Wnt pathway gene expression in normal B cells (Normal10)

description: Wnt pathway genes.


title: cancer, PhIP, replicate 3

status: Public on Aug 29 2013

type: RNA

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression data from PhIP-induced rat mammary cancer

hyb_protocol: Labeled cRNA was placed in a hybridization mixture containing control biotinylated probes according to manufacturer’s instructions. GeneChip arrays were hybridized with labeled cRNA for 16 h at 45°C with constant rotation (60 rpm).

scan_protocol: The arrays were washed and then stained with streptavidin-phycoerythrin conjugate (Molecular Probes, Tokyo, Japan) in a Fluidics Station 450 (Affymetrix) and subsequently scanned with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The scanned images were processed using Affymetrix GeneChip Analysis Suite software. Each data set was scaled such that the average intensity of all probe sets was adjusted to 500. Data were exported to flat text files and used for statistical analysis.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: PhIP-induced rat mammary cancer

label_protocol: Total RNA (8 µg) was used for the first-strand cDNA synthesis with a T7-(dT)24 primer (Proligo, Kyoto, Japan) and SuperScript III reverse transcriptase (Invitrogen Co., Carlsbad, CA, USA). Double-stranded cDNA was then synthesized with E. coli RNase, E. coli DNA polymerase and E. coli DNA ligase (Toyobo, Tokyo, Japan). Biotin-labeled fragmented cRNA was subsequently prepared with a BioArray HighYield RNA Transcript Labeling kit (Enzo, Farmingdale, NY, USA). Labeling was confirmed by formalin-containing agarose gel electrophoresis.

growth_protocol: 5-week-old female Sprague-Dawley rats were purchased, housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1degreeC) and humidity (50 ± 5%) under a regular 12-h light, 12-h dark cycle. They were fed a standard laboratory animal diet) and sterilized water ad libitum.

extract_protocol: total RNA was isolated by the acid guanidine phenol chloroform method (Isogen; Nippon Gene, Tokyo, Japan) and further purified with a silica-gel membrane (RNeasy Mini kit; Qiagen Inc., Valencia, CA, USA). The quality of all RNA samples was assessed by formalin-containing agarose gel electrophoresis.

treatment_protocol: At 7 weeks of age, the rats were either left untreated, given a single whole-body gamma-irradiation (0, 0.2, 0.5, 1 or 2 Gy) from a Cs-137 source. Three days after irradiation, MNU (20 or 40 mg/kg) was injected intraperitoneally or PhIP-HCl (40 mg/kg/day) was given by gavage for 5 consecutive days a week for 2 weeks with a 2-day interval. All rats were fed an AIN-76A diet containing 23.5% corn oil after 9 weeks of age.

tag: tissue

value: cancer

tag: etiology

value: PhIP

tag: h-ras

value: nonmutated

tag: background strain

value: Sprague-Dawley rats


title: Wnt pathway gene expression in normal B cells (Normal5)

city: Boston

first: Lili

last: Wang

state: MA

address: 77 Ave Louis Pasteur

country: USA

institute: Dana Farber Cancer Instutute

description: Wnt pathway genes.

hyb_protocol: Samples were hybridized to a microarray chip overnight at 45 degree in a solution containg several biotinylated control oligonucleotides

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
All expression profiles were processed using RMA implemented by the PreprocessDataset module in GenePattern, and Affymetrix probes were collapsed to unique genes (Gene Symbol) by selecting the probe with the maximal average expression for each gene. Batch effects were removed using ComBat, implemented by the ComBat module in GenePattern.
Complete table of RMA signals shown below. RMA signals, collapsed  to unique genes, are linked as supplementary files on the Series record.

organism: Homo sapiens

source_name: B cells

label_protocol: Samples were enzymatically fragmented and end-labled with a biotinylated nucleotide analog

extract_protocol: RNA were extracted using Trizol and further purified by RNeasy kit from Qiagen

treatment_protocol: For identification of Wnt targets, cells were treated with Wnt3a at 5ng/ml and 50ng/ml for 48 hours before harvest for RNA

tag: cell type

value: peripheral lymphocytes

tag: cd status

value: CD19 positive


title: Wnt pathway gene expression in CLL-B cells (CLL14)

description: Wnt pathway genes.

source_name: leukemia cells

value: CD19 CD5 positive


title: Wnt pathway gene expression in normal B cells (Normal6)

description: Wnt pathway genes.


title: cancer, gamma rays plus MNU, H-ras mutated, replicate 1

description: Gene expression data from rat mammary cancer induced by combination of radiation and MNU

value: radiation + MNU

value: mutated


title: Wnt pathway gene expression in normal B cells (Normal3)

description: Wnt pathway genes.


title: BNST/POA Day 60 Male 5

city: Los Angeles

first: Tuck

middle: Cheong

last: Ngun

state: CA

address: 695 Charles E Young Dr S Gonda 5524

department: Human Genetics

institute: UCLA

description:
Biological Replicate 4
60MOP5B

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Microarray data were processed using the statistical software program R (http://www.r-project.org/) and Bioconductor packages. The raw intensity data were first log2 transformed and then the outlier samples were detected based on the average inter-sample correlations. Three samples with average inter-sample correlations larger than two standard deviations (SDs) from the mean across all samples were removed from follow-up analysis. Then the samples were normalized by quantile normalization. Probes were considered robustly expressed if the detection p value was <0.05 in at least 20 samples (the total number of samples for every genetic/treatment group) in the data set. 57 samples with 13776 probes were retained for differential expression analysis.

organism: Mus musculus

source_name: BNST/POA Day 60 Male 5

label_protocol: Biotinylated cRNA were prepared by the UCLA Neuroscience Genomics Core.

extract_protocol: Total RNA was isolated from the BNST/POA using Qiagen AllPrep DNA/RNA Mini Kit (catalog no. 80204).

tag: strain

tag: age

value: 60 days

value: BNST/POA


title: cancer, PhIP, replicate 1


title: BNST/POA Day 60 Male 4

description:
Biological Replicate 3
60MOP4B

source_name: BNST/POA Day 60 Male 4


title: Striatum Day 4 Female 1

description: Biological Replicate 1

source_name: Striatum Day 4 Female 1

value: 4 days

value: Striatum


title: BNST/POA Day 60 Male 3

description:
Biological Replicate 2
60MOP3B

source_name: BNST/POA Day 60 Male 3


title: BNST/POA Day 60 Male 6

description:
Biological Replicate 5
60MOP6B

source_name: BNST/POA Day 60 Male 6


title: cancer, MNU, H-ras nonmutated, replicate 2

description: Gene expression data from MNU-induced rat mammary cancer

source_name: MNU-induced rat mammary cancer

value: MNU


title: Wnt pathway gene expression in normal B cells (Normal1)

description: Wnt pathway genes.


title: cancer, PhIP, replicate 2


title: BNST/POA Day 60 Male 1

description:
Biological Replicate 1
60MOP1B

source_name: BNST/POA Day 60 Male 1


title: cancer, MNU, H-ras nonmutated, replicate 3


title: cancer, MNU, H-ras nonmutated, replicate 4


title: Wnt pathway gene expression in normal B cells (Normal7)

description: Wnt pathway genes.


title: BNST/POA Day 60 Female+T 6

description:
Biological Replicate 4
60FTP6B

source_name: BNST/POA Day 60 Female+T 6


title: Wnt pathway gene expression in normal B cells (Normal2)

description: Wnt pathway genes.


title: cancer, MNU, H-ras mutated, replicate 5


title: BNST/POA Day 60 Female+T 5

description:
Biological Replicate 3
60FTP5B

source_name: BNST/POA Day 60 Female+T 5


title: BNST/POA Day 60 Female+T 2

description:
Biological Replicate 1
60FTP2B

source_name: BNST/POA Day 60 Female+T 2


title: 18_CoV6_PBMC_d3

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent Rhesus Macaque Gene Expression Microarray (Design ID 015421).

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

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

organism: Macaca mulatta

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

extract_protocol:
PBMCs were lysed in RLT buffer and RNA was extracted using QIAGEN RNeasy columns per the manufacturer's protocol.
Tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into 10-20 volumes (w/v) (e.g., 100mg/ml) RNAlater. After a 4ºC incubation overnight, samples were stored at -80ºC until further processing. Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation.
All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2-fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen, Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: 6 rhesus macaques were infected intratracheally with hCoV-EMC. PBMCs were collected at days 0, 1, 3, and 6, and lungs were collected from serial sacrifices of 3 animals each at day 3 and day 6. Infection produced a mild-moderate, self-limiting respiratory infection, and was not lethal.

value: PBMCs

tag: infection status

value: CoV

tag: timepoint

tag: animal identifier


title: control_322


title: BNST/POA Day 60 Female+T 4

description:
Biological Replicate 2
60FTP4B

source_name: BNST/POA Day 60 Female+T 4


title: cancer, MNU, H-ras nonmutated, replicate 1


title: cancer, MNU, H-ras mutated, replicate 3


title: Striatum Day 4 Female+T 1

description: Biological Replicate 1

source_name: Striatum Day 4 Female+T 1


title: cancer, MNU, H-ras mutated, replicate 2


title: cancer, MNU, H-ras mutated, replicate 4


title: C57Bl6/J_mammary gland_Lin-CD29hiCD24+

city: Rotterdam

first: Claudia

last: Gaspar

address: Dr. Molenwaterplein 40, PO Box 2040

department: Experimental Pathology

country: Netherlands

institute: ErasmusMC

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

scan_protocol: Standard Affymetrix protocols.

data_processing: After GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization were done using Partek Genomics Suite Software (Partek, Inc.).

label: Biotin

source_name: Normal mammary gland

label_protocol: Two-cycle Labelling kit according to Affymetrix’s instructions.

growth_protocol: Animals were housed in SPF conditions and fed ad libitum.

extract_protocol: Total RNA was isolated with RNeasy Micro kit (QIAGEN).

treatment_protocol: Tumors/mammary glands were collected, single cell suspensions were prepared, immuno labeled and FACS sorted. A total of 10,000 cells were collected for each population.

tag: genotype/variation

value: Apc+/+

tag: histology

value: Normal

tag: sorted population


title: BNST/POA Day 60 Female 3

description:
Biological Replicate 3
60FOP3B

source_name: BNST/POA Day 60 Female 3


title: BNST/POA Day 60 Female 4

description:
Biological Replicate 4
60FOP4B

source_name: BNST/POA Day 60 Female 4


title: 81_CoV5_lung RLL_d6_2

source_name: CoV5_lung RLL_d6

value: lung, right-lower lobe


title: cancer, gamma rays, replicate 3

description: Gene expression data from radiation-induced rat mammary cancer

source_name: radiation-induced rat mammary cancer

value: cancer

value: radiation

value: nonmutated


title: cancer, gamma rays, replicate 4

value: Sprague-Dawley rats


title: BNST/POA Day 60 Female 2

description:
Biological Replicate 2
60FOP2B

source_name: BNST/POA Day 60 Female 2


title: Wnt pathway gene expression in normal B cells (Normal4)

description: Wnt pathway genes.

source_name: B cells

value: peripheral lymphocytes

value: CD19 positive


title: C57Bl6/J_mammary glandH_Lin-

value: Lin-


title: C57Bl6/J_mammary gland_Lin-CD29+CD24+


title: BNST/POA Day 60 Female 5

description:
Biological Replicate 5
60FOP5B

source_name: BNST/POA Day 60 Female 5

value: 60 days


title: cancer, MNU, H-ras mutated, replicate 1

value: mutated


title: 10_CoV4_PBMC_d1


title: BNST/POA Day 60 Female 1

description:
Biological Replicate 1
60FOP1B

source_name: BNST/POA Day 60 Female 1

value: BNST/POA


title: C57Bl6/J_mammary glandG_Lin-CD29+CD24+


title: cancer, gamma rays, replicate 2


title: 4_CoV4_PBMC_d0


title: C57Bl6/J_mammary glandG_Lin-CD29hiCD24+


title: 44_CoV2_lung lesion_d3

source_name: CoV2_lung lesion_d3

value: lung lesion


title: 1_CoV1_PBMC_d0


title: C57Bl6/J_mammary glandF_Lin-CD29hiCD24+

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions.
For the normalization two technical replicates  of ACTB were used.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label_protocol: cDNAs were generated using High Capacity RNA-to-cDNA kit (Applied Biosystems) and employed for a pre-amplification step in Taqman PreAmp Master Mix for 14 cycles (Applied Biosysytems), according to manufacturer’s protocol. Real-Time PCR was performed by the 7900HT Fast Real-Time PCR System (Applied Biosystems). Replicate CT values were averaged.

tag: population


title: cancer, spontaneous, replicate 3

description: Gene expression data from spontaneous rat mammary cancer

source_name: spontaneous rat mammary cancer

value: spontaneous


title: cancer, spontaneous, replicate 2


title: 16_CoV4_PBMC_d3

value: PBMCs


title: BNST/POA Day 4 Male 3

description:
Biological Replicate 3
04MOP3B

source_name: BNST/POA Day 4 Male 3

value: 4 days


title: C57Bl6/J_mammary glandF_Lin-CD29hiCD24+

value: Apc+/+


title: C57Bl6/J_mammary glandF_Lin-CD29+CD24+

value: Normal


title: BNST/POA Day 4 Male 4

description:
Biological Replicate 4
04MOP4B

source_name: BNST/POA Day 4 Male 4


title: 39_CoV2_lung RLL_d3

source_name: CoV2_lung RLL_d3

value: lung, right-lower lobe

value: CoV


title: BNST/POA Day 4 Male 5

description:
Biological Replicate 5
04MOP5B

source_name: BNST/POA Day 4 Male 5


title: C57Bl6/J_mammary glandG_Lin-


title: C57Bl6/J_mammary glandF_Lin-


title: BNST/POA Day 4 Male 2

description:
Biological Replicate 2
04MOP2B

source_name: BNST/POA Day 4 Male 2


title: cancer, gamma rays, replicate 1

value: cancer

value: radiation


title: 9_CoV3_PBMC_d1


title: C57Bl6/J_mammary glandE_Lin-CD29hiCD24+


title: C57Bl6/J_mammary glandF_Lin-CD29+CD24+


title: cancer, spontaneous, replicate 1

value: nonmutated

value: Sprague-Dawley rats


title: 15_CoV3_PBMC_d3


title: Apc1572T_mammary tumorE_Lin-CD29+CD24+

source_name: Mammary gland tumor

value: Tumor


title: 5_CoV5_PBMC_d0


title: 2_CoV2_PBMC_d0


title: 53_CoV4_lung lesion 2_d3

source_name: CoV4_lung lesion 2_d3


title: BNST/POA Day 4 Male 1

description:
Biological Replicate 1
04MOP1B

source_name: BNST/POA Day 4 Male 1


title: BNST/POA Day 4 Female+T 4

description:
Biological Replicate 4
04FTP4B

source_name: BNST/POA Day 4 Female+T 4


title: C57Bl6/J_mammary glandE_Lin-CD29+CD24+

source_name: Normal mammary gland


title: 73_CoV3_lung RLL_d6

source_name: CoV3_lung RLL_d6


title: Apc1572T_mammary tumorE_Lin-CD29hiCD24+


title: Apc1572T_mammary tumorD_Lin-CD29hiCD24+


title: C57Bl6/J_mammary glandF_Lin-

value: Lin-


title: C57Bl6/J_mammary glandD_Lin-CD29hiCD24+


title: BNST/POA Day 4 Female+T 2

description:
Biological Replicate 2
04FTP2B

source_name: BNST/POA Day 4 Female+T 2


title: C57Bl6/J_mammary glandD_Lin-


title: C57Bl6/J_mammary glandD_Lin-CD29+CD24+


title: BNST/POA Day 4 Female+T 3

description:
Biological Replicate 3
04FTP3B

source_name: BNST/POA Day 4 Female+T 3


title: BNST/POA Day 4 Female+T 5

description:
Biological Replicate 5
04FTP5B

source_name: BNST/POA Day 4 Female+T 5


title: Apc1572T_mammary tumorD_Lin-CD29+CD24+


title: Apc1572T_mammary tumorE_Lin-


title: Apc1572T_mammary tumorC_Lin-CD29hiCD24+


title: Apc1572T_mammary tumorD_Lin-


title: Apc1572T_mammary tumorC_Lin-CD29+CD24+


title: Apc1572T_mammary tumorC_Lin-


title: 19_CoV1_PBMC_d6


title: BNST/POA Day 4 Female+T 1

description:
Biological Replicate 1
04FTP1B

source_name: BNST/POA Day 4 Female+T 1


title: Apc1572T_mammary tumorB_Lin-CD29hiCD24+


title: Apc1572T_mammary tumorC_Lin-CD29hiCD24+


title: 21_CoV5_PBMC_d6


title: 47_CoV4_lung RLL_d3

source_name: CoV4_lung RLL_d3


title: Apc1572T_mammary tumorB_Lin-CD29+CD24+


title: 12_CoV6_PBMC_d1


title: BNST/POA Day 4 Female 4

description:
Biological Replicate 4
04FOP4B

source_name: BNST/POA Day 4 Female 4


title: Apc1572T_mammary tumorB_Lin-


title: Apc1572T_mammary tumorC_Lin-CD29+CD24+


title: BNST/POA Day 4 Female 5

description:
Biological Replicate 5
04FOP5B

source_name: BNST/POA Day 4 Female 5


title: Apc1572T_mammary tumorB_Lin-CD29hiCD24+


title: Apc1572T_mammary tumorC_Lin-


title: 17_CoV5_PBMC_d3


title: control_119


title: Apc1572T_mammary tumorB_Lin-


title: Apc1572T_mammary tumorA_Lin-CD29hiCD24+


title: BNST/POA Day 4 Female 3

description:
Biological Replicate 3
04FOP3B

source_name: BNST/POA Day 4 Female 3


title: BNST/POA Day 4 Female 2

description:
Biological Replicate 2
04FOP2B

source_name: BNST/POA Day 4 Female 2


title: Apc1572T_mammary tumorB_Lin-CD29+CD24+


title: Apc1572T_mammary tumorA_Lin-CD29+CD24+


title: Apc1572T_mammary tumorA_Lin-CD29hiCD24+


title: 86_CoV5_lung lesion_d6

source_name: CoV5_lung lesion_d6


title: 61_CoV6_lung lesion 1_d3

source_name: CoV6_lung lesion 1_d3


title: Apc1572T_mammary tumorA_Lin-CD29+CD24+

source_name: Mammary gland tumor


title: BNST/POA Day 4 Female 1

description:
Biological Replicate 1
04FOP1B

source_name: BNST/POA Day 4 Female 1


title: Apc1572T_mammary tumorA_Lin-


title: 78_CoV3_lung lesion_d6

source_name: CoV3_lung lesion_d6


title: 8_CoV2_PBMC_d1


title: OPC differentiated on polylysine extract for 8h, Bio replicate 1

city: Cambridge

first: Szymon

last: Myrta

address: West Forvie Building, Robinson Way

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

description: OPC were differentiated for 4h on Poly L Lysine coated platest for 12h, following which RNA was harvested

hyb_protocol: The RNA was then prepared and hybridized to the Rat Gene 1.0ST array (Affymetrix) following protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the  GeneArray Scanner .

data_processing: Raw Affymetrix .CEL files were background-corrected, normalized and summarized using the RMA algorithm as implemented in the Affymetrix PowerTools software. Probe-sets that were not called present (Affymetrix signal detection statistic, P < 0.001) in all profiles of at least one sample group were excluded from analysis. Processed data was imported into the R statistical programming environment (http://www.r-project.org) and differential expression between sample groups assessed using the moderated t-test as implemented in the limma package for the Bioconductor suite of R bioinformatics software (http://bioconductor.org). In order to correct for hypothesis testing on such a scale, P-values relating to differential expression were corrected for multiple testing using FDR correction. Differential expression across sample groups was deemed significant at an FDR of 5% (q < 0.05).

source_name: Primary OPC cultures were isolated from neonatal Sprague Dawley (postnatal day 0-2) rat forebrains

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

growth_protocol: Primary OPC cultures were isolated from neonatal Sprague Dawley (postnatal day 0 –2) rat forebrains.

extract_protocol: RNA was isolated from the oligodendrocytes immediately after shake off and from those which were differentiated for 4h and 12h in Sato’s medium containing 0.5% FCS using an RNeasy Mini Kit (Qiagen). The quality of the RNA was checked with RNA Nano Chips (Agilent) on an Agilent 2100 Bioanalyzer (Agilent). Additionally, the RNA was purified using an RNeasy kit (Qiagen).

treatment_protocol: Differentiation was induced by Sato’s medium supplemented with 0.5% fetal calf serum (FCS).

value: Oligodendrocyte progenitor cells

value: Sprague Dawley

tag: differentiation treatment


title: Apc1572T_mammary tumorA_Lin-


title: 70_CoV1_lung lesion_d6

source_name: CoV1_lung lesion_d6


title: 65_CoV1_lung RLL_d6

source_name: CoV1_lung RLL_d6


title: OPC differentiated on polylysine extract for 8h, Bio replicate 3


title: 52_CoV4_lung lesion 1_d3

source_name: CoV4_lung lesion 1_d3


title: 7_CoV1_PBMC_d1


title: OPC differentiated on polylysine extract for 8h, Bio replicate 2


title: OPC differentiated on polylysine extract for 4h, Bio replicate 2

description: OPC were differentiated for 4h on Poly L Lysine coated platest for 4h, following which RNA was harvested


title: OPC differentiated on polylysine extract for 4h, Bio replicate 3


title: Tomato_Lateral_Bt_2

city: Sendai

first: Hideki

last: Takahashi

address: 1-1 Tsutsumidori-Amamiyamachi

institute: Tohoku University

description: Gene expression after 48hr in Bt-treated lateral roots of tomato

hyb_protocol: After fragmentation of 1650 ng of Cy3-labeled cRNA, the cRNA was applied to the Tomato Gene Expression Microarray 4x44K (Agilent Technologies, Santa Clara, CA, USA) and incubated at 65 °C for 17 h. After the hybridization, the array was washed with Agilent Washing Buffer 1 at 25 °C for 1 min and then with Agilent Washing Buffer 2 at 37 °C for 1 min.

scan_protocol: The probe array was scanned at 5 µm resolution using an Agilent Technologies Microarray Scanner.

data_processing:
One-color images of the scanned array were extraction using Agilent Feature Extraction (FE) Software 10.7.3.1.
Raw intensity values from each chip were normalized to the 75th percentile of the measurements using GeneSpring GX 9.0 Software. Relative changes in gene expression levels were compared between the samples treated with CF and diluted medium control.

organism: Solanum lycopersicum

source_name: Tomato, Lateral root, Bt, rep2

label_protocol: Isolated total RNA was amplified and labeled using a Low Input Quick Amp Labeling (LIQAL) Kit (Agilent Technologies, Santa Clara, CA, USA). Cyanine 3 (Cy3)-labeled cRNA was purified using RNeasy Mini Spin Column (Qiagen, Hilden, Germany).

growth_protocol: Solanum lycopersicum cv. ‘Oogata-fukuju’ plants were grown in 9-cm pots containing quartz sand at 24 °C in a growth chamber under continuous fluorescent light (70 µmol/m2/s) and fertilized with 1,000-fold-diluted Hyponex solution (Hyponex Japan) at 3 day intervals　Bacillus thuringiensis serovar fukuokaensis B88-82 was cultured in Nutrient Broth (NB) medium (Nissui, Tokyo, Japan) without NaCl at 25 °C for 2 days.

extract_protocol: Total RNA was isolated from two sets of the main and lateral root samples using an RNeasy Plant Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Cultures of B. thuringiensis adjusted to a final density of 1.8 × 108 cfu/ml were briefly centrifuged at 7,000 rpm for 10 min at 25 °C to pellet the bacterial cells. The supernatant was filtered through a nitrocellulose membrane (0.22 μm pore size) to produce the cell-free filtrate (CF). The roots of two-week-old tomato plants were carefully removed so as to minimize injury to the root tissue. After rinsing the roots with distilled water three times, the roots were dipped into 200 ml of CF. The CF-treated plants were incubated in a growth chamber at 25 °C under 14 h light (70 μmol/m2/s):10 h dark conditions for 48 h. The roots of control tomato plants were treated with diluted NB liquid medium and grown under the same conditions.

value: Lateral root

tag: treatment

value: Bt


title: OPC differentiated for 4h, Bio replicate 3

description: OPCs were harvested from Mixed glial culture and RNA was harvested from it

value: differentiated for 4h


title: Tomato_Lateral_Bt_1

source_name: Tomato, Lateral root, Bt, rep1

tag: tissue


title: OPC differentiated on polylysine extract for 4h, Bio replicate 1


title: Tomato_Main_Bt_1

description: Gene expression after 48hr in Bt-treated main roots of tomato

source_name: Tomato, Main root, Bt, rep1

value: Main root


title: Tomato_Main_Bt_2

source_name: Tomato, Main root, Bt, rep2


title: 14_CoV2_PBMC_d3

value: PBMCs


title: 56_CoV6_lung RLL_d3

source_name: CoV6_lung RLL_d3


title: OPC differentiated for 4h, Bio replicate 2


title: Tomato_Lateral_Control_1

description: Gene expression after 48hr in water-treated lateral roots of tomato

source_name: Tomato, Lateral root, Control, rep1

value: water-treated control


title: Tomato_Main_Control_2

description: Gene expression after 48hr in water-treated main roots of tomato

source_name: Tomato, Main root, Control, rep2


title: 6_CoV6_PBMC_d0


title: Tomato_Main_Control_1

source_name: Tomato, Main root, Control, rep1


title: 11_CoV5_PBMC_d1


title: OPC differentiated on myelin protein extract for 8h, Bio replicate 3

description: OPC were differentiated for 4h on Myelin Protein Extract for 12h, following which RNA was harvested

value: myelin protein extract for 8h


title: Tomato_Lateral_Control_2

source_name: Tomato, Lateral root, Control, rep2


title: OPC differentiated for 4h, Bio replicate 1


title: OPC differentiated on myelin protein extract for 8h, Bio replicate 2


title: 20_CoV3_PBMC_d6


title: 62_CoV6_lung lesion 2_d3

source_name: CoV6_lung lesion 2_d3

value: lung lesion


title: 13_CoV1_PBMC_d3

value: CoV


title: 81_CoV5_lung RLL_d6

source_name: CoV5_lung RLL_d6

value: lung, right-lower lobe


title: 3_CoV3_PBMC_d0


title: OPC differentiated on myelin protein extract for 4h, Bio replicate 2

description: OPC were differentiated for 4h on Myelin Protein Extract for 4h, following which RNA was harvested

value: myelin protein extract for 4h


title: 1S vs. 5S

status: Public on Aug 28 2013

city: Raleigh

first: Andrew

last: Frock

state: NC

address: 840 Main Campus Drive, Partners II, Room 3304

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

hyb_protocol: Microarray slides were pre-hybridized at 42°C for 45 min in 5X SSC, 0.1% SDS, 0.1% BSA, dipped five times in sterile dH2O, dipped twice in isopropanol, and dried in a slide spinner. cDNA was concentrated, resuspended in sterile dH2O, and heated to 95°C for 2 min. 2X hybridization buffer (5X SSC, 5X Denhardt's solution, 30% (v/v) formamide, 0.1% SDS) was added to equal part cDNA. This mixture was applied to the slide and covered with a 20x60 mm polyethylene hydrophobic coverslip. The slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18-20 hours. Slides were washed for 4 min in buffer 1 (2X SSC, 0.2% SDS), 4 min in buffer 2 (0.5X SSC, 0.2% SDS), and 4 min in buffer 3 (0.5X SSC). Then slides were dried using a slide spinner.

scan_protocol: Slides were scanned with an Axon GenePix 4000b scanner and GenePix Pro 6.0 software.

data_processing: After scanning the slides, the spots were quantified by GenePix Pro, and that data was brought into JMP and a log 2 transformation was done. ANOVA normalization was done on the eight (four slides x two channels per slide) distributions. Then row-by-row modeling was done. This results in a least square mean (LSM) value for each probe for each sample (Sample 1, 2, 3, and 4). If for a particular probe you subtract the LSM for Sample 2 from the LSM for Sample 1, you get a log 2 ratio for the difference of those two samples for that probe. This is reported in the VALUE column of the below tables. LSM values for each of the four samples are included in the supplementary file attached to GSE47072.

organism: Thermotoga maritima

source_name: 1 g/l yeast extract stationary phase

label_protocol: Superscript III (Invitrogen) was used to reverse transcribe RNA and incorporate 5-(3-aminoallyl)-dUTP (Ambion). cDNA was labeled with Cy5 or Cy3 dye (GE Healthcare).

growth_protocol: T. maritima was grown anaerobically in an oil bath at 80°C with shaking at 100 rpm. Culture bottles were made anaerobic by sealing, sparging with nitrogen, and adding Na2S•9H2O at a final concentration of 0.05% (w/v). For preparation of freezer stocks, 970 µl of cooled log-phase culture was added to 30 µl of dimethylsulfoxide and stored at -80°C. Freezer stocks were thawed and used to inoculate (1% v/v) artificial sea water (ASW) media (9) with 2.5 g/l maltose. After ~12 hours of growth, this culture was used to inoculate medium with varying concentrations of yeast extract (YE). This medium was based on a defined medium developed from ASW. The base medium consisted of (per L, final concentration): 15 g NaCl, 2 g Na2SO4, 2 g MgCl2•6H2O, 0.25 g NaHCO3, 20 mg KBr, 20 mg H3BO3, 20 mg KI, 3 mg Na2WO4, and 2 mg NiCl2•6H2O. The base medium was typically prepared at 2x concentration, adjusted to pH 7 with H2SO4, and sterilized by autoclaving. After autoclaving, 1.2 g KH2PO4, 2.5 g maltose monohydrate, 5 g NH4Cl, 5.4 mg FeCl3•6H2O, 1x trace elements (see below), and 1x vitamins (see below) were added (per L, final concentration). All of these components were prepared as concentrated, sterile-filtered stock solutions. YE concentration was varied by addition of a 25 g/L stock solution that was sterilized by filtration. Vitamin solution (1000x) consisted of (per L): 10 mg pyridoxine•HCl, 5 mg calcium pantothenate, 5 mg nicotinic acid, 5 mg riboflavin, 5 mg thiamine•HCl, 5 mg thioctic acid, 2 mg biotin, 2 mg folic acid, and 0.1 mg cyanocobalamin. Trace element solution (1000x) consisted of (per L): 1.5 g nitrilotriacetic acid (NTA), 0.5 g MnSO4•H2O, 0.2 g NiCl•6H2O, 0.1 g ZnSO4•7H2O, 0.01 g CuSO4•5H2O, and 0.01 g Na2MoO4•2H2O. NTA was dissolved by adding concentrated KOH to pH 6.5.

extract_protocol: At harvest, cultures were cooled in a dry ice-ethanol bath before centrifugation. Total RNA was extracted using TRIzol (Invitrogen) and purified using an RNeasy kit (Qiagen) with on-column DNase treatment.

tag: growth phase

value: stationary

tag: nutrient source

value: 1 g/l yeast extract

source_name: 5 g/l yeast extract stationary phase

value: 5 g/l yeast extract


title: 5S vs. 5E

source_name: 5 g/l yeast extract exponential phase

value: exponential


title: OPC differentiated on myelin protein extract for 8h, Bio replicate 1

source_name: Primary OPC cultures were isolated from neonatal Sprague Dawley (postnatal day 0-2) rat forebrains

value: Oligodendrocyte progenitor cells


title: 1E vs. 1S

source_name: 1 g/l yeast extract exponential phase


title: OPC differentiated on myelin protein extract for 4h, Bio replicate 3

value: Sprague Dawley


title: 5E vs. 1E


title: OPC differentiated on myelin protein extract for 4h, Bio replicate 1


title: 43.H.D

city: Linkoping

first: Colm

middle: Eamonn

last: Nestor

address: KEF, Hälsuniversitetet

country: Sweden

institute: Linkoping University

description:
X43D
mRNA profiling

hyb_protocol: The hybridization, staining, washing and scanning was performed as per the manufacturer’s instructions.

data_processing: Gene expression microarrays were analyzed using the R statistical programming language using functions of the gene expression microarray analysis package 'lumi'.

label_protocol: RNA extraction was performed using a miRneasy Mini Kit (Qiagen). For each sample, 250 ng of total RNA was amplified and labeled using an Illumina TotalPrep 96 RNA Amplification Kit as per the manufacturer’s instructions. The quantity of the labeled cRNA was measured using a NanoDrop spectrophotometer, and the quality and size distribution of the labeled cRNA assessed using an Agilent 2100 Bioanalyzer.

growth_protocol: PBMCs were prepared from fresh blood by means of centrifugation on Ficoll-Hypaque, washed, and stimulated with grass pollen extract (ALK-Abelló A/S; 100 μg/mL) at a density of 10^6 cells/mL and in a total volume per well of 2 mL of cell culture medium or diluent (PBS). After 7 days of incubation at 37°C and 5% CO2

extract_protocol: Total CD4+ T cells were purified from PBMCs by positive sorting using anti-CD4-coated paramagnetic microbeads and a MACS system (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).

treatment_protocol: PBMCS were cultured with grass pollen extract or diluent.

tag: challenge

value: Diluent

tag: diagnosis

value: H

tag: subject

value: CD4+ T-cells


title: 44.H.D

description:
X44D
mRNA profiling

scan_protocol: The hybridization, staining, washing and scanning was performed as per the manufacturer’s instructions.

tag: cell type


title: 38.H.A

description:
X38A
mRNA profiling

value: Allergen


title: 44.H.A

description:
X44A
mRNA profiling


title: 42.H.D

description:
X42D
mRNA profiling


title: 38.H.D

description:
X38D
mRNA profiling


title: 40.H.D

description:
X40D
mRNA profiling


title: 42.H.A

description:
X42A
mRNA profiling


title: 40.H.A

description:
X40A
mRNA profiling


title: 43.H.A

description:
X43A
mRNA profiling


title: 45.H.D

description:
X45D
mRNA profiling


title: 41.H.D

description:
X41D
mRNA profiling


title: 39.H.D

description:
X39D
mRNA profiling


title: 45.H.A

description:
X45A
mRNA profiling


title: 41.H.A

description:
X41A
mRNA profiling


title: 37.H.D

description:
X37D
mRNA profiling


title: 36.P.D

description:
X36D
mRNA profiling

value: P


title: 37.H.A

description:
X37A
mRNA profiling


title: 36.P.A

description:
X36A
mRNA profiling


title: 35.P.A

description:
X35A
mRNA profiling


title: 31.H.A

description:
X31A
mRNA profiling


title: 32.H.A

description:
X32A
mRNA profiling


title: 33.H.D

description:
X33D
mRNA profiling


title: 31.H.D

description:
X31D
mRNA profiling


title: 30.H.D

description:
X30D
mRNA profiling


title: 30.H.A

description:
X30A
mRNA profiling


title: 39.H.A

description:
X39A
mRNA profiling


title: 35.P.D

description:
X35D
mRNA profiling


title: 33.H.A

description:
X33A
mRNA profiling


title: 29.H.D

description:
X29D
mRNA profiling


title: 32.H.D

description:
X32D
mRNA profiling


title: 27.H.A

description:
X27A
mRNA profiling


title: 29.H.A

description:
X29A
mRNA profiling


title: 28.H.A

description:
X28A
mRNA profiling


title: 26.H.D

description:
X26D
mRNA profiling


title: 25.H.D

description:
X25D
mRNA profiling


title: 27.H.D

description:
X27D
mRNA profiling


title: 28.H.D

description:
X28D
mRNA profiling


title: 23.H.D

description:
X23D
mRNA profiling


title: 26.H.A

description:
X26A
mRNA profiling


title: 24.H.D

description:
X24D
mRNA profiling


title: 21.P.D

description:
X21D
mRNA profiling


title: 22.P.D

description:
X22D
mRNA profiling


title: 25.H.A

description:
X25A
mRNA profiling


title: 22.P.A

description:
X22A
mRNA profiling


title: 20.P.D

description:
X20D
mRNA profiling


title: 18.P.D

description:
X18D
mRNA profiling


title: 19.P.A

description:
X19A
mRNA profiling


title: 14.P.D

description:
X14D
mRNA profiling


title: 20.P.A

description:
X20A
mRNA profiling


title: 21.P.A

description:
X21A
mRNA profiling


title: 19.P.D

description:
X19D
mRNA profiling


title: 24.H.A

description:
X24A
mRNA profiling


title: 14.P.A

description:
X14A
mRNA profiling


title: 23.H.A

description:
X23A
mRNA profiling


title: 17.P.A

description:
X17A
mRNA profiling


title: 17.P.D

description:
X17D
mRNA profiling


title: 18.P.A

description:
X18A
mRNA profiling


title: 12.P.D

description:
X12D
mRNA profiling


title: 11.H.D

description:
X11D
mRNA profiling


title: 11.H.A

description:
X11A
mRNA profiling


title: 12.P.A

description:
X12A
mRNA profiling


title: 13.P.A

description:
X13A
mRNA profiling


title: 9.P.A

description:
X9A
mRNA profiling


title: 13.P.D

description:
X13D
mRNA profiling


title: 9.P.D

description:
X9D
mRNA profiling


title: 10.P.D

description:
X10D
mRNA profiling


title: 10.P.A

description:
X10A
mRNA profiling


title: yki_8-16h_embryonic_ChIP-seq_ChIP_Rep2

type: SRA

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: Yki91;target name: Yki;host: Rabbit;antigen: Full length Yki;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Ken Irvine Lab;short description: A gift to modENCODE from Hyangyee Oh and Ken Irvine to Nicolas Negre.

library_source: genomic

data_processing: Solexa_Alignment protocol. Raw image files were processed following the following Illumina-compatible pipeline:1.  The Raw images were first processed with the Casava 1.7.0.2.  Base-called sequences with confidence metrics were obtained using OLB-1.9.0.  All multiplexed samples were demultiplexed using Casava 1.7.0.3. Finally the BWA program was used to align the sequence reads to the Drosophila melanogaster (v5.32) genome, allowing up to 2 edit distance in the seed region and 3 in the full read length. Tags that aligned to more than one  location were excluded from our analysis for both ChIP sample and the corresponding control sample (input chromatin). Only properly aligned reads with mapping quality more than 30 were kept. MACS_Peak-calling protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software, version 2 (MACS2). MACS2 was supplied with the following parameters:tagSize = 50mfold = 2genomeSize = 120000000bandwidth = 100pvalue = 1e-5  Processed data are obtained using following parameters: genome version is flybase BDGPv5

molecule: genomic DNA

organism: Drosophila melanogaster

extract_protocol:
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.   2. For a 8-16 hours egg laying, new plates are added after a 2 hours pre-egglaying at 12 pm and flies are allowed to lay eggs for 8 hours.   3. Embryos are collected at 7.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 8am in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

tag: strain

value: Y cn bw sp

tag: developmental stage

value: Embryo 8-16h

tag: genotype


title: 8.P.A

description:
X8A
mRNA profiling


title: yki_8-16h_embryonic_ChIP-seq_ChIP_Rep1


title: insv_Kc_cells_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: insv;target name: INSV;host: Rabbit;antigen: MENQYQRIVSATAREDSQARRSKPLFLNAWSQTSSVDFEVLRSISAPDPQ VEVENRALRDKVRYLEAKLQQHKDLLSQIHATSARMQQASSLLAESRPPT PPAVQSHHILTPPSSEICAPAQNPQILDYKIISAPDDADAIEIRLAAESL NSLSTSADSDRLEICLGDENHQQSNHHNSQQQYRISNGIKRDGSSESADT PLQFIKRRKLQEIQLQEEIPRQNIKLPAKPQVKARNGSFTDLNKGQQQNM DNVMVSIGPNNTCVPASVFENINWSVCSLATRKLLVTIFDRETLATHSMT GKPSPAFKDQDKPLKRMLDPGKIQDIIFAVTHKCNASEKEVRNAITTKCA DENKMMKIQNVKRRSSGIKHEKENII;clonal: Polyclonal;purified: Size;company: Lab;catalog: Eric Lai Lab;short description: This is a gift from Eric Lai to Nicolas Negre for the modENCODE project. This antibody has been pre-adsorbed with 0-1h old Drosophila embryos before use in ChIP.

extract_protocol:
Cell lines (S2, Kc167...) are grown as described by the DGRC and the Cherbas Lab. After expanding the cell line, cells are transfered in a plate. Once confluent, 1.8% formaldehyde is added to the cell culture. Cells are harvested in presence of the formaldehyde with the help of a cell scrapper. After 15 minutes of incubation at room temperature, the cross-linking reaction is quenched with glycine for 5 minutes. Cells pellet are then washed 3 times with lysis buffer. Regular chromatin extraction before sonication is then performed.
Formaldehyde Cross-linking of Chromatin from any Drosophila tissue (Embryos, Larvae, Pupae, Adult flies).1. Homogenize the material (about 150-200 mg of embryos, pupae, adµlts, larvae, sufficient for four-five independent immuno-precipitations) in 5 ml of buffer A1 + 1.8% formaldehyde (290 µl of 37% solution) at room temperature using first a Potter homogenizer and then a Douncer with type A pestle (3 strokes). Wait 15? (total time starting from beginning of homogenization). Add glycin solution to 225 mM (540 µl of 2.5 M solution for 6 ml of cross-linked mixture), mix and incubate 5?. Put on ice. Keep on ice unless specified.2. Transfer the homogenate to a 15 ml tube. Centrifuge 5 min, at 4000 g at 4°C. Discard supernatant. Add 3 ml of buffer A1, resuspend pellet and spin down the same way. Repeat washing step 3 times.3. Wash once in 3 ml of lysis buffer without SDS. Spin down, 5 min at 4000g.4. Resuspend cross-linked material in 0.5 ml of lysis buffer and add SDS to 0.1% (2.5 µl) and N-lauroylsarcosine to 0.5% (12.5 µl). Incubate 10 min at 4°C in a rotating wheel.5. Sonicate in Polypropylene 15ml Falcon tubes according to .Diagenode instructions. The settings are: High power, 15 minutes, 30 seconds off, 30 seconds on. The water bath shoµld be kept cold either in a cold room or by a cold water pump.6. Rotate 10'. Transfer to eppendorf tubes and centrifuge 5', room temperature at maximum speed. Transfer supernatant to the new tube. Add another 0.5 ml of lysis buffer to the pellet, rotate for 10 min. Repeat centrifugation and combine supernatants. Centrifuge the combined supernatant 2x10 min at max speed. The supernatant from this stage will be referred as chromatin extract. Chromatin can be stored at ?80°C for several months at this stage. Add sodium azide to 0.02% for storage.7. [Optional : Purification of chromatin. Put chromatin extract in Centricon YM-100 column (4212), centrifuge 3x40' (or more) at 1000 g while adding lysis buffer. At least 3 vol. of lysis buffer should pass through column. Bring the final volume of chromatin extract to 1 ml by lysis buffer + protease inhibitors.]
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

tag: cell line

value: embryo-derived cell-line

value: late embryonic stage

value: se/e

tag: Sex

value: Female


title: 7.P.D

description:
X7D
mRNA profiling


title: yki_8-16h_embryonic_ChIP-seq_ChIP_Rep3


title: 8.P.D

description:
X8D
mRNA profiling


title: 6.P.A

description:
X6A
mRNA profiling


title: 7.P.A

description:
X7A
mRNA profiling


title: 5.P.A

description:
X5A
mRNA profiling


title: 5.P.D

description:
X5D
mRNA profiling


title: 4.P.A

description:
X4A
mRNA profiling


title: 4.P.D

description:
X4D
mRNA profiling


title: 2.P.D

description:
X2D
mRNA profiling


title: 6.P.D

description:
X6D
mRNA profiling


title: 3.P.D

description:
X3D
mRNA profiling


title: 3.P.A

description:
X3A
mRNA profiling


title: 1.P.A

description:
X1A
mRNA profiling


title: 2.P.A

description:
X2A
mRNA profiling


title: 1.P.D

description:
X1D
mRNA profiling


title: MTK12

city: San Antonio

first: Xiaodong

last: Cui

state: Texas

address: 126 Arrow Oaks

department: Electrical engineering

institute: Univ of Texas SA

description:
SAMPLE 16
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K12.

hyb_protocol: Biotin-labeled cRNA were hybridized with Illumina Rat-Ref-12-V1 BeadChips using Illumina standard protocol.

scan_protocol: The BeadChips are scanned using Illumina HiScanSQ scanner.

data_processing: The data is analyzed using Illumina GenomeStudio software.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K12

label_protocol: The RNA samples were labeled with Biotin using the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Cells were grown in RMPI-1640 with 10% FBS and collected at 70-80% confluency.

extract_protocol: Total RNAs were isolated with Trizol reagent (Invitrogen).

value: mesenchymal precursor cells

tag: infection

tag: complement

value: precursor miRNA miR-K12


title: MTK11

description:
SAMPLE 15
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K11.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K11

value: precursor miRNA miR-K11


title: MTK8

description:
SAMPLE 12
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K8.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K8

value: precursor miRNA miR-K8


title: MTK10

description:
SAMPLE 14
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K10.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K10

value: precursor miRNA miR-K10


title: MTVt

description:
SAMPLE 18
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with vector control.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with vector control

value: vector control


title: MTCL

description:
SAMPLE 17
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with the miRNA cluster.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with the miRNA cluster

value: the miRNA cluster


title: MTK4

description:
SAMPLE 8
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K4.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K4

value: precursor miRNA miR-K4


title: MTK9

description:
SAMPLE 13
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K9.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K9

value: precursor miRNA miR-K9


title: MTK3

description:
SAMPLE 7
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K3.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K3

value: precursor miRNA miR-K3


title: MTK6

description:
SAMPLE 10
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K6.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K6

value: precursor miRNA miR-K6


title: MTK5

description:
SAMPLE 9
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K5.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K5

value: precursor miRNA miR-K5


title: MTK7

description:
SAMPLE 11
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K7.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K7

value: precursor miRNA miR-K7


title: MTK1

description:
SAMPLE 5
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K1.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K1

value: precursor miRNA miR-K1


title: MTK2

description:
SAMPLE 6
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted and complemented with precursor miRNA miR-K2.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant, complemented with precursor miRNA miR-K2

value: precursor miRNA miR-K2


title: AP

description:
SAMPLE 1
MM cells.

source_name: mesenchymal precursor cells, non-infected


title: AWT

description:
SAMPLE 2
MM cells infected with wild-type KSHV.

source_name: mesenchymal precursor cells, infected with wild-type KSHV

value: wild-type KSHV


title: AREV

description:
SAMPLE 4
MM cells infected with a revertant virus of mutant KSHV with a cluster of 10 viral pre-miRNAs deleted.

source_name: mesenchymal precursor cells, infected with KSHV miR cluster deletion mutant


title: striatum of HdhQ111/Q111/mGluR5-/- rep2

city: London

first: Stephen

middle: Sean Gilbert

last: Ferguson

state: ON

address: 100 Perth Drive

department: Molecular Neurobiology

institute: Robarts Research Institute

description: striatum of HdhQ111/Q111/mGluR5-/- mouse

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed with Partek Genomcis Suite using the RMA normalization method
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

growth_protocol: Mouse striatum dissected from 90days male mice

extract_protocol: RNA was isolated using Trizol reagent as per manufacture's instructions (Invitrogen, Burlington, ON).  RNA was re-suspended in 20 μL of RNase free water and its concentration and quality were analyzed by NanoDrop™ (Thermo Scientific, Wilmington, USA) and gel electrophoresis, respectively.

tag: age

value: 90 days

value: striatum

tag: genetic background


title: AMT

description:
SAMPLE 3
MM cells infected with a mutant KSHV with a cluster of 10 viral pre-miRNAs deleted.

source_name: mesenchymal precursor cells, infected with revertant virus of KSHV miR cluster deletion mutant

value: mesenchymal precursor cells


title: striatum of HdhQ111/Q111/mGluR5+/+ rep1

description: striatum of HdhQ111/Q111/mGluR5+/+ mouse


title: striatum of HdhQ111/Q111/mGluR5-/- rep3

source_name: striatum of HdhQ111/Q111/mGluR5-/- mouse


title: striatum of HdhQ111/Q111/mGluR5+/+ rep3

source_name: striatum of HdhQ111/Q111/mGluR5+/+ mouse


title: striatum of HdhQ20/Q20 and mGluR5-/- rep3

description: striatum of HdhQ20/Q20 and mGluR5-/- mouse

value: HdhQ20/Q20 and mGluR5-/-


title: striatum of HdhQ20/Q20 and mGluR5-/- rep2

source_name: striatum of HdhQ20/Q20 and mGluR5-/- mouse


title: striatum of HdhQ20/Q20 and mGluR5-/- rep1


title: striatum of HdhQ20/Q20/mGluR5+/+ rep3

description: striatum of HdhQ20/Q20/mGluR5+/+ mouse

source_name: striatum of HdhQ20/Q20/mGluR5+/+ mouse


title: striatum of HdhQ111/Q111/mGluR5-/- rep1


title: striatum of HdhQ20/Q20/mGluR5+/+ rep2

description: striatum of HdhQ20/Q20/mGluR5+/+ mouse


title: CNR2

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: CNR

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

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

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

source_name: peritoneal macrophages from C57BL/6 mice fed CD

label_protocol: WTA-Ovation FFPE V2 kit and Encore biotin module (Nugen, San Carlos, CA) according to the manufacturer's protocol.

growth_protocol: Six week old C57BL/6 mice were fed either CD or HFD for 12 weeks.  The animals were injected with thyoglycollate and then euthanized, and peritoneal macrophages were collected by peritoneal lavage with PBS.

extract_protocol: Total RNA was extracted using RNAeasy kit (Qiagen, Valencia, CA) following manufacturer's protocol.

treatment_protocol: CD or HFD macrophage erythrophagocytosis was performed with CD-RBC, HFD-RBC, or no RBC.

tag: animal replicate

tag: treatment of macrophage donor

value: chow

tag: treatment of rbc donor

tag: treatment protocol

value: control diet macrophages exposed to nothing


title: HNR1

description: HNR

source_name: peritoneal macrophages from C57BL/6 mice fed HFD

value: highFat

value: high fat diet macrophages exposed to nothing


title: HHF2

description: HHF

value: high fat diet macrophages exposed to high fat diet red cells


title: CHF1

description: CHF

value: control diet macrophages exposed to high fat diet red cells


title: HNR2

description: HNR


title: CNR1

description: CNR


title: HC2

description: HC

value: high fat diet macrophages exposed to control diet red cells


title: HC1

description: HC


title: HHF1

description: HHF


title: Nodose nociceptors, biological replicate 1

first: Isaac

middle: M

last: Chiu

address: 3 Blackfan Circle

department: Neurology

institute: Boston Children's Hospital

description: FACS purified Nav1.8-Tomato positive cells from pooled nodose samples

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hr on Affymetrix mouse Gene ST version 1.0 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix CEL files were analyzed with the Robust Mutli-array Average (RMA) algorithm as the normalization method with quantile normalization, background correction, and median scalin. using the GenePattern (http://www.broadinstitute.org/cancer/software/genepattern) software platform.

source_name: Nodose ganglia from Nav1.8-Cre/R26Tomato mice

label_protocol: 100 ng total RNA was amplified using the GeneChip WT cDNA syntehsis and amplification kit (Affymetrix).  cDNA synthsis, biotinylation of cRNA, fragmentation, and labeling was according to standard Affymetrix protocols.

growth_protocol: Nav1.8-Cre mice were bred with Rosa26-TdTomato (ai14) reporter mice to generate nociceptor lineage reporter mouse progeny.

extract_protocol: RNA was extraced by sequential Trizol and Qiagen Rneasy micro column purification with genomic dna digest.

treatment_protocol: DRG, trigeminal or nodose ganglia were dissected from adult mice, treated with Collagenase/Dispase enzyme digestion for cell dissociation.  Tomato positive cells were purified by flow cytometry.

tag: tissue

value: Nodose facs purified nociceptors


title: Nodose nociceptors, biological replicate 2


title: Trigeminal nociceptors, biological replicate 2

description: FACS purified Nav1.8-Tomato positive cells from pooled Trigeminal samples

source_name: Trigeminal ganglia from Nav1.8-Cre/R26Tomato mice

value: Trigeminal facs purified nociceptors


title: CHF2

description: CHF


title: Nodose nociceptors, biological replicate 3


title: striatum of HdhQ111/Q111/mGluR5+/+ rep2


title: CC2

description: CC

value: control diet macrophages exposed to control diet red cells


title: Trigeminal nociceptors, biological replicate 4


title: DRG (lumbar) nociceptors, biological replicate 1

description: FACS purified Nav1.8-Tomato positive cells from pooled DRG samples

source_name: DRG (L3-L6) from Nav1.8-Cre/R26Tomato mice

value: DRG (lumbar) facs purified nociceptors


title: DRG (lumbar) nociceptors, biological replicate 3


title: Normal Non-PRA Serum Treated HUVEC Replicate 1 [7509301029_J]

city: New Haven

first: Dan

last: Jane-wit

state: CT

address: 10 Amistad St

department: Immunobiology

institute: Yale University School of Medicine

description:
Normal Non-PRA Serum Treated HUVEC Replicate 1
7509301029_J

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: HUVEC

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

growth_protocol: HUVEC grown in M199 media (20% FBS, 1.5% L-glutamine, 1.0% penicillin/streptomycin

extract_protocol: Qiagen Rneasy Kit

treatment_protocol: 4 hours in gelatin veronal buffer with 1:10 dilution of complement-inactivated PRA serum, vehicle, PRA serum, or non-PRA serum

value: HUVEC

tag: treatment

value: Non-PRA=Low Panel Reactive Antibody Serum from Healthy Donors

tag: treatment time

value: 4 hours


title: Trigeminal nociceptors, biological replicate 1


title: Normal Non-PRA Serum Treated HUVEC Replicate 2 [7509301029_K]

description:
Normal Non-PRA Serum Treated HUVEC Replicate 2
7509301029_K

tag: cell type


title: striatum of HdhQ20/Q20/mGluR5+/+ rep1

description: striatum of HdhQ20/Q20/mGluR5+/+ mouse

value: 90 days

value: striatum


title: DRG (lumbar) nociceptors, biological replicate 2


title: PRA Serum Treated HUVEC Replicate 2 [7509301029_H]

description:
PRA Serum Treated HUVEC Replicate 2
7509301029_H

value: PRA=High Panel Reactive Antibody Serum from Pre-Transplant Patients


title: Trigeminal nociceptors, biological replicate 3


title: Normal Non-PRA Serum Treated HUVEC Replicate 3 [7509301029_L]

description:
Normal Non-PRA Serum Treated HUVEC Replicate 3
7509301029_L


title: PRA Serum Treated HUVEC Replicate 3 [7509301029_I]

description:
PRA Serum Treated HUVEC Replicate 3
7509301029_I


title: PRA Serum Treated HUVEC Replicate 1 [7509301029_G]

description:
PRA Serum Treated HUVEC Replicate 1
7509301029_G


title: Vehicle Treated HUVEC Replicate 1 [7509301029_D]

description:
Vehicle Treated HUVEC Replicate 1
7509301029_D

value: Vehicle=Gelatin Veronal Buffer


title: Complement-Inactivated PRA Serum Treated HUVEC Replicate 1 [7509301029_A]

description:
Complement-Inactivated PRA Serum Treated HUVEC Replicate 1
7509301029_A

value: Heat Inactivated PRA 55C


title: Complement-Inactivated PRA Serum Treated HUVEC Replicate 2 [7509301029_B]

description:
Complement-Inactivated PRA Serum Treated HUVEC Replicate 2
7509301029_B


title: Vehicle Treated HUVEC Replicate 2 [7509301029_E]

description:
Vehicle Treated HUVEC Replicate 2
7509301029_E


title: Normal Non-PRA Serum Treated HUVEC Replicate 2 [7165895087_K]

description:
Normal Non-PRA Serum Treated HUVEC Replicate 2
7165895087_K


title: PRA Serum Treated HUVEC Replicate 3 [7165895070_I]

description:
PRA Serum Treated HUVEC Replicate 3
7165895070_I


title: Normal Non-PRA Serum Treated HUVEC Replicate 2 [7165895070_K]

description:
Normal Non-PRA Serum Treated HUVEC Replicate 2
7165895070_K


title: Vehicle Treated HUVEC Replicate 3 [7509301029_F]

description:
Vehicle Treated HUVEC Replicate 3
7509301029_F


title: CC1

description: CC

tag: strain

value: chow


title: Vehicle Treated HUVEC Replicate 3 [7165895070_F]

description:
Vehicle Treated HUVEC Replicate 3
7165895070_F


title: Normal Non-PRA Serum Treated HUVEC Replicate 3 [7165895070_L]

description:
Normal Non-PRA Serum Treated HUVEC Replicate 3
7165895070_L


title: PRA Serum Treated HUVEC Replicate 2 [7165895070_H]

description:
PRA Serum Treated HUVEC Replicate 2
7165895070_H


title: Complement-Inactivated PRA Serum Treated HUVEC Replicate 1 [7165895070_A]

description:
Complement-Inactivated PRA Serum Treated HUVEC Replicate 1
7165895070_A


title: Normal Non-PRA Serum Treated HUVEC Replicate 1 [7165895070_J]

description:
Normal Non-PRA Serum Treated HUVEC Replicate 1
7165895070_J


title: Complement-Inactivated PRA Serum Treated HUVEC Replicate 2 [7165895070_B]

description:
Complement-Inactivated PRA Serum Treated HUVEC Replicate 2
7165895070_B


title: PRA Serum Treated HUVEC Replicate 1 [7165895070_G]

description:
PRA Serum Treated HUVEC Replicate 1
7165895070_G


title: Normal Non-PRA Serum Treated HUVEC Replicate 3 [7165895087_L]

description:
Normal Non-PRA Serum Treated HUVEC Replicate 3
7165895087_L


title: Complement-Inactivated PRA Serum Treated HUVEC Replicate 3 [7509301029_C]

description:
Complement-Inactivated PRA Serum Treated HUVEC Replicate 3
7509301029_C


title: Vehicle Treated HUVEC Replicate 2 [7165895070_E]

description:
Vehicle Treated HUVEC Replicate 2
7165895070_E


title: Vehicle Treated HUVEC Replicate 1 [7165895070_D]

description:
Vehicle Treated HUVEC Replicate 1
7165895070_D


title: Normal Non-PRA Serum Treated HUVEC Replicate 1 [7165895087_J]

description:
Normal Non-PRA Serum Treated HUVEC Replicate 1
7165895087_J


title: PRA Serum Treated HUVEC Replicate 3 [7165895087_I]

description:
PRA Serum Treated HUVEC Replicate 3
7165895087_I


title: Complement-Inactivated PRA Serum Treated HUVEC Replicate 3 [7165895087_C]

description:
Complement-Inactivated PRA Serum Treated HUVEC Replicate 3
7165895087_C


title: DH_KYSE_FU4

city: Bedford Park

first: Damian

middle: James

last: Hussey

address: Flinders Drive

country: Australia

institute: Flinders University

description: miRNA

hyb_protocol: Affymetrix Hybridisation oven for 16 hours at 48 deg.C and 60 rpm, Arrays washed using FluidicsScript 450-0003.

scan_protocol: Affymetrix 3000 7G

data_processing: Cel files were analyzed with Partek genomics suite (version 6.5) using RMA background correction, quantile normalization and mean probe summarisation.

label_protocol: Genisphere FlashTag Biotin Labelling Kit

growth_protocol: Resistant sublines of KYSE410 (esophageal squamous cell carcinoms) and OE19 (esophageal adenocarcinoma) cell lines were generated using a pulsatile treatment approach which included repetitive treatment of cells with constant concentrations of cisplatin or 5-FU. Briefly, KYSE 410 cells were subjected to a 4-day exposure of 2 μM cisplatin or 5 μM 5-FU, and OE 19 cells were exposed to 5 μM cisplatin or 10 μM 5-FU for 3 days. The medium was not changed during this period, thereby providing a constant exposure to the chemotherapy agent. After removal of the chemotherapy agent, cells were allowed to recover, and then split when reaching approximately 70–80% confluency, followed by the next cycle of chemotherapy. All derived cell lines were shown to have significant resistance to the corresponding chemotherapy agent.

extract_protocol: Cells from the chemotherapy resistant variants and their original cell line were seeded into 6 replicate flasks each. Prior to harvest, resistant cell lines were allowed to grow for at least 24-48 hours in chemotherapy-free medium in order to avoid an acute toxicity response to the respective chemotherapeutic agent. Then, cells were harvested at a confluency of about 80% in TRIzol® (Invitrogen) and total RNA was extracted from the cells according to the manufacturer’s protocol. RNA concentration was measured using UV spectrophotometry (NanoDrop® ND-8000 Spectrophotometer, Thermo Fisher Scientific), and quality determined by visualization of distinct 28S and 18S rRNA species via electrophoresis through a 1% agarose gel. 500ng of total RNA was used for microarray studies.

value: KYSE


title: DH_KYSE_FU6

description: miRNA


title: Vehicle Treated HUVEC Replicate 2 [7165895087_E]

description:
Vehicle Treated HUVEC Replicate 2
7165895087_E


title: DH_KYSE_FU3

description: miRNA


title: PRA Serum Treated HUVEC Replicate 2 [7165895087_H]

description:
PRA Serum Treated HUVEC Replicate 2
7165895087_H


title: PRA Serum Treated HUVEC Replicate 1 [7165895087_G]

description:
PRA Serum Treated HUVEC Replicate 1
7165895087_G


title: DH_KYSE_con6

description: miRNA

value: control


title: DH_KYSE_FU1

description: miRNA


title: DH_KYSE_FU2

description: miRNA


title: DH_KYSE_con2

description: miRNA


title: DH_KYSE_con1

description: miRNA


title: Sarc3 [Illumina]

city: Silver Spring

first: BIJU

last: ISSAC

state: MD

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

description: SAMPLE 6

data_processing: The data was normalized using Quantile normalization and log (base2) transformed on GeneSpring 12.5 GX software from Agilent

source_name: chondrosarcoma

label_protocol: Biotinylated cRNA were prepared with the Ambion Message Amp kit for Illumina

growth_protocol: JJ012 and C28 cells were seeded on 60x15mm Petri dish at 5000000 cells density.in seeding media of 5ml.

extract_protocol: Qiazol was added to each dish and the cells were subject to active lysis. Lysates were frozen at -70 and total RNA was extracted with QiagenRNeasy Rneasy mini kit.

treatment_protocol: Cells were incubated 24 hours at 37Cin 5% CO2 incubator.

value: JJ012 cell line

tag: group

value: test


title: DH_KYSE_con4

description: miRNA


title: Sarc1 [Illumina]

description: SAMPLE 4


title: C28 (2) [Illumina]

description: SAMPLE 2

source_name: chondrocytes

value: C28 cell line


title: C28 (1) [Illumina]

description: SAMPLE 1


title: Sarc2 [Illumina]

description: SAMPLE 5


title: DH_KYSE_cis6

description: miRNA

value: cisplatin


title: Complement-Inactivated PRA Serum Treated HUVEC Replicate 1 [7165895087_A]

description:
Complement-Inactivated PRA Serum Treated HUVEC Replicate 1
7165895087_A


title: DH_KYSE_FU5

description: miRNA


title: Complement-Inactivated PRA Serum Treated HUVEC Replicate 3 [7165895070_C]

description:
Complement-Inactivated PRA Serum Treated HUVEC Replicate 3
7165895070_C


title: DH_KYSE_con3

description: miRNA


title: Vehicle Treated HUVEC Replicate 3 [7165895087_F]

description:
Vehicle Treated HUVEC Replicate 3
7165895087_F


title: DH_KYSE_con5

description: miRNA


title: Vehicle Treated HUVEC Replicate 1 [7165895087_D]

description:
Vehicle Treated HUVEC Replicate 1
7165895087_D


title: Complement-Inactivated PRA Serum Treated HUVEC Replicate 2 [7165895087_B]

description:
Complement-Inactivated PRA Serum Treated HUVEC Replicate 2
7165895087_B


title: 688_cKO.rep5

city: South San Francisco

first: Jessica

middle: Lynn

last: Larson

state: California

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 11.

data_processing: Agilent Feature Extraction software version 11 was used to create feature extraction files. The normal exponential convolution model was applied for the background correction, Loess and quantile were applied for within array and cross-array normalization. Gene differential expression was analyzed by the package of limma.

source_name: Universal mouse reference (UMR) from Stratagene

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

growth_protocol: Mice were bread to give the specific genotypes.

extract_protocol: Total RNA was isolated using RNAesy mini kit following  the manufacturer's instructions and including on column DNAse digestion.  RNA quality was verified by running samples on Agilent Bioanalyzer 2100.

treatment_protocol: DLK knockdown was induced by placing mice on a tamoxifen diet for 3 weeks. All wild type animals were on the tamoxifen diet as well.  Animals were taken down and hippocampus was dissected out and processed for RNA extraction.

tag: reference

value: adult hippocampus

tag: genotype

value: DLK conditional knockout


title: C28 (3) [Illumina]

description: SAMPLE 3

tag: cell line


title: DH_KYSE_cis4

description: miRNA


title: DH_KYSE_cis5

description: miRNA


title: DH_KYSE_cis2

description: miRNA


title: DH_OE19_cis6

description: miRNA


title: DH_OE19_con3

description: miRNA


title: DH_OE19_con4

description: miRNA


title: DH_OE19_con6

description: miRNA


title: DH_OE19_con5

description: miRNA


title: DH_OE19_cis5

description: miRNA


title: DH_OE19_con2

description: miRNA


title: DH_OE19_cis3

description: miRNA


title: 723_WT.rep5

value: Universal mouse reference (UMR) from Stratagene

value: DLK wild-type


title: 689_WT.rep4


title: 713_WT.rep2


title: 712_cKO.rep3


title: 705_cKO.rep4


title: 706_WT.rep1


title: 718_cKO.rep2


title: 698_cKO.rep1


title: DH_KYSE_cis3

description: miRNA


title: embryo_36hpf_mispair_rep2

city: Waterloo

first: Matt

last: Vijayan

address: 200 University Avenue W

institute: University of Waterloo

description:
36MP2
Gene expression in 36hpf embryos after microinjection of 4.4ng of glucocorticoid receptor mispair control oligonucleotide

hyb_protocol: 1.65 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing Agilent fragmentation buffer and  Agilent blocking agent following the manufacturers instructions. Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish Oligo Microarrays V2 (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene expression Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Gene expression was quantified with Agilent Feature Extraction 10.5.1.1.  Green processed signal from the Feature Extraction output was entered into Agilent GeneSpring 7.3.1 for analyis.  Data was normalized by flooring values below 0.05 to 0.05 and normalizing per chip to a set of positive control genes that were selected on the criteria that raw data was above 50 for all samples.

organism: Danio rerio

source_name: whole homogenized embryos_36 hpf_control treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA following the Agilent One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol v6 and purified using the Rneasy mini kit (Qiagen) and quantified with a Nanodrop spectrophotometer (Thermo Scientific)

extract_protocol: RNA was extracted from pools of embryos with the RNeasy Mini Kit (Qiagen) with on-column DNAse (Qiagen) treatment to remove genomic DNA contamination. Preliminary RNA quantification was performed via a Nanodrop spectrophotometer (260 nm; Thermo Scientific) and confirmed along with quality assessment by a Agilent 2100 bioanalyzer.

treatment_protocol: Zebrafish embryos were microinjected at the single-cell stage with either: active morpholino designed against the start site of translation for the glucocorticoid receptor transcript (sequence: 5’-CTCCAGTCCTCCTTGATCCATTTTG-3’, 4.4ng in 1nl injection volume) or a mispair control with five changed basepairs (5’-CTCCAGTCCTCCTTGATCCATTTTG-3’, 4.4ng in 1nl injection volume). Pools of 25 embryos were flash frozen at 24 and 36 hpf for RNA extraction. This experiment was repeated three times for three independent replicates.

value: embryo

tag: injected with

value: mispair control oligonucleotide

tag: hours post fertilization (hpf)


title: DH_KYSE_cis1

description: miRNA


title: DH_OE19_con1

description: miRNA


title: embryo_36hpf_mispair_rep3

description:
36MP3
Gene expression in 36hpf embryos after microinjection of 4.4ng of glucocorticoid receptor mispair control oligonucleotide


title: DH_OE19_cis1

description: miRNA


title: DH_OE19_cis4

description: miRNA


title: DH_OE19_cis2

description: miRNA


title: DH_OE19_FU6

description: miRNA


title: DH_OE19_FU3

description: miRNA


title: embryo_36hpf_mispair_rep1

description:
36MP1
Gene expression in 36hpf embryos after microinjection of 4.4ng of glucocorticoid receptor mispair control oligonucleotide


title: 714_WT.rep3


title: embryo_36hpf_morpholino_rep3

description:
36MO4
Gene expression in 36hpf embryos after microinjection of 4.4ng of glucocorticoid receptor morpholino oligonucleotide

source_name: whole homogenized embryos_36 hpf_morpholino treatment

value: active morpholino oligonucleotides to knockdown GR


title: IP with rabbit anti IKBa antibodies versus input

type: genomic

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: IP versus input of mouse fibroblast chromatin immunoprecipitated with IKB; technical replicate 3 of 3 with antibodies raised in rabbit

hyb_protocol: Microarrays containing PCR products representing over 7000 different mouse promoter regions spotted on Schott Nexterion® A+ slides slides were used.  5 micrograms of each labeled DNA were dried down by speedvac centrifugation with 50 ug of mouse Cot-1 DNA, 10 ug of yeast tRNA and resuspended in 80 ul of DIG-Easy hybridization buffer (Roche), denatured 10 minutes at 85ºC and incubated 1h at 45ºC to allow blocking of repetitive sequences by the Cot-1 DNA. Hybridization mix was then laid on 24x60 mm glass coverslip and applied to the microarray that had previously been pre-blocked in 1% BSA, 6x SSC and 0.5% SDS, 1 hour at 42ºC, rinsed 4 times in distilled water and dried by centrifugation. After 18 h hybridization inside a humidity control chamber in an InSlideOut hybridization oven, coverslips were removed in 250 ml 0.1x SSC / 0.1% SDS at 50ºC in a staining dish and slides were washed at room temperature in a staining dish on a shaking plate 3 times 5 min  in 250 ml of the same solution followed by 5 washes in 0.1X SSC alone. After drying by centrifugation 5 minutes at 1500 rpm slides were ready for scanning.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were background subtracted using the normexp method and balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, without scaling across chips.

source_name: NIH 3T3

label_protocol: 500 ng of DNA were  labelled with Cy3-CTP or Cy5-dCTP by random priming using Bioprime kit (Invitrogen) overnight at 37ºC and purified by solid phase extraction using the Bioprime kit spin columns. Fluorescent dye incorporation was assessed with a Nanodrop ND-1000 spectrophotometer.

growth_protocol: NIH-3T3 were grown in Dulbecco's media 10% Fetal Bovine Serum at 37C and 5%CO2.

extract_protocol: 6x10E7 NIH-3T3 cells were crosslinked in 0.5% formaldehyde for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 30 min on ice. The crosslinked chromatin was sheared to an average size of 1000 bp by ten 30-second pulses using a Dr. Hielscher sonicator (GmbH). The lysate was then centrifuged to remove cell debris, and the chromatin was visualized in an agarose gel. The chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 2 µg of the different antibodies  at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 500 µl elution buffer (1% SDS, 100 mM NaHCO3) for 1 h at RT. After centrifugation  the soluble chromatin was incubated overnight at 65C, followed by a 2 hour treatment with proteinase K to 500 µg/ml at 55C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

value: embryonic fibroblasts

tag: antibodies

value: rabbit anti IKB antibodies (06-494, Upstate, Millipore)

value: NIH 3T3


title: DH_OE19_FU1

description: miRNA


title: IP with mouse anti IKBa antibodies versus input

description: IP versus input of mouse fibroblast chromatin immunoprecipitated with IKB; technical replicate 2 of 3 with antibodies raised in mouse

value: mouse monoclonal anti IKB antibodies (sc-1643, Santa Cruz)


title: C28 (3)

description: control

hyb_protocol: target specific primers

data_processing: The real-time PCR reactions were run  Roche Lightcycler 480 real-time PCR instrument. The data was analyzed using MultiD Genex (MultiD,  Gothenburg, Sweden). Raw Data (Ct) were Inter-Plate calibrated. Outliers and negatives were filtered along with false positives. Missing values were filled/imputed. Data (ΔCt) was normalized to global mean. The fold change (2^ΔΔCt) was computed between test and control after determining quantification and log convertions to base 2. All significant miRNAs were subset and searched against miRWalk database (www.umm.uni-heidelberg.de/apps/zmf/mirwalk/index.html) on predicted and validated miroRNA , 6 reference gene assays (mirBase13) were used.

label: SYBR Green

label_protocol: 20 ng of total RNA per panel was reverse transcribed using miRCURYLNA RTmicroPCR, polyadenylation and cDNA synthesis kit (Exiqon, Woburn,MA) For each sample the cDNA was diluted and each reaction was combined with SYBR Green Master Mix (Exiqon) and added to the Ready-to-Use PCR Panels.

growth_protocol: JJ012 and C28 cells were seeded on 60x15mm Petri dish at 5000000 cells density in seeding media of 5ml.

extract_protocol: Qiazol was added to each dish and the cells were subject to active lysis. Lysates were frozen at -70 and total RNA was extracted with QiagenRNeasy  mini kit.

treatment_protocol: Cells were incubated 24 hours at 37C in 5% CO2 incubator.

value: C28 cell line control

value: chondrosarcoma


title: DH_OE19_FU4

description: miRNA


title: DH_OE19_FU2

description: miRNA


title: embryo_24hpf_morpholino_rep3

description:
24MO3
Gene expression in 24hpf embryos after microinjection of 4.4ng of glucocorticoid receptor morpholino oligonucleotide

source_name: whole homogenized embryos_24 hpf_morpholino treatment


title: IP with goat anti IKBa antibodies versus input

description: IP versus input of mouse fibroblast chromatin immunoprecipitated with IKB; technical replicate 1 of 3 with antibodies raised in goat

hyb_protocol: Microarrays containing PCR products representing over 7.000 different mouse promoter regions spotted on Schott Nexterion® A+ slides slides were used.  5 micrograms of each labeled DNA were dried down by speedvac centrifugation with 50 ug of mouse Cot-1 DNA, 10 ug of yeast tRNA and resuspended in 80 ul of DIG-Easy hybridization buffer (Roche), denatured 10 minutes at 85ºC and incubated 1h at 45ºC to allow blocking of repetitive sequences by the Cot-1 DNA. Hybridization mix was then laid on 24x60 mm glass coverslip and applied to the microarray that had previously been pre-blocked in 1% BSA, 6x SSC and 0.5% SDS, 1 hour at 42ºC, rinsed 4 times in distilled water and dried by centrifugation. After 18 h hybridization inside a humidity control chamber in an InSlideOut hybridization oven, coverslips were removed in 250 ml 0.1x SSC / 0.1% SDS at 50ºC in a staining dish and slides were washed at room temperature in a staining dish on a shaking plate 3 times 5 min  in 250 ml of the same solution followed by 5 washes in 0.1X SSC alone. After drying by centrifugation 5 minutes at 1500 rpm slides were ready for scanning.

value: goat anti IKB antibodies (sc-371-G, Santa Cruz)

extract_protocol: 6x10E7 NIH-3T3 cells were crosslinked in 0.5% formaldehyde for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 30 min on ice. The crosslinked chromatin was sheared to an average size of 1000 bp by ten 30-second pulses using a Dr. Hielscher sonicator (GmbH). The lysate was then centrifuged to remove cell debris, and the chromatin was visualized in an agarose gel. The chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 2 µg of the different antibodies at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 500 µl elution buffer (1% SDS, 100 mM NaHCO3) for 1 h at RT. After centrifugation  the soluble chromatin was incubated overnight at 65C, followed by a 2 hour treatment with proteinase K to 500 µg/ml at 55C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.


title: embryo_24hpf_mispair_rep3

description:
24MP3
Gene expression in 24hpf embryos after microinjection of 4.4ng of glucocorticoid receptor mispair control oligonucleotide

source_name: whole homogenized embryos_24 hpf_control treatment


title: Donor 18, Proliferative Medium, Rep3

city: Singapore

first: Jodhbir

last: Mehta

address: 11 Third Hospital Ave

department: Stem Cell and Tissue Engineering

country: Singapore

institute: Singapore Eye Research Institute

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 18) in Proliferative Medium, Rep 3

hyb_protocol: The labeled strands were hybridized in triplicate onto HumanHT-12 v4 Expression BeadChips using the Illumina IntelliHyb Seal.

data_processing: The data were analyzed withPartek Genomics Suite version 6.5 beta and normalized using Genechip robust multiarray averaging (GC-RMA) and batch removal tool.

source_name: Primary Corneal Endothelial Cells - Passage 3

label_protocol: Ambion® proprietary MEGAscript® in vitro transcription technology was used to generate biotinylated antisense cRNA.

growth_protocol: Isolation of human CECs using a two-step peel and digest method. Isolated human CECs were first established in M5 (Human Endothelial-SFM, was supplemented with 5% FBS and 1% antibiotic/antimycotic) overnight to allow for cell adherence and stabilization. The culture medium was subsequently replaced with M4 (Ham’s F12/M199, 5% FBS, 20 μg/ml ascorbic acid, 1% ITS, 1% antibiotic/antimycotic and 10 ng/ml bFGF) to promote the proliferation of the adhered CECs. When the growth of CECs reached 80% to 90% confluence (approximately two weeks), M4 medium was withdrawn and M5 medium was re-introduced to the CECs for at least seven days before passage. Confluent CECs were passaged via TE dissociation. For cellular expansion, the dissociated CECs were plated at the seeding density of 10^4 cells per cm^2.

extract_protocol: RNA was extracted with Trizol reagent. Clean-up and DNase treatment with QIAGEN RNeasy mini kit were performed in accordance to the manufacturer’s instruction. An Agilent RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer were used to determine the quality and integrity of RNA before microarray analysis.

treatment_protocol: Human CECs at the third passage were grown to confluence in M4 (Proliferative group), and were compared to CECs exposed to M5 (Maintenance group) for 7 days.

tag: protocol

value: Proliferative Medium


title: embryo_36hpf_morpholino_rep2

description:
36MO2
Gene expression in 36hpf embryos after microinjection of 4.4ng of glucocorticoid receptor morpholino oligonucleotide


title: Donor 17, Proliferative Medium, Rep1

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 17) in Proliferative Medium, Rep 1


title: Donor 18, Proliferative Medium, Rep2

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 18) in Proliferative Medium, Rep 2


title: embryo_24hpf_mispair_rep1

description:
24MP1
Gene expression in 24hpf embryos after microinjection of 4.4ng of glucocorticoid receptor mispair control oligonucleotide


title: C28 (1)

description: control


title: embryo_36hpf_morpholino_rep1

description:
36MO1
Gene expression in 36hpf embryos after microinjection of 4.4ng of glucocorticoid receptor morpholino oligonucleotide


title: embryo_24hpf_morpholino_rep2

description:
24MO2
Gene expression in 24hpf embryos after microinjection of 4.4ng of glucocorticoid receptor morpholino oligonucleotide


title: Donor 17, Proliferative Medium, Rep2

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 17) in Proliferative Medium, Rep 2


title: C28 (2)

description: control


title: Donor 18, Proliferative Medium, Rep1

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 18) in Proliferative Medium, Rep 1


title: Donor 18, Maintenance Medium, Rep3

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 18) in Maintenance Medium, Rep 3

value: Maintenance Medium


title: Sarc2

description: test

value: JJ012 cell line

value: chondrocytes


title: Sarc1

description: test


title: embryo_24hpf_morpholino_rep1

description:
24MO1
Gene expression in 24hpf embryos after microinjection of 4.4ng of glucocorticoid receptor morpholino oligonucleotide


title: Sarc3

description: test


title: Donor 18, Maintenance Medium, Rep2

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 18) in Maintenance Medium, Rep 2


title: Donor 18, Maintenance Medium, Rep1

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 18) in Maintenance Medium, Rep 1


title: Donor 17, Proliferative Medium, Rep3

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 17) in Proliferative Medium, Rep 3


title: Donor 17, Maintenance Medium, Rep3

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 17) in Maintenance Medium, Rep 3


title: Donor 17, Maintenance Medium, Rep2

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 17) in Maintenance Medium, Rep 2


title: Donor 17, Maintenance Medium, Rep1

description: Gene expression data of P3 human corneal corneal endothelial cells (Donor 17) in Maintenance Medium, Rep 1


title: YG001-T3

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization (see protocols.txt on the series record for full protocol)

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS using R2.12.1 with Loess function in marray v1.20.0, as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., >2^15) in either channel were not considered for the estimation of the LOESS curve.

label_protocol: robot amplification and labeling v1.0 (see protocols.txt on the series record for full protocol)

extract_protocol: RNA extraction cellLine (Trizol followed by RNeasy, see protocols.txt on the series record for full protocol)

value: 3T3-L1 undifferentiated

tag: genotype/variation

value: 3T3-L1 mature adipocytes


title: YG001-U3


title: YG001-U2


title: YG001-T4


title: YG001-U4


title: YG001-T2


title: 206_SIO

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: sample 206 treated with SIO

hyb_protocol: Manufacturer's recommendations

scan_protocol: Manufacturer's recommendations

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and quantile normalization  as normalization method.

label_protocol: Manufacturer's recommendations

growth_protocol: Cells derived from GBM surgical tissues (GBM146, GBM157, and GBM206) were established in Dr. Harley Kornblum’s laboratory at UCLA and were cultured as previously described

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen).

treatment_protocol: GBM sphere samples (GBM146, GBM157, and GBM 206) were treated with 1 µM Siomycin A or control (DMSO) for 24 hours

value: glioma stem cells

value: SIO


title: YG001-U1


title: 206_DMSO

description: sample 206 treated with DMSO

value: DMSO


title: Fetal mHeat-WT_E16.5_B6

city: Kyoto

first: Satoshi

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

description: 6-Fetal mHeat-WT_E16.5_B6.txt

hyb_protocol: Hybridization and washing steps were using Gene Expression Wash Pack (Agilent Technology) according to the manufacturer's instructions.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using DNA MicroArray Scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software version 9.5.3 and further analyzed using GeneSpring GX software version 11.0.2. Data were normalized to the 75 th percentile (median).

source_name: fetal mouse heart

label_protocol: 250 ng of total RNA was labelled with Cy3 using the Low RNA Fluorecent Linear Amplification Kit PLUS, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: CMPs were cultured on Collagen I coated dish in DMEM/F12 supplemented with 10% FBS, 40 ng/ml bFGF.

extract_protocol: Total RNA was extracted from each samples using the RNeasy Plus Mini Kit (QIAGEN).

tag: strain background

value: wild type

tag: age

value: embryonic day 16.5

value: Cardiac tissue


title: 157_DMSO

description: sample 157 treated with DMSO


title: Adult mouse total heart RNA_Clontech

description: 5-Adult mouse total heart RNA_Clontech.txt

source_name: Adult mouse heart


description: 3-Adult mouse cardiac mesenchymal progenitor from Atrial, Living.txt

tag: tissue source

value: mouse cardiac mesenchymal progenitor (mCMP)


title: YG001-C2


description: 4-Adult mouse cardiac mesenchymal progenitor from Ventricle, Living.txt


title: YG001-C3


title: 146_SIO

description: sample 146 treated with SIO


title: 146_DMSO

description: sample 146 treated with DMSO


title: 157_SIO

description: sample 157 treated with SIO


title: YG001-C1


title: YG001-C4