title: B6.MRLc1_testis_heat-exposed_10 days_rep2

city: Sapporo

first: Masataka

last: Chihara

state: Hokkaido

address: Kita 18, Nishi 9, Kita-ku

department: Department of Biomedical Sciences

institute: Graduate School of Veterinary Medicine, Hokkaido University

description: Gene expression after 10 days in heat-exposed mouse testis

hyb_protocol: 1.65 mg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 30 ml containing 25x fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 30 ml of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE (G4852A) for 17 hours at 65°C.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately for 2 minutes at 30°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Ver.9.5.3 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: B6.MRLc1, heat-exposed testis, 10 days, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (Thermo Scientific).

growth_protocol: All mice were maintained under specific pathogen-free conditions.

extract_protocol: Total RNA extracted from testes was purified using RNeasy Mini Kit (Qiagen)  following the manufacturer's recommendations. RNA samples were checked for RNA integrity on a Bioanalyzer2100 (Agilent Technologies).

treatment_protocol: Testes were isolated from mice at 10 days after a single scrotal heat stress of 43°C for 20 min.

value: B6.MRLc1-(D1Mit202–D1Mit403) carrying the telomeric region of MRL-type Chr 1 (67.97–81.63 cM)

tag: tissue

value: testis

tag: gender

value: male

tag: age

value: 3 months


title: EpiSC line_ 129C1_treated with IWP2_rep1

status: Public on Aug 01 2014

type: RNA

city: Tsukuba

first: Kuniya

last: Abe

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center

country: Japan

institute: RIKEN

description: Gene expression of undifferentiated EpiSCs.

hyb_protocol: One ug of Cy3-labelled cRNA was fragmented following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A) for 16hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immediately subjected to a microarray scanner.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner) using one color scan setting for 8x60k array slides ( Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters.

molecule: total RNA

organism: Mus musculus

source_name: EpiSC, 129C1_treated with IWP2, replicate 1

label_protocol: Twenty five nanogram of total RNA was labeled with Cy3-CTP with a Quick Amp Labeling Kit (Agilent Technologies). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: EpiSC lines were cultured in conventional medium, or in medium containing the Wnt signaling inhibitor. Murine ES cells were cultured in conventional medium or in medium containing 2i inhibitors.

extract_protocol: Total RNAs were extracted from samples using an AllPrep DNA/RNA Micro Kit (Qiagen, Hilden, Germany). The quality of RNA samples was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell type

value: stem cells

tag: method

value: established by the original protocol


title: Rat1 cells 60 min PE Treatment

city: Loma Linda

first: Daniel

middle: P

last: Morris

state: CA

address: Loma LInda University

department: Center for Perinatal Biology

country: USA

institute: Loma LInda University

description: 50 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

hyb_protocol: Cy5-labeled time point samples and an equimolar amount of rat reference RNA labeled with Cy3 were hybridized to a DNA chip containing the version 3 rat microarray (Operon Biotechnologies).  After hybridization, slides were washed sequentially. Details of hybridization and washing protocols can be found at http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/

scan_protocol: Scanned on a Gene Pix 5000 scanner in the Duke University Microarray Core facility.

data_processing:
Data was analyzed using GeneSpring.  Two color data was subject to Lowess normalization and background subtraction.   Ratio of sample/reference (Cy5/Cy3) signal for each time point was then divided by the averaged sample/reference (Cy5/Cy3) signal observed for the three untreated replicates in order to normalize the data series to zero time RNA levels. All time point sample values were retained to ensure that elimination of very low mRNA levels in untreated samples did not remove higher activated expression levels.
Following Lowess normalization and background subtraction, the ratio of sample/reference (Cy5/Cy3) signal for each time point was divided by the average sample/reference (Cy5/Cy3) signal observed for the three untreated replicates in order to normalize the data series to zero-time, untreated RNA levels. This normalized ratio, representing the fold-change in poly-A mRNA relative to untreated cells, was subject to Log 10 transformation to generate the reported values.
Non-numeric values indicate signal is absent in this point but present at other time points.
Log 10 transformation of the normalized poly-A mRNA levels at each time point relative to the average of the triplet untreated zero points.    Non-numeric values indicate signal is absent in this point but present at other time points.
Cy3 Reference counts following lowess normalization and background subtraction.  Non-numeric values indicate signal is absent in this point but present at other time points.
Cy5 Sample counts following lowess normalization and background subtraction.  Non-numeric values indicate signal is absent in this point but present at other time points.

organism: Rattus rattus

source_name: Rat-1 Fibroblast Serum PE 60 min

label_protocol: Total RNA was reverse transcribed using Super script II and Oligo dT primers.  RNA from individual time points was labeled with Cy5 while reference RNA was labeled with Cy3.  In order to ensure all upregulated points were captured by the reference RNA, it was created by combining an equal amounts of RNA from untreated cells with a mix form across the time series (30 min, 1h, 2h, 8h and 24h). Details of labeling protocols can be found at http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/

growth_protocol: A characterized rat-1 fibroblast cell line stably expressing HA-tagged human alpha-1a Adrenergic Receptor at 1.77±0.24 pmole/mg total protein was grown under 5% CO2 at  37°C in growth medium containing Dulbecco's Eagle Modified Medium supplemented with 10% fetal bovine serum (Hyclone, SH30071.03HI), penicillin (100 U/ml), streptomycin (100 µg/ml) and 0.5 mg/ml G418 to maintain selection.  Two days prior to use (42-50h), cells at 75% confluence were trypsinized and plated at 2 to 2.5 million cells per 15 cm dish in growth medium without G418 and grown to about 75% confluence in growth medium under 5% CO2 at 37°C until treatment.

extract_protocol: Following treatment, media was removed first by pouring then by aspiration for 5 secs followed by immediate addition of 10 ml of Trizol for total RNA extraction. Cells were then incubated in Trizol with rotation for 20 to 40 minutes at room temperature prior to storage at -80°C.  Later, 5 ml of these Trizol preparations in 15 ml tubes were thawed and the total RNA extracted as recommended by the manufacturer employing the tabletop centrifuge modification. Total RNA was resuspended to 1ug/ul in water.

treatment_protocol: Cells grown as described were stimulated by addition of filter sterilized phenylephrine (PE) stock in water to a final concentration of 10 uM, followed by gentle circular rotation to ensure mixing with minimal agitation.  At the appropriate time the media was removed quickly followed by immediate addition of Trizol for total RNA extraction.

tag: cell line

value: derived embyonic fibroblast from Fisher 2408 Rat

value: fibroblast

tag: treatment

value: phenylephrine

tag: time

value: 60 min

source_name: Rat-1 Fibroblast Combined Reference


title: B6.MRLc1_testis_heat-exposed_10 days_rep3

source_name: B6.MRLc1, heat-exposed testis, 10 days, replicate 3

tag: genotype

tag: genetic background


title: B6.MRLc1_testis_heat-exposed_10 days_rep1

source_name: B6.MRLc1, heat-exposed testis, 10 days, replicate 1


title: Rat1 cells 50 min PE Treatment

description: 40 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 50 min

value: 50 min


title: Rat1 cells 40 min PE Treatment

description: 30 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 40 min

value: 40 min


title: Rat1 cells 30 min PE Treatment

description: 25 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 30 min

value: 30 min


title: Rat1 cells 25 min PE Treatment

description: 20 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 25 min

value: 25 min


title: B6_testis_heat-exposed_10 days_rep3

source_name: B6, heat-exposed testis, 10 days, replicate 3

value: wt


title: X10

type: genomic

city: Amsterdam

first: Philip

middle: C

last: Schouten

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: According to manufacterer's protocol (Nimblegen Roche)

scan_protocol: 2 um double pass

data_processing: Nimblescan, grid tiff files, generate pair reports followed by using the NimbleScan DNAcopy procedure at default settings

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast Cancer aCGH

label_protocol: With the ENZO 42760 labeling kit for array CGH: 20 uL primers (vial 1) with 500 ng of genomic tumor DNA or Promega Female reference DNA (GG1521) in 19 ul of nuclease free water for 10 minutes at 99 C in pcr machine, followed by 10 minutes of cooling to 4 degrees. Snap freeze and spin. While on ice add 11 ul Cy3 mix (10ul Cy3+1ul Klenow DNA pol (vial 4)) to tumor DNA, and 11 ul Cy5 mix (10ul Cy3+1ul Klenow DNA pol (vial 4)) to reference DNA and incubate in PCR machine for 4 hours at 37 C. Then add 5ul stop buffer (vial 5).  To remove excess nucleotides with Qiagen MinElute PCR purification kit add 275 uL binding buffer (PB) to sample and reference. Put on minElute column and spin 60 sec on 16000 rcf. Add 700 ul Wash Buffer (PE) and centrifuge 60 secs at 16000 rcf. Dry columns by spinning another 60 secs at 16000 rcf. Elute the DNA in 2 steps by adding 2x 10.5 ul of elution buffer (EB). Pool equal amounts of tumor and reference DNA and speedvac into a pellet.

extract_protocol: 10 x 10 u slices containing at least 60% tumour cells were cleared of paraffin (2 x 5 min xylene, 2 x 30 s 100% ethanol, 30s 90% ethanol, 30 s 70% ethanol, and rinsed with H2O), treated with 1 M NaSCN at 37 C overnight, and sections of interest (>70% tumour cells) were scraped in 200 ul buffer ATL (Qiagen, cat. no. 51304).  27 ul of proteinase K (15 ug/ull, Roche, cat. no.3115879001) was immediately added, as well as at the end of the day, and at the beginning and end of the next day; samples were constantly shaken at 37 C during the time of digestion. The following day, 40 ul RNase A (20 ug/ul, Sigma, cat. no. R5500) was added to the sample, vortexed, and incubated for 2 min at room temperature. 400 ul of buffer AL (Qiagen, cat.no.51304) was added and incubated for 10 min at 70 C. 420 ul of 100% ethanol was added and vortexed. The sample mixture was spun on a spincolumn (Qiagen, cat. no. 51304) for 1 min at 8,000 rpm. The column was sequentially washed with 500 ul of the following reagents and spun for 1 min at 8,000 rpm: AW1, AW2, and  twice with 80% ethanol. The column was spun dry for 3 min at 14,000 rpm. The sample was eluted with 50 ul of AE buffer by spinning for 1 min at 8,000 rpm.  (Joosse, SA et al, Breast Cancer Res Treat, 2009)

value: breast cancer

tag: molecular subtype

value: TN

tag: er

tag: pr

tag: n stage

tag: t stage

tag: grade

value: Grade III

source_name: Promega Female Reference genomic DNA G1538

tag: source

value: pooled Female Reference DNA


title: B6_testis_heat-exposed_10 days_rep2

source_name: B6, heat-exposed testis, 10 days, replicate 2

tag: tissue

value: testis

value: male


title: X847

value: Grade II

source_name: Promega Female Reference genomic DNA G1537


title: NB4MTOEcells_ATRA72h

city: Sagamihara-City

first: Shinichiro

last: Takahashi

state: Kanagawa-Ken

address: 1-15-1, kitasato, minami-ku

institute: Kitasato University

description: MTRA

hyb_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

scan_protocol: We followed manufacturer's protocol, and used GenePix 4400A. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf) Raw data files (.TXT) were obtained automatically from CodeLink software.  The BLANK and MASK features are absent in this file.

data_processing: CodeLink Expression Analysis v5.0 software, Quantile normalization

source_name: NB4 cells transfected with pcDNA MT-1G expression vector, treated with ATRA for 72 hours

extract_protocol: RNA Mini Purification Kit (Qiagen, Miami, FL) was used.

treatment_protocol: NB4 cells transfected with pcDNA empty vector or pcDNA MT-1G expression vector, treated with ATRA for 72 hours.

tag: genotype/variation


title: Podocyte_Lupus_IgG_rep2

city: Izumo

first: Kunihiro

last: Ichinose

address: 89-1 Enya-cho

department: Department of Rheumatology

institute: Shimane University Faculty of Medicine

description: SLE IgG

scan_protocol: We followed manufacturer's protocol, and used GenePix 4400A. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

data_processing: CodeLink Expression Analysis v5.0 software; Quantile normalization; Quality flag L = low intensity, G = good

source_name: Podocytes_lupus IgG_24 h

label_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

growth_protocol: Conditionally immortalized human podocytes (AB 8/13) were kindly provided by Dr. Moin A. Saleem (University of Bristol, UK) and maintained in RPMI-1640 supplemented with 10% fetal calf serum (FCS) and 1% ITS Premix (BD Biosciences) at 33°C and shifted to 37°C for two weeks for differentiation.

extract_protocol: QIAGEN Rneasy(R) Mini Kit was used.

treatment_protocol: Cultured human podocytes with IgG purified from sera of normal individuals and lupus nephritis patient for 24 hr were collected for RNA.

value: conditionally immortalized human podocyte cells

tag: treated with

value: IgG from LN (lupus nephritis) patient for 24h


title: ControlNB4cells_ATRA72h

description: control RA

source_name: NB4 cells transfected with pcDNA empty vector, treated with ATRA for 72 hours

value: control


title: Podocyte_Norm_IgG_rep1

description: Normal IgG

source_name: Podocytes_normal IgG_24 h

tag: cell type

value: IgG from normal individual for 24h


title: X686

source_name: Promega Female Reference genomic DNA G1534


title: X703

value: luminal

source_name: Promega Female Reference genomic DNA G1535


title: X725

source_name: Promega Female Reference genomic DNA G1536


title: Rat1 cells 15 min PE Treatment

description: 15 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 15 min

value: derived embyonic fibroblast from Fisher 2408 Rat

value: fibroblast

value: phenylephrine

value: 15 min

source_name: Rat-1 Fibroblast Combined Reference


title: KSL Hp1gKD

city: Chiba

first: Satoru

last: Miyagi

state: Chiba

department: Graduate school of Medicine

institute: Chiba university

description: Gene expression in Hp1gKD c-Kit+ Lineage- cells

hyb_protocol: A total of 600 ng of the labeled cRNA was used for each hybridization. The process of hybridization and washing was performed using a  Expression Hybridization Kit (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: A DNA microarray scanner (Agilent ) was used for array scanning.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using following parameters (protocol GE1-107_sep09 and Grid:028005_D_F_20120201).

source_name: KSL, Hp1gKD, Day14, replicate 1

label_protocol: A total of 10 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent), amplified and labeled with Cyanine 3 using a Quick Amp Labeling Kit (Agilent)  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using TRIZOL LS solution (Invitrogen)  then purified using RNeasy micro plus kit (QIAGEN).

treatment_protocol: HSCs (CD34- c-Kit+ Sca1+  Lineage-) were sorted into 96-wellplates at 100 cells per well, and then incubated in α-MEM supplemented with 1% FBS, 50 μM 2-mercaptoethanol (2ME), 100 ng/ml mouse stem cell factor (SCF) , and 100 ng/ml human thrombopoietin (TPO)　for 24 h. Next, cells were transduced with lentivirus expressing shRNA at a multiplicity of infection (MOI) of 1,500-3,000 for 24 h. After transduction, cells were further incubated in the S-Clone SF-O3 (Sanko Junyaku) supplemented with 0.2% BSA, 50 μM 2-ME, 50 ng/ml SCF, and 50 ng/ml TPO for 14 days. Then, GFP+ c-Kit+ Lineage- hematopoietic progenitors were sorted and subjected into microarray analysis.

tag: strain

tag: cell fraction

value: c-Kit+ Lineage-

value: Female


title: KSL Hp1aKD

description: Gene expression in Hp1aKD c-Kit+ Lineage- cells

source_name: KSL, Hp1aKD, Day14, replicate 1


title: B6_testis_heat-exposed_10 days_rep1

source_name: B6, heat-exposed testis, 10 days, replicate 1

value: wt

tag: gender

tag: age

value: 3 months


title: KSL Tif1bKD

description: Gene expression in Tif1bKD c-Kit+ Lineage- cells

source_name: KSL, Tif1bKD, Day14, replicate 1


title: Rat1 cells 20 min PE Treatment

source_name: Rat-1 Fibroblast Serum PE 20 min

tag: cell line

tag: treatment

tag: time

value: 20 min


title: X527

source_name: Breast Cancer aCGH

value: breast cancer

tag: molecular subtype

tag: er

source_name: Promega Female Reference genomic DNA G1533

value: pooled Female Reference DNA


title: X493

value: TN

tag: pr

tag: n stage

value: Grade II

source_name: Promega Female Reference genomic DNA G1532


title: Rat1 cells 2 min PE Treatment

description: 2 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 2 min

value: 2 min


title: Rat1 cells 3 min PE Treatment

description: 3 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 3 min

value: 3 min


title: KSL LucKD

description: Gene expression in LucKD c-Kit+ Lineage- cells

source_name: KSL, LucKD, Day14, replicate 1


title: Rat1 cells untreated replicate 1

description: Biological replicate 1 of 3. Control, untreated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum untreated

value: untreated


title: Rat1 cells untreated replicate 3

description: Biological replicate 2 of 3. Control, untreated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.


title: Rat1 cells 7 min PE Treatment

description: 7 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 7 min

value: 7 min


title: Rat1 cells untreated replicate 2

value: derived embyonic fibroblast from Fisher 2408 Rat


title: X7

value: luminal

tag: t stage

tag: grade

source_name: Promega Female Reference genomic DNA G1543


title: Rat1 cells 5 min PE Treatment

description: 5 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 5 min

value: fibroblast

value: phenylephrine

value: 5 min


title: Rat1 cells 10 min PE Treatment

description: 10 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 10 min

value: 10 min


title: X270

value: Grade I

source_name: Promega Female Reference genomic DNA G1530

tag: source


title: T-HESC cells_TNF+IL1_rep 3

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

description: Cells were grown in DMEM/F12 medium supplemented with 10% fetal bovine serum, 1% ITS+, 1% penicillin/streptomycin, and 500 ng/mL puromycin.  Cells were serum starved for 24 hours before treatment.  Treatments were carried out for 48 hours.

hyb_protocol: 10 micrograms of biotinylated cRNA were mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.

scan_protocol: The slides were scanned in an Axon GenePix 4000B scanner.

data_processing: global median normalization, CodeLink Expression Analysis 4.1.0.4163

source_name: human endometrial stromal cell line (T-HESC) (ATCC CRL-4003)

label_protocol: Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Kit from Ambion from 1.0 micrograms total RNA starting material.

extract_protocol: The cultured endometrial cells were rinsed and TRI reagent (MRC) was added.  The cells were scraped into tubes and centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

value: Telomerase-immortalized endometrial stromal cell (T-HESC)

tag: atcc catalog number

value: TNFα +ILIβ

tag: dose

value: 5ng/ml TNF and 1ng/mlIL1

tag: serum starvation

value: 24 hours before treatment

tag: passage


title: T-HESC cells_TNF+IL1_rep 2


title: X209

tag: cell type

value: breast cancer

source_name: Promega Female Reference genomic DNA G1526

value: pooled Female Reference DNA


title: X295

source_name: Promega Female Reference genomic DNA G1531


title: T-HESC cells_TNF+IL1_rep 1


title: Caucasian_skin_2 (outlier)

status: Public on Jul 31 2014

city: Bethesda

first: Vincent

middle: J.

last: Hearing

state: MD

address: 37 Convent drive

department: Lab of cell biology

institute: National Cancer Institute

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing  protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: whole human skin from CA02

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA  InputLinear Amp Kit (Agilent Technologies) following the manufac-turer’s protocol.

extract_protocol: RNA was prepared from each biopsy using standard RNA extraction protocols (Trizol, Sigma, St Louis, MO), and were quality-checked using an Agilent 2100 Bioanalyzer platform (Agilent Technologies,Waldbronn, Germany).

treatment_protocol: 4mm human skin punch biopsies were taken from subjects

tag: tissue

value: whole human skin

tag: gender

value: female

tag: rin

tag: ethnic origin

value: Germany


title: Asian_skin_08 (outlier)

source_name: whole human skin from AS08

tag: age

value: Korea


title: X159

source_name: Breast Cancer aCGH

tag: molecular subtype

value: Grade III

source_name: Promega Female Reference genomic DNA G1524


title: X258

value: luminal

tag: er

value: Grade II

source_name: Promega Female Reference genomic DNA G1528


title: X268

tag: pr

source_name: Promega Female Reference genomic DNA G1529


title: X195

tag: n stage

source_name: Promega Female Reference genomic DNA G1525


title: T-HESC cells_IL1_rep 1

tag: cell line

tag: treatment

value: ILIβ


title: T-HESC cells_IL1_rep 3


title: X225

tag: t stage

tag: grade

source_name: Promega Female Reference genomic DNA G1527

tag: source


title: delta-qseB-delta-qseC_normalized signal

city: Wuhan

first: Jinlin

last: Liu

address: 152# Luoyu Street

department: College of Life Science

country: China

institute: Central China Normal University

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit (Agilent). 1μg of cRNA were mixed with blocking agent, fragmentation buffer and incubated at 60℃ for 30 min for fragmentation. GEx Hybridization Buffer were added and 100 μl mixture were hybridized at 65℃ for 17 hours with 10 rpm rotation. The arrays were washed two times using wash buffer 1 and 2 from Gene Expression Wash Buffer Kit (Agilent).

scan_protocol: Arrays were scanned using Agilent Microarray Scanner System G2565BA (Agilent) with resolution of 5μm. The scanner uses 100% and 10% PTM respectively and combines the two data automatically.

data_processing: The data were analyzed using Feature Extraction Software (Agilent). The signal intensity were normalized and transformed into log2 values.

organism: Actinobacillus pleuropneumoniae

source_name: strain ΔqseBΔqseC, serovar 1, mutant

label_protocol: cDNA were transcribed into cRNA using T7 RNA Polymerase and aaUTP (Ambion). cRNA were purified using QIAGEN RNeasy Mini kit (QIAGEN). 4μg cRNA were combined with DMSO and 0.3M NaHCO3 and then were added into Cy3 NHS ester (GE healthcare). The mixture were incubated at 25℃ for 1 hour. 4M Hydroxylamine were added and incubated at 25℃ for 15min. The labeled cRNA were purified using QIAGEN RNeasy Mini kit (QIAGEN).

growth_protocol: A. pleuropneumoniae strains were cultured in TSB medium supplemented with 10 μg/ml of nicotinamide adenine dinucleotide (NAD) and 10% (v/v) filtered cattle serum at 37℃. The samples were collected from mid-exponential phase and the total RNA were extracted using Trizol reagent according to the manufacturer’s instructions.

extract_protocol: RNA were extracted using RNA-Solv Reagent (Omega) according to the manufacturer’s instructions. Total RNA were purified using QIAGEN RNeasy Mini Kit (QIAGEN).

tag: strain

value: ΔqseBΔqseC

tag: phase

value: mid-exponential


title: 4074_normalized signal

source_name: strain 4074, serovar 1, w.t

value: mid-exponential phase


title: T-HESC cells_IL1_rep 2

value: Telomerase-immortalized endometrial stromal cell (T-HESC)

tag: atcc catalog number

tag: dose

tag: serum starvation

tag: passage


title: T-HESC cells_TNF_rep 3

value: TNFα


title: X116

tag: cell type

source_name: Promega Female Reference genomic DNA G1523


title: Caucasian_skin_9

source_name: whole human skin from CA09

tag: tissue

tag: gender

tag: age

tag: rin

tag: ethnic origin


title: Caucasian_skin_5

source_name: whole human skin from CA05


title: Caucasian_skin_10

source_name: whole human skin from CA10


title: X36

tag: molecular subtype

value: TN

tag: er

tag: pr

tag: n stage

source_name: Promega Female Reference genomic DNA G1522


title: Caucasian_skin_6

source_name: whole human skin from CA06


title: Caucasian_skin_8

source_name: whole human skin from CA08


title: T-HESC cells_vehicle control_rep 2

source_name: human endometrial stromal cell line (T-HESC) (ATCC CRL-4003)

tag: cell line

tag: treatment

value: vehicle

value: 24 hours before treatment


title: Caucasian_skin_4

source_name: whole human skin from CA04


title: Caucasian_skin_3

source_name: whole human skin from CA03


title: T-HESC cells_vehicle control_rep 3


title: T-HESC cells_TNF_rep 1

value: 5 ng/ml


title: Asian_skin_10

source_name: whole human skin from AS10

value: whole human skin

value: Philippinen


title: T-HESC cells_TNF_rep 2


title: Asian_skin_09

source_name: whole human skin from AS09

value: female


title: Asian_skin_07

source_name: whole human skin from AS07

value: Japan


title: Caucasian_skin_1

source_name: whole human skin from CA01

value: Russia


title: T-HESC cells_vehicle control_rep 1


title: Asian_skin_03

source_name: whole human skin from AS03


title: African_skin_09

source_name: whole human skin from AF09

value: Guinea-Bessau (Grandpa from Portugal)


title: African_skin_04

source_name: whole human skin from AF04

value: Ghana


title: African_skin_07

source_name: whole human skin from AF07

value: Nigeria


title: African_skin_06

source_name: whole human skin from AF06


title: African_skin_02

source_name: whole human skin from AF02


title: 24 h post 5 cGy + 2 Gy radiation, biological rep1 (PrimeView)

status: Public on Jul 30 2014

city: Hefei

first: Wei

last: Han

state: Anhui

address: #155 Shushanghu Road

institute: Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences

description:
Gene expression data from AG 1522 human fibroblasts 24 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_24h-1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on PrimeView Human Chip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed on a seventh-generation GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, US). Affymetrix GCOS software was used for image analysis to generate raw intensity data.

data_processing: The data were analyzed with Bioconductor.Normalization was performed with the RMA algorithm which included the global background adjustment and quantile normalization.

label: biotin

source_name: Human skin fibroblast AG 1522 cells, first exposed to 5 cGy then followed by 2 Gy X-ray radiation with 12 h interval, 24 h after the final radiation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Human skin fibroblast AG 1522 cells were cultured in modified α-MEM (Hyclone, Logan, US) supplemented with 20% fetal bovine serum (FBS) (Hyclone, Logan, US), 1% penicillin/streptomycin, 1% glutamine and 1% non-essential amino acids mix (Sigma-Aldrich, St. Louis, US). All cultures were grown in a humidified 5% CO2 atmosphere at 37℃. Prior to treatment, the confluence of cells obatined to 100%.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.Qualified total RNA was further purified using the RNeasy micro kit (QIAGEN, GmBH, Germany) and genomic contamination was removed by RNase-Free DNase Set (QIAGEN, GmBH, Germany).

treatment_protocol: The gene profiles for the 5 cGy groups i.e., those subjected to 5 cGy irradiation at different time points after irradiation, including 0 (baseline), 3, 6, 12 and 24 h, were examined.For the 2 Gy groups, i.e., those subjected to 2 Gy irradiation, at 0, 3, 6, 12 and 24 h after irradiation were examined.The gene profiles for the (5 cGy + 2 Gy) groups exposed to 5 cGy (priming dose) and then followed by 2 Gy (challenge dose), the time points 0, 3, 6, 12, 24 h after application of the challenging dose were examined.

value: skin fibroblast

value: 5 cGy followed by 2 Gy X-ray radiation

tag: time


title: 24 h post 5 cGy + 2 Gy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 24 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_24h-2


title: 12 h post 5 cGy + 2 Gy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 12 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_12h-2

source_name: Human skin fibroblast AG 1522 cells, first exposed to 5 cGy then followed by 2 Gy X-ray radiation with 12 h interval, 12 h after the final radiation


title: Asian_skin_05

source_name: whole human skin from AS05


title: African_skin_01

source_name: whole human skin from AF01


title: African_skin_08

source_name: whole human skin from AF08


title: Asian_skin_01

source_name: whole human skin from AS01


title: African_skin_10

source_name: whole human skin from AF10

value: Erythrea


title: 6 h post 5 cGy + 2 Gy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 6 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_6h-2

source_name: Human skin fibroblast AG 1522 cells, first exposed to 5 cGy then followed by 2 Gy X-ray radiation with 12 h interval, 6 h after the final radiation

value: 6 h


title: 3 h post 5 cGy + 2 Gy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 3 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_3h-3

source_name: Human skin fibroblast AG 1522 cells, first exposed to 5 cGy then followed by 2 Gy X-ray radiation with 12 h interval, 3 h after the final radiation

value: 3 h


title: African_skin_05

source_name: whole human skin from AF05


title: 24 h post 5 cGy + 2 Gy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 24 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_24h-3


title: 12 h post 5 cGy + 2 Gy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 12 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_12h-3


title: 6 h post 5 cGy + 2 Gy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 6 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_6h-3


title: 6 h post 5 cGy + 2 Gy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 6 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_6h-1


title: 12 h post 5 cGy + 2 Gy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 12 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_12h-1


title: 3 h post 5 cGy + 2 Gy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 3 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_3h-1


title: 3 h post 5 cGy + 2 Gy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 3 h after 5 cGy + 2 Gy X-ray radiation (12 h interval).
AG_5p2_3h-2


title: 24 h post 5 cGy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 24 h after 5 cGy X-ray radiation.
AG_5cGy_24h-1

source_name: Human skin fibroblast AG 1522 cells, 24 h after 5 cGy X-ray radiation

value: 5 cGy X-ray radiation


title: X25

source_name: Breast Cancer aCGH

value: breast cancer

value: luminal

tag: t stage

tag: grade

value: Grade II

source_name: Promega Female Reference genomic DNA G1521

tag: source

value: pooled Female Reference DNA


title: 12 h post 5 cGy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 12 h after 5 cGy X-ray radiation.
AG_5cGy_12h-3

source_name: Human skin fibroblast AG 1522 cells, 12 h after 5 cGy X-ray radiation


title: 3 h post 5 cGy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 3 h after 5 cGy X-ray radiation.
AG_5cGy_3h-3

source_name: Human skin fibroblast AG 1522 cells, 3 h after 5 cGy X-ray radiation


title: 6 h post 2 Gy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 6 h after 2 Gy X-ray radiation.
AG_2Gy_6h-2

source_name: Human skin fibroblast AG 1522 cells, 6 h after 2 Gy X-ray radiation

value: 2 Gy X-ray radiation


title: 6 h post 5 cGy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 6 h after 5 cGy X-ray radiation.
AG_5cGy_6h-3

source_name: Human skin fibroblast AG 1522 cells, 6 h after 5 cGy X-ray radiation


title: 24 h post 2 Gy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 24 h after 2 Gy X-ray radiation.
AG_2Gy_24h-1

source_name: Human skin fibroblast AG 1522 cells, 24 h after 2 Gy X-ray radiation


title: 3 h post 5 cGy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 3 h after 5 cGy X-ray radiation.
AG_5cGy_3h-1


title: 24 h post 5 cGy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 24 h after 5 cGy X-ray radiation.
AG_5cGy_24h-2


title: 12 h post 2 Gy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 12 h after 2 Gy X-ray radiation.
AG_2Gy_12h-2

source_name: Human skin fibroblast AG 1522 cells, 12 h after 2 Gy X-ray radiation


title: 6 h post 5 cGy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 6 h after 5 cGy X-ray radiation.
AG_5cGy_6h-1


title: 24 h post 2 Gy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 24 h after 2 Gy X-ray radiation.
AG_2Gy_24h-3


title: 3 h post 5 cGy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 3 h after 5 cGy X-ray radiation.
AG_5cGy_3h-2


title: 3 h post 2 Gy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 3 h after 2 Gy X-ray radiation.
AG_2Gy_3h-1

source_name: Human skin fibroblast AG 1522 cells, 3 h after 2 Gy X-ray radiation


title: 24 h post 2 Gy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 24 h after 2 Gy X-ray radiation.
AG_2Gy_24h-2


title: 3 h post 2 Gy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 3 h after 2 Gy X-ray radiation.
AG_2Gy_3h-3


title: 12 h post 5 cGy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 12 h after 5 cGy X-ray radiation.
AG_5cGy_12h-1


title: 12 h post 2 Gy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 12 h after 2 Gy X-ray radiation.
AG_2Gy_12h-3


title: 3 h post 2 Gy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 3 h after 2 Gy X-ray radiation.
AG_2Gy_3h-2


title: 6 h post 2 Gy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 6 h after 2 Gy X-ray radiation.
AG_2Gy_6h-1


title: 6 h post 5 cGy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 6 h after 5 cGy X-ray radiation.
AG_5cGy_6h-2


title: 12 h post 2 Gy radiation, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 12 h after 2 Gy X-ray radiation.
AG_2Gy_12h-1


title: 6 h post 2 Gy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 6 h after 2 Gy X-ray radiation.
AG_2Gy_6h-3


title: radiation sham, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts after 0 Gy sham X-ray radiation.
AG_0Gy_0h-3

source_name: Human skin fibroblast AG 1522 cells, 0 Gy X-ray radiation

value: 0 Gy X-ray radiation

value: control


title: radiation sham, biological rep4 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts after 0 Gy sham X-ray radiation.
AG_0Gy_0h-4


title: 24 h post 5 cGy radiation, biological rep3 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 24 h after 5 cGy X-ray radiation.
AG_5cGy_24h-3


title: 12 h post 5 cGy radiation, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts 12 h after 5 cGy X-ray radiation.
AG_5cGy_12h-2


title: Asian_skin_04

source_name: whole human skin from AS04

value: whole human skin

value: female

value: Korea


title: radiation sham, biological rep2 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts after 0 Gy sham X-ray radiation.
AG_0Gy_0h-2


title: LCL_untreated [N5707]

city: Haifa

first: Tamar

last: Paperna

address: Efron St. 1

department: Faculty of Medicine

country: Israel

institute: Technion

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Genome Studio software-detected intensity for values in sample columns and detection P values in the non-normalized matrix sheet. The data was log2 transformed and batch normalized using JMP genomics batch normalization application.

label_protocol: Illumina Protocol

growth_protocol: LCLs were cultured in RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, penicillin (100 U/ml), streptomycin (100μg/ml), and nystatin (12.5U/ml, Biological Industries).

extract_protocol: RNA was extracted from LCL cultures using the Roche RNA isolation kit. All RNA samples were checked for quality using Experion (Bio-Rad).

treatment_protocol: LCLs (1.4 million cells/ml) were incubated with 100 units/ml recombinant human IFN-β1a (InterferonSource) for 4 hours. Untreated cells were cultured in parallel and under identical culture conditions for comparison.

tag: in vitro treated ifnb

value: NO

value: Female

tag: ms subtype

value: Relapsing Remitting

tag: treatment status at phlebotomy

value: Naïve

tag: ethnicity (jewish/arab)

value: A


title: Diet study with EE2 in ovary of female largemouth bass, 70 ng EE2/g feed, replicate 2

status: Public on Jun 17 2014

city: Gainesville

first: Reyna

middle: Cristina

last: Colli-Dula

state: Florida

address: Mowry Drive 471

department: CEHT

institute: University of Florida

description:
70 ng EE2/g feed_G2
Gene expression after 60 days of a 70 ng EE2/g exposure in LMB female ovary.

hyb_protocol: Agilent protocol titled "One-color microarrays-based gene expression analysis" (document no. G4140-90040 v6.5) was used.

scan_protocol: Scanned on an Agilent G2505B microarray scanner.

data_processing: Data extraction was performed using Agilent Feature Extraction software. Background-subtracted raw expression data (gProcessedSignal) were imported into JMP Genomics v5 (SAS, Cary, NC). During import, data were log2-transformed and all control and non-uniform spots were removed prior to the final analysis. Raw intensity data for each microarray were median-centered before performing ANOVA.

organism: Micropterus salmoides

source_name: Ovary, 60 d, 70 ng EE2/g feed

growth_protocol: Adult female largemouth bass (LMB) were purchased from American Sport Fish Hatchery (Montgomery, AL). Fish were acclimated in aerated 150 gallon fiberglass tanks under constant conditions of 22.60 ± SD 1.41 °C for a minimum of 3 months prior to within the Aquatic Toxicology Laboratory at the University of Florida Center for Environmental and Human Toxicology (CEHT).

extract_protocol: Extracted total RNA from LMB samples using RNA STAT-60 (Tel-test, Friendswood, TX) according to manufacturer's protocol. RNA was reconstituted in RNAsecure (Ambion) and DNase-1 treated with DNA-free Turbo (Ambion).

treatment_protocol: Two different tanks containing female LMB (n= 6-10) were used for a dietary study, with one tank designed for control fish and the second one for EE2 exposure using feed containing 70 ng/g of EE2. All fish were fed 5 days per week for 60 days with floating pellets.

tag: tissue

value: gonad (ovary)

tag: gender

tag: developmental stage

value: adult

tag: treatment dosage

value: 70 ng EE2/g feed

tag: treatment duration

value: 60 days


title: Diet study with EE2 in ovary of female largemouth bass, control, replicate 2

description:
Control_G2
Gene expression after 60 days of control feed in LMB female ovary.

source_name: Ovary, 60 d, control

label_protocol: Agilent protocol titled "One-color microarrays-based gene expression analysis" (document no. G4140-90040 v6.5) was used.

tag: sample type


title: radiation sham, biological rep1 (PrimeView)

description:
Gene expression data from AG 1522 human fibroblasts after 0 Gy sham X-ray radiation.
AG_0Gy_0h-1

tag: cell type

value: skin fibroblast


title: Diet study with EE2 in ovary of female largemouth bass, 70 ng EE2/g feed, replicate 3

description:
70 ng EE2/g feed_G3
Gene expression after 60 days of a 70 ng EE2/g exposure in LMB female ovary.


title: Diet study with EE2 in ovary of female largemouth bass, 70 ng EE2/g feed, replicate 4

description:
70 ng EE2/g feed_G4
Gene expression after 60 days of a 70 ng EE2/g exposure in LMB female ovary.


title: Diet study with EE2 in ovary of female largemouth bass, control, replicate 3

description:
Control_G3
Gene expression after 60 days of control feed in LMB female ovary.


title: Diet study with EE2 in ovary of female largemouth bass, control, replicate 1

description:
Control_G1
Gene expression after 60 days of control feed in LMB female ovary.


title: SG17_EMD150_Maternal liver_EMD150_12days

status: Public on Jun 07 2014

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for Pharmacology and Toxicology

country: Germany

institute: Hannover Medical School

hyb_protocol: The labelled cRNA was  hybridized overnight onto the Affymetrix rat 230A gene chip (16h at 60 rpm in a 450C) in a hybridization chamber.

scan_protocol: The Affymetrix rat 230 A gene chip was first washed on fluidic station 400 and the arrays were scanned using the GeneArray Scanner from Affymetrix

data_processing: The data were normalized using Robust Multi-array Average (RMA) algorithm and Genedata Expressionist software was used for genomic profiling.

label: Biotin

organism: Rattus norvegicus

source_name: Maternal liver_EMD150_12d

label_protocol: cDNA was used as a template for in vitro transcription using the MEGAscript kit and biotinylated nucleotides to produce biotin labeled cRNA (Bioarray high yield RNA transcription labeling kit, Enzo life sciences).

extract_protocol: Total RNA was isolated from tissue samples (maternal liver, embryo liver, embryo bone, and whole embryo) using Qigen RNeasy mini spin kit. Double stranded cDNA was synthesized from total RNA using SuperscriptTM II enzyme (Invitrogen) and oligo dT24 T7 promoter primer. Synthesized cDNA was first cleaned using phase lock gel (Eppendorf) followed by ethanol precipitation.

treatment_protocol: Pregnant female Wistar rats were dosed daily with either EMD 82571 (50 or 150 mg/kg/day, low and high dose of EMD, respectively) or retinoic acid (12 mg/kg/day) on gestational days 6-11 and 6-17, respectively.

value: Maternal liver

value: EMD 82571 150 mg/kg/day

tag: strain

value: Wistar rat

tag: day


title: SG18_RA5_Maternal liver_RA5_12days

source_name: Maternal liver_RA5_12d

tag: treatment

value: Retinoic acid (12 mg/kg)


title: Diet study with EE2 in ovary of female largemouth bass, control, replicate 4

description:
Control_G4
Gene expression after 60 days of control feed in LMB female ovary.

value: control


title: SG08_Embryo liver_EMD150_20days

source_name: Embryo liver_EMD150_20d

value: Embryo Liver


title: Diet study with EE2 in ovary of female largemouth bass, 70 ng EE2/g feed, replicate 1

description:
70 ng EE2/g feed_G1
Gene expression after 60 days of a 70 ng EE2/g exposure in LMB female ovary.

value: female


title: SG21_RA56_Maternal liver_RA56_20days

source_name: Maternal liver_RA56_20d


title: SG19_RA56_Maternal liver_RA56_12days

source_name: Maternal liver_RA56_12d


title: SG09_Maternal liver_EMD150_20days

source_name: Maternal liver_EMD150_20d

value: Maternal Liver


title: SG15_Control_Maternal liver_12days

source_name: Maternal liver_12d


title: SG11_Embryo_EMD50_12days

value: Embryo

value: EMD 82571 50 mg/kg/day


title: SG05_Embryo liver_EMD50_20days

source_name: Embryo liver_EMD50_20d


title: SG14_RA56_Embryo_RA56_12days


title: SG20_RA56_Embryo liver_RA56_20days

source_name: Embryo liver_RA56_20d

value: Embryo liver


title: SG10_Control_Embryo_12days


title: SG16_EMD50_Maternal liver_EMD50_12days

source_name: Maternal liver_EMD50_12d


title: SG06_Maternal liver_EMD50_20days

source_name: Maternal liver_EMD50_20d


title: SG22_RA56_Embryo bone_RA56_20days

source_name: Embryo bone_RA56_20d

value: Embryo bone


title: SG04_Embryo bone_EMD50_20days

source_name: Embryo bone_EMD50_20d


title: SG07_Embryo bone_EMD150_20days

source_name: Embryo bone_EMD150_20d


title: SG12_Embryo_EMD150_12days


title: SG13_RA5_Embryo_RA5_12days


title: SG03_Control_Maternal liver_20days

source_name: Maternal liver_20d


title: SG02_Control_Embryo liver_20days

source_name: Embryo liver_20d


title: SG01_Control_Embryo bone_20days

source_name: Embryo bone_20d


title: hES-hn

status: Public on May 29 2014

city: Guangzhou

first: Wenyin

last: HE

state: Guangdong

address: No.63, Duobao road

institute: The third affiliated hospital of Guangzhou medical university

description: parthenogenesis embryonic stem cell

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v3.2

label: Cy5 and Cy3

source_name: hes

label_protocol: Standard Illumina Protocol

growth_protocol: cultured in ES medium or FM medium in vitro

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: natural growth without treatments

tag: pluripotent

value: stem cell

tag: disease state

value: parthenogenesis


title: GM18489

status: Public on May 09 2014

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description: Sample 63

hyb_protocol: The samples were bisulphite-converted and hybridized to the Infinium HumanMethylation450 BeadChip at the University of Chicago Functional Genomics facility.

scan_protocol: not provided

data_processing:
To ensure high data quality, probes were mapped to a bisulfite converted genome and only uniquely mapped probes were retained. Next we excluded probes that were not on the autosomes. Finally, we discarded any probes overlapping SNPs segregating in our panel, leaving 329,469 probes for analysis. We quantile-normalized these data to a standard normal first, across all probes within an individual and then across all individuals at a probe. Finally, we regressed out four principal components from the data to account for unobserved confounders.
Normalized data: Normalized average beta (PCs removed).
Un-normalized data: Unmethylated and methylated signal intensities and detection p-value.

label: cy3 and cy5

label_protocol: Standard illumina protocols

extract_protocol: DNA was extracted from lymphoblastoid Cell Line

value: Female

value: Lymphoblastoid Cell Line


title: FF-IPS-3

description: beta-thalassemia female stem cell

source_name: ips

value: beta-thalassemia


title: GM19193

description: Sample 55


title: hES-018

description: parthenogenesis embryonic stem cell


title: GM19207

description: Sample 57

value: Male


title: AF-IPS-9

description: normal female stem cell

value: normal


title: AF-IPS-2

description: normal female stem cell


title: AF-IPS-11

description: normal female stem cell


title: GM19114

description: Sample 62


title: GM19210

description: Sample 59


title: GM19140

description: Sample 50


title: GM19172

description: Sample 53


title: FF

description: beta-thalassemia female somatic cell

source_name: fibroblast

value: somatic


title: GM19209

description: Sample 58


title: GM19190

description: Sample 61


title: GM19138

description: Sample 49


title: GM19206

description: Sample 56


title: GM19108

description: Sample 60


title: hES-7

description: normal female embryonic stem cell


title: GM19137

description: Sample 48


title: GM18909

description: Sample 64


title: GM19171

description: Sample 52


title: hES-10

description: normal female embryonic stem cell


title: GM19141

description: Sample 51


title: AF-IPS-3

description: normal female stem cell


title: AF

description: normal female somatic cell

source_name: amino fluid


title: GM19119

description: Sample 47


title: GM19192

description: Sample 54


title: FF-IPS-1

description: beta-thalassemia female stem cell


title: GM18871

description: Sample 43


title: GM18853

description: Sample 39


title: GM18507

description: Sample 34


title: GM18862

description: Sample 41


title: GM18523

description: Sample 37


title: GM18505

description: Sample 33


title: GM18508

description: Sample 35


title: GM18510

description: Sample 31


title: GM18522

description: Sample 36


title: GM19101

description: Sample 44


title: GM18852

description: Sample 38


title: GM19116

description: Sample 46


title: GM18870

description: Sample 42


title: GM18504

description: Sample 32


title: GM19223

description: Sample 30


title: GM19201

description: Sample 26


title: GM19131

description: Sample 20


title: GM19144

description: Sample 22


title: GM18861

description: Sample 40


title: GM19143

description: Sample 21


title: GM19127

description: Sample 17


title: GM19204

description: Sample 28


title: GM19200

description: Sample 25


title: GM19130

description: Sample 19


title: GM19222

description: Sample 29


title: GM19203

description: Sample 27


title: GM19128

description: Sample 18


title: GM19159

description: Sample 23


title: GM19160

description: Sample 24


title: GM19099

description: Sample 16


title: GM19098

description: Sample 15


title: GM18858

description: Sample 11


title: GM18859

description: Sample 12


title: MGG8 iTPC POU3F2 SOX2 SALL2 OLIG2 replicate H3K27ac

status: Public on Apr 10 2014

type: SRA

city: Cambridge

first: Esther

last: Rheinbay

state: MA

address: 7 Cambridge Center

institute: Broad Institute

library_source: genomic

data_processing:
ChIP-Seq reads were aligned with Bowtie1; reads longer than 36 bases were truncated to 36 bases before alignment.
A filter to remove duplicate reads (identical starting position and direction) was applied
Peaks were identified as described in Rheinbay, Suva et al, Cell Reports 2013
Density maps were generated with IGVTools
Genome_build: hg19
Supplementary_files_format_and_content: BIGWIG, density maps.
Supplementary_files_format_and_content: BED: tab-delimited text file with the following columns: chr, start, end. ChIP-Seq peak calls.

source_name: MGG8 human glioblastoma serum-grown cell line

growth_protocol: MGG4 TPC and iTPC, MGG8 TPC and iTPC were cultured and passaged using standard neural stem cell conditions as described in Wakimoto et al, 2009 (PMID: 19351838) and Conti et al, 2005 (PMID: 16086633) MGG 4 FCS and MGG8 FCS were cultured in DMEM + 10% FCS and 1X P/S

extract_protocol:
As described in Mikkelsen et al., Nature 2007. Chromatin was fixed and sheared to 200-1000 bp using Branson Sonifer. After IP and adapter ligation, library fragments of 200-600 bp were isolated by Ampure XP bead purification. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the  Illumina Hiseq 2500 following the manufacturer's protocols.
Single read, Illumina

treatment_protocol: MGG4 and MGG 8 FCS were infected with lentiviral constructs containing individual ORFs of developmental transcription factors. Cells infected with various combinations of TF  were subsequently switched to neural stem conditions for a period of roughly one month and then subjected to ChIP-seq analysis.

tag: chip antibody

value: H3K27ac (Active Motif)


title: MGG8 DGC + POU3F2, SOX2 and SALL2 cDNA  H3K27ac


title: MGG8TPC SOX2 r1

source_name: MGG8 human glioblastoma stem cell line

value: Sox2 (R&D)


title: MGG8TPC OLIG2 r2

value: Olig2 (R&D)


title: MGG8TPC SOX2 r2


title: MGG8TPC SALL2

value: Sall2 (Bethyll)


title: MGG8TPC OLIG2 r1


title: MGG8TPC POU3F2

value: Pou3f2/Brn2 (Epitomics)


title: MGG8 DGC + POU3F2 and SOX2 cDNA H3K27ac


title: MGG8 iTPC POU3F2 SOX2 SALL2 OLIG2 H3K27ac


title: GM19102

description: Sample 45


title: MGG8 DGC + SOX2 cDNA H3K27ac


title: MGG8DGC H3K27ac


title: MGG6DGC H3K27ac

source_name: MGG6 human glioblastoma serum-grown cell line


title: GM18856

description: Sample 10


title: GM18855

description: Sample 9


title: MGG8 DGC + POU3F2 cDNA H3K27ac


title: MGG4DGC H3K27ac

source_name: MGG4 human glioblastoma serum-grown cell line


title: GM18519

description: Sample 7


title: MGG4 DGC + empty vector H3K27ac


title: MGG8 DGC + SALL2 cDNA H3K27ac


title: MGG4 iTPC POU3F2 SOX2 SALL2 OLIG2 H3K27ac


title: MGG28 primary tumor H3K27ac

source_name: Primary human tumor


title: GM18516

description: Sample 5


title: MGG30 primary tumor H3K27ac


title: MGG8TPC H3K27ac


title: GM18520

description: Sample 8


title: MGG8 DGC + OLIG2 cDNA H3K27ac


title: MGG6TPC H3K27ac

source_name: MGG6 human glioblastoma stem cell line


title: MGG8 DGC + empty vector H3K27ac


title: GM18502

description: Sample 4


title: GM18517

description: Sample 6


title: MGG27 primary tumor H3K27ac


title: MGG4TPC H3K27ac

source_name: MGG4 human glioblastoma stem cell line


title: GM18501

description: Sample 3


title: Gro-seq-siJMJD6-1-re2-HEK293T

status: Public on Jan 14 2014

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

description:
Gro-seq in HEK293T cells transfected with siRNA specific against JMJD6 (Qiagen)(repeat)
Nascent RNA sequencing

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: bigwig files report normalized total tags

source_name: HEK293T cell

growth_protocol: HEK293Tcells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
cells were washed 3 times with cold 1X phosphate buffered saline (PBS) buffer and then incubated in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5min on ice and harvested. Cells were first re-suspended and lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with 10 ml lysis buffer and then re-suspended in 100ml of freezing buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).
For run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase In, 1% sarkosyl, 500mM ATP, GTP, and Br-UTP, 2mM CTP) and incubated for 5 min at 30°C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Invitogen) following manufacturer’s instructions. NRO-RNA was then subjected to base hydrolysis on ice for 40 min and followed by treatment with DNase I and antarctic phosphatase. To purify the Br-UTP labeled nascent RNA, the NRO-RNA was immunoprecipitated with an anti-BrdU agarose beads (Santa Cruz Biotech) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween-20) for 1h at 4°C while rotating.  To repair the end, the immunoprecipitated BrU-RNA was re-suspended in 50mL reaction (43mL DEPC water, 5.2mL T4 PNK buffer, 1mL SUPERase In and 1mL T4 PNK (New England BioLabs)) and incubated at 37°C for 1h. RNA was then extracted, precipitated using acidic phenol-chloroform (Ambion) and subjected to poly-A tailing reaction by using poly-A polymerase (New England BioLabs) for 30 min at 37°C. Subsequently, reverse transcription was performed using oNTI223- primers (5’- pGATCGTCGGACTGTAGAACTCT; CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’) where the p indicates 5’ phosphorylation, ‘;’ indicates the abasic dSpacer furan and VN indicates degenerate nucleotides. Specifically, tailed RNA (8.0mL) was subjected to reverse transcription using superscript III (Invitrogen), after which the cDNA products were separated on a 10% polyacrylamide TBE-urea gel. The extended first-strand product (100-500bp) was excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1 (New England BioLabs). Re-linearized single strand cDNA (sscDNA) was separated in a 10% polyacrylamide TBE gel as described above and the product of needed size was excised (~170-400bp) for gel extraction. Finally, sscDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) according to the manufacturer’s instructions. Primers oNTI200 (5’-CAAGCAGAAGACGGCATA-3’) and oNTI201 (5’- AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG-3’) were used to generate DNAs for deep sequencing.

treatment_protocol: Cells were subjected to two rounds of siRNAs transfection in 3 days, followed by nuclei isolation.

tag: cell line

value: Human Embryonic Kidney 293 cells

tag: sirna transfection


title: Gro-seq-siBrd4-2-re2-HEK293T

description:
Gro-seq in HEK293T cells transfected with siRNA specific against Brd4 (Dharmacon)(repeat)
Nascent RNA sequencing


title: Gro-seq-siBrd4-1-re2-HEK293T

description:
Gro-seq in HEK293T cells transfected with siRNA specific against Brd4 (Qiagen)(repeat)
Nascent RNA sequencing


title: Gro-seq-siCTL-re2-HEK293T

description:
Gro-seq in HEK293T cells transfected with control siRNA (repeat)
Nascent RNA sequencing

value: siCTL


title: GM18499

description: Sample 2


title: Gro-seq-siJMJD6-2-re2-HEK293T

description:
Gro-seq in HEK293T cells transfected with siRNA specific against JMJD6 (Dharmacon)(repeat)
Nascent RNA sequencing


title: GM18498

description: Sample 1


title: Gro-seq-siBrd4-2-re1-HEK293T

description:
Gro-seq in HEK293T cells transfected with siRNA specific against Brd4 (Dharmacon)
Nascent RNA sequencing


title: Gro-seq-siJMJD6-1-re1-HEK293T

description:
Gro-seq in HEK293T cells transfected with siRNA specific against JMJD6 (Qiagen)
Nascent RNA sequencing


title: Gro-seq-siCTL-re1-HEK293T

description:
Gro-seq in HEK293T cells transfected with control siRNA
Nascent RNA sequencing


title: Gro-seq-siBrd4-1-re1-HEK293T

description:
Gro-seq in HEK293T cells transfected with siRNA specific against Brd4 (Qiagen)
Nascent RNA sequencing


title: Gro-seq-siJMJD6-2-re1-HEK293T

description:
Gro-seq in HEK293T cells transfected with siRNA specific against JMJD6 (Dharmacon)
Nascent RNA sequencing


title: BRAF(V600K)-G-rep3

status: Public on Dec 31 2013

city: Berlin

first: Markus

last: Morkel

address: Charitéplatz 1

department: Dept. of Pathology

institute: Charité - Universitätsmedizin Berlin

description: BRAF Mouse 3

hyb_protocol: Arrays were hybridized using the NuGen Procedure (at Company AROS, Aarhus, DK)

data_processing: Illumina Genome Studio GX 1.9.0, Quantile Normalisation

source_name: Lgr5-EGFP-positive crypt cells, BRAF(V600K) transgene negative

label_protocol: Probes were labelled using the NuGen Procedure (at Company AROS, Aarhus, DK)

growth_protocol: Mice were housed at a 12h/12h light/dark cycle and fed ad libitum. Transgenes were induced by doxycycline (4mg/ml) treatment provided in a 1% sucrose solution in the drinking water of transgenic mice. Single cell suspensions were isolated from intestinal crypts of mice aged 8-12weeks.

extract_protocol: Cells were sorted into Qiagen buffer RLT+1%beta-Mercaptoethanol, and RNA was extracted using RNeasy Micro columns

treatment_protocol: Cells were gated into different fractions, by high versus low green fluorescence (Lgr5-EGFP stem cell specific reporter) and high versus low red fluorescence (inducible TdTomato-BRAF(V600K) or TdTomato-luciferase control transgene). Resulting cell populations are labelled RG, R, G and NEG.

value: Lgr5-EGFP-positive crypt cells

tag: transgene

value: BRAF(V600K) transgene negative

tag: genetic background

value: B6/129S6 mixed

tag: organ

value: duodenum


title: GM18913

description: Sample 14

tag: gender


title: BRAF(V600K)-RG-rep2

description: BRAF Mouse 2

source_name: Lgr5-EGFP-positive crypt cells, BRAF(V600K) transgene positive

value: BRAF(V600K) transgene positive


title: BRAF(V600K)-NEG-rep2

description: BRAF Mouse 2

source_name: Lgr5-EGFP-negative crypt cells, BRAF(V600K) transgene negative

value: Lgr5-EGFP-negative crypt cells


title: GM18912

description: Sample 13

value: Female

value: Lymphoblastoid Cell Line


title: BRAF(V600K)-NEG-rep1

description: BRAF Mouse 1


title: BRAF(V600K)-NEG-rep3

description: BRAF Mouse 3


title: BRAF(V600K)-R-rep2

description: BRAF Mouse 2

source_name: Lgr5-EGFP-negative crypt cells, BRAF(V600K) transgene positive


title: BRAF(V600K)-R-rep1

description: BRAF Mouse 1


title: BRAF(V600K)-G-rep2

description: BRAF Mouse 2


title: BRAF(V600K)-R-rep3

description: BRAF Mouse 3


title: Preadipocytes treated with DMIOA, biological rep2

status: Public on Sep 17 2013

city: Winnipeg

first: Alemu

middle: Regassa

last: Hunde

state: Manitoba

address: 12 Dafoe Road

department: Animal Science

country: Canada

institute: University of Manitoba

description: Gene expression data from preadipocytes treated with DMIOA.

hyb_protocol: Following fragmentation, 12.5 µg of biotinylated total RNA were hybridized for 16 hours at 45C on Affymetrix Chicken Genome Array. Genechips were washed and stained using Fluidics station 450 (Affymetrix).

scan_protocol: The stained chips were scanned using Scanner 3000 (Affynetrix)

data_processing: Data were background corrected and normalised using GC-RMA

organism: Gallus gallus

source_name: preadipocytes isolated from laying hen

label_protocol: 15 µg of biotinylated aRNA were prepared according to the standard Affymetrix protocol (3' IVT Express Kit user manual, Affymetrix)

growth_protocol: The isolated preadipoctes were incubated in FBS containing 10% DMEM in an incubator with 5% CO2

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

treatment_protocol: Confluent preadipocytes were treated with adipogeneic cocktail (DMIOA) and DMIOA+20S oxysterol

value: Preadipocytes


title: luc_control-RG-rep1

description: Control Mouse 1

source_name: Lgr5-EGFP-positive crypt cells, luc transgene positive

value: luc transgene positive


title: BRAF(V600K)-RG-rep3

description: BRAF Mouse 3


title: Third leaf primordium-rep 1

status: Public on Dec 17 2013

city: Beijing

first: Rui

last: Chen

address: 5 Yiheyuan Road, Haidian District

department: College of Life Sciences

institute: Peking University

description: Dissected from rice embryos after the seeds were soaked in water for 2-3 days

hyb_protocol: The resulting cRNA was used for hybridization in the Affymetrix® Hybridization Oven 640 according to manufacturer’s instruction. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000. GeneChip Operating software (GCOS 1.4) were adopted for transforming pixels to intensities .

data_processing: Raw data was processed by an adjustment method to remove the bias raising from the two-cycle RNA linear amplification at probe level(Wang F, Chen R, Ji D, Bai S, Qian M, Deng M. 2013. Adjustment method for microarray data generated using two-cycle RNA labeling protocol. BMC Genomics 14(1): 31.), and then RMA was used for background correction, normalization and summary in Bioconductor.

organism: Oryza sativa Japonica Group

source_name: Third leaf primordium-rep 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by amplifying and labeling 50-300ng total RNA with Two-Cycle Eukaryotic Target Labeling Assay kit.

growth_protocol: Rice (O. sativa L. ssp. japonica cv. Zhonghua 15) seeds were soaked in water at 30oC for about a week. Then seedlings were transplanted in plastic pots and cultured at 30±2oC under 11 hours day/13 hours night cycle in growth chamber, or transplanted into the experimental field in growing season.

extract_protocol: Total RNA was isolated with TRIzol Reagent from Invitrogen Life Technologies.

tag: cultivar

value: Zhonghua 15

value: leaf


title: BRAF(V600K)-RG-rep1

description: BRAF Mouse 1


title: Bdf2-Flag

status: Public on Sep 24 2013

city: New York

first: Songtao

last: Jia

state: NY

address: 1114, Fairchild center

institute: Columbia University

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

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

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

organism: Schizosaccharomyces pombe

source_name: WT cells expressing Bdf2-flag

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

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

value: DNA from WCE

value: input

value: Bdf2-bound DNA

value: Flag


title: Preadipocytes treated with DMIOA+20S, biological rep2

description: Gene expression data from control preadipocytes treated withDMIOA+20S.


title: Preadipocytes treated with DMIOA, biological rep1


title: BRAF(V600K)-G-rep1

description: BRAF Mouse 1


title: luc_control-RG-rep2

description: Control Mouse 2


title: Third leaf primordium-rep 3

source_name: Third leaf primordium-rep 3


title: Non-treated control preadipocytes, biological rep1

description: Gene expression data from control preadipocytes.


title: Non-treated control preadipocytes, biological rep2


title: Stamen of stage 2-rep 1

description: Dissected from spikelets

source_name: Stamen of stage 2-rep 1

value: stamen


title: Preadipocytes treated with DMIOA+20S, biological rep1


title: Third leaf primordium-rep 2

source_name: Third leaf primordium-rep 2


title: luc_control-G-rep2

description: Control Mouse 2

source_name: Lgr5-EGFP-positive crypt cells, luc transgene negative

value: Lgr5-EGFP-positive crypt cells

value: luc transgene negative


title: luc_control-G-rep1

description: Control Mouse 1

value: B6/129S6 mixed


title: Ts1Cje-Ts63-Hippocampus

status: Public on Sep 05 2013

city: Medford

first: Heather

last: Wick

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

description: Hippocampus gene expression data from mouse Ts63

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Hybridization, Wash and Stain Kit according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned on a GeneArray Scanner 3000 7G, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Quality control and normalization were performed using the pipeline at the www.arrayanalysis.org website (Maastricht University, the Netherlands). Normalization was done using the Robust Multichip Average (RMA) algorithm and the MBNI custom CDF (http://brainarray.mbni.med.umich.edu/) version #14 for the mouse gene 1.0 ST array. Normalization output consisted of data for 21225 probe sets each corresponding to unique Entrez Gene IDs.

source_name: Total RNA from Hippocampus at 8-10 weeks of age

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate according to the GeneChip Whole Transcriptome Labeling and Hybridization protocol (http://www.affymetrix.com) combining the Ambion WT Expression kit (Life Technologies, Grand Island, NY) and the Affymetrix GeneChip Terminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Mice were housed in standard cages with food and water ad libitum under a controlled environment (temperature = 20°C; humidity = 60%) and a light/dark cycle of 12h. Ts1Cje males were backcrossed to C57Bl/6J females for several generations before experiments started.

extract_protocol: Ts1Cje females (N=6) and their wild-type littermates (N=5) were euthanized by cervical dislocation followed by decapitation. The cerebral cortex and the hippocampus were dissected on a cold platform and snap frozen in liquid nitrogen before storage at -80°C. Total RNA was isolated using the NucleoSpin RNA L and RNA II kits for the cortex and hippocampus respectively, following the manufacturer’s instructions (Macherey-Nagel, Bethlehem, PA). RNA concentrations were measured as absorbance at 260 nm on the Nanodrop instrument (Thermo Fisher Scientific, Waltham, MA). RNA quality was analyzed with the Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA) using the RNA 6000 Nano kit according to the manufacturer’s instructions. Only samples displaying an A260/A280 ratio of 2.0-2.1 and a RIN (RNA Integrity Number) > 9 were used for hybridization to the arrays.

value: female

tag: genotype

tag: tissue

value: hippocampus


title: Ts1Cje-WT95-Hippocampus

description: Hippocampus gene expression data from mouse WT95

value: WT


title: Ts1Cje-WT60-Hippocampus

description: Hippocampus gene expression data from mouse WT61

source_name: Total RNA from Hippocampus of 8-10 weeks of age


title: Ts1Cje-Ts61-Hippocampus

description: Hippocampus gene expression data from mouse Ts61


title: Ts1Cje-Ts94-Cortex

description: Cortex gene expression data from mouse Ts94

source_name: Total RNA from cortex at 8-10 weeks of age

value: brain cortex


title: Ts1Cje-WT98-Hippocampus

description: Hippocampus gene expression data from mouse WT98


title: Ts1Cje-Ts87-Hippocampus

description: Hippocampus gene expression data from mouse Ts87


title: Ts1Cje-WT65-Hippocampus

description: Hippocampus gene expression data from mouse WT65


title: Ts1Cje-Ts87-Cortex

description: Cortex gene expression data from mouse Ts87


title: Ts1Cje-Ts64-Hippocampus

description: Hippocampus gene expression data from mouse Ts64


title: Ts1Cje-Ts94-Hippocampus

description: Hippocampus gene expression data from mouse Ts94


title: Ts1Cje-WT95-Cortex

description: Cortex gene expression data from mouse WT95


title: Ts1Cje-Ts61-Cortex

description: Cortex gene expression data from mouse Ts61


title: Ts1Cje-Ts97-Cortex

description: Cortex gene expression data from mouse Ts97


title: Ts1Cje-WT98-Cortex

description: Cortex gene expression data from mouse WT98


title: Ts1Cje-Ts64-Cortex

description: Cortex gene expression data from mouse Ts64


title: Ts1Cje-Ts63-Cortex

description: Cortex gene expression data from mouse Ts63


title: Ts1Cje-WT62-Cortex

description: Cortex gene expression data from mouse WT62


title: Ts1Cje-WT60-Cortex

description: Cortex gene expression data from mouse WT61

source_name: Total RNA from cortex of 8-10 weeks of age


title: Ts1Cje-WT65-Cortex

description: Cortex gene expression data from mouse WT65


title: WT_1

status: Public on Aug 18 2013

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY (Version 2.12). Array data were subjected to robust multi-array average (RMA) normalization. Normalized data were used for calculating fold changes of up- and down-regulated genes using Student's test. Only data with a false discovery rate (FDR) adjusted p-value <0.05 and at least 2x differential expression were included in the analysis. Data underwent z-score transformation for display.

source_name: WT_Regulatory T-cells CD4+CD25+

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).

value: Regulatory T-cells CD4+CD25+

tag: genotype/variation

value: Foxp3cre control


title: WT_2

tag: cell type


title: WT_3

tag: strain


title: p300_1

source_name: p300_Regulatory T-cells CD4+CD25+


title: Ts1Cje-Ts97-Hippocampus

description: Hippocampus gene expression data from mouse Ts97


title: Ck-PGCLCs, Parental clone, day2, amp, rep2

status: Public on Aug 04 2013

city: Kyoto

first: Fumio

last: NAKAKI

address: Yoshidakonoe-cho, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto University

description: Male, C57BL/6;129, Blimp1-mVenus, stella-ECFP, Rosa26-rtTA

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data were normalized together with the default settings.

source_name: Ck-PGCLCs induced from BVSCR26rtTA ESCs, day2

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: Transfected ESCs were maintained under 2i+LIF condition and adapted to a feeder-free condition prior to induction. EpiLC differentiation was performed as reported previously (Hayashi et al., Cell, 2011).

extract_protocol: total RNA was extracted using Qiagen RNeasy according to manufacturer's instruction

treatment_protocol: After 36 hrs of differentiation, cells were harvested and cultured in a Lipidure-Coat 96-well plate (NOF) to be aggregated (started with 2,000 cells/well) in GK15 with 1.5 μg/ml of Dox (Clonetech) to induce TF-PGCLCs. Ck-PGCLCs were induced by BMP4 (500 ng/ml), BMP8A (500 ng/ml), SCF (100 ng/ml), LIF (1000 U/ml) and EGF (50 ng/ml) as previously described (Hayashi et al., Cell, 2011)

value: Male

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA

value: Ck-PGCLCs


title: p300_3


title: p300_2


title: Ts1Cje-WT62-Hippocampus

description: Hippocampus gene expression data from mouse WT62


title: AdERbetasiERalphaVeh rep2

status: Public on Jul 05 2013

city: Urbana

first: Zeynep

last: Madak Erdogan

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description: Gene expression data from MCF-7 cells, AdenoERbeta infection 72h, siERalpha treatment 24h, 0.1%EtOH for 24h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS 3000.

data_processing: The data were analyzed with  GCOS2.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: MCF-7 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 cells were maintained in MEM media with 5% Calf serum

treatment_protocol: MCF-7 cells expressing endogenous ERalpha were infected with adenovirus carrying either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 50. ERβ only cells were generated from these cells by knockdown of ERα in parental cells using the following siERα sequences from Dharmacon: forward, 5’-UCAUCGCAUUCCUUGCAAAdTdT-3’, and reverse, 5’-UUUGCAAGGAAUGCGAUGAdTdT-3’. siRNA experiments were performed as previously described, and resulted in knocknown of ERα mRNA and protein by greater than 95% (Chang et al, 2008). Briefly, cells were transfected with 20 nM siCtrl or siERα for 48 h after infection. Then cells were treated with 0.1% EtOH (Veh) or 10 nM E2 (Sigma-Aldrich) for 24h. All experiments were conducted with two or more replicates.

value: breast adenocarcinoma

tag: infected with

value: adenovirus carrying estrogen receptor beta (AdERb)

tag: transfected with

value: siERalpha

tag: treated with

value: 0.1% EtOH (Veh) for 24h


title: Ck-PGCLCs, Parental clone, day2, amp, rep1


title: AdERbetasiERalphaE2 rep2

description: Gene expression data from MCF-7 cells, AdenoERbeta infection 72h, siERalpha treatment 24h, 10 nM E2 for 24h

value: 10 nM E2 (Sigma-Aldrich) for 24h


title: AdERbetasiERalphaVeh rep1


title: Lung cancer Large Cell Neuroendocrine39

status: Public on May 24 2013

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

hyb_protocol: 20 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner

data_processing: The data was normalized by Robust Multi-Array average (RMA) algorithm (Genespring software; Agilent)

source_name: Lung Tumour

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

value: lung tumour

tag: age at surgery

value: M

tag: histology

value: LCNE

tag: pt stage

tag: pn stage

tag: pm stage

tag: follow-up time (months)

tag: status

value: DEAD

tag: disease free survival in months

tag: relapse (event=1; no event=0)


title: Lung cancer Large Cell Neuroendocrine34

tag: gender

value: ALIVE


title: Lung cancer Large Cell Neuroendocrine33

tag: tissue


title: Lung cancer Large Cell Neuroendocrine36

value: F


title: Lung cancer Large Cell Neuroendocrine31


title: Lung cancer Large Cell Neuroendocrine35


title: Normoxia +1h

status: Public on Aug 01 2013

city: Brussels

first: Olivier

last: Feron

address: Avenue E. Mounier, 52 - FATH5349

department: IREC

country: Belgium

institute: UCL

description: Gene expression data from B16 cells in normoxia 3+1h

hyb_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.

scan_protocol: Standard Affymetrix protocol

data_processing: GCOS

source_name: B16 normoxia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: in vitro B16 melanoma cells, in alpha MEM medium (Gibco) + P/S + vitamin + 10% FCS

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

treatment_protocol:
in serum free medium (alpha MEM + P/S) 2h before hypoxia
chronic hypoxia = 3h ; cyclic hypoxia = 3x1h hypoxia interrupted by 30 minutes reoxygenation
collecting time : at the end of hypoxia or after 1h reoxygenation

tag: cell line

value: B16 melanoma


title: Chronic hypoxia

description: Gene expression data from B16 cells in chronic hypoxia 3h

source_name: B16 chronic hypoxia


title: Lung cancer Large Cell Neuroendocrine38


title: Chronic hypoxia + 1h reoxygenation

description: Gene expression data from B16 in chronix hypoxia 3h + reoxygenation 1h

source_name: B16 chronic hypoxia + reoxygenation


title: Cyclic hypoxia

description: Gene expression data from B16 cells in cyclic hypoxia 3x1h

source_name: B16 cyclic hypoxia


title: Cyclic hypoxia + 1h reoxygenation

description: Gene expression data from B16 cells in cyclic hypoxia 3x1h + reoxygenation 1h

source_name: B16 cyclic hypoxia + reoxygenation


title: Lung cancer Large Cell Neuroendocrine37


title: Lung cancer Large Cell Neuroendocrine40


title: Lung cancer Large Cell Neuroendocrine30


title: Normoxia

description: Gene expression data from B16 cells in normoxia 3h


title: Lung cancer Large Cell Neuroendocrine28


title: Lung cancer Large Cell Neuroendocrine32


title: AdERbetasiERalphaE2 rep1

tag: cell type


title: Lung cancer Large Cell Neuroendocrine29


title: Lung cancer Large Cell Neuroendocrine24


title: Lung cancer Large Cell Neuroendocrine22


title: Lung cancer Large Cell Neuroendocrine26


title: Lung cancer Large Cell Neuroendocrine23


title: Lung cancer Large Cell Neuroendocrine27


title: Lung cancer Large Cell Neuroendocrine25


title: Lung cancer Large Cell Neuroendocrine20


title: Lung cancer Large Cell Neuroendocrine15


title: Lung cancer Large Cell Neuroendocrine18


title: Lung cancer Large Cell Neuroendocrine16


title: H4K16ac

source_name: WT cells

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

tag: strain

tag: sample type

value: DNA from WCE

tag: chip antibody

value: input

value: H4K16ac bound DNA


title: Lung cancer Large Cell Neuroendocrine21


title: Lung cancer Large Cell Neuroendocrine17


title: Lung cancer Large Cell Neuroendocrine19


title: Lung cancer Large Cell Neuroendocrine12


title: Lung cancer Basaloid41

value: BAS


title: Lung cancer Basaloid39


title: Lung cancer Basaloid42


title: Lung cancer Basaloid35


title: Lung cancer Basaloid36


title: Lung cancer Basaloid40


title: Lung cancer Basaloid37


title: Lung cancer Basaloid34


title: Lung cancer Large Cell Neuroendocrine13


title: Lung cancer Basaloid32


title: Lung cancer Large Cell Neuroendocrine11


title: Lung cancer Large Cell Neuroendocrine10


title: Lung cancer Basaloid33


title: Lung cancer Basaloid38


title: Lung cancer Basaloid24


title: Lung cancer Basaloid28


title: Lung cancer Basaloid31


title: Lung cancer Basaloid25


title: Lung cancer Basaloid17


title: Lung cancer Basaloid20


title: Lung cancer Basaloid26


title: Lung cancer Basaloid30


title: Lung cancer Basaloid27


title: Lung Squamous Cell Carcinoma63

value: SQC


title: Lung cancer Basaloid15


title: Lung cancer Basaloid23


title: Lung cancer Basaloid21


title: Lung cancer Basaloid16


title: Lung cancer Basaloid22


title: Lung cancer Basaloid18


title: Lung cancer Basaloid13


title: Lung cancer Basaloid9


title: Lung cancer Basaloid11


title: Lung cancer Basaloid8


title: Lung cancer Basaloid10


title: Lung cancer Large Cell Neuroendocrine9


title: Lung cancer Large Cell Neuroendocrine6


title: Lung cancer Large Cell Neuroendocrine7


title: Lung cancer Large Cell Neuroendocrine51


title: Lung cancer Large Cell Neuroendocrine8


title: Lung cancer Basaloid6


title: Lung cancer Basaloid4


title: Lung cancer Basaloid3


title: Lung Squamous Cell Carcinoma60


title: Lung Squamous Cell Carcinoma56


title: Lung cancer ADK85

value: ADC


title: Lung cancer ADK83


title: Lung Squamous Cell Carcinoma53


title: Lung cancer ADK82


title: Lung cancer Basaloid7


title: Lung Squamous Cell Carcinoma55


title: Lung Squamous Cell Carcinoma58


title: Lung cancer Carcinoid23

value: CARCI


title: Lung Squamous Cell Carcinoma57


title: Lung cancer ADK84


title: Lung cancer Carcinoid19


title: Lung cancer ADK87


title: Lung cancer Basaloid12


title: Lung cancer Carcinoid21


title: Lung Squamous Cell Carcinoma62


title: Lung cancer Carcinoid16


title: Lung Squamous Cell Carcinoma59


title: Lung cancer Carcinoid17


title: Lung cancer Carcinoid18


title: Lung Squamous Cell Carcinoma54


title: Lung cancer Carcinoid15


title: Lung cancer Carcinoid14


title: Lung cancer Carcinoid22


title: Lung cancer Carcinoid12


title: Lung cancer ADK81


title: Lung cancer Carcinoid11


title: Lung cancer Carcinoid13


title: Lung cancer Carcinoid20


title: Small Cell Lung Carcinoma22

value: SCC


title: Small Cell Lung Carcinoma20


title: Small Cell Lung Carcinoma21

value: TX


title: Lung cancer Carcinoid10


title: Small Cell Lung Carcinoma9


title: Small Cell Lung Carcinoma17


title: Small Cell Lung Carcinoma23


title: Small Cell Lung Carcinoma19


title: Small Cell Lung Carcinoma18


title: Small Cell Lung Carcinoma24


title: Small Cell Lung Carcinoma15


title: Lung cancer ADK80


title: Lung cancer ADK77


title: Non tumoral lung2

source_name: Non Tumoral Lung

value: NTL


title: Lung cancer Carcinoid9

value: lung tumour


title: Lung cancer ADK79


title: Lung cancer ADK78

value: M


title: Small Cell Lung Carcinoma12


title: Lung cancer Carcinoid8


title: Small Cell Lung Carcinoma10


title: Small Cell Lung Carcinoma16


title: Lung cancer Carcinoid7


title: Non tumoral lung13


title: Non tumoral lung14


title: Small Cell Lung Carcinoma14


title: Small Cell Lung Carcinoma11


title: Small Cell Lung Carcinoma13


title: Lung cancer Carcinoid6


title: Non tumoral lung1


title: Lung cancer Carcinoid5


title: Lung cancer Carcinoid4


title: Lung cancer Carcinoid2


title: Lung cancer Large Cell Neuroendocrine42

value: LCNE


title: Small Cell Lung Carcinoma8

value: DEAD


title: Small Cell Lung Carcinoma7


title: Lung cancer Carcinoid3

value: ND

value: NX


title: Lung cancer Large Cell Neuroendocrine41

value: ALIVE


title: Lung cancer Large Cell Neuroendocrine50


title: Lung cancer Basaloid14


title: Small Cell Lung Carcinoma6


title: Small Cell Lung Carcinoma4


title: Lung cancer Large Cell Neuroendocrine53


title: Lung cancer Large Cell Neuroendocrine48


title: Lung cancer Large Cell Neuroendocrine54


title: Lung cancer Large Cell Neuroendocrine52


title: Lung cancer Large Cell Neuroendocrine1


title: Lung cancer Large Cell Neuroendocrine55


title: Lung cancer Carcinoid1

value: F


title: Lung Squamous Cell Carcinoma47


title: Lung cancer Large Cell Neuroendocrine46


title: Lung cancer Large Cell Neuroendocrine45


title: Lung cancer Large Cell Neuroendocrine44


title: Lung cancer ADK74


title: Lung cancer Large Cell Neuroendocrine2


title: Lung Squamous Cell Carcinoma46


title: Small Cell Lung Carcinoma25


title: Lung cancer Large Cell Neuroendocrine49


title: Lung cancer Large Cell Neuroendocrine43


title: Lung cancer ADK72


title: Lung cancer ADK86


title: Lung cancer ADK71


title: Lung cancer Basaloid43


title: Lung cancer ADK70


title: Lung Squamous Cell Carcinoma44


title: Non tumoral lung12


title: Lung cancer ADK73


title: Lung cancer Large Cell Neuroendocrine47


title: Lung Squamous Cell Carcinoma61


title: Lung Squamous Cell Carcinoma49


title: Lung cancer ADK67


title: Lung Squamous Cell Carcinoma45


title: Lung cancer_Other5

value: Other


title: Lung Squamous Cell Carcinoma42


title: Lung cancer ADK69


title: Lung Squamous Cell Carcinoma43


title: Lung cancer ADK68


title: Lung cancer ADK66


title: Lung cancer ADK65


title: Lung cancer ADK62


title: Lung cancer ADK63


title: Lung Squamous Cell Carcinoma41


title: Lung cancer ADK60


title: Lung cancer ADK57


title: Lung cancer ADK61


title: Lung cancer ADK64


title: Lung cancer ADK58


title: Lung cancer ADK59


title: Lung cancer ADK56


title: Non tumoral lung9


title: Lung Squamous Cell Carcinoma38


title: Lung Squamous Cell Carcinoma37


title: Non tumoral lung10


title: Lung Squamous Cell Carcinoma40


title: Non tumoral lung8


title: Lung cancer ADK55


title: Lung cancer Large Cell Carcinoma3

value: LCC


title: Lung cancer ADK54


title: Lung Squamous Cell Carcinoma39


title: Lung Squamous Cell Carcinoma36


title: Lung cancer_Other4


title: Lung cancer ADK52


title: Lung cancer ADK51


title: Lung cancer ADK53


title: Lung cancer Large Cell Carcinoma2


title: Lung Squamous Cell Carcinoma32


title: Lung cancer ADK50


title: Lung Squamous Cell Carcinoma35


title: Lung Squamous Cell Carcinoma33


title: Lung Squamous Cell Carcinoma31


title: Non tumoral lung11


title: Lung cancer ADK48


title: Lung cancer ADK44


title: Lung Squamous Cell Carcinoma34


title: Lung cancer ADK47


title: Non tumoral lung7


title: Lung Squamous Cell Carcinoma29


title: Lung cancer ADK46


title: Lung cancer ADK49


title: Lung cancer ADK43


title: Lung Squamous Cell Carcinoma30


title: Lung cancer ADK42


title: Lung cancer ADK39


title: Lung cancer ADK41


title: Lung cancer ADK40


title: Lung cancer ADK36


title: Lung cancer ADK34


title: Lung cancer ADK38


title: Lung cancer ADK35


title: Lung Squamous Cell Carcinoma25


title: Lung cancer ADK37


title: Lung Squamous Cell Carcinoma23


title: Lung cancer ADK31


title: Lung Squamous Cell Carcinoma24


title: Lung Squamous Cell Carcinoma26


title: Lung Squamous Cell Carcinoma22


title: Non tumoral lung6


title: Lung Squamous Cell Carcinoma28


title: Lung cancer ADK30


title: Lung Squamous Cell Carcinoma27


title: Non tumoral lung5


title: Lung Squamous Cell Carcinoma20


title: Lung Squamous Cell Carcinoma21


title: Lung cancer ADK26


title: Lung cancer ADK25


title: Lung cancer ADK29


title: Lung cancer_Other3


title: Lung Squamous Cell Carcinoma17


title: Lung Squamous Cell Carcinoma18


title: Lung Squamous Cell Carcinoma19


title: Lung cancer ADK23


title: Lung cancer ADK22


title: Lung cancer ADK24


title: Lung cancer ADK27


title: Lung cancer ADK18


title: Lung Squamous Cell Carcinoma16


title: Lung Squamous Cell Carcinoma15


title: Lung cancer ADK17


title: Lung cancer ADK12


title: Lung cancer ADK15


title: Lung cancer ADK13


title: Lung cancer ADK21


title: Lung Squamous Cell Carcinoma13


title: Lung cancer ADK20


title: Lung cancer ADK14


title: Lung cancer ADK16


title: Lung cancer ADK10


title: Lung cancer ADK9


title: Lung cancer ADK19


title: Lung cancer ADK11


title: Lung Squamous Cell Carcinoma11


title: Lung cancer ADK28


title: Lung Squamous Cell Carcinoma10


title: Lung Squamous Cell Carcinoma14


title: Lung cancer_Other2


title: Lung cancer ADK8


title: Lung cancer ADK6


title: Lung Squamous Cell Carcinoma8


title: Lung Squamous Cell Carcinoma7


title: Non tumoral lung4


title: Lung cancer ADK2


title: Lung Squamous Cell Carcinoma9


title: Lung Squamous Cell Carcinoma3


title: Lung Squamous Cell Carcinoma5


title: Lung cancer Large Cell Carcinoma1


title: Lung Squamous Cell Carcinoma6


title: Lung cancer ADK3


title: Lung cancer ADK5


title: Lung cancer ADK45


title: Lung Squamous Cell Carcinoma1


title: Lung cancer ADK1


title: Duke_DnaseSeq_Mel_2183

status: Public on Sep 25 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

data_processing:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase

Raw data witheld due to privacy concerns.

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromDnase

tag: datatype

value: DnaseSeq

tag: datatype description

value: DNaseI HS Sequencing

tag: labversion

value: baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff:0.05

tag: cell

tag: cell organism

value: human

tag: cell description

value: Melanoma Cell line

tag: cell karyotype

value: cancer

tag: cell sex

value: U

value: baseAlignCounts.pl v 1