title: undiff control_E

status: Public on Jan 01 2016

scan_protocol: As per HumanHT-12 v3 Expression BeadChip - Illumina

data_processing: Data analysis was performed using Bioconductor software packages. The lumi package (Du et al. 2008; Lin et al. 2008) was used to perform variance stabilizing transformation and quantile normalization, and the limma package (Smyth 2004) was used for linear modeling and differential expression analysis.  Log2-fold gene expression changes were obtained, and p-values were adjusted according to the Benjamini-Hochberg method and considered significant if p-value < 0.01. We performed hypergeometric testing on Gene Ontology (GO) terms using the GOstats package (Gentleman 2004) and adjusted p-values for multiple testing, considering results

extract_protocol: RNA was isolated from samples collected in TRIzol® Reagent according to the single-step guanidinium acid-phenol method. RNA was further purified using the RNeasy Mini kit according to the manufacturer’s instructions, which included an on-column DNase treatment. RNA integrity was evaluated with the Agilent Bioanalyzer. The cDNA reverse transcription, cDNA purification, in vitro transcription of cRNA, and microarray hybridization, staining, and scanning were performed by the Yale Center for Genomic Analysis.  We used Illumina Human WG6 v3 Expression BeadChip arrays, which have 48,804 probe sets, of which over 27,000 represent coding transcripts with well-established annotation.  Sampel sizes were as follows; Depolarized groups, n=3; non-depolarized osteogenic control group, n=3; undifferentiated control group, n=2.

treatment_protocol: Whole bone marrow aspirate from a 25 year-old healthy man was purchased from Lonza through their Research Bone Marrow Donor Program, following approved guidelines of informed consent as previously documented (Sundelacruz et al. 2008, 2013b). Aspirate was plated at a density of 10 mL of aspirate per cm2 in control medium (DMEM with 10% fetal bovine serum (FBS), penicillin (100 U/mL), streptomycin (100 mg/mL), and 0.1 mM nonessential amino acids) supplemented with basic fibroblast growth factor (1 ng/mL) (Invitrogen). Cells were maintained in a humidified incubator at 37°C with 5% CO2. The hMSCs were isolated on the basis of their adherence to tissue culture plastic and were used for experiments between passages two and four.

value: Osteogenic (OS) cells


title: high K (depol)_D

type: RNA

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

country: USA

institute: University of Florida

hyb_protocol: Illumina Human WG6 v3 Expression BeadChip arrays

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole bone marrow aspirate from a 25 year-old healthy man was purchased from Lonza through their Research Bone Marrow Donor Program

label_protocol: As per HumanHT-12 v3 Expression BeadChip - Illumina

tag: gender

value: male

tag: tissue


title: Control

hyb_protocol: Microarray hybridization was performed using the Affy 3’ IVT Express Kit.

scan_protocol: Affymetrix GeneChip Fluidics, ArrayStation and Scanner as per manufacture protocol

data_processing: All microarray data were analyzed using Bioconductor packages in R. The quality of hybridized arrays was assessed using Affymetrix guidelines on the basis of scaling factor, background value, mean intensity of chip, and 3’ to 5’ ratios for spike-in control transcripts. The outlier analysis was performed using unsupervised clustering and principal component analysis. All high quality arrays were normalized using the MAS5 algorithm developed by Affymetrix. The absent/present calls for the transcripts were calculated using the MAS5 algorithm. The differentially expressed transcripts were identified on basis of fold change and Affymetrix transcripts calls. Transcripts with increased abundance were considered to be those that changed >2 fold in the experimental group compared to the control group, with present call in the experimental group. Transcripts with decreased abundance were considered to be those that changed >2 fold in the experimental group compared to the control group, with present call in control group. Differentially expressed transcripts were identified using customized script in R. The list of differentially expressed genes were annotated by Affymetrix.

organism: Xenopus laevis

source_name: embryos, stage 11

label_protocol: Affy 3’ IVT Express Kit.

extract_protocol: Microarray hybridization target preparations was performed using the Affy 3’ IVT Express Kit (Affymetrix, Santa Clara, CA) as per manufacturer’s protocol. Fragmented and biotin labeled/amplified RNA was hybridized in the GeneChip Xenopus laevis Genome 2.0 array (Affymetrix, Santa Clara, CA) as per the protocol provided by manufacturer.  The Affymetrix GeneChip® X. laevis Genome 2.0 Array has 32,400 probe sets representing more than 29,900 X. laevis transcripts. The quality of hybridized arrays was assessed using Affymetrix guidelines on the basis of scaling factor, background value, mean intensity of chip and 3’ to 5’ ratios for spike-in control transcripts. The outlier analysis was performed using unsupervised clustering and principal component analysis. All high quality arrays were normalized using MAS5 algorithm developed by Affymetrix. The absent/present calls for the transcripts were calculated using the MAS5 algorithm. The differentially expressed transcripts were identified on basis of fold change and Affymetrix transcripts calls. Overexpressed transcripts were at least 2-fold in the experimental group compared to the control group with present call in the experimental group. Under-expressed transcripts were at least 2 fold changed in the experimental group compared to the control group with present call in control group. Differentially expressed genes were annotated using the Affymetrix database or by performing BLAST analysis. All microarray data were analyzed using Bioconductor packages in R.

treatment_protocol: The procedure was performed by the Beth Israel Deaconess Medical Center (BIDMC) Genomics core (Boston, MA) at Harvard University.  A miRNeasy Mini  kit (Qiagen, Hilden, Germany) was used to isolate total RNA from the Xenopus embryos. There were 50 embryos pooled for each experimental sample.

tag: developmental stage

value: embryos, stage 11

tag: construct

value: Control


title: high K (depol)_F


title: 666 chimera

value: 666 chimera


title: undiff control_F


title: GlycineR

value: GlycineR


title: osteogenic control_B


title: osteogenic control_C


title: high K (depol)_E


title: osteogenic control_A


title: 1dpiT_2

hyb_protocol: Hybridizations were performed according to the GeneChip 3’IVT Express Kit User Manual:  12.5µg fragmented and labelled aRNA were hybridized for 17 hours at 45 degrees and 60 rpm. Arrays were washed and stained using the GeneChip Fluidic station FS450 with the wash and stain protocol FS450_0001.

scan_protocol: The Arrays were scanned using the Affymetrix GCS3000 System (Scanner). Cel files containing normalized intensity data (RMA normalisation) were generated using the Gene Expression Console (Affymetrix).

organism: Ambystoma mexicanum

source_name: spinal cord, 1d post Ivermectin injection

label_protocol: Microarrays were carried out in triplicate using a custom made axolotl Affymetrix Chip, and arrays were processed at the microarray facility at the MPI-CBG, Dresden Germany. Briefly, for each sample (n=3 / experimental group), 150 ng total RNA was used to reverse transcribe double stranded cDNA and subsequently in-vitro transcribe Cy3-labelled target cRNA as per the GeneChip 3’IVT Express Kit.

extract_protocol: Total RNA extraction for microarray analysis was done using TRIzol® Reagent. RNA was resuspended in 20µm of RNAase free water

treatment_protocol: All axolotls used in these experiments were bred in the axolotl facility at the University of Minnesota under the IACUC protocol #1201A08381. Axolotls of 2–3 cm were used for all in vivo experiments, and animals were kept in separate containers and fed daily with artemia; water was changed daily. Animals were anesthetized in 0.01% p-amino benzocaine (Sigma) before microinjection was performed.      Experimental Design: Ivermectin injection  Ivermectin or vehicle only (water) was pressure injected into the central canal of the spinal cord, and this was visualized by the addition of Fast Green into the solution. Directly after injection, a portion of the spinal cord was surgically removed and the animals were placed back into water in individual containers. One day post injury (1dpi) animals were anesthetized again and the area of the injury was removed. Tissue from 10 animals were pooled for each microarray replicate.

value: spinal chord


title: 1dpiT_3

data_processing: Cel files containing normalized intensity data (RMA normalisation) were generated using the Gene Expression Console (Affymetrix).


title: 1dpiT_1


title: 1dpi_1

source_name: spinal cord, 1d post crush


title: 1dpi_3


title: ouabain (depol)_A


title: 0dpi_2

source_name: Uninjured spinal cord tissue


title: 1dpi_2


title: 0dpi_1


title: undiff control_D


title: ouabain (depol)_B


title: hNEC, Vehicle, IAV, 48h, F2

status: Public on Dec 31 2015

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

state: MD

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

description: gene expression data

hyb_protocol: Hybridization to Affymetrix Human Gene ST 2.0 arrays was performed at 45oC for 16 hours at 60 rpm in the Affymetrix rotisserie hybridization oven.  The signal amplification protocol for washing and staining of eukaryotic targets was performed in an automated fluidics station (Affymetrix FS450) using Affymetrix protocol FS450_0002.

scan_protocol: The arrays were scanned in the GCS3000 laser scanner with autoloader and 3G upgrade (Affymetrix). Quality assessment of hybridizations and scans was performed with Expression Console software (Affymetrix).

data_processing: The data were analyzed with Partek Genomics Suite version 6.0 using Affymetrix default analysis settings and virus infected samples were normalized to matched mock samples. Quantile Normalization using RMA Background correction, with  Log Base 2, and   Median Polish probeset summarization in Partek Genomics Suite 6.0.

source_name: non-diseased human nasal epithelial tissue

label_protocol: Biotinylated ss-cDNA were prepared according to the Affymetrix GeneChip WT PLUS Reagent Kit according to the manufacturer’s recommended protocol from 100 nanograms of total RNA.

growth_protocol: Primary human nasal epithelial cells were obtained from non-diseased human donor tissue during endoscopic sinus surgery. The cells were differentiated at an air-liquid interface (ALI) in 24-well Falcon filter inserts (0.4-μM pore; 0.33cm2) coated with human type IV placental collagen.

extract_protocol: Trizol Reagent and the PureLink RNA Mini kit (Ambion/Life Technologies) were used for extraction and purification of RNA. Cells were processed according to the manufacturer’s protocol including the on-column DNAse treatment. Following elution of purified RNA from the PureLink columns with Nuclease-free water, quantitation was performed using a NanoDrop spectrophotometer and quality assessment determined by RNA Nano LabChip analysis on an Agilent BioAnalyzer 2100 or RNA Screen Tape on an Agilent TapeStation 2200.

treatment_protocol: Once fully differentiated, hNECs from females were exposed to E2 (10nM) or vehicle for 24h. Just prior to infection, the apical surface of hNEC cultures was washed with Dulbecco's phosphate-buffered saline with calcium and magnesium. The cultures were infected via the apical chamber with a multiplicity of infection (MOI) of 0.1 TCID50/cell or mock infected at 32°C in 200 ul of infection media.  After 2 hours, the inoculums were aspirated and the apical surfaces washed twice with DPBS before returning the cells to incubate at 32°C.

value: primary nasal epithelial cells

tag: treatment

value: Vehicle

tag: infection status

value: Infected

tag: hours post infection

tag: Sex

value: female


title: hNEC, E2, IAV, 24h, F4

description: gene expression data


title: hNEC, E2, IAV, 48h, F5

description: gene expression data


title: hNEC, Vehicle, IAV, 48h, F5

description: gene expression data


title: hNEC, E2, IAV, 24h, F3

description: gene expression data


title: hNEC, E2, IAV, 48h, F1

description: gene expression data


title: hNEC, E2, IAV, 24h, F1

description: gene expression data


title: hNEC, Vehicle, IAV, 24h, F5

description: gene expression data


title: hNEC, E2, IAV, 48h, F4

description: gene expression data


title: hNEC, Vehicle, IAV, 48h, F3

description: gene expression data


title: hNEC, Vehicle, IAV, 48h, F4

description: gene expression data


title: hNEC, E2, IAV, 48h, F3

description: gene expression data


title: hNEC, Vehicle, IAV, 24h, F3

description: gene expression data


title: hNEC, E2, IAV, 24h, F5

description: gene expression data


title: 0dpi_3


title: hNEC, Vehicle, IAV, 24h, F2

description: gene expression data


title: hNEC, E2, IAV, 48h, F2

description: gene expression data


title: hNEC, Vehicle, IAV, 48h, F1

description: gene expression data


title: Non-glial colonic cells

status: Public on Sep 01 2015

type: SRA

city: Athens

first: Brad

last: Nelms

state: GA

address: 120 E Green St

institute: University of Georgia

library_source: transcriptomic

data_processing:
Illumina Casava 1.8.2 software used for basecalling
Sequence reads were trimmed to remove the last 1 bp of the first read and the last 10 bp of the second read, then any reads that mapped to a “contamination library” by bowtie2 were removed (“contamination library” = ribosomal sequences, PhiX DNA, and chrM from the mm10 build)
Remaining reads were mapped to mm10 with tophat2 and parameters -r -35 --mate-std-dev 30 -G genes.gtf
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using CuffLinks with parameters -N -u -g genes.gtf -b genome.fa
Differential expression between GFP+ and GFP- samples was calculated using CuffDiff with parameters -b genome.fa -N genes.gtf, treating samples from ileum and colon as biological replicates
Genome_build: mm10
Supplementary_files_format_and_content: Output from CuffDiff; tab-delimited text files including FPKM for GFP+ (enteric glia) and GFP- (non-glia) samples, log2 fold change, and p-values for differential expression

organism: Mus musculus

source_name: Colon

extract_protocol:
Ileum and colon were dissected from PLP1-eGFP mice, treated with collagenase/dispase/trypsin to generate single cell suspensions, and sorted by FACS to purify GFP+ glial cells away from GFP-negative non-glial cells. Cells were sorted directly into Trizol. Cells from 3 animals/sample were pooled, and RNA was extracted using a modified version of the Qiagen RNAeasy Micro kit.
Per manufacturer's instructions, Integen-X Low Input Kit was used to create a library from 10ng of RNA per sample. Libraries were sequenced by Illumina HiSeq 2000 to generate 100bp paired end reads.

tag: strain

value: FVBN

value: colon

tag: facs population

value: GFP-

tag: age


title: Ileal glia

source_name: Ileum

value: ileum

value: GFP+


title: Non-glial ileal cells


title: Colonic glia


title: hNEC, E2, IAV, 24h, F2

description: gene expression data


title: HEY Ovarian Cancer 2D monolayer_01

status: Public on Apr 18 2016

hyb_protocol: cDNA and then amplified and labeled with biotin using Affymetrix 3’IVT Expression System according to the manufacturer’s instructions. Hybridization with the biotin-labeled RNA, staining, and scanning of the chips followed the prescribed procedure outlined in the Affymetrix technical manual.

scan_protocol: The Arrays were scanned using the Affymetrix GCS3000 System (Scanner). Cel files containing normalized intensity data (RMA normalization) were generated using the Gene Expression Console (Affymetrix).

data_processing: Signal intensity was scaled to an average intensity of 500 during comparison analysis.

source_name: HEY Ovarian Cancer 2D monolayer

label_protocol: RNA was converted to cDNA and then amplified and labeled with biotin using Affymetrix 3’IVT Expression System according to the manufacturer’s instructions.

growth_protocol: The HEY human ovarian cancer cell line was authenticated by short tandem repeat (STR) DNA profiling (Genetica, Inc.) and was compared to ATCC and previously published profiles (Gynecol Oncol. Oct 2012; 127(1): 241–248. ) Cells were cultured in a humidified incubator containing 5% CO2 at 37oC in RPMI with 10% fetal bovine serum and 1% Pen-Strep-Glutamine.  Spheroid formation was accomplished through the hanging drop method.  Briefly, trypsinized HEY cells were resuspended at 1 x 106 cells/mL in supplemented RPMI.  Multiple 25 µl droplets of the cell solution were then placed onto plate lids, inverted, and incubated for 72 hours to allow cells to aggregate into spheroids.

extract_protocol: HEY Human ovarian carcinoma cells treated with TGF-β were cultured on a 2-dimensional substrate or 3-dimensional substrate as described above.  Replicates of 4 separate experiments were performed on 4 different culturing days, cells isolated and stored in RNAlater Soln (Ambion) for no more than 7 days.  Up to 100µg of total RNA was isolated from all 8 samples using Qiagen’s RNeasy Mini Kit according to the manufacturer’s instructions. RNA integrity was verified with 1µl of total RNA on RNA 6000 chips (Agilent) using The Agilent 2100 Bioanalyzer.

treatment_protocol: To induce EMT, a final concentration of 10 ng/µl TGFβ was added to cells and incubated for 72 hours as monolayer cell culture or hanging drops during the creation of spheroids.  Following incubation, monolayer cells and spheroids were photographed using an Evos® FL Cell Imaging microscope (ThermoFisher Scientific) and then collected in 1X PBS.

tag: cell line

value: HEY Ovarian Cancer cells

tag: agent

value: TGFβ

tag: culture conditions

value: 2D monolayer


title: hNEC, Vehicle, IAV, 24h, F4

description: gene expression data


status: Public on Nov 03 2015

source_name: Control stage 45 (free-swimming tadpole).

extract_protocol: Embryos (collected N=10 per eppendorf tube, 5 biological replicates) washed in RNase and DNase free water were homogenized in TRIzol reagent (Life Technologies). Homogenized samples were stored at -80°C for up to one month. Total RNA was extracted according to the manufacturer’s instructions (Life Technologies).

treatment_protocol: Embryos were exposed in 0.1 X MMR from NF Stage 10 to NF Stage 45 to ivermectin (Sigma), 1 µM; 2’5’-Dideoxyadenosine (Sigma), 500 µM; Forskolin, 5 µM; Melanocyte stimulating hormone release inhibiting factor, 25 µM; SHU 9119, 500 nM. All compounds were obtained from Tocris, unless otherwise noted and prepared in Millipure (18 MΩ) water unless indicated. All drug treatments were performed using embryos from mixed batches of fertilizations, using at least 3 biological replicates. Control experiments were performed using embryos in normal media (0.1X MMR).

value: stage 45 (free-swimming tadpole).

value: larvae

tag: treated with

value: ivermectin from NF stage 10 onwards


title: Treatment stage 15 (early neurula)

source_name: Treatment stage 15 (early neurula)

value: stage 15 (early neurula)

value: developing embryo


title: C. elegans WT rep2

status: Public on Dec 29 2015

city: Vancouver

first: Stefan

last: Taubert

state: BC

address: 950 W 28th Ave, CMMT Room 2024

department: Medical Genetics

country: Canada

institute: UBC

description: Gene expression in 4th larval stage

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent).

data_processing: This dataset was normalized using the quantile normalization method (Bolstad et al., 2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization. A small number of probes (245) have replicate spots, and these were summarized by taking the median intensity. All arrays were of good quality and had similar foreground and background signal distributions for both mRNA and control probes. This suggests that quantile normalization is appropriate.  To identify differentially expressed genes, a linear model was fit to the comparison to estimate the mean M values and calculate moderated t-statistic, B statistic, false discovery rate and p-value for each gene for the comparison of interest. Adjusted p-values (AdjP) were produced as described (Holm, 1979). All procedures were carried out using functions in the R package limma in Bioconductor (Gentleman et al., 2004; Smyth, 2004)

organism: Caenorhabditis elegans

source_name: N2 wild-type strain

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent). Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to the microarrays (Agilent GPL10094: Agilent-020186 C. elegans (V2) Gene Expression Microarray (Feature Number version)).

growth_protocol: We grew synchronized mid-L4 stage worms (wild-type N2 worms and cdk-8(tm1238) mutants that had been outcrossed 6 times to corresponding WT) that were grown on nematode growth medium (NGM)-lite agar plates seeded with Escherichia coli strain OP50, incubated at 20°C. 4 independent biological repeats (individual worms growths) were collected per strain. ~4000 worms/sample were harvested in M9, washed 3x15ml M9, flash-frozen in liquid N2 and then stored in a -80oC freezer until RNA processing

extract_protocol: RNA was extracted by the Trizol extraction method as described in Taubert S et al., PLoS Genetics 2008 (PMID: 18454197). RNA quality was assessed on an Agilent 2100 Bioanalyzer using a Pico Chip (Agilent Technologies, Palo Alto, CA).

treatment_protocol: No treatment. WT vs mutant comparison.

value: whole worm

value: L4 stage (synchronized)

tag: genotype/variation

value: wild-type


title: C. elegans WT rep1

description: Gene expression in 4th larval stage


title: C. elegans cdk-8(tm1238) rep1

description: Gene expression in 4th larval stage

source_name: cdk-8( tm1238) mutant strain L4 stage synchronized


title: Control stage 15 (early neurula)

source_name: Control stage 15 (early neurula)


title: hNEC, Vehicle, IAV, 24h, F1

description: gene expression data

value: primary nasal epithelial cells

value: Vehicle

value: Infected

value: female


title: C. elegans WT rep4

description: Gene expression in 4th larval stage


title: C. elegans cdk-8(tm1238) rep4

description: Gene expression in 4th larval stage


title: C. elegans WT rep3

description: Gene expression in 4th larval stage


source_name: Treatment stage 45 (free-swimming tadpole).


title: C. elegans cdk-8(tm1238) rep3

description: Gene expression in 4th larval stage


title: C. elegans cdk-8(tm1238) rep2

description: Gene expression in 4th larval stage


title: 19.5 mg/kg Se Tank A Fish 2

status: Public on Jun 30 2015

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used. 1.54 ug of Cy3-labeled cRNA was used.

scan_protocol: Microarrays were kept in the dark until scanned at 5 um, channel G, Agilent HD (61x21.6mm) using the Agilent DNA Microarray Scanner with SureScan High ResolutionTechnology.

data_processing: Agilent Feature Extraction Software (v10.7) was used (GRID:028639_D_F_20100525). Normalized signal intensity provided here is Loess Normalization.

organism: Oncorhynchus mykiss

source_name: Liver; Dietary Organic Selenium

label_protocol: Agilent one color protocol for Cy3 following manufacturer's protocol

extract_protocol: Trizol protocol for total RNA following manufacturer's protocol

treatment_protocol: Dietary Organic Selenium exposure for 60 days

value: juvenile

value: liver


title: 31.8 mg/kg Se Tank A Fish 2


title: 31.8 mg/kg Se Tank B Fish 2


title: ouabain (depol)_C

value: male

value: Osteogenic (OS) cells


title: 31.8 mg/kg Se Tank A Fish 3


title: 19.5 mg/kg Se Tank B Fish 3


title: 19.5 mg/kg Se Tank B Fish 1


title: 31.8 mg/kg Se Tank A Fish 1


title: 31.8 mg/kg Se Tank C Fish 1


title: 19.5 mg/kg Se Tank C Fish 3


title: 31.8 mg/kg Se Tank C Fish 2


title: 19.5 mg/kg Se Tank C Fish 2


title: 10.7 mg/kg Se Tank C Fish 1


title: 31.8 mg/kg Se Tank B Fish 3


title: 19.5 mg/kg Se Tank C Fish 1


title: 19.5 mg/kg Se Tank A Fish 1


title: 31.8 mg/kg Se Tank C Fish 3


title: 19.5 mg/kg Se Tank B Fish 2


title: 7.1 mg/kg Se Tank B Fish 2


title: 7.1 mg/kg Se Tank C Fish 1


title: 31.8 mg/kg Se Tank B Fish 1


title: 10.7 mg/kg Se Tank A Fish 2


title: 10.7 mg/kg Se Tank A Fish 1


title: 10.7 mg/kg Se Tank C Fish 3


title: 7.1 mg/kg Se Tank B Fish 3


title: 10.7 mg/kg Se Tank B Fish 2


title: 7.1 mg/kg Se Tank C Fish 3


title: 7.1 mg/kg Se Tank B Fish 1


title: 10.7 mg/kg Se Tank A Fish 3


title: 10.7 mg/kg Se Tank B Fish 3


title: h T3_21

status: Public on Jun 17 2015

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software 10.7.3.1 was used to extract raw data.

data_processing: Normalized signal intensity provided was done by quanitle normalization; data were filterd at 1.5 prior to ANOVA

organism: Danio rerio

source_name: Liver

label_protocol: Agilent one color protocol for Cy3

extract_protocol: Trizol protocol for total RNA

value: Liver

value: high chlorothalonil


title: h T3_26


title: l T2_8

value: low chlorothalonil


title: l T2_19


title: Control Tank C Fish 3


title: 7.1 mg/kg Se Tank A Fish 1


title: c T1_3

value: control


title: h T3_11


title: c T1_23


title: Control Tank B Fish 3


title: c T1_10


title: Control Tank A Fish 2


title: c T1_19


title: c T1_24


title: l T2_6


title: Control Tank B Fish 2


title: Control Tank C Fish 1


title: 7.1 mg/kg Se Tank A Fish 3


title: l T2_17


title: c T1_25


title: Control Tank A Fish 3


title: l T2_22


title: h T3_14


title: Control Tank C Fish 2


title: Control Tank B Fish 1


title: AOCS_172

status: Public on May 19 2015

type: genomic

city: Herston

first: Ann-Marie

last: Patch

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Raw data for arrays used for methylation analysis

hyb_protocol: Samples were hybridized to Infinium Human Methylation 450K BeadChips (Illumina) according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned on Iscan (Illumina)

data_processing: Data was background corrected, normalized to internal controls and QC was performed at the probe and sample level. COMBAT was used to remove batch effects (Johnson et al., 2007)

molecule: genomic DNA

source_name: Fallopian Tube Cells

label_protocol: Bisulfite converted genomic DNAwas whole genome amplified and labeled using Illumina protocol

extract_protocol: DNA was extracted from fresh frozen tissues using AllPrep DNA/RNA Mini Kit (Qiagen). Genomic DNA (500ng) was bisulfite converted using EZ DNA methylation Kit (Zimo Research) following the manufacturer’s protocol with modification for Illumina Infinium Methyaltion arrays

value: Female

value: Fallopian Tube

tag: cell type

value: normal


title: MUS15

status: Public on May 15 2014

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

institute: University of Alberta

description: Gene expression in muscle biopsies from cancer patients.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent, using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities. The data was then imported into GeneSpring 7.3.1 and default normalization procedures, including a 75th percentile shift, were used.

source_name: muscle, female

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated using an RNeasy kit (Qiagen) according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: age (years)

tag: incidence site

value: Benign

tag: height (cm)

tag: preoperative weight (kg)

tag: bmi


title: MUS20

source_name: muscle, male

value: Male

value: Pharynx


title: MUS52

value: Ovary


title: MUS13

value: Uterus


title: MUS53


title: MUS22

value: Kidney


title: MUS10


title: MUS21


title: MUS12


title: MUS19

value: Lip and oral cavity


title: MUS09


title: MUS11


title: MUS18


title: MUS14


title: MUS17

value: Peritoneum


title: MUS37


title: MUS35


title: AOCS_178

tag: gender

tag: tissue


title: AOCS_176


title: AOCS_175


title: MUS08

tag: Sex


title: AOCS_174


title: AOCS_167_ICGC_DBDE_20130904_028

source_name: Ascites

value: Ascites

value: high grade serous ovarian cancer


title: AOCS_167_ICGC_DBDE_20130904_024

source_name: Tumourmetastasistodistantlocation

value: Tumourmetastasistodistantlocation


title: AOCS_167_ICGC_DBDE_20130904_027


title: AOCS_139_ICGC_DBDE_20130729_001

source_name: TumourMetastasisToDistantLocation

value: TumourMetastasisToDistantLocation


title: AOCS_177


title: M4266

value: Colon


title: M5028


title: M5019

value: Rectum


title: AOCS_173

value: Female


title: M4236


title: M4275


title: M4219

value: Pancreas


title: M4225


title: MUS07

value: Skin


title: M5017

value: Benign


title: AOCS_139_ICGC_DBDE_20130729_002


title: M4187

value: Male


title: M4255


title: M4161

value: Appendix


title: M4260


title: M4280

value: Biliary Tract, other & unspecified


title: M4282

value: appendix


title: M4177


title: M4245


title: M4249


title: AOCS_139_ICGC_DBDE_20130729_003


title: M4158


title: M4141


title: M4153


title: M4140


title: M4152


title: M4130


title: M4125


title: M4136

value: Liver & Intrahepatic Bile Ducts


title: M4108


title: M4107


title: M4109


title: M4085


title: M4123

value: Stomach


title: M4118


title: M4086


title: M4117


title: M4120


title: M4102


title: M4104


title: M4098


title: M4090


title: M4099


title: M4082


title: M4132


title: M4106


title: M4097


title: M4113


title: M4080


title: M4069


title: M4111


title: M4093


title: M4063

value: Rectosigmoid Junction


title: M4064

value: Gallbladder


title: M4057


title: M4059


title: M4048

value: Cecum


title: M4060


title: M4018


title: M4022


title: M4025

value: Ilium


title: M4001


title: M3070


title: M4036


title: M4052


title: M3075


title: M3068


title: M4054


title: M4028


title: M4020


title: M4026


title: M4021


title: M4014


title: M4004


title: M4005


title: M4234


title: M4050


title: M4034


title: M4287


title: M4056


title: M3071


title: M3060


title: M3055


title: M3065


title: M3057


title: M3053


title: M3047


title: M3037


title: M3009


title: M3023


title: M3056


title: M3025


title: M3061


title: M3008


title: M3031


title: M3019


title: M3005


title: M3038


title: M3007


title: M3043


title: M3021


title: M3027


title: M3026


title: M3016


title: M3050


title: M3034


title: M3033


title: M4070


title: M3013


title: M3049


title: M3002


title: M2070


title: M3032


title: M3001


title: M2066


title: M2060


title: M1014


title: M3003


title: Tshz1 mutant #3 [7018844095_E]

status: Public on Apr 01 2014

city: Heidelberg

first: Hagen

last: Wende

address: Im Neuenheimer Feld 366

department: Institute of Pharmacology

country: Germany

institute: Heidelberg University

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio

source_name: mouse olfactory bulb

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: strain

value: C57/BL6;129/Ola; CD1 mixed

tag: genotype nestin

value: +/Cre

tag: genotype tshz1

value: flox/GFP

value: 30 days

value: olfactory bulb


title: Tshz1 mutant #2 [7018844095_C]

description: replicate 2

tag: age


title: Tshz1 mutant #6 [7018844099_C]

description: replicate 6


title: Tshz1 mutant #5 [7018844099_A]

description: replicate 5


title: Tshz1 mutant #1 [7018844095_A]

description: replicate 1


title: M2069

value: Female


title: control #5 [7018844099_B]

description: replicate 5

value: flox/+


title: control #8 [7018844099_H]

description: replicate 8


title: control #4 [7018844095_H]

description: replicate 4


title: control #2 [7018844095_D]

description: replicate 2


title: Tshz1 mutant #4 [7018844095_G]

description: replicate 4


title: acH2AZ_mES_ChIPSeq

status: Public on Jul 20 2012

city: Boston

first: Kevin

last: Dong

state: MASSACHUSETTS

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

description: v6.5- mouse embryonic stem cells

library_source: genomic

data_processing:
ChIP-Seq reads for mouse and human were aligned to reference assemblies mm8 and hg18, respectively.
Bowtie version 0.12.8 was used with the default parameters, with reads discarded if they aligned to more than 10 places.
To create density files, the reads were extended to 200 bp and converted to BigWig using BedTools and UCSC wigToBigWig.
Supplementary_files_format_and_content: BigWig files containing the read densities for all regions.

growth_protocol:
Mouse v6.5 ES cells were cultured on fibroblast feeders in DMEM (Sigma) with 15% fetal bovine serum (Hyclone), GlutaMax (Invitrogen), MEM non-essential amino acids (Invitrogen), pen/strep (Invitrogen), ESGRO (Chemicon) and 2-mercaptoethanol (Sigma), incubating at 37oC, 5% CO2 [16]. Prior to harvest, these cells were passaged 2-3 times on feeder-free gelatinized tissue culture plates.
Mouse NP cells were generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).
Human H1 ES cells were cultured in TeSR media on Matrigel by Cellular Dynamics International. Cells were split with dispase and harvested at a passage number between 30 and 40. Prior to harvest, cells were karyotyped and stained for Oct4 to confirm pluripotency.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA or protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Genome Analyzer or HiSeq following the manufacturer's protocols.

value: Pluripotent embryonic stem cells

tag: passage

value: passage 5-10

tag: chip antibody

value: Acetyl-H2A.Z (Abcam ab18262)

value: 129SVJae x C57BL6


title: RNAPII_mES_ChIPSeq

description: v6.5- mouse embryonic stem cells

value: RNAPII (CTD4H8) (Covance MMS-128P)


title: H2AZ_mES_ChIPSeq

description: v6.5- mouse embryonic stem cells

value: H2A.Z (Millipore 07-594)


title: acH2AZ_mNP_ChIPSeq

description: Neural progenitor cells

value: ES-derived neural progenitor cells

value: passage 8-12


title: H2AZ_mNP_ChIPSeq

description: Neural progenitor cells


title: H2A.Z_hES_ChIPSeq

description: H1-human embryonic stem cells

value: H1 human embryonic stem cells

value: passage 30-40


title: Tshz1 mutant #8 [7018844099_G]

description: replicate 8

value: C57/BL6;129/Ola; CD1 mixed


title: TFIID_mES_ChIPSeq

description: v6.5- mouse embryonic stem cells

value: TFIID(TBP) (Santa Cruz sc-273X)


title: control #6 [7018844099_D]

description: replicate 6

value: +/Cre


title: H1_WCE_1

status: Public on Dec 23 2011

description: H1 ChIP Input Control

data_processing:
Alignment: Sequence reads were aligned to the human genome reference (hg19) using MAQ version 0.7.1 (Li et al., 2008, Genome Research 18, 1851-1858) with default parameters.  Reads mapping to multiple positions in the genome were placed randomly at one of those locations.
Read Density Maps:  BAM files were processed to WIG format using the 'count' command of igvtools (http://www.broadinstitute.org/igv/igvtools -- Robinson, et al. Integrative Genomics Viewer. Nature Biotechnology 29, 24-26 (2011)).  Reads were extended to 200 bp using the -e parameter, otherwise defaults were used.  The WIG files were then processed to BIGWIG format using the UCSC wigToBigWig utility (available here: http://hgdownload.cse.ucsc.edu/admin/exe/) with the -clip option specified.
Peak calling: Enriched intervals (binding sites) were identified using QuEST (Valouev et al., 2008, Nature methods 5, 829-834) and MACS (Zhang et al., 2008, Genome biology 9, R137). A control dataset derived by sequencing of at least two un-enriched input DNA samples (whole cell extract, WCE) was used to define a background model for binding assessment. These procedures yielded a list of enriched intervals for each CR, together with an estimate of statistical significance. As a first step, we retained all peaks with p < 10-8 or estimated FDR below 5%. We then applied a post-processing step, consolidating all the peaks called by the two algorithms, as described previously (Novershtern et al., 2011, Cell 144, 296-309). We call a peak only if it was found by either one method in at least two replicate ChIP-seq experiments, or by both methods in at least one replicate. We considered peaks to be overlapping if they are within a distance of 50bp.

source_name: H1 hESCs-WCE

growth_protocol: K562 erythrocytic leukaemia cells (ATCC CCL-243) were grown according to standard protocols in RPMI 1640 media (Invitrogen, 22400105) supplemented with 10% fetal bovine serum (FBS, Atlas Biologicals, F-0500-A) and 10% Penicillin/Streptomycin (Invitrogen, 15140122); H1 ES cells were grown in TeSR media on Matrigel (Cellular Dynamics), as described previously (Ernst, J., et al. (2011). Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49).

extract_protocol: Libraries of CR ChIP samples were prepared according to a modified version of the Illumina Genomic DNA protocol, as described previously (Mikkelsen et al., 2007). Briefly, ChIP DNA was ligated to Illumina adaptors and subjected to 22 cycles of PCR amplification. Amplified products between 200 and 800 bp were purified on a 2% agarose gel. Roughly 5 picomoles of DNA library was then applied to each lane of the flow cell and sequenced on Illumina GAII sequencers according to standard Illumina protocols.


title: H1_WCE_2

description: H1 ChIP Input Control

value: H1 ES cells were grown in TeSR media on Matrigel (Cellular Dynamics)


title: H1_SAP30

description: Chromatin IP against SAP30

source_name: H1 hESCs-SAP30 ChIP-seq

value: Active motif,3939731


title: control #3 [7018844095_F]

description: replicate 3

value: 30 days

value: olfactory bulb


title: control #1 [7018844095_B]

description: replicate 1

value: flox/+


title: H1_RBBP5_2

description: Chromatin IP against RBBP5

source_name: H1 hESCs-RBBP5 ChIP-seq


title: H1_SIRT6

description: Chromatin IP against SIRT6

source_name: H1 hESCs-SIRT6 ChIP-seq


title: H1_RBBP5_1

description: Chromatin IP against RBBP5


title: H1_SUZ12

description: Chromatin IP against SUZ12

source_name: H1 hESCs-SUZ12 ChIP-seq

value: Active motif,39357


title: H1_PHF8

description: Chromatin IP against PHF8

source_name: H1 hESCs-PHF8 ChIP-seq


title: H1_JMJD2A

description: Chromatin IP against JMJD2A

source_name: H1 hESCs-JMJD2A ChIP-seq


title: H1_JARID1C

description: Chromatin IP against JARID1C

source_name: H1 hESCs-JARID1C ChIP-seq


title: H1_HDAC6

description: Chromatin IP against HDAC6

source_name: H1 hESCs-HDAC6 ChIP-seq


title: H1_JARID1A_1

description: Chromatin IP against JARID1A

source_name: H1 hESCs-JARID1A ChIP-seq


title: H1_P300

description: Chromatin IP against P300

source_name: H1 hESCs-P300 ChIP-seq

value: Santa cruz, 48343 X


title: H1_HDAC2

description: Chromatin IP against HDAC2

source_name: H1 hESCs-HDAC2 ChIP-seq


title: H1_CHD1_1

description: Chromatin IP against CHD1

source_name: H1 hESCs-CHD1 ChIP-seq


title: H1_CHD1_2

description: Chromatin IP against CHD1


title: H1_EZH2

description: Chromatin IP against EZH2

source_name: H1 hESCs-EZH2 ChIP-seq

value: Active motif,39901


title: K562_WCE_2

description: K562 ChIP Input Control

value: K562 erythrocytic leukaemia cells (ATCC CCL-243)


title: K562_WCE_1

description: K562 ChIP Input Control


title: K562_WCE_3

description: K562 ChIP Input Control


title: K562_SIRT6

description: Chromatin IP against SIRT6

source_name: K562-SIRT6 ChIP-seq


title: K562_SUZ12

description: Chromatin IP against SUZ12

source_name: K562-SUZ12 ChIP-seq


title: K562_SAP30_2

description: Chromatin IP against SAP30

source_name: K562-SAP30 ChIP-seq


title: H1_JARID1A_2

description: Chromatin IP against JARID1A


title: H1_JARID1B

description: Chromatin IP against JARID1B

source_name: H1 hESCs-JARID1B ChIP-seq


title: H1_CHD7

description: Chromatin IP against CHD7

source_name: H1 hESCs-CHD7 ChIP-seq


title: K562_RNF2

description: Chromatin IP against RNF2

source_name: K562-RNF2 ChIP-seq


title: K562_REST

description: Chromatin IP against REST

source_name: K562-REST ChIP-seq


title: K562_RNAPIIS5P

description: Chromatin IP against RNAPIIS5P

source_name: K562-RNAPIIS5P ChIP-seq


title: K562_PHF8_2

description: Chromatin IP against PHF8

source_name: K562-PHF8 ChIP-seq


title: K562_RBBP5_1

description: Chromatin IP against RBBP5

source_name: K562-RBBP5 ChIP-seq


title: K562_PLU1_2

description: Chromatin IP against PLU1

source_name: K562-PLU1 ChIP-seq

value: A custom antibody


title: K562_RBBP5_2

description: Chromatin IP against RBBP5


title: Tshz1 mutant #7 [7018844099_E]

description: replicate 7

source_name: mouse olfactory bulb

value: flox/GFP


title: K562_RBBP5_3

description: Chromatin IP against RBBP5


title: control #7 [7018844099_F]

description: replicate 7


title: K562_PHF8_1

description: Chromatin IP against PHF8


title: K562_PLU1_1

description: Chromatin IP against PLU1


title: K562_PCAF

description: Chromatin IP against PCAF

source_name: K562-PCAF ChIP-seq


title: K562_P300

description: Chromatin IP against P300

source_name: K562-P300 ChIP-seq


title: K562_NSD2

description: Chromatin IP against NSD2

source_name: K562-NSD2 ChIP-seq


title: K562_MI2

description: Chromatin IP against MI2

source_name: K562-MI2 ChIP-seq


title: K562_KAT3A-CBP

description: Chromatin IP against KAT3A/CBP

source_name: K562-KAT3A/CBP ChIP-seq


title: K562_LSD1

description: Chromatin IP against LSD1

source_name: K562-LSD1 ChIP-seq


title: K562_JARID1C

description: Chromatin IP against JARID1C

source_name: K562-JARID1C ChIP-seq


title: K562_NCOR

description: Chromatin IP against NCOR

source_name: K562-NCOR ChIP-seq


title: K562_HDAC2_2

description: Chromatin IP against HDAC2

source_name: K562-HDAC2 ChIP-seq


title: K562_SAP30_1

description: Chromatin IP against SAP30

source_name: K562-SAP30 ChIP-seq


title: K562_HDAC6_1

description: Chromatin IP against HDAC6

source_name: K562-HDAC6 ChIP-seq


title: K562_HDAC6_2

description: Chromatin IP against HDAC6


title: K562_HDAC2_1

description: Chromatin IP against HDAC2


title: K562_HP1g

description: Chromatin IP against HP1g

source_name: K562-HP1g ChIP-seq


title: K562_HDAC1_1

description: Chromatin IP against HDAC1

source_name: K562-HDAC1 ChIP-seq

value: Santa cruz,6298X


title: K562_ESET

description: Chromatin IP against ESET

source_name: K562-ESET ChIP-seq

value: Santa cruz,166621X


title: K562_CHD1_2

description: Chromatin IP against CHD1

source_name: K562-CHD1 ChIP-seq


title: K562_EZH2

description: Chromatin IP against EZH2

source_name: K562-EZH2 ChIP-seq


title: K562_CHD1_1

description: Chromatin IP against CHD1


title: K562_CHD7

description: Chromatin IP against CHD7

source_name: K562-CHD7 ChIP-seq


title: K562_CBX2

description: Chromatin IP against CBX2

source_name: K562-CBX2 ChIP-seq


title: K562_HDAC1_2

description: Chromatin IP against HDAC1


title: YY1 ChIPSeq in V6.5 murine ES cells

status: Public on Nov 23 2010

data_processing:
Bed files:  Reads were aligned to the mm8 assembly using MAQ (version 0.7.1) with default parameters.  The MAQ output (http://maq.sourceforge.net/maq-manpage.shtml) was converted to BAM (http://samtools.sourceforge.net/SAM1.pdf).  All duplicate reads (reads mapping to the exact same genomic coordinates) were collapsed to one.  The BAM was converted to BED format as specified in the UCSC documentation (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).  The bed score field was calculated as (n/90)*1000, where n is the mapping quality score assigned by MAQ.  Any score calculated to be above 1000 was given a value of 1000.  The 'name' bed field was populated with the read name assigned by the sequencer.
WIG files:  WIG files were produced from BAM using the igvtools count command (http://www.broadinstitute.org/igv/node/173), using the -e parameter to extend the reads to 200 bp.  Default values were used for all other parameters.

source_name: Embryonic Stem Cells

extract_protocol: Described in Mikkelsen et al., Nature 2007. Chromatin was fixed and sheared to 200-600 bp using Branson Sonifer. After IP and adapter ligation library fragments of ~250 bp were isolated. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody catalog number

value: V6.5 on gelatin


title: YY1 ChIPSeq in Neural Progenitor cells

description: ES cells were differentiated into adherent neural cultures and plated on uncoated flasks in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

source_name: Neural Progenitor Cells

tag: cell type

value: ES-derived Neural Progenitor cells


title: K562_CBX8

description: Chromatin IP against CBX8

source_name: K562-CBX8 ChIP-seq


title: MoVB mouse vestibular sensory epithelia MPSS signature library

status: Public on Oct 01 2006

type: MPSS

city: Bethesda

first: Robert

last: Morell

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description:
Mouse vestibular tissue total RNA (MoVb.B16x) received from NIDCD was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4): 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634).  Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.
MoVb.B16x_sig21.5028W.d-20	6/4/2004	532451	14210	QC Passed
MoVb.B16x_sig21.5028T.d-20	6/2/2004	451211	11601	QC Passed
MoVb.B16x_sig21.5028W.a-20	5/27/2004	437296	10228	QC Passed
MoVb.B16x_sig21.5028T.c-20	5/25/2004	333984	7826	QC Passed
Total Beads successfully sequenced - 1754942

Processed Signatures - 13335

data_processing: Mean abundance for a signature derived from all MPSS runs for the sample, in transcripts per million (TPM)

source_name: Mouse vestibular sensory epithelia, male and female, total RNA

tag: Strain

tag: Age

value: 7 days

tag: Gender

value: male and female

tag: Tissue

value: vestibular sensory epithelia


title: MoSV stria vascularis MPSS library

description: Mouse vestibular tissue total RNA (MoVb.B16x) received from NIDCD was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4): 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634).  Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.

source_name: mouse stria vascularis

value: stria vascularis


title: MoCR mouse organ of Corti MPSS signature library

source_name: organ of Corti tissue

value: organ of Corti