title: abscission-R108-2 seeds Replicate 3

status: Public on Sep 24 2016

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

institute: INRAE

hyb_protocol: Hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnight. Slides were washed and dried prior to scanning.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche_NimbleGen MS200. DEVA Software v1.2.1 was used to extract pair_data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using R language, version 2.5.1 (R Development Core Team, 2011) and LIMMA package (Smyth G.K., 2005) from the Bioconductor project. For the processing steps, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse_transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine_3 (Cy3) or Cyanine_5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean_up column kits (Macherey_Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND_1000 (Nanodrop Technologies, DE, USA). Labelled samples (30 pmol) were combined and co_hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Medicago truncatula plants were grown at controlled temperature of 20/18°C 16 h light/dark. Seeds were then collected at different stages of development.

extract_protocol: Total RNAs were extracted from the frozen grinded seeds lots using the NucleoSpin Extract II, Total RNA Purification kit (Macherey-Nagel, GmbH & Co. KG, Germany) following manufacturer’s instructions

value: seed

tag: developmental stage

value: Seed abscission


title: vegfaa-/-

status: Public on Sep 25 2016

type: RNA

city: Bad Nauheim

first: Rubén

last: Marín-Juez

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute

description: Gene expression of vegfaa -/- ventricles

hyb_protocol: For the hybridisation the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) is used following the manufacture‘s protocol. For example, 600 ng cRNA is hybridised on a 8x60K microarray at 65 ◦C for 17 h using Agilent‘s recommended hybridisation chamber and oven. Finally the microarray is washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37◦C) Gene Expression Wash Buffer 2 for one minute.

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and 5 micron for HD Microarray formats, generating a 20 bit TIFF file respectively.

data_processing: Data of all samples are quantile normalised using the ranked median quantiles according to Bolstad et al. “A comparison of normalisation methods for high density oligonucleotide array data based on variance and bias”, Bioinformatics (19), 2003, Oxford Univ Press. Briefly, the mean signal of each target is ranked relative to all other targets. The ranked signal value is replaced with the median quantile value of the same rank. So the highest value in all samples becomes the mean of the highest values, the second highest value becomes the mean of the second highest values, and so on.

molecule: total RNA

organism: Danio rerio

source_name: vegfaa-/- ventricles

label_protocol: The Low Input QuickAmp Labeling Kit (Agilent Technologies) is used for generation of fluorescent cRNA (complementary RNA). By default cRNA is amplified by using oligo-dT primer for eukaryotic samples and a random primer for prokaryotic samples and labelled with cyanine 3-CTP following the manufacture‘s protocol.

extract_protocol: Total RNA was isolated using RNeasy Micro kit (Qiagen) following manufacturer’s instruction

tag: genotype/variation

value: vegfaa-/-

tag: tissue

value: ventricles

tag: age

value: 8 months


title: vegfaa+/+

description: Gene expression of vegfaa +/+ ventricles

source_name: vegfaa+/+ ventricles

value: vegfaa+/+


title: RNA from Met-low cells of B16-F10 cell line_2

city: Kanazawa

first: Kunio

last: Matsumoto

address: Kakuma

country: Japan

institute: Kanaawa University

description:
Gene Expression in Met-low cells of B16-F10 melanoma
Met-low_2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K (G4846A) 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 by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1  (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: B16-F10, Met-low cells, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low RNA Input Fluorescent Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: B16-F10 cell was cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was prepared using Sepazol reagent (Nakarai Tesque).  The quality of RNA samples were assessed by RNA 6000 nano kit (Agilent Bioanalyzer 2100).

treatment_protocol: B16-F10 cell were individually sorted and divided into Met-low or Met-high population using a FACS Aria II. Sorted cells were cultured for 3 days, independently.

value: Skin

tag: cell line

value: B16-F10 malignant melanoma cells

tag: sorted cells

value: Met-low cells


title: HDAC7 deficient pro-B cells, biological rep1

status: Public on Sep 26 2016

city: Barcelona

first: Maribel

last: Parra

state: Barcelona

address: Avda. Gran Via 199-203, L'Hospitalet de Llobregat

department: Cancer Epigenetics and Biology Programme (PEBC)

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

description: Gene expression data from HDAC7 deficient pro-B cells

hyb_protocol: PCR amplified biotinylated cDNA were hybridized against Affymetrix HT MG-430 PM Array Plate (Mouse Genome 430 PM strip)

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Affymatrix CEL files were background corrected and normalized using Bioconductor package “affy” using method rma.

label: biotin

source_name: Purified pro-B cells from HDAC7 deficient mice

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.

growth_protocol: B220+CD43+IgM- pro-B cells were isolated on a MoFlo sorter (Beckman-Coulter, Inc.) and resuspended in Trizol (Quiagen) reagent for further RNA extraction.

extract_protocol: RNA was extracted with a combination of Trizol and RNeasy minikit (Qiagen)

treatment_protocol: Biological triplicates of wold type and HDAC7 deficient pro-B cells.

tag: cell type

value: pro-B cells

tag: genotype

value: HDAC7 deficient


title: RNA from Met-high cells of B16-F10 cell line_1

description:
Gene Expression in Met-high cells of B16-F10 melanoma
Met-high_1

source_name: B16-F10, Met-high cells, replicate1

value: Met-high cells


title: abscission-abi5-2 mutant seeds Replicate 3

country: France

tag: tissus

tag: genetic background


title: RNA from Met-high cells of B16-F10 cell line_2

description:
Gene Expression in Met-high cells of B16-F10 melanoma
Met-high_2

source_name: B16-F10, Met-high cells, replicate2


title: abscission-abi5-2 mutant seeds Replicate 2


title: abscission-abi5-2 mutant seeds Replicate 1


title: abscission-R108-2 seeds Replicate 1


title: abscission-abi5-1 mutant seeds Replicate 3


title: abscission-R108-1 seeds Replicate 3


title: RNA from Met-low cells of B16-F10 cell line_1

description:
Gene Expression in Met-low cells of B16-F10 melanoma
Met-low_1

source_name: B16-F10, Met-low cells, replicate1


title: abscission-R108-1 seeds Replicate 1


title: wt pro-B cells, biological rep1

description: Gene expression data from wild type pro-B cells

source_name: Purified pro-B cells from wild type mice

value: wild type


title: abscission-abi5-1 mutant seeds Replicate 2


title: abscission-R108-1 seeds Replicate 2


title: 24dap-R108-2 seeds Replicate 1

value: 24 days after pollination


title: 24dap-R108-2 seeds Replicate 3


title: 24dap-abi5-2 mutant seeds Replicate 3


title: 24dap-abi5-2 mutant seeds Replicate 2


title: abscission-R108-2 seeds Replicate 2


title: 24dap-R108-2 seeds Replicate 2


title: abscission-abi5-1 mutant seeds Replicate 1


title: 24dap-abi5-2 mutant seeds Replicate 1


title: 24dap-R108-1 seeds Replicate 3


title: 24dap-abi5-1 mutant seeds Replicate 2


title: 24dap-abi5-1 mutant seeds Replicate 3


title: 24dap-R108-1 seeds Replicate 1


title: 24dap-abi5-1 mutant seeds Replicate 1


title: 16dap-R108-2 seeds Replicate 2

value: 16 days after pollination


title: 16dap-R108-2 seeds Replicate 3


title: 16dap-abi5-1 mutant seeds Replicate 1


title: blood-AR-rep9

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: 1190 Hornby Street

country: Canada

institute: PROOF Centre of Excellence

hyb_protocol: Affymetrix Human Genome U133 Plus 2.0 (Affymetrix, Inc, Santa Clara, CA, USA) microarrays were utilized at the Microarray Core Laboratory at Children’s Hospital, Los Angeles according to manufacturer instructions.

scan_protocol: standard Affymetrix protocol

data_processing: The microarrays were checked for quality using the “affy” (version 1.16.0) and “affyPLM” (version 1.14.0) BioConductor packages,40–42 as well as an internally developed method (Mahalanobis Distance Quality Control [MDQC],43 available in the “mdqc” Bionconductor package). Microarrays were first background-corrected, normalized and summarized to probe-set level data using the robust multichip average (RMA) method.44 All 54613 probe-sets were first submitted to a supervised, 2-class, univariate analysis (Significance Analysis of Microarrays) to identify potential differentially expressed probe-sets in whole blood.  A similar analysis was performed concurrently on the csSAM (sample composition) normalized whole blood expression data.

organism: Homo sapiens

source_name: PaxGene Wholeblood

label_protocol: standard Affymetrix protocol

extract_protocol: Whole blood RNA was extracted for selected samples. These samples were thawed, RNA isolated using PAXgene Blood RNA Kits (QIAGEN Inc, Germantown, MD, USA), and quality checked using an Agilent BioAnalyzer (Agilent Technologies Inc, Santa Clara, CA, USA).

treatment_protocol: Blood samples were collected in PAXgene tubes (PreAnalytiX, Hombrechtikon, Switzerland) and stored at -80°C until analysis.

tag: rejection status

value: AR

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: basophils


title: 16dap-abi5-2 mutant seeds Replicate 3


title: 16dap-R108-1 seeds Replicate 2


title: blood-NR-rep12

value: NR


title: blood-AR-rep8


title: 16dap-abi5-2 mutant seeds Replicate 2

value: seed


title: blood-NR-rep11


title: blood-NR-rep15


title: blood-AR-rep7


title: blood-NR-rep14


title: blood-NR-rep13


title: 16dap-abi5-1 mutant seeds Replicate 3


title: 16dap-abi5-1 mutant seeds Replicate 2


title: blood-AR-rep10


title: 16dap-R108-2 seeds Replicate 1


title: blood-AR-rep5


title: blood-AR-rep6


title: blood-NR-rep16


title: 24dap-R108-1 seeds Replicate 2


title: 16dap-R108-1 seeds Replicate 1


title: 16dap-R108-1 seeds Replicate 3


title: 16dap-abi5-2 mutant seeds Replicate 1


title: blood-NR-rep9


title: blood-NR-rep8


title: blood-NR-rep6


title: blood-AR-rep2


title: blood-AR-rep4


title: blood-NR-rep4


title: blood-NR-rep7


title: blood-NR-rep5


title: blood-AR-rep3


title: blood-NR-rep3


title: blood-NR-rep10


title: CSES20-NPCs

city: Jerusalem

first: Nissim

last: Benvenisty

state: Israel

address: Edmond Safra Campus Givat Ram

department: Genetics

country: Israel

institute: Hebrew University

description: gene expression

hyb_protocol: Affymetrix protocol, 11 µg cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console (RMA)

source_name: Down syndrome neural progenitor cells

label_protocol: 200 ng total RNA, Affymetrix protocol

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

tag: material

value: Cell line

tag: gender

value: male

value: neural progenitor cells derived from Down syndrome embryonic stem cells


title: blood-NR-rep1


title: CSES44-NPCs

description: gene expression


title: H9-NPCs

description: gene expression

source_name: Normal healthy control neural progenitor cells

value: female

value: neural progenitor cells derived from healthy human embryonic stem cells


title: blood-AR-rep1


title: mss11∆ Time point 3 (T3) vs Time point 4 (T4)

city: Hsinchu

first: Yu-Ting

last: Chen

address: No.101, Sec. 2, Guang-Fu Rd.

department: Institute of Molecular and Cellular Biology

country: Taiwan

institute: National Tsing Hua University, Taiwan

hyb_protocol: Pre-hybridized with 1% BSA 5x SSC and 0.1% SDS at  42 °C for 1hr. Subsequently washed with 0.1x SSC two times vigorously for 5 min at 25 °C. Then washed in ddH2O for 30 sec at 25 °C, and rinsed with isopropanol prior to drying and hybridizing. The array was hybridized with Cy-3 and Cy-5 labeled aRNA (+ 20µg of poly A and yeast tRNA) in Corning Microarray Hybridization Chamber (No.2551, Corning). The hybridization was reacted at 65˚C water bath for 16 hours. Array then washed in 2x SSC (+ 0.03 % SDS) at 65 °C for 2min.  Sub-washed in 2x SSC, 1x SSC, 0.2x SSC and 0.1x SSC, each at 25 °C for 2min prior to drying and scanning.

scan_protocol: The slide were scanned using Axon GenePix 4000B scanner (Axon Instruments, Inc., Union City, CA); Genepix software was used to pick up the spot.

data_processing: Lowess normalization was used to remove intensity-based variation across channels. The following linear model was then fitted for each of the spot on DNA microarrays: y ijkl = strain i + dye j + array k + ε ijkl, where strain i stands for the ith strain for i=1, 2, dye j stands for the jth dye effect for j=1,2, array k stands for the overall array effect and is a random effect, and ε ijkl is the residual term for random variation that is not caught by the above model. y ijkl is the intensity we want to model. The genes with significant strain effects are selected using False Discovery Rate (FDR)=0.05, which is equivalent to p-value ≤ 0.0148. The analysis was carried out with JMP Genomics (SAS Institute Inc., Cary, NC) and the R package qvalue

organism: Candida albicans

source_name: mss11 mutant sub-cultured in YPD medium at 30˚C for 6 hours

label_protocol: cDNA synthesis, aRNA synthesis and Cy-dye coupling was carried out by using Amino Allyl MessageAmp™ II aRNA Amplification Kit (AM1753, Ambion) following by manufacturer’s manual. Briefly, the first strand of cDNA was then prepared from total RNA using ArrayScript™ reverse transcriptase. After processing, DNA polymerase and RNase H was further used for second strand cDNA synthesis. In vitro transcription by using T7 RNA polymerase and purified cDNA as the template, the amino allyl UTP (aaUTP) incorporated aRNA (amino allyl-modified aRNA) was synthesized. aRNA was purified and performed Cy5  (Amersham Cy5 Mono-Reactive Dye Pack, PA25001, GE Healthcare) or Cy3 (Amersham Cy3 Mono-Reactive Dye Pack, PA23001, GE Healthcare) dye coupling. Cy dye coupled aRNA is purified by ultrafiltration using RNeasy® MinElute™ Cleanup kit (QIAGEN).

growth_protocol: Wild type (SC5314) and mss11∆ (CaMss11D1) Candida albicans strains were separately subcultured in 650 mL of 30˚C pre-warm YPD medium (in 2L falsk) (dilute to O.D. 600 nm at 0.1). Sampling at 3h (T1), 4.5h (T2), 6h (T3), 7.5h (T4), 9h (T5), 13h (T6).

extract_protocol: Total RNA was extracted by RNeasy® kit (74106, QIAGNE, Valencia, CA) following by manufacturer’s manual. Extracted total RNA was subsequently treated with Turbo DNA-free™ DNase (Ambion, Austin, TX) for 1 h at 37˚C to degrade residual DNA. The quality and quantity of total RNA are determined using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) or agarose gel electrophoresis and ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: The cell was removed to 50 mL conical tubes and centrifuged (3,220 g, 4˚C) to discard the supernatant completely; the cell was stored at -80˚C prior to RNA extraction.

tag: treatment

tag: strain

source_name: mss11 mutant sub-cultured in YPD medium at 30˚C for 7.5 hours


title: CSES21-NPCs

description: gene expression


title: CSES32-NPCs

description: gene expression


title: CSES15-NPCs

description: gene expression


title: mss11∆ Time point 5 (T5) vs Time point 6 (T6)

source_name: mss11 mutant sub-cultured in YPD medium at 30˚C for 9 hours

source_name: mss11 mutant sub-cultured in YPD medium at 30˚C for 13 hours


title: CSES7-NPCs

description: gene expression


title: mss11∆ Time point 6 (T6) vs Time point 1 (T1)

value: mss11 mutant sub-cultured in YPD medium at 30˚C for 13 hours

source_name: mss11 mutant sub-cultured in YPD medium at 30˚C for 3 hours


title: CSES13-NPCs

description: gene expression


title: blood-NR-rep2


title: W.T Time point 6 (T6) vs Time point 1 (T1)

source_name: wild type sub-cultured in YPD medium at 30˚C for 13 hours

source_name: wild type sub-cultured in YPD medium at 30˚C for 3 hours


title: W.T Time point 5 (T5) vs Time point 6 (T6)

source_name: wild type sub-cultured in YPD medium at 30˚C for 9 hours

value: wild type sub-cultured in YPD medium at 30˚C for 13 hours


title: W.T Time point 3 (T3) vs Time point 4 (T4)

source_name: wild type sub-cultured in YPD medium at 30˚C for 6 hours

source_name: wild type sub-cultured in YPD medium at 30˚C for 7.5 hours


title: mss11∆ Time point 4 (T4) vs Time point 5 (T5)

value: mss11 mutant sub-cultured in YPD medium at 30˚C for 7.5 hours

value: mss11 mutant sub-cultured in YPD medium at 30˚C for 9 hours


title: W.T Time point 2 (T2) vs Time point 3 (T3)

source_name: wild type sub-cultured in YPD medium at 30˚C for 4.5 hours

value: wild type sub-cultured in YPD medium at 30˚C for 6 hours


title: mss11∆ Time point 1 (T1) vs Time point 2 (T2)

value: mss11 mutant sub-cultured in YPD medium at 30˚C for 3 hours

source_name: mss11 mutant sub-cultured in YPD medium at 30˚C for 4.5 hours


title: Time point 4 W.T vs mss11∆ dye swap

value: wild type sub-cultured in YPD medium at 30˚C for 7.5 hours


title: Time point 5 W.T vs mss11∆ dye swap

value: wild type sub-cultured in YPD medium at 30˚C for 9 hours


title: mss11∆ Time point 2 (T2) vs Time point 3 (T3)

value: mss11 mutant sub-cultured in YPD medium at 30˚C for 4.5 hours

value: mss11 mutant sub-cultured in YPD medium at 30˚C for 6 hours


title: Time point 2 W.T vs mss11∆ dye swap

value: wild type sub-cultured in YPD medium at 30˚C for 4.5 hours


title: Time point 5 W.T vs mss11∆


title: Time point 1 W.T vs mss11∆ dye swap

value: wild type sub-cultured in YPD medium at 30˚C for 3 hours


title: log phase 5

city: Geneseo

first: Kevin

middle: T

last: Militello

state: New York

address: 1 College Circle

department: Biology

country: USA

institute: State University of New York at Geneseo

description: biological replicate 5 of 5

hyb_protocol: Microarray slides were hybridized with 0.3 mg of both cRNAs for 17 hours at 65oC in 1x Agilent hybridization buffer in an Agilent rotisserie on setting 10, washed with Agilent GE wash buffers 1 and 2, and rinsed with acetonitrile

scan_protocol: Arrays were scanned on an Agilent G2505B or G2505C scanner; images were quantified using the Agilent Feature Extract Software (most recent version)

data_processing: Agilent Feature Extract software performed background normalization and LOWESS correction for dye bias. Non-E. coli K-12 probes were removed from the dataset, as the BW25113 strain is a K-12 strain.

organism: Escherichia coli

source_name: untreated

label_protocol: Enriched RNA (0.5 mg) was converted to cRNA in the presence of Cy3-CTP or Cy5-CTP with the Quick Amp two-color labeling kit (Agilent) according to the manufacturer's instructions

growth_protocol: Escherichia coli cells were grown in LB at 37oC with shaking at 250 RPM

extract_protocol: Total RNA was isolated with the MasterPure RNA Isolation Kit (Epicentre), enriched for mRNA using the mRNA Prokaryotic mRNA Isolation Kit (Epicentre), and polyadenylated with kit all based on the manufacturer's instructions

treatment_protocol: Cells were grown in the absence and presence of 0.005 mg/mL 5-azacytidine to logarithmic phase (2 hours, A600=~0.45) or early stationary phase (8 hours, A600=~2.7)

tag: phase

value: log phase


title: W.T Time point 4 (T4) vs Time point 5 (T5)


title: Time point 2 W.T vs mss11∆


title: Time point 6 W.T vs mss11∆


title: Time point 6 W.T vs mss11∆ dye swap


title: Time point 3 W.T vs mss11∆


title: Time point 4 W.T vs mss11∆


title: Time point 3 W.T vs mss11∆ dye swap


title: early stationary phase 4

description: biological replicate 4 of 5

value: early stationary phase


title: early stationary phase 5

description: biological replicate 5 of 5


title: early stationary phase 2

description: biological replicate 2 of 5


title: W.T Time point 1 (T1) vs Time point 2 (T2)


title: Time point 1 W.T vs mss11∆

source_name: mss11mutant sub-cultured in YPD medium at 30˚C for 3 hours


title: early stationary phase 3

description: biological replicate 3 of 5


title: early stationary phase 1

description: biological replicate 1 of 5


title: log phase 4

description: biological replicate 4 of 5


title: log phase 1

description: biological replicate 1 of 5


title: log phase 3

description: biological replicate 3 of 5


title: log phase 2

description: biological replicate 2 of 5


title: preadipocytes at 120h in the lean line, biological rep2

city: Harbin

first: Hui

last: Zhang

state: Heilongjiang

address: Mucai street No. 59

department: College of Animal Science and Technology

country: China

institute: Northeast Agricultural University

description:
D.120H.2.CEL
Gene expression data from chicken preadipocytes oleate treated at 120h in the lean line.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

organism: Gallus gallus

source_name: chicken preadipocytes at 120h oleate treated in the lean line

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

growth_protocol: All birds were kept in similar environmental conditions and had access to feed and water ad libitum, and were fed with a commercial corn-soybean-based diet that met all NRC requirements (National Research Council, 1994).

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

treatment_protocol: Birds were slaughtered at 10-day-age and abdominal fat was isolated, digested in 2 mg/ml of collagenase type I (Invitrogen, Carlsbad, CA, USA) for 65 min at 37°C with shaking.

tag: line phenotype (abdomincal fat content)

value: lean

tag: age

tag: tissue

value: abdominal fat

value: preadipocytes

tag: treated with

value: oleate


title: preadipocytes at 120h in the fat line, biological rep3

description: Gene expression data from chicken preadipocytes oleate treated at 120h in the fat line.

source_name: chicken preadipocytes at 120h oleate treated in the fat line

value: fat

tag: cell type


title: preadipocytes at 120h in the lean line, biological rep1

description:
D.120H.1.CEL
Gene expression data from chicken preadipocytes oleate treated at 120h in the lean line.


title: preadipocytes at 120h in the lean line, biological rep3

description:
D.120H.3.CEL
Gene expression data from chicken preadipocytes oleate treated at 120h in the lean line.


title: S1

type: genomic

city: Beijing

first: Feifei

last: Ma

address: Road 2 Yabao

institute: Capital Institue of Pediatrics

description: MeDIP-Chip from deliveries of control fetuses

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc., Madison, WI, USA). For array hybridization, Roche NimbleGen's Human Promoter plus CpG Island array was used, which is a 3x720k format array design containing 27,728 CpG Islands and all well-characterized Promoter regions (from about -2,440bp to +610bp of the TSSs) totally covered by ~720,000 probes.

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner.

data_processing: Raw data was extracted as pair files by NimbleScan software. We perform Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample.

molecule: genomic DNA

source_name: MeDIP DNA from subject 1 placenta tissues of control fetuses

label_protocol: For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Genomic DNA was extracted from placenta tissues with premixed of  controls and  premixed of NTDs samples according to manufacturer’s instructions of DNeasy Blood and Tissue Kit (QIAGEN, Germany). Genomic DNA extracted from samples was quantified by Nanodrop ND-1000, and then analyzed by agarose gel electrophoresis to ensure the integrity and the quality of genomic DNA for the following experiment. After Fragmentation of the genomic DNA, the sheared DNA of each sample was quantified by Nanodrop ND-1000, and then analyzed by agarose gel electrophoresis to check the size of sheared DNA, which should between 200 – 1000 bp for the following experiment.

tag: sample type

value: MeDIP DNA

tag: tissue type

value: placenta

source_name: input DNA from subject 1 placenta tissues of control fetuses

value: input DNA


title: preadipocytes at 72h in the fat line, biological rep1

description:
G.72H.1.CEL
Gene expression data from chicken preadipocytes oleate treated at 72h in the fat line.

source_name: chicken preadipocytes at 72h oleate treated in the fat line


title: preadipocytes at 24h in the fat line, biological rep2

description:
G.24H.2.CEL
Gene expression data from chicken preadipocytes oleate treated at 24h in the fat line.

source_name: chicken preadipocytes at 24h oleate treated in the fat line


title: preadipocytes at 72h in the fat line, biological rep3

description:
G.72H.3.CEL
Gene expression data from chicken preadipocytes oleate treated at 72h in the fat line.


title: preadipocytes at 120h in the fat line, biological rep1

description:
G.120H.1.CEL
Gene expression data from chicken preadipocytes oleate treated at 120h in the fat line.


title: preadipocytes at 72h in the lean line, biological rep3

description:
D.72H.3.CEL
Gene expression data from chicken preadipocytes oleate treated at 72h in the lean line.

source_name: chicken preadipocytes at 72h oleate treated in the lean line


title: preadipocytes at 24h in the fat line, biological rep3

description:
G.24H.3.CEL
Gene expression data from chicken preadipocytes oleate treated at 24h in the fat line.


title: preadipocytes at 72h in the fat line, biological rep2

description:
G.72H.2.CEL
Gene expression data from chicken preadipocytes oleate treated at 72h in the fat line.


title: S3

description: MeDIP-Chip from deliveries of  fetuses with NTDs

source_name: MeDIP DNA from subject 1 placenta tissues of NTD's fetuses

source_name: input DNA from subject 1 placenta tissues of NTD's fetuses


title: preadipocytes at 72h in the lean line, biological rep2

description:
D.72H.2.CEL
Gene expression data from chicken preadipocytes oleate treated at 72h in the lean line.


title: preadipocytes at 12h in the fat line, biological rep1

description:
G.12H.1.CEL
Gene expression data from chicken preadipocytes oleate treated at 12h in the fat line.

source_name: chicken preadipocytes at 12h oleate treated in the fat line


title: preadipocytes at 120h in the fat line, biological rep2

description:
G.120H.2.CEL
Gene expression data from chicken preadipocytes oleate treated at 120h in the fat line.


title: preadipocytes at 24h in the lean line, biological rep3

description:
D.24H.3.CEL
Gene expression data from chicken preadipocytes oleate treated at 24h in the lean line.

source_name: chicken preadipocytes at 24h oleate treated in the lean line


title: preadipocytes at 72h in the lean line, biological rep1

description:
D.72H.1.CEL
Gene expression data from chicken preadipocytes oleate treated at 72h in the lean line.


title: preadipocytes at 12h in the fat line, biological rep3

description:
G.12H.3.CEL
Gene expression data from chicken preadipocytes oleate treated at 12h in the fat line.


title: preadipocytes at 24h in the lean line, biological rep1

description:
D.24H.1.CEL
Gene expression data from chicken preadipocytes oleate treated at 24h in the lean line.


title: preadipocytes at 12h in the lean line, biological rep3

description:
D.12H.3.CEL
Gene expression data from chicken preadipocytes oleate treated at 12h in the lean line.

source_name: chicken preadipocytes at 12h oleate treated in the lean line


title: preadipocytes at 12h in the fat line, biological rep2

description:
G.12H.2.CEL
Gene expression data from chicken preadipocytes oleate treated at 12h in the fat line.


title: preadipocytes at 120h control in the lean line, biological rep3

description:
D_c120h_3.CEL
Gene expression data from chicken preadipocytes normal cultured at 120h in the lean line.

source_name: chicken preadipocytes at 120h normal cultured in the lean line


title: preadipocytes at 120h control in the fat line, biological rep3

description:
G_C120h_3.CEL
Gene expression data from chicken preadipocytes normal cultured at 120h in the fat line.

source_name: chicken preadipocytes at 120h normal cultured in the fat line


title: preadipocytes at 24h in the fat line, biological rep1

description:
G.24H.1.CEL
Gene expression data from chicken preadipocytes oleate treated at 24h in the fat line.


title: preadipocytes at 120h control in the fat line, biological rep2

description:
G_C120h_2.CEL
Gene expression data from chicken preadipocytes normal cultured at 120h in the fat line.


title: preadipocytes at 24h control in the fat line, biological rep3

description:
G_C24h_3.CEL
Gene expression data from chicken preadipocytes normal cultured at 24h in the fat line.

source_name: chicken preadipocytes at 24h normal cultured in the fat line


title: S2


title: preadipocytes at 72h control in the fat line, biological rep2

description:
G_C72h_2.CEL
Gene expression data from chicken preadipocytes normal cultured at 72h in the fat line.

source_name: chicken preadipocytes at 72h normal cultured in the fat line


title: preadipocytes at 12h in the lean line, biological rep2

description:
D.12H.2.CEL
Gene expression data from chicken preadipocytes oleate treated at 12h in the lean line.


title: preadipocytes at 72h control in the lean line, biological rep3

description:
D_c72h_3.CEL
Gene expression data from chicken preadipocytes normal cultured at 72h in the lean line.

source_name: chicken preadipocytes at 72h normal cultured in the lean line


title: preadipocytes at 24h control in the fat line, biological rep1

description:
G_C24h_1.CEL
Gene expression data from chicken preadipocytes normal cultured at 24h in the fat line.


title: preadipocytes at 120h control in the lean line, biological rep2

description:
D_c120h_2.CEL
Gene expression data from chicken preadipocytes normal cultured at 120h in the lean line.


title: preadipocytes at 12h in the lean line, biological rep1

description:
D.12H.1.CEL
Gene expression data from chicken preadipocytes oleate treated at 12h in the lean line.


title: preadipocytes at 72h control in the fat line, biological rep3

description:
G_C72h_3.CEL
Gene expression data from chicken preadipocytes normal cultured at 72h in the fat line.


title: preadipocytes at 72h control in the lean line, biological rep2

description:
D_c72h_2.CEL
Gene expression data from chicken preadipocytes normal cultured at 72h in the lean line.


title: preadipocytes at 24h control in the fat line, biological rep2

description:
G_C24h_2.CEL
Gene expression data from chicken preadipocytes normal cultured at 24h in the fat line.


title: preadipocytes at 24h in the lean line, biological rep2

description:
D.24H.2.CEL
Gene expression data from chicken preadipocytes oleate treated at 24h in the lean line.


title: preadipocytes at 24h control in the lean line, biological rep2

description:
D_c24h_2.CEL
Gene expression data from chicken preadipocytes normal cultured at 24h in the lean line.

source_name: chicken preadipocytes at 24h normal cultured in the lean line


title: preadipocytes at 12h control in the fat line, biological rep2

description:
G_C12h_2.CEL
Gene expression data from chicken preadipocytes normal cultured at 12h in the fat line.

source_name: chicken preadipocytes at 12h normal cultured in the fat line


title: preadipocytes at 72h control in the lean line, biological rep1

description:
D_c72h_1.CEL
Gene expression data from chicken preadipocytes normal cultured at 72h in the lean line.


title: preadipocytes at 120h control in the lean line, biological rep1

description:
D_c120h_1.CEL
Gene expression data from chicken preadipocytes normal cultured at 120h in the lean line.


title: preadipocytes at 24h control in the lean line, biological rep3

description:
D_c24h_3.CEL
Gene expression data from chicken preadipocytes normal cultured at 24h in the lean line.


title: preadipocytes at 72h control in the fat line, biological rep1

description:
G_C72h_1.CEL
Gene expression data from chicken preadipocytes normal cultured at 72h in the fat line.


title: preadipocytes at 12h control in the fat line, biological rep1

description:
G_C12h_1.CEL
Gene expression data from chicken preadipocytes normal cultured at 12h in the fat line.


title: preadipocytes at 24h control in the lean line, biological rep1

description:
D_C24h_1.CEL
Gene expression data from chicken preadipocytes normal cultured at 24h in the lean line.


title: preadipocytes at 12h control in the fat line, biological rep3

description:
G_C12h_3.CEL
Gene expression data from chicken preadipocytes normal cultured at 12h in the fat line.


title: preadipocytes at 0h in the fat line, biological rep2

description:
G.OH.2.CEL
Gene expression data from chicken preadipocytes at 0h in the fat line.


title: preadipocytes at 12h control in the lean line, biological rep3

description:
D_C12h_3.CEL
Gene expression data from chicken preadipocytes normal cultured at 12h in the lean line.

source_name: chicken preadipocytes at 12h normal cultured in the lean line


title: preadipocytes at 12h control in the lean line, biological rep2

description:
D_C12h_2.CEL
Gene expression data from chicken preadipocytes normal cultured at 12h in the lean line.


title: preadipocytes at 120h control in the fat line, biological rep1

description:
G_C120h_1.CEL
Gene expression data from chicken preadipocytes normal cultured at 120h in the fat line.


title: preadipocytes at 12h control in the lean line, biological rep1

description:
D_C12h_1.CEL
Gene expression data from chicken preadipocytes normal cultured at 12h in the lean line.


title: preadipocytes at 0h in the lean line, biological rep2

description:
D.0H.2.CEL
Gene expression data from chicken preadipocytes at 0h in the lean line.


title: preadipocytes at -12h in the lean line, biological rep1

description:
D.minus.12H.1.CEL
Gene expression data from chicken preadipocytes at -12h in the lean line.


title: preadipocytes at 0h in the fat line, biological rep1

description:
G.OH.1.CEL
Gene expression data from chicken preadipocytes at 0h in the fat line.


title: preadipocytes at 0001 in the fat line, biological rep1

description:
G.0001.1.CEL
Gene expression data from chicken preadipocytes no cultured in the fat line.

source_name: chicken preadipocytes at 0001 time point in the fat line


title: preadipocytes at -12h in the lean line, biological rep3

description:
D.minus.12H.3.CEL
Gene expression data from chicken preadipocytes at -12h in the lean line.


title: preadipocytes at 0h in the lean line, biological rep3

description:
D.0H.3.CEL
Gene expression data from chicken preadipocytes at 0h in the lean line.


title: preadipocytes at -12h in the lean line, biological rep2

description:
D.minus.12H.2.CEL
Gene expression data from chicken preadipocytes at -12h in the lean line.


title: preadipocytes at -12h in the fat line, biological rep1

description:
G_minus_12h_1.CEL
Gene expression data from chicken preadipocytes at -12h in the fat line.


title: preadipocytes at 0h in the lean line, biological rep1

description:
D.0H.1.CEL
Gene expression data from chicken preadipocytes at 0h in the lean line.


title: preadipocytes at -12h in the fat line, biological rep2

description:
G_minus_12h_2.CEL
Gene expression data from chicken preadipocytes at -12h in the fat line.


title: R2KO_d28_lung_CD45_negative

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

description:
R2KO_d28_CD45-
Gene expression after silica aspiration in lung CD45-negative cells.

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally, 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 50μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven, and then washed at room temperature.

scan_protocol: The hybridized array was immediately scanned using the Agilent Technologies G2600D SG12494263 (Agilent Technologies, Inc.)

data_processing:
Raw data were extracted using Agilent Feature Extraction Software (Agilent Technologies, v11.0.1.1). The raw data for the same genes were then summarized automatically via the Agilent Feature Extraction protocol in order to generate raw data text files that contain expression data for each gene probed on the array. Array probes that displayed Flag A in samples were filtered out.
Data were preprocessed using R 2.15.1 (www.r-project.org) as follows: After averaging the expression values of duplicated probes, all expression values for the probes were log2 transformed and normalized between groups using the quantile method.

source_name: Lung, CD45-negative cells, Ccr2KO, day 28 post silica-aspiration

label_protocol: RNA labeling and hybridization were performed by using the Agilent’s Quick Amp Labeling Kit and Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 200ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (NanoDrop, Wilmington, USA).

growth_protocol: All mice were bred under specific pathogen-free conditions at the University of Tokyo and were 7-9 weeks old at the commencement of experiments. All animal experiments were conducted in accordance with the guidelines of the Animal Care and Use Committee of the University of Tokyo.

extract_protocol: RNA was prepared using TRIzol Reagent (Life Technologies) and RNeasy Mini Kits (QIAGEN) following the manufacturer's recommendations. RNA purity and integrity were confirmed based on its OD 260/280 ratio before analysis using an Agilent 2100 Bioanalyzer (Agilent Technologies). Each total RNA sample was pooled from 3 biological replicates (one experimental replicate).

treatment_protocol: Perfused lungs from B6 or Ccr2KO mice were enzymatically digested, then erythrocytes and silica particles were removed by Percoll gradient centrifugation. Lung CD45-negative cells were isolated by magnetically-labeled cell sorting from the resulting lung single cell suspensions.

tag: strain/background

tag: genotype/variation

value: lung

value: CD45-negative cells

tag: days post silica aspiration

value: day 28


title: B6_d28_lung_CD45_negative

description:
B6_d28_CD45-
Gene expression after silica aspiration in lung CD45-negative cells.

source_name: Lung, CD45-negative cells, WT, day 28 post silica-aspiration

value: WT


title: preadipocytes at 0001 in the lean line, biological rep3

description:
D.0001.3.CEL
Gene expression data from chicken preadipocytes no cultured in the lean line.

source_name: chicken preadipocytes at 0001 time point in the lean line


title: B6_d40_lung_CD45_negative

description:
B6_d40_CD45-
Gene expression after silica aspiration in lung CD45-negative cells.

source_name: Lung, CD45-negative cells, WT, day 40 post silica-aspiration

value: day 40


title: R2KO_d0_lung_CD45_negative

description:
R2KO_d0_CD45-
Gene expression after silica aspiration in lung CD45-negative cells.

source_name: Lung, CD45-negative cells, Ccr2KO, day 0 (untreated)

value: day 0


title: preadipocytes at 0001 in the lean line, biological rep2

description:
D.0001.2.CEL
Gene expression data from chicken preadipocytes no cultured in the lean line.


title: B6_d0_lung_CD45_negative

description:
B6_d0_CD45-
Gene expression after silica aspiration in lung CD45-negative cells.

source_name: Lung, CD45-negative cells, WT, day 0 (untreated)


title: preadipocytes at 0001 in the fat line, biological rep2

description:
G.0001.2.CEL
Gene expression data from chicken preadipocytes no cultured in the fat line.


title: preadipocytes at 0h in the fat line, biological rep3

description:
G.OH.3_2.CEL
Gene expression data from chicken preadipocytes at 0h in the fat line.


title: preadipocytes at -12h in the fat line, biological rep3

description:
G_minus_12h_3.CEL
Gene expression data from chicken preadipocytes at -12h in the fat line.


title: preadipocytes at 0001 in the lean line, biological rep1

description:
D.0001.1.CEL
Gene expression data from chicken preadipocytes no cultured in the lean line.


title: R2KO_d40_lung_CD45_negative

description:
R2KO_d40_CD45-
Gene expression after silica aspiration in lung CD45-negative cells.

source_name: Lung, CD45-negative cells, Ccr2KO, day 40 post silica-aspiration


title: preadipocytes at 0001 in the fat line, biological rep3

description:
G.0001.3.CEL
Gene expression data from chicken preadipocytes no cultured in the fat line.


title: Group520_Exp_Rno_Pal_91D_rep3

city: Chapel Hill

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

description:
gene expression
4580.gpr_Group520_Exp

hyb_protocol: Treated samples were co-hybridized with vehicle controls to individual arrays according to the manufacturer's protocol (Agilent Manual:G4140-90050 v. 5.0.1). All hybridizations were performed with three independent biological replicates for treated and control tissues (i.e., RNA samples were not pooled)

scan_protocol: Microarray slides were scanned at 532 nm (Cy3) and 635 nm (Cy5) on a GenePix 4000B scanner (Molecular Devices, Union City, CA). Images were analyzed for feature and background intensities using GenePix Pro 6.0 software (Molecular Devices).

data_processing: Microarrays incorporated independent labeling of each sample with two different dyes that were scanned using a GenePix 4000B scanner at 532 nm for Cy3 labeling (green dye), and 635 nm for Cy5 labeling (red dye). A portion of the microarray data (i.e. duodenum and jejejum tissues) have been previously processed, analyzed, and published in the following peer-reviewed articles available through PubMed: PMIDs 22561333 and 22155349. This current submission represents an updated analysis using all microarray data. Here, the mRNA microarray data were analyzed by pulling data for the median Cy3 dye signal, because the Cy5 dye signal has been shown to be susceptible to laboratory-introduced biases/errors (e.g., ozone). Data were then normalized by quantiles (Partek Genomics Suite, St Louis, Missouri).

organism: Rattus norvegicus

label_protocol: Independent labeling of each sample (Cy3 and Cy5, including dye swap) for each treatment group at each time point (8 and 91 days) was carried out.

growth_protocol: Details regarding chemicals, animals, vendors, and experimental methods have been previously published in the following articles available through PubMed: PMIDs 22561333 and 22155349.

extract_protocol: Preparation of duodenum and jejunum samples was carried out by collecting and flushing intestinal sections with ice-cold phosphate buffered saline. The duodenal and jejunal sections were cut longitudinally, and the epithelium was scraped using disposable sterile plastic spatulas (VWR International) into vials containing TRIzol (Invitrogen, Carlsbad, CA), snap-frozen in liquid nitrogen, and stored at -80 °C. Oral mucosa samples (viz. upper hard and soft palate) were collected from behind the upper front teeth back to the soft palate and were placed into vials containing TRIzol, snap-frozen in liquid nitrogen, stored at –80 °C. Frozen intestinal epithelial samples were homogenized using a Mixer Mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to the manufacturer's protocol with an additional acid phenol:chloroform extraction. Isolated RNA was resuspended in RNA storage solution (Ambion Inc., Austin,TX), quantified (A260), and quality was assessed by evaluation of the A260/A280 ratio and by visual inspection of 1 μg total RNA on a denaturing gel. Only high-quality RNA samples (A260/280>1.9) were examined using Rat and Mouse 4×44 K Agilent whole-genome oligonucleotide microarrays (version 1, Agilent Technologies, Inc., Santa Clara, CA).

treatment_protocol: In brief, SDD (CAS 7789-12-0; 99.95% pure) was obtained from Sigma-Aldrich, Inc. (Milwaukee, WI) and stored at room temperature and protected from light. Dose formulations were prepared at concentrations of 0.3, 4, 14, 60, 170, and 520 mg/l SDD in tap water, which is equivalent to ~0.1, 1.4, 5, 20.9, 59.3, and 180 ppm Cr(VI). Female Fischer 344 rats (Charles River Laboratories International, Inc.; Stone Ridge, NY) were received at ~4 weeks of age and allowed to acclimate for ~2 weeks. Rats were 83.1 to 126.4 g of weight at the start of exposure. Female B6C3F1 mice (Charles River, Raleigh, NC) were received at 4-5 weeks of age and allowed to acclimate for ~2 weeks. Mice were 13.3 to 22.9 g of weight at the start of exposure. All animals were allowed ad libitum access to irradiated NTP-2000 chow (Zeigler Bros., Gardners, PA) and drinking water (including test article) until study termination at days 8 or 91 of exposure. The in-life portion of these studies were conducted at Southern Research Institute (Birmingham, AL).

value: Female

value: Sodium Dichromate Dihydrate (SDD)

tag: dose

tag: dose units

value: mg/L

tag: replicate

tag: time-point

value: 91 Days

tag: animal id

value: palate


title: Group520_CT_Rno_Pal_91D_rep3

description:
gene expression
4579.gpr_Group520_CT

tag: gender

tag: treatment

value: Vehicle


title: Group520_CT_Rno_Pal_91D_rep2

description:
gene expression
4569.gpr_Group520_CT


title: Group60_Exp_Rno_Pal_91D_rep3

description:
gene expression
4576.gpr_Group60_Exp


title: Group520_Exp_Rno_Pal_91D_rep2

description:
gene expression
4570.gpr_Group520_Exp


title: Group520_CT_Rno_Pal_91D_rep1

description:
gene expression
4559.gpr_Group520_CT


title: Group60_Exp_Rno_Pal_91D_rep1

description:
gene expression
4556.gpr_Group60_Exp


title: Group520_Exp_Rno_Pal_91D_rep1

description:
gene expression
4560.gpr_Group520_Exp


title: Group170_Exp_Rno_Pal_91D_rep1

description:
gene expression
4558.gpr_Group170_Exp


title: Group170_CT_Rno_Pal_91D_rep1

description:
gene expression
4557.gpr_Group170_CT


title: Group170_Exp_Rno_Pal_91D_rep3

description:
gene expression
4578.gpr_Group170_Exp


title: Group170_Exp_Rno_Pal_91D_rep2

description:
gene expression
4568.gpr_Group170_Exp


title: Group03_CT_Rno_Pal_91D_rep1

description:
gene expression
4551.gpr_Group03_CT


title: Group4_Exp_Rno_Pal_91D_rep1

description:
gene expression
4554.gpr_Group4_Exp


title: Group170_CT_Rno_Pal_91D_rep2

description:
gene expression
4567.gpr_Group170_CT


title: Group60_CT_Rno_Pal_91D_rep1

description:
gene expression
4555.gpr_Group60_CT


title: Group4_CT_Rno_Pal_91D_rep1

description:
gene expression
4553.gpr_Group4_CT


title: Group4_Exp_Rno_Pal_91D_rep3

description:
gene expression
4574.gpr_Group4_Exp


title: Group4_Exp_Rno_Pal_91D_rep2

description:
gene expression
4564.gpr_Group4_Exp


title: Group170_CT_Rno_Pal_91D_rep3

description:
gene expression
4577.gpr_Group170_CT


title: Group60_CT_Rno_Pal_91D_rep3

description:
gene expression
4575.gpr_Group60_CT


title: Group03_Exp_Rno_Pal_91D_rep2

description:
gene expression
4562.gpr_Group03_Exp


title: Group4_CT_Rno_Pal_91D_rep2

description:
gene expression
4563.gpr_Group4_CT


title: Group60_CT_Rno_Pal_91D_rep2

description:
gene expression
4565.gpr_Group60_CT


title: Group03_Exp_Rno_Pal_91D_rep3

description:
gene expression
4572.gpr_Group03_Exp


title: Group03_CT_Rno_Pal_91D_rep3

description:
gene expression
4571.gpr_Group03_CT


title: Group520_Exp_Rno_Pal_8D_rep2

description:
gene expression
4540.gpr_Group520_Exp

value: 8 Days


title: Group60_Exp_Rno_Pal_91D_rep2

description:
gene expression
4566.gpr_Group60_Exp


title: Group03_CT_Rno_Pal_91D_rep2

description:
gene expression
4561.gpr_Group03_CT


title: Group520_Exp_Rno_Pal_8D_rep3

description:
gene expression
4550.gpr_Group520_Exp


title: Group03_Exp_Rno_Pal_91D_rep1

description:
gene expression
4552.gpr_Group03_Exp


title: Group4_CT_Rno_Pal_91D_rep3

description:
gene expression
4573.gpr_Group4_CT


title: Group520_Exp_Rno_Pal_8D_rep1

description:
gene expression
4530.gpr_Group520_Exp


title: Group170_Exp_Rno_Pal_8D_rep1

description:
gene expression
4528.gpr_Group170_Exp


title: Group520_CT_Rno_Pal_8D_rep1

description:
gene expression
4529.gpr_Group520_CT


title: Group170_CT_Rno_Pal_8D_rep1

description:
gene expression
4527.gpr_Group170_CT


title: Group60_Exp_Rno_Pal_8D_rep1

description:
gene expression
4526.gpr_Group60_Exp


title: Lamin B2 Kd_DLD1_Set3

city: Pune

first: Kundan

last: Sengupta

state: Maharashtra

address: Dr. Homi Bhabha Road, Pashan

country: India

institute: Indian Institute of Science Education and Research (IISER) Pune

hyb_protocol: Agilent’s In situ Hybridzation kit 5188-5242

scan_protocol: Not provided

data_processing: Data Agilent Feature Extraction Software version 10.5 (Protocol GE1_107_Sep09). Normalization Used 50th Percentile shift Normalization

source_name: DLD1 cells treated with siRNA against Lamin B2 (100nM) for 48 hours

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis)

extract_protocol: Trizol method

treatment_protocol: siRNA treatment using oligonucleotides against Lamin A/C and Lamin B2 for a duration of 48 hours.

tag: cell line

value: colorectal cancer


title: Lamin A Kd_DLD1_Set1

source_name: DLD1 cells treated with siRNA against Lamin A/C (100nM) for 48 hours


title: Lamin B2 Kd_DLD1_Set1


title: Lamin A Kd_DLD1_Set2


title: Lamin A Kd_DLD1_Set3


title: Group60_CT_Rno_Pal_8D_rep1

description:
gene expression
4525.gpr_Group60_CT


title: Group520_CT_Rno_Pal_8D_rep2

description:
gene expression
4539.gpr_Group520_CT


title: Lamin B2 Kd_DLD1_Set2


title: Group170_Exp_Rno_Pal_8D_rep2

description:
gene expression
4538.gpr_Group170_Exp


title: Group60_Exp_Rno_Pal_8D_rep2

description:
gene expression
4536.gpr_Group60_Exp


title: Group170_CT_Rno_Pal_8D_rep2

description:
gene expression
4537.gpr_Group170_CT


title: Group60_CT_Rno_Pal_8D_rep2

description:
gene expression
4535.gpr_Group60_CT


title: Group4_Exp_Rno_Pal_8D_rep2

description:
gene expression
4534.gpr_Group4_Exp


title: Control_DLD1_Set3

source_name: DLD1 cells not treated with siRNA


title: Group4_CT_Rno_Pal_8D_rep2

description:
gene expression
4533.gpr_Group4_CT


title: Control_DLD1_Set2


title: Control_DLD1_Set1


title: Group170_CT_Rno_Pal_8D_rep3

description:
gene expression
4547.gpr_Group170_CT


title: Group4_CT_Rno_Pal_8D_rep3

description:
gene expression
4543.gpr_Group4_CT


title: Group60_Exp_Rno_Pal_8D_rep3

description:
gene expression
4546.gpr_Group60_Exp


title: Group170_Exp_Rno_Pal_8D_rep3

description:
gene expression
4548.gpr_Group170_Exp


title: Group4_Exp_Rno_Pal_8D_rep1

description:
gene expression
4524.gpr_Group4_Exp


title: Group520_CT_Rno_Pal_8D_rep3

description:
gene expression
4549.gpr_Group520_CT


title: Group03_Exp_Rno_Pal_8D_rep2

description:
gene expression
4532.gpr_Group03_Exp


title: Group60_CT_Rno_Pal_8D_rep3

description:
gene expression
4545.gpr_Group60_CT


title: Group03_Exp_Rno_Pal_8D_rep3

description:
gene expression
4542.gpr_Group03_Exp


title: Group4_Exp_Rno_Pal_8D_rep3

description:
gene expression
4544.gpr_Group4_Exp


title: Group4_CT_Rno_Pal_8D_rep1

description:
gene expression
4523.gpr_Group4_CT


title: Group520_Exp_Mmu_Pal_90D_rep2


title: Group170_Exp_Mmu_Pal_90D_rep2


title: Group520_Exp_Rno_Jej_91D_rep3

description:
gene expression
4677.gpr_Group520_Exp

value: jejunum


title: Group03_CT_Rno_Pal_8D_rep3

description:
gene expression
4541.gpr_Group03_CT


title: Group520_Exp_Mmu_Pal_90D_rep1


title: Group520_CT_Mmu_Pal_90D_rep3


title: Group170_Exp_Mmu_Pal_90D_rep1


title: Group520_CT_Mmu_Pal_90D_rep1


title: Group03_CT_Rno_Pal_8D_rep1

description:
gene expression
4521.gpr_Group03_CT


title: Group520_Exp_Rno_Jej_91D_rep1

description:
gene expression
4657.gpr_Group520_Exp


title: Group03_Exp_Rno_Pal_8D_rep1

description:
gene expression
4522.gpr_Group03_Exp


title: Group170_Exp_Mmu_Pal_90D_rep3


title: Group03_CT_Rno_Pal_8D_rep2

description:
gene expression
4531.gpr_Group03_CT


title: Group520_Exp_Mmu_Pal_90D_rep3


title: Group520_CT_Rno_Jej_91D_rep3

description:
gene expression
4676.gpr_Group520_CT


title: Group170_CT_Mmu_Pal_90D_rep3


title: Group520_CT_Rno_Jej_91D_rep1

description:
gene expression
4656.gpr_Group520_CT


title: Group170_CT_Mmu_Pal_90D_rep1


title: Group60_CT_Mmu_Pal_90D_rep3


title: Group520_Exp_Rno_Jej_91D_rep2

description:
gene expression
4667.gpr_Group520_Exp


title: Group14_Exp_Mmu_Pal_90D_rep3


title: Group520_CT_Rno_Jej_91D_rep2

description:
gene expression
4666.gpr_Group520_CT


title: Group170_CT_Mmu_Pal_90D_rep2


title: Group60_Exp_Mmu_Pal_90D_rep2


title: Group170_Exp_Rno_Jej_91D_rep3

description:
gene expression
4675.gpr_Group170_Exp


title: Group60_Exp_Mmu_Pal_90D_rep1


title: Group60_Exp_Mmu_Pal_90D_rep3


title: Group60_CT_Mmu_Pal_90D_rep2


title: Group60_CT_Mmu_Pal_90D_rep1


title: Group14_Exp_Mmu_Pal_90D_rep1


title: Group14_Exp_Mmu_Pal_90D_rep2


title: Group170_CT_Rno_Jej_91D_rep3

description:
gene expression
4674.gpr_Group170_CT


title: Group170_CT_Rno_Jej_91D_rep1

description:
gene expression
4654.gpr_Group170_CT


title: Group4_CT_Mmu_Pal_90D_rep2


title: Group14_CT_Mmu_Pal_90D_rep3


title: Group4_Exp_Mmu_Pal_90D_rep2


title: Group4_Exp_Mmu_Pal_90D_rep1


title: Group14_CT_Mmu_Pal_90D_rep2


title: Group14_CT_Mmu_Pal_90D_rep1


title: Group60_Exp_Rno_Jej_91D_rep3

description:
gene expression
4673.gpr_Group60_Exp


title: Group520_CT_Mmu_Pal_90D_rep2


title: Group4_Exp_Mmu_Pal_90D_rep3


title: Group170_Exp_Rno_Jej_91D_rep1

description:
gene expression
4655.gpr_Group170_Exp


title: Group03_Exp_Mmu_Pal_90D_rep2


title: Group170_CT_Rno_Jej_91D_rep2

description:
gene expression
4664.gpr_Group170_CT


title: Group60_Exp_Rno_Jej_91D_rep2

description:
gene expression
4663.gpr_Group60_Exp


title: Group170_Exp_Rno_Jej_91D_rep2

description:
gene expression
4665.gpr_Group170_Exp


title: Group60_CT_Rno_Jej_91D_rep2

description:
gene expression
4662.gpr_Group60_CT


title: Group03_CT_Mmu_Pal_90D_rep3


title: Group520_Exp_Mmu_Pal_8D_rep2


title: Group4_CT_Mmu_Pal_90D_rep1


title: Group03_Exp_Mmu_Pal_90D_rep1


title: Group60_CT_Rno_Jej_91D_rep3

description:
gene expression
4672.gpr_Group60_CT


title: Group03_CT_Mmu_Pal_90D_rep1


title: Group03_CT_Mmu_Pal_90D_rep2


title: Group520_CT_Mmu_Pal_8D_rep3


title: Group03_Exp_Mmu_Pal_90D_rep3


title: Group520_Exp_Mmu_Pal_8D_rep3


title: Group4_CT_Mmu_Pal_90D_rep3


title: Group60_CT_Rno_Jej_91D_rep1

description:
gene expression
4652.gpr_Group60_CT


title: Group170_CT_Mmu_Pal_8D_rep3


title: Group520_Exp_Mmu_Pal_8D_rep1


title: Group170_Exp_Mmu_Pal_8D_rep1


title: Group60_Exp_Mmu_Pal_8D_rep2


title: Group170_CT_Mmu_Pal_8D_rep1


title: Group520_CT_Mmu_Pal_8D_rep2


title: Group4_Exp_Rno_Jej_91D_rep1

description:
gene expression
4651.gpr_Group4_Exp


title: Group170_Exp_Mmu_Pal_8D_rep2


title: Group170_CT_Mmu_Pal_8D_rep2


title: Group4_Exp_Rno_Jej_91D_rep2

description:
gene expression
4661.gpr_Group4_Exp


title: Group60_Exp_Rno_Jej_91D_rep1

description:
gene expression
4653.gpr_Group60_Exp


title: Group4_Exp_Rno_Jej_91D_rep3

description:
gene expression
4671.gpr_Group4_Exp


title: Group60_Exp_Mmu_Pal_8D_rep3


title: Group60_CT_Mmu_Pal_8D_rep2


title: Group520_CT_Mmu_Pal_8D_rep1


title: Group60_CT_Mmu_Pal_8D_rep1


title: Group60_Exp_Mmu_Pal_8D_rep1


title: Group170_Exp_Mmu_Pal_8D_rep3


title: Group14_Exp_Mmu_Pal_8D_rep2


title: Group03_Exp_Rno_Jej_91D_rep3

description:
gene expression
4669.gpr_Group03_Exp


title: Group4_CT_Rno_Jej_91D_rep3

description:
gene expression
4670.gpr_Group4_CT


title: Group14_Exp_Mmu_Pal_8D_rep3


title: Group14_Exp_Mmu_Pal_8D_rep1


title: Group4_CT_Rno_Jej_91D_rep1

description:
gene expression
4650.gpr_Group4_CT


title: Group14_CT_Mmu_Pal_8D_rep3


title: Group60_CT_Mmu_Pal_8D_rep3


title: Group03_Exp_Rno_Jej_91D_rep2

description:
gene expression
4659.gpr_Group03_Exp


title: Group03_Exp_Rno_Jej_91D_rep1

description:
gene expression
4649.gpr_Group03_Exp


title: Group4_Exp_Mmu_Pal_8D_rep3


title: Group4_CT_Mmu_Pal_8D_rep3


title: Group03_Exp_Mmu_Pal_8D_rep3


title: Group14_CT_Mmu_Pal_8D_rep2


title: Group520_Exp_Rno_Jej_8D_rep1

description:
gene expression
4687.gpr_Group520_Exp


title: Group4_Exp_Mmu_Pal_8D_rep2


title: Group4_CT_Mmu_Pal_8D_rep1


title: Group03_CT_Rno_Jej_91D_rep1

description:
gene expression
4648.gpr_Group03_CT


title: Group03_CT_Rno_Jej_91D_rep3

description:
gene expression
4668.gpr_Group03_CT


title: Group4_CT_Mmu_Pal_8D_rep2


title: Group03_CT_Rno_Jej_91D_rep2

description:
gene expression
4658.gpr_Group03_CT


title: Group03_CT_Mmu_Pal_8D_rep3


title: Group520_CT_Rno_Jej_8D_rep1

description:
gene expression
4686.gpr_Group520_CT


title: Group03_Exp_Mmu_Pal_8D_rep2


title: Group520_CT_Rno_Jej_8D_rep2

description:
gene expression
4696.gpr_Group520_CT


title: Group520_Exp_Mmu_Jej_90D_rep3


title: Group520_Exp_Rno_Jej_8D_rep2

description:
gene expression
4697.gpr_Group520_Exp


title: Group520_Exp_Rno_Jej_8D_rep3

description:
gene expression
4707.gpr_Group520_Exp


title: Group03_CT_Mmu_Pal_8D_rep1


title: Group03_CT_Mmu_Pal_8D_rep2


title: Group520_Exp_Mmu_Jej_90D_rep2


title: Group4_Exp_Mmu_Pal_8D_rep1


title: Group520_CT_Mmu_Jej_90D_rep3


title: Group03_Exp_Mmu_Pal_8D_rep1


title: Group520_CT_Rno_Jej_8D_rep3

description:
gene expression
4706.gpr_Group520_CT


title: Group14_CT_Mmu_Pal_8D_rep1


title: Group520_Exp_Mmu_Jej_90D_rep1


title: Group520_CT_Mmu_Jej_90D_rep2


title: Group170_Exp_Mmu_Jej_90D_rep3


title: Group520_CT_Mmu_Jej_90D_rep1


title: Group60_Exp_Mmu_Jej_90D_rep3


title: Group170_CT_Mmu_Jej_90D_rep3


title: Group170_CT_Mmu_Jej_90D_rep1


title: Group170_Exp_Mmu_Jej_90D_rep2


title: Group170_CT_Rno_Jej_8D_rep2

description:
gene expression
4694.gpr_Group170_CT


title: Group170_Exp_Mmu_Jej_90D_rep1


title: Group60_Exp_Mmu_Jej_90D_rep2


title: Group60_CT_Mmu_Jej_90D_rep2


title: Group60_Exp_Rno_Jej_8D_rep3

description:
gene expression
4703.gpr_Group60_Exp


title: Group60_Exp_Rno_Jej_8D_rep1

description:
gene expression
4683.gpr_Group60_Exp


title: Group14_Exp_Mmu_Jej_90D_rep2


title: Group60_Exp_Rno_Jej_8D_rep2

description:
gene expression
4693.gpr_Group60_Exp


title: Group14_Exp_Mmu_Jej_90D_rep3


title: Group170_Exp_Rno_Jej_8D_rep1

description:
gene expression
4685.gpr_Group170_Exp


title: Group60_Exp_Mmu_Jej_90D_rep1


title: Group60_CT_Mmu_Jej_90D_rep3


title: Group170_CT_Mmu_Jej_90D_rep2


title: Group170_Exp_Rno_Jej_8D_rep2

description:
gene expression
4695.gpr_Group170_Exp


title: Group170_CT_Rno_Jej_8D_rep1

description:
gene expression
4684.gpr_Group170_CT


title: Group170_CT_Rno_Jej_8D_rep3

description:
gene expression
4704.gpr_Group170_CT


title: Group14_CT_Mmu_Jej_90D_rep3


title: Group60_CT_Mmu_Jej_90D_rep1


title: Group14_CT_Mmu_Jej_90D_rep1


title: Group14_Exp_Mmu_Jej_90D_rep1


title: Group170_Exp_Rno_Jej_8D_rep3

description:
gene expression
4705.gpr_Group170_Exp


title: Group60_CT_Rno_Jej_8D_rep3

description:
gene expression
4702.gpr_Group60_CT


title: Group4_Exp_Mmu_Jej_90D_rep3


title: Group14_CT_Mmu_Jej_90D_rep2


title: Group4_Exp_Mmu_Jej_90D_rep2


title: Group4_CT_Mmu_Jej_90D_rep2


title: Group4_Exp_Rno_Jej_8D_rep3

description:
gene expression
4701.gpr_Group4_Exp


title: Group4_CT_Mmu_Jej_90D_rep3


title: Group60_CT_Rno_Jej_8D_rep2

description:
gene expression
4692.gpr_Group60_CT


title: Group4_Exp_Mmu_Jej_90D_rep1


title: Group03_Exp_Mmu_Jej_90D_rep3


title: Group03_Exp_Mmu_Jej_90D_rep2


title: Group4_CT_Mmu_Jej_90D_rep1


title: Group4_Exp_Rno_Jej_8D_rep2

description:
gene expression
4691.gpr_Group4_Exp


title: Group03_CT_Mmu_Jej_90D_rep2


title: Group60_CT_Rno_Jej_8D_rep1

description:
gene expression
4682.gpr_Group60_CT


title: Group4_CT_Rno_Jej_8D_rep2

description:
gene expression
4690.gpr_Group4_CT


title: Group4_CT_Rno_Jej_91D_rep2

description:
gene expression
4660.gpr_Group4_CT


title: Group4_Exp_Rno_Jej_8D_rep1

description:
gene expression
4681.gpr_Group4_Exp


title: Group03_CT_Mmu_Jej_90D_rep1


title: Group03_CT_Mmu_Jej_90D_rep3


title: Group4_CT_Rno_Jej_8D_rep3

description:
gene expression
4700.gpr_Group4_CT


title: Group520_Exp_Mmu_Jej_8D_rep1


title: Group520_CT_Mmu_Jej_8D_rep1


title: Group4_CT_Rno_Jej_8D_rep1

description:
gene expression
4680.gpr_Group4_CT


title: Group520_CT_Mmu_Jej_8D_rep3


title: Group03_Exp_Mmu_Jej_90D_rep1


title: Group520_Exp_Mmu_Jej_8D_rep3


title: Group520_CT_Mmu_Jej_8D_rep2


title: Group520_Exp_Mmu_Jej_8D_rep2


title: Group03_Exp_Rno_Jej_8D_rep3

description:
gene expression
4699.gpr_Group03_Exp


title: Group03_Exp_Rno_Jej_8D_rep2

description:
gene expression
4689.gpr_Group03_Exp


title: Group03_Exp_Rno_Jej_8D_rep1

description:
gene expression
4679.gpr_Group03_Exp


title: Group170_Exp_Mmu_Jej_8D_rep2


title: Group170_Exp_Mmu_Jej_8D_rep3


title: Group170_CT_Mmu_Jej_8D_rep2


title: Group60_Exp_Mmu_Jej_8D_rep3


title: Group170_Exp_Mmu_Jej_8D_rep1


title: Group170_CT_Mmu_Jej_8D_rep3


title: Group170_CT_Mmu_Jej_8D_rep1


title: Group60_Exp_Mmu_Jej_8D_rep1


title: Group60_Exp_Mmu_Jej_8D_rep2


title: Group03_CT_Rno_Jej_8D_rep1

description:
gene expression
4678.gpr_Group03_CT


title: Group03_CT_Rno_Jej_8D_rep3

description:
gene expression
4698.gpr_Group03_CT


title: Group520_Exp_Rno_Duo_91D_rep3

description:
gene expression
4611.gpr_Group520_Exp

value: duodenum


title: Group03_CT_Rno_Jej_8D_rep2

description:
gene expression
4688.gpr_Group03_CT


title: Group14_Exp_Mmu_Jej_8D_rep2


title: Group60_CT_Mmu_Jej_8D_rep2


title: Group14_Exp_Mmu_Jej_8D_rep3


title: Group520_Exp_Rno_Duo_91D_rep2

description:
gene expression
4601.gpr_Group520_Exp


title: Group60_CT_Mmu_Jej_8D_rep3


title: Group60_CT_Mmu_Jej_8D_rep1


title: Group14_CT_Mmu_Jej_8D_rep2


title: Group14_Exp_Mmu_Jej_8D_rep1


title: Group520_Exp_Rno_Duo_91D_rep1

description:
gene expression
4592.gpr_Group520_Exp


title: Group14_CT_Mmu_Jej_8D_rep1


title: Group4_Exp_Mmu_Jej_8D_rep1


title: Group520_CT_Rno_Duo_91D_rep3

description:
gene expression
4610.gpr_Group520_CT


title: Group170_Exp_Rno_Duo_91D_rep3

description:
gene expression
4609.gpr_Group170_Exp


title: Group520_CT_Rno_Duo_91D_rep2

description:
gene expression
4600.gpr_Group520_CT


title: Group4_Exp_Mmu_Jej_8D_rep2


title: Group03_Exp_Mmu_Jej_8D_rep1


title: Group170_Exp_Rno_Duo_91D_rep2

description:
gene expression
4599.gpr_Group170_Exp


title: Group4_CT_Mmu_Jej_8D_rep2


title: Group4_CT_Mmu_Jej_8D_rep1


title: Group520_CT_Rno_Duo_91D_rep1

description:
gene expression
4591.gpr_Group520_CT


title: Group03_CT_Mmu_Jej_8D_rep2


title: Group4_Exp_Mmu_Jej_8D_rep3


title: Group03_Exp_Mmu_Jej_8D_rep2


title: Group14_CT_Mmu_Jej_8D_rep3


title: Group4_CT_Mmu_Jej_8D_rep3


title: Group170_CT_Rno_Duo_91D_rep3

description:
gene expression
4608.gpr_Group170_CT


title: Group170_CT_Rno_Duo_91D_rep2

description:
gene expression
4598.gpr_Group170_CT


title: Group03_CT_Mmu_Jej_8D_rep3


title: Group03_Exp_Mmu_Jej_8D_rep3


title: Group170_CT_Rno_Duo_91D_rep1

description:
gene expression
4589.gpr_Group170_CT


title: Group170_Exp_Rno_Duo_91D_rep1

description:
gene expression
4590.gpr_Group170_Exp


title: Group520_Exp_Mmu_Duo_90D_rep2


title: Group520_Exp_Mmu_Duo_90D_rep1


title: Group03_CT_Mmu_Jej_8D_rep1


title: Group520_CT_Mmu_Duo_90D_rep3


title: Group520_Exp_Mmu_Duo_90D_rep3


title: Group170_Exp_Mmu_Duo_90D_rep3


title: Group520_CT_Mmu_Duo_90D_rep1


title: Group60_Exp_Rno_Duo_91D_rep3

description:
gene expression
4607.gpr_Group60_Exp


title: Group60_Exp_Rno_Duo_91D_rep1

description:
gene expression
4588.gpr_Group60_Exp


title: Group60_CT_Rno_Duo_91D_rep1

description:
gene expression
4587.gpr_Group60_CT


title: Group60_Exp_Rno_Duo_91D_rep2

description:
gene expression
4582.gpr_Group60_Exp


title: Group60_CT_Rno_Duo_91D_rep3

description:
gene expression
4606.gpr_Group60_CT


title: Group170_Exp_Mmu_Duo_90D_rep1


title: Group170_Exp_Mmu_Duo_90D_rep2


title: Group4_Exp_Rno_Duo_91D_rep3

description:
gene expression
4605.gpr_Group4_Exp


title: Group520_CT_Mmu_Duo_90D_rep2


title: Group60_Exp_Mmu_Duo_90D_rep3


title: Group170_CT_Mmu_Duo_90D_rep1


title: Group60_CT_Mmu_Duo_90D_rep3


title: Group170_CT_Mmu_Duo_90D_rep2


title: Group60_Exp_Mmu_Duo_90D_rep2


title: Group170_CT_Mmu_Duo_90D_rep3


title: Group60_CT_Mmu_Duo_90D_rep1


title: Group4_Exp_Rno_Duo_91D_rep2

description:
gene expression
4597.gpr_Group4_Exp


title: Group14_Exp_Mmu_Duo_90D_rep3


title: Group60_Exp_Mmu_Duo_90D_rep1


title: Group14_Exp_Mmu_Duo_90D_rep1


title: Group14_Exp_Mmu_Duo_90D_rep2


title: Group60_CT_Mmu_Duo_90D_rep2


title: Group14_CT_Mmu_Duo_90D_rep2


title: Group4_CT_Rno_Duo_91D_rep2

description:
gene expression
4596.gpr_Group4_CT


title: Group14_CT_Mmu_Duo_90D_rep3


title: Group14_CT_Mmu_Duo_90D_rep1


title: Group4_CT_Rno_Duo_91D_rep1

description:
gene expression
4585.gpr_Group4_CT


title: Group03_Exp_Mmu_Duo_90D_rep3


title: Group03_Exp_Mmu_Duo_90D_rep1


title: Group4_Exp_Mmu_Duo_90D_rep2


title: Group4_CT_Mmu_Duo_90D_rep2


title: Group03_Exp_Mmu_Duo_90D_rep2


title: Group03_Exp_Rno_Duo_91D_rep3

description:
gene expression
4603.gpr_Group03_Exp


title: Group03_Exp_Rno_Duo_91D_rep2

description:
gene expression
4594.gpr_Group03_Exp


title: Group4_Exp_Rno_Duo_91D_rep1

description:
gene expression
4586.gpr_Group4_Exp


title: Group4_Exp_Mmu_Duo_90D_rep1


title: Group60_CT_Rno_Duo_91D_rep2

description:
gene expression
4581.gpr_Group60_CT


title: Group4_CT_Mmu_Duo_90D_rep1


title: Group03_Exp_Rno_Duo_91D_rep1

description:
gene expression
4584.gpr_Group03_Exp


title: Group03_CT_Mmu_Duo_90D_rep3


title: Group520_Exp_Mmu_Duo_8D_rep3


title: Group03_CT_Rno_Duo_91D_rep3

description:
gene expression
4602.gpr_Group03_CT


title: Group520_Exp_Mmu_Duo_8D_rep2


title: Group03_CT_Mmu_Duo_90D_rep1


title: Group520_Exp_Mmu_Duo_8D_rep1


title: Group4_CT_Rno_Duo_91D_rep3

description:
gene expression
4604.gpr_Group4_CT


title: Group520_CT_Mmu_Duo_8D_rep2


title: Group03_CT_Mmu_Duo_90D_rep2


title: Group520_CT_Mmu_Duo_8D_rep3


title: WT LKS-Slam cells, biological rep3

city: Bonn

first: Viktor

last: Janzen

address: Sigmund-Freud-Str. 25

institute: University of Bonn

description: Gene expression data from LKS-Slam marker positive bone marrow cells

hyb_protocol: Fragmented and labeled cDNA was hybridized to Affymetrix arrays (MoGene-1.0-ST-v1 Gene Chip).

scan_protocol: Microarray experiments were performed using the Affymetrix™ platform according to manufacturer’s instructions. Each microarray was automatically washed, stained and then scanned (Affymetrix GeneChip Scanner 3000).

data_processing: Raw data were read out with the AGCC 3.0 Software and converted in CEL format files. A probe-level summary was determined using the Affymetrix™ GeneChip Operating Software using RMA algorithm. Normalization of raw data was performed by the Array Assist™ Software 4.0 (Stratagene, La Jolla, Canada), applying a GC-robust multichip average (RMA) algorithm. Significance was calculated using a t-test without multiple testing correction (Array Assist™ Software), selecting all transcripts with a minimum change in expression level of 2-fold together with a p-value less than 0.05.

label_protocol: Total RNA was amplified with the Nugene Ovation Pico Kit according to manufacturer's instructions.

extract_protocol: RNA extraction, amplification and hybridisation was done by MFT Services (Tübingen, Germany). Cells were thawed on ice and QIAshredder mini-spin columns (Qiagen) as well as needle and syringe homogenization were applied. Extraction of total RNA from each sample was performed (miRNeasy Kit; Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA quality was observed with Agilent 2100 Bioanalyzer using RNA 6000 Nano LabChip Kit (Agilent Technologies, Böblingen, Germany) following the manufacturer’s instructions.

treatment_protocol: At the age of six weeks Zeb2 fl/flMx1-Cre mice and WT mice were treated with pIC to induce gene deletion of Zeb2 in the bone marrow cells of the Zeb2 fl/flMx1-Cre mice. 8 weeks after induction the mice were euthanized and bone marrow extracted. Then a population of cells highly enriched for hematopoietic stem cells (LKS-Slam marker positive cells) was sorted by flow cytometry from each bone marrow sample. Cells were kept chilled from extraction from the bone, through the sort up until centrifugation. The cell pellets were shock frozen directly after the sort.

tag: genotype

value: C57Bl/6 WT

tag: age

value: 8 weeks after pIC induction (14 weeks total age)


title: Group03_CT_Rno_Duo_91D_rep1

description:
gene expression
4583.gpr_Group03_CT

tag: tissue


title: Group520_CT_Mmu_Duo_8D_rep1


title: WT LKS-Slam cells, biological rep2

source_name: LKS-Slam marker positive bone marrow cells


title: Group520_Exp_Rno_Duo_8D_rep3

description:
gene expression
4520.gpr_Group520_Exp


title: WT LKS-Slam cells, biological rep1


title: Zeb2KO LKS-Slam cells, biological rep2


title: Group170_Exp_Mmu_Duo_8D_rep2


title: Group170_Exp_Mmu_Duo_8D_rep1


title: Group170_CT_Mmu_Duo_8D_rep2


title: Zeb2KO LKS-Slam cells, biological rep1


title: Group520_CT_Rno_Duo_8D_rep3

description:
gene expression
4519.gpr_Group520_CT


title: Group170_CT_Mmu_Duo_8D_rep1


title: Group520_Exp_Rno_Duo_8D_rep1

description:
gene expression
4500.gpr_Group520_Exp


title: Group170_Exp_Rno_Duo_8D_rep3

description:
gene expression
4518.gpr_Group170_Exp


title: Group520_CT_Rno_Duo_8D_rep1

description:
gene expression
4499.gpr_Group520_CT


title: Group170_Exp_Mmu_Duo_8D_rep3


title: Group170_CT_Mmu_Duo_8D_rep3


title: Group520_CT_Rno_Duo_8D_rep2

description:
gene expression
4509.gpr_Group520_CT


title: Group170_Exp_Rno_Duo_8D_rep2

description:
gene expression
4508.gpr_Group170_Exp


title: Group520_Exp_Rno_Duo_8D_rep2

description:
gene expression
4510.gpr_Group520_Exp


title: Group170_Exp_Rno_Duo_8D_rep1

description:
gene expression
4498.gpr_Group170_Exp


title: NPCs-DSCR8

description:
gene expression
Edited Down syndrome neural progenitor cells clone 8

hyb_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

scan_protocol: Affymetrix protocol

label_protocol: Affymetrix protocol, 11 µg cRNA

extract_protocol: 200 ng total RNA, Affymetrix protocol

treatment_protocol: Total RNA was extracted using PerfectPure RNA Cultured Cell Kit (5 PRIME)

tag: material

value: Cell line

value: female

tag: cell type

value: neural progenitor cells derived from genome edited Down syndrome embryonic stem cells


title: Group60_Exp_Mmu_Duo_8D_rep1


title: Group60_Exp_Mmu_Duo_8D_rep2


title: NPCs-B233

description:
gene expression
Down syndrome neural progenitor cells

source_name: Down syndrome neural progenitor cells

value: neural progenitor cells derived from Down syndrome embryonic stem cells


title: Group60_CT_Mmu_Duo_8D_rep3


title: Group60_CT_Mmu_Duo_8D_rep2


title: NPCs-DSCR75

description:
gene expression
Edited Down syndrome neural progenitor cells clone 75


title: HUVECs from control mother 7

city: Singapore

first: Walter

last: Stunkel

address: 30 Medical Drive, Brenner Centre Lvl 4

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Using R limma package, normalised using quantile normalisation

label: Biotin

source_name: HUVECs from control mother

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

growth_protocol: HUVECs were isolated by perfusing the 5 cm of the umbilical vein with 5mL of collagenase solution (1 mg/mL). HUVECs were then grown for two passages in EGM-2 media (Lonza).

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

treatment_protocol: HUVECs were harvested in Trizol reagent during their exponential growth phase.

tag: materrnal condition

value: controls (mothers with no GDM)

tag: race

value: Chinese

value: Infant umbilical cord

value: human vascular endothelial cells (HUVECs)

tag: passage

value: passage 2


title: Group170_CT_Rno_Duo_8D_rep1

description:
gene expression
4497.gpr_Group170_CT

value: Female

value: mg/L


title: Group60_Exp_Mmu_Duo_8D_rep3

value: Sodium Dichromate Dihydrate (SDD)

value: 8 Days


title: HUVECs from control mother 4

value: Others


title: Group170_CT_Rno_Duo_8D_rep3

description:
gene expression
4517.gpr_Group170_CT

value: Vehicle

value: duodenum


title: HUVECs from control mother 8

value: Male


title: Group14_Exp_Mmu_Duo_8D_rep2


title: Group60_Exp_Rno_Duo_8D_rep2

description:
gene expression
4506.gpr_Group60_Exp


title: Group14_Exp_Mmu_Duo_8D_rep1


title: Zeb2KO LKS-Slam cells, biological rep3

value: 8 weeks after pIC induction (14 weeks total age)


title: Group60_Exp_Rno_Duo_8D_rep3

description:
gene expression
4516.gpr_Group60_Exp


title: Group60_Exp_Rno_Duo_8D_rep1

description:
gene expression
4496.gpr_Group60_Exp


title: Group60_CT_Mmu_Duo_8D_rep1


title: HUVECs from GDM mother 19

source_name: HUVECs from GDM mother

value: diagnosed with maternal gestational diabetes (GDM)


title: Group170_CT_Rno_Duo_8D_rep2

description:
gene expression
4507.gpr_Group170_CT


title: HUVECs from GDM mother 18


title: Group60_CT_Rno_Duo_8D_rep2

description:
gene expression
4505.gpr_Group60_CT


title: Group14_CT_Mmu_Duo_8D_rep2


title: Group60_CT_Rno_Duo_8D_rep3

description:
gene expression
4515.gpr_Group60_CT


title: Group14_CT_Mmu_Duo_8D_rep3


title: HUVECs from control mother 6

value: Malay


title: HUVECs from control mother 2


title: Group14_Exp_Mmu_Duo_8D_rep3


title: Group60_CT_Rno_Duo_8D_rep1

description:
gene expression
4495.gpr_Group60_CT


title: HUVECs from GDM mother 16


title: Group4_Exp_Mmu_Duo_8D_rep3


title: Group4_Exp_Mmu_Duo_8D_rep2


title: Group4_Exp_Rno_Duo_8D_rep2

description:
gene expression
4504.gpr_Group4_Exp


title: Group4_Exp_Mmu_Duo_8D_rep1


title: HUVECs from GDM mother 11


title: Group4_Exp_Rno_Duo_8D_rep1

description:
gene expression
4494.gpr_Group4_Exp


title: Group4_CT_Rno_Duo_8D_rep2

description:
gene expression
4503.gpr_Group4_CT


title: Group4_CT_Rno_Duo_8D_rep3

description:
gene expression
4513.gpr_Group4_CT


title: Group03_Exp_Rno_Duo_8D_rep3

description:
gene expression
4512.gpr_Group03_Exp


title: Group03_Exp_Mmu_Duo_8D_rep2


title: Group03_CT_Rno_Duo_8D_rep3

description:
gene expression
4511.gpr_Group03_CT


title: Group4_CT_Mmu_Duo_8D_rep1


title: Group03_CT_Rno_Duo_8D_rep2

description:
gene expression
4501.gpr_Group03_CT


title: Group03_Exp_Mmu_Duo_8D_rep1


title: Group03_CT_Rno_Duo_8D_rep1

description:
gene expression
4491.gpr_Group03_CT


title: Group4_CT_Rno_Duo_8D_rep1

description:
gene expression
4493.gpr_Group4_CT


title: Group03_CT_Mmu_Duo_8D_rep2


title: Group03_Exp_Rno_Duo_8D_rep2

description:
gene expression
4502.gpr_Group03_Exp


title: Group4_CT_Mmu_Duo_8D_rep2


title: Group03_CT_Rno_Duo_91D_rep2

description:
gene expression
4593.gpr_Group03_CT

value: 91 Days


title: Group03_CT_Mmu_Duo_8D_rep1


title: seedling roots, 3h OGs, bio rep 2

status: Public on Sep 23 2016

city: Berkeley

first: Clarice

last: de Azevedo Souza

state: CA

address: 2151 Berkeley Way

department: Department of Plant and Microbial Biology

institute: University of California, Berkeley

description: gene expression data from seedling roots 3 hours after elicitor treatment

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1 Genome Array GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer recommendation.

scan_protocol: GeneChip 7G scanner were used.

data_processing: The data were analyzed with Affymetrix® Expression Console™using Affymetrix default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 5.

organism: Arabidopsis thaliana

source_name: 7-day old seedling roots, 3h treatment

growth_protocol: Approximately 50-100 Arabidopsis seeds were sown on a nylon mesh in which roots passed through the mesh apertures (125 μm nominal hole size) allowing for separation of roots and shoots.

extract_protocol: Total RNA was extracted from seedling roots using Trizol LS (Invitrogen) according to the manufacturer's recommendations.

treatment_protocol: Mesh discs containing 7-day-old seedlings were transferred to Petri plates for the treatments indicated in the text and frozen immediately thereafter.

value: OGs

tag: time

value: 3 hours

tag: ecotype

tag: developmental stage

value: seedling

value: root


title: HUVECs from GDM mother 13

value: Infant umbilical cord

value: human vascular endothelial cells (HUVECs)

value: passage 2


title: seedling roots, 3h OGs, bio rep 1


title: seedling roots, 3h cellobiose, bio rep 3

value: cellobiose


title: Group03_Exp_Rno_Duo_8D_rep1

description:
gene expression
4492.gpr_Group03_Exp

value: Female

value: Sodium Dichromate Dihydrate (SDD)

tag: dose

tag: dose units

value: mg/L

tag: replicate

value: 8 Days


title: seedling roots, 3h cellobiose, bio rep 2


title: Group03_Exp_Mmu_Duo_8D_rep3

tag: gender

tag: time-point

tag: animal id

value: duodenum


title: Group4_CT_Mmu_Duo_8D_rep3

tag: treatment

value: Vehicle


title: Group03_CT_Mmu_Duo_8D_rep3


title: seedling roots, 3h chitin, bio rep 3

value: chitin


title: seedling roots, 3h OGs, bio rep 3


title: Mtb_INHd4_rep3

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

description: Biological replicate 3 of 3

hyb_protocol: Slide was hybridized for 16 hours at 42 in water bath with volume of 60 uL in solution of standard gene expression hybridization solution, and blocked in standard prehybridization solution. After hybridization, the slide was washed with standard wash protocol.

scan_protocol: scanned with PMT voltage adjusted for maximum dynamic range on Axon Genepix 4000B scanner

data_processing: Spots were gridded and quantitated in TIGR Spotfinder, data were processed in TIGR MIDAS with lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on

organism: Mycobacterium tuberculosis

source_name: Mtb log phase (Reference)

label_protocol: 2 ug total RNA was used as template for reverse transcription with random hexamer primers and aminoallyl-dUTP in a 2:3 ratio to dTTP in the nucleotide mix. After overnight incubation at 42°C, the reaction was stopped, RNA was hydrolyzed, and unincorporated nucleotides and free amines were removed with the Qiagen MinElute kit as per protocol, with amine-free phosphate wash and elution buffers. cDNA concentration and purity were measured by Nanodrop. Cy3 and Cy5 dyes were coupled to the aminoallyl-cDNA, which was then purified using a MinElute kit. Probe concentration, purity, and dye incorporation were measured by Nanodrop.

growth_protocol: Cultures were grown in 60mL 7H9 OADC 0.5% glycerol 0.05% Pan 50 µg/ml 0.05% tween-80 broth in 500 mL roller bottles to an OD600nm= 0.2 in a roller incubator at 37°C.

extract_protocol: Cells are collected by centrifugation and resuspended in 1mL buffer RLT from a Qiagen RNeasy kit. The suspension is transferred to Fast-Prep Blue Cap tubes and processed for 45 seconds at speed 6.5 in a Fast-Prep apparatus. After a brief incubation on ice the debris is spun down and the supernatant (~750uL) is removed to a fresh microcentrifuge tube. 525uL absolute ethanol is added and the samples are applied to RNeasy columns in two applications. At this point the RNA is purified as recommended by the Qiagen protocol.

treatment_protocol: 10mL was removed and harvested by centrifugation, then resuspended in 1mL Qiagen RNA protect and stored at 4°C. To remainder, isoniazid was added to final concentration 1ug/mL and cultures were returned to incubator for 4 days before harvest of remaining 50mL as for before treatment samples.

tag: strain

value: control

source_name: Mtb INH persisters (Test)

value: isoniazid


title: seedling roots, 3h cellobiose, bio rep 1

tag: tissue


title: seedling roots, 3h chitin, bio rep 2


title: Mtb_INHd4_rep1

description: Biological replicate 1 of 3


title: seedling roots, 3h control, bio rep 1

value: no treatment control


title: seedling roots, 3h control, bio rep 3

value: 3 hours


title: seedling roots, 3h chitin, bio rep 1

value: seedling


title: seedling roots, 25min cellobiose, bio rep 3

description: gene expression data from seedling roots 25min after elicitor treatment

source_name: 7-day old seedling roots, 25min treatment

value: root


title: seedling roots, 25min chitin, bio rep 3


title: seedling roots, 25min OGs, bio rep 1

value: OGs


title: seedling roots, 25min OGs, bio rep 2


title: seedling roots, 25min OGs, bio rep 3


title: seedling roots, 25min cellobiose, bio rep 1


title: seedling roots, 3h control, bio rep 2


title: Mtb_INHd4_rep2

description: Biological replicate 2 of 3


title: seedling roots, 25min chitin, bio rep 2


title: Group4_Exp_Rno_Duo_8D_rep3

description:
gene expression
4514.gpr_Group4_Exp


title: rep3 Mig GM+

city: La Jolla

first: Dong-Er

address: 3855 Health Sciences Drive

institute: UCSD Moores Cancer Center

description:
Mig+GM_3
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data was normalized using invariant set normalization with dCHIP.

source_name: Mig Lin-/c-Kit+ HSPCs with GM-CSF treatment

label_protocol: Total RNAs were labeled and hybridized on Illumina Mouse Ref-8 v2.0 Expression BeadChips following manufacturer’s protocol

growth_protocol: Lineage negative bone marrow cells were isolated from C57B6/J mice. Cells were cultured in StemSpan SFEM with 15% FBS, 10 ng/ml rmIL-3, 50 ng/ml rmSCF, 50 ng/ml rmFLT3L, 1% penicillin-streptomycin, and 1% glutamine, at the concentration of 2 x 10^5 cells/ml, and prestimulated overnight. Cells were retrovirally transduced with control MigR1 (Mig) or MigR1-HA-RUX1-ETO (RE) for 24 hours. After transduction, cells were washed, resuspended in StemSpan SFEM with or without addition of 10ng/ml of rmGM-CSF for 24 hours. After a total of 48 hours of RUNX1-ETO expression and 24 hours of GM-CSF treatment, GFP+/Lineage-/c-Kit+ cells were sorted for RNA isolation.

extract_protocol: RNA was isolated using column purification with the QIAGEN RNeasy mini kit in accordance with the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: MigR1 (Mig) HSPCs

value: 10ng/mL rmGM-CSF


title: rep3 AE GM-

description:
RE_3
Replicate 3

source_name: RE Lin-/c-Kit+ HSPCs without GM-CSF treatment

value: MigR1-RUNX1-ETO (RE) HSPCs

value: No Treatment


title: seedling roots, 25min chitin, bio rep 1


title: rep2 Mig GM-

description:
Mig_2
Replicate 2

source_name: Mig Lin-/c-Kit+ HSPCs without GM-CSF treatment


title: seedling roots, 25min control, bio rep 1


title: seedling roots, 25min cellobiose, bio rep 2

value: cellobiose


title: rep1 AE GM+

description:
RE+GM_1
Replicate 1

source_name: RE Lin-/c-Kit+ HSPCs with GM-CSF treatment


title: rep3 Mig GM-

description:
Mig_3
Replicate 3


title: seedling roots, 25min control, bio rep 3


title: rep3 AE GM+

description:
RE+GM_3
Replicate 3


title: rep2 AE GM-

description:
RE_2
Replicate 2


title: rep2 Mig GM+

description:
Mig+GM_2
Replicate 2


title: seedling roots, 25min control, bio rep 2


title: ostdl1a_S7_3

type: SRA

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
small RNA
ostdl1a mutant, anther development stage 7 (S7), rep 3.
Raw files for smallRNA-Seq were not provided by submitter

library_source: transcriptomic

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: Rice Genome Annotation Project 7.0
Supplementary_files_format_and_content: tag count file

organism: Oryza sativa

source_name: Rice spikelets

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol (Invitrogen) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-122-2001).

tag: genotype

value: ostdl1a mutant

value: anther development stage 7 (S7)


title: ostdl1a_S7_2

description:
small RNA
ostdl1a mutant, anther development stage 7 (S7), rep 2.
Raw files for smallRNA-Seq were not provided by submitter


title: rep2 AE GM+

description:
RE+GM_2
Replicate 2

tag: cell type


title: ostdl1a_S7_1

description:
small RNA
ostdl1a mutant, anther development stage 7 (S7), rep 1.
Raw files for smallRNA-Seq were not provided by submitter


title: rep1 Mig GM+

description:
Mig+GM_1
Replicate 1


title: ostdl1a_S5_3

description:
small RNA
ostdl1a mutant, anther development stage 5 (S5), rep 3.
Raw files for smallRNA-Seq were not provided by submitter

value: anther development stage 5 (S5)


title: rep1 Mig GM-

description:
Mig_1
Replicate 1


title: Group14_CT_Mmu_Duo_8D_rep1

first: Julia

value: Female

value: Vehicle

value: mg/L

value: 8 Days

value: duodenum


title: ostdl1a_S5_2

description:
small RNA
ostdl1a mutant, anther development stage 5 (S5), rep 2.
Raw files for smallRNA-Seq were not provided by submitter


title: patient 09, primary tumor, LOH status

city: Tokyo

first: Takuma

last: Morita

address: 1-5-45 Yushima, Bunkyo-ku

department: Maxillofacial Surgery

institute: Tokyo Medical and Dental University

description:
15-P_A_(OncoScan).CEL
15-P_C_(OncoScan).CEL
primary tumor of patient 09
LOH_09-P

hyb_protocol: The products were digested using HaeIII, mixed with the hybridization cocktail, denatured, and hybridized to the GeneChip OncoScan Arrays (Affymetrix)

scan_protocol: The hybridized arrays were finally washed and stained in a GeneChip Fluidics Station (Affymetrix) and scanned using a GeneChip Scanner (Affymetrix).

data_processing: Genome-wide copy number and loss of heterozygosity data were included in the .CEL files. The two files for each allele were collated for analysis in the .OSCHP files, which were quality checked using OncoScan Console Software (Affymetrix). Genome-wide copy number and CN-LOH data were visualized using Nexus Express for OncoScan Software (ver.3 BioDiscovery) and the Tuscan algorithm.  For statistical analysis, the status of copy number and LOH for each patient was calculated by Chromosome Analysis Suite (Affymetrix), and the obtained data in text file format was further analyzed by R statistical software (http://www.r-project.org/).

source_name: primary tumor of patient 09

label_protocol: Genomic DNA (80 ng per each sample) was labeled by OncoScan FFPE Assay Kit (Affymetrix) according to manufacturer's instruction.

extract_protocol: All samples were formalin-fixed paraffin-embedded (FFPE) tissues. Sections of 4 μm were cut from each FFPE tissue and mounted onto slides. After confirmation of the tumor area by pathological examination, the viable cancer cell populations were isolated from each slide-mounted section using scalpels. Dissected samples were collected for each sample and DNA extraction was performed using the QIAamp DNA FFPE Tissue Kit (QIAGEN) according to the manufacturer’s protocol. For each sample, genomic DNA was isolated, purified, and then eluted in ATE buffer, low EDTA, pH 8.3. The double-stranded genomic DNA was quantified using a Qubit 2.0 Fluorometer (Life Technologies) and diluted to 12 ng/μL.

tag: disease state

value: oral tongue squamous cell carcinoma (OTSCC)

tag: individual

value: patient 09

value: primary tumor (PT)

value: LOH


title: ostdl1a_S5_1

description:
small RNA
ostdl1a mutant, anther development stage 5 (S5), rep 1.
Raw files for smallRNA-Seq were not provided by submitter


title: patient 09, metastatic lymph node, LOH status

description:
15-L_A_(OncoScan).CEL
15-L_C_(OncoScan).CEL
metastatic lymph node of patient 09
LOH_09-L

source_name: metastatic lymph node of patient 09

value: metastatic lymph node (MLN)


title: FS1 Romidepsin 16h

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

institute: University Hospital Düsseldorf

description: FS1 treated with Romidepsin for 16h

data_processing: The data were normalised using quantile normalisation with Bioconductor R. Normalized values were tranformed into log2-values.

source_name: Sertoli cells

growth_protocol: TCam-2 and NCCIT cells were grown in RPMI, while 2102EP and JAR were grown in DMEM. Both media were supplemented with 10 % fetal calf serum (FCS) (PAA, Pasching, Austria), 1 % Penicillin / streptomycin (P / S) (PAN, Aidenbach, Germany), 200 mM L-Glutamine (Glu) (PAN, Aidenbach, Germany). MPAF and ARZ were grown in DMEM medium (10 % FCS, 1 % P / S, 200 mM Glu, 1x non-essential amino acids (PAA, Pasching, Austria), 100 nM ß-Mercaptoethanol (Sigma-Aldrich, Taufkirchen, Germany). FS1 cells were grown DMEM medium (20 % FCS, 1 % P / S, 200 mM Glu, 1x non-essential amino acids, 100 nM ß-Mercaptoethanol). All cells were grown at 37 °C and 7.5 % CO2.

extract_protocol: RNA was isolate by the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line


title: patient 08, metastatic lymph node, LOH status

description:
14-L_A_(OncoScan).CEL
14-L_C_(OncoScan).CEL
metastatic lymph node of patient 08
LOH_08-L

source_name: metastatic lymph node of patient 08

value: patient 08


title: patient 08, primary tumor, LOH status

description:
14-P_A_(OncoScan).CEL
14-P_C_(OncoScan).CEL
primary tumor of patient 08
LOH_08-P

source_name: primary tumor of patient 08


title: ostdl1a_S3_3

description:
small RNA
ostdl1a mutant, anther development stage 3 (S3), rep 3.
Raw files for smallRNA-Seq were not provided by submitter

value: anther development stage 3 (S3)


title: ostdl1a_S3_2

description:
small RNA
ostdl1a mutant, anther development stage 3 (S3), rep 2.
Raw files for smallRNA-Seq were not provided by submitter


title: FS1 Solvent 8h

description: FS1 treated with DMSO for 8h


title: patient 07, metastatic lymph node, LOH status

description:
11-L10_A_(OncoScan).CEL
11-L10_C_(OncoScan).CEL
metastatic lymph node of patient 07
LOH_07-L

source_name: metastatic lymph node of patient 07

value: patient 07


title: patient 10, primary tumor, LOH status

description:
16-P4_A_(OncoScan).CEL
16-P4_C_(OncoScan).CEL
primary tumor of patient 10
LOH_10-P

source_name: primary tumor of patient 10

value: patient 10


title: patient 10, metastatic lymph node, LOH status

description:
16-L53_A_(OncoScan).CEL
16-L53_C_(OncoScan).CEL
metastatic lymph node of patient 10
LOH_10-L

source_name: metastatic lymph node of patient 10


title: patient 07, primary tumor, LOH status

description:
11-P_A_(OncoScan).CEL
11-P_C_(OncoScan).CEL
primary tumor of patient 07
LOH_07-P

source_name: primary tumor of patient 07


title: FS1 Romidepsin 8h

description: FS1 treated with Romidepsin for 8h


title: patient 06, metastatic lymph node, LOH status

description:
7-L_A_(OncoScan).CEL
7-L_C_(OncoScan).CEL
metastatic lymph node of patient 06
LOH_06-L

source_name: metastatic lymph node of patient 06

value: patient 06


title: FS1 Solvent 16h

description: FS1 treated with DMSO for 16h


title: msp1_S7_3

description:
small RNA
msp1 mutant, anther development stage 7 (S7), rep 3.
Raw files for smallRNA-Seq were not provided by submitter

value: msp1 mutant

value: anther development stage 7 (S7)


title: patient 06, primary tumor, LOH status

description:
7-P_A_(OncoScan).CEL
7-P_C_(OncoScan).CEL
primary tumor of patient 06
LOH_06-P

source_name: primary tumor of patient 06


title: ostdl1a_S3_1

description:
small RNA
ostdl1a mutant, anther development stage 3 (S3), rep 1.
Raw files for smallRNA-Seq were not provided by submitter

value: ostdl1a mutant


title: ARZ Romidepsin 16h

description: ARZ treated with Romidepsin for 16h

source_name: neonatal primary fibroblasts

value: ARZ


title: msp1_S7_2

description:
small RNA
msp1 mutant, anther development stage 7 (S7), rep 2.
Raw files for smallRNA-Seq were not provided by submitter


title: ARZ Romidepsin 8h

description: ARZ treated with Romidepsin for 8h


title: patient 05, primary tumor, LOH status

description:
5-P_A_(OncoScan).CEL
5-P_C_(OncoScan).CEL
primary tumor of patient 05
LOH_05-P

source_name: primary tumor of patient 05

value: patient 05


title: patient 04, metastatic lymph node, LOH status

description:
4-L_A_(OncoScan).CEL
4-L_C_(OncoScan).CEL
metastatic lymph node of patient 04
LOH_04-L

source_name: metastatic lymph node of patient 04

value: patient 04


title: msp1_S5_3

description:
small RNA
msp1 mutant, anther development stage 5 (S5), rep 3.
Raw files for smallRNA-Seq were not provided by submitter

value: anther development stage 5 (S5)


title: msp1_S7_1

description:
small RNA
msp1 mutant, anther development stage 7 (S7), rep 1.
Raw files for smallRNA-Seq were not provided by submitter


title: msp1_S5_2

description:
small RNA
msp1 mutant, anther development stage 5 (S5), rep 2.
Raw files for smallRNA-Seq were not provided by submitter


title: msp1_S5_1

description:
small RNA
msp1 mutant, anther development stage 5 (S5), rep 1.
Raw files for smallRNA-Seq were not provided by submitter


title: ARZ Solvent 16h

description: ARZ treated with DMSO for 16h


title: patient 05, metastatic lymph node, LOH status

description:
5-L8_A_(OncoScan).CEL
5-L8_C_(OncoScan).CEL
metastatic lymph node of patient 05
LOH_05-L

source_name: metastatic lymph node of patient 05

value: oral tongue squamous cell carcinoma (OTSCC)