title: genomic DNA from 3999979020_R02C01

value: Hispanic


title: genomic DNA from 3999979011_R06C02

status: Public on Mar 10 2018

type: genomic

city: Los Angeles

first: Ritz

last: Beate

state: California

address: 650 Charles E Young Dr. South

department: Epidemiology

country: USA

institute: UCLA Fielding School of Public Health

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

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

data_processing: R software v3.4.2

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from whold blood samples using the Qiagen Gentra Puregene Blood Kit according to standard instructions

tag: disease state

value: Parkinson's disease (PD)

tag: age

tag: gender

value: Male

tag: ethnicity

value: Caucasian

tag: tissue

value: whole blood


title: Lung_WT_MyD88 fx_2h_rep2

type: RNA

city: RTP

first: Seddon

last: Thomas

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

description: Gene expression from MyD88 fx/fx lung treated with OVA/ stFLA for 2h.

hyb_protocol: Hybridization was done according to the manufacturer's instructions.

scan_protocol: Gene expression was quantified on the nCounter Digital AnalyzerTM.

data_processing: Raw data was normalized using the Nanostring nCounter software.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: 50 ng of each total RNA sample was labeled according to the manufacturer's instructions.

extract_protocol: Frozen lung lobes were homogenized and RNA isolated from whole lungs using the Qiagen Rneasy Mini Kit.

treatment_protocol: Mice were either untreated or sensitized oropharyngeally with 100 ug ovalbumin (OVA)/ 1250 ng standard flagellin (stFLA) for 2 or 6 hours in vivo.  After this time, lungs were isolated and snap frozen for RNA isolation.

tag: background

value: male

value: Lung

tag: timepoint

tag: treatment

value: OVA/ stFLA

tag: genotype

value: MyD88 fx/fx


title: genomic DNA from 3999979036_R05C01

value: PD-free control


title: genomic DNA from 3999979020_R01C01

value: Female


title: genomic DNA from 3999979011_R06C01


title: Lung_MyD88_KO_6h_rep3

description: Gene expression from MyD88 -/- lung treated with OVA/ stFLA for 6 h.


title: genomic DNA from 3999979011_R05C02


title: Lung_WT_MyD88 fx_0h_rep3

description: Gene expression from MyD88 fx/fx lung.


title: Lung_WT_MyD88 fx_0h_rep2

description: Gene expression from MyD88 fx/fx lung.


title: Lung_MyD88_KO_6h_rep2


title: Lung_WT_MyD88 fx_0h_rep1

description: Gene expression from MyD88 fx/fx lung.


title: genomic DNA from 3999979011_R02C02


title: genomic DNA from 3999979011_R02C01


title: Lung_MyD88_KO_2h_rep3

description: Gene expression from MyD88 -/- lung treated with OVA/ stFLA for 2 h.


title: genomic DNA from 3999979011_R05C01


title: genomic DNA from 3999979011_R01C02


title: Lung_MyD88_KO_2h_rep2


title: Mesial Temporal Lobe Epilepsy Tissue 1

city: NEW DELHI

first: APARNA

middle: BANERJEE

last: DIXIT

state: AIIMS

address: Room No 7003, 7th Floor, Convegence Block, AIIMS, ANSARI, NAGAR

department: A collaborative project between NBRC & AIIMS

country: India

institute: NATIONAL BRAIN RESERACH CENTRE

hyb_protocol: Labeled DNAs were hybridized to Human DNA methylation Microarray slides (G4495A, AMADID 023795) containing the annotated human 27,627 expanded CpG islands, 5081 UMR regions, 237,227 biological probes with median probe spacing of 97bp followingthe microarray manufacturer’s instructions.

scan_protocol: The slides were subsequently washed and scanned using Agilent scanner P/N G2565BA

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

source_name: Mesial Temporal Lobe Epilepsy tissue_MeDIP-WGA

label_protocol: 2μg of DNA from the WGAamplified sample (MeDIP-WGA), along with their corresponding whole genomic DNA (input), were labeled usingthe SureTag DNA labeling kit (5190-3400, Agilent)

growth_protocol: Tissues resected from 2 autopsy , 3 MTLE and 4 FCD type II were used for isolating Genomic DNA

extract_protocol: Genomic DNA was extracted using genomic DNAextraction kit (Qiagen, Hilden, Germany) and Methylated DNA was immunoprecipitated using standard protocols  with some modifications.  Briefly, 4 µg MseI digested genomic DNA was immunoprecipitated with 10 µg of monoclonal mouse anti 5-methylcytidine antibody (New England Biolab, Pickering, Ontario and Abcam Inc.Cambridge, MA 02139) a negative control normal mouse IgG (Abcam, ab81032) in a final volume of 500 μl IP buffer (10 mM sodium phosphate (pH 7.0), 140 mM NaCl, 0.05% Triton X-100). We incubated the mixture with 40 μl of Dynabeads and M-280 sheep antibody to mouse IgG (Dynal Biotech) for 12 hr at 4°C and washed it seven times with 700 μl of IP buffer. We then treated the beads with proteinase K for 4 hr at 50°C and recovered the methylated DNA by phenol-chloroform extraction followed by ethanol precipitation. The immunoprecipitated DNA and a sample of input DNA were amplified using GenomePlex Complete Whole Genome Amplification (WGA) kit (Sigma-Aldrich, Saint Louis, Missouri 63103 USA). At each step DNA integrity was analyzed by agarose gel electrophoresis.

treatment_protocol: autopsy were used as non-epileptic controls and MTLE  and FCD tissues were epileptic tissues

tag: subject status

value: Mesial temporal epilepsy (MTLE) patient

value: FEMALE

value: brain

source_name: Mesial Temporal Lobe Epilepsy input DNA

tag: sample type

value: whole genomic DNA (input)


title: Lung_MyD88_KO_0h_rep3

description: Gene expression from MyD88 -/- lung.


title: Lung_MyD88_KO_6h_rep1


title: Lung_MyD88_KO_2h_rep1


title: genomic DNA from 3999979011_R01C01


title: genomic DNA from 3999979010_R06C02


title: genomic DNA from 3999979010_R06C01


title: Lung_MyD88_KO_0h_rep2

description: Gene expression from MyD88 -/- lung.


title: genomic DNA from 3999979010_R05C02


title: genomic DNA from 3999979010_R04C01


title: genomic DNA from 3999979010_R02C02


title: genomic DNA from 3999979010_R03C01


title: genomic DNA from 3999979010_R05C01


title: Lung_AM_CD11c_cre+_MyD88 fx_6h_rep2

description: Gene expression from MyD88 fx/fx; Itgax-cre+/Tg Alveolar Macrophage

data_processing: Raw data was normalized using quantile normalization.

extract_protocol: RNA from sorted alveolar macrophages was isolated using the Trizol extraction protocol. RNA was concentrated and excess organic solvents removed using the Qiagen Rneasy MinElute Cleanup Kit.

treatment_protocol: Mice were sensitized oropharyngeally with 100 ug ovalbumin (OVA)/ 1250 ng standard flagellin (stFLA) for 6 hours in vivo.  After this time, lungs were isolated and digested with collagenease, DNase, hyaluronidase, and Liberase TM to generate a single cell suspension. Cells were stained for flow cytometry and sorted for autofluorescence hi and CD11c hi cells to include alveolar macrophages but not cDCs, moDCs, or inflammatory DCs.

tag: cell type

value: Sorted Alveolar Macrophage

value: MyD88 fx/fx; Itgax-cre+/Tg


title: Lung_AM_MyD88_KO_6h_rep1

description: Gene expression from MyD88 -/- Alveolar Macrophage


title: Lung_AM_CD11c_cre+_MyD88 fx_6h_rep1


title: Lung_AM_SPC_cre+_MyD88 fx_6h_rep1

description: Gene expression from MyD88 fx/fx; Sftpc-cre+/Tg Alveolar Macrophage

value: MyD88 fx/fx; Sftpc-cre+/Tg


title: Lung_AM_SPC_cre+_MyD88 fx_6h_rep2


title: Lung_AEC_MyD88_KO_2h_rep3

description: Gene expression from MyD88 -/- airway epithelial cells

extract_protocol: RNA from sorted AECs was isolated using the Trizol extraction protocol. RNA was concentrated and excess organic solvents removed using the Qiagen Rneasy MinElute Cleanup Kit.

treatment_protocol: Mice were sensitized oropharyngeally with 100 ug ovalbumin (OVA)/ 1250 ng standard flagellin (stFLA) for 2 hours in vivo.  After this time, lungs were isolated and digested with elastase and DNase to generate a single cell suspension. Cells were stained for flow cytometry and sorted for 7-AAD- CD31- CD34- CD45- EpCAM+ cells to include AECs but not endothelial cells or leukocytes.

value: Sorted Airway Epithelial Cells


title: genomic DNA from 3999979005_R05C02


title: genomic DNA from 3999979005_R06C02

value: Male


title: Lung_AM_WT_MyD88 fx_6h_rep1

description: Gene expression from MyD88 fx/fx Alveolar Macrophage


title: genomic DNA from 3999979005_R06C01

value: Parkinson's disease (PD)

value: Caucasian


title: Lung_AEC_MyD88_KO_2h_rep2

value: male


title: Lung_AEC_CD11c_cre+_MyD88 fx_2h_rep3

description: Gene expression from MyD88 fx/fx; Itgax-cre+/Tg airway epithelial cells

value: Lung


title: genomic DNA from 3999979005_R05C01

value: whole blood


title: genomic DNA from 3999979005_R04C01


title: genomic DNA from 3999979005_R02C02


title: Lung_AEC_CD11c_cre+_MyD88 fx_2h_rep1

value: OVA/ stFLA


title: Lung_AEC_CD11c_cre+_MyD88 fx_2h_rep2


title: genomic DNA from 3999979005_R02C01


title: genomic DNA from 3999979010_R01C02


title: Lung_AEC_SPC_cre+_MyD88 fx_2h_rep3

description: Gene expression from MyD88 fx/fx; Sftpc-cre+/Tg airway epithelial cells


title: genomic DNA from 3999979004_R05C01

value: PD-free control

value: Hispanic


title: genomic DNA from 3999979005_R01C02


title: Lung_AEC_SPC_cre+_MyD88 fx_2h_rep1


title: Lung_AM_WT_MyD88 fx_6h_rep2

value: MyD88 fx/fx


title: genomic DNA from 3999979004_R03C02


title: Lung_AEC_SPC_cre+_MyD88 fx_2h_rep2


title: genomic DNA from 3999979004_R06C01

value: Female


title: genomic DNA from 3999979004_R04C02


title: genomic DNA from 3999979004_R02C02

description: raw data unavailable for this sample


title: genomic DNA from 3999979004_R01C02


title: Lung_AEC_WT_MyD88 fx_2h_rep2

description: Gene expression from MyD88 fx/fx airway epithelial cells


title: Lung_AEC_MyD88_KO_2h_rep1


title: Lung_AEC_WT_MyD88 fx_2h_rep1


title: Lung_cDC_MyD88_KO_6h_OVA_stFLA_rep3

description: Gene expression from MyD88 -/-conventional Dendritic cell

extract_protocol: RNA from sorted cDCs was isolated using the Trizol extraction protocol. RNA was concentrated and excess organic solvents removed using the Qiagen Rneasy MinElute Cleanup Kit.

treatment_protocol: Mice were sensitized oropharyngeally with 100 ug ovalbumin (OVA)/ 1250 ng standard flagellin (stFLA) for 6 hours in vivo.  After this time, lungs were isolated and digested with collagenease, DNase, hyaluronidase, and Liberase TM to generate a single cell suspension. Cells were stained for flow cytometry and sorted for autofluorescence-, CD11c+, I-A(b) hi, CD88-, Ly6C- cells to include cDCs but not alveolar macrophages, moDCs, or inflammatory DCs.

value: Sorted conventional Dendritic cell


title: Lung_cDC_MyD88_KO_6h_OVA_stFLA_rep1


title: Lung_cDC_CD11c_cre+_MyD88 fx_6h_OVA_stFLA_rep3

description: Gene expression from MyD88 fx/fx; Itgax-cre+/Tgg conventional Dendritic cell


title: Lung_cDC_CD11c_cre+_MyD88 fx_6h_OVA_stFLA_rep2


title: Lung_cDC_CD11c_cre+_MyD88 fx_6h_OVA_stFLA_rep1


title: genomic DNA from 3999979002_R04C01


title: Lung_cDC_SPC_cre+_MyD88 fx_6h_OVA_stFLA_rep4

description: Gene expression from MyD88 fx/fx; Sftpc-cre+/Tg conventional Dendritic cell


title: genomic DNA from 3999979002_R03C01


title: genomic DNA from 3999979002_R02C01


title: genomic DNA from 3999979001_R06C02


title: Lung_cDC_SPC_cre+_MyD88 fx_6h_OVA_stFLA_rep3


title: genomic DNA from 3999979001_R06C01


title: Lung_cDC_SPC_cre+_MyD88 fx_6h_OVA_stFLA_rep1


title: Lung_cDC_MyD88_KO_6h_OVA_stFLA_rep2


title: genomic DNA from 3999979001_R05C01


title: genomic DNA from 3999979002_R06C01


title: genomic DNA from 3999979001_R05C02


title: genomic DNA from 3999979001_R04C02


title: genomic DNA from 3999979002_R05C01


title: Lung_cDC_WT_MyD88 fx_6h_OVA_stFLA_rep2

description: Gene expression from MyD88 fx/fx conventional Dendritic cell


title: Lung_cDC_WT_MyD88 fx_6h_OVA_stFLA_rep1


title: Lung_cDC_WT_MyD88 fx_6h_OVA_stFLA_rep4


title: Lung_cDC_WT_MyD88 fx_6h_OVA_stFLA_rep3


title: Lung_CD11c_cre+_MyD88 fx_6h_rep2

description: Gene expression from MyD88 fx/fx; Itgax-cre+/Tg lung treated with OVA/ stFLA for 6h.


title: genomic DNA from 3999979001_R03C02


title: genomic DNA from 3999979001_R04C01


title: genomic DNA from 3999979001_R03C01


title: Lung_CD11c_cre+_MyD88 fx_6h_rep1


title: Lung_CD11c_cre+_MyD88 fx_6h_rep3


title: genomic DNA from 3999979002_R01C01


title: genomic DNA from 3999979001_R02C01


title: Lung_cDC_SPC_cre+_MyD88 fx_6h_OVA_stFLA_rep2


title: genomic DNA from 3999979001_R01C02


title: genomic DNA from 3999979001_R01C01


title: genomic DNA from 3999979001_R02C02


title: 12_denerv_6_miRNA

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

country: Sweden

institute: SciLifeLab. Stockholm University

description: miRNA enriched

hyb_protocol: GeneChips were scanned using the Genechip Scanner 3000.  GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

scan_protocol: not provided

data_processing: normalised using RMA method. CHP files extracted from Affymetrix Expression Console Software v1.4.1.46

label: Biotin

organism: Rattus norvegicus

source_name: Denervated bladders from rats after bilat. pelvicus freezing

label_protocol: Protocol in chapter 3 was followed (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/mirna_array_strip_flashtag_manual.pdf)

growth_protocol: surgery (Sham samples) and surgery and bilateral ganglion freezing (for denerv samples)

extract_protocol: Biotin with Flash Tag Ligation

treatment_protocol: miRneasy plus RNeasy MinElute Cleanup

tag: strain

value: Sprague Dawley

value: female

value: ~3 months

value: urinary bladder

tag: in vivo treatments

value: surgery and bilateral ganglion freezing

tag: tissue harvesting

value: euthanization

value: over 95 percent smooth muscle


title: 11_denerv_5_miRNA

description: miRNA enriched


title: 7_denerv_1_miRNA

description: miRNA enriched


title: 9_denerv_3_miRNA

description: miRNA enriched


title: Lung_AM_MyD88_KO_6h_rep2

value: Sorted Alveolar Macrophage


title: 6_Sham_6_miRNA

description: miRNA enriched

source_name: Urinary bladders from sham op rats

value: surgery


title: 5_Sham_5_miRNA

description: miRNA enriched


title: 10_denerv_4_miRNA

description: miRNA enriched


title: Lung_cDC_MyD88_KO_6h_OVA_stFLA_rep1

description: Gene expression from MyD88 -/- lung treated with OVA/ stFLA for 6h

hyb_protocol: 5.5 μg micrograms of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console software.

source_name: Lung cDC MyD88 KO-6h OVA/stFLA

label_protocol: One hundred nanograms (100 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

treatment_protocol: Mice were either untreated or sensitized oropharyngeally with 100 ug ovalbumin (OVA)/ 1250 ng standard flagellin (stFLA) for 6 hours in vivo.  After this time, lungs were isolated and digested with collagenease, DNase, hyaluronidase, and Liberase TM to generate a single cell suspension. Cells were stained for flow cytometry and sorted for autofluorescence-, CD11c+, I-A(b) hi, CD88-, Ly6C- cells to include cDCs but not alveolar macrophages, moDCs, or inflammatory DCs.

value: male

value: Lung

value: Sorted cDC


description: Gene expression from MyD88 fx/fx; Sftpc-cre+/Tg lung treated with OVA/ stFLA for 6h

source_name: Lung cDC SPC cre+ MyD88 fx/fx-6h OVA/stFLA

value: OVA/ stFLA

value: MyD88 fx/fx; Sftpc-cre+/Tg


title: 2_Sham_2_miRNA

description: miRNA enriched


title: Lung_cDC_SPC_cre+_MyD88 fx_0h_rep2

description: Gene expression from MyD88 fx/fx; Sftpc-cre+/Tg lung

source_name: Lung cDC SPC cre+ MyD88 fx/fx-0h


description: Gene expression from MyD88 fx/fx; Itgax-cre+/Tg lung treated with OVA/ stFLA for 6h

source_name: Lung cDC CD11c cre+ MyD88 fx/fx-6h OVA/stFLA

value: MyD88 fx/fx; Itgax-cre+/Tg


title: Lung_cDC_WT_MyD88 fx_6h_OVA_stFLA_rep2

description: Gene expression from MyD88 fx/fx lung treated with OVA/ stFLA for 6h

source_name: Lung cDC WT MyD88 fx/fx-6h OVA/stFLA

value: MyD88 fx/fx


title: Lung_cDC_MyD88_KO_6h_OVA_stFLA_rep2


title: Lung_cDC_WT_MyD88 fx_6h_OVA_stFLA_rep1


title: 4_Sham_4_miRNA

description: miRNA enriched


title: Lung_cDC_MyD88_KO_0h_rep1

description: Gene expression from MyD88 -/- lung

source_name: Lung cDC MyD88 KO-0h


title: Lung_cDC_CD11c_cre+_MyD88 fx_0h_rep2

description: Gene expression from MyD88 fx/fx; Itgax-cre+/Tg lung

source_name: Lung cDC CD11c cre+ MyD88 fx/fx-0h


title: Lung_cDC_WT_MyD88 fx_0h_rep2

description: Gene expression from MyD88 fx/fx lung

source_name: Lung cDC WT MyD88 fx/fx-0h


title: Lung_cDC_MyD88_KO_0h_rep2

description: Gene expression from MyD88 -/- lung


title: Lung_cDC_CD11c_cre+_MyD88 fx_0h_rep1


title: Lung_cDC_WT_MyD88 fx_0h_rep1

description: Gene expression from MyD88 fx/fx lung


title: Lung_cDC_SPC_cre+_MyD88 fx_0h_rep1


title: 8_denerv_2_miRNA

description: miRNA enriched


title: 3_Sham_3_miRNA

description: miRNA enriched


title: st 38: Andrei_st_381-2_r1_001

type: SRA

city: Williamsburg

first: Margaret

last: Saha

state: VA

address: 540 Landrum Drive

department: Biology

institute: College of William and Mary

library_source: transcriptomic

data_processing:
Read quality was checked using FastQC (default parameters)
Trimmomatic (Version 0.36) was used to trim Illumina Truseq paired-end adapters and bases with phred quality scores < 5. Paramters: TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25
Trinity (Version 2.4.0) was used with all 9 RNA-Seq samples as input to assemble a de novo transcriptome. Parameters: --SS_lib_type RF --min_kmer_cov 2 --trimmomatic --seqType fq
Salmon (Version 0.8.2) was used for quantification (quasi-mapping-based-mode) generating TPM adundances for each sample using the de novo transcriptome as a reference. Parameters: --numBootstraps 50 -p 24 -l ISR --seqBias
Supplementary_files_format_and_content: Tab-delimited text file. Each row represents a transcript assembled by Trinity and each column contains TPM abundances for the specified sample.

organism: Xenopus andrei

source_name: group of 5 embryos

growth_protocol: Embryos were reared in 0.1X Marc’s Modified Ringers (MMR) with 50 µg/ml gentamicin at room temperature (22ºC)

extract_protocol:
Embryos were homogenized in TRI reagent and RNA was extracted with choloroform before separating aqueous and organic layers in a Phase Lock Gel Heavy tube (QuantaBio). RNA was purified using the MagMAX™- 96 for Microarrays (Thermo Fisher Scientific) kit according to the manufacturer’s instructions.
Illumina TruSeq Stranded rRNA depletion

treatment_protocol: At the desired stages, groups of embryos were flash frozen in liquid nitrogen and stored at -80ºC

value: group of 5 embryos

tag: nieuwkoop and faber stage


title: 1_Sham_1_miRNA

description: miRNA enriched

value: Sprague Dawley


title: st 30: Andrei_st_301-1_r1_001


title: st 40: Andrei_st_401-2_r1_001


title: st 18: Andrei_st_181-2_r1_001


title: st 12: Andrei_st_12-1_r1_001


title: st 10: Andrei_st_10-1_r1_001


title: st 35: Andrei_st_351-2_r1_001


title: st 0: Andrei_st_01-2_r1_001

value: 0 (unfertilized egg)


title: st 25: Andrei_st_251-2_r1_001


title: OVX+T osteoblast

city: Pu-Tzi

first: Wei-Bin

last: Hsu

state: Chia-Yi

address: No. 6, West Section, Chia-Pu Road

department: Sports center

country: Taiwan

institute: Chang Gung Memorial Hospital, Chiayi,

description: Gene expression data from osteoblast in the OVX mice with treadmill training

hyb_protocol: cDNA was hybridized to Affymetrix GeneChip Mouse Exon 1.0 ST Array according to the manufacturer’s instructions.

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

data_processing: Expression values were processed with Signal Space Transformation (SST) and Robust Multichip Average method, which included log2 transformation and quantile normalization.

source_name: osteoblast from ovariectomized mice with treadmill training

label_protocol: RNA was amplified (in vitro transcription) and generate biotin labeled Single-stranded cDNA according to manufacturer's instructions.

growth_protocol: The harvested tibias from each group were carefully cleaned of adherent soft tissue.  The epiphysis was cut off and the bone marrow cells flushed out using a 27-gauge needle syringe with phosphate buffered saline (PBS). The hollowed out bones were milled into 1-2mm2 bone chips and washed with PBS for three times. The bone chips then underwent two sequential 30-minute digestion runs using a commercial mixture [DMEM with 20ng/mL type II collagenase (Gibco)] at 37℃ in an oscillating water bath. After digestion, the bone pieces were vigorously washed with PBS for three times and transferred into a 10-cm Petri dish containing 20% FBS DMEM at a density of about 20-30 pieces per dish. Fresh medium was replaced three times per week.

extract_protocol: Total RNA was harvested and purified using miRNeasy Mini kit (Qiagen, Valencia, CA, USA)

value: female

value: long bone


title: 11_denerv_5_mRNA

hyb_protocol: Following fragmentation, 3.5ug of ssDNA were hybridized. See further information in chapter 3 (https://www.thermofisher.com/search/results?persona=DocSupport&refinementSearch=true&query=Manuals+%26+Protocols&navId=4294959596&refinementQuery=WT+PLUS+)

scan_protocol: GeneChips were scanned using the Genechip Scanner 3000.  GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

label: Biotin Allonamide Triphosphate

label_protocol: Biotin Allonamide Triphosphate and label incorporation Labelling reaction at 37 degrees

extract_protocol: miRneasy plus RNeasy MinElute Cleanup

treatment_protocol: surgery (Sham samples) and surgery and bilateral ganglion freezing (for denerv samples)

value: ~3 months

value: urinary bladder

value: surgery and bilateral ganglion freezing

value: over 95percent smooth muscle


title: OVX osteoblast

description: Gene expression data from osteoblast in theOVX mice

source_name: osteoblast from ovariectomized mice

value: ovariectomized


title: 7_denerv_1_mRNA

value: euthanization


title: 10_denerv_4_mRNA


title: 5_Sham_5_mRNA

value: surgery


title: 12_denerv_6_mRNA


title: 4_Sham_4_mRNA


title: 9_denerv_3_mRNA


title: 6_Sham_6_mRNA


title: Sham osteoblast

description: Gene expression data from osteoblast in the sham mice

source_name: osteoblast from sham mice

value: sham surgery


title: 1_Sham_1_mRNA


title: Hca-P

city: Panjin

first: HUANG

last: HUANG

state: Liaoning

address: NO.2 Dagong Road, New District of Liaodong Bay

department: School of Life and Medical Sciences

country: China

institute: Dalian University of Technology

description: Hybridization signals were scanned and analyzed by Genepix 4000B microarray scanner. The scanned images were imported into the GenePix Pro 6.2 software (Axon Instruments) for grid alignment and data extraction. Replicated miRNAs were averaged, and the miRNAs with intensities ≥50 in all samples were chosen to calculate the median normalization factor. The expressed miRNA data were normalized using the median normalization and chosen for the differentially expressed miRNA screening.

hyb_protocol: The miRCURYTMArray Power hyb kit was used according to the manufacturer’s instructions.

data_processing:
The scanned images were imported into the GenePix Pro 6.0 software (Axon Instruments) for grid alignment and data extraction.
Replicated miRNAs were averaged, and the miRNAs with intensities ≥50 in all samples were chosen to calculate the median normalization factor. The expressed miRNA data were normalized using the median normalization and chosen for the differentially expressed miRNA screening.

source_name: Hepatocellular Carcinoma cell

label_protocol: The miRCURYTMArray Power Labeling kit was used according to the manufacturer’s instructions for miRNA labeling.

growth_protocol: Mouse hepatocarcinoma Hca-P, Hca-F cell lines , which deriving from H22 cell line  have metastatic potential in the lymph nodes, (established and stored by Department of Pathology, Dalian Medical University) was subcutaneously injected into abdominal cavity of 615-mice and grown in abdominal cavity about 7 days, then mice were sacrificed and cells enriched from ascites were cultured in 90% RPMI-1640 (Gibco, USA) supplemented with 1 % penicillin/streptomycin antibiotics (Beyotime, China) and 10 % fetal bovine serum (Gibco, USA).  The non-metastatic mouse HCC Hepa1-6 cells, were obtained from the Cell Bank of Peking Union Medical University (Beijing, China); cultured in 90% DMEM (Gibco) supplemented with 1 % penicillin/streptomycin antibiotics (Beyotime, China) and 10 % fetal bovine serum (Gibco, USA).

extract_protocol: TRIzol® reagent (Invitrogen Life Technologies) was used according to the manufacturer’s instructions for isolating total RNA.

treatment_protocol: no treatment

value: suspension Hepatocellular Carcinoma cell (lower lymphatic metastasis ability)


title: Hepa1-6

description: Hybridization signals were scanned and analyzed by Genepix 4000B microarray scanner. The scanned images were imported into the GenePix Pro 6.1 software (Axon Instruments) for grid alignment and data extraction. Replicated miRNAs were averaged, and the miRNAs with intensities ≥50 in all samples were chosen to calculate the median normalization factor. The expressed miRNA data were normalized using the median normalization and chosen for the differentially expressed miRNA screening.

value: adherent Hepatocellular Carcinoma cell (no lymphatic metastasis ability)


title: H22

description: Hybridization signals were scanned and analyzed by Genepix 4000B microarray scanner. The scanned images were imported into the GenePix Pro 6.0 software (Axon Instruments) for grid alignment and data extraction. Replicated miRNAs were averaged, and the miRNAs with intensities ≥50 in all samples were chosen to calculate the median normalization factor. The expressed miRNA data were normalized using the median normalization and chosen for the differentially expressed miRNA screening.

value: suspension Hepatocellular Carcinoma cell (no lymphatic metastasis ability)


title: Hca-F

description: Hybridization signals were scanned and analyzed by Genepix 4000B microarray scanner. The scanned images were imported into the GenePix Pro 6.3 software (Axon Instruments) for grid alignment and data extraction. Replicated miRNAs were averaged, and the miRNAs with intensities ≥50 in all samples were chosen to calculate the median normalization factor. The expressed miRNA data were normalized using the median normalization and chosen for the differentially expressed miRNA screening.

value: suspension Hepatocellular Carcinoma cell (higher lymphatic metastasis ability)


title: 8_denerv_2_mRNA


title: J46

status: Public on Mar 09 2018

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

data_processing:
Reads were mapped to the mouse genome (Ensembl NCBIM37) using Bowtie2 v2.2.9.
The abundance was estimated using RSEM v1.3.0
The differential expression analysis was done using edgeR v3.2.4. The dispersion was set to 0.4 for a data set without replicates. Significance cut-off is q-value < 0.05.
Genome_build: NCBIM37
Supplementary_files_format_and_content: text file with expected_count, TPM, FPKM

source_name: Proximal jejunum

extract_protocol:
rRNAs were removed using Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) according to Illumina's instructions provided with the kit.
rRNA depleted samples were then fragmented .  Libraries were constructed using Illumina's TruSeq® Small RNA Sample Preparation protocol.

value: CBA/J

tag: Sex

value: male

tag: diet

value: Methionine adequate diet

tag: radiation dose

value: 8.5 Gy gamma radiation

value: Proximal jejunum


title: J61

value: Methionine supplemented diet


title: J59


title: J51

value: 0 Gy gamma radiation


title: J62


title: J50


title: J49


title: J60


title: J52


title: J47


title: J42


title: J35


title: J34


title: J3


title: 2_Sham_2_mRNA

value: Sprague Dawley

tag: gender

value: female

tag: age

value: ~3 months

value: urinary bladder


title: J2

tag: tissue


title: SHEP_NMYCER_8WG16_minusOHT

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

library_source: genomic

data_processing:
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1. and normalized to the sample with the smallest number of mapped reads (10.8 million reads for TFIIIC5 and NMYC samples, 11 million reads for RNAPII samples, 51 million reads for CTCF and RAD21 samples).
Wiggle files were generated using MACS v1.4.2 with default parameters but a p-value cutoff of 1e-6 (N-MYC, TF3C5) and keep-dup parameter =1. .bedGraph files were generated using bedtools genomecov.
Genome_build: hg19
Supplementary_files_format_and_content: Fixed step wiggle files with a resolution of 10bp or bedgraph files (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.

source_name: SH-EP-NMYCER

growth_protocol: Neuroblastoma cells were grown in RPMI-1640 (Sigma). Medium was supplemented with 10% fetal calf serum (Biochrom) and penicillin/streptomycin (Sigma).

extract_protocol:
Cells were treated with 1% formaldehyde for 10 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <500 bp using a Branson sonifier. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 18 cycles of PCR and library size was tested with the Biorad Experion system. The amount of library DNA was quantified using a picogreen assay

treatment_protocol: For siRNA transfections, cells were transfected using the RNAiMAX reagent and OptiMem medium (LifeTechnologies) according to the manufacturer's instructions. Cells were harvested 48 h after transfection. Cells were treated with CD532 (1µM) or DMSO for 4 (ChIP-seq) or 4 and 8 (RNA-seq) hours.To activate N-MYC-ER in SH-EP cells, cells were treated with 4-OHT (200nM) for 5 hours. Conditional shRNA-mediated depletion of TFIIIC5 was induced with doxycycline (1 µg/ml) for 48 hours.

value: EtOH

tag: antibody

value: RNAPII (8WG16, Covance, MMS-126R)


title: SHEP_NMYCER_8WG16_plusOHT


title: SHEP_NMYCER_input8WG16_plusOHT


title: J45


title: Cre- 24hrs post PH rep4

city: Edinburgh

first: Richard

middle: Sydney

last: Taylor

state: Midlothian

address: The University of Edinburgh, Easter Bush Campus

department: Roslin Institute

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Hybridization was performed with the in situ Hybridization Plus kit (Agilent) following the manufacturers single colour protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner with the one colour scan setting for 4x44k arrays.

data_processing:
Raw signal intensities were extracted with Agilent Feature Extraction v10.5 software.
Normalised (quantile) log2 intensity levels.

source_name: Liver, 24 hours post partial hepatectomy.

growth_protocol: Mice used for all experiments were 8–16 weeks old and were housed under pathogen–free conditions in the Animal Barrier Facility of the University of California, San Francisco

extract_protocol: RNA extraction was performed with the RNeasy Mini Kit (QIAGEN Inc.), and total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Two-thirds of the liver was surgically removed under isoflurane anesthesia. All surgeries were performed in the first half of the day.

value: Male


title: WHIM30 day 7 single cell suspension for mouse 101065

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

address: 203 E Cary St

institute: Virginia Commonwealth University

description: Suspension culture of cells from mammary tumors grown in mice (RNA collected 7 days after processing)

data_processing:
Alignment: STAR v2.5.2b was used for alignment with the following settings: --outSAMtype BAM Unsorted --outSAMorder Paired --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outFilterMultimapNmax 1
Read Counting: Salmon v0.8.2 was used for counting reads with the "quant" algorithm and library type set to "IU" using the transcriptome output of STAR.
Genome_build: A custom reference genome was built by concatenating the following three genome builds: GRCh38 human genome from the Genomic Data Commons (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files), GRCm38 M12 Gencode release of the Mouse genome (http://www.gencodegenes.org/mouse_releases/12.html), and the Xenotropic murine leukemia virus accession JF274252.1 (https://www.ncbi.nlm.nih.gov/nuccore/JF274252.1).  Prior to concatenation, human chromosomes were concatenated with "HUMAN_" and mouse chromosomes were concatenated with "MOUSE_".
Supplementary_files_format_and_content: The processed data files contain the output from Salmon and include Salmon calculated TPM, gene lengths, and raw counts for the human and mouse genomes.

source_name: Mammary tumor cells

growth_protocol: WHIM2 and WHIM30 mammary tumors were grown in NSG mice. WHIM2 and WHIM30 brain metastases were generated in NSG mice by intracardiac injection. WHIM2 and WHIM30 cell suspensions were generated from mammary tumor tissue removed from mice. Cells were collected immediately after processing (day 0) and also grown in suspension culture and collected after one week (day 7) for RNA isolation.

extract_protocol:
RNA was harvested from tissue/cell samples using the Qiagen Rneasy Mini Kit.
KAPA Stranded mRNA-Seq Kit was used for library preparation.

tag: histologic subtype

value: Triple-negative

tag: intrinsic subtype

value: Basal-like

tag: model type

value: Patient-derived xenograft

value: WHIM30 day 7 single cell suspension


title: WHIM30 day 0 single cell suspension for mouse 102106

description: Suspension culture of cells from mammary tumors grown in mice (RNA collected on day of processing)

value: WHIM30 day 0 single cell suspension


title: WHIM30 day 0 single cell suspension for mouse 101067


title: WHIM30 day 7 single cell suspension for mouse 101067


title: WHIM30 brain metastasis for mouse 100219

description: Brain metastasis tissue from mice generated by intracardiac injection of tumor cells

source_name: Brain metastasis tissue

value: WHIM30 brain metastasis


title: WHIM30 brain metastasis for mouse 100536


title: WHIM30 mammary gland tumor for mouse 102401

description: Tissue from mammary tumors grown in mice

source_name: Mammary tumor tissue

value: WHIM30 mammary gland tumor


title: WHIM30 mammary gland tumor for mouse 102402


title: Cre- 24hrs uninjured rep4

source_name: Healthy liver


title: Cre- 24hrs post PH rep2


title: Cre+ 24hrs post PH rep4


title: WHIM30 mammary gland tumor for mouse 102400


title: WHIM2 brain metastasis for mouse 101085

value: WHIM2 brain metastasis


title: Cre+ 24hrs uninjured rep2


title: Cre+ 24hrs post PH rep2


title: Cre- 24hrs uninjured rep3


title: Cre+ 24hrs uninjured rep4


title: Cre+ 24hrs post PH rep3


title: WHIM30 day 7 single cell suspension for mouse 102106


title: WHIM30 day 0 single cell suspension for mouse 101065


title: Cre- 24hrs post PH rep1


title: Cre+ 24hrs uninjured rep3


title: Cre+ 24hrs post PH rep1


title: Cre- 24hrs uninjured rep1


title: Cre- 24hrs post PH rep3


title: 3_Sham_3_mRNA

source_name: Urinary bladders from sham op rats

value: surgery

value: euthanization

value: over 95percent smooth muscle


title: Cre+ 24hrs uninjured rep1


title: WHIM2 day 7 single cell suspension for mouse 102594

value: WHIM2 day 7 single cell suspension


title: WHIM2 mammary gland tumor for mouse 102594

value: WHIM2 mammary gland tumor


title: WHIM2 day 0 single cell suspension for mouse 102594

value: WHIM2 day 0 single cell suspension


title: WHIM2 mammary gland tumor for mouse 102593


title: WHIM2 day 0 single cell suspension for mouse 102593


title: WHIM2 day 7 single cell suspension for mouse 102595


title: T35

data_processing:
Paired-end reads were mapped to NCBIM37 using Bowtie2 v2.2.9.
The abundance was estimated using RSEM ver. 1.30. and the differential expression analysis was done using EdgeR  in the Bioconductor package.

Genome_build: NCBIM37
Supplementary_files_format_and_content: text file with expected_count,  TPM and FPKM

source_name: B16-F10.1 metastasis

extract_protocol:
rRNAs were removed using Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) according to Illumina's instructions provided with the kit.
rRNA depleted samples were then fragmented .  Libraries were constructed using Illumina's TruSeq® Stranded Total RNA Sample Preparation protocol.

value: Methionine deficient (0%) diet

tag: host mouse strain

tag: host mouse sex

value: male

value: B16-F10.1 metastasis


title: WHIM2 day 7 single cell suspension for mouse 102593

value: Triple-negative


title: T40


title: Cre- 24hrs uninjured rep2

value: Male


title: T34


title: T29

value: Methionine restricted (25%) diet


title: WHIM2 mammary gland tumor for mouse 102595

value: Basal-like

value: Patient-derived xenograft


title: WHIM2 day 0 single cell suspension for mouse 102595


title: T28


title: T19

value: Methionine supplemented (300%) diet


title: T20


title: T16


title: T14


title: T27


title: Kidney_interleukin-18 knockout_6w-biological rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: whole kidney derived from 6 week-old IL-18KO strain

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 3µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for data processing.

source_name: whole kidney derived from 6w IL-18KO strain

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted from whole kidneys stored in RNA later (Ambion), derived from wild type and interleukin-18 knockout mice using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: no teatment

value: BALB/c

tag: organ

value: Kidney

tag: genotype

value: interleukin-18 knockout

value: 6 week-old


title: Kidney_wild type_12w-biological rep3

description: whole kidney derived from 12 week-old wild type strain

source_name: whole kidney derived from 12w wild type strain

tag: strain

value: wild type

value: 12 week-old


title: Kidney_wild type_6w-biological rep2

description: whole kidney derived from 6 week-old wild type strain

source_name: whole kidney derived from 6w wild type strain


title: Kidney_interleukin-18 knockout_6w-biological rep2


title: T13


title: Kidney_wild type_6w-biological rep3


title: Kidney_interleukin-18 knockout_6w-biological rep1


title: T12


title: Kidney_wild type_12w-biological rep1


title: B. breve UCC2003-malR6 v. B. breve UCC2003

city: Cork

first: Noreen

last: Lanigan

state: Cork

address: Biosciences Institute, University college Cork, cork, ireland.

department: Microbiology

country: Ireland

institute: University college cork

description: Gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

organism: Bifidobacterium breve UCC2003

source_name: B. breve UCC2003 grown in mMRS supplemented with 0.05% cysteine and 1% ribose

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 or Bifidobacterium breve UCC2003-atsR2 was grown in modified de Man, Rogosa and Sharpe (MRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), ,supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing 0.5% ribose or 0.5 % N-acetylglucosamine-6-sulfate. The strains were grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) to an optical density OD600 of 0.5

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

value: malR6 mutant


title: B. breve UCC2003-malR3 v. B. breve UCC2003

description: Gene expression array

value: malR3 mutant


title: Kidney_wild type_12w-biological rep2


title: B. breve UCC2003 v. B. breve UCC2003-malR6

description: Gene expression array


title: T7

value: Methionine adequate diet


title: Kidney_interleukin-18 knockout_12w-biological rep2

description: whole kidney derived from 12 week-old IL-18KO strain

source_name: whole kidney derived from 12w IL-18KO strain


title: Kidney_wild type_6w-biological rep1


title: B. breve UCC2003-malR5 v. B. breve UCC2003

description: Gene expression array

value: malR5 mutant


title: T3

value: male

value: B16-F10.1 metastasis


title: T2


title: B. breve UCC2003 v. B. breve UCC2003-malR3

description: Gene expression array


title: Kidney_interleukin-18 knockout_12w-biological rep3


title: B. breve UCC2003-malR2 v. B. breve UCC2003

description: Gene expression array

value: malR2 mutant


title: B. breve UCC2003 v. B. breve UCC2003-malR2

description: Gene expression array


title: B. breve UCC2003 v. B. breve UCC2003-bifR2

description: Gene expression array

value: bifR2 mutant


title: B. breve UCC2003-bifR1 v. B. breve UCC2003

description: Gene expression array

value: bifR1 mutant


title: B. breve UCC2003 v. B. breve UCC2003-malR5

description: Gene expression array


title: B. breve UCC2003-bifR2 v. B. breve UCC2003

description: Gene expression array


title: TCRβ+ vs. TCRβ- Mf replicate 3

city: Silver Spring

first: Miranda

middle: Sarah Melissa

last: Oakley

state: MD

address: 10993 New Hampshire Avenue

institute: FDA

description: Replicate 3 of 4

hyb_protocol: Microarray target and Hi-RPM hybridization buffer (Agilent Gene Expression Hybridization Kit Cat#5188-5242) were added on Agilent custom Mouse array (4x44K). The hybridization was performed on TECAN automated hybridization station HS 4800 Pro, followed protocol of Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) with TECAN HS Pro Hybridization. Briefly, the slide was hybridized under active liquid agitation and mixing in a bubble-free hybridization system. On-slide nitrogen drying was applied to avoid external drying step and drying artifacts.

scan_protocol: The hybridized microarray slides were protected with Agilent Ozone-Barrier slide cover before loading into Agilent microarray scanner G2505C, scanning at 5 micron resolution with XDR ratio of 0.10. Image Analysis was performed using Agilent Feature extraction software (version11.5)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: TCRβ+ Mf

label_protocol: 100 ng of template RNA was amplified and labeled with cy3 (TCRβ-) or cy5 (TCRβ+) dyes using the Low Input QuickAmp Labeling Kit (Agilent Technologies, Santa Clara, CA)

growth_protocol: C57BL/6 mice were infected with Plasmodium berghei ANKA parasites

extract_protocol: RNA was extracted from sorted cells using Trizol following manufacturer's instructions

treatment_protocol: TCRβ+ vs. TCRβ- Ly6G-CD11bhighCD14+F4/80+ splenic Mf were sorted from spleen tissue on day 6 post-infection

tag: cell

value: splenic Mf

value: Day 6 post Pb-A infection

source_name: TCRβ- Mf


title: MEF H2AX KO_2

city: Bethesda

first: Urbain

middle: S

last: Weyemi

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

hyb_protocol: Three replicates of each group were prepared, labeled, and hybridized to Affymetrix  Mouse Gene 2.0 ST arrays

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000

data_processing: Affymetrix Expression Console (EC) was used to generate CHP files from CEL files.Then, the CEL files were loaded into Partek Genomics Suite software, version 6.6 for normalization and differential expression analysis.

source_name: MEF

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 1 ug total RNA.  RNA was reverse transcribed with T7-oligo(dT) primer and biotin-labeled using Affymetrix One Cycle Target Labeling kit following manufacturer’s protocol

growth_protocol: Mouse embryonic fibroblasts (MEF) from both wild-type and H2AX mutant mice were obtained from the Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health.   Cells were grown at 37ºC with 5% CO2 in DMEM (Invitrogen, Carlsbad, USA), supplemented with 10% Fetal Bovine Serum (FBS, Atlanta Biologicals, GA, USA). All media were supplemented with 2 mM glutamine, penicillin and streptomycin (Invitrogen, Carlsbad, CA, USA).

extract_protocol: Total RNAs from MEF were extracted using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) following manufacturer’s instructions.

treatment_protocol: H2AX wild-type and H2AX knockout mouse embryonic fibroblasts were used. No special treatment was performed.

tag: cell type

value: mouse embryonic fibroblasts

value: H2A.X Knockout


title: MEF H2AX KO_3


title: Naphthalene-injured single-cell RNA-seq

city: Durham

first: Yoshihiko

last: Kobayashi

state: NC

address: 307 Research Dr

department: Cell Biology

institute: Duke University

data_processing:
Library was sequenced on Illumina NextSeq 500. Raw sequencing output were processed through 10X genomics Cell Rnager software suite using default setting. Reads were mapped to the mm10 transcriptome. Read counts were normalized to log2 reads per million mapped (rpm) and a cutoff of log2 rpm >= 1 was used to determine whether a given gene was expressed in a cell. To ensure that epithelial cells were included in dataset, we first included any cells expressing Epcam, Cdh1, Krt5, Krt8 or Krt14. From these cells, we excluded endothelial cells, blood cells and macrophages by filtering out all the cells expressing Esam, H2-ab1, H2-aa, Hba-a2, Hbb-bt or Cd68.
Genome_build: mm10
Supplementary_files_format_and_content: txt files which contain log2 RPM values

molecule: polyA RNA

source_name: CD-1 males and females, airway luminal surface epithelial cells

extract_protocol:
Surface epithelium was isolated by incubation with Dispase at room temperature for 30 min, followed by manually scraping surface epithelial sheet and incubated with trypsin-EDTA at 37 degree for 30 min. Remaining tissue immediately after removing surface epithelial sheet was dissociated with Collagenase II and Hyauluronidase at 37 degree for 30 min, followed by incubation with trypsin-EDTA at 37 degree for 30 min. Cells were passed through 40-um cell strainer, collected and processed according to 10X genomics single cell protocol.
Libraries were prepared using 10X genomics Chromium single cell 3' standard protocol.

value: Total epithelial cells in airway luminal surface

value: pooled male and female

value: airway luminal surface epithelial cells


title: Homeostatic single-cell RNA-seq

source_name: CD-1 males and females, airway submucosal glandular epithelial cells

value: Total epithelial cells in airway submucosal glands


title: MEF H2AX KO_1


title: Kidney_interleukin-18 knockout_12w-biological rep1

value: BALB/c

value: Kidney

value: interleukin-18 knockout

value: 12 week-old


title: MEF WT_1

value: H2AX. WT


title: MEF WT_3


title: Control_15min_rep1 versus AZT_15min_rep1

city: Lausanne

first: Arnau

last: Domenech

address: Biophore building

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers

scan_protocol: Fluorescence signals were detected by a GenePix 4200AL microarray scanner (Axon Instruments), with detection of excitation/emission at 562/576 nm for DyLight550 and excitation/emission at 652/672 nm for DyLight650

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization
raw data:  CY3 "NetA" and CY5 "NetB"

organism: Streptococcus pneumoniae D39

source_name: WT (ADP62) without compounds (15 min )

label_protocol: After quantification, around 15 µg of total RNA was converted into cDNA using reverse transcriptase and subsequently purified and labeled as has been described previously (de Jong et al., 2012). The random nonamers for the annealing were purchased from Bioké. For the transcription, the Superscript III and DTT were purchased from Invitrogen and AA-dUTP from Ambion. The amino allyl-modified cDNA was purified with the NucleoSpin Gel and PCR Clean-up kit (ref 740609.250, Macherey-Nagel). The cDNA concentrations were measured by spectrophotometry (NanoDrop ND-1000, Thermo Scientific). The purified cDNA samples were labeled either with DyLight550 (ref 62262, Thermo Scientific) or DyLight650 (ref 62265, Thermo Scientific). The DyLight labeled cDNA was purified, according to the previously described protocol (de Jong et al, 2012), using the similar kit from Macherey-Nagel. After incorporation of DyLight dyes in the cDNA, we measured the cDNA concentrations as described above.

growth_protocol: S. pneumoniae D39 bgaA::PssbB-luc, comC::ery (ADP62) was grown as standing culture without aeration at 37 °C to an optical density at 600nm of 0.15 in 50 ml C+Y medium, adjusted to pH 7.8

extract_protocol: The cells were collected by centrifugation at 8000 rpm for 5 min and frozen in liquid nitrogen for RNA isolation. The macaloïd method and the RNA isolation kit (ref 11828665001 Roche) were used, according to the previously described protocol (de Jong et al., 2012), for isolation of the total RNA. RNA concentrations and quality were measured by spectrophotometry (NanoDrop ND-1000, Thermo Scientific) and capillary electrophoresis (Agilent RNA 6000 Nano Assay Kit and Agilent 2100 Bioanalyzer, Agilent Technologies).

treatment_protocol: ADP62 was treated either with clavulanic acid (CLA, 2 µg/ml final concentration in the medium), aztreonam (AZT, 28 µg/ml final concentration) or without as a control. The cells were collected either 15 min after addition of compounds or 180 min after 1:100 dilution into medium containing antibiotic

tag: genotype/variation

value: Wild-type resembling

source_name: WT (ADP62) with 28 ug/ml aztreonam (15 min )


title: Control_15min_rep1 versus CLA_15min_rep1

description: S. pneumoniae D39 bgaA::PssbB-luc, comC::ery

source_name: WT (ADP62) with 2 ug/ml clavulanic (15 min )


title: TCRβ+ vs. TCRβ- Mf replicate 1

description: Replicate 1 of 4


title: TCRβ+ vs. TCRβ- Mf replicate 2

description: Replicate 2 of 4


title: Control_15min_rep1 versus Control_180min_rep1

source_name: WT (ADP62) without compounds (180 min )


title: Control_180min_rep1 versus CLA_180min_rep2

source_name: WT (ADP62) with 28 ug/ml aztreonam (180 min )


title: Control_180min_rep1 versus CLA_180min_rep1

source_name: WT (ADP62) with 2 ug/ml clavulanic (180 min )


title: MEF WT_2


title: Mouse Lung, CD-1, Dose 120, 104wk, biological replicate 10

status: Public on Mar 08 2018

city: Research Triangle Park

first: Michael

middle: B.

last: Black

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description:
SIRC_120_104w_275_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_275_CD-1_DEDSTY141-1_(HT_MG-430_PM)_D05.CEL

hyb_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit, page40-42 and GeneTitan® Instrument User Guide for Expression Array Plates.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6.

source_name: Whole lung, CD-1, WT, styrene inhalation, 120ppm, 104w

label_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit.

growth_protocol: Adult male C57Bl/6 WT, KO and TG and CD-1 mice were acquired from Taconic (Germantown, NY). Animals were kept in a humidity- and temperature-controlled, HEPA-filtered, mass air-displacement room. The room was maintained on a 12-hr light-dark cycle (7 AM-7 PM) at approximately 20-25°C with a relative humidity of approximately 35-65%. All animals were allowed access to Certified LabDiet 5002 diet and reverse osmosis water ad libitum.

extract_protocol: Trizol® (ThermalFisher) organic extraction with Phase Lock Gel™ -Heavy- tubes (5Prime). Aqueous phase placed in RB (QiaCube sample) tubes and loaded into QiaCube, the RNeasy Mini Protocol used.

treatment_protocol: During exposure periods, animals were placed individually in stainless-steel wire-mesh cages and exposed to styrene or air 5 days per week for 6 hours per day for either 1 or 4 weeks. On the morning following the last inhalation exposure, mice were euthanized by sodium pentobarbital and exsanguination. Doses were 0 ppm (air only), and 120 ppm styrene.

tag: strain/background

value: Wild Type (WT)

value: male

value: adult

value: Whole Lung

tag: treatment

value: styrene inhalation

tag: dose (ppm)

tag: time of exposure


title: K2D3_2

city: Hefei

first: Guanqing

last: Wu

state: Anhui

address: 218 Jixi Road

institute: Anhui Province PKD Center, Institute/Department of Urology, The First Affiliated Hospital of Anhui Medical University

description: Gene expression data from renal collecting duct epithelial cell line (Pkd2f3/-)

hyb_protocol: Following fragmentation, 13ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila 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. The trimmed mean target intensity of each array was arbitrarily set to 100.
RMA

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 cells were incubated in a humidified atmosphere of 5% CO2 at 37C with 10% FCS DMEM/F12 culture medium.

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

tag: tissue

value: kidney

tag: age

value: from 8-wk-old mouse kidney


title: B. breve UCC2003 v. B. breve UCC2003-bifR1

description: Gene expression array

value: wild type

value: bifR1 mutant


title: K2E8

description: Gene expression data from renal collecting duct epithelial cell line (Pkd2d3/-)


title: K2B3_2

source_name: renal collecting duct epithelial cell line (Pkd2f3/-)


title: TCRβ+ vs. TCRβ- Mf replicate 4

description: Replicate 4 of 4

value: splenic Mf

value: Day 6 post Pb-A infection


title: Frozen tissue ADBS

city: Marseille

first: Christophe

last: Chevillard

state: BDR

address: 27 bd Jean Moulin faculté de médecine

country: France

institute: INSERM

description: Total RNA extract from frozen tissue

hyb_protocol: The hybridization was performed for 17 hours at 10 rpm and 65°C in a Hybridization Oven (Robbins Scientific). Slide Wash was done according to the manufacturer's recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using Agilent DNA microarray scanner at 3 micron resolution. Raw data from scanned image files were extracted using Feature Extraction software (10.7.3.1). Spike-in used in the experiment gave reliable data and all arrays passed the quality control.

data_processing: The microarrays were therefore analyzed using both GeneSpring software (11.5.1). Threshold raw signals to 1.0. Normalization algorithm: Percentile shift. Percentile target: 75. Baseline option: baseline to median of all samples. Group comaraison: Moderated T-Test.

source_name: Human left ventricular free wall heart tissue

label_protocol: Microarrays were done using the Low Input Quick Amp Labeling One-Color Kit (Agilent Technologies) and the One-color RNA Spike-in Kit (Agilent Technologies) following the manufacturer's standard protocol (Agilent One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling). 100 ng of total RNA input was used. After cDNA synthesis, amplification, labeling and purification, the reaction efficacy was checked using the NanoDrop.

extract_protocol: Tissue (20-30mg of tissue) homogenization was carried out with the Precellys-24 device (Bertin Technologies, Ozyme), with ceramic beads (1.4mm in diameter, CK14), in 400 µl of lysis buffer RLT plus (Qiagen) supplemented with 4µl β-mercapto-ethanol. RNA was recovered with the RNeasy plus following the manufacturer's instructions (Qiagen). RNA integrity was assessed with a 2100 Bioanalyzer (Agilent). Total RNA (1µg), with a RIN > 7, was reverse-transcribed with the high Capacity cDNA Reverse Transcription Kit (Applied Biosystems).

value: Heart


title: SOM05CVW rep2

city: Villamayor

first: Marta

last: Montero-Barrientos

state: Salamanca

address: Río Duero 12

country: Spain

institute: CENIT SUPPORT SYSTEMS

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

scan_protocol: Microarray scanning, data acquisition and identification of probes showing a significant difference (p=0.05) in expression level between the two culture conditions considered were performed by Roche-NimbleGen as in previous studies (Rubio et al., 2014). Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
Background correction, normalization, and expression analysis from the data were performed using the RMA algorithm (Irizarry et al., 2003). A multi-class significance analysis of microarray (SAM) test was carried out on the expression values using a false discovery rate (FDR) of 0.15. The analysis was performed using the FlexArray 1.6.1.1 program through the R software. Transcripts showing significantly differential expression (FC>2) were annotated Gene Ontology (GO) terms.All the values (34,138) unfiltered are provided in this record.

organism: Trichoderma atroviride

source_name: T. atroviride IMI 352941 overgrowing V-138I

label_protocol: High quality purified RNAs were submitted to Roche-NimbleGene (40 μg per 3-microarray set) where cRNAs were synthesized, amplified and labeled and then used for subsequent hybridization. Labeling with Cy3 was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: T. atroviride T11 mycelia obtained from three different PDA cultures were used.

extract_protocol: Total RNAs were extracted using TRIZOL reagent (Invitrogen, Carlsbad, CA) from T11 mycelia, following the manufacturer’s instructions, it was treated with DNase I (Fermentas, Burlington, Canada) and then purified using the RNeasy MinElute Cleanup kit (Qiagen, Hilden, Germany).

treatment_protocol: Three T11 culture conditions were used. For this, isolate V-138I of V. dahliae was grown on PDA plates, covered with cellophane, at 25ºC for 4 days and T. atroviride IMI 352941 (T11) was sowed as described above. T11 mycelia were harvested when it was ca. 5 mm apart (CVV) and after Trichoderma had overgrown the host fungus V. dahliae (CVW). As control, T11 mycelium grown alone was harvested (CVT). Freeze-dried mycelia from T11 were ground in liquid nitrogen using a mortar and pestle.

tag: growth condition

value: overgrowing V-138I


title: K2B2

source_name: renal collecting duct epithelial cell line (Pkd2d3/-)


title: TCD-BM+ Tcells + ICA, biological rep5

city: ATLANTA

first: Daniel

last: Kalman

state: Georgia

address: 615 Michael Street Rm 155-1

department: Pathology and Laboratory Medicine

institute: Emory University

hyb_protocol: Labeled cDNA is hybridized to whole transcriptome Gene ST GeneChip microarrays at 45 degrees C for 16-18 hours. Hybridized microarrays are washed and stained on an Affymetrix GeneChip 450 fluidics station using the appropriate chip dependent fluidics script.

scan_protocol: Arrays are scanned and intensity data extracted using an Affymetrix 7G scanner and the Command Console software suite.

data_processing: The data analysis was done by processing the Affymetrix arrays using Partek Genome Studio (http://www.partek.com). The data were RMA normalized and the samples were grouped according to specified groupings: TCD/ICA, TCD/VEH, TCD+T/ICA and TCD+T/VEH. PCA analysis with outlier removal and unsupervised clustering were used to verify sample grouping. 1-way and 2-way ANOVA tests were performed to determine significant differential expression of genes among groups and identify common genes. The differential expression filtering was performed using an unadjusted p-value less than 0.05 and absolute fold-change greater than 1.5. The analysis steps performed using Partek software are discussed here (http://goo.gl/32Y8Aq).

source_name: Mouse transplanted with T cell depleted bone marrow + T cells and treated with ICA

label_protocol: Using Ambion WT Expression Kit, 250ng of good quality, intact Total RNA is reverse transcribed using a proprietary mix of oligo-dT and random primers designed to prime both poly-A and non-poly-A transcripts, while reducing ribosomal representation. Single stranded cDNA is converted to ds-cDNA, and then amplified in a 16hr IVT reaction. Amplified RNA is then converted back to ss-cDNA. Using the Affymetrix GeneChip WT Terminal Labeling and Hybridization kit, ss-cDNA is fragmented and terminal labeled.

growth_protocol: Mice were 8-12 weeks old at the time of bone marrow transplant and the beginning of treatment with either ICA or VEHICLE

treatment_protocol: The transplant model used was C57Bl/6 donors and B10.BR recipients. On day -1, recipient mice received 11Gy lethal total body irradiation. On day 0, recipient mice were transplanted with 5 x 106 allogeneic T cell depleted BM (TCD-BM) cells, with or without 2 x 106 purified allogeneic T cells.  Both TCD-BM only transplanted control animals, and TCD-BM + T cell transplanted animals, which develop GvHD, received a daily oral gavage of either 150 mg/kg ICA or Vehicle (DMSO (20%), PEG400 (40%), Citric Acid (2%)). Samples (ileum) were collected on day 21post-transplant.

value: small intestine:ileum

tag: time point

value: 21 days post-transplant

tag: description

value: Mouse with GvHD treated with ICA


title: SOM05CVV rep2

source_name: T. atroviride IMI 352941 grown at ca. 5 mm of Verticillium dahliae V-138I


title: Frozen tissue ACFS

description: Total RNA extract from frozen tissue


title: Frozen tissue ACS

description: Total RNA extract from frozen tissue


title: TCD-BM + Tcells+ VEHICLE, biological rep1

source_name: Mouse transplanted with T cell depleted bone marrow + T cells and treated with VEHICLE

value: Mouse with GvHD treated with VEHICLE


title: SOM05CVW rep1


title: SOM05CVT rep2

source_name: T. atroviride IMI 352941 grown alone

value: grown alone


title: Frozen tissue VAM

description: Total RNA extract from frozen tissue


title: SOM05CVT rep1


title: SOM05CVV rep3

value: grown at ca. 5 mm of Verticillium dahliae V-138I


title: Mouse Lung, CD-1, Dose 120, 104wk, biological replicate 7

description:
SIRC_120_104w_267_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_267_CD-1_DEDSTY141-1_(HT_MG-430_PM)_C05.CEL

value: Wild Type (WT)

tag: gender

value: male

value: adult


title: Mouse Lung, CD-1, Dose 120, 104wk, biological replicate 9

description:
SIRC_120_104w_271_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_271_Tu_CD-1_DEDSTY141-1_(HT_MG-430_PM)_C09.CEL

value: Whole Lung

value: styrene inhalation


title: TCD-BM+ Tcells + ICA, biological rep2


title: TCD-BM+ Tcells + ICA, biological rep4


title: Mouse Lung, CD-1, Dose 120, 104wk, biological replicate 6

description:
SIRC_120_104w_266_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_266_Tu_CD-1_DEDSTY141-1_(HT_MG-430_PM)_B09.CEL


title: SOM05CVT rep3


title: TCD-BM + Tcells+ VEHICLE, biological rep2


title: SOM05CVV rep1


title: Frozen tissue WMS

description: Total RNA extract from frozen tissue


title: SOM05CVW rep3


title: TCD-BM + VEHICLE, biological rep2

source_name: Mouse transplanted with T cell depleted bone marrow only and treated with VEHICLE

value: Bone marrow transplant control mouse treated with VEHICLE


title: Frozen tissue VLJ

description: Total RNA extract from frozen tissue


title: Mouse Lung, CD-1, Dose 120, 104wk, biological replicate 5

description:
SIRC_120_104w_264_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_264_Tu_CD-1_DEDSTY141-1_(HT_MG-430_PM)_B07.CEL


title: TCD-BM + VEHICLE, biological rep4


title: Frozen tissue PDS

description: Total RNA extract from frozen tissue


title: TCD-BM+ Tcells + ICA, biological rep3


title: TCD-BM + VEHICLE, biological rep3


title: Mouse Lung, CD-1, Dose 120, 104wk, biological replicate 4

description:
SIRC_120_104w_257_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_257_Tu_CD-1_DEDSTY141-1_(HT_MG-430_PM)_B05.CEL


title: TCD-BM+ Tcells + ICA, biological rep1


title: TCD-BM + Tcells+ VEHICLE, biological rep3


title: Mouse Lung, CD-1, Dose 120, 104wk, biological replicate 8

description:
SIRC_120_104w_270_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_270_CD-1_DEDSTY141-1_(HT_MG-430_PM)_C07_2.CEL


title: TCD-BM + Tcells+ VEHICLE, biological rep4


title: Mouse Lung, CD-1, Dose 120, 104wk, biological replicate 3

description:
SIRC_120_104w_240_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_240_CD-1_DEDSTY141-1_(HT_MG-430_PM)_A09.CEL


title: Frozen tissue JFG

description: Total RNA extract from frozen tissue


title: Frozen tissue LA

description: Total RNA extract from frozen tissue


title: TCD-BM + ICA, biological rep4

source_name: Mouse transplanted with T cell depleted bone marrow only and treated with ICA

value: Bone marrow transplant control mouse treated with ICA


title: Frozen tissue VLPL

description: Total RNA extract from frozen tissue


title: TCD-BM + VEHICLE, biological rep1


title: Mouse Lung, CD-1, Dose 120, 104wk, biological replicate 2

description:
SIRC_120_104w_239_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_239_Tu_CD-1_DEDSTY141-1_(HT_MG-430_PM)_A07.CEL


title: TCD-BM + ICA, biological rep5


title: TCD-BM + ICA, biological rep2


title: TCD-BM + ICA, biological rep1


title: Frozen tissue RIS

description: Total RNA extract from frozen tissue


title: Mouse Lung, CD-1, Dose 120, 104wk, biological replicate 1

description:
SIRC_120_104w_227_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_227_CD-1_DEDSTY141-1_(HT_MG-430_PM)_A05.CEL


title: Frozen tissue SMM

description: Total RNA extract from frozen tissue


title: Frozen tissue PGM

description: Total RNA extract from frozen tissue


title: TCD-BM + ICA, biological rep3


title: Mouse Lung, CD-1, Dose 0, 104wk, biological replicate 3

description:
SIRC_0_104w_135_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_135_Tu_CD-1_DEDSTY141-1_(HT_MG-430_PM)_B05.CEL

source_name: Whole lung, CD-1, WT, styrene inhalation, 0ppm, 104w


title: Mouse Lung, CD-1, Dose 0, 104wk, biological replicate 6

description:
SIRC_0_104w_145_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_145_CD-1_DEDSTY141-1_(HT_MG-430_PM)_C05.CEL


title: SVZ pericytes normoxia 6 hours without glucose rep 3

city: Lund

first: Robert

last: Carlsson

address: Sölvegatan 17

department: IKVL

institute: Lund University

description: 6 normoxia NOG_3.AVG_Signal

hyb_protocol: Illumina hybridization protocol (Manual 11322187 Revision A)

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevB

growth_protocol: SVZ pericytes were washed in PBS and normal DMEM conditioned DMEM was added (without glucose). For hypoxia the media or conditioned media was pre-bubbled in 0.5%-0.7% oxygen containing gas with an initial composition  of 85% N2, 10%Co2, 5%H2. There is then a little oxygen leakage into the hypoxia chamber that was measured to 0.5-0.7%. For RNA the cells were lysed directly in the hypoxia chamber for the hypoxic treatments and in normoxia in the normoxic conditions.

extract_protocol: QIAGEN mini totalRNA isolation

value: Subventricular zone (SVZ) adult brain pericytes

tag: treatment group

value: normoxia 6 hours without glucose


title: Frozen tissue BSL

description: Total RNA extract from frozen tissue

value: Heart


title: TG+STZ

city: Tokushima

first: Kazuhiro

last: Hasegawa

address: 3-18-15 Kuramoto-cho

department: Department of Nephrology

institute: Tokushima University Graduate School of Biomedical Sciences

description: TG+STZ

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.3.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_F_20101030) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Micro-dissected glomerular regions from TG+STZ mice.

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Eight-week-old male mice were treated with streptozotocin (STZ, Sigma-Aldrich, St. Louis, MO) dissolved in 100 mmol l−1 citrate buffer.

extract_protocol: RNA was prepared using the QIAzol Lysis Reagent and Rneasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.

treatment_protocol: Mice in the WT+STZ and TG+STZ groups were killed at 32weeks of age. We dissected the glomerular regions. Micro-dissected glomeruli were immediately used for total RNA isolation and subjected to analysis on microarray chips.

tag: strain background

value: Sirt1-overexpressing transgenic

value: 32 weeks of age

value: kidney


title: SVZ pericytes normoxia 6 hours with glucose rep 3

description: 6 normoxia glu_3.AVG_Signal

value: normoxia 6 hours with glucose


title: Mouse Lung, CD-1, Dose 0, 104wk, biological replicate 5

description:
SIRC_0_104w_144_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_144_Tu_CD-1_DEDSTY141-1_(HT_MG-430_PM)_B09.CEL


title: Mouse Lung, CD-1, Dose 0, 104wk, biological replicate 4

description:
SIRC_0_104w_142_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_142_CD-1_DEDSTY141-1_(HT_MG-430_PM)_B07.CEL


title: Mouse Lung, CD-1, Dose 0, 104wk, biological replicate 7

description:
SIRC_0_104w_149_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_149_CD-1_DEDSTY141-1_(HT_MG-430_PM)_C07.CEL


title: Mouse Lung, CD-1, Dose 0, 104wk, biological replicate 1

description:
SIRC_0_104w_129_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_129_CD-1_DEDSTY141-1_(HT_MG-430_PM)_A07.CEL


title: Mouse Lung, CD-1, Dose 0, 104wk, biological replicate 2

description:
SIRC_0_104w_130_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_130_CD-1_DEDSTY141-1_(HT_MG-430_PM)_A09.CEL


title: SVZ pericytes normoxia 6 hours without glucose rep 2

description: 6 normoxia NOG_2.AVG_Signal


title: WT+STZ

description: WT+STZ

source_name: Micro-dissected glomerular regions from WT+STZ mice.

value: wild type


title: Mouse Lung, CD-1, Dose 120, 78wk, biological replicate 2

description:
SIRC_120_78w_223_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_223_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_H09.CEL

source_name: Whole lung, CD-1, WT, styrene inhalation, 120ppm, 78w


title: Mouse Lung, CD-1, Dose 120, 78wk, biological replicate 3

description:
SIRC_120_78w_224_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_224_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_H10.CEL


title: Mouse Lung, CD-1, Dose 120, 78wk, biological replicate 1

description:
SIRC_120_78w_222_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_222_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_H08.CEL


title: SVZ pericytes normoxia 6 hours with glucose rep 1

description: 6 normoxia glu_1.AVG_Signal


title: SVZ pericytes normoxia 6 hours with glucose rep 2

description: 6 normoxia glu_2.AVG_Signal


title: SVZ pericytes normoxia 6 hours without glucose rep 1

description: 6 normoxia NOG_1.AVG_Signal


title: SVZ pericytes hypoxia 6 hours without glucose rep 3

description: 6 hypoxia NOG_3.AVG_Signal

value: hypoxia 6 hours without glucose


title: SVZ pericytes hypoxia 6 hours without glucose rep 2

description: 6 hypoxia NOG_2.AVG_Signal


title: Mouse Lung, CD-1, Dose 0, 78wk, biological replicate 5

description:
SIRC_0_78w_125_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_125_ACO9_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_G08.CEL

source_name: Whole lung, CD-1, WT, styrene inhalation, 0ppm, 78w


title: SVZ pericytes hypoxia 6 hours with glucose rep 3

description: 6 hypoxia glu_3.AVG_Signal

value: hypoxia 6 hours with glucose


title: Mouse Lung, CD-1, Dose 0, 78wk, biological replicate 4

description:
SIRC_0_78w_124_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_124_ACO9_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_G07.CEL

value: Wild Type (WT)


title: Mouse Lung, CD-1, Dose 0, 78wk, biological replicate 3

description:
SIRC_0_78w_123_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_123_ACO9_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_G06.CEL

value: male


title: Mouse Lung, CD-1, Dose 0, 78wk, biological replicate 2

description:
SIRC_0_78w_122_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_122_ACO9_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_G05.CEL

value: adult


title: Mouse Lung, CD-1, Dose 120, 52wk, biological replicate 3

description:
SIRC_120_52w_228_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_228_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_E10.CEL

source_name: Whole lung, CD-1, WT, styrene inhalation, 120ppm, 52w

value: Whole Lung


title: SVZ pericytes normoxia 2 hours without glucose rep 2

description: 2 normoxia NOG_2.AVG_Signal

value: normoxia 2 hours without glucose


title: SVZ pericytes normoxia 2 hours with glucose rep 4

description: 2 normoxia glu_4.AVG_Signal

value: normoxia 2 hours with glucose


title: SVZ pericytes normoxia 2 hours without glucose rep 4

description: 2 normoxia NOG_4.AVG_Signal


title: SVZ pericytes normoxia 2 hours without glucose rep 3

description: 2 normoxia NOG_3.AVG_Signal


title: SVZ pericytes hypoxia 6 hours with glucose rep 2

description: 6 hypoxia glu_2.AVG_Signal


title: SVZ pericytes hypoxia 6 hours without glucose rep 1

description: 6 hypoxia NOG_1.AVG_Signal


title: Mouse Lung, CD-1, Dose 120, 26wk, biological replicate 3

description:
SIRC_120_26w_213_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_213_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_B02.CEL

source_name: Whole lung, CD-1, WT, styrene inhalation, 120ppm, 26w

value: styrene inhalation


title: Mouse Lung, CD-1, Dose 0, 52wk, biological replicate 1

description:
SIRC_0_52w_116_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_116_ACO5_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_D02.CEL

source_name: Whole lung, CD-1, WT, styrene inhalation, 0ppm, 52w


title: SVZ pericytes normoxia 2 hours with glucose rep 2

description: 2 normoxia glu_2.AVG_Signal

value: Subventricular zone (SVZ) adult brain pericytes


title: SVZ pericytes normoxia 2 hours without glucose rep 1

description: 2 normoxia NOG_1.AVG_Signal


title: SVZ pericytes hypoxia 2 hours without glucose rep 4

description: 2 hypoxia NOG_4.AVG_Signal

value: hypoxia 2 hours without glucose


title: Mouse Lung, CD-1, Dose 120, 52wk, biological replicate 2

description:
SIRC_120_52w_220_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_220_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_E12.CEL


title: Mouse Lung, CD-1, Dose 120, 26wk, biological replicate 5

description:
SIRC_120_26w_215_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_215_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_B04.CEL


title: SVZ pericytes hypoxia 6 hours with glucose rep 1

description: 6 hypoxia glu_1.AVG_Signal


title: Mouse Lung, CD-1, Dose 0, 78wk, biological replicate 1

description:
SIRC_0_78w_121_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_121_ACO9_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_G04.CEL


title: Mouse Lung, CD-1, Dose 120, 26wk, biological replicate 4

description:
SIRC_120_26w_214_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_214_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_B03.CEL


title: Mouse Lung, CD-1, Dose 0, 52wk, biological replicate 3

description:
SIRC_0_52w_120_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_120_ACO5_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_H05.CEL


title: SVZ pericytes normoxia 2 hours with glucose rep 3

description: 2 normoxia glu_3.AVG_Signal


title: Mouse Lung, CD-1, Dose 0, 52wk, biological replicate 4

description:
SIRC_0_52w_163_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_163_ACO5_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_D04.CEL


title: Mouse Lung, CD-1, Dose 0, 52wk, biological replicate 2

description:
SIRC_0_52w_117_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_117_ACO5_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_D03.CEL


title: SVZ pericytes normoxia 2 hours with glucose rep 1

description: 2 normoxia glu_1.AVG_Signal


title: Mouse Lung, CD-1, Dose 120, 52wk, biological replicate 1

description:
SIRC_120_52w_219_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_219_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_E11.CEL


title: SVZ pericytes hypoxia 2 hours without glucose rep 2

description: 2 hypoxia NOG_2.AVG_Signal


title: Mouse Lung, CD-1, Dose 120, 26wk, biological replicate 1

description:
SIRC_120_26w_211_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_211_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_A08.CEL


title: SVZ pericytes hypoxia 2 hours without glucose rep 1

description: 2 hypoxia NOG_1.AVG_Signal


title: Mouse Lung, CD-1, Dose 120, 26wk, biological replicate 2

description:
SIRC_120_26w_212_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_212_STY_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_G07.CEL


title: SVZ pericytes hypoxia 2 hours without glucose rep 3

description: 2 hypoxia NOG_3.AVG_Signal


title: SVZ pericytes hypoxia 2 hours with glucose rep 4

description: 2 hypoxia glu_4.AVG_Signal

value: hypoxia 2 hours with glucose


title: S6

first: Beth

last: Kozel

address: 10 Center Dr

department: Translational vascular medicine branch

institute: NHLBI/NIH

data_processing:
Reads were aligned to mouse genome M13 using STAR on computational resources of the NIH HPC Biowulf cluster. (http://hpc.nih.gov).
Average 71 million paired-end reads mapped to mouse Gencode genes (release M13) were summarized by featureCounts.
(1) The total counts of reads across samples were normalized by DESeq2 package. (2) log2 transformation of the normalized counts for all genes across the samples.  Yielding data_table.xlsx.
In total, 19980 genes with 10 or more reads in all samples were selected and log2 transformed reads were used for downstream analysis.    Treatment effect of the samples were qualitatively assessed by the first few principal components of the expression data.
Genome_build: mouse genome M13 (corresponding to Ensembl release 88 and genome GRCm38)
Supplementary_files_format_and_content: *_gene.txt files generated by featureCounts
data_table.txt generated by DESeq2 package

growth_protocol: Aortic tissue from the left subclavian to the diaphragm was collected from 3 groups of  ~3 month old Eln+/- mice (n=4 each).  One group received regular drinking water.  A second group received minoxidil in drinking water from 2.5 months to 3 months of age.  The final group received minoxidil in drinking water from 2.5 months to 3 months and then received drug-free drinking water for 1 week prior to tissue harvest.

extract_protocol:
After collection, tissues were frozen in RNA-later until all tissues were available and could be processed for RNA as a group.  RNA extraction was done by RNeasy Fibrous Tissue Mini Kit (Qiagen) according to manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aorta

value: 3 mon

tag: genotype

value: Elastin +/-


title: S12

source_name: aorta, two_week_on_treatment_4

tag: strain


title: S5


title: S10

source_name: aorta, two_week_on_treatment_2


title: S8


title: S11

source_name: aorta, two_week_on_treatment_3


title: S9

source_name: aorta, two_week_on_treatment_1


title: SVZ pericytes hypoxia 2 hours with glucose rep 3

description: 2 hypoxia glu_3.AVG_Signal


title: SVZ pericytes hypoxia 2 hours with glucose rep 2

description: 2 hypoxia glu_2.AVG_Signal


title: Mouse Lung, CD-1, Dose 0, 26wk, biological replicate 5

description:
SIRC_0_26w_115_ACO1_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_115_ACO1_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_A12.CEL

source_name: Whole lung, CD-1, WT, styrene inhalation, 0ppm, 26w


title: Mouse Lung, CD-1, Dose 0, 26wk, biological replicate 1

description:
SIRC_0_26w_111_ACO1_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_111_ACO1_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_A07.CEL


title: Mouse Lung, CD-1, Dose 0, 26wk, biological replicate 4

description:
SIRC_0_26w_114_ACO1_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_114_ACO1_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_A11.CEL


title: S7


title: Mouse Lung, KO, Dose 0, 104wk, biological replicate 5

description:
SIRC_0_104w_557_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_557_KO_DEDSTY141-1_(HT_MG-430_PM)_F07.CEL

source_name: Whole lung, C57Bl/6, KO, styrene inhalation, 0ppm, 104w


title: Mouse Lung, KO, Dose 120, 104wk, biological replicate 4

description:
SIRC_120_104w_645_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_645_KO_DEDSTY141-1_(HT_MG-430_PM)_G05.CEL

source_name: Whole lung, C57Bl/6, KO, styrene inhalation, 120ppm, 104w


title: Mouse Lung, KO, Dose 120, 104wk, biological replicate 2

description:
SIRC_120_104w_633_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_633_KO_DEDSTY141-1_(HT_MG-430_PM)_F07.CEL


title: Mouse Lung, KO, Dose 120, 104wk, biological replicate 3

description:
SIRC_120_104w_644_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_644_KO_DEDSTY141-1_(HT_MG-430_PM)_F09.CEL


title: Mouse Lung, KO, Dose 120, 104wk, biological replicate 1

description:
SIRC_120_104w_630_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_630_KO_DEDSTY141-1_(HT_MG-430_PM)_F05.CEL


title: Mouse Lung, CD-1, Dose 0, 26wk, biological replicate 3

description:
SIRC_0_26w_113_ACO1_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_113_ACO1_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_A10.CEL


title: Mouse Lung, CD-1, Dose 0, 26wk, biological replicate 2

description:
SIRC_0_26w_112_ACO1_CD-1
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_26w_112_ACO1_CD-1_DEDSTY141-1_2016_(HT_MG-430_PM)_A09.CEL


title: SVZ pericytes hypoxia 2 hours with glucose rep 1

description: 2 hypoxia glu_1.AVG_Signal


title: Mouse Lung, KO, Dose 120, 104wk, biological replicate 5

description:
SIRC_120_104w_665_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_104w_665_KO_DEDSTY141-1_(HT_MG-430_PM)_G07.CEL


title: S4

source_name: aorta, control_4

value: control


title: Mouse Lung, KO, Dose 0, 104wk, biological replicate 6

description:
SIRC_0_104w_572_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_572_Tu_KO_DEDSTY141-1_(HT_MG-430_PM)_F09.CEL


title: S2

source_name: aorta, control_2


title: S3

source_name: aorta, control_3


title: S1

source_name: aorta, control_1


title: Mouse Lung, KO, Dose 0, 104wk, biological replicate 4

description:
SIRC_0_104w_552_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_552_KO_DEDSTY141-1_(HT_MG-430_PM)_F05.CEL


title: Mouse Lung, KO, Dose 120, 52wk, biological replicate 5

description:
SIRC_120_52w_620_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_620_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_F10.CEL

source_name: Whole lung, C57Bl/6, KO, styrene inhalation, 120ppm, 52w


title: Mouse Lung, KO, Dose 0, 104wk, biological replicate 1

description:
SIRC_0_104w_533_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_533_KO_DEDSTY141-1_(HT_MG-430_PM)_E05.CEL


title: Mouse Lung, KO, Dose 0, 78wk, biological replicate 2

description:
SIRC_0_78w_522_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_522_ACO11_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_G12.CEL

source_name: Whole lung, C57Bl/6, KO, styrene inhalation, 0ppm, 78w


title: Mouse Lung, KO, Dose 120, 78wk, biological replicate 3

description:
SIRC_120_78w_623_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_623_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_D05.CEL

source_name: Whole lung, C57Bl/6, KO, styrene inhalation, 120ppm, 78w


title: Mouse Lung, KO, Dose 120, 52wk, biological replicate 3

description:
SIRC_120_52w_618_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_618_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_F08.CEL


title: Mouse Lung, KO, Dose 120, 78wk, biological replicate 4

description:
SIRC_120_78w_624_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_624_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_D07.CEL


title: Mouse Lung, KO, Dose 0, 104wk, biological replicate 3

description:
SIRC_0_104w_544_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_544_KO_DEDSTY141-1_(HT_MG-430_PM)_E09.CEL


title: Mouse Lung, KO, Dose 0, 104wk, biological replicate 2

description:
SIRC_0_104w_541_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_104w_541_KO_DEDSTY141-1_(HT_MG-430_PM)_E07.CEL


title: Mouse Lung, KO, Dose 0, 78wk, biological replicate 1

description:
SIRC_0_78w_521_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_521_ACO11_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_G11.CEL


title: Mouse Lung, KO, Dose 0, 78wk, biological replicate 3

description:
SIRC_0_78w_523_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_523_ACO11_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_H01.CEL


title: Mouse Lung, KO, Dose 120, 78wk, biological replicate 5

description:
SIRC_120_78w_625_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_625_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_E05.CEL


title: Mouse Lung, KO, Dose 120, 78wk, biological replicate 2

description:
SIRC_120_78w_622_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_622_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_C07.CEL


title: Mouse Lung, KO, Dose 120, 52wk, biological replicate 4

description:
SIRC_120_52w_619_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_619_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_F09.CEL


title: Mouse Lung, KO, Dose 0, 52wk, biological replicate 5

description:
SIRC_0_52w_551_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_551_ACO7_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_E01.CEL

source_name: Whole lung, C57Bl/6, KO, styrene inhalation, 0ppm, 52w


title: Mouse Lung, KO, Dose 120, 52wk, biological replicate 2

description:
SIRC_120_52w_617_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_52w_617_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_F07.CEL


title: Mouse Lung, KO, Dose 0, 52wk, biological replicate 2

description:
SIRC_0_52w_518_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_518_ACO7_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_E02.CEL


title: Mouse Lung, KO, Dose 0, 52wk, biological replicate 4

description:
SIRC_0_52w_520_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_520_ACO7_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_E04.CEL


title: Mouse Lung, KO, Dose 0, 52wk, biological replicate 3

description:
SIRC_0_52w_519_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_519_ACO7_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_E03.CEL


title: Mouse Lung, KO, Dose 0, 78wk, biological replicate 4

description:
SIRC_0_78w_525_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_78w_525_ACO11_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_H02.CEL


title: Mouse Lung, KO, Dose 120, 78wk, biological replicate 1

description:
SIRC_120_78w_621_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_78w_621_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_C05.CEL


title: C3H, Liver, 21 days HFD, rep8 reanalysis

city: Munich

first: Barbara

last: Fridrich

address: Ingolstädter Landstraße 1

institute: Hemholtz Center Munich

description: Gene expression data from liver of radnom fed C3H mice, 21 days HFD

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.1) including median polish and Sketch-Quantile normalisation

source_name: C3H, Liver, 21 days HFD

label_protocol: GeneChip Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix)

growth_protocol: Single housed animals

extract_protocol: miRNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: As described in the paper. Briefly, mice were fed with a HFD (7, 14 or 21 days) or LFD (≤ 21 days) and gene transcription analyses in liver was performed.

value: 17 weeks

value: WT

value: high fat diet

tag: time


title: Mouse Lung, KO, Dose 120, 26wk, biological replicate 4

description:
SIRC_120_26w_615_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_120_26w_615_STY_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_C06.CEL

source_name: Whole lung, C57Bl/6, KO, styrene inhalation, 120ppm, 26w


title: C3H, Liver, 14 days HFD, rep6

description: Gene expression data from liver of radnom fed C3H mice, 14 days HFD

scan_protocol: According to the Affymetrix expression protocol

source_name: C3H, Liver, 14 days HFD

value: 16 weeks


title: C3H, Liver, 21 days HFD, rep2 reanalysis

value: male


title: C3H, Liver, 14 days HFD, rep5


title: C3H, Liver, 14 days HFD, rep3


title: C3H, Liver, 14 days HFD, rep8


title: C3H, Liver, 21 days HFD, rep4 reanalysis


title: C3H, Liver, 21 days HFD, rep1 reanalysis


title: C3H, Liver, 14 days HFD, rep7


title: C3H, Liver, 21 days HFD, rep7 reanalysis


title: Mouse Lung, KO, Dose 0, 52wk, biological replicate 1

description:
SIRC_0_52w_516_KO
Source of mice: Taconic Biosciences Inc., Germantown, NY
Gene expression data from mouse whole lungs.
SIRC_0_52w_516_ACO7_KO_DEDSTY141-1_2016_(HT_MG-430_PM)_D11.CEL

value: adult