title: CEMBA190212_9H_3_CEMBA190212_9H_4_B6_ad007


title: CEMBA190212_9H_3_CEMBA190212_9H_4_B6_ad006

status: Public on Oct 02 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CA

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA190212_9H_3_CEMBA190212_9H_4_B6_ad008


title: CEMBA190212_9H_3_CEMBA190212_9H_4_B3_ad004


title: CEMBA190212_9H_3_CEMBA190212_9H_4_B5_ad001


title: CEMBA190212_9H_3_CEMBA190212_9H_4_B6_ad004


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title: CEMBA190212_9H_1_CEMBA190212_9H_2_G5_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G5_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G5_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G5_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G4_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G4_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G4_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G6_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G4_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G4_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G4_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G3_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G3_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G3_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G3_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G4_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G3_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G3_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G2_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G2_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G2_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G2_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G12_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G2_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G2_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G12_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G12_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G12_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G12_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G12_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G12_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G3_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G11_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G11_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G11_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G11_ad012


title: CEMBA190212_9H_3_CEMBA190212_9H_4_A12_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G12_ad010


title: CEMBA190212_9H_3_CEMBA190212_9H_4_A2_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G11_ad004


title: CEMBA190212_9H_3_CEMBA190212_9H_4_A11_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G11_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G10_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G10_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G10_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G11_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G10_ad007


title: FAABL_replicate_7

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's HumanHT-12 V4.0 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.54 μm using the Illumina iScan scanner.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.I ndividual genes with pair-wise z-test P-values <0.05, average intensity >0, |Z-ratios| >1.5-fold, and fdr ≤0.3 were considered significant and were based on the maximum Z-ratio identified from multiple probes of the same gene.

molecule: total RNA

organism: Homo sapiens

source_name: FAABL

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol:
Gene expression analysis was performed on peripheral blood mononuclear cells (PBMCs) isolated from a subcohort of participants in the Healthy Aging in Neighborhoods of Diversity Across the Life Span (HANDLS) study of Baltimore City residents (28). HANDLS is a longitudinal epidemiological study of a diverse and representative sample of Baltimore City residents and was designed and implemented by the National Institute on Aging Intramural Research Program (NIA IRP). The subgroups for this study included age-matched African American (AA) or Caucasian (C)).  Exclusion criteria included history of HIV and HBV infection. All blood samples were collected in the morning during fasting. The isolation of the PBMCs was conducted within 3 hours of withdrawal, aliquoted, and stored at -80˚C. The Institutional Review Boards of the National Institute of Environmental Health Sciences and Morgan State University approved this study and a written informed consent was signed by all participants.
RNA was extracted using Trizol (Trizol Reagent, Invitrogen) according to manufacturer’s instructions, and  RNA concentration and integrity was assessed by Nanodrop and Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

tag: gender

value: Female

tag: ethnicity

value: African-American

tag: poverty status

value: Below

tag: tissue

value: PBMCs


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G10_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G10_ad002


title: FAABL_replicate_5


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G1_ad001


title: FAABL_replicate_4


title: FAABL_replicate_2


title: FAABL_replicate_3


title: FAABL_replicate_6


title: FAABL_replicate_1


title: FAAAB_replicate_5

source_name: FAAAB

value: Above


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G1_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G1_ad007


title: FAAAB_replicate_4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G1_ad010


title: FAAAB_replicate_2


title: FAAAB_replicate_1


title: FAAAB_replicate_3


title: FWBL_replicate_6

source_name: FWBL

value: White


title: FWBL_replicate_4


title: FAAAB_replicate_6


title: FWBL_replicate_5


title: FWBL_replicate_1


title: FWBL_replicate_3


title: FWBL_replicate_2


title: FWAB_replicate_7

source_name: FWAB


title: FWAB_replicate_6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G1_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F9_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F9_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F9_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_G1_ad002


title: FWAB_replicate_2


title: FWAB_replicate_5


title: FWAB_replicate_3


title: FWAB_replicate_4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F9_ad004


title: FWAB_replicate_1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F8_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F9_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F8_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F8_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F9_ad006


title: MAABL_replicate_6

source_name: MAABL

value: Male


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F7_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F8_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F8_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F7_ad007


title: MAABL_replicate_3


title: MAABL_replicate_5


title: MAABL_replicate_4


title: MAABL_replicate_7


title: MAABL_replicate_2


title: MAAAB_replicate_4

source_name: MAAAB


title: MAABL_replicate_1


title: MAAAB_replicate_6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F7_ad001


title: MAAAB_replicate_2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F7_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F7_ad002


title: MAAAB_replicate_5


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F8_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F7_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F6_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F6_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F7_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F6_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F6_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F6_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F6_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F6_ad002


title: MAAAB_replicate_1


title: MWBL_replicate_3

source_name: MWBL


title: MWBL_replicate_5


title: MWBL_replicate_6


title: MWAB_replicate_5

source_name: MWAB


title: MWAB_replicate_4


title: MWBL_replicate_4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F5_ad001


title: MAAAB_replicate_3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F5_ad012


title: MWAB_replicate_7


title: MWAB_replicate_6


title: MWAB_replicate_2


title: MWAB_replicate_3


title: MWBL_replicate_2


title: MWAB_replicate_1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F4_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F5_ad002


title: LM17 melanoma cell line resistant to PLX4032 treatment

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: CodeSet hybridization was performed according to the manufacturer's protocol.

scan_protocol: nCounter Analysis system (NanoString) was used to analyze fluorophore signals at 555 fields of view (FOV)

data_processing: Raw data were normalized and log2-transformed using the NanoStringNorm R package (Waggot 2017), setting the required parameters to the following values: Probe.Correction.Factor to “adjust”; CodeCount to “sum”; Background to “mean”; SampleContent to “top.geo.mean” and OtherNorm to “none”.

source_name: melanoma cell line

label_protocol: Labeling was performed according to the manufacturer's protocol

growth_protocol: The parental melanoma cell lines  and the PLX4032-resistant variants were cultured in RPMI medium supplemented with 10% FCS, HEPES buffer, glutamine and antibiotics. Cells were grown for 72 hours before recovery for RNA extraction (about 80% monolayer culture confluence).

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with Ambion miRVANA kit according to the protocol provided by the manufacturer.

treatment_protocol: The PLX4032-resistant cell line variants (LM11R, LM36R, LM47R, LM16R, LM43R, LM17R) were generated by repeated exposures to PLX4032 (3 µM) until the onset of resistance (2-8 months).

tag: cell line

tag: plx4032 sensitivity


title: LM17 melanoma cell line sensitive to PLX4032 treatment

value: Sensitive


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F5_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F4_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F4_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F4_ad007


title: LM16 melanoma cell line sensitive to PLX4032 treatment


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F5_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F4_ad006


title: MWBL_replicate_1


title: LM47 melanoma cell line sensitive to PLX4032 treatment


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F4_ad004


title: LM47 melanoma cell line resistant to PLX4032 treatment


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F5_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F3_ad012


title: LM16 melanoma cell line resistant to PLX4032 treatment


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F3_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F3_ad007


title: LM11 melanoma cell line resistant to PLX4032 treatment


title: LM36 melanoma cell line sensitive to PLX4032 treatment


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F4_ad002


title: LM11 melanoma cell line sensitive to PLX4032 treatment


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F3_ad010


title: D18-270046: OLE1.24M rep1

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description: K. phaffii ATAC-seq sample collected after growth in glycerol-containing medium. hGH-expressing strain with heterologous vector integrated upstream of OLE1.

data_processing:
NextSeq500 using v3 chemistry. Software: Control v2.2.0.2, RTA 2.4.11. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Sequence reads were aligned to the indicated targets with bowtie2 (version 2.3.2) with max fragment lenth (-X) set to 2000
PCR duplicates were removed with picard (version 2.9.0) and reads with mapping quality greater than 30 were selected and biological replicates were merged with samtools (version 1.5)
Chromatin accessibility peaks from raw ATAC-seq data were called using MACS2.
Nucleosome positioning and occupancy was determined using NucleoATAC with default settings.
Genome_build: Komagataella phaffi WT (PRJNA304977) with inserted transgenes where indicated
Supplementary_files_format_and_content: WT.v1.fa.gz is a fasta file of the Komagataella phaffi WT genome
Supplementary_files_format_and_content: WT_pAOX1_AOX1_ahGH.fa.gz  is a fasta file of the Komagataella phaffi WT genome with a human growth hormone transgene inserted at the AOX loci
Supplementary_files_format_and_content: WT_pDAS2_DAS2.ahGH.fa.gz is a fasta file of the Komagataella phaffi WT genome with a human growth hormone transgene inserted at the DAS2 loci
Supplementary_files_format_and_content: WT_pOLE1_OLE1_ahGH.fa.gz is a fasta file of the Komagataella phaffi WT genome with a human growth hormone transgene inserted at the OLE1 loci
Supplementary_files_format_and_content: *.narrowPeak.bed files contain peaks called by MAC2 from mapping of chromatin accessibility by ATAC-seq. Columns are as follows: 1) chromosome 2) start 3) end 4) peak name 5) integer score calculated as int(-10*log10qvalue) 6) . 7) fold-change at peak summit 8) -log10pvalue at peak summit 9) -log10qvalue at peak summit 10) relative summit position to peak start
Supplementary_files_format_and_content: *.nfrpos.bed.gz files contain nucleosome-free positions. Columns are (1) chrom, (2) left boundary (0-based), (3) right boundary (1-based), (4) mean occupancy, (5) minimum upper bound occupancy, (6) insertion density, (7) bias density
Supplementary_files_format_and_content: *.nucmap_combined.bed.gz files contain low and high resolution nucleosome calls. Columns are: (1) chrom, (2) dyad position (0-based), (3) dyad position(1-based), (4) z-score, (5) nucleosome occupancy estimate (6) lower bound for nucleosome occupancy estimate, (7) upper bound for nucleosome occupancy estimate (8) log likelihood ratio, (9) normalied nucleoatac signal value, (10) cross-correlation signal value before normalization, (11) number of potentially nucleosome-sized fragments, (12) number of fragments smaller than nucleosome sized, (13) "fuzziness" (measure of how wide signal peak is)

organism: Komagataella phaffii

source_name: bulk yeast cell culture

growth_protocol: BMGY containing 4% (v/v) glycerol was inoculated from a glycerol stock to an initial OD600 of 0.1 in a 24-well culture plate (Corning, Cat. # P-DW10ML24CS, Corning, NY) and cultured at ambient temperature and 600 rpm shaking. After 24h of biomass accumulation, cells were pelleted and resuspended in BMMY, containing 3% (v/v) methanol as both a carbon source and for induction of heterologous gene expression, for an additional 24h.

extract_protocol:
Two million cells per sample were prepared for transposition as described previously (doi:10.1101/gr.192294.115).
Spheroplasts were washed once with transposition buffer prior to transposition and PCR amplification for sequencing, which are described elsewhere (doi:10.1002/0471142727.mb2129s109). Amplified libraries were size selected using 0.4x followed by 0.8x Ampure XP beads according to manufacturer instructions (Beckman Coulter). Size-selected libraries were sequenced on an Illumina NextSeq to generate 40-nt paired-end reads.

tag: transgene expressed

value: rhGH

tag: integration locus

tag: carbon source

value: methanol

tag: alignment target


title: D18-270048: OLE1.24M rep3


title: D18-270047: OLE1.24M rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F3_ad006


title: D18-270045: DAS2.24M rep3

description: K. phaffii ATAC-seq sample collected after growth in glycerol-containing medium. hGH-expressing strain with heterologous vector integrated upstream of DAS2.


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F3_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F2_ad007


title: D18-270044: DAS2.24M rep2


title: D18-270043: DAS2.24M rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F3_ad004


title: D18-270042: AOX1.24M rep3

description: K. phaffii ATAC-seq sample collected after growth in glycerol-containing medium. hGH-expressing strain with heterologous vector integrated upstream of AOX1.


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F2_ad010


title: LM43 melanoma cell line sensitive to PLX4032 treatment


title: D18-270041: AOX1.24M rep2


title: LM36 melanoma cell line resistant to PLX4032 treatment


title: D18-270040: AOX1.24M rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F2_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F2_ad006


title: D18-270038: WT.24M rep2

description: K. phaffii ATAC-seq sample collected after growth in glycerol-containing medium. Null strain.

value: not applicable


title: D18-270039: WT.24M rep3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F2_ad008


title: D18-270011: OLE1.24G rep2

value: glycerol


title: D18-270010: OLE1.24G rep1


title: D18-270037: WT.24M rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F2_ad002


title: D18-270012: OLE1.24G rep3


title: D18-270008: DAS2.24G rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F2_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F12_ad010


title: D18-270009: DAS2.24G rep3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F12_ad007


title: D18-270007: DAS2.24G rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F12_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F3_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F12_ad008


title: D18-270006: AOX1.24G rep3


title: D18-270004: AOX1.24G rep1


title: D18-270003: WT.24G rep3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F12_ad004


title: D18-270002: WT.24G rep2


title: D18-270005: AOX1.24G rep2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F11_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F11_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F11_ad002


title: D18-270001: WT.24G rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F10_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F11_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F10_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F12_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F10_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F10_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F1_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F1_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F12_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F10_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E9_ad001


title: HuTu13 cells siControl, biological rep2 [array]

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

description:
13Co_B
Gene expression data from control HuTu13 cells.
Transfected with Control siRNA.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software.

data_processing: RMA of .CEL files using Bioconductor affy library and Brainarray custom CDF HGU133Plus2_Hs_ENTREZG_v21. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization.

label: biotin

source_name: HuTu13 cells (Mesenchymal) transfected with Control siRNA 2

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's instructions.

growth_protocol: HuTu cells are cultured with DMEM-F12, 1% GLN, 1% PS, 10% BIT9500 (serum substitute), 25 ng/ml human EGF, 25 ng/ml human bFGF.

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

treatment_protocol: Cells were transfected with siRNA by using RNAi MAX (ThermoFisher), according to the manufacturer's instructions.

tag: cell type

value: Primary Glioblastoma HuTu13 cells (Mesenchymal)

tag: experimental condition

value: Control siRNA


title: HuTu13 cells siControl, biological rep4 [array]

description:
13Co_D
Gene expression data from control HuTu13 cells.
Transfected with Control siRNA.

source_name: HuTu13 cells (Mesenchymal) transfected with Control siRNA 4


title: HuTu13 cells siControl, biological rep1 [array]

description:
13Co_A
Gene expression data from control HuTu13 cells.
Transfected with Control siRNA.

source_name: HuTu13 cells (Mesenchymal) transfected with Control siRNA 1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E9_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F1_ad007


title: HuTu10 cells siControl, biological rep4 [array]

description:
10Co_D
Gene expression data from control HuTu10 cells.
Transfected with Control siRNA.

source_name: HuTu10 cells (Proneural) transfected with Control siRNA 4

value: Primary Glioblastoma HuTu10 cells (Proneural)


title: HuTu13 cells siControl, biological rep3 [array]

description:
13Co_C
Gene expression data from control HuTu13 cells.
Transfected with Control siRNA.

source_name: HuTu13 cells (Mesenchymal) transfected with Control siRNA 3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E9_ad008

value: CA


title: MDA-MB-231 xenograft proton treated with 9 Gy of IR dose - replicate6

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

institute: IBSBC CNR

description: Biological replicate 6 of 6

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. Respective untreated cell lines, were used as a control. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from untreated MDA-MB-231 xenograft mouse was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: MDA-MB-231 xenograft mouse exposed to PRT, were collected after 72 hours post treatments.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: MDA-MB-231 Breast Cancer cell line xenograft

tag: original tissue

value: breast cancer tissue

tag: treatment

value: proton treated with 9 Gy of IR dose

tag: harvest time post treatment

value: 72 hours

source_name: Untreated MDA-MB-231 xenograft

value: MDA-MB-231 xenograft

value: none (no exposure to IR)


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E8_ad012

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

tag: Sex

value: male

tag: age


title: HuTu10 cells siControl, biological rep3 [array]

description:
10Co_C
Gene expression data from control HuTu10 cells.
Transfected with Control siRNA.

source_name: HuTu10 cells (Proneural) transfected with Control siRNA 3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E9_ad010

tag: strain


title: HuTu10 cells siControl, biological rep2 [array]

description:
10Co_B
Gene expression data from control HuTu10 cells.
Transfected with Control siRNA.

source_name: HuTu10 cells (Proneural) transfected with Control siRNA 2


title: MDA-MB-231 xenograft proton treated with 9 Gy of IR dose - replicate4

description: Biological replicate 4 of 6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E8_ad001


title: HuTu10 cells siControl, biological rep1 [array]

description:
10Co_A
Gene expression data from control HuTu10 cells.
Transfected with Control siRNA.

source_name: HuTu10 cells (Proneural) transfected with Control siRNA 1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E9_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_F1_ad001


title: MDA-MB-231 xenograft proton treated with 9 Gy of IR dose - replicate5

description: Biological replicate 5 of 6


title: MDA-MB-231 xenograft proton treated with 6 Gy of IR dose - replicate6

description: Biological replicate 6 of 6

value: proton treated with 6 Gy of IR dose


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E9_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E8_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E8_ad010


title: MDA-MB-231 xenograft proton treated with 9 Gy of IR dose - replicate2

description: Biological replicate 2 of 6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E8_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E7_ad001


title: MDA-MB-231 xenograft proton treated with 6 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: MDA-MB-231 xenograft proton treated with 9 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E8_ad004


title: MDA-MB-231 xenograft proton treated with 6 Gy of IR dose - replicate5

description: Biological replicate 5 of 6


title: MDA-MB-231 xenograft proton treated with 6 Gy of IR dose - replicate2

description: Biological replicate 2 of 6


title: MDA-MB-231 xenograft proton treated with 6 Gy of IR dose - replicate4

description: Biological replicate 4 of 6


title: PHx 48hr rep2

city: Durham

first: Anna Mae

last: Diehl

address: Research Drive

institute: Duke University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were quality assessed using FastQC v0.11.5, and were trimmed using TrimGalore v0.6.4
Alignments of trimmed reads were performed using STAR v2.6
Raw counts were generated using HTSeq v0.12.4. Differential expression analysis was implemented by DESeq2 in Bioconductor
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing raw counts

source_name: liver hepatocytes

growth_protocol: Mice were fed with normal diet

extract_protocol:
Hepatocytes were isolated using two-step collagenase perfusion method; RNA was extracted using TRIzol reagent protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10-12 weeks old mice underwent partial hepatectomy surgery

tag: protocol

value: PHx

tag: time point


title: PHx 48hr rep3


title: PHx 48hr rep1


title: MDA-MB-231 xenograft proton treated with 2 Gy of IR dose - replicate6

description: Biological replicate 6 of 6

tag: tissue

value: proton treated with 2 Gy of IR dose


title: MDA-MB-231 xenograft proton treated with 9 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: MDA-MB-231 xenograft proton treated with 6 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: MDA-MB-231 xenograft proton treated with 2 Gy of IR dose - replicate5

description: Biological replicate 5 of 6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E7_ad004


title: MDA-MB-231 xenograft proton treated with 2 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E7_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E6_ad007


title: PHx 0hr rep2


title: PHx 0hr rep1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E6_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E6_ad001


title: MDA-MB-231 xenograft proton treated with 2 Gy of IR dose - replicate2

description: Biological replicate 2 of 6


title: Hepatic mononuclear cells - SC+liver

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

description: Samples were collected 14 days after intrasplenic injection of tumor cells

data_processing:
Basecalls from the sequencer were first converted into FASTQs format with the bcl2fastq software provided by Illumina. Clean FASTQ files (adaptors were trimmed) were aligned to mice genome (GRCm38.p6) using the Cell Ranger software pipeline (version 2.2) provided by 10x Genomics using the STAR aligner using manufacturer recommended settings. UMI counts, and gene information as well as barcode matrix output from the Cell Ranger mentioned above were used for downstream analysis with pipeline of Seurat (version 2.3.4) R (version 3.6.0) Package. For data quality control, cells with less than 200 genes detected, cells with greater than 30% mitochondrial RNA content, and cells not expressing Ptprc (CD45) were excluded from analysis. After this step, 28,692 out of 34,080 cells passed the filters and were included in downstream analyses. Counts on the filtered matrix of each gene were then normalized with the total library size with the Seurat ‘NormalizeData’ function. To focus on more biologically meaningful variation, we use a subset of highly variable genes (2,000) identified by the function of ‘FindVariableGenes’ from Seurat to perform unsupervised clustering. In order to compare between two samples, ‘FindIntegrationAnchors’ and ‘IntegrateData’ functions were used to integrate samples from mice with and without liver tumors. Then each integrated feature was centered to mean of zero and was scaled by the standard deviation with the function ‘ScaleData’ in Seurat. Linear dimensionality reduction (Principal Component Analysis, PCA) was performed using the function ‘RunPCA’. To partition the cellular distance matrix into clusters, the graph-based ‘FindClusters’ function was used with the resolution set to 0.5. Next, UMAP plots were used to visualize the clusters of cells localized in the graph-based clusters by using ‘RunUMAP’ function with the same principal components described as above. Cluster markers were identified by finding differentially expressed genes between cells in a single cluster versus all cells in all other clusters using ‘FindAllMarkers’ function (Seurat). Clusters were further annotated by directly examined the expression levels of the markers identified above for each cell types with ‘Enrichr’ software (Kuleshov et al., 2016). The M1-like, M2-like, and cross presentation gene signature enrichment analysis were obtained from literature (Mould et al., 2019). The enrichment scores were calculated by averaging the expression level of each signature genes using the ‘Apply’ function (R)
Genome_build: mice genome (GRCm38.p6)
Supplementary_files_format_and_content: normal-matrix.mtx.gz,normal-features.tsv.gz,normal-barcodes.tsv.gz,tumor-matrix.mtx.gz,tumor-features.tsv.gz,tumor-barcodes.tsv.gz

source_name: Mononuclear cells

growth_protocol: On day 0, mice were intrasplenically injected with 500000 MC38 cells, followed by immediate splectomy. Mice were also subcutaneously injected with 3000000 MC38 cells. On day14, livers were collected and immune cells were isolated by density centrifugation. Three biological replicates were pooled for each sample.

extract_protocol:
Single cell sequencing was performed on hepatic mononuclear cells isolated by density centrifugation. In brief, normal livers and livers bearing MC38 tumours were resected, minced, and passed through a 100-mM cell strainer (BD Biosciences). Hepatocytes were depleted through a series of 100 x g centrifugation steps. The supernatant was layered onto 15 mL Ficoll-Paque media and centrifuged at 1000 x g for 20 minutes and stopped without a brake applied. The buffy layer was isolated, washed, and filtered. Three biological replicates were pooled. Single cell library preparation was carried out as per the 10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit v2 #1000014 (10 × Genomics, Pleasanton, CA, USA). Cell suspensions were loaded onto a Chromium Single-Cell Chip along with the reverse transcription (RT) master mix and single cell 5′ gel beads, aiming for 10,000 cells per channel. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed using a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA, USA). 13 cycles used for cDNA amplification. Amplified cDNA was purified using SPRI select beads (Beckman Coulter, Lane Cove, NSW, Australia) as per the manufacturer’s recommended parameters. PostcDNA amplification reaction QC and quantification was performed on the Agilent 2100 Bioanalyzer using the DNA High Sensitivity chip. For input into the gene expression library construction, 50ng cDNA and 14 cycles was used. Libraries were sequenced on an Illumina HiSeq 2500.
10X Genomics Chromium Single Cell 5' Library

value: liver

value: hepatic immune cells

tag: tumor information


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E6_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E6_ad006


title: MDA-MB-231 xenograft proton treated with 2 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: PHx 0hr rep3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E7_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E7_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E6_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E7_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E5_ad012


title: Hepatic mononuclear cells - SC

description: Samples were collected 14 days after intrasplenic injection of PBS

value: No tumor


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E5_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E5_ad004


title: FL12_Cerebrum

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
Illumina bcl2fastq software was used for basecalling
The raw reads were mapped to the mouse mm10 genome using STAR (version 2.6.1).
Expected counts, transcripts per million (TPM), and fragments per kilobase of exon per million reads (FPKM) values were obtained to measure gene expression using RSEM (version 1.3.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene-expression values for each samples

molecule: polyA RNA

source_name: Cerebrum

extract_protocol:
Total RNA was prepared using RNeasy Mini Kit (QIAGEN), ISOGEN (NIPPON GENE), or Sepasol (nakalai tesque).
Library construction was performed using the SureSelect Strand Specific RNA Library Prep Kit (Agilent Technologies) with poly(A) RNA or total RNA depleted of rRNA by Ribo-Zero rRNA Removal Kit (illumina).

value: 12 weeks

tag: condition

value: Flight

tag: genotype


title: FL06_Cerebrum

value: WT


title: FL11_Cerebrum


title: FL08_Cerebrum


title: FL10_Cerebrum


title: FL09_Cerebrum


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E5_ad007

value: CA


title: FL05_Cerebrum


title: NAE 18:3 3 h agb13

city: Denton

first: Ashley

middle: Elisabeth

last: Cannon

state: TX

address: 1155 Union Circle #305220

department: Biological Sciences

institute: The University of North Texas

description:
3hbeta183_3
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv

data_processing:
Reads were mapped to the reference using STAR and the default settings.
Expression analysis was completed using DESeq2.
Genome_build: TAIR10
Supplementary_files_format_and_content: "counttable.txt" files are output from STAR.
Supplementary_files_format_and_content: "normalized_countstable.csv" files are output normalized counts from DESeq2.

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were surface sterilized by treatment with 70% ethanol for 3 min followed by 20% bleach (5.25 % sodium hypochlorite, Clorox) with 0.01% Triton X-100 (Sigma-Aldrich) for 5 min and then rinsed five times with sterile ddH2O. After the final rinse, Arabidopsis seeds were maintained in 1 mL of sterile ddH2O, wrapped in two layers of aluminum foil, and placed in the dark at 4°C for three days. After three days, the seedlings were sown in 50 mL of ½ Murashige and Skoog (Sigma-Aldrich) media, pH 5.7 with 1% sucrose (Fisher Scientific) in a 250 mL sterile Erlenmeyer flask. The seeds were grown at 21°C, 80 -110 µmoles/m2s, on a shaker (Bellco Biotechnologies) set at speed level 3.

extract_protocol:
Each Arabidopsis seedling sample was ground to a fine powder and 500 µL of Hot Borate Buffer (200mM sodium tetraborate decahydrate - Sigma-Aldrich, 30 mM EGTA - Sigma-Aldrich, 1% SDS - Fisher, 1% deoxycholic acid - Sigma-Aldrich, 2% polyvinylpyrrolidone (PVP) 40K - Sigma-Aldrich, 0.5% IGEPAL CA-630 - Sigma-Aldrich, 10 mM DTT - Sigma-Aldrich) and 17.5 µL of 20 mg/mL Proteinase K (ThermoFisher) were added. After mixing, the sample and buffer solution were added to a lilac shredder column from a RNeasy Plant Mini Kit (Qiagen). The manufacturer's protocol from the RNeasy Plant Mini Kit was followed for the remainder of the extraction.
Poly(A) enrichment and library preparation were performed using the TruSeq Stranded mRNA prep kit (Illumina). Libraries were quantified by fluorometry, immobilized, and processed onto a flow cell, followed by 2 x 75 bp sequencing-by-synthesis on a Next-Seq 500 system (Illumina) with two mid-output cassettes (Illumina). Library construction and RNA sequencing were performed by the UNT Genomics Center (http://untgenomicscenter.squarespace.com/).

treatment_protocol: After four days, the seedlings were separated into groups of 515 using sterile toothpicks and moved to 20 mL of ½ Murashige and Skoog in a petri dish (100 x 25 mm, Fisher Scientific). The seedlings were treated with 0.2% DMSO (Sigma-Aldrich), 40 µM NAE 18:3 (Cayman Chemical) for 1 h or 3 h. After 1 h or 3h, whole seedlings were collected from each treatment group, flash frozen, and stored at -80°C.

tag: ecotype/background

tag: genotype/variation

value: Seedlings

tag: treatment time

value: 3 h

value: 4 days


title: NAE 18:3 3 h agb11

description:
3hbeta183_1
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E5_ad006


title: FL02_Cerebrum


title: FL04_Cerebrum


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E5_ad008


title: DMSO 3 h agb11

description:
3hbeta_1
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv

value: DMSO


title: DMSO 3 h agb13

description:
3hbeta_3
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv


title: GC12_Cerebrum


title: FL03_Cerebrum


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E4_ad001


title: FL01_Cerebrum


title: NAE 18:3 3 h agb12

description:
3hbeta183_2
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E4_ad007


title: FL07_Cerebrum


title: GC11_Cerebrum


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E4_ad010


title: GC10_Cerebrum


title: GC09_Cerebrum


title: NAE 18:3 3 h Col02

description:
3hcolo183_2
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E4_ad004


title: GC08_Cerebrum


title: LM43 melanoma cell line resistant to PLX4032 treatment

tag: cell line

tag: plx4032 sensitivity


title: GC07_Cerebrum


title: GC04_Cerebrum


title: GC05_Cerebrum


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E4_ad002


title: DMSO 3 h Col03

description:
3hcolo_3
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv

tag: treatment


title: GC03_Cerebrum


title: DMSO 3 h agb12

description:
3hbeta_2
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E4_ad008


title: GC01_Cerebrum


title: DMSO 3 h Col02

description:
3hcolo_2
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E3_ad012


title: GC02_Cerebrum


title: FL11_Kidney

source_name: Kidney


title: DMSO 3 h Col01

description:
3hcolo_1
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv


title: FL10_Kidney


title: NAE 18:3 3 h Col03

description:
3hcolo183_3
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E3_ad001


title: FL08_Kidney


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E4_ad006


title: GC06_Cerebrum


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E3_ad007


title: FL05_Kidney


title: FL02_Kidney


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E3_ad010


title: NAE 18:3 1 h agb12

description:
1hbeta183_2
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv

value: 1 h


title: GC12_Kidney


title: FL01_Kidney


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E3_ad006


title: NAE 18:3 1 h agb11

description:
1hbeta183_1
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: GC10_Kidney


title: NAE 18:3 3 h Col01

description:
3hcolo183_1
processed data file: 3h_countdata.txt
processed data file: 3h_normalized_countstable.csv


title: GC07_Kidney


title: GC11_Kidney


title: GC06_Kidney


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E3_ad004


title: FL12_Temporal_bone


title: GC02_Kidney


title: DMSO 1 h agb12

description:
1hbeta_2
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: FL11_Temporal_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E3_ad002


title: DMSO 1 h agb11

description:
1hbeta_1
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E3_ad008


title: FL10_Temporal_bone


title: NAE 18:3 1 h Col03

description:
1hcolo183_3
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: NAE 18:3 1 h agb13

description:
1hbeta183_3
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: FL09_Temporal_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E2_ad012


title: FL07_Temporal_bone


title: NAE 18:3 1 h Col02

description:
1hcolo183_2
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E2_ad007


title: FL08_Temporal_bone


title: GC11_Temporal_bone


title: GC10_Temporal_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E2_ad010


title: DMSO 1 h Col03

description:
1hcolo_3
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: GC12_Temporal_bone


title: DMSO 1 h agb13

description:
1hbeta_3
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E2_ad006


title: GC07_Temporal_bone


title: GC12_Thymus

description:
total RNA (depleted of rRNA)
900144Y

source_name: Thymus


title: GC08_Temporal_bone


title: GC09_Temporal_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E2_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E2_ad002


title: GC10_Thymus

description:
total RNA (depleted of rRNA)
900142Y


title: DMSO 1 h Col02

description:
1hcolo_2
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: GC11_Thymus

description:
total RNA (depleted of rRNA)
900143Y


title: DMSO 1 h Col01

description:
1hcolo_1
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: GC09_Thymus

description:
total RNA (depleted of rRNA)
900141Y


title: GC08_Thymus

description:
total RNA (depleted of rRNA)
900140Y


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E12_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E2_ad008


title: MDA-MB-231 xenograft proton treated with 2 Gy of IR dose - replicate4

description: Biological replicate 4 of 6

value: MDA-MB-231 Breast Cancer cell line xenograft

tag: original tissue

value: breast cancer tissue

tag: harvest time post treatment

value: 72 hours

value: MDA-MB-231 xenograft

value: none (no exposure to IR)


title: GC07_Thymus

description:
total RNA (depleted of rRNA)
900139Y


title: NAE 18:3 1 h Col01

description:
1hcolo183_1
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E12_ad010

tag: brain region

tag: Sex

value: male


title: GC05_Thymus

description:
total RNA (depleted of rRNA)
900137Y

tag: strain

tag: age


title: GC04_Thymus

description:
total RNA (depleted of rRNA)
900136Y


title: GC03_Thymus

description:
total RNA (depleted of rRNA)
900135Y


title: 136-E (RNA-Seq)

city: Leioa

first: Begoña

middle: M

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

data_processing:
Sequence reads were trimmed and filtered with Trimmomatic [v0.36] with the following criteria: (1) palindrome mode allowing up to two mismatches; (2) filter reads with an average Phred quality score within a sliding window of 5 nucleotides of 20; (3) filter reads with a length below 36.
The STAR RNA-seq aligner [v2.5.2b] was used to align clean reads to the Ovis aries reference genome using the 2-pass mode.
For each library, the featureCounts software from the SourceForge Subread package [v1.5.0-p1] was applied to assign uniquely aligned fragments to annotated genes in a strand specific manner.
To find new lncRNAs, an additional step was taken. The StringTie transcriptome assemler [v1.3.3b] was used to reconstruct the transcriptome from the previous mapping. It was run with default criteria and following manufacturers intructions.
Unknown, intronic and antisense transcripts were filtered by coding potential, length and exon number, and only candidate lncRNAs were were added to the count matrix of annotated genes.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text file matrix with the raw counts of sequencing reads from annotated genes and new lncRNAs. The genes are identified with the Ensembl ID, while the lncRNAs have the ID assigned by StringTie (MSTRG tag) and the samples are identified by the name of the title column of the SAMPLES section.

organism: Ovis aries

source_name: Encephalon

growth_protocol: The animals were kept under uniform housing conditions and nutritional regimens in Zaragoza (Spain). All experimental procedures were approved and licensed by the EthicalCommittee of the University of Zaragoza (ref: PI15/14). Requirements of the Spanish Policy for Animal Protection (RED53/2013) and the European Union Directive 2010/63 on protection of experimental animals were always fulfilled.

extract_protocol:
A sample from encephalon (parietal lobe cortex) was aseptically taken from each animal and tissue sections were preserved in RNAlater solution (Ambion, Austin, TX, USA) at −80 ⁰C. Total RNA was isolated from encephalon tissue using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) and PureLink RNA Mini Kit (Invitrogen). 60 mg tissue samples were homogenized in 1 ml of TRIzol Reagent using Precellys®24 homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France) combined with 1.4 and 2.8 mm ceramic beads mix lysing tubes (Bertin Technologies). RNA isolation was performed following manufacturer instructions and RNA was suspended in RNase free water and stored at −80 ⁰C. The TruSeq Small RNA library prep kit (Illumina, San Diego, CA, USA) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The animals were treated with three different treatments: one group was inoculated with nine different commercial vaccines, other one was inoculated only with the adjuvant (aluminium hydroxide, AL(OH)3), giving an equivalent dose of aluminium, and other was treated with PBS. Established legal periods between vaccinations were always fulfilled. The vaccination schedule was between February of 2015 and June of 2106, giving a total of 19 doses and 81.5 mg Al3+ per animal during that period.

value: Parietal lobe cortex

tag: group

value: Control

tag: breed

value: Rasa Aragonesa


title: 135-E (RNA-Seq)

tag: tissue


title: GC02_Thymus

description:
total RNA (depleted of rRNA)
900134Y

value: 12 weeks

tag: condition


title: 126-E (RNA-Seq)

value: Vaccine


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E12_ad008

value: CA


title: 137-E (RNA-Seq)


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E12_ad007


title: GC01_Thymus

description:
total RNA (depleted of rRNA)
900133Y

tag: genotype


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E12_ad006


title: FL12_Thymus

description:
total RNA (depleted of rRNA)
900132Y

value: Flight


title: FL09_Thymus

description:
total RNA (depleted of rRNA)
900129Y


title: 124-E (RNA-Seq)


title: FL11_Thymus

description:
total RNA (depleted of rRNA)
900131Y


title: 122-E (RNA-Seq)


title: FL10_Thymus

description:
total RNA (depleted of rRNA)
900130Y

value: WT


title: FL08_Thymus

description:
total RNA (depleted of rRNA)
900128Y


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E12_ad004


title: GC06_Thymus

description:
total RNA (depleted of rRNA)
900138Y


title: FL04_Thymus

description:
total RNA (depleted of rRNA)
900124Y


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E12_ad002


title: 117-E (RNA-Seq)

value: Adjuvant


title: FL05_Thymus

description:
total RNA (depleted of rRNA)
900125Y


title: FL07_Thymus

description:
total RNA (depleted of rRNA)
900127Y


title: FL06_Thymus

description:
total RNA (depleted of rRNA)
900126Y


title: 116-E (RNA-Seq)


title: FL03_Thymus

description:
total RNA (depleted of rRNA)
900123Y


title: FL02_Thymus

description:
total RNA (depleted of rRNA)
900122Y


title: 131-E (RNA-Seq)


title: FL01_Thymus

description:
total RNA (depleted of rRNA)
900121Y


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E12_ad001


title: 115-E (RNA-Seq)


title: 114-E (RNA-Seq)


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E11_ad007


title: FL10_Brown_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E11_ad004


title: FL09_Brown_adipose_tissue


title: FL11_Brown_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E11_ad002


title: FL06_Brown_adipose_tissue


title: FL08_Brown_adipose_tissue


title: FL05_Brown_adipose_tissue


title: FL04_Brown_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E10_ad012


title: FL02_Brown_adipose_tissue


title: GC12_Brown_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E10_ad004


title: FL03_Brown_adipose_tissue


title: FL01_Brown_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E11_ad012


title: GC10_Brown_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E10_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E10_ad002


title: GC09_Brown_adipose_tissue


title: FL12_Brown_adipose_tissue


title: GC07_Brown_adipose_tissue


title: GC08_Brown_adipose_tissue


title: 121-E (RNA-Seq)


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E10_ad006


title: GC11_Brown_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E10_ad001


title: GC06_Brown_adipose_tissue


title: FL07_Brown_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E1_ad012


title: GC04_Brown_adipose_tissue


title: GC05_Brown_adipose_tissue


title: GC03_Brown_adipose_tissue


title: FL12_White_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E1_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E11_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E1_ad001


title: GC02_Brown_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E1_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E1_ad004


title: FL07_White_adipose_tissue


title: FL11_White_adipose_tissue


title: FL05_White_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E1_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_E1_ad002


title: FL10_White_adipose_tissue


title: FL09_White_adipose_tissue


title: FL06_White_adipose_tissue


title: FL08_White_adipose_tissue


title: FL04_White_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D9_ad002


title: GC10_White_adipose_tissue


title: GC08_White_adipose_tissue


title: FL03_White_adipose_tissue


title: FL02_White_adipose_tissue


title: GC12_White_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D9_ad012


title: GC01_Brown_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D9_ad010


title: FL01_White_adipose_tissue


title: GC11_White_adipose_tissue


title: GC07_White_adipose_tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D9_ad006


title: GC06_White_adipose_tissue


title: GC09_White_adipose_tissue


title: GC03_White_adipose_tissue


title: GC05_White_adipose_tissue


title: GC04_White_adipose_tissue


title: GC12_Liver

source_name: Liver


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D8_ad012


title: GC02_White_adipose_tissue


title: GC01_White_adipose_tissue


title: GC10_Liver


title: GC11_Liver


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D9_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D8_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D8_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D8_ad008


title: GC09_Liver


title: GC08_Liver


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D7_ad001


title: GC07_Liver


title: GC04_Liver


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D8_ad007


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D7_ad006


title: GC05_Liver


title: GC06_Liver


title: GC02_Liver


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D7_ad004


title: GC01_Liver


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D7_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D6_ad007


title: FL11_Liver


title: FL07_Liver


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D6_ad004


title: GC03_Liver


title: FL09_Liver


title: G2_D6_L106 TP 6 days D3.8mg/m3

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway, Building 22

country: Canada

institute: Health Canada

hyb_protocol: An equimolar amount of UMRR cRNA was mixed with each experimental cRNA and was hybridized to Agilent SurePrint G3 Rat 8 × 60K microarrays (Agilent Technologies. Inc). Hybridization was conducted for 17 hours at 65oC.

scan_protocol: After washing, microarray slides were scanned in a Scanned on an Agilent G2505C scanner (Agilent). Data was retrieved using the Feature Extraction 11.0.1.1 software (Agilent). Data analysis is described below.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

organism: Rattus norvegicus

source_name: Lung

label_protocol: In brief, 200 ng of total RNA per individual rat lung sample or Universal Mouse Reference RNA UMRR (Agilent Technologies) was used to synthesise labelled cDNAs and cRNAs using the Linear Amplification Kit (Agilent Technologies). T7 RNA polymerase-transcribed cRNA from experimental samples were labelled with Cyanine-5 and UMRR was labelled with Cyanine-3.

growth_protocol: The animal exposure was performed as described in Gosens et al. (2016). In brief, adult male (8 week-old) Wistar Unilever outbred rats (strain HsdCpb:WU) were obtained from Harlan (Netherlands). Rats (332 ± 22 g) were acclimatized for two weeks in Macrolon type IV cages (2-5 individuals per cage) with food and water supplied ad libitum before the exposure. The experiments were conducted at the National Institute for Public Health (RIVM) at Bilthoven, The Netherlands, under permit number 201300190. Experimental procedures complied with the European directive on the protection of animals for scientific purposes (Directive 2010/63/EU).

extract_protocol: Total RNA was extracted from individual rat lung samples from each treatment group using the Direct-zol RNA MiniPrep kit for animal tissue (Zymo Research), following the manufacturer’s instructions. Total RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and RNA quality and integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). All samples showed RNA integrity numbers (RIN) above 7. Details of the microarray procedures can be found in Halappanavar et al. (2015).

treatment_protocol: This is a short-term inhalation study (STIS). It was conducted according to the OECD Test Guideline 403 for Acute Inhalation Toxicity Test number 403 using the C × T protocol considering a 6-h exposure equivalent per day (the maximum recommended). In brief, rats were exposed by inhalation (nose-only) to the 6 hour equivalent doses of 3 and 8.6 mg NPs / m3 of CuO nanomaterials (black material) positively charged coating (PEI) or 6 hour equivalent doses of 3.8 and 10.9 mg NPs / m3 of CuO nanomaterials negatively charged coating (ASC). Control animals were exposed to air only. Rats were exposed to five consecutive days and lung tissues were sampled on day 1 after the last exposure (referrred to as T6) and day 22 post-exposure (referred to as T27). Each treatment group consisted of minimum of 5 animals.

value: ASC

tag: sampleID

tag: time point

value: 6 days

tag: dose

source_name: Universal  Rat Reference RNA

tag: sample type

value: 14 rat cell lines


title: G2_D27_H122 TP 27 days D10.9mg/m3

value: 27 days


title: G2_D6_H115 TP 6 days D10.9mg/m3


title: G2_D27_L112 TP 27 days D3.8mg/m3


title: G2_D27_H121 TP 27 days D10.9mg/m3


title: G1_D6_H59 TP 6 days D8.6mg/m3

value: PEI


title: FL10_Liver


title: G1_D6_H60 TP 6 days D8.6mg/m3


title: G2_D6_H117 TP 6 days D10.9mg/m3


title: G1_D6_L50 TP 6 days D3mg/m3


title: FL04_Liver


title: FL05_Liver


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D6_ad002


title: FL03_Liver


title: FL12_Liver


title: FL06_Liver


title: G2_D6_L104 TP 6 days D3.8mg/m3


title: G1_D27_L55 TP 27 days D3mg/m3


title: G2_D6_H116 TP 6 days D10.9mg/m3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D6_ad008


title: FL02_Liver


title: FL08_Liver


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D6_ad010


title: FL01_Liver


title: GC11_Spleen

source_name: Spleen


title: G2_D27_L111 TP 27 days D3.8mg/m3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D5_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D5_ad012


title: GC10_Spleen


title: GC12_Spleen


title: GC07_Spleen


title: GC09_Spleen


title: GC05_Spleen


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D5_ad002


title: GC06_Spleen


title: D6_C5 TP 6 days D0mg/m3

value: Air


title: G1_D27_H66 TP 27 days D8.6mg/m3


title: GC03_Spleen


title: G1_D27_L56 TP 27 days D3mg/m3


title: G1_D27_H65 TP 27 days D8.6mg/m3


title: GC04_Spleen


title: GC01_Spleen


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D4_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D5_ad008


title: GC02_Spleen


title: G1_D6_L51 TP 6 days D3mg/m3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D5_ad010


title: FL12_Spleen


title: FL10_Spleen


title: GC08_Spleen


title: FL11_Spleen


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D5_ad006


title: FL08_Spleen


title: D27_C10 TP 27 days D0mg/m3


title: FL09_Spleen


title: FL06_Spleen


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D4_ad004


title: FL05_Spleen


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D4_ad002


title: G2_D6_L107 TP 6 days D3.8mg/m3


title: G2_D27_H120 TP 27 days D10.9mg/m3


title: FL04_Spleen


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D4_ad008


title: FL03_Spleen


title: FL01_Spleen


title: D6_C4 TP 6 days D0mg/m3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D3_ad007


title: FL02_Spleen


title: GC04_Mandibular_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D4_ad001


title: FL07_Spleen


title: GC02_Mandibular_bone


title: GC08_Mandibular_bone


title: GC07_Mandibular_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D3_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D4_ad007


title: FL02_Mandibular_bone


title: FL04_Mandibular_bone


title: FL01_Mandibular_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D3_ad002


title: G2_D27_L108 TP 27 days D3.8mg/m3


title: D6_C3 TP 6 days D0mg/m3


title: D27_C9 TP 27 days D0mg/m3


title: FL05_Mandibular_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D3_ad008


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D2_ad001


title: FL03_Mandibular_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D2_ad012


title: FL06_Mandibular_bone


title: G2_D6_H114 TP 6 days D10.9mg/m3


title: G2_D27_L110 TP 27 days D3.8mg/m3


title: D27_C8 TP 27 days D0mg/m3


title: GC06_Temporal_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D2_ad007


title: GC01_Mandibular_bone


title: G2_D27_H119 TP 27 days D10.9mg/m3


title: GC05_Temporal_bone


title: G1_D27_H64 TP 27 days D8.6mg/m3


title: G1_D27_L54 TP 27 days D3mg/m3


title: GC03_Mandibular_bone


title: FL06_Temporal_bone


title: FL05_Temporal_bone


title: GC04_Temporal_bone


title: FL04_Temporal_bone


title: GC01_Temporal_bone


title: G2_D6_H113 TP 6 days D10.9mg/m3


title: FL01_Temporal_bone


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D2_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D2_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D2_ad004


title: D27_C7 TP 27 days D0mg/m3


title: GC02_Temporal_bone


title: G2_D6_L105 TP 6 days D3.8mg/m3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D2_ad008


title: FL02_Temporal_bone


title: G1_D6_L49 TP 6 days D3mg/m3


title: G1_D27_H63 TP 27 days D8.6mg/m3


title: Tumor Kras/shp53, YTKO

description: Gene expression data from subcutaneous tumors derived from Kras/shp53-induced Gliomaspheres

data_processing:
Reads quality was checked using FastQC.
Reads were mapped to the mouse reference genome (mm10 build) using STAR (v2.5.3a).
Raw gene counts were obtained using the featureCounts function of the Rsubread R package (v1.22.3) and the UCSC gene annotation (mm10).
Genome_build: mm10
Supplementary_files_format_and_content: expression matrix (raw gene counts)

source_name: Subcutaneous tumor from Kras/shp53-induced Gliomaspheres

growth_protocol: Newborn astroglial cells were maintained, expanded in fibronectin-coated dishes with DMEM (Gibco) supplemented with 10% FBS, glutamine and antibiotics

extract_protocol:
RNA extraction from cells was performed with NucleoSpin 8 RNA Core Kit (Macherey-Nagel) according to the manufacturer’s instructions, using an automated system (Freedom EVO, Tecan).
RNA-seq libraries were prepared with TruSeq Stranded mRNA Library Prep (Illumina), according to manufacturer’s instructions.

treatment_protocol: At the appearance of palpable masses (between 2  weeks after injectione), one mouse injected subcutaneously with Kras/shp53-induced Gliomasphere cells received a TAM400/CreER diet (Envigo) to promote YAP/TAZ knockout in tumor cells (YAP/TAZ KO), whereas a second group, serving as control, continued to be fed with normal diet (YAP/TAZ wt).

tag: cells

tag: experimental conditions

value: TAM-treated


title: Blood_4

city: Freiburg

first: Patrice

last: Zeis

address: Stübeweg 51

country: Germany

description: library of ILCs d15 post NB infection

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000) was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters (Li and Durbin, 2010). The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapped by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the unique molecular identifier (UMI) followed by six bases representing the cell specific barcode. The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: peripheral Blood

growth_protocol: C57BL/6 mice were purchased from Charles River Laboratories. All mice were bred and housed under specific pathogen free conditions at the animal facilities of the University of Würzburg (ZEMM and Institute for Immunology and Virology), Memorial Sloan-Kettering Cancer Center, Max Planck Institute of Immunobiology and Epigenetics, Freiburg and Centre Immunologie Luminy and were used in accordance with institutional guidelines and as approved by the local authorities

extract_protocol:
Lungs were harvested, chopped into small pieces and incubated in digestion buffer DMEM (Gibco 31966021); 0.25 mg/ml LiberaseTM TL (Research Grade 05401020001, Roche); 10mM Hepes (Gipco 1563049) for 45 mins at 37°C on Eppendorf rotator at 120rpm. Digestion was stopped with 20ml RPMI 1640 medium Thermo Fisher Scientific; 31870074) added with 50μM 2-mercaptoethonal (AppliChem, A1108). Cells were meshed through 70um cell strainer (Falcon 3522350) and washed and collected in FACS Buffer or 1× MojoSort buffer (BioLegend; 480017). Bone marrow cells from ilia, femora, and tibiae were isolated by crushing the bones in 1× MojoSort buffer. Bone marrow cells were filtered (CellTrics, 30 μm; Sysmex) and washed and collected in 1x MojoSort buffer.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

value: peripheral Blood

value: 6-8 weeks


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D12_ad008

source_name: C57BL/6J Male P56 Mouse Brain

value: male


title: Tumor Kras/shp53, YTwt repB

value: Subcutaneous tumor from Kras/shp53-induced Gliomaspheres

value: Untreated


title: Blood_3

institute: Max Planck Institute of Immunobiology and Epigenetics

description: library of ILCs d15 post NB infection


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D12_ad010


title: Control mouse astroglial cells repC

description: Gene expression data from control astroglial cells

source_name: Control mouse astroglial cells

value: Control mouse astroglial cells

value: C57BL/6J; Yapf/f;Tazf/f


title: G1_D27_L53 TP 27 days D3mg/m3

tag: treatment


title: FL03_Temporal_bone

value: 12 weeks

value: Flight


title: G1_D6_H58 TP 6 days D8.6mg/m3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D2_ad002

value: CA


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D12_ad007


title: Blood_2

description: library of ILCs d15 post NB infection


title: D6_C2 TP 6 days D0mg/m3


title: GC03_Temporal_bone

value: WT


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D12_ad002


title: G1_D6_L48 TP 6 days D3mg/m3

value: 6 days


title: Blood_1

description: library of ILCs d15 post NB infection


title: G2_D27_H118 TP 27 days D10.9mg/m3

value: ASC

value: 14 rat cell lines


title: iv45_3

description: library of ivCD45+ ILCs d10 post NB infection

value: Lung


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D12_ad004


title: iv45_4


title: iv45_1


title: D27_C6 TP 27 days D0mg/m3

value: Air

value: 27 days


title: infLd7_7

description: library of ILCs d7 post NB infection mouse1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D12_ad001


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D10_ad012


title: G1_D27_L52 TP 27 days D3mg/m3

value: PEI


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D10_ad010


title: G1_D6_L47 TP 6 days D3mg/m3


title: infLd7_6

value: 6-8 weeks


title: infLd7_3


title: G1_D6_H61 TP 6 days D8.6mg/m3


title: infLd7_2


title: d7_4

description: library of ILCs d7 post NB infection mouse2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D10_ad006

value: male


title: infLd7_1


title: infLd7_5


title: infLd7_4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D10_ad008


title: G1_D6_H57 TP 6 days D8.6mg/m3


title: d7_1


title: iv45_2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D10_ad004


title: d7_3


title: d10_4

description: library of ILCs d10 post NB infection


title: D6_C1 TP 6 days D0mg/m3


title: d10_3

description: library of ILCs d10 post NB infection


title: d7_2


title: WT_M2_P2_I4

description: library of resting lung ILCs mouse2 sample8


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D1_ad002


title: G1_D27_H62 TP 27 days D8.6mg/m3


title: WT_M2_P2_I3

description: library of resting lung ILCs mouse2 sample7


title: G2_D6_L103 TP 6 days D3.8mg/m3


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D1_ad006


title: d10_1

description: library of ILCs d10 post NB infection


title: G2_D27_L109 TP 27 days D3.8mg/m3


title: WT_M2_P1_I8

description: library of resting lung ILCs mouse2 sample4


title: WT_M2_P1_I6

description: library of resting lung ILCs mouse2 sample2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C9_ad007


title: d10_2

description: library of ILCs d10 post NB infection


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C9_ad012


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D1_ad008


title: WT_M2_P2_I1

description: library of resting lung ILCs mouse2 sample5


title: WT_M2_P1_I5

description: library of resting lung ILCs mouse2 sample1


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C9_ad002


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D10_ad002


title: WT_M2_P1_I7

description: library of resting lung ILCs mouse2 sample3


title: Inf_M4_P2_I4

description: library of ILCs d15 post NB infection mouse4 plate8


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C9_ad008


title: WT_M1_P2_I9

description: library of resting lung ILCs mouse1 sample8


title: WT_M1_P2_I11

description: library of resting lung ILCs mouse1 sample6


title: WT_M2_P2_I2

description: library of resting lung ILCs mouse2 sample6


title: WT_M1_P2_I10

description: library of resting lung ILCs mouse1 sample5


title: WT_M1_P2_I12

description: library of resting lung ILCs mouse1 sample7


title: Inf_M3_P2_I9

description: library of ILCs d15 post NB infection mouse3 sample7


title: Inf_M3_P2_I8

description: library of ILCs d15 post NB infection mouse3 sample6


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C8_ad010


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C8_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C8_ad001


title: Inf_M4_P2_I3

description: library of ILCs d15 post NB infection mouse4 plate7


title: Inf_M4_P2_I2

description: library of ILCs d15 post NB infection mouse4 plate6


title: Inf_M4_P2_I1

description: library of ILCs d15 post NB infection mouse4 plate5


title: mergedInf_M4_P1_I11

description: library of ILCs d15 post NB infection mouse4 sample3


title: mergedInf_M4_P1_I10

description: library of ILCs d15 post NB infection mouse4 sample2


title: mergedInf_M4_P1_I12

description: library of ILCs d15 post NB infection mouse4 sample4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C8_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_D3_ad010


title: Inf_M3_P2_I5

description: library of ILCs d15 post NB infection mouse3 sample5


title: mergedWT_M1_P1_I4

description: library of resting lung ILCs mouse1 sample4


title: mergedWT_M1_P1_I3

description: library of resting lung ILCs mouse1 sample3


title: mergedInf_M3_P1_I6

description: library of ILCs d15 post NB infection mouse3 sample2


title: mergedWT_M1_P1_I2

description: library of resting lung ILCs mouse1 sample2


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C7_ad007


title: mergedInf_M3_P1_I5

description: library of ILCs d15 post NB infection mouse3 sample1


title: Gliomaspheres Kras/shp53 + TAM repB [exp2]

description:
astro_Cre_YT_Ras_sfere_P1_day7_TAM_repB
Gene expression data from Kras/shp53-induced Gliomaspheres, 7 days after inducing YAP/TAZ knockout.
processed data file: astro_YT_exp2_expressionMatrix_counts.txt

data_processing:
Reads quality was checked using FastQC.
Reads were mapped to the mouse reference genome (mm10 build) using STAR (v2.5.3a).
Raw gene counts were obtained using the featureCounts function of the Rsubread R package (v1.22.3) and the UCSC gene annotation (mm10).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: astro_YT_exp2_expressionMatrix_counts.txt: Tab-delimited expression matrix (raw gene counts).

source_name: Kras/shp53-induced Gliomaspheres, 7 days after YAP/TAZ knockout

growth_protocol: Gliomaspheres are cultured in suspension with DMEM-F12, 1% GLN, 1% PS, 1% N-2 supplement, 20 ng/ml mouse EGF, 20 ng/ml mouse bFGF.

treatment_protocol: Spheres were treated with 1µM 4OH TAM or left untreated for 1 week.

tag: cell type

value: Gliomaspheres from KRasG12V/shp53-transformed mouse astrocytes

tag: strain/background

tag: experimental condition

value: 4OH TAM


title: Gliomaspheres Kras/shp53 + TAM repA [exp2]

description:
astro_Cre_YT_Ras_sfere_P1_day7_TAM_repA
Gene expression data from Kras/shp53-induced Gliomaspheres, 7 days after inducing YAP/TAZ knockout.
processed data file: astro_YT_exp2_expressionMatrix_counts.txt


title: mergedWT_M1_P1_I1

description: library of resting lung ILCs mouse1 sample1

tag: strain


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C8_ad008

tag: brain region

tag: Sex

tag: age


title: mergedInf_M3_P1_I7

description: library of ILCs d15 post NB infection mouse3 sample3

tag: tissue


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C7_ad006


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C8_ad002


title: mergedInf_M3_P1_I8

description: library of ILCs d15 post NB infection mouse3 sample4


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C7_ad012


title: Gliomaspheres Kras/shp53 repB [exp2]

description:
astro_Cre_YT_Ras_sfere_P1_day7_repB
Gene expression data from control Kras/shp53-induced Gliomaspheres.
processed data file: astro_YT_exp2_expressionMatrix_counts.txt

source_name: Kras/shp53-induced Gliomaspheres

value: Untreated


title: Control mouse astrocytes repB [exp1]

description:
astro_YT_ctrl_no_doxy_repB
Gene expression data from control astrocytes.
processed data file: astro_YT_exp1_expressionMatrix_counts.txt

data_processing:
Reads quality was checked using FastQC.
Reads were mapped to the mouse reference genome (mm10 build) using STAR (v2.5.3a).
Raw gene counts were obtained using the featureCounts function of the Rsubread R package (v1.22.3) and the UCSC gene annotation (mm10).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: astro_YT_exp1_expressionMatrix_counts.txt: Tab-delimited expression matrix (raw gene counts).

source_name: Control mouse astrocytes

growth_protocol: Mouse astrocytes with HER2CA are cultured in DMEM-F12, 1% GLN, 1% PS, 1% N-2 supplement, 20 ng/ml mouse EGF, 20 ng/ml mouse bFGF, 1µg/µL Doxycycline. Gliomasphere are cultured in suspension in the same medium. Control mouse astrocytes are cultured in DMEM-F12, 1% GLN, 1% PS,1% N-2 supplement, 20 ng/ml mouse EGF, 20 ng/ml mouse bFGF, without Doxycycline.

treatment_protocol: HER2CA-transformed mouse astrocytes were treated for 15 days with 1µM 4OH TAM or left untreated.

value: Control mouse astrocytes

value: C57BL/6J; Yapf/f;Tazf/f


title: Gliomaspheres Kras/shp53 repA [exp2]

description:
astro_Cre_YT_Ras_sfere_P1_day7_repA
Gene expression data from control Kras/shp53-induced Gliomaspheres.
processed data file: astro_YT_exp2_expressionMatrix_counts.txt


title: Control mouse astrocytes repA [exp1]

description:
astro_YT_ctrl_no_doxy_repA
Gene expression data from control astrocytes.
processed data file: astro_YT_exp1_expressionMatrix_counts.txt


title: Mouse astrocytes HER2CA TAM Day 15 repA [exp1]

description:
astro_YT_doxy_day15_TAM_repA
Gene expression data from YAP/TAZ knockout astrocytes, 15 days after inducing HER2CA expression.
processed data file: astro_YT_exp1_expressionMatrix_counts.txt

source_name: Mouse YAP/TAZ knockout astrocytes + HER2CA Day 15

value: HER2CA-expressing mouse astrocytes

value: Doxycycline and 4OH TAM


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C7_ad001

value: CA


title: Mouse astrocytes HER2CA TAM Day 15 repB [exp1]

description:
astro_YT_doxy_day15_TAM_repB
Gene expression data from YAP/TAZ knockout astrocytes, 15 days after inducing HER2CA expression.
processed data file: astro_YT_exp1_expressionMatrix_counts.txt


title: Tumor Kras/shp53, YTwt repA

description:
MC38
Gene expression data from subcutaneous tumors derived from Kras/shp53-induced gliomaspheres.
processed data file: astro_YT_exp3_expressionMatrix_counts.txt

data_processing:
Reads quality was checked using FastQC.
Reads were mapped to the mouse reference genome (mm10 build) using STAR (v2.5.3a).
Raw gene counts were obtained using the featureCounts function of the Rsubread R package (v1.22.3) and the UCSC gene annotation (mm10).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: astro_YT_exp3_expressionMatrix_counts.txt: Tab-delimited expression matrix (raw gene counts).

source_name: Subcutaneous tumor from Kras/shp53-induced gliomaspheres

treatment_protocol: No treatment.


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C6_ad001

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C7_ad004


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C7_ad010


title: mergedInf_M4_P1_I9

description: library of ILCs d15 post NB infection mouse4 sample1


title: Gliomaspheres HER2CA repA [exp1]

description:
astro_YT_doxy_sfere_P1_repA
Gene expression data from HER2CA-expressing P1 Gliomaspheres.
processed data file: astro_YT_exp1_expressionMatrix_counts.txt

source_name: Gliomaspheres HER2CA

value: HER2CA-induced Gliomaspheres

value: Doxycycline and DMSO


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C7_ad008


title: Gliomaspheres HER2CA repB [exp1]

description:
astro_YT_doxy_sfere_P1_repB
Gene expression data from HER2CA-expressing P1 Gliomaspheres.
processed data file: astro_YT_exp1_expressionMatrix_counts.txt


title: LPS/IFNg treated Yap/Taz knockout_rep1

city: Singapore

first: Manvendra

middle: Kumar

last: Singh

state: Singapore

address: 8 College Road

department: Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS Medical School

data_processing:
Alignment using STAR version=STAR_2.5.1b
Mapping reads counting : featureCounts (Rsubread R package)
Genome_build: NCBI RefSeq annotation for mm10 (build 38.1) is used
Supplementary_files_format_and_content: RawReadCounts_WtKo_UntLps.txt.gz:  format - ".txt", Content - Raw read counts file from featureCount

source_name: Bone-marrow-derived macrophage (BMDM)

growth_protocol: BMDMs were isolated from the femurs and tibiae of control and YAP/TAZ-dKO mice. Femurs and tibiae were collected by cutting off the hind legs at the hip joint with sterile scissors, ensuring that joints were kept intact, and placed in sterile cold PBS. The excess muscle was removed carefully by leaving the bone with no muscle. Using sharp scissors soaked in 95% ethanol, the ends of the bones were cut. The bone cavity containing BMDMs was flushed out with 5 ml of sterile cold PBS. Cells were then centrifuged at 1000 rpm for 10 minutes for pellet collection. Pellets were resuspended and plated in 20 ml of macrophage medium [Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, catalog no. 11965092) containing 20% L929-conditioned medium, 1% penicillin/streptomycin and 10% FBS]. On day 3, an additional 15 ml of macrophage medium was added and on day 6, all the media were replaced with fresh macrophage media. On day 7, cells were detached using trypsin (Gibco, catalog no. 25200056) for 30 minutes to 1 hour at 4ÅãC. Cells were then washed, centrifuged, resuspended and seeded (1 Å~ 106 cells/well) in a 6-well tissue culture plates using the culture medium (DMEM containing 10% FBS and 1% penicillin/streptomycin).

extract_protocol:
Total RNA was prepared from BMDMs of 2-3 months old control and YAP/TAZ-dKO mice using either Favorgen RNA extraction kit (Favorgen Biotech, catalog no. FATRK 001-2) or PureLink RNA Mini Kit (Thermo Fisher, catalog no. 12183018A).
To perform the RNAseq, total RNA was prepared from BMDMs of 2-3 months old control and YAP/TAZ-dKO mice using either Favorgen RNA extraction kit (Favorgen Biotech, catalog no. FATRK 001-2) or PureLink RNA Mini Kit (Thermo Fisher, catalog no. 12183018A). Subsequently, strand-specific poly(A) RNAseq libraries were generated using NEBNext. Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB, catalog no. E7765S) and sequenced on Hiseq2000 sequencer.

treatment_protocol: We performed RNAseq analysis on BMDMs isolated from 2-3 months old control and YAP/TAZ-dKO mice and treated them with or without LPS/IFNg (LPS 100ng/ml + IFNγ 10ng/ml) for 12 hours.

value: 2-3 months


title: CEMBA190212_9H_1_CEMBA190212_9H_2_C6_ad004