title: mouse WT DRG rep2

city: Tarrytown

first: Tao

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

description:
wild type mouse lumar DRG
DRG.processed.umi.raw.counts.txt

data_processing:
Sample de-multiplexing, alignment, filtering, and UMI counting were conducted using Cell Ranger Single-Cell Software Suite59 (10X Genomics, v2.0.0).
The UMI data output from Cell Ranger Single-Cell Software Suite (10X Genomics, v2.0.0) was analyzed using Seurat package to assess the cell quality and identify cell types.
Cells with the number of detected genes less than 500 or over 15000, or with a UMI ratio of mitochondria encoded genes versus all genes over 0.1 were also removed. The UMI data was normalized by the ‘NormalizeData’ method in Seurat with default settings.
To avoid potential sample-to-sample variation caused by technical variation at various experiment steps, we employed Seurat data integration method. The top 2000 variable genes of each of the 5 samples were identified using ‘FindVariableFeatures’ with selection.method=‘vst’. Based on the union of these variable genes, the anchor cells in each sample were identified by ‘FindIntegrationAnchors’. All the samples were then integrated by ‘IntegrateData’. We subsequently scaled the integrated data (‘ScaleData’) and performed dimension reduction (‘RunPCA’).
Cells were then clustered based on the first 15 principal components by applying ‘FindNeighbors’ and ‘FindClusters’ (resolution=0.6, algorithm=1). Marker genes for each cluster were identified using ‘FindAllMarkers’. Parameters were used such that these genes were expressed in at least 25% of the cells in the cluster, and on average 2-fold higher than the rest of cells with a multiple-testing adjusted Wilcoxon test p value of less than 0.01.
The specificity of the canonical cell type-specific genes or cell cluster-specific genes were further examined by visualizations and used to define the cell type for each cluster.
Genome_build: mm10
Supplementary_files_format_and_content: a text file with genes in rows and cells in columns, and entries being UMI counts.

source_name: Dorsal root ganglion single cell

growth_protocol: Not applicable.

extract_protocol:
Lumbar DRGs were isolated from adult C57Bl6 mice and transferred to a dissociation buffer (Dulbecco's modified Eagle's medium supplemented with 10% heat-inactivated Fetal Calf Serum) (Gibco; cat # A38400-02). To generate a single cell suspension, DRGs were subjected to a 2 step-enzymatic dissociation followed by a mechanical dissociation.
RNA-seq libraries were constructed using Chromium Single Cell 3’ Library, Gel Beads & Multiplex Kit (10X Genomics).  Sequencing was performed on Illumina NextSeq500. Read 1 starts with a 26-bp UMI and cell barcode, followed by an 8-bp i7 sample index. Read 2 contains a 55-bp transcript read.

treatment_protocol: DRGs were first incubated with 0.125% collagenase P from Clostridium histolyticum (Roche Applied Science; cat # 11249002001) for 90 minutes in an Eppendorf Thermomixer C (37°C; intermittent 750 rpm shaking for about 10 sec every 2 minutes). Then, DRGs were transferred to a Hank's Balanced Salt Solution (HBSS, Mg2+ and Ca2+ free; Invitrogen) supplemented with 0.25% Trypsin (Worthington biochemical corp.; cat # LSoo3707) and 0.0025% EDTA and incubated for 10 minutes at 37°C in the Eppendorf Thermomixer C. Trypsin was neutralized by the addition of 2.5 mg/ml MgSO4 (Sigma; cat #M-3937) and DRGs were triturated with Pasteur pipettes. The resulting cell suspension was passed through a 70 µm mesh filter to remove remaining chunks of tissues and centrifuged for 5 minutes at 2500 rpm at room temperature. The pellet was resuspended in HBSS (Ca2+, Mg2+ free; Invitrogen) and the cell suspension was run on a 30% Percoll Plus gradient (Sigma GE17-5445-02) to further remove debris. Finally, cells were resuspended in PBS supplemented with 0.04% BSA at a concentration of 200 cells/µl and cell viability was determined using the automated cell analyzer NucleoCounter® NC-250™.

value: untreated


title: mouse WT DRG rep5

status: Public on Mar 31 2021

type: SRA

last: Yang

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: treatment


title: GF Male 3 [GM3]

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

data_processing:
QC by AlignerBoost
Mapping by AlignerBoost with STAR (v2.5.3)
Read counting by featureCount from the Subread package
DE gene calling by DESeq2
GO enrichment analysis by topGO, biomaRt R packages and REVIGO online server
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: raw counts

source_name: male_GF_adult skin keratinocytes

growth_protocol: All mouse experiments were conducted under protocols approved by the University of Pennsylvania Institutional Animal Care and Use Committee (Protocol #804065). Age-matched 6-8 weeks old mice were used for all experiments. Germ-free studies were conducted in the Penn Gnotobiotic Mouse facility. Indicated strains were bred and maintained as germ-free (GF) in flexible vinyl isolators at the Penn Gnotobiotic Mouse facility housed in the Veterinary Hospital at the University of Pennsylvania. SPF counterparts were purchased from Jackson Laboratories and allowed to acclimatize in the facility for one week prior to beginning any experiments. Colonized (COL) group of mice were born GF and then colonized with SPF microbiota for 2 weeks.

extract_protocol:
Mice were shaved, and skin was collected from dorsal region. Fat layer was scraped off using a scalpel and then skin was floated in dispase (1mg/ml) in 1X PBS overnight at 37oC for 1 hour in order to separate the epidermis from the dermis. The epidermis was stored in RNAlater.  Mouse epidermis that had been stored in RNA-Later (Thermo-Fisher) was blotted dry and approximately 20 mg of tissue was placed in a Lysing Matrix A tube (MP Bio) with 600 µl RLT buffer (Qiagen) containing 2-mercaptoethanol.  The tissue was homogenized with three, 1 min bursts of bead beating in a FastPrep 24 (MP Bio).  The lysate was centrifuged (14,000 x g, 3 min) and the supernatant was transferred to a new tube to which 1 volume of 70 % ethanol was added.   RNA was purified using a RNeasy Tissue Kit (Qiagen), as per manufacturer’s guidelines.
RNA was quantified on a Qubit and RNA-integrity was assessed using BioAnalyser according to manufacturer’s instructions. 1µg RNA was used to construct RNA-seq libraries using the stranded-TruSeq RNA Sample Prep Kit (Illumina), spiked with phiX and sequenced on the Illumina NextSeq-500 Platform across 3 runs of single-end 75 bp reads.

tag: Sex

value: male

tag: condition

value: GF

tag: tissue/cell type

value: adult skin keratinocytes


title: mouse WT DRG rep4


title: GF Female 3 [GF3]

source_name: female_GF_adult skin keratinocytes

value: female


title: GF Female 1 [GF1]


title: SPF Female 2 [SF2]

source_name: female_SPF_adult skin keratinocytes

value: SPF


title: mouse WT DRG rep1


title: SPF Female 4 [SF4]


title: SPF Male 2 [SM2]

source_name: male_SPF_adult skin keratinocytes


title: SPF Female 1 [SF1]


title: mouse WT DRG rep3


title: GF Male 4 [GM4]


title: COL Female 2 [CF2]

source_name: female_COL_adult skin keratinocytes

value: COL


title: GF Female 2 [GF2]


title: SPF Male 1 [SM1]


title: COL Male 2 [CM2]

source_name: male_COL_adult skin keratinocytes


title: COL Female 4 [CF4]


title: SPF Male 4 [SM4]


title: SPF Female 3 [SF3]


title: COL Male 1 [CM1]


title: Lin-negative single-cell of bilio-vascular tree fragments

city: PARIS

first: Axelle

last: Cadoret

address: 27 rue de Chaligny

department: UMRS938 CRSA

country: France

institute: INSERM

data_processing:
fastq files were generated using cellranger 3.0.2 mkfastq tool
matrix filles were generated using cellranger 3.0.2 count function, with mm10 reference transcriptome with 10000 cells as expected-cells number
output from cellranger was processed into Seurat v3.
filtered_feature_bc_matrix : filtered data from cellranger count outputs
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Liver

extract_protocol:
Illumina 10X Genomics 3’ v3 kit
single cell RNAseq 10X 3' v3 kit

tag: disease state

value: Normal

tag: tissue

value: Liver

tag: cell type

value: Lin-negative single-cell suspension from bilio-vascular tree fragments


title: GF Male 1 [GM1]


title: COL Female 3 [CF3]


title: COL Male 3 [CM3]


title: COL Female 1 [CF1]


title: SPF Male 3 [SM3]


title: WD5 rep3

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: small RNA

data_processing:
Reads were trimmed for BIOO adaptor sequence with cutadapt-1.2.1 (--adapter=TGGAATTCTCGGGTGCCAAGG), reads of size under 15 bases were discared.
Remaining reads were mapped using bowtie2 versus mm10 (--local --very-sensitive-local -k 24).
Aligned reads were finally annotated versus .Gff mirbase v21, ensembl ncrna rel73, tRNAs, and piRNAs from piRNAclusterDB.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of raw reads count for each Sample

source_name: spermatozoa

growth_protocol: 3-weeks-old male mice were divided into 2 groups. Males from the first group were kept on CD and the males of the other group were fed a WD for 3-4 months. This first generation of WD males was named WD1. At four months-old, 4 to 6 independent males of each group were then crossed with 7-weeks old C57BL/6J female mice (CD-fed) obtained from Charles River (Charles River Laboratories, France). The male progenies were kept and subjected to the same experimental procedure. At 3-weeks old, they were fed a WD and at 4-5 months crossed with a CD-female. This second generation of males was called WD2. This experimental design was repeated 3 times to obtain the WD5 group

extract_protocol:
Sperm were collected from epididym, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
100ng of total RNA were ligated, reverse transcribed and amplified (19 cycles) with the reagents from the NextFlex small RNAseq kit V3 (Bioo scientific). Amplified libraries were quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent), pooled and size-selected from 140 nt to 170 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were then sequenced on an Illumina Nextseq 500 Mid Flowcell with 75pb reads

value: spermatozoa

tag: age

value: 5-months old mice

tag: genotype

value: wild type

tag: generation number in hfd


title: WD5 rep2

description: small RNA


title: WD5 rep1

description: small RNA


title: GF Male 2 [GM2]


title: CD rep2

description: small RNA

growth_protocol: 3-weeks-old male mice were divided into 2 groups. Males from the first group were kept on CD and the males of the other group were fed a HFD for 3-4 months. This first generation of HFD males was named HFD1. At four months-old, 4 to 6 independent males of each group were then crossed with 7-weeks old C57BL/6J female mice (CD-fed) obtained from Charles River (Charles River Laboratories, France). The male progenies were kept and subjected to the same experimental procedure. At 3-weeks old, they were fed a HFD and at 4-5 months crossed with a CD-female. This second generation of males was called HFD2. This experimental design was repeated 3 times to obtain the HFD5 group


title: GF Female 4 [GF4]


title: WD1 rep3

description: small RNA


title: CD rep3

description: small RNA


title: CD rep1

description: small RNA


title: WD1 rep1

description: small RNA


title: COL Male 4 [CM4]


title: Sin3b_dad2

city: Nantes

first: Alice

last: Mollé

address: 30 bd Jean Monnet

institute: University of Nantes

library_source: genomic

data_processing:
Single-end reads were mapped to the hg19 genome by the BWA algorithm and reads mapping to non-canonical and mitochondrial chromosomes were also removed. For each sample, ChIP-seq peaks were detected using DFilter at a P-value threshold of 1x10-6. A set of consensus peaks was then obtained by taking the union of all peaks and counting reads these peaks using HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks files are generated with Dfilter

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cell

extract_protocol:
Cells were lysed and chromatin was fragmented with Micrococcal nuclease (MNase) and incubuated with 2 mg of anti-H3K27ac (39133, Active Motif) for immunoprecipitation
Libraries were prepared as follows. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were purified by double-sided SPRI size selection . The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were send to a sequencing platform core facility and sequenced on  a Next-seq 500 (Illumina).

value: Healthy

tag: family

value: Sin3B father

value: Peripheral blood mononuclear cell

tag: chip antibody

value: anti-H3K27ac (39133, Active Motif)


title: Sin3b_mom2

value: Sin3B mother


title: Sin3_input


title: Sin3A_mut1

value: SIN3A mutation

value: Sin3A mutant


title: Sin3b_mut1

value: SIN3B mutation

value: Sin3B mutant


title: Sin3A_mom

value: Sin3A mother


title: Sin3b_dad1


title: Sin3b_mut2


title: Sin3b_mom1


title: Sin3A_dad

value: Sin3A father


title: Sin3A_bro1

value: Sin3A brother


title: Sin3A_bro2


title: WD1 rep2

description: small RNA


title: MGHU3_NTZ 24h

city: Shen Zhen

first: Haiyan

last: Sun

state: Guang Dong

address: 47 Youyi Road, Luohu District

country: China

institute: The Third Affiliated Hospital of Shenzhen University (LuoHu Hospital Group)

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM/counts for each Sample

source_name: bladder carcinoma cell line

growth_protocol: MGHU3 cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% PS.

extract_protocol:
Magzol Reagent (Magen, China)
NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB,USA)

treatment_protocol: MGHU3 cells were grown on 100 mm culture dishes and cultured overnight.Then cells were treated with vehicle or Nitazoxanide for 24h before harvested for RNA-seq analysis.

tag: cell line

value: bladder carcinoma cell line

value: Nitazoxanide treatment


title: MGHU3_CTL

value: no treatment


title: Sin3A_mut2


title: TreatedVL_SLA_Patient5

type: RNA

city: Milan

first: Michaela

last: Fakiola

address: Via Francesco Sforza 35

country: Italy

institute: INGM

description: Day 30 stimulated

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were analyzed using lumi, beadarray and limma R packages. Raw data underwent background correction using negative ccontrol probes followed by quantile normalization and log2 transformation. Non-expressed (detection P-value > 0.05 in all arrays) and poor quality probes previously shown to have unreliable annotation were removed. Differential expression analyses were conducted using eBayes functions in limma.

label: biotin

source_name: Whole Blood

label_protocol: Biotinylated cRNA was generated following manufacturer protocols.

extract_protocol: RNA from whole blood samples was extracted using PAXgene Blood RNA kits (QIAGEN GmbH, Germany) according to manufacturer’s instructions. Globin mRNA was depleted using GLOBINclear™-Human kits (ThermoFischer Scientific, USA). RNA integrity and purity were checked using Tape Station 4200 (Agilent Technologies, USA).

treatment_protocol: Whole blood (5 mL) collected by venepuncture from active cases (i.e. pre-treatment; day 0) was stimulated with SLA (10μg /mL) with/without isotype control antibody (10μg /ml IgG2B clone #20116; R&D Systems, New Delhi, India) or anti-IL10 (10μg /mL IgG2B clone #25209; R&D Systems).  Whole blood collected at day 30 post-treatment was unstimulated or stimulated with SLA (10μg /mL) alone. Wells were harvested for RNA extraction following 4 hours of stimulation at 37°C 95% CO2. Stimulated whole blood was collected from culture wells and immediately placed into Paxgene tubes (QIAGEN GmbH, Germany) and stored at -80°C for RNA processing.

value: Treated VL SLA stimulated

tag: gender

value: Female

tag: subject


title: ActiveVL_SLA_Patient5

description: Day 0 stimulated

value: Active VL SLA stimulated


title: ActiveVL_SLA_aIL10_Patient2

description: Day 0 stimulated

value: Active VL SLA plus anti-IL10 antibody stimulated


title: ActiveVL_SLA_ISO_Patient6

description: Day 0 stimulated

value: Active VL SLA plus isotype control antibody stimulated

value: Male


title: ActiveVL_SLA_ISO_Patient2

description: Day 0 stimulated


title: TreatedVL_NIL_Patient5

description: Day 30 unstimulated

value: Treated VL unstimulated


title: TreatedVL_SLA_Patient2

description: Day 30 stimulated


title: ActiveVL_SLA_Patient12

description: Day 0 stimulated


title: ActiveVL_SLA_aIL10_Patient3

description: Day 0 stimulated


title: TreatedVL_SLA_Patient3

description: Day 30 stimulated


title: ActiveVL_SLA_ISO_Patient5

description: Day 0 stimulated


title: ActiveVL_SLA_aIL10_Patient5

description: Day 0 stimulated


title: ActiveVL_NIL_Patient12

description: Day 0 unstimulated

value: Active VL unstimulated


title: ActiveVL_SLA_aIL10_Patient11

description: Day 0 stimulated


title: ActiveVL_SLA_Patient3

description: Day 0 stimulated


title: ActiveVL_NIL_Patient11

description: Day 0 unstimulated


title: ActiveVL_SLA_ISO_Patient11

description: Day 0 stimulated


title: TreatedVL_NIL_Patient2

description: Day 30 unstimulated


title: TreatedVL_NIL_Patient11

description: Day 30 unstimulated


title: ActiveVL_SLA_aIL10_Patient10

description: Day 0 stimulated


title: ActiveVL_NIL_Patient3

description: Day 0 unstimulated


title: TreatedVL_SLA_Patient11

description: Day 30 stimulated


title: ActiveVL_SLA_Patient11

description: Day 0 stimulated


title: ActiveVL_NIL_Patient10

description: Day 0 unstimulated


title: ActiveVL_SLA_aIL10_Patient6

description: Day 0 stimulated


title: ActiveVL_NIL_Patient2

description: Day 0 unstimulated


title: ActiveVL_SLA_Patient10

description: Day 0 stimulated


title: ActiveVL_SLA_Patient6

description: Day 0 stimulated


title: ActiveVL_SLA_ISO_Patient10

description: Day 0 stimulated


title: TreatedVL_NIL_Patient6

description: Day 30 unstimulated


title: DM_2

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: RNA-seq for diabetic Macaca fascicularis RPE

data_processing:
Illumina Casava(v 1.7) software was used for basecalling.
FastQC (v 0.11.8) were used to removed low-quality reads
Retained reads were then aligned to Macaca 16 fascicularis genome (Macaca_fascicularis_5.0) using STAR (v 2.7.3a) in the pair-end  mode with default parameters.
Reads number mapped to each gene was counted using HTSeq (v 0.11.2).
The output matrix from HTSeq was input into the DESeq2 (v 1.26.0) for identification of differentially expressed genes between diabetes group and control group.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

organism: Macaca fascicularis

source_name: Retinal pigment epithelium

extract_protocol:
RPE cells were collected from 3 diabetic and 3 control subjects using an ophthalmic 6 spatula. Total RNA was purified using a TRIzol (Thermo Fisher Scientific) in accordance with the manufacturer’s protocol. The RNA sample quality was confirmed by the Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries were constructed using the TruSeq RNA-Seq kit (Illumina) following the manufacturer’s instructions. After evaluating the quality by Agilent 2100 Bioanalyzer, libraries were pooled and sequenced on Illumina Hiseq X10.

tag: group

value: Diabetes


title: TreatedVL_NIL_Patient4

description: Day 30 unstimulated


title: TreatedVL_SLA_Patient4

description: Day 30 stimulated


title: DM_1


title: DM_3


title: TreatedVL_SLA_Patient10

description: Day 30 stimulated


title: MM1S-T3-P22-WA

city: Wilrijk

first: Emilie

last: Logie

state: Antwerp

address: Universiteitsplein 1

department: Biomedical Sciences

country: Belgium

institute: University of Antwerp

description: MM1.S cell line

data_processing:
Quality of RNA-seq reads was assessed using FastQC (v0.11.5)
Sequenced reads were mapped to hg19 using the STAR alignment tool( v2.7.3a)
Raw gene counts were generated from STAR output. Count normalization was performed with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts and normalized gene counts

source_name: Multiple myeloma cells

growth_protocol: MM1 cells were grown in RPMI-1640 medium supplemented with 10% FBS and 1% P/S

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
Library preparation was outsourced to BGI facilities.

treatment_protocol: MM1 cells were treated with 1µM withaferin a for 3 h

tag: glucocorticoid sensitivity

value: sensitive

value: treated for 3 h with 1uM withaferin A

tag: passage

value: Cell passage number 22


title: CTRL_1

description: RNA-seq for control Macaca fascicularis RPE

value: Control


title: CTRL_2


title: ActiveVL_SLA_aIL10_Patient4

description: Day 0 stimulated


title: MM1R-T3-P4-WA

description: MM1.R cell line

value: resistant

tag: treatment

value: Cell passage number 4


title: ActiveVL_NIL_Patient4

description: Day 0 unstimulated


title: MM1R-T3-P7-WA

description: MM1.R cell line

value: Cell passage number 7


title: TreatedVL_NIL_Patient10

description: Day 30 unstimulated


title: ActiveVL_SLA_ISO_Patient4

description: Day 0 stimulated


title: TreatedVL_SLA_Patient1

description: Day 30 stimulated


title: ActiveVL_SLA_Patient4

description: Day 0 stimulated


title: TreatedVL_NIL_Patient1

description: Day 30 unstimulated


title: MM1S-T3-P23-WA

description: MM1.S cell line

value: Cell passage number 23


title: MM1S-T3-P16-WA

description: MM1.S cell line

value: Cell passage number 16


title: Fetal Brain Ethanol Affected rep 3

city: College Station

first: Michael

last: Golding

state: TX

address: 4466 TAMU

department: VTPP

institute: Texas A&M University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.4.0 with parameters -p 8  --segment-length 20
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks. Assemblies from all samples were merged using cuffmerge. Finally, cuffdiff was used to find differentially expressed genes and transcripts across all treatments.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Fetal Brain

extract_protocol:
Fetal brains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: fetal brain

value: GD 17

value: wild type


title: ActiveVL_NIL_Patient1

description: Day 0 unstimulated


title: MM1R-T3-P4-UT

description: MM1.R cell line

value: untreated


title: MM1R-T3-P6-WA

description: MM1.R cell line

value: Cell passage number 6


title: CTRL_3


title: Fetal Brain Ethanol Affected rep 1


title: MM1S-T3-P22-UT

description: MM1.S cell line


title: MM1R-T3-P7-UT

description: MM1.R cell line


title: Fetal Brain Ethanol Unaffected rep 3


title: ActiveVL_SLA_ISO_Patient1

description: Day 0 stimulated

value: Active VL SLA plus isotype control antibody stimulated

value: Male


title: ActiveVL_SLA_Patient1

description: Day 0 stimulated

value: Active VL SLA stimulated


title: Fetal Brain Ethanol Unaffected rep 1


title: Fetal Brain Ethanol Affected rep 2


title: MM1S-T3-P16-UT

description: MM1.S cell line

value: sensitive


title: MM1R-T3-P6-UT

description: MM1.R cell line


title: Fetal Brain Control rep 2


title: Fetal Brain Ethanol Unaffected rep 2


title: MM1S-T3-P23-UT

description: MM1.S cell line


title: Fetal Brain Control rep 3


title: Fetal Brain Control rep 1


title: OxyR analysis - WT iron replete

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

data_processing:
Base calls were done using CLC Genomic Workbench
Reads were aligned to the genome of Prevotella intermedia 17 using Genomic Workbench
Reads per gene were determined using Genomic Workbench
Statistical analysis was done using Genomic Workbench

organism: Prevotella intermedia

source_name: Bacterial cell

growth_protocol: Samples of wildtype and V3147 oxyR mutant P. intermedia were grown in an overnight culture of BHI media. The overnight cultures served to inoculate cultures of BHI media starting at an OD660 of approximately 0.05. Cultures were grown with and without dipyridyl to mid-log phase, centrifuged, and stored at -20 °C.

extract_protocol:
RNA isolation was carried out using the RNeasy mini-kit (Qiagen) following manufacturers protocol. Residual DNA was removed using the DNA-free DNase kit (Ambion) following manufacturers protocol.
For RNA-seq library generation, the Ovation complete Prokaryotic RNA-Seq DR multiplex kit (Nugen) was used. The library was generated following the manufacturers protocol and fragment sizes from sonication during library generation was confirmed using a bioanalyzer (Agilent Technologies). Libraries were sequenced by VCU nucleic acid sequencing core using Miseq Illumina sequencing.

treatment_protocol: Dipyridyl (Fe Chelator) - 150uM

tag: phase of growth

value: logarithmic phase of growth

tag: dp treatment

value: iron replete


title: ActiveVL_SLA_aIL10_Patient1

description: Day 0 stimulated

tag: disease state

value: Active VL SLA plus anti-IL10 antibody stimulated


title: OxyR analysis - WT iron deplete

value: iron deplete


title: OxyR analysis - mutant iron deplete


title: PD_1

city: Indianapolis

first: Chi

last: Zhang

state: IN

institute: INDIANA UNIVERSITY

data_processing:
RAW sequencing data were processed by Cell Ranger for making fastq file, alignment to mm10 genome, and generation of normalized gene expression matrices.
Seurat is used for the expression normalization with default parameter setting.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized expression value for each gene and cell.

source_name: Tumor

growth_protocol: C57BL/6 mice bearing orthotopic implanted MC38-derived tumors with different drug treatment. Tumors were harvested two weeks after initial treatment (5 tumor samples were pooled per arm).

extract_protocol: Libraries were prepared for sequencing using standard 10X genomics protocols

treatment_protocol: We had 4 different treatment conditions that are vehicle control, ATT-I (50 mg/kg, daily), anti-PD-1 (3 times/week, 5 times in total), or ATT-I + anti-PD-1 combo.

value: PD-1 treatment

tag: tissue

value: MC38-derived tumors


title: ATT-I

value: ATT-I treatment


title: WT

description: control

value: No treatment


title: Ldlr KO BMT scRNA-seq

city: Toronto

first: Corey

middle: A

last: Scipione

state: Ontario

address: 101 College Ave., TMDT 3-307 G,

department: Toronto General Hospital Research Institute

country: Canada

institute: University Health Network

description: intimal cell suspension

data_processing:
For RNA seq; RNA-seq reads were processed using the Tuxedo V2 protocol410. Briefly, reads were trimmed of adapter sequences associated with the Library Prep Kit using TrimGalore!, v0.5.0.  Trimmed reads were aligned to the mm10 genome using HISAT2 (v2.0.5) and transcript counts were determined using Stringtie (v2.0.4).
For single cell RNAseq; Digital gene expression matrices were generated with the Cell Ranger Pipeline v3.1 and aligned to the mm10-2020-A reference transcriptome. The resulting digital gene expression matrix was filtered, normalized, and clustered using R 4.0.2 and Seurat 3.2.145,46, as per MacParland et al.47. Briefly, features that were detected in less than 3 cells and cells with less than 200 features were excluded.   We further filtered out cells with greater than 5000 transcripts or a mitochondrial transcriptome of >25%.  Normalization was performed using LogNormalize feature with a scale factor of 100000.  PCA was performed on the top 2000 variable features that were identified using the “vst” selection method. This resulted in 4298 and 5396 cells for the non-BMT and BMT datasets, respectively.  The non-BMT and BMT datasets were integrated using the Harmony algorithm48 based on the first 15 principal components.  Cells were clustered using the Louvain algorithm based on the first 20 harmony dimensions with a resolution of 0.25. UMAP was used for non-linear reduction and two-dimensional data visualization.
Genome_build: mm10 (RNAseq) and mm10-2020A (scRNAseq)

source_name: WT to Ldlr KO BMT

extract_protocol:
For RNA sequencing the RNeasy micro kit (Cat. No. 74004, Qiagen) as per manufacturers protocol. For single cell sequencing the 10x Genomics Single Cell 3′ v2/v3 Reagent Kit user guide for the non-BMT (Ldlr-/-) and BMT (WT to Ldlr-/-) sample respectively.
For RNA sequencing the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®, using the manufacturer’s direct RNA input protocol (NEB). For single cell sequencing the v2 Chromium™ Single Cell 3ʹ Library Kit and the v3 Chromium™ Single Cell 3ʹ Library Kit was used for the non-BMT (Ldlr-/-) and BMT (WT to Ldlr-/-) sample respectively.

value: Bone marrow transplant

tag: diet

value: Standard Chow


title: OxyR analysis - mutant iron replete


title: Ldlr KO scRNA-seq

description: intimal cell suspension

source_name: Ldlr KO mice


title: Ldlr KO + BMT and 5dCRD 3 RNA-seq

molecule: polyA RNA

value: Cholesterol rich diet (5 days)


title: Combo

description: Combo

value: ATT-I, PD-1 treatment


title: Ldlr KO + BMT and 5dCRD 2 RNA-seq


title: Ldlr KO + 5dCRD 2 RNA-seq


title: Ldlr KO + 5dCRD 1 RNA-seq


title: Ldlr KO + BMT and 5dCRD 1 RNA-seq


title: Ldlr KO + BMT 3 RNA-seq


title: Ldlr KO + BMT 2 RNA-seq


title: Ldlr KO + BMT 1 RNA-seq


title: Muscle_4WP_Inter1_GS58_Rep1

type: genomic

city: Footscray

first: Sarah

middle: Amandine Caroline

last: Voisin

state: VIC

address: Ballarat Road

department: Institute for Health and Sport

country: Australia

institute: Victoria University

hyb_protocol: The amplification products were then fragmented, precipitated, resuspended, and then hybridised onto the BeadChips.

scan_protocol: The chips were washed and then stained prior to application on an HMEPIC array according to the manufacturer’s protocol. The HMEPIC arrays were then visualised and analysed using the Illumina HiScan instrument and GeneStudio software (Illumina).

data_processing:
Any sample with > 10% of probes with detection p-value > 0.01 was removed (default parameter of the champ.load function). All probes with missing β-values, with a detection p-value > 0.01, probes with a bead count < 3 in at least 5% of samples, non-CG probes and probes aligning to multiple locations in Pidsley et al. 2016 were removed, and probes located on the sex chromosomes were removed. SNP-related probes (“EUR” population probes in Zhou et al. 28) were also removed. β-values were obtained, and defined as  β-value =(intensity of the Methylated allele)/(intensity of the Unmethylated allele + intensity of the Methylated allele + 100)   Then, β-mixture quantile normalization (BMIQ) method was applied to adjust for the Type I and Type II probe designs for methylation profiles generated from the HM450 and HMEPIC arrays. To identify technical and biological sources of variation in each individual dataset, Singular Value Decomposition (SVD) was performed. In all pre-processed datasets, both the plate and the position on the plate were identified as significant technical effects. Thus, all β-values were converted to M-values and the ComBat function from the sva package used to adjust directly for these technical artefacts.
The Matrix signal intensities.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS58, Rep1

label_protocol: For bisulphite conversion of gDNA for subsequent methylation arrays, 500 ng total gDNA was bisulfite converted using the EZ DNA methylation kit (ZYMO research) as per the manufacturer’s instructions. Bisulfite converted DNA (bDNA) was then used for the methylation array protocol. riefly, bDNA was used for amplification of the regions of interest for binding to the Infinium BeadChip arrays.

extract_protocol: Total gDNA was extracted from 15 mg muscle tissue using the Allprep DNA/RNA/miRNA universal kit (Qiagen). The manufacturer’s protocol was modified to include the use of a Bullet Blender Gold Homogeniser (NextAdvance) in combination with dry ice for complete tissue digestion to ensure no enzymatic digestion of the DNA. Following isolation, DNA quantity and quality was measured using the dsDNA Broad Range Qubit kit (ThermoFisher scientific) on a Qubit Flourometer V2.0.

tag: subject id

tag: age

tag: Sex

value: M

tag: treatment/timepoint

value: Vastus lateralis


title: Muscle_PRE_Inter1_GS45_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS45, Rep1

value: F

value: at baseline during first intervention


title: Muscle_PRE_Inter1_GS43_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS43, Rep1


title: Muscle_8WP_Inter2_GS65_Rep1

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS65, Rep1


title: Muscle_4WP_Inter1_GS63_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS63, Rep1


title: Muscle_4WP_Inter1_GS37_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS37, Rep1


title: Ldlr KO 2 RNA-seq


title: Muscle_PRE_Inter1_GS55_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS55, Rep1


title: Muscle_4WP_Inter1_GS62_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS62, Rep1


title: Muscle_4WP_Inter2_GS57_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS57, Rep1


title: Ldlr KO 3 RNA-seq


title: Muscle_8WP_Inter2_GS61_Rep1

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS61, Rep1


title: Muscle_CON_Inter2_GS8_Rep1

description: Same individual as in GSM4577420, GSM4577441, GSM4577486

source_name: Vastus lateralis, at start of control period during second intervention, from individual GS8, Rep1


title: Ldlr KO 1 RNA-seq


title: Muscle_4WP_Inter1_GS34_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS34, Rep1


title: Muscle_4WP_Inter2_GS13_Rep1

description: Same individual as in GSM4577425, GSM4577434, GSM4577466

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS13, Rep1


title: Muscle_CON_Inter1_GS66_Rep1

source_name: Vastus lateralis, at start of control period during first intervention, from individual GS66, Rep1


title: Muscle_PRE_Inter2_GS9_Rep1

description: Same individual as in GSM4577422, GSM4577443, GSM4577464

source_name: Vastus lateralis, at baseline during second intervention, from individual GS9, Rep1

value: at baseline during second intervention


title: Muscle_PRE_Inter1_GS63_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS63, Rep1


title: TRT_Treated_Tumor_2

city: Orsay

first: Lionel

last: Larue

address: Centre universitaire Bat 101B-110-111-112 Rue Henri Becquerel CS 90030

department: CNRS UMR3347, INSERM  U1021

institute: Institut Curie

data_processing:
quality of the read was assessed using fastqc
the aligment was made on reference sequence (gencode m13 version - GRCm38.p5) using STAR algorithm
reads orientation was given using rseqc
Counts tables were generated through STAR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Read count values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Mouse Derived Isograft

growth_protocol: C57BL/6J mice were susbcutaneously injected by 1.10e5 1007 NRAS mouse melanoma cells in the right flank. 10 days after a single dose of treatment at Day 36, tumor were harvested.

extract_protocol:
total RNA was extracted using the miRneasy, Qiagen extraction kit according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina Truseq Stranded protocol using 1µg of total RNA. A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. RNA were fragmented and then cDNA were synthetized and ligated to TruSeq indexed adapters. Samples were amplified by PCR (12 cycles) to generate the final barecoded library.

treatment_protocol:
Mock treated mice were injected once with 100µL of saline, 36 days after cell-injection.
TRT treated mice were injected once with 18.5 MBq of [131I]ICF01012 in 100µL of saline, 36 days after cell-injection.

tag: cell type

value: 1007 NRAS murine melanoma cell line

tag: genotype

value: Tyr::NRAS; Cdkn2a-/-

tag: host strain


title: Muscle_PRE_Inter1_GS62_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS62, Rep1


title: Muscle_CON_Inter2_GS3_Rep1

description: Same individual as in GSM4577417, GSM4577442, GSM4577459, GSM4577480

source_name: Vastus lateralis, at start of control period during second intervention, from individual GS3, Rep1


title: Muscle_4WP_Inter1_GS50_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS50, Rep1


title: TRT_Treated_Tumor_1

tag: group


title: Muscle_CON_Inter1_GS42_Rep1

source_name: Vastus lateralis, at start of control period during first intervention, from individual GS42, Rep1


title: MOCK_Tumor_6

value: Saline


title: Muscle_4WP_Inter1_GS59_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS59, Rep1


title: Muscle_8WP_Inter2_GS11_Rep1

description: Same individual as in GSM4577423, GSM4577458, GSM4577483

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS11, Rep1


title: TRT_Treated_Tumor_3


title: MOCK_Tumor_5


title: MOCK_Tumor_2


title: Muscle_4WP_Inter2_GS11_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS11, Rep1


title: MOCK_Tumor_1


title: Muscle_4WP_Inter2_GS17_Rep1

description: Same individual as in GSM4577429, GSM4577454, GSM4577468

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS17, Rep1


title: Muscle_4WP_Inter1_GS31_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS31, Rep1


title: MB_RXB_15_Chronic Ethanol Diet with IMC Treatment

city: Cleveland

first: Chase

last: Neumann

state: OH

address: 99089 Carnegie Ave

institute: CCF

data_processing:
Trim Galore
FastQC
Star aligner
EdgeR differential expression
Genome_build: Mus Musculus Mm10
Supplementary_files_format_and_content: Norm_Counts_Ethanol_IMC.csv, normalized counts with MGI symbols and Entrez ID

source_name: Liver Tissue

extract_protocol:
Qiagen Rneasy Lipid Columns
Illumina TruSeq Directional Library Kit; Paired end 100bp

treatment_protocol: Vehicle vs. IMC

value: liver

value: Iodomethylcholine (IMC)

value: Chronic Ethanol Diet


title: Muscle_12WP_Inter2_GS13_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS13, Rep1


title: MOCK_Tumor_3


title: MB_RXB_11_Chronic Ethanol Diet with IMC Treatment


title: MOCK_Tumor_4


title: MB_RXB_09_Chronic Ethanol Diet with IMC Treatment


title: MB_RXB_07_Chronic Ethanol Diet with Vehicle Treatment

value: Vehicle


title: Muscle_12WP_Inter2_GS22_Rep1

description: Same individual as in GSM4577432, GSM4577448, GSM4577492

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS22, Rep1


title: Muscle_PRE_Inter1_GS29_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS29, Rep1


title: MB_RXB_05_Chronic Ethanol Diet with Vehicle Treatment


title: MB_RXB_13_Chronic Ethanol Diet with IMC Treatment


title: MB_RXB_03_Chronic Ethanol Diet with Vehicle Treatment


title: Muscle_PRE_Inter1_GS59_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS59, Rep1


title: MB_RXB_01_Chronic Ethanol Diet with Vehicle Treatment


title: MB_RXB_04_Pair Diet with IMC Treatment

value: Pair diet


title: MB_RXB_08_Pair Diet with IMC Treatment


title: MB_RXB_02_Pair Diet with IMC Treatment


title: MB_RXB_16_Pair Diet with Vehicle Treatment


title: MB_RXB_06_Pair Diet with IMC Treatment


title: MB_RXB_14_Pair Diet with Vehicle Treatment


title: MB_RXB_10_Pair Diet with Vehicle Treatment


title: srsf1-achko_cre_rep-3

city: Urbana

first: Waqar

last: Arif

state: IL

address: 506 S. Mathews Avenue

department: Biochemistry

institute: UIUC

description:
cre3_AACGTTCC-GGAGTACT_L001
cre injrected srsf1 acute hko replicate 3
processed data file:
srsf1_acute_hko_deseq2_output.csv
transcript_tpm_kallisto_table.csv

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Sequenced reads were trimmed for adaptor sequence and transcript abundances were computed using kallisto v0.46.0
kallisto index was generated using Gencode annotation, GRCm38_vM19
Differential gene expression analysis was performed with the kallisto abundance tables using tximport and DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Table of TPM values of annotated transcripts and DESeq2 output of differential gene expression

source_name: cre injrected srsf1 acute hko_hepatocytes

growth_protocol: Organisms were housed in flow cages, following the standard 12 hour light/dark cycle

extract_protocol:
Purified hepatocytes were flash frozen in liquid nitrogen, and RNA was harvested using Qiagen RNAeasy Kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for “TruSeq Stranded mRNAseq Sample Prep kit”

treatment_protocol: Acute knock-out model was achieved by injection of AAV8 viral vectors expressing iCRE (SRSF1 acHKO) or GFP (Controls)  into SRSF1 f/f mice at 8 weeks of age. Viral vector gene expression was driven by TBG promoter, allowing for hepatocyte-specific expression.

tag: strain background

value: 10 week

value: aav-tbg-icre

value: hepatocytes


title: Muscle_8WP_Inter2_GS56_Rep1

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS56, Rep1


title: MB_RXB_12_Pair Diet with Vehicle Treatment


title: Muscle_12WP_Inter2_GS17_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS17, Rep1


title: srsf1-achko_cre_rep-2

description:
cre2_ATGTAAGT-ACTCTATG_L001
cre injrected srsf1 acute hko replicate 2
processed data file:
srsf1_acute_hko_deseq2_output.csv
transcript_tpm_kallisto_table.csv


title: srsf1-achko_cre_rep-1

description:
cre1_CGGCGTGA-GCGCCTGT_L001
cre injrected srsf1 acute hko replicate 1
processed data file:
srsf1_acute_hko_deseq2_output.csv
transcript_tpm_kallisto_table.csv


title: Muscle_PRE_Inter2_GS11_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS11, Rep1


title: Muscle_PRE_Inter1_GS44_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS44, Rep1


title: ctrl_gfp_rep-3

description:
gfp3_GCAGAATT-ACCGGCCA_L001
gfp injected control replicate 3
processed data file:
srsf1_acute_hko_deseq2_output.csv
transcript_tpm_kallisto_table.csv

source_name: gfp injected control_hepatocytes

value: aav-tbg-gfp


title: Muscle_4WP_Inter1_GS33_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS33, Rep1


title: Muscle_4WP_Inter1_GS64_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS64, Rep1

value: M


title: Muscle_PRE_Inter1_GS42_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS42, Rep1

value: Vastus lateralis


title: Muscle_CON_Inter1_GS43_Rep1

source_name: Vastus lateralis, at start of control period during first intervention, from individual GS43, Rep1

value: F


title: ctrl_gfp_rep-1

description:
gfp1_GCACGGAC-GTCTCGCA_L001
gfp injected control replicate 1
processed data file:
srsf1_acute_hko_deseq2_output.csv
transcript_tpm_kallisto_table.csv


title: Muscle_PRE_Inter1_GS50_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS50, Rep1

value: at baseline during first intervention


title: Muscle_4WP_Inter1_GS52_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS52, Rep1


title: Muscle_4WP_Inter2_GS22_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS22, Rep1


title: Muscle_4WP_Inter1_GS66_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS66, Rep1


title: Muscle_4WP_Inter2_GS3_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS3, Rep1


title: Muscle_4WP_Inter1_GS49_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS49, Rep1


title: Holstein Friesian R microplus adult feeding replicate 3

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

description: Biological replicate 3 of 3. Holstein Friesian lymph node tissue. Rhipicephalus microplus adult tick attachment.

hyb_protocol: Equivalent picomoles (20 pmol) of Cy3-labelled cDNA from the common reference pool were hybridised with Cy5-labelled individual test cDNA. Overnight hybridisation at 65°C (rotation speed of 10), washing and post-processing were performed at the ACGT Microarray Facility (University of Pretoria, South Africa). Prior to slide scanning with the Axon GenePix 4000B scanner (Molecular Devices), slides were washed and dried by centrifugation

scan_protocol: Scanned on an Axon GenePix 4000B scanner (Molecular Devices) Images were measured, recorded, analysed and spots were inspected using Axon GenePix Pro 6.0 software (Molecular Devices)

data_processing: Axon GenePix Pro 6.0 software (Molecular Devices) and the linear model for microarray data analysis (LIMMA) within the R statistical environment (http://cran.r-project.org/) was employed. Adaptive background correction (offset = 50) was followed by within-array normalisation (Robust Spline) and between-array normalisation (G quantile). Fold change was determined between all transcripts within a cattle breed collected at different time-points using the empirical Bayesian statistics, which were subsequently expressed as P- values (corrected for false discovery rate).

organism: Bos taurus

source_name: Holstein Friesian superficial cervical lymph node, R microplus adult feeding

label_protocol:
First-strand cDNA synthesis was performed by incubating 4 µg RNA (from each biological replicate and the reference pool) with 250 pmol oligo(dT25) and 775 pmol random primer 9 for 10 minutes at 70˚C, followed by cooling on ice for 10 minutes. Reverse transcription and aminoallyl-dUTP (5-(3-aminoallyl)-2’deoxyuridine-5’ triphosphate) incorporation were performed simultaneously using 340 units SuperScript® III reverse transcriptase (Invitrogen™ life technologies, USA).
cDNA samples were coupled to 75 picomol Cy3 (reference pool) and Cy5 (samples) fluorescent dyes (GE Healthcare Life Sciences)at pH 9 dissolved in DMSO. Unincorporated dye was then removed.

extract_protocol: Total RNA was isolated using TRI-reagent fractionation (Sigma-Aldrich) and the RNeasy mini kit (QIAGEN, Germany) following the manufacturer’s instructions. Contaminating genomic DNA was removed with a DNase I treatment (QIAGEN, Germany).

treatment_protocol: Lymph node biopsies were collected, kept on ice and transferred to an RNA stabilizing solution (0.5 M EDTA, 1 M ammonium citrate, 5.3 M ammonium sulphate, adjusted to pH 5.2 with H2SO4).

value: Lymph node

tag: breed

value: Holstein

tag: sample type

source_name: Pooled cattle superficial cervical lymph nodes


title: Muscle_12WP_Inter2_GS3_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS3, Rep1


title: Muscle_4WP_Inter2_GS9_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS9, Rep1


title: Muscle_8WP_Inter2_GS66_Rep1

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS66, Rep1


title: Muscle_PRE_Inter1_GS46_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS46, Rep1


title: Muscle_4WP_Inter1_GS28_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS28, Rep1


title: Muscle_4WP_Inter2_GS18_Rep1

description: Same individual as in GSM4577438, GSM4577439, GSM4577460, GSM4577488

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS18, Rep1


title: Muscle_PRE_Inter2_GS3_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS3, Rep1

value: at baseline during second intervention


title: Muscle_4WP_Inter1_GS36_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS36, Rep1


title: Holstein Friesian R microplus adult feeding replicate 1

description: Biological replicate 1 of 3. Holstein Friesian lymph node tissue. Rhipicephalus microplus adult tick attachment.


title: Muscle_4WP_Inter1_GS51_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS51, Rep1


title: Muscle_PRE_Inter1_GS26_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS26, Rep1


title: Holstein Friesian R microplus adult feeding replicate 2

description: Biological replicate 2 of 3. Holstein Friesian lymph node tissue. Rhipicephalus microplus larvae adult attachment.

value: Rhipicephalus microplus adult tick attachment


title: Muscle_PRE_Inter2_GS13_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS13, Rep1


title: Muscle_4WP_Inter2_GS65_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS65, Rep1


title: Muscle_PRE_Inter1_GS66_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS66, Rep1


title: Holstein Friesian R microplus larval feeding replicate 3

description: Biological replicate 3 of 3. Holstein Friesian lymph node tissue. Rhipicephalus microplus larvae tick attachment.

source_name: Holstein Friesian superficial cervical lymph node, R microplus larval feeding


title: Muscle_8WP_Inter2_GS6_Rep1

description: Same individual as in GSM4577424, GSM4577446, GSM4577465

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS6, Rep1


title: Holstein Friesian R microplus larval feeding replicate 2

description: Biological replicate 2 of 3. Holstein Friesian lymph node tissue. Rhipicephalus microplus larvae tick attachment.


title: Holstein Friesian baseline replicate 2

description: Biological replicate 2 of 3. Holstein Friesian lymph node tissue. Baseline. No tick attachment.

source_name: Holstein Friesian superficial cervical lymph node, baseline

value: Baseline No tick attachment


title: Holstein Friesian baseline replicate 3

description: Biological replicate 3 of 3. Holstein Friesian lymph node tissue. Baseline. No tick attachment.

source_name: Pooled cattle superficial cervical lymph nodes


title: Holstein Friesian baseline replicate 1

description: Biological replicate 1 of 3. Holstein Friesian lymph node tissue. Baseline. No tick attachment.


title: Muscle_PRE_Inter1_GS40_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS40, Rep1


title: ctrl_gfp_rep-2

description:
gfp2_GGTACCTT-AAGACGTC_L001
gfp injected control replicate 2
processed data file:
srsf1_acute_hko_deseq2_output.csv
transcript_tpm_kallisto_table.csv

source_name: gfp injected control_hepatocytes

tag: treatment


title: Brahman R microplus adult feeding replicate 1

description: Biological replicate 1 of 3. Brahman lymph node tissue. Rhipicephalus microplus adult tick attachment.

source_name: Brahman superficial cervical lymph node, R microplus adult feeding

value: Brahman


title: Muscle_CON_Inter2_GS11_Rep1

description: Same individual as in GSM4577423, GSM4577458, GSM4577483

source_name: Vastus lateralis, at start of control period during second intervention, from individual GS11, Rep1


title: Brahman R microplus adult feeding replicate 3

description: Biological replicate 3 of 3. Brahman lymph node tissue. Rhipicephalus microplus adult tick attachment.


title: Brahman R microplus larval feeding replicate 3

description: Biological replicate 3 of 3. Brahman lymph node tissue. Rhipicephalus microplus larvae tick attachment.

source_name: Brahman superficial cervical lymph node, R microplus larval feeding


title: Brahman R microplus adult feeding replicate 2

description: Biological replicate 2 of 3. Brahman lymph node tissue. Rhipicephalus microplus larvae adult attachment.


title: Muscle_4WP_Inter1_GS48_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS48, Rep1


title: Brahman R microplus larval feeding replicate 2

description: Biological replicate 2 of 3. Brahman lymph node tissue. Rhipicephalus microplus larvae tick attachment.


title: Muscle_PRE_Inter2_GS17_Rep1

description: Same individual as in GSM4577429, GSM4577454, GSM4577468

source_name: Vastus lateralis, at baseline during second intervention, from individual GS17, Rep1


title: Brahman R microplus larval feeding replicate 1

description: Biological replicate 1 of 3. Brahman lymph node tissue. Rhipicephalus microplus larvae tick attachment.


title: Brahman baseline replicate 3

description: Biological replicate 3 of 3. Brahman lymph node tissue. Baseline. No tick attachment.

source_name: Brahman superficial cervical lymph node, baseline


title: Brahman baseline replicate 1

description: Biological replicate 1 of 3. Brahman lymph node tissue. Baseline. No tick attachment.


title: Holstein Friesian R microplus larval feeding replicate 1

description: Biological replicate 1 of 3. Holstein Friesian lymph node tissue. Rhipicephalus microplus larvae tick attachment.


title: Brahman baseline replicate 2

description: Biological replicate 2 of 3. Brahman lymph node tissue. Baseline. No tick attachment.


title: Bonsmara R microplus adult feeding replicate 2

description: Biological replicate 2 of 3. Bonsmara lymph node tissue. Rhipicephalus microplus larvae adult attachment.

source_name: Bonsmara superficial cervical lymph node, R microplus adult feeding

value: Bonsmara


title: Muscle_12WP_Inter2_GS9_Rep1

description: Same individual as in GSM4577422, GSM4577443, GSM4577464

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS9, Rep1


title: Bonsmara R microplus adult feeding replicate 1

description: Biological replicate 1 of 3. Bonsmara lymph node tissue. Rhipicephalus microplus adult tick attachment.


title: Bonsmara R microplus adult feeding replicate 3

description: Biological replicate 3 of 3. Bonsmara lymph node tissue. Rhipicephalus microplus adult tick attachment.


title: Bonsmara R microplus larval feeding replicate 3

description: Biological replicate 3 of 3. Bonsmara lymph node tissue. Rhipicephalus microplus larvae tick attachment.

source_name: Bonsmara superficial cervical lymph node, R microplus larval feeding


title: Muscle_12WP_Inter2_GS18_Rep1

description: Same individual as in GSM4577438, GSM4577439, GSM4577460, GSM4577488

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS18, Rep1


title: Muscle_PRE_Inter1_GS52_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS52, Rep1


title: Bonsmara R microplus larval feeding replicate 2

description: Biological replicate 2 of 3. Bonsmara lymph node tissue. Rhipicephalus microplus larvae tick attachment.


title: Bonsmara R microplus larval feeding replicate 1

description: Biological replicate 1 of 3. Bonsmara lymph node tissue. Rhipicephalus microplus larvae tick attachment.


title: Muscle_8WP_Inter2_GS52_Rep1

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS52, Rep1


title: Bonsmara baseline replicate 2

description: Biological replicate 2 of 3. Bonsmara lymph node tissue. Baseline. No tick attachment.

source_name: Bonsmara superficial cervical lymph node, baseline


title: Muscle_4WP_Inter1_GS27_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS27, Rep1


title: Muscle_4WP_Inter1_GS35_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS35, Rep1


title: Muscle_CON_Inter1_GS29_Rep1

source_name: Vastus lateralis, at start of control period during first intervention, from individual GS29, Rep1


title: Muscle_PRE_Inter2_GS65_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS65, Rep1


title: Muscle_12WP_Inter2_GS51_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS51, Rep1


title: Bonsmara baseline replicate 3

description: Biological replicate 3 of 3. Bonsmara lymph node tissue. Baseline. No tick attachment.

source_name: Pooled cattle superficial cervical lymph nodes


title: Muscle_4WP_Inter1_GS61_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS61, Rep1


title: Muscle_PRE_Inter1_GS41_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS41, Rep1


title: Bonsmara baseline replicate 1

description: Biological replicate 1 of 3. Bonsmara lymph node tissue. Baseline. No tick attachment.


title: Muscle_PRE_Inter1_GS51_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS51, Rep1


title: Muscle_PRE_Inter2_GS18_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS18, Rep1


title: Muscle_PRE_Inter1_GS32_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS32, Rep1


title: Muscle_CON_Inter2_GS17_Rep1

description: Same individual as in GSM4577429, GSM4577454, GSM4577468

source_name: Vastus lateralis, at start of control period during second intervention, from individual GS17, Rep1


title: Muscle_PRE_Inter1_GS61_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS61, Rep1


title: Muscle_PRE_Inter1_GS64_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS64, Rep1


title: GO3

city: Chennai

first: Sailaja

middle: V

last: Elchuri

state: Tamil Nadu

address: No18, College Road, Nungambakkam

department: Nanobiotechnology

country: India

institute: Vision Research Foundation

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip PrimeView. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console™ Software 1.3.1  using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Graphene Oxide Biological replicate 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were Trypsinized and collected after Treatments, washed thrice with 1X PBS.

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

tag: cell line

value: Breast Cancer cell line


title: Muscle_4WP_Inter1_GS26_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS26, Rep1


title: GN1

source_name: Graphene Nitrite Biological replicate 1


title: Muscle_PRE_Inter1_GS31_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS31, Rep1


title: GN2

source_name: Graphene Nitrite Biological replicate 2


title: GO2

source_name: Graphene Oxide Biological replicate 2


title: GN3

source_name: Graphene Nitrite Biological replicate 3


title: Muscle_12WP_Inter2_GS65_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS65, Rep1


title: GO1

source_name: Graphene Oxide Biological replicate 1


title: Muscle_CON_Inter2_GS18_Rep1

source_name: Vastus lateralis, at start of control period during second intervention, from individual GS18, Rep1


title: HOMC-B1

city: Aichi

first: Maho

last: Okuda

address: 1-1 Kanokoden, Chikusa-ku, Nagoya

department: Division of Cancer Biology

country: Japan

institute: Aichi Cancer Center Research Institute

description: Gene expression

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60 °C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray (G4851B) for 17 hours at 65 ˚C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ˚C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).

growth_protocol: They were maintained in RPMI1640 medium (Wako), supplemented with 10% fetal bovine serum (Gibco), penicillin (100 U/ml) and streptomycin (100 U/ml), at 37 °C in 5% CO2 and 95% air.

extract_protocol: RNA was prepared using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).

value: human omental mesothelial cell lines (HOMCs)


title: vagalton#84_Tri_T3_T4

city: Lebanon

first: Valerie

middle: Anne

last: Galton

state: New Hampshire

address: 1 Medical Center Drive

department: Physiology and Neurobiology

institute: Dartmouth Geisel School of Medicine

data_processing:
Illumina bcl2fastq used for basecalling
Sequences were trimmed of adaptor sequences, bases <Q15, and length >50bp using Trimmomatic
Reads passing QC were mapped to the human genome (GRCh38, version 38, Ensembl 78)  using bwa 0.7.10
A counts matrix was made using DESeq's summarizedExperiment
Genome_build: GRCh38 version 38 Ensembl 78
Supplementary_files_format_and_content: raw counts at the gene level for each sample

extract_protocol:
Liver samples were frozen on dry ice and total RNA was extracted using TRIzol solution from Invitrogen according to the manufacturer's instructions
Library synthesis for RNA-Seq was performed with 1 ug of high quality RNA [RIN 7.5 or higher] using the Illumina TruSeq mRNA Stranded library synthesis as described by the manufacturer

treatment_protocol: Mice were injected every other day with thyroid hormones or vehicle starting at postnatal day 2 until sacrifice

value: Postnatal day 14

value: Liver


title: Muscle_8WP_Inter2_GS2_Rep1

description: Same individual as in GSM4577415, GSM4577435, GSM4577476

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS2, Rep1


title: vagalton#85_Tri_T3_T4

description: vagalton_T4_20141104_85_Tri_T3_T4_FEMALE


title: HOMC-A4

description: Gene expression


title: Muscle_PRE_Inter1_GS58_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS58, Rep1


title: Muscle_4WP_Inter1_GS43_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS43, Rep1


title: C1

source_name: Control Biological replicate 3


title: vagalton#79_Tri_T3_T4

description: vagalton_T4_20141104_79_Tri_T3_T4_FEMALE


title: vagalton#80_Tri_T3_T4


title: MeT-5A

description: Gene expression

value: human normal pleura transformant


title: vagalton#77_Tri_T3_T4


title: vagalton#72_Tri_T3_T4


title: Muscle_PRE_Inter2_GS52_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS52, Rep1


title: vagalton#68_Tri_T3


title: Muscle_PRE_Inter1_GS38_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS38, Rep1


title: Muscle_PRE_Inter1_GS39_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS39, Rep1


title: vagalton#65_Tri_T3


title: vagalton#64_Tri_T3


title: Muscle_4WP_Inter1_GS65_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS65, Rep1


title: vagalton#61_Tri_T3


title: vagalton#62_Tri_T3


title: vagalton#60_Tri_T3


title: Muscle_PRE_Inter1_GS37_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS37, Rep1


title: Muscle_4WP_Inter1_GS44_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS44, Rep1


title: vagalton#70_Tri_T4


title: Muscle_8WP_Inter2_GS16_Rep1

description: Same individual as in GSM4577457, GSM4577469, GSM4577485

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS16, Rep1


title: Muscle_PRE_Inter2_GS56_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS56, Rep1


title: Muscle_4WP_Inter1_GS56_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS56, Rep1


title: HOMC-D4

description: Gene expression


title: Muscle_4WP_Inter1_GS29_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS29, Rep1


title: vagalton#69_Tri_T4


title: PBMC untreated donor D

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

institute: Hudson Institute of Medical Research

description: UT.D

data_processing:
RNA-seq analysis was performed in R (v3.6.1) using Bioconductor packages.
Read alignment was performed using the RSubread package (v2.0.0) with default settings and an index built from the Ensembl Homo sapiens GRCh38 primary assembly genome FASTA file.
Reverse-stranded gene counts were generated using the featureCounts function with the inbuilt hg38 human annotation.
Raw counts were processed using the edgeR package (v3.28.0). Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method.
Differential gene expression analyses were performed using the limma package (v3.42.0), with the voom, lmFit, eBayes and treat functions.
Genome_build: hg38
Supplementary_files_format_and_content: comma-delimited text file including raw counts for each sample

source_name: Peripheral blood mononuclear cells

growth_protocol: PBMC were isolated using SepMate tubes (Stemcell Technologies) and Histopaque density medium (Sigma-Aldrich). Cells were cultured at 1 million cells/mL in RPMI (Gibco) with 10% autologous serum.

extract_protocol:
mRNA was extracted using the PureLink RNA Mini Kit (Invitrogen) and RNA concentration quantified by Qubit (Invitrogen) and quality assessed by Bioanalyzer (Agilent).
PolyA RNA libraries were generated according to the Illumina TruSeq Stranded mRNA protocol using 400 ng total RNA. Libraries were pooled and sequenced by Illumina NextSeq500 sequencer in high output mode with v2.5 chemistry, using 75 base-pair single-end reads. PhiX spike-in was included at 1% for quality control.

treatment_protocol: Cells were treated with 1000 IU/mL recombinant human interferon alpha 2a (IFN) (Sigma-Aldrich). One hour later, 0.1 µM dexamethasone (Dex) (Sigma-Aldrich) was added and cells were cultured for 2 hours.

tag: individual

value: donor D

value: Peripheral blood mononuclear cells

value: UT

value: Female


title: vagalton#58_Tri_T4


title: Muscle_12WP_Inter2_GS52_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS52, Rep1

value: M

value: Vastus lateralis


title: PBMC untreated donor C

description: UT.C

value: donor C


title: vagalton#78_Tri_T3_T4

description: vagalton_T4_20141104_78_Tri_T3_T4_FEMALE


title: vagalton#54_Tri_T4


title: PBMC untreated donor B

description: UT.B

value: donor B

value: Male


title: Muscle_4WP_Inter2_GS51_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS51, Rep1


title: Muscle_12WP_Inter2_GS56_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS56, Rep1


title: vagalton#43_Tri_T4


title: Muscle_4WP_Inter1_GS53_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS53, Rep1


title: vagalton#46_Tri_T4


title: PBMC IFN donor C

description: IFN.C

value: IFN


title: Muscle_CON_Inter2_GS65_Rep1

source_name: Vastus lateralis, at start of control period during second intervention, from individual GS65, Rep1


title: vagalton#67_Tri

value: Vehicle


title: PBMC IFN donor B

description: IFN.B


title: Muscle_PRE_Inter2_GS8_Rep1

description: Same individual as in GSM4577420, GSM4577441, GSM4577486

source_name: Vastus lateralis, at baseline during second intervention, from individual GS8, Rep1

value: at baseline during second intervention


title: vagalton#40_Tri_T4


title: vagalton#71_Tri_T4


title: PBMC untreated donor A

description: UT.A

value: donor A


title: PBMC IFN donor D

description: IFN.D


title: vagalton#55_Tri


title: Muscle_4WP_Inter2_GS8_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS8, Rep1


title: PBMC IFN donor A

description: IFN.A


title: Muscle_4WP_Inter1_GS30_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS30, Rep1

value: F


title: vagalton#38_Tri

value: Postnatal day 14


title: Muscle_PRE_Inter2_GS51_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS51, Rep1


title: Muscle_4WP_Inter1_GS32_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS32, Rep1


title: PBMC Dex + IFN donor D

description: Dex.IFN.D


title: Muscle_8WP_Inter2_GS57_Rep1

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS57, Rep1


title: vagalton#37_Tri

value: Liver


title: Muscle_4WP_Inter1_GS46_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS46, Rep1


title: PBMC Dex + IFN donor C

description: Dex.IFN.C


title: Muscle_PRE_Inter1_GS47_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS47, Rep1

value: at baseline during first intervention


title: Muscle_PRE_Inter2_GS6_Rep1

description: Same individual as in GSM4577424, GSM4577446, GSM4577465

source_name: Vastus lateralis, at baseline during second intervention, from individual GS6, Rep1


title: PBMC Dex + IFN donor B

description: Dex.IFN.B


title: PBMC Dex + IFN donor A

description: Dex.IFN.A


title: vagalton#50_Cont


title: vagalton#59_Cont


title: PBMC Dex donor D

description: Dex.D

value: donor D

value: Dex


title: vagalton_#49_Cont


title: PBMC Dex donor C

description: Dex.C

value: Peripheral blood mononuclear cells


title: PBMC Dex donor B

description: Dex.B


title: vagalton#2019_Tri


title: Muscle_4WP_Inter1_GS42_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS42, Rep1


title: vagalton#47_Cont


title: PBMC Dex donor A

description: Dex.A

value: Female


title: vagalton#42_Cont


title: Muscle_PRE_Inter2_GS57_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS57, Rep1

value: M


title: Patient2 biological replicate 3

city: London

first: Manju

last: Kurian

address: Great Ormond Street Institute of Child Health, 30 Guilford Street

department: Developmental Neurosciences

country: United Kingdom

institute: University College of London

description:
processed data file: Raw_gene_counts_matrix.tab
processed data file: Normcounts_matrix_edgeR.tab

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, then mapped to GRCh38 whole genome using HISAT2 (v.2.1.0).
Fragments counts for genes were extracted with featureCounts (v.1.6.4) excluding duplicates, multimapping reads and chimeric fragments.
Differential gene expression was analysed using edgeR (v.3.24.1), filtering low counts with 0.35 minimum CPM in at least 3 samples.
Differential gene expression was performed comparing disease status (patients vs. control) and disease-specific genotype (patient 2 vs. patient 1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.tab: Tab-delimited text file with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Normcounts_matrix_edgeR.tab: Tab-delimited text file with normalized abundance measurements for every gene and every sample (output from edgeR).

source_name: midbrain dopaminergic neurons

growth_protocol: iPSC-derived midbrain dopaminergic neurons were produced following the protocol in Lehnen et al., Stem Cell Reports (2017).

extract_protocol:
Total RNA was isolated from midbrain dopaminergic neurons using the RNeasy mini kit (Qiagen) and RNA libraries were prepared from 100 ng of total RNA using KAPA mRNA HyperPrep kit (Roche).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: iPSCs-derived midbrain dopaminergic neurons

tag: genotype/variation

value: DDC compound heterozygous variants c.19C>T, c.299G>C

tag: diagnosis

value: AADC deficiency


title: Muscle_8WP_Inter2_GS22_Rep1

description: Same individual as in GSM4577432, GSM4577448, GSM4577492

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS22, Rep1

tag: tissue

value: Vastus lateralis


title: Muscle_CON_Inter1_GS33_Rep1

source_name: Vastus lateralis, at start of control period during first intervention, from individual GS33, Rep1

tag: subject id


title: Muscle_PRE_Inter1_GS27_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS27, Rep1

tag: age


title: Muscle_PRE_Inter1_GS60_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS60, Rep1

tag: Sex


title: Arabidopsis, shoots, irt1, + Fe, biological rep2

city: Bochum

first: Ute

last: Kraemer

address: Universitaetstrasse 150

country: Germany

institute: RUB University Bochum

hyb_protocol: Hybridisation to Affymetrix ATH1 genechips according to manufacturers instructions as GeneCore, EMBL, Heidelberg.

scan_protocol: Accordig to manufacturers instructions at GeneCore, EMBL, Heidelberg

data_processing: Data were analysed with Genespring software usign RMA normalisation and no transformation.

organism: Arabidopsis thaliana

source_name: 15 day-old irt1 seedlings grown under control conditions

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA

growth_protocol: For Fe deficiency treatments, contaminant metals were removed from the agar (Type M, above) through washing in EDTA solution, and Fe was omitted from the treatment media (- Fe) or supplied as 10 µM Fe-HBED (+ Fe). Seedlings were transferred to treatment media and harvested at ZT 3 h after 5 d of treatment.

extract_protocol: Total RNA extraction using RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Sterilized seeds were sown on 0.25x modified Hoagland solution, 1% (w/v) sucrose and 0.8% (w/v) agar Type M (Sigma). After stratification, vertically oriented square 120-mm polystyrene Petri dishes (Greiner Bio-On) were incubated in 11-h light (22°C, 145 µmol m−2 s−1 white light) and 13-h dark (18°C) cycles (Percival CU-41L4; CLF Climatics) for a 10-d pre-cultivation period prior to the initiation of treatments.

value: shoot


title: Muscle_PRE_Inter1_GS36_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS36, Rep1

tag: treatment/timepoint


title: Patient2 biological replicate 2

tag: cell type


title: Muscle_12WP_Inter2_GS66_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS66, Rep1


title: Arabidopsis, shoots, irt1, + Fe, biological rep1

tag: genotype


title: Muscle_PRE_Inter1_GS30_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS30, Rep1


title: Muscle_8WP_Inter2_GS3_Rep1

description: Same individual as in GSM4577417, GSM4577442, GSM4577459, GSM4577480

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS3, Rep1


title: Muscle_8WP_Inter2_GS13_Rep1

description: Same individual as in GSM4577425, GSM4577434, GSM4577466

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS13, Rep1


title: Patient1 biological replicate 2

value: DDC homozygous missense variant c.1039C>G


title: Muscle_4WP_Inter2_GS52_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS52, Rep1


title: Arabidopsis, shoots, wild-type, - Fe, biological rep2

source_name: 15 day-old wild-type seedlings grown under Fe deficiency for 5 days

value: wild-type


title: Arabidopsis, shoots, wild-type, - Fe, biological rep1


title: Patient1 biological replicate 1


title: Control biological replicate 3

value: Wild type

value: Healthy control


title: Arabidopsis, shoots, wild-type, + Fe, biological rep2

source_name: 15 day-old wild-type seedlings grown under control conditions


title: Muscle_PRE_Inter2_GS66_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS66, Rep1

value: at baseline during second intervention


title: Patient1 biological replicate 3


title: Arabidopsis, roots, irt1, + Fe, biological rep2

value: root


title: Control biological replicate 2


title: Arabidopsis, shoots, wild-type, + Fe, biological rep1


title: Muscle_PRE_Inter1_GS35_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS35, Rep1

value: F

value: at baseline during first intervention


title: Arabidopsis, roots, irt1, + Fe, biological rep1


title: Arabidopsis, roots, wild-type, - Fe, biological rep1


title: S7_31

city: Montpellier

first: Gabriel

last: Jimenez-Dominguez

state: Occitanie

address: 208 Avenue des apothicaires

department: Hérault

institute: Institut de Recherche en Cancérologie de Montpellier (IRCM)

description: er-rar-count.txt

data_processing:
Basecalling was performed using the two-channel SBS sequencing technology
TopHat (v2.1.0) splice junction mapper was used for RNA-Seq reads
RNA-Seq reads were aligned to the hg38 reference genome using the ultra high-throughput short read aligner Bowtie version: 2.2.6.0
Extraction of reads per gene was performed by the HTSeq-Count software
The read count matrix was normalized with edgeR (McCarthy et al., 2012) TMM algorithm
Sequencing Analysis Viewer 1,8,37 (Illumina) software was used for senquencing quality control. compressed .BCL files were generated by the NetSeq500 and demultiplexed by the bcl2fastq 2.0 (Illumina) software. Quality control on these files was performed by the FastQC v0,11,3 software.
Genome_build: hg38

source_name: MELN Invasive ductal carcinoma cell line

growth_protocol: MELN cells were cultured in phenol red-free Dulbecco’s modified Eagle medium (Gibco) containing 5% dextran-charcoal treated FCS (Invitrogen) and antibiotics (Gibco).

extract_protocol:
RNA was isolated using the Zymo Research kit (Zymo research)
Illumina TruSeq kit and submitted to NextSeq500

treatment_protocol: siRNAs were transfected using Interferrin (Polyplus). When indicated, cells were treated with 100nM Estradiol (E2) or/and  10μM of all-trans retinoic acid (RAR) and then harvested 18 hours later.

value: MCF-7 ERE-beta-globin Luciferase Neo

value: Breast

value: 100nM E2 and 10μM RA, siRNA LCoR and siRNA RIP140


title: Muscle_PRE_Inter1_GS65_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS65, Rep1

value: M


title: Arabidopsis, roots, wild-type, + Fe, biological rep2


title: Patient2 biological replicate 1

source_name: midbrain dopaminergic neurons

value: iPSCs-derived midbrain dopaminergic neurons


title: S7_30

description: er-rar-count.txt

value: 10μM RA, siRNA LCoR and siRNA RIP140


title: Muscle_4WP_Inter1_GS38_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS38, Rep1


title: Muscle_12WP_Inter2_GS8_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS8, Rep1


title: S7_32

description: er-rar-count.txt


title: Muscle_4WP_Inter1_GS55_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS55, Rep1


title: Muscle_4WP_Inter2_GS6_Rep2

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS6, Rep2


title: Muscle_PRE_Inter1_GS54_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS54, Rep1


title: Arabidopsis, roots, wild-type, + Fe, biological rep1


title: S7_28

description: er-rar-count.txt

value: 100nM E2, siRNA LCoR and siRNA RIP140


title: S7_29

description: er-rar-count.txt


title: Arabidopsis, roots, wild-type, - Fe, biological rep2


title: Muscle_PRE_Inter1_GS53_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS53, Rep1

value: Vastus lateralis


title: Arabidopsis_ab_high_150min_rep2

city: Kinokawa

first: Katsura

last: Izui

state: Wakayama

address: 930 Nishimitani

department: School of Biology-oriented Science and Technology

institute: Kinki University

description: Gene expression data from rosette leaves of Arabidopsis thaliana AB plant 7-week old that exposed to 14-16 ppm of formaldehyde for 150 minutes.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: The data were analyzed with R/Bioconductor using GC-RMA by gcrma package as normalization method.

label: Biotin

source_name: Rosette leaves of Arabidopsis thariana AB plant which exposed to 14-16 ppm of formaldehyde for 150 minutes.

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Seeds of Arabidopsis thariana AB plants were sown on modified MS-agar medium (half strength inorganic compounds for MS medium, 1.5 mg/L thiamine-HCl, 2.5 mg/L pyridoxine-HCl, 0.25 mg/L nicotinic acid, 15 g/L sucrose, 8 g/L agar and adjusted to pH 5.8 with KOH) containing 30 mg/L kanamycin and 40 mg/L gentamicin. After 1 week, the selected seedlings were transferred to the modified MS-agar medium without antibiotics, and were grown for 2 weeks. The 3-week old plants were transferred and grown in inorganic soil (ratio of vermiculite to perlite was 2 to 1) that absorbed 1 ml/L HYPONeX (HYPONeX Japan, Osaka, Japan) for 4 weeks at 22oC under 10 hours light (70-100 µmol/m2/sec.) in an incubator. For the acclimation before exposure, the 7-week old plants were kept under constant light (approx. 70 µmol/m2/sec.) at 24oC for 72 hours from 0:30 p.m. The plants were exposed to formaldehyde after 72 hours of acclimation. The environmental formaldehyde concentration was kept at less than 0.08 ppm until plants’ growth and experiments.

extract_protocol: Approximately 100 mg of rosette leaves was applied to total RNA extraction using Plant RNA isolation mini kit (Agilent) under its protocol.

treatment_protocol: After the acclimation of plants, formaldehyde exposure experiments were started at 0:30 p.m. and finished at 3:00 p.m. For the exposure, 3 plants were placed into the chamber (volume: 10 L) each exposure condition and these plants were treated as replications. During exposure, the chamber was ventilated by gas that was adjusted to each exposure concentration at flow rate of 200 ml/min, and kept humidity of 50-60% at 24oC under the light (approx. 70 µmol/m2/sec.). The exposure condition was non-treatment (acclimation condition, outside of the exposure chamber, less than 0.08 ppm), air-control (less than 0.04 ppm), low-concentration (1-2 ppm) and high-concentration (14-16 ppm). The rosette leaves of the exposed plants (approx. 100 mg/each sample) were placed into vials and were frozen by liquid nitrogen immediately.

tag: ecotype

value: Columbia

value: AB

value: 7-week old

value: Rosette leaf


title: Muscle_PRE_Inter1_GS28_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS28, Rep1


title: Arabidopsis_ab_low_150min_rep3

description: Gene expression data from rosette leaves of Arabidopsis thaliana AB plant 7-week old that exposed to 1-2 ppm of formaldehyde for 150 minutes.

source_name: Rosette leaves of Arabidopsis thariana AB plant which exposed to 1-2 ppm of formaldehyde for 150 minutes.


title: S7_25

description: er-rar-count.txt

value: Ethanol, siRNA LCoR and siRNA RIP140


title: Muscle_4WP_Inter1_GS45_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS45, Rep1


title: Muscle_8WP_Inter2_GS51_Rep1

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS51, Rep1


title: Arabidopsis_ab_high_150min_rep1


title: Muscle_12WP_Inter2_GS2_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS2, Rep1


title: Arabidopsis_ab_low_150min_rep1


title: S7_26

description: er-rar-count.txt


title: Arabidopsis_ab_low_150min_rep2


title: Muscle_4WP_Inter2_GS56_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS56, Rep1


title: S7_24

description: er-rar-count.txt

value: 100nM E2 and 10μM RA, RIP140 siRNA


title: Control biological replicate 1

value: Wild type

value: Healthy control


title: Arabidopsis_ab_high_150min_rep3


title: S7_27

description: er-rar-count.txt


title: S7_23

description: er-rar-count.txt


title: S7_22

description: er-rar-count.txt

value: 10μM RA, RIP140 siRNA


title: Muscle_4WP_Inter2_GS61_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS61, Rep1


title: Arabidopsis_ab_air_150min_rep2

description: Gene expression data from rosette leaves of Arabidopsis thaliana AB plant 7-week old that exposed to clean air (concentration of formaldehyde was less than 0.04 ppm) for 150 minutes.

source_name: Rosette leaves of Arabidopsis thariana AB plant which exposed to clean air (less than 0.04 ppm) for 150 minutes.


title: S7_21

description: er-rar-count.txt

source_name: MELN Invasive ductal carcinoma cell line

value: MCF-7 ERE-beta-globin Luciferase Neo


title: Arabidopsis_ab_air_150min_rep1


title: Arabidopsis_ab_air_150min_rep3


title: S7_20

description: er-rar-count.txt

value: Breast

value: 100nM E2, RIP140 siRNA


title: Muscle_8WP_Inter2_GS18_Rep1

description: Same individual as in GSM4577438, GSM4577439, GSM4577460, GSM4577488

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS18, Rep1

value: M


title: S7_18

description: er-rar-count.txt

value: Ethanol, RIP140 siRNA


title: S7_19

description: er-rar-count.txt


title: Muscle_4WP_Inter1_GS40_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS40, Rep1

value: F


title: Arabidopsis_ab_non_150min_rep3

description: Gene expression data from rosette leaves of Arabidopsis thaliana AB plant 7-week old that was non-treatment.

source_name: Rosette leaves of Arabidopsis thariana AB plant which was non-treatment.


title: Arabidopsis_ab_non_150min_rep2


title: Arabidopsis_ab_non_150min_rep1


title: S6_32

description: er-rar-count.txt

value: 100nM E2 and 10μM RA, LCoR siRNA


title: S7_17

description: er-rar-count.txt


title: Muscle_12WP_Inter2_GS61_Rep1

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS61, Rep1

value: Vastus lateralis


title: S6_31

description: er-rar-count.txt


title: Arabidopsis_wild_high_150min_rep2

description: Gene expression data from rosette leaves of 7-week old Arabidopsis thaliana that was exposed to 14-16 ppm of formaldehyde for 150 minutes.

source_name: Rosette leaves of Arabidopsis thaliana which was exposed to 14-16 ppm of formaldehyde for 150 minutes.

growth_protocol: Arabidopsis thaliana wild type plants were grown on modified MS-agar medium (half strength inorganic compounds for MS medium, 1.5 mg/L thiamine-HCl, 2.5 mg/L pyridoxine-HCl, 0.25 mg/L nicotinic acid, 15 g/L sucrose, 8 g/L agar and adjusted to pH 5.8 with KOH) for 3 weeks. The 3-week old plants were transferred and grown in inorganic soil (ratio of vermiculite to perlite was 2 to 1) that absorbed 1 ml/L HYPONeX (HYPONeX Japan, Osaka, Japan) for 4 weeks at 22oC under 10 hours light (70-100 µmol/m2/sec.) in an incubator. For the acclimation before exposure, the 7-week old plants were kept under constant light (approx. 70 µmol/m2/sec.) at 24oC for 72 hours from 0:30 p.m. The plants were exposed to formaldehyde after 72 hours of acclimation. The environmental formaldehyde concentration was kept at less than 0.08 ppm until plants’ growth and experiments.

extract_protocol: Approximately 100 mg of  rosette leaves were applied to total RNA extruction using Plant RNA isolation mini kit (Agilent) under its protocol.

value: Columbia

value: wild type


title: Muscle_4WP_Inter2_GS6_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS6, Rep1


title: Muscle_PRE_Inter1_GS49_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS49, Rep1

value: at baseline during first intervention


title: Muscle_4WP_Inter1_GS47_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS47, Rep1


title: Arabidopsis_wild_high_150min_rep3

value: 7-week old

value: Rosette leaf


title: Arabidopsis_wild_low_150min_rep3

description: Gene expression data from rosette leaves of 7-week old Arabidopsis thaliana that was exposed to 1-2 ppm of formaldehyde for 150 minutes.

source_name: Rosette leaves of Arabidopsis thaliana which was exposed to 1-2 ppm of formaldehyde for 150 minutes.


title: Arabidopsis_wild_high_150min_rep1


title: S6_29

description: er-rar-count.txt

value: 10μM RA, LCoR siRNA


title: Arabidopsis_wild_low_150min_rep2


title: S6_28

description: er-rar-count.txt

value: 100nM E2, LCoR siRNA


title: Arabidopsis_wild_low_150min_rep1


title: Peripheral brain tissue of rats with intracerebral hemorrhage group Replicate 3

city: Nantong

first: Jinglei

last: Wang

state: Jiangsu

address: 20 Xisi Road

institute: Affiliated Hospital of Nantong University

description: Biological replicate 3 of 3. ICH group.

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

organism: Rattus norvegicus

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: All rats were raised in a temperature-controlled room (22 ± 1 ˚C) with a 12-h light/dark cycle and food and water were available ad libitum.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: brain

value: day 1

tag: group

value: intracerebral hemorrhage


title: Muscle_PRE_Inter2_GS2_Rep1

description: Same individual as in GSM4577415, GSM4577435, GSM4577476

source_name: Vastus lateralis, at baseline during second intervention, from individual GS2, Rep1

value: at baseline during second intervention


title: S6_27

description: er-rar-count.txt

value: MCF-7 ERE-beta-globin Luciferase Neo

value: Breast


title: Arabidopsis_wild_air_150min_rep3

description: Gene expression data from rosette leaves of 7-week old Arabidopsis thaliana that was exposed to clean air (concentration of formaldehyde was less than 0.04 ppm) for 150 minutes.

source_name: Rosette leaves of Arabidopsis thaliana which was exposed to clean air (less than 0.04 ppm) for 150 minutes.


title: Muscle_PRE_Inter2_GS61_Rep1

source_name: Vastus lateralis, at baseline during second intervention, from individual GS61, Rep1

value: M


title: Peripheral brain tissue of rats with intracerebral hemorrhage group Replicate 2

description: Biological replicate 2 of 3. ICH group.


title: Muscle_PRE_Inter1_GS56_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS56, Rep1


title: Muscle_4WP_Inter1_GS54_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS54, Rep1


title: Peripheral brain tissue of rats with intracerebral hemorrhage group Replicate 1

description: Biological replicate 1 of 3. ICH group.


title: Arabidopsis_wild_air_150min_rep2


title: Muscle_8WP_Inter2_GS9_Rep1

description: Same individual as in GSM4577422, GSM4577443, GSM4577464

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS9, Rep1


title: S6_24

description: er-rar-count.txt

value: 100nM E2 and 10μM RA, No siRNA