title: 209, POST, PG

description: SAMPLE 82

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: efe (repetitions)

tag: sas (repetitions)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time


title: Elvitegravir treatment

status: Public on Mar 30 2022

type: SRA

city: Hong Kong

first: Wing Tung

last: Lee

address: Room Y934, 9/F, Lee Shau Kee Building, The Hong Kong Polytechnic University, Hung Hom, Kowloon

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University (PolyU)

library_source: transcriptomic

data_processing:
Raw reads from RNA-seq were checked by FastQC v0.11.9 and trimmed by trim_galore v0.6.7.
The filtered clean reads were mapped to reference genome by HISAT2 (version 2.2.1). StringTie and ASprofile were used for transcript assembly and quantification respectively.
Cufflinks software was then used to quantify transcripts and gene expression levels using mapped reads’ positional information on the gene.
Gene expression level was calculated in the form of fragments per kilobase million (FPKM) and calcalated by GenomicFeatures (Rpackage). Genes with undetected expression level in all the samples were excluded in the following analysis.
Genome_build: Mycobacterium bovis BCG strain Russia 368, complete genome
Supplementary_files_format_and_content: text file includes FPKM values for each Sample

molecule: total RNA

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: Elvitegravir treatment

extract_protocol:
RNeasy Plus Mini Kit (cat. no. 74134) was used to prepare the RNA sample
TruSeq Stranded Total RNA with Ribo-Zero Plus

tag: treatment

value: Elvitegravir


title: ABX464 treatment

source_name: ABX464 treatment


title: 321_AU8033_0

type: RNA

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

country: USA

institute: UNC Eshelman School of Pharmacy

description: mouse liver RNA

hyb_protocol: Fifteen micrograms of labeled cRNA was fragmented and prepared for hybridization on HT MG430 PM peg arrays.

scan_protocol: The Gene Titan robotic instrumentation (Affymetrix) was used to perform the hybridization, washing and scanning of the peg arrays.

data_processing: Probes containing SNPs in the genome of 45 CC strains were masked using the “kill-list” option in the APT module “apt-probeset-summarize”. Affymetrix CEL files were normalized using the Robust Multi-array Average (RMA) method with log2 transformation implemented in Affymetrix Power Tools (APT, v 1.17.0). A second pre-filtering step was then performed to eliminate lowly expressed probe sets defined as the maximum of log2 transformed expression level across samples less than an empirically chosen cutoff. Principal component analysis (PCA) and hierarchical clustering was used to evaluate the overall performance of the arrays. Seven (7) animals were identified as outliers (strains CC004, CC010, CC023, CC027, CC028, CC042, CC053, one animal each strain) and were removed from subsequent analysis.

label: biotin

organism: Mus musculus

source_name: mouse, liver

label_protocol: Double-stranded cDNA was synthesized from 50-150 ng (dependent on RNA yield) of total RNA, then transcribed to biotin-labeled cRNA using the 3’ Express IVT kit (Affymetrix).

growth_protocol: Eight (8) male mice from each of 45 CC lines  were purchased from the University of North Carolina, Chapel Hill.  Animals were acclimated for approximately 7 days prior to dosing. At the initiation of treatment, mice were approximately 8-10 weeks of age.

extract_protocol: Total cellular RNA was isolated using Trizol reagent (Invitrogen) and further purified using the QIAcube automated system (Qiagen). Following purification, the quantity of RNA was determined spectrophotometrically and the integrity of the RNA was evaluated with the Agilent 2100 Bioanalyzer.

treatment_protocol: Within each CC line, 4 animals were treated with a single dose of vehicle (0.5% w/v methylcellulose in purified water) and 4 were treated with TAK-875 (600 mg/kg). Test and control articles were administered by oral gavage in a dosing volume of 10 ml/kg. Animals were assigned to treatment groups using a randomization method based on bodyweight. Vehicle- and TAK-875-treated animals within each line were treated in pairs, and pairs within each line were randomized over the course of the study to minimize batch (treatment group) effects.

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: NH125 treatment

source_name: NH125 treatment


title: AEBSF (hydrochloride) treatment

source_name: AEBSF (hydrochloride) treatment

value: AEBSF (hydrochloride)


title: 322_AU8033_0

description: mouse liver RNA


title: Saquinavir (mesylate) treatment

source_name: Saquinavir (mesylate) treatment

value: Saquinavir (mesylate)


title: 316, POST, PG

type: genomic

city: Ribeirão Preto

first: Guilherme

middle: Da Silva

last: Rodrigues

address: Avenida Bandeirantes, 3900

country: Brazil

institute: Universidade de São Paulo

description: SAMPLE 79

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation Beadchip EPIC using standard Illumina protocol

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

data_processing:
Champ package for Rstudio was used to process data.
Matrix_Processed.txt value definition:  BMIQ normalized (provide the normalization method) Average Beta corrected by cell lineages

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from the collected whole blood, the technique adopted was automated by magnetic spheres, using the Maxwell MDx equipment.

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

value: PG

value: POST

tag: tissue

value: peripheral blood

tag: cell type

value: leukocytes


title: 279, POST, PG

description: SAMPLE 84

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: efe (repetitions)

tag: sas (repetitions)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time


title: Saquinavir treatment

source_name: Saquinavir treatment

tag: treatment

value: Saquinavir


title: 323_AU8033_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 244, POST, PG

description: SAMPLE 78

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: tissue

tag: cell type


title: 324_AU8033_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 319_AU8016_600

description: mouse liver RNA


title: Clemizole (hydrochloride) treatment

source_name: Clemizole (hydrochloride) treatment

tag: treatment

value: Clemizole (hydrochloride)


title: Letrazuril treatment

source_name: Letrazuril treatment

value: Letrazuril


title: Ebselen treatment

source_name: Ebselen treatment

value: Ebselen


title: PDT2-2

city: Chongqing

first: Xiaoyu

last: Wang

address: Shabei street

country: China

institute: Key Laboratory of Biorheological Science and Technology, Ministry of Education

data_processing:
Illumina CASAVA software used for basecalling.
After removing low-quality bases, using Rockhopper software, the sequencing clean reads was efficiently compared to the reference genome to obtain its position on the reference genome  information
The expected number of fragments per kilobase of transcription sequence per millions base pairs sequenced was calculated by using featureCounts software
Genome_build: Mycobacterium abscess ATCC 19977 genome
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

organism: Mycobacteroides abscessus

source_name: Mycobacterium abscess ATCC_19977 100µg/mL ALA+160J/cm2 light

growth_protocol: Mycobacterium abscess was Grown in Middlebrook 7H9 broth

extract_protocol:
Mycobacterium abscess solids were collected, then ground with liquid nitrogen, and RNA was collected with Trizol reagent. The Illumina truseq RNA sample preparation kit was used with 1 ug of total RNA to construct the sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The M. abscesses ATCC19977 strain was cultured in liquid 7H9 medium supplemented with 0.05% (v/v) Tween 80 and harvested when OD600 is 0.8, then adjusted OD600 to 0.1-0.2, and added the photosensitizer ALA (100µg/mL). Incubate at 37℃ for 12 hours, and process red light of 585-635nm with different energy (80,160J/cm2).

tag: strain

value: 100µg/mL ALA+160J/cm2 light


title: Pirodavir treatment

source_name: Pirodavir treatment

value: Pirodavir


title: PDT1-3

source_name: Mycobacterium abscess ATCC_19977 100µg/mL ALA+80J/cm2 light

value: 100µg/mL ALA+80J/cm2 light


title: PDT2-1


title: PDT2-3


title: 317_AU8016_600

description: mouse liver RNA


title: 503, PRE, PG

description: SAMPLE 76

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time

value: PRE


title: 520, PRE, PG

description: SAMPLE 75

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: tissue

tag: cell type


title: PDT1-2

tag: strain

tag: treatment


title: 539, PRE, PG

description: SAMPLE 74

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state


title: M-ab-3

source_name: Mycobacterium abscess ATCC_19977 0µg/mL ALA+0J/cm2 light

tag: strain

value: 0µg/mL ALA+0J/cm2 light


title: 313_AU8016_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: PDT1-1

tag: treatment


title: 315_AU8016_600

description: mouse liver RNA


title: M-ab-1


title: 545, PRE, PG

description: SAMPLE 72

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: time

tag: tissue

tag: cell type


title: M-ab-2

tag: strain

tag: treatment


title: 241, POST, PG

description: SAMPLE 77

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: agility (sec)

tag: 6mwt (m)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state


title: early stage hepatocellular carcinoma serum exosome 1

city: Shanghai

first: Peng

last: Chen

address: 88 ChongQing South Road

institute: Shanghai Jiao Tong University of medicine

description: serum exosome RNA-Seq

data_processing:
Illumina HiSeq 2000software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using HISAT v2.2.1 with parameters $HISAT_HOME/hisat -x 22_20-21M_hisat -1 $HISAT_HOME/example/reads/reads_1.fq -2 $HISAT_HOME/example/reads/reads_2.fq -S eg2.sam
The result of HISAT2 is the alignment result of each read after the optimal alignment. On this basis, Stringtie uses these reads fragments to assemble RNA sequences of true length for each RNA-seq, detailed can be seen in Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18. PMID: 25690850; PMCID: PMC4643835. We followed the specific protocol and applied StringTie  v2.1.4  with parameters stringtie --mix -G $ref/hg38_annotation.gff -o $sample1dir/out/transcripts.gtf \  $sample1dir/short_reads.cram $sample1dir/long_reads.bam
Assembly: hg18

source_name: isolated from serum

extract_protocol:
Exosomes were purified from the serum samples using ultracentrifugation method.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: exosome

tag: tumor stage

value: early stage hepatocellular carcinoma

value: liver


title: early stage hepatocellular carcinoma serum exosome 2

description: serum exosome RNA-Seq


title: 310_AU8016_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 510, PRE, PG

description: SAMPLE 71

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: time

tag: cell type


title: advanced stage hepatocellular carcinoma with portal vein tumor thrombosis serum 2

description: serum exosome RNA-Seq

tag: tissue

tag: tumor stage

value: advanced stage hepatocellular carcinoma


title: 312_AU8016_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 553, PRE, PG

description: SAMPLE 73

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

value: PG


title: advanced stage hepatocellular carcinoma with portal vein tumor thrombosis serum 3

description: serum exosome RNA-Seq

tag: tissue

tag: tumor stage


title: liver cirhosis serum exosome 3

description: serum exosome RNA-Seq

value: liver cirrohosis


title: advanced stage hepatocellular carcinoma with portal vein tumor thrombosis serum 1

description: serum exosome RNA-Seq


title: 316_AU8016_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 311_AU8016_0

description: mouse liver RNA


title: 506, PRE, PG

description: SAMPLE 70

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: time

value: peripheral blood

tag: cell type


title: 512, PRE, PG

description: SAMPLE 69

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: agility (sec)

tag: 6mwt (m)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: tissue

value: leukocytes


title: liver cirhosis serum exosome 2

description: serum exosome RNA-Seq

tag: tumor stage


title: liver cirhosis serum exosome 1

description: serum exosome RNA-Seq


title: 519, PRE, PG

description: SAMPLE 68

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb


title: 306_AU8008_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 307_AU8008_600

description: mouse liver RNA


title: 513, PRE, PG

description: SAMPLE 66

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: agility (sec)

tag: 6mwt (m)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time

tag: tissue

tag: cell type


title: H1299 cells, SH1, 3

city: Zhengzhou

first: zhuoyu

last: gu

state: China

address: No. 50, Jianshe East Road, Erqi District

institute: First Affiliated Hospital of Zhengzhou 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.
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.
Assembly: Homo_sapiens (NCBI_GCF_000001405.38_GRCh38.p12) https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.38
Supplementary files format and content: gene_diff.txt, gene_expression.txt

source_name: H1299 cells, SH1

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: cell line

value: lung adenocarcinoma

tag: age

value: Fifth generation

tag: genotype

value: hnRNPC knockdown


title: H1299 cells, SH1, 1


title: H1299 cells, SH1, 2


title: H1299 cells, NC1, 1

source_name: H1299 cells, NC1

value: hnRNPC shNC


title: 299, PRE, PG

description: SAMPLE 65

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb


title: 516, PRE, PG

description: SAMPLE 67

tag: age

tag: wc (cm)

tag: agility (sec)

tag: 6mwt (m)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time

tag: tissue

tag: cell type


title: H1299 cells, NC1, 2

tag: cell line

tag: genotype


title: 249, PRE, PG

description: SAMPLE 64

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: uric acid (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb


title: H1299 cells, NC1, 3

tag: cell line

tag: tissue

tag: age


title: 308_AU8008_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 304_AU8008_0

description: mouse liver RNA


title: H3

city: Jining

first: Daojing

last: Li

state: Shandong

address: No.89 Guhuai Road

department: Department of Neurology

institute: Affiliated Hospital of Jining Medical University

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: GRCh38
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: Peripheral blood mononuclear cell

extract_protocol:
Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA). Ribo zero ™  Magnetic Kit (epicentre) isolated and removed rRNA from total RNA.
A total amount of 1 μg RNA per sample was used. In brief, the Ribo-Zero™ Magnetic Kit(Epicentre) was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

tag: cell type

value: peripheral blood mononuclear cell

tag: disease state

value: patient with hemorrhagic transformation after acute ischemic stroke


title: C1

value: patient without hemorrhagic transformation after acute ischemic stroke


title: 244, PRE, PG

description: SAMPLE 63

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: time

value: PRE


title: H1

tag: cell type

tag: disease state


title: H2


title: C3


title: C2


title: 298_AU8005_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 305_AU8008_600

description: mouse liver RNA


title: 303_AU8008_0

description: mouse liver RNA


title: 302_AU8008_0

description: mouse liver RNA


title: 301_AU8008_0

description: mouse liver RNA


title: 209, PRE, PG

description: SAMPLE 62

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: tissue


title: AB3687 (FOX073-001_low)

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190744
TOLOSA_03

data_processing:
RNA-seq reads were mapped against human reference genome (GRCh38) using STAR software version 2.5.1b  with ENCODE parameters.
Genes were quantified using RSEM version 1.2.28  with default parameters and annotation file from GENCODE version 24
Differential expression analysis was performed with DESeq2 v1.18. R package  adjusting by sex on the model and using the Wald test to compare the experimental conditions
Genome_build: GRCh38 (primary assembly, gencode version 24)
Supplementary_files_format_and_content: raw counts (tsv)

source_name: fibroblasts

growth_protocol: Skin biopsies were obtained from sporadic and genetic forms of Parkinson’s disease and healthy controls. Fibroblasts were cultured in two conditions, high (25 mM) and low (5mM) glucose (DMEM; Gibco), and supplemented with 10% calf serum (CS) (Gibco) penicillin 100 U/mL, streptomycin 100 μg/mL, and heparin 125 μg/mL U/mL (DMEM/10% CS) (all Sigma, St Louis, Mo). Cells were grown at 37°C in 10% carbon dioxide and were passaged at confluence with a solution of trypsin/EDTA (Sigma).

extract_protocol:
RNA was performed using the Allprep DNA RNA Protein Minikit from Quiagen following manufacter instructions. Starting material included three times PBS washed cellular pellets of 106 cells. DNA and RNA concentration were determined on a NanoDrop ND-3300 Fluorospectrometer, and RNA integrity was examined with the Bioanalyzer 2100 (Agilent).
RNA sequencing (RNA-seq) was performed at the Centro Nacional de Análisis Genómico (CNAG) in Barcelona, Catalonia. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,) with minor modifications.

tag: disease state

value: healthy control

tag: cell type

value: fibroblasts

tag: glucose

value: low 5 mM

tag: gender

value: male

tag: batch


title: AB3686 (SP-17_low)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190743
TOLOSA_03

treatment_protocol: Fibroblasts were cultured in two conditions, high (25 mM) and low (5mM) glucose (DMEM; Gibco)

value: sporadic Parkinson's disease

value: female


title: AB3685 (SP-16_low

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190742
TOLOSA_03


title: 182, PRE, PG

description: SAMPLE 60

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

value: PG

tag: time


title: 297_AU8005_600

description: mouse liver RNA

source_name: mouse, liver

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 206, PRE, PG

description: SAMPLE 61

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: disease state

tag: tissue

value: peripheral blood

tag: cell type


title: AB3683 (SP-12_low)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190740
TOLOSA_03

value: LRRK2 Parkinson's disease (G2019S mutation)

tag: glucose

tag: gender

tag: batch


title: AB3682 (SP-11_low)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190739
TOLOSA_03


title: AB3681  (SP-09_low)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190738
TOLOSA_03


title: AB3684 (SP-13_low)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190741
TOLOSA_03


title: 241, PRE, PG

description: SAMPLE 59

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: time

value: leukocytes


title: 296_AU8005_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: AB3680 (SP-06_low)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190737
TOLOSA_03

tag: disease state

tag: cell type

tag: glucose

tag: gender

tag: batch


title: 295_AU8005_600

description: mouse liver RNA


title: AB3679 (SP-04_low)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190736
TOLOSA_03


title: AB3677 (SP-01_low)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190734
TOLOSA_03


title: AB3678 (SP-02_low)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
GSM2190735
TOLOSA_03


title: 210, PRE, PG

description: SAMPLE 55

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: tissue


title: AA0488 (FOX-073-001)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190731
TOLOSA_02

tag: disease state

tag: cell type

tag: glucose

value: high 25 mM

tag: gender

tag: batch


title: AA0489 (SP-16)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190732
TOLOSA_02


title: 279, PRE, PG

description: SAMPLE 58

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: time


title: 316, PRE, PG

description: SAMPLE 56

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: disease state

tag: tissue

tag: cell type


title: AA0490 (SP-17)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190733
TOLOSA_02

tag: glucose

tag: gender

tag: batch


title: 278, PRE, PG

description: SAMPLE 57

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: time


title: 294_AU8005_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: AA0486 (SP-12)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190729
TOLOSA_02

tag: disease state

tag: cell type

tag: glucose

tag: gender

tag: batch


title: AA0487 (SP-13)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190730
TOLOSA_02


title: 293_AU8005_0

description: mouse liver RNA


title: 288_AU8043_600

description: mouse liver RNA


title: AA0485 (SP-11)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190728
TOLOSA_02


title: 291_AU8005_0

description: mouse liver RNA


title: 287, PRE, PG

description: SAMPLE 54

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: tissue


title: 233, PRE, PG

description: SAMPLE 53

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time

tag: cell type


title: AA0483 (SP-06)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190726
TOLOSA_02

tag: glucose

tag: gender

tag: batch


title: 292_AU8005_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: AA0484 (SP-09)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190727
TOLOSA_02


title: AA0482 (SP-04)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190725
TOLOSA_02


title: AA0481 (SP-02)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190724
TOLOSA_02


title: AA0480 (SP-01)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
GSM2190723
TOLOSA_02


title: 522, POST, NGG

description: SAMPLE 52

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

value: NGG

value: POST

tag: tissue


title: 286_AU8043_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 287_AU8043_600

description: mouse liver RNA


title: 285_AU8043_600

description: mouse liver RNA


title: 521, POST, NGG

description: SAMPLE 51

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time

tag: cell type


title: 525, POST, NGG

description: SAMPLE 50

tag: age

tag: sbp (mmhg)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: tissue


title: LNCaP_sgNC_ENZ_1

city: Chicago

first: Sarki

last: Abdulkadir

state: IL

address: 303 E Superior St

institute: Northwestern University

library_source: genomic

data_processing:
Alignment: Sequenced reads were aligned to the hg38 reference human genome using Bowtie2.
Assembly: hg38
Supplementary files format and content: coverage

source_name: LNCaP prostate cancer cells

growth_protocol: LNCaP cells were routinely grown in RPMI media with 10% FBS and 1% Pen-strep.

extract_protocol:
Nuclei were isolated with nuclear lysis buffer and centrifuged at low speeds. The nuclei were resuspended in 50uL of transposase reaction mixture. Transposition was carried out at 37°C for 30 min, followed by DNA purification with DNA Clean and Concentrator-5 kit
library fragments were PCR-amplified with Nextera XT v2 adapter primers. Multiplexed libraries were sequenced on the NextSeq 500 (Illumina) for paired end 37nt

treatment_protocol: Cells were plated, and next day 5 µM of enzalutamide for 4 day treatment.

tag: condition

value: Control LNCaP cells

tag: cell line

value: LNCaP

tag: treatment

value: ENZ


title: LNCaP_sgPRRX2_ENZ_2

value: PRRX2 overexpressing LNCaP cells


title: LNCaP_sgPRRX2_ENZ_1


title: AC142 EV

city: Seattle

first: Kai

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of [] and random barcode length [] (on []). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
RNA Isolation method was . RNA Isolation kit was Homebrew Kit.
Library construction kit was Homebrew Kit. Samples were multiplexed. Type of Starting Material was total RNA.

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: extracellular vesicle

tag: rna isolation kit

value: Homebrew Kit


title: 537, POST, NGG

description: SAMPLE 47

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time

tag: cell type


title: 524, POST, NGG

description: SAMPLE 49

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: as

tag: cd

tag: pb

tag: tissue


title: DES_2 leaves

city: Gödöllő

first: Zsófia

last: Bánfalvi

address: Szent-Györgyi Albert u. 4.

department: Genetics and Biotechnology Institute

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

data_processing:
It was carried out by  Novogene (UK) Company Ltd. (Cambridge, UK)
Genome_build: Solanum tuberosum group Phureja DM1-3 v.6.1
Supplementary_files_format_and_content: txt, gene IDs and counts

organism: Solanum tuberosum

source_name: source leaf

growth_protocol: in pots in a greenhouse

extract_protocol:
Plant Mol Biol. 1988;11:255-269
Libraries were prepared by Novogene (UK) Company Ltd. (Cambridge, UK)

treatment_protocol: no treatment

value: leaf

value: mesophyll

value: 8-week-old plants

tag: line

value: DES

tag: genotype

value: control


title: DES_3 leaves


title: 284_AU8043_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: DES_1 leaves

tag: cell type

tag: age


title: 542, POST, NGG

description: SAMPLE 48

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: insulin ui/ml

tag: al

tag: ni

tag: li

tag: disease state

tag: time

value: peripheral blood

value: leukocytes


title: AC758 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 544, POST, NGG

description: SAMPLE 46

value: NGG

tag: tissue

tag: cell type


title: AC112 EV


title: aGI_3 leaves

tag: age

tag: line

value: aGI

tag: genotype


title: 282_AU8043_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 283_AU8043_0

description: mouse liver RNA


title: 278_AU8002_600

description: mouse liver RNA


title: LNCaP_sgNC_ENZ_2

value: Control LNCaP cells

tag: cell line

tag: treatment


title: aGI_2 leaves


title: 554, POST, NGG

description: SAMPLE 44

tag: disease state

tag: time

value: POST


title: 276_AU8002_600

description: mouse liver RNA


title: BQ11013 EV

tag: condition

tag: anatomical location


title: AC009 EV

tag: rna source

tag: rna isolation kit


title: 277_AU8002_600

description: mouse liver RNA


title: AC759 EV


title: BQ11004 EV


title: 527, POST, NGG

description: SAMPLE 43

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: tissue

tag: cell type


title: BQ9121 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: aGI_1 leaves

tag: age

tag: line

tag: genotype


title: 543, POST, NGG

description: SAMPLE 45

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: disease state

tag: time


title: 275_AU8002_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 555, POST, NGG

description: SAMPLE 42

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: tissue

tag: cell type


title: 212, POST, NGG

description: SAMPLE 41

tag: age

tag: sbp (mmhg)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: disease state

tag: time


title: 281_AU8043_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: LP285 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: AC-050 EV


title: EL4_GATA3_Dox_Tbet_DOX_2_WCE

city: London

first: Arnulf

last: Hertweck

address: Gower Street

department: UCL Cancer Institute

country: United Kingdom

institute: University College London

data_processing:
Raw reads were ﬁltered for base quality using FastQC with default parameters and adapters sequences were removed with Trim Galore!
Reads passing quality filtering criteria were aligned to GRCm38 using BWA with default settings
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: EL4 cell

growth_protocol: EL4 GFP+HA-GATA3 cells were transduced with retrovirus encoding a doxycycline-inducible FLAG-T-bet construct and selected with G418. Cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 4 mM L-alanyl-L-glutamine, 25 mM D-glucose, 1 mM sodium pyruvate, 10 mM HEPES, 100 U/ml penicillin and 100 µg/ml streptomycin

extract_protocol:
Cells were lysed with non-ionic detergent, the nuclei washed and then lysed with ionic detergent. Cells were sonicated on ice to solubilize and shear crosslinked DNA (27W for 10x 30 second pulses using a Misonix Sonicator 3000). The resulting whole cell lysate was cleared by centrifugation and then incubated overnight at 4°C with 50 µl of Protein G magnetic Dynabeads that had been pre-incubated with 5 µg of purified antibody (anti-FLAG, M2 Sigma; anti-HA, 3F10 Roche; anti-H3K27ac, ab4729 Abcam). Beads were washed 6 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65°C with rocking for 2 hrs and crosslinks then reversed in IP and input DNA by incubation at 65°C for 6 hrs. IP and input DNA were then purified by treatment with RNase A, proteinase K and isolated with KAPA Pure beads.
Libraries were constructed from ChIP DNA by standard Illumina protocols, except that DNA in the range 150-350 bp was gel-purified after PCR-amplification. The libraries were quantified using a Qubit fluorometer and Agilent bioanalyzer, pooled and subjected to 75 bp single-end sequencing with a NextSeq 550 sequencer

treatment_protocol: Cells were treated with 0-10ug/ml doxycycline for 48 hour prior to harvesting. Cells were stimulated with phorbol 12-myristate 13-acetate (50 ng/ml) and ionomycin (1 μM) for 4 hours prior to crosslinking. Cells were crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 20 minutes at room temperature before the reaction was quenched by addition of glycine as described. Cells were rinsed twice with 1xPBS and flash frozen in liquid nitrogen.

tag: cell line

value: EL4 cells

tag: ectopically expressed protein

value: HA-GATA3+ Dox-inducible FLAG-T-bet

tag: treatment

value: PMA+ionomycin; 2ug/ml Dox

tag: antibody


title: 167, POST, NGG

description: SAMPLE 40

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: tissue

tag: cell type


title: 274_AU8002_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 273_AU8002_0

description: mouse liver RNA


title: EL4_GATA3_Dox_Tbet_DOX_2_HA-GATA3_ChIP

tag: cell line

tag: ectopically expressed protein

tag: treatment

tag: antibody

value: anti-HA, 3F10 Roche


title: EL4_GATA3_Dox_Tbet_DOX_04_WCE

value: PMA+ionomycin; 0.4ug/ml Dox


title: 501, POST, NGG

description: SAMPLE 39

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: disease state

tag: time


title: EL4_GATA3_Dox_Tbet_DOX_10_HA-GATA3_ChIP

tag: cell line

tag: ectopically expressed protein

tag: treatment

value: PMA+ionomycin; 10ug/ml Dox

tag: antibody


title: 428, POST, NGG

description: SAMPLE 38

tag: tissue

tag: cell type


title: 2BQ0243 EV

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: extracellular vesicle

tag: rna isolation kit

value: Homebrew Kit


title: 505, POST, NGG

description: SAMPLE 37

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: as

tag: cd

tag: pb

tag: ni

tag: li


title: 271_AU8002_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: EL4_GATA3_Dox_Tbet_DOX_10_WCE

tag: cell line

tag: ectopically expressed protein

tag: treatment

tag: antibody


title: 511, POST, NGG

description: SAMPLE 36

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: disease state

tag: time

tag: tissue

tag: cell type


title: 267_OR5391_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: EL4_GATA3_Dox_Tbet_DOX_2_Flag-Tbet_ChIP

tag: cell line

tag: ectopically expressed protein

tag: treatment

tag: antibody

value: anti-FLAG, M2 Sigma


title: EL4_GATA3_Dox_Tbet_DOX_10_Flag-Tbet_ChIP


title: 272_AU8002_0

description: mouse liver RNA


title: 267, POST, NGG

description: SAMPLE 35

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: as

tag: cd

tag: pb

tag: ni

tag: li

value: peripheral blood


title: 268_OR5391_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: BQ6104 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: AC-048 EV


title: AC195 EV


title: 220, POST, NGG

description: SAMPLE 34

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: disease state

tag: time

tag: tissue

tag: cell type

value: leukocytes


title: EL4_GATA3_Dox_Tbet_DOX_04_Flag-Tbet_ChIP

tag: cell line

tag: ectopically expressed protein

tag: treatment

tag: antibody


title: 265_OR5391_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: AC064 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: EL4_GATA3_Dox_Tbet_DOX_04_HA-GATA3_ChIP


title: 202, POST, NGG

description: SAMPLE 33

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: disease state

value: NGG


title: BQ11014 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 2BQ0342 EV


title: 264_OR5391_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: AC-071 EV


title: CD8aa IEL Ctrl_rep_2

city: Bethesda

first: Jia

last: Nie

state: Maryland

address: Building 37, Room 3016

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Basecalling was performed using RTA 2.11.3
Barcode was demultiplexed with mkfastq in Cellranger 6.0.0
Alignment, tagging and gene counting were done with Cellranger 6.0.0
Genome_build: mm10
Supplementary_files_format_and_content: .h5 files of raw/filtered gene-by-barcode matrces

source_name: Gut epithelium

extract_protocol:
Chromium Single Cell V(D)J Reagent Kits (v1.1 Chemistry) per the manufacturer instructions (10X genomics)
Chromium Single Cell V(D)J Reagent Kits (v1.1 Chemistry) per the manufacturer instructions (10X genomics) were used for library. Libraries were pooled and sequenced on NextSeq 550 (HighOutput Kit V2.5, 75 cycle, parameter: R1: 26bp, I1: 8bp and R2: 55 bp).

tag: strain

tag: population

tag: genotype

value: Cd4 Cre- lrffl/fl

tag: tissue

value: Gut epithelium

tag: cell type

value: CD8aa intraepithelial lymphocytes


title: CD8aa splenocytes LRF KO_rep_1

source_name: Spleen

value: Cd4 Cre+ lrffl/fl

value: Spleen

value: CD8aa splenocytes


title: AC/BQ248 EV


title: 266_OR5391_600

description: mouse liver RNA


title: 280, POST, NGG

description: SAMPLE 31

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: time

value: POST


title: 261_OR5391_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 258_OR5035_600

description: mouse liver RNA


title: CD8aa IEL Ctrl_rep_1

tag: strain

tag: population

tag: genotype

tag: tissue

tag: cell type


title: 255, POST, NGG

description: SAMPLE 30

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: li

tag: disease state


title: AC/BQ259 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: AC084 EV


title: AC148 EV


title: 263_OR5391_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 197, POST, NGG

description: SAMPLE 29

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: time

tag: tissue

tag: cell type


title: Whole plant, Treated 2

city: Oeiras

first: Juan

middle: Ignacio

last: Vilchez

state: Lisbon

address: Avenida da Republica, -

department: Plant Division

country: Portugal

institute: ITQB - NOVA

data_processing:
RNA-Seq, 13-d-old plants at 7 d after treatment were harvested as whole seedlings.
RNA-Seq were pre-processed using Trimmomatic (version 0.36).
Subsequently, the clean reads were aligned to the TAIR10 reference genome using hisat2 (version 2.1.0) with the parameters‘--rna-strandness RF -p 30 --dta’.
The reads_count matrix was produced usinghtseq-count (version 0.9.1).
DEGs were identified using edgeR with the cut-offs offold-change ≥ 1.5 and false discovery rate ≤ 0.05. Three biological replicates of eachcondition were used to perform transcriptome analyses.
Assembly: TAIR10
Supplementary files format and content: Processed_data_DEG_total_CPM.xls (includes raw gene counts and counts per million reads mapped (CPM) values for each Sample)

organism: Arabidopsis thaliana

source_name: Whole plant

growth_protocol: A. thaliana seeds were surface sterilized with ethanol and bleach, and then washed with sterile water. Then they were placed in 1/2 MS plates, stratified at 4 degrees for 48 h and then germinated for 5 days. Finally the seedlings were transferred to vermiculite soil.

extract_protocol:
Plants were removed from soil and cleaned, flash frozen on dry ice, and RNA was harvested using RNeasy Plant Mini Kit for RNA extraction (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

treatment_protocol: Inoculums were applied 24 h after plants were transfered to soil. For Priestia megaterium YC4-R4 inoculum, bacteria was grow for 12 h in Luria Bertani medium (LB), up to 1 optical density at 600nm. Then they were resuspended in 0.45% NaCl as carrier. Mock inoculation was performed by applying same amount of free-bacteria 0.45% NaCl solution.

tag: ecotype

value: Whole plant (ground mixture)

tag: genotype

value: wild type

tag: treatment

value: Priestia megaterium inoculum

tag: age

value: 13 days after germination

tag: treatment time

value: 7 days after treatment


title: AC218 EV

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: extracellular vesicle

tag: rna isolation kit

value: Homebrew Kit


title: CD8aa splenocytes LRF KO_rep_2

tag: strain

tag: population


title: 256_OR5035_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: Whole plant, Treated 1

tag: tissue


title: 257_OR5035_600

description: mouse liver RNA


title: 219, POST, NGG

description: SAMPLE 32

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: disease state

value: NGG

tag: time

value: peripheral blood

tag: cell type

value: leukocytes


title: 262_OR5391_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 311, POST, NGG

description: SAMPLE 28

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: tissue


title: 255_OR5035_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 226, POST, NGG

description: SAMPLE 27

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: disease state

tag: time

tag: cell type


title: AC634 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 522, PRE, NGG

description: SAMPLE 26

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

value: PRE

tag: tissue


title: Whole plant, Mock 3

tag: ecotype

tag: genotype

tag: treatment

value: Mock inoculum

tag: age

tag: treatment time


title: 521, PRE, NGG

description: SAMPLE 25

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: disease state

tag: time

tag: cell type


title: 254_OR5035_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: Whole plant, Treated 3

tag: ecotype

tag: tissue

tag: genotype

tag: treatment

tag: age

tag: treatment time


title: BQ6136 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: Whole plant, Mock 1


title: Whole plant, Mock 2


title: 253_OR5035_0

description: mouse liver RNA


title: 525, PRE, NGG

description: SAMPLE 24

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: disease state

tag: time


title: AC087-6/25/2002-33 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 524, PRE, NGG

description: SAMPLE 23

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: tissue

tag: cell type


title: BQ0436 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: NoTumor scRNA LN

city: Palo Alto

first: Nathan

middle: Edward

last: Reticker-Flynn

state: CA

address: 3373 Hillview Ave

department: Pathology

institute: Stanford University

description: LNs were harvested in HBSS supplemented with 2% FBS (HBSSF) on ice. LNs were subjected to mincing and digestion with Collagenase 4 (Worthington) in RPMI-1640 for 10 minutes at 37°C prior to dissociation on 70μm strainers. Suspensions were washed twice with HBSSF, counted, and resuspended in PBS + 0.04% bovine serum albumin (Sigma). 10X Genomics library preparation was performed according to the manufacturer’s protocol by the Stanford Genome Sequencing Service Center.

data_processing:
Raw sequencing reads were filtered and adapters trimmed using Trimmomatic v0.36. Quality was assessed using FastQC v0.11.3.
Transcript abundance was quantified using Salmon v0.7.2 in quasi-mapping mode and using the sequence, GC, and position bias correction parameters.
Differential expression analysis was performed using DESeq2.
Assembly: GRCm38 GENCODE release M11
Supplementary files format and content: tab-delimeted files contain TPM values for each sample generated by Salmon

source_name: lymph node

growth_protocol: All cell lines are grown in DMEM supplemented with 10% FBS, glutamine, and penicillin/streptomycin

extract_protocol:
Cell lines were trypsinized, washed with complete serum, centrifuged, and washed with PBS. Following washing cell pellets were frozen at -80C. After thawing, cells were resuspended in buffer RLT and lysed using QiaShredders. Extraction was performed using the Qiagen RNEasy Plus mini kit according to the manufacturer's protocol.
Library construction (RNA-seq) was performed by MedGenome using the Illumina TruSeq stranded mRNA kit

tag: strain


title: LN6-987AL scRNA LN


title: 542, PRE, NGG

description: SAMPLE 22

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: disease state

tag: time


title: BQ6115 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 537, PRE, NGG

description: SAMPLE 21

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: tissue

tag: cell type


title: AC\BQ0280 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 544, PRE, NGG

description: SAMPLE 20

tag: disease state

tag: time


title: BQ6144 EV


title: 251_OR5035_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: POLG_G

city: Columbus

first: Matthew

last: Stratton

state: OH

address: 473 W 12th Ave

institute: Ohio State University

data_processing:
Cutadapt/Pearly to remove adapter contamination
FastQC
HISAT2 to map to MM10
Assemble reads in StringTie
edgeR for DE
Assembly: MM10
Supplementary files format and content: 1 excel file with FPKM

molecule: polyA RNA

source_name: Cardiac right ventricle

extract_protocol:
Modified Trizol to on column DNAse Treatment
Illumina TruSeq Stranded Poly(A) capture

tag: genotype

value: POLG Mutant

value: Cardiac right ventricle

tag: Sex

value: female


title: 247_AU8036_600

description: mouse liver RNA


title: 252_OR5035_0

description: mouse liver RNA


title: 248_AU8036_600

description: mouse liver RNA


title: POLG_H


title: POLG_F


title: 554, PRE, NGG

description: SAMPLE 18


title: 543, PRE, NGG

description: SAMPLE 19

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li


title: AC224 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 246_AU8036_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: BQ11019 EV


title: BQ9116 EV


title: POLG_E

tag: genotype

tag: tissue

tag: Sex


title: 527, PRE, NGG

description: SAMPLE 17

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: disease state

tag: time

tag: cell type


title: B16-F0 scRNA LN

tag: strain


title: WT_D

tag: genotype

value: WT

tag: tissue

tag: Sex


title: 244_AU8036_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 555, PRE, NGG

description: SAMPLE 16

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: cd

tag: pb

tag: ni

tag: li


title: 243_AU8036_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: WT_C

tag: genotype

tag: tissue

tag: Sex


title: AC644 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 212, PRE, NGG

description: SAMPLE 15

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: disease state

tag: time

tag: cell type


title: BQ6167 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: AC/BQ353 EV


title: 241_AU8036_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 242_AU8036_0

description: mouse liver RNA


title: WT_B

tag: genotype

tag: tissue

tag: Sex


title: 245_AU8036_600

description: mouse liver RNA


title: WT_A


title: 501, PRE, NGG

description: SAMPLE 13

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: cd

tag: pb

tag: ni

tag: li


title: AC170 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: AC104 EV


title: 428, PRE, NGG

description: SAMPLE 12

tag: disease state

tag: time

tag: tissue

tag: cell type


title: 505, PRE, NGG

description: SAMPLE 11

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: as


title: 167, PRE, NGG

description: SAMPLE 14

tag: age

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: cd

tag: pb

tag: ni

tag: li

tag: disease state

tag: time

tag: tissue

tag: cell type


title: #2AC/BQ134 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: AC080-6/13/2002-33 EV


title: 227_OR3252_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: AC-067 EV


title: 228_OR3252_600

description: mouse liver RNA


title: 220, PRE, NGG

description: SAMPLE 8

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd


title: 267, PRE, NGG

description: SAMPLE 9

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: pb

tag: ni

tag: li

tag: disease state

tag: time

tag: tissue

tag: cell type


title: AC839 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 202, PRE, NGG

description: SAMPLE 7

tag: age

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd


title: AC840 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 226_OR3252_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 225_OR3252_600

description: mouse liver RNA


title: 222_OR3252_0

description: mouse liver RNA


title: 219, PRE, NGG

description: SAMPLE 6

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: pb

tag: ni

tag: li

tag: disease state

tag: time

tag: tissue

tag: cell type


title: 223_OR3252_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: AC061-2/19/2002-33 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 218_OR3032_600

description: mouse liver RNA


title: AC081 EV


title: AC060 EV


title: 221_OR3252_0

description: mouse liver RNA


title: 280, PRE, NGG

description: SAMPLE 5

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: al

tag: as

tag: cd


title: 255, PRE, NGG

description: SAMPLE 4

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: pb

tag: ni

tag: li

tag: disease state

tag: time

tag: tissue

tag: cell type


title: 197, PRE, NGG

description: SAMPLE 3

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml


title: 511, PRE, NGG

description: SAMPLE 10

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: disease state


title: AC-054 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 224_OR3252_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 216_OR3032_600

description: mouse liver RNA


title: 214_OR3032_0

description: mouse liver RNA


title: BQ8123 EV


title: AC/BQ294 EV


title: 226, PRE, NGG

description: SAMPLE 1

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: hdl (mg/dl)

tag: ldl (mg/dl)

tag: triglycerides (mg/dl)

tag: insulin ui/ml

tag: time

tag: tissue

tag: cell type


title: AC250 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: 217_OR3032_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 215_OR3032_600

description: mouse liver RNA


title: 311, PRE, NGG

description: SAMPLE 2

tag: age

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: stature (m)

tag: bm (kg)

tag: wc (cm)

tag: hc (cm)

tag: bmi (kg/m2)

tag: efe (repetitions)

tag: sas (repetitions)

tag: agility (sec)

tag: 6mwt (m)

tag: uric acid (mg/dl)

tag: cholesterol (mg/dl)

tag: glucose (mg/dl)

tag: al

tag: as

tag: cd

tag: pb

tag: ni

tag: li

tag: disease state


title: #2BQ6114 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: BQ0422 EV


title: Genomic DNA from 293T-TFAP4

city: Yokohama

first: Yurina

last: Miyajima

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: SAMPLE 50

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

data_processing:
GenomeStudio software v2010.3
the 'processed data.txt' contains Average Beta.
the 'matrix signal intensities' contains unmethylated and methylated signal intensities.

label_protocol: Standard Illumina Protocol

growth_protocol: 293T cells were provided from RIKEN Bioresource Center (BRC) and were cultured in Dulbecco's modified Eagle's medium (DMEM) (Wako), supplemented with 10% FBS and penicillin/streptomycin (100 U/ml, 100 µg/ml) (Life Technologies).

extract_protocol: genomic DNA was extracted and purified using NucleoSpin Tissue (Macherey-Nagel) according to standard instructions

treatment_protocol: 293T cells were transduced genes of interest by using lentivirus vector system. Transduced cells were purified by antibiotics.

tag: cell line background

tag: source gender

value: Female

tag: tissue source

value: Kidney

tag: developmental stage

value: Embryo

tag: transduction


title: Genomic DNA from 293T-TCF21

description: SAMPLE 49


title: 213_OR3032_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: MWA+TIGIT

city: changzhou

first: yaping

last: chen

address: 185 juqian street

institute: soochow university

description: single cell rnaseq of sorted cd45 positive cells in tumor tissue

data_processing:
raw data were processed by cellranger 6.1.1
Genome_build: mm10
Supplementary_files_format_and_content: standard single cell format

source_name: CD45+ immune cells

growth_protocol: MC38 tumor cells were subcutaneously inoculated into the bilateral flanks of C57BL/6 mice.

extract_protocol:
On day 8 after MWA treatment, tumor on the left side were isolated, digested and isolated CD45+ cells. Libraries were constructed using 10x Genomics.
10X genomics V3.1

treatment_protocol: MWA was only carried out on the tumor on the right flank when the tumor volume reached approximately 300 mm3. TIGIT blockade was administered intraperitoneally three times every 3 days starting 1 day after MWA.

tag: strain

tag: tissue

value: CD45+ immune cells

tag: treatment

value: MWA+anti-TIGIT


title: MWA

value: MWA


title: Genomic DNA from 293T-SPIB

description: SAMPLE 48

value: SPIB


title: Genomic DNA from 293T-SPI1

description: SAMPLE 47


title: Genomic DNA from 293T-RUNX2

description: SAMPLE 46


title: WTSPL3

city: Beijing

first: Mingyang

address: 95 YongAn Road, Xicheng District

institute: Beijing Friendship Hospital, Capital Medical University

description: γδ T cells from spleen of healthy control

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v2.3.4.2
The read numbers of the corresponding genes were counted via HTSeq v0.6.1.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
γδ T cells from spleen and skin draining LN were isolated via FACS, and RNA was harvested using Qiagen RNeasy MinElute Cleanup Kit (Cat NO. 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male C57BL/6 mice were shaved and treated with a topical dose of 62.5mg imiquimod cream (3M) on their back for six consecutive days. At day 7, mice were sacrificed.

value: Spleen

value: healthy control


title: WTSPL2


title: 212_OR3032_0

city: Chapel Hill

first: Merrie

address: 301 Pharmacy Lane, Kerr Hall CB#7569

institute: UNC Eshelman School of Pharmacy

description: mouse liver RNA

data_processing: Probes containing SNPs in the genome of 45 CC strains were masked using the “kill-list” option in the APT module “apt-probeset-summarize”. Affymetrix CEL files were normalized using the Robust Multi-array Average (RMA) method with log2 transformation implemented in Affymetrix Power Tools (APT, v 1.17.0). A second pre-filtering step was then performed to eliminate lowly expressed probe sets defined as the maximum of log2 transformed expression level across samples less than an empirically chosen cutoff. Principal component analysis (PCA) and hierarchical clustering was used to evaluate the overall performance of the arrays. Seven (7) animals were identified as outliers (strains CC004, CC010, CC023, CC027, CC028, CC042, CC053, one animal each strain) and were removed from subsequent analysis.

extract_protocol: Total cellular RNA was isolated using Trizol reagent (Invitrogen) and further purified using the QIAcube automated system (Qiagen). Following purification, the quantity of RNA was determined spectrophotometrically and the integrity of the RNA was evaluated with the Agilent 2100 Bioanalyzer.


title: 207_IL16912_600

description: mouse liver RNA


title: 208_IL16912_600

description: mouse liver RNA


title: BQ6140 EV

tag: condition

value: Healthy Subject

value: Entire cardiovascular system

value: extracellular vesicle

value: Homebrew Kit


title: WTLN3

description: γδ T cells from lymphonode of healthy control

source_name: Lymphonode

value: Lymphonode


title: WTSPL1


title: 206_IL16912_600

description: mouse liver RNA


title: BQ0499 EV

tag: anatomical location


title: BQ6129 EV

tag: rna source


title: 205_IL16912_600

description: mouse liver RNA


title: 204_IL16912_0

description: mouse liver RNA


title: WTLN2


title: BQ0497 EV

tag: rna isolation kit


title: Genomic DNA from 293T-PTF1A

description: SAMPLE 45

tag: cell line background


title: BQ11002 EV


title: BQ9120 EV


title: #2BQ8119 EV


title: Genomic DNA from 293T-NR5A1

description: SAMPLE 42

tag: source gender


title: WTLN1


title: 211_OR3032_0

description: mouse liver RNA


title: 203_IL16912_0

description: mouse liver RNA


title: IMQSPL3

description: γδ T cells from spleen of IMQ-treated mice

value: imiquimod(IMQ) induced psoriasis


title: Genomic DNA from 293T-NRL

description: SAMPLE 43

tag: tissue source

value: NRL


title: 202_IL16912_0

description: mouse liver RNA


title: IMQSPL2


title: Genomic DNA from 293T-NR2F6

description: SAMPLE 40

tag: developmental stage


title: BQ11045 EV


title: Genomic DNA from 293T-PAX8

description: SAMPLE 44

tag: transduction


title: 201_IL16912_0

description: mouse liver RNA

tag: unc line name


title: Genomic DNA from 293T-NR1H4

description: SAMPLE 39


title: 199_IL16750_600

description: mouse liver RNA

tag: unc alias


title: Genomic DNA from 293T-NR4A1

description: SAMPLE 41


title: 198_IL16750_600

description: mouse liver RNA

tag: dose (mg/kg)


title: BQ0474 EV


title: Genomic DNA from 293T-NFIB

description: SAMPLE 37

value: NFIB


title: IMQSPL1


title: IMQLN3

description: γδ T cells from lymphonode of IMQ-treated mice


title: Genomic DNA from 293T-NFIX

description: SAMPLE 38

value: Female

value: NFIX


title: IMQLN2


title: Genomic DNA from 293T-NFE2

description: SAMPLE 35

value: Kidney

value: Embryo


title: AC075 EV


title: BQ211 EV


title: 196_IL16750_600

description: mouse liver RNA

tag: strain pair #


title: AC085 EV


title: IMQLN1


title: f1_tg_lfd_male_RNA_rep2

city: Sainte-Anne-de-Bellevue

first: Anne-Sophie

last: Pépin

state: QC

address: 21111 Lakeshore road

department: Department of Pharmacology and Therapeutics

country: Canada

institute: McGill University

data_processing:
ChIP:Sequencing reads were trimmed using Trimmomatic on single-end mode to remove adapters and filter out low-quality reads (version 0.36, parameters: 2:30:15 LEADING:30 TRAILING:30) (Bolger, Lohse and Usadel, 2014). Trimmed reads were aligned to the Mus Musculus mm10 genome assembly using Bowtie2 (version 2.3.4) (Salzberg, 2013). Unmapped reads were removed using SAMtools (version 1.9) (Li et al., 2009), and those with 3 mismatches or more were filtered out using Perlcode. BAM coverage files (BigWig) were generated using deeptools2 bamCoverage function (version 3.2.1, parameters: -of bigwig -bs 25 -p 20 --normalizeUsing RPKM -e 160 --ignoreForNormalization chrX) (Ramírez et al., 2016).
RNA: Reads were trimmed using Trim Galore (version 0.5.0, parameters for HiSeq: --phred33 --length 36 -q 5 --stringency 1 -e 0.1; parameters for NovaSeq: --paired --retain_unpaired --phred33 --length 36 -q 5 --stringency 1 -e 0.1) (Krueger, 2015). Trimmed reads were aligned to the Ensembl Genome Reference Consortium mouse reference 38 (GRCm38) primary assembly using hisat2 (version 2.1.0, parameters: -p 8 --dta) (Kim, Langmead and Salzberg, 2015). Aligned files with SAM format were converted to binary SAM format (BAM) and sorted by genomic position using SAMtools (version 1.9) (Li et al., 2009). Transcripts were assembled and gene abundances calculated using Stringtie (version 2.1.2, parameters: -p 8 -e -B -A) (Pertea et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, gtf [fpkm, tpm]

source_name: Liver

extract_protocol: Livers were collected at necropsy and the left lateral lobe was used for RNA extraction. RNA extraction was performed using Qiagen’s RNeasy Mini Kit following the manufacturer’s protocol.

treatment_protocol: Wildtype or KDM1A transgenic male mice were fed either a low- or high-fat diet (10% or 60% kcal fat, respectively) for 10-12 weeks starting at weaning. All females used for breeding and all F1 and F2 were fed a regular chow diet.

value: Liver

tag: age

value: 22 weeks

tag: genotype

value: Paternal KDM1A transgenic

tag: diet

value: Paternal low-fat diet

tag: Sex

value: male

tag: generation


title: AC049 EV

tag: condition

value: Healthy Subject

tag: anatomical location


title: Genomic DNA from 293T-NEUROD1

description: SAMPLE 34


title: f1_tg_lfd_male_RNA_rep3

tag: strain

tag: tissue


title: Genomic DNA from 293T-MYOG

description: SAMPLE 33

tag: cell line background

tag: source gender

value: MYOG


title: f1_tg_lfd_female_RNA_rep3

value: female


title: f1_tg_lfd_male_RNA_rep1


title: AC194 EV

value: Entire cardiovascular system

tag: rna source

value: extracellular vesicle

tag: rna isolation kit

value: Homebrew Kit


title: 194_IL16750_0

last: Mosedale

description: mouse liver RNA

tag: unc line name

tag: study pair #


title: 192_IL16750_0

description: mouse liver RNA

tag: unc alias

tag: dose (mg/kg)


title: 190_IL16750_0

description: mouse liver RNA

tag: strain pair #


title: Genomic DNA from 293T-MYF6

description: SAMPLE 32

tag: tissue source

tag: developmental stage

tag: transduction


title: 187_IL16680_600

description: mouse liver RNA


title: 188_IL16680_600

description: mouse liver RNA


title: AC0024 EV


title: Genomic DNA from 293T-NFE2L2

description: SAMPLE 36


title: AC249 EV


title: 186_IL16680_600

description: mouse liver RNA


title: 2BQ0381 EV


title: Genomic DNA from 293T-MSC

description: SAMPLE 31

value: MSC


title: Genomic DNA from 293T-LEF1

description: SAMPLE 30


title: f1_tg_lfd_female_RNA_rep2

tag: age

tag: genotype

tag: diet

tag: Sex

tag: generation


title: f1_tg_lfd_female_RNA_rep1

tag: strain

tag: tissue


title: f1_tg_hfd_male_RNA_rep3

value: Paternal high-fat diet


title: Genomic DNA from 293T-IRF8

description: SAMPLE 29

tag: cell line background

tag: source gender

value: Female


title: BQ8104 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: AC-059 EV


title: f1_tg_hfd_male_RNA_rep2


title: AC094 EV


title: 185_IL16680_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: Genomic DNA from 293T-IKZF3

description: SAMPLE 28

tag: tissue source

tag: developmental stage

tag: transduction


title: 184_IL16680_0

description: mouse liver RNA


title: f1_tg_hfd_male_RNA_rep1

tag: age

tag: genotype

tag: diet

tag: Sex

tag: generation


title: 182_IL16680_0

description: mouse liver RNA


title: 183_IL16680_0

description: mouse liver RNA


title: 2BQ0293 EV

tag: condition


title: Genomic DNA from 293T-HOXC9

description: SAMPLE 27

tag: cell line background

tag: source gender


title: Genomic DNA from 293T-HOXA9

description: SAMPLE 26


title: BQ0006 EV

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: ACBQ0279 EV


title: f1_tg_hfd_female_RNA_rep3

tag: strain

tag: tissue


title: f1_tg_hfd_female_RNA_rep2


title: Genomic DNA from 293T-GATA6

description: SAMPLE 25


title: 181_IL16680_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: AC/BQ278 EV


title: 178_OR15155_600

description: mouse liver RNA


title: 177_OR15155_600

description: mouse liver RNA


title: Genomic DNA from 293T-GATA3

description: SAMPLE 24

tag: tissue source

tag: developmental stage

tag: transduction


title: f1_crwt_lfd_male_RNA_rep3

tag: age

tag: genotype

value: Wildtype

tag: diet

tag: Sex

tag: generation


title: BQ11028 EV

tag: condition

tag: anatomical location

tag: rna source


title: AC618 EV

tag: rna isolation kit


title: Genomic DNA from 293T-FOXP1

description: SAMPLE 23

tag: cell line background

tag: source gender

value: Kidney


title: 176_OR15155_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)


title: f1_tg_hfd_female_RNA_rep1

tag: strain

tag: tissue


title: f1_crwt_lfd_male_RNA_rep2


title: BQ6133 EV


title: Genomic DNA from 293T-FOXA2

description: SAMPLE 22

tag: tissue source

tag: developmental stage

value: Embryo

tag: transduction


title: f1_crwt_lfd_male_RNA_rep1

value: Liver

tag: age

tag: genotype

tag: diet


title: Genomic DNA from 293T-FOSL2

description: SAMPLE 20


title: AC103 EV

tag: condition


title: Genomic DNA from 293T-FOXA1

description: SAMPLE 21


title: 175_OR15155_600

description: mouse liver RNA

tag: strain pair #

tag: study pair #


title: f1_crwt_lfd_female_RNA_rep3

value: 22 weeks

tag: Sex

tag: generation


title: BQ/2AC0245 EV

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: f1_crwt_lfd_female_RNA_rep2


title: 172_OR15155_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)


title: Genomic DNA from 293T-FOSB

description: SAMPLE 19

tag: cell line background

tag: source gender

tag: tissue source

value: FOSB


title: BQ/AC0463 EV


title: Genomic DNA from 293T-FEV

description: SAMPLE 18

tag: developmental stage

tag: transduction

value: FEV


title: 174_OR15155_0

description: mouse liver RNA


title: BQ258 EV


title: 173_OR15155_0

description: mouse liver RNA


title: 171_OR15155_0

description: mouse liver RNA


title: f1_crwt_lfd_female_RNA_rep1

tag: strain

tag: tissue

tag: age

tag: genotype

tag: diet

value: Paternal low-fat diet


title: f1_crwt_hfd_male_RNA_rep3

tag: Sex

value: male

tag: generation


title: Genomic DNA from 293T-ETV7

description: SAMPLE 17


title: Genomic DNA from 293T-ETV6

description: SAMPLE 16


title: f1_crwt_hfd_male_RNA_rep2


title: BQ9115 EV

tag: condition

value: Healthy Subject

tag: anatomical location

tag: rna source


title: 168_IL16557_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: strain pair #

tag: study pair #


title: 167_IL16557_600

description: mouse liver RNA

tag: dose (mg/kg)


title: Genomic DNA from 293T-ETV1

description: SAMPLE 14

tag: cell line background

tag: source gender

tag: tissue source

tag: developmental stage


title: f1_crwt_hfd_female_RNA_rep3

tag: strain

tag: tissue

tag: age

value: female


title: Genomic DNA from 293T-ETV4

description: SAMPLE 15

tag: transduction


title: f1_crwt_hfd_female_RNA_rep2

tag: genotype

tag: diet

tag: Sex

tag: generation


title: 2BQ0201 EV

tag: condition

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

tag: rna isolation kit


title: Genomic DNA from 293T-ETS2

description: SAMPLE 13


title: 166_IL16557_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)

tag: strain pair #

tag: study pair #


title: 165_IL16557_600

description: mouse liver RNA


title: BQ0435 EV

value: extracellular vesicle


title: f1_crwt_hfd_female_RNA_rep1

tag: strain


title: 163_IL16557_0

description: mouse liver RNA


title: Genomic DNA from 293T-ETS1

description: SAMPLE 12

tag: cell line background

tag: source gender

tag: tissue source

tag: developmental stage


title: BQ6120 EV

value: Homebrew Kit


title: 164_IL16557_0

description: mouse liver RNA


title: AC/BQ0392 EV


title: 162_IL16557_0

description: mouse liver RNA


title: 161_IL16557_0

description: mouse liver RNA


title: f0_tg_lfd_male_RNA_rep6

tag: tissue

tag: age

tag: genotype

value: KDM1A transgenic

tag: diet

value: low-fat diet


title: AC167 EV

tag: condition

tag: anatomical location


title: f0_tg_lfd_male_RNA_rep5

tag: Sex

tag: generation


title: f1_crwt_hfd_male_RNA_rep1

value: Paternal high-fat diet


title: Genomic DNA from 293T-ELF4

description: SAMPLE 10

value: Female

tag: transduction


title: 158_IL16513_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)


title: AC/BQ265 EV

tag: rna source

tag: rna isolation kit


title: BQ8113 EV


title: Genomic DNA from 293T-ELF2

description: SAMPLE 8

tag: cell line background

tag: source gender

value: Kidney


title: f0_tg_lfd_male_RNA_rep4

tag: strain


title: 2BQ0457 EV


title: BQ6109 EV


title: Genomic DNA from 293T-ELF1

description: SAMPLE 7

tag: tissue source

tag: developmental stage

value: Embryo


title: 156_IL16513_600

description: mouse liver RNA

tag: strain pair #

tag: study pair #


title: f0_tg_lfd_male_RNA_rep2

tag: tissue

value: Liver

tag: age

tag: genotype

tag: diet


title: Genomic DNA from 293T-ELK4

description: SAMPLE 11

tag: transduction


title: Genomic DNA from 293T-ELF3

description: SAMPLE 9


title: Genomic DNA from 293T-EHF

description: SAMPLE 6

value: EHF


title: f0_tg_lfd_male_RNA_rep3

value: 22 weeks

tag: Sex

tag: generation


title: f0_tg_hfd_male_RNA_rep6

value: high-fat diet


title: 155_IL16513_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)


title: BQ210 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: AC078 EV


title: Genomic DNA from 293T-EBF1

description: SAMPLE 5

tag: cell line background

tag: source gender

tag: tissue source

tag: developmental stage


title: BQ6119 EV


title: AC/BQ260 EV


title: Genomic DNA from 293T-CDX2

description: SAMPLE 3


title: 152_IL16513_0

description: mouse liver RNA

tag: strain pair #

tag: study pair #


title: AC110 EV


title: AC-063 EV


title: 154_IL16513_0

description: mouse liver RNA


title: 153_IL16513_0

description: mouse liver RNA


title: f0_tg_lfd_male_RNA_rep1

tag: strain

tag: tissue

tag: age

tag: genotype

tag: diet


title: f0_tg_hfd_male_RNA_rep3

tag: Sex

tag: generation


title: 157_IL16513_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: dose (mg/kg)


title: 151_IL16513_0

description: mouse liver RNA


title: BQ0277 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: f0_tg_hfd_male_RNA_rep2


title: 148_IL16441_600

description: mouse liver RNA


title: f0_tg_hfd_male_RNA_rep5


title: Genomic DNA from 293T-CEBPE

description: SAMPLE 4

tag: cell line background

tag: source gender

tag: tissue source

tag: developmental stage

tag: transduction

value: CEBPE


title: f0_tg_hfd_male_RNA_rep4

tag: strain

tag: tissue

tag: age

value: male


title: f0_tg_hfd_male_RNA_rep1

tag: genotype

tag: diet

tag: Sex


title: 145_IL16441_600

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: strain pair #

tag: study pair #


title: AC086 EV

tag: condition

value: Healthy Subject

tag: anatomical location

tag: rna source


title: CAM20.0156

city: Toronto

first: Yasin

last: Mamatjan

state: Ontario

address: 610 University Ave.

institute: Princess Margaret Cancer Center

description: Tumor methylation

hyb_protocol: Samples were fragmented, amplified and hybridized to the Illumina Infinium MethylationEPIC BeadChip as per standard Illumina protocols.

scan_protocol: per standard Illumina protocols

data_processing: Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version minfi_1.36.0). Beta values were calculated for each probe across all samples after post-processing.

source_name: fresh-frozen human meningioma

label_protocol: 250-500 ng of converted DNA was used as input, and labelled as per standard Illumina protocols.

extract_protocol: Genomic DNA was extracted from fresh-frozen tumor specimens and 250-500ng of bisulfite-treated DNA (EZ DNA Methylation Kit, Zymo, California, USA) per sample was used to obtain genome-wide DNA methylation profiles

treatment_protocol: During sample processing, genomic DNA from each specimen was processed.

value: meningioma

tag: molecule subtype

value: bisulfite-treated DNA


title: CAM20.0155

description: Tumor methylation


title: f0_crwt_lfd_male_RNA_rep6

value: Wildtype

tag: generation


title: 2BQ0453-8/11/2008-33 EV

last: Wang

description: EXR-KWANG1plasmaEV2BQ0453h8f11f2008h33-BS

value: Entire cardiovascular system

value: extracellular vesicle

tag: rna isolation kit

value: Homebrew Kit


title: CAM20.0154

description: Tumor methylation


title: f0_crwt_lfd_male_RNA_rep5

value: low-fat diet


title: Genomic DNA from 293T-ASCL2

description: SAMPLE 2

tag: cell line background

tag: source gender

value: Female

tag: tissue source

tag: developmental stage

tag: transduction


title: Genomic DNA from 293T mock

description: SAMPLE 1

value: Kidney

value: mock lentivirus vector


title: 144_IL16441_0

description: mouse liver RNA

tag: dose (mg/kg)


title: 147_IL16441_600

description: mouse liver RNA


title: f0_crwt_lfd_male_RNA_rep4

tag: strain

tag: tissue

value: Liver

tag: age

tag: genotype

tag: diet

tag: Sex


title: 143_IL16441_0

description: mouse liver RNA

tag: unc line name

tag: unc alias

tag: strain pair #

tag: study pair #


title: CAM20.0152

description: Tumor methylation

tag: molecule subtype


title: f0_crwt_lfd_male_RNA_rep3

tag: generation


title: BQ6127 EV

tag: condition

tag: anatomical location

tag: rna source

tag: rna isolation kit


title: AC108 EV


title: 146_IL16441_600

description: mouse liver RNA

tag: dose (mg/kg)


title: CAM20.0129

description: Tumor methylation


title: 142_IL16441_0

description: mouse liver RNA


title: f0_crwt_lfd_male_RNA_rep2

tag: strain


title: #2BQ8117 EV


title: f0_crwt_lfd_male_RNA_rep1

tag: tissue


title: CAM20.0128

description: Tumor methylation


title: f0_crwt_hfd_male_RNA_rep6

tag: age


title: AC036-2/28/2002-43 EV


title: BQ/AC0472 EV


title: f0_crwt_hfd_male_RNA_rep5

tag: genotype


title: 138_OR13140_600

description: mouse liver RNA


title: AC-1055 EV


title: ACBQ0439 EV


title: 141_IL16441_0

description: mouse liver RNA


title: CAM20.0153

description: Tumor methylation


title: CAM20.0126

description: Tumor methylation


title: 136_OR13140_600

description: mouse liver RNA


title: 137_OR13140_600

description: mouse liver RNA


title: CAM20.0125

description: Tumor methylation


title: 135_OR13140_600

description: mouse liver RNA


title: f0_crwt_hfd_male_RNA_rep4

tag: diet


title: BQ339 EV


title: CAM20.0124

description: Tumor methylation


title: CAM20.0122

description: Tumor methylation


title: CAM20.0127

description: Tumor methylation


title: f0_crwt_hfd_male_RNA_rep3

tag: Sex


title: f0_crwt_hfd_male_RNA_rep2


title: AC068-3/26/2002-33 EV


title: f0_crwt_hfd_male_RNA_rep1


title: CAM20.0120

description: Tumor methylation


title: #2AC/BQ137 EV


title: 134_OR13140_0

description: mouse liver RNA

tag: unc line name


title: CAM20.0119

description: Tumor methylation