title: Ric4

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Fastq file were mapped to Mus muculus genome GRCm38 (mm10) using STAR version 2.5.1b.
HTSeq-Counts command was then used to count the number of reads mapped to each gene.
The gene expression matrix was then generated based on the gene counts file for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw gene counts for each sample

source_name: Foxp3-deficient Rictor-deficient Treg cells

growth_protocol: Cells were directly isolated ex-vivo from the spleen of 4 weeks old female mice.

extract_protocol:
Total RNA was extracted and converted into double-stranded DNA (dsDNA), using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). dsDNA was then fragmented to 200- to 300-bp-sized fragments, using M220 Focused-ultrasonicator (Covaris), and these were used for the construction of libraries for Illumina sequencing.
Libraries were prepared from the extracted RNA using  the KAPA mRNA-Seq Kit (KAPA Biosystems, Wilmington, MA) per the manufacturers’ instructions.

treatment_protocol: Splenic Treg (CD4+RFP+ or CD4+YFP+) cells were double-sorted from 4 weeks old female Foxp3∆EGFPiCre/RFPR26YFP and Foxp3∆EGFPiCre/+Rictor∆/∆R26YFP mice. (n=4 per group). Cells were collected directly into TRIzol (Invitrogen).

value: Foxp3-deficient Rictor-deficient

tag: cell type


title: Ric3

status: Public on Apr 08 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype/variation

value: Splenic Treg (CD4+RFP+ or CD4+YFP+) cells


title: Ric5


title: mCre-pTm-R1

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
Illumina pipeline software v1.8 was used for base calling.
Raw fastq files were analyzed using Kallisto 0.43.0 ( -t 20 --single -l 300 -s 100 -b 100)
Kallisto output was used to test transcripts for expression differences using the Sleuth Wald test.
Files were compiled using R.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated files represent the adjusted q value for each condition and the beta value estimated by Sleuth

source_name: Splenic basophils

growth_protocol: Basophil isolation from female McpteCre +/- or -/-  DNMAML+/+ mice on B6 background from spleen, by digestion and flow sorting

extract_protocol:
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Diretional RNA-seq libraries were prepared from 25ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Naïve or day 14 T. muris infection (200 eggs), with IL-3 complex treatment on d-5 and d-2 before harvest to expand basophil numbers.

tag: genotype

value: Mcpt8Cre+/- DNMAML+/+

tag: condtion

value: d14 Trichuris muris infection IL-3c

tag: Sex

value: female

tag: background strain


title: genomic DNA from nevus sample 1341

type: genomic

city: Chapel Hill

first: Nancy

last: Thomas

state: NC

address: 405 Mary Ellen Jones Building

department: Dermatology

institute: University of North Carolina at Chapel Hill

description: nevus sample

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

scan_protocol: BeadArrays were imaged with the HiScan system using standard recommended Illumina scanner setting

data_processing: GenomeStudio M Module software

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: nevus sample

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from FFPE melanocytic samples using a proteinase K-based DNA lysis protocol

tag: tissue

value: nevus

tag: disease state

value: Nevus


title: genomic DNA from nevus sample 823

description: nevus sample


title: pCre-mTm-R3

value: Mcpt8Cre+/+ DNMAML+/+

value: Naïve IL-3c


title: genomic DNA from nevus sample 856

description: nevus sample


title: genomic DNA from nevus sample 862

description: nevus sample


title: deltaIcre5

source_name: Foxp3-deficient Treg cells


title: Ctrl_IPF [small RNA-seq]

city: Kaohsiung

first: Wei An

last: Chang

address: No.100, Shihcyuan 1st Rd., Sanmin Dist., Kaohsiung City 80708, Taiwan (R.O.C.)

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
Illumina official tool, BCL2FASTQ conversion Software v2.20 was used to convert BCL files from the Illumina sequencing platform.
TRIMMOMATIC v0.36 was used to clip the 3' adaptor sequence, trim low quality bases and discard reads shorter than 18 nucleotides.
BOWTIE v1.1.0 was used to align qualified reads on the reference genome sequence.
MiRDeep2 was used to estimate expression levels of known miRNAs, and also identifies novel miRNAs.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: excel files include miRNA ID, precursor miRNA ID, raw reads count and RPM values for each samples

source_name: Fibroblasts

growth_protocol: Human IPF lung fibroblasts (Disease Human Lung Fibroblasts, Idiopathic Pulmonary Fibrosis. Catalog No. CC-7231), purchased from Lonza Inc. (Walkersville, MD, USA), were incubated at 37°C in a 5% CO2-containing incubator in FGM™-2 Fibroblast Growth Medium-2 Bulletkit™ (Lonza, Catalog No. CC-3132) containing 0.5 mL human fibroblast growth factor-basic (hFGF-B), 0.5 mL insulin, 10 mL fetal bovine serum, and 0.5 mL GA-1000. The medium was changed every 2-3 days and the cells were passaged at 80-90% confluence for the following experiments.

extract_protocol:
total RNAs from Ctrl_IPF fibroblasts, Nintedanib_2uM_IPF fibroblasts and Nintedanib_4uM_IPF fibroblasts were extracted by Trizol Reagent according to the manufacturer’s instructions.
All RNA Sample preparation procedures were carried out according to the official Illumina protocol.  Agilent's SureSelect Strand-Specific RNA Library Preparation Kitwere used for library construction followed by AMPure XP Beads size selection.  The sequence was directly determined using Illumina's sequencing-by-synthesis (SBS) technology. Sequencing data (FASTQ files) were generated by Welgene's pipeline based on Illumina's basecalling program bcl2fastq v2.2.0.

treatment_protocol: Nintedanib (BIBF1120, Catalog No. S1010), purchased from Selleckchem (Houston, TX, USA), was dissolved in dimethyl sulfoxide (DMSO) (Sigma Chemical Co., St. Louis, MO, USA) to obtain various concentrations. The reagents were stored at -20°C until use in the experiments. In nintedanib-treated cultures, cells were treated with 1 μM, 2 μM, and 4 μM nintedanib for 24 h, 48 h, and 72 h. In control cultures, cells were treated with the carrier solvent (0.1% DMSO).

tag: source subject age

tag: gender

value: male

value: Lung

tag: cell line

value: Diseased Human Lung Fibroblasts, Idiopathic Pulmonary Fibrosis (DHLF-IPF)

tag: treatment

value: none (control)


title: genomic DNA from nevus sample 775

description: nevus sample


title: pCre-mTm-R2


title: pCre-mTm-R1


title: genomic DNA from nevus sample 820

description: nevus sample


title: Ric2


title: genomic DNA from nevus sample 828

description: nevus sample


title: deltaIcre4


title: deltaIcre1


title: genomic DNA from nevus sample 855

description: nevus sample


title: mCre-mTm-R3


title: mCre-mTm-R2


title: mCre-mTm-R1


title: WT5

source_name: WT Treg cells

value: wild type


title: genomic DNA from nevus sample 841

description: nevus sample


title: genomic DNA from nevus sample 759

description: nevus sample


title: genomic DNA from nevus sample 749

description: nevus sample


title: WT4


title: genomic DNA from nevus sample 776

description: nevus sample


title: genomic DNA from nevus sample 756

description: nevus sample


title: genomic DNA from melanoma sample 1630

description: melanoma sample

source_name: melanoma sample

value: primary invasive melanoma

value: Melanoma


title: genomic DNA from nevus sample 811

description: nevus sample


title: WT3


title: EEDnull_rep2

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

description:
null2
EEDnull_mm9.transcriptome_rep2

data_processing:
rsem v1.2.4 was used to align reads to mm9 transcriptome and generate expression values
Differentially expressed genes between control cells or cells expressing EZHIP were identified using EBSeq v1.20.0 (PPDE >= 0.95, Fold-change >=2)
Data was normalized using median normalization.
Genome_build: mm9
Supplementary_files_format_and_content: median normalized expression values

growth_protocol: MEFs were grown in Dulbecco's modified Eagle's medium with 10% FBS

extract_protocol:
RNA was isolated using Trizol reagent (IBI)
rRNA was depleted using NEBNext rRNA Depletion kit (E6310L). RNA-Seq libraries were generated using NEB E7530

treatment_protocol: Lentivurses for stable expression of H3.3K27M, and hEZHIPwere transduced in the cells. EED floxed cells were treated with cre-recombinanse hit-and-run lentivirus to generate EED knockout line and a single clone was selected for analyses.

value: Mouse embryonic fibroblasts

value: EED deletion line


title: genomic DNA from melanoma sample 1624

description: melanoma sample


title: EEDnull_rep1

description:
null1
EEDnull_mm9.transcriptome_rep1


title: control_rep2

description:
flox2
control_mm9.transcriptome_rep2

value: parental cells (EED floxed)


title: WT1

value: Splenic Treg (CD4+RFP+ or CD4+YFP+) cells


title: control_rep1

description:
flox1
control_mm9.transciptome_rep1


title: HDN4

type: RNA

city: Gaithersburg

first: Taylor

last: Cohen

state: MD

address: One Medimmune Way

institute: MedImmune

hyb_protocol: The biotin-labeled aRNA was purified with RNA binding beads and then fragmented at 94°C for 35 min in fragmentation buffer (40 mM Tris-acetate, pH 8.2, 100 mM Potassium Acetate and 30 mM Magnesium Acetate). Fragmented aRNA (10 µg) was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Array (Thermo Fisher Scientific) at 45 °C for 18 hrs.

scan_protocol: Affymetrix GeneChip Fluidics Station 450 was used for washing and staining of the arrays, and hybridized arrays were scanned using a GeneChip Scanner 300 7G (Thermo Fisher Scientific) according to the manufacturer’s user guide.

data_processing: Array files were normalized using the RMA method, and analyzed with Limma for differential expression analysis and GAGE for gene set (pathway) enrichment.

label: biotin

source_name: Neutrophil

label_protocol: Briefly, 75 ng of total RNA was reverse transcribed to first strand cDNA with T7-oligo(dT) primer using ArrayScript reverse transcriptase, followed by second strand cDNA synthesis to generate double-stranded cDNA (ds-cDNA). Subsequently, the ds-DNA was used as a template for in vitro transcription to synthesize biotin-labeled antisense-RNA (aRNA) molecules.

extract_protocol: Blood was collected 48h following infection, and high and low density neutrophils were purified by density centrifugation followed by neutrophil purification (Stem Cell Technologies)

treatment_protocol: Specific-pathogen-free 8 week old male BKS.Cg-Dok7<m>+/+Lepr,db>/J (The Jackson Laboratory) were infected IV (S. aureus 5e7 CFU strain SF8300)

tag: sample id

value: high density neutrophil

tag: age

value: 8 weeks


title: HDN1


title: deltaIcre3


title: EZHIP_rep2

description:
orf2
EZHIP_mm9.transcriptome_rep2

value: cells overexprssing EZHIP


title: genomic DNA from melanoma sample 1619

description: melanoma sample


title: genomic DNA from melanoma sample 1625

description: melanoma sample


title: genomic DNA from melanoma sample 1617

description: melanoma sample


title: genomic DNA from melanoma sample 1626

description: melanoma sample


title: genomic DNA from melanoma sample 1623

description: melanoma sample


title: K27M_rep2

description:
k27m2
K27M_mm9.transcriptome_rep2

value: cells overexprssing H3.3K27M


title: EZHIP_rep1

description:
orf1
EZHIP_mm9.transcriptome_rep1


title: HDN2


title: HDN5


title: LDN3

value: low density neutrophil


title: LDN4


title: genomic DNA from melanoma sample 1618

description: melanoma sample


title: LDN1


title: K27M_rep1

description:
k27m1
K27M_mm9.transcriptome_rep1


title: genomic DNA from melanoma sample 1616

description: melanoma sample


title: FB Rep 5

city: New Haven

first: Don

last: Nguyen

state: CT

address: 310 Cedar St

institute: Yale Shcool of Medicine

description:
Sample_EW48
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

data_processing:
Illumina software used for basecalling.
The R1 sequenced reads were trimmed for adaptor sequence, then mapped to mm10 and hg38 whole genome using the BMX-seq pipeline.
Reads mapped uniquely were counted to Gencode annotations for mm10(vM10) and hg38 (v24).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from the gene count matrix and median length of the transcripts of a gene annotation.
Genome_build: mm10 (GRCm38) and hg38 (GRCh38)
Supplementary_files_format_and_content: *.rpkm.csv: Comma-delimited text files include RPKM values for each gene (row) each Sample (column).

source_name: forebrain w/o tumors

growth_protocol: Brain metastatic cells were cultured under the same conditions as their parental lines and as recommended by the American Type Culture Collection. For human cell xenografts, 5-6 week old athymic nu/nu mice were injected intracardially (1-5x10e5 cells in 100ul PBS), subcutaneously (5x10e5 cells in 100ul PBS mixed with 50% growth factor reduce Matrigel).

extract_protocol:
Total RNA was extracted using the RNeasy Lipid Tissue mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Monolayer cell cultures were passaged every 3-4 days and cultured unperturbed for at least three days before harvesting. Tumor tissue was macrodissected including surrounding stromal regions and then flash frozen.

tag: mouse strain

value: athymic nu/nu mice


title: EEDnull Ring1b

description:
EEDnull
Immunoprecipitated DNA

library_source: genomic

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
Data was normalized using RPKM (1000000/aligned reads)
Deeptools was used to generate bigwig files for visuallization
mosaics was used to identify enriched regions of the genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig, bed (peaks)

source_name: Mouse embryonic fibroblasts

extract_protocol:
Cells were crosslinked with 1% PFA for 5 min. Lysed in (15 mM Tris, 1 mM CaCl2, 0.25% TritonX-100), treated with Mnase to genrate mono-nucleosomes. Chromatin was dialyzed against RIPA buffer (10mM Tris, 1% TritonX-100, 0.1% SDS, 0.1% Na-DOC) and supernatant was incubated with antibody overnight. Antibody was caputred using dynabeads for 3 hours. IPed material was eluted by boiling the beads in 1% SDS buffer at 65 degree C, after washing 5 times.
Libraries were constructed according to NEB Next Ultra protocol

treatment_protocol: Lentivurses for stable expression of H3.3K27M, H3.3K27R, hEZHIP were transduced in the cells. EED floxed cells were treated with cre-recombinanse hit-and-run lentivirus to generate EED knockout line and a single clone was selected for analyses.

tag: antibody

value: Ring1b (active motif 39663)


title: FB Rep 4

description:
Sample_EW47
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: HDN3

value: male


title: FB Rep 3

description:
Sample_EW39
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1614

description: melanoma sample


title: Control Ring1b

description:
Control
Immunoprecipitated DNA


title: LDN2


title: FB Rep 2

description:
Sample_EW38
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: K27R Ring1b

description:
K27R
Immunoprecipitated DNA

value: cells overexprssing H3.3K27R


title: LDN5


title: EZHIP Ring1b

description:
EZHIP
Immunoprecipitated DNA


title: genomic DNA from melanoma sample 1608

description: melanoma sample


title: FB Rep 1

description:
Sample_EW37
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: K27M Ring1b

description:
K27M
Immunoprecipitated DNA


title: Control H3K27me3

description:
Control
Immunoprecipitated DNA

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
Data was normalized using the reads aligned to exogenous reference (1000000/aligned reads to dm6)
Deeptools was used to generate bigwig files for visuallization
mosaics was used to identify enriched regions of the genome.
Genome_build: mm9, dm6
Supplementary_files_format_and_content: bigwig, bed (peaks)

value: H2K27me3 (Cell signaling C36B11)


title: EEDnull H3K27me3

description:
EEDnull
Immunoprecipitated DNA


title: genomic DNA from melanoma sample 1605

description: melanoma sample


title: genomic DNA from melanoma sample 1612

description: melanoma sample


title: K27R H3K27me3

description:
K27R
Immunoprecipitated DNA


title: K27M H3K27me3

description:
K27M
Immunoprecipitated DNA


title: EZHIP H3K27me3

description:
EZHIP
Immunoprecipitated DNA


title: genomic DNA from melanoma sample 1615

description: melanoma sample


title: genomic DNA from melanoma sample 1607

description: melanoma sample


title: EEDnull CBX2

description:
EEDnull
Immunoprecipitated DNA

value: CBX2 (Bethyl Lab A302-524A)


title: Control CBX2

description:
Control
Immunoprecipitated DNA


title: EZHIP CBX2

description:
EZHIP
Immunoprecipitated DNA


title: genomic DNA from melanoma sample 1595

description: melanoma sample

value: primary invasive melanoma


title: K27R CBX2

description:
K27R
Immunoprecipitated DNA


title: K27M CBX2

description:
K27M
Immunoprecipitated DNA


title: genomic DNA from melanoma sample 1523

description: melanoma sample

value: Melanoma


title: genomic DNA from melanoma sample 1596

description: melanoma sample


title: genomic DNA from melanoma sample 1299

description: melanoma sample


title: genomic DNA from melanoma sample 1505

description: melanoma sample


title: genomic DNA from melanoma sample 1524

description: melanoma sample


title: genomic DNA from melanoma sample 1599

description: melanoma sample


title: S100A8_4h_replicate 3

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
replicate 3
sample name: 3.4

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization protocol (Illumina)

scan_protocol: Standard scan protocol iScan system (Illumina)

data_processing: Data was normalized using Partek Genomics Suit

source_name: human blood monocytes

label_protocol: Illumina™ TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: Total cellular RNA isolation kit (Macherey-Nagel)

tag: donor

tag: stimulation

value: MRP8 5µg 4h

value: monocytes


title: genomic DNA from melanoma sample 1301

description: melanoma sample


title: LPS_4h_replicate 3

description:
replicate 3
sample name: 3.2

value: LPS 1ng 4h

tag: cell type


title: genomic DNA from melanoma sample 1492

description: melanoma sample


title: S100A9_4h_replicate 3

description:
replicate 3
sample name: 3.5

value: MRP14 5µg 4h


title: Con_4h_replicate 3

description:
replicate 3
sample name: 3.1

value: n 4h


title: genomic DNA from melanoma sample 1295

description: melanoma sample


title: genomic DNA from melanoma sample 1289

description: melanoma sample


title: S100A8_4h_replicate 2

description:
replicate 2
sample name: 2.4


title: S100A9_4h_replicate 2

description:
replicate 2
sample name: 2.5


title: genomic DNA from melanoma sample 1296

description: melanoma sample


title: genomic DNA from melanoma sample 1285

description: melanoma sample


title: S100A89_4h_replicate 2

description:
replicate 2
sample name: 2.3

value: MRP8/14 5µg 4h


title: genomic DNA from melanoma sample 1282

description: melanoma sample


title: genomic DNA from melanoma sample 1284

description: melanoma sample


title: genomic DNA from melanoma sample 1279

description: melanoma sample


title: genomic DNA from melanoma sample 1283

description: melanoma sample


title: genomic DNA from melanoma sample 1298

description: melanoma sample


title: genomic DNA from melanoma sample 1293

description: melanoma sample


title: genomic DNA from melanoma sample 1275

description: melanoma sample


title: LPS_4h_replicate 2

description:
replicate 2
sample name: 2.2


title: S100A9_4h_replicate 1

description:
replicate 1
sample name: 1.5


title: Con_4h_replicate 2

description:
replicate 2
sample name: 2.1


title: 05_KO_2

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

description: Gene expression of olvl28m13 knockout medaka.

hyb_protocol: Labeled cRNA was purified with RNeasy mini spin columns (QIAGEN) and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: After washing with Gene Expression Wash Buffer (Agilent Technologies), the slide glass was scanned on a Microarray Scanner (Agilent Technologies).

data_processing: Microarray data were analyzed using the GeneSpring software (Agilent Technologies).

organism: Oryzias latipes

source_name: olvl28m13 knockout, brain (ventral part of telenchephalon, hypothalamus and pituitary), replicate 2

label_protocol: cDNA synthesis and cRNA labeling reactions were performed with the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: olvl28m13 knockout medaka were generated using CRISPR/Cas9 system.

extract_protocol: Total RNA was prepared from three fish (n=3) to triplicate our observations using RNeasy tissue kit (QIAGEN).

treatment_protocol: Medaka were kept under LD conditions. Ventral part of telenchephalon, hypothalamus and pituitary were pooled from three fish (total 9 fish for each genetypes).

value: female

tag: genotype

value: olvl28m13 knockout


title: genomic DNA from melanoma sample 1265

description: melanoma sample


title: 04_KO_1

source_name: olvl28m13 knockout, brain (ventral part of telenchephalon, hypothalamus and pituitary), replicate 1


title: genomic DNA from melanoma sample 1271

description: melanoma sample


title: genomic DNA from melanoma sample 1267

description: melanoma sample


title: 03_WT_3

description: Gene expression of wild type medaka.

source_name: wild type, brain (ventral part of telenchephalon, hypothalamus and pituitary), replicate 3

value: wild type


title: genomic DNA from melanoma sample 1253

description: melanoma sample


title: 02_WT_2

description: Gene expression of wild type medaka.

source_name: wild type, brain (ventral part of telenchephalon, hypothalamus and pituitary), replicate 2


title: 01_WT_1

description: Gene expression of wild type medaka.

source_name: wild type, brain (ventral part of telenchephalon, hypothalamus and pituitary), replicate 1


title: Nintedanib_4uM_IPF

data_processing:
Illumina official tool, BCL2FASTQ conversion Software v2.20 was used to convert BCL files from the Illumina sequencing platform.
TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases.
Trimmed reads were aligned to the reference genome sequence using HISAT2 v2.1.0 aligner to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
Differential expression analysis was performed using CUFFDIFF of CUFFLINKS package v2.2.1 to produce gene/transcript read count and FPKM profiles for each group of samples, then functional enrichment assay was performed using clusterProfiler v3.6.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: excel files include gene ID, gene type, gene name, EntrezGene ID, locus and FPKM values for each samples

value: Lung

value: Diseased Human Lung Fibroblasts, Idiopathic Pulmonary Fibrosis (DHLF-IPF)

value: 4uM Nintedanib


title: Nintedanib_2uM_IPF

value: male

value: 2uM Nintedanib


title: S100A8_4h_replicate 1

description:
replicate 1
sample name: 1.4


title: 36_brain_d2ZT24_2

description: Gene expression under 48 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (48 h after the transition to LD), replicate 2

growth_protocol: Medaka fish (Oryzias latipes) were obtained from a local dealer and kept outdoor.

extract_protocol: Total RNA was prepared from three fish (n=2) to duplicate our observations using RNeasy tissue kit (QIAGEN).

treatment_protocol: Medaka kept under SD conditions were transferred to LD conditions. Ventral part of telenchephalon, hypothalamus and pituitary were collected from six fish every 4 h for three days during this transition


title: genomic DNA from melanoma sample 1264

description: melanoma sample


title: 06_KO_3

source_name: olvl28m13 knockout, brain (ventral part of telenchephalon, hypothalamus and pituitary), replicate 3


title: 35_brain_d2ZT24_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (48 h after the transition to LD), replicate 1


title: Ctrl_IPF

value: none (control)


title: genomic DNA from melanoma sample 1248

description: melanoma sample

value: primary invasive melanoma


title: LPS_4h_replicate 1

description:
replicate 1
sample name: 1.2


title: S100A89_4h_replicate 1

description:
replicate 1
sample name: 1.3


title: 34_brain_d2ZT20_2

description: Gene expression under 44 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (44 h after the transition to LD), replicate 2


title: genomic DNA from melanoma sample 1241

description: melanoma sample

value: Melanoma


title: LD_Riboseq rep2

description: Gene expression under on 16 h after transfer from SD to LD.

data_processing:
RNA-seq reads were aligned to medaka reference genome and annotation (Medaka2.2.4 (15 Nov2016), index and annotation packages) using TopHat (version 2.1.0).
The aligned short reads were counted using cufflinks (version 2.2.1).
Genome_build: Medaka2.2.4 (http://utgenome.org/medaka_v2/#!Medaka_gene_model.md1)
Supplementary_files_format_and_content: Excel file include FPKM for each sample.

growth_protocol: Medaka fish (Oryzias latipes) were obtained from a local dealer and kept under SD conditions.

extract_protocol:
Total RNA and ribosomal protected fragments of ventral part of telenchephalon, hypothalamus and pituitary were isolated with elimination of DNA contamination using DNase.
The cDNA libraries were prepared using TruSeq Ribo Profile Mammalian Library Prep kit (Illumina) following manufacturer protocols.

treatment_protocol: Medaka kept under SD conditions were transferred into LD conditions. After 16 h from the transition, brains (ventral part of telenchephalon, hypothalamus and pituitary) were collected.

tag: growth condition

value: 16 h after transfer from SD to LD.

tag: molecule subtype

value: Ribosomal protected fragments


title: Con_4h_replicate 1

description:
replicate 1
sample name: 1.1

value: monocytes


title: genomic DNA from melanoma sample 1246

description: melanoma sample


title: LD_Riboseq rep1

value: ventral part of telenchephalon, hypothalamus and pituitary


title: 33_brain_d2ZT20_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (44 h after the transition to LD), replicate 1


title: 32_brain_d2ZT16_2

description: Gene expression under 40 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (40 h after the transition to LD), replicate 2


title: genomic DNA from melanoma sample 1237

description: melanoma sample


title: 31_brain_d2ZT16_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (40 h after the transition to LD), replicate 1


title: LD_RNAseq rep1


title: S100A89_4h_replicate 3

description:
replicate 3
sample name: 3.3


title: LD_RNAseq rep2


title: 30_brain_d2ZT12_2

description: Gene expression under 36 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (36 h after the transition to LD), replicate 2


title: genomic DNA from melanoma sample 1278

description: melanoma sample

source_name: melanoma sample


title: genomic DNA from melanoma sample 1242

description: melanoma sample


title: genomic DNA from melanoma sample 1238

description: melanoma sample


title: M.2D Rep 3

description:
Sample_EW42
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

source_name: monolayer cell culture

tag: human cell line


title: 29_brain_d2ZT12_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (36 h after the transition to LD), replicate 1

tag: tissue


title: M.2D Rep 2

description:
Sample_EW41
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1236

description: melanoma sample

tag: disease state


title: 28_brain_d2ZT8_2

description: Gene expression under 32 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (32 h after the transition to LD), replicate 2


title: M.2D Rep 1

description:
Sample_EW40
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1233

description: melanoma sample


title: H.FBMet Rep 2

description:
Sample_EW31
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

organism:
Homo sapiens
Mus musculus

source_name: forebrain with tumors

value: athymic nu/nu mice


title: H.2D Rep 3

description:
Sample_EW26
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: H.FBMet Rep 1

description:
Sample_EW30
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: H.2D Rep 2

description:
Sample_EW25
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: 27_brain_d2ZT8_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (32 h after the transition to LD), replicate 1


title: 26_brain_d2ZT4_2

description: Gene expression under 28 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (28 h after the transition to LD), replicate 2


title: 25_brain_d2ZT4_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (28 h after the transition to LD), replicate 1


title: M.FBMet Rep 2

description:
Sample_EW45
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1232

description: melanoma sample


title: H.FBMet Rep 3

description:
Sample_EW32
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1234

description: melanoma sample


title: A.FBMet Rep 3

description:
Sample_EW36
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: H.2D Rep 1

description:
Sample_EW24
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1239

description: melanoma sample


title: 24_brain_d1ZT24_2

description: Gene expression under 24 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (24 h after the transition to LD), replicate 2


title: genomic DNA from melanoma sample 1223

description: melanoma sample


title: A.2D Rep 3

description:
Sample_EW29
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1219

description: melanoma sample


title: A.FBMet Rep 2

description:
Sample_EW35
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: 23_brain_d1ZT24_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (24 h after the transition to LD), replicate 1


title: A.FBMet Rep 1

description:
Sample_EW33
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: A.2D Rep 2

description:
Sample_EW28
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1231

description: melanoma sample


title: genomic DNA from melanoma sample 1218

description: melanoma sample


title: 22_brain_d1ZT20_2

description: Gene expression under 20 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (20 h after the transition to LD), replicate 2


title: A.2D Rep 1

description:
Sample_EW27
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: FBMet Rep 3

description:
Sample_EW20
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

data_processing:
Illumina software used for basecalling.
The R1 sequenced reads were trimmed for adaptor sequence, then mapped to mm10 and hg38 whole genome using the BMX-seq pipeline.
Reads mapped uniquely were counted to Gencode annotations for mm10 (vM10) and hg38 (v24).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from the gene count matrix and median length of the transcripts of a gene annotation.
Genome_build: mm10 (GRCm38) and hg38 (GRCh38)
Supplementary_files_format_and_content: *.rpkm.csv: Comma-delimited text files include RPKM values for each gene (row) each Sample (column).


title: 21_brain_d1ZT20_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (20 h after the transition to LD), replicate 1


title: HBMet Rep 3

description:
Sample_EW21
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

source_name: hindbrain with tumors


title: 2D Rep 3

description:
Sample_EW3
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: 20_brain_d1ZT16_2

description: Gene expression under 16 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (16 h after the transition to LD), replicate 2


title: HBMet Rep 2

description:
Sample_EW19
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1210

description: melanoma sample


title: genomic DNA from melanoma sample 1216

description: melanoma sample


title: 19_brain_d1ZT16_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (16 h after the transition to LD), replicate 1


title: 2D Rep 1

description:
Sample_EW1
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: 18_brain_d1ZT12_2

description: Gene expression under 12 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (12 h after the transition to LD), replicate 2


title: HBMet Rep 1

description:
Sample_EW17
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1212

description: melanoma sample


title: genomic DNA from melanoma sample 1203

description: melanoma sample


title: 2D Rep 2

description:
Sample_EW2
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: FBMet Rep 1

description:
Sample_EW16
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: WT_villi_scRNAseq

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
FastQC (version 0.11.3) was used to check the quality of raw sequencing reads (fastq)
Alignment: RNA-seq: TopHat2, version 2.1.0; ATAC-seq and ChIP-seq: Bowtie2, version 2.2.6
RNA-seq: Gene and transcript level computation done with CuffQuant, version 2.2.1
RNA-seq: Normalized abundance measurements generated by CuffNorm, version 2.2.1, calculate FPKM values using quartile normalization
RNA-seq: CuffDiff, version 2.2.1, geometric normalization, per-condition dispersion
ATAC-seq and ChIP-seq: Deeptools bamCoverage (v2.4.2, duplicate reads ignored, RPKM normalized and extended reads) was used to generate bigwig files from bam files.
ATAC-seq and ChIP-seq: Model-based Analysis of ChIP-Seq (MACS 1.4.1) was used for peak calling and to generate bed files from aligned reads. Shiftsize parameter was used for MACS based on the fragment size of Pippin Prep.
scRNA-seq: Cell Ranger v2.1.1 used for data processing. Read 1 technical information (26 bp to incorporate the UMIs and cell barcodes), read 2 biological information. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger mkfastq command. Subsequence UMI and cell barcode de-convolution was performed using 10X Genomics’ cellranger count command to generate the final digital gene expression matrices, t-SNE plot, and cloupe files.
Genome_build: mm9 (ChIP-seq); mm10 (scRNA-seq)

source_name: Single cells of WT duodenal villi

extract_protocol:
Freshly harvested duodenum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS at 4 °C. The tissue was then vigorously shaken to release the epithelium from underlying muscular tissue, and the supernatant was collected as the whole epithelium fraction; villi were collected from the top of a 70-μm cell strainer while crypts passed through. Cells were pelleted by centrifugation at 170 g at 4 °C and then washed by cold PBS. To dissociate single cells for single cell RNA-seq, isolated duodenal villi were further rotated with 5U/ml dispase (Stem Cell, #07913) and 200 U/ml of DNase I (Sigma D4513) at 37 °C for 30 min, and then washed by PBS with 1% BSA for twice, and filtered by 40-μm cell strainer. Each sample of dissociated duodenal villi was incubated with Dead Cell Removal MicroBeads (Miltenyi, USA) and passed through a magnetic column, removing the majority of dead cells/debris. The remaining live cells were counted using a trypan blue exclusion count assay with a hemocytometer and diluted for loading onto the Chromium Controller. Loading was performed to target capture of ~3,000 gel beads per sample for downstream analysis, and samples were processed through the Chromium Controller following the standard manufacturer’s specifications.
10X Genomics Chromium Single Cell 3’ v2 kit

treatment_protocol: Mice were injected i.p. with oil (vehicle for tamoxifen) for 2 consecutive days and were sacrificed 1 day after last injection.

value: duodenum villi

value: WT

value: oil vehicle


title: Hnf4ɣKO_Hnf4αChIP_rep2

data_processing:
FastQC (version 0.11.3) was used to check the quality of raw sequencing reads (fastq)
Alignment: RNA-seq: TopHat2, version 2.1.0; ATAC-seq and ChIP-seq: Bowtie2, version 2.2.6
RNA-seq: Gene and transcript level computation done with CuffQuant, version 2.2.1
RNA-seq: Normalized abundance measurements generated by CuffNorm, version 2.2.1, calculate FPKM values using quartile normalization
RNA-seq: CuffDiff, version 2.2.1, geometric normalization, per-condition dispersion
ATAC-seq and ChIP-seq: Deeptools bamCoverage (v2.4.2, duplicate reads ignored, RPKM normalized and extended reads) was used to generate bigwig files from bam files.
ATAC-seq and ChIP-seq: Model-based Analysis of ChIP-Seq (MACS 1.4.1) was used for peak calling and to generate bed files from aligned reads. Shiftsize parameter was used for MACS based on the fragment size of Pippin Prep.
scRNA-seq: Read 1 is 26 bp to incorporate the UMIs and cell barcodes, read 2 is 98 bp for the transcript information. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger mkfastq command. Subsequence UMI and cell barcode de-convolution was performed using 10X Genomics’ cellranger count command to generate the final digital gene expression matrices, t-SNE plot, and cloupe files.
Genome_build: mm9 (ChIP-seq); mm10 (scRNA-seq)

source_name: Hnf4gammaKO duodenum epithelium

extract_protocol:
Freshly harvested duodenum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS at 4 °C. The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The intestine pieces were discard and the supernatant was collected as whole epithelium fraction. Standard procedures were used for ChIP on mouse duodenum epithelial cells. Briefly, cells were isolated by 3mM EDTA/PBS and then cross-linked in 1% formaldehyde for 10 min at 4°C and then for 35 or 50 min at room temperature. Cells were washed with ice-cold PBS, resuspended with lysis buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris pH 8.0, and protease inhibitor cocktails) and further incubated at room temperature for 10 min. Cell lysates were sonicated using a Diagenode Bioruptor to generate 200 bp to 500 bp fragments, as determined by agarose gel electrophoresis. The supernatant of lysates were diluted 8-fold in binding buffer (20 mM Tris pH 8.0, 2 mM EDTA pH 8.0, 150 mM NaCl, 1% Triton X-100, and protease inhibitor cocktails) and incubated with 6 ug of Hnf4alpha (Santa Cruz sc-6556 X, lot #B1015) or Hnf4gamma (Santa Cruz sc-6558 X, lot #F0310) antibody coupled to Dynabeads (Invitrogen) at 4°C overnight. The immunoprecipitates were washed 5 times and rotated at 4°C with RIPA buffer (50 mM HEPES pH 7.6, 1 mM EDTA pH 8.0, 0.7% Na-deoxycholate, 1% NP-40, 0.5M LiCl) and a quick wash with TE buffer (0.1 mM EDTA pH 8.0 and 10 mM Tris pH 8.0). The DNA was recovered by incubating overnight in reverse cross-linking buffer (1% SDS, 0.1 M NaHCO3) at 65 °C. The DNA was purified by QIAquick PCR Purification Kit (QIAGEN) and quantified by using Picogreen (Life Technologies). ChIP enrichment was confirmed with qPCR for putative targets prior to library preparation.
Rubicon Genomics ThruPLEX DNA-seq Kit (Illumina)

value: duodenum epithelium

tag: chip antibody


title: SQ Rep 4

description:
Sample_EW15
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

source_name: subcutaneous tumors


title: WT_DSGFA_input_DNA

source_name: WT duodenum epithelium

extract_protocol:
Freshly harvested duodenum was flushed with cold PBS, opened longitudinally, cut into 1 cm pieces, and then rotated in 3 mM EDTA in PBS at 4 °C. The tissue was then violently shaken to release the epithelium from underlying muscular tissue. The intestine pieces were discard and the supernatant was collected as whole epithelium fraction. Standard procedures were used for ChIP on mouse duodenum epithelial cells. Briefly, cells were isolated by 3mM EDTA/PBS and then cross-linked 2 mM DSG (Thermo 20593) for 45 min, and then further cross-linked in 1% formaldehyde for 20 min at room temperature. Cells were washed with ice-cold PBS, resuspended with lysis buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris pH 8.0, and protease inhibitor cocktails), and further incubated at room temperature for 10 min. Cell lysates were sonicated using a Diagenode Bioruptor to generate 200 bp to 500 bp fragments, as determined by agarose gel electrophoresis. To recover the input DNA, the samples were incubated overnight in reverse cross-linking buffer (1% SDS and 0.1 M NaHCO3) at 65 °C. The DNA was purified by QIAquick PCR Purification Kit (QIAGEN) and quantified with Picogreen (Life Technologies). ChIP enrichment was confirmed with qPCR for putative targets prior to library preparation.
Rubicon Genomics ThruPLEX DNA-seq Kit (Illumina)


title: genomic DNA from melanoma sample 1192

description: melanoma sample

source_name: melanoma sample


title: genomic DNA from melanoma sample 1208

description: melanoma sample


title: M.FBMet Rep 1

description:
Sample_EW43
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

source_name: forebrain with tumors


title: SQ Rep 3

description:
Sample_EW14
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: SQ Rep 2

description:
Sample_EW13
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: 15_brain_d1ZT8_1

description: Gene expression under 8 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (8 h after the transition to LD), replicate 1

tag: gender

value: female


title: 16_brain_d1ZT8_2

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (8 h after the transition to LD), replicate 2


title: 14_brain_d1ZT4_2

description: Gene expression under 4 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (4 h after the transition to LD), replicate 2


title: SQ Rep 1

description:
Sample_EW12
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: 13_brain_d1ZT4_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (4 h after the transition to LD), replicate 1


title: genomic DNA from melanoma sample 1179

description: melanoma sample


title: genomic DNA from melanoma sample 852

description: melanoma sample


title: 12_brain_d0ZT24_2

description: Gene expression under 0 h before the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (0 h before the transition to LD), replicate 2


title: HB Rep 4

description:
Sample_EW11
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

source_name: hindbrain w/o tumors


title: HB Rep 3

description:
Sample_EW9
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: 10_brain_d0ZT20_2

description: Gene expression under 4 h before the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (4 h before the transition to LD), replicate 2


title: genomic DNA from melanoma sample 1202

description: melanoma sample


title: 11_brain_d0ZT24_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (0 h before the transition to LD), replicate 1


title: FB Rep 4

description:
Sample_EW10
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

source_name: forebrain w/o tumors


title: genomic DNA from melanoma sample 848

description: melanoma sample


title: 08_brain_d0ZT16_2

description: Gene expression under 8 h before the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (8 h before the transition to LD), replicate 2


title: HB Rep 2

description:
Sample_EW7
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: FB Rep 3

description:
Sample_EW8
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 1215

description: melanoma sample


title: genomic DNA from melanoma sample 849

description: melanoma sample


title: FB Rep 2

description:
Sample_EW6
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: 09_brain_d0ZT20_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (4 h before the transition to LD), replicate 1


title: 06_brain_d0ZT12_2

description: Gene expression under 12 h before the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (12 h before the transition to LD), replicate 2


title: LD_female_rep2

data_processing:
RNA-seq reads were aligned to medaka reference genome and annotation (Medaka2.2.4 (15 Nov2016), index and annotation packages) using HISAT2 (version 2.0.5).
The aligned short reads were counted using StringTie (version 1.3.3b).
Genome_build: Medaka2.2.4 (http://utgenome.org/medaka_v2/#!Medaka_gene_model.md1)
Supplementary_files_format_and_content: Excel file include FPKM for each sample.

extract_protocol:
Total RNA of ventral part of telenchephalon, hypothalamus and pituitary were isolated with elimination of DNA contamination using DNase.
According to TruSeq Stranded mRNA Sample Preparation Guide (Illumina), the cDNA libraries were prepared using TruSeq stranded mRNA LT sample prep kit (Illumina).

treatment_protocol: Medaka kept under SD conditions were either continuously maintained under SD or transferred into LD conditions. After 16 h from the transition, brains (ventral part of telenchephalon, hypothalamus and pituitary) were collected from six fishes for each condition.

value: under on 16 h after transfer from SD to LD.


title: FB Rep 1

description:
Sample_EW4
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 850

description: melanoma sample


title: LuOt Rep 2

description:
36667
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

source_name: lung tumors

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For orthotopic lung tumors, 1x10^5 cells were injected intratracheally.


title: Hnf4alphagammaDKO_villi_scRNAseq

source_name: Single cells of WT duodenal villi

treatment_protocol: Mice were injected with 100 mg/kg tamoxifen on the first day, 50 mg/kg tamoxifen on the second day, and were harvested 42h after tamoxifen injection

value: 100 mg/kg tamoxifen on the first day and 50 mg/kg tamoxifen on the second day


title: 04_brain_d0ZT8_2

description: Gene expression under 16 h before the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (16 h before the transition to LD), replicate 2


title: Hnf4alphaKOSmad4KO_viili_scRNAseq

treatment_protocol: Mice were injected i.p. with tamoxifen (50mg/kg/day)  for 4 consecutive days and were sacrificed 10 days after the first injection.

value: Villin-CreERT2; Hnf4alphaf/f; Smad4f/f

value: tamoxifen 50mg/kg/day


title: SD_female_rep2

value: under SD condition


title: LuOt Rep 1

description:
36666
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: FBMet Rep 2

description:
Sample_EW18
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: 03_brain_d0ZT8_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (16 h before the transition to LD), replicate 1


title: 17_brain_d1ZT12_1

description: Gene expression under 12 h after the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), LD (12 h after the transition to LD), replicate 1


title: BrMet Rep 3

description:
36674
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

source_name: brain tumors


title: 02_brain_d0ZT4_2

description: Gene expression under 20 h before the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (20 h before the transition to LD), replicate 2


title: BrMet Rep 2

description:
36673
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: 01_brain_d0ZT4_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (20 h before the transition to LD), replicate 1


title: genomic DNA from melanoma sample 693

description: melanoma sample

source_name: melanoma sample

value: primary invasive melanoma


title: genomic DNA from melanoma sample 691

description: melanoma sample

value: Melanoma


title: SD_female_rep1


title: BrMet Rep 1

description:
36672
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv


title: genomic DNA from melanoma sample 690

description: melanoma sample


title: genomic DNA from melanoma sample 793

description: melanoma sample


title: ScRNA-seq of airway macrophages

status: Public on Apr 07 2019

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

description:
1,134 Mixed cells stimulated at 0, 3, 6 days after LPS treatment
In read 1, the location of the UMIs are in nucleotide positions 12-21 of line #2.
In read 1, the location of the barcodes are in nucleotide positions 1-11 of line #2.

data_processing:
Raw cDNA reads in FASTQ files were trimmed using Cutadapt, where 5’ and 3’ quality trimming was carried out (q < 20) and both poly A tails and reads shorter than 25 base pairs were removed.
Trimmed reads were aligned to the hg38 human genome with GSNAP, setting “max-mismatches=0.05” and accounting for both known Ensembl splice sites and SNPs.
We quantified gene expression using HTSeq with “stranded=yes”, “mode=intersection-nonempty”, and “t=gene.”
We summed the number of unique molecular identifiers (UMIs) for each gene across runs to obtain a UMI count matrix that we used for all downstream analysis.
We quantified the number of genes with expression greater than zero in each cell and then removed 222 cells expressing fewer than 2,000 genes. Although samples comprising multiple cells were removed during the cell selection stage, to safeguard against undetected doublets, we removed seven outlier cells expressing > 11,800 genes or > 90,000 UMIs. We removed three additional cells for which < 40% of original reads mapped to a unique gene-annotated region. All remaining cells exhibited unique mapping rates > 50% and expressed genes of which < 30% were aligned to the mitochondrial genome. Prior to downstream analysis, we also removed select mitochondrial and ribosomal genes (those beginning with Mtat, Mt-, Mrpl, Mrps, Rpl, Rps) and very lowly expressed genes (those genes not expressed in at least 0.5% of cells). The final QCed dataset contained 902 cells with a mean of 20,199 UMI’s and 4,832 genes per cell.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Text files containing gene counts and metatadata describing the sample time for each cell
Supplementary_files_format_and_content: Janssen_expression_matrix_full_ENSMUSG.txt:D52
Supplementary_files_format_and_content: Janssen_expression_matrix_culled_mgi.txt:D52

source_name: Airway macrophages

extract_protocol:
Bronchoalveolar lavage (BAL) was performed with 10 serial lavages of 1ml PBS containing 5 mM EDTA. One animal was used for each time point. BAL cells were washed twice in PBS. FcgR was blocked using anti-CD16/CD32 for 20 minutes. For day 3 sample, neutrophils were depleted over a column by binding Ly6G prior to surface staining. Cells were incubated with primary antibody on ice for 30 minutes, washed twice, and then taken to FACS. Dead cells were excluded on the basis of scatter and DAPI exclusion. Monocytes were excluded based on size and light scattering characteristics. Antibodies and cell stains used are as follows: Anti-Ly6G (Biolegend, clone 1A8), anti-CD3 (ThermoFischer Scientific, clone 17A2), anti-CD19 (ThermoFischer Scientific, clone eBio1D3), anti-NK1.1 (ThermoFischer Scientific, clone PK136), DAPI (Biolegend, #422801), anti-CD64 (BD Biosciences, clone X54-5/7.1), anti-CD11c (ThermoFischer Scientific, clone N418), anti-CD11b (ThermoFischer Scientific, clone M1/70), and anti-F4/80 (ThermoFischer Scientific, clone BM8). FACS was performed using a BD FACSAria Cell Sorting System with BD FACSDiva Software (BD Biosciences, Franklin Lake, NJ) on unfixed specimens.
Sorted cells were dispensed into a 5,184-nanowell version 1 microchip using the ICELL8 platform (WaferGen Biosystems, Fremont, CA) from which single cells were selected for library preparation and sequencing. Library preparation was carried out using ICell8 single-cell poly-(A)+ transcriptome amplification hands-on workflow (with Triton X-100 for cell lysis), protocol D07-000040-003 rev4. Libraries were generated for a total of 1,134 selected cells, which were then sequenced as 100 base pair single-end reads on an Illumina HiSeq 2500 (Illumina, Inc., San Diego, CA) in three batches (two flow cell lanes per run).

treatment_protocol: 20 micrograms of LPS (Escherichia coli O55:B5 from List Biological Laboratories, Campbell, CA) in 50 microliters of PBS were instilled directly into the tracheas of mice sedated with isofluorane (Baxter, Deerfield, IL) using a modified feeding needle. Mice were sacrificed using peritoneal injection of pentobarbital sodium solution.

value: FACs sorted airway macrophages

tag: strain

value: 10-12 weeks


title: Moderate_Late_C

city: Rehovot

first: Jonathan

middle: Aryeh

last: Sobel

address: Benoziyo Building for Biological Sciences, room 277S, Weizmann Institute of Science

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of science

data_processing:
Reads were trimmed using cutadapt and mapped to genome mm10 using STAR  v2.4.2a with default parameters.
Counting proceeded over genes annotated in Gencode release mm10 using STAR.
Genome_build: mm10.
Supplementary_files_format_and_content: RNA-seq_raw_counts_Exercise_performance_project.csv
Supplementary_files_format_and_content: Raw read count for each gene in each sample

source_name: gastrocnemius muscle

growth_protocol: All animal experiments and procedures were conducted in conformity with the Institutional Animal Care and Use Committee (IACUC) guidelines. Three months old, males wild type mice were used. Mice were kept under 12 h light/dark regimen and fed either ad libitum or exclusively during the dark or light phase as indicated. ZT0 corresponded to lights on and Z12 to lights off in the animal facility.

extract_protocol:
Gastrocnemius muscles thawed for 1 minute at RT, then transferred to 2 ml TRI-reagent. Tissue was homogenized using disperser (IKA-T18) and then transferred to 1.7 ml tube and stand in RT for 5 minutes. 200 µL chloroform was added to each tissue sample for phase separation. Samples was then centrifuge for 15 minutes at 13,000 rpm at 4?c and transferred to tubes containing 500 µL Isopropanol. The upper phase was then isolated and stand at RT for 15 minutes and later centrifuged at 13,000 RPM at 4?c. Supernatant was removed and samples washed with 1ml of 75% cold EtOH and briefly vortexed. Sampled was then centrifuged for 10 minutes at 8,000 RPM at 4?c, and washed with 1ml of 75% cold EtOH and briefly vortexed. Pellet was dried, and later dissolved in 150 µL UPW. Samples was then incubated at 56 ?c for 10 minutes. RNA concentration was measured using Nanodrop.
The TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA) was used. The libraries were prepared according to the manufacturer’s protocol without further modifications

treatment_protocol: Mice were acclimated to treadmill running (Panlab Harvard Apparatus, Barcelona, Spain) a day prior to the sprint or the endurance exhaustion test: Pre-test: 10 min without movement follows 10 min at 0.1 m/sec with a 0% slope; 0.4mA shock intensity.Sprint cohort: phase I – 5 min at 8 cm/sec with a 0% slope; phase II – increases by 2 cm/sec every min. Mice ran until they reached failure, which was pre-define as 15 shocks per 60 sec or 25 shocks within 90sec or 30 within 120sec. Time to failure was recorded. Endurance  cohort: phase I – 5 min at 8 cm/sec with a 0% slope; phase II – increases by 2 cm/sec every min until reaching a final speed of 20cm/sec. Mice fully performed the high intensity protocol, or performed the moderate intensity test for 1 hour, subsequently their Gastrocnemius muscle was dissected and immediately frozen in liquid nitrogen.

tag: time

value: Late (ZT22)

tag: running protocole

value: Moderate

value: male


title: genomic DNA from melanoma sample 853

description: melanoma sample

data_processing: GenomeStudio M Module software

extract_protocol: Genomic DNA was extracted from FFPE melanocytic samples using a proteinase K-based DNA lysis protocol


title: Moderate_Late_B


title: Moderate_Late_A


title: genomic DNA from melanoma sample 1211

description: melanoma sample


title: Moderate_Early_B

value: Early (ZT14)


title: Moderate_Early_C


title: Moderate_Early_A


title: High_Late_C

value: High


title: High_Late_B


title: genomic DNA from melanoma sample 685

description: melanoma sample


title: genomic DNA from melanoma sample 682

description: melanoma sample


title: genomic DNA from melanoma sample 274

description: melanoma sample


title: genomic DNA from melanoma sample 684

description: melanoma sample


title: High_Late_A


title: 05_brain_d0ZT12_1

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (12 h before the transition to LD), replicate 1


title: LD_female_rep1

value: ventral part of telenchephalon, hypothalamus and pituitary


title: High_Early_C


title: High_Early_A


title: High_Early_B


title: HB Rep 1

description:
Sample_EW5
processed data file: mm10.rpkm.csv
processed data file: hg38.rpkm.csv

source_name: hindbrain w/o tumors

value: athymic nu/nu mice


title: Lalistat_24hr_replicate3

city: Baltimore

first: Wei

last: Shao

state: Maryland

address: 725 N Wolfe Street

department: Cell Biology

institute: Johns Hopkins University School of Medicine

hyb_protocol: Follow Agilent standard procedure. Conducted by Johns Hopkins University SKCCC microarray core

organism: Danio rerio

growth_protocol: Larvae from WT zebrafish mating

extract_protocol: There were 4 larvae each arm. RNA were extracted from 4 larvae using Zymo research Direct-zolTM RNA microPrep kit

treatment_protocol: larvae (5dpf) were treated with vehicle control DMSO (0.05%), U18666A (2uM) or lalistat (25uM) for 24hr

tag: age

tag: treatment

value: Lalistat


title: Basal_Late_B

value: Basal


title: Basal_Late_C


title: DMSO_24hr_replicate3

scan_protocol: Follow Agilent standard procedure. Conducted by Johns Hopkins University SKCCC microarray core

value: DMSO


title: genomic DNA from melanoma sample 273

description: melanoma sample


title: Lalistat_24hr_replicate1

data_processing: Follow Agilent standard procedure. Conducted by Johns Hopkins University SKCCC microarray core


title: DMSO_24hr_replicate2

label_protocol: Follow Agilent standard procedure. Conducted by Johns Hopkins University SKCCC microarray core


title: Lalistat_24hr_replicate2


title: Basal_Late_A


title: U18666A_24hr_replicate1


title: FBS

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

source_name: cultured cells PDAC Pa03c

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

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: Pancreatic ductal adenocarcinoma (PDAC)  cells

value: 10% FBS for 16hr


title: DMSO_24hr_replicate1


title: U18666A_24hr_replicate2


title: LPDS

description: replicate 1

value: 10% LPDS for 16hr


title: DMSO_2hr_replicate2

treatment_protocol: larvae (5dpf) were treated with vehicle control DMSO (0.02%) or lalistat (10uM) for 2hr


title: Basal_Early_C


title: genomic DNA from melanoma sample 228

description: melanoma sample

value: primary invasive melanoma


title: U18666A_24hr_replicate3


title: genomic DNA from melanoma sample 237

description: melanoma sample

value: Melanoma


title: Basal_Early_A


title: genomic DNA from melanoma sample 223

description: melanoma sample


title: DMSO_2hr_replicate1


title: Lalistat_2hr_replicate1

value: lalistat


title: SynCom_50Pi_Rep2_1

status: Public on Apr 06 2019

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

institute: The University of North Carolina at Chapel Hill

data_processing:
bcl2fastq 2.20.0 was used for basecalling
Quality assessment of the sequencing reads was performed using FastQC version 0.11.7
Trimmomatic version 0.36 was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Arabidopsis thaliana TAIR10 genome using HISAT2 version 2.1.0 with default parameters
The program featureCounts from the Subread package was used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis seedlings were grown on Johnson medium and solidified with 1 % bacto-agar. Media were supplemented with Pi (KH2PO4) at distinct concentrations; 1000 µM Pi was used for complete medium (+Pi) and 50 µM Pi was used in the Low Pi medium (-Pi).

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings according to Logemann, J. et al. Anal. Biochem. 163, 16–20 (1987). PMID: 2441623.
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare non-stranded Illumina RNA-seq libraries. Following library preparation, quality control and quantification were performed using a 2100 Bioanalyzer instrument (Agilent) and the Quant-iT PicoGreen dsDNA Reagent (Invitrogen), respectively.

treatment_protocol: Arabidopsis plants were germinated on Johnson medium (0.5 % sucrose) containing 1 mM Pi for 7 days in the vertical position and then transferred to 1000 µM Pi (high) and 50 µM Pi (low) media (without sucrose) in the presence or not of a 185-member  bacterial synthetic community. Plants were grown for another 12 days before harvesting

value: whole seedling

tag: phosphate availability

tag: bacteria presence

value: SynCom

tag: biorep


title: NoBacteria_50Pi_Rep1_3

tag: genotype

value: NoBacteria


title: SynCom_1000Pi_Rep2_2


title: SynCom_50Pi_Rep2_3


title: NoBacteria_50Pi_Rep1_2


title: genomic DNA from melanoma sample 252

description: melanoma sample


title: SynCom_50Pi_Rep2_2


title: SynCom_1000Pi_Rep2_1


title: SynCom_1000Pi_Rep2_3


title: NoBacteria_50Pi_Rep1_1


title: NoBacteria_1000Pi_Rep1_3


title: 07_brain_d0ZT16_1

description: Gene expression under 8 h before the transition to LD.

source_name: brain (ventral part of telenchephalon, hypothalamus and pituitary), SD (8 h before the transition to LD), replicate 1

value: female


title: Lalistat_2hr_replicate2


title: NoBacteria_1000Pi_Rep1_1


title: SynCom_50Pi_Rep1_3


title: SynCom_50Pi_Rep1_2


title: genomic DNA from melanoma sample 268

description: melanoma sample


title: SynCom_50Pi_Rep1_1


title: SynCom_1000Pi_Rep1_2


title: SynCom_1000Pi_Rep1_3


title: SynCom_1000Pi_Rep1_1


title: genomic DNA from melanoma sample 246

description: melanoma sample


title: NoBacteria_50Pi_Rep2_3


title: NoBacteria_50Pi_Rep2_2


title: genomic DNA from melanoma sample 244

description: melanoma sample


title: genomic DNA from melanoma sample 258

description: melanoma sample


title: genomic DNA from melanoma sample 265

description: melanoma sample


title: NoBacteria_1000Pi_Rep2_2


title: NoBacteria_1000Pi_Rep2_3


title: NoBacteria_1000Pi_Rep2_1


title: Root_phf1_high_2

data_processing:
bcl2fastq  2.20.0 was used for basecalling
Quality assessment of the sequencing reads was performed using FastQC version 0.11.7
Trimmomatic version 0.36 was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Arabidopsis thaliana TAIR10 genome using HISAT2 version 2.1.0 with default parameters
The program featureCounts from the Subread package was used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

source_name: Root

growth_protocol: Arabidopsis thaliana ecotype Col-0 and mutants phf1 and phr1 phl1 (both in the Col-0 background) were used. Seeds were surface sterilized (20 min 70% EtOH, 10 s 100% EtOH) and planted directly onto moist soil. Sown seeds were stratified for 3 days at 4 °C before being placed in a greenhouse under short-day conditions (6/18 day-night cycle; 19 to 21 °C) for 8 weeks

treatment_protocol: Each of the three Arabidopsis genotypes was grown in soil from all 18 plots (6 plots per P treatment). In addition, a 4th P regimen designated ‘Low+P’ was created by adding additional P to a set of pots with low P. The amount of P added to these pots is based on the difference in total P between Low and High P plots. The average difference between Low and High P over all the plots is 42 mg P per kg soil [41]. Per pot, this is 12.6 mg P (accounting for 300 g soil per pot). Thus, a 10 ml solution consisting of 4.2 mg P in the form of 20% K2HPO4 and 80% KH2PO4 was added to the pots in 3 applications (Week 2, 4 and 6) before watering (in order to distribute the P through the soil).

value: Root

tag: phosphate fertilization

value: high

tag: plot


title: Root_Col_0_low+Pi_2

value: low+Pi


title: Root_phf1_low+Pi_2


title: Root_phf1_high_3


title: Root_Col_0_low+Pi_1


title: Root_phr1_phl1_low+Pi_1


title: Root_Col_0_high_1


title: Root_Col_0_high_2


title: Root_phf1_medium_3

value: medium


title: Root_phf1_medium_2


title: Root_phf1_medium_1


title: Root_Col_0_medium_3


title: Root_Col_0_medium_1


title: Root_phf1_low_3

value: low


title: Root_phf1_low_2


title: Root_phf1_low_1


title: Root_phr1_phl1_low_2


title: NoBacteria_50Pi_Rep2_1


title: Root_phr1_phl1_low_1


title: Root_phf1_high_1


title: Root_phf1_low+Pi_1


title: Root_Col_0_low_2


title: Root_Col_0_high_3


title: Root_Col_0_low_1


title: Root_Col_0_medium_2


title: EBV-Rest B cell-d21-Donor2

city: Tampa

first: Mingxiang

last: Teng

state: FL

address: 12902 Magnolia Dr

department: Department of Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center and Research Institute

description: day 21

data_processing:
Read counts of GENCODE v28 genes and EBV genes were calculated using salmon 0.8.2 based on transcriptome
Log transformed and variance stabilized gene read counts were extracted using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: matrix of normalized gene read counts

source_name: Primary resting B cells

growth_protocol: Primary resting B Cells were rountinly cultured in RPMI1640 supplemented with 10% FCS.

extract_protocol:
RNA were extracted with Rneasy Mini Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood

tag: stages

value: Primary culture

tag: cell type

value: Primary B cell


title: EBV-Rest B cell-d14-Donor2

description: day 14

tag: tissue


title: EBV-Rest B cell-d14-Donor3

description: day 14


title: EBV-Rest B cell-d28-Donor1

description: day 28


title: EBV-Rest B cell-d21-Donor1

description: day 21


title: EBV-Rest B cell-d28-Donor3

description: day 28


title: EBV-Rest B cell-d28-Donor2

description: day 28


title: EBV-Rest B cell-d7-Donor2

description: day 7


title: Pre-immune rep2

city: Strasbourg

first: Kamel

last: Hammani

address: 12 Rue du général Zimmer

country: France

institute: IBMP-CNRS

data_processing:
Raw data were imported into CLC Genomics Workbench. Paired trimmed reads were aligned to the Arabidopsis chloroplast genome (accession number NC_000932.1) using CLC Genomics Workbench 6.5.1 (Qiagen) utilizing the following parameters: mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.5, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes.
Reads of the two replicates aligned in CLC Genomics Workbench were extracted as BAM files and sorted in Galaxy using the SortSam tool (version 2.7.1.1). Using the bamCoverage tool (version 3.0.2), sorted BAM files were converted into RPKM-normalized bigwig files and displayed in IGB. The differential enrichment of BSF/control of the two replicates was displayed across the entire chloroplast genome.
Genome_build: NC_000932.1, Arabidopsis thaliana chloroplast genome
Supplementary_files_format_and_content: bigwig

source_name: chloroplast; stroma extract

growth_protocol: Plants were grown under controlled conditions (12-h-light (20°C)/12-h-dark (18°C) at a PFD of 100 µmol photons m-2 sec-1)

extract_protocol:
Isolation of chloroplasts and stroma extracts as well as immunprecipitation protocol see: "Meurer, J., Schmid, L.M., Stoppel, R., Leister, D., Brachmann, A., and Manavski, N. (2017). PALE CRESS binds to plastid RNAs and facilitates the biogenesis of the 50S ribosomal subunit. Plant J 92:400-413."
Recovered RNA was used for generation of libraries with the ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) according to manufacturer's instructions

tag: cell compartment

value: chloroplast stroma

value: 2 weeks

tag: ecotype

value: WT


title: BSF rep2


title: bulk IL33KO tumor 4

city: New York

first: John Alec

middle: Gaite

last: Moral

address: 408 East 69th Street, Room Z-445G

department: Hepatopancreatobiliary Surgery

institute: Memorial Sloan Kettering Cancer Center

description: IL33KO bulk 4

data_processing:
Poly(A) capture and 100bp/100bp paired-end RNA sequencing on a HiSeq 4000 using the HiSeq 3000/4000 SBS Kit to obtain FASTQ files, which are mapped to the target genome using rnaStar aligner, using a 2 pass mapping method. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done (on the second pass the RemoveNoncanonical flag is used). After mapping the output SAM files are procssed using pICARD tools to:add read groups, AddOr ReplaceReadGroups, which converts it to the compressed BAM format. Expression count matrix is then computed from the mapped reads using HTSeq.
Normalized counts for all genes and samples were scaled using DESeq method and genes with mean counts less than 15 in both conditions were filtered out.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files

molecule: polyA RNA

source_name: orthotopic pancreas tumor

growth_protocol: KPC murine pancreatic cancer cell lines are maintained by in vitro prior to orthotopic injection into WT and IL33-/- mice.

extract_protocol:
KPC murine pancreatic tumors, implanted into 5 wild type and 5 IL33-/-, were harvested, processed into single cell suspension, and positively selected through magnetically-activated cell sorting  with CD45+ magnetic beads (Miltenyi Biotec catalog #130-052-301).  RNA was extracted using an RNeasy Plus Mini Kit (Qiagen catalog #74134)
TruSeq library preparation according to Illumina protocol (TruSeq Stranded mRNA LT Kit catalog #RS-122-2102)

treatment_protocol: Mice received no treatment in this study.

value: bulk tumor

value: orthotopic pancreas tumor

tag: strain

tag: Stage

value: tumor at 2 weeks


title: Pre-immune rep1


title: EBV-Rest B cell-d21-Donor3

description: day 21


title: bulk IL33KO tumor 3

description: IL33KO bulk 3


title: EBV-Rest B cell-d4-Donor3

description: day 4


title: EBV-Rest B cell-d7-Donor1

description: day 7


title: Root_Col_0_low_3


title: EBV-Rest B cell-d7-Donor3

description: day 7


title: bulk IL33KO tumor 2

description: IL33KO bulk 2


title: bulk IL33KO tumor 1

description: IL33KO bulk 1


title: bulk wild type tumor 5

description: WT bulk 5

value: wild type


title: EBV-Rest B cell-d4-Donor1

description: day 4


title: EBV-Rest B cell-d4-Donor2

description: day 4


title: bulk wild type tumor 4

description: WT bulk 4


title: BSF rep1


title: EBV-Rest B cell-d2-Donor3

description: day 2


title: bulk IL33KO tumor 5

description: IL33KO bulk 5


title: EBV-Rest B cell-d14-Donor1

description: day 14


title: bulk wild type tumor 3

description: WT bulk 3


title: bulk wild type tumor 1

description: WT bulk 1


title: EBV-Rest B cell-d2-Donor1

description: day 2


title: EBV-Rest B cell-d0-Donor2

description: day 0


title: bulk wild type tumor 2

description: WT bulk 2


title: EBV-Rest B cell-d0-Donor3

description: day 0


title: sorted IL33KO tumor infiltrating leukoctyes 5

description: IL33KO sorted 5

value: sorted tumor infiltrating leukoctyes


title: sorted IL33KO tumor infiltrating leukoctyes 3

description: IL33KO sorted 3


title: sorted IL33KO tumor infiltrating leukoctyes 2

description: IL33KO sorted 2


title: sorted IL33KO tumor infiltrating leukoctyes 1

description: IL33KO sorted 1


title: EBV-Rest B cell-d2-Donor2

description: day 2


title: sorted wild type tumor infiltrating leukoctyes 3

description: WT sorted 3


title: CD45.WT.M3_Salmonella

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

data_processing:
3' polyA RNA-seq
CellRanger 1.3.1
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: UMI count expression values for each gene (rows) in each cell (columns)

source_name: CD45+ immune cells from wild-type Salmonella-treated mouse rep. 3 [Fig. S5A-C]

extract_protocol: 10X Genomics Chromium Prep; 3' polyA RNA seq

value: intestinal immune cells

value: Salmonella enterica

tag: time point


title: Basal_Early_B

tag: time

value: Early (ZT14)

tag: running protocole

value: Basal

tag: gender

value: male


title: CD45.WT.M4_Salmonella

source_name: CD45+ immune cells from wild-type Salmonella-treated mouse rep. 4 [Fig. S5A-C]

tag: treatment


title: sorted wild type tumor infiltrating leukoctyes 5

description: WT sorted 5


title: sorted wild type tumor infiltrating leukoctyes 4

description: WT sorted 4


title: CD45.WT.M5_Control

source_name: CD45+ immune cells from wild-type control mouse rep. 5 [Fig. S5A-C]


title: sorted wild type tumor infiltrating leukoctyes 2

description: WT sorted 2


title: CD45.WT.M2_Salmonella

source_name: CD45+ immune cells from wild-type Salmonella-treated mouse rep. 2 [Fig. S5A-C]


title: CD45.WT.M4_Control

source_name: CD45+ immune cells from wild-type control mouse rep. 4 [Fig. S5A-C]


title: sorted IL33KO tumor infiltrating leukoctyes 4

description: IL33KO sorted 4


title: CD45.WT.M3_Control

source_name: CD45+ immune cells from wild-type control mouse rep. 3 [Fig. S5A-C]


title: CD45.WT.M1_Salmonella

source_name: CD45+ immune cells from wild-type Salmonella-treated mouse rep. 1 [Fig. S5A-C]


title: sorted wild type tumor infiltrating leukoctyes 1

description: WT sorted 1


title: CD45.WT.M2_Control

source_name: CD45+ immune cells from wild-type control mouse rep. 2 [Fig. S5A-C]


title: CD45.WT.M1_Control

source_name: CD45+ immune cells from wild-type control mouse rep. 1 [Fig. S5A-C]


title: Villin-cre CR6 3

first: Jessica

last: Neil

address: 430 East 29th Street

institute: Skirball Institute, NYU School of Medicine

data_processing:
Quality was assessed using FASTQC
Sequencing reads were aligned with STAR v2.6.1d against the GRCm38.p6 genome assembly
Normalized read counts were calculated using Cufflinks v2.2.1 against the same reference genome
Differential gene expression was determined with Cuffdiff
Gene ontology analysis performed using Qiagen’s Ingenuity Pathway Analysis (IPA, Qiagen)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Gene List was generated using excel

source_name: Villin-cre CR6_colonic epithelial cells

growth_protocol: Mice were aged until 8 weeks before starting treatment

extract_protocol:
Colonic epithelial cells were isolated and sorted as PI-CD45-EpCam+ into Trizol LS. RNA was isolated from the chloroform phase using the Rneasy mini kit as per manufacter's protocol
cDNA libraries were prepared with the Ovation Trio Low Input RNA–seq System V2 (NuGEN) and sequenced on Illumina’s HIseq platform using a paired-end protocol

treatment_protocol: Mice were given a cocktail of antibiotics for >10 days, followed by being infected with 3x106 pfu of murine norovirus CR6 strain (or left uninfected) for 10 days, followed by treatments with 3% DSS in drinking water for 6 days

value: IFNAR1f/f x Villin-cre

tag: infection status

value: Murine norovirus-CR6

tag: antibiotics/dss-treated mice

value: Antibiotics/DSS

value: Colonic epithelial cells


title: EBV-Rest B cell-d0-Donor1

description: day 0

value: Blood

value: Primary culture

value: Primary B cell


title: Villin-cre CR6 1


title: Flox CR6 3

source_name: Flox CR6_colonic epithelial cells


title: Villin-cre ABX 1

source_name: Villin-cre ABX_colonic epithelial cells

value: Uninfected


title: Villin-cre CR6 2


title: Villin-cre ABX 3


title: Flox CR6 2


title: Flox CR6 1


title: Flox ABX 2

source_name: Flox ABX_colonic epithelial cells


title: Sample 15

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata, 35

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

data_processing:
Adapter sequences were trimmed from the raw ATAC-seq reads with CutAdapt v1.12
Trimmed reads of each sample were mapped to the reference human genome build GRCh37/hg19 by using Bowtie2 v2.3.2 with default settings
Picard tools (http://broadinstitute.github.io/picard/) v1.126 was used to remove PCR duplicated reads and for insert size distribution analysis.
Reads mapping to mitochondrial DNA and the Y chromosome were filtered and only uniquely mapping paired reads with a quality score≥30 were kept for subsequent analysis.
The read start sites were adjusted to represent the center of the transposon binding event (5bp on forward strand and 4bp on reverse strand) as described.
Phantompeakqualtools v2.0 was used to calculate the strand cross-correlation and deepTools v2.0.1 was used to calculate correlation between samples
MACS2 v2.1.0 was used for peak calling with parameters “--nomodel--nolambda-keep-dup all--call-summits-g hs-B”, and peaks were filtered based on default settings and false discovery rate (FDR) < 0.1
Peaks in regions known to show artificially high signal were filtered using the hg19 blacklist file from ENCODE. BEDTools v2.26.0 was used for various analyses based on peak locations. Peaks located less than 50bp apart were merged in order to facilitate comparison between samples.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedGraph

source_name: Human islets

growth_protocol: Islets were cultured in CMRL 1066 medium supplemented with 10 mM nicotinamide, 10 mM HEPES buffer , 0.25 μg/ml fungizone, 50 μg/ml gentamicin, 2 mM L-glutamine, 10 μg/ml Ciprofloxacin, 10% (v/v) heat-inactivated human serum and 5.56 mM glucose. Some islets were frozen at -80 degrees celcius before use and some were used fresh.

extract_protocol:
Islets were washed twice with ice cold 1xPBS by spinning at 500g for 5mins at 4°C. Cell lysis was performed with ATAC lysis buffer (10mM Tris-HCl, pH 7.4, 3mM MgCl2, 10mM NaCl and 0.1% IGEPAL CA-630) by incubating on ice for 10mins and nuclei were then collected by spinning at 500g for 10mins at 4°C.
The transposition reaction mix (12.5μl of 2X TD buffer, 2μl of Tn5 transposase (Illumina, San Diego, CA, USA) and 10.5μl of nuclease free water was added to nuclei and incubated at 37°C for 1hour before the reaction was cleaned using MinElute cleanup kit (Qiagen, Hilden, Germany). Next, 10-12cycles of PCR were performed with transposed DNA using the Illumina Nextera dual index primers. The PCR product was cleaned using PCR purification kit (Qiagen).

value: pancreatic islets

tag: diagnosis

value: Diabetic


title: Sample 12

value: Healthy


title: Sample 14


title: Sample 13


title: Sample 10


title: Sample 9


title: Sample 11


title: WSB_169_S28_L006

city: Durham

first: Douglas

middle: A

last: Marchuk

address: 213 Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
adapter trimming (CutAdapt)
alignment to pseudoreference (TopHat v. 2.1.1)
remap to reference coordinates (Lapels)
read counting (HTseq)
differential expression (DESeq2)
Supplementary_files_format_and_content: .txt file with gene counts

extract_protocol: Not provided

value: brain

value: WSB/EiJ

tag: sequencing lane


title: WSB_138_S26_L006


title: WSB_m100_S23_L006


title: CAST_203_S22_L006

value: CAST/EiJ


title: WSB_120_S24_L006


title: Sample 8


title: Sample 7


title: CAST_202_S21_L006


title: WSB_135_S25_L006


title: WSB_147_S27_L006


title: Villin-cre ABX 2


title: Flox ABX 1


title: Flox ABX 3


title: NoBacteria_1000Pi_Rep1_2

city: Chapel Hill

source_name: whole seedling

value: whole seedling

tag: genotype

tag: phosphate availability

tag: bacteria presence

value: NoBacteria

tag: biorep


title: Sample 6

tag: tissue


title: CAST_201_S20_L006


title: CAST_200_S19_L006


title: CAST_170_S18_L006


title: CAST_142_S17_L006


title: Sample 3


title: Sample 4


title: Sample 2


title: Sample 1


title: WSB_169_S28_L005


title: WSB_m100_S23_L005


title: WSB_147_S27_L005


title: WSB_138_S26_L005


title: WSB_135_S25_L005


title: WSB_120_S24_L005


title: MS5-NPC

city: Seoul

first: Yanuar

middle: Alan

last: Sulistio

address: Wangsimni-ro 222

department: Biomedical Science

country: South Korea

institute: Hanyang University

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(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: H9 hESC-derived NPC

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

tag: cell line

tag: cell type

value: H9 hESC-derived NPC


title: CAST_202_S21_L005

tag: strain


title: H9

source_name: H9 hESC

value: H9 hESC


title: Sample 5


title: CAST_203_S22_L005


title: CAST_201_S20_L005


title: CAST_170_S18_L005


title: CAST_142_S17_L005


title: WT_4H_37C

city: Ottawa

first: François-Xavier

last: Campbell-Valois

state: ON

address: 75 rue Laurier est

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

data_processing:
All data processing steps were performed with Rockhopper (version 2.0.3)
Rockhopper was also used to map the reads.
Genome_build: Virulence plasmid: AL391753
Genome_build: Chromosome: CM001474

organism: Shigella flexneri

source_name: Shigella flexneri wild-type cells

growth_protocol: After incubation, red centered T3SS-positive bacteria were picked and inoculated in 2 mL of Difco Tryptic Soy Broth (TSB) (BD Biosciences, #211822), and incubated at 30°C for approximately 16 hours under constant shaking (225 rpm). The overnight cultures were then sub-cultured 1/200 in 4 mL of LB broth and incubated at 37°C for 4 hours with shaking (OD600» 1).

extract_protocol:
Immediately following incubation, 400 µL of culture was transferred into 800 µL of RNAprotect Bacterial Reagent (Qiagen, #76506), and treated as indicated by the supplier. The total RNA was then extracted using the RNeasy Mini Kit as indicated by the supplier (Qiagen, #74104).
Libraries were generated using the KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems), as per the manufacturer’s recommendations. TruSeq adapters and PCR primers were purchased from IDT. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

tag: serotype

value: wild-type, with streptomycine resistance

tag: antibiotic resistance

value: Streptomycin resistant


title: ipaD_4H_37C

source_name: Shigella flexneri ipaD cells

value: ipaD

value: Streptomycin and kanamycin resistant


title: Left atrial-patient-2

city: Shanghai

first: Ban

last: Liu

address: No. 301 Yanchang Road

country: China

institute: Tongji university

description: Gene expression in atrial fibrillation patient atrial tissues

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: Left atrial appendage,atrial fibrillation

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

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

treatment_protocol: Total RNAs were extracted from the atrial tissue using TRIzol reagent.

value: Left atrial appendage

value: Male

tag: age

value: atrial fibrillation


title: C4-2B MDV3100-resistant_2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: SAMPLE 4

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The data were processed and normalised using Illumina GenomeStudio

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS and 1% PS.

extract_protocol: Total RNA were extracted using Trizol according to manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

treatment_protocol: LNCaP and C4-2B, cells were continuously selected under 1 μM or 10 μM Enzalutamide (Selleckchem) respectively for at least 3 months. DMSO used as control.


title: LNCap MDV3100-resistant_1

description: SAMPLE 8

scan_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

source_name: LNCap

value: LNCap


title: LNCap MDV3100-resistant_2

description: SAMPLE 9

label_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.


title: LNCap MDV3100-resistant_3

description: SAMPLE 10


title: LNCap DMSO_3

description:
SAMPLE 7
selection protocol performed with DMSO

value: 0μM and with 0.1% DMSO


title: CAST_200_S19_L005


title: C4-2B DMSO_2

description:
SAMPLE 3
selection protocol performed with DMSO


title: LNCap DMSO_1

description:
SAMPLE 5
selection protocol performed with DMSO


title: control-1

description: Gene expression  in control atrial tissues

source_name: Left atrial appendage,control

tag: gender

value: healthy control


title: control-2


title: C4-2B MDV3100-resistant_1

description: SAMPLE 2


title: LNCap DMSO_2

description:
SAMPLE 6
selection protocol performed with DMSO


title: control-3


title: Left atrial-patient-3


title: Left atrial-patient-1


title: rat

status: Public on Apr 05 2019

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

data_processing:
CellRanger version 2.2.0 mkfastq tool was used for basecalling, which created 4 fastq files per sample from the 4 lanes of the flowcell. So, R1 has 4 fastq files; R2 has 4 fastq files; and I (index) has 4 fastq files.
R1 with a 16nt 10X barcode and a 10nt UMI
CellRanger version 2.2.0 count was used to create the matrix table for further processing.
The matrix was then loaded into Seurat version 2.3.4 for normalization, clustering and visualization.
Genome_build: GRch38,Sscrofa11 Release 91, mm10, Rnor6 Release 92
Supplementary_files_format_and_content: tab-delimited text file containing gene symbols with their respective expression for each cell/barcode.

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
CD45+ innate immune cells (T/B cell negative CD45+ cells) were sorted using a BD FACS AriaII. Live single cells were loaded into the 10x genomics machine.
Full length cDNA libraries were prepared by incubation of Gel Bead-In-EMulsions (GEMs) in a thermocycler machine with Chromium v2. GEMs containing cDNAs were broken and all single cell cDNA libraries were pooled together, cleaned using DynaBeads MyOne™ Silane beads (Fisher PN 37002D), and pre-amplified by PCR to generate sufficient mass for sequencing library construction.

value: Sprague Dawley

value: kidney

value: CD45+ innate immune cells

value: 3 months old

tag: Sex


title: C4-2B DMSO_1

description:
SAMPLE 1
selection protocol performed with DMSO


title: genome_dps_wce

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

data_processing:
dp3 genome
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings. Reads were trimmed to 50 bp and aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were extended to each library's estimated insert size. Genome-wide coverage counts were calculated, normalized to reads per million and saved in BigWig format
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

organism: Drosophila pseudoobscura

source_name: ML83-63 cells

growth_protocol: ML83-63 cells were cultured at 25C in M3+BPYE + 10% FCS

extract_protocol:
Cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer. Chromatin was sonicated by bioruptor to an average size of 250~500 bp. ~ 10 million cells was used for one ChIP-nexus.
DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using NEBNext End repair module. A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module.  Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

value: ML83-63 cells

tag: treatment

tag: chip antibody


title: genome_dps_h3k4me3_chipseq

value: anti-H3K4me3 rabbit polyclonal, Cell Signaling (#9727)


title: FTM4 (neck, old)

city: Yufu-shi

first: Takashi

last: Sakai

state: Oita

address: 1-1 Idaigaoka, Hasama-machi,

department: Faculty of Medicine

institute: Oita University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: lesional skin of neck, old FTM

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: STOCK a/a Tmem79ma Flgft/J

value: whole skin

value: female


title: WSN6: WSN Infection - Nuclear (6h)

city: Dallas

first: Beatriz

last: Fontoura

state: TX

address: 6000 Harryhines Blvd

institute: UT Southwestern Medical Center

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Cell Culture/WSN

growth_protocol: A549 cells were infected with A/WSN/1933 at an MOI of 5 for 6h.

extract_protocol: RNA from total cell lysate, or nuclear fraction, or cytoplasmic fraction was prepared using the RNeasy Plus mini Kit.

treatment_protocol: Total cell lysates as well as nuclear and cytoplasmic fractions were generated as we previously described (Zhang et al, J. Cell Biol. 2012, PMC3275370).

value: A549 cells

value: Influenza A/WSN/1933

tag: molecule subtype

value: Nuclear mRNA


title: FTM4 (flank, old)

source_name: non-lesional skin of flank, old FTM


title: MON6: Mock Infection - Nucleur (6h)

source_name: Cell Culture

value: mock


title: M-CSF treated cells

city: Farmington

first: Joseph

last: Lorenzo

address: 263 Farmington Avenue

department: Medicine

institute: UConn Health

description:
mean of 3 biologic replicate samples.  Each was analyzed independently by illumina array Standard deviation is provided for each gene
SAMPLE 1

hyb_protocol: Performed by the core facility at UConn Health

data_processing:
The data were analyzed by the core facility at UConn Health which has since shut down. The normalization method is unknown.
The core faciliy provided normalized data averaged across replicates together with the standard deviation and detection p-value.

source_name: bone marrow

extract_protocol:
isolation protocol: Freshly isolated murine C57BL/6 bone marrow cells were isolated and separated by fluorescence-activated cell sorting to a population that was CD3-, CD45R-, CD11b lo/-, CD115+.
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were cultured in MEM-alpha, 10% fetal bovine serumeither either  with M-CSF (30 ng/ml) alone or  M-CSF + RANKL (both at 30 ng.ml) for 3 days before adherant cells were extracted for RNA

value: bone marrow

tag: cell markers

value: 8 weeks

value: M-CSF treated


title: WSCY6: WSN Infection - Cytoplasmic (6h)

value: Cytoplasmic mRNA