title: aCGH analysis of AM patient-8

city: Nagoya

first: Akinobu

last: Ota

institute: Kinjo Gakuin University

description: Somatic genomic alterations of ameloblastoma in AM patient-8

hyb_protocol: Cy3-dUTP-labeled tumor-derived DNA or Cy5-dUTP-labeled coppresponding normal DNA were hybridized on a Agilent Human Genome CGH Microarray Kit 2 × 400K. After 40 h of hybridization at 65℃, the slides were washed according to the manufacturer instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x00k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parametersto obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Labeling and hybridization were performed according to the manufacturer's protocol. Briefly, 2 μg each of patients-derived DNA from tumor and normal counterpart were labeled by random priming with either, Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS, respectively(Agilent Technologies). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: For oligo-aCGH, genomic DNA was obtained from both tumor and normal tissues from 8 ameloblastoma patients using proteinase K/RNAse treatment and phenol–chloroform extraction according to standard procedures. DNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

value: ameloblastoma tumor

tag: Sex

value: Male

source_name: AM-008_normal tissue

value: normal tissue


title: NK CTV-1 16h donor 3

status: Public on Jun 11 2019

type: RNA

city: London

first: May

last: Sabry

address: Rowland Hill Street

department: Cancer Institute

country: United Kingdom

institute: University College London

description: Tumor-primed NK cells (16h)

hyb_protocol: Samples were hybridized with probes at 65°C for 18 hours before being placed into the automated nCounter™ Prep Station (NanoString Technologies), where samples were affixed to cartridges.

scan_protocol: Cartridges were immediately placed into the nCounter™ Digital Analyzer (Nanostring Technologies) and read at maximum resolution

data_processing: Using nSolver software, QC  was carried out using default QC parameter settings. Then, raw data files  were examined to ensure that counts of positive and negative controls as well as housekeeping/endogenous genes meet expectations. Thereafter, background noise was adjusted by background thresholding using a user-defined threshold count value of 20 counts. Normalization was accomplished using the geometric mean of the positive control counts, and housekeeping genes in the CodeSet Content. Differential expression was calculated by specifying NK alone samples as the baseline of the experiment using nSolver software.

label: Target-probe complex

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor-primed NK cells (16h)

label_protocol: Batches of 12 separate samples at one time were prepared as per manufacturer’s instructions.  Platform used was human myeloid innate immunity panel (Catalog number XT-CSO-HMMYLD1-12).

growth_protocol: NK cells were isolated from healthy donor PBMCs by positive selection for CD56 (CD56 MicroBeads; Miltenyi Biotec) according to the manufacturer’s instructions. Freshly isolated NK cells were maintained in complete medium (CM) (RPMI 1640 supplemented with 10% v/v fetal bovine serum and 2mM L-glutamine; all from Life Technologies). The  acute lymphoblastic leukemia cell line CTV-1 was maintained in CM.

extract_protocol: To prepare the samples, resting NK cells (5x10^5) were washed twice and incubated alone or mixed with mitomycin-C-treated CTV-1 cells (1x10^6) for 6 hours, or IL-2 (200 IU/ml) for 16 hours at 37°C in 5% v/v CO2. Thereafter, NK cells were selectively enriched from co-culture by CD56 isolation, and RNA was extracted from the samples using the RNAqueousTM Micro Kit (Thermo Fisher Scientific).

treatment_protocol: NK cell stimulation was achieved by co-incubating CD56+ NK cells (1x10^6) with CTV-1 (2x10^6) for 6 or 16 hours, or the exogenous cytokine IL-2 (200IU/ml) for  16 hours at 37ºC, 5% v/v CO2 in CM.

tag: tissue

value: peripheral blood

tag: cell type

value: natural killer cells


title: NK CTV-1 16h donor 2

description: Tumor-primed NK cells (16h)


title: WT_15

type: SRA

city: Cambridge

first: James

middle: A

last: Kraemer

state: MA

address: 31 Ames St, Building 68-570

department: Biology

country: USA

institute: Massachusetts Institute of Technology

library_source: transcriptomic

data_processing:
Paired-end reads were mapped to the MG1655 genome using bowtie2 using the arguments: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 -p 6 -l 40 -X 300.
Bowtie alignments were converted to csv files by mapping reads to gene extent regions
Genome_build: NC_000913.2
Supplementary_files_format_and_content: csv files were generated using custom python scripts. First column represents gene name and second column represents number of reads

molecule: total RNA

organism: Escherichia coli K-12

source_name: Bacterial liquid culture

growth_protocol: E. coli was grown to OD 0.2 before treatment or harvest in M9GAV + nucleobases (1x M9 salts, 0.4% glucose, 0.25% each of l-serine and l-threonine, 0.0375% each of l-asparagine and l-glutamine, 0.015% each of all 16 other natural amino acids, 1× Kao & Michayluk Vitamins, and 0.2 mM of each nucleobase).

extract_protocol:
RNA was extracted by hot trizol lysis and Direct-zol RNA MiniPrep (Zymo). rRNAs were removed using the Ribo-Zero Kit for Gram-negative bacteria (Illumina) and mRNAs were then fragmented with RNA fragmentation reagents (Ambion). First-strand cDNA synthesis was performed with random primers (Invitrogen) and Superscript III. After purifying cDNAs by phenol:chloroform:isoamyl alcohol extraction and precipitation, second-strand synthesis occurred with dUTP (Promega) instead of dTTP and RNase H (NEB), E.coli DNA ligase (NEB), and DNA Pol I (NEB). Sequencing libraries were built as with other libraries, except that the second strand was digested with USER (NEB) after the addition of Y-adaptors.
Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with either Phusion (NEB) or Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 250-600 bp.

treatment_protocol: 1 μL of a 1:10 dilution of ERCC RNA Spike-IN Mix 1 was added to frozen cell pellet immediately before extraction.

value: Escherichia coli K12 liquid culture

tag: growth stage

value: exponential phase

tag: genotype

value: rpoZ (WT)-kanR rpoC (WT)-tetAR, Ptac-relA'

tag: media

value: M9GAV + 0.2 mM nucleobases

tag: growth treatment

value: 50 µM IPTG added for 15 min to induce RelA'


title: aCGH analysis of AM patient-5

type: genomic

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

description: Somatic genomic alterations of ameloblastoma in AM patient-5

molecule: genomic DNA

source_name: AM-005_normal tissue


title: WtPH: Vector 2

city: Montreal

first: Jennifer

middle: Lynn

last: Estall

state: Quebec

address: 110 avenue des Pins ouest

country: Canada

institute: IRCM

description: microarray expression data from primary hepatocytes

hyb_protocol: standard Affymetrix procedure.

scan_protocol: standard Affymetrix procedure.

data_processing: The data were analyzed with RMA (log2) normalized data using the just.rma function in the affy package in Biocinductor

label: biotin

organism: Mus musculus

source_name: primary hepatocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 25 mM glucose DMEM supplemented with 0,2% BSA, 2 mM sodium pyruvate, and pen/strep.

extract_protocol: RNeasy Kit column extraction

treatment_protocol: Adenoviral infection (48 hours) followed by treatment for two hours with 2 ng/mL TNFalpha

tag: strain

value: liver

tag: cell line

value: WtPH

tag: genotype/variation

value: Control (baseline)

value: primary mouse hepatocytes

tag: isoform

value: Control (vector)

tag: treatment

value: vehicle (PBS)


title: NK IL2 donor 2

description: Lymphokine-activated NK cells

source_name: Lymphokine-activated NK cells


title: WtPH: Vector 3


title: Macro-8

city: Freiburg

first: Patrice

last: Zeis

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: library of 96 Cx3cr1gfp/+ Dermis Macrophages

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000) was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. In addition we annotated the EGFP sequence from the pEGFP-N1 vector (https://www.ncbi.nlm.nih.gov/nuccore/U55762) used to generate the CX3CR1-GFP reporter mice. This procedure resulted in 34,112 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9 + gfp sequence from pEGFP-N1 vector (https://www.ncbi.nlm.nih.gov/nuccore/U55762)
Supplementary_files_format_and_content: TSV files, columns represent CXR3CR1 high/mid/low macrophages, rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Dermis

growth_protocol: SPF animal facility, no earclipping

extract_protocol:
Mouse ears were digested with Dispase (0.25 U/ml), Collagenase II (1 mg/ml), and DNase I in HBSS with 10% FCS for 2 h at 1400 rpm and 37°C. Cells were filtered, stained and sorted as CD45+, CD11b+, CD64+, Lin- in a 384-well plate.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: untreated

value: ear skin

tag: age

value: 7 weeks

value: Cx3cr1gfp/+ Dermis Macrophages


title: Exp1 E19_Control 2

city: Los Angeles

first: Yong

last: Kim

state: CA

address: 10833 Le Conte Ave, 73-022 CHS

institute: UCLA

description: exosomal small RNA

data_processing:
Adapters and low-quality nucleotides were removed from raw fastq sequences using Cutadapt (v.1.11).
Adapter-free sequences were mapped to the Rat genome (rn5) using bowtie (v.1.1.2) using the parameters ‘-v 1 –k 100 –best –strata’.
Mapped reads were annotated to mature rat miRNA and piRNA. Rat miRNA annotations (rn5) were downloaded from miRBase. Rat piRNA annotations (rn4) were downloaded from piRNABank. Liftover of piRNA annotations rn4 to rn5 was performed since rn5 annotations were not available
Bowtie alignments were annotated to miRNA and piRNA coordinates by requiring the alignment start site to be between -3nt to +2nt positions near the annotated start site and the alignment end site be between -2nt and +3nt of the annotated end site. Multi-mapped reads are distributed 1/n, where n is the number of mapping locations.
DESeq2 (version 1.14.1) was used to further normalize and determine differential expression of miRNA and piRNA species between control and EtOH-treated groups. Reads were aligned to the spike-in control sequences, allowing no mismatches.
Genome_build: rn5, rn4
Supplementary_files_format_and_content: miRNA_piRNA_normalized_read_counts.xlsx

organism: Rattus norvegicus

source_name: amniotic fluid

extract_protocol:
Amniotic fluids were harvested at E16 and E19 and exosomes were isolated for RNA isolation
NEBNext Small RNA Library Prep set
exosomal RNA (20 ng each) was mixed with 1/15 amount of Spike-in RNA

treatment_protocol: Pregnant dams were treated with 0 or 2.5 g/kg of 20% EtOH by oral gavage on embryonic days 5, 8, 10, 12 and 15

value: Sprague-Dawley

value: control

value: Embryonic day 19

tag: sample type

value: amniotic fluid


title: aCGH analysis of AM patient-6

description: Somatic genomic alterations of ameloblastoma in AM patient-6

value: ameloblastoma tumor

value: Female

source_name: AM-006_normal tissue

value: normal tissue


title: Exp1 E19_Control 1

description: exosomal small RNA


title: Macro-7


title: WT_0

value: Escherichia coli K12 liquid culture

value: exponential phase

value: rpoZ (WT)-kanR rpoC (WT)-tetAR, Ptac-relA'

value: M9GAV + 0.2 mM nucleobases


title: Macro-6


title: aCGH analysis of AM patient-3

description: Somatic genomic alterations of ameloblastoma in AM patient-3

value: Male

source_name: AM-003_normal tissue


title: Exp1 E16_EtOH3

description: exosomal small RNA

value: EtOH

value: Embryonic day 16


title: aCGH analysis of AM patient-2

description: Somatic genomic alterations of ameloblastoma in AM patient-2

source_name: AM-002_normal tissue


title: NK CTV-1 6h donor 3

description: Tumor-primed NK cells (6h)

source_name: Tumor-primed NK cells (6h)

value: peripheral blood

value: natural killer cells


title: aCGH analysis of AM patient-7

description: Somatic genomic alterations of ameloblastoma in AM patient-7

source_name: AM-007_normal tissue


title: Macro-5

value: ear skin

value: 7 weeks

value: Cx3cr1gfp/+ Dermis Macrophages


title: Exp1 E16_EtOH2

description: exosomal small RNA

value: Sprague-Dawley


title: Exp1 E16_EtOH1

description: exosomal small RNA

value: amniotic fluid


title: Macro-4


title: aCGH analysis of AM patient-4

description: Somatic genomic alterations of ameloblastoma in AM patient-4

value: ameloblastoma tumor

source_name: AM-004_normal tissue


title: Exp1 E16_Control 3

description: exosomal small RNA

value: control


title: NK CTV-1 6h donor 1

description: Tumor-primed NK cells (6h)


title: Macro-3


title: NK alone donor 3

description: Control

source_name: Control


title: Macro_2


title: NK alone donor 2

description: Control


title: Exp1 E16_Control 2

description: exosomal small RNA


title: NK CTV-1 6h donor 2

description: Tumor-primed NK cells (6h)


title: Exp1 E16_Control 1

description: exosomal small RNA


title: NK alone donor 1

description: Control


title: w1118_THORAX_RU486_2

status: Public on Jun 10 2019

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to dm3  genome using an internal pipeline that employs bwa and STAR
Htseq was used to extract raw counts
Genome_build: dm3
Supplementary_files_format_and_content: Gene symbol raw count values in 2 column tab delimited txt file, one for each sample

organism: Drosophila melanogaster

source_name: thorax

extract_protocol:
trizol
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq  Stranded mRNA

treatment_protocol: 100uM RU486 for 10 days

value: thorax

tag: transgene/strain

value: 100uM RU486 for 10 days


title: w1118_THORAX_control_1

value: ethanol control


title: w1118_THORAX_control_2


title: w1118_THORAX_RU486_1


title: Act88F-GS_THORAX_control_3


title: Act88F-GS_THORAX_control_1


title: Act88F-GS_THORAX_control_2


title: elav-GS-Gal4_HEAD_RU486_3

source_name: head

value: head


title: Act88F-GS_THORAX_RU486_1


title: elav-GS-Gal4_HEAD_RU486_2


title: Act88F-GS_THORAX_RU486_2


title: LM_rep3

city: Braunschweig

first: Jasper

last: Schierstaedt

address: Messeweg 11-12

department: EP

institute: Julius kühn-Institute

data_processing:
To reveal transcriptional differences in S. Typhimurium 14028s exposed to the different media Illumina HiSeq sequencing were performed at the ZIEL - Institute for Food & Health, Core Facility Microbiome/NGS, Technische Universität München, Freising, Germany.
The sequence analyses were mapped to NC_003197.2 whole genome using Bowtie2 v0.6 with parameters -s -p -x -U -s -o
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1 with cufflinks parameters -I 1 -F 0.0 -j 0.0 -G, cuffmerge parameters -g cuffdiff parameters -FDR 0.05 -c 10 -library-norm-method geometric -dispersion-method pooled
Genome_build: NC_003197.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each treatment, fold change and significance levels

organism: Salmonella enterica

source_name: RNA from Salmonella grown in lettuce medium

growth_protocol: Salmonella was grown overnight at 37°C in LB broth . The cells were pelleted at  (1500 x g, 10 min), washed twice in 10 mM MgCl2 and OD600 = 1 was prepared. Two mL of this suspension were pipetted into dialysis tubes which were placed into 50 mL conical tubes containing 30 mL of  minimal medium (MM). 2x 0.5 mL from each dialysis tube were mixed with RNAprotect then pelleted and the pelletes used for RNA extraction.

extract_protocol:
The total RNA from the bacterial samples was extracted, the rRNA was removed and  then the RNA was fragmented using the ultrasonicator.
The library preparation was done with the TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: The minimal medium (MM) consisted of 20% M9 salts, 2 mM MgSO4 and 1.23 mM glucose in sterile deionized water. Tomato Medium (TM) and Lettuce medium (LM) contained 25% (v/v) plant extract and 20% M9 salts and 55% sterile deionized water. Plant root exudate media (LX, TX) consisted of lyophilized exudates (from about 25 plants, 4 h) resuspended in MgCl2. Soil suspensions consisted of 33% (v/v) soil in MgCl2.

tag: serovar

value: Typhimurium

tag: medium

value: lettuce medium


title: LM_rep1


title: elav-GS-Gal4_HEAD_RU486_1


title: WtPH: Vector 1

value: liver

value: WtPH

value: Control (baseline)

value: primary mouse hepatocytes

value: Control (vector)

value: vehicle (PBS)


title: elav-GS-Gal4_HEAD_control_3


title: Macro_1

value: ear skin

value: 7 weeks

value: Cx3cr1gfp/+ Dermis Macrophages


title: elav-GS-Gal4_HEAD_control_2


title: w1118_THORAX_RU486_3


title: elav-GS-Gal4_HEAD_control_1


title: LX_rep1

source_name: RNA from Salmonella grown in lettuce root exudates

value: lettuce root exudates


title: NK CTV-1 16h donor 1

description: Tumor-primed NK cells (16h)

source_name: Tumor-primed NK cells (16h)

value: peripheral blood

value: natural killer cells


title: Act88F-GS_THORAX_RU486_3

value: thorax

value: 100uM RU486 for 10 days


title: w1118_THORAX_control_3

value: ethanol control


title: MM_rep3

source_name: RNA from Salmonella grown in minimal medium

value: Typhimurium

value: minimal medium


title: S46_RNA_1

city: Quebec

first: Kanta

last: Chechi

address: 2275 Chemin Sainte Foy

department: Physiology

institute: Quebec Heart and Lung Institute, Laval University

data_processing:
Raw reads were trimmed for quality (phred33 ≥ 30) and length (n ≥ 32), and Illumina adapters were clipped off using Trimmomatic v. 0.35
Filtered reads were aligned to the GRCh37 human reference using Tophat v 2.0.14
Raw read counts of genes were obtained using htseq-count v.0.6.1
Base Calling was done using bcl2fastq v1.8.4 and raw reads were aligned to human reference using STAR  v2.4.0f1
Genome_build: GRCh37
Supplementary_files_format_and_content: raw files are either in bam or fastq format

source_name: Adipose tissue

extract_protocol:
Total RNA was isolated from tissue using the Rneasy Lipid Tissue Mini Kit (QIAGEN, Mississauga, Ontario) according to manufacturer's instructions. Purity of total RNA was determined as 260/280 nm absorbance ratio with expected values between 1.8-2.0 using Biodrop Duo (BioDrop, UK). In addition, RNA integrity of samples was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, California).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tisse

value: subcutaneous adipose

tag: ucp1 expression

value: High UCP1 -eAT

tag: disease state

value: CAD

tag: body type

value: Obese


title: LM_rep2

value: lettuce medium


title: S33_RNA_1

value: Low UCP1-eAT


title: S55_RNA_1


title: shCtrl_2nd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue < = 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa cell

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
The HeLa cells were ground into fine powder before RNA extraction. Total RNA was extracted by the hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina HiSeq 4000 was used to collect data from 150-bp pair-end sequencing (ABlife Inc., Wuhan, China).

treatment_protocol: shRNA transfection of HeLa cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for q-PCR analysis.

value: HeLa

tag: transfection

value: control plasmid


title: shCtrl_1st


title: MM_rep1


title: MM_rep2


title: shCRKL_2nd

value: CRKL knockdown


title: S30_RNA_1

value: Lean


title: S3_RNA_1

value: Non-CAD


title: LX_rep2

value: lettuce root exudates


title: shCRKL_1st


title: S28_RNA_1


title: Th17-1: Th17, biological rep1

city: Seattle

first: Raymond

last: Doty

state: WA

department: Division of Hematology

institute: University of Washington

description: Gene expression data from Th17 cells.

hyb_protocol: Samples were hybridized according to Affymetrix protocol. The chips were washed and stained using fluidics protocol FS450_0007.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 7G Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing:
Microarray data were analysed with the ‘limma’ package in R.
Matrix table includes: GC-RMA signal, normalized by z score and quantile

source_name: Th17 cells.

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

tag: cell type

value: T cells


title: S21_RNA_1


title: Th2-2: Th2, biological rep2

description: Gene expression data from Th2 cells.

source_name: Th2 cells.


title: Th2-1: Th2, biological rep1

description: Gene expression data from Th2 cells.


title: S17_RNA_1


title: LX_rep3


title: M55_RNA_1

value: mediastinal adipose


title: M46_RNA_1


title: S34_RNA_1


title: M34_RNA_1


title: Th1-1: Th1, biological rep1

description: Gene expression data from Th1 cells.

source_name: Th1 cells.


title: Naïve-1: Naïve, biological rep1

description: Gene expression data from naïve T cells.

source_name: naïve T cells.

value: Naïve


title: nTreg: natural Treg

description: Gene expression data from nTreg cells.

source_name: nTreg cells.

value: nTreg


title: M30_RNA_1


title: M28_RNA_1


title: M18_RNA_1


title: S18_RNA_1


title: Th17-2: Th17, biological rep2

description: Gene expression data from Th17 cells.


title: M17_RNA_1


title: M3_RNA_1


title: Naïve-2: Naïve, biological rep2


title: Th1-2: Th1, biological rep2

description: Gene expression data from Th1 cells.


title: Donor A - RFP+GFP+ Cells

first: Bryan

last: Bryson

address: 400 Technology Square

department: Biological Engineering

institute: MIT

description: normalizedCnt.csv [A-Live]

data_processing:
techinique replicates were pooled together then mapped to hg19 whole genome with tophat2 using parameters  --bowtie1    --no-coverage-search  --library-type fr-unstranded    -G  --transcriptome-index
reads per gene were calculated with htseq-count with ensembe 75 gene annoataion
reads counts were normalized by DESeq2 and then performed gene differential express analysis with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: csv text file

source_name: Monocyte derived macrophages

growth_protocol: Macrophages were infected with Mtb and subsequently extracellular bacteria were washed off. After washing, cells were allowed to proceed for 4 days prior to the addition of anhydrotetracycline. On day 5, cells were sorted for RFP+GFP+ or RFP+GFP- cells and sorted directly into RLT for RNA seq analysis.

extract_protocol:
Infected macrophages were isolated as described and RNA was purified using the RNeasy kit according to the manufacturer’s instructions (Qiagen). RNA was quantified by Nanodrop and quality assessed by Agilent 2100 Bioanalyzer.
Libraries were created from high quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina). Libraries were quantified by Qubit and sequenced on a HiSeq 2500 Sequencing System (Illumina). Each sample was sequenced with at least 30 million reads using single-end 50 base pair reads.

tag: sorted cells

value: RFP+GFP+


title: Donor B - RFP+GFP- Cells

description: normalizedCnt.csv [B-Dead]

value: RFP+GFP-


title: Donor B - RFP+GFP+ Cells

description: normalizedCnt.csv [B-Live]


title: E55_RNA_1

value: epicardial adipose

value: High UCP1 -eAT


title: Donor C - RFP+GFP+ Cells

description: normalizedCnt.csv [C-Live]


title: E34_RNA_1

value: Obese


title: E46_RNA_1

value: CAD


title: E33_RNA_1

value: Low UCP1-eAT


title: Donor A - RFP+GFP- Cells

description: normalizedCnt.csv [A-Dead]


title: E30_RNA_1


title: M33_RNA_1


title: Donor C - RFP+GFP- Cells

description: normalizedCnt.csv [C-Dead]


title: M21_RNA_1


title: E3_RNA_1


title: E28_RNA_1


title: E21_RNA_1


title: E18_RNA_1


title: E17_RNA_1


title: Nascent_RNA-seq_MCF-7_0.5M_biologicalRep2

city: Yokohama

first: Shruti

last: Bhagat

state: Kanagawa

address: W424, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Center for Integrative Medical Sciences

institute: RIKEN, Yokohama

data_processing:
For all our datasets we performed the following steps, (i) split reads by barcode, (ii) trimmed reads to remove barcode sequences and (iii) removed reads aligned to rRNA sequences (Human: GenBank U13369.1; Mouse: GenBank BK000964.3). These steps were performed using MOIRAI (Hasegawa et al., 2014) for human cell line data and using Trimmomatic v 0.36 (Bolger et al., 2014) and MOIRAI (Hasegawa et al., 2014) for mouse tissue data. For all CAGE based data and mouse RNA-seq data, sequences with base ‘N’ were also removed.
Non rRNA reads were mapped hg19 genome and human reference gene model Gencode v27lift37 comprehensive using  STAR v 2.5.0a with the following parameters for indexing: --runThreadN 12 --runMode genomeGenerate --genomeDir genome.fa --sjdbGTFfile Gencodeannotation.gtf and the following parameters for mapping: --runThreadN 12 --outSAMtype BAM SortedByCoordinate --out FilterMultimapNmax 1 --readFilesCommand zcat.
Transcription start sites for CAGE based data were identified using bedtools v 2.2.25 (Quinlan and Hall, 2010) as described here: http://fantom.gsc.riken.jp/5/sstar/Protocols:HeliScopeCAGE_read_alignment
Genome_build: Human: hg19 and Mouse:mm9
Supplementary_files_format_and_content: Bed 6 file for trasncription start sites. Scores represent aggregated tags with same starting position.

source_name: Breast

growth_protocol: MCF-7, HeLa-S3 and HepG2 cells were cultured at 37 ˚C under 5% CO2 in DMEM with L-Gln supplemented with 1 mM sodium pyruvate and 10% FBS. GM12878 and K562 cells were cultured at 37 ˚C under 5% CO2 in RPMI 1640 with L-Gln supplemented with 1 mM sodium pyruvate and 10% FBS.

extract_protocol:
The cDNA synthesis was carried out using 5 μg of total and nascent RNA (A260/280 and 260/230 ratios > 1.7). CAGE libraries were generated based on no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) precisely as described in Murata et al. (Methods Mol Biol. 2014;1164:67-85.).
Cultured medium was aspirated and cells were gently washed twice with 5 mL of ice-cold 1x D-PBS. To lyse cells, 1,400 μL of Buffer A (Nuclei ez lysis buffer (Sigma-Aldrich), 25 μM alpha-amanitin (FUJIFILM Wako Pure Chemical), 1× cOmplete Protease Inhibitor solution (Sigma-Aldrich) and 20 units of SUPERase IN RNase Inhibitor (Thermo Fisher Scientific)) was directly added to a dish. Cells treated with Buffer A were harvested using a cell scraper. 100 μL of the cell lysate was sampled and mixed with 700 μL of QIAzol (QIAGEN) for total RNA extraction. The remaining lysate was set on ice for 10 minutes. Then the lysate was centrifuged at 800 G for 5 minutes at 4 ˚C. The pellets were washed once with 200 μL of Buffer A.
Washed pellets were resuspended in 200 μL of Buffer B (1% NP-40, 20 mM HEPES, 300 mM NaCl, 2 M Urea, 0.2 mM EDTA, 1 mM DTT, 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution and 20 units SUPERase IN RNase Inhibitor), and incubated for 10 minutes on ice. Then, nuclear insoluble fraction was collected by 3,000 G centrifuge for 2 minutes at 4 ˚C. The pellets were washed once with 100 μL of Buffer B.
50 μL of DNase I solution containing 10 units of DNase I (Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and 20 units of SUPERase IN RNase Inhibitor was added to the pellets. The solution was incubated for 30 minutes at 37 ˚C while pipetting up and down several times every 10 minutes. 700 μL of QIAzol was directly added to the solution and thoroughly mixed. RNA was extracted by miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. An “on-column DNase I digestion” was carried out using RNase-free DNase set (QIAGEN). RNA was eluted in 30 μL of RNase-free water, and quality and quantity were measured by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent).

treatment_protocol: For the time course experiment, MCF-7 cells were serum-starved for 16 hours, and heregulin beta-1 was added to the medium at a final concentration of 10 nM. Cells were harvested at 0 (no treatment), 15, 30, 45, 60, 120, 180 and 360 minutes in triplicates.

tag: tissue

value: MCF-7 cell line

tag: urea treatment

tag: molecule subtype

value: Nascent RNA


title: Nascent_RNA-seq_MCF-7_1M_biologicalRep2


title: Nascent_RNA-seq_MCF-7_2M_biologicalRep2


title: Nascent_RNA-seq_MCF-7_1M_biologicalRep1


title: Nascent_RNA-seq_MCF-7_2M_biologicalRep1


title: Nascent_RNA-seq_MCF-7_0.5M_biologicalRep1


title: RNA-seq_MCF-7_biologicalRep2

value: Total RNA


title: RNA-seq_MCF-7_biologicalRep1


title: NET-CAGE_K562_0.5M_biologicalRep2

data_processing:
Library strategy: RNA-seq (CAGE)
For all our datasets we performed the following steps, (i) split reads by barcode, (ii) trimmed reads to remove barcode sequences and (iii) removed reads aligned to rRNA sequences (Human: GenBank U13369.1; Mouse: GenBank BK000964.3). These steps were performed using MOIRAI (Hasegawa et al., 2014) for human cell line data and using Trimmomatic v 0.36 (Bolger et al., 2014) and MOIRAI (Hasegawa et al., 2014) for mouse tissue data. For all CAGE based data and mouse RNA-seq data, sequences with base ‘N’ were also removed.
Non rRNA reads were mapped hg19 genome and human reference gene model Gencode v27lift37 comprehensive using  STAR v 2.5.0a with the following parameters for indexing: --runThreadN 12 --runMode genomeGenerate --genomeDir genome.fa --sjdbGTFfile Gencodeannotation.gtf and the following parameters for mapping: --runThreadN 12 --outSAMtype BAM SortedByCoordinate --out FilterMultimapNmax 1 --readFilesCommand zcat.
Transcription start sites for CAGE based data were identified using bedtools v 2.2.25 (Quinlan and Hall, 2010) as described here: http://fantom.gsc.riken.jp/5/sstar/Protocols:HeliScopeCAGE_read_alignment
Genome_build: Human: hg19 and Mouse:mm9
Supplementary_files_format_and_content: Bed 6 file for trasncription start sites. Scores represent aggregated tags with same starting position.

source_name: Bone marrow

extract_protocol:
The cDNA synthesis was carried out using 5 μg of total and nascent RNA (A260/280 and 260/230 ratios > 1.7). CAGE libraries were generated based on no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) precisely as described in Murata et al. (Methods Mol Biol. 2014;1164:67-85.).
Approximately 1.0 × 107 cells were used for total and nascent RNA fractionation. Culture medium was transferred to a conical centrifuge tube and centrifuged at 800 G for 5 minutes at 4 ˚C. The supernatant was removed and the cell pellets were washed with 5 mL of ice-cold D-PBS. To lyse cells, 1,000 μL of Buffer A (Nuclei ez lysis buffer (Sigma-Aldrich), 25 μM alpha-amanitin (FUJIFILM Wako Pure Chemical), 1× cOmplete Protease Inhibitor solution (Sigma-Aldrich) and 20 units of SUPERase IN RNase Inhibitor (Thermo Fisher Scientific)) was added to the cell pellets and resuspended by gentle vortex. 100 μL of the cell lysate was sampled and mixed with 700 μL of QIAzol for total RNA extraction. The remaining lysate was set on ice for 10 minutes. Then the lysate was centrifuged at 800 G for 5 minutes at 4 ˚C. The pellets were washed once with 600 μL of Buffer A.
Washed pellets were resuspended in 200 μL of Buffer B (1% NP-40, 20 mM HEPES, 300 mM NaCl, 2 M Urea, 0.2 mM EDTA, 1 mM DTT, 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution and 20 units SUPERase IN RNase Inhibitor), and incubated for 10 minutes on ice. Then, nuclear insoluble fraction was collected by 3,000 G centrifuge for 2 minutes at 4 ˚C. The pellets were washed once with 100 μL of Buffer B.
50 μL of DNase I solution containing 10 units of DNase I (Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and 20 units of SUPERase IN RNase Inhibitor was added to the pellets. The solution was incubated for 30 minutes at 37 ˚C while pipetting up and down several times every 10 minutes. 700 μL of QIAzol was directly added to the solution and thoroughly mixed. RNA was extracted by miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. An “on-column DNase I digestion” was carried out using RNase-free DNase set (QIAGEN). RNA was eluted in 30 μL of RNase-free water, and quality and quantity were measured by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent).

value: K562 cell line


title: NET-CAGE_K562_0.5M_biologicalRep1


title: Ctrl_ATMi_untreated_rep2

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol with Agilent SureScan microarray scanner (G2505C).

data_processing: Scanned images were processed with Agilent Feature Extraction v10.7 with default parameters to obtain raw data. Raw data were imported in R and processed using the limma package. After background correction with the normexp method, raw data were normalized with quantile method and log2 transformed. Intensity values from replicated probes were summarized calculating the mean expression.

source_name: hiPSC-derived neurons from healthy donor at DIV30

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations.

growth_protocol: hiPSC-derived neurons were terminally differentiated until 30 days in vitro (DIV30) stage from hNPCs that were seeded on Matrigel coated dishes in a medium made of   DMEM/F12 supplemented with 2mM glutamax, 100 units/ml penicillin, 100 mg/ml  streptomycin, 1:500 B27 supplement, 1:100 N2 supplement, 20 ng/ml EGF  and 20 ng/ml bFGF.

extract_protocol: Treated and untreated neurons were detached with Accutase Solution, harvested by centrifugation and lysed in QIAzol Lysis Reagent. Total RNA was then extracted and purified using the RNeasy Mini Kit according to the manifacturer's instructions.

treatment_protocol: DIV30 hiPSC-derived neurons were exposed to 30 μM CPT for 1h and subsequent drug washout for 3h. The untreated samples didn't receive CPT. In one condition, both untreated and CPT-treated neurons were pre-incubated for 1h with 10μM ATMi (KU-55933).

tag: condition


title: NET-CAGE_K562_2M_biologicalRep2

value: 2 M


title: NET-CAGE_K562_2M_biologicalRep1


title: NET-CAGE_K562_1M_biologicalRep2

value: 1 M


title: Ctrl_untreated_rep3


title: NET-CAGE_K562_1M_biologicalRep1


title: RFF4_CD8aa

city: Tokushima

first: Chieko

last: Ishifune

address: 3-18-15 Kuramoto

department: Department of Immunology and Parasitology

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GEx ver. 2.0 Microarrays (G4858A) for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity (Shift to 75 percentile) in Series supplementary file

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from sorted IELs and purified using the ReliaPrep RNA Cell Miniprep System (Promega). Samples are pooled from several isolation experiments. The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Small intestinal IELs were dispersed by 1mM EDTA and isolated by 40%/75% percoll.  For purification of TCRαβ+ CD8αα+ IELs,  CD4+ and TCRγδ+ cells were previously depleted from total IELs, and then stained with anti-TCRβ, TCRγδ, CD4, CD8α, and CD8β antibody.  TCRαβ+ CD8αα+ IELs (TCRgd- CD4- CD8b-) were soted for microarray analysis.

tag: strain

value: small intestine

tag: gender

value: pooled male and female

value: 8-12 weeks old

value: TCR{alpha}{beta}+ CD8{alpha}{alpha}+ intraepithelial lymphocytes

tag: genotype

value: CD4-Cre Rbpjf/f (RFF4)


title: Control_CD8aa

tag: age

value: Rbpjf/f (Control)


title: Ctrl_untreated_rep2


title: Ctrl_ATMi_3h_post_CPT_rep3


title: Ctrl_3h_post_CPT_rep2


title: Ctrl_ATMi_untreated_rep3


title: CAGE_K562_biologicalRep2


title: CAGE_K562_biologicalRep1


title: NET-CAGE_HepG2_2M_biologicalRep2

source_name: Liver

extract_protocol:
The cDNA synthesis was carried out using 5 μg of total and nascent RNA (A260/280 and 260/230 ratios > 1.7). CAGE libraries were generated based on no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) precisely as described in Murata et al. (Methods Mol Biol. 2014;1164:67-85.).
Approximately 1.0 × 107 cells were used for total and nascent RNA fractionation. Cultured medium was aspirated and cells were gently washed twice with 5 mL of ice-cold 1x D-PBS. To lyse cells, 1,400 μL of Buffer A (Nuclei ez lysis buffer (Sigma-Aldrich), 25 μM alpha-amanitin (FUJIFILM Wako Pure Chemical), 1× cOmplete Protease Inhibitor solution (Sigma-Aldrich) and 20 units of SUPERase IN RNase Inhibitor (Thermo Fisher Scientific)) was directly added to a dish. Cells treated with Buffer A were harvested using a cell scraper. 100 μL of the cell lysate was sampled and mixed with 700 μL of QIAzol (QIAGEN) for total RNA extraction. The remaining lysate was set on ice for 10 minutes. Then the lysate was centrifuged at 800 G for 5 minutes at 4 ˚C. The pellets were washed once with 200 μL of Buffer A.
Washed pellets were resuspended in 200 μL of Buffer B (1% NP-40, 20 mM HEPES, 300 mM NaCl, 2 M Urea, 0.2 mM EDTA, 1 mM DTT, 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution and 20 units SUPERase IN RNase Inhibitor), and incubated for 10 minutes on ice. Then, nuclear insoluble fraction was collected by 3,000 G centrifuge for 2 minutes at 4 ˚C. The pellets were washed once with 100 μL of Buffer B.
50 μL of DNase I solution containing 10 units of DNase I (Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and 20 units of SUPERase IN RNase Inhibitor was added to the pellets. The solution was incubated for 30 minutes at 37 ˚C while pipetting up and down several times every 10 minutes. 700 μL of QIAzol was directly added to the solution and thoroughly mixed. RNA was extracted by miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. An “on-column DNase I digestion” was carried out using RNase-free DNase set (QIAGEN). RNA was eluted in 30 μL of RNase-free water, and quality and quantity were measured by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent).

value: HepG2 cell line


title: cells transfected with 0.5nM miR199a-3p, 1

city: Paris

first: Paola

last: Arimondo

address: 28 rue du Dr Roux

department: Institut Pasteur

country: France

institute: CNRS

hyb_protocol: Genechip Expression hybridization controls and Genechip hybridization wash and stain kit (Affymetrix) according to manufacturer’s instructions.

scan_protocol: Microarrays were scannedon the Genechip scanner 3000 7G with autoloader according to manufacturer’s instructions.

data_processing:
The data were transformed en log2 with package oligo.Before normalisation quality controls were run on all probes corresponding to transcripts including the control probes with package affy. RMA normalisation was applied with package oligo on each condition with option “core”. Quality controls were run after normalisation on all probes corresponding to genes with package affy.
Differentially expressed genes between the treated and control conditions were determined choosing a threshold of Log2 fold change at 0.5 and a p-value < 0.05. P-value cut-off is FDR corrected.

source_name: WM266-4 cell line

label_protocol: Genechip WT PLUS reagent (Affymetrix) according to manufacturer’s instructions.

growth_protocol: Exponentially growing WM266-4 GFP cells were seeded at 160.000 cells/500 µL in 24-well plates

extract_protocol: Cells were recovered 48 h after transfection for further analysis. Total RNA extraction was performed on 500.000 cells, using Tri Reagent (Sigma-Aldrich) for total RNA isolation, following the manufacturer’s protocol and adding glycogen.

treatment_protocol: Cells were transfected with miR mimics at the mentioned concentrations and using LipofectamineTM 2000 Reagent (Life Technologies) according to manufacturer’s instructions. (Biological triplicates)

tag: disease

value: melanoma metastasis

tag: cell line


title: Ctrl_ATMi_3h_post_CPT_rep2


title: Ctrl_3h_post_CPT_rep1


title: cells transfected with 0.25nM miR199a-3p, 2


title: cells transfected with 0.5nM miR199a-3p, 2


title: cells transfected with ctrl miR (0.5nM), 2

value: ctrl miR (0.5nM)


title: retina P7

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

department: Neurobiology & Anatomy

institute: University of Utah

data_processing:
Base calls generated by Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61).
Fastq files were aligned to ensembl Mus musculus cDNA annotation (release 92) with salmon (v0.9.1).
The alignments were compiled with tximport (v1.8.0), and analyzed with DESeq2 (v1.20.0).
Genes were excluded from downstream analysis if they did not have at least 10 reads in at least one of the 14 datasets.
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: Tab-delimited file contains raw read counts, FPKM values, pairwise log2ratio and adjusted p-value (from DESeq2).

source_name: retina

extract_protocol:
For sorted migroglia: freshly dissected pure retinas were dissociated in PBS, 50 mM HEPES, 0.05 mg/ml DNase I (Sigma D4513), 0.025 mg/ml Liberase (Sigma 5401119001) for 35 min with intermediate trituration. Cells were passed through a 70 μm nylon cell strainer, washed with staining buffer (1X PBS, 2% BSA, 0.1% sodium azide, 0.05% EDTA), and red blood cells were lysed (eBioscience 00-4333-57). Cell counts were determined using a cell counter (Invitrogen Countess) and Fc block (BD Biosciences 553142) was added at 2 μl per 106 cells. Antibodies were applied for 30 min on ice (BV421-CD45 BD Bioscience 563890; APC-CCR2 Fisher Scientific FAB5538A100). Cells were washed, pelleted, and resuspended in 500 μl staining buffer. FACS was performed using a BD FACS Aria cell sorter at the University of Utah Flow Cytometry Core. Forward and side scatter were used to eliminate debris and the height and area of the forward scatter was used to discriminate singlets. Unstained cells were used as negative controls and were used to set gates. GFP+, CD45+, CCR2- were sorted directly into RLT buffer (Qiagen 79216) and stored at −20°C. Three biological replicates of retinal microglia were collected for each age. 1-2 litters were pooled for each sample at e16.5, 5-12 retinas were pooled for P7, and 7-14 retinas were pooled for P60. RNA from sorted cells was purified using an RNeasy Plus Micro kit (Qiagen 74034). Whole retina samples (central retina for e16.5) were dissected in 1x PBS on ice, placed in RLT buffer and stored at -20oC. RNA was extracted from whole retina samples with the RNeasy Plus Mini kit (Qiagen 74134).
The University of Utah High-Throughput Genomics Core ran Agilent High Sensitivity RNA ScreenTape Assay to determine RNA quality. For sorted microglia samples: cDNA libraries were generated using the NuGEN Ovation RNA-seq System v2 for ultra-low input samples, and individual bar-coded RNA-seq libraries were prepared for each sample. High quality whole retina RNA samples were transformed into sequencing libraries with TruSeq Stranded RNA Kit with Ribo-Zero Gold (Illumina RS-122-2301 and RS-122-2302).

value: WT


title: retina e16.5 2


title: Ctrl_ATMi_untreated_rep1


title: cells transfected with 0.5nM miR199a-3p, 3


title: retina P60


title: retina e16.5 3


title: NET-CAGE_HepG2_1M_biologicalRep2


title: cells transfected with 0.25nM miR199a-3p, 1


title: Ctrl_ATMi_3h_post_CPT_rep1


title: cells transfected with ctrl miR (0.5nM), 1


title: Ctrl_3h_post_CPT_rep3


title: cells transfected with ctrl miR (0.5nM), 3


title: NET-CAGE_HepG2_0.5M_biologicalRep2


title: retina e16.5 1


title: cells transfected with 0.25nM miR199a-3p, 3


title: mg P60 3

source_name: retinal microglia


title: mg P60 2


title: NET-CAGE_HepG2_1M_biologicalRep1


title: NET-CAGE_HepG2_0.5M_biologicalRep1


title: Ctrl_untreated_rep1


title: CAGE_HepG2_biologicalRep2


title: mg P60 1


title: mg P7 2


title: NET-CAGE_HeLa-S3_2M_biologicalRep2

source_name: Cervix

value: HeLa-S3 cell line


title: CAGE_HepG2_biologicalRep1


title: mg e16.5 1


title: mg P7 1


title: NET-CAGE_HeLa-S3_1M_biologicalRep2


title: NET-CAGE_HeLa-S3_1M_biologicalRep1


title: NET-CAGE_HeLa-S3_2M_biologicalRep1


title: CAGE_HeLa-S3_biologicalRep1


title: NET-CAGE_HeLa-S3_0.5M_biologicalRep1


title: e12.5_mouse_forelimb_H3K27ac_Input_rep2

first: Marie

last: Kmita

address: 110 Pine Ave W

institute: Institut de recherches cliniques de Montreal (IRCM)

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x.
Sam files were converted into tag directories using HOMER v4.9.1 and into bam files using Samtools v1.4.1 view function.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER with the following parameters:-fsize 1e20 -fragLength 150 –bigWig. Scores represent reads normalized per 10000000 reads

source_name: forelimb bud

extract_protocol:
ChIP experiments were performed in dissected proximal and distal forelimb buds of CD1 (wild type) and Prrx1Cre; EedDel/Flox (Eedc/-) mice at E12.5 following the same conditions as previously described (Berlivet et al., 2013). Chromatin was cross-linked for 13 minutes using formaldehyde and sonicated using Fisher Scientific, Model 100 sonic dismembrator to obtain fragments between 100-600 bp. Protein A and Protein G Dynabeads (Invitrogen) were incubated for 6 hours at 4℃ with 5ug Suz12 (D39F6, Cell Signaling), 4ug H3K27Ac (ab-4729, Abcam), and 4ug Ring1b (39663, Active Motif). The chromatin was coupled to the beads overnight at 4℃. The immunoprecipitated samples were then washed with different wash buffers depending on the antibody present. For SUZ12 antibody, 6 sequential RIPA washes (50mM Hepes-KOH (pH7.5), 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) were performed. For both H3K27Ac and RING1B sequential washes in low salt (1% Triton, 0,1% SDS, 150 mM NaCl, 20 mM Tris (pH8), 2 mM EDTA), high salt (1% Triton, 0,1% SDS, 500 mM NaCl, 20 mM Tris pH8, 2 mM EDTA), LiCl (1% NP-40, 250 mM LiCl, 10 mM Tris (pH8), 1 mM EDTA) and TE buffer (50 mM NaCl, 10 mM Tris (pH8), 1 mM EDTA) were performed. Lastly, the DNA was purified on QIAquick columns (Qiagen).
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina Hiseq 2500 in a 50 cycles paired-end configuration.

tag: developmental stage

value: forelimb bud

value: mixed background C57Bl/6 x 129

value: Prrx1Cre; EedDel/Flox

tag: antibody

value: none (input)


title: e12.5_mouse_distal_forelimb_Eedc/-_H3K27ac_ChIPseq_rep2

tag: tissue region

value: distal

value: H3K27ac Abcam:ab-4734


title: e12.5_mouse_forelimb_H3K27ac_Input_rep1


title: CAGE_HeLa-S3_biologicalRep2

value: Total RNA


title: aCGH analysis of AM patient-1

first: Akinobu

last: Ota

institute: Kinjo Gakuin University

description: Somatic genomic alterations of ameloblastoma in AM patient-1

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parametersto obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

extract_protocol: For oligo-aCGH, genomic DNA was obtained from both tumor and normal tissues from 8 ameloblastoma patients using proteinase K/RNAse treatment and phenol–chloroform extraction according to standard procedures. DNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

value: ameloblastoma tumor

tag: Sex

value: Male

source_name: AM-001_normal tissue

value: normal tissue


title: e12.5_mouse_distal_forelimb_Eedc/-_H3K27ac_ChIPseq_rep1

value: H3K27ac Abcam:ab-4733


title: mg P7 3


title: e12.5_mouse_proximal_forelimb_Eedc/-_H3K27ac_ChIPseq_rep1

value: proximal

value: H3K27ac Abcam:ab-4732


title: e12.5_mouse_proximal_forelimb_WT_H3K27ac_ChIPseq_rep1

value: H3K27ac Abcam:ab-4729


title: e12.5_mouse_distal_forelimb_WT_H3K27ac_ChIPseq_rep2

value: H3K27ac Abcam:ab-4731


title: e12.5_mouse_distal_forelimb_WT_H3K27ac_ChIPseq_rep1

value: WT

value: H3K27ac Abcam:ab-4730


title: e12.5_mouse_distal_forelimb_Eedc/-_RING1B_ChIPseq_rep2

value: forelimb bud

value: RING1B Actif Motif:39668


title: e12.5_mouse_forelimb_RING1B_Input_rep1

value: mixed background C57Bl/6 x 129


title: e12.5_mouse_forelimb_RING1B_Input_rep2

value: Prrx1Cre; EedDel/Flox

value: none (input)


title: e12.5_mouse_distal_forelimb_Eedc/-_RING1B_ChIPseq_rep1

value: distal

value: RING1B Actif Motif:39667


title: NET-CAGE_HeLa-S3_0.5M_biologicalRep2

value: HeLa-S3 cell line

value: Nascent RNA


title: mg e16.5 3


title: e12.5_mouse_proximal_forelimb_Eedc/-_RING1B_ChIPseq_rep1

value: RING1B Actif Motif:39666


title: mg e16.5 2


title: e12.5_mouse_distal_forelimb_WT_RING1B_ChIPseq_rep1

value: RING1B Actif Motif:39664


title: e12.5_mouse_proximal_forelimb_WT_RING1B_ChIPseq_rep1

value: proximal

value: RING1B Actif Motif:39663


title: e12.5_mouse_forelimb_Suz12_Input_rep2


title: e12.5_mouse_distal_forelimb_WT_RING1B_ChIPseq_rep2

value: RING1B Actif Motif:39665


title: e12.5_mouse_distal_forelimb_WT_SUZ12_ChIPseq_rep1

value: SUZ12 Cell Signaling:D39F6


title: e12.5_mouse_distal_forelimb_WT_SUZ12_ChIPseq_rep2

value: WT


title: e12.5_mouse_forelimb_Suz12_Input_rep1


title: NET-CAGE_MCF-7_2M_frozen_DMSO_biologicalRep2

extract_protocol:
The cDNA synthesis was carried out using 5 μg of total and nascent RNA (A260/280 and 260/230 ratios > 1.7). CAGE libraries were generated based on no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) precisely as described in Murata et al. (Methods Mol Biol. 2014;1164:67-85.).
Approximately 1.0 x 107 cells were prepared for different freezing conditions as follows. (i) Fresh: fresh MCF-7 cell pellets without cryopreservation were used as a control. 1,000 μL of Buffer A was directly added to the fresh cell pellets. (ii) Flash-frozen (Cryopreservation in pellet form): cell pellets were flash-frozen. Pellets without any medium were stored at -80 ˚C for 4 days. 1,000 μL of Buffer A (Nuclei ez lysis buffer (Sigma-Aldrich), 25 μM alpha-amanitin (FUJIFILM Wako Pure Chemical), 1× cOmplete Protease Inhibitor solution (Sigma-Aldrich) and 20 units of SUPERase IN RNase Inhibitor (Thermo Fisher Scientific)) was directly added to the frozen cell pellets. (iii) Cryopreservation with 10% Dimethyl sulfoxide (DMSO): the pellets were resuspended in 5 ml of DMEM containing 10% DMSO supplemented with FBS. The suspension was slowly frozen and stored for 4 days at -80 ˚C. Frozen cells were quickly thawed at 37 ˚C in a water bath. Then the suspension was centrifuged at 800 G for 5 minutes at 4 ˚C and the supernatant was removed. 1,000 μL of Buffer A was added to the cell pellets. (iv) Cryopreservation with CELLBANKER® 1 plus (NIPPON ZENYAKU KOGYO): the pellets were resuspended in 5 ml of CELLBANKER® 1 plus. The suspension was frozen at -80 ˚C and stored at -80 ˚C for 4 days. Frozen cells were quickly thawed at 37 ˚C in a water bath. Then the suspension was centrifuged at 800 G for 5 minutes at 4 ˚C and the supernatant was removed. 1,000 μL of Buffer A was added to the cell pellets. The lysate was set on ice for 10 minutes. Then the lysate was centrifuged at 800 G for 5 minutes at 4 ˚C. The pellets were washed once with 600 μL of Buffer A.
Washed pellets were resuspended in 200 μL of Buffer B (1% NP-40, 20 mM HEPES, 300 mM NaCl, 2 M Urea, 0.2 mM EDTA, 1 mM DTT, 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution and 20 units SUPERase IN RNase Inhibitor), and incubated for 10 minutes on ice. Then, nuclear insoluble fraction was collected by 3,000 G centrifuge for 2 minutes at 4 ˚C. The pellets were washed once with 100 μL of Buffer B.
50 μL of DNase I solution containing 10 units of DNase I (Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and 20 units of SUPERase IN RNase Inhibitor was added to the pellets. The solution was incubated for 30 minutes at 37 ˚C while pipetting up and down several times every 10 minutes. 700 μL of QIAzol was directly added to the solution and thoroughly mixed. RNA was extracted by miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. An “on-column DNase I digestion” was carried out using RNase-free DNase set (QIAGEN). RNA was eluted in 30 μL of RNase-free water, and quality and quantity were measured by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent).

value: MCF-7 cell line


title: NET-CAGE_MCF-7_2M_frozen_pellets_biologicalRep2


title: Young_1_C21

city: Rochester

first: Laura

last: Calvi

state: New York

address: 601 Elmwood Ave

department: Medicine

institute: University of Rochester Medical Center

data_processing:
DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Genome_build: GRCm38.p4 + Gencode-M6 Annotation
Supplementary_files_format_and_content: text file includes raw expression counts

source_name: Long-Term Hematopetic Stem Cell

growth_protocol: Mice were bred and mantained per standard rodent colony husbandry guidelines

extract_protocol:
Single long-term hematopoietuc stem cells (LT-HSC: Lineage-, Sca1+, cKit+, Flt3-, CD48-, CD150+) were captured on a 5–10 μm cell diameter integrated microfluidic chip (IFC) using the Fluidigm C1 Single-cell AutoPrep system (Fluidigm Corporation). Cells were pre-stained with Calcien AM/EthD-1 LIVE/DEAD cell viability assay (Life Technologies) and loaded onto the IFC at a concentration of 500–700 cells/ul.  Viable single cell confirmation was performed with phase-contrast fluorescence microscopy to assess the number and viability of cells per capture site. Only single, live cells were included in the analysis.
For RNA-seq analysis, cDNAs were prepared “on-IFC” using the SMARTer Ultra Low RNA kit for Illumina (Clontech) following fluidigm recomemdnations. Single-cell cDNA size distribution and concentration was assessed with PicoGreen (Life Technologies) and Agilent Bioanalyzer 2100 analysis (Agilent Technologies). Illumina libraries were constructed in 96-well plates using Illumina’s NexteraXT DNA Sample Preparation kit following the protocol supplied by Fluidigm. For each C1 experiment, a bulk RNA control and a negative control were processed in parallel, using the same reagent mixes as used on chip. Libraries were quantified by Agilent Bioanalyzer, using High Sensitivity DNA analysis kit, and also fluorometrically, using Qubit dsDNA HS Assay kits and a Qubit 2.0 Fluorometer (Technologies).
Fluidigm C1 full-length single-cell RNAseq

value: male

value: 3 months

value: Long-Term Hematopetic Stem Cell


title: Young_1_C51


title: e12.5_mouse_proximal_forelimb_WT_SUZ12_ChIPseq_rep1

value: forelimb bud

value: mixed background C57Bl/6 x 129


title: Young_1_C07


title: NET-CAGE_MCF-7_2M_frozen_cellbanker_biologicalRep1


title: NET-CAGE_MCF-7_2M_fresh_biologicalRep2


title: NET-CAGE_MCF-7_2M_frozen_cellbanker_biologicalRep2


title: Young_1_C41


title: NET-CAGE_MCF-7_2M_frozen_pellets_biologicalRep1


title: Young_1_C77


title: NET-CAGE_MCF-7_2M_fresh_biologicalRep1


title: Young_1_C24


title: Young_1_C92


title: Young_1_C02


title: Young_1_C23


title: NET-CAGE_MCF-7_2M_time120_biologicalRep3


title: NET-CAGE_MCF-7_2M_time120_biologicalRep4


title: NET-CAGE_MCF-7_2M_time180_biologicalRep3


title: NET-CAGE_MCF-7_2M_time360_biologicalRep3


title: NET-CAGE_MCF-7_2M_time60_biologicalRep3


title: NET-CAGE_MCF-7_2M_time45_biologicalRep3


title: Young_1_C61


title: NET-CAGE_MCF-7_2M_frozen_DMSO_biologicalRep1


title: Young_1_C79


title: Young_1_C86


title: NET-CAGE_MCF-7_2M_time0_biologicalRep3


title: NET-CAGE_MCF-7_2M_time30_biologicalRep3


title: Young_1_C57


title: Young_1_C28


title: NET-CAGE_MCF-7_2M_time180_biologicalRep2


title: Young_1_C40


title: NET-CAGE_MCF-7_2M_time360_biologicalRep2


title: NET-CAGE_MCF-7_2M_time120_biologicalRep2


title: NET-CAGE_MCF-7_2M_time60_biologicalRep2


title: Young_1_C04


title: Young_1_C84


title: Young_1_C88


title: HDAC5AA expressing retina rep3

city: Saint Louis

first: Valeria

last: Cavalli

state: Missouri

address: 660 S. Euclid Ave.

department: Anatomy and Neurobiology

institute: Washington University in St. Louis

data_processing:
Fastq files were aligned to mm10 using STAR-align
Aligned reads were counted using HTseq-count using default settings
Differential expression was performed using DESeq2
Genes with fewer than an average of 5 cpm were removed
Genome_build: mm10
Supplementary_files_format_and_content: Files were generated using DESeq2 and provide differential expression, rlog normalized counts per million, and adjusted p-values.

source_name: Retina

extract_protocol:
RNA was isolated using PureLink RNA Mini Kit (Life Technologies). Briefly, mice retinas were dissected out and homogenized in 300 µL lysis buffer plus mercaptoethanol using disposable pestles attached to a motor (Kontes). Lysates were passed 10 times through an insulin syringe and centrifuged at 12,000g at 4°C. Supernatant was transferred to a tube containing one volume of ethanol, mixed, and transferred to a Spin Column (PureLink RNA Mini Kit; Thermo).  PureLink DNAse treatment (Thermo) was performed in the column for 15 minutes. Purified RNA was stored at -80°C before
Ribosomal RNA was depleted using the Ribo-Zero rRNA Removal kit. cDNA Libraries were prepared using Clontech’s SMARTer kits for Illumina Sequencing (Clontech). The libraries were sequenced on HiSeq 3000 using 1x 50 single read.

treatment_protocol: AAV-GFP, AAV-HDAC5DAD and HDAC5AA  (Viral titer ranged between 5 x 10^12 vg/mL to 1 x 10^13 vg/mL) were intravitreally injected. After two weeks, optic nerve crushed was performed  by exposing the optic nerve and crushing with sterile jeweler's forceps for 3 seconds around 1 mm behind the optic disc. After 4 days, mice were sacrificed by CO2 and retinas were immediately dissected out.

tag: genotype/variation

value: HDAC5AA expressing retina with optic nerve crush

value: retina

value: Adult (around 6 weeks)


title: NET-CAGE_MCF-7_2M_time45_biologicalRep2

value: Nascent RNA


title: HDAC5AA expressing retina rep4


title: Young_1_C65


title: NET-CAGE_MCF-7_2M_time30_biologicalRep2


title: HDAC5AA expressing retina rep1


title: HDAC5AA expressing retina rep2


title: NET-CAGE_MCF-7_2M_time15_biologicalRep2


title: NET-CAGE_MCF-7_2M_time15_biologicalRep3


title: HDAC5DAD expressing retina rep4

value: HDAC5DAD expressing retina with optic nerve crush


title: HDAC5DAD expressing retina rep3


title: Young_1_C74


title: HDAC5DAD expressing retina rep2


title: Young_1_C62


title: HDAC5DAD expressing retina rep1


title: GFP expressing retina rep4

value: GFP expressing retina with optic nerve crush


title: GFP expressing retina rep3


title: Young_1_C26


title: NET-CAGE_MCF-7_2M_time360_biologicalRep1


title: GFP expressing retina rep2


title: Young_1_C49


title: Non injured retina rep4

description: RGC_GFPvUninjured.xlsx, RGC_HDAC5DADvUninjured.xlsx, RGC_HDAC5AAvUninjured.xlsx

value: Non injured retina


title: NET-CAGE_MCF-7_2M_time60_biologicalRep1


title: Non injured retina rep3


title: GFP expressing retina rep1


title: Young_1_C25


title: Young_1_C80


title: NET-CAGE_MCF-7_2M_time45_biologicalRep1


title: Non injured retina rep1


title: Non injured retina rep2


title: NET-CAGE_MCF-7_2M_time0_biologicalRep2


title: NET-CAGE_MCF-7_2M_time30_biologicalRep1


title: Ttol-2: Tolerance induced, biological rep2

description: Gene expression data from Nr4a1-oeverexpressed T cells.

source_name: Nr4a1-oeverexpressed T cells.

tag: cell type

value: T cells

value: Tolerance-induced


title: Ttol-1: Tolerance induced, biological rep1


title: Young_1_C46


title: NET-CAGE_MCF-7_2M_time15_biologicalRep1


title: Young_1_C66


title: Young_1_C53


title: NET-CAGE_MCF-7_2M_time180_biologicalRep1


title: NET-CAGE_MCF-7_2M_time0_biologicalRep1


title: Young_1_C31


title: CAGE_MCF-7_time120_biologicalRep4

value: Total RNA


title: Young_1_C81


title: Sample_48693

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

description: Condition 3: Uninjured hindlimb tendon (no burn and no tenotomy)

data_processing:
The quality of the fastq files from the sequencer were first checked using FastQC (v0.11.4).
used Kallisto to extract expression matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: Data matrix table is in text format

source_name: hindlimb tendon

extract_protocol:
Tissue was harvested from the Tenotomy site: between the insertion point in the gastrocnemius muscle and the attachment of the tendon at the calcaneous. Total RNA was extracted using Trizol™ reagent, and subsequently purified using a RNAeasy kit from Qiagen. RNA purity was confirmed before sequencing. Condition 1 is the uninjured right leg from the B/T, condition 2 is the injured left leg of B/T, and condition 3 is from uninjured WT non-B/T mouse.
TruSeq RNA-prep kit, according to manufacturer's protocol

treatment_protocol: A partial-thickness scald burn injury was administered to animals according to a previously described protocol by a single surgeon.3,57 Briefly, mice were anesthetized with inhaled isoflurane. Dorsal hair was closely clipped, and an aluminum block heated to 60°C was exposed to the dorsal region over 30% of the total body surface area for 18 s to achieve a partial-thickness burn injury. Each mouse then received a concurrent sterile dorsal hind limb tendon transection at the midpoint of the Achilles tendon (Achilles tenotomy) with placement of a single 5-0 vicryl suture to close the skin. Pain management was achieved with subcutaneous injections of buprenorphine (Buprenex, Reckitt Benckiser Pharmaceuticals) every 12 hr for 2 days.

value: 3 - Uninjured hindlimb tendon (no burn and no tenotomy)

value: C57BL/6 background


title: Young_1_C09

value: male


title: CAGE_MCF-7_time360_biologicalRep3

value: MCF-7 cell line


title: Sample_45866

description: Condition 2: Tenotomy site of a burn/tenotomy mouse (3 weeks after injury)

value: 2 - Tenotomy site of a burn/tenotomy mouse (3 weeks after injury)

tag: timepoint

value: three week tenotomy sites after burn tenotomy


title: CAGE_MCF-7_time180_biologicalRep3

tag: tissue


title: Sample_45867


title: Young_1_C20

value: 3 months

value: Long-Term Hematopetic Stem Cell


title: Sample_44743


title: CAGE_MCF-7_time120_biologicalRep3

tag: urea treatment


title: Long2

city: Seoul

first: Eunkyong

last: Ko

address: Gwanak ro

country: South Korea

institute: Seoul National University

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human HT-12 expression v.4 bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner.

data_processing:
The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)).   Array probes transformed by logarithm and normalized by quantile method.  Statistical significance of the expression data was determined using Fold change.  Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp).  All data analysis and visualization of differentially expressed genes was conducted using R 2.15.1 (www.r-project.org).
The file data2.xlsx contains both raw (AVG_Signal) and normalized signal for all replicates. The file data2.normalize.xlsx contains data summarized across the two replicates. The file data2-significant.xlsx contains genes identified with differential expression and gene ontology analysis by DAVID.

source_name: Human hepatocellular carcinoma cell Huh7

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: Cell lines were grown in Dulbecco’s modified Eagle’s medium (DMEM; Welgene, Gyeongsan-si, Korea) supplemented with 10 % fetal bovine serum (FBS; GenDepot, Barker, TX, USA) and cultured in a humidified 5 % CO2 incubator at 37°C.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Culture media were replaced daily, and cells were incubated for 4 days in 300 μM of H2O2 (H1009, Sigma).

value: Human hepatocellular carcinoma

tag: telomere length

value: long telomere


title: Sample_44742

description: Condition 1: Uninjured, contralateral hindlimb tendon of a burn/tenotomy mouse (3 weeks after injury)

tag: condition

value: 1 - Uninjured, contralateral hindlimb tendon of a burn/tenotomy mouse (3 weeks after injury)


title: Long


title: Rb_lo

city: Cleveland

first: Brian

last: Cobb

state: OH

address: 10900 Euclid Avenue, WRB 5132

department: Pathology

institute: Case Western Reserve University School of Medicine

data_processing:
Poor quality reads were trimmed with trimmomatic
Read alignment was performed using TopHat guided by Gencode vm4
Read counts were calculated using htseq-count and  Gencode vm4 annotations
RPKM values were calculated in R
Differential expression analysis between “hi” and “lo” samples was performed using the negative binomial test
implemented in DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: spreadsheet in Excel format

source_name: splenic CD4+ T cells

extract_protocol:
CD4+CD62L-CD44+FoxP3-CD45RbLo (RbLo TEM) and CD4+CD62L+CD44-FoxP-CD45RbHi (RbHi TN) cells were isolated from spleens of resting mice using FACS on a FACSAria.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured in wells of a 96 well plate coated with 2ug anti-CD3 antibody for 72 hours, harvested, and mRNA purified.

tag: strain

value: spleen

tag: activation

value: activated via CD3 for 72 hours


title: Sample_44740


title: Young_1_C69


title: CAGE_MCF-7_time60_biologicalRep3

tag: molecule subtype


title: NET-CAGE_HepG2_2M_biologicalRep1

value: HepG2 cell line

value: 2 M

value: Nascent RNA


title: Short2

value: short telomere


title: Rb_lo_o


title: Rb_hi_o


title: Short


title: CAGE_MCF-7_time45_biologicalRep3

value: Total RNA


title: Young_1_C56

tag: age


title: CAGE_MCF-7_time30_biologicalRep3


title: 20-K

city: Wauwatosa

first: John

middle: Henry

last: Dasinger

state: Wisconsin

address: 8701 W. Watertown Plank Road

institute: Medical College of Wisconsin

description:
K_CRLLS_CRLHS_10W.txt
K_MCWHS_CRLHS_10W.txt
BvsK_CRLHS_10W.txt

data_processing:
The raw sequences from HiSeq 2500 were first processed and trimmed
The trimmed short reads were mapped to the rat reference genome (rn5)
Bisulfite conversion rates were estimated from the number of unconverted cytosines at Klenow filled-in 3’MspI sites of sequencing reads that were short enough to read through these sites.
For each CpG site, the methylation rate (5mC) was calculated as the percentage of unconverted cytosines in each library
Metiline software was used to identify all methylation regions across the genome and subsequently identify differentially methylated regions (DMRs) between two groups of rats
A DMR was defined to contain at least five CpG sites, exhibit a 5mC difference of greater than 5% between two tested groups and a corrected p-value (q-value) <0.05
We divided genomic regions of interest into 3 groups including transcription start site (TSS), intragenic and intergenic. TSS regions were defined as 1 kb upstream or downstream of the TSS of a known gene. The intragenic was defined as a region between the start and end of a transcript. The intergenic regions were defined as regions between known transcripts.
Genome_build: Genome_build: rn5
Supplementary_files_format_and_content: processed files are the output of metiline's all methylation regions with default columns. Each txt file is named based on the comparison within. Comparisons are made between blood and kidney in files starting with "BvsK_" within same group, and across different groups either in blood in the files starting with "B_" or in the kidney in the files starting with "K_". each value uses the 4 samples in the group

source_name: Kidney T-cells

extract_protocol:
Perform the bisulfite conversion and subsequent clean-up using the QIAGEN EpiTect (or an equivalent) kit. Follow the manufacturer's protocol designated for DNA extracted from FFPE tissues for all samples, whether they are from FFPE material or not. Elute the DNA from the column with 22 μl of preheated (65 °C) EB buffer (from the EpiTect kit).
A total of 40 libraries were generated according to the previously described protocols by Gu et al. (Nature Protocols volume 6, pages 468–481 (2011)). The libraries underwent cluster generation using TruSeq PE Cluster Kit v4-cBot-HS and 100 cycles of paired-end sequencing using TruSeq SBS Kit v4-HS (Illumina). 13 or 14 libraries were multiplexed in one lane and sequenced on an Illumina HiSeq 2500 sequencer.

value: Kidney T-cells

tag: rat type

value: Dahl SS/JrHsdMcwiCrl rat (SS/CRL)

tag: chow

value: HS, 3 weeks

value: 10 weeks


title: Young_1_C73

value: male


title: 18-K


title: Young_1_C58

value: 3 months


title: 19-K


title: 17-K


title: Young_1_C06

value: Long-Term Hematopetic Stem Cell


title: 16-K

description:
K_CRLLS_CRLHS_10W.txt
K_MCWLS_CRLLS_10W.txt
BvsK_CRLLS_10W.txt

value: LS


title: 15-K


title: 14-K


title: Rb_hi


title: 11-K

description:
K_MCWLS_7W_10W.txt
BvsK_MCWLS_7W.txt

value: Dahl SS/JrHsdMcwi (SS/MCW)

value: 7 weeks


title: CAGE_MCF-7_time0_biologicalRep3

source_name: Breast

value: MCF-7 cell line


title: CAGE_MCF-7_time360_biologicalRep2


title: Young_1_C82


title: 12-K

description:
K_MCWLS_7W_10W.txt
BvsK_MCWLS_7W.txt


title: CAGE_MCF-7_time180_biologicalRep2


title: 9-K

description:
K_MCWLS_7W_10W.txt
BvsK_MCWLS_7W.txt


title: CAGE_MCF-7_time120_biologicalRep2


title: 10-K

description:
K_MCWLS_7W_10W.txt
BvsK_MCWLS_7W.txt


title: Young_1_C48


title: 8-K

description:
K_MCWHS_CRLHS_10W.txt
K_MCWLS_MCWHS_10W.txt
BvsK_MCWHS_10W.txt


title: CAGE_MCF-7_time60_biologicalRep2


title: CAGE_MCF-7_time15_biologicalRep3


title: 7-K


title: Young_1_C05


title: 6-K


title: 5-K


title: Young_1_C22


title: Young_1_C43


title: CAGE_MCF-7_time30_biologicalRep2


title: 4-K

description:
K_MCWLS_7W_10W.txt
K_MCWLS_CRLLS_10W.txt
K_MCWLS_MCWHS_10W.txt
BvsK_MCWLS_10W.txt


title: CAGE_MCF-7_time45_biologicalRep2


title: 13-K


title: Young_1_C87


title: Young_1_C83


title: 2-K


title: 3-K


title: CAGE_MCF-7_time15_biologicalRep2


title: Young_1_C17


title: 1-K


title: 20-B

description:
B_CRLLS_CRLHS_10W.txt
B_MCWHS_CRLHS_10W.txt
BvsK_CRLHS_10W.txt

source_name: Circulating T-cells

value: Circulating T-cells


title: 19-B


title: 17-B


title: 18-B


title: CAGE_MCF-7_time180_biologicalRep1


title: 15-B

description:
B_CRLLS_CRLHS_10W.txt
B_MCWLS_CRLLS_10W.txt
BvsK_CRLLS_10W.txt


title: Young_1_C03


title: Young_1_C68


title: 14-B


title: Young_1_C72


title: 11-B

description:
B_MCWLS_7W_10W.txt
BvsK_MCWLS_7W.txt


title: 12-B

description:
B_MCWLS_7W_10W.txt
BvsK_MCWLS_7W.txt


title: Young_1_C55


title: CAGE_MCF-7_time60_biologicalRep1


title: CAGE_MCF-7_time45_biologicalRep1


title: CAGE_MCF-7_time0_biologicalRep2


title: 10-B

description:
B_MCWLS_7W_10W.txt
BvsK_MCWLS_7W.txt


title: 8-B

description:
B_MCWHS_CRLHS_10W.txt
B_MCWLS_MCWHS_10W.txt
BvsK_MCWHS_10W.txt


title: Young_1_C76


title: CAGE_MCF-7_time360_biologicalRep1


title: Young_1_C14


title: 7-B


title: CAGE_MCF-7_time15_biologicalRep1


title: 6-B


title: CAGE_MCF-7_time30_biologicalRep1


title: 5-B


title: 16-B


title: 9-B

description:
B_MCWLS_7W_10W.txt
BvsK_MCWLS_7W.txt


title: Young_1_C63


title: Young_1_C44


title: CAGE_MCF-7_time0_biologicalRep1


title: Young_1_C89


title: 3-B

description:
B_MCWLS_7W_10W.txt
B_MCWLS_CRLLS_10W.txt
B_MCWLS_MCWHS_10W.txt
BvsK_MCWLS_10W.txt


title: 4-B


title: Young_1_C93


title: Young_1_C42


title: 2-B


title: Young_1_C13


title: NET-CAGE_MCF-7_6M_biologicalRep2

description: CNhi11025_171220_SN554_0340_ACBAYYACXX_NoIndex_L002_R1_001_TAC

value: 6 M


title: 1-B


title: Young_1_C95


title: NET-CAGE_MCF-7_4M_biologicalRep2

description: CNhi11025_171220_SN554_0340_ACBAYYACXX_NoIndex_L002_R1_001_GCG

value: 4 M


title: Young_1_C27


title: Young_1_C91


title: NET-CAGE_MCF-7_6M_biologicalRep1

description: CNhi11025_171220_SN554_0340_ACBAYYACXX_NoIndex_L002_R1_001_ATG

value: Nascent RNA


title: NET-CAGE_MCF-7_2M_biologicalRep4

description: CNhi11025_171220_SN554_0340_ACBAYYACXX_NoIndex_L002_R1_001_CAC

value: 2 M


title: NET-CAGE_MCF-7_4M_biologicalRep1

description: CNhi11025_171220_SN554_0340_ACBAYYACXX_NoIndex_L002_R1_001_AGT


title: Young_1_C10


title: NET-CAGE_MCF-7_8M_biologicalRep2

description: CNhi11025_171220_SN554_0340_ACBAYYACXX_NoIndex_L002_R1_001_GCT

value: 8 M


title: Young_1_C08


title: Young_1_C59


title: NET-CAGE_MCF-7_2M_biologicalRep2


title: Young_1_C90


title: NET-CAGE_MCF-7_8M_biologicalRep1

description: CNhi11025_171220_SN554_0340_ACBAYYACXX_NoIndex_L002_R1_001_ACG


title: skeletal muscle, 25(OH)D3 intervention, baseline sample, subject 3695

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.46.0).

source_name: m. vastus lateralis, 25(OH)D3 intervention, baseline sample, from subject 3695

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: This study is part of a larger clinical trial [PMID: 30053278]. In  brief, a 6-month, double-blind, placebo-controlled trial was performed, that included subjects randomly allocated to treatment who received daily supplements with either 10 µg 25(OH)D3 or a placebo capsule. Measurements were performed at baseline and after 6 months  of intervention. The study was carried out at Wageningen University and Hospital Gelderse Vallei, Ede, Netherlands (latitude: 51°N), between December 2014 and December 2015. The Medical Ethics Committee of Wageningen University and Research approved the study protocol and Hospital Gelderse Vallei approved local feasibility. All of the participants gave their written informed consent. The study was registered at clinicaltrials.gov as NCT02349282. Study population: Participants were recruited via registries of municipalities in Wageningen and the surroundings. A total of 78 men and women volunteered to participate in the main. Participants were included if they were ≥65 y of age, had a serum 25(OH)D concentration between 20 and 50 nmol/L (to convert to nanograms per milliliter, divide by 2.496), a BMI (in kg/m2) between 18.5 and 35, and who were prefrail or frail based on the frailty criteria of Fried et al. [PMID: 11253156]. Exclusion criteria were as follows: a serum calcium concentration >2.6 nmol/L or uncontrolled hypocalcemia, diagnosed malabsorption disorders, sarcoidosis, lymphoma, primary hyperparathyroidism, kidney stones (in the past 10 y), renal insufficiency, cancer, or the use of medication that may influence vitamin D metabolism [e.g., bisphosphonates, parathyroid hormone (PTH) treatment, anti-tuberculosis medications, anti-epileptic medications, bile acid sequestrate, or lipase inhibitors]. Furthermore, participants were excluded if they consumed >21 servings of alcoholic beverages/wk, were not willing or able to stop the use of vitamin D–containing supplements during the study, expected to increase their sun exposure (e.g., planned holiday), or had a surgery planned. For the gene expression analysis, samples of a subset of 22 subjects were included.

extract_protocol: Total RNA was prepared from the muscle biopsies (50 mg) using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: An independent investigator randomly allocated participants to 1 of the 2 intervention groups by a computer-generated list (SAS software 9.20; SAS Institute). Randomization was carried out in permuted blocks and stratified by sex and BMI (18.5–29.9 and 30–35). The 2 groups received daily supplements with either 10 µg 25(OH)D3, or placebo. Both the participants and investigators were blinded to treatment allocation, and study supplements were identical in appearance and taste. DSM Nutritional Products Ltd. provided the 25(OH)D3 (0.25% SD/S), vitamin D3, or placebo (microcrystalline cellulose; Avicel PH-102) in spray-dried form. Capsules were manufactured by Fisher Clinical Services GmbH. The actual content of the 25(OH)D3 capsules was 9.9 µg, which was tested by using HPLC. Participants were instructed to consume 1 capsule/d at breakfast. Treatment compliance was reported at 3 and 6 mo by capsule count of returned capsules, taking into account the number of days active in the study. Participants were considered compliant when ≥80% of the study supplements were taken. Before and after the intervention period, muscle biopsies were taken from the middle region of the vastus lateralis muscle under local anaesthesia (1% lidocaine, without epinephrine), ~15 cm above the patella and ~3 cm below entry through the fascia, using the percutaneous needle biopsy technique fromBergström [PMID: 5584523]. Samples were snap-frozen in liquid nitrogen, and stored at -80 degrees centigrade until RNA isolation.

value: muscle

value: Female

tag: subject id

tag: intervention group

value: 25-hydroxycholecalciferol (25(OH)D3)

tag: time of sampling

value: before intervention (baseline)


title: skeletal muscle, 25(OH)D3 intervention, intervention sample, subject 3695

source_name: m. vastus lateralis, 25(OH)D3 intervention, intervention sample, from subject 3695

tag: Sex

value: after intervention


title: skeletal muscle, 25(OH)D3 intervention, intervention sample, subject 3498

source_name: m. vastus lateralis, 25(OH)D3 intervention, intervention sample, from subject 3498

value: Male


title: NET-CAGE_MCF-7_1M_biologicalRep2

value: 1 M


title: skeletal muscle, placebo intervention, intervention sample, subject 3731

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3731

value: Placebo


title: skeletal muscle, placebo intervention, baseline sample, subject 3614

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3614


title: skeletal muscle, 25(OH)D3 intervention, intervention sample, subject 3516

source_name: m. vastus lateralis, 25(OH)D3 intervention, intervention sample, from subject 3516


title: skeletal muscle, placebo intervention, baseline sample, subject 3731

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3731


title: skeletal muscle, 25(OH)D3 intervention, baseline sample, subject 3516

source_name: m. vastus lateralis, 25(OH)D3 intervention, baseline sample, from subject 3516


title: Young_1_C16

source_name: Long-Term Hematopetic Stem Cell

value: male

value: 3 months

value: Long-Term Hematopetic Stem Cell


title: skeletal muscle, placebo intervention, intervention sample, subject 3614

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3614


title: skeletal muscle, 25(OH)D3 intervention, baseline sample, subject 3498

source_name: m. vastus lateralis, 25(OH)D3 intervention, baseline sample, from subject 3498


title: NET-CAGE_MCF-7_0.5M_biologicalRep2

value: MCF-7 cell line


title: Young_1_C01


title: NET-CAGE_MCF-7_2M_biologicalRep3

description: CNhi11025_171220_SN554_0340_ACBAYYACXX_NoIndex_L002_R1_001_ACC


title: Young_1_C36


title: NET-CAGE_MCF-7_1M_biologicalRep1


title: skeletal muscle, placebo intervention, baseline sample, subject 3375

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3375


title: skeletal muscle, placebo intervention, baseline sample, subject 3430

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3430


title: NET-CAGE_MCF-7_2M_biologicalRep1


title: skeletal muscle, placebo intervention, intervention sample, subject 3410

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3410


title: skeletal muscle, placebo intervention, intervention sample, subject 3430

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3430


title: skeletal muscle, placebo intervention, baseline sample, subject 3410

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3410


title: skeletal muscle, placebo intervention, intervention sample, subject 3375

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3375


title: skeletal muscle, placebo intervention, intervention sample, subject 3361

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3361


title: skeletal muscle, placebo intervention, baseline sample, subject 3361

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3361


title: Young_1_C96


title: Sample_44741

description: Condition 1: Uninjured, contralateral hindlimb tendon of a burn/tenotomy mouse (3 weeks after injury)

source_name: hindlimb tendon

value: 1 - Uninjured, contralateral hindlimb tendon of a burn/tenotomy mouse (3 weeks after injury)

value: C57BL/6 background

value: three week tenotomy sites after burn tenotomy


title: CAGE_MCF-7_biologicalRep2

source_name: Breast

value: Total RNA


title: Young_1_C12


title: CAGE_MCF-7_biologicalRep1


title: skeletal muscle, placebo intervention, intervention sample, subject 3360

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3360


title: NET-CAGE_MCF-7_0.5M_biologicalRep1

value: Nascent RNA


title: Young_1_C11


title: skeletal muscle, placebo intervention, baseline sample, subject 3360

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3360

value: muscle


title: Young_1_C47


title: skeletal muscle, placebo intervention, intervention sample, subject 3341

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3341

value: Female


title: skeletal muscle, placebo intervention, baseline sample, subject 3283

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3283


title: skeletal muscle, 25(OH)D3 intervention, intervention sample, subject 3322

source_name: m. vastus lateralis, 25(OH)D3 intervention, intervention sample, from subject 3322

value: 25-hydroxycholecalciferol (25(OH)D3)


title: Young_1_C30

source_name: Long-Term Hematopetic Stem Cell


title: IRF1_KO_IFN_L_rep2

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

data_processing:
Data were examined using Tuxedo pipeline for differential gene expression analysis. We used default parameters for these software programs and used a cutoff of 0.05 False Discovery Rate (FDR) by Benjamin-Hochberg method to determine differentially expressed genes with statistical significance.
We aligned to hg38 reference genome using HISAT2, version 2.0.5.
FPKM values were obtained using Cufflinks, patched version of 2.2.1.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM abundance measurements

growth_protocol: Cells were grown in Lonza's bronchial epithelial cell growth medium.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen).
To obtain the final sequencing library, 14 cycles of PCR were performed using Phusion Hot Start High-Fidelity DNA Polymerase (Finnzymes, Espoo, Finland). Three biological replicates were used and for each sample replicate we obtained ~50 million paired 50-mer reads (using Illumina HiSeq 2500 platform).

treatment_protocol: Cells were treated with IFNβ (0.2 ng/ml) and IFNλ1 (5ng/ml) for 24h.

tag: cell line

value: respiratory epithelial cells

tag: genotype/variation

value: IRF1 KO

tag: treated with

value: 5ng/ml IFNλ1 for 24h


title: IRF1_KO_IFN_L_rep3

tag: cell type


title: skeletal muscle, 25(OH)D3 intervention, intervention sample, subject 3295

source_name: m. vastus lateralis, 25(OH)D3 intervention, intervention sample, from subject 3295

tag: tissue

value: Male

value: after intervention


title: IRF1_KO_IFN_B_rep3

value: 0.2 ng/ml IFNβ for 24h


title: skeletal muscle, placebo intervention, baseline sample, subject 3341

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3341

value: Placebo

value: before intervention (baseline)


title: skeletal muscle, placebo intervention, intervention sample, subject 3283

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3283


title: skeletal muscle, 25(OH)D3 intervention, baseline sample, subject 3322

source_name: m. vastus lateralis, 25(OH)D3 intervention, baseline sample, from subject 3322


title: skeletal muscle, 25(OH)D3 intervention, baseline sample, subject 3295

source_name: m. vastus lateralis, 25(OH)D3 intervention, baseline sample, from subject 3295


title: Young_1_C35

value: male

value: 3 months

value: Long-Term Hematopetic Stem Cell


title: IRF1_KO_no IFN_rep2

source_name: BEAS-2B_IRF1_KO_no IFN


title: Young_1_C60


title: Young_1_C54


title: skeletal muscle, 25(OH)D3 intervention, baseline sample, subject 3279

source_name: m. vastus lateralis, 25(OH)D3 intervention, baseline sample, from subject 3279


title: IRF1_KO_no_IFN_rep3


title: Aged_1_C19

value: 24 Months


title: skeletal muscle, placebo intervention, intervention sample, subject 3258

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3258


title: Young_1_C71


title: 13-B

source_name: Circulating T-cells

value: Circulating T-cells

value: Dahl SS/JrHsdMcwiCrl rat (SS/CRL)

value: LS

value: 10 weeks


title: Aged_1_C38


title: skeletal muscle, placebo intervention, intervention sample, subject 3178

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3178

value: muscle


title: IRF1_KO_IFN_B_rep1

value: respiratory epithelial cells


title: skeletal muscle, placebo intervention, baseline sample, subject 3241

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3241


title: IRF1_KO_IFN_B_rep2

value: IRF1 KO


title: skeletal muscle, 25(OH)D3 intervention, baseline sample, subject 3106

source_name: m. vastus lateralis, 25(OH)D3 intervention, baseline sample, from subject 3106

value: 25-hydroxycholecalciferol (25(OH)D3)


title: skeletal muscle, placebo intervention, baseline sample, subject 3258

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3258

value: Female


title: skeletal muscle, 25(OH)D3 intervention, intervention sample, subject 3279

source_name: m. vastus lateralis, 25(OH)D3 intervention, intervention sample, from subject 3279

value: Male

value: after intervention


title: skeletal muscle, placebo intervention, baseline sample, subject 3178

source_name: m. vastus lateralis, placebo intervention, baseline sample, from subject 3178

value: Placebo


title: skeletal muscle, placebo intervention, intervention sample, subject 3241

source_name: m. vastus lateralis, placebo intervention, intervention sample, from subject 3241


title: skeletal muscle, 25(OH)D3 intervention, intervention sample, subject 3106

source_name: m. vastus lateralis, 25(OH)D3 intervention, intervention sample, from subject 3106


title: Parent_IFN_L_rep3

value: Wild type

value: 5ng/ml IFNλ1 for 24h


title: skeletal muscle, 25(OH)D3 intervention, intervention sample, subject 3090

source_name: m. vastus lateralis, 25(OH)D3 intervention, intervention sample, from subject 3090


title: IRF1_KO_IFN_L_rep1


title: skeletal muscle, 25(OH)D3 intervention, intervention sample, subject 3088

source_name: m. vastus lateralis, 25(OH)D3 intervention, intervention sample, from subject 3088


title: Aged_1_C66

source_name: Long-Term Hematopetic Stem Cell

value: male


title: skeletal muscle, 25(OH)D3 intervention, baseline sample, subject 3088

source_name: m. vastus lateralis, 25(OH)D3 intervention, baseline sample, from subject 3088

value: before intervention (baseline)


title: IRF1_KO_no_IFN_rep1


title: Parent_no_IFN_rep3


title: Aged_1_C67

value: 24 Months

value: Long-Term Hematopetic Stem Cell


title: Aged_1_C82


title: Aged_1_C29


title: Parent_IFN_B_rep3

value: 0.2 ng/ml IFNβ for 24h


title: skeletal muscle, 25(OH)D3 intervention, baseline sample, subject 3090

source_name: m. vastus lateralis, 25(OH)D3 intervention, baseline sample, from subject 3090


title: Aged_14_C24


title: skeletal muscle, 25(OH)D3 intervention, intervention sample, subject 3087

source_name: m. vastus lateralis, 25(OH)D3 intervention, intervention sample, from subject 3087


title: Parent_IFN_L_rep2


title: Parent_IFN_B_rep2