title: 20190925_1_3_S2

data_processing:
SMART-seq2 sequencing data were aligned with hisat2 using genome reference mm10. featureCounts was used to generate count matrix.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: count matrix in csv

extract_protocol:
To remove contaminating RBCs prior to sample isolation, all mice were first perfused with 10ml of 5mM EDTA/PBS at a flow rate of 5ml/min and then with 10ml PBS (without Ca/Mg) at a flow rate of 5ml/min. Samples were isolated from distinct proliferative microenvironments in the calvarium by a combination of plasma mediated laser ablation and micropipette aspiration (Image-seq samples, see manuscript for details).
Dissociation of tissues into single cells: All Image-seq and control samples were collected in Media 199 supplemented with 2% (v/v) FBS. Samples were pipetted up and down to generate a single cell suspension and 1ml of PBS (no Ca/Mg) was added to the cell suspension. Samples were incubated for 10min with 0.1µg of DAPI, and AML cells were sorted into individual wells of a 96well PCR plate filled with lysis buffer based on their GFP fluorescence. Samples were sealed and spun down immediately after sorting, flash frozen and stored at -80deg Celsius. Libraries were prepared using the MANTIS Liquid Handler (Formulatrix) and the Biomek FXP Single Arm System with Span-8 Pipettor (Beckman Coulter, A31843). Full-length cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, Inc.) and sequencing libraries prepared using the Nextera XT DNA library preparation kit (Illumina).

treatment_protocol: Image-seq mice were injected with 3 million HoxA9/Meis1 leukemia cells 3 days prior to the experiment, calcium binding dye alizarin red (AR) 2 days prior to the experiment and calcein blue (CB) on the day of the experiment.

value: HDP

tag: phenotype

value: AML cells


title: Brain WT Naive Rep1

status: Public on Aug 25 2022

type: SRA

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

country: USA

institute: Rutgers

library_source: transcriptomic

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software (Version 11.0.1) platform for analysis.
Imported reads were trimmed to remove adapters and low quality reads using CLC Genomics Workbench.
The reads are mapped to reference genome Mus musculus genome GRCm38.
The aligned reads were obtained using the RNA-Seq Analysis Tool of CLC Genomics Workbench using default settings.
Comparison of samples was performed using the "Differential Expression in RNA seq" function in CLC Genomics Workbench.
Genome_build: GRCm38
Supplementary_files_format_and_content: Total_counts_merged.csv: Comma-delimited file for CLC hit counts.

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Brain total cellular RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Thermo Fisher Scientific). The quality of RNA was first checked for integrity on an Agilent Bioanalyzer 2100; samples with RNA integrity number (RIN) >7.0 were used for subsequent processing. Total RNA was subjected to two rounds of poly(A) selection using oligo-d(T)25 magnetic beads (New England Biolabs). Illumina compatible RNAseq library was prepared using NEB next ultra RNAseq library preparation kit. The cDNA libraries were purified using AmpureXP beads and quantified on an Agilent Bioanalyzer and qubit analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: genotype

value: WT

tag: tissue

value: Brain

tag: age

value: 8-12 weeks (adult)

tag: treatment

value: Naive


title: sap3 KO, 60 min high light (800µE), replicate 1

type: RNA

city: ACTON

first: Marten

last: Moore

state: ACT

address: 134 Linnaeus Way

department: Research School of Biology

country: Australia

institute: The Australian National University

description:
gene expression from sap3 KO at 60 HL
SAP3_HL_REP_1

hyb_protocol: 3,8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Arabidopsis Gene 1.0 ST arrays for 16 h at 45 °C in a rotating chamber

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de). Summarized probe set signals were calculated by using the RMA (1) algorithm with the Affymetrix GeneChip Expression Console Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated. Probe sets with a fold change above 2.0 fold and a student’s t test P value lower than 0.05 were considered as significantly regulated.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: sap3 KO, 60 min high light (800µE)

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 15 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: Arabidopsis seeds were sown onto moist soil (Seed Raising and Cutting Mix, Martins, NSW, Australia) supplemented with 1 g/L dry volume of soil Osmocote Exact Mini slow release fertilizer (Scotts, NSW, Australia) and 1 L of 0.3 % (v/v) AzaMax (OCP, NSW, Australia). Seeds were covered with a plastic hood and stratified at 4 °C in the dark for at least 72 hours to break dormancy and coordinate germination. Stratified seeds were transferred to a temperature controlled Conviron S10H growth chamber (Conviron, Winnipeg, MB, Canada), fitted with a mixture of 250 W metal halide lamps (Venture Lighting, MH 250W/U) and high pressure sodium lamps (Phillips, SON‐T 250 W E E40 SL/12), for cultivation under a 10-hour photoperiod (08:00-18:00) of 80-100 μ mol photons m-2 s -1, 22.5/20.5 °C day/night temperatures, and 57/55 % day/night relative humidity.

extract_protocol: mRNA was extracted following the QIAGEN RNA extraction kit.

treatment_protocol: Three weeks old plants were transfered to 8 µmol photons m-2 s-1 (LL) for 10 days. Plants were transferred to 800 µmol photons m-2 s-1 (HL) for 10 min, while control plants remained in LL. Whole rosettes were harvested under control and HL conditions in the midday point of the light period to exclude circadian effects and immediately frozen in liquid nitrogen and stored at -80°C.

value: whole rosettes

tag: number of plants

tag: biological replicate number

value: SAP3 KO

value: high light (800µE) HL


title: 20190925_4_1_S4

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

growth_protocol: 8wk-old C57Bl6/J mice (#000664) were ordered from the Jackson Laboratory, housed in our animal facility for at least 2 weeks and used for experiments between 10-12 weeks of age

tag: condition

value: HDNP


title: 20191019_NoPro_B01_2_S35

value: NP


title: 20191001_1_2_S6


title: 20191019_NoPro_C01_2_S36


title: 20191019_NoPro_E01_2_S38


title: 20190925_1_2_S1


title: WT, low light control (8µE), pooled sample of 3 independent biological replicates

description:
gene expression from WT at LL control
WT_LL_REP_1-3

source_name: WT, low light control (8µE), pooled

value: WT (Col-0)

value: low light (8µE) LL


title: cml49 KO, 60 min high light (800µE), pooled sample of 3 independent biological replicates

description:
gene expression from cml49 KO at 60 HL
CML49_HL_REP_1-3

value: CML49 KO


title: 20190925_3_1_S3


title: 20191019_NoPro_B01_1_S31


title: 20191019_NoPro_D01_2_S37


title: sap3 KO, low light control (8µE), replicate 2

description:
gene expression from sap3 KO at LL control
SAP3_LL_REP_2

source_name: sap3 KO, low light control (8µE)


title: 20191019_NoPro_A01_2_S34


title: WT, 60 min high light (800µE), pooled sample of 3 independent biological replicates

description:
gene expression from WT at 60 HL
WT_HL_REP_1-3

source_name: WT, 60 min high light (800µE), pooled


title: 20191009_4_C04_S29


title: cml49 KO, low light control (8µE), pooled sample of 3 independent biological replicates

description:
gene expression from cml49 KO at LL control
CML49_LL_REP_1-3


title: 20191009_2_G02_S21

value: P


title: 20191009_2_H01_S14


title: 20191009_4_A04_S27


title: 20191009_2_E01_S11


title: 20191009_2_F02_S20


title: 20191009_2_F01_S12


title: 20191019_NoPro_D01_1_S33


title: 20191019_NoPro_C01_1_S32


title: 20191009_2_D02_S18


title: 20191009_2_D03_S26


title: 20191009_2_D01_S10


title: 20191009_2_B03_S24


title: 20191009_2_C02_S17


title: 20191009_2_B02_S16


title: 20191107_A01_S56


title: 20191009_2_A01_S7


title: 20191009_2_A02_S15


title: 20191009_2_B01_S8


title: 20191106_G12_S54


title: 20191105_F03_S52

value: IM


title: 20191106_F12_S53


title: 20191106_H12_S55


title: 20191105_D03_S50


title: 20191009_2_G01_S13


title: 20191105_A01_S45


title: 20191105_E03_S51


title: 20191105_B03_S48


title: 20191105_B01_S46


title: 20191104_H06_S44


title: 20191104_H05_S42


title: 20191009_2_C03_S25


title: 20191009_2_C01_S9


title: 20191104_H03_S33


title: 20191107_B01_S57


title: 20191104_G06_S43


title: 20191104_H02_S25


title: 20191104_H01_S20


title: 20191104_G05_S41


title: 20191105_C01_S47


title: 20191104_G03_S32


title: 20191104_G02_S24


title: 20191104_G01_S19


title: 20191104_F05_S40


title: 20191104_E05_S39


title: 20191104_F03_S31


title: 20191104_F01_S18


title: 20191105_C03_S49


title: 20191104_F02_S23


title: 20191104_E03_S30


title: 20191104_E01_S17


title: 20191104_D01_S16


title: 20191104_D03_S29


title: 20191104_E02_S22


title: 20191104_D05_S38


title: 20191104_D02_S21


title: 20191104_C01_S15


title: 20191104_C05_S37


title: 20191104_H04_S34


title: 20191104_C03_S28


title: 20191104_B03_S27


title: 20191104_A05_S35


title: 20191104_A03_S26


title: 20191104_A01_S14


title: 20191031_G01_S7


title: 20191031_F01_S6


title: 20191031_E03_S13


title: 20191031_E01_S5


title: 20191031_C03_S11


title: 20191031_C01_S4


title: 20191031_B01_S3


title: 20191031_B03_S10


title: 20191031_A03_S9


title: 20191031_D03_S12


title: 20191030_B01_S1


title: CCR2-DTR Trichinella-Infected

data_processing:
Demultiplexing with cellranger v2.1.0 mkfastq, bcl2fastq v2.20.0.422
Barcode and UMI deconvolution, alignment with cellranger v2.1.0 count
Genome_build: mm10
Supplementary_files_format_and_content: .h5 files (HDF5) for cellranger of deconvoluted gene expression matrix

extract_protocol:
Brain total cellular RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Thermo Fisher Scientific). The quality of RNA was first checked for integrity on an Agilent Bioanalyzer 2100; samples with RNA integrity number (RIN) >7.0 were used for subsequent processing. Total RNA was subjected to two rounds of poly(A) selection using oligo-d(T)25 magnetic beads (New England Biolabs). Illumina compatible RNAseq library was prepared using NEB next ultra RNAseq library preparation kit. The cDNA libraries were purified using AmpureXP beads and quantified on an Agilent Bioanalyzer and qubit analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: monocyte-depleted (CCR2-DTR)

tag: treatment/time point

value: 8 days post infection of Trichinella Spiralis

tag: cell type

value: CD45hi cells

value: 8-12 weeks adult mice


title: WT Trichinella-Infected

value: wild type

value: Brain


title: 20191104_B05_S36

value: AML cells


title: 20191031_A01_S2


title: WT Naïve


title: Skin_Young_rep1 [RNA-seq]

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description: Transcriptional profiling (RNA sequencing)

data_processing:
Fastq files quality check was performed using FastQC v0.11.5.
The fastq files were mapped to the mm9 genome using TopHat v2.1.0 (Trapnell, Roberts et al. 2012) with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene was calculated by HTSeq-Count 0.11.2 (Anders, Pyl et al. 2015) with -s no -a 0 -t exon -m intersection-nonempty parameters.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Htseq-count text files.

source_name: Skin, Young

growth_protocol: All wild-type mice were C57BL/6J obtained from Janvier or from internal breeding at the Leibniz Institute on Aging – Fritz Lipmann Institute (FLI). All animals were kept in a specific pathogen-free animal facility with a 12 h light/dark cycle. Dietary restriction experiments were performed on female mice. Young mice were aged 4 months, old mice were aged 22 months.

extract_protocol:
Mice were sacrificed by CO2 inhalation. Whole organs were extracted and cut into 2–4 pieces, respectively (100-300 mg/piece). Each sample was then quickly frozen in liquid nitrogen and stored at −80 °C until nuclei extraction was performed. In this study, we used 8 different organs or tissues: blood, brain, heart, kidney, liver, lung, muscle and skin.
RNA was isolated from Tissues using QUizol Reagent (ThermoFisher Scientific) according to the manufacturer’s instructions. RNA quantity was evaluated by Nanodrop 8000 (ThermoFisher Scientific) and the quality by using the Fragment Analyzer (Advanced Analytical) using the Standard Sensitivity RNA analysis Kit; 15nt DNF-471-0500 (Advanced Analytical). RNA samples were further processed for Total RNA-seq library preparation according to the manufacturer’s instructions (TruSeq RNA Sample preparation v2, Illumina).

treatment_protocol: One week before dietary restriction feeding, the animals were separated to single cages. Food weight and body weight were measured directly after separating the animals and before the dietary treatment starting. The daily food intake per animal was calculated and used for calculating the amount that refers to 70% for every animal dependent on its body weight. Food (ssniff #V1524-786) was given during the morning once per day to the DR (Dietary Restriction) animals. The AL (Ad libitum) animals had unlimited access to food during all the experimental time. Both DR and AL animals had unlimited access to the water. We studied 4 different groups of animals: ad libitum fed young (4 m, Young), ad libitum fed old (22 m, Old), long-term dietary restricted (LTDR; mice kept in DR from an age of 4 m to 22 m) and short-term dietary restricted (STDR; old mice kept for the last 2 months in DR before the sacrifice).

value: WT

value: Skin

value: Young (4 months)

tag: diet

value: Ad libitum


title: Skin_Young_rep2 [RNA-seq]


title: Skin_Young_rep3 [RNA-seq]


title: Skin_STDR_rep2 [RNA-seq]

source_name: Skin, STDR

value: Old (22 months)

value: Short-term dietary restriction

tag: Sex

value: Female


title: Skin_STDR_rep3 [RNA-seq]


title: Skin_Old_rep2 [RNA-seq]

source_name: Skin, Old


title: Skin_STDR_rep1 [RNA-seq]


title: 20191031_H01_S8


title: Skin_LTDR_rep1 [RNA-seq]

source_name: Skin, LTDR

value: Long-term dietary restriction


title: Muscle_Young_rep3 [RNA-seq]

source_name: Muscle, Young

value: Muscle


title: Skin_Old_rep1 [RNA-seq]


title: Muscle_STDR_rep1 [RNA-seq]

source_name: Muscle, STDR


title: Muscle_STDR_rep2 [RNA-seq]


title: Muscle_Young_rep2 [RNA-seq]


title: Skin_LTDR_rep2 [RNA-seq]


title: Muscle_Old_rep2 [RNA-seq]

source_name: Muscle, Old


title: Muscle_Old_rep1 [RNA-seq]


title: Muscle_Young_rep1 [RNA-seq]


title: Muscle_LTDR_rep3 [RNA-seq]

source_name: Muscle, LTDR


title: Muscle_LTDR_rep2 [RNA-seq]


title: Muscle_LTDR_rep1 [RNA-seq]


title: Lung_Young_rep3 [RNA-seq]

source_name: Lung, Young

value: Lung


title: Lung_Young_rep2 [RNA-seq]


title: Lung_STDR_rep3 [RNA-seq]

source_name: Lung, STDR


title: Lung_STDR_rep2 [RNA-seq]


title: Lung_Young_rep1 [RNA-seq]


title: Lung_Old_rep1 [RNA-seq]

source_name: Lung, Old


title: Lung_Old_rep2 [RNA-seq]


title: Lung_LTDR_rep2 [RNA-seq]

source_name: Lung, LTDR


title: Lung_LTDR_rep1 [RNA-seq]


title: Liver_Young_rep1 [RNA-seq]

source_name: Liver, Young

value: Liver


title: Liver_STDR_rep3 [RNA-seq]

source_name: Liver, STDR


title: Liver_Young_rep3 [RNA-seq]


title: Liver_Young_rep2 [RNA-seq]


title: Liver_STDR_rep2 [RNA-seq]


title: Liver_STDR_rep1 [RNA-seq]


title: Liver_Old_rep3 [RNA-seq]

source_name: Liver, Old


title: Liver_LTDR_rep3 [RNA-seq]

source_name: Liver, LTDR


title: Liver_Old_rep1 [RNA-seq]


title: Liver_Old_rep2 [RNA-seq]


title: Kidney_Young_rep3 [RNA-seq]

source_name: Kidney, Young

value: Kidney


title: Liver_LTDR_rep1 [RNA-seq]


title: Kidney_Young_rep2 [RNA-seq]


title: Liver_LTDR_rep2 [RNA-seq]


title: Kidney_STDR_rep3 [RNA-seq]

source_name: Kidney, STDR


title: Lung_STDR_rep1 [RNA-seq]


title: Kidney_Young_rep1 [RNA-seq]


title: Kidney_STDR_rep2 [RNA-seq]


title: Kidney_Old_rep2 [RNA-seq]

source_name: Kidney, Old


title: Kidney_Old_rep3 [RNA-seq]


title: Lung_LTDR_rep3 [RNA-seq]


title: Kidney_STDR_rep1 [RNA-seq]


title: Kidney_LTDR_rep3 [RNA-seq]

source_name: Kidney, LTDR


title: Kidney_LTDR_rep2 [RNA-seq]


title: Kidney_Old_rep1 [RNA-seq]


title: Heart_Young_rep1 [RNA-seq]

source_name: Heart, Young

value: Heart


title: Heart_STDR_rep3 [RNA-seq]

source_name: Heart, STDR


title: Heart_STDR_rep2 [RNA-seq]


title: Heart_Old_rep3 [RNA-seq]

source_name: Heart, Old


title: Heart_Young_rep2 [RNA-seq]


title: Heart_Old_rep2 [RNA-seq]


title: Heart_LTDR_rep3 [RNA-seq]

source_name: Heart, LTDR


title: Heart_LTDR_rep2 [RNA-seq]


title: Heart_STDR_rep1 [RNA-seq]


title: Brain_Young_rep3 [RNA-seq]

source_name: Brain, Young


title: Heart_LTDR_rep1 [RNA-seq]


title: Brain_Young_rep2 [RNA-seq]


title: Brain_STDR_rep2 [RNA-seq]

source_name: Brain, STDR


title: Brain_Young_rep1 [RNA-seq]


title: Brain_STDR_rep1 [RNA-seq]


title: Kidney_LTDR_rep1 [RNA-seq]


title: Brain_LTDR_rep2 [RNA-seq]

source_name: Brain, LTDR


title: Brain_Old_rep2 [RNA-seq]

source_name: Brain, Old


title: Blood_Young_rep2 [RNA-seq]

source_name: Blood, Young

value: Blood


title: Brain_LTDR_rep1 [RNA-seq]


title: Heart_Young_rep3 [RNA-seq]


title: Brain_Old_rep1 [RNA-seq]


title: Blood_STDR_rep3 [RNA-seq]

source_name: Blood, STDR


title: Blood_Young_rep1 [RNA-seq]


title: Heart_Old_rep1 [RNA-seq]


title: Blood_STDR_rep2 [RNA-seq]


title: Liver_Young_rep2 [ATAC-seq]

library_source: genomic

data_processing:
Fastq files quality check was performed with FastQC (v0.11.5). The adapter sequence was removed using fastx_clipper (FASTX Toolkit 0.0.13) with the -a CTGTCTCTTATACACATCTGACGCTGCCGACGA -Q33 -l 20 -n -v -M 10 parameters.
Fastq files mapping to mm9 genome was performed using Bowtie (v1.1.2) with --best --strata -m 1 parameters. Duplicate reads were removed using a custom script.
For making wig files macs14 (v1.4.2) was used. The wig files were converted to tdf using igvtools(v 2.4.19).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: tdf files

molecule: genomic DNA

source_name: Liver, Young

extract_protocol:
Mice were sacrificed by CO2 inhalation. Whole organs were extracted and cut into 2–4 pieces, respectively (100-300 mg/piece). Each sample was then quickly frozen in liquid nitrogen and stored at −80 °C until nuclei extraction was performed. In this ATAC-seq study, we used 2 different organs or tissues: kidney and liver.
10-30 mg of tissues were homogenized in a 2 ml Eppendorf tubes (with a tight pestle) with 15 strokes in 0.5 ml of liquid nitrogen on dry ice. Pulverized tissues were then suspended in cold 1X PBS, centrifuged at 2000g X 3 minutes at 4 C. After centrifugation, the supernatants were removed and the pellets were resuspended in tissue lysis buffer (with anti-protease). Tubes were rocked for 10 minutes at 4 C and then transferred to a glass douncer and homogenized with 15 strokes. After centrifuged at 800g X 5 minutes at 4 C, nuclei were resuspended in PBS, filtered with a 40 µm cell strainer and stained with Trypan blue and then counted. Approximately 50000 nuclei were transferred into a fresh tube and in 50 μl transposition reaction mixture containing 50 mM TAPS-NaOH (pH 8.5), 25 mM MgCl2, 50% DMF, 5 μl of Tn5 transposase, for 60 mins at 37 °C. Afterward, the DNA was purified with MinElute Purification Kit (Qiagen) and amplified with primers containing barcodes, as previously described (Picelli, S., et al., 2014).

treatment_protocol: One week before dietary restriction feeding, the animals were separated to single cages. Food weight and body weight were measured directly after separating the animals and before the dietary treatment starting. The daily food intake per animal was calculated and used for calculating the amount that refers to 70% for every animal dependent on its body weight. Food (ssniff #V1524-786) was given during the morning once per day to the DR (Dietary Restriction) animals. The AL (Ad libitum) animals had unlimited access to food during all the experimental time. Both DR and AL animals had unlimited access to the water. We studied 3 different groups of animals: ad libitum fed young (4 m, Young), ad libitum fed old (22 m, Old) and long-term dietary restricted (LTDR; mice kept in DR from an age of 4 m to 22 m).


title: Liver_Young_rep1 [ATAC-seq]


title: Blood_LTDR_rep1 [RNA-seq]

source_name: Blood, LTDR


title: Blood_STDR_rep1 [RNA-seq]


title: Liver_Old_rep2 [ATAC-seq]

source_name: Liver, Old


title: Blood_Old_rep2 [RNA-seq]

source_name: Blood, Old


title: Liver_Old_rep1 [ATAC-seq]


title: Liver_Old_rep3 [ATAC-seq]


title: Liver_LTDR_rep1 [ATAC-seq]

source_name: Liver, LTDR


title: Liver_LTDR_rep2 [ATAC-seq]


title: Blood_Young_rep3 [RNA-seq]


title: Kidney_Young_rep3 [ATAC-seq]

source_name: Kidney, Young


title: Kidney_Young_rep1 [ATAC-seq]


title: Kidney_Old_rep2 [ATAC-seq]

source_name: Kidney, Old


title: Kidney_Old_rep3 [ATAC-seq]


title: Kidney_Old_rep1 [ATAC-seq]


title: Blood_Old_rep1 [RNA-seq]


title: Kidney_LTDR_rep2 [ATAC-seq]

source_name: Kidney, LTDR


title: Kidney_LTDR_rep3 [ATAC-seq]


title: Blood_LTDR_rep2 [RNA-seq]


title: Kidney_LTDR_rep1 [ATAC-seq]


title: Kidney_Young_rep2 [ATAC-seq]


title: Erythroblasts, DKO biol rep 3

city: Milwaukee

first: Herve

last: Falet

state: WI

address: 8727 W Watertown Plank Rd

institute: Versiti Blood Research Institute

data_processing:
STAR aligner and MAPR-Seq workflow v3.0
Samples were sequenced to an average depth of 40 million reads.
Sequence reads were aligned to the reference genome, mm10, and reference transcriptome, GRCm38, using the STAR aligner and MAPR-Seq workflow v3.0.
Differential expression was calculated using EdgeR v3.8 and the gene-wise exact test on TMM-normalized levels.
All data was quality controlled using FastQC and RSeQC, followed by manual review and data visualization.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and log2FoldChange for each Sample

source_name: Spleen

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen).
RNA libraries were prepared using Illumina TruSeq Stranded mRNA, single indexed.

treatment_protocol: For the erythroblast analysis, spleen cells were stained with FITC-conjugated anti-CD71 and PE-conjugated anti-TER-119 (BD Biosciences) after homogenization and washing.

value: Spleen

value: Erythroblasts

value: Mpl-/- Dnm2Plt-/-

value: CD71+ sorting


title: Erythroblasts, DKO biol rep 2


title: FXR1 KD -2 Polysome RNA

first: Shobha

last: Vasudevan

address: 185 Cambridge St

department: Cancer Center

institute: Massachusetts General Hospital

description: RNA from polysome fractions of FXR1 Knockdown cells grown with serum (replicate 2)

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus

data_processing: HuGene 2.0 ST CEL files were normalized to produce gene-level expression values with the Robust Multiarray Average (RMA) using the affy R package (version 1.62.0) and Entrez Gene-specific R packages (version 24.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan

organism: Homo sapiens

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: RPMI1640 media supplemented with 10% fetal bovine serum (FBS), 2 mM L-Glutamine, 100 μg/mL streptomycin and 100 U/ml penicillin at 37°C in 5% CO2. Quiescent or G0 THP1 cells were prepared by washing with PBS followed by serum-starvation at a density of 2 × 105 cells/mL. Cells were furthur grown in serum starvation condition for 24 hr.

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

treatment_protocol: For knocking down expression of FXR1, Doxycycline (1 µgm/ml) was added every 24 hr. Treatment was done for three days.

tag: cell line

value: THP1 (Acute monocytic leukemia)

tag: cell state

value: Proliferative (with serum)

tag: gender

value: Male


title: FXR1 KD G0 -1 Input RNA

description: RNA from total cell lysates of FXR1 Knockdown cells grown without serum for 24 hr  (replicate 1)

value: Quiescent (without serum)


title: FXR1 KD G0 - 2 Input RNA

description: RNA from total cell lysates of FXR1 Knockdown cells grown without serum for 24 hr  (replicate 2)


title: Erythroblasts, DKO biol rep 1


title: Erythroblasts, Mpl, biol rep 2

value: Mpl-/- Dnm2Plt+/+


title: Erythroblasts, Mpl, biol rep 3


title: Vector Control polysome 1

description: Polysome associated RNA from vector control cells (replicate 1)

growth_protocol: RPMI1640 media supplemented with 10% fetal bovine serum (FBS), 2 mM L-Glutamine, 100 μg/mL streptomycin and 100 U/ml penicillin at 37°C in 5% CO2.

treatment_protocol: No treatment

value: proliferating (with serum)


title: FXR1 KD G0 -2 Polysome RNA

description: RNA from polysome fractions of FXR1 Knockdown cells grown without serum for 24 hr (replicate 2)


title: Tz Control -2 Input RNA

description: RNA from total cell lysates of control cells grown with serum  (replicate 2)


title: FXR1 KD -1 Polysome RNA

description: RNA from polysome fractions of FXR1 Knockdown cells grown with serum (replicate 1)


title: Vector Control polysome 2

description: Polysome associated RNA from vector control cells (replicate 2)


title: Tz Control G0 -1 Polysome RNA

description: RNA from polysome fractions of control cells grown without serum for 24 hr (replicate 1)


title: FXR1 KD G0 -1 Polysome RNA

description: RNA from polysome fractions of FXR1 Knockdown cells grown without serum for 24 hr (replicate 1)


title: Tz Control - 1 Polysome RNA

description: RNA from polysome fractions of control cells grown with serum (replicate 1)


title: Erythroblasts, Mpl, biol rep 1


title: FXR1 KD - 2 Input RNA

description: RNA from total cell lysates of FXR1 Knockdown cells grown with serum  (replicate 2)


title: FXR1 OE polysome 1

description: Polysome associated RNA from FXR1 OE cells (replicate 1)


title: Tz Control G0 -1 Input RNA

description: RNA from total cell lysates of control cells grown without serum for 24 hr  (replicate 1)


title: Tz Control G0 -2 Polysome RNA

description: RNA from polysome fractions of control cells grown without serum for 24 hr (replicate 2)


title: Vector Control Input 2

description: Total RNA from vector control cells (replicate 2)


title: FXR1 OE Input 2

description: Total RNA from FXR1 OE cells (replicate 2)


title: Erythroblasts, Dnm2, biol rep 3

value: Mpl+/+ Dnm2Plt-/-


title: FXR1 KD -1 Input RNA

description: RNA from total cell lysates of FXR1 Knockdown cells grown with serum  (replicate 1)


title: FXR1 OE polysome 2

description: Polysome associated RNA from FXR1 OE cells (replicate 2)


title: Tz Control - 1 Input RNA

description: RNA from total cell lysates of control cells grown with serum  (replicate 1)


title: FXR1 OE Input 1

description: Total RNA from FXR1 OE cells (replicate 1)


title: Tz Control G0 -2 Input RNA

description: RNA from total cell lysates of control cells grown without serum for 24 hr  (replicate 2)


title: Tz Control - 2 Polysome RNA

description: RNA from polysome fractions of control cells grown with serum (replicate 2)


title: Erythroblasts, Dnm2, biol rep 2


title: Vector Control Input 1

description: Total RNA from vector control cells (replicate 1)


title: Erythroblasts, WT, biol rep 3

value: Mpl+/+ Dnm2Plt+/+


title: Erythroblasts, WT, biol rep 2


title: Erythroblasts, WT, biol rep 1


title: E11.5 Sox9+ Progenitor Cells - Sample 2 [ATAC-seq]

city: Cincinnati

first: Daniel

middle: Todd

last: Swarr

state: OH- OHIO

address: 3333 Burnet Ave, ML 7009

department: Division of Neonatology & Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Reads were quality filtered and adapters were trimmed using Trimmomatic, version 0.39 (Bolger et al. 2014).
Reads were aligned to mouse genome mm10 using bowtie2 (Langmead and Salzberg 2012).
Duplicated reads were removed with picard tools, and blacklisted regions were filtered out using bedtools (Amemiya et al. 2019).
Peak calling was performed with MACS2 (version 2.2.1.20160309) using the additional parameters “—nomodel”, “—shift -100”, and “—extsize 200”.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 generated bedgraph file for pileup and control-lambda

source_name: SOX9-GFP+ lung epithelium

extract_protocol:
A single cell suspension was generated from embryonic lungs isolated from Tg(Sox9-EGFP)EB209Gsat reporter mice at either E11.5 or E16.5. SOX9+ lung epithelial cells were isolated by sorting for GFP+/CD326+/CD31-/CD45-/7-AAD- using a BD/FACSAria II cell sorter.
Nuclei were isolated, the transposase reaction was performed with Nextera Tn5 transposase (Illumina), and PCR amplification was performed according to previously published protocols (Buenrostro et al. 2015a).
Nextera Tn5 transposase (Illumina) per previously published protocols (Buenrostro et al. 2015a).

value: lung

tag: developmental stage

value: embryonic day E11.5


title: E16.5 Sox9+ Progenitor Cells - Sample 1 [ATAC-seq]

value: embryonic day E16.5


title: E16.5 Sox9+ Progenitor Cells - Sample 2 [ATAC-seq]


title: D7_Smart-seq2_H8_exp2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Single-cell RNA seq, Smart-Seq2

data_processing:
Smart-seq2: Reads were aligned to the GRCm38 mouse genome using TopHat aligner v2.1 (Trapnell et al. 2009) and Htseq-count v0.8 (Anders et al. 2015) was used to count the number of read alignments per gene in the resulting bam files (idattr = “gene_id” and stranded = “no”). Cells with <200,000 total reads, <1,000 genes detected and >30% of ERCC controls were excluded from analysis and genes with mean expression <1 were removed. The function computeSumFactors from the Bioconductor R package scran (Lun et al., 2016b) was used to compute the normalization factors for individual cells.
Genome_build: GRCm38
Supplementary_files_format_and_content: Smart-seq2 cell ID file: Csv file contains cell ID information for each sample Smart-seq2 dataset.
Smart-seq2 count file: Txt file contains raw count values with genes in rows and cells/samples in columns.
Smart-seq2 normalized count file: Txt file contains normalized and filtered count values with genes in rows and cells/samples in columns.;

source_name: Carotid artery

extract_protocol:
The Smart-seq2 protocol (Picelli et al., 2014) was used to generate amplified cDNA libraries from EYFP+RFP+ and EYFP+RFP- cells isolated from ligated left common carotid arteries of VSMC lineage-labeled animals (Myh11-EYFP-Ki67/RFP) 7 days after surgery and EYFP+ cells from unligated litter mate control animals in 2 separate experiments (experiment 1: 4 ligated arteries and 1 control arteries; experiment 2: 5 ligated arteries and 2 control arteries). Cells were processed as described (Dobnikar et al., 2018) with addition of ERCC spike controls (diluted 1:80,000,000, Invitrogen).
Sequencing libraries were generated using the Nextera XT kit and pooled libraries were sequenced using a paired end protocol (HiSeq 2500, Illumina).

tag: background


title: E16.5 Sox9+ Progenitor Cells - Sample 2 [RNA-seq]

data_processing:
Quality trimming and adapter clipping of sequencing reads was performed with Trimmmatic (Bolger et al. 2014).
Reads were then aligned against the mouse reference genome (mm10) using the STAR aligner (Dobin et al. 2013). Duplicate reads were flagged and removed using the MarkDuplicates program from Picard tools.
Per-gene read counts for GENECODE release M12 (GRCm38.p5) were computed using the Rsubread R package, with duplicate reads removed (Frankish et al. 2019; Liao et al. 2019).
The data were transformed using the VOOM function from the limma R package (Law et al. 2014)
Genome_build: mm10
Supplementary_files_format_and_content: voom-transformed expression matrix generated by limma
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
A single cell suspension was generated from embryonic lungs isolated from Tg(Sox9-EGFP)EB209Gsat reporter mice at either E11.5 or E16.5. SOX9+ lung epithelial cells were isolated by sorting for GFP+/CD326+/CD31-/CD45-/7-AAD- using a BD/FACSAria II cell sorter.
RNA was isolatedusing the RNEasy Micro Plus kit, after completing a trizol/chloroform extraction.
SMART-Seq v4 Ultra-Low Input RNA kits (TaKaRa Bio) were used to generated polyA selected libraries from total RNA.


title: D7_Smart-seq2_H7_exp2

description: Single-cell RNA seq, Smart-Seq2

tag: genotype


title: D7_Smart-seq2_H5_exp2

description: Single-cell RNA seq, Smart-Seq2


title: E11.5 Sox9+ Progenitor Cells - Sample 1 [ATAC-seq]

tag: tissue


title: D7_Smart-seq2_H6_exp2

description: Single-cell RNA seq, Smart-Seq2


title: E16.5 Sox9+ Progenitor Cells - Sample 3 [RNA-seq]


title: D7_Smart-seq2_H9_exp2

description: Single-cell RNA seq, Smart-Seq2


title: E11.5 Sox9+ Progenitor Cells - Sample 2 [RNA-seq]


title: E11.5 Sox9+ Progenitor Cells - Sample 1 [RNA-seq]


title: E11.5 Sox9+ Progenitor Cells - Sample 3 [RNA-seq]


title: E16.5 Sox9+ Progenitor Cells - Sample 1 [RNA-seq]


title: D7_Smart-seq2_H4_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_H1_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_H3_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_H12_exp2

description: Single-cell RNA seq, Smart-Seq2


title: Erythroblasts, Dnm2, biol rep 1

tag: strain


title: D7_Smart-seq2_H2_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_H11_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G8_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G9_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_H10_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G6_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G7_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G3_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G2_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G1_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G12_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G11_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F9_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F8_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G10_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F7_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F6_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F5_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F2_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F4_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F11_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F12_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E6_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F10_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F1_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E7_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E9_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G4_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_G5_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E5_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E3_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E11_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D8_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E1_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E10_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E8_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E4_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E12_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D9_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D3_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D7_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F3_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D6_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E2_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D2_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D12_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D4_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D5_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D11_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C4_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D1_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C8_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C7_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C3_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D10_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C6_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C9_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C5_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C2_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C10_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C11_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C1_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C12_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_B9_exp2

description: Single-cell RNA seq, Smart-Seq2


title: neocortex, huFOXP2, L4, rep1

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

institute: Yale University

data_processing:
STAR alignment
HTSeq count
Assembly: mm10
Supplementary files format and content: Tab-separated file representing counts for all samples

source_name: brain

extract_protocol:
Timed-pregnant CD-1 mice were used for in utero electroporation. Using day of vaginal plug as embryonic day 0.5, dams were anesthetized at E14.5, the uterine horn was exposed, and either empty plasmid or human/mouse FOXP2 cDNA and Gfp cDNA were electroporated into the ventricular wall (IUE refs from lab). At postnatal day 7, electroporated mice were sacrificed, their brains extracted into cooled aCSF, and then sectioned sagittally at 300µmin cooled aCSF. Sections were then microdissected, pooling for each mouse its neocortical layers 5-6 (infragranular, GFP-negative cells), L4 (granular, GFP-positive cells), and layers 2-3 (infragranular, GFP-negative cells), similar to previous techniques (Fertuzinhos, 2014).
Illumina TruSeq

value: brain

value: human FOXP2


title: neocortex, huFOXP2, L4, rep2


title: neocortex, huFOXP2, L2-3, rep2


title: neocortex, huFOXP2, L5-6, rep1


title: neocortex, huFOXP2, L2-3, rep1


title: D7_Smart-seq2_B7_exp2

description: Single-cell RNA seq, Smart-Seq2


title: neocortex, moFoxp2, L4, rep1

value: mouse FOXP2


title: neocortex, moFoxp2, L5-6, rep1


title: neocortex, GFP, L5-6, rep3

value: GFP


title: D7_Smart-seq2_B5_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_B6_exp2

description: Single-cell RNA seq, Smart-Seq2


title: neocortex, GFP, L2-3, rep3


title: neocortex, GFP, L4, rep3


title: neocortex, GFP, L4, rep2


title: neocortex, GFP, L5-6, rep2


title: neocortex, GFP, L2-3, rep2


title: neocortex, moFoxp2, L2-3, rep1


title: D7_Smart-seq2_B4_exp2

description: Single-cell RNA seq, Smart-Seq2


title: neocortex, huFOXP2, L5-6, rep2


title: neocortex, GFP, L5-6, rep1


title: D7_Smart-seq2_B8_exp2

description: Single-cell RNA seq, Smart-Seq2


title: neocortex, GFP, L4, rep1


title: D7_Smart-seq2_B2_exp2

description: Single-cell RNA seq, Smart-Seq2


title: neocortex, GFP, L2-3, rep1


title: D7_Smart-seq2_B1_exp2

description: Single-cell RNA seq, Smart-Seq2


title: Lp

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

data_processing:
De-multiplexed fastq files were tested with FastQC. Over-represented sequences and adapters were trimmed with the Qiagen CLC Workbench Software v. 10.0.1.
Reads were mapped with the Qiagen CLC Workbench Software v. 10.0.1, using the hg38 human reference genome using default mapping parameters.
Mapped unique gene reads were analysed with the R package DeSeq2 v. 1.22.2 in R version 3.5.1, and the contrasts M1 vs. ctrl and M2 vs. ctrl were calculated.
The DeSeq2 output for the ctrl, M1 and M2 samples is provided as Wxcel file processed_data_DeSeq2.xlsx.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: rawcounts_Bertrams.xlsx: Raw counts for each sample.
Supplementary_files_format_and_content: processed_data_DeSeq2.xlsx: DeSeq2 contrast of M1 vs. ctrl and M2 vs. ctrl.

source_name: blood derived monocyte

extract_protocol:
RNA was isolated by phenol chloroform extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Blood derived monocytes were cultured for 7 days in the presence of 1% human off-the-clot AB serum. On day 7, macrophage morphology was assessed by microscope, and cells were left untreated (ctrl), stimulated with 100ng/ml LPS + 20 ng/ml IFNgamma (M1) or 20 ng/ml IL4 + 20 ng/ml IL-13 or infected at MOI1 with WT or dFlaA Legionella Pneumophila Corby for 18h.

value: Blood derived monocyte

tag: treatment

value: Infected with Legionella Pneumophila Corby Wild Type


title: Lp_FlaA

value: Infected with Legionella Pneumophila Corby Flagellin Deficient


title: M2_C

description:
rawcounts_Bertrams.xlsx
processed_data_DeSeq2.xlsx

value: M2 polarized


title: D7_Smart-seq2_B12_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_B11_exp2

description: Single-cell RNA seq, Smart-Seq2


title: M1_C

value: M1 polarized


title: M2_B


title: M1_B


title: Ctrl_C

value: Untreated


title: M1_A


title: D7_Smart-seq2_B3_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_A9_exp2

description: Single-cell RNA seq, Smart-Seq2


title: M2_A


title: Ctrl_B


title: Ctrl_A


title: D7_Smart-seq2_A6_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_A7_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_A5_exp2

description: Single-cell RNA seq, Smart-Seq2


title: WT chondrocytes D14 RNA-seq-3

city: Hong Kong

first: Wai- Yee

last: Chan

state: Hong Kong

address: Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
CLC Genomics Workbench v 11.0.1
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: Excel files include RPKM values for each Sample

source_name: hESCs

growth_protocol: hESCs were maintained on Matrigel-coated plates (Corning) in mTesR medium (STEMCELL) before differentiation.

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Invitrogen) following the manufacturer’s instructions.
The library was establised by Novogene company (Beijing, China).

treatment_protocol: hESCs differentiation was following a previously publised protocol. Briefly, the cells were cultured in basal differentiation medium including DMED/F12, 2 mM L-glutamine, 1% (vol/vol) ITS, 1% (vol/vol) nonessential amino acids, 2% (vol/vol) B27, and 90 90 µM β-mercaptoethanol supplemented with appropriate chemicals. The key growth factors and chemicals used were as follows: WNT3A, NT4 (R&D systems), BMP4, GDF5, Activin-A (Peprotech), FGF2 (Biosource, Invitrogen), and Follistatin 300 (Sigma.)

value: hESCs

value: HESC-derived chondrocytes

value: WT

tag: time

value: Day 14


title: D7_Smart-seq2_A4_exp2

description: Single-cell RNA seq, Smart-Seq2


title: WRN chondrocytes D14 RNA-seq-1

value: WRN KD


title: D7_Smart-seq2_A1_exp2

description: Single-cell RNA seq, Smart-Seq2


title: WT chondrocytes D14 RNA-seq-2


title: WT chondrocytes D14 RNA-seq-1


title: WRN chondrocytes D14 RNA-seq-2


title: D7_Smart-seq2_A2_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_A12_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_A3_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_B10_exp2

description: Single-cell RNA seq, Smart-Seq2


title: SUM149 xenograft tumor cell pool2

city: Portland

first: Gordon

middle: B

last: Mills

state: Oregon

address: 2730 SW Moody Ave

department: Precision Oncology

institute: Oregon Health & Science University

data_processing:
basecalls were done by Illumina Casava1.8 software
sequenced reads were demultiplexed by Cell Ranger v6.0.0
sequenced reads were mapped to GRCh38 whole genome with all transcripts by Cell Ranger v6.0.0 with default parameters
sequenced reads were mapped to GRCh38 whole genome with only exons by velocyto v0.17
raw reads were loaded, merged and filtered in Python using scVelo
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited text files include CPM values of spliced RNA for each cells
Supplementary_files_format_and_content: comma-delimited text files include raw counts of spliced RNA for each cells

source_name: FVB mouse/breast cancer

growth_protocol: For xenograft assays 6 weeks old female NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice were purchased from Jackson Laboratory. Tumors were induced by unilateral orthotopic mammary fat pad injection of 2*106 SUM149 cells transfected with shCON or shCD9 lentivirus and suspended in 50 μL of culture medium/Matrigel Growth Factor Reduced Basement Membrane Matrix, Phenol Red-Free (Corning, CLS356231) in a 1:1 ratio. After 14 days, mice were randomized to treatment groups (n=8) based on tumor size.

extract_protocol:
tumor was harvested from FVB mouse mamary pad. Tumor tissue was dissociated with gentleMACS tissue dissociation kits (SUM149 xenograft tumors were disaggregated by gentleMACS kits (Miltenyi Biotec, #130-096-730), and incubated in TotelseqA hashtag antibodies (Biolegend, #394601, #394603, #394605, #394607, #394609, #394611, #394613, #394615) following the manufactural instructions. Live cells were isolated by EasySep Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies, #17899). Single cell suspensions were processed according to 10xGenomics scRNAseq sample preparation protocol (Chromium Single Cell 3’ v3.1 Reagent Kit, 10xGenomics). 1000 cells were targeted for each sample.)
RNA libraries were prepared for sequensing using standard library construction protocol by 10x Genomics

treatment_protocol: Mice were administered with vehicle or JQ1 (10mg/kg, daily, Selleckchem, #S7110) for 30 days. 3 tumors in each group were administered with vehicle for extra 10 days for regrowth assays.

value: mamary pad

value: JQ1 10mg/kg/day


title: WRN chondrocytes D14 RNA-seq-3


title: D7_Smart-seq2_A8_exp2

description: Single-cell RNA seq, Smart-Seq2


title: SUM149 xenograft tumor cell pool1


title: D7_Smart-seq2_A10_exp2

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_H9_exp1

description: Single-cell RNA seq, Smart-Seq2


title: 697_RNA_24hr

city: Memphis

last: Savic

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
Library strategy: ATAC-STARR-seq
Reads were mapped to the human genome using bowtie2
Peak calling on DNA input libraries was performed using MACS2 using the default q value of 0.05
BasicSTARRseq Bioconductor package was used to identify regions with significant STARR-seq signal over the input signal and call enhancers by identify the degree of enrichment in comparison to input
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files for each DNA library and csv output files from BasicSTARRseq Bioconductor package for each RNA-output time point containing p-values and enrichment scores for each called peak

source_name: 697 (ALL cell line)

growth_protocol: Nalm6 and 697 cells were maintained with RPMI-1640 with 10% charcoal-stripped FBS, 2mM Glutamine, and Pen/Strep

extract_protocol:
DNA input libraries for each cell line were generated according to the Greenleaf Lab FAST-ATAC protocol. RNA was extracted from cell lines using the Qiagen Rneasy Midi Kit (#75144) and polyA+ mRNA was isolated with the Oligotex mRNA Midi Kit (#70042).
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with prednisolone at a concentration of 5uM (Nalm6 cells) or 10uM (697 cells) for 6 or 24 hours

value: ALL

value: PRED (10uM, 24hrs)

tag: replicate


title: 697_DNA_Input_Library


title: D7_Smart-seq2_A11_exp2

description: Single-cell RNA seq, Smart-Seq2


title: Nalm6_RNA_24hr

source_name: Nalm6 (ALL cell line)

value: PRED (5uM, 24hrs)


title: Nalm6_RNA_6hr

value: PRED (5uM, 6hrs)


title: D7_Smart-seq2_H7_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Nalm6_DNA_Input_Library


title: 697_RNA_6hr

value: PRED (10uM, 6hrs)


title: Nalm6_RNA_0hr


title: D13

city: Parkville

first: Sean

last: Wilson

state: Victoria

address: 50 Flemington Road

institute: MCRI

description: D13+14 sample represents 4 barcoded replicates of 4 pooled organoids, each replicate derived from seperate monolayer differentiations of CRL1502.C32 iPSCs (D13 sample; also containing 4 barcoded replicates). D13+12 represents a single organoid derived from a D13 monolayer differentiation of CRL-2429/SIX2Cre/Cre:GAPDHdual iPSCs.

data_processing:
10x library demultiplexing: CellRanger 3.1.0
The 10x Genomics Cell Ranger pipeline (v3.1.0) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices.
HTO library demultiplexing: Cite-seq-count 1.4.3
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output files

source_name: Human iPSC kidney organoid

growth_protocol: iPSC lines were maintained and expanded at 37˚C, 5% CO2 and 5% O2 in Essential 8 medium (Thermo Fisher Scientific, Waltham, MA) on Matrigel- (BioStrategy, Victoria, Australia) coated plates with daily media changes and passaged every 2 – 3 days with EDTA in 1X PBS as described previously (Chen G. et al., Nature Methods, 2011).

extract_protocol:
Organoids were minced with a scalpel blade then dissociated in 1mL warmed Accutase, pipetting every 3 minutes for 15 minutes. The cell solution was placed on ice (2 minutes), passed through a 40um cell strainer, washed with TeSR-E6 and centrifuged (1500 rpm, 3 minutes). For D13 and D13+14 samples, barcoding was performed as described previously (Stoeckius M. et al., Genome Biol, 2018), incubating with 1µg hashtag oligo antibody (BioLegend TotalSeq-A0251 to A0258) for 20 minutes on ice prior to washing and pooling at equal cell ratios.  Prepared samples were resuspended in TeSR-E6 on ice and supplied for sequencing at a density of 300-1000 cells/uL.
10x libraries were constructed using 10x Chromium Next GEM Single Cell 3' Reagent kit v3.1. HTO librares were constructed following "BioLegend TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol".
Single cell RNA seq, with hastag oligo barcoding. Sequenced using Illumina Novoseq.

treatment_protocol: iPSC differentiation and organoid culture was performed using TeSR-E6 as described previously (Howden SE, et al., EMBO Rep, 2019; Takasato M, et al., Nat Protoc, 2016), with modifications to initial CHIR99021 exposure (5 days at 6µM) and extension of the monolayer differentiation period to 13 days with the addition of nephron progenitor maintenance media (Tanigawa S, et al., Cell Rep, 2016).

value: iPSC-derived kidney organoid


title: WGBS_697

data_processing:
Reads were mapped to the human genome using bowtie2
Methylation analysis is performed using Bismark
Genome_build: hg19
Supplementary_files_format_and_content: bed file of methylation values for each cell line

extract_protocol:
DNA was extracted from cell lines using the QIAamp DNA Mini Kit (cat# 51304)
Libraries were prepared for sequencing using standard Illumina protocols


title: D7_Smart-seq2_H6_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_H5_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_H4_exp1

description: Single-cell RNA seq, Smart-Seq2


title: WGBS_Nalm6


title: 697_RNA_0hr


title: 697_24hr_Rep3_RNAseq

data_processing:
Reads were mapped to the human genome using bowtie2
Differential enrichment analysis was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: text file of raw counts for each replicate

extract_protocol:
RNA was extracted from cell lines using the Norgen Total RNA Purification Kit (Norgen, #35300)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatement


title: D13 (HTO)


title: D13+14


title: D7_Smart-seq2_H3_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_H12_exp1

description: Single-cell RNA seq, Smart-Seq2


title: 697_0hr_Rep2_RNAseq


title: 697_6hr_Rep1_RNAseq


title: D7_Smart-seq2_H10_exp1

description: Single-cell RNA seq, Smart-Seq2


title: 697_24hr_Rep2_RNAseq


title: D13+12 SIX2Cre


title: D7_Smart-seq2_H11_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_H8_exp1

description: Single-cell RNA seq, Smart-Seq2


title: 697_24hr_Rep1_RNAseq


title: 697_0hr_Rep1_RNAseq


title: 697_0hr_Rep3_RNAseq


title: D7_Smart-seq2_G8_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D13+14 (HTO)


title: Nalm6_24hr_Rep1_RNAseq


title: 697_6hr_Rep3_RNAseq


title: D7_Smart-seq2_G9_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Nalm6_24hr_Rep2_RNAseq


title: Nalm6_24hr_Rep3_RNAseq


title: Nalm6_6hr_Rep3_RNAseq


title: Nalm6_6hr_Rep1_RNAseq


title: Nalm6_0hr_Rep2_RNAseq


title: 697_6hr_Rep2_RNAseq


title: D7_Smart-seq2_G6_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Nalm6_0hr_Rep3_RNAseq


title: D7_Smart-seq2_G5_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Nalm6_0hr_Rep1_RNAseq


title: H3K27ac_697_24hr_Rep3_ChIPseq

data_processing:
Reads were mapped to the human genome using bowtie2
Peak calling was performed using MACS2 using the default q value of 0.05
Differential enrichment analysis was performed using DESeq2 BigWig files were created using bedGraphToBigWig command in UCSC tools on bedgraphs output by MACS2
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files for each experimental sample

extract_protocol:
Cells were cross-linked, lysed, and sonicated according to the ENCODE project ChIPseq guidelines (https://www.encodeproject.org/about/experiment-guidelines/). 5ug of CTCF, GR, or H3K27ac antibody was used for IP
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with prednisolone at a concentration of 5uM (Nalm6 cells) or 10uM (697 cells) for 2, 6, 12, or 24 hours

tag: antibody

value: H3K27ac Rabbit pAb (Active Motif #39133)


title: D7_Smart-seq2_G4_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_697_24hr_Rep2_ChIPseq


title: D7_Smart-seq2_G3_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_697_12hr_Rep1_ChIPseq

value: PRED (10uM, 12hrs)


title: H3K27ac_697_6hr_Rep3_ChIPseq


title: D7_Smart-seq2_G12_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_697_12hr_Rep2_ChIPseq


title: H3K27ac_697_24hr_Rep1_ChIPseq


title: H3K27ac_697_12hr_Rep3_ChIPseq


title: D7_Smart-seq2_G11_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_697_2hr_Rep3_ChIPseq

value: PRED (10uM, 2hrs)


title: H3K27ac_697_6hr_Rep2_ChIPseq


title: H3K27ac_697_6hr_Rep1_ChIPseq


title: H3K27ac_697_2hr_Rep2_ChIPseq


title: D7_Smart-seq2_F9_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_697_2hr_Rep1_ChIPseq


title: Nalm6_6hr_Rep2_RNAseq


title: D7_Smart-seq2_G7_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F8_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_697_0hr_Rep3_ChIPseq


title: H3K27ac_697_0hr_Rep2_ChIPseq


title: D7_Smart-seq2_F7_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F6_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_Nalm6_24hr_Rep1_ChIPseq


title: H3K27ac_Nalm6_24hr_Rep3_ChIPseq


title: D7_Smart-seq2_G10_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_Nalm6_24hr_Rep2_ChIPseq


title: H3K27ac_Nalm6_12hr_Rep3_ChIPseq

value: PRED (5uM, 12hrs)


title: D7_Smart-seq2_F5_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_F4_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_Nalm6_12hr_Rep2_ChIPseq


title: H3K27ac_Nalm6_6hr_Rep3_ChIPseq


title: H3K27ac_Nalm6_12hr_Rep1_ChIPseq


title: H3K27ac_Nalm6_6hr_Rep1_ChIPseq


title: D7_Smart-seq2_F3_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_Nalm6_6hr_Rep2_ChIPseq


title: H3K27ac_Nalm6_2hr_Rep2_ChIPseq

value: PRED (5uM, 2hrs)


title: H3K27ac_Nalm6_2hr_Rep3_ChIPseq


title: CM D28 rep 4 [GC1003652]

city: Leuven

first: Tim

last: Herpelinck

address: Herestraat 49

department: Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing:
Single-strand sequences were aligned to the Homo sapiens GRh37 reference genome using STAR v.2.7.9a. Gene counts were obtained using subread.
DESeq2 v.1.26.0 was used to normalize the data and determine differentially expressed genes (based on log-fold change > 1 and adjusted p-value < 0.05). Differential expression was calculated using the likelihood ratio test as outlined in the DESeq2 documentation.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file of raw abundance counts from subread and normalized counts.

source_name: Periosteum-derived cells

growth_protocol: All cells were expanded up to passage 7 in high-glucose DMEM-GlutaMAX supplemented with 10% foetal bovine serum, 1% sodium pyruvate and 1% antibiotics-antimycotic solution (DMEM-C).

extract_protocol:
Cells from monolayer cultures were released enzymatically from the culture flasks by incubation with TrypLE Express (Life Technologies, UK) for 10 minutes, spun down at 200g for 10 minutes. Microtissues were gently flushed out of the microwells at the indicated time points and spun down at 200g for 10 minutes. Cells and microtissues were lysed in RLT lysis buffer (Qiagen, Germany) + 1% beta-mercaptoethanol (Sigma Aldrich, Germany), vortexed and stored at -80°C.
RNA was isolated from the lysates with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. cDNA libraries were generated using the Lexogen QuantSeq FWD Sample Preparation Kit.

treatment_protocol: Cells were seeded in microwell plates at 300,000 cells per well to cointain 1000 cells per microwell upon sedimentation. After sedimentation, cells spontaneously self-aggregate into spheroids. These were then treated up to 28 days with chondrogenic medium (CM), xeno-free chondrogenic medium (xfCM) or CM without growth factors (CM- no GF). Cells harvested from monolayer culture were used as baseline (DMEM-C).

value: Periosteum-derived cells

tag: passage

tag: platform

value: CM

tag: timepoint


title: D7_Smart-seq2_F2_exp1

description: Single-cell RNA seq, Smart-Seq2


title: CM D28 rep 3 [GC1003651]

tag: cell type


title: D7_Smart-seq2_F1_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_Nalm6_2hr_Rep1_ChIPseq

tag: cell line


title: D7_Smart-seq2_F12_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_697_0hr_Rep1_ChIPseq


title: H3K27ac_Nalm6_0hr_Rep3_ChIPseq


title: GR_697_24hr_Rep3_ChIPseq

value: GR Mouse mAb (BD #611227)


title: H3K27ac_Nalm6_0hr_Rep1_ChIPseq


title: D7_Smart-seq2_F11_exp1

description: Single-cell RNA seq, Smart-Seq2


title: CM D28 rep 1 [GC1003649]


title: GR_697_24hr_Rep2_ChIPseq


title: D7_Smart-seq2_F10_exp1

description: Single-cell RNA seq, Smart-Seq2


title: GR_697_24hr_Rep1_ChIPseq


title: CM D21 rep 4 [GC1003648]


title: CM D21 rep 3 [GC1003647]


title: D7_Smart-seq2_E9_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E8_exp1

description: Single-cell RNA seq, Smart-Seq2


title: H3K27ac_Nalm6_0hr_Rep2_ChIPseq


title: D7_Smart-seq2_E7_exp1

description: Single-cell RNA seq, Smart-Seq2


title: CM D21 rep 1 [GC1003645]


title: CM D21 rep 2 [GC1003646]


title: GR_697_12hr_Rep1_ChIPseq


title: CM D14 rep 4 [GC1003644]


title: GR_697_12hr_Rep2_ChIPseq


title: CM D28 rep 2 [GC1003650]


title: D7_Smart-seq2_E6_exp1

description: Single-cell RNA seq, Smart-Seq2


title: GR_697_6hr_Rep3_ChIPseq


title: D7_Smart-seq2_E4_exp1

description: Single-cell RNA seq, Smart-Seq2


title: GR_697_6hr_Rep2_ChIPseq


title: D7_Smart-seq2_E3_exp1

description: Single-cell RNA seq, Smart-Seq2


title: CM D14 rep 2 [GC1003642]


title: D7_Smart-seq2_E2_exp1

description: Single-cell RNA seq, Smart-Seq2


title: GR_697_6hr_Rep1_ChIPseq


title: GR_697_12hr_Rep3_ChIPseq


title: CM D14 rep 1 [GC1003641]


title: GR_697_2hr_Rep3_ChIPseq


title: D7_Smart-seq2_E1_exp1

description: Single-cell RNA seq, Smart-Seq2


title: cMPL-EPAZA-4

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description: Gene expression data from cMPL+ cells after treatment for 16 hours

hyb_protocol: cRNA was then hybridized to the Clariom D GeneChip probe array and includes a staining protocol with a fluorescent dye

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 7G (ThermoFisher Scientific)

data_processing:
The data were analyzed with Transcriptome analysis console (TAC) software (ThermoFisher Scientific)
Data generated from RMA normalized CEL expression data files merged itno expression dataset file using GenePattern<http://software.broadinstitute.org/cancer/software/genepattern/> module ExpressionFileCreator.

source_name: cMPL positive cells after 16 hours Treatment with EP and AZA

label_protocol: Biotinylated cRNA were prepared according to the protocol from amplified cRNA (ThermoFisher Scientific, Clariom D Pico Assay, Human Array).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions using the Rneasy Micro Kit (Qiagen).

treatment_protocol: Cord blood MNCs were treated for 16 hour in plain stem span media in the presence of TPO-RA (Thrombopoietin receptor agonists) 100ng/mL TPO or 5ug/mL eltrombopag (EP) with or without 0.3uM AZA. Cells were stained for cMPL and viable cMPL expressing cells sorted using Astrios and placed into RLT lysis buffer (Qiagen).

value: FACS sorted cMPL+ cells

tag: source

value: Cord blood MNCs


title: CM D7 rep 4 [GC1003640]


title: cMPL-EP-4

source_name: cMPL positive cells after 16 hours Treatment with EP

value: after 16 hours Treatment with EP


title: cMPL-TPOAZA-3

source_name: cMPL positive cells after 16 hours Treatment with TPO and AZA


title: cMPL-EP-3


title: GR_697_2hr_Rep2_ChIPseq

value: ALL


title: CM D14 rep 3 [GC1003643]


title: cMPL-TPOAZA-1 tech. rep.

source_name: cMPL positive cells after 16 hours Treatment with TPO and AZA - technical replicate


title: GR_697_2hr_Rep1_ChIPseq


title: cMPL-EPAZA-3

value: after 16 hours Treatment with EP and AZA


title: GR_Nalm6_24hr_Rep3_ChIPseq

value: PRED (5uM, 24hrs)


title: CM D7 rep 3 [GC1003639]


title: GR_Nalm6_24hr_Rep2_ChIPseq


title: D7_Smart-seq2_D9_exp1

description: Single-cell RNA seq, Smart-Seq2


title: cMPL-EP-2


title: cMPL-EPAZA-2


title: D7_Smart-seq2_E10_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E11_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_E12_exp1

description: Single-cell RNA seq, Smart-Seq2


title: CM 5H rep 4 [GC1003636]


title: CM D7 rep 1 [GC1003637]


title: CM D7 rep 2 [GC1003638]


title: GR_Nalm6_24hr_Rep1_ChIPseq


title: cMPL-EPAZA-1


title: D7_Smart-seq2_D8_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D7_exp1

description: Single-cell RNA seq, Smart-Seq2


title: GR_Nalm6_12hr_Rep3_ChIPseq


title: cMPL-TPO-3

source_name: cMPL positive cells after 16 hours Treatment with TPO

value: after 16 hours Treatment with TPO


title: CM 5H rep 2 [GC1003634]


title: CM 5H rep 1 [GC1003633]


title: D7_Smart-seq2_D6_exp1

description: Single-cell RNA seq, Smart-Seq2


title: GR_Nalm6_12hr_Rep2_ChIPseq


title: cMPL-TPO-2


title: cMPL-EP-1

source_name: cMPL positive cells after 16 hours Treatment with Ep

value: after 16 hours Treatment with Ep


title: tunR, rep2, 6 hrs, T101M + WalK(R555C) mutation

city: Toronto

first: Stephanie

last: Tan

state: ON

address: 661 University Ave

country: Canada

institute: University of Toronto

data_processing:
Adapters trimmed and demultiplexed using bcl2fastq by the Microbial Genome Sequencing Center (Pittsburgh, PA)
Trimmed reads were mapped to reference genome: S. aureus N315 (GCF_000009645.1) using Geneious Prime 2021.2.1
Expression analysis and comparisons performed using DeSeq2 algorithm integrated into Geneious Prime
Assembly: S. aureus N315 (GCF_000009645.1)
Supplementary files format and content: Raw Read Count,Raw Transcript Count,RPKM,TPM

organism: Staphylococcus aureus

source_name: bacteria

growth_protocol: 37C, 200RPM shaking, TSB media to OD600nm=1

extract_protocol:
RNA harvested using Qiagen Rneasy Mini Kit as instructed
rRNA depleted using RiboZero Plus kit (Illumina) and cDNA libraries generated with Stranded Total RNA Prep Ligation Kit (Illumina)

value: T101M + WalK(R555C) mutation

value: bacteria


title: DMEM-C D0 rep 7 [GC1003632]

value: Monolayer

value: DMEM-C


title: GR_Nalm6_12hr_Rep1_ChIPseq

value: PRED (5uM, 12hrs)


title: D7_Smart-seq2_D4_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D5_exp1

description: Single-cell RNA seq, Smart-Seq2


title: tunR, rep1, 6 hrs, T101M + WalK(R555C) mutation


title: tunR, rep3, 6 hrs, T101M + WalK(R555C) mutation


title: cMPL-TPOAZA-1

value: after 16 hours Treatment with TPO and AZA


title: GR_Nalm6_6hr_Rep2_ChIPseq

value: PRED (5uM, 6hrs)


title: walR, rep2, 6 hrs, WalR (T101M) mutation

value: WalR (T101M) mutation


title: walR, rep3, 6 hrs, WalR (T101M)mutation


title: DMEM-C D0 rep 5 [GC1003630]

value: Periosteum-derived cells


title: DMEM-C D0 rep 6 [GC1003631]


title: CM 5H rep 3 [GC1003635]

value: CM


title: D7_Smart-seq2_D2_exp1

description: Single-cell RNA seq, Smart-Seq2


title: cMPL-TPOAZA-2

value: FACS sorted cMPL+ cells

value: Cord blood MNCs


title: GR_Nalm6_6hr_Rep3_ChIPseq

value: ALL

value: GR Mouse mAb (BD #611227)


title: GR_Nalm6_6hr_Rep1_ChIPseq


title: D7_Smart-seq2_D3_exp1

description: Single-cell RNA seq, Smart-Seq2


title: walR, rep1, 6 hrs, WalR (T101M) mutation


title: DMEM-C D0 rep 4 [GC1003629]


title: GR_Nalm6_2hr_Rep3_ChIPseq

value: PRED (5uM, 2hrs)


title: D7_Smart-seq2_D1_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_D12_exp1

description: Single-cell RNA seq, Smart-Seq2


title: xfCM D21 rep 3 [GC1003627]

value: xfCM


title: xfCM D21 rep 4 [GC1003628]


title: wild type, rep 2, 6hrs

value: wild type


title: cMPL-TPO-1

value: after 16 hours Treatment with TPO


title: wild type, rep 3, 6hrs

value: bacteria


title: GR_Nalm6_2hr_Rep1_ChIPseq


title: wild type, rep 1, 6hrs


title: xfCM D21 rep 2 [GC1003626]


title: xfCM D21 rep 1 [GC1003625]


title: D7_Smart-seq2_D11_exp1

description: Single-cell RNA seq, Smart-Seq2


title: xfCM D14 rep 4 [GC1003624]


title: Tbx18-rep3

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
352_Cho_DESeq2_NormCounts_unpace.txt
Sample6_160709

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Rattus norvegicus (RN5) genomic reference with STAR (v2.4.0g1) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: RN5 from UCSC
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Rattus norvegicus

growth_protocol: Nenatal rat ventricular myocytes (NRVMs) were freshly isolated at postnatal age 1-3 days, and were cultured on a fibronectin-coated culture dishes in a M199-based media. For the first two days, the NRVMs were cultured in  10% fetal bovine serum (FBS)  and then in 2% FBS from day 3 and thereafter.

extract_protocol:
RNA was purified using QIAGEN miRNeasy Mini columns, and RNA quality assessed using Agilent Bioanalyzer.
100 ng of total RNA was used as input for library construction using the Illumina TruSeq mRNA Stranded Library Prep Kit. Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled, and sequenced on an Illumina HiSeq 3000 using (101 bp PE) at an average read depth of 30 million reads/sample.

treatment_protocol: The NRVMs were transduced with either Adeno-GFP or Adeno-Tbx18-IRES-GFP on the day of cell isolation.

value: Sprague Dawley

tag: viral transduction

tag: age

value: Postnatal day 1-3


title: Tbx18-rep2

description:
352_Cho_DESeq2_NormCounts_unpace.txt
Sample5_160708


title: D7_Smart-seq2_C9_exp1

description: Single-cell RNA seq, Smart-Seq2

tag: background


title: Tbx18-rep1

description:
352_Cho_DESeq2_NormCounts_unpace.txt
Sample4_160707


title: D7_Smart-seq2_C8_exp1

description: Single-cell RNA seq, Smart-Seq2

tag: genotype


title: CTCF_697_24hr_Rep1_ChIPseq

value: CTCF Rabbit pAb (Active Motif #61311)

value: PRED (10uM, 24hrs)


title: xfCM D14 rep 3 [GC1003623]


title: CTCF_697_24hr_Rep2_ChIPseq


title: CTCF_697_12hr_Rep1_ChIPseq

value: PRED (10uM, 12hrs)


title: CTCF_697_12hr_Rep2_ChIPseq


title: xfCM D14 rep 2 [GC1003622]


title: D7_Smart-seq2_D10_exp1

description: Single-cell RNA seq, Smart-Seq2


title: CTCF_697_6hr_Rep2_ChIPseq

value: PRED (10uM, 6hrs)


title: GFP-rep3

description:
352_Cho_DESeq2_NormCounts_unpace.txt
Sample3_160703

source_name: GFP-NRVMs

value: Ad-GFP


title: D7_Smart-seq2_C6_exp1

description: Single-cell RNA seq, Smart-Seq2

source_name: Carotid artery


title: xfCM D7 rep 4 [GC1003620]

value: Periosteum-derived cells


title: xfCM D14 rep 1 [GC1003621]


title: GFP-rep2

description:
352_Cho_DESeq2_NormCounts_unpace.txt
Sample2_160702


title: CTCF_697_6hr_Rep1_ChIPseq


title: CTCF_697_2hr_Rep2_ChIPseq

value: PRED (10uM, 2hrs)


title: D7_Smart-seq2_C4_exp1

description: Single-cell RNA seq, Smart-Seq2


title: GFP-rep1

description:
352_Cho_DESeq2_NormCounts_unpace.txt
Sample1_160701


title: D7_Smart-seq2_C5_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C7_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_C2_exp1

description: Single-cell RNA seq, Smart-Seq2


title: xfCM D7 rep 1 [GC1003617]


title: D7_Smart-seq2_C3_exp1

description: Single-cell RNA seq, Smart-Seq2


title: CTCF_697_2hr_Rep1_ChIPseq


title: xfCM D7 rep 2 [GC1003618]


title: D7_Smart-seq2_C1_exp1

description: Single-cell RNA seq, Smart-Seq2


title: TommW7

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files, log transfromed, normalized using quantile method and provided as an Excel spreadsheet. The background thresholds have been calculated per samples as the mean of the negative controls plus 2 times their standard deviation. Genes with counts less then the calculated background are considered not expressed and excluded from the subsequent analysis and not reported in the Normalzied_Data file.
Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system.

source_name: lymph node

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was processed following the NanoString manufacturer's protocol

extract_protocol: RNA was isolated from FFPE tissue

tag: tissue

value: lymph node

tag: status

value: Without Tumor


title: TommW6


title: TommW2


title: CTCF_697_0hr_Rep1_ChIPseq

value: ALL

tag: treatment


title: xfCM 5H rep 4 [GC1001712]


title: TommW3


title: CTCF_697_0hr_Rep2_ChIPseq


title: D7_Smart-seq2_C12_exp1

description: Single-cell RNA seq, Smart-Seq2


title: CTCF_Nalm6_24hr_Rep2_ChIPseq

value: PRED (5uM, 24hrs)


title: TommNC7

value: Untreated


title: xfCM D7 rep 3 [GC1003619]

value: xfCM


title: CTCF_Nalm6_24hr_Rep1_ChIPseq


title: D7_Smart-seq2_C11_exp1

description: Single-cell RNA seq, Smart-Seq2


title: xfCM 5H rep 2 [GC1001710]


title: CTCF_Nalm6_12hr_Rep2_ChIPseq

value: PRED (5uM, 12hrs)


title: xfCM 5H rep 1 [GC1001709]


title: CTCF_Nalm6_12hr_Rep1_ChIPseq


title: TommNC6


title: TommNC3


title: D7_Smart-seq2_B9_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_B8_exp1

description: Single-cell RNA seq, Smart-Seq2


title: xfCM D21 rep 6 [GC1001708]

value: CM - no GF


title: D7_Smart-seq2_B7_exp1

description: Single-cell RNA seq, Smart-Seq2


title: CTCF_Nalm6_6hr_Rep2_ChIPseq

value: PRED (5uM, 6hrs)


title: xfCM D21 rep 5 [GC1001707]


title: xfCM D21 rep 4 [GC1001706]


title: TommNC2


title: CTCF_Nalm6_6hr_Rep1_ChIPseq


title: D7_Smart-seq2_B6_exp1

description: Single-cell RNA seq, Smart-Seq2


title: xfCM 5H rep 3 [GC1001711]


title: CTCF_Nalm6_2hr_Rep2_ChIPseq

value: PRED (5uM, 2hrs)


title: TommC6

value: Depleted for Macrophages


title: TommC4


title: xfCM D21 rep 3 [GC1001705]


title: CTCF_Nalm6_2hr_Rep1_ChIPseq

value: CTCF Rabbit pAb (Active Motif #61311)


title: D7_Smart-seq2_B5_exp1

description: Single-cell RNA seq, Smart-Seq2


title: TommC2


title: D7_Smart-seq2_C10_exp1

description: Single-cell RNA seq, Smart-Seq2


title: xfCM D21 rep 2 [GC1001704]


title: D7_Smart-seq2_B4_exp1

description: Single-cell RNA seq, Smart-Seq2


title: xfCM D21 rep 1 [GC1001703]


title: CTCF_Nalm6_0hr_Rep2_ChIPseq

data_processing:
Reads were mapped to the human genome using bowtie2
Peak calling was performed using MACS2 using the default q value of 0.05
Differential enrichment analysis was performed using DESeq2
BigWig files were created using bedGraphToBigWig command in UCSC tools on bedgraphs output by MACS2
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files for each experimental sample


title: D7_Smart-seq2_B3_exp1

description: Single-cell RNA seq, Smart-Seq2

data_processing:
Smart-seq2: Reads were aligned to the GRCm38 mouse genome using TopHat aligner v2.1 (Trapnell et al. 2009) and Htseq-count v0.8 (Anders et al. 2015) was used to count the number of read alignments per gene in the resulting bam files (idattr = “gene_id” and stranded = “no”). Cells with <200,000 total reads, <1,000 genes detected and >30% of ERCC controls were excluded from analysis and genes with mean expression <1 were removed. The function computeSumFactors from the Bioconductor R package scran (Lun et al., 2016b) was used to compute the normalization factors for individual cells.
Genome_build: GRCm38
Supplementary_files_format_and_content: Smart-seq2 cell ID file: Csv file contains cell ID information for each sample Smart-seq2 dataset.
Smart-seq2 count file: Txt file contains raw count values with genes in rows and cells/samples in columns.
Smart-seq2 normalized count file: Txt file contains normalized and filtered count values with genes in rows and cells/samples in columns.;


title: CTCF_Nalm6_0hr_Rep1_ChIPseq

data_processing:
Reads were mapped to the human genome using bowtie2
Peak calling was performed using MACS2 using the default q value of 0.05
Differential enrichment analysis was performed using DESeq2

BigWig files were created using bedGraphToBigWig command in UCSC tools on bedgraphs output by MACS2
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files for each experimental sample


title: 697_24hr_Rep3_ATACseq

data_processing:
Reads were mapped to the human genome using bowtie2
Peak calling was performed using MACS2 using the default q value of 0.05
Differential analysis was performed using DESeq2
BigWig files were created using bedGraphToBigWig command in UCSC tools on bedgraphs output by MACS2
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files for each experimental sample

extract_protocol:
Cells were transposed following to the FAST-ATAC protocol from the Greenleaf Lab
Libraries were prepared for sequencing using standard Illumina protocols

value: PRED (10uM, 24hrs)


title: D7_Smart-seq2_B2_exp1

description: Single-cell RNA seq, Smart-Seq2

extract_protocol:
The Smart-seq2 protocol (Picelli et al., 2014) was used to generate amplified cDNA libraries from EYFP+RFP+ and EYFP+RFP- cells isolated from ligated left common carotid arteries of VSMC lineage-labeled animals (Myh11-EYFP-Ki67/RFP) 7 days after surgery and EYFP+ cells from unligated litter mate control animals in 2 separate experiments (experiment 1: 4 ligated arteries and 1 control arteries; experiment 2: 5 ligated arteries and 2 control arteries). Cells were processed as described (Dobnikar et al., 2018) with addition of ERCC spike controls (diluted 1:80,000,000, Invitrogen).
Sequencing libraries were generated using the Nextera XT kit and pooled libraries were sequenced using a paired end protocol (HiSeq 2500, Illumina).


title: CM Agarose D21 rep 2 [GC1001701]

value: Agarose

value: CM


title: 697_24hr_Rep2_ATACseq


title: D7_Smart-seq2_B12_exp1

description: Single-cell RNA seq, Smart-Seq2


title: CM Agarose D21 rep 1 [GC1001700]

value: Periosteum-derived cells


title: D7_Smart-seq2_B1_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_B11_exp1

description: Single-cell RNA seq, Smart-Seq2


title: DMEM-C D0 rep 2 [GC1001698]

value: Monolayer

value: DMEM-C


title: GR_Nalm6_2hr_Rep2_ChIPseq

value: GR Mouse mAb (BD #611227)


title: 697_6hr_Rep3_ATACseq

value: ALL

value: PRED (10uM, 6hrs)


title: 697_6hr_Rep2_ATACseq


title: DMEM-C D0 rep 1 [GC1001697]


title: 697_24hr_Rep1_ATACseq


title: 697_6hr_Rep1_ATACseq


title: Pto_HIMT_4_rep3

city: Verona

first: Elodie

last: Vandelle

state: Verona

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium supplemented with tomato extract, replicate 3

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >15 pmol Cy3/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing  25x Agilent fragmentation buffer and 10x Agilent blocking agent following manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to Agilent-078853 8x60K custom microarray chip for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarray chips were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing using the Agilent DNA Microarray Scanner with one color scan settings for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to XDR Hi100%, XDR Lo 10%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid:078853_D_F_20151012) to substract the background and obtain spatially-detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Data were background corrected and quantile normalized.

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with tomato extract for 4h, replicate 3

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 50 ng of RNA using the Low Input Quick Amp WT Labeling kit (Agilent Techonologies, Santa Clara, CA, USA) according to manufacturer's instructions for prokaryotic samples, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked using the NanoDrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA).

growth_protocol: Bacterial cells were cultured in hrp-inducing medium supplemented or not with kiwifruit or tomato extract (1%, v/v) for 1h or 4 h at 28°C with shaking (200 rpm)

extract_protocol: Two ml of each bacterial suspension were centrifuged and total RNA was extracted from cell pellets using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA). Total RNA quantity, integrity and purity were controlled using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA) and a Bioanalyzer Chip RNA 7500 serie II (Agilent).

value: bacterial cells


title: CM Agarose D21 rep 3 [GC1001702]


title: 697_0hr_Rep3_6-24hr_ATACseq


title: D7_Smart-seq2_B10_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Pto_HIMT_4_rep2

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium supplemented with tomato extract, replicate 2

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with tomato extract for 4h, replicate 2


title: D7_Smart-seq2_A8_exp1

description: Single-cell RNA seq, Smart-Seq2


title: 697_0hr_Rep2_6-24hr_ATACseq


title: TommC1

value: lymph node


title: KO-wat3

city: Nanjing

first: Yuncai

last: Zhou

state: Jiangsu

address: No. 818 Tianyuan East Road, Jiangning District

country: China

institute: Nanjing medical university

data_processing:
Illumina Casava 1.8 was used to recognize and trasfer the image results to reads.
The error rate was recorded as "e". The quality of base was characterized as Qphred, and the Qphred = -10log10 (e) .
The reads were filtered obey the rules as follows: first, filter the reads with adapter, second, delete the reads with uncertain base, finally, filter the reads containing more than 50% bases that has a Qphred ≤ 20.
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 according to the manufaturer's protocols.
Assembly: mm10
Supplementary files format and content: gene_count

source_name: White adipose tissue

growth_protocol: WT and  KO mice were fasted for 12 hrs, then anesthetized and sacrificed by neck broken. Cut off the auricular appendage and exhaled blood, then fulfill the vessels and wash with pre-cooling PBS.

extract_protocol:
Homogenate the tissues twice with a homogenizer, TRIZOL was used to extract total RNA.
2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Liver and inguinal WAT were collected and quick-frozen by liquid nitrogen.

value: White adipose tissue

tag: gender

value: male

value: global miR-322-503-351 deleted

value: fasted for 12 hrs


title: KO-wat2


title: H1299, 10Gy, exosome, rep1

city: Kunming

first: Tongxin

last: Yang

address: No.374 Dianmian Road

department: The Department of Urology

institute: The Second Affiliated Hospital of Kunming Medical University

description: MicroRNA expression after 10Gy-irradiated H1299 cell

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, 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 to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: H1299, exosome, 10Gy, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS 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.

growth_protocol: The adherent H1299 cells were cultured in RPMI-1640 medium containing 10% FBS.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Cell irradiation was performed using the Elekta linear accelerator at Source skin distance (SSD)=100cm, dose rate =400cGy/min, and the irradiation dose was 10 Gy.

tag: cell component

value: exosome

value: irradiation


title: H1299, 0Gy, exosome, rep1

description: MicroRNA expression after 0Gy-irradiated H1299 cell

source_name: H1299, exosome, 0Gy, replicate 1

value: control


title: DMEM-C D0 rep 3 [GC1001699]


title: D7_Smart-seq2_A7_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Pto_HIMT_4_rep1

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium supplemented with tomato extract, replicate 1

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with tomato extract for 4h, replicate 1


title: 697_0hr_Rep1_6-24hr_ATACseq

source_name: 697 (ALL cell line)

tag: replicate


title: D7_Smart-seq2_A6_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Pto_HIMT_1_rep3

description: Gene expression in Pto DC3000 cells grown 1h in hrp-inducing medium supplemented with tomato extract, replicate 3

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with tomato extract for 1h, replicate 3


title: KO-wat1


title: WT-wat3

value: wild type


title: Pto_HIMT_1_rep2

description: Gene expression in Pto DC3000 cells grown 1h in hrp-inducing medium supplemented with tomato extract, replicate 2

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with tomato extract for 1h, replicate 2


title: D7_Smart-seq2_A4_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Pto_HIMT_1_rep1

description: Gene expression in Pto DC3000 cells grown 1h in hrp-inducing medium supplemented with tomato extract, replicate 1

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with tomato extract for 1h, replicate 1


title: D7_Smart-seq2_A9_exp1

description: Single-cell RNA seq, Smart-Seq2


title: D7_Smart-seq2_A5_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Nalm6_24hr_Rep3_ATACseq

source_name: Nalm6 (ALL cell line)

value: PRED (5uM, 24hrs)


title: WT-wat2


title: D7_Smart-seq2_A3_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Nalm6_24hr_Rep2_ATACseq


title: Nalm6_24hr_Rep1_ATACseq


title: WT-wat1


title: D7_Smart-seq2_A2_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Pto_HIMK_4_rep3

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium supplemented with kiwifruit extract, replicate 3

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 4h, replicate 3


title: Pto_HIMK_4_rep2

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium supplemented with kiwifruit extract, replicate 2

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 4h, replicate 2


title: Nalm6_6hr_Rep3_ATACseq

value: PRED (5uM, 6hrs)


title: KO-liver3

source_name: Liver

value: Liver


title: D7_Smart-seq2_A12_exp1

description: Single-cell RNA seq, Smart-Seq2


title: Nalm6_6hr_Rep2_ATACseq


title: Nalm6_6hr_Rep1_ATACseq


title: D7_Smart-seq2_A1_exp1

description: Single-cell RNA seq, Smart-Seq2


title: KO-liver2


title: Pto_HIMK_4_rep1

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium supplemented with kiwifruit extract, replicate 1

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 4h, replicate 1


title: KO-liver1


title: Nalm6_0hr_Rep3_6-24hr_ATACseq


title: Pto_HIMK_1_rep2

description: Gene expression in Pto DC3000 cells grown 1h in hrp-inducing medium supplemented with kiwifruit extract, replicate 2

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 1h, replicate 2


title: WT-liver2


title: Pto_HIMK_1_rep1

description: Gene expression in Pto DC3000 cells grown 1h in hrp-inducing medium supplemented with kiwifruit extract, replicate 1

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 1h, replicate 1


title: Pto_HIM_4_rep3

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium, replicate 3

source_name: Pto DC3000 cells incubated in hrp-inducing medium for 4h, replicate 3


title: Donor 1510 MO -LIF 72h

first: Robin

last: Hallett

address: 101 College Street

department: Translation

institute: Northern Biologics

description: *** Raw data for this submission is unavailable (accidentally destroyed) ***

data_processing:
Reads were mapped to GRCh38
Assembly was completed using Stringtie
gene level FPKM were computed
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample (log2[FPKM+2])

source_name: Macrophages (M0) no LIF, day 3

growth_protocol: Human macrophages were differentiated in vitro from peripheral blood CD14+ monocytes using CSF1

extract_protocol: RNA was extracted using Rneasy Mini kit (Qiagen)

treatment_protocol: Macrophages were treated with LIF for 3 days (20nM)

value: Human monocyte derived macrophages

value: no LIF


title: 697_12hr_Rep3_ATACseq

value: ALL

value: PRED (10uM, 12hrs)


title: Donor 1510 MO +LIF 72h

source_name: Macrophages (M0) LIF, day 3

value: LIF


title: WT-liver1


title: Nalm6_0hr_Rep1_6-24hr_ATACseq


title: Pto_HIM_4_rep2

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium, replicate 2

source_name: Pto DC3000 cells incubated in hrp-inducing medium for 4h, replicate 2

value: bacterial cells


title: 697_12hr_Rep2_ATACseq


title: Donor 1604 MO +LIF 72h


title: Pto_HIM_4_rep1

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium, replicate 1

source_name: Pto DC3000 cells incubated in hrp-inducing medium for 4h, replicate 1


title: NSCs SETD4 OE 2

city: Hangzhou

first: sunli

last: cai

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Illumina NovaSeq 6000
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

growth_protocol: primary neural stem cells were isolated from the SVZ of adult C57BL/6 mice brain and maintained in Neuralbasal medium supplemented with 2% B27 in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
primary SVZ tissue were micro-dissected from adult C57BL/6 mice brain and dissociated by Neural Tissue Dissociation Kit - Papain (Miltenyi, 130-092-628)
RNA libraries were pereared for sequencing using standrard lllumina protocols

treatment_protocol: SETD4 overexpression was induced by treatment of 24 hour neural stem cells infected with ADV-SETD4-GFP, using ADV-GFP as a control.

value: brain

value: primary cell

value: neural stem cell

value: SETD4 overexpression


title: 697_12hr_Rep1_ATACseq

first: Daniel

source_name: 697 (ALL cell line)


title: Donor 1604 MO -LIF 72h


title: Donor 889 MO +LIF 72h


title: Pto_HIM_1_rep2

description: Gene expression in Pto DC3000 cells grown 1h in hrp-inducing medium, replicate 2

source_name: Pto DC3000 cells incubated in hrp-inducing medium for 1h, replicate 2


title: Pto_HIMK_1_rep3

description: Gene expression in Pto DC3000 cells grown 1h in hrp-inducing medium supplemented with kiwifruit extract, replicate 3

source_name: Pto DC3000 cells incubated in hrp-inducing medium supplemented with kiwifruit extract for 1h, replicate 3


title: NSCs ADV-GFP control 3

description: control.txt

value: WT

value: ADV-GFP


title: WT-liver3

value: male

value: fasted for 12 hrs


title: D7_Smart-seq2_A11_exp1

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

description: Single-cell RNA seq, Smart-Seq2

source_name: Carotid artery


title: Donor 889 MO -LIF 72h


title: 697_2hr_Rep2_ATACseq

value: PRED (10uM, 2hrs)


title: NSCs SETD4 OE 1


title: Pto_HIM_1_rep3

description: Gene expression in Pto DC3000 cells grown 1h in hrp-inducing medium, replicate 3

source_name: Pto DC3000 cells incubated in hrp-inducing medium for 1h, replicate 3


title: 697_2hr_Rep3_ATACseq


title: Pto_HIM_1_rep1

description: Gene expression in Pto DC3000 cells grown 1h in hrp-inducing medium, replicate 1

source_name: Pto DC3000 cells incubated in hrp-inducing medium for 1h, replicate 1


title: Nalm6_0hr_Rep2_6-24hr_ATACseq

source_name: Nalm6 (ALL cell line)


title: 697_2hr_Rep1_ATACseq


title: D7_Smart-seq2_A10_exp1

description: Single-cell RNA seq, Smart-Seq2


title: NSCs SETD4 OE 3


title: Sample 3_EB5 100% corrections

city: Wroclaw

first: Lukasz

last: Laczmanski

address: Weigla 12

country: Poland

institute: Hirszfeld Institute of Immunology and Experimental Therapy

data_processing:
The HISAT2 software (Kim, Paggi, et al. 2019) as used to align reads to the human reference genome (Hg38).
SAMtools software were used to convert .sam to .bam files.
The featureCounts algorithm performed transcript assembly, quantification of expression as fragments per kilobase of transcript per million mapped reads (FPKM) values, and normalization
Normalized FPKM values were used for the differential expression analysis, which was performed using an ‘edger’ R script
Assembly: HG38
Supplementary files format and content: tab-delimited text files include R edger's analysis.

source_name: fibroblasts

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen) according to manufacturer’s protocols
RNA-Sequencing libraries were prepared by KAPA RNA Hyper+RiboErase HMR Kit (Roche Corp.) according to the manufacturer’s standard protocol

value: fibroblasts

value: Fibroblasts after correction


title: NSCs ADV-GFP control 2

description: control.txt