title: anti-PRDM1, wildtype PRDM1, replicate 2

description: Cut&Run with PRDM1 antibody (CST), on CD22-CAR-T cells

value: pXD60 AAV6+Cpf1 mRNA


title: V223-SalivaRNAL_S168

status: Public on Dec 09 2022

type: SRA

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

country: USA

institute: National Institute on Aging

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed using cutadapter.
QIIME2.0 microbiome pipeline.
Centered log-ratio (CLR) transformation.
Assembly: hg38
Supplementary files format and content: *.genus.txt: Genus-level taxon datasets; CLR transformed values.
Library strategy: 16S RNA amplicon sequencing

molecule: genomic DNA

organism: human oral metagenome

source_name: Oral microbiome

extract_protocol:
DNA was isolated using a Zymo Research Quick-DNA Fecal/Soil Microbe Miniprep Kit (catalog D6010).
DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Saliva

tag: condition

value: not provided

tag: donor id


title: V219-SalivaRNAL_S270


title: SETD1AKO_FKBP-SETD1A_dTAG_CTDpS5 ChIP-Seq

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.1.0.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
Duplication reads were removed from aligned file by using picard-tools-1.56.
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

organism: Homo sapiens

growth_protocol: MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
For ChIP-seq, cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: HA-FKBP-hSETD1A expression vector, Cas9 expression vector and SETD1A sgRNA expression vector  were introduced with lentivirus and stable expressing single cell clone was established. Cells were treated with DMSO or 500 nM dTAG-13 for 24 hours.

tag: vector

tag: chip antibody

value: CTDpS5 (Cell Signaling)

tag: stimulation

tag: time


title: V218-Subgingival_S289

value: Subgingival sites


title: IgG control, replicate 3

city: West Haven

first: Ryan

middle: D

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

description: Cut&Run with IgG antibody, on parental CD8 T cells

data_processing:
CUT & RUN fastq sequencing data were analyzed according to a previously published protocol, with some modifications. Raw fastq files were first trimmed and cleaned using Trimmomatic  and Kseq. Cleaned fastq reads were then separately aligned to the human genome (hg38.p13) and the E. coli genome (GCF_000005845.2) using BWA mem with settings -M -t 8 -K 10000000.
Peaks were called from the hg38 BAM alignment files using MACS2 callpeak, comparing each experimental sample to each IgG control. The resulting peaks for a given sample were then merged with BEDTools. These peaks were then further merged, combining the peaks  from each biological condition (vector or PRDM1-cr1).
To define genes that are bound by PRDM1, we annotated the peak calls from the vector-treated samples using HOMER, assigning  each peak to the closest TSS (<=2.5kb). Overlaps between PRDM1-bound genes and DEGs were assessed by hypergeometric test, assuming 20,465 total human genes.
The number of aligned reads to each genome were then determined in order to calculate library scaling factors, as described in the EpiCypher CUTANA user manual. Specifically, the hg38- aligned read counts were scaled such that the reads aligned to the spike-in E. coli genome would be normalized across samples. The scaling factors were used to generate normalized bedgraph files, which were then converted into bigWig files. Replicate IgG control bigWig files were averaged by wiggleTools to create a single IgG control sample. Finally, signal visualization was performed using deepTools and Gviz.
Assembly: hg38.p13
Supplementary files format and content: .bw: bigWig normalized signal tracks. XDCut_Run01.mergedControl.bw contains the average signal for all 3 IgG replicates
Supplementary files format and content: .bed: *.200flank.bed has the MACS2 peak summits with surrounding 200bp. Sample5_7.MACS.merged.bed and Sample12_13.MACS.merged.bed are the merged peaks from Sample5+7 and Sample12+13, respectively.
Library strategy: Cut & Run

source_name: primary CD8 T cells

extract_protocol:
Vector CAR-T cells and PRDM1cr1 exon3-skip mutant CAR-T cells were FACS isolated, and CUT & RUN was performed following the EpiCypher CUTANA user manual. Briefly, 1 × 106 CAR-T cells were washed with cold PBS and resuspended in nuclei isolation buffer (100mM Hepes-KOH PH7.6, 100mM KCl, 5mM Mgcl2, 0.5% NP40 supplemented with Roche complete protease inhibitor) and incubated on ice for 10 min. Nuclei were washed twice with CUT & RUN wash buffer and incubated with activated concanavalin-A (ConA) beads for 10 min at RT. ConAbead- bound nuclei were incubated overnight at 4°C in CUT & RUN antibody buffer and antibodies including anti-Blimp1/PRDM1 (CST#9115), anti-H3K4me3 (positive control) and Rabbit IgG (negative control) antibodies. After antibody incubation, ConA-bead-bound nuclei were washed once with Cell Permeabilization Buffer then incubated with 2.5μL pAG-MNase for 10 min at RT. ConA-bound-nuclei were then washed twice with Cell Permeabilization Buffer. Targeted chromatin was digested and released by adding 1ul 100mM CaCl2 and incubated on ice for 2h. The reaction was stopped by addition of 33μl stop buffer.
1ul E. coli Spike-in DNA was added to each sample as internal control. DNA fragments were purified by using DNA cleanup columns. CUT & RUN sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primer Set 1 and 2). Library fragment size was analyzed by TapeStation (Agilent). The pass-QC libraries were sequenced on Illumina NovaSeq 150-bp paired-end reads.

tag: cell type

value: primary CD8 T cells

tag: genotype

value: parental

tag: treatment


title: Pou4f2_HA Rep1 Cut&Tag (1st sequencing)

city: Buffalo

first: Xiuqian

last: Mu

state: NY

address: 701 Ellicott Street

department: Ophthalmology

institute: University at Buffalo

description: Pou4f2_mergepeak_BAMPE2271_peaks.narrowPeak

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 3  mkoutput with Bcl2Fastq 2.20.0.422 and Cellranger-ATAC 1.1
Cellranger 3 and Cellranger-Atac 1.1 Count against mm10 genome to produce count matrix (h.5 format files, fragment tsv files, bam)
Seurat 4.0.1 used for marker gene analysis and visualization
Cut&Tag MACS2 Peak Calling -g mm using treatment and control (IgGRabbit) options
Feature Counts to DESeq2 for BULK-RNA analysis
Assembly: mm10
Supplementary files format and content: h5 File containing UMI corrected read counts, ATAC Fragment Files, narrowPeak peak calls from Cut&Tag
Library strategy: CUT&Tag

organism: Mus musculus

source_name: Mouse Retina

growth_protocol: Retinas with the desired genotypes at different developmental stages (E14.5, and E17.5) were collected in cold phosphate buffered solution (PBS) after timed mating. retinas were incubated in PBS with 100 μg/mL trypsin for 5 minutes at 37ºC and then triturated five times with a pipette. The soybean trypsin inhibitor was added to a final concentration of 100 μg/mL to stop digestion. Cells were collected by centrifugation at 500 g for 5 minutes, washed twice with PBS, and re-suspended in PBS. Cell sorting was performed on a BD FACS Fusion Cell Sorter. The viable and single cell events were selected for sorting through the forward and side scatter gates. The zsGreen signal was collected by a 488 laser with a 530/30 detector, and a 561 laser with a 582/15 detector was used to collect tdTomato expressing cells. The gating threshold for the fluorescence was set to relatively low levels to isolate cells that had just begun to express the two fluorescent proteins. The viability of purified cells was tested by trypan blue staining, and each sample had at least 80% of cells viable.

extract_protocol:
Nuclei isolation was performed following the protocol from 10X Genomics (CG000169). Briefly, 100,000-1,000,000 cells were collected by FACS and centrifuged at 300 g for 5 min at 4°C. Cell pellets were resuspended in 100 μl cold Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, 1%BSA), mixed by gently by pipetting then incubated for 2 min on ice. One milliliter of cold Wash Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1%BSA) was then added immediately and mixed by gentle pipetting. The cells were then spun down at 500 g for 5 min at 4°C, and resuspended in cold 1X Nuclei Buffer (10x Genomics, PN-2000153). The nuclei concentration and quality were determined with a hemocytometer.
scRNA-seq:  scRNA-seq was performed on 10X Chromium single cell platform using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1, in keeping with the manufacturer’s instructions (10X Genomics, CG000204). The sorted cells were loaded onto the 10X Genomics Chromium Controller targeting >5,000 cells per sample to generate scRNA-seq libraries. The quantity and quality of the libraries were evaluated by the Qubit Fluorometer and Agilent Fragment Analyzer. High-quality libraries were subsequently sequenced on a NovaSeq6000 sequencer (PE 26X100).
snATAC-seq:  scATAC-seq library preparation was performed following the protocol from 10X Genomics (CG000168 Rev B) using the Chromium Single Cell ATAC Reagent Kits (10X Genomics). The libraries were cleaned using SPRIselect reagent (Beckman Coulter). The quantity and quality of the libraries were evaluated by the Qubit Fluorometer and Agilent Fragment Analyzer. The libraries were subsequently sequenced on a NovaSeq6000 (PE50).
CUT&Tag:  The Cleavage Under Targets & Tagmentation (CUT&Tag) experiments were performed using reagents and following a protocol from EpiCypher.
scRNA-Seq (10 Genomics), snATAC-Seq (10 Genomics), CUT & Tag (Epicypher)

tag: antibody

value: rabbit, 3724, Cell Signaling

tag: strain

value: Mouse Retina

tag: developmental stage


title: Pou4f2_HA Rep1 Cut&Tag (2nd sequencing)


title: anti-PRDM1, wildtype PRDM1, replicate 1


title: Pou4f2-tdTomato-wt-E17.5 scATAC

library_source: genomic single cell

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 3  mkoutput with Bcl2Fastq 2.20.0.422 and Cellranger-ATAC 1.1
Cellranger 3 and Cellranger-Atac 1.1 Count against mm10 genome to produce count matrix (h.5 format files, fragment tsv files, bam)
Seurat 4.0.1 used for marker gene analysis and visualization
Cut&Tag MACS2 Peak Calling -g mm using treatment and control (IgGRabbit) options
Feature Counts to DESeq2 for BULK-RNA analysis
Assembly: mm10
Supplementary files format and content: h5 File containing UMI corrected read counts, ATAC Fragment Files, narrowPeak peak calls from Cut&Tag


title: SETD1AKO_FKBP-SETD1A_DMSO_CTDpS5 ChIP-Seq

value: DMSO


title: IgG control, replicate 2


title: V218-SalivaRNAL_S256


title: Pou4f2-tdTomato-wt-E14.5 scATAC


title: SETD1AKO_FKBP-SETD1A_dTAG_CTDpS7 ChIP-Seq

value: CTDpS7 (Cell Signaling)


title: V217-SalivaRNAL_S164


title: anti-H3K4me3, positive control

description: Cut&Run with H3K4me3 antibody, on parental CD8 T cells


title: IgG control, replicate 1


title: SETD1AKO_FKBP-SETD1A_DMSO_CTDpS7 ChIP-Seq


title: SETD1AKO_FKBP-SETD1A_dTAG_K4me1 ChIP-Seq

value: H3K4me1 (#ab8895, Abcam)


title: iCAFs

city: Tianjin

first: xudong

last: Wu

address: Qixiangtai Road

country: China

institute: Tianjin medical university

library_source: transcriptomic

data_processing:
Reads were aligned to the reference human genome assembly hg19 using hisat2 version 2.1.0 with default parameters. Assembling full-length transcripts and quantifications for each gene to generate Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) values were performed by StringTie v2.1.1.
Bigwig files were generated by deeptools v3.5.1 bamCoverage
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each Sample
Supplementary_files_format_and_content: Bigwig files for each Sample

molecule: total RNA

source_name: fibroblasts

growth_protocol: MRC5 cells were maintained in Growth Medium in a humidified 5% CO2 environment at 37°C.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEBNext Ultra RNA library Prep Kit for Illumina.

treatment_protocol: Empty vector, JUN WT or JUN AA overexpressed MRC5 were generated by infecting MRC5 with corresponding adenovirus. Induced CAFs (iCAFs) were generated by culturing MRC5 cells in MDA-MB-231-derived conditional medium for 7 days. To inhibit JUN phosphorylation, iCAFs were treated with vehicle (DMSO) or JNKi (1 µM) for 48 hours.

tag: cell line

value: induced CAFs (iCAFs)


title: V216-Subgingival_S34


title: iCAFs+JNKi

value: JNKi-treated iCAFs


title: V216-SalivaRNAL_S112


title: Atoh7-zsGreen-wt scATAC


title: SETD1AKO_FKBP-SETD1A_DMSO_K4me1 ChIP-Seq


title: Atoh7-zsGreen-wt-E17.5 scATAC


title: MRC5


title: SETD1AKO_FKBP-SETD1A_dTAG_K27Ac ChIP-Seq

value: H3K27ac (#39159, Active Motif)


title: V215-Subgingival_S262


title: V217-Subgingival_S57


title: Atoh7-zsGreen-Lacz-E14.5 scATAC


title: SETD1AKO_FKBP-SETD1A_DMSO_K27Ac ChIP-Seq


title: Atoh7/Pou4f2 double negative-E14.5 scATAC

value: Atoh7/Pou4f2-double negative


title: Atoh7-zsGreen-Lacz-E17.5 scATAC


title: SETD1AKO_FKBP-SETD1A_dTAG_K79me2 ChIP-Seq


title: V212-Subgingival_S288


title: Pou4f2-td-Tomato-wt-E17.5 scRNA

library_source: transcriptomic single cell


title: JUN_WT

value: JUN WT overexpression


title: SETD1AKO_FKBP-SETD1A_DMSO_K79me2 ChIP-Seq


title: con

value: empty vector overexpression


title: V215-SalivaRNAL_S298

value: Saliva


title: Atoh7-zsGreen-wt E17.5 scRNA


title: V212-SalivaRNAL_S222

value: not provided


title: SETD1AKO_FKBP-SETD1A_dTAG_K36me3 ChIP-Seq


title: V209-Subgingival_S69


title: JUN_AA

value: JUN AA overexpression


title: P8_CAFs_H3K4me1

data_processing:
Library strategy: CUT&Tag
Raw reads were aligned to the reference human genome assembly hg19 using Bowtie2  with ‘--local --very-sensitive --no-mixed --no-discordant -I 10 -X 700’ parameters. Only unique mapped reads with mapping quality greater than 20 were subjected to further analysis. Samtools was used to remove duplicated mapped reads. Peak calling was performed by MACS2 callpeak.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files for H3K4me1 were generated using  deeptools v3.5.1 bamCoverage
Supplementary_files_format_and_content: Bigwig files for H3K27ac in each patient were matched NFs-subtracted, which were generated by deeptools v3.5.1 bigwigCompare

source_name: primary fibroblasts

growth_protocol: Tumor tissues and corresponding para-tumoral non-malignant tissues were surgically removed from invasive breast cancer patients with axillary lymph node metastasis. Primary fibroblasts were maintained in Growth Medium in a humidified 5% CO2 environment at 37°C.

extract_protocol:
In brief, 30,000 primary fibroblasts were collected. The cells were washed twice using 1 ml wash buffer (20 mM HEPES PH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1×Protease Inhibitor Cocktail (PIC, Bimake), and then resuspended in 300 µl wash buffer. Concanavalin A coated beads were washed twice in binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1mM MnCl2, 1mM CaCl2) to be activated, followed by 10 µl activated beads addition to the resuspended cells. After incubation for 30 min at room temperature, the supernatant was removed. Beads were resuspended in 50 µL antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.0125% Digitonin, 2 mM EDTA, 0.1% BSA, 1×PIC). Then 0.5 µL primary antibody was added. Followed 2-hour incubation at room temperature, the supernatant was removed gently. Then the beads were resuspended in 100 µl Dig wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.0125% Digitonin, 1×PIC) containing 1 µl Guinea Pig anti-Rabbit IgG antibody and 1-hour-incubation at room temperature. The beads were washed three times in 800 µl Dig wash buffer, then resuspended in 100 µl Dig 300 wash buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5mM Spermidine, 0.0125% Digitonin, 1×PIC), followed by 0.04 μM pA-Tn5 adapter complex (Vazyme S603) addition and 1-hour incubation at room temperature. Then the beads were washed three times in 800 µl Dig 300 wash buffer and resuspended in 300 µL tagmentation buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.0125% Digitonin, 10 mM MgCl2, 1×PIC) and 1-hour incubation at 37°C. Then 10 µl of 0.5 M EDTA, 3 µl of 10% SDS and 1 µl of 20 mg/ml Proteinase K were added and incubated at 55°C for 1 hour to stop tagmentation. DNA was extracted by PCI and amplified with i5 and i7 primer in KAPA 2x PCR mix (KM2602). Amplification was performed using cycling program with heated lid, 72°C, 5 min; 98°C, 30 s; 17 cycles for 98°C, 10s; 60°C, 30 s; 72°C, 30 s; and 72°C for 5 min. DNA was size-selected to remove fragments above 1 kb and enrich the 200-1,000bp fragments by Ampure XP beads.
The purified DNA was used to construct libraries for sequencing.

value: cancer associated fibroblasts

tag: patient


title: Atoh7-zsGreen-wt-E14.5 scRNA


title: Atoh7-zsGreen-Lacz-E17.5 scRNA


title: P8_CAFs_H3K27ac


title: Pou4f2-tdTomato-wt-E14 scRNA


title: SETD1AKO_FKBP-SETD1A_dTAG_RNAP2 ChIP-Seq

value: RNAP2 (diagenode C15100055)


title: P8_NFs_H3K4me1

value: normal fibroblasts


title: V204-Subgingival_S102

value: Subgingival sites


title: V209-SalivaRNAL_S89


title: SETD1AKO_FKBP-SETD1A_DMSO_K36me3 ChIP-Seq


title: V204-SalivaRNAL_S79


title: Atoh7-zsGreen-Lacz-E14.5 scRNA

value: Mouse Retina


title: SETD1AKO_FKBP-SETD1A_DMSO_RNAP2 ChIP-Seq

value: DMSO


title: P8_NFs_H3K27ac


title: SETD1AKO_FKBP-SETD1A_dTAG_ATAC ATAC-Seq

description:
SETD1AKO_FKBP-SETD1A_dTAG_ATAC
ATAC


title: V203-Subgingival_S176


title: P5_CAFs_H3K4me1


title: AKR39, bulkRNA

city: New York

first: Andrew

middle: K

last: Ressler

institute: Columbia University

description:
P1_Hnrnpu_fl_het.csv
P1_Hnrnpu_fl_hom.csv
est_counts_genes_kallisto_P0_HNRNPUfl-andflfl.txt

data_processing:
For Bulk RNA Sequencing RTA (Illumina) was used for base calling and bcl12fastq2 (version 2.19) was used to convert BCL to fastq format, coupled with adaptor trimming. Pseudoalignment was performed to a kallisto index (Mouse: GRCm38) using kallisto (0.44.0).
For single-cell RNA-sequencing. 10X chromium pipeline defaults were used to generate barcoded matrices from BAM files. Then, Seurat v3.0 was used for downstream analyses, including DESeq2 for pseudobulk comparisons and MAST for analyses at single-cell resolution
Assembly: Grcm38 for Bulk RNA sequencing. Hg38 for human single-cell data
Supplementary files format and content: counts, Rdata, log2FoldChange
Supplementary files format and content: SampleDescriptions.csv includes all details on gender and batch of all samples included in this data repository.
Supplementary files format and content: hnrnpu_exp1and2_integrated_nfeatures2000_mtregress_dims11_respoint5_mt_umi.Rdata is processed Seurat object with all scRNA samples prior to naming of clusters to allow for any ad hoc analyses one might be interested in.

source_name: Hnrnpu conditional P1

growth_protocol: Human samples (PGP1, D11 and M20) are all DIV42-45 human cortical organoids. Method from Xiang et al. 2017 (doi: 10.1016/j.stem.2017.07.007)

extract_protocol:
Single nuclei dissociated with Papain + DNAse for organoids. For bulk RNA-sequencing, cortices were dissociated embryonically or perinatally and either flash frozen or RNA extracted by Qiagen RNAeasy kit. If frozen, samples place in RNA later and then extracted at later date using Qiagen RNAeasy kit
10X Chromium Single Cell 3' Standard library construction from JP Sulzberger genomics core at Columbia University. For bulk RNA sequencing Poly-A pull-down was used to enrich mRNAs from total RNA samples and libraries were constructed using Illumina TruSeq chemistry. Libraries were then sequenced using Illumina NovaSeq 6000

treatment_protocol: No treatment

value: P1 cortices

value: WT

value: No treatment


title: P5_CAFs_H3K27ac


title: AKR38, bulkRNA

description:
P1_Hnrnpu_fl_hom.csv
est_counts_genes_kallisto_P0_HNRNPUfl-andflfl.txt

value: HOM


title: SETD1AKO_FKBP-SETD1A_DMSO_ATAC ATAC-Seq

description:
SETD1AKO_FKBP-SETD1A_DMSO_ATAC
ATAC


title: V203-SalivaRNAL_S269


title: MV411_F12_dTAG_rep3

description: Sample 18

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: MOLM-13 cells and MV4-11 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was collected using Rneasy Mini Kit with DNase (QIAGEN)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: HA-FKBP-hSETD1A expression vector, Cas9 expression vector and SETD1A sgRNA expression vector  were introduced with lentivirus and stable expressing single cell clone was established. Cells were treated with DMSO or 500 nM dTAG-13 for 24 or 96 hours.


title: V202-Subgingival_S285


title: AKR34, bulkRNA


title: V202-SalivaRNAL_S286


title: AKR33, bulkRNA

description:
P1_Hnrnpu_fl_het.csv
est_counts_genes_kallisto_P0_HNRNPUfl-andflfl.txt

value: HET


title: MV411_F12_dTAG_rep1

description: Sample 16


title: P5_NFs_H3K4me1


title: P5_NFs_H3K27ac


title: V201-Subgingival_S52


title: MV411_Cas9_dTAG_rep3

description: Sample 15


title: P4_CAFs_H3K27ac


title: P4_CAFs_H3K4me1


title: MV411_F12_dTAG_rep2

description: Sample 17


title: AKR31, bulkRNA


title: V201-SalivaRNAL_S174


title: AKR28, bulkRNA


title: MV411_Cas9_dTAG_rep2

description: Sample 14


title: AKR37, bulkRNA


title: P4_NFs_H3K4me1


title: V200-Subgingival_S115


title: V200-SalivaRNAL_S61


title: AKR27, bulkRNA


title: MOLM-13_SETD1AKO_FKBP-SETD1A_F12_dTAG13_d4_exp2

description: Sample 12


title: P4_NFs_H3K27ac


title: AKR26, bulkRNA


title: V199-Subgingival_S183


title: P3_CAFs_H3K4me1


title: AKR25, bulkRNA


title: MOLM-13_SETD1AKO_FKBP-SETD1A_F12_dTAG13_d4_d1_exp1

description: Sample 11


title: P3_CAFs_H3K27ac


title: MOLM-13_SETD1AKO_FKBP-SETD1A_H7_dTAG13_d4_exp2

description: Sample 10


title: V199-SalivaRNAL_S147


title: AKR24, bulkRNA


title: AKR21, bulkRNA


title: V198-Subgingival_S173


title: P3_NFs_H3K4me1


title: P3_NFs_H3K27ac


title: V198-SalivaRNAL_S316


title: MOLM-13_SETD1AKO_FKBP-SETD1A_H7_dTAG13_d4_exp1

description: Sample 9


title: P2_CAFs_H3K4me1


title: sdmusrnaseq414, bulkRNA

description:
P0_Hnrnpu+-.csv
est_counts_genes_kallisto_P0_HNRNPU+-.txt

source_name: Hnrnpu constitutive P0

value: P0 cortices

value: C57BL/6NJ (005304 JAX stock) x FVB/NJ (001800 JAX stock)


title: MOLM-13_SETD1AKO_FKBP-SETD1A_F12_dTAG13_d1_exp1

description: Sample 7


title: V197-Subgingival_S260


title: MOLM-13_SETD1AKO_FKBP-SETD1A_F12_dTAG13_d1_exp2

description: Sample 8


title: P2_CAFs_H3K27ac


title: V197-SalivaRNAL_S83


title: sdmusrnaseq412, bulkRNA


title: sdmusrnaseq413, bulkRNA


title: MOLM-13_SETD1AKO_FKBP-SETD1A_H7_dTAG13_d1_exp2

description: Sample 6


title: MV411_Cas9_dTAG_rep1

description: Sample 13


title: V196-Subgingival_S28


title: P2_NFs_H3K27ac


title: P2_NFs_H3K4me1


title: sdmusrnaseq406, bulkRNA


title: sdmusrnaseq404, bulkRNA


title: MOLM-13_SETD1AKO_FKBP-SETD1A_F12_DMSO_d1_exp2

description: Sample 4


title: V196-SalivaRNAL_S194


title: P1_CAFs_H3K4me1


title: V195-Subgingival_S75


title: P1_CAFs_H3K27ac


title: sdmusrnaseq402, bulkRNA


title: MOLM-13_SETD1AKO_FKBP-SETD1A_F12_DMSO_d1_exp1

description: Sample 3


title: MOLM-13_SETD1AKO_FKBP-SETD1A_H7_DMSO_d1_exp2

description: Sample 2


title: sdmusrnaseq4010, bulkRNA


title: MOLM-13_SETD1AKO_FKBP-SETD1A_H7_dTAG13_d1_exp1

description: Sample 5


title: V195-SalivaRNAL_S264


title: P1_NFs_H3K4me1


title: V194-SalivaRNAL_S16


title: V194-Subgingival_S71


title: MOLM-13_SETD1AKO_FKBP-SETD1A_H7_DMSO_d1_exp1

description: Sample 1


title: P1_NFs_H3K27ac


title: sdmusrnaseq401, bulkRNA


title: Wnt2B Donor 2

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

data_processing:
Illumina software used for basecalling.
Reads quality was checked, trimmed and filtered by FastQC and Trimmomatic.
Raw data fastq files were generated on NextSeq using bcl2fastq2 V2.19 software
Reads mapping with Homo sapiens UCSC hg38 using HISAT2
Transcripts quantification using HTSeq
Gene differential expression using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Human dental pulp stem cells

extract_protocol:
After treatment, total RNA was isolated using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human dental pulp stem cells


title: iCAFs+JNKi_p-JUN

data_processing:
Raw reads were aligned to the reference human genome assembly hg19 using Bowtie2 with default parameters. Only unique mapped reads with mapping quality greater than 20 were subjected to further analysis. Samtools was used to remove duplicated mapped reads.
Bigwig files were generated by deeptools v3.5.1 bamCoverage
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files for each Sample

extract_protocol:
Briefly, cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. For selected experiments (ChIP for JUN and p-JUN), cells were double crosslinked with 2 mM EGS and 1% formaldehyde for 15 minutes at room temperature. Then it was quenched by 0.125 mol/L glycine for 5 minutes. Followed washing twice by PBS, the cells were resuspended and lysed. Then sonicating with a BioRuptor sonicator was performed. At 4°C, centrifugation at 15,000×g for 25 min was performed. Primary antibodies were added to the chromatin overnight at 4°C. Then 30ul protein A/G magnetic beads for IP were added. After 2-hour incubation at 4°C, the beads were washed three times by washing buffer. ChIP DNA was purified using PCR purification kits after reverse cross-linking at 65°C overnight.
Library construction was performed using Trueprep DNA library prep kit V2 for illumina.

value: JNKi-treated iCAFs

value: p-JUN


title: V193-Subgingival_S306

value: not provided


title: ARNS8, bulkRNA


title: V193-SalivaRNAL_S257

value: Saliva


title: iCAFs+JNKi_JUN

value: JUN


title: Wnt2B Donor 1


title: iCAFs+JNKi_H3K4me1


title: V192-Subgingival_S232


title: sdmusrnaseq4011, bulkRNA


title: ARNS6, bulkRNA


title: V192-SalivaRNAL_S143


title: iCAFs+JNKi_H3K27ac


title: ARNS5, bulkRNA


title: Wnt2B Donor 3


title: V191-Subgingival_S108


title: V191-SalivaRNAL_S73


title: iCAFs_JUN

value: induced CAFs (iCAFs)


title: IWP Donor 2


title: iCAFs_p-JUN


title: V188-Subgingival_S135

value: Subgingival sites


title: Tidelglusib Donor 3


title: IWP Donor 1


title: ARNS4, bulkRNA


title: iCAFs_H3K4me1


title: ARNS3, bulkRNA


title: ARNS2, bulkRNA


title: DGAR7, bulkRNA

description:
E13_Hnrnpu+-.csv
est_counts_genes_kallisto_E13_HNRNPU+-.txt

source_name: Hnrnpu constitutive E13

value: E13 cortices


title: Tidelglusib Donor 1


title: V188-SalivaRNAL_S273


title: Tidelglusib Donor 2


title: ARNS7, bulkRNA


title: V186-Subgingival_S29


title: IWP Donor 3


title: DGAR6, bulkRNA


title: DGAR5, bulkRNA


title: Control Donor 2


title: Control Donor 3


title: V186-SalivaRNAL_S204


title: DGAR4, bulkRNA


title: DGAR3, bulkRNA


title: V184-SalivaRNAL_S156


title: V181-SalivaRNAL_S78


title: DGAR1, bulkRNA


title: iCAFs_H3K27ac


title: JUN_AA_JUN

value: JUN AA overexpression


title: JUN_AA_H3K4me1


title: JUN_AA_p-JUN


title: JUN_AA_H3K27ac


title: V180-SalivaRNAL_S72


title: V184-Subgingival_S247


title: DGAR2, bulkRNA


title: V176-Subgingival_S32


title: Control Donor 1


title: V181-Subgingival_S165


title: V180-Subgingival_S267


title: JUN_WT_JUN

value: JUN WT overexpression


title: JUN_WT_p-JUN


title: JUN_WT_H3K4me1


title: con_p-JUN

value: empty vector overexpression


title: JUN_WT_H3K27ac


title: V176-SalivaRNAL_S299


title: con_JUN


title: C57Bl6J mice Tmem mice, CD45+ cardiac cell, RT 12Gyx1,, 28 days, 2 [scRNA-seq]

first: Achraf

last: Shamseddine

address: 1275 York Avenue

department: Radiation Oncology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Data was then analyzed using SEURAT version 3 (https://satijalab.org/seurat)
Assembly: MM10
Supplementary files format and content: *tsv, mtx

source_name: Cardiac

extract_protocol:
CD45+ cells freshyl isolated from the heart were washed in PBS and submitted for scRNA-seq library preparation using the 10X Genomics Platform.
Following QC, the single cell suspension was loaded onto Chromium Chip B (10X Genomics PN 2000060) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 4,500-9,300 cells proceeded using the Chromium Single Cell 3’ Reagent Kit v3 (10X Genomics PN 1000075) according to the manufacturer’s protocol.
cDNA amplification included 11 cycles and 44-87ng of the material was used to prepare sequencing libraries with 12 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 paired end run using the NovaSeq 6000 SP, S1, or S2 Reagent Kit (100 cycles) (Illumina).  An average of 201 million paired reads was generated per sample

treatment_protocol: Murine hearts were treated using small animal microirradiator to either sham or 12 Gy single fraction

value: Cardiac

value: CD45+ cells

value: STING KO

value: RT 12 Gy x 1

value: 28 days


title: C57Bl6J mice Tmem mice, CD45+ cardiac cell, RT 12Gyx1,, 28 days, 1 [scRNA-seq]


title: C57Bl6J mice, CD45+ cardiac cell, RT 12Gyx1,, 28 days, 2 [scRNA-seq]

value: WT


title: V175-Subgingival_S99


title: C57Bl6J mice, CD45+ cardiac cell, RT 12Gyx1,, 28 days, 1 [scRNA-seq]


title: C57Bl6J mice, CD45+ cardiac cell, Sham control, 28 days, 2 [scRNA-seq]

value: Sham


title: V175-SalivaRNAL_S203


title: con_H3K27ac


title: BC3-pH2.5-2

type: RNA

city: Chengdu

first: Yajing

state: Sichuan

address: No. 24, South Section 1, First Ring Road

department: College of Architecture and Environment

institute: Sichuan University

description: Gene expression data from Saccharomyces cerevisiae BC3 and fermented under pH 2.5 .

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Saccharomyces cerevisiae Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

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

data_processing:
The data were analyzed with Microarray Suite version 3.0 (MAS 3.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
q-value ≤ 5% and Fold Change ≥2 or≤0.5

label: biotin

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae BC3 in the YPD medium under pH 2.5

label_protocol: Biotinylated cRNA were prepared according to the Ambion #1792 cRNA

growth_protocol: at 35℃, 200 rpm growth for 4 h under pH 4.5 and 8 h under pH 2.5

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


title: B3-pH2.5-2

description: Gene expression data from Saccharomyces cerevisiae B3 and fermented under pH 2.5 .

source_name: Saccharomyces cerevisiae B3 in the YPD medium under pH 2.5


title: C3-pH2.5-2

description: Gene expression data from Saccharomyces cerevisiae C3 and fermented under pH 2.5 .

source_name: Saccharomyces cerevisiae C3 in the YPD medium under pH 2.5


title: C57Bl6J mice, CD45+ cardiac cell, Sham control, 28 days, 1 [scRNA-seq]


title: C3-pH2.5-1


title: BC3-pH2.5-1


title: B3-pH2.5-1


title: C57Bl6J mice, fibroblasts, RT 12Gy x 1, 28 days, 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GrCM38/mm10
Supplementary files format and content: tab-delimited excel files include TPM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Fibroblasts


title: V174-Subgingival_S182

value: not provided


title: KF-7-pH2.5-1

description: Gene expression data from Saccharomyces cerevisiae KF-7 and fermented under pH 2.5 .

source_name: Saccharomyces cerevisiae KF-7 in the YPD medium under pH 2.5


title: SETD1AKO_FKBP-SETD1A_dTAG_3h_K36me3 ChIP-Seq


title: con_input


title: SETD1AKO_FKBP-SETD1A_dTAG_9h_K36me3 ChIP-Seq


title: C57Bl6J mice, fibroblasts, RT 12Gy x 1, 28 days, 1


title: C57Bl6J mice, fibroblasts, Sham control, 28 days, 2


title: V174-SalivaRNAL_S233

value: Saliva


title: BC3-pH4.5-2

description: Gene expression data from Saccharomyces cerevisiae BC3 and fermented under pH 4.5 .

source_name: Saccharomyces cerevisiae BC3 in the YPD medium under pH 4.5


title: V172-Subgingival_S130


title: SETD1AKO_FKBP-SETD1A_dTAG_6h_K36me3 ChIP-Seq


title: con_H3K4me1


title: SETD1AKO_FKBP-SETD1A_dTAG_1h_K36me3 ChIP-Seq


title: V171-Subgingival_S49


title: KF-7-pH2.5-2


title: V171-SalivaRNAL_S282


title: V172-SalivaRNAL_S206


title: BC3-pH4.5-1


title: PAX7_Sort3

first: Emily

last: Lo

state: MD

address: 733 N Broadway

institute: Johns Hopkins

description: PAX7::GFP-sorted ESC-derived myogenic progenitor

data_processing:
Reads were trimmed using cutadapt v2.8.
Trimmed reads were mapped and quantified against human reference genome and transcriptome using salmon v1.3.0.
Salmon index was generated using human genome assembly GRCh37.p13 and GENCODE human transcriptome assembly Release 19.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression matrix, gene symbols as rows, sample names as columns

source_name: ESC-derived myogenic progenitor

growth_protocol: Briefly, before commitment, hESCs were expanded using a mouse embryonic fibroblast (MEFs; GlobalStem or AppliedStemCell) feeder layer and expansion media containing DMEM/F12, 20% knockout serum replacement, 1 mM L-glutamine, 100 mM MEM non-essential amino acids, 0.1 mM b-mercaptoethanol, and 10 ng/ml FGF2. For commitment, N2 media, which contained DMEM/F12 powder, glucose, sodium bicarbonate, insulin, putrescine, progesterone, sodium selenite, and transferrin, was conditioned by MEFs for 24 hours and sterile filtered. Commitment was performed with hESCs seeded in a 24-well culture plate coated with 1% Geltrex at a density of 1.5 x 105 cells/well. For the first 24 hours, the hESCs were fed MEF-conditioned N2 media containing 10 ng/ml FGF2 and 10uM Y-27632 (Cayman Chemical). For induction, on days 1-4 the N2 media was supplemented with 3µM CHIR99021 (Cayman Chemical) and on days 4-12 the N2 media was supplemented with 10µM DAPT (Cayman Chemical). Following approximately 30 days of commitment, the resulting hPDMs were expanded 5-6 passages in N2 media supplemented with 5% FBS, at which point the cells were seeded on scaffolds. The PAX7::GFP-sorted hPDMs were committed in the same fashion in N2 media containing 5% FBS, 1% P/S, and 10 ng/ml FGF2 following genetic manipulation with the CRISPR/Cas9 system to express a PAX7::GFP reporter. After the 30 day commitment protocol, the PAX7::GFP+ subpopulation was sorted for using fluorescence activated cell sorting (FACS).

extract_protocol:
RNA from 3 separate batches of passaged unsorted hPDMs and 3 batches of passaged PAX7-sorted hPDMs was isolated using Trizol reagent.
Libraries were prepared with 200 ng of RNA from each sample with the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit following manufacturer’s instructions. Sequencing was performed on the Illumina NovaSeq 6000 with 100 cycles and 800 million reads.

value: Myogenic progenitor


title: C3-pH4.5-1

description: Gene expression data from Saccharomyces cerevisiae C3 and fermented under pH 4.5 .

source_name: Saccharomyces cerevisiae C3 in the YPD medium under pH 4.5


title: C57Bl6J mice, fibroblasts, RT 12Gy x 1, 7 days, 2

value: 7 days


title: C57Bl6J mice, fibroblasts, RT 12Gy x 1, 7 days, 1


title: C3-pH4.5-2


title: C57Bl6J mice, fibroblasts, Sham control, 28 days, 1


title: SETD1AKO_FKBP-SETD1A_DMSO_9h_K36me3 ChIP-Seq

value: DMSO


title: V170-Subgingival_S162

source_name: Oral microbiome

value: Subgingival sites


title: B3-pH4.5-2

description: Gene expression data from Saccharomyces cerevisiae B3 and fermented under pH 4.5 .

source_name: Saccharomyces cerevisiae B3 in the YPD medium under pH 4.5


title: C57Bl6J mice, fibroblasts, Sham control, 7 days, 2


title: B3-pH4.5-1


title: PAX7_Sort2


title: C57Bl6J mice, fibroblasts, Sham control, 7 days, 1


title: V169-Subgingival_S111


title: V169-SalivaRNAL_S315


title: V170-SalivaRNAL_S211


title: C57Bl6J mice, fibroblasts, RT 12Gy x 1, 6 hours, 2

value: 6 hours


title: PAX7_Sort1


title: KF-7-pH4.5-2

description: Gene expression data from Saccharomyces cerevisiae KF-7 and fermented under pH 4.5 .

source_name: Saccharomyces cerevisiae KF-7 in the YPD medium under pH 4.5


title: V168-SalivaRNAL_S125


title: Unsort2

description: Unsorted ESC-derived myogenic progenitor

value: Unsorted


title: C57Bl6J mice, fibroblasts, RT 12Gy x 1, 6 hours, 1


title: Unsort3


title: Unsort1


title: V167-Subgingival_S91


title: C57Bl6J mice, fibroblasts, Sham control, 6 hours, 1


title: C57Bl6J mice, fibroblasts, Sham control, 6 hours, 2


title: V167-SalivaRNAL_S219


title: C57Bl6J mice, myocytes, RT 12Gy x 1, 28 days, 2

value: Myocytes


title: KF-7-pH4.5-1


title: C57Bl6J mice, myocytes, RT 12Gy x 1, 28 days, 1

value: Cardiac


title: V166-SalivaRNAL_S171


title: C57Bl6J mice, myocytes, Sham control, 28 days, 1


title: V164-Subgingival_S249


title: V164-SalivaRNAL_S53


title: C57Bl6J mice, myocytes, RT 12Gy x 1, 7 days, 2


title: V162-Subgingival_S142


title: V162-SalivaRNAL_S84


title: CON_DG_giological rep 06

city: Toyoake

first: Hideo

last: Hagihara

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Institute for Comprehensive Medical Science

institute: Fujita Health University

description: Gene expression data from the dentate gyrus of control mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 (GCS3000)

data_processing: The data were analyzed with Affymetrix Expression Cosole (version 1.1). The normalization used in RMA is quantile normalization.

source_name: Dentate gyrus of control mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

growth_protocol: 13–14 weeks old

extract_protocol: Trizol extraction of total RNA and cleanup byRNeasy Micro kit (QIAGEN) was performed according to the manufacturer's instructions.

treatment_protocol: No

value: Dentate gyrus


title: CON_DG_giological rep 05


title: CON_DG_giological rep 04


title: V166-Subgingival_S36


title: C57Bl6J mice, myocytes, Sham control, 28 days, 2


title: V157-Subgingival_S185


title: CON_DG_giological rep 03


title: C57Bl6J mice, myocytes, RT 12Gy x 1, 7 days, 1


title: CON_DG_giological rep 01


title: CON_DG_giological rep 02


title: V155-Subgingival_S278


title: KO_DG_biological rep 06

description: Gene expression data from the dentate gyrus of forebrain-specific calcineurin knockout mouse

source_name: Dentate gyrus of forebrain-specific calcineurin knockout mouse


title: C57Bl6J mice, myocytes, Sham control, 7 days, 2


title: KO_DG_biological rep 04


title: KO_DG_biological rep 05


title: C57Bl6J mice, myocytes, Sham control, 7 days, 1


title: KO_DG_biological rep 02


title: KO_DG_biological rep 03


title: C57Bl6J mice, myocytes, RT 12Gy x 1, 6 hours, 1


title: KO_DG_biological rep 01


title: V155-SalivaRNAL_S220


title: C57Bl6J mice, myocytes, Sham control, 6 hours, 2


title: V157-SalivaRNAL_S170


title: C57Bl6J mice, myocytes, RT 12Gy x 1, 6 hours, 2


title: C57Bl6J mice, myocytes, Sham control, 6 hours, 1


title: Isolated islets, 7-day old pig 3

city: Edmonton

first: Gina

last: Rayat

state: Alberta

department: Faculty of Medicine and Dentistry,

country: Canada

institute: Alberta Diabetes Institute, University of Alberta

hyb_protocol: Hybridization and washing of the microarrays were carried out according to the Affymetrix® GeneChip Expression Analysis Manual using GeneChip Hybridization Oven 640 and GeneChip Fluidics Station 450 respectively.

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

data_processing: Normalized data and further analysis of there microarray were performed using GeneSpring GX (Agilent Technologies) and Ingenuity Pathway Analysis software

label: Biotin

organism: Sus scrofa

source_name: Islets islolated from pancreas of 7-day old pig

label_protocol: Labelling of the Affymetrix® GeneChip microarrays of each sample were carried out according to the Affymetrix® GeneChip Expression Analysis Manual.

growth_protocol: 3 and 7 day old male Duroc/Large white cross-neonatal pigs were provided by the University of Alberta Swine Research Centre.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit and amplified according to the Affymetrix® protocol.

treatment_protocol: Digested (mechanical and 1mg/ml Type XI collagenase from Sigma) prancreas tissue was cultured for Ham’s F10 medium (Sigma), supplemented with 10 mmol/l D-glucose, 50 µmol/l isobutylmethylxanthine (ICN, Biomedicals, Montreal, QC, Canada), 0.5% BSA, 2 mmol/l L-glutamine, 3 mmol/l CaCl2, 10 mmol/l nicotinamide (BDH Biochemical, Poole, England), 100 U/ml penicillin, and 100 µg/ml streptomycin at 37°C, 5% CO2, and 95% air. The media of isolated islets was changed on days 1, 3, 5, and 7 post-isolations.

tag: age of pig


title: Isolated islets, 7-day old pig 4


title: V154-Subgingival_S62

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed using cutadapter.
QIIME2.0 microbiome pipeline.
Centered log-ratio (CLR) transformation.
Assembly: hg38
Supplementary files format and content: *.genus.txt: Genus-level taxon datasets; CLR transformed values.
Library strategy: 16S RNA amplicon sequencing


title: C57Bl6J mice, endothelial cells, RT 12Gy x 1, 28 days, 2

value: Endothelial cells


title: V151-Subgingival_S98


title: C57Bl6J mice, endothelial cells, RT 12Gy x 1, 28 days, 1

value: RT 12 Gy x 1


title: V151-SalivaRNAL_S276


title: V154-SalivaRNAL_S17


title: C57Bl6J mice, endothelial cells, Sham control, 28 days, 2

value: 28 days


title: Isolated islets, 7-day old pig 1


title: Isolated islets, 3-day old pig 4

source_name: Islets islolated from pancreas of 3-day old pig

value: 3 days


title: Isolated islets, 3-day old pig 3


title: V150-Subgingival_S281


title: Isolated islets, 3-day old pig 2


title: V150-SalivaRNAL_S100


title: C57Bl6J mice, endothelial cells, Sham control, 28 days,1

value: WT

value: Sham


title: C57Bl6J mice, endothelial cells, RT 12Gy x 1, 7 days, 2


title: Isolated islets, 7-day old pig 2


title: Isolated islets, 3-day old pig 1


title: C57Bl6J mice, endothelial cells, RT 12Gy x 1, 7 days, 1


title: Blood_60days_after_intervention_Patient18

type: genomic

city: Szczecin

first: Tomasz

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: DNA extracted from whole blood from patient with NAFLD

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

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

data_processing: Data were processed in R, normalized using BMIQ normalization.

label: Cy5 and Cy3

source_name: Whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA from the blood samples at first timepoint was extracted using Invisorb® Spin Blood Mini Kit (Stratec Biomedical AG, Germany) following the manufacturer’s instructions and salting out method from the second and third timepoint.

tag: time point


title: V148-Subgingival_S6

extract_protocol:
DNA was isolated using a Zymo Research Quick-DNA Fecal/Soil Microbe Miniprep Kit (catalog D6010).
DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: not provided


title: V148-SalivaRNAL_S153

value: Saliva

tag: condition


title: N18-CFMS 48H CSF1 rep2

city: Lille

first: Roland

last: Bourette

address: 1, rue du Professeur Calmette

country: France

institute: CNRS

description: Gene expression in N18-CFMS cells followinf a 48H CSF1 treatment

hyb_protocol: Labeled cDNA samples (600 ng) were used for 17- hour hybridization at 65°C to the SurePrint G3 mouse GE 8 × 60K Microarrays (Agilent Technologies). All procedures were carried out according to the manufacturer’s instructions.

scan_protocol: The hybridized microarrays were scanned with the Agilent DNA Microarray Scanner (G2505C).

data_processing: Signal intensity was quantified from the scanned image by using Feature Extraction software version 11.0.1 (Agilent Technologies).

source_name: N18-CFMS cell line

label_protocol: cRNA labeling, hybridization, and detection was carried out according to supplier’s instructions (Agilent Technologies). For each microarray, Cyanine 3-labeled cRNA was synthesized with the low input Quick Amp WT labeling kit from 100 ng of total RNA. RNA Spike-In was added to all tubes and used as positive controls of labeling and amplification steps.

growth_protocol: Cells were maintained in Gibco high-glucose Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) containing 10% fetal bovine serum (FBS, Invitrogen) supplemented with antibiotics (Zell Shield, Biovalley) and dihydrotestosterone (100 mM, Androstan, Sigma, #A8380) at 37°C in humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA from two independent experiments was extracted with the RNeasy Plus Kit (Qiagen) and was quantified with the NanoDrop ND-1000 (ThermoFisher Scientific). Quality of the extracted RNA was evaluated with the Agilent 2100 Bioanalyzer system (Agilent Technologies, Massy, France).

treatment_protocol: N18-Fms cells were stimulated by rmCSF-1 (100 ng/ml) for 24h or 48h, or left unstimulated.

value: CSF1 48H


title: C57Bl6J mice, endothelial cells, Sham control, 7 days, 2

source_name: Cardiac

value: 7 days


title: N18-CFMS 48H CSF1 rep1


title: V139-Subgingival_S117

tag: donor id


title: C57Bl6J mice, endothelial cells, Sham control, 7 days, 1


title: Blood_before_intervention_Patient17


title: Blood_30days_after_intervention_Patient17


title: Blood_60days_after_intervention_Patient17


title: Blood_before_intervention_Patient18


title: V139-SalivaRNAL_S254


title: N18-CFMS 24H CSF1 rep1

description: Gene expression in N18-CFMS cells followinf a 24H CSF1 treatment

value: CSF1 24H


title: C57Bl6J mice, endothelial cells, RT 12Gy x 1, 6 hours, 2


title: Blood_30days_after_intervention_Patient16


title: Blood_before_intervention_Patient16


title: V137-SalivaRNAL_S119


title: N18-CFMS 24H CSF1 rep2


title: C57Bl6J mice, endothelial cells, RT 12Gy x 1, 6 hours, 1


title: Blood_30days_after_intervention_Patient18


title: N18-CFMS Control rep2

description: Gene expression in untreated N18-CFMS cells

value: vehicule


title: V135-Subgingival_S201

value: Subgingival sites


title: N18-CFMS Control rep1


title: KAT7 mutant rep 4

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

data_processing:
Reads (49bp) were aligned to the mouse genome mm9 using the Rsubread package v1.4.0
Read counts were summarised at the gene level using the featureCounts function in Rsubread V1.4.0 using the in-built RefSeq annotation
Assembly: mm9
Supplementary files format and content: tab delimited text file with entrez gene id and gene length ain the first two columns, followed by 7 columns containing counts for each sample

molecule: polyA RNA

source_name: Brain

extract_protocol: Total RNA was isolated using Qiagen RNeasy kit (Qiagen, 74104) according to the manufacturer's instructions

value: Brain

value: Cortical neurons

value: KAT7 mutant

tag: age

tag: Sex

value: male


title: KAT7 mutant rep 3


title: V135-SalivaRNAL_S65


title: Blood_60days_after_intervention_Patient15


title: C57Bl6J mice, endothelial cells, Sham control, 6 hours, 1

value: Cardiac

value: Endothelial cells

value: 6 hours


title: V134-Subgingival_S131


title: KAT7 mutant rep 1


title: Blood_before_intervention_Patient14


title: Blood_60days_after_intervention_Patient16


title: ORFV2

city: Changchun

first: Jiyu

last: Guan

state: Jilin

address: 5333 Xi'an Road

institute: Jilin University

data_processing:
Basecalling was performed using CASAVA version 1.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Reads were aligned to the mm10 genome assembly using STAR version 2.7.3a
Assembly: mm10
Supplementary files format and content: bigWig files contain treat pileup read per million (RPM) normalized in bigWig format

source_name: B16-derived tumor tissue

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Cat. LS1040; Promega) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using Stranded mRNA-seq Lib Prep Kit for Illumina (Cat. RK20302; ABclonal). Paired-end sequencing was performed with Illumina NovaSeq platform.

value: B16-derived tumor tissue

value: ORFV


title: Blood_60days_after_intervention_Patient14


title: wt rep 3

value: wild type


title: V133-Subgingival_S212

value: not provided


title: Blood_30days_after_intervention_Patient14


title: KAT7 mutant rep 2


title: wt rep 2


title: ORFV3

value: WT


title: V133-SalivaRNAL_S180

value: Saliva


title: Blood_30days_after_intervention_Patient15


title: wt rep 1


title: Vehicle3

value: PBS


title: Blood_before_intervention_Patient15


title: V130-Subgingival_S311


title: ORFV1


title: Blood_before_intervention_Patient13


title: Vehicle2


title: C57Bl6J mice, endothelial cells, Sham control, 6 hours, 2

value: Sham


title: P6_CAFs

description:
NFs_CAFs_RNAseq_FPKM.txt
P6.RNAseq.bigwig

data_processing:
Reads were aligned to the reference human genome assembly hg19 using hisat2 version 2.1.0 with default parameters. Assembling full-length transcripts and quantifications for each gene to generate Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) values were performed by StringTie v2.1.1. For GSVA analyses of RNA-seq data from 7 pairs of primary NFs and matched CAFs, FPKM values were log2-transformed. The analyses were carried out by R package gsva (method=‘ssgsea’) against MSigDB gene sets v7.3.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each Sample
Supplementary_files_format_and_content: Bigwig files for each patient were matched NFs-subtracted, which were generated by deeptools v3.5.1 bigwigCompare

source_name: primary fibroblasts

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing by Beijing Genomics Institute (BGI).

value: cancer associated fibroblasts


title: V134-SalivaRNAL_S265


title: Blood_30days_after_intervention_Patient13


title: V130-SalivaRNAL_S210


title: P6_NFs

value: normal fibroblasts


title: Vehicle1


title: V126-Subgingival_S14

value: Subgingival sites


title: VEGF-HE2

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: Read 1 (R1) - Cell barcode and unique molecular identifier (UMI). Read 2 (R2) Biological read

data_processing:
Fastq files from scRNA-Seq experiments were aligned to the mouse genome (mm10) using CellRanger count v6.0.1
Gene expression was measured as UMI counts per cell using gene models from Ensembl (release 102) as the reference transcriptome
Assembly: mm10
Supplementary files format and content: HDF5 feature barcode matrix files generated using CellRanger Count.

source_name: Hemogenic Endothelium 1 (HE2) cells derived from HM-1 ES cell line

growth_protocol: Standard ES cell differentiation used serum and the purification of differentiating cells was conducted essentially as described in Obier et al. (2016) Serum Free I.V.D Culture Embryoid bodies (EBs) were generated from HM-1 mouse embryonic stem cells by plating at 5.0x105 cells/ml in serum free (SF) media into petri-grade dishes. BMP4 was added to a concentration of 5ng/ml. Cultures were left to incubate at 37°C and 5% CO2 for 60 hours before bFGF and Activin A were added at a concentration of 5ng/ml each. The cells were incubated for 16 hours at 37°C 5% CO2 and then sorted for FLK1+ cells as described in Obier et al. (2016). FLK1+ cells were plated in serum free media on 0.1% gelatine coated plates or for larger cultures flasks at 2.25x104 cells per cm. BMP4, Activin-A and bFGF were added to a concentration of 5ng/ml for 16 hours. Media was then removed, the blast culture was washed with PBS and fresh SF media was added containing BMP4 (5ng/ml), VEGF (5ng/ml), TPO (5ng/ml), SCF (100ng/ml), IL6 (10ng/ml) and IL3 (1ng/ml). For cytokine withdrawal experiments, one of BMP4, VEGF, IL6 or IL3 was not added at this stage. Blast cultures were left to incubate at 37°C and 5% CO2 for 72 hours before cells were harvested for cell sorting and FACS analysis. Inhibition of trypsin was achieved using Trypsin Inhibitor (Thermofisher) following the manufacturer’s instructions.

extract_protocol:
7x10^6 cells from the all-cytokine and 2.8x10^6 from the -VEGF blast cultures were were sorted for scRNA-Seq library preparation. Cells were stained with CD41-PECY (1:100), KIT-APC (1:100) and TIE2-PE (1:200) and sorted into HE1 (KIT+, TIE2+, CD41-) and HE2 (KIT+, TUE2+, CD41+) populations. Cells were resuspended in 80μl at a concentration of 100-1200 cells/μL for evaluation of viability prior to loading 10,000 cells per sample on a Chromium Single Cell Instrument (10x Genomics)
Library generation for scRNA-Seq was performed by the genomics Birmingham sequencing facility using the Chromium Single Cell 3' library and gel bead kit v3 (10x Genomics). Libraried were paired-end sequenced on an Illumina Novaseq 6000 using the cycle parameters recommended by 10x Genomics

value: HM-1 ES

tag: mouse strain


title: P5_CAFs

description:
NFs_CAFs_RNAseq_FPKM.txt
P5.RNAseq.bigwig


title: Blood_60days_after_intervention_Patient13


title: Blood_before_intervention_Patient12


title: All-HE1

source_name: Hemogenic Endothelium 1 (HE1) cells derived from HM-1 ES cell line


title: V122-Subgingival_S109

first: Bongsoo

institute: National Institute on Aging


title: eif4a3KD-CtrlOE, rep2

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

data_processing:
RNAseq reads were aligned to the mouse mm9 genome using Bowtie2 (v2.3.4.3)
Aligned bam files were sorted by samtools (v1.9) using the parameter -n
HTSeq software (v0.11.2) was used to count reads for each gene using parameters -r name -f bam
Read counts were normalized with the trimmed mean of M-values (TMM) method for differential expression analysis using edgeR (v3.26.8)
Genome_build: mm9
Supplementary_files_format_and_content: txt files - tab-delimited files containing TMM values for genes in each sample.

source_name: mESC J1

growth_protocol: Feeder-free murine ESCs were grown on 0.1% gelatin-coated tissue culture plates in ESC medium containing high-glucose DMEM, 15% fetal bovine serum (FBS), 100 μM nonessential amino acids, 1% nucleoside mix, 2 mM L-Glutamine, 50 U/mL Penicillin/Streptomycin, 0.1 mM 2-mercaptoethanol, and homemade recombinant leukemia inhibitory factor (LIF) tested for efficient self-renewal maintenance, at 37℃.

extract_protocol:
RNA was extracted with the Rneasy Plus kit (Qiagen, #74136) according to the manufacturer's instructions.
For ESCs, 1 µg total RNA from each sample was taken for the preparation of PolyA RNA-seq libraries, and massively parallel sequencing was performed with the HiSeq platform. Single-end 100 bp-length reads or paired-end 150 bp-length reads were produced.

treatment_protocol: The transfection of the feeder-free murine ESCs was performed using Lipofectamine 3000 according to the manufacturer's manual. After drug selection, the transfected ESCs were infected with the lentiviruses. The infected ESCs were selected with 1 μg/mL puromycin for 2.5 days. The cells were collected at Day 4.5 after infection.

value: Embryonic stem cells (ESCs)

value: mESC J1

value: eIF4A3 KD


title: Blood_60days_after_intervention_Patient10


title: Blood_60days_after_intervention_Patient12


title: V123-Subgingival_S30

last: Park


title: PDX-L5

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
Base calling and demultiplexing Bcl2fastq 1.8.4
Raw reads were processed with the miR&moRe pipeline (Bortoluzzi et al. 2012, Blood) and novel miRNA precursors were predicted with miRDeep2 (v2.0.0.7). Briefly, TruSeq adapter sequence (TGGAATTCTCGGGTGCCAAGG) was removed with the Fastxtoolkit v0.0.14 fastx_clipper and selected for reads between 15 and 30 nt, with 30 Phred average read quality, less than 2 bases with quality <20 within each read
Reads were aligned to human genome (hg38) and to precursor sequences (miRBase v21) with Bowtie v1.1.0, discarding reads aligning to > 5 genomic loci outside miRNA precursors (known and predicted) and having a sequence represented by < 10 reads.
Novel precursors with mirDeep scor < 1, Rfam alert, miR probability < 60 and length < 50nt were discarded.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read alignmenet count matrix to mature miRNAs, tab separated values
Supplementary_files_format_and_content: Small RNA genomic coordinates in GFF3 format

source_name: BCP-ALL

growth_protocol: BCP-ALL patient-derived cells were transplanted into NOD/SCID mice by tailvein injection. Cells were isolated from the spleen upon manifestation of leukemia.

extract_protocol:
Total RNA was isolated from 13 BCP-ALL patient derived xenograft with TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, US).
RNA libraries were prepared with TruSeq Small RNA Sample Preparation kit and sequenced by Illumina HiSeq (Illumina, San Diego, CA, US).

tag: engraftment

value: male


title: All-HE2


title: Blood_30days_after_intervention_Patient11


title: PDX-L7

value: female


title: V123-SalivaRNAL_S88

source_name: Oral microbiome


title: Blood_30days_after_intervention_Patient12


title: VEGF-HE1


title: V126-SalivaRNAL_S223


title: V122-SalivaRNAL_S305


title: Blood_60days_after_intervention_Patient11


title: eif4a3KD-CtrlOE, rep1

tag: cell type


title: PDX-S6


title: P5_NFs


title: Blood_30days_after_intervention_Patient10


title: V120-Subgingival_S172


title: CtrlKD-CtrlOE, rep2

value: Control


title: V120-SalivaRNAL_S226


title: Blood_before_intervention_Patient11


title: PDX-L6


title: PDX-L4


title: CtrlKD-CtrlOE, rep1


title: PDX-L3


title: V118-Subgingival_S2


title: eif4a3KD-ccnb1OE, rep2

value: eIF4A3 KD+Ccnb1 OE


title: V118-SalivaRNAL_S290


title: PDX-S4


title: PDX-S5


title: eif4a3KD-ccnb1OE, rep1


title: Blood_30days_after_intervention_Patient9


title: Islets, flox_base3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina NovaSeq6000 platform in a 100 base paired-end mode.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: Isolated islets

extract_protocol:
Total RNA was extracted Qiagen MiRNeasy kit
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

tag: genotype

value: Cdh13 exon2 floxed

tag: diet

value: normal chow diet

value: 8 weeks old


title: PDX-L2


title: Blood_before_intervention_Patient10


title: PDX-S3


title: Blood_60days_after_intervention_Patient9


title: V117-SalivaRNAL_S3

city: Baltimore

address: 251 Bayview Blvd

value: Saliva

value: not provided


title: V116-Subgingival_S301


title: Islets, flox_base2


title: Islets, flox_base1


title: PDX-L1


title: Blood_before_intervention_Patient9


title: PDX-S2


title: V114-Subgingival_S175


title: PDX-S1


title: ZT-2018102501

city: Wuhan

first: Yingying

last: Dong

address: 1095 Jie Fang Avenue

department: Department of Dermatology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
The raw reads were manufactured by removing containing adapter, poly‘N’, low quality and <17nt reads using FASTQC to acquire clean reads.
Mapping reads were got by mapping clean reads to reference genome of BWA
The miRDeep2 was used to recognize known mature miRNAs according to miRBase21 (www.miRBase.org) and to predict novel miRNAs.
The miRNA expression were counted by Reads Per Million (RPM) values
Differential expression between two sets of specimens was counted by edgeR algorithm based on two criteria of |log2（Fold Change）|≥1 and P-value < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: text files include all detected miRNAs

source_name: Exosome

extract_protocol:
Plasma exosomes and exosomal RNA of 20 samples were extracted and purified by exoRNeasy Maxi Kit.
Appropriately 50ng exosomal RNA of each samples was used to establish small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina

tag: age(years)

tag: gender

value: Female

tag: disease

value: non-segmental vitiligo (NSV) patient


title: V113-Subgingival_S157


title: Islets, flox_NC1

tag: strain

value: 14 weeks old


title: 2018072301-ASX


title: V114-SalivaRNAL_S191


title: Islets, flox_NC2


title: Blood_60days_after_intervention_Patient8

tag: patient


title: Blood_30days_after_intervention_Patient8


title: V116-SalivaRNAL_S93


title: Blood_30days_after_intervention_Patient7


title: V113-SalivaRNAL_S70


title: Islets, flox2

value: high-fat diet 6wks


title: V112-Subgingival_S12

value: Subgingival sites


title: 2018071602-YHJ


title: Blood_60days_after_intervention_Patient6


title: Islets, flox1


title: Blood_before_intervention_Patient8


title: Blood_before_intervention_Patient7


title: V112-SalivaRNAL_S27


title: Blood_before_intervention_Patient6


title: 2018071505-XSH


title: Islets, del_base3

value: Cdh13 exon2 deleted


title: V110-Subgingival_S263


title: YZY-2018072801


title: Islets, del_base2


title: Blood_before_intervention_Patient5


title: GTY-2018041603-1

value: Male


title: Blood_30days_after_intervention_Patient4


title: V110-SalivaRNAL_S237


title: V109-Subgingival_S312


title: V117-Subgingival_S23


title: Islets, del_NC3


title: Blood_60days_after_intervention_Patient5


title: V109-SalivaRNAL_S149


title: 2018071203-XXT


title: Blood_30days_after_intervention_Patient5


title: Blood_60days_after_intervention_Patient4


title: 2018071201-ZH


title: Islets, del_NC2


title: V108-Subgingival_S195


title: YH-2018051401-1


title: resistant, control, replicate 3

city: Columbia

first: Wesley

middle: C

last: Warren

state: MO

address: 1201 Rollins St.

department: Bond Life Sciences Center

institute: University of Missouri

data_processing:
Alignment with CellRanger v3.1.0 to GRCg6a
Assembly: GRCg6a
Supplementary files format and content: Aggregated counts matrix

molecule: cytoplasmic RNA

organism: Gallus gallus

source_name: spleen

extract_protocol:
After euthanizing the birds, the spleens were aseptically removed, homogenized and transferred the same day on ice for single-cell capture and library preparation of a targeted 3,000 cells/sample.
Single cell capture and cDNA library preparation were performed on the 10x Genomics Chromium Single Cell 3’ instrument (10x Genomics, Pleasanton, CA) according to the manufacturer’s recommendations. Pooled libraries were barcoded by sample and sequenced (2x150bp length) on an Illumina HiSeq 4000 (Illumina, Inc., San Diego, CA).

value: spleen

value: resistant

tag: treatment

value: control


title: V108-SalivaRNAL_S58


title: Blood_30days_after_intervention_Patient6

tag: time point


title: WX-N004-1

value: Health person


title: Islets, del3


title: Islets, del_NC1


title: Islets, flox3


title: Blood_before_intervention_Patient4


title: V105-Subgingival_S137

tag: tissue


title: susceptible, challenged, replicate 2

value: susceptible

value: challenged


title: Islets, del2


title: N027-LCY


title: V105-SalivaRNAL_S296

tag: condition


title: Blood_60days_after_intervention_Patient7


title: Blood_30days_after_intervention_Patient3


title: V104-Subgingival_S200

tag: donor id


title: resistant, challenged, replicate 2


title: TJ013-WXY


title: susceptible, challenged, replicate 3


title: susceptible, control, replicate 3


title: V104-SalivaRNAL_S313


title: Blood_60days_after_intervention_Patient3


title: Blood_60days_after_intervention_Patient2


title: Blood_30days_after_intervention_Patient2


title: TJ011-WTT


title: Alb-Cre;UBR7fl/fl #2

city: Guangxi

first: Bo

last: Tang

address: 6 Shuangyong Road

institute: Guangxi Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRCh38.91 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include normalized Conut values and raw fragment counts for each Sample

source_name: Mouse liver primary cells

growth_protocol: The conditionally immortalized mouse liver primary cells were cultured under growth permissive conditions at 37 °C in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: Wild-type and Alb-Cre;UBR7fl/fl mouse liver primary cells

value: Mouse liver primary cells

tag: genotype/variation


title: Blood_before_intervention_Patient3


title: susceptible, control, replicate 2


title: Islets, del_base1

value: normal chow diet

tag: age

value: 8 weeks old


title: Blood_before_intervention_Patient2


title: V103-Subgingival_S35

value: not provided


title: Alb-Cre;UBR7fl/fl #1


title: LQ-N007-1


title: susceptible, challenged, replicate 1


title: V103-SalivaRNAL_S259

value: Saliva


title: WT #3

value: wild type


title: TJ017-LYY


title: resistant, control, replicate 2


title: Islets, flox_NC3

value: Cdh13 exon2 floxed

value: 14 weeks old


title: WT #2


title: V102-Subgingival_S94

value: Subgingival sites


title: resistant, control, replicate 1


title: XWH-N008-1


title: V102-SalivaRNAL_S127


title: Blood_60days_after_intervention_Patient1


title: Blood_before_intervention_Patient1


title: TJ019-ZYH


title: WT #1


title: resistant, challenged, replicate 1


title: H2BK120ub_Alb-Cre;UBR7fl/fl

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC.
Quality reads were aligned to the hg19 reference genome using Bowtie version 1.1.2 with the following criteria: -n 1 -m 1–best–strata.
Duplicate reads were marked using SAMBLASTER before compression to BAM files
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using thengs.plotpackage function package in R program version 3.6.0
Genome_build: the UCSC Genome browser
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM for each Sample

growth_protocol: The conditionally immortalized mouse liver primary cells was cultured under growth permissive conditions at 37 °C in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Use ChIP-seq High Sensitivity kit (ab185908) to obtain cDNA library.
Operate according to the ChIP-seq High Sensitivity kit (ab185908) guide.

treatment_protocol: Wild-type mouse liver primary cells and Alb; Cre-UBR7fl/fl mouse liver primary cells

value: liver primary cells

value: Alb; Cre-UBR7fl/fl


title: TJ010-XYY

value: Male


title: susceptible, control, replicate 1

value: spleen


title: H2BK120ub_WT

source_name: Wild-type mouse liver primary cells


title: V101-SalivaRNAL_S103


title: Blood_30days_after_intervention_Patient1


title: V101-Subgingival_S231


title: CT-2018041103-1

value: non-segmental vitiligo (NSV) patient


title: microRNA counts from liver (ENCLB417KSE)

status: Public on Dec 08 2022

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR888CKV/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse liver
experiment encode accession: ENCSR888CKV
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB417KSE
size range: <30

hyb_protocol: Nanostring protocol

scan_protocol: Nanostring protocol

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (12.5 days)

label_protocol: Nanostring protocol

value: liver

value: tissue

tag: description

value: Liver from 88 embryonic 12.5 day mice

tag: biosample encode accession

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS479VPX at ENCODE; https://www.encodeproject.org/ENCBS479VPX/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA counts from liver (ENCLB554BFU)

description:
https://www.encodeproject.org/experiments/ENCSR942IBI/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse liver
experiment encode accession: ENCSR942IBI
assay title: microRNA counts
assembly: mm10
encode release date: 2015-12-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB554BFU
size range: <30

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (11.5 days)

value: Liver from 109 embyronic 11.5 day mice

value: ENCBS746POP at ENCODE; https://www.encodeproject.org/ENCBS746POP/


title: microRNA counts from midbrain (ENCLB457DMR)

description:
https://www.encodeproject.org/experiments/ENCSR921CNU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse midbrain
experiment encode accession: ENCSR921CNU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB457DMR
size range: <30

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (14.5 days)

value: midbrain

value: single midbrain from pup 1 pregnant 2 collected 7/30/2014

value: Barbara Wold, Caltech

value: ENCBS849BXE at ENCODE; https://www.encodeproject.org/ENCBS849BXE/


title: microRNA counts from heart (ENCLB570NSW)

description:
https://www.encodeproject.org/experiments/ENCSR883USZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse heart
experiment encode accession: ENCSR883USZ
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB570NSW
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl heart tissue postnatal (0 days)

value: heart

value: single heart from pup 1

value: 0 day

value: postnatal

value: not collected

value: ENCBS066TRB at ENCODE; https://www.encodeproject.org/ENCBS066TRB/


title: microRNA counts from forebrain (ENCLB224YWD)

description:
https://www.encodeproject.org/experiments/ENCSR966UUJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse forebrain
experiment encode accession: ENCSR966UUJ
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB224YWD
size range: <30

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (16.5 days)

value: forebrain

value: tissue

value: Forebrain pooled from embyonic 16.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS156DHU at ENCODE; https://www.encodeproject.org/ENCBS156DHU/


title: microRNA counts from forebrain (ENCLB031IPT)

description:
https://www.encodeproject.org/experiments/ENCSR966UUJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse forebrain
experiment encode accession: ENCSR966UUJ
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB031IPT
size range: <30

value: Forebrain from 41 embyonic 16.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS512LKA at ENCODE; https://www.encodeproject.org/ENCBS512LKA/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA counts from intestine (ENCLB959SUY)

description:
https://www.encodeproject.org/experiments/ENCSR888TKN/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse intestine
experiment encode accession: ENCSR888TKN
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB959SUY
size range: <30

source_name: Mus musculus strain B6NCrl intestine tissue mixed sex embryo (14.5 days)

value: intestine

value: single intestine from pup 1 pregnant 2 collected 7/15/2014

value: Barbara Wold, Caltech

value: ENCBS475HQA at ENCODE; https://www.encodeproject.org/ENCBS475HQA/


title: microRNA counts from midbrain (ENCLB162JQP)

description:
https://www.encodeproject.org/experiments/ENCSR921CNU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse midbrain
experiment encode accession: ENCSR921CNU
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB162JQP
size range: <30

value: midbrain

value: single midbrain from pup 1 pregnant 2 collected 7/24/2014

value: ENCBS825LGT at ENCODE; https://www.encodeproject.org/ENCBS825LGT/


title: microRNA counts from liver (ENCLB839VYO)

description:
https://www.encodeproject.org/experiments/ENCSR942IBI/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse liver
experiment encode accession: ENCSR942IBI
assay title: microRNA counts
assembly: mm10
encode release date: 2015-12-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB839VYO
size range: <30

value: liver

value: tissue

value: Liver from pooled embryonic 11.5 day mice

value: ENCBS522YOW at ENCODE; https://www.encodeproject.org/ENCBS522YOW/


title: microRNA counts from kidney (ENCLB028ZHA)

description:
https://www.encodeproject.org/experiments/ENCSR853PWX/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR853PWX
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB028ZHA
size range: <30

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (14.5 days)

value: kidney

value: 2 kidneys from pup 1 pregnant 2 collected 7/17/2014

value: embryonic

value: pooled male and female

value: ENCBS454WSU at ENCODE; https://www.encodeproject.org/ENCBS454WSU/


title: microRNA counts from forebrain (ENCLB668MQL)

description:
https://www.encodeproject.org/experiments/ENCSR866SQU/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR866SQU
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB668MQL
size range: <30

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (10.5 days)

value: forebrain

value: Forebrain from 69 embryonic 10.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS152ONW at ENCODE; https://www.encodeproject.org/ENCBS152ONW/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA counts from liver (ENCLB467FXI)

description:
https://www.encodeproject.org/experiments/ENCSR860OEN/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse liver
experiment encode accession: ENCSR860OEN
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB467FXI
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl liver tissue postnatal (0 days)

value: single liver from pup 3

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS301RUA at ENCODE; https://www.encodeproject.org/ENCBS301RUA/


title: microRNA counts from liver (ENCLB557PPR)

description:
https://www.encodeproject.org/experiments/ENCSR860OEN/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse liver
experiment encode accession: ENCSR860OEN
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB557PPR
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: liver

value: tissue

value: single liver from pup 1

value: ENCBS094UZQ at ENCODE; https://www.encodeproject.org/ENCBS094UZQ/


title: microRNA counts from forebrain (ENCLB349LIA)

description:
https://www.encodeproject.org/experiments/ENCSR866SQU/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR866SQU
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB349LIA
size range: <30

value: Forebrain from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS790BBA at ENCODE; https://www.encodeproject.org/ENCBS790BBA/


title: microRNA counts from kidney (ENCLB797GRZ)

description:
https://www.encodeproject.org/experiments/ENCSR853PWX/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR853PWX
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB797GRZ
size range: <30

value: kidney

value: 2 kidneys from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS731ALA at ENCODE; https://www.encodeproject.org/ENCBS731ALA/


title: microRNA counts from embryonic facial prominence (ENCLB739MXB)

description:
https://www.encodeproject.org/experiments/ENCSR828SVM/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR828SVM
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB739MXB
size range: <30

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (15.5 days)

value: embryonic facial prominence

value: Embryonic facial prominence from 62 embryonic 15.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS900XQR at ENCODE; https://www.encodeproject.org/ENCBS900XQR/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA counts from embryonic facial prominence (ENCLB038NOQ)

description:
https://www.encodeproject.org/experiments/ENCSR828SVM/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR828SVM
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB038NOQ
size range: <30

value: Embryonic facial prominence from 78 embryonic 15.5 day mice

value: ENCBS543BPM at ENCODE; https://www.encodeproject.org/ENCBS543BPM/


title: resistant, challenged, replicate 3

value: spleen

tag: genotype

value: resistant

value: challenged


title: microRNA counts from neural tube (ENCLB792LFB)

description:
https://www.encodeproject.org/experiments/ENCSR940THV/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse neural tube
experiment encode accession: ENCSR940THV
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB792LFB
size range: <30

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (11.5 days)

value: neural tube

value: tissue

value: Neural tube from 88 embyronic 11.5 day mice

value: embryonic

value: ENCBS183YVD at ENCODE; https://www.encodeproject.org/ENCBS183YVD/


title: microRNA counts from neural tube (ENCLB104HBO)

description:
https://www.encodeproject.org/experiments/ENCSR940THV/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 11.5 day (e11.5) mouse neural tube
experiment encode accession: ENCSR940THV
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB104HBO
size range: <30

value: Neural tube from 109 embyronic 11.5 day mice

value: pooled male and female

value: ENCBS402TUS at ENCODE; https://www.encodeproject.org/ENCBS402TUS/


title: microRNA counts from liver (ENCLB854TMN)

description:
https://www.encodeproject.org/experiments/ENCSR888CKV/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse liver
experiment encode accession: ENCSR888CKV
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB854TMN
size range: <30

value: liver

value: Liver from 120 embryonic 12.5 day mice

value: healthy

value: ENCBS236ISK at ENCODE; https://www.encodeproject.org/ENCBS236ISK/


title: microRNA counts from intestine (ENCLB759SIG)

description:
https://www.encodeproject.org/experiments/ENCSR888TKN/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse intestine
experiment encode accession: ENCSR888TKN
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB759SIG
size range: <30

value: intestine

value: single intestine from pup 1 pregnant 2 collected 7/17/2014

value: Barbara Wold, Caltech

value: ENCBS110AZU at ENCODE; https://www.encodeproject.org/ENCBS110AZU/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA counts from hindbrain (ENCLB275MPZ)

description:
https://www.encodeproject.org/experiments/ENCSR826DZM/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse hindbrain
experiment encode accession: ENCSR826DZM
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB275MPZ
size range: <30

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (15.5 days)

value: hindbrain

value: Hindbrain from 62 embryonic 15.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS948UKU at ENCODE; https://www.encodeproject.org/ENCBS948UKU/


title: microRNA counts from hindbrain (ENCLB697FIG)

description:
https://www.encodeproject.org/experiments/ENCSR826DZM/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse hindbrain
experiment encode accession: ENCSR826DZM
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB697FIG
size range: <30

value: tissue

value: Hindbrain from 78 embryonic 15.5 day mice

value: embryonic

value: ENCBS958AHU at ENCODE; https://www.encodeproject.org/ENCBS958AHU/


title: microRNA counts from heart (ENCLB457PNU)

description:
https://www.encodeproject.org/experiments/ENCSR823KMG/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR823KMG
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB457PNU
size range: <30

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (10.5 days)

value: heart

value: Heart from 51 embryonic 10.5 day mice

value: pooled male and female

value: ENCBS510GHM at ENCODE; https://www.encodeproject.org/ENCBS510GHM/


title: microRNA counts from heart (ENCLB392AOW)

description:
https://www.encodeproject.org/experiments/ENCSR823KMG/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR823KMG
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB392AOW
size range: <30

value: Heart from 69 embryonic 10.5 day mice

value: healthy

value: ENCBS366XOW at ENCODE; https://www.encodeproject.org/ENCBS366XOW/


title: microRNA counts from heart (ENCLB138ABS)

description:
https://www.encodeproject.org/experiments/ENCSR883USZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on postnatal 0 day mouse heart
experiment encode accession: ENCSR883USZ
assay title: microRNA counts
assembly: mm10
encode release date: 2015-11-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB138ABS
size range: <30
nucleic acid starting quantity: 100
nucleic acid starting quantity units: ng

value: single heart from pup 3

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS569APS at ENCODE; https://www.encodeproject.org/ENCBS569APS/


title: microRNA counts from embryonic facial prominence (ENCLB602RSG)

description:
https://www.encodeproject.org/experiments/ENCSR822RRV/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR822RRV
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB602RSG
size range: <30

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (10.5 days)

value: embryonic facial prominence

value: tissue

value: Craniofacial prominence from 69 embryonic 10.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS938XWJ at ENCODE; https://www.encodeproject.org/ENCBS938XWJ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA counts from hindbrain (ENCLB682QIM)

description:
https://www.encodeproject.org/experiments/ENCSR821ZGZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse hindbrain
experiment encode accession: ENCSR821ZGZ
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB682QIM
size range: <30

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (12.5 days)

value: hindbrain

value: Hindbrain from 88 embryonic 12.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS022IBY at ENCODE; https://www.encodeproject.org/ENCBS022IBY/


title: microRNA counts from stomach (ENCLB757KDU)

description:
https://www.encodeproject.org/experiments/ENCSR805WTW/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR805WTW
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB757KDU
size range: <30

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (14.5 days)

value: stomach

value: single stomach from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS715ONU at ENCODE; https://www.encodeproject.org/ENCBS715ONU/


title: microRNA counts from forebrain (ENCLB170OPR)

description:
https://www.encodeproject.org/experiments/ENCSR776CGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR776CGZ
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB170OPR
size range: <30

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (13.5 days)

value: forebrain

value: Forebrain from embryonic 13.5 day mice

value: healthy

value: ENCBS273RVL at ENCODE; https://www.encodeproject.org/ENCBS273RVL/


title: microRNA counts from intestine (ENCLB211IWF)

description:
https://www.encodeproject.org/experiments/ENCSR814KDR/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse intestine
experiment encode accession: ENCSR814KDR
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB211IWF
size range: <30

source_name: Mus musculus strain B6NCrl intestine tissue mixed sex embryo (16.5 days)

value: intestine

value: tissue

value: Intestine from 41 embyonic 16.5 day mice

value: ENCBS072GMU at ENCODE; https://www.encodeproject.org/ENCBS072GMU/


title: microRNA counts from embryonic facial prominence (ENCLB020XSS)

description:
https://www.encodeproject.org/experiments/ENCSR822RRV/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR822RRV
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB020XSS
size range: <30

value: embryonic facial prominence

value: Craniofacial prominence from 51 embryonic 10.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS199YOQ at ENCODE; https://www.encodeproject.org/ENCBS199YOQ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: microRNA counts from hindbrain (ENCLB530HWL)

description:
https://www.encodeproject.org/experiments/ENCSR821ZGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 12.5 day mouse hindbrain
experiment encode accession: ENCSR821ZGZ
assay title: microRNA counts
assembly: mm10
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB530HWL
size range: <30

value: hindbrain

value: Hindbrain from 120 embryonic 12.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS406RIE at ENCODE; https://www.encodeproject.org/ENCBS406RIE/


title: microRNA counts from forebrain (ENCLB839HFY)

description:
https://www.encodeproject.org/experiments/ENCSR776CGZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR776CGZ
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB839HFY
size range: <30

value: forebrain

value: Forebrain from embryonic 13.5 day mice

value: ENCBS793ZRY at ENCODE; https://www.encodeproject.org/ENCBS793ZRY/


title: microRNA counts from forebrain (ENCLB841GMI)

description:
https://www.encodeproject.org/experiments/ENCSR743UOB/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 15.5 day mouse forebrain
experiment encode accession: ENCSR743UOB
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB841GMI
size range: <30

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (15.5 days)

value: Forebrain from 78 embryonic 15.5 day mice

value: healthy

value: ENCBS811RMD at ENCODE; https://www.encodeproject.org/ENCBS811RMD/


title: microRNA counts from intestine (ENCLB776AYE)

description:
https://www.encodeproject.org/experiments/ENCSR814KDR/
***************
biological replicate number: 1
technical replicate number: 1
description: Nanostring miRNA Array on embryonic 16.5 day mouse intestine
experiment encode accession: ENCSR814KDR
assay title: microRNA counts
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB776AYE
size range: <30

value: intestine

value: tissue

value: Intestine pooled from embyonic 16.5 day mice

value: ENCBS856EWN at ENCODE; https://www.encodeproject.org/ENCBS856EWN/