title: SK-N-AS sgCDK8 MEKi rep1

tag: cell line


title: Young2-73

status: Public on Feb 22 2023

type: SRA

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

library_source: genomic single cell

data_processing:
ATAC-seq: Raw reads were trimmed using TrimGalore! software and inspected using FastQC
ATAC-seq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using Bowtie2 software, the resulting SAM files were converted to BAM files using SAMtools
ATAC-seq: Duplicate reads were removed using Picard tools
ATAC-seq: Mitochondrial reads removal and read shift were performed using ATACseqQC R package.
Assembly: NCBI37 (mm9)
Supplementary files format and content: Count matrix of reads mapped in chomatin regions open in HSC clones generated by single cell transplantations. Row names indicate the genomic coordinates of open chromatins.

molecule: genomic DNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Bone marrow cells were sorted by FACS
Illumina sequencing libraries were constructed according to a plate-based single cell ATACseq protocol

tag: strain

tag: phenotype

tag: cell type

value: Young-HSC


title: C1_12h

city: Chicago

first: Sarah

middle: J

last: Sun

state: Illinois

address: 900 E 57th Street

country: USA

institute: University of Chicago

library_source: transcriptomic

data_processing:
mm10
remove adapter sequences; trimmomatic-0.36; ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
read alignment; STAR; --sjdbOverhang 100
generate count matrix; featureCounts
processed_data: text file, raw counts matrix of reads overlapping each gene for each sample

molecule: total RNA

extract_protocol:
RNA extracted with Qiagen RNeasy kit
Illumina TruSeq

value: macrophage

tag: genotype

value: WT

tag: primary treatment

tag: timepoint

tag: secondary treatment


title: Young2-75


title: C1_7h


title: Young2-74


title: SK-N-AS sgCDK8 MEKi rep3

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

data_processing:
Quality control tests for unmapped reads were performed based on the FastQC v.0.11.9 software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and summarized with multiQC v1.7. The ERCC RNA Spike-In Mix (ThermoFisher Cat. No.: 4456740, https://tools.thermofisher.com/content/sfs/manuals/ERCC92.zip) was used as an external RNA control to estimate the variability in transcriptional performance (Bioconductor erccdashboard).
The spiked human reads were mapped to the hg38/gencode v30 human genome using STAR v2.6.1d  with standard parameters  --outSAMtype BAM SortedByCoordinate --outSAMunmapped None      --outSAMattributes NH HI NM MD AS XS --outReadsUnmapped Fastx --outSAMstrandField intronMotif --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan IndelSoftclipSingleend. Quality control for the mapped reads and for replicate reproducibility were performed using SARTools v1.7.3.
One sample (sgCCNC_MEKI_R1_dropped_lowQC) did not pass the QC tests and it was dropped out from any further analysis.
Gene level reads were summarized by counting the reads that overlapped the hg38/gencode v30 annotated gene exons, by using the featureCounts v1.6.3 method implemented in the Subread v2.0.0 package (http://subread.sourceforge.net).
Gene counts were normalized and used to quantify differential genes between the experimental and control conditions using the DESeq2 v1.32.0 method. Reads were normalized based on DESeq2 scaling factors. Gene expression was estimated based on log2(TPM+1) scores for normalized reads. Pair-wise genome-wide expression scatter dot plots, PCA, hierarchical clustering dendrograms and volcano plots were used to estimate the correlation of the  replicate samples correlation and the transcriptional dynamics across experimental phenotypes (SARTools v1.7.4, and Morpheus visualization platform, https://software.broadinstitute.org/morpheus). Genes with max(log2(TPM+1)) ≥ 1 across all samples were annotated as “expressed”.
Genome_build: hg38/gencode.v30
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with log2(TPM+1) expression scores for every gene and every sample.

organism: Homo sapiens

source_name: neuroblastoma

growth_protocol: SK-N-AS cells were infected with a single vector containing Cas9 and the indicated sgRNA.  Cells were then selected with puromycin.

extract_protocol:
After four days of treatment, RNA was harvested and purified with the Qiagen RNeasy Plus Mini Kit (Qiagen # 74134).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nine days after infection, cells were treated with either DMSO or 3 nM trametinib in triplicate.

value: SK-N-AS

tag: infection

tag: treatment

value: MEKi


title: SK-N-AS sgCDK8 DMSO rep3

value: DMSO


title: Young2-72


title: Young2-70


title: Young2-71


title: C1_4h


title: C1_2h


title: SK-N-AS sgCDK8 DMSO rep2


title: Young2-68


title: C2_2h


title: SK-N-AS sgCDK8 DMSO rep1


title: Young2-67


title: BG2_18h

value: beta glucan


title: Young2-66


title: Mel002-iLN

city: Los Angeles

first: Feiyang

last: Ma

state: CA

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

department: Molecular Biology Institute

institute: UCLA

library_source: transcriptomic single cell

data_processing:
The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell, generating 28 ́98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.
Raw reads were aligned to the human genome (hg38) and the digital expression matrix was generated using the cellranger count. Reads from individual samples were merged to generate the digital expression matrix using cellranger aggr.
R package Seurat was used to analyze the data.
Assembly: hg38
Supplementary files format and content: expression matrix

source_name: skin

extract_protocol:
Live CD45+HLA-DR+ cells were sorted from processed tumors.
Using the Chromium Single Cell 3′ Reagent Kit v3, single cell suspensions were partitioned into nanoliter droplets, known as gel- bead-in-emulsions (GEMs), to achieve single cell resolution. The cDNA generated within each individual GEM was tagged with a common 16-nt 10 ́ barcode and a 12-nt unique molecular barcode during the reverse transcription reaction. Purified cDNA was amplified in 11 cycles (98° 3 min, (98° 15 sec, 63° 20 sec, 72° 1 min) x 11, 72° 1 min) before being purified using SPRIselect beads. The cDNA concentration was then determined using an Agilent Bioanalyzer. Purified cDNA (10 μL) was used to generate the Illumina library for sequencing. For preparation of samples to be analyzed on the 10 ́ Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN- 1000073) and Chromium i7 Multiplex Kit (PN-120262) were used.

tag: tissue

value: skin

value: CD45+HLA-DR+ cells


title: Young2-65


title: SK-N-AS sgCCNC MEKi rep3

value: sgCCNC


title: BG2_15h


title: BG2_12h


title: Young2-64


title: Young2-63


title: Young2-61


title: BG2_7h


title: Young2-59


title: Young2-69


title: SK-N-AS sgCCNC MEKi rep1


title: SK-N-AS sgCCNC DMSO rep3


title: Young2-60


title: BG2_4h


title: SK-N-AS sgCCNC DMSO rep2


title: Young2-57


title: BG2_2h


title: Young2-56


title: SK-N-AS sgCCNC DMSO rep1


title: Young2-55


title: BG1_18h


title: SK-N-AS sgLacZ MEKi rep3

value: sgLacZ


title: Young2-53


title: Young2-54


title: BG1_15h


title: Young2-52


title: SK-N-AS sgLacZ MEKi rep2


title: SK-N-AS sgCCNC MEKi rep2


title: Young2-51


title: BG1_12h


title: Young2-62


title: SK-N-AS sgLacZ MEKi rep1


title: Young2-58


title: Young2-48


title: BG1_7h


title: Young2-49


title: Young2-47


title: BG1_4h


title: Young2-46


title: Young2-50


title: SK-N-AS sgLacZ DMSO rep3


title: SK-N-AS sgLacZ DMSO rep2


title: Young2-45


title: BG1_2h


title: Young2-44


title: SK-N-AS sgLacZ DMSO rep1


title: Young2-42


title: B-P-D6-5h-13_S64

value: pam3CSK4 5 hours


title: COVID_MISA_28

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

description: 10,000 cells loaded; Recovered: 3542 cells

data_processing:
All raw FASTQs reads were aligned to GRCh38 human reference using the STAR algorithm and quantified through the 10X Genomics cellranger v3.0.0 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<300 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate up to 50 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 25 were used to run and plot a tSNE plot for all cells.
Genome_build: Homo_sapiens : GRCh38
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

molecule: polyA RNA

source_name: PBMC (mixed 50:50 lymphocyte:leukocyte)

extract_protocol:
Blood samples were treated with RBC lysis. 50% of total blood cells were mixed with 50% of enriched lymphycytes (STEM Cell Kit)
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3.1 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 12 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using the NovaSeq S2 chip at a read depth of 32,000 reads/cell on an average of 4000 cells/sample.

tag: patient #

tag: clinical group

value: MIS-A

tag: collection time

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3.1


title: Young2-41


title: Young2-40


title: COVID_MISA_1

description: 10,000 cells loaded; Recovered: 4673 cells


title: Young2-39


title: B-N-D6-5h-13_S63


title: Young2-38


title: C-P-D6-5h-13_S62


title: C-N-D6-5h-13_S61


title: Young2-37


title: Young2-36


title: Young2-34


title: Young2-33


title: B-P-D6-1h-13_S60

value: pam3CSK4 1 hour


title: Young2-35


title: B-N-D6-1h-13_S59


title: COVID_D11_COVID_recovered

description: Cells Recovered: 2,714 cells; Mean reads per cell: 110,242

data_processing:
All raw FASTQs reads were aligned to GRCh38 human reference using the STAR algorithm and quantified through the 10X Genomics cellranger v3.0.0 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<300 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate up to 50 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 25 were used to run and plot a tSNE plot for all cells.
Genome_build: Homo_sapiens : GRCh38
Supplementary_files_format_and_content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

source_name: 50% of total blood cells were mixed with 50% of enriched lymphocytes

extract_protocol:
Blood samples were treated with RBC lysis. 50% of total blood cells were mixed with 50% of enriched lymphycytes (STEM Cell Kit).
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3.1 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 12 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using the NovaSeq S2 chip at a read depth of 32,000 reads/cell on an average of 4000 cells/sample.

value: peripheral blood with enriched lymphocytes

value: COVID Recovered

tag: dexamethasone status


title: COVID_D4_COVID_recovered

description: Cells Recovered: 4,510 cells; Mean reads per cell: 45,414


title: COVID_D9_COVID_recovered

description: Cells Recovered: 2,205 cells; Mean reads per cell: 116,996


title: dmut - 012.3mKaragogeos, 4.5.16

city: Heraklion

first: ZOUZANA

last: KOUNOUPA

state: Crete

address: Vassilika Vouton

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology Hellas

data_processing:
Torrent Suite™ Software 5.0 (Life Technologies): Run summary, QC metrics (RNASeqAnalysis plugin, version v5.0.2.1), FastQ generation (Ion Plugin Version v5.0.2.0).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Torrent Suite™ Software 5.0 (Life Technologies)
Trimmed sequence reads were mapped to GrCM38/mm10 using Torrent Suite™ Software 5.0 (Life Technologies), RNASeqAnalysis plugin, version v5.0.2.1 with default parameters
Read count extraction and normalization were performed using Torrent Suite™ Software 5.0 (Life Technologies), RNASeqAnalysis plugin, version v5.0.2.1
RNA seq analysis, statistical analysis and differential expression were werformed using CLC Genomics Workbench v 8.5
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: medial ganglionic eminence (MGE)

extract_protocol:
Τotal RNA from a pool of MGEs dissected from three E13.5 embryos per sample, was extracted and purified on columns (Qiagen RNeasy Plus Micro kit) ) and consequently was subjected to mRNA isolation, performed with Dynabeads mRNA DIRECT Micro Kit (Life Technologies) according to the manufacturer’s instructions.
Library construction was performed with the Ion Total RNA-seq kit (Life technologies) and the Ion XpressRNA kit (Life technologies) was used for barcoding.

value: medial ganglionic eminence (MGE)

value: MGE-derived cells

value: Rac1/Rac3 dmut

tag: age

tag: biological replicate


title: Young2-30

tag: strain

value: Young-HSC


title: Young2-29

tag: phenotype


title: Young2-43

tag: cell type


title: dmut - 015.2mKaragogeos, 29.3.16

tag: genotype


title: Young2-31


title: Young2-28


title: dmut - 014.1mKaragogeos, 29.3.16


title: C-P-D6-1h-13_S58

tag: cell line

value: macrophage

value: WT

tag: primary treatment


title: Young2-27


title: Young2-26


title: Young2-32


title: control - 011.3cKaragogeos, 4.5.16

value: Rac1/Rac3 wt


title: Young2-25


title: B-P-D4-5h-13_S56

value: beta glucan

tag: timepoint

tag: secondary treatment


title: B-N-D4-5h-13_S55


title: Young2-24


title: control - 013.2cKaragogeos, 29.3.16


title: C-N-D6-1h-13_S57


title: Young2-23


title: C-P-D4-5h-13_S54


title: Young2-22


title: Young2-21


title: Young2-19


title: Young2-20


title: control - 012.1cKaragogeos, 23.3.16


title: C-N-D4-5h-13_S53


title: 200594720025_R04C01

type: genomic

city: Rochester

first: Ellen

middle: L

last: Goode

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences

institute: Mayo Clinic

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Data were normalized separately for the two platforms. For Illumina Infinium Methylation EPIC, a Functional normalization was performed using the 'minfi' R/Bioconductor package. For Illumina InfiniumHumanMethylation 450 BeadChip, each batch was individually adjusted for plate effect, as follows: fit a linear model to the logit-transformed methylation values for each CpG locus and included a fixed effect term for plate; the logit-transformed locus means were then added back onto the unstandardized residuals derived from these models, before back transforming values on the logit-scale to a 0 to 1 scale. The batches were merged together and adjusted for batch effect using the same linear model approach.
Normalized Average Beta

source_name: Fresh Frozen Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

tag: gender

value: Female

tag: histology

value: Serous

tag: grade

value: High

tag: participationsite

tag: batch

value: epic


title: 200821620005_R08C01


title: Young2-17


title: 200821620048_R01C01


title: Young2-16


title: Young2-14


title: C-P-D4-1h-13_S50


title: Young2-13


title: B-N-D4-1h-13_S51


title: Young2-15


title: 200594720058_R02C01


title: C-N-D4-1h-13_S49


title: B-P-D2-5h-13_S48

value: pam3CSK4 5 hours


title: Young2-12


title: Young2-10


title: Young2-09


title: B-N-D2-5h-13_S47


title: 200594720025_R03C01


title: Young2-11


title: Young2-18


title: B-P-D4-1h-13_S52


title: 200821620005_R07C01


title: Young2-06


title: Young2-05


title: 200821620059_R02C01


title: C-N-D2-5h-13_S45


title: 200594720058_R08C01


title: Young2-03


title: 200594720025_R06C01


title: B-N-D2-1h-13_S43


title: Young2-01


title: 200821620038_R07C01


title: Young1-346


title: Young2-02


title: Young1-345


title: C-P-D2-1h-13_S42


title: C-N-D2-1h-13_S41


title: Young2-08


title: Young1-343


title: 200594720070_R06C01


title: Young1-344


title: 200594720058_R06C01


title: Young1-342


title: C-P-D2-5h-13_S46


title: 200594720058_R01C01


title: Young2-07


title: Young1-341


title: Young2-04


title: 200821620051_R08C01


title: B-P-D6-5h-12_S40


title: B-P-D2-1h-13_S44


title: Young1-340


title: B-N-D6-5h-12_S39


title: Young1-347


title: 200594720067_R06C01


title: Young1-339


title: 200821620037_R01C01


title: 200821620051_R07C01


title: B-P-D6-1h-12_S36


title: Young1-335


title: Young1-334


title: Young1-338


title: 200821620026_R06C01


title: Young1-332


title: Young1-333


title: B-N-D6-1h-12_S35


title: 200821620029_R06C01


title: Young1-336


title: Young1-330


title: C-P-D6-1h-12_S34


title: 200821620044_R06C01


title: Young1-329


title: Young1-328


title: Young1-327


title: Young1-326


title: 200821620036_R08C01


title: C-N-D6-1h-12_S33


title: B-P-D4-5h-12_S32


title: C-P-D6-5h-12_S38


title: 200821620036_R02C01


title: Young1-325


title: Young1-324


title: Young1-337


title: B-N-D4-5h-12_S31


title: C-N-D6-5h-12_S37


title: Young1-323


title: 200594720025_R05C01


title: Young1-321


title: Young1-331


title: C-P-D4-5h-12_S30


title: Young1-318


title: C-N-D4-5h-12_S29


title: Young1-317


title: Young1-319


title: 200821620038_R04C01


title: B-P-D4-1h-12_S28


title: 200821620005_R03C01


title: Young1-316


title: 200821620009_R05C01


title: B-N-D4-1h-12_S27


title: Young1-315


title: 200821620036_R07C01


title: C-P-D4-1h-12_S26


title: Young1-313


title: Young1-312


title: Young1-314


title: 200821620051_R05C01


title: 200821620048_R02C01


title: C-N-D4-1h-12_S25


title: Young1-311


title: Young1-309


title: Young1-310


title: B-P-D2-5h-12_S24


title: Young1-308


title: Young1-322


title: 200821620051_R04C01


title: 200821620036_R05C01


title: B-N-D2-5h-12_S23


title: Young1-307


title: Young1-305


title: 200594720070_R01C01


title: Young1-303


title: 200594720070_R04C01


title: Young1-301


title: Young1-302


title: B-P-D2-1h-12_S20


title: 200821620037_R08C01


title: Young1-299


title: B-N-D2-1h-12_S19


title: Young1-298


title: Young1-297


title: 200821620041_R04C01


title: C-P-D2-1h-12_S18


title: Young1-295


title: Young1-294


title: 200594720058_R05C01


title: Young1-296


title: Young1-293


title: DC4_381_NI_BIS96_B_MILD

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 85K EPIC Beadchip using standard Illumina protocol

scan_protocol: Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina).

data_processing:
Quality control, pre-processing and generation of β-values matrix were performed by using the RnBeads package (release 2.12.2) package, implemented R environment (version 4.1.3). SNP-enriched probes (139,721 sites), cross-reactive probes (34,264), unreliable measurements (4,369 sites), context-specific (1,180 sites), and on sex chromosomes probes (16,347sites), probes with many missing values (141 sites) were filtered out in the pre-processing step. As an outcome of the filtering procedures, 670,873 CpG sites and 187 samples were retained.
Matrix processed.txt: Normalized (BMIQ Quantile) average beta

label: cy3, cy5

source_name: Mild

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from peripheral blood lymphocytes of probands and their parents (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).

tag: tissue

tag: Sex

value: F

tag: clinical evolution

value: Mild


title: Young1-292


title: Young1-306


title: C-P-D2-5h-12_S22


title: B-P-D4-5h-11_S16


title: Young1-304


title: Young1-291


title: Young1-289


title: C-N-D2-5h-12_S21


title: B-N-D4-5h-11_S15


title: DC4_377_NI_BIS95_A_MILD

value: M

tag: age


title: Young1-287

tag: strain


title: C-P-D4-5h-11_S14


title: Young1-286

tag: phenotype


title: DC4_376_NI_BIS94_A_MILD


title: C-N-D4-5h-11_S13

tag: cell type


title: CaptureHiC-mm-Dup-het-FLHL-E115-Rep1-L16043-1

city: Berlin

first: Giulia

last: Cova

address: 63-73 Ihnestrasse

country: Germany

institute: Max Planck Institute

description: CaptureHiC-mm9-Dup-het-FLHL-E115-Rep1-50bp-MAPQ30-LOIC-5kb-L16043.WashU.txt

library_source: genomic

data_processing:
In a pre-processing step, the reads in fastq files were trimmed to 50 bp, if necessary, to obtain the same initial read length for all samples. Afterwards, mapping, filtering and deduplication of paired-end sequencing data was performed using the HiCUP pipeline v0.8.1(no size selection, Nofill: 1, Format: Sanger). The pipeline was set up with Bowtie2 v2.4.2 for mapping short reads to reference genome mm9. For merging biological replicates, the final bam files produced by the HiCUP pipeline were joined.
Juicer tools v1.19.02 was used to generate binned contact maps and to normalize maps by Knights and Ruiz (KR) matrix balancing.
For the generation of cHi-C maps, only read-pairs referring to the region of interest (chr19:44,440,001-46,400,000) and with MAPQ≥30 were considered.
In order to explicitly consider the duplicated region in the Dup mutant, we created cHi-C maps by applying the copy-number variation effects (LOIC)-normalization44 (python package iced v.0.5.345) to raw count maps.
Assembly: mm9

source_name: Embryonic Forelimb Hindlimb

extract_protocol:
Forelimb and hindlilmb buds were micro-dissected from E11.5 mouse embryos in 1xPBS, a single cell suspension was made using Trypsin, then samples were crosslinked using 2% PFA, snap frozen, and stored at -80 °C.
Snap frozen samples were first digested using DpnII, religated using the T4 DNA ligase (Thermo Fisher Scientific). The chimeric chromatin products were then decrosslinked overnight. RNase A treated chromatin was then precipitated.The precipiated chromatin was sheared using a Covaris sonicator (duty cycle: 10%; intensity: 5; cycles per burst: 200; time: 6 cycles of 60 s each; set mode: frequency sweeping; temperature: 4–7 °C). Adaptors were added to the sheared DNA and amplified according to the manufacturer’s instructions for Illumina sequencing (Agilent). The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing following the manufacturer’s instructions (Agilent).
Capture Hi-C

treatment_protocol: The capture HiC protocol was performed as decribed in Formation of new chromatin domains determines pathogenecity of genomic duplications. Franke et al., Nature 2016.

tag: genotype

value: Mutant_heterozygous inversion

tag: embryonic stage

tag: strain/background

value: G4 ESC


title: Young1-285


title: CaptureHiC-mm-Inv2-FLHL-E115-Rep2-L18176

description:
CaptureHiC-mm9-Inv2-FLHL-E115-Rep1Rep2Rep3merged-50bp-MAPQ30-KR-5kb-L18175-L18176-L18801.WashU.txt
CaptureHiC-mm9-Inv2-FLHL-E115-Rep1Rep2Rep3merged-vs-Wt-FLHL-E115-Rep1Rep2Rep3merged-MAPQ30-KR-5kb-diagNorm.WashU.txt

value: Mutant_homozygous inversion


title: C-N-D2-1h-12_S17

tag: cell line

tag: primary treatment

tag: timepoint


title: DC4_374_NI_BIS94_B_SEVERE

source_name: Severe

value: Severe


title: B-N-D4-1h-11_S11

tag: secondary treatment


title: CaptureHiC-mm-Inv2-FLHL-E115-Rep1-L18175


title: DC4_373_NI_BIS93_B_MILD


title: B-P-D4-1h-11_S12

value: pam3CSK4 1 hour


title: DC4_375_NI_BIS95_B_MILD


title: DC4_379_NI_BIS96_A_MILD


title: CaptureHiC-mm-Inv1-FLHL-E115-Rep1-L17927

description:
CaptureHiC-mm9-Inv1-FLHL-E115-Rep1Rep2Rep3-50bp-merged-MAPQ30-KR-5kb-L17927-L18799-L18800.WashU.txt
CaptureHiC-mm9-Inv1-FLHL-E115-Rep1Rep2Rep3merged-vs-Wt-FLHL-E115-Rep1Rep2Rep3merged-MAPQ30-KR-5kb-diagNorm.WashU.txt
Virtual4C-mm9-Inv1-merged-Lbx1-5kb.bedgraph
Virtual4C-mm9-Inv1-merged-Btrc-5kb.bedgraph
Virtual4C-mm9-Inv1-merged-Fgf8-5kb.bedgraph


title: Young1-282

value: Young-HSC


title: C-P-D4-1h-11_S10

value: macrophage

value: WT


title: DC4_372_NI_BIS93_A_MILD


title: C-N-D4-1h-11_S9


title: Young1-281


title: DC4_371_NI_BIS92_B_MILD


title: Young1-280


title: CaptureHiC-mm-Wt-FLHL-E115-Rep2-S11359

description:
CaptureHiC-mm9-Wt-FLHL-E115-Rep1Rep2Rep3-50bp-merged-MAPQ30-KR-5kb-L11359-L11678-S11359-L9627.WashU.txt
Virtual4C-mm9-Wt-merged-Lbx1-5kb.bedgraph
Virtual4C-mm9-Wt-merged-Btrc-5kb.bedgraph
Virtual4C-mm9-Wt-merged-Fgf8-5kb.bedgraph

value: Wild type


title: Young1-279


title: Young1-288


title: CaptureHiC-mm-Wt-FLHL-E115-tecRep1-L11678


title: Young1-278


title: C-P-D2-5h-11_S6


title: Young1-277


title: CaptureHiC-mm-Wt-FLHL-E115-Rep1-L11359


title: Young1-283


title: DC4_369_NI_BIS91_B_SEVERE


title: DC4_368_NI_BIS90_B_SEVERE


title: peri_p3_rep3

city: Boston

first: Yu

last: Liu

address: 72 East Concord Street

institute: Boston University

description: femur and tibia

data_processing: none provided by the submitter

source_name: periosteum

extract_protocol: SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and  amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing  library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed  by limited-cycle PCR to enrich and add index to the cDNA fragments. The final library was assessed with  Agilent TapeStation.

value: periosteum

value: Prx1+ CD45- CD105+ CD200 variable


title: Young1-276


title: C-N-D2-5h-11_S5


title: CaptureHiC-mm-Wt-FLHL-E115-Rep3-L9627-1


title: B-P-D2-1h-11_S4

value: beta glucan


title: peri_p3_rep2

description: femur and tibia


title: Young1-275


title: DC4_364_NI_BIS90_A_SEVERE


title: peri_p3_rep1

description: femur and tibia


title: peri_p2_rep3

description: femur and tibia


title: B-N-D2-1h-11_S3


title: DC4_366_NI_BIS91_A_SEVERE


title: DC4_367_NI_BIS89_B_SEVERE


title: Young1-274


title: DC4_370_NI_BIS92_A_MILD


title: DC4_363_NI_BIS89_A_MILD


title: B-P-D2-5h-11_S8


title: C-P-D2-1h-11_S2


title: peri_p2_rep2

description: femur and tibia


title: C-N-D2-1h-11_S1


title: B-N-D2-5h-11_S7


title: Young1-272


title: Young1-271


title: B-P-D14-5h-10_S96


title: peri_p2_rep1

description: femur and tibia


title: DC4_361_NI_BIS88_B_SEVERE


title: peri_p1_rep3

description: femur and tibia


title: B-N-D14-5h-10_S95


title: Young1-270


title: peri_p1_rep2

description: femur and tibia


title: DC4_360_NI_BIS87_A_SEVERE


title: C-P-D14-5h-10_S94


title: DC4_358_NI_BIS87_B_MILD


title: Young1-269


title: peri_p1_rep1

description: femur and tibia


title: C-N-D14-5h-10_S93


title: DC4_356_NI_BIS85_B_MILD


title: Young1-268


title: DC4_355_NI_BIS84_B_MILD


title: B-P-D14-1h-10_S92


title: Young1-273


title: Young1-267


title: Young1-266


title: B-N-D14-1h-10_S91


title: musc_p3_rep3

description: femur and tibia

source_name: skeletal muscle

value: skeletal muscle


title: musc_p3_rep1

description: femur and tibia


title: Young1-265


title: musc_p3_rep2

description: femur and tibia


title: C-P-D14-1h-10_S90


title: DC4_353_NI_BIS86_A_MILD


title: DC4_362_NI_BIS88_A_MILD


title: C-N-D14-1h-10_S89


title: DC4_352_NI_BIS82_B_MILD


title: Young1-264


title: musc_p2_rep2

description: femur and tibia


title: B-P-D12-5h-10_S88

value: pam3CSK4 5 hours


title: Young1-263


title: musc_p2_rep3

description: femur and tibia


title: DC4_351_NI_BIS85_A_SEVERE


title: musc_p2_rep1

description: femur and tibia


title: B-N-D12-5h-10_S87


title: musc_p1_rep3

description: femur and tibia


title: DC4_350_NI_BIS84_A_SEVERE


title: DC4_354_NI_BIS83_B_MILD

value: F


title: C-P-D12-5h-10_S86


title: Young1-261


title: Young1-262


title: B-P-D12-1h-10_S84


title: Young1-256


title: Young1-257


title: bm_p3_rep3

description: femur and tibia

source_name: bone marrow

value: bone marrow


title: musc_p1_rep1

description: femur and tibia


title: musc_p1_rep2

description: femur and tibia


title: DC4_345_NI_BIS80_A_SEVERE


title: Young1-255


title: bm_p3_rep2

description: femur and tibia


title: C-N-D12-5h-10_S85


title: B-N-D12-1h-10_S83


title: Young1-254


title: DC4_343_NI_BIS81_B_MILD

value: Mild


title: C-P-D12-1h-10_S82


title: C-N-D12-1h-10_S81


title: DC4_346_NI_BIS81_A_MILD


title: DC4_342_NI_BIS79_A_SEVERE

value: M


title: Young1-253


title: bm_p2_rep3

description: femur and tibia


title: DC4_349_NI_BIS83_A_SEVERE


title: B-P-D10-5h-10_S80


title: DC4_341_NI_BIS80_B_MILD


title: Young1-252


title: B-N-D10-5h-10_S79


title: DC4_340_NI_BIS79_B_SEVERE


title: DC4_347_NI_BIS82_A_SEVERE


title: Young1-251


title: bm_p2_rep2

description: femur and tibia


title: bm_p2_rep1

description: femur and tibia


title: DC4_336_NI_BIS78_A_MILD


title: C-P-D10-5h-10_S78


title: Young1-250


title: bm_p1_rep3

description: femur and tibia


title: C-N-D10-5h-10_S77


title: DC4_335_NI_BIS78_B_MILD


title: Young1-249


title: Young1-248


title: bm_p3_rep1

description: femur and tibia


title: DC4_333_NI_BIS77_A_SEVERE


title: B-P-D10-1h-10_S76


title: B-N-D10-1h-10_S75


title: DC4_332_NI_BIS76_A_MILD


title: Young1-247


title: bm_p1_rep2

description: femur and tibia


title: bm_p1_rep1

description: femur and tibia


title: C-P-D10-1h-10_S74


title: Young1-246


title: DC4_331_NI_BIS75_A_SEVERE


title: C-N-D10-1h-10_S73


title: DC4_329_NI_BIS77_B_MILD


title: WT_2

city: London

first: Elizabeth

last: Fisher

state: London

address: Queen Square

institute: University College London

description:
CLE413A3
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Dissected hippocampi were dissociated using the Adult Brain Dissociation Kit (Miltenyi Biotec #130-107-677) according to the manufacturer’s instructions. Cell suspensions were applied to 70 mm pre-moistened cell strainers and cells were collected by centrifugation for 10 min at 300 xg, 4 oC. Cell pellets were resuspended in ice-cold D-PBS using wide-bore, pre-moistened tips, prior to debris removal, which was carried out according to the manufacturer’s instructions. Final cell pellets were resuspended in 0.04% BSA in D-PBS (Miltenyi Biotec MACS BSA #130-091-376). Cell viability was assessed using a NanoEntek Eve Automated Cell Counter. The single-cell suspension was then loaded into the 10x Chromium.
Library was performed according to the manufacter’s instructions (single cell 3’ v1 protocol, 10x Genomics).

value: Hippocampus

value: Hippocampal

value: Wildtype

tag: strain background


title: Young1-245


title: Young1-244


title: Dp2Yey_1

description:
CLE413A2
10x Genomics


title: B-N-D8-5h-10_S71


title: DC4_327_NI_BIS74_A_SEVERE

value: Severe


title: DC4_326_NI_BIS76_B_MILD


title: B-P-D8-5h-10_S72


title: DC4_325_NI_BIS75_B_SEVERE


title: Young1-243

value: Young-HSC


title: Young1-242


title: C-P-D8-5h-10_S70

value: macrophage


title: RNA_Tumor CAG

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

country: China

institute: Nanjing University

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 4.0.0.
Single Cell 5' R2-only
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tumor

growth_protocol: The tumor was removed on the 18th day after 6-8 weeks of tumor bearing mice

extract_protocol:
After the tumor was removed, it was digested into single cell suspension with tumor tissue dissociation kit on ice, and 10x-RNA reagent were added
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After tumor bearing, PBS and CAG were administered by gavage every day

value: tumor

value: 10 weeks

value: WT

tag: treatment

value: Intragastric administration


title: WT_1

description:
CLE413A1
10x Genomics


title: C-N-D8-5h-10_S69


title: RNA_Tumor PBS


title: DC4_323_NI_BIS74_B_MILD


title: Young1-241


title: Dp2Yey_2

description:
CLE413A4
10x Genomics


title: ATAC_Tumor CAG

extract_protocol:
After the tumor was removed, it was digested into single cell suspension with tumor tissue dissociation kit on ice, and 10x-ATAC reagent were added
RNA libraries were prepared for sequencing using standard Illumina protocols


title: B-N-D8-1h-10_S67

value: beta glucan


title: B-P-D8-1h-10_S68

value: pam3CSK4 1 hour


title: DC4_321_NI_BIS72_A_MILD


title: Young1-240


title: ATAC_Tumor PBS


title: DC4_320_NI_BIS73_B_MILD


title: HepG2-

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

data_processing:
Adapters of reads were removed by cutadapt package28. Quality of clean reads was inspected by fastqc.
Single-end reads were mapped by Burrows–Wheeler Alignment tool (BWA) with parameters -n 1 -o 0 -e 0 -l 8 -k 0.
HTSeq was applied to count the read numbers of mature miRNAs in miRBase v22.
Genome_build: hg38
Supplementary_files_format_and_content: HepG2+_count.txt.gz, tab-seperated file, read counts
Supplementary_files_format_and_content: HepG2-_count.txt.gz, tab-seperated file, read counts

source_name: pulldown using negative probe

extract_protocol:
Probes based on back-splicing junction sequence are designed. The biotin-labeled positive probe or negative control probe whose sequence is reverse-complementary to positive probe, were respectively mixed with Pierce Streptavidin Magnetic Beads (ThermoFisher, USA) at room temperature for one hour. For lysis of cell samples, cell lysis solution was prepared: Protease Inhibitor Cocktail （Roche，Switzerland）and RNAase inhibitor（NEB，USA）were added prior to use. Cell samples were washed twice with RNA-free PBS prior to lysis. Cells were lysed using the cell lysis solution. Centrifuge at 14,000 rpm for 15 min and reserve the supernatant. The probe-bound beads were incubated overnight with RNA extract of samples at 4℃. Then, the bound miRNA was purified from complex with Trizol reagent by following the manufacturer’s procotol (ThermoFisher, USA).
The miRNA sequencing library was prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions. The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters, and finally sequenced for 50 cycles on Illumina HiSeq4000 sequencer following the manufacturer’s instructions.


title: DC4_319_NI_BIS71_A_SEVERE


title: Young1-238


title: C-P-D8-1h-10_S66


title: HepG2+

source_name: pulldown using circGLS2-specific probe


title: C-N-D8-1h-10_S65


title: Young1-237

source_name: Bone marrow


title: CMS+PHL rep3

city: Beijing

first: Yutao

last: Yang

state: Beijing

address: No.10, You An Men Wai Xi Tou Tiao

department: Department of Neurobiology

institute: Capital Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and then mapped to Rattus norvegicus whole genome using Hisat2.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell, Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: ftp://ftp.ensembl.org/pub/release-101/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz
Supplementary_files_format_and_content: gene_Fpkm.xls: Excel file includes FPKM values for each Sample.

organism: Rattus norvegicus

source_name: brain

extract_protocol:
mPFC tissues were removed, flash frozen on dry ice, and RNA was extracted using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: SD

value: Medial prefrontal cortex tissues (mPFC)

value: Chronic mild stress + Phloretin (CMS+PHL)


title: B-P-D14-5h-9_S64

value: pam3CSK4 5 hours


title: Young1-236


title: CMS+PHL rep2


title: B-N-D14-5h-9_S63


title: Young1-235


title: C-P-D14-5h-9_S62


title: DC4_315_NI_BIS70_A_SEVERE

value: M


title: Young1-234


title: Young1-239


title: DC4_313_NI_BIS69_A_MILD

value: F

value: Mild


title: C-N-D14-5h-9_S61


title: DC4_312_NI_BIS70_B_MILD


title: CMS rep3

value: Chronic mild stress (CMS)


title: Young1-233


title: Young1-232


title: DC4_318_NI_BIS72_B_MILD


title: DC4_309_NI_BIS67_A_SEVERE

value: Severe


title: Vehicle rep3

value: Vehicle


title: Young1-231

value: Young-HSC


title: DC4_311_NI_BIS68_A_MILD


title: Young1-230


title: DC4_308_NI_BIS66_A_MILD


title: C-P-D14-1h-9_S58

value: macrophage


title: B-N-D14-1h-9_S59


title: Vehicle rep2


title: DC4_316_NI_BIS71_B_MILD


title: C-N-D14-1h-9_S57


title: Young1-229


title: CMS+PHL rep1


title: DC4_307_NI_BIS69_B_SEVERE


title: B-P-D12-5h-9_S56


title: DC4_306_NI_BIS68_B_MILD


title: Young1-228


title: Vehicle rep1


title: B-P-D14-1h-9_S60


title: DC4_305_NI_BIS67_B_MILD


title: B-N-D12-5h-9_S55


title: CMS rep1


title: Young1-227


title: CMS rep2


title: IP_Col0K9

city: shanghai

first: li

last: peng

institute: PSC

description: WT

data_processing:
We cleaned the paired-end reads by Trimimomatic. After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
Clean reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 (version 2.2.8) with default parameters.
Enriched peaks were identified by MACS (version 1.4) with default parameters.
We defined the region of a target gene as the range from 1kb upstream of transcription start site (TSS) to transcription end site (TES). The target genes of each peak were annotated by annotatePeak function in ChIPseeker package.
The visualization of the average read coverage over gene body and additional up- and down-stream of the TSS and TES was performed by deepTools (version 2.4.1).
Assembly: TAIR10
Supplementary files format and content: bed files with peaks

organism: Arabidopsis thaliana

source_name: plant tissues

growth_protocol: All the plant seeds were sown and grown on 1/2 MS medium containing 1% sucrose. The seedlings were grown under a long- (16 h light/8 h dark)  photoperiod at 23 °C.

extract_protocol: Lysates were clarified from sonicated nuclei and histone modification were isolated with antibody in WT and mutants.

value: 12-day-old seedlings

tag: antibody

value: H3K9me2 (anti-H3K9me2, Abcam #ab1220)

tag: ecotype

value: Columbia


title: IP_28K9

tag: tissue


title: C-P-D12-5h-9_S54

value: WT


title: DC4_304_NI_BIS66_B_MILD

tag: Sex

tag: clinical evolution


title: Young1-226

extract_protocol:
Bone marrow cells were sorted by FACS
Illumina sequencing libraries were constructed according to a plate-based single cell ATACseq protocol

tag: strain


title: Input_H282


title: C-N-D12-5h-9_S53

extract_protocol:
RNA extracted with Qiagen RNeasy kit
Illumina TruSeq


title: DC4_303_NI_BIS65_B_SEVERE

tag: age


title: B-P-D12-1h-9_S52

tag: cell type

value: beta glucan

value: pam3CSK4 1 hour


title: Young1-223

tag: phenotype


title: DC4_302_NI_BIS64_B_MILD


title: B-N-D12-1h-9_S51

tag: genotype


title: DC4_301_NI_BIS63_B_MILD


title: Young1-222


title: IP A2atx128.1

data_processing:
We cleaned the paired-end reads by Trimimomatic. After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
Clean reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 (version 2.2.8) with default parameters.
Enriched peaks were identified by MACS (version 1.4) with default parameters.
We defined the region of a target gene as the range from 1kb upstream of transcription start site (TSS) to transcription end site (TES). The target genes of each peak were annotated by annotatePeak function in ChIPseeker package.
The visualization of the average read coverage over gene body and additional up- and down-stream of the TSS and TES was performed by deepTools (version 2.4.1).
Assembly: TAIR10
Supplementary files format and content: bigwig files with RPM value

growth_protocol: All the plant seeds were sown and grown on 1/2 MS medium containing 1% sucrose. The seedlings were grown under a long- (16 h light/8 h dark) photoperiod at 23 °C.

extract_protocol: Lysates were clarified from sonicated nuclei and ATX2-DNA complexes were isolated with antibody.

value: Flag (Sigma # F1804 )


title: Young1-221

data_processing:
ATAC-seq: Raw reads were trimmed using TrimGalore! software and inspected using FastQC
ATAC-seq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using Bowtie2 software, the resulting SAM files were converted to BAM files using SAMtools
ATAC-seq: Duplicate reads were removed using Picard tools
ATAC-seq: Mitochondrial reads removal and read shift were performed using ATACseqQC R package.
Assembly: NCBI37 (mm9)
Supplementary files format and content: Count matrix of reads mapped in chomatin regions open in HSC clones generated by single cell transplantations. Row names indicate the genomic coordinates of open chromatins.


title: DC4_299_NI_BIS62_B_MILD


title: IP A2atx1.2


title: C-P-D12-1h-9_S50

data_processing:
mm10
remove adapter sequences; trimmomatic-0.36; ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
read alignment; STAR; --sjdbOverhang 100
generate count matrix; featureCounts
processed_data: text file, raw counts matrix of reads overlapping each gene for each sample


title: Young1-220


title: DC4_298_NI_BIS61_B_MILD


title: IP A2atx1.1


title: B-P-D10-5h-9_S48


title: Young1-219


title: DC4_297_NI_BIS65_A_MILD


title: Young1-218


title: B-N-D10-5h-9_S47


title: IP A2.2


title: Young1-217


title: C-P-D10-5h-9_S46


title: DC4_296_NI_BIS64_A_MILD


title: Young1-224


title: IP A2.1


title: IP A2atx128.2


title: DC4_295_NI_BIS60_B_MILD


title: C-N-D10-5h-9_S45


title: IP Col0.2


title: DC4_294_NI_BIS59_B_MILD


title: Young1-216


title: Input_HCol0

description: WT


title: Young1-215


title: B-P-D10-1h-9_S44


title: C-N-D12-1h-9_S49


title: IP Col0.1


title: Input A2atx128


title: B-N-D10-1h-9_S43


title: DC4_292_NI_BIS63_A_SEVERE


title: C-P-D10-1h-9_S42


title: DC4_291_NI_BIS62_A_MILD


title: Input A2


title: C-N-D10-1h-9_S41


title: Young1-212


title: DC4_290_NI_BIS57_B_SEVERE


title: Young1-213


title: Input A2atx1


title: Young1-211


title: Input Col0


title: A2.2_IP

data_processing:
We cleaned the paired-end reads by Trimimomatic. After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
Clean reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 (version 2.2.8) with default parameters.
Enriched peaks were identified by MACS (version 1.4) with default parameters.
We defined the region of a target gene as the range from 1kb upstream of transcription start site (TSS) to transcription end site (TES). The target genes of each peak were annotated by annotatePeak function in ChIPseeker package.
The visualization of the average read coverage over gene body and additional up- and down-stream of the TSS and TES was performed by deepTools (version 2.4.1).
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files with peaks

tag: developmental stage


title: B-N-D8-1h-9_S39

tag: cell line


title: B-P-D8-1h-9_S40

tag: primary treatment


title: Young1-210


title: DC4_287_NI_BIS56_B_MILD


title: Young1-209


title: DC4_284_NI_BIS60_A_MILD


title: C-P-D8-1h-9_S38

tag: timepoint


title: DC4_293_NI_BIS58_B_SEVERE


title: C-N-D8-1h-9_S37

tag: secondary treatment


title: A2.1_IP


title: Col0.2_IP

value: wildtype


title: DC4_283_NI_BIS55_B_MILD


title: DC4_288_NI_BIS61_A_MILD


title: Young1-214


title: B-P-D6-1h-9_S36


title: Young1-207


title: DC4_282_NI_BIS54_B_MILD


title: B-N-D6-1h-9_S35


title: Young1-205


title: Young1-204


title: C-P-D6-1h-9_S34


title: DC4_280_NI_BIS58_A_MILD


title: A2_input


title: IP_X28.2 4Myc

extract_protocol: Lysates were clarified from sonicated nuclei and JMJ28-DNA complexes were isolated with antibody.

value: Myc


title: DC4_281_NI_BIS59_A_MILD


title: C-N-D6-1h-9_S33


title: Young1-203


title: Young1-202


title: B-P-D14-5h-8_S32

value: pam3CSK4 5 hours


title: IP_X28.1 4Myc


title: Young1-208


title: DC4_276_NI_BIS56_A_SEVERE

value: M


title: C-P-D14-5h-8_S30


title: B-N-D14-5h-8_S31


title: IP_Col0.1 wild-type

value: wild-type


title: IP_Col0.2 wild-type


title: Col0.1_IP


title: Young1-201


title: DC4_275_NI_BIS55_A_MILD

value: F

value: Mild


title: DC4_273_NI_BIS51_B_MILD


title: Young1-198


title: Young1-197


title: Input_X28 4Myc


title: C-N-D14-5h-8_S29


title: Col-0_input


title: Input_Col0 wild-type


title: B-P-D14-1h-8_S28


title: Young1-196


title: jmj28-2_H3K4me3_H3_B


title: DC4_279_NI_BIS57_A_MILD


title: B-N-D14-1h-8_S27


title: Young1-195


title: DC4_277_NI_BIS53_B_MILD


title: DC4_270_NI_BIS50_B_MILD


title: jmj28-2_H3K4me3_2_B


title: DC4_269_NI_BIS49_B_SEVERE

value: Severe


title: jmj28-2_H3K4me3_1_B


title: C-P-D14-1h-8_S26


title: C-N-D14-1h-8_S25


title: Young1-193

value: Young-HSC


title: DC4_268_NI_BIS48_B_MILD


title: DC4_267_NI_BIS53_A_SEVERE


title: Young1-192


title: Col-0_H3K4me3_2_B


title: B-P-D12-5h-8_S24

value: macrophage


title: DC4_265_NI_BIS47_B_SEVERE


title: Col-0_H3K4me3_H3_B

value: 12-day-old seedlings


title: Young1-191


title: B-N-D12-5h-8_S23


title: Young1-190


title: DC4_264_NI_BIS52_A_SEVERE


title: atx1/2_H3K4me3_H3_B


title: DC4_271_NI_BIS54_A_MILD


title: Young1-189


title: C-P-D12-5h-8_S22


title: C-N-D12-5h-8_S21


title: atx1/2_H3K4me3_2_B


title: DC4_262_NI_BIS46_B_SEVERE


title: Young1-188


title: Young1-194


title: Young1-187


title: B-N-D12-1h-8_S19


title: B-P-D12-1h-8_S20


title: P16RE_3

data_processing:
Real Time Analysis (RTA) and CASAVA v1.8 for base-calling
The abundances of transcripts were estimated by performing eXpress on the reference transcripts of NCBI
Genome_build: hg38
Supplementary_files_format_and_content: Both FPKM and read count matrix are tab-limited text files

source_name: Sorafenib-resistant organoid of patient 4, replicate 3

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The paired-end libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

tag: patient

tag: drug phenotype

value: resistant


title: DC4_261_NI_BIS50_A_SEVERE


title: DC4_260_NI_BIS49_A_SEVERE


title: C-P-D12-1h-8_S18


title: P16RE_2

source_name: Sorafenib-resistant organoid of patient 4, replicate 2


title: Col-0_H3K4me3_1_B

tag: antibody


title: Young1-186


title: DC4_259_NI_BIS48_A_MILD


title: B-P-D10-5h-8_S16


title: C-N-D12-1h-8_S17


title: DC4_258_NI_BIS47_A_MILD


title: Young1-185


title: Young1-184


title: DC4_263_NI_BIS51_A_SEVERE


title: B-N-D10-5h-8_S15


title: P16RE_1

source_name: Sorafenib-resistant organoid of patient 4, replicate 1


title: C-P-D10-5h-8_S14


title: P12_2

source_name: Sorafenib-sensitive organoid of patient 4, replicate 2

value: sensitive


title: DC4_257_NI_BIS46_A_SEVERE


title: DC4_256_NI_BIS45_A_SEVERE


title: atx1/2_H3K4me3_1_B

tag: ecotype


title: P12_1

source_name: Sorafenib-sensitive organoid of patient 4, replicate 1


title: DC4_254_NI_BIS45_B_MILD

source_name: Mild

tag: tissue


title: B-P-D10-1h-8_S12

value: WT


title: Young1-183


title: p26RE_3

source_name: Sorafenib-resistant organoid of patient 3, replicate 3


title: Young1-182


title: Young1-181


title: B-N-D10-1h-8_S11

value: beta glucan


title: Young1-179


title: DC4_252_NI_BIS44_B_SEVERE

source_name: Severe

tag: Sex


title: p26RE_2

source_name: Sorafenib-resistant organoid of patient 3, replicate 2


title: Young1-180


title: DC4_251_NI_BIS44_A_SEVERE

tag: clinical evolution


title: C-P-D10-1h-8_S10

value: pam3CSK4 1 hour


title: p26RE_1

source_name: Sorafenib-resistant organoid of patient 3, replicate 1


title: Young1-178

tag: strain


title: P12_3

source_name: Sorafenib-sensitive organoid of patient 4, replicate 3


title: C-N-D10-1h-8_S9


title: P11_3

source_name: Sorafenib-sensitive organoid of patient 3, replicate 3


title: Young1-177


title: DC4_249_NI_BIS43_B_MILD

tag: age


title: Young1-176

tag: cell type


title: DC4_248_NI_BIS42_A_SEVERE


title: P11_2

source_name: Sorafenib-sensitive organoid of patient 3, replicate 2


title: B-P-D8-5h-8_S8


title: P11_1

source_name: Sorafenib-sensitive organoid of patient 3, replicate 1


title: C-N-D10-5h-8_S13


title: B-N-D8-5h-8_S7


title: Young1-175

source_name: Bone marrow

tag: phenotype


title: DC4_247_NI_BIS42_B_MILD


title: P42RE_3

source_name: Sorafenib-resistant organoid of patient 2, replicate 3


title: DC4_246_NI_BIS41_B_SEVERE


title: C-P-D8-5h-8_S6

tag: genotype


title: P42RE_2

source_name: Sorafenib-resistant organoid of patient 2, replicate 2


title: Young1-174


title: C-N-D8-5h-8_S5


title: DC4_250_NI_BIS43_A_MILD


title: Young1-173


title: DC4_245_NI_BIS41_A_SEVERE


title: Young1-172


title: P42RE_1

source_name: Sorafenib-resistant organoid of patient 2, replicate 1


title: DC4_244_NI_BIS40_A_SEVERE


title: B-N-D6-1h-8_S3


title: DC4_243_NI_BIS40_B_SEVERE


title: B-P-D6-1h-8_S4


title: C-P-D6-1h-8_S2


title: Young1-170


title: P29_2

source_name: Sorafenib-sensitive organoid of patient 2, replicate 2


title: DC4_242_NI_BIS39_A_SEVERE


title: DC4_239_NI_BIS38_A_SEVERE


title: P29_1

source_name: Sorafenib-sensitive organoid of patient 2, replicate 1


title: C-N-D6-1h-8_S1


title: P27RE_3

source_name: Sorafenib-resistant organoid of patient 1, replicate 3


title: Young1-169


title: Young1-168


title: DC4_238_NI_BIS37_A_MILD


title: Infected, replicate 2, scRNAseq

first: Shaohui

last: Wang

address: 8700 Beverly BLVD

department: Surgery

institute: Cedars Sinai Medical Center

description: 10x Genomics

data_processing:
Raw sequencing data was demultiplexed and converted to FASTQ format using bcl2fastq v2.20. Cell Ranger v6.0.0 (10X Genomics) was used for barcode identification, read alignment, and UMI quantification with default parameters and aligning to the mouse reference genome GRCm38. In addition to the empty droplet filtering performed by Cell Ranger, poor-quality cells were removed by setting a maximum mitochondrial read of 15%.
Assembly: mm10 and HSV-1(MN136524)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: trigeminal ganglion

extract_protocol:
Mice were infected ocularly with HSV-1 McKrae and TG were harvested on day 35 PI. Thirty TG from 15 latently infected mice were pooled and washed with cold 1x HBSS six times, then incubated with 2 mg/ml collagenase D at 37oC degree for 1 hr to generate single cells. Dead cells were removed using a dead cell removal kit from STEMCELL (Seattle, WA, USA) according to the company protocol. CD45 positive cells were isolated using a mouse CD45 positive cell selection kit from STEMCELL according to company protocols. Isolated CD45 positive cells were mixed back with the original single cell suspension at a 1:1 ratio and used for single cell sequencing library preparation.
Single-cell RNAseq libraries were prepared according to the Single Cell 3′ v3.1 Reagent Kits User Guide (10x Genomics, Pleasanton, California). Cell suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-RT was performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA). GEMs were then harvested, and the cDNA was amplified and cleaned up using a SPRIselect Reagent Kit (Beckman Coulter, Brea, CA). Indexed sequencing libraries were constructed using a Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using a Collibri Library Quantification Kit (Thermo Fisher Scientific).

value: mixed

value: trigeminal ganglion

value: 6-8 weeks old


title: P27RE_2

source_name: Sorafenib-resistant organoid of patient 1, replicate 2


title: Infected, replicate 1, scRNAseq

description: 10x Genomics


title: Young1-166


title: P27RE_1

source_name: Sorafenib-resistant organoid of patient 1, replicate 1


title: DC3_228_HU_BIS36_A_SEVERE

source_name: Severe


title: DC3_231_HU_BIS38_B_SEVERE


title: Uninfected, scRNAseq

description: 10x Genomics


title: DC3_227_HU_BIS35_A_MILD

source_name: Mild


title: Young1-171


title: orgP10_2

source_name: Sorafenib-sensitive organoid of patient 1, replicate 2


title: Young1-167


title: P29_3

source_name: Sorafenib-sensitive organoid of patient 2, replicate 3


title: Young1-165


title: DC3_226_HU_BIS37_B_MILD


title: orgP10_3

source_name: Sorafenib-sensitive organoid of patient 1, replicate 3


title: Young1-163


title: Young1-164


title: DC3_225_HU_BIS36_B_MILD


title: RNA_P13RT

description: P13, recurrent

source_name: tumor

extract_protocol:
Samples were treated with 1mL TRIzol reagent according to manufacturer's instructions. Nanodrop ND-1000 was used for RNA density/purity detection. Agilent BioAnalyzer 2100 was used for RNA quality control. rRNA depletion was conducted before RNA-seq library preparation using TruSeq Stranded Total RNA Library Prep Kit.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: tumor


title: RNA_P13RN

description: P13, recurrent

source_name: Adjacent tissue

value: Adjacent tissue


title: F. nucleatum 2

city: Chengdu

first: Keyi

last: Zhang

address: No. 14, section 3, Renmin South Road

institute: West China Hospital of Stomatology, Sichuan University

data_processing:
Reads with adaptor were removed using Cutadpt v 1.10 .
Reads containing N (N indicates that base information cannot be determined) greater than 5% were removed using Cutadpt v 1.10.
Low-quality reads (the base number of quality value Q≤10 accounts for more than 20% of the entire read) were removed using Cutadpt v 1.10.
Cutadpt v 1.10 was used to count the original sequencing amount, effective sequencing amount, Q20, Q30, GC content, and comprehensive evaluation.
The reference genome comparison of the preprocessed valid data was performed using hisat v 2.0.4, and the gene position information specified in the genome annotation file gtf was counted separately, including: 1) Sequencing data and reference genome comparison Reads statistics; 2) Chromosome density distribution compared with reference genome by sequencing data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...

source_name: aorta

growth_protocol: Twenty-six 6-week-old C57/BL6 ApoE-/- mice were raised in a specific pathogen-free controlled animal laboratory under 12-h dark/light photophase and fed adaptively for 1 week. After that, 0.2mg/L trimethoprim and 1.0mg/L sulfa were added to the drinking water for 1 week, and the bilateral first molars were rubbed with chlorhexidine mouthwash.

extract_protocol:
The experimental procedures were performed in accordance with the standard test procedures provided by Illumina. Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Strain-specific library (mRNA-lncRNA-circRNA) was constructed by the method of removing rRNA depletion.

treatment_protocol: In the F.nucleatum group, 0.1ml F.nucleatum suspension was applied to the first molar in the mouth to establish the periodontitis model every alternate day for 12 weeks, while the control group was given 0.5ml 2%CMC.

value: aorta

tag: treatment

value: F. nucleatum-infected


title: Control 3

value: non-infected


title: F. nucleatum 1


title: F. nucleatum 3


title: DC3_224_HU_BIS34_A_MILD

extract_protocol: DNA was extracted from peripheral blood lymphocytes of probands and their parents (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).

value: M

value: Mild


title: Control 2


title: Young1-161

first: Claus

last: Nerlov

institute: Weatheral Institute of Molecular Medicine

source_name: Bone marrow

value: Young-HSC


title: DC3_223_HU_BIS35_B_MILD


title: RNA_P12RT

description: P12, recurrent


title: DC3_221_HU_BIS34_B_SEVERE

value: Severe


title: Young1-160


title: Control 1


title: RNA_P12RN

description: P12, recurrent


title: DC3_219_HU_BIS33_B_MILD


title: Young1-159


title: Young1-158


title: RNA_P11RN

description: P11, recurrent


title: RNA_P11RT

description: P11, recurrent


title: DC3_220_HU_BIS33_A_MILD

value: F


title: orgP10_1

source_name: Sorafenib-sensitive organoid of patient 1, replicate 1

value: sensitive


title: DC3_218_HU_BIS32_A_SEVERE


title: Young1-162


title: RNA_P10RT

description: P10, recurrent


title: Mpc2 KO GMPs biol rep 2

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

institute: University of Arizona

data_processing:
Reads were mapped and transcript abundances were calculated using Salmon v1.5.1
Differentially expressed genes were quantified with DESeq2 v2.11.40.6
Assembly: Gencode M27 transcriptome
Supplementary files format and content: Salmon generated .tabular.txt files containing TPM values for all transcripts
Supplementary files format and content: DESeq2 generated a .tabular.txt file containing a list of genes differentially regulated between Mpc2 KO and WT granulocyte-macrophage progenitors. Columns from left to right are gene id, mean normalized counts, log2 fold change, SE for log2 fold change, Wald stat, p value, and p value with FDR

source_name: bone marrow

extract_protocol:
NucleoSpin RNA XS (Macherey-Nagel)
SMARTseq V4  (Takara Bio) by Novogene

value: bone marrow

value: granulocyte-macrophage progenitors

value: Mpc2fl/fl; ROSA26 CreER+/-

value: male

value: tamoxifen chow for 2wks then mice were taken down


title: Mpc2 KO GMPs biol rep 3


title: Mpc2 KO GMPs biol rep 5


title: Mpc2 KO GMPs biol rep 4


title: Young1-157

city: Oxford

address: John Radcliffe Hospital, University of Oxford


title: DC3_217_HU_BIS32_B_MILD


title: RNA_P10RN

description: P10, recurrent


title: RNA_P13PT

description: P13, primary


title: RNA-seq_Young_4

data_processing:
RNAseq: Raw reads were trimmed using trimmomatic software and inspected using FastQC
RNAseq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using STAR software.
RNAseq: The featureCounts software was used to count reads on the basis of the RefSeq gene model
Assembly: NCBI37 (mm9)
Supplementary files format and content: Raw count matrices were generated by featureCounts software

extract_protocol:
Bone marrow cells were sorted by FACS and cDNA was generated according to Smart-seq+ protocol
Illumina sequencing libraries were constructed using the Nextera XT DNA Sample Preparation kit according to manufacturer's protocol.


title: Young1-156


title: DC3_215_HU_BIS31_A_MILD

data_processing:
Quality control, pre-processing and generation of β-values matrix were performed by using the RnBeads package (release 2.12.2) package, implemented R environment (version 4.1.3). SNP-enriched probes (139,721 sites), cross-reactive probes (34,264), unreliable measurements (4,369 sites), context-specific (1,180 sites), and on sex chromosomes probes (16,347sites), probes with many missing values (141 sites) were filtered out in the pre-processing step. As an outcome of the filtering procedures, 670,873 CpG sites and 187 samples were retained.
Matrix processed.txt: Normalized (BMIQ Quantile) average beta


title: Mpc2 KO GMPs biol rep 1


title: WT GMPs biol rep 5

value: ROSA26 CreER+/-


title: DC3_212_HU_BIS30_A_MILD


title: DC3_210_HU_BIS31_B_MILD


title: RNA_P13PN

description: P13, primary


title: RNA-seq_Young_3


title: WT GMPs biol rep 4


title: DC3_209_HU_BIS29_A_MILD


title: RNA_P12PT

description: P12, primary

value: tumor


title: RNA-seq_Young_2


title: RNA_P11PT

description: P11, primary


title: WT GMPs biol rep 3


title: RNA_P12PN

description: P12, primary

value: Adjacent tissue


title: WT GMPs biol rep 1


title: DC2_169_AU_BIS28_A_MILD


title: RNA-seq_Old_2

value: Old-HSC


title: WT GMPs biol rep 2


title: RNA_P11PN

description: P11, primary


title: DC2_93_AU_BIS23_A_MILD


title: DC2_143_AU_BIS27_A_MILD


title: RNA-seq_Old_1


title: Young_4

data_processing:
ATAC-seq: Raw reads were trimmed using TrimGalore! software and inspected using FastQC
ATAC-seq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using Bowtie2 software, the resulting SAM files were converted to BAM files using SAMtools
ATAC-seq: Duplicate reads were removed using Picard tools
ATAC-seq: Mitochondrial reads removal and read shift were performed using ATACseqQC R package.
ATAC-seq: Peak calling was perfoemd using MACS2 software and peaks within blacklist regions were filtered out before making the final bed file
Assembly: NCBI37 (mm9)
Supplementary files format and content: Count matrix of reads mapped in HSC open chromatin regoins. Row names indicate the genomic coordinates of open chromatins.

extract_protocol:
Bone marrow cells were sorted by FACS and DNA was generated according to Omni-ATAC-seq protocol
Illumina sequencing libraries were constructed using the Nextera DNA Sample Preparation kit according to manufacturer's protocol.


title: RNA_P10PN

description: P10, primary


title: RNA_P10PT

description: P10, primary


title: Young_3


title: DC2_122_AU_BIS26_A_MILD


title: RNA_P9T


title: RNA-seq_Young_1


title: DC2_115_AU_BIS29_B_MILD


title: RNA-seq_Old_3


title: Young_2


title: RST707-KO2

city: Memphis

first: Liqin

last: Zhu

state: TN

address: 262 Danny Thomas Place

department: Pharmacy and Pharmaceutical Sciences

institute: St. Jude Children’s Research Hospital

data_processing:
kallisto 0.46.1 were used to count the paired-end raw RNA-seq data with parameters: "quant --rf-stranded -i mm10.kidx --plaintext -t 2 --bias ".
gene-based raw counts were extracted from kallisto results by tximport R package as 'tximport("abundance.tsv", type = "kallisto", tx2gene = tx2gene)'
Assembly: mm10
Supplementary files format and content: gene-based raw counts

source_name: Prom1CreERT2; Ptenflx/flx; Tp53flx/flx; Rosa-ZsGreen (PPTR) genetic mouse models generated the liver cancer

growth_protocol: All cell lines were maintained in Dulbecco's Modified Eagle Medium (GIBCO, Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum (GIBCO, Life Technologies) and Penicillin-Streptomycin-Glutamine 100X, at 37°C in 5% CO2

extract_protocol:
Total RNA was extracted by RNeasy Kits (Qiagen, 74106) from replicate samples.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

tag: cell line


title: RST706-KO1

value: Prom1CreERT2; Ptenflx/flx; Tp53flx/flx; Rosa-ZsGreen (PPTR) genetic mouse models generated the liver cancer


title: RST709-KO2


title: DC2_105_AU_BIS28_B_MILD


title: Young_1


title: RNA_P8T


title: RST708-KO2


title: Old_4


title: DC2_123_AU_BIS30_B_MILD


title: Old_3


title: DC2_103_AU_BIS25_A_SEVERE


title: RNA_P8N


title: RST704-KO1


title: RST703-WT

value: WT


title: RNA_P7N


title: RNA_P7T


title: Old_2


title: Old_1


title: DC2_102_AU_BIS24_A_MILD

value: M


title: RST702-WT


title: DC1_66_AU_BIS27_B_MILD

value: Mild


title: DC1_67_AU_BIS22_A_MILD


title: RNA_P9N


title: RST701-WT


title: RST705-KO1


title: RNA_P6T


title: RNA_P6N


title: RNAseq-mm-Inv1-FLHL-E115-Rep2-L19727

description: RNAseq-mm9-Inv1-FLHL-E115-Rep1Rep2Merged-L19726-L19727.bw

data_processing:
Paired-end RNA-seq reads were mapped using the STAR mapper (splice junctions based on RefSeq; options: --alignIntronMin 20 –alignIntronMax 500000 – outFilterMismatchNmax 10).
Reads per gene were counted as described previously in Lupiáñez et al. Cell 2016, and used for differential expression analysis with the DEseq2 package.
mm9
Assembly: Mm9

source_name: Embryonic Forelimb Hindlimb

extract_protocol:
Total RNAs were extracted using the Rneasy Mini Kit (QIAGEN) according to the manufacturer's instructions.
Samples were poly-A enriched and sequenced using Illumina technology following standard protocols.

treatment_protocol: Limbs from E11.5 mouse embryos were dissected in PBS, snap frozen and stored at -80° C.

value: Embryonic Forelimb Hindlimb

value: Mutant_homozygous inversion

tag: embryonic stage

tag: strain/background

value: G4 ESC


title: DC1_65_AU_BIS26_B_SEVERE

value: Severe


title: Runx3_4


title: RNAseq-mm-Inv1-FLHL-E115-Rep1-L19726


title: RNA_P5T


title: RNAseq-mm-Dup-FLHL-E115-Rep2-L20035

description: RNAseq-mm9-Dup-FLHL-E115-Rep1Rep2Merged-L20034-L20035.bw

value: Mutant_Homozygous duplication


title: Runx3_1


title: DC1_63_AU_BIS25_B_MILD


title: RNAseq-mm-Dup-FLHL-E115-Rep1-L20034


title: DC1_62_AU_BIS24_B_SEVERE


title: EV_4

value: Control


title: RNA_P4T


title: RNAseq-mm9-Wt-FLHL-E115-Rep2-L19725

description: RNAseq-mm9-Wt-FLHL-E115-Rep1Rep2Merged-L19724-L19725.bw

value: Wild type


title: EV_3


title: RNA_P4N


title: EV_2


title: CaptureHiC-mm-Inv1-het-FLHL-E115_Rep3-L27265

description: CaptureHiC-mm9-Inv-het-FLHL-E115-Rep1Rep2Rep3-50bp-merged-MAPQ30-KR-5kb-L27263-L27264-L27265.WashU.txt

data_processing:
In a pre-processing step, the reads in fastq files were trimmed to 50 bp, if necessary, to obtain the same initial read length for all samples. Afterwards, mapping, filtering and deduplication of paired-end sequencing data was performed using the HiCUP pipeline v0.8.1(no size selection, Nofill: 1, Format: Sanger). The pipeline was set up with Bowtie2 v2.4.2 for mapping short reads to reference genome mm9. For merging biological replicates, the final bam files produced by the HiCUP pipeline were joined.
Juicer tools v1.19.02 was used to generate binned contact maps and to normalize maps by Knights and Ruiz (KR) matrix balancing.
For the generation of cHi-C maps, only read-pairs referring to the region of interest (chr19:44,440,001-46,400,000) and with MAPQ≥30 were considered.
In order to explicitly consider the duplicated region in the Dup mutant, we created cHi-C maps by applying the copy-number variation effects (LOIC)-normalization44 (python package iced v.0.5.345) to raw count maps.
Assembly: mm9

extract_protocol:
Forelimb and hindlilmb buds were micro-dissected from E11.5 mouse embryos in 1xPBS, a single cell suspension was made using Trypsin, then samples were crosslinked using 2% PFA, snap frozen, and stored at -80 °C.
Snap frozen samples were first digested using DpnII, religated using the T4 DNA ligase (Thermo Fisher Scientific). The chimeric chromatin products were then decrosslinked overnight. RNase A treated chromatin was then precipitated.The precipiated chromatin was sheared using a Covaris sonicator (duty cycle: 10%; intensity: 5; cycles per burst: 200; time: 6 cycles of 60 s each; set mode: frequency sweeping; temperature: 4–7 °C). Adaptors were added to the sheared DNA and amplified according to the manufacturer’s instructions for Illumina sequencing (Agilent). The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing following the manufacturer’s instructions (Agilent).
Capture Hi-C

value: Mutant_heterozygous inversion


title: RNAseq-mm9-Wt-FLHL-E115-Rep1-L19724


title: RNA_P3T


title: EV_1


title: RNA_P3N


title: CaptureHiC-mm-Inv1-het-FLHL-E115_Rep2-L27264


title: DC1_58_AU_BIS19_A_MILD


title: Runx3_3


title: DC1_59_AU_BIS22_B_MILD


title: DC1_64_AU_BIS21_A_MILD

value: F


title: CaptureHiC-mm-Inv1-het-FLHL-E115_Rep1-L27263


title: RNA_P2N


title: hematopoietic progenitors, KO9aa, Rep4

city: MADISON

first: Siqi

last: Shen

state: WI

address: 425 Henry Mall

institute: University of Wisconsin - Madison

description: 9aa-Ins-expressing mutant

data_processing:
ATAC-seq fragments were trimmed to remove adapter sequences using Trim Galore! V0.4.1 with the “—nextera” parameter and aligned to mouse (mm10) genome assembly using Bowtie2 (version 2.2.5) with GENCODE basic gene annotations (version M22)
Alignment files were converted to BAM format and Picard (version 2.26.0) was used to sort the aligned ATAC-seq files and remove duplicates
Peak calling for four biological replicates of each condition was achieved by MACS2 with the parameter –nolambda and others were set as default. To ensure that peaks are consistent in each condition, we use IDR (Irreproducible Discovery Rate) to compare peaks from pairs of replicates with --idr-threshold 0.05.
Assembly: mm10
Supplementary files format and content: narrowPeak: provide called peaks of signal enrichment based on pooled, normalized (interpreted) data. It is a BED6+4 format.

source_name: Fetal liver

growth_protocol: Cells were cultured in expansion media containing β-estradiol

extract_protocol:
From FACS isolated cells, nuclei was collected by centrifugation, resuspended, and incubated in tagmentation mix (10 mM TAPS, 5 mM MgCl2, pH 8.0 and 1.75 ul Tn5) at 37°C for 30 min. Tagmentation reactions were terminated by adding 10 µL 0.2% SDS followed by incubation at 55°C for 7 min. Adapter-tagged DNA was purified using MinElute PCR Purification kit (Qiagen) and amplified using KAPA HiFi Hotstart PCR kit (KAPA).
ATAC-seq libraries were sequenced on an Illumina NextSeq500 system using the 75-bp high-output sequencing kit

treatment_protocol: Cells were incubated with retroviruses for 3 d and washed and resuspended in PBS with 2% FBS prior to FACS isolation.

value: Fetal liver

value: Hematopoietic progenitors

value: Infected with 9aa-Ins vector


title: DC1_56_AU_BIS18_A_MILD


title: RNA_P2T

value: tumor


title: RNA_P5N

value: Adjacent tissue


title: hematopoietic progenitors, KO9aa, Rep3

description: 9aa-Ins-expressing mutant


title: DC1_54_AU_BIS17_A_SEVERE


title: CaptureHiC-mm-Inv2-FLHL-E115-tecRep3-L18801


title: RNA_P1T


title: DC1_53_AU_BIS21_B_MILD


title: DC1_60_AU_BIS20_A_MILD


title: DC1_61_AU_BIS23_B_MILD


title: CaptureHiC-mm-Inv2-FLHL-E115-Rep3-L18801


title: RNA_P1N


title: hematopoietic progenitors, KO9aa, Rep1

description: 9aa-Ins-expressing mutant


title: hematopoietic progenitors, KOWG, Rep4

description: GATA2-expressing mutant

value: Infected with GATA2 vector


title: CaptureHiC-mm-Inv1-FLHL-E115-Rep3-L18800


title: DC1_51_AU_BIS19_B_MILD

value: M


title: CaptureHiC-mm-Inv1-FLHL-E115-Rep2-L18799


title: hematopoietic progenitors, KOWG, Rep3

description: GATA2-expressing mutant


title: circRNA_P13RT

description: P13, recurrent

data_processing:
Real Time Analysis (RTA) and CASAVA v1.8 for base-calling
CIRI software was applied to identify the circRNAs. Reads spanning over back-splicing junction sites were collected to quantify all these circRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: circRNA_data.txt.gz is a tab-seperated file for circRNA read counts. circRNA_sequence.fa.gz is fasta-format file for assembled circRNA sequences.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
Total RNA was extracted from tissues and then the sequencing libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, San Diego, CA) and Ribonuclease R (Lucigen, Middleton, WI) according to the manufacturer’s instructions.


title: circRNA_P13RN

description: P13, recurrent


title: circRNA_P12RT

description: P12, recurrent


title: CaptureHiC-mm-Inv1-FLHL-E115-tecRep1-L17927


title: CaptureHiC-mm-Dup-FLHL-E115-tecRep3-L20288

description:
CaptureHiC-mm9-Dup-FLHL-E115-Rep1Rep2Rep3-50bp-merged-MAPQ30-LOIC-5kb-L20286-L20287-L20288.WashU.txt
CaptureHiC-mm9-Dup-FLHL-E115-Rep1Rep2Rep3merged-vs-Wt-FLHL-E115-Rep1Rep2Rep3merged-MAPQ30-KR-5kb-diagNorm.WashU.txt
Virtual4C-mm9-Dup-merged-Lbx1-5kb.bedgraph
Virtual4C-mm9-Dup-merged-Btrc-5kb.bedgraph
Virtual4C-mm9-Dup-merged-Fgf8-5kb.bedgraph


title: DC1_50_AU_BIS16_A_MILD

value: Mild


title: hematopoietic progenitors, KOWG, Rep2

description: GATA2-expressing mutant


title: DC1_49_AU_BIS18_B_MILD


title: hematopoietic progenitors, KOWG, Rep1

description: GATA2-expressing mutant


title: CaptureHiC-mm-Dup-FLHL-E115-Rep3-L20288


title: circRNA_P11RT

description: P11, recurrent


title: hematopoietic progenitors, WTEmp, Rep4

description: wild type

value: Infected with empty vector


title: CaptureHiC-mm-Dup-FLHL-E115-Rep2-L20287


title: hematopoietic progenitors, KO9aa, Rep2

description: 9aa-Ins-expressing mutant


title: DC1_48_AU_BIS15_A_MILD


title: circRNA_P12RN

description: P12, recurrent


title: hematopoietic progenitors, WTEmp, Rep3

description: wild type


title: DC1_52_AU_BIS20_B_SEVERE


title: DC1_40_AU_BIS13_A_SEVERE


title: DC1_39_AU_BIS16_B_MILD


title: circRNA_P10RT

description: P10, recurrent


title: hematopoietic progenitors, WTEmp, Rep1

description: wild type


title: DC1_47_AU_BIS14_A_MILD


title: CaptureHiC-mm-Dup-FLHL-E115-Rep1-L20286


title: circRNA_P10RN

description: P10, recurrent


title: hematopoietic progenitors, WTEmp, Rep2

description: wild type


title: circRNA_P11RN

description: P11, recurrent


title: circRNA_P13PN

description: P13, primary


title: DC1_38_AU_BIS15_B_MILD


title: hematopoietic progenitors, KOEmp, Rep2

description: mutant


title: D_15_3

city: Sacramento

first: Guiyan

address: 4645 2nd Ave

department: Department of Medical Pathology and Laboratory Medicine

institute: University of California at Davis

data_processing:
The NovaSeq 6000 uses RTA3 for its base calling. The version running on our machines is v3.4.4.
RNA-Seq data was analyzed using a Salmon-tximport-DESeq2 pipeline. The pair-ended reads (FASTQ format) were mapped to the reference mouse genome assembly (GRCm39, GENCODE release 27) and quantified with Salmon.
Gene-level counts were imported with tximport and differential expression analysis was performed with DESeq2 (version 1.18) with the corrected p value < 0.05 and fold change > 2.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include normalized read count values for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted using TRIzol Reagent. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using using NEBNext Ultra II non-directional RNA Library Prep kit (New England Biolabs, Inc., Ipswich, MA, USA). Library quality and concentration were assessed with Labchip and qPCR.

value: Liver

value: Male

value: Bulk liver

value: FXR KO

value: Western diet

tag: timepoint


title: D_15_4


title: hematopoietic progenitors, KOEmp, Rep1

description: mutant


title: hematopoietic progenitors, KOEmp, Rep4

description: mutant


title: D_15_2


title: DC1_34_AU_BIS12_A_MILD


title: DC1_31_AU_BIS12_B_MILD


title: CITE-seq WT replicate 4

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

institute: Canada's Michael Smith Genome Sciences Centre

data_processing:
library strategy: CITE-seq
Illumina RTA software used for basecalling.
Cellranger count was ran using cellranger version 3.0.2 and cellranger mm10 reference
Genome_build: mm10
Supplementary_files_format_and_content: Features_count_matrix.csv.gz contains a matrix where rows are genes or ADT, columns are cells (with cell information in the cell_annotation_matrix.csv), and values are counts for the given gene in the given cell. cell_annotation_matrix.csv contains a data frame with annotations (i.e. cell barcode, cell type, genotype, etc.) for each cell

source_name: E10.5 AGM

extract_protocol:
Embryos were dissected at E10.5 and AGM were processed for flow cytometry. Cells were stained with CD31-BV605 and the following CITE-seq antibodies at a final concentration of 0.2 ug/100 µL: TotalSeq™-A0012 anti-mouse CD117 (BioLegend #105843), TotalSeq™-A0443 anti-mouse CD41 (BioLegend #133937), TotalSeq™-A0110 anti-mouse CD43 (BioLegend #143211), TotalSeq™-A0157 anti-mouse CD45.2 (BioLegend #109853), TotalSeq™-A0191 anti-mouse/rat/human CD27 (BioLegend #124235), and TotalSeq™-A0073 anti-mouse/human CD44 (BioLegend #103045). Cells from 2-5 embryos were pooled for any given samples based on genotype
Libraries were prepared using the 10X Chromium Single Cell 3’ Reagent v3 chemistry kit as per the standard protocol from 10X Genomics (Pleasanton, California)

tag: developmental stage

value: WT


title: circRNA_P12PN

description: P12, primary


title: circRNA_P11PT

description: P11, primary


title: DC1_28_AU_BIS11_A_MILD


title: D_15_1


title: CITE-seq WT replicate 3


title: circRNA_P11PN

description: P11, primary


title: CITE-seq WT replicate 2


title: circRNA_P10PT

description: P10, primary


title: C_15_4

value: Control diet


title: DC1_27_AU_BIS10_A_MILD


title: DC1_37_AU_BIS14_B_MILD

value: F


title: hematopoietic progenitors, KOEmp, Rep3

description: mutant

value: Fetal liver


title: circRNA_P13PT

description: P13, primary


title: circRNA_P12PT

description: P12, primary


title: PLT-3, RNA-Seq

data_processing:
RNAseq: Raw reads were trimmed using trimmomatic software and inspected using FastQC
RNAseq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using STAR software.
RNAseq: The featureCounts software was used to count reads on the basis of the RefSeq gene model
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: Raw count matrices were generated by featureCounts software

value: PLT-HSC


title: C_15_3


title: DC1_24_AU_BIS11_B_MILD


title: CITE-seq WT replicate 1


title: DC1_32_AU_BIS13_B_MILD


title: circRNA_P10PN

description: P10, primary


title: C_15_2


title: PLT-2, RNA-Seq


title: DC1_23_AU_BIS10_B_MILD


title: C_15_1


title: circRNA_P9N


title: circRNA_P8T


title: B_15_4

value: Wild-type


title: PLT-1, RNA-Seq


title: PEM-6, RNA-Seq

value: PEM-HSC


title: B_15_3


title: DC1_20_AU_BIS09_B_MILD


title: DC1_21_AU_BIS08_A_MILD


title: circRNA_P8N

value: Adjacent tissue


title: B_15_2


title: DC1_17_AU_BIS07_A_SEVERE

value: Severe


title: PEM-5, RNA-Seq


title: B_15_1


title: DC1_16_AU_BIS06_A_MILD


title: circRNA_P7T

value: tumor


title: circRNA_P7N


title: PEM-4, RNA-Seq


title: A_15_5


title: DC1_15_AU_BIS08_B_SEVERE

value: M


title: circRNA_P9T


title: DC1_22_AU_BIS09_A_MILD

value: Mild


title: circRNA_P6T


title: PEM-2, RNA-Seq


title: circRNA_P6N


title: A_15_3

value: Liver


title: PEM-1, RNA-Seq


title: DC1_13_AU_BIS05_A_SEVERE


title: A_15_2

value: Male


title: circRNA_P5T


title: DC1_12_AU_BIS04_A_MILD


title: circRNA_P5N


title: MULTI-4, RNA-Seq

value: MUL-HSC


title: circRNA_P4T


title: D_10_7

value: Bulk liver

value: FXR KO


title: DC1_11_AU_BIS06_B_MILD


title: MULTI-3, RNA-Seq


title: D_10_D6

value: Western diet


title: DC1_10_AU_BIS05_B_SEVERE


title: MULTI-1, RNA-Seq


title: D_10_D5


title: DC1_08_AU_BIS04_B_SEVERE


title: circRNA_P4N


title: MULTI-2, RNA-Seq


title: DC1_14_AU_BIS07_B_MILD


title: PEM-3, RNA-Seq


title: circRNA_P3T


title: DC1_07_AU_BIS03_B_MILD


title: circRNA_P3N


title: DC1_06_AU_BIS03_A_SEVERE


title: C_10_C6

value: Control diet


title: DC1_04_AU_BIS02_A_SEVERE


title: ProB_3_S15

data_processing:
ATAC-seq: Raw reads were trimmed using TrimGalore! software and inspected using FastQC
ATAC-seq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using Bowtie2 software, the resulting SAM files were converted to BAM files using SAMtools
ATAC-seq: Duplicate reads were removed using Picard tools
ATAC-seq: Mitochondrial reads removal and read shift were performed using ATACseqQC R package.
ATAC-seq: Peak calling was perfoemd using MACS2 software and peaks within blacklist regions were filtered out before making the final bed file
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: Count matrix of reads mapped in progenitors' open chromatin regoins. Row names indicate the genomic coordinates of open chromatins.

extract_protocol:
Bone marrow cells were sorted by FACS and cDNA was generated according to Omni-ATAC-seq protocol
Illumina sequencing libraries were constructed using the Nextera DNA Sample Preparation kit according to manufacturer's protocol.

value: ProB


title: ProB_2_S14


title: D_10_2


title: ProB_1_S13


title: A_15_1


title: C_10_C5


title: circRNA_P2N


title: C_10_C4


title: DC1_03_AU_BIS02_B_MILD

value: F


title: MkP_3_S3

value: MkP


title: C_10_C3


title: circRNA_P1N


title: B_10_B6

value: Wild-type


title: MkP_1_S1


title: B_10_B5


title: DC1_01_AU_BIS01_B_MILD


title: GMP_Gata1_neg_3_S9

value: NMP


title: GMP_Gata1_neg_2_S8


title: B_10_B4


title: circRNA_P2T


title: B_10_B3


title: DN3_3_S18

value: Lin-CD4-CD8-CD44- CD25+


title: GMP_Gata1_neg_1_S7


title: Exocrine body of blank control group 2 [M_M2_NP2]

first: Shuang

last: Li

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

data_processing:
Remove 3 'connector and garbage sequence: obtain clean data
Length screening: the sequence with 18-25nt base length reserved for plants and 18-26nt base length reserved for animals
Comparison and analysis of various RNA databases: compare the remaining sequence (excluding miRNA) mRNA, RFam and Repbase databases, and filter them
MiRNA identification: obtain effective data and compare the precursor and genome for miRNA identification

extract_protocol:
The small RNA sequencing library was prepared using TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA) kit.
After the preparation of the library, the constructed library was sequenced using Illumina Hiseq2000/2500, with a single-ended reading length of 1X50bp.

value: bone marrow

value: M2 type macrophages

value: Exocrine body of blank control group 2

value: PBS for 48 hours

tag: molecule subtype

value: miRNA


title: Exocrine body of blank control group 3 [M_M2_NP3]

value: Exocrine body of blank control group 3


title: Exocrine body of blank control group 1 [M_M2_NP1]

value: Exocrine body of blank control group 1


title: skin wound tissue, pH8.4_GelMA hydrogel_bFGF, day4, biol rep 1

city: Whenzhou

first: Ruyi

last: Fan

address: Yongzhong

institute: Wenzhou Institute, University of Chinese Academy of Sciences

description:
Sample 19
pH8.4_GelMA hydrogel_bFGF 1

data_processing:
CLC Genomics Workbenchv 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 NCBI_GRCm39 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: NCBI_GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus

source_name: skin

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: A skin biopsy punch was used to make a circular full-thickness skin wound with a diameter of 8mm on both sides of the dorsal skin. The wounds were treated with different hydrogel scaffolds for 4 days.

value: skin

value: WT

value: Wounding

tag: group

value: pH8.4_GelMA hydrogel_bFGF, day4


title: skin wound tissue, pH8.4_GelMA hydrogel_bFGF, day4, biol rep 2

description:
Sample 20
pH8.4_GelMA hydrogel_bFGF 2


title: skin wound tissue, pH7.4_GelMA hydrogel_bFGF, day4, biol rep 3

description:
Sample 18
pH7.4_GelMA hydrogel_bFGF 3

value: pH7.4_GelMA hydrogel_bFGF, day4


title: Exocrine body of shear stress group 3 [M_M2_AP3]

value: Exocrine body of shear stress group 3

value: 48 hours under shear force


title: skin wound tissue, pH7.4_GelMA hydrogel_bFGF, day4, biol rep 2

description:
Sample 17
pH7.4_GelMA hydrogel_bFGF 2


title: DC1_02_AU_BIS01_A_MILD

first: Luciano

last: Calzari

institute: IRCCS Istituto Auxologico Italiano

value: M

value: Mild


title: Exocrine body of shear stress group 2 [M_M2_AP2]

value: Exocrine body of shear stress group 2


title: DN3_2_S17

value: Lin-CD4-CD8-CD44- CD25+


title: A_10_3

value: Liver

value: Male

value: Bulk liver

value: Wild-type

value: Control diet


title: A_10_5


title: DN3_1_S16


title: A_10_19


title: skin wound tissue, pH7.4_GelMA hydrogel_bFGF, day4, biol rep 1

description:
Sample 16
pH7.4_GelMA hydrogel_bFGF 1


title: skin wound tissue, pH6.4_GelMA hydrogel_bFGF, day4, biol rep 3

description:
Sample 15
pH6.4_GelMA hydrogel_bFGF 3

value: pH6.4_GelMA hydrogel_bFGF, day4


title: skin wound tissue, pH8.4_GelMA hydrogel_bFGF, day4, biol rep 3

description:
Sample 21
pH8.4_GelMA hydrogel_bFGF 3

value: skin


title: Control_EC_rep3

data_processing:
Illumina RTA 2.7.7 software used for basecalling.
RNA-Seq reads were aligned to the mm10 genome assembly using star version 2.5.2b
Genome_build: mm10
Supplementary_files_format_and_content: meis1_oe_gene_counts.txt contains a matrix where each row represents a gene, columns represent the different samples, and values are count

source_name: primary aortic endothelial cells

growth_protocol: 100,000 primary endothelial cells were plated per well of a 6-well plate precoated with Gelatin-Based Coating Solution (Cell Biologics) 24h prior transduction with Meis1-OE vector or YFP-CTRL. Transduction was stopped after 48h by complete media change and cells were FACS at 72h to select for incorporation of the vector. Transduced endothelial cells (YFP+CD31+VEC+) were re-plated in a 6-well plate, expanded to confluency, and harvested for RNA.

extract_protocol: Total RNA was extracted from 300,000 cells using TRIzol reagent (Invitrogen) and between 300-400 ng of RNA was sent for RNA-seq

value: Adult

value: WT

tag: transduction

value: control vector


title: CFU-E_3_S6

value: CFU-E


title: skin wound tissue, pH6.4_GelMA hydrogel_bFGF, day4, biol rep 2

description:
Sample 14
pH6.4_GelMA hydrogel_bFGF 2

tag: tissue

value: Wounding


title: circRNA_P1T

value: tumor


title: D_5_4

tag: Sex

value: FXR KO

value: Western diet


title: CFU-E_2_S5


title: skin wound tissue, pH6.4_GelMA hydrogel_bFGF, day4, biol rep 1

description:
Sample 13
pH6.4_GelMA hydrogel_bFGF 1


title: Control_EC_rep2


title: CFU-E_1_S4


title: D_5_3


title: Control_EC_rep1


title: Meis1-overexpressing_EC_rep3

value: overexpressed Meis1


title: skin wound tissue, pH8.4_GelMA hydrogel_aFGF, day4, biol rep 3

description:
Sample 12
pH8.4_GelMA hydrogel_aFGF 3

value: pH8.4_GelMA hydrogel_aFGF, day4


title: skin wound tissue, pH8.4_GelMA hydrogel_aFGF, day4, biol rep 2

description:
Sample 11
pH8.4_GelMA hydrogel_aFGF 2


title: MPP2_Gata1pos_4_S4

data_processing:
ATAC-seq: Raw reads were trimmed using TrimGalore! software and inspected using FastQC
ATAC-seq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using Bowtie2 software, the resulting SAM files were converted to BAM files using SAMtools
ATAC-seq: Duplicate reads were removed using Picard tools
ATAC-seq: Mitochondrial reads removal and read shift were performed using ATACseqQC R package.
ATAC-seq: Peak calling was perfoemd using MACS2 software and peaks within blacklist regions were filtered out before making the final bed file
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: Count matrix of reads mapped in MPP2 open chromatin regoins. Row names indicate the genomic coordinates of open chromatins.

value: Vwf-Gata1+ MPP2


title: MPP2_Gata1pos_3_S3


title: Meis1-overexpressing_EC_rep2


title: D_5_1

value: Liver

value: Male


title: D_5_2

value: Bulk liver


title: MkP_2_S2

value: MkP


title: Exocrine body of shear stress group 1 [M_M2_AP1]

value: bone marrow

value: M2 type macrophages

value: Exocrine body of shear stress group 1

value: 48 hours under shear force

value: miRNA


title: MPP2_Gata1pos_2_S2


title: skin wound tissue, pH8.4_GelMA hydrogel_aFGF, day4, biol rep 1

description:
Sample 10
pH8.4_GelMA hydrogel_aFGF 1

value: skin

value: WT


title: C_5_4

value: Control diet


title: C_5_3

value: FXR KO


title: A_10_2

value: Wild-type


title: skin wound tissue, pH7.4_GelMA hydrogel_aFGF, day4, biol rep 3

description:
Sample 9
pH7.4_GelMA hydrogel_aFGF 3

value: Wounding

value: pH7.4_GelMA hydrogel_aFGF, day4


title: C_5_2


title: skin wound tissue, pH7.4_GelMA hydrogel_aFGF, day4, biol rep 2

description:
Sample 8
pH7.4_GelMA hydrogel_aFGF 2


title: skin wound tissue, pH7.4_GelMA hydrogel_aFGF, day4, biol rep 1

description:
Sample 7
pH7.4_GelMA hydrogel_aFGF 1


title: MPP2_DP_3_S7

value: Vwf+Gata1+ MPP2


title: MPP2_DP_4_S8


title: C_5_1

value: Liver


title: HG3

city: Wuxi

first: Jun

last: Qiang

address: 9 Shanshi East road

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

description: The acute experimental group reduced the dissolved oxygen to (1. 02 ± 0. 10) mg · L- within 32 minutes

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 21.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test, Chi-squared nXn test, Student t test, or ANOVA based on the experiments design. The significance threshold was set to be 0.01 and 0.05 in each test.
Genome_build: http://asia.ensembl.org/Oreochromis_niloticus/Info/Index
Supplementary_files_format_and_content: excel,expression profiles

organism: Oreochromis niloticus

source_name: Gill tissue

growth_protocol: A total of 90 experimental fish were used for the main acute hypoxic stress experiment. Ninety experimental fish were randomly placed in six tanks (15 fish per tank), three treatment tanks and three 5mg/L control tanks.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Small RNA enrichment was done by excision of the 15 to 50 nt fraction from a polyacrylamide gel. Approximately 1 ug of enriched RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA).
And then we performed the single-end sequencing (36bp or 50bp ) on an Illumina Hiseq 2500 at the LC Sciences  following the vendor's recommended protocol.

treatment_protocol: The DO of the three treatment tanks was rapidly reduced to 96h-LH50 by pumping nitrogen into water from a nitrogen gas cylinder. Real-time reading with a DO meter were used to control the DO in water by adjusting oxygen intake. The sampling time was 96h.

value: the acute experimental group

value: Gill tissue

tag: tag


title: B_5_4

value: Male

value: Bulk liver

value: Western diet


title: MPP2_DP_2_S6

tag: strain


title: skin wound tissue, pH6.4_GelMA hydrogel_aFGF, day4, biol rep 3

description:
Sample 6
pH6.4_GelMA hydrogel_aFGF 3

value: pH6.4_GelMA hydrogel_aFGF, day4


title: HG2

description: The acute experimental group reduced the dissolved oxygen to (1. 02 ± 0. 10) mg · L- within 31 minutes


title: MPP2_DP_1_S5


title: B_5_2


title: HG1

description: The acute experimental group reduced the dissolved oxygen to (1. 02 ± 0. 10) mg · L- within 30 minutes


title: skin wound tissue, pH6.4_GelMA hydrogel_aFGF, day4, biol rep 2

description:
Sample 5
pH6.4_GelMA hydrogel_aFGF 2


title: B_5_3


title: PLT-3

data_processing:
ATAC-seq: Raw reads were trimmed using TrimGalore! software and inspected using FastQC
ATAC-seq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using Bowtie2 software, the resulting SAM files were converted to BAM files using SAMtools
ATAC-seq: Duplicate reads were removed using Picard tools
ATAC-seq: Mitochondrial reads removal and read shift were performed using ATACseqQC R package.
ATAC-seq: Peak calling was perfoemd using MACS2 software and peaks within blacklist regions were filtered out before making the final bed file
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: Count matrix of reads mapped in HSC open chromatin regoins. Row names indicate the genomic coordinates of open chromatins.

value: PLT-HSC


title: CG3

description: The culture conditions of the control group were the same as acclimation condition,

value: the control group


title: PLT-2


title: skin wound tissue, pH6.4_GelMA hydrogel_aFGF, day4, biol rep 1

description:
Sample 4
pH6.4_GelMA hydrogel_aFGF 1

value: skin