title: Single cell ATAC-seq - embryonic tdTomato MPs, Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/tdTomato Embryonic Day 12.5


title: NDT80_IGG_rep3

status: Public on Jul 15 2022

type: SRA

city: Merced

first: Clarissa

middle: Jane

last: Nobile

state: CA

address: 5200 North Lake Rd

department: Molecular and Cell Biology

country: USA

institute: University of California, Merced

description:
NDT80_GFP_bowtie2_sorted_dedup_spikein_normalized_size_filtered_sorted_macs2_fdr_nochrM_peaks_gfp_minus_igg.bed
NDT80_GFP_bowtie2_sorted_dedup_spikein_normalized_size_filtered_sorted_macs2_fdr_treat_pileup_final_fixed_gfp_minus_igg.bw

library_source: genomic

data_processing:
Library strategy: CUT&RUN
FastQ quality check with FastQC version 0.11.9
Adapter trimming with cutadapt version 3.5
Alignment to Candida albicans genome assembly 21 using Bowtie2 version 2.4.4
Remove PCR duplicated reads using MarkDuplicates functino of Picard version 2.26.6
Filter reads less than 20 bp and greater than 120 bp in length using SamTools version 1.14
Subsample reads from GFP or IgG samples based on E. coli read count in each paired sample using SamTools version 1.14
Peaks were called using Macs2 version 2.2.7.1
Genome_build: ASM18296v3
Supplementary_files_format_and_content: BigWig and BedGraph files were generated using from Macs2 version 2.2.7.1 during peak calling step

molecule: genomic DNA

organism: Candida albicans

source_name: Candida albicans in vitro biofilm samples

extract_protocol:
Nuclei isolation using zymolyase. TF-DNA complex were isolated with antibody.
Libraries were prepared using the NEBNextUltra II DNA Library Prepkit. Briefly, DNA was end-repaired and adapter ligated. After a DNA clean-up without size-selection, PCR enrichment of adapter-ligated samples was performed. After a second round of DNA clean-up, libraries are size selected by Polyacrylamide Gel Electrophoresis and cleaned up for sequencing.

tag: cut&run antibody

value: Rabbit IgG negative control antibody (Epicypher:cat# 13-0042)

tag: strain


title: NDT80_IGG_rep2


title: hiPSC, d45, replicate1

city: Mannheim

first: Philipp

last: Koch

state: Deutschland

country: Germany

institute: Hector Institute for Translational Brain Research

library_source: transcriptomic

data_processing:
Sequencing data was run through an RNAseq processing workflow by the Omics IT and Data Management Core Facility, German Cancer Research Center (DKFZ), as detailed in the 'data_processing_readme.txt' Series supplementary file.
Assembly: 1KGRef_PhiX
Supplementary files format and content: featureCounts.tsv: a matrix containing genes (features) as rows, and count information in columns

molecule: total RNA

organism: Homo sapiens

growth_protocol: IPSCs and NPCs were cultured on dishes coated with Geltrex™ (Life Technologies). IPSCs were maintained in DMEM/F12 with glutamine and HEPES (Life Technologies) supplemented with 1% Pen/Strep, 14 ng/ml sodium selenite (Sigma-Aldrich, S5261-10G), 64 µg/ml LAAP (Sigma-Aldrich, A8960-5G), 20 µg/ml insulin (Sigma-Aldrich, 91077C-1G), 2 ng/ml TGF-β1 (Cell Guidance Systems, GFH109), 200 ng/ml FGF-2 (Cell Guidance Systems, GFH146-1000) and 11 µg/ml transferrin (Sigma-Aldrich, T3705-5G). Base medium for NPCs and neurons was DMEM/F12 with glutamine (Life Technologies) containing N2 and B27 supplement (Life Technologies), 1% Pen/Strep, 1x GlutaMAX, 1x NEAA, 800 µg/ml D-glucose. For neural induction, monolayers of iPSCs were cultivated for 8-11 days in NPC base medium supplemented with 500 nM A83-01 (Biomol GmbH, Cay9001799-25), 200 nM LDN193189 (StemCell Technologies, 72148), 2 µM XAV939 (Cell Guidance Systems, SM38-50) and 1 mM cyclopamine (Biomol GmbH, Cay11321-10). NPCs were maintained in neural induction medium without cyclopamine. Neuronal differentiation of NPCs was initiated by switching to neuronal base medium supplemented with 1.8 mM CaCl2, 200 µM ascorbic acid, 1 µM LM22A (Sigma-Aldrich, SML0848-25MG), 1 µM LM22B (Tocris Bioscience, 6037), 2 µM PD-0332991 (Selleck Chemicals, 1116) and 5 µM DAPT (Cell Guidance Systems, SM15-50). The day of this medium change marked day 0 of differentiation. On day 3, cultures were dissociated using TrypLE™ Express (Life Technologies) and re-plated on dishes coated with 0.1 mg/ml poly-L-lysine and 3.75 µg/ml laminin (Sigma-Aldrich, L2020-1MG). Also on day 3, the previous neuronal medium was further supplemented with 3 µM CHIR99021 (Cell Guidance Systems, SM13-50), 10 µM forskolin (Cell Guidance Systems, SM18-100), 300 µM GABA (Sigma-Aldrich, A5835-10G). At day 11, DAPT and GABA and at day 18 CHIR99021 was removed. Subsequently, neurons matured in neuronal base medium containing 1.8 mM CaCl2, 200 µM ascorbic acid, 2 µM PD-0332991, 1 µM LM22A and 1 µM LM22B. All experiments in this study were performed after cultivation of the cells in neuronal base media (without additional additives) for 48 hours.

extract_protocol: RNA was isolated using TriFast™ (VWR, 30-2010) phenol:chloroform extraction.

tag: cell line

tag: cell type

value: hiPSC brain

tag: time point


title: hiPSC, d25, replicate2


title: AII_3

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

country: China

institute: Fujian University of Traditional Chinese Medicine

description: WT mice with 28-day Angiotensin-II (500ng/kg/min) treatment

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: GCRmm38/mm10(UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: renal

extract_protocol:
The renal were dissected and  stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with TRIzol® Reagent (Invitrogen,Carlsbad, CA, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by KAPA Library Quantification Kit (KAPA Biosystem, Wilmington, MA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEB Next rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit  (NEB,Ipswich, MA, USA)for Illumina was used to construct the libraries for sequencing following the manufacturer’s instructions.

tag: tissue

value: renal

tag: genotype

value: WT

tag: treatment 1

value: Angiotensin-II

tag: treatment 2

value: Saline

tag: group

value: AngII


title: WT OGAP-seq rep2

city: Sheffield

first: Sherif

last: El-Khamisy

state: South Yorkshire

address: Firth Court, University of Sheffield, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

description:
ND = No Doxycyclin (WT), PD = Post-doxycyclin (NuMA (TDIF)-KD), In = Input
AP-seq_TSS_TTS_Metagene_Profiles_Matrix.txt
AP-seq_Upstream_Exons_Downstream_Metagene_Profiles_Matrix.txt
AP-seq_Promoter_Counts_Matrix.txt

data_processing:
Data was mapped using BWA 0.7.17-r1188 with parameters -mem -M -k 25
Metagene matrices indicating coverage over the TSS/TTS and gene upstream, exonic, and downstream regions were generated using bam2geneprofile from the CGAT suite of tools with the parameters --reporter = gene, -m = tssprofile/geneprofile --merge-pairs
Counts of reads overlapping promoter regions were determined by creating a window 1000 base pairs upstream and downstream of the TSSs of protein coding genes using bedtools slop on a TSS bed, converting the resulting bed file to a GTF file and running featureCounts (parameters: -t exons -g gene) on the bam files over the promoter gtf
The mapped bam files were converted into bigwig files showing fold change relative to input by first performing narrow peak calling using MACS2 - parameters -g hs -B SPMR with the inputs as the control files. The sample and control lambda (derived from inputs) BEDgraph signal tracks were then compared using MACS2 bdgcomp with the option -m FE in order to generate sample BEDgraph files showing fold change relative to input, which were then converted to bigwigs.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file for visualising fold change in coverage relative to input, TSS/TTS and gene upstream, exonic, and gene downstream region metagene matrices assessing read density over various genomic features and a matrix containing read counts over promoter regions.
Supplementary_files_format_and_content: Read counts over promoter regions matrix
Supplementary_files_format_and_content: Metagene profile matrix for TSS/TTS regions

source_name: Retinal epithelium cell line

extract_protocol:
DNA was extracted from cells using the Qiagen Blood and Tissue Kit
ChIP libraries were prepared for sequencing using standard Illumina protocols

value: Retina

value: wild type


title: hiPSC, d5, replicate2


title: NDT80_IGG_rep1


title: AII_2


title: AII_1


title: hiPSC, d25, replicate1


title: Con_6

description: WT mice with 28-day Saline treatment

value: Control


title: WT_2_mESC_2020815

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

data_processing:
fastq files were obtained, as provided by sequencing facility (functional genomics center zurich)
Adapters were initially trimmed using TrimGalore with arguments “--stringency 3 –illumina”
Next, trimmed reads were polyA-tail-trimmed using TrimGalore with argument “--polyA”
Finally, processed files were mapped and analyzed using snakePipes' RNA-seq pipeline (v2.3.1) with arguments “--libraryType 1 –featureCountOptions ‘--primary’ –mode alignment,alignment-free,deepTolls_qc –sampleSheet mir290_vs_wt.conf”
Genome_build: ENSEMBL GRCm38 v98
Supplementary_files_format_and_content: counts

molecule: polyA RNA

source_name: Embryonic stem cells

growth_protocol: mESCs were cultured in DMEM, 15% serum 100 U/ml LIF, 0.1 mM 2-beta-mercaptoethanol, 1% Pen/Strep on gelatin coated plates.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina on 500ng of RNA

treatment_protocol: mESCs were transfected with one of the siPOOLs (obtained from siTOOLs Biotech GmbH) at a final concentration of 5nM using the Lipofectamine RNAiMax transfection reagent (Invitrogen). Cell were harvested after 36 hours of transfection.

value: 129/Ola background

value: Blastocyst

value: WT mESCs


title: WT OGAP-seq rep1


title: hiPSC, d5, replicate1


title: NDT80_GFP_rep3

value: GFP polyclonal antibody (Takara:cat # 632592)


title: Con_5

description: WT mice with 28-day Saline treatment


title: hiPSC, progenitors, replicate3


title: NuMA (TDIF)-KD H2O2 treated rep2

description:
PD_PH_2.bw
PD_PH_vs_ND_PH.genes.DEA.xls
PD_PH_vs_ND_PH.genes.significant.DEA.xls
ND = No Doxycyclin (WT), PD = Post-doxycyclin (NuMA (TDIF)-KD), NH = No H2O2, PH = Post H2O9

data_processing:
Data was mapped using STAR 2.5 with parameters -outFilterMismatchNmax 2
Differential expression analyses were carried out using DESeq2 after DESeq normalisation. A Benjamini-Hochberg procedure adjusted p-value of 0.05 was taken as the cutoff for differential expression.
The mapped bam files were converted into bigwig files using bam2wiggle from the CGAT suite of tools.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file for visualising RNA coverage and excel spreadsheets detailing p-values, expression levels (FPKM) and log fold-changes for all genes and significantly differentially expressed genes for the relevant comparisons.

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

tag: agent

value: NuMA (TDIF)-KD


title: NDT80_GFP_rep2


title: WT Input rep2


title: NuMA (TDIF)-KD H2O2 treated rep1

description:
PD_PH_1.bw
PD_PH_vs_ND_PH.genes.DEA.xls
PD_PH_vs_ND_PH.genes.significant.DEA.xls
ND = No Doxycyclin (WT), PD = Post-doxycyclin (NuMA (TDIF)-KD), NH = No H2O2, PH = Post H2O8


title: hiPSC, progenitors, replicate2


title: hiPSC, d45, replicate3


title: WT H2O2 treated rep2

description:
ND_PH_2.bw
ND_PH_vs_ND_NH.genes.DEA.xls
ND_PH_vs_ND_NH.genes.significant.DEA.xls
PD_PH_vs_ND_PH.genes.DEA.xls
PD_PH_vs_ND_PH.genes.significant.DEA.xls
ND = No Doxycyclin (WT), PD = Post-doxycyclin (NuMA (TDIF)-KD), NH = No H2O2, PH = Post H2O5


title: NDT80_GFP_rep1


title: Con_2

description: WT mice with 28-day Saline treatment


title: WT H2O2 treated rep1

description:
ND_PH_1.bw
ND_PH_vs_ND_NH.genes.DEA.xls
ND_PH_vs_ND_NH.genes.significant.DEA.xls
PD_PH_vs_ND_PH.genes.DEA.xls
PD_PH_vs_ND_PH.genes.significant.DEA.xls
ND = No Doxycyclin (WT), PD = Post-doxycyclin (NuMA (TDIF)-KD), NH = No H2O2, PH = Post H2O4


title: EFG1_IGG_rep_2

description:
EFG1_GFP_bowtie2_sorted_dedup_spikein_normalized_size_filtered_sorted_macs2_fdr_nochrM_peaks_gfp_minus_igg.bed
EFG1_GFP_bowtie2_sorted_dedup_spikein_normalized_size_filtered_sorted_macs2_fdr_treat_pileup_final_fixed_gfp_minus_igg.bw


title: EFG1_IGG_rep_3


title: WT untreated rep2

description:
ND_NH_2.bw
ND_PH_vs_ND_NH.genes.DEA.xls
ND_PH_vs_ND_NH.genes.significant.DEA.xls
ND = No Doxycyclin (WT), PD = Post-doxycyclin (NuMA (TDIF)-KD), NH = No H2O2, PH = Post H2O3


title: Con_1

description: WT mice with 28-day Saline treatment


title: EFG1_IGG_rep_1


title: WT untreated rep1

description:
ND_NH_1.bw
ND_PH_vs_ND_NH.genes.DEA.xls
ND_PH_vs_ND_NH.genes.significant.DEA.xls
ND = No Doxycyclin (WT), PD = Post-doxycyclin (NuMA (TDIF)-KD), NH = No H2O2, PH = Post H2O2


title: DKO BR3

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

data_processing:
Library strategy: CATCH-seq
Adapter trimming and quality filtering of the sequencing libraries was done using trim galore (0.6.2) (--paired).
The sequencing libraries were mapped against mm10 using Bismark (0.22.3). The mapping was done using the Bowtie 2 (2.4.1) backend in the paired-end mode with the following parameter values: --non_directional.
The counts of converted and unconverted cytosines in CpG context were extracted using bismark_methylation_extractor (--bedGraph --counts)
Genome_build: mm10
Supplementary_files_format_and_content: Coverage tracks produced by bismark_methylation_extractor.

source_name: Thymus

growth_protocol: All mice were bred and maintained under specific pathogen-free conditions at University of North Carolina (UNC) Genetic Medicine building, in a facility managed by the Division of Comparative Medicine at UNC Chapel Hill. The experimental procedures were approved by the UNC Institutional Animal Care and Use Committee.

extract_protocol:
Cells were lysed using Purelink genomic DNA mini kit (invitrogen). DNA was isolated following the manufacturer's instructions and was eluted in 50 ul molecular biology grade water.
A minimum of 1.1 ug of DNA was provided to Biodynami (Huntsville, Alabama) for bisulfite conversion, capture of the murine Zbtb7b locus and upstream region, library preparation and next generation sequencing. Biodynami NGS DNA library prep kit (cat no 30023) was used and methylated adapters were utilized. Bisulfite conversion of genomic DNA was performed with the epitect Bisulfite kit (Qiagen, catalogue number 59104). For the capture of the mm10 chromosome 3: 89,373,714-89,397,292 a Biodynami Custom Capture kit was developed and used.

treatment_protocol: Mice were euthanized by CO2 asphyxiation and thymi were isolated and dissociated to acquire single-cell suspensions. Total thymocytes were depleted of CD24hi cells by staining with biotinylated mouse anti-CD24 (clone:M1/69) purchased from Biolegend. Unwanted cells were depleted by binding to mouse streptavidin magnetic beads (anti-mouse Rapidspheres, cat no 19860, Stemcell Technologies) according to the manufacturer’s instructions. Enriched cells were stained with viability dye (eBioscience) to distinguish live cells from. Cells were stained with aGalactosyl-Ceramide loaded tetramer (conjugated with PE, obtained from NIH tetramer core), TCRb (clone:H57-597) conjugated with PERCP/Cy5.5 (Biolegend), anti-mouse CD4 AF488 (clone:RM4-5), CD8 (clone:53-6.7) conjugated with Brilliant Violet 650 or APC.  For the thymic differentiation related studies, live CD4+, CD8-, TCRb+, tetramer - cells were sorted and used in downstream applications. The purity of the samples after sorting was >98%.

tag: cell subset

tag: treatment

value: bisulfite conversion


title: Con_4

description: WT mice with 28-day Saline treatment


title: TET2CDTET3KO BR1


title: Fusarium solani, Xenorhabdus bovienii, 3days, rep3 [NKXb3]

city: Tianjin

first: Yu

last: Wang

address: Nankai University, Xuefu street, Nankai District

institute: Nankai University

data_processing:
TruSeq PE Cluster Kit v3-cBot-HS (Illumia)
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads fromrawdata.
Index of the reference genome was built using Hisat2 v2.0.5andpaired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Differential expression analysis of two groups was performed using the DESeq2 R package (1.16.1).
We used cluster Profiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: Fusarium_oxysporum_ncbi
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Fusarium solani

source_name: mycelium

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: mycelium

value: Next to Xenorhabdus bovienii, 3days


title: EFG1_GFP_rep_3


title: YY1 ChIP-seq Lin- XistΔ/Δ Rep2

city: Durham

first: Eda

last: Yildirim

state: NC

address: DUMC Box 3709

department: Cell Biology

institute: Duke University School of Medicine

data_processing:
ChIP-seq reads were trimmed using TrimGalore and then aligned to mm10 reference genome by Bowtie2 (v2.3.5.1, --qc-filter --very-sensitive).
Reads with alignment quality lower than 30 or reads aligned to mitochondrial DNA were removed using Samtools (v1.10).
For YY1 ChIP-seq, duplicated reads were removed by MarkDuplicates tool of Picard (v2.0.1; http://broadinstitute.github.io/picard/).
ChIP-seq results of two biological replicates were merged to make bigwig files, metagene profiles and heatmaps using deepTools (v3.5.0) (Ramirez et al., 2016) with CPM normalization method.
For YY1 ChIP-seq, peaks were called using findPeaks (-region -size 500 -minDist 500 -F 0 -L 4 -C 2) program in HOMER (v4.9.1) (Heinz et al., 2010) and consensus YY1 peak sites from all samples were calculated by DiffBind R package (v3.0.13, minOverlap = 2; https://bioconductor.org/packages/DiffBind/).
Genome_build: mm10
Supplementary_files_format_and_content: bed (YY1 peaks called by HOMER) and bigwig (H3K27me3 and H3K4me3 distribution).

source_name: YY1 ChIP-seq Lin- XistΔ/Δ

growth_protocol: Lin- cells were collected by depleting lineage-positive cells from the bone marrow.

extract_protocol:
ChIP experiments were performed as previously described with minor modifications (Kadota and Nagata, 2014). Briefly, to perform H3K27me3 and H3K4me3 ChIP, mouse bone marrow Lin- cells (~3x106) were crosslinked with 1% formaldehyde for 10 min at RT. The reaction was stopped by adding glycine (final concentration, 125 mM) for 5 min at RT. Crosslinked cells were treated with hypotonic buffer (10 mM HEPES-NaOH, pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.2 % NP-40, 1 mM DTT, 1 mM PMSF, 1x protease inhibitor cocktail (Sigma, P8340)) at 4ºC for 10 min and collected in a tube. The cells were lysed in 150 ml of ChIP lysis buffer (50 mM Tris-HCl, pH 7.9, 10 mM EDTA, 1% SDS, 1 mM PMSF, protease inhibitor cocktail (Sigma, P8340)) on ice for 10 min, and sonicated for 35 cycles (30’’ ON + 30’’ OFF) using Diagenode Bioruptor to shear the chromatin to 200-1,000 bp fragments. The lysate was diluted with 9x volumes of ChIP dilution buffer (16.7 mM Tris-HCl, pH 7.9, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 1 mM PMSF). The fragmented chromatin was pre-cleared using 15 ml of pre-washed Protein A/G agarose beads (Thermo Fisher, 20423) for 1 hour at 4ºC. The pre-cleared chromatin fragments were equally separated into two aliquots. Each aliquot was incubated with either 2 ml of anti-H3K27me3 (mAbcam6002; Abcam) or 2 ml of anti-H3K4me3 (ab8580; Abcam) antibodies at 4ºC overnight with rotation, followed by incubation with pre-washed Protein A/G agarose beads (Thermo Scientific, 20423) for 1-2 hours at 4ºC. DNA-protein complexes attached to agarose beads were washed at 4ºC with the following buffers: low salt wash buffer (20 mM Tris-HCl, pH 7.9, 100 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) for 10 min, high salt wash buffer (20 mM Tris-HCl, pH 7.9, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) for 10 min, the LiCl buffer (10 mM Tris-HCl, pH 7.9, 250 mM LiCl, 1% NP-40, 1% deoxycholate acid, 1 mM EDTA) for 10 min, and twice with TE buffer for 5 min. DNA-protein complexes were eluted by incubating the beads in elution buffer (1% SDS, 0.1 M NaHCO3) for 15 min at RT. Reverse crosslinking was performed by incubating samples in 200 mM of NaCl at 65ºC overnight followed by Proteinase K (20 mg/ml) treatment for 2 hrs at 55ºC. DNA was purified using MiniElute PCR purification kit (QIAGEN, 28006). To perform YY1 ChIP, bone marrow Lin- cells (~1.5x106) were crosslinked with 1% formaldehyde for 15 min at RT and the reaction was stopped by adding glycine (final concentration, 125 mM) for 5 min at RT. Crosslinked cells were treated with cell lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40, 1 mM DTT, 1 mM PMSF, 1x protease inhibitor cocktail (Sigma, P8340)) for 10 min at 4ºC. To digest chromatin into <1,000 bp fragments, the pellet was washed twice with MNase reaction buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1 mM CaCl2, 0.2% NP-40, 1 mM DTT, 1 mM PMSF, 1x protease inhibitor cocktail), resuspended in 200 ml of MNase reaction buffer containing 2.5U of MNase (NEB, M0247) and incubated for 10 min at 37ºC. MNase digestion was stopped by adding 20 ml of 0.5M EDTA into the reaction. Nuclear membrane was broken up by sonicating the lysate for 3 cycles (output level 6, 10’’ ON + 20’’ OFF) using Microson ultrasonic cell disruptor (Misonix). Lysate was spun at 21,000xg for 10 min at 4ºC, and the supernatant containing fragmented chromatin was incubated with 2 ml of anti-YY1 antibody (D5D92Z, Cell Signaling, 46395) overnight at 4ºC. DNA-protein complexes were pulled down with addition of 10 ml of pre-washed Protein G Magnetic Beads (Invitrogen, 10003D) and incubation for 1-2 hours at 4ºC. DNA-protein complexes were eluted in elution buffer (1% SDS, 0.1 M NaHCO3) by incubating at 65ºC for 40 min, and reverse crosslinked as described above. All ChIP DNA samples were purified using MinElute PCR purification kit (Qiagen,28006) and quantified using the fluorometric quantitation Qubit 2.0 system (Thermo Fisher Scientific).
ChIP-seq libraries were prepared using KAPA HyperPrep kit (KAPA, 07962347001). Libraries were sequenced on Illumina HiSeq 4000 (single-end; H3K27me3, and H3K4me3 ChIP-seq) and on Illumina NovaSeq 6000 (paired-end; YY1 ChIP-seq).

treatment_protocol: Bones (tibias and femurs) were dissected, and bone marrow (BM) was flushed with 1xPBS supplemented with 2% FBS (2% F/PBS) into a 50-ml tube (Falcon) using a 22.5 gauge needle. Cell suspension was pipetted up and down for several times and filtered through a 70μm cell strainer (Falcon, 352350) to obtain a single-cell suspension. Red blood cells in the cell suspension were lysed by ACK Lysing buffer (Gibco, A10492-01) according to the manufacturer's instructions. All antibodies were from BD Pharmingen unless noted. To label lineage-positive cells, the following antibody cocktail (1:200) containing biotinylated antibodies against CD11b (M1/70), Gr-1 (RB6-8C5), CD3ε (145-2C11), B220 (RA3-6B2), CD8a (53-6.7), CD4 (GK1.5), and TER-119 (TER-119) in combination with BV421-conjugated Streptavidin (BD, 5832259; 1:200) was used.

value: Bone marrow Lin- cells

value: Xist knockout

tag: Sex

value: Female

tag: age

value: 129Sv4/Jae x B6

tag: chip antibody

value: anti-YY1 (Cell Signaling, 46395)


title: EFG1_GFP_rep_2


title: Fusarium solani, Xenorhabdus bovienii, 3days, rep2 [NKXb2]


title: H3K27me3 ChIP-seq WT

description:
Wild type
MEF_WT_H3K27me3_129.bigwig
MEF_WT_H3K27me3_CAST.bigwig

data_processing:
Biological replicates of ChIP-seq data were pooled to maximize sequencing depth.
ChIP-seq reads were aligned to a N-masked mouse reference genome (in which all SNPs between 129S1/SvImJ and CAST/EiJ genome are replaced by “N”).
Reads with low alignment quality (MAPQ < 30) were removed, and the remaining aligned reads were split to 129S1/SvImJ or CAST/EiJ allele using SNPsplit.
Bigwig files were prepared using deepTools without normalization.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig, allele-specific genome track.

source_name: MEF

growth_protocol: Mouse embryonic fibroblasts (MEFs) were cultured in DMEM media containing 10% fetal bovine serum, 10 mM HEPES, 0.1 mM MEM Non-Essential Amino Acids (NEAA), 1% Penicillin/streptomycin and 0.2% 2-Mercaptoethanol.

extract_protocol:
DNA was purified using MiniElute PCR purification kit (QIAGEN, 28006).
ChIP-seq libraries were prepared using KAPA HyperPrep kit (KAPA, 07962347001).

treatment_protocol: ChIP experiments were performed as previously described with minor modifications (Kadota and Nagata, 2014). MEFs (~3x106) were crosslinked with 1% formaldehyde for 10 min (H3K27me3 and H3K27ac ChIP) or 15min (YY1 ChIP) at RT. The reaction was stopped by adding glycine (final concentration, 125 mM) for 5 min at RT. Crosslinked cells were lysed and the chromatin was digested to fragmetns smaller than 1000bp by sonication or MNase treatment. The digested chromatin was incuabted with 2 ul of anti-H3K27me3 (mAbcam6002; Abcam), anti-YY1 (Cell Signaling, 46395) or anti-H3K27ac (Abcam, ab4729) antibody 4ºC overnight with rotation, followed by incubation with pre-washed Protein A/G agarose (Thermo Scientific, 20423) or Protein G magnetic beads (Invitrogen, 10003D) for 1-2 hours at 4ºC. The agarose/beads was sequentially washed with low salt wash buffer (20 mM Tris-HCl, pH 7.9, 100 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) for 10 min, high salt wash buffer (20 mM Tris-HCl, pH 7.9, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) for 10 min, the LiCl buffer (10 mM Tris-HCl, pH 7.9, 250 mM LiCl, 1% NP-40, 1% deoxycholate acid, 1 mM EDTA) for 10 min, and twice with TE buffer for 5 min. DNA-protein complexes were eluted in elution buffer (1% SDS, 0.1 M NaHCO3). Reverse crosslinking was performed by incubating samples in 200 mM of NaCl at 65ºC overnight followed by Proteinase K (20 mg/ml) treatment for 2 hrs at 55ºC.

value: MEF

value: WT

value: 129S1/SvImJ x CAST/EiJ

value: anti-H3K27me3 (Abcam, 6002)


title: hiPSC, d5, replicate3

value: hiPSC brain


title: hiPSC, progenitors, replicate1


title: DKO BR2


title: H3K27me3 ChIP-seq XiΔXist

description:
Xist deletion on Xi
MEF_XistKO_H3K27me3_129.bigwig
MEF_XistKO_H3K27me3_CAST.bigwig

value: Xi[delta]Xist


title: Fusarium solani, Xenorhabdus bovienii, 3days, rep1 [NKXb1]


title: EFG1_GFP_rep_1


title: DKO BR1


title: Con_3

description: WT mice with 28-day Saline treatment

value: renal

value: Saline

value: Control


title: WT BR4

value: wild type

value: bisulfite conversion


title: ATAC-seq LSK- XistΔ/Δ Rep1

data_processing:
ATAC-seq reads were trimmed using TrimGalore and then aligned to mm10 reference genome by Bowtie2 (v2.3.5.1, --qc-filter --very-sensitive)
Reads with alignment quality lower than 30 or reads aligned to mitochondrial DNA were removed using Samtools (v1.10).
ATAC peaks were called using callpeak program (-q 0.01 -B -f BAMPE) in MACS2 (v2.2.7.1) and consensus ATAC peak sites were calculated by DiffBind.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak, ATAC peaks called by MACS2.

source_name: ATAC-seq LSK- XistΔ/Δ

growth_protocol: Bone marrow LSK+ (Lin-SCA-1+c-Kit+) and LSK- (Lin-SCA-1-c-KIT+) were sorted by FACS in 1xPBS.

extract_protocol:
ATAC experiments were performed as previously described with minor modifications (Buenrostro et al., 2015). Briefly, 10,000 bone marrow LSK+ or LSK- cells were lysed in ice-cold lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40) for 5 min and then washed twice with 10mM Tris-HCl, pH 7.4. Following the last wash, 25 ml of extracted nuclei was mixed with 25 ml of 2XTD buffer (66 mM Tris-Ac pH 7.8, 132 mM KAc, 20 mM MgAc, 32% Dimethyl Formamide) containing 1 ml of Tn5 with loaded tagmentation adapters. Transposition reaction mixture was incubated using a thermocycler rotating at 500 rpm for 1 hour at 37°C. Tagmented DNA fragments were purified using MinElute PCR Cleanup Kit (Qiagen, 28206) and amplified for 15 PCR cycles using Q5 polymerase (NEB, M0491). PCR products were run on a gel, and fragments of ~200-800 bp size were isolated and libraries were sequenced on MGI MGISEQ-2000 or Illumina NovaSeq 6000 with paired-end reads.
Libraries were constructed by PCR amplificaiton of tagmented DNA fragments.

treatment_protocol: Bones (tibias and femurs) were dissected, and bone marrow (BM) was flushed with 1xPBS supplemented with 2% FBS (2% F/PBS) into a 50-ml tube (Falcon) using a 22.5 gauge needle. Cell suspension was pipetted up and down for several times and filtered through a 70μm cell strainer (Falcon, 352350) to obtain a single-cell suspension. Red blood cells in the cell suspension were lysed by ACK Lysing buffer (Gibco, A10492-01) according to the manufacturer's instructions. All antibodies used for FACS staining were from BD Pharmingen unless noted. To label lineage-positive cells, the following antibody cocktail (1:200) containing biotinylated antibodies against CD11b (M1/70), Gr-1 (RB6-8C5), CD3ε (145-2C11), B220 (RA3-6B2), CD8a (53-6.7), CD4 (GK1.5), and TER-119 (TER-119) in combination with BV421-conjugated Streptavidin (BD, 5832259; 1:200) was used. To distinguish between LSK+ and LSK- cells, biotinylated lineage-specific antibody cocktail was used in combination with FITC-conjugated SCA-1 (D7; 1:100) and PE-conjugated c-KIT (2B8; 1:100) antibodies. Labelled cells were filtered through a 70 μm cell strainer before sorting. 7-Amino-Actinomycin D (7-AAD, BD559925; 1:200) solution was used to label the nonviable cells. For LSK+ and LSK- cells, sorting was conducted on MoFlo Astrios Cell Sorter (BD) or MA900 Multi-Application Cell Sorter (Sony). Approximately 10,000 cells were utilized per transposition reaction.

value: Bone marrow LSK- cells


title: WT BR3


title: hiPSC, d25, replicate3


title: Fusarium solani, medium, 3days, rep3 [CK3]

value: mycelium

value: Natural growth, 3 days


title: mesoderm R4

city: La Jolla

first: Shaina

last: Tran

address: 9500 Gilman Dr

institute: University of California, San Diego

description:
PeakMatrix.mtx
PeakMatrix_cols.csv
PeakMatrix_rows.csv
MotifMatrix.mtx
MotifMatrix_cols.csv
MotifMatrix_rows.csv
GeneScoreMatrix.mtx
GeneScoreMatrix_rows.csv
GeneScoreMatrix_cols.csv
TileMatrix.mtx
TileMatrix_rows.csv
TileMatrix_cols.csv

data_processing:
The mesoderm R1 snATAC reads were aligned to hg38 with snaptools bwa aligner
Aligned reads were converted to fragment files using Sinto
The mesoderm R3 and R4 snATAC reads were aligned with Cell Ranger ATAC
Aligned fragment files were further filtered, processed, and analyzed in ArchR
Genome_build: hg38
Supplementary_files_format_and_content: Mtx files were generated from ArchR. PeakMatrix.mtx contains all peaks for all 3 samples, MotifMatrix.mtx contains all motifs and deviation scores, GeneScoreMatrix.mtx contains all genes and gene scores, and TileMatrix.mtx contains ArchR's tile matrix for computing the peaks. Each matrix has corresponding metadata rows and columns csv files

source_name: hPSC-derived mesoderm cells

growth_protocol: mesoderm cells were derived from human pluripotent stem cells (H9) grown in E8 on Geltrex-coated plates

extract_protocol:
MinElute PCR Purification Kit (Qiagen) and size selection was performed with SPRISelect reagent (Beckman Coulter; 0.55× and 1.5×). Libraries were purified one more time with SPRISelect reagent (Beckman Coulter; 1.5×).
barcoded Tn5 transposomes

treatment_protocol: Three replicates were obtained from independent differentiations

tag: Stage

value: mesoderm


title: WT BR2


title: mesoderm R3


title: ATAC-seq LSK- WT Rep1

source_name: ATAC-seq LSK- WT

value: Wild type

value: Female

value: 129Sv4/Jae x B6


title: Fusarium solani, medium, 3days, rep1 [CK1]


title: ATAC-seq LSK+ XistΔ/Δ Rep1

source_name: ATAC-seq LSK+ XistΔ/Δ

value: Bone marrow LSK+ cells

value: Xist knockout


title: WT BR1


title: H3K9me3.prEpiSC

status: Public on Jul 14 2022

city: GuangZhou

first: Hanwen

last: Yu

state: GuangDong

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-*Sen Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Bioinformatic analyses ChIP-seq data generated in this study were performed by custom shell scripts in which raw data were first trimmed and filtered by TrimGalore with default parameter; then qualified read pairs were aligned to reference genome by Bowtie2 (release 2.4.1); after that biological and optical duplicates were removed with Sambamba (release 0.7.1); last we used MACS2 (release 2.2.7.1; parameters for broad peaks H3K9me3: --broad --broad-cutoff 0.05 -g hs -f BAMPE) to call peaks. All peaks were filtered with blacklisted regions. The highly reproducible peaks were identified by package IDR, which is a uniﬁed approach to measure the reproducibility of ﬁndings identiﬁed from replicate experiments and provides highly stable thresholds based on reproducibility. For downstream analysis, package deepTools (release 3.5.0) was used to generate genome coverage track files for UCSC visualization and heatmap based on scores of specific genomic regions, such as RPKM value.
Assembly: hg38
Supplementary files format and content: wig files were generated using deeptools; Scores represent RPKM values.
Library strategy: CUT&TAG

source_name: prEpiSC

growth_protocol: Human embryonic stem cells (hESCs) were cultured in matrigel-coated plates in the Essential 8 hESC medium (Thermo, catalog. no. A1517001). The medium was changed daily. hESCs were treated with 0.48 mM EDTA for dissociation and then passaged onto new Matrigel -coated plates every 4–5 days.

extract_protocol:
To obtain MII oocytes, the immature oocytes were collected and matured in vitro in medium (Cooper Surgical/SAGE, Trumbull, CT) supplemented with 75 mIU/ml FSH and LH for 24-28h. After the in vitro maturation, the MII oocytes were fertilized by intracytoplasmic sperm injection (ICSI), and then cultured in IVF medium (Vitrolife, catalog. no. 10136). 16-18h later, the fertilization were observed, 2PN zygotes were cultured in G1 medium (Vitrolife) at 37°C in 6% CO2, 5% O2 and 89% N2 for 3 days to 8-cell embryo stage, and then switched to G2 medium (Vitrolife) until the blastocyst stage. The 4-cell, 8-cell and morula embryos (zona pellucida and Polar body removed) were collected into the nuclear isolation buffer for AULIChIP-seq. The inner cell mass (ICM) and mural trophectoderm were separated by gently pipetting in a pipette with a diameter of 40-60 μm and collected into the nuclear isolation buffer.  Human ESCs were dissociated with Accutase (Thermo Fisher Scientific, catalog. no. A1110501) into single cells and washed with PBS solution twice. Then, 50 or 500 hESCs were collected into the nuclear isolation buffer.   Lysates were clarified from micrococcal nuclease-treated nuclei and histone-DNA complexes were isolated with anti-H3K9me3 antibody.
Libraries were prepared according to the Accel-NGS  2S Plus DNA Liibrary Kit from Swift Biosciences.

treatment_protocol: Without any chemical or genetic treatment on human embryos and embryonic stem cells prior to Pathul-seq.

value: prEpiSC

value: untreated


title: ATAC-seq LSK+ WT Rep1

source_name: ATAC-seq LSK+ WT


title: hESC 500cell H3K9me3 Input

data_processing:
Bioinformatic analyses ChIP-seq data generated in this study were performed by custom shell scripts in which raw data were first trimmed and filtered by TrimGalore with default parameter; then qualified read pairs were aligned to reference genome by Bowtie2 (release 2.4.1); after that biological and optical duplicates were removed with Sambamba (release 0.7.1); last we used MACS2 (release 2.2.7.1; parameters for broad peaks H3K9me3: --broad --broad-cutoff 0.05 -g hs -f BAMPE) to call peaks. All peaks were filtered with blacklisted regions. The highly reproducible peaks were identified by package IDR, which is a uniﬁed approach to measure the reproducibility of ﬁndings identiﬁed from replicate experiments and provides highly stable thresholds based on reproducibility. For downstream analysis, package deepTools (release 3.5.0) was used to generate genome coverage track files for UCSC visualization and heatmap based on scores of specific genomic regions, such as RPKM value.
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using deeptools; Scores represent RPKM values.

source_name: hESC 500cell H3K9me3 Input

growth_protocol: Human embryonic stem cells (hESCs) were cultured in matrigel-coated plates in the Essential 8 hESC medium (Thermo, catalog. no. A1517001). The medium was changed daily. Human ESCs were treated with 0.48 mM EDTA for dissociation and then passaged onto new Matrigel -coated plates every 4–5 days. Human trophoblast stem cells (hTSCs) were cultured in Col IV-coated plates in the hTSC medium.  The hTSC medium is prepared as the previous report (): DMEM/F12 (Gibco) supplemented with 0.2% FBS (ExCell Bio), 0.2% Primocin (InvivoGen), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific), 1% ITS-X (Thermo Fisher Scientific), 50 µg/ml Vitamin C (Sigma), 0.3% BSA (Thermo Fisher Scientific), 50 ng/ml hEGF (PeproTech), 2 mMCHIR99021 (Selleckchem), 0.5 mM A83-01 (Tocris), 1 mM SB431542 (Selleckchem), 0.8 mM VPA (Selleckchem), and 5 mM Y27632 (Millipore). To collect or passaging the cells, hTSCs were dissociated with TrypLE (Thermo Fisher Scientific) for 3 minutes.

extract_protocol:
Human ESCs and human TSCs were dissociated with Accutase (Thermo Fisher Scientific, catalog. no. A1110501) into single cells and washed with PBS solution twice. Then, hESCs and hTSCs were collected into the nuclear isolation buffer. Lysates were clarified from micrococcal nuclease-treated nuclei and histone-DNA complexes were isolated with anti-H3K9me3 antibody.
Libraries were prepared according to the Accel-NGS  2S Plus DNA Liibrary Kit from Swift Biosciences.

treatment_protocol: Without any chemical or genetic treatment on human embryos and embryonic stem cells prior to AULIChIP-seq.

value: Human trophoblast stem cells (hTSCs)


title: hESC 50cell H3K9me3 Input

source_name: hESC 50cell H3K9me3 Input


title: hESC H3K9me3 Input

source_name: hESC H3K9me3 Input


title: hTSC H3K27me3 IP rep1

source_name: hTSC H3K27me3 IP

value: H3K27me3 (Millipore 07-449)


title: hTSC Input rep1

source_name: hTSC Input


title: Fusarium solani, medium, 3days, rep2 [CK2]


title: hESC H3K9me3 IP

source_name: hESC H3K9me3 IP


title: treatment, 3 hours desiccation

city: Tehran

first: Fatemeh

last: Khani-Juyabad

address: North Sheikh Bahaee St., Deh-e Vanak

department: Microbiology

country: Iran

institute: Alzahra University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v 0.36.
Trimmed sequence reads were mapped to Nostoc sp. MG11 genome(GenBank accession number: JACXXN01) using Bowtie2 v 2.3.4.
Raw counts of sequencing reads extraction was performed using htseq (Version 0.9.1)
Assembly: JACXXN01
Supplementary files format and content: tab-delimited text files include Raw counts of sequencing reads for each Sample

organism: Nostoc sp. MG11

source_name: Nostoc sp. MG11 cells

growth_protocol: Nostoc sp. MG11 was grown at 25°C in BG11 medium under a continuous cool white fluorescence illumination.

extract_protocol:
Total RNA was extracted from sampels collected at 0 and 3 hours using Trizol (Invitrogen) following the instructions of manufacturer.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample Prep Kit v2 following manufacturer's protocols.

treatment_protocol: The cells were harvested after obtaining proper growth (0 h). Nostoc sp. MG11 cells were spread on the sterile plates and desiccated at 25°C under the continuous cool white fluorescence illumination for 3 hours.

value: Nostoc sp. MG11 cells

value: desiccation treatment

tag: time

value: Hour 3


title: hTSC Input rep2


title: mesoderm R1


title: hTSC H3K27me3 IP rep2

value: H3K27me3 (Millipore 07-450)


title: Control, 0 hour desiccation

value: control

value: Hour 0


title: TE H3K9me3 IP rep1

description:
hTE93-Ip_idr_peaks.bed
hTE93-Ip.bw

data_processing:
Bioinformatic analyses ChIP-seq data generated in this study were performed by custom shell scripts in which raw data were first trimmed and filtered by TrimGalore with default parameter; then qualified read pairs were aligned to reference genome by Bowtie2 (release 2.4.1); after that biological and optical duplicates were removed with Sambamba (release 0.7.1); last we used MACS2 (release 2.2.7.1; parameters for broad peaks H3K9me3: --broad --broad-cutoff 0.05 -g hs -f BAMPE) to call peaks. All peaks were filtered with blacklisted regions. The highly reproducible peaks were identified by package IDR, which is a uniﬁed approach to measure the reproducibility of ﬁndings identiﬁed from replicate experiments and provides highly stable thresholds based on reproducibility. For downstream analysis, package deepTools (release 3.5.0) was used to generate genome coverage track files for UCSC visualization and heatmap based on scores of specific genomic regions, such as RPKM value.
Genome_build: hg38
Supplementary_files_format_and_content: peak bed files.
Supplementary_files_format_and_content: wig files were generated using deeptools; Scores represent RPKM values.

source_name: human embryo

value: human embryo

value: TE


title: TE H3K9me3 Input


title: hTSC H3K9me3 IP rep2

source_name: hTSC H3K9me3 IP


title: H3K4me3.prEpiSC

value: H3K4me3 (Millipore 07-473)


title: hESC 50cell H3K9me3 IP

source_name: hESC 50cell H3K9me3 IP


title: TE H3K9me3 IP rep2

description:
hTE93-Ip_idr_peaks.bed
hTE93-Ip.bw


title: ICM H3K9me3 IP rep1

description:
hICM93-Ip_idr_peaks.bed
hICM93-Ip.bw

value: ICM


title: hESC 500cell H3K9me3 IP

source_name: hESC 500cell H3K9me3 IP


title: hTSC H3K9me3 IP rep1


title: Morula H3K9me3 IP rep2

description:
hM93-Ip_idr_peaks.bed
hM93-Ip.bw

value: Morula


title: Morula H3K9me3 Input


title: Morula H3K9me3 IP rep1

description:
hM93-Ip_idr_peaks.bed
hM93-Ip.bw


title: ICM H3K9me3 IP rep2

description:
hICM93-Ip_idr_peaks.bed
hICM93-Ip.bw


title: ICM H3K9me3 Input


title: 8Cell H3K9me3 IP rep2

description:
h8C93-Ip_idr_peaks.bed
h8C93-Ip.bw


title: 8Cell H3K9me3 Input


title: 8Cell H3K9me3 IP rep1

description:
h8C93-Ip_idr_peaks.bed
h8C93-Ip.bw


title: 4Cell H3K9me3 IP rep1

description:
h4C93-Ip_idr_peaks.bed
h4C93-Ip.bw


title: 4Cell H3K9me3 Input


title: A549_Ctrl_1st

city: Wuhan

first: Dong

last: Chen

state: Hubei

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

department: Center for Genome Analysis

institute: ABLife, Inc.

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

source_name: A549 cell

growth_protocol: Non-small cell lung cancer A549 cells were suspended in a DMEM medium containing 10% fetal bovine serum and 1% penicillin, and transformed into a 37 ° C, 5% CO2 incubator. Cell growth was observed under a microscope, and digestion and passage were performed when the cell fusion rate reached more than 80%.

extract_protocol:
Total RNA was isolated from A549 cells with Trizol. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase. Purified RNA was transcribed for cDNA by oligo dT primer. And then the insert fragment was synthesized by PCR amplification. A linearized vector digested by EcoRI and XhoI (NEB) and PCR insert were added to a PCR microtube for ligation with ClonExpress® II One Step Cloning Kit (Vazyme).
The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis. For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: Primer pairs used for Hot Fusion were designed with CE Design V1.04. Each of the primer comprises a fragment of gene specific sequence and a 17–30 bp sequence of the pIRES-hrGFP-1a vector. The pIRES-hrGFP-1a vector was digested by EcoRI and XhoI (NEB) at 37℃ for 2h~3h. Then enzyme-digested vector was run on 1.0% agarose gel and purified by Qiagen column kit. Plasmids were introduced into Escherichia coli strain by chemical transformation. Cells were plated onto LB agar plates containing 1µL/ml ampicillin, and incubated overnight at 37℃. Colonies were screened by colony PCR (28 cycles) with universal primers (located on the backbone vector).

value: Non-small cell lung cancer

value: A549 cell (control plasmid)


title: Normal ovarian tissue 3

city: Jinan

first: Zhen

last: Zhang

address: jingshi 18877

institute: shandong academy of medical sciences

data_processing:
The basic reads were converted into sequence data by base calling.
Low-quality reads were filtered, and the reads with 5¡¯ primer contaminants and poly (A) were removed.
The reads without 3¡¯adapter and insert tag, the reads shorter than 15 nt and longer than 41nt from the raw data were filtered, and the clean reads were obtained
Genome_build: human NCBI genome build 38
Supplementary_files_format_and_content: TPM

source_name: Ovary

extract_protocol:
Total RNA was extracted from tissues by using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ovary

tag: chemotherapy

value: No

tag: relapse


title: A549_APEX1_2nd

tag: cell line

value: APEX1 overexpression in A549 cell


title: A549_Ctrl_2nd


title: A549_Ctrl_3rd


title: Normal ovarian tissue 1


title: Malignant ovarian tissue 3


title: Normal ovarian tissue 2


title: Malignant ovarian tissue 1


title: Malignant ovarian tissue 2


title: shTaz_Seq1_rep3 [RNA-seq]

city: Jena

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

institute: Leibniz Institute on Aging

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by cutadapt (v2.10) , then mapped to mm10 whole genome using bowtie2-2.2.9 with default parameters
Differential gene expression was performed by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: RPKM table as a tab-delimited .txt file

extract_protocol:
HSPCs from C57BL/6 mice transplanted into Ly5.1 mice were sorted into RLT buffer (Qiagen) and purified by the Rneasy Micro kit (Qiagen).
Libraries were constructed using the NEBNextSingle Cell/Low Input RNA Library Prep Kit (E6420L). Ca. 400-3000 cells were used as input.

value: 22-28 months

tag: cell type

value: LT-HSC

tag: shRNA

value: shTaz Seq1


title: 4Cell H3K9me3 IP rep2

description:
h4C93-Ip_idr_peaks.bed
h4C93-Ip.bw

value: untreated


title: LSK_young [scRNA-seq]

data_processing:
FASTQ files from the sequencing runs were analyzed using the 10x Genomics Cell Ranger (v3.1.0) software. Briefly, the cellranger count function was used to count the UMIs/cell and the data sets were subsequently normalized by cellranger aggr.
The UMIs of the ADTs were counted and mapped using the Cite-seq-Count tool (https://hoohm.github.io/CITE-seq-Count/) using the following options: CITE-seq-Count -R1 R1.fastqgz -R2 R2.fastq.gz -cbf 1 -cbl 16 -umif 17 -umil 26 -cells # of cellranger output. All data for ADTs were log-transformed.
Genome_build: mm10
Supplementary_files_format_and_content: raw count matrix (cellranger output) for RNA quantification and log-normalized values for ADTs as a separate .txt file

extract_protocol:
HSPCs from transplanted Ly5.1 mice were sorted by flow cytometry. bone marrow (BM) cells were stained with the following antibodies for sorting. BM cells were incubated with a lineage mix of biotinylated antibodies together streptavidin eF450, anti-cKit-APC and anti-Sca-1-PE/Cy7. After sorting in PBS 0,04% BSA, cells were washed, counted with an automated cell counter (EVE, NanoEnTek) and adjusted to a concentration of 1000 cells/µL.
Libraries were constructed using the Chromium Single Cell 3′ Library Construction Kit v3
The mRNA-derived cDNAs were processed following the standard 10X Genomics protocol for cDNA library generation.  The scRNA-Seq libraries were sequenced an Illumina NextSeq 500 platform

value: 3-5 months

value: LSK


title: shTaz_Seq2_rep2 [RNA-seq]

value: shTaz Seq2


title: shTaz_Seq1_rep1 [RNA-seq]


title: A549_APEX1_3rd

tag: tissue


title: A549_APEX1_1st


title: shRen_rep3 [RNA-seq]

value: shRen


title: shRen_rep2 [RNA-seq]


title: rhombomere1_wildtype_rep1

type: RNA

city: Helsinki

first: Kaia

last: Achim

address: Viikinkaari 9

department: Faculty of Biological and Environmental Sciences

country: Finland

institute: University of Helsinki

hyb_protocol: 1.50 ug each sample was hybridized to Illumina’s MouseWG-6 Expression BeadChips, version 2 (BD-201-0602) at 58 C overnight (18 h) according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A.

scan_protocol: Chips were scanned with Illumina BeadArray Reader, BeadScan software version 3.5.

data_processing: The numerical results were extracted with Illumina’s GenomeStudio software v 1.0 without any normalization (raw data).

source_name: embryonic neural tube, rhombomere 1 neuroepithelium

label_protocol: Hybridization was detected with 1 ug/ml Cyanine3-streptavidine, GE Healthcare Limited UK (cat no PA43001).

growth_protocol: Gata2flox and En1-cre mouse strains were maintained in the ICR background, following the EU and national guidelines for laboratory animal husbandries.

extract_protocol: Tissues were dissected under dissection microscope. Genotyping sample was extracted from every embryo. Tissues were frozen in liquid nitrogen and stored in -80C until RNA extraction. RNA was extracted by TriZol.

treatment_protocol: Timed matings were set up according to need. Embryos were dissected at embryonic day (E) 12.5.

tag: genotype

value: wildtype

tag: developmental stage

value: neural tissue


title: shRen_rep1 [RNA-seq]


title: rhombomere1_wildtype_rep2


title: LT-HSC old rep 2 [scATAC-seq]

data_processing:
All processing steps were performed by the 10x Chromium cellranger-atac pipeline (v1.2.0)
Genome_build: mm10
Supplementary_files_format_and_content: peak Matrix containing counts per cell in a tab-delimited .txt file

extract_protocol:
10,000 cells (per sample, an equal number of cells (n=2500) from 4 mice were used) of young and old LT-HSCs were sorted into round-bottom 96 well plate containing 0.04% BSA/PBS.
For nuclei isolation, cells were lysed with chilled lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1%Nonidet P40, 0.01 % Digitonin, 1 % BSA) on ice for 3 min. Cells were washed with wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 1 % BSA). Supernatant was discarded and cells were resuspended in 1X Nuclei Buffer (10x Genomics, PN-2000153/ 2000207). Nuclei suspension was directly subjected to the transposition reaction and used for library preparation.

value: old


title: rhombomere1_wildtype_rep3


title: LT-HSC young rep 2 [scATAC-seq]

value: 3-4 months

value: young


title: rhombomere1_gata2cko_rep3


title: rhombomere1_gata2cko_rep1


title: rhombomere1_gata2cko_rep2


title: dorsal_mb_gata2cko_rep3

source_name: embryonic neural tube, dorsal midbrain neuroepithelium


title: dorsal_mb_gata2cko_rep2


title: dorsal_mb_ctrl_rep2

value: control


title: LT-HSC young rep6 [ATAC-seq]

data_processing:
All processing steps (Adapter trimming, adapter removal, removal of low complexity reads, PCR duplicate removal and mapping (BWA)), as well as conversion to bigWig files, were performed by the nextflow pipeline (https://github.com/nf-core/atacseq).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

extract_protocol:
HSPCs from young and old C57BL/6 mice were sorted into 2% BSA (PBS) and directly subjected to a modified ATAC-Seq protocol (PMID: 27526324).
Tagmented DNA was pre-amplified using 5 PCR cycles using barcoded Nextera PCR primers and the optimal numbers of cycle (30% of max) was determined by qPCR. After the second PCR, the DNA was purified by a MinElute PCR purification coumn (Qiagen) and subsequently size-selected by Ampure beads to obtain fragments between 50-1000bp.


title: dorsal_mb_ctrl_rep3


title: LT-HSC young rep4 [ATAC-seq]


title: ventral_mb_gata2cko_rep3

source_name: embryonic neural tube, ventral midbrain neuroepithelium


title: dorsal_mb_gata2cko_rep1


title: dorsal_mb_ctrl_rep1


title: LT-HSC old rep3 [ATAC-seq]


title: LT-HSC old rep2 [ATAC-seq]


title: 20d_rep_3

city: Tsukuba

first: takehito

last: sugasawa

state: Select State

address: Ibaraki

country: Japan

institute: University of tsukuba

data_processing:
The RNA-Seq reads were aligned to the mRatBN7.2 genome assembly using CLC genomics workbench 22.0 with the default settings.
A statistical differential expression test was used "Differential Expression for RNA-Seq tool" in the CLC software.
Supplementary files format and content: Excel file of statistic test and expression data.

organism: Rattus norvegicus

source_name: Red blood cell in rat

growth_protocol: Standard protocol

extract_protocol:
RNAs were extracted from the purified RBC, using RNAiso Blood (Cat#9112; Takara Bio)
Libraries were constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina, and NEBNext rRNA Depletion Kit (Cat# E7770 and E6310; New England Biolabs).

treatment_protocol: The following 3 experimental conditions were set for rat whole blood depending storage periods: Control (Cont; no storage), 10 days (10d), and 20 days (20d) group.

value: stored 20-day periods with citrate–phosphate–dextrose solution with adenine (CPDA) at 4°C

value: Red blood cells

value: 11 weeks

value: Wild type


title: 20d_rep_4


title: ventral_mb_gata2cko_rep1


title: ventral_mb_ctrl_rep1


title: 20d_rep_1


title: LT-HSC young rep5 [ATAC-seq]

value: LT-HSC


title: 10d_rep_4

value: stored 10-day periods with citrate–phosphate–dextrose solution with adenine (CPDA) at 4°C


title: E16.5

city: Los Angeles

first: Junjun

last: Jing

address: 2250 Alcazar Street

institute: Center for Craniofacial Molecular Biology, University of Southern California

data_processing:
Quality control, mapping, and count table assembly of the library were performed using the CellRanger pipeline version 3.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

source_name: molar

extract_protocol:
The tooth and its surrounding tissue were placed in 4mg/ml Dispase and 2mg/ml Collagenase on a thermomixer at 37°C for 15 to 30 min
cDNA libraries were prepared for sequencing using standard 10X Genomics protocols

tag: strain

value: molar


title: E14.5


title: ventral_mb_ctrl_rep3


title: P7.5


title: ventral_mb_gata2cko_rep2


title: P3.5


title: shPU1_Seq1_rep3 [RNA-seq]

description:
HPC5_shPU1_1_rep3
HPC5_normalzed_count_table.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by cutadapt (v2.10), then mapped to mm10 whole genome using bowtie2-2.2.9 with default parameters.
Differential gene expression was performed by DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: HPC5_normalized_count_table.txt: CPM table as a tab-delimited text file.

source_name: Cell line

growth_protocol: BM-HPC#5 cells were cultured in IMDM (+GlutaMAX, Thermo Fisher Scientific) supplemented with 10% FBS (Gibco), 1% penicillin-streptomycin (Sigma), 25 ng/mL recombinant mouse SCF (AF-250-03, PeproTech) and 10 ng/mL recombinant IL-6 (78052.1, STEMCELL Technologies).

extract_protocol:
RNA was isolated by the RNeasy Micro kit (Qiagen).
Libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit (kit) using the RNA purified by the NEBNext® Poly(A) mRNA Magnetic Isolation Module. 10 ng of total RNA were used as input.

tag: construct


title: 10d_rep_1


title: 20d_rep_2


title: LT-HSC old rep1 [ATAC-seq]

value: 22-28 months


title: myocardium, 4weeks, MI, rep2

city: Beijing

first: Qianqian

last: Guo

address: Dongcheng District, Hai Yun Cang on the 5th Zip

description: Gene expression after 4weeks in myocardial tissue of the infarct marginal zone of rat

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: myocardium, 4weeks, MI, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Rats are raised in the Barrier Animal Laboratory of Dongzhimen Hospital, Beijing University of Chinese Medicine, with a 12 h light/dark cycle and ad libitum food and water.

extract_protocol: Total RNA was extracted from myocardial tissue according to the mirVanaTM RNA Isolation Kit (AM1561, Applied Biosystems, USA). Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Rat models of acute myocardial infarction (AMI) were established by ligating the anterior descending branch of the left coronary artery, while sham-operated rats were only threaded without ligation as a control group.

value: Sprague–Dawley

tag: condition

value: AMI model

value: myocardium

tag: gender

value: male


title: E13.5


title: shPU1_Seq2_rep2 [RNA-seq]

description:
HPC5_shPU1_2_rep2
HPC5_normalzed_count_table.txt


title: ventral_mb_ctrl_rep2

value: neural tissue


title: myocardium, 4weeks, MI, rep3

institute: Dongzhimen Hospital, Beijing University of Chinese Medicine

source_name: myocardium, 4weeks, MI, replicate 3


title: myocardium, 4weeks, MI, rep1

source_name: myocardium, 4weeks, MI, replicate 1


title: Control_rep_4

tag: treatment


title: shPU1_Seq1_rep2 [RNA-seq]

description:
HPC5_shPU1_1_rep2
HPC5_normalzed_count_table.txt


title: shPU1_Seq2_rep1 [RNA-seq]

description:
HPC5_shPU1_2_rep1
HPC5_normalzed_count_table.txt


title: sRen_rep3 [RNA-seq]

description:
HPC5_shRen_rep3
HPC5_normalzed_count_table.txt

value: shRen

value: SGE-shRen


title: sRen_rep2 [RNA-seq]

description:
HPC5_shRen_rep2
HPC5_normalzed_count_table.txt


title: shPU1_Seq1_rep1 [RNA-seq]

description:
HPC5_shPU1_1_rep1
HPC5_normalzed_count_table.txt


title: myocardium, 4weeks, Non-MI, rep2

description: Gene expression after 4weeks in myocardial tissue of rat

source_name: myocardium, 4weeks, Non-MI, replicate 2


title: shPU1_Seq2_rep3 [RNA-seq]

description:
HPC5_shPU1_2_rep3
HPC5_normalzed_count_table.txt


title: Control_rep_3

tag: age


title: beaf_and_row_k_rep3

city: Jerusalem, Kiryat Shemona

first: Neta

last: Herman

address: Kiryat Shemona

department: Gentics, Nutrition

country: Israel

institute: Hebrew University Of Jerusalem, Migal

data_processing:
RNA-seq reads were aligned by STAR to the full genome sequences of Drosophila Melanogaster (UCSC version dm3)
Reads were counted per annotated gene using ESET (End Sequencing analysis Toolkit)
Genome_build: dm3
Supplementary_files_format_and_content: Table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown in Schneider’s Drosophila medium supplemented with 10% Fetal Bovine Serum and 1% penicillin/streptomycin

extract_protocol:
RNA purification was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol
3' RNA-seq library generation was performed based on a previous protocol ( Klein-Brill, A., Joseph-Strauss, D., Appleboim, A. & Friedman, N. Dynamics of Chromatin and Transcription during Transient Depletion of the RSC Chromatin Remodeling Complex. Cell Rep. (2019). doi:10.1016/j.celrep.2018.12.020). In brief, 100ng from each sample was incubated with oligo-dT reverse transcription (RT) primers containing 7bp barcode and 8bp UMI (Unique Molecular Identifier) at 72°C for 3 minutes and moved directly to ice. This was followed by a Reverse transcription reaction (SmartScribe kit Clontech) for 1 hour at 42°C and 70°C for 15 minutes. Next, samples were pooled and purified using SPRI beads X1.2 (Agencourt AMPure XP, Beckman Coulter). The pooled barcoded samples were then tagmented using Tn5 transposase (loaded with oligos Tn5MEDS-A) for 8 min at 55°C Followed by the addition of 0.2% SDS to strip off the Tn5 and SPRI X2 purification was performed. Finally, a PCR was performed with primers containing NGS sequences (KAPA HiFi HotStart ReadyMix, Kapa Biosystems, 12 cycles) and the library was cleaned using 0.8x SPRI beads.

treatment_protocol: Cells were diluted to 106 ml−1 and 4 μg of dsRNA per 1ml of cells were added. After 2 days the cells were diluted again to 106 ml−1 and 8 μg of dsRNA per 1ml of cells were added. After 2 days, the cells were washed twice with PBS, collected, and used for downstream experiments

value: S2 cells

value: dsRNA to BEAF-32 and row


title: 10d_rep_3


title: Control_rep_2

value: control


title: myocardium, 4weeks, Non-MI, rep3

source_name: myocardium, 4weeks, Non-MI, replicate 3


title: myocardium, 4weeks, Non-MI, rep1

source_name: myocardium, 4weeks, Non-MI, replicate 1


title: sRen_rep1 [RNA-seq]

description:
HPC5_shRen_rep1
HPC5_normalzed_count_table.txt


title: beaf_and_row_k_rep2


title: H4K20me1-ChIP Tet1 CM D7, B

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Processing pipeline: minute processing pipeline (https://github.com/NBISweden/minute)
Pipeline manager: Snakemake v5.30.1
Demultiplexing and deduplication: Reads were demultiplexed using cutadapt v3.2 (Martin 2011) allowing only one mismatch per barcode. Deduplication was performed on aligned BAM files, marking duplicates using je-suite (v2.0.RC) using UMI and location of first mate. Resulting marked files were parsed and duplicate pairs were removed.
Mapping: bowtie2 (v2.3.5.1) with --fast parameter
Scaling: ChIP coverage tracks were generated from BAM files using deepTools (v3.5.0) bamCoverage. Quantitative scaling of the ChIP-Seq tracks amongst conditions within each pool was based on their Input-Normalized Mapped Read Count (INRC). INRC was calculated by dividing the number of unique mm10-mapped reads by the respective number of Input reads:  #mapped[ChIP] / #mapped[Input] . This essentially corrected for an uneven representation of barcodes in the Input and we could demonstrate that the INRC is proportional to the amount of epitope present in each condition.   Naïve-untreated condition pooled was chosen as the reference sample, which was scaled to 1x coverage (also termed Reads per Genome Coverage, RPGC). All other conditions were scaled relative to the reference using the ratio of INRCs multiplied by the scaling factor determined for 1x normalization of the reference: ( #mapped[ChIP] / #mapped[Input] ) / ( #mapped[ChIP_Reference] / #mapped[Input_Reference] ) * scaling factor.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files are scaled according to MINUTE quantification with respect to the reference of each pool (J1 WT, 1xRPGC)

source_name: Tet1 CM D7

growth_protocol: Mouse ESCs were cultured in “Serum LIF” conditions, here the cells were maintained on 0.2% gelatin-coated dishes in Dulbecco's modified Eagle's medium (Sigma) supplemented with 16% fetal bovine serum (FBS, Sigma), 0.1 mM ß-mercaptoethanol (Invitrogen), 2 mM L-glutamine (Sigma), 1× MEM Non-essential amino acids (Sigma), 100 U/mL penicillin, 100 μg/mL streptomycin (Sigma), LIF (ESGRO, Millipore).

extract_protocol:
Cell lysis immediately followed by MNase digestion of native chromatin, T7-adapter ligation, pool-and-split multiplexing, immunoprecipitation and magnetic bead isolation of immunoprecipitated DNA.
ChIP-seq libraries were prepared using the MINUTE-ChIP protocol as described in Kumar & Elsässer 2019; PMID: 3153304 and sequenced on the Illumina NextSeq 500 (Paired End) platform.

treatment_protocol: Tet1 KO (clone H9) and Tet1 CM (clone D7) mESC lines were generated as described previously (Mulholland et al, 2020a, 2020b).

value: Embryonic Stem Cell

value: Tet1 CM D7

tag: chip antibody

value: H4K20me1 (ActiveMotif, #61015)

tag: minute-pool

value: Pool B

tag: supplementary file scaling

value: RPGC relative to WT J1

tag: supplementary file description

value: combined from four biological replicates

tag: replicate information

value: four biological replicates with different barcodes provided as separate FASTQ files


title: H3K27me1-ChIP Tet1 CM D7, A

tag: cell line

value: Pool A


title: H4K20me1-ChIP WT J1, B

source_name: WT J1

tag: cell type

value: WT J1

value: RPGC 1x genome coverage


title: H4K20me1-ChIP Tet1 KO H9, B

source_name: Tet1 KO H9

value: Tet1 KO H9


title: H3K27me1-ChIP WT J1, A


title: H3K27me1-ChIP Tet1 KO H9, A


title: beaf_and_row_k_rep1


title: H3K9me3-ChIP Tet1 CM D7, B

value: H3K9me3 (39161, ActiveMotif)


title: T1D patients with Calcified Carotid Plaque BC23

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

data_processing:
Data analysis was performed using CLC Genomics Workbench software 21.0.3 (Quiagen)
Reads from FASTq files was filtered for quality and aligned to the Ensembl-v99-hg38 version of the reference human genome and miRbase v.22.1  as annotation model
Normalization of the data was performed using TMM method (trimmed Mean of M-values)
Differential Expression analysis was performed using Generalized Linear Model (GLM) and Trimmed mean of M-values (TMM) normalized counts (CPM) were used as input data, considering significant Benjamini-Hochberg adjusted p-values ≤ 0.05
Assembly: Ensembl-v99-hg38
Supplementary files format and content: tab-delimited text files include raw data and cpm values (TMM-adjusted) for each Sample

source_name: blood

growth_protocol: This study was performed with the collaboration of the Unit of Metabolic Diseases, Department of Medicine, University of Padova, Italy, and the Center of Biomedical Research on Diabetes and Associated Metabolic Diseases, Department of Endocrinology, and Nutrition, University Hospital de la Santa Creu i Sant Pau, Barcelona, Spain. One hundred four subjects with T1D were recruited from the diabetic outpatient clinics at University Hospital Germans Trias i Pujol, Hospital Clinic of Barcelona, and University Hospital Arnau de Vilanova of Lleida in the North Western region of Spain (Catalonia). Inclusion criteria were as follows: age >18 years; type 1 diabetes for at least 1 year; estimated glomerular filtration rate (eGFR) >60 mL/1.73mq.min. Exclusion criteria were: previous cardiovascular diseases, defined as clinical coronary heart disease, stroke, or peripheral vascular disease (including any form of diabetic foot disease); and a urine albumin/creatinine excretion ratio >300 mg/g. Patients were enrolled in the study if they showed a uniformly CFP or CCP; the two groups were matched by sex and age. This study was carried out following the International Ethical Guidelines and the principles of the Declaration of Helsinki; the Local Ethics Committee of the participating centers approved the protocol (PI11/11, C0000046, and PI-13-095); all participants signed informed consent forms. Patients filled out a complete lifestyle questionnaire regarding medical history, current therapy, smoking habits, and physical activity. Plasma glucose, total serum cholesterol, HDL cholesterol, and triglyceride were measured using routine enzymatic methods. For NGS analysis, fasting blood samples were collected into EDTA-containing tubes, centrifuged at 3000g for 10 min and plasma aliquots were stored at -80°C until use.

extract_protocol:
Total RNA was isolated from plasma by miRNeasy Serum/plasma kit (Qiagen, Germany).
Small RNA libraries from plasma samples were obtained using QIAseq® miRNA Library kit (Qiagen, Hilden, Germany), according to the manufacturer protocol. NGS Library Quality Control (QC) analysis and quantification were performed before sequencing. Replicates were included.

tag: disease state

value: type 1 diabetes

value: blood

value: plasma


title: T1D patients with Calcified Carotid Plaque BC20

tag: tissue


title: row_k_rep2

value: S2 cells

value: dsRNA to row


title: T1D patients with Calcified Carotid Plaque BC17


title: H3K9me3-ChIP Tet1 KO H9, B

value: Embryonic Stem Cell


title: H3K9me3-ChIP WT J1, B


title: T1D patients with Calcified Carotid Plaque BC16


title: H4K20me3-ChIP Tet1 CM D7, B

value: Tet1 CM D7

value: H4K20me3 (07-463, Millipore)


title: H4K20me3-ChIP WT J1, B

value: Pool B


title: row_k_rep1


title: T1D patients with Calcified Carotid Plaque BC15


title: H4K20me3-ChIP Tet1 KO H9, B

value: RPGC relative to WT J1


title: T1D patients with Calcified Carotid Plaque BC13_BIS


title: beaf_k_rep3

value: dsRNA to BEAF-32


title: beaf_k_rep2


title: Control_rep_1

value: control

value: Red blood cells

value: 11 weeks

tag: genotype

value: Wild type


title: H4Kac-ChIP Tet1 CM D7, B

value: combined from four biological replicates

value: four biological replicates with different barcodes provided as separate FASTQ files


title: H4Kac-ChIP Tet1 KO H9, B

value: Tet1 KO H9


title: Input.prEpiSC

description: Input.prEpiSC

data_processing:
Bioinformatic analyses ChIP-seq data generated in this study were performed by custom shell scripts in which raw data were first trimmed and filtered by TrimGalore with default parameter; then qualified read pairs were aligned to reference genome by Bowtie2 (release 2.4.1); after that biological and optical duplicates were removed with Sambamba (release 0.7.1); last we used MACS2 (release 2.2.7.1; parameters for broad peaks H3K9me3: --broad --broad-cutoff 0.05 -g hs -f BAMPE) to call peaks. All peaks were filtered with blacklisted regions. The highly reproducible peaks were identified by package IDR, which is a uniﬁed approach to measure the reproducibility of ﬁndings identiﬁed from replicate experiments and provides highly stable thresholds based on reproducibility. For downstream analysis, package deepTools (release 3.5.0) was used to generate genome coverage track files for UCSC visualization and heatmap based on scores of specific genomic regions, such as RPKM value.
Assembly: hg38
Supplementary files format and content: wig files were generated using deeptools; Scores represent RPKM values.
Library strategy: CUT&TAG

source_name: prEpiSC

extract_protocol:
To obtain MII oocytes, the immature oocytes were collected and matured in vitro in medium (Cooper Surgical/SAGE, Trumbull, CT) supplemented with 75 mIU/ml FSH and LH for 24-28h. After the in vitro maturation, the MII oocytes were fertilized by intracytoplasmic sperm injection (ICSI), and then cultured in IVF medium (Vitrolife, catalog. no. 10136). 16-18h later, the fertilization were observed, 2PN zygotes were cultured in G1 medium (Vitrolife) at 37°C in 6% CO2, 5% O2 and 89% N2 for 3 days to 8-cell embryo stage, and then switched to G2 medium (Vitrolife) until the blastocyst stage. The 4-cell, 8-cell and morula embryos (zona pellucida and Polar body removed) were collected into the nuclear isolation buffer for AULIChIP-seq. The inner cell mass (ICM) and mural trophectoderm were separated by gently pipetting in a pipette with a diameter of 40-60 μm and collected into the nuclear isolation buffer.  Human ESCs were dissociated with Accutase (Thermo Fisher Scientific, catalog. no. A1110501) into single cells and washed with PBS solution twice. Then, 50 or 500 hESCs were collected into the nuclear isolation buffer.   Lysates were clarified from micrococcal nuclease-treated nuclei and histone-DNA complexes were isolated with anti-H3K9me3 antibody.
Libraries were prepared according to the Accel-NGS  2S Plus DNA Liibrary Kit from Swift Biosciences.

value: prEpiSC

value: untreated


title: H3K4me3-ChIP Tet1 CM D7, B

value: H3K4me3 (04-745, Millipore)


title: T1D patients with Calcified Carotid Plaque BC13

value: type 1 diabetes

value: blood

value: plasma


title: T1D patients with Calcified Carotid Plaque BC11


title: row_k_rep3

value: S2 cells

value: dsRNA to row


title: beaf_k_rep1


title: H3K4me3-ChIP WT J1, B

value: Embryonic Stem Cell

value: WT J1

value: Pool B

value: RPGC 1x genome coverage


title: Input Tet1 CM D7, B

value: Tet1 CM D7

value: RPGC relative to WT J1


title: control_rep3

value: No treatment


title: Input Tet1 KO H9, B

value: combined from four biological replicates

value: four biological replicates with different barcodes provided as separate FASTQ files


title: Input WT J1, B


title: H3K4me3-ChIP Tet1 KO H9, B

value: Tet1 KO H9


title: T1D patients with Calcified Carotid Plaque BC10


title: T1D patients with Calcified Carotid Plaque BC9


title: control_rep2


title: H3K27me3-ChIP Tet1 KO H9, A

value: H3K27me3 (07-449, Millipore)

value: Pool A


title: H4Kac-ChIP WT J1, B


title: T1D patients with Calcified Carotid Plaque BC8

value: type 1 diabetes


title: H3K27me3-ChIP WT J1, A


title: control_rep1


title: con_rowAB_rep3

data_processing:
ChIP-seq reads were aligned by bowtie2 software to the full genome sequence of Drosophila melanogaster (UCSC version dm3)
Duplicate reads were removed using the samtools rmdup function and uniquely mapped reads were kept (samtools view -q 10).
Peak calling was performed with the callpeak function of the MACS2 tool with a q-value<0.05
For visualization, bedGraph files were created by deepTools (a python tool) with bamCoverage function and normalization parameter set to RPKM
Genome_build: dm3
Supplementary_files_format_and_content: bigwig file for each replica, MACS2 narrowPeak peaks file

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Chromatin immobilization and barcoding performed as previously described (Gutin, J. et al. Fine-Resolution Mapping of TF Binding and Chromatin Interactions. Cell Rep. 22, 2797–2807 (2018).)

value: ROW


title: con_rowAB_rep2


title: Input Tet1 KO H9, A


title: H3K4me3-ChIP WT J1, A

value: H3K4me3 (04-745, Millipore)


title: Input Tet1 CM D7, A


title: H3K4me3-ChIP Tet1 KO H9, A


title: con_rowAB_rep1

value: S2 cells


title: Input WT J1, A


title: con_beafAB_rep3


title: T1D patients with Calcified Carotid Plaque BC5_BIS

value: blood

value: plasma


title: T1D patients with Calcified Carotid Plaque BC5


title: con_beafAB_rep2


title: R6/2.2-, 190808Fra_D19-8915

city: Cambridge

first: Maxwell

last: Gold

state: MA

address: 21 Ames St

institute: MIT

data_processing:
fastq files were aligned to mm10 genome assembly using Bowtie2
The ENCODE blacklist regions and PCR duplicates were removed (using SAMtools and Picard)
Peak calling was done using MACS2 (--nomodel –shift -100 –extsize 200 settings and q-value<0.05)
The consensus peak file for all samples was generated using Diffbind
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for fold changes at specific regions

source_name: HD, COR, 12W, NeuN neg

extract_protocol:
DNA was purified from brain cells using the DNeasy Blood & Tissue Kit (Qiagen), according to the manufacturer’s instructions (as described in pubmed 27146274)
DNA were prepared for high-throughput sequencing according to Illumina's instructions and sequenced on an Illumina platform following the manufacturer’s standard protocol (as described in pubmed 27146274)

value: Brain cells

value: HD

value: COR

tag: cell type neun status

value: NeuN neg


title: R6/2.2+, 190808Fra_D19-8914

source_name: HD, COR, 12W, NeuN pos

value: NeuN pos


title: 10d_rep_2

source_name: Red blood cell in rat

value: stored 10-day periods with citrate–phosphate–dextrose solution with adenine (CPDA) at 4°C

value: Red blood cells

value: 11 weeks

value: Wild type


title: con_beafAB_rep1


title: H3K4me3-ChIP Tet1 CM D7, A

value: Embryonic Stem Cell

value: Tet1 CM D7

value: RPGC relative to WT J1

value: combined from four biological replicates

value: four biological replicates with different barcodes provided as separate FASTQ files


title: T1D patients with Calcified Carotid Plaque BC8_BIS

value: type 1 diabetes


title: WT.6-, 190808Fra_D19-8913

source_name: WT, COR, 12W, NeuN neg

value: WT


title: T1D patients with Calcified Carotid Plaque BC2

value: blood

value: plasma


title: WT.5+, 190808Fra_D19-8908

source_name: WT, COR, 12W, NeuN pos

value: Brain cells


title: H3K27me3-ChIP Tet1 CM D7, A

value: H3K27me3 (07-449, Millipore)

value: Pool A


title: igg_rep2

data_processing:
ChIP-seq reads were aligned by bowtie2 software to the full genome sequence of Drosophila melanogaster (UCSC version dm3)
Duplicate reads were removed using the samtools rmdup function and uniquely mapped reads were kept (samtools view -q 10).
Peak calling was performed with the callpeak function of the MACS2 tool with a q-value<0.05
For visualization, bigwig files were created by deepTools (a python tool) with bamCoverage function and normalization parameter set to RPKM
Genome_build: dm3
Supplementary_files_format_and_content: bigwig file for each replica and bed peaks file per protein (antibody), MACS2 narrowPeak peaks file

source_name: fly heads

growth_protocol: All flies were raised at 25°C in 12-hour light: 12-hour dark cycles on standard diets

value: fly heads

value: Actin-gal4/+ (W1118) control

value: igG


title: R6/2.5-, 190808Fra_D19-8911

value: HD

value: COR

value: NeuN neg


title: T1D patients with Calcified Carotid Plaque B19


title: WT.6+, 190808Fra_D19-8912

value: NeuN pos


title: R6/2.5+, 190808Fra_D19-8910


title: T1D patients with Calcified Carotid Plaque B17


title: T1D patients with Calcified Carotid Plaque B18


title: WT.5-, 190808Fra_D19-8909


title: R6/2.4+, 190808Fra_D19-8906


title: T1D patients with Calcified Carotid Plaque B15


title: WT.4+, 190808Fra_D19-8904


title: h3k4me3_rep2


title: WT.4-, 190808Fra_D19-8905


title: h3k4me3_rep3


title: R6/2.3+, 190808Fra_D19-8902

source_name: HD, COR, 8W, NeuN pos


title: T1D patients with Calcified Carotid Plaque B14


title: R6/2.4-, 190808Fra_D19-8907


title: T1D patients with Calcified Carotid Plaque B16


title: R6/2.3-, 190808Fra_D19-8903

source_name: HD, COR, 8W, NeuN neg


title: WT.3+, 190808Fra_D19-8900

source_name: WT, COR, 8W, NeuN pos


title: WT.2+, 190808Fra_D19-8898


title: igg_rep1


title: h3k4me3_rep1


title: T1D patients with Calcified Carotid Plaque B13


title: woc_rep3

value: WOC


title: woc_rep2


title: WT.3-, 190808Fra_D19-8901

source_name: WT, COR, 8W, NeuN neg


title: R6/2.1-, 190808Fra_D19-8897


title: T1D patients with Calcified Carotid Plaque B12


title: R6/2.1+, 190808Fra_D19-8896


title: R6/2.2-, 190808Fra_D19-8899


title: R6/2.5-, 190808FraA_D19-8923

source_name: HD, STR, 12W, NeuN neg

value: STR


title: T1D patients with Calcified Carotid Plaque B11


title: T1D patients with Calcified Carotid Plaque B5


title: row_rep1

value: ROW


title: WT.5+, 190808FraA_D19-8920

source_name: WT, STR, 12W, NeuN pos


title: R6/2.4-, 190808FraA_D19-8919


title: row_rep3


title: WT.6+, 190808FraA_D19-8924


title: R6/2.4+, 190808FraA_D19-8918

source_name: HD, STR, 12W, NeuN pos


title: woc_rep1


title: R6/2.5+, 190808FraA_D19-8922


title: WT.1-, 190808Fra_D19-8895


title: T1D patients with Fibrous Carotid Plaque AC24

value: type 1 diabetes


title: WT.6-, 190808FraA_D19-8925

source_name: WT, STR, 12W, NeuN neg

value: WT


title: T1D patients with Calcified Carotid Plaque B3

value: blood


title: T1D patients with Calcified Carotid Plaque B4

value: plasma


title: WT.4+, 190808FraA_D19-8916

value: Brain cells


title: hp1c_rep2


title: R6/2.3+, 190627FraA_D19-7003

source_name: HD, STR, 8W, NeuN pos


title: hp1c_rep1


title: hp1c_rep3


title: T1D patients with Calcified Carotid Plaque B2

source_name: blood


title: R6/2.3-, 190627FraA_D19-7009

source_name: HD, STR, 8W, NeuN neg


title: WT.5-, 190808FraA_D19-8921


title: T1D patients with Calcified Carotid Plaque B1


title: T1D patients with Fibrous Carotid Plaque AC21


title: WT.4-, 190808FraA_D19-8917


title: T1D patients with Fibrous Carotid Plaque AC22


title: row_rep2


title: R6/2.2+, 190627FraA_D19-7002


title: WT.3-, 190627FraA_D19-7006

source_name: WT, STR, 8W, NeuN neg


title: WT.3+, 190627FraA_D19-7000

source_name: WT, STR, 8W, NeuN pos


title: hp1b_rep2


title: WT.2-, 190627FraA_D19-7005


title: WT.2+, 190627FraA_D19-6999


title: R6/2.2-, 190627FraA_D19-7008


title: T1D patients with Fibrous Carotid Plaque AC19


title: R6/2.1-, 190627FraA_D19-7007


title: T1D patients with Fibrous Carotid Plaque AC18


title: R6/2.1+, 190627FraA_D19-7001


title: WT.1+, 190627FraA_D19-6998


title: WBJPE166284.94

city: Hangzhou

first: Yuzi

last: Xu

state: Zhejiang

address: Yuhangtang Road

institute: Zhejiang University

data_processing:
Raw read counts for all genes were annotated based on GENCODE Release 35 (GRCh38.p13) (https://www.gencodegenes.org/human/)
The RNA-seq data were normalized by calculating CPM (counts per million) for genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: cartilage

extract_protocol:
Total RNA was isolated from homogenized cartilage using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Duesseldorf, Germany) following the manufacturer's instructions.
RNA-seq library preparation of the cartilage samples was performed using the BRB-seq protocol following manufacturer's protocols.

value: cartilage

tag: disease

value: osteoarthritic human cartilage


title: WBJPE166284.95


title: LT-HSC high old [scATAC-seq]

description:
Clca3a1_high
scATAC-Seq 10x Genomics (v1.1)
peakMatrix.txt

data_processing:
All processing steps were performed by the 10x Chromium cellranger-atac pipeline (v1.2.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peak matrix containing counts per cell in a tab-delimited text file.

extract_protocol:
10,000 cells (per sample, an equal number of cells (n=2500) from 4 mice were used) of Clca1high and Clca1low LT-HSCs were sorted into round-bottom 96 well plate containing 0.04% BSA/PBS.
For nuclei isolation, cells were lysed with chilled lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1% Nonidet P40, 0.01% Digitonin, 1% BSA) on ice for 3 min. Cells were washed with wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 1% BSA). Supernatant was discarded and cells were resuspended in 1X Nuclei Buffer (10x Genomics, PN-2000153/ 2000207). Nuclei suspension was directly subjected to the transposition reaction and used for library preparation.

tag: strain

value: 22-28 months

value: LT-HSC Clca3a1_high

tag: antibody

value: Clca3a1 antibody (DHSB; clone 10.1.1)


title: LT-HSC low old [scATAC-seq]

description:
Clca3a1_low
scATAC-Seq 10x Genomics (v1.1)
peakMatrix.txt

value: LT-HSC Clca3a1_low


title: T1D patients with Fibrous Carotid Plaque AC7


title: LT-HSC young rep2 [ATAC-seq]

description:
HSC_young_Rep2
ATAC-Seq (Nextera)

data_processing:
All processing steps (Adapter trimming, adapter removal, removal of low complexity reads, PCR duplicate removal and mapping (BWA)), as well as conversion to bigWig files, were performed by the nextflow pipeline (https://github.com/nf-core/atacseq).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

extract_protocol:
HSPCs from young and old C57BL/6 mice were sorted into 2% BSA (PBS) and directly subjected to a modified ATAC-Seq protocol (PMID: 27526324).
Tagmented DNA was pre-amplified using 5 PCR cycles using barcoded Nextera PCR primers and the optimal numbers of cycle (30% of max) was determined by qPCR. After the second PCR, the DNA was purified by a MinElute PCR purification column (Qiagen) and subsequently size-selected by Ampure beads to obtain fragments between 50-1000bp.

value: 3-5 months

value: LT-HSC


title: WBJPE166284.91


title: LT-HSC young rep3 [ATAC-seq]

description:
HSC_young_Rep3
ATAC-Seq (Nextera)


title: T1D patients with Fibrous Carotid Plaque AC4


title: WBJPE166284.90

value: healthy human cartilage


title: LT-HSC young rep1 [ATAC-seq]

description:
HSC_young_Rep1
ATAC-Seq (Nextera)


title: T1D patients with Fibrous Carotid Plaque AC12


title: WBJPE166284.88


title: LT-HSC low old rep2 [ATAC-seq]

description:
Clca3a1low_Rep2
ATAC-Seq (Nextera)


title: WT.1-, 190627FraA_D19-7004

value: NeuN neg


title: LT-HSC high old rep2 [ATAC-seq]

description:
Clca3a1high_Rep2
ATAC-Seq (Nextera)


title: WBJPE166284.92


title: LT-HSC low old rep3 [ATAC-seq]

description:
Clca3a1low_Rep3
ATAC-Seq (Nextera)


title: WBJPE166284.93


title: LT-HSC high old rep3 [ATAC-seq]

description:
Clca3a1high_Rep3
ATAC-Seq (Nextera)


title: T1D patients with Fibrous Carotid Plaque AC3


title: LT-HSC high old rep1 [ATAC-seq]

description:
Clca3a1high_Rep1
ATAC-Seq (Nextera)


title: T1D patients with Fibrous Carotid Plaque A18


title: LSK_young [CITE-seq]

description:
LSK_young_LSK_old_exprMatrix.txt
ADT_values.txt

data_processing:
Library strategy: CITE-seq
FASTQ files from the sequencing runs were analyzed using the 10x Genomics Cell Ranger (v3.1.0) software. Briefly, the cellranger count function was used to count the UMIs/cell and the data sets were subsequently normalized by cellranger aggr.
The UMIs of the ADTs were counted and mapped using the Cite-seq-Count tool (https://hoohm.github.io/CITE-seq-Count/) using the following options: CITE-seq-Count -R1 R1.fastqgz -R2 R2.fastq.gz -cbf 1 -cbl 16 -umif 17 -umil 26 -cells # of cellranger output. All data for ADTs were log-transformed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw count matrix (cellranger output) for RNA quantification and log-normalized values for ADTs as a separate text file.

extract_protocol:
HSPCs from young and old C57BL/6 mice were sorted by flow cytometry. Bone marrow (BM) cells were stained simultaneously with antibodies for sorting and CITE-Seq in three steps. BM cells were incubated with an anti-Clca3a1 antibody (DHSB, 10.1.1), then with a lineage mix of biotinylated antibodies together with an anti-syrian hamster PE/Cy7 antibody and finally the cells were stained with streptavidin eF450, anti-cKit-APC and anti-Sca1-FITC. At this last step all Total-seq antibodies were added: anti-PE (Biolegend, 408109) , anti-CD150 (Biolegend, 115945), anti-CD48 (Biolegend, 103447) + isotype controls. After sorting in PBS 0,04% BSA, cells were washed, counted with an automated cell counter (EVE, NanoEnTek) and adjusted to a concentration of 1000 cells/µL.
Libraries were constructed using the Chromium Single Cell 3′ Library Construction Kit v3.
ADT-derived cDNAs and mRNA-derived cDNAs were separated based on their size using 0.6X AMPure XP Beads (Beckman Coulter). The mRNA-derived cDNAs contained in the bead fraction were further processed following the standard 10X Genomics protocol for cDNA library generation. The ADT-derived cDNAs contained in the supernatant were further purified as follows: 1.4X beads were added to obtain a final AMPure XP beads concentration of 2X and samples were incubated 10 min at RT. Supernatant was discarded and beads were washed with Ethanol 80%, air-dried and resuspended in 50 uL water. The same procedure was repeated once. Beads were washed twice with Ethanol 80% and air-dried. The purified ADTs were subsequently eluted in 45 mL water at RT for 5 min. To generate the ADT sequencing library, 45 mL ADTs were used as template in a 100 uL PCR reaction with the NEBNext® High Fidelity Master Mix (NEB), a TruSeq small RNA RPIx (containing i7 index) primer and the 10X Genomics SI-PCR primer (see primer table). The PCR products were incubated with 1.6X AMPure XP beads at RT for 5 min. After washing the beads twice with Ethanol 80%, the ADT library was eluted in 30 mL water. The scRNA-Seq libraries and the ADT libraries were sequenced together on an Illumina NextSeq 500 platform.

value: LSK


title: LT-HSC low old rep1 [ATAC-seq]

description:
Clca3a1low_Rep1
ATAC-Seq (Nextera)


title: WBJPE166284.86


title: T1D patients with Fibrous Carotid Plaque AC1


title: T1D patients with Fibrous Carotid Plaque AC6


title: LSK_old [CITE-seq]


title: H9CerebralOrganoid, control, techRep1, bioRep3 (201026-B2c-susp)

city: Santa Cruz

first: Spencer

last: Seiler

address: 1156 High Street

department: Biomolecular Engineering

institute: UC Santa Cruz

description:
Sample 11
susp_d18_B2c_rsem_genes.results

data_processing:
toil-rnaseq pipeline v 4.0.3 (https://github.com/BD2KGenomics/toil-rnaseq).
Samples were demultiplexed using Illumina i5 and i7 barcodes
Multiple fastqs were merged on a per sample basis using toil-rnaseq
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt v 1.9 through toil-rnaseq
Trimmed sequence reads were mapped to hg38 UCSC assembly using GENCODE v 37 annotations with STAR v 2.7.9a alignment using parameters from ENCODE's DCC pipeline (parameters- outFilterMultimapNmax: 20, outFilterMismatchNmax: 999, outFilterMismatchNoverReadLmax: 0.04, alignSJoverhangMin: 8, alignSJDBoverhangMin: 1, sjdbScore: 1)
Gene and isoform counts were extracted using RSEM v 1.2.25
Assembly: hg38 UCSC assembly with GENCODE v 37 annotations
Supplementary files format and content: tab-delimited text files include gene IDs, expected counts, TPM, and FPKM values for each Sample

source_name: 3D organoid culture

growth_protocol: To generate cerebral organoids, adherent cultures were dissociated into single cells using Accutase Cell Dissociation Reagent (Gibco) and then aggregated in AggreWell 800 24-well plates (STEMCELL Technologies) at a density of 3,000,000 cells per well with 2mL of AggreWell Medium (STEMCELL Technologies) supplemented with Rho Kinase Inhibitor (Y-27632, 10 μM, Tocris, 1254) (day 0). The following day (day 1), 1mL of the AggreWell medium was manually replaced with supplemented medium containing WNT inhibitor (IWR1-ε, 3 μM, Cayman Chemical, 13659, days 1-10) and Nodal/Activin inhibitor (SB431542, Tocris, 1614, 5 μM, days 1-10). On day 2, aggregates were transferred onto a 37 μm filter (STEMCELL Technologies) by carefully aspirating with a  p1000 wide-bore pipette out of the AggreWell plate. The organoids were transferred into ultra-low adhesion 6-well plates (Corning) by inversion and rinsing of the filters with fresh AggreWell medium. Media was changed on days 3, 4, 5, 6, 8, and 10 by manually replacing 2 mL of conditioned media with fresh media. On day 11 and onward, the medium was changed to Neuronal Differentiation Medium containing Eagle Medium: Nutrient Mixture F-12 with GlutaMAX supplement (DMEM/F12, Thermo Fisher Scientific, 10565018), 1X N-2 Supplement (Thermo Fisher Scientific, 17502048), 1X Chemically Defined Lipid Concentrate (Thermo Fisher Scientific, 11905031) and 100 U/mL Penicillin/Streptomycin supplemented with 0.1\% recombinant human Fibroblast Growth Factor b (Alamone F-170) and 0.1\% recombinant human Epidermal Growth Factor (R&D systems 236-EG).

extract_protocol:
Zymo Research RNA Lysis Buffer was used to render cell lysate from whole organoid tissue.
RNA libraries were prepared using Smart-seq2 protocol for RNA-seq directly from the whole organoid lysate

treatment_protocol: Control-group “Suspension” organoids remained suspended in 6-well plates and were maintained with 2 mL media changes every other day for the remainder of the culture. Experimental-group “Automated” organoids were loaded onto the microfluidic chip and experienced media changes of 70 μL once every hour for the remainder of the culture.

value: H9 cerebral cortex organoid (Control-group)

value: Neural precursor cells

value: Suspension

tag: time

value: Day 18


title: H9CerebralOrganoid, control, techRep2, bioRep3 (201026-B2c-susp)

value: WT

tag: treatment


title: WBJPE166284.87


title: H9CerebralOrganoid, control, techRep1, bioRep1 (201026-B2a-susp)

description:
Sample 11
susp_d18_B2a_rsem_genes.results


title: T1D patients with Fibrous Carotid Plaque A15

value: type 1 diabetes

value: blood

value: plasma


title: T1D patients with Fibrous Carotid Plaque A16


title: WBJPE166284.84

value: cartilage

value: osteoarthritic human cartilage


title: H9CerebralOrganoid, control, techRep1, bioRep2 (201026-B2b-susp)

description:
Sample 11
susp_d18_B2b_rsem_genes.results


title: WBJPE166284.77


title: T1D patients with Fibrous Carotid Plaque A17


title: H9CerebralOrganoid, control, techRep2, bioRep2 (201026-B1b-susp)

description:
Sample 10
susp_d18_B1b_rsem_genes.results


title: H9CerebralOrganoid, control, techRep2, bioRep2 (201026-B2b-susp)


title: H9CerebralOrganoid, control, techRep1, bioRep2 (201026-B1b-susp)


title: H9CerebralOrganoid, control, techRep2, bioRep1 (201026-B1a-susp)

description:
Sample 10
susp_d18_B1a_rsem_genes.results


title: WBJPE166284.85


title: H9CerebralOrganoid, control, techRep1, bioRep1 (201026-B1a-susp)


title: T1D patients with Fibrous Carotid Plaque A14


title: WBJPE166284.73


title: T1D patients with Fibrous Carotid Plaque A13


title: WBJPE166284.62


title: H9CerebralOrganoid, control, techRep1, bioRep2 (201026-A2b-susp)

description:
Sample 9
susp_d18_A2b_rsem_genes.results


title: T1D patients with Fibrous Carotid Plaque A12


title: H9CerebralOrganoid, control, techRep2, bioRep1 (201026-A2a-susp)

description:
Sample 9
susp_d18_A2a_rsem_genes.results


title: T1D patients with Fibrous Carotid Plaque A11


title: WBJPE166284.60


title: WBJPE166284.58


title: H9CerebralOrganoid, control, techRep1, bioRep1 (201026-A2a-susp)


title: H9CerebralOrganoid, control, techRep1, bioRep3 (201026-A1c-susp)

description:
Sample 8
susp_d18_A1c_rsem_genes.results


title: WBJPE166284.66


title: T1D patients with Fibrous Carotid Plaque A10


title: WBJPE166284.54


title: H9CerebralOrganoid, control, techRep1, bioRep1 (201026-A1a-susp)

description:
Sample 8
susp_d18_A1a_rsem_genes.results


title: H9CerebralOrganoid, control, techRep2, bioRep2 (201026-A2b-susp)