title: PreB-Lig4-18hrs-AsisI-ENDseq-compareWith-Lig4-53BP1-clone2


title: PreB-Lig4-53BP1-12hrs-AsisI-ENDseq-DNA2i

status: Public on Sep 10 2021

type: SRA

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

country: China

library_source: genomic

data_processing:
library strategy: END-seq
END-seq reads were aligned to mm10 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: Abelson-transformed pre-B cell

growth_protocol: Abelson-transformed murine pre-B cells were grown in DMEM supplemented by 5% FBS, 1% pen/strep, 1% glutamine, 1% sodium pyruvate, 1% nonessential amino acids, and 55 μM β-mercaptoethanol

extract_protocol:
Live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads). libraries were prepared and sequenced following standard Illumina protocols

treatment_protocol: For G0/G1 cell cycle arrest, asynchronously cycling cells were treated with 3 μM imatinib/STI (Selleckchem, S2475) for 48 hr at 1x106 cells/mL. To induce AsiSI-ER cutting, cells were treated with 3 μg/mL doxycycline for 24 hr, followed by 1 μM 4-hydroxytamoxifen for an additional 18 hr

tag: cell type

value: Abelson-transformed pre-B cell

tag: treatment

value: 2uM DNA2i

tag: genotype

tag: asisi induction


title: PreB-Lig4-53BP1-18hrs-AsisI-ENDseq-clone2-contrl-for-APH-POLAi

institute: Center for Excellence in Molecular Cell Science

value: NT


title: PreB-Lig4-53BP1-18hrs-AsisI-ENDseq-clone1-POLAi

value: 1uM POLAi


title: PreB-Lig4-53BP1-18hrs-AsisI-ENDseq-clone2-APH

value: 5uM APH


title: PreB-Lig4-53BP1-18hrs-AsisI-ENDseq-clone1-APH


title: PreB-Lig4-53BP1-18hrs-AsisI-ENDseq-clone1


title: PreB-Lig4-18hrs-AsisI-ENDseq-50uM-APH

value: 50uM APH


title: PreB-Lig4-18hrs-AsisI-ENDseq-5uM-APH


title: PreB-Lig4-12hrs-AsisI-ENDseq-second-POLAi


title: PreB-Lig4-18hrs-AsisI-ENDseq-DMSO

value: DMSO


title: RAD21-depleted_2

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
processed data files:
nanog_rad21_merged_uniq_chimeric.txt
oct4_rad21_merged_uniq_chimeric.txt
prdm14_rad21_merged_uniq_chimeric.txt
sox2_rad21_merged_uniq_chimeric.txt

data_processing:
Library strategy: Tiled-Micro-Capture-C
MCC pipeline (https://github.com/jojdavies/Micro-Capture-C)
ICE normalization (Imakaev et al. Nature Methods 2012)
Genome_build: mm10
Supplementary_files_format_and_content: chimeric junctions files: tab-delimited text files listing the locations of the identified valid junctions

source_name: E14 mouse embryonic stem cells

growth_protocol: Cells were grown, treated and processed as described in the Methods section of the paper.

extract_protocol: Tiled-Micro-Capture-C (Tiled-MCC) combines Micro-Capture-C (MCC) library preparation with oligonucleotide capture enrichment for deep, targeted sequencing of chromatin interactions within regions of interest. Details are described in the Methods section of the paper.

tag: genetic modification

value: auxin

value: E14 mouse embryonic stem cells


title: PreB-WT-G2-6hrs-AsisI-ENDseq

value: G2 arrested+NT

value: WT


title: PreB-Lig4-53BP1-18hrs-AsisI-ENDseq-clone1-contrl-for-APH-POLAi


title: PreB-WT-G2-6hrs-AsisI-ENDseq-APH

value: G2 arrested+5uM APH


title: PreB-Lig4-18hrs-AsisI-ENDseq-HU

value: 10mM HU


title: CTCF_depleted_6

description:
processed data files:
nanog_CTCF_merged_uniq_chimeric.txt
oct4_CTCF_merged_uniq_chimeric.txt
prdm14_CTCF_merged_uniq_chimeric.txt
sox2_CTCF_merged_uniq_chimeric.txt

value: CTCF-AID


title: PreB-Lig4-12hrs-AsiSI-ENDseq-APH-rep2


title: PreB-Lig4-12hrs-AsiSI-ENDseq-POLAi


title: PreB-Lig4-12hrs-AsiSI-ENDseq-control-for-APH-POLAi-rep2


title: PreB-Lig4-12hrs-AsiSI-ENDseq-POLAi-rep2


title: PreB-Lig4-18hrs-AsisI-ENDseq


title: PreB-Lig4-12hrs-AsiSI-ENDseq-control-for-APH-POLAi


title: PreB-Lig4-12hrs-AsiSI-ENDseq-APH


title: PreB-Lig4-53BP1-6hrs-AsiSI-MRE11-clone1 [ChIP-seq]

data_processing:
ChIP-seq reads were aligned to mm10 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were fixed in 1% formaldehyde. Cells were sonicated, lysates clarified, and protein-DNA complexes immunoprecipitated.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads). libraries were prepared and sequenced following standard Illumina protocols

tag: chip antibody


title: PreB-Lig4-6hrs-AsiSI-MRE11 [ChIP-seq]


title: PreB-Lig4-53BP1-18hrs-AsisI-RPA-SSDS-clone1-contrl-for-APH-POLAi [ChIP-seq]

value: RPA


title: PreB-Lig4-53BP1-18hrs-AsisI-RPA-SSDS-clone2-contrl-for-APH-POLAi [ChIP-seq]


title: PreB-Lig4-53BP1-18hrs-AsisI-RPA-SSDS-clone1-POLAi [ChIP-seq]


title: PreB-Lig4-53BP1-18hrs-AsisI-RPA-SSDS-clone2-APH [ChIP-seq]


title: PreB-Lig4-53BP1-18hrs-AsisI-RPA-SSDS-clone2-POLAi [ChIP-seq]


title: PreB-Lig4-18hrs-AsisI-RPA-SSDS-control-for-HU [ChIP-seq]


title: PreB-Lig4-18hrs-AsisI-ENDseq-control-for-HU


title: PreB-Lig4-53BP1-18hrs-AsisI-RPA-SSDS-clone1-APH [ChIP-seq]


title: PreB-WT-18hrs-AsisI-ENDseq


title: PreB-Lig4-18hrs-AsiSI-RPA-SSDS-control-rep2 [ChIP-seq]


title: PreB-Lig4-18hrs-AsiSI-RPA-SSDS-APH-rep2 [ChIP-seq]

value: APH


title: PreB-Lig4-18hrs-AsisI-RPA-SSDS-HU [ChIP-seq]


title: PreB-Lig4-18hrs-AsiSI-RPA-SSDS-POLAi-rep2 [ChIP-seq]

value: POLA inhibitor


title: PreB-Lig4-18hrs-AsiSI-RPA-SSDS-APH [ChIP-seq]

value: Abelson-transformed pre-B cell


title: PreB-Lig4-18hrs-AsiSI-RPA-SSDS-POLAi [ChIP-seq]


title: PreB-Lig4-Rev1-18hrs-AsisI-SARseq-APH-rep2

data_processing:
library strategy: synthesis-associated with repair sequencing (SAR-seq)
SAR-seq reads were aligned to mm10 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were pelleted and resuspended in 1 mL cold PBS. Cold methanol was then added dropwise during slow vortexing to 90% final concentration. Samples were kept on ice for 20 minutes and then stored at -20C until processing.
Copper catalyzes azide-alkyne click chemistry. For biotin labeling via Click-iT reaction, cells were first washed 1x in PBS, permeabilized with 0.2% Triton-X100/PBS for 10 minutes on ice, and then washed 1x in PBS. Then the following were added in order: 3 mM copper sulfate (Sigma), 50 uM biotin azide (ThermoFisher, Cat. No. B10184), and 1X Click-iT additive (ThermoFisher, Cat. No. C10424) for 2 hours shaking at room temperature. Cells were then washed one time in PBS and lysed in 50 mM Tris pH 8.0 with 1% SDS and Proteinase K overnight at 37°C. DNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) according to manufacturer’s instructions, followed by 2.5:1 volume ethanol and 1:10 volume sodium acetate precipitation. DNA pellets were resuspended in TE buffer and sheared to 150-200 bp fragments using Covaris S220 sonicator at 10% duty cycle, 175 peak incident power, 200 cycles per burst, for 240 seconds. DNA was again precipitated by 2.5:1 volume ethanol and 1:10 volume sodium acetate and resuspended in TE buffer. Biotin-EdU fragments were pulled down using MyOne Streptavidin C1 Beads (ThermoFisher, Cat. No. 650-01). Before pulldown, 35 ul of Dynabeads were washed two times with 1 mL 1X Wash and Binding buffer (1X W&B) (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1 M NaCl, 0.1% Tween20) on a DynaMag-2 magnetic separator (Invitrogen, Cat. No. 12321D) and resuspended in 2X W&B (10 mM Tris-HCl pH8.0, 2 mM EDTA, 2 M NaCl, 0.2% Tween20). Equal volume of Dynabeads in 2X W&B were added to DNA in TE and incubated at 24°C shaking in a ThermoMixer C at 800 rpm for 30 minutes. Dynabeads bound to biotin-EdU fragments were washed three times in 1 mL of 1X W&B, two times in 1 mL EB, and one time in 1mL 1X T4 DNA Ligase Buffer (NEB). Dynabeads were resuspended in 50 L end-repair reaction mix (1X T4 DNA Ligase Buffer, 0.4 mM of dNTPs, 2.7 U of T4 DNA polymerase (NEB), 9 U of T4 Polynucleotide Kinase (NEB), and 1 U of Klenow fragment (NEB)) and incubated at 24°C shaking at 800 rpm for 30 minutes. Dynabeads were washed one time in 1mL 1X W&B, two times in 1mL EB, and one time in 1 mL NEBuffer 2 (NEB) and resuspended in 50 L of A-tailing reaction mix (1X NEB dA-Tailing Buffer and 20 U Klenow fragment exo- (NEB)), followed by incubation at 37°C shaking at 800 rpm for 30 minutes. Dynabeads were then washed again 1x in 1 mL NEBuffer 2 and resuspended in 115 L of ligation reaction mix (1X Quick Ligase Buffer (NEB), 6000 U Quick Ligase (NEB), 5 nM annealed TruSeq truncated adapter) and incubated at 25°C shaking at 600 rpm for 20 minutes. Ligation reaction was stopped by adding 50 mM EDTA, and Dynabeads were washed three times in 1 mL 1X W&B, three times in 1 mL EB, and finally resuspended in 8 uL EB + 10 uL 2X Kapa HiFI HotStart Ready Mix (Kapa Biosciences). 10 mM primers 5’-CAAGCAGAAGACGGCATACGA-GATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T-3’ and 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCC CTACACGACGCTCTTCCGATC*T-3’ (* indicates a phosphothiorate bond and a NNNNNN TruSeq index sequence) were added with 37 L PCR reaction mix (20uL 2X Kapa HiFI HotStart Ready Mix, 17 uL H2O) for final volume of 60 uL. DNA was amplified using PCR program: 98°C, 45 seconds; 15 cycles [98°C, 15 seconds; 63°C, 30 seconds; 72°C, 30 seconds]; 72°C, 5 minutes. PCR products were separated from DynaBeads and cleaned using 1.8X volume AMPure Beads XP. 150-200 bp bands were isolated on 2% agarose gel and purified using QIA-quick Gel Extraction Kit (Qiagen). Prior to sequencing using Illumina NextSeq 550 (75 bp single read), library concentrations were calculated by KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). To specifically sequence only EdU-incorporated strands of DNA (Strand-Specific SAR-seq), SAR-seq was followed exactly as above with additional steps prior to PCR amplification. After washing three times in 1 mL 1X W&B and three times in 1 mL EB post-ligation, Dynabeads were washed in 50 uL 1X SSC buffer and resuspended in 20 uL of 0.15 M NaOH for 10 minutes at room temperature to denature DNA strands. Beads were placed back on the DynaMag-2 magnetic separator and washed one time with 20 uL 0.1 M NaOH, one time with 1 mL 1X W&B, two times with 1 mL EB, and resuspended in 8 uL EB + 10 uL 2X Kapa HiFI HotStart Ready Mix. Primers and PCR reaction mix were added as above.

treatment_protocol: For G0/G1 cell cycle arrest, asynchronously cycling cells were treated with 3 μM imatinib/STI (Selleckchem, S2475) for 48 hr at 1x106 cells/mL. To induce AsiSI-ER cutting, cells were treated with 3 μg/mL doxycycline for 24 hr, followed by 1 μM 4-hydroxytamoxifen for an additional 18 hr with 20 uM EdU

tag: molecule subtype

value: EdU incorporated DNA


title: PreB-Lig4-Rev1-18hrs-AsisI-SARseq-contrl-for-APH-POLAi-rep2

value: NT


title: PreB-Lig4-Rev1-18hrs-AsisI-SARseq-APH-POLAi

value: 5uM APH+1uM POLA inhibitor


title: PreB-Lig4-18hrs-AsiSI-RPA-SSDS-control [ChIP-seq]


title: PreB-Lig4-Rev1-18hrs-AsisI-SARseq-POLAi-rep2

value: 1uM POLA inhibitor


title: PreB-Lig4-Rev1-18hrs-AsisI-SARseq-APH

value: 5uM APH


title: AgNO3-1

city: Xiamen

first: Jun

last: Yang

address: 1799 Jimei Road, Xiamen, 361021 PR China

institute: Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Raw reads were filtered to remove the adaptors and low-quality bases using cutadapt 2.10.
The filtered reads were mapped to the T. thermophila genome using HISAT.
Assembled the transcriptomes using StringTie.
The CUFFCOMPARE was used to compare all the assemblies to the genome annotation of T. thermophila.
The counted and normalized expression of lncRNA and protein-coding transcripts were estimated using all mapped reads by RSEM.
Genome_build: Tetrahymena thermophila
Supplementary_files_format_and_content: xls files include FPKM values for each Sample.

molecule: total RNA

organism: Tetrahymena thermophila

source_name: Tetrahymena thermophila total RNA

growth_protocol: Colonial cultures were maintained in the SSP medium

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

treatment_protocol: three replicates was silver nanoparticles treated for 24 hours.

value: treated with Ag+ for 24 hours

tag: strain


title: PreB-Lig4-Rev1-18hrs-AsisI-SARseq-contrl-for-APH-POLAi


title: PreB-Lig4-Rev1-18hrs-AsisI-SARseq-POLAi


title: PreB-Lig4-53BP1-18hrs-AsisI-SARseq-clone2-POLAi

value: 1uM POLAi


title: PreB-Lig4-53BP1-18hrs-AsisI-SARseq-clone2-APH


title: PreB-Lig4-53BP1-18hrs-AsisI-SARseq-clone1-POLAi


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-APH-Klenow-rep2

value: 5uM APH+Klenow-


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-APH-POLAi-DNApolI

value: 5uM APH+1uM POLAi+DNA Pol I


title: PreB-Lig4-53BP1-18hrs-AsisI-SARseq-clone1-APH


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-APH-POLAi-Klenow-

value: 5uM APH+1uM POLAi+Klenow-


title: PreB-Lig4-53BP1-18hrs-AsisI-SARseq-clone2-contrl-for-APH-POLAi


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-APH-POLAi-T4

value: 5uM APH+1uM POLAi+T4 DNA Pol


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-APH-T4-rep2

value: 5uM APH+T4 DNA Pol


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-APH-Klenow-


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-APH-DNApolI

value: 5uM APH+DNA Pol I


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-NT-Klenow-

value: NT+Klenow-


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-NT-T4-rep2

value: NT+T4 DNA Pol


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-NT-DNApolI-rep2

value: NT+DNA Pol I


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-NT-DNApolI

value: Abelson-transformed pre-B cell


title: PreB-Lig4-18hrs-AsisI-SARseq-5uM-APH

value: EdU incorporated DNA


title: PreB-Lig4-18hrs-AsisI-SARseq-50uM-APH

value: 50uM APH


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-NT-T4


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-APH-DNApolI-rep2


title: PreB-Lig4-53BP1-18hrs-AsisI-SARseq-clone1-contrl-for-APH-POLAi

value: NT


title: PreB-Lig4-18hrs-AsisI-SARseq-DMSO

value: DMSO


title: PreB-Lig4-18hrs-AsisI-SARseq-HU

value: 10mM HU


title: PreB-Lig4-18hrs-AsisI-SARseq-control-for-HU


title: PreB-Lig4-12hrs-AsiSI-SARseq-POLAi-rep2

value: 1uM POLA inhibitor


title: PreB-Lig4-12hrs-AsiSI-SARseq-APH-rep2

value: 5uM APH


title: PreB-Lig4-12hrs-AsiSI-SARseq-control-rep2


title: PreB-Lig4-12hrs-AsiSI-SARseq-APH


title: PreB-Lig4-12hrs-AsiSI-SARseq-POLAi


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-NT-Klenow-rep2


title: S3

city: Tianjin

first: Hailong

last: Li

state: China

address: nankai

institute: Nankai

data_processing:
Basecalls performed using CASAVA version 1.4
The software Bcl2fastq (V2.17.1.14) was used for base recognition of the original image data
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg19
Supplementary_files_format_and_content: peaks

organism: Homo sapiens

source_name: HFL6 cell

growth_protocol: Chromatin immunoprecipitation (ChIP) sequencing (ChIP-seq) was used to detect the interaction of the transcription factor FOXO3 with genes in HFL1 cells (1×107).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Crosslinking was terminated with glycine, and the cells were washed twice with precooled phosphate buffer saline (PBS) containing 1 mM PMSF in an ice bath. SDS lysis buffer containing 1 mM PMSF was prepared in an ice bath for 10 min to complete cell lysis.

value: embryonic lung fibroblast

tag: antibady

value: FOXO3 antibady

tag: cell line


title: PreB-Lig4-18hrs-AsisI-in-vitro-EDUseq-APH-T4


title: S1

source_name: HFL4 cell


title: input3

source_name: HFL3 cell


title: S2

source_name: HFL5 cell


title: input1

source_name: HFL1 cell


title: input2

source_name: HFL2 cell


title: PreB-WT-18hrs-AsisI-SARseq

value: WT


title: PreB-Lig4-12hrs-AsiSI-SARseq-control


title: PreB-Lig4-18hrs-AsisI-SARseq


title: PreB-Lig4-18hrs-AsisI-SARseq_strandness


title: CD4_Tcells_Vedolizumab_plus

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

country: Germany

institute: Universitätsklinikum Erlangen

data_processing:
Illumina RTA 1.18.66.3 was used for base calling
Base calling files were converted to FASTQ files and demultiplexed using Cell Ranger v3.0.1 (10x Genomics) mkfastq with standard parameters.
Cell Ranger v3.0.1 quant was used to map the demultiplexed reads to the reference genome (hg38), process cell barcodes, generate expression matrices of UMI (unique molecule identifier) counts per droplet and estimate the number of cells using standard parameters.
Scanpy v1.5.1 was used under Python v3.6.1 to remove low quality cells, discarding cells with less than 1000 UMI, less than 500 genes or more than 15000 UMI. Additionally, cells with more than 20% mitochondrial or more than 20% ribosomal gene content were removed. Prior to normalization, cells not expressing CD4 or CD3D expression is detected were removed. The data was normalized using the computeSumFactors function from the scran package v1.14.6 in R v3.6.3.
The filtered and normalized cells were clustered by similarity in gene expression using the UMAP algorithm for dimension reduction and the Leiden algorithm for community detection. Treg marker high regions were subclustered with the Leiden algorithm and subsequently all cells were categorized as ‘Treg’ or ‘Other’ based on the marker_gene_overlap function from Scanpy. All data visualizations were performed using Scanpy.
Differential expression analysis was performed by the diffxpy package from Scanpy. The fraction of cells expressing each gene was obtained for the two data sets using a custom made python script.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files with raw or normalized UMI counts per gene per cell after filtering in Scanpy plus metadata indicating cell type assignments. *raw.tsv.gz have been filtered for MT+RP, UMI and Gene. *normalized.tsv.gz additionally have been filtered in silico for CD3D+ and are normalized.

source_name: peripheral blood mononuclear cells (PBMC)

extract_protocol:
Vedolizumab negative (FVD-CD4+CD45RO+CD49d+Integrin beta7+VDZ-) and vedolizumab positive (FVD-CD4+CD45RO+CD49d+Integrin beta7+VDZ+) memory CD4 T cells were sorted by FACS. Purified cells were washed, counted and the viability was assessed by Trypan Blue staining. Viable cells were resuspended at a concentration of 1 Mio cells/ml in PBS + 2% FBS. 13000 cells were loaded onto a Chromium Single Cell A Chip (10x Genomics) with Chromium Single Cell 3' v3 Gel Beads (10x Genomics) to generate single cell bead emulsions for reverse transcription and cell bar coding according to the manufacturers instructions
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v3 and i7 Mutiplex kit (10X Genomics) according to the manufacturers instructions. Libraries were sequenced on an Illumina HiSeq 2500 using the recommended read lengths for Chromium Single Cell 3' v3 chemistry.

treatment_protocol: MACS-purified CD4+ T cells were stained for dead cells with Fixable Viability Dye (FVD) efluor780 (Invitrogen) and with following fluorochrome-conjugated extracellular antibodies: CD4 (FITC, VIT4, Miltenyi Biotec), CD45RO (BV510, UCHL1, Biolegend), CD49d (VioBlue, MZ18-24A9, Miltenyi Biotec), Integrin beta 7 (PE, FIB27, Biolegend) and 10 µg/ml of AF647 labelled vedolizumab.

value: human CD4 memory T cells expressing alpha4 and beta7 integrin

value: Incubated with 10 µg/ml vedolizumab (VDZ) for 30 minutes

tag: facs marker

value: FVD- / CD4+ / CD45RO+ / CD49d+ / Integrin beta7+ / VDZ+


title: AZA treated 2

city: Badalona

first: Jeannine

last: Diesch

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Research

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
library strategy: Amplicon sequencing
Basecalls performed using CASAVA version 1.9
Reads were trimmed keeping only the shRNA loop sequence using fastx_trimmer (-f 2, -l 22), collapsed using fastx_collapser and then aligned with the Epi9 reference
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files; aligned count data containing shRNA ID, EntrezID and gene symbol

source_name: SKK-1_AZA treated

growth_protocol: Cells were maintained in RPMI 1640 (Gibco) supplemented with 10% of FBS, 1% penicillin-streptomycin and 1% L-Gutamine (Gibco) at 37ºC in 5% CO2.

extract_protocol:
gDNA was extracted from >8 x 10^6 cells using standard techniques
Libraries were prepared by PCR amplification of shRNA guide strands with custom primers (p7+loop, CAAGCAGAAGACGGCATACGATAGTGAAGCCACAGATGTA; p5+miR3’, AATGATACGGCGACCACCGACTAAAGTAGCCCCTTGAATTC) using AmpliTaq Gold polymerase (Thermofisher). PCR products were gel extracted (340bp band) and sequenced using a custom sequencing primer (miR30EcoRISeq, TAGCCCCTTGAATTCCGAGGCAGTAGGCA)

treatment_protocol: SKK-1 cells were transduced in triplicates with the Epi9 library containing 7296 shRNAs targeting 912 chromatin regulators. After puromycin treatment each replicate was split in two and one half treated with 0.25 µM AZA every two days. 14 days afterwards cells were harvested and gDNA extracted.

tag: tissue source

value: acute myeloid leukemia

tag: genotype/variation

value: transduced with the the Epi9 library containing 7296 shRNAs targeting 912 chromatin regulators

value: 14days azacitidine treatment before harvest


title: Untreated 2


title: Untreated 1


title: AZA treated 3


title: AZA treated 1


title: Untreated 3


title: C646 replicate 2

data_processing:
library strategy: SLAMseq (Thiol (SH)-Linked Alkylation for the Metabolic sequencing of RNA)
Basecalls performed using CASAVA version 1.9
Reads were processed using SlamDunk v0.4.1 running the full analysis procedure (slamdunk all) and aligning against the human genome (UCSC version GRCh38), trimming 12 bp from the 5' end (-5 12), reporting up to 100 alignments for multimappers (-n 100) and activating multimapper retainment strategy (-m), filtering for variants with a variant fraction of 0.2 (-mv 0.2), filtering with a base-quality cutoff of 27 (-mbq 27) and stringency filter set to 2 (requiring ≥ 2 T>C conversions per read).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files; SlamDunk v0.4.1 output containing UTR coordinates named by EntrezID, raw and normalized read counts, as well as T>C conversion statistics. For details see: http://t-neumann.github.io/slamdunk/docs.html

source_name: MOLM-13 cells

extract_protocol:
RNA was extracted using Rneasy Mini kit (Qiagen) and processed using the SLAMseq Anabolic Kinetics Kit (Lexogen Gmbh, Austria) according to the manufacturer’s instructions
Libraries were prepared from 500ng alkylated RNA using the QuantSeq 3’mRNA-Seq for Illumina (FWD) and PCR Add-on Kit for Illumina (Lexogen Gmbh, Austria)

treatment_protocol: MOLM-13 cells were either treated with 10 µM C646 or DMSO (3 replicates each) for 1 hour, labelled with 100 µM 4sU for another hour and SLAM-seq performed

tag: tissue

tag: time

value: 4su labeling for 60 min before harvest:


title: C646 replicate 3


title: C646 replicate 1


title: DMSO control 3


title: DMSO control 2


title: DMSO control 1


title: ppx3

city: Eilat

first: Eran

last: Yanowski

address: North beach

country: Israel

institute: National Center for Mariculture

description: 384 plate holding single-cells

data_processing:
Illumina NextSeq 500 sequencer, at a sequencing depth of 20,000–50,000 reads per cell.
Sequenced reads were mapped to mouse reference genome mm10 using HISAT (v.0.1.6)
specific mitochondrial genes and immunoglobulin (Ig) genes were removed.
cells with either fewer than 300 UMIs or a total fraction of mitochondrial gene expression exceeding 50% were removed
Gene features with high variance to the mean (Tvm) were selected using the parameter Tvm > 0.2 and minimal total UMIs > 100.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
Supplementary_files_format_and_content: The file sample_metadata_excel.xlsx includes cell barcodes for each cell ID.

source_name: Isolated islets of Langerhans

growth_protocol: 12 week-old male mice were subjected to partial pancreatectomy or sham-operations. Aminals were let 4-weeks off recover (for pancreas regeneration) before obtaining isolated islets

extract_protocol:
Islets were isolated from pancreata using Collagenase digestion and Histopaque gradient separation, hand-picked, dissociated using Trypsin, FACS-sorted to single cells and seeded separately in 384 well-plates with lysis buffer.
Single cells are lysed, and the 3' ends of mRNAs are annealed to UMIs containing a T7 promoter. The mRNA is reverse-transcribed to cDNA and amplified by IVT. The RNA strands are fragmented and annealed to sequencing adapters, followed by RT to generate barcoded cDNA libraries that are ready for sequencing. single-cell MARSseq

treatment_protocol: Prior to surgical procedure, 10-week old male mice were treated with Tamoxifen (8mg) for two weeks.

value: islets of Langerhans

tag: cell source

value: Sox9-lineage traced cells

value: Sox9-CreER; tdTomato

tag: Sex

value: male

tag: tomato status

value: Negative

value: partial pancreatectomy


title: CD4_Tcells_Vedolizumab_minus

tag: cell type

tag: treatment

value: FVD- / CD4+ / CD45RO+ / CD49d+ / Integrin beta7+ / VDZ-


title: ppx 1

description: 384 plate holding single-cells

value: Positive


title: ppx2

description: 384 plate holding single-cells


title: Control Replicate 1

type: RNA

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

country: USA

institute: Yale University

scan_protocol: not provided

data_processing: Raw data were normalized and analyzed by GeneSpring GX software version 11.5 (Agilent Technologies).

label: biotin

source_name: Human hepatic cell line (Huh7 cells)

label_protocol: Data were generated at the NYU Langone Genome Technology Center.

growth_protocol: Human hepatic cells (Huh7) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% FBS

extract_protocol: cells were harvested in Trizol and RNA was purified using the RNeasy Isolation Kit (Qiagen). The purity and integrity of total RNA was verified using the Agilent Bioanalyzer and hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the manufacturer’s instructions. Two biological replicates for each condition were used for analysis.

treatment_protocol: 120 μg/ml native LDL (nLDL, to cholesterol enrich), 5 μM statin (to cholesterol deplete) or vehicle control for 24 h

value: control


title: Statin Replicate 2

hyb_protocol: according to the manufacturer’s instructions

value: statin


title: Sham 3

description: 384 plate holding single-cells

value: sham


title: LDL Replicate 1

value: LDL


title: Statin Replicate 1


title: LDL Replicate 2


title: D1_21_PA

city: Bethesda

first: Samantha

middle: Grace

last: Tilson

state: Maryland

address: 10 Center Dr., Building 10, Room 10S257

department: Liver Diseases Branch

institute: NIH, NIDDK

data_processing:
Initial QC, basecalling, alignment, filtering, peak-calling, counts, etc. was performed using the CCBR pipeliner tool (https://ccbr.github.io/Pipeliner/).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: RawCounts_Subread_Genes.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Hepatocyte-like cell

growth_protocol: Human induced pluripotent stem cells were differentiated into hepatocyte-like cells over 30 days using an established, chemically-defined protocol. On day 23 of the differentiation protocol, cells were split and placed into 3D culture in matrigel. The HLCs were grown for 6 days in matrigel before being treated with lipids for 24 hours and collected for RNA sequencing.

extract_protocol:
RNA was extracted with the Qiagen RNeasy Micro Kit per the manufacturer's instructions.
20 ng of total RNA was used for the construction of sequencing libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Cells were treated for 24 hours with control medium or medium supplemented with 0.25mM oleic acid or 0.25mM palmitic acid.

tag: genotype

value: PNPLA3 KO

value: Hepatocyte-like cells

value: FSPS13B #21

tag: differentiation

value: HLC Differentiation #1

value: PA


title: Control Replicate 2


title: D2_6_PA

value: FSPS13B #6

value: HLC Differentiation #2


title: Sham 2

description: 384 plate holding single-cells

value: islets of Langerhans

value: Sox9-lineage traced cells

value: Sox9-CreER; tdTomato

value: mixed sample:Positive first 4 rows, negative the rest


title: D1_6_PA


title: D2_21_OA

value: OA


title: Sham 1

description: 384 plate holding single-cells

value: male

value: Positive


title: D2_6_OA


title: D1_21_OA


title: D1_21_C

value: Control


title: D2_21_PA


title: D2_6_C


title: CFIm68 si2 passage 3

city: Montreal

first: Thomas

middle: F.

last: Duchaine

state: Quebec

address: 3655 Promenade Sir William Osler

country: Canada

institute: McGill University

data_processing:
Raw reads were preprocessed to remove any adapter sequences using Trimmomatic v0.36 and mapped to mm10 genome with STAR v2.7.2b. Subsequent identification and quantification of PAS peaks were performed according to Lianoglou et al. (2013)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files contain read tracks
Supplementary_files_format_and_content: counts files were generated using featureCounts against a curated PAS list

source_name: fibroblast cells

growth_protocol: Cells were maintained in DMEM supplemented with 10% calf serum in a humidified incubator at 37C with 5% CO2

extract_protocol:
Qiazol (Qiagen) was added directly to PBS rinsed cells for RNA collection. Column extraction of total RNA was done using NEB or Qiagen kits following instructions.
Libraries were prepared using Lexogen QuantSeq 3' mRNA-seq (REV) library prep kit following instructions.

treatment_protocol: Cells were reverse transfect with siRNAs at a final concentration of 10uM for 72 hours using Lipofectamine RNAiMAX (ThermoFisher)

tag: sirna

value: CFIm68 si2


title: CFIm68 si1 passage 3

value: CFIm68 si1


title: CFIm68 si2 passage 4


title: CFIm68 si2 passage 5


title: CFIm59 si2 passage 8

value: CFIm59 si2


title: CFIm68 si1 passage 5


title: CFIm59 si2 passage 7


title: CFIm68 si1 passage 4


title: D2_G342_PA

value: PNPLA3 I148M

value: Hepatocyte-like cells

value: FSPS13B G342


title: D1_6_C

value: PNPLA3 KO

value: HLC Differentiation #1


title: D1_G342_C


title: D1_G342_OA


title: CFIm59 si1 passage 7

value: CFIm59 si1


title: CFIm25 si2 passage 8

value: CFIm25 si2


title: CFIm59 si1 passage 8


title: CFIm59 si2 passage 6


title: D2_21_C

value: FSPS13B #21

value: HLC Differentiation #2


title: CFIm59 si1 passage 6


title: D1_30_PA

value: WT

value: FSPS13B #30

value: PA


title: CFIm25 si1 passage 8

value: CFIm25 si1


title: D2_9_PA

value: FSPS13B #9


title: CFIm25 si2 passage 7


title: D1_9_PA


title: D2_30_OA

value: OA


title: D2_9_OA


title: D1_30_OA


title: control siRNA passage 8

value: control siRNA


title: CFIm25 si1 passage 7


title: D2_G342_C

value: Control


title: CFIm25 si1 passage 6


title: D2_G342_OA

value: PNPLA3 I148M


title: control siRNA passage 5


title: control siRNA passage 6


title: D1_G342_PA

value: Hepatocyte-like cells


title: D2_9_C


title: control siRNA passage 4


title: CFIm25 si2 passage 6


title: control siRNA passage 3


title: spt6-1004 Input ChIP-Seq replicate 2

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: ChIP-Seq of Input in spt6-1004 S. cerevisiae cells grown at 30oC

data_processing:
Reads were trimmed using cutadapt (base quality threshold of 20)
Reads were aligned to a combined S. cerevisiae + S. pombe genome using Bowtie2
Average fragment size of DNA molecules sequenced was determined by cross-correlation (done in R using the SPP package)
Reads mapping to S. cerevisiae genome were separated from the reads mapping to the S. pombe genome
Coverage files (wig format) were produced using the igvtools count function, extending reads by (length of fragment sizes - average read length) for each library.
wig format files were converted to the bedgraph format
Spike in normalization was done as described previously (Orlando et al., 2014), correcting for variations in the input samples.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: The bedGraph files contain spike-in normalized coverage of DNA fragments obtained after immunoprecipitation. Average fragment length determined using cross-correlation

organism: Saccharomyces cerevisiae

source_name: log phase S. cerevisiae

growth_protocol: S.cerevisiae cells were grown to OD600 ≈ 0.6 (~2x10^7 cells/ml) in YPD at 30ºC

extract_protocol:
ChIP-seq was performed as described previously (Gopalakrishnan et al. 2019, Nucleic acids research) and is reproduced here. Cultures were cross-linked by the addition of formaldehyde to a final concentration of 1% followed by incubation with shaking at room temperature for 20 minutes. Glycine was added to a final concentration of 125 mM and the incubation was continued for 10 minutes. The cells were pelleted and washed twice with cold 1x TBS (100mM Tris, 150 mM NaCl, pH 7.5) and once with cold water. The cell pellets were then suspended in 800 µl cold LB140 buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1x cOMPLETE Protease Inhibitor tablet (Roche)). One ml of glass beads was added and the cells were lysed by bead beating for 8 minutes at 4oC with incubation on ice for 3 minutes after every one minute. The lysate was collected and centrifuged at 12,500 rpm for 5 minutes and the resulting pellet was washed once with 800 µl cold LB140 buffer. The pellet was resuspended in 580 µl cold LB140 buffer and sonicated in a QSonica Q800R machine for 20 minutes (30 seconds on, 30 seconds off, 70% amplitude). The sonicated samples were centrifuged at 12,500 rpm for 30 minutes and the resulting supernatant was taken for the immunoprecipitation step. 300-500 µg of S. cerevisiae chromatin was mixed with 33-55 µg (10%) of S. pombe chromatin and the volume was brought up to 800 µl with WB140 buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate). This was used as the input for the immunoprecipitation reaction. Antibody was added to the input and the samples incubated overnight at 4oC with end-over-end rotation. Fifty µl of Protein G sepharose beads (GE healthcare) pre-washed twice in WB140 was added to the IPs and samples were incubated for 4 hours at 4oC with end-over-end rotation. . The beads were washed twice with WB140, twice with WB500 (50 mM HEPES-KOH, pH 7.5, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), twice with WBLiCl (10 mM Tris pH 7.5, 250 mM LiCl, 1mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate) for two minutes each and once with TE (10 mM Tris pH 7.4, 1 mM EDTA) for five minutes. The immunoprecipitated material was eluted twice with 100 µl TES (50 mM Tris pH 7.4, 1 mM EDTA, 1% SDS) at 65oC for 30 minutes. The eluates were incubated at 65oC overnight to reverse the crosslinking. Two hundred µl of TE was added to the eluates followed by RNase A/T1 to a final concentration of 0.02 µg/µl. The samples were incubated at 37oC for 2 hours. Proteinase K was added to a final concentration of 0.4 mg/ml and samples were incubated at 42oC for 2 hours. DNA was purified using Zymo DCC (for ChIP-Seq).
The library preparation was done as described in Wong et al., 2013, Current protocols in molecular biology

tag: temperature

tag: chip target

value: none (input)


title: spt6-1004 Input ChIP-Seq replicate 3

tag: strain


title: spt6-1004 Input ChIP-Seq replicate 1


title: D1_9_C

tag: cell line


title: D2_30_C


title: CD4/ALK4-KO_rep1

city: Athens

first: Maria

last: Semitekolou

address: 4 Soranou Ephessiou St.

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

data_processing:
Quality Control was performed at the fastq raw data file for each sample using the “FASTQC” software.
FastQ files were aligned to mm10 mouse genome using HISAT2 (Kim et al., 2015).
Counts were defined using HTSeq htseq-count command with the  “intersection non empty” option (Anders et al., 2015)
The count files were used as Input for DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files provide raw read counts for every sample
Supplementary_files_format_and_content: csv file providing Differential Expression Analysis output for KO samples vs Wild Type

source_name: Lung-tumor infiltrating CD4+ T cells

extract_protocol:
Lung tissues from CD4/ALK4-KO or WT mice bearing LLC-OVA lung tumors were collected, minced and incubated with Liberase TL and DNase. Single-cell suspensions were prepared and the tumor-infiltrating leukocyte cell fraction was collected at the interface between 40% and 80% discontinuous percoll gradient. CD4+ T cells were isolated from the tumor-infiltrating leukocyte fraction and RNA was extracted using commercially available kits.
RNAseq libraries were prepared with the illumina TruSeq RNA v2 kit using 1 μg of total RNA, checked with the Agilent bioanalyzer DNA1000 chip, quantitated with the qubit HS spectrophotometric method and pooled in equimolar amounts for Sequencing. Approximately 25Million, 75 bp long, Single-End reads were generated for each sample with illumina NextSeq500 sequencer.

treatment_protocol: 5x10e5 LLC-OVA cells were intravenously inoculated into CD4CreERT2+/-/Acvr1bfl/fl (CD4/ALK4-KO) or WT mice and the lung tumors formed were excised after 18-22 days.

value: Lung tumor

value: CD4+ T cells

tag: strain background


title: control siRNA passage 7


title: wild-type Input ChIP-Seq replicate 2

description: ChIP-Seq of Input in wild-type S. cerevisiae cells grown at 30oC

value: wild-type


title: CD4/ALK4-KO_rep2


title: Wild_Type_rep2


title: Cdh-cre Myct1 fl/fl Endothelium

city: Palo Alto

first: Christoph

last: Thaiss

state: CA

address: 3181 Porter Dr.

department: Immunology and Pathology

institute: Arc Institute

data_processing:
Cell Ranger 2.1.1 pipeline used for data processing
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Endothelial Cells

extract_protocol:
Tumor were harvested from 4 individual mice and pulled together to digest and process for signle cell suspension with a cocktail of Collagenase-II, Dispase-II, and Deoxyribonuclease
Single-cell RNA-seq libraries were prepared using version 1 Chromium Single-cell 3′ Library, Gel Bead & Mutiplex Kit (10X Genomics).

value: Tumor

value: Cdh-cre Myct1 fl/fl


title: Wild_Type_rep1


title: wild-type Input ChIP-Seq replicate 3


title: WT Endothelium


title: D1_30_C

value: HLC Differentiation #1


title: spt6-1004 Rpb1 ChIP-Seq replicate 3

description: ChIP-Seq of Rpb1 in spt6-1004 S. cerevisiae cells grown at 30oC


title: D2_30_PA

value: WT

value: HLC Differentiation #2


title: wild-type Input ChIP-Seq replicate 1


title: HWNHFBGX3_Autg.3.t0_17s004153.1.1_Paulsen_lane117s004153

city: Heidelberg

first: Joschka

last: Hey

state: Deutschland

address: Im Neuenheimer Feld 280

department: Cancer epigenomics

institute: DKFZ

data_processing:
RNA-seq data was processed with the nf-core RNA-seq pipeline (Ewels et al., 2020) (v. 1.2). Default parameters were used unless mentioned otherwise. Sequences were aligned to the mouse reference genome mm10 by application of the software HISAT2, with --unstranded option. For single-end data the -singleEnd option was applied. Transcripts were assembled using StringTie and gene code gene annotation release M20 (Frankish et al., 2019). Gene counts were generated with Stringties prepDE.py script (setting: -eb).
For the identification of differentially expressed genes, the R package DESeq2 was used (Love, Huber, & Anders, 2014). For group-wise comparison of baseline replicates, the littermate was included in the design formula to adjust for batch effects. For the LPS stimulation experiment the date of library preparation was included. The adjusted p-value as well as log2 fold change required to fulfil statistical significance is mentioned in the figure legends.
Genome_build: mm10
Supplementary_files_format_and_content: Count file as tab-delimited text file. Excel sheet containing differentially expressed genes; Scnn1b-transgene vs wildtype at baseline

source_name: airway macrophages

growth_protocol: One ml dispase (BD Biosciences, Heidelberg, Germany) was intratracheally instilled into the lungs and plugged inside by instillation of 300 ml low melting agarose (1%). When agarose is solid, whole lung was extracted including the tracheobronchial tree, put into 2 ml dispase and left for 35 min at RT. Reaction was stopped with complete DMEM, lungs were mashed with a plunger, tracheobronchial tree was removed and cell suspension put through a 100 mm cell strainer (BD Biosciences, Heidelberg, Germany). After red blood cell lysis (RBC lysis buffer, eBiosciences, Dreieich, Germany) cell suspension was enriched by magnetic bead separation using CD45+ magnetic beads, according to manufacturer’s instructions (Miltenyi Biotech, Bergisch Gladbach, Germany). After positive selection cells were counted and antibody-concentration used according to obtained cell numbers, as prior determined by titration. Cells were incubated for 5 min with purified rat IgG2b anti-mouse CD16/CD32 receptor antibody (BD Biosciences, Heidelberg, Germany) in FACS buffer containing 1 % BSA (SERVA Electrophoresis GmbH, Heidelberg, Germany) and 5 mM EDTA (Sigma-Aldrich, Darmstadt, Germany), following staining with fluorochrome-conjugated antibodies against murine CD45.2, Siglec-F and CD11c (see Supplementary table 5). Samples were stained with 7-AAD (0.25 mg/ml per 1x106 cells; Biolegend, London, UK) 5min prior to sort, for dead cell exclusion. Sorting was performed at the EMBL Flow Core Facility, Heidelberg, Germany. AMs were sorted using a standard BD Fusion equipped with 100-mW 405-nm, 100-mW 488-nm, 80-mW 561-nm, 80-mW 640-nm lasers and an ND2.0 filter in front of the FSC photodiode, a nozzle size of 100 μm, and corresponding BD FACSFlow sheath pressure of 20 psi, matched with a transducer frequency of 32 kHz. Input pressure was adjusted to ensure that every fifth to sixth drop was populated by an event. Purity check of sorted cells was performed on selected samples from each run confirming purities ranging 95-99 %.

extract_protocol:
DNA and RNA were isolated using TRIzol reagent (Sigma Aldrich, Darmstadt, Germany) and further AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) purification, following the manufacturer’s instructions. For RNA isolation (RNase-free DNAse set, Qiagen) DNAse I digestion was performed on the column. Proteinase K digestion was applied for RNA and DNA isolation (Puregene Proteinase K, Qiagen). Prior to library preparation, DNA and RNA quality was checked by Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA). All RNA samples reached an RNA integrity number (RIN) > 8.5.
For the paired-end baseline as well as LPS- and medium-treated replicates of wt- and tg-AM, sequencing libraries were prepared by the DKFZ Genomics and Proteomics Core Facility from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit according to the manufacturer’s instructions. For sequencing, samples were sequenced on a HiSeq 2000 v4, paired-end, 125 bp platform (Illumina). Single-end baseline replicates were prepared by the EMBL Genomics Core Facility from total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.  Sequencing was performed on a Next Seq 500, single-end, 75 bp platform.

value: lung

value: airway macrophages

tag: batch


title: spt6-1004 Rpb1 ChIP-Seq replicate 2


title: HWNHFBGX3_Autg.2.t0_17s004152.1.1_Paulsen_lane117s004152


title: HWNHFBGX3_Autg.1.t0_17s004151.1.1_Paulsen_lane117s004151


title: spt6-1004 Rpb1 ChIP-Seq replicate 1


title: wild-type Rpb1 ChIP-Seq replicate 3

description: ChIP-Seq of Rpb1 in wild-type S. cerevisiae cells grown at 30oC


title: il11ra mutant fin, 24 hpa, rep3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus Ensembl zebrafish genome version danRer11 (GRCz11) using STAR 2.7.3a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.26. The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers
Genome_build: danRer11
Supplementary_files_format_and_content: library size normalized counts

organism: Danio rerio

source_name: Caudal fin

extract_protocol:
Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in -80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
200-500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina)

tag: developmental stage

value: adult

value: il11ra mutant

value: fin amputation

tag: time point

value: 24 hpa


title: HW7VVBGX3_t0.Wt2_17s004140.1.1_Paulsen_lane117s004140

value: wildtype

tag: tissue


title: HW7VVBGX3_t0.Wt3_17s004141.1.1_Paulsen_lane117s004141


title: wild-type Rpb1 ChIP-Seq replicate 2


title: Wild-type fin, 24 hpa, rep3

value: wild type


title: il11ra mutant fin, 24 hpa, rep2


title: wild-type Rpb1 ChIP-Seq replicate 1


title: il11ra mutant fin, 24 hpa, rep1


title: wild-type Spt5-V5 ChIP-Seq replicate 3

description: ChIP-Seq of Spt5-V5 in wild-type S. cerevisiae cells grown at 30oC


title: spt6-1004 Spt5-V5 ChIP-Seq replicate 3

description: ChIP-Seq of Spt5-V5 in spt6-1004 S. cerevisiae cells grown at 30oC


title: spt6-1004 Spt5-V5 ChIP-Seq replicate 2


title: il11ra mutant ventricle, 96 hpci, rep2

source_name: Cardiac ventricle

value: cardiac cryoinjury

value: 96 hpci


title: spt6-1004 Spt5-V5 ChIP-Seq replicate 1


title: wild-type Spt5-V5 ChIP-Seq replicate 2


title: wild-type Spt5-V5 ChIP-Seq replicate 1


title: Wild-type ventricle, 96 hpci, rep2


title: il11ra mutant ventricle, 96 hpci, rep1


title: Wild-type ventricle, 96 hpci, rep1


title: Wild-type fin, 24 hpa, rep2


title: spt6-1004 Abd1-HA ChIP-Seq replicate 1

description: ChIP-Seq of Abd1-HA in spt6-1004 S. cerevisiae cells grown at 30oC


title: spt6-1004 Abd1-HA ChIP-Seq replicate 2


title: HW7VVBGX3_t0.Wt1_17s004139.1.1_Paulsen_lane117s004139


title: SAN-rep-3-neg

city: Warszawa

first: Cecilia

middle: Lanny

last: Winata

address: Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

data_processing:
Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10.
Sequenced reads were trimmed for adaptor sequence (cutadapt -a CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG -q 20 -O 10 -m 25 -o), and masked for low-complexity or low-quality sequence, then mapped to indexed Danio rerio.GRCz11.cdna. (Ensembl Genes 92)
transcripts were quantified using Salmon algorithm (Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C: Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 2017, 14(4):417-419) and further pre-processed using quantile normalization and centralization as described in (Wirth et al., Expression cartography of human tissues using self organizing maps. BMC Bioinformatics 2011, 12:306).
Data were then used to train a self-organizing map (SOM), translating the expression profiles of all 19,854 genes measured into a two-dimensional map of 30x30 metagene profiles using the Bioconductor R-package ‘oposSOM’ (Loffler-Wirth H, Kalcher M, Binder H: oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor. Bioinformatics 2015, 31(19):3225-3227).
We validated the oposSOM differential expression analysis using results of DESeq2 as an independent method analysis to compare between GFP+ and ROH fractions.
Genome_build: Zebrafish Genes (GRCz11) (Ensembl Genes 92)
Supplementary_files_format_and_content: tab delimited file format.

molecule: polyA RNA

source_name: Heart Cells

extract_protocol:
Hearts from transgenic line sqet33mi59BEt were extracted at 72hpf, flash frozen on ice, cells were lysed and sorted into two fractions by FACS and RNA was harvested using Trizol reagent.
cDNA synthesis was performed using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (TakaRa) was used for cDNA synthesis. RNA-seq libraries were generated by Illumina Nextera XT kit according to manufacturer's protocol. Sequencing libraries were purified with Agencourt AMPure XP PCR purification beads (Beckman Coulter, USA) and fragment distribution was assessed by using High Sensitivity D1000 ScreenTape and Agilent 2200 TapeStation system (Agilent Technologies, USA). KAPA library quantification kit (Kapa Biosystems, USA) was used to quantify the libraries. RNA-seq was performed with paired-end sequencing (2×75bp reads) on the NextSeq 500 (Illumina, USA).

tag: transgenic line

value: 72 hpf

value: heart

tag: gfp status

value: negative


title: wild-type Abd1-HA ChIP-Seq replicate 2

description: ChIP-Seq of Abd1-HA in wild-type S. cerevisiae cells grown at 30oC

value: wild-type


title: SAN-rep-3-pos

source_name: Heart Cells from sinoatrial ring

value: positive


title: wild-type Abd1-HA ChIP-Seq replicate 3


title: wild-type Abd1-HA ChIP-Seq replicate 1


title: SAN-rep-2-pos


title: healthy control-3

city: zhengzhou

first: Mingyue

last: Shi

address: no.7 weiwu road

institute: Henan Provincial People’s Hospital

description: healthy control-3

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Oﬀ-Line Base Caller software, v1.8)
Sequence quality was examined using the FastQC software.
The trimmed reads (trimmed 5’, 3’-adaptor bases using cut-adapt) were aligned to reference genome using Hisat2 software.
The transcript abundances for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown.
The diﬀerentially expressed genes and transcripts were fltered using R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown, then use CPAT
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: PBMCs

extract_protocol:
Total RNA was extracted from above samples by using Trizol reagent (Invitrogen)
KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing library.

value: PBMCs

tag: disease state

value: healthy

tag: disease subtype


title: healthy control-2

description: healthy control-2

tag: cell type


title: Wild-type fin, 24 hpa, rep1

tag: genotype

tag: treatment


title: SAN-rep-2-neg


title: spt6-1004 Abd1-HA ChIP-Seq replicate 3


title: SAN-rep-1-pos


title: SAN-rep-1-neg


title: R/R-AML-2

value: AML

value: refractory/relapsed AML


title: R/R-AML-1


title: S-AML-2

value: refractory secondary AML


title: R/R-AML-3


title: healthy control-1

description: healthy control-1


title: S-AML-1


title: S-AML-3


title: AML-4

value: de novo AML


title: AML-3


title: BrainChip_Veh_TopChannel_S4

first: Iosif

last: Pediaditakis

address: 27 Drydock avenue

institute: Emulate Inc.

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
Genome_build: GRCh38
Supplementary_files_format_and_content: Unique gene hit counts

source_name: (iPSC)-derived dopaminergic neurons, primary asrocytes, primary microglia, primary pericytes from the brain channel of the Brain-Chip

growth_protocol: Brain-Chip and cell seeding: A mixture of dopaminergic neurons, astrocytes, microglia, and pericytes was seeded in the upper brain channel of the Brain-Chips at the following concentrations: 2 million cells/mL for dopaminergic neurons, 2 million cells/mL for astrocytes, 0.1 million cells/mL for microglia, and 0.1 million cells/mL for pericytes. After cell seeding, the upper channel of the Brain-Chip was maintained in DopaNeurons medium and incubated overnight at 37°C (Day 0). The following day (Day 1), the lower vascular channel was rinsed with human serum-free endothelial medium supplemented with 2% platelet-poor plasma-derived serum, 10 μM Y27632, and then BMECs were seeded at a concentration of 16-20 million cells/mL to ensure the very tight endothelial monolayer found in the human blood-brain barrier, and the chips were flipped immediately to allow  BMECs to adhere to the ECM-coated part of the membrane. After 2 h incubation, the chips were flipped back to let the rest of BMECs sit on the bottom and sides of the channel to form a capillary lumen. The vascular channel of the Brain-Chip was maintained overnight. On Day 2, the Brain-Chips were connected to the Zoë® culture module and perfused continuously through the brain and vascular channel at a flow rate of 30 μl hr-1 and 60 μl hr-1 respectively, using each channels' respective media.The conventional cell cultures and the Brain-Chips were seeded using the same ECM composition as well as cell composition and seeding density. Building of a neurovascular unit model in vitro, requires seeding of the different cell types at different time points. Specifically, the first experimental day (D0) the dopaminergic neurons, astrocytes, microglia, and pericytes are seeded on the apical side, followed by the seeding of the endothelial cells (D1) on the basolateral side of the 0.47 cm2 Transwell-Clear permeable inserts (0.4-μm pore size). For the apical compartment we used iCell DopaNeurons Media, while for the basolateral compartment we used HBMEC medium. The cells maintained under static conditions throughout the duration of the experiment (D8). The culture medium was replaced daily in both compartments.

extract_protocol:
RNA was extracted using TRIzol (Life Technologies) according to manufacturer’s guidelines
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Addition of exogenous alpha-synuclein to brain channel: Human recombinant αSyn monomers and pre-formed fibrils were purchased from Abcam (Monomers; ab218819, Fibrils; ab218819), and were diluted in DopaNeurons Media to a final concentration of 4 μg/mL.  For treatment, freshly prepared monomers and fibrils were used.  On Day 2, the upper channel of the Brain-Chip was exposed to monomeric or fibrillar αSyn. After three days of exposure (D5), the medium was changed, and the culture was maintained using DopaNeurons Media (αSyn free) for three more days (D8).

tag: applied mechanostimulation

value: flow (30 µl/hr)


title: AML-2


title: BrainChip_Veh_TopChannel_S3

value: (iPSC)-derived dopaminergic neurons, primary asrocytes, primary microglia, primary pericytes


title: BrainChip_Veh_TopChannel_S1


title: BrainChip_Veh_TopChannel_S2


title: CCC_Veh_S4

source_name: (iPSC)-derived dopaminergic neurons, primary asrocytes, primary microglia, primary pericytes from the upper compartment of the transwell


title: AML-1


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC087.T1

city: San Francisco

first: Bushra

last: Samad

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

description: Tumor associated conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Colorectal  tumor specimen

data_processing:
RNAseq reads were first aligned to reference of rRNA and mitochondrial rRNA using BWA-mem
The remaining reads were aligned to the Ensembl GRCh38.85 transcriptome build using STAR
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: Colon & Rectum

extract_protocol:
The mRNA was isolated via DinaBead Direct, then converted into amplified cDNA using Tecan Ovation RNA-Seq System V2 kit, following the manufacturer protocol.
The dsDNA went through tagmentation, amplification and clean up with AMPure XP beads steps, using the Illumina Nextera XT DNA Library Prep Kit. Quality control analysis was performed on the resulting pooled libraries with the Agilent Bioanalyzer HS DNA chip to assess fragment size distribution and concentration

value: Colorectal cancer

tag: sorted compartment

value: CD4+ and CD8+ T cells

tag: specimen

value: primary Colorectal  tumor specimen

tag: cd38 level


title: CCC_Veh_S3


title: CD4+ and CD8+ T cells from metastasic Colorectal  tumor specimen, IPICRC078.T2

description: Tumor associated conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a metastasic Colorectal  tumor specimen

value: metastasic Colorectal  tumor specimen


title: CCC_Veh_S1


title: CCC_Veh_S2


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC075.T1


title: BrainChip_BottomChannel_aSyn_Monomer_S3

source_name: (iPSC)-derived brain endothelial cells from the vascular channel of the Brain-Chip

value: (iPSC)-derived brain endothelial cells

value: flow (60 µl/hr)


title: BrainChip_BottomChannel_aSyn_Monomer_S4


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC077.T1


title: CD4+ and CD8+ T cells from metastasic Colorectal  tumor specimen, IPICRC071.T2


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC072.T1


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC064.T1


title: BrainChip_BottomChannel_aSyn_Monomer_S1


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC062.T1


title: BrainChip_BottomChannel_aSyn_Monomer_S2


title: BrainChip_BottomChannel_aSyn_Fibrils_S1


title: CD4+ and CD8+ T cells from primary Colorectal  juxta-tumoral tumor specimen (reactive normal tissue), IPICRC057.N1

description: Tumor associated conventional T cell both CD4+ and CD8+ sorted by flow cytometry from a primary Colorectal  juxta-tumoral tumor specimen (reactive normal tissue)


title: BrainChip_BottomChannel_aSyn_Fibrils_S3


title: BrainChip_BottomChannel_aSyn_Fibrils_S2


title: BrainChip_BottomChannel_aSyn_Fibrils_S4


title: CD4+ and CD8+ T cells from primary Colorectal  juxta-tumoral tumor specimen (reactive normal tissue), IPICRC058.N1


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC053.T1


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC055.T1


title: Injured vs. Control ventricles

city: Giessen

first: Sven

last: Reischauer

state: Hessen

address: Auweg 129

department: Cardiology/Angiology

institute: Medical Clinic I - JLU

hyb_protocol: cRNA is hybridised on 8x60K microarrays at 65°C for 17 h

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and 5 micron for HD Microarray formats

data_processing: Agilent's Feature Extraction software version 11 is used to read and process the TIFF files.

source_name: Control

label_protocol: For 1st strand synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer) is used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP is performed.

extract_protocol: TRIzol RNA extraction

value: adult ventricle

source_name: Cryoinjury


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC039.T1


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC048.T1


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC037.T1


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC058.T1


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC035.T1


title: WT_17-med-am-ATAC

data_processing:
Processing of the ATAC-seq reads were performed using the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline; 10.5281/zenodo.156534.svg) using default parameters. As a reference genome mm10 was used. Each baseline replicate achieved a minimum of 50 million non-duplicated, non-mitochondrial reads. The irreproducible discovery rate was less than two for each group of replicates and the fraction of reads in called peak regions above 0.5.
Differential accessibility was performed using the R package DiffBind (Stark, 2011). In short, a common peak set was identified by the presence of a peak in at least two samples. As a method for differential analysis edgeR was further applied (Robinson, Mccarthy, & Smyth, 2010). For the LPS stimulation experiment the date of RNA isolation was included as a blocking factor to adjust for batch effects. To define the LPS treatment effect in Fig. 4, count values were extracted for every consensus peak and a multi-factor design including the batch, genotype, treatment and interaction term (~batch+genotype+treatment+genotype:treatment) was constructed using DESeq2. Only the treatment covariate was extracted using the following contrast: c("treatment","medium", "LPS"). LPS responsive regions with an adjusted p-value <0.05 and a log2 fold-change > 2 were considered as significant. Annotation of all differentially accessible regions was performed with the R package ChIPseeker (Yu, Wang, & He, n.d.) and TxDb.Mmusculus.UCSC.mm10.knownGene (BC, 2019).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with differentially expressed genes; multi-factor model including treatment and genotype covariate

growth_protocol: Mice were anesthetized by intraperitoneal injection of 120 mg/kg ketamine and 16 mg/kg xylazin (Sigma-Aldrich, Darmstadt, Germany) and exsanguinated. Primary AMs were collected by flushing the lungs 3 times with 800  ml of PBS supplemented with 5 mM EDTA (Sigma-Aldrich, Darmstadt, Germany). The lavage was repeated twice.

extract_protocol:
DNA and RNA were isolated using TRIzol reagent (Sigma Aldrich, Darmstadt, Germany) and further AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) purification, following the manufacturer’s instructions. For RNA isolation (RNase-free DNAse set, Qiagen) DNAse I digestion was performed on the column. Proteinase K digestion was applied for RNA and DNA isolation (Puregene Proteinase K, Qiagen). Prior to library preparation, DNA and RNA quality was checked by Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA). All RNA samples reached an RNA integrity number (RIN) > 8.5.
ATAC libraries have been prepared according to the Omni-ATAC protocol (Corces et al., 2017a) with minor modifications. In short, 50000 viable cells were pelleted and wahsed in PBS. Subsequently, nuclei were isolated using cold lysis buffer (0.01% Digitonin [Sigma-Aldrich, Munich, Germany], 1% NP40 [Genaxxon Bioscience, Ulm, Germany], 0.1% Tween-20 [Sigma-Aldrich, Munich, Germany]). Resuspension of the nuclei was done in ATAC washing buffer (10 mM Tris-HCl pH 7.4 [Sigma-Aldrich, Munich, Germany], 10 mM NaCl [Sigma-Aldrich, Munich, Germany], 3 mM MgCl2 [Sigma-Aldrich, Munich, Germany]).The tagmentation reaction was performed in 2x transposition buffer (20 mM Tris-HCl pH 7.6 [Sigma-Aldrich, Munich, Germany], 3 mM MgCl2 [Sigma-Aldrich, Munich, Germany], 20% Dimethyl Formamide [Sigma-Aldrich, Munich, Germany]) by the addition of 2.5µl of Tagment DNA Enzyme 1 (Illumina, San Diego, CA) and rotating the mixture at 1000 rpm for 30 minutes at 37°C. The reaction was stopped by the addition of 20µl of 5M Guanidinium thiocyanate (Sigma-Aldrich, Munich, Germany). Transposed chromatin was then purified using 30µl of AMPure XP beads beads (Beckman Coulter, Brea, CA)), and 110 µl of PEG buffer (2.5 M NaCl [Sigma-Aldrich, Munich, Germany], 20% PEG 8000 [Sigma-Aldrich, Munich, Germany]). Library amplification was separated in a two-step procedure. First, 25 µl of NEBNext High Fidelity 2x Master Mix (NEB, Ipswich, MA), 0.8 µl of 10 µM Custom Nextera PCR Primer 1, and 0.8 µl of 10 µM Custom Nextera PCR Barcode was added to 25µl of the transposed DNA, using the following program: 5 minutes at 72°C, 30 seconds at 98°C, 5 cycles of 10 seconds at 98°C, 30 seconds at 63°C, and 1 minute at 72°C, and, finally, 1 minute at 72°C. 5µl of the pre-amplified PCR mixture were used to determine how many additional cycles were needed to reach sufficient amplification of each library. For this, Sybr Green I nucleic acid gel stain (Thermo Fisher Scientific, Waltham, MA) was added and quantitative PCR performed with light cycler instrument (Roche, Basel, Switzerland) by applying the following program: 30 seconds at 98°C, 20 cycles of 10 seconds at 98°C, 30 seconds at 63°C, 1 minutes at 72°C, and, finally, 1 minute at 72°C. In a second step, the previous identified PCR cycles were applied to the remaining pre-amplified mixture. The libraries were then purified with a left sided size selection applying 1.4x of AMPure XP beads (Beckman Coulter, Brea, CA) and finally resuspended in 1x elution buffer (Qiagen, Hilden, Germany). Fragment size distribution was checked by Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and concentrations were quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA). Sequencing was performed in multiplexes at the DKFZ Genomics and Proteomics Core Facility using the HiSeq 2000 v4 paired-end 125 bp platform (Illumina).

treatment_protocol: For LPS and mucus treatment, lavages from 3-4 animals were pooled to obtain sufficient numbers of AMs . For baseline gene expression individual lavages were used. Collected cells were seeded into a flat-bottom 96-well plate in complete DMEM (1g/L D-Glucose, L-Glutamine, Pyruvat; Gibco, Dreieich, Germany) containing 10 % heat-inactivated FCS (Gibco, Dreieich, Germany), 1x penicillin-streptomycin (Gibco, Dreieich, Germany) 2 mM L-glutamine (Gibco, Dreieich, Germany) to a final count of 1x105 AMs/well, for LPS treatment, according to cell composition determined by cytospin. For baseline gene expression all cells were seeded. After 1 hr incubation at 37 °C, 5 % CO2, the non-adherent cells were gently washed from the plate with prewarmed PBS. For baseline gene expression, adherent cells were resuspended in 200 ml Trizol (Thermo Fisher Scientific GmbH, Dreieich, Germany). For LPS treatment, adherent cells were exposed to 100 ng/ml LPS from P. aeruginosa (Sigma-Aldrich, Darmstadt, Germany) for 6, 12, and 24 hrs or complete DMEM as control. For mucus treatment AMs were exposed to different concentrations of bovine submaxillary gland mucus (Merck Millipore, Darmstadt, Germany). Supernatants were collected and the cells were resuspended in 200 ml Trizol for RNA extraction.

tag: strain

value: wildtype

value: lung

value: airway macrophages

value: medium


title: CD4+ and CD8+ T cells from primary Colorectal  tumor specimen, IPICRC054.T1


title: WT_18-med-am-ATAC


title: WT_16-lps-am-ATAC

value: lipopolysaccharide


title: lcSSc_5

city: Zürich

first: Peter

last: Leary

address: Winterthurerstrasse 190

department: Functional Genomics Center Zürich

country: Switzerland

institute: ETH Zürich

description: CD14+ monocytes from lcSSc patient

data_processing: raw counts

source_name: CD14+ blood monocyte

growth_protocol: CD14+ monocytes isolated from blood using magnetic sorting

extract_protocol:
RNA was isolated using QuickRNA Microprep (ZymoResearch).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lcSSc


title: TG_17-med-am-ATAC


title: WT_17-lps-am-ATAC


title: TG_19-med-am-ATAC


title: WT_18-lps-am-ATAC


title: WT_16-med-am-ATAC


title: CD4+ and CD8+ T cells from metastasic Colorectal  tumor specimen, IPICRC040.T2


title: TG_17-lps-am-ATAC


title: TG_18-lps-am-ATAC


title: TG_19-lps-am-ATAC


title: Exercised vs. Lazy ventricles

source_name: Lazy

source_name: Exercise


title: KO Hypoxia-1

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

description: Cells published in PMID: 22225988

hyb_protocol: Illumina Total Prep (Ambion)

scan_protocol: Standard Illumina protocol

data_processing: Illumina Beadstudio data were quantile normalized using Bioconductor's Limma package

source_name: PyMT mammary tumor epithelial cells

label_protocol: Standard Illumina protocol

growth_protocol: Cells were maintained as described in PMID: 22225988, standard growth medium was DMEM/F12 supplemented with 2% FBS (cat. #16000044)

extract_protocol: Cells were lysed on the plate with RNABee reagent (Tel-Test, Friendswood, TX) and total RNA prepared as per manufacturer instructions

treatment_protocol: Cells were grown in replicates in 6-well standard tissue culture plates in DMEM/F12 + 2% FBS to ~80% confluence then left at normoxia or exposed to hypoxia (0.5% oxygen) for 6h prior to washing and cell harvest

value: HIF-1 KO

tag: protocol

value: Hypoxia

value: late-stage tumor ER-negative epithelial cells


title: lcSSc_3

description: CD14+ monocytes from lcSSc patient


title: KO Hypoxia-2

description: Cells published in PMID: 22225988


title: WT_18-med-am-RNA

data_processing:
RNA-seq data was processed with the nf-core RNA-seq pipeline (Ewels et al., 2020) (v. 1.2). Default parameters were used unless mentioned otherwise. Sequences were aligned to the mouse reference genome mm10 by application of the software HISAT2, with --unstranded option. For single-end data the -singleEnd option was applied. Transcripts were assembled using StringTie and gene code gene annotation release M20 (Frankish et al., 2019). Gene counts were generated with Stringties prepDE.py script (setting: -eb).
For the identification of differentially expressed genes, the R package DESeq2 was used (Love, Huber, & Anders, 2014). For group-wise comparison of baseline replicates, the littermate was included in the design formula to adjust for batch effects. For the LPS stimulation experiment the date of library preparation was included. The adjusted p-value as well as log2 fold change required to fulfil statistical significance is mentioned in the figure legends.
Genome_build: mm10
Supplementary_files_format_and_content: Count file as tab-delimited text file. Excel-file with differentially expressed genes;  Scnn1b-transgene vs wildtype upon LPS and medium treatment (RNA_Treat_DEG.xlsx)
Supplementary_files_format_and_content: Excel-file with differentially expressed genes; multi-factor model including treatment and genotype covariate (RNA_Treat_DEG_Model.xlsx)

extract_protocol:
 I thought we ended up using FACS sorted AM
For the paired-end baseline as well as LPS- and medium-treated replicates of wt- and tg-AM, sequencing libraries were prepared by the DKFZ Genomics and Proteomics Core Facility from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit according to the manufacturer’s instructions. For sequencing, samples were sequenced on a HiSeq 2000 v4, paired-end, 125 bp platform (Illumina). Single-end baseline replicates were prepared by the EMBL Genomics Core Facility from total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.  Sequencing was performed on a Next Seq 500, single-end, 75 bp platform.

tag: batch


title: TG_18-med-am-ATAC


title: lcSSc_4

description: CD14+ monocytes from lcSSc patient


title: KO Hypoxia-3

description: Cells published in PMID: 22225988


title: WT Hypoxia-1

description: Cells published in PMID: 22225988


title: WT Hypoxia-3

description: Cells published in PMID: 22225988


title: WT Hypoxia-2

description: Cells published in PMID: 22225988


title: KO Normoxia-2

description: Cells published in PMID: 22225988

value: Normoxia


title: PreB-Lig4-12hrs-AsisI-ENDseq-control-for-second-POLAi

city: Shanghai

first: Wei

last: Wu

address: 320 yueyang road

institute: Center for Excellence in Molecular Cell Science

data_processing:
library strategy: END-seq
END-seq reads were aligned to mm10 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Abelson-transformed pre-B cell

extract_protocol:
Live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads). libraries were prepared and sequenced following standard Illumina protocols

value: Abelson-transformed pre-B cell

value: NT

tag: asisi induction


title: WT_16-med-am-RNA

source_name: airway macrophages


title: KO Normoxia-3

description: Cells published in PMID: 22225988


title: TG_19-med-am-RNA


title: lcSSc_1

description: CD14+ monocytes from lcSSc patient


title: TG_18-med-am-RNA


title: HC_5

description: CD14+ monocytes from healthy control

value: Healthy control


title: WT_18-lps-am-RNA


title: WT_17-lps-am-RNA


title: WT_16-lps-am-RNA


title: WT_17-med-am-RNA


title: lcSSc_2

description: CD14+ monocytes from lcSSc patient


title: WT Normoxia-3

description: Cells published in PMID: 22225988


title: KO Normoxia-1

description: Cells published in PMID: 22225988


title: HC_4

description: CD14+ monocytes from healthy control


title: TG_19-lps-am-RNA


title: TG_17-lps-am-RNA


title: HC_3

description: CD14+ monocytes from healthy control


title: TG_18-lps-am-RNA


title: HC_2

description: CD14+ monocytes from healthy control


title: WT_3-wildtype-am-RNA


title: WT_2-wildtype-am-RNA


title: HC_1

description: CD14+ monocytes from healthy control


title: WT_1-wildtype-am-RNA


title: TG_2-transgene-am-RNA


title: TG_3-transgene-am-RNA


title: Sample4 TRICOV22_K [CITE-seq]

city: Birmingham

first: Graham

last: Taylor

address: Vincent Drive

department: Institute of Immunology and Immunotherapy

institute: University of Birmingham

description: Sample4_GEXFB_filtered_feature_bc_matrix.h5

data_processing:
Library strategy: CITE-Seq
Processing of raw reads including 10X barcode-aware demultiplexing from BCL to FASTQ files, transcriptome alignment to human genome assembly GRCh38 and unique molecular identifier (UMI) counting were performed using the 10X Cell Ranger pipeline version 3.1.0 with GRCh38-version 3.0.0 as the reference.
Seurat v3.1.5 S6 was used for sample merging, quality control (QC), clustering and reporting.
Both gene expression (RNA) and antibody-derived tag (ADT) assays were loaded from the CellRanger count platform into a Seurat object for each sample excluding cells with less than 200 genes and features detected in less than 3 cells.
The four samples were then merged to create a single aggregated object. QC was conducted on both assays separately.
For the RNA assay, to mitigate the influence of sex on clustering and differential expression, the XIST and RSP4Y1 genes were removed.
Cells with a number of features between 200 and 600, counts of greater than 1000 and mitochondrial percentage less than 15% were kept for further processing.
The gene expression data was normalised using the ‘LogNormalize’ method with the scale.factor set to the default 10000. 1500 variable features were identified using the ‘vst’ method of the ‘FindVariableFeatures’ function.
The assay was finally scaled with the number of counts and mitochondrial percentage variables regressed.
The ADT assay was first used to identify dead cells or cell doublets by removing double positive instances of lineage markers according to the following criteria: CD14 > 60 & CD19 > 50, CD19 > 40 & CD3 > 40, CD14 > 80 & CD3 > 50 and CD3 < 50 & gamma-delta > 400.
The assay was then centred log-ratio (CLR) normalised and scaled with default parameters. The remaining object comprised 10,031 cells with 17,583 features.
Both the RNA and ADT assays were used to compute 50 principal components. These principal components were then used as input into the ‘FindNeighbours’ function and subsequently the ‘FindClusters’ function with resolution set to the default value of 1, resulting in 19 clusters which were visualised using tSNE.
The clusters were manually annotated from expression of lineage markers both at the transcript (RNA) and protein (ADT) levels.
Genome_build: GRCh38
Supplementary_files_format_and_content: Feature matrix in H5 format.

source_name: Peripheral Blood Mononuclear Cells

extract_protocol: Single cell libraries were constructed using 10X Genomics Single Cell 3' Reagents Kits v3 according to manufacturer’s instructions and sequenced on an Illumina NextSeq 500 platform.

treatment_protocol: Cryopreserved PBMCs were recovered and feature barcoded using Biolegend CITE-seq antibodies. All four samples were processed at the same time.

tag: diagnosis

value: Kawasaki Disease

tag: timepoint

value: Acute (pre-treatment)

value: Peripheral Blood Mononuclear Cells

tag: donor id


title: WT Normoxia-1

description: Cells published in PMID: 22225988


title: TG_1-transgene-am-RNA

tag: tissue


title: dcSSc_3

description: CD14+ monocytes from dcSSc patient

value: dcSSc


title: dcSSc_2

description: CD14+ monocytes from dcSSc patient


title: TG_15-transgene-am-ATAC

data_processing:
Processing of the ATAC-seq reads were performed using the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline; 10.5281/zenodo.156534.svg) using default parameters. As a reference genome mm10 was used. Each baseline replicate achieved a minimum of 50 million non-duplicated, non-mitochondrial reads. The irreproducible discovery rate was less than two for each group of replicates and the fraction of reads in called peak regions above 0.5.
Differential accessibility was performed using the R package DiffBind (Stark, 2011). In short, a common peak set was identified by the presence of a peak in at least two samples. As a method for differential analysis edgeR was further applied (Robinson, Mccarthy, & Smyth, 2010). For the LPS stimulation experiment the date of RNA isolation was included as a blocking factor to adjust for batch effects. To define the LPS treatment effect in Fig. 4, count values were extracted for every consensus peak and a multi-factor design including the batch, genotype, treatment and interaction term (~batch+genotype+treatment+genotype:treatment) was constructed using DESeq2. Only the treatment covariate was extracted using the following contrast: c("treatment","medium", "LPS"). LPS responsive regions with an adjusted p-value <0.05 and a log2 fold-change > 2 were considered as significant. Annotation of all differentially accessible regions was performed with the R package ChIPseeker (Yu, Wang, & He, n.d.) and TxDb.Mmusculus.UCSC.mm10.knownGene (BC, 2019).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with differentially accessible regions; Scnn1b-transgene vs wildtype at baseline


title: Sample2 TRICOV20_A [CITE-seq]

description: Sample2_GEXFB_filtered_feature_bc_matrix.h5

value: MIS-C


title: TG_19-transgene-am-ATAC

value: lung


title: NR8383_Control

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression after 24hr in rat alveolar macrophages as vehicle cotrol

hyb_protocol: Each labeled cRNA probe was used separately for hybridization to a 4~44 K Whole Rat Genome Microarray (G4131F; Agilent Technologies) at 65C for 17 h.

scan_protocol: Hybridized microarray slides were washed according to the manufacturerfs instructions and scanned with a DNA Microarray Scanner (Agilent) at 5 ƒÊm resolution.

data_processing: The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 12.0.3.1.

organism: Rattus norvegicus

source_name: Rat alveolar macrophages, 24hr, Control, 4 replicates

label_protocol: Cyanine-3-labeled cRNA was prepared from RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 spectrophotometer.

growth_protocol: Rat alveolar macrophage cells (NR8383) obtained the American Type Culture Collection were cultured at 37 ‹C in 75-cm2 cell culture flasks in F-12K with 10 % (v/v) heat-inactivated fetal bovine serum (FBS) in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit (Qiagen, Japan) following the manufacturerfs instructions. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., US), and sample qualities were monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies, US).

treatment_protocol: F-12K + FBS medium was removed by centrifugation. Cell cultures were replaced with six kinds of the SCFs working solutions (SCF1, SCF2, or SCF3), respectively. The cultures were seeded into each well of a 6-well plate and grown for 24 hours at 37 ?C in a humidified incubator with 5% CO2. Cell concentrations at this point were approximately 3.0 x 10^5 cells/mL.

tag: cell line

value: Rat alveolar macrophages  (NR8383)

value: Vehicle control

tag: time


title: dcSSc_5

description: CD14+ monocytes from dcSSc patient

tag: disease subtype


title: Sample3 TRICOV20_F [CITE-seq]

description: Sample3_GEXFB_filtered_feature_bc_matrix.h5

value: Convalescent

tag: cell type


title: TG_13-transgene-am-ATAC

tag: genotype

value: airway macrophages


title: TG_14-transgene-am-ATAC


title: Sample1 TRICOV19_A [CITE-seq]

description: Sample1_GEXFB_filtered_feature_bc_matrix.h5


title: NR8383_SCF1

description: Gene expression after 24hr in SCF1-exposed rat alveolar macrophages

source_name: Rat alveolar macrophages, 24hr, SCF1, 4 replicates

tag: treatment


title: NR8383_SCF2

description: Gene expression after 24hr in SCF2-exposed rat alveolar macrophages

source_name: Rat alveolar macrophages, 24hr, SCF2, 4 replicates


title: WT_19-wildtype-am-ATAC

value: wildtype


title: WT_14-wildtype-am-ATAC


title: NR8383_SCF3

description: Gene expression after 24hr in SCF3-exposed rat alveolar macrophages

source_name: Rat alveolar macrophages, 24hr, SCF3, 4 replicates


title: WT_13-wildtype-am-ATAC


title: dcSSc_4

description: CD14+ monocytes from dcSSc patient


title: dcSSc_1

description: CD14+ monocytes from dcSSc patient


title: WT_5-wildtype-am-WGBS_TAG

data_processing:
Raw reads were processed using Trimmomatic (Bolger, Lohse, & Usadel, 2014) (version 0.36)  and aligned against the mouse reference genome mm10 using bwa mem (Li, 2013) (version 0.7.8) with default parameters, except for invoking “-T 0”. After alignment duplicates were marked by applying Picard MarkDuplicates (http://broadinstitute.github.io/picard; version 1.125). Methylation calling was performed with MethylDackel (https://github.com/dpryan79/MethylDackel; v. 0.3.0). According to M-bias plot quality control, the five base pairs at the two ends of the reads were excluded from methylation calling. All samples used for downstream analysis had a bisulfite conversion rate of above 98% and more than 95% of all reference CpG were covered. In total each wt- and tg-AM group had a total coverage of at least 20-times.
Bsmooth algorithm of bsseq (Hansen, Langmead, & Irizarry, 2012) (version 1.20.0) was used to smooth the methylation profiles of all samples with default parameters. DMRs in a pair-wise comparison between tg- and wt-AM were called with DSS (Park & Wu, n.d.) (v. 2.32.0). Regions with at least 3 CpGs, a minimum length of 50bp, a minimum delta of 0.1 and a Benjamin-Hochberg corrected p-value < 0.05 were selected.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of differentially methylated regions; Scnn1b-transgene vs wildtype at baseline

extract_protocol:
DNA and RNA were isolated using TRIzol reagent (Sigma Aldrich, Darmstadt, Germany) and further AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) purification, following the manufacturer’s instructions. For RNA isolation (RNase-free DNAse set, Qiagen) DNAse I digestion was performed on the column. Proteinase K digestion was applied for RNA and DNA isolation (Puregene Proteinase K, Qiagen). Prior to library preparation, DNA and RNA quality was checked by Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA). All RNA samples reached an RNA integrity number (RIN) > 8.5.
Tagmentation based WGBS followed the protocol described in (Peat & Smallwood, 2018) with 20 ng genomic DNA as input. From each tagmentation reaction, four sequencing libraries with different barcodes were generated, and further pooled in equimolar amounts with a final concentration of 10 nM. Library pools were sequenced at the DKFZ Genomics and Proteomics Core Facility using paired-end, 125 bp, on one lane of a HiSeq2000 v4 sequencer (Illumina).


title: Sample4 TRICOV22_K [RNA-seq]

data_processing:
Processing of raw reads including 10X barcode-aware demultiplexing from BCL to FASTQ files, transcriptome alignment to human genome assembly GRCh38 and unique molecular identifier (UMI) counting were performed using the 10X Cell Ranger pipeline version 3.1.0 with GRCh38-version 3.0.0 as the reference.
Seurat v3.1.5 S6 was used for sample merging, quality control (QC), clustering and reporting.
Both gene expression (RNA) and antibody-derived tag (ADT) assays were loaded from the CellRanger count platform into a Seurat object for each sample excluding cells with less than 200 genes and features detected in less than 3 cells.
The four samples were then merged to create a single aggregated object. QC was conducted on both assays separately.
For the RNA assay, to mitigate the influence of sex on clustering and differential expression, the XIST and RSP4Y1 genes were removed.
Cells with a number of features between 200 and 600, counts of greater than 1000 and mitochondrial percentage less than 15% were kept for further processing.
The gene expression data was normalised using the ‘LogNormalize’ method with the scale.factor set to the default 10000. 1500 variable features were identified using the ‘vst’ method of the ‘FindVariableFeatures’ function.
The assay was finally scaled with the number of counts and mitochondrial percentage variables regressed.
The ADT assay was first used to identify dead cells or cell doublets by removing double positive instances of lineage markers according to the following criteria: CD14 > 60 & CD19 > 50, CD19 > 40 & CD3 > 40, CD14 > 80 & CD3 > 50 and CD3 < 50 & gamma-delta > 400.
The assay was then centred log-ratio (CLR) normalised and scaled with default parameters. The remaining object comprised 10,031 cells with 17,583 features.
Both the RNA and ADT assays were used to compute 50 principal components. These principal components were then used as input into the ‘FindNeighbours’ function and subsequently the ‘FindClusters’ function with resolution set to the default value of 1, resulting in 19 clusters which were visualised using tSNE.
The clusters were manually annotated from expression of lineage markers both at the transcript (RNA) and protein (ADT) levels.
Genome_build: GRCh38
Supplementary_files_format_and_content: Feature matrix in H5 format.


title: WTM3

city: Guangzhou

first: Liping

last: Wang

state: Guangdong

address: No. 232, Outer Ring East Road, Guangzhou University Town, Panyu District

institute: Guangzhou University of Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver tissue of male C57BL/6J mice

extract_protocol:
livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 3 μg of RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: Sex

value: male

tag: age

value: 52 weeks post natal

value: wild type


title: WT_4-wildtype-am-WGBS_TAG


title: WT_3-wildtype-am-WGBS_TAG


title: Sample3 TRICOV20_F [RNA-seq]


title: WTM2


title: Sample2 TRICOV20_A [RNA-seq]


title: WT_1-wildtype-am-WGBS_TAG


title: TG_5-transgene-am-WGBS_TAG


title: Abcb11M3

source_name: liver tissue of male  Abcb11-/- mice


title: TG_3-transgene-am-WGBS_TAG


title: TG_1-transgene-am-WGBS_TAG


title: Delta-tocotrienol 6

city: Piscataway

first: Hong

state: NJ

address: 164 Frelinghuysen

department: Chemical Biology

institute: Rutgers the State Univesrity of New Jersey

description:
Delta-tocotrienol treatment
T6

data_processing:
Firstly, we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. We mapped clean reads to reference using Bowtie2 and then calculate gene expression level with RSEM. Finally, we identify DEGs (differentially expressed genes) between samples.
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step
Genome_build: mm10
Supplementary_files_format_and_content: fpkm and read count

source_name: Prostate dorsal-lateral-ventral glands

extract_protocol:
RNA was extracted using Qiagen Rneasy kit.
After extracting the total RNA from the tissues, mRNA is then enriched by using the oligo (dT) magnetic beads from the total RNA. By using the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and poly (A) addition. Finally, sequencing adapters are ligated to the fragments. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via BGISEQ-500.

treatment_protocol: In this study, male prostate-specific Pten-/- mice at the age of 6 weeks were separated randomly into 3 groups (6 per group), the control group (fed AIN93M diet), the metabolic syndrome group (fed 60% kcal high-fat diet), and the treatment group (fed AIN93M diet containing 0.05% delta-tocotrienol).  The fasting blood glucose and insulin levels measured at the age of 6 (before the use of the different diet), 10, and 20 weeks. All mice were sacrficed at 20 weeks of age after an 8 hour day timr fasting. Prostate dorsal-lateral-ventral glands were separated under dissection microscope for extracting the total RNA for quantification sequencing.

value: Fvb

value: prostate-specific Pten-/-

value: Prostate dorsal-lateral-ventral glands

tag: pathology

value: High-grade prostatic intraepithelial neoplasia (HG-PIN)


title: Abcb11M1

tag: strain


title: Delta-tocotrienol 5

description:
Delta-tocotrienol treatment
T5


title: Abcb11M2


title: Delta-tocotrienol 3

description:
Delta-tocotrienol treatment
T3


title: WTF3

source_name: liver tissue of female C57BL/6J mice

value: female


title: WTF2