title: ATAC_MatN_KEP_aIL1B_2

city: Amsterdam

first: Elzo

last: de Wit

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequencing reads were aligned to the mm10 mouse reference genome using bwa mem version 0.7.17-r1188.
Mapped reads were filtered for mapping quality >15 using samtools version 1.10.
bigWig coverage files were generated with deepTools using the reads per genomic content (RPGC) scaling.
Assembly: mm10
Supplementary files format and content: bigWig files contain coverage for each sample scaled to 1x genome coverage.

extract_protocol:
LT-HSCs, MPPs, CMPs and GMPs were enriched by neutrophil depletion. Bone marrow single cell suspensions were incubated with 10μg/ml anti-Ly6G (1A8, BioXcell) before neutrophil depletion using sheep anti-rat magnetic beads (Dynabeads, Life Technologies) and subsequently stained with cell surface markers. For sorting pre-neutrophils and neutrophils from bone marrow, blood and lung, cells were first incubated with 500μg/ml purified mouse IgG+10% FCS (BM) or rat anti-mouse CD16/CD32 antibody (blood and lung), stained with cell surface markers and sorted using gating strategies for HSPC populations or CD45+ CD11b+ Ly6G+ 7-AAD- markers for sequencing of blood and lung neutrophils.
Nuclei of the sorted cells were isolated, permeabilized and tagmented by using commercially available Tn5 transposase (Illumina, Nextera DNA Library Preparation Kit). DNA fragments underwent a first 9-cycle PCR amplifications using KAPA HiFi HotStart ReadyMix (7958935001, Roche), and we selected the fragments between 150 and 700 bp in size using with SPRI beads (A63881, Backman Coulter). The size-selected fragments were amplified for a second 9-cycle PCR reactions, and the resulted libraries were purified using SPRI beads.

value: Bone marrow

value: MatN

value: KEP


title: pituitary gland, Amh_KO

status: Public on Apr 08 2025

type: SRA

city: Wuhan

first: Jie

last: Mei

state: Hubei

address: No.7, Donghu South Road, Wuchang District

department: Institute of Hydrobiology

country: China

institute: Chinese Academy of Sciences

description: Library name: Sample 2

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed and aligned to the ENSEMBL GRCz11 zebrafish transcriptome to generate feature-barcode matrices using CellRanger (v5.0.1) with the default parameters.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Danio rerio

source_name: pituitary gland

extract_protocol:
After dissection, zebrafish pituitaries from WT or amh-/- females were washed with cold PBS or fresh Ringer’s solution for 5-10 min, followed by mechanical and enzymatic dissociation in protease solution (0.25% trypsin (Life Technologies), 400 mg/ml collagenase D (Sigma) and 1 mM EDTA in PBS) and incubated at 28.5 °C for 20-30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution (6 mM CaCl2 and 30% foetal bovine serum (FBS) in PBS). The samples were filtered with a 40 μm cell strainer, centrifuged (2000 rpm, 5 min, 4 °C) and then resuspended in 1X PBS.
Single-cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 according to the manufacturer’s instructions.

tag: tissue

value: pituitary gland

tag: genotype

value: knockout Amh


title: SV20 GT, TBX3, ChIP

city: Vancouver

first: Tabea

middle: L

last: Stephan

state: BC

address: 2329 West Mall

country: Canada

institute: University of British Columbia

library_source: genomic

data_processing:
aligned to hg19/GRCH37 using STAR (v2.5.0)
Bam files filtered using encode_task_filter.py from the ENCODE chip-seq-pipeline2, dublicate reads mapped using Picard (v2.1.1.1), unmapped, unpaired, low quality (MAPQ<5), non-primary alignment reads removed using SAM flag filter '-F 1804' using SAMtools (v1.3)
peaks were called using MACS2
Bigwig files were generated using MACS2 and deeptools
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: Gut tube stage

growth_protocol: SV20 iPSCs were differentiated as previously described (Si-Tayeb et al., 2010 and Teng Ang et al., 2018). Briefly, cells were grown on Geltrex-coated plates to 100% confluency and subsequently differentiated into mesendodermal progenitors using RPMI media supplemented with 1x B27 minus insulin, Activin A (100ng/ml), FGF2 (20ng/ml) and BMP4 (10ng/ml) for 48h. Definitive endodermal cells were further differentiated with Activin A (100 ng/ml) and 1x B27 minus insulin only for additional 48h. Alternatively, definitive endodermal cells were generated using STEMdiff definitive Endoderm Kit (Stemcell Technologies). Subsequently, cells were specified to hepatic endodermal cells for 96h in RPMI supplemented with 1x B27 with insulin, BMP4 (20ng/ml) and FGF2 (10ng/ml) at 4% O2 or for 24h in IMDM/F12 supplemented with A8301 (1uM), BMP4 (30ng/ml), FGF2 (10ng/ml) and TTNPB (75nM) for 24h followed by Activin A (10ng/ml), BMP4 (30ng/ml), 8-bromo-cAMP (1mM) and C-59 (1µM, first 24h)/CHIR99201(1µM, next 48h) for 96h in atmospheric O2. Hepatoblasts were generated with BMP4 (10ng/ml), OSM (10ng/ml), Dexamethasone (10µM), RO4929097 (2µM), Forskolin (10µM), insulin (10µg/ml), transferrin (15µg/ml), AAP (200µg/ml) and SB505124 (1µM, just first 48h) in full IMDM/F12 media for 6 days in atmospheric O2 or by incubation at 4% O2 and in RPMI supplemented with 1x B27 with insulin and HGF (20ng/ml) only.

extract_protocol:
1 million (histone modification ChIP-seq) to 10 million (transcription factor ChIP-seq) cells were cross-linked with 1 % fresh methanol-free formaldehyde for 10 min at room temperature (RT). The cross-linking was stopped with the addition of fresh glycine to a final concentration of 0.125M and incubation for 5 min at RT. Cells were subsequently washed twice with cold PBS, pelleted and resuspended in cold ChIP lysis buffer and lysed for 15 min on ice while dounce homogenizing 20x during the incubation. After re-pelleting, nuclei were resuspended in ChIP nuclear lysis buffer for 30-60 min on ice. Chromatin was sheared by sonication for 20 cycles at 60 hz for 30 sec on/30 sec off. Cellular debris was removed by centrifugation. Chromatin was pre-cleared by rotating at 4 °C for 1h with Protein A/G Ultralink beads (Thermo Fisher Scientific, Pierce) in ChIP dilution buffer. Chromatin was incubated with primary antibodies overnight at 4°C while rotating. Protein A/G Ultralink beads (Thermo Fisher Scientific, Pierce) were added to the immunoprecipitation (chromatin + antibody) mix and incubated at 4°C for further 4 hours. Unbound fraction of the IgG chromatin solution was kept as input DNA. Beads were subsequently washed for 5 min at 4°C once each in low salt buffer, high salt buffer, lithium chloride buffer, followed by two washes in TE buffer, before eluting the DNA by incubating the beads in 125µl-250µl fresh elution buffer for 15 min at RT while vortexing/rotating. To reverse the cross-linking, samples were incubated overnight at 65°C in 0.192M NaCl, 40mM Tris-Cl, pH6.5, 10mM EDTA, 0.08mg/ml Proteinase K and 0.1 mg/ml RNaseA. DNA was subsequently extracted and purified by phenol-chloroform extraction and precipitated in Ethanol at -80°C before being resuspended in 50µl of H2O.
samples were library prepped using the NEBNext Ultra II DNA library Prep Kit for Illumina following manufacturer’s recommendations

value: Gut tube stage

tag: cell line

tag: cell type

value: differentiated iPSC

tag: chip antibody

value: 22HCLC, Thermo Fisher Scientific


title: ATAC_MatN_KEP_aIL1B_3

organism: Mus musculus

source_name: Bone marrow

tag: treatment


title: ATAC_MatN_WT_aIL1B_3

value: WT


title: 12_2KO-DMX-03

city: Bethesda

first: Pablo

last: Tapia

state: Maryland

address: 50 South Dr

department: Cell Biology and Physiology Center, National Heart, Lung, and Blood

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Basecalling was performed using Real Time Analysis version 2 (RTA2) software.
RTA2 software was used for basecalling and STAR algorithm version 2.5.2b with default settings was used to align the data to the human GRCh38/hg38 genome assembly to generate BAM files.
Differential gene expression analysis was performed using DESeq2 software version v1.14.1.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for all samples. Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Excel file containing DESeq2-normalized gene counts and the results of the performed differential analyses

molecule: total RNA

source_name: iBMDM

growth_protocol: iBMDM cells were maintained in RPMI 1640 medium supplemented with FBS 10% in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104). For each sample, 0.5 μg of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: iBMDM cells were treated with murine agonist STING DMXAA 10 µg/mL at different times

value: iBMDM

value: immortalized bone marrow-derived macrophage

value: TFEB/TFE3 KO

value: STING agonist


city: Barcelona

first: Ferran

last: Aguilar

state: Barcelona

address: Travessera de Gràcia, 11

country: Spain

institute: EF-CLIF

description:
S39
Whole-blood RNA-seq from ACLF treated (S39).
mRNAseq

data_processing:
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability.
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: *.tsv: RSEM expected counts.

source_name: Whole blood

extract_protocol:
RNA was isolated from blood stored in Tempus tubes using the Tempus™ Spin RNA Isolation Kit (reference 4380204, Applied Biosystems). RNA quality was assessed using Agilent RNA 6000 Nano and Pico Chips (Agilent Technologies, Cat.# 5067-1511 and Cat.# 5067-151, respectively) and concentration via Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat.# Q32855).
Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina Inc., Cat.# 20020612) and TruSeq RNA CD Index Plate (Illumina Inc., Cat.# 20019792) following TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E). Briefly, starting from 500 ng of total RNA, rRNA and globin mRNA were depleted and remaining RNA was purified, fragmented and primed for cDNA synthesis. cDNA first strand was synthesized with SuperScript-II Reverse Transcriptase (Thermo Fisher Scientific, Cat.#18064-014) for 10 min at 25°C, 15 min at 42°C, 15 min at 70°C and pause at 4°C. cDNA second strand was synthesized with Illumina reagents at 16°C for 1 hour. Then, A-tailing and adaptor ligation were performed. Finally, enrichment of libraries was achieved by PCR (30 sec at 98°C; 15 cycles of 10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C; 5min at 72°C and pause at 4°C). Afterwards, libraries were visualized on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626), quantified using Qubit dsDNA HS DNA Kit (Thermo Fisher Scientific, Cat. # Q32854) and sequenced in a NovaSeq-6000 (Illumina Inc.) by at least 40 million paired-end 100nt reads.

tag: group

value: ACLF treated

value: Whole blood


title: 11_2KO-DMX-02


title: ATAC_MatN_KEP_aIL1B_1


description:
S103
Whole-blood RNA-seq from ACLF treated (S103).
mRNAseq


description:
S34
Whole-blood RNA-seq from ACLF treated (S34).
mRNAseq


title: WT 3

city: Nanjing

first: Yuzhuo

last: Xu

address: 12 Xue-fu Road, Pukou District

institute: Nanjing University

description: Library name: Sample3

data_processing:
FastQc were used for data quality control.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SeqPrep and Sickle.
Paired-end clean reads were aligned to the reference genome using the HISAT2 2.1.0; RSEM was used to calculate FPKM.
Differential expression analysis was performed using the DESeq v1.26.0.
Assembly: GRCm39
Supplementary files format and content: xls files include counts and tpm values for each sample

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA sample prep kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mouse embryonic stem cell


title: 10_2KO-DMX-01


description:
S101
Whole-blood RNA-seq from ACLF treated (S101).
mRNAseq


title: ATAC_MatN_WT_aIL1B_1


title: PHx_12h_2

city: jinan

first: Jiabei

last: Lian

state: Shandong

address: No.44, Wenhauxi Road, Lixia District, Jinan, China

department: College of Basic Medical Sciences

institute: Shandong University

description:
Library name: PHx_12h_2
12 h after 70% partial hepatectomy

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample, which have been adjusted for batch effects across the two sample submissions to ensure data consistency and comparability.

source_name: liver

growth_protocol: Hepatocytes were freshly isolated from different time points (6 h,12 h,24 h,48 h,72 h,7 d,14 d,21 d) of the liver regeneration after PHx in mice for RNA extraction.

extract_protocol:
Total mRNA was isolated by TRIzol (Takara) or FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: liver

value: partial hepatectomy


title: WT 2

description: Library name: Sample2


title: WT 1

description: Library name: Sample1


description:
S95
Whole-blood RNA-seq from ACLF treated (S95).
mRNAseq


title: 09_NC-DMX-03


title: ATAC_MatN_KEP_CTRL_3

value: Bone marrow

value: MatN

value: CTRL


title: 08_NC-DMX-02


title: pituitary gland, WT

description: Library name: Sample 1

value: pituitary gland


description:
17K042
Whole-blood RNA-seq from Healthy Subjects (17K042).
mRNAseq

value: Healthy Subjects


title: WT CRE 1

description: Library name: Sample4


title: 07_NC-DMX-01


title: Zbtb24-KO2-H3K9me3

city: 昆明市

first: youqi

last: liu

state: 云南省

address: wujiaying

institute: Kunming University Of Science And Technology

description:
Library name: Zbtb24-KO2-H3K9me3
Zb_KO.bw

data_processing:
Raw sequencing reads were processed to remove adapter sequences using Cutadapt.
FastQC was employed to evaluate raw and post-trimming data quality, including metrics such as per-base sequence quality and GC content.
Low-quality reads were filtered using Trimmomatic, with sliding-window trimming and removal of reads below length thresholds.
FASTQ files from technical replicates under identical experimental conditions were concatenated using the cat command to enhance data robustness.
Processed reads were aligned to the reference genome (e.g., hg38 or mm10) using Bowtie2 in end-to-end mode for high sensitivity.
SAM files were converted to compressed BAM format (samtools view),BAM files were sorted by chromosomal coordinates (samtools sort),Index files (.bai) were generated for efficient downstream analysis (samtools index).
BigWig File Generation via bamCoverage
Normalized BigWig files were generated using bamCoverage from deepTools, with parameters such as bin size = 150 bp and RPM normalization for genome-wide signal visualization.
Assembly: GRCm38
Supplementary files format and content: bw
Library strategy: CUT&Tag

source_name: mouse embryonic stem cells (mESCs)

growth_protocol: Mouse ES cells were cultured with the medium consist of DMEM (Gibco), 15% fetal bovine serum (FBS, Gibco (16000-004), 10ng/ml Recombinant Murine LIF, 0.1 mM non-essential amino acids (11146-050, Gibco), 0.1 mM PenStrep (15140-122, Gibco), 0.1 mM β-mercaptoethanol (21985-023, Gibco),1 mM GlutaMAX-1(35050-061, Gibco). The medium was changed daily, and cells were passaged every two days.

extract_protocol:
The sample used to perform CUT&Tag are prepared based on the commonly used method. AS for CUT&Tag, Cells were harvested and counted. Number of 50000~100000 cells were used for CUT&Tag.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stable cell lines were obtained. Mouse ESCs were cultured for 2 days then collected for DNA extractiona and CUT&Tag profiling by high throughput sequencing.

value: mouse embryonic stem cells (mESCs)


title: ATAC_MatN_KEP_CTRL_1

value: KEP


description:
17K029
Whole-blood RNA-seq from Healthy Subjects (17K029).
mRNAseq


title: Zbtb24-KO1-H3K9me3

description:
Library name: Zbtb24-KO1-H3K9me3
Zb_KO.bw


title: ATAC_MatN_WT_CTRL_4

value: WT


title: ATAC_MatN_KEP_CTRL_2


title: WT-rep3-H3K9me3

description:
Library name: WT-rep3-H3K9me3
WT.bw


title: 06_2KO-Control-03

value: iBMDM


title: ATAC_MatN_WT_aIL1B_2


title: 05_2KO-Control-02

value: immortalized bone marrow-derived macrophage


description:
17K013
Whole-blood RNA-seq from Healthy Subjects (17K013).
mRNAseq


title: ATAC_MatN_WT_CTRL_3


title: WT-rep2-H3K9me3

description:
Library name: WT-rep2-H3K9me3
WT.bw


description:
17K010
Whole-blood RNA-seq from Healthy Subjects (17K010).
mRNAseq


description:
17K008
Whole-blood RNA-seq from Healthy Subjects (17K008).
mRNAseq


title: 03_NC-Control-03


title: ATAC_MatN_WT_CTRL_2


title: WT-rep1-H3K9me3

description:
Library name: WT-rep1-H3K9me3
WT.bw


description:
17K007
Whole-blood RNA-seq from Healthy Subjects (17K007).
mRNAseq


title: Hells-KO2-H3K9me3

description:
Library name: Hells-KO2-H3K9me3
He_KO.bw

value: Hells-KO


description:
17K032
Whole-blood RNA-seq from Healthy Subjects (17K032).
mRNAseq


description:
17K004
Whole-blood RNA-seq from Healthy Subjects (17K004).
mRNAseq


title: Hells-KO1-H3K9me3

description:
Library name: Hells-KO1-H3K9me3
He_KO.bw


title: Cdca7-KO3-H3K9me3

description:
Library name: Cdca7-KO3-H3K9me3
Cd_KO.bw


title: Cdca7-KO4-H3K9me3

description:
Library name: Cdca7-KO4-H3K9me3
Cd_KO.bw


title: 6_5364NIH_MartinaDMXAA3_RNA_mm_iUDI0073

value: Macrophages

value: Wild Type

value: DMXAA 10 µg/mL 3h


title: ATAC_ImmN_KEP_aIL1B_1

value: ImmN


title: 01_NC-Control-01

value: STING agonist


title: 5_5364NIH_MartinaDMXAA2_RNA_mm_iUDI0072


description:
17K003
Whole-blood RNA-seq from Healthy Subjects (17K003).
mRNAseq

value: Whole blood


title: ATAC_ImmN_WT_aIL1B_3

value: Bone marrow


title: ATAC_ImmN_KEP_aIL1B_2


title: 04_2KO-Control-01


description:
pS52
Whole-blood RNA-seq from ACLF with septic shock treated (pS52).
mRNAseq

value: ACLF with septic shock treated


title: Cdca7-KO2-H3K9me3

description:
Library name: Cdca7-KO2-H3K9me3
Cd_KO.bw


title: 4_5364NIH_MartinaDMXAA1_RNA_mm_iUDI0071


title: gWAT MKO HFD_rep3

city: Seoul, Republic of Korea

first: Sangseob

last: Kim

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.38. (Trimmomatic option : ILLUMINACLIP:[TruSeq3-PE-2.fa]:2:30:10:5:true ,LEADING:3 , TRAILING:3 , SLIDINGWINDOW:4:15, MINLEN:36)
To estimate expression levels, the RNA-Seq reads were mapped to Mus musculus genome (mm10) using HISAT2 version 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie version 1.3.4d software in default options.
The read count data of filtered genes was normalized by RLE (Relative Log Expression) normalization with DESeq2. The nbinomWaldTest function in DESeq2 was used to test for differential expression. The output prints foldChange, p-value and FDR values which corrected by the Benjamin-Hochberg procedure. DEGs was determined by |fold change|>=2 and p-value <0.05. For DEGs, hierarchical clustering analysis was performed with complete linkage method and Euclidean distance as a measure of similarity.
Gene-enrichment analysis and KEGG pathway analysis for DEGs were also performed based on Gene Ontology (http://geneontology.org/) and KEGG pathway (https://www.genome.jp/kegg/) database respectively. All statistical analysis and visualization of differentially expressed genes was conducted using R.3.5.1 (www.r-project.org).
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: gonadal white adipose tissue

growth_protocol: Mice were fed a NCD or HFD and were kept on a 12-h light/12-h dark cycle with free access to food and water at 22±1 °C.

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen) and processed as per manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s protocol.

treatment_protocol: Mice were fed a NCD or HFD for 12 weeks at the age of 8 weeks.

value: gonadal white adipose tissue

value: MKO

value: HFD


title: ATAC_ImmN_WT_aIL1B_2


title: 3_5364NIH_MartinaControl3_RNA_mm_iUDI0070

value: Untreated


title: ATAC_MatN_WT_CTRL_1

value: MatN

value: CTRL


title: Whole-blood RNA-seq from preACLF with sepsis shock (pS63)

description:
pS63
Whole-blood RNA-seq from preACLF with septic shock (pS63).
mRNAseq

value: preACLF with septic shock


title: ATAC_ImmN_WT_aIL1B_1

value: WT


title: 02_NC-Control-02

value: iBMDM

value: immortalized bone marrow-derived macrophage


title: gWAT MKO HFD_rep2


title: ATAC_ImmN_KEP_aIL1B_3

value: KEP


title: 2_5364NIH_MartinaControl2_RNA_mm_iUDI0069

value: Macrophages

value: Wild Type


title: gWAT MKO HFD_rep1


title: ATAC_ImmN_KEP_CTRL_3

value: ImmN


title: 1_5364NIH_MartinaControl1_RNA_mm_iUDI0068


description:
03K003
Whole-blood RNA-seq from Healthy Subjects (03K003).
mRNAseq

value: Healthy Subjects

value: Whole blood


title: gWAT WT HFD_rep2


title: Whole-blood RNA-seq from preACLF with sepsis shock (S77)

description:
S77
Whole-blood RNA-seq from preACLF with septic shock (S77).
mRNAseq


description:
S19
Whole-blood RNA-seq from ACLF with septic shock treated (S19).
mRNAseq

value: ACLF with septic shock treated


title: 01_Martina-TFEB_TFEB

data_processing:
Basecalls performed using Illumina bcl2fastq2 version 2.20
ChIP-seq reads were aligned to the human GRCh38/hg38 genome assembly using Burrows-Wheeler Aligner algorithm with default settings.
Data were filtered as follows: Duplicate reads were removed, and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7 [2]. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Assembly: mm10
Supplementary files format and content: bigWIG files were generated using wigToBigWig version 4 software

extract_protocol:
Chromatin was isolated from cells by adding lysis buffer (1% SDS, 10 mM EDTA and 50mM Tris-HCl, pH 8.1 containing protease inhibitors), followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). Genomic DNA regions of interest were isolated using monoclonal antibody against Flag.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara) following the manufacturer's protocol. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end) following the manufacturer's protocols.

value: DMXAA 10 µg/mL


title: gWAT WT HFD_rep1

value: gonadal white adipose tissue


title: ATAC_ImmN_WT_CTRL_3

value: Bone marrow


title: p300KO UUO kidney 3

city: seoul

first: HYUNSIK

last: KIM

address: 50-1 Yonsei-ro

institute: yonsei univ

data_processing:
Sequencing reads were trimmed by BBDuk(> average Q20)
Mapping by Bowie2 to Reference genome and calcaulation read count using Bedtools
TMM+CPM normalization by EdgeR
DEG master file production by ExDEGA
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count

source_name: kidney

growth_protocol: The mice were housed in a SPF facility, with a controlled temperature and humidity under conditions of a 12-h light/12-h dark cycle. To generate p300 null allele, LoxP sites were inserted into the flanking regions of the p300 gene on exon 9.

extract_protocol:
Total RNA from mouse kidney was extrated using Trizol reagent(TAKARA, japan).
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Using 8 to 10-week-old mice, UUO surgery was opeated. And mice was sacrificed at 8days after surgery

value: kidney

value: PTC specific p300 Knock out


title: Whole-blood RNA-seq from preACLF with sepsis shock (S18)

description:
S18
Whole-blood RNA-seq from preACLF with septic shock (S18).
mRNAseq


description:
S15
Whole-blood RNA-seq from ACLF with septic shock treated (S15).
mRNAseq


title: gWAT MKO NCD_rep3

value: MKO

value: NCD


title: p300KO UUO kidney 2


title: Whole-blood RNA-seq from preACLF with sepsis shock (S16)

description:
S16
Whole-blood RNA-seq from preACLF with septic shock (S16).
mRNAseq

value: preACLF with septic shock


title: ATAC_ImmN_WT_CTRL_1

value: WT

value: CTRL


description:
S76
Whole-blood RNA-seq from ACLF with septic shock treated (S76).
mRNAseq


title: gWAT MKO NCD_rep2


title: p300KO UUO kidney 1


title: gWAT MKO NCD_rep1


title: ATAC_PreN_KEP_aIL1B_3

value: PreN

value: KEP


description:
S13
Whole-blood RNA-seq from ACLF with septic shock treated (S13).
mRNAseq


title: WT UUO kidney 3

value: Wild type


title: Whole-blood RNA-seq from preACLF with sepsis shock (S14)

description:
S14
Whole-blood RNA-seq from preACLF with septic shock (S14).
mRNAseq


title: gWAT WT HFD_rep3

value: HFD


title: ATAC_ImmN_KEP_CTRL_1

value: ImmN


title: ATAC_ImmN_KEP_CTRL_2


title: WT UUO kidney 2


title: 00_Marina-TFEB_Input

value: iBMDM

value: Macrophages

value: Untreated


title: gWAT WT NCD_rep3

value: gonadal white adipose tissue


description:
pS60
Whole-blood RNA-seq from ACLF with septic shock treated (pS60).
mRNAseq

value: ACLF with septic shock treated

value: Whole blood


title: gWAT WT NCD_rep2


title: ATAC_PreN_KEP_aIL1B_1

value: Bone marrow


title: WT UUO kidney 1

value: kidney


title: ATAC_ImmN_WT_CTRL_2


title: Whole-blood RNA-seq from preACLF with sepsis shock (pS49)

description:
pS49
Whole-blood RNA-seq from preACLF with septic shock (pS49).
mRNAseq


title: gWAT WT NCD_rep1

value: NCD


title: WT sham kidney 3

value: Sham


description:
pS22
Whole-blood RNA-seq from ACLF with septic shock treated (pS22).
mRNAseq


title: ATAC_PreN_WT_aIL1B_2

value: WT


title: ATAC_PreN_WT_aIL1B_3


title: APC-KO duodenum crypt tom+ cells, scATAC-seq rep3

city: Boston

first: Ramesh

middle: A

last: Shivdasani

state: MA

address: 450Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: 10x Genomics

data_processing:
The barcoded processing, peak calling and gene counting were done using the Cell Ranger software v2.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: metadata.csv contains cell type annotation metadata

source_name: Duodenum

growth_protocol: To activate CreER-T2 in Atoh1CreER-T2;R26RTom  or Atoh1Cre;Apcfl/fl;R26RTom mice, we administered 2 doses of 1 mg/mL tamoxifen (Sigma-Aldrich, T5648; stocks prepared in cornflower oil) by intraperitoneal (IP) injection 24 h apart; and 12 h later we harvested intestinal TOM+  crypt cells for scATAC-seq.

extract_protocol:
Pieces of small intestine were rinsed in PBS, then rotated in 5 mM EDTA (pH 8) in PBS for 45 min at 4°C with manual shaking every 10 min and a change of solution after 30 min. Released epithelium was passed through a 70-µm strainer to separate villi from crypts and was dissociated into single cells by rotating in 4% TrypLE solution (ThermoFisher, A1217702) for 30-45 min at 37°C. Single cells were diluted in Dulbecco’s modified Eagle medium (DMEM, Corning. 17-205-CV) containing 2% FBS. Tom+ cells were isolated on a FACSAria II SORP flow cytometer, with elimination of dead (DAPI+) cells, pelleted by centrifugation, and trypan blue-excluding cells were counted manually.
Library was performed according to the manufacter’s instructions (single cell ATAC v1.1 protocol, 10x Genomics). Briefly, Transposed nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The transposed DNA elements contained in every single GEM was amplified, which contains an Ilumina P5 sequence and the 10x Barcode. The pooled barcoded ATAC sites was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P7 sequences and a sample index were added.

value: Duodenum

value: Epithelium

value: Tamoxifen (1mg/ml)


title: APC-KO duodenum crypt tom+ cells, scATAC-seq rep2

description: 10x Genomics

treatment_protocol: To activate CreER-T2 in Atoh1CreER-T2;R26RTom  or Atoh1Cre;Apcfl/fl;R26RTom mice, we administered 2 doses of 1 mg/mL tamoxifen (Sigma-Aldrich, T5648; stocks prepared in cornflower oil) by intraperitoneal (IP) injection 24 h apart; and 12 h later we harvested intestinal TOM+  crypt cells for scATAC-seq.


description:
S29
Whole-blood RNA-seq from ACLF with septic shock treated (S29).
mRNAseq


title: WT sham kidney 1

value: Wild type


title: WT sham kidney 2


title: APC-KO duodenum crypt tom+ cells, scATAC-seq rep1

description: 10x Genomics


title: ATAC_PreN_WT_aIL1B_1

value: PreN


title: Whole-blood RNA-seq from preACLF with sepsis shock (pS21)

description:
pS21
Whole-blood RNA-seq from preACLF with septic shock (pS21).
mRNAseq

value: preACLF with septic shock


title: Whole-blood RNA-seq from preACLF with sepsis shock (S26)

description:
S26
Whole-blood RNA-seq from preACLF with septic shock (S26).
mRNAseq


description:
S05
Whole-blood RNA-seq from ACLF with septic shock treated (S05).
mRNAseq


title: Cotl1-/--HFD_4

city: Suwon

first: Seon-Yong

last: Jeong

address: 206, World cup-ro, Yeongtong-gu

department: Department of Medical Genetics

institute: Ajou University School of Medicine

description:
Library name: Sample 8
Column name in Adipose_tissue_all_counts_data.txt: Cotl1-/--HFD_4_RPKM

data_processing:
Preprocessing Low quality reads and adapter sequences were filtered according to the following criteria. -Tool : cutadapt version : 2.8 parameter : quality-cutoff (20) parameter : minimum-length (50)
Alignment Filtered reads were mapped to the reference genome related to the species. The parameters have been set based on ENCODE standard options. -Reference Data Species : Mus_musculus Resource : Ensembl Genome Assembly : GRCm38.p6 (GCA_000001635.8) Genemodel version : 99 -Tool : STAR citation : Reference 2 version : 2.7.1a parameter : outFilterType (BySJout) parameter : outFilterMultimapNmax (20) parameter : alignSJoverhangMin (8) parameter : alignSJDBoverhangMin (1) parameter : outFilterMismatchNmax (999) parameter : outFilterMismatchNoverLmax (0.04) parameter : alignIntronMin (20) parameter : alignIntronMax (1000000) parameter : alignMatesGapMax (1000000)
Assembly: GRCm38.p6
Supplementary files format and content: RPKM values for each Sample

source_name: white adipose tissue

extract_protocol:
Wild-type and Cotl1 knockout male mice (4 weeks) were fed a 60% HFD for 12 weeks, and WAT was dissected. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and used for RNA-seq
cDNA libraries were synthesized by using TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA)

value: white adipose tissue

tag: Sex

value: male

tag: diet

value: HFD


title: ATAC_PreN_KEP_CTRL_1

value: KEP

value: CTRL


title: WT duodenum crypt tom+ cells, scATAC-seq rep2

description: 10x Genomics


title: ATAC_PreN_KEP_aIL1B_2


title: Cotl1-/--HFD_3

description:
Library name: Sample 7
Column name in Adipose_tissue_all_counts_data.txt: Cotl1-/--HFD_3_RPKM


title: ATAC_PreN_KEP_CTRL_2


title: Cotl1-/--HFD_2

description:
Library name: Sample 6
Column name in Adipose_tissue_all_counts_data.txt: Cotl1-/--HFD_2_RPKM


title: WT duodenum crypt tom+ cells, scATAC-seq rep1

description: 10x Genomics


title: Whole-blood RNA-seq from preACLF with sepsis shock (S04)

description:
S04
Whole-blood RNA-seq from preACLF with septic shock (S04).
mRNAseq

value: Whole blood


title: Cotl1-/--HFD_1

description:
Library name: Sample 5
Column name in Adipose_tissue_all_counts_data.txt: Cotl1-/--HFD_1_RPKM


title: APC-KO duodenum crypt tom+ cells, scRNA-seq rep2

description: 10x Genomics

data_processing:
The barcoded processing and gene counting were done using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include STAR raw counts for each Sample
Supplementary files format and content: metadata.csv contains cell type annotation metadata

growth_protocol: To activate CreER-T2 in Atoh1CreER-T2;R26RTom  or Atoh1Cre;Apcfl/fl;R26RTom mice, we administered 2 doses of 1 mg/mL tamoxifen (Sigma-Aldrich, T5648; stocks prepared in cornflower oil) by intraperitoneal (IP) injection 24 h apart; and 12 h later we harvested intestinal TOM+  crypt cells for scRNA-seq.

extract_protocol:
Pieces of small intestine were rinsed in PBS, then rotated in 5 mM EDTA (pH 8) in PBS for 45 min at 4°C with manual shaking every 10 min and a change of solution after 30 min. Released epithelium was passed through a 70-µm strainer to separate villi from crypts and was dissociated into single cells by rotating in 4% TrypLE solution (ThermoFisher, A1217702) for 30-45 min at 37°C. Single cells were diluted in Dulbecco’s modified Eagle medium (DMEM, Corning. 17-205-CV) containing 2% FBS. Tom+ cells were isolated on a FACSAria II SORP flow cytometer, with elimination of dead (DAPI+) cells, pelleted by centrifugation, and trypan blue-excluding cells were counted manually.
Library preparation was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: Intestine Epithelium


title: ATAC_PreN_WT_CTRL_3

value: Bone marrow


title: ATAC_PreN_KEP_CTRL_3


title: ATAC_PreN_WT_CTRL_2


title: APC-KO duodenum crypt tom+ cells, scRNA-seq rep1

description: 10x Genomics

treatment_protocol: To activate CreER-T2 in Atoh1CreER-T2;R26RTom  or Atoh1Cre;Apcfl/fl;R26RTom mice, we administered 2 doses of 1 mg/mL tamoxifen (Sigma-Aldrich, T5648; stocks prepared in cornflower oil) by intraperitoneal (IP) injection 24 h apart; and 12 h later we harvested intestinal TOM+  crypt cells for scRNA-seq.


title: B16-F10-3

city: Shenzhen

first: Xuefei

last: Li

address: 1068 Xueyuan Avenue, Shenzhen University Town, Nanshan

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

description: Library name: Sample 3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
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 v1.6.0 was used to count the reads numbers mapped to each gene.
Assembly: GRCm39 (GCA_000001635.9)
Supplementary files format and content: text files (.txt) containing raw, unnormalized read counts per gene (rows) across samples (columns), with gene identifiers (e.g., Ensembl IDs).

source_name: Tumor (from B16-F10 melanoma model)

extract_protocol:
Total RNA was extracted from tissue samples using standard methods. RNA quality assessment was performed using three approaches: Nanodrop spectrophotometer was used for preliminary concentration and purity assessment. Qubit fluorometer was used for precise RNA quantification. RNA integrity (RIN value) was assessed using the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system.
A total of 1 µg of RNA per sample was used as input for RNA library preparation. Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations. Index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-), followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. Overhangs were converted into blunt ends via exonuclease/polymerase activities, and 3' ends of DNA fragments were adenylated.  NEBNext Adaptor with a hairpin loop structure was ligated to prepare for hybridization. cDNA fragments of 250–300 bp were size-selected using the AMPure XP system (Beckman Coulter, USA). Then, 3 µl of USER Enzyme (NEB, USA) was used at 37°C for 15 min, followed by 5 min at 95°C before PCR amplification. PCR was performed using Phusion High-Fidelity DNA Polymerase, Universal PCR primers, and Index (X) Primer. Finally, PCR products were purified using the AMPure XP system, and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Tumor (from B16-F10 melanoma model)

value: melanoma

value: B16-F10; pLV[Exp]-Puro-EF1A>GCaMP6s

value: B16-F10 tumor-bearing mice treated with OT-1 CD8+ T cells; isolated by FACS based on GCaMP6s expression


title: Whole-blood RNA-seq from preACLF with sepsis shock (S02)

description:
S02
Whole-blood RNA-seq from preACLF with septic shock (S02).
mRNAseq


title: ATAC_PreN_WT_CTRL_1

value: WT


title: WT duodenum crypt tom+ cells, scRNA-seq rep2

description: 10x Genomics

value: Duodenum

value: Tamoxifen (1mg/ml)


description:
S54
Whole-blood RNA-seq from ACLF with septic shock treated (S54).
mRNAseq

value: ACLF with septic shock treated


title: WT duodenum crypt tom+ cells, scRNA-seq rep1

description: 10x Genomics


title: WT-HFD_2

description:
Library name: Sample 2
Column name in Adipose_tissue_all_counts_data.txt: WT-HFD_2_RPKM


title: ATAC_GMP_KEP_aIL1B_3

value: GMP


title: WT-HFD_3

description:
Library name: Sample 3
Column name in Adipose_tissue_all_counts_data.txt: WT-HFD_3_RPKM

value: white adipose tissue


description:
S06
Whole-blood RNA-seq from ACLF with septic shock treated (S06).
mRNAseq


title: Whole-blood RNA-seq from preACLF with sepsis shock (S63)

description:
S63
Whole-blood RNA-seq from preACLF with septic shock (S63).
mRNAseq

value: preACLF with septic shock


title: ATAC_GMP_KEP_aIL1B_2


title: Enterocytes, ATAC rep2

data_processing:
Sequence reads were trimmed for adaptor sequence using cutadapt verion 1.14
Trimmed sequence reads were mapped to mm10 using Bowtie2 2.3.5
bigwig files were quantile normalized over 25bp windows using Haystack Hotspots
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: Organoids were grown in media containing advanced DMEM, 1% B27 (Gibco), 0.5% N2-supplement (Gibco), 125 mM N-Acetylcysteine (Sigma), 10% Rspo1-conditioned medium (Harvard Digestive Disease Center), 100 ng/ml rNOG (Peprotech), 100 ng/ml rEGF (Peprotech) and 10 μM Y-27632 (Sigma). The GSK3-inhibitor CHIR99021 (Sigma, 5 μM) was added to the media to mimic canonical Wnt-activation in WnthiBMPlo conditions, and mixtures of recombinant(r) BMPs (rBMP2/4/7, 50ng/ml combined) added to the media without rNOG and RSPO1 for WntloBMPhi conditions.

extract_protocol:
Nuclei were harvested at specified time points and transposed using Tn5, and Nextera DNA library kit was used for the construction of sequencing libraries.
ATAC libraries were prepared by NEBNext High Fidelity 2X PCR Master mix

treatment_protocol:
To induce secretory differentiation organoids were treated with DAPT (10 μM, Sigma-Aldrich D5942) for 3 days and then continued on DAPT for 4 additional days as control or treated with DAPT and GSK3-inhibitor CHIR99021 (Sigma, 5 μM) to mimic canonical Wnt-activation in WnthiBMPlo conditions or with DAPT and mixtures of recombinant(r) BMPs (rBMP2/4/7, 50ng/ml combined) without rNOG and RSPO1 for WntloBMPhi conditions for 4 additional days.
Lgr5 GFP+ ISC or villi enterocytes from VilCreER-T2;Apcfl/fl mice 3 weeks after tamoxifen induction IP (1mg/ml) were harvested for bulkATAC-seq.


title: Enterocytes, ATAC rep1


description:
S36
Whole-blood RNA-seq from ACLF with septic shock treated (S36).
mRNAseq


title: ATAC_GMP_WT_aIL1B_3


title: WT-HFD_4

description:
Library name: Sample 4
Column name in Adipose_tissue_all_counts_data.txt: WT-HFD_4_RPKM

value: male

value: HFD


title: RNA_Lung_Neutrophil_KEP_4

data_processing:
Sequencing reads were aligned to the mm10 mouse reference genome using the STAR aligner version 2.7.9a.
Mapped reads were filtered for mapping quality >10 using samtools version 1.10.
Gene counts were generated using the "summarizeOverlaps" function from R/Bioconductor package GenomicAlignments, with the counting mode set to "Union".
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Lung

extract_protocol:
LT-HSCs, MPPs, CMPs and GMPs were enriched by neutrophil depletion. Bone marrow single cell suspensions were incubated with 10μg/ml anti-Ly6G (1A8, BioXcell) before neutrophil depletion using sheep anti-rat magnetic beads (Dynabeads, Life Technologies) and subsequently stained with cell surface markers. For sorting pre-neutrophils and neutrophils from bone marrow, blood and lung, cells were first incubated with 500μg/ml purified mouse IgG+10% FCS (BM) or rat anti-mouse CD16/CD32 antibody (blood and lung), stained with cell surface markers and sorted using gating strategies for HSPC populations or CD45+ CD11b+ Ly6G+ 7-AAD- markers for sequencing of blood and lung neutrophils. RNA was isolated following RNeasy Mini Kit (Qiagen) protocol, using 80% ethanol instead of RPE buffer.
Smart-seq2 library preparation was performed according to the Smart-seq2 protocol, using 2100 Bioanalyzer System (Agilent) for quality control.

value: Lung

value: Neutrophil

value: KEP


title: ATAC_GMP_KEP_aIL1B_1

data_processing:
Sequencing reads were aligned to the mm10 mouse reference genome using bwa mem version 0.7.17-r1188.
Mapped reads were filtered for mapping quality >15 using samtools version 1.10.
bigWig coverage files were generated with deepTools using the reads per genomic content (RPGC) scaling.
Assembly: mm10
Supplementary files format and content: bigWig files contain coverage for each sample scaled to 1x genome coverage.

extract_protocol:
LT-HSCs, MPPs, CMPs and GMPs were enriched by neutrophil depletion. Bone marrow single cell suspensions were incubated with 10μg/ml anti-Ly6G (1A8, BioXcell) before neutrophil depletion using sheep anti-rat magnetic beads (Dynabeads, Life Technologies) and subsequently stained with cell surface markers. For sorting pre-neutrophils and neutrophils from bone marrow, blood and lung, cells were first incubated with 500μg/ml purified mouse IgG+10% FCS (BM) or rat anti-mouse CD16/CD32 antibody (blood and lung), stained with cell surface markers and sorted using gating strategies for HSPC populations or CD45+ CD11b+ Ly6G+ 7-AAD- markers for sequencing of blood and lung neutrophils.
Nuclei of the sorted cells were isolated, permeabilized and tagmented by using commercially available Tn5 transposase (Illumina, Nextera DNA Library Preparation Kit). DNA fragments underwent a first 9-cycle PCR amplifications using KAPA HiFi HotStart ReadyMix (7958935001, Roche), and we selected the fragments between 150 and 700 bp in size using with SPRI beads (A63881, Backman Coulter). The size-selected fragments were amplified for a second 9-cycle PCR reactions, and the resulted libraries were purified using SPRI beads.

value: Bone marrow


title: Lgr5+ ISC, ATAC rep2

value: Intestine Epithelium


title: RNA_Lung_Neutrophil_KEP_2


title: Whole-blood RNA-seq from preACLF with sepsis shock (S35)

description:
S35
Whole-blood RNA-seq from preACLF with septic shock (S35).
mRNAseq

value: Whole blood


title: ATAC_GMP_WT_aIL1B_2


title: PBMC from sample HV3_5

description: PBMC from sample HV3_5

data_processing:
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: RSEM expected counts

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
RNA wa extracted from PBMCs using the tryzol reagent.RNA quality was assessed using Agilent RNA 6000 Nano and Pico Chips (Agilent Technologies, Cat.# 5067-1511 and Cat.# 5067-151, respectively) and concentration via Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat.# Q32855
Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina Inc., Cat.# 20020612) and TruSeq RNA CD Index Plate (Illumina Inc., Cat.# 20019792) following TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E). Briefly, starting from 500 ng of total RNA, rRNA and globin mRNA were depleted and remaining RNA was purified, fragmented and primed for cDNA synthesis. cDNA first strand was synthesized with SuperScript-II Reverse Transcriptase (Thermo Fisher Scientific, Cat.#18064-014) for 10 min at 25°C, 15 min at 42°C, 15 min at 70°C and pause at 4°C. cDNA second strand was synthesized with Illumina reagents at 16°C for 1 hour. Then, A-tailing and adaptor ligation were performed. Finally, enrichment of libraries was achieved by PCR (30 sec at 98°C; 15 cycles of 10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C; 5min at 72°C and pause at 4°C). Afterwards, libraries were visualized on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626), quantified using Qubit dsDNA HS DNA Kit (Thermo Fisher Scientific, Cat. # Q32854) and sequenced in a NovaSeq-6000 (Illumina Inc.) by at least 40 million paired-end 100nt reads

treatment_protocol: PBMC were seeded at a density of 1.5x106 cells/ml and incubated with either albumin (Albutein®), recombinant albumin expressed in Oryza sativa (rHSA) (Sigma) (both at 15 mg/ml) or vehicle control for twenty-four hours at 37ºC in a 5% CO2 incubator. In some experiments, PBMCs were incubated with the FcRn blocking antibody, ADM31 (Aldevron) (10 g/ml) before the addition of albumin. Isolation of total RNA from cells was performed by TRIzol. RNA concentration and integrity, library preparation and RNA-Seq analysis was performed as already described for whole-blood RNA-seq.

tag: disease group

value: HV


title: PBMC from sample HV3_4

description: PBMC from sample HV3_4


title: Lgr5+ ISC, ATAC rep1


title: DAPT + WntloBMPhi, ATAC rep2

value: DAPT(10uM) + rBMP2/4/7 (50ng/ml combined) - RPSO2 and -rNOG


title: ATAC_GMP_WT_aIL1B_1

value: WT


title: RNA_Lung_Neutrophil_KEP_1


title: PBMC from sample HV3_3

description: PBMC from sample HV3_3

value: rHSA


title: ATAC_GMP_KEP_CTRL_2

value: CTRL


title: WT-HFD_1

description:
Library name: Sample 1
Column name in Adipose_tissue_all_counts_data.txt: WT-HFD_1_RPKM


title: RNA_Lung_Neutrophil_KEP_3


title: RNA_Lung_Neutrophil_WT_4


title: DAPT + WnthiBMPlo, ATAC rep2

value: Duodenum


title: ATAC_GMP_KEP_CTRL_1

value: GMP


title: PBMC from sample HV3_1

description: PBMC from sample HV3_1

value: Veh


title: RNA_Lung_Neutrophil_WT_3


title: ATAC_GMP_WT_CTRL_3


title: PBMC from sample HV3_2

description: PBMC from sample HV3_2

value: HSA


title: DAPT + WnthiBMPlo, ATAC rep1


title: RNA_Lung_Neutrophil_WT_2


title: PBMC from sample HV2_5

description: PBMC from sample HV2_5


title: RNA_Lung_Neutrophil_WT_1


title: ATAC_GMP_WT_CTRL_1


title: PBMC from sample HV2_4

description: PBMC from sample HV2_4


title: ATAC_GMP_WT_CTRL_2


title: DAPT Only, ATAC rep2


title: PBMC from sample HV2_3

description: PBMC from sample HV2_3


title: DAPT Only, ATAC rep1

value: DAPT (10uM)


title: RNA_Blood_Neutrophil_KEP_4

source_name: Blood

value: Blood


title: Crypt TOM+, Day12, RNA rep2

data_processing:
sequence reads were mapped to mm10 using STAR aligner
Read count extraction were performed using STAR aligner v2.6.0c
Assembly: mm10
Supplementary files format and content: tab-delimited text files include STAR raw counts for each Sample

growth_protocol: For mature goblet cell isolation Atoh1CreER-T2;R26RTom mice were treated with 1 dose of tamoxifen injection IP (1mg/ml) and villi TOM+ were cells harvested 36 h later. For Paneth cell isolation Atoh1CreER-T2;R26RTom mice were treated with 1 dose of tamoxifen injection IP (1mg/ml) and crypt TOM+ cells were harvested 12 days later. TOM+PTPRC+ and TOM-PTPRC+ crypt cells from LGR5Cre/+; R26Tom mice intestine were isolated by flow cytometry 5 days after tamoxifen injection IP (1mg/ml) to specifically enrich for Epithelial derived lymphoid-like cells (EDLCs) and intraepithelial lymphocytes (IELs) respectively.

extract_protocol:
RNA was harvested from sorted viable (DAPI-) TOM+ or EPCAM+ mouse cells, PTPRC+ mouse EDLCs (TOM+), and IELs (TOM-) using Rneasy mini plus kit (Qiagen) and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene Corporation Inc.

value: Atoh1Cre/+; R26Tom

value: 1mg/ml Tamoxifen


title: ATAC_CMP_KEP_aIL1B_3

value: CMP

value: KEP


title: RNA_Blood_Neutrophil_KEP_2

value: Neutrophil


title: Crypt TOM+, Day12, RNA rep1

treatment_protocol: For mature goblet cell isolation Atoh1CreER-T2;R26RTom mice were treated with 1 dose of tamoxifen injection IP (1mg/ml) and villi TOM+ were cells harvested 36 h later. For Paneth cell isolation Atoh1CreER-T2;R26RTom mice were treated with 1 dose of tamoxifen injection IP (1mg/ml) and crypt TOM+ cells were harvested 12 days later. TOM+PTPRC+ and TOM-PTPRC+ crypt cells from LGR5Cre/+; R26Tom mice intestine were isolated by flow cytometry 5 days after tamoxifen injection IP (1mg/ml) to specifically enrich for Epithelial derived lymphoid-like cells (EDLCs) and intraepithelial lymphocytes (IELs) respectively.

value: Intestine Epithelium


title: DAPT + WntloBMPhi, ATAC rep1


title: Villi TOM+, 36h, RNA rep2


title: ATAC_CMP_KEP_aIL1B_1

value: Bone marrow


title: RNA_Blood_Neutrophil_KEP_1


title: PBMC from sample HV1_5

description: PBMC from sample HV1_5

value: HV


title: ATAC_CMP_WT_aIL1B_3

value: WT


title: Villi TOM+, 36h, RNA rep1


title: RNA_Blood_Neutrophil_WT_4


title: PBMC from sample HV1_4

description: PBMC from sample HV1_4


title: NGKO_3

first: Bowen

last: Wang

value: mouse embryonic stem cell

value: NanogKO


title: RNA_Blood_Neutrophil_WT_3


title: PBMC from sample HV1_3

description: PBMC from sample HV1_3

value: rHSA


title: ATAC_CMP_WT_aIL1B_2


title: NGKO_2


title: ATAC_CMP_KEP_aIL1B_2


title: NGKO_1


title: RNA_Blood_Neutrophil_WT_2


title: RNA_Blood_Neutrophil_KEP_3


title: ATAC_CMP_KEP_CTRL_2

value: CTRL


title: RNA_Blood_Neutrophil_WT_1


title: ATAC_CMP_WT_aIL1B_1


title: PBMC from sample HV2_1

description: PBMC from sample HV2_1

value: Veh


title: RNA_MatN_KEP_aIL1B_3

value: MatN


title: PBMC from sample HV1_2

description: PBMC from sample HV1_2

value: HSA


title: NGFF_2

value: NanogF/F


title: RNA_MatN_KEP_aIL1B_2


title: PBMC from sample AD5_4

description: PBMC from sample AD5_4

value: AD


title: NGFF_1


title: RNA_MatN_KEP_aIL1B_1


title: PBMC from sample AD5_3

description: PBMC from sample AD5_3


title: ATAC_CMP_WT_CTRL_3


title: ATAC_CMP_WT_CTRL_2


title: PBMC from sample HV2_2

description: PBMC from sample HV2_2


title: OtKO_3


title: OtKO_2


title: PBMC from sample AD5_2

description: PBMC from sample AD5_2


title: ATAC_CMP_WT_CTRL_1


title: PBMC from sample HV1_1

description: PBMC from sample HV1_1


title: ATAC_CMP_KEP_CTRL_3


title: PBMC from sample AD5_5

description: PBMC from sample AD5_5


title: NGFF_3


title: RNA_ImmN_KEP_aIL1B_2

value: ImmN


title: ATAC_CMP_KEP_CTRL_1

value: CMP


title: PBMC from sample AD5_1

description: PBMC from sample AD5_1


title: RNA_ImmN_KEP_aIL1B_3

value: KEP


title: PBMC from sample AD4_5

description: PBMC from sample AD4_5


title: OtKO_1


title: ATAC_MPP_KEP_aIL1B_2

value: MPP


title: ATAC_MPP_KEP_aIL1B_3


title: RNA_ImmN_KEP_aIL1B_1


title: PBMC from sample AD4_4

description: PBMC from sample AD4_4


title: OtFF_3


title: RNA_PreN_KEP_aIL1B_3

value: PreN


title: RNA_PreN_KEP_aIL1B_2

value: Bone marrow


title: OtFF_2


title: ATAC_MPP_KEP_aIL1B_1


title: ATAC_MPP_WT_aIL1B_3


title: PBMC from sample AD4_3

description: PBMC from sample AD4_3


title: RNA_PreN_KEP_aIL1B_1


title: SX123_3

value: Sox2F/F;Sox1/3-/- -CRE


title: PBMC from sample AD4_2

description: PBMC from sample AD4_2


title: ATAC_MPP_WT_aIL1B_2

value: WT


title: OtFF_1

value: mouse embryonic stem cell


title: PBMC from sample AD4_1

description: PBMC from sample AD4_1


title: SX123_2


title: ATAC_MPP_WT_aIL1B_1


title: ATAC_MPP_KEP_CTRL_3


title: PBMC from sample AD3_3

description: PBMC from sample AD3_3


title: SX123_1


title: RNA_GMP_KEP_aIL1B_1

value: GMP


title: RNA_CMP_KEP_aIL1B_3


title: ATAC_MPP_KEP_CTRL_1


title: SX13KO_2


title: PBMC from sample AD3_1

description: PBMC from sample AD3_1


title: RNA_CMP_KEP_aIL1B_2


title: SX13KO_3


title: RNA_CMP_KEP_aIL1B_1


title: PBMC from sample AD3_2

description: PBMC from sample AD3_2


title: ATAC_MPP_KEP_CTRL_2


title: SX13KO_1


title: PBMC from sample AD2_2

description: PBMC from sample AD2_2


title: PBMC from sample AD2_3

description: PBMC from sample AD2_3

value: rHSA


title: ATAC_MPP_WT_CTRL_2

value: CTRL


title: SX2FFCRE_3


title: ATAC_MPP_WT_CTRL_3


title: RNA_GMP_KEP_aIL1B_3


title: RNA_MPP_KEP_aIL1B_2


title: SX2FFCRE_2


title: PBMC from sample AD2_1

description: PBMC from sample AD2_1

value: Veh


title: RNA_GMP_KEP_aIL1B_2


title: ATAC_MPP_WT_CTRL_1


title: RNA_MPP_KEP_aIL1B_1


title: SX2FFCRE_1


title: ATAC_LTHSC_KEP_aIL1B_3

value: LTHSC


title: PBMC from sample AD1_3

description: PBMC from sample AD1_3


title: ATAC_LTHSC_KEP_aIL1B_2


title: PBMC from sample AD1_2

description: PBMC from sample AD1_2

value: HSA


title: RNA_LTHSC_KEP_aIL1B_3


title: SX2FF_2

description:
SX2FFCRE_vs_SX2FF.deseq2.annot.xls.gz
SX123_vs_SX2FF.deseq2.annot.xls.gz


title: PBMC from sample AD1_1

description: PBMC from sample AD1_1


title: ATAC_LTHSC_WT_aIL1B_3


title: SX2FF_3


title: RNA_LTHSC_KEP_aIL1B_2


title: ATAC_LTHSC_WT_aIL1B_2


title: SXKO_3


title: ATAC_LTHSC_KEP_aIL1B_1


title: ATAC_LTHSC_WT_aIL1B_1


title: RNA_LTHSC_KEP_aIL1B_1


title: SXKO_2


title: RNA_MatN_WT_aIL1B_2

value: MatN


title: RNA_MatN_WT_aIL1B_3


title: SXKO_1


title: ATAC_LTHSC_KEP_CTRL_3


title: RNA_MPP_KEP_aIL1B_3


title: RNA_MatN_WT_aIL1B_1


title: ATAC_LTHSC_KEP_CTRL_2


title: ATAC_LTHSC_KEP_CTRL_1


title: RNA_ImmN_WT_aIL1B_3


title: SXFF_3


title: SXFF_2


title: RNA_ImmN_WT_aIL1B_2


title: SXFF_1


title: RNA_PreN_WT_aIL1B_3


title: ATAC_LTHSC_WT_CTRL_3


title: ATAC_LTHSC_WT_CTRL_2


title: WAT, KO, rep3

city: Suita

first: Akifumi

last: Uota

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Department of Metabolic Medicine, Osaka University Graduate School of Medicine

data_processing:
Adapter sequences were trimmed using Cutadapt v4.0.
Trimmed reads were mapped to the mouse mm10 genome using Bowtie2 v2.3.5.1.
The mapped reads were generated for visualization using DeepTools v3.5.1.
The peaks were identified using MACS2 v2.2.7.1.
Assembly: mm10
Supplementary files format and content: BAM, narrowPeak

source_name: adipose tissue

extract_protocol:
Genomic DNA was extracted from tissues using ATAC-Seq Kit (Active Motif).
Library preparation was performed using ATAC-Seq Kit (Active Motif).

value: adipose tissue


title: SX2FF_1


title: ATAC_LTHSC_WT_CTRL_1


title: RNA_PreN_WT_aIL1B_2


title: WAT, flox, rep2


title: WAT, KO, rep2


title: RNA_GMP_WT_aIL1B_3


title: RNA_PreN_WT_aIL1B_1


title: RNA_GMP_WT_aIL1B_2


title: Ctrl, replicate 1, RNA_seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

description: Library name: Ctrl_1

data_processing:
The raw reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version: cutadapt-1.9).
Filtered reads were mapped against the mm10 assembly of the Mus musculus genome (National Center for Biotechnology Information) using hisat2 (Version 2.2.1).
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Full-length cDNA was generated using SMART-Seq HT Kit (Takara), paired-end DNA libraries was generated and indexed using NexteraTM XT Library Prep Kit and then NexteraTM XT Index Kit.

value: colon

value: immune cell

value: Control


title: DCA, replicate 2, RNA_seq

description: Library name: DCA_2

value: DCA


title: DCA, replicate 1, RNA_seq

description: Library name: DCA_1


title: Ctrl, replicate 2, RNA_seq

description: Library name: Ctrl_2


title: WAT, KO, rep1


title: scRNA-seq_WT3_KEP3_HTO

description: 10x Genomics with hashtag oligos for 1 WT and 1 KEP mouse

data_processing:
Sequencing reads were aligned to the refdata-gex-mm10-2020-A genome (10X Genomics) and the gene and hashtag oligo count matrices of non-empty droplets were generated using the CellRanger 7.1.0 software.
Assembly: refdata-gex-mm10-2020-A (10X Genomics)
Supplementary files format and content: Matrix market (mtx) file includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text file includes barcodes for each sample.
Supplementary files format and content: Tab-delimited text file includes features (genes and hashtag oligos) for each sample.
Supplementary files format and content: RDS file includes a SingleCellExperiment R/Bioconductor object with raw and normalised counts, dimensionality reduction matrices, cell QC metrics, phase and cell type assignments, and inferred pseudotime values.

extract_protocol:
Hematopoietic stem and progenitor cells (HSPCs) were enriched by neutrophil depletion. Bone marrow single cell suspensions were incubated with 10μg/ml anti-Ly6G (1A8, BioXcell) before neutrophil depletion using sheep anti-rat magnetic beads (Dynabeads, Life Technologies) and subsequently stained with cell surface markers. Cells were incubated with TotalSeq B anti-mouse hashtags (BioLegend) to enable de-multiplexing. Sorted single cell suspensions of CD34+cKIT+ cells were diluted to a final concentration of 1000 cells/μl in 1xPBS containing 0.04% BSA (400ug/ml).
The Chromium X platform of 10X Genomics was used for single cell partitioning and barcoding. Per single cell suspension, each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 3’ Gene Expression libraries and Cell Hashing libraries via Feature barcode technology were prepared according to the manufacturer’s protocol (CG000317, 10X Genomics). All libraries were quantified on a 2100 Bioanalyzer Instrument following the Agilent Technologies Protocol (Agilent DNA 7500 kit, G2938-90024). Sequence library pools were composed and quantified by qPCR, according to the KAPA Library Quantification Kit Illumina® Platforms protocol (KR0405, KAPA Biosystems).

value: Hematopoietic stem and progenitor cells

value: WT+KEP

tag: library type

value: HTO


title: CS16

city: Pasadena

first: Magdalena

last: Zernicka Goetz

state: CALIFORNIA

address: CALIFORNIA INSTITUTE OF TECHNOLOGY

institute: California Institute of Technolog

data_processing:
Cell Ranger software from 10X Genomics was installed for data pre-processing. Raw sequencing data were organized, with the requirement that sequencing reads be demultiplexed into FASTQ format files for each sample. Using cellranger mkfastq to demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files. Reads were mapped to the human hg38 genome and counted with GRCh38-3.0.0 annotation using cellranger count. The data pre-processing workflow was streamlined and standardized to maintain consistency across samples.
Assembly: hg38,GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: amnion

extract_protocol:
All tissues for sequencing and spatial work were collected in HypoThermosol FRS preservation solution (H4416-100ML Merck) and stored at 4 °C until processing. Tissue dissociation was conducted within 24 h of tissue retrieval.Tissues were cut into <1 mm3 segments before being digested with Trypsin/EDTA 0.25% phenol red (25200072 Thermo Fisher Scientific) for 10-15 min at 37 °C with intermittent shaking. Digested tissue was passed through a 100 µm filter and cells collected by centrifugation (500g for 5 min at 4 °C). Cells were washed with PBS and then resuspended in PBS 0.04% BSA before cell counting.
cells were loaded according to the manufacturer’s protocol for the Chromium Next GEM Single Cell 5 v2 (Dual index) kit for CS17 amnion and Chromium Next GEM Single Cell 3 v3.1 (Dual index) kit for CS19 and CS22 amnion from 10X Genomics to attain 7,000 cells per reaction. Library preparation was carried out according to the manufacturer’s protocol. Libraries were sequenced, aiming at a minimum coverage of 20,000 raw reads per cell, on the Illumina HiSeq4000 or Novaseq 6000 systems using the sequencing format: read 1, 26 cycles; i7 index, 8 cycles, i5 index, 0 cycles; read 2, 98 cycles.

value: amnion

value: amnion cells


title: WAT, flox, rep1


title: RNA_GMP_WT_aIL1B_1

first: Elzo

last: de Wit

value: Bone marrow

value: GMP

value: WT


title: RNA_CMP_WT_aIL1B_3

value: CMP


title: scRNA-seq_WT3_KEP3_GEX

value: GEX


title: CS17


title: pituitary gland, WT_rep2_IP

first: Jie

last: Mei

description: Library name: Sample 12

data_processing:
Raw reads were filtered by Trimmomatic (v0.35) to remove adapter sequences and low-quality reads. Clean reads were aligned to the zebrafish GRCz11 genome using BWA with the default options. Then, MACS2 (v2.1.2) was used for peak calling.
Assembly: GRCz11
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: pituitary gland

extract_protocol:
Nuclei were harvested from a mass of zebrafish pituitary cells. Nuclei were washed and incubated with 10 μl concanavalin A-coated magnetic beads. Bead-bound cells were then resuspended with dig-wash buffer (20 mM HEPES, pH 7.5; 150 mM NaCl; 0.5 mM spermidine; 1X protease inhibitor cocktail; 0.05% digitonin; and 2 mM EDTA) and a 1:50 dilution of primary anti-phospho-Smad1/5/9 antibody (Cell Signaling Technology, 13820, Rabbit, USA) or control IgG on a rotating platform overnight at 4 °C. The beads were washed in dig-wash buffer, and the primary antibody was removed using a magnetic stand and then incubated with a secondary antibody (1:100) for 60 min. After incubation, the beads were washed in dig-Hisalt buffer and incubated with the proteinA-Tn5 adapter complex for 1 h. Next, the cells were resuspended in Tagmentation buffer (10 mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1 h. The DNA fragments were purified using phenol‒chloroform-isoamyl alcohol extraction and ethanol precipitation.
The sequencing libraries were prepared according to the manufacturer’s instructions and cleaned using XP beads (Beckman Counter)

value: pituitary gland

value: IP


title: scRNA-seq_WT2_KEP2_HTO

source_name: Bone marrow


title: RNA_ImmN_WT_aIL1B_1

value: ImmN


title: WAT, flox, rep3

value: adipose tissue


title: RNA_CMP_WT_aIL1B_1


title: RNA_MPP_WT_aIL1B_3

value: MPP


title: pituitary gland, WT_rep2_IgG

description: Library name: Sample 11

value: IgG


title: scRNA-seq_WT1_KEP1_HTO


title: pituitary gland, WT_rep1_IP

description: Library name: Sample 10


title: RNA_MPP_WT_aIL1B_2


title: pituitary gland, WT_rep1_IgG

description: Library name: Sample 9


title: Anti-IgG Hepatocyte Organoids

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
CUT&Tag reads were aligned to the mm10 genome using BWA.
Peaks were called using MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Hepatocyte organoids

growth_protocol: The isolated hepatocytes were filtered through a 70 μm filter, washed twice with cold AdDMEM/F12, counted and mixed with Matrigel and loaded into suspension plates. 24-well plates were used with 20,000-50,000 cells per well. After Matrigel was solidified, Hep-Medium was added. 4 days later, Hepatocyte organoids were digested as single cells. Genomic DNA was extracted and subjected to CUT&Tag.

extract_protocol:
The library preparation was performed with a CUT&Tag Assay Kit (Vazyme) by the manufacturer’s instructions.
To amplify libraries, 15μL DNA was mixed with 5μL of a universal i5 and 5μL of auniquely barcoded i7 primer. A volume of 25 μL  2× CAM was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 3 min (gap filling); 95 °C for 3 min; 9~20 cycles of 98 °C for 10 s and 60 °C for 5 s; final extension at 72 °C for 1 min and hold at 4 °C. libraries clean-up was performed VAHTS DNA Clean beads.

value: Hepatocyte organoids

tag: antibody

value: anti-IgG


title: pituitary gland, Bmpr2a_rep2_IP

description: Library name: Sample 8

value: knockout Bmpr2a


title: RNA_LTHSC_WT_aIL1B_2

value: LTHSC


title: pituitary gland, Bmpr2a_rep2_IgG

description: Library name: Sample 7


title: scRNA-seq_WT1_KEP1_GEX

value: Hematopoietic stem and progenitor cells

value: WT+KEP


title: Anti-ONECUT2 Hepatocyte Organoids


title: pituitary gland, Bmpr2a_rep1_IP

description: Library name: Sample 6


title: RNA_LTHSC_WT_aIL1B_3

value: Bone marrow


title: RNA_LTHSC_WT_aIL1B_1


title: pituitary gland, Bmpr2a_rep1_IgG

description: Library name: Sample 5


title: RNA_CMP_WT_aIL1B_2


title: Anti-ATF3 Hepatocyte Organoids


title: RNA_MatN_KEP_CTRL_2

value: MatN

value: KEP

value: CTRL


title: Normoxia Nnt-wt mouseID=NMW12

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

data_processing:
RNA preparation, library construction, sequencing on NovaSeq 6000 platform and raw data filtering was performed by Novogene (China).
Reads were aligned to the mouse genome (Mus_musculus.GRCm39.108) using STAR  (-runThreadN 2 --genomeDir --readFilesIn  --readFilesCommand gunzip -c --outFileNamePrefix  --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattrIHstart 0 --outFilterType BySJout --sjdbGTFfile /Mus_musculus.GRCm39.108.gtf --quantMode TranscriptomeSAM
Reads were quantified using HTSeq
Assembly: Mus_musculus.GRCm39.108
Supplementary files format and content: Raw counts using HTSeq

source_name: Gastrocnemius muscle

extract_protocol:
Directly after normoxia/hypoxia exposure, mice were killed by dicapitation. Gastrocnemius was isolated, snap frozen in liquid nitrogen and stored at -80°C until further analysis. Total RNA was extracted by grinding frozen muscle tissue and dissolving approximately 15 mg in 1 ml Trizol. Further RNA isolation was performed according to manufacture's  instructions (Thermo Fisher). RNA concentration was measured using NanoDrop one spectrophotometer (Thermo Fisher). RNA integrity was measured using RNA Screentape on the 2200 Tapestation (Agilent).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for directional library. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification(In-house kit: Novogene NGS Stranded RNA Library Prep Set (PT044)). The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms (NovaSeq 6000 platform using S4 flow cells), according to effective library concentration and data amount.

treatment_protocol: Gene expression profiles from gastrocnemius of fasted Nnt-wt male mice exposed to hypoxia (12%O2) or normoxia for 6 hours  (n=12 per group). Mice were weaned on 21 days and housed individually till killed. Mice had ad libitum access to chow diet till from 23.00 on 23 days, exposed to hypoxia (12% O2) or normoxia from 5.00 on 24 days for 6 hours and killed directly after exposure. Mice had ad libitum access to water at all times.

value: Gastrocnemius muscle

value: male

tag: strain

value: Nnt-wt

tag: age

value: 24 days

value: normoxia


title: pituitary gland, Amh_rep2_IgG

description: Library name: Sample 3

value: pituitary gland

value: knockout Amh


title: RNA_MatN_KEP_CTRL_1

city: Amsterdam

address: Plesmanlaan 121


title: scRNA-seq_WT2_KEP2_GEX

value: GEX


title: pituitary gland, Amh_rep1_IP

city: Wuhan

address: No.7, Donghu South Road, Wuchang District

description: Library name: Sample 2

value: IP


title: Normoxia Nnt-wt mouseID=NMW9


title: RNA_ImmN_KEP_CTRL_3

value: ImmN


title: Normoxia Nnt-wt mouseID=NMW8


title: pituitary gland, Amh_rep1_IgG

description: Library name: Sample 1

value: IgG


title: Normoxia Nnt-wt mouseID=NMW7


title: RNA_ImmN_KEP_CTRL_2


title: Normoxia Nnt-wt mouseID=NMW6


title: RNA_PreN_KEP_CTRL_3

value: PreN


title: RNA_ImmN_KEP_CTRL_1


title: RNA_PreN_KEP_CTRL_2


title: Normoxia Nnt-wt mouseID=NMW5


title: RNA_PreN_KEP_CTRL_1


title: pituitary gland, Amh_rep2_IP

description: Library name: Sample 4


title: RNA_MPP_WT_aIL1B_1

value: MPP

value: WT


title: Normoxia Nnt-wt mouseID=NMW11


title: RNA_GMP_KEP_CTRL_2

value: Bone marrow

value: GMP


title: RNA_MatN_KEP_CTRL_3

value: MatN

value: KEP

value: CTRL


title: Normoxia Nnt-wt mouseID=NMW4

value: Gastrocnemius muscle

value: male

value: Nnt-wt


title: Normoxia Nnt-wt mouseID=NMW2

value: 24 days

value: normoxia


title: Hypoxia Nnt-wt mouseID=HMW12

value: hypoxia


title: RNA_GMP_KEP_CTRL_3


title: RNA_GMP_KEP_CTRL_1


title: RNA_CMP_KEP_CTRL_2

value: CMP


title: Normoxia Nnt-wt mouseID=NMW10


title: RNA_CMP_KEP_CTRL_3


title: Normoxia Nnt-wt mouseID=NMW1


title: Hypoxia Nnt-wt mouseID=HMW11


title: Hypoxia Nnt-wt mouseID=HMW10


title: RNA_CMP_KEP_CTRL_1


title: RNA_MPP_KEP_CTRL_3


title: RNA_MPP_KEP_CTRL_2


title: Hypoxia Nnt-wt mouseID=HMW8


title: RNA_MPP_KEP_CTRL_1


title: Hypoxia Nnt-wt mouseID=HMW6


title: RNA_LTHSC_KEP_CTRL_3

value: LTHSC


title: Hypoxia Nnt-wt mouseID=HMW5


title: Hypoxia Nnt-wt mouseID=HMW4


title: RNA_LTHSC_KEP_CTRL_2


title: Normoxia Nnt-wt mouseID=NMW3


title: RNA_LTHSC_KEP_CTRL_1


title: Hypoxia Nnt-wt mouseID=HMW3


title: Hypoxia Nnt-wt mouseID=HMW2


title: RNA_MatN_WT_CTRL_1


title: RNA_MatN_WT_CTRL_3


title: Hypoxia Nnt-wt mouseID=HMW1


title: RNA_MatN_WT_CTRL_2


title: Roots, reoxygenation, rep3

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

data_processing:
Raw reads were processed with BBDUK2 using the following settings: qtrim=w trimq=20 maq=10 rref=bbmap/resources/adapters.fa k=23 mink=11 hdist=1 tbo tpe minlength=35 removeifeitherbad=t
Reads were mapped against lupin genome (LupAngTanjil_v1.0, from Ensembl Plants 55) using STAR with the following settings: --outSAMattributes All --outSAMattrIHstart 0 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 50000 --alignMatesGapMax 100000 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3
The BAM files were used for ab initio transcriptome assembly with StringTie
Gene expression values were calculated with RSEM
Assembly: LupAngTanjil_v1.0
Supplementary files format and content: A regular output of RSEM, i.e. tab-delimited fields: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

organism: Lupinus angustifolius

source_name: Roots

growth_protocol: Seeds of Lupinus angustifolius cv. Sonet were surface sterilized by soaking them in 70% (vol/vol) ethanol for 5 min, followed by rinsing five times with sterile, deionized water. Subsequently, the seeds were soaked in water for 30 min and then germinated for 3 d at 21°C on water-soaked tissue paper in a growth chamber kept in the dark.

extract_protocol:
Poly(A) RNA was isolated using PolyATtract mRNA Isolation System IV (Promega)
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol

treatment_protocol: After three days of germination, hypoxia was induced in seedlings with 3-4 cm roots by submerging the plants in containers filled with tap water (oxygen concentration in water: 8.7 mg/L). The water level was maintained approximately 4 cm above the plants, and the plants were cultured under the same conditions. Reoxygenation after hypoxia was performed under seed germination conditions.

value: Roots

value: 3 days old

value: Reoxygenation

tag: time

value: 6 hours


title: Roots, reoxygenation, rep1


title: Roots, submergence, rep3

value: Submergence

value: 15 hours


title: Hypoxia Nnt-wt mouseID=HMW9


title: RNA_ImmN_WT_CTRL_2

institute: Netherlands Cancer Institute

value: Bone marrow

value: ImmN

value: WT


title: RNA_ImmN_WT_CTRL_3

value: CTRL


title: PHx_21d_1

description: Library name: PHx_21d

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: Tab_delimited text files include FPKM values for each Sample

source_name: liver

growth_protocol: Hepatocytes were freshly isolated from undamaged and different time points (6 h,12 h,24 h,48 h,72 h,7 d,14 d,21 d) of the liver regeneration after PHx in mice for RNA extraction or embedded in Matrigel and collected the hepatocyte organoids in the passage.

extract_protocol:
Total mRNA was isolated by TRIzol (Takara) or FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme)  following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: primary hepatocyte

value: partial hepatectomy

value: 21 d after 70% partial hepatectomy


title: Hypoxia Nnt-wt mouseID=HMW7

value: Gastrocnemius muscle

value: male

value: Nnt-wt

value: 24 days

value: hypoxia


title: RNA_ImmN_WT_CTRL_1


title: Roots, submergence, rep2

value: Roots

value: 3 days old


title: Roots, submergence, rep1

value: Submergence


title: RNA_PreN_WT_CTRL_3

value: PreN


title: PHx_14d_1

description: Library name: PHx_14d

value: 14 d after 70% partial hepatectomy


title: PHx_7d_1

description: Library name: PHx_7d

value: 7 d after 70% partial hepatectomy


title: RNA_PreN_WT_CTRL_2

value: Bone marrow

value: WT


title: Roots, reoxygenation, rep2

value: Reoxygenation

value: 6 hours


title: RNA_PreN_WT_CTRL_1

value: CTRL


title: PHx_72h_1

description: Library name: PHx_72h

value: liver

value: primary hepatocyte

value: partial hepatectomy

value: 72 h after 70% partial hepatectomy


title: Roots, control, rep1

value: Control conditions

value: control


title: Hep_Orgs_rep1

description: Library name: HepOrg1

source_name: Organoid

value: Organoid

value: Hepatocyte organoids

value: Hepatocyte Organoids


title: Roots, control, rep2

value: Roots

value: 3 days old


title: PHx_48h_1

description: Library name: PHx_48h

value: 48 h after 70% partial hepatectomy


title: PHx_24h_1

description: Library name: PHx_24h

value: 24 h after 70% partial hepatectomy


title: Hep_Orgs_rep2

description: Library name: HepOrg2


title: PHx_12h_1

description: Library name: PHx_12h

value: 12 h after 70% partial hepatectomy


title: RNA_GMP_WT_CTRL_1

value: Bone marrow

value: GMP

value: WT


title: Roots, control, rep3


title: PHx_6h_1

description: Library name: PHx_6h

value: liver

value: 6 h after 70% partial hepatectomy


title: RNA_CMP_WT_CTRL_3

value: CMP

value: CTRL


title: RNA_CMP_WT_CTRL_2


title: RNA_GMP_WT_CTRL_3


title: Undamaged_control_rep1

description: Library name: control_I

value: primary hepatocyte

value: Undamaged


title: RNA_GMP_WT_CTRL_2


title: RNA_CMP_WT_CTRL_1


title: Hep_Org_P1_6d [ATAC-seq]

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
ATAC-Seq reads were aligned to the mm10 genome using BWA.
Peaks were called using MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2.1.2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: liver tissue was isolated from undamaged and at different time points (6 h,12 h,24 h,48 h) of the liver regeneration after PHx in mice and preparation of single hepatocyte organoid from P0_4d and P1_6d for ATAC-Seq.

extract_protocol:
Preparation of single hepatocyte organoid: Pipette up and down to destroy the cell/extracellular matrix mixture with a micropipette and then transfer the organoid suspension to a 15 mL centrifuge tube on ice. Optionally, turn the tube up and down from time to thaw the mixture thoroughly. Centrifuge for 5 min at 500-800 x g and 4 °C and discard the supernatant. Add 1 mL of trypsin solution to the pellet and pipette it to mix. Incubate at 37 °C for 5-10 min and then stop digestion by adding 2x the volume of wash medium. Centrifuge for 5 min at 800 x g and 4 °C and discard the supernatant. Resuspend the pellet with a culture medium and count the cells using a hemacytometer.
ATAC-seq was performed as previously reported. Briefly, nucleus was extracted from samples, and the nucleus pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37℃ for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit.

value: Organoid

value: Hepatocyte organoids isolated from mice hepatocyte, passaged once and cultured for 6 days


title: RNA_MPP_WT_CTRL_3

value: MPP


title: Hep_Org_P0_4d [ATAC-seq]

value: Hepatocyte organoids

value: Hepatocyte organoids isolated from mice hepatocyte and cultured for 4 days without passage


title: RNA_MPP_WT_CTRL_2


title: P15

type: genomic

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

hyb_protocol: Agilent Microarray Hybridization protocol

scan_protocol: Agilent DNA Microarray Scanner

data_processing: Data were analyzed and visualized using Agilent CytoGenomics 4.0 software (Agilent Technologies, CA)

source_name: Bone Marrow

label_protocol: Agilent SureTag Enzymatic labeling kit

extract_protocol: QIAamp DNA Mini Kit

tag: condition

value: Experiment

value: Bone Marrow

source_name: Peripheral Blood

value: Control

value: Peripheral Blood


title: Undamaged_control_rep2

description: Library name: Control_2


title: PS3

type: RNA

city: Changchun

first: Tingshuang

last: Xu

state: Jilin

address: No. 1 Xinmin Street

institute: First Hospital of Jilin University

hyb_protocol: Cy3  labeled  small  RNAs  were  hybridized  to  Arraystar  Human  Small  RNA  Arrays  in Agilent  Hybridization  Oven.

scan_protocol: the array was scanned by an Agilent Scanner G2505C

data_processing: Intensity data were extracted using Agilent Feature Extraction software.

source_name: patients with RA

label_protocol: 100ng  total  RNAs  were  dephosphorylated  to  form  a  unified  3-OH  end.  3-OH  ended  RNA  were  then  denaturated  by  DMSO  and  enzymatically  labeled  with  Cy3.

extract_protocol: total RNA was extracted from serum samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA quantity and quality were evaluated using a spectrophotometer (NanoDrop® ND-1000 UV-Vis, Nanogen Inc.). RNA integrity was assessed using a Bioanalyzer 2100 or gel electrophoresis

treatment_protocol: Exosomes were extracted from serum cells of patients with RA and healthy controls, using the exoEasy Maxi Kit

value: Serum exosome

tag: gender

value: female


title: Ap-treated and costimulated_donor10

city: Heidelberg

first: Yvonne

last: Samstag

address: INF 305

department: Institute of Immunology

country: Germany

institute: Heidelberg University Hospital

description: total RNA was isolated from T cells pretreated with Ap for 1 h and costimulated for 4 h

hyb_protocol: hybridization of the sample mixed with reporter codeset and capture probeset was done at 65°C for 20 h (according to manufacture's protocol)

scan_protocol: samples were purified, immobilized on cartridges and scanned on the nCounter® SPRINT Profiler (nanoString Technologies)

data_processing: the raw RCC files were uploaded onto the nSolver software, raw counts were measured, stable houskeeping genes for normalization was identified using NormFinder, an excel plug-in software, and data were subsequently normalized to obtain normalized counts. The normalized counts were used for the final evaluations.

label: nCounter® Reporter Codeset and Capture Probeset

source_name: T cells, CD3x28 costimulated, 4 h

label_protocol: for each sample, 5uL of total RNA was mixed with 3uL of reporter codeset and 2uL of capture probeset (according to manufacture's protocol)

extract_protocol: total RNA was extracted using Direct-zol RNA isolation following manufacture's protocol

tag: cells

value: T cells

tag: donor id

value: Donor 10

value: Ap-treated and costimulated


title: PHx_48h_Tissue [ATAC-seq]

city: jinan

first: Jiabei

last: Lian

address: No.44, Wenhauxi Road, Lixia District, Jinan, China

tag: tissue

value: liver

tag: genotype

value: partial hepatectomy

value: 48 h after 70% partial hepatectomy


title: PS2


title: P19


title: P16


title: P20


title: DMSO-treated and costimulated_donor10

description: total RNA was isolated from T cells pretreated with DMSO for 1 h and costimulated for 4 h

value: DMSO-treated and costimulated


title: P14


title: P17


title: PHx_24h_Tissue [ATAC-seq]

value: 24 h after 70% partial hepatectomy


title: Con3

source_name: healthy control

value: male


title: RNA_LTHSC_WT_CTRL_3

data_processing:
Sequencing reads were aligned to the mm10 mouse reference genome using the STAR aligner version 2.7.9a.
Mapped reads were filtered for mapping quality >10 using samtools version 1.10.
Gene counts were generated using the "summarizeOverlaps" function from R/Bioconductor package GenomicAlignments, with the counting mode set to "Union".
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

extract_protocol:
LT-HSCs, MPPs, CMPs and GMPs were enriched by neutrophil depletion. Bone marrow single cell suspensions were incubated with 10μg/ml anti-Ly6G (1A8, BioXcell) before neutrophil depletion using sheep anti-rat magnetic beads (Dynabeads, Life Technologies) and subsequently stained with cell surface markers. For sorting pre-neutrophils and neutrophils from bone marrow, blood and lung, cells were first incubated with 500μg/ml purified mouse IgG+10% FCS (BM) or rat anti-mouse CD16/CD32 antibody (blood and lung), stained with cell surface markers and sorted using gating strategies for HSPC populations or CD45+ CD11b+ Ly6G+ 7-AAD- markers for sequencing of blood and lung neutrophils. RNA was isolated following RNeasy Mini Kit (Qiagen) protocol, using 80% ethanol instead of RPE buffer.
Smart-seq2 library preparation was performed according to the Smart-seq2 protocol, using 2100 Bioanalyzer System (Agilent) for quality control.

value: Bone marrow

tag: cell type

value: LTHSC

value: WT

value: CTRL


title: P22

value: Experiment

value: Control


title: P12

value: Bone Marrow

value: Peripheral Blood


title: PS4

value: Serum exosome

value: female


title: CT-treated and costimulated_donor10

description: total RNA was isolated from T cells pretreated with CT for 1 h  and costimulated for 4 h

value: T cells

value: Donor 10

tag: treatment

value: CT-treated and costimulated


title: PHx_12h_Tissue [ATAC-seq]

value: liver

value: partial hepatectomy

value: 12 h after 70% partial hepatectomy


title: untreated and costimulated_donor10

description: total RNA was isolated from T cells kept untreated and costimulated for 4 h

value: untreated and costimulated


title: RNA_MPP_WT_CTRL_1

value: Bone marrow

value: MPP


title: RNA_LTHSC_WT_CTRL_2

value: LTHSC

value: WT


title: RNA_LTHSC_WT_CTRL_1

value: CTRL


title: PHx_6h_Tissue [ATAC-seq]

value: 6 h after 70% partial hepatectomy


title: Con2


title: P11

value: Experiment

value: Bone Marrow

value: Control


title: P10

value: Peripheral Blood


title: Con1

value: Serum exosome

value: female


title: untreated and unstimulated_donor10

description: total RNA was isolated from T cells kept untreated and unstimulated for 4 h

value: T cells

value: Donor 10

value: untreated and unstimulated


title: P9


title: P8


title: SV20, Panc, rep 3

city: Vancouver

first: Tabea

last: Stephan

address: 2329 West Mall

institute: University of British Columbia

description: Library name: Panc rep 3

data_processing:
aligned to hg19/GRCH37 using DRAGEN
TPM values were calculated in DRAGEN and differential gene expression was calculated using DESeq2
Assembly: hg19
Supplementary files format and content: TPM values
Supplementary files format and content: excel sheet with all TPM values from all samples

source_name: Pancreas stage

growth_protocol: SV20 iPSCs were differentiated as previously described (Teng Ang et al., 2018). Briefly, cells were grown on Geltrex-coated plates to 100% confluency and subsequently differentiated into definitive endoderm using the StemDiff Endoderm kit from Stemcell Technologies.Cells were then differentiation into posterior foregut cells, hepatic endoderm and subsequently into hepatoblasts as described in Teng Ang et al., 2018.

extract_protocol:
RNA was extracted from collected cell pellets using TRIzol (Thermo Fisher Scientific).
samples were library prepped at the BRC Sequencing core

value: Pancreas stage

tag: cell line

value: differentiated iPSC


title: 2208L-Res2 Rep3, scRNAseq

city: Houston

first: Xiang

last: Zhang

state: TEXAS

address: One Baylor Plaza, Alkek N1130

department: Breast Center

institute: Baylor College of Medicine

description: cellplex 10x Genomics

data_processing:
sample and expression library were demultiplexed by using cellranger multi pipeline, v7.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi), with the barcode assignment confidence 0.84
Assembly: mm10
Supplementary files format and content: tab-seperated values files and matrix files

source_name: Breast tumor

extract_protocol:
Tumors were resected in ice-cold PBS and dissociated using tumor dissociation buffer (DMEM with 10%FBS, 1 mg/ml collagenase II, 2mg/ml dispase II and 100K unit/ml DNase I). Tissues were mechanically dissociated using a cell strainer pestle and incubated in 37°C incubator for 1 hour. A single-cell suspension was obtained by filtering the tissue lysate through a 70 μm cell strainer. The single-cell suspension was then resuspended in red blood cell lysis buffer. After centrifugation, cells were resuspended in FACS buffer and stained for V450-CD45 for cell sorting. CD45+ cells were sorted out and kept in PBS for library preparation.
The single-cell gene expression Library was prepared according to the Chromium Single Cell Gene Expression 3’v3.1 kit (10x Genomics). Briefly, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each single cell.
scRNA-seq, sample multiplexed by using Cellplex

value: Breast tumor

value: CD45+ immune cells


title: Undamaged_Tissue [ATAC-seq]

institute: Shandong University

value: liver

value: Undamaged


title: SV20, Panc, rep 2

description: Library name: Panc rep 2

value: WT


title: Ap-treated and costimulated_donor9

value: Donor 9

value: Ap-treated and costimulated


title: 2208L-Res2 Rep1, scRNAseq

description: cellplex 10x Genomics


title: SV20, Panc, rep 1

description: Library name: Panc rep 1


title: 2208L-Res2 Rep2, scRNAseq

description: cellplex 10x Genomics


title: SV20, Panc, rep 3, TBX3 OE

description: Library name: Panc rep 3, TBX3 OE

value: TBX3 OE


title: 2208L-Res1 Rep3, scRNAseq

description: cellplex 10x Genomics


title: DMSO-treated and costimulated_donor9

value: DMSO-treated and costimulated


title: INFECTED 12 HRS N4

city: Santiago

first: Pablo

middle: González

last: Muñoz

state: Santiago

address: Avenida Libertador Bernardo O Higgins 340

country: Chile

institute: Pontifical Catholic University of Chile

data_processing:
Galaxy webserver (usegalaxy.org)
Sequences were trimmed for adaptor sequence and low quality sequences using Trimmomatic tool
Trimmed sequences reads were mapped to mm10 reference genome
Mapped reads were counted using HT-seq Count tool
Normalized counts were used to GSEA analysis
Assembly: mm10
Supplementary files format and content: norm_counts.txt

source_name: Bone marrow Dendritic  Cells

growth_protocol: Dendritic cells were differentiated from hind limb bone marrow precursors of C57BL/6 mice in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS), 100 UI/ml Penicillin/Streptomycin (All from Thermo Fisher Scientific), and 10 ng/ml of recombinant murine granulocyte-macrophage-colony-stimulating factor (GM-CSF)

extract_protocol:
Total RNA was harvested with trizol, 1ug of total RNA was used for the construction of  sequencing libraries
Libraries were preparated using TruSeq stranded mRNA LT kit (Illumina) following manufacturer's protocols.

treatment_protocol: Differentiated dendritic cells were infected with HSV-1 strain F or MOCK treated for 12 hours.

value: Bone marrow Dendritic  Cells

value: Infected with HSV-1 (F) MOI :3


title: SV20, Panc, rep 2, TBX3 OE

description: Library name: Panc rep 2, TBX3 OE


title: CT-treated and costimulated_donor9

value: CT-treated and costimulated


title: untreated and costimulated_donor9

value: T cells

value: untreated and costimulated


title: SV20, Panc, rep1, TBX3 OE

description: Library name: Panc rep 1, TBX3 OE


title: INFECTED 12 HRS N3


title: 2208L-Res1 Rep2, scRNAseq

description: cellplex 10x Genomics


title: P7

value: Experiment

value: Bone Marrow

value: Control

value: Peripheral Blood


title: Ap-treated and costimulated_donor8

value: Donor 8


title: P3


title: INFECTED 12 HRS N2

value: Infected with HSV-1 (F)-GFP MOI :3


title: DMSO-treated and costimulated_donor8


title: P1


title: 2208L-Res1 Rep1, scRNAseq

description: cellplex 10x Genomics

value: Breast tumor

value: CD45+ immune cells


title: SV20, HEP rep 3

description: Library name: HEP rep 3

source_name: Hepatoblast stage

value: Hepatoblast stage

value: differentiated iPSC

value: WT


title: 2208L Rep3, scRNAseq

description: cellplex 10x Genomics


title: INFECTED 12 HRS N1

value: Infected with HSV-1 (F)MOI :3


title: SV20, HEP rep 2

description: Library name: HEP rep 2


title: P6


title: P5


title: P2


title: 2208L Rep2, scRNAseq

description: cellplex 10x Genomics


title: untreated and unstimulated_donor9

value: Donor 9

value: untreated and unstimulated


title: 2208L Rep1, scRNAseq

description: cellplex 10x Genomics


title: MOCK 12 HRS N4

value: Bone marrow Dendritic  Cells

value: Treatment with MOCK


title: MOCK 12 HRS N3


title: SV20, HE rep 3

description: Library name: HE rep 3

source_name: Hepatic endodderm stage

value: Hepatic endodderm stage


title: SV20, HEP rep 1

description: Library name: HEP rep 1


title: Cortex, WT P1 rep2

city: Buffalo

first: Soo-Kyung

last: Lee

address: 109 Cooke Hall, University at Buffalo, North Campus

department: Biological Sciences

institute: University at Buffalo

data_processing:
The paired-end RNA-seq reads were mapped to the mouse reference genome using STAR (v2.6.1d) with the default settings.
Then RSEM (v1.3.3) was used to quantify the gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes expected_count values for each Sample

source_name: Cortex

extract_protocol:
RNA was extracted from a single hemisphere of the cortex using Rneasy mini kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using Illumina Truseq Stranded RNA library prep kit following manufacturer's protocols.

value: Cortex

value: whole cortical cells


title: MOCK 12 HRS N2


title: untreated and unstimulated_donor8

value: T cells


title: Cortex, WT P1 rep1


title: MOCK 12 HRS N1


title: Ap-treated and costimulated_donor7

value: Donor 7

value: Ap-treated and costimulated