title: colon, M3

city: Nanjing

first: Yimeng

address: China pharmoceutical university

institute: China pharmoceutical university

description: Library name: Sample6

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool, BMKCloud (www.biocloud.net) online platform.
Hisat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases: Nr (NCBI non-redundant protein sequences);Pfam (Protein family); KOG/COG (Clusters of Orthologous Groups of proteins); Swiss-Prot (A manually annotated and reviewed protein sequence database); KO (KEGG Ortholog database); GO (Gene Ontology).
Assembly: The StringTie Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from Hisat2 alignment results.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: colon

extract_protocol:
The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
RNA concentration and purity was measured using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: colon

tag: condition

value: high-fat diet


title: colon, M1

status: Public on Jul 18 2025

type: SRA

last: Chen

country: China

description: Library name: Sample4

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: strain


title: Mouse sample 5 (CORWT-P2)

city: Pok Fu Lam

first: Peikai

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description:
WT mouse treat by pioglitazone from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz

data_processing:
The human fastq read-pairs were aligned to human reference genome using the HISAT2 aligner
The mouse fastq read-pairs were aligned to mouse reference genome (mm10) using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The human BAM files were quantified to human gene model by GENCODE (v25) using Cufflinks and HTSeq-count
The mouse BAM files were quantified to mouse gene model by GENCODE (vM11) using Cufflinks and HTSeq-count
Assembly: GRCh38 and mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample for all genes
Supplementary files format and content: tab-delimited text files include raw count values for each Sample for all genes

source_name: Cortex

growth_protocol:
In the human samples, human ES cells were differentiated by Neuron Differentiation Kit (Catalog #08500) and the induced NPCs were cultured using Neurobasal medium.
In the mouse samples, mouse neural precursor cells (mNPCs) were isolated from the various brain tissues of E12.5 mice, and the cells were cultured in DMEM/F12 culture media supplemented with 2% B27, 100 units/mL penicilin, 100ug/mL streptomycin, 20ng/mL epidermal growth factor and 10 ng/mL fibroblast growth factor.

extract_protocol:
RNA extraction from dissociated cells was done by using Ambiion RNA extraction kit (CAT#AM-1560). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ndufs4 wildtype (WT) and knockout (KO) mice were grouped into four groups: WT + V (vehicle), WT + P (pioglitazone), KO + V and KO + P. All mice were treated with equivalent volume (15μl/g) of vehicle or pioglitazone via daily intraperitoneal injection (I.P.) since day 25.

value: Cortex

tag: sequencing batch

value: batch 2

tag: sequencing date

tag: num reads

tag: cell type

value: primary brain cells

tag: genotype

value: Wild-type

tag: treatment

value: pioglitazone


title: Human sample 5 (C8V-P2)

description:
frame shift mutation, overexpression Ndufs4 by lentivirus infection
human.n11.COUNTS.txt.gz
human.n11.FPKM.txt.gz

organism: Homo sapiens

tag: cell line

value: ES1 induced NPC

value: no treatment


title: colon, M2

description: Library name: Sample5


title: Human sample 4 (C8-P5)

description:
frame shift mutation
human.n11.COUNTS.txt.gz
human.n11.FPKM.txt.gz


title: colon, B2

description: Library name: Sample2

value: isobutyrate


title: Vehicle-2

city: guangzhou

first: XING

last: HE

state: ( 86 ) CHINA

address: 中山大学南校区生命科学学院A334

institute: 生命科学学院

description: Library name: Sample 2

data_processing:
Adapter sequences were automatically detected and trimmed using TrimGalore v0.6.10 with default parameters.
Clean reads were aligned to the human reference genome (GRCh38) using STAR v2.7.11b in two-pass mode.
Resulting BAM files were sorted using Samtools v1.20.
Gene-level read counts were obtained using the featureCounts function from the Subread package v2.0.6.
Transcripts per million (TPM) values were calculated based on read counts and gene lengths.
Assembly: GRCh38
Supplementary files format and content: Csv file containing Transcripts per million (TPM) values.

source_name: PBMC

growth_protocol: PBMC cells were cultured in 1640 with 1% sodium pyruvate and 10% (vol/vol) fetal bovine serum.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent, and sequencing was conducted by Sangon Biotech. Bioanalyzer (Agilent 2100 Bioanalyzer) was used to assess the quality of samples.
Total RNA was isolated from cells using TRIzol reagent (Invitrogen), and sequencing was performed by Sangon Biotech. Sample quality was assessed using a Bioanalyzer (Agilent 2100 Bioanalyzer). RNA-seq libraries of polyadenylated RNA were prepared using mRNA-seq V2 Library Prep Kit and sequenced on MGISEQ-2000 platform.

treatment_protocol: PBMCs infected with H1N1 in the absence or presence of diethyl-ester OAA.

value: PBMC

value: Vehicle


title: Mouse sample 6 (CORKO-V1)

description:
Ndufs4 knock out mouse treat by vehicle from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz

value: vehicle


title: Mouse sample 3 (WTME-P1)

source_name: Medulla

value: Medulla

value: batch 1


title: Mouse sample 4 (WTME-V1)

description:
WT mouse treat by vehicle from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz


title: colon, B3

description: Library name: Sample3


title: Human sample 3 (C8-P2)


title: Vehicle-1

address: 中山大学南校区生命科学学院A334

description: Library name: Sample 1


title: Mouse sample 29 (S16-30-LCG6376)

description:
Ndufs4 knock out mouse treat by pioglitazone from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz

value: batch 3


title: Mouse sample 2 (KOME-V1)


title: Human sample 2 (C3-P2)


title: colon, B1

description: Library name: Sample1


title: IRI_sytox-CD45-

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

data_processing:
Sequencing outputs were demultiplexed using cellranger mkfastq
Fastq files were aligned to Rattus norvegicus Rnor_6.0 reference using cellranger count
Assembly: Rnor_6.0 (rn6)
Supplementary files format and content: Processed data files are gzipped cellranger count output directory (filtered_feature_bc_matrix).

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
Chopped tissue were isolated using the Multi Tissue Dissociation kit2 and gentleMACS Dissociator. Viable and CD45- cells were sorted and collected using FACSAria III for single cell RNA-seq.
Libraries were prepared using the Next GEM single cell 3' kit (10x Genomics) according to the manufacturer's protocol. Targeted 6,000 cells for each sample.

value: Renal cells

tag: cell sorting

value: Sytox-, Cd45+

value: IRI

value: kidney


title: HDAC3 knockout-aortic valves, pooled 4 valves, H3K27ac

city: Worcester

first: Chinmay

last: Trivedi

state: MA

address: 368 Plantation St, AS7-1047

department: Medicine

country: USA

institute: University of Massachusetts Medical School

description: Library name: Mutant- H3K27ac

library_source: genomic

data_processing:
Reads were trimmed, aligned to the mm10 genome using Bowtie2 and filtered for quality. Peaks were called with MACS, annotated with ChIPseeker, and visualized using HOMER and DolphinNext.
Assembly: Mouse mm10
Supplementary files format and content: Hdac3.bedGraph.gz
Supplementary files format and content: pHdac3.bedGraph.gz
Supplementary files format and content: IgG.bedGraph.gz
Supplementary files format and content: H3K27ac-KO.bedGraph.gz
Supplementary files format and content: H3K27ac-Con.bedGraph.gz
Library strategy: Cut&Tag

molecule: genomic DNA

source_name: Aortic valves

extract_protocol:
Aortic valves were dissected from 12- week old mice and snap frozen in liquid nitrogen and stored in -800C. Nuclei were isolated and followed Active Motif’s protocol (catalog #53160) with minor modification. The nuclei were bound with concanavalin A beads and incubated w with antibodies targeting phospho-HDAC3, HDAC3, H3K27ac, or IgG control. Secondary antobodies were incubated for an hour followed by pA-Tn5 transposomes for another hour. The DNA was tagmented and extracted as per the protocol.
Indexed libraries were prepared following Active Motif’s protocol (catalog #53160) and sequenced on an Illumina MiSeq platform with 25-bp paired-end reads.

value: Aortic valves

value: HDAC3 F/F, PostnCre

tag: age

value: 12 weeks

tag: cut&tag antibody

value: H3K27ac (Abcam, #ab 4729)


title: Mouse sample 1 (KOME-P1)

value: primary brain cells

value: pioglitazone


title: Human sample 1 (C6-P5)

description:
Wild-type ES cells induce NPC, passage 5
human.n11.COUNTS.txt.gz
human.n11.FPKM.txt.gz

value: batch 2

value: ES1 induced NPC

value: Wild-type

value: no treatment


title: Z-138_SNP_array_data_replicate2

type: genomic

city: Barcelona

first: Renée

last: Beekman

address: Carrer Dr. Aiguader 88

country: Spain

institute: CRG

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner.

data_processing: Genotypes from the CEL files were defined using the crlmm package (v. 1.58.0), with the following quality thresholds: confidence scores >0.7 and SNR scores > 5.

label: Biotin

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted using Qiagen DNA extraction kits

tag: disease stage

value: mantle cell lymphoma


title: IRI_sytox-

value: Whole kidney cells

value: Sytox-


title: Human sample 6 (C6-P2)

description:
Wild-type ES cells induce NPC, passage 2
human.n11.COUNTS.txt.gz
human.n11.FPKM.txt.gz


title: Vehicle-H1N1-1

address: 中山大学南校区生命科学学院A334

description: Library name: Sample 4

value: PBMC


title: Aortic valves, control, pooled 4 valves, IgG

description: Library name: IgG

value: HDAC3 F/+

value: CST Isotype control (66362S)


title: Vehicle-3

address: 中山大学南校区生命科学学院A334

description: Library name: Sample 3

value: Vehicle


title: MHCC97H, MEX3C

city: Guangzhou

first: Yun

middle: yun

last: Xiao

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
RIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using seqtk v1.0-r82-dirty, discarding reads left with < 20 bp
RIP-seq reads were aligned to the UCSC hg19 genome. Only uniquely mapping reads with at most two mismatches were retained.
To create RIP-seq coverage plots, the locations of the mapped RIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing ripseek with the significance cut-off q-value <=0.01
bigWig files were generated using the bedtools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS; HyClone, Logan, UT, USA) at 37 °C in a 5% CO2 incubator.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes and 1 M glycine was added for 5 min to stop the fixation.The cells are collected by scraping and lysing in lysis buffer supplemented with protease and RNasin. Samples were then immunoprecipitated using 5μg anti-MEX3C antibodies coupled to protein A Dynabeads. The immunoprecipitates were washed extensively with lysis buffer 4-6 times. RNA was extracted using Trizol following the manufacturer's instructions.
Total RIP-RNA was purified with RNeasy Micro Kit according to manufacturer's instructions (Qiagen, Hilden, Germany).TruSeq Stranded Total RNA with Ribo-Zero kit (Illumina, San Diego, CA) has been used for library preparation following the manufacturer's instructions. Both RNA samples and final libraries were quantified by using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and quality tested by Agilent 2100 Bioanalyzer RNA Nano assay (Agilent Technologies, Santa Clara, CA). Libraries were then processed with Illumina cBot for cluster generation on the flowcell, following the manufacturer’s instructions and sequenced on 150 bp pair-ends mode at the on Novaseq6000 (Illumina, San Diego, CA). The library construction and sequencing were performed at Shanghai Biotechnology Corporation.

value: Hepatocellular carcinoma cells


title: sham_sytox-CD45-

value: Renal cells

value: Sytox-, Cd45+

value: sham

value: kidney


title: Aortic valves, control, pooled 4 valves, phosho-HDAC3

description: Library name: phospho-HDAC3

value: Aortic valves

value: 12 weeks

value: phospho-HDAC3 (Ser424)  (CST, #3815S)


title: sham_sytox-


title: MHCC97H, Input


title: H3K9me2 ChIP-seq in Setdb1 KO

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

description:
Library name: K9me2_Setdb1KO
K9me2_Setdb1KO

data_processing:
Trim adapter and low quality reads using Trim_galore
Map reads on mouse genome by Bowtie2
Remove PCR duplicates by Picard
Assembly: mm10
Supplementary files format and content: bigWig

source_name: MEF

growth_protocol: Mouse embryonic fibroblasts were maintained in Dulbecco's modified Eagle's medium (Nacalai tesque, 08458-16) containing 10% fetal bovine serum (Biosera, FB1061), MEM Non-Essential medium and 2-Mercaptoethanol (Nacalai tesque, 21417-52).

extract_protocol:
ChIP DNA was extracted by Native ChIP protocol
At least 2 × 105 cells were lysed in 50 µl Buffer 1 (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris-HCl (pH7.5), 0.3 M Sucrose, 0.5 mM DTT, and protease inhibitors (Nacalai tesque, 04080-11), then were added 50 µl Buffer2 (Buffer 1 + 1% NP40) to the sample. After the incubation for 10 min on ice, the sample was added 800 µl Buffer 3 (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris-HCl (pH7.5), 1.2 M Sucrose, 0.5 mM DTT, and protease inhibitors). After centrifugation at 9000 rpm for 10 min at 4°C, the sample was added 100 µl MNase buffer (0.32 M Sucrose, 50 mM Tris-HCl (pH7.5), 4 mM MgCl2, 1 mM CaCl2, and phenylmethylsulfonyl fluoride (PMSF)) followed by incubation for 20 min at 37 °C with 0.3 U MNase (TAKARA, 2910 A). After the incubation, the reaction was stopped by 10 µl 0.5 M EDTA. After centrifugation at 15,000 rpm for 10 min at 4°C, the supernatant was added 900 µl Incubation buffer (50 mM NaCl, 20 mM Tris-HCl (pH7.5), 5 mM EDTA, 0.01% NP40, ad PMSF). In all, 10% of the sample was used for input, and the remains proceeded the following procedure. The sample was mixed with the antibody-beads complex which was formed by incubation of 20 µl protein A/G beads (Santa Cruz, sc-2003) with antibody in Incubation buffer on ice for 1 h. After rotating for overnight at 4°C, the complex was washed by 500 µl Wash buffer A (75 mM NaCl, 50 mM Tris-HCl (pH7.5), 10 mM EDTA, and 0.01% NP40), 500 µl Wash buffer B (100 mM NaCl, 50 mM Tris-HCl (pH7.5), 10 mM EDTA, and 0.01% NP40), and 500 µl wash buffer C (175 mM, 50 mM Tris-HCl (pH7.5), 10 mM EDTA, and 0.01% NP40). The ChIP DNA was eluted by RNase and Protease treatment followed by DNA purification using PCR purification kit (QIAGEN).

value: MEF

value: Setdb1 KO

tag: batch


title: Aortic valves, control, pooled 4 valves, HDAC3

description: Library name: HDAC3

value: HDAC3 (Abcam, #ab7030)


title: Subject_C26_Nasal (scTCR-seq)

status: Public on Jul 17 2025

city: Cambridge

first: Menna

last: Clatworthy

address: Cambridge Biomedical Campus, Francis Crick Ave, Trumpington

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description:
Library name: Sample_Fq_38
single cell VDJ (TCR)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software v6.0.1 (10x Genomics
Assembly: GRCH38
Supplementary files format and content: Compressed tab-separated values files, unfiltered single cell barcode gene expression matrix

molecule: polyA RNA

source_name: Nasal

extract_protocol:
Nasal tissue samples were minced, digested in a DNAse/Liberase solution for 30 minutes, strained and washed to create a single cell suspension. Paired whole blood was centrifuged layered on Histopaque 1077, with PBMC layer extracted and washed. Nasal and PBMC samples were loaded as single cell suspensions without sorting
ScRNAseq gene expression libraries were contructed in accordance with the manufacturer protocol, with TCR enrichment using the Chromium Single Cell Human TCR Amplification Kit (Single cell 5' v2 protocol, 10x Genomics

value: Nasal

value: Healthy control


title: Subject_C21_Blood (scTCR-seq)

description:
Library name: Sample_Fq_14
single cell VDJ (TCR)

source_name: Blood

value: Blood


title: Subject_C17_Nasal (scTCR-seq)

description:
Library name: Sample_Fq_19
single cell VDJ (TCR)


title: Subject_C24_Nasal (scTCR-seq)

description:
Library name: Sample_Fq_11
single cell VDJ (TCR)


title: Subject_C17_Blood (scTCR-seq)

description:
Library name: Sample_Fq_18
single cell VDJ (TCR)


title: Subject_C24_Blood (scTCR-seq)

description:
Library name: Sample_Fq_10
single cell VDJ (TCR)


title: Subject_C19_Blood (scTCR-seq)

description:
Library name: Sample_Fq_8
single cell VDJ (TCR)


title: Subject_C20_Blood (scTCR-seq)

description:
Library name: Sample_Fq_4
single cell VDJ (TCR)


title: Subject_C19_Nasal (scTCR-seq)

description:
Library name: Sample_Fq_9
single cell VDJ (TCR)


title: Aortic valves, pooled 4 valves, H3K27ac

description: Library name: Control- H3K27ac

value: HDAC3 F/+, PostnCre

value: H3K27ac (Abcam, #ab 4729)


title: Subject_12_Nasal (scTCR-seq)

description:
Library name: MC9785409
single cell VDJ (TCR)

value: Conval COVID


title: Subject_12_Blood (scTCR-seq)

description:
Library name: MC9785406
single cell VDJ (TCR)


title: Subject_11_Blood (scTCR-seq)

description:
Library name: MC9785405
single cell VDJ (TCR)


title: Subject_10_Blood (scTCR-seq)

description:
Library name: MC9785403
single cell VDJ (TCR)


title: Subject_10_Nasal (scTCR-seq)

description:
Library name: MC9785404
single cell VDJ (TCR)


title: Subject_9_Nasal (scTCR-seq)

description:
Library name: MC9785402
single cell VDJ (TCR)


title: Z-138_SNP_array_data_replicate1

value: mantle cell lymphoma


title: Subject_8_Blood (scTCR-seq)

description:
Library name: MC9785399
single cell VDJ (TCR)


title: Subject_9_Blood (scTCR-seq)

description:
Library name: MC9785401
single cell VDJ (TCR)


title: Subject_8_Nasal (scTCR-seq)

description:
Library name: MC9785400
single cell VDJ (TCR)


title: Subject_7_Nasal (scTCR-seq)

description:
Library name: MC9785398
single cell VDJ (TCR)

value: Active COVID


title: Subject_7_Blood (scTCR-seq)

description:
Library name: MC9785397
single cell VDJ (TCR)


title: Subject_C21_Nasal (scTCR-seq)

description:
Library name: Sample_Fq_15
single cell VDJ (TCR)


title: Subject_6_Blood (scTCR-seq)

description:
Library name: MC9785395
single cell VDJ (TCR)


title: Subject_5_Blood (scTCR-seq)

description:
Library name: MC9785393
single cell VDJ (TCR)


title: Subject_5_Nasal (scTCR-seq)

description:
Library name: MC9785394
single cell VDJ (TCR)


title: Subject_3_Nasal (scTCR-seq)

description:
Library name: Sample_Fq5_COVID
single cell VDJ (TCR)


title: Subject_3_Blood (scTCR-seq)

description:
Library name: Sample_Fq6_COVID
single cell VDJ (TCR)


title: Subject_4_Nasal (scTCR-seq)

description:
Library name: MC9785392
single cell VDJ (TCR)


title: Subject_4_Blood (scTCR-seq)

description:
Library name: MC9785391
single cell VDJ (TCR)


title: Subject_C20_Nasal (scTCR-seq)

description:
Library name: Sample_Fq_5
single cell VDJ (TCR)


title: Subject_2_Blood (scTCR-seq)

description:
Library name: Sample_Fq3_COVID
single cell VDJ (TCR)


title: Subject_1_Blood (scTCR-seq)

description:
Library name: Sample_Fq1_COVID
single cell VDJ (TCR)


title: Subject_1_Nasal (scTCR-seq)

description:
Library name: Sample_Fq2_COVID
single cell VDJ (TCR)


title: MOSH-10

city: Shenzhen

first: Yunchong

last: Guo

address: Zhenyuan Road, Xinhu Street, Guangming District

institute: The seventh affiliated hospital，Sun Yat-sen University

description: Library name: p10

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak(except for input sample)

source_name: Sperm

extract_protocol:
Cells were fixed with 1% formaldehyde for 10minutes.After quenching and celllysis,chromatin was sonicated using a E220 focused-ultrasonicator(Covaris)
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXT flex DNA Barcodes from Bio Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Sperm


title: MOSH-8

description: Library name: p8


title: MOSH-9

description: Library name: p9


title: MOSH-6

description: Library name: p6


title: MOSH-2

description: Library name: p2


title: Control-4

description: Library name: c4


title: Control-3

description: Library name: c3


title: HS5

city: Wuxi

first: Qitao

state: Jiangsu

address: No. 299, Qingyang Road, Liangxi District

department: Department of Dermatology

institute: The Affiliated Wuxi People's Hospital of Nanjing Medical University

description:
Library name: Sample 11
10x Genomics

library_source: transcriptomic single cell

data_processing:
To account for multiple biological and experimental characteristics, the Harmony algorithm was used to integrate the 78,503 total cells. After clustering the merged datasets and examining PTPRC (CD45) expression, the cells were divided into immune and non-immune cell clusters. We extracted the immune cell clusters for subsequent analysis. 41,438 single cells in total remained and were included in the downstream analyses. Further analysis, such as quality control and unsupervised clustering, was performed using the Seurat (4.4.0, http://satijalab.org/ seurat/) R toolkit.
Assembly: Human GRCh38
Supplementary files format and content: rds

source_name: scalp

extract_protocol:
Fresh skin samples were immediately washed, minced, and digested at 37°C for one hour to prepare single-cell suspensions using a composite enzyme solution with the following components:3.5 mg/ml Collagenase II, 1 mg/ml Collagenase IV, 0.02 mg/ml DNase I, 30 U/ml Hyaluronidase, 30 U/ml Keratinase, 400 µg/ml Liberase, 1.2 units/ml Dispase II. Following red blood cell lysis, AO/PI (Acridine Orange/Propidium Iodide) staining and trypan blue microscopy were performed for cell counting. Flow cytometry was performed to assess the proportion of CD45⁺ cells. 10 µL of CD45 antibody (555482; 25ug/ml; BD Biosciences) was added to the suspension for incubation, followed by cell sorting using a flow cytometer (BD FACS Aria III). Data were analyzed using BD FACSDiva 9.0.1 software.
ScRNA-seq was submitted for Shanghai Genechem Co., Ltd. Single-cell library sequencing was conducted on the Illumina HiSeq X Ten, with 150 nt paired-end sequencing. The Chromium instrument and the Single Cell 3’ Reagent kit V3.1 (Dual Index) were used to prepare individually barcoded single-cell RNA-Seq libraries following the manufacturer’s protocol (10X Genomics). Briefly, sample partitioning and molecular barcoding were done on the Chromium Controller (10x Genomics), where we loaded cellular suspensions together with the Single-cell 3’ Gel Beads on a Single-cell 3’ chip, in which gel beads in emulsion (GEM) generation took place. RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell reagent kit V3.1 (10X Genomics). Sequencing was performed with Illumina NovaSeq.

value: scalp

value: primary tissues

value: All cells

tag: disease

value: healthy


title: HS3

description:
Library name: Sample 9
10x Genomics


title: HS1

description:
Library name: Sample 7
10x Genomics


title: HS2

description:
Library name: Sample 8
10x Genomics


title: HS4

description:
Library name: Sample 10
10x Genomics


title: Subject_6_Nasal (scTCR-seq)

description:
Library name: MC9785396
single cell VDJ (TCR)


title: PB2

description:
Library name: Sample 5
10x Genomics

source_name: skin

value: skin

value: CD45+ cells

value: psoriasis


title: PB3

description:
Library name: Sample 6
10x Genomics


title: PB1

description:
Library name: Sample 4
10x Genomics


title: Subject_2_Nasal (scTCR-seq)

description:
Library name: Sample_Fq4_COVID
single cell VDJ (TCR)


title: PS3

description:
Library name: Sample 3
10x Genomics


title: MOSH-2 treated with Semaglutide

description: Library name: f2


title: RNA-seq, MiaPaCa-2 HIF1α KO cells, Hypoxia, replicate 2

city: Jackson

first: Shashi

last: Anand

state: MS

address: 2500 N State St

department: Cell and Molecular Biology

institute: University of Mississippi Medical Center

description: Library name: Sample 11

data_processing:
Raw sequencing reads underwent quality control check, and paired-end clean reads were aligned to human hg19 reference genome using TopHat2 software. Differential gene expression analysis was performed using the DESeq2 R package (version 1.30.1).
Assembly: GRCh37 or hg19
Supplementary files format and content: FPKM

source_name: Pancrease

growth_protocol: Pancreatic cancer cells were cultured in RPMI media supplemented with 10% FBS and allowed them to grow in a CO2 incubator at 37°C and 5% CO2.

extract_protocol:
After treatment, total RNA was isolated using QIAGEN RNAeasy Kit as per manufacturer's instruction manual.
RNA samples were submitted for sequencing and bioinformatic analysis at Novogene corporation. RNA quality and quantity was assessed and served as input for poly A+ mRNA enrichment. The enriched mRNA was fragmented and reverse transcribed to cDNA, cDNA fragments were then ligated with specific adaptor sequences and used for library preparation. The cDNA library was sequenced using the Illumina NovaSeq 6000 platform.

treatment_protocol: Cells were subjected to either normoxia (20% O2) or hypoxia (1.0% O2) treatment. Hypoxia treatment was given in in a hypoxia chamber equipped with an oxygen controller (BioSpherix, Parish, NY) for respective time intervals.

value: Pancrease

value: Human Pancreatic Cancer Cells

value: HIF1α KO (Hypoxia)


title: RNA-seq, MiaPaCa-2 MYB KO cells, Hypoxia, replicate 2

description: Library name: Sample 8

value: MYB KO (Hypoxia)


title: RNA-seq, MiaPaCa-2 MYB KO cells, Hypoxia, replicate 3

description: Library name: Sample 9


title: RNA-seq, MiaPaCa-2 HIF1α KO cells, Hypoxia, replicate 3

description: Library name: Sample 12


title: RNA-seq, MiaPaCa-2 HIF1α KO cells, Hypoxia, replicate 1

description: Library name: Sample 10


title: PS1

description:
Library name: Sample 1
10x Genomics


title: RNA-seq, MiaPaCa-2 Control cells, Hypoxia, replicate 3

description: Library name: Sample 6

value: Control (Hypoxia)


title: RNA-seq, MiaPaCa-2 MYB KO cells, Hypoxia, replicate 1

description: Library name: Sample 7


title: MOSH-5

description: Library name: p5


title: RNA-seq, MiaPaCa-2 Control cells, Hypoxia, replicate 1

description: Library name: Sample 4


title: RNA-seq, MiaPaCa-2 Control cells, Hypoxia, replicate 2

description: Library name: Sample 5


title: MOSH-7

description: Library name: p7


title: RNA-seq, MiaPaCa-2 Control cells, Normoxia, replicate 3

description: Library name: Sample 3

value: Control (Normoxia)


title: RNA-seq, MiaPaCa-2 Control cells, Normoxia, replicate 2

description: Library name: Sample 2


title: RNA-seq, MiaPaCa-2 Control cells, Normoxia, replicate 1

description: Library name: Sample 1


title: Plate 2, biological replicate 2, tagmentation technical replicate 5

city: Berkeley

first: Brenna

middle: C

last: Remick

state: CA

address: 415 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Library name: Library T

data_processing:
zUMIs (https://github.com/sdparekh/zUMIs/) was used to demultiplex samples, collapse UMIs, and align reads to human (GRCh38) and myxoma virus (GCF_000843685.1) reference genomes.
Differential gene expression analysis was conducted by iterating through each MYXV ORF and using DESeq2 (1.42.1) to compare gene expression to that of mCherry-expressing control samples.
Assembly: GRCh38, GCF_000843685.1
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

growth_protocol: BLaER1 cells were cultured in RPMI 1640 medium (Gibco) supplemented with L-glutamine, sodium pyruvate, 100 U/ml penicillin-streptomycin, and 10% (v/v) FBS (Gibco).

extract_protocol:
Cells were lysed in TRK lysis buffer (Omega Bio-tek) and incubated with Proteinase K. RNA was isolated using 30% PEG beads prepared in house (Thermo Sera-Mag Speed Beads #45152105050250 resuspended in 2M NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.01% Igepal CA-630, 0.05% sodium azide, 30% PEG 8000) at a 1:2 ratio of lysate to beads. Samples were treated with DNase I (Thermo) in the presence of RNasin Plus Ribonuclease Inhibitor (Promega).
Prime-seq (https://www.protocols.io/view/prime-seq-81wgb1pw3vpk) was adapted for library preparation. During cDNA synthesis, prime-seq uses poly(A) priming, template switching, early barcoding, and UMIs to generate 3′ tagged RNA-seq libraries. Following reverse transcription into cDNA, samples from all wells of a 96-well plate were pooled with 30% PEG beads at a ratio of 1:1 lysate to beads. Pooled samples were then treated with Exonuclease I (Thermo). cDNA was then amplified using Terra PCR Direct Polymerase Mix (Takara) for 9 cycles. Libraries were then tagmented (4-5 technical replicates per library) and amplified using Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: In an arrayed format, BLaER1 cells were transduced to express individual myxoma virus (MYXV) ORFs under the control of a doxycycline-inducible promoter. Transduced cells were selected with puromycin and then transdifferentiated into monocytes in 96-well plates, such that each well contained BLaER1 monocytes expressing a different MYXV ORF. To transdifferentiate BLaER1 cells into monocytes, 70,000 cells per well were cultured in RPMI media containing 10 ng/ml of human recombinant (hr) IL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech), and 100 nM β-Estradiol (Sigma-Aldrich) for 5 days. BLaER1 monocytes were treated with 1 µg/ml doxycycline hyclate (Sigma-Aldrich) for 24 hours to induce expression of MYXV ORFs.

value: monocyte

value: WT

value: doxycycline, 24 hours


title: Plate 2, biological replicate 1, tagmentation technical replicate 5

description: Library name: Library R


title: Plate 1, biological replicate 2, tagmentation technical replicate 4

description: Library name: Library O


title: Plate 2, biological replicate 1, tagmentation technical replicate 4

description: Library name: Library N


title: Plate 2, biological replicate 2, tagmentation technical replicate 4

description: Library name: Library P


title: Plate 1, biological replicate 1, tagmentation technical replicate 4

description: Library name: Library Q


title: PS2

description:
Library name: Sample 2
10x Genomics


title: Plate 1, biological replicate 1, tagmentation technical replicate 3

description: Library name: Library M


title: Plate 2, biological replicate 2, tagmentation technical replicate 3

description: Library name: Library L


title: Plate 1, biological replicate 2, tagmentation technical replicate 3

description: Library name: Library K


title: Plate 2, biological replicate 1, tagmentation technical replicate 3

description: Library name: Library J


title: Plate 2, biological replicate 2, tagmentation technical replicate 2

description: Library name: Library H


title: Plate 1, biological replicate 2, tagmentation technical replicate 2

description: Library name: Library G


title: Plate 1, biological replicate 1, tagmentation technical replicate 2

description: Library name: Library E


title: Plate 2, biological replicate 1, tagmentation technical replicate 1

description: Library name: Library B


title: Plate 2, biological replicate 2, tagmentation technical replicate 1

description: Library name: Library D


title: Plate 1, biological replicate 2, tagmentation technical replicate 1

description: Library name: Library C


title: Plate 2, biological replicate 1, tagmentation technical replicate 2

description: Library name: Library F


title: Plate 1, biological replicate 1, tagmentation technical replicate 1

description: Library name: Library A


title: JSL1 IRF7 Alt cells, clone 12. PIC stimulation, replicate D

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

description:
Library name: Alt-12_PIC_D
Alt-12_PIC_D column in the 2024_Panthi-IRF7_TPMs.csv file

data_processing:
Raw fastq files were trimmed to remove adapters and low quality reads with bbduk v38.79 (https://sourceforge.net/projects/bbmap/) using the parameters “ref=/bbmap/resources/adapters.fa ktrim=r k=23 mink=11 hdist=1 minlength=35 tpe tbo qtrim=r trimq=10”.
Transcripts were counted using salmon v1.10.0 in pseudoalignment mode with the quant command using the parameters “-l A--validateMappings --rangeFactorizationBins 4 --seqBias --gcBias --recoverOrphans”
Transcripts were collapsed to the gene level and differential abundance calculations were performed with DESeq2
Assembly: Homo sapiens GRCh38 (hg38) transcriptome, annotation v1.09 from Ensembl
Supplementary files format and content: quant.sf files are raw output from Salmon of transcript counts/TPMs. The TPMs CSV file is all TPMs collapsed to gene level.

source_name: JSL1 (Jurkat-derived)

growth_protocol: All CRISPR-edited Jurkat cells were maintained in RPMI medium (Corning) supplemented with 5% heat-inactivated fetal bovine serum (GIBCO) and 2 mM penicillin-streptomycin. The cells were cultured at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Following an 8-hour treatment with either polyIC or IFN-Alpha 2a, cells were collected, and RNA was isolated using TRIzol reagent according to the manufacturer’s instructions (Thermo Fisher Scientific, Catalog Number: 15596026). The RNA integrity was assessed using an Agilent Bioanalyzer, ensuring all samples had an RNA Integrity Number greater than 8.
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. Converted the RNA molecules into complementary DNA (cDNA). cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: CRISPR-edited clones were treated with either high molecular weight (HMW) polyinosinic-polycytidylic acid (polyIC, Invivogen) at a final concentration of 10 μg/ml or recombinant interferon-alpha 2a (IFN-Alpha 2a, PBL Assay Science) at a final concentration of 500 U/ml for 8 hours. For stimulation, the cells were adjusted to a density of 1 × 10⁶ cells/ml and incubated in medium alone or with the specified treatments for the indicated duration.

value: JSL1 (Jurkat-derived)

value: Immortalized T cell

value: IRF7 Alt, clone 12

value: PIC at 10ug/mL for 8hrs

value: D


title: JSL1 IRF7 Alt cells, clone 12. PIC stimulation, replicate B

description:
Library name: Alt-12_PIC_B
Alt-12_PIC_B column in the 2024_Panthi-IRF7_TPMs.csv file

value: B


title: JSL1 IRF7 Alt cells, clone 12. Unstim, replicate B

description:
Library name: Alt-12_Unstim_B
Alt-12_Unstim_B column in the 2024_Panthi-IRF7_TPMs.csv file

value: Unstim


title: JSL1 IRF7 Alt cells, clone 12. IFNa stimulation, replicate A

description:
Library name: Alt-12_IFNa_A
Alt-12_IFNa_A column in the 2024_Panthi-IRF7_TPMs.csv file

value: IFNa at 500U/mL for 8hrs

value: A


title: JSL1 IRF7 Alt cells, clone 12. PIC stimulation, replicate A

description:
Library name: Alt-12_PIC_A
Alt-12_PIC_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 12. IFNa stimulation, replicate B

description:
Library name: Alt-12_IFNa_B
Alt-12_IFNa_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 12. Unstim, replicate A

description:
Library name: Alt-12_Unstim_A
Alt-12_Unstim_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 12. PIC stimulation, replicate C

description:
Library name: Alt-12_PIC_C
Alt-12_PIC_C column in the 2024_Panthi-IRF7_TPMs.csv file

value: C


title: JSL1 IRF7 Can cells, clone 22. PIC stimulation, replicate D

description:
Library name: Can-22_PIC_D
Can-22_PIC_D column in the 2024_Panthi-IRF7_TPMs.csv file

value: IRF7 Can, clone 22


title: JSL1 IRF7 Can cells, clone 22. PIC stimulation, replicate C

description:
Library name: Can-22_PIC_C
Can-22_PIC_C column in the 2024_Panthi-IRF7_TPMs.csv file


title: Plate 1, biological replicate 2, tagmentation technical replicate 5

description: Library name: Library S


title: JSL1 IRF7 Can cells, clone 22. PIC stimulation, replicate B

description:
Library name: Can-22_PIC_B
Can-22_PIC_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 22. Unstim, replicate B

description:
Library name: Can-22_Unstim_B
Can-22_Unstim_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 22. IFNa stimulation, replicate B

description:
Library name: Can-22_IFNa_B
Can-22_IFNa_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 22. PIC stimulation, replicate A

description:
Library name: Can-22_PIC_A
Can-22_PIC_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 22. Unstim, replicate A

description:
Library name: Can-22_Unstim_A
Can-22_Unstim_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 22. IFNa stimulation, replicate A

description:
Library name: Can-22_IFNa_A
Can-22_IFNa_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 1. PIC stimulation, replicate D

description:
Library name: KO-1_PIC_D
KO-1_PIC_D column in the 2024_Panthi-IRF7_TPMs.csv file

value: IRF7 KO, clone 1


title: JSL1 IRF7 KO cells, clone 1. PIC stimulation, replicate C

description:
Library name: KO-1_PIC_C
KO-1_PIC_C column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 1. IFNa stimulation, replicate B

description:
Library name: KO-1_IFNa_B
KO-1_IFNa_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 1. PIC stimulation, replicate B

description:
Library name: KO-1_PIC_B
KO-1_PIC_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 1. PIC stimulation, replicate A

description:
Library name: KO-1_PIC_A
KO-1_PIC_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 1. Unstim, replicate A

description:
Library name: KO-1_Unstim_A
KO-1_Unstim_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. PIC stimulation, replicate C

description:
Library name: Alt-3_PIC_C
Alt-3_PIC_C column in the 2024_Panthi-IRF7_TPMs.csv file

value: IRF7 Alt, clone 3


title: JSL1 IRF7 Alt cells, clone 3. IFNa stimulation, replicate C

description:
Library name: Alt-3_IFNa_C
Alt-3_IFNa_C column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. PIC stimulation, replicate B

description:
Library name: Alt-3_PIC_B
Alt-3_PIC_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. Unstim, replicate C

description:
Library name: Alt-3_Unstim_C
Alt-3_Unstim_C column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. Unstim, replicate B

description:
Library name: Alt-3_Unstim_B
Alt-3_Unstim_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. IFNa stimulation, replicate A

description:
Library name: Alt-3_IFNa_A
Alt-3_IFNa_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. Unstim, replicate A

description:
Library name: Alt-3_Unstim_A
Alt-3_Unstim_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. PIC stimulation, replicate C

description:
Library name: Can-10_PIC_C
Can-10_PIC_C column in the 2024_Panthi-IRF7_TPMs.csv file

value: IRF7 Can, clone 10


title: JSL1 IRF7 Can cells, clone 10. IFNa stimulation, replicate C

description:
Library name: Can-10_IFNa_C
Can-10_IFNa_C column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. PIC stimulation, replicate B

description:
Library name: Can-10_PIC_B
Can-10_PIC_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. IFNa stimulation, replicate B

description:
Library name: Can-10_IFNa_B
Can-10_IFNa_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. Unstim, replicate B

description:
Library name: Can-10_Unstim_B
Can-10_Unstim_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. PIC stimulation, replicate A

description:
Library name: Can-10_PIC_A
Can-10_PIC_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. IFNa stimulation, replicate A

description:
Library name: Can-10_IFNa_A
Can-10_IFNa_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 1. Unstim, replicate B

description:
Library name: KO-1_Unstim_B
KO-1_Unstim_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. IFNa stimulation, replicate 3

description:
Library name: Alt-3_IFNa_3
Alt-3_IFNa_3 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 1. IFNa stimulation, replicate A

description:
Library name: KO-1_IFNa_A
KO-1_IFNa_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. Unstim, replicate A

description:
Library name: Can-10_Unstim_A
Can-10_Unstim_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. PIC stimulation, replicate 3

description:
Library name: Alt-3_PIC_3
Alt-3_PIC_3 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. PIC stimulation, replicate 3

description:
Library name: Can-10_PIC_3
Can-10_PIC_3 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. Unstim, replicate 3

description:
Library name: Alt-3_Unstim_3
Alt-3_Unstim_3 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. Unstim, replicate 3

description:
Library name: Can-10_Unstim_3
Can-10_Unstim_3 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. IFNa stimulation, replicate 3

description:
Library name: Can-10_IFNa_3
Can-10_IFNa_3 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 8. Unstim, replicate 3

description:
Library name: KO-8_Unstim_3
KO-8_Unstim_3 column in the 2024_Panthi-IRF7_TPMs.csv file

value: IRF7 KO, clone 8


title: JSL1 IRF7 Alt cells, clone 3. PIC stimulation, replicate A

description:
Library name: Alt-3_PIC_A
Alt-3_PIC_A column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 WT cells. PIC stimulation, replicate 1

description:
Library name: WT_PIC_3
WT_PIC_3 column in the 2024_Panthi-IRF7_TPMs.csv file

value: IRF7 WT


title: JSL1 IRF7 Alt cells, clone 3. IFNa stimulation, replicate B

description:
Library name: Alt-3_IFNa_B
Alt-3_IFNa_B column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. IFNa stimulation, replicate 2

description:
Library name: Alt-3_IFNa_2
Alt-3_IFNa_2 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 WT cells. IFNa stimulation, replicate 1

description:
Library name: WT_IFNa_3
WT_IFNa_3 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. Unstim, replicate 2

description:
Library name: Alt-3_Unstim_2
Alt-3_Unstim_2 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. IFNa stimulation, replicate 2

description:
Library name: Can-10_IFNa_2
Can-10_IFNa_2 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. Unstim, replicate 2

description:
Library name: Can-10_Unstim_2
Can-10_Unstim_2 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 8. PIC stimulation, replicate 2

description:
Library name: KO-8_PIC_2
KO-8_PIC_2 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 8. IFNa stimulation, replicate 2

description:
Library name: KO-8_IFNa_2
KO-8_IFNa_2 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 WT cells. PIC stimulation, replicate C

description:
Library name: WT_PIC_2
WT_PIC_2 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. Unstim, replicate C

description:
Library name: Can-10_Unstim_C
Can-10_Unstim_C column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 8. Unstim, replicate 2

description:
Library name: KO-8_Unstim_2
KO-8_Unstim_2 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 WT cells. IFNa stimulation, replicate C

description:
Library name: WT_IFNa_2
WT_IFNa_2 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 WT cells. Unstim, replicate 2

description:
Library name: WT_Unstim_2
WT_Unstim_2 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 8. IFNa stimulation, replicate 3

description:
Library name: KO-8_IFNa_3
KO-8_IFNa_3 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. IFNa stimulation, replicate 1

description:
Library name: Alt-3_IFNa_1
Alt-3_IFNa_1 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. PIC stimulation, replicate 1

description:
Library name: Can-10_PIC_1
Can-10_PIC_1 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Can cells, clone 10. Unstim, replicate 1

description:
Library name: Can-10_Unstim_1
Can-10_Unstim_1 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 8. PIC stimulation, replicate 1

description:
Library name: KO-8_PIC_1
KO-8_PIC_1 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 WT cells. PIC stimulation, replicate B

description:
Library name: WT_PIC_1
WT_PIC_1 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 8. Unstim, replicate 1

description:
Library name: KO-8_Unstim_1
KO-8_Unstim_1 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 KO cells, clone 8. IFNa stimulation, replicate 1

description:
Library name: KO-8_IFNa_1
KO-8_IFNa_1 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 IRF7 Alt cells, clone 3. Unstim, replicate 1

description:
Library name: Alt-3_Unstim_1
Alt-3_Unstim_1 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 WT cells. IFNa stimulation, replicate B

description:
Library name: WT_IFNa_1
WT_IFNa_1 column in the 2024_Panthi-IRF7_TPMs.csv file


title: JSL1 WT cells. Unstim, replicate 3

description:
Library name: WT_Unstim_3
WT_Unstim_3 column in the 2024_Panthi-IRF7_TPMs.csv file


title: P4-4 (Patient 4, Region 4)

city: Stockholm

first: Nidhi

last: Sharma

state: Stockholm

address: Tomtebodavägen 23, Solna

department: Oncology-Pathology

country: Sweden

institute: Science for life laboratory, Karolinska Institute

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.  Softwares used: bedtools (2.29.2), bioconductor-summarizedexperiment (1.20.0), bioconductor-tximeta (1.8.0), deseq2 (1.28.0), dupradar (1.18.0), fastqc (0.11.9), nextflow (20.11.0-edge), nf-core/rnaseq (3.0), picard (2.23.9), preseq (2.0.3), qualimap (2.2.2-dev), rseqc (3.0.1), salmon (1.4.0), samtools (1.10), star (2.6.1d), stringtie (2.1.4), subread (2.0.1), trimgalore (0.6.6), ucsc (377)
Assembly: Homo sapiens, GRCh38)
Supplementary files format and content: tab-delimited file contains raw gene counts for each sample.

source_name: Brain

extract_protocol:
The sections collected in tubes were first washed in PBS to remove the blood, centrifuged, and the tissue pellets were used for subsequent DNA, RNA, and protein extraction with the AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Hilden, Germany) as per the manufacturer’s protocol. The quality control and concentration of the RNA samples were measured using the Agilent 2100 Bioanalyzer system.
Illumina RiboZero GOLD was used for ribosomal depletion from samples and Illumina TruSeq Stranded total RNA was used for RNA library construction. Multiplex sequencing in 0.25 lane on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with more than 50M reads/sample and a sequencing depth of 2 x 150 pairs, using 'NovaSeqXp' workflow in 'S4' mode flowcell. Out of 16 samples, 4 samples (P1-R2, P4-R2, P2-R3, P2-R4) failed the reception control library quality control step and were not sequenced.
RNA-seq, Illumina TruSeq Stranded total RNA, Illumina RiboZero GOLD, -, 1301

value: Brain

tag: patient

tag: region

tag: disease state

value: MBM


title: JSL1 WT cells. Unstim, replicate 1

description:
Library name: WT_Unstim_1
WT_Unstim_1 column in the 2024_Panthi-IRF7_TPMs.csv file

value: JSL1 (Jurkat-derived)

value: Immortalized T cell


title: P4-3 (Patient 4, Region 3)

tag: tissue


title: P3-4 (Patient 3, Region 4)


title: P4-1 (Patient 4, Region 1)


title: P3-1 (Patient 3, Region 1)


title: P3-3 (Patient 3, Region 3)


title: P2-1 (Patient 2, Region 1)


title: P1-4 (Patient 1, Region 4)


title: P1-3 (Patient 1, Region 3)


title: P2-2 (Patient 2, Region 2)


title: P1-1 (Patient 1, Region 1)


title: polysomalRNA_GAL_CTRL_REP3

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

country: France

institute: Institut Curie

data_processing:
RNA-seq data have been analyzed with the Institut Curie RNA-seq Nextflow pipeline (v3.1.4, https://doi.org/10.5281/zenodo.7443721). Briefly, raw reads were first trimmed with Trimgalor. Reads were aligned on the human reference genome (hg19) using STAR (STAR_2.6.1a_08-27). Genes abundance has been then estimated using STAR (STAR_2.6.1a_08-27). .
Assembly: Hg19
Supplementary files format and content: Semicolon delimited text file includes raw counts for each sample

extract_protocol:
RNA was isolated using the TRIzol-chloroform method and treated with DNase I (TURBO DNA-free; Invitrogen™, #AM1907) according to the manufacturer’s instructions. After DNase treatment, RNA was quantified using a Nanodrop 2000 spectrophotometer (Thermo Scientific™), and 1 μg total RNA was used to synthesize cDNA using SuperScript III Reverse Transcriptase (200 U/μL; Invitrogen™, #18080044) and random hexamer primers (Invitrogen™, #SO142), according to the manufacturer’s instructions. Quantitative PCR (qPCR) was performed using the Power SYBR Green PCR Master Mix (Thermo Scientific™, #4367559) on a CFX96 Real-Time PCR Detection System (Bio-Rad Laboratories Inc).
RNA sequencing libraries were prepared from 500ng to 1µg of total RNA or mRNA-enriched from heavy polysome fractions using the Illumina TruSeq Stranded mRNA Library preparation kit which allows to perform a strand specific sequencing. Nanodrop spectrophotometer was used to assess purity of RNA based on absorbance ratios (260/280 and 260/230) and BioAnalyzer for RNA integrity (RIN>9). A first step of polyA+ selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. The libraries were equimolarly pooled and subjected to qPCR quantification using the KAPA library quantification kit (Roche).

value: melanoma

tag: fraction

value: polysomal RNA


title: polysomalRNA_GAL_CTRL_REP2


title: polysomalRNA_GAL_CTRL_REP1


title: totalRNA_GAL_CTRL_REP2

value: total RNA


title: JSL1 IRF7 Alt cells, clone 3. PIC stimulation, replicate 1

description:
Library name: Alt-3_PIC_1
Alt-3_PIC_1 column in the 2024_Panthi-IRF7_TPMs.csv file

value: PIC at 10ug/mL for 8hrs


title: totalRNA_GAL_CTRL_REP1


title: polysomalRNA_GLU_GAPDH_REP3


title: polysomalRNA_GLU_GAPDH_REP2


title: totalRNA_GLU_GAPDH_REP1


title: totalRNA_GLU_GAPDH_REP3


title: polysomalRNA_GLU_GAPDH_REP1


title: polysomalRNA_GLU_PKM2_REP3


title: totalRNA_GLU_GAPDH_REP2


title: totalRNA_GLU_PKM2_REP3


title: totalRNA_GLU_PKM2_REP2


title: totalRNA_GLU_PKM2_REP1


title: polysomalRNA_GLU_HK2_REP3


title: polysomalRNA_GLU_PKM2_REP1


title: polysomalRNA_GLU_HK2_REP1


title: totalRNA_GLU_HK2_REP3


title: totalRNA_GLU_HK2_REP1


title: polysomalRNA_GLU_HK2_REP2


title: polysomalRNA_GLU_CTRL_REP2


title: polysomalRNA_GLU_CTRL_REP3


title: totalRNA_GLU_HK2_REP2


title: polysomalRNA_GLU_CTRL_REP1


title: totalRNA_GLU_CTRL_REP3


title: totalRNA_GLU_CTRL_REP2


title: totalRNA_GAL_CTRL_REP3


title: totalRNA_GLU_CTRL_REP1


title: h-hADSCs_3,  scRNAseq

first: Liming

last: Gui

address: 1120 Lianhua Street

department: Obstetrics and Gynaecology

institute: Peking University Shenzhen Hospital

description:
10X Genomics
h-hADSCs_matrix.mtx.gz
h-hADSCs_feature.tsv.gz
h-hADSCs_barcodes.tsv.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support.10xgenomics.com/single-cell-expression/software/pipelines/latests/what-is-cell-ranger)
The Fragments Per Kilobase of transcript sequence per Million mapped reads (FPKM) value for each gene was calculated based on its length and the number of mapped reads
Differential expression analysis was conducted between two groups, with two biological replicates per group, using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-separated value files and matrix files

source_name: Subcutaneous adipose tissue

growth_protocol: The isolation of hADSCs was carried out using the previously described method15  with modifications. hADSCs were cultured in DMEM/F-12 medium (Gibco) supplemented 10% fetal bovine serum (Gibco), 1%Glumax (Gibco), 1%NEAA(Gibco) and 1% penicillin/ streptomycin (Gibco) at 37 °C in a humidified 5% CO2 incubator. The characteristics of hADSCs were examined as below: hADSCs morphology was observed by an inverted microscope (Leica). Flow cytometry by FACSCanto II (BD) was used to detect hADSCs-related surface markers including CD31, HLA-DR, CD73, CD90, CD105 and CD29. The osteogenic and adipogenic differentiation potential of hADSCs was identified using inductive media according to the protocols provided by the manufacturers (HyCyte™). Calcium mineral deposits were stained with Alizarin Red, while lipid droplets were stained with Oil Red O.

extract_protocol:
Freshly collected h-hADSCs and c-hADSCs were separately digested, then washed in PBS twice and resuspended in PBS with 0.04% w/v BSA.
Library was performed according to the manufacter's instructions (single cell 3' V2 protocol, 10x Genomics). Briefly, hADSCs were resuspended in the master mix and loaded together with patiti0ning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The oply-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R! primer sequence. Unique Molecular Identifier (UMI) and the 10X Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and apropiated sized fragments were selected with SPRIselect library construction. During the library construction llumina R2 primer sequence, paired-ended constructs with P5 and P7 sequence and a sample index were added

treatment_protocol: Primary hADSCs treated with HEP14 (h-hADSCs) or vehicle(c-hADSCs) at passage 4 were used for for performing RNA-Sequencing.

value: Subcutaneous adipose tissue

value: human Adipose-Derived Stem Cells, hADSCs

value: WT

value: HEP14 for 48h


title: h-hADSCs_4,  scRNAseq


title: h-hADSCs_2,  scRNAseq


title: c-hADSCs_3,  scRNAseq

description:
10X Genomics
c-hADSCs_matrix.mtx.gz
c-hADSCs_feature.tsv.gz
c-hADSCs_barcodes.tsv.gz

value: vehicle for 48h


title: h-hADSCs_1,  scRNAseq


title: c-hADSCs_1, scRNAseq


title: c-hADSCs_2,  scRNAseq


title: h-hADSCs_2

data_processing:
Clean reads were then mapped to the reference genome using the HISAT2 (v2.0.5) software
The featureCounts (v1.5.0-p3) tool was utilized to count the number of reads mapped to each gene.
The Fragments Per Kilobase of transcript sequence per Million mapped reads (FPKM) value for each gene was calculated based on its length and the number of mapped reads
Differential expression analysis was conducted between two groups, with two biological replicates per group, using the DESeq2 R package (1.20.0).
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: human Adipose-Derived Stem Cells, hADSCs

extract_protocol:
Total RNA was then extracted from the ovarian tissue using TRIzol reagentaccording to the manufacturer's instructions (Invitrogen)
These libraries were sequenced on the Illumina NovaSeq 6000 platform (Novogene) to generate high-quality sequencing data

treatment_protocol: Primary hADSCs treated with HEP14 or vehicle at passage 4 were used for for performing RNA-Sequencing.


title: h-hADSCs_3


title: polysomalRNA_GLU_PKM2_REP2


title: c-hADSCs_3


title: h-hADSCs_1


title: c-hADSCs_1


title: Euploid wtGATA1 Day 11 progenitors

first: Eric

last: Wafula

state: PA

address: 2714-2720 South Street

department: DBHi

institute: Children's Hospital of Philadelphia

description:
EuploidwtGATA1D11_barcodes.tsv.gz
EuploidwtGATA1D11_features.tsv.gz
EuploidwtGATA1D11_matrix.mtx.gz

data_processing:
Raw base calls (BCL) files were demultiplexed into FASTQ files using CellRanger (v7.1.0) mkfastq, then processed with counts to generate feature-barcode counts matrices aligned to the 10x Genomics Human reference GRCh38 (Ensembl98). Contaminating ambient RNA expression was corrected using SoupX (v1.6.2). Doublets and cells with high mitochondrial RNA were removed using DoubletFinder (v2.0.3) to obtained processed data.
Assembly: GRCh38
Supplementary files format and content: Tab-separated filtered feature-barcode files, including barcodes, genes, and count matrices

source_name: iPSC

growth_protocol: iPSCs were maintained on a mouse embryonic fibroblast feeder layer with HES-10 (10 ng/mL of beta fibroblast growth factor) media. All cells were maintained at 37 °C, 5% CO2, and 5% O2.

extract_protocol:
Sorted HPCs were resuspended in 0.04% BSA in PBS at 1000 cells/μL, and 2 x 104 cells per sample were loaded onto gel beads-in-emulsion wells (10x Genomics). After cell lysis, cDNA libraries were reverse-transcribed from extracted RNA using the Chromium Single Cell Platform (10x Genomics).
Sorted HPCs were resuspended in 0.04% BSA in PBS at 1000 cells/μL, and 2 x 104cells per sample were loaded onto gel beads-in-emulsion wells (10x Genomics).cDNA libraries were prepared from extracted RNA using the Chromium Single Cell Platform (10x Genomics). cDNA quality and integrity were measured byTapeStationHigh Sensitivity DNA analysis (Agilent) beforesequencingwitha standard 3’ assay with theNovaSeq6000 platform and S1 Reagent Kit v1.5 (Illumina)

treatment_protocol: Hematopoietic progenitors were differentiated from the iPSCs over 7-11 days via embryoid body formation in StemPro-34 with pre-defined cytokines to pattern towards mesoderm induction, hematoendothelial specification, and hematopoietic differentiation. Differentiating cells were maintained on a rotary shaker at 100 rpm.

value: iPSC

value: iPSC-derived hematopoietic progenitors

value: Hematopoietic differentiation via embryoid body formation


title: c-hADSCs_2


title: T21 wtGATA1 Day 11 progenitors

description:
T21wtGATA1D11_barcodes.tsv.gz
T21wtGATA1D11_features.tsv.gz
T21wtGATA1D11_matrix.mtx.gz

value: DS145 EM9


title: T21 GATA1s Day 11 progenitors

description:
T21GATA1sD11_barcodes.tsv.gz
T21GATA1sD11_features.tsv.gz
T21GATA1sD11_matrix.mtx.gz


title: Euploid GATA1s Day 11 progenitors

description:
EuploidGATA1sD11_barcodes.tsv.gz
EuploidGATA1sD11_features.tsv.gz
EuploidGATA1sD11_matrix.mtx.gz


title: Euploid wtGATA1 Day 9 progenitors

description:
EuploidwtGATA1D9_barcodes.tsv.gz
EuploidwtGATA1D9_features.tsv.gz
EuploidwtGATA1D9_matrix.mtx.gz


title: T21 wtGATA1 Day 9 progenitors

description:
T21wtGATA1D9_barcodes.tsv.gz
T21wtGATA1D9_features.tsv.gz
T21wtGATA1D9_matrix.mtx.gz


title: Control No4

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
CPM estimates, generated with cpm function from edgeR version 3.17
Assembly: GRCm38.p6
Supplementary files format and content: raw counts with kallisto quant version 0.4.6.
Supplementary files format and content: CPM estimates, generated with cpm function from edgeR version 3.17

source_name: Hepatic endothelial cells

extract_protocol:
Isolation of hepatic endothelial cells was performed as described before (PMID: 32916216). Mice were deeply anesthetized with Isolfluran (Baxter) and sacrificed by cervical dislocation. Livers were perfused in situ via the portal vein with a 0.05% collagenase/amino acid/saccharide solution (C2674, Sigma-Aldrich). Livers were dissected and mechanically disrupted. Liver tissue from three mice was pooled and digested at 38 °C in collagenase/Gey’s balanced salt solution (G9779, Sigma-Aldrich). Then, the tissue was filtered through a 250 μm mesh. Non-parenchymal cells were separated by a 19.3 % Nycodenz (1002424, Axis-Shield, Alere Technologies) gradient. Subsequently, magnetic-activated cell sorting (MACS) was used with anti-CD146 MicroBeads (ME-9F1, 130-092-007, Miltenyi Biotech) to purify endothelial cells.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

value: Hepatic endothelial cells


title: Euploid GATA1s Day 7 progenitors technical replicate 2

description:
EuploidGATA1sD7_barcodes.tsv.gz
EuploidGATA1sD7_features.tsv.gz
EuploidGATA1sD7_matrix.mtx.gz

value: iPSC-derived CD41+/235+ hematopoietic progenitors


title: T21 GATA1s Day 9 progenitors

description:
T21GATA1sD9_barcodes.tsv.gz
T21GATA1sD9_features.tsv.gz
T21GATA1sD9_matrix.mtx.gz


title: Control No2


title: Control No1


title: Euploid GATA1s Day 7 progenitors technical replicate 1


title: Euploid wtGATA1 Day 7 progenitors technical replicate 2

description:
EuploidwtGATA1D7_barcodes.tsv.gz
EuploidwtGATA1D7_features.tsv.gz
EuploidwtGATA1D7_matrix.mtx.gz


title: Maf-LSEC-KO No3

value: Maf-knockout


title: Control No3


title: T21 GATA1s Day 7 progenitors T21 wtGATA1 Day 7 technical replicate 2

description:
T21GATA1sD7_barcodes.tsv.gz
T21GATA1sD7_features.tsv.gz
T21GATA1sD7_matrix.mtx.gz


title: Maf-LSEC-KO No2


title: T21 wtGATA1 Day 7 progenitors technical replicate 1

description:
T21wtGATA1D7_barcodes.tsv.gz
T21wtGATA1D7_features.tsv.gz
T21wtGATA1D7_matrix.mtx.gz


title: Maf-LSEC-KO No1


title: Control2

city: Iowa City

first: Snehajyoti

last: Chatterjee

state: IA

address: 169 Newton Road

department: Neuroscience & Pharmacology

institute: University of Iowa

description:
Library name: Control2
Fresh Frozen Spatial Transcriptome Sequencing

data_processing:
Raw files were processed with spaceranger-3.0.0
Outputs for each samples are provided in tar.gz files.
Assembly: mm10
Supplementary files format and content: Output provided in tar.gz file
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
The mice were euthanized by cervical dislocation, and the whole brains were flash-frozen in -70C isopentane. The flash-frozen brains were stored at -80C. Brains were embedded in optimal cutting temperature medium (OCT) and then cryosectioned at −20°C with the Leica CM3050 S Cryostat. Coronal sections measuring 10 microns thick were prepared from the brain area containing the dorsal hippocampus. They were placed on chilled Visium Spatial Gene Expression Slides (10X Genomics). The Visium slides were fixed, stained, and imaged with Hematoxylin and Eosin on an Olympus BX61 microscope. The tissue was subsequently permeabilized, then Poly-A mRNAs captured by the poly(dT) primers pre-coated on the slide. Reverse transcription and synthesis of the second strand were employed to amplify cDNA samples from the Visium slides. These samples were subsequently transferred, purified, and quantified for library preparation.
Sequencing libraries were prepared according to the Visium Spatial Gene Expression User Guide (10X Genomics). The libraries were sequenced on a NovaSeq 6000 (Illumina)

value: brain

value: Vehicle


title: shJab3

city: Wuhan

last: Zhang

state: Hubei

address: Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuchang District

department: Department of Hematology

institute: Wuhan University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug oftotal RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit folowing manufacturer's protocols.

value: cell line

value: Leukemic cells

value: Jab1 knockdown

value: Virus transfection


title: Euploid GATA1s Day 9 progenitors

description:
EuploidGATA1sD9_barcodes.tsv.gz
EuploidGATA1sD9_features.tsv.gz
EuploidGATA1sD9_matrix.mtx.gz


title: PCB2

description:
Library name: PCB2
Fresh Frozen Spatial Transcriptome Sequencing

value: PCB


title: T21 GATA1s Day 7 progenitors T21 wtGATA1 Day 7 technical replicate 1


title: PCB1

description:
Library name: PCB1
Fresh Frozen Spatial Transcriptome Sequencing


title: shJab2


title: shNC3

value: WT


title: shJab1


title: shNC1


title: Maf-LSEC-KO No4


title: DRG, naive, 3M, scRNA-seq, rep2

city: St. Louis

first: Valeria

last: Cavalli

state: MO

address: 1 Bookings Dr.

institute: Washington University in St. Louis

description:
Library name: Sample 2
10X Genomics

data_processing:
A digital expression matrix was obtained using the 10X Genomics Cell Ranger pipeline.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dorsal root ganglion (L4-L5)

extract_protocol:
L4 and L5 DRG’s from 3 month old female mice were collected into cold HBSS with 10% 1M HEPES, then transferred to fresh made pre-warmed dissociation medium (15U/mL Papain suspension, 20mg/mL L-cysteine, 10mg/mL Deoxyribonuclease I , 10% 1M HEPES in HBSS) incubated in 37oC for 20 min. Samples were incubated with collagenase (150µg/mL) in 37oC for 20 min after washing with pre-warmed HBSS twice. After washing with pre-warmed HBSS twice, the single cell suspension was resuspend by gently triturating in complete medium (Neurobasal™-A Medium, with B-27™ Plus Supplement ; GlutaMAX™ Supplement) following by passing through 70-micron cell strainers. Single cell suspension was resuspend in HBSS with 10% 1M HPEPS and 0.1% Fetal Bovine Serum following by staining with LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit (ThermoFisher; Catalog# L34965). Live single cells were sorted by MoFlo. Sorted cells were washed in DPBS+0.04%BSA solution and manually counted using a hemocytometer. Solution was adjusted to a concentration of 700-1000cell/microliter
Single cell RNA-Seq libraries were prepared using GemCode Single-Cell 3′ Gel Bead and Library Kit (10x Genomics). polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform.

value: Dorsal root ganglion (L4-L5)

tag: strain

tag: Sex

value: female


title: Euploid wtGATA1 Day 7 progenitors technical replicate 1

value: iPSC

tag: cell type


title: HEK293T_99xGly_c8_-DOX

city: Boston

first: Raghu

last: Chivukula

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to the reference human genome GRCh38 and genome annotation from Ensembl release 104 using STAR v2.7.1a.
Reads aligned to each gene were counted using featureCounts from Subread v1.6.2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

growth_protocol: HEK293T cells were grown in high glucose DMEM supplemented with 10% fetal bovine serum and 1X penicillin-streptomycin at 37°C and 5% CO2.

extract_protocol:
Cells were rinsed in PBS and lysed in QIAzol (Qiagen). RNA was extracted using a miRNeasy micro cleanup kit (Qiagen).
Libraries were prepared from 500 ng of RNA using a KAPA RNA HyperPrep Kit with RiboErase (Roche) and KAPA Unique Dual-Indexed Adapters (Roche) with 12 cycles of PCR.

treatment_protocol: Where indicated, culture medium was supplemented with 10 ng/mL doxycycline (DOX).

tag: genotype


title: DRG, 21M, snRNA-seq, rep2

description:
Library name: Sample 3
PIP-seq

data_processing:
A digital expression matrix was obtained using the Fluent BioSciences Pipseeker (v3.3.0) pipeline.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Dorsal root ganglion (L3-L5)

extract_protocol:
L3, L4 and L5 DRGs were collected from mice and immediately placed on dry ice. DRG were stored in -80 until processing. Nuclei were isolated using the Illumina Nuclei Isolation Kit (Illumina; Catalog# 20132795). The DRG were dissociated using a KIMBLE 2mL Dounce homogenizer (Sigma; Catalog# D8938) in Nuclei Extraction Buffer (NEB) and passed through a 40-micron cell strainer. The nuclei were briefly centrifuged and then passed through a 10-micron cell strainer. The nuclei were resuspended in Nuclei Suspension Buffer (NSB) and counted for intact nuclei using 7-AAD stain (Sigma; Catalog# SML1633). Nuclei were processed using the Illumina Single Cell 3’ RNA Prep, T20 Kit (Illumina; Catalog# FB0005366, FB0005373, FB0005362, FB0005382)
Single nucleus RNA-Seq libraries were prepared using the Illumina V Library Prep Kit (Illumina; Catalog# 20132789, FB0005374, FB0005373).

value: Dorsal root ganglion (L3-L5)

value: male


title: DRG, 3M, snRNA-seq, rep1

description:
Library name: Sample 1
PIP-seq


title: DRG, 21M, snRNA-seq, rep1

description:
Library name: Sample 2
PIP-seq


title: T21 wtGATA1 Day 7 progenitors technical replicate 2

value: DS145 EM9

tag: treatment

value: Hematopoietic differentiation via embryoid body formation


title: HEK293T_99xGly_c26_+DOX

tag: cell line

value: DOX


title: HEK293T_99xGly_c26_-DOX


title: DRG, naive, 3M, scRNA-seq, rep1

description:
Library name: Sample 1
10X Genomics


title: TRIPLE_2

city: Pamplona

first: Alfonso

last: Calvo

state: Navarra

address: Avenida Pío XII 55

institute: CIMA Universidad de Navarra

description: Library name: TRIPLE_312

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode vM36 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Tumor

growth_protocol: Murine RP (Rb1/Tp53 KO) cells were subcutaneously injected in one flank of 8-week-old female F1 mice (resulting from C57Bl/6j x 129S1/Sv cross). When tumor volume reached approximately 50 mm3, mice were randomized and treated with the following drug combination: Dasatinib (Dasa) at 30 mg/kg daily+anti-PD-1+anti-CTLA4 (100 microg/mouse for each antibody). Control animals were treated with vehicle.

extract_protocol:
For transcriptomic analysis, RNA was extracted from frozen tumors or cells using NucleoSpin RNA kit (Macherey-Nagel) according to manufacturer’s instructions.
After quality control with Tape Station (Agilent), samples were sequenced by Macrogen. Truseq mRNA Library NovaSeq6000 150PE (150 x 2 bp) with 30 M total reads/sample was built. Sequencing consisted of readings of a hundred and fifty base pairs in 5’-3’ direction and vice versa.

value: Tumor


title: HEK293T_99xGly_c5_-DOX


title: TRIPLE_1

description: Library name: TRIPLE_065


title: TRIPLE_3

description: Library name: TRIPLE_378


title: HEK293T_99xGly_c5_+DOX


title: HEK293T_99xGly_c8_+DOX


title: CTR_2

description: Library name: CTR_385


title: CTR_3

description: Library name: CTR_705


title: HEK293T_15xGly_c12_-DOX


title: HEK293T_15xGly_c9_-DOX


title: DASATINIB_ITC_4

description: Library name: NB42

growth_protocol: Murine RP (Rb1/Tp53 KO) cells were subcutaneously injected in one flank of 8-week-old female F1 mice (resulting from C57Bl/6j x 129S1/Sv cross). When tumor volume reached approximately 50 mm3, mice were randomized and treated with: Dasatinib (Dasa) at 30 mg/kg daily, anti-PD-1+anti-CTLA4 (100 microg/mouse for each antibody), or the combination Dasa+anti-PD-1+anti-CTLA4 (Dasa+ITc). Control animals were treated with vehicle.

extract_protocol:
For transcriptomic analysis, RNA was extracted from frozen RP tumors using NucleoSpin RNA kit (Macherey-Nagel) according to manufacturer’s instructions.
After quality control with Tape Station (Agilent), samples were sequenced by Macrogen. Truseq mRNA Library NovaSeq6000 150PE (150 x 2 bp) with 30 M total reads/sample was built. Sequencing consisted of readings of a hundred and fifty base pairs in 5’-3’ direction and vice versa.


title: DASATINIB_ITC_3

description: Library name: NB40


title: CTR_1

description: Library name: CTR_016


title: HEK293T_15xGly_c12_+DOX


title: DASATINIB_ITC_2

description: Library name: NB39


title: shNC2


title: HEK293T_15xGly_c10_-DOX


title: HEK293T_15xGly_c10_+DOX


title: DASATINIB_ITC_1

description: Library name: NB37


title: HEK293T_15xGly_c9_+DOX


title: ITC_3

description: Library name: NB35


title: ITC_2

description: Library name: NB34


title: Retinal organoids at day 170 of differentiation, 12h light (flickering 40 Hz) and 12h dark for 7 days, sc seq

city: Brno

first: Tomas

last: Barta

address: Kamenice 3

country: Czech Republic

institute: Masaryk University

description: Library name: scRNA-seq_Photostimulated_40Hz

data_processing:
Bulk RNA sequencing: The adapters and quality trimming of raw fastq reads was performed using Trimmomatic v0.39 with settings CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35.  Single-cell RNA analysis: All data analysis and visualizations were conducted using R. We performed quality control checks for each sample in R for each sample and removed any cells with <1000 reads or 500 genes or >10% mitochondrial reads. Doublets were predicted using DoubletFinder and filtered from the data. The Seurat R package (version 5.1.0) was then used to process the data.
Assembly: Bulk RNA sequencing: human reference genome (Ensembl GRCh38 annotation) using STAR v2.7.3a with default settings, except for --outFilterMismatchNoverLmax 0.66 and --twopassMode Basic.  Single-cell RNA sequencing: human reference genome refdata-gex-GRCh38-2020-A
Supplementary files format and content: Bulk RNA sequencing: Mapped sequencing reads were assigned to specified genomic features using featureCounts (Rsubread library). Normalized (VST-transformed) reads are in bulk_normalized_counts_vst.csv file  Single-cell RNA sequencing: RDS files for dark and photostimulated at 40 Hz, respectively

source_name: Retinal organoid

extract_protocol:
Bulk RNA sequencing: Retinal organoids were washed twice with PBS and dissociated in RNA Blue Reagent (Top-Bio). Samples were either stored at −80 °C or processed immediately. Organoids were homogenized using an insulin syringe, and total RNA was extracted using the Direct-zol™ RNA MicroPrep Kit (ZYMO RESEARCH, Cat. No.: R2062), following the manufacturer’s protocol.  Single-cell RNA sequencing: Organoid dissociation was carried out using the Neurosphere Dissociation Kit (#130-095-943, Miltenyi Biotec) according to the manufacturer’s instructions. Briefly, organoids were washed twice with cold HBSS (#14025092, Gibco) and transferred into Eppendorf tubes containing 960 μL of preheated Buffer X (each set of 15 organoids was dissociated in a separate tube). Then, 25 μL of Enzyme P, 10 μL of Buffer Y, and 5 μL of Enzyme A were added and mixed gently. The tubes were placed on a thermal mixer with a block (Eppendorf) for 10 minutes at 37°C and 800 rpm. The organoids were dissociated using a fire-polished Pasteur pipette by pipetting up and down 10 times slowly. They were then incubated again under the same conditions for 5 minutes in the thermal mixer and pipetted up and down 10 times with the Pasteur pipette. After adding cold HBSS containing 5% FBS to the single-cell suspension, the mixture was passed through a 40 μm cell strainer placed on a 15 mL tube. Cells were counted, and the tubes were centrifuged at 300×g for 10 minutes at room temperature. The supernatant was aspirated completely, and the cells were resuspended in cold HBSS containing 5% FBS at a concentration of 1000 cells/μL and kept on ice. (Total single cell number 1.500.000/sample)
Bulk RNA sequencing: RNA integrity was checked on the Fragment Analyzer using RNA Kit 15 nt (Agilent Technologies). 500ng of total RNA was used as input for library preparation using QuantSeq 3′ mRNA-Seq FWD with UDI 12 nt Kit (v.2) (Lexogen) in combination with UMI Second Strand Synthesis Module for QuantSeq FWD. Quality control for library quantity and size distribution was done using QuantiFluor dsDNA System (Promega) and High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies). Final library pool was sequenced on NextSeq using High Output Kit v2.5 75 cycles (Illumina) in single-end mode.  Single-cell RNA sequencing: Library preparation was conducted using the same protocol. The quality and quantity of the prepared libraries were assessed using the High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies) and the QuantiFluor dsDNA System (Promega). The libraries were then sequenced using the AVITI sequencing platform (Element Biosciences), employing the AVITI 2×75 Sequencing Kit Cloudbreak FS High Output (150 Gb). Sequencing reads were processed using Cell Ranger software version 8.0.1 (10x Genomics), with FASTQ files aligned to the human reference genome refdata-gex-GRCh38-2020-A, also provided by 10x Genomics, to generate gene expression matrices for downstream analyses.

value: Retinal organoid

value: hiPSC M8

value: wt

value: photostimulation - 40 Hz


title: Retinal organoids at day 170 of differentiation, cultured in the dark, sc seq

description: Library name: scRNA-seq_Dark

value: dark


title: DASATINIB_3

description: Library name: NB28


title: ITC_1

description: Library name: NB32


title: DASATINIB_4

description: Library name: NB29


title: DASATINIB_2

description: Library name: NB27


title: D7

city: Haidian

first: Awais

last: Ali

state: Beijing

address: Room No. 106, International Student Dormitory, Chinese Academy of Agricultural Sciences

institute: Majorbio

description:
Library name: D7
10X Arg (18g/kg), Replicate 7

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Assembly: Gallus_gallus  genome  GCF_016699485.2
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...

organism: Gallus gallus

source_name: Liver

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions. The RNA-seq transcriptome librariy was prepared following Illumina Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: Liver


title: D6

description:
Library name: D6
10X Arg (18g/kg), Replicate 6


title: D5

description:
Library name: D5
10X Arg (18g/kg), Replicate 5


title: D8

description:
Library name: D8
10X Arg (18g/kg), Replicate 8


title: D4

description:
Library name: D4
10X Arg (18g/kg), Replicate 4


title: DASATINIB_1

description: Library name: NB26


title: C_3

description: Library name: NB23


title: D2

description:
Library name: D2
10X Arg (18g/kg), Replicate 2


title: C_2

description: Library name: NB22


title: D1

description:
Library name: D1
10X Arg (18g/kg), Replicate 1


title: C_1

description: Library name: NB20


title: C8

description:
Library name: C8
5X Arg (9 g/kg), Replicate 8


title: knock out #3

city: Atlanta

first: Michael

last: Deans

address: 201 Dowman Drive Atlanta

institute: Emory University School of Medicine

description: Library name: 20648X7

data_processing:
quality inspection with FastQC (version 0.12.1)
trimming of sequence reads to 120bp with Cutadapt (version 4.3)
alignment of sequence reads with HISAT2 (version 2.2.1)
analysis of differential gene expression with R packages Rsubread, featureCounts, and DESeq2
Assembly: GRCm39
Supplementary files format and content: size factor normalized values for wildtype samples
Supplementary files format and content: size factor normalized values for knock out samples

source_name: organ of corti

extract_protocol:
RNA was harvested using Qiagen RNeasy
libraries where prepared from total RNA after rRNA depletion using NEBNext Ultra II

value: organ of corti

value: Prox1 knock-out (Emx2-cre; floxed-Prox1)


title: knock out #4

description: Library name: 20648X8


title: C7

description:
Library name: C7
5X Arg (9 g/kg), Replicate 7


title: knock out #2

description: Library name: 20648X6


title: C5

description:
Library name: C5
5X Arg (9 g/kg), Replicate 5


title: C6

description:
Library name: C6
5X Arg (9 g/kg), Replicate 6


title: knock out #1

description: Library name: 20648X5


title: C3

description:
Library name: C3
5X Arg (9 g/kg), Replicate 3


title: C2

description:
Library name: C2
5X Arg (9 g/kg), Replicate 2


title: wildtype #2

description: Library name: 20648X2

value: wildtype


title: wildtype #3

description: Library name: 20648X3


title: C_4

description: Library name: NB24


title: C1

description:
Library name: C1
5X Arg (9 g/kg), Replicate 1


title: wildtype #1

description: Library name: 20648X1


title: B8

description:
Library name: B8
Arg (1.8 g/kg), Replicate 8


title: LSEC WT

first: Volker

last: Ast

address: Theodor-Kutzer-Ufer 1-3

department: NGS Core Facility

institute: University Hospital Mannheim

description: 10X genomics

data_processing:
DATA PRE-PROCESSING: The raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 6.0.2), which performed demultiplexing, barcode assignment, alignment to the mouse reference genome mm10, filtering, barcode counting, and UMI counting.
DATA PROCESSING: On the filtered matrix output of Cell Ranger, the empty droplets were identified using low UMI counts (500 UMIs), and Otsu’s Method, as described in Ben-Moshe et al1. The mean UMI counts of the empty droplets were then subtracted from each cell. Further analyses were performed using the Seurat package (version 5.0.1). Cells with total UMI counts lower than 1500 or total gene counts lower than 750 were removed. Cell clustering was based on PCA dimensionality reduction using 16 or 20 PCs (for the WT and KO data, respectively) and a resolution value of 0.3. For further analysis, mitochondrial (“ˆmt-”) and ribosomal (“Rp”) genes were manually removed from the gene list since they are prone to batch-related expression variability. Additionally, doublets were identified and removed using the DoubleFinder Package (version 2.0.3). Cell type-specific markers were then utilized to interpret the single-cell clusters: Adgre1 and Clec4f for macrophages, Ptprc and Cd52 for immune cells, Acta1 for hepatic stellate cells, Arg1 for hepatocytes, and Pecam1 for endothelial cells. The clustering was used to subset only the endothelial cells. The last subset was done excluding the cells that expressed Vwf to delete the vascular endothelial cells. This processing was done independently for each sequencing run. Finally, the processed WT and KO Seurat Objects were merged. Data were normalized and scaled using the SCTransform function. Cell clustering was based on PCA dimensionality reduction using 22 PCs and a resolution value of 0.3. The resulting clusters were then manually annotated after extracting cluster markers using the FindAllMarkers Seurat function.
Assembly: mm10
Supplementary files format and content: Tab separated values files (TSV) and matrix files (MTX)

extract_protocol:
Mice were deeply anesthetized with Isolfluran (Baxter) and sacrificed by cervical dislocation. Livers were perfused in situ via the portal vein with a 0.05% collagenase/amino acid/saccharide solution (C2674, Sigma-Aldrich). Livers were dissected and mechanically disrupted. Liver tissue from three mice was pooled and digested at 38 °C in collagenase/Gey’s balanced salt solution (G9779, Sigma-Aldrich). Then, the tissue was filtered through a 250 μm mesh. Non-parenchymal cells were separated by a 19.3 % Nycodenz (1002424, Axis-Shield, Alere Technologies) gradient. Subsequently, magnetic-activated cell sorting (MACS) was used with anti-CD146 MicroBeads (ME-9F1, 130-092-007, Miltenyi Biotech) to purify endothelial cells. LSEC suspensions were adjusted to a concentration of approximately 1,000 cells/µL in PBS to ensure optimal capture efficiency for 10x Genomics Chromium Next GEM technology.
Single-cell suspensions were loaded into the 10x Genomics Chromium Controller (10x Genomics) to generate Gel Bead-in-Emulsions (GEMs), following the manufacturer's instructions (10x Genomics protocol number: CG000317 Rev A). A targeted cell recovery of 10,000 cells was used to ensure sufficient capture while minimizing doublet formation. Inside each GEM, reverse transcription was performed using reagents from the 10x Genomics Chromium Single Cell 3’ Reagent Kit v3.1. Barcoded mRNA transcripts were converted into cDNA within the emulsion droplets. Following reverse transcription, cDNA was purified with Silane Dynabeads (Thermo Fisher Scientific), and the cDNA libraries were amplified by polymerase chain reaction (PCR) to generate sufficient material for sequencing. Amplified cDNA was subjected to fragmentation, end repair, and A-tailing using the Chromium Single Cell 3’ Library Construction Kit. Adapter ligation and final amplification were performed to generate sequencing-ready libraries. Sample quality was assessed using an Agilent Bioanalyzer (Agilent Technologies) to ensure library integrity and appropriate fragment sizes.

value: Liver Sinusoidal Endothelial cells

value: WT


title: LSEC MAF KO

description: 10X genomics

value: KO


title: B6

description:
Library name: B6
Arg (1.8 g/kg), Replicate 6


title: B7

description:
Library name: B7
Arg (1.8 g/kg), Replicate 7


title: WT Neutrophils, lung, sorted from infected WT mice, 72h pi. Rep.2

city: New York

first: YAHUI

last: GUO

state: NY

address: 407 East 68th street, ZRC1641

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center (MSKCC)

description: 400k cells were used

data_processing:
CUT&RUN datasets were processed by trimming paired reads for adaptors and low-quality sequences using Trimmomatic (v0.39) and aligning to the mm10 reference genome with Bowtie 2 (v2.4.1).
Peaks were identified using MACS2 (v2.2.7.1) with input samples as control, employing narrow peak parameters and cutoff - analysis - ple-5 - keep - dup all -B - SPMR. Irreproducible discovery rate (IDR) calculations were performed using ENCODE project scripts (IDR v2.0.4.2).
Reproducible peaks with an IDR value of 0.05 or less in each condition were retained, aggregated, and merged to create the final atlas, which was annotated with the UCSC Known Gene model.
Reads were mapped to this atlas and counted using the summarize Overlaps function from the Genomic Alignment package (v1.34.1).
Assembly: GRCm38.p6
Supplementary files format and content: Bigwig
Library strategy: CUT&RUN

source_name: lung

growth_protocol: To prepare single cell lung suspensions for flow cytometry. After perfusing murine lungs, they were placed in a gentle MACS™ C tube and mechanically homogenized in 5 ml RPMI-1640, 10% FBS, and 0.1 mg/ml DNAse using a gentle MACS™ Octo Dissociator (Miltenyi Biotech) without the use of collagenase. The lung cell suspensions were then lysed of RBCs, enumerated, and stained with fluorophore-conjugated antibodies prior to flow cytometric analysis. We used BD Aria for flow cytometric sorting, cell always stays on ice or sorted at 4℃. Neutrophils were identified as CD45+ CD11b+ Ly6Clo Ly6G+ cells

extract_protocol:
For CUT&RUN, 400,000 sorted neutrophils were used for H3K4me3 and STAT1 analysis. Anti-H3K4me3 (Epicypher, cat. no. 13-0028) or polyclonal anti-STAT1 antibodies (Proteintech, cat. no. 10144-2-AP) were employed for each target. Sorted cells were washed with PBS and resuspended in Antibody Buffer (1 ´ eBioscience Perm/Wash Buffer, 1´ Roche cOmplete EDTA-free Protease Inhibitor, 0.5 µM Spermidine, and 2 µM EDTA in H2O). They were incubated overnight at 4°C with control IgG, H3K4me3, or STAT1 antibodies diluted 1:100 in Antibody Buffer in a 96-well V-bottom plate. Following antibody incubation, cells were washed twice with Buffer 1 (1´ eBioscience Perm/Wash Buffer, 1´ Roche cOmplete EDTA-free Protease Inhibitor, 0.5 µM Spermidine in H2O) and resuspended in 50 µL of Buffer 1 plus 1´ pA/G-MNase (Cell Signaling, cat. no. 57813). This mixture was incubated on ice for 1 hour, then washed twice with Buffer 2 (0.05% w/v Saponin, 1´ Roche cOmplete EDTA-free Protease Inhibitor, 0.5 µM Spermidine in 1X PBS) three times. Cells were resuspended in Calcium Buffer (Buffer 2 plus 2 µM CaCl2) and incubated on ice for 30 minutes to activate the pA/G-MNase reaction. An equal volume of 2´ STOP Buffer (Buffer 2 plus 20 µM EDTA plus 4 µM EGTA) and 1 pg of Saccharomyces cerevisiae spike-in DNA (Cell Signaling, cat. no. 29987) were added. Samples were incubated at 37 °C for 15 minutes, followed by DNA isolation and purification using the Qiagen MinElute Kit per the manufacturer’s instructions.
Immunoprecipitated DNA was quantified by PicoGreen, and the size was evaluated using an Agilent BioAnalyzer: fragments between 100 and 600 bp were size selected using aMPure XP beads (Beckman Coulter, cat. no. A63882).  KAPA HTP Library Preparation Kit (Kapa Biosystems, cat. no. KK8234) was used to prepare Illumina sequencing libraries according to the manufacturer’s instructions with 0.001–0.5 ng input DNA and 14 cycles of PCR. Barcoded libraries were run on the NovaSeq 6000 in a PE100 run using S4 kit version 1.5 with XP mode to generate approximately 23 million paired reads per sample.

treatment_protocol: cells sorted from naïve mice have no treatment; cells sorted from infected mice, mice were infected with ECA10 A. fumigatus for 72h

value: lung

value: neutrophils

value: 72h pi with 3*10^7 CEA10


title: B4

description:
Library name: B4
Arg (1.8 g/kg), Replicate 4


title: WT Neutrophils, lung, sorted from infected WT mice, 72h pi. Rep.3

description: 400k cells were used


title: WT Neutrophils, lung, sorted from infected WT mice, 72h pi. Rep.1

description: 400k cells were used


title: B3

description:
Library name: B3
Arg (1.8 g/kg), Replicate 3


title: B2

description:
Library name: B2
Arg (1.8 g/kg), Replicate 2


title: wildtype #4

description: Library name: 20648X4


title: C4

description:
Library name: C4
5X Arg (9 g/kg), Replicate 4


title: WT Neutrophils, lung, sorted from infected WT mice, 72h pi.

description: 400k cells were used


title: B1

description:
Library name: B1
Arg (1.8 g/kg), Replicate 1


title: A8

description:
Library name: A8
Control (0 g/kg), Replicate 8


title: WT Neutrophils, BM, sorted from naïve WT mice

description: 400k cells were used

source_name: bone marrow

value: bone marrow

value: naïve


title: STAT1 KO Neutrophils, lung, sorted from infected WT mice, 72h pi.

description: 400k cells were used

value: STAT1 KO


title: A6

description:
Library name: A6
Control (0 g/kg), Replicate 6


title: Ovary, aged_HEP14_4

city: Shenzhen

source_name: ovary

treatment_protocol: young (7~8 weeks), adult (27~28 weeks), aged mice (73~74 weeks) treated with vehicle, and aged mice (73~74 weeks) treated with HEP14 (aged+HEP14 mice).

value: ovary

value: 73~74 weeks


title: Control1

description:
Library name: Control1
Fresh Frozen Spatial Transcriptome Sequencing

value: brain

value: Vehicle


title: Ovary, aged_HEP14_2


title: Ovary, aged_HEP14_3


title: Ovary, aged_HEP14_1


title: A5

description:
Library name: A5
Control (0 g/kg), Replicate 5

value: Liver


title: Ovary, aged_4


title: A4

description:
Library name: A4
Control (0 g/kg), Replicate 4


title: B5

description:
Library name: B5
Arg (1.8 g/kg), Replicate 5


title: Ovary, aged_3


title: A3

description:
Library name: A3
Control (0 g/kg), Replicate 3


title: A1

description:
Library name: A1
Control (0 g/kg), Replicate 1