title: umbilical cord plasma, Gen3G, PubM2149

description: Library name: Gen3G_UCP_PubM2149

tag: tissue

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)


title: umbilical cord plasma, Gen3G, PubM2669

status: Public on Jul 31 2026

type: SRA

city: Sherbrooke

first: Luigi

last: Bouchard

country: Canada

institute: Université de Shebrooke

description: Library name: Gen3G_UCP_PubM2669

library_source: transcriptomic

data_processing:
The extra-cellular RNA processing toolkit (exceRpt) pipeline version 4.6.3 (PMID : 30956140) was used to process miRNA sequencing data from fastq files.
Low quality reads (Phred score < 20 for more than  80% of the read) and adapters sequences were removed with the FASTX-Toolkit integrated in the exceRpt pipeline. High quality sequences were mapped to the human genome (GRCh37) and miRBase version 21 using the STAR alignment algorithm version 2.4.2a.
Read count extraction was performed using the Rscript provided for processing exceRpt output for multiple samples (PMID : 30956140).
Assembly: GRCh37
Supplementary files format and content: Comma-seperated value file, include non-normalized read counts for each microRNA detected in each samples.

molecule: total RNA

organism: Homo sapiens

source_name: umilical cord plasma

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit and protocol (Thermo Fisher Scientific, catalogue # AM1556), in a randomized order, from up to 500 μL of UCP (130 µL to 500 µL, based on availability) kept at -80 °C until extraction. Prior to extraction, a volume of miRNeasy Serum/Plasma  Caenorhabditis elegans cel-miR-39-3p mimic Spike-In Control (Qiagen, catalog # 219610) was added to each sample, folowing a 1 μL for each 250 μL of plasma ratio. Elution of total RNA was performed in 75 µL of nuclease-free water, and 70 µL of this RNA eluate was then precipitated, dried and resuspended in 5 μL of nuclease-free water as previously described (PMID: 35246451). The whole volume was used for library preparation.
Samples were randomized before library preparation. The libraries were created using the the Truseq Small RNA Sample Prep kit (Illumina, BC, Canada; catalogue # RS-200- 0012) following  the standard procedure adapted to samples of low RNA concentration by Burgos et al (PMID: 23525801). To maintain an optimal reaction ratio, half of the reagents volumes were used for RNA ligation with adapters at 3′ and 5′ ends, reverse transcription, barcoding (index 1-48: one index per sample) and PCR amplification (15 cycles). Libraries were purified by migration in a Novex polyacrylamide TBE Gel, 6% (ThermoFisher Scientific, Waltham, United States, catalog #EC265BOX). Fragments between 145 and 160 bp were excised and eluted from the gel with 300 µL of nuclease-free water at room temperature, during an overnight incubation at 500 RPM on a microplate shaker (VWR, ON, Canada, catalog #12620-930). Libraries were concentrated by precipitation following manufacturer's instructions, briefly with a 30 minutes incubation at -80°C, and resuspended in 25 µL of 10 mM Tris-HCl pH 8.5 buffer. Libraries sequencing, including quality control and sample pooling, was performed at the Centre d’expertise et de services Génome Québec (Montréal, Canada). The Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) was used to assess the quality of each library (i.e., concentration, library length and primer dimers absence).  Librairies were pooled equimolarly (200 pM final molarity; 48 libraries with different indexes per lane), denatured and clustered on an Illumina NovaSeq S1 flowcell following the Xp protocol from manufacturer’s recommendations. The sequencing run was performed for 100 cycles in single-end mode, on a NovaSeq 6000 platform.

value: umilical cord plasma

tag: fetal sex

value: male

tag: gestational age_at_birth_(weeks)

tag: delivery type

value: vaginal

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: Primary PCa, patient with no bone metastasis, donor NR_10

city: Melbourne

first: xin

last: liu

address: 305 Graattan St

country: Australia

institute: Peter mac

description: Library name: NR_10_RARP

data_processing:
RNA-seq analysis was performed in R (v4.1.0). Clean reads (no adapter contamination, < 20% undecided bases, > 50% high quality bases) were aligned using the RSubread package (v2.8.1). An index was built using the Ensembl Homo sapiens GRCh38 primary assembly genome file and alignment was performed using subjunc with default settings.
Gene counts were obtained using featureCounts using the Ensembl Homo sapiens GRCm38 version 105 GTF annotation file, with isPairedEnd = TRUE, useMetaFeatures = TRUE and strandSpecific = 0.
Ensembl gene IDs were annotated using the biomaRt package (v2.50.1) and a DGEList object was created with the counts and gene annotation using the edgeR package (v3.36.0). A design matrix was constructed incorporating the sample group (NBmRC, BmRC, LN or Bone met).
Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method. Counts were transformed using the voom method and a linear model was fit using the edgeR voomLmFit function, incorporating sample weights and using donor as a blocking factor.
Differential gene expression analyses were performed using the limma (v3.50.0) package. Groups were compared using the contrasts.fit function and moderated t-statistics were calculated using the treat function with a 1.2-fold cut-off. Differentially expressed genes were determined using a false discovery rate-adjusted (FDR) p-value < 0.05.
Assembly: hg38
Supplementary files format and content: PCa_Met_processed.xlsx contains processed counts (tab 1) and voom-transformed expression values (tab 2).

source_name: Primary adenocarcinoma

extract_protocol:
Total RNA was extracted from fresh frozen tissue (n = 50) using the AllPrep DNA/RNA Mini kit (Qiagen, Maryland U.S.A) according to manufacturer’s instructions. RNA yield was quantified using the Qubit RNA High Sensitivity Assay (Invitrogen) with the Qubit 2.0 Fluorometer. RNA quality was assessed using the RNA 6000 Pico Kit on the Agilent 2100 Bioanalyzer.
One microgram of total RNA (RIN > 6.5) was used as input into the TruSeq RNA Sample Preparation Kit v2 (Illumina). cDNA fragments were end repaired, adenylated, adaptors-ligated, purified and PCR enriched. Two samples did not pass pre-sequencing QC (RC_02_RARP, RC_17_RARP). Sequencing (n = 48) was performed on the Illumina HiSeq3000 (PE-150, 20 million paired reads per sample) by Novogene Bioinformatics (Hong Kong).

value: Primary adenocarcinoma

tag: donor

tag: cancer type

value: Prostate cancer

tag: group

value: NBmRC

tag: group description

value: NBmRC denotes non-metastatic primary tumor tissue

tag: age at_diagnosis

tag: path ggs

tag: clinical tumor_stage


title: umbilical cord plasma, Gen3G, PubM2829

description: Library name: Gen3G_UCP_PubM2829

tag: tissue

tag: fetal sex

value: female

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)


title: PCa bone metastases, donor RC_09

description: Library name: RC_09_MET

source_name: Bone metastases

value: Bone metastases

value: Bone met denotes tissue from PCa bone metastases


title: Primary PCa, patient with bone-metastatic disease, donor RC_07

description: Library name: RC_07_RARP

value: BmRC

value: BmRC denotes primary tumor tissue from patient with bone-metastatic PCa


title: umbilical cord plasma, Gen3G, PubM2785

description: Library name: Gen3G_UCP_PubM2785

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)


title: umbilical cord plasma, Gen3G, PubM2183

description: Library name: Gen3G_UCP_PubM2183

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: umbilical cord plasma, Gen3G, PubM2576

description: Library name: Gen3G_UCP_PubM2576


title: Primary PCa, patient with no bone metastasis, donor NR_06

description: Library name: NR_06_RARP

tag: donor

tag: cancer type

tag: group

tag: group description

tag: age at_diagnosis

tag: path ggs


title: umbilical cord plasma, Gen3G, PubM2541

description: Library name: Gen3G_UCP_PubM2541

tag: tissue

tag: fetal sex

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)


title: PCa bone metastases, donor RC_01

description: Library name: RC_01_MET

tag: clinical tumor_stage


title: umbilical cord plasma, Gen3G, PubM2058

description: Library name: Gen3G_UCP_PubM2058

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity


title: Primary PCa, patient with no bone metastasis, donor NR_13

description: Library name: NR_13_RARP

tag: donor

tag: cancer type


title: Primary PCa, patient with bone-metastatic disease, donor NR_05

description: Library name: NR_05_RARP

tag: group

tag: group description


title: umbilical cord plasma, Gen3G, PubM2005

description: Library name: Gen3G_UCP_PubM2005

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: Primary PCa, patient with no bone metastasis, donor NR_04

description: Library name: NR_04_RARP

tag: tissue

tag: age at_diagnosis

tag: path ggs


title: umbilical cord plasma, Gen3G, PubM2831

description: Library name: Gen3G_UCP_PubM2831

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)


title: Primary PCa, patient with no bone metastasis, donor NR_11

description: Library name: NR_11_RARP

tag: clinical tumor_stage


title: umbilical cord plasma, Gen3G, PubM2777

description: Library name: Gen3G_UCP_PubM2777

tag: delivery type

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity


title: Primary PCa, patient with no bone metastasis, donor NR_03

description: Library name: NR_03_RARP

tag: donor

tag: cancer type

tag: group

tag: group description


title: Primary PCa, patient with no bone metastasis, donor NR_02

description: Library name: NR_02_RARP

tag: tissue

tag: age at_diagnosis


title: umbilical cord plasma, Gen3G, PubM2662

description: Library name: Gen3G_UCP_PubM2662

tag: fetal sex

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: umbilical cord plasma, Gen3G, PubM2274

description: Library name: Gen3G_UCP_PubM2274

tag: gestational age_at_birth_(weeks)

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)


title: Primary PCa, patient with bone-metastatic disease, donor NR_09

description: Library name: NR_09_RARP

tag: path ggs

tag: clinical tumor_stage


title: Primary PCa, patient with bone-metastatic disease, donor NR_01

description: Library name: NR_01_RARP

tag: donor


title: CD8 T Cells Control_3

city: Wuhan

first: jianhong

last: zhao

state: Hubei

address: Donghu Road, No. 115

country: China

institute: Wuhan University

description: Library name: CD8 T Cells Control3

data_processing:
Raw sequencing reads were processed using Skewer for adapter trimming and low-quality read filtering.
Quality assessment of raw and cleaned sequencing data was performed with FastQC software (v0.11.2, RRID: SCR_014583).
Differential expression analysis between experimental groups was conducted using the DESeq2 R package.
Hierarchical cluster analysis of differentially expressed genes (DEGs) was performed in R software (v3.2.0). All p-values were adjusted for multiple testing using the Benjamini-Hochberg (BH) procedure.
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEGs were implemented in R software (v3.2.0) based on the hypergeometric distribution, to identify significantly enriched functional terms and pathways.Gene Set Enrichment Analysis (GSEA) was carried out using GSEA software (v2.2.2, RRID: SCR_003199) to evaluate the enrichment of predefined gene sets.
Assembly: GRCm38/mm10
Supplementary files format and content: sgDnmt3a vs sgNTC-gene-exp.csv
Supplementary files format and content: Zymosterol vs Control-gene-exp.csv

organism: Mus musculus

source_name: CD8+ T cells

extract_protocol:
Total RNA was extracted from three types of samples: tumor tissues from sgNTC/sgDnmt3a MC38-bearing C57BL/6 mice, MC38 cells with or without 5-Aza treatment, and CD8+ T cells with or without zymosterol treatment. RNA isolation was performed using the QIAwave RNA Mini Kit (Qiagen, Cat. No. 74536) following the manufacturer's standard operating procedure.
Strand-specific RNA sequencing libraries were constructed with the TruSeq RNA Sample Preparation Kit (Illumina, Cat. No. RS-122-2001) according to the manufacturer's protocol. All libraries were sequenced on the Illumina NovaSeq 6000 platform by Genergy Biotechnology Corporation (Shanghai, China).

tag: cell line

value: CD8+ T cells

tag: treatment

value: Vehicle


title: umbilical cord plasma, Gen3G, PubM2449

description: Library name: Gen3G_UCP_PubM2449

tag: delivery type

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity


title: CD8 T Cells Control_2

description: Library name: CD8 T Cells Control2


title: umbilical cord plasma, Gen3G, PubM2405

description: Library name: Gen3G_UCP_PubM2405

tag: tissue

tag: fetal sex

value: cesarean

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))


title: umbilical cord plasma, Gen3G, PubM2487

description: Library name: Gen3G_UCP_PubM2487

tag: gestational age_at_birth_(weeks)

tag: birth weight_(g)

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: CD8 T Cells Control_1

description: Library name: CD8 T Cells Control1


title: Primary PCa, patient with bone-metastatic disease, donor NR_08

description: Library name: NR_08_RARP

tag: cancer type

tag: group

tag: group description

tag: age at_diagnosis

tag: path ggs

tag: clinical tumor_stage


title: umbilical cord plasma, Gen3G, PubM2231

description: Library name: Gen3G_UCP_PubM2231

tag: delivery type

tag: z-score birth_weight

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)


title: CD8 T Cells Zymosterol_3

description: Library name: CD8 T Cells Zymosterol3

tag: cell line

tag: treatment

value: treated with 20 μM zymosterol for 24 h


title: umbilical cord plasma, Gen3G, PubM2784

description: Library name: Gen3G_UCP_PubM2784

tag: tissue

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))


title: CD8 T Cells Zymosterol_2

description: Library name: CD8 T Cells Zymosterol2


title: umbilical cord plasma, Gen3G, PubM2568

description: Library name: Gen3G_UCP_PubM2568

tag: birth weight_(g)

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: CD8 T Cells Zymosterol_1

description: Library name: CD8 T Cells Zymosterol1


title: sgNTC_3

description: Library name: sgNTC3

source_name: Tumor tissue

value: Tumor tissue

tag: cell type

value: MC38 mouse colorectal cancer cell line

tag: genotype

value: WT


title: umbilical cord plasma, Gen3G, PubM2519

description: Library name: Gen3G_UCP_PubM2519

value: umilical cord plasma

tag: delivery type

value: vaginal

tag: z-score birth_weight

tag: birth lenght_(cm)


title: umbilical cord plasma, Gen3G, PubM2447

description: Library name: Gen3G_UCP_PubM2447

value: male

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)


title: umbilical cord plasma, Gen3G, PubM2378

description: Library name: Gen3G_UCP_PubM2378

tag: tissue


title: sgNTC_1

description: Library name: sgNTC1

tag: cell line


title: umbilical cord plasma, Gen3G, PubM2489

description: Library name: Gen3G_UCP_PubM2489

tag: fetal sex

tag: gestational age_at_birth_(weeks)


title: sgDnmt_3a_3

description: Library name: sgDnmt3a3

value: Dnmt3a knockout


title: umbilical cord plasma, Gen3G, PubM2466

description: Library name: Gen3G_UCP_PubM2466

tag: gestationnal weight_gain_(kg)

tag: maternal parity


title: sgDnmt_3a_2

description: Library name: sgDnmt3a2


title: umbilical cord plasma, Gen3G, PubM2320

description: Library name: Gen3G_UCP_PubM2320

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))


title: umbilical cord plasma, Gen3G, PubM2833

description: Library name: Gen3G_UCP_PubM2833

tag: birth weight_(g)

tag: sample glycemia_(mmol/l)


title: sgDnmt_3a_1

description: Library name: sgDnmt3a1

tag: cell type


title: umbilical cord plasma, Gen3G, PubM2754

description: Library name: Gen3G_UCP_PubM2754

tag: batch (run_and_region)


title: LUAD stage III tumor sample S3N

city: 广州

first: 丽娟

last: 邵

state: 广东省

address: 梅花村街道

institute: 广东药科大学附属第一医院

description: Library name: S3N

data_processing:
Raw sequencing data (BCL files) were converted to FASTQ format using bcl2fastq v2.20.0. FASTQ files were then processed with Cell Ranger v7.0.0 using the 'cellranger count' pipeline with reference genome GRCh38. The resulting gene-by-cell UMI count matrices were used for downstream analysis.
Assembly: GRCh38 (Ensembl v104)
Supplementary files format and content: Processed data files are provided in two formats: (1) Filtered gene-barcode matrices in MEX format (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) containing UMI counts for each sample; (2) Seurat RDS files containing the integrated dataset with clustering and annotation results.

source_name: lung

growth_protocol: Fresh lung tissue samples (tumor and matched adjacent non-malignant) were obtained from patients undergoing surgical resection. Tissues were immediately placed in cold preservation medium and processed within 2 hours.

extract_protocol:
Tissues were minced into small pieces and enzymatically dissociated using a mixture of collagenase and DNase I. The resulting cell suspension was filtered through a 40 μm strainer to remove debris and aggregates. Red blood cells were lysed using ACK lysis buffer. Viable single cells were collected and resuspended in PBS with 0.04% BSA.
Single-cell RNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3' Kit (v3.1, 10x Genomics) following the manufacturer's protocol. Briefly, single-cell suspensions were loaded onto a Chromium controller to generate single-cell Gel Beads-in-Emulsion (GEMs). After reverse transcription, cDNA was amplified and indexed libraries were prepared.

treatment_protocol: No treatment was applied prior to sample collection.

value: lung

tag: disease state

value: LUAD

tag: Stage

value: stage III


title: siNC-transfected chondrocytes_2

city: 山西

first: Jie

last: Yuan

address: The Second Hospital of Shanxi Medical University

description: Library name: Wt2

data_processing:
Base calling and demultiplexing were performed by the sequencing provider to generate FASTQ files.
Assembly: GRCm39
Supplementary files format and content: Excel workbook gene_count_matrix.xlsx containing gene-level processed expression values across six samples: WT1, WT2, WT3, Rala1, Rala2, and Rala3.

source_name: mouse temporomandibular joint

extract_protocol:
Total RNA was extracted from each sample for bulk RNA sequencing.
RNA-seq libraries were constructed from total RNA and sequenced as paired-end reads on the Illumina NovaSeq 6000

value: mouse temporomandibular joint

value: mouse temporomandibular joint condylar chondrocytes

tag: genotype

value: wild type

tag: treatment

value: siNC-transfected chondrocytes


title: siNC-transfected chondrocytes_3

institute: The Second Hospital of Shanxi Medical University

description: Library name: Wt3


title: siNC-transfected chondrocytes_1

description: Library name: Wt1


title: LUAD stage III tumor sample S3T

institute: 广东药科大学附属第一医院

description: Library name: S3T

source_name: lung tumor

value: lung tumor


title: siRalA-transfected chondrocytes_3

description: Library name: Rala_3

value: RalA knockdown

value: siRalA-transfected chondrocytes


title: LUAD stage I tumor sample S1N

institute: 广东药科大学附属第一医院

description: Library name: S1N

value: stage I


title: LUAD stage I tumor sample S1T

institute: 广东药科大学附属第一医院

description: Library name: S1T


title: siRalA-transfected chondrocytes_2

description: Library name: Rala_2


title: siRalA-transfected chondrocytes_1

description: Library name: Rala_1


title: Adjacent normal tissue N2B (matched to T2B)

institute: 广东药科大学附属第一医院

description: Library name: N2B


title: CHIP_Input_TTX_AP5_shNup153_2

city: Dresden

first: Abhinav

last: Soni

state: Saxony

address: Tatzberg 41

department: Nuclear architecture in neural plasticity and aging

country: Germany

institute: German Center for Neurodegenerative Diseases, Dresden

description:
Library name: L192431
Input CHIP sample collected from primary cortical neurons treated with AAV-shNup153-2 from DIV8 to DIV13 and silenced with TTX/AP5. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.

library_source: genomic

data_processing:
To align ChIP-seq reads, the nf-core/atacseq pipeline was used (v2.0). After alignment and filtering of reads, the nf-core pipeline generated separate bigwig files, which were used for visualization of reads in the IGV browser.
Assembly: mm10
Supplementary files format and content: Processed data files includes bigwig files for each samples.

molecule: genomic DNA

source_name: Primary cortical neurons

growth_protocol: Embryonic cortices (embryonic day 17.5-19.5) (C57/BL6 mice) from one litter were dissected and pooled together to be processed as a single biological replicate. Dissociated primary cortical neurons were plated in Poly-Dl-Ornithine Hydrobromide coated plates. Cells were maintained in incubators at 37°C with a CO2 concentration of 5%. 30% medium was replaced at DIV4 and DIV8 with Brain Phys Neuronal Culture Medium (STEMCELL Tec), supplemented with 2% SM1-NC (STEMCELL Tec).

extract_protocol:
CHIP samples were subjected to Illumina library preparation using the NEBnext Ultra II DNA library preparation chemistry (New England Biolabs, E7645L). The libraries were size-selected with XP beads. The resulting libraries were checked for quality and quantified using a Fragment Analyzer (Agilent) NGS Fragment Kit (1-6000bp). The final libraries were subjected to 100bp paired-end sequencing on the Illumina NovaSeq6000 platform at a depth of 35-55 million fragments per library.
PCNs were collected in theTTX-AP5 state at DIV13. PCNs were fixed by adding 16% formaldehyde (VWR International) directly to the media to a final concentration of 1% for 10 minutes at RT. Residual formaldehyde was quenched by adding 1M glycine (Carl Roth) directly to the media to a final concentration of 0.1M for 15 minutes at RT. After quenching, PCNs were washed twice with cold PBS solution containing protease inhibitor (Sigma Aldrich) (PBS-PI) for five minutes each. Cells were scraped from the plates and collected in a 1.5ml tube, pelleted by centrifugation at 300 G, and washed with PBS-PI. Samples were either stored at -80°C or processed directly for chromatin immunoprecipitation. For ChIP-Seq of H3K27ac, 1.5mM EGS (ethylene glycol bis succinimidyl succinate) was applied for 15 minutes at RT prior to formaldehyde fixation, followed by two 5-minute washes with PBS. A total of two biological replicates were used for ChIP-Seq for each condition. Samples were thawed and lysed in 1 ml of ChIP lysis buffer for 10 min at 4°C on a rotator. Samples were washed in ChIP Wash buffer for 10 min at 4°C and resuspended in ChIP buffer for sonication. Samples were sonicated using a focused-ultrasonicator (Covaris).  After confirming the size of the fragments, the samples were pre-cleaned with 10 µl of Dynabeads Protein G (Life Technologies) for 1 hour at 4°C, and then the samples were incubated with 2 ug of primary antibodies at 4°C overnight on a rotator. The next day, Dynabeads were added into the samples for 2 hours, and the tubes were rotated at 4°C. Dynabeads were separated from the samples using a magnetic stand DynaMagTM (Thermo Fisher). The beads were sequentially washed with low-salt buffer, high-salt buffer, lithium chloride buffer and twice with TE 1X buffer (IDTE). The bound chromatin was eluted from the Dynabeads by incubating it in 100 ul of elution buffer. Following RNase A and proteinase K treatments, DNA was purified using a standard phenol chloroform extraction method.
ChIP samples were subjected to Illumina fragment library preparation using the NEBnext Ultra II DNA library preparation chemistry (New England Biolabs, E7645L). Briefly, DNA fragments were end-repaired, A-tailed and ligated to unique-dual indexed Illumina Truseq adapters (IDT, prehybridized UDI-UMI Adapters for Illumina, 0.15 µM adapter per reaction). The resulting libraries were PCR-amplified for 15 cycles using universal primers (primer 1: CAAGCAGAAGACGGCATACGAGAT and Primer 2: AATGATACGGCGACCACCGA*G; *: Phosphothioate bond) and purified using XP beads (Beckman Coulter). The libraries were size-selected with XP beads. The resulting libraries were checked for quality and quantified using a Fragment Analyzer (Agilent) NGS Fragment Kit (1-6000bp). The final libraries were subjected to 100bp paired-end sequencing on the Illumina NovaSeq6000 platform at a depth of 35-55 million fragments per library.

value: Primary cortical neurons

value: AAV treatment from DIV8 to DIV13 followed by neuronal activity silencing with TTX/AP5 in primary cortical neurons


title: Adjacent normal tissue N2A (matched to T2A)

institute: 广东药科大学附属第一医院

description: Library name: N2A


title: CHIP_Input_TTX_AP5_shControl

description:
Library name: L192430
Input CHIP sample collected from primary cortical neurons treated with AAV-shControl from DIV8 to DIV13 and silenced with TTX/AP5. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.


title: CHIP_H3K27ac_TTX_AP5_shNup153_2_Replicate2

description:
Library name: L192425
H3K27ac CHIP sample collected from primary cortical neurons treated with AAV-shNup153-2 from DIV8 to DIV13 and silenced with TTX/AP5. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.


title: Adjacent normal tissue N1B (matched to T1B)

institute: 广东药科大学附属第一医院

description: Library name: N1B


title: Adjacent normal tissue N1A (matched to T1A)

institute: 广东药科大学附属第一医院

description: Library name: N1A


title: LUAD stage III tumor sample T2B

institute: 广东药科大学附属第一医院

description: Library name: T2B


title: LUAD stage III tumor sample T2A

institute: 广东药科大学附属第一医院

description: Library name: T2A


title: CHIP_H3K27ac_TTX_AP5_shNup153_2_Replicate1

description:
Library name: L192424
H3K27ac CHIP sample collected from primary cortical neurons treated with AAV-shNup153-2 from DIV8 to DIV13 and silenced with TTX/AP5. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.


title: CHIP_H3K27ac_TTX_AP5_shControl_Replicate1

description:
Library name: L192422
H3K27ac CHIP sample collected from primary cortical neurons treated with AAV-shControl from DIV8 to DIV13 and silenced with TTX/AP5. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.


title: CHIP_H3K27ac_TTX_AP5_shControl_Replicate2

description:
Library name: L192423
H3K27ac CHIP sample collected from primary cortical neurons treated with AAV-shControl from DIV8 to DIV13 and silenced with TTX/AP5. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.


title: LUAD stage I tumor sample T1B

institute: 广东药科大学附属第一医院

description: Library name: T1B


title: LUAD stage I tumor sample T1A

institute: 广东药科大学附属第一医院

description: Library name: T1A


title: TrCo+PT-1LVAN (TrCo_A9VP4_Plate8)

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description: Library name: TrCo_and_PT-1LVAN_TrCo_A9VP4_Plate8

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)  The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.         The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates.      Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files. Tab-delimited files (HIC files) describing the chromatin contacts will be generated with in-house developing package using the filtered BAM files.
Assembly: hg38
Supplementary files format and content: An ALLC file contains 7 columns with DNA methylation information of a single cell at single base resolution. The columns are 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.   A contact file contains long range chromatin contacts of a single cell after removing the ones overlapping blacklists. The columns are 1. Strand1, 2. Chromosome1, 3. Position1, 4. place holder column, always be 0, 5. Strand2, 6. Chromosome2, 7. Position2, 8. place holder column, always be 1.
Library strategy: snm3C-seq

source_name: Transverse Colon

extract_protocol:
Nuclei extraction protocol can be found at https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1
Library preparation protocol can be found at https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1

value: Transverse Colon


title: umbilical cord plasma, Gen3G, PubM2159

description: Library name: Gen3G_UCP_PubM2159

value: umilical cord plasma

tag: delivery type

value: cesarean

tag: z-score birth_weight

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)


title: Slc31a1 cKO BMSCs

city: Changchun

first: Yuhang

last: Jiang

state: Jilin

address: No.461 Xinjiang Road

department: Institute of Translational Medicine

institute: The First Hospital of Jilin University

description:
Library name: Sample 2
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline (10x Genomics) for demultiplexing, barcode processing, alignment to the mm10 mouse reference genome, UMI counting, and generation of gene-by-cell count matrices.
Downstream single-cell analysis was performed using the Seurat R package. Quality control excluded cells with fewer than 200 detected genes or greater than 10% mitochondrial gene content, and putative doublets were removed using DoubletFinder.
Filtered data were log-normalized and scaled before principal component analysis (PCA). Cell clustering was performed using a shared nearest neighbor (SNN) modularity optimization algorithm, and UMAP was used for visualization.
Prrx1-positive mesenchymal lineage cells were subset for re-clustering. Differential gene expression was analyzed using the Wilcoxon rank-sum test, and pathway enrichment analysis was performed using the KEGG database.
Assembly: Mus musculus mm10 (GRCm38)
Supplementary files format and content: Processed data consist of Cell Ranger filtered gene/feature-barcode expression matrices for each sample. Matrix files may be provided as Matrix Market files (matrix.mtx.gz) with matching barcodes.tsv.gz. Values represent UMI counts per gene per cell.

source_name: Bonemarrow

growth_protocol: Slc31a1flox/flox mice and Prrx1-Cre+/-; Slc31a1flox/flox conditional knockout mice were maintained on a C57BL/6J background under specific pathogen-free conditions with a 12 h light/dark cycle and free access to food and water. Bone marrow cells were flushed from femurs and tibias of mice with alpha-MEM and seeded in culture plates in complete medium consisting of alpha-MEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 ug/mL streptomycin at 37 degrees C with 5% CO2. Non-adherent cells were removed after 48 h.

extract_protocol:
Adherent BMSCs were harvested from culture, washed, and prepared as single-cell suspensions for 10x Genomics loading. Cell viability was confirmed to be greater than 85% before library preparation. In the 10x Genomics Chromium workflow, cells were partitioned into gel bead-in-emulsions (GEMs), and mRNA from individual cells was reverse-transcribed and barcoded to generate single-cell cDNA libraries.
Single-cell RNA-seq libraries were prepared by OE Biotech Co., Ltd. (Shanghai, China) using the 10x Genomics Chromium platform and Chromium Single Cell 3' Reagent Kits v3 according to the manufacturer's protocol. Gel bead-in-emulsions were generated, followed by reverse transcription, cDNA amplification, and library construction using standard 10x Genomics workflows. Qualified libraries were sequenced on an Illumina NovaSeq 6000 platform to generate paired-end reads.

treatment_protocol: No exogenous in vitro drug, dietary, or osteogenic induction treatment was applied to the cells used for this scRNA-seq comparison before single-cell capture. The experimental perturbation was genetic deletion of Slc31a1 in Prrx1-lineage mesenchymal cells (Prrx1-Cre+/-; Slc31a1flox/flox) compared with Slc31a1flox/flox wild-type littermate controls.

tag: tissue

value: Bonemarrow

tag: cell line

value: BMSC

value: Mesenchymal stem cells

value: KO

value: No

tag: batch


title: WT BMSCs

description:
Library name: Sample 1
10X Genomics

value: WT


title: TrCo+PT-1LVAN (TrCo_A9VP4_Plate6)

description: Library name: TrCo_and_PT-1LVAN_TrCo_A9VP4_Plate6


title: TrCo+PT-1LVAN (TrCo_A9VP4_Plate7)

description: Library name: TrCo_and_PT-1LVAN_TrCo_A9VP4_Plate7


title: Slc31a1-cKO BMSCs Input

description: Library name: Sample 4

data_processing:
Raw sequencing reads were trimmed to remove adapter sequences and low-quality bases. Clean reads were aligned to the mouse reference genome mm10 using Bowtie2. PCR duplicate reads were removed. H3K9ac peaks were called using MACS2 with corresponding input DNA as control. H3K9ac signal distribution around transcription start sites and selected genomic loci, including the Id1 locus, was visualized using deepTools and Integrative Genomics Viewer.
Assembly: Mus musculus mm10 / GRCm38
Supplementary files format and content: Processed data include normalized bigWig files representing genome-wide H3K9ac ChIP-seq enrichment signals for each sample. The bigWig files can be used for genome browser visualization of normalized H3K9ac signals.

growth_protocol: All mice were maintained on a C57BL/6J background under specific pathogen-free conditions with a 12-hour light/dark cycle and free access to food and water. Mesenchymal lineage-specific Slc31a1 conditional knockout mice were generated by crossing Slc31a1 flox/flox mice with Prrx1-Cre mice, and Slc31a1 flox/flox littermates were used as wild-type controls. Bone marrow cells were flushed from femurs and tibias of 4-week-old mice with alpha-MEM. Cells were seeded in 60-mm culture plates and cultured in complete medium consisting of alpha-MEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C in 5% CO2. Non-adherent cells were removed by PBS washing after 48 hours, and adherent BMSCs were maintained.

extract_protocol:
For H3K9ac ChIP-seq, WT and Slc31a1 cKO BMSCs were crosslinked with 1% formaldehyde for 10 minutes at room temperature, and the reaction was quenched with 125 mM glycine for 5 minutes. Cells were washed with cold PBS, collected, and lysed in ChIP lysis buffer containing protease inhibitors. Chromatin was sheared by sonication to an average fragment size of approximately 200–500 bp. A fraction of sheared chromatin was saved as input DNA after clarification, and the remaining chromatin was incubated overnight at 4°C with anti-H3K9ac antibody. Immune complexes were captured using Protein A/G magnetic beads, washed sequentially with low-salt, high-salt, LiCl, and TE buffers, and eluted. ChIP DNA and corresponding input DNA were purified for downstream library preparation.
Purified H3K9ac ChIP DNA and corresponding input DNA were used for sequencing library preparation with a low-input DNA library preparation kit according to the manufacturer’s protocol. Libraries were amplified, purified, and assessed for quality and concentration before sequencing. Qualified libraries were sequenced on an Illumina platform.

treatment_protocol: No pharmacological or chemical treatment was applied to the ChIP-seq samples. The experimental variable was genotype: wild-type Slc31a1 flox/flox control BMSCs versus Prrx1-Cre; Slc31a1 flox/flox conditional knockout BMSCs. WT and Slc31a1 cKO BMSCs were cultured and processed under the same conditions before H3K9ac ChIP-seq.

tag: chip antibody


title: TrCo+PT-1LVAN (TrCo_A9VP4_Plate5)

description: Library name: TrCo_and_PT-1LVAN_TrCo_A9VP4_Plate5


title: Slc31a1-cKO BMSCs H3K9ac ChIP

description: Library name: Sample 2


title: WT BMSCs Input

description: Library name: Sample 3


title: umbilical cord plasma, Gen3G, PubM2430

description: Library name: Gen3G_UCP_PubM2430

tag: fetal sex

value: female

tag: gestational age_at_birth_(weeks)

value: vaginal

tag: birth weight_(g)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))


title: WT BMSCs H3K9ac ChIP

description: Library name: Sample 1

tag: cell type

tag: genotype


title: umbilical cord plasma, Gen3G, PubM2733

description: Library name: Gen3G_UCP_PubM2733

tag: delivery type

tag: z-score birth_weight

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: TrCo+PT-1LVAN (TrCo_A9VP4_Plate4)

description: Library name: TrCo_and_PT-1LVAN_TrCo_A9VP4_Plate4

tag: tissue


title: umbilical cord plasma, Gen3G, PubM2018

description: Library name: Gen3G_UCP_PubM2018

value: male

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)


title: TrCo+PT-1LVAN (TrCo_A9VP4_Plate3)

description: Library name: TrCo_and_PT-1LVAN_TrCo_A9VP4_Plate3


title: Slc31a1 cKO BMSCs

description:
Library name: Sample 2
Clean reads were aligned to the mouse reference genome mm10 using Bowtie2.

data_processing:
Raw paired-end reads were trimmed to remove adapter sequences and low-quality bases. Clean reads were aligned to the mouse reference genome mm10 using Bowtie2. PCR duplicate reads, mitochondrial reads, and reads mapping to blacklisted genomic regions were removed. Open chromatin peaks were called using MACS2. Peak annotation and genomic distribution analyses were performed using HOMER, ChIPseeker, or equivalent R packages. Differential chromatin accessibility analysis was performed between WT and Slc31a1 cKO BMSCs. Normalized bigWig files were generated for genome browser visualization.
Assembly: Mus musculus mm10 / GRCm38
Supplementary files format and content: Processed data include normalized bigWig files representing genome-wide ATAC-seq accessibility signal for each sampls. The bigWig files can be used for genome browser visualization of normalized chromatin accessibility signals.

growth_protocol: All mice were maintained on a C57BL/6J background under specific pathogen-free conditions with a 12-hour light/dark cycle and free access to food and water. Mesenchymal lineage-specific Slc31a1 conditional knockout mice were generated by crossing Slc31a1 flox/flox mice with Prrx1-Cre mice; Slc31a1 flox/flox littermates were used as wild-type controls. Bone marrow cells were flushed from femurs and tibias of 4-week-old mice with alpha-MEM. Cells were seeded in 60-mm culture dishes and cultured in complete medium consisting of alpha-MEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C in 5% CO2. Non-adherent cells were removed by PBS washing after 48 hours.

extract_protocol:
ATAC-seq was performed using freshly harvested WT and Slc31a1 cKO BMSCs. Approximately 50,000 viable cells per sample were washed with cold PBS and lysed in ice-cold nuclei isolation buffer. Nuclei were collected by centrifugation and subjected to Tn5 transposition in transposition buffer at 37°C for 30 minutes. Tagmented DNA was then purified for library amplification.
Tagmented DNA generated by Tn5 transposition was amplified by PCR using indexed primers. Libraries were purified using AMPure XP beads and assessed for size distribution and concentration using an Agilent Bioanalyzer or equivalent platform. Qualified ATAC-seq libraries were sequenced on an Illumina platform to generate paired-end reads.

treatment_protocol: No pharmacological or chemical treatment was applied to the ATAC-seq samples. The experimental variable was genotype: wild-type Slc31a1 flox/flox control BMSCs versus Prrx1-Cre; Slc31a1 flox/flox conditional knockout BMSCs. WT and Slc31a1 cKO BMSCs were harvested and processed under the same conditions for ATAC-seq.

tag: cell line

tag: treatment


title: WT BMSCs

description:
Library name: Sample 1
Clean reads were aligned to the mouse reference genome mm10 using Bowtie2.


title: Primary PCa, patient with bone-metastatic disease, donor RC_11

description: Library name: RC_11_RARP

value: Primary adenocarcinoma

tag: donor

tag: cancer type

value: Prostate cancer

tag: group

value: BmRC

tag: group description

value: BmRC denotes primary tumor tissue from patient with bone-metastatic PCa

tag: age at_diagnosis

tag: path ggs

tag: clinical tumor_stage


title: PCa bone metastases, donor RC_10

description: Library name: RC_10_MET

value: Bone metastases

value: Bone met denotes tissue from PCa bone metastases


title: WT3

city: Saint Louis

first: laura

last: schuettpelz

state: MO

address: 660 S. Euclid

institute: washington university

description: Library name: Sample 8

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 101 top-level assembly with STAR version 2.7.9a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3.
Assembly: Ensembl_R101
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Bone marrow

extract_protocol:
HSCs were double sorted directly into lysis buffer. RNA was isolated using the NucleoSpin RNA XS Kit (Machery-Nagel, Bethlehem, PA, USA).
Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol.

value: Bone marrow

value: primary cells

tag: cell type

value: Hematopoietic stem cell

tag: genotype


title: TrCo+PT-1LVAN (TrCo_A9VP4_Plate1)

description: Library name: TrCo_and_PT-1LVAN_TrCo_A9VP4_Plate1

value: Transverse Colon


title: TrCo+PT-1LVAN (TrCo_A9VP4_Plate2)

description: Library name: TrCo_and_PT-1LVAN_TrCo_A9VP4_Plate2


title: TrCo+PT-1LGRB (TrCo_A9HOW_Plate8)

description: Library name: TrCo_and_PT-1LGRB_TrCo_A9HOW_Plate8


title: sgNTC_2

description: Library name: sgNTC2

value: Tumor tissue

value: MC38 mouse colorectal cancer cell line


title: TrCo+PT-1LGRB (TrCo_A9HOW_Plate6)

description: Library name: TrCo_and_PT-1LGRB_TrCo_A9HOW_Plate6


title: umbilical cord plasma, Gen3G, PubM2776

description: Library name: Gen3G_UCP_PubM2776

value: umilical cord plasma

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: birth weight_(g)

tag: z-score birth_weight

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)


title: TrCo+PT-1LGRB (TrCo_A9HOW_Plate7)

description: Library name: TrCo_and_PT-1LGRB_TrCo_A9HOW_Plate7

tag: tissue


title: WT2

description: Library name: Sample 9

tag: cell line

value: WT


title: umbilical cord plasma, Gen3G, PubM2633

description: Library name: Gen3G_UCP_PubM2633

value: female

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: batch (run_and_region)


title: WT4

description: Library name: Sample 7

tag: cell type

tag: genotype


title: TrCo+PT-1LGRB (TrCo_A9HOW_Plate4)

description: Library name: TrCo_and_PT-1LGRB_TrCo_A9HOW_Plate4


title: KO1

description: Library name: Sample 5

value: KO


title: TrCo+PT-1LGRB (TrCo_A9HOW_Plate5)

description: Library name: TrCo_and_PT-1LGRB_TrCo_A9HOW_Plate5


title: KO2

description: Library name: Sample 4


title: WT5

description: Library name: Sample 6


title: TrCo+PT-1LGRB (TrCo_A9HOW_Plate3)

description: Library name: TrCo_and_PT-1LGRB_TrCo_A9HOW_Plate3


title: WT1

description: Library name: Sample 10


title: KO3

description: Library name: Sample 3


title: SkGcn+PT-1LVAN (SkGcn_C1PWV_Plate8)

description: Library name: SkGcn_and_PT-1LVAN_SkGcn_C1PWV_Plate8

source_name: Gastrocnemius Medialis

value: Gastrocnemius Medialis


title: TrCo+PT-1LGRB (TrCo_A9HOW_Plate1)

description: Library name: TrCo_and_PT-1LGRB_TrCo_A9HOW_Plate1


title: KO5

description: Library name: Sample 1


title: TrCo+PT-1LGRB (TrCo_A9HOW_Plate2)

description: Library name: TrCo_and_PT-1LGRB_TrCo_A9HOW_Plate2


title: Experiment 216 (lung from WT and Clec1a deficient mice at day 1 after secondary E Coli infection) HTO

city: Nantes

first: Elise

last: Chiffoleau

address: 30 Bd jean Monnet CHU

country: France

description:
Library name: Sample 5_HTO
10X genomics
TO216_barcodes.tsv.gz
TO216_features.tsv.gz
TO216_matrix.mtx.gz
TO216_feature_reference.csv

library_source: other

data_processing:
Libraries were sequenced with an Illumina NovaSeq 6000. Sequenced data were processed using the Cellranger-7.2.0 pipeline for sample demultiplexing, sequence alignment, barcode processing and unique molecular identity (UMI) counting. Filtered matrixes were processed and cells containing more than 5% of mitochondrial genes were filtered off.
Dataset integration, clustering and differential gene expression was performed using the Seurat package (v4.4.0).
Gene Set Enrichment Analysis (GSEA) was performed using the fgsea package (v.1.32.4).
GSEA results were visualized using ggplot2 (v3.5.2).
Assembly: mm10
Supplementary files format and content: Tab separated values barcodes, features and matrix files as tsv formats

molecule: protein

extract_protocol:
Cells were incubated with TotalSeq barcoded-antibodies for each sample, in order to identify their origin after RNA library creation. Approximately 16,000 cells per reaction were processed using a 10X Chromium Next Controller following the 3’ V3 protocol.
RNA libraries were then prepared using the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (PN-120267) and Chromium Next GEM Single Cell 3′ Library and Gel Bead Kit v3.1 (PN-1000121) (10X Genomics)

treatment_protocol: C57BL/6 Clec1a KO or WT mice were intratracheally injected with 75 µl of E. coli DH5-α suspension (MCF=0,7), lungs were instilled intratracheally with 3 mL of dispase solution at day 1 or 3 after infection, recovered and placed into a tube containing 3 mL of dispase diluted by 1:10 in HBSS for 30 min at room temperature. Lungs were dissociated and cells were sorted by FACS ARIA in order to reduce the predominant neutrophil population and to enrich in endothelial cells for scRNAseq experiments, purified cells were mixed with as follow (6·105 CD45+ Ly6G- cells, 3·105 CD45+ cells and 1·105 CD45- CD31+ cells).

value: lung

tag: strain

value: mixed sample (C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates)

tag: Sex

value: male

tag: treatment

value: HTO1:WT1 day 1 ; HTO2:WT2 day 1 ; HTO3:KO1 day 1 ; HTO4:KO2 day 1 secondary infection

tag: age

value: 8-12 weeks old

tag: time

value: day 1 after E. Coli infection

tag: library

value: HTO

tag: multiplexed sample

value: sample 5


title: Experiment 173 (lung from WT and Clec1a deficient mice at day 1 after primary E Coli infection) HTO

description:
Library name: Sample 4_HTO
10X genomics
TO173_barcodes.tsv.gz
TO173_features.tsv.gz
TO173_matrix.mtx.gz
TO173_feature_reference.csv

value: HTO5:WT1 day 1 ; HTO6:WT2 day 1 ; HTO7:KO1 day 1 ; HTO8:KO2 day 1 primary infection

value: sample 4


title: Experiment 171 (lung from WT and Clec1a deficient mice at day 3 after primary E Coli infection) HTO

description:
Library name: Sample 3_HTO
10X genomics
TO171_barcodes.tsv.gz
TO171_features.tsv.gz
TO171_matrix.mtx.gz
TO171_feature_reference.csv

value: HTO1:WT1 day 3 ; HTO2:WT2 day 3 ; HTO3:KO1 day 3 ; HTO4:KO2 day 3 primary infection

value: day 3 after E. Coli infection

value: sample 3


title: SkGcn+PT-1LVAN (SkGcn_C1PWV_Plate3)

description: Library name: SkGcn_and_PT-1LVAN_SkGcn_C1PWV_Plate3


title: Experiment 120 (lung from WT and Clec1a deficient mice at day 3 after primary E Coli infection) HTO

description:
Library name: Sample 2_HTO
10X genomics
TO120_barcodes.tsv.gz
TO120_features.tsv.gz
TO120_matrix.mtx.gz
TO120_feature_reference.csv

value: HTO5:WT1 day 3 ; HTO6:WT2 day 3 ; HTO7:KO1 day 3 ; HTO8:KO2 day 3 primary infection

value: sample 2


title: SkGcn+PT-1LVAN (SkGcn_C1PWV_Plate6)

description: Library name: SkGcn_and_PT-1LVAN_SkGcn_C1PWV_Plate6


title: SkGcn+PT-1LVAN (SkGcn_C1PWV_Plate7)

description: Library name: SkGcn_and_PT-1LVAN_SkGcn_C1PWV_Plate7


title: Experiment 119 (lung from WT and Clec1a deficient mice at day 1 after primary E Coli infection) HTO

description:
Library name: Sample 1_HTO
10X genomics
TO119_barcodes.tsv.gz
TO119_features.tsv.gz
TO119_matrix.mtx.gz
TO119_feature_reference.csv

value: HTO1:WT1 day 1 ; HTO2:WT2 day 1 ; HTO3:KO1 day 1 ; HTO4:KO2 day 1 primary infection

value: sample 1


title: Experiment 217 (lung from WT and Clec1a deficient mice at day 3 after secondary E Coli infection) HTO

description:
Library name: Sample 6_HTO
10X genomics
TO217_barcodes.tsv.gz
TO217_features.tsv.gz
TO217_matrix.mtx.gz
TO217_feature_reference.csv

value: lung

value: HTO5:WT1 day 3 ; HTO6:WT2 day 3 ; HTO7:KO1 day 3 ; HTO8:KO2 day 3 secondary infection

value: sample 6


title: SkGcn+PT-1LVAN (SkGcn_C1PWV_Plate2)

description: Library name: SkGcn_and_PT-1LVAN_SkGcn_C1PWV_Plate2

value: Gastrocnemius Medialis


title: Experiment 217 (lung from WT and Clec1a deficient mice at day 3 after secondary E Coli infection) scRNAseq

description:
Library name: Sample 6_mRNA
10X genomics
TO217_barcodes.tsv.gz
TO217_features.tsv.gz
TO217_matrix.mtx.gz
TO217_feature_reference.csv

value: mixed sample (C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates)

value: male

value: 8-12 weeks old

value: mRNA


title: SkGcn+PT-1K2DA (SkGcn_C1MKW_Plate8)

description: Library name: SkGcn_and_PT-1K2DA_SkGcn_C1MKW_Plate8


title: SkGcn+PT-1K2DA (SkGcn_C1MKW_Plate7)

description: Library name: SkGcn_and_PT-1K2DA_SkGcn_C1MKW_Plate7


title: Experiment 171 (lung from WT and Clec1a deficient mice at day 3 after primary E Coli infection) scRNAseq

description:
Library name: Sample 3_mRNA
10X genomics
TO171_barcodes.tsv.gz
TO171_features.tsv.gz
TO171_matrix.mtx.gz
TO171_feature_reference.csv


title: Experiment 216 (lung from WT and Clec1a deficient mice at day 1 after secondary E Coli infection) scRNAseq

description:
Library name: Sample 5_mRNA
10X genomics
TO216_barcodes.tsv.gz
TO216_features.tsv.gz
TO216_matrix.mtx.gz
TO216_feature_reference.csv

value: HTO1:WT1 day 1 ; HTO2:WT2 day 1 ; HTO3:KO1 day 1 ; HTO4:KO2 day 1 secondary infection

value: day 1 after E. Coli infection

value: sample 5


title: Experiment 173 (lung from WT and Clec1a deficient mice at day 1 after primary E Coli infection) scRNAseq

description:
Library name: Sample 4_mRNA
10X genomics
TO173_barcodes.tsv.gz
TO173_features.tsv.gz
TO173_matrix.mtx.gz
TO173_feature_reference.csv

value: HTO5:WT1 day 1 ; HTO6:WT2 day 1 ; HTO7:KO1 day 1 ; HTO8:KO2 day 1 primary infection

value: sample 4


title: SkGcn+PT-1K2DA (SkGcn_C1MKW_Plate6)

description: Library name: SkGcn_and_PT-1K2DA_SkGcn_C1MKW_Plate6


title: SkGcn+PT-1K2DA (SkGcn_C1MKW_Plate5)

description: Library name: SkGcn_and_PT-1K2DA_SkGcn_C1MKW_Plate5


title: Experiment 119 (lung from WT and Clec1a deficient mice at day 1 after primary E Coli infection) scRNAseq

description:
Library name: Sample 1_mRNA
10X genomics
TO119_barcodes.tsv.gz
TO119_features.tsv.gz
TO119_matrix.mtx.gz
TO119_feature_reference.csv


title: Experiment 120 (lung from WT and Clec1a deficient mice at day 3 after primary E Coli infection) scRNAseq

description:
Library name: Sample 2_mRNA
10X genomics
TO120_barcodes.tsv.gz
TO120_features.tsv.gz
TO120_matrix.mtx.gz
TO120_feature_reference.csv

value: HTO5:WT1 day 3 ; HTO6:WT2 day 3 ; HTO7:KO1 day 3 ; HTO8:KO2 day 3 primary infection

value: day 3 after E. Coli infection


title: SkGcn+PT-1K2DA (SkGcn_C1MKW_Plate4)

description: Library name: SkGcn_and_PT-1K2DA_SkGcn_C1MKW_Plate4


title: cDC1, Clec1a WT6_n4_ns

description:
Library name: Sample 240
TO241_DGEseq.unq.refseq.umi.dat

data_processing:
An average of 5 million 75 bp single-end reads were obtained for each sample.
Samples were demultiplexed and aligned to the GRCm38 (mm10) genome using the DGE bioinformatics pipeline.
Post-sequencing, data demultiplexing was performed using Illumina bcl2fastq.
The resulting FASTQ files were analyzed using the 3’ Sequencing RNA Profiling (SRP) pipeline
Assembly: mm10
Supplementary files format and content: Digital gene expression (DGE) profiles were generated by counting the number of unique UMIs associated with each RefSeq gene for each sample and expressed in .dat format

source_name: spleen

extract_protocol:
5,000 cells were incubated in lysis buffer containing 0.16uL 10% Triton X-100, 0.08 uL RNAse Out (40U/µL, Invitrogen) and 3.75 µL RNAse DNAse free water
Lyzed cells were loaded on a 96-plate using an OT-2 library prep robot (Opentrons). 1uL barcoded RT-primers with universal adapters, well-specific barcodes, and unique molecular identifiers were then added to the wells and incubated at 72°C for 3 min before reverse transcription. Barcoded complementary DNAs from multiple samples were then pooled, amplified, and tagmented using a transposon fragmentation approach which enriches for 3′ ends of complementary DNA.

treatment_protocol: Spleen from WT and Clec1a KO mice were recovered, minced and incubated with collagenase IV for 45 minutes at 37°C (Roche, cat: 11088882001). The resulting cell suspension was then enriched in cDC1s by incubation with a DC isolation kit (Milteny, cat: 130-091-169) and sorted with an AutoMACS separator. The resulting cell suspension was then stained with fluorochrome-conjugated antibodies and purified cDC1s were sorted by FACS (based on the expression of CD11c, MHC-II and XCR1) using a Cytek Aurora spectral flow cytometer. Purified cDC1s were then plated in flat-bottom 96-well plates and stimulated with E. coli (MOI = 10), MCA-OVA UV-treated cells (ratio 1:10) or recombinant mouse IFNβ (1000 U/ml, BioTechne R&D Systems cat: 8234-MB-010) for 6h. Then, cells were extensively washed and harvested for RNAseq experiments.

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: type 1 conventional dendritic cells

value: Clec1a WT

value: Non stimulated


title: SkGcn+PT-1K2DA (SkGcn_C1MKW_Plate2)

description: Library name: SkGcn_and_PT-1K2DA_SkGcn_C1MKW_Plate2

value: Gastrocnemius Medialis


title: cDC1, Clec1a WT6_n4_necrocoli

description:
Library name: Sample 239
TO241_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells plus E Coli


title: cDC1, Clec1a WT6_n4_ifn

description:
Library name: Sample 237
TO241_DGEseq.unq.refseq.umi.dat

value: stimulated with type I IFN


title: cDC1, Clec1a WT6_n3_necro

description:
Library name: Sample 233
TO241_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: stimulated with necrotic cells


title: cDC1, Clec1a WT6_n3_ifn

description:
Library name: Sample 232
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT6_n3_necrocoli

description:
Library name: Sample 234
TO241_DGEseq.unq.refseq.umi.dat


title: SkGcn+PT-1K2DA (SkGcn_C1MKW_Plate1)

description: Library name: SkGcn_and_PT-1K2DA_SkGcn_C1MKW_Plate1


title: cDC1, Clec1a WT6_n2_ns

description:
Library name: Sample 230
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT6_n2_necro

description:
Library name: Sample 228
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT6_n2_ecoli

description:
Library name: Sample 226
TO241_DGEseq.unq.refseq.umi.dat

value: stimulated with E Coli


title: cDC1, Clec1a WT6_n2_necrocoli

description:
Library name: Sample 229
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT6_n1_ns

description:
Library name: Sample 225
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT6_n1_necro

description:
Library name: Sample 223
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT6_n1_ifn

description:
Library name: Sample 222
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT6_n1_necrocoli

description:
Library name: Sample 224
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT6_n1_ecoli

description:
Library name: Sample 221
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n4_necro

description:
Library name: Sample 218
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n3_ns

description:
Library name: Sample 215
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n4_ecoli

description:
Library name: Sample 216
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n3_necro

description:
Library name: Sample 213
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n3_necrocoli

description:
Library name: Sample 214
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n3_ifn

description:
Library name: Sample 212
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n3_ecoli

description:
Library name: Sample 211
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n2_ns

description:
Library name: Sample 210
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n2_necrocoli

description:
Library name: Sample 209
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n2_necro

description:
Library name: Sample 208
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n2_ecoli

description:
Library name: Sample 206
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n2_ifn

description:
Library name: Sample 207
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n1_ns

description:
Library name: Sample 205
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n1_necrocoli

description:
Library name: Sample 204
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT5_n1_necro

description:
Library name: Sample 203
TO241_DGEseq.unq.refseq.umi.dat


title: UH rep4

city: changsha

first: Huilin

middle: huilin

last: Yang

state: huannan

address: Donghu Street

institute: Hunan Agricultural University

description: Library name: sample 16

data_processing:
Illumina Novaseq platform were used for basecalling.
Please refer to QC report for methods of sample quality control.
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

organism: Pardosa pseudoannulata

source_name: whole spider

extract_protocol:
Fast RNA-seg Lib Prep Kit V2(Cat.No.RK20306)；
RNA libraries were prepared for sequencing using standard Illumina protocols
Messenger RNAwaspurified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was  synthesized using random hexamer primers followed by the second  strand cDNA synthesis. The library was ready after end repair, A-tailing,  adapter ligation, size selection, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification  and bioanalyzer for size distribution detection.
Messenger RNAwaspurified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was  synthesized using random hexamer primers.
After library quality control, different libraries were pooled based on the  effective concentration and targeted data amount, then subjected to  Illumina sequencing.

value: whole spider

tag: sample group

value: UH

value: Urea treatment


title: UH rep3

description: Library name: sample 15


title: cDC1, Clec1a WT5_n1_ifn

description:
Library name: Sample 202
TO241_DGEseq.unq.refseq.umi.dat


title: UH rep2

description: Library name: sample 14


title: UH rep1

description: Library name: sample 13


title: UM rep4

description: Library name: sample 12

value: UM


title: cDC1, Clec1a KO6_n4_ns

description:
Library name: Sample 200
TO241_DGEseq.unq.refseq.umi.dat

value: Clec1a KO


title: UM rep3

description: Library name: sample 11


title: UM rep2

description: Library name: sample 10


title: cDC1, Clec1a KO6_n4_necrocoli

description:
Library name: Sample 199
TO241_DGEseq.unq.refseq.umi.dat


title: UM rep1

description: Library name: sample 9


title: UL rep4

description: Library name: sample 8

value: UL


title: cDC1, Clec1a KO6_n4_necro

description:
Library name: Sample 198
TO241_DGEseq.unq.refseq.umi.dat

value: spleen


title: UL rep2

description: Library name: sample 6


title: cDC1, Clec1a KO6_n4_ifn

description:
Library name: Sample 197
TO241_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates


title: UL rep1

description: Library name: sample 5


title: Ck rep4

description: Library name: sample 4

value: Ck


title: cDC1, Clec1a KO6_n4_ecoli

description:
Library name: Sample 196
TO241_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells


title: Ck rep3

description: Library name: sample 3


title: cDC1, Clec1a KO6_n3_ns

description:
Library name: Sample 195
TO241_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: Ck rep1

description: Library name: sample 1


title: B3

city: Huzhou

first: Yunliang

last: Yao

state: Zhejiang

address: 759 East Second Ring Road

department: Medical School

institute: Huzhou Normal University

description:
Library name: B3
DNBelab C platform single-cell RNA sequencing sample B3; filtered cell count 14363; median genes per cell 1712; mean UMI 5291.42.

data_processing:
DNBC4tools v2.1.2 (DNBelab C Series single-cell RNA analysis pipeline) was used with default parameters for sample de-multiplexing, cell-barcode and UMI processing, alignment of transcript reads to the mouse GRCm39/mm39 reference genome, single-cell 3' UMI counting, and generation of a gene-by-cell count matrix for each library. Valid cell-associated barcodes were identified automatically from the UMI-count distribution of each barcode to remove background beads.
Seurat v3.0.2 was used for quality-control filtering, normalization, multi-sample integration, dimensionality reduction (PCA), and clustering (Louvain).
SingleR v1.0.0 and SCINA were used for cell-type annotation, followed by manual curation using canonical marker genes.
clusterProfiler v3.14.0 (KEGG v2021.09, GO v2021.0918) was used for functional enrichment; CellChat v0.5.0 was used for cell-cell communication analysis.
Quality control in Seurat: cells expressing fewer than 200 genes were excluded; sample-specific upper thresholds ranged from 21,617-24,401 UMIs and 5,504-5,969 detected genes per cell; cells with >20% mitochondrial transcripts, ribosomal transcript proportions above sample-specific thresholds of 31.0-37.1%, or >1% erythrocyte-associated transcripts were removed. Putative doublets were identified and removed using Scrublet. Analyses were performed in R v3.6.
Assembly: GRCm39/mm39
Supplementary files format and content: barcodes.tsv.gz: cell barcode table
Supplementary files format and content: features.tsv.gz: feature/gene annotation table
Supplementary files format and content: matrix.mtx.gz: gene-by-cell count matrix in Matrix Market format

molecule: polyA RNA

source_name: knee joint synovium

growth_protocol: Female C57BL/6 mice were purchased from GemPharmatech Co., Ltd. Mice were used at 8 weeks of age and acclimatized for one week before experimentation. Animals were housed under specific-pathogen-free (SPF) conditions with controlled temperature and humidity and a 12-h light/dark cycle. All animal procedures were approved by the Institutional Animal Care and Use Committee of Huzhou Normal University and performed in accordance with institutional guidelines.

extract_protocol:
Synovial tissue was dissected from the inflamed knee joints of six C&AIA mice during the effector phase of disease. Tissue from two mice was pooled before processing, yielding three pooled biological samples (B1, B2, B3). Tissues were enzymatically dissociated into single-cell suspensions using 1-2 mg/mL Collagenase Type II and 0.1 mg/mL DNase I in serum-free medium, with incubation at 37 C for 45-60 min under continuous agitation. Cell viability and concentration were assessed before library construction.
Single-cell RNA-seq libraries were prepared using the DNBelab C Series High-throughput Single-Cell RNA Library Preparation Set (MGI, cat. no. 940-001818-00). Single-cell suspensions were converted into barcoded scRNA-seq libraries through droplet encapsulation, emulsion breakage, collection of mRNA-capture beads, reverse transcription, and cDNA amplification and purification. Amplified cDNA was sheared to 300-500 bp and indexed sequencing libraries were constructed according to the manufacturer's protocol. Library quality was assessed using the Qubit ssDNA Assay Kit (Thermo Fisher Scientific) and an Agilent Bioanalyzer 2100. For each sample a cDNA (gene expression) library and a paired cell-barcode oligo library were generated (target ~400M and ~60M reads, respectively). Libraries were sequenced on the DNBSEQ-T7 platform using paired-end sequencing: read 1 was 30 bp (10-bp cell barcode 1, 10-bp cell barcode 2 and 10-bp unique molecular identifier), read 2 was 100 bp covering the transcript sequence, and a 10-bp index read was used for sample identification.

treatment_protocol: Female C57BL/6 mice were used to establish the collagen- and antibody-induced arthritis (C&AIA) model, the disease model profiled in this study. On day 0, mice were immunized subcutaneously at the base of the tail with 0.1 ml of type II collagen emulsion (100 ug collagen per mouse). On day 21, mice received an anti-type II collagen monoclonal antibody cocktail (1 mg per mouse). On day 22, lipopolysaccharide (LPS) was administered to synchronize and enhance disease onset. Mice were monitored for arthritis development, and inflamed knee joint synovium was harvested at the effector phase for single-cell RNA sequencing.

value: knee joint synovium

value: Female

value: wild type


title: cDC1, Clec1a KO6_n3_necrocoli

description:
Library name: Sample 194
TO241_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: stimulated with necrotic cells plus E Coli


title: B2

description:
Library name: B2
DNBelab C platform single-cell RNA sequencing sample B2; filtered cell count 10668; median genes per cell 1406.5; mean UMI 5392.78.

value: collagen- and antibody-induced arthritis (C&AIA)


title: B1

description:
Library name: B1
DNBelab C platform single-cell RNA sequencing sample B1; filtered cell count 11111; median genes per cell 1506; mean UMI 5432.73.


title: cDC1, Clec1a KO6_n3_necro

description:
Library name: Sample 193
TO241_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: cDC1, Clec1a WT5_n1_ecoli

description:
Library name: Sample 201
TO241_DGEseq.unq.refseq.umi.dat

value: Clec1a WT

value: stimulated with E Coli


title: Telencephalon_WT_rep3

city: Hangzhou

first: Xiaoping

last: Han

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

description:
Library name: Telencephalon_WT_rep3_scRNA-seq
UURNA-seq

data_processing:
Raw FASTQ files were split by i7 indexes of DNBSEQ-T7 using splitBarcode (v0.1.6) then converted to BAM format. The 30-bp cell barcodes and 7-bp unique molecular identifiers (UMIs) were extracted and tagged. Reads with poor barcode or UMI quality (more than 8/37 bases showing quality < 10) were tagged with XQ and removed afterwards. The known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each barcode or UMI. The corrected BAM files were converted to FASTQ files with barcodes and UMIs trimmed. Cutadapt was then used to trim poly-A. Before Read-2 files were used for alignment, seqtk was performed to reverse the sequences. Reads were aligned to mm10 using STAR in single-end mode. The aligned BAM files were then merged with the unaligned ones to recover barcode and UMI information. The TagReadWithGeneExon function was employed to recognize reads mapped to the exonic and intronic regions of genes. Then the tagged BAM files were split by the third 10-bp barcodes (barcode 3) of each read, which is designed to distinguish different samples. BAM files with different i7 indexes were all merged if they shared the same barcode 3. Finally, the top 20,000 barcodes in each BAM file were extracted and their expression matrices were quantified.
Assembly: mm10
Supplementary files format and content: Compressed Tab-delimited text files containing gene expression matrices
Supplementary files format and content: Compressed Tab-delimited text files containing metadata of cells analyzed

molecule: nuclear RNA

source_name: Telencephalon

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Library preparations were performed with the UURNA-seq protocol

value: Telencephalon

value: WT

value: Male

value: 8 weeks

tag: mouse id


title: Telencephalon_WT_rep2

description:
Library name: Telencephalon_WT_rep2_scRNA-seq
UURNA-seq

tag: tissue


title: cDC1, Clec1a KO6_n3_ifn

description:
Library name: Sample 192
TO241_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: Clec1a KO

value: stimulated with type I IFN


title: Telencephalon_KO_rep3

description:
Library name: Telencephalon_KO_rep3_scRNA-seq
UURNA-seq

value: Mecp2 KO

value: 9 weeks


title: Telencephalon_WT_rep1

description:
Library name: Telencephalon_WT_rep1_scRNA-seq
UURNA-seq


title: cDC1, Clec1a KO6_n3_ecoli

description:
Library name: Sample 191
TO241_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells


title: UL rep3

description: Library name: sample 7

value: whole spider

value: UL

value: Urea treatment


title: Telencephalon_KO_rep2

description:
Library name: Telencephalon_KO_rep2_scRNA-seq
UURNA-seq

value: 7 weeks


title: cDC1, Clec1a KO6_n2_ns

description:
Library name: Sample 190
TO241_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: Non stimulated


title: SpinalCord_WT_rep3

description:
Library name: SpinalCord_WT_rep3_scRNA-seq
UURNA-seq

source_name: SpinalCord

value: SpinalCord


title: Telencephalon_KO_rep1

description:
Library name: Telencephalon_KO_rep1_scRNA-seq
UURNA-seq

value: Telencephalon


title: SpinalCord_WT_rep2

description:
Library name: SpinalCord_WT_rep2_scRNA-seq
UURNA-seq

value: WT

value: Male


title: KO4

description: Library name: Sample 2

value: Bone marrow

tag: cell line

value: primary cells

value: Hematopoietic stem cell

value: KO


title: cDC1, Clec1a KO6_n2_necrocoli

description:
Library name: Sample 189
TO241_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: Clec1a KO

value: stimulated with necrotic cells plus E Coli


title: SkGcn+PT-1LVAN (SkGcn_C1PWV_Plate5)

description: Library name: SkGcn_and_PT-1LVAN_SkGcn_C1PWV_Plate5

value: Gastrocnemius Medialis


title: SpinalCord_WT_rep1

description:
Library name: SpinalCord_WT_rep1_scRNA-seq
UURNA-seq

value: 8 weeks


title: SkGcn+PT-1LVAN (SkGcn_C1PWV_Plate4)

description: Library name: SkGcn_and_PT-1LVAN_SkGcn_C1PWV_Plate4


title: SpinalCord_KO_rep3

description:
Library name: SpinalCord_KO_rep3_scRNA-seq
UURNA-seq

value: Mecp2 KO

value: 9 weeks


title: cDC1, Clec1a KO6_n2_necro

description:
Library name: Sample 188
TO241_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: stimulated with necrotic cells


title: Ck rep2

description: Library name: sample 2

value: whole spider

value: Ck

value: Urea treatment


title: SpinalCord_KO_rep2

description:
Library name: SpinalCord_KO_rep2_scRNA-seq
UURNA-seq

value: SpinalCord

value: Male

value: 7 weeks


title: SkGcn+PT-1LVAN (SkGcn_C1PWV_Plate1)

description: Library name: SkGcn_and_PT-1LVAN_SkGcn_C1PWV_Plate1


title: Pituitary_WT_rep3

description:
Library name: Pituitary_WT_rep3_scRNA-seq
UURNA-seq

source_name: Pituitary

value: Pituitary

value: WT


title: SpinalCord_KO_rep1

description:
Library name: SpinalCord_KO_rep1_scRNA-seq
UURNA-seq


title: cDC1, Clec1a KO6_n2_ifn

description:
Library name: Sample 187
TO241_DGEseq.unq.refseq.umi.dat

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: Clec1a KO

value: stimulated with type I IFN


title: Pituitary_WT_rep2

description:
Library name: Pituitary_WT_rep2_scRNA-seq
UURNA-seq

value: 8 weeks


title: cDC1, Clec1a KO6_n2_ecoli

description:
Library name: Sample 186
TO241_DGEseq.unq.refseq.umi.dat

value: stimulated with E Coli


title: Pituitary_WT_rep1

description:
Library name: Pituitary_WT_rep1_scRNA-seq
UURNA-seq


title: Pituitary_KO_rep3

description:
Library name: Pituitary_KO_rep3_scRNA-seq
UURNA-seq

value: Mecp2 KO

value: 9 weeks


title: SkGcn+PT-1K2DA (SkGcn_C1MKW_Plate3)

description: Library name: SkGcn_and_PT-1K2DA_SkGcn_C1MKW_Plate3

value: Gastrocnemius Medialis


title: cDC1, Clec1a WT6_n4_necro

description:
Library name: Sample 238
TO241_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: Clec1a WT

value: stimulated with necrotic cells


title: cDC1, Clec1a KO6_n1_ns

description:
Library name: Sample 185
TO241_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: Pituitary_KO_rep2

description:
Library name: Pituitary_KO_rep2_scRNA-seq
UURNA-seq

value: Male

value: 7 weeks


title: Pituitary_KO_rep1

description:
Library name: Pituitary_KO_rep1_scRNA-seq
UURNA-seq

value: Pituitary


title: cDC1, Clec1a KO6_n1_necrocoli

description:
Library name: Sample 184
TO241_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with necrotic cells plus E Coli


title: Diencephalon_WT_rep3

description:
Library name: Diencephalon_WT_rep3_scRNA-seq
UURNA-seq

source_name: Diencephalon

value: Diencephalon

value: WT


title: Diencephalon_WT_rep2

description:
Library name: Diencephalon_WT_rep2_scRNA-seq
UURNA-seq

value: 8 weeks


title: cDC1, Clec1a KO6_n1_necro

description:
Library name: Sample 183
TO241_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: Clec1a KO


title: Diencephalon_WT_rep1

description:
Library name: Diencephalon_WT_rep1_scRNA-seq
UURNA-seq


title: cDC1, Clec1a WT6_n3_ecoli

description:
Library name: Sample 231
TO241_DGEseq.unq.refseq.umi.dat

value: stimulated with E Coli


title: cDC1, Clec1a WT6_n3_ns

description:
Library name: Sample 235
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a WT6_n4_ecoli

description:
Library name: Sample 236
TO241_DGEseq.unq.refseq.umi.dat


title: cDC1, Clec1a KO6_n1_ifn

description:
Library name: Sample 182
TO241_DGEseq.unq.refseq.umi.dat

value: stimulated with type I IFN


title: Diencephalon_KO_rep3

description:
Library name: Diencephalon_KO_rep3_scRNA-seq
UURNA-seq

value: Mecp2 KO

value: 9 weeks


title: Diencephalon_KO_rep2

description:
Library name: Diencephalon_KO_rep2_scRNA-seq
UURNA-seq


title: Diencephalon_KO_rep1

description:
Library name: Diencephalon_KO_rep1_scRNA-seq
UURNA-seq


title: cDC1, Clec1a WT6_n2_ifn

description:
Library name: Sample 227
TO241_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: Clec1a WT


title: cDC1, Clec1a KO6_n1_ecoli

description:
Library name: Sample 181
TO241_DGEseq.unq.refseq.umi.dat


title: Cerebellum_WT_rep3

description:
Library name: Cerebellum_WT_rep3_scRNA-seq
UURNA-seq

source_name: Cerebellum

value: Cerebellum

value: Male


title: cDC1, Clec1a KO5_n4_ns

description:
Library name: Sample 180
TO241_DGEseq.unq.refseq.umi.dat

value: Non stimulated


title: Cerebellum_WT_rep2

description:
Library name: Cerebellum_WT_rep2_scRNA-seq
UURNA-seq


title: Cerebellum_WT_rep1

description:
Library name: Cerebellum_WT_rep1_scRNA-seq
UURNA-seq


title: Cerebellum_KO_rep3

description:
Library name: Cerebellum_KO_rep3_scRNA-seq
UURNA-seq


title: cDC1, Clec1a KO5_n4_necrocoli

description:
Library name: Sample 179
TO241_DGEseq.unq.refseq.umi.dat

value: spleen


title: Cerebellum_KO_rep1

description:
Library name: Cerebellum_KO_rep1_scRNA-seq
UURNA-seq


title: cDC1, Clec1a KO5_n4_necro

description:
Library name: Sample 178
TO241_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: BrainStem_WT_rep2

description:
Library name: BrainStem_WT_rep2_scRNA-seq
UURNA-seq

source_name: BrainStem

value: BrainStem


title: BrainStem_WT_rep3

description:
Library name: BrainStem_WT_rep3_scRNA-seq
UURNA-seq

value: WT


title: cDC1, Clec1a KO5_n4_ifn

description:
Library name: Sample 177
TO241_DGEseq.unq.refseq.umi.dat


title: BrainStem_KO_rep3

description:
Library name: BrainStem_KO_rep3_scRNA-seq
UURNA-seq


title: BrainStem_WT_rep1

description:
Library name: BrainStem_WT_rep1_scRNA-seq
UURNA-seq

value: 8 weeks


title: BrainStem_KO_rep2

description:
Library name: BrainStem_KO_rep2_scRNA-seq
UURNA-seq

value: 7 weeks


title: cDC1, Clec1a KO5_n4_ecoli

description:
Library name: Sample 176
TO241_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: Clec1a KO


title: cDC1, Clec1a KO5_n3_ns

description:
Library name: Sample 175
TO241_DGEseq.unq.refseq.umi.dat


title: BrainStem_KO_rep1

description:
Library name: BrainStem_KO_rep1_scRNA-seq
UURNA-seq


title: H3K27me3_Telencephalon_WT

description:
Library name: H3K27me3_Telencephalon_WT_CUTnTag
CUT&Tag

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were aligned to mm10 using bowtie2 (v2.5.2). Reads with quality > 2 were selected and sorted by query names. BAM files were converted to BEDPE files then to fragment files (sorted BED files). Fragments in the blacklist regions of mm10 (https://www.encodeproject.org/files/ENCFF547MET/) were removed. BED files were converted to BW files for subsequent visualization.
The raw sorted BED files (blacklist regions were not removed) are supported as supplementary files for individual samples.
Assembly: mm10
Supplementary files format and content: BED  files including sorted fragments
Library strategy: CUT&Tag

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Concanavalin A (ConA) coated magnetic beads were freshly activated with Ca²⁺ and Mn²⁺. Nuclei were extracted and a total of 10,000 nuclei were incubated with activated ConA beads. Supernatant was next removed, and beads were incubated with antibody (1:50) on a rotator at 4°C overnight, followed by incubated with secondary antibody (1:100) for 1 hr at room temperature. Beads were washed three times and suspended in dig300-wash buffer pre-mixed with pG-Tn5 (1:100), incubated for 1 hr at room temperature. After washing beads for three times, tag buffer was added to each well, then incubated on a rotator at 37 °C for 1 hr. After centrifugation, beads were washed once and resuspended. Lysis buffer was added to each well, and incubated for 2 hr at 65 °C. After adding 10% Tween20, TruePrep CUT&Tag Amplification Mix (Vazyme), 10 mM MGI-P5, and 10 mM MGI-P7 primer were added. Then PCR program was performed. Finally, 1.5 × VAHTS DNA Clean Beads were used to purify the library.

value: Telencephalon

tag: antibody


title: cDC1, Clec1a KO5_n3_necrocoli

description:
Library name: Sample 174
TO241_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells plus E Coli


title: H3K9me3_Telencephalon_WT

description:
Library name: H3K9me3_Telencephalon_WT_CUTnTag
CUT&Tag

value: H3K9me3 (Active Motif, #39161)


title: H3K4me1_Telencephalon_WT

description:
Library name: H3K4me1_Telencephalon_WT_CUTnTag
CUT&Tag


title: cDC1, Clec1a KO5_n3_necro

description:
Library name: Sample 173
TO241_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old


title: Mecp2_Thymus_WT

description:
Library name: Mecp2_Thymus_WT_CUTnTag
CUT&Tag

source_name: Thymus

value: Thymus

value: MECP2 (Proteintech, 10861-1-AP)


title: Mecp2_Stomach_WT

description:
Library name: Mecp2_Stomach_WT_CUTnTag
CUT&Tag

source_name: Stomach

value: Stomach


title: Mecp2_SmallIntestine_WT

description:
Library name: Mecp2_SmallIntestine_WT_CUTnTag
CUT&Tag

source_name: SmallIntestine

value: SmallIntestine

value: Male


title: Mecp2_Pituitary_WT

description:
Library name: Mecp2_Pituitary_WT_CUTnTag
CUT&Tag

value: Pituitary


title: PBMC+4809 (PBMC_4809_Plate8)

description: Library name: PBMC_and_4809_PBMC_4809_Plate8

source_name: Peripheral Blood

value: Peripheral Blood


title: Mecp2_Muscle_WT

description:
Library name: Mecp2_Muscle_WT_CUTnTag
CUT&Tag

source_name: Muscle

value: Muscle


title: cDC1, Clec1a KO5_n3_ecoli

description:
Library name: Sample 171
TO241_DGEseq.unq.refseq.umi.dat

value: spleen

value: type 1 conventional dendritic cells

value: stimulated with E Coli


title: cDC1, Clec1a KO5_n2_ns

description:
Library name: Sample 170
TO241_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: Non stimulated


title: PBMC+4809 (PBMC_4809_Plate7)

description: Library name: PBMC_and_4809_PBMC_4809_Plate7


title: Mecp2_Lung_WT

description:
Library name: Mecp2_Lung_WT_CUTnTag
CUT&Tag

source_name: Lung

value: Lung

value: WT

value: 8 weeks


title: cDC1, Clec1a KO5_n2_necrocoli

description:
Library name: Sample 169
TO241_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: Clec1a KO

value: stimulated with necrotic cells plus E Coli


title: Mecp2_Kidney_WT

description:
Library name: Mecp2_Kidney_WT_CUTnTag
CUT&Tag

source_name: Kidney

value: Kidney

value: MECP2 (Proteintech, 10861-1-AP)


title: Mecp2_Epididymis_WT

description:
Library name: Mecp2_Epididymis_WT_CUTnTag
CUT&Tag

source_name: Epididymis

value: Epididymis

value: Male


title: PBMC+4809 (PBMC_4809_Plate5)

description: Library name: PBMC_and_4809_PBMC_4809_Plate5

value: Peripheral Blood


title: Mecp2_BrownFat_WT

description:
Library name: Mecp2_BrownFat_WT_CUTnTag
CUT&Tag

source_name: BrownFat

value: BrownFat


title: cDC1, Clec1a KO5_n2_necro

description:
Library name: Sample 168
TO241_DGEseq.unq.refseq.umi.dat

source_name: spleen

value: spleen

value: stimulated with necrotic cells


title: PBMC+4809 (PBMC_4809_Plate4)

description: Library name: PBMC_and_4809_PBMC_4809_Plate4


title: neural_Telencephalon_WT_rep3

description:
Library name: neural_Telencephalon_WT_rep3_scATAC-seq
UUATAC-seq

library_source: genomic single cell

data_processing:
Raw FASTQ files were split by i7 indexes of DNBSEQ-T7 using splitBarcode (v0.1.6) then converted to BAM format. The 30-bp barcodes were tagged and reads with low quality were removed. Barcodes were next corrected and combined with the i7 indexes to label cells. The barcode-corrected BAM files were split by barcode 3 which label samples. Cell barcodes (i7 indexes + 30-bp barcodes) were added to the query name of each read. BAM files were then converted to FASTQ files with 30-bp barcodes and reverse complementary mosaic end (ME) sequences trimmed. Reads were aligned to mm10 using BWA (version 0.7.15) in paired-end mode. The aligned and sorted BAM files were shifted using the alignmentSieve function in deepTools (version 3.5.1) to correct the 9-bp gap. The shifted BAM files were next merged per sample and converted to BEDPE files (BED format). BEDPE files were cleaned to fragment files for subsequent analyses.
Assembly: mm10
Supplementary files format and content: Compressed BED  files containing sorted fragments
Supplementary files format and content: Compressed Tab-delimited text files containing metadata of cells analyzed

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Library preparations were performed with the UUATAC-seq protocol

value: Telencephalon


title: PBMC+4809 (PBMC_4809_Plate3)

description: Library name: PBMC_and_4809_PBMC_4809_Plate3


title: Mecp2_BoneMarrow_WT

description:
Library name: Mecp2_BoneMarrow_WT_CUTnTag
CUT&Tag

source_name: BoneMarrow

value: BoneMarrow


title: cDC1, Clec1a KO5_n2_ecoli

description:
Library name: Sample 166
TO241_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: type 1 conventional dendritic cells

value: stimulated with E Coli


title: neural_Telencephalon_WT_rep2

description:
Library name: neural_Telencephalon_WT_rep2_scATAC-seq
UUATAC-seq

source_name: Telencephalon

value: WT

value: 8 weeks


title: neural_Telencephalon_WT_rep1

description:
Library name: neural_Telencephalon_WT_rep1_scATAC-seq
UUATAC-seq


title: neural_Telencephalon_KO_rep3

description:
Library name: neural_Telencephalon_KO_rep3_scATAC-seq
UUATAC-seq

value: Mecp2 KO

value: 9 weeks


title: PBMC+4809 (PBMC_4809_Plate2)

description: Library name: PBMC_and_4809_PBMC_4809_Plate2


title: cDC1, Clec1a KO5_n1_ns

description:
Library name: Sample 165
TO241_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: Clec1a KO

value: Non stimulated


title: neural_Telencephalon_KO_rep2

description:
Library name: neural_Telencephalon_KO_rep2_scATAC-seq
UUATAC-seq

value: Male

value: 7 weeks


title: PBMC+4809 (PBMC_4809_Plate1)

description: Library name: PBMC_and_4809_PBMC_4809_Plate1

value: Peripheral Blood


title: neural_Telencephalon_KO_rep1

description:
Library name: neural_Telencephalon_KO_rep1_scATAC-seq
UUATAC-seq


title: cDC1, Clec1a KO5_n1_necrocoli

description:
Library name: Sample 164
TO241_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with necrotic cells plus E Coli


title: neural_SpinalCord_WT_rep3

description:
Library name: neural_SpinalCord_WT_rep3_scATAC-seq
UUATAC-seq

source_name: SpinalCord

value: SpinalCord


title: PBMC+11714 (PBMC_11714_Plate8)

description: Library name: PBMC_and_11714_PBMC_11714_Plate8


title: neural_SpinalCord_WT_rep2

description:
Library name: neural_SpinalCord_WT_rep2_scATAC-seq
UUATAC-seq


title: neural_SpinalCord_WT_rep1

description:
Library name: neural_SpinalCord_WT_rep1_scATAC-seq
UUATAC-seq


title: cDC1, Clec1a KO5_n1_necro

description:
Library name: Sample 163
TO241_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: PBMC+11714 (PBMC_11714_Plate7)

description: Library name: PBMC_and_11714_PBMC_11714_Plate7


title: neural_SpinalCord_KO_rep2

description:
Library name: neural_SpinalCord_KO_rep2_scATAC-seq
UUATAC-seq


title: PBMC+11714 (PBMC_11714_Plate6)

description: Library name: PBMC_and_11714_PBMC_11714_Plate6


title: cDC1, Clec1a KO5_n1_ecoli

description:
Library name: Sample 161
TO241_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates


title: neural_Pituitary_WT_rep2

description:
Library name: neural_Pituitary_WT_rep2_scATAC-seq
UUATAC-seq

source_name: Pituitary

value: Pituitary


title: neural_Pituitary_WT_rep1

description:
Library name: neural_Pituitary_WT_rep1_scATAC-seq
UUATAC-seq


title: PBMC+11714 (PBMC_11714_Plate5)

description: Library name: PBMC_and_11714_PBMC_11714_Plate5


title: cDC1, Clec1a WT2_n4_ns

description:
Library name: Sample 160
TO240_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells

value: Clec1a WT


title: neural_Pituitary_KO_rep3

description:
Library name: neural_Pituitary_KO_rep3_scATAC-seq
UUATAC-seq


title: neural_Pituitary_KO_rep2

description:
Library name: neural_Pituitary_KO_rep2_scATAC-seq
UUATAC-seq


title: H3K4me3_Telencephalon_WT

description:
Library name: H3K4me3_Telencephalon_WT_CUTnTag
CUT&Tag

value: Telencephalon

value: WT

value: 8 weeks


title: PBMC+11714 (PBMC_11714_Plate4)

description: Library name: PBMC_and_11714_PBMC_11714_Plate4


title: cDC1, Clec1a WT2_n4_ecoli

description:
Library name: Sample 156
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: stimulated with E Coli


title: neural_Pituitary_KO_rep1

description:
Library name: neural_Pituitary_KO_rep1_scATAC-seq
UUATAC-seq

value: Mecp2 KO


title: PBMC+11714 (PBMC_11714_Plate3)

description: Library name: PBMC_and_11714_PBMC_11714_Plate3


title: cDC1, Clec1a KO5_n3_ifn

description:
Library name: Sample 172
TO241_DGEseq.unq.refseq.umi.dat

value: Clec1a KO

value: stimulated with type I IFN


title: neural_Diencephalon_WT_rep2

description:
Library name: neural_Diencephalon_WT_rep2_scATAC-seq
UUATAC-seq

source_name: Diencephalon

value: Diencephalon

value: Male


title: PBMC+11714 (PBMC_11714_Plate2)

description: Library name: PBMC_and_11714_PBMC_11714_Plate2

value: Peripheral Blood


title: cDC1, Clec1a WT2_n3_necrocoli

description:
Library name: Sample 154
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with necrotic cells plus E Coli


title: neural_Diencephalon_WT_rep1

description:
Library name: neural_Diencephalon_WT_rep1_scATAC-seq
UUATAC-seq


title: Mecp2_Ovary_WT

description:
Library name: Mecp2_Ovary_WT_CUTnTag
CUT&Tag

source_name: Ovary

value: Ovary

value: MECP2 (Proteintech, 10861-1-AP)


title: PBMC+4809 (PBMC_4809_Plate6)

description: Library name: PBMC_and_4809_PBMC_4809_Plate6


title: PBMC+11714 (PBMC_11714_Plate1)

description: Library name: PBMC_and_11714_PBMC_11714_Plate1


title: neural_Diencephalon_KO_rep3

description:
Library name: neural_Diencephalon_KO_rep3_scATAC-seq
UUATAC-seq

value: 9 weeks


title: neural_Diencephalon_WT_rep3

description:
Library name: neural_Diencephalon_WT_rep3_scATAC-seq
UUATAC-seq


title: neural_Diencephalon_KO_rep2

description:
Library name: neural_Diencephalon_KO_rep2_scATAC-seq
UUATAC-seq

value: 7 weeks


title: cDC1, Clec1a WT2_n3_ns

description:
Library name: Sample 155
TO240_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: type 1 conventional dendritic cells

value: Clec1a WT

value: Non stimulated


title: cDC1, Clec1a KO5_n2_ifn

description:
Library name: Sample 167
TO241_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old


title: cDC1, Clec1a WT2_n3_necro

description:
Library name: Sample 153
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: Mecp2_Breast_WT

description:
Library name: Mecp2_Breast_WT_CUTnTag
CUT&Tag

source_name: Breast

value: Breast

value: WT

value: 8 weeks


title: neural_Cerebellum_WT_rep3

description:
Library name: neural_Cerebellum_WT_rep3_scATAC-seq
UUATAC-seq

source_name: Cerebellum

value: Cerebellum

value: Male


title: neural_Diencephalon_KO_rep1

description:
Library name: neural_Diencephalon_KO_rep1_scATAC-seq
UUATAC-seq

value: Diencephalon

value: Mecp2 KO


title: cDC1, Clec1a WT2_n3_ifn

description:
Library name: Sample 152
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with type I IFN


title: neural_Cerebellum_WT_rep2

description:
Library name: neural_Cerebellum_WT_rep2_scATAC-seq
UUATAC-seq


title: P+9216 (P_9216_AR_Plate7)

description: Library name: P_and_9216_P_9216_AR_Plate7

source_name: Placenta

value: Placenta


title: neural_Cerebellum_WT_rep1

description:
Library name: neural_Cerebellum_WT_rep1_scATAC-seq
UUATAC-seq


title: neural_Cerebellum_KO_rep3

description:
Library name: neural_Cerebellum_KO_rep3_scATAC-seq
UUATAC-seq

value: 9 weeks


title: cDC1, Clec1a WT2_n3_ecoli

description:
Library name: Sample 151
TO240_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: stimulated with E Coli


title: neural_Cerebellum_KO_rep1

description:
Library name: neural_Cerebellum_KO_rep1_scATAC-seq
UUATAC-seq


title: cDC1, Clec1a WT2_n2_ns

description:
Library name: Sample 150
TO240_DGEseq.unq.refseq.umi.dat

value: type 1 conventional dendritic cells

value: Clec1a WT


title: neural_BrainStem_WT_rep3

description:
Library name: neural_BrainStem_WT_rep3_scATAC-seq
UUATAC-seq

source_name: BrainStem

value: BrainStem


title: cDC1, Clec1a WT2_n2_necrocoli

description:
Library name: Sample 149
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: stimulated with necrotic cells plus E Coli


title: P+9216 (P_9216_AR_Plate8)

description: Library name: P_and_9216_P_9216_AR_Plate8


title: neural_BrainStem_WT_rep2

description:
Library name: neural_BrainStem_WT_rep2_scATAC-seq
UUATAC-seq

value: WT


title: neural_BrainStem_WT_rep1

description:
Library name: neural_BrainStem_WT_rep1_scATAC-seq
UUATAC-seq

value: 8 weeks


title: P+9216 (P_9216_AR_Plate4)

description: Library name: P_and_9216_P_9216_AR_Plate4


title: neural_Cerebellum_KO_rep2

description:
Library name: neural_Cerebellum_KO_rep2_scATAC-seq
UUATAC-seq

value: Cerebellum

value: 7 weeks


title: cDC1, Clec1a WT2_n2_necro

description:
Library name: Sample 148
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: P+9216 (P_9216_AR_Plate2)

description: Library name: P_and_9216_P_9216_AR_Plate2


title: neural_BrainStem_KO_rep2

description:
Library name: neural_BrainStem_KO_rep2_scATAC-seq
UUATAC-seq

value: Mecp2 KO

value: Male


title: pan_tissue_WhiteFat_WT

description:
Library name: pan_tissue_WhiteFat_WT_scATAC-seq
UUATAC-seq

source_name: WhiteFat

value: WhiteFat


title: P+9216 (P_9216_AR_Plate3)

description: Library name: P_and_9216_P_9216_AR_Plate3

value: Placenta


title: P+9216 (P_9216_AR_Plate1)

description: Library name: P_and_9216_P_9216_AR_Plate1


title: neural_BrainStem_KO_rep1

description:
Library name: neural_BrainStem_KO_rep1_scATAC-seq
UUATAC-seq


title: cDC1, Clec1a WT2_n2_ecoli

description:
Library name: Sample 146
TO240_DGEseq.unq.refseq.umi.dat

value: spleen


title: pan_tissue_Eye_WT

description:
Library name: pan_tissue_Eye_WT_scATAC-seq
UUATAC-seq

source_name: Eye

value: Eye


title: pan_tissue_Thyroid_WT

description:
Library name: pan_tissue_Thyroid_WT_scATAC-seq
UUATAC-seq

source_name: Thyroid

value: Thyroid


title: P+9216 (P_9216_AR_Plate5)

description: Library name: P_and_9216_P_9216_AR_Plate5


title: cDC1, Clec1a WT2_n1_ns

description:
Library name: Sample 145
TO240_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: type 1 conventional dendritic cells

value: Non stimulated


title: P+9213 (P_9213_AR_Plate8)

description: Library name: P_and_9213_P_9213_AR_Plate8


title: pan_tissue_BrownFat_WT

description:
Library name: pan_tissue_BrownFat_WT_scATAC-seq
UUATAC-seq

value: BrownFat


title: pan_tissue_Epididymis_WT

description:
Library name: pan_tissue_Epididymis_WT_scATAC-seq
UUATAC-seq

value: Epididymis


title: pan_tissue_AdrenalGland_WT

description:
Library name: pan_tissue_AdrenalGland_WT_scATAC-seq
UUATAC-seq

source_name: AdrenalGland

value: AdrenalGland

value: WT


title: cDC1, Clec1a WT2_n1_necrocoli

description:
Library name: Sample 144
TO240_DGEseq.unq.refseq.umi.dat

value: 8-12 weeks old

value: Clec1a WT

value: stimulated with necrotic cells plus E Coli


title: pan_tissue_WhiteFat_KO

description:
Library name: pan_tissue_WhiteFat_KO_scATAC-seq
UUATAC-seq

value: Mecp2 KO

value: 9 weeks


title: cDC1, Clec1a WT2_n1_necro

description:
Library name: Sample 143
TO240_DGEseq.unq.refseq.umi.dat

value: stimulated with necrotic cells


title: P+9213 (P_9213_AR_Plate6)

description: Library name: P_and_9213_P_9213_AR_Plate6

value: Placenta


title: cDC1, Clec1a WT2_n1_ifn

description:
Library name: Sample 142
TO240_DGEseq.unq.refseq.umi.dat

value: spleen

value: stimulated with type I IFN


title: pan_tissue_Testis_KO

description:
Library name: pan_tissue_Testis_KO_scATAC-seq
UUATAC-seq

source_name: Testis

value: Testis

value: Male


title: P+9213 (P_9213_AR_Plate5)

description: Library name: P_and_9213_P_9213_AR_Plate5


title: pan_tissue_Telencephalon_KO

description:
Library name: pan_tissue_Telencephalon_KO_scATAC-seq
UUATAC-seq

value: Telencephalon


title: cDC1, Clec1a WT2_n1_ecoli

description:
Library name: Sample 141
TO240_DGEseq.unq.refseq.umi.dat

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: type 1 conventional dendritic cells

value: stimulated with E Coli


title: pan_tissue_Stomach_KO

description:
Library name: pan_tissue_Stomach_KO_scATAC-seq
UUATAC-seq

source_name: Stomach

value: Stomach


title: P+9213 (P_9213_AR_Plate4)

description: Library name: P_and_9213_P_9213_AR_Plate4


title: pan_tissue_Spleen_KO

description:
Library name: pan_tissue_Spleen_KO_scATAC-seq
UUATAC-seq

source_name: Spleen

value: Spleen


title: cDC1, Clec1a WT1_n4_ns

description:
Library name: Sample 140
TO240_DGEseq.unq.refseq.umi.dat

source_name: spleen

value: 8-12 weeks old

value: Non stimulated


title: P+9213 (P_9213_AR_Plate3)

description: Library name: P_and_9213_P_9213_AR_Plate3