title: control 1

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
Reads were aligned to GRCm38/mm10 genome using Hisat2 (Mortazavi et al., 2008).  FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Data were analyzed using DESeq2 v1.20.0 (Anders et al., 2013) to determine differentially regulated genes between wild type and Acly KO mice (p-value < .05). The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: Acly gene count data.csv is gene count data
Supplementary files format and content: AclykovsAclywt_deg.xls is analysis of differential gene expression

source_name: sciatic nerve

growth_protocol: The Acly floxed allele (Zhao et al., 2016) was obtained from Jackson Laboratories (MMRRC stock #43555, and was maintained on the C57BL/6 genetic background and mated to mP0TOTA-Cre (Mpz-cre) (Feltri et al., 1999).

extract_protocol:
Using control and Acly cKO mice at 5 weeks of age (n=3 Acly cKO/2 controls), RNA was purified from sciatic nerves using RNA Clean & Concentrator-5 (#R1013)
1000 ng total RNA was sent to Novogene for library preparation after PolyA selection and Illumina sequencing (Novaseq 6000). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

value: sciatic nerve

value: Acly f/f

value: 5 weeks


title: Tg_F_H2O_Pris_D221-2_CD4_ATAC

status: Public on Feb 01 2024

type: SRA

city: Stanford

first: Diana

middle: Remy

last: Dou

state: CA

address: 269 Campus Drive, CCSR 2130

country: USA

institute: Stanford University

library_source: genomic

data_processing:
The adaptor of paired-end ATAC-seq data were first trimmed by an in-house software, and then aligned to mm10 genome using bowtie2.
The mitochondrial reads and reads with low alignment score (<10) were removed.
The aligned sam files were converted to bam files and sorted by Samtools.
Picard was used to remove duplicate reads and MACS2 was used to call peaks.
Bedtools was used to generate readCounts from called peaks
Each ATAC-seq peak was annotated by its nearby genes using GREAT under the basal plus extension default setting
Raw bulk ATAC-seq read counts normalized and analyzed using DESeq2
Assembly: mm10
Supplementary files format and content: Bedtools generated matrix of ATAC readCounts from called peaks
Supplementary files format and content: ATAC readCounts file

molecule: genomic DNA

organism: Mus musculus

source_name: CD4+ spleen

extract_protocol:
At 52 weeks post-injection, spleens were harvested and mechanically dissociated. CD4+ cells were isolated from freshly dissociated mouse spleen using the EasySep Mouse CD4+ T cell Isolation Kit (STEMCELL Technologies, 19852).
Freshly isolated CD4+ cells were prepared using the Omni-ATAC protocol to generate ATAC-seq libraries.

treatment_protocol: 12-14 week old C57BL6/J mice of inidcated genotypes were injected with 0.5 mL pristane or PBS (control mock injection) and continuously fed water with or without doxycycline for 52 weeks post-injection

tag: tissue

value: CD4+ spleen

tag: strain

tag: post-treatment (wks)

tag: Sex

value: Female

tag: genotype

value: tgXist/-

tag: treatment

value: Pristane

tag: molecule type

value: transposed genomic DNA


title: Tg_F_H2O_Pris_D222-2_CD4_ATAC


title: Tg_F_H2O_Pris_D221-1_CD4_ATAC


title: 72P_WT4_6M

city: Trondheim

first: Barbara

last: van Loon

address: Erling Skjalgsons gate 1

country: Norway

institute: Norwegian University of Science and Technology

description: 75bp SE

library_source: transcriptomic

data_processing:
Sequenced on Illumina HiSeq4000 with each sample being sequenced across all 8 lanes
Illumina bcl2fastq 2.20.0.422 used for basecalling
Sequenced reads were mapped to GRCm38.6 whole genome using STAR v2.4.0 with parameters --chimSegmentMin 30 --runThreadN 12 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000
Counting was performed using HTSeq (Anders et a., 2015 Bioinformatics) v0.6.0 (htseq-count) using reverse stranded settings, counting exon features and reporting Ensembl Gene Ids.
Assembly: GRCm38.6
Supplementary files format and content: Count matrix output from HTSeq (details above), no normalization was performed on the provided matrix.

molecule: total RNA

source_name: Prefrontal cortex

extract_protocol:
RNA was extracted from the pellets using RNAEasy Mini Kit (Qiagen, #74104).
Lexogen SENSE mRNA library preparation kit (polyA stranded)

value: Prefrontal cortex

value: Aag WT

tag: time

value: 6 months


title: Acly cKO3

molecule: polyA RNA

value: Acly f/f Mpz-cre


title: Acly cKO2


title: Treated (biological replicate 3)

city: Palo Alto

first: Jason

last: Ross

address: 265 Campus Drive

description: HSCs isolated from Treated animals

data_processing:
For 'Gene_Biotype', only 'protein_coding' genes are included
Assembly: The paired-end reads were aligned to the reference Mouse genome downloaded from Ensembl database (genome-build GRCm38.p6; genome-version GRCm38; genome-build-accession NCBI: GCA_000001635.8)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: bone-marrow

extract_protocol:
Approximately 1,000 total HSCs (KLS FLT3–CD34–CD150+) were FACS-sorted from aged control mice or aged mice that received antibody-conditioning 9 days earlier and immediately added to lysis buffer
Libraries were prepared using Takara SMART-Seq v4 Ultra low Input RNA kit and sequencing was performed with NovaSeq with approximately 20 million paired reads per sample by MedGenome Inc.

treatment_protocol: Treated mice received anti-NEO1/anti-CD62p/anti-CD47/anti-cKIT, HSCs were isolated at day 9.

value: bone-marrow

tag: cell type

value: HSC

value: Treated


title: 70P_WT4_5D

description: 75bp SE

value: 5 days


title: 71P_WT4_6W

description: 75bp SE

value: 6 weeks


title: 69P_KO4_6M

description: 75bp SE

value: Aag KO


title: 68P_KO4_6W

description: 75bp SE


title: Treated (biological replicate 2)

description: HSCs isolated from Treated animals


title: 67P_KO4_5D

description: 75bp SE


title: 63P_WT3_6M

description: 75bp SE


title: Treated (biological replicate 1)

description: HSCs isolated from Treated animals


title: 61P_WT3_5D

description: 75bp SE


title: 59P_KO3_6W

description: 75bp SE


title: 60P_KO3_6M

description: 75bp SE


title: control 2

value: sciatic nerve

value: Acly f/f


title: Control (biological replicate 3)

description: HSCs isolated from Control animals


title: 62P_WT3_6W

description: 75bp SE


title: Control (biological replicate 2)

description: HSCs isolated from Control animals


title: 53P_WT2_6W

description: 75bp SE


title: 51P_KO2_6M

description: 75bp SE


title: 50P_KO2_6W

description: 75bp SE


title: Wt_M_M51_GEx

library_source: transcriptomic single cell

data_processing:
FASTQ files were trimmed, filtered, and aligned using the cellranger arc pipeline from 10X genomics.
multiome single cell gene expression profiles were clustered and visualized using Seurat.
multiome single cell ATAC profiles were clustered and visualized using ArchR.
Assembly: mm10
Supplementary files format and content: Filtered cell by gene counts matrices (scRNA) and fragments files (scATAC) generated by 10X cellranger arc pipeline.

source_name: CD45+ spleen

extract_protocol:
At 16 weeks post-injection, spleens were harvested, mechanically dissociated and live (7aad-) CD45+ cells were isolated via FACS.
Multi-ome (paired single cell gene expression and single cell ATAC) libraries were constructed using commercially available reagents and protocols from 10X Genomics.

treatment_protocol: 8-10 week old SJL/J mice of inidcated genotypes were injected with 0.5 mL pristane and continuously fed water with or without doxycycline for 16 weeks post-injection

value: CD45+ spleen

value: SJL/J

value: Male

value: Wt

value: Dox+Pristane

value: cDNA


title: Wt_M_M51_atac

library_source: genomic single cell

value: transposed genomic DNA


title: Acly cKO1

value: 5 weeks


title: 58P_KO3_5D

description: 75bp SE

value: Prefrontal cortex


title: 54P_WT2_6M

description: 75bp SE

value: Aag WT

value: 6 months


title: 52P_WT2_5D

description: 75bp SE


title: 49P_KO2_5D

description: 75bp SE


title: 44P_WT1_6W

description: 75bp SE


title: Wt_M_M131_atac


title: 45P_WT1_6M

description: 75bp SE


title: 42P_KO1_6M

description: 75bp SE


title: CpG2-OVA-SQB

city: Boston

first: Yang

last: Zeng

address: 360 Longwood Avenue

institute: Dana Farber Cancer Institute

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mouse GRCm38 genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2 followed by differential expression analysis using DESeq2.
Assembly: Mouse GRCm38 reference
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

extract_protocol:
The samples were send to Genewiz for Processing. RNA was extracted by the CRO company using the Qiagen Rnease mini kit.
RNA sequencing (RNA-seq) was carried out by Genewiz using an ultra-low input RNA-seq package that includes polyA selection. Sequencing was performed with an Illumina HiSeq with 150-bp pair-ended reads.

treatment_protocol: The immature BMDCs were treated with different vaccines as mentioned above for 1 day and collected by TRIzol (Invitrogen).

value: Bone marrow

value: Dendritic cells

tag: developmental stage

value: Primary cells

value: vaccine stimulation


title: 43P_WT1_5D

description: 75bp SE

value: 5 days


title: Wt_M_M131_GEx


title: 40P_KO1_5D

description: 75bp SE

value: Aag KO


title: Wt_M_M112_GEx

value: CD45+ spleen


title: 36H_WT4_6M

description: 75bp SE

source_name: Hippocampus

value: Hippocampus


title: Wt_M_M112_atac

value: SJL/J

value: Male


title: 34H_WT4_5D

description: 75bp SE


title: Control (biological replicate 1)

description: HSCs isolated from Control animals

value: bone-marrow

value: HSC


title: 35H_WT4_6W

description: 75bp SE

value: 6 weeks


title: 33H_KO4_6M

description: 75bp SE


title: 32H_KO4_6W

description: 75bp SE


title: Wt_F_F120_GEx

value: Female

value: Wt

value: Pristane

value: cDNA


title: Wt_F_F120_atac

value: transposed genomic DNA


title: 26H_WT3_6W

description: 75bp SE

value: Aag WT


title: Wt_F_D671_GEx


title: 31H_KO4_5D

description: 75bp SE


title: 27H_WT3_6M

description: 75bp SE

value: 6 months


title: 25H_WT3_5D

description: 75bp SE


title: 24H_KO3_6M

description: 75bp SE


title: Tg_M_M64_GEx

value: tgXist/-

value: Dox+Pristane


title: Wt_F_D671_atac


title: 23H_KO3_6W

description: 75bp SE

value: Aag KO


title: 22H_KO3_5D

description: 75bp SE

value: 5 days


title: Tg_M_M64_atac

value: CD45+ spleen


title: 41P_KO1_6W

description: 75bp SE

value: Prefrontal cortex


title: 18H_WT2_6M

description: 75bp SE

value: Hippocampus


title: 17H_WT2_6W

description: 75bp SE


title: 15H_KO2_6M

description: 75bp SE


title: Tg_M_M60_GEx

value: SJL/J

value: Male


title: Tg_M_M60_atac


title: 14H_KO2_6W

description: 75bp SE

value: 6 weeks


title: 13H_KO2_5D

description: 75bp SE


title: 5H_KO1_6W

description: 75bp SE


title: 8H_WT1_6W

description: 75bp SE


title: 7H_WT1_5D

description: 75bp SE


title: 6H_KO1_6M

description: 75bp SE


title: Tg_M_M133_atac


title: 4H_KO1_5D

description: 75bp SE


title: Tg_M_M101_GEx


title: RE-RE_ADX_7.ZT12

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

data_processing:
Sequencing reads were pre-processed using the nf-core/rnaseq v1.2 pipeline, and read quality was assessed by FastQC v0.11.8.
TrimGalore v0.5.0 was used to trim sequencing reads, eliminate Illumina adaptor remains, and discard short reads.
The resulting reads were mapped onto the mouse genome using HiSAT2 v2.1.0 and quantified using featureCounts v1.6.2.
TMM-normalized FPKM values were calculated using Bioconductor package edgeR v3.30.0 and log2-transformed with a pseudo count of 0.01.
The expression data was adjusted for batch effect using the Bioconductor package sva v3.36.0.
13500 genes with average non-transformed FPKM expression > 0.5 in at least one time point of at least one experimental condition were considered for further analysis.
Assembly: GRCm38, release 81
Supplementary files format and content: Tab-delimited text file with log2-transformed FPKM gene expression values for each sample.

source_name: tibialis anterior muscle

extract_protocol:
After homogenization of tibialis anterior muscle with Qiazol reagent (Qiagen #1023537) RNA was isolated using miRNeasy Mini Kit (Qiagen #1038703). RNA quality was checked using Nanodrop and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent).
RNA-seq libraries were sequenced in single-end mode with a read length of 60 base pairs with an average of 25 million reads for each sample at the Genomic Unit of CNIC (Illumina HiSeq 4000).

treatment_protocol: Tibialis anterior muscle was collected and snap frozen with liquid nitrogen at two different time point intervals during 24hr period (ZT0 and ZT12).

value: female

tag: age

value: 18 weeks

tag: feeding

value: ad libitum

tag: zeitgeber time

value: whole muscle

value: Adrenalectomy


title: Tg_M_M101_atac

value: transposed genomic DNA


title: RE-RE_ADX_8.ZT12

value: 16 weeks


title: 16H_WT2_5D

description: 75bp SE

value: Aag WT


title: Tg_M_D795_GEx

value: tgXist/-

value: Dox+Pristane

value: cDNA


title: Tg_M_D739_GEx

value: CD45+ spleen


title: RE-RE_ADX_1.ZT0

value: 11 weeks


title: 9H_WT1_6M

description: 75bp SE

value: Hippocampus

value: 6 months


title: RE-RE_ADX_6.ZT12


title: RE-RE_ADX_2.ZT0

value: 15 weeks


title: RE-RE_ADX_4.ZT0

value: 8 weeks


title: RE-RE_SHAM_8.ZT12

value: female

value: 14 weeks

value: Sham


title: Tg_M_M133_GEx

value: SJL/J

value: Male


title: RE-RE_SHAM_6.ZT12

value: ad libitum

value: whole muscle


title: RE-RE_ADX_5.ZT12

value: 12 weeks

value: Adrenalectomy


title: Tg_M_D739_atac

value: tgXist/-

value: Dox+Pristane

value: transposed genomic DNA


title: RE-RE_SHAM_7.ZT12

value: 13 weeks


title: RE-RE_SHAM_4.ZT0


title: Tg_M_D795_atac

value: CD45+ spleen


title: Tg_M_D665_GEx

value: cDNA


title: Tg_M_D665_atac


title: RE-RE_SHAM_2.ZT0

value: 11 weeks


title: RE-RE_SHAM_3.ZT0

value: 9 weeks


title: Tg_M_D651_GEx


title: RE-RE_SHAM_1.ZT0

value: female


title: WT_ADX+DEX_8.ZT12

value: wild-type

value: 14 weeks

value: Adrenalectomy + dexamethasone (Dex) treated


title: Tg_M_D651_atac

value: SJL/J

value: Male


title: WT_ADX+DEX_7.ZT12

value: ad libitum

value: whole muscle


title: RE-RE_ADX_3.ZT0

value: Adrenalectomy


title: WT_ADX+DEX_6.ZT12


title: eWAT,high fat diet for 17 weeeks [HFD-3]

city: Nantong

first: Jinyu

last: Ma

address: 19 Qixiu Road, Nantong 226001, China.

country: China

institute: Nantong University

data_processing:
Filtering of Clean Reads(version 0.18.0)
Alignment with Ribosome RNA (version 2.2.8)
Alignment with Reference Genome(HISAT2. 2.4)
Quantification of Gene Abundance(StringTie v1.3.1 and RSEM)
Differentially expressed genes(DESeq2)
Assembly: Ensembl_release104
Supplementary files format and content: fpkm values of  each samples
Supplementary files format and content: reads count data obtained in gene expression level analysis

source_name: eWAT,high fat diet for 17 weeeks

extract_protocol:
Briefly, total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. The resulting enriched mRNA was fragmented into short fragments using fragmentation buffer and reversely transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina
The purified double-stranded cDNA fragments were end repaired, a base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads. Ligated fragments were then subjected to size selection by agarose gel electrophoresis and PCR amplification. The resulting cDNA library was sequenced using Illumina Novaseq6000 at Gene Denovo Biotechnology Co.

value: Epididymal adipose tissue

value: wild type

value: high fat diet


title: WT_ADX+DEX_5.ZT12


title: Wt_M_H2O_PBS_D419_CD4_RNA

data_processing:
RNA-seq data was aligned to mm10 using STAR
RSEM was used to generate gene expression read counts.
DESeq2 was used to normalize and analyze RNA-seq read counts
Assembly: mm10
Supplementary files format and content: RSEM generated matrix of RNA-seq raw readCounts

extract_protocol:
At 52 weeks post-injection, spleens were harvested and mechanically dissociated. CD4+ cells were isolated from freshly dissociated mouse spleen using the EasySep Mouse CD4+ T cell Isolation Kit (STEMCELL Technologies, 19852).
Freshly isolated CD4+ cells were prepared using the stranded mRNA Library Prep (Illumina, 20020594) to generate polyA-selected RNA-sequencing libraries. Cleanup performed on magnets with AMPure XP beads (Beckman Coulter, A63880).

value: CD4+ spleen

value: Wt

value: PBS


title: RE-RE_SHAM_5.ZT12

value: 12 weeks

value: Sham


title: WT_ADX+DEX_3.ZT0

value: female


title: eWAT,high fat diet for 17 weeeks [HFD-2]


title: WT_ADX+DEX_2.ZT0

value: wild-type


title: eWAT,high fat diet for 17 weeeks [HFD-1]


title: WT_ADX+ADR_6.ZT12

value: 13 weeks

value: Adrenalectomy + adrenaline (Adr) treated


title: WT_ADX+ADR_7.ZT12


title: eWAT,high fat diet for 17 weeeks [CD44-2]


title: eWAT,high fat diet for 17 weeeks [CD44-3]


title: eWAT,high fat diet for 17 weeeks [CD44-1]


title: WT_ADX+ADR_4.ZT0

value: 14 weeks


title: WT_ADX+ADR_3.ZT0


title: WT_ADX+DEX_1.ZT0

value: Adrenalectomy + dexamethasone (Dex) treated


title: PD1+Tim3+WT, mRNA-derived cDNA

city: Shinjuku-ku

first: Taeko

last: Hayakawa

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology, Institute for Advanced Medical Research

country: Japan

institute: Keio University School of Medicine

description: poly A RNA

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2
(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix(.h5)

source_name: tumor

extract_protocol:
On day 10, after adoptive transfer TILs were isolated andCD8+TIM3+PD1+TILs were sorted and used as ascRNA-seq sample.
Library was performed according to the manufacter’s instructions (Chromium Next GEM SIngle Cell 5'Reagent Kits v2, 10x Genomics).

value: tumor

tag: cell line

value: CD8 TIL


title: WT_ADX+ADR_5.ZT12

value: ad libitum

value: whole muscle


title: PD1+Tim3+KO, mRNA-derived cDNA

description: poly A RNA


title: WT_ADX+ADR_1.ZT0


title: WT, mRNA-derived cDNA

description: poly A RNA

extract_protocol:
On day 14, after tumor inoculation TILs were isolated andCD45+TILs mice weresorted andused as a scRNA-seq sample.
Library was performed according to the manufacter’s instructions (Chromium Next GEM SIngle Cell 5'Reagent Kits v2, 10x Genomics).

value: CD45 TIL


title: WT_ADX+DEX_4.ZT0

value: 11 weeks


title: WT_ADX_4.ZT12

value: Adrenalectomy


title: WT_ADX_3.ZT0


title: WT_ADX_2.ZT0

value: 15 weeks


title: WT_ADX_6.ZT12

value: 16 weeks


title: CD4Cre, mRNA-derived cDNA

description: poly A RNA


title: WT_ADX_1.ZT0


title: LLC, KO, scRNAseq

city: Shanghai

first: junhao

last: hu

address: 100 Haike Road, Zhangjiang High tech Park, Pudong

institute: The Interdisciplinary Research Center on Biology and Chemistry

description: 10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger software v6.1.1.
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: LLC tumor

extract_protocol:
Tumors were gently minced into small pieces using scissors, and subsequently transferred into a 15 ml tube containing the digestion solution (2 mg/ ml Collagenase type IV (C5138, Sigma), 2.5 mg/ ml Dispase II (4942078001, Sigma), 40 µg/ ml DNase (10104159001, Sigma) in DMEM). Tumors were digested for 30 minutes at 37°C with continuous rotation. Following digestion, the resulting cell suspensions were filtered through 70 µm cell strainers (CSS010070, Jetbiofil) placed on 50 ml tubes. The cell suspensions were subsequently centrifuged at 300×g for 7 minutes at 4°C. The supernatants were aspirated completely. The cell pellets were re-suspended in 5 ml 1x ACK buffer on ice for 3 minutes to lyse the erythrocytes. Next, 8 ml PBS was added into the tubes to stop reaction. In the end, the cells were centrifuge at 300xg for 7 minutes at 4°C and resuspended with PBS for further analysis.
Library was performed accoring to manufacter's instructions (single cell 3' v3.1 protocol, 10X Genomics)

value: LLC tumor

value: Cspg4-CreER^T2::Gucyc1b1 flox/flox


title: WT_SHAM_6.ZT12

value: female

value: 10 weeks

value: Sham


title: WT_SHAM_8.ZT12

value: wild-type

value: 12 weeks


title: WT_ADX+ADR_2.ZT0

value: 14 weeks

value: Adrenalectomy + adrenaline (Adr) treated


title: WT_ADX+ADR_8.ZT12

value: 13 weeks


title: WT_SHAM_7.ZT12

value: ad libitum


title: vivo CellHashing for PD1+Tim3+ CD8 T cell rep2 [T cells, HTO-derived cDNA_rep2]

description: Hashtag-derived oligonucleotide(HTO1,2,3)

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1
(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix(.h5)

molecule: protein

source_name: B16-OVA tumor

extract_protocol:
Three weeks after tumor injection, CD3e+CD8+ TILs, CD3e+CD8+PD1+Tim3+ Lag3+ TILs before tamoxifen treatment and tdTomato+ after tamoxifen treatment were isolated by FACS AriaIII as a single-cell RNA-seq sample.
Library was performed according to the manufacter’s instructions (Chromium Next GEM SIngle Cell 5'Reagent Kits v2, 10x Genomics).

value: B16-OVA tumor

value: CD8+PD1+Tim3+ TIL

value: NR4a1 flox/flox NR4a2 flox/flox OT-I Tg/+ tdTomato+

value: tamoxifen


title: WT_ADX_7.ZT12

value: 17 weeks

value: whole muscle

value: Adrenalectomy


title: vivo PD1+Tim3+ CD8 T cell of WT and Nr4a rep2 [TAM rep2]

description: poly A RNA


title: fetal liver, TiO2, 13.11 h, replicate 16

city: Gentofte

first: Albin

last: Sandelin

address: Markvangen 26

country: Denmark

institute: University of Copenhagen

data_processing:
Basecalling done bg Novogene as part of paid service. Sequencing produced a total of 828 libraries (414 paired end), with a median read depth of 24*106 reads (mean 25*106 reads, min 19.9 and max 46.6106), all of which passed initial QC controls performed by multiqc56. We detected base-pair overrepresentation in the first 11 bp of each read, as expected due to biases in random primers, and removed them using the trimfq command from seqtk (https://github.com/lh3/seqtk). Reads were mapped to gencode mouse transcriptome version M2357, which is an annotation of the genome assembly version GRCm38. In order to perform pseudo-mapping with Salmon58, we created an index using k-mer size 31 bp and supplying the genome in order to create decoy k-mers to account for biases due to un-annotated transcribed genomic regions (as described in Salmon documentation). We mapped libraries to the resulting index using Salmon quant using the following options: gcBias, seqBias, validateMappings, numBootstraps=10 and minScoreFraction=0.8. Finally, we annotated the resulting quant files using the R library tximeta59 and removed all features that lacked annotation. We performed all initial exploratory analyses and plots (e.g. PCA) using TPM-normalized data, and used the raw count data for the differential expression analysis. Before fitting statistical models, we normalised the count data from Salmon using TMM, retained only transcripts with more than 10 reads in at least 70% of the samples of the same condition, and applied voom correction for mean/variance relationship using the limma package60.
Assembly: gencode mouse transcriptome version M23
Supplementary files format and content: TPM matrix summarizing all samples

source_name: fetal liver

growth_protocol: Animals : Nulliparous C57BL/6JRj mice (Janvier, Saint Berthevin Cedex, France) from the same barrier were time-mated and pregnancy confirmed by the presence of vaginal plug the morning after mating (designated gestation day (GD) 0). Dams arrived at the institute at GD 11 or 12 and were allowed to acclimate for 6-7 days prior to exposure. Mice were pair housed in clear 1290D euro standard polypropylene cages with Aspen bedding (Tapvei, Estonia), enrichment (mouse house 80-ACRE011, Techniplast, Italy; small aspen blocks, Tapvei, Estonia) and nesting material (Enviro Dri, Lillico, Biotechnology, UK), under controlled conditions and access to food (Altromin 1314 for breeding, Brogaaarden, Denmark) and tap water ad libitum. Animals were weighed on the day of arrival and the day prior to exposure to confirm pregnancy.

extract_protocol:
Isolation of pups and maternal/fetal organs: At 2, 5, 12 and 24 h, dams were terminally anesthetized by subcutaneous injection of 0.2 ml of Zoletil mixture (tiletamin/zolazepam, xylazin og fentanyl) and killed by exanguination by withdrawal of heart blood into Eppendorf tubes containing 36 ml K2EDTA (n=7-9 per exposure/time point). The uterus was excised and opened. Fetuses were excised from their embryonic sac, their viability confirmed, killed by decapitation, sexed by visual inspection, and their position in the uterus noted. From each litter, the first female fetus encountered in the right uterine horn, counting from the cervix, was selected and saved for analyses. The placenta was dissected into chorion and decidua by blunt/stump dissection under. From dams, the liver and right lung were dissected. Dissected organs were snap frozen in liquid nitrogen and kept at -80ºC. Fetal livers were dissected later. Maternal blood was centrifuged at 2000xg at 4°C for 5 min and plasma was stored in aliquots at -80°C until analysis. A maximum of one female fetus from each dam were used for any one outcome. RNA extraction: Total RNA was isolated from frozen maternal lung and liver, chorion, decidua and fetal liver. Briefly, 20 - 50 mg of tissue was homogenized with a blender in 700 ul lysis buffer with 7 ul mercapto-ethanol. RNA extraction was carried out utilizing magnetic beads technology, on a chemagic Prepito® (Perkin Elmer, Waltham, Massachusetts), as recommended by the manufacturer. Concentration and purity were measured on a NanoDrop1000 spectrophotometer, with all samples showing an A260/280 ratio between 1.9 and 2.1. RNA integrity was analyzed by 2100 Bioanalyzer (Agilent Technologies) with Agilent RNA 6000 Pico Kit (Agilent Technologies) as recommended by manufacturer. All samples used for RNAseq displayed RNA integrity number (RIN) above 7. cDNA library construction and paired end sequencing was carried out by Novogene (Hongkong). To exclude ribosomal RNA, polyA selection was done.
Novogene paid service

treatment_protocol: Exposure: Lipopolysaccharide (LPS; E. Coli serotype 00:55 B5 LPS (Sigma Lot nr. 025M4040V)) was diluted to the final concentration (0.02 µg/µl) in double distilled pyrogen-free water (Chem-Lab, Zedelgem, Belgium). In the morning of GD 17, the pregnant mice were divided into control and LPS treatment groups, evenly distributing weights among the groups. Animals were placed in a whole-body inhalation chamber with an attached anaesthetic vaporizer  delivering 3-4% isoflurane in filtered air, and were intratracheally instilled with 50 µl of vehicle (control group) or 1 μg LPS in 50 µl vehicle, followed by 200μl of air. Vehicle and LPS were administered through a 0.58 mm polyethylene tube (Ref: 427411, Becton Dickinson, Brøndby, Denmark) attached to a plastic syringe. After instillation, animals were returned to their cage, briefly placed on heating pads and checked upon regularly until euthanization.

value: fetal liver

value: WT


title: WT_SHAM_3.ZT0

value: female

value: 9 weeks


title: WT_ADX_5.ZT12

value: wild-type

value: 16 weeks


title: WT_SHAM_2.ZT0

value: 10 weeks

value: Sham


title: WT_SHAM_1.ZT0


title: WT_SHAM_5.ZT12


title: WT_SHAM_4.ZT0

value: 11 weeks


title: fetal liver, H2O, 13.11 h, replicate 50


title: fetal liver, TiO2, 13.11 h, replicate 15


title: T cells, HTO-derived cDNA

description: Hashtag-derived oligonucleotide(HTO1,2,3,4)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1
(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix(.h5)

extract_protocol:
On day 10, after adoptive transfer CD8+ TILs of each implanted mice were used as a single-cell RNA-seq sample.
Library was performed according to the manufacter?s instructions (Chromium Next GEM SIngle Cell 5'Reagent Kits v2, 10x Genomics).

value: WT & NR4aDKO


title: fetal liver, H2O, 15.11 h, replicate 46


title: fetal liver, LPS, 15.11 h, replicate 39

value: LPS


title: Tex_GEM

description: poly A RNA

value: B16-OVA tumor

value: CD8+PD1+Tim3+ TIL


title: fetal liver, TiO2, 19.11 h, replicate 5


title: T cells, HTO-derived cDNA [vivo CellHashing for CD3 of WT and Nr4a KO]

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO1,2,3,4,5,6)

data_processing:
Adapter trimming of sequencing data was performed by using cutadapt 2.10. Filtered reads were chunked to 16 parts for parallel processing by using Seqkit 0.9.0.
Filtered cell barcode reads were annotated by Python script provided by BD with minor modification for compatible to Python3.7, associated cDNA reads were mapped to Ensembl cDNA and ncRNA (build GRCm38, release-101) by using Bowtie2-2.3.4.1 by the following parameters: -N 1 - -very-sensitive-local --seed 656565 --reorder, and associated Hashtag reads were mapped to Known barcode sequence+BAAAAA by using Bowtie2-2.4.2 by the following parameters:-D 50 -R 20 -N 0 -L 8 -i S,1,0.75 --norc --seed 656565 --reorder --trim-to 3:21 --score-min L,-9,0 --mp 3,3 --np 3 --rdg 3,3.
Cell barcode information of each read was added to the bowtie2-mapped BAM files, and read counts of same gene symbols of each cell barcode were counted. Inflection point of the knee-plot of cell barcode/read number was detected by using DropletUtils package in R 3.5.3, and cell barcodes below the inflection threshold were filtered out.
Each hashtag read was normalized by total read counts into the smallest total read counts linearly and each cell were annotated to each hashtag based on fold-change between first- and second-most highly counted hashtags. Cells were ordered ascending by the fold-change, and top 3.82 % cells were filtered out as doublet cells (probability of the % of doublet was estimated by Poisson's distribution calculated by load cell number and total number of Rhapsody wells).
Distribution-based error correction for background subtraction of gene-expression matrix was performed as described previously (Shichino et al., Commun Biol 2022) with the following parameters (maximum expression of log2(x+1) was over 8, maximum average expression of first component was over 5.5, and minimum difference of average expression between first- and second-components was over 5).
Assembly: GRCm38 release 101
Supplementary files format and content: gene-expression matrix (.txt.gz)
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: B16F10 subcutaneouse tumor

extract_protocol:
intratumor CD3⁺ cells were isolated using an autoMACS Pro Separator by positive selection after Percoll enrichment. To obtain scRNA-seq data, we used an BD Rhapsody system (BD Biosciences) and TAS-Seq.
Resulted cells were trapped and reverse-transcribed using an BD Rhapsody system (BD) according to the manufacturer’s instructions, followed by the preparation of cDNA libraries and hashtag libraries by TAS-Seq method (Shichino et al. Commun. Biol,, 2022). The library preparation and sequencing analysis were conductd by ImmunoGeneTeqs, Inc (Chiba, Japan) by using Novaseq 6000 sequencer (Illumina, San Diego, CA, USA) and Novaseq S4 200 cycles v1.5 kit (Illumina).

value: B16F10 subcutaneouse tumor

value: CD3e-enriched T cells


title: fetal liver, LPS, 19.11 h, replicate 30


title: LLC, CT, scRNAseq

description: 10X Genomics

value: LLC tumor

value: Gucy1b1 flox/flox


title: fetal liver, LPS, 19.11 h, replicate 29

value: fetal liver


title: T cells , mRNA-derived cDNA [vivo CD3 WT and Nr4a KO]

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
cell names in processed files are as follows: [HTO ID]_[DataID]_[Cell barcode number]


title: fetal liver, H2O, 19.11 h, replicate 23

value: WT


title: vivo CellHashing for PD1+Tim3+ CD8 T cell rep1 [T cells, HTO-derived cDNA_rep1]

value: NR4a1 flox/flox NR4a2 flox/flox OT-I Tg/+ tdTomato+

value: tamoxifen


title: fetal liver, LPS, 19.11 h, replicate 26


title: fetal liver, LPS, 19.11 h, replicate 28


title: vivo Nr4a dKO PD1+Tim3+ CD8 T cell rep2

description: vivo Nr4a dKO PD1+Tim3+ CD8 T cell rep2

data_processing:
Adapter trimming and quality filtering of resulting fastq files were performed by using Cutadapt-v1.18.
Trimmed reads were mapped to the Refseq mm10 RNA by using Bowtie2-2.2.5.
Tag numbers of each gene represented the expression level of each gene and were used as count data.
Assembly: mm10
Supplementary files format and content: The raw read counts were normalized with transcripts per million (TPM).

extract_protocol:
On day 10, after adoptive transfer CD3e+CD8+PD1+Tim3- and CD3e+CD8+PD1+Tim3+ TILs of each implanted mouse were isolated and used as a RNA-seq sample
RNA was harvested using Rnaeasy mini plus kit (Qiagen)


title: fetal liver, H2O, 19.11 h, replicate 22


title: fetal liver, LPS, 19.11 h, replicate 27


title: fetal liver, H2O, 19.11 h, replicate 21


title: fetal liver, LPS, 19.11 h, replicate 25


title: fetal liver, H2O, 19.11 h, replicate 20


title: fetal liver, LPS, 13.11 h, replicate 47


title: vivo Nr4a dKO PD1+Tim3+ CD8 T cell rep1

description: vivo Nr4a dKO PD1+Tim3+ CD8 T cell rep1


title: vivo WT PD1+Tim3+ CD8 T cell rep1

description: vivo WT PD1+Tim3+ CD8 T cell rep1


title: fetal liver, LPS, 15.11 h, replicate 38


title: fetal liver, H2O, 19.11 h, replicate 24


title: vivo PD1+Tim3+ CD8 T cell of WT and Nr4a rep1 [TAM rep1]

description: poly A RNA


title: fetal liver, H2O, 15.11 h, replicate 45


title: fetal liver, TiO2, 13.11 h, replicate 14


title: fetal liver, LPS, 13.11 h, replicate 46


title: vivo Nr4a dKO PD1+Tim3- CD8 T cell rep1

description: vivo Nr4a dKO PD1+Tim3- CD8 T cell rep1

value: CD8+PD1+Tim3- TIL


title: fetal liver, LPS, 13.11 h, replicate 45


title: vivo WT PD1+Tim3- CD8 T cell rep2

description: vivo WT PD1+Tim3- CD8 T cell rep2


title: fetal liver, H2O, 13.11 h, replicate 49


title: fetal liver, H2O, 13.11 h, replicate 48


title: vivo WT PD1+Tim3- CD8 T cell rep1

description: vivo WT PD1+Tim3- CD8 T cell rep1


title: fetal liver, H2O, 13.11 h, replicate 47


title: fetal liver, LPS, 13.11 h, replicate 43


title: vitro dKO 48hr rep2

source_name: CD8+ T cell

extract_protocol:
After 24 or 48 hr,  the cultured cells in vitro were harvested as a bulk RNA sequencing sample.
RNA was collected using Rnaeasy mini plus kit (Qiagen)

value: CD8+ T cell


title: fetal liver, H2O, 13.11 h, replicate 45


title: fetal liver, H2O, 13.11 h, replicate 46


title: vitro dKO 48hr rep1


title: fetal liver, LPS, 13.11 h, replicate 42


title: vitro WT 48hr rep2


title: fetal liver, LPS, 13.11 h, replicate 41


title: vivo WT PD1+Tim3+ CD8 T cell rep2

description: vivo WT PD1+Tim3+ CD8 T cell rep2


title: vivo Nr4a dKO PD1+Tim3- CD8 T cell rep2

description: vivo Nr4a dKO PD1+Tim3- CD8 T cell rep2


title: fetal liver, LPS, 13.11 h, replicate 40


title: vitro WT 48hr rep1


title: fetal liver, H2O, 13.11 h, replicate 44


title: fetal liver, H2O, 13.11 h, replicate 43


title: fetal liver, H2O, 13.11 h, replicate 42


title: vitro WT 24hr rep2


title: fetal liver, LPS, 13.11 h, replicate 44


title: fetal liver, LPS, 13.11 h, replicate 39


title: vitro dKO 24hr rep1


title: vitro dKO 24hr rep2


title: fetal liver, H2O, 12.11 h, replicate 20


title: fetal liver, LPS, 12.11 h, replicate 21


title: fetal liver, LPS, 12.11 h, replicate 19


title: fetal liver, H2O, 12.11 h, replicate 19


title: vitro WT 24hr rep1


title: fetal liver, LPS, 12.11 h, replicate 18


title: fetal liver, H2O, 12.11 h, replicate 18


title: exp2_hh_nfil3_ko_hybrid_2

city: St. Louis

first: Feiya

last: Ou

state: MO

address: 4939 Children's Place

department: Pathology & Immunology

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.
RNA-seq reads were aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software
Raw gene counts were imported to R using the EdgeR package for downstream analyses. After filtering out lowly expressed genes, counts were trimmed mean of M-values (TMM)-normalized for differential expression analysis.
464 genes were identified as being differentially expressed between WT cDC1 and cDC2 with greater than 4-fold changes and FDR below 0.001.
Supplementary files format and content: exp1_all.gene_counts.tsv: tab-delimited file includes gene counts for each sample in exp1
Supplementary files format and content: exp2_all.gene_counts.tsv: tab-delimited file includes gene counts for each sample in exp2
Supplementary files format and content: exp1_processed_data.xlsx: spreadsheet includes differential expression results for each sample in exp1

source_name: spleen

extract_protocol:
Total RNA was extracted from sort-purified cDC populations using NucleoSpin RNA XS (Macherey-Nagel). Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 9.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: spleen

value: hybrid cDC

value: Irf8 +32H/H Nfil3-/-


title: fetal liver, H2O, 12.11 h, replicate 17


title: exp2_hh_nfil3_ko_hybrid_1


title: fetal liver, TiO2, 15.11 h, replicate 11


title: exp2_hh_d123_hybrid_2


title: fetal liver, TiO2, 15.11 h, replicate 10


title: fetal liver, H2O, 15.11 h, replicate 44


title: exp2_hh_d123_hybrid_1


title: fetal liver, H2O, 15.11 h, replicate 43


title: fetal liver, LPS, 15.11 h, replicate 36


title: fetal liver, LPS, 15.11 h, replicate 35


title: fetal liver, LPS, 15.11 h, replicate 37


title: fetal liver, H2O, 15.11 h, replicate 42


title: fetal liver, LPS, 15.11 h, replicate 34


title: fetal liver, LPS, 12.11 h, replicate 20


title: exp2_hh_hybrid_1

value: Irf8 +32H/H


title: exp2_hh_hybrid_2


title: fetal liver, H2O, 15.11 h, replicate 40


title: exp2_hh_nfil3_ko_dc1_2


title: fetal liver, H2O, 5.11 h, replicate 46


title: fetal liver, H2O, 15.11 h, replicate 39


title: fetal liver, H2O, 15.11 h, replicate 41


title: exp2_wt_dc1_2


title: fetal liver, LPS, 15.11 h, replicate 33

value: LPS


title: fetal liver, TiO2, 5.11 h, replicate 9


title: fetal liver, TiO2, 5.11 h, replicate 10


title: fetal liver, LPS, 5.11 h, replicate 46


title: fetal liver, LPS, 15.11 h, replicate 32


title: fetal liver, H2O, 15.11 h, replicate 38


title: fetal liver, LPS, 5.11 h, replicate 44


title: fetal liver, H2O, 5.11 h, replicate 45


title: exp2_hh_dc1_2


title: exp2_hh_dc1_1


title: fetal liver, H2O, 5.11 h, replicate 44


title: exp1_hh_dc2_2


title: fetal liver, LPS, 5.11 h, replicate 43


title: fetal liver, H2O, 5.11 h, replicate 43


title: exp1_hh_dc2_1


title: fetal liver, H2O, 5.11 h, replicate 42


title: fetal liver, LPS, 5.11 h, replicate 42


title: exp1_hh_hybrid_2


title: fetal liver, LPS, 5.11 h, replicate 41


title: fetal liver, LPS, 5.11 h, replicate 40


title: exp1_hh_hybrid_1


title: exp2_hh_nfil3_ko_dc1_1


title: exp2_wt_dc1_1


title: fetal liver, H2O, 5.11 h, replicate 40


title: fetal liver, LPS, 5.11 h, replicate 39


title: fetal liver, H2O, 5.11 h, replicate 39


title: exp1_hh_dc1_2


title: fetal liver, LPS, 5.11 h, replicate 38


title: fetal liver, LPS, 5.11 h, replicate 45


title: exp1_hh_dc1_1


title: fetal liver, H2O, 5.11 h, replicate 38


title: fetal placenta, H2O, 13.11 h, replicate 40

source_name: fetal placenta

value: fetal placenta


title: fetal placenta, LPS, 12.11 h, replicate 17


title: exp1_h+_dc2_2


title: fetal liver, H2O, 5.11 h, replicate 41


title: exp1_h+_hybrid_2


title: fetal placenta, H2O, 13.11 h, replicate 41


title: fetal placenta, H2O, 15.11 h, replicate 37


title: fetal placenta, H2O, 13.11 h, replicate 39


title: fetal placenta, TiO2, 13.11 h, replicate 13


title: fetal placenta, TiO2, 13.11 h, replicate 12


title: exp1_h+_hybrid_1


title: exp1_h+_dc1_1


title: fetal placenta, LPS, 5.11 h, replicate 37


title: fetal placenta, LPS, 15.11 h, replicate 31


title: fetal placenta, H2O, 15.11 h, replicate 36


title: exp1_wt_dc2_1


title: exp1_h+_dc2_1


title: fetal placenta, TiO2, 19.11 h, replicate 4


title: exp1_h+_dc1_2


title: fetal placenta, LPS, 19.11 h, replicate 24


title: M430_Granulocytes

type: genomic

city: Gdańsk

first: Marcin

last: Jakalski

address: Dębinki 7

department: 3P Medicine Laboratory

country: Poland

institute: Medical University of Gdańsk

description:
granulocyte sample from normal control
203219760193_R05C01

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Human MethylationEPIC Beadchips using standard Illumina protocol.

scan_protocol: Illumina iScan System as per manufacturer’s protocol

data_processing:
Illumina® GenomeStudio, normalized with R package wateRmelon (QN + BMIQ)
Processed data files include: Average M value

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Granulocytes

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from granulocytes and monocytes using Qiagen DNeasy Kit according to standard instructions

value: Granulocytes

tag: gender

value: Male

tag: donor id

tag: loy status

value: non-LOY

tag: sample type

value: genomic DNA

tag: disease state

value: control


title: fetal placenta, H2O, 19.11 h, replicate 18

tag: tissue


title: fetal placenta, H2O, 5.11 h, replicate 37


title: fetal placenta, LPS, 19.11 h, replicate 23


title: fetal placenta, H2O, 19.11 h, replicate 19


title: exp1_wt_dc1_2


title: fetal placenta, H2O, 19.11 h, replicate 17


title: fetal placenta, LPS, 19.11 h, replicate 22


title: M430_Monocytes

description:
monocyte sample from normal control
203219760193_R04C01

source_name: Monocytes

value: Monocytes


title: fetal placenta, LPS, 19.11 h, replicate 21

value: WT


title: M433_Granulocytes

description:
granulocyte sample from normal control
203219760193_R08C01


title: Bone-marrow, 35 d.p.i., B220-B220intB220+CD138+, BCR-seq

city: Pittsburgh

first: Harinder

last: Singh

state: PA

address: 5051 Centre Avenue

department: Center for Systems Immunology and Department of Immunology

institute: University of Pittsburgh

description:
10X genomics - 5Prime - V1.1
filtered_contig_annotations.csv
filtered_contig.fasta
Experiment5_D35_BM_BCR

data_processing:
For all scRNA-Seq experiments, UMI counts were calculated using CellRanger (v.3.1.0) and reference genome set to mm10. CellRanger filtered feature sparse matrix counts files from the CD138+ splenocyte sample obtained on 35 d.p.i. (HDF5 format) were supplied for unsupervised analysis using ICGS2 algorithm with default parameters. Cell-type predictions were initially obtained from ICGS2 based on marker enrichment and then further refined based on manual curation with literature-associated markers. Non-B-lineage cells were identified according to their marker genes, and thereby excluded from the downstream analysis. The obtained ICGS2 clusters were filtered to include B cell and plasma cell clusters for downstream UMAP visualization.
For all single-cell experiments, the ICGS generated cell clusters defined for Day 35 cells from Experiment1 were used as the reference sets in the cellHarmony pipeline4. For each scRNA-Seq dataset, the marker genes defined for each ICGS2 cluster from Day 35 sample were used as the reference cluster markers and log-transformed normalized gene expression files were provided as the input for cellHarmony pipeline. The correlation cutoff parameter in cellHarmony was set to 0.7 to include only the cells with stronger matches to the reference cell clusters, thereby excluding low quality cells.
Single-cell VDJ sequencing data were processed using Cellranger vdj (v.3.1.0) with refdata-cellranger-vdj-GRCm 38-alts-ensembl-3.1.0 reference from 10x Genomics. Barcode information obtained from the CellRanger VDJ output and gene expression were used for coupling the BCR and transcriptomes respectively. Transcriptomes were labeled based on ICGS2 clusters obtained on 35 d.p.i. or cellHarmony clusters in the case of other datasets. Cells that did not contain both the BCR and gene expression features were excluded for any downstream analysis. The hypermutation rate and affinity maturation were determined for these cells as described previously2. For clonal analysis, cells were defined based on the following criteria. Clones were identified based on cells that bear identical V(D)J rearrangements in their heavy and light chain loci (kappa or lambda), including sharing of amino acid sequences encoded in VH CDR3 regions. If a cell contained multiple kappa and/or gamma chain rearrangements, then the productively rearranged light chain gene was used for clonal identity. This analysis was performed for 22 NP-specific VH genes and 19 KLH-specific VH genes.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scBCR-seq

extract_protocol:
Splenic and bone marrow cells (tibia, femur and iliac crest) were isolated from C57BL/6J mice immunized with NP-KLH, alum and LPS on 14, 21 and 35 d.p.i.. Splenocytes and BM cells were washed and prepared as single-cell suspensions in MACS buffer. Enriched CD138+ cells were obtained by using Easysepä Release Mouse Biotin Positive Selection Kit. Cell concentration was adjusted to 100 x 106 cells per mL and incubated with 50 μL of normal rat serum for 5 minutes. Biotinylated anti-CD138 (281.2) antibody (1.0 μg/mL) was added to the cells and incubated for 5 minutes. Next the cells were incubated (5 minutes) with Easysepä Biotin positive selection antibody (50 μL/mL) followed by addition of Easysepä Rapidspheres (100 μL/mL) (5 minutes). MACS buffer was added to the cocktail and an Easysepä magnet was used to remove cells that were not bound to rapidspheres. After three washes, CD138+ cells were obtained by incubating with Easysepä Release Buffer for 5 minutes and placing the cells in a magnet to release them from the Rapidspheres. Purity of enriched CD138+ cells was determined by flow cytometry after labeling a small fraction of the cells with viability dye eFluor 780 (eF780), APC Streptavidin and PE-Dazzle Red 594 B220 (RA3-6B2) for 30 minutes at 4˚C. For the isolation of CD138+ subsets by flow cytometry, enriched CD138+ cells after Rapidspheres release, were labeled with viability dye eFluor 780 (eF780), APC-Streptavidin, PE-Dazzle Red 594 B220 (RA3-6B2), PerCP-Cy5.5 CD44 (IM7) and FITC CD11a (M17/4) for 30 minutes at 4˚C and were sorted as B220+CD138+CD44-CD11a-, B220+CD138+CD44+CD11a+, B220intCD138+CD44+CD11a+ and B220-CD138+CD44+CD11a+ subsets using FACSAria II (BD) with 70 μm nozzle at 4˚C.
Enriched CD138+ splenocytes or flow sorted CD138+ splenic and BM subsets were suspended in 5% FBS and loaded along with oil and beads containing unique barcodes onto the Chromium controller (10x Genomics) to form an emulsion. Single cells contained in oil droplets were then lysed and mRNA was captured by the beads and subjected to reverse transcription and cDNA amplification to generate libraries for sequencing, according to the manufacturer’s protocol, as described previously2. From the cDNA libraries, one aliquot was used for fragmentation and preparation for transcriptome profiling, and another for amplification of VDJ regions using the BCR kit. Samples were then sequenced using a NovaSeq 6000 (Illumina) in which 30,000 and 5,000 reads were generated with the mRNA and BCR libraries respectively.

treatment_protocol: Seven to eight week old mice were immunized intraperitoneally with 100 μg NP(23)-KLH, NP(25)-KLH or NP(27)-KLH (Biosearch Technologies) mixed with 50% (v/v) imject alum (Thermo Fisher Scientific) and 1 μg LPS (Sigma).

value: Bone marrow

value: NP-KLH + Alum + LPS


title: exp1_wt_dc1_1


title: Bone-marrow, 35 d.p.i., B220-B220intB220+CD138+, scRNA-seq

description:
10X genomics - 5Prime - V1.1
filtered_feature_bc_matrix.h5
Experiment5_D35_BM_GEX

data_processing:
For all scRNA-Seq experiments, UMI counts were calculated using CellRanger (v.3.1.0) and reference genome set to mm10. CellRanger filtered feature sparse matrix counts files from the CD138+ splenocyte sample obtained on 35 d.p.i. (HDF5 format) were supplied for unsupervised analysis using ICGS2 algorithm with default parameters. Cell-type predictions were initially obtained from ICGS2 based on marker enrichment and then further refined based on manual curation with literature-associated markers. Non-B-lineage cells were identified according to their marker genes, and thereby excluded from the downstream analysis. The obtained ICGS2 clusters were filtered to include B cell and plasma cell clusters for downstream UMAP visualization.
For all single-cell experiments, the ICGS generated cell clusters defined for Day 35 cells from Experiment1 were used as the reference sets in the cellHarmony pipeline4. For each scRNA-Seq dataset, the marker genes defined for each ICGS2 cluster from Day 35 sample were used as the reference cluster markers and log-transformed normalized gene expression files were provided as the input for cellHarmony pipeline. The correlation cutoff parameter in cellHarmony was set to 0.7 to include only the cells with stronger matches to the reference cell clusters, thereby excluding low quality cells.
Single-cell VDJ sequencing data were processed using Cellranger vdj (v.3.1.0) with refdata-cellranger-vdj-GRCm 38-alts-ensembl-3.1.0 reference from 10x Genomics. Barcode information obtained from the CellRanger VDJ output and gene expression were used for coupling the BCR and transcriptomes respectively. Transcriptomes were labeled based on ICGS2 clusters obtained on 35 d.p.i. or cellHarmony clusters in the case of other datasets. Cells that did not contain both the BCR and gene expression features were excluded for any downstream analysis. The hypermutation rate and affinity maturation were determined for these cells as described previously2. For clonal analysis, cells were defined based on the following criteria. Clones were identified based on cells that bear identical V(D)J rearrangements in their heavy and light chain loci (kappa or lambda), including sharing of amino acid sequences encoded in VH CDR3 regions. If a cell contained multiple kappa and/or gamma chain rearrangements, then the productively rearranged light chain gene was used for clonal identity. This analysis was performed for 22 NP-specific VH genes and 19 KLH-specific VH genes.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: fetal placenta, LPS, 13.11 h, replicate 38


title: Spleen, 35 d.p.i., B220-B220intB220+CD138+, BCR-seq

description:
10X genomics - 5Prime - V1.1
filtered_contig_annotations.csv
filtered_contig.fasta
Experiment5_D35_SP_BCR

source_name: Spleen

value: Spleen


title: exp1_wt_dc2_2


title: fetal placenta, LPS, 19.11 h, replicate 20


title: M423_Granulocytes

description:
granulocyte sample from normal control
203219760193_R02C01


title: fetal placenta, H2O, 19.11 h, replicate 15


title: M423_Monocytes

description:
monocyte sample from normal control
203219760193_R01C01


title: M422_Granulocytes

description:
granulocyte sample from normal control
203220070094_R08C01

value: LOY


title: fetal placenta, LPS, 19.11 h, replicate 19


title: fetal placenta, H2O, 15.11 h, replicate 35


title: M422_Monocytes

description:
monocyte sample from normal control
203220070094_R07C01


title: Spleen, 35 d.p.i., B220-B220intB220+CD138+, scRNA-seq

description:
10X genomics - 5Prime - V1.1
filtered_feature_bc_matrix.h5
Experiment5_D35_SP_GEX


title: fetal placenta, H2O, 13.11 h, replicate 38


title: M42_Monocytes

description:
monocyte sample from normal control
203219760034_R06C01


title: fetal placenta, LPS, 13.11 h, replicate 37


title: Bone-marrow, 35 d.p.i., B220-B220intCD138+, BCR-seq

description:
10X genomics - 5Prime - V1
filtered_contig_annotations.csv
filtered_contig.fasta
Experiment4_D35_BM_BCR


title: Bone-marrow, 35 d.p.i., B220-B220intCD138+, scRNA-seq

description:
10X genomics - 5Prime - V1
filtered_feature_bc_matrix.h5
Experiment4_D35_BM_GEX


title: fetal placenta, LPS, 13.11 h, replicate 36


title: fetal placenta, H2O, 19.11 h, replicate 16


title: Spleen, 35 d.p.i., B220-B220intCD138+, BCR-seq

description:
10X genomics - 5Prime - V1
filtered_contig_annotations.csv
filtered_contig.fasta
Experiment4_D35_SP_BCR


title: M413_Granulocytes

description:
granulocyte sample from normal control
203220070094_R04C01


title: fetal placenta, H2O, 13.11 h, replicate 36


title: fetal placenta, H2O, 13.11 h, replicate 37


title: fetal placenta, LPS, 15.11 h, replicate 30


title: M419_Granulocytes

description:
granulocyte sample from normal control
203220070094_R06C01


title: fetal placenta, LPS, 13.11 h, replicate 34


title: Spleen, 35 d.p.i., B220-B220intCD138+, scRNA-seq

description:
10X genomics - 5Prime - V1
filtered_feature_bc_matrix.h5
Experiment4_D35_SP_GEX


title: fetal placenta, LPS, 13.11 h, replicate 35


title: fetal placenta, H2O, 13.11 h, replicate 35


title: fetal placenta, LPS, 13.11 h, replicate 33


title: Spleen, 35 d.p.i., B220-CD138+, BCR-seq

description:
10X genomics - 5Prime - V1
filtered_contig_annotations.csv
filtered_contig.fasta
Experiment3_D35_SP_BCR


title: M390_Granulocytes

description:
granulocyte sample from normal control
203220070094_R01C01


title: fetal placenta, H2O, 13.11 h, replicate 33


title: Spleen, 35 d.p.i., B220-CD138+, scRNA-seq

description:
10X genomics - 5Prime - V1
filtered_feature_bc_matrix.h5
Experiment3_D35_SP_GEX


title: M39_Granulocytes

description:
granulocyte sample from normal control
203219760034_R05C01


title: fetal placenta, H2O, 13.11 h, replicate 34


title: fetal placenta, TiO2, 13.11 h, replicate 11


title: fetal placenta, LPS, 13.11 h, replicate 32


title: fetal placenta, LPS, 13.11 h, replicate 31


title: Spleen, 14 d.p.i., NP-specific B cells, BCR-seq

description:
10X genomics - 5Prime - V1
filtered_contig_annotations.csv
filtered_contig.fasta
Experiment2_D14_SP_BCR


title: M39_Monocytes

description:
monocyte sample from normal control
203219760034_R04C01


title: fetal placenta, LPS, 13.11 h, replicate 30


title: Spleen, 14 d.p.i., NP-specific B cells, scRNA-seq

description:
10X genomics - 5Prime - V1
filtered_feature_bc_matrix.h5
Experiment2_D14_SP_GEX


title: M384_Granulocytes

description:
granulocyte sample from normal control
203219730005_R07C01


title: fetal placenta, LPS, 12.11 h, replicate 16


title: fetal placenta, H2O, 13.11 h, replicate 32


title: fetal placenta, H2O, 12.11 h, replicate 16


title: M382_Monocytes

description:
monocyte sample from normal control
203219730005_R05C01


title: fetal placenta, H2O, 12.11 h, replicate 15


title: fetal placenta, H2O, 12.11 h, replicate 14


title: M396_Granulocytes

description:
granulocyte sample from normal control
203220070094_R02C01


title: fetal placenta, LPS, 12.11 h, replicate 14


title: Spleen, 21 d.p.i., CD138+, BCR-seq

description:
10X genomics - 5Prime - V1
filtered_contig_annotations.csv
filtered_contig.fasta
Experiment1_D21_SP_BCR


title: fetal placenta, LPS, 12.11 h, replicate 13


title: M381_Granulocytes

description:
granulocyte sample from normal control
203219730005_R03C01


title: Spleen, 35 d.p.i., CD138+, BCR-seq

description:
10X genomics - 5Prime - V1
filtered_contig_annotations.csv
filtered_contig.fasta
Experiment1_D35_SP_BCR


title: fetal placenta, TiO2, 15.11 h, replicate 9


title: fetal placenta, H2O, 12.11 h, replicate 13


title: Spleen, 35 d.p.i., CD138+, scRNA-seq

description:
10X genomics - 5Prime - V1
filtered_feature_bc_matrix.h5
groups.Day_35-OutliersRemoved-refined.txt
MarkerGenes_withannotations.txt
Experiment1_D35_SP_GEX


title: M380_Granulocytes

description:
granulocyte sample from normal control
203219730005_R02C01


title: fetal placenta, LPS, 15.11 h, replicate 29


title: fetal placenta, TiO2, 15.11 h, replicate 8


title: M380_Monocytes

description:
monocyte sample from normal control
203219730005_R01C01


title: fetal placenta, H2O, 15.11 h, replicate 34


title: Spleen, 21 d.p.i., CD138+, scRNA-seq

description:
10X genomics - 5Prime - V1
filtered_feature_bc_matrix.h5
Experiment1_D21_SP_GEX


title: fetal placenta, LPS, 15.11 h, replicate 28


title: M359_Granulocytes

description:
granulocyte sample from normal control
203219730049_R08C01


title: Renal capsule aged rep 1

city: South San Francisco

first: Andrey

last: Shaw

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation was done using 10X Cell Ranger pipeline v6.0.2
Assembly: GRCm38
Supplementary files format and content: Tab-separated filtered counts files split into barcodes, features, and matrix.

source_name: Kidney

extract_protocol:
Following extraction of renal capsules from kidneys, renal capsules were transferred to 1 ml digestion buffer with LiberaseTM (1.5 U/ml; 5401127001, Millipore Sigma) and DNaseI (50 U/ml; D4527, Millipore Sigma) in RPMI-1640. Tissues were shredded using scissors and incubated for enzymatic digestion (37⁰C, 800 rpm, 15 min); samples were then sieved via a 100 μm then 70 μm  MACS® SmartStrainers (130-098-463, 130-098-462, Miltenyi Biotec) and 10 ml ice-cold 10% fetal bovine serum (FBS) in RPMI-1640 were added to stop digestion. Samples were kept on ice for further processing.
Sample processing for scRNA-seq was done using Chromium Next GEM Single Cell 3’ Kit v3.1 (1000269, 10X Genomics) according to manufacturer’s instructions.

treatment_protocol: no treatment

value: Kidney

value: renal capsule

value: whole tissue


title: fetal placenta, LPS, 12.11 h, replicate 15


title: fetal placenta, LPS, 15.11 h, replicate 27


title: M355_Granulocytes

description:
granulocyte sample from normal control
203219730049_R07C01


title: fetal placenta, H2O, 15.11 h, replicate 32


title: Renal capsule young rep 2


title: fetal placenta, H2O, 15.11 h, replicate 33


title: Renal capsule young rep 1


title: M355_Monocytes

description:
monocyte sample from normal control
203219730049_R06C01


title: fetal placenta, LPS, 15.11 h, replicate 26


title: M354_Granulocytes

description:
granulocyte sample from normal control
203219730049_R05C01


title: M353_Granulocytes

description:
granulocyte sample from normal control
203219730049_R04C01


title: fetal placenta, H2O, 15.11 h, replicate 30


title: fetal placenta, H2O, 15.11 h, replicate 31


title: RCAMs,aged,rep2

data_processing:
Data was processed using HTSeqGenie, a gsnap based NGS workflow that runs the BCB endorsed RNASeq workflows (https://bioconductor.org/packages/release/bioc/html/HTSeqGenie.html).
Assembly: GRCm38
Supplementary files format and content: Tab-separated files with raw gene counts for each sample

source_name: Renal Capsule

extract_protocol:
RNeasy Micro Kit (74004, Qiagen)
Truseq Stranded mRNA kit (Illumina)
Regular input RNA-Seq: total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies). For sequencinglibrary generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies).Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 millions single-end 50-base pairreads for each sample.
Low input RNA-Seq: total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific catalog#: Q32852) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies catalog#: 5067-5576). cDNA library was generated from 2 nanograms of total RNA using Smart-Seq V4 Ultra Low Input RNA Kit (Takara catalog#: 634894). 150 picograms of cDNA was used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina catalog#: FC-131-1024). Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific catalog#: Q32851) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies catalog#: 5067-5582).Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 millions single-end 50-base pairreads for each sample.

value: Renal Capsule


title: RCAMs,aged,rep1


title: Renal capsule aged rep 2


title: M350_Granulocytes

description:
granulocyte sample from normal control
203219730049_R02C01


title: fetal placenta, LPS, 5.11 h, replicate 36

value: LPS


title: RCAMs,aged,rep3


title: RCAMs,young,rep4


title: fetal placenta, H2O, 5.11 h, replicate 36

value: fetal placenta


title: M34_Granulocytes

description:
granulocyte sample from normal control
203219760034_R02C01

value: Granulocytes


title: fetal placenta, LPS, 15.11 h, replicate 25


title: RCAMs,young,rep3


title: M34_Monocytes

description:
monocyte sample from normal control
203219760034_R01C01

value: Male


title: fetal placenta, H2O, 15.11 h, replicate 29


title: M336_Monocytes

description:
monocyte sample from normal control
203219730049_R01C01

value: non-LOY


title: RCAMs,aged,rep4


title: RCAMs,young,rep2


title: fetal placenta, H2O, 15.11 h, replicate 28


title: M33_Monocytes

description:
monocyte sample from normal control
203219730222_R06C01

value: genomic DNA


title: Ing4Ing5_DKO_1459_4

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

data_processing:
Thebase calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the mouse genome by Rsubread version 2.12.3
Fragment (read-pair) counts were summarized by RefSeq Gene ID using the Rsubread featureCounts function
Genes were identified using Rsubreads inbuilt mm39 annotation
Assembly: mm39
Supplementary files format and content: tab-delimited text files wre written from the R prompt; columns represent RefSeq Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

source_name: embryonic mouse heart

extract_protocol:
Total RNA was isolated from E8.75 or E8.25 embryo hearts using an RNA isolation kit (Qiagen RNeasy Micro Kit; Qiagen 74004) according to manufacturer’s instructions.
RNA-sequencing libraries from 100 ng of RNA per sample were generated using a kit (TruSeq Stranded RNA library Prep Kit; Illumina 20020594) and indices (Illumina 20020492) following the manufacturer’s instructions.

tag: mouse id

tag: mouse litter

tag: Sex

value: M

value: embryonic mouse heart


title: M33_Granulocytes

description:
granulocyte sample from normal control
203219730222_R07C01

value: control


title: M352_Granulocytes

description:
granulocyte sample from normal control
203219730049_R03C01


title: fetal placenta, TiO2, 5.11 h, replicate 8

tag: genotype

value: WT

tag: treatment


title: Kidney,Macrophages,rep3

tag: cell type

value: Macrophages


title: fetal placenta, LPS, 15.11 h, replicate 24


title: Ing4Ing5_DKO_1459_3

value: F


title: Kidney,Macrophages,rep4


title: fetal placenta, TiO2, 5.11 h, replicate 7


title: Ing4Ing5_DKO_1459_2


title: Kidney,Macrophages,rep2


title: M31_Granulocytes

description:
granulocyte sample from normal control
203219760178_R02C01


title: Kidney,Macrophages,rep1


title: Ing4Ing5_DKO_1459_1


title: M31_Monocytes

description:
monocyte sample from normal control
203219760178_R01C01

value: Monocytes


title: fetal placenta, H2O, 5.11 h, replicate 35


title: Renal Capsule,Macrophages,rep4


title: M384_Monocytes

description:
monocyte sample from normal control
203219730005_R06C01


title: M306_Monocytes

description:
monocyte sample from normal control
203219760034_R07C01

value: LOY


title: RCAMs,young,rep1


title: M321_Granulocytes

description:
granulocyte sample from normal control
203219760034_R08C01


title: fetal placenta, LPS, 5.11 h, replicate 34


title: M22_Granulocytes

description:
granulocyte sample from normal control
203219750076_R08C01


title: Renal Capsule,Macrophages,rep3


title: WT_1027_5


title: fetal placenta, H2O, 5.11 h, replicate 34


title: M22_Monocytes

description:
monocyte sample from normal control
203219750076_R07C01


title: WT_1027_1


title: Renal Capsule,Macrophages,rep1


title: fetal placenta, LPS, 5.11 h, replicate 33


title: fetal placenta, LPS, 5.11 h, replicate 35


title: Kidney,Capsule,aged,rep3


title: fetal placenta, H2O, 5.11 h, replicate 33


title: M20_Granulocytes

description:
granulocyte sample from normal control
203219730222_R05C01


title: WT_1026_7


title: M20_Monocytes

description:
monocyte sample from normal control
203219730222_R04C01


title: fetal placenta, LPS, 5.11 h, replicate 32


title: WT_1027_6


title: Ing4Ing5_DKO_1459_5


title: Brain, MCMV, 12 Months Post Infection [snMultiATAC]

city: New Orleans

first: Kevin

last: Zwezdaryk

state: LA

address: 1430 Tulane Ave, Mail code #8638

department: Micro/Immuno

institute: Tulane University

description:
10x Genomics
Kevin008_snMultiATAC

data_processing:
bcl2fast2/2.20 and 10x Cellranger-arc-2.0.0 were used to generate Fastq files, perform alignment,filtering,barcode counting,UMI counting and aggregation.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5

source_name: Brain

growth_protocol: Mice were maintained  on a diurnal light cycle and provided food and water ad libitum

extract_protocol:
Mice were euthanized via injection with a sublethal dose of ketamine and xylazine followed by exsanguination. Mice were perfused with ice-cold PBS, brain was collected and flash frozen in liquid nitrogen. Brain was processed according to the 10X Genomics Protocol Revision D. Brain was lysed with 0.1x lysis buffer and homogenized wtih scissors and a pellet pestle. Homogenate was incubated for 3 minutes on ice. Suspension was filtered through at 70um filter and run through a 30% Percoll Plus gradient to remove myelin. Cells were then washed, visualized on a microscope to determine nuclear membrane integrity, and counted.
Library construction was performed according to 10x Genomics Chromium™ Next GEM Single Cell Multiome ATAC+Gene Expression Reagent Kit protocol
single cell gene expression RNA-seq and transposed DNA ATAC-seq

treatment_protocol: Mice were either mock infected or infected with 5x10^4 plaque forming units of murine cytomegalovirus (MCMV) at 8 weeks of age. Infections were repeated every 3 months (at 3 months post initial infection (MPI), 6 MPI, and 9 MPI) and scrificed at 14 months of age.

value: Brain

tag: strain

value: BALB/c

value: 14 Months

value: Female

value: MCMV Smith Strain Infected


title: Kidney,Capsule,aged,rep2

value: Renal Capsule

value: whole tissue


title: fetal placenta, H2O, 5.11 h, replicate 32

value: fetal placenta


title: Kidney,Capsule,aged,rep1


title: M14_Monocytes

description:
monocyte sample from normal control
203219730222_R01C01

value: Male

value: non-LOY

value: genomic DNA


title: M12_Granulocytes

description:
granulocyte sample from normal control
203219760178_R06C01

value: Granulocytes

value: control


title: fetal placenta, LPS, 5.11 h, replicate 31

value: WT

value: LPS


title: Brain, MCMV, 12 Months Post Infection [snMultiGEX]

description:
10x Genomics
Kevin008_snMultiGEX

molecule: nuclear RNA

tag: age


title: Kidney,Capsule,young,rep3


title: fetal placenta, H2O, 5.11 h, replicate 31


title: Brain, Mock, 12 Months Post Infection [snMultiGEX]

description:
10x Genomics
Kevin007_snMultiGEX

value: Untreated


title: Kidney,Capsule,young,rep2


title: UAD106_Granulocytes

description:
granulocyte sample from AD patient
203219730112_R02C01

value: Alzheimer's disease


title: Renal Capsule,Macrophages,rep2

value: Macrophages


title: fetal placenta, LPS, 5.11 h, replicate 30


title: UAD100_Monocytes

description:
monocyte sample from AD patient
203219760031_R08C01

value: Monocytes


title: fetal placenta, H2O, 5.11 h, replicate 30


title: UAD100_Granulocytes

description:
granulocyte sample from AD patient
203219730112_R01C01


title: late, TCR library, CD3 sorted intracranial CT2A

city: DURHAM

first: Jessica

last: Waibl Polania

state: NC

address: 303 Research Dr., RM 217

institute: Duke University

description:
10x Genomics
l1_filtered_contig_annotations.csv
l2_filtered_contig_annotations.csv
l3_filtered_contig_annotations.csv
l4_filtered_contig_annotations.csv

data_processing:
The Cell Ranger pipeline (10X Genomics) was used to perform sample demultiplexing and to generate FASTQ files for the gene expression and ADT libraries. FASTQ files were demultiplexed from the raw sequencing reads (bcl2fastq, v2.20), aligned to the mouse mm10 reference genome (cellranger, v4.0.0), and raw gene count matrices were generated using STAR (v2.7.5c).
Downstream analysis was performed using the R software Seurat package49(v4.0.3,http://satijalab.org/seurat/). Hashtag oligos, which corresponded to biological replicates, were demultiplexed usingthe HTODemux function and appended to the meta-data for each sample. Low-quality cells, expressing less than 200 genes, and genes expressed by fewer than three cells were removed. The gene expression matrix for each genotype was then concatenated using the merge function in Seurat. The percentage of mitochondrial gene content was calculated using the Mouse.MitoCarta3.050gene set and the PercentageFeatureSet function in Seurat. The Seurat object was converted to a SingleCellExperiment object, and outlier exclusion was performed in scater (v.1.18.6). Using the isOutlier function in scater, cells were discarded if their percentage of mitochondrial gene content, number of expressed genes, or number of reads for a given cell was considered an outlier. A total of 6,742 CD8+cells passed QC and the SingleCellExperiment object was then converted back into a Seurat object. Normalization and regression of cell cycle scoring and percent mitochondrial gene content were performed using the SCTransform function in Seurat. Principal component analysis (PCA) was performed on all genes, and the number of principal components to be utilized in further analysis was determined heuristically using the elbow method. Eleven principal components were used for clustering and dimensionality reduction using FindNeighbors, RunUMAP, and a resolution of 0.5 was used for FindClusters in Seurat. This approach identified six distinct cell clusters. All subsequent analyses were conducted with this cleaned object.
For TCRSeq analysis, scRepertoire standard workflow was utilized51. In brief filtered contig outputs from the 10X Genomics Cell Ranger Pipeline were loaded into R (v4.1.2) and combined into a list using combineTCR. Next combineExpression was used to attach clonotypic information to the Seurat object. Visualizations were made using the scRepertoire vignette.
For exhaustion signature score generation, the built in AddModuleScore function from Seurat was utilized with a gene list from Im et al. 201619. A detailed list can be found in Table S1. For pseudotime analysis, the object was passed into Monocle v3 without any changes to the UMAP dimensional reduction.
Assembly: mm10
Supplementary files format and content: raw read counts in gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes. *barcodes.tsv = Barcode sequences that correspond to column indices in matrix.mtx. *features.tsv = Gene IDs.
Supplementary files format and content: filtered_contig_annotations files are the output from the 10X CellRanger pipeline for TCR clones. There are 4 processed contig files per sample (e1-e4, l1-l4) these represent biological replicates that were assigned from hashtag oligo expression. When processing, all 4 processed files should be used per sample. These files may be grouped together, then analyzed using packages, such as scRepertoire (https://ncborcherding.github.io/vignettes/vignette.html) .

source_name: brain tumor

extract_protocol:
CD3+ tumor infiltrates were isolated using FACS sorting. Single-cell suspensions were loaded on the 10x Genomics Chromium controller, and mRNA converted to cDNA libraries. Single-cell libraries were sequenced on a Novaseq 6000 150PE S-Prime flowcell. Libraries were sequenced in single index mode with the following read lengths: 28x8x91. 10x 5' Chromium chemistry
GEMs are generated by combining barcoded Single Cell 5’ Gel Beads, Master Mix, Partitioning Oil and single cells on a Chromium microfluidic Chip. Immediately following GEM generation, the Gel Bead is dissolved and any co-partitioned cell is lysed. Oligonucleotides containing an Illumina R1 sequence (read 1 sequencing primer), a 16 nt 10x Barcode, a 10 nt unique molecular identifier (UMI), and 13 nt template switch oligo (TSO) are released and mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents and poly(dT) RT primers. Incubation of the GEMs produces 10x Barcoded, full-length cDNA from polyadenylated mRNA. GEMs are then broken and pooled and the 10x Barcoded first-strand cDNA is purified from the post GEM-RT reaction mixture and amplified. Full-length V(D)J segments (10x Barcoded) are enriched from amplified cDNA via PCR amplification with universal primer for 5’ adapter and successive nested primers specific to the TCR and/or BCR constant regions. Enrichment and library preparation of the TCR and BCR constant regions takes place in two separate workflows using the same amplified cDNA stock. Enzymatic fragmentation and size selection are used to generate variable length fragments that collectively span the V(D)J segments of the enriched TCR and/or BCR transcripts prior to library construction. P5, P7, a dual sample index, and an Illumina R2 sequence (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and Sample Index PCR. The final libraries contain the P5 and P7 priming sites used in Illumina sequencing. Sequence is generated using Illumina short read paired end sequencing.

value: brain tumor

value: CD3+ cells

value: 6-8 weeks

tag: time point

value: day 19


title: early, TCR library, CD3 sorted intracranial CT2A

description:
10x Genomics
e1_filtered_contig_annotations.csv
e2_filtered_contig_annotations.csv
e3_filtered_contig_annotations.csv
e4_filtered_contig_annotations.csv

value: day 13


title: WT_1026_3

value: F

value: embryonic mouse heart


title: fetal placenta, LPS, 5.11 h, replicate 29

value: fetal placenta


title: Cultured airway basal cells, LAMA3-transduced, rep 2

city: London

first: Robert

middle: E.

last: Hynds

address: 20c Guilford Street

department: UCL GOS Institute of Child Health

country: United Kingdom

institute: University College London

data_processing:
FASTQ files were processed using the nf-core/rnaseq pipeline (v3.11.2).
Normalized counts were output from DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing the normalized counts for each sample (from DESeq2)

source_name: Primary EB tracheal basal cell culture

growth_protocol: Primary tracheal biopsies were obtained from a patient with epidermolysis bullosa with informed consent. Cells were cultured according to the methods described in Butler et al. (PMID: 26840431).

extract_protocol:
RNA was extracted using a Purelink RNA Mini Kit.
DNA libraries were constructed using the KAPA mRNA HyperPrep kit (Roche).

treatment_protocol: Cultured basal cells were transduced with a lentivirus to overexpress the LAMA3A gene. Non-transduced cells were subjected to identical culture procedures without transduction.

value: Primary EB tracheal basal cell culture


title: Cultured airway basal cells, LAMA3-transduced, rep 1


title: M14_Granulocytes

description:
granulocyte sample from normal control
203219730222_R02C01

value: Granulocytes

value: Male

value: non-LOY

value: genomic DNA


title: Cultured airway basal cells, LAMA3-transduced, rep 3


title: Brain, Mock, 12 Months Post Infection [snMultiATAC]

description:
10x Genomics
Kevin007_snMultiATAC

value: Brain

value: BALB/c

value: 14 Months

value: Female

value: Untreated


title: late, antibody derived trancript (ADT) library, CD3 sorted intracranial CT2A

description:
10x Genomics
late_matrix.mtx.gz
late_features.tsv.gz
late_barcodes.tsv.gz

value: brain tumor

value: CD3+ cells

value: WT


title: fetal placenta, H2O, 5.11 h, replicate 29


title: Cultured airway basal cells, non-transduced, rep 3


title: early, antibody derived trancript (ADT) library, CD3 sorted intracranial CT2A

description:
10x Genomics
early_matrix.mtx.gz
early_features.tsv.gz
early_barcodes.tsv.gz

value: 6-8 weeks

value: day 13


title: fetal placenta, LPS, 5.11 h, replicate 28

value: LPS


title: UAD094_Granulocytes

description:
granulocyte sample from AD patient
203219760031_R05C01

value: Alzheimer's disease


title: late, gene expression (GEX) library, CD3 sorted intracranial CT2A

value: day 19


title: UAD095_Granulocytes

description:
granulocyte sample from AD patient
203219760031_R06C01

value: Granulocytes


title: maternal placenta, H2O, 13.11 h, replicate 31

source_name: maternal placenta

value: maternal placenta


title: Cultured airway basal cells, non-transduced, rep 1

value: Primary EB tracheal basal cell culture


title: UAD094_Monocytes

description:
monocyte sample from AD patient
203219760031_R04C01

value: Monocytes

value: Male

value: non-LOY

value: genomic DNA


title: Kidney,Capsule,young,rep1

value: Renal Capsule

value: whole tissue


title: early, gene expression (GEX) library, CD3 sorted intracranial CT2A

value: brain tumor


title: SNU1079, combination, 48h

city: Houston

first: yan

last: zhu

state: TX

address: 1515 Holcombe Blvd.

institute: MD Anderson

data_processing:
We identified genomic loci with peaks that were enriched for H3K27ac of every sample by MACS.
A pipeline had been established in which fastq files were analyzed to output bed files containing enriched peaks. Through this pipeline, sequences underwent FASTQC tool for quality-control measures and were aligned to the reference genome (hg19) using the Bowtie2 tool, and   MACS2 algorithms determined H3K27Ac peak enrichment.
For global H3K27Ac enrichment analysis, BED files were generated using ± 50 base pairs of the enrichment summit and plots were generated using seqMINER.
Assembly: HG19
Supplementary files format and content: peaks.txt

source_name: liver

growth_protocol: All cell lines were cultured in high glucose Dulbecco’s Modified Eagle Medium (DMEM, Corning, #10-017-CV) containing 10% (v/v) fetal bovine serum (FBS, Gibco, #26140079) and 1% (v/v) penicillin/streptomycin (Gibco, 15-140-122) in an incubator at 37°C with 5% CO2.

extract_protocol:
After harvest, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction were quenched with 125 mM glycine. After chromatin were fragmented to 200 to 600 bp by sonication, chromatin templates from 10 million cells were used for ChIP experiment. Samples were immunoprecipitated with 2μg of H3K27ac (Abcam, #ab4729) antibody overnight at 4 °C followed by washing steps. After reverse cross-linking, the ChIP DNA fragment were purified and repaired using End-It™ DNA End-Repair Kit followed by treatment with Taq polymerase to generate single-base 3´ overhangs used for adaptor ligation.
Following the ligation of a pair of Illumina adaptors to the repaired ends, the ChIP DNA were amplified using the adaptor primers. ENCODE guidelines were used to maintain the quality of all data sets, including the read depth.

treatment_protocol: Four group (vehicle, ARV825, AZD8055, and combination) of CCA cell lines (SNU1079 and SSP25) with 48h of drug treatment

value: liver

value: cholangiocarcinoma

value: wildtype

value: Combination, 48h

tag: antibody

value: H3K27ac (Abcam, #ab4729) antibody


title: UAD093_Granulocytes

description:
granulocyte sample from AD patient
203219760031_R02C01

value: LOY

value: Alzheimer's disease


title: fetal placenta, H2O, 5.11 h, replicate 28

value: fetal placenta

value: WT


title: RE-RE_OHDA_4.ZT12

data_processing:
Sequencing reads were pre-processed using the nf-core/rnaseq v1.2 pipeline, and read quality was assessed by FastQC v0.11.8.
TrimGalore v0.5.0 was used to trim sequencing reads, eliminate Illumina adaptor remains, and discard short reads.
The resulting reads were mapped onto the mouse genome using HiSAT2 v2.1.0 and quantified using featureCounts v1.6.2.
TMM-normalized FPKM values were calculated using Bioconductor package edgeR v3.30.0 and log2-transformed with a pseudo count of 0.01.
14500 genes with average non-transformed FPKM expression > 0.5 in at least one time point of at least one experimental condition were considered for further analysis.
Assembly: GRCm38, release 81
Supplementary files format and content: Tab-delimited text file with log2-transformed FPKM gene expression values for each sample.

source_name: tibialis anterior muscle

extract_protocol:
After homogenization of tibialis anterior muscle with Qiazol reagent (Qiagen #1023537) RNA was isolated using miRNeasy Mini Kit (Qiagen #1038703). RNA quality was checked using Nanodrop and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent).
RNA-seq libraries were sequenced in paired-end mode with a read length of 150 base pairs with an average of 2 x 25 million reads for each sample at Berry Genomics (Illumina NovaSeq 6000).

value: female

value: 18 weeks

tag: feeding

value: ad libitum

tag: zeitgeber time

value: whole muscle

value: OHDA treatment; 50mg/kg dose


title: maternal placenta, H2O, 13.11 h, replicate 30

value: maternal placenta


title: SNU1079, AZD8055, 48h

tag: cell line


title: maternal placenta, TiO2, 15.11 h, replicate 7


title: RE-RE_OHDA_3.ZT12

value: 15 weeks


title: SNU1079, ARV825, 48h


title: maternal placenta, H2O, 15.11 h, replicate 27


title: UAD087_Granulocytes

description:
granulocyte sample from AD patient
203219640142_R07C01

value: Granulocytes

tag: gender

value: Male

tag: donor id

tag: loy status

value: genomic DNA


title: maternal placenta, TiO2, 13.11 h, replicate 10

tag: tissue


title: RE-RE_OHDA_2.ZT0

value: 12 weeks


title: UAD086_Granulocytes

description:
granulocyte sample from AD patient
203219760180_R07C01

tag: sample type

tag: disease state


title: SNU1079, control, 48h

value: liver

value: cholangiocarcinoma

value: wildtype


title: maternal placenta, H2O, 13.11 h, replicate 29


title: RE-RE_OHDA_1.ZT0

tag: Sex

value: 16 weeks


title: UAD078_Monocytes

description:
monocyte sample from AD patient
203219640088_R04C01

value: Monocytes

value: non-LOY

value: Alzheimer's disease


title: SSP25, combination, 48h [aa-1]

data_processing:
In mRNA-seq analysis, differential RNA expression patterns will be identified through DESeq2 and EdgeR algorithms
Assembly: GRCh37
Supplementary files format and content: txt file contains raw count from each sample

extract_protocol:
Kit from ThermoFisher with CAT# 12183025
A total amount of 2 μg RNA per sample was used as input material for library construction. Strand-specific sequencing libraries were generated through the dUTP method by using the resulting RNA from NEBNext Ultra Directional RNA Library Prep Kit for Illumina.

tag: genotype

value: Combination, 48h


title: SSP25, AZD8055, 48h [azd-1]

tag: treatment


title: Cultured airway basal cells, non-transduced, rep 2

tag: cell type

value: Primary EB tracheal basal cell culture

value: WT


title: UAD097_Granulocytes

description:
granulocyte sample from AD patient
203219760031_R07C01


title: maternal placenta, TiO2, 13.11 h, replicate 9

data_processing:
Basecalling done bg Novogene as part of paid service. Sequencing produced a total of 828 libraries (414 paired end), with a median read depth of 24*106 reads (mean 25*106 reads, min 19.9 and max 46.6106), all of which passed initial QC controls performed by multiqc56. We detected base-pair overrepresentation in the first 11 bp of each read, as expected due to biases in random primers, and removed them using the trimfq command from seqtk (https://github.com/lh3/seqtk). Reads were mapped to gencode mouse transcriptome version M2357, which is an annotation of the genome assembly version GRCm38. In order to perform pseudo-mapping with Salmon58, we created an index using k-mer size 31 bp and supplying the genome in order to create decoy k-mers to account for biases due to un-annotated transcribed genomic regions (as described in Salmon documentation). We mapped libraries to the resulting index using Salmon quant using the following options: gcBias, seqBias, validateMappings, numBootstraps=10 and minScoreFraction=0.8. Finally, we annotated the resulting quant files using the R library tximeta59 and removed all features that lacked annotation. We performed all initial exploratory analyses and plots (e.g. PCA) using TPM-normalized data, and used the raw count data for the differential expression analysis. Before fitting statistical models, we normalised the count data from Salmon using TMM, retained only transcripts with more than 10 reads in at least 70% of the samples of the same condition, and applied voom correction for mean/variance relationship using the limma package60.
Assembly: gencode mouse transcriptome version M23
Supplementary files format and content: TPM matrix summarizing all samples

extract_protocol:
Isolation of pups and maternal/fetal organs: At 2, 5, 12 and 24 h, dams were terminally anesthetized by subcutaneous injection of 0.2 ml of Zoletil mixture (tiletamin/zolazepam, xylazin og fentanyl) and killed by exanguination by withdrawal of heart blood into Eppendorf tubes containing 36 ml K2EDTA (n=7-9 per exposure/time point). The uterus was excised and opened. Fetuses were excised from their embryonic sac, their viability confirmed, killed by decapitation, sexed by visual inspection, and their position in the uterus noted. From each litter, the first female fetus encountered in the right uterine horn, counting from the cervix, was selected and saved for analyses. The placenta was dissected into chorion and decidua by blunt/stump dissection under. From dams, the liver and right lung were dissected. Dissected organs were snap frozen in liquid nitrogen and kept at -80ºC. Fetal livers were dissected later. Maternal blood was centrifuged at 2000xg at 4°C for 5 min and plasma was stored in aliquots at -80°C until analysis. A maximum of one female fetus from each dam were used for any one outcome. RNA extraction: Total RNA was isolated from frozen maternal lung and liver, chorion, decidua and fetal liver. Briefly, 20 - 50 mg of tissue was homogenized with a blender in 700 ul lysis buffer with 7 ul mercapto-ethanol. RNA extraction was carried out utilizing magnetic beads technology, on a chemagic Prepito® (Perkin Elmer, Waltham, Massachusetts), as recommended by the manufacturer. Concentration and purity were measured on a NanoDrop1000 spectrophotometer, with all samples showing an A260/280 ratio between 1.9 and 2.1. RNA integrity was analyzed by 2100 Bioanalyzer (Agilent Technologies) with Agilent RNA 6000 Pico Kit (Agilent Technologies) as recommended by manufacturer. All samples used for RNAseq displayed RNA integrity number (RIN) above 7. cDNA library construction and paired end sequencing was carried out by Novogene (Hongkong). To exclude ribosomal RNA, polyA selection was done.
Novogene paid service


title: SSP25, ARV825, 48h [arv-1]


title: maternal placenta, LPS, 15.11 h, replicate 23

value: LPS


title: RE-RE_SHAM_2.ZT0

tag: strain

value: female

value: 11 weeks

value: ad libitum

value: whole muscle

value: Sham


title: UAD089_Granulocytes

description:
granulocyte sample from AD patient
203219760031_R01C01

value: Granulocytes

value: Male

value: genomic DNA


title: maternal placenta, H2O, 15.11 h, replicate 26

value: maternal placenta


title: SSP25, control, 48h [SSP-1]

value: liver

value: cholangiocarcinoma

value: wildtype


title: SNU1079, combination, 48h [SNU-AA]


title: UAD069_Granulocytes

description:
granulocyte sample from AD patient
203219640088_R02C01

value: non-LOY

value: Alzheimer's disease


title: UAD088_Granulocytes

description:
granulocyte sample from AD patient
203219640142_R08C01


title: WT_OHDA_8.ZT12

value: wild-type

tag: age

value: 13 weeks

value: OHDA treatment; 50mg/kg dose


title: UAD066_Monocytes

description:
monocyte sample from AD patient
203219760202_R08C01

value: Monocytes


title: maternal placenta, TiO2, 19.11 h, replicate 3

value: WT


title: RE-RE_SHAM_1.ZT0

value: female

value: 10 weeks

value: ad libitum


title: RE-RE_SHAM_4.ZT12

value: 11 weeks

value: whole muscle

value: Sham


title: UAD064_Monocytes

description:
monocyte sample from AD patient
203219760202_R07C01

value: Male

value: LOY

value: genomic DNA


title: maternal placenta, LPS, 19.11 h, replicate 18

value: maternal placenta

value: LPS


title: WT_OHDA_7.ZT12

value: 12 weeks


title: SNU1079, AZD8055, 48h [SNU-AZD]

value: liver

value: cholangiocarcinoma

value: wildtype


title: UAD066_Granulocytes

description:
granulocyte sample from AD patient
203219760180_R01C01

value: Granulocytes

value: non-LOY

value: Alzheimer's disease


title: maternal placenta, H2O, 19.11 h, replicate 14

value: WT


title: WT_OHDA_6.ZT12

value: female

value: wild-type

value: ad libitum

value: OHDA treatment; 50mg/kg dose


title: maternal placenta, LPS, 19.11 h, replicate 17


title: UAD069_Monocytes

description:
monocyte sample from AD patient
203219640088_R01C01

value: Monocytes

value: Male


title: SNU1079, control, 48h [SNU-CRL]


title: RE-RE_SHAM_3.ZT12

value: 11 weeks

value: whole muscle

value: Sham


title: WT_OHDA_5.ZT12

value: 15 weeks


title: WT_OHDA_4.ZT0

value: 16 weeks


title: UAD058_Granulocytes

description:
granulocyte sample from AD patient
203219760202_R02C01

value: LOY

value: genomic DNA


title: maternal placenta, H2O, 19.11 h, replicate 13

value: maternal placenta


title: UAD058_Monocytes

description:
monocyte sample from AD patient
203219760202_R01C01


title: Akata BCR 3

first: Erik

middle: K

last: Flemington

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Sequencing reads were aligned to the hg38 and EBV genomes using STAR
Only the first base of every read was used to build a bigwig coverage file
Assembly: hg38 and chrEBV_Akata_inverted
Supplementary files format and content: bigWig

source_name: Akata

extract_protocol:
RNA was extracted from cell pellets using TRIzol Reagent (ThermoFisher Scientific, cat no. 15596018) according to the manufacturer's protocol
Libraries were prepared using the CAGE Preparation Kit from KK DNAForm.

value: Akata

value: anti-IgG


title: maternal placenta, LPS, 19.11 h, replicate 16

value: WT

value: LPS


title: maternal placenta, H2O, 19.11 h, replicate 12


title: UAD045_Granulocytes

description:
granulocyte sample from AD patient
203219720005_R01C01

value: Granulocytes

value: Alzheimer's disease


title: Akata BCR 4


title: UAD038_Monocytes

description:
monocyte sample from AD patient
203219730179_R05C01


title: WT_OHDA_2.ZT0

value: female

value: wild-type

value: ad libitum

value: OHDA treatment; 50mg/kg dose


title: Akata BCR 2


title: Akata BCR 1


title: maternal placenta, LPS, 19.11 h, replicate 15


title: WT_OHDA_3.ZT0

value: whole muscle


title: WT_OHDA_1.ZT0


title: SNU1079, ARV825, 48h [SNU-ARV]

value: liver

value: cholangiocarcinoma

value: wildtype


title: UAD061_Monocytes

description:
monocyte sample from AD patient
203219760202_R03C01

value: Monocytes

value: Male

value: non-LOY


title: UAD033_Granulocytes

description:
granulocyte sample from AD patient
203219730179_R04C01

value: LOY

value: genomic DNA


title: WT_SHAM_7.ZT12

value: 12 weeks

value: Sham


title: maternal placenta, LPS, 19.11 h, replicate 14

value: maternal placenta

value: WT

value: LPS


title: Akata Ctl 3

value: Akata


title: Akata Ctl 4


title: maternal placenta, LPS, 19.11 h, replicate 13


title: UAD033_Monocytes

description:
monocyte sample from AD patient
203219730179_R03C01

value: Alzheimer's disease


title: WT_SHAM_6.ZT12

value: female

value: wild-type

value: 18 weeks

value: ad libitum


title: UAD030_Granulocytes

description:
granulocyte sample from AD patient
203219730179_R01C01

value: Granulocytes


title: maternal placenta, H2O, 19.11 h, replicate 11


title: WT_SHAM_5.ZT12

value: 16 weeks

value: whole muscle


title: UAD028_Granulocytes

description:
granulocyte sample from AD patient
203219730117_R08C01

value: Male


title: Akata Ctl 2


title: Akata Ctl 1


title: maternal placenta, LPS, 13.11 h, replicate 29


title: WT_SHAM_4.ZT0


title: UAD028_Monocytes

description:
monocyte sample from AD patient
203219730117_R07C01

value: Monocytes

value: LOY


title: Mutu Zta 3

source_name: Mutu

value: Mutu

value: Zta


title: WT_SHAM_3.ZT0

value: 17 weeks

value: Sham


title: maternal placenta, LPS, 15.11 h, replicate 22

value: maternal placenta

value: WT

value: LPS


title: Mutu Zta 2


title: UAD011_Granulocytes

description:
granulocyte sample from AD patient
203219730117_R04C01

value: genomic DNA

value: Alzheimer's disease


title: Mutu Zta 1


title: Mutu Ctl 3

value: Ctl


title: UAD011_Monocytes

description:
monocyte sample from AD patient
203219730117_R03C01


title: UAD008_Monocytes

description:
monocyte sample from AD patient
203219730200_R08C01

value: non-LOY


title: WT_SHAM_1.ZT0

value: female

value: wild-type

value: 13 weeks

value: ad libitum


title: maternal placenta, H2O, 13.11 h, replicate 28


title: maternal placenta, LPS, 13.11 h, replicate 27


title: Mutu Ctl 2


title: D6,liver,WT,WD diet+Vehicle(Cancer)

first: lan

last: Zhong

address: Jimo Road 150

institute: Shanghai East hospital

data_processing:
Reads were filtered by Cutadapt-1.9 and verified using FastQC-0.11.9.
Filtered reads were aligned to the mus musculus reference genome using HISAT2-2.2.1.
The mapped reads were assembled using StringTie-2.1.6
All transcriptomes were merged to reconstruct a comprehensive transcriptome using gffcompare-0.9.8.
StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM.
Assembly: GRCm38/mm10

source_name: Liver

growth_protocol: Five-week-old male C57BL/6j mice were fed a WD diet (fat, 40%; Fructose,20%; Cholesterol,2%; Nutrition).

extract_protocol:
After 40 weeks, the mice were sacrificed and liver, serum and visceral adipose tissue (VAT) were collected.
Total RNA was extracted using Trizolreagent(thermofisher,15596018)following the manufacturer's procedure.

treatment_protocol: After 32 weeks of WD feeding, all mice received 1 injection of PBS or MSCs via the tail vein.

tag: model

value: WD-induced NASH

value: Liver

value: WD diet+Vehicle(Cancer)


title: Mutu Ctl 1

value: Mutu


title: UAD008_Granulocytes

description:
granulocyte sample from AD patient
203219730117_R01C01

value: Granulocytes

value: Male


title: UAD005_Granulocytes

description:
granulocyte sample from AD patient
203219730200_R07C01

value: LOY


title: D4,liver,WT,WD diet+Vehicle

value: WT

value: WD diet+Vehicle


title: Akata BCR 3

data_processing:
Aligned using bowtie2
Duplicates marked and removed using Picard
Bam files converted to bigwig using DeepTools
Assembly: hg38 and chrEBV_Akata_inverted
Supplementary files format and content: bigWig

source_name: B cell lymphoma

extract_protocol:
The ATAC-seq protocol from Buenrostro J, Wu B, Chang H, Greenleaf W. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol. 2015;109:21.29.1-21.29-9.
Nextera DNA Library Prep Kit (Illumina, catalog # FC-121-1030)

value: B cell lymphoma

value: Akata

value: anti-IgG


title: D3,liver,WT,WD diet+Vehicle


title: UAD005_Monocytes

description:
monocyte sample from AD patient
203219730200_R06C01

value: Monocytes

value: genomic DNA

value: Alzheimer's disease


title: Akata BCR 2