title: TCTN2_vko

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

description: 10x Genomics

data_processing:
Illumina sequencing reads were aligned to the human mRNA reference genome (GRCh38) using the 10x Genomics CellRanger pipeline (version 3.0.2) with default parameters.
Assembly: GRCh38
Supplementary files format and content: tar compressed  files include filtered_gene_bc_matrices after running CellRanger pipeline

source_name: embryonic

growth_protocol: hNTO were cultured in a 96-well U-shaped ultra-low plate with N2/B27 medium (DMEM/F12:Neurobasal medium 1:1, contains 0.5% N2 supplement, 0.5% B27 supplement, 1% GlutaMAX,  1%NEAA, 1% P/S). Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 11 of differentiation.

extract_protocol:
To generate neural progenitor cell fate, the following reagents were used during specific time periods: From day 0 to day 6, a combination of 50 ng/ml Noggin and 10 μM SB431542 was employed. From day 4 to day 8, 3 μM CHIR99021 was added. Additionally, from day 4 to day 11, 0.1 μM RA was introduced to drive the neural progenitor cells towards a caudal fate. To induce the expression of BMP4 and SHH proteins, which are generated from each organizer center, 200 ng/ml DOX was added from day 7 to day 11. After the aforementioned steps, dorso-ventral patterned neural tube organoids were generated.
Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 (10x Genomics, Cat# PN-1000121) according to the manufacturer’s protocol for 10000 cells recovery.

value: embryonic

value: human embryonic stem cells

value: human neural tube organoids (hNTOs)

value: TCTN2 KO


title: TCTN2_dko

status: Public on Feb 06 2024

type: SRA

country: China

description: 10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: day 5 rep 2

city: St. Louis

first: Matthew

last: Mosley

state: MO

address: 660 S. Euclid Ave.

department: Developmental Biology

country: USA

institute: Washington University in St. Louis School of Medicine

library_source: transcriptomic

data_processing:
Clean reads were obtained by filtereing reads containing adapters, poly-N reads, and low quality reads.
Fastq files were aligned to the reference genome using STAR version 2.7.3a.
Gene counts were determined using the featureCounts function in the R package Rsubread.
Assembly: Caenorhabditis elegans WBcel235.94
Supplementary files format and content: Gene counts for each sample in tab-delimitted text format.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Whole body

extract_protocol:
Animals were wahsed off plates with M9 buffer and allowed to settle by gravity. Samples were lysed by addition of TRIzol (ThermoFisher) with repeated flash-freeze/thaw cycles in liquid nitrogen. Total RNA was obtained by phenol chloroform extraction and purified according to the RNeasy Micro kit protocl (Qiagen), including on-column DNase treatment.
mRNA was enriched using oligo(dT) beads, and the Ribo-Zero kit (Illumina) was used to remove rRNA. First, mRNA was fragmented randomly by adding fragmentation buffer, then cDNA was synthesized by using mRNA template and random hexamers primer, after which a second-strand synthesis buffer (Illumina) , dNTPs, RNase H, and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

value: Whole body

tag: time point

value: day 5


title: Non-migrant eye, 30dpf, 3

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC

data_processing:
Good-quality raw reads were aligned against the turbot genome assembly (ASM318616v1) using STAR v2.7.0e alignment software
Reads were assigned to unique genes with HTseq software v0.10.0
Assembly: ASM318616v1
Supplementary files format and content: text file including raw counts for each sample

organism: Scophthalmus maximus

source_name: Non-migrant eye

extract_protocol:
Total RNA was extracted from the tissues and purified using the RNeasy Mini Kit (Qiagen) following the manufacturer’s intructions.
BGISEQ-500 stranded mRNA library

value: Non-migrant eye

tag: age


title: Non-migrant eye, 30dpf, 2


title: day 5 rep 1


title: NIH-3T3 cells, no4sU, replicate B

city: Würzburg

first: Kevin

last: Berg

address: Versbacher Str. 7

country: Germany

institute: University of Würzburg

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt, reads with length < 18 were removed
Trimmed sequence reads were mapped to rRNA (U13369.1) and Mycoplasma database using bowtie2 (v. 2.3.0). Mapped reads were filtered out
Trimmed and filtered sequence reads were mapped to the mouse genome (ensembl 102) using STAR v. 2.7.10b (parameters: --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --alignEndsType Extend5pOfReads12 --outSAMattributes nM MD NH –outSAMunmapped Within)
Subsequent analyses were conducted in R.
Assembly: mus musculus (ensembl 102)
Supplementary files format and content: Tab-separated values files
Library strategy: SLAM-seq

organism: Mus musculus

growth_protocol: NIH-3T3 cells were grown in DMEM supplemented with 100 IU/mL Penicillin and, 100 g/mL Streptomycin and supplemented with 10% NCS at 37°C, 5% CO2

extract_protocol:
Cells subject to 4sU-labeling were harvested using TRI reagent (Sigma) and RNA isolation was conducted using the Zymo DirectZol RNA-microprep kit (R2062) as described by the manufacturer and re-suspended in 1X PBS buffer
SLAM-seq was conducted using IAA to mediate U>C conversions at 50oC/20 minutes. The reaction was quenched using excess DTT. RNA was then purified using RNeasy Mini elute kit (Qiagen)

treatment_protocol: Cells were treated with 800 µM 4sU for 15, 30, 60, 90 and 120 minutes.

value: fibroblast cells

value: WT

tag: treatment

tag: time


title: Non-migrant eye, 30dpf, 1


title: NIH-3T3 cells, no4sU, replicate A


title: Non-migrant eye, 15dpf, 3


title: day 4 rep 2

value: day 4


title: WT_NTO

description: 10x Genomics


title: Donor891_16h_IL7+12

city: South San Francisco

first: Regina

middle: Junhui

last: Lin

state: CA

address: 210 E Grand Ave

institute: Allogene Therapeutics, Inc.

data_processing:
RSEM (gencode v25 mapped to GRCh37) was used to quantify transcript abundance, and to generate   expected counts for each gene.
Differential expression (DE) was assessed with edgeR.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Microsoft Excel Comma Separated Value files include differentially expressed gene analysis using the edgeR quasi-likelyhood (QL) framework for each comparison. Adjusted p-values (padj) were calculated using the Benjamini–Hochberg method. Significant differentially expressed (DE) genes were defined by fold change (≥2) and Benjamini–Hochberg false discovery rate (FDR<=0.05).

source_name: T cells

growth_protocol: Healthy donor T cells were activated and transduced with lentivirus encoding iTurboCAR.7.12, then expanded in 100 U/ml human IL-2 for a total of 14 days before cryopreservation. iTurboCAR.7.12 T cells were recovered from cryopreservation and FACS-sorted to enrich for live, iTurboCAR+ T cells.

extract_protocol:
Cells were pelleted, resuspended in RNAlater solution and stored at -80°C. RNA was then harvested using Trizol reagent.
Library construction was performed using TruSeq Stranded mRNA protocol.

treatment_protocol: FACS-sorted iTurboCAR+ T cells were either treated with vehicle control (untreated), AP1903 (1 μg/ml), or recombinant human IL-7 (10 ng/ml) and human IL-12p70 (10 ng/ml) for 4 hours or 16 hours.

value: FACS-sorted iTurboCAR+ T cells

tag: donor

value: hIL-7 and hIL-12p70 (10 ng/ml each), 16 hours


title: Non-migrant eye, 15dpf, 2


title: HeLa, GFP-TAF1 expression, GFP, greenCUT&RUN, -Ca2+ control

city: Freiburg im Breisgau

first: Tanja

last: Bhuiyan

address: Albertstrasse 25

department: Institute of Experimental and Clinical Pharmacology and Toxicology

institute: University of Freiburg

library_source: genomic

data_processing:
Reads were processed using bcl2fastq version: 2.20.0.422. for Novaseq output
CUT&RUN reads were trimmed using Trim-galore v0.6.4
Alignment to human and drosophila genomes was carried out using bowtie2 v2.3.5.1 according to Nizamuddin et al., 2021. The total number of aligned reads, representing both human and drosophila spike-in, was calculated using the Flagstat program of samtools (version 1.10).
Spike-in normalized genome coverage (BigWig) files were created with DeepTools bamCoverage v3.5.1.0.0 using a blacklist region file for hg38, bin size 50 bases and 1x normalization (RPCG). The scaling factor was calculated 10⁶/spike-in reads for CUT&RUN and 10⁵/spike-in reads for greenCUT&RUN
Peaks were identified using HOMER with default parameters, except for the inclusion of –C 0. Normalization of reads during peak calling was conducted using spike-in according to Nizamuddin et al., 2021 #69. Peaks in the experiment were called against control samples.
To merge peaks, bedtools intersect intervals (v 2.30.0+galaxy1) was used with 1 bp required overlap.
Assembly: hg38 (human) and BDGP5 (drosophila)
Supplementary files format and content: bigWig, bed

molecule: genomic DNA

source_name: HeLa

growth_protocol: DMEM, 10% FBS, 1 mM sodium pyruvate, cells were cultured at 37 °C with 5% CO2

extract_protocol:
Standard CUT&RUN according to Skene et al., 2018
NEB Next Ultra II library preparation kit (NEB #E7645L) without size selection according to manufacturer’s instructions with modifications: we increased the end prep duration to 60 min at 50 °C instead of 30 min at 65 °C and used only 10 s annealing and extension time instead of 75 s, and 15 PCR cycles during the amplification step

treatment_protocol: 1 ug/mL doxycycline overnight (17-22 h)

value: HeLa

value: 1 ug/mL doxycycline

tag: cut&run antibody

value: GFP-nanobody-MNase


title: day 4 rep 1


title: Non-migrant eye, 15dpf, 1


title: Donor891_16h_No Tx

value: Vehicle control, 16 hours


title: day 3 rep 3

value: day 3


title: Migrant eye, 57dpf, 3

source_name: Migrant eye

value: Migrant eye


title: HeLa, GFP-TAF1 expression, GFP, greenCUT&RUN


title: day 3 rep 2


title: Donor177_16h_IL7+12


title: Migrant eye, 57dpf, 2


title: HeLa, GFP-NLS-TAF2d1142-1171 expression, rep1, GFP, greenCUT&RUN, -Ca2+ control


title: day 3 rep 1


title: Donor177_16h_AP1903

value: AP1903 (1 ug/ml), 16 hours


title: Migrant eye, 57dpf, 1


title: Donor177_16h_No Tx


title: day 2 rep 3

value: day 2


title: Migrant eye, 30dpf, 3


title: Donor891_4h_IL7+12

value: hIL-7 and hIL-12p70 (10 ng/ml each), 4 hours


title: day 4 rep 3

value: Whole body


title: day 2 rep 2


title: HeLa, GFP-NLS-TAF2d1009-1199 expression, rep2, GFP, greenCUT&RUN, -Ca2+ control


title: Migrant eye, 30dpf, 2


title: Migrant eye, 30dpf, 1


title: day 2 rep 1


title: Donor891_4h_AP1903

value: AP1903 (1 ug/ml), 4 hours


title: HeLa, GFP-NLS-TAF2d1009-1199 expression, rep2, GFP, greenCUT&RUN


title: HeLa, GFP-NLS-TAF2d1009-1199 expression, rep1, GFP, greenCUT&RUN, -Ca2+ control


title: Donor891_16h_AP1903


title: Donor891_4h_No Tx

value: Vehicle control, 4 hours


title: Migrant eye, 15dpf, 3


title: day 1 rep 3

value: day 1


title: day 1 rep 2


title: HeLa, GFP-NLS-TAF2d1009-1199 expression, rep1, GFP, greenCUT&RUN


title: Donor177_4h_IL7+12


title: Migrant eye, 15dpf, 2


title: HeLa, GFP-TAF2 expression, GFP, greenCUT&RUN, -Ca2+ control


title: day 1 rep 1


title: HeLa, GFP-NLS-TAF2d1142-1171 expression, rep1, GFP, greenCUT&RUN


title: Donor177_4h_No Tx


title: Migrant eye, 15dpf, 1


title: Donor177_4h_AP1903


title: HeLa, GFP-TAF2 expression, GFP, greenCUT&RUN


title: shTbl1xr1-D2-rep1

status: Public on Feb 05 2024

city: Guangzhou

first: Yiwei

last: Lai

state: Guangdong

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine Key Laboratory of Regenerative Biology, CAS

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
RNA-seq data was mapped to mm10 (Ensembl 93) reference genome with STAR, and gene expression was quantified in an RSEM-based pipeline. DEGs were determined by DESeq2 (V1.30.1) and were defined as an absolute fold change > 1.5 and P value < 0.05.
Assembly: RNA-seq data was mapped to mm10 (Ensembl 93) reference genome with a STAR-based RSEM pipeline.
Supplementary files format and content: Count matrixes generated by RSEM.

source_name: Liver

extract_protocol:
Total RNA was extracted from mouse liver using TRIzol (MRC, RN190) following the manufacturer’s instructions.
Bulk RNA-seq libraries were prepared using MGIEasy RNA Library Prep Set (MGI, 1000006384) according to the manufacturer’s instructions.

value: Liver


title: shTbl1xr1-D2-rep2


title: shTbl1xr1-D2-rep3


title: shNC-D2-rep3

value: shNC


title: shNC-D2-rep4


title: shNC-D2-rep2


title: shNC-D2-rep1


title: shTbl1xr1-D2-rep4


title: 3-1_M12_S119,HyperSeq, scRNASeq

city: Kensington

first: Yike

last: Xie

state: NSW

address: Lowy 2, Cnr High and Botany St

country: Australia

institute: UNSW Sydney

description: A single cell was imaged by a hyperspectral microscope and then captured by CellCelector

data_processing:
The sequencing reads were demultiplexed using bcl2fastq 2.20 (Illumina, San Diego, CA, USA), mapped and counted to human genome reference (GRCh38) for MCF-7 cells using STAR aligner. HTSeq 2.0 was used to map the sequencing reads of MCF-7 cells into exon level. Quality of datasets were evaluated based on the number of genes expressed in the count matrix, the total counts per cell and the percentage of counts in mitochondrial genes. Genes that were expressed in less than ten cells were excluded. Datasets were normalised by the total reads, multiplied by 1,000,000 (cpm). During analyses but doublet deconvolution, datasets were log2 transformed after addition of a pseudo count of 1. GSEAPY was used for pathway analysis.
Assembly: GRCh38
Supplementary files format and content: fastq files of each cell are provided

source_name: Breast

extract_protocol:
MCF-7 cells were washed twice with PBS, then placed into equilibrated Hank’s balanced salt solution (HBSS) (Thermo Fisher Scientific, Waltham MA, USA) and maintained at 37°C during hyperspectral imaging. Subsequently, imaged cells were captured by CellCelector to a 384-well PCR plate with lysis buffer.
Library was prepared following Smart-seq2 protocol. Briefly, cells were picked into 384 well lysis plates followed by reverse transcription, template switching and 26 cycles of PCR to generate and amplify the cDNA. MANTIS automated liquid handler (Tecan, Zürich, Switzerland) was used during the process. cDNA was normalised to 0.1 - 1ng/µl according to the qualification by Quant-iT™ PicoGreen™ dsDNA Assay Kit (Thermo Fisher Scientific, Waltham MA, USA) via automated liquid handling robot Mosquito (SPT Labtech, Melbourn, Cambridgeshire, UK). Nextera XT kit (Illumina, San Diego, CA, USA) with 14 cycles of amplification was used for tagmenting MCF-7 cells. Purification was conducted to remove primer by Agencourt Ampure XP (Beckman Coulter, Brea CA, USA) magnetic beads at a ratio of 0.7x for two times. Libraries were quantified using Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany).

value: Breast

value: Breast cancer cells


title: 3-1_N12_S120,HyperSeq, scRNASeq


title: 3-1_F12_S112,HyperSeq, scRNASeq


title: 3-1_E12_S111,HyperSeq, scRNASeq


title: 3-1_J12_S116,HyperSeq, scRNASeq


title: 3-1_L10_S94,HyperSeq, scRNASeq


title: 3-1_D11_S98,HyperSeq, scRNASeq


title: 3-1_M10_S95,HyperSeq, scRNASeq


title: 3-1_K10_S93,HyperSeq, scRNASeq


title: 3-1_H12_S114,HyperSeq, scRNASeq


title: 3-1_J10_S92,HyperSeq, scRNASeq


title: 3-1_I12_S115,HyperSeq, scRNASeq


title: 3-1_H10_S90,HyperSeq, scRNASeq


title: 3-1_C11_S97,HyperSeq, scRNASeq


title: 3-1_G12_S113,HyperSeq, scRNASeq


title: 3-1_K12_S117,HyperSeq, scRNASeq


title: 3-1_F10_S88,HyperSeq, scRNASeq


title: 3-1_N10_S96,HyperSeq, scRNASeq


title: 3-1_E10_S87,HyperSeq, scRNASeq


title: 3-1_G10_S89,HyperSeq, scRNASeq


title: 3-1_J9_S80,HyperSeq, scRNASeq


title: 3-1_L12_S118,HyperSeq, scRNASeq


title: 3-1_L9_S82,HyperSeq, scRNASeq


title: 3-1_H9_S78,HyperSeq, scRNASeq


title: 3-1_K9_S81,HyperSeq, scRNASeq


title: 3-1_I9_S79,HyperSeq, scRNASeq


title: 3-1_H11_S102,HyperSeq, scRNASeq


title: 3-1_G9_S77,HyperSeq, scRNASeq


title: 3-1_E9_S75,HyperSeq, scRNASeq


title: 3-1_D9_S74,HyperSeq, scRNASeq


title: 3-1_K8_S69,HyperSeq, scRNASeq


title: 3-1_F8_S64,HyperSeq, scRNASeq


title: 3-1_L8_S70,HyperSeq, scRNASeq


title: 3-1_N7_S60,HyperSeq, scRNASeq


title: 3-1_H7_S54,HyperSeq, scRNASeq


title: 3-1_J8_S68,HyperSeq, scRNASeq


title: 3-1_L7_S58,HyperSeq, scRNASeq


title: 3-1_K7_S57,HyperSeq, scRNASeq


title: 3-1_G8_S65,HyperSeq, scRNASeq


title: 3-1_G7_S53,HyperSeq, scRNASeq


title: 3-1_N6_S48,HyperSeq, scRNASeq


title: 3-1_M6_S47,HyperSeq, scRNASeq


title: 3-1_E8_S63,HyperSeq, scRNASeq


title: 3-1_C9_S73,HyperSeq, scRNASeq


title: 3-1_J7_S56,HyperSeq, scRNASeq


title: 3-1_C8_S61,HyperSeq, scRNASeq


title: 3-1_J6_S44,HyperSeq, scRNASeq


title: 3-1_M7_S59,HyperSeq, scRNASeq


title: 3-1_F9_S76,HyperSeq, scRNASeq


title: 3-1_F7_S52,HyperSeq, scRNASeq


title: 3-1_D7_S50,HyperSeq, scRNASeq


title: 3-1_H6_S42,HyperSeq, scRNASeq


title: 3-1_G6_S41,HyperSeq, scRNASeq


title: 3-1_F6_S40,HyperSeq, scRNASeq


title: 3-1_I8_S67,HyperSeq, scRNASeq


title: 3-1_I7_S55,HyperSeq, scRNASeq


title: 3-1_E6_S39,HyperSeq, scRNASeq


title: 3-1_D6_S38,HyperSeq, scRNASeq


title: 3-1_L6_S46,HyperSeq, scRNASeq


title: 3-1_C6_S37,HyperSeq, scRNASeq


title: 3-1_J5_S32,HyperSeq, scRNASeq


title: 3-1_D5_S26,HyperSeq, scRNASeq


title: 3-1_K5_S33,HyperSeq, scRNASeq


title: 3-1_H5_S30,HyperSeq, scRNASeq


title: 3-1_K6_S45,HyperSeq, scRNASeq


title: 3-1_L4_S22,HyperSeq, scRNASeq


title: 3-1_H4_S18,HyperSeq, scRNASeq


title: 3-1_I4_S19,HyperSeq, scRNASeq


title: 3-1_M4_S23,HyperSeq, scRNASeq


title: 3-1_G5_S29,HyperSeq, scRNASeq


title: 3-1_G4_S17,HyperSeq, scRNASeq


title: 3-1_J3_S8,HyperSeq, scRNASeq


title: 3-1_I5_S31,HyperSeq, scRNASeq


title: 3-1_M3_S11,HyperSeq, scRNASeq


title: 3-1_N4_S24,HyperSeq, scRNASeq


title: 3-1_K4_S21,HyperSeq, scRNASeq


title: 3-1_J4_S20,HyperSeq, scRNASeq


title: 3-1_G3_S5,HyperSeq, scRNASeq


title: 3-1_I3_S7,HyperSeq, scRNASeq


title: HET, replicate 4, CC, bulkATAC

city: Houston

first: Michael

last: Green

state: Texas

address: 7455 Fannin Street

department: Department of Lymphoma/Myeloma

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read trimming, read alignment using bwa, filtering low-quality, unmapped and duplicated reads. BIGWIG files were generated using deeptools RPKM normalization.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: mm10
Supplementary files format and content: Tab-separated count matrix file and RPKM normalized bigwig files

source_name: Spleen

extract_protocol:
DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (D4014, Zymo Research)
ATAC-seq libraries were generated following the Omni-ATAC protocol. Libraries were barcoded and amplified with KAPA HiFi HotStart ReadyMix (KK2602, Roche). Library size distribution and concentration was evaluated using the Agilent 4200 TapeStation system and Qubit dsDNA HS Assay Kit (ThermoFisher Scientific), respectively.

value: Spleen

tag: strain

value: 8-10 weeks


title: 3-1_F3_S4,HyperSeq, scRNASeq


title: HET, replicate 4, CB, bulkATAC


title: 3-1_L3_S10,HyperSeq, scRNASeq


title: HET, replicate 3, CB, bulkATAC


title: HET, replicate 3, CC, bulkATAC


title: HET, replicate 2, CC, bulkATAC


title: D374Y mCherry-APOB

city: Stockholm

first: Stephen

last: Malin

address: Bioclinicum J8:20, Visionsgatan 4

country: Sweden

institute: Karolinska Institutet

data_processing:
Data analysis was performed in R using Seurat v4 (45) with the gene Gm42418 removed from the data set. Liver cells were identified  with Total-seq cell hashing antibodies from Biolegend. A0301 defines this liver sample
Assembly: MM10
Supplementary files format and content: H5ad file format of 10x count matrix

growth_protocol: mice were housed in a specific pathogen-free vivarium at the Karolinska Institute. The light/dark period was 12h/12h, and mice were kept under standard temperature and humidity conditions (20-22 °C, 45-55% RH). All mice had ad libitum access to food and water. Breeding mice were fed chow diet R36 (12.6 MJ/kg, 18% protein, 4% fat; Lantmännen, Sweden). Experimental mice received chow diet (R70, Lantmännen, Sweden, 12.5 MJ/kg, 14% protein, 4.5% fat) or HFD (R638, Lantmännen, Sweden, 15.6 MJ/kg, 17.2% protein, 21% fat, 0.15% cholesterol) as stated in each experiment

extract_protocol:
live CD45+ mCherry+ cells were sorted from the liver. A small sample from one lobe was cut into small pieces and digested in 0.2 mg/mL collagenase IV for 30 min at 37 °C in RPMI 1640. The cell suspension was passed through an 18 g syringe 10 times to remove any clumps and then a 70uM cell strainer. The cell suspension was then washed with FACS buffer before being sorted by a Sony SH800S cell sorter. Cells were additionlay stained with Total-seq cell hashing antibodies from Biolegend. A0301 defines this liver sample
Cells were processed immediately for GEM generation and barcoding on a 10X Chromium using Next GEM 3’ v3.1 reagents (10X Genomics) followed by sequencing and processing on Cellranger. equenced on a NovaSeq 6000 on an SP flow cell with the following run set up: Run setup 28-8-0-91 , 1% Phix.

value: D374Y mCherry-APOB

value: Day 10 after tamoxifen chow diet


title: HET, replicate 1, CC, bulkATAC


title: WT, replicate 3, CC, bulkATAC


title: WT, replicate 2, CC, bulkATAC


title: HET, replicate 1, CB, bulkATAC


title: WT, replicate 4, CB, bulkATAC


title: WT, replicate 4, CC, bulkATAC


title: WT, replicate 3, CB, bulkATAC


title: shRNA-Ddx5(IL-1β+TNF-α), 3

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome:Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: 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, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. 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.
Enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Gene Set Enrichment Analysis: Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre- defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO、KEGG、Reactome、DO and DisGeNET data sets were used for GSEA independently.
SNP analysis: GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10.
AS analysis: Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.5) software was used to analysis the AS event.
PPI analysis of differentially expressed genes: PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.
Assembly: mm10
Supplementary files format and content: fpkm

extract_protocol:
We conducted the experiment with ATDC5 (a chondrocyte line). This cell line uses lentivirus to introduce shRNA expression cassettes , which permit stable integration into and expression from the host genome in the cell line, and constructed a DDX5 knockdown stable cell line, and by adding IL-1 β+ TNF- α stimulation induces inflammatory cell lines in vitro. Then, the identified differentially expressed genes were RNA-seq using the Ingnuity platform.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: mouse teratocarcinoma cells

value: DDX5 knockdown


title: shRNA-NC(IL-1β+TNF-α), 3

value: wildtype


title: WT, replicate 2, CB, bulkATAC


title: WT, replicate 1, CB, bulkATAC


title: shRNA-Ddx5(IL-1β+TNF-α), 2


title: shRNA-NC(IL-1β+TNF-α), 2


title: shRNA-Ddx5(IL-1β+TNF-α), 1


title: HOMO, replicate 2, CB, bulkATAC


title: HOMO, replicate 2, CC, bulkATAC


title: HOMO, replicate 3, CC, bulkATAC


title: HOMO, replicate 1, CC, bulkATAC


title: shRNA-Ddx5, 3

value: DDX5 knockdowm

value: No stimulation


title: shRNA-Ddx5, 2


title: WT, replicate 3, CC, bulkATAC


title: HOMO, replicate 3, CB, bulkATAC


title: HOMO, replicate 1, CB, bulkATAC


title: shRNA-Ddx5, 1


title: shRNA-NC 3


title: HET, replicate 2, CB, bulkATAC


title: WT, replicate 1, CC, bulkATAC


title: shRNA-NC 2


title: WT, replicate 2, CC, bulkATAC


title: WT, replicate 2, CB, bulkATAC


title: shRNA-NC(IL-1β+TNF-α), 1


title: shRNA-NC 1


title: wt3

city: Paris

first: Evgeniya

last: Petrova

address: 24 Boulevard du Montparnasse

department: Imagine Institute

country: France

institute: INSERM UMR1163

data_processing:
Sequencing data were processed with Illumina Pipeline software (Casava)
Reads were cleaned of adapter sequences and low-quality sequences using an in-house program (https://github.com/baj12/clean_ngs).
Trimmed sequence reads were mapped to GrCM38/mm10 using TopHat program (version 1.4.1.1, default parameters)
Read count extraction and normalization were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: excel file with normalized counts by DEseq2

source_name: Back skin

extract_protocol:
RNA was extracted using RNeasy Firbous Tissue kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
Directional libraries were prepared from total RNA using the Truseq Stranded mRNA sample preparation kit (Illumina 15031047) following the manufacturer’s instructions. Clusters were generated for the resulting libraries, with Illumina HiSeq SR Cluster Kit v3 reagents. Runs were carried out over 51 cycles, including seven indexing cycles, to obtain 51-bp single-end reads.

value: Back skin

value: WT

tag: Sex

value: male

tag: age (days)


title: wt4


title: WT, replicate 1, CB, bulkATAC


title: HET, replicate 1, CC, bulkRNA

data_processing:
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read alignment using STAR-aligner. Count matrices were created using featureCounts of subread package.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files and fragments files

extract_protocol:
GC B cells were isolated from mice spleens at day 10 post-immunization using the Germinal Center B Cell (PNA) MicroBead Kit (Miltenyi Biotec,130-110-479). RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN) according to the manufacturers protocol. RNA concentration was determined using the Qubit RNA High Sensitivity Kit (Thermo Fisher Q32855) and RNA integrity was assessed using High Sensitivity RNA ScreenTape analysis (Agilent 5067-5579) on the Agilent 4200 TapeStation system.
mRNA-seq library preparation was performed using KAPA RNA HyperPrep Kit with RiboErase (HMR), following the manufacturer’s protocol. Library size distribution and concentration were evaluated using the Agilent 4200 TapeStation system and Qubit dsDNA HS Assay Kit (ThermoFisher Scientific), respectively.


title: wt1


title: Spink5ko4


title: HET, replicate 1, CB, bulkRNA


title: Spink5ko2

value: female


title: Spink5ko3


title: WT, replicate 2, CB, bulkRNA


title: WT, replicate 2, CC, bulkRNA


title: S31,Pilot experiment, scRNASeq


title: WT, replicate 1, CC, bulkRNA


title: Spink5ko1


title: WT, replicate 1, CB, bulkRNA


title: S29,Pilot experiment, scRNASeq


title: HOMO, replicate 2, CB, bulkRNA

data_processing:
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read alignment using STAR-aligner. Count matrices were created using featureCounts of subread package.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: mm10
Supplementary files format and content: Tab-separated matrix file


title: HOMO, replicate 2, CC, bulkRNA


title: S28,Pilot experiment, scRNASeq


title: S30,Pilot experiment, scRNASeq


title: HOMO, replicate 1, CB, bulkRNA


title: S27,Pilot experiment, scRNASeq


title: S25,Pilot experiment, scRNASeq


title: WT, replicate 3, CB, bulkRNA


title: wt2


title: HOMO, replicate 1, CC, bulkRNA


title: S24,Pilot experiment, scRNASeq


title: S20,Pilot experiment, scRNASeq


title: HET, replicate 2, CC, bulkRNA


title: HET, replicate 2, CB, bulkRNA


title: WT, replicate 1, CC, bulkRNA


title: WT, replicate 3, CC, bulkRNA


title: WT, replicate 2, CB, bulkRNA


title: WT, replicate 1, CB, bulkRNA


title: S23,Pilot experiment, scRNASeq


title: S22,Pilot experiment, scRNASeq


title: D374Y week 4 HFD CD20 2

data_processing:
Cluster generation and sequencing was carried out by using the Illumina HiSeqV4 system with a read length of 50 nucleotides (single-read) or NovaSeq with a read length of 150 nucleotides (paired-end) and aligned to the mouse transcriptome genome assembly version of July 2007 (NCBI37/mm9) using TopHat version 1.4.1 or mouse genome assembly version of December 2011 (GRCm38/mm10) using STAR 2.4.2a (38) in the transcriptome-guided alignment mode.
Assembly: MM9 or MM10 as indicated in the description field
Supplementary files format and content: Tab-separated values of raw counts for each sample generated using HT-SEQ

extract_protocol:
livers were solubilized in Qiazol lysis reagent using Tissuelyser (Qiagen) and extracted RNA was isolated to upper fraction by chloroform. Purification was performed with RNeasy mini kit including on-column DNAse treatment, using a Qiacube robot.
RNA was selected using Poly(A) RNA Selection Kit (Lexogen) and sequencing libraries prepared with Lexogen QuantSeq V2. DNA fragments 200-800 bp for RNA-seq were selected.

value: Liver

value: week 4 HFD anti CD20


title: S19,Pilot experiment, scRNASeq

value: Breast


title: S18,Pilot experiment, scRNASeq

value: Breast cancer cells


title: S17,Pilot experiment, scRNASeq


title: D374Y week 4 HFD CD20 1


title: D374Y week 4 HFD CD20 3


title: S16,Pilot experiment, scRNASeq


title: S14,Pilot experiment, scRNASeq


title: APOE cKO Day 10 Clodronate 3

value: APOE cKO

value: Day 10 chow Clodronate liposomes


title: D374Y week 4 HFD PBS 2

value: week 4 HFD PBS


title: S26,Pilot experiment, scRNASeq


title: S15,Pilot experiment, scRNASeq


title: WT, replicate 2, CC, bulkRNA

value: Spleen

value: 8-10 weeks


title: S13,Pilot experiment, scRNASeq


title: APOE cKO Day 10 Clodronate 1


title: APOE cKO Day 10 Clodronate 2


title: S11,Pilot experiment, scRNASeq


title: S12,Pilot experiment, scRNASeq


title: APOE cKO Day 10 Dil 2

value: Day 10 chow Dil liposomes


title: S8,Pilot experiment, scRNASeq


title: APOE cKO Day 10 Dil 3


title: S6,Pilot experiment, scRNASeq


title: S9,Pilot experiment, scRNASeq


title: APOE cKO Day 10 Dil 1


title: S5,Pilot experiment, scRNASeq


title: D374Y week 8 HFD Clodronate 2

value: week 8 HFD Clodronate liposomes


title: D374Y littermate control week 8 HFD Dil 3

value: D374Y littermate control

value: week 8 HFD Dil liposomes


title: S4,Pilot experiment, scRNASeq


title: D374Y week 12 HFD 4

value: week 12 HFD


title: D374Y littermate control week 8 HFD Dil 1


title: D374Y week 8 HFD Clodronate 1


title: S3,Pilot experiment, scRNASeq


title: D374Y littermate control week 8 HFD Dil 2


title: D374Y week 4 HFD PBS 1


title: S1,Pilot experiment, scRNASeq


title: HS2 H1N1 infected, then SARS-CoV-2 infected 48 hours later, Day 2, animal 3

city: West haven

first: Antariksh

last: Tyagi

state: CT

address: 830 West Campus Dr

institute: Yale University

data_processing:
Low quality reads were trimmed and adaptor contamination were removed using Trim Galore (v0.5.0)
Trimmed reads were mapped to the MesAur1.0 reference genome using HISAT2
Gene expression levels were quantified using StringTie (v1.3.3b)
Assembly: MesAur1.0
Supplementary files format and content: tab-delimited text file of raw counts

organism: Mesocricetus auratus

source_name: Nasal epithelium

extract_protocol:
RNA was extracted (RNeasy Mini Kit; Qiagen) and potential DNA contamination were removed with 30 minute incubation in RNase-free DNase (Qiagen). Total RNA quality was determined by estimating the A260/A280 and A260/A230 ratios by nanodrop.   RNA integrity was determined by running an Agilent Bioanalyzer gel, with samples with values of 5 or greater used for library preparation. Using the Kapa RNA HyperPrep Kit with RiboErase (KR1351), rRNA was depleted starting from 25-1000ng of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA.  Samples were then fragmented using heat and magnesium.
1st strand synthesis was performed using random priming.  2nd strand synthesis incorporated dUTPs into the 2nd strand cDNA.  Adapters were then ligated and the library amplified.
Indexed libraries were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems, Roche) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ?0.5 ng/ul were used for sequencing.   Sample concentrations were normalized to 1.2 nM and loaded onto an Illumina NovaSeq flow cell at a concentration that yielded at least 30 million passing filter clusters per sample. Samples were sequenced using 150bp paired-end sequencing on an Illumina NovaSeq according to Illumina protocols

treatment_protocol: We infected 6-8 week old Syrian hamsters intranasally with Influenza (Influenza virus A/Michigan/45/2015 (H1N1) pdm09), followed by infection with SARS-CoV-2 (SARS-CoV-2 Wuhan/IVDC-HB-01/2019) given intranasally 48 hours later. Four infection groups were used: H1N1 infection only (n=6), SARS-CoV-2 infection only (n=6), H1N1 infection followed by SARS-CoV-2 infection 48 hours later (n=6), and mock infected (n=4)

value: Nasal epithelium

value: Wild type

value: Influenza virus A/Michigan/45/2015 (H1N1) pdm09 followed by SARS-CoV-2 Wuhan/IVDC-HB-01/2019


title: S2,Pilot experiment, scRNASeq


title: D374Y week 12 HFD 2

value: Liver


title: HS2 H1N1 infected, then SARS-CoV-2 infected 48 hours later, Day 2, animal 2


title: HS1 H1N1 infected, then SARS-CoV-2 infected 48 hours later, Day 1, animal 3


title: S10,Pilot experiment, scRNASeq


title: D374Y week 12 HFD 3


title: D374Y littermate control week 12 HFD 2


title: S7,Pilot experiment, scRNASeq


title: D374Y week 12 HFD 1


title: D374Y littermate control week 12 HFD 1


title: HS1 H1N1 infected, then SARS-CoV-2 infected 48 hours later, Day 1, animal 1


title: APOE cKO week 12 HFD 3


title: S2 SARS-CoV-2 infected, Day 2 animal 3

value: SARS-CoV-2 Wuhan/IVDC-HB-01/2019


title: D374Y littermate control week 12 HFD 3


title: APOE cKO week 12 HFD 2


title: APOE cKO week 12 HFD 1


title: S1 SARS-CoV-2 infected, Day 1 animal 2


title: S1 SARS-CoV-2 infected, Day 1 animal 3


title: APOE cKO littermate control week 12 HFD 3

value: APOE cKO littermate control


title: APOE cKO littermate control week 12 HFD 2


title: APOE cKO littermate control week 12 HFD 1


title: S2 SARS-CoV-2 infected, Day 2 animal 2


title: S1 SARS-CoV-2 infected, Day 1 animal 1


title: H2 H1N1 infected, Day 2 animal 2

value: Influenza virus A/Michigan/45/2015 (H1N1) pdm09


title: D374Y week 8 HFD 4

value: week 8 HFD


title: D374Y week 8 HFD 5


title: D374Y week 8 HFD 3


title: HS1 H1N1 infected, then SARS-CoV-2 infected 48 hours later, Day 1, animal 2


title: H1 H1N1 infected, Day 1 animal 2


title: HS2 H1N1 infected, then SARS-CoV-2 infected 48 hours later, Day 2, animal 1


title: D374Y week 8 HFD 1


title: H2 H1N1 infected, Day 2 animal 3


title: D374Y littermate control week 8 HFD 3


title: D374Y littermate control week 8 HFD 2


title: H2 H1N1 infected, Day 2 animal 1


title: samp_D Control, mock infected animal D

value: Mock inoculated


title: samp_C Control, mock infected animal C


title: D374Y week 8 HFD 2


title: APOE cKO week 8 HFD 4

value: APOE cKO


title: APOE cKO week 12 HFD 4


title: H1 H1N1 infected, Day 1 animal 3


title: S2 SARS-CoV-2 infected, Day 2 animal 1


title: samp_A Control, mock infected animal A


title: H1 H1N1 infected, Day 1 animal 1


title: APOE cKO littermate control week 8 HFD 3


title: R1192C_MUT, replicate 3, bulkATAC

data_processing:
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read trimming, read alignment using bwa, filtering low-quality, unmapped and duplicated reads. BIGWIG files were generated using deeptools RPKM normalization.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: hg38
Supplementary files format and content: Tab-separated count matrix file and RPKM normalized bigwig files

source_name: Raji

value: Raji

value: Smarca4 R1192C/+


title: R1192C_MUT, replicate 2, bulkATAC


title: APOE cKO littermate control week 8 HFD 2


title: R1192C_MUT, replicate 1, bulkATAC


title: APOE cKO littermate control week 8 HFD 1


title: samp_B Control, mock infected animal B


title: D374Y littermate control week 8 HFD 1


title: WT, replicate 3, bulkATAC


title: APOE cKO week 8 HFD 1


title: WT, replicate 4, bulkATAC


title: WT, replicate 2, bulkATAC


title: WT, replicate 1, bulkATAC


title: APOE cKO week 8 HFD 3


title: APOE cKO week 8 HFD 5


title: RAW 264.7, Irf7 KO1 Untreated rep 3

city: Bryan

first: Kristin

middle: L

last: Patrick

address: 8447 Riverside Pkwy, MREB 3102

department: Microbial Pathogenesis and Immunology

institute: Texas A&M University, College of Medicine

description: Irf7 KO DEGs UN Table.xlsx

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Reads were trimmed using cutadapt.
Quality scores were assessed using FastQC.
Reads were aligned to the Mus musculus genome build GRCm39 using STAR3.
Individual sample reads were quantified using HTseq4 and normalized via Relative Log Expression (RLE) using DESeq2 R library.
Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library.
Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction.
Assembly: Mus musculus genome build mm10
Supplementary files format and content: raw data fastq.gz
Supplementary files format and content: fastq.gz

growth_protocol: DMEM supplemented with 10% FBS and 2% Hepes. Cells cultured at 37C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Zymo Research Direct-zol kits were used to isolate RNA with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100 ng/ml LPS added to complete media (CM) for 4h

value: macrophage-like

value: Irf7 KO

value: Untreated


title: APOE cKO week 8 HFD 2


title: GFP_LOW, replicate 1, 72hr, IgG

data_processing:
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read trimming, read alignment using BOWTIE2, filtering low-quality, unmapped and duplicated reads. BIGWIG files were generated using deeptools RPKM normalization.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: hg38
Supplementary files format and content: RPKM bw files
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed using CUTANA™ ChIC/CUT&RUN kit (EpiCypher, Cat. 14-1048), according to manufacturer’s instructions
Following DNA purification, libraries were prepared using KAPA HyperPrep Kit (Roche, KK8504). Three replicates were performed for each condition. 100bp paired-end sequencing was performed on Illumina sequencer


title: GFP_LOW, replicate 2, 72hr, IgG


title: GFP_LOW, replicate 3, 72hr, IgG


title: RAW 264.7, GFP KO Untreated rep 2

description: Irf7 KO DEGs UN Table.xlsx

value: GFP gRNA Control


title: RAW 264.7, Irf7 KO1 Untreated rep 1

description: Irf7 KO DEGs UN Table.xlsx


title: RAW 264.7, Irf7 KO1 Untreated rep 2

description: Irf7 KO DEGs UN Table.xlsx


title: GFP_HIGH, replicate 3, 72hr, IgG


title: RAW 264.7, GFP KO Untreated rep 3

description: Irf7 KO DEGs UN Table.xlsx


title: GFP_HIGH, replicate 2, 72hr, IgG


title: RAW 264.7, GFP KO Untreated rep 1

description: Irf7 KO DEGs UN Table.xlsx


title: GFP_LOW, replicate 2, 48hr, IgG


title: RAW 264.7, Irf7 KO1 +LPS rep 3

description: Irf7 KO DEGs +4H LPS Table.xlsx

value: 4h LPS


title: GFP_HIGH, replicate 2, 48hr, IgG


title: GFP_LOW, replicate 1, 48hr, IgG


title: RAW 264.7, GFP KO +LPS rep 3

description: Irf7 KO DEGs +4H LPS Table.xlsx


title: RAW 264.7, Irf7 KO1 +LPS rep 1

description: Irf7 KO DEGs +4H LPS Table.xlsx


title: GFP_LOW, replicate 2, 24hr, IgG


title: GFP_LOW, replicate 3, 48hr, IgG


title: 4T1 tumor, with peak, replicate 2 [N25]

city: CLEVELAND

first: Haidong

last: Huang

state: OH

address: 9500 EUCLID AVE RK-15

department: Cancer Biology

institute: Cleveland Clinic Foundation

data_processing:
Fastq files containing reads were quality-controlled with fastQC and aligned to the mouse genome mm10 using STAR aligner with ‘quantMode’ mode to generate gene counts.
Assembly: mm10
Supplementary files format and content: raw counts for each sample

source_name: 4T1-TNBC tumors

extract_protocol:
Tissues were snap-frozen in liquid nitrogen immediately after dissected. RNAs were isolated from these tissues using Trizol reagent.
Oligo(dT) purified RNAs were used to construct libraries for paired-end unstranded sequencing

value: 4T1-TNBC tumors

value: with peak


title: RAW 264.7, Irf7 KO1 +LPS rep 2

description: Irf7 KO DEGs +4H LPS Table.xlsx


title: 4T1 tumor, before peak, replicate 1 [NO1]

value: before peak


title: 4T1 tumor, before peak, replicate 2 [NO2]


title: 4T1 tumor, with peak, replicate 1 [L25]


title: 4T1 tumor, with peak, replicate 3 [O5DL]


title: 4T1 tumor, before peak, replicate 3 [NO3]


title: GFP_HIGH, replicate 3, 48hr, IgG


title: C&R_D12_JB_IgG

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

data_processing:
C&R were mapped on the mouse genome (mm39 masked  for JF1 SNPs) using Bowtie2 .
Alignments filtering was realized with samtools (view -f 2 -q 20), and the coverage was obtained using bamCoverage (--scaleFactor “spike-in DNA” --normalizeUsing RPKM --binSize 25)
Peaks were called with MACS2 using Cut&Run sample performed with an IgG as a control (callpeak -f BAMPE --keep-dup all)
Assembly: mm39
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

growth_protocol: ES cell lines were maintained in gelatin-coated dishes with ESGRO complete plus medium (Millipore, SF001-500P) containing LIF, BMP4, and a GSK3-β inhibitor. ES-derived neural precursor cells were generated using in vitro corticogenesis as described in Montibus et al 2021 (PMID: 32405722).

extract_protocol:
Cut&Run was performed using the CUTANA™ CUT&RUN Kit (Epicypher) on non-fixed nuclei according to the manufacturer's instructions.
Illumina sequencing libraries were prepared using the CUTANA™ CUT&RUN Library Prep Kit (EpiCypher 14-1001 & 14-1002) according to the manufacturer's recommendations, and sequencing on a NovaSeq 6000 instrument (Illumina) were performed by IntegraGen SA.

value: ES-derived neural precursor cells

value: JF1 x C57BL/6

value: In vitro corticogenesis Day 12

tag: chip antibody

value: IgG Epicypher, 13-0042K


title: GFP_LOW, replicate 1, 24hr, IgG


title: C&R_D12_JB_H3K27me3

value: H3K27me3 Diagenode, C15410195


title: GFP_HIGH, replicate 1, 24hr, IgG


title: GFP_HIGH, replicate 1, 48hr, IgG


title: GFP_HIGH, replicate 1, 72hr, IgG


title: RAW 264.7, GFP KO +LPS rep 2

description: Irf7 KO DEGs +4H LPS Table.xlsx


title: RAW 264.7, GFP KO +LPS rep 1

description: Irf7 KO DEGs +4H LPS Table.xlsx


title: GFP_LOW, replicate 3, 24hr, IgG


title: Otx2_D1

city: Austin

first: Muyoung

last: Lee

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description: processed data file: TPM_table2.txt

data_processing:
Adapter/quality trimming was done with Trim Galore v0.6.10 (Babraham Bioinformatics, https://github.com/FelixKrueger/TrimGalore)
Quantification of transcript expressions was done using Salmon v1.10.2 (PMID: 28263959) based on the mm10 reference, and the data were aggregated to the gene level using the R package tximport v1.22.0 (PMID: 26925227).
Assembly: mm10
Supplementary files format and content: TPM_table.txt, length-scaled TPM values of genes (rows) from each sample (column)

source_name: pre-implantation embryo

extract_protocol:
Total RNA was extracted from cells using the RNeasy Plus Mini Kit (Qiagen) (74136). The mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module kit (E7490L).
The RNAs-seq libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (E7770L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol. RNA-seq was then performed with paired-end 150bp on the NovaSeq 6000 (Illumina).

value: pre-implantation embryo

value: mouse embryonic stem (ES) cells

value: Otx2 SBFB

value: Doxycycline (500ng/ml) was applied to the cells for 1 day.


title: Otx2_D3

description: processed data file: TPM_table2.txt

value: Doxycycline (500ng/ml) was applied to the cells for 3 days.


title: C&R_ES_JB_H3K27me3

value: ES cells


title: GFP_HIGH, replicate 2, 24hr, IgG

value: Raji


title: Otx2_12h

description: processed data file: TPM_table2.txt

value: Doxycycline (500ng/ml) was applied to the cells for 12 hours.


title: GFP_HIGH, replicate 3, 72hr, PU.1


title: GFP_LOW, replicate 1, 72hr, PU.1


title: Otx2_D5

description: processed data file: TPM_table2.txt

value: Doxycycline (500ng/ml) was applied to the cells for 5 days.


title: Otx2_0h

description: processed data file: TPM_table2.txt

value: Doxycycline was not applied to the cells.


title: GFP_LOW, replicate 3, 48hr, PU.1


title: GFP_HIGH, replicate 2, 72hr, PU.1


title: GFP_LOW, replicate 2, 48hr, PU.1


title: GFP_LOW, replicate 1, 48hr, PU.1


title: Gcm1_12h

description: processed data file: TPM_table2.txt

value: Gcm1 SBFB


title: GFP_LOW, replicate 3, 72hr, PU.1


title: Otx2_6h

description: processed data file: TPM_table2.txt

value: Doxycycline (500ng/ml) was applied to the cells for 6 hours.


title: Otx2_3h

description: processed data file: TPM_table2.txt

value: Doxycycline (500ng/ml) was applied to the cells for 3 hours.


title: Gcm1_3h

description: processed data file: TPM_table2.txt


title: GFP_HIGH, replicate 1, 72hr, PU.1


title: Gcm1_D5

description: processed data file: TPM_table2.txt


title: Gcm1_D3

description: processed data file: TPM_table2.txt


title: GFP_HIGH, replicate 3, 48hr, PU.1


title: GFP_LOW, replicate 2, 72hr, PU.1


title: GFP_HIGH, replicate 1, 48hr, PU.1


title: Dlx5_D1

description: processed data file: TPM_table2.txt

value: Dlx5 SBFB


title: GFP_HIGH, replicate 3, 24hr, IgG


title: GFP_LOW, replicate 3, 24hr, PU.1


title: Gcm1_0h

description: processed data file: TPM_table2.txt


title: Dlx5_D5

description: processed data file: TPM_table2.txt


title: Dlx5_12h

description: processed data file: TPM_table2.txt


title: GFP_HIGH, replicate 2, 48hr, PU.1


title: GFP_LOW, replicate 2, 24hr, PU.1


title: Dlx5_D3

description: processed data file: TPM_table2.txt


title: Gcm1_D1

description: processed data file: TPM_table2.txt


title: GFP_HIGH, replicate 3, 24hr, PU.1


title: Dlx5_0h

description: processed data file: TPM_table2.txt


title: GFP_LOW, replicate 1, 24hr, PU.1


title: Dlx5_3h

description: processed data file: TPM_table2.txt


title: Dlx5_6h

description: processed data file: TPM_table2.txt


title: GFP_LOW, replicate 2, 24hr, bulkRNA treated

data_processing:
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read alignment using STAR-aligner. Count matrices were created using featureCounts of subread package.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: hg38
Supplementary files format and content: Tab-separated matrix file

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN) according to the manufacturers protocol.
mRNA-seq library preparation was performed using KAPA RNA HyperPrep Kit with RiboErase (HMR), following the manufacturer’s protocol. Library size distribution and concentration was evaluated using the Agilent 4200 TapeStation system and Qubit dsDNA HS Assay Kit (ThermoFisher Scientific), respectively.


title: Gcm1_6h

description: processed data file: TPM_table2.txt


title: GFP_HIGH, replicate 1, 24hr, PU.1


title: GFP_LOW, replicate 3, 24hr, bulkRNA untreated

value: DMSO


title: Pdx1_noDox_ctrl

description: processed data file: TPM_table.txt

value: Pdx1 SBFB

value: Doxycycline was not applied to the cells. The cells were maintained to day 7.


title: GFP_LOW, replicate 3, 24hr, bulkRNA treated


title: GFP_LOW, replicate 2, 24hr, bulkRNA untreated


title: GFP_LOW, replicate 1, 24hr, bulkRNA treated


title: Pdx1_D3_Dox_remv

description: processed data file: TPM_table.txt

value: pre-implantation embryo

value: 3 day of doxycycline treatment (500ng/ml) and then the doxycycline was removed. The cells were maintained to day 7.


title: GFP_LOW, replicate 1, 24hr, bulkRNA untreated


title: GFP_HIGH, replicate 2, 24hr, PU.1


title: D374Y week 4 HFD CD8 2

value: Liver

value: week 4 HFD anti CD8


title: GFP_HIGH, replicate 3, 24hr, bulkRNA treated


title: D374Y week 4 HFD 3

value: week 4 HFD


title: D374Y week 4 HFD CD8 3


title: Otx2_noDox_ctrl

description: processed data file: TPM_table.txt

value: mouse embryonic stem (ES) cells

value: Otx2 SBFB


title: D374Y week 4 HFD CD8 1


title: Otx2_Dox_ctrl

description: processed data file: TPM_table.txt

value: Doxycycline (500ng/ml) was continuously applied to the cells. The cells were maintained to day 7.


title: D374Y week 4 HFD 1


title: GFP_HIGH, replicate 3, 24hr, bulkRNA untreated

value: Raji


title: GFP_HIGH, replicate 2, 24hr, bulkRNA treated


title: Pdx1_D1_Dox_remv

description: processed data file: TPM_table.txt

value: 1 day of doxycycline treatment (500ng/ml) and then the doxycycline was removed. The cells were maintained to day 7.


title: D374Y littermate control week 4 HFD 2

value: D374Y littermate control


title: GFP_HIGH, replicate 2, 24hr, bulkRNA untreated


title: APOE cKO week 4 HFD CD8 2

value: APOE cKO


title: D374Y littermate control week 4 HFD 1


title: APOE cKO week 4 HFD 3


title: Otx2_D5_Dox_remv

description: processed data file: TPM_table.txt

value: 5 day of doxycycline treatment (500ng/ml) and then the doxycycline was removed. The cells were maintained to day 7.


title: APOE cKO week 4 HFD CD8 1


title: GFP_HIGH, replicate 1, 24hr, bulkRNA treated


title: APOE cKO week 4 HFD 2


title: Pdx1_Dox_ctrl

description: processed data file: TPM_table.txt


title: Otx2_D3_Dox_remv

description: processed data file: TPM_table.txt


title: Otx2_D1_Dox_remv

description: processed data file: TPM_table.txt


title: Gcm1_noDox_ctrl

description: processed data file: TPM_table.txt

value: Gcm1 SBFB


title: D374Y week 4 HFD 2


title: GFP_HIGH, replicate 1, 24hr, bulkRNA untreated

value: DMSO


title: APOE cKO littermate control week 4 HFD 2

value: APOE cKO littermate control


title: APOE cKO week 4 HFD 1


title: APOE cKO littermate control week 4 HFD 3


title: Pdx1_D5_Dox_remv

description: processed data file: TPM_table.txt

value: Pdx1 SBFB


title: D374Y Day 10 chow Clodronate 2

value: Day 10 chow Clodronate liposomes


title: APOE cKO littermate control week 4 HFD 1


title: Gcm1_D5_Dox_remv

description: processed data file: TPM_table.txt

value: pre-implantation embryo


title: R1192C_MUT, replicate 4, bulkATAC

value: Smarca4 R1192C/+


title: R1192C_MUT, replicate 2, bulkATAC


title: R1192C_MUT, replicate 3, bulkATAC


title: Gcm1_Dox_ctrl

description: processed data file: TPM_table.txt


title: D374Y Day 10 chow Dil 3

value: Liver

value: Day 10 chow


title: Gata3_noDox_ctrl

description: processed data file: TPM_table.txt

value: mouse embryonic stem (ES) cells

value: Gata3 SBFB

value: Doxycycline was not applied to the cells. The cells were maintained to day 7.


title: D374Y Day 10 chow Clodronate 1


title: D374Y Day 10 chow Dil 2


title: R1192C_MUT, replicate 1, bulkATAC


title: WT, replicate 3, bulkATAC


title: Gata3_Dox_ctrl

description: processed data file: TPM_table.txt

value: Doxycycline (500ng/ml) was continuously applied to the cells. The cells were maintained to day 7.


title: WT, replicate 2, bulkATAC


title: Gata3_D5_Dox_remv

description: processed data file: TPM_table.txt


title: D374Y littermate control Day 10 chow Clodronate 3


title: D374Y Day 10 chow Dil 1


title: WT, replicate 1, bulkATAC


title: D374Y littermate control Day 10 chow Clodronate 2


title: D374Y Day 10 chow Clodronate 3


title: R1192C_MUT, replicate 3, bulkRNA

value: Raji


title: Gata3_D3_Dox_remv

description: processed data file: TPM_table.txt

value: 3 day of doxycycline treatment (500ng/ml) and then the doxycycline was removed. The cells were maintained to day 7.


title: Gata3_D1_Dox_remv

description: processed data file: TPM_table.txt

value: 1 day of doxycycline treatment (500ng/ml) and then the doxycycline was removed. The cells were maintained to day 7.


title: R1192C_MUT, replicate 2, bulkRNA


title: Gcm1_D3_Dox_remv

description: processed data file: TPM_table.txt


title: Torpor Supraoptic Nucleus Replicate 5

city: New Haven

first: Madeleine

last: Junkins

state: Connecticut

address: 333 Cedar Street

department: Cellular & Molecular Physiology; Neuroscience

data_processing:
Raw sequencing reads were filtered and trimmed to retain high-quality reads using Trimmomatic v0.39 (Bolger et al., 2014) with default parameters.
Filtered high-quality reads from all samples were aligned to Ictidomys tridecemlineatus reference genome using STAR aligner v2.7.7a with default parameters (Dobin et al., 2013).
Aligned reads were counted by the featureCounts module within the Subread package v2.0.1 with default parameters (Liao et al., 2014).
Processing, normalization, and statistical analysis of read counts was performed using the EdgeR v3.38.4 package in R v4.2.1 (Robinson et al., 2010)
Statistical analysis of differential expression of genes between groups was performed using the GLM approach and the quasi-likelihood F-test, as implemented in the EdgeR package.
Assembly: The SpeTri2.0 [GCA_000236235.1] reference genome and the gene annotation were obtained from the Broad Institute through the National Center for Biotechnology Information (Ictidomys tridecemlineatus; assembly SpeTri2.0; NCBI Ictidomys tridecemlineatus Annotation Release 102; all files accessed on 8/17/2020).  Reference genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/GCF_015476345.1_ZJU1.0_genomic.fna.gz; Gene annotation: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/236/235/GCF_000236235.1_SpeTri2.0/GCF_000236235.1_SpeTri2.0_genomic.gff.gz; the gene annotation was filtered to include only protein-coding genes.
Supplementary files format and content: Processed data file in Excel format (.xlsx) contains normalized read counts, normalized mean read counts, P-values, adjusted FDR values, and fold change (log2) for statistical comparison of expression values between 2 groups.

organism: Ictidomys tridecemlineatus

source_name: Supraoptic Nucleus of Hypothalamus

growth_protocol: The brain was rapidly dissected and a vibratome (Leica VT1200) was used to cut 300-600 μm coronal slices. The supraoptic nuclei were manually dissected out from the slices using 27G needles and placed immediately into RNA lysis buffer from the Quick-RNA Microprep Kit (Zymo, R1050).

extract_protocol:
Total RNA was isolated from tissue using the Quick-RNA Microprep Kit (Zymo, R1050). RNA concentration and integrity number (RIN) were assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). RNA concentrations were in the range of ~5.1 – 42.4 ng/µL and RIN values were in the range of 7.3 – 8.8.
Sequencing libraries were prepared using the Kapa mRNA Hyper Prep kit (KAPA Biosystems, Wilmington, MA).

value: Supraoptic Nucleus of Hypothalamus

tag: state

value: Torpor


title: Gcm1_D1_Dox_remv

description: processed data file: TPM_table.txt

value: Gcm1 SBFB


title: Dlx5_noDox_ctrl

description: processed data file: TPM_table.txt

value: Dlx5 SBFB


title: Torpor Supraoptic Nucleus Replicate 3


title: Torpor Supraoptic Nucleus Replicate 4


title: WT, replicate 4, bulkATAC


title: D374Y Day 10 chow 2


title: D374Y Day 10 chow 1


title: R1192C_MUT, replicate 1, bulkRNA


title: Dlx5_Dox_ctrl

description: processed data file: TPM_table.txt


title: WT, replicate 3, bulkRNA


title: WT, replicate 4, bulkRNA


title: Dlx5_D5_Dox_remv

description: processed data file: TPM_table.txt

value: 5 day of doxycycline treatment (500ng/ml) and then the doxycycline was removed. The cells were maintained to day 7.


title: D374Y littermate control Day 10 chow 2

value: D374Y littermate control


title: Torpor Supraoptic Nucleus Replicate 1


title: Dlx5_D3_Dox_remv

description: processed data file: TPM_table.txt

value: pre-implantation embryo


title: IBA Supraoptic Nucleus Replicate 5

value: IBA


title: APOE cKO Day 10 chow 4

value: Liver

value: APOE cKO


title: Torpor Supraoptic Nucleus Replicate 2


title: D374Y littermate control Day 10 chow 1

value: Day 10 chow


title: D374Y littermate control Day 10 chow Clodronate 1

value: Day 10 chow Clodronate liposomes


title: WT, replicate 2, bulkRNA


title: WT, replicate 1, bulkRNA


title: APOE cKO Day 10 chow 3


title: GFP_LOW, replicate 3, 72hr, bulkRNA

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN) according to the manufacturers protocol.
mRNA-seq library preparation was performed using KAPA RNA HyperPrep Kit with RiboErase (HMR), following the manufacturer’s protocol. Library size distribution and concentration were evaluated using the Agilent 4200 TapeStation system and Qubit dsDNA HS Assay Kit (ThermoFisher Scientific), respectively.


title: RNA-seq_D12_JB_rep2

data_processing:
RNA-seq were mapped on the mouse genome (mm39 masked  for JF1 SNPs) using TopHat2 with a transcript annotation file from UCSC (refGene track).
The read count per gene was obtained with the HTseq-count script on properly paired reads and RefGene transcript annotation file.
Differential expression analysis between groups was based on read count using DESeq2 and edgeR R packages.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include count values per gene

extract_protocol:
The total RNA were extracted using the RNeasy MiniKit (Qiagen, 74104) following the manufacturer's protocol. RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).
TruSeq Stranded mRNA library preparation or NEBNext® Ultra™ II mRNA-Seq library preparation  and sequencing on illumina  HiSeq4000  or Illumina NovaSeq 6000 were performed by Integragen, SA (Evry, France), according to the manufacturer's protocol.

value: ES-derived neural precursor cells

value: JF1 x C57BL/6

value: In vitro corticogenesis Day 12


title: IBA Supraoptic Nucleus Replicate 4


title: RNA-seq_D12_BJ_rep2

value: C57BL/6 x JF1


title: APOE cKO Day 10 chow 2


title: IBA Supraoptic Nucleus Replicate 3


title: APOE cKO Day 10 chow 1


title: RNA-seq_ES_JB_rep2

value: ES cells


title: GFP_LOW, replicate 3, 24hr, bulkRNA

value: Raji


title: IBA Supraoptic Nucleus Replicate 1

value: Supraoptic Nucleus of Hypothalamus


title: GFP_LOW, replicate 3, 48hr, bulkRNA


title: RNA-seq_ES_BJ_rep2


title: Active Supraoptic Nucleus Replicate 5

value: Active


title: GFP_LOW, replicate 2, 72hr, bulkRNA


title: C&R_ES_JB_IgG

data_processing:
C&R were mapped on the mouse genome (mm39 masked  for JF1 SNPs)using Bowtie2 .
Alignments filtering was realized with samtools (view -f 2 -q 20), and the coverage was obtained using bamCoverage (--scaleFactor “spike-in DNA” --normalizeUsing RPKM --binSize 25)
Peaks were called with MACS2 using Cut&Run sample performed with an IgG as a control (callpeak -f BAMPE --keep-dup all)
Assembly: mm39
Supplementary files format and content: bigWig
Library strategy: Cut&Run

value: IgG Epicypher, 13-0042K


title: Active Supraoptic Nucleus Replicate 4


title: Dlx5_D1_Dox_remv

description: processed data file: TPM_table.txt

value: mouse embryonic stem (ES) cells

value: Dlx5 SBFB

value: 1 day of doxycycline treatment (500ng/ml) and then the doxycycline was removed. The cells were maintained to day 7.


title: C&R_ES_JB_CTCF

value: CTCF Diagenode, C15410210


title: GFP_LOW, replicate 2, 24hr, bulkRNA


title: APOE cKO littermate control Day 10 chow 3

value: Liver

value: APOE cKO littermate control


title: APOE cKO littermate control Day 10 chow 2

value: Day 10 chow


title: C&R_D12_BJ_IgG


title: APOE cKO littermate control Day 10 chow 1


title: GFP_LOW, replicate 1, 72hr, bulkRNA


title: IBA Supraoptic Nucleus Replicate 2

value: IBA


title: D374Y week 20 HFD 4

value: week 20 HFD


title: Active Supraoptic Nucleus Replicate 1


title: C&R_ES_BJ_IgG


title: C&R_D12_BJ_CTCF

value: ES-derived neural precursor cells


title: D374Y week 20 HFD 3


title: GFP_LOW, replicate 1, 48hr, bulkRNA


title: Active Supraoptic Nucleus Replicate 2


title: APOE cKO littermate control Day 10 chow 4


title: GFP_LOW, replicate 1, 24hr, bulkRNA


title: C&R_ES_BJ_CTCF


title: GFP_LOW, replicate 2, 48hr, bulkRNA


title: D374Y week 20 HFD 2


title: C&R_ES_BJ_ZFP57

value: ZFP57 Abcam, ab45341


title: GFP_HIGH, replicate 3, 72hr, bulkRNA


title: D374Y week 20 HFD 1


title: treatment2

city: shanghai

first: zengguang

last: wang

address: No. 639 Zhizaoju Road, Shanghai 200001

institute: Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software to obtain mapped reads.FeatureCounts 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.
Assembly: Rattus_norvegicus_Ensembl_104
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

organism: Rattus norvegicus

source_name: tenocytes

extract_protocol:
Total RNA was extracted from the tenocytes using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapterligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system

value: tenocytes

value: complete medium containing 50ng/ml IL-1b


title: treatment3


title: C&R_D12_BJ_H3K27me3

value: C57BL/6 x JF1

value: In vitro corticogenesis Day 12

value: H3K27me3 Diagenode, C15410195


title: Active Supraoptic Nucleus Replicate 3

value: Supraoptic Nucleus of Hypothalamus

value: Active


title: treatment1


title: D374Y littermate control week 20 HFD 2

value: D374Y littermate control


title: GFP_HIGH, replicate 3, 24hr, bulkRNA

value: Raji


title: C&R_ES_BJ_H3K27me3

value: ES cells


title: control3

value: complete medium


title: D374Y littermate control week 20 HFD 1

value: Liver


title: control2


title: 4C-seq_Trappc9_PE_D12_BJ

data_processing:
Due to the primer design, paired end reads were used to determine the viewpoint allele and the interacting sequence. To do this, only the expected sequence, corresponding to the viewpoint of the informative reads, was mapped to the mm39 hybrid genome using bowtie2 (--trim5 10 --trim3 “viewpoint specific” --local --very-sensitive-local). Only alignments mapped to the viewpoint coordinates and with a minimal quality were conserved to determine the origin allelic of the viewpoint in the reads (samtools view -q 10 [ viewpoint coordinates]). To determine the sequence in interaction, the expected sequence with DpnII restriction site was mapped to the mm39 masked genome using bowtie2 (--trim5 “viewpoint specific” --trim3 “viewpoint specific” --local --very-sensitive-local). these alignments were filtered for mapping quality (samtools view -q 10 ) and were split according to the origin allelic of the viewpoint. To construct the allelic interactome, the alignments were processed the FourCSeq Bioconductor package to count the reads mapped exactly to the end of a DpnII fragment and to generate a smoothed rpm normalized coverage.
Assembly: mm39
Supplementary files format and content: bigwig, allelic coverage
Library strategy: 4C-seq

extract_protocol:
4C Template Preparation was carried out as previously described with some modifications (Harmen J G van de Werken et al,). Briefly, 1x107 cell suspensions were cross-linked with formaldehyde (final concentration 2%) for 10 min. After cell lysis and permeabilization by SDS and Triton X-100 treatments, samples were digested with 600U DpnII at 37ºC in 1X NEBuffer DpnII (4 h with 200U, overnight with 200U and 4 h with 200U). The restriction enzyme was inactivated with SDS and Triton X-100. The first ligation was performed overnight at 18°C in a large volume, 7.2 ml of 1X ligase buffer and with 50U T4 DNA Ligase. The cross-linking was reversed with 600ug Proteinase K at 65°C overnight. After phenol/chloroform purification, the DNA was digested with 50U of NlaIII overnight at 37°C. After phenol/chloroform purification, a second ligation was performed overnight at 18°C in 14ml of 1X ligase buffer and with 100U of T4 DNA Ligase. The 4C Template was concentrated with an ethanol precipitation and then purified using the DNA Clean & Concentrator Zymo-25 kit.
To produce a 4C-seq library, 3,2 µg of 4C template was amplified into 16 PCR reactions with viewpoint specific sequencing primers and 56 U of Expand Long Template Polymerase. PCR reactions were pooled and purified using High Pure PCR Product Purification Kit. 4C-seq library of different viewpoints were combined before sequencing on an HiSeq 4000 or NovaSeq 6000 instrument (Illumina) by IntegraGen SA.


title: APOE cKO week 20 HFD 3

value: APOE cKO


title: 4C-seq_Trappc9_PE_ES_BJ


title: APOE cKO week 20 HFD 2


title: GFP_HIGH, replicate 2, 48hr, bulkRNA


title: GFP_HIGH, replicate 2, 24hr, bulkRNA


title: control1


title: GFP_HIGH, replicate 1, 72hr, bulkRNA


title: APOE cKO week 20 HFD 1


title: 4C-seq_Kcnk9_D12_BJ


title: GFP_HIGH, replicate 3, 48hr, bulkRNA


title: APOE cKO littermate control week 20 HFD 2

value: APOE cKO littermate control


title: GFP_HIGH, replicate 1, 48hr, bulkRNA


title: 4C-seq_Peg13_DMR_D12_BJ_2


title: GFP_HIGH, replicate 2, 72hr, bulkRNA


title: APOE cKO littermate control week 20 HFD 1

value: week 20 HFD


title: GFP_HIGH, replicate 1, 24hr, bulkRNA


title: TCR:eVAT Lean and eVAT Obese and Spleen Lean and Spleen Obese (exp4)

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as count matrices using Cell Ranger (10x Genomics).
Cells with no or multiple hashes, high mitochondrial content, low gene number, low UMI number, or lineage markers of contaminants were filtered out in Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: eVAT Lean #3 (Hash1), eVAT Obese #3 (Hash3), eVAT Obese #4 (Hash4), Spleen Lean #3 (Hash7), Spleen Obese #3 (Hash9), Spleen Obese #4 (Hash10)

extract_protocol:
Immunocytes were released by mechanical disruption followed by filtering and washed in RPMI containing 5% fetal calf serum (FCS). Red blood cells were lysed prior to filtering using ACK lysing buffer Cells were then purified by fluorescence-activated cell sorting. Single cells were then sent to the Broad Institute Genomics Platform, which performed encapsulation following 10x Genomics protocols.
scRNA-seq and scTCR-seq; 10x Genomics library prep, 3' v3 chemistry or 5' v2 chemistry

value: eVAT

value: CD45+ TCRb+ CD4+ Tregs

value: Male

value: LFD or HFD

tag: hashid

value: Hash1-ACCCACCAGTAAGAC, Hash3-CTTGCCGCATGTCAT, Hash4-AAAGCATTCTTCACG, Hash7-GAGTCTGCCAGTATC, Hash9-TGCCTATGAAACAAG, Hash10-CCGATTGTAACAGAC


title: 4C-seq_Peg13_DMR_ES_BJ_2

value: C57BL/6 x JF1


title: GFP_LOW, replicate 3, 72hr, bulkATAC

extract_protocol:
DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (D4014, Zymo Research)
ATAC-seq libraries were generated following the Omni-ATAC protocol. Libraries were barcoded and amplified with KAPA HiFi HotStart ReadyMix (KK2602, Roche). Library size distribution and concentration was evaluated using the Agilent 4200 TapeStation system and Qubit dsDNA HS Assay Kit (ThermoFisher Scientific), respectively.


title: TCR:eVAT Lean and eVAT Obese and Spleen Lean and Spleen Obese (exp3)

source_name: eVAT Lean #1 (Hash4), eVAT Lean #2 (Hash5), eVAT Obese #1 (Hash2), eVAT Obese #2 (Hash3), Spleen Lean #1 (Hash9), Spleen Lean #2 (Hash10), Spleen Obese #1 (Hash7), Spleen Obese #2 (Hash8)

value: Hash4-AAAGCATTCTTCACG, Hash5-CTTTGTCTTTGTGAG, Hash2-GGTCGAGAGCATTCA, Hash3-CTTGCCGCATGTCAT, Hash9-TGCCTATGAAACAAG, Hash10-CCGATTGTAACAGAC, Hash7-GAGTCTGCCAGTATC, Hash8-TATAGAACGCCAGGC


title: dOptix_library_2

city: New York

first: Felix

last: Simon

state: New York

address: 24 Waverly Place

department: Biology

institute: NYU

description: 10x genomics

data_processing:
Fastq files were generated using cell ranger cellranger/6.0.1 with default parameters
We mapped the reads to the D. melanogaster genome assembly BDGP6.88 using cellranger 6.0.1 with default parameters except the "cell_number" parameter that was set to 7000.
Building of the filtered and annotated seurat objects is detailed in the "Methods" section of the corresponding paper.
Assembly: BDGP6.88
Supplementary files format and content: Processed data files named "Library_filtered_feature_bc_matrix.zip" contain the "Filtered feature-barcode matrices MEX" cellranger count output for the corresponding library.
Supplementary files format and content: Processed data files named "Library_filtered_normalized.RDS" are the filtered and annotated seurat objects for the corresponding libraries.

organism: Drosophila melanogaster

source_name: Optic lobe

extract_protocol:
Whole brains were extracted in ice-cold Schneider's media. The brains were then transferred into DPBS, we used an epifluorescence microscope to remove brains with ectopic mOPC GFP expression, and placed the brains back in Schneider’s media. The brains were then incubated at 25˚C in Schneider’s media with 2mg/mL Collagenase and 2mg/mL Dispase, for 1hr 30min (adult brains) or for 30min (pupal brains), then washed 3 times with ice-cold Schneider’s media to stop the dissociation. Optic lobes were then separated from the central brain, transferred in ice-cold DPBS + 0.04% BSA, and washed twice with ice-cold DPBS + 0.04% BSA. For pupal brains, the separation between central brain and optic lobes can be seen as a difference in texture: the optic lobe forms a smoother and cohesive structure that can be removed using a fine tungsten needle. Optic lobes and 150μL of DPBS + 0.04% BSA were then transferred to a low-bind Eppendorf, and dissociated by pipetting vigorously 50 times, resting the cells for 1 minute on ice, and pipetting 50 times more. The cell suspension was then checked under a dissecting microscope, and we pipetted up to 50 more times if the size of remaining clumps was too significant. We did not try to dissociate small clumps since they are most likely neuropils, not soma, and indeed we empirically noticed a better quality of the data obtained after lowering pipetting repetitions. The suspension was then passed through a 20µm mini-PluriStrainer, and the filter was washed with 400μL of DPBS + 0.04% BSA which we also collected (pipetting from the opposite side may be necessary to collect the entire cell suspension).
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index )

value: Optic lobe

tag: group

value: dOptix


title: myofibroblast, WT, treated, rep5

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

data_processing:
Libraries were sequenced by illumine sequencer Novaseq of 150 bp pair-end reads.
Reads were mapped to mouse genome GRCm38 (mm10) v89 using STAR6 aligner and counts per gene were quantified by featureCounts7 with settings of pair-end (-p) and exon mapping (-t exon).
Preprocessing filtering removed genes not expressed in more than one sample.
Genes were considered detected if they have a count of at least 5 counts in at least 5 samples.
Assembly: mm10
Supplementary files format and content: tab seperated raw count file (combined all samples)

source_name: Primary renal myofibroblasts

extract_protocol:
Primary renal myofibroblasts were harvested and RNA was extracted with RNeasy mini kit (Qiagen) following the manufacturer’s instruction.
Libraries were generated with the poly-A selection method (mRNA Direct kit, Life Technologies) and sequenced with the NovaSeq 6000 S4 platform (23150 bp) at a target of 30 million reads per library.

value: Primary renal myofibroblasts

value: WT


title: vOptix_library_1

description: 10x genomics

tag: tissue

value: vOptix


title: GFP_LOW, replicate 3, 48hr, bulkATAC

tag: cell line

value: Raji


title: pxb_library

description: 10x genomics

value: pxb


title: myofibroblast, WT, treated, rep4

tag: cell type


title: GFP_LOW, replicate 3, 24hr, bulkATAC

tag: genotype


title: dOptix_library_1

description: 10x genomics


title: FBC:eVAT Lean and eVAT Obese and Spleen Lean and Spleen Obese (exp4)

description:
exp4_barcodes.tsv.gz
exp4_features.tsv.gz
exp4_matrix.mtx.gz


title: FBC:eVAT Lean and eVAT Obese and Spleen Lean and Spleen Obese (exp3)

description:
exp3_barcodes.tsv.gz
exp3_features.tsv.gz
exp3_matrix.mtx.gz


title: 4C-seq_Kcnk9_ES_BJ

value: ES cells


title: GEX:eVAT Lean and eVAT Obese and Spleen Lean and Spleen Obese (exp4)


title: GFP_LOW, replicate 2, 72hr, bulkATAC


title: myofibroblast, WT, treated, rep3


title: myofibroblast, WT, treated, rep2


title: GFP_LOW, replicate 2, 48hr, bulkATAC


title: zebrafish dEN dissected tissue

city: Wako

first: Yuki

last: Tanimoto

state: Saitama

address: 2-1 Hirosawa

department: CBS

country: Japan

institute: RIKEN

description: 10x Genomics

data_processing:
The obtained scRNAseq data of 3,381 cells were analyzed by Seurat.47 As a quality control, cells with more than 6% mitochondrial genes, less than 200 unique genes, and more than 17500 UMIs were removed. Barcodes with less than 500 UMIs had been already removed by cellranger count pipeline. The remaining 3,043 cells were then data normalized by LogNormalize method with scale.factor = 10000. For further calculation of UMAP and clustering, variable genes were determined with FindVariableFeatures function with selection.method = “vst”, and the top 2000 most highly variable genes were used for further clustering. The expression of each gene was shifted so that the mean expression across cells is 0, and scaled so that the variance across cells is 1 by ScaleData function. PCA was run on the scaled data and then UMAP and clustering were performed with the FindNeighbors function with the top 35 PCs, the FindClusters function with resolution = 0.5, and the RunUMAP function with the top 35 PCs. Dot plots and violin plots were generated by Seurat and cell types were determined by the expression of marker genes that define specific cell types.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: HTML output file obtained from Seurat analysis using R markdown

organism: Danio rerio

source_name: dorsal entopeduncular nucleus and its surrounding brain tissue

growth_protocol: regular laboratory cultivation condition

extract_protocol:
Dissection was performed on 6 individuals of TgBAC(npy:GAL4VP16);Tg(UAS:GFP) fish and 12 dissected tissue pieces from the left and right hemispheres were obtained in total. The dEN and its surrounding regions were carefully dissected with micro-scissors and fine forceps in ice-cold and oxygenized Neurobasal medium (ThermoFisher Scientific 21103049) supplemented with 1x B-27 (ThermoFisher Scientific 17504044) under a fluorescent dissection microscope, as shown in the Figure S5A. The dissected tissue was dissociated with the Papain Dissociation Kit (Worthington; LK003150) with 0.1% 2-mercaptoethanol for 15 minutes with gentle shaking at 28.5 degrees Celsius. Then, the cells were dissociated by gentle trituration 15 times with a glass Pasteur pipet coated with 2% BSA in PBS and spun at 300xg for 5 minutes. The cells were resuspended in papain inhibitor solution (Worthington) and incubated for 10 minutes with gentle shaking at 28.5 degrees Celsius. Then, the cells were further dissociated by gentle trituration 20 times with a glass Pasteur pipet attached with a regular 200-µl tip coated with 2% BSA in PBS. The dissociated cell suspension was then filtered with pluriStrainer Mini 40 µm (pluriSelect) coated with 2% BSA in PBS and spun at 300xg for 5 minutes. The resulting cell suspension was resuspended in 2% BSA in PBS, and then cell debris and dead cells were removed by FACS (FACSAria SORP, BD Biosciences) using Hoechst (to sort out cells from cell debris) and Propidium Iodide (to sort out living cells from dead cells). After FACS sorting, a small fraction of the cell suspension was used to estimate the total number of the cells and their viability using a dead cell stain Trypan Blue (elabscience). The obtained suspension contained 16,000 cells with 85.0% viability.
The resulting single-cell suspension was loaded on the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, PN-1000269), and the cDNA library was prepared according to the manufacturer’s instructions. The obtained cDNA library underwent Next generation sequencing by illumina Hiseq X (GENEWIZ) with 400,429,716 total reads and 85.9% of sequencing saturation. The obtained sequence was then analyzed by “Cell Ranger count” pipeline provided by 10x Genomics with default options. The reads were aligned to zebrafish reference transcriptome (ENSEMBL Zv11, release 99) and EGFP CDS, which were built by “Cell Ranger mkref” command based on zebrafish reference genome GRCz11 and annotation Ensembl 99. This resulted in 3,381 estimated number of cells with 4890 median unique molecular identifier (UMI) counts per cell.

value: Neurons/glia/blood cells from telencephalon


title: GEX:eVAT Lean and eVAT Obese and Spleen Lean and Spleen Obese (exp3)


title: myofibroblast, WT, untreated, rep5

value: control


title: GFP_LOW, replicate 1, 72hr, bulkATAC


title: myofibroblast, WT, untreated, rep4


title: GEX:eVAT Tregs 14wk LFD and eVAT Tregs 14/16wk LFD/LFD and eVAT Tregs 14/16wk LFD/HFD (exp2)

source_name: eVAT Tregs 14wk LFD #2 (Hash3), eVAT Tregs 14/16wk LFD/LFD #2 (Hash2), eVAT Tregs 14/16wk LFD/HFD #2 (Hash1)

value: eVAT

value: 14wk LFD or 14/16wk LFD/LFD or 14/16wk LFD/HFD


title: GFP_LOW, replicate 1, 48hr, bulkATAC


title: myofibroblast, WT, untreated, rep2


title: myofibroblast, WT, untreated, rep3


title: GFP_HIGH, replicate 3, 72hr, bulkATAC


title: RNA-seq_D12_JB_rep1

value: ES-derived neural precursor cells

value: JF1 x C57BL/6

value: In vitro corticogenesis Day 12


title: GFP_HIGH, replicate 3, 48hr, bulkATAC


title: GFP_LOW, replicate 2, 24hr, bulkATAC


title: GEX:eVAT Tregs 14wk LFD and eVAT Tregs 14/16wk LFD/LFD and eVAT Tregs 14/16wk LFD/HFD (exp1)

source_name: eVAT Tregs 14wk LFD #1 (Hash3), eVAT Tregs 14/16wk LFD/LFD #1 (Hash1), eVAT Tregs 14/16wk LFD/HFD #1 (Hash2)

value: CD45+ TCRb+ CD4+ Tregs

value: Male


title: myofibroblast, WT, treated, rep1


title: RNA-seq_D12_BJ_rep1

value: C57BL/6 x JF1


title: GFP_HIGH, replicate 3, 24hr, bulkATAC


title: myofibroblast, KO, treated, rep5

value: KO


title: RNA-seq_ES_JB_rep1


title: myofibroblast, KO, treated, rep4

value: Primary renal myofibroblasts


title: myofibroblast, KO, treated, rep3


title: vOptix_library_2

description: 10x genomics

value: Optic lobe


title: RNA-seq_ES_BJ_rep1


title: GFP_HIGH, replicate 2, 48hr, bulkATAC


title: myofibroblast, KO, treated, rep2


title: myofibroblast, KO, treated, rep1


title: GFP_HIGH, replicate 2, 72hr, bulkATAC


title: 4C-seq_Peg13_DMR_ES_JB


title: GEX:eVAT SVF 14wk LFD and eVAT SVF 14/16wk LFD/LFD and eVAT SVF 14/16wk LFD/HFD (exp2)

source_name: eVAT SVF 14wk LFD #2 (Hash3), eVAT SVF 14/16wk LFD/LFD #2 (Hash2), eVAT SVF 14/16wk LFD/HFD #2 (Hash1)

value: Live SVF


title: GEX:eVAT SVF 14wk LFD and eVAT SVF 14/16wk LFD/LFD and eVAT SVF 14/16wk LFD/HFD (exp1)

source_name: eVAT SVF 14wk LFD #1 (Hash3), eVAT SVF 14/16wk LFD/LFD #1 (Hash1), eVAT SVF 14/16wk LFD/HFD #1 (Hash2)


title: GFP_HIGH, replicate 2, 24hr, bulkATAC

value: Raji


title: myofibroblast, WT, untreated, rep1

value: WT


title: myofibroblast, KO, untreated, rep5


title: 4C-seq_Peg13_DMR_ES_BJ

value: ES cells


title: GFP_HIGH, replicate 1, 24hr, bulkATAC


title: GFP_HIGH, replicate 1, 48hr, bulkATAC


title: patient13_postACT_1

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

data_processing:
The scTCR-Seq reads were aligned to the GRCh38 reference genome (refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0) and quantified using cellranger vdj (10X Genomics, version 4.0.0).
Assembly: GRCh38
Supplementary files format and content: csv file ("all_contig_annotations.csv" output from Cellranger) containing the mapping of unique cells to TCR

source_name: melanoma

extract_protocol:
Resected tumors were chopped into 1-2 mm2 pieces and, along with post-infusion biopsies, cryopreserved in 90% human serum + 10% dimethyl sulfoxide (DMSO) and additional pieces were snap frozen for bulk RNA extraction. For single-cell experiments, both frozen and fresh material were used as starting material. PBMCs were isolated from blood collected in EDTA tubes and cryopreserved in 90% human serum + 10% DMSO. The day of the assay, pathofrozen pieces were thawed in RPMI + 10% FBS and chopped in small pieces using a scalpel. Tissue was dissociated in RPMI + 2% Gelatin (#G7041, Sigma-Aldrich) + 200 IU/mL Collagenase I (#17100-017, ThermoFisher Scientific) + 400 IU/mL Collagenase IV (#17104-019, ThermoFisher Scientific) + 5 IU/mL Deoxyribonuclease I (#D4527, Sigma-Aldrich) + 0.1% RNasin Plus RNase Inhibitor (#N2618, Promega) for 15-30min (depending of sample size and consistency) at 37°C and shaken at 160rpm. Digested cells were filtered using a 70 mm strainer and resuspended in PBS + 1% Gelatin + 0.1% RNasin. Cells were manually counted with hematocymeter then stained for viability with 50uM/mL of Calcein AM (#C3099, Thermo Fisher Scientific) and FcR blocked (#130-059-901, Miltenyi Biotec) for 15min at RT. After incubation and washing, cells were stained with CD45-APC (#304012, BioLegend) for 20min at 4°C. After washing, cells were resuspended in PBS + 0.04% BSA (Sigma-Aldrich) + 0.1% RNasin and DAPI staining (Invitrogen) was performed.
40’000 CD45+ cells and 40’000 total live cells were sorted on a MoFlo Astrios (Beckman Coulter) and collected in separated 0.2mL PCR tubes containing 10ml in PBS + 0.04% BSA + 0.1% RNasin. After sorting, cells were manually counted with hemocytometer and viability was assessed using Trypan blue exclusion. Ex vivo CD45 cells from tumor were resuspended at a density of 600-1200 cells/ml when possible with a viability of >90% and subjected to a 10x Chromium instrument for single-cell analysis. Single-cell RNA libraries were generated using the Chromium Next GEM Single Cell 5’ Library and Gel beads kit v1.1 for the CD45-sorted population or using the Chromium Next GEM Single Cell 3’ Library and Gel beads kit v3.1 for the live-sorted cells, according to the manufacturer’s instructions. For each sample, 15’000 cells were loaded into the Chromium machine when possible (i.e. the total of sorted cells if <15’000), encapsulated and barcoded following the manual (CG000388 for 3’ or CG000207 for 5’ technology). After encapsulation and reverse transcription, 14 PCR cycles were used to amplify cDNA. All library construction steps were performed according to the manufacturer's protocol. For the FACS sorting of post-ACT biopsies, depending of the percentage of CD45+ fraction in the sample, two sorting strategies were adopted. If the CD45+ fraction was inferior to 75% of total viable cells, 40’000 CD45+ and 40’000 CD45- viable cells were sorted in two separated tubes. If the CD45+ fraction was superior to 75% of total viable cells, 40’000 total viable cells were collected in one tube.  All cells were sorted on a MoFlo Astrios (Beckman Coulter) and collected in separated 0.2mL PCR tubes containing 10l in PBS + 0.04% BSA + 0.1% RNasin. After sort, cells were manually counted with hemacytometer and viability was assessed using Trypan blue exclusion. If CD45+ and CD45- were sorted separately, cells were mixed with a ratio of 70% CD45+ and 30% CD45-. All cells were resuspended at a density of 600-1200 cells/mL if possible with a viability >90% and subjected to a 10x Chromium instrument for single-cell analysis. Only the CD45+ compartment was analyzed in this study.

value: melanoma

tag: patient

value: post-ACT

tag: biopsy site


title: R1192C_MUT, replicate 4, bulkRNA

value: Smarca4 R1192C/+


title: R1192C_MUT, replicate 3, bulkRNA


title: patient10_postACT_1


title: myofibroblast, KO, untreated, rep1

tag: treatment

value: control


title: patient7_postACT_1

tag: time


title: myofibroblast, KO, untreated, rep2


title: myofibroblast, KO, untreated, rep3


title: S59

data_processing:
Sequencing reads were aligned and quantified to the mouse genome GRCm38 (mm10-3.0.0 provided by 10x Genomics) using 10x Genomics cellranger count (v3.1.0).
For each of the four samples, quality control and preprocessing were performed individually. Genes present in less than 50 cells and cells below the 10th and above the 90th percentile in terms of both the number of genes and number of counts were filtered out. Cells with percentage of mitochondrial content greater than 40% and haemoglobin gene accounting more than 1% of total counts were also filtered. In addition, cells above the 99th percentile in terms of percentage of total counts being stress genes (Hochane et al. 2019) were removed.
Assembly: mm10
Supplementary files format and content: tab seperated matrix files

source_name: kidney

extract_protocol:
Mouse kidneys was perfused, excised, minced, digested to obtain single cell suspension as described before. Cells were collected by centrifugation, subjected to live-death dye and sorted by flow cytometry using BD FACS ARIA system.
Isolated living single cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3′ Library, Gel Bead & Multiplex Kit, and Chip Kit V3, loading an estimated 7,000–12,000 cells per library/well, and following the manufacturer's instructions. Indexed libraries were sequenced using Illumina NovaSeq 6000 platform, where 150bp pair-end sequences were obtained.

value: kidney


title: R1192C_MUT, replicate 1, bulkRNA


title: patient8_postACT_1


title: R1192C_MUT, replicate 2, bulkRNA


title: S57


title: patient5_postACT_1


title: WT, replicate 4, bulkRNA


title: patient1_postACT_1


title: myofibroblast, KO, untreated, rep4


title: 4C-seq_Peg13_DMR_D12_BJ

value: ES-derived neural precursor cells


title: S42

value: wwp2 KO


title: GFP_HIGH, replicate 1, 72hr, bulkATAC

data_processing:
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read trimming, read alignment using bwa, filtering low-quality, unmapped and duplicated reads. BIGWIG files were generated using deeptools RPKM normalization.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: hg38
Supplementary files format and content: Tab-separated count matrix file and RPKM normalized bigwig files


title: patient13_preACT_2

value: pre-ACT


title: WT, replicate 3, bulkRNA


title: WT, replicate 2, bulkRNA


title: HET, replicate 4, 10X multiome scRNA

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting were done using the Cell Ranger ARC software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
Analyses were performed in R (version 4.2.1) using various R packages. FASTQ files were processed using cellranger-arc count (10x genomics). This pipeline aligns reads to the mm10 mouse reference genome, performs barcode error correction, PCR duplicate marking, peak calling, and ATAC and gene expression molecule counting to produce expression and fragment count matrices.  The gene expression matrices and ATAC fragments were loaded into R and processed with Signac (version 1.9.0, https://github.com/timoast/signac) and Seurat (version 4.3.0, https://github.com/satijalab/seurat) for downstream analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files and fragments files

molecule: nuclear RNA

source_name: Spleen

extract_protocol:
GC B cells were isolated from mice spleens at day 10 post-immunization using the Germinal Center B Cell (PNA) MicroBead Kit (Miltenyi Biotec,130-110-479). To improve the quality of single cell ATAC libraries, pre-enriched cells were stained with Zombie Green (BioLegend) and sorted by FACS. Cells were washed in PBS containing 0.04% BSA 2 times. Determine the cell concentration using a Countess II FL Automated Cell counter and viable cell number was counted by the trypan blue dye exclusion method, before proceeding to nuclei isolation. Pellet 100,000~200,000 cells at 300 rcf for 5 min at 4 °C, remove all supernatant and resuspend in lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA, 1 mM DTT and 1 U/µl RNase inhibitor). Incubate for 5 min on ice. After a total of 3 washes, nuclei were resuspended in diluted nuclei buffer (10x Genomics) and nuclei concentration was determined.
Proceed immediately to Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338). Briefly, 10,000 nuclei/sample were loaded on the Chromium Controller. The 10X libraries were then prepared following the manufacturer’s instruction (Next GEM Single Cell Multiome)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression

value: Spleen

tag: age

value: 8-10 weeks

value: Germinal Center B Cells


title: patient12_preACT_1


title: patient13_preACT_1


title: HET, replicate 4, 10X multiome scATAC

description: 10x Genomics