title: Transgenic C-IKKα mouse, 15C

description:
Back skin cells derived from the 6-month-old C15 C-IKKα transgenic mouse
C15

source_name: C-IKKα sample; 6-month-old 15C (FBV) mouse skin


title: Transgenic C-IKKα mouse, 14C

status: Public on Nov 14 2024

type: SRA

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

description:
Back skin cells derived from the 6-month-old C14 C-IKKα transgenic mouse
C14

library_source: transcriptomic

data_processing:
Reads were aligned to GRCm39 mouse genome with “Rbowtie2”
counts extracted with featureCounts function from “Rsubread” and gencode annotation release 27 (gencode.vM27.annotation.gtf)
Gene set enrichment analyses were conducted with GSEA (version 4.1.0) software 74, using the normalized count values.
Assembly: GRCm39
Supplementary files format and content: normalized counts

molecule: total RNA

organism: Mus musculus

source_name: C-IKKα sample; 6-month-old 14C (FBV) mouse skin

extract_protocol:
Total RNA from back skin derived from wild type or transgenic N-IKKα and C-IKKα  was extracted using TRIzol reagent (ThermoFisher) and purified with RNeasy MinElute Cleanup Kit (Qiagen).
cDNA library was constructed using Stranded mRNA Library Preparation Kit and sequenced in the Illumina Novaseq platform, using 150bp paired-end sequencing reads.

tag: tissue

value: Back skin

tag: genotype

value: C-IKK{alpha}

tag: cell type

value: Skin cells

tag: age

tag: strain background

value: FVB


title: Transgenic N-IKKα mouse, 12N

description:
Back skin cells derived from the 6-month-old N12 N-IKKα transgenic mouse
N12

source_name: N-IKKα sample; 6-month-old 12N (FBV) mouse skin

value: N-IKK{alpha}


title: Transgenic C-IKKα mouse, 13C

description:
Back skin cells derived from the 6-month-old C13 C-IKKα transgenic mouse
C13

source_name: C-IKKα sample; 6-month-old 13C (FBV) mouse skin


title: HD_21

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

data_processing:
CLC Genomics Workbench 23.0.5 (Qiagen)
Adapter sequences were trimmed and sequences with less than 15 pb or without adapter nor UMI (Unique Molecular Index) were discarded
A sequential alignment strategy was used to map sequences on several databases: reference GRCh38 human genome was used, miRBase v.22.1 was considered the first annotation model, and sequences were collected as mature miRNAs
Before normalization and differential expression (DE) analysis, data were filtered, considering small RNAs with a minimum number of reads count (mean read count>2.5/group). DE analysis was performed using Generalized Linear Model (GLM) and Trimmed Mean of M-values (TMM) normalized counts (CPM) were used as input data, considering significant Benjamini-Hochberg adjusted p-values ≤ 0.05
Assembly: GRCh38 human genome
Supplementary files format and content: excel file included raw counts for each sample
Supplementary files format and content: excel file included CPM for each sample; P (IIM) vs S (HD)
Supplementary files format and content: excel file included CPM for each sample; CAM vs NCAM

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from EVs samples using the miRNeasy Serum/Plasma Advanced kit (Qiagen, Germany),
library preparation of sncRNAs from EVs samples was obtained using QIAseq® miRNA Library kit (Qiagen, Germany),

value: Peripheral blood

value: Extracellular vesicles

value: healthy donor (HD)


title: CAM_5

value: CAM


title: HD_22


title: Transgenic N-IKKα mouse, 11N

description:
Back skin cells derived from the 6-month-old N11 N-IKKα transgenic mouse
N11

source_name: N-IKKα sample; 6-month-old 11N (FBV) mouse skin


title: HD_20


title: HD_19


title: Transgenic N-IKKα mouse, 10N

description:
Back skin cells derived from the 6-month-old N10 N-IKKα transgenic mouse
N10

source_name: N-IKKα sample; 6-month-old 10N (FBV) mouse skin


title: Transgenic N-IKKα mouse, 9N

description:
Back skin cells derived from the 6-month-old N9 N-IKKα transgenic mouse
N9

source_name: N-IKKα sample; 6-month-old 9N (FBV) mouse skin


title: CAM_4


title: Transgenic N-IKKα mouse, 8N

description:
Back skin cells derived from the 6-month-old N8 N-IKKα transgenic mouse
N8

source_name: N-IKKα sample; 6-month-old 8N (FBV) mouse skin


title: CAM_3


title: Wild type mouse, WT5

description:
Back skin cells derived from the 6-month-old WT5 wild type mouse
WT5

source_name: WT sample; 6-month-old WT5 (FBV) mouse skin

value: WT


title: IIM_15

value: inflammatory myopathies (IIM)


title: CAM_2


title: Wild type mouse, WT4

description:
Back skin cells derived from the 6-month-old WT4 wild type mouse
WT4

source_name: WT sample; 6-month-old WT4 (FBV) mouse skin


title: IIM_14


title: HD_18


title: Wild type mouse, WT2

description:
Back skin cells derived from the 6-month-old WT2 wild type mouse
WT2

source_name: WT sample; 6-month-old WT2 (FBV) mouse skin


title: HD_17


title: Wild type mouse, WT1

description:
Back skin cells derived from the 6-month-old WT1 wild type mouse
WT1

source_name: WT sample; 6-month-old WT1 (FBV) mouse skin


title: C

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description:
10x Genomics
S075_08_mmepiAT_C

library_source: transcriptomic single cell

data_processing:
CellRanger v6.1.2 used for demultiplexing + read mapping + barcode assignment + UMI counting
scDblFinder used for removing doublets
Seurat v4.1.0 used for quality control + normalization + sample integration + dimensionality reduction + cell clustering
SCpubr v1.0 used for data visualization
Assembly: mm10-2020A (10x Genomics)
Supplementary files format and content: Filtered feature-barcode count matrices from CellRanger

molecule: nuclear RNA

source_name: epididymal adipose tissue

extract_protocol:
Nuclei were isolated from snap frozen epiAT in ice cold Nuclei Extraction Buffer (Miltenyi, #130-128-024) supplemented with 0.2U/µl recombinant RNase Inhibitor (Takara, #2313) and 1x cOmpleteTM EDTA-free Protease Inhibitor (Roche, #5056489001) using the gentleMACSTM Octo Dissociator (Miltenyi, #130-096-427) using C-tubes (Miltenyi, #130-093-237). Nuclei were subsequently filtered through a 50µm cell strainer (Sysmex, #04-0042-2317) and washed two times in PBS-BSA (1% w/v) containing 0.2U/µl RNase inhibitor. For snRNAseq 5 mice were pooled per condition.
10 x Genomics Single Cell Gene Expression 3' v3.1

value: epididymal adipose tissue

tag: strain

tag: treatment

value: 18 weeks old, chow diet


title: IIM_12


title: HH

description:
10x Genomics
S075_05_mmepiAT_HH

value: 31 weeks old, high fat diet 25 weeks


title: Wild type mouse, WT3

description:
Back skin cells derived from the 6-month-old WT3 wild type mouse
WT3

source_name: WT sample; 6-month-old WT3 mouse skin


title: HD_16


title: HC

description:
10x Genomics
S019_04_mmepiAT_HC

value: 26 weeks old, 12 week HFD followed by 8 weeks chow diet


title: HD_15


title: IIM_13


title: Wild type mouse, WT6

description:
Back skin cells derived from the 6-month-old WT6 wild type mouse
WT6

source_name: WT sample; 6-month-old WT6 (FBV) mouse skin


title: CCH

description:
10x Genomics
S075_04_mmepiAT_CCH

value: 30 weeks, old 26 weeks chow diet then 4 weeks high fat diet


title: IIM_16


title: H

description:
10x Genomics
S075_07_mmepiAT_H

value: 18 weeks old, 12 weeks high fat diet


title: HHC

description:
10x Genomics
S019_03_mmepiAT_HHC

value: 39 weeks old, 25 week HFD followed by 8 weeks chow diet


title: HD_14


title: HD_11


title: HD_12


title: CC

description:
10x Genomics
S019_02_mmepiAT_CC

value: 26 weeks old, chow diet


title: IIM_10


title: TRAP_HHC_long_2

description:
TRAP-seq
S087_08

library_source: other

data_processing:
FastQC v0.11.9 used for quality control
TrimGalore v0.6.6 used for trimming
HISAT2 v2.2.1 used for aligning reads against mouse reference genome
subread v2.0.1 used for gene quantification
edgeR used for count normalization and differential expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited raw count matrix of all samples

molecule: other

source_name: Epididymal adipose tissue

extract_protocol:
Nuclei and ribosomes were isolated from snap frozen epiAT from AdipoERCre x NuTRAP mice in ice cold Nuclei Extraction Buffer (Miltenyi, #130-128-024) supplemented with 0.2U/µl recombinant RNase Inhibitor (Takara, #2313) and 1x cOmpleteTM EDTA-free Protease Inhibitor (Roche, #5056489001) and 10 mM sodium butyrate using the gentleMACSTM Octo Dissociator (Miltenyi, #130-096-427) using C-tubes (Miltenyi, #130-093-237). Nuclei suspension was filtered through a 50µm strainer and centrifuged at 4˚C, 500 x g for 5 minutes. The supernatant was transferred into a new tube and supplemented with 2mM DTT, 100µg/ml cycloheximide and 1mg/ml sodium heparin and kept on ice. Per sample 25µl GFP-Trap® Magnetic Agarose beads (ChromoTEK GmbH, #gtma-20) were washed 2ml in polysome lysis buffer (50mM TRIS-HCl pH 7.5, 100mM NaCl, 12mM MgCl2, 1% Igepal CA-630 (Sigma-Aldrich, #I8896), 1x protease inhibitor). The supernatant was mixed with the beads and incubated at 4˚C, on a rotator for 1-2 hours. Subsequently, tubes were put on a magnetic stand and the supernatant was removed. The beads were washed three times with polysome lysis buffer supplemented with 2mM DTT (Sigma-Aldrich, # D0632-10G), 100µg/ml cycloheximide (Sigma, # D0632-10G) and 1mg/ml sodium heparin (VWR, # ACRO411210010) and resuspended in 1ml Trizol (ThermoFisher, #15596). Trizol preserved samples were kept at -80˚C until RNA isolation. RNA was isolated by adding 200µl of chloroform (Sigma-Aldrich, #288306) to samples, followed by shaking and centrifugation at 4˚C, 12’000 x g for 15 minutes. The aqueous phase was transferred into a new tube and RNA was isolated and DNase treated with the RNA Clean and Concentrator-5 kit (Zymo Research, #R1016) following the manufacturer’s instructions.
RNA libraries were prepared by performing reverse transcription and template switching using Maxima H Minus reverse transcriptase (ThermoFisher, #EP0753), a template switch oligo and an oligodT primer to generate full length cDNA. cDNA was amplified using the Kapa Hotstart 2x ReadyMix (Roche Diagnostics, #7958935001). 1-3ng cDNA were then tagmentated using 1.3µg Tn5 and amplified using Kapa HiFi plus dNTPs (Roche Diagnostics, #07958846001) and the following PCR settings: 72˚C 5 minutes, 98˚C 30 seconds, 10 cycles of 98˚C for 10 seconds, 63˚C for 30 seconds, 72˚C for 1 minute, hold at 4˚C. Libraries were quantified using the KAPA library quantification kit (Roche Diagnostis, #079602), and sequenced at PE150 on a NovaSeq 6000 at Novogene.

treatment_protocol: control

value: Epididymal adipose tissue

value: adipocytes

value: AdipoERCre x NuTRAP on C576BL6 background

tag: replicate

value: biol rep 2

value: 39 weeks old, 25 weeks HFD, then 8 weeks chow diet


title: IIM_9

value: Peripheral blood

value: Extracellular vesicles


title: TRAP_CCC_long_2

description:
TRAP-seq
S087_07

value: 39 weeks old, chow diet


title: IIM_11

value: inflammatory myopathies (IIM)


title: Transgenic N-IKKα mouse, 7N

description:
Back skin cells derived from the 6-month-old N7 N-IKKα transgenic mouse
N7

source_name: N-IKKα sample; 6-month-old N7 (FBV) mouse skin

value: Back skin

value: N-IKK{alpha}

value: Skin cells

value: FVB


title: IIM_8


title: HCH

description:
10x Genomics
S075_03_mmepiAT_YoYo

value: epididymal adipose tissue

value: 30 weeks old, 12 weeks high fat diet, then 8 weeks chow diet, then 4 weeks high fat diet


title: TRAP_HH_long_2

description:
TRAP-seq
S087_06

value: 31 weeks old, 25 weeks HFD


title: HD_10

value: healthy donor (HD)


title: TRAP_CC_long_2

description:
TRAP-seq
S087_05

value: Epididymal adipose tissue

value: 31 weeks old, chow diet


title: HD_13


title: HD_9


title: TRAP_HHC_long_1

description:
TRAP-seq
S087_04

value: adipocytes

value: AdipoERCre x NuTRAP on C576BL6 background

value: biol rep 1


title: TRAP_CCC_long_1

description:
TRAP-seq
S087_03


title: IIM-7

value: Peripheral blood


title: CCC

description:
10x Genomics
S019_01_mmepiAT_CCC


title: HD_8

value: Extracellular vesicles


title: TRAP_CC_long_1

description:
TRAP-seq
S087_01


title: TRAP_HC_short_3

description:
TRAP-seq
S086_12

value: biol rep 3

value: 26 weeks old, 12 weeks HFD then 8 weeks chow diet


title: HD_7


title: TRAP_CC_short_3

description:
TRAP-seq
S086_11

value: 26 weeks old, chow diet


title: TRAP_HH_long_1

description:
TRAP-seq
S087_02


title: HD_6


title: TRAP_H_short_3

description:
TRAP-seq
S086_10

value: 18 weeks old, 12 weeks HFD


title: TRAP_C_short_3

description:
TRAP-seq
S086_09

value: 18 weeks old, chow diet


title: CAM_1

value: CAM


title: HD_5


title: p21002-s004_4x0339_wk8_PD1-ICOS_high

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.7.3a.(Dobin et al.)
Transcript abundance was estimated in STAR during alignment using the algorithm of htseq-count (Anders et al., 2015)
Assembly: panTro6
Supplementary files format and content: comma delimited text file containing gene symbol, raw read counts for each sample (in columns) for each annotated transcript (in rows).

organism: Pan troglodytes

source_name: CD4+ T cell

extract_protocol:
Cells were sorted at 4C by flow cytometry into tubes containing RPMI.  Following centrifugation, cells were homogenized in 350uL Buffer RLT containing 1% 2-Mercaptoethanol and extracted using the RNeasy Micro kit (Qiagen) with on-column DNase digestion.
RNA quality was assessed using a Fragment Analyzer (Agilent), and then 0.5 nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions.  Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation Kit (Illumina).  Libraries were validated by capillary electrophoresis on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding 20 million reads per sample.

value: CD4+ T cell

tag: population

value: PD-1/ICOS high

tag: time


title: IIM_4

value: inflammatory myopathies (IIM)


title: TRAP_HC_short_2

description:
TRAP-seq
S086_08

value: biol rep 2


title: TRAP_CC_short_2

description:
TRAP-seq
S086_07

value: Epididymal adipose tissue


title: IIM_3


title: p21002-s013_4x0312_wk8_PD1-ICOS_high


title: TRAP_H_short_2

description:
TRAP-seq
S086_06


title: HD_4

value: healthy donor (HD)


title: HD_3


title: TRAP_C_short_2

description:
TRAP-seq
S086_05

value: adipocytes


title: TRAP_HC_short_1

description:
TRAP-seq
S086_04

value: AdipoERCre x NuTRAP on C576BL6 background


title: IIM_6


title: IIM_2


title: TRAP_CC_short_1

description:
TRAP-seq
S086_03

value: biol rep 1


title: IIM_5

value: Peripheral blood


title: TRAP_H_short_1

description:
TRAP-seq
S086_02


title: HD_1

value: Extracellular vesicles


title: IIM_1


title: TRAP_C_short_1

description:
TRAP-seq
S086_01


title: HC_short_H3K27me3_3_AdipoERCre

library_source: genomic

data_processing:
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
Bowtie2 v2.4.4 used for read mapping
samtools v1.13 used for sorting bam files
bedtools v2.30 used for converting sorted bam files into bedgraph files
SEACR v1.3 used for calling peaks
Assembly: mm10
Supplementary files format and content: tab delimited called peak regions for each sample
Library strategy: Cut&Tag

molecule: genomic DNA

source_name: Epididymal Adipose Tissue

extract_protocol:
Nuclei and ribosomes were isolated from snap frozen epiAT from AdipoERCre x NuTRAP mice in ice cold Nuclei Extraction Buffer (Miltenyi, #130-128-024) supplemented with 0.2U/µl recombinant RNase Inhibitor (Takara, #2313) and 1x cOmpleteTM EDTA-free Protease Inhibitor (Roche, #5056489001) and 10 mM sodium butyrate using the gentleMACSTM Octo Dissociator (Miltenyi, #130-096-427) using C-tubes (Miltenyi, #130-093-237). Cut and Tag was performed as previously described  by Henikoff with minor adjustments .. All buffers were supplemented with 1 x cOmplete EDTA-free Protease inhibitor and 10mM sodium butyrate. Briefly, nuclei bound to beads were aliquoted into 96-well LoBind plates (Eppendorf, #0030129547) and incubated with primary antibodies – anti-H3K4me3 (abcam, #ab8580), anti-H3K27me3 (Cell Signaling Technology, #C36B11), anti-H3K27ac (abcam, #ab4729), anti-H3K4me1 (abcam, #ab8895) –  overnight at 4˚C.With the plate on a magnet the primary antibody solution was removed, the beads were resuspended in secondary antibody solution (guinea pig anti-rabbit IgG (antibodies-online gmbh, #ABIN101961)) and incubated at room temperature. pA-Tn5 was bound to antibodies, transposition performed at 37 ˚C and stopped using TAPS-Wash solution. Nuclei were lysed and pA-Tn5 decrosslinked using SDS-release solution. PCR was performed using Kapa HiFi plus dNTPs (Roche Diagnostics, #07958846001) with the following PCR settings: 72˚C 5 minutes, 98˚C 30 seconds, 15 cycles of 98˚C 10 seconds, 63˚C 30 seconds, 72˚C final extension for 1 minute, hold at 4˚C.
PCR was performed using Kapa HiFi plus dNTPs (Roche Diagnostics, #07958846001) with the following PCR settings: 72˚C 5 minutes, 98˚C 30 seconds, 15 cycles of 98˚C 10 seconds, 63˚C 30 seconds, 72˚C final extension for 1 minute, hold at 4˚C.

value: Epididymal Adipose Tissue

value: Adipocytes

tag: histone mark

value: biol rep 3


title: spleen, PDAC_BF, scRNAseq

city: Omaha

first: Michael

middle: A

last: Hollingsworth

state: NE

address: BCC 8.12.384, 601 S Saddle Creek Road

department: Eppley Cancer Institute

institute: University of Nebraska Med Center

description: 10x Genomics

data_processing:
Transcript reads were aligned to the GRCh38 Human Genome reference by the Cell Ranger 3.0.0 pipeline (10x Genomics, Inc.) to generate matrix files containing cell barcodes, UMIs (unique molecular identifiers), and transcript counts.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen PDAC

extract_protocol:
Spleens were cut and stomached in the Stomacher 80 Biomaster. After red blood cell lysis, dead cells were removed using Dead Cell Removal MicroBeads (Miltenyi; Catalog-No.: 130-090-101).
Splenocytes were given to the UNMC Genomics Core Facility, which then prepared the scRNA-seq libraries using 10x Genomics' Chromium Single Cell Platform 3' (Version 3), following standard protocol.

value: Spleen PDAC

value: Folfirinox


title: HD_2


title: spleen, PDAC_62, scRNAseq

description: 10x Genomics

value: Untreated


title: spleen, PDAC_64, scRNAseq

description: 10x Genomics


title: spleen, PDAC_34, scRNAseq

description: 10x Genomics

value: Folfiri + Radiation


title: CC_short_H3K27me3_2_AdipoERCre

value: 26 weeks old, chow diet


title: HC_short_H3K27me3_2_AdipoERCre

value: 26 weeks old, 12 weeks HFD then 8 weeks chow diet


title: spleen, normal_30, scRNAseq

description: 10x Genomics

source_name: Spleen normal

value: Spleen normal


title: spleen, normal_23, scRNAseq

description: 10x Genomics


title: H_short_H3K27me3_2_AdipoERCre

value: biol rep 2

value: 18 weeks old, 12 weeks HFD


title: C_short_H3K27me3_2_AdipoERCre

value: 18 weeks old, chow diet


title: HC_short_H3K27me3_1_AdipoERCre

value: AdipoERCre x NuTRAP on C576BL6 background


title: CC_short_H3K27me3_1_AdipoERCre

value: biol rep 1


title: Multi-Organ, Array-seq

city: Chicago

first: Denis

last: Cipurko

state: IL

address: 900 E 57th St

department: Biological Sciences Division

institute: University of Chicago

data_processing:
Raw data processing: Fastq files from Array-seq and Visium sequencing experiments were generated using BaseSpace DRAGEN Analysis v1.3.0. To generate spatial count matrices, fastq files were processed using STARsolo from the STAR package version 2.7.10a with the mm10 mouse or CRCh38 human reference genome.  Array-seq data alignment and filtering: A custom python script was used to join STARsolo output count matrices and spot coordinates and generate a png image of points matching the x, y positions of each barcoded spot, colored based on UMI counts. The digitally generated Array-seq spot image is manually aligned with the H&E image of the same section using Illustrator. A custom python script is used to detect tissue in the H&E image and filter Array-seq data spots not under tissue.  VIsium data alignment: Visium datasets were filtered for spots under tissue and aligned to H&E images by joining the tissue positions list csv, generated by the Spaceranger v1.2.0 software to the AnnData object generated from the STARSolo count matrix.  Clustering and differential expression: For spatial gene expression analysis using Scanpy, resulting count matrices were further filtered to keep (1) genes with at least 20 UMIs across all spots, and (2) spots with more than 120 UMIs in total. For clustering, data was normalized, log10 transformed, and clustered using principal component analysis (PCA), k-nearest neighbors (k-NN) identification, and the Leiden clustering algorithm. For differential expression analysis, we used the tl.rank_genes_groups() function in Scanpy. To map tissue subregions to spatial cluster obtained with the Leiden algorithm, we used the top 15 differentially expressed genes from each cluster for manual annotation. For plotting, spatial count or cluster identity were overlaid on the greyscale H&E image using the Seaborn package.
Assembly: mm10 mouse or CRCh38 human reference genome
Supplementary files format and content: Raw count matrix data from STARSolo: Barcodes.tsv.gz, Features.tsv.gz, and matrix.mtx.gz
Supplementary files format and content: H5ad files contain raw count matricies with spot annotation of tissue subregion and scaled x,y coordinates.
Supplementary files format and content: Png files of each tissue H&E section. Spot coordinates align to pixel coordinates of corresponding H&E image files.
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: Multiple Organ Types (Brain, Kidney, Liver)

extract_protocol:
10 µm fresh-frozen, OCT-embedded tissue sections on Array-seq slides were thawed at 37°C for 1 minute and fixed for 30-45 minutes at -20°C in 100% methanol. Following fixation, slides were dried for 1 minute at room temperature, and incubated with 2 U/µL Ribolock in 5X SSC for 5 minutes at room temperature. The SSC buffer was removed from the slide surface, sections were stained for 3 minutes at room temperature with hematoxylin, washed in nuclease-free water, and stained for 1 minute at room temperature with eosin diluted 1:10 in 0.45 M Tris-Acetic acid buffer, pH = 6.0. The slide was washed in nuclease-free water and kept at room temperature until dry and imaged at 20X magnification using an Olympus VS2000 slide scanner. Tissue sections were then permeabilized with 0.1% pepsin in 0.1 M HCl at 37°C for 15-20 minutes. After permeabilization, sections were washed once with 0.1X saline-sodium citrate (SSC) buffer. Tissue sections then underwent reverse transcription, tissue removal, exonuclease I treatment. cDNAs were eluted from the array by incubating for 10 minutes at room temperature in 0.1 M KOH and neutralized by adding 0.2X volume of 1M Tris-HCl.
cDNAs were purified using a DNA Clean & Concentrator-5 kit and amplified using single-primer PCR using the KAPA HiFi HotStart ReadyMix kit. Amplified cDNAs were cleaned up using magnetic SPRISelect beads. 100 ng of amplified cDNA was tagmented using Tagment DNA TDE1 Enzyme and buffer for 5 min at 55°C and amplified by PCR using the Illumina Read1 primer and Illumina Read2-i7 reverse primers. Libraries were cleaned up using SPRISelect beads followed by gel purification using 2% E-Gel EX Agarose Gels and MinElute columns and quantified with the Qubit dsDNA High Sensitivity Assay Kit. Resulting libraries were sequenced on Illumina sequencing platforms.

value: 6 weeks

tag: st method

value: Array-seq

tag: Sex

value: Female


title: C_short_H3K27me3_1_AdipoERCre

value: Epididymal Adipose Tissue

value: Adipocytes


title: H_short_H3K27me3_1_AdipoERCre


title: CC_short_H3K27me3_3_AdipoERCre

value: biol rep 3


title: Kidney, Visium, Rep. 4

source_name: Kidney

value: Kidney

value: Visium


title: Kidney, Visium, Rep. 3


title: C_short_H3K27me3_3_AdipoERCre


title: H_short_H3K27ac_3_AdipoERCre


title: 3T3-L1 cells, shRNA #2, Day0, bio rep 2

city: Cleveland

first: Xuan

last: Xu

state: OH

address: 2109 Adelbert Rd

institute: Case Western Reserve University

data_processing:
Remove reads containing adapters.
Remove reads containing N > 10% (N represents the base cannot be determined).
Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Reads were aligned to the mouse genome (Ensembl m38.102) using TopHat version 2.1.0, SamTools version 1.3.1, and Bowtie2 version 2.2.6
Gene expression count tables were generated using HTSeq version 0.6.1
Assembly: Ensembl m38.102
Supplementary files format and content: comma-separated values text file includes normalized counts for each sample

growth_protocol: 3T3-L1 preadipocyte were maintained in DMEM supplemented with 10% FBS snd antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was collected using QIAshredder and RNeasy mini kit (Qiagen)
RNA libraries were prepared using Illumina TruSeq RNA Library Prep Kit following manufacture's protocol

treatment_protocol: Adipogenic differentiation was induced at day 0 (2 days post confluence) by adding the induction medium, which is the complete culture medium supplemented with the DMI cocktail (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine, and 167 nM insulin). At day 3, the induction medium was removed and the maintenance medium (complete culture medium supplemented with 167 nM insulin) was added. At day 7, the maintenance medium was removed, and complete culture medium was added. The cells were harvested for RNA extraction at day 11.

tag: cell line

value: preadipocyte

value: Zbtb9 knockdown

value: adipogenic differentiation


title: Kidney, Visium, Rep. 1


title: Kidney, Visium, Rep. 2


title: 3D Kidney, Array-seq


title: CC_short_H3K27ac_2_AdipoERCre

value: 26 weeks old, chow diet


title: HC_short_H3K27ac_2_AdipoERCre

value: biol rep 2

value: 26 weeks old, 12 weeks HFD then 8 weeks chow diet


title: Kidney, Array-seq, Rep. 4


title: Kidney, Array-seq, Rep. 1


title: C_short_H3K27ac_2_AdipoERCre

value: 18 weeks old, chow diet


title: HC_short_H3K27ac_1_AdipoERCre

value: AdipoERCre x NuTRAP on C576BL6 background


title: spleen, normal_8, scRNAseq

description: 10x Genomics

value: Spleen normal


title: CC_short_H3K27ac_1_AdipoERCre

value: biol rep 1


title: lib95640

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base call quality-trimming step was applied to remove low-confidence base calls from the ends of read using trimmomatic v0.39 (LEADING:3 SLIDINGWINDOW:4:20 MINLEN:8)
Trimmed sequence read were mapped to GRCm38.91 using star (v2.7.11a)
Duplicates were removed from aligned reads using Picard (v3.1.0) and samtools (v1.16)
Gene counts were generated using htseq-count v2.0.2
Assembly: GRCm38.91
Supplementary files format and content: tab-delimited text file with raw gene counts for each sample

source_name: Skin

extract_protocol: Total RNA was extracted from skin from the UVB-treated site (+UVB) and a non-treated control site (-UVB) and processed for bulk RNA sequencing.

treatment_protocol: Foxp3-WT and Foxp3-DE2 mice were treated with 6 doses of UVB light (100mJ/cm2) on a shaved patch of skin (3cm x 2cm) on the back flank of each mouse.

value: Skin

value: 6x200mj/cm2 UVB


title: lib95639


title: H_short_H3K27ac_1_AdipoERCre

value: Epididymal Adipose Tissue

value: 18 weeks old, 12 weeks HFD


title: Mouse Main Olfactory Bulb, Array-seq

source_name: Main Olfactory Bulb

value: Main Olfactory Bulb

value: 6 weeks

value: Array-seq

value: Female


title: H_short_H3K27ac_2_AdipoERCre

value: Adipocytes


title: C_short_H3K27ac_1_AdipoERCre


title: upf1_CHX_T_2

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Reads were trimmed using Trim Galore
Reads were mapped on the S. cerevisiae reference genome (R64-2-1, including the 2-micron plasmid) and ERCC spike-in RNA sequences, using HISAT2 V2.2.0, with default parameters and maximum intron size of 5000.
Gene count was obtained with featureCounts v2.0.0.
Gene count was normalized using estimatesizefactorsformatrix() function from DESeq2 package (R software), using snoRNA counts.
Normalized densities were computed for each sample as : normalized gene count / gene length
Assembly: R64-2-1
Supplementary files format and content: tab delimited file, containing normalized tag/nt for each sample

organism: Saccharomyces cerevisiae

growth_protocol: WT and upf1-delta yeast cells were grown to mid-log phase (OD600 0.5) at 30°C in YPD medium.

extract_protocol:
Total RNA was extracted using standard hot phenol procedure. Extracted RNA was ethanol-precipitated, resuspended in nuclease-free H2O (Ambion) and quantified using a NanoDrop 2000c spectrophotometer and/or a Qubit fluorometer with the Qubit RNA HS Assay kit (Life Technologies).
For each sample, 1.5 µg of total RNA was mixed with 3 µl of diluted ERCC RNA spike-in mix and then digested for 1h at 30°C with 1 unit of Terminator 5´-Phosphate-Dependent Exonuclease (Epicentre) in 1X Reaction Buffer A containing 10 units of SUPERase-In RNase inhibitor (Invitrogen). After phenol/chloroform extraction, Terminator-digested RNA was precipitated with ethanol, and then resuspended in nuclease-free H2O. Libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) and the IDT for Illumina – TruSeq RNA UD indexes (Illumina).

treatment_protocol: Cells were treated for 15 minutes with cycloheximide (100 μg/ml, final concentration) or with an equal volume of DMSO.

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 upf1*::kanMX4

value: CHX


title: C_short_H3K27ac_3_AdipoERCre

value: biol rep 3


title: HC_short_H3K27ac_3_AdipoERCre

value: 26 weeks old, 12 weeks HFD then 8 weeks chow diet


title: lib95638


title: upf1_CHX_T_1


title: HC_short_H3K4me3_3_AdipoERCre


title: CC_short_H3K4me3_3_AdipoERCre

value: 26 weeks old, chow diet


title: H_short_H3K4me3_3_AdipoERCre

value: AdipoERCre x NuTRAP on C576BL6 background


title: upf1_DMSO_T_2

value: DMSO


title: Kidney, Array-seq, Rep. 2

value: Kidney


title: Kidney, Array-seq, Rep. 3


title: C_short_H3K4me3_3_AdipoERCre

value: 18 weeks old, chow diet


title: upf1_DMSO_T_1


title: CC_short_H3K4me3_2_AdipoERCre

value: biol rep 2


title: lib95634

value: Skin

value: 6x200mj/cm2 UVB


title: H_short_H3K4me3_2_AdipoERCre

value: Epididymal Adipose Tissue

value: 18 weeks old, 12 weeks HFD


title: WT_CHX_T_2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: HC_short_H3K4me3_2_AdipoERCre


title: HC_short_H3K4me3_1_AdipoERCre

value: biol rep 1


title: WT_CHX_T_1


title: lib95629

value: Untreated


title: H_short_H3K4me3_1_AdipoERCre

value: Adipocytes


title: WT_DMSO_T_2


title: C_short_H3K4me3_1_AdipoERCre


title: CC_short_H3K4me3_1_AdipoERCre


title: lib95628


title: HC_short_H3K4me1_3_AdipoERCre


title: CC_short_H3K4me1_3_AdipoERCre


title: lib95635


title: WT_DMSO_T_1


title: lib95627


title: U2OS Cells_Unstressed

city: Baltimore

first: Emmanouil

last: Maragkakis

state: MD

address: 251 Bayview Blvd, 10B133 Baltimore

department: Laboratory of Genetics and Genomics (LGG)

institute: National Institute on aging

data_processing:
Basecalled using Guppy (v3.4.5)
5’ adaptors were identified and removed using Cutadapt (v2.8)
Reads were first aligned against ribosomal sequences obtained from SILVA. Non-ribosomal reads were subsequently mapped against the human genome hg38 using minimap2 (version 2.17)
Reads were also aligned against the human transcriptome.
The poly(A) tail lengths were extracted from sequenced reads using the nanopolish polya package, with quality control scores as “PASS” selectively used in our analysis.
Assembly: hg38 for homo sapiens and  mm10 for mouse.
Supplementary files format and content: Tab-delimited text files include transcript id based raw counts and respective average trasncript length values for each Sample
Supplementary files format and content: Counts and lengths for each trasncript were calculated.

source_name: U2OS Cells

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA from HeLa cells was isolated using Trizol reaget (Invitrogen, Cat# 15596-018) following the manufacturer’s protocl. 75 µg of total RNA was used to isolate poly(A) mRNAs. 500-1000 ng of poly(A) mRNA was used for library preparation
RNA libraries for dRNA-Seq were prepared using direct RNA sequencing kit (Oxford Nanopore Technologies, SQK-RNA002)  following manufacturer's protocols.
Long read direct RNA-seq using Oxford Nanopore Technology

treatment_protocol: For arsenite treatment, 80-85% confluent HeLa cells were treated with 500 µM of arsenite (Sigma) whereas for combined arsenite and cycloheximide treatment, cells were treated with 500 µM of HeLa cells and 25 µg/ml of cycloheximide for 1 hour. Similarly for combined arsenite and ISRIB treatment, cells were treated with 500 µM of arsenite and 200 nM of ISRIB for 1 hour.

value: U2OS Cells

value: WT

value: Unstressed


title: lib95633


title: C_short_H3K4me1_3_AdipoERCre

value: biol rep 3


title: H_short_H3K4me1_3_AdipoERCre

value: AdipoERCre x NuTRAP on C576BL6 background


title: HC_short_H3K4me1_2_AdipoERCre

value: 26 weeks old, 12 weeks HFD then 8 weeks chow diet


title: lib95626


title: U2OS Cells_Arsenite

value: Arsenite


title: CC_short_H3K4me1_2_AdipoERCre

value: 26 weeks old, chow diet


title: lib95630


title: U2OS Cells_G3BP-mutated Unstressed

value: G3BP1 mutant


title: C_short_H3K4me1_2_AdipoERCre

value: biol rep 2

value: 18 weeks old, chow diet


title: lib95625

value: Skin


title: U2OS Cells_G3BP-mutated + Arsenite


title: C_short_H3K4me3_2_AdipoERCre

value: Epididymal Adipose Tissue


title: CC_short_H3K4me1_1_AdipoERCre


title: CC4:4-1

city: Beijing

first: Xiaobin

last: Luo

address: Tsinghua Garden, Haidian District

country: China

institute: Tsinghua University

description:
NovaSeq X Plus platform (PE150) with the NovaSeq Reagent Kit
L1EIC0602172-EXP44_1

data_processing:
In terms of DNA, the aligned reads for each sample were then reconstructed using a reference-based method implemented by StringTie. To ascertain differentially expressed genes (DEGs) between two samples, transcript levels were evaluated using the transcripts per million (TPM) technique, and RSEM was employed to estimate gene abundances. Differential expression analysis was conducted using DESeq2, where DEGs demonstrating a | log2 fold change (FC) | ≥ 1 and a false discovery rate (FDR) < 0.05 (DESeq2) or FDR < 0.001 (DEGseq) were identified as significantly differentially expressed. Additionally, functional enrichment analyses such as GO and KEGG pathway assessments were conducted to determine significant enrichment of DEGs in GO terms and metabolic pathways, with a Bonferroni-corrected P-value < 0.05 against the entire transcriptome background. These analyses were performed using Goatools for GO and a Python script for KEGG pathway analysis.
Raw paired-end DNA reads were initially processed for trimming and quality control using the FAST tool with its default settings. Subsequently, the purified reads were individually mapped to the reference genome in orientation mode using HISAT2 software.
Assembly: not provided
Supplementary files format and content: raw count data of all samples have been provided on gene-exp.csv excel data

organism: Rattus norvegicus

source_name: sciatic nerve tissue

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Qiagen) according to the manufacturer’s instructions.
RNA quality was determined using the 5300 Bioanalyser (Agilent) and quantified with the ND-2000 (NanoDrop Technologies). Only RNA samples meeting specific criteria (OD260/280 = 1.8 ~ 2.2, OD260/230 ≥ 2.0, RQN ≥ 7.0, 28S: 18S ≥ 1.0, > 1μg) were used to construct the sequencing library. RNA purification, reverse transcription, library creation, and sequencing were conducted by Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China).
The mRNA-seq transcriptome library was generated according to the Illumina® Stranded mRNA Prep, Ligation protocol (San Diego, USA) using 1 μg of total RNA. Initially, messenger RNA was isolated using the polyA selection method with oligo (dT) beads and subsequently fragmented using a fragmentation buffer. Following this, double-stranded cDNA was produced using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, USA) with random hexamer primers.
The resulting cDNA underwent end-repair, phosphorylation, and adapter ligation according to the library preparation protocol. cDNA target fragments of 300 bp were size-selected on 2% Low Range Ultra Agarose and amplified by PCR using Phusion DNA polymerase (NEB) for 15 cycles.
After post-quantification using Qubit 4.0, the sequencing libraries were sequenced on either a NovaSeq X Plus platform (PE150) with the NovaSeq Reagent Kit or a DNBSEQ-T7 platform (PE150) with the DNBSEQ-T7RS Reagent Kit (FCL PE150) version 3.0.

value: sciatic nerve tissue


title: H_short_H3K4me1_1_AdipoERCre

value: biol rep 1

value: 18 weeks old, 12 weeks HFD


title: Hela Cells_Dominant -ve NOT8* Unstressed

source_name: Hela Cells

value: Hela Cells


title: VP4:2_2

description:
NovaSeq X Plus platform (PE150) with the NovaSeq Reagent Kit
L1EIC0602170-VP42_2


title: HHC_long_H3K27me3_3_AdipoERCre

value: Adipocytes

value: 39 weeks old, 25 weeks HFD, then 8 weeks chow diet


title: Hela Cells_Dominant -ve NOT8* + Arsenite

value: WT


title: CCC_long_H3K27me3_3_AdipoERCre

value: biol rep 3

value: 39 weeks old, chow diet


title: VP4:2_1

description:
NovaSeq X Plus platform (PE150) with the NovaSeq Reagent Kit
L1EIC0602169-VP42_1


title: Hela Cells_Unstressed (Control)(GFP)

value: Unstressed (Control)(GFP)


title: HH_long_H3K27me3_3_AdipoERCre

value: AdipoERCre x NuTRAP on C576BL6 background

value: 31 weeks old, 25 weeks HFD


title: H_short_H3K4me1_2_AdipoERCre


title: HH_long_H3K27me3_2_AdipoERCre


title: HC_short_H3K4me1_1_AdipoERCre

value: 26 weeks old, 12 weeks HFD then 8 weeks chow diet


title: CC4:4-2

description:
NovaSeq X Plus platform (PE150) with the NovaSeq Reagent Kit
L1EIC0602173-EXP44_2


title: Hela Cells_Dominant -ve DCP2* Unstressed

value: Unstressed


title: Control 2

description:
NovaSeq X Plus platform (PE150) with the NovaSeq Reagent Kit
L1EIC0602164-CON2

value: Control


title: CC_long_H3K27me3_2_AdipoERCre

value: biol rep 2

value: 31 weeks old, chow diet


title: Control 1

description:
NovaSeq X Plus platform (PE150) with the NovaSeq Reagent Kit
L1EIC0602163-CON1

value: sciatic nerve tissue


title: Hela Cells_Arsenite (GFP)

value: Arsenite (GFP)


title: CCC_long_H3K27me3_1_AdipoERCre

value: Epididymal Adipose Tissue

value: biol rep 1


title: Hela Cells_Dominant -ve DCP2* + Arsenite

value: Hela Cells

value: Arsenite


title: HHC_long_H3K27ac_3_AdipoERCre

value: Adipocytes

value: 39 weeks old, 25 weeks HFD, then 8 weeks chow diet


title: HeLa cells, Arsenite, XRN1 siRNA, 60 min, rep 2

data_processing:
Basecalled using Guppy (v3.4.5)
5’ adaptors were identified and removed using Cutadapt (v2.8)
Reads were first aligned against ribosomal sequences obtained from SILVA. Non-ribosomal reads were subsequently mapped against the human genome hg38 using minimap2 (version 2.17)
Reads were also aligned against the human transcriptome.
The poly(A) tail lengths were extracted from sequenced reads using the nanopolish polya package, with quality control scores as “PASS” selectively used in our analysis.
Assembly: hg38
Supplementary files format and content: *counts_length.tab: Tab-delimited text files include transcript id based raw counts and respective average trasncript length values for each Sample
Supplementary files format and content: *polyA.tab: PolyA length
Supplementary files format and content: DESeq2 differential gene expression (Arsenite-Control)

source_name: HeLa cell line

extract_protocol:
Total RNA from HeLa cells was isolated using Trizol reaget (Invitrogen, Cat# 15596-018) following the manufacturer’s protocl. 75 µg of total RNA was used to isolate poly(A) mRNAs. 500-1000 ng of poly(A) mRNA was used for library preparation
RNA libraries for dRNA-Seq were prepared using direct RNA sequencing kit (Oxford Nanopore Technologies, SQK-RNA002)  following manufacturer's protocols.

treatment_protocol:
For arsenite treatment, 80-85% confluent HeLa cells were treated with 500 µM of arsenite (Sigma) whereas for combined arsenite and cycloheximide treatment, cells were treated with 500 µM of HeLa cells and 25 µg/ml of cycloheximide for 1 hour. Similarly for combined arsenite and ISRIB treatment, cells were treated with 500 µM of arsenite and 200 nM of ISRIB for 1 hour.
For siRNA treatment, HeLa cells were transfected with 20 nM of siRNA specific to XRN1 using Neon Transfection system 100 µl kit (ThermoFisher, MPK100) for 72 hours.

value: HeLa cell line

value: WT

value: Arsenite, XRN1 siRNA

tag: time (arsenite_treatment)

value: 60 minute

tag: kit

tag: flow-cell


title: Ischemic_25min_Insulin_5

city: Rochester

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

institute: Mayo Clinic

description:
ischemia for 25 mins with insulin
IS_25ins_5

data_processing:
Original image data file from high-throughput sequencing platforms is transformed to sequenced reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) formatfiles, which contain sequences of reads and corresponding base quality.
Reads with adapter contamination were removed. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Alignments were performed with HISAT2 v2.05. Novel transcripts were predicted using StringTie v1.3.3b.
FeatureCounts v1.5.0-p3 was used to obtain raw read counts and normalized FPKM values.
Assembly: Rattus norvegicus v6.0, Ensembl v102
Supplementary files format and content: comma-separated csv file containing raw counts for each sample
Supplementary files format and content: comma-separated csv file containing fpkm values for each sample

source_name: Right atrial tissue

extract_protocol:
Traditional phenol/chloroform-based extraction was performed for the RNA extraction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, thefirst strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis usingeither dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification,and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzymedigestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distributiondetection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective libraryconcentration and data amount.

tag: tissue

value: Right atrial tissue

value: Pretreatment of insulin for 30 mins and tissue perfusion was turned off to micmick global heart ischemia, then tissue was reperfused for 30 mins


title: HHC_long_H3K27me3_2_AdipoERCre

tag: genotype

value: AdipoERCre x NuTRAP on C576BL6 background


title: CC_long_H3K27me3_1_AdipoERCre

tag: cell type


title: CCC_long_H3K27ac_3_AdipoERCre

value: biol rep 3

value: 39 weeks old, chow diet


title: HHC_long_H3K27me3_1_AdipoERCre


title: HH_long_H3K27ac_3_AdipoERCre

value: 31 weeks old, 25 weeks HFD


title: HHC_long_H3K27ac_2_AdipoERCre

value: biol rep 2


title: HH_long_H3K27ac_2_AdipoERCre

value: Epididymal Adipose Tissue


title: HeLa cells, mock siRNA, rep 2

value: mock siRNA

value: 0 minute


title: C_short_H3K4me1_1_AdipoERCre

value: biol rep 1

value: 18 weeks old, chow diet


title: Ischemic_25min_Insulin_4

description:
ischemia for 25 mins with insulin
IS_25ins_4


title: Ischemic_25min_Insulin_3

description:
ischemia for 25 mins with insulin
IS_25ins_3


title: HHC_long_H3K27ac_1_AdipoERCre

value: Adipocytes

value: 39 weeks old, 25 weeks HFD, then 8 weeks chow diet


title: CC4:2-2

description:
NovaSeq X Plus platform (PE150) with the NovaSeq Reagent Kit
L1EIC0602167-EXP42_2

value: sciatic nerve tissue


title: CC4:2-1

description:
NovaSeq X Plus platform (PE150) with the NovaSeq Reagent Kit
L1EIC0602166-EXP42_1


title: HeLa cells, Arsenite, mock siRNA, 60 min, rep 2

value: HeLa cell line

value: WT

value: Arsenite, mock siRNA


title: CCC_long_H3K27ac_1_AdipoERCre


title: 3T3-Mouse Cells_Unstressed

source_name: 3T3-Mouse Cells

value: 3T3-Mouse Cells

value: Unstressed


title: HH_long_H3K27ac_1_AdipoERCre

value: AdipoERCre x NuTRAP on C576BL6 background


title: CC_long_H3K27ac_1_AdipoERCre

value: 31 weeks old, chow diet


title: Ischemic_25min_Insulin_2

description:
ischemia for 25 mins with insulin
IS_25ins_2

value: Right atrial tissue

value: Pretreatment of insulin for 30 mins and tissue perfusion was turned off to micmick global heart ischemia, then tissue was reperfused for 30 mins


title: 3T3-Mouse Cells_Arsenite

value: Arsenite


title: Ischemic_25min_Insulin_1

description:
ischemia for 25 mins with insulin
IS_25ins_1


title: CCC_long_H3K4me3_3_AdipoERCre

value: Epididymal Adipose Tissue

value: biol rep 3

value: 31 weeks old, 25 weeks HFD


title: Ischemic_25min_6

description:
ischemia for 25 mins without insulin
IS_25_6

value: 30 mins perfusion following by 25 mins ischemia and 30 mins reperfusion


title: HH_long_H3K4me3_3_AdipoERCre

value: Adipocytes


title: Brain, TNFKO + 5mg-kg LPS, m10, d0.5

description:
BR_d0.5_10
Brain_cpm_counts.txt

data_processing:
Sequencing read files were processed to generate UMI (unique molecular identifier) count matrices using the python toolkit from the bcbio-nextgen project version 1.1.5 (https://bcbio-nextgen.readthedocs.io/en/latest/). In brief, reads were aligned to the mouse mm10 transcriptome with RapMap (https://github.com/COMBINE-lab/RapMap). Quality control metrics were compiled with a combination of FastQC (http:bioinformatics.babraham.ac.uk/projects/fastqc/), Qualimap, MultiQC (https://github.com/ewels/MultiQC). Samples were demultiplexed using barcodes stored in Read 1 (first 6 bases) and raw UMI count matrices were computed using UMIs stored in Read 1 (bases 7 to 16) (https://github.com/vals/umis). Differential expression (DE) analysis was done using custom scripts in R (http://www.R-project.org). Raw count matrices were filtered to keep genes with at least 20 counts per million (cpm) or 5 UMIs in 2 samples and normalized across samples using the calcNormFactor function in edgeR (https://github.com/StoreyLab/edge).
Assembly: mm10
Supplementary files format and content: All count matrices are in tsv format. The first seven columns contain sample metadata (Organ, Treatment, Mouse ID, Mouse genotype, etc.). The remaining columns consist of normalized cpm counts. Matrices include all replicates for the organ.

source_name: Brain

extract_protocol:
Whole-tissue RNA extraction was performed as described previously (Surya et al., 2020). Briefly, tissues stored in RNA-preserving solution were thawed and transferred to 2 mL tubes containing 700-1500 µL (depending on tissue) of PureZOL (Bio-Rad, 7326890) or homemade Trizol-like solution (38% phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate, 5% glycerol). Tissues were lysed by adding 2.8-mm ceramic beads (OMNI International, 19-646) and running 1-3 cycles of 5-45 s at 3500 rpm on the PowerLyzer 24 (QIAGEN). For liver, brain, and small intestine samples, tissues were lysed with 3-5 mL using M tubes (Miltenyi biotec, 130-096-335) and running 1-4 cycles of the RNA_02.01 program on the gentleMACS Octo Dissociator (Miltenyi biotec). Next, lysates were processed in deep 96-well plates (USA Scientific 1896-2000) by adding chloroform for phase separation by centrifugation, followed by precipitation of total RNA in the aqueous phase using magnetic beads coated with silane (Dynabeads MyOne Silane; TermoFisher Scientific 37002D), buffer RLT (QIAGEN 79216), and ethanol. Genomic DNA contamination was removed by on-bead DNase I (ThermoFisher Scientific AM2239) treatment at 37 °C for 20 min. After washing steps with 80% ethanol, RNA was eluted from beads. This RNA extraction protocol was performed on the Bravo Automated Liquid Handling Platform (Agilent). Sample concentrations were measured using a Nanodrop One (Termo Scientific). RNA quality was confirmed using a Tapestation 4200 (Agilent Technologies). For each tissue sample, full-length cDNA was synthesized in 20 µl final reaction volume containing the following: (1) 10 µl of 10 ng/µl RNA; (2) 1 µl containing 2 pmoles of a custom RT primer biotinylated in 5’ and containing sequences from 5’ to 3’ for the Illumina read 1 primer, a 6-bp sample barcode (up to 384), a 10-bp unique molecular identifier (UMI), and an anchored oligo(dT)30 for priming; and (3) 9 µl of RT mix containing 4 µl of 5X RT buffer, 1 µl of 10 mM dNTPs, 2 pmoles of template switching oligo (TSO), and 0.25 µl of Maxima H Minus Reverse Trascriptase (Thermo Scientific, EP0753). First, barcoded RT primers were added to RNA, which were then denatured at 72°C for 1 min and snap cooled on ice. Second, the RT mix was added, and plates were incubated at 42°C for 120 min. For each library, double stranded cDNA from up to 384 samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research, D4013), and residual RT primers were removed using exonuclease I (New England Biolabs, M0293).
Full-length cDNAs were amplified with 5 to 8 cycles of single-primer PCR using the Advantage 2 PCR Kit (clontech 639206) and cleaned up using SPRIselect magnetic beads (Beckman Coulter B23318). cDNA was quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific 32851) and 50 ng of cDNA per pool of samples was tagmented using the Tagment DNA Enzyme I (Illumina 20034197) and amplified using the NEBNext Ultra II Q5 Master Mix (NEW ENGLAND BioLabs M0544L). Libraries were gel purified using 2% E-Gel EX Agarose Gels (ThermoFisher Scientific G402002), quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851) and a Tapestation 4200 (Agilent Technologies), and sequenced on the NextSeq 550 platform (Illumina).

value: Brain

tag: mouse id

tag: time point

value: 12 hours

value: 5mg-kg LPS


title: Brain, TNFKO + 5mg-kg LPS, m12, d0.5

description:
BR_d0.5_12
Brain_cpm_counts.txt


title: Ischemic_25min_5

description:
ischemia for 25 mins without insulin
IS_25_5

value: WT


title: HHC_long_H3K4me3_2_AdipoERCre

value: biol rep 2

value: 39 weeks old, 25 weeks HFD, then 8 weeks chow diet


title: Brain, TNFKO + 5mg-kg LPS, m11, d0.5

description:
BR_d0.5_11
Brain_cpm_counts.txt


title: HH_long_H3K4me3_2_AdipoERCre

value: 39 weeks old, chow diet


title: Ischemic_25min_3

description:
ischemia for 25 mins without insulin
IS_25_3


title: CCC_long_H3K4me3_1_AdipoERCre

value: AdipoERCre x NuTRAP on C576BL6 background

value: biol rep 1


title: CC_long_H3K27ac_2_AdipoERCre

value: 31 weeks old, chow diet


title: CC_long_H3K4me3_2_AdipoERCre


title: Brain, TNFKO + 5mg-kg LPS, m9, d0.5

description:
BR_d0.5_9
Brain_cpm_counts.txt


title: HHC_long_H3K4me3_1_AdipoERCre


title: Ischemic_25min_2

description:
ischemia for 25 mins without insulin
IS_25_2

value: Right atrial tissue


title: CC_long_H3K4me3_1_AdipoERCre


title: HHC_long_H3K4me1_3_AdipoERCre


title: Brain, 5mg-kg LPS, m8, d0.5

description:
BR_d0.5_8
Brain_cpm_counts.txt


title: CCC_long_H3K4me1_3_AdipoERCre


title: HH_long_H3K4me1_3_AdipoERCre


title: Ischemic_25min_1

description:
ischemia for 25 mins without insulin
IS_25_1


title: HHC_long_H3K4me3_3_AdipoERCre


title: Brain, 5mg-kg LPS, m7, d0.5

description:
BR_d0.5_7
Brain_cpm_counts.txt


title: HHC_long_H3K4me1_2_AdipoERCre


title: HH_long_H3K4me1_2_AdipoERCre


title: Ischemic_0min_6

description:
Non-ischemic control
IS_0_6

value: Non-ischemic control, tissue perfusion duration and glucose are the same as the other two groups


title: Brain, 5mg-kg LPS, m6, d0.5

description:
BR_d0.5_6
Brain_cpm_counts.txt


title: Ischemic_0min_5

description:
Non-ischemic control
IS_0_5


title: CC_long_H3K4me1_2_AdipoERCre

value: Epididymal Adipose Tissue


title: HHC_long_H3K4me1_1_AdipoERCre


title: Brain, 5mg-kg LPS, m5, d0.5

description:
BR_d0.5_5
Brain_cpm_counts.txt


title: CCC_long_H3K4me1_1_AdipoERCre


title: Ischemic_0min_4

description:
Non-ischemic control
IS_0_4


title: CC_long_H3K4me1_1_AdipoERCre


title: HH_long_H3K4me1_1_AdipoERCre


title: Ischemic_0min_3

description:
Non-ischemic control
IS_0_3


title: Brain, CTRL, m3, d0.5

description:
BR_d0.5_3
Brain_cpm_counts.txt

value: PBS


title: HHC_long_ATAC_3

data_processing:
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
Bowtie2 v2.4.4 used for read mapping
samtools v1.13 used for sorting bam files
bedtools v2.30 used for converting sorted bam files into bedgraph files
SEACR v1.3 used for calling peaks
Assembly: mm10
Supplementary files format and content: tab delimited called peak regions for each sample

extract_protocol:
Nuclei and ribosomes were isolated from snap frozen epiAT from AdipoERCre x NuTRAP mice in ice cold Nuclei Extraction Buffer (Miltenyi, #130-128-024) supplemented with 0.2U/µl recombinant RNase Inhibitor (Takara, #2313) and 1x cOmpleteTM EDTA-free Protease Inhibitor (Roche, #5056489001) and 10 mM sodium butyrate using the gentleMACSTM Octo Dissociator (Miltenyi, #130-096-427) using C-tubes (Miltenyi, #130-093-237).  Nuclei were resuspended in ATAC-seq solution (10mM TAPS pH 8.5, 5mM MgCl2, 10% DMF, 0.2µg/µl transposase (Tn5)) and incubated at 37˚C for 30 minutes, thereafter 100µl DNA binding buffer (Zymo Research, #D4003-1) were added and samples were stored at -20˚C. Thereafter DNA was extracted using the Zymo DNA Clean and Concentrator-5 (Zymo Research, #D4004).
Library amplification was performed using Kapa HiFi plus dNTPs (Roche Diagnostics, #07958846001) and the following PCR settings: 72˚C 5 minutes, 98˚C 30 seconds, 10 cycles of 98˚C 10 seconds, 63˚C 30 seconds, 72˚C 1 minute, hold at 4˚C.

value: biol rep 3


title: Ischemic_0min_2

description:
Non-ischemic control
IS_0_2


title: HHC_long_ATAC_2


title: CCC_long_ATAC_2


title: Brain, CTRL, m2, d0.5

description:
BR_d0.5_2
Brain_cpm_counts.txt


title: Ischemic_0min_1

description:
Non-ischemic control
IS_0_1


title: Brain, CTRL, m1, d0.5

description:
BR_d0.5_1
Brain_cpm_counts.txt


title: HH_long_ATAC_2

value: 31 weeks old, 25 weeks HFD


title: HHC_long_ATAC_1

value: Adipocytes


title: Small Intestine, TNFKO + 5mg-kg LPS, m12, d0.5

description:
SI_d0.5_12
Small Intestine_cpm_counts.txt

source_name: Small Intestine

value: Small Intestine


title: CC_long_ATAC_2


title: CCC_long_ATAC_1


title: Bos taurus,pre_4_IP RNA

city: Changchun

first: Xiaorui

last: Yang

address: Xincheng Street

institute: Jilin Agricultural University

data_processing:
*library strategy: m6A-seq
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: BOVINE(ensemble V107)
Supplementary files format and content: bigWig

organism: Bovidae

source_name: ovary

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: ovary

value: before the onset of puberty


title: Small Intestine, TNFKO + 5mg-kg LPS, m11, d0.5

description:
SI_d0.5_11
Small Intestine_cpm_counts.txt

value: 12 hours

value: 5mg-kg LPS


title: Bos taurus,pre_2_IP RNA


title: Bos taurus,pre_4_input RNA


title: HC_short_ATAC_3

value: 26 weeks old, 12 weeks HFD then 8 weeks chow diet


title: Small Intestine, TNFKO + 5mg-kg LPS, m10, d0.5

description:
SI_d0.5_10
Small Intestine_cpm_counts.txt


title: HH_long_ATAC_1


title: CC_long_ATAC_1


title: Brain, CTRL, m4, d0.5

description:
BR_d0.5_4
Brain_cpm_counts.txt

value: Brain


title: Small Intestine, TNFKO + 5mg-kg LPS, m9, d0.5

description:
SI_d0.5_9
Small Intestine_cpm_counts.txt


title: H_short_ATAC_3

value: AdipoERCre x NuTRAP on C576BL6 background

value: 18 weeks old, 12 weeks HFD


title: CC_short_ATAC_3

value: 26 weeks old, chow diet


title: C_short_ATAC_3

value: 18 weeks old, chow diet


title: Bos taurus,pre_1_IP RNA


title: HC_short_ATAC_2

value: biol rep 2


title: H_short_ATAC_2

value: Epididymal Adipose Tissue


title: Bos taurus,pre_1_input RNA


title: CC_short_ATAC_2


title: Small Intestine, 5mg-kg LPS, m8, d0.5

description:
SI_d0.5_8
Small Intestine_cpm_counts.txt


title: Small Intestine, 5mg-kg LPS, m6, d0.5

description:
SI_d0.5_6
Small Intestine_cpm_counts.txt


title: Bos taurus,post_4_IP RNA

value: after the onset of puberty


title: HH_long_ATAC_3

value: biol rep 3


title: Small Intestine, 5mg-kg LPS, m7, d0.5

description:
SI_d0.5_7
Small Intestine_cpm_counts.txt


title: C_short_ATAC_2


title: Small Intestine, 5mg-kg LPS, m5, d0.5

description:
SI_d0.5_5
Small Intestine_cpm_counts.txt


title: HC_short_ATAC_1

value: biol rep 1


title: Bos taurus,post_4_input RNA


title: Bos taurus,post_3_IP RNA


title: H_short_ATAC_1

value: Adipocytes


title: Bos taurus,post_3_input RNA


title: NPC_nuclei T2-rep1

city: Sydney

first: Ramin

last: M Farahani

state: NSW

address: Westmead Hospital, Darcy Road

department: molecular biomedicine

country: Australia

institute: University of Sydney

description:
T2na
Nuclear neRNAs at t=2h post-induction of differentiation

data_processing:
RNA-seq reads were aligned to Ensembl GRCm38 M. musculus reference transcriptome using Hisat2
StringTie was utilized to assemble and quantify expressed transcripts. Bam files were also transported to SeqMonk and analyzed using RNAseq quatitation pipeline of the software.
The transcript abundance and differential expression tables were generated using Ballgown.
EdgeR package combined with SeqMonk RNAseq pipeline were used for statistical analysis of between-group differences,
Gene ontology (GO) enrichment analysis was done using string database.
Assembly: GRCm38(mm10)
Supplementary files format and content: xlsx files generated using ballgown and Seqmonk RNAseq pipeline: scores represent log2fold change.

source_name: Mouse neural progenitor cells

growth_protocol: The established mouse multipotent neural stem cells (C17.2) were purchased from CellBank Australia (Children’s Medical Research Institute, Australia). Growth medium for NPCs consisted of DMEM/F12 supplemented with 10% fetal Bovine serum and Antibiotic-Antimycotic (100X, Life Technologies).

extract_protocol:
RNA was harvested using Bioline RNA isolation kit. After rRNA depletion, library preparation was achieved using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) with 1 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce neural differentiation, NPCs were cultured in Knockout™ DMEM (Gibco), GlutaMAX™ supplement, and N2 supplement (Gibco).

tag: strain

value: CD1 x C57BL/6

value: Neural induction


title: Small Intestine, CTRL, m4, d0.5

description:
SI_d0.5_4
Small Intestine_cpm_counts.txt

value: Small Intestine

tag: treatment

value: PBS


title: NPC_nuclei T1-rep1

description:
T1na
Nuclear neRNAs at t=1h post-induction of differentiation

value: mouse multipotent neural stem cells (C17.2)


title: NPC_nuclei T0-rep2

description:
T0nb
Nuclear neRNAs at t=0h post-induction of differentiation


title: NPC_nuclei T1-rep2

description:
T1nb
Nuclear neRNAs at t=1h post-induction of differentiation


title: Small Intestine, CTRL, m2, d0.5

description:
SI_d0.5_2
Small Intestine_cpm_counts.txt

value: 12 hours


title: NPC_nuclei T2-rep2

description:
T2nb
Nuclear neRNAs at t=2h post-induction of differentiation


title: NPC_nuclei T0-rep1

description:
T0na
Nuclear neRNAs at t=0h post-induction of differentiation


title: CC_short_ATAC_1

source_name: Epididymal Adipose Tissue

tag: replicate


title: Bos taurus,post_2_input RNA

value: ovary


title: Bos taurus,post_2_IP RNA


title: NPC_mitochondira T2-rep1

description:
T2ma
Mitochondrial neRNAs at t=2h post-induction of differentiation


title: Bos taurus,pre_2_input RNA

value: before the onset of puberty


title: NPC_mitochondira T1-rep2

description:
T1mb
Mitochondrial neRNAs at t=1h post-induction of differentiation


title: Small Intestine, CTRL, m1, d0.5

description:
SI_d0.5_1
Small Intestine_cpm_counts.txt


title: Small Intestine, CTRL, m3, d0.5

description:
SI_d0.5_3
Small Intestine_cpm_counts.txt


title: Cells grown on methanol and thiosulfate (biol rep 1)

city: Bonn

first: Christiane

last: Dahl

address: Meckenheimer Allee 168

department: Institut für Mikrobiologie & Biotechnologie

country: Germany

data_processing:
RNAseq Pipeline v2.0
Raw sequencing data are preprocessed to generate clean data for downstream analysis. In this step, quality of raw sequencing ischecked and filtered to retain only high quality bases by performing adapter trimming, quality filtering and per-read quality pruning.
Quality is interpreted as the probability of an incorrect base call or, equivalently, the base call accuracy. The quality score islogarithmically based, so a quality score of 10 reflects a base call accuracy of 90%, but a quality score of 20 reflects a base callaccuracy of 99% and a quality score of 30 reflects a base call accuracy of 99.9%. These probability values are the results from thebase calling algorithm and depend on how much signal was captured for the base incorporation.
Sequencing reads representing reads with quality score at least Q30 is above 90% is of very good quality. For a reasonably goodsample source material, according to Illumina specifications, one could expect >75% reads with at least Q30 Phred quality.
Raw sequencing data was processed using fastp software to remove poor quality bases (below Phred Quality 20) using thesliding window approach where  if the average quality of the bases drops below Q20, those bases are removed from the reads. After quality trimming, program checks for presence of any adapters in the reads and removes from the reads. Further, shorterreads which are <30bp length are also removed to retain only high quality sequencing reads for each sample in the analysis. Incase of paired-end reads, both the sequencing reads which pass the QC criteria are considered for downstream analysis.
High quality sequence reads were aligned to the reference genome using STAR (Spliced Transcripts Alignment to a Reference) along with the known gene models.
Assembly: NC_014313.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes significant fold changes for each gene
Supplementary files format and content: tab-delimited text file includes fold changes for each gene

organism: Hyphomicrobium denitrificans

source_name: bacterial cell

growth_protocol: H. denitrificans ΔtsdA was cultured in 50 ml minimal medium containing either 24.4 mM methanol or 24.4 mM methanol plus 2 mM thiosulfate in 200 ml Erlenmeyer flasks at 30°C with shaking at 200 rpm to early log phase.

extract_protocol:
From the frozen pellets, the RNA was purified with the FastGene RNA Premium Kit (NIPPON Genetics EUROPE, Düren, Germany) according to the manufacturer’s instructions. A modification was introduced regarding the cell lysis step. After addition of the lysis buffer that contained 1% (v/v) 2-mercaptoethanol, cells were disrupted by bead beating (Bead Ruptor 12 Bead Mill Homogenizer, Omni International, Kennesaw, GA, USA) for three cycles of 30 s at maximum speed and incubation on ice for 1 min. RNA quality was checked on 1% agarose gels and its concentration was measured using NanoPhotometer NP80 (IMPLEN, Munich, Germany).
The RNA was shipped on dry ice to Eurofins Genomics GmbH (Ebersberg, Germany). The subsequent analysis pipeline included rRNA depletion, library preparation (mRNA fragmentation, strand specific cDNA synthesis), Illumina paired end sequencing (2 x 150 bp, minimum 10 MB reads)), and bioinformatic analysis (mapping against the reference genome, identification and quantification of transcripts, pairwise comparison of expression levels and determination of significant fold differences) and was conducted by the company.
Strand-specific cDNA library. RNA-seq Technology: Genome Sequencer Illumina NovaSeq. Sequence mode: NovaSeq 6000 S4 PE150 XP

treatment_protocol: Cells from 20 ml culture were harvested and flash frozen in liquid N2 and stored at -70°C.

value: bacterial cell

value: delta tsdA

tag: condition

value: methanol and thiosulfate

value: growth in batch culture


title: Skin, TNFKO + 5mg-kg LPS, m12, d0.5

description:
SK_d0.5_12
Skin_cpm_counts.txt

value: Skin

value: 5mg-kg LPS


title: NPC_mitochondira T1-rep1

description:
T1ma
Mitochondrial neRNAs at t=1h post-induction of differentiation


title: NPC_mitochondira T0-rep2

description:
T0mb
Mitochondrial neRNAs at t=0h post-induction of differentiation


title: Cells grown on methanol (biol rep 2)

value: methanol


title: Skin, TNFKO + 5mg-kg LPS, m11, d0.5

description:
SK_d0.5_11
Skin_cpm_counts.txt


title: NPC_mitochondira T0-rep1

description:
T0ma
Mitochondrial neRNAs at t=0h post-induction of differentiation


title: ATAC-seq T2

description: ATAC-seq at t=2h post-induction of differentiation

data_processing:
ATACseq reads were aligned to Ensembl GRCm38 M. musculus reference genome.
trimmed sequences were mapped to mouse genome (GRCm38 - mm10) using Bowtie2 software
peak calling was performed using MACS2
heatmap of coverage at TSS was generated with deepTools
Gene ontology (GO) enrichment analysis was done using string database.
Assembly: GRCm38(mm10)
Supplementary files format and content: csv file containing MACS2 peaks annotated via SeqMonk (csv)

extract_protocol:
A total of 50,000 nuclei from NPCs were used for ATAC-seq as described elsewhere (Buenrostro et al., Curr Protoc Mol Biol. 2015).
ATAC-seq libraries were constructed using Illumina Tagment DNA TDE1 Enzyme and Buffer Kit
Nextera adapters and TDE1 enzyme.


title: Skin, TNFKO + 5mg-kg LPS, m10, d0.5

description:
SK_d0.5_10
Skin_cpm_counts.txt


title: ATAC-seq T1.5

description: ATAC-seq at t=1.5h post-induction of differentiation


title: Cells grown on methanol (biol rep 1)


title: NPC_mitochondira T2-rep2

description:
T2mb
Mitochondrial neRNAs at t=2h post-induction of differentiation


title: ATAC-seq T1

description: ATAC-seq at t=1h post-induction of differentiation


title: ATAC-seq T0

description: ATAC-seq at t=0h (control)


title: Skin, TNFKO + 5mg-kg LPS, m9, d0.5

description:
SK_d0.5_9
Skin_cpm_counts.txt


title: E-cadherin knock out 2

first: Rene-Marc

last: Mege

address: 15 Rue Helene Brion

institute: Institut Jacques Monod

data_processing:
After sequencing, a primary analysis based on AOZAN software (ENS, Paris) was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). Obtained fastq files were then aligned using STAR algorithm (version 2.5.2b) and quality control of the alignment obtained with Picard tools (version 2.8.1). Reads were then counted using Featurecount (version Rsubread 1.24.1) and the statistical analyses on the read counts were performed with the DESeq2 package version 1.14.1 to determine the proportion of differentially expressed genes between the two conditions. From the initial DESeq2 file containing 11191 genes without duplicates, we then performed the Gene Set Enrichment Analysis with the ClusterProfiler package on R~\cite{yu_clusterprofiler_2012}. We used the canis familiaris (Cf) annotation and performed the GSEA from ENSEMBL to SYMBOL annotations without permutation and with p-value and p-value adjusted cutoffs set at 0.05.
We then looked at the Molecular Signatures Database (MSigDB) to find if these up or downregulated genes were present in the gene sets related to specific cellular processes as cell-cell adhesion or cell death, apoptosis and oxidative stress or cell substrate adhesion regulation
Assembly: canis familiaris (Cf) annotation and performed the GSEA from ENSEMBL to SYMBOL annotations
Supplementary files format and content: WT_KO_Analysis.xlsx

organism: Canis lupus familiaris

growth_protocol: MDCK WT and MDCK E-cad KO cells were grown in DMEM + 10% FBS and 1% PS until 70-80% confluency.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, Cat.No./ID:74104). Briefly cells were lysed with RLT buffer and disrupt using cell shredder. Following RNA collection following the kit protocol, RNA concentrations were obtained using nanodrop or a fluorometric Qubit RNA assay (Life Technologies, Grand Island, New York, USA).
250 ng of high quality total RNA sample ($RIN > 8$) was processed using Stranded mRNA Prep kit (Illumina) according to manufacturer instructions. Briefly, after purification of poly-A containing mRNA molecules, mRNA molecules are fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during the second strand synthesis will permit to achieve the strand specificity. Addition of a single A base to the cDNA is followed by ligation of Illumina adapters. Libraries were quantified by Q bit and profiles were assessed using the DNA High Sensitivity LabChip kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode.

value: Kidney

value: MDCK Type II Ecadherin KO

value: Madin-Darby canine kidney(MDCK)cells

value: MDCK Type II

value: e-cadherin loss of function


title: F1.KPN.SIP.av2

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description:
F1.KPN.SIP.av2
VW8.KPN 28.1.G

data_processing:
The quality of raw data was assessed using FastQC (v.0.11.9) and MultiQC (v.1.9) prior to processing the data.
The first 12 bases as well as low-quality bases (Phred score < 20) were trimmed from each sequence using Cutadapt (v1.18).
STAR (v.2.7.4.a) was applied to align sequences to the mouse genome (GRCm38) and to determine counts per gene.
After log2 transformation and quantile normalization, data were visualized using PCA plots to assess the quality of data after alignment and possible batch effects.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized values for each Sample

growth_protocol: Intestinal organoids were maintained in Advanced DMEM/F12 (ADF) media supplemented with penicillin (100ug/ml), 5ml 200 mM Glutamax, 5ml 10mM Hepes, B27 supplement (Invitrogen) and N2 supplement (Invitrogen). In addition to ADF we also use 50ng/ml recombinant Mouse EGF (Tebu-BIO), mouse Noggin-FC supernatant (~100ng/ml) and R-Spondin-FC supernatant(~ 500ng/ml). Cultures were maintained at 37 degrees celsius and checked monthly for mycoplasma contamination.

extract_protocol:
RNA was isolated using Bioke Nucleospin RNA isolation kit (Bioke) according to the manufacturer’s protocol. DNA degradation was performed using Bioke RNase-Free DNase. We assessed the quality of our RNA samples using Agelent 2100 Bioanalyzer (Agilent Technologies) and only high quality RNA samples were selected based on RIN value.
The organoid RNAseq libraries were prepared using KAPA mRNA HyperPrep (Roche) following the manufacturer’s protocol. They were barcoded, quantified using the Qubit DNA HS kit from Thermofisher and Tapestation 4200 from Agilent, pooled and multiplex sequencing was performed on the Illumina Novaseq6000 platform.

value: Small Intestine

value: In Vitro organoids

value: KPN

tag: batch


title: F1.KPN.SIP.bv2

description:
F1.KPN.SIP.bv2
VW7.KPN 20.5.A


title: Skin, 5mg-kg LPS, m8, d0.5

description:
SK_d0.5_8
Skin_cpm_counts.txt

value: 12 hours


title: Skin, 5mg-kg LPS, m7, d0.5

description:
SK_d0.5_7
Skin_cpm_counts.txt


title: F1.KP.CO.av2.OE

description:
F1.KP.CO.av2.OE
VW5.KP 8.5.A

source_name: Colon

value: Colon

value: KP


title: F1.KP.SIP.bv2

description:
F1.KP.SIP.bv2
VW6.KP 7.5.D


title: WT, control, sample 3

value: control


title: Skin, 5mg-kg LPS, m6, d0.5

description:
SK_d0.5_6
Skin_cpm_counts.txt


title: F1.KPN.SIP.av1

description:
F1.KPN.SIP.av1
VW4.KPN 28.1.G


title: Skin, 5mg-kg LPS, m5, d0.5

description:
SK_d0.5_5
Skin_cpm_counts.txt


title: F1.KPN.SIP.bv1

description:
F1.KPN.SIP.bv1
VW3.KPN 20.5.A


title: ATAC-seq T0.5

description: ATAC-seq at t=0.5h post-induction of differentiation

value: mouse multipotent neural stem cells (C17.2)

value: CD1 x C57BL/6

value: Neural induction


title: F1.KP.CO.av1.OE

description:
F1.KP.CO.av1.OE
VW1.KP 8.5.A


title: DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes 9

type: genomic

city: Ariel

first: Mali

last: Salmon-Divon

address: Ariel university, Ariel Israel, Ramat HaGolan St 65, Ari'el

country: Israel

institute: Department of Molecular Biology, Ariel University

description:
RDD9
DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes

hyb_protocol: Standard Illumina Procedure for MethylationEPIC platform with FFPE restoration step

data_processing:
ChAMP package in R environment (v 2.21.1)
BMIQ normalized beta

label: Cy3 and Cy5

source_name: skin

extract_protocol: ChemagicSTAR FFPE DNA Extraction Protocol

value: skin

tag: disease state

value: histiocytoses

value: male


title: Cells grown on methanol and thiosulfate (biol rep 2)

value: bacterial cell

value: delta tsdA

value: methanol and thiosulfate

value: growth in batch culture


title: WT, control, sample 1

source_name: Kidney

value: Kidney

value: MDCK Type II

value: Madin-Darby canine kidney(MDCK)cells


title: C_short_ATAC_1

value: Epididymal Adipose Tissue

value: Adipocytes

value: AdipoERCre x NuTRAP on C576BL6 background

value: biol rep 1

value: 18 weeks old, chow diet


title: Skin, CTRL, m3, d0.5

description:
SK_d0.5_3
Skin_cpm_counts.txt

source_name: Skin

value: Skin

value: 12 hours

value: PBS


title: E-cadherin knock out 3

value: MDCK Type II Ecadherin KO

value: e-cadherin loss of function


title: DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes 8

description:
RDD8
DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes

scan_protocol: Standard Illumina Procedure for MethylationEPIC platform with FFPE restoration step

value: skin

value: histiocytoses

value: female


title: F1.KPNA2.CO.c

description:
F1.KPNA2.CO.c
AK60

value: Colon

value: In Vitro organoids


title: mVT2-tomo-seq

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

institute: University Hospital Würzburg

data_processing:
Of the paired-ended reads, read 1 contains the UMI in the first 6 bases and the section barcode in the following 7 bases. Read 2 contains the gene expression information and is used for alignment. Trimming was performed using TrimGalore (v.0.6.10) with default parameters. Reads were mapped to the mouse genome (GRCm38) using STAR (v.2.7.9a) setting --outSAMstrandField to intronMotif and --outFilterMultimapNmax to 1 with other parameters set to default.
Assembly: GRCm38
Supplementary files format and content: coutc files contain number of reads
Supplementary files format and content: coutb files contain number of observed UMI
Supplementary files format and content: coutt files contain number of unique UMI-corrected transcripts per gene per section

source_name: ventral tongue

extract_protocol:
RNA was extracted from the sections using the NucleoSpin RNA XS isolation kit (Macherey Nagel) following the manufacturer's instructions.
RNA was processed using the previously described CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end reads.

value: ventral tongue

value: wild-type

tag: section thickness

value: 14 micrometre


title: Skin, CTRL, m2, d0.5

description:
SK_d0.5_2
Skin_cpm_counts.txt


title: mVT1-tomo-seq


title: F1.KPNA2.CO.c.OE

description:
F1.KPNA2.CO.c.OE
AK59


title: DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes 7

description:
RDD7
DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes

source_name: colon

label_protocol: Standard Illumina Procedure for MethylationEPIC platform with FFPE restoration step

value: colon

tag: Sex


title: Inguinal Lymph Node, TNFKO + 5mg-kg LPS, m12, d0.5

description:
iLN_d0.5_12
Inguinal Lymph Node_cpm_counts.txt

source_name: Inguinal Lymph Node

value: Inguinal Lymph Node

value: 5mg-kg LPS


title: Skin, CTRL, m1, d0.5

description:
SK_d0.5_1
Skin_cpm_counts.txt


title: F1.KPNA2.CO.b

description:
F1.KPNA2.CO.b
AK58


title: mHP2-tomo-seq

source_name: hard palate

value: hard palate


title: DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes 10

description:
RDD10
DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes


title: WT, control, sample 2

value: Kidney

tag: cell line

value: MDCK Type II

value: Madin-Darby canine kidney(MDCK)cells

value: control


title: F1.KPNA2.CO.b.OE

description:
F1.KPNA2.CO.b.OE
AK57


title: DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes 5

description:
RDD5
DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes

source_name: lymph node

value: lymph node


title: DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes 4

description:
RDD4
DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes

source_name: brain

value: brain

value: male


title: Skin, CTRL, m4, d0.5

description:
SK_d0.5_4
Skin_cpm_counts.txt

value: Skin

value: 12 hours

value: PBS


title: Inguinal Lymph Node, TNFKO + 5mg-kg LPS, m11, d0.5

description:
iLN_d0.5_11
Inguinal Lymph Node_cpm_counts.txt


title: mDT2-tomo-seq

source_name: dorsal tongue

value: dorsal tongue


title: DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes 6

description:
RDD6
DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes

value: skin

value: histiocytoses

value: female


title: DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes 2

description:
RDD2
DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes


title: F1.KPNA2.CO.a

description:
F1.KPNA2.CO.a
AK56

value: Colon

value: In Vitro organoids


title: Inguinal Lymph Node, TNFKO + 5mg-kg LPS, m10, d0.5

description:
iLN_d0.5_10
Inguinal Lymph Node_cpm_counts.txt

value: Inguinal Lymph Node

value: 5mg-kg LPS


title: DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes 3

description:
RDD3
DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes

source_name: nasopharynx

value: nasopharynx


title: Inguinal Lymph Node, 5mg-kg LPS, m8, d0.5

description:
iLN_d0.5_8
Inguinal Lymph Node_cpm_counts.txt


title: mDT1-tomo-seq

value: wild-type

value: 14 micrometre


title: F1.AP.CO.c

description:
F1.AP.CO.c
AK9

value: AP


title: Inguinal Lymph Node, 5mg-kg LPS, m7, d0.5

description:
iLN_d0.5_7
Inguinal Lymph Node_cpm_counts.txt


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 13

description:
LCH13
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

source_name: lung

value: lung


title: F1.KPNA2.SIP.a

description:
F1.KPNA2.SIP.a
AK55

source_name: Small Intestine

value: Small Intestine


title: Inguinal Lymph Node, TNFKO + 5mg-kg LPS, m9, d0.5

description:
iLN_d0.5_9
Inguinal Lymph Node_cpm_counts.txt


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 12

description:
LCH12
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

source_name: bone

value: bone

value: male


title: mBM2-tomo-seq

source_name: buccal mucosa

value: buccal mucosa


title: mHP1-tomo-seq

value: hard palate


title: F1.AK.CO.c

description:
F1.AK.CO.c
AK7

value: AK


title: Inguinal Lymph Node, 5mg-kg LPS, m5, d0.5

description:
iLN_d0.5_5
Inguinal Lymph Node_cpm_counts.txt

value: 12 hours


title: DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes 1

description:
RDD1
DNA from histyocitic infiltrated tissues of Rosai-Dorfman-Destombes

source_name: breast

value: breast

value: histiocytoses

value: female


title: Inguinal Lymph Node, CTRL, m4, d0.5

description:
iLN_d0.5_4
Inguinal Lymph Node_cpm_counts.txt

value: Inguinal Lymph Node

value: PBS


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 14

description:
LCH14
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

value: skin


title: BMEo PBS treated3

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

data_processing:
The sequences which passed QC were mappted to mm10 using Hisat2.
Htseq was used to obtain gene expression counts.
DESeq2 was used to normalize gene counts and differentially expressed gene detection.
Assembly: mm10
Supplementary files format and content: Matrix table with normalized gene counts for every sample.

source_name: bone marrow derived eosinophils

growth_protocol: The bone marrow cells are cultured at 10^6/ml in medium containing RPMI with 20% FBS, 100IU/ml penicillin and 10μg/ml streptomycin, 2mM glutamine, 25mM HEPES and 1× nonessential amino acids and 1mM sodium pyruvate and 50μM 2-MEsupplemented with 100ng/ml SCF(stem sell factor) and 100ng/ml FLT3-L from day 0 to 4. On day4, cells were resuspend with medium with 20 ng/ml IL-5. On day8, the cells were moved to a new plastic plate and maintained in fresh medium supplemmented with 20 ng/ml IL-5. Hereafter, half of the culture medium was changed to fresh medium containing IL-5 every other day. On day14 cells were subjected to the experiment.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA MicroPrep kit and was cleaned up with the NEBNext rRNA Depletion kit v2.
The libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Cells were harvested, and dead cells were removed using the Mojo Sort Mouse Dead Cell Removal Kit. Following this step, cells were treated with or without 2.5 ng/mL IL-33 for 3 hours.

value: bone marrow derived eosinophils

value: WT


title: F1.BPNA2.SIP.a

description:
F1.BPNA2.SIP.a
AK49

value: In Vitro organoids


title: F1.AP.SIP.c

description:
F1.AP.SIP.c
AK8

value: AP


title: mBM1-tomo-seq

value: wild-type

value: 14 micrometre


title: Inguinal Lymph Node, 5mg-kg LPS, m6, d0.5

description:
iLN_d0.5_6
Inguinal Lymph Node_cpm_counts.txt

value: 5mg-kg LPS


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 10

description:
LCH10
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

source_name: skin

value: male


title: BMEo PBS treated1


title: BMEo IL-33 treated 3


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 9

description:
LCH9
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

source_name: muscle

value: muscle


title: Inguinal Lymph Node, CTRL, m2, d0.5

description:
iLN_d0.5_2
Inguinal Lymph Node_cpm_counts.txt


title: BMEo PBS treated2


title: BMEo IL-33 treated 1


title: F1.AK.CO.b

description:
F1.AK.CO.b
AK5

source_name: Colon

value: Colon

value: AK


title: Inguinal Lymph Node, CTRL, m1, d0.5

description:
iLN_d0.5_1
Inguinal Lymph Node_cpm_counts.txt

value: 12 hours


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 11

description:
LCH11
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

value: histiocytoses


title: F1.BPNA2.SIP.b

description:
F1.BPNA2.SIP.b
AK51

value: Small Intestine


title: F1.BPNA2.SIP.c

description:
F1.BPNA2.SIP.c
AK53


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 7

description:
LCH7
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

value: lung


title: Inguinal Lymph Node, CTRL, m3, d0.5

description:
iLN_d0.5_3
Inguinal Lymph Node_cpm_counts.txt

value: Inguinal Lymph Node

value: PBS


title: F1.BPNA2.CO.c

description:
F1.BPNA2.CO.c
AK54


title: Bone Marrow, TNFKO + 5mg-kg LPS, m12, d0.5

description:
BM_d0.5_12
Bone Marrow_cpm_counts.txt

source_name: Bone Marrow

value: Bone Marrow


title: F1.BPNA2.CO.a

description:
F1.BPNA2.CO.a
AK50


title: BMEo IL-33 treated 2

value: bone marrow derived eosinophils

value: WT


title: F1.BPNA2.CO.b

description:
F1.BPNA2.CO.b
AK52

value: In Vitro organoids


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 8

description:
LCH8
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

value: brain


title: F1.K.SIP.c.OE

description:
F1.K.SIP.c.OE
AK48

value: K


title: F1.K.CO.c.OE

description:
F1.K.CO.c.OE
AK47


title: Bone Marrow, TNFKO + 5mg-kg LPS, m9, d0.5

description:
BM_d0.5_9
Bone Marrow_cpm_counts.txt

value: 5mg-kg LPS


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 4

description:
LCH4
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

value: bone

value: male


title: F1.K.SIP.a

description:
F1.K.SIP.a
AK46


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 6

description:
LCH6
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

value: skin

value: female


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 5

description:
LCH5
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis


title: Bone Marrow, 5mg-kg LPS, m8, d0.5

description:
BM_d0.5_8
Bone Marrow_cpm_counts.txt

value: 12 hours