title: FGF_Neurog2_3

data_processing:
We checked the quality of the raw FASTQ reads using FastQC.
We performed quality control and adapter trimming of the raw FASTQ reads using Cutadapt low quality read (< 20bp)
The trimmed reads were mapped to the mouse reference genome (mm10) by using Bowtie2 (parameter: --very-sensitive -X 1000 --dovetail).
We used Genrich in ATAC-seq mode to identify accessible regions and bam2counts to generate a count table matrix for each sample.
We performed differential accessibility analysis using R/Bioconductor package DESeq2 (version 1.36.0, fold change (FC) > 2 and adjusted P-value < 0.05) and annotated the accessible regions using Chipseeker (TSS ± 3.0 Kb) . We used bamcoverage and deeptools to generate heatmaps of accessible sites.
Assembly: mm10
Supplementary files format and content: Excel tables (.xlsx) containing rlog normalised peak counts for each sample

growth_protocol: Following decapitation of postnatal (P5-P6) wild-type C57BL/6J mice, the skin and the skull were removed, and the brain was extracted avoiding any tissue damage and placed into the 10 mM HEPES solution for dissection. After separating the two hemispheres, the meninges were removed and a piece of cerebral cortex was dissected using fine forceps and collected in a tube with astrocyte medium (Fetal calf serum-FCS (10% (v/v); Horse serum-HS (5% (v/v)); glucose (3,5 mM); B27 supplement; Penicillin/Streptomycin (final dilution 1:100) in DMEM/F12+GlutaMAX). Tissue was mechanical dissociated with a 5 ml pipette and placed into uncoated plastic flasks for cell expansion in astrocyte medium supplemented with two growth factors EGF (10 ng/ml) +bFGF (10 ng/ml) or with the bFGF (10 ng/ml) only as specified for each experiment. After 4-5 days, the medium was exchanged and supplied with the fresh growth factors. After 10 days of culturing, cultured cells were rinsed with DPBS and contaminating oligodendrocyte precursor cells were removed by brusquely shaking the culture flasks several times. Astroglial cells were then detached from the flask by trypsinization and seeded onto poly-D-lysine (PDL)-coated glass coverslips at a density of 8x104 cells per well in a 24-well plate with astrocyte medium.

extract_protocol:
Astrocytes were collected by trypsinization 48 h after retroviral transduction, washed, resuspended in DPBS and analysed using a FACS Aria II instrument (BD Biosciences) in the FACSFlowTM medium. Debris and aggregated cells were gated out by forward-scatter area (FSC-A) and side-scatter area (SSC-A). Forward scatter area (FSC-A) vs. forward scatter width (FSC-W) was used to discriminate doublets from single cells. To set the gates for the sorting, untransduced astrocytes were recorded. Sorted cells were collected in the DPBS, counted and divided into two batches: 50000 cells were immediately processed for the ATAC-seq and the remainder of the cells were collected for the RNA-seq library preparation.
Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq), a method to detect chromatin accessibility genome-wide, was performed following the published protocol [102,103]. Briefly, right after the FACS sorting, 50000 cells were lysed, nuclei were extracted and resuspended in transposase reaction mix (25 μl 2x TD buffer (Illumina); 2,5 μl Transposase (Illumina); 22,5 μl nuclease free water), following by transposition reaction for 30 minutes at 370C. To stop the transposition reaction, samples were purified using a Qiagen MinElute PCR (Qiagen) purification kit according to the manufacturer instructions. Open chromatin fragments were first amplified for 5 cycles and then for additional 7-8 cycles, as determined by RT-qPCR reaction, using the combination of primer Ad1_noMX (5’ AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG 3’) and the Nextera Index Kit (Illumina) primer N701-N706. Libraries were purified using a Qiagen MinElute PCR purification kit (Qiagen) and their quality was assessed using the Bioanalyzer High-Sensitivity DNA kit (Agilent) according to the manufacturer’s instructions. The concentration of each library was measured by Qubit using provided protocol.  Libraries were pooled for sequencing mix containing 20 ng of each library. Prior to the sequencing, pooled libraries were additionally purified with AMPure beads (ratio 1:1) to remove contaminating primer dimers and quantified using Qubit and Bioanalyzer High-Sensitivity DNA kit (Agilent). 50-bp paired-end deep sequencing was carried out on HiSeq 4000 (Illumina).

treatment_protocol: For the ATAC-seq experiments, the cells were kept in the astrocyte medium and collected 48 h after viral transduction (Control, Hmgb2, Neurog2, or  Neurog2+Hmgb2 transcription factor). Astrocytes were detached from the flask by trypsinization, prepared for the FACS and sorted for the following ATAC-seq experiments according to the fluorophore expression.

tag: genotype

value: Neurog2 overexpression/bFGF


title: Visceral_ASC_obese_basal_rep3

status: Public on Mar 06 2025

type: RNA

city: Barcelona

first: Gemma

last: Arderiu

address: Avda. S. Antoni M. Claret 167

department: Cardiovascular area

country: Spain

institute: Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau IIB-Sant Pau

description: miRNA expression data from ASCs

hyb_protocol: Biotin-labeled RNA was hybridized to affymetrix miRNA 4.0 GeneChips for 16 hours (48ºC, 60 rpm) using a GeneChip 645 hybridization oven and washed and stained on the GeneChip Fluidics Station 450 using protocol FS450_0002.

scan_protocol: Scanning of microarrays was performed using the Affymetrix GeneChip 3000 7G scanner. AGGC software was used for scanner images adquisition.

data_processing: Raw data was normalized in Transcriptome Analysis Console (TAC 4.0.2.15) software using RMA-DABG algorithm and CHP files were generated.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Adipose-derived stem cell

label_protocol: 500 ng of RNA was labeled using Applied Biosystems FlashTag Biotin HSR RNA labeling kit according to manufacturer's instructions.

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM)-Low Glucose (Thermo Fisher Scientific) supplemented with 10% FBS, 100 U/ml penicillin and 0.1 mg/ml streptomycin (Invitrogen) in a humidified environment at 37°C with 5% CO2 and were used between passages 2 and 4.

extract_protocol: miRNA was isolated using a mirVana™ miRNA Isolation Kit with phenol (Life Technologies Corporation) according to the manufacturer's instructions.

treatment_protocol: To induce ASCs differentiation into ECs, ASCs were cultured in DMEM-Low Glucose supplemented with 10 ng/ml bFGF (233-FB, R&D Systems). Cells were supplied with fresh medium every 3 days and cultured for a total of 9 days

tag: tissue

value: Visceral adipose tissue

tag: categorization

value: obese

tag: state

value: basal

tag: gender

value: female


title: S_coelicolor_M512lpm_4d biol rep 2

type: SRA

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

country: Germany

institute: Institute for Bioinformatics and Medical Informatics

description:
Library name: S_coelicolor_M512lpm_4d
RNA isolated after 4days of growth from S. coelicolor M512 expressing the liposidomycin gene cluster

library_source: transcriptomic

data_processing:
All reads mappings were performed against the cosmid references (lpm: NCBI accession number GU219978, cpz: NCBI accession number FJ490409, Publication https://doi.org/10.1038/nchembio.1310)
The mappings of all samples were conducted with HISAT2 v2.1.0. Spliced alignment of reads was disabled (HISAT2 parameter --no-spliced-alignment). Library type was set to reverse (--rna-strandness).
The resulting mapping files in SAM format were converted to BAM format and unmapped reads were removed using SAMtools v1.9
From the bam files coverage was calculated for each strand using deepTools 3.5.6 with the command bamCoverage (—filterRNAstrand reverse/forward)
Assembly: All reads mappings were performed against the cosmid references (lpm: NCBI accession number GU219978, cpz: NCBI accession number FJ490409, Publication https://doi.org/10.1038/nchembio.1310)
Supplementary files format and content: Cosmid wide coverage per position as .bw file for each strand in each sample

organism: Streptomyces coelicolor

source_name: whole cell

growth_protocol: For the cultivation of Streptomyces coelicolor strains, spore stocks were used to inoculate 50 mL TSB medium as a pre-culture and grown at 30 °C and 200 rpm for 3 days. One mL of the pre-culture was used to inoculate 70 mL of production medium (PM) and cultivation was continued under the same conditions for 4 days. All cultivations were carried out in 300 mL baffled Erlenmeyer flasks containing a stainless steel spring.

extract_protocol:
RNA was isolated from 5 mL culture volume of Streptomyces coelicolor M512 either expressing the caprazamycin or liposidomycin gene cluster (S. coelicolor M512/cpzLK09 and S. coelicolor M512/lpmLK01) using the RNeasy plus kit (Qiagen, Hilden, Germany). Cells were transferred into lysing matrix B tubes (2 mL) and lysed in a MP FastPrep-24 (all supplied by MP Biomedicals, USA) for two times 15 s at 4000 m/s with a cooling step on ice for 4 min between the two rounds of shaking. RNA was eluted in RNase-free water and measured at the nanodrop 1000 spectrometer (VWR International, USA). Contaminating DNA was digested using the RNase-free DNase kit (Qiagen, Hilden, Germany). The RNA was purified using the RNA clean-up kit (Macherey-Nagel, Düren, Germany) and tested for the absence of DNA by PCR.
The total RNA was quantified with a Qubit RNA BR Assay Kit (Thermo Fisher) and RNA integrity was checked by an Agilent 2100 BioAnalyzer with the RNA 6000 Pico kit (Agilent). Library preparation was performed with Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Microbiome according to the manufacturer’s instructions. In brief, 100 ng of total RNA per sample were subjected to rRNA depletion, followed by cDNA library construction, adapter ligation and 15 cycles of barcoding PCR. Obtained libraries were quantified with Qubit 1x DNA HS Assay Kit (Thermo Fisher) and the fragment distribution was checked by an Agilent 2100 BioAnalyzer using the High Sensitivity DNA Kit (Agilent). Libraries were subsequently pooled and sequenced on an Illumina NovaSeq 6000 device using the NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) with a run mode of 75,10,10,0. The average number of obtained reads was 27-43 million. The sequencing was demultiplexed with the latest version of the nextflow pipeline: nf-core/demultiplex. For demultiplexing bcl2fastq was used and the quality was checked with fastp.

value: whole cell

tag: strain

tag: cell type

value: bacterial

value: SCP1-, SCP2-, DeltaactII-ORF4, DeltaredD containing the liposidomycin gene cluster from S. sp. SN1061-M, KanR

tag: treatment

value: cell lysis, RNA isolation and purification


title: TMD8_input

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

country: USA

institute: University of Michigan Medical School

library_source: genomic

data_processing:
Single-end or paired-end reads were aligned to hg19 using BWA-ALN (v 0.7.17).
Bam files were filtered (samtools view) to remove reads flagged as secondary alignments, not passing quality control, PCR or optical duplicates, and supplementary alignments (flags: 0x100, 0x200, 0x400, 0x800), and for paired-end read to retain only paired reads in a proper pair (flags: 0x1, 0x2)          .
Reads were filtered to retain only individual reads (single-end) or read-pairs (paired-end) mapping to <=2 sites genome-wide (X0 tag <=2 for single-end or both paired-end reads).
Display files were generated with deeptools bamCoverage (options: "--binSize 25 --normalizeUsing CPM --extendReads")
Assembly: hg19
Supplementary files format and content: bigwig (hg19 fragment coverage, normalized to fragments per million post-filtering)

molecule: genomic DNA

growth_protocol: All cell lines were cultured in RPMI 1640 + Glutamax supplemented with 10% fetal calf serum, penicillin/streptomycin, nonessential amino acids, 1 mM sodium pyruvate, and 55 micromolar 2-mercaptoethanol

extract_protocol:
Five to twenty million cells were cross-linked in PBS + 1% formaldehyde for 10 minutes at room temperature (histone marks) or 37C (TFs), quenched with 1/20th volume of 2.5M glycine, washed twice in cold PBS with protease inhibitors, and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted at 3000g, and resuspended in cold SDS lysis buffer (0.3% SDS for H3K27ac and 1% SDS for TFs, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes. Nuclei were fragmented on a Q800R2 Sonifier (QSonica) as follows: three cycles of amplitude = 50, pulse times: 30s on / 30s off, total on time = 3:20 m, temperature = 80C (histone marks) or two cycles of amplitude = 70, pulse times: 45s on / 15s off, total on time = 8:50 m, temperature = 40C (TFs). Samples were diluted 1:3 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4°C overnight with 2-5 ug of antibody. Antibody-chromatin complexes were captured with protein G–conjugated beads, washed, and eluted. After reversal of cross-linking, RNase and proteinase K treatment were performed and DNA was purified with Ampure XP beads for library preparation. Input sample was prepared by the same approach without immunoprecipitation.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated (Quick T4 DNA ligase, NEB) to barcoded illumina adaptors (Single-Indexed Adapter Kit, KAPA, #KK8700). Each reaction was followed by clean-up with AMPure XP beads. Ligation products were amplified by PCR for 14-18 cycles with illumina indexing primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection.

tag: cell line

value: Diffuse large B-cell lymphoma cell line

tag: chip antibody


title: FGF_Neurog2_2

city: Planegg-Martinsried

first: Jovica

last: Ninkovic

address: Großhaderner Straße 9

department: Department of Cell Biology and Anatomy III

institute: Biomedical Center (BMC),LMU - Munich

organism: Mus musculus

source_name: Cortex (Grey matter)

value: Cortex (Grey matter)

value: Primary culture

value: Astrocytes

value: Wildtype


title: Visceral_ASC_obese_basal_rep1

description: miRNA expression data from ASCs

value: male


title: S_coelicolor_M512lpm_2d biol rep 2

description:
Library name: S_coelicolor_M512lpm_2d
RNA isolated after 2days of growth from S. coelicolor M512 expressing the liposidomycin gene cluster


title: FGF_Neurog2_1


title: HBL1_input


title: S_coelicolor_M512cpz_4d biol rep 3

description:
Library name: S_coelicolor_M512cpz_4d
RNA isolated after 4days of growth from S. coelicolor M512 expressing the caprazamycin gene cluster

value: SCP1-, SCP2-, DeltaactII-ORF4, DeltaredD containing the caprazamycin gene cluster from S. sp. MK730-62F2, KanR


title: RCK8_input


title: S_coelicolor_M512cpz_2d biol rep 1

description:
Library name: S_coelicolor_M512cpz_2d
RNA isolated after 2days of growth from S. coelicolor M512 expressing the caprazamycin gene cluster


title: Visceral_ASC_obese_differentiated_Ecs_rep1

description: miRNA expression data from ASCs differentiated into Ecs

value: differenciated


title: FGF_Neurog2_Hmgb2_3

value: Neurog2+Hmgb2 overexpression/bFGF


title: U2392_input


title: FGF_Neurog2_Hmgb2_2


title: Subcutaneous_ASC_obese_differentiated_Ecs_rep4

value: Subcutaneous adipose tissue


title: Subcutaneous_ASC_obese_differentiated_Ecs_rep2

value: obese


title: Visceral_ASC_obese_basal_rep2

description: miRNA expression data from ASCs

value: Visceral adipose tissue

value: basal


title: FGF_Neurog2_Hmgb2_1


title: dpf-3(xe68);alg-2(ok304), rep3

city: Québec

first: Louis-Mathieu

last: Harvey

address: 9, rue McMahon

country: Canada

institute: CRCHUQ-UL

description:
Library name: Sample 18
small RNA analysis

data_processing:
The samples are debarcoded
The adaptors are removed and only reads of size >16 are kept
Small RNAs are mapped to genome and cDNA using Bowtie 0.12.7 and at most 2 mismatches are considered
The reads were normalized to the total small RNAs including miRNAs, 22G-RNAs and 21U-RNAs
Assembly: C. elegans WS215
Supplementary files format and content: miRNA Reads Per million

organism: Caenorhabditis elegans

source_name: worm

growth_protocol: Animals were grown on NGM plates with OP50 at 25°C.

extract_protocol:
Total RNA was extracted from young adult animals pellets using Trizol
The extracted RNA was used as input for the NEBNext Multiplex Small RNA Library Kit and size selection is performed for miRNAs on gel (Bands corresponding to ~140 bp)

value: worm

tag: developmental stage

value: Young adult


title: Subcutaneous_ASC_obese_differentiated_Ecs_rep1


title: dpf-3(xe68);alg-2(ok304), rep2

description:
Library name: Sample 17
small RNA analysis


title: Subcutaneous_ASC_obese_differentiated_Ecs_rep3

value: female


title: FGF_Hmgb2_3

value: Hmgb2 overexpression/bFGF


title: dpf-3(xe68);alg-2(ok304), rep1

description:
Library name: Sample 16
small RNA analysis


title: DB_input

source_name: DB

value: DB

value: Diffuse large B-cell lymphoma cell line


title: Karpas422_input


title: alg-2(ok304), rep3

description:
Library name: Sample 15
small RNA analysis

value: alg-2(ok304) II


title: FGF_Hmgb2_2

value: Cortex (Grey matter)

value: Primary culture

value: Astrocytes


title: SUDHL5_input


title: alg-2(ok304), rep2

description:
Library name: Sample 14
small RNA analysis


title: BJAB_input

source_name: BJAB

value: BJAB


title: Subcutaneous_ASC_obese_basal_rep4

description: miRNA expression data from ASCs


title: FGF_Hmgb2_1

value: Wildtype


title: FGF_Control_3

value: Control/bFGF


title: alg-2(ok304), rep1

description:
Library name: Sample 13
small RNA analysis


title: HT_input

source_name: HT

value: HT


title: Subcutaneous_ASC_obese_basal_rep2

description: miRNA expression data from ASCs

value: Subcutaneous adipose tissue

value: obese

value: male


title: Subcutaneous_ASC_obese_basal_rep1

description: miRNA expression data from ASCs

value: basal


title: WSUDLCL2_input


title: dpf-3(xe68);alg-1(gk214), rep3

description: small RNA analysis

value: worm

value: Young adult


title: FGF_Control_2


title: FGF_Control_1


title: dpf-3(xe68);alg-1(gk214), rep2

description: small RNA analysis


title: Subcutaneous_ASC_obese_basal_rep3

description: miRNA expression data from ASCs

value: female


title: U2392_H3K27ac_ChIP-Seq

value: H3K27ac (Active Motif, Cat #39133)


title: Subcutaneous_ASC_lean_differentiated_Ecs_rep3

value: lean

value: differenciated


title: Subcutaneous_ASC_lean_differentiated_Ecs_rep4


title: EGF_FGF_Hmgb2_4

value: Cortex (Grey matter)

value: Hmgb2 overexpression/EGF+bFGF


title: dpf-3(xe68);alg-1(gk214), rep1

description: small RNA analysis


title: TMD8_H3K27ac_ChIP-Seq

value: Diffuse large B-cell lymphoma cell line


title: Subcutaneous_ASC_lean_differentiated_Ecs_rep2


title: alg-1(gk214), rep3

description: small RNA analysis


title: SUDHL5_H3K27ac_ChIP-Seq


title: EGF_FGF_Hmgb2_3

value: Primary culture

value: Astrocytes


title: EGF_FGF_Hmgb2_2

value: Wildtype


title: alg-1(gk214), rep2

description: small RNA analysis


title: RCK8_H3K27ac_ChIP-Seq


title: EGF_FGF_Neurog2_Hmgb2_3

value: Neurog2+Hmgb2 overexpression/EGF+bFGF


title: Subcutaneous_ASC_ lean_basal_rep4

description: miRNA expression data from ASCs

value: Subcutaneous adipose tissue


title: Subcutaneous_ASC_ lean_basal_rep3

description: miRNA expression data from ASCs


title: alg-1(gk214), rep1

description: small RNA analysis


title: EGF_FGF_Hmgb2_1


title: EGF_FGF_Neurog2_Hmgb2_2


title: dpf-3(xe68), rep2

description: small RNA analysis

value: dpf-3(xe68) I


title: Subcutaneous_ASC_ lean_basal_rep2

description: miRNA expression data from ASCs

value: male


title: Subcutaneous_ASC_lean_differentiated_Ecs_rep1


title: H3K4me3_FL_HH24_galGal6_WT_Rep2

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health

data_processing:
Tn5 adaptor sequences were trimmed using cutadapt (--minimum-length 20 --quality-cutoff 20)
Reads were aligned to appropriate genome builds using bowtie2 ( --very-sensitive -X 700)
Duplicates were removed using Picard v2.23.4. Unmapped, low quality reads (MAPQ < 10), and chromosomal reads were removed with samtools
Assembly: mouse: mm39, chicken: galGal6
Supplementary files format and content: bigWig profiles of normalized counts (CPM) were generated using deeptools v3.5.4 (Ramírez, Fidel, et al., 2016).

organism: Gallus gallus

source_name: FL

extract_protocol:
Cells were fixed with 1% MeOH-free formaldehyde for 10min, quenched with glycine and lysed with lysis buffer (10mM Tris pH 8.0, 100mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA, 0.1% Sodium deoxycholate, 0.5% N-lauroylsarcosine). DNA was sheared to 200-700bp using a Covaris E220. Antibodies were incubated overnight at 4C. Bound DNA was precipitated with protein G beads, cleaned up and tagmented with Tn5 for 5min at 37C. Reverse cross-linking was done with Proteinase K, and cleaned up using the MinElute Reaction Cleanup kit (Qiagen).
Libraries were amplified with dual indexing Nextera primers, followed by purification and appropriate size-selection using AmPureXP beads
ChIPmentation

treatment_protocol: dissected embryonic hearts are dissociated with Trypsin/EDTA for 10 minutes (FL) or 15 minutes (heart) to get single-cell suspension. dissociated cells were filtered through a 100µm (embryonic heart) or 70µm (limb) MACS® SmartStrainer

value: FL

value: WT


title: Subcutaneous_ASC_ lean_basal_rep1

description: miRNA expression data from ASCs

value: basal


title: HT_H3K27ac_ChIP-Seq

value: HT


title: H3K4me3_FL_HH22_galGal6_WT_Rep1


title: WSUDLCL2_H3K27ac_ChIP-Seq

value: H3K27ac (Active Motif, Cat #39133)


title: BJAB_H3K27ac_ChIP-Seq

value: BJAB


title: HBL1_H3K27ac_ChIP-Seq


title: N2, rep3

description: small RNA analysis

value: worm

value: Young adult

value: N2 (Bristol)


title: H3K4me1_FL_HH24_galGal6_WT_Rep2


title: WSUDLCL2_ATAC-seq

data_processing:
Paired-end reads were aligned to hg19 using BWA-ALN (v 0.7.17).
Bam files were filtered (samtools view) to retain only paired reads in a proper pair (flags: 0x1, 0x2), and to remove reads flagged as secondary alignments, not passing quality control, PCR or optical duplicates, and supplementary alignments (flags: 0x100, 0x200, 0x400, 0x800).
Reads were filtered to retain only read-pairs mapping to <=2 sites genome-wide (X0 tag <=2 for both reads).
Display files were generated with deeptools bamCoverage (options: "--binSize 25 --normalizeUsing CPM --extendReads")
Assembly: hg19
Supplementary files format and content: bigwig (hg38 fragment coverage, normalized to fragments per million post-filtering)

extract_protocol:
Nuclei were isolated from 50,000 cells for each sample using Nuclei EZ prep-Nuclei Isolation Kit (Sigma-Aldrich, USA). The transposition reaction mix (25μl of 2X TD buffer, 2.5μl of Tn5 transposase (Illumina, San Diego, CA, USA), 15ul of PBS and 7.5μl of nuclease free water) was added to nuclei and incubated at 37°C for 1hour in an orbital shaker at 300RPM. 50uL Qiagen buffer PB was added to each sample to stop the reaction and DNA was isolated with AMPure XP beads (Beckman Coulter).
15 cycles of PCR were performed with transposed DNA using the dual index primers and NEBNext PCR Master Mix, followed by AMPure XP purification.

value: Diffuse large B-cell lymphoma cell line


title: DB_H3K27ac_ChIP-Seq

value: DB


title: dpf-3(xe68), rep3

description: small RNA analysis


title: EGF_FGF_Neurog2_Hmgb2_1

value: Cortex (Grey matter)

value: Primary culture

value: Astrocytes


title: EGF_FGF_Neurog2_2

value: Wildtype

value: Neurog2 overexpression/EGF+bFGF


title: H3K4me3_FL_HH24_galGal6_WT_Rep1


title: EGF_FGF_Neurog2_3


title: dpf-3(xe68), rep1

description: small RNA analysis

value: dpf-3(xe68) I


title: H3K4me1_FL_HH24_galGal6_WT_Rep1

value: FL


title: U2392_ATAC-seq


title: H3K4me1_FL_HH22_galGal6_WT_Rep1

value: WT


title: N2, rep2

description: small RNA analysis


title: N2, rep1

description: small RNA analysis


title: TMD8_ATAC-seq


title: H3K27ac_FL_HH24_galGal6_WT_Rep2


title: H3K27ac_FL_HH24_galGal6_WT_Rep1


title: MFh6_rep2

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Koyto Univ.

data_processing:
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.6.6), Trimmomatic (ver. 0.39) and cutadapt (ver. 3.1) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.104) using STAR (ver. 2.7.9b).
The read count of gene features was performed with the featureCounts tool (ver. 2.0.1)
Assembly: ce11
Supplementary files format and content: txt
Supplementary files format and content: tab-delimited text files include featureCount values for each sample

source_name: Whole

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Clontech)

treatment_protocol: Three-day-old worms were cultured for six hours on mNGM plates covered with OP50 (control group) or M. furfur.

value: Whole

value: Bristol N2

value: wild-type

value: feeding M. furfur


title: EGF_FGF_Control_3

value: Control/EGF+bFGF


title: EGF_FGF_Control_2


title: HT_ATAC-seq

value: HT


title: H3K4me3_heart_HH24_galGal6_WT_Rep2

source_name: heart

value: heart


title: OPh6_rep2

value: feeding OP50


title: MFh6_rep1


title: RCK8_ATAC-seq

value: Diffuse large B-cell lymphoma cell line


title: H3K27ac_FL_HH22_galGal6_WT_Rep1


title: HBL1_ATAC-seq


title: DB_ATAC-seq

value: DB


title: H3K4me3_heart_HH22_galGal6_WT_Rep2


title: H3K4me3_heart_HH24_galGal6_WT_Rep1


title: spleen, 24 h experimental treatment S. iniae challenge, striped bass, rep5

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

description:
sb_strep_t24h_5
sb-strep-counts.txt

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using  FastQC (v.0.11.9) and Trimmomatic (v.0.38). This was used to trim low-quality ends from reads and for Illumina adapter removal.
All reads were filtered for the removal of 18S, 5.8S, and 28S sequences using the STAR Gapped Mapper (v.2.7.8a) and Samtools (v.1.12) for alignment of sequences to the Morone 18S, 5.8S, and 28S sequences available on GenBank and output of unaligned reads used for subsequent analysis. This was completed as QC indicated the sequence reads for WB_t01h_5 had high alignment (44.46%) to these sequences. This individual was dropped from subsequent analysis.
The STAR Gapped Mapper (v.2.7.8a) and Samtools (v.1.12) were used to align all filtered reads generated for the other 47 samples to the respective SB or WB reference transcriptomes using default parameters.
Read-counts were generated using the default parameters of HTSeq (v.0.9.0).
Gene expression fold-changes were determined between groups were determined in a pairwise fashion using edgeR (v.4.0.16) with TMM (Weighted trimmed mean of M-values) as the normalization method, Generalized Linear Model (GLM) Quasi Likelihood F-Test,  and “robust” filter to strengthen estimations against potential outliers.
Assembly: The reference SB transcriptome was built from the protein-coding sequences available on NCBI associated with the current reference genome (GCF_004916995.1; NCSU_SB_2.0). The WB reference transcriptome is a shotgun assembly built from the sequence data available in GenBank GAZY00000000.1 (GAZY01000001-GAZY01183659).
Supplementary files format and content: tab-deliminated text files of read counts representing the total number of reads aligned to each genomic feature for striped bass (sb-strep-counts.txt) and white bass (wb-strep-counts.txt).

organism: Morone saxatilis

source_name: spleen

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
RNA library preparation, sequencing and data analysis were conducted at Azenta Life Sciences (South Plainfield, NJ, USA) as follows: Total RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis match was allowed for index sequence identification.

treatment_protocol: Striped bass (SB) and white bass (WB) in the control group (t00h) were given a mock saline treatment via intraperitoneal (IP) injection and sampled immediately prior to fish in experimental aquaria being challenged with 100 uL of Streptococcus iniae isolate ARS 98-60 via IP injection. Fish were observed twice daily for the recording and removal of any dead or moribund fish, and fish were formally sampled at three timepoints after the challenge had been initiated, 1 hour post treatment (t01h), 4 hours post treatment (t04h), and 24 hours post treatment (t24h).

tag: animal

value: striped bass (SB)

value: spleen

value: Streptococcus iniae intraperitoneal injection

tag: time

value: 24 h after bacteria treatment


title: EGF_FGF_Neurog2_1

value: Cortex (Grey matter)

value: Primary culture

value: Astrocytes

value: Wildtype

value: Neurog2 overexpression/EGF+bFGF


title: H3K4me3_heart_HH22_galGal6_WT_Rep1

value: WT


title: SUDHL5_ATAC-seq


title: Short-term HFD mouse 146 [H146]

city: Aberdeen

first: Elaina

last: Collie-Duguid

address: 23 St Machar Drive

country: United Kingdom

institute: University of Aberdeen

description: allsamplescounts.txt

data_processing:
Processed in Illumina Basespace (4.1.0)
Reads trimmed with Illumina Basespace app FASTQ Toolkit (2.0.0) to remove reads with phred score <20 and length <20nt and to remove adapter sequences
Aligned to mm10 Mus musculus genome using STAR (2.0) aligner
Differential expression analysis using DESeq2 (1.6)
Assembly: mm10
Supplementary files format and content: matrix txt file containing counts for every sample: matrix column names listed in M33-M48.

source_name: liver

extract_protocol:
RNA was extracted using TriReagent and chloroform.  1µg of RNA was used to construct each library.
Sequencing libraries were prepared using the TruSeq stranded total RNA with Ribo-zero (RS-122-2301) following the low sample protocol.

treatment_protocol: Male C57BL/6J wild-type mice were fed HFD supplemented +/- 0.04% fenretinide for 7 days (short-term) or 20 weeks (long-term). Mice were killed by cardiac exsanguination under CO2-induced anaesthesia, liver removed and flash frozen in liquid nitrogen and stored at -80oC until processed. For downstream analysis, groups were analysed by pairwise comparison.

value: liver

tag: Sex

value: Male

value: C57BL/6J wild-type

value: 7 days 45% HFD


title: H3K4me1_heart_HH24_galGal6_WT_Rep2

value: heart


title: A549-siATF5-2

city: Sapporo

first: Hisashi

last: Haga

address: Kita-10 Nishi-8, Kita-ku

institute: Hokkaido University

hyb_protocol: Biotynylated cDNA were hybridized on Clariom™ S Array, Human with Hybridization Oven 645, Affymetrix, Inc. GeneChips  were washed with GeneChip™ Hybridization, Wash, and Stain Kit and stained in the Fluidics Station 450、Affymetrix, Inc.

scan_protocol: GeneChips were scanned using the Scanner 3000 7G, Affymetrix, Inc.

data_processing: The data were analyzed with GeneChip® Command Console and Transcriptome Analysis Console with SST-RMA for normalization (Thermo Fisher Scientific Inc.).

source_name: A549 cells with siATF5-2 cultured on stiff matrix

label_protocol: Following cDNA synthesis and fragmentation of 5.5 ug total cDNA, biotinylated cDNA were prepared.

growth_protocol: KP4 or A549 cells (5x10^4 cells) were seeded on 0.5 mL of collagen gels in 35 mm plastic dishes or collagen-coated 35 mm plastic dishes and cultured for 48 h.

extract_protocol: For KP4-stiff, KP4-soft, A549-stiff, A549-soft samples, we extracted RNA with TriPure Isolation Reagent (11667165001, Roche) followed by purification with Fast Gene RNA Premium kit (FG-81050, NIPPON Genetics). On other cases, RNA was extracted by FastGene RNA Basic Kit (FG-80250, NIPPON Genetics).

treatment_protocol: KP4 or A549 cells were transfected with 8 pmol siRNA or a NC non-targeting RNA duplex via the Lipofectamine RNAiMAX Transfection Reagent (13778150, Invitrogen). After 24 h, the cells were harvested, seeded on collagen-coated plastic or glass dishes.

value: with siATF5-2 cultured on stiff matrix


title: BJAB_ATAC-seq

value: BJAB

value: Diffuse large B-cell lymphoma cell line


title: spleen, 24 h experimental treatment S. iniae challenge, striped bass, rep3

description:
sb_strep_t24h_3
sb-strep-counts.txt

value: striped bass (SB)

value: spleen


title: spleen, 24 h experimental treatment S. iniae challenge, striped bass, rep4

description:
sb_strep_t24h_4
sb-strep-counts.txt

value: Streptococcus iniae intraperitoneal injection

value: 24 h after bacteria treatment


title: Short-term HFD mouse 144 [H144]

description: allsamplescounts.txt


title: EGF_FGF_Control_1

value: Cortex (Grey matter)

value: Primary culture

value: Control/EGF+bFGF


title: H3K4me1_heart_HH24_galGal6_WT_Rep1


title: OPh6_rep1

value: Whole

value: Bristol N2

value: wild-type

value: feeding OP50


title: A549-siATF5-1

source_name: A549 cells with siATF5-1 cultured on stiff matrix

value: with siATF5-1 cultured on stiff matrix


title: spleen, 24 h experimental treatment S. iniae challenge, striped bass, rep1

description:
sb_strep_t24h_1
sb-strep-counts.txt


title: H3K4me1_heart_HH22_galGal6_WT_Rep2

value: WT


title: H3K4me1_heart_HH22_galGal6_WT_Rep1

value: heart


title: Short-term HFD mouse 142 [H142]

description: allsamplescounts.txt

value: liver

value: Male

value: C57BL/6J wild-type

value: 7 days 45% HFD


title: KP4-siATF5-2

source_name: KP4 cells with siATF5-2 cultured on stiff matrix

value: with siATF5-2 cultured on stiff matrix


title: spleen, 24 h experimental treatment S. iniae challenge, striped bass, rep6

description:
sb_strep_t24h_6
sb-strep-counts.txt

value: striped bass (SB)

value: spleen

value: Streptococcus iniae intraperitoneal injection


title: spleen, 24 h experimental treatment S. iniae challenge, striped bass, rep2

description:
sb_strep_t24h_2
sb-strep-counts.txt

value: 24 h after bacteria treatment


title: Long-term HFD mouse 45 [H45]

description: allsamplescounts.txt

value: 20 weeks 45% HFD


title: KP4-siATF5-1

source_name: KP4 cells with siATF5-1 cultured on stiff matrix


title: spleen, 4 h experimental treatment S. iniae challenge, striped bass, rep6

description:
sb_strep_t04h_6
sb-strep-counts.txt

value: 4 h after bacteria treatment


title: H3K27ac_heart_HH24_galGal6_WT_Rep2


title: KP4-NC

source_name: KP4 cells with NC RNA cultured on stiff matrix

value: with NC RNA cultured on stiff matrix


title: Long-term HFD mouse 33 [H33]

description: allsamplescounts.txt


title: spleen, 4 h experimental treatment S. iniae challenge, striped bass, rep5

description:
sb_strep_t04h_5
sb-strep-counts.txt


title: H3K27ac_heart_HH24_galGal6_WT_Rep1


title: spleen, 4 h experimental treatment S. iniae challenge, striped bass, rep4

description:
sb_strep_t04h_4
sb-strep-counts.txt


title: A549-NC

source_name: A549 cells with NC RNA cultured on stiff matrix


title: Long-term HFD mouse 28 [H28]

description: allsamplescounts.txt


title: H3K27ac_heart_HH22_galGal6_WT_Rep2


title: AAA

city: Toronto

first: Clinton

last: Robbins

state: ON

address: 101 College Street

institute: UHN

description:
Library name: Sample 3
ApoE-/-, cigarette smoke exposed with measureable aortic dilatation, 16 weeks HFD

library_source: transcriptomic single cell

data_processing:
The sequenced data was processed into expression matrices with the Cell Ranger Single Cell Software Suite 2.2.0 by 10X Genomics (http://10xgenomics.com/).
Raw base call files from HiSeq2500 sequencer were demultiplexed into library specific FASTQ files.
Sequencing reads were aligned to the mouse transcriptome using STAR aligner
Subsequently, cell barcodes and Unique Molecular Identifiers (UMIs), underwent filtering and correction.
Reads associated with the retained barcodes were quantified and used to build a transcript count table.
Assembly: mm10
Supplementary files format and content: Barcode, genes and expression matrix

source_name: Aorta

growth_protocol: ApoE-/- mice were exposed to room air or cigarette smoke and fed a high fat diet for 16 weeks. C57Bl/6 control was chow fed

extract_protocol:
A total of 5159 cells from three different experimental groups (Naïve: 738, Room Air: 1736, Smoke: 584, and Aneurysm: 2685) were analyzed. Viability for the samples were as follows: Naïve (73%), RA (91%), Aneurysm (94%). Following counting, the appropriate volume for each sample was calculated for a target capture 2000-4000 cells. Samples below the required cell concentration as defined by the user guide (i.e., <400 cells/µl) were pelleted and re-suspended in a reduced volume and counted again using a haemocytometer prior to loading onto the 10x Genomics single-cell-A chip.
Libraries were prepared as outlined in the 10x Genomics Single Cell 3′ v2 Reagent Kit user guide
Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles. Samples were sequenced to a read depth of ~60,000 reads/cell and run through the 10X Genomics cell ranger platform.

treatment_protocol: C57BL/6 mice (n=5, control), Apoe-/- mice exposed room air (n=5, Room Air) and Apoe-/- mice exposed to cigarette smoke that developed measurable aneurysms (n=4, Aneurysm). Apoe-/- mice were on a Western diet and exposed to cigarette smoke for 16 weeks. Suprarenal aortas were isolated and pooled for each group and total CD45+CD31- and CD45-CD31+ cells were FACS sorted using the MoFlo Astrios BRVY.

value: Aorta

value: CD45+ leukocytes


title: A549-stiff

source_name: A549 cells cultured on stiff matrix

value: cultured on stiff matrix


title: Short-term HFD mouse 143 [H143]

description: allsamplescounts.txt


title: Long-term HFD mouse 25 [H25]

description: allsamplescounts.txt


title: H3K27ac_heart_HH22_galGal6_WT_Rep1

value: WT


title: spleen, 4 h experimental treatment S. iniae challenge, striped bass, rep3

description:
sb_strep_t04h_3
sb-strep-counts.txt


title: KP4-soft

source_name: KP4 cells cultured on soft matrix

value: cultured on soft matrix


title: spleen, 4 h experimental treatment S. iniae challenge, striped bass, rep2

description:
sb_strep_t04h_2
sb-strep-counts.txt


title: RA

description:
Library name: Sample 2
ApoE-/-, room air exposed, 16 weeks HFD


title: HiC_heart_HH22_galGal6_WT_Rep2

data_processing:
Pair-end reads were aligned using BWA mem v0.7.17 to reference genome
Chimeric reads handling, filtering, removal of duplicates and contact matrices were generated using Juicer v1.6.0 CPU version (Durand et al 2016)
Assembly: galGal6
Supplementary files format and content: hic

extract_protocol:
~1 million cells per replicate were fixed in 2% formaldehyde, lysed and digested with DpnII. Digested ends were marked with biotin-14-dATP. After reverse cross-linking, DNA was sheared to 300-600bp fragment size.
Biotinylated junctions were enriched using Streptavidin T1 beads. Fragments were ends-repaired before adaptor ligation and indexing via PCR amplification. Purification and size selection were carried out using AMPure XP beads
Modified in-situ Hi-C protocol (Melo, U. S. et al. 2020)

treatment_protocol: dissected embryonic hearts were dissociated with Trypsin/EDTA for 15 minutes to get single-cell suspension. dissociated cells were filtered through a 100µm MACS® SmartStrainer

value: heart


title: Short-term FEN-HFD mouse 66 [F66]

description: allsamplescounts.txt

value: liver

value: Male

value: 7 days 45% HFD + 0.04% Fenretinide


title: KP4-stiff

source_name: KP4 cells cultured on stiff matrix


title: HiC_heart_HH22_galGal6_WT_Rep1


title: Control

description:
Library name: Sample 1
C57Bl/6 fed a chow diet


title: spleen, 1 h experimental treatment S. iniae challenge, striped bass, rep6

description:
sb_strep_t01h_6
sb-strep-counts.txt

value: 1 h after bacteria treatment


title: Short-term FEN-HFD mouse 62 [F62]

description: allsamplescounts.txt

value: C57BL/6J wild-type


title: ATAC-seq_FL_HH24_galGal6_WT_Rep2

data_processing:
Tn5 adaptor sequences were trimmed using cutadapt (--minimum-length 20 --quality-cutoff 20)
Reads were aligned to appropriate genome builds using bowtie2 ( --very-sensitive -X 1000)
Duplicates were removed using Picard v2.23.4. Unmapped, low quality reads (MAPQ < 10), and chromosomal reads were removed with samtools
bigWig profiles of normalized counts (CPM) were generated using deeptools v3.5.4 (Ramírez, Fidel, et al., 2016).
Assembly: mouse: mm39, chicken: galGal6
Supplementary files format and content: bigWig

extract_protocol:
50.000 cells were lysed for nuclei, and used for each reaction of tagmentation as previously described for Omni-ATAC (Corces, M., Trevino, A., Hamilton, E. et al. 2017). Tagmented DNA were purified using MinElute Reaction Cleanup kit.
Libraries were amplified with dual indexing Nextera primers, followed by purification and double size-selection using AmPureXP beads

value: FL


title: A549-soft

source_name: A549 cells cultured on soft matrix


title: Cigarette Smoke no AAA

description: Library name: 2CS

data_processing:
The sequenced data was processed into expression matrices with the Cell Ranger software (version 2.2.0) from 10X Genomics (http://10xgenomics.com/).
Raw base call files from HiSeq2500 sequencer were demultiplexed into library specific FASTQ files.
Sequencing reads were aligned to the mouse transcriptome using STAR aligner.
Subsequently, cell barcodes and Unique Molecular Identifiers (UMIs) underwent filtering and correction.
Reads associated with the retained barcodes were quantified and used to build a transcript count table.
Assembly: mm10
Supplementary files format and content: Raw and filtered Barcode, features and expression matrix

molecule: nuclear RNA

growth_protocol: ApoE-/- mice were exposed to room air or cigarette smoke and fed a high fat diet for 20 weeks.

extract_protocol:
Nuclei were isolated using 10x Genomics’ Chromium Nuclei Isolation Kit (10x Genomics, cat. no. 1000493) lysis buffer with the debris removal substituted by the Miltenyi Anti-Nucleus beads. Frozen tissue pieces were weighed on dry ice before transferring into a petris dish. 500ul of Lysis buffer comprised of Lysis Reagent (10x Genomics, cat. no. 2000558), Reducing Agent B (10x Genomics, cat. no. 2000087), and Surfactant A (10x Genomics, cat. no. 2000559) was added to the frozen tissue on ice. The tissue was chopped into smaller pieces with tissue scissors and then transferred to a 2ml glass douncer (Millipore Sigma, cat. no D8938). 8 strokes with the loose pestle A was required to fully dissociate the tissue. The total lysis time was 5 minutes. After dissociation, 500ul of lysate was transferred to the Nuclei Isolation Column (10x Genomics, cat. no. 2000562) and spun at 16,000 rcf for 20 seconds at 4C to remove leftover tissue. Following the centrifugation, the sample was vortexed for 10 seconds at 3000 rpm. An aliquot from the lysate was used to calculate the nuclei numbers using a 1:1 dilution with AOPI. This count was used to calculate the volume of buffer to resuspend the nuclei. The sample was spun at 500 rcf for 3 min at 4C. The supernatant was removed and the nuclei pellet was resuspended in Nuclei Separation buffer composed of Nuclei Extraction buffer (Miltenyi Biotec, cat. no. 130-128-024), PBS, BSA and Rnase Inhibitor (Millipore Sigma, cat. no. 3335402001). Miltenyi Anti-nucleus beads (Cat. No.130-132-997) were then added to the sample; 50ul for each million nuclei. The nuclei were incubated with the beads for 15 minutes on ice after which an additional 2ml of the Nuclei Separation buffer was added to the sample. Then the sample was passed through a LS column (Miltenyi Biotec, cat. no.130-042-401) attached to the MACS MultiStand (Miltenyi Biotec, cat. no. 130-042-303) with QuadroMACS separator (Miltenyi Biotec, cat. no. 130-042-302). The column was then washed twice with 1ml of the Nuclei Separation buffer. After the washes, the column was placed on a 15ml collection tube and 1ml of the Nuclei Separation buffer was added into the column and plunged into the tube. The purified nuclei were spun at 500 rcf for 5 minutes. The supernatant was removed and the nuclei pellet was washed with Wash Buffer comprised of 1x PBS, 10% BSA and RNase Inhibitor. The nuclei suspension was centrifuged at 4C for 5 min at 500 rcf and the nuclei pellet was resuspended in wash buffer. Nuclei counting was done using a 1:1 dilution with AOPI on a haemocytometer (Thermo Fisher, cat. no. 22-600-100). Following counting, the appropriate volume for each sample was calculated for a target capture of 20,000 cells and then the nuclei were loaded onto 10x 3’ GEM X chip. After droplet generation, samples were transferred to a pre-chilled strip tube (USA Scientific, US14024700), and incubated in a Bio-Rad thermos cycler. Sample cDNA was recovered using Recovery Agent provided by 10x and subsequently cleaned up using a Silane DynaBead (Thermo Fisher) mix as outlined by the user guide Chromium GEM-X Single Cell 3’ Reagent Kits v4.
Purified cDNA was amplified for 11 cycles before being cleaned up using SPRIselect beads (Beckman Coulter). Samples were run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Chromium GEM-X Single Cell 3’ Reagent Kits v4 user guide with modifications to the PCR cycles based on the calculated cDNA concentration.
The molarity of each library was calculated based on library size as measured bioanalyzer (Agilent Technologies) and qPCR amplification data (Roche, cat. no. 07960140001). Gene Expression libraries were sequenced on Illumina’s NovaSeqX with the following run parameters: read 1 – 28 cycles, read 2 – 90 cycles, index 1 – 10 cycles and index 2 – 10 cycles.

treatment_protocol: Following euthanasia, the abdominal aorta was extracted and slow-frozen using a Mr. Frosty

value: total cells

value: ApoE-/-


title: spleen, 1 h experimental treatment S. iniae challenge, striped bass, rep5

description:
sb_strep_t01h_5
sb-strep-counts.txt

value: striped bass (SB)

value: spleen

value: Streptococcus iniae intraperitoneal injection


title: Short-term FEN-HFD mouse 61 [F61]

description: allsamplescounts.txt


title: spleen, 1 h experimental treatment S. iniae challenge, striped bass, rep4

description:
sb_strep_t01h_4
sb-strep-counts.txt


title: Long-term FEN-HFD mouse 29 [F29]

description: allsamplescounts.txt

value: 20 weeks 45% HFD + 0.04% Fenretinide


title: spleen, 1 h experimental treatment S. iniae challenge, striped bass, rep3

description:
sb_strep_t01h_3
sb-strep-counts.txt


title: infected tomato+ GC+ B cells 21 days after influenza infection NT, NALT and cLN VDJ

city: Goteborg

first: Davide

last: Angeletti

address: Medicinaregatan 7a

country: Sweden

institute: University of Gothenburg

description:
Library name: NTseqVDJ
10x genomics 5´ v2

data_processing:
Raw fastq files were processed through the 10x cellranger pipeline  with reference genome mm10.
Assembly: mm10
Supplementary files format and content: tab separated value files, matrix files and filtered contig files

source_name: nasal tissue + NALT+ cLN

extract_protocol:
The sorted cells were individually tagged, pooled and washed before loading to Chromium Controller and using the Chromium Next GEM Single Cell 5´ Kit v2 (10x Genomics).
Libraries were created using the Library Construction Kit, 5´Feature Barcode Kit, Chromium Single Cell Mouse BCR Amplification Kit, Dual Index Kit TT Set A (PN-1000215) and Dual Index Kit TN Set A (PN-1000250) (10x Genomics) ).Their quality and quantity was assessed using the Agilent Tapestation system and the Qubit Fluorometer (Invitrogen), before being sent for sequencing to the SNP&SEQ Technology Platform, Science for Life Laboratory (Uppsala Biomedical Centre, Uppsala University, Sweden).

treatment_protocol: Mice were infected with Pr8 i.n. at 21dpi mice were sacrificed and nasal tissue, NALT and cervical lymph nodes were isolated, digested and processed.

value: nasal tissue + NALT+ cLN

value: GC B cell

tag: immunophenotype

value: B220+ GL7+ Tomato+ IgD- CD38-

tag: age

value: 8-12 weeks

tag: number of_mice

value: 8 infected

value: influenza A virus PR8 21dpi

tag: hashtags

value: nasal tissue (TotalSeq-C0301 anti-mouse Hashtag 1).  ; NALT (TotalSeq-C0302 anti-mouse Hashtag 2). Cervical lymph node (TotalSeq-C0303 anti-mouse Hashtag 3).


title: Long-term FEN-HFD mouse 24 [F24]

description: allsamplescounts.txt

tag: tissue

value: liver

value: Male

tag: genotype


title: Room Air Control

description: Library name: 1RA

value: Aorta


title: spleen, 1 h experimental treatment S. iniae challenge, striped bass, rep2

description:
sb_strep_t01h_2
sb-strep-counts.txt

value: 1 h after bacteria treatment


title: ATAC-seq_heart_HH24_galGal6_WT_Rep2

value: heart

value: WT


title: ATAC-seq_FL_HH22_galGal6_WT_Rep1

source_name: FL

value: FL


title: infected tomato+ GC+ B cells 21 days after influenza infection NT, NALT and cLN CSP

description:
Library name: NTseqCSP
10x genomics 5´ v2


title: Long-term FEN-HFD mouse 22 [F22]

description: allsamplescounts.txt

value: C57BL/6J wild-type


title: Short-term FEN-HFD mouse 65 [F65]

description: allsamplescounts.txt

value: 7 days 45% HFD + 0.04% Fenretinide


title: Long-term FEN-HFD mouse 21 [F21]

description: allsamplescounts.txt

value: 20 weeks 45% HFD + 0.04% Fenretinide


title: infected tomato+ GC+ B cells 21 days after influenza infection NT, NALT and cLN

description:
Library name: NTseqGEX
10x genomics 5´ v2

value: nasal tissue + NALT+ cLN


title: Cigarette Smoke AAA

description: Library name: 3CSAAA

value: total cells

value: ApoE-/-


title: spleen, 4 h experimental treatment S. iniae challenge, striped bass, rep1

description:
sb_strep_t04h_1
sb-strep-counts.txt

value: striped bass (SB)

value: spleen

value: Streptococcus iniae intraperitoneal injection

value: 4 h after bacteria treatment


title: spleen, 1 h experimental treatment S. iniae challenge, striped bass, rep1

description:
sb_strep_t01h_1
sb-strep-counts.txt


title: spleen, 0 h control treatment S. iniae challenge, striped bass, rep6

description:
sb_strep_t00h_6
sb-strep-counts.txt

value: control saline intraperitoneal injection

value: 0 hr after control treatment


title: Forelimb, E11.5, H3K4me3, biol rep 1, ChIP

city: Seville

first: Ismael

last: Sospedra-Arrufat

address: Carretera de Utrera km1, UPO

institute: CABD

description: ChIPmentation

data_processing:
Basecalling was performed using FastQC 0.11.9
Pig ChIP-seq libraries were sequenced 50-bp paired-end, except for H3K4me1. This last, together with mouse libraries were sequenced 100-bp paired-end reads, and subsequently cropped to 50-bp from 3' end with Trimmomatic 0.39.
Paired-end reads were aligned to GRCm38/mm10 mouse assembly or susScrofa11.1/susScr11 pig assembly using Bowtie2 2.3.5.
SAM to BAM conversions were performed using Samtools 1.9 with read deduplication using the ‘rmdup’ command.
BAM to BigWig conversions were performed using bamCoverage tool from Deeptools 3.5 toolkit, with the normalization option set for ‘RPKM’ (Reads Per Kilobase per Million mapped reads).
Peakcalling was performed using the IDR framework (idr 0.1 version) on BED files from biological replicate pairs, with a global IDR <0.01 cut-off, and ‘broad’ peaks parameters.
Assembly: Mouse GRCm38/mm10 or pig SusScrofa11.1/susScr11
Supplementary files format and content: BigWig, BED.

source_name: Forelimb

growth_protocol: Wild-type mouse and pig embryos were generated by natural matting and collected on desired gestational day.

extract_protocol:
Nuclei homogenization was performed mechanically and chromatin crosslinking at 1% formaldehyde for 5 min at RT. Chromatin was sonicated (300-500 bp DNA smear) using a Covaris M220 sonicator.
ChIP-seq libraries were generated using NEBNext High-Fidelity 2x PCR Master Mix (NEB). The optimum number for enrichment cycles for each library was determined empirically by qPCR, using the same kit, and 1 μL of each ChIP per 10 μL reaction. DNA concentration was quantified by Qbit (Invitrogen).

value: Forelimb

value: wild-type

tag: Stage

value: anti-H3K4me3 (Abcam ab8580)

tag: replicate


title: FoMV_ZmH2B_3

city: Beijing

first: Ying

last: Ding

address: No.2 Yuanmingyuan West Road, Haidian

country: China

institute: Chinese Academy of Agricultural Sciences

description: Library name: FoMV_ZmH2B_3

data_processing:
The raw reads were filtered using ht2-filter in the HTQC package (1.92.1) with default parameters to remove low-quality reads. The filtered reads were compared to the reference maize genome (Zea mays RefGen_V4) using TopHat (2.0.11) to remove host genome sequences. The mapped reads were assembled, and fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks.
Assembly: Zea mays

organism: Zea mays

source_name: leaves

extract_protocol:
RNA was extracted using Trizol reagent
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.

value: leaves


title: ATAC-seq_heart_HH24_galGal6_WT_Rep1

source_name: heart

value: heart

value: WT


title: Forelimb, E11.5, H3K4me3, biol rep 2, ChIP

description: ChIPmentation


title: ATAC-seq_heart_HH22_galGal6_WT_Rep2


title: FoMV_ZmH2B_2

description: Library name: FoMV_ZmH2B_2


title: spleen, 0 h control treatment S. iniae challenge, striped bass, rep5

description:
sb_strep_t00h_5
sb-strep-counts.txt

source_name: spleen


title: FoMV_ZmH2B_1

description: Library name: FoMV_ZmH2B_1


title: spleen, 0 h control treatment S. iniae challenge, striped bass, rep4

description:
sb_strep_t00h_4
sb-strep-counts.txt


title: Forelimb, E11.5, H3K4me1, biol rep 2, ChIP

description: ChIPmentation

value: anti-H3K4me1 (Abcam ab8895)


title: ATAC-seq_FL_HH24_galGal6_WT_Rep1

value: FL


title: ATAC-seq_heart_HH22_galGal6_WT_Rep1


title: ATAC-seq_FL_HH22_galGal6_WT_Rep2


title: RNA-seq_heart_HH24_galGal6_WT_Rep2

data_processing:
Paired-end reads were aligned and quantified using STARv2.7.9a using reference genome sequences and annotations from GENCODE (vM32, primary) for mouse and Ensembl (GRCg7b) for chicken
Gene-level counts were obtained for each sample with --quantMode geneCounts
bigWig profiles of normalized counts (RPKM) were generated using deeptools v3.5.4 (Ramírez, Fidel, et al., 2016).
Assembly: galGal6
Supplementary files format and content: bigWig

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy-Mini Kit.
Ribosomal RNA was depleted before stranded library preparation with Kapa HyperPrep Kit

treatment_protocol: dissected embryonic hearts are dissociated with Trypsin/EDTA for 15 minutes to get single-cell suspension. dissociated cells were filtered through a 100µm MACS® SmartStrainer before snapfrozen in liquid nitrogen


title: RNA-seq_heart_HH24_galGal6_WT_Rep1


title: spleen, 0 h control treatment S. iniae challenge, striped bass, rep2

description:
sb_strep_t00h_2
sb-strep-counts.txt


title: Forelimb, E11.5, H3K27ac, biol rep 2, ChIP

description: ChIPmentation

value: anti-H3K27ac (Abcam, ab4729)


title: spleen, 0 h control treatment S. iniae challenge, striped bass, rep3

description:
sb_strep_t00h_3
sb-strep-counts.txt


title: FoMV_EV_2

description: Library name: FoMV_EV_2


title: FoMV_EV_1

description: Library name: FoMV_EV_1


title: spleen, 0 h control treatment S. iniae challenge, striped bass, rep1

description:
sb_strep_t00h_1
sb-strep-counts.txt


title: Forelimb, E11.5, H3K27ac, biol rep 1, ChIP

description: ChIPmentation


title: RNA-seq_heart_HH22_galGal6_WT_Rep2


title: RNA-seq_heart_HH22_galGal6_WT_Rep1


title: MorpPF [PRRS_Saline_M_57]

status: Public on Mar 05 2025

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

data_processing:
Quality-scores line in fastq files processed with Casava1.8 used an ASCII offset of 33.
Sequences were trimmed for adaptor sequences and masked for low-complexity and low-quality.
150 nt paired-end reads were assembled into transcript isoforms and mapped to the pig genome (assembly 11.1) using Kallisto v0.43 (Bray et al., 2016).
Assembly: Sus scrofa genome (version 11.1)
Supplementary files format and content: Morphine_Prefrontal_57samples_GEO_counts.csv: Comma-separated text file includes transcripts per million (TPM) values for each sample, one column per sample.

organism: Sus scrofa

source_name: PrefrontalCortex

extract_protocol:
RNA was extracted from all samples using standards protocols. TRIzol reagent (Life Technologies, Grand Island, New York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was used for purification.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the antisense strand and read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on 4 lanes first and 5 lanes later for 101 cycles from one end of the fragments using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

value: Prefrontal cortex

tag: maternal immune activation

value: Porcine reproductive and respiratory syndrome (PRRS)

value: Saline

value: Male

value: 21 days


title: MorpPF [PRRS_Saline_M_56]


title: MorpPF [PRRS_Saline_M_55]


title: MorpPF [PRRS_Saline_M_53]


title: MorpPF [PRRS_Saline_M_51]


title: MorpPF [PRRS_Saline_M_52]


title: MorpPF [PRRS_Saline_M_54]


title: MorpPF [PRRS_Saline_M_49]


title: MorpPF [PRRS_Saline_M_48]


title: Forelimb, E11.5, H3K4me1, biol rep 1, ChIP

description: ChIPmentation


title: MorpPF [PRRS_Saline_M_47]


title: MorpPF [PRRS_Saline_M_46]


title: MorpPF [PRRS_Saline_M_45]


title: MorpPF [PRRS_Saline_M_44]


title: FoMV_EV_3

description: Library name: FoMV_EV_3


title: MorpPF [PRRS_Saline_F_42]

value: Female


title: MorpPF [PRRS_Saline_F_40]


title: MorpPF [PRRS_Saline_M_43]


title: MorpPF [PRRS_Saline_F_39]


title: MorpPF [PRRS_Saline_F_41]


title: MorpPF [PRRS_Saline_F_33]


title: MorpPF [PRRS_Saline_F_31]


title: MorpPF [PRRS_Saline_F_36]


title: MorpPF [PRRS_Saline_F_30]


title: MorpPF [PRRS_Saline_F_28]


title: MorpPF [PRRS_Saline_F_35]


title: MorpPF [PRRS_Saline_F_29]


title: MorpPF [PRRS_Saline_M_50]


title: MorpPF [PRRS_Saline_F_38]


title: MorpPF [PRRS_Saline_F_27]


title: MorpPF [PRRS_Saline_F_34]


title: MorpPF [PRRS_Saline_F_26]


title: MorpPF [PRRS_Morphine_M_23]

value: Morphine


title: MorpPF [PRRS_Morphine_M_22]


title: MorpPF [PRRS_Morphine_M_21]


title: MorpPF [PRRS_Morphine_M_20]


title: MorpPF [PRRS_Morphine_F_16]


title: MorpPF [PRRS_Morphine_F_17]


title: MorpPF [Control_Saline_M_12]

value: Control


title: MorpPF [Control_Saline_M_13]


title: MorpPF [PRRS_Morphine_F_15]


title: MorpPF [PRRS_Saline_F_37]


title: MorpPF [Control_Saline_F_8]


title: MorpPF [PRRS_Saline_F_32]


title: MorpPF [Control_Saline_F_11]


title: MorpPF [PRRS_Morphine_F_14]


title: MorpPF [Control_Saline_F_10]


title: MorpPF [Control_Morphine_M_7]


title: MorpPF [Control_Morphine_M_6]


title: MorpPF [Control_Morphine_F_1]


title: MorpPF [PRRS_Morphine_M_24]


title: MorpPF [Control_Morphine_F_2]


title: MorpPF [Control_Morphine_F_3]


title: BM MNCs, Healthy Donor, HD10-c

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

description: long read scRNA-seq

data_processing:
The primary data analysis, including barcode and unique molecular identifier demultiplexing, was performed using the EPI2ME software.
Assembly: hg38
Supplementary files format and content: raw count expression matrix

source_name: Bone Marrow

extract_protocol:
BM MNCs from two CCUS patients and two eHDs were assessed for concentration and viability using a Life Technologies Countess 3 FL cell counter and trypan blue exclusion staining. Suspensions with 70% or higher viability were used for capture. Two to five sample suspensions were captured for each sample, targeting 50,000 cells per sample. Single-cell capture was performed on the Chromium iX using 10x Genomics’ Next GEM 3’ scRNAseq V3.1 protocol (CG000315_ChromiumNextGEMSingleCell3-GeneExpression, v3.1, DualIndex_RevE), up to and including cDNA amplification and cleanup.
The purified, amplified cDNA was assessed for quality and concentration using an Agilent HS DNA Bioanalyzer and the Qubit HS dsDNA Assay (both from Thermo Fisher). Ten nanograms of the resultant barcoded, full-length cDNA transcripts were used as templates for Nanopore full-length cDNA library preparation. The transcripts were first amplified with custom biotinylated primers. The resultant biotinylated cDNA was captured following bead cleanup using streptavidin beads. A second round of PCR was performed on the eluted cDNA, and the product was used to generate nanopore libraries using the Ligament Sequencing Kit V14 (Nanopore, SQK-LSK114). Purified libraries were quantified using the Qubit HS dsDNA Assay, and 100 fmoles of library were loaded to R10.4.1 flow cells (FLO-PRO114M) and sequenced on a PromethION24 sequencer. Libraries were sequenced for 72 hours with a 200-bp minimum read length using the super accurate base-calling mode. Single-cell full-length cDNA libraries were prepared using the 10X Genomics microfluidics-based Chromium platform. Subsequently, these libraries underwent sequencing on a Nanopore PromethION Flow Cell. Each PromethION Flow Cell typically yields approximately 80 million cell-assigned reads, allowing for the analysis of up to around 8,000 cells per flow cell. Multiple libraries were prepared from the same sample to ensure an adequate number of cells and achieve a higher sequencing depth, and several sequencing runs were conducted for each library.

value: Bone Marrow

tag: cell type

value: Bone Marrow Mononuclear cells

tag: group

value: Healthy Donor


title: Unlabeled

city: Irvine

first: Annie

last: Trinh

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: Library name: Unlabeled

data_processing:
For BrdU-labeled samples loaded on R9.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN106D), basecalling on raw current signals was performed using Guppy v6.5.7. DNA sequences were aligned to the hg19 human reference genome using Minimap2 v2.24 and chimeric reads were removed using samtools v1.15.1. To identify BrdU-containing reads, DNAscent v3.1.254 was used to detect the BrdU base analog within individual reads. CpG methylation was called using nanopolish v0.13.255. For BrdU-labeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114) and unlabeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M), basecalling and alignment to the hg19 human reference genome were performed using Dorado v0.6.2. Chimeric reads were removed using samtools v1.15.1. To identify BrdU-containing reads, DNAscent v4.0.1 was used to detect the nucleoside analog within individual reads. CpG methylation was called using Dorado v0.6.2. Nanoplot v1.41.6 was used to assess and visualize read-level statistics such as number of reads, read length N50, mean and median read length, and mean and median read quality.
Assembly: GRCh37 (hg19)
Supplementary files format and content: For nanopore long-read samples, processed data are available in bedMethyl files (.bed) and read-level calls (.tsv). For Repli-ATAC samples, processed data are provided as .bigWig files.

growth_protocol: HUES64 hESCs were cultured on Geltrex (Thermo Fisher Scientific, A1413302) coated tissue culture plates with mTeSR (STEMCELL Technologies) media. Cells were incubated at 37°C with 5% CO2. Media was changed daily and cells were passaged upon reaching 80% confluency using ReleSR (STEMCELL Technologies).

extract_protocol:
For samples labeled with 50 µM BrdU or nocodazole, cells were lysed via incubation in SDS-PK buffer (0.5% wt/vol) sodium dodecyl sulfate (SDS), 50mM Tris-HCl, 0.01M EDTA, 1M NaCl and 0.2mg/ml proteinase K) at 56°C for 2h. Genomic DNA was isolated using phenol-chloroform extraction and isopropanol precipitation. For samples labeled with 500 µM BrdU, genomic DNA was isolated using the Puregene Cell Kit (8 x 10^8) (Qiagen, 158043) or Monarch® Genomic DNA Purification Kit (NEB, T3010S) according to the manufacturer’s instructions.
For samples labeled with 50 µM BrdU or nocodazole, libraries were prepared from purified and fragmented genomic DNA using a Ligation Sequencing Kit (Oxford Nanopore Technologies, SQK-LSK110) according to the manufacturer’s instructions. Briefly, DNA repair and end-prep were performed using NEBNext® FFPE DNA Repair Mix (NEB, M6630) and NEBNext® Ultra II End Repair/dA-tailing Module (NEB, E7546). Adapter ligation and clean-up were performed using the NEBNext® Quick Ligation Module (NEB, E6056). Long Fragment Buffer from the Ligation Sequencing Kit was used in the clean-up step to enrich for DNA fragments of >3 kb. Libraries were loaded onto R9.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN106D) and sequenced using a MinION Mk1b device (Oxford Nanopore Technologies) for 16 hours. Minimum read length was set to 200 bp. For samples labeled with 500 µM BrdU and samples not labeled with BrdU, libraries were prepared using a Ligation Sequencing Kit (Oxford Nanopore Technologies, SQK-LSK114) according to the manufacturer’s instructions, similarly to previously described. Libraries for samples labeled with 500 µM BrdU were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114) and sequenced using a MinION Mk1b device for 32 hours. Libraries generated from unlabeled samples were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M) and sequenced on a PromethION P2 solo device (Oxford Nanopore Technologies) for 72 hours. Minimum read length was set to 1000 bp. All sequencing data was collected using MinKNOW v23.07.5.

treatment_protocol: For the nocodazole experiment, hESCs were treated with 2 µg/ml nocodazole for 16h prior to DNA extraction. For the BrdU pulse-chase experiments, BrdU pulses are conducted by adding BrdU to the culture medium at the desired final concentration and incubating for the specified durations (10 minutes, 20 minutes, 30 minutes, or 1 hour). Cells are then either collected immediately (0h chase) or washed three times with DPBS and incubated in fresh mTeSR medium for 16 hours (16h chase). For mock treatments, BrdU is replaced with an equivalent volume of Ultrapure H2O. Cells subjected to mock treatments undergo the same incubation times as their BrdU-treated counterparts, with samples collected at 0h or following a 16h incubation.

tag: cell line

value: human embryonic stem cells

tag: treatment

value: Unlabeled (no BrdU)


title: MorpPF [Control_Morphine_M_5]


title: MorpPF [Control_Morphine_M_4]


title: MorpPF [PRRS_Morphine_M_25]


title: BM MNCs, Healthy Donor, HD10-b

description: long read scRNA-seq


title: MorpPF [PRRS_Morphine_F_18]


title: MorpPF [PRRS_Morphine_F_19]


title: BM MNCs, Healthy Donor, HDMCBM-c

description: long read scRNA-seq


title: BM MNCs, Healthy Donor, HD10-a

description: long read scRNA-seq


title: BM MNCs, Healthy Donor, HDMCBM-a

description: long read scRNA-seq


title: MorpPF [Control_Saline_F_9]


title: BM MNCs, Healthy Donor, HDMCBM-b

description: long read scRNA-seq


title: BM MNCs, CCUS, CCUS-52-e

description: long read scRNA-seq

value: CCUS


title: BM MNCs, CCUS, CCUS-52-d

description: long read scRNA-seq


title: BM MNCs, CCUS, CCUS-52-a

description: long read scRNA-seq


title: BM MNCs, CCUS, CCUS-52-c

description: long read scRNA-seq


title: BM MNCs, CCUS, CCUS-52-b

description: long read scRNA-seq


title: BM MNCs, CCUS, CCUS-70-d

description: long read scRNA-seq


title: BM MNCs, CCUS, CCUS-70-e

description: long read scRNA-seq


title: BM MNCs, CCUS, CCUS-70-c

description: long read scRNA-seq


title: BM MNCs, CCUS, CCUS-70-b

description: long read scRNA-seq


title: WT(nip)-12h-3

city: 长沙

first: 别帅骏

last: 别

state: 长沙

address: 芙蓉区远大二路892号

department: 实验大楼

institute: 湖南省农业科学院

description:
Library name: sample9
HRY8-12h-3

data_processing:
DESeq2 software (version 1.12.3)
Rice leaves of Nipponbare (Nip), OsCBM1-RNAi and OsCBM1-OE plants were collected in liquid nitrogen at 12 hours after inoculation Xoo at booting stage.
Total RNA was extracted according to TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA purity and quantity were verified using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA). Transcriptome sequencing and analysis were performed by OE Biotech Co. (Shanghai, China); and transcriptome libraries were con-structed using the VAHTS Universal V5 RNA-seq Library Preparation Kit
Supplementary files format and content: tab-delimited text files inculde FPKM and counts values for Sample

organism: Oryza sativa

source_name: plant leaves

extract_protocol:
RNA was harvested using Rneasy mini plus kit .1.3ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were perpared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocol

value: plant leaves

value: WT(nip)

value: Bacterial inoculation and cold treatment


title: WT(nip)-12h-1

description:
Library name: sample7
HRY8-12h-1


title: HFF，DMSO，rep3

city: Shanghai

first: Peng

last: Yu

state: Shanghai

address: 2205 Songhu Road, Yangpu District,Shanghai, China

institute: Fudan University

data_processing:
TrimGalore (v.0.6.6) was used to filter out low quality reads and bases in the 3’ end of FASTQ files, then the clean data files were consequentially aligned to human GRCh38 reference genome by STAR (v.2.2.1), and only unique mapping reads were included for further analysis. StringTie 111 was used to quantify the gene expression level and normalize by TPM (transcripts per million).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: HFF

extract_protocol:
RNA was harvested using TRIzol Reagent (ThermoFisher) according to the manufacturer's instructions .
1 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using KAPA RNA hyperPrep Kit following manufacturer's protocols.

value: HFF

value: fibroblast


title: HFF，DMSO，rep1


title: OsCBM1-OE41-12h-1

description:
Library name: sample4
HRY7-12h-1


title: HFF，4OHT，rep2


title: OsCBM1-RNAi55-12h-2

description:
Library name: sample2
HRY4-12h-2


title: OsCBM1-OE41-12h-2

description:
Library name: sample5
HRY7-12h-2


title: OsCBM1-RNAi55-12h-3

description:
Library name: sample3
HRY4-12h-3


title: HFF，4OHT，rep1


title: OsCBM1-RNAi55-12h-1

description:
Library name: sample1
HRY4-12h-1


title: AE2S 3

city: Erlangen

first: Christian

last: Büttner

address: Schwabachanlage 10

department: Institut of Human Genetics

institute: University Hospital Erlangen

data_processing:
After sequencing on a Illumina Hiseq 2500 platform Reads were demultiplexed with bcl2fastq with one mismatch allowed in the dual barcodes and trimmed with cutadapt (-trim-n ,-max-n 0.1; -q 20,20; -minimum-length 50; trimming Truseq adapters).
Preprocessed FASTQ were aligned to the GRCh38 genome with STAR aligner (Version 2.7.8.a).
Unique mappings were counted in a strand specific manner on the exonic regions from Ensembl gene model version 103 using featureCounts (Version 2.0.1).
Differential expression and rlog transformed expression values were calculated using the DESeq2 package (version 1.30) in the R statistical environment version 4.0.3.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files with rlog-transformed expression values for each sample.

source_name: brain vascular pericytes

growth_protocol: Human brain vascular pericytes (InnoProt, Derio, Spain) were cultured in pericyte medium (InnoProt, Derio, Spain) containing 2 % fetal bovine serum, 1 % pericyte growth supplement and 1 % penicillin/streptomycin solution. Cells were cultured on Poly-L-Lysine (2 µg/cm2, ScienCell) and incubated at 37 °C and 95% O2 / 5% CO2 until they reach confluence. Medium was changed every second day.

extract_protocol:
RNA was extracted using the Rneasy Kit (Qiagen) and DNase digested.
RNA libraries for RNA-seq were prepared from 500 ng of total RNA applying the TruSeq Stranded mRNA Kit manufacturers protocol using 12 PCR cycles during final amplification.

treatment_protocol: Ammonium iron (II) sulfate hexahydrate (AE2S, Ref No. 9719, Sigma-Aldrich) was applied at a concentration of 300 µM, TDA Reagent for microbiology (FeCl3, Ref No. 80353, Sigma-Aldrich), was applied art a concentration of 200 µM.

value: brain vascular pericytes


title: AE2S 4


title: HFF，4OHT，rep3


title: HFF，DMSO，rep2


title: FeCl3 4


title: FeCl3 2


title: FeCl3 1


title: AE2S 2


title: Control 4

value: Pericyte medium


title: Control 3


title: AE2S 1


title: FeCl3 3


title: OsCBM1-OE41-12h-3

description:
Library name: sample6
HRY7-12h-3


title: BM MNCs, CCUS, CCUS-70-a

description: long read scRNA-seq


title: Control 2


title: WT(nip)-12h-2

description:
Library name: sample8
HRY8-12h-2


title: Control 1


title: APC_872, wt, water, colon, healthy

city: London

first: Maria

last: Glymenaki

address: Du Cane Road

institute: Imperial College London

description:
IGF119438
APC-872Colon-healthy

data_processing:
Sequencing data were mapped against a reference transcriptome with STAR alignment, followed by quantification using RSEM as detailed in alternate protocol 7 of the STAR software package.
Gene counts were generated using featureCounts.
Subsequent analysis was performed using DESeq2 pipeline following the RNA-Seq workflow.
Assembly: org.Mm.eg.db
Supplementary files format and content: normalized_counts_DESEq_*.txt: Tab-delimited text files including normalized count values after running DESeqDataSetFromMatrix to prepare the data for DESeq analysis.

source_name: Colon

extract_protocol:
Lysis buffer (Qiagen) was directly added to the tissue and RNA was extracted using the miRNeasy Micro Kit (Qiagen). RNA was treated with RNase-Free DNase Set (Qiagen) followed by RNA clean-up.
RNA sequencing analysis was performed by Imperial BRC Genomics Facility (Imperial College London). Library was prepared using total RNA for cells.

treatment_protocol: Tissue was harvested, washed with sterile PBS and stored in RNAprotect Tissue Reagent in -80°C.

value: Colon

value: wt

value: water

tag: disease stage

value: no tumor

tag: parental origin

tag: mouse id

tag: paired tumour and non-tumour sample from the same animal

value: No


title: APC_870, wt, water, colon, healthy

description:
IGF119436
APC-870Colon-healthy

tag: Sex

value: Female


title: APC_869, wt, tyramine, colon, healthy

description:
IGF119435
APC-869Colon-healthy

value: tyramine


title: APC_866, APCmin/+, water, colon, healthy

description:
IGF119433
APC-866Colon-healthy

value: APCmin/+

value: Male


title: APC_867, APCmin/+, tyramine, colon, healthy

description:
IGF119434
APC-867Colon-healthy


title: APC_871, wt, tyramine, colon, healthy

description:
IGF119437
APC-871Colon-healthy


title: APC_865, APCmin/+, water, colon, healthy

description:
IGF119432
APC-865Colon-healthy


title: APC_863, wt, tyramine, colon, healthy

description:
IGF119431
APC-863Colon-healthy


title: APC_862, wt, water, colon, healthy

description:
IGF119430
APC-862Colon-healthy


title: APC_858, APCmin/+, water, colon, healthy

description:
IGF119426
APC-858Colon-healthy


title: APC_860, APCmin/+, tyramine, colon, healthy

description:
IGF119428
APC-860Colon-healthy


title: APC_857, wt, tyramine, colon, healthy

description:
IGF119425
APC-857Colon-healthy


title: APC_856, APCmin/+, tyramine, colon, healthy

description:
IGF119424
APC-856Colon-healthy


title: APC_861, wt, tyramine, colon, healthy

description:
IGF119429
APC-861Colon-healthy


title: APC_859, APCmin/+, tyramine, colon, healthy

description:
IGF119427
APC-859Colon-healthy


title: APC_853, APCmin/+, water, colon, healthy

description:
IGF119421
APC-853Colon-healthy


title: APC_870, wt, water, ileum, healthy

description:
IGF119416
APC-870Ileum-healthy

source_name: Ileum

value: Ileum


title: APC_872, wt, water, ileum, healthy

description:
IGF119418
APC-872Ileum-healthy


title: APC_854, wt, water, colon, healthy

description:
IGF119422
APC-854Colon-healthy


title: APC_701, APCmin/+, water, colon, healthy

description:
IGF119419
APC-701Colon-healthy


title: APC_871, wt, tyramine, ileum, healthy

description:
IGF119417
APC-871Ileum-healthy


title: APC_712, APCmin/+, tyramine, colon, healthy

description:
IGF119420
APC-712Colon-healthy


title: APC_868, APCmin/+, water, ileum, healthy

description:
IGF119414
APC-868Ileum-healthy


title: APC_725, wt, tyramine, ileum, healthy

description:
IGF119415
APC-725Ileum-healthy


title: APC_866, APCmin/+, water, ileum, healthy

description:
IGF119412
APC-866Ileum-healthy

value: Yes


title: APC_864, APCmin/+, tyramine, ileum, healthy

description:
IGF119411
APC-864Ileum-healthy


title: APC_863, wt, tyramine, ileum, healthy

description:
IGF119410
APC-863Ileum-healthy


title: APC_862, wt, water, ileum, healthy

description:
IGF119409
APC-862Ileum-healthy


title: APC_723, wt, tyramine, ileum, healthy

description:
IGF119408
APC-723Ileum-healthy


title: APC_867, APCmin/+, tyramine, ileum, healthy

description:
IGF119413
APC-867Ileum-healthy


title: APC_860, APCmin/+, tyramine, ileum, healthy

description:
IGF119407
APC-860Ileum-healthy


title: APC_859, APCmin/+, tyramine, ileum, healthy

description:
IGF119406
APC-859Ileum-healthy


title: APC_707, APCmin/+, tyramine, ileum, healthy

description:
IGF119402
APC-707Ileum-healthy


title: APC_715, APCmin/+, tyramine, ileum, healthy

description:
IGF119403
APC-715Ileum-healthy


title: APC_855, APCmin/+, tyramine, colon, healthy

description:
IGF119423
APC-855Colon-healthy


title: APC_853, APCmin/+, water, ileum, healthy

description:
IGF119400
APC-853Ileum-healthy


title: APC_703, APCmin/+, tyramine, ileum, healthy

description:
IGF119398
APC-703Ileum-healthy


title: APC_858, APCmin/+, water, ileum, healthy

description:
IGF119405
APC-858Ileum-healthy


title: APC_854, wt, water, ileum, healthy

description:
IGF119401
APC-854Ileum-healthy


title: APC_713, APCmin/+, water, ileum, healthy

description:
IGF119394
APC-713Ileum-healthy


title: APC_717, wt, tyramine, ileum, healthy

description:
IGF119397
APC-717Ileum-healthy


title: APC_710, wt, tyramine, ileum, healthy

description:
IGF119391
APC-710Ileum-healthy


title: APC_712, APCmin/+, tyramine, ileum, healthy

description:
IGF119393
APC-712Ileum-healthy


title: APC_708, wt, water, ileum, healthy

description:
IGF119389
APC-708Ileum-healthy


title: APC_857, wt, tyramine, ileum, healthy

description:
IGF119404
APC-857Ileum-healthy


title: APC_711, wt, water, ileum, healthy

description:
IGF119392
APC-711Ileum-healthy


title: APC_709, APCmin/+, water, ileum, healthy

description:
IGF119390
APC-709Ileum-healthy


title: APC_702, wt, tyramine, ileum, healthy

description:
IGF119385
APC-702Ileum-healthy


title: APC_701, APCmin/+, water, ileum, healthy

description:
IGF119384
APC-701Ileum-healthy


title: APC_714, wt, tyramine, ileum, healthy

description:
IGF119395
APC-714Ileum-healthy


title: APC_866, APCmin/+, water, ileum, tumour

description:
IGF119381
APC-866Ileum-tumour

value: tumor


title: APC_719, APCmin/+, water, ileum, healthy

description:
IGF119399
APC-719Ileum-healthy


title: APC_864, APCmin/+, tyramine, ileum, tumour

description:
IGF119379
APC-864Ileum-tumour


title: APC_700, APCmin/+, tyramine, ileum, healthy

description:
IGF119383
APC-700Ileum-healthy


title: APC_706, APCmin/+, tyramine, ileum, healthy

description:
IGF119388
APC-706Ileum-healthy


title: APC_699, APCmin/+, water, ileum, healthy

description:
IGF119382
APC-699Ileum-healthy


title: APC_865, APCmin/+, water, ileum, tumour

description:
IGF119380
APC-865Ileum-tumour


title: APC_705, wt, water, ileum, healthy

description:
IGF119387
APC-705Ileum-healthy


title: APC_858, APCmin/+, water, ileum, tumour

description:
IGF119377
APC-858Ileum-tumour


title: APC_856, APCmin/+, tyramine, ileum, tumour

description:
IGF119376
APC-856Ileum-tumour


title: APC_716, wt, water, ileum, healthy

description:
IGF119396
APC-716Ileum-healthy


title: APC_718, APCmin/+, tyramine, ileum, tumour

description:
IGF119374
APC-718Ileum-tumour


title: APC_853, APCmin/+, water, ileum, tumour

description:
IGF119375
APC-853Ileum-tumour


title: APC_706, APCmin/+, tyramine, ileum, tumour

description:
IGF119372
APC-706Ileum-tumour


title: APC_700, APCmin/+, tyramine, ileum, tumour

description:
IGF119371
APC-700Ileum-tumour


title: APC_704, APCmin/+, water, ileum, healthy

description:
IGF119386
APC-704Ileum-healthy


title: PANC1, p53 ChIP

city: Göttingen

first: Shiv

middle: K.

last: Singh

address: Robert-Koch-Straße 40

department: Gastroenterology, GI-Oncology and Endocrinology

institute: University Medical Center Göttingen

description: Library name: PANC1_p53_ChIP

data_processing:
Quality control using FastQC.
Alignment to hg38 using bowtie2.
Filtering of not properly aligned, low quality reads
Duplicate removal using samtools
Peak calling using MACS2 callpeak with standard parameters.
Assembly: hg38
Supplementary files format and content: Peak file

source_name: cell line

extract_protocol:
Cells were fixed in 1% PFA in PBS for 20 min, after quencing and lysis, chromatin was sonicated on a Bioruptor Pico (Diagenode).
Libraries were constructed using Microplex Library Preparation Kit v3 (Diagenode).

value: cell line


title: APC_699, APCmin/+, water, ileum, tumour

description:
IGF119370
APC-699Ileum-tumour


title: PANC1, input

description: Library name: PANC1_input


title: MiaPaCa2, input

description: Library name: MiaPaCa2_input


title: PANC1, sip53, 3

description: Library name: PANC1_sip53_3

data_processing:
Quality control using FastQC, Kraken, and FastQ Screen
Reads were trimmed using Trimmomatic and mapped to hg38 using STAR.
Reads were counted using HTSeq-count
Assembly: hg38
Supplementary files format and content: count files

molecule: polyA RNA

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Libraries were constructed using 1 µg of RNA and the TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: Double siRNA transfection using Lipofectamine (at 0h and 24 h after seeding).

value: siRNA against p53


title: PANC1, sip53, 1

description: Library name: PANC1_sip53_1


title: PANC1, siCtrl, 3

description: Library name: PANC1_siCtrl_3

value: negative control siRNA


title: PANC1, sip53, 2

description: Library name: PANC1_sip53_2


title: PANC1, siCtrl, 2

description: Library name: PANC1_siCtrl_2


title: MiaPaCa2, p53 ChIP

description: Library name: MiaPaCa2_p53_ChIP


title: MiaPaCa2, siCtrl, 2

description: Library name: MiaPaCa2_siCtrl_2


title: MiaPaCa2, siCtrl, 3

description: Library name: MiaPaCa2_siCtrl_3


title: MiaPaCa2, sip53, 2

description: Library name: MiaPaCa2_sip53_2


title: MiaPaCa2, siCtrl, 1

description: Library name: MiaPaCa2_siCtrl_1


title: PANC1, siCtrl, 1

description: Library name: PANC1_siCtrl_1


title: MiaPaCa2, sip53, 3

description: Library name: MiaPaCa2_sip53_3


title: CUT&RUN of genetic modified HUDEP-2 cell lines: HA CUT&RUN of HUDEP-2 cell line B replicate2

city: Ann Arbor

first: Kaiwen

last: Deng

state: Michigan

address: 3305 NCRC Building 520

department: DCMB

institute: University of Michigan

description: CUT&RUN was performed using 1million nuclei with spefic antibodies(1:100 dilute); library was prepared with NEBNext UltraII DNA Library Prep Kit for Illumina

data_processing:
All samples were processed using the CUT&RUNTools with the default trimming and alignment settings. Paired-end sequencing reads were first trimmed with Trimmomatic and a built-in algorithm of the tool. Subsequently, reads were aligned to the reference human genome GRCh38 assembly with bowtie2. Alignment results were recorded in BAM files and sorted, indexed, marked duplications with Picard MarkDuplicate function, and then filtered with SAMtools to discard unmapped reads. Fragments of sizes less than 120 bp were kept for downstream analysis. MACS2 version 2.1.4 was used to call peaks from the BAM files with narrowPeak setting, q-value cutoff of 0.01, and with --SPMR which normalizes the signal intensity.
Assembly: GRCh38
Supplementary files format and content: bigWig files (.bw) stored the normalized pile-ups of the reads
Supplementary files format and content: narrow peak files (.narrowPeak) stored the peaks called by MACS2

source_name: HUDEP-2 Clone B

growth_protocol: HUDEP-2 cells were maintained in StemSpan SFEM (STEMCELL Technologies, 09650) supplemented with SCF (50 ng/ml), EPO (3 IU/ml), Dexamethasone (10-6 M), Doxycycline (1 mg/ml). Cells were passaged every two to three days to maintain a density between 1x105 to 8x105 cells/ml.

extract_protocol:
CUT&RUN experiments were carried out as described(Liu et al. Cell 2018; Skene et al. Nat Protoc 2018) with modiﬁcations. Brieﬂy, nuclei from 1million cells were isolated with NE buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 1nM MnCl2, 0.5 mM Spermidine, and 1x EDTA-free protease inhibitor cocktails from Sigma (CPI)). Nuclei were conjugated to Concanavalin A-coated magnetic beads (Bangs Laboratories) by incubation at room temperature for 10 minutes. Nuclei:bead slurry was incubated with primary antibody in antibody buffer (20 mM HEPES-NaOH, pH 7.5, 150mM NaCl, 0.5 mM Spermidine, 1xCPI, 0.05% Digitonin and 2mM EDTA) at 4°C overnight. After washing away unbound antibody with Dig-wash buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x CPI and 0.05% Digitonin) for 2 times, protein A/G-MNase (Epicypher) was added according to manufacturer’s instructions and incubated for 2 hours at 4°C. The samples were washed twice with Dig-wash buffer and once with Low-salt rinse buffer (20 mM HEPES-NaOH pH 7.5, 0.5 mM Spermidine, and 0.05% Digitonin)6. Protein A/G-MNase was then activated by incubating samples in 0°C ice water with Incubation buffer (3.5 mM HEPES-NaOH pH 7.5, 10mM CaCl2, and 0.05% Digitonin). After MNase digestion for 2 hours, the reaction was stopped by replacing with equal volume of STOP buffer (170 mM NaCl, 20 mM EGTA, 0.05% Digitonin, 50 µg/mL RNase A and 25 µg/mL glycogen). The protein-DNA complexes were released by incubation at 37°C for 30 minutes. After proteinase K digestion at 55°C for 1 hour, the samples were then subjected to DNA purification by phenol chloroform extraction. Targeted DNA were evaluated by Qubit ﬂuorometer and bioanalyzer for quality control followed by library preparation.
Library preparation was performed following the modified protocol for TF-targeted short fragments using NEBNext Ultra II DNA Library Prep Kit following manufacturer's instructions. Brieﬂy, the dA-tailing reaction was modified to 50 °C for 1 hr. After adaptor ligation, 1.75 x volume of size-selection beads was added to increase the recovery of short fragments. DNA was then PCR amplified for 12 cycles with reduced amount of universal and individual index primers. After PCR ampliﬁcation, size selection of 160-350bp fragments was carried out by sequentially adding 0.6 x and 0.6 x volume of beads. Quantity and size distribution of libraries were measured by Qubit ﬂuorometer and Bioanalyzer, respectively.

treatment_protocol: All HUDEP-2 cell clones were cultured in the same condition for expansion, without any additional treatment.

value: HUDEP-2 Clone B


title: CUT&RUN of genetic modified HUDEP-2 cell lines: HA CUT&RUN of HUDEP-2 cell line B replicate3


title: MiaPaCa2, sip53, 1

description: Library name: MiaPaCa2_sip53_1


title: APC_860, APCmin/+, tyramine, ileum, tumour

description:
IGF119378
APC-860Ileum-tumour


title: CUT&RUN of genetic modified HUDEP-2 cell lines: MYC CUT&RUN of HUDEP-2 cell line B replicate3


title: APC_713, APCmin/+, water, ileum, tumour

description:
IGF119373
APC-713Ileum-tumour


title: CUT&RUN of genetic modified HUDEP-2 cell lines: MYC CUT&RUN of HUDEP-2 cell line B replicate2


title: CUT&RUN of genetic modified HUDEP-2 cell lines: HA CUT&RUN of HUDEP-2 cell line B replicate1


title: CUT&RUN of genetic modified HUDEP-2 cell lines: TR4 CUT&RUN of HUDEP-2 cell line T replicate3

source_name: HUDEP-2 Clone T

value: HUDEP-2 Clone T


title: CUT&RUN of genetic modified HUDEP-2 cell lines: MYC CUT&RUN of HUDEP-2 cell line T replicate3


title: CUT&RUN of genetic modified HUDEP-2 cell lines: MYC CUT&RUN of HUDEP-2 cell line B replicate1


title: CUT&RUN of genetic modified HUDEP-2 cell lines: TR4 CUT&RUN of HUDEP-2 cell line T replicate2


title: CUT&RUN of genetic modified HUDEP-2 cell lines: MYC CUT&RUN of HUDEP-2 cell line T replicate2


title: CUT&RUN of genetic modified HUDEP-2 cell lines: TR4 CUT&RUN of HUDEP-2 cell line T replicate1


title: CUT&RUN of genetic modified HUDEP-2 cell lines: TR4 CUT&RUN of HUDEP-2 cell line TB replicate3

source_name: HUDEP-2 Clone TB

value: HUDEP-2 Clone TB


title: CUT&RUN of genetic modified HUDEP-2 cell lines: MYC CUT&RUN of HUDEP-2 cell line T replicate1


title: CUT&RUN of genetic modified HUDEP-2 cell lines: TR4 CUT&RUN of HUDEP-2 cell line TB replicate2


title: CUT&RUN of genetic modified HUDEP-2 cell lines: HA CUT&RUN of HUDEP-2 cell line TB replicate3


title: CUT&RUN of genetic modified HUDEP-2 cell lines: MYC CUT&RUN of HUDEP-2 cell line TB replicate3


title: CUT&RUN of genetic modified HUDEP-2 cell lines: HA CUT&RUN of HUDEP-2 cell line TB replicate2


title: CUT&RUN of genetic modified HUDEP-2 cell lines: TR4 CUT&RUN of HUDEP-2 cell line TB replicate1


title: CUT&RUN of genetic modified HUDEP-2 cell lines: MYC CUT&RUN of HUDEP-2 cell line TB replicate2


title: CUT&RUN of genetic modified HUDEP-2 cell lines: MYC CUT&RUN of HUDEP-2 cell line TB replicate1


title: CUT&RUN of genetic modified HUDEP-2 cell lines: HA CUT&RUN of HUDEP-2 cell line TB replicate1


title: HCT116, tyramine treatment, 1.6mM, biol rep5

data_processing:
Sequencing data were mapped against a reference transcriptome with STAR alignment, followed by quantification using RSEM as detailed in alternate protocol 7 of the STAR software package.
Gene counts were generated using featureCounts.
Subsequent analysis was performed using DESeq2 pipeline following the RNA-Seq workflow
Assembly: org.Hs.eg.db
Supplementary files format and content: tab-delimited text files including normalized count values after running DESeqDataSetFromMatrix to prepare the data for DESeq analysis

growth_protocol: HCT116 cells were maintained in RPMI 1640 medium (Gibco) supplemented with 10% FBS, 100 units/mL penicillin, 100 μg/mL streptomycin, and 2 mmol/L L-glutamine (Gibco).

extract_protocol:
Lysis buffer (Qiagen) was directly added to the cells and RNA was extracted using the RNeasy Mini Kit (Qiagen).  RNA was treated with RNAse-Free DNase Set (Qiagen) followed by RNA clean-up.
RNA sequencing analysis was performed by Imperial BRC Genomics Facility (Imperial College London). Library was prepared using total RNA for cells.

treatment_protocol: Cells were maintained in culture medium supplemented with 5% dextran-coated charcoal-stripped FBS for 72 hrs to remove hormones and growth factors before any treatment. HCT116 cells were  treated with 1.2 mM or 1.6 mM tyramine or left untreated for 24 hrs.

value: colorectal cancer cells

value: tyramine treatment, 1.6mM


title: HCT116, tyramine treatment, 1.6mM, biol rep6


title: CUT&RUN of genetic modified HUDEP-2 cell lines: IgG CUT&RUN of HUDEP-2 cell line TB


title: CUT&RUN of genetic modified HUDEP-2 cell lines: IgG CUT&RUN of HUDEP-2 cell line B


title: CUT&RUN of genetic modified HUDEP-2 cell lines: IgG CUT&RUN of HUDEP-2 cell line T


title: HCT116, tyramine treatment, 1.6mM, biol rep2


title: HCT116, tyramine treatment, 1.6mM, biol rep1


title: HCT116, tyramine treatment, 1.6mM, biol rep4


title: HCT116, tyramine treatment, 1.2mM, biol rep6

value: tyramine treatment, 1.2mM


title: HCT116, tyramine treatment, 1.2mM, biol rep5


title: HCT116, tyramine treatment, 1.2mM, biol rep4


title: HCT116, tyramine treatment, 1.2mM, biol rep2


title: HCT116, untreated, biol rep5

value: no


title: HCT116, untreated, biol rep6


title: HCT116, tyramine treatment, 1.2mM, biol rep1


title: HCT116, untreated, biol rep4


title: HCT116, untreated, biol rep3


title: HCT116, untreated, biol rep2


title: HCT116, untreated, biol rep1


title: Sample5

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

description:
Library name: S5
10x Genomics 3' gene expression v3.1

data_processing:
Samples were demultixpled, aligned, and counted using CellRanger v8.0.1.
Assembly: Mmul10
Supplementary files format and content: Tab separated value files and matrix files

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Fresh frozen tissue samples were homogenized and used to generate nuclei suspensions as detailed in accompanying manuscripts.
Libraries were constructed using the manufacturer protocol for the 10x Genomics dual index 3' gene expression assay v3.1

value: brain

value: saline


title: Sample4

description:
Library name: S4
10x Genomics 3' gene expression v3.1


title: Sample2

description:
Library name: S2
10x Genomics 3' gene expression v3.1


title: HCT116, tyramine treatment, 1.6mM, biol rep3


title: rat BMEC, low shear, 4

city: Morgantown

first: Moriah

last: Katt

state: WV

address: 1306 Evansdale Dr

institute: West Virginia University

data_processing:
STAR
featurecounts
Assembly: hg38
Supplementary files format and content: csv, counts

source_name: brain vasculature

extract_protocol:
Qiagen Miniprep RNA Kit
polyA enrichment

value: brain vasculature

value: low shear


title: rat BMEC, low shear, 1


title: rat BMEC, low shear, 3


title: rat BMEC, low shear, 2


title: rat BMEC, high shear, 3

value: high shear


title: rat BMEC, high shear, 4


title: rat BMEC, high shear, 2


title: rat BMEC, high shear, 1


title: HCT116, tyramine treatment, 1.2mM, biol rep3


title: Sample1

description:
Library name: S1
10x Genomics 3' gene expression v3.1


title: Sample3

description:
Library name: S3
10x Genomics 3' gene expression v3.1